1Siesta Version : v4.1-b4-351 2Architecture : x86_64-linux-n-62-26-19 3Compiler version: GNU Fortran (GCC) 9.3.0 4Compiler flags : mpifort -m64 -fPIC -O3 -march=native -ftree-vectorize -fexpensive-optimizatioons -funroll-loops -fprefetch-loop-arrays -fno-second-underscore -flto 5PP flags : -I/dtu/sw/dcc/SL73/2020-aug/generic/build-tools/1.0/include -I/dtu/sw/dcc/SL773/2020-aug/generic/gcc/9.3.0/include -I/dtu/sw/dcc/SL73/2020-aug/generic/gcc/9.3.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/zlib/1.2.11/include -I/dtu/sw/dcc/SL73/2020-aug/generic/numactl/2.0.12/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/libxml2/2.9.10/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/hwloc/2.2.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/knem/1.1.4/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/ucx/1.8.1/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/openmpi/4.0.4/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/szip/2.1.1/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/hdf5/1.12.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/pnetcdf/1.12.1/include -I/dtu/sw/dcc/SL73/2020-aug/generic/gen-zlib/1.2.11/include -I/dtu/sw/dcc/SL73/2020-aug/generic/openssl/1.1.1/include -I/dtu/sw/dcc/SL73/2020-aug/generic/libssh2/1.8.2/include -I/dtu/sw/dcc/SL73/2020-aug/generic/curl/7.65.1/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/netcdf/4.7.4/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/flook/0.8.1/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/fftw/3.3.8/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/parmetis/4.0.3/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/scalapack/2.1.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/lapack/3.9.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/blis/0.7.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/scotch/6.0.9/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/mumps/5.3.3/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/elpa/2020.05.001/include -DSIESTA__ELPA -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DCDF -DCDF4 -DSIESTA__FLOOK -DNCDF -DNCDF_4 -DNCDF_PARALLEL -DTS_NOCHECKS -DSIESTA__METIS -DSIESTA__MUMPS -DSIESTA__MRRR -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/elpa/2020.05.001/include/elpa 6Libraries : libncdf.a libfdict.a -lnetcdff -lnetcdf -lpnetcdf -lhdf5_hl -lhdf5 -lz -lzmuumps -lmumps_common -lesmumps -lscotch -lscotcherr -lpord -lparmetis -lmetis -lelpa -lscalapack -llapack -lblis -L/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/flook/0.8.1/lib -Wl,-rpath=/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/flook/0.8.1/lib -lflookall -ldl -flto -fuse-linker-plugin -lmetis 7PARALLEL version 8NetCDF support 9NetCDF-4 support 10NetCDF-4 MPI-IO support 11METIS ordering support 12Lua support 13 14* Running on 8 nodes in parallel 15>> Start of run: 22-JAN-2021 23:12:41 16 17 *********************** 18 * WELCOME TO SIESTA * 19 *********************** 20 21reinit: Reading from standard input 22reinit: Dumped input in INPUT_TMP.93070 23************************** Dump of input data file **************************** 24SystemName Water molecule -- md verlet 25SystemLabel h2o 26NumberOfAtoms 3 27NumberOfSpecies 2 28MeshCutoff 100 Ry 29%block ChemicalSpeciesLabel 30 1 8 O # Species index, atomic number, species label 31 2 1 H 32%endblock ChemicalSpeciesLabel 33LatticeConstant 8.0 Ang 34%block LatticeVectors 351.0 0.0 0.0 360.0 1.0 0.0 370.0 0.0 0.8 38%endblock LatticeVectors 39AtomicCoordinatesFormat Ang 40%block AtomicCoordinatesAndAtomicSpecies 41 0.000 0.000 0.000 1 42 0.757 0.586 0.000 2 43-0.757 0.586 0.000 2 44%endblock AtomicCoordinatesAndAtomicSpecies 45Solution.Method diagon 46MeshCutoff 100 Ry 47WriteCoorStep .true. 48WriteForces .true. 49WriteMDHistory .true. 50MD.UseSaveXV T 51MD.TypeOfRun Verlet 52MD.InitialTemperature 600 K 53MD.Initial.Time.Step 1 54MD.Final.Time.Step 20 55MD.Length.Time.Step 0.2 fs 56************************** End of input data file ***************************** 57 58reinit: ----------------------------------------------------------------------- 59reinit: System Name: Water molecule -- md verlet 60reinit: ----------------------------------------------------------------------- 61reinit: System Label: h2o 62reinit: ----------------------------------------------------------------------- 63 64initatom: Reading input for the pseudopotentials and atomic orbitals ---------- 65Species number: 1 Atomic number: 8 Label: O 66Species number: 2 Atomic number: 1 Label: H 67 68Ground state valence configuration: 2s02 2p04 69Reading pseudopotential information in formatted form from O.psf 70 71Valence configuration for pseudopotential generation: 722s( 2.00) rc: 1.14 732p( 4.00) rc: 1.14 743d( 0.00) rc: 1.14 754f( 0.00) rc: 1.14 76Ground state valence configuration: 1s01 77Reading pseudopotential information in formatted form from H.psf 78 79Valence configuration for pseudopotential generation: 801s( 1.00) rc: 1.25 812p( 0.00) rc: 1.25 823d( 0.00) rc: 1.25 834f( 0.00) rc: 1.25 84For O, standard SIESTA heuristics set lmxkb to 3 85 (one more than the basis l, including polarization orbitals). 86Use PS.lmax or PS.KBprojectors blocks to override. 87For H, standard SIESTA heuristics set lmxkb to 2 88 (one more than the basis l, including polarization orbitals). 89Use PS.lmax or PS.KBprojectors blocks to override. 90 91<basis_specs> 92=============================================================================== 93O Z= 8 Mass= 16.000 Charge= 0.17977+309 94Lmxo=1 Lmxkb= 3 BasisType=split Semic=F 95L=0 Nsemic=0 Cnfigmx=2 96 i=1 nzeta=2 polorb=0 (2s) 97 splnorm: 0.15000 98 vcte: 0.0000 99 rinn: 0.0000 100 qcoe: 0.0000 101 qyuk: 0.0000 102 qwid: 0.10000E-01 103 rcs: 0.0000 0.0000 104 lambdas: 1.0000 1.0000 105L=1 Nsemic=0 Cnfigmx=2 106 i=1 nzeta=2 polorb=1 (2p) 107 splnorm: 0.15000 108 vcte: 0.0000 109 rinn: 0.0000 110 qcoe: 0.0000 111 qyuk: 0.0000 112 qwid: 0.10000E-01 113 rcs: 0.0000 0.0000 114 lambdas: 1.0000 1.0000 115------------------------------------------------------------------------------- 116L=0 Nkbl=1 erefs: 0.17977+309 117L=1 Nkbl=1 erefs: 0.17977+309 118L=2 Nkbl=1 erefs: 0.17977+309 119L=3 Nkbl=1 erefs: 0.17977+309 120=============================================================================== 121</basis_specs> 122 123atom: Called for O (Z = 8) 124 125read_vps: Pseudopotential generation method: 126read_vps: ATM3 Troullier-Martins 127Valence charge for ps generation: 6.00000 128 129xc_check: Exchange-correlation functional: 130xc_check: Ceperley-Alder 131V l=0 = -2*Zval/r beyond r= 1.1278 132V l=1 = -2*Zval/r beyond r= 1.1278 133V l=2 = -2*Zval/r beyond r= 1.1278 134V l=3 = -2*Zval/r beyond r= 1.1138 135All V_l potentials equal beyond r= 1.1278 136This should be close to max(r_c) in ps generation 137All pots = -2*Zval/r beyond r= 1.1278 138 139VLOCAL1: 99.0% of the norm of Vloc inside 34.126 Ry 140VLOCAL1: 99.9% of the norm of Vloc inside 77.774 Ry 141atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.37759 142atom: Maximum radius for r*vlocal+2*Zval: 1.18566 143GHOST: No ghost state for L = 0 144GHOST: No ghost state for L = 1 145GHOST: No ghost state for L = 2 146GHOST: No ghost state for L = 3 147 148KBgen: Kleinman-Bylander projectors: 149 l= 0 rc= 1.294105 el= -1.742414 Ekb= 9.135903 kbcos= 0.326910 150 l= 1 rc= 1.294105 el= -0.676589 Ekb= -8.124878 kbcos= -0.395047 151 l= 2 rc= 1.448233 el= 0.002386 Ekb= -2.039267 kbcos= -0.003484 152 l= 3 rc= 1.561052 el= 0.003508 Ekb= -0.799141 kbcos= -0.000344 153 154KBgen: Total number of Kleinman-Bylander projectors: 16 155atom: ------------------------------------------------------------------------- 156 157atom: SANKEY-TYPE ORBITALS: 158atom: Selected multiple-zeta basis: split 159 160SPLIT: Orbitals with angular momentum L= 0 161 162SPLIT: Basis orbitals for state 2s 163 164SPLIT: PAO cut-off radius determined from an 165SPLIT: energy shift= 0.020000 Ry 166 167 izeta = 1 168 lambda = 1.000000 169 rc = 3.305093 170 energy = -1.723766 171 kinetic = 1.614911 172 potential(screened) = -3.338677 173 potential(ionic) = -11.304675 174 175 izeta = 2 176 rmatch = 2.510382 177 splitnorm = 0.150000 178 energy = -1.471299 179 kinetic = 2.446434 180 potential(screened) = -3.917732 181 potential(ionic) = -12.476133 182 183SPLIT: Orbitals with angular momentum L= 1 184 185SPLIT: Basis orbitals for state 2p 186 187SPLIT: PAO cut-off radius determined from an 188SPLIT: energy shift= 0.020000 Ry 189 190 izeta = 1 191 lambda = 1.000000 192 rc = 3.937239 193 energy = -0.658841 194 kinetic = 5.005986 195 potential(screened) = -5.664827 196 potential(ionic) = -13.452360 197 198 izeta = 2 199 rmatch = 2.541963 200 splitnorm = 0.150000 201 energy = -0.367441 202 kinetic = 7.530509 203 potential(screened) = -7.897949 204 potential(ionic) = -16.611953 205 206POLgen: Perturbative polarization orbital with L= 2 207 208POLgen: Polarization orbital for state 2p 209 210 izeta = 1 211 rc = 3.937239 212 energy = 2.398520 213 kinetic = 4.716729 214 potential(screened) = -2.318209 215 potential(ionic) = -8.603170 216atom: Total number of Sankey-type orbitals: 13 217 218atm_pop: Valence configuration (for local Pseudopot. screening): 219 2s( 2.00) 220 2p( 4.00) 221Vna: chval, zval: 6.00000 6.00000 222 223Vna: Cut-off radius for the neutral-atom potential: 3.937239 224 225atom: _________________________________________________________________________ 226 227<basis_specs> 228=============================================================================== 229H Z= 1 Mass= 1.0100 Charge= 0.17977+309 230Lmxo=0 Lmxkb= 2 BasisType=split Semic=F 231L=0 Nsemic=0 Cnfigmx=1 232 i=1 nzeta=2 polorb=1 (1s) 233 splnorm: 0.15000 234 vcte: 0.0000 235 rinn: 0.0000 236 qcoe: 0.0000 237 qyuk: 0.0000 238 qwid: 0.10000E-01 239 rcs: 0.0000 0.0000 240 lambdas: 1.0000 1.0000 241------------------------------------------------------------------------------- 242L=0 Nkbl=1 erefs: 0.17977+309 243L=1 Nkbl=1 erefs: 0.17977+309 244L=2 Nkbl=1 erefs: 0.17977+309 245=============================================================================== 246</basis_specs> 247 248atom: Called for H (Z = 1) 249 250read_vps: Pseudopotential generation method: 251read_vps: ATM3 Troullier-Martins 252Valence charge for ps generation: 1.00000 253 254xc_check: Exchange-correlation functional: 255xc_check: Ceperley-Alder 256V l=0 = -2*Zval/r beyond r= 1.2343 257V l=1 = -2*Zval/r beyond r= 1.2189 258V l=2 = -2*Zval/r beyond r= 1.2189 259All V_l potentials equal beyond r= 1.2343 260This should be close to max(r_c) in ps generation 261All pots = -2*Zval/r beyond r= 1.2343 262 263VLOCAL1: 99.0% of the norm of Vloc inside 28.493 Ry 264VLOCAL1: 99.9% of the norm of Vloc inside 64.935 Ry 265atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.45251 266atom: Maximum radius for r*vlocal+2*Zval: 1.21892 267GHOST: No ghost state for L = 0 268GHOST: No ghost state for L = 1 269GHOST: No ghost state for L = 2 270 271KBgen: Kleinman-Bylander projectors: 272 l= 0 rc= 1.364359 el= -0.467325 Ekb= -2.005361 kbcos= -0.336422 273 l= 1 rc= 1.434438 el= 0.001430 Ekb= -0.501708 kbcos= -0.021697 274 l= 2 rc= 1.470814 el= 0.002365 Ekb= -0.190555 kbcos= -0.002281 275 276KBgen: Total number of Kleinman-Bylander projectors: 9 277atom: ------------------------------------------------------------------------- 278 279atom: SANKEY-TYPE ORBITALS: 280atom: Selected multiple-zeta basis: split 281 282SPLIT: Orbitals with angular momentum L= 0 283 284SPLIT: Basis orbitals for state 1s 285 286SPLIT: PAO cut-off radius determined from an 287SPLIT: energy shift= 0.020000 Ry 288 289 izeta = 1 290 lambda = 1.000000 291 rc = 4.828263 292 energy = -0.449375 293 kinetic = 0.929372 294 potential(screened) = -1.378747 295 potential(ionic) = -1.915047 296 297 izeta = 2 298 rmatch = 3.854947 299 splitnorm = 0.150000 300 energy = -0.336153 301 kinetic = 1.505294 302 potential(screened) = -1.841447 303 potential(ionic) = -2.413582 304 305POLgen: Perturbative polarization orbital with L= 1 306 307POLgen: Polarization orbital for state 1s 308 309 izeta = 1 310 rc = 4.828263 311 energy = 0.706972 312 kinetic = 1.396397 313 potential(screened) = -0.689424 314 potential(ionic) = -1.169792 315atom: Total number of Sankey-type orbitals: 5 316 317atm_pop: Valence configuration (for local Pseudopot. screening): 318 1s( 1.00) 319Vna: chval, zval: 1.00000 1.00000 320 321Vna: Cut-off radius for the neutral-atom potential: 4.828263 322 323atom: _________________________________________________________________________ 324 325prinput: Basis input ---------------------------------------------------------- 326 327PAO.BasisType split 328 329%block ChemicalSpeciesLabel 330 1 8 O # Species index, atomic number, species label 331 2 1 H # Species index, atomic number, species label 332%endblock ChemicalSpeciesLabel 333 334%block PAO.Basis # Define Basis set 335O 2 # Species label, number of l-shells 336 n=2 0 2 # n, l, Nzeta 337 3.305 2.510 338 1.000 1.000 339 n=2 1 2 P 1 # n, l, Nzeta, Polarization, NzetaPol 340 3.937 2.542 341 1.000 1.000 342H 1 # Species label, number of l-shells 343 n=1 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol 344 4.828 3.855 345 1.000 1.000 346%endblock PAO.Basis 347 348prinput: ---------------------------------------------------------------------- 349 350Dumping basis to NetCDF file O.ion.nc 351Dumping basis to NetCDF file H.ion.nc 352coor: Atomic-coordinates input format = Cartesian coordinates 353coor: (in Angstroms) 354 355siesta: WARNING: XV file not found 356 357siesta: Atomic coordinates (Bohr) and species 358siesta: 0.00000 0.00000 0.00000 1 1 359siesta: 1.43052 1.10738 0.00000 2 2 360siesta: -1.43052 1.10738 0.00000 2 3 361 362siesta: System type = molecule 363 364initatomlists: Number of atoms, orbitals, and projectors: 3 23 34 365 366siesta: ******************** Simulation parameters **************************** 367siesta: 368siesta: The following are some of the parameters of the simulation. 