1======================================================================= 2 SIESTA CHANGES: TOP IS MOST RECENT 3======================================================================= 4 5 6** CHANGES ALONG trunk 7----------------------------------------------------------------------- 82016-06-23 trunk-525 9Merged 4.0-500 10 11* Update list of contributors. 12* Electric-field/slab-dipole-correction fix. 13* Fix to avoid ps reparametrization in bessel case 14* Remove Util/pseudo-xml 15* Other minor changes in README files 16 17 18----------------------------------------------------------------------- 19... 20... 21----------------------------------------------------------------------- 222016-05-29 trunk-504 23Update makefile in Util/Gen-basis after ldau inclusion 24 25Some extra modules are needed in Gen-basis 26 27modified: 28 Util/Gen-basis/Makefile 29 30----------------------------------------------------------------------- 312016-05-18 trunk-503 32Merged fix lp:1582978 (from rel-4.0) 33 34----------------------------------------------------------------------- 352016-05-10 trunk-502 36Revise mentions to now-standalone ATOM program. Revert Tests/test.mk. 37 38* The ATOM program is not bundled with Siesta due to licensing 39 differences. Mentions to it throughout the documentation and 40 example files have been updated accordingly. 41 42* The file Tests/test.mk has been reverted to the revno 488 version. 43 Note that the proper way to run the tests for a given version is 44 to descend into the 'Tests' directory directly below the compilation 45 directory ('Obj' or other) rather than going to the top-level 'Tests'. 46 47* Syntax changes for compiler complaints reported by Mariella Ippolito 48 from CINECA. 49 50* Completion of changes to licensing headers. 51 52modified: 53 Docs/siesta.tex 54 Examples/README 55 Examples/Vps/README 56 Src/SiestaXC/vv_vdwxc.F90 57 Src/fsiesta_mpi.F90 58 Src/write_inp_wannier.F90 59 Src/ldau.F 60 Src/ldau_specs.f 61 Tests/test.mk 62 + Header changes in a number of files 63 64----------------------------------------------------------------------- 652016-05-05 trunk-501 66Fix in 'fat' utility. Write spin info in 'eigfat2plot' 67 68The 'fat' program in Util/COOP computes the projections of specific 69band states onto sets of orbitals. Due to an error, the program did 70not function correctly when a subset of upper bands was selected with 71the '-b' and '-B' flags. 72 73The 'eigfat2plot' utility in Util/Bands now prints an extra field giving 74the spin of the state. 75 76modified: 77 Util/Bands/eigfat2plot.f90 78 Util/COOP/fat.f90 79 Util/COOP/main_vars.f90 80 81----------------------------------------------------------------------- 822016-05-03 trunk-500 83Fix for handling of geometry info in bands/wfns calculation 84 85The computation of bands and/or wavefunctions in 'siesta_analysis' 86requires an initial setup of the k-point sets involved. These are 87input in ad-hoc fdf blocks with two possible options for the scaling: 88'pi/a' and 'ReciprocalLatticeVectors'. 89 90The 'pi/a' option needs a lattice constant, which is determined by 91issuing an 'fdf_get' call, whereas the reciprocal lattice vector 92option triggers a call to 'redcel' to determine the unit cell. 93 94An immediate problem is the absence of lattice constant or unit-cell 95information in the fdf file. This may happen, for example, when the 96'use-struct-file' or 'use-save-xv' options are in effect. The program 97would either stop when not finding the lattice constant, or, worse, 98would implicitly compute a zero unit cell and crash later with 99linear-algebra related errors such as faulty Cholesky 100decompositions. (The zero-unit-cell case is an unfortunate consequence 101of the implicit convention that an absent unit cell means that the 102user wants an automatic one.) 103 104A second problem is that, even if the required geometry information is 105given in the fdf file, the band/wfn calculation might be happening at 106the end of a cell relaxation or MD run, so the actual unit cell is not 107that in the fdf file. This should be considered bad practice, but it 108might happen. 109 110The minimal solution adopted (encoded in routine get_kpoints_scale) 111consists of attempting to read the lattice constant for the 'pi/a' 112case, as before, but to use the unit-cell information in the 113'siesta_geom' module for the reciprocal-lattice-vectors case. This 114information is not enough for the 'pi/a' option, since no record is 115kept of any centering options for cubic systems, so 'a' cannot be 116directly determined from the volume of the unit cell. Note that the 117setup information is handled at the beginning of the run (during the 118initialization in 'siesta_init'. 119 120A message is printed to warn the user about possible inconsistencies 121if the unit-cell changes by the end of the run. In any case, the 122practice of computing bands or wavefunctions at the end of a 123geometry-changing run should be discouraged. 124 125added: 126 Src/get_kpoints_scale.f90 127modified: 128 Src/Makefile 129 Src/bands.F 130 Src/writewave.F 131 132----------------------------------------------------------------------- 1332016-05-02 trunk-499 134Allowed neglecting KB projectors with LDA+U 135 136- The LDA+U projectors are now not dependent 137 on the NeglNonOverlapInt option which only 138 deals with KB projectors. 139 140- Streamlined calculation of rmaxo/rmaxkb in 141 hsparse, ldau, nlefsm, 142 143 Basically they looped over the entire structure 144 to find only the species orbital/projector 145 ranges. 146 Thus it is more efficient in those routines. 147 148modified: 149 Src/Makefile 150 Src/hsparse.F 151 Src/ldau.F 152 Src/nlefsm.f 153 Src/siesta_init.F 154 Src/state_init.F 155 156----------------------------------------------------------------------- 1572016-05-02 trunk-498 158Fixed imports 159 160modified: 161 Src/ldau_specs.f 162 Src/m_cite.F90 163 164----------------------------------------------------------------------- 1652016-05-01 trunk-497 166Added LDA+U citation of the implementation paper 167 168modified: 169 Src/ldau_specs.f 170 Src/m_cite.F90 171 172----------------------------------------------------------------------- 1732016-04-29 trunk-495 174Fixed rmaxh for correct range of Hamiltonian elements 175 176- The rmaxh was too short in case of LDAU projectors 177 bigger than the KB projectors. 178 179 This fixes the calculation of the correct rmaxh 180 when the LDAU projectors are used. 181 182modified: 183 Src/atomlist.f 184 Src/siesta_init.F 185 186----------------------------------------------------------------------- 1872016-04-29 trunk-494 188Cleaned LDA+U 189 190- Moved H_ldau to sparse_matrices. 191 This makes the global memory of "standard" matrix 192 elements common in the common module. 193 This requires that it is passed on every call to 194 Hubbard_term. 195 196- Moved several saved variables in the hubbard_term 197 to the module level. 198 This makes it easier to distinguish global variables. 199 200- Removed all commented out debugging statements. 201 202- Improved the logic of the options in the LDA+U implementation 203 204 REMARK: The logic is exactly the same but clearer from the 205 input options point of view. 206 207 1. ldau_init is now forced to .true. if ldau_shift is true. 208 2. There is no need to store the current geometry setup 209 Now the H_ldau is reset when state_init is called. 210 211- Removed a print-out of: 212 213 "Adding Hamiltonian contribution." 214 215 This is implicit in each SCF cycle (from after the 216 initial occupations have been calculated). 217 218 I have tested this on an MD run as well. 219 220modified: 221 Src/Makefile 222 Src/final_H_f_stress.F 223 Src/ldau.F 224 Src/ldau_specs.f 225 Src/scfconvergence_test.F 226 Src/setup_hamiltonian.F 227 Src/sparse_matrices.F 228 Src/state_init.F 229 230----------------------------------------------------------------------- 2312016-04-29 ldau-499 232Cleaned up the ldau modules by moving variables 233 234- The ldau_specs module had several variables defined 235 as module variables while they where only needed 236 in one subroutine. 237 They have been moved there. 238 239 Now also the projector arrays are deallocated after 240 having created the actual projectors used. 241 242 Thus saving additional memory. 243 244modified: 245 Src/ldau.F 246 Src/ldau_specs.f 247 248----------------------------------------------------------------------- 2492016-04-28 ldau-498 250Removed _tmp/tmp_ in ldau shells, removed double references 251 252- Removed all double references in the code of ldaushells 253 from the derived type. 254 255- Changed tmp names to standard conforming names. 256 This is more intuitive to grasp. 257 258modified: 259 Src/Makefile 260 Src/basis_types.f 261 Src/ldau_specs.f 262 263----------------------------------------------------------------------- 2642016-04-28 ldau-497 265Die if requesting non-existing PAO LDAU projectors 266 267- If the requested quantum number LDAU is not found 268 in the list of PAO objects then siesta will die. 269 270modified: 271 Src/ldau_specs.f 272 273----------------------------------------------------------------------- 2742016-04-28 ldau-496 275Cosmetic update of ldau code 276 277- Easier logistic in the loops in ldau 278 279- Cosmetic changes for the interface of hubbard_term which 280 now passes the local number of orbitals. 281 282- Beautification of the DEBUG_PAO print-out. 283 284modified: 285 Src/final_H_f_stress.F 286 Src/hsparse.F 287 Src/ldau.F 288 Src/register_rfs.F90 289 Src/setup_hamiltonian.F 290 291----------------------------------------------------------------------- 2922016-04-28 ldau-495 293Fix possible double counting of Hldau 294 295- If recompute_H_after_scf it is required that 296 we use H_tmp in final_H_f_stress. 297 298 This is now fixed. 299 300modified: 301 Src/final_H_f_stress.F 302 303----------------------------------------------------------------------- 3042016-04-28 ldau-494 305Almost fixed parallel version 306 307- Implemented Alberto's fixes for the basis specifications 308 in parallel with some minor corrections. 309 310 This is because the basis_specs are only on Node == 0. 311 However, the specifications should be broadcasted 312 to the other nodes. 313 314 This is now performed by dublicating the LDAU radial 315 functions to the other nodes and retaining the 316 data on all nodes. 317 318 I have added the remaining Bcast which where required. 319 320- Added bcast of the LDAU variables in broadcast_basis. 321 Several variables are required Bcasted. 322 323- Reduced memory requirements slightly 324 325- Reverted globalization of DEldau as entered by 326 Nick in r488. 327 This is not needed as the DEldau is calculated 328 from globalized occupations. 329 330- Removed un-needed ldaushell in the basis_species. 331 Only the *_tmp is used so we do not need the second. 332 333- Fix for "SpinPolarized false" regarding occupations 334 335- TODO move Hldau to sparse_matrices such that it may 336 be calculated "one time" and stored in a generic place. 337 338modified: 339 Src/Makefile 340 Src/atm_types.f 341 Src/basis_types.f 342 Src/broadcast_basis.F 343 Src/final_H_f_stress.F 344 Src/hsparse.F 345 Src/ldau.F 346 Src/ldau_specs.f 347 Src/setup_hamiltonian.F 348 349----------------------------------------------------------------------- 3502016-04-28 ldau-493 351Fixed r491 with rofi array size 352 353- Correspondance with Javier brought this 354 fix. 355 356modified: 357 Src/ldau_specs.f 358 359----------------------------------------------------------------------- 3602016-04-27 ldau-492 361Added die when user reads basis + LDAU 362 363- Reading the basis from NetCDF or ascii files 364 is not allowed when using LDA+U. 365 366 This feature is simply not implemented yet. 367 (but could be) 368 369modified: 370 Src/initatom.f 371 372----------------------------------------------------------------------- 3732016-04-27 ldau-491 374Fixes for pointers and possible seg-fault 375 376- Pointers in ldau.F where only nullified in 377 the first run. However, they should be 378 in each SCF. 379 Fixed. 380 381- Print-out of LDAU parameters in the basis-specification 382 This makes easy identification of the used LDA+U 383 basis. 384 385- A possible seg-fault for accessing array elements beyond 386 dimension was found in the ldau_specs.f. 387 388 A possible fix has been added. 389 390 TODO: Check validity for other systems. 391 For Javier's initial test MnO the results are identical. 392 393modified: 394 Src/basis_types.f 395 Src/ldau.F 396 Src/ldau_specs.f 397 398----------------------------------------------------------------------- 3992016-04-25 ldau-490 400Second patches by Nick Andersen 401 402* The files that have been added or modified are: 403 404- hsparse.F: Call to basis_parameters only if switch_ldau 405- matel_registry.F90: Cosmetic changes on show_pool 406- register_rfs.F90: Writing of part of the output only done if 407 the directive DEBUG_PAO is switched 408- siesta_init.F: Remove the call to test_register 409 410----------------------------------------------------------------------- 4112016-04-25 ldau-488 412First patches by Nick Andersen 413 414* The files that have been added or modified are: 415 416- final_H_f_stress.F: Globalization of the sum of DEldau added 417- ldau.F: Writing on some of the output only on Node 0, 418 globalization of dnmax 419- siesta_init.F: Initialization of Eldau and DEldau 420 421----------------------------------------------------------------------- 4222016-04-25 ldau-487 423Corrected version in the CHANGES file 424 425----------------------------------------------------------------------- 4262016-04-25 ldau-486 427Calculation of the Hubbard-like matrix elements, and their contribution 428to forces and stresses 429 430* The files that have been added or modified are: 431 432- atmfuncs.f: New function ldau_gindex added 433- basis_io.F: The information of the LDA+U projectors is dumped into 434 the corresponding files 435- compute_energies.F90: The Hubbard energy is added to the total energy 436- compute_max_diff.F: The maximum difference between the input and the 437 output density matrices is saved in the public 438 variable dDmax_current, that is required within 439 the hubbard_term subroutine in order to know 440 whether the population of the LDA+U projector is 441 updated or not. 442- final_H_f_stress.F: Last call to hubbard_term in order to compute the 443 forces and stresses once the self-consistency is 444 achieved 445- hsparse.F: The eventual overlap with the LDA+U projectors is 446 considered, as it was done with the KB projectors 447- initatom.f: Call to the subroutine ldau_proj_gen to generate the 448 LDA+U projectors 449- m_energies.F90: The Hubbard energies are included in the variables 450- scfconvergence_test.F: The criterion on the convergence of the population of 451 the LDA+U is added to the requirements to determine 452 whether the SCF is achieved 453- setup_hamiltonian.F: Call to hubbard_term to add the contribution of the 454 Hubbard-like terms to the Hamiltonian 455- write_subs.F: The information of the Hubbard like energies is dumped 456- ldau.F: New subroutine that computes the Hubbard-like 457 contribution to matrix elements, forces, and stresses 458- Makefile: Customaty changes to include the new files and dependencies 459- Docs/siesta.tex: A new section on the LDA+U calculations has been written 460 461----------------------------------------------------------------------- 4622016-02-22 ldau-485 463Generation of the LDA+U projections compatible with new matel 464 465* The files that have been added or modified are: 466- ldau_specs.f: Module ldau_specs to read the input file, 467 generate the projectors and populate the derived types. 468- atm_transfer.f: Call to populate_species_info_ldau to populate the 469 variables in the species derived type related with the 470 LDA+U projectors. 471- atm_types.f: New variables related with the LDA+U projectors 472 defined in the derived type species. 473 Essentially, they are a copy of the corresponding variables 474 for the KB projector 475- atom.F: The following subroutines declared public: 476 schro_eq, rc_vs_e, build_vsoft 477- basis_specs.f: The subroutine label2species is declared public. 478 It will be used afterwards in read_ldau_specs. 479- basis_types.f: New derived type ldaushell_t defined, and the 480 corresponding subroutines for initialization, print, etc 481 are introduced. 482- broadcast_basis.F:The broadcast of the species derived type has been 483 generalized to include also the corresponding variables 484 related with the LDA+U projectors 485- initatom.f: Here we read the info related with the LDA+U projs 486 in the fdf file (calling the subroutine read_ldau_specs) 487 and we call the subroutine in charge of generating them 488 (ldau_proj_gen) 489- register_rfs.F90: Subroutine modified to include the LDA+U projectors 490 in the pool 491- Makefile: Customaty changes to include the new files and dependencies 492 493 494added: 495 Src/ldau_specs.f 496modified: 497 Src/Makefile 498 Src/atm_transfer.f 499 Src/atm_types.f 500 Src/atom.F 501 Src/basis_specs.f 502 Src/basis_types.f 503 Src/broadcast_basis.F 504 Src/initatom.f 505 Src/register_rfs.F90 506 507 508----------------------------------------------------------------------- 5092016-03-21 trunk-493 510Merged Ramon SO changes + fixes 511 512- Merged Ramon's SO changes. 513 514- Changed alot of interfaces from Ramon initial 515 commit. 516 This is to better conform with the transiesta merge 517 to happen shortly. 518 519- Clarified a lot of output for the user when performing 520 SO / non-collinear calculations. 521 522- Reduce memory usage from Ramon's version considerably in 523 terms of the sparsity pattern. 524 In Ramon's implementation the H_kin/H_vkb/H_so where 525 full spin-matrices. 526 However, this is not needed. 527 H_kin/H_vkb == same for all spin 528 H_so == only has 6 components 529 530- Fixed calculation of total energy if one requests mixing charge 531 532- Fixed potential memory overflow in dfscf where V was 533 allocated on the stack. 534 535- Moved spin-spiral options to m_spin module 536 537- Enabled one flag for controlling the spin-configuration 538 539 Magnetization non-polarized/polarized/non-collinear/spin-orbit 540 541 with some variations of short-hands. 542 These are merely added for consistency 543 544 Magnetization NP/P/NC/SO 545 546 This removes the obscure choice of several options for _one_ 547 selection of computational type. 548 549 For backwards compatibility the old flags still exist and are 550 the basis for the initial option for Magnetization. 551 552- Diagonalization options moved to a common module 553 TODO extend this to streamline r/c-diag. 554 TODO externalize the diagonalization modules for easier 555 abstraction. 556 557removed: 558 Src/m_diagon.F 559added: 560 Src/diag3g.F 561 Src/diag3k.F 562 Src/m_diagon_opt.F90 563 Src/moments.F 564 Src/pdos2g.F 565 Src/pdos2k.F 566 Src/pdos3g.F 567 Src/pdos3k.F 568 Src/spinorbit.f 569 Tests/SpinOrbit/ 570 Tests/SpinOrbit/FePt-L1_0-so/ 571 Tests/SpinOrbit/FePt-L1_0-so/README 572 Tests/SpinOrbit/FePt-L1_0-so/X-alignment/ 573 Tests/SpinOrbit/FePt-L1_0-so/X-alignment/x-axis/ 574 Tests/SpinOrbit/FePt-L1_0-so/X-alignment/x-axis/Fe.psf 575 Tests/SpinOrbit/FePt-L1_0-so/X-alignment/x-axis/Pt.psf 576 Tests/SpinOrbit/FePt-L1_0-so/X-alignment/x-axis/fept.fdf 577 Tests/SpinOrbit/FePt-L1_0-so/X-alignment/x-axis/fept.out 578 Tests/SpinOrbit/FePt-L1_0-so/X-alignment/y-axis/ 579 Tests/SpinOrbit/FePt-L1_0-so/X-alignment/y-axis/Fe.psf 580 Tests/SpinOrbit/FePt-L1_0-so/X-alignment/y-axis/Pt.psf 581 Tests/SpinOrbit/FePt-L1_0-so/X-alignment/y-axis/fept.fdf 582 Tests/SpinOrbit/FePt-L1_0-so/X-alignment/y-axis/fept.out 583 Tests/SpinOrbit/FePt-L1_0-so/X-alignment/z-axis/ 584 Tests/SpinOrbit/FePt-L1_0-so/X-alignment/z-axis/Fe.psf 585 Tests/SpinOrbit/FePt-L1_0-so/X-alignment/z-axis/Pt.psf 586 Tests/SpinOrbit/FePt-L1_0-so/X-alignment/z-axis/fept.fdf 587 Tests/SpinOrbit/FePt-L1_0-so/X-alignment/z-axis/fept.out 588 Tests/SpinOrbit/FePt-L1_0-so/Z-alignment/ 589 Tests/SpinOrbit/FePt-L1_0-so/Z-alignment/x-axis/ 590 Tests/SpinOrbit/FePt-L1_0-so/Z-alignment/x-axis/Fe.psf 591 Tests/SpinOrbit/FePt-L1_0-so/Z-alignment/x-axis/Pt.psf 592 Tests/SpinOrbit/FePt-L1_0-so/Z-alignment/x-axis/fept.fdf 593 Tests/SpinOrbit/FePt-L1_0-so/Z-alignment/x-axis/fept.out 594 Tests/SpinOrbit/FePt-L1_0-so/Z-alignment/y-axis/ 595 Tests/SpinOrbit/FePt-L1_0-so/Z-alignment/y-axis/Fe.psf 596 Tests/SpinOrbit/FePt-L1_0-so/Z-alignment/y-axis/Pt.psf 597 Tests/SpinOrbit/FePt-L1_0-so/Z-alignment/y-axis/fept.fdf 598 Tests/SpinOrbit/FePt-L1_0-so/Z-alignment/y-axis/fept.out 599 Tests/SpinOrbit/FePt-L1_0-so/Z-alignment/z-axis/ 600 Tests/SpinOrbit/FePt-L1_0-so/Z-alignment/z-axis/Fe.psf 601 Tests/SpinOrbit/FePt-L1_0-so/Z-alignment/z-axis/Pt.psf 602 Tests/SpinOrbit/FePt-L1_0-so/Z-alignment/z-axis/fept.fdf 603 Tests/SpinOrbit/FePt-L1_0-so/Z-alignment/z-axis/fept.out 604 Tests/SpinOrbit/FePt-L1_0-so/config 605 Tests/SpinOrbit/FePt-L1_0-so/makefile 606 Tests/SpinOrbit/FePt-L1_0-so/script-fept.sh 607 Tests/SpinOrbit/Pt2-so-bis/ 608 Tests/SpinOrbit/Pt2-so-bis/README 609 Tests/SpinOrbit/Pt2-so-bis/X-alignment/ 610 Tests/SpinOrbit/Pt2-so-bis/X-alignment/x-axis/ 611 Tests/SpinOrbit/Pt2-so-bis/X-alignment/x-axis/Pt.psf 612 Tests/SpinOrbit/Pt2-so-bis/X-alignment/x-axis/pt2.fdf 613 Tests/SpinOrbit/Pt2-so-bis/X-alignment/x-axis/pt2.out 614 Tests/SpinOrbit/Pt2-so-bis/X-alignment/y-axis/ 615 Tests/SpinOrbit/Pt2-so-bis/X-alignment/y-axis/Pt.psf 616 Tests/SpinOrbit/Pt2-so-bis/X-alignment/y-axis/pt2.fdf 617 Tests/SpinOrbit/Pt2-so-bis/X-alignment/y-axis/pt2.out 618 Tests/SpinOrbit/Pt2-so-bis/X-alignment/z-axis/ 619 Tests/SpinOrbit/Pt2-so-bis/X-alignment/z-axis/Pt.psf 620 Tests/SpinOrbit/Pt2-so-bis/X-alignment/z-axis/pt2.fdf 621 Tests/SpinOrbit/Pt2-so-bis/X-alignment/z-axis/pt2.out 622 Tests/SpinOrbit/Pt2-so-bis/Z-alignment/ 623 Tests/SpinOrbit/Pt2-so-bis/Z-alignment/x-axis/ 624 Tests/SpinOrbit/Pt2-so-bis/Z-alignment/x-axis/Pt.psf 625 Tests/SpinOrbit/Pt2-so-bis/Z-alignment/x-axis/pt2.fdf 626 Tests/SpinOrbit/Pt2-so-bis/Z-alignment/x-axis/pt2.out 627 Tests/SpinOrbit/Pt2-so-bis/Z-alignment/y-axis/ 628 Tests/SpinOrbit/Pt2-so-bis/Z-alignment/y-axis/Pt.psf 629 Tests/SpinOrbit/Pt2-so-bis/Z-alignment/y-axis/pt2.fdf 630 Tests/SpinOrbit/Pt2-so-bis/Z-alignment/y-axis/pt2.out 631 Tests/SpinOrbit/Pt2-so-bis/Z-alignment/z-axis/ 632 Tests/SpinOrbit/Pt2-so-bis/Z-alignment/z-axis/Pt.psf 633 Tests/SpinOrbit/Pt2-so-bis/Z-alignment/z-axis/pt2.fdf 634 Tests/SpinOrbit/Pt2-so-bis/Z-alignment/z-axis/pt2.out 635 Tests/SpinOrbit/Pt2-so-bis/config 636 Tests/SpinOrbit/Pt2-so-bis/makefile 637 Tests/SpinOrbit/Pt2-so-bis/script-pt2.sh 638modified: 639 Docs/siesta.tex 640 Src/Makefile 641 Src/bands.F 642 Src/born_charge.F 643 Src/cdiag.F 644 Src/compute_dm.F 645 Src/compute_energies.F90 646 Src/compute_norm.F 647 Src/compute_rhog.F 648 Src/dfscf.f 649 Src/dhscf.F 650 Src/diag2g.F 651 Src/diag2k.F 652 Src/diagg.F 653 Src/diagk.F 654 Src/diagon.F 655 Src/final_H_f_stress.F 656 Src/grdsam.F 657 Src/initatom.f 658 Src/iodm_netcdf.F90 659 Src/ioeig.f 660 Src/local_DOS.F 661 Src/m_broyden_mixing.f 662 Src/m_energies.F90 663 Src/m_fire_mixing.f 664 Src/m_pulay.F90 665 Src/m_spin.F90 666 Src/mixer.F 667 Src/new_dm.F 668 Src/pdos.F 669 Src/periodic_table.f 670 Src/post_scf_work.F 671 Src/projected_DOS.F 672 Src/rdiag.F 673 Src/reoptical.F 674 Src/rhoofd.F 675 Src/save_density_matrix.F 676 Src/scfconvergence_test.F 677 Src/setup_H0.F 678 Src/setup_hamiltonian.F 679 Src/siesta_analysis.F 680 Src/siesta_init.F 681 Src/sparse_matrices.F 682 Src/state_analysis.F 683 Src/state_init.F 684 Src/vmat.F 685 Src/write_subs.F 686 Src/writewave.F 687 Src/xc.f 688 689----------------------------------------------------------------------- 6902016-03-07 trunk-492 691Initial k-displacements are now 0 692 693modified: 694 Src/kgridinit.F 695 Src/kpoint_grid.F90 696 Src/kpoint_pdos.F90 697 Src/m_ts_kpoints.F90 698 Src/setup_kscell.F 699 700----------------------------------------------------------------------- 7012016-03-07 trunk-491 702Fixed k-grid displacement reading 703 704- There was no need for not reading 0 as a displacement 705 in the kgrid_monkhorst_pack block. 706 707 Previously siesta would error when: 708 %block kgrid_monkhorst_pack 709 1 0 0 0 710 0 1 0 0 711 0 0 1 0 712 %endblock 713 while now this will works 714 715modified: 716 Src/kgridinit.F 717 Src/kpoint_grid.F90 718 Src/kpoint_pdos.F90 719 Src/m_ts_kpoints.F90 720 Src/setup_kscell.F 721 722----------------------------------------------------------------------- 7232016-03-05 trunk-490 724Automatic reading of #atoms, and species without denoting count 725 726- The NumberOfSpecies flag is now not needed any more. 727 728 This reflects an easier usage as it first reads the lines 729 in the ChemicalSpeciesLabel block and counts the number 730 of species from this block. 731 732 A small bug has also been fixed in that the first 733 number is now correctly inserted in the slot 734 that it intents. 735 736 The NumberOfSpecies flag still has precedence in case 737 you want a reduced number of elements. 738 739 +manual 740 741- The NumberOfAtoms is now not needed any more. 742 743 Similar to the NumberOfSpecies flag we now count the 744 number of atoms from the block by default. 745 746 The NumberOfAtoms flag still has precedence in case 747 you want a reduced number of atoms. 748 749 +manual 750 751- Output of chemical species is now more concise and aligned. 752 This is just a visual change. 753 754modified: 755 Docs/siesta.tex 756 Src/chemical.f 757 Src/coor.F 758 759----------------------------------------------------------------------- 7602016-03-03 trunk-489 761[merge] Tests fix, REFERENCE_DIR and SIESTA 762 763- After having build siesta in the Obj directory 764 a natural procedure would be to go to Tests 765 and run the tests: 766 make 767 However, the default SIESTA is not pointing to 768 the Obj. 769 Further the REFERENCE_DIR is not pointing to the 770 correct reference directory when in the top Tests 771 directory. 772 773 Hence the procedure is: 774 1. cd Obj 775 2. ../Src/obj_setup.sh 776 3. <create arch.make> 777 4. make 778 5. cd ../Tests/ 779 6. make 780 781modified: 782 Tests/test.mk 783 7842016-02-26 trunk-488 785Add generic citation helper 786 787- It was previously difficult to figure 788 out which papers where of significance when 789 using SIESTA. 790 This addition adds the capability of on-the-fly 791 creation of .bib files for users to easier find 792 the papers that are being used in their corresponding 793 run. 794 795added: 796 Src/m_cite.F90 797modified: 798 Src/Makefile 799 Src/m_efield.F 800 Src/siesta_init.F 801 Src/ts_init.F90 802 803----------------------------------------------------------------------- 8042016-02-17 trunk-486 805Fixed auxiliary array usage for ksv and optical 806 807- ksv: 808 This routine used Hkin as a work-array for calculating 809 certain quantities for polarization calculations. 810 811 This may lead to inadvertently destroying reliance 812 across calculations which are not intended. 813 814 This bug has been fixed by introducing the allocation 815 of the work-array in the ksv routine, directly. 816 817 Furthermore, we have explicitly added the => null() 818 when initializing several of the pointers. 819 820- optical: 821 This routine used Eold, Dold and Hkin as 822 work-arrays for calculating optical properties. 823 824 We have fixed these issues and moved allocation into 825 the routine. 826 827 Furthermore there were several "saved" variables 828 which were not needed to be saved. 829 830 All variables were re-calculated on each entry-point. 831 This has also been fixed. 832 833 Streamlined the algorithm for calculating transition-rates. 834 835- phirphi_opt: 836 Reduced memory by ENDLESS. 837 It allocated an enourmous amount of memory of which only 1 element 838 was used at a time. 839 If the full matrix is going to be needed, then re-instantiate the 840 comments !N. 841 The si-optical test yields the same result and I see no problem 842 in the current algorithm. 843 844modified: 845 Src/born_charge.F 846 Src/ksv.f 847 Src/optical.F 848 Src/phirphi_opt.f 849 Src/siesta_analysis.F 850 851----------------------------------------------------------------------- 8522016-02-17 trunk-485 853Add GPL notices and headers 854 855* Include proper headers 856* Add Docs/Contributors.txt and NOTICE.txt files. 857* Update READMEs and LICENSE files in several directories. 858* Remove Pseudo/atom, Util/test-xml 859* Remove DOM files from Src/xmlparser 860* Replace old copyright notice in Src/Confs 861 862This revision touches a large number of files due to the 863change in licensing and copyright. 864 865The other major change is the removal of the Pseudo/atom subtree, 866which is now distributed independently. 867 868----------------------------------------------------------------------- 8692016-02-05 trunk-484 870Merge fixes from rel-4.0 branch 871 872* Fix Tests/test.mk and Genbasis makefile 873 874The reference directory's path was incorrect in Tests/test.mk 875 876In Util/Gen-basis/Makefile, the treatment of COMP_LIBS can be improved 877with a form suggested by Pedro Brandimarte, which will work even if 878there are multiple files in COMP_LIBS. 879 880* Fix peak alloc report in MPI 881 882When alloc-report-level is 1 or 3, a report should be printed at every 883peak. This hanged in MPI runs. Now only the root node peaks are 884printed. 885 886(Thanks to Nick R. Papior) 887 888* Some older .CHANGES files have been moved to the 'branch-changes' 889 directory, and older release notes moved to the 890 'older-release-notes' directory. 891 892modified: 893 Tests/test.mk 894 Util/Gen-basis/Makefile 895 Src/alloc.F90 896 Docs/siesta.tex 897added: 898 Docs/branch-changes/ 899 Docs/older-release-notes/ 900 901----------------------------------------------------------------------- 9022015-12-18 10:25:00 GMT trunk-483 903Add lapack and blas code in Libs to support OMM and SVD 904 905* To enable quick compilation with no external libraries, some 906 lapack/blas routines have been added to the Src/Libs directory. 907 908 A minimal example of arch.make: Src/Sys/nolibs.make 909 910 Note that some optional features do depend on the availability of 911 external libraries, such as netCDF and fftw. 912 913added: 914 Src/Libs/svd_omm_lapack.f 915modified: 916 Src/Libs/blas.f 917 Src/Libs/makefile 918 Src/Sys/nolibs.make 919 Util/Gen-basis/Makefile 920 921----------------------------------------------------------------------- 9222015-12-17 16:25:00 GMT trunk-482 923New versions of grid2cube and gnubands. Laplacian of grid functions 924 925* Updated new.gnubands in Util/Bands to enhance spin processing 926 and optional production of labels in tick marks. 927 928 (Nick R. Papior) 929 930* A new experimental program g2c_ng in Util/Grid offers extended 931 and cleaner functionality over the classic grid2cube. 932 933* A new program cdf_laplacian in Util/Grid computes the laplacian 934 of a grid function in netCDF format. 935 936 (A. Garcia) 937 938added: 939 Util/Grid/cdf_laplacian.F90 940 Util/Grid/g2c_ng.f 941 Util/Grid/m_gridfunc.F90 942 Util/Grid/m_struct.f90 943modified: 944 Util/Bands/Makefile 945 Util/Bands/README 946 Util/Bands/new.gnubands.f90 947 Util/Grid/README 948 Util/Grid/makefile 949 Util/build_all.sh 950 951 952----------------------------------------------------------------------- 9532015-11-26 15:10:00 GMT trunk-481 954Increase the number of allowed iterations in minvec 955 956The default value of 100 was inadequate for the needs of 957k-point supercells for large multipliers. 958 959modified: 960 Src/minvec.f 961 962----------------------------------------------------------------------- 9632015-11-26 13:50:00 GMT trunk-480 964Fix bug in heapsort routine 965 966(Thanks to Nick Papior) 967 968* The recent re-implementation of the heapsort algorithm in routine 969 'ordix' in 'sorting.f' (trunk revno 468) was buggy. 970 971 This affected: 972 973 - The siesta.BONDS file, which did not have optimal ordering of the 974 bond-lengths. 975 976 - Some calculations using k-points, as routine 'minvec', used in the 977 definition of the effective k-point supercell, calls 'ordix'. 978 (The reference outputs for the 'var_cell' and 'si2x1h' tests have 979 been modified.) 980 981 - (probably) The re-use of density-matrix information, as the ordering 982 of interactions in 'hsparse' also depended on 'ordix' through calls to 983 'ordvec'. 984 985 - (maybe) The operation of the "rho-mixing" routines, which use 'ordix' 986 for the sorting of stars. 987 988modified: 989 Src/sorting.f 990 Tests/Reference/si2x1h.out 991 Tests/Reference/var_cell.out 992 993----------------------------------------------------------------------- 9942015-10-04 00:40:00 GMT trunk-479 995Assorted fixes and cleanup. Update reference outputs 996 997- Replace pointers by allocatables in {zm,cell}_broyden_optim. 998- Split-off read_options from siesta_options to reduce 999 dependencies and clarify hidden symbol associations. 1000- Remove dependency in sparse_matrices 1001- Fix dependencies in makefiles in Util 1002- Remove Reference-xml 1003- Update Reference-out files 1004- Provide a simple-minded mechanism to flag differences in the 1005 test outputs ('make check'). 1006 1007removed: 1008 Tests/Reference-xml/ 1009 Tests/Reference/partial.out 1010added: 1011 Src/read_options.F90 1012 Tests/Reference/TranSiesta-TBTrans/ts_au_100/au_100.AVTRANS 1013 Tests/Reference/TranSiesta-TBTrans/ts_au_100/au_100.TEIG 1014 Tests/Reference/TranSiesta-TBTrans/ts_au_100_0.25V/au_100.AVTRANS 1015 Tests/Reference/TranSiesta-TBTrans/ts_au_100_0.25V/au_100.TEIG 1016 Tests/Reference/TranSiesta-TBTrans/ts_au_100_repetition/au_100.AVTRANS 1017 Tests/Reference/TranSiesta-TBTrans/ts_au_100_repetition/au_100.TEIG 1018 Tests/Reference/TranSiesta-TBTrans/ts_au_100_repetition_0.25V/au_100.AVTRANS 1019 Tests/Reference/TranSiesta-TBTrans/ts_au_100_repetition_0.25V/au_100.TEIG 1020 Tests/TranSiesta-TBTrans/copy_to_reference.sh 1021 Tests/TranSiesta-TBTrans/run_tests.sh 1022modified: 1023 Docs/siesta.tex 1024 Src/Makefile 1025 Src/cell_broyden_optim.F 1026 Src/diagon.F 1027 Src/final_H_f_stress.F 1028 Src/obj_setup.sh 1029 Src/projected_DOS.F 1030 Src/proximity_check.F 1031 Src/siesta_analysis.F 1032 Src/siesta_forces.F 1033 Src/siesta_init.F 1034 Src/siesta_move.F 1035 Src/siesta_options.F90 1036 Src/sparse_matrices.F 1037 Src/state_analysis.F 1038 Src/state_init.F 1039 Src/struct_init.F 1040 Src/write_md_record.F 1041 Src/write_subs.F 1042 Src/zm_broyden_optim.F 1043 Tests/Makefile 1044 Tests/README 1045 Tests/Reference/* 1046 Tests/cmp_digest.sh 1047 Tests/partial/README 1048 Tests/test.mk 1049 Util/Denchar/Src/Makefile 1050 Util/Gen-basis/Makefile 1051 Util/STM/ol-stm/Src/Makefile 1052 Util/SiestaSubroutine/README 1053 Util/TBTrans/Makefile 1054 Util/TBTrans_rep/Makefile 1055 Util/VCA/Makefile 1056 Util/build_all.sh 1057 1058 1059 1060 1061 1062 1063----------------------------------------------------------------------- 10642015-09-29 10:25:00 GMT trunk-478 1065Fixes: OCCS file, pdoskp, processorY 1066 1067* The OCCS file, containing the occupation at each k-point, 1068 is now created only during the scf cycle, in 'diagon'. This 1069 fixes problems that appeared when 'diagk' was called from 1070 other routines. 1071 1072* Some arrays in pdoskp were not dimensioned correctly on 1073 input in pdoskp. 1074 1075* Added a sanity check for the user-entered ProcessorY. 1076 1077(Thanks to Nick P. Andersen) 1078 1079modified: 1080 Src/diagk.F 1081 Src/diagk_file.F 1082 Src/diagon.F 1083 Src/initparallel.F 1084 Src/pdoskp.F 1085 1086----------------------------------------------------------------------- 10872015-09-17 13:25:00 GMT trunk-477 1088Fixes: pi/a mode in bands; low-n interpolation; others 1089 1090* Fix handling of n<3 cases in interpolation.f90 1091* Made global variable 'saved' in matel_registry 1092 (J. Soler, with thanks to Nick P. Andersen) 1093 1094* Fix uninitialized variable in interpolation.f90. 1095* Proper check on number of atoms in zmatrix.F. 1096* Avoid underflow in sorting.f. 1097 1098 (Thanks to P. Brandimarte) 1099 1100* In bands.F, only check for LatticeConstant input 1101 in the "pi/a" case. 1102 1103modified: 1104 Src/bands.F 1105 Src/interpolation.f90 1106 Src/matel_registry.F90 1107 Src/sorting.f 1108 Src/zmatrix.F 1109 1110----------------------------------------------------------------------- 11112015-07-16 15:05:00 GMT trunk-476 1112Fix the geometry and DM and H logic for consistency in analysis 1113 1114-*-*-*-*-* 1115IMPORTANT NOTE: This patch will slightly change the output 1116of most calculations and the detailed results of any 1117post-processing. Keep this in mind if you need to maintain coherency 1118within a project. See the rest of the text for ways to restore 1119backward compatibility. The reference output files in Tests/Reference 1120have *not* been updated yet. 1121-*-*-*-*-* 1122 1123This is the initial patch in a long-overdue clarification work related 1124to the "outer geometry loop" in Siesta and its interaction with the 1125analysis of the electronic structure. 1126 1127The most important changes, following the actual refactoring logic, are: 1128 1129* Superfluous calls to 'superx' to propagate the new coordinates to 1130 the auxiliary supercell in 'siesta_move' have been removed, as they 1131 are already done by 'state_init'. 1132 1133* The above change has the side effect of leaving inconsistent sets of 1134 unit cell and supercell coordinates in 'siesta_analysis' if the unit 1135 cell coordinates used in the latter are those 'moved' by the 1136 geometry-update routines. To avoid this, and to do the analysis 1137 using the actual coordinates used in the computation of the 1138 electronic structure, the coordinates are reset to those values 1139 (using the *_last arrays) in 'siesta_analysis'. The old behavior 1140 can be recovered by using by setting the backward compatibility 1141 switch 'compat-pre-v4-dynamics' to 'true'. 1142 1143 1144* To guarantee that the DM and H used in the analysis correspond to 1145 the latest electronic structure computed, there should be no mixing 1146 at the end of the scf loop. This behavior, which was optional until 1147 now (controlled by the value of scf-mix-after-convergence) is now 1148 the default. The use of DM_out instead of DM_mixed provides also a 1149 truly variational total-energy and more consistent forces. If the 1150 scf cycle is carried out mixing H, H(DM_in) is recovered by 1151 re-setting H to Hold in siesta_forces at the end of the cycle. 1152 1153 Also, to preserve the right H for analysis it is necessary to 1154 avoid overwriting it in post_scf_work. This is now done by default, 1155 except if the option 'scf-recompute-h-after-scf' is 'true'. 1156 1157 There is another switch for pre-v4.0 compatibility in this context: 1158 If 'compat-pre-v4-dm-h' is 'true', the 'scf-mix-after-convergence' 1159 and 'scf-recompute-h-after-scf' options are activated too. 1160 1161 Some comments have been added to siesta_forces to document possible 1162 further clarifications. 1163 1164* For clarity, each MD or geometry-optimization flavor has now its own 1165 self-contained logic block in 'siesta_move'. This has uncovered a 1166 few issues that have been corrected: 1167 1168 - The quenched forms of the Verlet and Parrinello-Rahman (PR) 1169 schemes, which are actually relaxations, did not check for 1170 convergence before moving the atoms (PR did not check at any 1171 point). Now the 'constrained' forces and stress are checked 1172 before invoking the routines. In the case of PR, a 'target stress' 1173 can optionally be subtracted from the constrained stress (a 1174 further form of constraint that was previously only available 1175 (internally) in the standard relaxation routines). A future update 1176 might put all these constraint conditions in 'fixed', but care 1177 should be taken to study their interaction with the MD 1178 variable-cell routines. A future revision might look into the 1179 effectiveness of the variable-cell routines. 1180 There is a new example in Tests for quenched MD relaxation. 1181 1182 - The geometry output in 'siesta_move' is now exclusively done for 1183 checkpointing purposes, and typically involves the 'moved' 1184 geometries. The current geometry output is done in 'state_init', 1185 and any final output in 'siesta_analysis'. 1186 1187 - Some output calls have been removed where they did not make much 1188 sense (as in the FC or server blocks). 1189 1190 - The deprecated 'phonon' support has been removed. 1191 1192* Siesta_analysis outputs the 'current' final geometry, and not the 1193 'moved' one. The old behavior can be recovered by using the 1194 'compat-pre-v4-dynamics' switch. 1195 1196* The default 'dynamics' option has been changed from 'verlet' to 'CG'. 1197 There should really be a new 'single-point' default which completely 1198 avoids 'siesta_move'. The old behavior can be recovered by using the 1199 'compat-pre-v4-dynamics' switch. 1200 1201* Single-point calculations do not write .STRUCT_NEXT_ITER files, and 1202 the coordinates in the XV file are the current ones, unmoved. 1203 Extra output in siesta_options is avoided for this case. 1204 1205* The headings for the beginning of the dynamics blocks are now 1206 more concrete. 1207 1208Other minor changes: 1209 1210* Fix the IO field widths in the bonds routine to support more atoms. 1211 1212* Add a few more deallocations in several routines, and change the 1213 'routine' field in some deallocations to match the allocations 1214 (notably for arrays in the 'sparse_matrices' module) 1215 1216* Cosmetic changes in the output format for dynamics headings 1217 1218* Atomic displacements for force-constant runs are output in Ang. 1219 1220removed: 1221 Src/phonon.F 1222added: 1223 Src/m_target_stress.F 1224 Tests/si2x1h-quench/ 1225 Tests/si2x1h-quench/makefile 1226 Tests/si2x1h-quench/si2x1h-quench.fdf 1227 Tests/si2x1h-quench/si2x1h-quench.pseudos 1228modified: 1229 Docs/siesta.tex 1230 Src/Makefile 1231 Src/atomlist.f 1232 Src/bonds.f 1233 Src/dhscf.F 1234 Src/diag2g.F 1235 Src/diag2k.F 1236 Src/final_H_f_stress.F 1237 Src/fixed.F 1238 Src/ioxv.F 1239 Src/m_check_supercell.f 1240 Src/m_pulay.F90 1241 Src/new_dm.F 1242 Src/post_scf_work.F 1243 Src/save_density_matrix.F 1244 Src/siesta_analysis.F 1245 Src/siesta_forces.F 1246 Src/siesta_init.F 1247 Src/siesta_move.F 1248 Src/siesta_options.F90 1249 Src/sparse_matrices.F 1250 Src/state_analysis.F 1251 Src/state_init.F 1252 Src/write_subs.F 1253 1254----------------------------------------------------------------------- 12552015-07-08 11:00:00 GMT trunk-475 1256Minor fixes and cosmetic changes after Wannier merge 1257 1258* Associate auxiliary array auxloc in slave nodes even if 1259 not used in mpi_reduce call (Nick P. Andersen). 1260 1261* Add missing files in Test/wannier. 1262 1263* Streamline the wannier interface output. 1264 1265added: 1266 Tests/wannier/makefile 1267 Tests/wannier/wannier.pseudos 1268modified: 1269 Src/compute_pw_matrix.F90 1270 Src/m_digest_nnkp.F90 1271 Src/write_inp_wannier.F90 1272 1273----------------------------------------------------------------------- 12742015-07-07 08:30:00 GMT trunk-474 1275Merge code for interoperation with Wannier90 1276 1277(Javier Junquera, after work by Richard Korytar, and Alberto Garcia) 1278 1279Siesta can now read the .nnkp file produced by Wannier90 and output 1280the *.amn, *.mmn, *.eig (see below), and UNK* files needed by 1281post-processing with that program, which generates maximally-localized 1282Wannier functions. 1283 1284The most relevant changes in the code needed to support this 1285functionality are detailed below. For practical guidance, see the 1286manual, the simple test in Tests/wannier, and the suite of Wannier90 1287examples adapted for Siesta in 1288 1289 http://personales.unican.es/junqueraj/Wannier-examples.tar.gz 1290 1291 1292* To implement support for "projection functions", which might not be 1293 pure radial functions, but hybrids with mixed angular momentum and 1294 varying spatial orientation, as well as to provide support of 1295 arbitrary kinds of radial functions for future developments, the 1296 'matel' framework has been extended: 1297 1298 Matel (actually renamed to 'new_matel') now accepts two generalized 1299 indexes instead of the two pairs of indexes previously used. The 1300 generalized indexes can represent either a normal "radial function", 1301 as in previous Siesta usage, or a "projection function". The indexes 1302 are obtained via a "check-in" into a registry of functions, which 1303 keeps track of the nature of the functions and provides the needed 1304 evaluators and accessors for 'new_matel'. 1305 1306 The relevant code is in 'matel_registry', 'new_matel', and 1307 'register_rfs'. The latter shows how to "register" the usual radial 1308 functions for PAOs, KB projectors, etc. 1309 1310* Bloch states are computed and saved, instead of being recomputed as 1311 needed, to avoid problems with irreproducible random phases and 1312 linear combinations within degenerate subspaces. 1313 1314* At this point the parallelization of the new code is only "over 1315 orbitals". It is not yet possible to parallelize the operations over 1316 the k-points on the grid. The production of the UNK* files can be 1317 slow if there are many k-points and bands. 1318 1319* There is not yet support for "spinor wavefunctions". In the case of 1320 spin-polarized calculations, separate spin-up and spin-down 1321 processings are needed. 1322 1323* There is not yet support for interaction with Wannier90 in "library 1324 mode", due to licensing issues. 1325 1326* The "eigenvalue file" for Wannier90 has extension .eigW to avoid 1327 clashes with the standard Siesta eigenvalue file in case-insensitive 1328 filesystems. 1329 1330removed: 1331 Src/matel.f 1332added: 1333 Src/amn.F90 1334 Src/broadcast_projections.F 1335 Src/compute_pw_matrix.F90 1336 Src/delk.F 1337 Src/diagonalizeHk.F90 1338 Src/m_digest_nnkp.F90 1339 Src/m_noccbands.f 1340 Src/m_orderbands.F 1341 Src/m_overkkneig.F90 1342 Src/m_planewavematrix.F90 1343 Src/m_planewavematrixvar.F90 1344 Src/m_trialorbitalclass.f90 1345 Src/m_writedelk.F 1346 Src/matel_registry.F90 1347 Src/mmn.F90 1348 Src/new_matel.f 1349 Src/register_rfs.F90 1350 Src/reordpsi.F 1351 Src/siesta2wannier90.F90 1352 Src/write_inp_wannier.F90 1353 Tests/wannier/ -- New test 1354 Tests/wannier/wannier.fdf 1355 Tests/wannier/wannier.nnkp 1356modified: 1357 Docs/siesta.tex 1358 Src/Makefile 1359 Src/alloc.F90 -- New z3 and z4 generics 1360 Src/m_mpi_utils.F 1361 Src/atm_types.f -- Fields for global index storage 1362 Src/atmfuncs.f -- Global index management 1363 Src/dhscf.F -- New routine to compute PW matrix elements 1364 Src/mneighb.f -- Added 'x0' module variable 1365 Src/parallelsubs.F -- Catch special blocksize case 1366 Src/mesh.F -- Extra bookeeping 1367 Src/meshdscf.F 1368 Src/meshsubs.F 1369 Src/kinefsm.f -- New matel 1370 Src/naefs.f 1371 Src/nlefsm.f 1372 Src/overfsm.f 1373 Src/overlap.f 1374 Src/phirphi.f 1375 Src/phirphi_opt.f 1376 Src/siesta_analysis.F -- Actual w90 processing 1377 Src/siesta_init.F 1378 Src/siesta_options.F90 1379 Src/spher_harm.f -- Two implementations of YLMEXP. 1380 1381 1382----------------------------------------------------------------------- 13832015-06-29 15:20:00 GMT trunk-473 1384Merge code for 'server' operation via sockets and i-PI interface 1385 1386(Michele Ceriotti, Jose Soler) 1387 1388* A new infrastructure for socket handling in f90 has been 1389implemented by Michele Ceriotti (EPFL), who is also the author 1390of the i-PI framework. From its web-page: 1391 1392 i-PI is a Path Integral Molecular Dynamics (PIMD) wrapper code 1393 designed to be used together with ab initio evaluation of the 1394 interactions between the atoms. i-PI should be run as a separate 1395 program, and communicates with one or more instances of an 1396 electronic structure code using internet (or UNIX) sockets. The 1397 communication is regulated by a simple protocol, and requires 1398 patching the client code to handle the exchange of data with i-PI. 1399 1400This revision implements the interface to the i-PI protocol. In 1401Siesta, the new socket functionality can also be used as a new form of 1402'server' operation. 1403 1404See Util/Sockets for examples of the f90 socket interface, 1405Util/SiestaSubroutine for examples of the server operation (including 1406via sockets) and Tests/i-pi-test for a simple test of interoperability 1407with i-PI. 1408 1409added: 1410 Src/fsiesta_sockets.F90 1411 Src/fsockets.f90 1412 Src/iosockets.F90 1413 Src/sockets.c 1414 Tests/ipi-test/ 1415 Util/SiestaSubroutine/SimpleTest/README 1416 Util/SiestaSubroutine/SimpleTest/socket.fdf 1417 Util/SiestaSubroutine/SimpleTest/sockets.sh 1418 Util/Sockets/ 1419renamed: 1420 Util/SiestaSubroutine/SimpleTest/Src/simple_pipes_parallel.f90 => 1421 Util/SiestaSubroutine/SimpleTest/Src/simple_parallel.f90 1422modified: 1423 Docs/siesta.tex 1424 Src/Makefile 1425 Src/fsiesta_mpi.F90 1426 Src/fsiesta_pipes.F90 1427 Src/siesta_master.f90 1428 Src/siesta_options.F90 1429 Src/struct_init.F 1430 Util/README 1431 Util/SiestaSubroutine/FmixMD/Src/para.f90 1432 Util/SiestaSubroutine/README 1433 Util/SiestaSubroutine/SimpleTest/Src/Makefile 1434 Util/SiestaSubroutine/SimpleTest/h2o.fdf 1435 Util/SiestaSubroutine/SimpleTest/test.sh 1436 Util/SiestaSubroutine/SimpleTest/Src/simple_parallel.f90 1437 1438----------------------------------------------------------------------- 14392015-06-22 9:35:00 GMT trunk-472 1440Revert previous change affecting FA and FC files. FAC/FCC files. 1441 1442* At revno 464, a change was introduced to output the constrained 1443 forces to the FA and FC files. This had unintended consequences for 1444 some analysis tools. 1445 1446 The change has been reverted, and the FC/FA files are now created as 1447 before. In addition, if constraints are used, new FCC/FAC files 1448 will be created with the constrained forces. 1449 1450 The vibra utility will default to use the FCC files if the 1451 GeometryConstraints block exists, and in any case the 1452 force-constants file to use can be specified with the Vibra.FC fdf 1453 option. 1454 1455 To support these changes, the write_forces subroutine has now 1456 the geometry step as an additional argument. 1457 1458 The writing of forces has been moved to its appropriate place in the 1459 write_subs modules. 1460 1461* Some more cosmetic changes in the Vibra package. 1462 1463modified: 1464 Docs/siesta.tex 1465 Src/Makefile 1466 Src/iofa.f 1467 Src/ofc.f 1468 Src/siesta_analysis.F 1469 Src/siesta_forces.F 1470 Src/state_analysis.F 1471 Src/write_subs.F 1472 Util/Vibra/Docs/CHANGES 1473 Util/Vibra/Docs/vibra.tex 1474 Util/Vibra/Examples/README 1475 Util/Vibra/Examples/si54.bands 1476 Util/Vibra/Examples/si54.fdf 1477 Util/Vibra/Src/Makefile 1478 Util/Vibra/Src/fcbuild.f 1479 Util/Vibra/Src/recoor.f 1480 Util/Vibra/Src/vibra.f 1481 1482----------------------------------------------------------------------- 14832015-06-17 8:50:00 GMT trunk-471 1484Fix SiestaXC makefile. Clarifiy docs for WriteDenchar 1485 1486* Fix a typo in SiestaXC/makefile that was preventing 1487 the correct processing of the "dist" target. 1488 (J. Soler) 1489 1490* Update the WriteDenchar documentation in the Siesta manual. 1491 (G. Huhs) 1492 1493modified: 1494 Docs/siesta.tex 1495 Src/SiestaXC/makefile 1496 1497----------------------------------------------------------------------- 14982015-06-10 12:30:00 GMT trunk-470 1499Build fixes in Util and SiestaXC 1500 1501* Bring up to date the code in STM/ol-stm. 1502 1503* Fixes for compilation of various programs 1504 in Util after the NR changeover. 1505 1506added: 1507 Util/Gen-basis/local_die.F 1508 Util/STM/ol-stm/Src/handlers.f 1509modified: 1510 Src/SiestaXC/atomxc.F90 1511 Src/SiestaXC/mesh1d.f90 1512 Util/Denchar/Src/Makefile 1513 Util/Gen-basis/Makefile 1514 Util/Gen-basis/gen-basis.F 1515 Util/STM/ol-stm/Src/Makefile 1516 Util/STM/ol-stm/Src/atompla.f 1517 Util/STM/ol-stm/Src/extrapolate.f 1518 Util/STM/ol-stm/Src/fftw3_mymod.f90 1519 Util/STM/ol-stm/Src/readstm.f 1520 Util/STM/ol-stm/Src/reinitstm.f 1521 Util/STM/ol-stm/Src/stm.f 1522 Util/SiestaSubroutine/FmixMD/Src/Makefile 1523 Util/build_all.sh* 1524 1525----------------------------------------------------------------------- 15262015-06-02 09:45:00 GMT trunk-469 1527Cosmetic fix for errorf.f 1528 1529Put proper end statements 1530 1531modified: 1532 Src/errorf.f 1533 1534----------------------------------------------------------------------- 15352015-06-02 07:10:00 GMT trunk-468 1536Replacement of NR routines. Fix for charge-conf variables. 1537 1538* Replaced FFT 1d routine by a version based on Temperton's GPFA 1539 1540 Calls to the 'four1' routine have been replaced by calls to 1541 'fft_gpfa_ez' with the same arguments. This routine lives 1542 in a new module in 'm_fft_gpfa.F', which also contains the 1543 legacy code by Temperton and the original entry points. 1544 1545 The cdf_fft program in Util/Grid now uses Temperton's GPFA package. 1546 1547 (A. Garcia) 1548 1549* Replaced tred2/tqli by Lapack calls in m_filter (E. Artacho) 1550 1551* Replaced derf/derfc by Netlib versions (E. Artacho) 1552 1553* Replaced random number routine (E. Artacho) 1554 1555* Some routines from Numerical Recipes reimplemented 1556 1557 Some routines from Numerical Recipes have been reimplemented with 1558 (mostly) the same algorithms. 1559 1560 (Jose Soler, with minor changes by A. Garcia) 1561 1562 - spline interpolation routines rewritten and moved to interpolation module 1563 - polint Lagrange interpolation rewritten and moved to interpolation module 1564 - ordix subroutine recoded 1565 - chebfd re-styled to remove remaining similarities with NR chebft 1566 - choldc and cholsl fully re-styled and renamed as cholDcmp and cholLinSys 1567 - zbrent substituted by a simple bisection root finder 1568 - amoeba method re-implemented 1569 1570 (+ Interface to external routine 'die' simplified: it now 1571 requires a string argument) (A. Garcia) 1572 1573* Bugfix for soft confinement charge 1574 1575 A shell was not initialized properly if the PAO.Basis block was 1576 not defined. Now the initialization routine is called before 1577 setting up the orbital. 1578 1579 Also changed the comments about the magnitude of the charge 1580 confinement width. 1581 1582 (Nick P. Andersen) 1583 1584----------------(Inserted missing records)----------------------------- 15852015-03-04 11:47:32 +0100 [trunk-467] 1586Fix import of idyn in save_density_matrix (rc-4.0) 1587 1588 * The idyn variable was not imported from siesta_options 1589 in standard "siesta" mode 1590 1591 (thanks to J. Junquera) 1592 1593 modified: 1594 Src/save_density_matrix.F 1595------------------------------------------------------------ 15962015-02-03 15:28:00 +0100 [trunk-466] 1597Fixed IO statements for molecularmechanics module 1598 1599 (Nick .P. Andersen) 1600 1601 * IO print-outs was still abundant in parallel runs. 1602 Now only the IO node will print out. 1603 1604 * The manual has been corrected to correctly state 1605 that any unit is allowed in the MM.* block. 1606 1607 modified: 1608 Docs/siesta.tex 1609 Src/molecularmechanics.F90 1610------------------------------------------------------------ 16112015-01-07 11:35:12 +0100 [trunk-465] 1612Merge fix from rc-4.0: MPI tag in SiestaXC/mesh3d 1613 1614 * The variable Mpitag was not initialized, leading to problems whenever 1615 its value was not zero or considered as MPI_ANY_TAG in a Recv operation. 1616 1617 (Nick P. Andersen) 1618 1619 modified: 1620 Src/SiestaXC/mesh3d.F90 1621------------------------------------------------------------ 16222014-11-08 17:26:37 +0100 [trunk-464] 1623Merge fixes from rc-4.0: constr. forces, MPI compilation, mm.potentials 1624 1625 -- Fabiano Corsetti: Fix output to show constrained forces 1626 1627 * Changed the calling of the iofa and ofc routines inside write_subs, 1628 so that the forces with constraints are written to file in each case 1629 instead of the uncorrected forces. 1630 1631 modified: 1632 Src/write_subs.F 1633 1634 1635 -- Alberto Garcia: Fix 'clean' rule in MPI Makefile 1636 1637 The interface library libmpi_f90.a was not removed when issuing a 1638 'make clean', possibly leading to strange errors if the MPI 1639 compilation environment was later changed. 1640 1641 modified: 1642 Src/MPI/Makefile 1643 1644 -- Nick P Andersen: Fix shortcomings in reading of empirical potential block 1645 1646 * The number of potential lines is now arbitrary. 1647 * Units handling has been improved, to allow arbitrary 1648 length and energy units. 1649 1650 modified: 1651 Src/molecularmechanics.F90 1652 1653----------------------------------------------------------------------- 16542014-11-08 16:15:00 GMT trunk-463 1655Added restart file for smooth continuation of annealing runs 1656 1657* Added the writing and reading of an .ANNEAL_RESTART file, along the 1658 same lines of the .VERLET_RESTART file. This fixes a small problem 1659 for restarting annealing calculations when a continuous smooth run 1660 is desired. 1661 1662(Fabiano Corsetti) 1663 1664added: 1665 Tests/anneal-cont/ 1666 Tests/anneal-cont/README 1667 Tests/anneal-cont/makefile 1668 Tests/anneal-cont/script.sh 1669modified: 1670 Docs/siesta.tex 1671 Src/dynamics.f 1672 1673----------------------------------------------------------------------- 16742014-05-29 12:40:00 GMT trunk-462 1675Improved MPI version of siesta as a subroutine (J.M.Soler) 1676 1677* The MPI version of fsiesta now creates a directory for each siesta 1678 process, and writes in it all output and continuation files 1679 1680* New example Util/SiestaSubroutine/ProtoNEB/ 1681 1682added: 1683 Util/SiestaSubroutine/ProtoNEB/ 1684 Util/SiestaSubroutine/ProtoNEB/NH3-point01.fdf 1685 Util/SiestaSubroutine/ProtoNEB/NH3-point02.fdf 1686 Util/SiestaSubroutine/ProtoNEB/NH3-point03.fdf 1687 Util/SiestaSubroutine/ProtoNEB/NH3.fdf 1688 Util/SiestaSubroutine/ProtoNEB/Src/ 1689 Util/SiestaSubroutine/ProtoNEB/Src/Makefile 1690 Util/SiestaSubroutine/ProtoNEB/Src/protoNEB.F90 1691modified: 1692 Src/fsiesta_mpi.F90 1693 Util/SiestaSubroutine/README 1694 1695----------------------------------------------------------------------- 16962014-05-29 10:45:00 GMT trunk-461 1697%files added to Util/JobList options (J.M.Soler) 1698 1699added: 1700 Util/JobList/Examples/Ice/dummyFile 1701modified: 1702 Util/JobList/Examples/Ice/iceChecks.jobs 1703 Util/JobList/README 1704 Util/JobList/Src/jobList.f90 1705 1706----------------------------------------------------------------------- 17072014-05-29 10:30:00 GMT trunk-460 1708New GGA and VDW functionals (M.Fritz & J.M.Soler) 1709 1710* Added 4 GGA functionals by Capelle et al 1711 Refs: L.S.Pedroza et al, PRB 79, 201106 (2009) and 1712 M.M.Odashima et al, J. Chem. Theory Comp. 5, 798 (2009) 1713 1714* Added 2 VDW-DF functionals of 1715 V.R.Cooper, PRB 81, 161104(R) (2010) 1716 K. Berland and P. Hyldgaard, PRB 89, 035412 (2014) 1717 1718* Fixed PW91 and BLYP GGA functionals 1719 1720* Corrected a minor bug in vdwxc.F90 (parameter nq->mq) 1721 1722* Updated and extended XC testers 1723 1724* Added some test outputs in SiestaXC/Testers/Reference 1725 1726* m_timer.F90 added to SIESTA_SRCS in SiestaXC/makefile 1727 1728(+ fix syntax error in Pseudo/atom/pxf.F90) 1729(+ increase patch level in Pseudo/atom/version.h) 1730 1731added: 1732 Docs/gga.CHANGES 1733 Src/SiestaXC/Testers/Reference/ 1734 Src/SiestaXC/Testers/Reference/test1.out 1735 Src/SiestaXC/Testers/Reference/test2.out 1736 Src/SiestaXC/Testers/Reference/test3.out 1737 Src/SiestaXC/Testers/Reference/test4.out 1738 Src/SiestaXC/Testers/test6.f90 1739 Src/SiestaXC/Testers/test6.m 1740renamed: 1741 Src/SiestaXC/Testers/test2.f90 => Src/SiestaXC/Testers/test2.F90 1742modified: 1743 Docs/siesta.tex 1744 Pseudo/atom/Docs/atom.tex 1745 Pseudo/atom/pseudoXML.f 1746 Pseudo/atom/pxf.F90 1747 Pseudo/atom/velect.f 1748 Pseudo/atom/version.h 1749 Src/SiestaXC/Testers/makefile 1750 Src/SiestaXC/Testers/test1.f90 1751 Src/SiestaXC/Testers/test3.F90 1752 Src/SiestaXC/Testers/test4.F90 1753 Src/SiestaXC/Testers/test5.f90 1754 Src/SiestaXC/atomxc.F90 1755 Src/SiestaXC/cellxc.F90 1756 Src/SiestaXC/ggaxc.f 1757 Src/SiestaXC/ldaxc.f 1758 Src/SiestaXC/makefile 1759 Src/SiestaXC/siestaxc.F90 1760 Src/SiestaXC/vdwxc.F90 1761 Src/SiestaXC/vv_vdwxc.F90 1762 Src/SiestaXC/xcmod.f90 1763 Src/atom.F 1764 Src/xc.f 1765 Src/SiestaXC/Testers/test2.F90 1766 1767----------------------------------------------------------------------- 17682014-03-25 12:40:00 GMT trunk-459 1769Fix bug when reading spin-polarized deformation charge 1770 1771When reading a spin-polarized deformation charge (in netCDF form) 1772the added atomic-superposition charge was too large by a factor of two. 1773 1774modified: 1775 Src/dhscf.F 1776 1777----------------------------------------------------------------------- 17782014-03-05 09:15:00 GMT trunk-458 1779Fixes and new features in fdf 1780 1781* Fix handling of empty value for fdf_string 1782 1783When a line contains only a label, fdf_string incorrectly tried to 1784read beyond the first token. It has now been fixed, assigning an 1785empty string to the function value. 1786 1787* Nullify fdf buffer pointer at declaration 1788 1789(+ fix the assignment of the name for the debug file) 1790 1791* New list functionality in fdf (Nick P Andersen) 1792 1793See Src/fdf/sample.F90 and sample.fdf for examples. 1794 1795* A more flexible fdf_init (JM Soler) 1796 1797The routine fdf_init can be called without arguments in the most 1798common case when reading from standard input (unit 5). See the new 1799code in fdf.F90 for details. Note that Siesta does not yet use the new 1800possibilities. 1801 1802added: 1803 Docs/fdf.CHANGES 1804modified: 1805 Src/fdf/fdf.F90 1806 Src/fdf/parse.F90 1807 Src/fdf/sample.F90 1808 Src/fdf/sample.fdf 1809 version.info 1810 1811----------------------------------------------------------------------- 18122014-03-05 09:10:00 GMT trunk-457 1813Fix printed charges for transiesta in spin-polarized case 1814 1815* When using spin the shown charges were wrong, however, the computations 1816 are correct. 1817 The charges are now consistent. 1818 (Thanks to Paula Abufager and Nicolas Lorente for pointing this out) 1819 1820modified: 1821 Src/m_ts_in_siesta.F 1822 1823----------------------------------------------------------------------- 18242014-02-20 11:30:00 GMT trunk-456 1825Bug fixes and feature changes in charge-density mixing 1826 1827* The criterion for participation of a node in the DIIS procedure was 1828faulty. 1829 1830* For spin-polarized systems, the rho(G=0) components were not mixed, 1831 as they should. 1832 1833* Several option labels have changed: 1834 1835The "old" ThomasFermiK2 option has been renamed to 1836 1837SCF.Kerker.q0sq [ physical energy ] 1838 1839The default remains 0.0 Ry, although the program now prints several 1840possible heuristic values: 1841 1842- The actual Thomas-Fermi wavevector squared 1843- The square of 2*pi/L, where L is the length of the longest cell vector. 1844 1845SCF.RhoG.DIIS.Cutoff (physical energy) 1846 1847determines the sub-set of G vectors which will undergo the DIIS 1848procedure. Default: 9 Ry. 1849 1850SCF.RhoG.DIIS.Depth 1851 1852determines the maximum number of previous steps considered in the DIIS 1853procedure. Default: 0 1854 1855SCF.RhoG.Metric.Preconditioner.Cutoff (physical energy) 1856 1857determines the value of "q1^2" in the weighing of the different G 1858components in the scalar products among residuals in the DIIS 1859procedure. Following the KF ansatz, this parameter is chosen so that 1860the smallest (non-zero) G has a weight 20 times larger than that of 1861the smallest G vector in the DIIS set. Default: The KF prescription. 1862 1863SCF.DebugRhogMixing 1864 1865controls the level of debugging output in the mixing procedure 1866(basically whether the first few stars worth of Fourier components are 1867printed). Default: False. Note that this feature will only display 1868the components in the master node... 1869 1870* By default, the DIIS procedure uses a method based on 1871 singular-value-decomposition to find the coefficients. 1872 1873 To turn off SVD, use 'SCF.RhoG.DIIS.UseSVD F' 1874 1875 To modify the threshold for removal of small singular values (set by 1876 default to a ratio of 1.0e-8 with respect to the maximum 1877 sing. value) use 'SCF.RhoG.DIIS.RcondSVD <value>' 1878 1879 Use 'debug-diis T' to see debugging information. 1880 1881modified: 1882 Docs/siesta.tex 1883 Src/Makefile 1884 Src/m_rhog.F90 1885 Src/m_diis.F90 1886 Tests/h2o-rhog-mixing/h2o-rhog-mixing.fdf 1887 1888----------------------------------------------------------------------- 18892014-02-10 09:40:00 GMT trunk-455 1890Charge-density mixing 1891 1892With the fdf option 1893 1894 MixCharge T 1895 1896the self-consistent-field convergence acceleration will be carried out 1897by mixing the charge density (actually the Fourier-components of the 1898charge). Both a simple Kerker-preconditioning and a DIIS procedure with 1899a subset of the Fourier components are implemented. 1900 1901The implementation follows the ideas in Kresse+Furthmuller, 1902Comp.Mat.Sci. 6, 15-50 (1996), KF in what follows). 1903 1904Relvant parameters: 1905 1906 ThomasFermiK2 (physical energy) 1907 1908determines the Thomas-Fermi wavevector squared (in Ry) featuring in 1909the Kerker mixing, which is always performed on all components of 1910rho(G), even those treated with the DIIS scheme. Default: 0 Ry. 1911 1912 1913 RhoGMixingCutoff (physical energy) 1914 1915determines the sub-set of G vectors which will undergo the DIIS 1916procedure. Only those with kinetic energies below this cutoff will be 1917considered. The optimal extrapolation of the rho(G) elements will be 1918replaced in the fourier series before performing the Kerker 1919mixing. Default: 9 Ry. 1920 1921 RhoG-DIIS-Depth 1922 1923determines the maximum number of previous steps considered in the DIIS 1924procedure. Default: 0 1925 1926 RhoG-SP-Preconditioner-Cutoff (physical energy) 1927 1928determines the value of "q1^2" in the weighing of the different G 1929components in the scalar products among residuals in the DIIS 1930procedure. Following the KF ansatz, this parameter is chosen so that 1931the smallest (non-zero) G has a weight 20 times larger than that of 1932the smallest G vector in the DIIS set. Default: The KF prescription. 1933 1934 DebugDIIS 1935 1936controls the level of debugging output in the DIIS procedure. Default: 1937False. 1938 1939 DebugRhogMixing 1940 1941controls the level of debugging output in the mixing procedure 1942(basically whether the first few stars worth of Fourier components are 1943printed). Default: False. Note that this feature will only display 1944the components in the master node... 1945 1946 SCF.MixCharge.SCF1 1947 1948controls whether mixing is done in the first scf step. Default: 1949false. (This seems to speed up convergence in some cases. More data is 1950needed.) 1951 1952 The information about rhog_in and rhog_out in first scf iteration is 1953not added to the DIIS history. This seems to improve the convergence. 1954 1955* Added h2o-rhog-mixing test 1956 1957Note that the default convergence criteria remains based on the 1958differences in the density matrix, but in this case the differences 1959are from step to step, not the more fundamental DM_out-DM_in. Perhaps 1960some other criterion should be made the default (max |Delta rho(G)|, 1961convergence of the free-energy...) 1962 1963Note that with charge mixing the Harris energy as it is currently 1964computed in Siesta loses its meaning, since there is no "DM_in". The 1965program prints zeroes in the Harris energy field. 1966 1967Note that the KS energy is correctly computed throughout the scf cycle, 1968as there is an extra step for the calculation of the charge stemming from 1969DM_out, which also updates the energies. Forces and final energies are 1970correctly computed with the final DM_out, regardless of the setting of 1971the option for mixing after scf convergence. 1972 1973The program now prints a more accurate summary of the criterion used 1974for scf cycle termination. 1975 1976Note that the criterion for total-energy convergence now uses the free 1977electronic energy, which is the appropriate magnitude to monitor in 1978the general case of possibly fractional occupancies. 1979 1980The mixing flavor should be made into a first-class option variable, 1981instead of being encoded in two separate logicals (mix_charge, 1982mixH)... 1983 1984The new code uses a circular stack implemented using a 1985"reference-counting" paradigm. 1986 1987----------------------------------------------------------------------- 19882014-01-31 15:15:00 GMT trunk-454 1989Allow the handling of ghosts of synthetic atoms 1990 1991Species with "atomic number" < -200 are now correctly treated as 1992ghosts of synthetic atoms. 1993 1994(Thanks to A. Vozny and A. Suarez) 1995 1996modified: 1997 Docs/siesta.tex 1998 Src/atm_transfer.f 1999 Src/atom.f 2000 Src/chemical.f 2001 Src/periodic_table.f 2002 2003----------------------------------------------------------------------- 20042014-01-16 15:35:00 GMT trunk-453 2005Added a simple ps-->inp converter for ATOM 2006 2007This program is useful when the INP file is no longer available. 2008 2009It has a few limitations: note in particular that it cannot possibly 2010reconstruct the partial core radius. 2011 2012(A. Garcia) 2013 2014added: 2015 Pseudo/atom/Util/Ps2Inp/ 2016 Pseudo/atom/Util/Ps2Inp/die.F 2017 Pseudo/atom/Util/Ps2Inp/flib_spline.f90 2018 Pseudo/atom/Util/Ps2Inp/make_ps_input.f90 2019 Pseudo/atom/Util/Ps2Inp/pseudopotential.f 2020 2021----------------------------------------------------------------------- 20222014-01-15 11:40:00 GMT trunk-452 2023Fixed a wrong threshold for the bias for transiesta runs 2024 2025* Due to a programming error, at low bias the Voltage was considered 2026 to be too low at 0.1 V instead of at 10^(-4) V. 2027 2028modified: 2029 Src/m_ts_options.F90 2030 2031----------------------------------------------------------------------- 20322013-12-04 14:00:00 GMT trunk-451 2033Use electronic entropy from current SCF step. EHarris update fix. 2034 2035* The electronic entropy is computed (in 'compute_dm') once the 2036 electronic structure is known. The -TS term in the electronic free 2037 energy was previously computed using the information from the 2038 previous SCF step (by having it added to Etot in 2039 'setup_hamiltonian', using an intermediate variable). Now it is 2040 added in 'scfconvergence_test' and it corresponds to the current SCF 2041 step. (The last entropy computed in the scf cycle is also added to 2042 the final Etot in 'post_scf_work'.) There is not much theoretical 2043 justification for the previous choice, and the new one looks more 2044 appropriate in general, and notably if E_KS(out) is computed (as 2045 with H mixing). 2046 2047* The Harris energy update DEharr is computed in 'compute_dm', and 2048 corresponds to Tr(H*(DM_out-DM_in)). 2049 2050 In 'post_scf_work' there was a statement 2051 2052 Eharrs = Etot + DEharr 2053 2054 Since this Etot is computed with DM_mixed (the DM predicted by 2055 'mixer' for a hypothetical next SCF iteration) or with DM_out 2056 (depending on whether a final mixing is done at the end of the 2057 cycle) this value for Eharrs is suspect. This value was never 2058 actually printed, since printing routines used 'Eharrs1', which is 2059 the last value of Eharrs computed in the SCF cycle (set in 2060 'scfconvergence_test'). To reproduce that behavior, the above 2061 statement has been removed, and Eharris1 replaced by Eharrs 2062 everywhere. 2063 2064* Added a message detailing which DM is used in 'post_scf_work', 2065 and suggesting the use of "SCF.MixAfterConvergence F" 2066 2067modified: 2068 Src/Makefile 2069 Src/compute_dm.F 2070 Src/final_H_f_stress.F 2071 Src/local_DOS.F 2072 Src/m_energies.F90 2073 Src/post_scf_work.F 2074 Src/scfconvergence_test.F 2075 Src/setup_hamiltonian.F 2076 Src/siesta_init.F 2077 Src/write_md_record.F 2078 Src/write_subs.F 2079 2080----------------------------------------------------------------------- 20812013-11-22 15:30:00 GMT trunk-450 2082Fix SiestaXC/mesh3d to avoid overflow of distributions and/or tasks 2083 2084(Thanks to Nick P. Andersen) 2085 2086Due to two bugs in mesh3d.F90, the number of mesh distributions 2087and/or communication tasks overflowed in some cases, specially 2088when using vdW and a variable cell. Fixed. 2089 2090modified: 2091 Src/SiestaXC/cellxc.F90 : improved output to debugXC 2092 Src/SiestaXC/mesh3d.F90 : bug fixes + improved debugXC output 2093 2094----------------------------------------------------------------------- 20952013-11-15 15:20:00 GMT trunk-449 2096Fix Tbtrans runs at Gamma when using Transiesta k-point data 2097 2098(Thanks to Nick P. Andersen) 2099 2100When a calculation was performed with k-points in transiesta and a 2101subsequent tbtrans calculation was performed ONLY at the Gamma point, 2102the calculated transmission was wrong. 2103 2104This has now been fixed. 2105 2106modified: 2107 Util/TBTrans_rep/tbtrans.F90 2108 2109----------------------------------------------------------------------- 21102013-10-31 19:30:00 GMT trunk-448 2111Minor fixes in XC library (JMS) 2112 2113- Due to roundoff errors, the first mesh point generated by mesh1d 2114 might be slightly outside the given range. This has been fixed. 2115- The maximum number of mesh distributions in mesh3d has been increased. 2116- To reduce the executable file, the allocation of some large arrays in 2117 vdwxc.F90 and vv_vdwxc.F90 has changed from static to dynamic. 2118- To avoid compiler warnings, some real-to-integer conversions in 2119 vv_vdwxc.F90 have been changed from implicit to explicit. 2120 2121modified: 2122 Src/SiestaXC/makefile 2123 Src/SiestaXC/mesh1d.f90 2124 Src/SiestaXC/mesh3d.F90 2125 Src/SiestaXC/vdwxc.F90 2126 Src/SiestaXC/vv_vdwxc.F90 2127 2128----------------------------------------------------------------------- 21292013-10-22 14:10:00 GMT trunk-447 2130Improve the estimation of the orbital distribution blocksize 2131 2132For small problems or a too-large number of processors (heuristically, 2133when nprocs*24 > norbs), the estimation of the default blocksize for 2134orbital distribution could lead to some processors being idle, or to a 2135large imbalance in the distribution. 2136 2137This has been fixed. The imbalance (the ratio of maximum to minimum 2138number of orbitals assigned to a processor) is now not larger than 2 for 2139those badly designed runs. 2140 2141The imbalance is printed to the output file. 2142 2143(A. Garcia) 2144 2145modified: 2146 Src/initparallel.F 2147 Src/m_dminim.F90 2148 Src/m_zminim.F90 2149 Src/parallelsubs.F 2150 Docs/siesta.tex 2151 2152----------------------------------------------------------------------- 21532013-10-16 12:30:00 GMT trunk-446 2154Output file names for dhscf packed in a derived type (JMS) 2155 2156 The file names passed to dhscf, for output densities and potentials 2157on the grid, have been packed into a derived type defined in files.f 2158 Also, a new density file .RHOXC, with the density passed to cellxc 2159(i.e. including the nonlocal core corrections), can be written by 2160activating SaveRhoXC in the .fdf file. 2161 As a minor point, file .VNA was being written in every call to 2162dhscf (provided that SaveNeutralAtomPotential was active). Now it is 2163written only when dhscf is called by siesta_analysis, as the other 2164output files. 2165 2166modified: 2167 Docs/siesta.tex 2168 Src/Makefile 2169 Src/dhscf.F 2170 Src/files.f 2171 Src/grdsam.F 2172 Src/local_DOS.F 2173 Src/setup_hamiltonian.F 2174 Src/siesta_analysis.F 2175 Src/siesta_options.F90 2176 2177----------------------------------------------------------------------- 21782013-09-30 10:30:00 GMT trunk-445 2179New mixing options and simplification of scf loop 2180 2181* If the option 2182 2183 MixHamiltonian T 2184 2185is used, the program will mix the Hamiltonian instead of the density 2186matrix to achieve self-consistency. 2187 2188Note that the "dDmax" column in the output will reflect the changes in 2189H, not in the DM. 2190 2191The Kohn-Sham energy will converge more uniformly, as it is computed 2192using a DM_out, instead of a (mixed) DM_in. 2193 2194 2195* Optionally avoid mixing DM or H after scf-convergence 2196 2197If the option 2198 2199 SCF.MixAfterConvergence F 2200 2201is used, the program will exit the scf loop without a final mixing. 2202The DM coming out of the cycle will then be DM_out (regardless of 2203whether we are mixing H or the DM). The hamiltonian coming out of the 2204cycle is H_out (generated with DM_out), but H_in ("Hold" in the code) 2205is also kept if the option is set, so it could be reset if needed in 2206the future. 2207 2208Not mixing after convergence will improve the quality of the final 2209Kohn-Sham energy and forces in calculations that use DM mixing. 2210The effect should be very small for well-converged calculations. 2211 2212The DM is saved during the scf cycle for restarting purposes (unless 2213overridden by the user). If there is no mix after convergence, the 2214final DM_out is saved. 2215 2216 2217* A number of options have been added to control the behavior of the 2218Pulay mixer: 2219 2220- Pulay mixing might kick in only after a specified number of history 2221steps have been built up: 2222 2223 pulay_minimum_history = fdf_get("SCF.PulayMinimumHistory",2) 2224 2225- Pulay mixing might not work well if far from the fixed point. This 2226option will avoid inserting the current X_in, X_out pair in the 2227history stack if the maximum difference is above the specified number. 2228 2229 max_dmax_for_pulay = fdf_get("SCF.PulayDmaxRegion",1000.0_dp) 2230 2231There is no effect by default. 2232 2233- The "damping" term applied after the DIIS minimization can be 2234different from that used for linear mixing: 2235 2236 alpha_pulay = fdf_get("SCF.Pulay.Damping",-1.0_dp) 2237 2238By default, alpha_pulay would be set to the linear-mixing parameter. 2239 2240- The damping of the DIIS-predicted X_in is done to avoid introducing 2241linear dependencies into the Pulay history stack. Alternatively (or 2242simultaneously) one can use the most recent X_in, X_out pair in a 2243linear mixing step, and use a possibly different mixing 2244parameter. This would be akin to a "kick", but without removing all 2245the history information. 2246 2247 linear_mixing_after_pulay = fdf_get("SCF.LinearMixingAfterPulay",.false.) 2248 alpha_after_pulay = fdf_get("SCF.MixingWeightAfterPulay",0.5_dp) 2249 2250- Instead of direct matrix inversion, the more robust SVD algorithm can 2251be used to perform the DIIS extrapolation: 2252 2253 use_svd_in_pulay = fdf_get("SCF.Pulay.UseSVD",.false.) 2254 debug_svd_in_pulay = fdf_get("SCF.Pulay.DebugSVD",.true.) 2255 ! Note that 1.0e-6 seems too conservative 2256 rcond_svd_pulay = fdf_get("SCF.Pulay.RcondSVD",1.0e-8_dp) 2257 2258 2259* The loop logic in 'siesta_forces' has been revised to make it more 2260clear, maintaining the old behavior with the exception of: 2261 2262- The maximum number of scf iterations is that set by the user, 2263instead of one less, since the final forces phase is not counted as an 2264iteration. 2265 2266- Upon the beginning of a GF TranSiesta run, when mixing H, the 2267hamiltonian will be recomputed with the proper bias, instead of 2268inheriting H from the previous normal Siesta initialization. 2269 2270(+ The DM is now normalized in 'compute_dm' and 'new_dm') 2271 2272(+ replaced the "siesta:" prefix by "scf:" in the relevant scf cycle 2273output) 2274 2275(+ changed the order of the monitor_forces_in_scf block, so that it is 2276executed before mixing). 2277 2278 2279added: 2280 Src/compute_max_diff.F 2281 Src/m_svd.F90 2282 Src/save_density_matrix.F 2283modified: 2284 Docs/siesta.tex 2285 Src/Makefile 2286 Src/compute_dm.F 2287 Src/final_H_f_stress.F 2288 Src/m_pulay.F90 2289 Src/m_ts_global_vars.f90 2290 Src/m_ts_options.F90 2291 Src/mixer.F 2292 Src/new_dm.F 2293 Src/normalize_dm.F 2294 Src/post_scf_work.F 2295 Src/scfconvergence_test.F 2296 Src/setup_hamiltonian.F 2297 Src/siesta_forces.F 2298 Src/siesta_options.F90 2299 Src/sparse_matrices.F 2300 Src/state_init.F 2301 Src/write_subs.F 2302 2303----------------------------------------------------------------------- 23042013-08-28 10:30:00 GMT trunk-444 2305Bug fixes to the preconditioner in the OMM modules 2306(Fabiano Corsetti) 2307 2308modified: 2309 Docs/siesta.tex 2310 Src/m_dminim.F90 2311 Src/m_zminim.F90 2312 2313----------------------------------------------------------------------- 23142013-07-31 16:05:00 GMT trunk-443 2315Update to gnubands program 2316 2317(Nick P. Andersen) 2318 2319Added a fermi shift flag (-F), and energy range flags (-e -E) to 2320specify in which range one needs the window. This energy range 2321specification can be used at the same time as the band-index 2322specification. 2323 2324Fixed a bug when printing for spin-polarized calculations. 2325 2326modified. 2327 Util/Bands/new.gnubands.f90 2328 2329----------------------------------------------------------------------- 23302013-07-31 16:00:00 GMT trunk-442 2331Synch patch-logs from siesta-3.0 branch up to siesta-3.2 release 2332 2333Did a "merge" followed by a "revert ." to keep only the patch logs, to 2334maintain the ability to merge fixes applied initially to the 2335siesta-3.0 branch. 2336 2337(no changes) 2338 2339----------------------------------------------------------------------- 23402013-07-05 15:40:00 GMT trunk-441 2341Cosmetic fixes to please Cray compiler. Arch.make files for PRACE computers 2342 2343(Fabiano Corsetti) 2344 2345* Some cosmetic changes for Cray compiler. 2346 2347* Added some arch.make files for PRACE computers to Src/Sys 2348 2349added: 2350 Src/Sys/arch.make.curie 2351 Src/Sys/arch.make.fermi 2352 Src/Sys/arch.make.hermit 2353 Src/Sys/arch.make.juqueen 2354 Src/Sys/arch.make.marenostrum 2355 Src/Sys/arch.make.supermuc 2356modified: 2357 Src/m_partial_charges.F 2358 Src/rhoofd.F 2359 Src/vmat.F 2360 2361----------------------------------------------------------------------- 23622013-07-04 16:00:00 GMT trunk-440 2363Avoid allocation of auxiliary index arrays in the general case 2364 2365* Some auxiliary index arrays intended only for O(N) calculations were 2366 allocated unconditionally. This has been fixed. 2367 2368modified: 2369 Src/initparallel.F 2370 2371----------------------------------------------------------------------- 23722013-06-21 11:10:00 GMT trunk-439 2373Siesta as subroutine using MPI. Vydrov-VanVoorhis vdW functional 2374 2375(Implemented by Jose Soler) 2376 2377* Siesta as a subroutine using MPI. 2378 2379A new version of fsiesta (siesta forces as a subroutine) that uses MPI 2380to keep different siesta jobs, with their corresponding memory 2381allocations, separated as different MPI processes. Each siesta job can 2382itself run in parallel using its own MPI communicator. 2383 2384See Util/SiestaSubroutine for more information. 2385 2386* Implementation of Vydrov-VanVoorhis (VV) vdW functional. 2387 2388Ref: O.A.Vydrov & T.vanVoorhis, JCP 133, 244103 (2010) 2389Conditions have been added in vdwxc to trap the VV case, calling the 2390corresponding routines in vv_vdwxc, where most of the new code is. 2391 2392 2393* Minor changes: 2394 2395Array copy in mesh3d expanded in do loops to circunvent an apparent 2396compiler bug 2397 2398Incresed length of some character strings that hold file names 2399 2400Increased parameter minloc in rhoofd and vmat for better efficiency 2401 2402Two minor bugs corrected in vdwxc.f90 2403 2404vdw_exchng changed to vdw_localxc in m_vdwxc 2405 2406The coefficients for interpolation of phi(d1,d2) in the upper boundary 2407of d1 and d2 have been corrected in vdwxc:bcucof. But since these 2408boundary values may be never encountered, this correction is probably 2409irrelevant. Additionally, a couple of comments have been corrected, 2410and the reference output of the graphite_vdw_df test has been updated. 2411 2412A trap has been added in rdiag and cdiag to handle the trivial 2413eigenvalue problem for matrices of dimension one, which was not 2414treated correctly by the LAPACK routines. 2415 2416Consistency of array names in calls to re_alloc and de_alloc 2417 2418added: 2419 Src/SiestaXC/Testers/test2.m 2420 Src/SiestaXC/Testers/test5.f90 2421 Src/SiestaXC/Testers/test5.m 2422 Src/SiestaXC/vv_vdwxc.F90 2423 Src/fsiesta_mpi.F90 2424 Src/siesta_master.f90 2425 Util/SiestaSubroutine/SimpleTest/ 2426 Util/SiestaSubroutine/SimpleTest/Src/ 2427 Util/SiestaSubroutine/SimpleTest/Src/Makefile 2428 Util/SiestaSubroutine/SimpleTest/Src/phonons.f90 2429 Util/SiestaSubroutine/SimpleTest/Src/simple_mpi_parallel.f90 2430 Util/SiestaSubroutine/SimpleTest/Src/simple_pipes_parallel.f90 2431 Util/SiestaSubroutine/SimpleTest/Src/simple_serial.f90 2432 Util/SiestaSubroutine/SimpleTest/h2o.fdf 2433 Util/SiestaSubroutine/SimpleTest/h2o.out 2434 Util/SiestaSubroutine/SimpleTest/test.sh 2435renamed: 2436 Src/fsiesta.F90 => Src/fsiesta_pipes.F90 2437modified: 2438 Docs/siesta.tex 2439 Pseudo/atom/pseudoXML.f 2440 Pseudo/atom/velect.f 2441 Src/MPI/mpi_siesta.f90 2442 Src/Makefile 2443 Src/SiestaXC/Testers/makefile 2444 Src/SiestaXC/Testers/test2.f90 2445 Src/SiestaXC/Testers/test3.F90 2446 Src/SiestaXC/Testers/test4.F90 2447 Src/SiestaXC/atomxc.F90 2448 Src/SiestaXC/cellxc.F90 2449 Src/SiestaXC/lib-00-README 2450 Src/SiestaXC/lib-makefile 2451 Src/SiestaXC/makefile 2452 Src/SiestaXC/mesh3d.F90 2453 Src/SiestaXC/siestaxc.F90 2454 Src/SiestaXC/vdwxc.F90 2455 Src/SiestaXC/xcmod.f90 2456 Src/atmfuncs.f 2457 Src/cdiag.F 2458 Src/fft.F 2459 Src/m_timer.F90 2460 Src/moreParallelSubs.F90 2461 Src/new_dm.F 2462 Src/pxf.F90 2463 Src/rdiag.F 2464 Src/reinit.F 2465 Src/rhoofd.F 2466 Src/setspatial.f 2467 Src/siesta_end.F 2468 Src/siesta_forces.F 2469 Src/siesta_init.F 2470 Src/siesta_move.F 2471 Src/struct_init.F 2472 Src/vmat.F 2473 Tests/Reference/graphite_vdw_df.out 2474 Tests/graphite_vdw_df/graphite_vdw_df.fdf 2475 Util/SiestaSubroutine/README 2476 Util/Vibra/Src/outbands.f 2477 Util/Vibra/Src/vibrator.f 2478 version.info 2479 Src/fsiesta_pipes.F90 2480 2481 2482----------------------------------------------------------------------- 24832013-06-10 14:20:00 GMT trunk-438 2484Bug fixes in constraints routine 2485 2486* Make sure that the atomic indices are in the correct range. 2487 2488* Add code to guarantee the enlargement of an array in the 2489general case. 2490 2491(Thanks to Nick P. Andersen) 2492 2493modified: 2494 Src/fixed.F 2495 2496----------------------------------------------------------------------- 24972013-06-10 14:10:00 GMT trunk-437 2498New option for KB projector generation (J. Junquera) 2499 2500With the option 2501 2502KB.New.Reference.Orbitals T 2503 2504the routine to generate KB projectors will use slightly different 2505parameters for the construction of the reference orbitals involved 2506(Rmax=60 bohr both for integration and normalization). 2507 2508modified: 2509 Docs/siesta.tex 2510 Src/atom.F 2511 Src/atom_options.F90 2512 2513----------------------------------------------------------------------- 25142013-06-05 13:00:00 GMT trunk-436 2515Charge confinement and filteret basis generation options 2516 2517Two experimental features related to basis-set generation: 2518 2519* Charge confinement feature for basis set generation 2520(Emilio Artacho) 2521 2522Present soft confinement produces bad polarisation orbitals if the 2523original atomic orbitals are unbound or very wide (automatic 2524polarisation still gives too wide orbitals). 2525 2526A Q/r potential with Yukawa decay can now be added to the atomic and 2527soft-confinement potentials. Soft-confinement sshould now be used only 2528for the soft tail cutting with r_in ~ 0.9 r_c. 2529 2530See the manual for more details. 2531 2532* New 'filteret' basis-set scheme. 2533(Julian Gale) 2534 2535New options to use the filterets (functions appearing in the filtering 2536mechanism proposed by Anglada and Soler) as a systematic basis 2537set. The size of the basis set is controlled by the filter cut-off for 2538the orbitals. 2539 2540See the manual for more details. 2541 2542(Thanks to Tristana Sondon for help in merging) 2543 2544added: 2545 Tests/Reference/chargeconf-h2o.out 2546 Tests/Reference/h2o_filteret_basis.out 2547 Tests/chargeconf-h2o/ 2548 Tests/chargeconf-h2o/chargeconf-h2o.fdf 2549 Tests/chargeconf-h2o/chargeconf-h2o.pseudos 2550 Tests/chargeconf-h2o/makefile 2551 Tests/h2o_filteret_basis/ 2552 Tests/h2o_filteret_basis/h2o_filteret_basis.fdf 2553 Tests/h2o_filteret_basis/h2o_filteret_basis.pseudos 2554 Tests/h2o_filteret_basis/makefile 2555modified: 2556 Docs/siesta.tex 2557 Src/atm_transfer.f 2558 Src/atm_types.f 2559 Src/atmparams.f 2560 Src/atom.F 2561 Src/basis_specs.f 2562 Src/basis_types.f 2563 Src/initatom.f 2564 Src/m_filter.f90 2565 Src/old_atmfuncs.f 2566 2567----------------------------------------------------------------------- 25682013-06-05 12:40:00 GMT trunk-435 2569Compilation fixes for tbtrans. Cosmetic changes 2570 2571The old symbol "DAT_double" was still being used in one of the 2572routines of the new tbtrans program (in Util/TBTrans_rep). References 2573related to new timer_tree module were missing in both versions of 2574tbtrans. 2575 2576In parallel operation, the "bye" routine now produces output only 2577in the master node. 2578 2579In runs which are requested to end after the initial processing of 2580the structure, XMOL output is produced if requested. 2581 2582modified: 2583 Src/siesta_init.F 2584 Src/sys.F 2585 Util/TBTrans/Makefile 2586 Util/TBTrans_rep/Makefile 2587 Util/TBTrans_rep/m_tbt_iotshs.F90 2588 Util/TBTrans_rep/m_tbt_read_tshs.F90 2589 2590----------------------------------------------------------------------- 25912013-03-31 19:00:00 GMT trunk-434 2592Experimental timer with call-tree awareness 2593 2594A new timer, based on wall time in the master node, and keeping track 2595of the tree-structure of the timed sections, can be enabled by setting 2596 2597UseTreeTimer T 2598 2599in the fdf file. 2600 2601It works in tandem with the default timer, and it currently produces a 2602report at the end of the output file in which the parent-child 2603relationships are represented by simple indentation. 2604 2605Some new timing calls have been added in the code. 2606 2607added: 2608 Src/die.F 2609 Src/timer_tree.f90 2610modified: 2611 Src/Makefile 2612 Src/SiestaXC/makefile 2613 Src/fft.F 2614 Src/m_hsx.F 2615 Src/m_iodm.F 2616 Src/m_timer.F90 2617 Src/m_walltime.f90 2618 Src/matel.f 2619 Src/molecularmechanics.F90 2620 Src/setup_H0.F 2621 Src/setup_hamiltonian.F 2622 Src/siesta_forces.F 2623 Src/siesta_init.F 2624 Src/timer.F90 2625 2626 2627----------------------------------------------------------------------- 26282013-03-26 12:35:00 GMT trunk-433 2629Implemented the non-O(N) version of the Ordejon-Mauri functional 2630 2631(Work by Fabiano Corsetti) 2632 2633* This re-implementation of Ordejon-Mauri will be referred to as the Orbital 2634 Minimization Method (OMM); it is now a third available option for the keyword 2635 SolutionMethod, alongside diagon and OrderN. 2636* The OMM is not an O(N) functional at present, since no localization is imposed 2637 on the trial orbitals; in future, it can be extended to include this option 2638* The functional is contained in two new modules: m_dminim (double 2639 precision routines) and m_zminim (double complex routines) 2640* The modules works in serial with LAPACK, or in parallel with MPI and 2641 ScaLAPACK 2642* The double precision module (for Gamma point calculations) has the option of 2643 using sparse matrix-dense matrix multiplications, with custom-coded algorithms 2644 that interface between SIESTA's native sparse matrix scheme and (Sca)LAPACK's 2645 dense matrix scheme 2646* The SIESTA manual has been updated to include a list of all OMM-related 2647 keywords, with detailed explanations and notes to the user 2648 2649added: 2650 Docs/CHANGES.minim 2651 Src/m_dminim.F90 2652 Src/m_zminim.F90 2653 Tests/OMM_h2o/ 2654 Tests/OMM_h2o/Makefile 2655 Tests/OMM_h2o/OMM_h2o.fdf 2656 Tests/OMM_h2o/OMM_h2o.pseudos 2657 Tests/OMM_si/ 2658 Tests/OMM_si/Makefile 2659 Tests/OMM_si/OMM_si.fdf 2660 Tests/OMM_si/OMM_si.pseudos 2661 Tests/Reference-xml/OMM_h2o.xml 2662 Tests/Reference-xml/OMM_si.xml 2663 Tests/Reference/OMM_h2o.out 2664 Tests/Reference/OMM_si.out 2665modified: 2666 Docs/siesta.tex 2667 Src/Makefile 2668 Src/compute_dm.F 2669 Src/local_DOS.F 2670 Src/post_scf_work.F 2671 Src/projected_DOS.F 2672 Src/siesta_analysis.F 2673 Src/siesta_options.F90 2674 Src/write_subs.F 2675 Tests/Makefile 2676 2677----------------------------------------------------------------------- 26782013-01-24 14:30:00 GMT trunk-432 2679Export some MPI symbols explicitly. Remove obsolete symbols 2680 2681Author: A. Garcia 2682 2683Some PGI compilers do not consider symbols public by default 2684when they are inherited through a chain of module 'uses'. This 2685affected in particular some MPI symbols in the mpi_siesta module. 2686The symbols are now made 'public' explicitly. 2687 2688The symbols DAT_single, DAT_double, etc, which were necessary to 2689deal with machines (old Crays) with different meanings for single 2690and double precision, have now been removed from the MPI interface 2691modules. They still appear in some routines as aliases for imports. 2692 2693modified: 2694 Src/MPI/mpi.F 2695 Src/MPI/mpi_siesta.f90 2696 Src/m_glob_sparse.F90 2697 Src/m_ts_electrode.F90 2698 Src/m_ts_gf.F90 2699 Src/m_ts_in_siesta.F 2700 Src/m_ts_scattering.F 2701 2702----------------------------------------------------------------------- 27032013-01-21 11:15:00 GMT trunk-431 2704Fix possible problems in temporary file name 2705 2706Author: A. Garcia 2707 2708The name of the temporary file used to dump the contents of the fdf file 2709could be malformed in certain situations. The algorithm has now been 2710changed. 2711 2712(Thanks to Romuald Carpentier) 2713 2714(+ Remove fossil DEBUG sections) 2715 2716modified: 2717 Src/reinit.F 2718 2719----------------------------------------------------------------------- 27202013-01-21 10:45:00 GMT trunk-430 2721Rationalize fdf logging and debugging 2722 2723Author: A. Garcia 2724 2725In runs with many processors, the default logging behavior was affecting 2726performance. The policy is now as follows. 2727 2728* Debugging and logging. 2729 2730By default, all the fdf requests are logged, printing the final value 2731extracted (if it is the default value, it is identified as such). 2732In MPI operation, only the master node does the logging, unless the 2733"output-level" is set to a value >= 2. This can be done directly in 2734the fdf file: 2735 2736fdf-output 2 # Turn on logging for all nodes 2737fdf-output 0 # Turn off logging completely 2738 2739No debugging is done, unless the "debug-level" is set to a value greater 2740than zero. The most meaningful way to use this feature is to set the 2741debugging level before the fdf data structures are built. This can be 2742achieved by calling the routine fdf_setdebug with the appropriate level 2743and file name *before* the call to fdf_init. This gives full control 2744over the behavior. This is not currently used in Siesta. 2745 2746Alternatively, if the library is compiled with the pre-processor symbol 2747FDF_DEBUG defined, it will set the debug level to 2 (exhaustive) for all 2748nodes in the system. (It will also set the output level to 2 (all nodes)). 2749 2750If the debugging level (>=2) is only specified in the fdf file itself, 2751the library will provide a print-out of the final data structure generated 2752(in all nodes). 2753 2754fdf-debug 2 2755 2756(+ Support for FDF_DEBUG in the Makefile) 2757(+ Cosmetic improvement to the numerical field in the log files) 2758 2759modified: 2760 Src/Makefile 2761 Src/fdf/fdf.F90 2762 Src/fdf/fdf.Standard 2763 Src/reinit.F 2764 2765----------------------------------------------------------------------- 27662013-01-18 10:30:00 GMT trunk-429 2767JobList utility to organize and run multiple jobs 2768 2769Author: J. Soler 2770 2771The JobList directory contains utilities to organize, to run or queue, 2772and to collect results of multiple siesta jobs. It is particularly 2773suited for preliminary convergence tests, and it uses only fortran 2774codes and minimal shell scripts. 2775 2776added: 2777 Util/JobList/ 2778modified: 2779 Src/siesta_end.F 2780 Src/siesta_init.F 2781 Util/README 2782----------------------------------------------------------------------- 27832012-12-13 17:15:00 GMT Alberto Garcia <albertog@icmab.es> trunk-428 2784Bugfix in spin calculations for TBTrans_rep 2785 2786(This fixes a problem in the new TBtrans by N.P. Andersen) 2787 2788* The current and the averaged arrays were not initialized correctly 2789 for the case of spin: 2790 2791 - TAv, TEigAv, TDOSAv, PDOSAv, Current 2792 2793modified: 2794 Util/TBTrans_rep/tbtrans.F90 2795 2796----------------------------------------------------------------------- 27972012-12-10 09:00:00 GMT Alberto Garcia <albertog@icmab.es> trunk-427 2798More fixes and tests for new transiesta/tbtrans_rep code 2799 2800Several new bug fixes and clarifications have been added to the new 2801TranSiesta/TBTrans code, as well as more tests. Be sure to see the file 2802Docs/TranSiestaUpdate.pdf for information about the new features and 2803behavior changes. 2804 2805* Added deallocation routine to glob_sparse module 2806* Added preliminary code for doing calculations in TBtrans without 2807 inner cell distances (for now this has no importance but provides 2808 a stepping stone for future development) 2809* Bugfix for 'forces' run (bcast of coordinates was not performed) 2810* Wrap mulliken-charges message in MPI runs 2811 2812* Added new test cases: 2813 2814 - The voltage test case au_111_capacitor sometimes exhibits problems of 2815 accuracy, dependent on compiler and execution options, due to the small 2816 conductance. More rigorous tests have been added: 2817 2818 + ts_au_100 2819 + ts_au_100_repetition 2820 + ts_au_100_0.25V 2821 + ts_au_100_repetition_0.25V 2822 2823 which optionally exercise both the new "repetition" option and the 2824 applied bias. They are based on an Au-chain in between gold 100 surfaces. 2825 2826 - These tests are quite large and thus take a significant amount of CPU 2827 time. They might not be needed if the old tests still perform well and 2828 the outputs agree with those in the Tests/Reference. 2829 2830added: 2831 Tests/Reference/TranSiesta-TBTrans/ts_au_100/ 2832 Tests/Reference/TranSiesta-TBTrans/ts_au_100_0.25V/ 2833 Tests/Reference/TranSiesta-TBTrans/ts_au_100_repetition/ 2834 Tests/Reference/TranSiesta-TBTrans/ts_au_100_repetition_0.25V/ 2835 Tests/TranSiesta-TBTrans/ts_au_100/ 2836 Tests/TranSiesta-TBTrans/ts_au_100_0.25V/ 2837 Tests/TranSiesta-TBTrans/ts_au_100_repetition/ 2838 Tests/TranSiesta-TBTrans/ts_au_100_repetition_0.25V/ 2839modified: 2840 Docs/TranSiestaUpdate.pdf 2841 Src/iopipes.F90 2842 Src/m_glob_sparse.F90 2843 Src/m_hs_matrix.f90 2844 Src/m_ts_electrode.F90 2845 Src/m_ts_gf.F90 2846 Src/m_ts_in_siesta.F 2847 Src/mixer.F 2848 Src/ts_init.F90 2849 Util/TBTrans_rep/m_tbt_options.F90 2850 Util/TBTrans_rep/tbtrans.F90 2851 2852 2853----------------------------------------------------------------------- 28542012-11-20 09:00:00 GMT Alberto Garcia <albertog@icmab.es> trunk-426 2855Bug fixes for new transiesta/tbtrans_rep code 2856 2857Several bug fixes and clarifications have been added to the new 2858TranSiesta/TBTrans code. Be sure to see the file 2859Docs/TranSiestaUpdate.pdf for information about the new features and 2860behavior changes. 2861 2862* Corrected the DOS calculations with spin factors 2863* Bugfix for units in AtomPDOS and COOP calculations (TBtrans_rep) 2864* Renamed FDF-option TS.ReUseGF to TS.TBT.ReUseGF (TBtrans_rep) 2865* Fixed options not being seen (TS.TBT.CalcIEig) 2866* Added all output files to the documentation 2867* Added Header information for all TBtrans_rep data files 2868* Added dummy routine in m_glob_sparse for non-MPI compilations 2869* Avoid f2003 features for pointer handling 2870* Use alloc module in m_hs_matrix 2871* Handling of FDF-log files corrected in TBtrans_rep (late merge) 2872 2873modified: 2874 Docs/TS-npa.CHANGES 2875 Docs/TranSiestaUpdate.pdf 2876 Docs/siesta.tex 2877 Src/Makefile 2878 Src/m_glob_sparse.F90 2879 Src/m_hs_matrix.f90 2880 Src/m_ts_contour.f90 2881 Src/m_ts_electrode.F90 2882 Src/m_ts_gf.F90 2883 Src/ts_init.F90 2884 Util/TBTrans_rep/atompdos.F90 2885 Util/TBTrans_rep/coop.F90 2886 Util/TBTrans_rep/m_tbt_options.F90 2887 Util/TBTrans_rep/m_tbt_out.f90 2888 Util/TBTrans_rep/tbt_reinit.F90 2889 Util/TBTrans_rep/tbtrans.F90 2890 2891----------------------------------------------------------------------- 28922012-11-14 18:00:00 GMT Alberto Garcia <albertog@icmab.es> trunk-425 2893Use scratch fdf log files for non-master nodes 2894 2895Unless the FDF_DEBUG preprocessor compilation option is in effect, 2896non-master nodes in MPI operation do not use named log files. Instead, 2897they use "scratch" files which the operating system opens in 2898appropriate places. This will reduce clutter. 2899 2900(Note that this feature is in general dangerous if the files are 2901large, as they can inadvertently fill up filesystems or otherwise 2902create havoc. However, the fdf log files are quite small.) 2903 2904(Contributed by Nick P. Andersen) 2905 2906(+ rearranged the statements that update INCFLAGS in the fdf 2907makefile. This could trap some incorrect settings of this variable in 2908the top arch.make) 2909 2910modified: 2911 Src/fdf/fdf.F90 2912 Src/fdf/makefile 2913 2914----------------------------------------------------------------------- 29152012-10-31 9:10:00 GMT Alberto Garcia <albertog@icmab.es> trunk-424 2916Bug fixes for array bounds 2917 2918There were array bounds problems in: 2919 2920- The new code to print the initial spin polarization, for the case 2921 of non-collinear spin. 2922 2923- The 'transition_rate' routine: ek and ek_local were wrongly 2924 dimensioned to no_l, instead of no_u. 2925 2926- The mesh1d file in SiestaXC 2927 2928(+ removed old debugging code in 'domain_decomposition') 2929 2930modified: 2931 Src/domain_decom.F 2932 Src/new_dm.F 2933 Src/transition_rate.F 2934 Src/SiestaXC/mesh1d.f90 2935 2936----------------------------------------------------------------------- 29372012-10-30 9:50:00 GMT Alberto Garcia <albertog@icmab.es> trunk-423 2938Transiesta and TBTrans enhancements by Nick P. Andersen 2939 2940A number of enhancements to the TranSiesta and TBTrans subsystems have 2941been added by Nick Papior Andersen, of the Technical Univ. of Denkmark. 2942 2943A full list of the changes follows. Users are advised to read the file 2944Docs/TranSiestaUpdate.pdf, as well as the manual, to get a primer on 2945the new features and things to watch out for and explore in the new 2946version. 2947 2948* Added the repetition of the electrode unit cells to limit the Transiesta 2949 calculation time. 2950 - Through the options: 2951 + TS.ReplicateA1Left 2952 + TS.ReplicateA2Left 2953 + TS.ReplicateA1Right 2954 + TS.ReplicateA2Right 2955 - We take advantage of Bloch's theorem to accomplish this. 2956 2957* All contour related variables have been assigned a contour type which 2958 gathers the information about the energy points. This will provide a cleaner 2959 interface for those wishing to extend the contour method. 2960 2961* Changed the contour energy points to be shown in eV, rather than Ry 2962 - I.e. they can not be compared in the out-file directly 2963 2964* Simplified the contour distribution so as to not have any parallel arrays 2965 2966* The surface Green's function files are now created during option reading 2967 This accomodates two important things: 2968 1. The GF files are now entirely moved out of the transiesta routine for 2969 clarity, 2970 2. Any wrong setup of the system will be caught immediately instead of after 2971 the diagon run. 2972 2973* The GF files have been renamed using <systemlabel>.TSGF[L|R] 2974 2975* Added proper checks of the atomic coordinates when using the electrodes, 2976 will now exit if not correctly setup. (checks down to 1e-4) 2977 2978* Added checks of the unit cell setup, so that in transiesta runs the 2979 unitcell must have a distinct z-direction 2980 2981* Added checks of the electrodes to show a warning if the electrodes extend 2982 into a third neighbouring cell in the transport direction. 2983 2984* Clarified the fermi level in the electrodes, it was in fact the electrode 2985 fermi level shift 2986 2987* Added a lot of systematic output for clarification about the Transiesta 2988 parsing of the system. It will provide how the systems are setup in buffer 2989 regions, electrode region and scattering region. 2990 2991* Informational output regarding the charge re-distribution during the SCF 2992 cycles. 2993 2994* Fully parallelized the Greens function creation. 2995 2996* Bugfix in the Transiesta package regarding the DM.UseSaveDM T 2997 2998* Added a general operator which yields the parallelised number of iterations 2999 of an arbitrary loop (.PARCOUNT.), see parallel.F90 3000 3001* Memory-optimized several routines in the transiesta package 3002 3003* GFGammaGF has recieved an overhaul which speeds it up by a factor of two 3004 and limits memory substantially! 3005 3006* Renamed <systemlabel>.CONTOUR to <systemlabel>.TSCC 3007 3008* Added a ts_init routine for gathering of the required initializations 3009 3010* Added notices to users about the use of non-optimal energy points in 3011 transiesta runs. 3012 3013* In case of electrodes not matching with the Transiesta setup it will print 3014 out a high-precision block which can be used for the FDF block. 3015 3016* Added 'chargecorrection' feature, maybe not exact enough to be used, 3017 however, it can be used to force the charges to be "correct" 3018 3019* Changed the Transiesta k-points to be written to file <systemlabel>.TSKP 3020 instead of overwriting the <systemlabel>.KP 3021 3022* Cleaned up a lot of code in all transiesta modules. 3023 One can still clean up some more code, however, we have made good ground. 3024 3025* Added a precision for transiesta in precision.F90 3026 - Currently not used, however, could be the future of limiting Transiesta memory 3027 3028* Added -DTRANSIESTA_DEBUG statements to also debug Transiesta 3029 3030* Added a new TBTrans utility which can be found in Util/TBTtrans_rep 3031 - Fully parallel across energy points and forward parallel across k-points 3032 - This is tightly integrated with transiesta 3033 - Has all the features in Transiesta (parallel GF creation, repetition, etc.) 3034 - Has reenabled the calculation of Atomic PDOS 3035 + Needs to be checked 3036 - Has reenabled the calculation of COOP 3037 + Needs to be checked 3038 - Prepared to automatically add flags for user defined formats. 3039 - The GF files have been renamed using <systemlabel>.TBTGF[L|R] 3040 - The regions output also shows which atoms are in the PDOS region 3041 - Added a tbt_kgrid_Monkhorst_Pack block which is only read by TBtrans, 3042 if it does not exist, it will read kgrid_Monkhorst_Pack instead. 3043 3044* Bugfix in Tests/script_ts to be able to use bash 3045 3046* Added a new test: 3047 - Tests/TranSiesta-TBTrans/ts_au_repetition/ 3048 This will default to use the new TBTrans_rep code. 3049 3050*** General SIESTA changes: 3051 3052* Added a new fdf option MinSCFIterations to prevent the second iteration 3053 jump in MD simulations. 3054 3055* Increased the width of the output field for dDmax, to improve 3056 the monitoring of the convergence of the density matrix. 3057 3058* Added IPO flags for the Makefile to be able to abstract from that. 3059 Libraries should not be compiled with IPO for obvious reasons. 3060* Bugfix in the configure command upon checking the NetCDF linking (netcdf 3061 is now generally a two library linking, which requires "-marks) 3062* Added 'obsolete' and 'deprecated' keys for the FDF library 3063 3064* For creating the Hamiltonian at various k-points new modules have been added: 3065 - m_hs_matrix.f90 3066 + Used to generate a square (dense) matrix from the sparse matrix. 3067 Supplying a k-point will create the equivalent k-point Hamiltonian 3068 + One can also use this to acquire the transfer matrices 3069 + Symmetrizing the hamiltonian and trimming it is also enabled. 3070 - m_glob_sparse.f90 3071 + Will globalize any arrays which are distributed in SIESTA mpi runs 3072 + Used in MPIruns in combination with m_hs_matrix. 3073 3074* Added a makefile for the manual (make siesta, make final, make extra) 3075* Added hyperref to the manual 3076 3077* Added note about GCC 4.7.1 not being compatible with the forces type run, 3078 they have disregarded the piped files in the compiler. Revert to GCC 4.6 3079 or older. 3080 3081removed: 3082 Docs/siesta.ind 3083 Src/m_ts_contour.F 3084added: 3085 Docs/Makefile 3086 Docs/TS-npa.CHANGES 3087 Docs/TranSiestaUpdate.pdf 3088 Src/kpoint_convert.f90 3089 Src/m_glob_sparse.F90 3090 Src/m_hs_matrix.f90 3091 Src/m_ts_cctype.f90 3092 Src/m_ts_contour.f90 3093 Src/m_ts_gf.F90 3094 Src/m_ts_voltage.F90 3095 Src/ts_init.F90 3096 Src/ts_show_regions.f90 3097 Tests/Reference/TranSiesta-TBTrans/ts_au_repetition/ 3098 Tests/Reference/TranSiesta-TBTrans/ts_au_repetition/au_111_capacitor.AVTRANS 3099 Tests/Reference/TranSiesta-TBTrans/ts_au_repetition/au_111_capacitor.TEIG 3100 Tests/Reference/TranSiesta-TBTrans/ts_au_repetition/au_111_capacitor.TRANS 3101 Tests/Reference/TranSiesta-TBTrans/ts_au_repetition/au_111_capacitor.out 3102 Tests/Reference/TranSiesta-TBTrans/ts_au_repetition/elec_au_111_abc.out 3103 Tests/Reference/TranSiesta-TBTrans/ts_au_repetition/tbt_au_111_capacitor.out 3104 Tests/TranSiesta-TBTrans/ts_au_repetition/ 3105 Tests/TranSiesta-TBTrans/ts_au_repetition/Au.psf 3106 Tests/TranSiesta-TBTrans/ts_au_repetition/au_111_capacitor.fdf 3107 Tests/TranSiesta-TBTrans/ts_au_repetition/elec_au_111_abc.fdf 3108 Tests/TranSiesta-TBTrans/ts_au_repetition/makefile 3109 Tests/TranSiesta-TBTrans/ts_au_repetition/script.sh 3110 Util/TBTrans_rep/ 3111 Util/TBTrans_rep/Makefile 3112 Util/TBTrans_rep/atompdos.F90 3113 Util/TBTrans_rep/coop.F90 3114 Util/TBTrans_rep/m_lowdin.f90 3115 Util/TBTrans_rep/m_tbt_iotshs.F90 3116 Util/TBTrans_rep/m_tbt_kpoints.F90 3117 Util/TBTrans_rep/m_tbt_options.F90 3118 Util/TBTrans_rep/m_tbt_out.f90 3119 Util/TBTrans_rep/m_tbt_read_tshs.F90 3120 Util/TBTrans_rep/tbt_init.F90 3121 Util/TBTrans_rep/tbt_reinit.F90 3122 Util/TBTrans_rep/tbtrans.F90 3123 Util/TBTrans_rep/transmission.f90 3124 Util/TBTrans_rep/tt_eig.f90 3125modified: 3126 Docs/README 3127 Docs/siesta.tex 3128 Src/MPI/Makefile 3129 Src/Makefile 3130 Src/compute_dm.F 3131 Src/configure 3132 Src/dhscf.F 3133 Src/diagkp.F 3134 Src/fdf/fdf.F90 3135 Src/m_ts_aux_rout.F 3136 Src/m_ts_electrode.F90 3137 Src/m_ts_in_siesta.F 3138 Src/m_ts_io.F90 3139 Src/m_ts_kpoints.F90 3140 Src/m_ts_options.F90 3141 Src/m_ts_scattering.F 3142 Src/parallel.F 3143 Src/precision.F 3144 Src/scfconvergence_test.F 3145 Src/siesta_forces.F 3146 Src/siesta_init.F 3147 Src/siesta_options.F90 3148 Src/version.F90 3149 Src/write_subs.F 3150 Tests/TranSiesta-TBTrans/README 3151 Tests/script_ts.mk 3152 Util/SiestaSubroutine/README 3153 Util/TBTrans/Makefile 3154 3155----------------------------------------------------------------------- 31562012-10-25 10:45:00 GMT Alberto Garcia <albertog@icmab.es> trunk-422 3157Fix handling of debugging preprocessor symbol in fdf 3158 3159The generic DEBUG symbol has been replaced by FDF_DEBUG. 3160 3161The declaration of the recently added 'filedebug' local variable has 3162been moved out of a preprocessor block. 3163 3164modified: 3165 Src/fdf/fdf.F90 3166 3167----------------------------------------------------------------------- 31682012-10-24 14:45:00 GMT Alberto Garcia <albertog@icmab.es> trunk-421 3169Add rp and rv options to XML pseudopotential handling 3170 3171The RPBE and revPBE XC flavors were not correctly handled by 3172the XML routines. 3173 3174modified: 3175 Pseudo/atom/pseudoXML.f 3176 Util/pseudo-xml/xml2psf_helper.f 3177 3178----------------------------------------------------------------------- 31792012-10-24 13:50:00 GMT Alberto Garcia <albertog@icmab.es> trunk-420 3180Enable MD continuation runs even if the restart file is not available 3181 3182(Fabiano Corsetti) 3183 3184If the user has selected MD.UseSaveXV to continue an MD run from a 3185previously computed set of positions and velocities (in the XV file), 3186but the appropriate restart file is not found, the positions x(t) and 3187velocities v(t-dt) are read from the XV file, and the positions are 3188then backward-propagated by one time step using the Euler method to 3189start the MD run from time (t-dt) with a consistent set of positions 3190and velocities. 3191 3192In previous versions the program complained if the appropriate restart 3193file was not available. This patch enables cross-restarts (i.e., an 3194Annealing calculation followed by a Nose simulation) within the simple 3195"reuse-the-XV-file" framework. The last point computed in the previous 3196simulation will be basically repeated in the continuation run. For 3197"seamless" continuations, the flavor-specific restart file is needed. 3198 3199N.B.: The value of the time step of the previous run (from which the 3200XV file has been generated) should be equal to that of the current 3201run. This information is not saved in the XV file, and so it is not 3202possible for the code to tell whether the two runs are consistent. 3203 3204N.B. 2: The backward-propagation is only used for runs with more than 3205one time step, and is done in routine 'struct_init'. 3206 3207This fix applies to Verlet, Nose, PR, and NPR runs. 3208 3209* New tests: 3210 3211 md-single-run, md-cont, md-cont-no-restart-file 3212 3213 md-anneal-cont 3214 3215(+ used correct fdf option for annealing flavor in md_anneal test) 3216 3217added: 3218 Tests/md-anneal-cont/ 3219 Tests/md-anneal-cont/README 3220 Tests/md-anneal-cont/makefile 3221 Tests/md-anneal-cont/script.sh 3222 Tests/md-cont/ 3223 Tests/md-cont-no-restart-file/ 3224 Tests/md-cont-no-restart-file/README 3225 Tests/md-cont-no-restart-file/makefile 3226 Tests/md-cont-no-restart-file/script.sh 3227 Tests/md-cont/README 3228 Tests/md-cont/makefile 3229 Tests/md-cont/script.sh 3230 Tests/md-single-run/ 3231 Tests/md-single-run/README 3232 Tests/md-single-run/makefile 3233 Tests/md-single-run/script.sh 3234modified: 3235 Docs/siesta.ind 3236 Docs/siesta.tex 3237 Src/Makefile 3238 Src/dynamics.f 3239 Src/iomd.f 3240 Src/struct_init.F 3241 Tests/md_anneal/md_anneal.fdf 3242 3243----------------------------------------------------------------------- 32442012-10-24 13:30:00 GMT Alberto Garcia <albertog@icmab.es> trunk-419 3245Add option to turn off time-reversal symmetry for k-points 3246 3247If the fdf option TimeReversalSymmetryForKpoints is set to "false", 3248the program will keep all the k-points in the BZ, without using the (k,-k) 3249implicit symmetry which is valid in the absence of external magnetic 3250fields or spin-orbit coupling. This feature is added for completeness and 3251test purposes. 3252 3253In spin-polarized calculations, the code now prints a summary of the 3254initial spin polarization when the density-matrix is initialized. 3255 3256modified: 3257 Docs/siesta.tex 3258 Src/Makefile 3259 Src/find_kgrid.F 3260 Src/kpoint_grid.F90 3261 Src/kpoint_pdos.F90 3262 Src/new_dm.F 3263 3264----------------------------------------------------------------------- 32652012-10-24 13:20:00 GMT Alberto Garcia <albertog@icmab.es> trunk-418 3266Use actual number of electrons in optical calculations 3267 3268The 'optical' routine now uses the actual number of electrons (rather 3269than the nominal number of valence electrons) for non-spin-polarized 3270calculations. This affects only systems with a net charge. Note that 3271spin-polarized calculations were already using the actual number 3272of electrons. 3273 3274(Thanks to Alexander Vozny) 3275 3276modified: 3277 Src/Makefile 3278 Src/optical.F 3279 3280----------------------------------------------------------------------- 32812012-10-23 14:10:00 GMT Alberto Garcia <albertog@icmab.es> trunk-417 3282Allow doping feature for all systems 3283 3284The "SimulateDoping" option is now enabled for "bulk" systems, in the 3285interest of generality and to fix an inconsistency in the logic for 3286charge removal. (Thanks to N. P. Andersen) 3287 3288modified: 3289 Src/dhscf.F 3290 3291----------------------------------------------------------------------- 32922012-10-23 14:05:00 GMT Alberto Garcia <albertog@icmab.es> trunk-416 3293Fix spin loop in initialization in Eig2DOS program 3294 3295The initialization code was missing a loop over spin. 3296 3297(+ changes to fix compiler-dependent complaints) 3298 3299(Thanks to N.P. Andersen) 3300 3301( + Update reference outputs for si_fatbands test ) 3302 3303 3304modified: 3305 Tests/Reference-xml/si_fatbands.xml 3306 Tests/Reference/si_fatbands.out 3307 Util/Eig2DOS/Eig2DOS.f90 3308 3309----------------------------------------------------------------------- 33102012-10-23 14:00:00 GMT Alberto Garcia <albertog@icmab.es> trunk-415 3311New options for wavefunction output. 'Fatbands' analysis. Mprop enhancements 3312 3313(A. Garcia) 3314 3315* Enhanced 'bands' routine to write out the wavefunctions 3316 3317If the fdf symbol 3318 3319WFS.Write.For.Bands 3320 3321is set to .true., the program will write out the wavefunctions 3322corresponding to the bands specified in the BandLines block. 3323 3324There are now different file names for wavefunction output: 3325 3326SystemLabel.bands.WFSX : produced by BandLines + WFS.Write.For.Bands 3327SystemLabel.fullBZ.WFSX : for COOP/COHP-related use 3328SystemLabel.selected.WFSX : produced by WaveFuncKPoints 3329 3330Note that for down-stream processing, some of these files might have 3331to be renamed to simply 'SystemLabel.WFSX'. 3332 3333A subset of the bands (for both the BandLines and COOP/COHP cases) can 3334be specified by the fdf keywords: 3335 3336WFS.Band.Min (int, default: 1) 3337WFS.Band.Max (int, default: number of orbitals) 3338 3339The energy window options 3340 3341WFS.Energy.Min 3342WFS.Energy.Max 3343 3344are not in effect for BandLines. 3345 3346 3347* New 'Fatbands' functionality 3348 3349A new utility program ('fat') has been added to generate 'fatband' 3350information. It processes .WFSX files (typically produced during a 3351"bands" calculation) and .HSX files to produce 'EIGFAT' files 3352containing both the eigenvalues ("eig") and the value of the 3353projection of the wavefunction on a given orbital set ("fat"). Most of 3354the code is shared with the PDOS/COOP/COHP program mprop, hence its 3355location in the Util/COOP directory. 3356 3357A new plotting converter, eigfat2plot, has been placed in the 3358Util/Bands directory. It is suitable for simple 'gnuplot' use. 3359 3360Added Tests/si_fatbands 3361 3362 3363* Modified Denchar to read WFSX files 3364 3365Denchar now reads directly the newer-format WFSX files, 3366which are more compact. 3367 3368Also, added a new full example in Util/Denchar/Examples, and 3369two python scripts for contour plots, courtesy of Pablo Aguado. 3370 3371* Moved gnubands.f program to new directory Util/Bands 3372* Added new 'gnubands' program, with more options (Util/Bands/new.gnubands) 3373 3374* Mprop enhancements 3375 3376- New energy-range and band-index options in mprop. 3377 3378* Upgrade of the Util/COOP/mprop program, with new options and 3379 clarification of existing ones: 3380 3381- Allow specification of subsets of bands in Util/COOP/mprop 3382 3383New options "-b min_band -B max_band" to allow the use of restricted 3384band sets in the generation of PDOS, COOP, and COHP curves. 3385 3386- Clearer energy-range options in mprop program 3387 3388The -m/-M options now refer to eigenvalues. Together with the band 3389options (-b/-B), they determine the eigenvectors actually taken into 3390account. 3391 3392- Add plotting window options to mprop. Cosmetics 3393 3394The plotting window can now be specified with the -w/-W options. By 3395default it is determined on the basis of the eigenvalue range. 3396 3397(+ add missing declaration to dm_creator.f90) 3398 3399added: 3400 Tests/Reference-xml/si_fatbands.xml 3401 Tests/Reference/si_fatbands.out 3402 Tests/si_fatbands/ 3403 Tests/si_fatbands/makefile 3404 Tests/si_fatbands/si_fatbands.fdf 3405 Tests/si_fatbands/si_fatbands.pseudos 3406 Util/Bands/ 3407 Util/Bands/Makefile 3408 Util/Bands/README 3409 Util/Bands/eigfat2plot.f90 3410 Util/Bands/f2kcli.F90 3411 Util/Bands/fat.gplot 3412 Util/Bands/m_getopts.f90 3413 Util/Bands/new.gnubands.f90 3414 Util/COOP/Tests/si_fatbands/ 3415 Util/COOP/Tests/si_fatbands/README 3416 Util/COOP/Tests/si_fatbands/fatbands.mpr 3417 Util/COOP/fat.f90 3418 Util/Denchar/Examples/2dplot.py 3419 Util/Denchar/Examples/FullExample.fdf 3420 Util/Denchar/Examples/Si.psf 3421 Util/Denchar/Examples/surf.py 3422 Util/Denchar/Src/readwavesx.f 3423renamed: 3424 Util/gnubands.f => Util/Bands/gnubands.f 3425modified: 3426 Docs/siesta.ind 3427 Docs/siesta.tex 3428 Src/Makefile 3429 Src/bands.F 3430 Src/diagk.F 3431 Src/siesta_analysis.F 3432 Src/writewave.F 3433 Util/COOP/Makefile 3434 Util/COOP/README 3435 Util/COOP/Tests/README 3436 Util/COOP/dm_creator.F90 3437 Util/COOP/main_vars.f90 3438 Util/COOP/mprop.f90 3439 Util/COOP/subs.f90 3440 Util/Denchar/Docs/CHANGES 3441 Util/Denchar/Docs/denchar.tex 3442 Util/Denchar/Src/Makefile 3443 Util/Denchar/Src/denchar.f 3444 Util/Eig2DOS/Eig2DOS.f90 3445 Util/README 3446 3447----------------------------------------------------------------------- 34482012-10-23 13:50:00 GMT Alberto Garcia <albertog@icmab.es> trunk-414 3449Hirshfeld and Voronoi charges. Bader analysis output 3450 3451The Hirshfeld and Voronoi methods are partial-charge estimations based 3452directly on the charge density. They thus complement the Mulliken analysis 3453which depends on the density-matrix. 3454 3455Relevant fdf keywords: 3456 3457WriteHirshfeldPop T 3458WriteVoronoiPop T 3459 3460See the manual for details. 3461 3462(Code for Hirshfeld and Voronoi analysis contributed by P. Ordejon. 3463Integrated into the dhscf workflow by A. Garcia.) 3464 3465* Implementation of Bader charge output 3466 3467If the option 3468 3469 SaveBaderCharge T 3470 3471is used, the program will write the electronic charge density with an 3472extra set of model core charges, useful for post-processing by a Bader 3473"atoms in molecules" analysis. See the manual for important details. 3474 3475The grid2cube program in Util has been extended to deal with the .BADER 3476file. 3477 3478* New test: h2o-pop 3479 3480----------------------------------------------------------------------- 34812012-09-25 10:12:00 GMT Alberto Garcia <albertog@icmab.es> trunk-413 3482Use a 'unique' string in fdf log files 3483 3484In MPI operation, the fdf subsystem writes log files (and optionally 3485debug files) to the /tmp filesystem. Up to now the file names were not 3486unique across jobs, which led to failures. Now a string based on the 34875 least significant digits of the current time is added to the file 3488prefix. 3489 3490Also, removed the printing of a log message regarding the number of 3491lines processed while setting up the fdf data structures, which could 3492potentially confuse some systems. 3493 3494modified: 3495 Src/reinit.F 3496 Src/fdf/fdf.F90 3497 3498----------------------------------------------------------------------- 34992012-08-27 10:10:00 GMT Alberto Garcia <albertog@icmab.es> trunk-412 3500Nullify pointers in diagkp 3501 3502Pointers were not properly nullified in diagkp. 3503 3504(Thanks to Nick P. Andersen) 3505 3506(+ clean up extra path dependencies in Denchar Makefile) 3507 3508modified: 3509 Src/diagkp.F 3510 3511----------------------------------------------------------------------- 35122012-06-21 10:10:00 GMT Alberto Garcia <albertog@icmab.es> trunk-411 3513Fix bug in fdf_bbackspace. No .ion.nc files for ghosts 3514 3515A bug in fdf_bbackspace made it take two steps back when at the end of 3516an fdf block. This has now been fixed, removing also the superfluous 3517'pline' argument. 3518 3519When dealing with ghost atoms, the .ion.nc files containing ionic 3520information in netCDF format cannot yet be read back properly. Their 3521generation has been deactivated for now. Users can still use the 3522standard .ion files in ASCII format with the option 'UserBasis T'. 3523 3524modified: 3525 Docs/siesta.tex 3526 Src/basis_io.F 3527 Src/basis_specs.f 3528 Src/fdf/fdf.F90 3529 3530----------------------------------------------------------------------- 35312012-06-15 15:09:00 GMT Alberto Garcia <albertog@icmab.es> trunk-410 3532Improved the estimation of the size of the automatic cell 3533 3534If not specified, Siesta generates automatically a unit cell for 3535"molecular" or "atomic" systems. The criterion is that the cell is big 3536enough to avoid interactions between orbitals in two different cells. 3537 3538Up to now, the estimation of the size of the orbitals was given by 3539the cutoff of Vna. But if the basis set contains large orbitals which 3540are not occupied in the ground state, this estimate is too short. 3541 3542The "size of the atom" is now estimated as the largest of rc(Vna) and 3543the cutoffs of all the orbitals. 3544 3545modified: 3546 Src/Makefile 3547 Src/automatic_cell.f 3548 3549----------------------------------------------------------------------- 35502012-04-13 15:05:00 GMT Alberto Garcia <albertog@icmab.es> trunk-409 3551Extended the functionality of the 'eig2dos' program 3552 3553A new directory Util/Eig2DOS holds an updated version of the 3554venerable 'eig2dos' program, with a new command-line interface 3555that allows to specify all the parameters and new capabilities: 3556 3557-- Optional use of the k-point weight information in a .KP file. 3558-- Selection of a range of bands for the calculation of the DOS. 3559 3560Invoke the program as 'Eig2DOS -h' for a synopsis. 3561 3562(A. Garcia) 3563 3564added: 3565 Util/Eig2DOS/ 3566 Util/Eig2DOS/Eig2DOS.f90 3567 Util/Eig2DOS/Makefile 3568 Util/Eig2DOS/m_getopts.f90 3569renamed: 3570 Util/eig2dos.f => Util/Eig2DOS/original.eig2dos.f 3571modified: 3572 Docs/siesta.ind 3573 Docs/siesta.tex 3574 Util/README 3575 3576----------------------------------------------------------------------- 35772012-04-04 10:40:00 GMT Alberto Garcia <albertog@icmab.es> trunk-408 3578Close netCDF file descriptors for DM and DMHS files 3579 3580The descriptors for the DM.nc and DMHS.nc netCDF files are kept open 3581during the SCF cycle, but should be closed at the end of it to avoid 3582resource exhaustion in, say, MD runs. This was not done due to a 3583programming error. They are now closed at the beginning of the next 3584SCF cycle. 3585 3586(Thanks to Nick Papior Andersen) 3587 3588modified: 3589 Src/iodm_netcdf.F90 3590 Src/iodmhs_netcdf.F90 3591 3592----------------------------------------------------------------------- 35932012-03-09 15:00:00 GMT Alberto Garcia <albertog@icmab.es> trunk-407 3594Extend DM normalization diagnostics 3595 3596In order to conserve the number of electrons N, the density matrix 3597(DM) has to be normalized: Tr[S*DM]=N, where S is the overlap matrix. 3598 3599The DM might not be normalized because it has been re-used (and 3600re-arranged) from a previous geometry step, or because of some error 3601in its computation during the scf cycle. The two cases are now 3602reported differently: 3603 3604In the first scf step, the fractional tolerance is 0.001 (tighter than 3605the previous default of 0.01), and a "Note" is printed. 3606 3607In subsequent steps, the fractional tolerance can be specified 3608by means of the fdf symbol 3609 3610DM.Normalization.Tolerance Tol 3611 3612and is 1.0e-5 by default. The program now aborts if this threshold is 3613breached. 3614 3615NOTE: The DM might not be normalized upon entry to the (first 3616geometry) scf loop because of a possible "folding" of the overlap 3617matrix in gamma-point calculations with small unit cells: the overlaps 3618of a given unit-cell orbital with multiple images are accumulated 3619instead of being kept separate. Then, the trace Tr[S*DM_atomic] will 3620not give the number of electrons. 3621The folding (which is reported if detected by the program) is done for 3622efficiency reasons, but might cause problems for further analysis 3623(i.e., Mulliken charges, or COOP/COHP calculations). 3624 3625modified: 3626 Src/Makefile 3627 Src/normalize_dm.F 3628 Src/setup_hamiltonian.F 3629 Src/siesta_options.F90 3630 3631----------------------------------------------------------------------- 36322012-03-08 16:55:00 GMT Alberto Garcia <albertog@icmab.es> trunk-406 3633Fix reading of position constraints in block 3634 3635In %block GeometryConstraints, the simple option 3636 3637 position i j k l ... 3638 3639to list atoms to be kept fixed, was not implemented correctly. 3640 3641(Thanks to J. Junquera for the bug report and fix) 3642 3643modified: 3644 Src/fixed.F 3645 3646----------------------------------------------------------------------- 36472012-03-08 10:40:00 GMT Alberto Garcia <albertog@icmab.es> trunk-405 3648Change position of force-monitoring block 3649 3650The optional calculation of forces inside the scf loop is now done 3651after printing the current energies. Otherwise the output for etot 3652would correspond to that for the following iteration, and EHarris 3653would be wrong. 3654 3655modified: 3656 Src/siesta_forces.F 3657 3658----------------------------------------------------------------------- 36592012-03-07 14:25:00 GMT Alberto Garcia <albertog@icmab.es> trunk-404 3660Add force convergence diagnostic 3661 3662When the option to monitor the forces during the SCF cycle is in effect, the 3663program will print the maximum absolute value of the change in forces from one 3664step to the next. Other statistics could be implemented. 3665 3666modified: 3667 Src/siesta_forces.F 3668 3669----------------------------------------------------------------------- 36702012-03-06 15:15:00 GMT Alberto Garcia <albertog@icmab.es> trunk-403 3671Allow monitoring of forces during SCF cycle 3672 3673Using the fdf symbol 3674 3675MonitorForcesInSCF T 3676 3677the program will compute the forces and stresses at every scf step. 3678Use in combination with WriteForces. 3679 3680modified: 3681 Src/Makefile 3682 Src/siesta_forces.F 3683 Src/siesta_options.F90 3684 3685----------------------------------------------------------------------- 36862012-02-23 9:40:00 GMT Alberto Garcia <albertog@icmab.es> trunk-402 3687Update of Andrei Postnikov's utilities to V0.4 3688 3689Added also the fmpdos program, an alternative to pdosxml. 3690 3691added: 3692 Util/Contrib/APostnikov/00README 3693 Util/Contrib/APostnikov/fmpdos.f 3694 Util/Contrib/APostnikov/test_mdc.f 3695modified: 3696 Util/Contrib/APostnikov/Makefile 3697 Util/Contrib/APostnikov/README 3698 Util/Contrib/APostnikov/eig2bxsf.f 3699 Util/Contrib/APostnikov/md2axsf.f 3700 Util/Contrib/APostnikov/rho2xsf.f 3701 Util/Contrib/APostnikov/vib2xsf.f 3702 Util/Contrib/APostnikov/wraxsf1.f 3703 Util/Contrib/APostnikov/wraxsf2.f 3704 3705----------------------------------------------------------------------- 37062012-02-22 13:50:00 GMT Alberto Garcia <albertog@icmab.es> trunk-401 3707Assorted cosmetic and compilation fixes 3708 3709* Include missing LDFLAGS symbol in some Util makefiles 3710 3711modified: 3712 Util/COOP/Makefile 3713 Util/Contrib/APostnikov/Makefile 3714 Util/test-xml/makefile 3715 3716* Obsolete debug information was still being written to unit 23 in 3717 domain_decom, including a call to "flush". 3718 3719modified: 3720 Src/domain_decom.F 3721 3722* Fix makefile symbols in Util/STM/ol-stm 3723 The new domain_decomposition symbols and dependencies were missing. 3724 3725modified: 3726 Util/STM/ol-stm/Src/Makefile 3727 3728* Updated bug reporting guidelines 3729 3730added: 3731 Docs/REPORTING_BUGS 3732modified: 3733 Docs/siesta.tex 3734 README 3735 3736* Do not count ghost atoms when printing ionic charge 3737 3738This was purely cosmetic, but misleading: the variable 3739zvaltot now records only the sum of (pseudo)protons in 3740non-ghost species. 3741 3742(+ cosmetic fix in the printing of lmxkb for ghosts 3743species in .ion files) 3744 3745modified: 3746 Src/atomlist.f 3747 Src/basis_types.f 3748 3749* Fix the script in Tests/partial 3750 Now it can automatically compile the 'fractional' program 3751 3752modified: 3753 Tests/partial/script.sh 3754 3755* Add Util/clean_all.sh script 3756* Remove scratch fdf directories in Util/GenBasis and Util/Vibra 3757 3758removed: 3759 Util/Gen-basis/fdf/ 3760 Util/Vibra/Src/fdf/ 3761added: 3762 Util/clean_all.sh 3763 3764 3765 3766----------------------------------------------------------------------- 37672012-02-21 17:50:00 GMT Alberto Garcia <albertog@icmab.es> trunk-400 3768Assorted bugfixes and cosmetics 3769 3770Bugfixes for recent features: 3771 3772* Include support for domain_decom in Denchar makefile 3773 3774Cosmetic changes: 3775 3776 - State that the units for mprop distances are Ang 3777 - Clarify error message in ts_iohs regarding nspin 3778 - Write eigenvalues in eV in CML file (ioeig) 3779 - Use $(AR) instead of 'ar' in all makefiles 3780 - Specify Ry units for H in DMHS netcdf files 3781 - Fix call to 'memory' in Denchar/stsofr.f 3782 3783modified: 3784 Src/Libs/makefile 3785 Src/MPI/Makefile 3786 Src/Sys/DOCUMENTED-TEMPLATE.make 3787 Src/iodmhs_netcdf.F90 3788 Src/ioeig.f 3789 Src/m_ts_io.F90 3790 Src/wxml/makefile 3791 Src/xmlparser/makefile 3792 Util/COOP/subs.f90 3793 Util/Denchar/Src/Makefile 3794 Util/Denchar/Src/stsofr.f 3795 3796----------------------------------------------------------------------- 37972012-02-21 17:05:00 GMT Alberto Garcia <albertog@icmab.es> trunk-399 3798Some cleanup and new options for O(N) solver code 3799 3800The O(N) solver code is being cleaned up, and more options are being 3801added, but should still be used with care and for systems for which 3802it is appropriate. 3803 3804* More documentation and better variable names and structure in some 3805 files. 3806 3807* Stop if O(N) chemical potential calculation is requested in parallel 3808 3809 The code in chempot is not correctly parallelized yet. Now the 3810 program stops at the beginning of the run if any of the relevant fdf 3811 options is enabled. 3812 3813* Implement graph-based domain decomposition for O(N) routines 3814 3815 Based on code by Rogeli Grima (BSC). 3816 3817 It is enabled by defining 3818 3819 UseDomainDecomposition T 3820 3821 in the fdf file. NOTE that if you use NetCDF you also need: 3822 3823 WriteDMNetcdf F 3824 WriteDMHS-netcdf F 3825 3826 until a non-local call to LocalToGlobalOrb is fixed. 3827 3828 The METIS library (www.cs.umn.edu/~metis) is also needed. Calls to 3829 this library are wrapped in preprocessor blocks controlled by the 3830 symbol 3831 3832 ON_DOMAIN_DECOMP 3833 3834 which needs to be specified at (parallel) compile time if domain 3835 decomposition is desired. 3836 3837 Now, by default, Julian's Gale spatial decomposition code is 3838 bypassed, unless the fdf variable 3839 3840 UseSpatialDecomposition 3841 3842 is set. The default is now to use block-cyclic decomposition, but 3843 any serious calculation should use one of the two more sophisticated 3844 approaches. A further refinement is in the pipeline. 3845 3846* Add the Util/ON directory with lwf2cdf program 3847 3848 This utility program converts the information in the LWF file 3849 to netCDF format. 3850 3851(A. Garcia, May-July 2011, Feb 2012) 3852(Backported from 3.1) 3853 3854----------------------------------------------------------------------- 38552012-02-21 14:15:00 GMT Alberto Garcia <albertog@icmab.es> trunk-398 3856Avoid broadcast after fdf operation in m_ts_options 3857 3858With the new fdf interface all nodes get the appropriate values 3859without a broadcast. There was a fossil mpi_bcast in m_ts_options. 3860 3861modified: 3862 Src/m_ts_options.F90 3863 3864----------------------------------------------------------------------- 38652012-02-20 16:45:00 GMT Alberto Garcia <albertog@icmab.es> trunk-397 3866More documentation for tests. New .make file. 3867 3868* Added a new README file for the Tests directory and for the 3869 new-style Transiesta-TBTrans tests 3870 3871* Add arch.make file for Marenostrum IBM supercomputer using ESSL 3872 3873 Added the necessary LAPACK libraries in order to compile using ESSL on IBM. 3874 ESSL are a set of system-optimized BLAS functions and subroutines. 3875 3876 Use the following lines in your arch.make: 3877 COMP_LIBS = essl_lapack.a 3878 LIBS = -lessl 3879 3880 The new file Src/Sys/marenostrum-mpi-essl-netcdf-64.make is appropriate 3881 for 64 bit operation. 3882 3883 (Thanks to Oscar Paz) 3884 3885 added: 3886 Src/Sys/marenostrum-mpi-essl-netcdf-64.make 3887 Src/Libs/essl_lapack.f 3888 modified: 3889 Src/Libs/makefile 3890 Src/Makefile 3891 3892* Make sure 'partial' is compiled in test 3893 3894 The 'partial' test is not completely set up for transparent operation, 3895 and the needed executable in Util/VCA needs to be pre-compiled. 3896 3897 The script stops with a message if this is not done (note that this 3898 test is not executed by default from the top Makefile). 3899 3900 modified: 3901 Tests/partial/script.sh 3902 3903----------------------------------------------------------------------- 39042012-02-20 16:30:00 GMT Alberto Garcia <albertog@icmab.es> trunk-396 3905Fixes: pointer initialization, logical assignment 3906 3907In cgvc_zmatrix, two scratch pointers were not properly initialized 3908before use. 3909 3910In nlefsm, two logical arrays were initialized with '0', instead of 3911'.false.' (Thanks to Carlos Sanz for pointing this out). 3912 3913modified: 3914 Src/cgvc_zmatrix.F 3915 Src/nlefsm.f 3916 3917----------------------------------------------------------------------- 39182012-02-20 15:50:00 GMT Alberto Garcia <albertog@icmab.es> trunk-395 3919Avoid broadcast after fdf operation in tbtrans 3920 3921With the new fdf interface all nodes get the appropriate values 3922without a broadcast. Tbtrans (in routine reinit_tb) still called 3923mpi_bcast. This led to errors in some systems. 3924 3925modified: 3926 Util/TBTrans/reinit_tb.F 3927 3928----------------------------------------------------------------------- 39292012-02-20 13:50:00 GMT Alberto Garcia <albertog@icmab.es> trunk-394 3930Update TranSiesta tests. Cosmetics 3931 3932* Update the TranSiesta-TBTrans test directories 3933 3934 TranSiesta-TBTrans specific tests now reside in 3935 Tests/TranSiesta-TBTrans. These tests (currently ts_fast and ts_au) 3936 only make sense if the "transiesta" flavor of Siesta has been compiled 3937 in (by executing "make transiesta" in a fresh build directory), so 3938 they are not executed by default. 3939 3940 Reference outputs can now be found in 3941 Tests/Reference/TranSiesta-TBTrans. Note that these reference 3942 outputs have not yet been updated: they correspond to siesta-3.1. 3943 3944 The manual has been updated to refer to the Examples/TranSiesta 3945 directory (which has been created) for the guided calculation. 3946 3947 removed: 3948 Tests/transiesta/Fast/ 3949 Tests/transiesta/au_111_capacitor/ 3950 Tests/transiesta/bulk_au_111/ 3951 Tests/transiesta/elec_au_111_abc/ 3952 added: 3953 Tests/Reference/TranSiesta-TBTrans/ 3954 Tests/Reference/TranSiesta-TBTrans/ts_au/ 3955 Tests/Reference/TranSiesta-TBTrans/ts_fast/ 3956 Tests/TranSiesta-TBTrans/ts_au/ 3957 Examples/TranSiesta 3958 renamed: 3959 Tests/transiesta/ => Tests/TranSiesta-TBTrans/ 3960 Tests/ts_fast/ => Tests/TranSiesta-TBTrans/ts_fast/ 3961 modified: 3962 Tests/TranSiesta-TBTrans/ts_fast/makefile 3963 Tests/TranSiesta-TBTrans/ts_fast/script.sh 3964 Tests/Makefile 3965 Tests/script_ts.mk 3966 Docs/siesta.tex 3967 3968* Removed call to BLAS routine zdotc in tbtrans. Replaced it 3969 by an explicit loop. 3970 3971* Clarify the mention of "hybrid" functionals in the manual 3972 3973 modified: 3974 Docs/siesta.tex 3975 3976* Remove order-N test from standard list. Add note. 3977 3978 As it does not run well in parallel, the order-N 3979 test has been removed from the standard list 3980 in the Makefile for the Tests directory. 3981 3982 added: 3983 Tests/h2o_orderN/000README 3984 modified: 3985 Tests/Makefile 3986 3987----------------------------------------------------------------------- 39882012-02-16 15:25:00 GMT Alberto Garcia <albertog@icmab.es> trunk-393 3989Fix pointer initialization in moremeshsubs 3990 3991Two workspace pointers were not properly nullified before allocation. 3992 3993Thanks to Olivier Coulaud for the report and the fix. 3994 3995modified: 3996 Src/moremeshsubs.F 3997 3998----------------------------------------------------------------------- 39992012-02-16 10:35:00 GMT Alberto Garcia <albertog@icmab.es> trunk-392 4000Proper closing of files in m_iorho 4001 4002Due to a programming error, the calls to io_close in read_rho and 4003check_rho were incorrectly placed. 4004 4005Thanks to Carlos Sanz for the report and the fix. 4006 4007modified: 4008 Src/m_iorho.F 4009 4010----------------------------------------------------------------------- 40112012-02-15 18:05:00 GMT Alberto Garcia <albertog@icmab.es> trunk-391 4012Clarify flow of data in setup_H0 4013 4014The routine setup_H0 pre-computes the matrix elements of the kinetic 4015and non-local pseudopotential pieces of the Hamiltonian, which do not 4016depend on the density matrix. 4017 4018Routines kinefsm and nlfesm also compute Ekin and Enl, respectively, 4019but since they are not called anymore in the SCF cycles, Ekin and Enl 4020are not updated, and are only printed at the first and last 4021iterations. 4022 4023In order to make this more explicit, H0 has been substituted by two 4024arrays, H_kin and H_vkb, to hold the pieces of H. Ekin and Enl are now 4025computed in setup_hamiltonian, with the appropriate density matrix. A 4026minor cosmetic issue now is that, in setup_H0, the routines 'kinefsm' 4027and 'nlefsm' must be called with a value of 1 for nspin, as befits the 4028structure of H_kin and H_vkb. The density matrix array is not 4029referenced. 4030 4031Other changes: 4032 4033* The variable 'nh' has been substituted by its equivalent maxnh 4034throughout the code. 4035 4036* The use of H0 as a work array in calls to the ksv_pol routine has 4037been made clearer by importing H_kin and renaming it 'Work'. 4038 4039modified: 4040 Docs/KNOWN.ISSUES.BSC-patch 4041 Src/Makefile 4042 Src/born_charge.F 4043 Src/compute_dm.F 4044 Src/final_H_f_stress.F 4045 Src/hsparse.F 4046 Src/kinefsm.f 4047 Src/nlefsm.f 4048 Src/normalize_dm.F 4049 Src/post_scf_work.F 4050 Src/setup_H0.F 4051 Src/setup_hamiltonian.F 4052 Src/siesta_analysis.F 4053 Src/siesta_init.F 4054 Src/sparse_matrices.F 4055 Src/state_init.F 4056 4057----------------------------------------------------------------------- 40582011-10-28 10:45:00 GMT Alberto Garcia <albertog@icmab.es> trunk-390 4059Avoid temporary arrays in SiestaXC/mesh3d 4060 4061Calls with a re-shaped array as argument, and with 4062array-section arguments, were inducing some compilers 4063to create temporary arrays. 4064 4065modified: 4066 Src/SiestaXC/mesh3d.F90 4067 4068----------------------------------------------------------------------- 40692011-10-28 10:35:00 GMT Alberto Garcia <albertog@icmab.es> trunk-389 4070Re-instate reading of charge netcdf files 4071 4072This feature had been turned off after the BSC merge pending 4073clarification. 4074 4075modified: 4076 Src/dhscf.F 4077 4078----------------------------------------------------------------------- 40792011-10-28 10:15:00 GMT Alberto Garcia <albertog@icmab.es> trunk-388 4080Grid file utilities. User-specified mesh sizes 4081 4082Two new programs are available to generate grid files 4083(density, potential): 4084 4085-- grid_rotate: cyclically rotates the coordinates of 4086 a grid file. 4087-- grid_supercell: generates the grid file appropriate 4088 for a supercell. 4089 4090The user can now specify the mesh sizes to be used 4091by the program, by inserting a block definition in 4092the fdf file: 4093 4094%block Mesh-sizes 4095 40 56 120 4096%endblock Mesh-sizes 4097 4098This feature is useful when coupled to the above utilities, 4099since the "magic" fft numbers might not be appropriate. 4100 4101added: 4102 Docs/Grid.CHANGES 4103 Util/Grid/grid_rotate.F90 4104 Util/Grid/grid_supercell.F90 4105modified: 4106 Src/Makefile 4107 Src/meshsubs.F 4108 Util/Grid/makefile 4109 4110----------------------------------------------------------------------- 41112011-09-16 09:15:00 GMT Alberto Garcia <albertog@icmab.es> trunk-387 4112Fix bug in BandLines processing 4113 4114The processing of the BandLines block was faulty, resulting 4115in most cases in the skipping of the 'bands' calculation. 4116 4117modified: 4118 Src/bands.F 4119 4120----------------------------------------------------------------------- 41212011-09-12 09:15:00 GMT Alberto Garcia <albertog@icmab.es> trunk-386 4122Fix fdf_defined to take blocks into account 4123 4124The new version of fdf_defined was only checking 4125for the existence of single labels. It has been 4126fixed to check for blocks too. 4127 4128modified: 4129 Src/fdf/fdf.F90 4130 Src/fdf/sample.F90 4131 4132----------------------------------------------------------------------- 41332011-08-30 09:50:00 GMT Alberto Garcia <albertog@icmab.es> trunk-385 4134Fix two minor bugs in Denchar 4135 4136Some compilers had trouble with a block pointer. It has 4137been made into a normal variable. 4138 4139An attempt was made to close an I/O unit that had not 4140ben opened in the spin-unpolarized case. 4141 4142(Thanks to T. Sondon) 4143 4144modified: 4145 Util/Denchar/Src/atompla.f 4146 Util/Denchar/Src/rhoofr.f 4147 4148----------------------------------------------------------------------- 41492011-08-26 12:40:00 GMT Alberto Garcia <albertog@icmab.es> trunk-384 4150Print information about grid distributions 4151 4152New code has been added to show information about 4153the different grid data distributions. 4154 4155modified: 4156 Src/moremeshsubs.F 4157 4158----------------------------------------------------------------------- 41592011-05-19 15:20:00 GMT Alberto Garcia <albertog@icmab.es> trunk-383 4160Fix and clarify code for KB projector orthogonalization 4161 4162In routine kbproj, a saved variable was used to keep track 4163of the number of previous KB projectors with the same l. This 4164variable was only reset upon a change in l. This can lead 4165to errors if a species with a single l=0 KB complex is used. 4166 4167The code has been streamlined, passing explicitly an index 4168that determines the sequence number of the projector. 4169 4170modified: 4171 Src/atom.f 4172 4173----------------------------------------------------------------------- 41742011-05-03 16:10:00 GMT Alberto Garcia <albertog@icmab.es> trunk-382 4175Fix declaration in cgwf.F 4176 4177A previous commit introduced a spurious dummy argument 4178"node", which should really be imported from a module. 4179 4180modified: 4181 Src/cgwf.F 4182 4183----------------------------------------------------------------------- 41842011-05-03 14:15:00 GMT Alberto Garcia <albertog@icmab.es> trunk-381 4185Clarify mixing code in TranSiesta mode 4186 4187If the TranSiesta code is compiled in, the user can choose between two 4188mixing options in the self-consistent cycle: density-matrix, or 4189Hamiltonian. The option chosen takes effect both for the initial 4190normal Siesta-style calculation, if needed, and for the "transiesta 4191mode" section. 4192 4193The code in mixer.F and elsewhere has been streamlined, to make it 4194clear what the mixed objects are and avoid extraneous global 4195dependencies. 4196 4197modified: 4198 Src/Makefile 4199 Src/m_ts_global_vars.f90 4200 Src/mixer.F 4201 Src/new_dm.F 4202 Src/state_init.F 4203 4204----------------------------------------------------------------------- 42052011-05-03 14:05:00 GMT Alberto Garcia <albertog@icmab.es> trunk-380 4206Make auxiliary variable double precision in line minimization 4207 4208In routine linmin4, the complex variable "c" was declared 4209as single-precision. It is now a double. 4210 4211modified: 4212 Src/cgwf.F 4213 4214----------------------------------------------------------------------- 42152011-05-03 13:00:00 GMT Alberto Garcia <albertog@icmab.es> trunk-379 4216Fix mixing bug in Transiesta + tbtrans wrap + pulayx warnings 4217 4218* Fix mixing bug in TranSiesta 4219 4220In TranSiesta mode, the program first might carry out a calculation at 4221zero bias and with periodic boundary conditions, just as a normal 4222Siesta calculation. Then the program goes into "transiesta mode" 4223proper, during which a new mixing cycle takes place. 4224 4225In late June 2010, a change in the structure of the mixing code 4226introduced a bug: the counter holding the number of history records 4227was not properly initialized upon the ending of the preliminary 4228siesta-style calculation. 4229 4230The mixing counter is now properly reset. 4231 4232modified: 4233 Src/scfconvergence_test.F 4234 4235* In tbtrans some auxiliary files were written to by all the nodes. 4236 4237(+ Also, make sure that the transiesta capability appears at 4238the top of the transiesta output file) 4239 4240modified: 4241 Src/Makefile 4242 Util/TBTrans/tbtrans.F 4243 4244* Avoid reporting unstable inversion in pulayx 4245 4246Typically, inversion problems in the DIIS procedure occur when the 4247error estimate for a step is very small compared to the previous 4248ones. This is harmless, and the reporting of a failure in the output 4249file is confusing. 4250 4251In case it is needed, a hook to allow a full diagnosis 4252can be compiled in with the preprocessor flag 4253 4254DEBUG_PULAY_INVERSE 4255 4256(+ Also, initialize "found" variable in new_dm.F in transiesta mode) 4257 4258modified: 4259 Src/m_pulay.F90 4260 Src/new_dm.F 4261 4262* Increase field sizes in OCCS file 4263 4264Some fields overflowed when a large number of k-points was used. 4265 4266modified: 4267 Src/diagk.F 4268 Src/diagk_file.F 4269 4270----------------------------------------------------------------------- 42712011-05-03 12:45:00 GMT Alberto Garcia <albertog@icmab.es> trunk-378 4272Fix manual re: non-collinear GGA and zmatrix input. FoX cosmetics 4273 4274* The manual incorrectly stated that GGA was not compatible with 4275non-collinear-spin calculations. 4276 4277The order of the spherical coordinates for the second atom in the 4278zmatrix format input is now explicitly stated. 4279 4280modified: 4281 Docs/siesta.tex 4282 4283* Cosmetic changes to avoid xlf compiler diagnostics in dummy FoX 4284 4285If the "trap undefined variables" option is enabled in the xlf 4286compiler, some stray symbols in the dummy version of the FoX library 4287produce diagnostics. They have been re-wrapped. 4288 4289(Thanks to Oscar Paz) 4290 4291modified: 4292 Src/FoX/common/m_common_attrs.F90 4293 Src/FoX/utils/fox_m_utils_uri.F90 4294 4295----------------------------------------------------------------------- 42962011-04-14 09:10:00 GMT Alberto Garcia <albertog@icmab.es> trunk-377 4297Avoid the creation of temporary and log files for fdf in parallel 4298 4299The standard mode of operation of the new fdf library is "cluster", in 4300which the root node reads and processes the fdf file(s) and sends 4301relevant information to the rest of the nodes. At the end of the setup 4302process every node has a private copy of a pre-parsed fdf structure 4303that can be consulted quickly. 4304 4305In the first version by Raul de la Cruz the root node sent raw text 4306information to the other nodes, and these used a temporary scratch 4307file to dump it to. Later these nodes invoked the digesting routine on 4308the scratch file to create the memory structure. 4309 4310Now the root node serializes its own memory structure and sends it 4311over to the other nodes. These just need to de-serialize the 4312information and re-create the memory structure. 4313 4314Log files were also produced by all nodes by default. Now non-root 4315nodes create the log files under "/tmp", with names of the form 4316"tmp/fdf.log.N", where N is a representation of the MPI rank. Only 4317the root node creates a "fdf.log" file in the working directory. 4318This is useful for cluster settings in which non-root nodes might not 4319be able to write efficiently to common areas. 4320 4321Any debug files are created in the same way, with names of the form 4322"tmp/fdf.debug.N". At the end of the run they will contain a dump 4323of the fdf memory structure. 4324 4325Alberto Garcia, April 2011 4326 4327modified: 4328 Docs/KNOWN.ISSUES.BSC-patch 4329 Src/fdf/fdf.F90 4330 Src/fdf/parse.F90 4331 4332 4333----------------------------------------------------------------------- 43342011-03-29 13:30:00 GMT Alberto Garcia <albertog@icmab.es> trunk-376 4335Remove earlier patch for calculation of chemical potential 4336 4337Undo the changes to chempot (and the calling sequences in ordern and 4338compute_dm) introduced in November 2007 by P. Ordejon, as they are not 4339completely correct. This routine determines an approximate chemical 4340potential for O(N) calculations. Note that parallel operation is still 4341not possible. 4342 4343(Did not take back the changes in denmat.F and denmatlomem.F, which 4344simply force an unconditional rescaling of the density matrix to 4345produce the correct charge density.) 4346 4347(+ Fixed the code so that arbitrarily large Chebyshev's orders 4348are in principle possible in Chempot) 4349 4350(+ Instrumented the O(N) line-minimization routine to print extra 4351information if the preprocessor symbol DEBUG_LINMIN4 is used) 4352 4353modified: 4354 Src/cgwf.F 4355 Src/chempot.F 4356 Src/compute_dm.F 4357 Src/ordern.F 4358 4359----------------------------------------------------------------------- 43602011-03-22 10:10:00 GMT Alberto Garcia <albertog@icmab.es> trunk-375 4361Clarify folding warning for gamma-point calculations 4362 4363For gamma-point calculations with unit cells not large enough to avoid 4364interactions with images, a warning was produced even though it was 4365only relevant for calculations intended for COOP/COHP analysis. The 4366warning now appears only in that case. 4367 4368The manual has been updated to cover the point above, and also to make 4369it clear that the Use.New.Diagk option is not compatible with the 4370Diag.Parallel.Over.K mode. 4371 4372(+ cosmetic changes to avoid compiler warnings related to duplicate 4373use statements) 4374 4375modified: 4376 Docs/siesta.ind 4377 Docs/siesta.tex 4378 Src/Makefile 4379 Src/hsparse.f 4380 Src/m_ts_scattering.F 4381 4382----------------------------------------------------------------------- 43832011-03-14 10:10:00 GMT Alberto Garcia <albertog@icmab.es> trunk-374 4384Experimental output comparison tool 4385 4386A simple "output digest" script in awk extracts key information fields from the output 4387file with default precisions, and generates a small file. These digest files can then 4388be compared to check for differences. 4389 4390This is an experimental feature. It is not yet integrated in the automatic test 4391framework. Note that the reference output files in Tests/Reference have not yet 4392been updated, pending a review. 4393 4394added: 4395 Tests/cmp_digest.sh ! Script to compare digest files 4396 Tests/out_digest.awk ! Digest generator 4397 Tests/out_digest_template.awk ! Template for optional precision changes 4398modified: 4399 Src/obj_setup.sh ! It now creates a symbolic link to the ref directory. 4400 4401----------------------------------------------------------------------- 44022011-03-09 16:00:00 GMT Alberto Garcia <albertog@icmab.es> trunk-373 4403Fix two bugs in Vibra package 4404 4405The code to read the coordinates-and-masses block did not process the 4406masses properly. It now also warns when there are not enough values in 4407each line (a common error). 4408 4409Variable 'nlines' was not properly set in routine 'klines'. 4410 4411modified: 4412 Util/Vibra/Src/klines.f 4413 Util/Vibra/Src/recoor.f 4414 4415----------------------------------------------------------------------- 44162011-03-04 14:45:00 GMT Alberto Garcia <albertog@icmab.es> trunk-372 4417Re-enable write_rho routine 4418 4419The write_rho routine had been modified for debugging purposes, but 4420was not re-enabled. It now has been brought back to normal. 4421 4422modified: 4423 Src/m_iorho.F 4424 4425----------------------------------------------------------------------- 44262011-02-25 10:20:00 GMT Alberto Garcia <albertog@icmab.es> trunk-371 4427Fixes in pdosxml and denchar 4428 4429(Ported from siesta-3.0 branch) 4430 4431*Some compilers might have trouble with the shorthand 4432array syntax used in the update of data arrays in m_pdos.f90. 4433The bounds are now explicitly indicated. 4434 4435(Thanks to Miguel Pruneda) 4436 4437modified: 4438 Util/pdosxml/m_pdos.f90 4439 4440* In 2D wavefunction mode, denchar was printing two blank lines 4441between coordinate blocks. 4442 4443modified: 4444 Util/Denchar/Src/denchar.f -- removed duplicate 'use' statement 4445 Util/Denchar/Src/rhoofr.f -- interblock spacing 4446 Util/Denchar/Src/wavofr.f -- " 4447 4448----------------------------------------------------------------------- 44492011-02-18 15:55:00 GMT Alberto Garcia <albertog@icmab.es> trunk-370 4450Re-initialize data array in timer routine 4451 4452Apparently it fixes some strangeness with some compilers. 4453 4454(by Jose Soler) 4455 4456modified: 4457 Src/m_timer.F90 4458 4459----------------------------------------------------------------------- 44602011-02-18 15:50:00 GMT Alberto Garcia <albertog@icmab.es> trunk-369 4461Remove mentions to SLEPC 4462 4463The mentions to SLEPC were fossils from a side branch and they have been 4464removed. 4465 4466modified: 4467 Src/siesta_init.F 4468 4469----------------------------------------------------------------------- 44702011-02-03 11:15:00 GMT Alberto Garcia <albertog@icmab.es> trunk-368 4471Incorporation of BSC code: mesh optimization; parallel fdf library 4472 4473* The ongoing collaboration with the Barcelona Supercomputer Center 4474(through the department of Computer Applications in Science and 4475Engineering) has resulted in two new main enhancements: 4476 4477- New code to improve the load-balance among processors in the 4478operations carried out in the real-space mesh (involved in the 4479computation of charge density, exchange-correlation potential, and 4480matrix elements of the hamiltonian, among others). 4481 4482Since the different operations have different work-load patterns, it 4483has been necessary to define and handle three separate data 4484distributions, with appropriately optimized communication patterns. 4485Most of the new code is contained in new specialized modules, and 4486there are calls for data distribution handling in higher-level 4487modules, notably dhscf. 4488 4489An overview of the rationale and implementation of the new functionality 4490can be found in 4491 4492An efficient implementation of a QM-MM method in SIESTA, 4493C. F. Sanz-Navarro, R. Grima, A. Garcia, E. A. Bea, A. Soba, 4494J.M. Cela, and P. Ordejon, 4495Theoretical Chemistry Accounts. Online pub Sep 2010. 4496DOI: 10.1007/s00214-010-0816-5 4497 4498We are working on a set of developer-oriented notes to facilitate 4499future enhancements. 4500 4501- A new fdf library which avoids the 'master node bottleneck': each 4502MPI processor now holds a copy of the relevant information, and can 4503satisfy fdf queries without the need for interprocess communication or 4504file access. 4505 4506The most noticeable change is in the processing of fdf blocks. The previous 4507version of the library provided a Fortran unit number from which the 4508user code could read the block contents. Now the user is given an 4509abstract handle with which to perform explicitly the operations of reading 4510lines, parse, and extract useful information. This paradigm was already 4511present as a wrapper in previous versions of Siesta, but it is now mandatory. 4512 4513The two new developments, while formally independent, have been merged 4514at the same time due to historical and logistical reasons. Even though 4515the mesh enhancements affect directly only a relatively small number 4516of files, many others have been modified: some by changes in memory 4517allocation syntax and indentation, and some to clarify code patterns 4518or interfaces (see below). The new treatment of fdf blocks and the 4519removal of the explicit broadcast step in some existing fdf calls has 4520meant changes to many other files. In all, this patch affects several 4521dozen files in the Siesta distribution. 4522 4523* Other significant changes 4524 4525- The interface to the spherical-harmonics module in matel has been 4526changed to avoid the creation of temporary arrays at run time. Also, 4527some internal arrays in the spherical-harmonics module are now 4528pre-allocated to avoid overhead. 4529 4530- Throughout the code most 'allocatable' arrays have been turned into 4531pointers, to be able to exploit the functionality in the alloc module 4532to resize them concisely. It can be argued that we have gone too far 4533in some cases. 4534 4535We have invested a lot of effort in this work, but it is very likely 4536that some issues have escaped us. A list of those known at this 4537time can be found in the file Docs/KNOWN.ISSUES.BSC-patch 4538 4539removed: 4540 Src/FoX/arch.make 4541 Src/doping.F 4542 Src/fdf/fdf.f 4543 Src/fdf/fdf.h 4544 Src/fdf/fdf_mod.f 4545 Src/fdf/fdfdefs.h 4546 Src/fdf/io_for_fdf_tests.f 4547 Src/fdf/io_sample.f 4548 Src/fdf/parse.f 4549 Src/fdf/sample.f 4550 Src/m_efield.F 4551 Tests/bsc-compare.sh 4552 Tests/std-compare.sh 4553 Util/Denchar/Src/fdf/.dummy_dir 4554 Util/Gen-basis/fdf/.dummy_directory 4555 Util/TBTrans/Libs/ 4556 Util/TBTrans/Libs/.dummy_directory 4557 Util/TBTrans/MPI/ 4558 Util/TBTrans/MPI/.dummy_dir 4559 Util/TBTrans/fdf/ 4560 Util/VCA/fdf/.dummy_directory 4561 Util/Vibra/Src/fdf/.dummy_directory 4562added: 4563 .bzrignore 4564 Docs/BSC.CHANGES 4565 Docs/KNOWN.ISSUES.BSC-patch 4566 Src/FoX/arch.make 4567 Src/Libs/dgetrs_lapack.f 4568 Src/Libs/dspev_lapack.f 4569 Src/Sys/altix-32b-par.make 4570 Src/Sys/altix-32b-ser.make 4571 Src/Sys/atto-pgf95-openmpi.make 4572 Src/Sys/finisterrae.make.moved 4573 Src/Sys/g95-macosx-netcdf.make 4574 Src/Sys/gfortran-macosx-netcdf.make 4575 Src/Sys/intel-mpi-checks-metis.make 4576 Src/Sys/intel10-openmpi.make 4577 Src/Sys/intel11-openmpi.make 4578 Src/Sys/macosx-openmpi.make 4579 Src/Sys/marenostrum-lanczos.make 4580 Src/Sys/marenostrum-mpi-metis-64.make 4581 Src/Sys/mn-32b-par.make 4582 Src/Sys/mn-32b-ser.make 4583 Src/Sys/mn-openmp.make 4584 Src/Sys/nano-intel10-mvapich.make 4585 Src/Sys/pgf95-pgimpi.make 4586 Src/Sys/rogeli-intel-par.make 4587 Src/bsc_cellxc.F 4588 Src/bsc_xcmod.F 4589 Src/cellxc_mod.F 4590 Src/debugmpi.F 4591 Src/doping_uniform.F 4592 Src/fdf.Standard 4593 Src/fdf/XY.fdf 4594 Src/fdf/arch.make 4595 Src/fdf/fdf.F90 4596 Src/fdf/hostfile 4597 Src/fdf/io_fdf.F90 4598 Src/fdf/iso_fortran_env.F90 4599 Src/fdf/parse.F90 4600 Src/fdf/prec.F90 4601 Src/fdf/sample.F90 4602 Src/fdf/submit.sh 4603 Src/fdf/tags 4604 Src/fdf/utils.F90 4605 Src/final_H_f_stress.F 4606 Src/m_diagon.F 4607 Src/m_dscfcomm.F 4608 Src/m_efield.F 4609 Src/mesh.F 4610 Src/meshcomm.F 4611 Src/meshphi.F 4612 Src/moremeshsubs.F 4613 Src/qsort.F 4614 Src/schecomm.F 4615 Src/setup_H0.F 4616 Src/walltime.c 4617 Src/xc.f 4618 Tests/mgc-force/ 4619 Tests/mgc-force/makefile 4620 Tests/mgc-force/mgc-force.fdf 4621 Tests/mgc-force/mgc-force.pseudos 4622 Util/Denchar/Src/timer_local.f 4623renamed: 4624 Src/atom.f => Src/atom.F 4625 Src/forhar.f => Src/forhar.F 4626 Src/hsparse.f => Src/hsparse.F 4627 Src/meshmatrix.F => Src/meshdscf.F 4628 Src/parallelsubs.f => Src/parallelsubs.F 4629 Src/rhooda.f => Src/rhooda.F 4630 Src/rhoofd.f => Src/rhoofd.F 4631 Src/sparse_matrices.F90 => Src/sparse_matrices.F 4632 Src/timer.f90 => Src/timer.F90 4633 Src/vmat.f => Src/vmat.F 4634modified: 4635 Docs/siesta.ind 4636 Docs/siesta.tex 4637 Src/MPI/generate.sh 4638 Src/MPI/mpi.F 4639 Src/MPI/mpi__include.f90 4640 Src/Makefile 4641 Src/SiestaXC/lib-makefile 4642 Src/SiestaXC/makefile 4643 Src/Sys/finisterrae.make 4644 Src/Sys/gfortran-netcdf.make 4645 Src/Sys/marenostrum-mpi-32.make 4646 Src/Sys/nano-intel-mpi-cdf.make 4647 Src/Sys/nano-intel-mpi.make 4648 Src/alloc.F90 4649 Src/arw.f 4650 Src/atm_transfer.f 4651 Src/atm_types.f 4652 Src/atmfuncs.f 4653 Src/atomlist.f 4654 Src/atomlwf.F 4655 Src/bands.F 4656 Src/basis_io.F 4657 Src/basis_specs.f 4658 Src/basis_types.f 4659 Src/bonds.f 4660 Src/born_charge.F 4661 Src/broadcast_basis.F 4662 Src/broyden_optim.F 4663 Src/cdiag.F 4664 Src/cell_broyden_optim.F 4665 Src/cell_fire_optim.F 4666 Src/cgvc.F 4667 Src/cgvc_zmatrix.F 4668 Src/cgwf.F 4669 Src/chemical.f 4670 Src/chempot.F 4671 Src/compute_dm.F 4672 Src/conjgr.f 4673 Src/constr.f 4674 Src/coor.F 4675 Src/denmat.F 4676 Src/denmatlomem.F 4677 Src/densematrix.f 4678 Src/detover.F 4679 Src/dfscf.f 4680 Src/dhscf.F 4681 Src/diag2g.F 4682 Src/diag2k.F 4683 Src/diagg.F 4684 Src/diagk.F 4685 Src/diagk_file.F 4686 Src/diagkp.F 4687 Src/diagon.F 4688 Src/diagpol.f 4689 Src/diagsprl.F 4690 Src/dipole.F 4691 Src/dnaefs.f 4692 Src/dynamics.f 4693 Src/egandd.F 4694 Src/eggbox.F 4695 Src/electrostatic.f 4696 Src/ener3.F 4697 Src/ener3lomem.F 4698 Src/fdf/Otherfile 4699 Src/fdf/README 4700 Src/fdf/coords.fdf 4701 Src/fdf/fdf.Standard 4702 Src/fdf/makefile 4703 Src/fdf/sample.fdf 4704 Src/fermid.F 4705 Src/fft.F 4706 Src/find_kgrid.F 4707 Src/fire_optim.F 4708 Src/fixed.F 4709 Src/get_target_stress.f 4710 Src/globalise.F 4711 Src/gradient.F 4712 Src/gradientlomem.F 4713 Src/grdsam.F 4714 Src/initatom.f 4715 Src/initparallel.F 4716 Src/iocg.f 4717 Src/iodm.F 4718 Src/iodm_netcdf.F90 4719 Src/iodmhs_netcdf.F90 4720 Src/ioeig.f 4721 Src/iofa.f 4722 Src/iogrid_netcdf.F90 4723 Src/iokp.f 4724 Src/iolwf.F 4725 Src/iomd.f 4726 Src/iopipes.F90 4727 Src/ioxv.F 4728 Src/iozm.F 4729 Src/kgrid.F 4730 Src/kgridinit.F 4731 Src/kinefsm.f 4732 Src/kpoint_grid.F90 4733 Src/kpoint_pdos.F90 4734 Src/ksv.f 4735 Src/ksvinit.F 4736 Src/linpack.F 4737 Src/listsc.f 4738 Src/local_DOS.F 4739 Src/m_broyden_mixing.f 4740 Src/m_fire_mixing.f 4741 Src/m_history.f90 4742 Src/m_iodm.F 4743 Src/m_iorho.F 4744 Src/m_iostruct.f 4745 Src/m_memory.F 4746 Src/m_mpi_utils.F 4747 Src/m_pulay.F90 4748 Src/m_sparse.F 4749 Src/m_spin.F90 4750 Src/m_ts_in_siesta.F 4751 Src/m_ts_kpoints.F90 4752 Src/m_ts_options.F90 4753 Src/matel.f 4754 Src/memory.F 4755 Src/memoryinfo.F 4756 Src/meshsubs.F 4757 Src/metaforce.F 4758 Src/mixer.F 4759 Src/mneighb.f 4760 Src/molecularmechanics.F90 4761 Src/moreParallelSubs.F90 4762 Src/mulliken.F 4763 Src/naefs.f 4764 Src/new_dm.F 4765 Src/nlefsm.f 4766 Src/normalize_dm.F 4767 Src/obc.f 4768 Src/old_atmfuncs.f 4769 Src/optical.F 4770 Src/ordern.F 4771 Src/outcoor.f 4772 Src/overfsm.f 4773 Src/overlap.f 4774 Src/pdos.F 4775 Src/pdosg.F 4776 Src/pdosk.F 4777 Src/pdoskp.F 4778 Src/phirphi.f 4779 Src/phirphi_opt.f 4780 Src/phonon.F 4781 Src/pixmol.f 4782 Src/plcharge.F 4783 Src/poison.F 4784 Src/post_scf_work.F 4785 Src/precision.F 4786 Src/projected_DOS.F 4787 Src/proximity_check.F 4788 Src/pseudopotential.f 4789 Src/pxf.F90 4790 Src/radfft.f 4791 Src/radial.f 4792 Src/rdiag.F 4793 Src/read_xc_info.F 4794 Src/readsp.F 4795 Src/redcel.F 4796 Src/reinit.F 4797 Src/reoptical.F 4798 Src/reord.f 4799 Src/rhoofdsp.f 4800 Src/savepsi.F 4801 Src/scfconvergence_test.F 4802 Src/setatomnodes.F 4803 Src/setspatial.f 4804 Src/setup_hamiltonian.F 4805 Src/setup_kscell.F 4806 Src/shaper.f 4807 Src/show_distribution.f 4808 Src/siesta.F 4809 Src/siesta_analysis.F 4810 Src/siesta_end.F 4811 Src/siesta_forces.F 4812 Src/siesta_init.F 4813 Src/siesta_move.F 4814 Src/siesta_options.F90 4815 Src/sorting.f 4816 Src/spher_harm.f 4817 Src/state_analysis.F 4818 Src/state_init.F 4819 Src/struct_init.F 4820 Src/vmatsp.f 4821 Src/vmb.F 4822 Src/write_md_record.F 4823 Src/write_subs.F 4824 Src/writewave.F 4825 Src/wxml/m_wxml_array_str.f90 4826 Src/wxml/m_wxml_buffer.f90 4827 Src/wxml/m_wxml_core.f90 4828 Src/wxml/m_wxml_dictionary.f90 4829 Src/wxml/m_wxml_elstack.f90 4830 Src/zm_broyden_optim.F 4831 Src/zm_fire_optim.F 4832 Src/zmatrix.F 4833 Tests/Makefile 4834 Util/Contrib/APostnikov/Makefile 4835 Util/Denchar/Src/Makefile 4836 Util/Denchar/Src/atompla.f 4837 Util/Denchar/Src/denchar.f 4838 Util/Denchar/Src/local_reinit.f 4839 Util/Denchar/Src/readpla.f 4840 Util/Denchar/Src/readsts.f 4841 Util/Gen-basis/Makefile 4842 Util/Gen-basis/gen-basis.F 4843 Util/HSX/iohs.F 4844 Util/Helpers/Makefile 4845 Util/Optimizer/Makefile 4846 Util/TBTrans/Makefile 4847 Util/TBTrans/green4.F 4848 Util/TBTrans/m_tbt_gf.F90 4849 Util/TBTrans/m_tbt_options.F90 4850 Util/TBTrans/mkqgrid.f 4851 Util/TBTrans/reinit_tb.F 4852 Util/TBTrans/tbtrans.F 4853 Util/VCA/Makefile 4854 Util/Vibra/Src/Makefile 4855 Util/Vibra/Src/fcbuild.f 4856 Util/Vibra/Src/klines.f 4857 Util/Vibra/Src/recoor.f 4858 Util/Vibra/Src/vibrator.f 4859 version.info 4860 Src/atom.F 4861 Src/forhar.F 4862 Src/hsparse.F 4863 Src/meshdscf.F 4864 Src/parallelsubs.F 4865 Src/rhooda.F 4866 Src/rhoofd.F 4867 Src/sparse_matrices.F 4868 Src/timer.F90 4869 Src/vmat.F 4870 4871 4872 4873 4874 4875 4876----------------------------------------------------------------------- 48772011-01-07 15:15:00 GMT Alberto Garcia <albertog@icmab.es> trunk-367 4878Initialized pointers in moreParallelSubs. Timer call 4879 4880* Several pointers were used without nullification in routine copyfile in 4881file moreParallelSubs.F90. 4882 4883* A "turn-off" call to timer was needed in cdiag in case of early termination. 4884 4885modified: 4886 Src/cdiag.F 4887 Src/moreParallelSubs.F90 4888 4889----------------------------------------------------------------------- 48902010-11-30 13:15:00 GMT Alberto Garcia <albertog@icmab.es> trunk-366 4891Work around bugs in Intel compilers: FoX generics, k-grid 4892 4893* Work around a bug in Intel12 compiler in k-grid setup 4894 4895A dummy internal write is used to re-focus the compiler 4896treatment of a few integer variables. 4897 4898modified: 4899 Src/find_kgrid.F 4900 Src/kgrid.F 4901 Src/kgridinit.F 4902 4903* Avoid use of generics in declarations in FoX format routine 4904 4905The use of generic functions in declaration statements was confusing 4906the Fortran compiler (version >= 11). They have been replaced by calls 4907to the specific versions. 4908 4909modified: 4910 Src/FoX/fsys/fox_m_fsys_format.F90 4911 4912----------------------------------------------------------------------- 49132010-11-26 15:00:00 GMT Alberto Garcia <albertog@icmab.es> trunk-365 4914Fix setting of applied electric field in parallel 4915 4916Due to a programming error, the user-specified electric 4917field was not correctly set in non-master nodes. 4918 4919Thanks to Alexander Vozny for the bug report. 4920 4921modified: 4922 Src/m_efield.F 4923 4924----------------------------------------------------------------------- 49252010-11-18 08:45:00 GMT Alberto Garcia <albertog@icmab.es> trunk-364 4926Clarify the output of the timing routine 4927 4928The timing routine now prints zeros instead of NaNs in the 4929communications section if the variable MPI_TIMING is not defined, 4930and an informational note. 4931 4932modified: 4933 Src/m_timer.F90 4934 4935----------------------------------------------------------------------- 49362010-11-18 08:40:00 GMT Alberto Garcia <albertog@icmab.es> trunk-363 4937Modify bonds routine to print real locations of neighbors 4938 4939In routine bonds (called at the beginning and at the end of the 4940program) we now print the real location of the neighbor atom in space, 4941and not, as in earlier versions, the location of the equivalent 4942representative in the unit cell. 4943 4944modified: 4945 Src/bonds.f 4946 4947----------------------------------------------------------------------- 49482010-11-12 16:20:00 GMT Alberto Garcia <albertog@icmab.es> trunk-362 4949Merge 3.0 fixes: ps reparametrization, getopts, ioncat, atm manual 4950 4951* Cosmetic fixes in Gen-basis/{ioncat,ionplot.sh} 4952 4953modified: 4954 Util/Gen-basis/ioncat.f 4955 Util/Gen-basis/ionplot.sh 4956 4957* Fix test in m_getopts 4958 4959A double if test gives problems with some compilers when 4960bounds checking is in effect. 4961 4962modified: 4963 Src/m_getopts.f90 4964 4965* Improved grid for re-parametrization of pseudopotentials 4966 4967When the option Reparametrize.Pseudos is in effect, the program 4968resamples the pseudopotential data into a new logarithmic grid with 4969parameters chosen so that the grid-point separation at the typical rcs 4970for orbitals is small enough (of the order of 0.01 bohr). The previous 4971choice of parameters resulted in grid-point separations of the order 4972of 0.005 bohr near the origin, which apparently is not fine enough for 4973s orbitals, leading to oscillations in the gradient near the origin. 4974 4975A new set of default parameters has been chosen to provide a finer 4976grid spacing (1.e-5 bohr) near the origin and 0.01 bohr around r=10 4977bohr. This results in grids with around 10000 points, which is still 4978manageable. 4979 4980( Also, a few extra diagnostic files are produced if the option 4981 Write.Ion.Plot.Files is in effect, and the .psdump file now 4982 contains the core charge ) 4983 4984modified: 4985 Src/atmparams.f 4986 Src/atom.f 4987 Src/basis_specs.f 4988 Src/pseudopotential.f 4989 Docs/siesta.tex 4990 4991* Update atom manual 4992 4993- Include a mention of the "fractional atomic number" capability. 4994 4995- Update the link to Jose Luis Martins' version of the atom program, and 4996 the contact information in the README file. 4997 4998modified: 4999 Pseudo/atom/Docs/atom.tex 5000 Pseudo/atom/README 5001 5002----------------------------------------------------------------------- 50032010-10-01 10:00:00 GMT Alberto Garcia <albertog@icmab.es> trunk-361 5004Improved documentation of VDW-KBM functional 5005 5006(J. Soler) 5007 5008modified: 5009 Docs/siesta.tex 5010 Src/SiestaXC/atomxc.F90 5011 Src/SiestaXC/cellxc.F90 5012 Src/SiestaXC/siestaxc.F90 5013 Src/SiestaXC/vdwxc.F90 5014 Src/SiestaXC/xcmod.f90 5015 5016----------------------------------------------------------------------- 50172010-08-05 15:10:00 GMT Alberto Garcia <albertog@icmab.es> trunk-360 5018(Admin) Incorporate logs of recent patches from 3.0 branch 5019 5020The siesta-3.0 branch can be considered as a sort of "bug-fix" branch 5021for "trunk". Hence, periodic merges are needed. This merges 5022have up to now been done in a "cherry-picking" manner, since 3.0 5023contains other material that is not supposed to go into trunk. This 5024has the unfortunate feature that the patch logs are not incorporated 5025into the trunk, and a "bzr missing" command will keep reporting 5026spurious differences. 5027 5028The logs of all the recently applied patches, corresponding to 3.0 5029patches up to 3.0-rc2, have now been incorporated by doing a normal 5030merge followed by "bzr revert ." to remove all file changes (changes 5031already incorporated in local revnos from 349 up to this one). This 5032has the effect of marking those patches in siesta-3.0 as "known" to 5033this branch, and will simplify the porting of future patches from the 50343.0 branch. Note that the patch logs do not appear in "bzr log" unless 5035the "-n0" option is used. This is desirable, as a casual user might 5036find the output confusing. 5037 5038Note that revno 355 in this branch already incorporated (without 5039explicit mention in the commit log, due to an oversight) the relevant 50403.0 patches up to 3.0-rc1. 5041 5042The version string has been set to trunk-360 in both version.info and 5043siesta.tex. 5044 5045----------------------------------------------------------------------- 50462010-08-05 14:40:00 GMT Alberto Garcia <albertog@icmab.es> trunk-359 5047Fixes for portability (FoX str, pulay, MD rewind, reshape) 5048 5049* The PGI compiler had trouble with the "str" function exported from 5050 FoX. The call has been replaced by an internal write to an auxiliary 5051 variable. 5052 5053* In m_pulay, some compilers evaluated both sub-clauses of an "and" 5054 expression, even if the first was .false.. This led to a division by 5055 zero in a mod operation. The expression has been replaced by more 5056 robust code. 5057 5058* The MD file repositioning code in iomd.f gave problems in some 5059 systems. It has been removed, and substituted by an explicit 5060 'position="append"' clause in the open statement. 5061 5062* In SiestaXC/mesh3d.F90, work around a gfortran bug in the reshape 5063 intrinsic by specifying a zero lower bound. The bug only appears 5064 if bounds checking is in effect. 5065 5066modified: 5067 Src/m_pulay.F90 5068 Src/siesta_cmlsubs.F90 5069 Src/iomd.f 5070 Src/SiestaXC/mesh3d.F90 5071 5072----------------------------------------------------------------------- 50732010-08-05 14:05:00 GMT Alberto Garcia <albertog@icmab.es> trunk-358 5074Cosmetic fixes (larger fields in atm files, vibra manual) 5075 5076* Use larger output fields for atm diagnostic files 5077 5078The atm program generates, among others, the files FOURIER_QMAX and 5079ECONF_DIFFS, which contain information useful for optimization 5080runs. The output fields were quite tight and sometimes 5081overflowed. They have beeen made larger. 5082 5083modified: 5084 Pseudo/atom/prdiff.f 5085 Pseudo/atom/wrapup.f 5086 5087* Clarify the meaning of the supercell options in the Vibra manual 5088 5089New wording to make it clear that the supercell options refer 5090to the number of augmentation shells around the unit cell. 5091 5092modified: 5093 Util/Vibra/Docs/vibra.tex 5094 5095----------------------------------------------------------------------- 50962010-08-05 14:00:00 GMT Alberto Garcia <albertog@icmab.es> trunk-357 5097Compute and print band-structure energy. Updates to Util/COOP/mprop 5098 5099* The band-structure energy Ebs = Tr(DM*H) is now computed at every 5100 iteration and printed at the beginning and end of the SCF cycle, both 5101 in the output file and in the CML file. The calculation is done in 5102 compute_dm, so DM is the "output DM" from the diagonalization of H. 5103 5104* The mprop program has been updated to output the integrated 5105 band-structure energy as a function of energy as a third column in 5106 the integrated-dos file. The " -n " option has been documented. 5107 5108* Creation of Util/COOP/Docs, and addition of some notes on the units 5109 and meaning of the COOP and COHP curves. 5110 5111added: 5112 Util/COOP/Docs/ 5113 Util/COOP/Docs/UnitsAndMeaningOfCurves.txt 5114 Util/COOP/Tests/README 5115modified: 5116 Src/Makefile 5117 Src/compute_dm.F 5118 Src/m_energies.F90 5119 Src/write_subs.F 5120 Util/COOP/README 5121 Util/COOP/main_vars.f90 5122 Util/COOP/mprop.f90 5123 Util/COOP/subs.f90 5124 5125----------------------------------------------------------------------- 51262010-08-05 13:00:00 GMT Alberto Garcia <albertog@icmab.es> trunk-356 5127Make the HSX format the default for H,S files 5128 5129The old HS format was highly inefficient, as each piece of data was 5130written to its own record. In addition, it only contained information 5131about the inter-orbital vectors Xij if k-points were used in the 5132calculation. 5133 5134The new HSX file format was introduced at the time of the first 5135COOP/COHP implementation. It is more tightly packed, and the real 5136arrays (H, S, and Xij) are written in single-precision. 5137 5138The HSX format is now the default in Siesta (TranSiesta has its own 5139format). 5140 5141The programs hsx2hs and hs2hsx in Util/HSX are provided to facilitate 5142the transition. Note however that an HS file written by Siesta during 5143a Gamma-only calculation will not contain information about the 5144inter-orbital vectors Xij, and hs2hsx will refuse to create an HSX 5145file from it. 5146 5147See Util/HSX/README for more details. 5148 5149The file iohs.F has been moved to Util/HSX from the main source 5150directory. 5151 5152added: 5153 Util/HSX/hs2hsx.f90 5154 Util/HSX/hsx2hs.f90 5155 Util/HSX/makefile 5156renamed: 5157 Src/iohs.F => Util/HSX/iohs.F 5158modified: 5159 Docs/siesta.tex 5160 Src/Makefile 5161 Src/setup_hamiltonian.F 5162 Util/HSX/README 5163 Util/HSX/hsx_m.f90 5164 5165----------------------------------------------------------------------- 51662010-08-05 10:55:00 GMT Alberto Garcia <albertog@icmab.es> trunk-355 5167Hook to output the initial charge density 5168 5169If the fdf variable SaveInitialChargeDensity is "true", the program 5170generates a RHO_INIT (and a RhoInit.grid.nc file if netCDF is compiled 5171in) containing the charge density used to start the first 5172self-consistency step, and it stops. Note that if an initial density 5173matrix (DM file) is used, it is not normalized. This is useful to 5174generate the charge density associated to "partial" DMs. 5175 5176modified: 5177 Docs/siesta.tex 5178 Src/dhscf.F 5179 Src/setup_hamiltonian.F 5180 Src/siesta_options.F90 5181 5182----------------------------------------------------------------------- 51832010-08-05 10:10:00 GMT Alberto Garcia <albertog@icmab.es> trunk-354 5184Fixes and new functionality in Pulay mixing 5185 5186* The "kick" functionality intended to "shake" periodically the Pulay 5187mixing procedure was incorrectly implemented. This has now been fixed, 5188with the added feature that the Pulay history is completely reset 5189after a kick. 5190 5191* Additionally, support has been added to specify whether the first 5192density-matrix residual of the SCF cycle and the first residual after 5193a kick are included in the Pulay history. It can be argued that in 5194these cases the "output" DM might be significantly different from the 5195"input" DM. To preserve backwards compatibility, these residuals are 5196kept in the Pulay history unless the fdf variable 5197 5198 DM.Pulay.Avoid.First.After.Kick 5199 5200is set to "true" in the input file. 5201 5202* The above changes have forced a temporary disabling of the "Pulay on 5203 file" feature, which will be re-implemented in a form that works 5204 well in parallel. 5205 5206* Updated the manual. 5207 5208(A. Garcia) 5209 5210renamed: 5211 Src/m_pulay.F => Src/m_pulay.F90 5212modified: 5213 Src/mixer.F 5214 Src/siesta_options.F90 5215 Src/m_pulay.F90 5216 Docs/siesta.tex 5217 5218----------------------------------------------------------------------- 52192010-08-05 10:00:00 GMT Alberto Garcia <albertog@icmab.es> trunk-353 5220Fixes and improvements in the optical spectra code 5221 5222* Fixed a bug in optical.F: the call to subroutine kgridinit nwas 5223 causing problems and providing results that were not compatible any 5224 longer with those of subroutine kgrid. 5225 5226* Modified call to subroutine transition_rate: wmin and wmax passed to 5227 subroutine so that only the relevant transition probabilities are 5228 explicitly calculated. 5229 5230* Added a new test (Tests/si-optical) to exercise the optical code. 5231 5232(Daniel Sanchez Portal) 5233 5234added: 5235 Tests/Reference-xml/si-optical.xml 5236 Tests/Reference/si-optical.out 5237 Tests/si-optical/ 5238 Tests/si-optical/makefile 5239 Tests/si-optical/si-optical.fdf 5240 Tests/si-optical/si-optical.pseudos 5241modified: 5242 Docs/CHANGES 5243 Src/optical.F 5244 Src/transition_rate.F 5245 5246----------------------------------------------------------------------- 52472010-08-04 15:40:00 GMT Alberto Garcia <albertog@icmab.es> trunk-352 5248Updates and fixes to the TranSiesta/tbtrans code (F.D. Novaes) 5249 5250This patch includes bug fixes (in TranSiesta and tbtrans), a cleanup 5251involving removal of dead code, proper declarations of variables, and 5252a new prototype test framework for TranSiesta and tbtrans. 5253 52541. Fixed the issues related to the density matrix in a TS run, due to the 5255changes in new_dm.F 5256 5257* The new module m_ts_iodm.F is the equivalent of m_iodm.F, created to 5258handle .TSDE files. These, are just like .DM files but where the Escf 5259sparse matrix and the Fermi Energy are written at the end of the 5260file. The makefile was modified in order to include this module. 5261 5262* The new_dm module now has a cleaner Transiesta related structure. 5263The possibility of doing a "continuation run" (where a .TSDE file is 5264read and the run starts with a TS calculated density matrix), is 5265handled by calling the routine read_dynamic_ts_dm. Since Transiesta 5266also stores and reads Escf, the variable EDM_tmp has been created and 5267is used in the same way as D_tmp. The routine change_sparsity is also 5268used for Escf. But these parts of the code have not been tested yet, 5269since it would require a change in the sparsity., by atomic 5270rearrangements. 5271 5272 5273added: 5274 Src/m_ts_iodm.F 5275modified: 5276 Src/Makefile 5277 Src/new_dm.F 5278 5279 52802. Changed the way mixH or mixDM are internally handled. Added a 5281global_vars module. 5282 5283* Created the module m_ts_global_vars.f90 that contains the TS 5284variables that are accessed in different parts of the code and are not 5285passed as dummy arguments. 5286 5287* Considerable changes were made in the way the possibility of mixing 5288either the density matrix or the hamiltonian is handled internally. 5289The VIn and VOut pointers are still used, but now, instead of 5290allocating some memory and copying the values of Dscf (H) to them, 5291they directly point to either the Dscf and Dold matrices OR to H and 5292HOld. The latter vector is allocated only whe mixH=.true., and this 5293implies that in this case more memory will be required since Dold is 5294also allocated because it is used in other parts of the code. In any 5295case, this leads to a smaller amount of allocated memory. The coding 5296is clearer also, specially at the siesta_forces routine. 5297 5298 5299added: 5300 Src/m_ts_global_vars.f90 5301modified: 5302 Src/Makefile 5303 Src/compute_dm.F 5304 Src/dhscf.F 5305 Src/m_ts_iodm.F 5306 Src/m_ts_options.F90 5307 Src/mixer.F 5308 Src/new_dm.F 5309 Src/scfconvergence_test.F 5310 Src/setup_hamiltonian.F 5311 Src/siesta_forces.F 5312 Src/state_init.F 5313 Src/write_subs.F 5314 53153. Cleaning of m_ts modules; set grid variables to be defined with 5316grid_p; and smaller changes. 5317 5318* Removed unused variables and dummy arguments (all m_ts modules). 5319Also specified what is used from each module with the idiom "use 5320MODULE, only:" 5321 5322* For the TSVHFix and TSvoltage2 subroutines (m_ts_in_siesta.F90 5323module), fixed the precision of the "v" variable (real space 5324potential) to be grid_p. 5325 5326* The following cosmetic declaration changes were made: 5327 5328real*8 --> real(dp) 5329complex*16 --> complex(dp) 5330double precision --> real(dp) 5331 5332where "dp" comes from the precision module. 5333 5334* IOnode was incorrectly set to be node=1, now it is node=0 5335 (m_ts_in_siesta.F) 5336 5337* Removed the initH variable from several routines. (new_dm, 5338scfconvergence_test, setup_hamiltonian,siesta_forces) 5339 5340 5341modified: 5342 Src/compute_dm.F 5343 Src/m_ts_contour.F 5344 Src/m_ts_electrode.F90 5345 Src/m_ts_in_siesta.F 5346 Src/m_ts_io.F90 5347 Src/m_ts_options.F90 5348 Src/m_ts_scattering.F 5349 Src/new_dm.F 5350 Src/scfconvergence_test.F 5351 Src/setup_hamiltonian.F 5352 Src/siesta_forces.F 5353 53544. Assortment of changes/fixes in TBTrans. 5355 5356* The original version of TBTrans (by M. Brandbyge) was not 5357parallelized. Some of the original properties computed by tbtrans 5358(the transmission function and the pdos) have been "ported" to work 5359also in the parallelized version of the code, but some have not. Those 5360who have not, have been, for now, deleted (atompdos, coop and NetCDF 5361related things). 5362 5363* The transmission function is now multiplied by two in the 5364case of non spin-polarized calculations. As a consequence, the 5365computed current is multiplied too. 5366 5367* The printed value of the pdos (averaged over all the k-points), when 5368running in parallel with more than one node, was not correct: only the values 5369coming from the node=0 were being printed. This has been fixed. 5370 5371* Some smaller changes were done on the way the results are written in the output 5372files (e.g. including blank lines in between values for each k-point, so that 5373the file can be directly plotted with xmgrace). Also changed the name of the 5374routine "Tsiokp" (m_tbt_kpoints.F90) to "get_kp_on_node" since it represents 5375better what it really does. 5376 5377removed: 5378 Util/TBTrans/atompdos.F 5379 Util/TBTrans/coop.f 5380 Util/TBTrans/OutputRegionData.F 5381 Util/TBTrans/OutputRegionData.NoLowdin.F 5382 Util/TBTrans/netcdfwrite.F 5383modified: 5384 Util/TBTrans/Makefile 5385 Util/TBTrans/m_tbt_gf.F90 5386 Util/TBTrans/m_tbt_kpts.F90 5387 Util/TBTrans/m_tbt_options.F90 5388 Util/TBTrans/tbtrans.F 5389 53905. Created a test directory (ts_fast) to test TranSIESTA and 5391TBTrans. (F.D.Novaes/A.Garcia) 5392 5393* An automatic test for transiesta and tbtrans can be run by going to 5394the $OBJDIR/Tests directory, and typing: 5395 5396 make ts 5397 5398and to clean: 5399 5400 make clean_ts 5401 5402For now, only the tests contained in the ts_fast directory will be 5403executed, and more tests with similar structure will be added in the 5404near future. The script first runs the electrode calculation, then 5405the scattering region calculation and finally tbtrans. If during any 5406of these steps there is an error message sent to stderr, the script 5407will stop and the following step will not start. The error message is 5408printed to an output file (err_elec.out or err_scat.out or 5409err_tbt.out). It only creates the "completed" file if it reaches the 5410end. 5411 5412Parallel compilations can be tested by changing to the ts_fast directory 5413and (for example) typing: 5414 5415 make TS="/opt/openmpi.gcc.gfortran/bin/mpirun -np 2 ../../../transiesta" 5416 5417By default, tbtrans will be (re)compiled using the arch.make located 5418in the $OBJDIR. To use an already compiled version of tbtrans (again, 5419inside the ts_fast directory) type: 5420 5421 make TBT=/some/path/to/tbtrans 5422 5423NOTE: Since the compilation of tbtrans is automatic and unattended, 5424you will need to specify in your arch.make the linear algebra libraries 5425needed for tbtrans in your system. For example: 5426 5427 TBTRANS_LINALG=linalg.a # Or maybe only: zgeev_lapack.a zgesv_lapack.a 5428 5429* The functionality for the TS tests is kept in the new file scrip_ts.mk. 5430 5431added: 5432 Tests/script_ts.mk 5433 Tests/ts_fast/ 5434 Tests/ts_fast/H.psf 5435 Tests/ts_fast/elec.fast.fdf 5436 Tests/ts_fast/makefile 5437 Tests/ts_fast/scat.fast.fdf 5438 Tests/ts_fast/script.sh 5439modified: 5440 Tests/Makefile 5441 5442----------------------------------------------------------------------- 54432010-08-04 15:10:00 GMT Alberto Garcia <albertog@icmab.es> trunk-351 5444Fix for out-of-box atoms in meshsubs 5445 5446In InitAtomMesh, during the calculation of the relative position of an 5447atom with respect to the grid, make sure we consider the equivalent 5448position inside the cell, even if the atom is outside. 5449 5450(Possible problem detected by P. Ordejon, fixed by J. Soler) 5451 5452modified: 5453 Src/meshsubs.F 5454 5455----------------------------------------------------------------------- 54562010-08-03 15:35:00 GMT Alberto Garcia <albertog@icmab.es> trunk-350 5457Port several small patches from 3.0 branch up to 3.0-rc2 5458 5459* Fix initialization of target_stress in some cell-only relaxations 5460 5461When using the RelaxCellOnly option in tandem with Broyden relaxation, 5462the target stress was not properly initialized. 5463 5464(Thanks to Marcos Verissimo Alves for pointing out the bug and fix) 5465 5466 modified: 5467 Src/cell_broyden_optim.F 5468 5469* Print value of dipole if applying correcting field 5470 5471If the SlabDipoleCorrection option is active, print the computed 5472value of the total system dipole at every iteration, to help 5473diagnose possible problems. 5474 5475Added note in the manual warning about the use of non-corrected 5476density matrices with this option. 5477 5478(+ fix MPI wrap of output in m_efield) 5479 5480 modified: 5481 Src/Makefile 5482 Src/dhscf.F 5483 Src/m_efield.F 5484 Docs/siesta.tex 5485 5486* Correction of error in siesta.tex (as discovered by J. Junquera) 5487 5488The FDF labels DM.Energy.Tolerance and DM.Harris.Tolerance 5489were wrongly stated as "real" instead of "real energy", and their 5490default value stated with no units when its units are eV. 5491 5492 modified: 5493 Docs/siesta.tex 5494 5495----------------------------------------------------------------------- 54962010-08-03 15:15:00 GMT Alberto Garcia <albertog@icmab.es> trunk-349 5497Tentative fix for DM reuse bug 5498 5499In some cases the re-use of the DM after a geometry change led to 5500large values of ddmax and instabilities in SCF convergence. The 5501tentative cause was the re-allocation of Dscf right after the call to 5502hsparse for the new geometry, and before new_dm, combined with a 5503"sparsity pattern change" in-place. When the re-allocation is deferred 5504to new_dm, and the plain "change_sparsity" routine is used, the 5505problem seems to disappear. 5506 5507Thanks to Oswaldo Dieguez for his sleuthing work. 5508 5509More testing is needed to close the bug definitively. 5510 5511Modified: 5512 Src/Makefile 5513 Src/new_dm.F 5514 Src/state_init.F 5515 5516----------------------------------------------------------------------- 55172010-06-23 12:20:00 GMT Jose A Torres <jose.torres.alonso@uam.es> trunk-348 5518 5519Use DEBUG_XC preprocessor symbol to wrap SiestaXC debugging (J. Gale) 5520 5521 * Comments wrapped by ! DEBUG in several SiestaXC routines (and in 5522 related sections of siesta_init and siesta_end) have been replaced 5523 by #ifdef DEBUG_XC ... #endif so that the writing of debugging files 5524 can be turned off easily at compile time. 5525 5526 Note that this has forced the change in file extension of a few 5527 files in Src/SiestaXC, with concommitant changes in the makefiles. 5528 5529renamed: 5530 Src/SiestaXC/atomxc.f90 => Src/SiestaXC/atomxc.F90 5531 Src/SiestaXC/cellxc.f90 => Src/SiestaXC/cellxc.F90 5532 Src/SiestaXC/fft3d.f90 => Src/SiestaXC/fft3d.F90 5533 Src/SiestaXC/fftr.f90 => Src/SiestaXC/fftr.F90 5534 Src/SiestaXC/siestaxc.f90 => Src/SiestaXC/siestaxc.F90 5535 Src/SiestaXC/vdwxc.f90 => Src/SiestaXC/vdwxc.F90 5536modified: 5537 Src/SiestaXC/lib-arch.make 5538 Src/SiestaXC/lib-makefile 5539 Src/SiestaXC/makefile 5540 Src/SiestaXC/mesh3d.F90 5541 Src/siesta_end.F 5542 Src/siesta_init.F 5543 Src/SiestaXC/atomxc.F90 5544 Src/SiestaXC/cellxc.F90 5545 Src/SiestaXC/fft3d.F90 5546 Src/SiestaXC/fftr.F90 5547 Src/SiestaXC/siestaxc.F90 5548 Src/SiestaXC/vdwxc.F90 5549 5550----------------------------------------------------------------------- 55512010-06-23 12:02:00 GMT Jose A Torres <jose.torres.alonso@uam.es> trunk-347 5552 5553Make sure that units are closed with io_close (J. Gale) 5554 5555 * 'Close' replaced by call to 'io_close' in several routines to 5556 prevent luns overload. 5557 5558 * Unused declarations of io_assign and io_close removed from diagon.F 5559 and ksv.f 5560 5561 (Julian Gale) 5562 5563 modified: 5564 Src/diagon.F 5565 Src/ksv.f 5566 Src/m_timer.F90 5567 Src/moreParallelSubs.F90 5568 Src/write_orb_indx.f90 5569----------------------------------------------------------------------- 55702010-06-23 02:19:00 GMT Jose A Torres <jose.torres.alonso@uam.es> trunk-346 5571 5572Support for LMKLL and KBM vdW functionals in ATOM (A. Garcia) 5573 5574 The pseudopotential generation program now accepts the "vl" xc code to 5575 request the Lee et al. (LMKLL) version of the vdW functional 5576 (arXiv:1003.5255v1 (2010)), and the "vk" xc code for the vdW 5577 parametrization of Klimes et al. (KBM) (JPCM 22, 022201 (2009)). 5578 5579 The id strings in .xml pseudo files are, respectively, 5580 'Lee-et-al--LMKLL', and 'Klimes-et-al--KBM'. For consistency, the id 5581 string for the Dion functional has been extended to 5582 'Dion-et-al--DRSLL' 5583 5584 The ATOM manual has been updated, and the version number set to 5585 3.3.1. 5586 5587 Obsolete xc routines (pre-SiestaXC) have been removed from the 5588 Pseudo/atom directory. 5589 5590 removed: 5591 Pseudo/atom/blypxc.f 5592 Pseudo/atom/ggaxc.f 5593 Pseudo/atom/ldaxc.f 5594 Pseudo/atom/pw92xc.f 5595 Pseudo/atom/pzxc.f 5596 Pseudo/atom/revpbexc.f 5597 Pseudo/atom/rpbexc.f 5598 modified: 5599 Pseudo/atom/Docs/atom.tex 5600 Pseudo/atom/Makefile 5601 Pseudo/atom/pseudoXML.f 5602 Pseudo/atom/velect.f 5603----------------------------------------------------------------------- 56042010-04-20 00:53:00 GMT Jose A Torres <jose.torres.alonso@uam.es> trunk-345 5605 5606Updated makefile dependencies (J. M. Soler) 5607 5608modified: 5609 Src/Makefile 5610 Src/SiestaXC/makefile 5611 5612----------------------------------------------------------------------- 56132010-04-20 00:48:00 GMT Jose A Torres <jose.torres.alonso@uam.es> trunk-344 5614 5615Added parametrization of Klimes et al for vdW-DF (J. M. Soler) 5616 5617modified: 5618 Docs/siesta.tex ! Added VDW/KBM 5619 Src/SiestaXC/Testers/test1.f90 ! Call to B88 GGA exchange 5620 Src/SiestaXC/atomxc.f90 ! Added VDW/KBM comment 5621 Src/SiestaXC/cellxc.f90 ! Added VDW/KBM comment 5622 Src/SiestaXC/ggaxc.f ! Added Becke-88 exchange routine 5623 Src/SiestaXC/siestaxc.f90 ! Added VDW/KBM comment 5624 Src/SiestaXC/vdwxc.f90 ! Call to B88 exchange 5625 Src/SiestaXC/xcmod.f90 ! Call to vdw_set_author for KBM 5626 5627----------------------------------------------------------------------- 56282010-04-20 00:44:00 GMT Jose A Torres <jose.torres.alonso@uam.es> trunk-343 5629 5630Documentation completed on LMKLL flavour of vdW-DF (J. M. Soler) 5631 5632modified: 5633 Docs/siesta.tex 5634 Src/SiestaXC/siestaxc.f90 5635 Src/SiestaXC/vdwxc.f90 5636 5637----------------------------------------------------------------------- 56382010-04-20 00:38:00 GMT Jose A Torres <jose.torres.alonso@uam.es> trunk-342 5639 5640A bug corrected in testers (J. M. Soler) 5641 5642modified: 5643 Src/SiestaXC/Testers/test2.f90 ! Avoid using DRSLL & LMKLL together 5644 Src/SiestaXC/Testers/test3.F90 5645 Src/SiestaXC/Testers/test4.F90 5646 5647----------------------------------------------------------------------- 56482010-04-20 00:34:00 GMT Jose A Torres <jose.torres.alonso@uam.es> trunk-341 5649 5650Added the vdW functional flavour of K.Lee et al, arXiv:1003.5255v1 (2010) (J.M. Soler) 5651 5652modified: 5653 Src/SiestaXC/Testers/test1.f90 ! Added PW86 5654 Src/SiestaXC/Testers/test2.f90 ! Added VDW/LMKLL 5655 Src/SiestaXC/Testers/test3.F90 ! Added VDW/LMKLL 5656 Src/SiestaXC/Testers/test4.F90 ! Added VDW/LMKLL 5657 Src/SiestaXC/atomxc.f90 ! Call to vdw_exchng 5658 Src/SiestaXC/cellxc.f90 ! Call to vdw_exchng 5659 Src/SiestaXC/ggaxc.f ! Added PW86 and PW86R exchange functionals 5660 Src/SiestaXC/vdwxc.f90 ! Added vdw_exchng and vdw_set_author 5661 Src/SiestaXC/xcmod.f90 ! Call to vdw_set_author 5662 5663----------------------------------------------------------------------- 56642010-03-08 12:23:00 GMT Jose A Torres <jose.torres.alonso@uam.es> trunk-340 5665 5666Update FoX to version 4.1.0 (A. Walker) 5667 5668 Version 4.1.0 of FoX, used to produce our XML output was released 5669 on 2010-02-09. This patch updates the version shipped with Siesta 5670 to this version. 5671 5672 Changes that affect Siesta are that the build process for FoX can 5673 now take advantage of possible parallelization (make -j), we can 5674 ask FoX to generate an abort signal if it kills the process and 5675 the inclusion of work arounds for compiler bugs in recent versions 5676 of the pgi compiler. Some of these changes existed in an (unrelased) 5677 version of FoX shipped with Siesta since revision 320. 5678 5679 modified: 5680 Src/FoX/FoX-config.in 5681 Src/FoX/LICENSE 5682 Src/FoX/Makefile 5683 Src/FoX/common/FoX_common.F90 5684 Src/FoX/configure 5685 Src/FoX/wxml/FoX_wxml.f90 5686 Src/FoX/wxml/m_wxml_core.F90 5687 version.info 5688 5689----------------------------------------------------------------------- 56902010-02-04 03:50:00 GMT Jose A Torres <jose.torres.alonso@uam.es> trunk-339 5691 5692 Fix bug in previous patch regarding CG DM extrapolation (A. Garcia) 5693 5694 The logic of a previous patch was wrong, and the resulting 5695 code prevented the proper restructuring of a reused DM in 5696 the course of CG relaxations. 5697 5698 To make it clear now: For "CG" calculations, the default is not to 5699 extrapolate the DM (unless requested by explicitly setting 5700 'DM.AllowExtrapolation' to "true"). The previous step's DM is reused. 5701 5702 modified: 5703 Docs/siesta.tex 5704 Src/new_dm.F 5705 5706----------------------------------------------------------------------- 57072010-02-04 03:36:00 GMT Jose A Torres <jose.torres.alonso@uam.es> trunk-338 5708 5709 Avoid extrapolation of DM during geometry optimization (A. Garcia) 5710 5711 When performing a geometry optimization (CG, Broyden, etc) (idyn=0 in 5712 the code), there might be sudden jumps in the geometry (e.g., at the 5713 end of a line-minimization) that render a extrapolation of the DM 5714 risky. Hence DM extrapolation is turned off in this case. 5715 5716 One might argue that DM re-use should be avoided too. 5717 5718 modified: 5719 Docs/siesta.tex 5720 Src/new_dm.F 5721 5722----------------------------------------------------------------------- 57232010-02-03 02:34:00 GMT Jose A Torres <jose.torres.alonso@uam.es> trunk-337 5724 5725Patch for problem in the iVec computers (J. M. Soler) 5726 5727 A persistent problem in Australia's iVec supercomputers was traced to an 5728 apparent ifort compiler error, producing a core dump in re_alloc's line 5729 array(c(1,1):c(2,1)) = old_array(c(1,1):c(2,1)) 5730 that disappeared when substituted by 5731 do i = c(1,1),c(2,1) 5732 array(i) = old_array(i) 5733 enddo 5734 Since, in the offending call, no array copy was really neaded, the problem 5735 was solved insted by adding copy=.false. in that call by initMesh. 5736 5737 Independently of the former, a number of corrections or improvements 5738 were done in various files, to solve small deficiencies located during 5739 the process of debugging the previous problem. 5740 5741 modified: 5742 Src/SiestaXC/debugxc.f90 ! Corrected file name in closeDebugOutputFile 5743 Src/SiestaXC/ggaxc.f ! Added spin bounds in array copy 5744 Src/SiestaXC/mesh3d.F90 ! Added several checks for range of iDistr 5745 Src/fermid.F ! Removed a duplicated printout 5746 Src/meshsubs.F ! Added copy=.false. in call to re_alloc 5747 5748----------------------------------------------------------------------- 57492010-02-03 02:28:00 GMT Jose A Torres <jose.torres.alonso@uam.es> trunk-336 5750 5751Corrected call to MPI_AllReduce in SiestaXC/Testers/test4.F90 (J.M. Soler) 5752 5753 modified: 5754 Src/SiestaXC/Testers/test1.f90 ! Increased number of densities tried 5755 Src/SiestaXC/Testers/test4.F90 ! Corrected call to MPI_AllReduce 5756 5757----------------------------------------------------------------------- 57582010-02-03 02:22:00 GMT Jose A Torres <jose.torres.alonso@uam.es> trunk-335 5759 5760MPI_grid_real kind adapted to new standard (J.M. Soler) 5761 5762 modified: 5763 Src/MPI/mpi.F ! MPI_grid_real=DAT_double unless def GRID_SP 5764 5765----------------------------------------------------------------------- 57662010-02-03 00:17:00 GMT Jose A Torres <jose.torres.alonso@uam.es> trunk-334 5767 5768A bug corrected by J.D.Gale in the am05 functional (J.M. Soler) 5769 5770 modified: 5771 Src/SiestaXC/Testers/makefile ! Copy ../*.mod 5772 Src/SiestaXC/am05.f90 ! Bug corrected 5773 Src/SiestaXC/ggaxc.f ! Corrected call to am05wbs 5774 5775----------------------------------------------------------------------- 57762010-02-02 10:57:00 GMT Jose A Torres <jose.torres.alonso@uam.es> trunk-333 5777 5778Two minor bugs found by Alberto Garcia (J.M. Soler) 5779 5780 modified: 5781 Src/SiestaXC/Testers/test3.F90 ! Add MPI_Finalize 5782 Src/SiestaXC/Testers/test4.F90 ! Add MPI_Finalize 5783 Src/SiestaXC/lib-makefile ! Add am05.o 5784 5785----------------------------------------------------------------------- 57862010-02-01 20:55:00 GMT Jose A Torres <jose.torres.alonso@uam.es> trunk-332 5787 5788Include AM05 functional in SiestaXC/Testers (J.M. Soler) 5789 5790 The recently-added AM05 functional has been added to those tested by the 5791 SiestaXC/Testers. 5792 5793 modified: 5794 Src/SiestaXC/Testers/test1.f90 5795 Src/SiestaXC/Testers/test2.f90 5796 Src/SiestaXC/Testers/test3.F90 5797 Src/SiestaXC/Testers/test4.F90 5798 5799--------------------------------------------------------------------- 58002010-01-15 18:40:00 GMT Jose A Torres <jose.torres.alonso@uam.es> trunk-331 5801 5802 Two mesh-related bugs (From J.M.Soler) 5803 5804 In routine phiOnMesh, function 'size' was used with unassociated pointers. 5805 This is a bug, although most compilers tolerate it. Unrelated to this, 5806 in routine divideBox1D, the limits of the first and last boxes was not 5807 correctly initialized. 5808 5809 modified: 5810 Src/SiestaXC/mesh3d.F90 ! Initialize partBox(1,1) and partBox(2,nParts) 5811 Src/meshsubs.F ! Check pointer associations 5812 5813--------------------------------------------------------------------- 58142010-01-15 18:40:00 GMT Jose A Torres <jose.torres.alonso@uam.es> trunk-330 5815 5816 Two bugs in MPI communications (From J.M.Soler) 5817 5818 The length increase of strings XCfunc and XCauth in trunk-320-JMS-3 had not 5819 been considered in their MPI communication calls. Also, unrelated to this, 5820 a conditional return made node 0 not participate in a global broadcast, 5821 leaving the other nodes hunging. 5822 5823 modified: 5824 Src/m_efield.F ! Removed conditional return 5825 Src/read_xc_info.F ! Corrected string length in MPI_Bcast 5826 5827--------------------------------------------------------------------- 58282010-01-15 18:40:00 GMT Jose A Torres <jose.torres.alonso@uam.es> trunk-329 5829 5830 Bug correction in mesh3d (From J.M.Soler) 5831 5832 A case not taken care of, in routine sameMeshDistr, created an 5833 out-of-bounds condition that was noticed by J.D.Gale and others. 5834 Also, a use statement was added for MPI routines in m_mpi_utils. 5835 5836 modified: 5837 Src/SiestaXC/mesh3d.F90 ! Bug corrected in sameMeshDistr 5838 Src/m_mpi_utils.F ! Added use statement for MPI routines 5839 Src/meshsubs.F ! Variable JDGdistr saved and initialized 5840 5841--------------------------------------------------------------------- 58422010-01-15 18:10:00 GMT Jose A Torres <jose.torres.alonso@uam.es> trunk-328 5843 5844 Print vacuum level (From J.M.Soler) 5845 5846 The vacuum level, defined as the effective potential at grid points with 5847 zero density, is printed in the standard output. This is done whenever 5848 there are such points and either SaveElectrostaticPotential or 5849 SaveTotalPotential are true. This will be useful to calculate the work 5850 function of a surface. 5851 5852 added: 5853 Src/vacuum_level.f90 ! Computes the vacuum level 5854 modified: 5855 Docs/siesta.tex ! Document side effect of SaveTotalPotential 5856 Src/Makefile ! Add vacuum_level.o. Update dependencies 5857 Src/dhscf.F ! Call vacuum_level and print it 5858 Src/moreParallelSubs.F90 ! Make public miscAllReduceInt 5859 5860--------------------------------------------------------------------- 58612010-01-15 18:10:00 GMT Jose A Torres <jose.torres.alonso@uam.es> trunk-327 5862 5863 Make doping routine call global fdf version (From J.M.Soler) 5864 5865 An error was occurring because all nodes were calling the old (serial) fdf 5866 routines, which should be called only by node=0. The fdf_global version can 5867 handle such global calls. 5868 5869 modified: 5870 Src/Makefile ! Updated dependencies 5871 Src/doping.F ! Call global fdf version 5872 5873--------------------------------------------------------------------- 58742010-01-15 17:55:00 GMT Jose A Torres <jose.torres.alonso@uam.es> trunk-326 5875 5876 New GGA functionals with PBE form and parameters from Capelle et al (From J.M.Soler) 5877 5878 The four new functionals, with author labels PBE(JsJrLO), PBE(JsJrHEG), 5879 PBE(GcGxLO), and PBE(GcGxHGE), have the PBE functional form, but use 5880 modified values for parameters beta, mu, and kappa. 5881 Refs: L.S.Pedroza et al, PRB 79, 201106 (2009) 5882 M.M.Odashima et al, J. Chem. Theory Comp. 5, 798 (2009) 5883 5884 modified: 5885 Src/SiestaXC/ggaxc.f ! New functionals implemented 5886 Src/SiestaXC/xcmod.f90 ! Increased length for XCfunc and XCauth strings 5887 Src/atom.f ! Let xc_check continue even if func. not known 5888 Src/read_xc_info.F ! Increased length for XCfunc and XCauth strings 5889 5890--------------------------------------------------------------------- 58912010-01-15 17:40:00 GMT Jose A Torres <jose.torres.alonso@uam.es> trunk-325 5892 5893Document in manual the file on orbital indexes (From J.M.Soler) 5894 5895Added to the manual documentation on file (label).ORB_INDX 5896 5897modified: 5898 Docs/siesta.ind 5899 Docs/siesta.tex ! File ORB_INDX documented. 5900 5901--------------------------------------------------------------------- 59022010-01-15 17:40:00 GMT Jose A Torres <jose.torres.alonso@uam.es> trunk-324 5903 5904Write orbital indexes (From J.M.Soler) 5905 5906 To assist users in interpreting files like (label).DM and (label).HS, a new 5907 file called (label).ORB_INDX is written with info on the orbital index order. 5908 5909 added: 5910 Src/write_orb_indx.f90 ! Writes (label).ORB_INDX 5911 5912 modified: 5913 Src/Makefile ! Added write_orb_indx.o + Dependencies updated 5914 Src/atmfuncs.f ! Orbital symmetry names completed up to g orbitals 5915 Src/compute_dm.F ! Added call to write_orb_indx 5916 5917--------------------------------------------------------------------- 59182010-01-15 17:02:00 GMT Jose A Torres <jose.torres.alonso@uam.es> trunk-323 5919 5920Name of functional updated in AM05XC to correctly be AM05 (From J. Gale) 5921 5922modified: 5923 Src/SiestaXC/ggaxc.f 5924 5925--------------------------------------------------------------------- 59262010-01-15 16:43:00 GMT Jose A Torres <jose.torres.alonso@uam.es> trunk-322 5927 5928Changes to the default precision of grid magnitudes (From A. Garcia) 5929 5930The grid functions (charge densities, potentials, etc) are now in 5931double precision by default. The 'phi' array that holds the values of 5932the basis orbitals on the real-space grid is kept in single precision. 5933 5934The following pre-processing symbols at compile time control the 5935precision selection: 5936 5937#ifdef GRID_SP 5938 integer, parameter :: grid_p = sp 5939 integer, parameter :: phi_grid_p = sp 5940#elif defined(GRID_DP) 5941 integer, parameter :: grid_p = dp 5942 integer, parameter :: phi_grid_p = dp 5943#else 5944 integer, parameter :: grid_p = dp 5945 integer, parameter :: phi_grid_p = sp 5946#endif 5947 5948GRID_DP will lead to a sizable memory increase, as 'phi' is the main 5949user of memory on the grid. On the other hand, the gains in accuracy 5950are negligible, as the operations over 'phi' are accumulated in double 5951precision variables. 5952 5953GRID_SP recovers the old Siesta default. It will not free much 5954memory, and it will show some numerical differences. 5955 5956modified: 5957 Docs/siesta.ind 5958 Docs/siesta.tex 5959 Src/meshsubs.F 5960 Src/precision.F 5961 5962--------------------------------------------------------------------- 59632010-01-15 16:43:00 GMT Jose A Torres <jose.torres.alonso@uam.es> trunk-321 5964 5965 Fixed the precision of real and complex variables in m_ts* modules. (From F.D.Novaes) 5966 5967 * For the TSVHFix and TSvoltage2 subroutines (m_ts_in_siesta.F90 module), 5968 fixed the precision of the "v" variable (real space potential) 5969 to be grid_p. 5970 5971 * In all the modified modules, the following changes were made: 5972 5973 real*8 --> real(dp) 5974 complex*16 --> complex(dp) 5975 double precision --> real(dp) 5976 5977 where "dp" comes from the precision module. 5978 5979 modified: 5980 Src/m_ts_aux_rout.F 5981 Src/m_ts_contour.F 5982 Src/m_ts_electrode.F90 5983 Src/m_ts_in_siesta.F 5984 Src/m_ts_io.F90 5985 Src/m_ts_scattering.F 5986 5987--------------------------------------------------------------------- 59882009-12-07 18:43:00 GMT Jose A Torres <jtorres.sp@gmail.com> trunk-320 5989 5990 Make WriteXML option consistent (XML.Write) and document (From A. Walker) 5991 5992 Document the two new XML options: XML.AbortOnErrors and 5993 XML.AbortOnWarnings in siesta.tex (documentation is in the 5994 XML appendix). 5995 5996 Rename undocumented WriteXML option to XML.Write for 5997 consistancy. Document this option in siesta.tex. 5998 5999 modified: 6000 Docs/siesta.tex 6001 Src/siesta_cmlsubs.F90 6002 6003--------------------------------------------------------------------- 60042009-12-07 18:28:00 GMT Jose A Torres <jtorres.sp@gmail.com> trunk-319 6005 6006Update FoX library and add XML.AbortOnErrors and XML.AbortOnWarnings (From A. Walker) 6007 6008It is sometimes useful for warnings or errors generated by the FoX 6009libary to result in an abort to generate a core dump or stack trace to 6010see where in Siesta the call causing the error is being made. It is 6011now possible to turn on this behaviour at runtime using two new fdf 6012boolean tags: 6013 6014 XML.AbortOnErrors XML.AbortOnWarnings 6015 6016Both are boolean and default to .false. (which mirrors the current 6017stopping behaviour). 6018 6019These features have been made possible by an update in the FoX library 6020that adds an interface to allow errors and warnings to result in an 6021abort signal. In the update there is also a fix to work around a PGI 6022bug for the overloaded wxml interfaces (aparently not used in Siesta) 6023and a change to the prng to avoid using initalised data in prng_init. 6024 6025added: 6026 Src/FoX/arch.make 6027modified: 6028 Src/FoX/Makefile 6029 Src/FoX/common/FoX_common.F90 6030 Src/FoX/common/m_common_error.F90 6031 Src/FoX/common/makefile 6032 Src/FoX/fsys/fox_m_fsys_abort_flush.F90 6033 Src/FoX/utils/fox_m_utils_uuid.F90 6034 Src/FoX/utils/makefile 6035 Src/FoX/wcml/m_wcml_molecule.F90 6036 Src/FoX/wcml/makefile 6037 Src/FoX/wxml/m_wxml_core.F90 6038 Src/FoX/wxml/m_wxml_overloads.F90 6039 Src/FoX/wxml/makefile 6040 Src/siesta_cml.f90 6041 Src/siesta_cmlsubs.F90 6042 6043------------------------------------------------------------------------------ 60442009-12-04 16:21:00 GMT Jose A Torres <jtorres.sp@gmail.com> trunk-318 6045 6046Fixes to compilation of Utils (From A. Garcia) 6047 6048After the merge of SiestaXC the building of many Util programs was broken. 6049The problems have been fixed. 6050 6051modified: 6052 Pseudo/atom/Makefile 6053 Pseudo/atom/divdif.f 6054 Util/Denchar/Src/Makefile 6055 Util/Gen-basis/Makefile 6056 Util/Helpers/Makefile 6057 Util/Optimizer/Makefile 6058 Util/STM/ol-stm/Src/Makefile 6059 Util/STM/simple-stm/plstm.f 6060 Util/TBTrans/Makefile 6061 Util/VCA/Makefile 6062 6063------------------------------------------------------------------------------ 60642009-11-27 19:56:00 GMT Jose A Torres <jtorres.sp@gmail.com> trunk-317 6065 6066Minor change in cellxc.f90 to make it compatible with xlf 6067 6068In cellxc.f90 6069The code: 6070timeDisp=huge(timeDisp) 6071Seems to give compilation problems when using xlf 6072It has been replaced by 6073timeDisp=huge(1.0_dp) 6074 6075modified: 6076 Src/SiestaXC/cellxc.f90 6077 6078------------------------------------------------------------------------------ 60792009-11-27 19:35:00 GMT Jose A Torres <jtorres.sp@gmail.com> trunk-316 6080 6081Position of checking statement corrected in cellxc.f90 6082 6083The variable GGA was being used before being defined in 6084SiestaXC/cellxc.f90. This modification fixes that bug. 6085The following block: 6086" if (present(dVxcdD) .and. GGA) & 6087 call die(errHead//'dVxcdD available only for LDA') 6088" 6089Has been moved to a new position, just after GGA has been defined. 6090 6091modified: 6092 Src/SiestaXC/cellxc.f90 6093 6094------------------------------------------------------------------------------ 60952009-11-27 18:56:00 GMT Jose A Torres <jtorres.sp@gmail.com> trunk-315 6096 6097Modularize efield and doping modules. Restructure CML interfaces. (From A. Garcia) 6098 6099* The code in efield.F (now m_efield.F) has been split in several 6100 routines. 6101 6102* The code in doping.F has been split in several routines. 6103 6104* Siesta_cml is now the main interface to CML in Siesta. 6105 Siesta_cmlsubs is a client of siesta_cml and only exports 6106 siesta_cml_init and siesta_cml_exit. 6107 6108 For unknown reasons, it has been necessary to declare all the 6109 symbols in siesta_cml explicitly "public" and add the "private" 6110 global statement to avoid compiler crashes (intel V10) upon 6111 compiling several modules. A number of explicit "only" clauses have 6112 been added to a few CML import statements in several modules. 6113 6114removed: 6115 Src/efield.F 6116added: 6117 Src/m_efield.F 6118modified: 6119 Src/Makefile 6120 Src/dhscf.F 6121 Src/doping.F 6122 Src/post_scf_work.F 6123 Src/setup_hamiltonian.F 6124 Src/siesta_cml.f90 6125 Src/siesta_cmlsubs.F90 6126 Src/siesta_end.F 6127 Src/siesta_move.F 6128 Src/state_init.F 6129 6130------------------------------------------------------------------------------ 61312009-11-27 18:45:00 GMT Jose A Torres <jtorres.sp@gmail.com> trunk-314 6132 6133Fix test scripts for correct executable path (From A. Garcia) 6134 6135* Some scripts in Tests/Scripts still referred to the old "Src"-style 6136 siesta executable. 6137 6138* Tests/test.mk had a path to the executable which assumed that it ran 6139 under the default Obj directory. 6140 6141modified: 6142 Tests/Scripts/matterhorn-gm.sge 6143 Tests/Scripts/matterhorn-mpich.sge 6144 Tests/Scripts/nano.pbs 6145 Tests/Scripts/nano4.sh 6146 Tests/Scripts/simple_parallel.sh 6147 Tests/test.mk 6148 6149------------------------------------------------------------------------------ 61502009-11-25 09:34:00 GMT Jose A Torres <jtorres.sp@gmail.com> trunk-313 6151 6152siestaXC.f90 renamed siestaxc.f90 (From J. Soler) 6153 6154To avoid case ambiguities, that cause compilation problems, the name of file 6155siestaXC.f90 has been renamed as siestaxc.f90 6156 6157renamed: 6158 Src/SiestaXC/siestaXC.f90 => Src/SiestaXC/siestaxc.f90 6159modified: 6160 Src/SiestaXC/lib-00-README ! siestaXC.mod -> siestaxc.mod 6161 Src/SiestaXC/lib-makefile ! siestaXC.f90,o -> siestaxc.f90,o 6162 Src/SiestaXC/makefile ! siestaXC.f90,o -> siestaxc.f90,o 6163 6164------------------------------------------------------------------------ 61652009-11-23 09:54:00 GMT Jose A Torres <jtorres.sp@gmail.com> trunk-312 6166 6167Support for the Armiento and Mattson's functional added (From J. Gale) 6168 6169Support for the AM05 functional has been added to routines in SiestaXC 6170and Pseudo. This is done using the AM05 subroutines distributed by 6171Armiento and Mattson, under the terms of the conditions contained within 6172the header to their software allowing modification and redistribution 6173provider the original copyright header remains. 6174 6175A new module, am05, contained within the file SiestaXC/am05.f90, has been 6176added containing the code from Armiento and Mattsson. Within ggaxc.f90 6177a wrapper has been added, am05xc, to pass the variables from ggaxc to 6178am05 subroutines and handle the return arguments appropriately. 6179 6180In the atom program the two-letter symbol "am" has been added for AM05. 6181In SIESTA the GGA Authors are "AM05". 6182 6183A test of the AM05 functional added in h2o_am05. 6184 6185added: 6186 Pseudo/atom/am05.f 6187 Src/SiestaXC/am05.f90 6188 Tests/Pseudos/H_am05.psf 6189 Tests/Pseudos/O_am05.psf 6190 Tests/Reference/h2o_am05.out 6191 Tests/h2o_am05/ 6192 Tests/h2o_am05/README 6193 Tests/h2o_am05/h2o_am05.fdf 6194 Tests/h2o_am05/h2o_am05.pseudos 6195 Tests/h2o_am05/makefile 6196modified: 6197 Docs/siesta.tex 6198 Pseudo/atom/Docs/atom.tex 6199 Pseudo/atom/pseudoXML.f 6200 Pseudo/atom/velect.f 6201 Src/Makefile 6202 Src/SiestaXC/atomxc.f90 6203 Src/SiestaXC/cellxc.f90 6204 Src/SiestaXC/ggaxc.f 6205 Src/SiestaXC/makefile 6206 Src/SiestaXC/siestaXC.f90 6207 Src/SiestaXC/xcmod.f90 6208 Src/atom.f 6209 6210------------------------------------------------------------------------ 62112009-11-10 20:30:00 GMT Jose M Soler <jose.soler@uam.es> trunk-311 6212 6213Avoid repetition of routine name in allocation report 6214 6215Since the introduction of the routine name in the allocation report, in 6216revno 301, some arrays appeared with a repeated routine name, since this 6217is also given in the array name. Also, the module name has been added in 6218calls to re_alloc, within module neighbour. 6219 6220modified: 6221 Src/SiestaXC/atomxc.f90 ! Call to alloc_default commented out 6222 Src/SiestaXC/cellxc.f90 ! 'routine' removed from call to alloc_default 6223 Src/matel.f ! 'routine' removed from call to alloc_default 6224 Src/mneighb.f ! Module name used in calls to re_alloc 6225 6226 6227------------------------------------------------------------------------ 62282009-11-10 18:25:00 GMT Jose A. Torres <jtorres.sp@gmail.com> trunk-310 6229 6230Increased parameter nr in vdwxc, to avoid an out-of-bounds condition(J. Soler) 6231 6232An out of bounds condition was occurring in vdwxc when called by atom 6233pseudopotential generation program. With ifort, this lead to program 6234crash or to an overflow of the system memory. To solve this, parameter 6235nr been increased from 1024 to 2048, and a check has been added. 6236 6237modified: 6238 Src/SiestaXC/vdwxc.f90 ! Parameter nr increased 6239 6240------------------------------------------------------------------------ 62412009-11-10 17:59:00 GMT Jose A. Torres <jtorres.sp@gmail.com> trunk-309 6242 6243Clarification of the use of *_last geometry information (A. Garcia) 6244 6245The variables xa_last (formerly xalast), ucell_last, and scell_last 6246are used to hold the information related to the last geometry for 6247which the electronic structure has been computed. This is necessary 6248since the "siesta_move" routine updates the geometry after every step. 6249By using the "*_last" variables instead of "xa", "ucell", and "scell", 6250we make sure that "siesta_analysis", when calculating the 6251polarization, optical properties, etc, uses the coordinates actually 6252used to compute the electronic structure. 6253 6254The *_last variables are set at the beginning of "siesta_move", before 6255the actual displacements. Due to a bug in the program, however, this 6256was being done only at the final scheduled step ('fincoor'), instead 6257of inconditionally after every step. Thus they could be used undefined 6258if, for example, a relaxation finishes before the scheduled number of 6259steps (which is typical). 6260 6261While fixing this bug, it became apparent that some other sections of 6262"siesta_analysis" are using the "predicted" coordinates (the output of 6263coordinates in various formats) instead of the last "used" 6264coordinates. This can be considered a feature or a bug. 6265 6266Similarly, the computation of the spin polarization uses a density 6267matrix that is actually the result of a mixing after the last SCF 6268step. 6269 6270(Fix prepared by A. Garcia after the discovery of the bug by J. Gale) 6271 6272modified: 6273 Src/atomlist.f 6274 Src/born_charge.F 6275 Src/local_DOS.F 6276 Src/siesta_analysis.F 6277 Src/siesta_geom.F90 6278 Src/siesta_move.F 6279 6280------------------------------------------------------------------------ 62812009-11-10 17:53:00 GMT Jose A. Torres <jtorres.sp@gmail.com> trunk-308 6282 6283Fix bug in electric field initialization (J. Junquera) 6284 6285When using the ExternalElectricField option (block), a bug prevented 6286the actual use of the field to generate the potential ramp on the grid 6287(but not the calculation of an extra contribution to the energy). 6288 6289 6290modified: 6291 Src/efield.F 6292 6293------------------------------------------------------------------------ 62942009-11-06 19:34 GMT Jose A. Torres <jtorres.sp@gmail.com> trunk-307 6295 6296Error fixed for MPI_Waitall, Call to write_raw_efs limited to I/O node (J.Gale) 6297 6298Introduced some patches from J.Gale's branch: 6299 6300* Error in mpi_siesta.f90 fixed for MPI_Waitall. The interface had 6301 the wrong set of arguments passed through. 6302 6303 + call MPI_WAITALL(COUNT, ARRAY_OF_REQUESTS, ARRAY_OF_STATUSES, IERROR) 6304 --- 6305 - call MPI_WAITALL(COUNT, ARRAY_OF_REQUESTS, INDEX, STATUS, IERROR) 6306 6307* Call to write_raw_efs from state_analysis now limited to I/O node only. 6308 6309 + if (IOnode) call write_raw_efs(stress,na_u,fa,FreeE) 6310 --- 6311 - call write_raw_efs(stress,na_u,fa,FreeE) 6312 6313* Some comments changed in Src/m_timer.F90 6314 6315 6316modified: 6317 Src/MPI/mpi_siesta.f90 ! 6318 Src/m_timer.F90 6319 Src/state_analysis.F 6320 6321------------------------------------------------------------------------ 63222009-11-03 11:15:00 GMT Jose M Soler <jose.soler@uam.es> trunk-306 6323Correct number of orbital nodes with 'nodes' option 6324 6325The (mainly obsolete) 'nodes' option for basis orbital generation was 6326producing orbitals with one excess radial node (i.e. one and two nodes 6327for double zeta, instead of zero and one node). Corrected. 6328 6329A goto statement, out of a start-stop-timer piece of code, lead to 6330a program die within timer in some cases. Corrected. 6331 6332modified: 6333 Src/atom.f ! Radial nodes decresed for 'nodes' option 6334 Src/m_timer.F90 ! A small correction of output format 6335 Src/rdiag.F ! Added call to stop_timer within rdiag3 section 6336 6337------------------------------------------------------------------------ 63382009-10-15 21:00:00 GMT Jose M Soler <jose.soler@uam.es> trunk-305 6339Match arguments between re_alloc and de_alloc calls 6340 6341For a correct accounting of array allocations, both the 'name' and 6342'routine' arguments should be identical (including case sensitivity) 6343in the corresponding calls to re_alloc and de_alloc of an array. 6344The two arguments are combined into an internal name as 6345trim(routine)//' '//name, so that (name='rho',routine='dhscf') 6346is equivalent to (name='dhscf rho'). This is the name printed in 6347the allocation report. 6348 6349When the array is allocated and deallocated in different subroutines, 6350it is clearer not to use the 'routine' argument, or give it the value 6351of the array 'owner' (for example its module name). 6352 6353Our most complicated case is that of arrays declared in one or more 6354subroutines and allocated in a subroutine called by them (as done in 6355find_kgrid). In this case, the 'routine' name must be that of the 6356allocating subroutine, but the arrays of the different calling 6357routines will be reported as a single array. Thus, array kpoint of 6358routine kpoint_grid and array kpoints_pdos of routine kpoint_pdos 6359will be reported together as array points of routine find_kgrid. 6360 6361I see no solution if more than one called subroutine (not in the 6362same module) were allocating or deallocating an array, but there 6363is no such a case in siesta. 6364 6365For the previous reasons, until now, only the 'name' argument was used. 6366But this made it difficult to identify the siesta routines allocating 6367many arrays. So from now on, the whole routine+name will be used. 6368 6369The calls to printmemory have been commented out: its output has 6370become unrealistic, since most allocations occur in re_alloc and 6371they are no longer transmitted to routine memory. 6372 6373modified: 6374 Src/SiestaXC/fft3d.f90 6375 Src/SiestaXC/mesh3d.F90 6376 Src/alloc.F90 6377 Src/atomlwf.F 6378 Src/bands.F 6379 Src/basis_types.f 6380 Src/bonds.f 6381 Src/cgvc_zmatrix.F 6382 Src/detover.F 6383 Src/dhscf.F 6384 Src/fft.F 6385 Src/find_kgrid.F 6386 Src/fire_optim.F 6387 Src/forhar.f 6388 Src/hsparse.f 6389 Src/kinefsm.f 6390 Src/ksv.f 6391 Src/m_broyden_mixing.f 6392 Src/m_fire_mixing.f 6393 Src/m_iodm.F 6394 Src/m_pulay.F 6395 Src/m_sparse.F 6396 Src/memory.F 6397 Src/meshmatrix.F 6398 Src/molecularmechanics.F90 6399 Src/moreParallelSubs.F90 6400 Src/new_dm.F 6401 Src/nlefsm.f 6402 Src/old_atmfuncs.f 6403 Src/outcoor.f 6404 Src/overfsm.f 6405 Src/pdos.F 6406 Src/pdosg.F 6407 Src/pdosk.F 6408 Src/pdoskp.F 6409 Src/phirphi.f 6410 Src/poison.F 6411 Src/pseudopotential.f 6412 Src/reord.f 6413 Src/rhoofd.f 6414 Src/rhoofdsp.f 6415 Src/savepsi.F 6416 Src/setup_hamiltonian.F 6417 Src/siesta_analysis.F 6418 Src/siesta_end.F 6419 Src/siesta_init.F 6420 Src/siesta_move.F 6421 Src/spher_harm.f 6422 Src/state_init.F 6423 Src/vmat.f 6424 Src/vmatsp.f 6425 Src/zm_broyden_optim.F 6426 Src/zm_fire_optim.F 6427 Src/zmatrix.F 6428 6429------------------------------------------------------------------------ 64302009-10-13 08:05:00 GMT Alberto Garcia <albertog@icmab.es> trunk-304 6431Array indexp distributed among parallel processors (J. Soler) 6432 6433* Array indexp translates the mesh index from the extended supercell 6434 to the part of unit cell stored locally by each node. It has been 6435 distributed, so that now it translated to myBox from myExtBox, which 6436 are my processor's mesh box and the same box extended by lateral 6437 'wings'. 6438 6439* Documentation of meshsubs has been considerably extended 6440 6441 6442------------------------------------------------------------------------ 64432009-10-12 16:05:00 GMT Alberto Garcia <albertog@icmab.es> trunk-303 6444Add dependency line in SiestaXC. Add missing Supercell docs 6445 6446* A dependency for timer.o was missing in the SiestaXC makefile, thus 6447breaking the multithreaded compilation ("make -j N") feature. (A. Walker) 6448 6449* The documentation for the Supercell option had been inadvertently 6450 left out of the manual after the reorganization. 6451 6452------------------------------------------------------------------------ 64532009-10-12 13:35:00 GMT Alberto Garcia <albertog@icmab.es> trunk-302 6454Assorted fixes after vdw merge 6455 6456* Fix copy operation for modules in SiestaXC, to work around down-casing 6457 by Intel compiler and the possible need of visibility of included modules 6458 for other compilers. (Thanks to A. Walker) 6459 6460* Add XC dependency to TranSiesta compilation (F.D. Novaes) 6461 6462* Wrap pre-broadcast section in rdiag (J. Gale) 6463 6464* Trap for potential out of bounds access to string in m_timer.F90 (J. Gale) 6465 6466* Format change in atomlist (J. Gale) 6467 6468 Format of write statement modified to allow for the fact that the 6469 number of orbitals and projectors is much larger than the number of 6470 atoms, often leading to overflow. 6471 6472* License header update in SiestaXC directory. 6473* Use lib-arch.make to compile stand-alone library, for clarity. 6474 6475------------------------------------------------------------------------ 64762009-10-05 14:15:00 GMT Alberto Garcia <albertog@icmab.es> trunk-301 6477New siestaXC library including van der Waals functional 6478 6479Implementation of the non local van der Waals density functional 6480of Dion et al (PRL 92, 246401 (2004), PRL 103, 096102 (2009)). 6481 6482The codes for the new functional are 6483 6484XC.functional VDW 6485XC.authors DRSLL 6486 6487in Siesta and 'vw' (or 'vf') in Atom. 6488 6489All the exchange-correlation routines have been placed in a library 6490called siestaXC, whose unique entry point is module m_siestaXC. The 6491sources are in subdirectory Src/SiestaXC, whose makefile allows to 6492create a self-contained distribution in file siestaXC.tgz, that can 6493be used in programs other than siesta. The library sources that are 6494used by siesta also outside the library (like alloc.F90) remain in 6495Src, and are copied by SiestaXC/makefile into siestaXC.tgz. 6496 6497The library is used to compile siesta itself, with a scheme similar 6498to that used for MPI, fdf and FoX. Pseudo/atom has been also adapted 6499to use the siestaXC library. 6500 6501The implementation of the non local van der Waals density functional 6502has led to a whole rewritting of cellxc and a major one of atomxc. 6503File xc has been splitted in m_atomxc, m_ldaxc, and m_ggaxc, which 6504are now modules. The VDW-specific routines are in module m_vdwxc. 6505 6506The new parallelization of cellxc has led to several new modules, of 6507which mesh3d is the largest one. It allows new distributions of mesh 6508points among processors, that can change dynamically. Other relevant 6509modules are fftr, for 3-D FFTs of real functions. fft3d has changed 6510to allow (complex) 3-D FFTs using the new distributions of mesh points. 6511Module mesh1d provides radial (1-D) mesh utilities. Module m_debugXC 6512writes reports debugXC.node$$ with details of mesh distributions. 6513 6514The new m_timer module, together with changes in MPI/mpi_siesta, allows 6515the profiling of MPI communication times, for each routine that calls 6516timer, after compiling with -DMPI_TIMING. Routine timer itself remains 6517external, but it uses m_timer operationally. 6518 6519The full accounting and reporting of allocated arrays is now done in 6520module alloc, and printed in (SystemLabel).alloc. The old 'memory' 6521routine now passes information to alloc for this accounting, rather 6522than the other way around. Therefore, the 'total' allocation sizes 6523given by memory routine are no longer complete, though they are still 6524printed. 6525 6526(Jose Soler (UAM), with help by Alberto Garcia (ICMAB), Rogeli Grima 6527(BSC) , and Jose Maria Cela (BSC)) 6528 6529 6530------------------------------------------------------------------------ 65312009-09-29 10:30:00 GMT Alberto Garcia <albertog@icmab.es> trunk-300 6532TranSiesta updates. Assorted fixes and cleanup. Update outputs and banner. 6533 6534* Make local copy of reinit in Util/Denchar 6535* Add comment to the manual re: MeshSubDivisions 6536* Put unit of current in tbtrans. Updated outputs in Tests/transiesta 6537* Merge changes to TS code by F. Novaes 6538* Change Copyright dates. Now they are of the form 1996- 6539* Remove xmlparser/Test directory. Remove test-xml fossils 6540* Update out and xml reference files. Update Tests/Makefile 6541* Fix script.mk and Tests/partial/script.sh 6542 6543------------------------------------------------------------------------ 65442009-09-29 10:30:00 GMT Alberto Garcia <albertog@icmab.es> trunk-299 6545Update of TS section of manual. Assorted fixes. 6546 6547* Update of the TranSiesta section of the manual (P. Ordejon, F. Novaes) 6548 6549* Fixes and streamlined compilation of tbtrans program in Util/TBTrans 6550 (F. Novaes, A. Garcia) 6551 6552* Update of 'doping' routine for doped slabs (P. Ordejon) 6553 6554* New 'si2x1h-dipole' test for the dipole correction feature (P. Ordejon) 6555 6556* Fixes to the building system (A. Walker, A. Garcia) 6557 6558* Fixes in 'bands.F' routine (A. Walker, J. Gale) 6559 6560* Added Util/WFS/info_wfsx.f program (A. Garcia) 6561 6562* New utility Util/Helpers/get_chem_labels (A. Garcia) 6563 6564* Added zero-point-motion to Util/Vibra/Src/vibrator.f (J. Gale) 6565 6566* Fix to avoid the handling of 'reduced_vlocal' when reading .ion files. 6567 (A. Garcia) 6568 6569* Remove obsolete files from Src/fdf and clarify usage (A. Garcia) 6570 6571------------------------------------------------------------------------ 65722009-09-11 11:30:00 GMT Alberto Garcia <albertog@icmab.es> trunk-298 6573Re-organization of the manual. Building fixes. Update of Contrib utils 6574 6575* The manual has been thoroughy re-sectioned, and some obscure points 6576clarified. 6577 6578* In some cases, it has been necessary to make minor changes to the 6579code to be consistent with the behavior implied by the manual: 6580 6581-- The forces file (.FA) is always created. 6582 6583-- There is no longer a coupling of the WriteCoorStep and WriteMDXMol 6584 options. 6585 6586* Fix of the long-standing "mis-feature/bug" in the generation of 6587 perturbative polarization orbitals. The fix is turned off by 6588 default, unless the variable PAO.OldStylePolOrbs is set to 6589 ".false.". (See manual.) 6590 6591* Changes to streamline compilation, and new version of 6592 the arch.make template in Src/Sys/DOCUMENTED_TEMPLATE.make 6593 There are minor changes needed in arch.make files: 6594 6595 - Use of NETCDF_INCFLAGS instead of simply INCFLAGS 6596 - Deprecation of the use of DEFS instead of FPPFLAGS 6597 6598 A new Util/build_all.sh script automates the building 6599 of all the utility programs. 6600 6601* Simplification of TranSiesta compilation: 6602 6603 The target "transiesta" in the makefile defines its 6604 own -DTRANSIESTA pre-processor flag, so the user does 6605 not need to worry about it. 6606 6607 Additionally, the makefile checks whether the last 6608 compilation taking place in the building directory 6609 was a "plain siesta", or a "transiesta", and complains 6610 in case of a mismatch. 6611 6612* Removal of all remaining mentions to the "Src" directory in the 6613 automated tests in Tests. 6614 6615* Update of Andrei Postnikov's utilities in Util/Contrib/APostnikov to 6616 V. 0.3, and integration into the standard building mechanism. 6617 6618(Alberto Garcia, with help from E. Artacho, J. Soler, O. Dieguez, and 6619J. Junquera. The polarization-orbital fix is due to E. Anglada.) 6620 6621 6622------------------------------------------------------------------------ 66232009-09-02 13:50:00 GMT Alberto Garcia <albertog@icmab.es> trunk-297 6624Code to treat slabs with net dipole and charged slabs (P. Ordejon) 6625 6626If the FDF option 'SlabDipoleCorrection' is set to "true", Siesta 6627calculates the electric field required to compensate the dipole of the 6628system. The potential added to the grid corresponds to that of a 6629dipole layer at the middle of the vacuum layer. For slabs, this 6630exactly compensates the electric field at the vacuum, created by the 6631dipole moment of the system, thus allowing to deal with asymmetric 6632slabs (including systems with an adsorbate on one surface) and compute 6633properties such as the work funcion of each of the surfaces. 6634 6635The FDF option SimulateDoping, if "true", instructs the program to add 6636a background charge density to simulate doping. The new "doping" 6637routine calculates the net charge of the system, and adds a 6638compensating background charge that makes the system neutral. This 6639background charge is constant at points of the mesh near the atoms, 6640and zero at points far from the atoms. This simulates situations like 6641doped slabs, where the extra electrons (holes) are compensated by 6642oposite charges at the material (the ionized dopant impurities), but 6643not at the vacuum. This serves to simulate properly doped systems in 6644which there are large portions of vacuum, such as doped slabs. 6645 6646New test: sic-slab 6647 6648During the implementation of these features, a bug related to the 6649calculation of the distance between Bravais planes was discovered 6650and fixed in efield. 6651 6652------------------------------------------------------------------------ 66532009-08-30 17:15:00 GMT Alberto Garcia <albertog@icmab.es> trunk-296 6654TS manual and updates. Building rationalization. Hsparse speedup 6655 6656* Added TranSIESTA sections to the manual (Docs/siesta.tex) (by 6657 J.A. Torres). 6658 6659* TranSIESTA and TBTrans updates (by F.D. Novaes): 6660 6661- Reimplementation of getGF_Tri, that obtains the Green's Function 6662 using the fact that the Hamiltonian is tridiagonal. 6663 6664- Fixed the generation of listudg in the transiesta routine 6665 (m_ts_in_siesta.F). Now, when the TS.UpdateDMCR is set to 6666 .false. the cross terms between the electrodes and the contact region 6667 of the density matrix are also updated in the TS iteration 6668 process. If set to .true., only the elements of the contact region 6669 are changed during the self consistent cycle. 6670 6671- In weightDM and weightDMC (m_ts_scattering.F), changed the weights 6672 of the cross terms elements, since when using Tri_Diag the 6673 non-equilibrium contributions are zero the way it used to be. 6674 6675- In new_dm.F, added a condition that does not sets the energy-density 6676 matrix to zero in the first iteration of the SCF cycle. 6677 6678- (with A. Garcia) New building scheme for TBTrans. 6679 6680* Building rationalization (by A. Garcia): 6681 6682- Move auxiliary programs from Src to individual directories in Util 6683 6684 -- gen-basis and ioncat now live in Util/Gen-basis 6685 -- mixps and fractional have been moved to Util/VCA 6686 -- The programs to test the MPI installation are now in Util/MPI_test 6687 6688- Update building mechanisms in Util/STM 6689 6690(Some of the above building improvements use new functionality in 6691the fdf and MPI makefiles that allows these modules to be compiled in 6692"private subdirectories" anywhere: see Denchar and TBTrans for examples.) 6693 6694* Hsparse has been dramatically speeded-up by removing a superfluous 6695 inner loop (by A. Garcia). 6696 6697* Other updates to the manual by A. Garcia 6698 6699 6700** CHANGES ALONG siesta-2.6 series of trunk 6701 6702----------------------------------------------------------------------- 67032009-08-20 09:25:00 GMT Alberto Garcia <albertog@icmab.es> 2.6.32 6704Documentation updates. Building and cosmetic fixes. Eggbox checker. 6705 6706* Added a draft of release_notes_3.0 6707 6708* New experimental directory Docs/ExtraDocs containing files with 6709 information relevant to a specific feature. They should complement 6710 the "manual", which is really a reference manual and not very useful 6711 for feature discovery. This is work in progress and subject to major 6712 changes. 6713 6714* Updated the content of a number of README files. 6715 6716* Updated several sections of Docs/siesta.tex. 6717 6718* Created new Util/test-xml directory to keep a separate version of 6719 the XML checker. 6720 6721* New Util/Scripting/eggbox_checker.py script for eggbox diagnostics. 6722 6723* Added Src/Sys/DOCUMENTED-TEMPLATE.make to help users with the subtle 6724 points of arch.make generation. More documentation about the 6725 building process in several places. 6726 6727* Warn about deprecation of PHONON interface. 6728 6729* Update siesta.tex with DM reuse information. Better header 6730 information in new_dm.F. Remove references to iodm in Siesta 6731 files. It is still needed for some utility programs. 6732 6733* Clarify target of 'goto' in atomlwf (this was a bug introduced in 6734 previous patches). 6735 6736* Give the Src/obj_setup.sh the ability to override the Src link in 6737 the object directory. Now it should be possible to completely update 6738 the object directory even if it moves. 6739 6740* Proper test for gfortran macros 6741 6742 gfortran now defines the __GFORTRAN__ macro, so it is 6743 no longer necessary to define GFORTRAN in makefiles, but 6744 it is still supported. The proper idiom for the gfortran 6745 test in f2kcli is now: 6746 6747 #if !defined(GFORTRAN) && !defined(__GFORTRAN__) 6748 6749* Removed the Src/filter debug directory. 6750 6751* Updates to some makefiles and many cosmetic fixes. 6752 6753----------------------------------------------------------------------- 67542009-08-14 16:20:00 GMT Alberto Garcia <albertog@icmab.es> 2.6.31 6755Speed-up of density-matrix building in diagk 6756 6757By computing only the products of eigenvector components which are 6758really needed, the building of the density-matrix has been 6759significantly speeded-up in diagk. A similar idea can be applied in 6760diagkp and diag2k (here saving in memory too), but these are not 6761implemented yet. 6762 6763NOTE that the diagk_file version of the routine is still significantly 6764faster, and should be the method of choice when NetCDF is compiled in. 6765 6766modified: 6767 Src/diagk.F 6768 6769----------------------------------------------------------------------- 67702009-08-07 16:20:00 GMT Alberto Garcia <albertog@icmab.es> 2.6.30 6771Assorted fixes, dealing mostly with the building system 6772 6773* (IMPORTANT) The default building directory is now Obj, instead of Src. 6774 This change is necessary to support multiple compilation with the 6775 same source. See Obj/README for more details. 6776 6777* Many fixes to smooth compilation in several systems, notably on IBM 6778 computers. 6779 6780* The default makefile in Pseudo/atom is now the 'modern' version with 6781 CML support. 6782 6783* Clearer diagnostics in case of FoX configuration problems. 6784 6785* Removed obsolete .make files from Src/Sys. Added 64bit versions of 6786 the MareNostrum files. 6787 6788* The 'MaximumWallClockTime' option is no longer available. 6789 6790* Fixes in the NetCDF iodm* routines to properly handle a pointer. 6791 6792removed: 6793 Src/Sys/eth-hreidar-mpi.make 6794 Src/Sys/lahey-lam.make 6795 Src/Sys/lahey-mpich.make 6796 Src/Sys/lahey-nolibs.make 6797 Src/Sys/lahey.make 6798 Src/Sys/osfdxml-mpich.make 6799 Src/Sys/osfdxml.make 6800 Src/Sys/osfdxmlcdf.make 6801 Src/Sys/pgf90-lam.make 6802 Src/Sys/pgf90-mpich.make 6803 Src/Sys/pgf90-nolibs.make 6804 Src/Sys/pgf90.make 6805 Src/Sys/sgi-altix.make 6806 Src/Sys/sgi.make 6807 Src/Sys/sgi64-cdf.make 6808 Src/Sys/sgi64-lam-cdf.make 6809 Src/Sys/sgi64-lam.make 6810 Src/Sys/sgi64-mpi_fermat.make 6811 Src/Sys/sgi64-mpich-cdf.make 6812 Src/Sys/sgi64-mpich.make 6813 Src/Sys/sgin32-mpi.make 6814 Src/Sys/sun-nolibs.make 6815 Src/Sys/t3e.make 6816 Util/COOP/precision.f 6817added: 6818 Obj/ 6819 Obj/README 6820 Src/Sys/marenostrum-mpi-64.make 6821 Src/Sys/marenostrum-mpi-netcdf-64.make 6822renamed: 6823 Pseudo/atom/makefile => Pseudo/atom/makefile-old 6824 Pseudo/atom/makefile-xml => Pseudo/atom/Makefile 6825 Src/Sys/marenostrum-mpi.make => Src/Sys/marenostrum-mpi-32.make 6826 Util/COOP/sys.f90 => Util/COOP/sys_local.f90 6827 Util/Vibra/Vibra/ => Util/Vibra/Src/ 6828modified: 6829 Docs/siesta.ind 6830 Docs/siesta.tex 6831 Src/FoX/configure 6832 Src/Makefile 6833 Src/Sys/README 6834 Src/Sys/cscs-cray-mpi.make 6835 Src/Sys/cscs-cray.make 6836 Src/Sys/cscs-ibm-blanc.make 6837 Src/Sys/finisterrae.make 6838 Src/Sys/marenostrum-mpi-netcdf-32.make 6839 Src/iodm_netcdf.F90 6840 Src/iodmhs_netcdf.F90 6841 Src/molecularmechanics.F90 6842 Src/obj_setup.sh 6843 Src/siesta_options.F90 6844 Src/timer.F 6845 Util/COOP/Makefile 6846 Util/COOP/mprop.f90 6847 Util/Denchar/Src/Makefile 6848 Util/DensityMatrix/makefile 6849 Util/Grid/makefile 6850 Util/Projections/makefile 6851 Util/Vibra/Src/Makefile 6852 Util/WFS/makefile 6853 Util/pdosxml/makefile 6854 Util/pseudo-xml/makefile 6855 Pseudo/atom/makefile-old 6856 Pseudo/atom/Makefile 6857 Src/Sys/marenostrum-mpi-32.make 6858 6859----------------------------------------------------------------------- 68602009-07-03 14:00:00 GMT Alberto Garcia <albertog@icmab.es> 2.6.29 6861TranSiesta: New saving options and file format (M. Paulsson, F.D. Novaes) 6862 6863 * Changed format and filenames for saved TSHS files. 6864 * Enabled transiesta to save a TSHS file for each step in a FC run. 6865 * Transiesta keyword TS.onlyS (T/F) to save overlap matrix in .TSHS 6866 file format and quit without any SCF cycle. 6867 * New "onlyS" option to stop after generating the overlap matrix. 6868 * Disabled proximity check for onlyS run. 6869 6870(+ Fix a few glitches in FoX-enabled compilation of TranSiesta) 6871 6872Thanks to M. Paulsson and F.D. Novaes for this patch. 6873 6874** NOTE: The Intel compiler V. 11.{0,1} does not compile correctly 6875 this version. 6876 6877removed: 6878 Util/TBTrans/TSiohs2.F 6879modified: 6880 Src/Makefile 6881 Src/m_ts_electrode.F90 6882 Src/m_ts_io.F90 6883 Src/m_ts_options.F90 6884 Src/proximity_check.F 6885 Src/setup_hamiltonian.F 6886 Src/siesta_forces.F 6887 Src/state_init.F 6888 Src/write_subs.F 6889 Util/TBTrans/Makefile 6890 Util/TBTrans/TSiohs.F 6891 Util/TBTrans/work.pcl 6892 6893 6894----------------------------------------------------------------------- 68952009-06-24 12:50:00 GMT Alberto Garcia <albertog@icmab.es> 2.6.28 6896Update of CMLComp output. Integration of FoX library (A. Walker, T. White) 6897 6898A subset of the FoX library has been integrated into the source tree. 6899It is configured and built by the Siesta Makefile, and is compatible 6900with the use of VPATH for multiple compilation. 6901 6902The XML output from Siesta now conforms to the CMLComp subset of 6903version 2.2 of the Chemical Markup Language (CML). 6904 6905A new directory Util/CMLComp has been created to hold the ccViz tool 6906to convert the XML output file into an XHTML file that can be opened 6907with any browser. 6908 6909FoX is also used (optionally) by atm to produce pseudopotential files 6910in XML format, replacing the older wxml library by A. Garcia. 6911 6912Thanks to Andrew Walker and Toby White for most of the technology 6913involved in this patch. A. Garcia fixed a few issues of the 6914interaction of FoX with the rest of the build process. 6915 6916NOTE: The output reference XML files in Tests/Reference-xml have 6917been updated. A review of the test list and a final check is due 6918before release. 6919 6920 6921----------------------------------------------------------------------- 69222009-06-24 12:25:00 GMT Alberto Garcia <albertog@icmab.es> 2.6.27 6923Fix TranSiesta compilation issue after recent patches (F.D. Novaes) 6924 6925A compilation error occurred because "found" variable is no longer used 6926in mixer.F (chages in io of density matrix) 6927 6928Made "found" an optinal argument in TSiodm of the m_ts_io.F90 module. 6929 6930In new_dm.F, in the call for TSiodm made explicit the use of the 6931optional "found", since it is used to determine if it should start 6932with a TS calculation, or a diagon calcualtion. 6933 6934In mixer.F, the call for TSiodm no longer uses the "found" variable. 6935 6936modified: 6937 Src/m_ts_io.F90 6938 Src/mixer.F 6939 Src/new_dm.F 6940 6941 6942----------------------------------------------------------------------- 69432009-06-24 12:15:00 GMT Alberto Garcia <albertog@icmab.es> 2.6.26 6944Fix behavior of extra pdos sampling for gamma case 6945 6946The new "extra sampling" feature for the PDOS 6947incorrectly changed the behavior of the program for 6948gamma-only calculations. Now "gamma_pdos" is set to 6949.true. if the user does not specify any extra 6950sampling requirements. 6951 6952Thanks to Jaime Ferrer for spotting the bug. 6953 6954modified: 6955 Src/kpoint_pdos.F90 6956 6957----------------------------------------------------------------------- 69582009-06-15 12:45:00 GMT Alberto Garcia <albertog@icmab.es> 2.6.25 6959Fix bug in verlet restart in parallel (A. Aguado) 6960 6961The variable old_dt was read by Node zero from the VERLET_RESTART 6962file, but was not broadcast to the other nodes. 6963 6964Symptoms of this bug were crashes with a Cholesky-type error, poor 6965energy conservation, and bad self-consistency of the density matrix 6966when running restarted microcanonical simulations in parallel. 6967 6968Thanks to Andres Aguado <aguado@metodos.fam.cie.uva.es> 6969for diagnosing and fixing the bug. 6970 6971modified: 6972 Src/dynamics.f 6973 6974----------------------------------------------------------------------- 69752009-06-15 12:45:00 GMT Alberto Garcia <albertog@icmab.es> 2.6.24 6976Fixes: denchar, pathscale_mpi. DM(HS) history files. Makefiles 6977 6978* Added nano .make and script files. Fixed ag test. 6979 6980- The ag test had a very small MeshCutoff, and crashed. 6981- Added netCDF-enabled .make file for nano. 6982- Updated README file in Src/Sys 6983- Added pbs and sh scripts for test execution on nano. 6984 6985* More complete DM and DMHS history files 6986 6987The DM and DMHS history files have now names of 6988the form DM-NNNN.nc and DMHS-NNNN.nc, respectively, 6989to hold information for all geometry steps. This 6990expanded history option is turned off by default. 