369siesta: A complete list of the parameters used, including default values, 370siesta: can be found in file out.fdf 371siesta: 372redata: Spin configuration = none 373redata: Number of spin components = 1 374redata: Time-Reversal Symmetry = T 375redata: Spin spiral = F 376redata: Long output = F 377redata: Number of Atomic Species = 2 378redata: Charge density info will appear in .RHO file 379redata: Write Mulliken Pop. = NO 380redata: Matel table size (NRTAB) = 1024 381redata: Mesh Cutoff = 100.0000 Ry 382redata: Net charge of the system = 0.0000 |e| 383redata: Min. number of SCF Iter = 0 384redata: Max. number of SCF Iter = 1000 385redata: SCF convergence failure will abort job 386redata: SCF mix quantity = Hamiltonian 387redata: Mix DM or H after convergence = F 388redata: Recompute H after scf cycle = F 389redata: Mix DM in first SCF step = T 390redata: Write Pulay info on disk = F 391redata: New DM Occupancy tolerance = 0.000000000001 392redata: No kicks to SCF 393redata: DM Mixing Weight for Kicks = 0.5000 394redata: Require Harris convergence for SCF = F 395redata: Harris energy tolerance for SCF = 0.000100 eV 396redata: Require DM convergence for SCF = T 397redata: DM tolerance for SCF = 0.000100 398redata: Require EDM convergence for SCF = F 399redata: EDM tolerance for SCF = 0.001000 eV 400redata: Require H convergence for SCF = T 401redata: Hamiltonian tolerance for SCF = 0.001000 eV 402redata: Require (free) Energy convergence for SCF = F 403redata: (free) Energy tolerance for SCF = 0.000100 eV 404redata: Using Saved Data (generic) = F 405redata: Use continuation files for DM = F 406redata: Neglect nonoverlap interactions = F 407redata: Method of Calculation = Diagonalization 408redata: Electronic Temperature = 299.9869 K 409redata: Fix the spin of the system = F 410redata: Dynamics option = Verlet MD run 411redata: Initial MD time step = 1 412redata: Final MD time step = 20 413redata: Length of MD time step = 0.2000 fs 414redata: Initial Temperature of MD run = 600.0000 K 415redata: Perform a MD quench = F 416mix.SCF: Pulay mixing = Pulay 417mix.SCF: Variant = stable 418mix.SCF: History steps = 2 419mix.SCF: Linear mixing weight = 0.250000 420mix.SCF: Mixing weight = 0.250000 421mix.SCF: SVD condition = 0.1000E-07 422redata: Save all siesta data in one NC = F 423redata: *********************************************************************** 424 425%block SCF.Mixers 426 Pulay 427%endblock SCF.Mixers 428 429%block SCF.Mixer.Pulay 430 # Mixing method 431 method pulay 432 variant stable 433 434 # Mixing options 435 weight 0.2500 436 weight.linear 0.2500 437 history 2 438%endblock SCF.Mixer.Pulay 439 440Size of DM history Fstack: 1 441Total number of electrons: 8.000000 442Total ionic charge: 8.000000 443 444* ProcessorY, Blocksize: 2 3 445 446 447* Orbital distribution balance (max,min): 3 2 448 449 Kpoints in: 1 . Kpoints trimmed: 1 450 451siesta: k-grid: Number of k-points = 1 452siesta: k-grid: Cutoff (effective) = 3.200 Ang 453siesta: k-grid: Supercell and displacements 454siesta: k-grid: 1 0 0 0.000 455siesta: k-grid: 0 1 0 0.000 456siesta: k-grid: 0 0 1 0.000 457 458diag: Algorithm = D&C 459diag: Parallel over k = F 460diag: Use parallel 2D distribution = T 461diag: Parallel block-size = 3 462diag: Parallel distribution = 2 x 4 463diag: Used triangular part = Lower 464diag: Absolute tolerance = 0.100E-15 465diag: Orthogonalization factor = 0.100E-05 466diag: Memory factor = 1.0000 467 468 469ts: ************************************************************** 470ts: Save H and S matrices = F 471ts: Save DM and EDM matrices = F 472ts: Only save the overlap matrix S = F 473ts: ************************************************************** 474 475************************ Begin: TS CHECKS AND WARNINGS ************************ 476************************ End: TS CHECKS AND WARNINGS ************************** 477 478 479 ==================================== 480 Begin MD step = 1 481 ==================================== 482 483outcoor: Atomic coordinates (Ang): 484 0.00000000 0.00000000 0.00000000 1 1 O 485 0.75700000 0.58600000 0.00000000 2 2 H 486 -0.75700000 0.58600000 0.00000000 2 3 H 487 488outcell: Unit cell vectors (Ang): 489 8.000000 0.000000 0.000000 490 0.000000 8.000000 0.000000 491 0.000000 0.000000 6.400000 492 493outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 494outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 495outcell: Cell volume (Ang**3) : 409.6000 496<dSpData1D:S at geom step 1 497 <sparsity:sparsity for geom step 1 498 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 499 <dData1D:(new from dSpData1D) n=69, refcount: 1> 500refcount: 1> 501new_DM -- step: 1 502Initializing Density Matrix... 503DM filled with atomic data: 504<dSpData2D:DM initialized from atoms 505 <sparsity:sparsity for geom step 1 506 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 8> 507 <dData2D:DM n=69 m=1, refcount: 1> 508refcount: 1> 509No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 510New grid distribution: 1 511 1 1: 25 1: 13 1: 5 512 2 1: 25 1: 13 6: 10 513 3 1: 25 1: 13 11: 15 514 4 1: 25 1: 13 16: 20 515 5 1: 25 14: 25 1: 5 516 6 1: 25 14: 25 6: 10 517 7 1: 25 14: 25 11: 15 518 8 1: 25 14: 25 16: 20 519 520InitMesh: MESH = 50 x 50 x 40 = 100000 521InitMesh: (bp) = 25 x 25 x 20 = 12500 522InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 523ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 524New grid distribution: 2 525 1 7: 25 6: 25 1: 6 526 2 7: 25 1: 5 1: 6 527 3 7: 25 1: 5 7: 20 528 4 1: 6 1: 5 7: 20 529 5 1: 6 6: 25 1: 6 530 6 1: 6 1: 5 1: 6 531 7 7: 25 6: 25 7: 20 532 8 1: 6 6: 25 7: 20 533New grid distribution: 3 534 1 1: 9 7: 25 1: 7 535 2 11: 25 1: 6 1: 8 536 3 1: 9 7: 25 8: 20 537 4 11: 25 1: 6 9: 20 538 5 10: 25 7: 25 1: 7 539 6 1: 10 1: 6 9: 20 540 7 10: 25 7: 25 8: 20 541 8 1: 10 1: 6 1: 8 542Setting up quadratic distribution... 543ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 544PhiOnMesh: Number of (b)points on node 0 = 2280 545PhiOnMesh: nlist on node 0 = 5165 546 547stepf: Fermi-Dirac step function 548 549siesta: Program's energy decomposition (eV): 550siesta: Ebs = -82.119669 551siesta: Eions = 815.854478 552siesta: Ena = 175.155695 553siesta: Ekin = 377.531314 554siesta: Enl = -69.272321 555siesta: Eso = 0.000000 556siesta: Edftu = 0.000000 557siesta: DEna = -17.548253 558siesta: DUscf = 2.107478 559siesta: DUext = 0.000000 560siesta: Exc = -117.110096 561siesta: eta*DQ = 0.000000 562siesta: Emadel = 0.000000 563siesta: Emeta = 0.000000 564siesta: Emolmec = 0.000000 565siesta: Ekinion = 0.000000 566siesta: Eharris = -466.820729 567siesta: Etot = -464.990661 568siesta: FreeEng = -464.990661 569 570 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 571 scf: 1 -466.820729 -464.990661 -464.990661 1.433758 -4.421566 7.362816 572timer: Routine,Calls,Time,% = IterSCF 1 0.021 1.60 573 scf: 2 -466.222677 -465.720515 -465.720515 0.059267 -3.209848 2.873260 574 scf: 3 -465.834534 -465.817252 -465.817252 0.028397 -2.390871 0.344099 575 scf: 4 -465.822842 -465.820237 -465.820237 0.010402 -2.315513 0.265656 576 scf: 5 -465.822394 -465.821750 -465.821750 0.021596 -2.104162 0.064327 577 scf: 6 -465.821894 -465.821832 -465.821832 0.000473 -2.074057 0.029944 578 scf: 7 -465.821907 -465.821875 -465.821875 0.000931 -2.076615 0.020268 579 scf: 8 -465.821906 -465.821892 -465.821892 0.000897 -2.081282 0.012963 580 scf: 9 -465.821896 -465.821895 -465.821895 0.000620 -2.087336 0.005007 581 scf: 10 -465.821894 -465.821895 -465.821895 0.000099 -2.089924 0.002495 582 scf: 11 -465.821895 -465.821895 -465.821895 0.000039 -2.090352 0.001641 583 scf: 12 -465.821895 -465.821895 -465.821895 0.000042 -2.090515 0.000723 584 585SCF Convergence by DM+H criterion 586max |DM_out - DM_in| : 0.0000415343 587max |H_out - H_in| (eV) : 0.0007228882 588SCF cycle converged after 12 iterations 589 590Using DM_out to compute the final energy and forces 591No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 592 593siesta: E_KS(eV) = -465.8219 594 595siesta: E_KS - E_eggbox = -465.8219 596 597siesta: Atomic forces (eV/Ang): 598 1 0.000000 -0.692488 0.000000 599 2 0.665998 0.319146 -0.000000 600 3 -0.665998 0.319146 -0.000000 601---------------------------------------- 602 Tot -0.000000 -0.054197 0.000000 603---------------------------------------- 604 Max 0.692488 605 Res 0.417713 sqrt( Sum f_i^2 / 3N ) 606---------------------------------------- 607 Max 0.692488 constrained 608 609Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -4.36 -2.33 -1.07 -0.00 0.08 0.36 610(Free)E + p*V (eV/cell) -465.1609 611Target enthalpy (eV/cell) -465.8219 612 613siesta: Stress tensor (static) (eV/Ang**3): 614 -0.002568 0.000000 0.000000 615 -0.000000 -0.001104 0.000000 616 -0.000000 0.000000 -0.000417 617 618siesta: Pressure (static): 2.18394413 kBar 619 620siesta: Stress tensor (total) (eV/Ang**3): 621 -0.002718 0.000223 0.000048 622 0.000223 -0.001456 -0.000003 623 0.000048 -0.000003 -0.000667 624 625siesta: Pressure (total): 2.58550296 kBar 626 627siesta: Temp_ion = 600.000 K 628 629 ==================================== 630 Begin MD step = 2 631 ==================================== 632 633outcoor: Atomic coordinates (Ang): 634 0.00019082 -0.00042428 0.00038907 1 1 O 635 0.75258336 0.59326734 -0.00010629 2 2 H 636 -0.75560632 0.58544359 -0.00605717 2 3 H 637 638outcell: Unit cell vectors (Ang): 639 8.000000 0.000000 0.000000 640 0.000000 8.000000 0.000000 641 0.000000 0.000000 6.400000 642 643outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 644outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 645outcell: Cell volume (Ang**3) : 409.6000 646<dSpData1D:S at geom step 2 647 <sparsity:sparsity for geom step 2 648 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 649 <dData1D:(new from dSpData1D) n=69, refcount: 1> 650refcount: 1> 651new_DM -- step: 2 652Re-using DM from previous geometries... 653Number of DMs in history: 1 654 DM extrapolation coefficients: 6551 1.00000 656New DM after history re-use: 657<dSpData2D:SpM extrapolated using coords 658 <sparsity:sparsity for geom step 2 659 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 660 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 661refcount: 1> 662No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 663New grid distribution: 1 664 1 1: 25 1: 13 1: 5 665 2 1: 25 1: 13 6: 10 666 3 1: 25 1: 13 11: 15 667 4 1: 25 1: 13 16: 20 668 5 1: 25 14: 25 1: 5 669 6 1: 25 14: 25 6: 10 670 7 1: 25 14: 25 11: 15 671 8 1: 25 14: 25 16: 20 672 673InitMesh: MESH = 50 x 50 x 40 = 100000 674InitMesh: (bp) = 25 x 25 x 20 = 12500 675InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 676ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 677New grid distribution: 2 678 1 7: 25 6: 25 1: 6 679 2 7: 25 1: 5 1: 6 680 3 7: 25 1: 5 7: 20 681 4 1: 6 1: 5 7: 20 682 5 1: 6 6: 25 1: 6 683 6 1: 6 1: 5 1: 6 684 7 7: 25 6: 25 7: 20 685 8 1: 6 6: 25 7: 20 686New grid distribution: 3 687 1 1: 9 7: 25 1: 7 688 2 11: 25 1: 6 1: 8 689 3 1: 9 7: 25 8: 20 690 4 11: 25 1: 6 9: 20 691 5 10: 25 7: 25 1: 7 692 6 1: 10 1: 6 9: 20 693 7 10: 25 7: 25 8: 20 694 8 1: 10 1: 6 1: 8 695Setting up quadratic distribution... 696ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 697PhiOnMesh: Number of (b)points on node 0 = 2280 698PhiOnMesh: nlist on node 0 = 5155 699 700 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 701 scf: 1 -465.816427 -465.820181 -465.820181 0.005385 -2.111993 0.037620 702 scf: 2 -465.820026 -465.820165 -465.820165 0.001400 -2.135079 0.054200 703 scf: 3 -465.820268 -465.820241 -465.820241 0.000823 -2.121472 0.003760 704 scf: 4 -465.820243 -465.820242 -465.820242 0.000040 -2.121462 0.002010 705 scf: 5 -465.820243 -465.820243 -465.820243 0.000061 -2.121522 0.000704 706 707SCF Convergence by DM+H criterion 708max |DM_out - DM_in| : 0.0000609123 709max |H_out - H_in| (eV) : 0.0007043356 710SCF cycle converged after 5 iterations 711 712Using DM_out to compute the final energy and forces 713No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 714 715siesta: E_KS(eV) = -465.8202 716 717siesta: Atomic forces (eV/Ang): 718 1 0.095186 -0.645321 -0.005307 719 2 0.653330 0.267011 0.001260 720 3 -0.751421 0.332279 -0.006813 721---------------------------------------- 722 Tot -0.002905 -0.046031 -0.010861 723---------------------------------------- 724 Max 0.751421 725 Res 0.421473 sqrt( Sum f_i^2 / 3N ) 726---------------------------------------- 727 Max 0.751421 constrained 728 729Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -4.57 -2.24 -1.07 0.01 0.06 0.56 730(Free)E + p*V (eV/cell) -465.1489 731Target enthalpy (eV/cell) -465.8202 732 733siesta: Stress tensor (static) (eV/Ang**3): 734 -0.002699 0.000124 -0.000011 735 0.000124 -0.001048 0.000006 736 -0.000013 0.000006 -0.000417 737 738siesta: Pressure (static): 2.22442332 kBar 739 740siesta: Stress tensor (total) (eV/Ang**3): 741 -0.002850 0.000348 0.000037 742 0.000347 -0.001400 0.000003 743 0.000035 0.000004 -0.000667 744 745siesta: Pressure (total): 2.62598215 kBar 746 747siesta: Temp_ion = 593.670 K 748 749 ==================================== 750 Begin MD step = 3 751 ==================================== 752 753outcoor: Atomic coordinates (Ang): 754 0.00038393 -0.00086401 0.00077801 1 1 O 755 0.74841457 0.60063598 -0.00021211 2 2 H 756 -0.75449770 0.58501324 -0.01211693 2 3 H 757 758outcell: Unit cell vectors (Ang): 759 8.000000 0.000000 0.000000 760 0.000000 8.000000 0.000000 761 0.000000 0.000000 6.400000 762 763outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 764outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 765outcell: Cell volume (Ang**3) : 409.6000 766<dSpData1D:S at geom step 3 767 <sparsity:sparsity for geom step 3 768 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 769 <dData1D:(new from dSpData1D) n=69, refcount: 1> 770refcount: 1> 771new_DM -- step: 3 772Re-using DM from previous geometries... 773Number of DMs in history: 1 774 DM extrapolation coefficients: 7751 1.00000 776New DM after history re-use: 777<dSpData2D:SpM extrapolated using coords 778 <sparsity:sparsity for geom step 3 779 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 780 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 781refcount: 1> 782No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 783New grid distribution: 1 784 1 1: 25 1: 13 1: 5 785 2 1: 25 1: 13 6: 10 786 3 1: 25 1: 13 11: 15 787 4 1: 25 1: 13 16: 20 788 5 1: 25 14: 25 1: 5 789 6 1: 25 14: 25 6: 10 790 7 1: 25 14: 25 11: 15 791 8 1: 25 14: 25 16: 20 792 793InitMesh: MESH = 50 x 50 x 40 = 100000 794InitMesh: (bp) = 25 x 25 x 20 = 12500 795InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 796ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 797New grid distribution: 2 798 1 7: 25 6: 25 1: 6 799 2 7: 25 1: 5 1: 6 800 3 7: 25 1: 5 7: 20 801 4 1: 6 1: 5 7: 20 802 5 1: 6 6: 25 1: 6 803 6 1: 6 1: 5 1: 6 804 7 7: 25 6: 25 7: 20 805 8 1: 6 6: 25 7: 20 806New grid distribution: 3 807 1 1: 9 7: 25 1: 7 808 2 11: 25 1: 6 1: 8 809 3 1: 9 7: 25 8: 20 810 4 11: 25 1: 6 9: 20 811 5 10: 25 7: 25 1: 7 812 6 1: 10 1: 6 9: 20 813 7 10: 25 7: 25 8: 20 814 8 1: 10 1: 6 1: 8 815Setting up quadratic distribution... 816ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 817PhiOnMesh: Number of (b)points on node 0 = 2280 818PhiOnMesh: nlist on node 0 = 5157 819 820 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 821 scf: 1 -465.818370 -465.818576 -465.818576 0.005419 -2.142786 0.042838 822 scf: 2 -465.818357 -465.818545 -465.818545 0.001629 -2.169296 0.063249 823 scf: 3 -465.818677 -465.818642 -465.818642 0.000965 -2.153498 0.004086 824 scf: 4 -465.818645 -465.818643 -465.818643 0.000042 -2.153554 0.002206 825 scf: 5 -465.818645 -465.818644 -465.818644 0.000063 -2.153702 0.000661 826 827SCF Convergence by DM+H criterion 828max |DM_out - DM_in| : 0.0000633661 829max |H_out - H_in| (eV) : 0.0006609259 830SCF cycle converged after 5 iterations 831 832Using DM_out to compute the final energy and forces 833No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 834 835siesta: E_KS(eV) = -465.8186 836 837siesta: Atomic forces (eV/Ang): 838 1 0.188648 -0.577837 -0.010141 839 2 0.627572 0.205217 0.002848 840 3 -0.821685 0.335052 -0.013557 841---------------------------------------- 842 Tot -0.005465 -0.037568 -0.020851 843---------------------------------------- 844 Max 0.821685 845 Res 0.420735 sqrt( Sum f_i^2 / 3N ) 846---------------------------------------- 847 Max 0.821685 constrained 848 849Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -4.66 -2.12 -1.07 0.02 0.02 0.74 850(Free)E + p*V (eV/cell) -465.1497 851Target enthalpy (eV/cell) -465.8186 852 853siesta: Stress tensor (static) (eV/Ang**3): 854 -0.002778 0.000247 -0.000025 855 0.000247 -0.000960 0.000012 856 -0.000026 0.000012 -0.000417 857 858siesta: Pressure (static): 2.21917654 kBar 859 860siesta: Stress tensor (total) (eV/Ang**3): 861 -0.002910 0.000460 0.000013 862 0.000460 -0.001323 0.000015 863 0.000012 0.000015 -0.000667 864 865siesta: Pressure (total): 2.61649890 kBar 866 867siesta: Temp_ion = 587.525 K 868 869 ==================================== 870 Begin MD step = 4 871 ==================================== 872 873outcoor: Atomic coordinates (Ang): 874 0.00058155 -0.00131758 0.00116671 1 1 O 875 0.74448386 0.60808247 -0.00031684 2 2 H 876 -0.75370080 0.58471000 -0.01818183 2 3 H 877 878outcell: Unit cell vectors (Ang): 879 8.000000 0.000000 0.000000 880 0.000000 8.000000 0.000000 881 0.000000 0.000000 6.400000 882 883outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 884outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 885outcell: Cell volume (Ang**3) : 409.6000 886<dSpData1D:S at geom step 4 887 <sparsity:sparsity for geom step 4 888 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 889 <dData1D:(new from dSpData1D) n=69, refcount: 1> 890refcount: 1> 891new_DM -- step: 4 892Re-using DM from previous geometries... 