6991 6992(+ experimental analysis scripts in Util/SCF) 6993 6994* Better makefiles for some Util subdirectories 6995 6996The WFS, DensityMatrix, and pseudo-xml subdirectories 6997of Util now have makefiles instrumented to use the 6998new OBJDIR variable. 6999 7000* Cosmetic fix for Pathscale MPI 7001 7002File mpi.F was not processed correctly by the Pathscale compiler. 7003 7004* Fix double empty-line bug in denchar 7005 7006The 2D data files contained extra blank lines in between blocks. 7007 7008* Proper citation for ATOM in Pseudo/atom/README 7009 7010 7011added: 7012 Src/Sys/nano-intel-mpi-cdf.make 7013 Tests/Scripts/nano.pbs 7014 Tests/Scripts/nano4.sh 7015 Util/SCF/README 7016 Util/SCF/g_dm.py 7017 Util/SCF/g_dm3.py 7018 Util/SCF/g_els_out.py 7019 Util/SCF/g_hh.py 7020 Util/SCF/g_hist.py 7021 Util/WFS/makefile 7022modified: 7023 Docs/siesta.ind 7024 Docs/siesta.tex 7025 Pseudo/atom/README 7026 Src/MPI/mpi.F 7027 Src/Sys/README 7028 Src/iodm_netcdf.F90 7029 Src/iodmhs_netcdf.F90 7030 Src/state_init.F 7031 Tests/ag/ag.fdf 7032 Util/Denchar/Src/rhoofr.f 7033 Util/DensityMatrix/makefile 7034 Util/pseudo-xml/makefile 7035 version.info 7036 7037 7038----------------------------------------------------------------------- 70392009-06-15 11:00:00 GMT Alberto Garcia <albertog@icmab.es> 2.6.23 7040Implementation of PBEsol functional (J. Gale) 7041 7042Implemented the PBE functional for solids of Perdew et al, PRL 100, 7043136406 (2008). 7044 7045The xc_authors string in Siesta is 'PBEsol'. In atom, the two-letter 7046symbol is 'ps' 7047 7048The XML interface in Pseudo/atom and the converter in Util/pseudo-xml 7049have been updated. 7050 7051 Docs/siesta.tex 7052 Pseudo/atom/Docs/atom.tex 7053 Pseudo/atom/makefile-xml 7054 Pseudo/atom/pseudoXML.f 7055 Pseudo/atom/velect.f 7056 Pseudo/atom/xc.f 7057 Src/atom.f 7058 Src/xc.f 7059 Util/pseudo-xml/xml2psf_helper.f 7060 7061----------------------------------------------------------------------- 70622009-06-15 11:00:00 GMT Alberto Garcia <albertog@icmab.es> 2.6.22 7063Optional k-point sampling for PDOS calculations (J. Gale) 7064 7065Separate grid of K-points introduced for PDOS so that greater 7066resolution can be achieved. To do this, a new module based on the SCF 7067kpoint module has been introduced with separate data structures for 7068the PDOS k-points. In the case that no PDOS grid is specified then the 7069SCF grid is used as present. 7070 7071Handle the case where a gamma point calculation is performed for the 7072SCF and then a non-gamma calculation is requested for the PDOS 7073evaluation. Here the need for the auxiliary cell is trapped in 7074siesta_init by a call to the new routine init_projected_dos. If 7075do_pdos is true, then the gamma flag is set to be false if gamma_pdos 7076is false. 7077 7078Note added to the manual to suggest that PDOS evaluations be performed 7079using a restart if the SCF case involves the gamma point while the 7080PDOS grid involves general k-points. 7081 7082(AG added the si_pdos_kgrid test) 7083 7084added: 7085 Src/kpoint_pdos.F90 7086 Tests/Reference-xml/si_pdos_kgrid.xml 7087 Tests/Reference/si_pdos_kgrid.out 7088 Tests/si_pdos_kgrid/ 7089 Tests/si_pdos_kgrid/makefile 7090 Tests/si_pdos_kgrid/si_pdos_kgrid.fdf 7091 Tests/si_pdos_kgrid/si_pdos_kgrid.pseudos 7092modified: 7093 Docs/siesta.tex 7094 Src/Makefile 7095 Src/projected_DOS.F 7096 Src/siesta_init.F 7097 7098----------------------------------------------------------------------- 70992009-05-07 10:35:00 GMT Alberto Garcia <albertog@icmab.es> 2.6.21 7100Parallel fixes: Diag.ParallelOverK for wf generation; idle nodes 7101 7102* Patches in diagg and diagk for the corner case in which a node has no 7103assigned orbitals (Julian Gale). 7104 7105* The option to parallelize over k-points is only implemented for the 7106SCF loop. The bands routine had already been coded to fall back on the 7107standard parallelization over orbitals, but the wwave routine (used to 7108generate wavefunctions for analysis) had not. This bug has been 7109corrected, and now both routines print a warning to the user when the 7110Diag.ParallelOverK option is used. 7111 7112modified: 7113 Src/bands.F 7114 Src/diagg.F 7115 Src/diagk.F 7116 Src/writewave.F 7117 Docs/siesta.tex 7118 Docs/siesta.ind 7119 7120----------------------------------------------------------------------- 71212009-04-02 12:55:00 GMT Alberto Garcia <albertog@icmab.es> 2.6.20 7122More flexible compilation of Util code 7123 7124By a simple change to the makefiles (involving an OBJDIR variable that 7125can be set to "Src" or to the name of the optional compiler-dependent 7126object directory), the code in Util can be compiled with multiple 7127options. 7128 7129The use of VPATH within Util also allows the re-use of common utility 7130files such as f2kcli.F90. 7131 7132Work in progress. Really a temporary solution util Util is integrated in 7133the architecture-or-compiler-dependent object directories. 7134 7135+ The pdos program in Util/pdosxml has been renamed to pdosxml. 7136 7137removed: 7138 Util/COOP/f2kcli.F90 7139 Util/pdosxml/f2kcli.F90 7140added: 7141 Util/Projections/makefile 7142renamed: 7143 Util/pdosxml/pdos.f90 => Util/pdosxml/pdosxml.f90 7144modified: 7145 Util/COOP/Makefile 7146 Util/Grid/makefile 7147 Util/Vibra/Vibra/Makefile 7148 Util/Vibra/Vibra/vibrator.f 7149 Util/pdosxml/README 7150 Util/pdosxml/makefile 7151 Util/pdosxml/pdosxml.f90 7152 7153----------------------------------------------------------------------- 71542009-04-02 12:50:00 GMT Alberto Garcia <albertog@icmab.es> 2.6.19 7155New version of denchar in Util/Denchar 7156 7157A new version of denchar, able to process complex wavefunctions and 7158multiple k-points, has been put back in the Util/Denchar/Src directory. 7159It can be compiled by re-using code in the top Src directory. 7160 7161(Thanks to Pablo Ordejon) 7162 7163removed: 7164 Src/denchar.F 7165 Src/m_denchar_geom.f 7166 Src/m_denchar_init.F 7167 Src/m_denchar_io.F 7168 Src/m_denchar_neighb.f 7169 Src/m_denchar_work.f 7170 Util/Denchar/README-Source 7171added: 7172 Util/Denchar/Src/ 7173 Util/Denchar/Src/Makefile 7174 Util/Denchar/Src/README 7175 Util/Denchar/Src/atompla.f 7176 Util/Denchar/Src/colinear.f 7177 Util/Denchar/Src/denchar.f 7178 Util/Denchar/Src/fdf/ 7179 Util/Denchar/Src/fdf/makefile 7180 Util/Denchar/Src/itochar.f 7181 Util/Denchar/Src/length.f 7182 Util/Denchar/Src/matvect.f 7183 Util/Denchar/Src/neighb.f 7184 Util/Denchar/Src/planed.f 7185 Util/Denchar/Src/ranger.f 7186 Util/Denchar/Src/readpla.f 7187 Util/Denchar/Src/readsts.f 7188 Util/Denchar/Src/readwaves.f 7189 Util/Denchar/Src/redata_denchar.f 7190 Util/Denchar/Src/reinit.f 7191 Util/Denchar/Src/rhoofr.f 7192 Util/Denchar/Src/stsofr.f 7193 Util/Denchar/Src/wavofr.f 7194 Util/Denchar/Src/wrout.f 7195modified: 7196 Docs/siesta.tex 7197 Src/Makefile 7198 Util/Denchar/Docs/CHANGES 7199 Util/Denchar/Docs/denchar.tex 7200 7201 7202----------------------------------------------------------------------- 72032009-04-02 12:45:00 GMT Alberto Garcia <albertog@icmab.es> 2.6.18 7204Added general-purpose optimizer in Util/Optimizer 7205 7206Alpha version of the general-purpose optimization program, useful, 7207among other things, for pseudopotential and basis-set generation. 7208 7209added: 7210 7211 Util/Optimizer/ 7212 Util/Optimizer/Examples/ 7213 Util/Optimizer/Examples/Basis-Optim-Bond/ 7214 Util/Optimizer/Examples/Basis-Optim-Bond/H.psf 7215 Util/Optimizer/Examples/Basis-Optim-Bond/O.psf 7216 Util/Optimizer/Examples/Basis-Optim-Bond/SWARM_PARAMS 7217 Util/Optimizer/Examples/Basis-Optim-Bond/TEMPLATE 7218 Util/Optimizer/Examples/Basis-Optim-Bond/VARS 7219 Util/Optimizer/Examples/Basis-Optim-Bond/run_script.sh 7220 Util/Optimizer/Examples/Basis_Harris/ 7221 Util/Optimizer/Examples/Basis_Harris/DeltaRho.grid.nc 7222 Util/Optimizer/Examples/Basis_Harris/H.psf 7223 Util/Optimizer/Examples/Basis_Harris/O.psf 7224 Util/Optimizer/Examples/Basis_Harris/PARAMS 7225 Util/Optimizer/Examples/Basis_Harris/README 7226 Util/Optimizer/Examples/Basis_Harris/TEMPLATE 7227 Util/Optimizer/Examples/Basis_Harris/VARS 7228 Util/Optimizer/Examples/Basis_Harris/run_script.sh 7229 Util/Optimizer/Examples/Basis_Optim/ 7230 Util/Optimizer/Examples/Basis_Optim/H.psf 7231 Util/Optimizer/Examples/Basis_Optim/O.psf 7232 Util/Optimizer/Examples/Basis_Optim/PARAMS 7233 Util/Optimizer/Examples/Basis_Optim/README 7234 Util/Optimizer/Examples/Basis_Optim/TEMPLATE 7235 Util/Optimizer/Examples/Basis_Optim/VARS 7236 Util/Optimizer/Examples/Basis_Optim/run_script.sh 7237 Util/Optimizer/Examples/Basis_Optim_Accel/ 7238 Util/Optimizer/Examples/Basis_Optim_Accel/DeltaRho.grid.nc 7239 Util/Optimizer/Examples/Basis_Optim_Accel/H.psf 7240 Util/Optimizer/Examples/Basis_Optim_Accel/O.psf 7241 Util/Optimizer/Examples/Basis_Optim_Accel/PARAMS 7242 Util/Optimizer/Examples/Basis_Optim_Accel/README 7243 Util/Optimizer/Examples/Basis_Optim_Accel/TEMPLATE 7244 Util/Optimizer/Examples/Basis_Optim_Accel/VARS 7245 Util/Optimizer/Examples/Basis_Optim_Accel/run_script.sh 7246 Util/Optimizer/Examples/Pseudo-Optim-Constrained/ 7247 Util/Optimizer/Examples/Pseudo-Optim-Constrained/PARAMS 7248 Util/Optimizer/Examples/Pseudo-Optim-Constrained/PSGEN.TEMPLATE 7249 Util/Optimizer/Examples/Pseudo-Optim-Constrained/README 7250 Util/Optimizer/Examples/Pseudo-Optim-Constrained/SWARM_PARAMS 7251 Util/Optimizer/Examples/Pseudo-Optim-Constrained/Test.inp 7252 Util/Optimizer/Examples/Pseudo-Optim-Constrained/VARS 7253 Util/Optimizer/Examples/Pseudo-Optim-Constrained/run_script.sh 7254 Util/Optimizer/Makefile 7255 Util/Optimizer/README 7256 Util/Optimizer/amoeba.f 7257 Util/Optimizer/io.f 7258 Util/Optimizer/minimizer.f90 7259 Util/Optimizer/parse.f 7260 Util/Optimizer/precision.f90 7261 Util/Optimizer/simplex.f90 7262 Util/Optimizer/swarm.f90 7263 Util/Optimizer/sys.f 7264 Util/Optimizer/vars_module.f90 7265 7266----------------------------------------------------------------------- 72672009-04-02 12:40:00 GMT Alberto Garcia <albertog@icmab.es> 2.6.17 7268New utility programs and features 7269 7270* Orbital projection program 7271 7272Integrated a new version of the "orbmol" program, by Rurali and 7273Lorente, including the k-points functionality later implemented by 7274Tabares and Ordejon. The program is now called "orbmol_proj", and 7275is more economical in memory and hopefully run-time. 7276 7277The program uses the new WFSX wavefunction format (the new program 7278wfs2wfsx.f can be used for legacy data). 7279 7280* New tool for creation of partial density matrices 7281 7282A new program 'dm_creator' has been created in Util/COOP. 7283Given an HSX and a WFSX file, and an optional energy range, dm_creator 7284computes a "partial density matrix" with only those states in the 7285energy range. This density matrix can then be used with Denchar 7286for plotting (or for other more or less devious applications...) 7287 7288* Scripting 7289 7290- New cutoff.py example script 7291- Enhancements to the ASE interface: 7292 - "copy" method for Atom class 7293 - pseudopotential handler for ListOfAtoms 7294 7295* Enhanced WFS utilities 7296 7297The wavefunction-handling programs have been moved to Util/WFS. Added 7298wfsnc2wfsx (useful for New-Diagk calculations) and wfs2wfsx. 7299 7300* Enhanced grid utilities in Util/Grid 7301 7302- Increase bounds of work array in Util/Grid/libfft.f 7303- Added octave/matlab scripts for plane averages 7304 7305* New Util/HSX directory 7306 7307Up to now it only contains an experimental module hsx_m.f90 to process HSX files. 7308 7309* New program dm_filter in Util/DensityMatrix 7310 7311The DM filter program produces a new density-matrix in which only the 7312contributions of specified orbitals are retained (with minor modifications it can 7313delete those and keep the rest). 7314 7315added: 7316 Util/COOP/dm_creator.F90 7317 Util/COOP/iodm_netcdf.F90 7318 Util/COOP/write_dm.f 7319 Util/DensityMatrix/README 7320 Util/DensityMatrix/dmfilter.f90 7321 Util/Grid/average_x.m 7322 Util/Grid/average_z.m 7323 Util/HSX/ 7324 Util/HSX/hsx_m.f90 7325 Util/Projections/ 7326 Util/Projections/Example/ 7327 Util/Projections/Example/Na-on-Na-4A/ 7328 Util/Projections/Example/Na-on-Na-4A/Na.psf 7329 Util/Projections/Example/Na-on-Na-4A/coo.gplot 7330 Util/Projections/Example/Na-on-Na-4A/coo.mpr 7331 Util/Projections/Example/Na-on-Na-4A/molecule.fdf 7332 Util/Projections/Example/Na-on-Na-4A/orbmol.gplot 7333 Util/Projections/Example/Na-on-Na-4A/orbmol.input 7334 Util/Projections/Example/Na-on-Na-4A/pdos.mpr 7335 Util/Projections/Example/Na-on-Na-4A/system.fdf 7336 Util/Projections/Example/Na-on-Na-6A/ 7337 Util/Projections/Example/Na-on-Na-6A/Na.psf 7338 Util/Projections/Example/Na-on-Na-6A/coo.gplot 7339 Util/Projections/Example/Na-on-Na-6A/coo.mpr 7340 Util/Projections/Example/Na-on-Na-6A/molecule.fdf 7341 Util/Projections/Example/Na-on-Na-6A/orbmol.gplot 7342 Util/Projections/Example/Na-on-Na-6A/orbmol.input 7343 Util/Projections/Example/Na-on-Na-6A/pdos.mpr 7344 Util/Projections/Example/Na-on-Na-6A/system.fdf 7345 Util/Projections/README 7346 Util/Projections/orbmol_proj.f90 7347 Util/Scripting/cutoff.py 7348 Util/WFS/ 7349 Util/WFS/wfs2wfsx.f 7350 Util/WFS/wfsnc2wfsx.f90 7351renamed: 7352 Util/readwf.f => Util/WFS/readwf.f 7353 Util/readwfx.f => Util/WFS/readwfx.f 7354 Util/wfsx2wfs.f => Util/WFS/wfsx2wfs.f 7355modified: 7356 Src/diagk_file.F 7357 Src/iowfs_netcdf.F90 7358 Util/COOP/Makefile 7359 Util/COOP/README 7360 Util/COOP/io_hs.f90 7361 Util/COOP/mprop.f90 7362 Util/COOP/subs.f90 7363 Util/DensityMatrix/cdf2dm.f90 7364 Util/DensityMatrix/dm2cdf.f90 7365 Util/DensityMatrix/makefile 7366 Util/Grid/libfft.f 7367 Util/Scripting/Siesta/Interface.py 7368 7369 7370----------------------------------------------------------------------- 73712009-04-02 11:00:00 GMT Alberto Garcia <albertog@icmab.es> 2.6.16 7372Assorted new (small) features 7373 7374* Write Neutral-atom potential on the grid 7375 7376If the fdf symbol SaveNeutralAtomPotential is set to 'True', the neutral-atom 7377potential is written to file SystemLabel.VNA (and optionally to Vna.grid.nc) 7378This feature is exercised in the h2o test. 7379 7380* Warnings for multiple images at Gamma, with optional forcing of supercell 7381 7382For a gamma-point calculation, it is still possible to have overlap of multiple 7383images. This could be because the cell is not big enough, if the user wants 7384to save CPU time and sacrifice a bit of accuracy. 7385 7386This is harmless for the calculation of the electronic structure, as the program 7387just adds up all the relevant matrix elements, with phase factor 1. 7388 7389For a COOP/COHP calculation, the resulting xij array is *wrong*, as 7390only the vector for one representative of the class of interactions is 7391kept. Thus a warning is produced by hsparse. 7392 7393A new fdf symbol, "ForceAuxCell", has been introduced to allow the user to 7394request a (more expensive) "k-point" calculation with an auxiliary cell if 7395needed. At this point, the very first iteration might give different results, 7396since the initial normalization of the density-matrix is different. 7397 7398* Update the Src/ioncat.f program 7399 7400It can now process the core charge and the charge associated to the 7401local pseudopotential 7402 7403* Write also a (new format) HSX file whenever an HS file is requested. 7404 7405* Add new .make files to Src/Sys 7406 7407* Show message from 'die' also on standard error 7408 7409* Disallow repeated species labels 7410 7411* Use species label instead of atomic symbol in dump files. 7412 7413* Set near-zero lattice vector components to zero 7414 7415If the LatticeParameters option is used, and due to roundoff error in the 7416trigonometry, some components of the lattice vectors turned out very small 7417but non-zero. Now they are set to zero for cosmetic reasons. 7418 7419* Disallow the use of non-diagonal supercells 7420 7421Their use is not well-defined in all cases. 7422 7423 7424 7425 7426 7427----------------------------------------------------------------------- 74282009-04-02 10:30:00 GMT Alberto Garcia <albertog@icmab.es> 2.6.15 7429Assorted fixes (hsparse warnings, xc_check...) 7430 7431* Fix for overzealous multiple-image detection in hsparse 7432 7433Hsparse raised a warning regarding connectivity of multiple images 7434without actually checking that the currently considered neighbor did 7435indeed overlap with the base atom. 7436 7437* Add missing line in Util/Grid/grid2cube.f 7438 (P. Ordejon) 7439 7440* Initialize nspin_data in Util/pdosxml/m_pdos.f90. Update cli code. 7441 (Reported by P. Ordejon) 7442 7443* Fix revPBE section in xc_check in atom.f 7444 7445* Fixed calculation of fermi level for charged systems in Util/COOP/mprop.f90 7446 (Thanks to Manuel Cobian) 7447 7448* Fixed labels and file names in some tests. 7449 (Reported by I. Silanes, IFCA) 7450 7451* Fix declarations in function numb in chempot 7452 (Thanks to Manuel Cobian) 7453 7454* Increase the number of fields for energy differences in Pseudo/atom/prdiff.f 7455 (Reported by V. Maslyuk) 7456 7457added: 7458 Tests/pd_ice/pd_ice.pseudos 7459renamed: 7460 Tests/h3po4_atomlists_1 => Tests/h3po4_1 7461 Tests/h3po4_atomlists_1/h3po4.fdf => Tests/h3po4_1/h3po4_1.fdf 7462 Tests/h3po4_atomlists_1/h3po4.pseudos => Tests/h3po4_1/h3po4_1.pseudos 7463 Tests/h3po4_atomlists_2 => Tests/h3po4_2 7464 Tests/h3po4_atomlists_2/h3po4.fdf => Tests/h3po4_2/h3po4_2.fdf 7465 Tests/h3po4_atomlists_2/h3po4.pseudos => Tests/h3po4_2/h3po4_2.pseudos 7466 Tests/h3po4_atomlists_3 => Tests/h3po4_3 7467 Tests/h3po4_atomlists_3/h3po4.fdf => Tests/h3po4_3/h3po4_3.fdf 7468 Tests/h3po4_atomlists_3/h3po4.pseudos => Tests/h3po4_3/h3po4_3.pseudos 7469 Tests/pd_h2o => Tests/pd_ice 7470modified: 7471 Pseudo/atom/prdiff.f 7472 Src/atom.f 7473 Src/chempot.F 7474 Src/hsparse.f 7475 Tests/h3po4_1/makefile 7476 Tests/h3po4_2/makefile 7477 Tests/h3po4_3/makefile 7478 Tests/pd_ice/makefile 7479 Tests/ptcda/ptcda.fdf 7480 Util/COOP/io_hs.f90 7481 Util/COOP/main_vars.f90 7482 Util/COOP/mprop.f90 7483 Util/Grid/grid2cube.f 7484 Util/pdosxml/f2kcli.F90 7485 Util/pdosxml/m_pdos.f90 7486 Tests/h3po4_1/h3po4_1.fdf 7487 Tests/h3po4_2/h3po4_2.fdf 7488 Tests/h3po4_3/h3po4_3.fdf 7489 7490 7491----------------------------------------------------------------------- 74922009-03-28 17:20:00 GMT Alberto Garcia <albertog@icmab.es> 2.6.14 7493Added a translator for pseudopotential files in XML format 7494 7495Directory Util/pseudo-xml contains code by J. Junquera and A. Garcia 7496to convert pseudopotential files in the XML format designed by 7497Junquera, Garcia, and Verstraete (to be published) to ".psf" format. 7498 7499Also: 7500 - Use of "force_underflow" to avoid very small numbers in output. 7501 - Use exact traditional marker messages in psf file. 7502 7503added: 7504 Util/pseudo-xml/Fe.xml 7505 Util/pseudo-xml/io.f 7506 Util/pseudo-xml/makefile 7507 Util/pseudo-xml/pseudopotential.f 7508 Util/pseudo-xml/sys.f90 7509 Util/pseudo-xml/xml2psf.f90 7510 Util/pseudo-xml/xml2psf_helper.f 7511renamed: 7512 Src/pseudo-xml => Util/pseudo-xml 7513modified: 7514 Docs/siesta.tex 7515 Pseudo/atom/pseudoXML.f 7516 Util/README 7517 Util/pseudo-xml/README 7518 7519 7520----------------------------------------------------------------------- 75212009-03-19 11:00:00 GMT Alberto Garcia <albertog@icmab.es> 2.6.13 7522Fix evaluation of atomic radial functions near r=0 7523 7524Spherical functions with l=0 must have a zero gradient at the 7525origin. However, after a change somewhere between v0.9 and v0.11, the 7526splines used have been constructed using the "natural" boundary 7527condition of zero second derivative. This causes numerical problems 7528stemming from the discontinuity of the gradient, notably extraneous 7529forces when atoms move slightly away from exact grid-point positions. 7530 7531The problem has been fixed by specifying explicitly "yp1=0" in the 7532construction of the splines. It has also been necessary to augment the 7533rad_setup_d2 and radial_read_ascii functions with extra arguments, so 7534that tables in .ion or .ion.nc files can be processed adequately. 7535 7536The changes affect the orbitals and the projectors (their tables 7537contain R(r)/r**l, so they have zero derivative at zero for all l), 7538the pseudocore charge, the local pseudopotential charge density, and 7539Vna. Only the "reduced Vlocal" function (which is not really used by 7540Siesta) uses a natural spline, as it has a finite slope at r=0 (maybe 7541because this is not a "volume function" but a synthetic one). 7542 7543A related problem is the extrapolation to r=0 of magnitudes computed 7544on the radial grid. Typically the construction procedure starts or 7545ends with the first non-zero value of the radius, and a final 7546extrapolation is done. This can be linear, quadratic, or "flat" 7547(involving just a copy of the value at the first nonzero 7548radius...). In particular, a "flat" extrapolation was used for the 7549pseudocore charge (which led again to extraneous contributions to 7550forces) and for the effective charge density associated to the local 7551pseudopotential (in this case there does not seem to be a sizable 7552contribution to the forces). A quadratic extrapolation is now used 7553for those magnitudes. 7554 7555The gradient was not computed properly in a "danger area" with an 7556approximate radius 2* r_c /500, where 500 is the number of points in 7557the interpolation table and r_c is the cutoff of the function 7558considered. Thus for a very localized pseudo-core charge (rc=1.5 bohr) 7559the effects might be felt when the atoms move by up to around 0.006 7560bohr from a grid point. 7561 7562The bug might have affected phonon calculations starting from 7563high-symmetry atomic positions, since a very small displacement might 7564then give meaningless results. Other effects might be extra noise in 7565molecular dynamics calculations when an atom falls by chance in the 7566"danger area", and puzzlingly high residual forces for particular 7567values of atomic coordinates, which might have complicated the analysis 7568of the eggbox effect. 7569 7570Credits: D. Sanchez Portal found the spline issue. A. Garcia coded the 7571 fix, found the extrapolation bug, and analyzed the issues involved. 7572 7573+: The "ioncat" program has been updated to process the pseudo-core charge 7574 and the local-pseudopotential charge density. 7575+: A new function rchlocal has been added to atmfuncs.f 7576 7577modified: 7578 Src/atmfuncs.f 7579 Src/atom.f 7580 Src/basis_io.F 7581 Src/electrostatic.f 7582 Src/ioncat.f 7583 Src/radial.f 7584 Docs/siesta.tex 7585 7586----------------------------------------------------------------------- 75872009-03-19 10:00:00 GMT Alberto Garcia <albertog@icmab.es> 2.6.12 7588Fix of non-collinear-spin patch 7589 7590Due to an oversight, the patch leading to version 2.6.9 was missing 7591two essential fdf calls relating to spin polarization in module m_spin. 7592Requests for spin-polarized or non-collinear-spin calculations were 7593silently ignored. 7594 7595This has now been fixed and the documentation of the m_spin module 7596improved. 7597 7598Thanks to Oswaldo Dieguez for reporting the bug. 7599 7600modified: 7601 Src/m_spin.F90 7602 Docs/siesta.tex 7603 7604----------------------------------------------------------------------- 76052009-03-16 16:30:00 GMT Alberto Garcia <albertog@icmab.es> 2.6.11 7606Re-design of DM re-use code plus reallocation bug fix 7607 7608* A redesigned m_new_dm module prepares a starting density matrix for a 7609new geometry iteration. This DM can be: 7610 76111. Synthesized directly from atomic occupations (not idempotent) 76122. Read from file 76133. Extrapolated from (two) previous steps 76143.a The DM of the previous iteration 7615 7616In cases 2 and 3, a check is done to guarantee that the structure 7617of the read or extrapolated DM conforms to the current sparsity. 7618If it does not, the information is re-arranged. 7619 7620Special cases: 7621 Harris: The matrix is always initialized 7622 Force calculation: The DM should be written to disk 7623 at the time of the "no displacement" 7624 calculation and read from file at 7625 every subsequent step. 7626 Variable-cell calculation: 7627 If the auxiliary cell changes, the DM is forced to be 7628 initialized (conceivably one could rescue some important 7629 information from an old DM, but it is too much trouble 7630 for now). NOTE that this is a change in policy with respect 7631 to previous versions of the program, in which a (blind?) 7632 re-use was allowed. 7633 7634 7635* The physical dimensions of the DM array were not allowed to shrink 7636upon reallocation, thus introducing mismatches between the actual size 7637and what several subroutines expected. This bug, which affected with 7638particular severity spin-polarized calculations, has now been fixed. 7639 7640* New symbols for control of DM reuse and extrapolation 7641 7642The FDF symbols: 7643 7644DM.AllowReuse (default .TRUE.) 7645DM.AllowExtrapolation (default .TRUE.) 7646 7647control whether the DM can be re-used from one geometry step to another, and 7648whether it can be extrapolated using information from the two previous steps. 7649 7650If DM.AllowReuse is .false., the DM is not read from file even if DM.UseSaveDM is .true. 7651 7652The default for ReinitialiseDM has been changed to ".true.". Hence the DM is 7653reset (and not read from file) when the auxiliary supercell shape changes, as sanity 7654dictates. 7655 7656* Re-design of new_dm and extrapol 7657 7658 * Use new functionality in module m_sparse to simplify the logic and 7659 hide the ---old index arrays. 7660 7661 * Initdm is now part of the new_dm module. 7662 7663 (* While debugging a hard-to-track zeroth allocation of DMsaved made a 7664 note in alloc.F90) 7665 7666* Split of read/write functionality in iodm. Sparsity module. Input check 7667 7668 * A new module m_iodm based in iodm has been added (the old code remains). 7669 Reading and writing are now done by separate routines, read_dm and write_dm, 7670 respectively. 7671 7672 * New module m_sparse, containing code to check for sparsity changes and 7673 to re-structure a sparse matrix to conform to a new pattern (inspired by 7674 code in extrapol). 7675 7676 * Initdm now calls read_dynamic_dm, which generates a completely fresh 7677 DM. Then the input sparsity pattern is compared to the current one, 7678 and updated if needed. If the file cannot be used, perform a proper bailout 7679 (supersedes a previous patch by Emilio and Andrew on iodm.f) 7680 7681 7682removed: 7683 Src/extrapol.F 7684 Src/initdm.F 7685added: 7686 Src/compute_norm.F 7687 Src/m_iodm.F 7688 Src/m_sparse.F 7689modified: 7690 Docs/CHANGES 7691 Src/Makefile 7692 Src/alloc.F90 7693 Src/diagk.F 7694 Src/hsparse.f 7695 Src/iodm.F 7696 Src/mixer.F 7697 Src/new_dm.F 7698 Src/post_scf_work.F 7699 Src/siesta_init.F 7700 Src/siesta_options.F90 7701 Src/sparse_matrices.F90 7702 Src/state_init.F 7703 Src/version.F90 7704 version.info 7705 7706------------------------------------------------------------------ 77072009-02-22 22:00:00 GMT Alberto Garcia <albertog@icmab.es> 2.6.10 7708Fixed non-collinear spin calculation in parallel 7709 7710 * The diagonalization with mixed spins requires doubling 7711 the effective blocksize for scalapack. This has been 7712 fixed. 7713 7714 Credits: Volodymyr Maslyuk, Alberto Garcia 7715 7716 Note that the option Diag.ParallelOverK cannot yet 7717 be used with non-collinear spin. 7718 7719 Other fixes: 7720 7721 * In non-collinear spin calculations there is no CML output. 7722 Thus the relevant CML module should not be opened. 7723 7724 New test: fe_noncol_kp 7725 7726added: 7727 Tests/fe_noncol_kp/ 7728 Tests/fe_noncol_kp/fe_noncol_kp.fdf 7729 Tests/fe_noncol_kp/fe_noncol_kp.pseudos 7730 Tests/fe_noncol_kp/makefile 7731modified: 7732 Docs/siesta.tex 7733 Src/Makefile 7734 Src/cdiag.F 7735 Src/diag2g.F 7736 Src/diag2k.F 7737 Src/diagon.F 7738 Src/m_spin.F90 7739 Src/mulliken.F 7740 Tests/fe_clust_noncollinear/fe_clust_noncollinear.fdf 7741 7742------------------------------------------------------------------ 77432009-02-06 14:30:00 GMT Alberto Garcia <albertog@icmab.es> 2.6.9 7744Implementation of new filtering logic 7745 7746See the manual for instructions on how to use the new 7747FDF symbols FilterCutoff and FilterTol. 7748 7749* Note that there are no safeguards for failures of the filtering 7750routine. In particular, if FilterTol is set to a "large" value, some 7751orbitals will not be filtered correctly, and the tables will be 7752corrupted. 7753 7754* The implementation of automatic meshcutoff is not ready yet. 7755 7756* Updated the "filter" tests. 7757 7758* In atom, moved the call to 'comcore' after orbital setup. This is 7759needed to apply an orbital-determined cutoff to the partial-core 7760charge. The orbitals themselves are generated with the "raw" core 7761charge from the pseudopotential file, and then filtered. Then the PCC 7762is filtered. 7763 7764* Apart from the fdf symbols discussed in the manual, the following 7765undocumented ones can be used for now: (see the code) 7766 7767PCC.Filter 7768PAO.Filter 7769VNA.Filter 7770 7771(booleans). Fine-tune which things are filtered. 7772(make sure other options and defaults are compatible) 7773 7774XXX.FilterFactor: fine-tune the default factors used 7775 7776XXX.FilterCutoff: fine-tune the cutoff 7777 7778XXX.FilterTol: set the diagnostic Kin Energy tolerance 7779for an estimate of the hardness of the function. This 7780defaults to 0.003 Ry. 7781 7782removed: 7783 Tests/Reference-xml/pb_filter_all.xml 7784 Tests/Reference-xml/pb_filter_basis.xml 7785 Tests/Reference-xml/pb_filter_pcc.xml 7786 Tests/Reference-xml/pb_filter_vna.xml 7787 Tests/Reference/pb_filter_all.out 7788 Tests/Reference/pb_filter_basis.out 7789 Tests/Reference/pb_filter_nopcc.out 7790 Tests/Reference/pb_filter_pcc.out 7791 Tests/Reference/pb_filter_vna.out 7792 Tests/Reference/var_cell_filter.out 7793 Tests/pb_filter_basis/ 7794 Tests/pb_filter_basis/makefile 7795 Tests/pb_filter_basis/pb_filter_basis.fdf 7796 Tests/pb_filter_basis/pb_filter_basis.pseudos 7797 Tests/pb_filter_nopcc/ 7798 Tests/pb_filter_nopcc/makefile 7799 Tests/pb_filter_nopcc/pb_filter_nopcc.fdf 7800 Tests/pb_filter_nopcc/pb_filter_nopcc.pseudos 7801 Tests/pb_filter_pcc/ 7802 Tests/pb_filter_pcc/makefile 7803 Tests/pb_filter_pcc/pb_filter_pcc.fdf 7804 Tests/pb_filter_pcc/pb_filter_pcc.pseudos 7805 Tests/pb_filter_vna/ 7806 Tests/pb_filter_vna/makefile 7807 Tests/pb_filter_vna/pb_filter_vna.fdf 7808 Tests/pb_filter_vna/pb_filter_vna.pseudos 7809 Tests/var_cell_filter/ 7810 Tests/var_cell_filter/makefile 7811 Tests/var_cell_filter/var_cell_filter.fdf 7812 Tests/var_cell_filter/var_cell_filter.pseudos 7813 Tests/var_cell_stress/ 7814 Tests/var_cell_stress/makefile 7815 Tests/var_cell_stress/var_cell_stress.fdf 7816 Tests/var_cell_stress/var_cell_stress.pseudos 7817added: 7818 Docs/filtering.CHANGES 7819 Tests/Reference-xml/pb_filter_cutoff.xml 7820 Tests/Reference-xml/pb_filter_tol.xml 7821 Tests/Reference/pb_filter_cutoff.out 7822 Tests/Reference/pb_filter_tol.out 7823 Tests/pb_filter_tol/ 7824 Tests/pb_filter_tol/makefile 7825 Tests/pb_filter_tol/pb_filter_tol.fdf 7826 Tests/pb_filter_tol/pb_filter_tol.pseudos 7827renamed: 7828 Tests/pb_filter_all => Tests/pb_filter_cutoff 7829 Tests/pb_filter_all/pb_filter_all.fdf => Tests/pb_filter_cutoff/pb_filter_cutoff.fdf 7830 Tests/pb_filter_all/pb_filter_all.pseudos => Tests/pb_filter_cutoff/pb_filter_cutoff.pseudos 7831modified: 7832 Docs/CHANGES 7833 Docs/siesta.ind 7834 Docs/siesta.tex 7835 Src/atom.f 7836 Tests/pb_filter_cutoff/makefile 7837 Tests/std-Makefile 7838 version.info 7839 Tests/pb_filter_cutoff/pb_filter_cutoff.fdf 7840 7841------------------------------------------------------------------ 78422008-12-06 17:50:00 GMT Alberto Garcia <albertog@icmab.es> 2.6.8 7843Optimize and fix COOP/COHP/PDOS analysis program 7844 7845The mprop program in Util/COOP has been revamped to decrease 7846drastically the amount of memory needed and to speed up execution. 7847Now it should be competitive with, and more flexible than, Siesta's 7848built-in PDOS computation. 7849 7850In the process of optimization several bugs were found and fixed. 7851Users are advised to revise the results of old calculations, 7852particularly if k-points or multiple-zeta orbital were used. 7853 7854(+ The OCCS file needs to be opened at the right place in diagk) 7855 7856 7857added: 7858 Tests/Reference-xml/si64_coop.xml 7859 Tests/Reference/si64_coop.out 7860modified: 7861 Src/diagk.F 7862 Tests/si64_coop/si64_coop.fdf 7863 Util/COOP/Makefile 7864 Util/COOP/Tests/n_chain/coo.N-N.gplot 7865 Util/COOP/io_hs.f90 7866 Util/COOP/main_vars.f90 7867 Util/COOP/mprop.f90 7868 Util/COOP/read_curves.f90 7869 Util/COOP/subs.f90 7870 7871------------------------------------------------------------------ 78722008-11-28 16:15:00 GMT Alberto Garcia <albertog@icmab.es> 2.6.7 7873Assorted bug fixes: iodm, pdos, fdf, cdf_fft 7874 7875* Fix latest patch for iodm.F (formatting, messages) 7876* Fix long-standing bug in pdos XML output 7877* Cosmetic fix in experimental file Util/Grid/cdf_fft.f90 7878* Fix obscure bug in fdf 7879 7880modified: 7881 Src/fdf/fdf.f 7882 Src/iodm.F 7883 Src/wxml/m_wxml_text.F90 7884 Util/Grid/cdf_fft.f90 7885 7886 ------------------------------------------------------------ 7887 revno: 271 7888 committer: Alberto Garcia <albertog@icmab.es> 7889 branch nick: trunk-ag 7890 timestamp: Mon 2008-10-27 22:42:54 +0100 7891 message: 7892 Do not use volume factor in cdf_fft 7893 7894 The factor only makes sense for charge-density files. 7895 7896 modified: 7897 Util/Grid/cdf_fft.f90 7898 ------------------------------------------------------------ 7899 revno: 270 7900 committer: Alberto Garcia <albertog@icmab.es> 7901 branch nick: trunk-ag 7902 timestamp: Mon 2008-10-27 22:37:48 +0100 7903 message: 7904 Close the output channel in fdf_shutdown 7905 7906 If fdf is re-invoked, an error was triggered because 7907 fdf_shutdown did not close the previous run's output channel. 7908 Bug spotted by Eduardo Hernandez. 7909 7910 modified: 7911 Src/fdf/fdf.f 7912 ------------------------------------------------------------ 7913 revno: 269 7914 committer: Alberto Garcia <albertog@icmab.es> 7915 branch nick: trunk-ag 7916 timestamp: Mon 2008-10-27 22:35:55 +0100 7917 message: 7918 Fix a long-standing bug in pdos xml output 7919 7920 In Src/wxml/m_wxml_text.F90, the arguments to the sign function were 7921 reversed, causing badly formatted records in the pdos xml file. 7922 Thanks to Rogeli Grima for spotting the bug. 7923 7924 modified: 7925 Src/wxml/m_wxml_text.F90 7926 7927 7928------------------------------------------------------------------ 79292008-11-28 14:25:00 GMT Alberto Garcia <albertog@icmab.es> 2.6.6 7930Avoid MPI deadlock when DM file is not acceptable (A. Walker) 7931 7932 Since r263.1.1 it was possible for the test 7933 7934 if ( maxnd .lt. ndmax ) then 7935 okdim = .false. 7936 ... skip DM reading ... 7937 7938 7939 to be true on some nodes and false on others 7940 as ndmax was local to the node. This condition 7941 leads to some nodes to wait at globalize_max 7942 in m_pulay.F (near line 53) and the other to wait 7943 at the MPI_Wait in iodm.F (near line 293). Avoid 7944 this by detecting whether maxnd and ndmax are 7945 different between nodes. The test is done on all nodes and 7946 all must be ok to use the .DM file. 7947 7948 modified: 7949 Src/iodm.F 7950 version.info 7951 7952------------------------------------------------------------------ 79532008-10-15 10:50:00 GMT Alberto Garcia <albertog@icmab.es> 2.6.5 7954Assorted fixes (deprecated constructs, zmatrix, cg restarts) (A. Walker) 7955 7956 ------------------------------------------------------------------------- 7957 2008-10-13 Andrew Walker 2.6.4--awalker-trunk-fixes-5 7958 Remove use of features deleted in Fortran 95 7959 7960 Specifically, one use of PAUSE and one GOTO an 7961 ENDDO statment. GOTO now jumps to the next line 7962 and the PAUSE is replaced to an (MPI safe) call 7963 to die(). 7964 7965 modified: 7966 Docs/CHANGES.awalker-trunk-fixes 7967 Src/atomlwf.F 7968 Src/m_ts_aux_rout.F 7969 version.info 7970 7971 ------------------------------------------------------------------------- 7972 2008-10-13 Andrew Walker 2.6.4--awalker-trunk-fixes-4 7973 Simple bugfix for fixed cell restarts. 7974 7975 In the case of a tightend ftol after a sucessful CG run, relaxed 7976 is set to .true. by the read from iocg. This results in the test 7977 for convergence being skipped within conjgr. Setting relaxed to 7978 .false. here avoids this. In the case of a variable cell relaxed 7979 is set below anyway and the converence test is always performed. 7980 A better solution (moving the test out into a seperate routine) 7981 will follow in a later version. 7982 7983 modified: 7984 Docs/CHANGES.awalker-trunk-fixes 7985 Src/cgvc.F 7986 version.info 7987 7988 ------------------------------------------------------------------------- 7989 2008-10-13 Andrew Walker 2.6.4--awalker-trunk-fixes-3 7990 NAG issues with transiesta 7991 7992 Even with -dcfuns the NAG f95 compiler does not like the 7993 "non-standard double precision complex intrinsic function" 7994 dcexp. Use the generic exp instead. 7995 7996 modified: 7997 Docs/CHANGES.awalker-trunk-fixes 7998 Src/m_ts_electrode.F90 7999 Src/m_ts_in_siesta.F 8000 Src/m_ts_scattering.F 8001 8002 ------------------------------------------------------------------------- 8003 2008-10-13 Andrew Walker 2.6.4--awalker-trunk-fixes-2 8004 Fix errors in some zmatrix tests 8005 8006 According to the documentation and code in zmatrix.F the 8007 fdf flags to control zmatrix force tolerance and optimizer 8008 step size are ZM.ForceTolLength, ZM.ForceTolAngle, 8009 ZM.MaxDisplLength and ZM.MaxDisplAngle - in some tests 8010 they were shortened to ...Ang and ...Len. This patch 8011 corrects this. The values in the tests were set to the 8012 defaults so test output is not changed. 8013 8014 modified: 8015 Docs/CHANGES.awalker-trunk-fixes 8016 Tests/benzene/benzene.fdf 8017 Tests/fire_benzene/fire_benzene.fdf 8018 Tests/h2oZ/h2oZ.fdf 8019 Tests/zmatrix/zmatrix.fdf 8020 8021 ------------------------------------------------------------------------- 8022 2008-10-13 Andrew Walker 2.6.4--awalker-trunk-fixes-1 8023 Make obj_setup.sh executable. 8024 8025 This needs to be executed in order to do VPATH make. 8026 8027 added: 8028 Docs/CHANGES.awalker-trunk-fixes 8029 modified: 8030 Src/obj_setup.sh* 8031 version.info 8032 8033 8034------------------------------------------------------------------ 80352008-09-12 13:45:00 Alberto Garcia <albertog@icmab.es> 2.6.4 8036Extended Ordejon-Mauri ordern functional to atoms with odd number of electrons 8037 8038Patch by: Emilio Artacho <emilio@esc.cam.ac.uk> 8039timestamp: Sat 2008-08-30 18:38:45 +0100 8040 8041In the initial assigning of LWF centers to atoms, it assigns n/2 to 8042atoms with n even, and (n+1)/2 or (n-1)/2 in an alternating sequence 8043to atoms with odd number. The sequence runs in the order of input in 8044the atomic coordinates block; the user can control the assignment by 8045defining the order there. 8046 8047modified: 8048 Docs/siesta.tex 8049 Src/atomlwf.F 8050 8051------------------------------------------------------------------ 80522008-09-12 13:25:00 Alberto Garcia <albertog@icmab.es> 2.6.3 8053Siesta moves on with fresh DM instead of stopping when wrong DM file 8054 8055Patch by: Emilio Artacho <emilio@esc.cam.ac.uk> 8056timestamp: Thu 2008-08-28 15:53:19 +0100 8057 8058Simple patch removing chkdim calls in iodm.F and substituting them by 8059if statements. If the dimensions are wrong it sends back found=.false. 8060 8061There is a 'goto' statement introduced to minimise impact on present 8062structure (pending the up-and-coming revision of DM handling) 8063 8064modified: 8065 Src/iodm.F 8066 8067------------------------------------------------------------------ 80682008-09-11 11:50:00 Alberto Garcia <albertog@icmab.es> 2.6.2 8069Incorporate new filtering functionality 8070 8071Pending the merge of the new atom-clean structure, the new filtering 8072functionality of Jose Soler and Eduardo Anglada has been incorporated 8073temporarily into this branch. 8074 8075The filtering routines are in Src/m_filter.f90, a self-contained 8076module with no dependencies. A new subdirectory Src/filter with 8077the same code is meant to serve as a test framework for now. 8078Eventually it would be turned into a "library" subdirectory, 8079and Src/m_filter.f90 removed. 8080 8081The old filtering routines have been removed. 8082Minimal documentation has been added to Docs/siesta.tex. 8083 8084removed: 8085 Src/filter.f90 8086 Src/filter_subs.f 8087added: 8088 Src/filter/ 8089 Src/filter/README 8090 Src/filter/ba-6s-orb.dat 8091 Src/filter/core.dat 8092 Src/filter/f2kcli.F90 8093 Src/filter/m_filter.f90 8094 Src/filter/m_getopts.f90 8095 Src/filter/makefile 8096 Src/filter/test_filter.f90 8097 Src/filter/ti-3p-orb.dat 8098 Src/filter/ti-4p-orb.dat 8099 Src/m_filter.f90 8100modified: 8101 Docs/CHANGES 8102 Docs/siesta.ind 8103 Docs/siesta.tex 8104 Src/Makefile 8105 Src/atom.f 8106 Src/version.F90 8107 version.info 8108 8109 81102008-09-11 11:10:00 GMT Alberto Garcia <albertog@icmab.es> 2.6.1 8111Fix bug related to vna introduced at a previous patch 8112 8113A patch introduced in 2.5.29 in meshsubs.F was wrong. Vna must 8114be kept in "gradients" calculations. Its intent has been set 8115to "inout" and the extra initialization removed. 8116 8117The bug was spotted by Rogeli Grima. 8118 8119modified: 8120 Src/meshsubs.F 8121 Src/version.F90 8122 version.info 8123 8124____________________________________________________________________ 8125** CHANGES ALONG siesta@uam.es--2006/siesta-devel--reference--2.5 8126-------------------------------------------------------------------- 8127 81282008-07-18 08:30:00 GMT Alberto Garcia <albertog@icmab.es> patch-33 8129 8130Summary: Fix in dhscf.F . Added OUT directories int Tests/transiesta 8131 8132(F.D. Novaes) 8133 8134* Corrected the position of MPI #endif in dhscf. 8135 8136* Added output files of transiesta runs in OUT directories 8137and of tbtrans runs in OUT_TBT in the tests located in Tests/transiesta 8138 81392008-07-16 15:30:00 GMT Alberto Garcia <albertog@icmab.es> patch-32 8140 8141Summary: Added tests for Transiesta and /Util/TBTrans (F.D. Novaes) 8142 8143Tests/transiesta contains some (not quite automatic) 8144tests for transiesta and tbtrans. 8145 8146Util/TBTrans contains the source code for tbtrans. 8147 8148README_TRANSIESTA in the top directory explains 8149the basic features and organization for transiesta. 8150 81512008-07-16 07:40:00 GMT Alberto Garcia <albertog@icmab.es> patch-31 8152 8153Summary: Added support for Lapack routine zgesv for transiesta 8154 8155For systems without pre-compiled libraries, zgesv_lapack.f has 8156been added to Src/Libs. It is added by default to linalg.a 8157 81582008-07-15 08:40:00 GMT Alberto Garcia <albertog@icmab.es> patch-30 8159 8160Summary: Merge of Transiesta code -- F. D. Novaes version 8161 8162Brief Description: 8163 8164The TranSIESTA code consists in a a set of additional routines for the 8165SIESTA package for the computation of electronic transport 8166properties. It was originally developed by Mads Brandbyge, Jose-Luiz 8167Mozos, Pablo Ordejon, Jeremy Taylor and Kurt Stokbro (Phys. Rev. B 65, 8168165401 (02)), and first implemented in the SIESTA 1.3p version. 8169 8170The present distribution was adapted to the SIESTA 2.5 structure. With 8171respect to the first implementation, it has the additional feature of 8172allowing for the use of a k-point sampling other than the gamma point 8173(for the 2D Brillouin zone perpendicular to the transport 8174direction). These modifications were done by F. D. Novaes 8175(fdnovaes@icmab.es) 8176 8177Source code Structure: 8178 8179In this implementation, the original TranSIESTA routines were grouped 8180in a set of modules, that all begin with m_ts (m_ts_electrode.F90, 8181e.g.), together with the addition of some new subroutines. These 8182modules are located in the Src directory. The interface for 8183TranSIESTA also requires the modification of some of the SIESTA 8184routines. Presently, this is controlled by compilation directives 8185(#ifdef TRANSIESTA), so that only when compiling with the -DTRANSIESTA 8186FPPFLAGS option that the objects will contain the modifications. 8187 8188Compiling: 8189 8190Add -DTRANSIESTA to the FPPFLAGS variable in the arch.make file, and 8191type 8192 8193make transiesta 8194 8195The Makefile was modified in such a way to link the m_ts modules and 8196create a binary called transiesta. 8197 8198 81992008-07-08 13:45:00 GMT Alberto Garcia <albertog@icmab.es> patch-29 8200 8201Summary: Patches by A. Walker: undefined variables and pointers, intents 8202 8203The original names of the patch files are retained for reference. 8204 8205* NAG-01-null.patch -- makes various undefined pointers disassociated 8206(in fft3d.F, dfscf.f, pseudopotential.f, hsparse.f, optical.F, 8207writewave.F and zmatrix) and wraps a pointer declaration that is only 8208used under -DMPI with the ifdef in optical.F. 8209 8210* NAG-02-intent.patch -- attempts to deal with a couple of issues with 8211the intent of variables. Intent(out) results in the variable being 8212undefined at the start of the called subroutine (and in the caller, if 8213it is not changed). In vmb.F there is a call to fixed with a couple of 8214variables being used in two places (on intent(in) and another 8215intent(out)) - I don't know what the strictly correct behavior is in 8216this case, but under NAG this results in the intent(in) variable being 8217undefined in fixed. I've worked around this with a pair temporary 8218variables. The alternative is to rework the interface to fixed using 8219intent(inout). The second issue is similar and in meshsubs.f: Vna 8220ended up undefined if gradient was true. I've dealt with this by 8221setting Vna to 0.0, but a reworking using intent(inout) may also be a 8222better solution. 8223 8224* NAG-03-dhfcs.patch -- deals with a couple of pointers in 8225dhscf.F. These need to have the save attribute or they will be 8226undefined rather than disassociated on the second and subsequent 8227calls. I've also added a comma to a data block. 8228 8229* NAG-04-filter.patch Changes the dimensions of f0 from nr to n so to 8230avoid a mismatch in array dimensions of x in the call to the 8231interpolation function at line 169. As far as I can tell this is the 8232correct fix: yold is known at the xold positions and ynew will be 8233calculated at the xnew positions, so ynew (which is f0) should be of 8234the same dimensions as xnew (which is x), and yold (f) should be of 8235the same dimensions as xold (r). 8236 8237* NAG-05-init -- In dynamics.f initialize magv and magf in the uphill 8238case. In forhar.f initialize stressl array. In m_cell.f initialize 8239celli as it is used in the case of a zmatrix molecule without a cell 8240before the box size is calculated. In m_kinetic.F90 initialize 8241thermostat parameters. 8242 8243 82442008-06-29 22:45:00 GMT Alberto Garcia <albertog@icmab.es> patch-28 8245 8246Summary: Minor cosmetic fixes to avoid compilation warnings 8247 8248* Fix cycle statement in m_denchar_work.f 8249 8250* Fix cycle statements in pdos routines -- warning in atomlwf.F 8251 8252* Some debugging support for KB generation 8253 8254If Atom.Debug.KB.Generation is "true", 'AtomLabel-KBproj'.index 8255files are produced showing the non-interpolated projectors. 8256 8257* Fixes for NAG compiler contributed by Toby White: 8258 8259chempot: intent of mu in numb routine. 8260writewave: remove references to paste routine 8261fft3d.F: explicit array-ness of trigs in calls to setup routines. 8262 82632008-06-29 22:40:00 GMT Alberto Garcia <albertog@icmab.es> patch-27 8264 8265Summary: Fixed bug affecting MP occupation smearing. 8266 8267Fixed a bug (reported by Francois Willaime of CEA/Saclay) 8268which affected calculations in metals using the Hermite-Gauss 8269broadening scheme proposed by Methfessel and Paxton 8270(OccupationFunction MP). 8271 8272The following test on state occupancy was performed: 8273 8274if (qe.gt.occtol) 8275 8276where qe is the state occupancy, and occtol, the tolerance (set to 827710**-12 by default). If one uses the Methfessel-Paxton smearing, qe 8278may take negative values and this test therefore yields wrong results. 8279 8280The bug has be fixed by replacing the test by 8281 8282if (abs(qe).gt.occtol) 8283 8284in all diag*.F routines. 8285 8286 82872008-06-29 18:20:00 GMT Alberto Garcia <albertog@icmab.es> patch-26 8288 8289Summary: Remove residual (k,-k) pairs of k-points 8290 8291The original algorithm sometimes left pairs of k-points related 8292by inversion. A new routine "trim_kpoint_list" in find_kgrid.F 8293now takes care of them. 8294 8295A file NON_TRIMMED_KP_LIST is created with the "raw" list produced 8296by the first part of the process, for debugging purposes. 8297 8298NOTE: Some pairs are *still* not removed properly. A fix is in the works. 8299 8300Credits: Eduardo Machado (CEA) implemented a preliminary version 8301 modifying the original algorithm. 8302 8303* Write KP file unconditionally (regardless of WriteKpoints setting) 8304 83052008-06-29 18:15:00 GMT Alberto Garcia <albertog@icmab.es> patch-25 8306 8307Summary: Assorted geometry-related cosmetic fixes 8308 8309* Do not pretend to update zmatrix info during MD runs 8310 8311The zmatrix form of structural information is only kept up 8312to date when performing geometry relaxations. In molecular 8313dynamics runs, only the cartesian coordinates are updated, and 8314the zmatrix variables are kept frozen at their initial values. 8315 8316This is potentially confusing, so a warning is now issued and 8317the zmatrix "updates" are no longer printed. 8318 8319* Fix shape script in Utils/MD 8320 8321* Compute bond information for all server steps 8322 8323 If the server option is used, the program will compute the bond-length 8324 information at every step. 8325 8326 The first file has now extension ".BONDS_INITIAL", and every successive 8327 one, simply ".BONDS". The final one is still "SystemLabel.BONDS_FINAL". 8328 8329* More flexibility and error detection in reading of atomic coordinates 8330 8331(Patch by Andrew Walker) 8332 8333In coor.F, new logic has been implemented to detect malformed input lines 8334in the AtomicCoordinatesAndAtomicSpecies block. As a by-product, comments 8335and blank lines can now be present in the block. 8336 8337 8338(Unrelated) 8339 8340* Temporarily move xml-pseudopotential to xmlparser directory 8341 The file is not ready for production, but could interfere with the 8342 automatic dependency analysis. 8343 83442008-06-29 17:45:00 GMT Alberto Garcia <albertog@icmab.es> patch-24 8345 8346Summary: Generalized SCF convergence criteria. Optional enforcement 8347 8348New criterion for SCF convergence based on the Harris energy. This 8349is useful if only energies are needed, as the Harris energy tends 8350to converge faster than the Kohn-Sham energy. 8351 8352This new criterion joins the two already implemented: 8353 8354- The standard criterion is based on the convergence of the density 8355matrix, with the relevant parameter being DM.Tolerance. 8356 8357- Optionally, one can require that the total energy changes are 8358also below a prescribed tolerance: 8359 8360DM.RequireEnergyConvergence T 8361 8362In this case, DM.EnergyTolerance is the total-energy tolerance 8363 8364The new criterion is requested by 8365 8366DM.RequireHarrisConvergence T 8367 8368DM.HarrisTolerance is the harris-energy tolerance (default 1e-4 eV) 8369 8370(Note that DM convergence is not needed in this case). 8371 8372The user is responsible for using the correct energies in further 8373processing, e.g., the Harris energy if the Harris criterion is used. 8374 8375To help in basis-optimization tasks, a new file BASIS_HARRIS_ENTHALPY 8376is provided, holding the same information as BASIS_ENTHALPY but using 8377the Harris energy instead of the Kohn-Sham energy. 8378 8379 8380The energy criteria are implemented using "convergers", new objects 8381defined and implemented in m_convergence.f90. It is probably overkill 8382as of now, but it can be enhanced to provide new functionality. 8383 8384 8385* Added Andrew Walker's patch for convergence enforcement 8386 8387If the fdf symbol SCFMustConverge is set to 'true', the program will abort 8388if convergence is not achieved after the specified number of iterations 8389(set with MaxSCFIterations, or currently 50 by default). 8390 8391* Added explicit support for flush and abort for gfortran in pxf.F 8392 83932008-06-29 17:30:00 GMT Alberto Garcia <albertog@icmab.es> patch-23 8394 8395Summary: Patch by Andrew Walker for maximum wall-clock time 8396 8397If MaximumWallClockTime is set (to a time specification of 8398the form 8399 8400 15 s 8401 7 mins 8402 2 hours 8403 3 days 8404 ... ) 8405 8406the program will abort if the specific wall-time is exceeded. 8407The checks are done with the granularity of the calls to 'timer' (i.e., 8408there might be some slack). If the maximum time is 0 (the default), or is 8409negative, the time is unlimited. 8410 8411 8412* Added -DFC_HAVE_FLUSH -DFC_HAVE_ABORT to the gfortran*.make files 8413 84142008-06-29 16:30:00 GMT Alberto Garcia <albertog@icmab.es> patch-22 8415 8416Summary: Integration of new STM-images code. Better makefiles. 8417 8418Util/STM/ol-stm contains the code by Pablo Ordejon and Nicolas Lorente 8419that implements the Tersoff-Hamann approximation to STM images, with a 8420previous step of extrapolation of wave functions from a reference 8421plane. It is thus more accurate than the simple code to be found now 8422in Util/STM/simple-stm. 8423 8424Note that for now the fftw3 library needs to be available for this 8425code to work. 8426 8427Bug fixes found upon integration: 8428 8429- Bug fix in Util/STM/ol-stm/Src/extrapol.f: the interpretation of the 8430layout of the lattice vectors in the "cell" array was wrong. 8431 8432- fftw3 "estimation" call moved outside a loop in extrapol.f (there is 8433more scope for optimization here). 8434 8435* The makefiles for several utilities have been streamlined, 8436and the compilation of the ol-stm program uses a VPATH 8437functionality to avoid duplicating code in the top-level 8438Src directory. The old neighb/ranger routines are retained for now. 8439 8440Some changes were needed to implement this correctly: 8441 8442iodm.F: 8443 8444- Removed support for old-style control files. 8445- Wrapping of LocalToGlobalOrbital call in iodm.F in a MPI preprocessor block. 8446 8447spher_harm.f: Used dot_product instead of ddot. 8448 8449* Other changes: 8450 8451Src/Sys/cscs-ibm-blanc.make: netcdf compilation. 8452Util/Grid/makefile: more targets, FC_SERIAL support. 8453Util/Macroave/Src/Makefile: FC_SERIAL support. 8454 8455Fix for Finisterrae .make file and .sge script in Tests/Scripts. 8456 84572008-06-29 15:30:00 GMT Alberto Garcia <albertog@icmab.es> patch-21 8458 8459Summary: A faster diagk with eigenvector storage 8460 8461The new k-point-mode diagonalization routine diagk_file stores 8462the eigenvectors on file to avoid re-computation after fermi-level 8463determination. The file is in netCDF form, allowing a more 8464flexible dispatching of eigenvectors to and from the master node. 8465(At the time of building the new density matrix, the eigenvectors 8466are read by and transferred from the root node in blocks.) 8467 8468This routine should be very useful for relatively large systems, but 8469the speedup is noticeable for all but the very small. 8470 8471In order to use the new routine, netCDF support should be compiled in, 8472and the symbol UseNewDiagk must be set to "true" in the fdf 8473file. Specifying a number of eigenvectors to store is possible through 8474the symbol NumberOfEigenstates. Note that for now, for safety, all 8475eigenvectors for a given k-point and spin are computed by the 8476diagonalization routine, but only that number specified by the user 8477are stored. If they are insufficient, the program stops. A rule of 8478thumb to select the number of eigenvectors to store is to count the 8479number of electrons and divide by two, and then apply a "safety 8480factor" of around 1.1-1.2 to take into account fractional occupations 8481and band overlaps. 8482 8483A new file "OCCS" is produced with information about the number of 8484states occupied. 8485 8486Note that this routine is NOT yet set up to be used for band-structure 8487computations, or to "write out" wavefunctions. It should only be used 8488in the SCF loop, i.e., from routine "diagon". 8489 8490The old diagk routine is kept, for use in smaller systems and to be 8491called from driver routines which provide other functionality. 8492 8493The size of the transfer block is set to n_eigenvectors/Nodes (note 8494that the user is responsible for setting n_eigenvectors). The loops in 8495the density-matrix building section have been rearranged. Now each DM 8496scan loop (with potential inefficiencies for indirection) has more 8497work to do, and it is no longer cost-effective to fill the dense 8498matrices Dk and Ek first. 8499 8500The size of the block could in principle be increased for free to 8501Min(no_l), and psi_block made into a pointer to Haux. Preliminary 8502tests seem to indicate a lower performance, however (?). 8503 8504To Do: 8505 8506Clarify the use of work arrays. Haux and Saux should probably be allocated 8507inside the diagonalization routines, and not in diagon. 8508 8509 8510* The timing sections have been split into "build HS", "eigenvalues/eigenvectors" 8511and "buildD" components. 8512 85132008-06-29 13:30:00 GMT Alberto Garcia <albertog@icmab.es> patch-20 8514 8515Summary: NetCDF I/O of Grid magnitudes. Density re-starts 8516 8517New module iogrid_netcdf implements a general-purpose dumper 8518of grid magnitudes in netCDF format. If netCDF support is 8519enabled, files with extension .grid.nc are produced for 8520whatever grid magnitude is requested to be saved (charge density 8521(Rho), deformation density (DeltaRho), potential, etc). 8522 8523The use of grid descriptors for each node and the addressable netCDF 8524file format greatly simplify the communication needs for the 8525output of grid variables. 8526 8527Module iogrid_netcdf implements a "grid descriptor calculator" for 8528the standard uniform distribution, but the routine which outputs 8529grid functions is in principle able to work with any distribution. 8530 8531Util/Grid contains new utilities for conversion and analysis 8532of the .grid.nc files. 8533 8534If the keywords SCF.Read.Charge.NetCDF or 8535SCF.Read.Deformation.Charge.NetCDF are true, the charge density 8536(respectively the deformation charge density) is read from file 8537Rho.IN.grid.nc (respectively DeltaRho.IN.grid.nc). 8538 8539This feature allows the easier re-use of electronic-structure 8540information from a previous run. It is not necessary that the basis 8541sets are "similar" (a requirement if density-matrices are to be read 8542in). The deformation charge is particularly useful to give a good 8543starting point for slightly different geometries. 8544 8545To Do: 8546 8547- Improve the handling of possibly conflicting features, such as the 8548use of the Harris functional or the mixing of the DM after the first 8549iteration. 8550 8551- Extend the flexibility of the reading options (to use them, for 8552example, in molecular dynamics or phonon calculations). Currently the 8553density is only read once, at the beginning of the run. 8554 8555- Support reading of charge densities in FFT boxes of different sizes 8556 (via resampling). Auxiliary code for this is in Util/Grid/cdf_fft.f90. 8557 8558 8559- References to the NetCDF directory under Src and to NETCDF_INTERFACE 8560 in the Makefile have been removed. 8561 8562 8563IMPLEMENTATION NOTES: 8564 8565The grid magnitudes are stored in single precision in the .grid.nc files. 8566 8567 8568* Added .make and script file for Finisterrae at CESGA 8569 8570 85712008-06-29 13:00:00 GMT Alberto Garcia <albertog@icmab.es> patch-19 8572 8573Summary: Bug fix in grid2val. Added permute program to Macroave suite. 8574 8575* Fix bug in grid2val (utility to compute values of grid functions 8576 at arbitrary points). 8577 8578The cell vectors were declared as single precision, while in fact they 8579are stored as double precision by Siesta. 8580 8581Added also tips on compilation. 8582 8583* Added permute.F program to Macroave suite 8584 8585Sometimes it is useful to have "x" as the direction perpendicular to 8586the slab. Macroave is hard-wired to work with "z", so the program 8587"permute.F" has been written to carry out a preliminary rotation of 8588the axes in the grid file. 8589 8590Streamlined the compilation steps in Util/Macroave/Src. 8591 85922008-06-29 12:50:00 GMT Alberto Garcia <albertog@icmab.es> patch-18 8593 8594Summary: NetCDF I/O for DM, H, and S 8595 8596Experimental support for DM output in netCDF form, optionally with 8597complete history of a SCF cycle. 8598 8599The netCDF format allows for flexible and portable I/O, and supports 8600the extension of arrays into a "time-record" dimension. 8601 8602A DM-only netCDF file (DM.nc) with the same information as the 8603traditional DM file is created if Write.DM.NetCDF is 'true' (default 8604with netCDF support). In this case, the DM values are written in 8605routine mixer (as is common practice in Siesta, despite the fact that 8606the resulting DM does not correspond to the last electronic structure 8607computed). 8608 8609If WriteDMHS.NetCDF is true (default with netCDF support), a DMHS.nc 8610file containing the overlap matrix S, DM_in, H, and DM_out is written 8611to in compute_dm, right after the computation of DM_out. 8612 8613The default in both cases is not to use the optional time dimension 8614and overwrite the previous SCF step's information. 8615To keep the whole history of (the last) SCF cycle, use 8616WriteDM.History.NetCDF or WriteDMHS.History.NetCDF, respectively. 8617The DMHS history might be useful to diagnose SCF convergence issues. 8618(See new test Test/h2o_netcdf) 8619 8620With the new DM to netCDF (dm2cdf) and netCDF to DM (cdf2dm) converters in 8621the Util/DensityMatrix directory, the information in the .nc files can be easily converted 8622to and from the legacy DM format, allowing the re-use of DM information 8623in computers with incompatible floating point formats. 8624 8625Util/SCF/dm.py is a simple example of processing of netCDF with a Python script. 8626 8627To use the netCDF functionality, Siesta must have been compiled with 8628the appropriate netCDF libraries. Example .make files can be found in 8629the Src/Sys directory (notably gfortran-netcdf.make and 8630marenostrum-mpi-netcdf-XX.make files). 8631 8632The .nc files can also be displayed with the shell utility "ncdump", 8633installed by default when the netCDF library is compiled. 8634 8635 8636IMPLEMENTATION NOTES: 8637 8638- The DM, H, and S information is stored in the .nc files in *single precision*. 8639To change this in the future, an fdf symbol might be used to trigger the replacement 8640of "float" by "double" in the definition of the variables in the netCDF files. Care 8641should be taken to adapt all the other utilities. Single precision seems to be 8642perfectly adequate, however. 8643 8644- No attempt has been made to optimize the memory use or allocation/deallocation 8645 overhead, giving priority to clarity. The netCDF format allows a huge simplification 8646of the MPI communications involved in the I/O, so this is a minor issue. 8647 8648- The functionality is included in the iodm_netcdf.F90 and iodmhs_netcdf.F90 files. 8649 The new flags are stored and processed in the siesta_options.F90 module. 8650 86512008-05-06 12:30:00 GMT Alberto Garcia <albertog@icmab.es> patch-17 8652 8653Summary: Update of atom to 3.2.8: xml, optimization hooks, tutorial update. 8654 8655* Integrated Javier Junquera's XML-generating routines 8656 Added pseudoXML.f and supporting files. 8657 (Note that the XML support in Siesta itself is not yet implemented, 8658 pending retroffiting of the VCA and other enhancements. The relevant 8659 files have been put in a new directory 'Src/pseudo-xml'. 8660 8661* Write pseudo wavefunctions in PSWFFMT 8662 8663* Updated version.h to include the variable "atom_id", now used 8664 in various places to set the creator string. 8665 8666* A simpler makefile has been written when XML support is not needed 8667so that no symbols from the main Siesta directory need to be 8668included. The full makefile is called makefile-xml. To use it it is 8669only necessary to have built libwxml.a in the Src hierarchy of Siesta 8670(after creating the necessary arch.make) 8671 8672* ATOM now recognizes the FREE_FORMAT_RC_INPUT directive, useful 8673for optimization runs. 8674 8675* A new estimation of ps hardness (qmax) is written to FOURIER_QMAX file. 8676 8677* The fourier area calculation has been moved to the "down" section, 8678since the "up" potentials are not always generated. 8679 8680* Avoid very small numbers that might need a three-character 8681exponent field in formatted output. 8682 8683* The Tutorial has been brought up to date, using the version employed 8684in the latest Siesta schools. Note that the location of the 8685scripts used to run the examples has changed. They are now in the 8686Pseudo/atom/Tutorial/Utils directory. 8687 8688* Extended the periodic-table structures in input.f and nucl_z.f 8689 8690 86912008-05-06 10:30:00 GMT Alberto Garcia <albertog@icmab.es> patch-16 8692 8693Summary: Make the production of small ionic files optional -- fdf.log 8694 8695* Files with prefix ORB, KB, CHCORE, SPLIT_SCAN, etc, and 8696pseudopotential dump files, which are useful for plotting basis 8697orbitals and other ion-related information, are now optional. To 8698create them, the user should set 8699 8700 WriteIonPlotFiles T 8701 8702in the fdf file. 8703 8704Note that the same functionality is available in gen-basis. 8705 8706The corresponding option variable "write_ion_plot_files" is now kept 8707in an "atom-specific" options module, to avoid a dependency cascade. 8708 8709* Fixed the makefile sections for some auxiliary programs. 8710 8711* The file "out.fdf" has been renamed to "fdf.log" 8712 87132008-04-08 16:30:00 GMT Alberto Garcia <albertog@icmab.es> patch-15 8714 8715Summary: Implemented a Grimme-type molecular-mechanics potential for dispersion effects 8716 8717A dispersion potential of the Grimme type (similar to the C6 type but 8718with a different damping function) has been implemented. See 8719S. Grimme, J. Comput. Chem. Vol 27, 1787-1799 (2006)). 8720 8721The parameters are specified in the MM.Potentials block, using the 8722"Grimme" keyword. 8723 8724Hooks for changing the "d" and "s6" parameters are provided 8725(MM.Grimme.D and MM.Grimme.S6). 8726 8727A minor cosmetic addition: the kind of molecular mechanics potential 8728between species is now printed upon encoutering the relevant line in 8729the block. 8730 87312008-04-08 15:00:00 GMT Alberto Garcia <albertog@icmab.es> patch-14 8732 8733Summary: Changes for portability and cosmetics 8734 8735Portability: 8736 8737 * Use character(*) in MPI character modules. 8738 8739 Previously character(1) was used, leading to complaints by some compilers. 8740 8741Usability: 8742 8743 * Extra fdf symbol for struct_file input specification 8744 8745 The manual mentions "Use.Struct.File" as the relevant alias, but 8746 the code used "MD.Use.Struct.File". Both are now accepted. 8747 8748Makefile and makefile templates: 8749 8750 * Fix mixps section in Makefile 8751 * Add .make file for snake at ICMAB 8752 * Fix tabs in eth-hreidar-mpi.make 8753 87542008-03-08 23:56:00 GMT Alberto Garcia <albertog@icmab.es> patch-13 8755 8756Summary: Remove 'multiple images' warning in gamma-point-only calculations 8757 8758The calculation of the xij array (vector distances to interacting 8759neighbors) was enabled in 2.5.1 also for the case of gamma-point-only 8760calculations. This is needed for the post-processing of COOP curves. 8761In a gamma-point-only calculation several atoms might still 8762see images of themselves as interacting if the cell is not that 8763big. The xijorb code warned about that, even though the calculation of 8764the matrix elements is of course correct, as k=0 and there are no 8765phase factors to worry about. The warning has been now turned off. 8766 87672008-03-08 23:55:00 GMT Alberto Garcia <albertog@icmab.es> patch-12 8768 8769Summary: Fix the constraint of static C.M. in initial velocities 8770 8771Routine vmb sets the initial velocities according to an approximate 8772Maxwell-Boltzmann distribution, with the extra constraint of static 8773center of mass. Due to an oversight, the routine only enforced this 8774constraint for the case of a single species. It has been fixed. 8775 87762008-01-11 16:25:00 GMT Alberto Garcia <albertog@icmab.es> patch-11 8777 8778Summary: Proper fix of cell management for zmatrix case. Enthalpy cosmetics 8779 8780A recent previous patch (8) broke the unit cell handling in the zmatrix case. 8781It has been fixed. 8782 8783The assorted "enthalpy" output has been rationalized, 8784reserving the use of the word "enthalpy" for the original case 8785of "target enthalpy". 8786 8787(Fixed syntax error in std-test.mk) 8788 87892008-01-11 14:05:00 GMT Alberto Garcia <albertog@icmab.es> patch-10 8790 8791Summary: Make diagonalization the default solution method regardless of size 8792 8793Make diagonalization the default solution method regardless of system size. 8794 87952008-01-11 14:00:00 GMT Alberto Garcia <albertog@icmab.es> patch-9 8796 8797Summary: Fix test.mk scripts 8798 8799The std-test.mk script did not copy the output file to the main test directory. 8800The bsc-test.mk did not remove all the scratch files. 8801 8802Fixed a typo in the input to the si2x1h test. 8803 88042008-01-11 13:55:00 GMT Alberto Garcia <albertog@icmab.es> patch-8 8805 8806Summary: Fix for structural supercell construction 8807 8808Due to the accidental mis-use of a module variable, the routine coor 8809did not generate the supercell correctly when a %supercell block was used. 8810 8811Added and additional warning if such a block is used when the structure is 8812input in Zmatrix form. 8813 88142007-12-17 14:25:00 GMT Alberto Garcia <albertog@icmab.es> patch-7 8815 8816Summary: Fix memory leak in dhscf 8817 8818The array dvxcdn was allocated but never deallocated in dhscf. Actually, 8819it was never used in cellxc, so it has now been dimensioned trivially 8820to (1,1,1). The bug was introduced in the bsc-master-2.1 branch, at 8821patch 27. 8822 88232007-11-22 18:45:00 GMT Alberto Garcia <albertog@icmab.es> patch-6 8824 8825Summary: New 'fdf' target in Makefile for tests 8826 8827(E. Anglada) 8828 8829New target for the test option: fdf calls. 8830Requested by BSC so they can test the new fdf. 8831 8832New files (new tests and missing xml output files for reference) 8833A/ Tests/var_cell_stress 8834A Tests/Reference-xml/fire_benzene.xml 8835A Tests/Reference-xml/si_coop.xml 8836A Tests/var_cell_stress/.arch-ids/=id 8837A Tests/var_cell_stress/.arch-ids/makefile.id 8838A Tests/var_cell_stress/.arch-ids/var_cell_stress.fdf.id 8839A Tests/var_cell_stress/.arch-ids/var_cell_stress.pseudos.id 8840A Tests/var_cell_stress/makefile 8841A Tests/var_cell_stress/var_cell_stress.fdf 8842A Tests/var_cell_stress/var_cell_stress.pseudos 8843 8844 8845Modified files 8846M Src/siesta_move.F : remove debug info 8847M Src/remove_intramol_pressure.f90 : remove debug info 8848M Tests/std-Makefile Xmlcheck enabled by default. New targets: fdf, all 8849M Tests/std-test.mk 8850M Tests/si2x1h/si2x1h.fdf New option 8851M Src/atom.f Remove debug info. 8852 88532007-11-22 18:30:00 GMT Alberto Garcia <albertog@icmab.es> patch-5 8854 8855Summary: xml tester update (Eduardo Anglada) 8856 8857New files: 8858A Src/xmlparser/corresponding_node.f90 8859A Src/xmlparser/string_utilities.f90 8860 8861Changes in the xml output: 8862M Src/state_analysis.F 8863M Src/siesta_move.F 8864M Src/setup_hamiltonian.F 8865M Src/siesta_forces.F 8866M Src/scfconvergence_test.F 8867M Src/post_scf_work.F 8868 8869Changes in the xml tester: 8870M Src/wxml/m_wxml_core.f90 8871M Src/wxml/flib_wstml.f90 8872M Src/xmlparser/makefile 8873M Src/xmlparser/m_dom_element.f90 8874M Src/xmlparser/m_strings.f90 8875M Src/xmlparser/compare_m.f90 8876M Src/xmlparser/test.f90 8877 8878Changes in the tests makefiles 8879M Tests/std-Makefile 8880M Tests/std-test.mk 8881 8882Upgraded xml reference outputs: 8883... 8884 88852007-11-22 17:55:00 GMT Alberto Garcia <albertog@icmab.es> patch-4 8886 8887Summary: Fixes for denchar compilation and wavefunction output 8888 8889* The makefile section for denchar had several errors. 8890 8891* siesta_analysis used maxwk as a local variable, instead of importing 8892 it from writewave, thus preventing the call to wwave from working. 8893 8894* (NOTE: the need for a lattice constant or cell vectors in the fdf file 8895 if the wavefunctions need to be output should be removed) 8896 88972007-11-22 17:45:00 GMT Alberto Garcia <albertog@icmab.es> patch-3 8898 8899Summary: Fixed computation of chemical potential in O(N) (P.Ordejon) 8900 8901* Chempot, rather than updated, has been substituted by the version 8902in the "cecam" branch of the 2.0 fixes branch. However, some constructions 8903have been updated to the post-BSC-cleaning structure: 8904 8905- Use of the smarter mneighb routine. 8906- Some arrays are now pointers instead of allocatables. 8907 8908* A new test (Tests/h2o_4) has been added. 8909 8910* NOTE that the new code does not yet work in Parallel. 8911 89122007-11-22 17:40:00 GMT Alberto Garcia <albertog@icmab.es> patch-2 8913 8914Summary: Optimization enhancements (fire algorithm, step control). 8915 8916 8917* Step-size control has been add to the Broyden optimizers (Standard, ZM, 8918 and Cell-only). There is no theoretical justification for this procedure, 8919 so the Hessian is not likely to improve very much... it is probably best 8920 to combine a size-limited CG series with another small-Jinv Broyden series. 8921 8922* New FORCE_STRESS for direct output of the energy, forces, and stress 8923 (in internal Siesta units). 8924 8925* Re-implemented the FIRE optimization algorithm, both for geometry 8926 and (experimentally) for SCF. 8927 8928 The advantages for the SCF mixing are: 8929 8930 * Trivial algorithm (also in parallel) 8931 * Initial dt can be just set to alpha. 8932 * Adaptive changes to alpha. 8933 * There should be no need for kicks. 8934 8935 (Set DM.FIRE.Mixing to T to enable) 8936 Could also set DM.Fire.Nmin to 2, 3, 4 instead of the default 5 8937 (Actually, this number could be akin to the DM.Number{Pulay,Broyden}...) 8938 8939* Added .make files for opterons and matgas cluster at ICMAB in parallel. 8940 8941* Compilation fixes(uncovered by a new version of g95) 8942 8943 * External statements referring to obsolete names 8944 * Continuation lines. 8945 * Statement order. 8946 8947 89482007-11-22 17:35:00 GMT Alberto Garcia <albertog@icmab.es> patch-1 8949 8950Summary: Merged COOP/COHP functionality 8951 8952Merged the COOP/COHP/PDOS code from the 2.1 branch complex. 8953 8954¡-- Functionality changes: 8955 8956* The wavefunction file is now in WFSX format (well-packed, single-precision, and thus 8957significantly smaller). The Util/wfsx2wfs program can be used to re-generate the old format. 8958 8959* The xijo array (for relative positions between interacting orbitals) is always produced. 8960 8961-- New features: 8962 8963Option COOP.Write triggers the creation of a wavefunction file (for the SCF-k-point set) 8964and an HSX file (enhanced HS format) that can later be processed by Util/COOP/mprop 8965for the off-line generation of COOP/COHP/(P)DOS. 8966 8967 8968____________________________________________________________________ 8969** CHANGES ALONG siesta@uam.es--2006/siesta-devel--reference--2.3 8970-------------------------------------------------------------------- 8971 89722007-11-22 17:30:00 GMT Alberto Garcia <albertog@icmab.es> patch-2 8973 8974Summary: Add a proper account of the BSC changes that went into the merge 8975 8976In the Docs/CHANGES file, a new section detailing the changes made 8977along the BSC branches has been prepared, and the history of the 8978reference--2.1 branch after the branching has been reinstated. 8979The BSC section is in chronological order, to ease the understading. 8980 8981 89822007-11-21 10:30:00 GMT Alberto Garcia <albertog@icmab.es> patch-1 8983 8984Summary: Direct merge into master branch of initial BSC changes 8985 8986The changes along the BSC branches, up to the end of the restructuring 8987of siesta.F and associated changes, have been merged into a direct 8988descendant of the main development line. The BSC work originally 8989started as a branch of siesta-devel--reference--2.1--patch-29. Development 8990along 2.1 continued, and a new continuation branch 2.3 has been created 8991specifically for this merge. 8992 8993A description of the changes along the BSC branches follows, in 8994chronological order. To re-take the history of the 2.1 branch before 8995the merge, search for "2.1-before-BSC-merge" forward. 8996 8997==================================================== 8998*** BSC-Changes from January 2007 up to the merge into reference--2.3 8999 in November 2007 (initial restructuring). 9000==================================================== 9001 9002Revision: siesta-bsc--reference--2.1--patch-1 9003Archive: siesta@uam.es--2006 9004Creator: Alberto Garcia <albertog@icmab.es> 9005Date: Thu Jan 25 14:17:04 CET 2007 9006Standard-date: 2007-01-25 13:17:04 GMT 9007New-files: Src/.arch-ids/compute_dm.F.id 9008 Src/.arch-ids/mixer.F.id 9009 Src/.arch-ids/post_scf_work.F.id 9010 Src/.arch-ids/scfconvergence_test.F.id 9011 Src/.arch-ids/setup_hamiltonian.F.id 9012 Src/.arch-ids/siesta_analysis.F.id 9013 Src/.arch-ids/siesta_end.F.id 9014 Src/.arch-ids/siesta_init.F.id 9015 Src/.arch-ids/siesta_move.F.id 9016 Src/.arch-ids/siesta_todo.F.id 9017 Src/.arch-ids/state_init.F.id 9018 Src/Sys/.arch-ids/marenostrum-mpi.make.id 9019 Src/Sys/marenostrum-mpi.make Src/compute_dm.F 9020 Src/mixer.F Src/post_scf_work.F 9021 Src/scfconvergence_test.F Src/setup_hamiltonian.F 9022 Src/siesta_analysis.F Src/siesta_end.F Src/siesta_init.F 9023 Src/siesta_move.F Src/siesta_todo.F Src/state_init.F 9024 Tests/.arch-ids/bsc-Makefile.id 9025 Tests/.arch-ids/bsc-test.mk.id 9026 Tests/.arch-ids/compara.id 9027 Tests/.arch-ids/compare.sh.id 9028 Tests/Reference/.arch-ids/force_constants.out.id 9029 Tests/Reference/force_constants.out Tests/bsc-Makefile 9030 Tests/bsc-test.mk Tests/compara Tests/compare.sh 9031 Tests/force_constants/.arch-ids/=id 9032 Tests/force_constants/.arch-ids/FC.fdf.id 9033 Tests/force_constants/.arch-ids/force_constants.fdf.id 9034 Tests/force_constants/.arch-ids/force_constants.pseudos.id 9035 Tests/force_constants/.arch-ids/makefile.id 9036 Tests/force_constants/FC.fdf 9037 Tests/force_constants/force_constants.fdf 9038 Tests/force_constants/force_constants.pseudos 9039 Tests/force_constants/makefile 9040New-directories: Tests/force_constants 9041 Tests/force_constants/.arch-ids 9042Modified-files: Src/Makefile Src/siesta.F Src/version.F90 9043 version.info 9044New-patches: siesta@uam.es--2006/siesta-bsc--reference--2.1--patch-1 9045Summary: First stage of siesta.F splitting at BSC 9046Keywords: 9047 9048The first coding session at BSC on January 19, 2007 resulted in a first 9049splitting of siesta.F into blocks. 9050 9051A new module "siesta_todo.F" was created holding most of the variables 9052declared in siesta.F, as well as all the 'use' statements. External 9053subroutines are kept for now in siesta.F. "siesta_todo.F" also 9054contains the output routines which were formerly internal routines of 9055the main program. 9056 9057Several new files were created: 9058 9059siesta_init 9060 state_init 9061 setup_hamiltonian 9062 compute_dm 9063 mixer 9064 scfconvergence_test 9065 post_scf_work 9066 siesta_move 9067siesta_analysis 9068siesta_end 9069 9070siesta.F is now much smaller, and has calls to those routines plus 9071the minimum logic to control the geometry and scf loops. No attempt 9072has been made to tidy up any of the blocks yet. 9073 9074The scf loop has been re-structured to separate the "last" pass which 9075was performed after scf convergence. Some more work is needed to 9076clarify the behavior in borderline and non-standard cases. 9077 9078The Makefile was updated. 9079 9080Added new file Src/Sys/marenostrum-mpi.make. 9081 9082Added new file Tests/compare.sh to automate comparisons with reference 9083output (works best if the reference output is from the same platform, 9084to avoid rounding differences). 9085 9086Added new test Tests/force_constants to exercise the idyn=6 code. 9087 9088Revision: siesta-bsc--reference--2.1--patch-2 9089Archive: siesta@uam.es--2006 9090Creator: Alberto Garcia <albertog@icmab.es> 9091Date: Wed Jan 31 11:06:37 CET 2007 9092Standard-date: 2007-01-31 10:06:37 GMT 9093New-files: Src/.arch-ids/struct_init.F.id Src/struct_init.F 9094 Tests/Reference/.arch-ids/force_2.out.id 9095 Tests/Reference/force_2.out Tests/force_2/.arch-ids/=id 9096 Tests/force_2/.arch-ids/FC.fdf.id 9097 Tests/force_2/.arch-ids/force_2.fdf.id 9098 Tests/force_2/.arch-ids/force_2.pseudos.id 9099 Tests/force_2/.arch-ids/makefile.id 9100 Tests/force_2/FC.fdf Tests/force_2/force_2.fdf 9101 Tests/force_2/force_2.pseudos Tests/force_2/makefile 9102New-directories: Tests/force_2 Tests/force_2/.arch-ids 9103Modified-files: Src/Makefile Src/atomlist.f Src/initatom.f 9104 Src/redata.F Src/siesta_init.F Src/siesta_todo.F 9105New-patches: agarcia@siesta.arch--2006/siesta-bsc--agarcia--2.1--patch-1 9106 agarcia@siesta.arch--2006/siesta-bsc--agarcia--2.1--patch-2 9107 siesta@uam.es--2006/siesta-bsc--reference--2.1--patch-2 9108Summary: Created struct_init for initial geometry setup. New test force_2 9109Keywords: 9110 9111Struct_init has been detached from siesta_init to perform a self-contained 9112geometry setup. 9113 9114Notes: 9115 9116* Ns is now set in initatom, and it is "intent(in)" in redata. 9117 9118* Those variables which have to do with structural input 9119are read twice: once in struct_init, and then in redata, pending a 9120re-structuring of the latter. In some cases local variables are 9121used. 9122 9123* iza is still set up in initatomlists. This means that some of the 9124structural output has to be kept in siesta_init for now. The fix is to 9125compute iza in coor or in read_struct. 9126 9127* va and vcell are zeroed out if an XV file is not used. But the 9128zmatrix i/o routine is in principle able to read vcell (?). 9129 9130* Put the calls to struct_init and initatomlists closer. 9131Do the array initialization inside of initatomlists. 9132 9133New test "force_2" for force-constant calculation with a smaller 9134runtime than "force_constants" 9135 9136(Note: the initial coordinate output and other details are now output 9137in a different order from that in the base version) 9138 9139Revision: siesta-bsc--reference--2.1--patch-3 9140Archive: siesta@uam.es--2006 9141Creator: Alberto Garcia <albertog@icmab.es> 9142Date: Wed Jan 31 11:11:28 CET 2007 9143Standard-date: 2007-01-31 10:11:28 GMT 9144New-files: Src/.arch-ids/write_md_record.F.id 9145 Src/write_md_record.F 9146Modified-files: Docs/CHANGES Src/Makefile Src/siesta.F 9147 Src/siesta_init.F Src/siesta_move.F Src/state_init.F 9148 version.info 9149New-patches: agarcia@siesta.arch--2006/siesta-bsc--agarcia--2.1--patch-3 9150 siesta@uam.es--2006/siesta-bsc--reference--2.1--patch-3 9151Summary: Consolidate geometry updates at the end of loop 9152Keywords: 9153 9154* Move comment about start of geometry loop to the right place in 9155 siesta.F 9156 9157* For idyn cases 6 (force constant), 7 (phonon interface), and 8 9158(server calculation), move the coordinate updates from the beginning 9159to the end of the geometry loop. The logic of geometry output to file XV 9160has been maintained. For cases 6 and 7, any output to a MD history file 9161is now done with the current (distorted) coordinates, instead of with 9162the restored (undisplaced) coordinates (bug of original version). 9163 9164Note that the logic of XV output for the true MD cases has been maintained. 9165(next step's geometry, current step's velocities). 9166 9167The MD output (together with any pixmol output) has been encapsulated 9168in a new file write_md_record.F 9169 9170Revision: siesta-bsc--reference--2.1--patch-4 9171Archive: siesta@uam.es--2006 9172Creator: Alberto Garcia <albertog@icmab.es> 9173Date: Wed Jan 31 11:15:47 CET 2007 9174Standard-date: 2007-01-31 10:15:47 GMT 9175Modified-files: Docs/CHANGES Src/m_check_supercell.f 9176 version.info 9177New-patches: agarcia@siesta.arch--2006/siesta-bsc--agarcia--2.1--patch-4 9178 siesta@uam.es--2006/siesta-bsc--reference--2.1--patch-4 9179Summary: Initialize vol2 correctly in m_check_supercell.f 9180Keywords: 9181 9182(This patch is needed so that tests run in a predictable manner: 9183the uninitialized vol2 had an influence on code path and led to 9184erratic differences in outputs). 9185The base version (in siesta-devel--bsc--base--2.1, a branch of 9186siesta-devel--reference--2.1--patch-29) has also been corrected. 9187 9188 9189Revision: siesta-bsc--reference--2.1--patch-5 9190Archive: siesta@uam.es--2006 9191Creator: Alberto Garcia <albertog@icmab.es> 9192Date: Wed Jan 31 11:17:22 CET 2007 9193Standard-date: 2007-01-31 10:17:22 GMT 9194New-files: Src/.arch-ids/kpoint_grid.F90.id 9195 Src/.arch-ids/proximity_check.F.id Src/kpoint_grid.F90 9196 Src/proximity_check.F 9197Modified-files: Docs/CHANGES Src/Makefile Src/bands.F 9198 Src/kgridinit.F Src/siesta_analysis.F Src/siesta_init.F 9199 Src/siesta_todo.F Src/state_init.F version.info 9200New-patches: agarcia@siesta.arch--2006/siesta-bsc--agarcia--2.1--patch-5 9201 siesta@uam.es--2006/siesta-bsc--reference--2.1--patch-5 9202Summary: Kgrid setup streamlined. Bands. Proximity check. Hsparse allocation 9203Keywords: 9204 9205* The kgrid handling is now done through a new module kpoint_grid, which exports 9206the new routine setup_Kpoint_grid, and holds kpoint and other arrays. 9207 9208The kgrid is initialized for the first geometry in siesta_init, and then 9209updated in the geometry loop (the conditions of the update are those of the 9210original reference version: varcel or server calculation) 9211 9212Kgridinit (still outside the new module) has had its nkpnt argument 9213made "intent(out)". 9214 9215* The setup of the band k-points has been moved to a new routine 9216'setup_bands' in module 'band' in file 'bands.F', which also holds 9217now nbk, maxbk, and bk. The setup routine is called right before the 9218band calculation *after* the geometry loop, instead of at the beginning 9219of the run (with the initial geometry). 9220The influence of nbk on 'gamma' has been removed, as it could conflict with 9221the self-consistent calculation. 9222 9223(* The similar Writewave and KSV initializations have not been 9224refactored yet) 9225 9226* The 'proximity check' code has been put into a new subroutine with 9227that name. Some of the local loop variables have been renamed. 9228 9229* After the call to hsparse, the code for allocation of some arrays 9230has been simplified. 9231 9232(This was the end of the second iteration of work at BSC by JMC, MQ, and AG 9233on 30 January). 9234 9235Revision: siesta-bsc--reference--2.1--patch-6 9236Archive: siesta@uam.es--2006 9237Creator: Alberto Garcia <albertog@icmab.es> 9238Date: Wed Feb 7 08:20:02 CET 2007 9239Standard-date: 2007-02-07 07:20:02 GMT 9240New-files: Src/.arch-ids/local_DOS.F.id 9241 Src/.arch-ids/new_dm.F.id 9242 Src/.arch-ids/normalize_dm.F.id 9243 Src/.arch-ids/projected_DOS.F.id Src/local_DOS.F 9244 Src/new_dm.F Src/normalize_dm.F Src/projected_DOS.F 9245Modified-files: Docs/CHANGES Src/Makefile Src/compute_dm.F 9246 Src/mixer.F Src/post_scf_work.F Src/setup_hamiltonian.F 9247 Src/siesta.F Src/siesta_analysis.F Src/siesta_end.F 9248 Src/siesta_init.F Src/siesta_move.F Src/state_init.F 9249 version.info 9250New-patches: mquero@siesta.arch--2006/siesta-bsc--mquero--2.1--patch-2 9251 siesta@uam.es--2006/siesta-bsc--reference--2.1--patch-6 9252Summary: Work by Manuel Quero before the meeting on Feb 7th 9253Keywords: 9254 9255New routines: 9256 9257* new_dm (code formerly in state_init) 9258* normalize_dm (code formerly in setup_hamiltonian) 9259* local_DOS 9260* projected_DOS (code formerly in siesta_analysis) 9261 9262All the new routines split off from siesta.F have been placed in modules. 9263 9264(kgrid and kgridinit are still not in the kgrid module, as they are used 9265in the KSV and optical sections -- more analysis is needed) 9266 9267(Jose Soler's new version of the siesta_todo module is still not used) 9268 9269(Code edited by Alberto Garcia from a package sent by Manuel Quero) 9270 9271 9272Revision: siesta-bsc--reference--2.1--patch-7 9273Archive: siesta@uam.es--2006 9274Creator: Alberto Garcia <albertog@icmab.es> 9275Date: Wed Feb 7 08:28:59 CET 2007 9276Standard-date: 2007-02-07 07:28:59 GMT 9277New-files: Src/.arch-ids/born_charge.F.id Src/born_charge.F 9278 Tests/born/.arch-ids/=id Tests/born/.arch-ids/FC.fdf.id 9279 Tests/born/.arch-ids/born.fdf.id 9280 Tests/born/.arch-ids/born.pseudos.id 9281 Tests/born/.arch-ids/makefile.id Tests/born/FC.fdf 9282 Tests/born/born.fdf Tests/born/born.pseudos 9283 Tests/born/makefile 9284New-directories: Tests/born Tests/born/.arch-ids 9285Modified-files: Docs/CHANGES Src/Makefile Src/siesta_move.F 9286 Tests/Makefile Tests/compare.sh version.info 9287New-patches: agarcia@siesta.arch--2006/siesta-bsc--agarcia--2.1--patch-6 9288 agarcia@siesta.arch--2006/siesta-bsc--agarcia--2.1--patch-7 9289 agarcia@siesta.arch--2006/siesta-bsc--agarcia--2.1--patch-8 9290 siesta@uam.es--2006/siesta-bsc--reference--2.1--patch-7 9291Summary: Moved the Born-effective-charge code 9292Keywords: 9293 9294Created a new module in born_charge.F. 9295 9296The code is now executed by a call to born_charge() right after the 9297end of the force calculation at the end of the geometry loop. There is 9298no need to save xalast for this, as the coordinates have not yet been 9299moved. (Note that KSV_pol is called with xa instead of xalast). 9300 9301Created new test 'born' and updated compare.sh 9302 9303 9304Revision: siesta-bsc--master--2.1--patch-1 9305Archive: ref@bsc--2007 9306Creator: Alberto Garcia <albertog@icmab.es> 9307Date: Thu Feb 8 10:52:48 CET 2007 9308Standard-date: 2007-02-08 09:52:48 GMT 9309New-files: Src/.arch-ids/m_siesta.jose.F.id 9310 Src/m_siesta.jose.F 9311Modified-files: Docs/CHANGES Src/local_DOS.F Src/m_cell.f 9312 Src/siesta.F Src/siesta_analysis.F Src/siesta_move.F 9313 Src/siesta_todo.F version.info 9314New-patches: ag@bsc--2007/siesta-bsc--ag--2.1--patch-2 9315 ref@bsc--2007/siesta-bsc--master--2.1--patch-1 9316Summary: Use of xalast in analysis routines. Exit of geometry loop 9317Keywords: 9318 9319The conditions for the setting and use of xalast have been clarified. 9320 9321The analysis routines (KSVpol, optical, dhscf (in plotting mode), 9322local_DOS) now use the xalast array, which always refers to the atomic 9323positions for which the density matrix was computed at the last 9324geometry iteration performed (i.e., it is set before moving the atoms). 9325 9326For consistency, new arrays ucell_last and scell_last are similarly handled. 9327 9328Apart from those routines, the new setting conditions for xalast affect the 9329computation of the virial correction to the "molecular pressure". 9330 9331In the geometry loop, the ending condition for istep has been 9332corrected: it is not increased if the structure is relaxed. 9333 9334(Work done at BSC in the morning of Feb 7) 9335 9336 9337Revision: siesta-bsc--master--2.1--patch-2 9338Archive: ref@bsc--2007 9339Creator: Alberto Garcia <albertog@icmab.es> 9340Date: Thu Feb 8 11:35:15 CET 2007 9341Standard-date: 2007-02-08 10:35:15 GMT 9342New-files: Src/.arch-ids/siesta_options.F.id 9343 Src/siesta_options.F 9344Removed-files: Src/.arch-ids/m_smearing.f.id 9345 Src/.arch-ids/redata.F.id Src/m_smearing.f Src/redata.F 9346Modified-files: Docs/CHANGES Src/Makefile Src/compute_dm.F 9347 Src/local_DOS.F Src/mixer.F Src/new_dm.F 9348 Src/post_scf_work.F Src/projected_DOS.F 9349 Src/proximity_check.F Src/scfconvergence_test.F 9350 Src/setup_hamiltonian.F Src/siesta.F 9351 Src/siesta_analysis.F Src/siesta_init.F 9352 Src/siesta_move.F Src/siesta_todo.F Src/state_init.F 9353 Src/struct_init.F Src/write_md_record.F version.info 9354New-patches: ag@bsc--2007/siesta-bsc--ag--2.1--patch-3 9355 ref@bsc--2007/siesta-bsc--master--2.1--patch-2 9356Summary: Creation of a module to hold the siesta options 9357Keywords: 9358 9359A new module 'siesta_options' has been created to hold the program 9360options (typically those variables that can be specified in the fdf file). 9361The catch-all module 'siesta_todo' has been slimmed down accordingly. 9362 9363Routine redata has been put in the module, renamed as 'read_options'. 9364 9365A few other option-setting statements in the old siesta.F have been put 9366into read_options. 9367 9368Some others remain scattered: 9369 93701. Those in the Broyden routines. 93712. Those needed to process the initial geometry, read in struct_init. 9372 9373(Work done at the BSC on Feb 7) 9374 9375 9376Revision: siesta-bsc--master--2.1--patch-3 9377Archive: ref@bsc--2007 9378Creator: Alberto Garcia <albertog@icmab.es> 9379Date: Thu Feb 8 11:58:38 CET 2007 9380Standard-date: 2007-02-08 10:58:38 GMT 9381New-files: Src/.arch-ids/siesta_geom.F90.id 9382 Src/siesta_geom.F90 9383Modified-files: Docs/CHANGES Src/Makefile Src/atomlist.f 9384 Src/coor.F Src/diagsprl.F Src/iozm.F Src/local_DOS.F 9385 Src/m_cell.f Src/m_iostruct.f Src/outcoor.f Src/pdos.F 9386 Src/siesta_analysis.F Src/siesta_init.F 9387 Src/siesta_move.F Src/siesta_options.F Src/siesta_todo.F 9388 Src/struct_init.F Src/writewave.F Src/zmatrix.F 9389 version.info 9390New-patches: ag@bsc--2007/siesta-bsc--ag--2.1--patch-4 9391 ref@bsc--2007/siesta-bsc--master--2.1--patch-3 9392Summary: New geometry module 9393Keywords: 9394 9395A new module siesta_geom has been created to hold basic geometry 9396information. 9397 9398Thus the atomic coordinates no longer live in 'atomlists', and the unit 9399cell no longer lives in 'm_cell'. Supercell variables have also be put 9400in the new module. 9401 9402+ Some more slimming down of 'siesta_todo'. 9403 9404Revision: siesta-bsc--master--2.1--patch-4 9405Archive: ref@bsc--2007 9406Creator: Alberto Garcia <albertog@icmab.es> 9407Date: Thu Feb 8 12:15:51 CET 2007 9408Standard-date: 2007-02-08 11:15:51 GMT 9409New-files: Src/.arch-ids/sparse_matrices.F90.id 9410 Src/sparse_matrices.F90 9411Modified-files: Docs/CHANGES Src/Makefile Src/born_charge.F 9412 Src/compute_dm.F Src/local_DOS.F Src/mixer.F Src/new_dm.F 9413 Src/normalize_dm.F Src/post_scf_work.F 9414 Src/projected_DOS.F Src/setup_hamiltonian.F 9415 Src/siesta_analysis.F Src/siesta_init.F 9416 Src/siesta_move.F Src/siesta_todo.F Src/state_init.F 9417 version.info 9418New-patches: ag@bsc--2007/siesta-bsc--ag--2.1--patch-5 9419 ref@bsc--2007/siesta-bsc--master--2.1--patch-4 9420Summary: New stub module for sparse matrices 9421Keywords: 9422 9423A stub module to hold the sparse matrices ('sparse_matrices') has been 9424created. It just holds the relevant variables, without any attempt to 9425create derived types yet. 9426 9427(Work done at BSC in the afternoon of Feb 7) 9428 9429Revision: siesta-bsc--master--2.1--patch-5 9430Archive: ref@bsc--2007 9431Creator: Alberto Garcia <albertog@icmab.es> 9432Date: Fri Feb 9 11:48:32 CET 2007 9433Standard-date: 2007-02-09 10:48:32 GMT 9434New-files: Tests/.arch-ids/bsc-compare.sh.id 9435 Tests/bsc-compare.sh 9436Renamed-files: Tests/.arch-ids/Makefile.id Tests/.arch-ids/std-Makefile.id 9437 Tests/.arch-ids/compare.sh.id Tests/.arch-ids/std-compare.sh.id 9438 Tests/.arch-ids/test.mk.id Tests/.arch-ids/std-test.mk.id 9439 Tests/Makefile Tests/std-Makefile 9440 Tests/compare.sh Tests/std-compare.sh 9441 Tests/test.mk Tests/std-test.mk 9442Modified-files: Tests/README Tests/bsc-Makefile 9443 Tests/bsc-test.mk Tests/std-compare.sh 9444New-patches: ref@bsc--2007/siesta-bsc--master--2.1--patch-5 9445Summary: More options for running tests 9446Keywords: 9447 9448Several versions of Makefile and test.mk are provided in Tests: 9449 9450bsc-Makefile, bsc-test.mk : For BSC work 9451std-Makefile, std-test.mk : Standard, complete versions 9452 9453The user should link the chosen versions to Makefile and test.mk 9454 9455 9456Revision: siesta-bsc--master--2.1--patch-6 9457Archive: ref@bsc--2007 9458Creator: Alberto Garcia <albertog@icmab.es> 9459Date: Fri Feb 16 03:07:23 CET 2007 9460Standard-date: 2007-02-16 02:07:23 GMT 9461New-files: Src/.arch-ids/find_kgrid.F.id 9462 Src/.arch-ids/setup_kscell.F.id Src/find_kgrid.F 9463 Src/setup_kscell.F 9464Removed-files: Src/.arch-ids/repol.F.id Src/repol.F 9465Renamed-files: Src/.arch-ids/ksvinit.f.id Src/.arch-ids/ksvinit.F.id 9466 Src/ksvinit.f Src/ksvinit.F 9467Modified-files: Src/Makefile Src/bands.F Src/born_charge.F 9468 Src/dhscf.F Src/diagg.F Src/diagk.F Src/fermid.F 9469 Src/kpoint_grid.F90 Src/ksv.f Src/ksvinit.F 9470 Src/siesta_analysis.F Src/siesta_init.F 9471 Src/siesta_todo.F Src/state_init.F Src/writewave.F 9472 Tests/born/born.fdf 9473New-patches: ag@bsc--2007/siesta-bsc--ag--2.1--patch-7 9474 ag@bsc--2007/siesta-bsc--ag--2.1--patch-8 9475 ag@bsc--2007/siesta-bsc--ag--2.1--patch-11 9476 ag@bsc--2007/siesta-bsc--ag--2.1--patch-12 9477 ag@bsc--2007/siesta-bsc--ag--2.1--patch-13 9478 ref@bsc--2007/siesta-bsc--master--2.1--patch-6 9479Summary: Encapsulation of k-point handling 9480Keywords: 9481 9482The different k-point grids now live in different modules, 9483and are set up (or their size estimated) early in siesta_init. 9484 9485The scf kgrid has its own module, kpoint_grid, and a more 9486sophisticated (but equivalent) logic inside. (Except for a cosmetic 9487change when the auxiliary k-point supercell is the trivial one but 9488with permuted rows). 9489 9490The others, notably the polarization grid, are just 9491encapsulated, without much change. 9492 9493Patches applied: 9494 9495 * ag@bsc--2007/siesta-bsc--ag--2.1--patch-7 9496 New utilities for scf kgrid construction 9497 9498 * ag@bsc--2007/siesta-bsc--ag--2.1--patch-8 9499 Fix use of uninitialized maxk 9500 9501 * ag@bsc--2007/siesta-bsc--ag--2.1--patch-11 9502 Move band initialization back to siesta_init 9503 9504 * ag@bsc--2007/siesta-bsc--ag--2.1--patch-12 9505 Encapsulate k-point processing for wavefunction printout 9506 9507 * ag@bsc--2007/siesta-bsc--ag--2.1--patch-13 9508 Encapsulation of polarization k-point setup 9509Revision: siesta-bsc--master--2.1--patch-7 9510Archive: ref@bsc--2007 9511Creator: Alberto Garcia <albertog@icmab.es> 9512Date: Fri Feb 16 03:08:19 CET 2007 9513Standard-date: 2007-02-16 02:08:19 GMT 9514Modified-files: Src/atomlist.f Src/struct_init.F 9515New-patches: ag@bsc--2007/siesta-bsc--ag--2.1--patch-10 9516 ref@bsc--2007/siesta-bsc--master--2.1--patch-7 9517Summary: Initialize iza in struct_init 9518Keywords: 9519 9520The array iza might be needed by ioxv in struct_init, but it was initialized 9521only later in atomlist. 9522 9523 9524Revision: siesta-bsc--master--2.1--patch-8 9525Archive: ref@bsc--2007 9526Creator: Alberto Garcia <albertog@icmab.es> 9527Date: Fri Feb 16 03:10:07 CET 2007 9528Standard-date: 2007-02-16 02:10:07 GMT 9529Modified-files: Src/Makefile Src/born_charge.F 9530 Src/compute_dm.F Src/coor.F Src/hsparse.f Src/local_DOS.F 9531 Src/m_broyden_mixing.f Src/mixer.F Src/new_dm.F 9532 Src/normalize_dm.F Src/post_scf_work.F 9533 Src/projected_DOS.F Src/proximity_check.F 9534 Src/scfconvergence_test.F Src/setup_hamiltonian.F 9535 Src/siesta.F Src/siesta_analysis.F Src/siesta_end.F 9536 Src/siesta_geom.F90 Src/siesta_init.F Src/siesta_move.F 9537 Src/siesta_options.F Src/siesta_todo.F 9538 Src/sparse_matrices.F90 Src/state_init.F 9539 Src/struct_init.F Src/write_md_record.F Src/xcmod.F 9540New-patches: ag@bsc--2007/siesta-bsc--ag--2.1--patch-14 9541 mqag@bsc--2007/siesta-bsc--mqag--2.1--patch-3 9542 mqag@bsc--2007/siesta-bsc--mqag--2.1--patch-4 9543 ref@bsc--2007/siesta-bsc--master--2.1--patch-8 9544Summary: Siesta_todo slimming by M. Quero 9545Keywords: 9546 9547Module imports in siesta_todo have been almost eliminated. 9548 9549Only the variables declared explicitly as local in the old siesta.F 9550remain in siesta_todo. (Work done by Manuel Quero after the third meeting) 9551 9552(Note: the cosmetic changes in neighb.f, ranger.f, and struct_init.F90, 9553have not been applied) 9554 9555A bug in born_charge.F has been fixed by AG. 9556 9557Patches applied: 9558 9559 * mqag@bsc--2007/siesta-bsc--mqag--2.1--patch-3 9560 Progressive emptying of siesta_todo 9561 9562 * mqag@bsc--2007/siesta-bsc--mqag--2.1--patch-4 9563 Add siesta_geom imports to born_charge.F 9564 9565Revision: siesta-bsc--master--2.1--patch-9 9566Archive: ref@bsc--2007 9567Creator: Alberto Garcia <albertog@icmab.es> 9568Date: Thu Feb 15 22:39:24 CET 2007 9569Standard-date: 2007-02-15 21:39:24 GMT 9570Modified-files: Src/born_charge.F 9571New-patches: ref@bsc--2007/siesta-bsc--master--2.1--patch-9 9572Summary: Fix import of no_l in born_charge 9573Keywords: 9574 9575Revision: siesta-bsc--master--2.1--patch-10 9576Archive: ref@bsc--2007 9577Creator: Alberto Garcia <albertog@icmab.es> 9578Date: Thu Feb 15 23:13:10 CET 2007 9579Standard-date: 2007-02-15 22:13:10 GMT 9580Renamed-files: Src/.arch-ids/siesta_options.F.id Src/.arch-ids/siesta_options.F90.id 9581 Src/.arch-ids/zheevds.f.id Src/.arch-ids/zheevds.F90.id 9582 Src/.arch-ids/zmatrix.F.id Src/.arch-ids/zmatrix.F90.id 9583 Src/siesta_options.F Src/siesta_options.F90 9584 Src/zheevds.f Src/zheevds.F90 9585 Src/zmatrix.F Src/zmatrix.F90 9586Modified-files: Src/siesta_options.F90 Src/zheevds.F90 9587 Src/zmatrix.F90 9588New-patches: ag@bsc--2007/siesta-bsc--ag--2.1--patch-16 9589 mqag@bsc--2007/siesta-bsc--mqag--2.1--patch-5 9590 ref@bsc--2007/siesta-bsc--master--2.1--patch-10 9591Summary: Some conversions to Fortran90 by M. Quero 9592Keywords: 9593 9594zmatrix.F90, zheevs.F90, siesta_options.F90 9595 9596 9597Revision: siesta-bsc--master--2.1--patch-11 9598Archive: ref@bsc--2007 9599Creator: Alberto Garcia <albertog@icmab.es> 9600Date: Sat Feb 17 20:34:42 CET 2007 9601Standard-date: 2007-02-17 19:34:42 GMT 9602New-files: Docs/.arch-ids/BSC-Issues.id Docs/BSC-Issues 9603 Src/.arch-ids/state_analysis.F.id 9604 Src/.arch-ids/stress.F90.id 9605 Src/.arch-ids/write_subs.F.id 9606 Src/Sys/.arch-ids/intel-checks.make.id 9607 Src/Sys/intel-checks.make Src/state_analysis.F 9608 Src/stress.F90 Src/write_subs.F 9609Removed-files: Tests/.arch-ids/compara.id Tests/compara 9610Modified-files: Docs/CHANGES Src/Makefile Src/alloc.F90 9611 Src/bsd.f Src/coor.F Src/fixed.F Src/kpoint_grid.F90 9612 Src/ksvinit.F Src/local_DOS.F Src/m_mpi_utils.F 9613 Src/parallel.f Src/post_scf_work.F Src/pulayx.F 9614 Src/scfconvergence_test.F Src/setup_hamiltonian.F 9615 Src/siesta.F Src/siesta_analysis.F Src/siesta_geom.F90 9616 Src/siesta_init.F Src/siesta_move.F Src/siesta_todo.F 9617 Src/sparse_matrices.F90 Src/state_init.F 9618 Src/struct_init.F Src/zheevds.F90 Tests/bsc-Makefile 9619 Tests/bsc-compare.sh Tests/bsc-test.mk 9620 Tests/h2oZ/h2oZ.fdf version.info 9621New-patches: mq@bsc--2007/mq--feb16--1.0--patch-1 9622 ref@bsc--2007/siesta-bsc--master--2.1--patch-11 9623Summary: Fourth session at the BSC 9624Keywords: 9625 9626* New routine state_analysis.F split from siesta_move.F 9627 9628* Some variables taken out of siesta_todo and moved to 9629various places: 9630 9631 - New module m_stress in stress.F90 holds stress et al 9632 (Some variables could actually be turned into locals 9633 in several routines, except perhaps 'stress'.) 9634 - mscell et al moved to siesta_geom 9635 - nh and nhmax moved to sparse_matrices 9636 9637* write_subs now holds the siesta_write_XX routines 9638 formerly in siesta_todo 9639 9640* Some allocatables changed to pointers in fixed.F and pulayx.F 9641 (First step: just use re_alloc instead of allocate/memory 9642 In a second step work arrays will live outside) 9643 9644* Cosmetic changes in m_mpi_utils.F90 (in the context of the 9645analysis of the MPI interface) 9646 9647* Changes in coor.F: 9648 - mscell, nsc changed to coor_mscell and coord_nsc 9649 - routine superx_coor taken out of the coor scope, to 9650 avoid clashes with the imported variables in coor. 9651 (this supercell does not have anything to do with the 9652 auxiliary supercell for matrix elements) 9653 9654AG upon merging: 9655 9656* Fix typo in zmatrix declarations 9657* Declare etime in bsd.f 9658* New trick in Makefile to remove the dependency 9659 of siesta_cmlsubs.o on version.o after doing "make dep". 9660* Put an explicit unit cell in h2oZ.fdf to avoid a bug. 9661Revision: siesta-bsc--master--2.1--patch-12 9662Archive: ref@bsc--2007 9663Creator: Alberto Garcia <albertog@icmab.es> 9664Date: Mon Feb 19 00:08:23 CET 2007 9665Standard-date: 2007-02-18 23:08:23 GMT 9666New-files: Src/.arch-ids/overlap.f.id Src/overlap.f 9667Modified-files: Src/Makefile Src/local_DOS.F 9668 Src/post_scf_work.F Src/setup_hamiltonian.F Src/siesta.F 9669 Src/siesta_analysis.F Src/siesta_init.F 9670 Src/siesta_todo.F Src/state_analysis.F Src/state_init.F 9671 Src/stress.F90 Src/write_subs.F 9672New-patches: ag@bsc--2007/vars-mem--ag--0.1--base-0 9673 ag@bsc--2007/vars-mem--ag--0.1--patch-1 9674 ag@bsc--2007/vars-mem--ag--0.1--patch-2 9675 ref@bsc--2007/siesta-bsc--master--2.1--patch-12 9676Summary: Clarification of the scope of the stress variables 9677Keywords: 9678 9679A number of changes to rationalize the use of 'stress': 9680 9681* New routine 'overlap': a simplified version of overfsm adequate 9682for calling from state_init, where only the overlap matrix is needed, 9683and the stress was zero. 9684 9685* Routine setup_hamiltonian now globalizes the stress, and calls 9686the 'twobody' routine. Variable 'stressl' made into a local. 9687 9688* local_DOS, and the writing of charge and potentials, do no need 9689to use the 'stress' variable at all. 9690 9691Revision: siesta-bsc--master--2.1--patch-13 9692Archive: ref@bsc--2007 9693Creator: Alberto Garcia <albertog@icmab.es> 9694Date: Mon Feb 19 00:09:35 CET 2007 9695Standard-date: 2007-02-18 23:09:35 GMT 9696Modified-files: Src/Makefile Src/siesta.F 9697 Src/siesta_analysis.F 9698New-patches: ag@bsc--2007/vars-mem--ag--0.1--patch-3 9699 ref@bsc--2007/siesta-bsc--master--2.1--patch-13 9700Summary: Creation of siesta_forces 9701Keywords: 9702 9703Finally, siesta_forces has been created, clarifying in the process the 9704parameters of siesta_write_energies. 9705 9706Revision: siesta-bsc--master--2.1--patch-14 9707Archive: ref@bsc--2007 9708Creator: Alberto Garcia <albertog@icmab.es> 9709Date: Mon Feb 19 00:13:17 CET 2007 9710Standard-date: 2007-02-18 23:13:17 GMT 9711New-files: Src/.arch-ids/siesta_forces.F.id 9712 Src/siesta_forces.F 9713Modified-files: Src/Makefile Src/born_charge.F 9714 Src/siesta_analysis.F Src/siesta_init.F 9715 Src/siesta_todo.F Src/state_init.F 9716New-patches: ag@bsc--2007/vars-mem--ag--0.1--patch-4 9717 ag@bsc--2007/vars-mem--ag--0.1--patch-5 9718 ref@bsc--2007/siesta-bsc--master--2.1--patch-14 9719Summary: Replacement of some allocatables by pointers and automatics 9720Keywords: 9721 9722eo, qo : pointers 9723fa, cfa, fal : pointers 9724 9725polxyz, polR : automatic arrays, as they are small 9726 9727(+ really add siesta_forces.F from previous patch) 9728Revision: siesta-bsc--master--2.1--patch-15 9729Archive: ref@bsc--2007 9730Creator: Alberto Garcia <albertog@icmab.es> 9731Date: Sat Feb 24 15:04:53 CET 2007 9732Standard-date: 2007-02-24 14:04:53 GMT 9733New-files: Src/.arch-ids/m_energies.F90.id 9734 Src/.arch-ids/m_steps.F90.id Src/m_energies.F90 9735 Src/m_steps.F90 9736Removed-files: Src/.arch-ids/m_siesta.jose.F.id 9737 Src/m_siesta.jose.F 9738Modified-files: Src/Makefile Src/compute_dm.F 9739 Src/kpoint_grid.F90 Src/local_DOS.F Src/mixer.F 9740 Src/new_dm.F Src/post_scf_work.F 9741 Src/scfconvergence_test.F Src/setup_hamiltonian.F 9742 Src/siesta.F Src/siesta_analysis.F Src/siesta_forces.F 9743 Src/siesta_init.F Src/siesta_move.F Src/siesta_todo.F 9744 Src/state_analysis.F Src/state_init.F 9745 Src/write_md_record.F Src/write_subs.F 9746New-patches: ag@bsc--2007/ag--vars--1.0--base-0 9747 ag@bsc--2007/ag--vars--1.0--patch-1 9748 ag@bsc--2007/ag--vars--1.0--patch-2 9749 ag@bsc--2007/ag--vars--1.0--patch-3 9750 ag@bsc--2007/ag--vars--1.0--patch-4 9751 ref@bsc--2007/siesta-bsc--master--2.1--patch-15 9752Summary: New m_energies and m_steps modules. Back to old k-point behavior 9753Keywords: 9754 9755More steps in the slimming of siesta_todo: 9756 9757* Module m_energies contains the energy components 9758* Module m_steps contains inicoor, fincoor, istp, final 9759* Variable dDmax has been turned into an argument of 9760 mixer and scfconvergence_test 9761 9762*The old code had a bug in the update of k-points with cell changes: 9763the kscell matrix was kept constant, instead of re-calculating it. 9764This was fixed in the re-structured version, but of course the fix 9765leads to differences in the outputs of some tests, notably var_cell. 9766 9767The bug has been re-activated in kpoint_grid.F90 by commenting out 9768the update of kscell. 9769 9770The resetting of kscell to the unit matrix in case of gamma 9771calculations has been deferred for the same reason. 9772 9773 9774 9775 9776Revision: siesta-bsc--master--2.1--patch-16 9777Archive: ref@bsc--2007 9778Creator: Alberto Garcia <albertog@icmab.es> 9779Date: Sun Feb 25 21:04:19 CET 2007 9780Standard-date: 2007-02-25 20:04:19 GMT 9781New-files: Src/.arch-ids/m_auxpul.F90.id 9782 Src/.arch-ids/m_dipol.F90.id Src/.arch-ids/m_eo.F90.id 9783 Src/.arch-ids/m_forces.F90.id 9784 Src/.arch-ids/m_kinetic.F90.id 9785 Src/.arch-ids/m_ntm.F90.id 9786 Src/.arch-ids/m_numbs_neighb.F90.id 9787 Src/.arch-ids/m_rmaxh.F90.id 9788 Src/.arch-ids/m_spin.F90.id Src/m_auxpul.F90 9789 Src/m_dipol.F90 Src/m_eo.F90 Src/m_forces.F90 9790 Src/m_kinetic.F90 Src/m_ntm.F90 Src/m_numbs_neighb.F90 9791 Src/m_rmaxh.F90 Src/m_spin.F90 9792Removed-files: Src/.arch-ids/spin_init.f.id Src/spin_init.f 9793Renamed-files: Src/.arch-ids/stress.F90.id Src/.arch-ids/m_stress.F90.id 9794 Src/stress.F90 Src/m_stress.F90 9795Modified-files: Docs/CHANGES Src/.arch-ids/m_stress.F90.id 9796 Src/.arch-ids/state_analysis.F.id 9797 Src/.arch-ids/write_subs.F.id Src/Makefile 9798 Src/atomlist.f Src/born_charge.F Src/broyden_optim.F 9799 Src/cgvc.F Src/cgvc_zmatrix.F Src/compute_dm.F 9800 Src/dhscf.F Src/diagkp.F Src/dynamics.f Src/fixed.F 9801 Src/kpoint_grid.F90 Src/ksv.f Src/local_DOS.F 9802 Src/m_denchar_geom.f Src/m_energies.F90 Src/m_steps.F90 9803 Src/m_stress.F90 Src/mixer.F Src/molecularmechanics.F90 9804 Src/new_dm.F Src/normalize_dm.F Src/phonon.F 9805 Src/post_scf_work.F Src/projected_DOS.F 9806 Src/proximity_check.F Src/setup_hamiltonian.F 9807 Src/siesta.F Src/siesta_analysis.F Src/siesta_geom.F90 9808 Src/siesta_init.F Src/siesta_move.F 9809 Src/siesta_options.F90 Src/siesta_todo.F 9810 Src/sparse_matrices.F90 Src/state_analysis.F 9811 Src/state_init.F Src/struct_init.F Src/write_md_record.F 9812 Src/write_subs.F version.info 9813New-patches: ag@bsc--2007/ag--vars--1.0--patch-5 9814 ag@bsc--2007/ag--vars--1.0--patch-6 9815 ag@bsc--2007/ag--vars--1.0--patch-7 9816 ag@bsc--2007/ag--vars--1.0--patch-8 9817 mq@bsc--2007/mq--feb21--1.0--base-0 9818 mq@bsc--2007/mq--feb21--1.0--patch-1 9819 mq@bsc--2007/mq--feb21--1.0--patch-2 9820 ref@bsc--2007/siesta-bsc--master--2.1--patch-16 9821Summary: Merge of removal of integer and real variables from siesta_todo 9822Keywords: 9823 9824Inital work done at BSC by M. Quero from Feb 19 to 23, 2007. A. Garcia 9825then consolidated some of the modules and removed others, turning some 9826variables into locals or arguments (See ag@bsc--2007/ag--vars--1.0) 9827 9828Some fine tuning still needs to be done, and note that the 9829'high-level' handling of major variables, for example as 9830 9831 call siesta_forces(geom,force_stress) 9832 9833has not started yet. 9834 9835New modules: 9836 9837m_auxpul.F90 : Pulay variables. Will go into a "pulay" module. 9838m_dipol.F90 : Dipole 9839m_spin.F90 : nspin, qs, efs, plus routine init_spin (replaces 9840 spin_init). Readsp not included, as it needs work. 9841m_eo.F90 : eo, qo arrays 9842m_forces.F90 : fa, cfa, and ntcon. At the same level as stress.F90, 9843 which has been renamed to m_stress.F90 9844m_kinetic.F90 : Kinetic energies of Parrinello/Rahman variables 9845m_ntm.F90 : Mesh multipliers. Should probably go in meshsubs. 9846m_numbs_neighb.F90 : Variables related to the neighbor calculations. 9847m_rmaxh.F90 : Hamiltonian maximum range. Should be clarified. 9848 9849* Module atomlist now includes no_l 9850* Module siesta_geom now includes va (atomic velocities), plus 9851 a new variable volume_of_some_cell to pass volume information (to 9852 mimic a very likely bug in the old code) 9853* Array xijo is now in sparse_matrices 9854 9855 9856 9857Revision: siesta-bsc--master--2.1--patch-17 9858Archive: ref@bsc--2007 9859Creator: Alberto Garcia <albertog@icmab.es> 9860Date: Mon Feb 26 09:21:36 CET 2007 9861Standard-date: 2007-02-26 08:21:36 GMT 9862New-files: Src/.arch-ids/show_distribution.f.id 9863 Src/show_distribution.f Tests/born_spin/.arch-ids/=id 9864 Tests/born_spin/.arch-ids/FC.fdf.id 9865 Tests/born_spin/.arch-ids/born_spin.fdf.id 9866 Tests/born_spin/.arch-ids/born_spin.pseudos.id 9867 Tests/born_spin/.arch-ids/makefile.id 9868 Tests/born_spin/FC.fdf Tests/born_spin/born_spin.fdf 9869 Tests/born_spin/born_spin.pseudos 9870 Tests/born_spin/makefile 9871New-directories: Tests/born_spin Tests/born_spin/.arch-ids 9872Modified-files: Docs/CHANGES Src/Makefile 9873 Src/broadcast_basis.F Src/iohs.F Src/ksv.f Src/optical.F 9874 Src/savepsi.F Src/siesta_init.F Src/writewave.F 9875 Tests/std-Makefile version.info 9876New-patches: ag@bsc--2007/ag--bugs--1.0--base-0 9877 ag@bsc--2007/ag--bugs--1.0--patch-1 9878 ref@bsc--2007/siesta-bsc--master--2.1--patch-17 9879 siesta@uam.es--2006/siesta-devel--reference--2.1--patch-31 9880 siesta@uam.es--2006/siesta-devel--reference--2.1--patch-42 9881 siesta@uam.es--2006/siesta-devel--reference--2.1--patch-43 9882 siesta@uam.es--2006/siesta-devel--reference--2.1--patch-45 9883 siesta@uam.es--2006/siesta-devel--reference--2.1--patch-46 9884Summary: Fixes for troublesome bugs in reference code 9885Keywords: 9886 9887Retrofitted from -devel--reference. 9888 9889Patches applied: 9890 9891 * siesta@uam.es--2006/siesta-devel--reference--2.1--patch-31 9892 Parallel bug fix and cleanup in writewave.F 9893 9894 * siesta@uam.es--2006/siesta-devel--reference--2.1--patch-42 9895 zval wrongly treated as MPI_integer in broadcast_basis 9896 9897 * siesta@uam.es--2006/siesta-devel--reference--2.1--patch-43 9898 Wrap io_close for MPI in iohs.F 9899 9900 * siesta@uam.es--2006/siesta-devel--reference--2.1--patch-45 9901 Clean up handling of ntote in ksv and optical 9902 9903 * siesta@uam.es--2006/siesta-devel--reference--2.1--patch-46 9904 Fix allocation of temporary array in savepsi in parallel 9905 9906 9907Revision: siesta-bsc--master--2.1--patch-18 9908Archive: ref@bsc--2007 9909Creator: Alberto Garcia <albertog@icmab.es> 9910Date: Wed Feb 28 12:30:16 CET 2007 9911Standard-date: 2007-02-28 11:30:16 GMT 9912New-files: Src/.arch-ids/m_gamma.F90.id Src/m_gamma.F90 9913Removed-files: Src/.arch-ids/siesta_todo.F.id 9914 Src/siesta_todo.F 9915Modified-files: Docs/CHANGES Src/Makefile Src/born_charge.F 9916 Src/compute_dm.F Src/hsparse.f Src/local_DOS.F 9917 Src/matel.f Src/mixer.F Src/new_dm.F Src/normalize_dm.F 9918 Src/post_scf_work.F Src/projected_DOS.F 9919 Src/proximity_check.F Src/reinit.F 9920 Src/scfconvergence_test.F Src/setup_hamiltonian.F 9921 Src/siesta.F Src/siesta_analysis.F Src/siesta_end.F 9922 Src/siesta_forces.F Src/siesta_geom.F90 9923 Src/siesta_init.F Src/siesta_move.F 9924 Src/siesta_options.F90 Src/state_analysis.F 9925 Src/state_init.F Src/struct_init.F Src/sys.F 9926 Src/write_md_record.F Src/write_subs.F version.info 9927New-patches: ag@bsc--2007/ag--vars--1.0--patch-9 9928 mq@bsc--2007/mq--feb26--1.0--patch-1 9929 mq@bsc--2007/mq--feb26--1.0--patch-2 9930 ref@bsc--2007/siesta-bsc--master--2.1--patch-18 9931Summary: Final cleanup of siesta_todo 9932Keywords: 9933 9934(During and after meeting at BSC on Feb 26, 2007) 9935 9936* New module m_gamma. 9937* 'shape' put in siesta_geom. 9938* 'sname' put in siesta_options. 9939* Signaling role of 'foundxv' taken over by 'xv_file_read' in ioxv.F 9940 9941* All the other variables have been made local to the appropriate routines. 9942 9943+ Cosmetic changes in state_init and hsparse: conversion of implicit 9944 loops with goto to explicit 'do while' loops. 9945 9946+ Conversion of scfconvergence_test and proximity_check into modules. 9947 9948 9949Revision: siesta-bsc--master--2.1--patch-19 9950Archive: ref@bsc--2007 9951Creator: Alberto Garcia <albertog@icmab.es> 9952Date: Thu Mar 1 13:00:45 CET 2007 9953Standard-date: 2007-03-01 12:00:45 GMT 9954Modified-files: Docs/CHANGES Src/alloc.F90 version.info 9955New-patches: ag@bsc--2007/ag--vars--1.0--patch-10 9956 ref@bsc--2007/siesta-bsc--master--2.1--patch-19 9957Summary: Add character(len=*) routines to alloc.F90 9958Keywords: 9959 9960New module procedures realloc_s1 and dealloc_s1 9961 9962Revision: siesta-bsc--master--2.1--patch-20 9963Archive: ref@bsc--2007 9964Creator: Alberto Garcia <albertog@icmab.es> 9965Date: Thu Mar 15 17:08:31 CET 2007 9966Standard-date: 2007-03-15 16:08:31 GMT 9967Modified-files: Docs/CHANGES Src/fixed.F Src/setspatial.f 9968 Tests/bsc-Makefile Tests/std-Makefile version.info 9969New-patches: ag@bsc--2007/ag--vars--1.0--patch-12 9970 ag@bsc--2007/ag--vars--1.0--patch-13 9971 ref@bsc--2007/siesta-bsc--master--2.1--patch-20 9972Summary: Pointers in fixed and setspatial. si2x1h test added to bsc-Makefile 9973Keywords: 9974 9975Revision: siesta-bsc--master--2.1--patch-21 9976Archive: ref@bsc--2007 9977Creator: Alberto Garcia <albertog@icmab.es> 9978Date: Thu Mar 15 17:10:48 CET 2007 9979Standard-date: 2007-03-15 16:10:48 GMT 9980Removed-files: Src/.arch-ids/m_auxpul.F90.id 9981 Src/m_auxpul.F90 9982Renamed-files: Src/.arch-ids/pulayx.F.id Src/.arch-ids/m_pulay.F.id 9983 Src/pulayx.F Src/m_pulay.F 9984Modified-files: Docs/CHANGES Src/Makefile Src/m_pulay.F 9985 Src/mixer.F Src/state_init.F version.info 9986New-patches: ag@bsc--2007/ag--vars--1.0--patch-14 9987 ref@bsc--2007/siesta-bsc--master--2.1--patch-21 9988Summary: Re-organization of pulay module 9989Keywords: 9990 9991Pulayx is now part of a module "m_pulay", which contains the 9992nauxpul and auxpul variables. Module m_auxpul has been removed. 9993 9994The calling sequence for pulayx has been simplified, as some of 9995the arguments are now module variables. Argument maxo was innecesary. 9996Internal work arrays are now pointers. 9997 9998The changes affect mixer and state_init (which calls a new routine 9999init_pulay_arrays) 10000 10001 10002Revision: siesta-bsc--master--2.1--patch-22 10003Archive: ref@bsc--2007 10004Creator: Alberto Garcia <albertog@icmab.es> 10005Date: Thu Mar 15 17:19:58 CET 2007 10006Standard-date: 2007-03-15 16:19:58 GMT 10007New-files: Src/.arch-ids/m_neighbors.f90.id 10008 Src/m_neighbors.f90 10009Removed-files: Src/.arch-ids/m_numbs_neighb.F90.id 10010 Src/.arch-ids/xijorb.f.id Src/m_numbs_neighb.F90 10011 Src/xijorb.f 10012Modified-files: Docs/CHANGES Src/Makefile Src/alloc.F90 10013 Src/born_charge.F Src/hsparse.f Src/overlap.f 10014 Src/post_scf_work.F Src/proximity_check.F 10015 Src/setup_hamiltonian.F Src/siesta_analysis.F 10016 Src/state_init.F version.info 10017New-patches: ag@bsc--2007/ag--vars--1.0--patch-15 10018 ag@bsc--2007/ag--vars--1.0--patch-16 10019 ag@bsc--2007/ag--vars--1.0--patch-17 10020 ag@bsc--2007/ag--vars--1.0--patch-18 10021 ag@bsc--2007/ag--vars--1.0--patch-19 10022 ref@bsc--2007/siesta-bsc--master--2.1--patch-22 10023Summary: Reorganization of hsparse/xijorb calls with new neighbor module 10024Keywords: 10025 10026* Deactivated 's' routines in alloc.F90, as they are seen as extremely 10027dangerous. 10028 10029* New module m_neighbors houses maxna, jna, r2ij, and xij, and the new 10030routine init_neighbor_arrays, which simplifies the logic of the block 10031formerly in state_init. The initialization routine is invoked with a 10032larger rmax, appropriate for the workings of hsparse, so that there is 10033no need to check again for the appropriate sizes. Actually, this rmax 10034is the largest ever needed by the calculation of neighbors, so maxna 10035is set once and for all. 10036 10037* Old module m_numb_neighbs has been removed. 10038 10039This new module (which supersedes m_numb_neighb) could be used 10040by other second-level routines (nlefsm, phirphi, etc). 10041 10042* Hsparse is now called just once from state_init. It allocates listh 10043(and xijo, if applicable), and returns the size "nh" of the sparse 10044matrices. 10045 10046* maxnh is always set to nh (and not to some larger value if nh > (the 10047old maxnh)). 10048 10049* The sparse arrays are always re_alloc'ated, as these calls are very 10050cheap if they have the right size. 10051 10052* The code for xijorb and hsparse is almost identical. It has been 10053merged, adding two new arguments to hsparse: gamma and xijo, so that 10054hsparse fills xijo also if gamma is false. Multiple-image detection is 10055still active. 10056 10057* Routine xijorb has been deleted. 10058 10059* Allocatables have been turned into pointers inside hsparse. 10060 10061Revision: siesta-bsc--master--2.1--patch-23 10062Archive: ref@bsc--2007 10063Creator: Alberto Garcia <albertog@icmab.es> 10064Date: Thu Mar 15 17:22:35 CET 2007 10065Standard-date: 2007-03-15 16:22:35 GMT 10066New-files: Src/.arch-ids/obj_setup.sh.id Src/obj_setup.sh 10067Modified-files: Docs/CHANGES Src/MPI/Makefile 10068 Src/MPI/generate.sh Src/Makefile Src/fdf/makefile 10069 version.info 10070New-patches: ag@bsc--2007/ag--vars--1.0--patch-20 10071 agarcia@siesta.arch--2006/vpath--agarcia--0.1--patch-1 10072 agarcia@siesta.arch--2006/vpath--agarcia--0.1--patch-2 10073 agarcia@siesta.arch--2006/vpath--agarcia--0.1--patch-3 10074 ref@bsc--2007/siesta-bsc--master--2.1--patch-23 10075Summary: VPATH-aware compilation for multiple executable versions 10076Keywords: 10077 10078Added Src/obj_setup.sh script, to be called from any directory on 10079which the build is going to take place, and modified slightly some 10080makefiles to make them VPATH-proof. The Tests directory is replicated 10081in the "build" directory (and a fake symbolic link called "Src" added 10082so that all the test-running scripts work without change). 10083 10084(The pristine Src should be "clean", without any object files) 10085 10086Example. From the top Siesta directory: 10087 10088mkdir Objs 10089cd Objs 10090sh ../Src/obj_setup.sh 10091../Src/configure --enable-fast 10092make 10093cd Tests 10094make clean; make 10095cd # Now a parallel version 10096mkdir ParaObjs 10097cd ParaObjs 10098sh ../Src/obj_setup.sh 10099cp ../Src/Sys/parallel.make ./arch.make 10100make 10101cd Tests 10102make clean; make 10103 10104Revision: siesta-bsc--master--2.1--patch-24 10105Archive: ref@bsc--2007 10106Creator: Alberto Garcia <albertog@icmab.es> 10107Date: Mon Mar 19 09:37:33 CET 2007 10108Standard-date: 2007-03-19 08:37:33 GMT 10109Modified-files: Docs/CHANGES Src/Makefile Src/alloc.F90 10110 Src/atom.f Src/detover.F Src/dfscf.f Src/fft3d.F 10111 Src/meshmatrix.F Src/old_atmfuncs.f Src/optical.F 10112 Src/overfsm.f Src/rhoofd.f Src/rhoofdsp.f Src/savepsi.F 10113 Src/siesta_analysis.F Src/spher_harm.f 10114 Src/transition_rate.F Src/vmat.f Src/vmatsp.f Src/xc.f 10115 version.info 10116New-patches: ag@bsc--2007/vars--mqag--1.0--base-0 10117 ag@bsc--2007/vars--mqag--1.0--patch-1 10118 ag@bsc--2007/vars--mqag--1.0--patch-2 10119 ag@bsc--2007/vars--mqag--1.0--patch-3 10120 ag@bsc--2007/vars--mqag--1.0--patch-4 10121 ag@bsc--2007/vars--mqag--1.0--patch-5 10122 ag@bsc--2007/vars--mqag--1.0--patch-6 10123 ag@bsc--2007/vars--mqag--1.0--patch-7 10124 ag@bsc--2007/vars--mqag--1.0--patch-8 10125 ag@bsc--2007/vars--mqag--1.0--patch-9 10126 ag@bsc--2007/vars--mqag--1.0--patch-10 10127 ag@bsc--2007/vars--mqag--1.0--patch-11 10128 ag@bsc--2007/vars--mqag--1.0--patch-12 10129 ag@bsc--2007/vars--mqag--1.0--patch-13 10130 ref@bsc--2007/siesta-bsc--master--2.1--patch-24 10131Summary: Allocatables to pointers I 10132Keywords: 10133 10134First merge of the changes Based on work by Manuel Quero from Feb 28 to Mar 16. 10135Allocatable arrays have been turned into pointers in several routines. 10136 10137Patches applied: 10138 10139 * ag@bsc--2007/vars--mqag--1.0--base-0 10140 tag of ref@bsc--2007/siesta-bsc--master--2.1--patch-23 10141 10142 * ag@bsc--2007/vars--mqag--1.0--patch-1 10143 Siesta_analysis, sphere_harm 10144 10145 * ag@bsc--2007/vars--mqag--1.0--patch-2 10146 Transition_rate 10147 10148 * ag@bsc--2007/vars--mqag--1.0--patch-3 10149 Vmat and vmatsp 10150 10151 * ag@bsc--2007/vars--mqag--1.0--patch-4 10152 Added _z1, _z2, and _r4 support to alloc.F90 10153 10154 * ag@bsc--2007/vars--mqag--1.0--patch-5 10155 Detover, allocating complex arrays 10156 10157 * ag@bsc--2007/vars--mqag--1.0--patch-6 10158 Fft3d 10159 10160 * ag@bsc--2007/vars--mqag--1.0--patch-7 10161 Old_atmfuncs 10162 10163 * ag@bsc--2007/vars--mqag--1.0--patch-8 10164 Savepsi 10165 10166 * ag@bsc--2007/vars--mqag--1.0--patch-9 10167 Explicit array-ness in calls to spline 10168 10169 * ag@bsc--2007/vars--mqag--1.0--patch-10 10170 Meshmatrix and routines which use DscfL 10171 10172 * ag@bsc--2007/vars--mqag--1.0--patch-11 10173 xc.f 10174 10175 * ag@bsc--2007/vars--mqag--1.0--patch-12 10176 Overfsm 10177 10178 * ag@bsc--2007/vars--mqag--1.0--patch-13 10179 Optical 10180 10181 10182Revision: siesta-bsc--master--2.1--patch-25 10183Archive: ref@bsc--2007 10184Creator: Alberto Garcia <albertog@icmab.es> 10185Date: Tue Mar 20 23:49:17 CET 2007 10186Standard-date: 2007-03-20 22:49:17 GMT 10187Modified-files: Docs/CHANGES Src/Makefile Src/bonds.f 10188 Src/hsparse.f Src/m_neighbors.f90 Src/nlefsm.f Src/pdos.F 10189 Src/pdosg.F Src/pdosk.F Src/pdoskp.F Src/phirphi.f 10190 Src/poison.F Src/proximity_check.F Src/radfft.f 10191 Src/reord.f Src/setup_hamiltonian.F Src/shaper.f 10192 Tests/mgco3/mgco3.fdf version.info 10193New-patches: ag@bsc--2007/vars--mqag--1.0--patch-14 10194 ag@bsc--2007/vars--mqag--1.0--patch-15 10195 ag@bsc--2007/vars--mqag--1.0--patch-16 10196 ag@bsc--2007/vars--mqag--1.0--patch-17 10197 ag@bsc--2007/vars--mqag--1.0--patch-18 10198 ag@bsc--2007/vars--mqag--1.0--patch-19 10199 ag@bsc--2007/vars--mqag--1.0--patch-20 10200 ag@bsc--2007/vars--mqag--1.0--patch-21 10201 ref@bsc--2007/siesta-bsc--master--2.1--patch-25 10202Summary: Allocatables to pointers II 10203Keywords: 10204 10205Second merge of the changes Based on work by Manuel Quero from Feb 28 to Mar 16. 10206Allocatable arrays have been turned into pointers in several routines. 10207 10208+ Clarification of the use of the new m_neighbors module. 10209+ vpath-aware "make dep" target 10210 10211Patches applied: 10212 10213 * ag@bsc--2007/vars--mqag--1.0--patch-14 10214 radfft 10215 10216 * ag@bsc--2007/vars--mqag--1.0--patch-15 10217 poison 10218 10219 * ag@bsc--2007/vars--mqag--1.0--patch-16 10220 reord 10221 10222 * ag@bsc--2007/vars--mqag--1.0--patch-17 10223 phirphi 10224 10225 * ag@bsc--2007/vars--mqag--1.0--patch-18 10226 PDOS routines 10227 10228 * ag@bsc--2007/vars--mqag--1.0--patch-19 10229 Clarification of m_neighbors use. Nlefsm converted 10230 10231 * ag@bsc--2007/vars--mqag--1.0--patch-20 10232 bonds. Vpath-aware makedepend 10233 10234 * ag@bsc--2007/vars--mqag--1.0--patch-21 10235 shaper 10236 10237 10238Revision: siesta-bsc--master--2.1--patch-26 10239Archive: ref@bsc--2007 10240Creator: Alberto Garcia <albertog@icmab.es> 10241Date: Tue Apr 10 09:03:36 CEST 2007 10242Standard-date: 2007-04-10 07:03:36 GMT 10243Removed-files: Src/.arch-ids/numbvect.f.id Src/numbvect.f 10244Modified-files: Docs/CHANGES Src/Makefile Src/alloc.F90 10245 Src/atomlist.f Src/atomlwf.F Src/bands.F 10246 Src/basis_types.f Src/born_charge.F Src/broyden_optim.F 10247 Src/cellxc.F Src/chempot.F Src/coor.F Src/denmat.F 10248 Src/denmatlomem.F Src/forhar.f Src/hsparse.f 10249 Src/initatom.f Src/kinefsm.f Src/ksv.f Src/listsc.f 10250 Src/m_broyden_mixing.f Src/m_iostruct.f 10251 Src/molecularmechanics.F90 Src/nlefsm.f Src/obc.f 10252 Src/ofc.f Src/old_atmfuncs.f Src/ordern.F Src/outcoor.f 10253 Src/pseudopotential.f Src/setatomnodes.F 10254 Src/show_distribution.f Src/siesta_geom.F90 10255 Src/struct_init.F version.info 10256New-patches: ag@bsc--2007/vars--mqag--1.0--patch-22 10257 ag@bsc--2007/vars--mqag--1.0--patch-23 10258 ag@bsc--2007/vars--mqag--1.0--patch-24 10259 ag@bsc--2007/vars--mqag--1.0--patch-25 10260 ag@bsc--2007/vars--mqag--1.0--patch-26 10261 ag@bsc--2007/vars--mqag--1.0--patch-27 10262 ag@bsc--2007/vars--mqag--1.0--patch-28 10263 ag@bsc--2007/vars--mqag--1.0--patch-29 10264 ag@bsc--2007/vars--mqag--1.0--patch-30 10265 ag@bsc--2007/vars--mqag--1.0--patch-31 10266 ag@bsc--2007/vars--mqag--1.0--patch-32 10267 ag@bsc--2007/vars--mqag--1.0--patch-33 10268 ag@bsc--2007/vars--mqag--1.0--patch-34 10269 ag@bsc--2007/vars--mqag--1.0--patch-35 10270 ag@bsc--2007/vars--mqag--1.0--patch-36 10271 ag@bsc--2007/vars--mqag--1.0--patch-37 10272 ag@bsc--2007/vars--mqag--1.0--patch-38 10273 ag@bsc--2007/vars--mqag--1.0--patch-39 10274 ag@bsc--2007/vars--mqag--1.0--patch-40 10275 ag@bsc--2007/vars--mqag--1.0--patch-41 10276 ag@bsc--2007/vars--mqag--1.0--patch-42 10277 ref@bsc--2007/siesta-bsc--master--2.1--patch-26 10278Summary: Allocatables to pointers III 10279Keywords: 10280 10281Third installment in the merging of the allocatables->pointers work at BSC. 10282 10283Patches applied: 10284 10285 * ag@bsc--2007/vars--mqag--1.0--patch-22 10286 cisa in siesta_geom 10287 10288 * ag@bsc--2007/vars--mqag--1.0--patch-23 10289 MolecularMechanics 10290 10291 * ag@bsc--2007/vars--mqag--1.0--patch-24 10292 Forhar 10293 10294 * ag@bsc--2007/vars--mqag--1.0--patch-25 10295 Deallocate basis spec arrays 10296 10297 * ag@bsc--2007/vars--mqag--1.0--patch-26 10298 Fix names in re_alloc/de_alloc statements 10299 10300 * ag@bsc--2007/vars--mqag--1.0--patch-27 10301 kinefsm 10302 10303 * ag@bsc--2007/vars--mqag--1.0--patch-28 10304 ksv 10305 10306 * ag@bsc--2007/vars--mqag--1.0--patch-29 10307 listsc 10308 10309 * ag@bsc--2007/vars--mqag--1.0--patch-30 10310 m_broyden_mixing 10311 10312 * ag@bsc--2007/vars--mqag--1.0--patch-31 10313 Rationalization of chempot 10314 10315 * ag@bsc--2007/vars--mqag--1.0--patch-32 10316 Setatomnodes. Stop if bad load balancing 10317 10318 * ag@bsc--2007/vars--mqag--1.0--patch-33 10319 obc rationalization 10320 10321 * ag@bsc--2007/vars--mqag--1.0--patch-34 10322 ofc rationalization 10323 10324 * ag@bsc--2007/vars--mqag--1.0--patch-35 10325 outcoor 10326 10327 * ag@bsc--2007/vars--mqag--1.0--patch-36 10328 pseudopotential 10329 10330 * ag@bsc--2007/vars--mqag--1.0--patch-37 10331 elem in atomlist and struct_init 10332 10333 * ag@bsc--2007/vars--mqag--1.0--patch-38 10334 atomlwf 10335 10336 * ag@bsc--2007/vars--mqag--1.0--patch-39 10337 bands 10338 10339 * ag@bsc--2007/vars--mqag--1.0--patch-40 10340 broyden_optim 10341 10342 * ag@bsc--2007/vars--mqag--1.0--patch-41 10343 cellxc 10344 10345 * ag@bsc--2007/vars--mqag--1.0--patch-42 10346 denmat and denmatlomem 10347 10348Revision: siesta-bsc--master--2.1--patch-27 10349Archive: ref@bsc--2007 10350Creator: Alberto Garcia <albertog@icmab.es> 10351Date: Wed Apr 11 13:04:23 CEST 2007 10352Standard-date: 2007-04-11 11:04:23 GMT 10353Removed-files: Src/.arch-ids/m_neighbors.f90.id 10354 Src/.arch-ids/neighb.f.id Src/.arch-ids/ranger.f.id 10355 Src/m_neighbors.f90 Src/neighb.f Src/ranger.f 10356Modified-files: Docs/CHANGES Src/Makefile Src/atomlwf.F 10357 Src/basis_io.F Src/bonds.f Src/born_charge.F 10358 Src/chempot.F Src/compute_dm.F Src/dhscf.F Src/dnaefs.f 10359 Src/hsparse.f Src/initatom.f Src/kinefsm.f Src/ksv.f 10360 Src/meshsubs.F Src/mneighb.f Src/naefs.f Src/nlefsm.f 10361 Src/optical.F Src/overfsm.f Src/overlap.f Src/phirphi.f 10362 Src/phirphi_opt.f Src/post_scf_work.F 10363 Src/proximity_check.F Src/setup_hamiltonian.F 10364 Src/shaper.f Src/siesta_analysis.F Src/siesta_init.F 10365 Src/state_init.F version.info 10366New-patches: ag@bsc--2007/vars--mqag--1.0--patch-43 10367 ag@bsc--2007/vars--mqag--1.0--patch-44 10368 ag@bsc--2007/vars--mqag--1.0--patch-45 10369 ag@bsc--2007/vars--mqag--1.0--patch-46 10370 ag@bsc--2007/vars--mqag--1.0--patch-47 10371 ag@bsc--2007/vars--mqag--1.0--patch-48 10372 ref@bsc--2007/siesta-bsc--master--2.1--patch-27 10373Summary: Allocatables to pointers IV -- new neighbor code + nspecies fix 10374Keywords: 10375 10376Further changes for allocatables->pointers conversion. 10377 10378Neighb and ranger removed in favor of 'mneighb' approach, as it is 10379more robust and less confusing. 10380 10381There has been a slight change in mneighb: maxnna is now a module 10382variable, and not an argument of mneighb. Maxnna is given an initial 10383value, and the module arrays initialized to that size in the first 10384invocation. 10385 10386Patches applied: 10387 10388 * ag@bsc--2007/vars--mqag--1.0--patch-43 10389 First stages of changeover to mneighb paradigm 10390 10391 * ag@bsc--2007/vars--mqag--1.0--patch-44 10392 New functionality in mneighb. Convert chempot 10393 10394 * ag@bsc--2007/vars--mqag--1.0--patch-45 10395 Converted phirphi*, ksv, and optical 10396 10397 * ag@bsc--2007/vars--mqag--1.0--patch-46 10398 Final changeover to new neighb paradigm 10399 10400 * ag@bsc--2007/vars--mqag--1.0--patch-47 10401 dhscf. Minor change in meshsubs. Cosmetic cleanup of mneighb. 10402 10403Also: Fix setting of number of species for user basis option 10404 10405The number of species was not set correctly if the options User.Basis 10406or User.Basis.Netcdf were used. 10407 10408 10409 10410Revision: siesta-bsc--master--2.1--patch-28 10411Archive: ref@bsc--2007 10412Creator: Alberto Garcia <albertog@icmab.es> 10413Date: Mon May 7 16:32:55 CEST 2007 10414Standard-date: 2007-05-07 14:32:55 GMT 10415Modified-files: Docs/CHANGES Src/Makefile Src/cellxc.F 10416 Src/initatom.f version.info 10417New-patches: ref@bsc--2007/siesta-bsc--master--2.1--patch-28 10418Summary: Explicit array-ness in calls in initatom and cellxc 10419Keywords: 10420 10421The Marenostrum compiler complains if actual arguments with 10422array indexes beginning at 0 are written in the old f77 style: 10423 10424Thus one has to write in initatom: 10425 10426 call .... 10427 nkbl(0:,is), erefkb(1,0:,is),lmxo(is), 10428 10429instead of: 10430 call .... 10431 nkbl(0,is), erefkb(1,0,is),lmxo(is), 10432 10433* In cellxc, a similar specification is necessary: 10434 10435 call HowManyMeshPerNode(MeshNsm,Pleft3,Nodes,NMeshPN, 10436 . PMesh(1:,3)) 10437 10438Revision: siesta-bsc--master--2.1--patch-29 10439Archive: ref@bsc--2007 10440Creator: Alberto Garcia <albertog@icmab.es> 10441Date: Tue May 8 00:03:35 CEST 2007 10442Standard-date: 2007-05-07 22:03:35 GMT 10443Modified-files: Docs/CHANGES Src/cellxc.F version.info 10444New-patches: ref@bsc--2007/siesta-bsc--master--2.1--patch-29 10445Summary: Fix wrong allocations in cellxc.F 10446Keywords: 10447 10448A few typos in the conversion of allocatables to pointers in cellxc caused 10449crashes. Fixed allocation of dbuffer and bvxc. 10450 10451Revision: siesta-bsc--master--2.1--patch-30 10452Archive: ref@bsc--2007 10453Creator: Alberto Garcia <albertog@icmab.es> 10454Date: Tue May 8 22:04:56 CEST 2007 10455Standard-date: 2007-05-08 20:04:56 GMT 10456Modified-files: Docs/CHANGES Src/initatom.f version.info 10457New-patches: ref@bsc--2007/siesta-bsc--master--2.1--patch-30 10458Summary: Explicit array extents in initatom.f 10459Keywords: 10460 10461More fixes for compiler handling of array arguments: 10462 10463The actual argument (in call to atom in initatom.f): 10464 10465 nzeta(0:,1,is) 10466 10467is wrong. It should be: nzeta(0:,1:,is) 10468 10469The 0: form was put in a previous patch to avoid an mismatched interface 10470error with the Marenostrum compiler. But once this is done, apparently 10471one has to go all the way with explicit array extents. Otherwise bad 10472code is produced by other compilers (at least by Intel's). 10473 10474This is mildly confusing, as the dummy arguments are declared 10475in f77 style in atom.f: 10476 10477 integer, intent(in) :: nzeta(0:lmaxd,nsemx) 10478 10479(or are they?). 10480 10481There might be other instances of this usage. 10482 10483Revision: siesta-bsc--master--2.1--patch-31 10484Archive: ref@bsc--2007 10485Creator: Alberto Garcia <albertog@icmab.es> 10486Date: Thu May 10 13:02:23 CEST 2007 10487Standard-date: 2007-05-10 11:02:23 GMT 10488Modified-files: Src/Makefile Src/extrapol.F Src/hsparse.f 10489 Src/new_dm.F Src/state_init.F 10490New-patches: ref@bsc--2007/siesta-bsc--master--2.1--patch-31 10491Summary: Avoid shrinking of density-matrix arrays for extrapol. 10492Keywords: 10493 10494Routine extrapol has to deal with density-matrices with possibly different 10495sparsity patterns. It is essential that their "value" and "list" arrays be 10496large enough to allow proper processing. 10497 10498After the cleanup, the allocation section after the call to hsparse in 10499state_init called re_alloc inconditionally, regardless of whether the 10500total size of Dscf (nh) had increased or not. Sometimes this led to a 10501*shrinking* ofthe arrays, and bounds errors in extrapol. The option 10502'shrink=.false.' has now been used. (Also, for good measure, shrinking 10503is avoided in the allocation of listh, now done inside hsparse.) 10504 10505Extrapol has been turned into a module, and the assumed-shape idiom used 10506to declare the relevant arrays (otherwise bounds errors would result from 10507the comparison with the nominal nmax). 10508 10509* Other: cosmetic change in the 'dep' target to deal properly with 10510degenerate vpaths. 10511Revision: siesta-bsc--master--2.1--patch-32 10512Archive: ref@bsc--2007 10513Creator: Alberto Garcia <albertog@icmab.es> 10514Date: Fri May 11 16:57:28 CEST 2007 10515Standard-date: 2007-05-11 14:57:28 GMT 10516Modified-files: Docs/CHANGES Src/state_init.F version.info 10517New-patches: ref@bsc--2007/siesta-bsc--master--2.1--patch-32 10518Summary: Fix typo in state_init.F 10519Keywords: 10520 10521A loose 'endif' in state_init.F has been removed. 10522 10523Update of CHANGES for patch-31. 10524 10525 10526Revision: siesta-bsc--master--2.1--patch-33 10527Archive: ref@bsc--2007 10528Creator: Alberto Garcia <albertog@icmab.es> 10529Date: Thu May 17 17:59:40 CEST 2007 10530Standard-date: 2007-05-17 15:59:40 GMT 10531Modified-files: Docs/CHANGES Src/siesta_forces.F 10532 version.info 10533New-patches: ref@bsc--2007/siesta-bsc--master--2.1--patch-33 10534Summary: Execute SCF loop when nscf=1 10535Keywords: 10536 10537When nscf=1, the scf loop was not entered, and 10538the program went directly to the "post-scf" section. 10539 10540Now, unless nscf<=0, the scf loop is executed at least once. 10541 10542Revision: siesta-bsc--master--2.1--patch-34 10543Archive: ref@bsc--2007 10544Creator: Alberto Garcia <albertog@icmab.es> 10545Date: Wed Jun 6 10:23:24 CEST 2007 10546Standard-date: 2007-06-06 08:23:24 GMT 10547Modified-files: Docs/CHANGES Src/siesta_forces.F 10548 version.info 10549New-patches: ref@bsc--2007/siesta-bsc--master--2.1--patch-34 10550Summary: Clarify bounds of SCF loop in siesta_forces. 10551Keywords: 10552 10553The exit criterion of the scf loop in siesta_forces 10554has been clarified: It now exits before completing 10555the last scheduled iteration (i.e., iteration number 10556nscf) as it is assumed (notably for Harris-functional 10557calculations) that it corresponds to the final pass 10558for force and stress calculation. 10559 10560The check on the sign of wmix has been deleted. 10561 10562================================ 10563 10564The changes on branch ref@bsc--2007/siesta-bsc--master--2.3 were 10565mainly merges of new features and fixes along devel-2.1. The patches 10566were first put in ag@bsc--2007/merge-devel--ag--2.3 (up to patch-18) 10567and were then copied verbatim into 10568ref@bsc--2007/siesta-bsc--master--2.3. 10569 10570Some other bug-fixes along bsc--2.1--master were also merged into the 105712.3--master branch. 10572 10573The only other changes were: 10574 10575* Fix typo in state_init.F 10576 10577* BSC cosmetic change to zmatrix.F90 taken back. 10578 In detail: synched patch-38, and copied zmatrix.F from reference-2.1 10579 after doing a 'tla mv zmatrix.F0 zmatrix.F. 10580 10581* siesta_geom was needed in zmatrix.F 10582 10583Revision: siesta-bsc--master--2.3--patch-25 10584Archive: ref@bsc--2007 10585Creator: Alberto Garcia <albertog@icmab.es> 10586Date: Wed Jun 6 10:33:04 CEST 2007 10587Standard-date: 2007-06-06 08:33:04 GMT 10588Modified-files: Docs/CHANGES Src/kpoint_grid.F90 10589 version.info 10590New-patches: ref@bsc--2007/siesta-bsc--master--2.3--patch-25 10591Summary: Avoid MP-grid permutations in trivial gamma case 10592Keywords: 10593 10594For completeness, the effective Monkhorst-Pack grid is 10595printed even if only the gamma point is used. The algorithm 10596to generate it might sometimes permute the lattice vectors. 10597This is now corrected. 10598 10599 10600====END OF LOG OF BSC CHANGES================================== 10601 106022.1-before-BSC-merge 10603____________________________________________________________________ 10604** CHANGES ALONG siesta@uam.es--2006/siesta-devel--reference--2.1 10605-------------------------------------------------------------------- 10606 106072007-06-05 13:30 GMT Alberto Garcia <albertog@icmab.es> patch-63 10608 10609Summary: Correct pseudo in ch4 test 10610 106112007-06-05 13:30 GMT Alberto Garcia <albertog@icmab.es> patch-62 10612 10613Summary: Wrap write_struct and zmatrix output for MPI 10614 10615In siesta.F, the geometry output calls before moving the atoms 10616were done by all nodes. 10617 106182007-06-04 15:40 GMT Alberto Garcia <albertog@icmab.es> patch-61 10619 10620Summary: Zmatrix optimization enhancements. Sign change in MM stress. 10621 10622* Added constant-volume optimization option to the Zmatrix code. 10623 10624* Broyden option for Zmatrix optimization. 10625 10626* The zmatrix optimization code for the "variable cell" case has been 10627partially fixed. It now fails to work only if some of the coordinates 10628of an atom specifed in "cartesian" form are variables (i.e., allowed 10629to relax) and others are not. 10630 10631For example: 10632 10633cartesian 10634... 10635 1 0.3 0.4 0.5 1 0 1 10636... 10637 10638will fail as the second coordinate is not allowed to relax. 10639 10640 1 0.4 0.2 -0.7 0 0 0 OK 10641 1 0.4 0.2 -0.7 1 1 1 OK 10642 10643 10644* New file cell_broyden_optim.F implements "cell-only" optimizations. 10645 10646This feature is enabled by setting the symbol 10647 10648MD.RelaxCellOnly 10649 10650to .true.. 10651 10652Only the cell parameters are relaxed (by the Broyden method). The 10653atomic coordinates are re-scaled to the new cell, keeping the 10654fractional coordinates constant. For Zmatrix calculations, the 10655fractional position of the first atom in each molecule is kept fixed, 10656and no attempt is made to rescale the bond distances or angles. 10657 10658* Removal of intra-molecular pressure 10659 10660If the symbol 10661 10662MD.RemoveIntramolecularPressure 10663 10664is set to .true., the contribution to the stress coming from the 10665internal degrees of freedom of the molecules will be subtracted. This 10666is done in an approximate manner, using the virial form of the stress, 10667and assumming that the "mean force" over the coordinates of the 10668molecule represents the "inter-molecular" stress. The correction term 10669was already computed in earlier versions ("Pmol"). The correction is 10670now computed molecule-by-molecule if the Zmatrix format is used. 10671 10672NOTE: The reported "Molecular Pressure" might change slightly from 10673previous versions as the "current" and not the "next iteration" coordinates 10674are used for the computation of the virial term. 10675 10676 10677If the intra-molecular stress is removed, the corrected static and 10678total stresses are printed in addition to the uncorrected items. 10679 10680The corrected Voigt form is also printed. 10681 10682(New test ch4 to exemplify this feature) 10683 10684 10685* Correction of the sign of the stress in molecularmechanics.F90 10686 10687For MM potentials, attractive interactions are represented by 10688*positive* C coefficients in the MM.Potentials block. Then the 10689MM energy is negative, as it should be. However, the sign of 10690the stress was wrong in the original implementation. Now (also 10691printed as MM-Stress) it should come out as a positive contribution 10692(negative pressure), forcing the cell to contract. 10693 10694(Updated graphite_full test) 10695 10696 10697* New Utils/MM_Examples directory. 10698 10699An example of the use of MM potentials to introduce van der Waals 10700interactions in an approximate manner (for the artificial example 10701of fcc He). 10702 10703* Additional enthalpy-analog output. 10704 10705The enthalpy is computed in two ways: as the "target enthalpy" using 10706the target pressure, and as the "real" enthalpy using the trace of the 10707current stress tensor as an estimation of the pressure. Ideally, both 10708values should be identical at convergence, but the "target enthalpy" 10709might have significant errors coming from the tolerances. 10710 10711 10712* NEW STRUCTURE OUTPUT FILES: 10713 10714OUT.UCELL.ZMATRIX 10715 10716It contains the structural information in fdf form, with 10717blocks for unit-cell vectors and for Zmatrix coordinates. The 10718Zmatrix block is in a ``canonical'' form with the following 10719characteristics: 10720 107211. No symbolic variables or constants are used. 107222. The position coordinates of the first atom in each molecule 10723 are absolute cartesian coordinates. 107243. Any coordinates in ``cartesian'' blocks are also absolute cartesians. 107254. There is no provision for output of constraints. 107265. The units used are those initially specified by the user, and are 10727 noted also in fdf form. 10728 10729Note that the geometry reported is the last one for which forces and 10730stresses were computed. 10731 10732NEXT_ITER.UCELL.ZMATRIX 10733 10734In the same format but with a possibly updated geometry. 10735 10736Label.STRUCT_NEXT_ITER. 10737 10738Structure in crystallographic format (same as Label.STRUCT_OUT) for a 10739possibly updated geometry. 10740 10741(Call performed in siesta_write_positions, which is called after the 10742structure has moved after the application of forces/stress.) 10743 10744 10745* New .make file for Hreidar at ETH Zurich. 10746 107472007-05-09 14:40 GMT Alberto Garcia <albertog@icmab.es> patch-8 10748 10749Summary: New features for variable-cell optimization. MM Stress sign fix 10750 10751* New file cell_broyden_optim.F implements "cell-only" optimizations. 10752This feature is enabled by setting the symbol 10753 10754MD.RelaxCellOnly 10755 10756to .true.. 10757 10758* Removal of intra-molecular pressure 10759If the symbol 10760 10761MD.RemoveIntramolecularPressure 10762 10763is set to .true., the contribution to the stress coming from the 10764internal degrees of freedom of the molecules will be subtracted. This 10765is done in an approximate manner, using the virial form of the stress, 10766and assumming that the "mean force" over the coordinates of the 10767molecule represents the "inter-molecular" stress. The correction term 10768was already computed in earlier versions ("Pmol"). The correction is 10769now computed molecule-by-molecule if the Zmatrix format is used. 10770 10771* More stress output items. 10772 10773If the intra-molecular stress is removed, the corrected static and 10774total stresses are printed in addition to the uncorrected items. 10775 10776The corrected Voigt form is also printed. 10777 10778* New form for the enthalpy 10779 10780The enthalpy is computed in two ways: as the "target enthalpy" using 10781the target pressure, and as the "real" enthalpy using the trace of the 10782current stress tensor as an estimation of the pressure. Ideally, both 10783values should be identical at convergence, but the "target enthalpy" 10784might have significant errors coming from the tolerances. 10785 10786* Correction of the sign of the stress in molecularmechanics.F90 10787 10788For MM potentials, attractive interactions are represented by 10789*positive* C coefficients in the MM.Potentials block. Then the 10790MM energy is negative, as it should be. However, the sign of 10791the stress was wrong in the original implementation. Now (also 10792printed as MM-Stress) it should come out as a positive contribution 10793(negative pressure), forcing the cell to contract. 10794 10795* New Utils/MM_Examples directory. 10796 10797An example of the use of MM potentials to introduce van der Waals 10798interactions in an approximate manner (for the artificial example 10799of fcc He). 10800 10801* New .make file for Hreidar at ETH Zurich. 10802 108032007-06-4 14:40 GMT Alberto Garcia <albertog@icmab.es> patch-60 10804 10805Summary: Origin shift was applied after possible coordinate scaling 10806 10807In routine coor, the origin shift was applied after the section in 10808which the coordinates are re-scaled (from Ang to Bohr, or from fractional 10809to cartesian, etc). However, it is clear in the manual that the shift 10810vector is in the same units and format as the input coordinates. 10811 10812The shift is now applied right after reading the coordinate block. 10813 10814NOTE: This does not apply to the Zmatrix routine, which has *its own* 10815conventions for origin shift, neither to coordinates read from an XV 10816file or a Struct file. 10817 108182007-06-4 14:30 GMT Alberto Garcia <albertog@icmab.es> patch-59 10819 10820Summary: Undefined var in kgridinit, iohs MPI write, pdosg array bound 10821 10822* Initialize "genlogic" to .false. before it is used in kgridinit. 10823 10824* Fix index in write statement in iohs in parallel affecting list array. 10825 10826* Fix dimension of dpr in pdosg. Clarify names of variables in pdos. 10827 In pdosg, dpr was wrongly dimensioned to no_l (modern notation) instead of no_u. 10828 108292007-05-17 900:12 GMT Alberto Garcia <albertog@icmab.es> patch-58 10830 10831Summary: Refinements of XML tester. New ioncat program 10832 10833Eduardo Anglada's bugfixes to the XML tester package: 10834 10835* Apply bugfixes to compare_m.f90. 10836* Initialize variable 'len' in m_reader.f90 to suit buggy compilers. 10837* Use the 'normalize' DOM function to consolidate adjacent text nodes. 10838 (rather than changing the pcdata processing in the SAX parser). 10839* Add removal of tolerances.dat and diff output to the 'clean' target 10840 in test.mk 10841 10842New features: 10843 10844* Use the command-line options processor. Valid options: 10845 10846 -d : enable debugging output. 10847 -t FILE : specify tolerances file. 10848 -g LOGTOL: specify (minus log10 of) global tolerance 10849 -s : stop after first error 10850 -e NUM : stop after NUM errors 10851 10852* By default, the tester does not stop after errors. 10853 10854* Enhance xmlparser/Tests/compare.sh to accept options. 10855 10856* Modified f2kcli.F90 to fit gfortran (this compiler 10857already implements all the functionality, so a 10858preprocessor symbol is used to disable the module). 10859 10860* Added Src/Sys/gfortran.make 10861 10862------------- 10863 10864* New program "ioncat" in Src to analyze the content of .ion files. 10865 10866 Usage: ioncat [options] Species_Label 10867 Options: 10868 10869 -s : Show header information 10870 -i : Print indexes of unique orbitals 10871 -j : Print indexes of unique KB projectors 10872 -o ORBINDEX : Generate table for orbital ORBINDEX 10873 -k KBINDEX : Generate table for KB proj KBINDEX 10874 -v : Generate table for Vna potential 10875 -Z : Zoom in near rc for table generation 10876 -h : Print this help message 10877 10878The accompanying script ionplot.sh shows how to drive 10879ioncat to plot the results. 10880 108812007-05-13 20:00:12 GMT Alberto Garcia <albertog@icmab.es> patch-57 10882 10883Summary: MareNostrum fixes. zdrot to blas. obj_setup. compare_m syntax 10884 10885* Add "." to MPI_INCLUDE, and INCFLAGS to default rules in MN's .make file. 10886* Remove old MN .make file. 10887* Do not link Reference-xml in obj_setup.sh 10888* Move zdrot routine from dc_lapack.f to blas.f 10889 108902007-05-12 18:00:12 GMT Alberto Garcia <albertog@icmab.es> patch-56 10891 10892Summary: Fixes for compilation of test-xml and MPI tests 10893 10894* A warning is now printed if the user tries to invoke 'make' 10895from the xmlparser or MPI directories to compile test-xml or 10896the MPI tests, so that the proper VPATH is used. 10897 10898* Add pxf.o dependency to test-xml 10899 10900* Add INCFLAGS to default suffix rule to Intel mkl .make file. 10901 109022007-05-07 09:50:12 GMT Alberto Garcia <albertog@icmab.es> patch-55 10903 10904Summary: Portability fixes: xmlparser split. New mpich pe in matterhorn 10905 10906* Split the compilation of libxmlparser.a and the xml-test program, as the 10907 PGI compiler cannot deal with the DOM part. 10908* Compile test programs in Src/MPI at main compilation time. (It is harder 10909 to do it later if vpath is used.) 10910 10911* New mpich .make files for matterhorn 10912 (the oci.q queue does not support myrinet). New script in Tests/Scripts. 10913 109142007-04-30 08:50:12 GMT Alberto Garcia <albertog@icmab.es> patch-54 10915 10916Summary: Portability fixes (matterhorn/pgf90). Wider basis enthalpy field. 10917 10918 * agarcia@siesta.arch--2006/siesta-fix--matterhorn--0.1--patch-1 10919 More denchar and gen-basis objs 10920 10921 * agarcia@siesta.arch--2006/siesta-fix--matterhorn--0.1--patch-2 10922 Wider field in BASIS_ENTHALPY 10923 10924 * agarcia@siesta.arch--2006/siesta-fix--matterhorn--0.1--patch-3 10925 Fix matterhorn Sys files for VPATH compilation 10926 10927 109282007-04-27 16:15:12 GMT Alberto Garcia <albertog@icmab.es> patch-53 10929 10930Summary: Merge of XML tester by Eduardo Anglada 10931Keywords: 10932 10933* New command-line interface 10934* Merged new functionality into old test.mk 10935 10936* Some of the new tests are not yet properly integrated. 10937 (reference output files and xml files have to be 10938 re-generated). 10939 109402007-04-17 13:54:12 GMT Alberto Garcia <albertog@icmab.es> patch-52 10941 10942Summary: New method for split-norm calculation 10943 10944The method for generating multiple-zeta orbitals is based on fitting a 10945function of the form r^l (C_1*r^2 +C_2) at a certain point of the 10946initial (1st zeta) orbital. 10947 10948The criterion spelled out in the Siesta JPC paper seems to imply that 10949the split-norm parameter refers to the norm of the tail of the initial 10950orbital (i.e., the region to the right of the fitting point). However, 10951the actual code in Siesta takes it to mean the norm of the tail *plus* 10952the norm of the parabolic function in the inner region. The reasons 10953are mostly historical, having to do with finding a "good enough, universal" 10954default value for the split-norm parameter. 10955 10956The problem with the "parabola+tail" method is that it does not always 10957work, and this is bad for an unsupervised method like the simplex. For 10958example, if the first-zeta orbital has a relatively large slope at or 10959near rc , the smallest parabola one can fit (for radii very close to 10960rc) has a significant norm, and there is a minimum value for the 10961split-norm parameter. Thus the method will not work if the user (or 10962simplex) requests a split-norm greater than this value, and Siesta 10963will stop. This behavior is not uncommon. 10964 10965On the other hand, the norm of the tail region is of course smooth and 10966covers monotonically the whole range 0-1. It has very low contrast 10967near rc, meaning that in order to fit a 2nd-zeta orbital with a 10% 10968reduction in rc, one might need to use "tail-split-norms" of 0.001 or 10969smaller. 10970 10971New code for multiple split orbitals has been written to address these 10972issues, while at the same time maintaining backwards compatibility with 10973the old procedure. The code is controlled by the new fdf symbols: 10974 10975* PAO.NewSplitCode 10976 10977Enables a new, simpler way to match the multiple-zeta radii. 10978 10979If an old-style (tail+parabola) calculation is being done, perform a 10980scan of the tail+parabola norm in the whole range of the 1st-zeta 10981orbital, and store that in split_table. The construction of the 109822nd-zeta orbital involves simply scanning split_table to find the 10983appropriate place. Due to the idiosyncracies of the old algorithm, 10984the new one is not guaranteed to produce exactly the same results, 10985as it might settle on a neighboring grid point for the matching. 10986 10987* PAO.SplitTailNorm 10988 10989split_table is set to sqrt(1-norm(r)), to more closely match the 10990spirit of the JPC paper (the square root is introduced to make the 10991split norm values larger for 2nd-zeta radii in the vicinity of rc). 10992 10993* PAO.FixSplitTable 10994 10995The old-style split-table is fixed by applying a damping function that 10996takes it to zero at the 1st-zeta orbital radius. This option enables 10997PAO.NewSplitCode. 10998 10999 11000By default, all three symbols are .false., resulting in the use of the old 11001code. In this case, the program now stops if the requested split_norm 11002is smaller than the values on the table, and prints an explanation. 11003 110042007-04-17 09:54:12 GMT Alberto Garcia <albertog@icmab.es> patch-51 11005 11006 Summary: 11007 Fix tag in MPI send/receive in mulliken 11008 Revision: 11009 siesta-devel--reference--2.1--patch-51 11010 11011 * The undefined variable 'io' was used as tag... changed to itot, the 11012 orbital index. 11013 11014 * Trimmed mpibuff before writing. 11015 11016 11017 11018 modified files: 11019 Src/mulliken.F 11020 11021 new patches: 11022 agarcia@siesta.arch--2006/mulliken--agarcia--0.1--patch-1 11023 11024 110252007-03-19 14:18:58 GMT Alberto Garcia <albertog@icmab.es> patch-50 11026 11027 Summary: 11028 Add molecular mechanics documentation 11029 Revision: 11030 siesta-devel--reference--2.1--patch-50 11031 11032 Patches applied: 11033 11034 * agarcia@siesta.arch--2006/mulliken--agarcia--0.1--patch-1 11035 Fix tag in MPI send and receive in calculation of overlap 11036 11037 11038 modified files: 11039 Docs/siesta.ind Docs/siesta.tex 11040 110412007-03-14 22:30:31 GMT Alberto Garcia <albertog@icmab.es> patch-49 11042 11043Summary: VPATH-aware compilation for multiple executable versions 11044 11045Added Src/obj_setup.sh script, to be called from any directory on 11046which the build is going to take place, and modified slightly some 11047makefiles to make them VPATH-proof. The Tests directory is replicated 11048in the "build" directory. 11049 11050(The pristine Src directory should be "clean", without objects, or else 11051the compilation in the build directories will get confused) 11052 11053Example. From the top Siesta directory: 11054 11055mkdir Objs 11056cd Objs 11057sh ../Src/obj_setup.sh 11058../Src/configure --enable-fast 11059make 11060cd Tests 11061make clean; make 11062cd # Now a parallel version 11063mkdir ParaObjs 11064cd ParaObjs 11065sh ../Src/obj_setup.sh 11066cp ../Src/Sys/parallel.make ./arch.make 11067make 11068cd Tests 11069make clean; make 11070 110712007-03-09 9:40:31 GMT Alberto Garcia <albertog@icmab.es> patch-48 11072 11073Summary: Option to use fractional rc's for multiple zeta 11074 11075If the rc's for multiple-zeta orbitals are given as negative numbers 11076in the PAO.Basis block, they are interpreted as the corresponding 11077fractions of the rc for the first-zeta orbital. 11078 11079This is useful in basis optimization, to avoid having to include 11080explicitly the constraint that rc(izeta>1) < rc(izeta=1). 11081 11082Note however that, if the rc's are significantly larger than the 11083natural size of the atomic orbital, multiple-zeta orbitals will tend 11084to be very similar to the first (this is now flagged by the program as 11085a warning). The best procedure to avoid this is to use an explicit 11086split-norm value. 11087 110882007-03-08 19:30:31 GMT Alberto Garcia <albertog@icmab.es> patch-47 11089 11090Summary: First implementation of basis_enthalpy calculation 11091 11092New file BASIS_ENTHALPY contains the "effective basis enthalpy" 11093of Anglada et al. The pressure is determined from the fdf symbol 11094"BasisPressure", with a 0.2 GPa default. 11095 11096Further work: different weights to different species. 11097 110982007-02-25 20:30:31 GMT Alberto Garcia <albertog@icmab.es> patch-46 11099 11100Summary: Fix allocation of temporary array in savepsi in parallel 11101 11102Some nodes might not have any occupied orbitals assigned to them, so 11103one has to be careful in the allocation of a buffer array in MPI. 11104Allocate using the dimensions on the master node. 11105 11106+ Add 'show_distribution' routine to warn (for now) the user 11107 when there are nodes which do not handle any orbitals. 11108 11109+ Add experimental 'compare' target to Makefile. 11110 11111+ Add 'born_spin' test. 11112 111132007-02-23 16:17:31 GMT Alberto Garcia <albertog@icmab.es> patch-45 11114 11115 Summary: 11116 Clean up handling of ntote in ksv and optical 11117 Revision: 11118 siesta-devel--reference--2.1--patch-45 11119 11120 11121 modified files: 11122 Src/ksv.f Src/optical.F 11123 11124 111252007-02-23 16:16:10 GMT Alberto Garcia <albertog@icmab.es> patch-44 11126 11127 Summary: 11128 Wrap writes for MPI 11129 Revision: 11130 siesta-devel--reference--2.1--patch-44 11131 11132 11133 modified files: 11134 Src/broyden_optim.F Src/siesta.F 11135 11136 111372007-02-23 15:37:15 GMT Alberto Garcia <albertog@icmab.es> patch-43 11138 11139 Summary: 11140 Wrap io_close for MPI in iohs.F 11141 Revision: 11142 siesta-devel--reference--2.1--patch-43 11143 11144 The calls to io_close were not restricted to the master node. 11145 11146 11147 11148 modified files: 11149 Src/iohs.F 11150 11151 111522007-02-23 15:14:11 GMT Alberto Garcia <albertog@icmab.es> patch-42 11153 11154 Summary: 11155 zval wrongly treated as MPI_integer in broadcast_basis 11156 Revision: 11157 siesta-devel--reference--2.1--patch-42 11158 11159 After the introduction of the hybrid-atom capability, zval is a real 11160 number. It was however treated as MPI_integer in broadcast_basis. 11161 11162 11163 modified files: 11164 Src/broadcast_basis.F 11165 11166 111672007-02-22 17:35:07 GMT Alberto Garcia <albertog@icmab.es> patch-41 11168 11169 Summary: 11170 New compilation and test-running files for arina 11171 Revision: 11172 siesta-devel--reference--2.1--patch-41 11173 11174 New file Src/Sys/arina-mlib.make for the new library setup 11175 at the itanium machine at the UPV. Src/Confs/arina-mpi.conf 11176 is now obsolete. 11177 11178 Update of Tests/Scripts/arina.pbs. 11179 11180 11181 new files: 11182 Src/Sys/.arch-ids/arina-mlib.make.id Src/Sys/arina-mlib.make 11183 11184 modified files: 11185 Docs/CHANGES Docs/siesta.ind Src/Confs/arina-mpi.conf 11186 Tests/Scripts/arina.pbs version.info 11187 11188 111892007-02-21 11:09:21 GMT Alberto Garcia <albertog@icmab.es> patch-40 11190 11191 Summary: 11192 Update reference output for benzene test. New script for matterhorn 11193 Revision: 11194 siesta-devel--reference--2.1--patch-40 11195 11196 * The old Reference/benzene.out contained debugging output. 11197 * Updated script to run parallel jobs under SGE on matterhorn. 11198 * Declare etime in bsd.f 11199 11200 11201 modified files: 11202 Docs/CHANGES Docs/siesta.tex Src/bsd.f 11203 Tests/Reference/benzene.out Tests/Scripts/matterhorn-gm.sge 11204 version.info 11205 11206 112072007-02-21 10:49:20 GMT Alberto Garcia <albertog@icmab.es> patch-39 11208 11209 Summary: 11210 Fix units conversion in Util/Optical/optical.f 11211 Revision: 11212 siesta-devel--reference--2.1--patch-39 11213 11214 (Daniel Sanchez) 11215 11216 Optical.f is a program to analyze the file .EPSIMG and obtain the 11217 optical properties. A unit conversion was done from eV to Ry instead 11218 of to Ha. 11219 11220 11221 modified files: 11222 Docs/CHANGES Docs/siesta.tex Src/version.F90 11223 Util/Optical/optical.f version.info 11224 11225 112262007-02-21 10:38:40 GMT Alberto Garcia <albertog@icmab.es> patch-38 11227 11228 Summary: 11229 Fix of zmatrix code to deal with degenerate case 11230 Revision: 11231 siesta-devel--reference--2.1--patch-38 11232 11233 (Colin Glass, Alberto Garcia) 11234 11235 The first three atoms in a zmatrix molecule are special. The torsion 11236 angle of the third is specified with respect to a plane formed by the 11237 first two atoms and a notional atom located along the z axis from the 11238 second. If the second atom is located also along the z axis from the 11239 first, the plane is undefined. 11240 11241 The routine to compute the cartesian coordinates from the Zmatrix 11242 coordinates deals now with the third atom in a more controlled way, 11243 and uses the phi angle of the second atom (which should be specified 11244 even if theta=0) to determine correctly the reference plane for the 11245 torsion. 11246 11247 Notation: the atoms used as reference for the calculation of the 11248 position of the current atom are: 11249 11250 i: determines the bond length 11251 j: together with i, determines the angle theta 11252 k: together with i and j, determines the reference plane for the torsion. 11253 11254 In case of alignment of i,j, and k, we use the azimuth (phi) of i with 11255 respect to j to fix the reference plane. 11256 11257 If "i" is the first atom in the Zmatrix, its Zmatrix coordinates are X 11258 Y Z, and we cannot use its "phi angle" as reference, but in fact this 11259 angle can be easily computed as phi_ref = phi_ji - pi, where phi_ji is 11260 the azimuth of the j atom with respect to i. 11261 11262 Routine z2cgen is passed phi_ref after checking the above conditions. 11263 11264 This fix only applies only to the calculation of the coordinates of the third 11265 atom, but it could presumably be generalized to intercept singular cases 11266 at any link of the zmatrix, at which i, j, and k could lie along a line. 11267 11268 * New checks to detect attempts to use "fractional coordinates" when 11269 the unit cell is not yet defined at the time of reading the Zmatrix. 11270 11271 * New test "benzene" 11272 11273 11274 new files: 11275 Tests/Reference/.arch-ids/benzene.out.id 11276 Tests/Reference/benzene.out Tests/benzene/.arch-ids/=id 11277 Tests/benzene/.arch-ids/benzene.fdf.id 11278 Tests/benzene/.arch-ids/benzene.pseudos.id 11279 Tests/benzene/.arch-ids/makefile.id Tests/benzene/benzene.fdf 11280 Tests/benzene/benzene.pseudos Tests/benzene/makefile 11281 11282 modified files: 11283 Docs/CHANGES Src/version.F90 Src/zmatrix.F Tests/Makefile 11284 version.info 11285 11286 new directories: 11287 Tests/benzene Tests/benzene/.arch-ids 11288 11289 new patches: 11290 agarcia@siesta.arch--2006/siesta--zmatrix--0.1--base-0 11291 agarcia@siesta.arch--2006/siesta--zmatrix--0.1--patch-1 11292 agarcia@siesta.arch--2006/siesta--zmatrix--0.1--patch-2 11293 agarcia@siesta.arch--2006/siesta--zmatrix--0.1--patch-3 11294 agarcia@siesta.arch--2006/siesta--zmatrix--0.1--patch-4 11295 agarcia@siesta.arch--2006/siesta--zmatrix--0.1--patch-5 11296 agarcia@siesta.arch--2006/siesta--zmatrix--0.1--patch-6 11297 agarcia@siesta.arch--2006/siesta--zmatrix--0.1--patch-7 11298 agarcia@siesta.arch--2006/siesta--zmatrix--0.1--patch-8 11299 agarcia@siesta.arch--2006/siesta--zmatrix--0.1--patch-9 11300 11301 113022007-02-20 16:23:24 GMT Alberto Garcia <albertog@icmab.es> patch-37 11303 11304 Summary: 11305 Correction to k-point grid update fix 11306 Revision: 11307 siesta-devel--reference--2.1--patch-37 11308 11309 The previous k-point fix was incorrect, as it changed the interface of 11310 kgridinit and kgrid, which are used in other parts of the program. A 11311 cleaner approach uses a module to hold the information about the 11312 k-point grid for selfconsistency. 11313 11314 The k-point grid used for achieving self-consistency is now 11315 re-computed inside the geometry loop if: 11316 11317 The calculation is a cell-optimization one (i.e., if MD.VariableCell 11318 is .true.), or if it is a "siesta-server" run. This is the old default. 11319 11320 Additionally, if the user sets the fdf flag "ChangeKgridInMD" to 11321 .true., the grid will be recomputed also during MD runs that potentially 11322 change the unit cell: Parrinello-Rahman, Nose-Parrinello-Rahman, and 11323 Anneal. 11324 11325 New test: born 11326 11327 11328 new files: 11329 Src/.arch-ids/find_kgrid.F.id Src/.arch-ids/kpoint_grid.F90.id 11330 Src/Sys/.arch-ids/intel-checks.make.id 11331 Src/Sys/intel-checks.make Src/find_kgrid.F Src/kpoint_grid.F90 11332 Tests/Reference/.arch-ids/born.out.id Tests/Reference/born.out 11333 Tests/born/.arch-ids/=id Tests/born/.arch-ids/FC.fdf.id 11334 Tests/born/.arch-ids/born.fdf.id 11335 Tests/born/.arch-ids/born.pseudos.id 11336 Tests/born/.arch-ids/makefile.id Tests/born/FC.fdf 11337 Tests/born/born.fdf Tests/born/born.pseudos 11338 Tests/born/makefile 11339 11340 modified files: 11341 Docs/CHANGES Docs/siesta.ind Docs/siesta.tex Src/Makefile 11342 Src/kgrid.F Src/kgridinit.F Src/siesta.F Tests/Makefile 11343 version.info 11344 11345 new directories: 11346 Tests/born Tests/born/.arch-ids 11347 11348 113492007-02-02 10:14:02 GMT Alberto Garcia <albertog@icmab.es> patch-36 11350 11351 Summary: 11352 Add graphite_c6_full test for more realistic vdW test 11353 Revision: 11354 siesta-devel--reference--2.1--patch-36 11355 11356 The original graphite test prepared by J. Gale to show an 11357 example of adding two-body potentials to simulate van der Waals 11358 interactions has been added as graphite_c6_full. It is not 11359 executed by default as it requires significant CPU time. 11360 11361 + Minor cosmetic changes in filter_subs.f and kgridinit.F 11362 11363 11364 11365 new files: 11366 Tests/Pseudos/.arch-ids/C.pbe.psf.id Tests/Pseudos/C.pbe.psf 11367 Tests/graphite_c6_full/.arch-ids/=id 11368 Tests/graphite_c6_full/.arch-ids/graphite_c6_full.fdf.id 11369 Tests/graphite_c6_full/.arch-ids/graphite_c6_full.pseudos.id 11370 Tests/graphite_c6_full/.arch-ids/makefile.id 11371 Tests/graphite_c6_full/graphite_c6_full.fdf 11372 Tests/graphite_c6_full/graphite_c6_full.pseudos 11373 Tests/graphite_c6_full/makefile 11374 11375 modified files: 11376 Docs/CHANGES Src/filter_subs.f Src/kgridinit.F version.info 11377 11378 new directories: 11379 Tests/graphite_c6_full Tests/graphite_c6_full/.arch-ids 11380 11381 113822007-01-31 16:53:19 GMT Alberto Garcia <albertog@icmab.es> patch-35 11383 11384 Summary: 11385 Merge filtering package by Eduardo Anglada 11386 Revision: 11387 siesta-devel--reference--2.1--patch-35 11388 11389 Code that implements the ideas in 11390 11391 Anglada E, Soler JM 11392 Filtering a distribution simultaneously in real and Fourier space 11393 PHYSICAL REVIEW B 73 (11): Art. No. 115122 MAR 2006 11394 11395 has been merged. 11396 11397 The filtering is selected by fdf directives of the form: 11398 11399 PAO.Filter .true. 11400 VNA.filter .true. 11401 PCC.filter .true. 11402 11403 and the default parameters are determined by heuristics based 11404 on the value of the MeshCutoff. 11405 11406 (A manual entry is being written) 11407 11408 New tests: 11409 11410 Tests/pb_bulk 11411 Tests/pb_bulk_1000 11412 Tests/pb_filter_all 11413 Tests/pb_filter_basis 11414 Tests/pb_filter_nopcc 11415 Tests/pb_filter_pcc 11416 Tests/pb_filter_vna 11417 Tests/var_cell_filter 11418 11419 11420 new files: 11421 Src/.arch-ids/filter.f90.id Src/.arch-ids/filter_subs.f.id 11422 Src/filter.f90 Src/filter_subs.f 11423 Tests/Pseudos/.arch-ids/Pb.psf.id Tests/Pseudos/Pb.psf 11424 Tests/Reference/.arch-ids/pb_bulk.out.id 11425 Tests/Reference/.arch-ids/pb_bulk_1000.out.id 11426 Tests/Reference/.arch-ids/pb_filter_all.out.id 11427 Tests/Reference/.arch-ids/pb_filter_basis.out.id 11428 Tests/Reference/.arch-ids/pb_filter_nopcc.out.id 11429 Tests/Reference/.arch-ids/pb_filter_pcc.out.id 11430 Tests/Reference/.arch-ids/pb_filter_vna.out.id 11431 Tests/Reference/.arch-ids/var_cell_filter.out.id 11432 Tests/Reference/pb_bulk.out Tests/Reference/pb_bulk_1000.out 11433 Tests/Reference/pb_filter_all.out 11434 Tests/Reference/pb_filter_basis.out 11435 Tests/Reference/pb_filter_nopcc.out 11436 Tests/Reference/pb_filter_pcc.out 11437 Tests/Reference/pb_filter_vna.out 11438 Tests/Reference/var_cell_filter.out 11439 Tests/pb_bulk/.arch-ids/=id 11440 Tests/pb_bulk/.arch-ids/makefile.id 11441 Tests/pb_bulk/.arch-ids/pb_bulk.fdf.id 11442 Tests/pb_bulk/.arch-ids/pb_bulk.pseudos.id 11443 Tests/pb_bulk/makefile Tests/pb_bulk/pb_bulk.fdf 11444 Tests/pb_bulk/pb_bulk.pseudos Tests/pb_bulk_1000/.arch-ids/=id 11445 Tests/pb_bulk_1000/.arch-ids/makefile.id 11446 Tests/pb_bulk_1000/.arch-ids/pb_bulk_1000.fdf.id 11447 Tests/pb_bulk_1000/.arch-ids/pb_bulk_1000.pseudos.id 11448 Tests/pb_bulk_1000/makefile 11449 Tests/pb_bulk_1000/pb_bulk_1000.fdf 11450 Tests/pb_bulk_1000/pb_bulk_1000.pseudos 11451 Tests/pb_filter_all/.arch-ids/=id 11452 Tests/pb_filter_all/.arch-ids/makefile.id 11453 Tests/pb_filter_all/.arch-ids/pb_filter_all.fdf.id 11454 Tests/pb_filter_all/.arch-ids/pb_filter_all.pseudos.id 11455 Tests/pb_filter_all/makefile 11456 Tests/pb_filter_all/pb_filter_all.fdf 11457 Tests/pb_filter_all/pb_filter_all.pseudos 11458 Tests/pb_filter_basis/.arch-ids/=id 11459 Tests/pb_filter_basis/.arch-ids/makefile.id 11460 Tests/pb_filter_basis/.arch-ids/pb_filter_basis.fdf.id 11461 Tests/pb_filter_basis/.arch-ids/pb_filter_basis.pseudos.id 11462 Tests/pb_filter_basis/makefile 11463 Tests/pb_filter_basis/pb_filter_basis.fdf 11464 Tests/pb_filter_basis/pb_filter_basis.pseudos 11465 Tests/pb_filter_nopcc/.arch-ids/=id 11466 Tests/pb_filter_nopcc/.arch-ids/makefile.id 11467 Tests/pb_filter_nopcc/.arch-ids/pb_filter_nopcc.fdf.id 11468 Tests/pb_filter_nopcc/.arch-ids/pb_filter_nopcc.pseudos.id 11469 Tests/pb_filter_nopcc/makefile 11470 Tests/pb_filter_nopcc/pb_filter_nopcc.fdf 11471 Tests/pb_filter_nopcc/pb_filter_nopcc.pseudos 11472 Tests/pb_filter_pcc/.arch-ids/=id 11473 Tests/pb_filter_pcc/.arch-ids/makefile.id 11474 Tests/pb_filter_pcc/.arch-ids/pb_filter_pcc.fdf.id 11475 Tests/pb_filter_pcc/.arch-ids/pb_filter_pcc.pseudos.id 11476 Tests/pb_filter_pcc/makefile 11477 Tests/pb_filter_pcc/pb_filter_pcc.fdf 11478 Tests/pb_filter_pcc/pb_filter_pcc.pseudos 11479 Tests/pb_filter_vna/.arch-ids/=id 11480 Tests/pb_filter_vna/.arch-ids/makefile.id 11481 Tests/pb_filter_vna/.arch-ids/pb_filter_vna.fdf.id 11482 Tests/pb_filter_vna/.arch-ids/pb_filter_vna.pseudos.id 11483 Tests/pb_filter_vna/makefile 11484 Tests/pb_filter_vna/pb_filter_vna.fdf 11485 Tests/pb_filter_vna/pb_filter_vna.pseudos 11486 Tests/var_cell_filter/.arch-ids/=id 11487 Tests/var_cell_filter/.arch-ids/makefile.id 11488 Tests/var_cell_filter/.arch-ids/var_cell_filter.fdf.id 11489 Tests/var_cell_filter/.arch-ids/var_cell_filter.pseudos.id 11490 Tests/var_cell_filter/makefile 11491 Tests/var_cell_filter/var_cell_filter.fdf 11492 Tests/var_cell_filter/var_cell_filter.pseudos 11493 11494 modified files: 11495 Docs/CHANGES Src/Makefile Src/atom.f version.info 11496 11497 new directories: 11498 Tests/pb_bulk Tests/pb_bulk/.arch-ids Tests/pb_bulk_1000 11499 Tests/pb_bulk_1000/.arch-ids Tests/pb_filter_all 11500 Tests/pb_filter_all/.arch-ids Tests/pb_filter_basis 11501 Tests/pb_filter_basis/.arch-ids Tests/pb_filter_nopcc 11502 Tests/pb_filter_nopcc/.arch-ids Tests/pb_filter_pcc 11503 Tests/pb_filter_pcc/.arch-ids Tests/pb_filter_vna 11504 Tests/pb_filter_vna/.arch-ids Tests/var_cell_filter 11505 Tests/var_cell_filter/.arch-ids 11506 11507 115082007-01-25 17:34:07 GMT Alberto Garcia <albertog@icmab.es> patch-34 11509 11510 Summary: 11511 k-point sampling update when kgrid_cutoff is specified 11512 Revision: 11513 siesta-devel--reference--2.1--patch-34 11514 11515 The user can specify a kgrid_cutoff or a Monkhorst-Pack grid 11516 to determine the k-point sampling. If there are unit-cell 11517 changes during the calculation, the k-point set does not 11518 change if a MP grid has been specified (the sampling accuracy changes 11519 implicitly). 11520 11521 On the other hand, the k-point set should change in principle if a 11522 kgrid_cutoff has been given and the cell volume changes, but due to a 11523 programming error the k-point grid was fixed after the first 11524 iteration. 11525 11526 The error affects variable-cell calculations specifying a 11527 kgrid_cutoff. "Variable-cell" means that the unit cell changes 11528 during a calculation, as in cell optimization and the MD flavors 11529 Parrinello-Rahman, Nose-Parrinello-Rahman, and Annealing runs. 11530 11531 A user might want to avoid sudden changes in the k-point set 11532 while performing molecular dynamics runs or cell optimizations, 11533 notably if the calculations are not very well converged. In that 11534 case a MP grid, and not a kgrid_cutoff, should be specified. 11535 11536 A related problem that has been fixed in this patch is the 11537 possible overriding of the user's MP displacement specification after 11538 the first iteration. 11539 11540 There is no backwards compatibility after this bugfix. To recover the 11541 old behavior when a kgrid_cutoff was specified, the user should check 11542 the old output, extract the information about the MP grid generated 11543 automatically by the program, and put it in an MP block. 11544 11545 (Regeneration of reference outputs) 11546 11547 modified files: 11548 Docs/CHANGES Docs/siesta.ind Docs/siesta.tex Src/kgrid.F 11549 Src/kgridinit.F Src/siesta.F Tests/Reference/batio3.out 11550 Tests/Reference/bessel.out Tests/Reference/constant_volume.out 11551 Tests/Reference/fe.out Tests/Reference/fe_broyden.out 11552 Tests/Reference/floating.out Tests/Reference/graphite_c6.out 11553 Tests/Reference/h2o.out Tests/Reference/h2oZ.out 11554 Tests/Reference/h2o_basis.out Tests/Reference/h2o_dos.out 11555 Tests/Reference/h2o_findp_bug.out 11556 Tests/Reference/h2o_op_broyden.out 11557 Tests/Reference/h2o_orderN.out 11558 Tests/Reference/h2o_radialgrid.out 11559 Tests/Reference/h2o_reparam.out Tests/Reference/md_anneal.out 11560 Tests/Reference/md_nose.out Tests/Reference/md_npr.out 11561 Tests/Reference/md_pr.out Tests/Reference/md_verlet.out 11562 Tests/Reference/mgco3.out Tests/Reference/oxyn.out 11563 Tests/Reference/partial.out Tests/Reference/si2x1h.out 11564 Tests/Reference/si64.out Tests/Reference/si_bandpoints.out 11565 Tests/Reference/sih.out Tests/Reference/sih_fire.out 11566 Tests/Reference/sih_op_broyden.out 11567 Tests/Reference/var_cell.out Tests/Reference/zmatrix.out 11568 version.info 11569 115702007-01-22 19:50:32 GMT Alberto Garcia <albertog@icmab.es> patch-33 11571 11572 Summary: 11573 Initialize vol2 correctly in m_check_supercell.f 11574 Revision: 11575 siesta-devel--reference--2.1--patch-33 11576 11577 11578 modified files: 11579 Src/m_check_supercell.f 11580 11581 115822007-01-22 14:30:00 GMT Alberto Garcia <albertog@icmab.es> patch-32 11583 11584Summary: New treatment of fractional atoms in VCA. Bug fix in lmxo 11585 11586Instead of mixing with a "zero" pseudopotential, pseudopotentials 11587for a "fractionally occupied" site can be generated by simply 11588multiplying the potential and charges by the appropriate factor, 11589using the 'fractional' program, which resides in the top source 11590directory. 11591 11592There is no longer any need for the "zero" pseudopotential files. 11593 11594Bug fix: lmxo was not being set correctly for synthetic atoms. 11595 11596Test update: 'oxyn' and 'partial' reference outputs have been 11597regenerated. 'partial' now uses the 'fractional' program. 11598 11599NOTE: there are some instabilities in the outputs on the intel 11600compiler+library platform. 11601 11602 116032007-01-10 9:24:00 GMT Alberto Garcia <albertog@icmab.es> patch-31 11604 11605(Interim manual entry -- to be replaced by the automatic version later) 11606 11607Summary: Parallel bug fix and cleanup in writewave.F 11608Keywords: 11609 11610(Julian Gale) 11611 11612The code in writewave.F has been cleaned up a bit and a fix for a bug 11613appearing in parallel execution has been fixed. 11614 116152007-01-10 9:00:00 GMT Alberto Garcia <albertog@icmab.es> patch-30 11616 11617Summary: Update of CHANGES and siesta.tex for rmax.radial.grid feature 11618 11619 116202006-12-18 16:00:00 GMT Alberto Garcia <albertog@icmab.es> patch-29 11621 11622(Interim manual entry -- to be replaced by the automatic version later) 11623 11624Summary: Point at infinity set closer in atom for reparametrized calculations 11625Keywords: 11626 11627If the reference energy of a KB projector is not specified, the 11628program first computes a solution of Schrodinger's equation which is 11629zero at r(nrval), i.e., the largest radius, which is typically of the 11630order of 120 bohr (this is determined by the pseudopotential file). 11631 11632If the pseudopotential is reparametrized the number of radial points 11633needed increases substantially. This uncovers a weakness in the 11634routines in arw.f: they do not rescale the wavefunction as they 11635integrate the equation, so overflows can occur in some situations 11636(this has been seen with the pgf90 on opterons and with the NAG 11637compiler on a Mac). 11638 11639One solution (error-prone) could be to re-write the arw routines. 11640Another one is to re-define the point-at-infinity so that overflows do 11641not occur. It has been found that setting Rmax.Radial.Grid (new fdf 11642symbol) to 50.0 (implicit bohr units) removes the problem, while 11643maintaining numerical accuracy up to 10^-4 eV in total energy. (The 11644eigenvalues for KB generation (reported as "el" in the output) are of 11645course higher, and in some cases the corresponding rc is slightly 11646larger.) This insensitivity is due to the fact that all the relevant 11647KB projector information is constructed from the shape of the radial 11648function inside a much smaller box of radius 6 bohrs (harwired in the 11649program). 11650 11651PAOs (which need a similar integration to infinity if an energy shift 11652is used) are not affected at all by the change. 11653 11654The new fdf symbol Rmax.Radial.Grid does not need to be used if 11655Reparametrize.Pseudos is set (its default is then set to 50.0). 11656 11657 116582006-12-17 22:30:00 GMT Alberto Garcia <albertog@icmab.es> patch-28 11659 11660 (Manual entry) 11661 11662 Summary: 11663 Update of CHANGES file and Reference outputs (Siesta-BSC-base-C1) 11664 Revision: 11665 siesta-devel--reference--2.1--patch-28 11666 11667 Final packaging for the Siesta-BSC-base candidate. 11668 11669 116702006-12-17 18:36:41 GMT Alberto Garcia <albertog@icmab.es> patch-27 11671 11672 Summary: 11673 Safeguard in floating point comparison in sorting routine 11674 Revision: 11675 siesta-devel--reference--2.1--patch-27 11676 11677 To avoid instabilities leading to compiler-dependent 11678 behavior, a smearing in the .LT. tests has been introduced 11679 in routine ordix in module sorting. 11680 11681 The smearing parameter has been set to 11682 11683 double precision, parameter :: delta = 1.0d-12 11684 11685 11686 11687 modified files: 11688 Src/sorting.f Src/version.F90 version.info 11689 11690 new patches: 11691 siesta@uam.es--2006/siesta--release--2.0--patch-27 11692 11693 116942006-12-17 18:26:01 GMT Alberto Garcia <albertog@icmab.es> patch-26 11695 11696 Summary: 11697 Allow lifting of even/odd restrictions in radial grid 11698 Revision: 11699 siesta-devel--reference--2.1--patch-26 11700 11701 The old code in arw.f needed to work with an odd number of points in 11702 the radial grid. That restriction has been lifted by coding a new 11703 "Simpson" integration routine (routine integrator in arw.f). 11704 11705 Those sections of atom.f in which the number of points is redefined 11706 to make it odd (thus shifting the cutoff radii in the process) have 11707 been wrapped in if tests. If the fdf symbol 'Restricted.Radial.Grid' is 11708 set to .false., those sections will not be executed. 11709 11710 Together with the 'Reparametrize.Pseudos' feature, this change will 11711 allow a tighter mapping between the rc's specified externally (e.g., 11712 by a simplex driver) and those actually used by the program. 11713 11714 * New test: 11715 11716 h2o_radialgrid 11717 11718 new files: 11719 Tests/h2o_radialgrid/.arch-ids/=id 11720 Tests/h2o_radialgrid/.arch-ids/h2o_radialgrid.fdf.id 11721 Tests/h2o_radialgrid/.arch-ids/h2o_radialgrid.pseudos.id 11722 Tests/h2o_radialgrid/.arch-ids/makefile.id 11723 Tests/h2o_radialgrid/h2o_radialgrid.fdf 11724 Tests/h2o_radialgrid/h2o_radialgrid.pseudos 11725 Tests/h2o_radialgrid/makefile 11726 11727 modified files: 11728 Docs/siesta.ind Docs/siesta.tex Src/Makefile Src/arw.f 11729 Src/atom.f Src/basis_specs.f Src/version.F90 Tests/Makefile 11730 Tests/h2o_basis/h2o_basis.fdf version.info 11731 11732 new directories: 11733 Tests/h2o_radialgrid Tests/h2o_radialgrid/.arch-ids 11734 11735 117362006-12-17 18:01:18 GMT Alberto Garcia <albertog@icmab.es> patch-25 11737 11738 Summary: 11739 Allow user-directed switching of 'findp bug' 11740 Revision: 11741 siesta-devel--reference--2.1--patch-25 11742 11743 * In order to make it easier to compare with previous calculations, 11744 a new symbol, PAO.Keep.Findp.Bug, is now read. If .true., the old 11745 code in findp is enabled. 11746 11747 * Other fixes: 11748 11749 - Removal of a spurious io_close call in atom.f 11750 - More clear warning when rc(nzeta > 1) /= 0 if a per-shell 11751 split-norm is specified. 11752 11753 * New test: 11754 11755 h2o_findp_bug 11756 11757 11758 new files: 11759 Tests/Reference/.arch-ids/h2o_findp_bug.out.id 11760 Tests/Reference/h2o_findp_bug.out 11761 Tests/h2o_findp_bug/.arch-ids/=id 11762 Tests/h2o_findp_bug/.arch-ids/h2o_findp_bug.fdf.id 11763 Tests/h2o_findp_bug/.arch-ids/h2o_findp_bug.pseudos.id 11764 Tests/h2o_findp_bug/.arch-ids/makefile.id 11765 Tests/h2o_findp_bug/h2o_findp_bug.fdf 11766 Tests/h2o_findp_bug/h2o_findp_bug.pseudos 11767 Tests/h2o_findp_bug/makefile 11768 11769 modified files: 11770 Docs/siesta.ind Docs/siesta.tex Src/Sys/macosx-xlf.make 11771 Src/atom.f Src/basis_specs.f Tests/Makefile 11772 11773 new directories: 11774 Tests/h2o_findp_bug Tests/h2o_findp_bug/.arch-ids 11775 11776 117772006-12-14 18:34:34 GMT Alberto Garcia <albertog@icmab.es> patch-24 11778 11779 Summary: 11780 Fixes for latest features. 11781 Revision: 11782 siesta-devel--reference--2.1--patch-24 11783 11784 * In basis_specs.f, the explicit rc's for multiple-zeta orbitals were set 11785 erroneously to zero. Now the user is warned of a possible conflict with 11786 the specified split_norm parameter. 11787 11788 * In pseudopotential.f, a call to io_close was missing in the dumping routine. 11789 11790 * Function symbol was called inside I/O statements in pixmol, coxmol, 11791 and coceri. 11792 11793 * Molecularmechanics.F90 always printed a sentence about two-body potentials, 11794 even if they were not used. Removed. 11795 11796 * oxyn and partial tests added to Tests/Makefile. 11797 11798 * Tests/partial/script.sh now compiles mixps if it is not built. 11799 11800 * Src/Sys/macosx-xlf.make modified to compile parsing.f without optimization. 11801 11802 * Tests/h2o/h2o.fdf is back to the classic version (removal of 11803 reparametrization option) 11804 11805 11806 modified files: 11807 Src/Sys/macosx-xlf.make Src/basis_specs.f Src/basis_types.f 11808 Src/coceri.f Src/coxmol.f Src/molecularmechanics.F90 11809 Src/periodic_table.f Src/pixmol.f Src/pseudopotential.f 11810 Src/version.F90 Tests/Makefile Tests/h2o/h2o.fdf 11811 Tests/partial/script.sh version.info 11812 11813 118142006-12-14 11:13:48 GMT Alberto Garcia <albertog@icmab.es> patch-23 11815 11816 Summary: 11817 Add grid function evaluator program 11818 Revision: 11819 siesta-devel--reference--2.1--patch-23 11820 11821 11822 New program /Util/grid2val : a "stream evaluator" for functions 11823 defined on the grid. 11824 11825 11826 new files: 11827 Util/.arch-ids/grid2val.f.id Util/grid2val.f 11828 11829 modified files: 11830 Src/version.F90 Util/README version.info 11831 11832 new patches: 11833 agarcia@siesta.arch--2006/siesta--alchemy--0.1--patch-24 11834 11835 118362006-12-14 10:52:11 GMT Alberto Garcia <albertog@icmab.es> patch-22 11837 11838 Summary: 11839 New auxiliary files for compilation and execution 11840 Revision: 11841 siesta-devel--reference--2.1--patch-22 11842 11843 Added pdlaprnt.f file from PBLAS to Src/MPI, with an optional Makefile symbol 11844 to enable its compilation. That routine is missing in some system libraries, 11845 and it is needed to compile the pblas test. 11846 11847 Modified Confs/matterhorn* to add a warning related to the need to compile 11848 some files without optimization 11849 11850 Added Confs/macosx-nag-cdf.sh 11851 11852 Tests/Scripts now contains cryst-mpd.sge and simple_parallel.sh for runs 11853 on a Rocks cluster (batch and single-node-interactive) using mpd. 11854 11855 Added Src/Sys/mare-nostrum.make (experimental) 11856 11857 11858 11859 new files: 11860 Src/Confs/.arch-ids/macosx-nag-cdf.conf.id 11861 Src/Confs/macosx-nag-cdf.conf Src/MPI/.arch-ids/pdlaprnt.f.id 11862 Src/MPI/pdlaprnt.f Src/Sys/.arch-ids/mare-nostrum.make.id 11863 Src/Sys/mare-nostrum.make 11864 Tests/Scripts/.arch-ids/cryst-mpd.sge.id 11865 Tests/Scripts/cryst-mpd.sge 11866 11867 modified files: 11868 Src/Confs/matterhorn-gm.conf Src/Confs/matterhorn-serial.conf 11869 Src/MPI/Makefile Tests/Scripts/matterhorn-gm.sge 11870 11871 new patches: 11872 agarcia@siesta.arch--2006/siesta-devel--agarcia--2.1--patch-24 11873 agarcia@siesta.arch--2006/siesta-devel--agarcia--2.1--patch-37 11874 11875 118762006-12-13 15:12:04 GMT Alberto Garcia <albertog@icmab.es> patch-21 11877 11878 Summary: 11879 Packaging of soft-confinement code in a subroutine 11880 Revision: 11881 siesta-devel--reference--2.1--patch-21 11882 11883 The computation of the soft-confinement potential has been moved to 11884 the routine "build_vsoft" at the end of the atom module. 11885 11886 The naming convention for the relevant files has changed. There is 11887 now a file per (l,nsm) shell, with a name of the form 11888 11889 AtomLabel.Ll.nsm.confpot 11890 11891 where l is the angular momentum. 11892 11893 11894 modified files: 11895 Src/atom.f Src/version.F90 version.info 11896 11897 118982006-12-13 14:05:57 GMT Alberto Garcia <albertog@icmab.es> patch-20 11899 11900 Summary: 11901 Update CHANGES. Set version to 2.1.20 11902 Revision: 11903 siesta-devel--reference--2.1--patch-20 11904 11905 11906 modified files: 11907 Docs/CHANGES Src/version.F90 version.info 11908 119092006-12-13 13:55:55 GMT Alberto Garcia <albertog@icmab.es> patch-19 11910 11911 Summary: 11912 Printout of info on interatomic distances 11913 Revision: 11914 siesta-devel--reference--2.1--patch-19 11915 11916 A new routine "bonds" based on "shaper" has been created to compute 11917 the interatomic distances. Output is to file "slabel.BONDS" upon first 11918 reading the structural information, and to file "slabel.BONDS_FINAL" 11919 after the last geometry iteration. The neighbors are identified by 11920 atom number and symbol, but the positions reported are those of the 11921 equivalent atom in the unit cell. 11922 11923 Distances are computed up to a maximum of Max.Bond.Distance (default 11924 6.0 Bohr). 11925 11926 A new routine "sort" based on indexx from Numerical Recipes has been 11927 added to file "recipes.f". 11928 11929 11930 new files: 11931 Src/.arch-ids/bonds.f.id Src/bonds.f 11932 11933 modified files: 11934 Docs/siesta.ind Docs/siesta.tex Src/Makefile Src/recipes.f 11935 Src/siesta.F version.info 11936 11937 new patches: 11938 agarcia@siesta.arch--2006/siesta--alchemy--0.1--patch-23 11939 agarcia@siesta.arch--2006/siesta-devel--agarcia--2.1--patch-38 11940 11941 119422006-12-13 11:26:57 GMT Alberto Garcia <albertog@icmab.es> patch-18 11943 11944 Summary: 11945 Simple molecular mechanics and metadynamics 11946 Revision: 11947 siesta-devel--reference--2.1--patch-18 11948 11949 (From Julian Gale's jgale@siesta.arch--2005/siesta-general--jgale--2.1) 11950 11951 * molecularmechanics.f90 - new routine added and called from siesta.F to 11952 compute a C6/C8/C10 dispersion term using either the undamped Cn/r**n 11953 or the Tang-Toennes damped forms. 11954 11955 * siesta.F has been modified and a routine metaforce.F added to 11956 introduce a Gaussian force between a pair of atoms. This is useful for 11957 a metadynamics approach. 11958 11959 New test: graphite_c6 (stripped-down version) 11960 11961 new files: 11962 Src/.arch-ids/metaforce.F.id 11963 Src/.arch-ids/molecularmechanics.F90.id Src/metaforce.F 11964 Src/molecularmechanics.F90 11965 Tests/Reference/.arch-ids/graphite_c6.out.id 11966 Tests/Reference/graphite_c6.out 11967 Tests/graphite_c6/.arch-ids/=id 11968 Tests/graphite_c6/.arch-ids/graphite_c6.fdf.id 11969 Tests/graphite_c6/.arch-ids/graphite_c6.pseudos.id 11970 Tests/graphite_c6/.arch-ids/makefile.id 11971 Tests/graphite_c6/graphite_c6.fdf 11972 Tests/graphite_c6/graphite_c6.pseudos 11973 Tests/graphite_c6/makefile 11974 11975 modified files: 11976 Src/Makefile Src/basis_specs.f Src/redata.F Src/siesta.F 11977 Tests/Makefile 11978 11979 new directories: 11980 Tests/graphite_c6 Tests/graphite_c6/.arch-ids 11981 11982 new patches: 11983 agarcia@siesta.arch--2006/siesta-devel--agarcia--2.1--patch-49 11984 agarcia@siesta.arch--2006/siesta-devel--agarcia--2.1--patch-51 11985 11986 119872006-12-13 10:49:32 GMT Alberto Garcia <albertog@icmab.es> patch-17 11988 11989 Summary: 11990 Scripting utilities 11991 Revision: 11992 siesta-devel--reference--2.1--patch-17 11993 11994 Util/Scripting contains some proof-of-concept and prototype 11995 python modules and scripts. 11996 11997 Most of the functionality is based on the ASE package of the CAMPOS 11998 project. See http://oldwww.fysik.dtu.dk/CAMPOS 11999 12000 The necessary modules are in the Siesta directory. The package can 12001 also be installed in the appropriate Python directory using the 12002 setup.py file provided. The scripts in the top directory could 12003 then be transported anywhere. 12004 12005 Note that the location of the siesta executable must be specified 12006 in the scripts at this point. 12007 12008 Directory scripts/ contains some general-purpose utilities. 12009 12010 new files: 12011 Util/Scripting/.arch-ids/=id 12012 Util/Scripting/.arch-ids/README.id 12013 Util/Scripting/.arch-ids/amoeba.py.id 12014 Util/Scripting/.arch-ids/ase.py.id 12015 Util/Scripting/.arch-ids/ase_newton.py.id 12016 Util/Scripting/.arch-ids/ase_relax.py.id 12017 Util/Scripting/.arch-ids/ase_verlet.py.id 12018 Util/Scripting/.arch-ids/bond.py.id 12019 Util/Scripting/.arch-ids/client.py.id 12020 Util/Scripting/.arch-ids/h2o.py.id 12021 Util/Scripting/.arch-ids/setup.py.id 12022 Util/Scripting/.arch-ids/simplex_optim.py.id 12023 Util/Scripting/README Util/Scripting/Siesta/.arch-ids/=id 12024 Util/Scripting/Siesta/.arch-ids/Interface.py.id 12025 Util/Scripting/Siesta/.arch-ids/__init__.py.id 12026 Util/Scripting/Siesta/.arch-ids/calculator.py.id 12027 Util/Scripting/Siesta/.arch-ids/read_struct.py.id 12028 Util/Scripting/Siesta/.arch-ids/server.py.id 12029 Util/Scripting/Siesta/.arch-ids/siesta.py.id 12030 Util/Scripting/Siesta/Interface.py 12031 Util/Scripting/Siesta/__init__.py 12032 Util/Scripting/Siesta/calculator.py 12033 Util/Scripting/Siesta/read_struct.py 12034 Util/Scripting/Siesta/server.py 12035 Util/Scripting/Siesta/siesta.py Util/Scripting/amoeba.py 12036 Util/Scripting/ase.py Util/Scripting/ase_newton.py 12037 Util/Scripting/ase_relax.py Util/Scripting/ase_verlet.py 12038 Util/Scripting/bond.py Util/Scripting/client.py 12039 Util/Scripting/h2o.py Util/Scripting/scripts/.arch-ids/=id 12040 Util/Scripting/scripts/.arch-ids/plot_struct_jmol.py.id 12041 Util/Scripting/scripts/.arch-ids/plot_struct_rasmol.py.id 12042 Util/Scripting/scripts/.arch-ids/pr_after_nose.py.id 12043 Util/Scripting/scripts/.arch-ids/struct_to_bplot.py.id 12044 Util/Scripting/scripts/.arch-ids/struct_to_cif.py.id 12045 Util/Scripting/scripts/.arch-ids/struct_to_pdb.py.id 12046 Util/Scripting/scripts/.arch-ids/transf.py.id 12047 Util/Scripting/scripts/plot_struct_jmol.py 12048 Util/Scripting/scripts/plot_struct_rasmol.py 12049 Util/Scripting/scripts/pr_after_nose.py 12050 Util/Scripting/scripts/struct_to_bplot.py 12051 Util/Scripting/scripts/struct_to_cif.py 12052 Util/Scripting/scripts/struct_to_pdb.py 12053 Util/Scripting/scripts/transf.py Util/Scripting/setup.py 12054 Util/Scripting/simplex_optim.py 12055 12056 modified files: 12057 Docs/siesta.ind Docs/siesta.tex 12058 12059 new directories: 12060 Util/Scripting Util/Scripting/.arch-ids Util/Scripting/Siesta 12061 Util/Scripting/Siesta/.arch-ids Util/Scripting/scripts 12062 Util/Scripting/scripts/.arch-ids 12063 12064 new patches: 12065 agarcia@siesta.arch--2006/siesta-devel--agarcia--2.1--patch-5 12066 agarcia@siesta.arch--2006/siesta-devel--agarcia--2.1--patch-6 12067 agarcia@siesta.arch--2006/siesta-devel--agarcia--2.1--patch-12 12068 agarcia@siesta.arch--2006/siesta-devel--agarcia--2.1--patch-15 12069 agarcia@siesta.arch--2006/siesta-devel--agarcia--2.1--patch-19 12070 agarcia@siesta.arch--2006/siesta-devel--agarcia--2.1--patch-25 12071 12072 120732006-12-12 18:20:47 GMT Alberto Garcia <albertog@icmab.es> patch-16 12074 12075 Summary: 12076 Change handling of default charge for basis generation 12077 Revision: 12078 siesta-devel--reference--2.1--patch-16 12079 12080 Formerly, if the user did not specify the charge to be used 12081 for the generation of the basis, it was assumed to be zero. Thus 12082 there was no way to distinguish a "zero value" from a "non specified 12083 value". This caused problems in some cases if the pseudopotential 12084 was generated with an ionic configuration. A "zero charge" would not 12085 then override the ionic charge setting. 12086 12087 modified files: 12088 Src/atom.f Src/basis_types.f 12089 12090 new patches: 12091 agarcia@siesta.arch--2006/siesta-devel--agarcia--2.1--patch-46 12092 agarcia@siesta.arch--2006/siesta-devel--agarcia--2.1--patch-47 12093 agarcia@siesta.arch--2006/siesta-devel--agarcia--2.1--patch-48 12094 12095 120962006-12-12 18:18:34 GMT Alberto Garcia <albertog@icmab.es> patch-15 12097 12098 Summary: 12099 More flexible basis-generation options 12100 Revision: 12101 siesta-devel--reference--2.1--patch-15 12102 12103 * Allow more symbols as PAO.BasisSize specification: 12104 12105 SZ 12106 SZP, SZSP, SZ1P, SZP1 12107 DZ 12108 DZP, DZSP, DZP1, DZ1P 12109 DZDP, DZP2, DZ2P 12110 TZ 12111 TZP, TZSP, TZP1, TZ1P 12112 TZDP, TZP2, TZ2P 12113 TZTP, TZP3, TZ3P 12114 12115 np or pn means n polarization shells. 12116 sp, dp, tp: singly, doubly, triply polarized 12117 12118 (Julian Gale, Alberto Garcia) 12119 12120 * Per-shell split-valence specification 12121 12122 Using the idiom "S number" anywhere on the first line of a shell entry 12123 in PAO.Basis, one can select the split norm parameter for the multiple 12124 zeta generation on that shell. If no indication is given, the program will 12125 use the global default split_norm (0.15) or one introduced through the 12126 appropriate fdf symbol. Optimizing a basis set using S numbers is more 12127 robust than using extra rc's. 12128 12129 Example: 12130 12131 %block PAO.Basis 12132 Ta 3 3.28 12133 n=6 0 2 S 0.25 E 44.5 1.98 12134 5.872 0.0 12135 1.000 1.000 12136 n=6 1 1 E 89.0 0.6 12137 7.5896 12138 1.000 12139 n=5 2 2 S 0.37 E 31.1 1.717 12140 5.633 0.0 12141 1.000 1.0 12142 %endblock PAO.Basis 12143 12144 (Alberto Garcia) 12145 12146 * A new global fdf symbol PAO.SplitNormH controls the split-norm 12147 parameter for hydrogen atoms (defined as those with atomic number 1). 12148 There is no default: it falls back to the value of PAO.SplitNorm 12149 (Julian Gale) 12150 12151 * Implemented default soft-confinement settings through fdf symbols 12152 (Julian Gale) 12153 It is triggered by fdf_boolean('PAO.SoftDefault',.false.) 12154 Then, the following symbols are searched for, with the 12155 indicated defaults: 12156 12157 softRc = fdf_double('PAO.SoftInnerRadius',0.9d0) 12158 softPt = fdf_double('PAO.SoftPotential',40.0d0) 12159 12160 * Negative values of rinn in the E section of PAO.Basis mean that 12161 rinn will be the given fraction of the PAO cutoff. 12162 12163 * Simplified the handling of defaults for soft confinement and 12164 split_norm values by setting them in basis_specs.f 12165 12166 * Documented new features in siesta.tex 12167 (added also the options for reparametrization of pseudopotentials) 12168 12169 * Assorted cosmetic fixes for module accesibility 12170 12171 12172 new files: 12173 Tests/Reference/.arch-ids/h2o_basis.out.id 12174 Tests/Reference/h2o_basis.out Tests/h2o_basis/.arch-ids/=id 12175 Tests/h2o_basis/.arch-ids/h2o_basis.fdf.id 12176 Tests/h2o_basis/.arch-ids/h2o_basis.pseudos.id 12177 Tests/h2o_basis/.arch-ids/makefile.id 12178 Tests/h2o_basis/h2o_basis.fdf 12179 Tests/h2o_basis/h2o_basis.pseudos Tests/h2o_basis/makefile 12180 12181 modified files: 12182 Docs/siesta.ind Docs/siesta.tex Src/atom.f Src/basis_specs.f 12183 Src/basis_types.f Src/gen-basis.F Src/initatom.f 12184 Src/parallel.f Src/parsing.f Src/periodic_table.f 12185 Src/precision.F Src/wxml/m_wxml_error.f90 Src/xcmod.F 12186 Tests/Makefile Tests/h2o/h2o.fdf version.info 12187 12188 new directories: 12189 Tests/h2o_basis Tests/h2o_basis/.arch-ids 12190 12191 new patches: 12192 agarcia@siesta.arch--2006/siesta--alchemy--0.1--patch-22 12193 agarcia@siesta.arch--2006/siesta-devel--agarcia--2.1--patch-42 12194 agarcia@siesta.arch--2006/siesta-devel--agarcia--2.1--patch-45 12195 12196 121972006-12-12 17:01:53 GMT Alberto Garcia <albertog@icmab.es> patch-14 12198 12199 Summary: 12200 Update CHANGES 12201 Revision: 12202 siesta-devel--reference--2.1--patch-14 12203 12204 12205 modified files: 12206 Docs/CHANGES version.info 12207 12208 122092006-12-12 16:55:30 GMT Alberto Garcia <albertog@icmab.es> patch-13 12210 12211 Summary: 12212 Reparametrization of pseudopotentials 12213 Revision: 12214 siesta-devel--reference--2.1--patch-13 12215 12216 * By changing the a and b parameters of the logarithmic grid, a new one 12217 with a more homogeneous overall grid-point separation can be used for 12218 the generation of basis sets and projectors. For example, by using 12219 a=5x10-4 and b=10, the grid point separations at r=0 and 10 bohrs are 0.005 12220 and 0.01 bohrs, respectively. More points are needed to reach r's of the order 12221 of a hundred bohrs, but the extra computational effort is negligible. 12222 12223 This behavior is triggered by the boolean fdf symbol Reparametrize.Pseudos. 12224 12225 Further tuning can be achieved by the use of two other fdf symbols. The 12226 processing syntax and defaults are: 12227 12228 new_a = fdf_double("NewAParameter",5.0e-4_dp) 12229 new_b = fdf_double("NewBParameter",10.0_dp) 12230 12231 * New test: h2o_reparam 12232 12233 * Bug fix: 12234 12235 In routine findp in atom.f, the radius was wrongly computed as 12236 12237 r = b*(exp(a*(i-1)) + 1) 12238 12239 instead of 12240 12241 r = b*(exp(a*(i-1)) - 1) 12242 12243 The bug was dramatically exposed when using a re-parametrization in which 12244 b is no longer small (10.0 vs 1.0e-4). 12245 12246 12247 12248 new files: 12249 Tests/Reference/.arch-ids/h2o_reparam.out.id 12250 Tests/Reference/h2o_reparam.out 12251 Tests/h2o_reparam/.arch-ids/=id 12252 Tests/h2o_reparam/.arch-ids/h2o_reparam.fdf.id 12253 Tests/h2o_reparam/.arch-ids/h2o_reparam.pseudos.id 12254 Tests/h2o_reparam/.arch-ids/makefile.id 12255 Tests/h2o_reparam/h2o_reparam.fdf 12256 Tests/h2o_reparam/h2o_reparam.pseudos 12257 Tests/h2o_reparam/makefile 12258 12259 modified files: 12260 Src/Makefile Src/atmparams.f Src/atom.f Src/basis_specs.f 12261 Src/pseudopotential.f Tests/Makefile 12262 12263 new directories: 12264 Tests/h2o_reparam Tests/h2o_reparam/.arch-ids 12265 12266 new patches: 12267 agarcia@siesta.arch--2006/siesta--alchemy--0.1--patch-20 12268 agarcia@siesta.arch--2006/siesta--alchemy--0.1--patch-21 12269 agarcia@siesta.arch--2006/siesta-devel--agarcia--2.1--patch-41 12270 12271 122722006-12-12 14:26:27 GMT Alberto Garcia <albertog@icmab.es> patch-12 12273 12274 Summary: 12275 Changes to support synthetic atoms (VCA) 12276 Revision: 12277 siesta-devel--reference--2.1--patch-12 12278 12279 Support for dealing with "synthetic atoms" has been added. Their basic 12280 feature is that they cannot be assigned a true integer atomic number: 12281 12282 - One could mix the pseudopotentials of two elements to generate 12283 an appropriate hybrid to be used in a "virtual crystal approximation". 12284 (See description of mixps program below) 12285 (Note that the ATOM program also allows the treatment of "atoms" with 12286 a fractional Z. This is an alternative choice for mixtures involving 12287 atoms which are contiguous in the periodic table. 12288 See Pseudo/atom/Tutorial/ON) 12289 12290 - By mixing a true atom's pseudopotential with a "null" pseudopotential, 12291 a "partial occupation" can be simulated. 12292 12293 Comparatively minor changes were needed to have Siesta process correctly 12294 synthetic species: 12295 12296 * Atomic numbers greater than 200 signal a synthetic atom. The symbol 12297 returned (in module periodic_table) is SX, where X is an integer from 12298 1 to 9. 12299 In order to generate an appropriate "neutral atom" configuration, some 12300 extra information is needed about the "ground state" of the synthetic 12301 atom. It is taken from a SyntheticAtoms block (read in basis_specs.f). 12302 For example: 12303 12304 %block Chemical_Species_label 12305 1 201 ON-0.50000 12306 %endblock Chemical_Species_label 12307 %block SyntheticAtoms 12308 1 # Species index 12309 2 2 3 4 # n numbers for valence states with l=0,1,2,3 12310 2.0 3.5 0.0 0.0 # occupations of valence states with l=0,1,2,3 12311 %endblock SyntheticAtoms 12312 12313 * Changes in data structures and helper functions to support synthetic 12314 species: 12315 12316 New logical component "synthetic" in basis_types.f 12317 In atm_types, zval is now a real number. 12318 In atmfuncs, izvalfis has been renamed zvalfis, and now returns a real. 12319 (Same in old_atmfuncs, where the izvaltb array has been renamed zvaltb 12320 and now holds real numbers). 12321 Atm_transfer uses zvalfis. 12322 In basis_io, zval is now printed as a real number. Filename length enlarged 12323 to support long labels. 12324 12325 Calculation of total number of "pseudoprotons" in atomlist. Printed 12326 in siesta, together with the total number of electrons. 12327 12328 Electrostatic.f uses real instead of integer nuclear charges. 12329 Optical.F and ksv.F use now a real "total number of electrons" 12330 12331 * Pseudopotential module changes: 12332 12333 - New routine read_ps_conf to crack the information about the configuration 12334 used to generate the pseudopotential (and used in atom to set the vps 12335 charge). Synthetic species do not have the appropriate text block in the 12336 .psf file, so the ability to process a new field ("gen_zval") has been 12337 added to read_pseudo_formatted (this extra field is optional and appears 12338 only in "synthetic" .psf files). 12339 12340 - New routine write_pseudo_formatted added. 12341 12342 * Atom.f changes: 12343 12344 - The code now in pseudopotential::read_ps_conf has been removed. 12345 - The species label and not the atomic number is now used for 12346 identification of the species. 12347 - Routine prinput now outputs a SyntheticAtoms block if needed. 12348 12349 * The output format in Outcoor.f has been changed to allow for long 12350 species labels. The label now comes last, and the atom number next 12351 to last. This could break non-supported user scripts. 12352 12353 12354 A new program (mixps) has been written to mix pseudopotentials. It 12355 takes as command-line arguments the names (actually labels) of the two 12356 atoms involved (A and B), and the mixing parameter. Then it combines 12357 the information in A.psf and B.psf and creates a new file AB-0.xxxxx.psf, 12358 where 0.xxxxx is the mixing parameter (to five decimal places) specified. 12359 It outputs also a SyntheticAtoms block suitable for use by Siesta, and 12360 a MIXLABEL file which contains the final label used (useful for scripts). 12361 12362 This program is located in the top directory to ease compilation. 12363 12364 The new directory Util/VCA contains some documentation and the 12365 Programs zerops.f and zerops_rel.f to generate "null 12366 pseudopotentials". The resulting pseudos can also be found in 12367 Tests/Pseudos. 12368 12369 12370 New tests: 12371 12372 oxyn: Molecule made up of ON hybrids 12373 partial: Molecule made up of O-Zero hybrids (a very artificial 12374 partial occupation) 12375 12376 The 'partial' test introduces a new idiom for tests: the use of 12377 a general script to perform more complicated operations. The handling 12378 of paths is still very primitive. 12379 12380 NOTES: 12381 12382 - The basis set is generated by Siesta using the "mixed" 12383 pseudopotential. There is no provision at this time to "mix" basis 12384 sets, or in general to build a basis set using information about the 12385 basis sets for the atoms involved in the mix. On the other hand, basis 12386 sets for synthetic atoms can be optimized as usual. 12387 12388 - PseudoCore charges are mixed if they exist in the individual atoms' 12389 pseudopotential files. This might lead to extra non-linearities in the 12390 solid-state calculation. 12391 12392 - Once Siesta reads the new .psf file for the hybrid, it generates a 12393 local-pseudopotential charge and a local pseudopotential from it. Note 12394 that this means that the local pseudopotential is not a true mix of 12395 the local pseudopotentials of the individual atoms. 12396 12397 - Once Siesta reads the "neutral-atom configuration" from the 12398 SyntheticAtoms block, it generates the appropriate neutral-atom potential 12399 using the local pseudopotential and the atomic charge density. 12400 12401 new files: 12402 Pseudo/atom/Tutorial/ON/.arch-ids/=id 12403 Pseudo/atom/Tutorial/ON/.arch-ids/ON.tm2.inp.id 12404 Pseudo/atom/Tutorial/ON/.arch-ids/README.id 12405 Pseudo/atom/Tutorial/ON/ON.tm2.inp 12406 Pseudo/atom/Tutorial/ON/README 12407 Src/.arch-ids/flib_spline.f90.id Src/.arch-ids/mixps.f.id 12408 Src/flib_spline.f90 Src/mixps.f Tests/.arch-ids/script.mk.id 12409 Tests/Pseudos/.arch-ids/ON-0.34560.psf.id 12410 Tests/Pseudos/.arch-ids/Zero.nrl.psf.id 12411 Tests/Pseudos/.arch-ids/Zero.rel.psf.id 12412 Tests/Pseudos/ON-0.34560.psf Tests/Pseudos/Zero.nrl.psf 12413 Tests/Pseudos/Zero.rel.psf 12414 Tests/Reference/.arch-ids/oxyn.out.id 12415 Tests/Reference/.arch-ids/partial.out.id 12416 Tests/Reference/oxyn.out Tests/Reference/partial.out 12417 Tests/oxyn/.arch-ids/=id Tests/oxyn/.arch-ids/makefile.id 12418 Tests/oxyn/.arch-ids/oxyn.fdf.id 12419 Tests/oxyn/.arch-ids/oxyn.pseudos.id Tests/oxyn/makefile 12420 Tests/oxyn/oxyn.fdf Tests/oxyn/oxyn.pseudos 12421 Tests/partial/.arch-ids/=id 12422 Tests/partial/.arch-ids/makefile.id 12423 Tests/partial/.arch-ids/script.sh.id Tests/partial/makefile 12424 Tests/partial/script.sh Tests/script.mk Util/VCA/.arch-ids/=id 12425 Util/VCA/.arch-ids/README.id Util/VCA/.arch-ids/zerops.f.id 12426 Util/VCA/.arch-ids/zerops_rel.f.id Util/VCA/README 12427 Util/VCA/zerops.f Util/VCA/zerops_rel.f 12428 12429 modified files: 12430 Docs/siesta.ind Docs/siesta.tex Src/Makefile 12431 Src/atm_transfer.f Src/atm_types.f Src/atmfuncs.f Src/atom.f 12432 Src/atomlist.f Src/basis_io.F Src/basis_specs.f 12433 Src/basis_types.f Src/chemical.f Src/electrostatic.f Src/ksv.f 12434 Src/old_atmfuncs.f Src/optical.F Src/outcoor.f 12435 Src/periodic_table.f Src/pseudopotential.f Src/siesta.F 12436 Src/sys.F Util/README version.info 12437 12438 new directories: 12439 Pseudo/atom/Tutorial/ON Pseudo/atom/Tutorial/ON/.arch-ids 12440 Tests/oxyn Tests/oxyn/.arch-ids Tests/partial 12441 Tests/partial/.arch-ids Util/VCA Util/VCA/.arch-ids 12442 12443 new patches: 12444 agarcia@siesta.arch--2006/siesta--alchemy--0.1--base-0 12445 agarcia@siesta.arch--2006/siesta--alchemy--0.1--patch-1 12446 agarcia@siesta.arch--2006/siesta--alchemy--0.1--patch-2 12447 agarcia@siesta.arch--2006/siesta--alchemy--0.1--patch-3 12448 agarcia@siesta.arch--2006/siesta--alchemy--0.1--patch-4 12449 agarcia@siesta.arch--2006/siesta--alchemy--0.1--patch-5 12450 agarcia@siesta.arch--2006/siesta--alchemy--0.1--patch-6 12451 agarcia@siesta.arch--2006/siesta--alchemy--0.1--patch-7 12452 agarcia@siesta.arch--2006/siesta--alchemy--0.1--patch-8 12453 agarcia@siesta.arch--2006/siesta--alchemy--0.1--patch-9 12454 agarcia@siesta.arch--2006/siesta--alchemy--0.1--patch-11 12455 agarcia@siesta.arch--2006/siesta--alchemy--0.1--patch-12 12456 agarcia@siesta.arch--2006/siesta--alchemy--0.1--patch-13 12457 agarcia@siesta.arch--2006/siesta--alchemy--0.1--patch-14 12458 agarcia@siesta.arch--2006/siesta--alchemy--0.1--patch-16 12459 agarcia@siesta.arch--2006/siesta--alchemy--0.1--patch-17 12460 agarcia@siesta.arch--2006/siesta--alchemy--0.1--patch-18 12461 agarcia@siesta.arch--2006/siesta--alchemy--0.1--patch-19 12462 agarcia@siesta.arch--2006/siesta--alchemy--0.1--patch-25 12463 agarcia@siesta.arch--2006/siesta-devel--agarcia--2.1--patch-39 12464 agarcia@siesta.arch--2006/siesta-devel--agarcia--2.1--patch-40 12465 12466 12467 Summary: 12468 Update CHANGES 12469 Revision: 12470 siesta-devel--reference--2.1--patch-11 12471 124722006-12-12 09:56:36 GMT Alberto Garcia <albertog@icmab.es> patch-10 12473 12474 Summary: 12475 Appropriate supercell for elongated unit cells 12476 Revision: 12477 siesta-devel--reference--2.1--patch-10 12478 12479 The algorithm used to construct the auxiliary supercell for the 12480 calculation of matrix elements with k-point sampling simply multiplies 12481 each lattice vector by the appropriate factor (diagonal 12482 supercell). This causes a problem when the unit cell is elongated (see 12483 for example the mgco3 test in Tests/). In these cases, some lattice 12484 points are actually closer than the shortest cell vector would 12485 indicate, with the result that the supercell is too small and some 12486 atoms "see" multiple images. This appears in the program as a warning 12487 of the type: 12488 12489 xijorb: WARNING: orbital pair 1 341 is multiply connected 12490 12491 The resulting numerical errors are typically very small. 12492 12493 The fix involves an iterative increase of the supercell factors until 12494 the minimum-distance criterion is satisfied. (See new file 12495 m_check_supercell.f) 12496 12497 The old behavior can be recovered by setting the fdf variable 12498 NaiveAuxiliaryCell to .true. . 12499 12500 new files: 12501 Src/.arch-ids/m_check_supercell.f.id Src/m_check_supercell.f 12502 12503 modified files: 12504 Docs/siesta.tex Src/Makefile Src/siesta.F version.info 12505 12506 new patches: 12507 siesta@uam.es--2006/siesta--release--2.0--patch-18 12508 siesta@uam.es--2006/siesta--release--2.0--patch-22 12509 12510 125112006-12-11 16:29:55 GMT Alberto Garcia <albertog@icmab.es> patch-9 12512 12513 Summary: 12514 Fixes for Siesta-as-Server (from 2.0.1) 12515 Revision: 12516 siesta-devel--reference--2.1--patch-9 12517 12518 A number of fixes were needed for the proper functioning of the 12519 Siesta-as-Server package (also known as "SiestaAsSubroutine") 12520 (in addition to the purely cosmetic of openning the right CML context, 12521 already committed): 12522 12523 - iopipes.F90 had to be properly parallelized. 12524 12525 - fsiesta.f90 has been moved from Util/... to the main source directory 12526 in order to be compiled with the proper flushing routine. 12527 A couple of issues having to do with optional arguments have also been fixed. 12528 12529 - The makefile in Util/SiestaSubroutine/FmixMD/Src has been modified to 12530 deal with the new place for fsiesta.f90. 12531 12532 - Two new tests have been added. One of them tests the driving of a parallel 12533 Siesta calculation. A new script "test.sh" automates these tests. 12534 12535 In the main code, it has been noted that the "Forces" option (i.e., 12536 the computation of energy, forces, and stresses from geometry read 12537 through pipes from a client program) should be assimilated to a 12538 "variable cell" calculation, in the sense that the unit cell might be 12539 different from call to call. Appropriate checks have been included to 12540 regenerate k-point and supercell information if needed. 12541 12542 In the same vein, if the client inputs a null unit cell, Siesta should 12543 generate an automatic one, at any step. A new routine "automatic_cell.f" 12544 has been written and is now called at the beginning of the initialization 12545 section, and after every reading of geometry from pipes. 12546 12547 A null unit cell will be input whenever siesta_forces is not passed 12548 the optional "cell" parameter. This might happen during MD or relaxation 12549 for a molecule. The actual unit cell used will then vary from step to 12550 step. To avoid this, the cell should be passed explicitly in siesta_forces, 12551 at every step (as it is done in the 'driver?' exampl). 12552 12553 Other changes: 12554 12555 - New Sys/intel9-cmkl8-mpi.make file for parallel compilation in Rocks cluster. 12556 12557 - A new script in Tests/Scripts automates the handling of mpd daemons 12558 in an interactive single-nod run (when allowed). 12559 12560 Changes over 2.0.1 fix: 12561 12562 * fsiesta.f90 renamed to fsiesta.F90 to enable NAG-specific module handling. 12563 * Makefile: rerun of "make dep". 12564 12565 new files: 12566 Src/.arch-ids/automatic_cell.f.id 12567 Src/Sys/.arch-ids/intel9-cmkl8-mpi.make.id 12568 Src/Sys/intel9-cmkl8-mpi.make Src/automatic_cell.f 12569 Tests/Scripts/.arch-ids/simple_parallel.sh.id 12570 Tests/Scripts/simple_parallel.sh 12571 Util/SiestaSubroutine/FmixMD/.arch-ids/parallel.sh.id 12572 Util/SiestaSubroutine/FmixMD/.arch-ids/test.sh.id 12573 Util/SiestaSubroutine/FmixMD/Src/.arch-ids/para.f90.id 12574 Util/SiestaSubroutine/FmixMD/Src/.arch-ids/simple.f90.id 12575 Util/SiestaSubroutine/FmixMD/Src/para.f90 12576 Util/SiestaSubroutine/FmixMD/Src/simple.f90 12577 Util/SiestaSubroutine/FmixMD/parallel.sh 12578 Util/SiestaSubroutine/FmixMD/test.sh 12579 12580 removed files: 12581 Util/SiestaSubroutine/FmixMD/Src/.arch-ids/fsiesta.f90.id 12582 Util/SiestaSubroutine/FmixMD/Src/fsiesta.f90 12583 12584 modified files: 12585 Src/Makefile Src/fsiesta.F90 Src/iopipes.F90 Src/siesta.F 12586 Util/SiestaSubroutine/FmixMD/README 12587 Util/SiestaSubroutine/FmixMD/Src/Makefile 12588 Util/SiestaSubroutine/FmixMD/Src/fmixmd.f90 12589 Util/SiestaSubroutine/README 12590 12591 renamed files: 12592 Util/SiestaSubroutine/.arch-ids/fsiesta.f90.id 12593 ==> Src/.arch-ids/fsiesta.F90.id 12594 Util/SiestaSubroutine/FmixMD/Src/.arch-ids/makefile.id 12595 ==> Util/SiestaSubroutine/FmixMD/Src/.arch-ids/Makefile.id 12596 Util/SiestaSubroutine/FmixMD/Src/makefile 12597 ==> Util/SiestaSubroutine/FmixMD/Src/Makefile 12598 Util/SiestaSubroutine/fsiesta.f90 12599 ==> Src/fsiesta.F90 12600 12601 new patches: 12602 siesta@uam.es--2006/siesta--release--2.0--patch-23 12603 12604 126052006-12-11 15:58:25 GMT Alberto Garcia <albertog@icmab.es> patch-8 12606 12607 Summary: 12608 Fixes from release-2.0 branch 12609 Revision: 12610 siesta-devel--reference--2.1--patch-8 12611 12612 A new set of fixes carried over from the 2.0 release branch. 12613 See individual patch logs or the 2.0.1 release notes for 12614 more information. 12615 12616 Patches applied: 12617 12618 * siesta@uam.es--2006/siesta--release--2.0--patch-11 12619 Fix syntax error in preprocessor block in mpi.F 12620 12621 * siesta@uam.es--2006/siesta--release--2.0--patch-12 12622 Add COMP_LIBS to gen-basis link stage 12623 12624 * siesta@uam.es--2006/siesta--release--2.0--patch-13 12625 Export all the environment in sge_run.sh 12626 12627 * siesta@uam.es--2006/siesta--release--2.0--patch-14 12628 Fix bug in iohs.F (write statement) 12629 12630 * siesta@uam.es--2006/siesta--release--2.0--patch-16 12631 Fix format issue in DxFormat.f90 12632 12633 * siesta@uam.es--2006/siesta--release--2.0--patch-17 12634 Fixes in Makefile: denchar deps and netcdf interface 12635 12636 * siesta@uam.es--2006/siesta--release--2.0--patch-19 12637 Parallel handling of spin check for KSV 12638 12639 * siesta@uam.es--2006/siesta--release--2.0--patch-20 12640 Enhancement of iohs to deal with k-points 12641 12642 * siesta@uam.es--2006/siesta--release--2.0--patch-21 12643 Bugfix in iohs for parallel execution 12644 12645 * siesta@uam.es--2006/siesta--release--2.0--patch-25 12646 Set target stress to zero in constant-volume variable-cell runs 12647 12648 12649 modified files: 12650 Src/MPI/mpi.F Src/Makefile Src/arch.make.in Src/cgvc.F 12651 Src/configure Src/configure.ac Src/iohs.F Src/siesta.F 12652 Tests/Scripts/sge_run.sh Tests/fe/fe.fdf Tests/h2o/h2o.fdf 12653 Util/Contrib/FElMellouhi/DxFormat.f90 12654 12655 new patches: 12656 agarcia@siesta.arch--2006/siesta-devel--agarcia--2.1--patch-13 12657 agarcia@siesta.arch--2006/siesta-devel--agarcia--2.1--patch-16 12658 agarcia@siesta.arch--2006/siesta-devel--agarcia--2.1--patch-29 12659 agarcia@siesta.arch--2006/siesta-devel--agarcia--2.1--patch-36 12660 agarcia@siesta.arch--2006/siesta-devel--agarcia--2.1--patch-43 12661 jgale@siesta.arch--2005/siesta-general--jgale--2.1--patch-25 12662 siesta@uam.es--2006/siesta--release--2.0--patch-11 12663 siesta@uam.es--2006/siesta--release--2.0--patch-12 12664 siesta@uam.es--2006/siesta--release--2.0--patch-13 12665 siesta@uam.es--2006/siesta--release--2.0--patch-14 12666 siesta@uam.es--2006/siesta--release--2.0--patch-16 12667 siesta@uam.es--2006/siesta--release--2.0--patch-17 12668 siesta@uam.es--2006/siesta--release--2.0--patch-19 12669 siesta@uam.es--2006/siesta--release--2.0--patch-20 12670 siesta@uam.es--2006/siesta--release--2.0--patch-21 12671 siesta@uam.es--2006/siesta--release--2.0--patch-25 12672 12673 126742006-12-11 15:32:32 GMT Alberto Garcia <albertog@icmab.es> patch-7 12675 12676 Summary: 12677 Enhancements to the vibra package 12678 Revision: 12679 siesta-devel--reference--2.1--patch-7 12680 12681 (Julian Gale) 12682 12683 An option has been introduced to compute infra-red intensities. In 12684 order to do this the Born effective charges must have been computed 12685 along with the force constants and the .BC file must be present in the 12686 current directory. The intensities are estimated according to formula 12687 (6) in the paper by Fernandez-Torre et al in J. Phys. Chem. A, 108, 12688 10535-10541 (2004). 12689 12690 Explicit copy of fdf.mod to deal with faulty arch.make's. 12691 12692 Removal of chkdim call from klines. 12693 12694 AG: Fixes for portability in Makefile and vibrator.f 12695 12696 Patches applied: 12697 12698 * jgale@siesta.arch--2005/siesta-general--jgale--2.1--patch-1 12699 Call to chkdim removed from klines 12700 12701 * jgale@siesta.arch--2005/siesta-general--jgale--2.1--patch-19 12702 Copying of fdf module to Vibra directory for build automated 12703 12704 * jgale@siesta.arch--2005/siesta-general--jgale--2.1--patch-20 12705 Calculation of the IR intensities added to the Vibra package 12706 12707 12708 modified files: 12709 Util/Vibra/Docs/CHANGES Util/Vibra/Docs/vibra.tex 12710 Util/Vibra/Vibra/Makefile Util/Vibra/Vibra/klines.f 12711 Util/Vibra/Vibra/vibrator.f 12712 12713 new patches: 12714 agarcia@siesta.arch--2006/siesta-devel--agarcia--2.1--patch-50 12715 jgale@siesta.arch--2005/siesta-general--jgale--2.1--patch-1 12716 jgale@siesta.arch--2005/siesta-general--jgale--2.1--patch-19 12717 jgale@siesta.arch--2005/siesta-general--jgale--2.1--patch-20 12718 12719 127202006-12-11 15:30:16 GMT Alberto Garcia <albertog@icmab.es> patch-6 12721 12722 Summary: 12723 New "fire-quench" damped-dynamics optimization algorithm 12724 Revision: 12725 siesta-devel--reference--2.1--patch-6 12726 12727 (Emilio Artacho) 12728 12729 A damped dynamics (named FIRE) by Bitzek et al, PRL 97, 170201 (2006). 12730 Introduced in subroutine verlet2 (velocity Verlet), in dynamics.f, 12731 just after the power quench option. Convergence is controlled by 12732 MaxForceTol. No variable cell option included at this point. The 12733 parameters controlling the algorithm have been taken from the original 12734 paper and harwired into the routine. 12735 Controlled by MD.FireQuench (logical), partly tunable by changing 12736 the initial time step MD.LengthTimeStep, and the block AtomicMass. 12737 12738 (New test sih_fire ) 12739 12740 12741 12742 new files: 12743 Tests/Reference/.arch-ids/sih_fire.out.id 12744 Tests/Reference/sih_fire.out Tests/sih_fire/.arch-ids/=id 12745 Tests/sih_fire/.arch-ids/makefile.id 12746 Tests/sih_fire/.arch-ids/sih_fire.fdf.id 12747 Tests/sih_fire/.arch-ids/sih_fire.pseudos.id 12748 Tests/sih_fire/makefile Tests/sih_fire/sih_fire.fdf 12749 Tests/sih_fire/sih_fire.pseudos 12750 12751 modified files: 12752 Docs/siesta.ind Docs/siesta.tex Src/Makefile Src/dynamics.f 12753 Src/redata.F Src/siesta.F Tests/Makefile 12754 12755 new directories: 12756 Tests/sih_fire Tests/sih_fire/.arch-ids 12757 12758 new patches: 12759 eartacho@siesta.arch--2005/siesta-devel--eartacho--2.1--patch-4 12760 12761 127622006-12-11 14:19:35 GMT Alberto Garcia <albertog@icmab.es> patch-5 12763 12764 Summary: 12765 New block BandPoints accepts arbitrary k-points 12766 Revision: 12767 siesta-devel--reference--2.1--patch-5 12768 12769 (Emilio Artacho) 12770 12771 Instead of introducing lines of k-points for band calculations, 12772 BandPoints allows for arbitrary k-points. Useful for other purposes 12773 such as obtaining densities of states etc. 12774 12775 New test: Tests/si_bandpoints 12776 Reference values in Tests/Reference/si_bandpoints.bands 12777 12778 new files: 12779 Tests/Reference/.arch-ids/si_bandpoints.bands.id 12780 Tests/Reference/si_bandpoints.bands 12781 Tests/si_bandpoints/.arch-ids/=id 12782 Tests/si_bandpoints/.arch-ids/makefile.id 12783 Tests/si_bandpoints/.arch-ids/si_bandpoints.fdf.id 12784 Tests/si_bandpoints/.arch-ids/si_bandpoints.pseudos.id 12785 Tests/si_bandpoints/makefile 12786 Tests/si_bandpoints/si_bandpoints.fdf 12787 Tests/si_bandpoints/si_bandpoints.pseudos 12788 12789 modified files: 12790 Docs/siesta.ind Docs/siesta.tex Src/bands.F Tests/Makefile 12791 12792 new directories: 12793 Tests/si_bandpoints Tests/si_bandpoints/.arch-ids 12794 12795 new patches: 12796 eartacho@siesta.arch--2005/siesta-devel--eartacho--2.1--patch-1 12797 eartacho@siesta.arch--2005/siesta-devel--eartacho--2.1--patch-2 12798 eartacho@siesta.arch--2005/siesta-devel--eartacho--2.1--patch-3 12799 12800 128012006-10-02 09:09:00 GMT Alberto Garcia <albertog@icmab.es> patch-4 12802 12803 Summary: 12804 Update CHANGES 12805 Revision: 12806 siesta-devel--reference--2.1--patch-4 12807 12808 12809 modified files: 12810 Docs/CHANGES 128112006-10-02 09:08:05 GMT Alberto Garcia <albertog@icmab.es> patch-3 12812 12813 Summary: 12814 Implementation of the Wu-Cohen functional 12815 Revision: 12816 siesta-devel--reference--2.1--patch-3 12817 12818 A new routine "wcxc" has been added to xc.f (courtesy of Marivi 12819 Fdez. Serra and Julian Gale, with contributions from Alberto Garcia). 12820 12821 The new xc code (for both Atom and Siesta) is "wc". 12822 12823 modified files: 12824 Docs/CHANGES Docs/siesta.ind Docs/siesta.tex 12825 Pseudo/atom/ChangeLog Pseudo/atom/Docs/atom.tex 12826 Pseudo/atom/makefile Pseudo/atom/velect.f 12827 Pseudo/atom/version.h Pseudo/atom/xc.f Src/atom.f Src/xc.f 12828 Src/xcmod.F 12829 128302006-05-24 18:56:49 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-2 12831 12832 Summary: 12833 New logic for k-point grid generation from kgrid_cutoff 12834 Revision: 12835 siesta-devel--reference--2.1--patch-2 12836 12837 The previous algorithm created a diagonal supercell so that the length 12838 of the shortest vector was greater than twice the kgrid_cutoff. But 12839 there might be an equivalent supercell (same volume, generating the 12840 same lattice points), but with shorter vectors (more "spherical"). Half of 12841 the shortest resulting lattice vector is the effective cutoff. This 12842 effective cutoff was just reported, but the more spherical 12843 cell was not used anymore. The kgrid was generated as the reciprocal cell of 12844 the chosen diagonal supercell. In some cases, the program ended 12845 up using a much shorter cutoff than requested. 12846 12847 The fix, as suggested by Jose Soler, is to start the procedure with 12848 the most "spherical" unit cell, thus generating an optimal supercell 12849 in the spirit of the Moreno-Soler paper. 12850 12851 A number of other changes have been made to the code: 12852 12853 1. Minvec has been turned into a module, and the routine now reports 12854 also the transformation matrix. (Change to gchkmx needed, including 12855 an auxiliary array to avoid aliasing of arguments). 12856 12857 2. Even though the program can find the optimal k-grid displacements, 12858 those given by the user in a Monkhorst-Pack block are not overriden 12859 (in case there are good reasons for the choice, such as the need to 12860 have the gamma point in the set). The program will nevertheless print 12861 a line telling the user about the more suitable displacement(s). 12862 12863 3. The program now reports the effective cutoff even for Gamma-point-only 12864 calculations. 12865 12866 4. The multiplication factors of the effective supercell are made 12867 explicitly positive (changing kdsc and mr after the call to idiag). This 12868 might fix a long-standing issue with non-diagonal MP supercells. 12869 12870 Version info updated for development branch. 12871 12872 Note: There is *no provision for backward compatibility*, although it is 12873 still possible to re-use the kgrid supercells reported by previous versions 12874 to reproduce the old behavior for a given kgrid_cutoff. 12875 12876 To Do: Tidy up the kgridinit/kgrid code redundancy. 12877 12878 The manual has been updated to reflect the new algorithm outline, and 12879 to stress the format of the MP supercell input. 12880 12881 Also, the manual now mentions the Divide and Conquer issue, and 12882 the version number on the cover has been changed to 2.0.X. 12883 12884 12885 12886 modified files: 12887 Docs/siesta.tex Src/Makefile Src/chkgmx.f Src/kgrid.F 12888 Src/kgridinit.F Src/minvec.f Src/siesta.F version.info 12889 12890 128912006-05-24 14:00:50 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-1 12892 12893 Summary: 12894 Merge patches from release-2.0 branch 12895 Revision: 12896 siesta-devel--reference--2.1--patch-1 12897 12898 Assorted bugfixes backported to the development branch: 12899 12900 * siesta@uam.es--2006/siesta--release--2.0--patch-1 12901 Remove external declaration of 'timer' in spher_harm and radfft. 12902 12903 * siesta@uam.es--2006/siesta--release--2.0--patch-2 12904 Bug fix in dlaed6 in dc_lapack.f 12905 12906 * siesta@uam.es--2006/siesta--release--2.0--patch-3 12907 Use dc_lapack.f together with any system libraries 12908 12909 * siesta@uam.es--2006/siesta--release--2.0--patch-4 12910 Fix import of dp in optical.F 12911 12912 * siesta@uam.es--2006/siesta--release--2.0--patch-5 12913 Fix reading of nspin variable in pdosxml 12914 12915 * siesta@uam.es--2006/siesta--release--2.0--patch-6 12916 Add revPBE to xc_check in atom.f -- tidy 12917 12918 * siesta@uam.es--2006/siesta--release--2.0--patch-7 12919 Fix version.F90 triad. 12920 12921 * siesta@uam.es--2006/siesta--release--2.0--patch-8 12922 Siesta-server steps treated correctly for CML output 12923 12924 * siesta@uam.es--2006/siesta--release--2.0--patch-9 12925 Fix file prefix identification in m_denchar_init 12926 12927 12928 new files: 12929 Src/Confs/.arch-ids/intel9mkl8-safe.conf.id 12930 Src/Confs/intel9mkl8-safe.conf 12931 12932 modified files: 12933 Pseudo/atom/Tutorial/ae.sh Pseudo/atom/Tutorial/pg.sh 12934 Pseudo/atom/Tutorial/pt.sh Src/Libs/dc_lapack.f Src/atom.f 12935 Src/configure Src/configure.ac Src/m_denchar_init.F 12936 Src/optical.F Src/radfft.f Src/siesta.F Src/spher_harm.f 12937 Util/pdosxml/m_pdos.f90 version.info 12938 12939 12940____________________________________________________________________ 12941** CHANGES ALONG siesta@uam.es--2005/siesta--pre-release--2.0 12942-------------------------------------------------------------------- 12943 129442006-02-24 16:06:00 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-30 12945 12946 2.0 release point 12947 Will move to new branch siesta--release--2.0 12948 129492006-02-24 15:39:13 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-29 12950 12951 Summary: 12952 Add pathscale .make files 12953 Revision: 12954 siesta--pre-release--2.0--patch-29 12955 12956 12957 new files: 12958 Src/Sys/.arch-ids/pathscale-mpi.make.id 12959 Src/Sys/.arch-ids/pathscale.make.id Src/Sys/pathscale-mpi.make 12960 Src/Sys/pathscale.make 12961 12962 modified files: 12963 Src/Sys/cscs-cray-mpi.make 12964 12965 129662006-02-24 14:55:21 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-28 12967 12968 Summary: 12969 Remove version.o dependency from Makefile 12970 Revision: 12971 siesta--pre-release--2.0--patch-28 12972 12973 12974 modified files: 12975 Src/Makefile 12976 12977 129782006-02-24 12:06:18 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-27 12979 12980 Summary: 12981 Update Reference outputs + cosmetic changes in version.F90 12982 Revision: 12983 siesta--pre-release--2.0--patch-27 12984 12985 * New outputs in Tests/Reference 12986 * New SGE script in Tests/Scripts 12987 * Cosmetic change to version line in version.F90 12988 12989 12990 new files: 12991 Tests/Reference/.arch-ids/si2x1h.out.id 12992 Tests/Reference/si2x1h.out 12993 Tests/Scripts/.arch-ids/sge_run.sh.id Tests/Scripts/sge_run.sh 12994 12995 modified files: 12996 Src/version.F90 Tests/Makefile Tests/Reference/batio3.out 12997 Tests/Reference/bessel.out Tests/Reference/constant_volume.out 12998 Tests/Reference/fe.out Tests/Reference/fe_broyden.out 12999 Tests/Reference/floating.out Tests/Reference/h2o.out 13000 Tests/Reference/h2oZ.out Tests/Reference/h2o_dos.out 13001 Tests/Reference/h2o_op_broyden.out 13002 Tests/Reference/h2o_orderN.out Tests/Reference/md_anneal.out 13003 Tests/Reference/md_nose.out Tests/Reference/md_npr.out 13004 Tests/Reference/md_pr.out Tests/Reference/md_verlet.out 13005 Tests/Reference/mgco3.out Tests/Reference/si64.out 13006 Tests/Reference/sih.out Tests/Reference/sih_op_broyden.out 13007 Tests/Reference/var_cell.out Tests/Reference/zmatrix.out 13008 13009 130102006-02-24 11:48:08 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-26 13011 13012 Summary: 13013 Update top-file README and SIESTA_LICENCE 13014 Revision: 13015 siesta--pre-release--2.0--patch-26 13016 13017 13018 new files: 13019 .arch-ids/SIESTA_LICENCE.id SIESTA_LICENCE 13020 13021 modified files: 13022 README 13023 13024 130252006-02-24 11:33:10 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-25 13026 13027 Summary: 13028 Include information about pdf manual files 13029 Revision: 13030 siesta--pre-release--2.0--patch-25 13031 13032 13033 new files: 13034 Docs/.arch-ids/README.id Docs/README 13035 Util/Denchar/Docs/.arch-ids/README.id Util/Denchar/Docs/README 13036 13037 modified files: 13038 Docs/release.notes_2.0 Pseudo/atom/Docs/README README 13039 Util/Denchar/Docs/denchar.tex 13040 13041 130422006-02-24 10:56:42 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-24 13043 13044 Summary: 13045 Remove ancillary files from top of distribution 13046 Revision: 13047 siesta--pre-release--2.0--patch-24 13048 13049 Old release-related and administrative files have been removed from 13050 the code distribution, as well as the Specs directory. 13051 13052 13053 13054 removed files: 13055 .arch-ids/PACKAGING.id .arch-ids/Siesta-licence.pdf.id 13056 .arch-ids/Siesta-licence.txt.id .arch-ids/build_parallel.sh.id 13057 .arch-ids/build_serial.sh.id .arch-ids/copyright.id 13058 .arch-ids/cover.collab.id .arch-ids/cover.indeps.id 13059 .arch-ids/cover.parallel.id .arch-ids/dempi.py.id 13060 .arch-ids/put_copyright.sh.id .arch-ids/user.list.id PACKAGING 13061 Siesta-licence.pdf Siesta-licence.txt Specs/.arch-ids/=id 13062 Specs/.arch-ids/Broyden.specs.id Specs/Broyden.specs 13063 build_parallel.sh build_serial.sh copyright cover.collab 13064 cover.indeps cover.parallel dempi.py put_copyright.sh 13065 user.list 13066 13067 removed directories: 13068 Specs Specs/.arch-ids 13069 13070 130712006-02-24 10:52:25 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-23 13072 13073 Summary: 13074 Update MD restart info and output options in manual 13075 Revision: 13076 siesta--pre-release--2.0--patch-23 13077 13078 13079 modified files: 13080 Docs/siesta.ind Docs/siesta.tex 13081 13082 130832006-02-23 22:24:47 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-22 13084 13085 Summary: 13086 Deactivated pre-commit hook to update version.info. Set to 2.0-release 13087 Revision: 13088 siesta--pre-release--2.0--patch-22 13089 13090 The atomatic updating of version.info has been deactivated 13091 (in file {arch}/=hook) in the pre-release branch so that the 13092 version string can be fixed to "siesta-2.0-release". 13093 13094 13095 modified files: 13096 version.info {arch}/=hook 13097 13098 130992006-02-23 22:21:50 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-21 13100 13101 Summary: 13102 Declare variable in md_out.F90 13103 Revision: 13104 siesta--pre-release--2.0--patch-21 13105 13106 13107 modified files: 13108 Src/md_out.F90 13109 13110 131112006-02-23 19:09:10 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-20 13112 13113 Summary: 13114 Use slabel-prefixed restart files in dynamics.f 13115 Revision: 13116 siesta--pre-release--2.0--patch-20 13117 13118 13119 modified files: 13120 Src/dynamics.f 13121 13122 131232006-02-23 15:08:40 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-19 13124 13125 Summary: 13126 Close MD netCDF file at each step. Wrap netcdf code completely 13127 Revision: 13128 siesta--pre-release--2.0--patch-19 13129 13130 * Surround all the MD netcdf code with preprocessor directives. 13131 * Close MD netcdf file at each step to avoid leaving it in an 13132 undefined state. 13133 13134 13135 modified files: 13136 Src/md_out.F90 Src/siesta.F 13137 13138 131392006-02-23 11:59:15 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-18 13140 13141 Summary: 13142 Remove -u flag from g95-cdf.conf 13143 Revision: 13144 siesta--pre-release--2.0--patch-18 13145 13146 13147 modified files: 13148 Src/Confs/g95-cdf.conf 13149 13150 131512006-02-23 11:50:54 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-17 13152 13153 Summary: 13154 Update affiliations in Siesta-licence.txt 13155 Revision: 13156 siesta--pre-release--2.0--patch-17 13157 13158 13159 modified files: 13160 Siesta-licence.txt 13161 13162 131632006-02-23 11:40:55 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-16 13164 13165 Summary: 13166 Update dependencies in Makefile 13167 Revision: 13168 siesta--pre-release--2.0--patch-16 13169 13170 13171 modified files: 13172 Src/Makefile 13173 13174 131752006-02-23 11:27:25 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-15 13176 13177 Summary: 13178 Correct typos 13179 Revision: 13180 siesta--pre-release--2.0--patch-15 13181 13182 13183 modified files: 13184 Src/atom.f Src/m_denchar_geom.f Src/m_denchar_init.F 13185 Src/m_denchar_io.F Src/outcoor.f 13186 13187 131882006-02-23 10:58:05 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-14 13189 13190 Summary: 13191 Enable experimental netCDF output for MD + md.py script in Util/MD 13192 Revision: 13193 siesta--pre-release--2.0--patch-14 13194 13195 * Simple netCDF output enabled in siesta.F (netCDF needs to be compiled in). 13196 Produces a slabel.MD.nc file. 13197 * A new experimental python script for processing of the new netCDF format MD 13198 file has been added to Util/MD. 13199 * Add option to write MD history to md_anneal test. 13200 13201 * Vienese output file now called slabel.MD_CAR. 13202 13203 13204 13205 13206 new files: 13207 Src/Confs/.arch-ids/g95-cdf.conf.id Src/Confs/g95-cdf.conf 13208 Util/MD/.arch-ids/md.py.id Util/MD/md.py 13209 13210 modified files: 13211 Src/md_out.F90 Src/siesta.F Tests/md_anneal/md_anneal.fdf 13212 13213 132142006-02-23 10:29:37 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-13 13215 13216 Summary: 13217 Removed Outs directory from Tests 13218 Revision: 13219 siesta--pre-release--2.0--patch-13 13220 13221 The old tests outputs will move to a web-page, but will not be part of the distribution. 13222 13223 13224 removed files: 13225 Tests/Outs/.arch-ids/=id Tests/Outs/.arch-ids/README.id 13226 Tests/Outs/.arch-ids/batio3.out.id 13227 Tests/Outs/.arch-ids/constant_volume.out.id 13228 Tests/Outs/.arch-ids/fe.out.id 13229 Tests/Outs/.arch-ids/fe_broyden.out.id 13230 Tests/Outs/.arch-ids/h2o.out.id 13231 Tests/Outs/.arch-ids/h2oZ.out.id 13232 Tests/Outs/.arch-ids/h2o_dos.out.id 13233 Tests/Outs/.arch-ids/h2o_orderN.out.id 13234 Tests/Outs/.arch-ids/mgco3.out.id 13235 Tests/Outs/.arch-ids/si.out.id 13236 Tests/Outs/.arch-ids/si64.out.id 13237 Tests/Outs/.arch-ids/sih.out.id 13238 Tests/Outs/.arch-ids/var_cell.out.id Tests/Outs/README 13239 Tests/Outs/batio3.out Tests/Outs/constant_volume.out 13240 Tests/Outs/fe.out Tests/Outs/fe_broyden.out Tests/Outs/h2o.out 13241 Tests/Outs/h2oZ.out Tests/Outs/h2o_dos.out 13242 Tests/Outs/h2o_orderN.out Tests/Outs/mgco3.out 13243 Tests/Outs/si.out Tests/Outs/si64.out Tests/Outs/sih.out 13244 Tests/Outs/var_cell.out 13245 13246 removed directories: 13247 Tests/Outs Tests/Outs/.arch-ids 13248 13249 132502006-02-23 10:25:10 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-12 13251 13252 Summary: 13253 XML output fixes 13254 Revision: 13255 siesta--pre-release--2.0--patch-12 13256 13257 * Units attribute in XML output now specified with siestaUnits prefix. 13258 * Namespace and stylesheet declarations in siesta_cmlsubs.F90 13259 * Bug fixes and extensions in wxml/flib_cml.f90 and wxml/flib_wstml.f90 13260 13261 13262 modified files: 13263 Src/efield.F Src/ioeig.f Src/meshsubs.F Src/ordern.F 13264 Src/redata.F Src/siesta.F Src/siesta_cmlsubs.F90 13265 Src/wxml/flib_wcml.f90 Src/wxml/flib_wstml.f90 13266 13267 new patches: 13268 twhite@siesta.arch--2005/siesta-devel--release--1.5--patch-4 13269 twhite@siesta.arch--2005/siesta-devel--xmltidy--1.5--patch-3 13270 twhite@siesta.arch--2005/siesta-devel--xmltidy--1.5--patch-4 13271 13272 132732006-02-23 08:46:59 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-11 13274 13275 Summary: 13276 Upgrade to latest Starlink fortran.m4 - m4 copyright merge 13277 Revision: 13278 siesta--pre-release--2.0--patch-11 13279 13280 * Upgrade fortran.m4 to latest version which properly 13281 supports case-insensitive filesystems. 13282 13283 (Undocumented in previous patch: copyright stamping of m4 files) 13284 (Configure.ac has now Version 2.0 instead of 1.4) 13285 13286 13287 modified files: 13288 Src/aclocal.m4 Src/configure Src/m4/fortran.m4 13289 13290 new patches: 13291 twhite@siesta.arch--2005/siesta-devel--release--1.5--patch-3 13292 13293 132942006-02-23 08:42:23 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-10 13295 13296 Summary: 13297 Mention DivAndConq problem in manual 13298 Revision: 13299 siesta--pre-release--2.0--patch-10 13300 13301 Patches applied: 13302 13303 * twhite@siesta.arch--2005/siesta-devel--release--1.5--patch-1 13304 Documentation update 13305 13306 * twhite@siesta.arch--2005/siesta-devel--release--1.5--patch-2 13307 m4 copyright notices 13308 13309 13310 modified files: 13311 Docs/siesta.tex Src/aclocal.m4 Src/configure.ac 13312 Src/m4/ACX_MPI.m4 Src/m4/TW_CHECK_BLACS.m4 13313 Src/m4/TW_CHECK_FC_90.m4 Src/m4/TW_CHECK_FC_95.m4 13314 Src/m4/TW_CHECK_FC_FPP.m4 Src/m4/TW_CHECK_FC_FPP_90.m4 13315 Src/m4/TW_CHECK_FC_TR15580.m4 Src/m4/TW_CHECK_FC_TR15581.m4 13316 Src/m4/TW_CHECK_SCALAPACK.m4 Src/m4/TW_FC_CHECK_ABORT.m4 13317 Src/m4/TW_FC_CHECK_DCFUNS.m4 Src/m4/TW_FC_CHECK_FLUSH.m4 13318 Src/m4/TW_FC_ID.m4 Src/m4/TW_FC_ID_FLAGS.m4 13319 Src/m4/TW_FC_KINDS.m4 Src/m4/TW_FIND_FC_BLAS.m4 13320 Src/m4/TW_FIND_LAPACK.m4 Src/m4/TW_PATH_NETCDF.m4 13321 Src/m4/TW_TRY_DC_LAPACK.m4 Src/m4/ac_config_aux_dirs.m4 13322 13323 new patches: 13324 twhite@siesta.arch--2005/siesta-devel--release--1.5--patch-1 13325 twhite@siesta.arch--2005/siesta-devel--release--1.5--patch-2 13326 13327 133282006-02-22 10:19:05 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-9 13329 13330 Summary: 13331 Removed Out directories from Examples 13332 Revision: 13333 siesta--pre-release--2.0--patch-9 13334 13335 13336 removed files: 13337 Examples/Fe/Out/.arch-ids/=id 13338 Examples/Fe/Out/.arch-ids/Fe.out.id Examples/Fe/Out/Fe.out 13339 Examples/H2O/Out/.arch-ids/=id 13340 Examples/H2O/Out/.arch-ids/h2o.out.id Examples/H2O/Out/h2o.out 13341 Examples/MgO/Out/.arch-ids/=id 13342 Examples/MgO/Out/.arch-ids/MgO.out.id Examples/MgO/Out/MgO.out 13343 Examples/SiH/Out/.arch-ids/=id 13344 Examples/SiH/Out/.arch-ids/sih.ANI.id 13345 Examples/SiH/Out/.arch-ids/sih.out.id Examples/SiH/Out/sih.ANI 13346 Examples/SiH/Out/sih.out 13347 13348 modified files: 13349 Examples/README 13350 13351 removed directories: 13352 Examples/Fe/Out Examples/Fe/Out/.arch-ids Examples/H2O/Out 13353 Examples/H2O/Out/.arch-ids Examples/MgO/Out 13354 Examples/MgO/Out/.arch-ids Examples/SiH/Out 13355 Examples/SiH/Out/.arch-ids 13356 13357 133582006-02-16 13:53:40 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-8 13359 13360 Summary: 13361 Update configure 13362 Revision: 13363 siesta--pre-release--2.0--patch-8 13364 13365 13366 modified files: 13367 Src/configure 13368 13369 133702006-02-16 13:53:17 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-7 13371 13372 Summary: 13373 Update version number and add copyright to configure.ac 13374 Revision: 13375 siesta--pre-release--2.0--patch-7 13376 13377 13378 modified files: 13379 Src/configure Src/configure.ac 13380 13381 133822006-02-16 13:49:09 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-6 13383 13384 Summary: 13385 Divide and Conquer default was wrong in manual 13386 Revision: 13387 siesta--pre-release--2.0--patch-6 13388 13389 13390 modified files: 13391 Docs/siesta.tex 13392 13393 133942006-02-15 15:32:54 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-5 13395 13396 Summary: 13397 Clarify Pulay line in redata output 13398 Revision: 13399 siesta--pre-release--2.0--patch-5 13400 13401 (D. Grimwood) The text output next to the value of "maxsav" was ambiguous. 13402 13403 13404 modified files: 13405 Src/redata.F 13406 13407 134082006-02-14 09:14:02 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-4 13409 13410 Summary: 13411 Small cosmetic changes 13412 Revision: 13413 siesta--pre-release--2.0--patch-4 13414 13415 Patches applied: 13416 13417 * eartacho@siesta.arch--2005/siesta--my-changes--0.3--patch-1 13418 Cosmetics output 13419 13420 13421 modified files: 13422 Src/atomlist.f Src/siesta.F 13423 13424 new patches: 13425 eartacho@siesta.arch--2005/siesta--my-changes--0.3--patch-1 13426 13427 134282006-02-13 17:09:08 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-3 13429 13430 Summary: 13431 Update to CHANGES file 13432 Revision: 13433 siesta--pre-release--2.0--patch-3 13434 13435 13436 modified files: 13437 Docs/CHANGES 13438 134392006-02-13 17:02:08 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-2 13440 13441 Summary: 13442 Added a Drude term for optical properties of metals 13443 Revision: 13444 siesta--pre-release--2.0--patch-2 13445 13446 Up to now only the contribution from inter-band transitions was 13447 taken into account for the calculation of the dielectric function. 13448 This is enough for insulators or semiconductors. However, for 13449 metals it is necessary to include a term associated with intra-band 13450 transitions. Here we assume that it has the form of the Drude 13451 dielectric function 13452 13453 epsilon_intraband(w)= 1 -wp^2/w*(w+i*gamma), 13454 13455 where wp^2 is calculated by SIESTA, while gamma (the inverse of 13456 the relaxation time) is considered an empirical parameter with 13457 which we can play during the analysis of the data. 13458 13459 (Updated also Util/Optical) 13460 13461 modified files: 13462 Src/optical.F Src/transition_rate.F Util/Optical/README 13463 Util/Optical/input.f Util/Optical/optical.f 13464 Util/Optical/si.EPSIMG 13465 13466 new patches: 13467 dsanchez@siesta.arch--2005/siesta--optical--0.2--patch-1 13468 13469 134702006-02-13 16:59:36 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-1 13471 13472 Summary: 13473 Cosmetic changes for switch to 2.0 13474 Revision: 13475 siesta--pre-release--2.0--patch-1 13476 13477 * version triad in version.F90 set to 2.0.0 13478 * release_notes_1.5 moved to release_notes_2.0 13479 * Top-level README updated 13480 * Docs/siesta.tex updated. 