893Number of DMs in history: 1 894 DM extrapolation coefficients: 8951 1.00000 896New DM after history re-use: 897<dSpData2D:SpM extrapolated using coords 898 <sparsity:sparsity for geom step 4 899 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 900 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 901refcount: 1> 902No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 903New grid distribution: 1 904 1 1: 25 1: 13 1: 5 905 2 1: 25 1: 13 6: 10 906 3 1: 25 1: 13 11: 15 907 4 1: 25 1: 13 16: 20 908 5 1: 25 14: 25 1: 5 909 6 1: 25 14: 25 6: 10 910 7 1: 25 14: 25 11: 15 911 8 1: 25 14: 25 16: 20 912 913InitMesh: MESH = 50 x 50 x 40 = 100000 914InitMesh: (bp) = 25 x 25 x 20 = 12500 915InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 916ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 917New grid distribution: 2 918 1 7: 25 6: 25 1: 6 919 2 7: 25 1: 5 1: 6 920 3 7: 25 1: 5 7: 20 921 4 1: 6 1: 5 7: 20 922 5 1: 6 6: 25 1: 6 923 6 1: 6 1: 5 1: 6 924 7 7: 25 6: 25 7: 20 925 8 1: 6 6: 25 7: 20 926New grid distribution: 3 927 1 1: 9 7: 25 1: 7 928 2 11: 25 1: 6 1: 8 929 3 1: 9 7: 25 8: 20 930 4 11: 25 1: 6 9: 20 931 5 10: 25 7: 25 1: 7 932 6 1: 10 1: 6 9: 20 933 7 10: 25 7: 25 8: 20 934 8 1: 10 1: 6 1: 8 935Setting up quadratic distribution... 936ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 937PhiOnMesh: Number of (b)points on node 0 = 2280 938PhiOnMesh: nlist on node 0 = 5142 939 940 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 941 scf: 1 -465.820425 -465.817046 -465.817046 0.005478 -2.174308 0.048300 942 scf: 2 -465.816746 -465.816994 -465.816994 0.001854 -2.204200 0.072884 943 scf: 3 -465.817162 -465.817118 -465.817118 0.001108 -2.186186 0.004326 944 scf: 4 -465.817121 -465.817120 -465.817120 0.000043 -2.186298 0.002361 945 scf: 5 -465.817121 -465.817121 -465.817121 0.000066 -2.186524 0.000657 946 947SCF Convergence by DM+H criterion 948max |DM_out - DM_in| : 0.0000661789 949max |H_out - H_in| (eV) : 0.0006574628 950SCF cycle converged after 5 iterations 951 952Using DM_out to compute the final energy and forces 953No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 954 955siesta: E_KS(eV) = -465.8171 956 957siesta: Atomic forces (eV/Ang): 958 1 0.277221 -0.489565 -0.015329 959 2 0.589580 0.134809 0.005051 960 3 -0.874471 0.326442 -0.020353 961---------------------------------------- 962 Tot -0.007671 -0.028314 -0.030632 963---------------------------------------- 964 Max 0.874471 965 Res 0.415564 sqrt( Sum f_i^2 / 3N ) 966---------------------------------------- 967 Max 0.874471 constrained 968 969Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -4.67 -1.94 -1.07 0.04 -0.02 0.91 970(Free)E + p*V (eV/cell) -465.1625 971Target enthalpy (eV/cell) -465.8171 972 973siesta: Stress tensor (static) (eV/Ang**3): 974 -0.002802 0.000365 -0.000039 975 0.000365 -0.000840 0.000017 976 -0.000041 0.000018 -0.000417 977 978siesta: Pressure (static): 2.16755911 kBar 979 980siesta: Stress tensor (total) (eV/Ang**3): 981 -0.002916 0.000568 -0.000013 982 0.000567 -0.001212 0.000026 983 -0.000015 0.000026 -0.000667 984 985siesta: Pressure (total): 2.56076871 kBar 986 987siesta: Temp_ion = 581.660 K 988 989 ==================================== 990 Begin MD step = 5 991 ==================================== 992 993outcoor: Atomic coordinates (Ang): 994 0.00078581 -0.00178287 0.00155504 1 1 O 995 0.74077682 0.61558010 -0.00041966 2 2 H 996 -0.75323565 0.58453060 -0.02425445 2 3 H 997 998outcell: Unit cell vectors (Ang): 999 8.000000 0.000000 0.000000 1000 0.000000 8.000000 0.000000 1001 0.000000 0.000000 6.400000 1002 1003outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 1004outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 1005outcell: Cell volume (Ang**3) : 409.6000 1006<dSpData1D:S at geom step 5 1007 <sparsity:sparsity for geom step 5 1008 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 1009 <dData1D:(new from dSpData1D) n=69, refcount: 1> 1010refcount: 1> 1011new_DM -- step: 5 1012Re-using DM from previous geometries... 1013Number of DMs in history: 1 1014 DM extrapolation coefficients: 10151 1.00000 1016New DM after history re-use: 1017<dSpData2D:SpM extrapolated using coords 1018 <sparsity:sparsity for geom step 5 1019 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 1020 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 1021refcount: 1> 1022No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 1023New grid distribution: 1 1024 1 1: 25 1: 13 1: 5 1025 2 1: 25 1: 13 6: 10 1026 3 1: 25 1: 13 11: 15 1027 4 1: 25 1: 13 16: 20 1028 5 1: 25 14: 25 1: 5 1029 6 1: 25 14: 25 6: 10 1030 7 1: 25 14: 25 11: 15 1031 8 1: 25 14: 25 16: 20 1032 1033InitMesh: MESH = 50 x 50 x 40 = 100000 1034InitMesh: (bp) = 25 x 25 x 20 = 12500 1035InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 1036ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 1037New grid distribution: 2 1038 1 7: 25 6: 25 1: 6 1039 2 7: 25 1: 5 1: 6 1040 3 7: 25 1: 5 7: 20 1041 4 1: 6 1: 5 7: 20 1042 5 1: 6 6: 25 1: 6 1043 6 1: 6 1: 5 1: 6 1044 7 7: 25 6: 25 7: 20 1045 8 1: 6 6: 25 7: 20 1046New grid distribution: 3 1047 1 1: 9 7: 25 1: 7 1048 2 11: 25 1: 6 1: 8 1049 3 1: 9 7: 25 8: 20 1050 4 11: 25 1: 6 9: 20 1051 5 10: 25 7: 25 1: 7 1052 6 1: 10 1: 6 9: 20 1053 7 10: 25 7: 25 8: 20 1054 8 1: 10 1: 6 1: 8 1055Setting up quadratic distribution... 1056ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 1057PhiOnMesh: Number of (b)points on node 0 = 2280 1058PhiOnMesh: nlist on node 0 = 5148 1059 1060 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 1061 scf: 1 -465.822505 -465.815584 -465.815584 0.005536 -2.206361 0.053481 1062 scf: 2 -465.815190 -465.815505 -465.815505 0.002068 -2.239444 0.082159 1063 scf: 3 -465.815719 -465.815664 -465.815664 0.001246 -2.219332 0.004454 1064 scf: 4 -465.815667 -465.815666 -465.815666 0.000044 -2.219493 0.002451 1065 scf: 5 -465.815667 -465.815667 -465.815667 0.000069 -2.219790 0.000667 1066 1067SCF Convergence by DM+H criterion 1068max |DM_out - DM_in| : 0.0000685652 1069max |H_out - H_in| (eV) : 0.0006665344 1070SCF cycle converged after 5 iterations 1071 1072Using DM_out to compute the final energy and forces 1073No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 1074 1075siesta: E_KS(eV) = -465.8157 1076 1077siesta: Atomic forces (eV/Ang): 1078 1 0.357351 -0.381728 -0.021336 1079 2 0.541476 0.056758 0.007843 1080 3 -0.908865 0.305859 -0.026716 1081---------------------------------------- 1082 Tot -0.010038 -0.019110 -0.040209 1083---------------------------------------- 1084 Max 0.908865 1085 Res 0.406974 sqrt( Sum f_i^2 / 3N ) 1086---------------------------------------- 1087 Max 0.908865 constrained 1088 1089Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -4.61 -1.71 -1.07 0.06 -0.07 1.07 1090(Free)E + p*V (eV/cell) -465.1862 1091Target enthalpy (eV/cell) -465.8157 1092 1093siesta: Stress tensor (static) (eV/Ang**3): 1094 -0.002776 0.000473 -0.000055 1095 0.000473 -0.000689 0.000022 1096 -0.000057 0.000022 -0.000417 1097 1098siesta: Pressure (static): 2.07290364 kBar 1099 1100siesta: Stress tensor (total) (eV/Ang**3): 1101 -0.002875 0.000666 -0.000041 1102 0.000666 -0.001067 0.000035 1103 -0.000043 0.000036 -0.000668 1104 1105siesta: Pressure (total): 2.46218793 kBar 1106 1107siesta: Temp_ion = 576.057 K 1108 1109 ==================================== 1110 Begin MD step = 6 1111 ==================================== 1112 1113outcoor: Atomic coordinates (Ang): 1114 0.00099863 -0.00225730 0.00194286 1 1 O 1115 0.73727520 0.62309927 -0.00051950 2 2 H 1116 -0.75311530 0.58446723 -0.03033721 2 3 H 1117 1118outcell: Unit cell vectors (Ang): 1119 8.000000 0.000000 0.000000 1120 0.000000 8.000000 0.000000 1121 0.000000 0.000000 6.400000 1122 1123outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 1124outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 1125outcell: Cell volume (Ang**3) : 409.6000 1126<dSpData1D:S at geom step 6 1127 <sparsity:sparsity for geom step 6 1128 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 1129 <dData1D:(new from dSpData1D) n=69, refcount: 1> 1130refcount: 1> 1131new_DM -- step: 6 1132Re-using DM from previous geometries... 1133Number of DMs in history: 1 1134 DM extrapolation coefficients: 11351 1.00000 1136New DM after history re-use: 1137<dSpData2D:SpM extrapolated using coords 1138 <sparsity:sparsity for geom step 6 1139 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 1140 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 1141refcount: 1> 1142No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 1143New grid distribution: 1 1144 1 1: 25 1: 13 1: 5 1145 2 1: 25 1: 13 6: 10 1146 3 1: 25 1: 13 11: 15 1147 4 1: 25 1: 13 16: 20 1148 5 1: 25 14: 25 1: 5 1149 6 1: 25 14: 25 6: 10 1150 7 1: 25 14: 25 11: 15 1151 8 1: 25 14: 25 16: 20 1152 1153InitMesh: MESH = 50 x 50 x 40 = 100000 1154InitMesh: (bp) = 25 x 25 x 20 = 12500 1155InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 1156ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 1157New grid distribution: 2 1158 1 7: 25 6: 25 1: 6 1159 2 7: 25 1: 5 1: 6 1160 3 7: 25 1: 5 7: 20 1161 4 1: 6 1: 5 7: 20 1162 5 1: 6 6: 25 1: 6 1163 6 1: 6 1: 5 1: 6 1164 7 7: 25 6: 25 7: 20 1165 8 1: 6 6: 25 7: 20 1166New grid distribution: 3 1167 1 1: 9 7: 25 1: 7 1168 2 11: 25 1: 6 1: 8 1169 3 1: 9 7: 25 8: 20 1170 4 11: 25 1: 6 9: 20 1171 5 10: 25 7: 25 1: 7 1172 6 1: 10 1: 6 9: 20 1173 7 10: 25 7: 25 8: 20 1174 8 1: 10 1: 6 1: 8 1175Setting up quadratic distribution... 1176ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 1177PhiOnMesh: Number of (b)points on node 0 = 2280 1178PhiOnMesh: nlist on node 0 = 5157 1179 1180 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 1181 scf: 1 -465.824488 -465.814152 -465.814152 0.005593 -2.238780 0.058254 1182 scf: 2 -465.813675 -465.814061 -465.814061 0.002266 -2.274780 0.090906 1183 scf: 3 -465.814305 -465.814240 -465.814240 0.001374 -2.252739 0.004488 1184 scf: 4 -465.814242 -465.814241 -465.814241 0.000044 -2.252940 0.002485 1185 scf: 5 -465.814243 -465.814242 -465.814242 0.000071 -2.253301 0.000685 1186 1187SCF Convergence by DM+H criterion 1188max |DM_out - DM_in| : 0.0000707186 1189max |H_out - H_in| (eV) : 0.0006854927 1190SCF cycle converged after 5 iterations 1191 1192Using DM_out to compute the final energy and forces 1193No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 1194 1195siesta: E_KS(eV) = -465.8142 1196 1197siesta: Atomic forces (eV/Ang): 1198 1 0.427546 -0.255523 -0.028495 1199 2 0.485153 -0.027808 0.011183 1200 3 -0.924359 0.273262 -0.032175 1201---------------------------------------- 1202 Tot -0.011660 -0.010069 -0.049487 1203---------------------------------------- 1204 Max 0.924359 1205 Res 0.396557 sqrt( Sum f_i^2 / 3N ) 1206---------------------------------------- 1207 Max 0.924359 constrained 1208 1209Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -4.46 -1.43 -1.07 0.07 -0.11 1.21 1210(Free)E + p*V (eV/cell) -465.2211 1211Target enthalpy (eV/cell) -465.8142 1212 1213siesta: Stress tensor (static) (eV/Ang**3): 1214 -0.002698 0.000570 -0.000071 1215 0.000570 -0.000507 0.000024 1216 -0.000073 0.000024 -0.000418 1217 1218siesta: Pressure (static): 1.93467501 kBar 1219 1220siesta: Stress tensor (total) (eV/Ang**3): 1221 -0.002786 0.000754 -0.000070 1222 0.000753 -0.000890 0.000043 1223 -0.000072 0.000043 -0.000669 1224 1225siesta: Pressure (total): 2.32020994 kBar 1226 1227siesta: Temp_ion = 570.578 K 1228 1229 ==================================== 1230 Begin MD step = 7 1231 ==================================== 1232 1233outcoor: Atomic coordinates (Ang): 1234 0.00122168 -0.00273785 0.00233000 1 1 O 1235 0.73395763 0.63060788 -0.00061510 2 2 H 1236 -0.75334561 0.58450753 -0.03643217 2 3 H 1237 1238outcell: Unit cell vectors (Ang): 1239 8.000000 0.000000 0.000000 1240 0.000000 8.000000 0.000000 1241 0.000000 0.000000 6.400000 1242 1243outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 1244outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 1245outcell: Cell volume (Ang**3) : 409.6000 1246<dSpData1D:S at geom step 7 1247 <sparsity:sparsity for geom step 7 1248 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 1249 <dData1D:(new from dSpData1D) n=69, refcount: 1> 1250refcount: 1> 1251new_DM -- step: 7 1252Re-using DM from previous geometries... 1253Number of DMs in history: 1 1254 DM extrapolation coefficients: 12551 1.00000 1256New DM after history re-use: 1257<dSpData2D:SpM extrapolated using coords 1258 <sparsity:sparsity for geom step 7 1259 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 1260 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 1261refcount: 1> 1262No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 1263New grid distribution: 1 1264 1 1: 25 1: 13 1: 5 1265 2 1: 25 1: 13 6: 10 1266 3 1: 25 1: 13 11: 15 1267 4 1: 25 1: 13 16: 20 1268 5 1: 25 14: 25 1: 5 1269 6 1: 25 14: 25 6: 10 1270 7 1: 25 14: 25 11: 15 1271 8 1: 25 14: 25 16: 20 1272 1273InitMesh: MESH = 50 x 50 x 40 = 100000 1274InitMesh: (bp) = 25 x 25 x 20 = 12500 1275InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 1276ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 1277New grid distribution: 2 1278 1 7: 25 6: 25 1: 6 1279 2 7: 25 1: 5 1: 6 1280 3 7: 25 1: 5 7: 20 1281 4 1: 6 1: 5 7: 20 1282 5 1: 6 6: 25 1: 6 1283 6 1: 6 1: 5 1: 6 1284 7 7: 25 6: 25 7: 20 1285 8 1: 6 6: 25 7: 20 1286New grid distribution: 3 1287 1 1: 9 7: 25 1: 7 1288 2 11: 25 1: 6 1: 8 1289 3 1: 9 7: 25 8: 20 1290 4 11: 25 1: 6 9: 20 1291 5 10: 25 7: 25 1: 7 1292 6 1: 10 1: 6 9: 20 1293 7 10: 25 7: 25 8: 20 1294 8 1: 10 1: 6 1: 8 1295Setting up quadratic distribution... 1296ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 1297PhiOnMesh: Number of (b)points on node 0 = 2280 1298PhiOnMesh: nlist on node 0 = 5159 1299 1300 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 1301 scf: 1 -465.826246 -465.812696 -465.812696 0.005646 -2.271391 0.062517 1302 scf: 2 -465.812123 -465.812581 -465.812581 0.002445 -2.309972 0.098920 1303 scf: 3 -465.812867 -465.812791 -465.812791 0.001491 -2.286210 0.004446 1304 scf: 4 -465.812793 -465.812792 -465.812792 0.000045 -2.286444 0.002473 1305 scf: 5 -465.812794 -465.812793 -465.812793 0.000073 -2.286860 0.000720 1306 1307SCF Convergence by DM+H criterion 1308max |DM_out - DM_in| : 0.0000727731 1309max |H_out - H_in| (eV) : 0.0007199451 1310SCF cycle converged after 5 iterations 1311 1312Using DM_out to compute the final energy and forces 1313No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 1314 1315siesta: E_KS(eV) = -465.8128 1316 1317siesta: Atomic forces (eV/Ang): 1318 1 0.484837 -0.112395 -0.037547 1319 2 0.422663 -0.117614 0.015030 1320 3 -0.921334 0.228886 -0.036337 1321---------------------------------------- 1322 Tot -0.013834 -0.001123 -0.058854 1323---------------------------------------- 1324 Max 0.921334 1325 Res 0.386491 sqrt( Sum f_i^2 / 3N ) 1326---------------------------------------- 1327 Max 0.921334 constrained 1328 1329Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -4.26 -1.09 -1.07 0.08 -0.16 1.32 1330(Free)E + p*V (eV/cell) -465.2652 1331Target enthalpy (eV/cell) -465.8128 1332 1333siesta: Stress tensor (static) (eV/Ang**3): 1334 -0.002578 0.000653 -0.000085 1335 0.000653 -0.000299 0.000024 1336 -0.000087 0.000024 -0.000419 1337 1338siesta: Pressure (static): 1.75998393 kBar 1339 1340siesta: Stress tensor (total) (eV/Ang**3): 1341 -0.002657 0.000827 -0.000098 1342 0.000827 -0.000683 0.000047 1343 -0.000100 0.000047 -0.000671 1344 1345siesta: Pressure (total): 2.14185153 kBar 1346 1347siesta: Temp_ion = 564.978 K 1348 1349 ==================================== 1350 Begin MD step = 8 1351 ==================================== 1352 1353outcoor: Atomic coordinates (Ang): 1354 0.00145635 -0.00322110 0.00271624 1 1 O 1355 0.73080041 0.63807188 -0.00070500 2 2 H 1356 -0.75392545 0.58463466 -0.04254092 2 3 H 1357 1358outcell: Unit cell vectors (Ang): 1359 8.000000 0.000000 0.000000 1360 0.000000 8.000000 0.000000 1361 0.000000 0.000000 6.400000 1362 1363outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 1364outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 1365outcell: Cell volume (Ang**3) : 409.6000 1366<dSpData1D:S at geom step 8 1367 <sparsity:sparsity for geom step 8 1368 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 1369 <dData1D:(new from dSpData1D) n=69, refcount: 1> 1370refcount: 1> 1371new_DM -- step: 8 1372Re-using DM from previous geometries... 