13481 13482 modified files: 13483 Docs/release.notes_2.0 Docs/siesta.tex README Src/version.F90 13484 version.info 13485 13486 renamed files: 13487 Docs/.arch-ids/release.notes_1.5.id 13488 ==> Docs/.arch-ids/release.notes_2.0.id 13489 Docs/release.notes_1.5 13490 ==> Docs/release.notes_2.0 13491 134922006-02-13 16:06:52 GMT Alberto Garcia <wdpgaara@lg.ehu.es> base-0 13493 13494 Summary: 13495 tag of siesta@uam.es--2005/siesta--copyright-stamp--1.5--patch-3 13496 Revision: 13497 siesta--pre-release--2.0--base-0 13498 13499 (automatically generated log message) 13500 13501-------------------------------------------------------------------- 13502** A Special branch was used for copyright stamping, leading up to 13503 13504 siesta@uam.es--2005/siesta--copyright-stamp--1.5--patch-3 13505 13506____________________________________________________________________ 13507** CHANGES ALONG siesta@uam.es--2005/siesta-devel--reference--1.5 13508-------------------------------------------------------------------- 13509 135102006-02-13 15:00:00 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-37 13511 13512 Summary: 13513 Update to CHANGES file 13514 Revision: 13515 siesta-devel--reference--1.5--patch-37 13516 135172006-02-13 14:43:00 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-36 13518 13519 Summary: 13520 More documentation and fixes for Examples, Tutorials, and Util 13521 Revision: 13522 siesta-devel--reference--1.5--patch-36 13523 13524 * Expanded and created README files for Examples, Tutorials, and Util 13525 * Cleaned up Denchar (removed Tests directory from distribution) 13526 and Vibra (new compilation scheme, using the top-level arch.make) 13527 * Fixed end-of-file handling in sies2arc. 13528 13529 13530 13531 new files: 13532 Tests/.arch-ids/README.id Tests/README 13533 Tutorials/.arch-ids/README.id Tutorials/README 13534 Util/Vibra/Vibra/.arch-ids/io.f.id Util/Vibra/Vibra/io.f 13535 13536 removed files: 13537 Util/Basis/.arch-ids/=id Util/Basis/.arch-ids/gen-basis.sh.id 13538 Util/Basis/.arch-ids/kbs.gplot.id 13539 Util/Basis/.arch-ids/kbs.gps.id 13540 Util/Basis/.arch-ids/orbs.gplot.id 13541 Util/Basis/.arch-ids/orbs.gps.id 13542 Util/Basis/.arch-ids/setup_plot.sh.id 13543 Util/Basis/.arch-ids/subkb.gplot.id 13544 Util/Basis/.arch-ids/suborb.gplot.id 13545 Util/Basis/.arch-ids/vdens.gplot.id 13546 Util/Basis/.arch-ids/vdens.gps.id Util/Basis/gen-basis.sh 13547 Util/Basis/kbs.gplot Util/Basis/kbs.gps Util/Basis/orbs.gplot 13548 Util/Basis/orbs.gps Util/Basis/setup_plot.sh 13549 Util/Basis/subkb.gplot Util/Basis/suborb.gplot 13550 Util/Basis/vdens.gplot Util/Basis/vdens.gps 13551 Util/Denchar/Src/.arch-ids/=id 13552 Util/Denchar/Src/MPI/.arch-ids/=id 13553 Util/Denchar/Src/NetCDF/.arch-ids/=id 13554 Util/Denchar/Src/fdf/.arch-ids/=id 13555 Util/Denchar/Tests/.arch-ids/=id 13556 Util/Denchar/Tests/Si/.arch-ids/=id 13557 Util/Denchar/Tests/Si/2D/.arch-ids/=id 13558 Util/Denchar/Tests/Si/2D/.arch-ids/Si.CON.DEL.id 13559 Util/Denchar/Tests/Si/2D/.arch-ids/Si.CON.SCF.id 13560 Util/Denchar/Tests/Si/2D/.arch-ids/Si.CON.WF1.id 13561 Util/Denchar/Tests/Si/2D/.arch-ids/Si.CON.WF2.id 13562 Util/Denchar/Tests/Si/2D/.arch-ids/Si.CON.WF3.id 13563 Util/Denchar/Tests/Si/2D/.arch-ids/Si.CON.WF4.id 13564 Util/Denchar/Tests/Si/2D/.arch-ids/Si.CON.WF5.id 13565 Util/Denchar/Tests/Si/2D/.arch-ids/Si.CON.WF6.id 13566 Util/Denchar/Tests/Si/2D/.arch-ids/Si.CON.WF7.id 13567 Util/Denchar/Tests/Si/2D/.arch-ids/Si.CON.WF8.id 13568 Util/Denchar/Tests/Si/2D/.arch-ids/Si.fdf.id 13569 Util/Denchar/Tests/Si/2D/.arch-ids/Si.psf.id 13570 Util/Denchar/Tests/Si/2D/.arch-ids/contour.gplot.id 13571 Util/Denchar/Tests/Si/2D/Si.CON.DEL 13572 Util/Denchar/Tests/Si/2D/Si.CON.SCF 13573 Util/Denchar/Tests/Si/2D/Si.CON.WF1 13574 Util/Denchar/Tests/Si/2D/Si.CON.WF2 13575 Util/Denchar/Tests/Si/2D/Si.CON.WF3 13576 Util/Denchar/Tests/Si/2D/Si.CON.WF4 13577 Util/Denchar/Tests/Si/2D/Si.CON.WF5 13578 Util/Denchar/Tests/Si/2D/Si.CON.WF6 13579 Util/Denchar/Tests/Si/2D/Si.CON.WF7 13580 Util/Denchar/Tests/Si/2D/Si.CON.WF8 13581 Util/Denchar/Tests/Si/2D/Si.fdf 13582 Util/Denchar/Tests/Si/2D/Si.psf 13583 Util/Denchar/Tests/Si/2D/contour.gplot 13584 Util/Denchar/Tests/Si/3D/.arch-ids/=id 13585 Util/Denchar/Tests/Si/3D/.arch-ids/Si.DRHO.cube.id 13586 Util/Denchar/Tests/Si/3D/.arch-ids/Si.RHO.cube.id 13587 Util/Denchar/Tests/Si/3D/.arch-ids/Si.WF1.cube.id 13588 Util/Denchar/Tests/Si/3D/.arch-ids/Si.WF2.cube.id 13589 Util/Denchar/Tests/Si/3D/.arch-ids/Si.WF3.cube.id 13590 Util/Denchar/Tests/Si/3D/.arch-ids/Si.WF4.cube.id 13591 Util/Denchar/Tests/Si/3D/.arch-ids/Si.WF5.cube.id 13592 Util/Denchar/Tests/Si/3D/.arch-ids/Si.WF6.cube.id 13593 Util/Denchar/Tests/Si/3D/.arch-ids/Si.WF7.cube.id 13594 Util/Denchar/Tests/Si/3D/.arch-ids/Si.WF8.cube.id 13595 Util/Denchar/Tests/Si/3D/.arch-ids/Si.fdf.id 13596 Util/Denchar/Tests/Si/3D/.arch-ids/Si.psf.id 13597 Util/Denchar/Tests/Si/3D/Si.DRHO.cube 13598 Util/Denchar/Tests/Si/3D/Si.RHO.cube 13599 Util/Denchar/Tests/Si/3D/Si.WF1.cube 13600 Util/Denchar/Tests/Si/3D/Si.WF2.cube 13601 Util/Denchar/Tests/Si/3D/Si.WF3.cube 13602 Util/Denchar/Tests/Si/3D/Si.WF4.cube 13603 Util/Denchar/Tests/Si/3D/Si.WF5.cube 13604 Util/Denchar/Tests/Si/3D/Si.WF6.cube 13605 Util/Denchar/Tests/Si/3D/Si.WF7.cube 13606 Util/Denchar/Tests/Si/3D/Si.WF8.cube 13607 Util/Denchar/Tests/Si/3D/Si.fdf 13608 Util/Denchar/Tests/Si/3D/Si.psf 13609 Util/Denchar/Tests/SiH3/.arch-ids/=id 13610 Util/Denchar/Tests/SiH3/2D/.arch-ids/=id 13611 Util/Denchar/Tests/SiH3/2D/.arch-ids/H.psf.id 13612 Util/Denchar/Tests/SiH3/2D/.arch-ids/Si.psf.id 13613 Util/Denchar/Tests/SiH3/2D/.arch-ids/SiH3.CON.DEL.id 13614 Util/Denchar/Tests/SiH3/2D/.arch-ids/SiH3.CON.DOWN.id 13615 Util/Denchar/Tests/SiH3/2D/.arch-ids/SiH3.CON.MAG.id 13616 Util/Denchar/Tests/SiH3/2D/.arch-ids/SiH3.CON.UP.id 13617 Util/Denchar/Tests/SiH3/2D/.arch-ids/SiH3.CON.WF1.DOWN.id 13618 Util/Denchar/Tests/SiH3/2D/.arch-ids/SiH3.CON.WF1.UP.id 13619 Util/Denchar/Tests/SiH3/2D/.arch-ids/SiH3.CON.WF2.DOWN.id 13620 Util/Denchar/Tests/SiH3/2D/.arch-ids/SiH3.CON.WF2.UP.id 13621 Util/Denchar/Tests/SiH3/2D/.arch-ids/SiH3.CON.WF3.DOWN.id 13622 Util/Denchar/Tests/SiH3/2D/.arch-ids/SiH3.CON.WF3.UP.id 13623 Util/Denchar/Tests/SiH3/2D/.arch-ids/SiH3.CON.WF4.DOWN.id 13624 Util/Denchar/Tests/SiH3/2D/.arch-ids/SiH3.CON.WF4.UP.id 13625 Util/Denchar/Tests/SiH3/2D/.arch-ids/SiH3.CON.WF5.DOWN.id 13626 Util/Denchar/Tests/SiH3/2D/.arch-ids/SiH3.CON.WF5.UP.id 13627 Util/Denchar/Tests/SiH3/2D/.arch-ids/SiH3.CON.WF6.DOWN.id 13628 Util/Denchar/Tests/SiH3/2D/.arch-ids/SiH3.CON.WF6.UP.id 13629 Util/Denchar/Tests/SiH3/2D/.arch-ids/SiH3.fdf.id 13630 Util/Denchar/Tests/SiH3/2D/H.psf 13631 Util/Denchar/Tests/SiH3/2D/Si.psf 13632 Util/Denchar/Tests/SiH3/2D/SiH3.CON.DEL 13633 Util/Denchar/Tests/SiH3/2D/SiH3.CON.DOWN 13634 Util/Denchar/Tests/SiH3/2D/SiH3.CON.MAG 13635 Util/Denchar/Tests/SiH3/2D/SiH3.CON.UP 13636 Util/Denchar/Tests/SiH3/2D/SiH3.CON.WF1.DOWN 13637 Util/Denchar/Tests/SiH3/2D/SiH3.CON.WF1.UP 13638 Util/Denchar/Tests/SiH3/2D/SiH3.CON.WF2.DOWN 13639 Util/Denchar/Tests/SiH3/2D/SiH3.CON.WF2.UP 13640 Util/Denchar/Tests/SiH3/2D/SiH3.CON.WF3.DOWN 13641 Util/Denchar/Tests/SiH3/2D/SiH3.CON.WF3.UP 13642 Util/Denchar/Tests/SiH3/2D/SiH3.CON.WF4.DOWN 13643 Util/Denchar/Tests/SiH3/2D/SiH3.CON.WF4.UP 13644 Util/Denchar/Tests/SiH3/2D/SiH3.CON.WF5.DOWN 13645 Util/Denchar/Tests/SiH3/2D/SiH3.CON.WF5.UP 13646 Util/Denchar/Tests/SiH3/2D/SiH3.CON.WF6.DOWN 13647 Util/Denchar/Tests/SiH3/2D/SiH3.CON.WF6.UP 13648 Util/Denchar/Tests/SiH3/2D/SiH3.fdf 13649 Util/Denchar/Tests/SiH3/3D/.arch-ids/=id 13650 Util/Denchar/Tests/SiH3/3D/.arch-ids/H.psf.id 13651 Util/Denchar/Tests/SiH3/3D/.arch-ids/Si.psf.id 13652 Util/Denchar/Tests/SiH3/3D/.arch-ids/SiH3.DRHO.cube.id 13653 Util/Denchar/Tests/SiH3/3D/.arch-ids/SiH3.RHO.DOWN.cube.id 13654 Util/Denchar/Tests/SiH3/3D/.arch-ids/SiH3.RHO.UP.cube.id 13655 Util/Denchar/Tests/SiH3/3D/.arch-ids/SiH3.WF5.DOWN.cube.id 13656 Util/Denchar/Tests/SiH3/3D/.arch-ids/SiH3.WF5.UP.cube.id 13657 Util/Denchar/Tests/SiH3/3D/.arch-ids/SiH3.fdf.id 13658 Util/Denchar/Tests/SiH3/3D/H.psf 13659 Util/Denchar/Tests/SiH3/3D/Si.psf 13660 Util/Denchar/Tests/SiH3/3D/SiH3.DRHO.cube 13661 Util/Denchar/Tests/SiH3/3D/SiH3.RHO.DOWN.cube 13662 Util/Denchar/Tests/SiH3/3D/SiH3.RHO.UP.cube 13663 Util/Denchar/Tests/SiH3/3D/SiH3.WF5.DOWN.cube 13664 Util/Denchar/Tests/SiH3/3D/SiH3.WF5.UP.cube 13665 Util/Denchar/Tests/SiH3/3D/SiH3.fdf 13666 Util/Vibra/Vibra/Sys/.arch-ids/=id 13667 Util/Vibra/Vibra/Sys/.arch-ids/cray.make.id 13668 Util/Vibra/Vibra/Sys/.arch-ids/freebsd.make.id 13669 Util/Vibra/Vibra/Sys/.arch-ids/hp.make.id 13670 Util/Vibra/Vibra/Sys/.arch-ids/ibm.make.id 13671 Util/Vibra/Vibra/Sys/.arch-ids/ibmessl.make.id 13672 Util/Vibra/Vibra/Sys/.arch-ids/linux.make.id 13673 Util/Vibra/Vibra/Sys/.arch-ids/osf.make.id 13674 Util/Vibra/Vibra/Sys/.arch-ids/osfdxml.make.id 13675 Util/Vibra/Vibra/Sys/.arch-ids/sgi.make.id 13676 Util/Vibra/Vibra/Sys/.arch-ids/t3e.make.id 13677 Util/Vibra/Vibra/Sys/.arch-ids/unknown.make.id 13678 Util/Vibra/Vibra/Sys/cray.make 13679 Util/Vibra/Vibra/Sys/freebsd.make Util/Vibra/Vibra/Sys/hp.make 13680 Util/Vibra/Vibra/Sys/ibm.make 13681 Util/Vibra/Vibra/Sys/ibmessl.make 13682 Util/Vibra/Vibra/Sys/linux.make Util/Vibra/Vibra/Sys/osf.make 13683 Util/Vibra/Vibra/Sys/osfdxml.make 13684 Util/Vibra/Vibra/Sys/sgi.make Util/Vibra/Vibra/Sys/t3e.make 13685 Util/Vibra/Vibra/Sys/unknown.make 13686 Util/Vibra/Vibra/fdf/.arch-ids/=id 13687 Util/Vibra/Vibra/fdf/.arch-ids/Coords.dat.id 13688 Util/Vibra/Vibra/fdf/.arch-ids/Otherfile.id 13689 Util/Vibra/Vibra/fdf/.arch-ids/README.id 13690 Util/Vibra/Vibra/fdf/.arch-ids/TODO.id 13691 Util/Vibra/Vibra/fdf/.arch-ids/coords.fdf.id 13692 Util/Vibra/Vibra/fdf/.arch-ids/fdf.Standard.id 13693 Util/Vibra/Vibra/fdf/.arch-ids/fdf.f.id 13694 Util/Vibra/Vibra/fdf/.arch-ids/fdf.f90.id 13695 Util/Vibra/Vibra/fdf/.arch-ids/fdf.h.id 13696 Util/Vibra/Vibra/fdf/.arch-ids/fdfdefs.h.id 13697 Util/Vibra/Vibra/fdf/.arch-ids/io.f.id 13698 Util/Vibra/Vibra/fdf/.arch-ids/io_sample.f.id 13699 Util/Vibra/Vibra/fdf/.arch-ids/makefile.id 13700 Util/Vibra/Vibra/fdf/.arch-ids/sample.f.id 13701 Util/Vibra/Vibra/fdf/.arch-ids/sample.f90.id 13702 Util/Vibra/Vibra/fdf/.arch-ids/sample.fdf.id 13703 Util/Vibra/Vibra/fdf/Coords.dat Util/Vibra/Vibra/fdf/Otherfile 13704 Util/Vibra/Vibra/fdf/README Util/Vibra/Vibra/fdf/TODO 13705 Util/Vibra/Vibra/fdf/coords.fdf 13706 Util/Vibra/Vibra/fdf/fdf.Standard Util/Vibra/Vibra/fdf/fdf.f 13707 Util/Vibra/Vibra/fdf/fdf.f90 Util/Vibra/Vibra/fdf/fdf.h 13708 Util/Vibra/Vibra/fdf/fdfdefs.h Util/Vibra/Vibra/fdf/io.f 13709 Util/Vibra/Vibra/fdf/io_sample.f Util/Vibra/Vibra/fdf/makefile 13710 Util/Vibra/Vibra/fdf/sample.f Util/Vibra/Vibra/fdf/sample.f90 13711 Util/Vibra/Vibra/fdf/sample.fdf 13712 13713 modified files: 13714 Docs/siesta.ind Docs/siesta.tex Examples/README README 13715 Tests/Makefile Util/Denchar/Docs/denchar.tex 13716 Util/PyAtom/README.scripts Util/README Util/Vibra/Docs/CHANGES 13717 Util/Vibra/Docs/vibra.tex Util/Vibra/README 13718 Util/Vibra/Vibra/Makefile Util/Vibra/Vibra/fcbuild.f 13719 Util/Vibra/Vibra/klines.f Util/Vibra/Vibra/outbands.f 13720 Util/Vibra/Vibra/parse.f Util/Vibra/Vibra/recoor.f 13721 Util/Vibra/Vibra/vibrator.f Util/sies2arc/sies2arc.f 13722 13723 renamed files: 13724 Util/Denchar/Src/.arch-ids/README.id 13725 ==> Util/Denchar/.arch-ids/README-Source.id 13726 Util/Denchar/Src/README 13727 ==> Util/Denchar/README-Source 13728 13729 removed directories: 13730 Util/Basis Util/Basis/.arch-ids Util/Denchar/Src 13731 Util/Denchar/Src/.arch-ids Util/Denchar/Src/MPI 13732 Util/Denchar/Src/MPI/.arch-ids Util/Denchar/Src/NetCDF 13733 Util/Denchar/Src/NetCDF/.arch-ids Util/Denchar/Src/fdf 13734 Util/Denchar/Src/fdf/.arch-ids Util/Denchar/Tests 13735 Util/Denchar/Tests/.arch-ids Util/Denchar/Tests/Si 13736 Util/Denchar/Tests/Si/.arch-ids Util/Denchar/Tests/Si/2D 13737 Util/Denchar/Tests/Si/2D/.arch-ids Util/Denchar/Tests/Si/3D 13738 Util/Denchar/Tests/Si/3D/.arch-ids Util/Denchar/Tests/SiH3 13739 Util/Denchar/Tests/SiH3/.arch-ids Util/Denchar/Tests/SiH3/2D 13740 Util/Denchar/Tests/SiH3/2D/.arch-ids 13741 Util/Denchar/Tests/SiH3/3D 13742 Util/Denchar/Tests/SiH3/3D/.arch-ids Util/Vibra/Vibra/Sys 13743 Util/Vibra/Vibra/Sys/.arch-ids Util/Vibra/Vibra/fdf 13744 Util/Vibra/Vibra/fdf/.arch-ids 13745 13746 new patches: 13747 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-50 13748 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-51 13749 13750 137512006-02-12 20:04:44 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-35 13752 13753 Summary: 13754 Re-organization of Tutorials and Tests 13755 Revision: 13756 siesta-devel--reference--1.5--patch-35 13757 13758 Updated script in Tutorials/Bases so that it works out of the box 13759 Removed Tutorials/Intro 13760 Moved Tests from Src to top directory 13761 Removed mgo test and added si2x1h test (formerly in Tutorials/Intro) 13762 13763 13764 new files: 13765 Tests/si2x1h/.arch-ids/=id Tests/si2x1h/.arch-ids/makefile.id 13766 Tests/si2x1h/.arch-ids/si2x1h.fdf.id 13767 Tests/si2x1h/.arch-ids/si2x1h.pseudos.id Tests/si2x1h/makefile 13768 Tests/si2x1h/si2x1h.fdf Tests/si2x1h/si2x1h.pseudos 13769 13770 removed files: 13771 Src/Tests/mgo/.arch-ids/=id Src/Tests/mgo/.arch-ids/Kgrid.id 13772 Src/Tests/mgo/.arch-ids/makefile.id 13773 Src/Tests/mgo/.arch-ids/mgo.STRUCT_IN.id 13774 Src/Tests/mgo/.arch-ids/mgo.fdf.id 13775 Src/Tests/mgo/.arch-ids/mgo.pseudos.id 13776 Src/Tests/mgo/.arch-ids/mydefaults.fdf.id Src/Tests/mgo/Kgrid 13777 Src/Tests/mgo/makefile Src/Tests/mgo/mgo.STRUCT_IN 13778 Src/Tests/mgo/mgo.fdf Src/Tests/mgo/mgo.pseudos 13779 Src/Tests/mgo/mydefaults.fdf Tutorials/Intro/.arch-ids/=id 13780 Tutorials/Intro/Fe/.arch-ids/=id 13781 Tutorials/Intro/Fe/.arch-ids/Fe.fdf.id 13782 Tutorials/Intro/Fe/.arch-ids/Fe.psf.id 13783 Tutorials/Intro/Fe/.arch-ids/README.id 13784 Tutorials/Intro/Fe/.arch-ids/bands.sh.id 13785 Tutorials/Intro/Fe/.arch-ids/dos.gplot.id 13786 Tutorials/Intro/Fe/Fe.fdf Tutorials/Intro/Fe/Fe.psf 13787 Tutorials/Intro/Fe/README Tutorials/Intro/Fe/bands.sh 13788 Tutorials/Intro/Fe/dos.gplot Tutorials/Intro/MgO/.arch-ids/=id 13789 Tutorials/Intro/MgO/.arch-ids/Mg.psf.id 13790 Tutorials/Intro/MgO/.arch-ids/MgO.fdf.id 13791 Tutorials/Intro/MgO/.arch-ids/O.psf.id 13792 Tutorials/Intro/MgO/.arch-ids/README.id 13793 Tutorials/Intro/MgO/.arch-ids/cont.gplot.id 13794 Tutorials/Intro/MgO/.arch-ids/plot.sh.id 13795 Tutorials/Intro/MgO/.arch-ids/raw.in.id 13796 Tutorials/Intro/MgO/Mg.psf Tutorials/Intro/MgO/MgO.fdf 13797 Tutorials/Intro/MgO/O.psf Tutorials/Intro/MgO/README 13798 Tutorials/Intro/MgO/cont.gplot Tutorials/Intro/MgO/plot.sh 13799 Tutorials/Intro/MgO/raw.in Tutorials/Intro/Si/.arch-ids/=id 13800 Tutorials/Intro/Si/.arch-ids/README.fit.id 13801 Tutorials/Intro/Si/.arch-ids/README.id 13802 Tutorials/Intro/Si/.arch-ids/README.plot.id 13803 Tutorials/Intro/Si/.arch-ids/Si.fdf.id 13804 Tutorials/Intro/Si/.arch-ids/Si.psf.id 13805 Tutorials/Intro/Si/.arch-ids/Si_strele.fdf.id 13806 Tutorials/Intro/Si/.arch-ids/bands.sh.id 13807 Tutorials/Intro/Si/.arch-ids/cont.gplot.id 13808 Tutorials/Intro/Si/.arch-ids/dos.gplot.id 13809 Tutorials/Intro/Si/.arch-ids/fit.sh.id 13810 Tutorials/Intro/Si/.arch-ids/plot.sh.id 13811 Tutorials/Intro/Si/.arch-ids/raw.in.id 13812 Tutorials/Intro/Si/README Tutorials/Intro/Si/README.fit 13813 Tutorials/Intro/Si/README.plot Tutorials/Intro/Si/Si.fdf 13814 Tutorials/Intro/Si/Si.psf Tutorials/Intro/Si/Si_strele.fdf 13815 Tutorials/Intro/Si/bands.sh Tutorials/Intro/Si/cont.gplot 13816 Tutorials/Intro/Si/dos.gplot Tutorials/Intro/Si/fit.sh 13817 Tutorials/Intro/Si/plot.sh Tutorials/Intro/Si/raw.in 13818 Tutorials/Intro/Si_surface/.arch-ids/=id 13819 Tutorials/Intro/Si_surface/.arch-ids/H.psf.id 13820 Tutorials/Intro/Si_surface/.arch-ids/Si.psf.id 13821 Tutorials/Intro/Si_surface/.arch-ids/Si2x1.fdf.id 13822 Tutorials/Intro/Si_surface/H.psf 13823 Tutorials/Intro/Si_surface/Si.psf 13824 Tutorials/Intro/Si_surface/Si2x1.fdf 13825 Tutorials/Intro/Water_molecule/.arch-ids/=id 13826 Tutorials/Intro/Water_molecule/.arch-ids/README.id 13827 Tutorials/Intro/Water_molecule/README 13828 Tutorials/Intro/Water_molecule/h2o/.arch-ids/=id 13829 Tutorials/Intro/Water_molecule/h2o/.arch-ids/H.psf.id 13830 Tutorials/Intro/Water_molecule/h2o/.arch-ids/O.psf.id 13831 Tutorials/Intro/Water_molecule/h2o/.arch-ids/cont.gplot.id 13832 Tutorials/Intro/Water_molecule/h2o/.arch-ids/h2o.fdf.id 13833 Tutorials/Intro/Water_molecule/h2o/.arch-ids/plot.sh.id 13834 Tutorials/Intro/Water_molecule/h2o/.arch-ids/raw.in.id 13835 Tutorials/Intro/Water_molecule/h2o/H.psf 13836 Tutorials/Intro/Water_molecule/h2o/O.psf 13837 Tutorials/Intro/Water_molecule/h2o/cont.gplot 13838 Tutorials/Intro/Water_molecule/h2o/h2o.fdf 13839 Tutorials/Intro/Water_molecule/h2o/plot.sh 13840 Tutorials/Intro/Water_molecule/h2o/raw.in 13841 Tutorials/Intro/Water_molecule/h2o_cell/.arch-ids/=id 13842 Tutorials/Intro/Water_molecule/h2o_cell/.arch-ids/H.psf.id 13843 Tutorials/Intro/Water_molecule/h2o_cell/.arch-ids/O.psf.id 13844 Tutorials/Intro/Water_molecule/h2o_cell/.arch-ids/h2o_cell.fdf.id 13845 Tutorials/Intro/Water_molecule/h2o_cell/H.psf 13846 Tutorials/Intro/Water_molecule/h2o_cell/O.psf 13847 Tutorials/Intro/Water_molecule/h2o_cell/h2o_cell.fdf 13848 Tutorials/Intro/Water_molecule/h2o_relax/.arch-ids/=id 13849 Tutorials/Intro/Water_molecule/h2o_relax/.arch-ids/O.psf.id 13850 Tutorials/Intro/Water_molecule/h2o_relax/.arch-ids/h2o_relax.fdf.id 13851 Tutorials/Intro/Water_molecule/h2o_relax/O.psf 13852 Tutorials/Intro/Water_molecule/h2o_relax/h2o_relax.fdf 13853 13854 modified files: 13855 Tests/Makefile Tests/Scripts/arina.pbs 13856 Tests/Scripts/matterhorn-gm.sge Tests/test.mk 13857 Tutorials/Bases/000README Tutorials/Bases/gen-basis.sh 13858 13859 renamed files: 13860 13861 All in Src/Tests... 13862 13863 new directories: 13864 Tests/.arch-ids Tests/Outs/.arch-ids Tests/Pseudos/.arch-ids 13865 Tests/Reference/.arch-ids Tests/Scripts/.arch-ids 13866 Tests/batio3/.arch-ids Tests/bessel/.arch-ids 13867 Tests/constant_volume/.arch-ids Tests/fe/.arch-ids 13868 Tests/fe_broyden/.arch-ids Tests/floating/.arch-ids 13869 Tests/h2o/.arch-ids Tests/h2oZ/.arch-ids 13870 Tests/h2o_dos/.arch-ids Tests/h2o_op_broyden/.arch-ids 13871 Tests/h2o_orderN/.arch-ids Tests/md_anneal/.arch-ids 13872 Tests/md_nose/.arch-ids Tests/md_npr/.arch-ids 13873 Tests/md_pr/.arch-ids Tests/md_verlet/.arch-ids 13874 Tests/mgco3/.arch-ids Tests/si2x1h Tests/si2x1h/.arch-ids 13875 Tests/si64/.arch-ids Tests/sih/.arch-ids 13876 Tests/sih_op_broyden/.arch-ids Tests/var_cell/.arch-ids 13877 Tests/zmatrix/.arch-ids 13878 13879 removed directories: 13880 Src/Tests/.arch-ids Src/Tests/Outs/.arch-ids 13881 Src/Tests/Pseudos/.arch-ids Src/Tests/Reference/.arch-ids 13882 Src/Tests/Scripts/.arch-ids Src/Tests/batio3/.arch-ids 13883 Src/Tests/bessel/.arch-ids Src/Tests/constant_volume/.arch-ids 13884 Src/Tests/fe/.arch-ids Src/Tests/fe_broyden/.arch-ids 13885 Src/Tests/floating/.arch-ids Src/Tests/h2o/.arch-ids 13886 Src/Tests/h2oZ/.arch-ids Src/Tests/h2o_dos/.arch-ids 13887 Src/Tests/h2o_op_broyden/.arch-ids 13888 Src/Tests/h2o_orderN/.arch-ids Src/Tests/md_anneal/.arch-ids 13889 Src/Tests/md_nose/.arch-ids Src/Tests/md_npr/.arch-ids 13890 Src/Tests/md_pr/.arch-ids Src/Tests/md_verlet/.arch-ids 13891 Src/Tests/mgco3/.arch-ids Src/Tests/mgo 13892 Src/Tests/mgo/.arch-ids Src/Tests/si64/.arch-ids 13893 Src/Tests/sih/.arch-ids Src/Tests/sih_op_broyden/.arch-ids 13894 Src/Tests/var_cell/.arch-ids Src/Tests/zmatrix/.arch-ids 13895 Tutorials/Intro Tutorials/Intro/.arch-ids Tutorials/Intro/Fe 13896 Tutorials/Intro/Fe/.arch-ids Tutorials/Intro/MgO 13897 Tutorials/Intro/MgO/.arch-ids Tutorials/Intro/Si 13898 Tutorials/Intro/Si/.arch-ids Tutorials/Intro/Si_surface 13899 Tutorials/Intro/Si_surface/.arch-ids 13900 Tutorials/Intro/Water_molecule 13901 Tutorials/Intro/Water_molecule/.arch-ids 13902 Tutorials/Intro/Water_molecule/h2o 13903 Tutorials/Intro/Water_molecule/h2o/.arch-ids 13904 Tutorials/Intro/Water_molecule/h2o_cell 13905 Tutorials/Intro/Water_molecule/h2o_cell/.arch-ids 13906 Tutorials/Intro/Water_molecule/h2o_relax 13907 Tutorials/Intro/Water_molecule/h2o_relax/.arch-ids 13908 13909 renamed directories: 13910 Src/Tests 13911 ==> Tests 13912 13913 new patches: 13914 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-45 13915 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-46 13916 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-47 13917 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-48 13918 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-49 13919 13920 139212006-02-12 18:54:18 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-34 13922 13923 Summary: 13924 Added more options to MD output. Unit cell printed always 13925 Revision: 13926 siesta-devel--reference--1.5--patch-34 13927 13928 (Undocumented changes) 13929 13930 If MD output is enabled, a file called MD_CAR is written with cell and 13931 coordinate information in a vienese format. 13932 13933 Also if MD output is enabled, and if NetCDF support is compiled in, a 13934 file called MD.nc is produced. 13935 13936 * The unit cell vectors are printed regardless of the setting of VariableCell. 13937 13938 13939 new files: 13940 Src/.arch-ids/md_out.F90.id Src/md_out.F90 13941 13942 modified files: 13943 Src/Makefile Src/siesta.F 13944 13945 new patches: 13946 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-42 13947 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-43 13948 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-44 13949 13950 139512006-02-12 18:49:03 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-33 13952 13953 Summary: 13954 Assorted fixes: removed ionew module, wrapping, variable declarations. 13955 Revision: 13956 siesta-devel--reference--1.5--patch-33 13957 13958 * Removed ionew.F. 13959 All references to 'io_assign' and 'io_close' are resolved by io.f. 13960 IOnode is taken from module 'parallel'. 13961 13962 * Wrap write statements in die in xc.f 13963 13964 * Fix compilation of denchar and gen-basis 13965 13966 * Declare variable in mpi_utils 13967 13968 13969 13970 removed files: 13971 Src/.arch-ids/ionew.F.id Src/ionew.F 13972 13973 modified files: 13974 Src/Makefile Src/arw.f Src/atomlist.f Src/denchar.F 13975 Src/gen-basis.F Src/iodm.F Src/iopipes.F90 13976 Src/m_denchar_init.F Src/m_denchar_io.F Src/m_denchar_work.f 13977 Src/m_mpi_utils.F Src/pdos.F Src/pseudopotential.f 13978 Src/setatomnodes.F Src/siesta.F Src/xc.f 13979 Tutorials/Pseudos/README 13980 13981 new patches: 13982 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-37 13983 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-39 13984 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-40 13985 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-41 13986 13987 139882006-02-12 18:45:29 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-32 13989 13990 Summary: 13991 Better user-interface for Broyden optimization 13992 Revision: 13993 siesta-devel--reference--1.5--patch-32 13994 13995 Broyden optimization is now selected by 13996 13997 MD.TypeOfRun Broyden 13998 (The fdf symbol Optim.Broyden is still honored, but is deprecated) 13999 14000 Broyden optimization options are prefixed by MD.Broyden, instead of 14001 Optim.Broyden. 14002 14003 Updated the manual. 14004 14005 14006 14007 14008 modified files: 14009 Docs/siesta.ind Docs/siesta.tex Src/Makefile 14010 Src/Tests/h2o_op_broyden/h2o_op_broyden.fdf 14011 Src/Tests/sih_op_broyden/sih_op_broyden.fdf 14012 Src/Tests/var_cell/var_cell.fdf Src/broyden_optim.F 14013 Src/redata.F Src/siesta.F 14014 14015 renamed files: 14016 Src/.arch-ids/optim.F.id 14017 ==> Src/.arch-ids/broyden_optim.F.id 14018 Src/optim.F 14019 ==> Src/broyden_optim.F 14020 14021 new patches: 14022 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-38 14023 14024 140252006-02-09 12:12:10 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-31 14026 14027 Summary: 14028 (atom) More output for ps optimization. More Fe examples in Tutorial 14029 Revision: 14030 siesta-devel--reference--1.5--patch-31 14031 14032 Added output of Fourier norm of pseudopotential to FOURIER_AREA file, to aid 14033 in automatic optimization. 14034 14035 Put more examples in ../atom/Tutorial/Fe, including a small-core pseudopotential. 14036 14037 14038 new files: 14039 Pseudo/atom/Tutorial/Fe/.arch-ids/Fe.3d74s1.inp.id 14040 Pseudo/atom/Tutorial/Fe/.arch-ids/Fe.sc.inp.id 14041 Pseudo/atom/Tutorial/Fe/.arch-ids/Fe.sc.opt.inp.id 14042 Pseudo/atom/Tutorial/Fe/.arch-ids/Fe.test.sc.inp.id 14043 Pseudo/atom/Tutorial/Fe/Fe.3d74s1.inp 14044 Pseudo/atom/Tutorial/Fe/Fe.sc.inp 14045 Pseudo/atom/Tutorial/Fe/Fe.sc.opt.inp 14046 Pseudo/atom/Tutorial/Fe/Fe.test.sc.inp 14047 14048 modified files: 14049 Pseudo/atom/Tutorial/Fe/README Pseudo/atom/potran.f 14050 Pseudo/atom/wrapup.f version.info 14051 14052 new patches: 14053 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-33 14054 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-34 14055 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-35 14056 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-36 14057 14058 140592006-02-07 10:19:22 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-30 14060 14061 Summary: 14062 Update Release Notes 14063 Revision: 14064 siesta-devel--reference--1.5--patch-30 14065 14066 14067 removed files: 14068 Util/Contrib/APostnikov/.arch-ids/rho2xsf_bac.f.id 14069 Util/Contrib/APostnikov/rho2xsf_bac.f 14070 14071 modified files: 14072 Docs/release.notes_1.5 Util/pdosxml/README 14073 14074 140752006-02-07 08:59:43 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-29 14076 14077 Summary: 14078 Changes to the manual 14079 Revision: 14080 siesta-devel--reference--1.5--patch-29 14081 14082 The manual has been updated. Notable changes: 14083 14084 * Parallelization issues (J. Gale) 14085 * Configure support and other new features and issues (E. Artacho, A. Garcia) 14086 14087 14088 modified files: 14089 Docs/siesta.ind Docs/siesta.tex version.info 14090 14091 new patches: 14092 eartacho@siesta.arch--2005/siesta--my-changes--0.2--base-0 14093 eartacho@siesta.arch--2005/siesta--my-changes--0.2--patch-1 14094 eartacho@siesta.arch--2005/siesta--my-changes--0.2--patch-2 14095 eartacho@siesta.arch--2005/siesta--my-changes--0.2--patch-3 14096 eartacho@siesta.arch--2005/siesta--my-changes--0.2--patch-4 14097 jgale@siesta.arch--2005/siesta--my-changes--0.2--patch-1 14098 14099 141002006-02-07 08:51:40 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-28 14101 14102 Summary: 14103 Change ground state configuration of Pd 14104 Revision: 14105 siesta-devel--reference--1.5--patch-28 14106 14107 In order to be able to specify spin polarization, the d-shell must 14108 not be completely full. For Pd, the configuration 4d10 has been 14109 changed to 4d9-5s1. 14110 14111 14112 modified files: 14113 Src/periodic_table.f 14114 14115 141162006-02-06 18:50:36 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-27 14117 14118 Summary: 14119 Update CHANGES file and version.info 14120 Revision: 14121 siesta-devel--reference--1.5--patch-27 14122 14123 14124 modified files: 14125 Docs/CHANGES version.info 14126 141272006-02-06 15:07:50 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-26 14128 14129 Summary: 14130 Declare all variables. Replace 'stop' with 'die'. 14131 Revision: 14132 siesta-devel--reference--1.5--patch-26 14133 14134 All variables should now be explicitly declared. 14135 14136 Stop statements have been replaced by calls to "die" for proper 14137 behavior under MPI. "die" calls MPI_Abort, which should terminate 14138 the whole set of processes even if called only by the master node. 14139 14140 14141 modified files: 14142 Src/Libs/machine.F Src/Makefile Src/alloc.F90 Src/arw.f 14143 Src/atm_transfer.f Src/atom.f Src/atomlwf.F Src/bands.F 14144 Src/basis_io.F Src/basis_types.f Src/bessph.f Src/cellxc.F 14145 Src/cgwf.F Src/chempot.F Src/chkgmx.f Src/denchar.F 14146 Src/dfscf.f Src/dhscf.F Src/dipole.F Src/dynamics.f 14147 Src/efield.F Src/fermid.F Src/fft3d.F Src/gen-basis.F 14148 Src/grdsam.F Src/idiag.f Src/initdm.F Src/io.f Src/iocg.f 14149 Src/iohs.F Src/iolwf.F Src/ipack.f Src/m_broyddj.f90 14150 Src/m_broyddj_nocomm.f90 Src/m_denchar_neighb.f Src/m_iorho.F 14151 Src/m_walltime.f90 Src/madelung.f Src/mneighb.f Src/outcoor.f 14152 Src/parallelsubs.f Src/phirphi_opt.f Src/poison.F Src/pulayx.F 14153 Src/ranger.f Src/readsp.F Src/recipes.f Src/redcel.F 14154 Src/rhoofd.f Src/rhoofdsp.f Src/siesta.F Src/sys.F Src/timer.F 14155 Src/transition_rate.F Src/vmb.F Src/writewave.F Src/xc.f 14156 14157 new patches: 14158 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-20 14159 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-22 14160 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-23 14161 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-26 14162 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-27 14163 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-28 14164 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-29 14165 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-30 14166 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-32 14167 14168 141692006-02-06 15:02:25 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-25 14170 14171 Summary: 14172 Unwrap setting of ParallelOverK in siesta. Wrap KSV and BEC IO. 14173 Revision: 14174 siesta-devel--reference--1.5--patch-25 14175 14176 ParallelOverK was set inside an #ifdef MPI block, but it was used in the 14177 main code later on. Unwrapped. 14178 14179 Wrapp IO in KSV and Born Effective Charges code for MPI. 14180 14181 14182 modified files: 14183 Src/ksv.f Src/siesta.F 14184 14185 new patches: 14186 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-24 14187 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-31 14188 14189 141902006-02-06 14:59:54 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-24 14191 14192 Summary: 14193 Proper account of WriteEigenvalues. EIG file always written 14194 Revision: 14195 siesta-devel--reference--1.5--patch-24 14196 14197 Eigenvalues are only written to the OUT file if WriteEigenvalues 14198 (or LongOutput) is set to .true. in the fdf file. The EIG file is 14199 always written. 14200 14201 14202 14203 modified files: 14204 Src/siesta.F 14205 14206 new patches: 14207 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-21 14208 14209 142102006-02-06 14:58:05 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-23 14211 14212 Summary: 14213 Integrated some third-party code by A. Postnikov and F. ElMellouhi 14214 Revision: 14215 siesta-devel--reference--1.5--patch-23 14216 14217 Contributed code is in Util/Contrib 14218 14219 14220 14221 new files: 14222 Util/Contrib/.arch-ids/=id Util/Contrib/.arch-ids/README.id 14223 Util/Contrib/APostnikov/.arch-ids/=id 14224 Util/Contrib/APostnikov/.arch-ids/Makefile.id 14225 Util/Contrib/APostnikov/.arch-ids/README.id 14226 Util/Contrib/APostnikov/.arch-ids/displa.f.id 14227 Util/Contrib/APostnikov/.arch-ids/eig2bxsf.f.id 14228 Util/Contrib/APostnikov/.arch-ids/fillbox.f.id 14229 Util/Contrib/APostnikov/.arch-ids/hit.f.id 14230 Util/Contrib/APostnikov/.arch-ids/intpl04.f.id 14231 Util/Contrib/APostnikov/.arch-ids/inver3.f.id 14232 Util/Contrib/APostnikov/.arch-ids/itochar.f.id 14233 Util/Contrib/APostnikov/.arch-ids/makebox.f.id 14234 Util/Contrib/APostnikov/.arch-ids/md2axsf.f.id 14235 Util/Contrib/APostnikov/.arch-ids/read_ev.f.id 14236 Util/Contrib/APostnikov/.arch-ids/read_xv.f.id 14237 Util/Contrib/APostnikov/.arch-ids/rho2xsf.f.id 14238 Util/Contrib/APostnikov/.arch-ids/rho2xsf_bac.f.id 14239 Util/Contrib/APostnikov/.arch-ids/test_md.f.id 14240 Util/Contrib/APostnikov/.arch-ids/vib2xsf.f.id 14241 Util/Contrib/APostnikov/.arch-ids/w_arrow.f.id 14242 Util/Contrib/APostnikov/.arch-ids/w_movie.f.id 14243 Util/Contrib/APostnikov/.arch-ids/wraxsf1.f.id 14244 Util/Contrib/APostnikov/.arch-ids/wraxsf2.f.id 14245 Util/Contrib/APostnikov/.arch-ids/xv2xsf.f.id 14246 Util/Contrib/APostnikov/Makefile 14247 Util/Contrib/APostnikov/README 14248 Util/Contrib/APostnikov/displa.f 14249 Util/Contrib/APostnikov/eig2bxsf.f 14250 Util/Contrib/APostnikov/fillbox.f 14251 Util/Contrib/APostnikov/hit.f 14252 Util/Contrib/APostnikov/intpl04.f 14253 Util/Contrib/APostnikov/inver3.f 14254 Util/Contrib/APostnikov/itochar.f 14255 Util/Contrib/APostnikov/makebox.f 14256 Util/Contrib/APostnikov/md2axsf.f 14257 Util/Contrib/APostnikov/read_ev.f 14258 Util/Contrib/APostnikov/read_xv.f 14259 Util/Contrib/APostnikov/rho2xsf.f 14260 Util/Contrib/APostnikov/rho2xsf_bac.f 14261 Util/Contrib/APostnikov/test_md.f 14262 Util/Contrib/APostnikov/vib2xsf.f 14263 Util/Contrib/APostnikov/w_arrow.f 14264 Util/Contrib/APostnikov/w_movie.f 14265 Util/Contrib/APostnikov/wraxsf1.f 14266 Util/Contrib/APostnikov/wraxsf2.f 14267 Util/Contrib/APostnikov/xv2xsf.f 14268 Util/Contrib/FElMellouhi/.arch-ids/=id 14269 Util/Contrib/FElMellouhi/.arch-ids/DxFormat.f90.id 14270 Util/Contrib/FElMellouhi/.arch-ids/DxView.cfg.id 14271 Util/Contrib/FElMellouhi/.arch-ids/DxView.net.id 14272 Util/Contrib/FElMellouhi/.arch-ids/README.id 14273 Util/Contrib/FElMellouhi/DxFormat.f90 14274 Util/Contrib/FElMellouhi/DxView.cfg 14275 Util/Contrib/FElMellouhi/DxView.net 14276 Util/Contrib/FElMellouhi/README Util/Contrib/README 14277 14278 new directories: 14279 Util/Contrib Util/Contrib/.arch-ids Util/Contrib/APostnikov 14280 Util/Contrib/APostnikov/.arch-ids Util/Contrib/FElMellouhi 14281 Util/Contrib/FElMellouhi/.arch-ids 14282 14283 new patches: 14284 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-25 14285 14286 142872006-02-02 15:24:55 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-22 14288 14289 Summary: 14290 Auxiliary files for configuration tests in atom + "err=" fix 14291 Revision: 14292 siesta-devel--reference--1.5--patch-22 14293 14294 * New files AE_ECONF, PT_ECONF, and ECONF_DIFFS are produced if 14295 a pseudopotential test is run with the customary structure for the 14296 input file (first an ae series, then a corresponding pt series). 14297 14298 The last line of ECONF_DIFFS contains the max abs value of the 14299 excitation energy differences, as well as the mean abs and rms values. 14300 14301 This is useful for externally-driven optimization of pseudopotentials. 14302 14303 * Also, to help some compilers, add err= clause to read stmt in atom/input.f 14304 14305 modified files: 14306 Pseudo/atom/atm.f Pseudo/atom/input.f Pseudo/atom/prdiff.f 14307 version.info 14308 14309 new patches: 14310 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-17 14311 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-19 14312 14313 143142006-02-02 14:03:43 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-21 14315 14316 Summary: 14317 Fix matel to avoid non-zero gradients of overlaps in some cases 14318 Revision: 14319 siesta-devel--reference--1.5--patch-21 14320 14321 Problem: (As restated by A. Postnikov in the Siesta list, after a message 14322 by Hongjun Xiang <xhongjun@MAIL.USTC.EDU.CN>) 14323 -------- 14324 14325 erroneous values of some gradients as delivered by matel. 14326 I.e., the analytical gradient of the overlap of each basis function 14327 with itself is not zero, contrary to expectation. An example for Al s-function: 14328 ia,io,ioa,ja,jo,joa: 1 1 1 1 1 1 xij= 0.0000 0.0000 0.0000 14329 S = 1.00000E+00 grad S = 0.00000E+00 0.00000E+00 -9.71745E-03 14330 T = 4.00390E-01 grad T = 0.00000E+00 0.00000E+00 -1.54155E-02 14331 The values in the last column must be zero. 14332 14333 Jose Soler wrote: 14334 14335 The simplest and most apropriate solution to this problem is to simply 14336 change the line 14337 DFFR0 = HUGE 14338 into 14339 DFFR0 = 0 14340 14341 That changes the boundary condition of the spline interpolation from 14342 (d2FFR/dR2)_0=0 to (dFFR/dR)_0=0 and makes the error in the force of 14343 order 1.e-12 rather than 1.e-2. 14344 14345 Done. 14346 14347 14348 modified files: 14349 Src/matel.f 14350 14351 new patches: 14352 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-18 14353 14354 143552006-02-02 14:00:17 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-20 14356 14357 Summary: 14358 New organization of MD tests -- dynamics stubs for MD output 14359 Revision: 14360 siesta-devel--reference--1.5--patch-20 14361 14362 * The MD tests are now md_{verlet,nose,pr,npr,anneal}. Sample outputs 14363 have been added to Src/Tests/Reference. 14364 14365 * Code stubs have been added to dynamics.f to output synchronous MD 14366 information. (with a view to merge D. Grimwood's approach in the 14367 future). See also md_utils.f90 for a skeleton of an MD writer (format 14368 to be agreed upon). 14369 14370 14371 new files: 14372 Src/.arch-ids/md_utils.f90.id 14373 Src/Tests/Reference/.arch-ids/md_nose.out.id 14374 Src/Tests/Reference/.arch-ids/md_verlet.out.id 14375 Src/Tests/Reference/md_nose.out 14376 Src/Tests/Reference/md_verlet.out 14377 Src/Tests/md_verlet/.arch-ids/=id 14378 Src/Tests/md_verlet/.arch-ids/makefile.id 14379 Src/Tests/md_verlet/.arch-ids/md_verlet.fdf.id 14380 Src/Tests/md_verlet/.arch-ids/md_verlet.pseudos.id 14381 Src/Tests/md_verlet/makefile Src/Tests/md_verlet/md_verlet.fdf 14382 Src/Tests/md_verlet/md_verlet.pseudos Src/md_utils.f90 14383 14384 modified files: 14385 Src/Tests/Makefile Src/Tests/Reference/h2oZ.out 14386 Src/Tests/Reference/md_anneal.out 14387 Src/Tests/Reference/md_npr.out Src/Tests/Reference/md_pr.out 14388 Src/Tests/Reference/zmatrix.out Src/Tests/md_anneal/makefile 14389 Src/Tests/md_anneal/md_anneal.fdf Src/Tests/md_nose/makefile 14390 Src/Tests/md_nose/md_nose.fdf Src/dynamics.f 14391 14392 renamed files: 14393 Src/Tests/Reference/.arch-ids/si.out.id 14394 ==> Src/Tests/Reference/.arch-ids/md_anneal.out.id 14395 Src/Tests/Reference/si.out 14396 ==> Src/Tests/Reference/md_anneal.out 14397 Src/Tests/md/.arch-ids/=id 14398 ==> Src/Tests/md_nose/.arch-ids/=id 14399 Src/Tests/md/.arch-ids/makefile.id 14400 ==> Src/Tests/md_nose/.arch-ids/makefile.id 14401 Src/Tests/md/.arch-ids/md.fdf.id 14402 ==> Src/Tests/md_nose/.arch-ids/md_nose.fdf.id 14403 Src/Tests/md/.arch-ids/md.pseudos.id 14404 ==> Src/Tests/md_nose/.arch-ids/md_nose.pseudos.id 14405 Src/Tests/md/md.fdf 14406 ==> Src/Tests/md_nose/md_nose.fdf 14407 Src/Tests/md/md.pseudos 14408 ==> Src/Tests/md_nose/md_nose.pseudos 14409 Src/Tests/si/.arch-ids/=id 14410 ==> Src/Tests/md_anneal/.arch-ids/=id 14411 Src/Tests/si/.arch-ids/makefile.id 14412 ==> Src/Tests/md_anneal/.arch-ids/makefile.id 14413 Src/Tests/si/.arch-ids/si.STRUCT_IN.id 14414 ==> Src/Tests/md_anneal/.arch-ids/md_anneal.STRUCT_IN.id 14415 Src/Tests/si/.arch-ids/si.fdf.id 14416 ==> Src/Tests/md_anneal/.arch-ids/md_anneal.fdf.id 14417 Src/Tests/si/.arch-ids/si.pseudos.id 14418 ==> Src/Tests/md_anneal/.arch-ids/md_anneal.pseudos.id 14419 Src/Tests/si/si.STRUCT_IN 14420 ==> Src/Tests/md_anneal/md_anneal.STRUCT_IN 14421 Src/Tests/si/si.fdf 14422 ==> Src/Tests/md_anneal/md_anneal.fdf 14423 Src/Tests/si/si.pseudos 14424 ==> Src/Tests/md_anneal/md_anneal.pseudos 14425 14426 new directories: 14427 Src/Tests/md_anneal/.arch-ids Src/Tests/md_nose/.arch-ids 14428 Src/Tests/md_verlet Src/Tests/md_verlet/.arch-ids 14429 14430 removed directories: 14431 Src/Tests/md/.arch-ids Src/Tests/si/.arch-ids 14432 14433 renamed directories: 14434 Src/Tests/md 14435 ==> Src/Tests/md_nose 14436 Src/Tests/si 14437 ==> Src/Tests/md_anneal 14438 14439 new patches: 14440 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-14 14441 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-16 14442 14443 144442006-01-27 17:17:14 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-19 14445 14446 Summary: 14447 Update CHANGES file 14448 Revision: 14449 siesta-devel--reference--1.5--patch-19 14450 14451 14452 modified files: 14453 Docs/CHANGES version.info 14454 144552006-01-27 17:12:51 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-18 14456 14457 Summary: 14458 Added rPBE and revPBE xc functionals to the ATM ps generation program 14459 Revision: 14460 siesta-devel--reference--1.5--patch-18 14461 14462 * Code for rPBE taken from Siesta xc.f previous to the 14463 hybrid-DFT-related architectural changes by J. Gale. 14464 14465 * revPBE is just PBE with a parameter change. 14466 14467 * Version bumped up to 3.2.2. 14468 14469 * Manual updated (a ps version is no longer in the source tree. 14470 Users are advised to generate it or to download it). 14471 14472 14473 14474 new files: 14475 Pseudo/atom/.arch-ids/revpbexc.f.id 14476 Pseudo/atom/.arch-ids/rpbexc.f.id 14477 Pseudo/atom/Docs/.arch-ids/README.id Pseudo/atom/Docs/README 14478 Pseudo/atom/revpbexc.f Pseudo/atom/rpbexc.f 14479 14480 removed files: 14481 Pseudo/atom/Docs/.arch-ids/atom_2up.ps.id 14482 Pseudo/atom/Docs/atom_2up.ps 14483 14484 modified files: 14485 Pseudo/atom/ChangeLog Pseudo/atom/Docs/atom.tex 14486 Pseudo/atom/Tutorial/000README Pseudo/atom/ggaxc.f 14487 Pseudo/atom/header.f Pseudo/atom/input.f Pseudo/atom/makefile 14488 Pseudo/atom/velect.f Pseudo/atom/version.h 14489 Pseudo/atom/wrapup.f Pseudo/atom/xc.f 14490 14491 new patches: 14492 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-15 14493 14494 144952006-01-27 17:09:47 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-17 14496 14497 Summary: 14498 Clean restarts for Parrinello-Rahman and Nose-PR MD (interim fix) 14499 Revision: 14500 siesta-devel--reference--1.5--patch-17 14501 14502 * Added md_pr and md_npr tests for PR and NPR MD. 14503 14504 * Streamlined 'pr' and 'npr' in dynamics.f with vector notation, and 14505 implemented an ad-hoc restarting mechanism using files to hold 14506 the 'old' coordinates and cell vectors (and Nose variables in 'npr'). 14507 14508 Routine 'anneal' is left unchanged for now. 14509 14510 14511 new files: 14512 Src/Tests/Reference/.arch-ids/md_npr.out.id 14513 Src/Tests/Reference/.arch-ids/md_pr.out.id 14514 Src/Tests/Reference/md_npr.out Src/Tests/Reference/md_pr.out 14515 Src/Tests/md_npr/.arch-ids/=id 14516 Src/Tests/md_npr/.arch-ids/makefile.id 14517 Src/Tests/md_npr/.arch-ids/md_npr.fdf.id 14518 Src/Tests/md_npr/.arch-ids/md_npr.pseudos.id 14519 Src/Tests/md_npr/makefile Src/Tests/md_npr/md_npr.fdf 14520 Src/Tests/md_npr/md_npr.pseudos Src/Tests/md_pr/.arch-ids/=id 14521 Src/Tests/md_pr/.arch-ids/makefile.id 14522 Src/Tests/md_pr/.arch-ids/md_pr.fdf.id 14523 Src/Tests/md_pr/.arch-ids/md_pr.pseudos.id 14524 Src/Tests/md_pr/makefile Src/Tests/md_pr/md_pr.fdf 14525 Src/Tests/md_pr/md_pr.pseudos 14526 14527 modified files: 14528 Src/Makefile Src/dynamics.f 14529 14530 new directories: 14531 Src/Tests/md_npr Src/Tests/md_npr/.arch-ids Src/Tests/md_pr 14532 Src/Tests/md_pr/.arch-ids 14533 14534 new patches: 14535 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-6 14536 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-7 14537 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-8 14538 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-9 14539 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-10 14540 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-11 14541 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-12 14542 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-13 14543 14544 145452006-01-27 17:00:35 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-16 14546 14547 Summary: 14548 Bug fixes: ang in dynamics, gen-basis compilation, D&C in Fe test 14549 Revision: 14550 siesta-devel--reference--1.5--patch-16 14551 14552 * Remove duplicate variable ang in dynamics@pr 14553 * Add m_walltime to gen-basis obj list 14554 * Move function call with side effects outside if stmt in chemical.f 14555 * Import node from parallel in timer 14556 14557 * Do not use Divide and Conquer in Fe test (to maintain *some* 14558 continuity in the test results -- but the test itself is very 14559 numerically unstable...) 14560 14561 modified files: 14562 Src/Makefile Src/Tests/fe/fe.fdf Src/chemical.f Src/dynamics.f 14563 Src/timer.F version.info 14564 14565 new patches: 14566 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--base-0 14567 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-1 14568 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-2 14569 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-3 14570 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-4 14571 agarcia@siesta.arch--2006/siesta-devel--agarcia--1.5--patch-5 14572 14573 14574 145752006-01-24 16:48:19 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-14 14576 14577 Summary: 14578 Coherent restarting for MD jobs (interim fix) 14579 Revision: 14580 siesta-devel--reference--1.5--patch-14 14581 14582 The XV file contains the positions and velocities *at different 14583 times*. This poses problems for the continuation of MD runs. 14584 14585 Until we can re-design the MD output code, an interim fix has been 14586 prepared: 14587 14588 For the velocity-Verlet algorithm (in routine 'verlet2'), the fix is to read the 14589 'old' forces as well as the 'current' positions and 'old' velocities. 14590 Forces are written to VERLET_FORCES at each step, and are read in the 14591 first step if the XV file has been read. 14592 14593 For the modified Verlet algorithm (in routine 'nose'), the fix is to read the 14594 'old' positions, AND the values of the Nose variables (current and old). 14595 14596 The information is written to NOSE_RESTART at each step, and is read in the 14597 first step if the XV file has been read. 14598 14599 The code in ioxv.F has been put in a module, to hold the new variable 14600 xv_file_read. 'dynamics.f' has also been turned into a module. 14601 14602 Fixes for the other MD flavors are forthcoming. 14603 14604 14605 14606 new files: 14607 Src/Tests/md/.arch-ids/=id Src/Tests/md/.arch-ids/makefile.id 14608 Src/Tests/md/.arch-ids/md.fdf.id 14609 Src/Tests/md/.arch-ids/md.pseudos.id Src/Tests/md/makefile 14610 Src/Tests/md/md.fdf Src/Tests/md/md.pseudos 14611 14612 modified files: 14613 Src/Makefile Src/Sys/intel9-mkl8.make Src/Tests/Makefile 14614 Src/dynamics.f Src/ioxv.F Src/m_mpi_utils.F Src/siesta.F 14615 Src/sys.F 14616 14617 new directories: 14618 Src/Tests/md Src/Tests/md/.arch-ids 14619 14620 new patches: 14621 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.5--patch-32 14622 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.5--patch-33 14623 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.5--patch-34 14624 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.5--patch-35 14625 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.5--patch-36 14626 14627 146282006-01-24 13:46:16 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-13 14629 14630 Summary: 14631 Parallel over K option extended to band calculations + assorted fixes 14632 Revision: 14633 siesta-devel--reference--1.5--patch-13 14634 14635 (By Julian Gale) 14636 14637 * K point parallelism was previously only enabled for the regular SCF procedure. It has 14638 now been extended to the determination of the band structure. 14639 14640 * The case sensitivity for some zmatrix input commands has been handled by 14641 converting the input line to lower case. 14642 14643 * A new module "files" has been added that contains the system label and a 14644 parameter that is used to define the label length in subroutines to 14645 ensure consistency. 14646 14647 * nrowsDscfL caused an error due to an out of bounds reference in 14648 dfscf.f rhoofd.f rhoofdsp.f vmat.f, and vmatsp.f. Fixed. 14649 14650 14651 14652 new files: 14653 Src/.arch-ids/files.f.id Src/files.f 14654 14655 modified files: 14656 Src/Makefile Src/bands.F Src/cdiag.F Src/coceri.f Src/coxmol.f 14657 Src/dfscf.f Src/iocg.f Src/iodm.F Src/ioeig.f Src/iofa.f 14658 Src/iohs.F Src/iokp.f Src/iolwf.F Src/iomd.f Src/ioxv.F 14659 Src/iozm.F Src/m_iostruct.f Src/ofc.f Src/optical.F 14660 Src/parallel.f Src/pdos.F Src/phonon.F Src/pixmol.f 14661 Src/plcharge.F Src/pulayx.F Src/redata.F Src/reinit.F 14662 Src/rhoofd.f Src/rhoofdsp.f Src/siesta.F 14663 Src/siesta_cmlsubs.F90 Src/vmat.f Src/vmatsp.f Src/writewave.F 14664 Src/zmatrix.F 14665 14666 new patches: 14667 jgale@siesta.arch--2005/siesta--my-changes--0.1--patch-8 14668 jgale@siesta.arch--2005/siesta--my-changes--0.1--patch-9 14669 jgale@siesta.arch--2005/siesta--my-changes--0.1--patch-10 14670 jgale@siesta.arch--2005/siesta--my-changes--0.1--patch-13 14671 14672 146732006-01-24 10:49:10 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-12 14674 14675 Summary: 14676 Added code to compute Born effective charges 14677 Revision: 14678 siesta-devel--reference--1.5--patch-12 14679 14680 (Code from Tom Archer and Miguel Pruneda) 14681 14682 The Born effective charge tensor is calculated by finite differences, 14683 using the polarization differences in the small displacements 14684 generated in the FC type of run. 14685 14686 They can be used by Vibra to obtain LO-TO splittings and infrared 14687 activities but VIBRA still needs to be updated to do so (Tom Archer has a 14688 working version). 14689 14690 14691 new files: 14692 Src/.arch-ids/obc.f.id Src/obc.f 14693 14694 modified files: 14695 Docs/siesta.tex Src/Makefile Src/siesta.F 14696 14697 new patches: 14698 eartacho@siesta.arch--2005/siesta--my-changes--0.1--patch-4 14699 eartacho@siesta.arch--2005/siesta--my-changes--0.1--patch-5 14700 14701 147022006-01-24 10:34:24 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-11 14703 14704 Summary: 14705 XML output additions and fixes 14706 Revision: 14707 siesta-devel--reference--1.5--patch-11 14708 14709 * Correct cml namespace 14710 * Print out positions & cell at every step. 14711 * Backported from xmlf90 - PMR added lattice & latticeVectors to CML, so we can use it. 14712 14713 modified files: 14714 Src/ioxv.F Src/outcoor.f Src/siesta.F Src/siesta_cmlsubs.F90 14715 14716 new patches: 14717 twhite@siesta.arch--2005/siesta-devel--xmltidy--1.5--patch-1 14718 twhite@siesta.arch--2005/siesta-devel--xmltidy--1.5--patch-2 14719 14720 147212006-01-23 15:26:33 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-10 14722 14723 Summary: 14724 Proper configure test for NetCDF 14725 Revision: 14726 siesta-devel--reference--1.5--patch-10 14727 14728 Patches applied: 14729 14730 * twhite@siesta.arch--2005/siesta-devel--netcdf--1.5--patch-1 14731 14732 14733 14734 modified files: 14735 Src/NetCDF/Makefile Src/aclocal.m4 Src/arch.make.in 14736 Src/configure Src/configure.ac Src/m4/TW_PATH_NETCDF.m4 14737 14738 new patches: 14739 twhite@siesta.arch--2005/siesta-devel--netcdf--1.5--patch-1 14740 14741 147422006-01-18 16:51:14 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-9 14743 14744 Summary: 14745 Update CHANGES file 14746 Revision: 14747 siesta-devel--reference--1.5--patch-9 14748 14749 14750 modified files: 14751 Docs/CHANGES 14752 14753 147542006-01-18 16:45:48 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-8 14755 14756 Summary: 14757 Bug fix regarding limited eigenvectors & spin (by Pablo Ordejon) 14758 Revision: 14759 siesta-devel--reference--1.5--patch-8 14760 14761 When telling siesta not to find all eigenvectors, and with spin polarisation, 14762 there were still some misadjustments. 14763 14764 14765 14766 14767 modified files: 14768 Src/siesta.F 14769 14770 new patches: 14771 eartacho@siesta.arch--2005/siesta--my-changes--0.1--patch-3 14772 14773 147742006-01-18 16:44:22 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-7 14775 14776 Summary: 14777 Several bugs fixed in optical and pulayx 14778 Revision: 14779 siesta-devel--reference--1.5--patch-7 14780 14781 BUGs Fixed: 14782 14783 subroutines optical, transition_rate and diagpol: 14784 *The subroutine was not able to deal correctly with the 14785 calculation of the optical properties of a molecule using 14786 only gamma point. 14787 *The scissor correction was not applied at the right place 14788 *The populations used to calculate the dielectric constant 14789 were incorrect (by a factor of two). Fortunately this only 14790 translate in an incorrect normalization factor which, at the 14791 end, was corrected (inadvertently) due to the use of Ry instead 14792 of atomic units. 14793 subroutine pulayx: 14794 *The case of the subroutine inver failing was not conveniently 14795 treated in all the cases due to the use of the function mod. 14796 14797 Other changes: 14798 subroutine optical: 14799 *The default mesh for the calculation of the optical properties of 14800 molecules and atoms has been changed to gamma point. Thus, in these 14801 cases the Optical.Mesh block does not need to be specified. 14802 *Some cosmetics 14803 subroutine reoptical: 14804 *Some cosmetics. 14805 *Ensuring the default option 'polycrystal' for the polarization type. 14806 subroutine ksv_pol: 14807 *Modification of the call to subroutine diagpol, which now has 14808 and additional parameter. 14809 subroutine phirphi_opt.f 14810 *Cosmetics and minor changes 14811 Docs/siesta.tex 14812 *Has been changed according to this new default 14813 *A new reference has been added to the list of SIESTA references. 14814 *Sanchez-Portal's affiliation has been updated. 14815 14816 14817 14818 modified files: 14819 Docs/siesta.ind Docs/siesta.tex Src/diagpol.f Src/ksv.f 14820 Src/optical.F Src/phirphi_opt.f Src/pulayx.F Src/reoptical.F 14821 Src/transition_rate.F 14822 14823 new patches: 14824 dsanchez@siesta.arch--2005/siesta--optical--0.1--patch-1 14825 14826 148272006-01-17 14:16:51 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-6 14828 14829 Summary: 14830 Assignments moved outside inner loop in kinefsm to save cputime 14831 Revision: 14832 siesta-devel--reference--1.5--patch-6 14833 14834 Patches applied: 14835 14836 * jgale@siesta.arch--2005/siesta--my-changes--0.1--patch-2 14837 Assignments moved outside inner loop in kinefsm to save cputime. 14838 14839 14840 modified files: 14841 Src/kinefsm.f 14842 14843 new patches: 14844 jgale@siesta.arch--2005/siesta--my-changes--0.1--patch-2 14845 14846 148472006-01-17 14:05:29 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-5 14848 14849 Summary: 14850 Added compilation support for SGI-Altix and Intel9+MKL8 14851 Revision: 14852 siesta-devel--reference--1.5--patch-5 14853 14854 New files in Src/Sys for SGI-Altix and (library locations site-dependent) 14855 Intel Fortran Compiler V.7 with Intel MKL V.8. 14856 14857 14858 new files: 14859 Src/Sys/.arch-ids/intel9-mkl8.make.id 14860 Src/Sys/.arch-ids/sgi-altix.make.id Src/Sys/intel9-mkl8.make 14861 Src/Sys/sgi-altix.make 14862 14863 new patches: 14864 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.5--patch-27 14865 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.5--patch-28 14866 jgale@siesta.arch--2005/siesta--my-changes--0.1--patch-4 14867 14868 148692006-01-17 14:01:54 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-4 14870 14871 Summary: 14872 Zmatrix information output and re-starting options (+fixes) 14873 Revision: 14874 siesta-devel--reference--1.5--patch-4 14875 14876 The program now writes a summary of the zmatrix *explicit* variables 14877 at each step of the optimization phase. 14878 14879 New option MD.UseSaveZM added to preserve Zmatrix information accross runs. 14880 14881 New zmatrix test. 14882 14883 Other fixes: 14884 14885 - Remove comment from optim.F implying that it does not work for variable cell 14886 relaxations. 14887 14888 - Fix computation of lattice angles in wxml/flib_wcml.f90. 14889 14890 14891 new files: 14892 Src/.arch-ids/iozm.F.id Src/.arch-ids/m_cell.f.id 14893 Src/Tests/Reference/.arch-ids/zmatrix.out.id 14894 Src/Tests/Reference/zmatrix.out 14895 Src/Tests/zmatrix/.arch-ids/=id 14896 Src/Tests/zmatrix/.arch-ids/Zmatrix.data.id 14897 Src/Tests/zmatrix/.arch-ids/makefile.id 14898 Src/Tests/zmatrix/.arch-ids/zmatrix.fdf.id 14899 Src/Tests/zmatrix/.arch-ids/zmatrix.pseudos.id 14900 Src/Tests/zmatrix/Zmatrix.data Src/Tests/zmatrix/makefile 14901 Src/Tests/zmatrix/zmatrix.fdf 14902 Src/Tests/zmatrix/zmatrix.pseudos Src/iozm.F Src/m_cell.f 14903 14904 modified files: 14905 Docs/siesta.ind Docs/siesta.tex Src/Makefile 14906 Src/Tests/Makefile Src/Tests/Reference/h2oZ.out Src/optim.F 14907 Src/siesta.F Src/wxml/flib_wcml.f90 Src/zmatrix.F 14908 14909 new directories: 14910 Src/Tests/zmatrix Src/Tests/zmatrix/.arch-ids 14911 14912 new patches: 14913 agarcia@siesta.arch--2005/siesta-devel--ag-uspex--1.5--base-0 14914 agarcia@siesta.arch--2005/siesta-devel--ag-uspex--1.5--patch-1 14915 agarcia@siesta.arch--2005/siesta-devel--ag-uspex--1.5--patch-2 14916 agarcia@siesta.arch--2005/siesta-devel--ag-uspex--1.5--patch-3 14917 agarcia@siesta.arch--2005/siesta-devel--ag-uspex--1.5--patch-4 14918 agarcia@siesta.arch--2005/siesta-devel--ag-uspex--1.5--patch-5 14919 agarcia@siesta.arch--2005/siesta-devel--ag-uspex--1.5--patch-6 14920 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.5--patch-18 14921 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.5--patch-23 14922 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.5--patch-29 14923 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.5--patch-30 14924 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.5--patch-31 14925 jgale@siesta.arch--2005/siesta--my-changes--0.1--patch-3 14926 jgale@siesta.arch--2005/siesta--my-changes--0.1--patch-7 14927 14928 149292006-01-17 10:47:32 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-3 14930 14931 Summary: 14932 XC: Add revPBE functional -- fix call to blypxc for non-collinear spin 14933 Revision: 14934 siesta-devel--reference--1.5--patch-3 14935 14936 A new routine has been added to xc.f to implement the "revPBE" functional 14937 (which only differs from PBE in the change of a parameter). The new "author" 14938 code in the fdf file is "revPBE". 14939 14940 The call to blypxc was not correct in the case of non-collinear spin. Fixed. 14941 14942 14943 14944 modified files: 14945 Docs/siesta.tex Src/siesta.F Src/xc.f 14946 14947 new patches: 14948 eartacho@siesta.arch--2005/siesta--my-changes--0.1--patch-2 14949 jgale@siesta.arch--2005/siesta--my-changes--0.1--patch-6 14950 14951 149522006-01-17 10:42:36 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-2 14953 14954 Summary: 14955 Units of energy in MDE are now eV 14956 Revision: 14957 siesta-devel--reference--1.5--patch-2 14958 14959 Patches applied: 14960 14961 * eartacho@siesta.arch--2005/siesta--my-changes--0.1--patch-1 14962 Bug fixed: units of energy in MDE now eV 14963 14964 14965 modified files: 14966 Src/iomd.f 14967 14968 new patches: 14969 eartacho@siesta.arch--2005/siesta--my-changes--0.1--patch-1 14970 14971 149722005-12-09 11:21:52 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-1 14973 14974 Summary: 14975 Broyden algorithm for geometry optimization. Assorted fixes. 14976 Revision: 14977 siesta-devel--reference--1.5--patch-1 14978 14979 * Broyden algorithm for geometry optimization 14980 14981 It is a drop-in replacement for the conjugate-gradients algorithm (including 14982 the variable-cell case). It seems to work better in all cases analyzed, 14983 even with the standard defaults. 14984 14985 (selected by the new Optim.Broyden boolean fdf variable. See the manual 14986 for a full set of options, but note that the defaults seem to work well) 14987 14988 The code is in the new routine optim.F, which just calls the same code in 14989 m_broyddj.f90 used for the SCF minimization. Actually, a special 14990 version without interprocess communication has been prepared, so that 14991 in a parallel run, with the coordinates and forces replicated in all 14992 processors, all will be doing the same kinds of operations. 14993 14994 Some new tests have been added: h2o_op_broyden, sih_op_broyden. 14995 The var_cell test is now done with the Broyden algorithm. 14996 14997 * Wrap some calls and I/O statements for MPI operation. 14998 (I/O in redata, calls to coxmol and coceri) 14999 15000 * Give XV file priority over struct-file input 15001 15002 * Update FFLAGS in cscs-cray-mpi.make 15003 15004 * New Tests/Reference directory to hold recent output files (for checks on 15005 new installations, rather than correctness tests). 15006 15007 * Add proper CML references for the zmatrix case. 15008 15009 * Atom cosmetic fixes: non-standard write in atom/vionic.f, 15010 generic f95 aux file. 15011 15012 * Annealing proto-code. Some experimental code to achieve a given 15013 temperature "exactly" after a Md.TauRelax time. This is not physical, just 15014 expeditive. The code is not yet enabled. 15015 15016 The si test has been changed to an example of annealing. 15017 15018 15019 15020 15021 new files: 15022 Pseudo/atom/.arch-ids/auxf95.f.id Pseudo/atom/auxf95.f 15023 Src/.arch-ids/m_broyddj_nocomm.f90.id Src/.arch-ids/optim.F.id 15024 Src/Tests/Reference/.arch-ids/=id 15025 Src/Tests/Reference/.arch-ids/batio3.out.id 15026 Src/Tests/Reference/.arch-ids/bessel.out.id 15027 Src/Tests/Reference/.arch-ids/constant_volume.out.id 15028 Src/Tests/Reference/.arch-ids/fe.out.id 15029 Src/Tests/Reference/.arch-ids/fe_broyden.out.id 15030 Src/Tests/Reference/.arch-ids/floating.out.id 15031 Src/Tests/Reference/.arch-ids/h2o.out.id 15032 Src/Tests/Reference/.arch-ids/h2oZ.out.id 15033 Src/Tests/Reference/.arch-ids/h2o_dos.out.id 15034 Src/Tests/Reference/.arch-ids/h2o_op_broyden.out.id 15035 Src/Tests/Reference/.arch-ids/h2o_orderN.out.id 15036 Src/Tests/Reference/.arch-ids/mgco3.out.id 15037 Src/Tests/Reference/.arch-ids/si.out.id 15038 Src/Tests/Reference/.arch-ids/si64.out.id 15039 Src/Tests/Reference/.arch-ids/sih.out.id 15040 Src/Tests/Reference/.arch-ids/sih_op_broyden.out.id 15041 Src/Tests/Reference/.arch-ids/var_cell.out.id 15042 Src/Tests/Reference/batio3.out Src/Tests/Reference/bessel.out 15043 Src/Tests/Reference/constant_volume.out 15044 Src/Tests/Reference/fe.out Src/Tests/Reference/fe_broyden.out 15045 Src/Tests/Reference/floating.out Src/Tests/Reference/h2o.out 15046 Src/Tests/Reference/h2oZ.out Src/Tests/Reference/h2o_dos.out 15047 Src/Tests/Reference/h2o_op_broyden.out 15048 Src/Tests/Reference/h2o_orderN.out 15049 Src/Tests/Reference/mgco3.out Src/Tests/Reference/si.out 15050 Src/Tests/Reference/si64.out Src/Tests/Reference/sih.out 15051 Src/Tests/Reference/sih_op_broyden.out 15052 Src/Tests/Reference/var_cell.out 15053 Src/Tests/h2o_op_broyden/.arch-ids/=id 15054 Src/Tests/h2o_op_broyden/.arch-ids/h2o_op_broyden.fdf.id 15055 Src/Tests/h2o_op_broyden/.arch-ids/h2o_op_broyden.pseudos.id 15056 Src/Tests/h2o_op_broyden/.arch-ids/makefile.id 15057 Src/Tests/h2o_op_broyden/h2o_op_broyden.fdf 15058 Src/Tests/h2o_op_broyden/h2o_op_broyden.pseudos 15059 Src/Tests/h2o_op_broyden/makefile Src/Tests/mgo/.arch-ids/=id 15060 Src/Tests/mgo/.arch-ids/Kgrid.id 15061 Src/Tests/mgo/.arch-ids/makefile.id 15062 Src/Tests/mgo/.arch-ids/mgo.STRUCT_IN.id 15063 Src/Tests/mgo/.arch-ids/mgo.fdf.id 15064 Src/Tests/mgo/.arch-ids/mgo.pseudos.id 15065 Src/Tests/mgo/.arch-ids/mydefaults.fdf.id Src/Tests/mgo/Kgrid 15066 Src/Tests/mgo/makefile Src/Tests/mgo/mgo.STRUCT_IN 15067 Src/Tests/mgo/mgo.fdf Src/Tests/mgo/mgo.pseudos 15068 Src/Tests/mgo/mydefaults.fdf 15069 Src/Tests/sih_op_broyden/.arch-ids/=id 15070 Src/Tests/sih_op_broyden/.arch-ids/makefile.id 15071 Src/Tests/sih_op_broyden/.arch-ids/sih_op_broyden.fdf.id 15072 Src/Tests/sih_op_broyden/.arch-ids/sih_op_broyden.pseudos.id 15073 Src/Tests/sih_op_broyden/makefile 15074 Src/Tests/sih_op_broyden/sih_op_broyden.fdf 15075 Src/Tests/sih_op_broyden/sih_op_broyden.pseudos 15076 Src/m_broyddj_nocomm.f90 Src/optim.F 15077 15078 modified files: 15079 Docs/siesta.tex Pseudo/atom/makefile Pseudo/atom/vionic.f 15080 Src/Makefile Src/Sys/cscs-cray-mpi.make Src/Tests/Makefile 15081 Src/Tests/si/si.fdf Src/Tests/sih/sih.fdf 15082 Src/Tests/var_cell/var_cell.fdf Src/coor.F Src/dynamics.f 15083 Src/redata.F Src/siesta.F version.info 15084 15085 new directories: 15086 Src/Tests/Reference Src/Tests/Reference/.arch-ids 15087 Src/Tests/h2o_op_broyden Src/Tests/h2o_op_broyden/.arch-ids 15088 Src/Tests/mgo Src/Tests/mgo/.arch-ids Src/Tests/sih_op_broyden 15089 Src/Tests/sih_op_broyden/.arch-ids 15090 15091 new patches: 15092 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.5--base-0 15093 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.5--patch-1 15094 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.5--patch-2 15095 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.5--patch-3 15096 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.5--patch-4 15097 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.5--patch-5 15098 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.5--patch-6 15099 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.5--patch-7 15100 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.5--patch-8 15101 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.5--patch-9 15102 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.5--patch-10 15103 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.5--patch-11 15104 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.5--patch-12 15105 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.5--patch-13 15106 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.5--patch-14 15107 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.5--patch-15 15108 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.5--patch-16 15109 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.5--patch-17 15110 15111 151122005-11-06 11:39:29 GMT Alberto Garcia <wdpgaara@lg.ehu.es> base-0 15113 15114 Summary: 15115 tag of siesta@uam.es--2005/siesta-devel--reference--1.4--patch-18 15116 Revision: 15117 siesta-devel--reference--1.5--base-0 15118 15119 (automatically generated log message) 15120 (Detailed patch list omitted) 15121 15122____________________________________________________________________ 15123** CHANGES ALONG siesta@uam.es--2005/siesta-devel--reference--1.4 15124-------------------------------------------------------------------- 15125 151262005-11-06 11:32:34 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-18 15127 15128 Added Release Notes for interim release 1.5 15129 Modified version.F90 to set version number to 1.5.0 15130 Modified top-level README 15131 151322005-11-06 11:04:34 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-17 15133 15134 Updated this (Docs/CHANGES) file 15135 151362005-11-04 17:14:34 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-16 15137 15138 Summary: 15139 New starlink autoconf. CML update. MD scripts. New walltime analysis. 15140 Revision: 15141 siesta-devel--reference--1.4--patch-16 15142 15143 * Merge from Toby White's ac-update branch -- New starlink autoconf 15144 (Add m4/fortran.m4 to list of files to be merged into aclocal.m4) 15145 15146 * Merge CML generation patches along twhite@siesta.arch--2005/siesta-devel--xml--1.4, 15147 up to patch-3: 15148 15149 XML changes to conform better to CML schema 15150 Add stylesheet decelaration. 15151 fix lattice 15152 15153 (Note: siesta_cml.f90 patches applied in effect to siesta_cmlsubs.F90) 15154 15155 * Add simple MD analysis scripts 15156 15157 * Improve walltime printing: 15158 15159 A new module m_walltime implements a "wall_time(t)" call similar to 15160 "cpu_time(t)", including checks for wraparound of the system counter. 15161 With the new routine, timer has been enhanced to print also elapsed times. 15162 The new table (and a line for IterSCF) goes to standard output. 15163 15164 To Do: Rationalize MPI calls. 15165 Integrate both cpu and walltime information in the same table. 15166 15167 15168 * Do not rewind alloc_report file, to allow for multiple batches of information. 15169 15170 15171 new files: 15172 Src/.arch-ids/m_walltime.f90.id Src/m_walltime.f90 15173 Util/MD/.arch-ids/=id Util/MD/.arch-ids/tpe.sh.id 15174 Util/MD/.arch-ids/voigt.sh.id Util/MD/tpe.sh Util/MD/voigt.sh 15175 15176 modified files: 15177 Src/Makefile Src/aclocal.m4 Src/alloc.F90 Src/atomlist.f 15178 Src/configure Src/coor.F Src/m4/TW_FC_KINDS.m4 15179 Src/m4/fortran.m4 Src/m_iostruct.f Src/m_wallclock.f90 15180 Src/outcoor.f Src/siesta.F Src/siesta_cmlsubs.F90 Src/timer.F 15181 Src/wxml/flib_wcml.f90 Src/wxml/flib_wstml.f90 15182 Src/wxml/m_wxml_core.f90 Src/wxml/m_wxml_text.F90 version.info 15183 15184 renamed files: 15185 Util/PyAtom/.arch-ids/shape.sh.id 15186 ==> Util/MD/.arch-ids/shape.sh.id 15187 Util/PyAtom/shape.sh 15188 ==> Util/MD/shape.sh 15189 15190 new directories: 15191 Util/MD Util/MD/.arch-ids 15192 15193 new patches: 15194 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-79 15195 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-80 15196 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-81 15197 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-82 15198 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-83 15199 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-84 15200 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-85 15201 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-86 15202 twhite@siesta.arch--2005/siesta-devel--xml--1.4--base-0 15203 twhite@siesta.arch--2005/siesta-devel--xml--1.4--patch-1 15204 twhite@siesta.arch--2005/siesta-devel--xml--1.4--patch-2 15205 twhite@siesta.arch--2005/siesta-devel--xml--1.4--patch-3 15206 twhite@siesta.arch--2005/siesta-test--ac-update--1.4--patch-1 15207 twhite@siesta.arch--2005/siesta-test--ac-update--1.4--patch-2 15208 15209======================================================================= 15210 152112005-11-04 15:22:47 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-15 15212 15213 Summary: 15214 Merge of J. Gale's branch: O(N), D&C, zmatrix, dEtol + bug fixes 15215 Revision: 15216 siesta-devel--reference--1.4--patch-15 15217 15218 * Order N lower memory option expanded 15219 15220 (1) Lower memory version of gradient and denmat have been added: Here the algorithm is 15221 adapted along the lines of ener3lomem.F such that the size of the buxstore(2) 15222 communication arrays is reduced by a factor of 2 relative to the standard versions. 15223 Since these arrays can be the largest ones, it makes it feasible to run larger 15224 order N jobs. 15225 15226 Files involved: denmatlomem.F, gradientlomem.F, egandd.F 15227 15228 (2) Parallel division of work in order N: A check is now added to ensure that the 15229 number of domains created is larger than the number of processors so that no processor 15230 should be without work. 15231 15232 Files involved: initparallel.F 15233 15234 (3) Reduce alloc/dealloc in order N set up: The algorithm for subroutines in on_subs.F 15235 has been changed to ensure that the resizing of arrays is performed just once in 15236 each case. 15237 15238 Files involved: on_subs.F 15239 15240 * Divide and conquer could now be made the default algorithm for diagonalisation: 15241 (Actual setting pending) 15242 15243 Files involved: redata.F, rdiag.F, cdiag.F 15244 15245 * Z-matrix optimisation included 15246 15247 (1) Z-matrix added: This allows a Z-matrix block to be specified for the structural 15248 input, with the ability to specify symbolic variables, constants and constraints, 15249 as well as offering control over the optimisation process. 15250 15251 Files: zmatrix.F, siesta.F, cgvc_zmatrix.F, coor.F, conjgr.F 15252 15253 Also added example and test case. 15254 15255 (2) parsing routine extended: The option to return an array that indicates the order 15256 in which parameters were read has been added. 15257 15258 Files: parsing.f 15259 15260 (3) Makefile: New routines zmatrix.F, gradientlomem.F & denmatlomem.F added 15261 15262 (4) New units added: Units relevant to angular degrees of freedom added 15263 15264 Files: fdf/fdf.f 15265 15266 (5) Mesh output returned to standard form: The output of the mesh details had been changed 15267 and so the format has been restored to the existing format (same information - different 15268 line spacing) 15269 15270 Files: meshsubs.F 15271 15272 (6) coor.f renamed to coor.F 15273 15274 * Energy convergence criterion added for SCF 15275 * Introduce new fdf symbol DM.RequireEnergyConvergence to make the test 15276 optional. (At least, to reproduce old test results) 15277 15278 BUG FIXES 15279 15280 - initparallel.F modified so that ncell is set based on absolute size of ucell 15281 to allow for negative cell parameters 15282 - Format for Qtot from mulliken increased to f12.3 to avoid ****** 15283 - Banner changed to better handle 1 node being run with MPI 15284 15285 Corrections to order N from Toby: 15286 - setatomnodes.f - error in referencing of y index when counting number of atoms in X blocks 15287 - declared sizes of numc/numcold corrected to nbasisloc in extrapolon.f 15288 15289 * Initializations: 15290 15291 - lastna in meshsubs.F 15292 - ilm in spher_harm.f 15293 - rngmax in ranger.f 15294 - CartesianB and CartesianF in zmatrix.F 15295 15296 ( Note ** : stressl MUST NOT be initialized to zero in cellxc (inout) ) 15297 15298 Other: 15299 15300 - User pxfabort in sys.F 15301 - Add intents to arguments in ranger.f 15302 - Replace "shrink=false" by "copy=.false." in re_alloc of listh in siesta.F 15303 - Use units module in zmatrix.F 15304 - Import IOnode in zmatrix.F 15305 - Add deg in units.f90 15306 15307 * Declare iamove as (*) in ranger 15308 * Initialize ianneal in redata.F 15309 * Fix bug in alloc_err bounds array 15310 15311 * Go back to "traditional" h2o test (without Broyden). 15312 * Reset target pressure to 100 Gpa in var_cell test. 15313 15314 ** Add elec_corr_setup call to user.basis case. 15315 15316 new files: 15317 Examples/Zmatrix/.arch-ids/=id 15318 Examples/Zmatrix/.arch-ids/h2oZ.fdf.id 15319 Examples/Zmatrix/h2oZ.fdf Src/.arch-ids/cgvc_zmatrix.F.id 15320 Src/.arch-ids/conjgr_old.f.id Src/.arch-ids/coor.F.id 15321 Src/.arch-ids/denmatlomem.F.id 15322 Src/.arch-ids/gradientlomem.F.id Src/.arch-ids/zmatrix.F.id 15323 Src/Tests/Outs/.arch-ids/h2oZ.out.id Src/Tests/Outs/h2oZ.out 15324 Src/Tests/h2oZ/.arch-ids/=id 15325 Src/Tests/h2oZ/.arch-ids/h2oZ.fdf.id 15326 Src/Tests/h2oZ/.arch-ids/h2oZ.pseudos.id 15327 Src/Tests/h2oZ/.arch-ids/makefile.id Src/Tests/h2oZ/h2oZ.fdf 15328 Src/Tests/h2oZ/h2oZ.pseudos Src/Tests/h2oZ/makefile 15329 Src/cgvc_zmatrix.F Src/conjgr_old.f Src/coor.F 15330 Src/denmatlomem.F Src/gradientlomem.F Src/zmatrix.F 15331 15332 removed files: 15333 Src/.arch-ids/coor.f.id Src/coor.f 15334 15335 modified files: 15336 Docs/siesta.ind Docs/siesta.tex Src/Makefile 15337 Src/Tests/Makefile Src/Tests/h2o/h2o.fdf 15338 Src/Tests/var_cell/var_cell.fdf Src/alloc.F90 Src/cdiag.F 15339 Src/cgvc.F Src/cgwf.F Src/conjgr.f Src/egandd.F 15340 Src/extrapolon.f Src/fdf/fdf.f Src/globalise.F Src/initatom.f 15341 Src/initparallel.F Src/iocg.f Src/m_iostruct.f 15342 Src/m_mpi_utils.F Src/meshsubs.F Src/mulliken.F Src/on_subs.F 15343 Src/parsing.f Src/ranger.f Src/rdiag.F Src/redata.F 15344 Src/setatomnodes.F Src/siesta.F Src/spher_harm.f Src/sys.F 15345 Src/units.f90 Src/version.F90 version.info 15346 15347 new directories: 15348 Examples/Zmatrix Examples/Zmatrix/.arch-ids Src/Tests/h2oZ 15349 Src/Tests/h2oZ/.arch-ids 15350 15351 new patches: 15352 jgale@siesta.arch--2005/siesta-devel--jgale--1.4--base-0 15353 jgale@siesta.arch--2005/siesta-devel--jgale--1.4--patch-1 15354 jgale@siesta.arch--2005/siesta-devel--jgale--1.4--patch-2 15355 jgale@siesta.arch--2005/siesta-devel--jgale--1.4--patch-3 15356 jgale@siesta.arch--2005/siesta-devel--jgale--1.4--patch-4 15357 jgale@siesta.arch--2005/siesta-devel--jgale--1.4--patch-5 15358 jgale@siesta.arch--2005/siesta-devel--jgale--1.4--patch-6 15359 jgale@siesta.arch--2005/siesta-devel--jgale--1.4--patch-7 15360 jgale@siesta.arch--2005/siesta-devel--jgale--1.4--patch-8 15361 jgale@siesta.arch--2005/siesta-devel--jgale--1.4--patch-9 15362 jgale@siesta.arch--2005/siesta-devel--jgale--1.4--patch-10 15363 jgale@siesta.arch--2005/siesta-devel--jgale--1.4--patch-11 15364 jgale@siesta.arch--2005/siesta-devel--jgale--1.4--patch-12 15365 jgale@siesta.arch--2005/siesta-devel--jgale--1.4--patch-13 15366 jgale@siesta.arch--2005/siesta-devel--jgale--1.4--patch-14 15367 jgale@siesta.arch--2005/siesta-devel--jgale--1.4--patch-15 15368 jgale@siesta.arch--2005/siesta-devel--jgale--1.4--patch-16 15369 jgale@siesta.arch--2005/siesta-devel--jgale--1.4--patch-17 15370 jgale@siesta.arch--2005/siesta-devel--jgale--1.4--patch-18 15371 jgale@siesta.arch--2005/siesta-devel--jgale--1.4--patch-19 15372 jgale@siesta.arch--2005/siesta-devel--jgale--1.4--patch-20 15373 siesta@uam.es--2005/siesta-devel--jg-merge--1.4--base-0 15374 siesta@uam.es--2005/siesta-devel--jg-merge--1.4--patch-1 15375 siesta@uam.es--2005/siesta-devel--jg-merge--1.4--patch-2 15376 siesta@uam.es--2005/siesta-devel--jg-merge--1.4--patch-3 15377 siesta@uam.es--2005/siesta-devel--jg-merge--1.4--patch-4 15378 siesta@uam.es--2005/siesta-devel--jg-merge--1.4--patch-5 15379 siesta@uam.es--2005/siesta-devel--jg-merge--1.4--patch-6 15380 siesta@uam.es--2005/siesta-devel--jg-merge--1.4--patch-7 15381 siesta@uam.es--2005/siesta-devel--jg-merge--1.4--patch-8 15382 siesta@uam.es--2005/siesta-devel--jg-merge--1.4--patch-9 15383 siesta@uam.es--2005/siesta-devel--jg-merge--1.4--patch-10 15384 siesta@uam.es--2005/siesta-devel--jg-merge--1.4--patch-11 15385 siesta@uam.es--2005/siesta-devel--jg-merge--1.4--patch-12 15386 siesta@uam.es--2005/siesta-devel--jg-merge--1.4--patch-13 15387 siesta@uam.es--2005/siesta-devel--jg-merge--1.4--patch-14 15388 siesta@uam.es--2005/siesta-devel--jg-merge--1.4--patch-15 15389 siesta@uam.es--2005/siesta-devel--jg-merge--1.4--patch-16 15390 siesta@uam.es--2005/siesta-devel--jg-merge--1.4--patch-17 15391 siesta@uam.es--2005/siesta-devel--jg-merge--1.4--patch-18 15392 siesta@uam.es--2005/siesta-devel--jg-merge--1.4--patch-19 15393 siesta@uam.es--2005/siesta-devel--jg-merge--1.4--patch-20 15394 twhite@siesta.arch--2005/siesta-devel--zmatrix--1.4--patch-1 15395 twhite@siesta.arch--2005/siesta-devel--zmatrix--1.4--patch-3 15396 15397======================================================================= 15398 153992005-10-04 13:59:58 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-14 15400 15401 Summary: 15402 Assorted bug and portability fixes -- more wrappers 15403 Revision: 15404 siesta-devel--reference--1.4--patch-14 15405 15406 * Fix mpi bug (incorrect use of temporary arrays for reduction 15407 operation) in mulliken.F. 15408 15409 * Merge O(N) spatial-decomposition bugfixes from From Toby White's 15410 dedicated branch (up to patch-10): 15411 15412 globalise.F - declare variables. 15413 initparallel.F - don't make too many spatial cells. 15414 setatomnodes.F - correct initialization so that non-2-3-5 15415 case works. 15416 15417 * Portability fixes, mostly dealing with MPI support. 15418 15419 * More wrapping of MPI calls in several routines. New program 15420 mpi_test.F90 to test wrappers. 15421 15422 * Assorted bug fixes (wrapping of fdf calls) and cosmetic changes. 15423 15424 15425 new files: 15426 Src/.arch-ids/mpi_test.F90.id 15427 Src/Confs/.arch-ids/matterhorn-serial.conf.id 15428 Src/Confs/matterhorn-serial.conf 15429 Src/Tests/Scripts/.arch-ids/=id 15430 Src/Tests/Scripts/.arch-ids/arina.pbs.id 15431 Src/Tests/Scripts/.arch-ids/matterhorn-gm.sge.id 15432 Src/Tests/Scripts/arina.pbs 15433 Src/Tests/Scripts/matterhorn-gm.sge Src/mpi_test.F90 15434 15435 modified files: 15436 Src/MPI/Makefile Src/MPI/generate.sh Src/MPI/mpi.F 15437 Src/Makefile Src/Sys/cscs-cray-mpi.make Src/Sys/cscs-cray.make 15438 Src/Tests/Makefile Src/Tests/h2o/h2o.fdf Src/alloc.F90 15439 Src/arch.make.in Src/cgvc.F Src/fft3d.F Src/globalise.F 15440 Src/initparallel.F Src/linpack.F Src/m_broyden_mixing.f 15441 Src/m_fdf_global.F90 Src/m_mpi_utils.F Src/memoryinfo.F 15442 Src/mulliken.F Src/nlefsm.f Src/overfsm.f Src/redata.F 15443 Src/setatomnodes.F Src/siesta.F version.info 15444 15445 renamed files: 15446 Src/.arch-ids/m_wrappers.F90.id 15447 ==> Src/.arch-ids/m_fdf_global.F90.id 15448 Src/m_wrappers.F90 15449 ==> Src/m_fdf_global.F90 15450 15451 new directories: 15452 Src/Tests/Scripts Src/Tests/Scripts/.arch-ids 15453 15454 new patches: 15455 agarcia@siesta.arch--2005/siesta--mpiwrap--1.4--base-0 15456 agarcia@siesta.arch--2005/siesta--mpiwrap--1.4--patch-1 15457 agarcia@siesta.arch--2005/siesta--mpiwrap--1.4--patch-2 15458 agarcia@siesta.arch--2005/siesta--mpiwrap--1.4--patch-3 15459 agarcia@siesta.arch--2005/siesta--mpiwrap--1.4--patch-4 15460 agarcia@siesta.arch--2005/siesta--mpiwrap--1.4--patch-5 15461 agarcia@siesta.arch--2005/siesta--mpiwrap--1.4--patch-6 15462 agarcia@siesta.arch--2005/siesta--mpiwrap--1.4--patch-7 15463 agarcia@siesta.arch--2005/siesta--mpiwrap--1.4--patch-8 15464 agarcia@siesta.arch--2005/siesta--mpiwrap--1.4--patch-9 15465 agarcia@siesta.arch--2005/siesta--mpiwrap--1.4--patch-10 15466 agarcia@siesta.arch--2005/siesta--mpiwrap--1.4--patch-11 15467 agarcia@siesta.arch--2005/siesta--mpiwrap--1.4--patch-12 15468 agarcia@siesta.arch--2005/siesta--mpiwrap--1.4--patch-13 15469 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-72 15470 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-73 15471 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-74 15472 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-75 15473 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-76 15474 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-77 15475 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-78 15476 twhite@siesta.arch--2005/siesta-bugfix--spatial--1.4--patch-8 15477 twhite@siesta.arch--2005/siesta-bugfix--spatial--1.4--patch-9 15478 twhite@siesta.arch--2005/siesta-bugfix--spatial--1.4--patch-10 15479 15480======================================================================= 15481 154822005-10-04 13:49:31 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-13 15483 15484 Summary: 15485 New kind of structure input -- constant-volume variable-cell - no sig 15486 Revision: 15487 siesta-devel--reference--1.4--patch-13 15488 15489 * Using the option UseStructFile, the structural information will be 15490 read from SiestaLabel.STRUCT_IN. This option is incompatible with 15491 UseSaveXV, and will prevail. 15492 15493 * Siesta now always produces a SiestaLabel.STRUCT_OUT file. 15494 15495 The .STRUCT_XX files have the cell vectors in Ang and the atomic 15496 positions in atomic coordinates. 15497 15498 * The option MD.ConstantVolume will result in a constant-volume 15499 variable-cell simulation (i.e., only the cell shape and the atomic 15500 positions change). 15501 15502 * After every MD or relaxation step, Siesta now writes the "enthalpy" 15503 E+pV, where p is actually the target pressure. 15504 15505 * New tests: var_cell and constant_volume. 15506 15507 * Changed si test to use the new UseStructFile feature. 15508 15509 * Removed "sig" fossils from source. 15510 15511 15512 15513 new files: 15514 Src/.arch-ids/m_iostruct.f.id 15515 Src/Tests/Outs/.arch-ids/constant_volume.out.id 15516 Src/Tests/Outs/.arch-ids/var_cell.out.id 15517 Src/Tests/Outs/constant_volume.out Src/Tests/Outs/var_cell.out 15518 Src/Tests/constant_volume/.arch-ids/=id 15519 Src/Tests/constant_volume/.arch-ids/constant_volume.fdf.id 15520 Src/Tests/constant_volume/.arch-ids/constant_volume.pseudos.id 15521 Src/Tests/constant_volume/.arch-ids/makefile.id 15522 Src/Tests/constant_volume/constant_volume.fdf 15523 Src/Tests/constant_volume/constant_volume.pseudos 15524 Src/Tests/constant_volume/makefile 15525 Src/Tests/si/.arch-ids/si.STRUCT_IN.id 15526 Src/Tests/si/si.STRUCT_IN Src/Tests/var_cell/.arch-ids/=id 15527 Src/Tests/var_cell/.arch-ids/makefile.id 15528 Src/Tests/var_cell/.arch-ids/var_cell.fdf.id 15529 Src/Tests/var_cell/.arch-ids/var_cell.pseudos.id 15530 Src/Tests/var_cell/makefile Src/Tests/var_cell/var_cell.fdf 15531 Src/Tests/var_cell/var_cell.pseudos Src/m_iostruct.f 15532 15533 removed files: 15534 Src/.arch-ids/sig.f.id Src/Tests/.arch-ids/cmpsig.f.id 15535 Src/Tests/.arch-ids/do.sh.id Src/Tests/Sigs/.arch-ids/=id 15536 Src/Tests/Sigs/.arch-ids/batio3.sig.id 15537 Src/Tests/Sigs/.arch-ids/fe.sig.id 15538 Src/Tests/Sigs/.arch-ids/h2o.sig.id 15539 Src/Tests/Sigs/.arch-ids/h2o_dos.sig.id 15540 Src/Tests/Sigs/.arch-ids/h2o_orderN.sig.id 15541 Src/Tests/Sigs/.arch-ids/si64.sig.id 15542 Src/Tests/Sigs/.arch-ids/sih.sig.id Src/Tests/Sigs/batio3.sig 15543 Src/Tests/Sigs/fe.sig Src/Tests/Sigs/h2o.sig 15544 Src/Tests/Sigs/h2o_dos.sig Src/Tests/Sigs/h2o_orderN.sig 15545 Src/Tests/Sigs/si64.sig Src/Tests/Sigs/sih.sig 15546 Src/Tests/cmpsig.f Src/Tests/do.sh Src/sig.f 15547 15548 modified files: 15549 Docs/siesta.ind Docs/siesta.tex Src/Makefile 15550 Src/Tests/Makefile Src/Tests/Outs/si.out Src/Tests/si/makefile 15551 Src/Tests/si/si.fdf Src/Tests/test.mk Src/cgvc.F Src/outcell.f 15552 Src/siesta.F version.info 15553 15554 new directories: 15555 Src/Tests/constant_volume Src/Tests/constant_volume/.arch-ids 15556 Src/Tests/var_cell Src/Tests/var_cell/.arch-ids 15557 15558 removed directories: 15559 Src/Tests/Sigs Src/Tests/Sigs/.arch-ids 15560 15561 new patches: 15562 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-70 15563 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-71 15564 15565======================================================================= 15566 155672005-10-04 13:43:52 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-12 15568 15569 Summary: 15570 Flexible precision for grid arrays (and some O(N) work arrays) 15571 Revision: 15572 siesta-devel--reference--1.4--patch-12 15573 15574 * Arrays on the grid were previously single-precision. Now they can be 15575 made double precision by defining the pre-processor symbol GRID_DP, i.e.: 15576 15577 DEFS= -DGRID_DP in arch.make, or, if using configure: 15578 15579 DEFS="GRID_DP" ./configure 15580 15581 * When doing I/O of the grid arrays to file, SINGLE PRECISION is used, 15582 regardless of the internal representation chosen. 15583 15584 * iorho.F has been turned into m_iorho.F, and the subroutine 'iorho' 15585 split in three: 'write_rho' (the only one currently in use within Siesta), 15586 'read_rho', and 'check_rho'. dhscf.F has been updated accordingly. 15587 15588 * forhar.F has been turned into a module. 15589 15590 * An extra pre-processor symbol ON_DP has been introduced to switch the 15591 precision of some work arrays defined in module 'on_main' in file onmod.F. 15592 15593 * Some cosmetic changes in makefiles (notably for denchar support). 15594 15595 modified files: 15596 Src/MPI/mpi.F Src/Makefile Src/Tests/h2o/h2o.fdf Src/cellxc.F 15597 Src/chempot.F Src/dfscf.f Src/dhscf.F Src/diagon.F 15598 Src/dipole.F Src/efield.F Src/fft3d.F Src/forhar.f 15599 Src/m_iorho.F Src/m_memory.F Src/memory.F Src/meshmatrix.F 15600 Src/meshsubs.F Src/onmod.F Src/poison.F Src/precision.F 15601 Src/reord.f Src/rhooda.f Src/rhoofd.f Src/rhoofdsp.f 15602 Src/siesta.F Src/vmat.f Src/vmatsp.f version.info 15603 15604 renamed files: 15605 Src/.arch-ids/iorho.F.id 15606 ==> Src/.arch-ids/m_iorho.F.id 15607 Src/iorho.F 15608 ==> Src/m_iorho.F 15609 15610 new patches: 15611 agarcia@siesta.arch--2005/siesta--grid-reals--1.4--base-0 15612 agarcia@siesta.arch--2005/siesta--grid-reals--1.4--patch-1 15613 agarcia@siesta.arch--2005/siesta--grid-reals--1.4--patch-2 15614 agarcia@siesta.arch--2005/siesta--grid-reals--1.4--patch-3 15615 agarcia@siesta.arch--2005/siesta--grid-reals--1.4--patch-4 15616 agarcia@siesta.arch--2005/siesta--grid-reals--1.4--patch-5 15617 agarcia@siesta.arch--2005/siesta--grid-reals--1.4--patch-6 15618 agarcia@siesta.arch--2005/siesta--grid-reals--1.4--patch-7 15619 agarcia@siesta.arch--2005/siesta--grid-reals--1.4--patch-8 15620 agarcia@siesta.arch--2005/siesta--grid-reals--1.4--patch-9 15621 agarcia@siesta.arch--2005/siesta--grid-reals--1.4--patch-10 15622 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-69 15623 15624======================================================================= 15625 156262005-10-04 13:39:54 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-11 15627 15628 Summary: 15629 O(N) spatial bugfixes merge + simple wallclock stamper 15630 Revision: 15631 siesta-devel--reference--1.4--patch-11 15632 15633 * (use m_wallclock) call wallclock("some description") will 15634 write out in file "CLOCK" the elapsed wall-clock time at that 15635 point in the program. 15636 15637 * Merge O(N) spatial-decomposition bugfixes, up to patch-7 of T. White's branch: 15638 15639 deallocation order change 15640 use units in initdm 15641 spatial bugfix 15642 extrapolon array declarations 15643 Don't allow ON.MaxIter = 0 in redata. 15644 fix misdeclaration in extrapolon.F 15645 15646 15647 15648 new files: 15649 Src/.arch-ids/m_wallclock.f90.id Src/m_wallclock.f90 15650 15651 modified files: 15652 Src/Makefile Src/diagon.F Src/extrapolon.f Src/initdm.F 15653 Src/redata.F Src/setatomnodes.F Src/setspatial.f Src/siesta.F 15654 Src/spatial.F version.info 15655 15656 new patches: 15657 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-67 15658 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-68 15659 twhite@siesta.arch--2005/siesta-bugfix--spatial--1.4--base-0 15660 twhite@siesta.arch--2005/siesta-bugfix--spatial--1.4--patch-1 15661 twhite@siesta.arch--2005/siesta-bugfix--spatial--1.4--patch-2 15662 twhite@siesta.arch--2005/siesta-bugfix--spatial--1.4--patch-3 15663 twhite@siesta.arch--2005/siesta-bugfix--spatial--1.4--patch-4 15664 twhite@siesta.arch--2005/siesta-bugfix--spatial--1.4--patch-5 15665 twhite@siesta.arch--2005/siesta-bugfix--spatial--1.4--patch-6 15666 twhite@siesta.arch--2005/siesta-bugfix--spatial--1.4--patch-7 15667 15668======================================================================= 15669 156702005-09-07 09:24:37 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-10 15671 15672 Summary: 15673 Fix bug in xc.f 15674 Revision: 15675 siesta-devel--reference--1.4--patch-10 15676 15677 * In pzxc, DECPDN was erroneously given the value that should have 15678 been assigned to DECFDN when rs>1.0. This bug only affects (apparently 15679 very mildly, if at all) spin-polarized calculations with CA xc. 15680 15681 (Reported on Aug. 12, 2005 by Zhiqin Zhao <zzhao@ee.duke.edu>) 15682 15683 15684 modified files: 15685 Pseudo/atom/xc.f Src/xc.f version.info 15686 15687 new patches: 15688 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-66 15689 15690======================================================================= 15691 156922005-09-07 09:23:39 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-9 15693 15694 Summary: 15695 Add output of Voigt components of stress tensor in Kbar. 15696 Revision: 15697 siesta-devel--reference--1.4--patch-9 15698 15699 * The output is done after every geometry iteration, and not at the end. 15700 15701 modified files: 15702 Src/siesta.F 15703 15704 new patches: 15705 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-64 15706 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-65 15707 15708======================================================================= 15709 157102005-09-07 09:07:43 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-8 15711 15712 Summary: 15713 Changes for portability -- new Test building framework 15714 Revision: 15715 siesta-devel--reference--1.4--patch-8 15716 15717 * New building method for tests (in Src/Tests) that allows stand-alone 15718 running of each test, and easier changes in the running method. 15719 15720 * Updates to the autoconf procedures, mostly in the area of parallel support. 15721 New Src/Confs directory created to hold small files containing the right 15722 invocation of configure for several computers. 15723 15724 * Updated MPI makefile (by Toby White) 15725 15726 * Changes to support several architectures and compilers, 15727 including clusters at ETH and the Univ. of Zurich, and the Cray at 15728 the CSCS. Apart from .make (and Confs/*.sh files), some files had 15729 to be changed due to quirks in pgf90...: 15730 15731 * electrostatic.f has to be compiled without optimization. 15732 * some module interfaces have to be made even more explicit. 15733 15734 * Modification of the structure of the siesta_cml hierarchy, as well as 15735 that of the timestamp support subroutines. 15736 15737 15738 new files: 15739 Src/.arch-ids/siesta_cmlsubs.F90.id Src/Confs/.arch-ids/=id 15740 Src/Confs/.arch-ids/arina-mpi.conf.id 15741 Src/Confs/.arch-ids/arina-serial.conf.id 15742 Src/Confs/.arch-ids/matterhorn-gm.conf.id 15743 Src/Confs/.arch-ids/pegasus-mpi.conf.id 15744 Src/Confs/arina-mpi.conf Src/Confs/arina-serial.conf 15745 Src/Confs/matterhorn-gm.conf Src/Confs/pegasus-mpi.conf 15746 Src/Sys/.arch-ids/cscs-cray-mpi.make.id 15747 Src/Sys/.arch-ids/cscs-cray.make.id 15748 Src/Sys/.arch-ids/pgf90-matterhorn-gm.make.id 15749 Src/Sys/.arch-ids/pgf90-matterhorn-mpich.make.id 15750 Src/Sys/.arch-ids/pgf95-matterhorn.make.id 15751 Src/Sys/cscs-cray-mpi.make Src/Sys/cscs-cray.make 15752 Src/Sys/pgf90-matterhorn-gm.make 15753 Src/Sys/pgf90-matterhorn-mpich.make 15754 Src/Sys/pgf95-matterhorn.make Src/Tests/.arch-ids/test.mk.id 15755 Src/Tests/Outs/.arch-ids/fe_broyden.out.id 15756 Src/Tests/Outs/.arch-ids/mgco3.out.id 15757 Src/Tests/Outs/.arch-ids/si.out.id 15758 Src/Tests/Outs/fe_broyden.out Src/Tests/Outs/mgco3.out 15759 Src/Tests/Outs/si.out Src/Tests/Pseudos/.arch-ids/C.psf.id 15760 Src/Tests/Pseudos/.arch-ids/Mg.psf.id Src/Tests/Pseudos/C.psf 15761 Src/Tests/Pseudos/Mg.psf 15762 Src/Tests/batio3/.arch-ids/makefile.id 15763 Src/Tests/batio3/makefile 15764 Src/Tests/bessel/.arch-ids/makefile.id 15765 Src/Tests/bessel/makefile Src/Tests/fe/.arch-ids/makefile.id 15766 Src/Tests/fe/makefile 15767 Src/Tests/fe_broyden/.arch-ids/makefile.id 15768 Src/Tests/fe_broyden/makefile 15769 Src/Tests/floating/.arch-ids/makefile.id 15770 Src/Tests/floating/makefile 15771 Src/Tests/h2o/.arch-ids/makefile.id Src/Tests/h2o/makefile 15772 Src/Tests/h2o_dos/.arch-ids/makefile.id 15773 Src/Tests/h2o_dos/makefile 15774 Src/Tests/h2o_orderN/.arch-ids/makefile.id 15775 Src/Tests/h2o_orderN/makefile Src/Tests/mgco3/.arch-ids/=id 15776 Src/Tests/mgco3/.arch-ids/makefile.id 15777 Src/Tests/mgco3/.arch-ids/mgco3.fdf.id 15778 Src/Tests/mgco3/.arch-ids/mgco3.pseudos.id 15779 Src/Tests/mgco3/makefile Src/Tests/mgco3/mgco3.fdf 15780 Src/Tests/mgco3/mgco3.pseudos Src/Tests/si/.arch-ids/=id 15781 Src/Tests/si/.arch-ids/makefile.id 15782 Src/Tests/si/.arch-ids/si.fdf.id 15783 Src/Tests/si/.arch-ids/si.pseudos.id Src/Tests/si/makefile 15784 Src/Tests/si/si.fdf Src/Tests/si/si.pseudos 15785 Src/Tests/si64/.arch-ids/makefile.id Src/Tests/si64/makefile 15786 Src/Tests/sih/.arch-ids/makefile.id Src/Tests/sih/makefile 15787 Src/Tests/test.mk Src/m4/.arch-ids/TW_FC_KINDS.m4.id 15788 Src/m4/TW_FC_KINDS.m4 Src/siesta_cmlsubs.F90 15789 15790 removed files: 15791 Src/.arch-ids/doversion.sh.id Src/doversion.sh 15792 15793 modified files: 15794 Src/Libs/makefile Src/MPI/Makefile Src/MPI/generate.sh 15795 Src/Makefile Src/NetCDF/Makefile Src/Sys/compaq-mpi.make 15796 Src/Sys/darwin.make Src/Sys/g95-nolibs.make Src/Sys/hpcx.make 15797 Src/Sys/ibm-regatta-p4.make Src/Sys/ibmp3-mpi.make 15798 Src/Sys/ibmp3.make Src/Sys/intel-mkl.make 15799 Src/Sys/intel-nolibs.make Src/Sys/itanium2-mpi.make 15800 Src/Sys/itanium2.make Src/Sys/lahey-lam.make 15801 Src/Sys/lahey-mpich.make Src/Sys/lahey-nolibs.make 15802 Src/Sys/lahey.make Src/Sys/macosx-nag-mpi.make 15803 Src/Sys/macosx-nag.make Src/Sys/macosx-xlf.make 15804 Src/Sys/nolibs.make Src/Sys/osfdxml-mpich.make 15805 Src/Sys/osfdxml.make Src/Sys/osfdxmlcdf.make 15806 Src/Sys/pgf90-lam.make Src/Sys/pgf90-mpich.make 15807 Src/Sys/pgf90-nolibs.make Src/Sys/pgf90.make Src/Sys/sgi.make 15808 Src/Sys/sgi64-cdf.make Src/Sys/sgi64-lam-cdf.make 15809 Src/Sys/sgi64-lam.make Src/Sys/sgi64-mpi_fermat.make 15810 Src/Sys/sgi64-mpich-cdf.make Src/Sys/sgi64-mpich.make 15811 Src/Sys/sgin32-mpi.make Src/Sys/sun-nolibs.make 15812 Src/Sys/t3e.make Src/Tests/Makefile Src/Tests/h2o/h2o.fdf 15813 Src/aclocal.m4 Src/arch.make.in Src/configure Src/configure.ac 15814 Src/denmat.F Src/egandd.F Src/ener3.F Src/ener3lomem.F 15815 Src/fdf/makefile Src/gradient.F Src/m4/TW_CHECK_SCALAPACK.m4 15816 Src/ordern.F Src/pdos.F Src/siesta.F Src/siesta_cml.f90 15817 Src/timestamp.f90 Src/wxml/makefile Src/xmlparser/makefile 15818 version.info 15819 15820 renamed files: 15821 Src/.arch-ids/siesta_cml.F90.id 15822 ==> Src/.arch-ids/siesta_cml.f90.id 15823 Src/siesta_cml.F90 15824 ==> Src/siesta_cml.f90 15825 15826 new directories: 15827 Src/Confs Src/Confs/.arch-ids Src/Tests/mgco3 15828 Src/Tests/mgco3/.arch-ids Src/Tests/si Src/Tests/si/.arch-ids 15829 15830 new patches: 15831 agarcia@siesta.arch--2005/siesta--cscs-fix--1.4--base-0 15832 agarcia@siesta.arch--2005/siesta--cscs-fix--1.4--patch-1 15833 agarcia@siesta.arch--2005/siesta--cscs-fix--1.4--patch-2 15834 agarcia@siesta.arch--2005/siesta--cscs-fix--1.4--patch-3 15835 agarcia@siesta.arch--2005/siesta--cscs-fix--1.4--patch-4 15836 agarcia@siesta.arch--2005/siesta--cscs-fix--1.4--patch-5 15837 agarcia@siesta.arch--2005/siesta--cscs-fix--1.4--patch-6 15838 agarcia@siesta.arch--2005/siesta--cscs-fix--1.4--patch-7 15839 agarcia@siesta.arch--2005/siesta--cscs-fix--1.4--patch-8 15840 agarcia@siesta.arch--2005/siesta--cscs-fix--1.4--patch-9 15841 agarcia@siesta.arch--2005/siesta--cscs-fix--1.4--patch-10 15842 agarcia@siesta.arch--2005/siesta--cscs-fix--1.4--patch-11 15843 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-48 15844 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-49 15845 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-50 15846 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-51 15847 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-52 15848 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-53 15849 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-54 15850 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-55 15851 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-56 15852 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-57 15853 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-58 15854 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-59 15855 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-60 15856 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-61 15857 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-62 15858 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-63 15859 agarcia@siesta.arch--2005/siesta-devel--tests--1.4--base-0 15860 agarcia@siesta.arch--2005/siesta-devel--tests--1.4--patch-1 15861 agarcia@siesta.arch--2005/siesta-devel--tests--1.4--patch-2 15862 agarcia@siesta.arch--2005/siesta-devel--tests--1.4--patch-3 15863 agarcia@siesta.arch--2005/siesta-devel--tests--1.4--patch-4 15864 twhite@siesta.arch--2005/siesta-bugfix--mpimake--1.4--base-0 15865 twhite@siesta.arch--2005/siesta-bugfix--mpimake--1.4--patch-1 15866 twhite@siesta.arch--2005/siesta-bugfix--mpimake--1.4--patch-2 15867 twhite@siesta.arch--2005/siesta-bugfix--mpimake--1.4--patch-3 15868 twhite@siesta.arch--2005/siesta-bugfix--mpimake--1.4--patch-4 15869 twhite@siesta.arch--2005/siesta-bugfix--mpimake--1.4--patch-5 15870 15871======================================================================= 15872 158732005-08-08 14:02:46 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-7 15874 15875 Summary: 15876 BUGfix -- stressl was initialized to zero in cellxc. 15877 Revision: 15878 siesta-devel--reference--1.4--patch-7 15879 15880 * (Bug introduced in: 15881 siesta@uam.es--2005/siesta-devel--reference--1.4--patch--3) 15882 15883 The wrong intent specification had led to an incorrect zeroing 15884 of stressl in cellxc.F, what resulted in very wrong values for 15885 the stress tensor and the pressure. Fixed. 15886 15887 15888 modified files: 15889 Src/cellxc.F version.info 15890 15891 new patches: 15892 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-46 15893 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-47 15894 15895======================================================================= 15896 158972005-08-05 14:25:41 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-6 15898 15899 Summary: 15900 Integration of xml parser (SAX version) -- pdosxml direct compilation 15901 Revision: 15902 siesta-devel--reference--1.4--patch-6 15903 15904 * Copied xmlf90/sax, and adapted the makefile. 15905 Modified appropriately the main Makefile. 15906 15907 * Util/pdosxml/pdos is an exhibit for the use of the XML parser (SAX version) 15908 The makefile has been changed to pick up the relevant library and modules 15909 from ../../Src 15910 15911 15912 new files: 15913 Src/xmlparser/.arch-ids/=id 15914 Src/xmlparser/.arch-ids/flib_sax.f90.id 15915 Src/xmlparser/.arch-ids/m_buffer.f90.id 15916 Src/xmlparser/.arch-ids/m_charset.f90.id 15917 Src/xmlparser/.arch-ids/m_converters.f90.id 15918 Src/xmlparser/.arch-ids/m_debug.f90.id 15919 Src/xmlparser/.arch-ids/m_dictionary.f90.id 15920 Src/xmlparser/.arch-ids/m_elstack.f90.id 15921 Src/xmlparser/.arch-ids/m_entities.f90.id 15922 Src/xmlparser/.arch-ids/m_fsm.f90.id 15923 Src/xmlparser/.arch-ids/m_io.f90.id 15924 Src/xmlparser/.arch-ids/m_reader.f90.id 15925 Src/xmlparser/.arch-ids/m_xml_error.f90.id 15926 Src/xmlparser/.arch-ids/m_xml_parser.f90.id 15927 Src/xmlparser/.arch-ids/makefile.id Src/xmlparser/flib_sax.f90 15928 Src/xmlparser/m_buffer.f90 Src/xmlparser/m_charset.f90 15929 Src/xmlparser/m_converters.f90 Src/xmlparser/m_debug.f90 15930 Src/xmlparser/m_dictionary.f90 Src/xmlparser/m_elstack.f90 15931 Src/xmlparser/m_entities.f90 Src/xmlparser/m_fsm.f90 15932 Src/xmlparser/m_io.f90 Src/xmlparser/m_reader.f90 15933 Src/xmlparser/m_xml_error.f90 Src/xmlparser/m_xml_parser.f90 15934 Src/xmlparser/makefile 15935 15936 modified files: 15937 Src/Makefile Util/pdosxml/makefile version.info 15938 15939 new directories: 15940 Src/xmlparser Src/xmlparser/.arch-ids 15941 15942 new patches: 15943 agarcia@siesta.arch--2005/siesta--xmlparser--1.4--base-0 15944 agarcia@siesta.arch--2005/siesta--xmlparser--1.4--patch-1 15945 agarcia@siesta.arch--2005/siesta--xmlparser--1.4--patch-2 15946 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-45 15947 15948======================================================================= 15949 159502005-08-05 14:17:41 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-5 15951 15952 Summary: 15953 Get rid of NODAT hack 15954 Revision: 15955 siesta-devel--reference--1.4--patch-5 15956 15957 (From Toby White) 15958 15959 * In MPI/mpi.F, rename all MPI_(realprecision) constants to 15960 DAT_(real_precision) according to machine type. Then 15961 recreate MPI_(realprecision) so now it always points to 15962 correct precision. Remove NODAT hack. 15963 * Go through all .F and .F90 files, and remove all 15964 references to NODAT and DAT_anything. 15965 15966 (AG: In merging, the new redata.F has been discarded, as the 15967 version closest to reference had done away with direct MPI calls. 15968 Also, m_mpi_utils has been updated to remove the NODAT sections) 15969 15970 modified files: 15971 Src/MPI/mpi.F Src/MPI/pi3.F Src/alloc.F90 Src/bands.F 15972 Src/broadcast_basis.F Src/cellxc.F Src/cgvc.F Src/cgwf.F 15973 Src/chempot.F Src/denmat.F Src/detover.F Src/dhscf.F 15974 Src/diag2g.F Src/diag2k.F Src/diagg.F Src/diagk.F Src/diagkp.F 15975 Src/diagsprl.F Src/dipole.F Src/efield.F Src/eggbox.F 15976 Src/ener3.F Src/ener3lomem.F Src/fft3d.F Src/globalise.F 15977 Src/gradient.F Src/initparallel.F Src/iodm.F Src/iohs.F 15978 Src/iolwf.F Src/iopipes.F90 Src/iorho.F Src/ioxv.F 15979 Src/kgridinit.F Src/m_mpi_utils.F Src/meshmatrix.F 15980 Src/mulliken.F Src/optical.F Src/ordern.F Src/pdosg.F 15981 Src/pdosk.F Src/pdoskp.F Src/phonon.F Src/pulayx.F Src/pxf.F90 15982 Src/readsp.F Src/reoptical.F Src/repol.F Src/savepsi.F 15983 Src/siesta.F Src/siesta_cml.F90 Src/timer.F 15984 Src/transition_rate.F Src/vmb.F Src/writewave.F Src/xcmod.F 15985 15986 modified directories: 15987 Src/m4 15988 15989 new patches: 15990 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-43 15991 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-44 15992 twhite@siesta.arch--2005/siesta-bugfix--parallel-tidy--1.4--patch-1 15993 twhite@siesta.arch--2005/siesta-bugfix--parallel-tidy--1.4--patch-2 15994 15995======================================================================= 15996 159972005-08-02 14:07:31 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-4 15998 15999 Summary: 16000 16001 Revision: 16002 siesta-devel--reference--1.4--patch-4 16003 16004 16005 Patches applied: 16006 16007 * agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-41 16008 Support for LAM at ETH, pgf90 16009 16010 * agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-42 16011 Print out stress tensor in kbar 16012 16013 16014 new files: 16015 Src/Sys/.arch-ids/pgf90-lam.make.id Src/Sys/pgf90-lam.make 16016 16017 modified files: 16018 Src/MPI/Makefile Src/MPI/generate.sh Src/siesta.F 16019 16020 new patches: 16021 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-41 16022 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-42 16023 16024======================================================================= 16025 160262005-08-02 13:36:28 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-3 16027 16028 Summary: 16029 Integration of Broyden mixing. Real kinds discovery for MPI 16030 Revision: 16031 siesta-devel--reference--1.4--patch-3 16032 16033 * A new method for SCF convergence acceleration, based on 16034 the Broyden-Vanderbilt-Louie-Johnson scheme, has been implemented. 16035 16036 The major new pieces of code are m_broyden_mixing.f (similar in structure 16037 to pulayx) and m_broyddj.f90, which implements the method and takes care 16038 of hiding all the storage complexity. 16039 16040 [ The patches (later taken back) 16041 16042 * agarcia@siesta.arch--2005/siesta-devel--ag-bau--1.4--patch-5 16043 Annealing framework 16044 16045 * agarcia@siesta.arch--2005/siesta-devel--ag-bau--1.4--patch-6 16046 Fine-tuning of annealing framework 16047 16048 contain an early attempt to couple the Broyden scheme to a 16049 simulated-anealing kind of procedure. ] 16050 16051 * To aid in the parallelization of m_broyddj.f90, a new set of MPI wrapper 16052 routines (in module m_mpi_utils) has been implemented. These simplify the 16053 calls to the most common MPI routines, and are generic, thus avoiding the 16054 need to worry about the MPI type qualifiers. 16055 16056 * Similar wrappers for fdf calls have been implemented in m_wrappers.F90. 16057 They are mainly used in redata.F, which has been slimmed down significantly. 16058 16059 * A new stub module m_options is a prototype for a program-wide repository 16060 of runtime options, to be phased in in stages. 16061 16062 * Some of the arrays in m_broyddj.f90 can be single or double precision. 16063 Precision is selected through the pre-processor symbol BROYDEN_DP, which 16064 is checked-for in precision.F. The same will be done in the future for 16065 the arrays on the grid. 16066 16067 * The input variables related to the Broyden mixing method are documented 16068 in the manual. The H2O test has been converted to use the Broyden method, 16069 and a new fe_broyden test added. 16070 16071 * Misc: Added top-level Specs directory to hold Specification documents (...). 16072 Added Specs/Broyden.spec. 16073 16074 ----------- 16075 * A simple program "kind_explorer" now finds the kind 16076 parameters for real numbers, and feeds them to configure.sh 16077 in the MPI building process. 16078 16079 To Do: Somehow connect the mpif.h kind parameters and 16080 the native ones. 16081 16082 * Add some comments in precision.F 16083 16084 ----------- 16085 16086 * Portability and cosmetic fixes: 16087 16088 Include spatial.o in denchar object list 16089 Initialize stressl in cellxc 16090 Removed size() on deallocated array in diagon.F 16091 Fix SYS in g95-nolibs.make 16092 16093 16094 new files: 16095 Specs/.arch-ids/=id Specs/.arch-ids/Broyden.specs.id 16096 Specs/Broyden.specs Src/.arch-ids/m_broyddj.f90.id 16097 Src/.arch-ids/m_broyden_mixing.f.id 16098 Src/.arch-ids/m_history.f90.id Src/.arch-ids/m_mpi_utils.F.id 16099 Src/.arch-ids/m_options.f90.id Src/.arch-ids/m_smearing.f.id 16100 Src/.arch-ids/m_wrappers.F90.id 16101 Src/MPI/.arch-ids/kind_explorer.f90.id 16102 Src/MPI/kind_explorer.f90 Src/Tests/fe_broyden/.arch-ids/=id 16103 Src/Tests/fe_broyden/.arch-ids/fe_broyden.fdf.id 16104 Src/Tests/fe_broyden/.arch-ids/fe_broyden.pseudos.id 16105 Src/Tests/fe_broyden/fe_broyden.fdf 16106 Src/Tests/fe_broyden/fe_broyden.pseudos Src/m_broyddj.f90 16107 Src/m_broyden_mixing.f Src/m_history.f90 Src/m_mpi_utils.F 16108 Src/m_options.f90 Src/m_smearing.f Src/m_wrappers.F90 16109 16110 modified files: 16111 Docs/siesta.ind Docs/siesta.tex Src/MPI/Makefile Src/Makefile 16112 Src/Sys/g95-nolibs.make Src/Tests/Makefile 16113 Src/Tests/h2o/h2o.fdf Src/Tests/si64/si64.fdf Src/atmfuncs.f 16114 Src/cellxc.F Src/chkdim.f Src/diagon.F Src/precision.F 16115 Src/redata.F Src/siesta.F Src/sys.F version.info 16116 16117 new directories: 16118 Specs Specs/.arch-ids Src/Tests/fe_broyden 16119 Src/Tests/fe_broyden/.arch-ids 16120 16121 new patches: 16122 agarcia@siesta.arch--2005/siesta-devel--ag-bau--1.4--base-0 16123 agarcia@siesta.arch--2005/siesta-devel--ag-bau--1.4--patch-1 16124 agarcia@siesta.arch--2005/siesta-devel--ag-bau--1.4--patch-2 16125 agarcia@siesta.arch--2005/siesta-devel--ag-bau--1.4--patch-3 16126 agarcia@siesta.arch--2005/siesta-devel--ag-bau--1.4--patch-4 16127 agarcia@siesta.arch--2005/siesta-devel--ag-bau--1.4--patch-5 16128 agarcia@siesta.arch--2005/siesta-devel--ag-bau--1.4--patch-6 16129 agarcia@siesta.arch--2005/siesta-devel--ag-bau--1.4--patch-7 16130 agarcia@siesta.arch--2005/siesta-devel--ag-bau--1.4--patch-8 16131 agarcia@siesta.arch--2005/siesta-devel--ag-bau--1.4--patch-9 16132 agarcia@siesta.arch--2005/siesta-devel--ag-bau--1.4--patch-10 16133 agarcia@siesta.arch--2005/siesta-devel--ag-bau--1.4--patch-11 16134 agarcia@siesta.arch--2005/siesta-devel--ag-bau--1.4--patch-12 16135 agarcia@siesta.arch--2005/siesta-devel--ag-bau--1.4--patch-13 16136 agarcia@siesta.arch--2005/siesta-devel--ag-bau--1.4--patch-14 16137 agarcia@siesta.arch--2005/siesta-devel--ag-bau--1.4--patch-15 16138 agarcia@siesta.arch--2005/siesta-devel--ag-bau--1.4--patch-16 16139 agarcia@siesta.arch--2005/siesta-devel--ag-bau--1.4--patch-17 16140 agarcia@siesta.arch--2005/siesta-devel--ag-bau--1.4--patch-18 16141 agarcia@siesta.arch--2005/siesta-devel--ag-bau--1.4--patch-19 16142 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-33 16143 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-34 16144 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-35 16145 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-36 16146 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-37 16147 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-38 16148 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-39 16149 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-40 16150 16151======================================================================= 16152 161532005-06-08 12:55:52 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-2 16154 16155 Summary: 16156 Siesta 1.4.55 and .56, recipes.f as module, g95, version id 16157 Revision: 16158 siesta-devel--reference--1.4--patch-2 16159 16160 * agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-26 16161 Patch for Siesta 1.4.55 16162 16163 Version: 1.4.55 16164 Date: 2005/06/02 11:30 GMT 16165 Title: U option in matel 16166 Author: Jose M. Soler <jose.soler@uam.es> 16167 16168 Added ability of matel of calculating electrostatic interaction 16169 between two atom-centered charge distributions ('U' option). 16170 This option is not used in siesta, but has been included to 16171 maintain a unique version of matel from other codes. 16172 16173 Files: 16174 atmfuncs.f xphiatm, yphiatm, and zphiatm moved to matel 16175 fermid.F derf and derfc moved to recipes.f 16176 matel.f New option 'U' 16177 recipes.f Functions derf and derfc moved here from fermid.F 16178 16179 * agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-27 16180 Change local name of izamax in linpack.F 16181 16182 * agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-28 16183 Two array copies rewritten as do loops in alloc.F90 16184 16185 * agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-29 16186 fsiesta: sleep 10 seconds before start of siesta 16187 16188 * agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-30 16189 Siesta 1.4.56 plus modularization of recipes.f 16190 16191 (Part of 1.4.56 committed in two previous patches) 16192 -- linpack.F 16193 -- alloc.F90 16194 16195 Version: 1.4.56 16196 Date: 2005/06/02 12:30 GMT 16197 Title: Patches to compiler/system bugs 16198 Author: Eduardo Anglada <eduardo.anglada@uam.es> 16199 16200 Miscellaneous patches to apparent compiler or system bugs. 16201 16202 Files: 16203 atom.f Single quotes changed to double quotes 16204 16205 * (A. Garcia) 16206 16207 - Modularization of recipes.f, and thus 16208 changes in atom.f, electrostatic.f, radial.f, radfft.f, fermid.F, and matel.f 16209 16210 - Fix of calls to spline and splint in matel to pass whole array section. 16211 16212 * agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-31 16213 Support for g95 -- atom.f fix -- Makefile fix 16214 16215 * Added Src/Sys/g95-nolibs.make 16216 (g95 can be obtained from http://g95.sourceforge.net/) 16217 * Fixed a bug in atom.f introduced in the previous patch. 16218 * Put recipes.o near the front of the modules list to 16219 satisfy dependencies. 16220 16221 * agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-32 16222 Add arch version string to executable 16223 16224 A hook has been added to {arch}/=hook, which is called 16225 by a simple script in $HOME/.arch-params/hook: 16226 16227 #!/bin/sh 16228 hook="$ARCH_TREE_ROOT/{arch}/=hook" 16229 if [ -x "$hook" ] ; then 16230 "$hook" $@ 16231 fi 16232 16233 The only useful task of the hook is a "pre-commit" 16234 generation of a version.info file, which is 16235 also being commited in this patch. 16236 16237 * A script Src/doversion.sh inserts the contents 16238 of version.info into an appropriate place in version.F90. 16239 16240 NOTE: This does not quite work, as by the time the hook is 16241 run, the changeset has already been finalized, and the 16242 new version.info is not committed. 16243 16244 new files: 16245 .arch-ids/version.info.id Src/.arch-ids/doversion.sh.id 16246 Src/Sys/.arch-ids/g95-nolibs.make.id Src/Sys/g95-nolibs.make 16247 Src/doversion.sh version.info 16248 16249 modified files: 16250 Src/Makefile Src/alloc.F90 Src/atmfuncs.f Src/atom.f 16251 Src/electrostatic.f Src/fermid.F Src/linpack.F Src/matel.f 16252 Src/radfft.f Src/radial.f Src/recipes.f Src/version.F90 16253 Util/SiestaSubroutine/fsiesta.f90 16254 16255 new patches: 16256 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-25 16257 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-26 16258 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-27 16259 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-28 16260 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-29 16261 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-30 16262 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-31 16263 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-32 16264 16265======================================================================= 16266 162672005-05-31 11:01:07 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-1 16268 16269 Summary: 16270 Fix Src/Tests/Makefile and h2o.fdf 16271 Revision: 16272 siesta-devel--reference--1.4--patch-1 16273 16274 Changes to the test makefile and h2o.fdf 16275 had been inadvertently commited. 16276 16277 16278 modified files: 16279 Src/Tests/Makefile Src/Tests/h2o/h2o.fdf 16280 16281======================================================================= 16282 162832005-05-31 10:47:37 GMT Alberto Garcia <wdpgaara@lg.ehu.es> base-0 16284 16285 Summary: 16286 tag of siesta@uam.es--2004/siesta-devel--reference--1.4--patch-46 16287 Revision: 16288 siesta-devel--reference--1.4--base-0 16289 16290 (automatically generated log message) 16291 16292 new patches: 16293 agarcia@siesta.arch--2004/siesta-devel--agarcia--1.4--base-0 16294 agarcia@siesta.arch--2004/siesta-devel--agarcia--1.4--patch-1 16295 agarcia@siesta.arch--2004/siesta-devel--agarcia--1.4--patch-2 16296 agarcia@siesta.arch--2004/siesta-devel--agarcia--1.4--patch-3 16297 agarcia@siesta.arch--2004/siesta-devel--agarcia--1.4--patch-4 16298 agarcia@siesta.arch--2004/siesta-devel--agarcia--1.4--patch-5 16299 agarcia@siesta.arch--2004/siesta-devel--agarcia--1.4--patch-6 16300 agarcia@siesta.arch--2004/siesta-devel--agarcia--1.4--patch-7 16301 agarcia@siesta.arch--2004/siesta-devel--agarcia--1.4--patch-8 16302 agarcia@siesta.arch--2004/siesta-devel--agarcia--1.4--patch-9 16303 agarcia@siesta.arch--2004/siesta-devel--agarcia--1.4--patch-10 16304 agarcia@siesta.arch--2004/siesta-devel--agarcia--1.4--patch-11 16305 agarcia@siesta.arch--2004/siesta-devel--agarcia--1.4--patch-12 16306 agarcia@siesta.arch--2004/siesta-devel--agarcia--1.4--patch-13 16307 agarcia@siesta.arch--2004/siesta-devel--agarcia--1.4--patch-14 16308 agarcia@siesta.arch--2004/siesta-devel--agarcia--1.4--patch-15 16309 agarcia@siesta.arch--2004/siesta-devel--agarcia--1.4--patch-16 16310 agarcia@siesta.arch--2004/siesta-devel--agarcia--1.4--patch-17 16311 agarcia@siesta.arch--2004/siesta-devel--agarcia--1.4--patch-18 16312 agarcia@siesta.arch--2004/siesta-devel--agarcia--1.4--patch-19 16313 agarcia@siesta.arch--2004/siesta-devel--agarcia--1.4--patch-20 16314 agarcia@siesta.arch--2004/siesta-devel--pseudoxml--1.4--patch-1 16315 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--base-0 16316 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-1 16317 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-2 16318 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-3 16319 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-4 16320 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-5 16321 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-6 16322 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-7 16323 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-8 16324 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-9 16325 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-10 16326 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-11 16327 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-12 16328 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-13 16329 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-14 16330 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-15 16331 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-16 16332 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-17 16333 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-18 16334 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-19 16335 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-20 16336 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-21 16337 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-22 16338 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-23 16339 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-24 16340 siesta@uam.es--2004/siesta-candidate--reference--1.1--base-0 16341 siesta@uam.es--2004/siesta-candidate--reference--1.1--patch-1 16342 siesta@uam.es--2004/siesta-candidate--reference--1.3--base-0 16343 siesta@uam.es--2004/siesta-candidate--reference--1.3--patch-1 16344 siesta@uam.es--2004/siesta-candidate--reference--1.3--patch-2 16345 siesta@uam.es--2004/siesta-devel--reference--0.11--base-0 16346 siesta@uam.es--2004/siesta-devel--reference--0.11--patch-1 16347 siesta@uam.es--2004/siesta-devel--reference--1.0--base-0 16348 siesta@uam.es--2004/siesta-devel--reference--1.0--patch-1 16349 siesta@uam.es--2004/siesta-devel--reference--1.0--patch-2 16350 siesta@uam.es--2004/siesta-devel--reference--1.0--patch-3 16351 siesta@uam.es--2004/siesta-devel--reference--1.0--patch-4 16352 siesta@uam.es--2004/siesta-devel--reference--1.0--patch-5 16353 siesta@uam.es--2004/siesta-devel--reference--1.2--base-0 16354 siesta@uam.es--2004/siesta-devel--reference--1.2--patch-1 16355 siesta@uam.es--2004/siesta-devel--reference--1.2--patch-2 16356 siesta@uam.es--2004/siesta-devel--reference--1.2--patch-3 16357 siesta@uam.es--2004/siesta-devel--reference--1.2--patch-4 16358 siesta@uam.es--2004/siesta-devel--reference--1.2--patch-5 16359 siesta@uam.es--2004/siesta-devel--reference--1.2--patch-6 16360 siesta@uam.es--2004/siesta-devel--reference--1.2--patch-7 16361 siesta@uam.es--2004/siesta-devel--reference--1.4--base-0 16362 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-1 16363 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-2 16364 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-3 16365 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-4 16366 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-5 16367 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-6 16368 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-7 16369 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-8 16370 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-9 16371 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-10 16372 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-11 16373 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-12 16374 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-13 16375 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-14 16376 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-15 16377 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-16 16378 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-17 16379 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-18 16380 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-19 16381 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-20 16382 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-21 16383 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-22 16384 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-23 16385 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-24 16386 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-25 16387 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-26 16388 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-27 16389 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-28 16390 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-29 16391 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-30 16392 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-31 16393 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-32 16394 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-33 16395 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-34 16396 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-35 16397 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-36 16398 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-37 16399 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-38 16400 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-39 16401 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-40 16402 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-41 16403 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-42 16404 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-43 16405 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-44 16406 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-45 16407 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-46 16408 siesta@uam.es--2004/siesta-release--reference--0.9--base-0 16409 siesta@uam.es--2004/siesta-release--reference--0.11--base-0 16410 siesta@uam.es--2004/siesta-release--reference--0.11--patch-1 16411 siesta@uam.es--2004/siesta-release--reference--1.1--base-0 16412 siesta@uam.es--2004/siesta-release--reference--1.1--patch-1 16413 siesta@uam.es--2004/siesta-release--reference--1.1--patch-2 16414 siesta@uam.es--2004/siesta-release--reference--1.3--base-0 16415 twhite@siesta.arch--2004/siesta-devel--autoconf--1.4--base-0 16416 twhite@siesta.arch--2004/siesta-devel--autoconf--1.4--patch-1 16417 twhite@siesta.arch--2004/siesta-devel--autoconf--1.4--patch-2 16418 twhite@siesta.arch--2004/siesta-devel--autoconf--1.4--patch-3 16419 twhite@siesta.arch--2004/siesta-devel--autoconf--1.4--patch-4 16420 twhite@siesta.arch--2004/siesta-devel--autoconf--1.4--patch-5 16421 twhite@siesta.arch--2004/siesta-devel--autoconf--1.4--patch-6 16422 twhite@siesta.arch--2004/siesta-devel--autoconf--1.4--patch-7 16423 twhite@siesta.arch--2004/siesta-devel--autoconf--1.4--patch-8 16424 twhite@siesta.arch--2004/siesta-devel--tw-bugfix--1.4--base-0 16425 twhite@siesta.arch--2004/siesta-devel--tw-bugfix--1.4--patch-1 16426 twhite@siesta.arch--2004/siesta-devel--tw-bugfix--1.4--patch-2 16427 twhite@siesta.arch--2004/siesta-devel--tw-bugfix--1.4--patch-3 16428 twhite@siesta.arch--2004/siesta-devel--tw-bugfix--1.4--patch-4 16429 twhite@siesta.arch--2004/siesta-devel--tw-bugfix--1.4--patch-5 16430 twhite@siesta.arch--2004/siesta-devel--tw-bugfix--1.4--patch-6 16431 twhite@siesta.arch--2004/siesta-devel--tw-bugfix--1.4--patch-7 16432 twhite@siesta.arch--2004/siesta-devel--tw-bugfix--1.4--patch-8 16433 twhite@siesta.arch--2004/siesta-devel--tw-bugfix--1.4--patch-11 16434 twhite@siesta.arch--2004/siesta-devel--tw-bugfix-2--1.4--patch-3 16435 twhite@siesta.arch--2004/siesta-devel--tw-bugfix-2--1.4--patch-4 16436 twhite@siesta.arch--2004/siesta-devel--tw-bugfix-2--1.4--patch-6 16437 twhite@siesta.arch--2004/siesta-devel--tw-bugfix-2--1.4--patch-7 16438 twhite@siesta.arch--2004/siesta-devel--tw-bugfix-2--1.4--patch-9 16439 twhite@siesta.arch--2004/siesta-devel--tw-bugfix-2--1.4--patch-10 16440 twhite@siesta.arch--2004/siesta-devel--tw-bugfix-2--1.4--patch-11 16441 twhite@siesta.arch--2004/siesta-devel--tw-bugfix-2--1.4--patch-13 16442 twhite@siesta.arch--2004/siesta-devel--tw-bugfix-2--1.4--patch-14 16443 twhite@siesta.arch--2004/siesta-devel--tw-bugfix-2--1.4--patch-15 16444 twhite@siesta.arch--2004/siesta-devel--tw-bugfix-2--1.4--patch-17 16445 twhite@siesta.arch--2004/siesta-devel--tw-bugfix-2--1.4--patch-18 16446 twhite@siesta.arch--2004/siesta-devel--tw-bugfix-2--1.4--patch-20 16447 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--base-0 16448 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-1 16449 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-2 16450 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-3 16451 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-4 16452 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-5 16453 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-6 16454 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-7 16455 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-8 16456 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-9 16457 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-10 16458 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-11 16459 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-12 16460 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-13 16461 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-14 16462 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-15 16463 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-16 16464 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-17 16465 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-18 16466 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-19 16467 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-20 16468 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-21 16469 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-22 16470 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-23 16471 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--base-0 16472 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-1 16473 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-2 16474 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-3 16475 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-4 16476 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-5 16477 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-6 16478 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-7 16479 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-8 16480 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-9 16481 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-10 16482 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-11 16483 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-12 16484 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-13 16485 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-14 16486 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-15 16487 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-16 16488 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-17 16489 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-18 16490 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-19 16491 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-20 16492 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-21 16493 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-22 16494 twhite@siesta.arch--2005/siesta-devel--tw-bugfix--1.4--patch-1 16495 twhite@siesta.arch--2005/siesta-devel--tw-bugfix--1.4--patch-2 16496 twhite@siesta.arch--2005/siesta-devel--tw-bugfix--1.4--patch-3 16497 twhite@siesta.arch--2005/siesta-devel--tw-bugfix--1.4--patch-4 16498 twhite@siesta.arch--2005/siesta-devel--tw-bugfix--1.4--patch-5 16499 twhite@siesta.arch--2005/siesta-devel--tw-bugfix--1.4--patch-7 16500 twhite@siesta.arch--2005/siesta-devel--tw-bugfix--1.4--patch-8 16501 twhite@siesta.arch--2005/siesta-devel--tw-bugfix--1.4--patch-9 16502 16503 16504____________________________________________________________________ 16505** CHANGES ALONG siesta@uam.es--2004/siesta-devel--reference--1.4 16506-------------------------------------------------------------------- 16507 165082005-05-31 10:40:32 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-46 16509 16510 Summary: 16511 Fixes, compilation symbols, flush & abort 16512 Revision: 16513 siesta-devel--reference--1.4--patch-46 16514 16515 * Fixes for Intel compiler. 16516 * Checks for alloc/dealloc completion status 16517 * Pre-processing symbols 16518 * Portable flush and abort subroutines (Toby White) 16519 * Cosmetic changes (Toby White, Julian Gale, Alberto Garcia) 16520 16521 Patches applied: 16522 16523 * agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-10 16524 Allow all nodes to write in sys.F 16525 16526 * agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-11 16527 Fix typo in sys.F 16528 16529 * agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-12 16530 Workaround for allocatable issues in Intel compiler 16531 16532 * agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-13 16533 Add checks for alloc/dealloc completion status 16534 16535 * agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-14 16536 Add m_memory to previous patch 16537 16538 * agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-15 16539 New pre-processing symbols for WXML and Scalapack_extra 16540 16541 * agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-16 16542 Add flush to nag.f 16543 16544 * agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-17 16545 Remove debug output in memory.F 16546 16547 * agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-18 16548 Cosmetic issues: transfer, count. 16549 16550 * agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-19 16551 fix format in sys.F -- proc id 16552 16553 * agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-20 16554 remove memorys from memory.F 16555 16556 * agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-21 16557 Portable flush and abort routines (Toby White) 16558 16559 * agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-22 16560 Flush output after every step 16561 16562 * agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-23 16563 frstme and fmt i/o issues in iodm -- chmods 16564 16565 * agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-24 16566 Some fixes by Julian Gale (from Siesta 1.4.54) 16567 16568 * twhite@siesta.arch--2005/siesta-devel--tw-bugfix--1.4--patch-1 16569 Rename trasnfer -> atm_transfer 16570 16571 * twhite@siesta.arch--2005/siesta-devel--tw-bugfix--1.4--patch-2 16572 Rename count -> alloc_count 16573 16574 * twhite@siesta.arch--2005/siesta-devel--tw-bugfix--1.4--patch-3 16575 Include system name in cml output 16576 16577 * twhite@siesta.arch--2005/siesta-devel--tw-bugfix--1.4--patch-4 16578 Fix flush & abort issues 16579 16580 * twhite@siesta.arch--2005/siesta-devel--tw-bugfix--1.4--patch-5 16581 fix for previous changeset 16582 16583 * twhite@siesta.arch--2005/siesta-devel--tw-bugfix--1.4--patch-7 16584 iodm fix 16585 16586 * twhite@siesta.arch--2005/siesta-devel--tw-bugfix--1.4--patch-8 16587 Periodic flush of stdout 16588 16589 * twhite@siesta.arch--2005/siesta-devel--tw-bugfix--1.4--patch-9 16590 reset dm.formattedinput on second time around. 16591 16592 16593 new files: 16594 Src/.arch-ids/m_memory.F.id Src/.arch-ids/pxf.F90.id 16595 Src/m4/.arch-ids/TW_FC_CHECK_ABORT.m4.id 16596 Src/m4/TW_FC_CHECK_ABORT.m4 Src/m_memory.F Src/pxf.F90 16597 16598 modified files: 16599 Src/Makefile Src/Sys/README Src/Sys/itanium2-mpi.make 16600 Src/Sys/itanium2.make Src/Sys/osfdxml.make Src/Sys/sgi.make 16601 Src/Tests/Makefile Src/Tests/h2o/h2o.fdf Src/aclocal.m4 16602 Src/alloc.F90 Src/atm_transfer.f Src/cgwf.F Src/configure 16603 Src/configure.ac Src/diagon.F Src/fdf/Coords.dat 16604 Src/fdf/Otherfile Src/fdf/TODO Src/fdf/coords.fdf 16605 Src/fdf/fdf.Standard Src/fdf/fdf.h Src/fdf/fdfdefs.h 16606 Src/fdf/makefile Src/fdf/sample.fdf Src/gen-basis.F 16607 Src/ibm_pessl.f Src/initatom.f Src/iodm.F Src/iopipes.F90 16608 Src/m4/TW_FC_CHECK_FLUSH.m4 Src/memory.F Src/nag.f Src/pdos.F 16609 Src/pdoskp.F Src/redata.F Src/scalapack_extra.F Src/siesta.F 16610 Src/sys.F Src/wxml/flib_wstml.f90 Src/wxml/m_wxml_core.f90 16611 Src/wxml/m_wxml_dictionary.f90 Src/wxml/m_wxml_error.f90 16612 Src/wxml/m_wxml_text.F90 Src/xlf.f 16613 16614 renamed files: 16615 Src/.arch-ids/scalapack_extra.f.id 16616 ==> Src/.arch-ids/scalapack_extra.F.id 16617 Src/.arch-ids/transfer.f.id 16618 ==> Src/.arch-ids/atm_transfer.f.id 16619 Src/scalapack_extra.f 16620 ==> Src/scalapack_extra.F 16621 Src/transfer.f 16622 ==> Src/atm_transfer.f 16623 Src/wxml/.arch-ids/m_wxml_text.f90.id 16624 ==> Src/wxml/.arch-ids/m_wxml_text.F90.id 16625 Src/wxml/m_wxml_text.f90 16626 ==> Src/wxml/m_wxml_text.F90 16627 16628 new patches: 16629 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-10 16630 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-11 16631 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-12 16632 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-13 16633 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-14 16634 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-15 16635 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-16 16636 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-17 16637 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-18 16638 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-19 16639 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-20 16640 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-21 16641 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-22 16642 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-23 16643 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-24 16644 twhite@siesta.arch--2005/siesta-devel--tw-bugfix--1.4--patch-1 16645 twhite@siesta.arch--2005/siesta-devel--tw-bugfix--1.4--patch-2 16646 twhite@siesta.arch--2005/siesta-devel--tw-bugfix--1.4--patch-3 16647 twhite@siesta.arch--2005/siesta-devel--tw-bugfix--1.4--patch-4 16648 twhite@siesta.arch--2005/siesta-devel--tw-bugfix--1.4--patch-5 16649 twhite@siesta.arch--2005/siesta-devel--tw-bugfix--1.4--patch-7 16650 twhite@siesta.arch--2005/siesta-devel--tw-bugfix--1.4--patch-8 16651 twhite@siesta.arch--2005/siesta-devel--tw-bugfix--1.4--patch-9 16652 16653========================================================================= 16654 166552005-04-28 07:41:26 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-45 16656 16657 Summary: 16658 Merge of CVS 1.4.52 by J. Gale: hybrid XC + fixes 16659 Revision: 16660 siesta-devel--reference--1.4--patch-45 16661 16662 Changes: 16663 16664 * Version CVS 1.4.52 (see below) plus the following fixes: 16665 16666 * Use of real (sp) constant in max expression in cellxc.F 16667 * Make xcmod entities private by default. 16668 * Fix Makefile to remove duplicates of sys.o and parsing.o, 16669 and to include dependencies on xcmod.o 16670 16671 --------------------------------------------------------------------------- 16672 Version: 1.4.52 16673 Date: 2005/04/08 8:30 GMT 16674 Title: Hybrid DFT 16675 Author: Julian Gale <julian@power.curtin.edu.au> 16676 16677 The ability to create hybrid density functionals has been added. 16678 Note that this currently excludes Hartree-Fock exchange. 16679 16680 Files: 16681 16682 Makefile xcmod added to MOD & GEN-BASIS objects list 16683 atom.f Calls to atomxc modified to reflect change in arguments 16684 Pseudopotential functional consistency check modified 16685 to only apply to the single functional case. 16686 cellxc.F XC functional information now accessed from module 16687 Modified to handle hybrid functionals 16688 DVol now divided through prior to adding to VXC to 16689 avoid divide at end and extra multiplications. 16690 dfscf.f Use reference to phiatm removed as not needed 16691 dhscf.F Setting of XC data removed from subroutine and from 16692 calls to cellxc & forhar 16693 forhar.f Call to cellxc modified inline with argument changes 16694 and XC information is no longer passed through. Order 16695 of memory deallocations reversed. 16696 gen-basis.F Call to setXC added 16697 rhoofd.f Use reference to phiatm removed as not needed 16698 siesta.F Call to setXC added 16699 siesta.tex Documentation added for hybrid functionals 16700 vmat.f Use reference to phiatm removed as not needed 16701 vmatsp.f Use reference to phiatm removed as not needed 16702 xc.f atomxc has been modified to handle hybrid functionals 16703 XC information is now access through a module 16704 Auxillary space for storage of DVol now allocated locally 16705 xcmod.F New module added to hold information about the XC 16706 functionals & their weights. Also contains routine to 16707 setup XC information. 16708 16709 16710 16711 new files: 16712 Src/.arch-ids/xcmod.F.id Src/xcmod.F 16713 16714 modified files: 16715 Docs/CHANGES Docs/siesta.tex Src/Makefile Src/atom.f 16716 Src/cellxc.F Src/dfscf.f Src/dhscf.F Src/forhar.f 16717 Src/gen-basis.F Src/rhoofd.f Src/siesta.F Src/version.F90 16718 Src/vmat.f Src/vmatsp.f Src/xc.f 16719 16720 new patches: 16721 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-8 16722 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-9 16723 16724========================================================================= 16725 167262005-04-26 08:09:25 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-44 16727 16728 Summary: 16729 Streamline wxml after XML merge 16730 Revision: 16731 siesta-devel--reference--1.4--patch-44 16732 16733 Some changes had to be made to the wxml subsystem 16734 to avoid problems with the pgf90 compiler and to 16735 avoid the use of the transfer intrinsic. 16736 16737 16738 16739 new files: 16740 Src/wxml/.arch-ids/m_wxml_array_str.f90.id 16741 Src/wxml/m_wxml_array_str.f90 16742 16743 modified files: 16744 Src/Sys/itanium2-mpi.make Src/rhoofdsp.f Src/vmatsp.f 16745 Src/wxml/flib_wcml.f90 Src/wxml/flib_wstml.f90 16746 Src/wxml/m_wxml_buffer.f90 Src/wxml/m_wxml_core.f90 16747 Src/wxml/m_wxml_dictionary.f90 Src/wxml/m_wxml_escape.f90 16748 Src/wxml/makefile 16749 16750 new patches: 16751 agarcia@siesta.arch--2004/siesta-devel--agarcia--1.4--patch-16 16752 agarcia@siesta.arch--2004/siesta-devel--agarcia--1.4--patch-17 16753 agarcia@siesta.arch--2004/siesta-devel--agarcia--1.4--patch-18 16754 agarcia@siesta.arch--2004/siesta-devel--agarcia--1.4--patch-19 16755 agarcia@siesta.arch--2004/siesta-devel--agarcia--1.4--patch-20 16756 agarcia@siesta.arch--2004/siesta-devel--pseudoxml--1.4--patch-1 16757 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--base-0 16758 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-1 16759 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-2 16760 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-3 16761 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-4 16762 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-5 16763 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-6 16764 agarcia@siesta.arch--2005/siesta-devel--agarcia--1.4--patch-7 16765 16766========================================================================= 16767 167682005-04-08 15:40:10 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-43 16769 16770 Summary: 16771 Fix typo in iodm.F 16772 Revision: 16773 siesta-devel--reference--1.4--patch-43 16774 16775 16776 modified files: 16777 Src/iodm.F 16778 16779========================================================================= 16780 167812005-04-08 15:39:41 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-42 16782 16783 Summary: 16784 Wrap long line in mulliken.F 16785 Revision: 16786 siesta-devel--reference--1.4--patch-42 16787 16788 16789 modified files: 16790 Src/mulliken.F 16791 16792========================================================================= 16793 167942005-04-08 13:34:34 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-41 16795 16796 Summary: 16797 Merge from devel-twhite: Fmt IO for DM. 16798 Revision: 16799 siesta-devel--reference--1.4--patch-41 16800 16801 Unformatted DM files are not transferrable between machines 16802 (indeed, between compilers on the same machine). This allows 16803 for formatted files, which are larger and less efficient, but 16804 allow transfer. The default remains unformatted. 16805 16806 * iodm.F: 16807 . three new fdf variables 16808 DM.FormattedFiles - formatted input & output of DM files 16809 DM.FormattedInput - formatted input DM. 16810 DM.FormattedOutput - formatted output DM 16811 . In the case of formatted i/o, a file with the extension .DMF is used 16812 . All i/o is the same as new-style unformatted, except formatted 16813 - I11 for integers 16814 - ES22.15 for floats 16815 (this preserves max accuracy for standard 32-bit integers and 64-bit doubles. 16816 . Also tidy up declarations, and correct comments. 16817 16818 * redata.F: correct spelling error in comment. 16819 16820 * Docs/siesta.tex: Document three new options 16821 16822 * Remove executablt flag from Src/pdos.F, Src/pdosk.F, and Docs/CHANGES 16823 * Add executable flag to Src/configure 16824 16825 modified files: 16826 Docs/CHANGES Docs/siesta.tex Src/iodm.F Src/redata.F 16827 Src/version.F90 16828 16829 new patches: 16830 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-22 16831 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-23 16832 16833========================================================================= 16834 168352005-04-08 13:20:28 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-40 16836 16837 Summary: 16838 add code for abort with NAG compiler 16839 Revision: 16840 siesta-devel--reference--1.4--patch-40 16841 16842 Patches applied: 16843 16844 * twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-22 16845 Allow for formatted DM files. 16846 16847 * twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-23 16848 Fix permissions 16849 16850 16851 modified files: 16852 Src/nag.f 16853 16854========================================================================= 16855 168562005-04-07 21:28:56 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-39 16857 16858 Summary: 16859 Merge of xml work by Jon Wakelin and Toby White 16860 Revision: 16861 siesta-devel--reference--1.4--patch-39 16862 16863 Jon Wakelin started the XML-fication of the output, and 16864 after his departure from Cambridge Toby White made 16865 substantial improvements. 16866 16867 For the details of the changes, please see the patch logs 16868 for version twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4 16869 16870 16871 16872 16873 16874 new files: 16875 Src/.arch-ids/siesta_cml.F90.id Src/.arch-ids/units.f90.id 16876 Src/siesta_cml.F90 Src/units.f90 16877 Src/wxml/.arch-ids/m_wcml_coma.f90.id 16878 Src/wxml/.arch-ids/m_wxml_error.f90.id 16879 Src/wxml/m_wcml_coma.f90 Src/wxml/m_wxml_error.f90 16880 16881 modified files: 16882 Docs/siesta.tex Src/MPI/mpi.F Src/MPI/mpi__include.f90 16883 Src/Makefile Src/Tests/Makefile Src/Tests/batio3/batio3.fdf 16884 Src/Tests/bessel/bessel.fdf Src/Tests/do.sh 16885 Src/Tests/fe/fe.fdf Src/Tests/floating/floating.fdf 16886 Src/Tests/h2o_orderN/h2o_orderN.fdf Src/Tests/si64/si64.fdf 16887 Src/atomlist.f Src/basis_specs.f Src/cdiag.F Src/cgwf.F 16888 Src/diagk.F Src/efield.F Src/fermid.F Src/ioeig.f Src/ionew.F 16889 Src/memory.F Src/memoryinfo.F Src/meshsubs.F Src/mulliken.F 16890 Src/ordern.F Src/outcell.f Src/outcoor.f Src/parallel.f 16891 Src/pdos.F Src/periodic_table.f Src/phonon.F Src/redata.F 16892 Src/siesta.F Src/timestamp.f90 Src/version.F90 16893 Src/wxml/flib_wcml.f90 Src/wxml/flib_wstml.f90 16894 Src/wxml/m_wxml_buffer.f90 Src/wxml/m_wxml_core.f90 16895 Src/wxml/m_wxml_dictionary.f90 Src/wxml/m_wxml_elstack.f90 16896 Src/wxml/m_wxml_escape.f90 Src/wxml/m_wxml_overloads.f90 16897 Src/wxml/m_wxml_text.f90 Src/wxml/makefile 16898 {arch}/siesta-devel/siesta-devel--reference/siesta-devel--reference--1.4/siesta@uam.es--2004/patch-log/patch-24 16899 16900 renamed files: 16901 Src/.arch-ids/timestamp.f.id 16902 ==> Src/.arch-ids/timestamp.f90.id 16903 Src/timestamp.f 16904 ==> Src/timestamp.f90 16905 16906 new patches: 16907 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--base-0 16908 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-1 16909 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-2 16910 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-3 16911 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-4 16912 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-5 16913 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-6 16914 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-7 16915 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-8 16916 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-9 16917 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-10 16918 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-11 16919 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-12 16920 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-13 16921 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-14 16922 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-15 16923 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-16 16924 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-17 16925 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-18 16926 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-19 16927 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-20 16928 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-21 16929 twhite@siesta.arch--2004/siesta-devel--xml-merge--1.4--patch-22 16930 16931========================================================================= 16932 169332005-04-07 14:35:49 GMT Alberto Garcia <wdpgaara@lg.ehu.es> patch-38 16934 16935 Summary: 16936 Siesta 1.4.51 (dummy import to rename extrapolon + CHANGES, version.F90) 16937 Revision: 16938 siesta-devel--reference--1.4--patch-38 16939 16940 16941 Version: 1.4.51 16942 Date: 2005/04/07 15:30 GMT 16943 Title: Extrapol fixes -- cdiag fix (Toby White) 16944 Author: Toby White <tow21@cam.ac.uk> 16945 16946 The only real change in this patch is the actual renaming of extrapolon.F 16947 to extrapolon.f, which was documented but not performed in patch-37. It was 16948 put in the cvs version. 16949 16950 Also, CHANGES and version.F90 are in "cvs form". 16951 16952 16953 modified files: 16954 Docs/CHANGES Src/version.F90 16955 16956 renamed files: 16957 Src/.arch-ids/extrapolon.F.id 16958 ==> Src/.arch-ids/extrapolon.f.id 16959 Src/extrapolon.F 16960 ==> Src/extrapolon.f 16961========================================================================= 16962 16963Version: 1.4.51 16964Date: 2005/04/07 15:30 GMT 16965Title: Extrapol fixes -- cdiag fix (Toby White) 16966Author: Toby White <tow21@cam.ac.uk> 16967 16968* siesta 1.4.50 (=patch-36) erroneously deleted three lines from 16969 cdiag.F which initialize vl & vu. Restore them. 16970* also in rdiag.F make sure that all real variables are initialized 16971 to _dp instead of d0; and use parameters one and zero throughout. 16972 16973* extrapol.F checks for the number of rows of M held on 16974 the current node - if zero, it exits immediately. However, 16975 there is an MPI_AllReduce in the middle. If this is 16976 skipped on some nodes, the results are unpredictable. 16977 This patch fixes the problem such that the MPI_AllReduce 16978 is always executed. 16979* in addition, : 16980 . change all d0 variables to _dp; 16981 . use sys::die instead of stop on error 16982 . remove unnecessary if check (if zero don't add, which 16983 actually slows code down.) 16984 . remove unnecessary "use parallelsubs" 16985 . Add intents to all arguments 16986 . remove unused dummy variable nmrow 16987* siesta.F; remove omitted arg from call to extrapol 16988* extrapolon.F: similar changes; 16989 . change all d0 to _dp 16990 . use sys::die instead of stop on error 16991 . remove unnecessary if check (if zero don't add, which 16992 actually slows code down.) 16993 . remove unnecessary "use mpi_siesta" 16994 . use parallel to bring in node instead of arg list. 16995 . Add intents to all arguments. 16996 . remove unused dummy variable node 16997 . improve logic flow to avoid goto's 16998 . rename file to extrapolon.f since it no longer requires preprocessing. 16999* ordern.F, remove omitted arg from call to extrapolon 17000 17001 version.F90, Docs/CHANGES 17002 17003(siesta-devel--reference--1.4--patch-37) 17004 17005======================================================================= 17006Version: 1.4.51 17007Date: 2005/04/07 15:30 GMT 17008Title: Extrapol fixes -- cdiag fix (Toby White) 17009Author: Toby White <tow21@cam.ac.uk> 17010 17011* siesta 1.4.50 (=patch-36) erroneously deleted three lines from 17012 cdiag.F which initialize vl & vu. Restore them. 17013* also in rdiag.F make sure that all real variables are initialized 17014 to _dp instead of d0; and use parameters one and zero throughout. 17015 17016* extrapol.F checks for the number of rows of M held on 17017 the current node - if zero, it exits immediately. However, 17018 there is an MPI_AllReduce in the middle. If this is 17019 skipped on some nodes, the results are unpredictable. 17020 This patch fixes the problem such that the MPI_AllReduce 17021 is always executed. 17022* in addition, : 17023 . change all d0 variables to _dp; 17024 . use sys::die instead of stop on error 17025 . remove unnecessary if check (if zero don't add, which 17026 actually slows code down.) 17027 . remove unnecessary "use parallelsubs" 17028 . Add intents to all arguments 17029 . remove unused dummy variable nmrow 17030* siesta.F; remove omitted arg from call to extrapol 17031* extrapolon.F: similar changes; 17032 . change all d0 to _dp 17033 . use sys::die instead of stop on error 17034 . remove unnecessary if check (if zero don't add, which 17035 actually slows code down.) 17036 . remove unnecessary "use mpi_siesta" 17037 . use parallel to bring in node instead of arg list. 17038 . Add intents to all arguments. 17039 . remove unused dummy variable node 17040 . improve logic flow to avoid goto's 17041 . rename file to extrapolon.f since it no longer requires preprocessing. 17042* ordern.F, remove omitted arg from call to extrapolon 17043 17044 version.F90, Docs/CHANGES 17045 17046(siesta-devel--reference--1.4--patch-37) 17047 17048======================================================================= 17049Version: 1.4.52 17050Date: 2005/04/08 8:30 GMT 17051Title: Hybrid DFT 17052Author: Julian Gale <julian@power.curtin.edu.au> 17053 17054The ability to create hybrid density functionals has been added. 17055Note that this currently excludes Hartree-Fock exchange. 17056 17057Files: 17058 17059Makefile xcmod added to MOD & GEN-BASIS objects list 17060atom.f Calls to atomxc modified to reflect change in arguments 17061 Pseudopotential functional consistency check modified 17062 to only apply to the single functional case. 17063cellxc.F XC functional information now accessed from module 17064 Modified to handle hybrid functionals 17065 DVol now divided through prior to adding to VXC to 17066 avoid divide at end and extra multiplications. 17067dfscf.f Use reference to phiatm removed as not needed 17068dhscf.F Setting of XC data removed from subroutine and from 17069 calls to cellxc & forhar 17070forhar.f Call to cellxc modified inline with argument changes 17071 and XC information is no longer passed through. Order 17072 of memory deallocations reversed. 17073gen-basis.F Call to setXC added 17074rhoofd.f Use reference to phiatm removed as not needed 17075siesta.F Call to setXC added 17076siesta.tex Documentation added for hybrid functionals 17077vmat.f Use reference to phiatm removed as not needed 17078vmatsp.f Use reference to phiatm removed as not needed 17079xc.f atomxc has been modified to handle hybrid functionals 17080 XC information is now access through a module 17081 Auxillary space for storage of DVol now allocated locally 17082xcmod.F New module added to hold information about the XC 17083 functionals & their weights. Also contains routine to 17084 setup XC information. 17085======================================================================= 17086Version: 1.4.51 17087Date: 2005/04/07 15:30 GMT 17088Title: Extrapol fixes -- cdiag fix (Toby White) 17089Author: Toby White <tow21@cam.ac.uk> 17090 17091* siesta 1.4.50 (=patch-36) erroneously deleted three lines from 17092 cdiag.F which initialize vl & vu. Restore them. 17093* also in rdiag.F make sure that all real variables are initialized 17094 to _dp instead of d0; and use parameters one and zero throughout. 17095 17096* extrapol.F checks for the number of rows of M held on 17097 the current node - if zero, it exits immediately. However, 17098 there is an MPI_AllReduce in the middle. If this is 17099 skipped on some nodes, the results are unpredictable. 17100 This patch fixes the problem such that the MPI_AllReduce 17101 is always executed. 17102* in addition, : 17103 . change all d0 variables to _dp; 17104 . use sys::die instead of stop on error 17105 . remove unnecessary if check (if zero don't add, which 17106 actually slows code down.) 17107 . remove unnecessary "use parallelsubs" 17108 . Add intents to all arguments 17109 . remove unused dummy variable nmrow 17110* siesta.F; remove omitted arg from call to extrapol 17111* extrapolon.F: similar changes; 17112 . change all d0 to _dp 17113 . use sys::die instead of stop on error 17114 . remove unnecessary if check (if zero don't add, which 17115 actually slows code down.) 17116 . remove unnecessary "use mpi_siesta" 17117 . use parallel to bring in node instead of arg list. 17118 . Add intents to all arguments. 17119 . remove unused dummy variable node 17120 . improve logic flow to avoid goto's 17121 . rename file to extrapolon.f since it no longer requires preprocessing. 17122* ordern.F, remove omitted arg from call to extrapolon 17123 17124 version.F90, Docs/CHANGES 17125 17126(siesta-devel--reference--1.4--patch-37) 17127 17128======================================================================= 17129Version: 1.4.50 17130Date: 2005/03/29 07:30 GMT 17131Title: Parallel diag np/q fix 17132Author: Julian Gale <julian@power.curtin.edu.au> 17133 17134The variables np/nq were being used without initialisation in some 17135cases of parallel diagonalisation, according to options. This has 17136been rectified, as well as removing the variable "iter" which was 17137unused. 17138 17139Files: 17140 17141cdiag.F np/nq set and iter removed 17142rdiag.F np/nq set and iter removed 17143version.F90 / CHANGES as per usual 17144======================================================================= 17145Version: 1.4.49 17146Date: 2005/03/23 05:00 GMT 17147Title: CG variable save fix 17148Author: Julian Gale <julian@power.curtin.edu.au> 17149 17150The "save" attribute has been added back for cgaux in cgvc.F as 17151this is required by conjgr.f for correct execution. The deallocation 17152order of gfa & gxa has been reversed for cleaness too. 17153 17154Files: 17155 17156cgvc.F Save attribute added to cgaux 17157version.F90 / CHANGES as per usual 17158======================================================================= 17159Version: 1.4.48 17160Date: 2005/03/21 07:30 GMT 17161Title: CG variable re-initialization + constant fix in meshsubs.F 17162Author: Toby White <tow21@cam.ac.uk> 17163 17164* cgvc.F: cgcntrl is still not initialized correctly if usesavecg is not 17165 set. This patch fixes this. 17166 Update variable declarations & include intent; make kBar a parameter. 17167 Correct subroutine documentation. 17168 Replace all d0 with _dp. 17169 Replace specific dabs with generic abs. 17170 17171* meshsubs.F: Fix constant. 17172 17173version.F90 / CHANGES 17174 17175ARCH patches: siesta-devel--reference--1.4--patch-30 and --patch-34 17176======================================================================= 17177Version: 1.4.47 17178Date: 2005/03/16 04:00 GMT 17179Title: CG bug fix 17180Author: Julian Gale <julian@power.curtin.edu.au> 17181 17182The initialisation of cntrl in conjgr.f introduced in 1.4.42 17183has been removed since this is already done in the calling 17184routine and causes the minimiser to fail by reseting it on 17185every call. 17186 17187conjgr.f Line with cntrl = 0.0 removed and style updated a bit 17188version.F90 / CHANGES 17189======================================================================= 17190Version: 1.4.46 17191Date: 2005/03/11 07:30 GMT 17192Title: PDOS - Parallel over K points 17193Author: Julian Gale <julian@power.curtin.edu.au> 17194 17195The option to parallelise a calculation by distributing K points 17196over processors has been extended to the partial density of states 17197calculation. 17198 17199Changes: 17200 17201pdos.F Option Diag.ParallelOverK checked for in fdf and if true 17202 the routine now calls pdoskp instead of pdosk 17203pdoskp.F New routine added to perform parallel PDOS over K points 17204version.F90 / CHANGES 17205======================================================================= 17206Version: 1.4.45 17207Date: 2005/03/10 03:00 GMT 17208Title: Diag tag snag 17209Author: Julian Gale <julian@power.curtin.edu.au> 17210 17211Changes: 17212 17213A couple of incorrect tags have been updated to reflect the fact 17214that they should now be prefixed with "Diag." - spotted by 17215Nichols. 17216 17217siesta.tex ParallelOverK -> Diag.ParallelOverK 17218redata.F DivideAndConquer -> Diag.DivideAndConquer 17219version.F90 / CHANGES 17220======================================================================= 17221Version: 1.4.44 17222Date: 2005/03/08 04:30 GMT 17223Title: FSM deallocation order change 17224Author: Julian Gale <julian@power.curtin.edu.au> 17225 17226Changes: 17227 17228nlefsm.f / overfsm.f / nlefsm.f - order of deallocations reversed 17229to try to keep stack clean 17230 17231version.F90 / CHANGES as per usual 17232======================================================================= 17233Version: 1.4.43 17234Date: 2005/03/04 19:30 GMT 17235Title: Introduction of RPBE (GGA) 17236Author: Marivi Fernandez-Serra <Marivi.Fernandez-Serra@lpmcn.univ-lyon1.fr> 17237 17238Changes: 17239 RPBE GGA has been introduced 17240 17241Files: 17242 xc.f, atom.f, version.F90, siesta.tex, CHANGES 17243======================================================================= 17244Version: 1.4.42 17245Date: 2005/02/25 15:00 GMT 17246Title: Assorted changes for correctness (Toby White) 17247Author: Toby White <tow21@cam.ac.uk> 17248 17249Changes: 17250 17251(patch 20 in siesta-devel--reference--1.4): 17252 17253* Src/wxml: interim update of wxml library. 17254 17255(patch 24 in siesta-devel--reference--1.4): 17256 17257* in cdiag.F, properly initialize vl & vu. 17258 17259* in atom.F, make sure com_vlocal is called for floating 17260 orbitals and Bessel orbitals, (so that vlocaltab is 17261 initialized), 17262 17263* in denmat.F, ft & fts were never initialized before use 17264 (potentially very dangerous) This patch fixed that, and 17265 also only defines and allocates them for the serial 17266 version (they're never used in parallel - this should save 17267 memory) 17268 17269 (** This addresses the same issue as J. Gale's fix 17270 in 1.4.41 **) 17271 17272 - also change all double precision constants to use _dp 17273 17274* in matel.f, when reallocing y and dydr, use copy=.false., 17275 since we don't need to preserve their values (this also 17276 prevents an attempt to use uninitialized variables when 17277 doing the copying) 17278 17279* grdsam.F: initialize lstcll before use 17280 17281* conjgr.f: initialize all of cntrol before use 17282 17283* siesta.F: when fixspin==.false., and qspin>1, qs was not being 17284 initialized before use. Fixed here. Also replace use of dble 17285 intrinsic with real(..., kind=dp). 17286 17287* Tests/batio3/batio3.fdf: GridCellSampling block was wrong. 17288 17289ARCH info: 17290 17291Revision: siesta-devel--reference--1.4--patch-20 17292Archive: siesta@uam.es--2004 17293Creator: Alberto Garcia <wdpgaara@lg.ehu.es> 17294Date: Fri Feb 4 18:44:57 CET 2005 17295Standard-date: 2005-02-04 17:44:57 GMT 17296New-files: Src/wxml/.arch-ids/flib_wcml.f90.id 17297 Src/wxml/.arch-ids/flib_wstml.f90.id 17298 Src/wxml/.arch-ids/m_wxml_escape.f90.id 17299 Src/wxml/.arch-ids/m_wxml_overloads.f90.id 17300 Src/wxml/flib_wcml.f90 Src/wxml/flib_wstml.f90 17301 Src/wxml/m_wxml_escape.f90 17302 Src/wxml/m_wxml_overloads.f90 17303Modified-files: Src/wxml/flib_wxml.f90 17304 Src/wxml/m_wxml_core.f90 Src/wxml/m_wxml_text.f90 17305 Src/wxml/makefile 17306 17307Revision: siesta-devel--reference--1.4--patch-24 17308Archive: siesta@uam.es--2004 17309Creator: Alberto Garcia <wdpgaara@lg.ehu.es> 17310Date: Thu Feb 24 21:58:10 CET 2005 17311Standard-date: 2005-02-24 20:58:10 GMT 17312Modified-files: Src/Tests/batio3/batio3.fdf Src/atom.f 17313 Src/cdiag.F Src/conjgr.f Src/denmat.F Src/grdsam.F 17314 Src/matel.f Src/siesta.F 17315 17316======================================================================= 17317Version: 1.4.41 17318Date: 2005/02/25 08:00 GMT 17319Title: Denmat serial fix 17320Author: Julian Gale <julian@power.curtin.edu.au> 17321 17322Changes: 17323 17324The initialisaiton of ft & fst when compiled in serial was missing 17325from denmat.F. It has now been added. 17326 17327Files: 17328 17329denmat.F ft & fst zeroed in #else for serial case 17330version.F90 / CHANGES as per usual 17331 17332======================================================================= 17333Version: 1.4.40 17334Date: 2005/02/13 17:35 GMT 17335Title: Fixes by Toby White (including spatial parallelization) 17336Author: Toby White <tow21@cam.ac.uk> 17337 17338Changes: 17339 17340* rdiag.F: initialize vu & vl correctly 17341* siesta.F: correctly set muldeb & signat in MPI environment 17342* cdiag.F correct real constants to complex constants 17343 17344* remove the following routines from files in Libs: 17345 ZHEGVD 17346 ZHPMV 17347 ZHPR2 17348 DGETC2 17349 DSPMV 17350 DSPR2 17351 DSYGVD 17352 17353* When spatial parallelization is given too many nodes, it ends 17354 up allocating no cells to some. This resulted in some array 17355 allocations not being done, which meant accesses to these arrays 17356 were reading uninitialized memory. Random numbers were introduced 17357 into the density. Fixed by: 17358** setatomnodes.F: emit warning that some nodes are unused. Also 17359 fix print statements to properly give results 17360 from all nodes. 17361** siesta.F: rewrite allocation of arrays to properly allocate 17362 empty arrays. Also remove extraneous declarations 17363 and unused Uses. 17364 17365* pulayx.F was trying to access empty arrays. 17366 17367* Add pathf90 to compiler search list, and run autoconf 17368 17369* Open specifier in alloc.F90 was wrong: you're not allowed to 17370 open an already-connected file with status='unknown' (this 17371 cause NAG to crash). Replace with position='append' to ensure 17372 that nodes other than zero have the file pointer placed at the 17373 end of the file (otherwise behaviour is unspecified) 17374 17375* Add datestamp to siesta filename for tracking purposes, and 17376 copy to siesta executable directory. 17377 17378* Remove POSITION= specifier entirely. NAG still complains, and the 17379 default seems to work. 17380* In setatomnodes.F, the calculation of npgrid[xyz]ptr was slightly 17381 broken in systems with large amount of empty space; if, for example, 17382 five cells were available in the x direction, but only three were 17383 filled with atoms, then the rest of npgridxptr ought to be set to the 17384 final cell number - in actuality only its final element was. This 17385 resulted in siesta getting confused later. FIxed here. 17386 17387* in memory.F90, ensure that "maximum memory" outputs are 17388 synced correctly in the output stream. (otherwise they 17389 are interspersed randomly with other output) 17390* in alloc.F90, when alloc_err is encountered, do a proper 17391 MPI_Abort and flush to ensure timely crashing, and output 17392 of the error message. (otherwise all information is lost, 17393 one process dies, and the others continue until they hang) 17394 17395* remove unused declaration in atomlwf 17396* allocate array in memory.F to stop NAG complaining. 17397* ifdef MPI correctly in flushrap.F90 17398 17399Plus: (by AG) 17400 17401* Change in J. Junquera's affiliation in Util/Denchar/Docs/denchar.tex 17402(siesta-devel--reference--1.4--patch-22) 17403 17404ARCH info: 17405 17406Revision: siesta-devel--reference--1.4--patch-23 17407Archive: siesta@uam.es--2004 17408Creator: Alberto Garcia <wdpgaara@lg.ehu.es> 17409Date: Sun Feb 13 18:22:13 CET 2005 17410Standard-date: 2005-02-13 17:22:13 GMT 17411Modified-files: Docs/CHANGES Src/Libs/blas.f 17412 Src/Libs/dc_lapack.f Src/Libs/lapack.f Src/aclocal.m4 17413 Src/alloc.F90 Src/atomlwf.F Src/cdiag.F Src/configure 17414 Src/m4/fortran.m4 Src/memory.F Src/pulayx.F Src/rdiag.F 17415 Src/setatomnodes.F Src/siesta.F 17416 {arch}/siesta-devel/siesta-devel--reference/siesta-devel--reference--1.4/siesta@uam.es--2004/patch-log/patch-15 17417Summary: Assorted fixes by Toby White (including spatial parallelization) 17418Keywords: 17419 17420Patches applied: 17421 17422 * twhite@siesta.arch--2004/siesta-devel--tw-bugfix-2--1.4--patch-9 17423 more minor bugfixes 17424 17425 * twhite@siesta.arch--2004/siesta-devel--tw-bugfix-2--1.4--patch-10 17426 remove unnecessary blas/lapack routines. 17427 17428 * twhite@siesta.arch--2004/siesta-devel--tw-bugfix-2--1.4--patch-11 17429 fix for empty nodes 17430 17431 * twhite@siesta.arch--2004/siesta-devel--tw-bugfix-2--1.4--patch-13 17432 another empty node fix. 17433 17434 * twhite@siesta.arch--2004/siesta-devel--tw-bugfix-2--1.4--patch-14 17435 add pathf90 to configure list. 17436 17437 * twhite@siesta.arch--2004/siesta-devel--tw-bugfix-2--1.4--patch-15 17438 open specifier in alloc.F90 fix. 17439 17440 * twhite@siesta.arch--2004/siesta-devel--tw-bugfix-2--1.4--patch-17 17441 Fix alloc.F90 open, and correct setatomnodes 17442 17443 * twhite@siesta.arch--2004/siesta-devel--tw-bugfix-2--1.4--patch-18 17444 improve output and error diagnostics 17445 17446 * twhite@siesta.arch--2004/siesta-devel--tw-bugfix-2--1.4--patch-20 17447 minor fixes 17448 17449 * twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-10 17450 merge from upstream 17451 17452 * twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-11 17453 bugfix merge 17454 17455 * twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-12 17456 17457 17458 * twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-13 17459 fix for empty nodes 17460 17461 * twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-14 17462 merge from --reference--1.4 17463 17464 * twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-15 17465 assorted changes from my bugfix branch 17466 17467======================================================================= 17468Version: 1.4.39 17469Date: 2005/02/04 17:05 GMT 17470Title: Denchar bugs fixed 17471Author: Javier Junquera <javier.junquera@unican.es> 17472 17473Some bugs that appeared during the compilation or execution 17474of denchar have been fixed. 17475 17476Files: 17477 17478Makefile - inclusion of parallelsubs.o in OTHER_DENCHAR_OBJS 17479denchar.F - variable FILEIN set to 'stdin', 17480 avoiding the call to command_argument_count() 17481m_denchar_work.f - change in some write formats in order to 17482 avoid double space between data of consecutive 17483 rows in the output. 17484version.F90, CHANGES 17485Denchar/Docs/denchar.tex : Change in affiliation 17486======================================================================= 17487Version: 1.4.38 17488Date: 2005/02/04 05:30 GMT 17489Title: O(N) extrapolation fix 17490Author: Julian Gale <julian@power.curtin.edu.au> 17491 17492The order N code was failing in parallel when the structure 17493of the Hamiltonian changed between geomtry steps. The code 17494has been modified to solve this. The arrays cold / listcold 17495now only keep the rows for which the current node has principal 17496responsibility for. The extrapolation and I/O of LWFs now 17497acts just on this part of C and is then globalised to all 17498processors. 17499 17500Files: 17501 17502atomlwf.F Dimensions of cold/listcold decreased by using nbasisloc 17503egandd.F Reallocation of arrays now occurs when iopt = 0 and 17504 not just on the first call. The copy=.true. and 17505 shrink=.false. attributes have also been added. 17506extrapolon.F Now acts only on 1->nbasisloc rather than 1->nbasisCloc 17507iolwf.F Now acts only on 1->nbasisloc rather than 1->nbasisCloc 17508 and nbasisloc is added as a pased argument. 17509ordern.F Handling of cold/listcold changed and call to 17510 globaliseC added after extrapolon call. 17511version.F90, CHANGES 17512======================================================================= 17513Version: 1.4.37 17514Date: 2005/01/25 03:00 GMT 17515Title: Mesh subdivisions control from input 17516Author: Julian Gale <julian@power.curtin.edu.au> 17517 17518The value of nsm, which was previously a parameter, can now be 17519adjusted from the input deck using the "MeshSubDivisions" option. 17520The order of array deallocation in dhscf.F has also been reversed. 17521 17522Files: 17523 17524dhscf.F, meshsubs.F, version.F90, CHANGES, siesta.tex 17525======================================================================= 17526Version: 1.4.36 17527Date: 2005/01/25 06:10 GMT 17528Title: Grdsam array size fix 17529Author: Julian Gale <julian@power.curtin.edu.au> 17530 17531The size of the array dpt has been corrected to depend on maxpt+1 17532rather than na. Order of array deallocations has been reversed to 17533be deallocation friendly. 17534 17535Files: 17536 17537grdsam.F, version.F90, CHANGES 17538======================================================================= 17539Version: 1.4.35 17540Date: 2005/01/08 16:20 GMT 17541Title: Removed old Denchar source 17542Author: Alberto Garcia <wdpgaara@lg.ehu.es> 17543 17544Removed all files under Util/Denchar/Src. 17545(The source for Denchar has been in the top directory 17546for a while) 17547 17548Changes to version.F90 and CHANGES. 17549 17550======================================================================= 17551Version: 1.4.34 17552Date: 2005/01/07 13:45 GMT 17553Title: Bugfixes by Toby White: decls, inits, typos, autoconf 17554ARCH patches: siesta-devel--reference--1.4--patch-14, 17555 siesta-devel--reference--1.4--patch-15 17556Author: Toby White (committed by Alberto Garcia) and Alberto Garcia 17557 17558* Removal of "use" statement for m_radfft from atom.f 17559* Fix declarations in mneighb.f similarly to neighb.f 17560* Fix typo in fft3d.F 17561* Fix MPI/Makefile to properly inherit FFLAGS_MPI 17562* Initialise variables properly in meshsubs.F 17563* Add ifort to list of compilers tested for in configure 17564 17565 17566ARCH info: 17567 17568Revision: siesta-devel--reference--1.4--patch-14 17569Archive: siesta@uam.es--2004 17570Creator: Alberto Garcia <wdpgaara@lg.ehu.es> 17571Date: Fri Jan 7 14:32:44 CET 2005 17572Standard-date: 2005-01-07 13:32:44 GMT 17573Modified-files: Docs/CHANGES Src/atom.f Src/diagk.F 17574 Src/fermid.F Src/version.F90 Src/writewave.F 17575New-patches: agarcia@siesta.arch--2004/siesta-devel--agarcia--1.4--patch-12 17576 agarcia@siesta.arch--2004/siesta-devel--agarcia--1.4--patch-13 17577 agarcia@siesta.arch--2004/siesta-devel--agarcia--1.4--patch-14 17578 agarcia@siesta.arch--2004/siesta-devel--agarcia--1.4--patch-15 17579 siesta@uam.es--2004/siesta-devel--reference--1.4--patch-14 17580Summary: Siesta 1.4.32 and 1.4.33, plus radfft removal from atom 17581Keywords: cvs-date=2004/12/20,cvs-date=2005/01/05, merge from agarcia 17582 17583Revision: siesta-devel--reference--1.4--patch-15 17584Archive: siesta@uam.es--2004 17585Creator: Alberto Garcia <wdpgaara@lg.ehu.es> 17586Date: Fri Jan 7 14:47:48 CET 2005 17587Standard-date: 2005-01-07 13:47:48 GMT 17588Modified-files: Docs/CHANGES Src/MPI/Makefile Src/aclocal.m4 17589 Src/configure Src/fft3d.F Src/m4/fortran.m4 17590 Src/meshsubs.F Src/mneighb.f 17591New-patches: siesta@uam.es--2004/siesta-devel--reference--1.4--patch-15 17592 twhite@siesta.arch--2004/siesta-devel--tw-bugfix-2--1.4--patch-3 17593 twhite@siesta.arch--2004/siesta-devel--tw-bugfix-2--1.4--patch-4 17594 twhite@siesta.arch--2004/siesta-devel--tw-bugfix-2--1.4--patch-6 17595 twhite@siesta.arch--2004/siesta-devel--tw-bugfix-2--1.4--patch-7 17596 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-8 17597 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-9 17598Summary: Bugfixes by Toby White: decls, inits, typos, autoconf 17599Keywords: Merged from -devel--twhite--patch-9 17600 17601 17602======================================================================= 17603Version: 1.4.33 17604Date: 2005/01/05 16:15 GMT 17605Title: Fixed bugs in diagk.F for writting of wave functions 17606Author: Pablo Ordejon <ordejon@icmab.es> 17607 17608Some bugs introduced in the recent changes of diagk.F in the writting 17609of the wave functions are corrected. 17610 17611Files: 17612 17613diagk.F All eigenvectors are computed when writing of wave 17614 functions is required; the right information about 17615 eigenvalues is now passed. 17616writewave.F Correct call to diagg.f to include new variable 17617 neigwanted 17618version.F90 / CHANGES 17619 17620======================================================================= 17621Version: 1.4.32 17622Date: 2004/12/20 8:30 GMT 17623Title: Fermi occupancy initialisation 17624Author: Julian Gale <julian@power.curtin.edu.au> 17625 17626The occupancies are explicitly initialised to zero in fermid & 17627fermispin to ensure that the checking of occupancies in the build 17628of the density matrix is correct. 17629 17630Files: 17631 17632fermid.F Initialisation of occupancies upto maxe added and 17633 cosmetic f90 changes made. 17634version.F90 / CHANGES 17635 17636======================================================================= 17637Version: 1.4.31 17638Date: 2004/12/10 16:40 GMT 17639Title: bugfixes for Julian's diagon improvements 17640ARCH patches: siesta-devel--reference--1.4--patch-12, 17641 siesta-devel--reference--1.4--patch-13 17642Author: Toby White (committed by Alberto Garcia) 17643 17644* scalapack_extra needs an extra couple of routines now. With 17645 these siesta will now compile with Sun's S3L library for 17646 its blas/scalapack. 17647* In cdiag.F, ztrsm was being called with an incorrectly typed 17648 7th argument. This silently introduced random numbers into the 17649 energy. 17650* previous bugfix omitted kind= keyword from cmplx 17651* also apply same bugfix to pblas pztrsm calls. 17652 17653ARCH info: 17654 17655Revision: siesta-devel--reference--1.4--patch-12 17656Archive: siesta@uam.es--2004 17657Creator: Alberto Garcia <wdpgaara@lg.ehu.es> 17658Date: Fri Dec 10 16:26:27 CET 2004 17659Standard-date: 2004-12-10 15:26:27 GMT 17660Modified-files: Docs/CHANGES Src/cdiag.F 17661 Src/scalapack_extra.f 17662 {arch}/siesta-devel/siesta-devel--reference/siesta-devel--reference--1.4/siesta@uam.es--2004/patch-log/patch-4 17663 {arch}/siesta-devel/siesta-devel--reference/siesta-devel--reference--1.4/siesta@uam.es--2004/patch-log/patch-6 17664Modified-directories: {arch}/siesta-devel/siesta-devel--reference/siesta-devel--reference--1.4 17665 {arch}/siesta-devel/siesta-devel--reference/siesta-devel--reference--1.4/siesta@uam.es--2004 17666 {arch}/siesta-devel/siesta-devel--reference/siesta-devel--reference--1.4/siesta@uam.es--2004/patch-log 17667New-patches: siesta@uam.es--2004/siesta-devel--reference--1.4--patch-12 17668 twhite@siesta.arch--2004/siesta-devel--autoconf--1.4--patch-8 17669 twhite@siesta.arch--2004/siesta-devel--tw-bugfix--1.4--patch-8 17670 twhite@siesta.arch--2004/siesta-devel--tw-bugfix--1.4--patch-11 17671 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-5 17672 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-6 17673Summary: bugfixes for Julian's diagon improvements 17674Keywords: scalapack blas ztrsm 17675 17676Revision: siesta-devel--reference--1.4--patch-13 17677Archive: siesta@uam.es--2004 17678Creator: Alberto Garcia <wdpgaara@lg.ehu.es> 17679Date: Fri Dec 10 17:30:24 CET 2004 17680Standard-date: 2004-12-10 16:30:24 GMT 17681Modified-files: Docs/CHANGES Src/cdiag.F 17682New-patches: siesta@uam.es--2004/siesta-devel--reference--1.4--patch-13 17683 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-7 17684Summary: fix ztrsm bugfix 17685 17686 17687 17688======================================================================= 17689Version: 1.4.30 17690Date: 2004/12/10 15:45 GMT 17691Title: Add missing autoconf files (no arch change) 17692Author: Alberto Garcia <wdpgaara@lg.ehu.es> 17693 17694While committing patch-10 from arch, CVS did not flag 17695some files as "not added". They are added now. 17696These files should have been part of 1.4.28. 17697 17698Files: 17699 17700aclocal.m4 arch.make.in config.guess 17701config.sub configure configure.ac : New files 17702 17703ARCH info: No change (new files were part of 17704 siesta-devel--reference--1.4--patch-10) 17705======================================================================= 17706Version: 1.4.29 17707Date: 2004/12/10 7:30 GMT 17708Title: New parallel denmat 17709Author: Julian Gale <julian@power.curtin.edu.au> 17710 17711The multiplication of cHc / cSc by c in denmat has been rewritten in 17712terms of using numct/listct, instead of numf/listf to go directly 17713to ftG/fstG, rather than via chcc/cscc. A number of related clean ups 17714in the parallel order N have been made. 17715 17716Files: 17717 17718atomlwf.F The arrays nbNode and nbAtom have been removed 17719denmat.F Algorithm changed for chc/csc x c step / 17720 arrays chcc & cscc eliminated / globaliseF not 17721 called anymore. 17722egandd.F Arrays f & fs no longer passed to denmat.F 17723ener3.F The array nbNode is no longer "use"d 17724ener3lomem.F The array nbNode is no longer "use"d 17725globalise.F Local elements of buxg are now explicitly zeroed for 17726 safety during rezero call. 17727onmod.F The arrays nbNode and nbAtom have been removed 17728ordern.F The arrays nbNode and nbAtom have been removed 17729version.F / CHANGES - as per usual 17730======================================================================= 17731Version: 1.4.28 17732Date: 2004/12/09 18:00 GMT 17733Title: Autoconf (siesta-devel--reference--1.4--patch-10) 17734Author: Toby White (committed by Alberto Garcia) 17735 17736Changes: 17737 17738 * Add requisite files for autoconf. 17739 - aclocal.m4 & configure are generated files. 17740 17741 * Remove cleaning of aux_ files from Makefile 17742 17743ARCH info: 17744 17745Revision: siesta-devel--reference--1.4--patch-10 17746Archive: siesta@uam.es--2004 17747Creator: Alberto Garcia <wdpgaara@lg.ehu.es> 17748Date: Tue Dec 7 21:54:51 CET 2004 17749Standard-date: 2004-12-07 20:54:51 GMT 17750New-files: Src/.arch-ids/aclocal.m4.id 17751 Src/.arch-ids/arch.make.in.id 17752 Src/.arch-ids/config.guess.id 17753 Src/.arch-ids/config.sub.id 17754 Src/.arch-ids/configure.ac.id 17755 Src/.arch-ids/configure.id Src/aclocal.m4 17756 Src/arch.make.in Src/config.guess Src/config.sub 17757 Src/configure Src/configure.ac Src/m4/.arch-ids/=id 17758 Src/m4/.arch-ids/ACX_MPI.m4.id 17759 Src/m4/.arch-ids/TW_CHECK_BLACS.m4.id 17760 Src/m4/.arch-ids/TW_CHECK_FC_90.m4.id 17761 Src/m4/.arch-ids/TW_CHECK_FC_95.m4.id 17762 Src/m4/.arch-ids/TW_CHECK_FC_FPP.m4.id 17763 Src/m4/.arch-ids/TW_CHECK_FC_FPP_90.m4.id 17764 Src/m4/.arch-ids/TW_CHECK_FC_TR15580.m4.id 17765 Src/m4/.arch-ids/TW_CHECK_FC_TR15581.m4.id 17766 Src/m4/.arch-ids/TW_CHECK_SCALAPACK.m4.id 17767 Src/m4/.arch-ids/TW_FC_CHECK_DCFUNS.m4.id 17768 Src/m4/.arch-ids/TW_FC_CHECK_FLUSH.m4.id 17769 Src/m4/.arch-ids/TW_FC_ID.m4.id 17770 Src/m4/.arch-ids/TW_FC_ID_FLAGS.m4.id 17771 Src/m4/.arch-ids/TW_FIND_FC_BLAS.m4.id 17772 Src/m4/.arch-ids/TW_FIND_LAPACK.m4.id 17773 Src/m4/.arch-ids/TW_PATH_NETCDF.m4.id 17774 Src/m4/.arch-ids/TW_TRY_DC_LAPACK.m4.id 17775 Src/m4/.arch-ids/ac_config_aux_dirs.m4.id 17776 Src/m4/.arch-ids/fortran.m4.id Src/m4/ACX_MPI.m4 17777 Src/m4/TW_CHECK_BLACS.m4 Src/m4/TW_CHECK_FC_90.m4 17778 Src/m4/TW_CHECK_FC_95.m4 Src/m4/TW_CHECK_FC_FPP.m4 17779 Src/m4/TW_CHECK_FC_FPP_90.m4 17780 Src/m4/TW_CHECK_FC_TR15580.m4 17781 Src/m4/TW_CHECK_FC_TR15581.m4 17782 Src/m4/TW_CHECK_SCALAPACK.m4 17783 Src/m4/TW_FC_CHECK_DCFUNS.m4 17784 Src/m4/TW_FC_CHECK_FLUSH.m4 Src/m4/TW_FC_ID.m4 17785 Src/m4/TW_FC_ID_FLAGS.m4 Src/m4/TW_FIND_FC_BLAS.m4 17786 Src/m4/TW_FIND_LAPACK.m4 Src/m4/TW_PATH_NETCDF.m4 17787 Src/m4/TW_TRY_DC_LAPACK.m4 Src/m4/ac_config_aux_dirs.m4 17788 Src/m4/fortran.m4 17789New-directories: Src/m4 Src/m4/.arch-ids 17790Modified-files: Src/Makefile 17791New-patches: siesta@uam.es--2004/siesta-devel--reference--1.4--patch-10 17792 twhite@siesta.arch--2004/siesta-devel--autoconf--1.4--base-0 17793 twhite@siesta.arch--2004/siesta-devel--autoconf--1.4--patch-1 17794 twhite@siesta.arch--2004/siesta-devel--autoconf--1.4--patch-2 17795 twhite@siesta.arch--2004/siesta-devel--autoconf--1.4--patch-3 17796 twhite@siesta.arch--2004/siesta-devel--autoconf--1.4--patch-4 17797 twhite@siesta.arch--2004/siesta-devel--autoconf--1.4--patch-5 17798 twhite@siesta.arch--2004/siesta-devel--autoconf--1.4--patch-6 17799 twhite@siesta.arch--2004/siesta-devel--autoconf--1.4--patch-7 17800 twhite@siesta.arch--2004/siesta-devel--tw-bugfix--1.4--base-0 17801 twhite@siesta.arch--2004/siesta-devel--tw-bugfix--1.4--patch-1 17802 twhite@siesta.arch--2004/siesta-devel--tw-bugfix--1.4--patch-2 17803 twhite@siesta.arch--2004/siesta-devel--tw-bugfix--1.4--patch-7 17804 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-4 17805Summary: Autoconf files -- merge of siesta-devel--twhite--1.4--patch-4 17806Keywords: 17807 17808 17809 17810======================================================================= 17811Version: 1.4.27 17812Date: 2004/12/09 17:30 GMT 17813Title: Fixes by Toby White (siesta-devel--reference--1.4--patch-9) 17814Author: Alberto Garcia <wdpgaara@lg.ehu.es> 17815 17816Changes: 17817 17818 * minor fixes to let NAG run with fewer complaints 17819 * - neigh.f: initialize CELAST & RGLAST before use 17820 use precision module 17821 add intents to arguments 17822 - meshmatrix.F: do not test size of unallocated array 17823 - matel.f & meshsubs.f: make sure literal constants have 17824 correct precision 17825 * Rearrange Libs: 17826 - move IEEECK from blas.f to lapack.f 17827 - replace machine.f with LAPACK3E version which is not 17828 broken by optimization. 17829 - Src/Libs/makefile & Src/Makefile: add separate targets 17830 for libblas.a and liblapack.a 17831 * Src/Makefile fixes: 17832 - clear SUFFIXES at the start (fixes .mod Modula-2 problems) 17833 - Fix sed quoting in version rule (and tidy it up a bit) 17834 17835ARCH info: 17836 17837Revision: siesta-devel--reference--1.4--patch-9 17838Archive: siesta@uam.es--2004 17839Creator: Alberto Garcia <wdpgaara@lg.ehu.es> 17840Date: Tue Dec 7 20:22:24 CET 2004 17841Standard-date: 2004-12-07 19:22:24 GMT 17842Renamed-files: Src/Libs/.arch-ids/machine.f.id Src/Libs/.arch-ids/machine.F.id 17843 Src/Libs/machine.f Src/Libs/machine.F 17844Modified-files: Src/Libs/README Src/Libs/blas.f 17845 Src/Libs/lapack.f Src/Libs/machine.F Src/Libs/makefile 17846 Src/Makefile Src/matel.f Src/meshmatrix.F Src/meshsubs.F 17847 Src/neighb.f 17848Modified-directories: Src/Libs/.arch-ids 17849New-patches: siesta@uam.es--2004/siesta-devel--reference--1.4--patch-9 17850 twhite@siesta.arch--2004/siesta-devel--tw-bugfix--1.4--patch-3 17851 twhite@siesta.arch--2004/siesta-devel--tw-bugfix--1.4--patch-4 17852 twhite@siesta.arch--2004/siesta-devel--tw-bugfix--1.4--patch-5 17853 twhite@siesta.arch--2004/siesta-devel--tw-bugfix--1.4--patch-6 17854 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--base-0 17855 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-1 17856 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-2 17857 twhite@siesta.arch--2004/siesta-devel--twhite--1.4--patch-3 17858Summary: Merge of siesta-devel--twhite--1.4--patch-3 17859Keywords: 17860 17861** Transitional fixes: 17862 17863 Removed obsolete files: 17864 17865 Src/fdf: fdf2.f fdf3.f 17866 Src/NetCDF: netcdf.f90.orig netcdf_overloads.f90.orig 17867 Util/Denchar/Src/NetCDF: netcdf.f90.orig netcdf_overloads.f90.orig 17868 Docs/Tech: basis_generation.html index.html 17869 17870======================================================================= 17871Version: 1.4.26 17872Date: 2004/12/05 3:30 GMT 17873Title: Fixes for test example bugs 17874Author: Julian Gale <julian@power.curtin.edu.au> 17875 17876dfscf.f Setting of Parallel_Run variable corrected 17877gradient.F Reinitialisation of bux1/2 moved for correct 17878 operation of serial version. 17879pdos.F Deallocation of tmp moved to correct place 17880siesta.F Initialisation of Escf given explicit limits 17881======================================================================= 17882Version: 1.4.25 17883Date: 2004/12/02 4:00 GMT 17884Title: Fix for parallel ON grad 17885Author: Julian Gale <julian@power.curtin.edu.au> 17886 17887The algorithm used in gradient.F to calculate the gradients of the 17888LWF coefficients has been subtly modified. In the previous version 17889it was found that every so often a contribution from one Node to 17890a gradient only present on another node was occuring. This is now 17891avoided by computing the first term in the gradient using globalised 17892versions of bux1/2 & ft/fst. Consequently it is now restricted to 17893only those basis functions in grad for which the local node is 17894responsible. However, bux1 has to be globalised as well as bux2. 17895 17896Files: 17897dhscf.F Call to create mapping of Dscf to DscfL wrapped by check 17898 on number of processors, rather than local number of 17899 orbitals in line with changes for version 1.4.24 17900gradient.F Algorithm modifed as described above 17901version.F90, CHANGES 17902======================================================================= 17903Version: 1.4.24 17904Date: 2004/11/28 12:00 GMT 17905Title: Zero work on nodes fixes 17906Author: Julian Gale <julian@power.curtin.edu.au> 17907 17908A few changes have been made to handle the case where a spatial 17909decomposition is used but there are no orbitals assigned to a 17910given node. 17911 17912Files: 17913denmat.F Trap for nbasisloc = 0 in referencing arrays 17914dfscf.f Local parallel variables set based on number of nodes 17915ordern.F Trap for nbasisloc = 0 in referencing arrays 17916rhoofd.f Local parallel variables set based on number of nodes 17917vmat.f Local parallel variables set based on number of nodes 17918version.F90, CHANGES 17919======================================================================= 17920Version: 1.4.23 17921Date: 2004/11/24 12:00 GMT 17922Title: Increased maxclustersize in diagonalisation 17923Author: Julian Gale <julian@power.curtin.edu.au> 17924 17925The default value of maxclustersize in rdiag/cdiag has been increased 17926from 0 to 12. In the case of degenerate eigenvalue clusters, this will 17927save one call to the diag routines if the number is less than 12. 17928 17929Files: 17930 17931cdiag.F maxclustersize initialised to 12 17932rdiag.F maxclustersize initialised to 12 17933version.F90, CHANGES 17934======================================================================= 17935Version: 1.4.22 17936Date: 2004/11/23 1:00 GMT 17937Title: Fix to setting of neigwanted for spin polarisation 17938Author: Julian Gale <julian@power.curtin.edu.au> 17939 17940Small fix to siesta.F in the setting of neigwanted. Previous 17941version failed for spin polarisation because qtot needed to 17942be replaced by qs(is) in the calculation of neigmin. Check 17943against neigmin moved to last for safety too. 17944 17945Files: 17946 17947siesta.F Setting of neigmin corrected for nspin>1 17948version.F90, CHANGES 17949======================================================================= 17950Version: 1.4.21 17951Date: 2004/11/22 8:40 GMT 17952Title: New spin polarised order N and diagonalisation routines 17953Author: Julian Gale <julian@power.curtin.edu.au> 17954 17955Three major changes and lots of small ones. The key changes are: 17956 17957(A) Matrix diagonalisation: 17958 17959Matrix diagonalisation routines have been rewritten to give greater 17960control over diagonalisation algorithms. Changes include: 17961 17962(1) Option to use expert or simple interface 17963(2) Option to use "all in one" call of diagonaliser or components 17964(3) Parallel divide and conquer added 17965(4) Option for pre- and post- rotation of standard eigensolutions added 17966(5) SIESTA specific lapack calls added to reduce memory usage in 17967 divide and conquer algorithms 17968(6) Work space sizes now set to value that is likely to give the 17969 best performance rather than the minimum 17970(7) Names of control options now pre-fixed with "Diag." 17971(8) Facility for changing algorithm as a function of no. of SCF 17972 cycle included 17973(9) A 2-D decomposition is now the default for scalapack since this 17974 is found to give radically improved scaling in the parallel 17975 performance. 17976 17977(B) Order N: 17978 17979Parallel code has been rewritten based on 0.15 version, with a spatial 17980decomposition strategy. This is based on an approach that minimises 17981communication at the expense of memory by only passing between two 17982nodes once per array during the key order N routines. The routines 17983are designed to be efficient for large problems - i.e. when the size 17984of the interaction range is small compared to region size stored on 17985each node. 17986 17987(C) Spin-polarised order N: 17988 17989Separate Fermi lelvels can now be set for alpha and beta spin so as 17990to perform spin polarised order N. Look forward to double the 17991convergence problems though! 17992 17993Files: 17994 17995Docs/ 17996 17997siesta.tex Modified to reflect the option changes for the 17998 new version. 17999 18000Src/ 18001 18002alloc.F90 Unused variables removed 18003 REPORT_LEVEL now broadcast to all nodes 18004 Output now enable for level 4 case in parallel 18005atmfuncs.f lmxkbfis accessed from module 18006atmparams.f Default value of nsmx now = 2, rather than 1. 18007atomlist.f Size of variable in write statement increased 18008atomlwf.F New order N version with spin polarisation 18009bands.F Reference to dot removed 18010 occtol pased through to diag routines 18011 Unused variables removed 18012cart2frac.f Routine added to convert Cartesian to fractional coordinates 18013 for use in spatial decomposition. 18014cdiag.F Blacs communicators now only setup once 18015 Rewritten to allow access to full (sca)lapack functionality 18016 Parallel divide and conquer added 18017 2-D decomposition added 18018cellxc.F Double precision -> real(dp) 18019 Unused variables removed 18020chkgmx.f Function dot replaced by blas routine ddot 18021cgwf.F New order N version with spin polarisation 18022chempot.F Double precision -> real(dp) + module use onlys added 18023 Order of dense matrix initialise loop swaped for efficiency 18024 Timing calls placed in chempot rather than calling routine 18025chkgmx.f Function dot replaced by blas routine ddot 18026conjgr.f Function dot replaced by blas routine ddot 18027denmat.F New order N version with spin polarisation 18028detover.F Unused variables removed 18029dfscf.f Double precision -> real(dp) 18030 Small modifications of some operations to try to achieve 18031 better performance. 18032dhscf.F Function dot replaced by blas routine ddot 18033 Modifications made for spatial decomposition when nuo = 0 18034 Double precision -> real(dp) 18035 Call to readsp moved to frstme section and results saved 18036 Calls to mesh subroutines - arguments changed 18037diagg.F Handling of small occupancies in DM build revised 18038diagk.F Handling of small occupancies in DM build revised 18039 Calculation of eigenvectors now restricted to the minimum needed 18040diagkp.F Handling of small occupancies in DM build revised 18041 Calculation of eigenvectors now restricted to the minimum needed 18042diag2g.F Handling of small occupancies in DM build revised 18043diag2k.F Handling of small occupancies in DM build revised 18044 Calculation of eigenvectors now restricted to the minimum needed 18045diagg.F Handling of small occupancies in DM build revised 18046diagsprl.F Handling of small occupancies in DM build revised 18047 Calculation of eigenvectors now restricted to the minimum needed 18048 Note that it appeared that twice as many eigenvectors as possible 18049 were being calculated. 18050 calculated previous 18051diagon.F New parameters passed through - iscf & occtol 18052 Call to readsp moved to frstme section and results saved 18053diagpol.f Call to cdiag modified 18054 Memory handling modified 18055 Local array aux removed 18056dsyevds.f Setting of LOPT modified on return from dsytrd 18057efield.F Function dot replaced by blas routine ddot 18058egandd.F New order N version with spin polarisation 18059eggbox.F Unused variables removed 18060ener3.F New order N version with spin polarisation 18061ener3lomem.F Lower memory version of ener3 18062extrapol.F Trapped added for parallel case where nuo is zero 18063extrapolon.F New order N version with spin polarisation 18064fermid.F Unused variables removed 18065fft3d.F MPI sub groups only created on first call 18066fixed.F Function dot replaced by blas routine ddot 18067globalise.F Routine for communication in order N added 18068gradient.F New order N version with spin polarisation 18069grdsam.F Fa / stress removed and order of dealloc improved 18070hsparse.f Calculation of numh & listh separated 18071initdm.F Trap added for parallel case where nuo is zero 18072initparallel.F Routine added to initialise parallel parameters 18073iodm.F Variable declaration made more f90 like 18074iohs.F Unused variables removed 18075iolwf.F New order N version. Only new format files supported 18076iorho.F Variable declarations moved to ifdef MPI block 18077 Unused variables removed 18078kgrid.F Error message for non-normalised weights replaced by 18079 correction of weights. 18080ksv.f Function dot replaced by blas routine ddot 18081ksvinit.f Unused variables removed 18082linpack.F Unused variables removed 18083Makefile New routines added 18084matel.f Double precision -> real(dp) 18085 Unused variables removed 18086 Upper bounds for arrays specified on call to ylmexp to 18087 avoid out of bounds error messages when debugging. 18088memoryinfo.F DiagScale & TryMemoryIncrease removed 18089meshmatrix.F Variable declarations moved to ifdef MPI block 18090meshsubs.F Function dot replaced by blas routine ddot 18091 Unused variables removed 18092minvec.f Function dot replaced by blas routine ddot 18093 Unused variables removed 18094mneighb.f Module version of neighb added for order N 18095m_denchar_neighb.f Function dot replaced by blas routine ddot 18096mulliken.F Minor tidy 18097onmod.F New order N version with spin polarisation 18098on_subs.F New order N version with spin polarisation 18099ordern.F New order N version with spin polarisation 18100outcell.f Double precision -> real(dp) 18101outcoor.f Double precision -> real(dp) 18102overfsm.f Double precision -> real(dp) 18103parallel.f Default blocksize set to 24 18104parallelsubs.f Support for spatial decomposition added 18105pdos.F Unused variables removed, including array aux 18106pdosg.F Call to rdiag modified 18107 Unused variables removed 18108 Memory handling for diagonalisation changed 18109pdosk.F Call to cdiag modified 18110 Unused variables removed 18111 Memory handling for diagonalisation changed 18112phirphi_opt.f Reference to dot removed 18113phonon.F Double precision -> real(dp) 18114plcharge.F Declaration of maxnhg moved to MPI block 18115poison.F Style changed (partly) to resemble rest of code 18116propor.f Convert to lower case style 18117pulayx.F Indenting standardised 18118radfft.f Unused variables removed 18119 Double precision -> real(dp) 18120 Order of memory allocation/deallocation optimised 18121ranger.f Double precision -> real(dp) 18122 Function dot replaced by blas routine ddot 18123rdiag.F 2-D decomposition added 18124 Blacs communicators now only setup once 18125 Rewritten to allow access to full (sca)lapack functionality 18126 Parallel divide and conquer added 18127readsp.F Duplicate definition of 'use parallel' removed 18128redata.F Separate eta values for alpha & beta spin added 18129 Occupancy tolerance made an input parameter 18130 DiagScale & TryMemoryIncrease removed 18131 DiagMemory option -> Diag.Memory for consistency 18132 with new options in cdiag.F / rdiag.F 18133redcel.F Double precision -> real(dp) 18134reoptical.F Unused variables removed 18135rhoofd.f Modifications made for spatial decomposition when nuo = 0 18136rhoofdsp.f Unused variables removed 18137parallelsubs.f Spatial decomposition included 18138propor.f Numbered do loops removed 18139setatomnodes.F Routine added to assign atoms to Nodes 18140setspatial.f Spatial decomposition included 18141shaper.f Double precision -> real(dp) 18142sig.f Double precision -> real(dp) 18143 Unused variables removed 18144siesta.F New parameters passed to diagon / bands 18145 Unused variables removed 18146 Trap on error message for order N / PDOS combination added 18147 so that it is only output if do_pdos is actually true. 18148 Variable neigwanted added to restrict eigenstate computation 18149 for gamma point case. 18150spatial.F Spatial decomposition included 18151spher_harm.f Function dot replaced by blas routine ddot 18152 Referencing of passed arrays in YLMYLM shifted by 1 (Y & 18153 DYDR now start at 0) 18154siesta.F Call to ordern changed & eta now eta(2) 18155 Pressure now output for variable cell optimisation 18156sys.F Unused variables removed 18157transition_rate.F Unused variables removed 18158typecell.f Double precision -> real(dp) 18159uncell.f Routine added for conversion of vectors to cell parameters 18160vmat.f Trap for nuo = 0 added in parallel 18161 Double precision -> real(dp) 18162vmatsp.f Unused variables removed 18163vmb.F Double precision -> real(dp) 18164writewave.F Reference to dot removed 18165 Calls to diag routines modified 18166 Unused variables removed 18167xc.f Double precision -> real(dp) 18168 Unused variables removed 18169zheevds.f Lower memory version of lapack routine zheevd 18170 18171Src/Libs/ 18172 18173lapack.f Routines required for new rdiag/cdiag added 18174======================================================================= 18175Version: 1.4.20 18176Date: 2004/11/19 8:40 GMT 18177Title: Fixed import of symbols from basis_types and basis_specs modules 18178Author: Alberto Garcia <wdpgaara@lg.ehu.es> 18179 18180Files: 18181 Src/initatom.f 18182 gen-basis.F 18183 basis_specs.f : Added "private" clause to basis_specs 18184 and imported symbols explicitly in 18185 initatom and gen-basis. 18186 18187 version.F90: Customary changes. 18188 18189======================================================================= 18190Version: 1.4.19 18191Date: 2004/11/13 15:00 GMT 18192Title: Added pdosxml utility, ps rc table, MPI test files, "only" clauses 18193Author: Alberto Garcia <wdpgaara@lg.ehu.es> 18194 18195Files: 18196 Util/pdosxml/ : Directory containing PDOS file processor 18197 which uses the Fortran XML parser. 18198 18199 Pseudo/atom/Contrib/atom_table.txt: 18200 Table by Jose Luis Martins with suggested 18201 values for the configurations and rc 18202 parameters for pseudopotential generation. 18203 18204 Src/MPI/blacs_prb.f90 18205 pblas_prb.f90 18206 pblas.dat 18207 pi3.F : Files to test the MPI installation, and 18208 the blacs and pblas libraries. 18209 Src/MPI/Makefile : Support for the test files. 18210 Src/MPI/generate.sh: Fix a typo (SV, VS overloads) 18211 18212 Src/atom.f 18213 basis_types.f : Added "only" clauses in import of 18214 basis_types module. 18215 Src/Makefile : Added dependency for sys.o 18216 18217 version.F90: Customary changes. 18218 18219======================================================================= 18220Version: 1.4.18 18221Date: 2004/08/30 11:00 GMT 18222Title: Bug in noncollinear spin input angles, reported by Ivan Runger 18223Author: Jose M. Soler <jose.soler@uam.es> 18224 18225With the noncollinear spin option, the input spin angles were not 18226converted to radians 18227 18228Files: 18229 initdm.F : Factor pi/180 added to angles 18230 version.F90: Customary changes. 18231 18232======================================================================= 18233Version: 1.4.17 18234Date: 2004/07/19 12:00 GMT 18235Title: More code cleanup after optical props import 18236Author: Alberto Garcia <wdpgaara@lg.ehu.es> 18237 18238A number of mostly cosmetic changes were necessary to make the code 18239acceptable by the Intel Compiler. 18240 18241Files: 18242 18243 fermid.F : Changed into a module 18244 18245 Makefile bands.F conjgr.f dfscf.f 18246 diag2g.F diag2k.F diagg.F diagk.F diagkp.F diagsprl.F 18247 diagon.F optical.F phirphi_opt.f rdiag.F 18248 timer.F transition_rate.F writewave.F: Assorted cosmetic changes. 18249 18250 scalapack_extra.f: New file to hold SCALAPACK routines not 18251 in old versions. 18252 Sys/itanium2-mpi.make: Use scalapack_extr 18253 18254 version.F90: Customary changes. 18255 18256======================================================================= 18257Version: 1.4.16 18258Date: 2004/07/14 10:40 18259Title: HighestOccupiedBand fix 18260Author: Julian Gale <julian@power.curtin.edu.au> 18261 18262The setting of the highest occupied orbital has been changed to 18263come from the top downwards to avoid problems with the 18264SingleExcitation option. 18265 18266Files: 18267 18268diagg.F Setting of HighestOccupiedBand changed 18269diagk.F Setting of HighestOccupiedBand changed 18270diagkp.F Setting of HighestOccupiedBand changed 18271 18272+ usual changes to CHANGES, version.F90 18273======================================================================= 18274Version: 1.4.15 18275Date: 2004/07/13 11:30 18276Title: Optical properties & improved gamma point diagonalisation 18277Author: Daniel Sanchez-Portal and 18278 Julian Gale <julian@power.curtin.edu.au> 18279 18280Optical property calculation reintroduced, modified for improved 18281efficiency, and parallelised. It should be noted that while it works 18282in parallel there is scope for improvement of the performance. 18283 18284Arrays Haux, Saux & psi which are dense moved into a new module. 18285 18286Memory requirements for gamma point divide and conquer option reduced 18287by adding SIESTA specific routine that avoids copying. 18288 18289Parallel divide and conquer for gamma point added. 18290 18291Node & Nodes placed in parallel module. 18292 18293Memory accounting made more reliable. 18294 18295Files: 18296 18297In Src/ 18298 18299Makefile New routines & modules added 18300alloc.F90 Subroutine count changed so that memory is always 18301 called to ensure that total memory count is correct. 18302atmfuncs.f rphiatm made public for benefit of phirphi_opt 18303atomlwf.F Node/Nodes now accessed from parallel module 18304bands.F Node/Nodes now accessed from parallel module 18305 Haux, Saux & psi accessed from module 18306broadcast_basis.F Node/Nodes now accessed from parallel module 18307cdiag.F Node/Nodes now accessed from parallel module 18308cellxc.F Node/Nodes now accessed from parallel module 18309cgvc.F Node now accessed from parallel module 18310cgwf.F Node/Nodes now accessed from parallel module 18311chempot.F Node/Nodes now accessed from parallel module 18312chkgmx.F Removed 18313chkgmx.f chkgmx.F but with no need for cpp since Node is 18314 now accessed from parallel module 18315denchar.F Node/Nodes now accessed from parallel module 18316denmat.F Node/Nodes now accessed from parallel module 18317densematrix.f Module containing Haux, Saux & psi added 18318detover.F Node/Nodes now accessed from parallel module 18319dhscf.F Node now accessed from parallel module 18320diagg.F No. of eigenvectors argument added to rdiag call 18321 Node/Nodes now accessed from parallel module 18322diag2g.F Node/Nodes now accessed from parallel module 18323diag2k.F Node/Nodes now accessed from parallel module 18324diagk.F Node/Nodes now accessed from parallel module 18325diagkp.F Node/Nodes now accessed from parallel module 18326diagon.F Arrays Haux, Saux & psi now accessed from module 18327 Node/Nodes now accessed from parallel module 18328diagpol.f Arrays Haux & Saux now passed in 18329diagsprl.F Node/Nodes now accessed from parallel module 18330dipole.F Node/Nodes accessed from parallel module 18331dnaefs.f Call to chkdim removed 18332dsyevds.f Modified version of Lapack routine to save memory 18333dynamics.F Renamed to dynamics.f 18334dynamics.f As per dynamics.F except that Node is accessed from 18335 parallel module & uses module precision 18336efield.F Use of "double precision" replaced by real(dp) 18337 Node/Nodes accessed from parallel module 18338eggbox.F Node now accessed from parallel module 18339egandd.F Node/Nodes accessed from parallel module 18340ener3.F Node/Nodes accessed from parallel module 18341extrapol.F Node/Nodes accessed from parallel module 18342extrapolon.F Node/Nodes accessed from parallel module 18343fermid.F Node/Nodes accessed from parallel module 18344 Precision taken from module 18345fft3d.F Node/Nodes accessed from parallel module 18346fixed.F Node/Nodes accessed from parallel module 18347gauleg.f File removed since it is no longer used 18348gen-basis.F Node/Nodes accessed from parallel module 18349gradient.F Node/Nodes accessed from parallel module 18350grdsam.F Node accessed from parallel module 18351hsparse.f Node/Nodes accessed from parallel module 18352idiag.f Fast return added for case where MOLD is diagonal 18353 already to avoid crash in kgrid 18354initdm.F Node/Nodes accessed from parallel module 18355iodm.F Node/Nodes accessed from parallel module 18356iohs.F Node/Nodes accessed from parallel module 18357iolwf.F Node/Nodes accessed from parallel module 18358ionew.F Node accessed from parallel module 18359iorho.F Node/Nodes accessed from parallel module 18360ioxv.F Node accessed from parallel module 18361kgrid.F Node accessed from parallel module 18362kgridinit.F Cosmetic changes & Node accessed from parallel module 18363kinefsm.f Call to chkdim removed 18364 Node/Nodes accessed from parallel module 18365ksv.F Renamed to ksv.f as cpp now not needed 18366ksv.f As per ksv.F, but Node accessed from parallel module 18367 Arrays Haux, Saux & psi now accessed from module 18368 Size of psi arrays is reduced by a factor of nspin 18369 which is not actually needed. 18370 Output that was in the main routine is now here. 18371listsc.f Redundant reference to external chkdim removed 18372madelung.F Renamed to madelung.f as cpp now not needed 18373madelung.f As per madelung.F, but Node accessed from parallel module 18374memory.F Node/Nodes accessed from parallel module 18375meshmatrix.F Use of "double precision" replaced by real(dp) 18376 Node/Nodes accessed from parallel module 18377meshsubs.F Node/Nodes accessed from parallel module 18378minvec.f Precision now set from module 18379mulliken.F Node/Nodes accessed from parallel module 18380naefs.f Call to chkdim removed 18381nlefsm.f Redundant reference to external chkdim removed 18382 maxna now passed in so that it's size is increased 18383 prior to possible optical calculation 18384 Node/Nodes accessed from parallel module 18385ofc.f Redundant reference to external chkdim removed 18386on_subs.F Node/Nodes accessed from parallel module 18387optical.F Added from version 0.15 & updated 18388 Node/Nodes accessed from parallel module 18389ordern.F Node/Nodes accessed from parallel module 18390overfsm.f Node/Nodes accessed from parallel module 18391parallel.f Node/Nodes placed in module 18392parallelsubs.f Split out of parallel.f to contain subroutines 18393 Default BlockSize increased to 24 18394pdos.F Node/Nodes accessed from parallel module 18395 Arrays Haux, Saux & psi now accessed from module 18396pdosg.F No. of eigenvectors argument added to rdiag call 18397 Node/Nodes accessed from parallel module 18398pdosk.F Node/Nodes accessed from parallel module 18399phirphi.f Use of chkdim removed 18400 Calls to matel now wrapped by check on whether dk is 18401 significant to avoid redundant calculation. 18402 Node/Nodes accessed from parallel module 18403phirphi_opt.f Added from version 0.15 & updated 18404 Calls to matel now wrapped by check on whether dk is 18405 significant to avoid redundant calculation. 18406 Node/Nodes accessed from parallel module 18407phonon.F Reference to chkdim being external removed 18408 Node/Nodes accessed from parallel module 18409plcharge.F Node/Nodes accessed from parallel module 18410poison.F Node/Nodes accessed from parallel module 18411propor.f Precision now set from module 18412pulayx.F Node/Nodes accessed from parallel module 18413radfft.f Redundant reference to external chkdim removed 18414rdiag.F Rewritten version added 18415 Node/Nodes accessed from parallel module 18416readsp.F Node/Nodes now accessed from parallel module 18417redata.F Node/Nodes now accessed from parallel module 18418 Default MemoryFactor reduced to 1.2 18419reinit.F Node/Nodes now accessed from parallel module 18420reoptical.F Added from version 0.15 & updated 18421 Node/Nodes now accessed from parallel module 18422repol.F Use of "double precision" replaced by real(dp) 18423 Node/Nodes now accessed from parallel module 18424savepsi.F Node/Nodes now accessed from parallel module 18425shaper.f Redundant reference to external chkdim removed 18426siesta.F Pointers Haux, Saux & psi nullified 18427 Calls to optical added 18428 Resizing of arrays after nlefsm added if required 18429 based on maxna 18430 Output for KSV now moved into KSV_pol 18431 Node/Nodes accessed from parallel module 18432sys.F Node/Nodes now accessed from parallel module 18433timer.F Node now accessed from parallel module 18434 Made implicit real(dp) rather than double precision 18435transition_rate.F Added from version 0.15 & updated 18436 Node/Nodes accessed from parallel module 18437vmb.F Use of "double precision" replaced by real(dp) 18438 Node/Nodes accessed from parallel module 18439xijorb.f Node/Nodes accessed from parallel module 18440writewave.F Arrays Haux, Saux & psi now accessed from module 18441 Node/Nodes accessed from parallel module 18442 18443In Src/Libs/ 18444 18445lapack.f Extra-routines added for rdiag.F 18446 18447In Util/ 18448 18449optical Directory renamed to Optical for style consistency 18450 18451In Util/Optical 18452 18453README Reinstated from version 0.15 18454input.f Reinstated from version 0.15 18455optical.f Reinstated from version 0.15 18456si.EPSIMG Reinstated from version 0.15 18457 18458In Docs/ 18459 18460siesta.tex Optical option documented 18461CHANGES This documentation added! 18462======================================================================= 18463Version: 1.4.14 18464Date: 2004/06/23 14:30 18465Title: Diag speed up 18466Author: Julian Gale <julian@power.curtin.edu.au> 18467 18468Saving of CPU time in diag*.F by skipping build of density matrix 18469when the band occupancy is less than a small threshold. 18470 18471Files: 18472 18473Src/diag2g.F HighestOccupiedBand pointer added to limit D build 18474Src/diag2k.F HighestOccupiedBand pointer added to limit D build 18475Src/diagg.F HighestOccupiedBand pointer added to limit D build 18476Src/diagk.F HighestOccupiedBand pointer added to limit D build 18477Src/diagkp.F HighestOccupiedBand pointer added to limit D build 18478 Sizes of listhptr/listdptr/numh/numd changed to maxuo 18479Src/diagsprl.F HighestOccupiedBand pointer added to limit D build 18480======================================================================= 18481Version: 1.4.13 18482Date: 2004/06/23 9:30 18483Title: Even more code cleanup 18484Author: Julian Gale <julian@power.curtin.edu.au> 18485 18486Some minor fixes to compilation and other small changes 18487 18488Files: 18489 18490Src/atom.f Check on value of nsemx being exceeded for qPAO added 18491Src/electrostatic.f npairs is now used from atm_types so that the value is 18492 the same on all nodes 18493Src/dfscf.f indxuo now accessed from module 18494Src/dhscf.F First dimension of DVxcdn made equal to ntpl for 18495 correct bounds checking in cellxc.F even though 18496 never referenced 18497 indxuo no longer passed through 18498Src/grdsam.F indxuo no longer passed through 18499Src/meshmatrix.F indxuo now accessed from module 18500Src/parallel.f Default blocksize increased to 16 18501Src/rhooda.f indxuo now accessed from module 18502Src/rhoofd.f indxuo now accessed from module 18503Src/rhoofdsp.f indxuo now accessed from module 18504Src/siesta.F ifdef NODAT wrapping of mpi_siesta use statement 18505 added to select correct quantity for using 18506 indxuo no longer passed to grdsam & dhscf 18507Src/vmat.f indxuo now accessed from module 18508Src/vmatsp.f indxuo now accessed from module 18509======================================================================= 18510Version: 1.4.12 18511Date: 2004/06/10 21:00 18512Title: More code cleanup 18513Author: Alberto Garcia <wdpgaara@lg.ehu.es> 18514 18515* Declaration of variables in some files. 18516 (implicit statements for real variables remain...) 18517 18518File siesta/Src/dot.f 18519File siesta/Src/electrostatic.f 18520File siesta/Src/fermid.F 18521File siesta/Src/idiag.f 18522File siesta/Src/linpack.F 18523File siesta/Src/paste.f 18524File siesta/Src/poison.F 18525File siesta/Src/pseudopotential.f 18526File siesta/Src/ranger.f 18527File siesta/Src/reclat.f 18528File siesta/Src/timer.F 18529File siesta/Src/xc.f 18530 18531* Some changes to the MPI compilation setup. File mpif2sane.f90 intended 18532 to replace the direct inclusion of mpif.h in the future. 18533 18534File siesta/Src/MPI/Makefile (new symbol for NAG compiler) 18535File siesta/Src/MPI/mpi.F (remove some mpi_2XX symbols) 18536File siesta/Src/MPI/mpi__include.f90 ( " ) 18537File siesta/Src/MPI/mpif2sane.f90 is new. 18538File siesta/Src/Sys/macosx-nag-mpi.make is new. 18539 18540======================================================================= 18541Version: 1.4.11 18542Date: 2004/06/08 12:00 18543Title: Use of accessibility clauses to help compilers + cleanup 18544Author: Alberto Garcia <wdpgaara@lg.ehu.es> 18545 18546* Some compilers (notably Intel's) have trouble compiling certain 18547sections of the code, probably because of limitations in their 18548namespace-handling internal structures in some versions. To help 18549them, and also as a matter of good programming practice, it is 18550advisable to follow these basic guidelines: 18551 185521. Make all modules "private" by default. Public entities should be 18553given the "public" attribute explicitly. This prevents the leaking of 18554symbols from other used modules. 185552. Use the "only:" qualifier to import symbols from modules. This is 18556particularly necessary for program units which use a lot of modules, such 18557as siesta.F itself. 18558 18559Files changed: 18560 18561 Src: pdos.F redata.F siesta.F cdiag.F rdiag.F 18562 atmfuncs.f old_atmfuncs.f basis_types.f atm_types.f 18563 atom.f transfer.f ionew.F initatom.f atomlist.f 18564 dfscf.f rhoofd.f rhoofdsp.f vmat.f vmatsp.f 18565 18566 Src/MPI: mpi.F mpi__include.f90 (removed mpi.f90) 18567 18568* On_subs has been turned into a module. 18569 18570 Src: on_subs.F egandd.F 18571 18572* The calculation of the electrostatic correction tables has been moved out 18573 of the basis-generation modules and placed in a new one (electrostatic.f). 18574 Gen-basis and the rest of the basis-generation code are now more decoupled 18575 from the rest of the program, and a number of duplicate routines have 18576 been removed. The module old_atmfuncs.f has been streamlined, with the 18577 removal of a number of obsolete routines and data structures. 18578 18579Files: 18580 18581 Src: old_atmfuncs.f atom.f transfer.f initatom.f gen-basis.F 18582 Makefile basis_io.F 18583 18584* Fixed MPI/Makefile to make the NODAT option pass through for the 18585 compilation of the MPI modules. 18586 18587 Src/MPI/Makefile 18588 18589* New directory Src/wxml for XML-writing modules. The new code is being 18590 progressively integrated into Siesta. 18591 18592 Files: 18593 Src: pdos.F (some new calls, and extra file) 18594 Makefile (support for wxml) 18595 18596 Src/wxml: New directory 18597 18598 (Developers: use "-d" flag to cvs update to pick up the new directory) 18599 18600* Removal of unused symbols, declaration of implicitly-typed variables, 18601 use of standard kinds for real variables (some files only) 18602 18603 Src: chkgmx.F bessph.f pseudopotential.f atm_types.f basis_types.f 18604 atom.f transfer.f basis_io.F 18605 18606* Tab removal and other cosmetic changes: 18607 18608 Src: iopipes.F90 chempot.F fermid.F alloc.F90 matel.f meshsubs.F 18609 neighb.f ranger.f ran3.f overfsm.f 18610 18611* Wrapping of MPI I/O (Julian Gale): 18612 18613 Src: diagon.F (spiral case was not wrapped) 18614 18615* Change in deallocation order (Julian Gale): 18616 18617 Src: rhoofd.f vmat.f 18618 18619* In timer.F, the call to the CPUTIM routine has been eliminated in favor 18620 of the f95 standard cpu_time. A new file "cpu_time.f90" has been added 18621 for compilers which are not f95-compliant (PGI). Current SYS symbols 18622 in .make files are redundant but harmless. 18623 18624 Files: Src: timer.F cpu_time.f90 (new file) 18625 Src/Sys: pgf90*.make (use cpu_time in SYS) 18626 18627* New .make files for compilation on a new machine with itanium2 processors 18628 and myrinet networking (using Intel's 7.1 compiler) 18629 18630 Files: Src/Sys: itanium2.make itanium2-mpi.make 18631 18632* Pseudo/atom/Tutorial: 18633 scripts ae.sh, pg.sh, and pt.sh made more robust. 18634 New file subps.gps for shell interoperability. 18635 18636 version.F90 : Customary changes 18637 Docs/CHANGES : Customary changes 18638 18639======================================================================== 18640Description: New .make and SYS files to support IBM's pessl library 18641Version: 1.4.10 18642Date: 2004/02/04 16:00 18643Title: Support for pessl on IBM machines 18644Author: Alberto Garcia <wdpgaara@lg.ehu.es> 18645 18646Description: New .make and SYS files to support IBM's pessl library 18647 18648Files: 18649 18650 Src/Sys/ibm-regatta-p4.make: New file 18651 Src/ibm_pessl.f : New file with extra code 18652 version.F90 : Customary changes 18653 Docs/CHANGES : Customary changes 18654 18655======================================================================= 18656Version: 1.4.9 18657Date: 2004/02/01 18:00 18658Title: Miscellaneous fixes for portability 18659Author: Alberto Garcia <wdpgaara@lg.ehu.es> 18660 18661Description: Consolidation of various fixes for portability. 18662 18663Files: 18664 18665Src/basis_types.f : use kind(dp) instead of real*8 18666Src/iodm.F : use ionew 18667Src/pseudopotential.f : use ionew 18668Src/pdos.F : Remove unused variables, arguments, and functions. 18669Src/siesta.F : Remove unused arguments in call to pdos. 18670 Remove hollerith constructs. 18671Src/periodic_table.f : Make mass data real, instead of double precision. 18672Src/xlf.f : New file for IBM-XL support (flush routine) 18673Src/f2kcli.F90 : New file for command-line argument parsing. 18674Src/iopipes.F90 : Add conditional block for NAG compilation. 18675 18676Src/Makefile : Remove f2kcli from gen-basis and siesta (mpich problems) 18677Src/gen-basis.F : Remove f2kcli code. 18678 18679Src/denchar.F 18680 m_denchar_geom.f 18681 m_denchar_init.F 18682 m_denchar_io.F 18683 m_denchar_neighb.f 18684 m_denchar_work.f : New files for denchar in top directory. 18685Util/Denchar/Docs/denchar.tex: Manual for denchar updated. 18686Util/Denchar/Docs/CHANGES : Updated to reflect change in code location. 18687Util/Denchar/Src/Makefile : Disabled. 18688 18689Util/Contour/grid2d.f : float to dble. Open statements changed. 18690Util/PyAtom: shape.sh : extracts cell shape data from output file. 18691 18692 18693Src/NetCDF/Makefile: add default line. Add FFLAGS_NETCDF symbol. 18694Src/Libs/makefile : do not include machine.o in dc_lapack.a 18695Src/Sys/pgf90.make : Add dc_lapack.a to COMP_LIBS. Tab for atom.o. CDF optional 18696Src/Sys/pgf90-mpich.make : As above plus some documentation on MPI stuff 18697Src/Sys/macosx-xlf.make 18698Src/Sys/macosx-nag.make : New files for MacOS X support. 18699Src/Sys/nag-darwin-nolibs.make : Removed. Obsolete 18700 18701Util/PyAtom/local.biggles.py: change Vlocal to Reduced_vlocal. 18702 18703======================================================================= 18704Version: 1.4.8 18705Date: 2004/01/26 16:00 18706Title: Fixes in inver, pulay, fermispin, plstm. 18707Author: Pablo Ordejon <ordejon@icmab.es> 18708 18709Description: Fixes to correct bugs and/or improve the stability 18710 of the inversion routines, the Pulay mixing and the fixed 18711 spin calculations. These fixes correct the degradation 18712 of performance of selfconsistency convergence 18713 of Siesta 1.3 compared to 1.2. 18714 Small change on utility plstm.f to avoid problems 18715 in some compilers. 18716 18717Files: 18718 cgwf.F : New interface with inver 18719 dynamics.F : New interface with inver 18720 diagg.F : Corrects call to fermispin 18721 diagk.F : Corrects call to fermispin 18722 diagkp.F : Corrects call to fermispin 18723 fermid.F : Now contains fermispin subroutine; 18724 fermispin now calculates and returns entropy. 18725 fermispin.F : Elliminated; content included now in fermid.F 18726 inver.f : New interface, returns error message if 18727 unsuccessful execution 18728 pulayx.F : New interface with inver; corrected stability 18729 version.F90 : Customary changes 18730 Makefile : Elliminated reference to fermispin.F 18731 Docs/CHANGES : Customary changes 18732 Util/plstm.f : Changed input flags 18733 18734======================================================================= 18735Version: 1.4.7 18736Date: 2004/01/22 17:00 18737Title: Bug in normalization of DOS 18738Author: Javier Junquera <jjunquer@physics.rutgers.edu> 18739 18740Description: The Density Of States was divided twice by the number 18741 of k-points. This bug is present since version 1.2.41. 18742 18743Files: 18744 pdosk.F : The number of k-points, NK, has dropped 18745 from the normalization factor, NORM 18746 version.F90 : Customary changes 18747 Docs/CHANGES : Customary changes 18748 18749======================================================================= 18750Version: 1.4.6 18751Date: 2004/01/19 16:30 18752Title: Siesta as a subroutine 18753Author: Jose M. Soler <jose.soler@uam.es> 18754 18755Description: A new utility routine module that can be used by external 18756 programs to communicate with siesta processes (running separatedly) 18757 to send coordinates and receive forces, as if siesta were a 18758 conventional force-field subroutine. 18759 18760Files: 18761 iopipes.F90 : New module with the routines to communicate with the 18762 user's driver program through Unix pipes 18763 redata.F : Accepts new option MD.TypeOfRun=forces 18764 reinit.F : Appends a number to file INPUT_TMP 18765 siesta.F : Calls to the communication routines added 18766 Makefile : Added file iopipes.o 18767 Util/SiestaSubroutine : New directory. Contains the module fsiesta, 18768 with the routines to be called by the user's 18769 program, and the subdirectory FmixMD with an 18770 example. See its file README for details. 18771 Docs/siesta.tex : Explains the new option MD.TypeOfRun=forces 18772 18773======================================================================= 18774Version: 1.4.5 18775Date: 2003/12/05 13:45 18776Title: Bug fix (initdm) 18777Author: Jose M. Soler <jose.soler@uam.es> 18778 18779Description: 18780 A small denominator has been added to avoid a division by zero when 18781one tries to polarize a closed-shell atom. A warning has also been 18782added for this case. 18783 18784Files: 18785 initdm.F: small denominator and warning added 18786 18787======================================================================= 18788Version: 1.4.4 18789Date: 2003/11/18 19:00 18790Title: Bug fix (initwave) 18791Author: Javier Junquera <jjunquer@physics.rutgers.edu> 18792 18793Description: 18794 Two allocatables variables were incorrectly deallocated 18795 18796Files: 18797 writewave.F: inquiry for the status of values and integs before deallocate 18798 18799======================================================================= 18800Version: 1.4.3 18801Date: 2003/11/07 17:00 18802Title: Bug fix (Plrho) 18803Author: Jose M. Soler <jose.soler@uam.es> 18804 18805Description: 18806 An index was incorrectly initialized, causing problems in spin 18807polarized systems 18808 18809Files: 18810 Util/Plrho/iorho.f : Instruction ind=0 moved inside spin loops 18811 18812======================================================================= 18813Version: 1.4.2 18814Date: 2003/11/05 17:30 18815Title: Bux fix (initwave) 18816Author: Javier Junquera <jjunquer@physics.rutgers.edu> 18817 18818Description: 18819 18820 A memory problem, that appeared when more than 4 values were 18821 introduced in each line of the block WaveFuncKPoints, has been fixed. 18822 The variables values and integs in the subroutine initwave 18823 (module writewave) have been redefined as allocatable. 18824 18825Files: 18826 writewave.F : variables values and integs defined as allocatable 18827 version.F90, CHANGES : Customary changes 18828 siesta.tex : Change of affiliation 18829 18830======================================================================= 18831Version: 1.4.1 18832Date: 2003/09/10 18:30 18833Title: version.F --> version.F90 18834Author: Alberto Garcia <wdpgaara@lg.ehu.es> 18835 18836Description: 18837 18838Rewrite version.F as a free-format f90 file (and thus change the 18839extension to .F90). Modify Makefile accordingly. 18840 18841Files: 18842 version.F : removed 18843 version.F90 : new file 18844 Makefile : updated to reflect new .F90 extensions. 18845 18846======================================================================= 18847Version: 1.4.0 18848Date: 2003/07/30 20:45 18849Title: This is 1.4.0 in main trunk 18850Author: Emilio Artacho <emilio@esc.cam.ac.uk> 18851 18852Description: 18853 This is 1.4.0 in main trunk. Any revision on 1.3 should be 18854done in the 1.3 branch as well as on this trunk 18855 18856Files: 18857 build_serial and build_parallel (remove Tests) 18858 siesta.tex: removed reference to msiesta in constr.f 18859 version.F CHANGES siesta.ind 18860======================================================================= 18861Version: 1.3 and 1.4.0 not yet 18862Date: 2003/07/19 19:15 18863Title: Pre Tagging and branching 1.3 and 1.4.0: Miscellanea 18864Author: Emilio Artacho <emilio@esc.cam.ac.uk> 18865 18866Description: 18867 Some pre-branching changes: Mesh cutoff to 100Ry default; 18868 Makefile to show contents of FFLAGS etc in output; 18869 Manual: index entry for geometry constraints + warning about XV 18870 for supercell. 18871 18872Files: 18873 Makefile, redata.F, siesta.tex, siesta.ind, version.F, CHANGES 18874======================================================================= 18875Version: 1.3 not yet 18876Date: 2003/07/23 14:15 18877Title: Minor bug corrections 18878Author: Pablo Ordejon <ordejon@icmab.es> 18879 18880Description: 18881 A minor bug in the parallel execution in writewave.F has 18882been fixed. Two bugs in the output of Denchar have been 18883fixed. 18884 18885Files: 18886 Src/writewave.f: Parallel execution bug corrected 18887 Util/Denchar/Src/wrout.F: Bug in writting of output corrected 18888 Util/Denchar/Src/itochar.F: Bug in writting of output corrected 18889 Util/Denchar/Docs/denchar.tex, CHANGES: Customary changes 18890 siesta.tex, CHANGES, version.F, release_notes_1.3: Customary changes 18891======================================================================= 18892Version: 1.3 and 1.4.0 not yet 18893Date: 2003/07/19 19:15 18894Title: Pre Tagging and branching 1.3 and 1.4.0 18895Author: Emilio Artacho <emilio@esc.cam.ac.uk> 18896 18897Description: 18898 The 1.3 package was to be defined at this stage. 18899But not yet, since Examples have to be updated with 1.3 and a few 18900last minute things popped up. Later, it will be tagged 18901and a branch opened for bug corrections of 1.3 (new versions 18902with fixes will be produced and distributed when/if needed) while 18903the main branch trunk becomes 1.4.0 for further development. 18904 18905Files: 18906 CHANGES, siesta.tex, version.F 18907======================================================================= 18908Version: 1.2.45 18909Date: 2003/07/17 22:00 18910Title: Slight change in Makefile 18911Author: Emilio Artacho <emilio@esc.cam.ac.uk> 18912 18913Description: 18914 The Makefile has been slightly changes to avoid problems with 18915the sed processing from version.F to temp.F and temp0.F 18916 18917Files: 18918 Makefile + customary (Licence files added). 18919======================================================================= 18920Version: 1.2.44 18921Date: 2003/07/15 14:00 18922Title: Parallel eggbox 18923Author: Julian Gale <j.gale@imperial.ac.uk> 18924 18925Description: 18926 18927The eggbox routine was tripping up parallel execution of the code 18928and so this has been handled. 18929 18930Files: 18931 18932diagon.F : Order of memory deallocation reversed to be stack friendly 18933eggbox.F : Calls to fdf are now handled in parallel and data is 18934 : broadcast where necessary 18935siesta.F : First call to eggbox is now for all processors 18936version.F & CHANGES 18937======================================================================= 18938Version: 1.2.43 18939Date: 2003/07/14 1:30 18940Title: Fixed fermid 18941Author: Julian Gale <j.gale@imperial.ac.uk> 18942 18943Description: 18944 18945The routine fermid.F has been bug fixed. The variable NH was not 18946broadcast when read in parallel and not explicitly saved between 18947calls. Also the ocf string was set to two different defaults in 18948STEPF vs ENPY, which has been standardised. 18949 18950Files: 18951fermid.F : Changes as listed above. 18952version.F and CHANGES 18953======================================================================= 18954Version: 1.2.42 18955Date: 2003/07/11 11:00 18956Title: Berry phase continuity for polarization calculation 18957Author: Daniel Sanchez-Portal 18958 18959Description: 18960 18961The Berry phase is obtained as a surface integral (in reciprocal 18962space) of a so-called quantum phase. 18963When evaluating the integrand we have an arbitrariness of 2pin 18964in each point of the 2D mesh. This arbitrariness has 18965to be eliminated by enforcing the continuity of the integrand. 18966A few code lines have been added to subroutine ksv.F in order 18967to ensure this continuity. 18968 18969Files: 18970ksv.F : few lines of code added and new array phaseold(2) 18971version.F and CHANGES 18972======================================================================= 18973Version: 1.2.41 18974Date: 2003/07/09 11:30 18975Title: Parallel PDOS, gamma point and K point weighting 18976Author: Julian Gale <j.gale@imperial.ac.uk> 18977 18978Description: 18979 18980The PDOS option has been extended to allow for the gamma point, 18981K point weighting and parallel execution. 18982 18983Files: 18984 18985Makefile : pdosg.F added 18986pdos.f : renamed to pdos.F 18987pdos.F : modified version of pdos.f to handle parallel execution 18988pdosg.F : routine for PDOS calculation at gamma point added 18989pdosk.f : renamed to pdosk.F 18990pdosk.F : modified version of pdosk.f to handle parallel execution 18991siesta.F : Parallel call to pdos now allowed and variables broadcasted 18992siesta.tex : Comment on order-N in parallel added 18993version.F and CHANGES 18994======================================================================= 18995Version: 1.2.40 18996Date: 2003/07/02 19:30 18997Title: renaming of module mpi to mpi_siesta 18998Author: Emilio Artacho <emilio@esc.cam.ac.uk> 18999 19000Description: 19001 19002Renaming of module mpi to mpi_siesta to avoid name clashes 19003 19004Files: 19005 19006alloc.F90, *.F 19007version.F and siesta.tex and CHANGES 19008======================================================================= 19009Version: 1.2.39 19010Date: 2003/06/30 19:00 19011Title: renaming of realloc and dealloc to re_alloc and de_alloc 19012Author: Emilio Artacho <emilio@esc.cam.ac.uk> 19013 19014Description: 19015 19016Renaming of realloc and dealloc to re_alloc and de_alloc 19017to avoid problems with some (not so standard but important) 19018compilers. 19019 19020Files: 19021 19022alloc.F90, siesta.F, atomlist.f, on_subs.F, 19023cdiag.F, rdiag.F, coor.f, dfscf.f, matel.f, 19024version.F and siesta.tex and CHANGES 19025======================================================================= 19026Version: 1.2.38 19027Date: 2003/06/30 18:00 19028Title: Small bug in siesta.F 19029Author: Pablo Ordejon <ordejon@icmab,es> 19030 19031Description: 19032 19033A small bug in siesta.F that showed up in alpha machines has 19034been corrected, about the handling of undefined wfk. 19035 19036Files: 19037 19038siesta.F 19039Customary version.F siesta.tex CHANGES 19040======================================================================= 19041Version: 1.2.37 19042Date: 2003/06/30 15:35 19043Title: Update of Util: README and inclusion og grid1d + release.notes 19044Author: Emilio Artacho <emilio@esc.cam.ac.uk> 19045 19046Description: 19047 19048Grid1d utility added (very simple extracting of 1D information from 19049anthing in the 3D grid in the RHO format). It interpolates. 19050Update in Util/README and in release.notes_1.3 19051 19052Files: 19053 19054Util/ grid1d.f grid1d-raw.in grid1d-noraw.in README 19055Docs/ release.notes_1.3 19056Customary version.F siesta.tex CHANGES 19057======================================================================= 19058Version: 1.2.36 19059Date: 2003/06/30 13:15 19060Title: Corrected parallel Mulliken for iopt = 3 19061Author: Julian Gale <j.gale@imperial.ac.uk> 19062 19063Description: 19064 19065The use of Mulliken level 3 in parallel was causing the code to print 19066out incorrect results and hang. This was due to referencing of the 19067local number of basis functions where the global number should be used. 19068This is now fixed so that the serial and parallel results should be 19069congruent for this option. 19070 19071Files: 19072 19073mulliken.F : nbasistot now passed in instead of nbasis (global vs 19074 : local). nbasis (local) is computed locally and the 19075 : iopt = 3 code has been corrected to ensure that the 19076 : orbitals are printed in the global order 19077siesta.F : no_u passed to mulliken instead of no_l 19078version.F, CHANGES : customary changes 19079======================================================================= 19080Version: 1.2.35 19081Date: 2003/06/30 12:00 19082Title: Write Wavefunctions capability, bug corrections and new utils 19083Author: Pablo Ordejon <ordejon@icmab.es> 19084 19085Description: 19086 190871) The capability to write wavefunctions coefficients of selected 19088 wavefunctions at selected k-points has been implemented. 19089 Dumps the coefficients to a binary file (a utility program 19090 to convert it to readable form is also provided in Util), 19091 and also to the main output if desired. 19092 Note that a new logical variable (getPSI) has been 19093 included in the interface of diagg and diagk, so that they 19094 calculated the wavefunctions that the user wishes to print. 19095 190962) Several bugs (mainly in parallel mode runs) are corrected 19097 190983) Three new utility programs are included 19099 19100Files: 19101/Docs 19102 siesta.tex : customary changes; explanation of utility to write wfs 19103 siesta.ind : customary changes 19104 CHANGES : customary changes 19105/Src 19106 bands.F : comply to new interface of diagg and diagk; 19107 bug (intr. in 1.2.31) corrected in call to diag routines 19108 diagg.F : capability to write wfs; new logical flag in interface 19109 diagk.F : capability to write wfs; new logical flag in interface 19110 diagon.F : capability to write wfs to file 19111 fermid.F : parallel mode bug fix 19112 inver.f : augmented for robustness in case LAPACK fails 19113 Makefile : miscellaneous changes 19114 pulayx.F : augmented for robustness in case residual is exacly null 19115 siesta.F : changes for capability to write wavefunctions 19116 version.F : customary changes 19117 vmb.F : parallel mode bug fix 19118 writewave.F: new: module that handles the wfs writting 19119/Util 19120 README : update list of utility programs 19121 grid2cube.f: new: converts siesta grid files to Gaussian Cube format 19122 pltstm.f : new: a simple program to simulate STM images 19123 readwf.f : new: utility to read wfs file to user-friendly format 19124======================================================================= 19125Version: 1.2.34 19126Date: 2003/06/30 9:00 19127Title: Correction in order-N - C save 19128Author: Julian D. Gale <j.gale@ic.ac.uk> 19129 19130Description: 19131 19132The contents of the C array is now preserved when reallocating after 19133the call to cspa since this is not read again. 19134 19135Files: 19136 19137ordern.F : Contents of C copied to rtmp2 and back again after realloc 19138version.F, CHANGES : customary changes 19139======================================================================= 19140Version: 1.2.33 19141Date: 2003/06/26 16:20 UTC 19142Title: Portability bug fixes and enhancements 19143Author: Alberto Garcia <wdpgaara@lg.ehu.es> 19144 19145Description: 19146 19147A number of fixes related to portability problems: 19148 19149* Handling of array shapes in radfft. Related: explicit interface 19150for ordern and hsparse routines. 19151 19152* Bug fix in new fermid.F routines. 19153 19154* Initialization bug fix in on_subs.F. 19155 19156* Support for systems without the LAPACK 'divide and conquer' routines 19157in their system libraries. 19158 19159* Warning for MPI data type codes. 19160 19161* Improved compilation in subdirectories. 19162 19163* Apparently cosmetic changes intended for the NAG compiler. 19164 19165 19166Files: 19167 19168ordern.F, hsparse.f : Now wrapped in modules m_ordern and m_hsparse, 19169 respectively. No file name change. 19170interfaces.f : Removed. 19171siesta.F : Now 'use's m_ordern and m_hsparse. 19172 Initialization of two logical variables. 19173 19174radfft.f : Now wrapped in module m_radfft. 19175 No file name change. 19176matel.f, atom.f, 19177basis_io.F : Now 'use' m_radfft. 19178 19179atom.f : Cosmetic changes, and simplification of ghost 19180 signals. 19181 19182Makefile : Support for new module dependencies. 19183 Better handling of compilation in subdirectories, 19184 in particular ranlib handling. 19185 19186fermid.F : variable ocupfncft now saved. 19187on_subs.F : ncmax initialized before its use. 19188poison.F : (cosmetic?) modulo instead of mod 19189inver.f : (cosmetic?) reversed declaration order. 19190 19191(these changes committed at an earlier date:) 19192Libs/ : 19193lapack.f, dc_lapack.f : Split divide and conquer routines. 19194makefile : Better logic for support of 'dc'-less systems. 19195 19196MPI/ : 19197Makefile : Warning about kind numbers. 19198 19199Sys/ : 19200.make files : Explicit RANLIB macro. 19201 Alpha files might require dc_lapack split. 19202README : Explain dc_lapack issue. 19203lahey-nolibs.make 19204pgf90-nolibs.make : New files. 19205nag-darwin-nolibs-make: NAG MacOSX macros (some hfs issues) 19206 19207version.F, CHANGES : customary changes 19208======================================================================= 19209Version: 1.2.32 19210Date: 2003/06/23 16:00 19211Title: Correction in order-N + PDOS in manual 19212Author: Julian D. Gale <j.gale@ic.ac.uk> 19213 19214Description: 19215 19216Two small corrections have been made. The first fixes an out of bounds 19217error that can occur when restarting an order-N calculation and the 19218second is the removal of the limitations for PDOS from the text in the 19219manual to reflect recent modifications. 19220 19221Files: 19222ordern.F : maxnc is now the larger of ncmax and maxnc after 19223 reallocation to ensure that passed first dimension is 19224 correct for listc/listcold 19225siesta.tex : Text concerning PDOS updated 19226version.F, CHANGES, siesta.tex, siesta.ind: customary changes 19227======================================================================= 19228Version: 1.2.31 19229Date: 2003/06/23 12:00 19230Title: Methfessel-Paxton smearing function 19231Author: Pablo Ordejon <ordejon@icmab.es> 19232 19233Description: 19234 19235 The smearing function scheme of Methfessel and Paxton has been 19236implemented. For metals, it allows for a much better convergence 19237to the ground state properties even with large smearing temperatures. 19238Improved convergence to self-consistency and k-points is also 19239achieved. 19240 A few changes have been made in the old Fermi-Dirac function, too. 19241In particular, the old function stepf included a factor 2 that 19242has been removed (to make the definition of the Fermi-Dirac 19243and Methfessel-Paxton functions correspond to the usual ones), 19244and added elsewhere. Therefore, the diagonalization 19245routines have been updated accordingly. 19246 Also, the calculation of the entropy has been removed from siesta.F, 19247because in the Methfessel-Paxton scheme this term depends 19248on the eigenvalues, which are not available in the main program. 19249The calculation of the entropy is done now in fermid.F, and 19250passed to siesta.F through the diagonalization routines. 19251 19252Files: 19253siesta.F : changes to remove entropy and calculation 19254diag2g.F, diag2k.F, diagg.F, diagk.F, diagkp.F, diagon.F, diagsprl.F: 19255 changed to pass Entropy to siesta.F, and redefined stepf 19256fermid.F : Methfessel-Paxton included; redefined stepf 19257fermispin.F : redefined stepf 19258version.F, CHANGES, siesta.tex, siesta.ind: customary changes 19259======================================================================= 19260Version: 1.2.30 19261Date: 2003/06/23 11:45 19262Title: Miscellaneous corrections 19263Author: Pablo Ordejon <ordejon@icmab.es> 19264 19265Description: 19266 19267 Several corrections have been made (thanks to those who reported the 19268problems): 19269 192701) Maxwell-Boltzmann initial velocities were not obbeying the constraints 19271 imposed in fixed.F (problem reported by Masaya Ishida). This has now 19272 been fixed, so that dynamics runs do obbey the constraints. 192732) A correction in the dynamics routines has been made to account for the 19274 number of imposed constraints in the definition of the temperature. 19275 As a consequence, a new variable has been included in the argument list 19276 of constr.f to output the number of constraints imposed by the user. 192773) The example of the constr.f provided to make the relative height of two 19278 atoms constant, only worked for the case of two atoms with the same mass. 19279 I have rewriten it for the general case of two different masses, and 19280 changed the example in the manual and the fixed.F routine accordingly. 192814) Some changes in the initiallization of the MD variables, to make the start 19282 of the run more in accord with the imposed initial velocities. 192835) The inver.f90 routine provided by William Mattson has been removed, 19284 because it caused some problems in handling nonorthogonal cells, in the 19285 variable cell dynamics (problem reported by Benoit Braida). I have written 19286 a new inver.f code that used LAPACK routines to invert a matrix. All the 19287 calls to the old inver2 and the old inver.f90 routines are now re-directed 19288 to the new inver. The appropriate LAPACK routines that were not included in 19289 Libs/lapack.f have been included. 192906) The fdf reading of the Divide-and-Conquer option is now only done in the 19291 first call to the diagonalization routines, to avoid huge out.fdf files 19292 when a large number of k-points is used. 192937) A recent change in matel.f made by A. Garcia to avoid problems with the 19294 NAG compiled have been reverted, since it causes problems in other 19295 compilers. This still needs to be worked out!! 192968) A bug in mulliken.F that caused the overlap population matrix between atoms 19297 not to be symmetric when k-points were used (pointed out by P. Alemany) has 19298 been corrected. 192999) A small bug (found by S. Reich) in vibrator.F has been corrected. Besides, 19300 fdbuild.F has been slightly changed to include more significant digits in 19301 the output. Finally, some input files and updated output files have been 19302 provided so that the user can reproduce the examples of Vibra. 19303 19304 19305Files: 19306/Docs 19307 siesta.tex : customary changes; explanation of new interface of constr.f 19308 and correction to example case 19309 CHANGES : changes as customary 19310/Src 19311 cdiag.F : read fdf option D&C only fisrt time 19312 cgwf.F : call to new inver routine 19313 constr.F : interface with new output variable ntcon 19314 dynamics.F : miscellaneous: temp. definition with constraints; 19315 new init. of some dynamics 19316 fixed.F : new interface with constr.f; define tot. nr. of constraints; 19317 correct example case 19318 inver.f : new file - new inversion routine 19319 inver.f90 : removed 19320 matel.f : recent change by A. Garcia reverted 19321 mulliken.F : bug corrected: lines 219 and 226 19322 pulayx.F : call to new inversion routine; comment invert2 (not used now) 19323 rdiag.F : read fdf option D&C only fisrt time 19324 siesta.F : misc. changes in calls to dynamics and constraint routines 19325 version.F : customary changes 19326 vmb.F : changes to account for constraints in definig initial velocities 19327/Src/Include 19328 constr.f : interface with new output variable ntcon 19329/Src/Libs 19330 lapack.f : routines necessary to invert matrices included 19331/Util/Vibra 19332 README : update email address 19333/Util/Vibra/Docs 19334 CHANGES : new file; records changes in Vibra package 19335 vibra.tex : some changes in user guide 19336/Util/Vibra/Examples 19337 README : new file; explanation to run examples 19338 si2.bands : updated output file 19339 si2.FC : updated output file 19340 si2.fdf : updated input file 19341 si2-siesta : new file; input for Siesta, necessary to reproduce example 19342 si2.vectors: updated output file 19343 si54.bands : updated output file 19344 si54.FC : updated output file 19345 si54-siesta: new file; input for Siesta, necessary to reproduce example 19346 Si.inp : new file; input for Siesta, necessary to reproduce example 19347/Util/Vibra/Vibra 19348 fcbuild.f : increase number of digits in the output of atomic coords 19349 vibrator.f : bug fix 19350======================================================================= 19351Version: 1.2.29 19352Date: 2003/06/06 18:15 19353Title: Two small bugs 19354Author: Jose M. Soler <jose.soler@uam.es> 19355 19356Description: 19357 Some arrays were not allocated in the rare case that there was a 19358single basis orbital in the whole system. Also, the dimension of the 19359input array in routine four1 was incorrect. 19360 19361Files: 19362 siesta.F : corrected use of dimension maxnh 19363 recipes.f : dimension of array DATA increased from NN to 2*NN 19364======================================================================= 19365Version: 1.2.28 19366Date: 2003/06/05 23:30 19367Title: Eggbox correction (by Tom Archer) plus cosmetics 19368Author: Emilio Artacho <emilio@esc.cam.ac.uk> 19369 19370Description: 19371 A possibility for eggbox correction is included assuming atom additivity 19372and species dependent components, by which various fourier components 19373for the eggbox of isolated atoms of each species are given to Siesta 19374and Siesta substracts it from energy and forces. 19375 A little output cosmetics has been introduced as well 19376 19377Files: 19378 eggbox.F : new 19379 siesta.F, Makefile: to call eggbox 19380 coor.f, atom.f, reinit.F, basis_types.f, memory.f, 19381 atomlist.f, initatom.f, redata.f and siesta.F : changes only in writes 19382 version.F, siesta.tex, siesta.ind and CHANGES as customary 19383======================================================================= 19384Version: 1.2.27 19385Date: 2003/06/04 14:00 19386Title: Print of the ionic and total charge densities. 19387Author: Javier Junquera <javier.junquera@ulg.ac.be> 19388 19389Description: 19390The soft diffuse ionic charge, whose electrostatic potential is the 19391local part of the pseudopotential, can be printed now at the points 19392of the grid (file SystemLabel.IOCH), together with the total 19393(ionic+electronic) charge density (file SystemLabel.TOCH). 19394The new input variables that control the writting are, respectively, 19395SaveIonicCharge, and SaveTotalCharge. 19396 19397When using the Harris functional, the Harris energy is printed at 19398the end of each molecular dynamic step, instead of the Kohn-Sham energy. 19399The SystemLabel.MDE file is also written using the harris' energy instead 19400of the Kohn-Sham energy. 19401 19402Files: 19403 siesta.F : New variables to define the files SystemLabel.IOCH, and 19404 SystemLabel.TOCH. 19405 : Calls to dhscf have changed. The name of two extra files 19406 : have been added to the argument list. 19407 : Printing of the Harris energy. 19408 : Change in the definitions of getot, and in the call to 19409 : iomd when harris functional is used. 19410 grdsam.F : Calls to dhscf have changed. The name of two extra files 19411 : have been added to the argument list. 19412 dhscf.F : Two new variables with the names of the two files. 19413 : Call the new subroutine LocalChargeOnMesh, and write 19414 : the ionic and total charge densities. 19415 meshsubs.F: New subroutine LocalChargeOnMesh. 19416 siesta.tex, siesta.ind, CHANGES, version.F: Customary changes 19417======================================================================= 19418Version: 1.2.26 19419Date: 2003/06/03 14:30 19420Title: Fixed bug in parallel polarisation 19421Author: Julian Gale <j.gale@imperial.ac.uk> 19422 19423Description: 19424The calculation of polarisation was giving incorrect answers in 19425parallel due to corruption of the saved wavefunction in psiprev. 19426Was due to trying to combine the calculation and saving aspects 19427to minimise communication. Saving of wavefunction now performed 19428as a separate operation. 19429 19430Files: 19431 ksv.F : savepsi is now called after detover where needed and 19432 : the logical flag that was passed to this routine has 19433 : been removed. 19434 detover.F : The savepsi option has been removed along with the 19435 : incoming logical argument. 19436 version.F / CHANGES 19437======================================================================= 19438Version: 1.2.25 19439Date: 2003/05/22 19:30 19440Title: Fixed bug in BLYP forces (Marivi Fernandez-Serra) 19441Author: Emilio Artacho <emilio@esc.cam.ac.uk> 19442 19443Description: 19444 The implementation of the derivatives for the forces in the BLYP 19445functional had a bug, found and fixed by Marivi Fernandez-Serra. 19446 (a few hours before, Alberto Garcia committed basis_type.f to 19447solve some compilation problems with some compilers). 19448 19449Files: 19450 xc.f in Src 19451 blypxc.f in Pseudo/atom 19452 basis_type.f 19453 siesta.tex, siesta.ind, CHANGES, version.F 19454======================================================================= 19455Version: 1.2.24 19456Date: 2003/05/21 22:00 19457Title: Various (single excitation, flush, print pressure, etc) 19458Author: Emilio Artacho <emilio@esc.cam.ac.uk> 19459 19460Description: 19461 194621. Single excitation: possibility of lowest excited state by 19463 swapping the populations of HOMO and LUMO (if no spin polarisation, 19464 it is half swapping). Introduce SingleExcitation logical flag. 19465 It is done for ispin=1 and ik=1. 194662. The SIG file (who used it?) is now only appearing is asked with the 19467 SignatureRecords flag. 194683. Option of Mulliken at every SCF (for dealing with SCF problems) 19469 by turning true the MullikenInSCF flag 194704. Flushes the ANI, MD, and MDE files at every time step by closing 19471 the files. It reopens (append) at every instance. It solves the 19472 problem originated by some compilers that keep data in buffers. 19473 These data are lost if the program dies. It is still to be solved for 19474 the standard output. The same (not elegant but robust) solution 19475 can be used if instead of writing to standard output, siesta would 19476 write to a file. 194775. In MD runs the stress tensor and (solid) pressure are printed at 19478 every step. Both the static (ellectronic contribution) and total 19479 (adding kinetic term of nuclei). At the end of the run it is printed 19480 as always, only the static. The MDE file now writes total solid pressure 19481 and volume together with E_tot, E_KS, T, and step. 19482 19483Files: 19484 fermid.F : Single excitation 19485 siesta.F : Signature records, Mulliken in SCF 19486 mulliken.F : Consmetics 19487 iomd.f : flush MD and MDE 19488 pixmol.f : flush ANI 19489 siesta.tex, siesta.ind, CHANGES, version.F 19490======================================================================= 19491Version: 1.2.23 19492Date: 2003/05/01 11:00 19493Title: Corrected FFT and ordern 19494Author: Julian D. Gale <j.gale@imperial.ac.uk> 19495 19496Description: 19497 19498Two bugs have been fixed: 19499(1) In the FFT routine, the dimensions were exceed then the contents of 19500 trigs were not always recalculated after increasing the dimensions. 19501(2) In order N the contents of several arrays were not preserved during 19502 resizing leading to loss of data for the subsequent geometry steps. 19503 19504Files: 19505 19506diagon.F : The order of deallocation of the arrays is reversed to be more 19507 stack friendly. 19508fft3d.F : OldMesh reinitialised to 0 if the size of the array trigs is 19509 altered to ensure that array is refilled correctly. 19510hpcx.make : the -bmaxdata flag has been added in order to access the 19511 full memory 19512ordern.F : Contents of several arrays are preserved on resizing. 19513======================================================================= 19514Version: 1.2.22 19515Date: 2003/04/14 15:10 19516Title: Corrected k-grid cutoff 19517Author: Jose M. Soler <jose.soler@uam.es> 19518 19519Description: 19520 19521For some nonorthorrombic k-sampling grids, the cutoff was overestimated 19522A call to minvec was introduced to find the true minimum supercell vector 19523 19524Files: 19525 19526kgridinit.F : Introduced call to minvec 19527 19528======================================================================= 19529Version: 1.2.21 19530Date: 2003/04/14 15:00 19531Title: Cleaning of foreign code 19532Author: Jose M. Soler <jose.soler@uam.es> 19533 19534Description: 19535 19536To avoid any legal problems, the few routines not written by the siesta 19537team have been cleaned or modified to make them different enough from 19538the original ones. However, apropriate statements of the original 19539procedence/authorship have been kept in all the files affected. 