1373Number of DMs in history: 1 1374 DM extrapolation coefficients: 13751 1.00000 1376New DM after history re-use: 1377<dSpData2D:SpM extrapolated using coords 1378 <sparsity:sparsity for geom step 8 1379 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 1380 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 1381refcount: 1> 1382No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 1383New grid distribution: 1 1384 1 1: 25 1: 13 1: 5 1385 2 1: 25 1: 13 6: 10 1386 3 1: 25 1: 13 11: 15 1387 4 1: 25 1: 13 16: 20 1388 5 1: 25 14: 25 1: 5 1389 6 1: 25 14: 25 6: 10 1390 7 1: 25 14: 25 11: 15 1391 8 1: 25 14: 25 16: 20 1392 1393InitMesh: MESH = 50 x 50 x 40 = 100000 1394InitMesh: (bp) = 25 x 25 x 20 = 12500 1395InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 1396ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 1397New grid distribution: 2 1398 1 7: 25 6: 25 1: 6 1399 2 7: 25 1: 5 1: 6 1400 3 7: 25 1: 5 7: 20 1401 4 1: 6 1: 5 7: 20 1402 5 1: 6 6: 25 1: 6 1403 6 1: 6 1: 5 1: 6 1404 7 7: 25 6: 25 7: 20 1405 8 1: 6 6: 25 7: 20 1406New grid distribution: 3 1407 1 1: 9 7: 25 1: 7 1408 2 11: 25 1: 6 1: 8 1409 3 1: 9 7: 25 8: 20 1410 4 11: 25 1: 6 9: 20 1411 5 10: 25 7: 25 1: 7 1412 6 1: 10 1: 6 9: 20 1413 7 10: 25 7: 25 8: 20 1414 8 1: 10 1: 6 1: 8 1415Setting up quadratic distribution... 1416ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 1417PhiOnMesh: Number of (b)points on node 0 = 2280 1418PhiOnMesh: nlist on node 0 = 5148 1419 1420 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 1421 scf: 1 -465.827623 -465.811135 -465.811135 0.005697 -2.304019 0.066179 1422 scf: 2 -465.810470 -465.810996 -465.810996 0.002600 -2.344794 0.106018 1423 scf: 3 -465.811323 -465.811236 -465.811236 0.001593 -2.319551 0.004336 1424 scf: 4 -465.811238 -465.811237 -465.811237 0.000046 -2.319812 0.002420 1425 scf: 5 -465.811239 -465.811238 -465.811238 0.000075 -2.320274 0.000746 1426 1427SCF Convergence by DM+H criterion 1428max |DM_out - DM_in| : 0.0000748213 1429max |H_out - H_in| (eV) : 0.0007455693 1430SCF cycle converged after 5 iterations 1431 1432Using DM_out to compute the final energy and forces 1433No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 1434 1435siesta: E_KS(eV) = -465.8112 1436 1437siesta: Atomic forces (eV/Ang): 1438 1 0.528754 0.044583 -0.048470 1439 2 0.355975 -0.211275 0.019307 1440 3 -0.900191 0.173350 -0.038840 1441---------------------------------------- 1442 Tot -0.015462 0.006657 -0.068003 1443---------------------------------------- 1444 Max 0.900191 1445 Res 0.379700 sqrt( Sum f_i^2 / 3N ) 1446---------------------------------------- 1447 Max 0.900191 constrained 1448 1449Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -3.99 -0.72 -1.08 0.08 -0.20 1.42 1450(Free)E + p*V (eV/cell) -465.3180 1451Target enthalpy (eV/cell) -465.8112 1452 1453siesta: Stress tensor (static) (eV/Ang**3): 1454 -0.002418 0.000719 -0.000098 1455 0.000719 -0.000067 0.000022 1456 -0.000100 0.000022 -0.000420 1457 1458siesta: Pressure (static): 1.55127875 kBar 1459 1460siesta: Stress tensor (total) (eV/Ang**3): 1461 -0.002491 0.000886 -0.000125 1462 0.000885 -0.000449 0.000048 1463 -0.000127 0.000049 -0.000673 1464 1465siesta: Pressure (total): 1.92939855 kBar 1466 1467siesta: Temp_ion = 558.944 K 1468 1469 ==================================== 1470 Begin MD step = 9 1471 ==================================== 1472 1473outcoor: Atomic coordinates (Ang): 1474 0.00170368 -0.00370328 0.00310132 1 1 O 1475 0.72777823 0.64545572 -0.00078757 2 2 H 1476 -0.75484680 0.58482756 -0.04866440 2 3 H 1477 1478outcell: Unit cell vectors (Ang): 1479 8.000000 0.000000 0.000000 1480 0.000000 8.000000 0.000000 1481 0.000000 0.000000 6.400000 1482 1483outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 1484outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 1485outcell: Cell volume (Ang**3) : 409.6000 1486<dSpData1D:S at geom step 9 1487 <sparsity:sparsity for geom step 9 1488 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 1489 <dData1D:(new from dSpData1D) n=69, refcount: 1> 1490refcount: 1> 1491new_DM -- step: 9 1492Re-using DM from previous geometries... 1493Number of DMs in history: 1 1494 DM extrapolation coefficients: 14951 1.00000 1496New DM after history re-use: 1497<dSpData2D:SpM extrapolated using coords 1498 <sparsity:sparsity for geom step 9 1499 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 1500 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 1501refcount: 1> 1502No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 1503New grid distribution: 1 1504 1 1: 25 1: 13 1: 5 1505 2 1: 25 1: 13 6: 10 1506 3 1: 25 1: 13 11: 15 1507 4 1: 25 1: 13 16: 20 1508 5 1: 25 14: 25 1: 5 1509 6 1: 25 14: 25 6: 10 1510 7 1: 25 14: 25 11: 15 1511 8 1: 25 14: 25 16: 20 1512 1513InitMesh: MESH = 50 x 50 x 40 = 100000 1514InitMesh: (bp) = 25 x 25 x 20 = 12500 1515InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 1516ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 1517New grid distribution: 2 1518 1 7: 25 6: 25 1: 6 1519 2 7: 25 1: 5 1: 6 1520 3 7: 25 1: 5 7: 20 1521 4 1: 6 1: 5 7: 20 1522 5 1: 6 6: 25 1: 6 1523 6 1: 6 1: 5 1: 6 1524 7 7: 25 6: 25 7: 20 1525 8 1: 6 6: 25 7: 20 1526New grid distribution: 3 1527 1 1: 9 7: 25 1: 7 1528 2 11: 25 1: 6 1: 8 1529 3 1: 9 7: 25 8: 20 1530 4 11: 25 1: 6 9: 20 1531 5 10: 25 7: 25 1: 7 1532 6 1: 10 1: 6 9: 20 1533 7 10: 25 7: 25 8: 20 1534 8 1: 10 1: 6 1: 8 1535Setting up quadratic distribution... 1536ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 1537PhiOnMesh: Number of (b)points on node 0 = 2280 1538PhiOnMesh: nlist on node 0 = 5156 1539 1540 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 1541 scf: 1 -465.828465 -465.809378 -465.809378 0.005743 -2.336487 0.069145 1542 scf: 2 -465.808628 -465.809217 -465.809217 0.002728 -2.379010 0.112021 1543 scf: 3 -465.809581 -465.809484 -465.809484 0.001679 -2.352565 0.004172 1544 scf: 4 -465.809487 -465.809486 -465.809486 0.000046 -2.352846 0.002335 1545 scf: 5 -465.809487 -465.809486 -465.809486 0.000077 -2.353345 0.000762 1546 1547SCF Convergence by DM+H criterion 1548max |DM_out - DM_in| : 0.0000769218 1549max |H_out - H_in| (eV) : 0.0007618424 1550SCF cycle converged after 5 iterations 1551 1552Using DM_out to compute the final energy and forces 1553No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 1554 1555siesta: E_KS(eV) = -465.8095 1556 1557siesta: Atomic forces (eV/Ang): 1558 1 0.557694 0.213138 -0.061641 1559 2 0.287744 -0.307150 0.023970 1560 3 -0.861960 0.107623 -0.039323 1561---------------------------------------- 1562 Tot -0.016522 0.013611 -0.076993 1563---------------------------------------- 1564 Max 0.861960 1565 Res 0.379190 sqrt( Sum f_i^2 / 3N ) 1566---------------------------------------- 1567 Max 0.861960 constrained 1568 1569Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -3.68 -0.31 -1.08 0.07 -0.24 1.48 1570(Free)E + p*V (eV/cell) -465.3777 1571Target enthalpy (eV/cell) -465.8095 1572 1573siesta: Stress tensor (static) (eV/Ang**3): 1574 -0.002227 0.000767 -0.000108 1575 0.000767 0.000185 0.000016 1576 -0.000110 0.000016 -0.000420 1577 1578siesta: Pressure (static): 1.31503237 kBar 1579 1580siesta: Stress tensor (total) (eV/Ang**3): 1581 -0.002297 0.000926 -0.000148 1582 0.000926 -0.000191 0.000045 1583 -0.000150 0.000045 -0.000674 1584 1585siesta: Pressure (total): 1.68911367 kBar 1586 1587siesta: Temp_ion = 552.124 K 1588 1589 ==================================== 1590 Begin MD step = 10 1591 ==================================== 1592 1593outcoor: Atomic coordinates (Ang): 1594 0.00196437 -0.00418035 0.00348492 1 1 O 1595 0.72486521 0.65272304 -0.00086105 2 2 H 1596 -0.75609514 0.58506128 -0.05480281 2 3 H 1597 1598outcell: Unit cell vectors (Ang): 1599 8.000000 0.000000 0.000000 1600 0.000000 8.000000 0.000000 1601 0.000000 0.000000 6.400000 1602 1603outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 1604outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 1605outcell: Cell volume (Ang**3) : 409.6000 1606<dSpData1D:S at geom step 10 1607 <sparsity:sparsity for geom step 10 1608 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 1609 <dData1D:(new from dSpData1D) n=69, refcount: 1> 1610refcount: 1> 1611new_DM -- step: 10 1612Re-using DM from previous geometries... 1613Number of DMs in history: 1 1614 DM extrapolation coefficients: 16151 1.00000 1616New DM after history re-use: 1617<dSpData2D:SpM extrapolated using coords 1618 <sparsity:sparsity for geom step 10 1619 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 1620 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 1621refcount: 1> 1622No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 1623New grid distribution: 1 1624 1 1: 25 1: 13 1: 5 1625 2 1: 25 1: 13 6: 10 1626 3 1: 25 1: 13 11: 15 1627 4 1: 25 1: 13 16: 20 1628 5 1: 25 14: 25 1: 5 1629 6 1: 25 14: 25 6: 10 1630 7 1: 25 14: 25 11: 15 1631 8 1: 25 14: 25 16: 20 1632 1633InitMesh: MESH = 50 x 50 x 40 = 100000 1634InitMesh: (bp) = 25 x 25 x 20 = 12500 1635InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 1636ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 1637New grid distribution: 2 1638 1 7: 25 6: 25 1: 6 1639 2 7: 25 1: 5 1: 6 1640 3 7: 25 1: 5 7: 20 1641 4 1: 6 1: 5 7: 20 1642 5 1: 6 6: 25 1: 6 1643 6 1: 6 1: 5 1: 6 1644 7 7: 25 6: 25 7: 20 1645 8 1: 6 6: 25 7: 20 1646New grid distribution: 3 1647 1 1: 9 7: 25 1: 7 1648 2 11: 25 1: 6 1: 8 1649 3 1: 9 7: 25 8: 20 1650 4 11: 25 1: 6 9: 20 1651 5 10: 25 7: 25 1: 7 1652 6 1: 10 1: 6 9: 20 1653 7 10: 25 7: 25 8: 20 1654 8 1: 10 1: 6 1: 8 1655Setting up quadratic distribution... 1656ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 1657PhiOnMesh: Number of (b)points on node 0 = 2280 1658PhiOnMesh: nlist on node 0 = 5160 1659 1660 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 1661 scf: 1 -465.828612 -465.807322 -465.807322 0.005784 -2.368610 0.071337 1662 scf: 2 -465.806501 -465.807142 -465.807142 0.002825 -2.412395 0.116778 1663 scf: 3 -465.807536 -465.807432 -465.807432 0.001746 -2.385053 0.003963 1664 scf: 4 -465.807434 -465.807433 -465.807433 0.000047 -2.385347 0.002222 1665 scf: 5 -465.807435 -465.807434 -465.807434 0.000079 -2.385875 0.000768 1666 1667SCF Convergence by DM+H criterion 1668max |DM_out - DM_in| : 0.0000790960 1669max |H_out - H_in| (eV) : 0.0007684553 1670SCF cycle converged after 5 iterations 1671 1672Using DM_out to compute the final energy and forces 1673No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 1674 1675siesta: E_KS(eV) = -465.8074 1676 1677siesta: Atomic forces (eV/Ang): 1678 1 0.572288 0.390264 -0.077252 1679 2 0.218588 -0.403542 0.028940 1680 3 -0.808529 0.033082 -0.037612 1681---------------------------------------- 1682 Tot -0.017653 0.019804 -0.085924 1683---------------------------------------- 1684 Max 0.808529 1685 Res 0.387797 sqrt( Sum f_i^2 / 3N ) 1686---------------------------------------- 1687 Max 0.808529 constrained 1688 1689Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -3.33 0.14 -1.08 0.06 -0.27 1.52 1690(Free)E + p*V (eV/cell) -465.4437 1691Target enthalpy (eV/cell) -465.8074 1692 1693siesta: Stress tensor (static) (eV/Ang**3): 1694 -0.002006 0.000797 -0.000115 1695 0.000797 0.000454 0.000006 1696 -0.000117 0.000006 -0.000421 1697 1698siesta: Pressure (static): 1.05343383 kBar 1699 1700siesta: Stress tensor (total) (eV/Ang**3): 1701 -0.002076 0.000950 -0.000169 1702 0.000949 0.000088 0.000037 1703 -0.000171 0.000037 -0.000676 1704 1705siesta: Pressure (total): 1.42295126 kBar 1706 1707siesta: Temp_ion = 544.184 K 1708 1709 ==================================== 1710 Begin MD step = 11 1711 ==================================== 1712 1713outcoor: Atomic coordinates (Ang): 1714 0.00223876 -0.00464808 0.00386667 1 1 O 1715 0.72203511 0.65983728 -0.00092356 2 2 H 1716 -0.75765021 0.58530755 -0.06095548 2 3 H 1717 1718outcell: Unit cell vectors (Ang): 1719 8.000000 0.000000 0.000000 1720 0.000000 8.000000 0.000000 1721 0.000000 0.000000 6.400000 1722 1723outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 1724outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 1725outcell: Cell volume (Ang**3) : 409.6000 1726<dSpData1D:S at geom step 11 1727 <sparsity:sparsity for geom step 11 1728 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 1729 <dData1D:(new from dSpData1D) n=69, refcount: 1> 1730refcount: 1> 1731new_DM -- step: 11 1732Re-using DM from previous geometries... 1733Number of DMs in history: 1 1734 DM extrapolation coefficients: 17351 1.00000 1736New DM after history re-use: 1737<dSpData2D:SpM extrapolated using coords 1738 <sparsity:sparsity for geom step 11 1739 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 1740 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 1741refcount: 1> 1742No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 1743New grid distribution: 1 1744 1 1: 25 1: 13 1: 5 1745 2 1: 25 1: 13 6: 10 1746 3 1: 25 1: 13 11: 15 1747 4 1: 25 1: 13 16: 20 1748 5 1: 25 14: 25 1: 5 1749 6 1: 25 14: 25 6: 10 1750 7 1: 25 14: 25 11: 15 1751 8 1: 25 14: 25 16: 20 1752 1753InitMesh: MESH = 50 x 50 x 40 = 100000 1754InitMesh: (bp) = 25 x 25 x 20 = 12500 1755InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 1756ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 1757New grid distribution: 2 1758 1 7: 25 6: 25 1: 6 1759 2 7: 25 1: 5 1: 6 1760 3 7: 25 1: 5 7: 20 1761 4 1: 6 1: 5 7: 20 1762 5 1: 6 6: 25 1: 6 1763 6 1: 6 1: 5 1: 6 1764 7 7: 25 6: 25 7: 20 1765 8 1: 6 6: 25 7: 20 1766New grid distribution: 3 1767 1 1: 9 7: 25 1: 7 1768 2 11: 25 1: 6 1: 8 1769 3 1: 9 7: 25 8: 20 1770 4 11: 25 1: 6 9: 20 1771 5 10: 25 7: 25 1: 7 1772 6 1: 10 1: 6 9: 20 1773 7 10: 25 7: 25 8: 20 1774 8 1: 10 1: 6 1: 8 1775Setting up quadratic distribution... 