19540Three routines in recipes.f were eliminated: ratint because it always 19541called polint internally, and splin/splinu because they were equivalent 19542to spline/splint. 19543 19544Files: 19545 19546arw.f : Code cleaned and language updated. 19547 Many comments added or corrected. 19548arw.F : Eliminated (changed to arw.f) 19549atom.f : Calls to ratint changed by polint 19550basis_io.F : Calls to ratint changed by polint 19551cellxc.F : Header comments slightly changed 19552matel.f : Calls to splin/splinu changed to spline/splint 19553periodic_table.f : Code updated. Some comments added 19554recipes.f : Routines ratint, splin, and splinu eliminated. 19555 Code updated and comments added 19556siesta.F : Copyright statements in header changed 19557xc.f : Header comments slightly changed 19558Makefile : arw.o made dependent of ionew.o 19559 19560======================================================================= 19561Version: 1.2.20 19562Date: 2003/1/20 16:00 19563Title: HPCx changes 19564Author: Julian Gale <j.gale@ic.ac.uk> 19565 19566Description: 19567 19568A small number of changes have been made for easy compilation on an 19569IBM Regatta machine to enable use with the HPCx service in the UK 19570(and elsewhere). 19571 19572Files: 19573 19574alloc.F90 : if NODAT option added for -DNODAT to avoid MPI problems 19575bands.F : if NODAT option added for -DNODAT to avoid MPI problems 19576broadcast_basis.F : if NODAT option added for -DNODAT to avoid MPI problems 19577cellxc.F : if NODAT option added for -DNODAT to avoid MPI problems 19578cgvc.F : if NODAT option added for -DNODAT to avoid MPI problems 19579cgwf.F : if NODAT option added for -DNODAT to avoid MPI problems 19580chempot.F : if NODAT option added for -DNODAT to avoid MPI problems 19581denmat.F : if NODAT option added for -DNODAT to avoid MPI problems 19582detover.F : if NODAT option added for -DNODAT to avoid MPI problems 19583dhscf.F : if NODAT option added for -DNODAT to avoid MPI problems 19584diag2g.F : if NODAT option added for -DNODAT to avoid MPI problems 19585diag2k.F : if NODAT option added for -DNODAT to avoid MPI problems 19586diagg.F : if NODAT option added for -DNODAT to avoid MPI problems 19587diagk.F : if NODAT option added for -DNODAT to avoid MPI problems 19588diagkp.F : if NODAT option added for -DNODAT to avoid MPI problems 19589diagon.F : if NODAT option added for -DNODAT to avoid MPI problems 19590diagsprl.F : if NODAT option added for -DNODAT to avoid MPI problems 19591dipole.F : if NODAT option added for -DNODAT to avoid MPI problems 19592efield.F : if NODAT option added for -DNODAT to avoid MPI problems 19593ener3.F : if NODAT option added for -DNODAT to avoid MPI problems 19594fft3d.F : if NODAT option added for -DNODAT to avoid MPI problems 19595gradient.F : if NODAT option added for -DNODAT to avoid MPI problems 19596iodm.F : if NODAT option added for -DNODAT to avoid MPI problems 19597iohs.F : if NODAT option added for -DNODAT to avoid MPI problems 19598iolwf.F : if NODAT option added for -DNODAT to avoid MPI problems 19599iorho.F : if NODAT option added for -DNODAT to avoid MPI problems 19600ioxv.F : if NODAT option added for -DNODAT to avoid MPI problems 19601kgridinit.F : if NODAT option added for -DNODAT to avoid MPI problems 19602meshmatrix.F : if NODAT option added for -DNODAT to avoid MPI problems 19603mulliken.F : if NODAT option added for -DNODAT to avoid MPI problems 19604ordern.F : if NODAT option added for -DNODAT to avoid MPI problems 19605phonon.F : if NODAT option added for -DNODAT to avoid MPI problems 19606pulayx.F : if NODAT option added for -DNODAT to avoid MPI problems 19607readsp.F : if NODAT option added for -DNODAT to avoid MPI problems 19608redata.F : if NODAT option added for -DNODAT to avoid MPI problems 19609repol.F : if NODAT option added for -DNODAT to avoid MPI problems 19610savepsi.F : if NODAT option added for -DNODAT to avoid MPI problems 19611siesta.F : if NODAT option added for -DNODAT to avoid MPI problems 19612timer.F : if NODAT option added for -DNODAT to avoid MPI problems 19613vmb.F : if NODAT option added for -DNODAT to avoid MPI problems 19614Sys/hpcx.make : arch.make for HPCx service 19615======================================================================= 19616Version: 1.2.19 19617Date: 2003/1/10 17:00 19618Title: FFT fixed for large meshes 19619Author: Julian Gale <j.gale@ic.ac.uk> 19620 19621Description: 19622 19623For very large mesh dimensions the array trigs in the FFT was not 19624able to cope. Hence this array has been made dynamic. Also a few 19625minor changes have been made, firstly to cellxc.F, to solve some 19626MPI issues at APAC, and secondly to siesta.F, to optionally avoid 19627problems with convergence where the auxiliary mesh changes during 19628a variable cell optimisation. 19629 19630Files: 19631 19632cellxc.F : The parallelisation has been altered to involve fewer 19633 : transfers, but of larger packets. Should improve 19634 : performance were latency is high and avoids problems 19635 : with MPI counters becoming too large. 19636fft3d.F : The array trigs is now dynamically allocated to allow 19637 : for larger meshes. 19638siesta.F : An option has been added to fix the auxiliary cell size 19639 : to avoid poor convergence behaviour. 19640siesta.tex : New option FixAuxiliaryCell documented 19641======================================================================= 19642Version: 1.2.18 19643Date: 2002/10/09 10:30 19644Title: Fix to spiral spin in parallel 19645Author: Julian Gale <j.gale@ic.ac.uk> 19646 19647Description: 19648 19649Parallel runs were crashing due to an fdf call that was not wrapped to 19650only be from Node 0 in readsp.f. This routine is now MPI'd to handle 19651the fdf call safely. 19652 19653Files: 19654 19655readsp.f : Removed from distribution 19656readsp.F : Added - readsp.f with wrapping of fdf calls for parallel 19657 : execution. 19658======================================================================= 19659Version: 1.2.17 19660Date: 2002/09/13 17:00 19661Title: Changes in xc.f, other cosmetic changes. 19662Author: Alberto Garcia 19663 19664Description: 19665 19666* There was a subtle numerical instability in the pzxc routine 19667when dealing with very small densities (as for large r in the 19668atomic program). Jose Soler has rewritten the offending section. 19669 19670* Added blypxc routine to xc.f 19671 19672* Cosmetic change in basis_specs.f. The printing of basis 19673 specification now skips over shells with nzeta=0... 19674 19675Files: 19676 19677xc.f , basis_specs.f 19678 19679======================================================================= 19680Version: 1.2.16 19681Date: 2002/09/02 17:00 19682Title: Divide and Conquer + fixes 19683Author: Julian Gale <j.gale@ic.ac.uk> 19684 19685Description: 19686 19687The option to use divide and conquer Lapack algorithms has been added 19688to rdiag and cdiag, as well as tidying up the source code a bit here. 19689Also a bug in the order N part for eta .ne. 0 has been corrected, as 19690well as a few fixes for parallel execution related to recently introduced 19691functionality. There are also a few bits of cleaning highlighted as a 19692result of running the code through the NAG compiler. 19693 19694Files: 19695 19696siesta.tex : DivideAndConquer option documented 19697alloc.F90 : optional attribute added for name/routine + checking for 19698 : these terms being present before being addressed added 19699 : in alloc_err 19700basis_types.f : Missing comma in format descriptor added 19701cdiag.F : Divide and Conquer option added for serial execution + 19702 : code tidied 19703cgwf.F : Indentation tidied (tabs removed) 19704chempot.F : Indentation tidied (tabs removed) 19705dhscf.F : Spin-spiral I/O handled for parallel version 19706diagg.F : Aux array no longer passed to rdiag 19707gradient.F : Bug fixed for eta .ne. 0 case 19708kgrid.F : Spin-spiral I/O handled for parallel version 19709kgridinit.F : Spin-spiral I/O handled for parallel version 19710mulliken.F : Indentation tidied (tabs removed) 19711on_subs.F : Duplicate definition of numbtmp removed 19712pdosk.f : Explicit declaration of type for dfloat added 19713pulayx.F : Indentation tidied (tabs removed) 19714rdiag.F : Divide and Conquer option added for serial execution + 19715 : code tidied. Argument "fv" removed, and allocation now 19716 : done using alloc module. 19717redata.F : State of divide and conquer flag output 19718siesta.F : Ekinion zeroed at the start to avoid case where it is 19719 : uninitialised. Plus sequence of testing of state of S 19720 : is altered to avoid a "size" operation on an unallocated 19721 : pointer. 19722transfer.f : Indentation tided (tabs removed) 19723version.f : version number incremented 19724vmb.F : Indentation tided (tabs removed) 19725Lib/blas.f : Updated to include the divide and conquer required routines. 19726Lib/lapack.f : Updated to include the divide and conquer required routines. 19727Sys/sgi64-mpi_fermat.make : -lscs flag added for DaC routines 19728======================================================================= 19729Version: 1.2.15 19730Date: 2002/07/14 17:00 19731Title: Cosmetic changes for School 19732Author: Alberto Garcia 19733 19734Description: 19735 19736The atomic generation routines have been enhanced to provide 19737more information for plotting. Gen-basis now accepts only one 19738species. 19739Tutorials directory added. 19740The manual has been updated to mention the existence of the ATOM 19741manual. 19742 19743======================================================================= 19744Version: 1.2.14 19745Date: 2002/06/28 17:00 19746Title: Non-collinear GGA 19747Author: Jose M. Soler <jose.soler@uam.es> 19748 19749Description: 19750 19751Support for non-collinar GGA. The local xc energy is made dependent 19752of the gradient of the density and of the MAGNITUDE of magnetization, 19753but not of the gradient of the magnetization direction. 19754Implemented by Victor M. Garcia <victor@condmat.uniovi.es> 19755 19756Files: 19757 19758xc.f: Modified the subrutine GGAXC to allow for non-collinear spin. 19759 19760======================================================================= 19761Version: 1.2.13 19762Date: 2002/06/24 12:45 19763Title: Spin spiral 19764Author: Jose M. Soler <jose.soler@uam.es> 19765 19766Description: 19767 19768Support for spin-spiral states, implemented by Victor M. Garcia 19769<victor@condmat.uniovi.es> 19770 19771Files: 19772 19773dhscf.F: Call to rhoofdsp and vmatsp. 19774diagon.F: Call to diagsprl. 19775kgridinit.F: If spiral, skip time reversal symmetry (include all k's) 19776kgrid.F If spiral, skip time reversal symmetry (include all k's) 19777diagsprl.F New. Diagonalizes the Hamiltonian for spin spiral. 19778ipack.f New. Packs/unpacks several integer indexes into/out of one 19779readsp.f New. Reads spiral wave vector 19780rhoofdsp.f New. Substitutes rhoofd for spiral configurations. 19781vmatsp.f New. Substitutes vmat for spiral configurations. 19782Makefile Add diagsprl.F, ipack.f, readsp.f, rhoofdsp.f, and vmatsp.f 19783 19784======================================================================= 19785Version: 1.2.12 19786Date: 2002/06/20 17:00 19787Title: Simplification of fdf module 19788Author: Alberto Garcia 19789 19790Description: 19791 19792The fdf module provides f90 interfaces for the f77 routines in 19793fdf.f, as well as new, pure-f90 routines. Until now there was 19794also an overloaded routine "fdf_get" which could stand for any 19795of the specific scalar routines. Unfortunately, either the Intel 19796or the PGI compiler chokes with its implementation. It is almost 19797certain that these are compiler errors. However, in the interest 19798of portability, the "fdf_get" interface has been removed. 19799 19800For the same reason, the routine fdf_parsed_string (currently not 19801used in Siesta) has been removed. 19802 19803Changed Files: 19804 19805fdf/fdf_mod.f 19806in Src: 19807basis_specs.f coor.f initatom.f chemical.f fdf_mod.f spin_init.f 19808 19809======================================================================= 19810Version: 1.2.11 19811Date: 2002/06/11 17:00 19812Title: Changes for (partial) support of Intel Fortran Compiler 19813Author: Alberto Garcia 19814 19815Description: 19816 19817The Intel Fortran Compiler is apparently strong at optimization but 19818very weak at following standard practice. It is not trivial to 19819integrate full support for it, but the current version of Siesta (at 19820least the serial incarnation) can still be made to compile portably 19821with a few kludges. At this point there is no support for MPI or 19822NetCDF. 19823 198241. Changes in fdf/fdf_mod.f: addition of redundant internal interfaces. 198252. fdf/makefile: kludge to make the fdf directory visible in the 19826 "subprogram catalog", and to deal with new extension for module files. 198273. Makefile: clean procedure updated. 198283. New intel*.make files in Sys. 19829 19830Thanks to Eduardo Anglada for helping with the catalog issue. 19831 19832Changed Files: 19833 19834fdf/fdf_mod.f 19835fdf/makefile 19836Makefile 19837Src/Sys/intel-mkl.make: New file. Uses optimized mkl libraries 19838Src/Sys/intel-nolibs.make: IFC needs a special library... 19839 19840======================================================================= 19841Version: 1.2.10 19842Date: 2002/06/07 15:00 19843Title: Bugs in non-collinear spin 19844Author: Jose M. Soler <jose.soler@uam.es> 19845 19846Description: 19847 198481. Avoid out-of-bounds in array qos 19849 198502. Definition of hermiticity relations for the Hamiltonian and 19851 density matrix in diag2g.F and diag2k.F 19852 198534. Modified the density matrix in diag2k.F to take ino account the 19854 time reversal symmetry. 19855 198565. Modified siesta.F to skip the eigenvectors calculation if there is 19857 only one SCF step. 19858 19859All these bugs were found and corrected by Victor M. Garcia 19860<victor@condmat.uniovi.es> 19861 19862Files: 19863 19864diag2g.F Correct hamiltonian hermicity 19865diag2k.F Correct hamiltonian hermicity and time-reversal in DM 19866mulliken.F Avoid out-of-bounds in array qos 19867siesta.F Avoid writting noncalculated eigenvalues 19868siesta.tex Date and version updated 19869 19870======================================================================= 19871Version: 1.2.9 19872Date: 2002/04/30 15:00 GMT 19873Title: Vmat fix 19874Author: Julian Gale <j.gale@ic.ac.uk> 19875 19876Description: 19877 19878An error in the diagonal elements of Vlocal has been corrected, as well 19879as a few more minor items. 19880 19881Files: 19882 19883meshmatrix.F Case where no mesh points are allocated to a node during 19884 parallel execution is handled properly with respect to 19885 zero length arrays. 19886on_subs.F Duplicate definition of numbtmp removed 19887vmat.f Error in diagonal elements of Vlocal corrected 19888xc.f Variable name corrected in pzxc from DECPDN -> DECFDN 19889======================================================================= 19890Version: 1.2.8 19891Date: 2002/04/11 19892Title: Bug fixed in vmat.f, rhoofd.f, and dfscf.f 19893Author: Javier Junquera <Javier.Junquera@ulg.ac.be> 19894 19895Description: 19896 198971. A bug has been fixed in the subroutines that calculate 19898 the integrals in the real space mesh. 19899 If the longest orbital of a given specie is unoccupied in 19900 the free atom, then some points were wrongly skipped 19901 while calculating the integrals. 19902 The definition of the cutoff radiae has been modified in 19903 vmat, rhoofd and dfscf 19904 Files: vmat.f, rhoofd.f, dfscf.f 19905 199062. The maximum number of iterations to converge the Fermi 19907 energy has been increased to 100. For some systems 50 is not 19908 a large enough number. 19909 File: fermid.F 19910 199113. Customary changes in file Src/version.F and Docs/CHANGES 19912 File: version.F, Docs/CHANGES 19913 19914======================================================================= 19915Version: 1.2.7 19916Date: 2002/02/06 19917Title: PDOS calculation back into siesta.F... 19918Author: Alberto Garcia <wdpgaara@lg.ehu.es> 19919 19920Description: 19921 19922The PDOS calculation had been deactivated in siesta.F due to an error. 19923It has been put back in. File: siesta.F 19924 19925======================================================================= 19926Version: 1.2.6 19927Date: 2002/02/04 19928Title: Interface with F90 Denchar Utility 19929Author: Javier Junquera <Javier.Junquera@ulg.ac.be> 19930 19931Description: 19932 199331. The interface between Siesta and Denchar has been implemented 19934 using Fortran 90. 19935 File: plcharge.F 19936 199372. The interface routine is called again from Siesta. 19938 (This call was commented in the fortran 90 Siesta branch. 19939 File: siesta.F 19940 199413. Subroutine plcharge is included in the object list. 19942 File: Makefile 19943 199444. Almost all the routines in the utility package Denchar have been 19945 rewritten in Fortran 90 in order 19946 to make it compatible with the 1.X version of Siesta. 19947 Files: Util/Denchar 19948 199495. Customary changes in file Src/version.F and Docs/siesta.tex 19950 File: version.F 19951======================================================================= 19952Version: 1.2.5 19953Date: 2002/01/17 19954Title: Bug fix in pdos.f, reorg of ghost routine, lmxkb info for users 19955Author: Alberto Garcia <wdpgaara@lg.ehu.es> 19956 19957Description: 19958 199591. Fixed a writing bug in pdos.f (for spin-polarized calculations). 19960 File: pdos.f 19961 199622. Make f-channel the highest-l projector used. 19963 Inform the user about the possibility of 19964 using a lower lmxkb. 19965 File: basis_specs.f 19966 199673. Reorganize routine ghost (avoid computing excited state if 19968 not necessary). Remove references to "atom.h". 19969 File: atom.f 19970======================================================================= 19971Version: 1.2.4 19972Date: 2001/12/14 18:15 GMT 19973Title: Order N improvements/tidy 19974Author: Julian Gale <j.gale@ic.ac.uk> 19975 19976Description: 19977 19978The key changes relate to improvements in the order N part. The form of 19979cspa and eandg has been changed, in particular. Now the parameters maxnf, 19980maxnft and maxnhij are found in eandg, not in cspa. This allows an 19981accurate determination of the sizes in parallel and leads to much 19982improved parallel scaling of cspa, removing this bottleneck for very 19983large calculations. There are also improvements to ener3.F and gradient.F 19984to reduce memory requirements and improve performance. There are also a 19985large number of minor changes where unused variables have been cleared 19986out. 19987 19988Files: 19989 19990atmfuncs.f Unused variables removed to be tidy and reduce warnings 19991atom.f Unused variables removed to be tidy and reduce warnings 19992atomlwf.F Considerably changed to achieve reasonable parallel 19993 scaling and efficiency. The parameters nfmax, nftmax 19994 and nhijmax are no longer determined here since the 19995 values were always overestimates when operating in 19996 parallel and this allows the code to be more readily 19997 distributed over processors. The determination of the 19998 sparse indexing and the initialisation of the LWFs has 19999 been separated so that parallelism can be achieved without 20000 altering the effect on the random initialisation. The 20001 building of the sparse indices is now distributed by 20002 search atom over Nodes. 20003bands.F Unused variables removed to be tidy and reduce warnings 20004basis_io.F Unused variables removed to be tidy and reduce warnings 20005cgwf.F Variables maxnf, maxnft and maxnhij removed as arguments 20006 and no longer passed to eandg. 20007detover.F Dimensions of psitmp for passing corrected and full 20008 matrix used in savepsi option. Also referencing of 20009 variable "je" return to the global frame as "jeg" 20010 where necessary. Unused variables removed. 20011dfscf.f Unused variables removed to be tidy and reduce warnings 20012diag2g.F Unused variables removed to be tidy and reduce warnings 20013diag2k.F Unused variables removed to be tidy and reduce warnings 20014diagpol.f Unused variable "io" removed 20015egandd.F Structure changed due to the fact that maxnhij, maxnft 20016 and maxnf are now determined here, rather than in cspa. 20017ener3.F Re-structured for greater parallel efficiency / lower 20018 memory use. 20019forhar.f Unused variables removed to be tidy and reduce warnings 20020gradient.F Variables nfmax/nhijmax globalised 20021initatom.f Unused variable "js" removed 20022ionew.F Declaration of "used" removed since variable is unused 20023 in io_status 20024kgridinit.F Unused variable "d" removed 20025ksv.F Unused variable "mxhov2" removed 20026matel.f Unused variable "js" removed 20027meshsubs.F Unused variables removed to be tidy and reduce warnings 20028old_atmfuncs.f Declaration of "maxo" removed since variable is unused 20029on_subs.F New routines added that are variants on the old ones 20030 for determining just the array dimension parameters 20031 nfmax, nftmax, nhijmax. 20032ordern.F Modified to reflect the removal of nfmax, nftmax and 20033 nhijmax 20034parallel.f Unused variables removed to be tidy and reduce warnings 20035phonon.F Unused variables removed to be tidy and reduce warnings 20036pulayx.F Unused variable "iii" removed 20037rhooda.f Unused variable "in" removed 20038rhoofd.f Unused variables removed to be tidy and reduce warnings 20039siesta.F Unused variables removed to be tidy and reduce warnings 20040vmat.f Unused variables removed to be tidy and reduce warnings 20041======================================================================= 20042Version: 1.2.3 20043Date: 2001/11/20 12:30 GMT 20044Title: iorho parallel fix / order N improvements 20045Author: Julian Gale <j.gale@ic.ac.uk> 20046 20047Description: 20048 20049The handling of blocksizes has been corrected in iorho.F, since 20050the data distribution model coded was not quite the same as in 20051dhscf.F. The routine has been changed to make things consistent. 20052Further improvements have been to the order N part to reduce the 20053memory and increase the speed. In particular, the set up of the 20054indexing arrays has been examined. In axb_build1, the array ind 20055has been switched from a 2-D to 1-D array which is set up as necessary 20056using the sparsed stored indices. Also the broadcast of data has 20057been altered to group data so that each Node only broadcasts once. 20058The size of the local scratch arrays in denmat have also been reduced 20059by finding the optimum value of nfmax. 20060 20061Files: 20062 20063 atomlwf.F Rounding error allowed for in checking of number 20064 of electrons. 20065 denmat.F Memory reduced further / performance increased. 20066 Main change is to value of nfmax used to size 20067 local temporary arrays. 20068 egandd.F Array indgf is distributed across nodes. 20069 gradient.F Memory reduced further / performance increased. 20070 iorho.F Calculation of blocksizes for I/O in parallel 20071 was in error. Now fixed. 20072 on_subs.F The array ind has been removed and replaced by a 20073 1-D array which is filled as necessary from nindv 20074 which is sparse. Also data is broadcast by Node 20075 rather than by orbital. Array indgf is distributed 20076 across nodes. 20077 outcoor.f I/O modified to handle up to 999,999 atoms 20078 siesta.F I/O modified to handle up to 999,999 atoms 20079======================================================================= 20080Version: 1.2.2 20081Date: 2001/11/05 16:00 GMT 20082Title: Memory re-linearised in order N 20083Author: Julian Gale <j.gale@ic.ac.uk> 20084 20085Description: 20086 20087In the process of originally parallelising the order N part, 20088the linear scaling of the memory usage with system size was 20089lost. This has now been restored which should lead to memory 20090savings for large jobs in parallel. 20091 20092Files: 20093 denmat.F Modified to change size of all 2-D or higher 20094 arrays so that two dense indices are never 20095 used. 20096 egandd.F Call to ind_gf reinstated and fttof passed to 20097 gradient. Left-hand dimension of fttof/listft 20098 corrected to maxnft. 20099 ener3.F Modified to change size of all 2-D or higher 20100 arrays so that two dense indices are never 20101 used. 20102 gradient.F Modified to change size of all 2-D or higher 20103 arrays so that two dense indices are never 20104 used. 20105 on_subs.F Subroutine ind_gf reinstated as fttof is now 20106 used again. 20107 MPI/Makefile Two blank lines removed that break the make 20108 on SGI machines. 20109======================================================================= 20110Version: 1.2.1 20111Date: 2001/10/11 17:30 GMT 20112Title: Accelerated direct spin polarised calculations 20113Author: Julian Gale <j.gale@ic.ac.uk> 20114 20115Description: 20116 20117The use of the DirectPhi option has been accelerated for spin 20118polarised calculations by only calculating the values of Phi 20119on the mesh once. This is achieved by moving the loop over 20120spin inside rhoofd and vmat. Also a bug in the print out of the 20121spin polarisation when running in parallel has been fixed. 20122 20123Files: 20124 dfscf.f Call to matrixOtoM modified. 20125 dhscf.F Calling of rhoofd and vmat modified. 20126 meshmatrix.F Spin loops moved within matrixOtoM and matrixMtoO. 20127 rhoofd.f Looping over spin components now included internally. 20128 Dlocal array stored in triangular fashion. 20129 siesta.F Qspin now globalised before print out of spin 20130 polarisation. 20131 vmat.f Looping over spin components now included internally. 20132 Vlocal array stored in triangular fashion. 20133======================================================================= 20134Version: 1.2.0 [No change] 20135Date: 2001/10/04 20136Title: Bug fixes in basis_io.F 20137Author: Alberto Garcia <wdpgaara@lg.ehu.es> 20138 20139Description: 20140 20141Fixed bugs having to do with: 20142 201431. The use of the .ion files generated by an independent siesta or 20144gen-basis run. 201452. The default mass for floating orbitals 20146 20147(Discovered just after the release of siesta-1.1) 20148 20149Files: 20150 basis_io.F: Second derivative of elec_corr structures was not 20151 updated after generation in elec_corr_setup. 20152 Changed filename from XX.ion_nc to XX.ion.nc 20153 basis_specs.f: Do not make default mass too big for floating orbitals. 20154======================================================================= 20155Version: 1.2.0 20156Date: 2001/09/26 20157Title: Merge from rel-1-1-branch at 1.1 release point (siesta-1-1) 20158Author: Alberto Garcia <wdpgaara@lg.ehu.es> 20159 20160 Starting point for new cycle of development. 20161 20162 Changes and fixes in preparation of the 1.1 release 20163 merged back to main trunk: 20164 20165* Fixed mismatched MPI block in siesta.F (related to PDOS change). 20166 file: siesta.F 20167 20168* Total DOS file is now just *.DOS. 20169 20170* Better output for PDOS file. Used "xml" format to ease (?) 20171 processing (evolving ideas). 20172 files: pdos.f pdosk.f 20173 20174* Added new "h2o_dos" test in Src/Tests. 20175 20176* Added "xml" output for .ion data. 20177 files: xml.f basis_io.F radial.f initatom.f 20178 20179* Committed Bug fix for O(N) calculations (Julian Gale) 20180 file: gradient.F Src/Tests/Makefile (enabled h2o_orderN) 20181 20182* Added new sgi64-mpi_fermat.make file (Julian Gale) 20183 20184* Array shape fixes in xc.f (cosmetic) (Julian Gale) 20185 20186* Added top README file. 20187 20188* Removed obsolete source files from Src directory. 20189 files: iorder.f order.f ordvec.f ylmylm.f lofilm.f 20190 resize.F ylmexp.f symbol.f rlylm.f die.F 20191 20192* Added user.list (Please update), build_parallel.sh, and other 20193 release-related files, and updated some others. These files are 20194 not part of any distribution. 20195 20196* Updated CONDITIONS (list of developers) 20197 20198* Many User Guide updates (J. Junquera, E. Artacho, A. Garcia) 20199 20200* Removed .vps, out.fdf, and siesta.size files from Examples directory. 20201 20202* Updated .out files in Src/Tests and Examples/*/Out 20203 20204* Added Util/PyAtom/pdos.py script (experimental -- not in release) 20205 20206* Set Version to 1.2.0 20207 20208======================================================================= 20209Version: 1.0.62 20210Date: 2001/09/24 12:00 GMT 20211Title: Projected Density of States. 20212Author: Javier Junquera <javier.junquera@uam.es> 20213 20214Description: 20215 20216The Total Density Of States (Total DOS), and its projection 20217on the basis orbitals (Projected Density Of States, PDOS), 20218are computed and dumped to files ('.TOT.DOS' and '.PDOS' respectively). 20219 20220This only works in a serial run. An error message will be issued 20221when we try to use it in a parallel execution. 20222 20223It is only implemented when the hamiltonian 20224is solved by diagonalization with k-points. 20225 20226Files: 20227 siesta.F Call to pdos subroutine is added 20228 pdos.f New subroutine, interface between siesta and the one that 20229 computes the PDOS 20230 pdosk.f New subroutine. Computes the PDOS 20231 Makefile pdos.o and pdosk.o added to object list 20232 Docs/siesta.tex, Docs/siesta.ind 20233 Documentation of new block usage. 20234======================================================================== 20235Version: 1.0.61 20236Date: 2001/09/16 18:00 GMT 20237Title: New input/output facilities for ps and basis information 20238Author: Alberto Garcia <wdpgaara@lg.ehu.es> 20239 20240Description: 20241 20242Pseudopotential information can now be read by SIESTA in formatted 20243form from '.psf' files (which are now also generated by ATOM). This 20244will make it easier to transport ps files among computers. The 20245old *.psatom.data files are no longer valid. 20246 20247Also, the PAO, KB projector, and Vlocal and charges data are dumped to 20248'.ion' (and '.ion_nc' if NetCDF is available) files, which can later 20249be used to re-generate the atomic information if the 'user-basis' 20250(or 'user-basis-netcdf') option is specified in SIESTA. A header section 20251containing information about the specifications for basis construction 20252and about the pseudopotential used is also included. 20253 20254Files: 20255 chemical.f New module to centralize the chemical species info. 20256 pseudopotential.f 20257 New routine to read formatted '.psf' files. 20258 New routine to print a header containing basic ps info. 20259 20260 basis_io.F Modifications to the routines which read and write the 20261 '.ion' files. 20262 atm_types.f basis_specs.f basis_types.f atm_types.f initatom.f 20263 transfer.f 20264 Minor changes to support the above changes. 20265 20266 Pseudo/atom/wrapup.f 20267 New file VPSFMT output 20268 Pseudo/atom/Samples/pg.sh 20269 File VPSFMT copied to <name>.psf 20270 Pseudo/atom/Docs/User.Guide 20271 Updated 20272 20273 Docs/siesta.tex, Docs/siesta.ind 20274 Documentation of new file usage. 20275======================================================================== 20276Version: 1.0.60 20277Date: 2001/09/11 17:00 GMT 20278Title: Corrections and modification to limit runaway memory 20279Author: Julian D. Gale <j.gale@ic.ac.uk> 20280 20281Description: 20282 20283This is a collection of corrections for a few bugs, typos, 20284and problems noticed on certain platforms. It appears that 20285on Linux boxes, under Absoft f90, and on DEC platforms the 20286f90 implementation fails to properly free memory when 20287deallocated. Because of the size of phi/listp2/lstpht, this 20288can rapidly lead to the memory being exhausted on some machines. 20289Hence a workaround has been added to PhiOnMesh so that these 20290arrays are only redimensioned when absolutely necessary - 20291i.e. they are too small. A tolerance has also been added to 20292the initial dimension (of 1%) to hopefully minimise 20293reallocations. 20294 20295Files: 20296 atom.f Spelling of "analysis" corrected 20297 matel.f Dimensions of arrays adjusted to prevent crash when 20298 running in parallel (contraction prevented). Debug 20299 statements commented out. 20300 meshsubs.F Reallocation of phi/lstpht/listp2 avoided one possible 20301 to avoid memory increasing on platforms that fail to 20302 properly deallocate arrays from memory. 20303 mulliken.F Spelling of "analysis" corrected 20304 Loops over 1,Nodes corrected to 0,Nodes-1 20305 redata.F Spelling of "analysis" corrected / alignment of write 20306 tidied 20307 siesta.F Call to ioeig corrected to pass no_u instead of no_l 20308======================================================================== 20309Version: 1.0.59 20310Date: 2001/07/10 10:00 GMT 20311Title: Changes to support pgf90 and non-MPI version 20312Author: Alberto Garcia <wdpgaara@lg.ehu.es> 20313 20314Description: 20315 20316A. The pgf90 compiler had trouble compiling certain sections of the 20317code. These had been rewritten slightly to help it. 20318 20319 Files: 20320 Src/fdf/parse.f: Use token_arr instead of tokens to avoid compiler 20321 bug. 20322 Src/fdf/fdf_mod.f, fdf.f : Use fdf_block_old wrapper routine to 20323 avoid compiler bug that led to an 20324 infinite loop. 20325 Src/alloc.F90: Fix declaration of character variable. 20326 Sys/pgf90*.make: Name NetCDF library explicitly, instead of using -L. 20327 20328B. The process to generate a de-MPI'ized version suitable for general 20329 users has been streamlined somewhat. 20330 20331 Files: 20332 20333 build_serial.sh: Use the same Makefile. Copy also .f90 files 20334 Src/Makefile: Test for existence of MPI directory before cleaning. 20335======================================================================= 20336Version: 1.0.58 20337Date: 2001/06/29 12:00 GMT 20338Title: removed local variables NSM and NMESHG in cellxc 20339Author: Jose M. Soler <jose.soler@uam.es> 20340 20341Description: 20342 20343Variables NSM and NMESHG are now imported from module mesh and 20344should not be redeclared locally. 20345 20346Files: 20347 cellxc.F: removed local variables NSM and NMESHG 20348======================================================================= 20349Version: 1.0.57 20350Date: 2001/05/18 20:15 GMT 20351Title: serial version of cellxc.F and xc.f returned to f77 20352Author: Jose M. Soler <jose.soler@uam.es> 20353 20354Description: 20355 20356The serial part of cellxc and atomxc was returned to f77, to make 20357it more transportable as a separated package. Required node and 20358mesh arguments for parallel esecution are now obtained directly 20359within cellxc, rather than passed as arguments. 20360 20361Files: 20362 cellxc.F: serial part returned to f77 20363 Node and Nodes obtained by calling MPI 20364 NMESHG and NSM obtained from module mesh 20365 dhscf.F: call to cellxc 20366 forhar.f: call to cellxc 20367 meshsubs.F: added static valiables NMESHG and NSM 20368 siesta.F: removed save declarations 20369 xc.f: returned to f77 20370======================================================================= 20371Version: 1.0.56 20372Date: 2001/05/18 20:00 GMT 20373Title: Corrected bug in MATEL which produced numerical errors 20374Author: Jose M. Soler <jose.soler@uam.es> 20375 20376Description: 20377 20378A change in the call to RADFFT was missing in basis_io.F and 20379read_user_basis.F. Instead, RADFFT has been returned to its previous 20380state, to avoid reproducing this error. This corrects the small 20381numeric differences in the output introduced in version 1.0.50. 20382Additionally, calls to realloc were simplified in MATEL. 20383 20384Files: 20385 matel.f: simplified realloc procedures 20386 radfft.f: commented out return of spillage in last element 20387======================================================================= 20388Version: 1.0.55 20389Date: 2001/05/11 20390Title: Grid cell sampling bug fix 20391Author: Emilio Artacho <Emilio.Artacho@uam.es> 20392 20393Description: 20394 20395The energy was not being averaged by the grid-cell-sampling option, 20396since the calculation of Etot (and Eharris and FreeEner) was done 20397only in the before-last iteration, before grid-cell sampling. Fixed. 20398 20399Files: 20400 siesta.F 20401 (customary version.F, CHANGES and siesta.tex) 20402======================================================================= 20403Version: 1.0.54 20404Date: 2001/05/01 20405Title: Mesh memory correction 20406Author: Julian Gale <j.gale@ic.ac.uk> 20407 20408Description: 20409 20410Out of bounds memory writes were occuring for a small number of arrays 20411in routines relating to the mesh for some cases. This was related to 20412the local variable "maxloc" being used in two different contexts with 20413a common value. A new separate value has now been introduced for the 20414case where a value which was too small was being assigned. 20415 20416Files: 20417 dfscf.f : Sizing of ibc, C, gC and xgC corrected. 20418 rhoofd.f : Sizing of ilc and Clocal corrected. 20419 vmat.f : Sizing of ilc and Clocal corrected. 20420======================================================================= 20421Version: 1.0.53 20422Date: 2001/04/26 20423Title: New inver 20424Author: William Mattson <wmattson@uiuc.edu> (committed by JDG) 20425 20426Description: 20427 20428It turns out that the subroutine inver fails for certain matrices 20429and returns "NaN"s. This was observed by William Mattson from 20430Richard Martin's group and he has kindly provided a routine 20431that fixes the problem. 20432 20433Files: 20434 inver.f : Removed in favour of inver.f90 20435 inver.f90 : Replaces inver.f 20436======================================================================= 20437Version: 1.0.52 20438Date: 2001/03/27 08:45 GMT 20439Title: Matel fixes 20440Author: Julian D. Gale <j.gale@ic.ac.uk> 20441 20442Description: 20443 20444A number of corrections have been made, primarily to matel. The 20445main change to matel is to explicitly zero INDF and INDFF when 20446reallocated in case this is not the default action and also to 20447trap when IOPER increases so as to increase the size of the 20448appropriate arrays. A few other bugs have been cleared up for 20449parallel execution. 20450 20451Files: 20452 ksv.F : Dimension of ek changed to nuotot. 20453 matel.f : INDF / INDFF zeroed after realloc calls. 20454 : Test for INDF being associated added to avoid 20455 : call to SIZE when INDF is a null pointer. 20456 : Change in third dimension (IOPER) now trapped. 20457 parallel.f : New subroutine to set the default blocksize 20458 : added - checks that if the number of orbitals 20459 : is small then the blocksize is lowered to ensure 20460 : some work on each processor. 20461 siesta.F : Setting of level for alloc routines corrected 20462 : for parallel execution. 20463 : Call to new routine for setting default blocksize 20464 : added and calls for parallel setup moved until 20465 : later in the routine so that no_u is defined. 20466======================================================================= 20467Version: 1.0.51 20468Date: 2001/02/28 05:00 GMT 20469Title: Improved memory for parallel order N 20470Author: Julian D. Gale <j.gale@ic.ac.uk> 20471 20472Description: 20473 20474The key routines for order N calculation have been modified 20475to lower the peak memory usage by reordering certain operations 20476to reduce the amount of local workspace at the expense of a 20477communication overhead in some cases for multiprocessor systems. 20478A few other changes have been made as a result of compilation 20479and testing of the latest version on the Cray and under the 20480pgf90 compiler. 20481 20482Files: 20483 ener3.F : Memory usage reduced for parallel execution 20484 denmat.F : Memory usage reduced for parallel execution 20485 gradient.F : Memory usage reduced for parallel execution 20486 dhscf.f : Typo in message corrected 20487 fdf/fdf_mod.f : Local variable default2 added to fdf_sp to 20488 : handle type conversion on calling fdf_single 20489 periodic_table.f: lmax lowered to 3 in cnfig to avoid write beyond 20490 : bounds error when called by routines where lmax is 20491 : already 3 20492 Makefile : atmparams.o added to object list for make of base 20493======================================================================= 20494Version: 1.0.50 20495Date: 2001/01/31 17:30 GMT 20496Title: Miscellaneous corrections 20497Author: Jose M. Soler <jose.soler@uam.es> 20498 20499Description: 20500 20501More modular reading of .RHO files in plrho. 20502Calls memory from realloc to keep the correct total allocated memory. 20503Authorship correction of some periodic_table routines. 20504 20505Files: 20506 alloc.F90 : Call memory. Corrected CRAY sizes. 20507 arw.F : Document moving of some routines 20508 iorho.F : Returns correct sizes instead of stopping 20509 matel.f : Last function value made zero after radfft call 20510 parallel.f : Default initialization of Blocksize and ProcessorY 20511 periodic_table.f: Authorship correction of some routines 20512 Plrho/iorho.f : Serial version of iorho 20513 Plrho/plrho.f : Use iorho to read .RHO files 20514 Plrho/plrho.f77 : Fortran77 version 20515 Plrho/plrho_guide.txt : Document previous changes 20516======================================================================= 20517Version: 1.0.49 20518Date: 2001/01/29 19:00 GMT 20519Title: Merge of 'newatom' branch 20520Author: Alberto Garcia <wdpgaara@lg.ehu.es> 20521 20522Description: 20523 20524The basis-generation subsystem has been improved by rationalizing some 20525data structures and making some code simpler. A major simplification 20526involves doing the work in serial mode and broadcasting only the final 20527data structures. A more powerful 'parse' mechanism has been implemented 20528to help with the complex processing of data blocks which define the 20529basis. A complete list of changes follows. 20530 20531Files: 20532 atom.f: Back to serial mode. Streamlined somewhat, but still basically 20533 unchanged. Lots of more work needed. 20534 atom.F: Removed. 20535 atm_types.f: Data structures to hold PAO, KB proj, and vlocal info. 20536 atminit.F: Removed. Its functionality is now in... 20537 initatom.f: Includes logic to deal with user-defined bases (new format). 20538 atomlist.f: Now computes total number of orbitals and KB projectors. 20539 Includes superx. 20540 base.F: A new, standalone, program for basis generation. 20541 basis_io.F: Reads and writes basis information in two formats: pure 20542 ASCII and NetCDF (if compiled in). Note that the .F suffix 20543 does not have anything to do with MPI... it is needed to 20544 preprocess NetCDF blocks. 20545 basis_specs.f: New routines for basis definition. See documentation 20546 in the file itself. 20547 basis_types.f : Data structures for basis specification, and routines 20548 to interface with the old-style arrays needed by 'atom'. 20549 broadcast_basis.F: New file. 20550 cdiag.F: Make H and S real arrays with an extra dimension, so that 20551 the (formal) interface errors do not stop the program in 20552 debugging runs. Now the interface mismatch is passed on 20553 to the library side. 20554 cellxc.F: Arrays xmesh and aux are now assumed size to avoid 20555 interface mismatches. 20556 chkdim.F chkdim.f: Calls routine 'die' to avoid explicit MPI code. 20557 coceri.f: Uses 'periodic_table' module (q.v.) and automatic arrays. 20558 coor.f coxmol.f pixmol.f: Use 'periodic_table' 20559 dfscf.F: fal array dimensioned to na instead of nua. 20560 diagon.F: Aux array size was too small for 'diagk' case. 20561 diag*.{f,F} propor.f: Use new module 'sys' (q.v.) 20562 die.F: Removed. Functionality in module sys.F (q.v.) 20563 dump2cdf.F dump_ascii.f: Removed. Functionality now in basis_io.F 20564 gauleg.f lofilm.F 20565 rlylm.f ylmexp.f 20566 ylmylm.f: Removed and integrated into new module 'spher_harm.f', to 20567 make the interfaces explicit. 20568 ionew.F: New prototype module to deal with logical unit numbers and 20569 the variable IOnode (to simplify MPI I/O). 20570 matel.f: Array syntax explicit in some calls to match the interfaces 20571 in spher_harm. 20572 meshsubs.F: Dummy argument fal was wrongly dimensioned (to na instead 20573 of nua) in routine neutralatomonmesh. Inocuous but wrong. 20574 old_atmfuncs.f: It now does the allocation and clearing of the 20575 old-style atomic tables which use to be done in 'atom'. 20576 periodic_table.f: New module with purely 'atomic' routines, taken from... 20577 arw.F: 'atomic' routines moved to module 'periodic_table'. 20578 plcharge.F: Removed. Functionality provided by .RHO files and the 20579 helper programs in Util/Contour and Util/Plrho 20580 pseudopotential.f: New module to read and hold the data from ps files. 20581 (Currently, the data is recopied in 'atom') 20582 radial.f: Dynamic table size. 20583 recipes.f: Use automatic arrays when needed. 20584 redata.F: Issues note about .RHO file substituting denchar info. 20585 redbasis.f: Removed. 20586 siesta.F: New initatom interface. PDOS stub (not implemented yet). 20587 Remove call to plcharge. Use 'parse' module. Initialize 20588 array listhold after allocation. Explicit calls to 20589 routine superx after every kind of atomic move. 20590 sorting.f: New module, which includes: 20591 ordix.f ordvec.f order.f iorder.f: removed 20592 superx.f: put in module atomlist (and also as internal sub in coor.f) 20593 hsparse.f minvec.f: Changed to .f extension. Use 'sorting'. 20594 spher_harm.f: New module holding the Spherical Harmonics routines, 20595 with explicit interfaces. 20596 symbol.f: Removed. Included in module 'periodic_table'. 20597 sys.F: New module. Implements routines 'die' and 'bye'. These can 20598 be called to terminate an MPI job from anywhere in the program. 20599 transfer.f: Streamlined. 20600 types.f: Removed. Now called atm_types.f 20601 Makefile: Changed to reflect the additions and deletions. 20602 NetCDF/README: New file explaining some compatibility issues. 20603 fdf/fdf.f: Change name of block data. 20604 fdf/fdf_mod.f: New features. See documentation in file. 20605 fdf/fdf2.f fdf3.f: removed. 20606 fdf/parse.f: New file. A more powerful parser. See docs in file. 20607 fdf/makefile: updated. 20608 Docs/siesta.tex: Use makeidx package. Updated to reflect new changes. 20609======================================================================= 20610Version: 1.0.48 20611Date: 2001/01/23 17:30 GMT 20612Title: Bug Fix (nlcc + spin) 20613Author: Pablo Ordejon <ordejon@icmab.es> 20614 20615Description: 20616 20617Fixed bug reported by J. Junquera (on Jan 20 2001) and 20618G. Canto (Jan 22 2001). The bug produced wrong values 20619of the stress and forces for calculations with spin 20620polarization and non-linear core corrections (simultaneously). 20621 20622Files: 20623 meshsubs.F : Routine PartialCoreOnMesh corrected. 20624 Customary Docs/CHANGES and Src/version.F changes. 20625======================================================================== 20626Version: 1.0.47 20627Date: 2001/01/12 19:30 GMT 20628Title: Dynamic (re)allocation in MATEL 20629Author: Jose M. Soler <jose.soler@uam.es> 20630 20631Description: 20632 20633As a leftover of f77 static allocation requirement, the array 20634dimensions in MATEL are found using obscure formulas. F90 and the 20635alloc module allow a simpler and cheaper reallocation on the fly. 20636 20637Files: 20638 matel.f : Arrays reallocated on the fly, using alloc module 20639 Suppressed matel_init and matel_module 20640 Removed pure-spherical-harmonic requirement for orbitals 20641 atmfuncs.f: Allowed IO=0 in LOFIO and MOFIO (with result L=0) 20642 kinefsm.f : Removed 'use matel_module' statement 20643 naefs.f : " 20644 nlefsm.f : " 20645 overfsm.f : " 20646 phirphi.f : " 20647 radfft.f : G(NK) returns spilling of G(k) beyond Kmax 20648 siesta.F : Supressed call to matel init 20649 Added alloc_report initialization and printout 20650 Makefile : matel moved from module to normal routine 20651 Added dependence of matel.o on alloc.o 20652 Supressed dependences on matel_module 20653 siesta.tex: Added documentation of new option AllocReportLevel 20654======================================================================== 20655Version: 1.0.46 20656Date: 2001/01/09 11:00 GMT 20657Title: Bug fis in iomd.f 20658Author: Pablo Ordejon <ordejon@icmab.es> 20659 20660Description: 20661 20662A problem with the reading/writing in the MD files is solved. 20663The problem consisted in the inability of some compilers 20664to write once the EOF character was reached. 20665 20666 20667Files: 20668 iomd.f: Backspace command added 20669 Customary Docs/CHANGES and Src/version.F changes. 20670======================================================================== 20671Version: 1.0.45 20672Date: 2000/12/13 12:00 GMT 20673Title: Interface to K. Parlinski's PHONON program 20674Author: Alberto Garcia <wdpgaara@lg.ehu.es> 20675 20676Description: 20677 20678K. Parlinski's program PHONON can analyze the crystal structure and 20679provide a set of symmetry-irreducible atomic displacements with which 20680to compute the dynamical matrix and obtain the phonon dispersion 20681relations and other lattice-dynamical magnitudes. Siesta can now read 20682PHONON-provided information (basically in the MD.ATforPhonon and 20683PhononLabels blocks), carry out the required calculations (in a form 20684similar to that used for brute-force FC approach) and write a 20685SystemLabel.PHONON file that can be post-processed by PHONON. 20686 20687Files: 20688 phonon.F: Module implementing the interface routines. 20689 redata.F: Logic to decide when a PHONON calculation (idyn=7) is 20690 to be undertaken. 20691 siesta.F: Calls to phonon.F routines. 20692 Makefile: Addition of phonon.F. 20693 siesta.tex: Brief documentation of the interface. 20694 Customary Docs/CHANGES and Src/version.F changes. 20695======================================================================== 20696Version: 1.0.44 20697Date: 2000/12/12 19:46 GMT 20698Title: BUG FIXED. Ref. br-20001209-002 20699Author: Alberto Garcia <wdpgaara@lg.ehu.es> 20700 20701Description: 20702 20703Corrected bug reported by P. Ordejon: 20704Siesta was not parsing correctly the valence configuration 20705information if the pseudopotential file was generated in 20706a spin-polarized calculation. 20707 20708Files: 20709 atom.F: New code to process configuration string. 20710 Customary Docs/CHANGES and Src/version.F changes. 20711======================================================================== 20712Version: 1.0.43 20713Date: 2000/12/12 19:00 GMT 20714Title: Eigenvalue-only diagonalization for k-sampling 20715Author: Jose M. Soler <jose.soler@uam.es> 20716 20717Description: 20718 20719In the case of k-sampling, an initial diagonalization is now performed to 20720find the eigenvalues, the Fermi level and the occupation weights. 20721Since the eigenvectors cannot be stored because of memory limitations, 20722the diagonalization is later repeated to find them and the density matrix. 20723By calling the LAPACK diagonalization routine with an eigenvalue-only flag, 20724a major part of the CPU time of the first diagonalization can be saved. 20725 20726Files: 20727 cdiag.F: Add argument NEVEC with the number of desired eigenvectors 20728 If NEVEC==0, call ZHEGV with job='N' (eigenvalues only). 20729 Otherwise, find all eigenvectors, like previously. 20730 Supress FV argument in CDIAG and allocate it internally. 20731 Use realloc to allocate arrays. 20732 diag2g.F: " 20733 diagpol.f: " 20734 diagk.F: First call to CDIAG with NEVEC=0. Second with NEVEC=NUO 20735 diag2k.F: " 20736 diagkp.F: " 20737 Customary Docs/CHANGES, Docs/siesta.tex, and Src/version.F changes. 20738======================================================================== 20739Version: 1.0.42 20740Date: 2000/12/12 15:30 GMT 20741Title: BUG FIXED. Siesta 1.X. Ref. br-20001209-001 20742Author: Pablo Ordejon <ordejon@icmab.es> 20743 20744Description: 20745 20746Bug fixed: Siesta 1.X. Ref. br-20001209-001 20747 20748Corrected bug reported by A. Garcia: 20749Extrapolation of the density matrix for FC calculations, 20750when no DM file was present. Besides, an error was detected 20751in extrapol.F for the case of k-point sampling (where maxo 20752is different from maxuo) 20753 20754Files: 20755 siesta.F: Treat differently the extrapolation for FC calcs. with 20756 no DM files. 20757 extrapol.F: Fix bug (dimensions of aux matrix were wrong for 20758 k-point sampling calculations). 20759 Customary Docs/CHANGES and Src/version.F changes. 20760======================================================================== 20761Version: 1.0.41 20762Date: 2000/11/29 18:00 CET 20763Title: BUG FIXED. Routines 'initbands' in bands.F and 'fixed' in fixed.F 20764Author: Daniel Sanchez-Portal <sanchezp@uiuc.edu> 20765 20766Description: 20767 20768Two bugs corrected in 'initbands': 20769* Variable scale, defined as character*30, was broadcast and character*1 20770* switch added so kpoints are only broadcast to the other nodes if 20771 there is enough space to calculate and store them (nk.le.maxk) 20772One bug in subroutine 'fixed': 20773* The node reading the input was not specified 20774 20775Files: 20776 fixed.F: Fix bug 20777 bands.F: Fix bug 20778 Customary Docs/CHANGES and Src/version.F changes. 20779======================================================================== 20780Version: 1.0.40 20781Date: 2000/11/25 11:30 GMT 20782Title: BUG FIXED. Routine 'parabola' in atom.F 20783Author: Alberto Garcia <wdpgaara@lg.ehu.es> 20784 20785Description: 20786 20787Updated routine 'parabola' which deals with multiple zeta orbital 20788matching and was updated on branch siesta-0 after the fork (for some 20789reason the change was not detected earlier). This fix will cause 20790noticeable numerical differences in the 'split' routine output 20791concerning the kinetic, potential, and total energy of zeta>1 orbitals 20792in some limited cases (Fe in the Examples directory being one of 20793them). The orbital itself seems not to be noticeably affected. 20794 20795Files: 20796 atom.F : Updated routine parabola. 20797 Customary Docs/CHANGES and Src/version.F changes. 20798======================================================================== 20799Version: 1.0.39 20800Date: 2000/11/24 13:15 CET 20801Title: BUGS FIXED. endif missing in MPI part of cellxc.F 20802Author: Pablo Ordejon <ordejonicmab.es> 20803 20804Description: 20805 20806Bug fixed: endif missing in MPI part of cellxc.F 20807 20808Files: 20809 cellxc.F : Fix bug 20810 Customary Docs/CHANGES and Src/version.F changes. 20811======================================================================== 20812Version: 1.0.39 20813Date: 2000/11/23 16:15 CET 20814Title: BUGS FIXED: supercell call in dynamics loop + update of k-points 20815Author: Pablo Ordejon <ordejonicmab.es> 20816 20817Description: 20818 20819Several bugs have been corrected, that produced wrong results for 20820dynamics runs with k-points. The first affected the case of fixed 20821cells, and the second the case of variable cells: 20822 - The supercel setup for k-points was wrongly done only out of the 20823 dynamics loop for fixed dell. Corrected to setup within te loop. 20824 - The k-points were not updated for the variable cell case. 20825 Corrected to update them. 20826 20827Files: 20828 siesta.F : Fix bugs for supercell and k-points updates. 20829 Customary Docs/CHANGES and Src/version.F changes. 20830======================================================================== 20831Version: 1.0.38 20832Date: 2000/11/1 21:30 CET 20833Title: adding Harris forces for the first SCF step. 20834Author: Javier Junquera <javier.junquera@uam.es> 20835 20836Description: 20837 20838 When Harris functional is being used in a molecular 20839 dynamics simulation, the initial charge density of each step 20840 is always the sum of atomic charges. 20841 20842Files: 20843 siesta.F : Skip the extrapolation of the density matrix 20844 Initialize the density matrix in each SCF step 20845 redata.F: New variable harrisfun. Switch that fixes if 20846 Harris functional is going to be used. 20847 Customary Docs/CHANGES 20848======================================================================== 20849Version: 1.0.38 20850Date: 2000/11/1 13:00 CET 20851Title: adding Harris forces for the first SCF step. 20852Author: Javier Junquera <javier.junquera@uam.es> 20853 20854Description: 20855 20856 The computation of the forces for the Harris functional 20857 in the first SCF step has been implemented. This functional 20858 is a not self-consistent version of DFT. It is extremly 20859 cheap but not very accurate for system which involves 20860 great charge transfer. Suitable for long runs of 20861 molecular dynamics simulations. 20862 20863Files: 20864 siesta.F : Skip the diagonalization in the last step. 20865 meshsubs.F : Bug corrected in PartialCoreonMesh subroutine. 20866 Problem related with the distance of a given point 20867 of the grid to a given atom. If that distant is zero 20868 the point is not considered, and that's wrong. 20869 cellxc.F, xc.f : Derivatives of exchange-correlation potential 20870 respect the charge density. Only implemented 20871 for Perdew-Zunger parametrization (LDA) 20872 dfscf.f : Improved efficiency. 20873 dhscf.F : Reads the functional in which the computation of the forces 20874 will be based. Call to cellxc updated. Call to dfscf updated. 20875 New call to forhar. 20876 forhar.f: New subroutine where the potentials needed by dfscf for 20877 the Harris functional forces are built. 20878 redata.F: Automatic set up of DM.UseSaveDM, MaxSCFIterations and 20879 DM.MixSCF1 when Harris' forces are selected. 20880 Makefile: Added forhar.f 20881 Customary version.F, Docs/CHANGES and Docs/siesta.tex 20882======================================================================== 20883Version: 1.0.37 20884Date: 2000/10/09 20:15 CET 20885Title: correcting ibmp3.make and version.F 20886Author: Emilio Artacho <Emilio.Artacho@uam.es> 20887 20888Files: Sys/ibmp3.make 20889 version.F, CHANGES, siesta.tex 20890======================================================================== 20891Version: 1.0.37 20892Date: 2000/10/05 19:15 CET 20893Title: Improved efficiency vmat & rhoofd (buffer) / various for compiling 20894Author: Emilio Artacho <Emilio.Artacho@uam.es> 20895 20896Description: 20897 20898(1) vmat and rhoofd were less efficient than 0.12 corresponding ones 20899at least for some systems. The 'buffer' that keeps a piece of a matrix 20900in a non-sparse form has been increased (by 100) so that fewer unpdates 20901of this buffer have to be done in the whole procedure (J.M.Soler). 20902The efficiency is comparable now (even better). 20903 20904(2) Siesta has been compiled in the IBM SP2 machine in Lyon, both 20905parallel and scalar. Parallel compilation has also been done for 20906a large parallel Compaq machine in Grenoble. Makefiles and related. 20907 20908NOTE: The IBM didn't know about complex.2double, I removed it from mpi.F 20909 (not used) 20910 20911Files: 20912 rhoofd.f, vmat.f : improved efficiency 20913 ibmp3.make, ibmp3-mpi.make, compaq-mpi.make : (in Sys/) 20914 MPI/mpi.F, MPI/Makefile 20915 Customary version.F, Docs/CHANGES and Docs/siesta.tex 20916======================================================================== 20917Version: 1.0.36 20918Date: 2000/09/13 11:00 GMT 20919Title: Fix for plotting files / vmat speed up 20920Author: Julian Gale <j.gale@ic.ac.uk> 20921 20922Description: 20923 20924The format of files for use in Plrho was changed due to necessity for 20925the parallelisation because the density matrix was not stored on any 20926one node in a complete form. Hence Plrho has had to be modified to 20927reflect this. Also a bug in iorho relating to this change has been 20928fixed. 20929Also the implicit loops have been removed from several places in vmat 20930to improve performance with current compilers. In addition, a few 20931other performance enhancements have been introduced through the use 20932of local variables to reduce the number of multiplications in important 20933parts of the code. 20934 20935Files: 20936 20937 iorho.F : The wrong dimension was being used in the inner loop 20938 : and has therefore been corrected. 20939 plrho.f : Format of files from iorho changed to new form. 20940 vmat.f : Implicit loops / sum function removed + VClocal added 20941 : to reduce number of multiplications. 20942======================================================================== 20943Version: 1.0.35 20944Date: 2000/08/10 13:00 GMT 20945Title: Change in .DM format 20946Author: Julian Gale <j.gale@ic.ac.uk> 20947 20948Description: 20949 20950The main change is to the way in which the .DM file is written. The 20951form of the statements has been changed to something much closer to 20952how it used to be written before the parallelisation forced some 20953changes. This was done because of poor performance during disk writes 20954on a cluster of machines with a remote mounted disk and will generally 20955benefit the speed of writes, though not always quite as dramatically 20956as in this case. Also a couple of minor changes were made to avoid 20957compiler hiccups and warning messages. 20958 20959Files: 20960 alloc.F90 : argument "type" declared as (len=*) in type_mem for 20961 : the benefit of the PG compiler 20962 cellxc.F : 0.0d0 -> 0.0 in a couple of places to avoid type 20963 : conversion warnings 20964 iodm.F : form of write statements adjusted to maximum number 20965 : of writes per statement within parallel constraints 20966======================================================================== 20967Version: 1.0.34 20968Date: 2000/07/29 17:30 GMT 20969Title: Change to PCC to remove spurious forces 20970Author: Julian Gale <j.gale@ic.ac.uk> 20971 20972Description: 20973 20974Certain runs on a high symmetry system were found to give large 20975symmetry breaking forces for some atoms on a special position 20976but not all when using partial core corrections in the pseudo 20977potential. The problem was trace back to very small values of 20978the distance between the mesh points and atoms. 20979 20980Files: 20981 meshsubs.F : r > tiny check has been added to trap small distances 20982 : that lead to spurious forces 20983 siesta.F : comments stating that KSV_pol is not sorted for parallel 20984 : use have been removed as this is no longer true 20985======================================================================== 20986Version: 1.0.33 20987Date: 2000/07/05 16:00 GMT 20988Title: Re-organization of atomic information. Other structural changes. 20989Author: Alberto Garcia <wdpgaara@lg.ehu.es> 20990 20991Description: 20992 20993-- Completely new replacement for atmfuncs module. 20994 20995Created a set of derived types to hold the information relative 20996to the atomic basis and pseudopotentials. The new structures are 20997somewhat more flexible and lean than the old ones. The functions in 20998atmfuncs have been re-implemented accordingly. 20999 21000A new module 'types.f' holds the derived types (which might still be 21001streamlined somewhat). In 'transfer.f', the information is transferred 21002from the old atomic structures to the new ones. The old atmfuncs 21003module has been renamed to 'old_atmfuncs'. The new structures are also 21004used in dump2cdf.F, which creates self-describing files with the 21005atomic information (see below). 21006 21007Atom.F and redbasis.F are left mostly untouched for now. 21008 21009The old dimensioning parameters (still useful for old_atmfuncs, atom, and 21010redbasis) are kept in 'atmparams'. 21011 21012Created a "radial function" derived type (not general enough, but 21013useful for atmfuncs) which encapsulates the linear grid and the 21014'splint' operation needed to interpolate on it. Presumably other types 21015appropriate for logarithmic meshes, more general functions, etc, could 21016be defined as well. The code is in 'radial.f', although the type 21017definition is still in types.f. 21018 21019-- Matel.f 21020 21021Allocatable arrays local to matel turned into automatic arrays, which 21022are allocated and deallocated automatically by the compiler. (The SGI 21023had problems deallocating one of the arrays). This solution (also 21024used in parsing.f) is the cleanest one for relatively small 21025arrays. For larger sizes, the process could run into stack limits 21026(which could in principle be circumvented by the use of the "limit(s)" 21027or "ulimit(s)" shell command). 21028 21029-- Siesta.F atomlist.f atminit.F 21030 21031Some streamlining of the code. Created a new module "atomlist" which 21032holds isa, xa, lasto, etc, and contains initatomlists and superc 21033(which does nothing but reallocate arrays if needed and expanding xa, 21034etc to the virtual supercell). Eventually, "atomlist" could be use(d) 21035by the routines which need those arrays. Regarding the treatment of 21036the "real" and the "virtual" supercell, "ncells", "na", "no", etc, 21037meant different things in different places, and one had to be very 21038careful about it. In the new version, the program knows nothing about 21039the supercell specified in the input file (as the manual says it 21040should). It only deals with "na_u" and "no_u", respectively the number 21041of atoms and the number of orbitals in the unit cell. If the use of 21042k-points forces the use of a "virtual" supercell, one needs also 21043"na_s" and "no_s". Those variables also live in module 21044'atomlist'. Also, "nuo" (the number of orbitals local to the node) has 21045been renamed to "no_l". 21046 21047atminit.F could really be part of the atomic suite in the future. 21048 21049-- OrderN issue: If the user requests k-points for an ordern calculation, 21050the program fails as some arrays are accessed beyond their dimensions. 21051Inserted a trap for (.not. gamma) before the call to ordern to check it. 21052Eventually the supercell variables should be made private to the small group 21053of routines which really need them... 21054 21055-- Use of new 'alloc' module by Jose. 21056 21057It has been integrated as Src/alloc.F90, with some minor changes and 21058fixes (and a change of the module name to just 'alloc' instead of 21059'alloc_module'). It is used by siesta.F, coor.f, and atomlist.f to 21060deal with the atomlist arrays. 21061 21062 -- Redata.F coor.f init_spin.f 21063 21064Eliminated the call to 'recoor' inside redata and replaced it by a 21065call from siesta to a new routine 'coor'. This almost eliminates the 21066need to call 'resize', except to initialize nspin. For now, 21067'init_spin' does only that bit, but it could be extended to do the 21068rest of the spin-related readings. 21069 21070-- NetCDF hooks 21071 21072Included support for the use of data files which are self-describing 21073and thus readable in a wide variety of ways. I have chosen the netCDF 21074format, which I think is powerful enough for our purposes. If the user 21075compiles Siesta with the NetCDF option (enabled in arch.make with a 21076couple of lines), the program will generate files with extensions 21077".dump.nc" for each of the species, containing the orbitals, KB projs, 21078etc. The 'ncdump' utility which comes with netCDF can be used to 21079produce a human readable form of the files, and other tools (such as 21080Python, or other compiled Fortran programs) can be used to provide any 21081desired information. The basis information can also be read from the 21082.dump.nc NetCDF files by renaming them to .basis.nc and specifying 21083'new-user-basis' in the fdf file. (This capability is restricted for now to 21084NetCDF-capable implementations). 21085 21086-- NetCDF interface 21087 21088A new directory NetCDF contains the F90 interface to the NetCDF 21089library Version 3.5 (whose source is kept in a separate cvs 21090repository, in case it is needed). Note that the interface is 21091relatively new, and only works with that version of NetCDF. 21092 21093-- MPI interface 21094 21095Upgraded the MPI F90 interface by using kind numbers for the 21096generation of the module procedures which are then overloaded. A 21097single file "Interfaces.f90" is now produced. Cray users can now avoid 21098editing mpi.f90, as the necessary type fiddlings are done in a 21099preprocessor block in mpi.F. 21100 21101-- Slight change to the arch.make macros. 21102 21103In order to support the new MPI and NetCDF interfaces, new macros have 21104to be defined in the arch.make file. Examples for Linux, SGI64, and 21105Osfdxml-cdf have been created in the Src/Sys file. (All of them with 21106NetCDF support which can be overridden). 21107 21108 21109-- Use of kind parameters in declarations and tagging of real constants. 21110 21111Started using the 'kinds' defined in precision.F (note the change to 21112allow a possible Cray-related preprocessing) in some files. The only 21113way to avoid precision-related pitfalls is to stick to consistent 21114declarations and the tagging of all real constants. See in particular 21115routine 'linmin' in file 'cgwf.F'. 21116 21117-- Parse routine 21118 21119Some of the %blocks in Siesta have lots of structure. Reading or 21120modifying it can be difficult. We are looking for ways to make 21121'parse' more powerful. Eventually, it will live in a module of its own 21122together with extra data structures which won't have to be declared in 21123the calling routine. For now, a new module 21124('parsing') has been created. As a more 21125techical note also mentioned above, the allocatable 21126arrays have been replaced with automatic ones. 21127 21128-- FDF2 module 21129 21130As an exercise, created another fdf interface module which 21131contains a generic 'fdf_get' routine. It is called 'fdf2' and used 21132for illustration purposes in 'coor.f' and 'spin_init.f'. 21133 21134-- IONode 21135 21136Routines which formerly called MPI_Comm_Rank to find out whether 21137it was OK to do IO can now just import the logical variable 'IOnode' from 21138module 'ionew'. (Eventually ionew will contain all the stuff now in 'io'). 21139The variable is initialized by a call to 'io_setup' in siesta.F. 21140 21141-- Interface blocks 21142 21143File interfaces.f contains interface blocks for ordern and 21144hsparse. Eventually, it would be desirable to provide explicit 21145interfaces for all the routines in the package (via interface blocks 21146or by the use of modules). 21147 21148Changed, New, and Replaced files: Too many to list here (see the more 21149relevant cases in description above). 21150 21151======================================================================== 21152Version: 1.0.32 21153Date: 2000/06/19 22:00 GMT 21154Title: Handling of nonpositive density in exchange-correlation routines 21155Author: Jose M. Soler <jose.soler@uam.es> 21156 21157Description: 21158 21159The handling of negative or zero densities has been corrected and 21160homogenized across xc routines. The DENMIN parameter has been 21161decreased to 1.d-15, to avoid small energy errors. Documentation for 21162the noncollinear spin option added to cellxc interface. 21163 21164Files: 21165 xc.f : Corrected overflow bug. DENMIN decreased 21166 cellxc.F : Corrected ISPIN loop limit. ABS(D) changed by MAX(0.d0,D) 21167======================================================================== 21168Version: 1.0.31 21169Date: 2000/06/16 16:00:00 GMT 21170Title: Fix of order N, stress fixing and tidying of prmem. 21171Author: Julian D. Gale <j.gale@ic.ac.uk> 21172 21173Description: 21174 21175The problem with the serial version of order N dimension checking 21176has been corrected and the references to prmem removed as they 21177are now defunct. Also the ability to fix stresses has been added 21178to the geometry constraints. 21179 21180Files: 21181 cellxc.F : trapping of densities less than denmin added to 21182 : avoid floating point crashes in XC routines 21183 fixed.F : stress fixing option added 21184 ksv.F : prmem removed from list of external routines 21185 Makefile : prmem.o removed from list of objects 21186 neighb.f : prmem removed from comment as no longer needed 21187 on_subs.F : bug in axb_build1 corrected due to listb references 21188 prmem.f : removed as no longer used 21189 ranger.f : prmem removed from list of external routines 21190 siesta.F : extra MPI_Barrier added after final printmemory to 21191 : tidy parallel output 21192 : call to prmem removed as no longer used 21193 siesta.tex : stress fixing documented 21194 version.f : Version number incremented to 1.0.31 21195======================================================================== 21196Version: 1.0.30 21197Date: 2000/05/16 01:30:00 GMT 21198Title: Removed single precision in recipes.f 21199Author: Jose M. Soler <jose.soler@uam.es> 21200 21201Description: 21202 21203A conversion to single precision, originally in the Numerical Recipes 21204routine four1, was removed. Apparently this was the main source of 21205minor numerical discrepancies between different computers. 21206Also, all constants were transformed from single to double precision. 21207The output files in siesta/Examples were also updated. 21208 21209Files: 21210 recipes.f : Removed calls to SNGL 21211 Examples/H2O/Out/h2o.out : Updated (with cefeo/osfdxml.make) 21212 Examples/H2O/Out/out.fdf : " 21213 Examples/H2O/OrderN/h2o.fdf : " 21214 Examples/H2O/OrderN/out.fdf : " 21215 Examples/SiH/Out/sih.fdf : " 21216 Examples/SiH/Out/out.fdf : " 21217 Examples/Fe/Out/Fe.fdf : " 21218 Examples/Fe/Out/out.fdf : " 21219 version.f : Updated version number and date 21220 Docs/siesta.tex : Updated date 21221 Docs/CHANGES : This entry 21222======================================================================== 21223Version: 1.0.29 21224Date: 2000/05/01 13:00:00 GMT 21225Title: Band calculation bug fixes etc 21226Author: Julian Gale <j.gale@ic.ac.uk> 21227 21228Description: 21229 21230A couple of problems concerned with band structure calculations 21231which were brought to light by one of Daniels students have been 21232fixed as well as a missing format descriptor from an error 21233message. 21234 21235Files: 21236 atom.F : missing "i4" output descriptor for error message 21237 : added concerning insufficient L projectors 21238 bands.F : mscell(3,3) declared locally and added to redcel call 21239 : references to nuo changed to nuotot in several places 21240 : as this was leading to incorrect output to the .bands 21241 : file 21242 ksv.F : redcel removed from list of external routines 21243 version.f : Version number incremented to 1.0.29 21244======================================================================== 21245Version: 1.0.28 21246Date: 2000/04/28 17:00:00 GMT 21247Title: New compilation scheme. Reading from stdin. Matel fix. 21248Author: Alberto Garcia <wdpgaara@lg.ehu.es> 21249 21250Description: 21251 21252For a number of reasons, the architecture support in the makefiles is 21253now implemented by including "arch.make" (that is, a fixed-name file, 21254instead of "$SIESTA_SYS.make"). All references to SIESTA_SYS have been 21255eliminated, so even if it is still in the environment nothing should be 21256messed up. A new makefile variable SIESTA_ARCH is used for identification 21257purposes. 21258 21259Also, reinit now allows the FDF input to be read through standard 21260input, as in siesta < h2o.fdf. To support debugging sessions, siesta 21261will read from INPUT_DEBUG if this file exists (and warn about it). 21262NOTE: In some platforms, the siesta executable must reside in the same 21263directory as the files for things to work properly (this happens to 21264the parallel version in Linux). 21265 21266A minor (cosmetic) fix to matel: some arrays did not need to be saved, 21267as they were deallocated upon exit. 21268 21269Files: 21270 Docs/siesta.tex : Revamping and removal of obsolete sections. 21271 matel.f : Array declarations. 21272 version.f : Version number incremented to 1.0.28 21273 reinit.F : Support for dual input. 21274 resize.F : More graceful exit. 21275 Makefile : arch.make support. 21276 Sys/*.make : Some pruning of old files, updates. 21277 MPI/Makefile : arch.make support. 21278======================================================================== 21279Version: 1.0.27 21280Date: 2000/04/12 4:00:00 GMT 21281Title: Spin polarisation corrections 21282Author: Julian Gale <j.gale@ic.ac.uk> 21283 21284Description: 21285 21286Three bugs relating to spin polarised calculations have been fixed 21287as well as an issue relating to the use of a variable in atom.F 21288detected by a compiler. 21289 21290Files: 21291 atom.F : q renamed to qtmp in choverlp 21292 dhscf.F : Dscf -> Dscf(1,ispin) in call to rhoofd 21293 : Hmat -> Hmat(1,ispin) in call to vmat 21294 siesta.F : S(jo) -> S(ind) in calculation of qspin() 21295 version.f : Version number incremented to 1.0.27 21296======================================================================== 21297Version: 1.0.26 21298Date: 2000/03/30 9:30:00 GMT 21299Title: Slight fixes to timing and vibrations 21300Author: Julian Gale <j.gale@ic.ac.uk> 21301 21302Description: 21303 21304As a result of running on the Cray with uninitialised variables set to 21305NaN a few small possible problems were indentified for machines which 21306do not default to static memory. Also a few similar issues were found 21307in the course of testing parallel frequency calculations and have 21308been cleaned up. 21309 21310Files: 21311In Src/ 21312 ofc.f : Reading of .FC file altered to avoid crash on Cray. 21313 siesta.F : Tempion initialised to zero and printing for FC option 21314 : modified. 21315 timer.F : Variables "count_rate" and "wt" saved between calls 21316 : in elap1. 21317 version.f : Version number incremented to 1.0.26 21318In Util/Vibra/Vibra 21319 fcbuild.f : Logical "overflow" initialised to false 21320 Makefile : ARCH environment variable changed to SIESTA_SYS for 21321 : consistency with main program 21322 vibrator.f : Logical "overflow" initialised to false 21323 : Variable "nk" initialised to zero 21324 : Call to outbands suppressed if nk = 0 21325 : Typo corrected - "Writting" -> "Writing" 21326 Sys/t3e.make : Make options for Cray T3E added 21327======================================================================== 21328Version: 1.0.25 21329Date: 2000/03/29 8:30:00 GMT 21330Title: 21331Author: Julian Gale <j.gale@ic.ac.uk> 21332 21333Description: 21334 21335There have been several major changes for this release : 21336 21337(1) The array listh has now been distributed across the processors 21338(2) The storage format of the main sparse arrays, H, S, Dscf, listh etc 21339 has been changed to be more compact. Hence for any given spin these 21340 arrays are now 1-D instead of 2-D, thus eliminating the storage of 21341 any zeros (except the tolerance at the end of listh to avoid recalling 21342 hsparse). The start of any row, n, of the sparse matrix can now be found 21343 at "listhptr(n)+1". 21344(3) dhscf.F has been heavily modified to make it more modular. Hence it 21345 has largely been reduced to a series of subroutine calls which use 21346 routines from meshsubs.F and meshmatrix.F. All references to the 21347 density matrix in mesh-local stored form have been abstracted to a 21348 module so that it and its pointers are not directly seen at the dhscf 21349 level. Likewise the transformations from orbital to mesh-local storage 21350 via MPI have been localised in 2 subroutines so that the majority of 21351 high level mesh routines no longer call MPI. 21352(4) The dimension of the array within has been corrected to maxphi in all_phi 21353 as this can lead to floating point errors otherwise. 21354(5) The storage of phi has been re-ordered according to Jose's suggestion 21355 so that it is ordered by mesh points rather than orbitals. This has 21356 led to the removal of the call to transp and some related arrays as 21357 the data is already in the transposed form. Similarly the 21358 calculation of Phi has been simplified (at the expensive of some 21359 potential CPU savings) leading to removal of options, such as SaveMemory. 21360(6) An extra check has been added to the mesh initialisation. For non-right 21361 angled unit cells there used to be the possibility that the mesh cut-off 21362 might not be greater than the requested value. A new check has been 21363 added that guarantees that it will be satisfied by increasing NTM. 21364(7) The value of ncmax is now initialised to zero in iolwf if no file is 21365 found otherwise the value could be NaN and is then used to allocate 21366 memory in ordern leading to a memory error. 21367(8) Parallelisation of KSV added 21368(9) Bug in grdsam fixed - pt was not preserved between calls 21369 21370Files: 21371 atmfuncs.F : The dimension of "within" has been corrected to maxphi in all_phi 21372 : The default value of nzetmx has been increased to 3 21373 atom.F : Calls to prmem removed as the memory is dynamically created. 21374 atomlwf.F : Modified to allow for local nature of numh,listhptr,listh including 21375 : globalisation of numft which is now needed as a result 21376 bands.F : Modified to allow for local nature of numh,listhptr,listh 21377 cgwf.F : Modified due to new sparse form of arrays 21378 chempot.F : Modified due to new sparse form of arrays + loop conversion to f90 21379 denmat.F : Modified due to new sparse form of arrays + local nature of storage 21380 : numh/listh/listhptr 21381 detover.f : Re-named to detover.F as CPP options are present 21382 detover.F : Modified due to new sparse form of arrays 21383 : Aux re-sized to nocc x nocc and parallelisation added 21384 dfscf.F : Renamed to dfscf.f as all MPI calls have been removed 21385 dfscf.f : Argument maxorb removed and Dscf/DscfL changed to new format 21386 : Internal logical Parallel introduced to handle choice of Dscf or DscfL 21387 : The gradients are now calculated using a call to all_phi for speed 21388 dhscf.F : Globalisation of dipol(3) moved into dipole.F 21389 : Argument maxorb removed and Hmat/Dscf changed to new format 21390 : dipol(1:3) initialise to zero to avoid floating point crash in grdsam.F 21391 : for "bulk" case 21392 diag2g.F : Modified due to new sparse form of arrays + loop conversion to f90 21393 diag2k.F : Modified due to new sparse form of arrays + loop conversion to f90 21394 diagg.F : Modified due to new sparse form of arrays + loop conversion to f90 21395 diagk.F : Modified due to new sparse form of arrays + loop conversion to f90 21396 diagkp.F : Modified to allow for local nature of numh,listhptr,listh 21397 : Globalisation of pointers to H and S added 21398 diagon.F : Modified due to new sparse form of arrays 21399 diagpol.f : Modified due to new sparse form of arrays + loop conversion to f90 21400 : Modified to allow for parallel execution by changing the order of 21401 : referencing Haux/Saux and looping on the left by nuotot and on the 21402 : right by nuo. 21403 dipole.F : Globalisation of dipole now in subroutine 21404 dynamics.F : Contents of array "sold" now preserved between calls 21405 egandd.F : Modified due to new sparse form of arrays + frstme variable removed 21406 ener3.F : Modified due to new sparse form of arrays + local nature of storage 21407 : numh/listh/listhptr 21408 extrapol.F : mm2/mnew changed to 2-D array of size (maxnh,nspin) + maxno->maxnh + 21409 : modifications to allow for the fact that the sparse indexing arrays 21410 : are now local only 21411 extrapolon.F : version of extrapol created for order(N) using the old sparse matrix form 21412 : as the format has yet to be changed in this section of the code 21413 gradient.F : Modified due to new sparse form of listh + local nature of storage 21414 : numh/listh/listhptr 21415 grdsam.F : Argument maxorb removed and Hmat/Dscf changed to new format + loops 21416 : changed to f90 form for compactness 21417 : Array pt preserved between calls as the contents are only read once 21418 : and dimensions corrected to 3 x (maxpt+1). 21419 hsparse.F : Modified due to new sparse form of listh + local nature of storage 21420 : numh/listh/listhptr. 21421 : Trap for nuo = 0 added for setting nlhmax 21422 idiag.f : shared do loop termination removed 21423 initdm.F : Dscf/Dold changed to 2-D array of size (maxnh,nspin) + maxno->maxnh + 21424 : listh now in 1-D form and a pointer to the start of the rows is added 21425 : and passed through to iodm.F 21426 iodm.F : dm changed to 2-D array of size (maxnh,nspin) + maxno->maxnh 21427 iohs.F : Format of saved H/S/xij changed to match new linear form 21428 iolwf.F : ncmax initialised to 0 if found = .false. 21429 kinefsm.F : Renamed to kinefsm.f as all MPI calls have been removed 21430 kinefsm.f : Renamed kinefsm.F with Node and Nodes added to argument list 21431 : Dscf made into 2-D array and maxnd is equal to maxnh 21432 ksv.F : Modified due to new sparse form of arrays and parallelisation. 21433 : Copy of psi into psiprev moved to detover/savepsi 21434 listsc.f : Trivial typo - corrected in a comment 21435 Makefile : new routines added to list and dependances on meshmatrix.F and meshsubs.F 21436 matel.f : Calls to prmem removed as the memory is dynamically created. 21437 meshmatrix.F : A collection of a module that contains data for the matrix Dscf 21438 : stored locally with respect to the mesh rather than the orbitals 21439 : and two subroutines that transform forward and backwards between 21440 : the two local arrangements 21441 meshsubs.F : A collection of subroutines that perform tasks on the mesh. The is a 21442 : composed of code that used to all be in dhscf.F but with changes to 21443 : the code that calculates the wavefunctions at the mesh points. This 21444 : part has been changed so that the data is ordered by mesh point and 21445 : simplified according to Jose's algorithm 21446 minvec.F : shared do loop termination removed 21447 mulliken.F : Modified due to new sparse form of arrays + local nature of storage 21448 : numh/listh/listhptr 21449 nlefsm.F : Renamed to nlefsm.f as all MPI calls have been removed 21450 nlefsm.f : Renamed nlefsm.F with Node and Nodes added to argument list 21451 on_subs.F : Two versions of the subroutine axb_build have now been added 21452 : suffixed by 1 or 2. axb_build2 is the same as the old routine 21453 : whereas axb_build1 is a modified form to allow for the more 21454 : dense sparse storage algorithm used in the main part of the 21455 : code, but not yet in the ordern section. 21456 ordern.F : Modified due to new sparse form of arrays and call to extrapol 21457 : replaced by call to extrapolon 21458 overfsm.F : Renamed to overfsm.f as all MPI calls have been removed 21459 overfsm.f : Renamed overfsm.F with Node and Nodes added to argument list 21460 : Escf made into 2-D array and maxnd is equal to maxnh 21461 phirphi.f : Modified due to new sparse form of arrays and for parallel form. 21462 : nuotot, Node and Nodes added to argument list 21463 plcharge.f : Renamed to plcharge.F as it now requires MPI use 21464 plcharge.F : Created from plcharge.f but modified to reflect the new sparse 21465 : array indexing form and the fact that this information is local. 21466 pulayx.F : Modified due to new sparse form of arrays + local nature of storage 21467 : numh/listh/listhptr 21468 redata.F : Default value of MemoryScale has been changed to 1.0 21469 rhooda.f : The accessing of data has been modified to reflect the fact that 21470 : quantities are now order by mesh points, leading to the removal 21471 : of some of the indexing arrays. Also the argument list has been 21472 : shortened because a number of parameters are now in the "mesh" 21473 : /"meshphi" modules. 21474 rhoofd.F : Renamed to rhoofd.f as all MPI calls have been removed 21475 rhoofd.f : Created from rhoofd.F and modified so that the much of the grid 21476 : related data is stored in modules rather than being passed as 21477 : arguments. The choice between Parallel and serial forms of use 21478 : Dscf is made internally now and the new sparse format is included. 21479 savepsi.F : New routine to copy psi to psiprev in ksv.F while handling the 21480 : parallel distribution of data. 21481 siesta.F : Sparse storage of H,H0,S,xijo,Dscf,Dscfsave changed to save memory 21482 : H,H0 and S now only allocated after first call to hsparse 21483 : Some loops converted to f90 form to condense code 21484 : Node and Nodes added to argument list of kinefsm/nlefsm/overfsm/ 21485 : xijorb 21486 : Commented out calls to prmem removed for tidyness 21487 : Variable nnomax has been removed. 21488 : The extra safety margin added to the length of listh has been 21489 : reduced to 5% from 10% - because the array is 1-D there should 21490 : less need for changes as variation betweens will now cancel 21491 : each other out partially. 21492 transp.f : Deleted as it is no longer needed 21493 version.f : version number incremented to 1.0.25 21494 vlist.F : Removed to simplify dhscf.F as it was never called. 21495 vmat.F : Renamed to vmat.f as all MPI calls have been removed 21496 vmat.f : Created from vmat.F and modified so that the much of the grid 21497 : related data is stored in modules rather than being passed as 21498 : arguments. The choice between Parallel and serial forms of use 21499 : Vs is made internally now and the new sparse format is included. 21500 xijorb.F : Renamed to xijorb.f as all MPI calls have been removed 21501 xijorb.f : Renamed xijorb.F with Node and Nodes added to argument list 21502 xijorb.f : xijo changed to 2-D array of size (3,maxnh) and nomax->maxnh 21503======================================================================== 21504Version: 1.0.24b (version array not changed in program) 21505Date: 2000/03/28 11:00:00 GMT 21506Title: Minor cosmetic changes. Wall-time output 21507Authors: Alberto Garcia <wdpgaara@lg.ehu.es> 21508 21509Description: 21510 21511The timing routine now generates an extra file "WALLTIME" with 21512*elapsed* time. Added routines 'elap1' and 'timer1'. 21513 21514Some minor changes to the FDF package, to remove output to unit 0 and 21515to improve the makefile. An extra routine fdf_inhibit, has been added 21516for future use. 21517 21518Minor changes to MPI/Makefile to simplify the 'clean' procedure. 21519 21520Files: 21521 21522timer.F 21523fdf/fdf.f 21524 fdf_mod.f 21525 makefile 21526MPI/Makefile 21527======================================================================== 21528Version: 1.0.24 21529Date: 2000/01/27 11:30:00 GMT 21530Title: Errors in siesta.F corrected 21531Author: Julian Gale <j.gale@ic.ac.uk> 21532 21533Description: 21534 The first dimension of the array ebk has been corrected to nuotot 21535 instead of nuo in siesta.F, the dimension being passed to bands 21536 being adjusted accordingly, so that the parallel operation is 21537 correct. Also "bands" is now only called if nbk > 0 as there is 21538 no setup to be done within "bands". 21539Files: 21540 siesta.F 21541======================================================================== 21542Version: 1.0.23 21543Date: 2000/01/27 9:30:00 GMT 21544Title: Error in allocation of ebk corrected in siesta.F 21545Author: Julian Gale <j.gale@ic.ac.uk> 21546 21547Description: 21548 The array ebk in siesta.F was allocated within the check to see 21549if nbk was greater than maxbk. However, this only happened if nbk 21550> 1 leading to an error for a single K point. Allocation has now 21551been moved until after maxbk is known. 21552 21553Files: 21554 siesta.F 21555======================================================================== 21556Version: 1.0.22 21557Date: 2000/01/24 16:00:00 GMT 21558Title: Fixes to bands.F / dhscf.F / atom.F 21559Author: Julian Gale <j.gale@ic.ac.uk> 21560 21561Description: 21562 A number of bugs have been uncovered and fixed as described below. 21563Files: 21564 atom.F : in SPLIT a value of rphi was accessed where uninitialised 21565 bands.F : the use of fdf for reading the BandLines was incorrect 21566 : and has been amended. Also, for simplicity and safety 21567 : a "band" module has been created containing a routine 21568 : "initbands" which initialises the data for bands and a 21569 : true call to "bands" which actually performs the band 21570 : structure calculation. This avoids the passing of 21571 : uninitialised data arrays during the initialisation 21572 : phase. 21573 dhscf.F : the arrays used to store the previous calls atomic 21574 : coordinates failed to reflect the fact that the 21575 : supercell might increase in size for a variable cell 21576 : run with multiple K points. Hence now the sizes are 21577 : checked first and SAMEXA is set to false if the sizes 21578 : differ and the arrays are re-dimensioned. Also the 21579 : size of NeedDscfL has been corrected to NUO instead 21580 : of NORB, as has the referencing during DHSCF4 which 21581 : included redundant work for supercells. 21582 initdm.F : the names of variables have been altered to reflect 21583 : the fact that the routine operates on just the unit 21584 : cell and not the supercell when addressing certain 21585 : indices. This is a purely cosmetic change for 21586 : consistency with other parts of the program. 21587 siesta.F : the calls to bands have been modified to reflect the 21588 : new form of initbands/bands. This has led to a cleaner 21589 : allocation of dynamic memory. 21590======================================================================== 21591Version: 1.0.21 21592Date: 2000/01/11 10:30:00 GMT 21593Title: Fixes and cosmetic improvements to avoid compiler warnings 21594Author: Julian Gale <j.gale@ic.ac.uk> 21595 21596Description: 21597 Two bugs have been fixed, namely the loss of constraint information 21598 in fixed.F due to deallocation of the arrays between calls and an 21599 uninitialised array access in "split" due to the wrong looping upper 21600 bound. Also cosmetic changes have been made to remove compiler 21601 warnings about features which do not strictly comply with the f90 21602 standard (deprecated features) for cleaner compilation on some 21603 machines. 21604Files: 21605 arw.F : numbered do loops on executable line removed 21606 atom.F : loop over 1->nrmax changed to 1->nrval to avoid floating 21607 : point error due to accessing an uninitialised array 21608 : element 21609 detover.f : dcmplx -> cmplx / dimag -> aimag / dreal -> real 21610 dhscf.F : shared do loop termination removed 21611 diagon.F : ParallelOverK only set on first call now and saved 21612 dismin.f : shared do loop termination removed 21613 egandd.F : parameter "nc" no longer passed to ctrans1 21614 ener3.F : commented dimensions of numhij corrected 21615 fixed.F : arrays ctype / iac / xc allocated on first call and never 21616 : deallocated 21617 inver.f : shared do loop termination removed 21618 linpack.F : dcmplx -> cmplx / dimag -> aimag / dreal -> real 21619 minvec.F : shared do loop termination removed 21620 on_subs.F : parameter "nc" no longer used - array dimension set using 21621 : ncmin and ncmax 21622 pulayx.F : shared do loop termination removed 21623======================================================================== 21624Version: 1.0.20 21625Date: 2000/01/08 00:01:00 GMT 21626Title: Improved performance with DirectPhi option 21627Author: Jose M. Soler <jose.soler@uam.es> 21628 21629Description: 21630 The performance with option DirectPhi, in which the orbitals are 21631 calculated 'on the fly' at grid points, has been improved by 21632 obtaining all the orbitals of one atom in a single call. 21633 Also, routines rhoofd and vmat have been slightly rewritten to 21634 avoid references to large global arrays within the inermost loop. 21635Files: 21636 atmfuncs.f : New routine all_phi 21637 rhoofd.F : Calls all_phi instead of phiatm 21638 vmat.f : Calls all_phi instead of phiatm 21639======================================================================== 21640Version: 1.0.19 21641Date: 2000/01/04 13:00:00 GMT 21642Title: Correction to memory allocation in egandd.F 21643Authors: Julian Gale <j.gale@ic.ac.uk> 21644 21645Description: 21646 Memory allocation in egandd.F didn't reflect the fact that the 21647 bands are distributed across the nodes for some arrays leading 21648 to unnecessarily large memory usage in parallel. 21649File: 21650 egandd.F 21651======================================================================== 21652Version: 1.0.18 21653Date: 2000/01/04 12:50:00 CET 21654Title: Bug fix in grid-cell sampling (improved mesh-cutoff convergence) 21655Author: Emilio.Artacho@uam.es 21656 21657Description: 21658 Bug discovered by Daniel SP, forces where not adequately updated 21659File: 21660 grdsam.F (plus customary siesta.tex, CHANGES, version.f) 21661======================================================================== 21662Version: 1.0.17 21663Date: 1999/12/19 12:30:00 GMT 21664Title: Fixes to ordern and vlist 21665Authors: Julian Gale <j.gale@ic.ac.uk> 21666 21667Description: 21668 21669A couple of bug fixes have been introduced : 21670 21671(1) The array nindv was being passed from eandg to axb_build with 21672 the wrong size declaration on the second call. This led to an 21673 out of bounds error which showed up as a crash in iolwf for 21674 some runs. The arrays ind and nindv are now locally created 21675 in axb_build with the sizes needed for a given call to avoid 21676 any possible errors during calling. 21677(2) The list of arguments for vlist was inconsistent with the call 21678 from dhscf.F. The auxillary array parameters are now handled 21679 using local dynamic memory. This error was not really detected 21680 as vlist never seems to get called. 21681 21682Files: 21683 21684egandd.F : ind and nindv have been removed 21685on_subs.F : ind and nindv are now locally allocated in axb_build 21686vlist.F : MaxInd and ind removed from argument list and ind is now 21687 : dynamically allocated 21688======================================================================== 21689Version: 1.0.16 21690Date: 1999/12/17 9:15:00 GMT 21691Title: Fixes to ordern/iolwf + supercell creation 21692Authors: Julian Gale <j.gale@ic.ac.uk> 21693 21694Description: 21695 21696A number of small changes have been made; 21697 21698(1) There were errors in the handling of restarts for ordern 21699 calculations due to dynamic memory allocation which have 21700 been fixed. 21701(2) The use of listcold between ordern and extrapol was 21702 inconsistent for parallel runs. listcold now only stores 21703 the lists for the local orbitals on the current node to 21704 save memory and make everything consistent with extrapol. 21705(3) The allocation of memory in SIESTA has been corrected for 21706 an error that occured when a supercell was built. 21707(4) The save attribute has been added to bcell in dhscf.F 21708 21709Files: 21710 21711dhscf.F : bcell variable given save attribute 21712iolwf.F : modifications made to reflect changes to new size 21713 : of listcold and dimension error for maxc trapped 21714 : so that new value can be returned as ncmax 21715ordern.F : listcold now dimensioned as (maxnc,maxoloc) to save 21716 : memory and for consistency in extrapol. Handling of 21717 : dynamic memory overflow in iolwf added. 21718siesta.F : allocation of arrays that depend on nua moved to handle 21719 : the fact that redata can change the value of nua for a 21720 : supercell calculation 21721======================================================================== 21722Version: 1.0.15 21723Date: 1999/12/13 16:20:00 GMT 21724Title: Improvements to building behavior 21725Authors: Alberto Garcia <wdpgaara@lg.ehu.es> 21726 21727Description: 21728 21729A number of changes to improve compilation portability. 21730 21731Files: 21732 21733precision.f90: Removed 21734precision.f : Added. It now uses fixed format, as the rest of the program. 21735Makefile : Better cleaning, and precision changes. 21736fdf/makefile : fdf_mod.o is now added to the library. 21737Libs/lapack.f: machine-constants routines segregated to machine.f. 21738Libs/machine.f: file to be compiled without optimization. 21739Libs/makefile: added support for machine.o build. 21740MPI/Makefile : moved '.generated' to 'generate'. 21741Sys/ibmp3.make and Sys/ibm.f: partial support for IBM machines (Emilio) 21742 21743======================================================================== 21744Version: 1.0.14 21745Date: 1999/12/01 9:15:00 GMT 21746Title: Memory leak checks + diagonalisation modification 21747Authors: Julian Gale <j.gale@ic.ac.uk> 21748 21749Description: 21750 21751This version contains 3 principal changes : 21752 21753(1) To guard against memory leaks, the save attribute has been added 21754 to near all allocatable arrays so that the machine can detect 21755 when an array is attempted to be allocated having not been 21756 previous deallocated. As a result, a memory leak was found in 21757 outcoor.f on the array xap and has been fixed. 21758(2) It appears that most of the time a parallel diagonalisation can 21759 continue quite satisfactorily when SCALAPACK returns the warning 21760 about non-converged eigenvalues due to clustering without any 21761 effect on the results. Hence a new parameter MemoryScale has been 21762 introduced which is the scale factor by which the memory available 21763 to SCALAPACK is increased when TryMemoryIncrease is true. If this 21764 value is set equal to 1.0, instead of the default 1.5, then the 21765 SCF procedure continues without actually increasing the memory. 21766(3) The print out of memory information has now been modified to 21767 reflect the fact that the word lengths are different on a Cray 21768 and this is handled by a cpp directive at compile time. Hence the 21769 file memoryinfo.f has become memoryinfo.F 21770 21771Files: 21772 21773coceri.f : save attribute added to allocatable arrays 21774detover.f : save attribute added to allocatable arrays 21775diagpol.f : save attribute added to allocatable arrays 21776matel.f : save attribute added to allocatable arrays 21777numbvect.f : save attribute added to allocatable arrays 21778ordvec.f : save attribute added to allocatable arrays 21779outcoor.f : save attribute added to allocatable arrays 21780 + memory leak fixed on xap 21781parse.f : save attribute added to allocatable arrays 21782phirphi.f : save attribute added to allocatable arrays 21783radfft.f : save attribute added to allocatable arrays 21784ranger.f : save attribute added to allocatable arrays 21785recipes.f : save attribute added to allocatable arrays 21786reord.f : save attribute added to allocatable arrays 21787shaper.f : save attribute added to allocatable arrays 21788xc.f : save attribute added to allocatable arrays 21789ylmylm.f : save attribute added to allocatable arrays 21790atminit.F : save attribute added to allocatable arrays 21791atomlwf.F : save attribute added to allocatable arrays 21792bands.F : save attribute added to allocatable arrays 21793cdiag.F : ierror = -2 if TryMemoryIncrease = .true. 21794 and MemoryScale = 1.0 21795cgvc.F : save attribute added to allocatable arrays 21796chempot.F : save attribute added to allocatable arrays 21797diagk.F : handling of ierror modified 21798diag2k.F : handling of ierror modified 21799diagkp.F : save attribute added to allocatable arrays 21800diagg.F : handling of ierror modified 21801diag2g.F : handling of ierror modified 21802diagon.F : save attribute added to allocatable arrays 21803dynamics.F : save attribute added to allocatable arrays 21804egandd.F : save attribute added to allocatable arrays 21805extrapol.F : save attribute added to allocatable arrays 21806fixed.F : save attribute added to allocatable arrays 21807grdsam.F : save attribute added to allocatable arrays 21808hsparse.F : save attribute added to allocatable arrays 21809initdm.F : save attribute added to allocatable arrays 21810iodm.F : save attribute added to allocatable arrays 21811iolwf.F : save attribute added to allocatable arrays 21812kinefsm.F : save attribute added to allocatable arrays 21813ksv.F : save attribute added to allocatable arrays 21814memoryinfo.F : handling of Cray word lengths added 21815mulliken.F : save attribute added to allocatable arrays 21816nlefsm.F : save attribute added to allocatable arrays 21817on_subs.F : save attribute added to allocatable arrays 21818overfsm.F : save attribute added to allocatable arrays 21819pulayx.F : save attribute added to allocatable arrays 21820redata.F : MemoryScale read in 21821rdiag.F : ierror = -2 if TryMemoryIncrease = .true. 21822 and MemoryScale = 1.0 21823siesta.F : save attribute added to allocatable arrays 21824xijorb.F : save attribute added to allocatable arrays 21825======================================================================== 21826Version: 1.0.13 21827Date: 1999/11/26 18:15:00 GMT 21828Title: Return to Main Trunk 21829Authors: Alberto Garcia <wdpgaara@lg.ehu.es> 21830 21831Description: 21832 21833The changes made to the code along the "merged" branch have been 21834merged back to the main trunk. A few cosmetic changes have also 21835been made. Note that it is not practical to include all the commit 21836messages pertaining to the merged branch again. For all practical purposes, 21837there is a "wall" between 0.12.19 (tagged 'fork') and 1.0.13. 21838 21839Files: 21840 21841CHANGES: It contains the description of the latest changes along 21842 the merged branch. For full details, see the log history 21843 in each file. 21844redbasis.f: Removal of references to atom.h 21845atom.h: Removal. (Note that some "hardwired" parameters remain 21846 in the atmfuncs module -- they will be dealt with in 21847 the future.) 21848======================================================================== 21849Version: 1.0.12 21850Date: 1999/11/24 18:00:00 GMT 21851Title: Direct evaluation of phi added 21852Authors: Julian Gale <j.gale@ic.ac.uk> 21853 21854Description: 21855 21856An option has been added to calculate the value of the orbitals at 21857the mesh points on the fly to avoid the use of the PHI array in 21858DHSCF on lower routines. This allows a large saving in memory to 21859be made in some cases, with a penalty in CPU time. For very large 21860jobs it makes the difference between running and not running though 21861if memory is tight. Also an MPI barrier has been added in siesta.F 21862before the memory is printed to tidy up the output. 21863 21864Files: 21865 21866dfscf.F : value of phi is now used from called to phiatm rather than C 21867dhscf.F : DirectPhi option added 21868rhooda.f : DirectPhi option added 21869rhoofd.F : DirectPhi option added 21870siesta.F : MPI barrier added before call to printmemory 21871vmat.F : DirectPhi option added 21872siesta.ind : SaveMemory and DirectPhi options described 21873siesta.tex : SaveMemory and DirectPhi options described 21874======================================================================== 21875Version: 1.0.11 21876Date: 1999/11/18 16:30:00 GMT 21877Title: Sys reorganization. Bugfix in atom.F. Misc cosmetic changes. 21878Authors: Alberto Garcia <wdpgaara@lg.ehu.es> 21879 21880Description: 21881 21882 * The Sys directory has been reorganized. Obsolete files have 21883 been removed. A new file "nolibs.make" has been added to support 21884 systems without any libraries (this would be the equivalent of 21885 'unknown.make'). 21886 * Bug fix in atom.F: The global variable Q was being inadvertently 21887 re-used in a subroutine. 21888 * Fix to avoid interface errors (when checking enabled) in ranger.f 21889 * diagkp.F: Addition of a dummy routine so that some compilers do 21890 not complain of an empty file. 21891 21892Files: 21893 21894Makefile: Clarified the status of Sys.f files. 21895atom.F: Bug fix. 21896diagkp.F: Addition of dummy routine. 21897diagon.F: fdf is now 'used'. 21898ranger.f: interface errors "corrected" (more needs to be done in the future) 21899Sys/*.make: Elimination of obsolete files and addition of new ones. 21900 21901======================================================================== 21902Version: 1.0.10 21903Date: 1999/11/17 17:00:00 21904Title: listsc and matel converted into modules 21905Authors: Jose M. Soler <jose.soler@uam.es> / Julian Gale (j.gale@ic.ac.uk) 21906 21907Description: 21908 The clumsy ENTRY construction in listsc and matel was translated 21909 into fortran90 modules (JMS). Plus a number of small fixes for 21910 errors during compilation + runtime errors, primarily connected 21911 with the diagonalisation modifications. Also documentation 21912 modifications. 21913 21914Files: 21915 Makefile : declare listsc and matel as modules. 21916 atom.F : data statement converted into array declaration + 21917 : nrcfile initialised 21918 dfscf.F : use statement 21919 diagkp.F : routine wrapped in preprocessor directive - for MPI only 21920 diagon.F : diagkp declared as external 21921 diagpol.f : error flag for cdiag call added + handling 21922 hsparse.F : use statement 21923 kinefsm.F : use statement 21924 linpack.F : renamed from linpack.f 21925 : compiler directives added to handle precision of BLAS routines 21926 : dcabs1 renamed to sdcabs1 to avoid conflict with libraries 21927 : routines ending in "1" were removed as they were redundant 21928 listsc.f : converted into module 21929 matel.f : converted into module 21930 naefs.f : use statement 21931 nlefsm.F : use statement 21932 overfsm.F : use statement 21933 phirphi.f : use statement 21934 rhoofd.F : use statement 21935 siesta.F : use statement + lower limit of maxkb + initialisating Escf 21936 version.f : increased number 21937 vmat.F : use statement 21938 fdf/makefile : copying of module files now uses wildcard 21939 Docs/siesta.tex : version no. changed + parallel related options added 21940 Docs/siesta.ind : new options added with provisional page numbers 21941======================================================================== 21942Version: 1.0.9 21943Date: 1999/11/16 19:00:00 21944Title: Ongoing cleanup of atomic routines. FDF module. LAPACK and BLAS 21945Author: Alberto Garcia 21946 21947Description: 21948 21949A number of unrelated changes. 21950 21951* Systems without lapack and blas can now use source provided 21952 (use "cvs update -d" to pick up new directory Libs) 21953* Removed some blas routines from linpack (now duplicated in Libs/blas.f) 21954* Initialization of some variables (notably ends of arrays) in atom.F. 21955 Typically, the first element of arrays indexed over the radial 21956 coordinate was not initialized properly. They showed up as "initialized" 21957 in runs with checks enabled. This fix might improve the accord between 21958 runs with different number of processors. 21959* Use of "assigned" unit numbers for reading in atom.F and redbasis.f 21960 (Formerly an arbitrary "unit=1" was used) 21961* Changed redbasis.F back to redbasis.f, as no MPI-specific code is left. 21962* Wrap of I/O in subroutine 'user' in atom.F. Rationalization of some of 21963 the reading. More work needs to be done. 21964* Be more careful about underflow in atom.F. A check has been added to 21965 avoid computation of exp(-big), where 'big' could be so large as to 21966 cause underflows (and some systems to stop). A configurable maximum 21967 value for 'big' (currently 60.d0) has been introduced. 21968* Fdf declarations are now in a module. Note that this is the simplest 21969 step one can take to bring fdf into a f90 "flavor". The only change 21970 to the code has been to introduce a private unit allocator. 21971* The Makefile has been changed to support the new features. Also, the 21972 MPILIB mechanism has been slightly modified. It should now work 21973 on machines (such as the SGI) whose makes complained if MPILIB was 21974 empty (in serial mode). 21975 21976Files: 21977 Makefile 21978 bands.F 21979 cgvc.F 21980 dhscf.F 21981 efield.F 21982 fixed.F 21983 grdsam.F 21984 initdm.F 21985 iocg.f 21986 iodm.F 21987 ioeig.f 21988 iofa.f 21989 iohs.F 21990 iokp.f 21991 iolwf.F 21992 iomd.f 21993 iorho.F 21994 ioxv.F 21995 kgridinit.F 21996 ksv.F 21997 linpack.f 21998 ofc.f 21999 outcoor.f 22000 plcharge.f 22001 pulayx.F 22002 recoor.F 22003 redata.F 22004 redcel.F 22005 reinit.F 22006 repol.F 22007 resize.F 22008 siesta.F 22009 version.f 22010 fdf/ makefile 22011 Libs/makefile 22012 Libs/lapack.f 22013 Libs/blas.f 22014 22015======================================================================== 22016Version: 1.0.8 22017Date: 1999/11/16 17:00:00 22018Title: Diagonalisation improvements and parallelisation over K points 22019Author: Julian Gale (j.gale@ic.ac.uk) 22020 22021Description: 22022 22023 The diagonalisation procedure has been slightly modified. So far 22024 many parallel diagonalisations have failed because of the memory 22025 being insufficient to separate clustered eigenvalues. The 22026 solution is obviously to provide more memory, which can be done 22027 using the "DiagMemory" option. However, it is not easy to know 22028 a priori how much extra memory is needed which leads to lots of 22029 job restarts from scratch. Hence, an option "TryMemoryIncrease" 22030 has been added to try to solve this problem internally to 22031 minimise the number of failing runs. The specific changes that 22032 have resulted are : 22033 22034 (1) cdiag/rdiag now return an argument ierror which indicates the 22035 success or failure of diagonalisation. Ierror = 0 implies 22036 success, 1 implies fatal failure and -1 implies that failure 22037 was due to insufficient memory being available to separate 22038 clustered eigenvalues and that a repeat should be tried 22039 with more memory. 22040 (2) the fdf option "TryMemoryIncrease" has been added with the 22041 default value ".true.". This implies that a parallel job 22042 will attempt to increase the memory available to diagonalisation 22043 by increasing "MemoryFactor" internally with the aim of 22044 achieving a successful diagonalisation without restarting 22045 the job externally 22046 (3) in routines that call cdiag/rdiag the ierror flag is now 22047 handled by calling "die" if there is a fatal error. If there 22048 was insufficient memory then the arrays are re-initialised 22049 and the diagonalisation repeated to see if it is successful 22050 - this only happens if TryMemoryIncrease is true. 22051 (4) For the case of multiple K points, nspin .le. 2, an 22052 option to parallelise over K points has been added in the 22053 new routine "diagkp" based on "diagk". This option gives 22054 good parallel performance for small unit cell metallic 22055 systems where the number of K points is much larger than 22056 the number of orbitals. 22057Files: 22058 Makefile 22059 cdiag.F 22060 diagg.F 22061 diag2g.F 22062 diagk.F 22063 diag2k.F 22064 diagkp.F 22065 diagon.F 22066 memoryinfo.f 22067 rdiag.F 22068 redata.F 22069 siesta.F 22070 version.f 22071======================================================================== 22072Version: 1.0.7 22073Date: 1999/11/15 13:30:00 22074Title: KSV routines re-introduced for serial mode only + save attribute 22075Author: Julian Gale (j.gale@ic.ac.uk) 22076 22077Description: 22078 Daniel's polarisation modifcations have now been introduced back 22079 into the merged version for SERIAL only execution at the 22080 moment. There have been a few changes in the routines as well : 22081 22082 (1) Dynamic memory has been introduced 22083 (2) KSV_pol has been split into an initialisation routine KSV_init 22084 that calculates just the dimensions needed and KSV_pol which 22085 does the actual calculation. 22086 (3) The code that performs the determinant calculation has been 22087 placed in a separate subroutine called linpack.f 22088 (4) The function dcabs1 in the Linpack routines has been modified 22089 to avoid a bug due to the optimising compiler on the Cray 22090 22091 The "save" attribute has been added to allocatable arrays - this 22092 should help track down any memory leaks as an attempt to allocate 22093 an already allocated array from a previous call should result in 22094 an error. So far this has been done for the main routines where 22095 larger amounts of memory are allocated - should be extended to 22096 all arrays eventually. 22097 Also, in dhscf.F the maximum loop index in the calculation of X0 22098 prior to calling DIPOLE has been changed to NUA instead of NA 22099 otherwise the incorrect dipole moment is obtained. 22100Files: 22101 Makefile 22102 cdiag.F 22103 cellxc.F 22104 denmat.F 22105 detover.f 22106 dhscf.F 22107 diagpol.f 22108 ener3.F 22109 fft3d.F 22110 gradient.F 22111 iorho.F 22112 ksv.F 22113 ksvinit.f 22114 linpack.f 22115 ordern.F 22116 phirphi.f 22117 poison.F 22118 rdiag.F 22119 repol.F 22120 rhoofd.F 22121 siesta.F 22122 transp.f 22123 version.f 22124 vmat.F 22125======================================================================== 22126Version: 1.0.6 22127Date: 1999/11/11 10:00:00 22128Title: Improved choice of default processorY value added 22129Author: Julian Gale (j.gale@ic.ac.uk) 22130 22131Description: 22132 New features introduced for this version are : 22133 22134 (1) Nearly all parameters that might be exceeded during a run have 22135 been replaced with dynamic memory. The remaining parameter 22136 statements are large to set run behaviour, rather than array 22137 sizes. Some array dimensioning parameters remain, but these 22138 related to numbers which are unlikely to change (such as the 22139 maximum angular moment possible for an orbital etc) 22140 (2) Variable declarations have been tidied up to produce fewer 22141 compiler warning concerning unused variables. This particularly 22142 applies to the scalar version 22143 (3) A small number of bug fixes, including initialisation of ql to 22144 zero to avoid a crash when semi-core states are present. 22145Files: 22146 coceri.f 22147 dot.f 22148 dnaefs.f 22149 naefs.f 22150 neighb.f 22151 ordvec.f 22152 outcoor.f 22153 parallel.f 22154 parse.f 22155 phirphi.f 22156 prmem.f 22157 radfft.f 22158 ranger.f 22159 recipes.f 22160 reord.f 22161 shaper.f 22162 version.f 22163 xc.f 22164 ylmylm.f 22165 atminit.F 22166 arw.F 22167 atomlwf.F 22168 bands.F 22169 cdiag.F 22170 cellxc.F 22171 cgvc.F 22172 chempot.F 22173 chkdim.F 22174 denmat.F 22175 dfscf.F 22176 dhscf.F 22177 diag2g.F 22178 diag2k.F 22179 diagk.F 22180 diagon.F 22181 dynamics.F 22182 efield.F 22183 egandd.F 22184 ener3.F 22185 fermid.F 22186 fft3d.F 22187 fixed.F 22188 gradient.F 22189 hsparse.F 22190 initdm.F 22191 iorho.F 22192 kgrid.F 22193 kgridinit.F 22194 kinefsm.F 22195 ksv.F 22196 mulliken.F 22197 nlefsm.F 22198 on_subs.F 22199 ordern.F 22200 overfsm.F 22201 pulayx.F 22202 redata.F 22203 rdiag.F 22204 redbasis.F 22205 rhoofd.F 22206 siesta.F 22207 timer.F 22208 vmat.F 22209 xijorb.F 22210======================================================================== 22211Version: 1.0.5 22212Date: 1999/11/01 16:00:00 22213Title: Improved choice of default processorY value added 22214Author: Julian Gale (j.gale@ic.ac.uk) 22215 22216Description: 22217 The program now chooses a default value of ProcessorY based on 22218 the total number of Nodes so that the processors are divided 22219 as evenly as possible in the two directions with the Y direction 22220 being the smaller factor. Currently only 2, 3 and 5 are used 22221 as possible factors. More could be easily added, but probably 22222 would be of limited use. 22223Files: 22224 siesta.F 22225 parallel.f 22226======================================================================== 22227Version: 1.0.4 22228Date: 1999/10/28 13:00:00 22229Title: Input parameter to control workspace for diagonalisation added 22230Author: Julian Gale (j.gale@ic.ac.uk) 22231 22232Description: 22233 A new input option "DiagMemory" has been introduced which allows 22234 the user to control how much workspace memory is made available 22235 to Scalapack. The memory that is given, the more likely it is 22236 that all eigenvalues will be converged as the separation of 22237 clustered values in this package is dependent on this. The 22238 default value is 2. A value of less than 1 will lead to failure! 22239Files: 22240 Makefile 22241 cdiag.F 22242 memoryinfo.f 22243 rdiag.F 22244 redata.F 22245======================================================================== 22246Version: 1.0.3 22247Date: 1999/10/27 9:00:00 22248Title: Memory tracking added + minor bug fixes 22249Author: Julian Gale (j.gale@ic.ac.uk) 22250 22251Description: 22252 In order to monitor the dynamic memory usage of SIESTA, a routine 22253 memory has been added which must be called everytime an array is 22254 allocated or deallocated. There is also a routine "printmemory" 22255 which can be called at anytime to output the peak memory use so 22256 far. Hopefully this should enable the detection of memory leaks 22257 and assist in determining whether a job fails to run due to lack 22258 of memory. 22259 Also a few minor bugs have been fixed where uninitialised variables 22260 were being accessed on restarting from an existing density matrix 22261 or from a conjugate gradients history file. 22262Files: 22263 Makefile 22264 siesta.F 22265 memory.F 22266 memoryinfo.f 22267 atminit.F 22268 atom.F 22269 atomlwf.F 22270 bands.F 22271 cdiag.F 22272 cellxc.F 22273 cgvc.F 22274 chempot.F 22275 denmat.F 22276 dhscf.F 22277 diagon.F 22278 dynamics.F 22279 egandd.F 22280 ener3.F 22281 extrapol.F 22282 fft3d.F 22283 gradient.F 22284 grdsam.F 22285 hsparse.F 22286 initdm.F 22287 iodm.F 22288 iolwf.F 22289 iorho.F 22290 kinefsm.F 22291 listsc.f 22292 matel.f 22293 mulliken.F 22294 nlefsm.F 22295 ofc.f 22296 on_subs.F 22297 ordern.F 22298 overfsm.F 22299 pulayx.F 22300 poison.F 22301 ranger.F 22302 rdiag.F 22303 reord.f 22304 rhoofd.F 22305 transp.f 22306 vmat.F 22307======================================================================== 22308************************************************************************ 22309********* OLD (SERIAL ONLY) VERSION CHANGELOG ***************** 22310///////// This version is kept in the cvs branch ///////////////// 22311///////// 'siesta-0' ///////////////// 22312************************************************************************ 22313======================================================================== 22314Version: 0.12.19 22315Date: 1999/09/4 05:00:00 22316Title: Minor change in subroutine redbasis and reKBblock 22317Author: Daniel Sanchez (daniel@roma.physics.uiuc.edu) 22318 22319Description: 22320 Variable polorb included in the call of the subroutine 22321 reKBblock 22322File: 22323 redbasis.f 22324 redbasis_subs.f 22325===================================================================== 22326Version: 0.12.18 22327Date: 1999/08/12 23:00:00 22328Title: Minor changes to avoid compilation warnings 22329Author: Daniel Sanchez (daniel@roma.physics.uiuc.edu) 22330 22331Description: 22332 Some minor changes in subroutines atom_subs.f, atom_functionss.f 22333 and KSV.f to try to eliminate some compilation warnings (reported 22334 by Pablo Ordejon) using Linux compiler 22335Files: 22336 atom_subs.f 22337 atom_functions.f 22338 KSV.f 22339 Include/diagon.h : Value of the parameter maxhs set equal to 2. 22340======================================================================== 22341Version: 0.12.17 22342Date: 1999/08/04 14:00:00 22343Title: Corrected bug in coceri.f 22344Author: Emilio Artacho (emilio.artacho@uam.es) 22345 22346Description: 22347 Coordinate output for cerius (coceri.f) was wrong because of 22348 a transposition of the inverse matrix of lattice vectors (to get 22349 to fractional coordinates. 22350 22351Files: 22352 coceri.f 22353 usual (CHANGES, version.h, siesta.tex) 22354======================================================================== 22355Version: 0.12.16 22356Date: 1999/08/03 01:30:00 22357Title: Corrected bug in redbasis.f 22358Author: Daniel Sanchez (daniel@roma.physics.uiuc.edu) 22359 22360Description: 22361 Variables semic and lsemic were not correctly initialized, 22362 this causes an error in hp machines. 22363 22364Files: 22365 redbasis.f : Variables semic and lsemic are now initialized 22366======================================================================== 22367Version: 0.12.15 22368Date: 1999/08/02 19:30:00 22369Title: Restored variable savevh (bug introduced in recent change) 22370Author: Jose M. Soler (jose.soler@uam.es) 22371 22372Description: 22373 Somehow I introduced an 'amass' within the name savevh 22374 22375Files: 22376 siesta.f : Restored declaration of variable savevh 22377======================================================================== 22378Version: 0.12.14 22379Date: 1999/07/30 02:45:00 22380Title: Double-z orbitals orthogonalized to inner states 22381Author: Daniel Sanchez-Portal (daniel@roma.physics.uiuc.edu) 22382 22383Description: 22384 With the option "split", the double-z orbitals are 22385 explicitely orthogonalized to the inner (semicore) 22386 states. 22387 Minor bug corrected in subroutine draw_basis 22388Files: 22389 atom_subs.f 22390 version.h 22391 Docs/CHANGES 22392======================================================================== 22393Version: 0.12.13 22394Date: 1999/07/29 08:30:00 22395Title: More general type of "semicore" states allowed. 22396Author: Daniel Sanchez-Portal (daniel@roma.physics.uiuc.edu) 22397 22398Description: 22399 Several modifications in the atomic routines allow now 22400 for a more general type of "semicore"-like states in the 22401 calculations. 22402 For example, if the pseudopotential of Ti is generated 22403 from a ionic configuration 3s2 3p6 3d2, the program will 22404 understand that the readed pseudopotentials belong to the 22405 states 3s and 3p rather than to the states 4s and 4p. 22406 The program can handle a different (independent) basis set 22407 for the 3s and 4s shell (for example), generated using the 22408 standard techniques, but now the PAO corresponding to 22409 the 4s state will have one node. 22410 22411 Another difference is that now the basis set is generated 22412 using the same configuration (self-consistent density) used 22413 to generate the pseudopotentials ( previously the atom 22414 was neutralize by rescaling the charge density). 