1776ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 1777PhiOnMesh: Number of (b)points on node 0 = 2280 1778PhiOnMesh: nlist on node 0 = 5160 1779 1780 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 1781 scf: 1 -465.827955 -465.804903 -465.804903 0.005820 -2.400206 0.072693 1782 scf: 2 -465.804027 -465.804708 -465.804708 0.002887 -2.444730 0.120153 1783 scf: 3 -465.805125 -465.805015 -465.805015 0.001792 -2.416822 0.003718 1784 scf: 4 -465.805017 -465.805016 -465.805016 0.000048 -2.417122 0.002087 1785 scf: 5 -465.805017 -465.805017 -465.805017 0.000081 -2.417670 0.000765 1786 1787SCF Convergence by DM+H criterion 1788max |DM_out - DM_in| : 0.0000813554 1789max |H_out - H_in| (eV) : 0.0007652749 1790SCF cycle converged after 5 iterations 1791 1792Using DM_out to compute the final energy and forces 1793No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 1794 1795siesta: E_KS(eV) = -465.8050 1796 1797siesta: Atomic forces (eV/Ang): 1798 1 0.572260 0.572324 -0.095260 1799 2 0.150856 -0.498730 0.034146 1800 3 -0.741443 -0.048750 -0.033528 1801---------------------------------------- 1802 Tot -0.018327 0.024844 -0.094642 1803---------------------------------------- 1804 Max 0.741443 1805 Res 0.406886 sqrt( Sum f_i^2 / 3N ) 1806---------------------------------------- 1807 Max 0.741443 constrained 1808 1809Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -2.94 0.61 -1.08 0.04 -0.30 1.53 1810(Free)E + p*V (eV/cell) -465.5142 1811Target enthalpy (eV/cell) -465.8050 1812 1813siesta: Stress tensor (static) (eV/Ang**3): 1814 -0.001763 0.000808 -0.000119 1815 0.000808 0.000735 -0.000008 1816 -0.000120 -0.000008 -0.000420 1817 1818siesta: Pressure (static): 0.77347879 kBar 1819 1820siesta: Stress tensor (total) (eV/Ang**3): 1821 -0.001835 0.000955 -0.000185 1822 0.000955 0.000382 0.000023 1823 -0.000187 0.000023 -0.000677 1824 1825siesta: Pressure (total): 1.13768208 kBar 1826 1827siesta: Temp_ion = 534.844 K 1828 1829 ==================================== 1830 Begin MD step = 12 1831 ==================================== 1832 1833outcoor: Atomic coordinates (Ang): 1834 0.00252685 -0.00510210 0.00424614 1 1 O 1835 0.71926225 0.66676230 -0.00097310 2 2 H 1836 -0.75948657 0.58553533 -0.06712086 2 3 H 1837 1838outcell: Unit cell vectors (Ang): 1839 8.000000 0.000000 0.000000 1840 0.000000 8.000000 0.000000 1841 0.000000 0.000000 6.400000 1842 1843outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 1844outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 1845outcell: Cell volume (Ang**3) : 409.6000 1846<dSpData1D:S at geom step 12 1847 <sparsity:sparsity for geom step 12 1848 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 1849 <dData1D:(new from dSpData1D) n=69, refcount: 1> 1850refcount: 1> 1851new_DM -- step: 12 1852Re-using DM from previous geometries... 1853Number of DMs in history: 1 1854 DM extrapolation coefficients: 18551 1.00000 1856New DM after history re-use: 1857<dSpData2D:SpM extrapolated using coords 1858 <sparsity:sparsity for geom step 12 1859 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 1860 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 1861refcount: 1> 1862No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 1863New grid distribution: 1 1864 1 1: 25 1: 13 1: 5 1865 2 1: 25 1: 13 6: 10 1866 3 1: 25 1: 13 11: 15 1867 4 1: 25 1: 13 16: 20 1868 5 1: 25 14: 25 1: 5 1869 6 1: 25 14: 25 6: 10 1870 7 1: 25 14: 25 11: 15 1871 8 1: 25 14: 25 16: 20 1872 1873InitMesh: MESH = 50 x 50 x 40 = 100000 1874InitMesh: (bp) = 25 x 25 x 20 = 12500 1875InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 1876ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 1877New grid distribution: 2 1878 1 7: 25 6: 25 1: 6 1879 2 7: 25 1: 5 1: 6 1880 3 7: 25 1: 5 7: 20 1881 4 1: 6 1: 5 7: 20 1882 5 1: 6 6: 25 1: 6 1883 6 1: 6 1: 5 1: 6 1884 7 7: 25 6: 25 7: 20 1885 8 1: 6 6: 25 7: 20 1886New grid distribution: 3 1887 1 1: 9 7: 25 1: 7 1888 2 11: 25 1: 6 1: 8 1889 3 1: 9 7: 25 8: 20 1890 4 11: 25 1: 6 9: 20 1891 5 10: 25 7: 25 1: 7 1892 6 1: 10 1: 6 9: 20 1893 7 10: 25 7: 25 8: 20 1894 8 1: 10 1: 6 1: 8 1895Setting up quadratic distribution... 1896ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 1897PhiOnMesh: Number of (b)points on node 0 = 2280 1898PhiOnMesh: nlist on node 0 = 5162 1899 1900 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 1901 scf: 1 -465.826408 -465.802068 -465.802068 0.005850 -2.431079 0.073161 1902 scf: 2 -465.801165 -465.801868 -465.801868 0.002914 -2.475795 0.122029 1903 scf: 3 -465.802293 -465.802179 -465.802179 0.001815 -2.447669 0.003446 1904 scf: 4 -465.802182 -465.802181 -465.802181 0.000048 -2.447971 0.001936 1905 scf: 5 -465.802182 -465.802181 -465.802181 0.000084 -2.448529 0.000752 1906 1907SCF Convergence by DM+H criterion 1908max |DM_out - DM_in| : 0.0000836940 1909max |H_out - H_in| (eV) : 0.0007523455 1910SCF cycle converged after 5 iterations 1911 1912Using DM_out to compute the final energy and forces 1913No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 1914 1915siesta: E_KS(eV) = -465.8022 1916 1917siesta: Atomic forces (eV/Ang): 1918 1 0.558659 0.756315 -0.115186 1919 2 0.085976 -0.591018 0.039513 1920 3 -0.662915 -0.136258 -0.027047 1921---------------------------------------- 1922 Tot -0.018280 0.029038 -0.102720 1923---------------------------------------- 1924 Max 0.756315 1925 Res 0.436449 sqrt( Sum f_i^2 / 3N ) 1926---------------------------------------- 1927 Max 0.756315 constrained 1928 1929Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -2.53 1.10 -1.08 0.01 -0.32 1.51 1930(Free)E + p*V (eV/cell) -465.5882 1931Target enthalpy (eV/cell) -465.8022 1932 1933siesta: Stress tensor (static) (eV/Ang**3): 1934 -0.001499 0.000801 -0.000118 1935 0.000801 0.001022 -0.000025 1936 -0.000119 -0.000025 -0.000419 1937 1938siesta: Pressure (static): 0.47908955 kBar 1939 1940siesta: Stress tensor (total) (eV/Ang**3): 1941 -0.001576 0.000942 -0.000196 1942 0.000942 0.000685 0.000005 1943 -0.000198 0.000005 -0.000676 1944 1945siesta: Pressure (total): 0.83704156 kBar 1946 1947siesta: Temp_ion = 523.909 K 1948 1949 ==================================== 1950 Begin MD step = 13 1951 ==================================== 1952 1953outcoor: Atomic coordinates (Ang): 1954 0.00282832 -0.00553801 0.00462286 1 1 O 1955 0.71652200 0.67346312 -0.00100766 2 2 H 1956 -0.76157441 0.58571142 -0.07329651 2 3 H 1957 1958outcell: Unit cell vectors (Ang): 1959 8.000000 0.000000 0.000000 1960 0.000000 8.000000 0.000000 1961 0.000000 0.000000 6.400000 1962 1963outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 1964outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 1965outcell: Cell volume (Ang**3) : 409.6000 1966<dSpData1D:S at geom step 13 1967 <sparsity:sparsity for geom step 13 1968 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 1969 <dData1D:(new from dSpData1D) n=69, refcount: 1> 1970refcount: 1> 1971new_DM -- step: 13 1972Re-using DM from previous geometries... 1973Number of DMs in history: 1 1974 DM extrapolation coefficients: 19751 1.00000 1976New DM after history re-use: 1977<dSpData2D:SpM extrapolated using coords 1978 <sparsity:sparsity for geom step 13 1979 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 1980 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 1981refcount: 1> 1982No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 1983New grid distribution: 1 1984 1 1: 25 1: 13 1: 5 1985 2 1: 25 1: 13 6: 10 1986 3 1: 25 1: 13 11: 15 1987 4 1: 25 1: 13 16: 20 1988 5 1: 25 14: 25 1: 5 1989 6 1: 25 14: 25 6: 10 1990 7 1: 25 14: 25 11: 15 1991 8 1: 25 14: 25 16: 20 1992 1993InitMesh: MESH = 50 x 50 x 40 = 100000 1994InitMesh: (bp) = 25 x 25 x 20 = 12500 1995InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 1996ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 1997New grid distribution: 2 1998 1 7: 25 6: 25 1: 6 1999 2 7: 25 1: 5 1: 6 2000 3 7: 25 1: 5 7: 20 2001 4 1: 6 1: 5 7: 20 2002 5 1: 6 6: 25 1: 6 2003 6 1: 6 1: 5 1: 6 2004 7 7: 25 6: 25 7: 20 2005 8 1: 6 6: 25 7: 20 2006New grid distribution: 3 2007 1 10: 25 7: 25 1: 8 2008 2 1: 9 7: 25 1: 7 2009 3 11: 25 1: 6 9: 20 2010 4 11: 25 1: 6 1: 8 2011 5 1: 10 1: 6 9: 20 2012 6 1: 10 1: 6 1: 8 2013 7 10: 25 7: 25 9: 20 2014 8 1: 9 7: 25 8: 20 2015Setting up quadratic distribution... 2016ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 2017PhiOnMesh: Number of (b)points on node 0 = 2280 2018PhiOnMesh: nlist on node 0 = 5158 2019 2020 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 2021 scf: 1 -465.823934 -465.798801 -465.798801 0.005874 -2.461036 0.072715 2022 scf: 2 -465.797889 -465.798598 -465.798598 0.002902 -2.505386 0.122330 2023 scf: 3 -465.799030 -465.798917 -465.798917 0.001815 -2.477399 0.003155 2024 scf: 4 -465.798919 -465.798918 -465.798918 0.000049 -2.477697 0.001774 2025 scf: 5 -465.798919 -465.798918 -465.798918 0.000086 -2.478257 0.000730 2026 2027SCF Convergence by DM+H criterion 2028max |DM_out - DM_in| : 0.0000860883 2029max |H_out - H_in| (eV) : 0.0007303893 2030SCF cycle converged after 5 iterations 2031 2032Using DM_out to compute the final energy and forces 2033No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 2034 2035siesta: E_KS(eV) = -465.7989 2036 2037siesta: Atomic forces (eV/Ang): 2038 1 0.531276 0.938771 -0.137353 2039 2 0.025241 -0.678896 0.044988 2040 3 -0.575759 -0.227602 -0.018238 2041---------------------------------------- 2042 Tot -0.019242 0.032272 -0.110603 2043---------------------------------------- 2044 Max 0.938771 2045 Res 0.474881 sqrt( Sum f_i^2 / 3N ) 2046---------------------------------------- 2047 Max 0.938771 constrained 2048 2049Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -2.11 1.59 -1.08 -0.03 -0.33 1.46 2050(Free)E + p*V (eV/cell) -465.6630 2051Target enthalpy (eV/cell) -465.7989 2052 2053siesta: Stress tensor (static) (eV/Ang**3): 2054 -0.001232 0.000776 -0.000113 2055 0.000776 0.001310 -0.000045 2056 -0.000114 -0.000045 -0.000417 2057 2058siesta: Pressure (static): 0.18102095 kBar 2059 2060siesta: Stress tensor (total) (eV/Ang**3): 2061 -0.001314 0.000911 -0.000202 2062 0.000911 0.000993 -0.000018 2063 -0.000204 -0.000018 -0.000674 2064 2065siesta: Pressure (total): 0.53165483 kBar 2066 2067siesta: Temp_ion = 511.306 K 2068 2069 ==================================== 2070 Begin MD step = 14 2071 ==================================== 2072 2073outcoor: Atomic coordinates (Ang): 2074 0.00314252 -0.00595143 0.00499628 1 1 O 2075 0.71379133 0.67990638 -0.00102515 2 2 H 2076 -0.76388068 0.58580116 -0.07947908 2 3 H 2077 2078outcell: Unit cell vectors (Ang): 2079 8.000000 0.000000 0.000000 2080 0.000000 8.000000 0.000000 2081 0.000000 0.000000 6.400000 2082 2083outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 2084outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 2085outcell: Cell volume (Ang**3) : 409.6000 2086<dSpData1D:S at geom step 14 2087 <sparsity:sparsity for geom step 14 2088 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 2089 <dData1D:(new from dSpData1D) n=69, refcount: 1> 2090refcount: 1> 2091new_DM -- step: 14 2092Re-using DM from previous geometries... 2093Number of DMs in history: 1 2094 DM extrapolation coefficients: 20951 1.00000 2096New DM after history re-use: 2097<dSpData2D:SpM extrapolated using coords 2098 <sparsity:sparsity for geom step 14 2099 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 2100 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 2101refcount: 1> 2102No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 2103New grid distribution: 1 2104 1 1: 25 1: 13 1: 5 2105 2 1: 25 1: 13 6: 10 2106 3 1: 25 1: 13 11: 15 2107 4 1: 25 1: 13 16: 20 2108 5 1: 25 14: 25 1: 5 2109 6 1: 25 14: 25 6: 10 2110 7 1: 25 14: 25 11: 15 2111 8 1: 25 14: 25 16: 20 2112 2113InitMesh: MESH = 50 x 50 x 40 = 100000 2114InitMesh: (bp) = 25 x 25 x 20 = 12500 2115InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 2116ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 2117New grid distribution: 2 2118 1 7: 25 6: 25 1: 6 2119 2 7: 25 1: 5 1: 6 2120 3 7: 25 1: 5 7: 20 2121 4 1: 6 1: 5 7: 20 2122 5 1: 6 6: 25 1: 6 2123 6 1: 6 1: 5 1: 6 2124 7 7: 25 6: 25 7: 20 2125 8 1: 6 6: 25 7: 20 2126New grid distribution: 3 2127 1 10: 25 7: 25 1: 8 2128 2 1: 9 7: 25 1: 7 2129 3 11: 25 1: 6 9: 20 2130 4 11: 25 1: 6 1: 8 2131 5 1: 10 1: 6 9: 20 2132 6 1: 10 1: 6 1: 8 2133 7 10: 25 7: 25 9: 20 2134 8 1: 9 7: 25 8: 20 2135Setting up quadratic distribution... 2136ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 2137PhiOnMesh: Number of (b)points on node 0 = 2280 2138PhiOnMesh: nlist on node 0 = 5158 2139 2140 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 2141 scf: 1 -465.820558 -465.795135 -465.795135 0.005891 -2.489876 0.071339 2142 scf: 2 -465.794227 -465.794922 -465.794922 0.002851 -2.533297 0.120993 2143 scf: 3 -465.795351 -465.795240 -465.795240 0.001789 -2.505813 0.003006 2144 scf: 4 -465.795242 -465.795241 -465.795241 0.000050 -2.506101 0.001746 2145 scf: 5 -465.795242 -465.795242 -465.795242 0.000088 -2.506652 0.000700 2146 2147SCF Convergence by DM+H criterion 2148max |DM_out - DM_in| : 0.0000884347 2149max |H_out - H_in| (eV) : 0.0006997261 2150SCF cycle converged after 5 iterations 2151 2152Using DM_out to compute the final energy and forces 2153No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 2154 2155siesta: E_KS(eV) = -465.7952 2156 2157siesta: Atomic forces (eV/Ang): 2158 1 0.492001 1.116680 -0.161843 2159 2 -0.030291 -0.760960 0.050512 2160 3 -0.481563 -0.321035 -0.007178 2161---------------------------------------- 2162 Tot -0.019853 0.034685 -0.118509 2163---------------------------------------- 2164 Max 1.116680 2165 Res 0.519912 sqrt( Sum f_i^2 / 3N ) 2166---------------------------------------- 2167 Max 1.116680 constrained 2168 2169Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -1.68 2.08 -1.08 -0.08 -0.33 1.38 2170(Free)E + p*V (eV/cell) -465.7378 2171Target enthalpy (eV/cell) -465.7952 2172 2173siesta: Stress tensor (static) (eV/Ang**3): 2174 -0.000959 0.000734 -0.000103 2175 0.000734 0.001593 -0.000070 2176 -0.000105 -0.000070 -0.000414 2177 2178siesta: Pressure (static): -0.11733489 kBar 2179 2180siesta: Stress tensor (total) (eV/Ang**3): 2181 -0.001048 0.000864 -0.000202 2182 0.000863 0.001299 -0.000047 2183 -0.000204 -0.000047 -0.000672 2184 2185siesta: Pressure (total): 0.22486389 kBar 2186 2187siesta: Temp_ion = 497.089 K 2188 2189 ==================================== 2190 Begin MD step = 15 2191 ==================================== 2192 2193outcoor: Atomic coordinates (Ang): 2194 0.00346850 -0.00633812 0.00536583 1 1 O 2195 0.71104917 0.68606096 -0.00102348 2 2 H 2196 -0.76636963 0.58576911 -0.08566438 2 3 H 2197 2198outcell: Unit cell vectors (Ang): 2199 8.000000 0.000000 0.000000 2200 0.000000 8.000000 0.000000 2201 0.000000 0.000000 6.400000 2202 2203outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 2204outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 2205outcell: Cell volume (Ang**3) : 409.6000 2206<dSpData1D:S at geom step 15 2207 <sparsity:sparsity for geom step 15 2208 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 2209 <dData1D:(new from dSpData1D) n=69, refcount: 1> 2210refcount: 1> 2211new_DM -- step: 15 2212Re-using DM from previous geometries... 2213Number of DMs in history: 1 2214 DM extrapolation coefficients: 22151 1.00000 2216New DM after history re-use: 2217<dSpData2D:SpM extrapolated using coords 2218 <sparsity:sparsity for geom step 15 2219 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 2220 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 2221refcount: 1> 2222No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 2223New grid distribution: 1 2224 1 1: 25 1: 13 1: 5 2225 2 1: 25 1: 13 6: 10 2226 3 1: 25 1: 13 11: 15 2227 4 1: 25 1: 13 16: 20 2228 5 1: 25 14: 25 1: 5 2229 6 1: 25 14: 25 6: 10 2230 7 1: 25 14: 25 11: 15 2231 8 1: 25 14: 25 16: 20 2232 2233InitMesh: MESH = 50 x 50 x 40 = 100000 2234InitMesh: (bp) = 25 x 25 x 20 = 12500 2235InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 2236ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 2237New grid distribution: 2 2238 1 7: 25 6: 25 1: 6 2239 2 7: 25 1: 5 1: 6 2240 3 7: 25 1: 5 7: 20 2241 4 1: 6 1: 5 7: 20 2242 5 1: 6 6: 25 1: 6 2243 6 1: 6 1: 5 1: 6 2244 7 7: 25 6: 25 7: 20 2245 8 1: 6 6: 25 7: 20 2246New grid distribution: 3 2247 1 10: 25 7: 25 1: 8 2248 2 1: 9 7: 25 1: 7 2249 3 11: 25 1: 6 1: 12 2250 4 11: 25 1: 6 13: 20 2251 5 1: 10 1: 6 9: 20 2252 6 1: 10 1: 6 1: 8 2253 7 10: 25 7: 25 9: 20 2254 8 1: 9 7: 25 8: 20 2255Setting up quadratic distribution... 2256ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 2257PhiOnMesh: Number of (b)points on node 0 = 2280 2258PhiOnMesh: nlist on node 0 = 5154 2259 2260 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 2261 scf: 1 -465.816314 -465.791102 -465.791102 0.005900 -2.517391 0.069033 2262 scf: 2 -465.790246 -465.790909 -465.790909 0.002759 -2.559326 0.117979 2263 scf: 3 -465.791306 -465.791201 -465.791201 0.001738 -2.532710 0.002962 2264 scf: 4 -465.791202 -465.791202 -465.791202 0.000051 -2.532983 0.001759 2265 scf: 5 -465.791203 -465.791202 -465.791202 0.000091 -2.533516 0.000662 2266 2267SCF Convergence by DM+H criterion 2268max |DM_out - DM_in| : 0.0000907306 2269max |H_out - H_in| (eV) : 0.0006619509 2270SCF cycle converged after 5 iterations 2271 2272Using DM_out to compute the final energy and forces 2273No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 2274 2275siesta: E_KS(eV) = -465.7912 2276 2277siesta: Atomic forces (eV/Ang): 2278 1 0.441830 1.287286 -0.188179 2279 2 -0.079310 -0.835948 0.056041 2280 3 -0.383245 -0.414763 0.005803 2281---------------------------------------- 2282 Tot -0.020724 0.036575 -0.126335 2283---------------------------------------- 2284 Max 1.287286 2285 Res 0.569103 sqrt( Sum f_i^2 / 3N ) 2286---------------------------------------- 2287 Max 1.287286 constrained 2288 2289Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -1.26 2.56 -1.07 -0.13 -0.32 1.28 2290(Free)E + p*V (eV/cell) -465.8105 2291Target enthalpy (eV/cell) -465.7912 2292 2293siesta: Stress tensor (static) (eV/Ang**3): 2294 -0.000692 0.000676 -0.000090 2295 0.000676 0.001866 -0.000097 2296 -0.000092 -0.000097 -0.000410 2297 2298siesta: Pressure (static): -0.40809477 kBar 2299 2300siesta: Stress tensor (total) (eV/Ang**3): 2301 -0.000787 0.000799 -0.000197 2302 0.000799 0.001596 -0.000081 2303 -0.000199 -0.000081 -0.000669 2304 2305siesta: Pressure (total): -0.07541061 kBar 2306 2307siesta: Temp_ion = 481.452 K 2308 2309 ==================================== 2310 Begin MD step = 16 2311 ==================================== 2312 2313outcoor: Atomic coordinates (Ang): 2314 0.00380505 -0.00669398 0.00573087 1 1 O 2315 0.70827692 0.69189841 -0.00100055 2 2 H 2316 -0.76900398 0.58557972 -0.09184747 2 3 H 2317 2318outcell: Unit cell vectors (Ang): 2319 8.000000 0.000000 0.000000 2320 0.000000 8.000000 0.000000 2321 0.000000 0.000000 6.400000 2322 2323outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 2324outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 2325outcell: Cell volume (Ang**3) : 409.6000 2326<dSpData1D:S at geom step 16 2327 <sparsity:sparsity for geom step 16 2328 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 2329 <dData1D:(new from dSpData1D) n=69, refcount: 1> 2330refcount: 1> 2331new_DM -- step: 16 2332Re-using DM from previous geometries... 2333Number of DMs in history: 1 2334 DM extrapolation coefficients: 23351 1.00000 2336New DM after history re-use: 2337<dSpData2D:SpM extrapolated using coords 2338 <sparsity:sparsity for geom step 16 2339 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 2340 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 2341refcount: 1> 2342No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 2343New grid distribution: 1 2344 1 1: 25 1: 13 1: 5 2345 2 1: 25 1: 13 6: 10 2346 3 1: 25 1: 13 11: 15 2347 4 1: 25 1: 13 16: 20 2348 5 1: 25 14: 25 1: 5 2349 6 1: 25 14: 25 6: 10 2350 7 1: 25 14: 25 11: 15 2351 8 1: 25 14: 25 16: 20 2352 2353InitMesh: MESH = 50 x 50 x 40 = 100000 2354InitMesh: (bp) = 25 x 25 x 20 = 12500 2355InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 2356ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 2357New grid distribution: 2 2358 1 7: 25 6: 25 1: 6 2359 2 7: 25 1: 5 1: 6 2360 3 7: 25 1: 5 7: 20 2361 4 1: 6 1: 5 7: 20 2362 5 1: 6 6: 25 1: 6 2363 6 1: 6 1: 5 1: 6 2364 7 7: 25 6: 25 7: 20 2365 8 1: 6 6: 25 7: 20 2366New grid distribution: 3 2367 1 10: 25 7: 25 1: 9 2368 2 1: 9 7: 25 1: 7 2369 3 11: 25 1: 6 1: 12 2370 4 11: 25 1: 6 13: 20 2371 5 1: 10 1: 6 9: 20 2372 6 1: 10 1: 6 1: 8 2373 7 10: 25 7: 25 10: 20 2374 8 1: 9 7: 25 8: 20 2375Setting up quadratic distribution... 2376ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 2377PhiOnMesh: Number of (b)points on node 0 = 2280 2378PhiOnMesh: nlist on node 0 = 5150 2379 2380 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 2381 scf: 1 -465.811301 -465.786787 -465.786787 0.005905 -2.543370 0.065815 2382 scf: 2 -465.785995 -465.786608 -465.786608 0.002629 -2.583279 0.113293 2383 scf: 3 -465.786974 -465.786877 -465.786877 0.001662 -2.557886 0.002915 2384 scf: 4 -465.786878 -465.786878 -465.786878 0.000051 -2.558141 0.001769 2385 scf: 5 -465.786879 -465.786878 -465.786878 0.000093 -2.558646 0.000618 2386 2387SCF Convergence by DM+H criterion 2388max |DM_out - DM_in| : 0.0000928756 2389max |H_out - H_in| (eV) : 0.0006183721 2390SCF cycle converged after 5 iterations 2391 2392Using DM_out to compute the final energy and forces 2393No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 2394 2395siesta: E_KS(eV) = -465.7869 2396 2397siesta: Atomic forces (eV/Ang): 2398 1 0.383104 1.447635 -0.215601 2399 2 -0.121575 -0.902798 0.061472 2400 3 -0.282922 -0.507135 0.020484 2401---------------------------------------- 2402 Tot -0.021394 0.037702 -0.133645 2403---------------------------------------- 2404 Max 1.447635 2405 Res 0.620050 sqrt( Sum f_i^2 / 3N ) 2406---------------------------------------- 2407 Max 1.447635 constrained 2408 2409Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -0.85 3.01 -1.06 -0.19 -0.30 1.16 2410(Free)E + p*V (eV/cell) -465.8802 2411Target enthalpy (eV/cell) -465.7869 2412 2413siesta: Stress tensor (static) (eV/Ang**3): 2414 -0.000431 0.000605 -0.000074 2415 0.000605 0.002124 -0.000127 2416 -0.000076 -0.000127 -0.000406 2417 2418siesta: Pressure (static): -0.68729157 kBar 2419 2420siesta: Stress tensor (total) (eV/Ang**3): 2421 -0.000533 0.000721 -0.000187 2422 0.000721 0.001880 -0.000118 2423 -0.000189 -0.000118 -0.000664 2424 2425siesta: Pressure (total): -0.36507305 kBar 2426 2427siesta: Temp_ion = 464.721 K 2428 2429 ==================================== 2430 Begin MD step = 17 2431 ==================================== 2432 2433outcoor: Atomic coordinates (Ang): 2434 0.00415079 -0.00701517 0.00609075 1 1 O 2435 0.70545855 0.69739337 -0.00095429 2 2 H 2436 -0.77174566 0.58519793 -0.09802279 2 3 H 2437 2438outcell: Unit cell vectors (Ang): 2439 8.000000 0.000000 0.000000 2440 0.000000 8.000000 0.000000 2441 0.000000 0.000000 6.400000 2442 2443outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 2444outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 2445outcell: Cell volume (Ang**3) : 409.6000 2446<dSpData1D:S at geom step 17 2447 <sparsity:sparsity for geom step 17 2448 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 2449 <dData1D:(new from dSpData1D) n=69, refcount: 1> 2450refcount: 1> 2451new_DM -- step: 17 2452Re-using DM from previous geometries... 2453Number of DMs in history: 1 2454 DM extrapolation coefficients: 24551 1.00000 2456New DM after history re-use: 2457<dSpData2D:SpM extrapolated using coords 2458 <sparsity:sparsity for geom step 17 2459 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 2460 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 2461refcount: 1> 2462No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 2463New grid distribution: 1 2464 1 1: 25 1: 13 1: 5 2465 2 1: 25 1: 13 6: 10 2466 3 1: 25 1: 13 11: 15 2467 4 1: 25 1: 13 16: 20 2468 5 1: 25 14: 25 1: 5 2469 6 1: 25 14: 25 6: 10 2470 7 1: 25 14: 25 11: 15 2471 8 1: 25 14: 25 16: 20 2472 2473InitMesh: MESH = 50 x 50 x 40 = 100000 2474InitMesh: (bp) = 25 x 25 x 20 = 12500 2475InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 2476ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 2477New grid distribution: 2 2478 1 7: 25 6: 25 1: 6 2479 2 7: 25 1: 5 1: 6 2480 3 7: 25 1: 5 7: 20 2481 4 1: 6 1: 5 7: 20 2482 5 1: 6 6: 25 1: 6 2483 6 1: 6 1: 5 1: 6 2484 7 7: 25 6: 25 7: 20 2485 8 1: 6 6: 25 7: 20 2486New grid distribution: 3 2487 1 10: 25 7: 25 1: 9 2488 2 1: 9 7: 25 1: 7 2489 3 11: 25 1: 6 1: 12 2490 4 11: 25 1: 6 13: 20 2491 5 1: 10 1: 6 9: 20 2492 6 1: 10 1: 6 1: 8 2493 7 10: 25 7: 25 10: 20 2494 8 1: 9 7: 25 8: 20 2495Setting up quadratic distribution... 2496ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 2497PhiOnMesh: Number of (b)points on node 0 = 2280 2498PhiOnMesh: nlist on node 0 = 5157 2499 2500 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 2501 scf: 1 -465.805658 -465.782304 -465.782304 0.005902 -2.567614 0.061722 2502 scf: 2 -465.781591 -465.782138 -465.782138 0.002460 -2.604980 0.106968 2503 scf: 3 -465.782470 -465.782384 -465.782384 0.001560 -2.581151 0.002864 2504 scf: 4 -465.782385 -465.782385 -465.782385 0.000052 -2.581384 0.001776 2505 scf: 5 -465.782386 -465.782385 -465.782385 0.000095 -2.581854 0.000571 2506 2507SCF Convergence by DM+H criterion 2508max |DM_out - DM_in| : 0.0000947792 2509max |H_out - H_in| (eV) : 0.0005705775 2510SCF cycle converged after 5 iterations 2511 2512Using DM_out to compute the final energy and forces 2513No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 2514 2515siesta: E_KS(eV) = -465.7824 2516 2517siesta: Atomic forces (eV/Ang): 2518 1 0.316990 1.595820 -0.244320 2519 2 -0.156118 -0.960644 0.066821 2520 3 -0.182932 -0.596518 0.036395 2521---------------------------------------- 2522 Tot -0.022060 0.038658 -0.141104 2523---------------------------------------- 2524 Max 1.595820 2525 Res 0.670747 sqrt( Sum f_i^2 / 3N ) 2526---------------------------------------- 2527 Max 1.595820 constrained 2528 2529Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -0.47 3.44 -1.06 -0.25 -0.28 1.01 2530(Free)E + p*V (eV/cell) -465.9455 2531Target enthalpy (eV/cell) -465.7824 2532 2533siesta: Stress tensor (static) (eV/Ang**3): 2534 -0.000185 0.000523 -0.000055 2535 0.000523 0.002364 -0.000158 2536 -0.000056 -0.000158 -0.000402 2537 2538siesta: Pressure (static): -0.94922559 kBar 2539 2540siesta: Stress tensor (total) (eV/Ang**3): 2541 -0.000293 0.000631 -0.000173 2542 0.000631 0.002147 -0.000158 2543 -0.000175 -0.000158 -0.000659 2544 2545siesta: Pressure (total): -0.63820445 kBar 2546 2547siesta: Temp_ion = 447.340 K 2548 2549 ==================================== 2550 Begin MD step = 18 2551 ==================================== 2552 2553outcoor: Atomic coordinates (Ang): 2554 0.00450411 -0.00729815 0.00644477 1 1 O 2555 0.70258095 0.70252389 -0.00088269 2 2 H 2556 -0.77455674 0.58458985 -0.10418430 2 3 H 2557 2558outcell: Unit cell vectors (Ang): 2559 8.000000 0.000000 0.000000 2560 0.000000 8.000000 0.000000 2561 0.000000 0.000000 6.400000 2562 2563outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 2564outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 2565outcell: Cell volume (Ang**3) : 409.6000 2566<dSpData1D:S at geom step 18 2567 <sparsity:sparsity for geom step 18 2568 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 2569 <dData1D:(new from dSpData1D) n=69, refcount: 1> 2570refcount: 1> 2571new_DM -- step: 18 2572Re-using DM from previous geometries... 2573Number of DMs in history: 1 2574 DM extrapolation coefficients: 25751 1.00000 2576New DM after history re-use: 2577<dSpData2D:SpM extrapolated using coords 2578 <sparsity:sparsity for geom step 18 2579 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 2580 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 2581refcount: 1> 2582No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 2583New grid distribution: 1 2584 1 1: 25 1: 13 1: 5 2585 2 1: 25 1: 13 6: 10 2586 3 1: 25 1: 13 11: 15 2587 4 1: 25 1: 13 16: 20 2588 5 1: 25 14: 25 1: 5 2589 6 1: 25 14: 25 6: 10 2590 7 1: 25 14: 25 11: 15 2591 8 1: 25 14: 25 16: 20 2592 2593InitMesh: MESH = 50 x 50 x 40 = 100000 2594InitMesh: (bp) = 25 x 25 x 20 = 12500 2595InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 2596ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 2597New grid distribution: 2 2598 1 7: 25 6: 25 1: 6 2599 2 7: 25 1: 5 1: 6 2600 3 7: 25 1: 5 7: 20 2601 4 1: 6 1: 5 7: 20 2602 5 1: 6 6: 25 1: 6 2603 6 1: 6 1: 5 1: 6 2604 7 7: 25 6: 25 7: 20 2605 8 1: 6 6: 25 7: 20 2606New grid distribution: 3 2607 1 1: 9 7: 25 1: 7 2608 2 11: 25 1: 6 1: 12 2609 3 11: 25 1: 6 13: 20 2610 4 10: 25 7: 25 12: 20 2611 5 10: 25 7: 25 1: 11 2612 6 1: 10 1: 6 9: 20 2613 7 1: 9 7: 25 8: 20 2614 8 1: 10 1: 6 1: 8 2615Setting up quadratic distribution... 2616ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 2617PhiOnMesh: Number of (b)points on node 0 = 2280 2618PhiOnMesh: nlist on node 0 = 5152 2619 2620 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 2621 scf: 1 -465.799542 -465.777779 -465.777779 0.005893 -2.589914 0.056799 2622 scf: 2 -465.777167 -465.777637 -465.777637 0.002254 -2.624252 0.099058 2623 scf: 3 -465.777921 -465.777848 -465.777848 0.001435 -2.602313 0.002811 2624 scf: 4 -465.777849 -465.777848 -465.777848 0.000052 -2.602521 0.001779 2625 scf: 5 -465.777849 -465.777849 -465.777849 0.000096 -2.602948 0.000520 2626 2627SCF Convergence by DM+H criterion 2628max |DM_out - DM_in| : 0.0000963363 2629max |H_out - H_in| (eV) : 0.0005203030 2630SCF cycle converged after 5 iterations 2631 2632Using DM_out to compute the final energy and forces 2633No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 2634 2635siesta: E_KS(eV) = -465.7778 2636 2637siesta: Atomic forces (eV/Ang): 2638 1 0.244244 1.730244 -0.274173 2639 2 -0.182636 -1.008848 0.072004 2640 3 -0.084690 -0.681752 0.053367 2641---------------------------------------- 2642 Tot -0.023082 0.039645 -0.148802 2643---------------------------------------- 2644 Max 1.730244 2645 Res 0.719544 sqrt( Sum f_i^2 / 3N ) 2646---------------------------------------- 2647 Max 1.730244 constrained 2648 2649Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -0.11 3.83 -1.04 -0.32 -0.25 0.85 2650(Free)E + p*V (eV/cell) -466.0066 2651Target enthalpy (eV/cell) -465.7778 2652 2653siesta: Stress tensor (static) (eV/Ang**3): 2654 0.000047 0.000429 -0.000032 2655 0.000429 0.002583 -0.000191 2656 -0.000033 -0.000191 -0.000394 2657 2658siesta: Pressure (static): -1.19398292 kBar 2659 2660siesta: Stress tensor (total) (eV/Ang**3): 2661 -0.000066 0.000527 -0.000153 2662 0.000527 0.002392 -0.000202 2663 -0.000154 -0.000202 -0.000651 2664 2665siesta: Pressure (total): -0.89459372 kBar 2666 2667siesta: Temp_ion = 429.838 K 2668 2669 ==================================== 2670 Begin MD step = 19 2671 ==================================== 2672 2673outcoor: Atomic coordinates (Ang): 2674 0.00486329 -0.00753969 0.00679223 1 1 O 2675 0.69963406 0.70727168 -0.00078377 2 2 H 2676 -0.77739994 0.58372313 -0.11032556 2 3 H 2677 2678outcell: Unit cell vectors (Ang): 2679 8.000000 0.000000 0.000000 2680 0.000000 8.000000 0.000000 2681 0.000000 0.000000 6.400000 2682 2683outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 2684outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 2685outcell: Cell volume (Ang**3) : 409.6000 2686<dSpData1D:S at geom step 19 2687 <sparsity:sparsity for geom step 19 2688 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 2689 <dData1D:(new from dSpData1D) n=69, refcount: 1> 2690refcount: 1> 2691new_DM -- step: 19 2692Re-using DM from previous geometries... 