22415 22416 22417Files: 22418 initatom.f 22419 atom.f 22420 atom_subs.f 22421 atom_functions.f 22422 redbasis.f 22423 redbasis_subs.f 22424 mulliken.f 22425 plcharge.f 22426 version.h 22427 Util/Denchar/Src/redata.f 22428 Util/Denchar/Src/phiatm.f 22429 Src/Include/atom.h 22430 Docs/CHANGES 22431 Docs/siesta.tex 22432======================================================================== 22433Version: 0.12.12 22434Date: 1999/07/26 20:30:00 22435Title: listh array restricted to unit cell 22436Author: Jose M. Soler (jose.soler@uam.es) 22437 22438Description: 22439 The listh array, which frequently took most of the memory when using 22440 k-sampling, is now restricted to the unit cell, and recalculated on 22441 the fly outside it, using a faster algorithm. 22442 22443Files: 22444 dfscf.f : Call to listh for orbitals out of the unit cell 22445 hsparse.f : Call to listh0 to initialize listh function 22446 listh.f : New algorithm. Now a function for a given orbital. 22447 rhoofd.f : Call to listh for orbitals out of the unit cell 22448 siesta.f : Dimension of listh reduced from supercell to unit cell 22449 vmat.f : Call to listh for orbitals out of the unit cell 22450 Makefile : listsc.o depends on siesta.h 22451======================================================================== 22452Version: 0.12.11 22453Date: 1999/07/20 7:30:00 22454Title: Several KB projectors for each angular momentum 22455Author: Daniel Sanchez-Portal (daniel@roma.physics.uiuc.edu) 22456 22457Description: 22458 Several new routines have been added to the files atom_subs.f 22459 and redbasis_subs.f to allow the use of several KB projectors 22460 for each angular momentum. The implementation follows the 22461 work by Blochl, PRB 41, 5414 (1990). 22462 22463Files: 22464 atom_subs.f: Several new routines 22465 redbasis_subs.f: New routine to read the block PS.KBprojectors 22466 redbasis.f: Added a call to routine reKBblock, two new arguments 22467 atom.f: to new arguments in the call of this routine, 22468 and some other changes 22469 initatom.f: Modified the calls to routines atom and redbasis. 22470 matel.f: New parameter mxzkb (max. number of KB projectors per l) 22471 nlefsm.f: Value of the parameter maxkba from 16 to 25. 22472 version.h 22473 Include/atom.h:New parameter nkbmx(max. number of KB projectors per l) 22474 Include/matel.h:New parameter mxzkb(max. number of KB projectors per l) 22475 Docs/siesta.tex 22476 Docs/CHANGES 22477======================================================================== 22478Version: 0.12.10 22479Date: 1999/07/13 14:15:00 22480Title: Plrho support for bonding wireframe 22481Author: Jose M. Soler (jose.soler@uam.es) 22482 22483Description: 22484 A new routine (platom) was added to read the XV file and draw a 22485wireframe of bonds connecting atoms. Since it is still rather primitive 22486and unstable, its call is commented out in plrho. 22487 22488Files: 22489 platom.f : Bond-wireframe routine (new) 22490 plin3d.f : Plots a line in 3 dimensions (new) 22491 plrho.f : Added call to platom (still commented out) 22492 plrho.h : zbuff array added to common block 22493 pltr3d.f : zbuff array moved to common block 22494 ray.f : Added eps to denominator to avoid division by zero 22495 plrho_guide.txt : Added brief explanation on platom 22496======================================================================== 22497Version: 0.12.9 22498Date: 1999/07/13 14:00:00 22499Title: First call to overfsm moved out of SCF loop 22500Author: Jose M. Soler (jose.soler@uam.es) 22501 22502Description: 22503 In order to be able to make some post-processing calculations which 22504may require the overlap matrix, with MaxSCFiterations=0 (reading the 22505converged density matrix), the first call to overfsm was moved before 22506the start of the SCF loop. 22507 22508Files: 22509 siesta.f : First call to overfsm moved out of SCF loop 22510======================================================================== 22511Version: 0.12.8 22512Date: 1999/07/2 5:00:00 22513Title: Small modifications on the routine KSV_pol 22514Author: Daniel Sanchez-Portal (daniel@roma.physics.uiuc.edu) 22515 22516Description: 22517 Just adding an exit point if no calculation has been requested 22518 22519Files: 22520 Src/KSV.f 22521 Docs/CHANGES 22522======================================================================== 22523Version: 0.12.8 22524Date: 1999/07/1 7:00:00 22525Title: Some modifications on the routine KSV_pol 22526Author: Daniel Sanchez-Portal (daniel@roma.physics.uiuc.edu) 22527 22528Description: 22529 Some small changes in the routine KSV_pol, which calculates 22530 the electronic polarization. 22531 22532Files: 22533 Src/KSV.f New argument shape, and some minor modifications 22534 Src/siesta.f Calls to the routine KSV_pol modify for the new parameter 22535 Docs/CHANGES 22536======================================================================== 22537Version: 0.12.7 22538Date: 1999/06/30 1:00:00 22539Title: Electronic polarization calculation using the Berry phase method 22540 (and other minor changes) 22541Author: Daniel Sanchez-Portal (daniel@roma.physics.uiuc.edu) 22542 22543Description: 22544 The calculation of the electronic polarization for bulk systems 22545 using the Berry phase approach of R.D.King-Smith and D.Vanderbilt 22546 (PRB 47, 1651 (1993)). The calculation is slightly different than 22547 the usual approach used within plane-waves calculatios, and 22548 calculations using gaussian basis sets, due to the numerical 22549 (arbitrary radial shape) character of the basis used in SIESTA. 22550 The matrix elements of the position operator in the basis set is 22551 used, instead of the plane-wave that appears in the initial 22552 formulation of the method. This method can only be applied 22553 to insulators. 22554 22555 The calculation of this matrix elements is performed by matel 22556 only when the calculation of the polarization is requested, to 22557 avoid the allocation of the extra-memory (relatively big compare 22558 with which was usually used by matel) when it is not necessary. 22559 22560 Other small modifications in the atomic routines: 22561 *When the basis set is generated from a charged atomic 22562 configuration (this must be explicetely requested in the input, 22563 it is not related with the configuration used to generate the 22564 pseudopotentials) a message is print by the subroutine atom. 22565 *Radius of the orbitals for cations are now different (shorter) 22566 than those of the neutral atom. For anions they are calculated 22567 from the neutral atom. 22568 *Some changes in subroutine USER to avoid problems with 22569 the interpolation of the orbitals (readed from the numerical 22570 tables) near zero. 22571 22572 Corrected a small bug in SIESTA: 22573 Usually the coordinates are moved after the last self-consistent 22574 calculation of the density-matrix. These changed coordinates 22575 are then inconsistent with the density-matrix and forces used 22576 to calculate the forces, virial, LDOS, files to plot density, 22577 etc... I have corrected this by saving the last coordinates 22578 for what the electronic structure is actually calculated, and 22579 using these coordinates to perform all these final calculations. 22580 22581Files 22582 Src/detover.f, KSV.f, phirphi.f, diagpol.f, repol.f (new files) 22583 Src/atom_functions.f (added three new functions) 22584 Src/matel.f (strongly modified) 22585 Src/siesta.f, matel.h, siesta.h (modified) 22586 Src/atom.f, atom_subs.f, siesta.f (slight modifications) 22587 Src/Makefile 22588 customary siesta.tex, siesta.ind, version.h, CHANGES 22589======================================================================== 22590Version: 0.12.6 [to 0.11.5 in rel-0-11-fixes branch] 22591Date: 1999/06/18 12:30:00 22592Title: BUG Fixed in iorho.f concerning formatted/unformatted reading 22593Author: Emilio Artacho (emilio.artacho@uam.es) 22594 22595Description: 22596 A formatted read was done for unformatted files and vice-versa. 22597 It DID NOT affect the normal working of siesta since it was always 22598 using an unformatted file, and compilers were wise enough to 22599 disregard the * format. (In that case, how did we find it? I 22600 don't know, ask Jorge Kohanoff). 22601 22602Files: 22603 iorho.f and customary 22604======================================================================== 22605Version: 0.12.6 [to 0.11.5 in rel-0-11-fixes branch] 22606Date: 1999/06/10 17:45:00 22607Title: BUG Fixed: save alat in outcoor.f (bug only for certain compilers) 22608Author: Emilio Artacho (emilio.artacho@uam.es) 22609 22610Files: 22611 outcoor.f and customary 22612======================================================================== 22613Version: 0.12.5 22614Date: 1999/06/09 12:30:00 22615Title: Denchar utility: it provides now atomic coordinates in 2D-plot coors 22616Author: Javier Junquera (javier@polar.fmc.uam.es) 22617 22618Description: 22619 The package provides the possibility of giving the coordinates 22620 of any atoms of the calculated system in the reference frame of 22621 the 2D plot (the third coordinate would correspond to the one 22622 perpendicular to the plane and is zero for atoms within the plane). 22623 The atoms wanted are specified by giving their indices as in the 22624 siesta run, in the fdf block 2D.AtomsInPlane . 22625 22626Files (all in Util/Denchar): 22627 Src/atompla.f (new) 22628 Src/denchar.f, planed.f, rhoofr.f, readpla.f, wrout.f, Makefile (modif) 22629 Docs/denchar.tex 22630 Examples/ (all modified) 22631 customary siesta.tex, version.h, CHANGES 22632======================================================================== 226330.12.4 = 0.11.4 released as 0.11.f1 22634======================================================================== 22635Version: 0.12.4 [0.11.4 in rel-0-11-fixes branch] 22636Date: 1999/06/09 10:45:00 22637Title: Rounding off release: Examples update and matel.h 22638Author: Emilio Artacho (emilio.artacho@uam.es) 22639 22640Files: 22641 Examples/*/Out/* updated for latest version 22642 Include/matel.h changed MAXR to 128 and MAXQ to 1024 for consistency 22643 (1 before, and the compiler complained) 22644======================================================================== 22645Version: 0.12.4 [0.11.4 in rel-0-11-fixes branch] 22646Date: 1999/06/08 16:00:00 22647Title: Fixed bug in vmat.f 22648Author: Jose M. Soler (jose.soler@uam.es) 22649 22650Description: 22651 It was introduced in 0.10.20, and affected only Gamma-point 22652 calculations with substantial overlap between equivalent orbitals 22653 from different cells. Fixed. 22654 22655Files: 22656 vmat.f 22657 customary siesta.tex, version.h, CHANGES 22658======================================================================== 22659Version: 0.12.3 [0.11.3 in rel-0-11-fixes branch] 22660Date: 1999/06/08 12:30:00 22661Title: Fixed bug in atomlwf.f 22662Author: Pablo Ordejon (ordejon@icmab.es) 22663 22664Description: 22665 The number of electron is now passed from ordern.f to atomlwf.f 22666 This fixes problems when charged cells and Order-N are combined. 22667 Also, checks are done to avoid the use of Ordejon-Mauri functional 22668 with charged cells. 22669 22670Files: 22671 ordern.f, atomlwf.f 22672 customary siesta.tex, version.h, CHANGES 22673======================================================================== 22674Version: 0.12.2 (No PL change) 22675Date: 1999/06/04 16:30:00 22676Title: Minor cosmetic changes. New .make files 22677Author: Alberto Garcia <wdpgaara@lg.ehu.es> 22678 22679Description: 22680 * Minor cosmetic change in siesta.f to avoid 22681 check bounds warnings or errors at compile 22682 time. 22683 * Re-structuring of matel.f to help some 22684 compilers. 22685 * Changes to some of the Sys/*.make files. Addition 22686 of some more. 22687 22688 (No user-visible changes.) 22689 22690Files: 22691 siesta.f: 22692 matel.f: 22693 Sys/ 22694 g77.make: ranlib used by default (BSD compatibility) 22695 g77-libs.make: New file. Uses system BLAS and LAPACK. 22696 nag-f90.make, nag-f95.make, pgf77.make, pgf90.make: New files. 22697======================================================================== 22698Version: 0.12.2 22699Date: 1999/06/03 12:30:00 22700Title: Changes to fdf behavior. Use of io_assign 22701Author: Alberto Garcia <wdpgaara@lg.ehu.es> 22702 22703Description: 22704 * When calling fdf_init with 'stdin' as input file, 22705 some systems complain about the impossibility of 22706 rewinding unit 5. The fix consists of creating 22707 a scratch file FDF_STDIN and passing it to 22708 fdf_init. 22709 * fdf has been updated to avoid using standard 22710 input directly (same mechanism). 22711 * Call to io_assign in atom.f (instead of 22712 opening and closing unit 12) 22713 22714 (No user-visible changes.) 22715 22716Files: 22717 redata.f: Modified to use FDF_STDIN. 22718 fdf/fdf.f: Now deals more robustly with stdin. 22719 atom.f: Call to io_assign 22720 Makefile: Explicit dependencies for fdf files. 22721 customary version.h, CHANGES 22722======================================================================== 22723Version: 0.11.1 0.12.1 22724Date: 1999/06/02 19:20:00 22725Title: Fixed bug in rhoofd.f 22726Author: Jose M. Soler (jose.soler@uam.es) 22727 22728Description: 22729 It was introduced in 0.10.20, and affected only Gamma-point 22730 calculations with substantial overlap between equivalent orbitals 22731 from different cells. Fixed. 22732 22733Files: 22734 rhoofd.f 22735 customary siesta.tex, version.h, CHANGES 22736======================================================================== 22737Version: 0.11.0 0.12.0 22738Date: 1999/05/26 12:00:00 22739Title: Fixed bug in siesta.f, iomd was called with idyn instead of varcel 22740Author: Emilio Artacho (emilio.artacho@uam.es) 22741 22742Files: 22743 Src/siesta.f 22744 (plus customary) 22745======================================================================== 22746Version: 0.11.0 0.12.0 22747Date: 1999/05/25 16:00:00 22748Title: Bug fixes 22749Author: Pablo Ordejon (ordejon@icmab.es) 22750 22751Files: 22752 Src/bands.f Call to diagk corrected 22753 Src/redata.f fs_dafault defined as logical 22754 Src/version.h, Docs/CHANGES Usual changes 22755======================================================================== 22756Version: 0.11.0 0.12.0 22757Date: 1999/05/17 21:00:00 22758Title: Option to calculate a fixed spin state 22759Author: Pablo Ordejon (ordejon@icmab.es) 22760 22761Files: 22762 Src/fermispin.f New. Calculates occupations with fixed spin 22763 Src/diagg.f Calls fermispin if spin is fixed 22764 Src/diagk.f Calls fermispin if spin is fixed 22765 Src/diagon.f Pass fixed spin info to diag routines 22766 Src/redata.f Read new variables FixSpin and TotalSpin 22767 Src/siesta.f Changes for fixed spin calcs. 22768 Docs/CHANGES Changes for fixed spin calcs. 22769 Docs/siesta.tex Changes for fixed spin calcs. 22770 Docs/siesta.ind Changes for fixed spin calcs. 22771 Docs/release.notes_0.11 Changes for fixed spin calcs. 22772======================================================================== 22773Version: 0.11.0 0.12.0 22774Date: 1999/05/17 20:00:00 22775Title: Fixed bug in cgvc.f 22776Author: Emilio Artacho (emilio.artacho@uam.es) 22777 22778Files: 22779 cgvc.f : It was using inver.f for matrix inversion, not good 22780 changed for reclat 22781 version.h, CHANGES, siesta.tex as usual 22782======================================================================== 22783Version: 0.11.0 0.12.0 22784Date: 1999/05/05 17:15:00 22785Title: Fixed bug in madelung (mulecule) + fixed dim enlargement 22786Author: Emilio Artacho (emilio.artacho@uam.es) 22787 22788Files: 22789 madelung : bug: it checked whether it was a mUlecule (fixed) 22790 rhoofd, vmat : maxloc: 200 -> 300 22791 matel : NQ: 512 -> 1024 22792 kinefsm, overfsm : nomax: 10000 -> 20000 22793 nlefsm : maxna: 500 -> 1000 22794 maxno: 1000 -> 2000 22795 maxo: 10000 -> 20000 22796 hsparse, xijorb : maxna: 500 -> 1000 22797 maxnkb: 1000 -> 2000 22798 maxo: 10000 -> 20000 22799 shaper : maxna: 500 -> 1000 22800 initdm : maxat: 500 -> 1000 22801======================================================================== 22802Version: 0.12.0 <=> 0.11.0 <=> 0.10.32 22803======================================================================== 22804Version: 0.10.32 22805Date: 1999/04/26 18:30:00 22806Title: Corrected a bug which produced too large values of NFFR in MATEL 22807Author: Jose M. Soler (jose.soler@uam.es) 22808 22809Description: 22810 A bug in searching previously stored functions produced too large 22811 tables of FFR, with the same function repeated two times. 22812 Value IR=0 was also excluded from the comparison. 22813 After these changes, the dimension of FFR could even be reduced. 22814 22815Files: 22816 matel.f : Bug corrected 22817 Docs/siesta.tex : Removed the description of the now-solved problem 22818 Docs/siesta.ind (correpondingly) 1999/04/27 10:45 22819 Include/constr.f : Updated as in Src (unrelated to matel) 22820======================================================================== 22821Version: 0.10.31 22822Date: 1999/04/26 16:00:00 22823Title: Reorganization of Sys. New environment variable SIESTA_SYS 22824Author: Alberto Garcia <wdpgaara@lg.ehu.es> 22825 22826Description: 22827 * New, deleted, and modified files in Sys. 22828 * The environmental variable determining system/compiler/library 22829 settings is now SIESTA_SYS, instead of ARCH. 22830 * Some additions to the manual section dealing with compilation. 22831 (Changed version number since SIESTA_SYS is a 'major' change) 22832 22833Files: 22834 22835 Src/Sys/ 22836 sgi.make : Now uses sgi.f. 22837 sgi.f : Includes timing routine. 22838 sgimath.make: Now uses sgimath.f. 22839 sgimath.f : New file. 22840 g77-libs.make : (New file) For g77 systems with -llapack and -lblas. 22841 freebsd.make: (Deleted) Use g77 or g77-libs instead. 22842 diag_lapack.f: (New file) Included by relevant .f files. 22843 22844 Util/ 22845 msiesta : Added comments. Changed ARCH to SIESTA_SYS 22846 rrsiesta : Added comments. 22847 22848 Src/ 22849 Makefile : Changed ARCH to SIESTA_SYS 22850 22851 Docs/ 22852 siesta.tex : Re-wrote section on compilation. Updated to 0.10.31 22853======================================================================== 22854Version: 0.10.30 22855Date: 1999/04/23 12:30:00 22856Title: SGI system-dependent makefile options 22857Author: Emilio Artacho (emilio.artacho@uam.es) 22858 22859Description: 22860 Some problems with the mathematical library of SGI were found by 22861 Julian Gale for the diagonalization. Also, some compiler options 22862 had to be changed for some SGI's OS flavors. 22863 22864Files: 22865 sgi.make : No libraries, uses general.f, and some flags changed 22866 sgimath.make: The previous version, with old flags and the math library 22867======================================================================== 22868Version: 0.10.30 22869Date: 1999/04/20 17:00:00 22870Title: Revision and actualization of examples 22871Author: Emilio Artacho (emilio.artacho@uam.es) 22872 22873Description: 22874 Siesta examples are now: 22875 * H2O molecules as simplest, first contact. Plus ordern possibility. 22876 (unchanged, only updated) 22877 * Interstitial H in bulk Si, with a supercell of 64+1 atoms. SZ. 22878 Relaxation (40 Mb and 20 cefeo minutes). 22879 * bcc ferromagnetic bulk Fe, with GGA and partial core correction. 22880 Band structure and magnetic moment. 22881 Previous Si64 supercell example has been removed. 22882 22883Files: 22884 Examples/H2O : h2o.fdf Out/h2o.out, out.fdf, siesta.size 22885 Fe : analogous 22886 SiH : analogous plus sih.ANI (Xmol movie) 22887 Vps : Fe.inp and Fe.vps added 22888 Customary siesta.tex, version.h and CHANGES 22889======================================================================== 22890Version: 0.10.29 22891Date: 1999/04/16 19:30:00 22892Title: sies2arc utility 22893Author: Julian Gale (j.gale@ic.ac.uk) 22894 22895Description: 22896 Utility for extracting the coordinates from a SIESTA output file and 22897 converting them into an arc file Movie for Cerius2/InsightII. 22898 22899Files: 22900 Util/sies2arc/sies2arc.f main program 22901 linepro.f parses input lines 22902 wtof.f converts word to a floating point number 22903 cell.f converts cell parameters to cell vectors 22904 constants contains fundamental constants 22905======================================================================== 22906Version: 0.10.29 22907Date: 1999/04/14 21:45:00 22908Title: Cosmetics in redata + printing Max constrained forces 22909Author: Emilio Artacho (emilio.artacho@uam.es) 22910 22911Files: 22912 siesta.f, redata.f, siesta.tex, version.h, CHANGES 22913======================================================================== 22914Version: 0.10.29 22915Date: 1999/04/13 19:00:00 22916Title: Changes in scripts + manual 22917Author: Emilio Artacho (emilio.artacho@uam.es) 22918 22919Description: 22920 Hopefully last changes for 0.11: 22921 - Scripts (msiesta etc) to avoid compilation of atom.f and related 22922 everytime 22923 - Manual: revision of explanations of scripts, and other details 22924 - Options Ang and Bohr as synonims of NotScaledCartesianAng etc. 22925 - Slight changes in siesta.f, outcoor.f, pulayx.f to avoid multiple 22926 fdf reading. 22927 22928Files: 22929 msiesta, rsiesta, rrsiesta, qsiesta, qrrsiesta 22930 siesta.f, outcoor.f, recoor.f, pulayx.f 22931 siesta.tex, siesta.ind, CHANGES, version.h 22932======================================================================== 22933Version: 0.10.28 22934Date: 1999/04/13 13:15:00 22935Title: Output: append in MD files + various in manual and siesta.f 22936Author: Emilio Artacho (emilio.artacho@uam.es) 22937 22938Description: 22939 - MD history files are now accumulative for different runs (so that 22940 a restart of rrsiesta does not leaves us with a stupid face). 22941 - If coordinates are not written to standard output, they are by 22942 default accumulated in XMol format in file.ANI 22943 - Output of max constrained force in standard output 22944 - Manual describes it, plus inclusion of cond-mat ref ICSSS. 22945 22946Files: 22947 pixmol.f iomd.f : accumulative (incorporates winding to end with 22948 routines windu and windf in iomd.f) 22949 siesta.f : ANI default and writing constrained max force 22950 siesta.tex siesta.ind : manual 22951 CHANGES, version.h 22952======================================================================== 22953Version: 0.10.28 22954Date: 1999/04/09 19:45:00 22955Title: Variable cell CG optimization 22956Author: Emilio Artacho (emilio.artacho@uam.es) 22957 22958Description: 22959 Variable cell CG optimization activated and described in the manual. 22960 See MD.VariableCell. It allows external pressure and non-hydrostatic 22961 stresses. 22962 22963Files: 22964 cgvc.f : activated variable cell (before was shortcut) 22965 redata.f : changed some names and defaults. 22966 siesta.tex, siesta.ind 22967 Customary version.h, CHANGES 22968======================================================================== 22969Version: 0.10.27 22970Date: 1999/04/08 15:40:00 22971Title: Minimal description of partial-core included in atom's User.Guide 22972Author: Emilio Artacho (emilio.artacho@uam.es) 22973 22974Files: 22975 Pseudo/atom/Docs/User.guide 22976======================================================================== 22977Version: 0.10.27 22978Date: 1999/04/08 13:00:00 22979Title: EIG2DOS utility for DOS & acknowl in manual & coceri to Ang 22980Author: Emilio Artacho (emilio.artacho@uam.es) 22981 22982Files: 22983 Util/eig2dos.f 22984 Docs/siesta.tex, siesta.ind 22985 coceri.f : output for cerius has now lattice parameters in Ang. 22986 Customary version.h, CHANGES 22987======================================================================== 22988Version: 0.10.27 22989Date: 1999/03/11 20:30:00 22990Title: Capability for charged systems, and minor corrections 22991Author: P. Ordejon (ordejon@condmat01.geol.uniovi.es) 22992 22993Description: 22994 The capability to deal with charged systems is implemented. 22995 For atoms and molecules, the energy is corrected with 22996 a standard Madeliung term, for faster convergence vs cell size. 22997 22998 Also, some minor changes in some routines have been made, 22999 to avoid compilation warning due to non-initialized or 23000 not used variables. 23001 23002Files: 23003 Src/Makefile 23004 Src/atomlwf.f Corrections to avoid compilation warnings 23005 Src/bands.f Corrections to avoid compilation warnings 23006 Src/chempot.f Corrections to avoid compilation warnings 23007 Src/madelung.f New file. Calculates Madelung correction 23008 Src/mulliken.f Corrections to avoid compilation warnings 23009 Src/ordern.f Corrections to avoid compilation warnings 23010 Src/propor.f Corrections to avoid compilation warnings 23011 Src/siesta.f Changes to allow for charged systems 23012 Src/redata.f Introduce new variable (NetCharge) for charged systems 23013 Src/typecell.f New file. Identifies SC, FCC and BCC cells 23014 Src/version.h 23015 Src/Sys/cdiag_general.f 23016 Corrections to avoid compilation warnings 23017 Src/Sys/rdiag_general.f 23018 Corrections to avoid compilation warnings 23019 Docs/CHANGES This file 23020 Docs/siesta.ind Index for 0.10.27 version 23021 Docs/siesta.tex Manual for 0.10.27 version 23022======================================================================== 23023Version: 0.10.26 23024Date: 1999/03/05 14:30:00 23025Title: Description of output files of atomic program in User.Guide 23026Author: Emilio Artacho (emilio.artacho@uam.es) 23027 23028Description: 23029 The contents of the different files generated by Alberto's atomic 23030 program are described in his User.Guide file. 23031 23032Flies: 23033 Pseudo/atom/Docs/User.Guide 23034======================================================================== 23035Version: 0.10.26 23036Date: 1999/03/04 17:20:00 23037Title: Re-introduced arguments listC and endC in rhoofd and vmat 23038Author: Jose M. Soler (jose.soler@uam.es) 23039 23040Description: 23041 Although unused in the present version, arguments listC and endC 23042 are used in a special version of J.Junquera to save memory with 23043 k-sampling. Also changed the dimensions of some arrays to avoid 23044 compilation warnings. 23045 23046Files: 23047 dhscf.f : Calls to rhoofd and vmat 23048 minvec.f : New array iaux 23049 neighb.f : Dimension of iamove 23050 ranger.f : Dimension of iamove 23051 rhoofd.f : Restored arguments listC, endC 23052 vmat.f : Restored arguments listC, endC 23053 xc.f : Dimensions of ds and vxunif in pbxc 23054======================================================================== 23055Version: 0.10.26 23056Date: 1999/03/02 01:31:00 (local time at Oviedo) 23057Title: Change definition of variables in ordern.f 23058Author: Pablo Ordejon (ordejon@condmat01.geol.uniovi.es) 23059 23060Description: 23061 Variables g and hg, which were defined as real*8 in ordern.f, 23062 are changed to real*4, to concord with their definition 23063 in cgwf.f (which is called by ordern.f). 23064 This change does not affect the results, but saves a 23065 little bit of memory. 23066 23067Files: 23068 Src/ordern.f: change definition of variables g and hg to real*4 23069 Src/version.h: version 0.10.26 23070 Docs/CHANGES: describe changes. 23071======================================================================== 23072Version: 0.10.26 23073Date: 1999/02/28 20:15:00 (local time at Oviedo) 23074Title: Package VIBRA to compute phonons. 23075Author: Pablo Ordejon (ordejon@condmat01.geol.uniovi.es) 23076 23077Description: 23078 Package VIBRA to compute phonon frequencies and 23079 normal modes has been incorporated into the SIESTA 23080 distribution. Changes in Siesta to compute the 23081 force constant matrix (used by VIBRA) have also 23082 been introduced, as a new MD option (to displace 23083 atoms one by one and compute the force constants) 23084 23085Files: 23086 Util/Vibra: New directory, with VIBRA sources, docs and examples 23087 Util/README: List new packages 23088 Src/siesta.f: Modified to compute the force constant matrix 23089 Src/ofc.f: New file. Writes the force constant matrix to a file 23090 Src/redata.f: Modified to read new dynamics variables 23091 Src/Makefile: Modified to include ofc.f 23092 Src/version.h: Tag version 0.10.26 23093 Docs/siesta.tex: Description of new variables 23094 Docs/siesta.ind: Update of index 23095 Docs/CHANGES: Describe changes 23096======================================================================== 23097Version: 0.10.25 23098Date: 1999/02/27 14:30:00 (local time at Oviedo) 23099Title: Incorporate O(N) automatic calculation of Chemical Potential 23100 and correct bug in former siesta.f commit. 23101Author: Pablo Ordejon (ordejon@condmat01.geol.uniovi.es) 23102 23103Description: 23104 The automatic estimate of the Chemical Potential, in Order-N 23105 operation, is now incorporated in the Order-N routines. 23106 The estimate is done by the projection method of Goedecker, 23107 (PRB 51, 9455 (1995)), modified for non-orthogonal basis like 23108 proposed by Stephan et al. (PRB 57, 6391 (1998), PRB 58, 13472 23109 (1998)). 23110 Also, a small bug in the last siesta.f version was 23111 fixed (ns elliminated from call to ordern.f). 23112 23113Files: 23114 chempot.f: New file 23115 ordern.f: Modified to call chempot.f 23116 redata.f: Modified to read Chemical Potential related information 23117 siesta.f: Modified to include calculation of Chemical Potential, 23118 and small bug fixed (ellimination of ns from call to 23119 ordern) 23120 version.h: Tag version 0.10.25 23121 Include/ordern.h: Modified to include maxnh in the parameters list. 23122 Docs/siesta.tex Description of new variables 23123 Docs/siesta.ind Update of index 23124 Docs/CHANGES Describe changes 23125======================================================================== 23126Version: 0.10.24 23127Date: 1999/02/26 15:45:00 MET 23128Title: Various structural and cosmetic changes 23129Author: Alberto Garcia <wdpgaara@lg.ehu.es> 23130 23131Description: 23132 23133Structural changes: 23134 23135* .h files now reside in Src/Include, and need to be copied to the Src 23136directory before the first compilation. (Manual updated) 23137 23138* System-dependent code now resides completely in Sys. Some files 23139(e.g., cdiag_general.f, rdiag_general.f, poison_general.f) have been 23140created from their counterparts in Src, and the latter removed. File 23141inclusion in architecture-dependent files is now kept to just one 23142level. 23143 23144* Removed Sys/osf.f. Its functionality was identical to bsd.f 23145* Added g77.make and modified freebsd.make in Sys. 23146 23147* Makefile updated to include support for plusFORT-style checks and 23148to remove an spurious mention to cdiag. 23149 23150Code changes: 23151 23152* Array config in atm_pot dimensioned to (0:4) instead of (0:3) 23153* Some variables should be arrays in ggaxc and pbexc (fixed) 23154 23155* (Daniel Sanchez-Portal) Various fixes in atomic routines. 23156 23157* Gave explicit lenghts to "x" output descriptors and 23158Hollerith variables. 23159 23160* Removal of unused variables (too many files to list). 23161 23162* Removal of unused arguments: 23163 23164 Pulayx : listd 23165 Rhoofd : listc, endc 23166 Vmat : listc, endc 23167 Polarization: b 23168 Initguess, cspa: ns 23169 23170* Expansion of TABs in some files (tabs could cause problems with 23171some compilers). 23172======================================================================== 23173Version: 0.10.23 23174Date: 1999/02/25 23:45:00 23175Title: Bug corrected in plcharge.f and DENCHAR 23176Author: Daniel Sanchez-Portal (daniel@roma.physics.uiuc.edu) 23177 23178Description: 23179 Program DENCHAR used an obsolote version of the atomic 23180 subroutines. In fact, the version used was obsolete even 23181 the first time that the program was added to the SIESTA 23182 program. I doubt that the program had ever properly run, 23183 due to this mismatch in versions. 23184 By passing I added a couple of format statements in some 23185 write sentences in the routines grid2d.f and rhoofr.f 23186 23187Files: 23188 plcharge.f (in SIESTA) 23189 redata.f, phiatm.f, rhoofr.f (in DENCHAR). 23190 grid2d.f (in Contour) 23191======================================================================== 23192Version: 0.10.23 23193Date: 1999/02/24 24:00:00 23194Title: Bug corrected in atom_subs.f 23195Author: Daniel Sanchez-Portal (daniel@roma.physics.uiuc.edu) 23196 23197Description: 23198 Bug corrected in atom_subs.f. In the previous versions 23199 the variable norb in the routine atm_pop was not initialized. 23200 Dimesions for the arrays in subroutines polarization and rc_vs_e 23201 are now provided by the file atom.h 23202 Minor semi-cosmetic changes in atom_subs.f atom.f and atom_functions.f 23203 23204Files: 23205 atom_subs.f, atom.f, atom_functions.f 23206======================================================================== 23207Version: 0.10.23 23208Date: 1999/02/21 22:05:00 23209Title: Conjugate gradient continuation file and flag 23210Author: Emilio Artacho (emilio.artacho@uam.es) 23211 23212Description: 23213 The conjugate gradient relaxation is no longer controlled by siesta 23214 but by cgvc. It stores auxiliary CG arrays in file belovedsystem.CG . 23215 Restarting with MD.UseSaveCG and MD.UseSaveXV and the .CG and .XV 23216 files from a previously interrupted CG relaxation, allows a smooth 23217 continuation of it. An irrelevant bug has been corrected. 23218 It is prepared for variable cell relaxation. In fact the code is 23219 there, ready, just called by MD.VariableCell true, but I am not still 23220 sure whether there is a bug in it, and I have disabled it 23221 provisionally. 23222 23223Files: 23224 cgvc.f, iocg.f : new 23225 siesta.f, redata.f, Makefile 23226 siesta.tex, siesta.ind, version.h, CHANGES 23227======================================================================== 23228Version: 0.10.23 23229Date: 1999/02/21 18:15:00 23230Title: Introduction of k-sampling artillery into MD for variable cell 23231Author: Emilio Artacho (emilio.artacho@uam.es) 23232 23233Description: 23234 the calls within siesta prior to the MD cycle, related to k-sampling 23235 (kgrid, superc, etc) havev been introduced within for variabel cell 23236 MD, in which such things have to be recalculated. 23237 23238Files: 23239 siesta.f, iomd.f 23240 CHANGES, siesta.tex version.h 23241======================================================================= 23242Version: 0.10.22 23243Date: 1999/02/21 17:15:00 23244Title: Description in the manual of previous changes; ibmesslp3.make; 23245Author: Emilio Artacho (emilio.artacho@uam.es) 23246 23247Description: 23248 Actualization of siesta.tex with the new output features. 23249 New Sys file; ibmesslp3, adapted to the Power3 processor at Lyon 23250 23251Files; 23252 siesta.tex, siesta.ind 23253 CHANGES, version.h 23254 Sys/ibmesslp3.make 23255======================================================================== 23256Version: 0.10.22 23257Date: 1999/02/21 1:15:00 23258Title: Substantial output change; Gnubands utility; 23259Author: Emilio Artacho (emilio.artacho@uam.es) 23260 23261Description: 23262 Output has been made flexibler by the addition of several flags 23263 for optional printing of some (typically long) pieces: forces, 23264 k-points, bands, eigenvalues, coordinates etc, can now be switched 23265 on and off independently. 23266 The default is now NOT to print most of those. A general FDF flag 23267 "LongOutput" has been devised for turning on the printing of most of 23268 them at once. Some cosmetics has been added to the output. 23269 The initial atomic coordinates are now written after ioxv. Before 23270 the fdf coordinates were always written, independent of whether the 23271 XV file was read or not. 23272 Several new files are now generated, in some cases only if the 23273 information does not go to standard output. Others keep the history 23274 of MD simulations (one of them for Xmol animation). 23275 23276 Utility program GNUBANDS reads from standard input the .bands 23277 file grnerated by SIESTA and writes in standard output in a format 23278 directly readablo by Gnuplot. 23279 23280Files: 23281 Makefile, siesta.f, redata.f, outcoor.f, recoor.f : modified 23282 atom.f, atom_subs.f, bands.f, superx.f : cosmetics 23283 iokp.f, iomd.f, iofa.f, ioeig.f, pixmol.f : new 23284 Util/gnubands.f : new 23285 version.h, CHANGES 23286 siesta.tex, siesta.ind 23287======================================================================== 23288Version: 0.10.22 23289Date: 1999/02/21 1:15:00 23290Title: BUG FIXED in atomlwf.f 23291Author: Pablo Ordejon (ordejon@condmat01.geol.uniovi.es) 23292 23293Description: 23294 Program would crash on IBMs when dimensioning ordern subroutines. 23295 Alphas would behave strangely (ask for more dimensions after having 23296 been dimensioned) but not crash. 23297 23298Files: 23299 atomlwf.f 23300======================================================================== 23301Version: 0.10.21 23302Date: 1999/02/20 15:20:00 23303Title: Modifications mixing algorithms 23304Author: Pablo Ordejon (ordejon@condmat01.geol.uniovi.es) 23305 23306Description: 23307 Fixed errors of version 0.10.21. 23308 Changed output of si64 example. 23309 23310Files: 23311 Src/Makefile 23312 Src/pulayx.f 23313 Examples/Si64/Out/si64.out 23314 Examples/Si64/Out/out.fdf 23315 Examples/Si64/Out/siesta.size 23316======================================================================== 23317Version: 0.10.21 23318Date: 1999/02/20 14:45:00 23319Title: Modifications mixing algorithms 23320Author: Pablo Ordejon (ordejon@condmat01.geol.uniovi.es) 23321 23322Description: 23323 The Pulay mixing algorithms have been modified and improved, 23324 and some new imput variables related to the mixing have been introduced. 23325 The Pulay mixing is now done mixing parts of both the input and 23326 output matrices of former steps (whereas in the previous versions 23327 only input matrices were used). This allows to perform the 23328 Pulay mixing on EVERY SCF cycle. The algorithm and use is described 23329 in the user guide siesta.tex. 23330 New input variables are defined, to: 23331 1) Skip the Pulay mixing once in a while, and use linear mixing with 23332 a different alpha (suggested by G. Fabricius). New variables: 23333 DM.NumberKick, DM.KickMixingWeight 23334 2) Define whether mixing is done in first SCF iteration (usually it 23335 should not be done, but can be useful for SCF restarts). 23336 New variable: DM.MixSCF1 23337 Also, the mixing.f routine for linear mixing has been elliminated. 23338 Now, linear mixing is also done by pulayx.f 23339 23340Files: 23341 Src/siesta.f: Modifications for new variables, ellimination of 23342 mixing.f and new behavior of pulayx.f 23343 Src/redata.f: New mixing variables 23344 Src/pulay.f: New algorithm for mixing 23345 Src/mixing.f: SUPPRESSED 23346 Src/version.h: new version 23347 Docs/siesta.tex: new variables explained 23348 Docs/siesta.ind: new version 23349======================================================================== 23350Version: 0.10.20 23351Date: 1999/02/19 20:15:00 23352Title: New version of DENCHAR (0.1.1) 23353Author: Javier Junquera (junquera@condmat01.geol.uniovi.es) 23354 23355Description: 23356Changes to the input of charge, suggested by E. Artacho. 23357The names of the variables have been changed: all variable 23358names are added a '2D.' in the beginning of the variable name 23359(in order to distinguish variables proper of DENCHAR in fdf 23360input files) and some names have been reduced. 23361Also, the fdf input file is now dumped at the beginning 23362of the output. 23363Also, version number has been added, and will be maintained 23364and upgraded in future versions. 23365 23366Files: 23367 Util/Denchar/Src: Makefile: New file (dropped somehow in past version) 23368 denchar.f: Small input changes 23369 iodm.f: Small output changes 23370 readpla.f: Small input changes 23371 rhoofr.f: Small input and output changes 23372 wrout.f: New file 23373 Util/Denchar/Examples: AtomicIndex.fdf: Removed 23374 AtomicIndices.fdf: New (old AtomicIndex.fdf, modified 23375 for now input variables) 23376 ThreePoints.fdf: modified for now input variables 23377 TwoLines.fdf: modified for now input variables 23378 NormalVector.fdf: modified for now input variables 23379 Util/Denchar/Docs: denchar.tex: New version manual. 23380======================================================================== 23381Version: 0.10.20 23382Date: 1999/02/18 14:15:00 23383Title: Scalar rhoofd, vmat, triangular but not inverted 23384Author: Jose M. Soler (jose.soler@uam.es) 23385 23386Description: 23387 After some checks on ibms, decs, and sgi, there was an important 23388 variability on architecture for the inverted loops in rhoofd and vmat. 23389 This version recovers old structure (suited for scalar) but 23390 incorporates triangularizations that increase spped in a factor of 2 23391 compared with the old version. 23392 23393Files: 23394 rhoofd.f, vmat.f 23395 version.h, siesta.tex, CHANGES 23396======================================================================== 23397Version: 0.10.19 23398Date: 1999/02/16 14:30:00 23399Title: Structure for vmat more efficient on some platforms 23400Author: Julian D. Gale (j.gale@ic.ac.uk) 23401 23402Description: 23403 Analogous (to some extent) to rhoofd 23404 23405Files: 23406 vmat.f 23407 version.h, siesta.tex, CHANGES 23408======================================================================== 23409Version: 0.10.19 23410Date: 1999/02/4 12:45:00 23411Title: Structure for rhoofd more efficient on some platforms 23412Author: Julian D. Gale (j.gale@ic.ac.uk) 23413 23414Description: 23415 *Triangular sum instead of whole square-matrix sum: it doubles speed 23416 *Inverted order in do-loops, for a better parallelisation 23417 23418Files: 23419 rhoofd.f 23420 version.h, siesta.tex, CHANGES 23421======================================================================== 23422Version: 0.10.18 23423Date: 1999/01/31 19:15:00 23424Title: Bug fixed in atom + saving mixed DM + correcting spellings 23425Author: Emilio Artacho (emilio.artacho@uam.es) 23426 23427Description: 23428 *DM is now saved after mixing and mixing is done even in last iteration! 23429 Useful for O(N) scf step by step, and for achieving convergence with 23430 small mixings in different steps. 23431 *BUG FIXED: basis type = user had a wrong output format. 23432 *Misspellings corrected 23433 23434Files: 23435 siesta.f, denmat.f: mixing and DM saving 23436 atom_subs.f: bug fix 23437 several for misspellings 23438 version.h, CHANGES 23439======================================================================== 23440Version: 0.10.18 23441Date: 1999/01/31 11:45:00 23442Title: RCS Id label inclusion in every file of Src/ and Docs/ (fdf excl.) 23443Author: Emilio Artacho (emilio.artacho@uam.es) 23444 23445Description: 23446 A first line in every SIESTA file (in the Src and Docs directories) 23447 has been added with the RCS Id information which tells the version 23448 number of each file for developer and user information. 23449Note: It originally stores emilio in that line since I made the commit, 23450 but it does not mean anything on authorship nor responsilbility on the 23451 particular files. It will be changing to more adequate names with 23452 future changes. 23453 23454Files: 23455 Src/ (incl. Include/ and Sys/, but not fdf/) 23456 Docs/ 23457======================================================================== 23458Version: 0.10.18 23459Date: 1999/01/19 10:00:00 23460Title: IBM-ESSL version of rdiag (continued) 23461Author: Jose M. Soler (jose.soler@uam.es) 23462 23463Description: 23464 include 'eispack.f', previously in cdiag.f has been moved also to 23465 bsd.f, cray.f, general.f, ibm.f, and osf.f. 23466 23467Files: 23468 Sys/bsd.f : Added include '../eispack.f' 23469 Sys/cray.f : Added include '../eispack.f' 23470 Sys/general.f : Added include '../eispack.f' 23471 Sys/ibm.f : Added include '../eispack.f' 23472 Sys/osf.f : Added include '../eispack.f' 23473======================================================================== 23474Version: 0.10.18 23475Date: 1999/01/18 18:30:00 23476Title: IBM-ESSL version of rdiag 23477Author: Jose M. Soler (jose.soler@uam.es) 23478 23479Description: 23480 A new version of rdiag, written by Jorge Kohanoff, which calls the 23481 IBM-ESSL library routine DSYGV, was added. Additionally, the line 23482 include 'eispack.f' in cdiag.f has been moved to ibmessl.f, which 23483 is the file actually compiled. 23484 23485Files: 23486 Sys/ibmessl.f : Added new version of rdiag 23487 Added include '../eispack.f' 23488 cdiag.f : Removed include 'eispack.f' 23489======================================================================== 23490Version: 0.10.17 23491Date: 1998/12/10 23:00:00 23492Title: Several fixes to dynamics subroutines. 23493Author: Pablo Ordejon (ordejon@condmat01.geol.uniovi.es) 23494 23495Description: 23496 This version patches several problems detected in the molecular 23497 dynamics routines: 23498 1) problems with natoms=1 23499 2) output of cell velocities for several variable cell shape 23500 dynamics options 23501 3) error of reading of MD.BulkModulus variable (units included 23502 in the reading) 23503 Also, problems with DENCHAR program by J.Junquera are fixed 23504Files: 23505 Src/siesta.f : Calls to dynamics rutines: print out pressure. 23506 Src/redata.f : Correct reading of MD.BulkModulus 23507 Src/dynamics.f : Correct bug for natoms=1 23508 Util/Denchar/Src/denchar.f : fdf_init declared as external 23509 Util/Denchar/Src/colinear.f : Bug fixed 23510======================================================================== 23511Version: 0.10.16 23512Date: 1998/12/02 16:00:00 23513Title: New utility DENCHAR for 2D charge density plotting 23514 (Alternative to Contour by E. Artacho) 23515Author: Javier Junquera (junquera@condmat01.geol.uniovi.es) 23516 23517Description: 23518 Utility to read the density matrix and other information generated by 23519 SIESTA and generate 2D grids in arbitrary planes for 2D contour drawing. 23520 The SIESTA package has been modified to dump the necessary information 23521 to new output files. This package is an alternative to the program 23522 Coutour (By E. Artacho). 23523 DENCHAR allows to plot the charge in an arbitrary plane using 23524 a grid of arbitrary fineness (independent of the grid used in SIESTA). 23525 The total charge density, the spin components, the magnetization 23526 (difference of charges of spin up and down) and the difference between 23527 the selfconsistent charge and the sum of atomic densities can be plotted. 23528 DENCHAR uses FDF to read the data of the plane in which the contours 23529 are plotted, and some other information (like names of the density 23530 matrix and other output files from SIESTA). A manual is provided, 23531 as well as a directory with examples. 23532 DENCHAR contains the FDF package from A. Garcia and J. Soler, 23533 and many routines from SIESTA. 23534 23535Files: 23536 Util/Denchar/Docs/denchar.tex : NEW. user guide 23537 23538 Util/Denchar/Examples/AtomicIndex.fdf | 23539 Util/Denchar/Examples/NormalVector.fdf | 23540 Util/Denchar/Examples/TwoLines.fdf | 23541 Util/Denchar/Examples/ThreePoints.fdf | : NEW. example input files 23542 23543 Util/Denchar/Src/Makefile | 23544 Util/Denchar/Src/chkdim.f | 23545 Util/Denchar/Src/colinear.f | 23546 Util/Denchar/Src/denchar.f | 23547 Util/Denchar/Src/dmna.f | 23548 Util/Denchar/Src/dot.f | 23549 Util/Denchar/Src/fdf.f | 23550 Util/Denchar/Src/fdf.h | 23551 Util/Denchar/Src/fdfdefs.h | 23552 Util/Denchar/Src/io.f | 23553 Util/Denchar/Src/iodm.f | 23554 Util/Denchar/Src/length.f | 23555 Util/Denchar/Src/matvect.f | 23556 Util/Denchar/Src/neighb.f | 23557 Util/Denchar/Src/paste.f | 23558 Util/Denchar/Src/phiatm.f | 23559 Util/Denchar/Src/planed.f | 23560 Util/Denchar/Src/prmem.f | 23561 Util/Denchar/Src/ranger.f | 23562 Util/Denchar/Src/readpla.f | 23563 Util/Denchar/Src/redata.f | 23564 Util/Denchar/Src/rhoofr.f | 23565 Util/Denchar/Src/rlylm.f | 23566 Util/Denchar/Src/splint.f | 23567 Util/Denchar/Src/volcel.f | : NEW. code sources and makefiles 23568======================================================================== 23569Version: 0.10.15 23570Date: 1998/12/01 15:30:00 23571Title: Three bug corrections related with k-sampling 23572Author: Jose M. Soler (jose.soler@uam.es) 23573 23574Description: 23575 If bands were asked without k-sampling for energy, a conflict occurred 23576 between routines diagon and bands, which share common blocks. Argument 23577 gamma has been added to diagon, in order to ensure that it uses complex 23578 diagonalization (even only for gamma) when the bands routine is used. 23579 Also, an incorrect call to redcel in bands produced a core dump when 23580 using the option BandLinesScale=ReciprocalLatticeVectors. 23581 Finally, a bug in dhscf has been corrected, which produced an incorrect 23582 value of the dipole moment when k-sampling was used. 23583Files: 23584 bands.f : Corrected call to redcell 23585 dhscf.f : Corrected calculation of x0 before calling dipole 23586 diagon.f : Added argument gamma 23587 siesta.f : Call to diagon 23588======================================================================== 23589Version: 0.10.14 23590Date: 1998/11/23 17:30:00 23591Title: Placing imported routines in separated files 23592Author: Jose M. Soler (jose.soler@uam.es) 23593 23594Description: 23595 Routines not written by us, which were scattered across many files, 23596 have been placed in separated files, for copyright reasons. 23597 Apropriate acknowledgements have been added in the manual. 23598Files: 23599 arw.f : NEW. Contains routines bcorgn, bcrmax, cnfig, egofb, 23600 lmxofz, numin, numout, nrmlzg, polint, qvlofz, 23601 vhrtre, yofe, previously in atom_subs.f: 23602 atom_subs.f: Routines bcorgn, bcrmax, cnfig, egofb, lmxofz, 23603 numin, numout, nrmlzg, polint, qvlofz, 23604 vhrtre, yofe, moved to arw.f 23605 Routines ratint, spline, splint moved to recipes.f 23606 Routines paste, pasteb moved to paste.f 23607 cft.f : NEW. Contains routine cft, previously in poison.f 23608 cdiag.f : Routines eisch1, tql2c, htribk moved to eispack.f 23609 eispack.f : NEW. Contains eisch1, tql2c, htribk, previosly in cdiag.f 23610 four1.f : SUPRESSED. Routine four1 now in recipes.f 23611 ordix.f : SUPRESSED. Routine ordix now in recipes.f 23612 paste.f : NEW. Contains routines paste, pasteb, previously in 23613 atom_subs.f 23614 poison.f : Routine cft moved to file cft.f 23615 recipes.f : NEW. Contains routines four1, ordix, ratint, splin, 23616 spline, splint, splinu, previously in other files. 23617 splin.f : SUPRESSED. Routines splin, splinu now in recipes.f 23618 Makefile : Adapted to the changes above 23619 Docs/siesta.tex : New section of acknowledgements, plus some update 23620 of the Projected Changes and Additions section 23621======================================================================== 23622Version: 0.10.14 23623Date: 1998/11/17 21:15:00 23624Title: New utility: 2D contour plotting 23625Author: Emilio Artacho (emilio.artacho@uam.es) 23626 23627Description: 23628 Utility to read 3D-grid functions information generated by SIESTA 23629 (.RHO, .DRHO, etc.) and generate 2D grids in arbitrary planes for 23630 2D contour drawing. It does not affect the rest of the SIESTA pack. 23631 23632Files: 23633 Util/Contour/grid2d.f : the program 23634 Util/Contour/raw.in, noraw.in : input examples 23635 Util/Contour/gnux11, gnups : gnuplot use examples 23636 Util/Contour/README : short explanation 23637======================================================================== 23638Version: 0.10.14 23639Date: 1998/10/23 21:00:00 23640Title: Alphabetic index at the end of the manual (please check and keep) 23641Author: Emilio Artacho (emilio.artacho@uam.es) 23642 23643Description: 23644 An alphabetic index is added at the end of the manual. It is made by 23645 introducing \index{whatever} commands in the siesta.tex file, 23646 running 'latex siesta', then 'makeindex siesta', and then 'latex 23647 siesta' again. 23648Files: 23649 siesta.tex 23650 siesta.ind (index generated by makeindex) 23651======================================================================== 23652Version: 0.10.14 23653Date: 1998/10/23 18:30:00 23654Title: Bug corrections, mainly with k-sampling 23655Author: Jose M. Soler (jose.soler@uam.es) 23656 23657Description: 23658 Parameters maxna and maxno were reduced to their minimun acceptable 23659 values (without margin for atom movements) when other parameters 23660 were changed, increasing the number of recompilations. 23661 Array conect in hsparse was incorrectly initialized with k-sampling. 23662 Array listno in listsc was written out-of-bounds when its dimension 23663 was too small. 23664Files: 23665 siesta.f : avoid reducing maxna and maxno 23666 hsparse.f : corrected initialization of array conect 23667 listsc.f : conditional writting of listno 23668======================================================================== 23669Version: 0.10.13 23670Date: 1998/10/18 14:00:00 23671Title: Plotting DeltaRho (Rho-Rho_atoms), msiesta, and manual revision *.h 23672Author: Emilio Artacho (emilio.artacho@uam.es) 23673 23674Description: 23675 New SaveDeltaRho FDF option to save the electronic density minus the 23676 sum of the atomic densities. File SystemLabel.DRHO 23677Files: 23678 dhscf.f: Does the icalculating and calling to iorho (who writes). 23679 New argument at interface: fildrh, name of file to write. 23680 siesta.f: Adapt to new dhscf.f interface and generate new name. 23681 grdsam.f: Adapt to new dhscf.f interface. 23682 Util/msiesta: If init, cp *.h to working directory 23683 siesta.tex: Documented + redocumenting .h files and generation. 23684 version.h and CHANGES 23685======================================================================== 23686Version: 0.10.12 23687Date: 1998/10/14 21:00:00 23688Title: One more optional input in block PAO.Basis 23689Author: Daniel Sanchez-Portal (daniel@polar.fmc.uam.es) 23690 23691Description: 23692 -Now variable PAO.BasisType can assume different values for 23693 different species. New optional input in data block PAO.Basis 23694Files: 23695 atom.f : 23696 atom_subs.f : 23697 redbasis_subs.f: 23698 redbasis.f : 23699 initatom.f : 23700 version.h : Changed the date but not the number of last version, 23701 which is still 0.10.12 23702 Docs/siesta.tex : Added description of the new parameter 23703======================================================================== 23704Version: 0.10.12 23705Date: 1998/10/13 17:00:00 23706Title: BUG FIX in siesta, atom_subs and redbasis_subs 23707Author: Daniel Sanchez-Portal (daniel@polar.fmc.uam.es) 23708 23709Description: 23710 -New version of subroutine mulliken did not work properly because 23711 new arguments were not included in its call in main program 23712 -Corrected some bugs (lack of initialization for some variables) 23713 in some subroutines from atom_subs.f, redbasis_subs.f (detected 23714 while runing in a Linux machine). 23715 -Corrected length of common blocks in atom_subs.f to avoid 23716 errors in some compilers (detected while compiling in a Linux 23717 machine). 23718 23719Files: 23720 siesta.f : Corrected call of subroutine mulliken 23721 atom_subs.f : Bug fix 23722 redbasis_subs.f: Bug fix 23723 version.h : Changed the date but not the number of last version, 23724 which is still 0.10.12 23725 Examples/H2O/Out : Updated outputs 23726 Examples/H2O/OrderN/Out : Updated outputs 23727 Examples/Si64/Out : Updated outputs 23728 Docs/siesta.tex : Added description of the data block PAO.BasisSizes 23729======================================================================== 23730Version: 0.10.12 23731Date: 1998/10/10 20:00:00 23732Title: BUG FIX in outcoor + New flag in outcoor + Cosmetics 23733Author: Emilio Artacho (emilio.artacho@uam.es) 23734 23735Description: 23736 - outcoor would generate wrong fractional coordinates because of a 23737 matrix transposition (fixed). 23738 - New 'WriteCoorStepNot' for not writing coordinates at each time step 23739 - Cosmetics for output in various files. 23740 - Output formats in new atom-related: it should be '1x' instead of 'x' 23741 23742Files: 23743 outcoor.f : bug + flag 23744 mulliken.f : formats to 1x 23745 matel.f : cosmetics (Estee Lauder) 23746 redata.f : " 23747 atom.f : " 23748 atom_subs.f : " 23749 siesta.tex : new flag + some small changes 23750 version.h 23751======================================================================== 23752Version: 0.10.11 23753Date: 1998/10/9 19:00:00 23754Title: New implementation of the subroutine atom, and more flexible input 23755 for the basis set 23756Author: Daniel Sanchez-Portal(daniel@polar.fmc.uam.es) 23757 23758Description: 23759 General restructuring of atom subroutine(s), cutting it to pieces, 23760 redefining functions for interface with SIESTA, and redefining the 23761 input for the basis, being now much more flexible. 23762 23763 Semicore states (in a simple version) can be now introduced. 23764 23765 A BUG was FIXED for perturbative polarization orbitals. 23766 23767Files: 23768 23769atom.f: 23770 Strongly modified. The routine has been completely restructured. Different 23771 calculations (local pseudopot., basis set, neutral-potential, etc...) are now 23772 performed by different routines which are called by the 'main' routine atom. 23773 These new routines are included in the file atom_subs.f. 23774 Semicore states can be automatically included, though in a quite naive way. 23775atom_functions.f: 23776 NEW. Include all the 'atom dependent' functions. Most of the old ones 23777 (phiatm, rcut, ...) have been modified, and new functions have been coded. 23778atom.h: 23779 Type declaration for the parameters included in the file. Parameter 23780 ntbmax increased to 500. 23781atomlwf.f: 23782 subroutine atomlwf: lmax, lmaxs and nzls erased from the input 23783 subroutine initguess: lmax, lmaxs and nzls erased from the input, information 23784 now provided by functions lomaxfis and nztfl 23785atom_subs.f: 23786 32 new subrotuines have been added. Fixed a BUG in the interpolation of 23787 polarization orbitals. As a consecuence, the contribution to the forces 23788 coming from this orbitals, in spite of being consitent with energy, show 23789 an oscillatory behaviour which could worse the convergence with the grid 23790 spacing. 23791 The effect could be more important only for H, or other elements having 23792 'p' polarization orbitals. 23793chcore.f: 23794 Deleted (now included in atom_functions.f) 23795dnaefs.f: 23796 Argument izs removed, information now provided by izofis function 23797epskb.f : 23798 Deleted (now included in atom_functions.f) 23799initatom.f: 23800 Several arguments have been removed from the call to this routine. 23801 Included a call to subroutine redbasis (before calling subroutine atom). 23802 Checks for several dimensions have been deleted. 23803Makefile: 23804 Added files: atom_functions.f, redbasis.f redbasis_subs.f 23805 Deleted files: chcore.f epskb.f phiatm.f psover.f rcore.f rcut.f uion.f 23806 All the deteled routines, together with other 'atom depedent' functions, 23807 now included in the file atom_functions.f 23808 File initatom.f now depends on dimensions in atom.h 23809matel.f : 23810 Deleted arguments lmaxs, lmxkbs, maxls and nzls in subroutine matel0. 23811 The information is now provided by functions lomaxfis, lmxkbfis and nztfl. 23812mulliken.f : 23813 Added arguments isa, iphorb and iaorb. Changes in the ouput 23814 format for the population analisys: Now a label with the 23815 symmetry of each orbital is also printed. 23816naefs.f: 23817 Argument izs removed, information now provided by izofis function 23818ordern.f: 23819 lmax, lmaxs and nzls erased from the input 23820outcoor.f: 23821 Argument atm_label removed, information now provided by 23822phiatm.f : 23823 Deleted (now included in atom_functions.f) 23824rcore.f : 23825 Deleted (now included in atom_functions.f) 23826rcut.f : 23827 Deleted (now included in atom_functions.f) 23828redata.f : 23829 Several arguments have been removed from the call to this routine. 23830 All the information about atomic orbitals, pseudopotentials and atomic 23831 masses is now read by subroutine redbasis called by subroutine initatom. 23832 Default masses for floating Bessel functions set to 1.0d30 a.u. 23833 Dynamics type is always set to 'cg' if the system contains just one atom. 23834redbasis.f: 23835 NEW. Reads the information about atomic orbitals, pseudopotentials and atomic 23836 masses. Called by subroutine initatom. 23837redbasis_subs.f: 23838 NEW. This file include nine routines used by redbasis to read the input (fdf) 23839 file in several possible formats. 23840siesta.f : 23841 Several arrays containing information about the chemical 23842 species and the basis set have been removed. Calls 23843 of routines redata, initatom, matel0,naefs, dnaefs, ordern, 23844 and outcoor have also been modified. 23845Include/atom.h: 23846 Type declaration for the parameters included in the file. Parameter 23847 ntbmax increased to 500. 23848Include/siesta.h : 23849 Parameters maxl, maxos, maxs, maxzet have been suppressed. 23850Examples/H2O/Out : Updated outputs 23851Examples/H2O/OrderN/Out : Updated outputs 23852Examples/Si64/Out : Updated outputs 23853Docs/siesta.tex : Updated basis set description 23854======================================================================== 23855Version: 0.10.10 23856Date: 1998/08/28 19:00:00 23857Title: Efficient k-sampling implementation 23858Author: Jose M. Soler (jose.soler@uam.es) 23859 23860Description: 23861 The need to use very large supercells, in order to do k-sampling, 23862 has been eliminated, making k-sampling efficient. Other canges are: 23863 - BUG corrected in dhscf => now finds more adjusted cutoffs. 23864 - Now k-sampling and bands are compatible with non-collinear spin 23865 - Suppressed automatic k-sampling when using SuperCell 23866 - Auxiliary arrays now shared by diagon and bands 23867 - Optimized matrix multiplication algorithm in diagon 23868 - Added LAPACK complex diagonalization routine for osfdxml systems 23869 - neighb initialized before each use 23870 - Suppressed writting the density matrix in denmat 23871 - Avoid decreasing array dimensions in ranger 23872 - Array xijo now dimensioned only when necessary 23873 23874Files: 23875 Makefile : Added routines diagg, diagk, diag2g, diag2k, digcel, 23876 redcel, superc, and superx 23877 Suppressed routine diagnc 23878 atomlwf.f : Initialization of neighb done always 23879 bands.f : Calls diagk and diag2k 23880 Auxiliary space shared with diagon trough common block 23881 denmat.f : Suppressed writting the density matrix 23882 dfscf.f : Added argument indxuo to add forces to atom in unit cell 23883 dhscf.f : Calculate things only in the unit cell (many changes) 23884 Corrected a BUG to find the mesh cutoff for nonothorhombic cells 23885 dynamics.f: Corrected the name of the routines in error message 23886 diagnc.f : SUPRESSED (now diag2g) 23887 diagg.f : NEW. Diagonalization for gamma only 23888 diagk.f : NEW. Diagonalization with k sampling 23889 Optimized matrix multiplication algorithm 23890 diag2g.f : NEW. Same as diagg for non-collinear spin 23891 diag2k.f : NEW. Same as diagk for non-collinear spin 23892 diagon.f : Calls diagg, diagk, diag2g and diag2k to do the work 23893 Auxiliary space shared with bands trough common block 23894 diagon.h : Suppressed maxspn. Added maxhs and maxpsi 23895 digcel.f : NEW. Finds diagonal unit cell and supercell combination 23896 dnaefs.f : Distiction of unit cell and supercell. neighb initialized 23897 grdsam.f : Call to dhscf 23898 hsparse.f : Slight comment corrections (code not changed) 23899 initatom.f: Suppress repeated arguments 23900 iohs.f : Array xij not written when only gamma point is used 23901 kgrid.f : Suppressed automatic k-sampling for SuperCell use 23902 kinefsm.f : Distiction of unit cell and supercell. neighb initialized 23903 listsc.f : NEW. Expands neighbour lists from unit cell to supercell 23904 naefs.f : Distiction of unit cell and supercell. neighb initialized 23905 nlefsm.f : Distiction of unit cell and supercell. neighb initialized 23906 overfsm.f : Distiction of unit cell and supercell. neighb initialized 23907 ranger.f : Avoid decreasing array dimensions 23908 recoor.f : Expand coordinates to supercell 23909 redata.f : Supercell atomic coord. now done by new supcel routine 23910 Specified SuperCell now becomes operative unit cell 23911 redcel.f : NEW. Reads the unit-cell/supercell vectors 23912 rhooda.f : Added argument indxuo to work only within unit cell 23913 rhoofd.f : Added argument indxuo to work only within unit cell 23914 siesta.f : Calculate things only in the unit cell (many changes) 23915 siesta.h : Suppressed parameter maxkba 23916 Added parameter maxxij to dimension array xijo 23917 Name of parameter dimaux changed to maxpul 23918 superc.f : NEW. Finds the required supercell and expands arrays to it. 23919 superx.f : NEW. Expands coordinates from unit cell to supercell. 23920 version.h : New version 0.10.10 23921 vmat.f : Added argument indxuo to work only within unit cell 23922 vmb.f : Return if nat=1 23923 xijorb.f : Name of argument 'cell' changed to 'scell'. 23924 Include/siesta.h : Suppressed parameter maxkba 23925 Include/diagon.h : Suppressed maxspn. Added maxhs and maxpsi 23926 Sys/bsd.f : cdiag added to system-dependent routines 23927 Sys/cray.f : cdiag added to system-dependent routines 23928 Sys/general.f : cdiag added to system-dependent routines 23929 Sys/ibm.f : cdiag added to system-dependent routines 23930 Sys/ibmessl.f : cdiag added to system-dependent routines 23931 Sys/osf.f : cdiag added to system-dependent routines 23932 Sys/osfdxml.f : New version of cdiag to use LAPACK routine zhegv 23933 Sys/sgi.f : cdiag added to system-dependent routines 23934 Docs/siesta.tex : Updated k-sampling instructions 23935 Docs/siesta/CHANGES 23936 Examples/H2O/Out/* : Updated outputs 23937 Examples/Si64/Out/* : Updated outputs 23938======================================================================== 23939Version: 0.10.9 23940Date: 1998/07/14 11:30:00 23941Title: Increased tolerance in shaper routine 23942Author: Jose M. Soler (jose.soler@uam.es) 23943 23944Description: 23945 In some cases, the system shape was incorrectly reported as bulk 23946 because the tolerance in routine linvec (1.e-10) was too small. 23947 23948Files: 23949 shaper.f : Tolerance in routine linvec increased to 1.e-6 23950======================================================================== 23951Version: 0.10.8 23952Date: 1998/07/13 16:15:00 23953Title: Corrected calculation of local density of states 23954Author: Jose M. Soler (jose.soler@uam.es) 23955 23956Description: 23957 After previous change, LDOS was incorrectly calculated, because the 23958 hamiltonian was reinitialized but the dhscf part was not included 23959 before calling diagon to find the LDOS density matrix. 23960 23961Files: 23962 siesta.f : Eliminate the reinitialization of H 23963======================================================================== 23964Version: 0.10.7 23965Date: 1998/06/26 17:30:00 23966Title: Grid-cell sampling for accelerated grid convergence 23967Author: Emilio Artacho (emilio.artacho@uam.es) 23968 23969Description: 23970 Sampling displacements of the system with respect to the grid 23971 across the grid cell is used to symmetrize energies, forces, stresses 23972 and dipoles. It allows a better convergence with grid cutoff by 23973 reducing the egg-box effect. The displacements are introduced 23974 within the block GridCellSampling (see the manual) 23975 23976Files: 23977 grdsam.f : new subroutine doing the sampling at the end of an SCF cycle 23978 siesta.f 23979 dhscf.f : sampling is done by calling dhscf for each displacement 23980 Makefile 23981 siesta.tex 23982======================================================================== 23983Version: 0.10.6 and 0.9.2 23984Date: 1998/06/22 21:45:00 23985Title: Corrected MAXL dimension in ylmexp. (SEVERE BUG for L>2) 23986Author: Jose M. Soler (jose.soler@uam.es) 23987 23988Description: 23989 Due to an insuficient dimension, the overlap was incorrect for L>2, 23990 including the f Kleinman-Bylander operators. 23991 23992Files: 23993 ylmexp.f : maxLM = maxL**2 changed to (maxL+1)**2 23994 ylmylm.f : Same correction 23995======================================================================== 23996Version: 0.10.5 23997Date: 1998/06/22 21:45:00 23998Title: Corrected supercell hamiltonian symmetrization 23999Author: Jose M. Soler (jose.soler@uam.es) 24000 24001Description: 24002 The condition if (ncells .lt. 1) was incorrect, because ncells must 24003 be at least one. As a consecuence, no supercell symmetrization was 24004 done. Now it has been corrected to if (ncells .gt. 1) 24005 24006Files: 24007 diagon.f : if (ncells .lt. 1) changed to if (ncells .gt. 1) 24008 Examples/Si64/Out/si64.out : Updated output 24009 Examples/Si64/Out/out.fdf : Updated output 24010 Examples/Si64/Out/siesta.size : Updated output 24011======================================================================== 24012Version: 0.10.4 24013Title: Remove unused subroutine ylmr 24014Author: Jose M. Soler (jose.soler@uam.es) 24015 24016Files: 24017 atom_subs.f : Subroutine ylmr removed 24018======================================================================= 24019Version: 0.10.3 24020Date: 1998/06/22 21:45:00 24021Title: No mixing in last iteration and when wmix=0 24022Author: Jose M. Soler (jose.soler@uam.es) 24023 24024Description: 24025 An unexpected behavior occurred when only one iteration was done, 24026 because in the first iteration, the whole new density matrix is 24027 taken, irrespective of the mixing weight (this is because the first 24028 density matrix is not idenpotent). Now, the mixing subroutines are 24029 not called in the last iteration, even if it is also the first one. 24030 24031Files: 24032 siesta.f : Conditions to call mixing and pulayx 24033======================================================================== 24034Version: 0.10.2 24035Date: 1998/06/22 21:45:00 24036Title: Added non-collinear spin 24037Author: Jose M. Soler (jose.soler@uam.es) 24038 24039Description: 24040 In the non-collinear-spin density functional, spinor wavefunctions 24041 and 2x2 spin density matrices allow the spin to change direction 24042 at every point. Ref: T. Oda et al, PRL 80, 3622 (1998). 24043 Non-collinear-spin density matrix has 4 components (nspin=4). 24044 No k-sampling allowed in this version for non-collinear-spin. 24045 24046Files: 24047 bands.f : Return if nspin=4 24048 dfscf.f : Free-atom and SCF contributions separated and initialized 24049 dhscf.f : Handle the nspin=4 case 24050 diagnc.f : (New) Eigenvalue problem in spinor space (doubled) 24051 diagnc.h : (New) Dimension parameters for diagnc 24052 initdm.f : Initialize the non-collinear-spin density matrix 24053 mulliken.f : Handle the nspin=4 case 24054 redata.f : Read the NonCollinearSpin fdf label 24055 rdiag.f : Word ERROR added in error message 24056 siesta.f : Handle the nspin=4 case. Call diagnc 24057 xc.f : Diagonalize the spin density matrix in routine ldaxc 24058 Makefile : Add diagnc 24059 siesta.tex : Add NonCollinearSpin and modify DM.InitSpin options 24060======================================================================== 24061Version: 0.10.1 and 0.9.1 24062Date: 1998/05/18 13:21:16 24063Title: msiesta not to find .h files in subdirectories 24064Author: Alberto Garcia <wdpgaara@lg.ehu.es> 24065 24066Description: 24067 An unexpected behavior of msiesta was that it could find (and use 24068 to replace) .h files in subdirectories of the working directory. 24069 This was due to the use of 'find' by msiesta, now supressed. 24070 24071Files: 24072 Util/msiesta : use of find supressed. 24073======================================================================== 24074Version: 0.10.0 <=> 0.9.0 <=> 0.8.53 24075======================================================================== 24076Version: 0.8.53 24077Date: 1998/05/5 21:30:00 24078Title: Revising script files + comment on them in the manual 24079Author: Emilio Artacho (emilio.artacho@uam.es) 24080 24081Description: 24082 Script files qsiesta and qrrsiesta allow running in the absence of other 24083 scripts from the working directory. 24084 24085 msiesta copies Include/ordern.h and Include/diagon.h in working directory 24086 if init. 24087 24088 Manual has a comment on the convenience of "touch" *.h in a working 24089 directory if recompiling after some time (after other systems have been 24090 compiled. 24091 24092Files: 24093 qsiesta, qrrsiesta, msiesta 24094 siesta.tex 24095======================================================================== 24096Version: 0.8.52 24097Date: 1998/05/4 20:25:00 24098Title: Printing Qtot before DM normalization in O(N) solution 24099Author: Pablo Ordejon (ordejon@condmat01.geol.uniovi.es) 24100 24101Description: 24102 Write Qtot before and after the DM renormalization, in O(N) calculations. 24103 This is usefull to bracket the value of eta. 24104 24105Files: 24106 ordern.f : Change the format of the printout of qtot 24107 denmat.f : Write qtot before normalization 24108======================================================================== 24109Version: 0.8.51 24110Date: 1998/05/3 22:30:00 24111Title: Removing unused variables + adding parenthesis: Avoiding warnings 24112Author: Emilio Artacho (emilio.artacho@uam.es) 24113 24114Description: 24115 From the compilation of SIESTA 0.8.50 with g77 -Wall (linux), warnings 24116 concerning unused variables and ambiguous math expressions have been 24117 used for their correction. Unused variables have been removed and 24118 parenthesis have been added to math expressions. 24119 24120Files: (and variables removed) 24121 Sys/cray.f : times (in cputim.f) 24122 Sys/ibm.f : times (in cputim.f) 24123 Sys/ibmessl.f : i, j, np (in poison.f) 24124 Sys/osfdxml.f : i, j, np (in poison.f) 24125 atom.f : loctype, namaux 24126 atom_subs.f : 24127 bands.f : ie 24128 bessph.f : 24129 cdiag.f : 24130 constr.f : fz 24131 cputim.f : times 24132 denmat.f : iunit 24133 dhscf.f : epsxc, qatm, qscf, ro, wspin 24134 diagon.f : found 24135 efield.f : 24136 fermid.f : 24137 four1.f : 24138 gradient.f : 24139 hsparse.f : kno, jno, ina 24140 idiag.f : 24141 initatom.f : il 24142 initdm.f : fname 24143 iorho.f : sname 24144 kgrid.f : 24145 nlefsm.f : kna 24146 ordvec.f : jv 24147 outcoor.f : i, iunit, title 24148 overfsm.f : 24149 poison.f : 24150 prmem.f : namety 24151 psover.f : is 24152 radfft.f : 24153 ranger.f : drm, dxm, iv, ivx, nxlast, volmin 24154 rdiag.f : 24155 redata.f : alat_defect, smassr, iscale, flc 24156 reord.f : iaux, j1, j2, j3 24157 rlylm.f : 24158 siesta.f : overflowna, pi 24159 splin.f : 24160 vmat.f : p0 24161 xc.f : 24162 xijorb.f : kno, jno, ina 24163======================================================================== 24164Version: 0.8.50 (continued, no code change but cosmetics) 24165Date: 1998/04/29 20:45:00 24166Title: Output cosmetics + adding E_KS output for each SCF loop end. 24167Author: Emilio Artacho (emilio.artacho@uam.es) 24168 24169Description: 24170 Surface reflectivity and different light sources have been introduced. 24171 The illumination data may be specified in light.dat file. 24172 24173Files: 24174 siesta.f (E_KS writing + cosmetics) 24175 ordern.f (output cosmetics) 24176 chkdim.f (") 24177 cgwf.f (") 24178 siesta.tex (Alberto added to front page of manual) 24179======================================================================== 24180Version: 0.8.50 24181Date: 1998/04/15 16:00:00 24182Title: Variable illumination in plrho 24183Author: Jose M. Soler (jose.soler@uam.es) 24184 24185Description: 24186 Surface reflectivity and different light sources have been introduced. 24187 The illumination data may be specified in light.dat file. 24188 24189Files (all in siesta/Util/Plrho): 24190 ray.f : New function, which returns a pixel light intensity (ray) 24191 pltr3d.f : Call to ray 24192 plrho.f : Added include 'ray.f' statement 24193 light.dat : New. Example of illumination data file 24194 plrho_guide.txt : Documentation of these changes 24195======================================================================== 24196Version: 0.8.50 24197Date: 1998/04/15 16:00:00 24198Title: Printed Fermi energy 24199Author: Jose M. Soler (jose.soler@uam.es) 24200 24201Description: 24202 Fermi energy re-printed after the eigenvalues 24203 24204Files: 24205 siesta.f : Added a write line. 24206======================================================================== 24207Version: 0.8.49 24208Date: 1998/04/14 21:40:00 24209Title: Reading atomic masses + cosmetics + fix bugs (linux.make, outcell) 24210Author: Emilio Artacho (Emilio.Artacho@uam.es) 24211 24212Description: 24213 Atomic masses can be now read through an fdf block: AtomicMass. 24214 The species not included in the block assume standard value for the 24215 species. If block not present, standard values for all (as before). 24216 24217 linux.make lacked RANLIB definition. Fixed. 24218 24219 outcell.f wrote cell volume in wrong units. Fixed. 24220 24221 Cosmetics: initatom does not write poems any more. And others. 24222 24223Files: 24224 remass.f : new for mass reading 24225 redata.f : calls it plus cosmetics 24226 Makefile 24227 outcell.f: bug fixed 24228 initatom.f 24229 atom.f 24230 prversion.f 24231 siesta.tex 24232======================================================================== 24233Version: 0.8.48 24234Date: 1998/04/04 17:15:00 24235Title: Temperature in output 24236Author: Pablo Ordejon (ordejon@condmat01.geol.uniovi.es) 24237 24238Description: 24239 24240The temperature is writen on output for any MD flavour. 24241(Error corrected in if statement) 24242 24243Files: 24244 siesta.f 24245======================================================================== 24246Version: 0.8.48 24247Date: 1998/04/04 17:15:00 24248Title: Optimized memory for Order-N routines 24249Author: Pablo Ordejon (ordejon@condmat01.geol.uniovi.es) 24250 24251Description: 24252 24253Redefined the dimension of several matrices in the Order-N routines, 24254which were oversized. The result is a reduction in executable size 24255for Order-N calculations. The reduction is related to the maxnhf 24256parameter. 24257 24258Files: 24259 denmat.f: eliminate nhfmax parameter. sustitute by nfmax 24260 in chcc and cscc matrices definitions 24261 egandd.f: substitute maxnhf by maxnf in definition of f and fs 24262 gradient.f: eliminate nhfmax parameter. sustitute by nfmax 24263 in f and fs matrices definitions 24264======================================================================== 24265Version: 0.8.47 24266Date: 1998/03/25 13:00:00 24267Title: New Util scripts. Makefile extensions 24268Author: Alberto Garcia <wdpgaara@lg.ehu.es> 24269 24270Description: 24271 24272The scripts in Util have been rewritten using Bourne shell constructs. Only 24273minor changes in their functionality have been introduced (mostly more 24274robust warnings). 24275 24276Added support for Cray and SGI machines. For the latter, a default 24277binary architecture -mips4 is assumed. Added a $(COMMENTS) symbol 24278to sgi.make (echoed in Makefile) to warn the user. 24279 24280Files: 24281Directory Util: prdate, msiesta, rsiesta, rrsiesta, qsiesta, qrrsiesta 24282Directory Src/Sys: cray.f, cray.make, sgi.f, sgi.make: new files. 24283Directory Src: Makefile: Made 'nodebug' compilation the default. 24284 Corrected outcoor entry. Echoed $(COMMENTS). 24285======================================================================== 24286Version: 0.8.46 24287Date: 1998/03/18 13:45:00 24288Title: Suppressed an incorrect call to matel0 24289Author: Jose M. Soler (jose.soler@uam.es) 24290 24291Description: 24292 Suppressed an extra call to matel0, which was inadvertently left in 24293 siesta.f in last version. 24294 Variables I1=1 and I2=2 introduced in matel to avoid a compilation 24295 message with the -C option (array bounds check) 24296 24297Files: 24298 siesta.f 24299 matel.f 24300======================================================================== 24301Version: 0.8.45 24302Date: 1998/03/16 16:32:00 24303Title: Commentaries changed. 24304Author: Daniel Sanchez-Portal (daniel@polar.fmc.uam.es) 24305 24306Subroutine initatom.f : 24307 Arrays rcls, contrf, lmaxs, lmxkbs, nzls 24308 have to be considered as belonging to the output rather than to the 24309 input of the routine. The commentary on the begining of the routine 24310 has been changed in that sense. 24311Subroutine atom.f : 24312 The same as initatom.f 24313 24314Subroutine r_vs_e and polarization: 24315 Some lines have been commented to avoid the 'uncontroled' ouput 24316 that appered when the programme was run in some machines. 24317 24318Files: 24319 initatom.f : Updated header commentaries 24320 atom.f : Updated header commentaries 24321 atom_subs.f : Some lines commented in routines r_vs_e and polarization 24322======================================================================== 24323Version: 0.8.44 24324Date: 1998/03/13 13:30:00 24325Title: Optimized diagonalization 24326Author: Jose M. Soler (jose.soler@uam.es) 24327 24328Description: 24329 Some loops for the generation of the density matrix from the 24330 eigenvectors were interchanged, to improve memory access. 24331 New versions for rdiag and cdiag, using lapack routine dsygv 24332 of the DEC dxml library. 24333 These changes reduce CPU time by more than 50% in many cases. 24334 24335Files: 24336 diagon.f : Exchanged some loops 24337 Sys/*.f : Added include '../rdiag.f' sentence 24338 Sys/osfdxml.f : Added new rdiag version, calling a lapack routine 24339 Makefile : Supressed rdiag 24340 Examples/H2O/Out/* : Updated outputs 24341 Examples/H2O/OrderN/* : Updated outputs 24342 Examples/Si64/Out/* : Updated outputs 24343======================================================================== 24344Version: 0.8.44 24345Date: 1998/03/13 13:30:00 24346Title: Reorganized system-dependent versions 24347Author: Jose M. Soler (jose.soler@uam.es) 24348 24349Description: 24350 In order to handle more easly the system-dependent versions, the 24351 'general' (source code) versions are kept in the Src directory. 24352 The files Src/Sys/*.f, containing the system-dependent versions, 24353 now contain sentences like include '../poison.f', when necessary. 24354 24355Files: 24356 Src/poison.f : (new) General version 24357 Src/cputim.f : (new) General version 24358 Src/Sys/*.f : explicit source code of general versions substituted 24359 by sentences like include '../poison.f' 24360======================================================================== 24361Version: 0.8.44 24362Date: 1998/03/13 13:30:00 24363Title: Creation of matel.h 24364Author: Jose M. Soler (jose.soler@uam.es) 24365 24366Description: 24367 Although the sizes of the arrays in routine matel are independent of 24368 system size, and neglegible for large systems, they were dimensioned 24369 for the largest systems (5 species with spd DZP) and they took most 24370 of the memory for small systems. A new file matel.h, written by a 24371 new matel0 entry point in matel.f, was introduced to solve this, 24372 using the run-compile loop method. 24373 24374Files: 24375 Include/matel.h : (new) basic dimension parameters for matel 24376 matel.h : same as Include/matel.h 24377 matel.f : new matel0 entry point 24378 siesta.f : call to matel0 24379======================================================================== 24380Version: 0.8.44 24381Date: 1998/03/13 13:30:00 24382Title: Corrected decomposition of final energies 24383Author: Jose M. Soler (jose.soler@uam.es) 24384 24385Description: 24386 A missing term -Uatm in the ion-electron interaction energy, printed 24387 in the 'Final energy' output was added. 24388 Ecorrec was changed to eta*DQ (only the printed name). 24389 Ekinion was included in the final energy decomposition. 24390 24391Files: 24392 siesta.f 24393======================================================================== 24394Version: 0.8.43 24395Date: 1998/03/10 11:30:00 24396Title: Changed tolerace in routine livec 24397Author: Jose M. Soler (jose.soler@uam.es) 24398 24399Description: 24400 Changed tolerace to 1.d-10 in routine livec, called by shaper, 24401 in order to solve a problem found by Pablo for a slab. 24402 24403Files: 24404 shaper.f : Parameter TOL of LIVEC changed to 1.D-10 24405======================================================================== 24406Version: 0.8.42 24407Date: 1998/02/23 12:05:03 24408Title: Implemented Version string management 24409Author: Jose M. Soler (jose.soler@uam.es), 24410 Alberto Garcia (wdpgaara@lg.ehu.es) 24411 24412Description: 24413 The version of the code in use is written in version.h, and is 24414 printed in every siesta run. That version number is consistent 24415 with the one appearing on the manual front page, as well as the 24416 corresponding date. 24417 Odd version numbers (like 0.9) are distribution releases, 24418 with possible bug fixes: 0.9 fix 3. 24419 Even version numbers (like 0.10) are development versions, 24420 which include new implementacions as patches: 0.10 pl 5 24421 (pl: patch level). 24422 24423Files: 24424 version.h : has version number stored within 24425 prversion.f : prints version 24426 siesta.f : calling version files 24427 Makefile : version file dependencies 24428======================================================================== 24429Version: 0.8.41 24430Date: 1998/02/20 19:31:22 24431Title: Examples directory restructured 24432Author: Jose M. Soler (jose.soler@uam.es), 24433 24434Description: 24435 Two exmaples now: H2O and Si64. Both diagonalizing. 24436 24437Files: (within siesta/Examples/) 24438 Vps/ (pseudopotentials) 24439 README 24440 H.inp 24441 O.inp 24442 Si.inp 24443 H.vps 24444 O.vps 24445 Si.vps 24446 H2O/ 24447 h2o.fdf 24448 Out/ 24449 h2o.out 24450 out.fdf 24451 siesta.size 24452 Si64/ 24453 si64.fdf 24454 Out/ 24455 si64.out 24456 out.fdf 24457 siesta.size 24458======================================================================== 24459Version: 0.8.40 24460Date: 1998/02/20 14:37:00 24461Title: FIX: CG order-N minimization parameters 24462Author: Pablo Ordejon (ordejon@condmat01.geol.uniovi.es) 24463 24464Description: 24465Changed minimization parameters to solve convergence problem 24466in order-N solution of H2O. 24467 24468Files: 24469 cgwf.f 24470======================================================================== 24471Version: 0.8.39 24472Date: 1998/02/19 18:31:38 24473Title: Moving the executable in utility *siesta scripts 24474Author: Emilio Artacho (emilio.artacho@uam.es) 24475 24476Description: 24477 The utility files for automatized running of siesta (msiesta, rsiesta, 24478 and qsiesta) have been slightly modified: the executable code siesta 24479 is moved to the working directory, so that different systems can run 24480 simultaneously without interfering, as long as the working directories 24481 are different. 24482 Simultaneous compilation is not advised. 24483 24484 qrrsiesta has been added: it does recurrent run-recompile in batch 24485 queues (both this one and qsiesta are prepared for NQS batch system, 24486 available at least for DEC systems) 24487 24488Files: (in Util/) 24489 rsiesta 24490 msiesta 24491 qsiesta 24492 qrrsiesta : (new) equivalent to rrsiesta for NQS batch system 24493======================================================================== 24494Version: 0.8.38 24495Date: 1998/02/19 17:02:22 24496Title: Printing of hostname and date/time transferred to script 24497Author: Jose M. Soler (jose.soler@uam.es), 24498 24499Description: 24500 Date, time and hostname are printed in the output file at the 24501 beginning and the end of a siesta run. The prdate subroutine used 24502 to do it using system calls which demanded large amounts of extra 24503 memory. Now, that function has been transferred to a script (prdate) 24504 which is called by the rsiesta script. The original subroutine has 24505 been kept empty. 24506 24507Files: 24508 prdate (in Util/) (new) 24509 rsiesta (in Util/) 24510 prdate.f : now empty, it does nothing, kept for possible future. 24511======================================================================== 24512Version: 0.8.37 24513Date: 1998/02/19 17:02:22 24514Title: Dipole moment, now also calculated for chains and slabs 24515Author: Jose M. Soler (jose.soler@uam.es) 24516 24517Description: 24518 Related to ExternalElectricField. Possibility of calculating 24519dipole moment for chains and slabs, not only for molecules, as 24520long as it is normal to the direction(s) of repetition. 24521 24522Files: 24523 dhscf.f 24524 dipole.f : (sign of dipole moment corrected) 24525======================================================================== 24526Version: 0.8.36 24527Date: 1998/02/19 17:02:22 24528Title: Implemented constraints for dynamics/relaxations 24529Author: Jose M. Soler (jose.soler@uam.es) 24530 24531Description: 24532 Fixes constraints to the change of atomic coordinates during 24533 geometry relaxation or molecular dynamics, usinf FDF data block 24534 GeometryConstraints. Allowed constraints are: 24535 -cellside: fixes the unit-cell side lengths to 24536 their initial values (not implemented yet). 24537 -cellangle: fixes the unit-cell angles to 24538 their initial values (not implemented yet). 24539 -position: fixes the positions of the specified atoms to 24540 their initial values. 24541 -center: fixes the center (mean position, not center of mass) of a 24542 group of atoms to its initial value (not implemented yet). 24543 -rigid: fixes the relative positions of a group of atoms, without 24544 restricting their displacement or rotation as a rigit unit 24545 (not implemented yet). 24546 -routine: Additionally, the user may write a problem-specific routine 24547 called constr, which inputs the atomic forces and stress 24548 tensor and outputs them orthogonalized to the constraints. 24549 Example: 24550 %block GeometryConstraints 24551 cellside c 24552 cellangle alpha beta gamma 24553 position from -1 to -10 24554 rigid 1 2 24555 center 1 2 0.0 0.0 1.0 24556 routine constr 24557 %endblock GeometryConstraints 24558 24559Files: 24560 constr.f : (new) User-written subroutine for constr-definition 24561 (also in Src/Include/ for hanling like .h files) 24562 fixed.f : (new) Relaxation and dynamics with constrined forces 24563 siesta.f : Calls fixed 24564 Makefile : Added fixed.f and constr.f 24565 siesta.tex : Documented 24566======================================================================== 24567Version: 0.8.35 24568Date: 1998/02/19 17:02:22 24569Title: Implemented ExternalElectricField 24570Author: Jose M. Soler (jose.soler@uam.es) 24571 24572Description: 24573 An external electric field can be applied to molecules, 24574 chains and slabs, using an FDF data block. Example: 24575 %block ExternalElectricField 24576 0.000 0.000 0.100 V/Ang 24577 %endblock ExternalElectricField 24578 The field must be perpendicular to bulk directions 24579 (like those parallel to a slab), or otherwise siesta will 24580 automatically orthogonalize it (and print a warning). 24581 The field is applied using the real space grid of dhscf. 24582 The discontinuity of the potential is automatically 24583 placed in the vacuum region, between repeated 24584 molecules/chains/slabs. 24585 24586Files: 24587 cross.f : (new) Vector poduct (used by efield) 24588 dhscf.f : Calls to efield and shaper 24589 efield.f : (new) External electric field implementation 24590 fdf.f : Added electric field units 24591 Makefile : Added cross.f and efield.f 24592 siesta.f : Call to shaper 24593 shaper.f : New argument to return the bulk directions 24594 siesta.tex : ExternalElectricField documented 24595======================================================================== 24596Version: 0.8.34 24597Date: 1998/02/19 17:02:22 24598Title: Calculate XC potential only where there is density 24599Author: Jose M. Soler (jose.soler@uam.es) 24600 24601Description: 24602 Up to this point the XC potential was calculated for the whole grid. 24603 Now it is calculated only for those points for which there is a finite 24604 electronic density. 24605 24606Files: 24607 xc.f 24608======================================================================== 24609Version: 0.8.33 24610Date: 1998/02/17 16:31:04 24611Title: FIX: divided-by-zero problem in MD T=0. Miscellanea. 24612Author: Pablo Ordejon (ordejon@condmat01.geol.uniovi.es) 24613 24614Description: 24615 Small modifications to correct problems with initial temperature 24616 for MD (when T=0). Additionally: 24617 - Parameter namax added to coceri.f and outcoor.f 24618 - Small modifications of extrapolation procedure between 24619 succesive minimizations in orderN (make linear extrapolation 24620 ONLY when last minimization took less than 50 iterations) 24621 - Redefine parameter restart (from 50 to 300) in cgwf.f 24622 24623Files: 24624 vmb.f : T=0 problem fixed 24625 siesta.f : id. 24626 outcoor.f: parameter namax added 24627 coceri.f : id. 24628 ordern.f : extrapolation 24629 cgwf.f : restart parameter 24630======================================================================== 24631Version: 0.8.32 24632Date: 1998/02/17 16:31:04 24633Title: Velocities in XV for all dynamics options 24634Author: Pablo Ordejon (ordejon@condmat01.geol.uniovi.es) 24635 24636Description: 24637 The velocities are now written in file .XV . Before they were all 24638 zero except for the Verlet option. It allows their use on restart. 24639 24640Files: 24641 dynamics.f 24642======================================================================== 24643Version: 0.8.31 24644Date: 1998/02/11 19:07:00 24645Title: FIX: Non-standard FORTRAN in Emilio's 0.8.37 and 0.8.39 patches 24646Author: Alberto Garcia (wdpgaara@lg.ehu.es) 24647 24648Description: 24649 Data statement out of order in redata.f, initdm.f, and recoor.f 24650 Adjustable array illegal in f77 in outcoor.f and coceri.f 24651 24652Files: 24653 outcoor.f 24654 coceri.f 24655 initdm.f 24656 recoor.f 24657 redata.f 24658======================================================================== 24659Version: 0.8.30 24660Date: 1997/12/31 12:46:41 24661Title: Non conventional order in p and d orbitals (Mulliken) 24662Author: Emilio Artacho (emilio.artacho@uam.es) 24663 24664Description: 24665 Noted that the order how the p and d orbitals are stored, and 24666 appear in places like Mulliken output, is not conventional. It was 24667 no bug, it was supposed to be so, but it was not clear. It has been 24668 made clear now in the manual, in the WriteMullikenPop explanation, 24669 among other instances. The order is: y, z, x for the p's, and 24670 xy, yz, z^2, xz and x^2-y^2, for the d's. 24671 24672Files: 24673 siesta.tex (in Docs/) : documented. 24674======================================================================== 24675Version: 0.8.29 24676Date: 1997/12/27 12:31:09 24677Title: Initial spin-polarization input for spin-polarized calculations 24678Author: Emilio Artacho (emilio.artacho@uam.es) 24679 24680Description: 24681 Modification in DM initialization: 24682 - Now it is done in new separate subroutine initdm.f 24683 - It allows the introduction of initial spin polarizations 24684 atom by atom with new %block DM.InitSpin: there is one line per 24685 atom to be spin-polarized, containing the atom index and the desired 24686 initial spin-polarization. Example: 24687 %block DM.InitSpin 24688 5 -1. 24689 3 + 24690 7 - 24691 + 1 24692 -.5 2 24693 %endblock DM.InitSpin 24694 24695Files: 24696 initdm.f : (new) DM initialization, including spin if required. 24697 siesta.f : calling initdm.f 24698 Makefile : include reference to initdm.f 24699 siesta.tex : documentation on DM.InitSpin block 24700 minvec.f : spelling (no effect of code) 24701 idiag.f : id. 24702======================================================================== 24703Version: 0.8.28 24704Date: 1997/12/23 19:58:24 24705Title: Storage of density matrices for Pulay convergence acceleration 24706Author: Pablo Ordejon (ordejon@condmat01.geol.uniovi.es) 24707 24708Description: 24709 Pulay mixing routines have been modified. 24710 * An option is included to store the intermediate information 24711 in files or in memory. The fdf variable is DM.PulayOnFile. 24712 If true, SIESTA will use files SystemLabel.P1 and SystemLabel.P2 24713 to store the intermediate information. If false, it will 24714 be stored in auxiliary arrays in memory. 24715 * The I/O from disk has been optimized, to decreasse the size 24716 of the Pulay files and also the number of I/O operations 24717 * IMPORTANT: A new parameter has been included in siesta.h !!!! 24718 This is necessary to open space for the Pulay auxiliary 24719 storage arrays. This means that old siesta.h files will NOT 24720 work with the new version, unless the new variable is defined. 24721 24722Files: 24723 pulayx.f 24724 redata.f 24725 siesta.f 24726 siesta.h 24727 siesta.tex 24728======================================================================== 24729Version: 0.8.27 24730Date: 1997/12/23 19:58:24 24731Title: Initial temperature for molecular dynamics 24732Author: Pablo Ordejon (ordejon@condmat01.geol.uniovi.es) 24733 24734Description: 24735 A new MD feature has been implemented: the possibility of 24736 specifying an initial temperature for the MD sumulation. 24737 The fdf variable is MD.InitialTemperature. 24738 The atomic velocities are randomly assigned according to the 24739 Maxwell-Boltzmann distribution (imposing the constraint of 24740 zero center of mass velocity). 24741 24742Files: 24743 vmb.f : (new) 24744 redata.f 24745 siesta.f 24746 Makefile : include vmb.f 24747 siesta.tex 24748======================================================================== 24749Version: 0.8.26 24750Date: 1997/12/23 19:58:24 24751Title: Renormalize the charge for ordern 24752Author: Pablo Ordejon (ordejon@condmat01.geol.uniovi.es) 24753 24754Description: 24755 The density matrix routine for O(N) has been slightly modified, 24756 to renormalize the DM so that the total charge is the correct 24757 one. This is quite necessary to achieve selfconsistency with 24758 the O(N) functional, although is not well justified (in principle 24759 is not variational!!). 24760 24761Files: 24762 egandd.f: Small modifications to renormalize the charge 24763 denmat.f: Modified to renormalize the density matrix 24764======================================================================== 24765Version: 0.8.25 24766Date: 1997/12/23 19:58:24 24767Title: FIX: Corrected scale of the time step 24768Author: Pablo Ordejon (ordejon@condmat01.geol.uniovi.es) 24769 24770Description: 24771 An IMPORTANT error in the dynamics routines has been corrected. 24772 The routines had a unit conversion error that affected the 24773 scale of the time step (the dynamics were correct, 24774 but the time units were scaled). 24775 24776Files: 24777 dynamics.f: Corrects serious error of units in foverm variable 24778======================================================================== 24779Version: 0.8.24 24780Date: 1997/12/22 20:49:04 24781Title: Input/Output: Coordinates, Lattice Parameters, Pseudopotentials, 24782 Maximum and Mean Forces, Splitgauss 24783Author: Emilio Artacho (emilio.artacho@uam.es) 24784 24785Description: 24786 * Coordinates input has been separated to new subroutine (recoor) 24787 that hangs from redata. 24788 * Output of cell vectors and parameters separated into new routine 24789 (outcell) (only for intermediate and final writing in case of 24790 lattice relaxation or MD Parrinello-Rahman) 24791 * More flexible output of coordinates (both intermediate and final): 24792 - It can write in any of the formats that can be used for input 24793 (except ScaledCartesian if there was no lattice parameter in input) 24794 - Output format specified in new fdf: AtomCoorFormatOut. 24795 Default (if not given): uses same as for input 24796 (AtomicCoordinatesFormat) 24797 For both fdf's the value 'Fractional' can be used instead of 24798 'ScaledByLatticeVectors' 24799 New subroutine (outcoor) 24800 * Optional writing of atomic coordinates in separate files with 24801 adequate formats for being read by: 24802 - XMOL (symbol and x y z in Ang) WriteCoorXmol true 24803 - CERIUS (cell pars, sym, x y z in fractional) WriteCoorCerius true 24804 New subroutines (coxmol, coceri) 24805 * Writes maximum force and residual mean square force 24806 after total force 24807 * Writes atomic coordinates as x, y, z, is, Symbol, number. It can 24808 be taken to the fdf input file as is. 24809 * New possibility of introducing lattice vectors: 24810 %block LatticeParameters 24811 a b c alpha beta gamma 24812 %endblock LatticeParameters 24813 It checks whether both blocks (LatticeParameters and LatticeVectors) 24814 are present, and stops with ERROR if it is the case. Otherwise 24815 it generates the vectors according to whatever is present or 24816 automatically if none. 24817 * redata now writes the vectors in rows (instead of columns as before) 24818 and without the 'redata: ' so that they can be incorporated 24819 as written to the input. 24820 * Pseudopotentials will be read from 'syslabel'.vps instead of .psatom.data. 24821 For backwards compatibility, if .vps is not found, then .psatom.data 24822 is looked for. In this case a warning is given. 24823 * Making Siesta write a message saying when it reads XV 24824 * Scale factor for splitgauss is now a scale factor and not the alpha 24825 in exp(-alpha*r**2). Scale factor is 1/sqrt(alpha) 24826 * Parrinello-Rahman MD (with or w/o quench) now writes stress tensor and 24827 lattice parameters for every time step 24828 * Mulliken: formatted output (pure cosmetics) 24829 24830Files: 24831 recoor.f : (new) reads coordinates 24832 outcell.f: (new) writes cell vectors 24833 outcoor.f: (new) writes coordinates 24834 coxmol.f : (new) writes coordinates in XMol format in a separate file 24835 coceri.f : (new) writes coordinates in CERIUS format in a separate file 24836 ioxv.f : writes message 24837 mulliken.f : Cosmetics 24838 redata.f : calling 24839 siesta.f : calling 24840 atom.f : reading .vps + scale factor for splitgauss. 24841 Makefile 24842 siesta.tex 24843======================================================================== 24844Version: 0.8.23 24845Date: 1997/12/11 17:42:24 24846Title: Added check for excesive proximity between atoms 24847Author: Jose M. Soler (jose.soler@uam.es) 24848 24849Description: 24850 The program warns about atoms being closer than a specific distance: 24851 one Bohr by default, which can be modified by 24852 WarningMinimumAtomicDistance 24853 Helpful to avoid the frequent errors in coordinate input, which, 24854 when atoms are extremely close originates an overlap matrix error. 24855 24856Files: 24857 siesta.f 24858 siesta.tex 24859======================================================================== 24860Version: 0.8.22 24861Date: 1997/12/11 17:42:24 24862Title: Plotting charge density, LDOS(x,y,z), Potentials 24863Author: Jose M. Soler (jose.soler@uam.es) 24864 24865Description: 24866 Plotting SIESTA's outputs in real space. All plots are done in 24867 two steps: 24868 * Running SIESTA with an option for it to write a file with the 24869 information to be plotted: 24870 - SaveRho : logical: valence charge density 24871 (pseudocore) 24872 - SaveElectrostaticPotential : logical: Pseudopots + Hartree 24873 - SaveTotalPotential : logical: id + XC 24874 - LocalDensityOfStates : data block: charge density 24875 associated to an energy range 24876 specified in the block: 24877 %block LocalDensityOfStates 24878 -3.50 0.00 eV 24879 %endblock LocalDensityOfStates 24880 These informations are stored in corresponding files (.RHO, .VH, 24881 .VT, .LDOS, respectively). It is stored: information about the 24882 real-space grid (defined by the cutoff => fineness of plot depends 24883 on cutoff!!) and values of the specific funtion at the grid points. 24884 * Generating a plot for X11 and/or Postscript, etc. 24885 This is done with the utility plrho program now at Util/Plrho. 24886 It requires the presence in the computer of the graphic library 24887 PGPLOT, set of FORTRAN subroutines to plot on different devices. 24888 It is public domain and not difficult to install. 24889 Plrho plots isosurfaces (surfaces of constant value of the 24890 particular function, like traditional plots of orbitals) in 3D 24891 using perspective and shading. It allows plotting two functions 24892 at the same time: First function (say Rho) as isosurface, and 24893 the value of the second function (say electrostatic potential) 24894 is plotted on the Rho isosurface with a color coding (similar 24895 to GRASP for biopolymers). 24896 24897Files: 24898 iorho.f 24899 siesta.f 24900 dhscf.f 24901 siesta.tex 24902 Util/README 24903 Util/Plrho/ new directory wi th new files: 24904 plrho.f, plrho.h, paste.f, plsurf.f, rotate.f, icolor.f, pltr3d.f, 24905 plrho_guide.txt, plrho.dat, and README 24906======================================================================== 24907Version: 0.8.21 24908Date: 1997/11/5 10:59:49 24909Title: FIX: Correcting input/output for coordinates and velocities .XV 24910Author: Jose M. Soler (jose.soler@uam.es) 24911 24912Description: 24913 (1) Corrected output unit for writing coordinates and velocities 24914 Fri Oct 24 18:16:00 1997 24915 (2) An incorrect 'write(iu,*) na' changed to read 24916 Wed Nov 5 10:59:49 1997 24917 24918Files: 24919 ioxv.f 24920======================================================================== 24921Version: 0.8.20 24922Date: 1997/10/24 18:16:00 24923Title: Shift all atomic coordinates by shifting the origins 24924Author: Jose M. Soler (jose.soler@uam.es) 24925 24926Description: 24927 Vector specifying a rigid shift to apply to the atomic coordinates, 24928 given in the same format and units as these. Notice that the atomic 24929 positions (shifted or not) need not be within the cell formed by 24930 LatticeVectors, since periodic boundary conditions are always 24931 assumed. 24932 %block AtomicCoordinatesFormat 24933 1.000 3.000 2.000 24934 %endblock AtomicCoordinatesFormat 24935 24936Files: 24937 redata.f 24938 siesta.tex 24939======================================================================== 24940Version: 0.8.19 24941Date: 1997/10/22 10:12:06 24942Title: FIX: Added a tolerance in vector-length comparisons in minvec.f 24943Author: Jose M. Soler (jose.soler@uam.es) 24944 24945Description: 24946 Some systems entered an infinite loop in the first call to DHSCF 24947 (building grid etc) due to a strict comparison of two vectors in 24948 minvec.f. Added a tolerance, problem solved. (It used to happen 24949 in a Linux system at least). 24950 24951Files: 24952 minvec.f 24953======================================================================== 24954Version: 0.8.18 24955Date: 1997/10/16 18:14:16 24956Title: Off-site orbitals: fixes and changes for new basis handling 24957Author: Daniel Sanchez-Portal (daniel@polar.fmc.uam.es) 24958 24959Description: 24960 Off-site orbitals: to use them new species has to be defined, and 24961 each orbital center has to be regarded as an 'atom' of that 'species' 24962 and coordinates have to be assigned to it. Two kinds 24963 * Orbitals that would correspond to some atom, but the atom is not 24964 there. The species is to be given the corresponding atomic number 24965 with negative sign. Siesta will put the orbitals of that atom 24966 in the given ccordinates but without pseudopotentail and without 24967 its electrons. Useful for calculating the basis-set superposition 24968 error (BSSE). 24969 * Bessel functions. Corresponding node at r_c. EnergyShift has no 24970 meaning here. The r_c has to be gicen in the PAO_basis_and_PS_lmax 24971 block. 24972 24973Files: 24974 redata.f 24975 atom_subs.f 24976 atom.f 24977======================================================================== 24978Version: 0.8.17 24979Date: 1997/10/15 18:08:52 24980Title: New makefile options for IBMs and DECs without libraries + RANLIB 24981Author: Alberto Garcia (wdpgaara@lg.ehu.es) and Emilio Artacho 24982 24983Description: 24984 - unknown.make: Added dummy RANLIB command to warn the user. 24985 - New makefile ARCH options for IBMs and DECs without libraries: 24986 osf and ibm 24987 24988Files: 24989 unknown.make 24990 ibm.f 24991 ibm.make 24992 osf.f 24993 osf.make 24994 siesta.tex 24995======================================================================== 24996Version: 0.8.16 24997Date: 1997/9/26 17:30:03 24998Title: Supercell: fixes and improvements 24999Author: Jose M. Soler (jose.soler@uam.es) 25000 25001Description: 25002 - Imposed the translational supercell symmetry on forces. 25003 - Changed the call to hsparse and xijorb to improve the performance of 25004 diagon when there is a supercell. 25005 - Changed the k-grid default to gamma of the SUPER cell. 25006 - Improved performance of diagon for a supercell. 25007 25008Files: 25009 siesta.f 25010 kgrid.f 25011 xijorb.f 25012 diagon.f 25013 hsparse.f 25014 iorder.f 25015 ordvec.f 25016 Makefile 25017 siesta.tex 25018======================================================================== 25019Version: 0.8.15 25020Date: 1997/9/26 17:30:03 25021Title: FIX: Stress & forces with part core + automatic cell generation 25022Author: Jose M. Soler (jose.soler@uam.es) 25023 25024Description: 25025 - Corrected force and stress with partial core correction. 25026 - Added printout of the number of mesh points. 25027 - Corrected error in automatic cell generation. 25028 25029Files: 25030 dhscf.f 25031 diagon.f 25032 siesta.f 25033 redata.f 25034 siesta.tex 25035======================================================================== 25036Version: 0.8.14 25037Date: 1997/8/28 15:25:16 25038Title: siesta.PAO.BasisType --> PAO.BasisType 25039Author: Daniel Sanchez-Portal (daniel@polar.fmc.uam.es) 25040 25041Description: 25042 Old FDF label siesta.PAO.BasisType is now PAO.BasisType. 25043 Its possible values: split, nodes, nonodes, user, and splitgauss. 25044 25045Files: 25046 atom.f 25047 Examples/h2o.fdf 25048 Examples/h2o.gga.fdf 25049======================================================================== 25050Version: 0.8.13 25051Date: 1997/8/25 18:42:20 25052Title: Manual (quick start, introduction) + Utilities (new rrsiesta) 25053Author: Jose M. Soler (jose.soler@uam.es) 25054 25055Description: 25056 * Manual siesta.tex: 25057 - Largely expanded INTRODUCTION section. 25058 - New QUICK START section. 25059 - New k-sampling options documented. 25060 - New error&warning messages and two known problems documented. 25061 * Script utilities: 25062 - New rrsiesta: Really-run-siesta. Keeps recompiling until siesta 25063 really runs. 25064 - rsiesta: Extracts from output all errors and warnings and prints 25065 them at the end. 25066 25067Files: 25068 Util/rrsiesta (new) 25069 Util/rsiesta 25070 siesta.tex 25071======================================================================== 25072Version: 0.8.12 25073Date: 1997/8/25 18:42:20 25074Title: k-sampling, supercells, and bands 25075Author: Jose M. Soler (jose.soler@uam.es) 25076 25077Description: 25078 * Supercell: New fdf block that allows automatic generation of a 25079 supercell out of the repetition of the unit cell. Coordinates 25080 have to be given only for atoms in the unit cell. 25081 %block SuperCell 25082 M(1,1) M(2,1) M(3,1) 25083 M(1,2) M(2,2) M(3,2) 25084 M(1,3) M(2,3) M(3,3) 25085 %endblock SuperCell 25086 and the supercell is defined as 25087 SuperCell(ix,i) = \sum_j CELL(ix,j)*M(j,i). 25088 Diagonalization is done for the unit cell. 25089 DHSCF works with the supercell. 25090 * k-sampling: Improved. But it can only be done if a supercell is 25091 defined such that any atom only sees one image of any other. 25092 * Bands: k-lines are introduced to obtain eigenvalues along them 25093 for conventional band (spaghetti) plots. 25094 25095Files: 25096 idiag.f (new) 25097 bands.f (new) 25098 diagon.f 25099 kgrid.f 25100 redata.f 25101 siesta.f 25102 siesta.h 25103 Src/Include/siesta.h 25104 Makefile 25105 siesta.tex 25106======================================================================== 25107Version: 0.8.11 25108Date: 1997/8/8 18:53:19 25109Title: FIX: Found the bug in stress calculation 25110Author: Jose M. Soler (jose.soler@uam.es) 25111 25112Description: 25113 There was a term missing in the stress calculation associated to the 25114 derivative of 1/r in the electrostatic energy (at last it was not 25115 related with the orbitals' scale factors as speculated before). 25116 There was an additional term missing for GGA. The whole has been 25117 restructured. The new contribution is calculated in poison 25118 25119Files: 25120 Sys/osfdxml.f : Added stress to argument list of poison. 25121 Sys/bsd.f : id. 25122 Sys/general.f : id. 25123 Sys/ibmessl.f : id. 25124 xc.f 25125 dhscf.f 25126 Makefile 25127======================================================================== 25128Version: 0.8.10 25129Date: 1997/8/8 18:09:25 25130Title: Input for controlling Pulay mixing 25131Author: Emilio Artacho (emilio.artacho@uam.es) 25132 25133Description: 25134 The fdf variable DM.NumberPulay is introduced. It controls Pulay 25135 mixing by stating that Pulay is to be performed every n iterations 25136 (the others being linear mixing) n being the value given in 25137 DM.NumberPulay. If less than 2 it performs no Pulay mixing. 25138 The mixing itself was introduced before by Pablo but another 25139 input was used. 25140 25141Files: 25142 pulayx.f 25143 redata.f 25144 siesta.f 25145 siesta.tex 25146======================================================================== 25147Version: 0.8.9 25148Date: 1997/8/8 18:09:25 25149Title: Input for controlling initial spin density: Ferro or Antiferro 25150Author: Emilio Artacho (emilio.artacho@uam.es) 25151 25152Description: 25153 The new FDF logical variable DM.InitSpinAF is introduced. 25154 It defines the initial spin density for a spin polarized calculation. 25155 The spin density is initially constructed with the maximum possible 25156 spin polarization for each atom in its atomic configuration. 25157 This variable defines the relative orientation of the atomic 25158 spins: 25159 false: gives ferromagnetic order (all spins up). 25160 true: gives antiferromagnetic order. Up and down are assigned 25161 according to order in the block 25162 AtomicCoordinatesAndAtomicSpecies: up for the odd atoms, 25163 down for even. 25164Files: 25165 redata.f 25166 siesta.f 25167 siesta.tex 25168======================================================================== 25169Version: 0.8.8 25170Date: 1997/8/7 12:05:06 25171Title: Utility scripts rsiesta, msiesta, and qsiesta 25172Author: Jose M. Soler (jose.soler@uam.es) 25173 25174Description: 25175 Shell scripts introduced to run siesta from an arbitrary directory. 25176 All three use the environment variable SIESTA_DIR (../Src by default) 25177 25178Files: 25179 Util/msiesta makes (compiles) siesta 25180 Util/rsiesta runs siesta directly 25181 Util/qsiesta submits a siesta batch job, using NQS batch system 25182======================================================================== 25183Version: 0.8.7 25184Date: 1997/8/7 12:05:06 25185Title: Directory Include/ and ranger.f and ranger.h 25186Author: Jose M. Soler (jose.soler@uam.es) 25187 25188Description: 25189 * New directory Src/Include where all the recommended initial *.h 25190 (atom, dhscf, siesta, diagon, ordern) are stored, instead the 25191 Src/*.h0 25192 * Subroutine ranger.f separated from neighb.f, and new ranger.h 25193 25194Files: 25195 Src/Include/atom.h, dhscf.h, diagon.h, ordern.h, siesta.h and ranger.h 25196 ranger.f (new) 25197 neighb.f 25198 Makefile 25199======================================================================== 25200Version: 0.8.6 25201Date: 1997/8/5 19:36:47 25202Title: Automatic basis implementation 25203Author: Daniel Sanchez-Portal (daniel@polar.fmc.uam.es) 25204 25205Description: 25206 Implemented into SIESTA the possibility of automatic generation of 25207 the basis orbitals requiring minimal (or even none) information 25208 at the input fdf file. General basis information for automatic basis 25209 generation: 25210 * PAO.EnergyShift: It defines the different (first-z) orbitals' r_c's 25211 by their excitation energy. Giving this number the basis generated 25212 is automatically a compensated basis (default 20 mRy). 25213 * PAO.SplitNorm: A standard to define default sensible radii for the 25214 split-valence type of basis. It gives the amount of norm that 25215 the second-zeta split-off piece has to carry. The split radius 25216 is defined accordingly. If multiple-zeta is used, the corresponding 25217 radii are obtained by imposing smaller fractions of the SplitNorm 25218 (1/2, 1/4 ...) value as norm carried by the higher zetas. (def 0.15) 25219 * PAO.BasisSize: Defines basis sizes: SZ or MINIMAL for single-z; 25220 DZ for double-z; and DZP or STANDARD for DZ plus polarization. 25221 (def DZP). 25222 * PAO.PolarizationOrbitals: true: adds polarization orbitals of 25223 perturbative kind. 25224 * PAO.SplitPolarizationOrbitals: true means to split the polarization 25225 orbitals of perturbative kind. 25226 These new inputs plus the old 25227 * siesta.PAO.BasisType (now split, splitgauss, nodes, nonodes, user), 25228 permit the definition of the basis with no need of the old 25229 block PAO_basis_and_PS_lmax. If this block is not present, then the 25230 new block Chemical_species_label is needed, which inputs the different 25231 species for the different atoms: 25232 %block ChemicalSpeciesLabel 25233 1 6 C 25234 %endblock ChemicalSpeciesLabel 25235 Note that just writing this block and nothing else for the basis, siesta 25236 generates a quite sensible basis for the atoms involved (in this case 25237 just carbon): DZP, cutting with an energy shift of 20 mRy (approx 25238 4.2 Bohr for carbon), splitting with 0.15 of the norm, etc. If the 25239 PAO_basis_and_PS_lmax is there, then only those data which are specified 25240 with a zero will be generated automatically. Nonzero specifications in 25241 this block have priority. 25242 A file is written for each atom called 'label'.PAO.basis with the 25243 numerical basis used. Same format as read by PAO.BasisType = user. 25244 25245Files: 25246 parse.f : (new) routine which parses an input line into names 25247 and numbers 25248 atom.f : Basis changes heavily here. 25249 initatom.f: changed interface and added calls to chkdim 25250 redata.f : PAO_basis_and_PS_lmax is now optional. 25251 Added Chemical_species_label block. 25252 Added argument atm_label. 25253 siesta.f : changed interfaces to redata and initatom 25254 Makefile : added parse.f 25255======================================================================== 25256Version: 0.8.5 25257Date: 1997/8/4 18:12:39 25258Title: FIX: Corrected a SEVERE bug for spin polarization 25259Author: Jose M. Soler (jose.soler@uam.es) 25260 25261Description: 25262 Corrected a SEVERE bug for spin polarization. Correct ispin 25263 index in eigenvalue printout. 25264 25265Files: 25266 siesta.f 25267======================================================================== 25268Version: 0.8.4 25269Date: 1997/7/24 15:46:34 25270Title: Pulay mixing 25271Author: Pablo Ordejon (ordejon@condmat01.geol.uniovi.es) 25272 25273Description: 25274 Introduced new routine to perform Pulay mixing: 25275 Modified and partly re-written by P. Ordejon, July'97, on a routine 25276 original of In-Ho Lee, Beckman Inst., Univ. of Illinois, Mar. 25 '97. 25277 It represents an SCF convergence accelerator nased on storing the 25278 history of convergence for a few cycles and guessing the next based 25279 on that story. 25280 25281Files: 25282 pulayx.f 25283 siesta.f 25284 Makefile 25285======================================================================== 25286Version: 0.8.3 25287Date: 1997/7/21 14:45:48 25288Title: Alaternative local pseudopotential for shallow cores 25289Author: Daniel Sanchez-Portal (daniel@polar.fmc.uam.es) 25290 25291Description: 25292 The local pseudopot is usially the one generated by a positive charge 25293 equal to the net of the core, but spread in a Gaussian of the width 25294 of the core. The core radius is taken as the radius outside which 25295 the pseudopotentials all (s,p,d..) go like Z/r within a tolerance. 25296 This cutoff is also defining the range of the KB projectors 25297 However, atoms with shallow cores (Ga, Ge, ...) demand a very 25298 long core radius, not necessarily because the different pseudopots 25299 remain different for long radii, but because the charge of the core 25300 spreads and the Z/r behavior comes too slowly. 25301 For these cases (controlled by an if, if the value of that core 25302 radius is too long) an alternative local pseudopotential is defined: 25303 A smooth curve ( Vloc(r)=v3exp(v1*r^2+v2*r^3) ) for r < Rc(KB) 25304 is matched to the pseudopot coming from r > Rc(KB). Rc(KB) is the 25305 new core radius (for the KB) very close to the one used in the 25306 atomic program, and the one for which diff pseudopots converge to one. 25307 There is also the possibility of using 25308 Vloc(r)=v4exp(v1*r^2+v2*r^3+v3*r^4) for matching not only value and 25309 first derivative, but also second derivative. 25310 The program does everything. ATOM informs in output. 25311 25312Files: 25313 atom.f 25314 atom_subs.f 25315======================================================================== 25316Version: 0.8.2 25317Date: 1997/7/16 15:00:22 25318Title: Makefile: a unique file for different architectures 25319Author: Alberto Garcia (wdpgaara@lg.ehu.es) 25320 25321Description: 25322 Compilation procedure for SIESTA using one only Makefile file. The 25323 user has to define the system variable ARCH taking one of the 25324 prepared possibilities in Src/Sys (like export ARCH=linux). 25325 The new directoy Src/Sys has the .make files for the different 25326 architectures (compiler names, flags and other pecularities) and 25327 the fortran subroutines that depend on the machine: cputim.f 25328 and others like poison.f that may call propriety libraries. 25329 general.f is all purpose, all architecture, and selfcontained 25330 for the use on any platform. 25331 This way, the old architecture adapted files in Src (poison, 25332 cputim, for different systems) disappear. 25333 25334Files: 25335 Makefile 25336 Sys/osfdxml.f 25337 Sys/bsd.f 25338 Sys/general.f 25339 Sys/ibmessl.f 25340 Sys/ibmessl.make 25341 Sys/linux.make 25342 Sys/osfdxml.make 25343 Sys/freebsd.make 25344 Sys/hp.make 25345 makefile, Makefile.DEC, Makefile.IBM, Makefile.linux, 25346 poison.general.f, cputim.general.f, poison.DEC.f, poison.IBM.f, 25347 poison.f, cputim.DEC.f, cputim.IBM.f, and cputim.f all disappear. 25348======================================================================== 25349Version: 0.8.1 25350Date: 1997/7/15 21:39:57 25351Title: k-sampling 25352Author: Jose M. Soler (jose.soler@uam.es) 25353 25354Description: 25355 k-sampling implementation. It is only partial since dhscf.f and all 25356 dealings in the grid are left untouched (and real). It is therefore 25357 only possible to do k-samplings on cells such that any atom sees only 25358 one image of any other atom. K-sampling in this case is then just 25359 mutiplying by phases in the right places. 25360 25361Files: 25362 atom.f 25363 cdiag.f 25364 dhscf.f 25365 diagon.f 25366 fermid.f 25367 kgrid.f (new) 25368 rdiag.f 25369 rdiagon.f (supressed) 25370 siesta.f 25371 siesta.h 25372 xijorb.f (new) Vectors among atom centers 25373 Makefile 25374 siesta.tex 25375======================================================================== 25376Version: SIESTA 0.8 25377Date: 1997/7/15 21:39:57 25378Title: Several: Output files + shaper + dipole + prdate + automatic cell 25379Author: Jose M. Soler (jose.soler@uam.es) 25380 25381Description: 25382 * Several routines saving information to files: 25383 - iodm.f : the 'save' file is SystemLabel.DM 25384 - iolwf.f : the 'save' file is SystemLabel.LWF 25385 - iohs.f : writes/reads H y S 25386 - iorho.f : writes/reads rho in the mesh 25387 - ioxv.f : writes/reads positions and velocities 25388 * Dipole moment is calculated from grid integration 25389 * shaper.f obtains the shape of a system: molecule, chain, slab, solid 25390 * prdate: prints time, date and computer name at the beginning and 25391 the end of the calculation in the output file. 25392 * Automatic cell: if there is no lattice parameter nor lattice vectors 25393 specified in input, they are all generated such that there is no 25394 overlap between cells (plus a 10% extra) (shape: molecule) 25395 If the lattice parameter is given but not the lattice vectors a 25396 cubic cell is assumed. 25397 25398Files: 25399 dipole.f 25400 dhscf.f 25401 iodm.f 25402 iolwf.f 25403 iohs.f 25404 iorho.f 25405 ioxv.f 25406 redata.f 25407 shaper.f 25408 prdate.f 25409 siesta.f 25410 Makefile 25411 siesta.tex 25412======================================================================== 25413 25414 PRIOR TO SIESTA 0.8: Some important changes 25415 (see Log.Messages for details) 25416 25417======================================================================== 25418Date: 1997/6/23 16:28:07 25419Title: SIESTA optimization, including adaptation to dxml of DEC 25420Author: Jose M. Soler (jose.soler@uam.es) 25421======================================================================== 25422Date: 1997/6/6 17:33:15 25423Title: OrderN options (Kim, Ordejon-Mauri, file) 25424 siesta.h generation 25425Author: Pablo Ordejon (ordejon@condmat01.geol.uniovi.es) 25426======================================================================== 25427Date: 1997/5/6 16:54:33 25428Title: Mulliken populations in output 25429Author: Pablo Ordejon (ordejon@condmat01.geol.uniovi.es) 25430======================================================================== 25431Date: 1997/4/16 20:20:15 25432Title: Smooth core charge for local pseudopot: core overlap handling 25433Author: Daniel Sanchez-Portal (daniel@polar.fmc.uam.es) 25434======================================================================== 25435Date: Once upon a time 25436Title: Atomic program package for pseudopotential generation: 25437 Berkeley's code, maintained by Alberto Garcia, is incorporated 25438 into directory Pseudo 25439Author: Alberto Garcia (wdpgaara@lg.ehu.es) 25440======================================================================== 25441 25442 25443