2693Number of DMs in history: 1 2694 DM extrapolation coefficients: 26951 1.00000 2696New DM after history re-use: 2697<dSpData2D:SpM extrapolated using coords 2698 <sparsity:sparsity for geom step 19 2699 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 2700 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 2701refcount: 1> 2702No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 2703New grid distribution: 1 2704 1 1: 25 1: 13 1: 5 2705 2 1: 25 1: 13 6: 10 2706 3 1: 25 1: 13 11: 15 2707 4 1: 25 1: 13 16: 20 2708 5 1: 25 14: 25 1: 5 2709 6 1: 25 14: 25 6: 10 2710 7 1: 25 14: 25 11: 15 2711 8 1: 25 14: 25 16: 20 2712 2713InitMesh: MESH = 50 x 50 x 40 = 100000 2714InitMesh: (bp) = 25 x 25 x 20 = 12500 2715InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 2716ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 2717New grid distribution: 2 2718 1 7: 25 6: 25 1: 6 2719 2 7: 25 1: 5 1: 6 2720 3 7: 25 1: 5 7: 20 2721 4 1: 6 1: 5 7: 20 2722 5 1: 6 6: 25 1: 6 2723 6 1: 6 1: 5 1: 6 2724 7 7: 25 6: 25 7: 20 2725 8 1: 6 6: 25 7: 20 2726New grid distribution: 3 2727 1 1: 9 7: 25 1: 7 2728 2 11: 25 1: 6 1: 12 2729 3 11: 25 1: 6 13: 20 2730 4 10: 25 7: 25 13: 20 2731 5 10: 25 7: 25 1: 12 2732 6 1: 10 1: 6 9: 20 2733 7 1: 9 7: 25 8: 20 2734 8 1: 10 1: 6 1: 8 2735Setting up quadratic distribution... 2736ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 2737PhiOnMesh: Number of (b)points on node 0 = 2280 2738PhiOnMesh: nlist on node 0 = 5141 2739 2740 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 2741 scf: 1 -465.793155 -465.773378 -465.773378 0.005878 -2.610080 0.051107 2742 scf: 2 -465.772876 -465.773261 -465.773261 0.002014 -2.640942 0.089660 2743 scf: 3 -465.773495 -465.773435 -465.773435 0.001287 -2.621195 0.002754 2744 scf: 4 -465.773436 -465.773435 -465.773435 0.000053 -2.621374 0.001778 2745 scf: 5 -465.773436 -465.773436 -465.773436 0.000097 -2.621749 0.000469 2746 2747SCF Convergence by DM+H criterion 2748max |DM_out - DM_in| : 0.0000974537 2749max |H_out - H_in| (eV) : 0.0004688341 2750SCF cycle converged after 5 iterations 2751 2752Using DM_out to compute the final energy and forces 2753No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 2754 2755siesta: E_KS(eV) = -465.7734 2756 2757siesta: Atomic forces (eV/Ang): 2758 1 0.167116 1.848366 -0.304309 2759 2 -0.200929 -1.046859 0.077013 2760 3 0.009704 -0.761478 0.070813 2761---------------------------------------- 2762 Tot -0.024108 0.040029 -0.156483 2763---------------------------------------- 2764 Max 1.848366 2765 Res 0.764792 sqrt( Sum f_i^2 / 3N ) 2766---------------------------------------- 2767 Max 1.848366 constrained 2768 2769Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 0.23 4.18 -1.03 -0.40 -0.21 0.67 2770(Free)E + p*V (eV/cell) -466.0612 2771Target enthalpy (eV/cell) -465.7734 2772 2773siesta: Stress tensor (static) (eV/Ang**3): 2774 0.000259 0.000328 -0.000007 2775 0.000328 0.002774 -0.000226 2776 -0.000008 -0.000226 -0.000387 2777 2778siesta: Pressure (static): -1.41337462 kBar 2779 2780siesta: Stress tensor (total) (eV/Ang**3): 2781 0.000141 0.000416 -0.000129 2782 0.000416 0.002608 -0.000248 2783 -0.000130 -0.000248 -0.000641 2784 2785siesta: Pressure (total): -1.12569938 kBar 2786 2787siesta: Temp_ion = 412.798 K 2788 2789 ==================================== 2790 Begin MD step = 20 2791 ==================================== 2792 2793outcoor: Atomic coordinates (Ang): 2794 0.00522646 -0.00773696 0.00713241 1 1 O 2795 0.69661095 0.71162233 -0.00065564 2 2 H 2796 -0.78023947 0.58256753 -0.11643997 2 3 H 2797 2798outcell: Unit cell vectors (Ang): 2799 8.000000 0.000000 0.000000 2800 0.000000 8.000000 0.000000 2801 0.000000 0.000000 6.400000 2802 2803outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 2804outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 2805outcell: Cell volume (Ang**3) : 409.6000 2806<dSpData1D:S at geom step 20 2807 <sparsity:sparsity for geom step 20 2808 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 2809 <dData1D:(new from dSpData1D) n=69, refcount: 1> 2810refcount: 1> 2811new_DM -- step: 20 2812Re-using DM from previous geometries... 2813Number of DMs in history: 1 2814 DM extrapolation coefficients: 28151 1.00000 2816New DM after history re-use: 2817<dSpData2D:SpM extrapolated using coords 2818 <sparsity:sparsity for geom step 20 2819 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 2820 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 2821refcount: 1> 2822No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 2823New grid distribution: 1 2824 1 1: 25 1: 13 1: 5 2825 2 1: 25 1: 13 6: 10 2826 3 1: 25 1: 13 11: 15 2827 4 1: 25 1: 13 16: 20 2828 5 1: 25 14: 25 1: 5 2829 6 1: 25 14: 25 6: 10 2830 7 1: 25 14: 25 11: 15 2831 8 1: 25 14: 25 16: 20 2832 2833InitMesh: MESH = 50 x 50 x 40 = 100000 2834InitMesh: (bp) = 25 x 25 x 20 = 12500 2835InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 2836ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 2837New grid distribution: 2 2838 1 7: 25 6: 25 1: 6 2839 2 7: 25 1: 5 1: 6 2840 3 7: 25 1: 5 7: 20 2841 4 1: 6 1: 5 7: 20 2842 5 1: 6 6: 25 1: 6 2843 6 1: 6 1: 5 1: 6 2844 7 7: 25 6: 25 7: 20 2845 8 1: 6 6: 25 7: 20 2846New grid distribution: 3 2847 1 1: 9 7: 25 1: 7 2848 2 11: 25 1: 6 1: 12 2849 3 11: 25 1: 6 13: 20 2850 4 10: 25 7: 25 13: 20 2851 5 10: 25 7: 25 1: 12 2852 6 1: 10 1: 6 9: 20 2853 7 1: 9 7: 25 8: 20 2854 8 1: 10 1: 6 1: 8 2855Setting up quadratic distribution... 2856ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 2857PhiOnMesh: Number of (b)points on node 0 = 2280 2858PhiOnMesh: nlist on node 0 = 5133 2859 2860 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 2861 scf: 1 -465.786693 -465.769250 -465.769250 0.005859 -2.627921 0.044728 2862 scf: 2 -465.768862 -465.769160 -465.769160 0.001744 -2.654910 0.078906 2863 scf: 3 -465.769342 -465.769295 -465.769295 0.001118 -2.637624 0.002694 2864 scf: 4 -465.769296 -465.769296 -465.769296 0.000053 -2.637772 0.001772 2865 scf: 5 -465.769296 -465.769296 -465.769296 0.000098 -2.638089 0.000418 2866 2867SCF Convergence by DM+H criterion 2868max |DM_out - DM_in| : 0.0000980020 2869max |H_out - H_in| (eV) : 0.0004175824 2870SCF cycle converged after 5 iterations 2871 2872Using DM_out to compute the final energy and forces 2873No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 2874 2875siesta: E_KS(eV) = -465.7693 2876 2877siesta: Atomic forces (eV/Ang): 2878 1 0.086676 1.948808 -0.334338 2879 2 -0.210727 -1.074325 0.081824 2880 3 0.099157 -0.834697 0.088436 2881---------------------------------------- 2882 Tot -0.024894 0.039786 -0.164078 2883---------------------------------------- 2884 Max 1.948808 2885 Res 0.805315 sqrt( Sum f_i^2 / 3N ) 2886---------------------------------------- 2887 Max 1.948808 constrained 2888 2889Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 0.52 4.47 -1.01 -0.47 -0.17 0.47 2890(Free)E + p*V (eV/cell) -466.1091 2891Target enthalpy (eV/cell) -465.7693 2892 2893siesta: Stress tensor (static) (eV/Ang**3): 2894 0.000449 0.000220 0.000020 2895 0.000220 0.002936 -0.000260 2896 0.000019 -0.000260 -0.000379 2897 2898siesta: Pressure (static): -1.60544029 kBar 2899 2900siesta: Stress tensor (total) (eV/Ang**3): 2901 0.000327 0.000296 -0.000102 2902 0.000296 0.002792 -0.000295 2903 -0.000103 -0.000295 -0.000631 2904 2905siesta: Pressure (total): -1.32916947 kBar 2906 2907siesta: Temp_ion = 396.830 K 2908 2909siesta: Program's energy decomposition (eV): 2910siesta: Ebs = -102.634166 2911siesta: Eions = 815.854478 2912siesta: Ena = 174.892324 2913siesta: Ekin = 349.711175 2914siesta: Enl = -60.959680 2915siesta: Eso = 0.000000 2916siesta: Edftu = 0.000000 2917siesta: DEna = -1.911074 2918siesta: DUscf = 0.725809 2919siesta: DUext = 0.000000 2920siesta: Exc = -112.373371 2921siesta: eta*DQ = 0.000000 2922siesta: Emadel = 0.000000 2923siesta: Emeta = 0.000000 2924siesta: Emolmec = 0.000000 2925siesta: Ekinion = 0.102584 2926siesta: Eharris = -465.666712 2927siesta: Etot = -465.666712 2928siesta: FreeEng = -465.666712 2929 2930siesta: Final energy (eV): 2931siesta: Band Struct. = -102.634166 2932siesta: Kinetic = 349.711175 2933siesta: Hartree = 411.788122 2934siesta: Edftu = 0.000000 2935siesta: Eso = 0.000000 2936siesta: Ext. field = 0.000000 2937siesta: Exch.-corr. = -112.373371 2938siesta: Ion-electron = -1128.692329 2939siesta: Ion-ion = 13.797108 2940siesta: Ekinion = 0.102584 2941siesta: Total = -465.666712 2942siesta: Fermi = -2.638089 2943 2944siesta: Atomic forces (eV/Ang): 2945siesta: 1 0.086676 1.948808 -0.334338 2946siesta: 2 -0.210727 -1.074325 0.081824 2947siesta: 3 0.099157 -0.834697 0.088436 2948siesta: ---------------------------------------- 2949siesta: Tot -0.024894 0.039786 -0.164078 2950 2951siesta: Stress tensor (static) (eV/Ang**3): 2952siesta: 0.000449 0.000220 0.000020 2953siesta: 0.000220 0.002936 -0.000260 2954siesta: 0.000019 -0.000260 -0.000379 2955 2956siesta: Cell volume = 409.600000 Ang**3 2957 2958siesta: Pressure (static): 2959siesta: Solid Molecule Units 2960siesta: -0.00001091 0.00000261 Ry/Bohr**3 2961siesta: -0.00100203 0.00023986 eV/Ang**3 2962siesta: -1.60544029 0.38430011 kBar 2963(Free)E+ p_basis*V_orbitals = -465.184129 2964(Free)Eharris+ p_basis*V_orbitals = -465.184129 2965 2966siesta: Electric dipole (a.u.) = -0.042630 0.591839 -0.059918 2967siesta: Electric dipole (Debye) = -0.108354 1.504305 -0.152297 2968 2969cite: Please see "h2o.bib" for an exhaustive BiBTeX file. 2970cite: Please clearly indicate Siesta version in published work: v4.1-b4-351 2971cite: This calculation has made use of the following articles 2972cite: which are encouraged to be cited in a published work. 2973 Primary SIESTA paper 2974 DOI: www.doi.org/10.1088/0953-8984/14/11/302 2975 2976>> End of run: 22-JAN-2021 23:12:45 2977Job completed 2978Siesta Version : v4.1-b4-351 2979Architecture : x86_64-linux-n-62-26-19 2980Compiler version: GNU Fortran (GCC) 9.3.0 2981Compiler flags : mpifort -m64 -fPIC -O3 -march=native -ftree-vectorize -fexpensive-optimizatioons -funroll-loops -fprefetch-loop-arrays -fno-second-underscore -flto 2982PP flags : -I/dtu/sw/dcc/SL73/2020-aug/generic/build-tools/1.0/include -I/dtu/sw/dcc/SL773/2020-aug/generic/gcc/9.3.0/include -I/dtu/sw/dcc/SL73/2020-aug/generic/gcc/9.3.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/zlib/1.2.11/include -I/dtu/sw/dcc/SL73/2020-aug/generic/numactl/2.0.12/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/libxml2/2.9.10/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/hwloc/2.2.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/knem/1.1.4/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/ucx/1.8.1/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/openmpi/4.0.4/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/szip/2.1.1/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/hdf5/1.12.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/pnetcdf/1.12.1/include -I/dtu/sw/dcc/SL73/2020-aug/generic/gen-zlib/1.2.11/include -I/dtu/sw/dcc/SL73/2020-aug/generic/openssl/1.1.1/include -I/dtu/sw/dcc/SL73/2020-aug/generic/libssh2/1.8.2/include -I/dtu/sw/dcc/SL73/2020-aug/generic/curl/7.65.1/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/netcdf/4.7.4/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/flook/0.8.1/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/fftw/3.3.8/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/parmetis/4.0.3/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/scalapack/2.1.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/lapack/3.9.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/blis/0.7.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/scotch/6.0.9/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/mumps/5.3.3/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/elpa/2020.05.001/include -DSIESTA__ELPA -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DCDF -DCDF4 -DSIESTA__FLOOK -DNCDF -DNCDF_4 -DNCDF_PARALLEL -DTS_NOCHECKS -DSIESTA__METIS -DSIESTA__MUMPS -DSIESTA__MRRR -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/elpa/2020.05.001/include/elpa 2983Libraries : libncdf.a libfdict.a -lnetcdff -lnetcdf -lpnetcdf -lhdf5_hl -lhdf5 -lz -lzmuumps -lmumps_common -lesmumps -lscotch -lscotcherr -lpord -lparmetis -lmetis -lelpa -lscalapack -llapack -lblis -L/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/flook/0.8.1/lib -Wl,-rpath=/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/flook/0.8.1/lib -lflookall -ldl -flto -fuse-linker-plugin -lmetis 2984PARALLEL version 2985NetCDF support 2986NetCDF-4 support 2987NetCDF-4 MPI-IO support 2988METIS ordering support 2989Lua support 2990 2991* Running on 8 nodes in parallel 2992>> Start of run: 22-JAN-2021 23:12:46 2993 2994 *********************** 2995 * WELCOME TO SIESTA * 2996 *********************** 2997 2998reinit: Reading from standard input 2999reinit: Dumped input in INPUT_TMP.98208 3000************************** Dump of input data file **************************** 3001SystemName Water molecule -- md verlet 3002SystemLabel h2o 3003NumberOfAtoms 3 3004NumberOfSpecies 2 3005MeshCutoff 100 Ry 3006%block ChemicalSpeciesLabel 3007 1 8 O # Species index, atomic number, species label 3008 2 1 H 3009%endblock ChemicalSpeciesLabel 3010LatticeConstant 8.0 Ang 3011%block LatticeVectors 30121.0 0.0 0.0 30130.0 1.0 0.0 30140.0 0.0 0.8 3015%endblock LatticeVectors 3016AtomicCoordinatesFormat Ang 3017%block AtomicCoordinatesAndAtomicSpecies 3018 0.000 0.000 0.000 1 3019 0.757 0.586 0.000 2 3020-0.757 0.586 0.000 2 3021%endblock AtomicCoordinatesAndAtomicSpecies 3022Solution.Method diagon 3023MeshCutoff 100 Ry 3024WriteCoorStep .true. 3025WriteForces .true. 3026WriteMDHistory .true. 3027MD.UseSaveXV T 3028MD.TypeOfRun Verlet 3029MD.InitialTemperature 600 K 3030MD.Initial.Time.Step 1 3031MD.Final.Time.Step 20 3032MD.Length.Time.Step 0.2 fs 3033************************** End of input data file ***************************** 3034 3035reinit: ----------------------------------------------------------------------- 3036reinit: System Name: Water molecule -- md verlet 3037reinit: ----------------------------------------------------------------------- 3038reinit: System Label: h2o 3039reinit: ----------------------------------------------------------------------- 3040 3041initatom: Reading input for the pseudopotentials and atomic orbitals ---------- 3042Species number: 1 Atomic number: 8 Label: O 3043Species number: 2 Atomic number: 1 Label: H 3044 3045Ground state valence configuration: 2s02 2p04 3046Reading pseudopotential information in formatted form from O.psf 3047 3048Valence configuration for pseudopotential generation: 30492s( 2.00) rc: 1.14 30502p( 4.00) rc: 1.14 30513d( 0.00) rc: 1.14 30524f( 0.00) rc: 1.14 3053Ground state valence configuration: 1s01 3054Reading pseudopotential information in formatted form from H.psf 3055 3056Valence configuration for pseudopotential generation: 30571s( 1.00) rc: 1.25 30582p( 0.00) rc: 1.25 30593d( 0.00) rc: 1.25 30604f( 0.00) rc: 1.25 3061For O, standard SIESTA heuristics set lmxkb to 3 3062 (one more than the basis l, including polarization orbitals). 3063Use PS.lmax or PS.KBprojectors blocks to override. 3064For H, standard SIESTA heuristics set lmxkb to 2 3065 (one more than the basis l, including polarization orbitals). 3066Use PS.lmax or PS.KBprojectors blocks to override. 3067 3068<basis_specs> 3069=============================================================================== 3070O Z= 8 Mass= 16.000 Charge= 0.17977+309 3071Lmxo=1 Lmxkb= 3 BasisType=split Semic=F 3072L=0 Nsemic=0 Cnfigmx=2 3073 i=1 nzeta=2 polorb=0 (2s) 3074 splnorm: 0.15000 3075 vcte: 0.0000 3076 rinn: 0.0000 3077 qcoe: 0.0000 3078 qyuk: 0.0000 3079 qwid: 0.10000E-01 3080 rcs: 0.0000 0.0000 3081 lambdas: 1.0000 1.0000 3082L=1 Nsemic=0 Cnfigmx=2 3083 i=1 nzeta=2 polorb=1 (2p) 3084 splnorm: 0.15000 3085 vcte: 0.0000 3086 rinn: 0.0000 3087 qcoe: 0.0000 3088 qyuk: 0.0000 3089 qwid: 0.10000E-01 3090 rcs: 0.0000 0.0000 3091 lambdas: 1.0000 1.0000 3092------------------------------------------------------------------------------- 3093L=0 Nkbl=1 erefs: 0.17977+309 3094L=1 Nkbl=1 erefs: 0.17977+309 3095L=2 Nkbl=1 erefs: 0.17977+309 3096L=3 Nkbl=1 erefs: 0.17977+309 3097=============================================================================== 3098</basis_specs> 3099 3100atom: Called for O (Z = 8) 3101 3102read_vps: Pseudopotential generation method: 3103read_vps: ATM3 Troullier-Martins 3104Valence charge for ps generation: 6.00000 3105 3106xc_check: Exchange-correlation functional: 3107xc_check: Ceperley-Alder 3108V l=0 = -2*Zval/r beyond r= 1.1278 3109V l=1 = -2*Zval/r beyond r= 1.1278 3110V l=2 = -2*Zval/r beyond r= 1.1278 3111V l=3 = -2*Zval/r beyond r= 1.1138 3112All V_l potentials equal beyond r= 1.1278 3113This should be close to max(r_c) in ps generation 3114All pots = -2*Zval/r beyond r= 1.1278 3115 3116VLOCAL1: 99.0% of the norm of Vloc inside 34.126 Ry 3117VLOCAL1: 99.9% of the norm of Vloc inside 77.774 Ry 3118atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.37759 3119atom: Maximum radius for r*vlocal+2*Zval: 1.18566 3120GHOST: No ghost state for L = 0 3121GHOST: No ghost state for L = 1 3122GHOST: No ghost state for L = 2 3123GHOST: No ghost state for L = 3 3124 3125KBgen: Kleinman-Bylander projectors: 3126 l= 0 rc= 1.294105 el= -1.742414 Ekb= 9.135903 kbcos= 0.326910 3127 l= 1 rc= 1.294105 el= -0.676589 Ekb= -8.124878 kbcos= -0.395047 3128 l= 2 rc= 1.448233 el= 0.002386 Ekb= -2.039267 kbcos= -0.003484 3129 l= 3 rc= 1.561052 el= 0.003508 Ekb= -0.799141 kbcos= -0.000344 3130 3131KBgen: Total number of Kleinman-Bylander projectors: 16 3132atom: ------------------------------------------------------------------------- 3133 3134atom: SANKEY-TYPE ORBITALS: 3135atom: Selected multiple-zeta basis: split 3136 3137SPLIT: Orbitals with angular momentum L= 0 3138 3139SPLIT: Basis orbitals for state 2s 3140 3141SPLIT: PAO cut-off radius determined from an 3142SPLIT: energy shift= 0.020000 Ry 3143 3144 izeta = 1 3145 lambda = 1.000000 3146 rc = 3.305093 3147 energy = -1.723766 3148 kinetic = 1.614911 3149 potential(screened) = -3.338677 3150 potential(ionic) = -11.304675 3151 3152 izeta = 2 3153 rmatch = 2.510382 3154 splitnorm = 0.150000 3155 energy = -1.471299 3156 kinetic = 2.446434 3157 potential(screened) = -3.917732 3158 potential(ionic) = -12.476133 3159 3160SPLIT: Orbitals with angular momentum L= 1 3161 3162SPLIT: Basis orbitals for state 2p 3163 3164SPLIT: PAO cut-off radius determined from an 3165SPLIT: energy shift= 0.020000 Ry 3166 3167 izeta = 1 3168 lambda = 1.000000 3169 rc = 3.937239 3170 energy = -0.658841 3171 kinetic = 5.005986 3172 potential(screened) = -5.664827 3173 potential(ionic) = -13.452360 3174 3175 izeta = 2 3176 rmatch = 2.541963 3177 splitnorm = 0.150000 3178 energy = -0.367441 3179 kinetic = 7.530509 3180 potential(screened) = -7.897949 3181 potential(ionic) = -16.611953 3182 3183POLgen: Perturbative polarization orbital with L= 2 3184 3185POLgen: Polarization orbital for state 2p 3186 3187 izeta = 1 3188 rc = 3.937239 3189 energy = 2.398520 3190 kinetic = 4.716729 3191 potential(screened) = -2.318209 3192 potential(ionic) = -8.603170 3193atom: Total number of Sankey-type orbitals: 13 3194 3195atm_pop: Valence configuration (for local Pseudopot. screening): 3196 2s( 2.00) 3197 2p( 4.00) 3198Vna: chval, zval: 6.00000 6.00000 3199 3200Vna: Cut-off radius for the neutral-atom potential: 3.937239 3201 3202atom: _________________________________________________________________________ 3203 3204<basis_specs> 3205=============================================================================== 3206H Z= 1 Mass= 1.0100 Charge= 0.17977+309 3207Lmxo=0 Lmxkb= 2 BasisType=split Semic=F 3208L=0 Nsemic=0 Cnfigmx=1 3209 i=1 nzeta=2 polorb=1 (1s) 3210 splnorm: 0.15000 3211 vcte: 0.0000 3212 rinn: 0.0000 3213 qcoe: 0.0000 3214 qyuk: 0.0000 3215 qwid: 0.10000E-01 3216 rcs: 0.0000 0.0000 3217 lambdas: 1.0000 1.0000 3218------------------------------------------------------------------------------- 3219L=0 Nkbl=1 erefs: 0.17977+309 3220L=1 Nkbl=1 erefs: 0.17977+309 3221L=2 Nkbl=1 erefs: 0.17977+309 3222=============================================================================== 3223</basis_specs> 3224 3225atom: Called for H (Z = 1) 3226 3227read_vps: Pseudopotential generation method: 3228read_vps: ATM3 Troullier-Martins 3229Valence charge for ps generation: 1.00000 3230 3231xc_check: Exchange-correlation functional: 3232xc_check: Ceperley-Alder 3233V l=0 = -2*Zval/r beyond r= 1.2343 3234V l=1 = -2*Zval/r beyond r= 1.2189 3235V l=2 = -2*Zval/r beyond r= 1.2189 3236All V_l potentials equal beyond r= 1.2343 3237This should be close to max(r_c) in ps generation 3238All pots = -2*Zval/r beyond r= 1.2343 3239 3240VLOCAL1: 99.0% of the norm of Vloc inside 28.493 Ry 3241VLOCAL1: 99.9% of the norm of Vloc inside 64.935 Ry 3242atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.45251 3243atom: Maximum radius for r*vlocal+2*Zval: 1.21892 3244GHOST: No ghost state for L = 0 3245GHOST: No ghost state for L = 1 3246GHOST: No ghost state for L = 2 3247 3248KBgen: Kleinman-Bylander projectors: 3249 l= 0 rc= 1.364359 el= -0.467325 Ekb= -2.005361 kbcos= -0.336422 3250 l= 1 rc= 1.434438 el= 0.001430 Ekb= -0.501708 kbcos= -0.021697 3251 l= 2 rc= 1.470814 el= 0.002365 Ekb= -0.190555 kbcos= -0.002281 3252 3253KBgen: Total number of Kleinman-Bylander projectors: 9 3254atom: ------------------------------------------------------------------------- 3255 3256atom: SANKEY-TYPE ORBITALS: 3257atom: Selected multiple-zeta basis: split 3258 3259SPLIT: Orbitals with angular momentum L= 0 3260 3261SPLIT: Basis orbitals for state 1s 3262 3263SPLIT: PAO cut-off radius determined from an 3264SPLIT: energy shift= 0.020000 Ry 3265 3266 izeta = 1 3267 lambda = 1.000000 3268 rc = 4.828263 3269 energy = -0.449375 3270 kinetic = 0.929372 3271 potential(screened) = -1.378747 3272 potential(ionic) = -1.915047 3273 3274 izeta = 2 3275 rmatch = 3.854947 3276 splitnorm = 0.150000 3277 energy = -0.336153 3278 kinetic = 1.505294 3279 potential(screened) = -1.841447 3280 potential(ionic) = -2.413582 3281 3282POLgen: Perturbative polarization orbital with L= 1 3283 3284POLgen: Polarization orbital for state 1s 3285 3286 izeta = 1 3287 rc = 4.828263 3288 energy = 0.706972 3289 kinetic = 1.396397 3290 potential(screened) = -0.689424 3291 potential(ionic) = -1.169792 3292atom: Total number of Sankey-type orbitals: 5 3293 3294atm_pop: Valence configuration (for local Pseudopot. screening): 3295 1s( 1.00) 3296Vna: chval, zval: 1.00000 1.00000 3297 3298Vna: Cut-off radius for the neutral-atom potential: 4.828263 3299 3300atom: _________________________________________________________________________ 3301 3302prinput: Basis input ---------------------------------------------------------- 3303 3304PAO.BasisType split 3305 3306%block ChemicalSpeciesLabel 3307 1 8 O # Species index, atomic number, species label 3308 2 1 H # Species index, atomic number, species label 3309%endblock ChemicalSpeciesLabel 3310 3311%block PAO.Basis # Define Basis set 3312O 2 # Species label, number of l-shells 3313 n=2 0 2 # n, l, Nzeta 3314 3.305 2.510 3315 1.000 1.000 3316 n=2 1 2 P 1 # n, l, Nzeta, Polarization, NzetaPol 3317 3.937 2.542 3318 1.000 1.000 3319H 1 # Species label, number of l-shells 3320 n=1 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol 3321 4.828 3.855 3322 1.000 1.000 3323%endblock PAO.Basis 3324 3325prinput: ---------------------------------------------------------------------- 3326 3327Dumping basis to NetCDF file O.ion.nc 3328Dumping basis to NetCDF file H.ion.nc 3329coor: Atomic-coordinates input format = Cartesian coordinates 3330coor: (in Angstroms) 3331 3332ioxv: Reading coordinates and velocities from file 3333! Info in XV file prevails over previous structure input 3334WARNING: h2o.VERLET_RESTART not found--reading only XV file and moving back 1 time step using Euler 3335 3336siesta: Atomic coordinates (Bohr) and species 3337siesta: 0.00988 -0.01458 0.01347 1 1 3338siesta: 1.31633 1.34439 -0.00121 2 2 3339siesta: -1.47440 1.10059 -0.22001 2 3 3340 3341siesta: System type = molecule 3342 3343initatomlists: Number of atoms, orbitals, and projectors: 3 23 34 3344 3345siesta: ******************** Simulation parameters **************************** 3346siesta: 3347siesta: The following are some of the parameters of the simulation. 3348siesta: A complete list of the parameters used, including default values, 3349siesta: can be found in file out.fdf 3350siesta: 3351redata: Spin configuration = none 3352redata: Number of spin components = 1 3353redata: Time-Reversal Symmetry = T 3354redata: Spin spiral = F 3355redata: Long output = F 3356redata: Number of Atomic Species = 2 3357redata: Charge density info will appear in .RHO file 3358redata: Write Mulliken Pop. = NO 3359redata: Matel table size (NRTAB) = 1024 3360redata: Mesh Cutoff = 100.0000 Ry 3361redata: Net charge of the system = 0.0000 |e| 3362redata: Min. number of SCF Iter = 0 3363redata: Max. number of SCF Iter = 1000 3364redata: SCF convergence failure will abort job 3365redata: SCF mix quantity = Hamiltonian 3366redata: Mix DM or H after convergence = F 3367redata: Recompute H after scf cycle = F 3368redata: Mix DM in first SCF step = T 3369redata: Write Pulay info on disk = F 3370redata: New DM Occupancy tolerance = 0.000000000001 3371redata: No kicks to SCF 3372redata: DM Mixing Weight for Kicks = 0.5000 3373redata: Require Harris convergence for SCF = F 3374redata: Harris energy tolerance for SCF = 0.000100 eV 3375redata: Require DM convergence for SCF = T 3376redata: DM tolerance for SCF = 0.000100 3377redata: Require EDM convergence for SCF = F 3378redata: EDM tolerance for SCF = 0.001000 eV 3379redata: Require H convergence for SCF = T 3380redata: Hamiltonian tolerance for SCF = 0.001000 eV 3381redata: Require (free) Energy convergence for SCF = F 3382redata: (free) Energy tolerance for SCF = 0.000100 eV 3383redata: Using Saved Data (generic) = F 3384redata: Use continuation files for DM = F 3385redata: Neglect nonoverlap interactions = F 3386redata: Method of Calculation = Diagonalization 3387redata: Electronic Temperature = 299.9869 K 3388redata: Fix the spin of the system = F 3389redata: Dynamics option = Verlet MD run 3390redata: Initial MD time step = 1 3391redata: Final MD time step = 20 3392redata: Length of MD time step = 0.2000 fs 3393redata: Initial Temperature of MD run = 600.0000 K 3394redata: Perform a MD quench = F 3395mix.SCF: Pulay mixing = Pulay 3396mix.SCF: Variant = stable 3397mix.SCF: History steps = 2 3398mix.SCF: Linear mixing weight = 0.250000 3399mix.SCF: Mixing weight = 0.250000 3400mix.SCF: SVD condition = 0.1000E-07 3401redata: Save all siesta data in one NC = F 3402redata: *********************************************************************** 3403 3404%block SCF.Mixers 3405 Pulay 3406%endblock SCF.Mixers 3407 3408%block SCF.Mixer.Pulay 3409 # Mixing method 3410 method pulay 3411 variant stable 3412 3413 # Mixing options 3414 weight 0.2500 3415 weight.linear 0.2500 3416 history 2 3417%endblock SCF.Mixer.Pulay 3418 3419Size of DM history Fstack: 1 3420Total number of electrons: 8.000000 3421Total ionic charge: 8.000000 3422 3423* ProcessorY, Blocksize: 2 3 3424 3425 3426* Orbital distribution balance (max,min): 3 2 3427 3428 Kpoints in: 1 . Kpoints trimmed: 1 3429 3430siesta: k-grid: Number of k-points = 1 3431siesta: k-grid: Cutoff (effective) = 3.200 Ang 3432siesta: k-grid: Supercell and displacements 3433siesta: k-grid: 1 0 0 0.000 3434siesta: k-grid: 0 1 0 0.000 3435siesta: k-grid: 0 0 1 0.000 3436 3437diag: Algorithm = D&C 3438diag: Parallel over k = F 3439diag: Use parallel 2D distribution = T 3440diag: Parallel block-size = 3 3441diag: Parallel distribution = 2 x 4 3442diag: Used triangular part = Lower 3443diag: Absolute tolerance = 0.100E-15 3444diag: Orthogonalization factor = 0.100E-05 3445diag: Memory factor = 1.0000 3446 3447 3448ts: ************************************************************** 3449ts: Save H and S matrices = F 3450ts: Save DM and EDM matrices = F 3451ts: Only save the overlap matrix S = F 3452ts: ************************************************************** 3453 3454************************ Begin: TS CHECKS AND WARNINGS ************************ 3455************************ End: TS CHECKS AND WARNINGS ************************** 3456 3457 3458 ==================================== 3459 Begin MD step = 1 3460 ==================================== 3461 3462outcoor: Atomic coordinates (Ang): 3463 0.00522750 -0.00771363 0.00712840 1 1 O 3464 0.69657098 0.71141855 -0.00064012 2 2 H 3465 -0.78022066 0.58240920 -0.11642319 2 3 H 3466 3467outcell: Unit cell vectors (Ang): 3468 8.000000 0.000000 0.000000 3469 0.000000 8.000000 0.000000 3470 0.000000 0.000000 6.400000 3471 3472outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 3473outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 3474outcell: Cell volume (Ang**3) : 409.6000 3475<dSpData1D:S at geom step 1 3476 <sparsity:sparsity for geom step 1 3477 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 3478 <dData1D:(new from dSpData1D) n=69, refcount: 1> 3479refcount: 1> 3480new_DM -- step: 1 3481Initializing Density Matrix... 3482DM filled with atomic data: 3483<dSpData2D:DM initialized from atoms 3484 <sparsity:sparsity for geom step 1 3485 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 8> 3486 <dData2D:DM n=69 m=1, refcount: 1> 3487refcount: 1> 3488No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 3489New grid distribution: 1 3490 1 1: 25 1: 13 1: 5 3491 2 1: 25 1: 13 6: 10 3492 3 1: 25 1: 13 11: 15 3493 4 1: 25 1: 13 16: 20 3494 5 1: 25 14: 25 1: 5 3495 6 1: 25 14: 25 6: 10 3496 7 1: 25 14: 25 11: 15 3497 8 1: 25 14: 25 16: 20 3498 3499InitMesh: MESH = 50 x 50 x 40 = 100000 3500InitMesh: (bp) = 25 x 25 x 20 = 12500 3501InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 3502ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 3503New grid distribution: 2 3504 1 7: 25 6: 25 1: 6 3505 2 7: 25 1: 5 1: 6 3506 3 7: 25 1: 5 7: 20 3507 4 1: 6 1: 5 7: 20 3508 5 1: 6 6: 25 1: 6 3509 6 1: 6 1: 5 1: 6 3510 7 7: 25 6: 25 7: 20 3511 8 1: 6 6: 25 7: 20 3512New grid distribution: 3 3513 1 1: 9 7: 25 1: 7 3514 2 11: 25 1: 6 1: 12 3515 3 11: 25 1: 6 13: 20 3516 4 10: 25 7: 25 13: 20 3517 5 10: 25 7: 25 1: 12 3518 6 1: 10 1: 6 9: 20 3519 7 1: 9 7: 25 8: 20 3520 8 1: 10 1: 6 1: 8 3521Setting up quadratic distribution... 3522ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 3523PhiOnMesh: Number of (b)points on node 0 = 2280 3524PhiOnMesh: nlist on node 0 = 5133 3525 3526stepf: Fermi-Dirac step function 3527 3528siesta: Program's energy decomposition (eV): 3529siesta: Ebs = -82.264876 3530siesta: Eions = 815.854478 3531siesta: Ena = 174.893053 3532siesta: Ekin = 371.577802 3533siesta: Enl = -66.805890 3534siesta: Eso = 0.000000 3535siesta: Edftu = 0.000000 3536siesta: DEna = -14.792749 3537siesta: DUscf = 1.911589 3538siesta: DUext = 0.000000 3539siesta: Exc = -115.961161 3540siesta: eta*DQ = 0.000000 3541siesta: Emadel = 0.000000 3542siesta: Emeta = 0.000000 3543siesta: Emolmec = 0.000000 3544siesta: Ekinion = 0.000000 3545siesta: Eharris = -467.439257 3546siesta: Etot = -465.031834 3547siesta: FreeEng = -465.031834 3548 3549 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 3550 scf: 1 -467.439257 -465.031834 -465.031834 1.369148 -4.721235 6.832340 3551timer: Routine,Calls,Time,% = IterSCF 1 0.020 1.51 3552 scf: 2 -466.126578 -465.691169 -465.691169 0.055536 -3.619916 2.524245 3553 scf: 3 -465.778310 -465.765100 -465.765100 0.023489 -2.942223 0.377120 3554 scf: 4 -465.770671 -465.768050 -465.768050 0.011237 -2.860531 0.279514 3555 scf: 5 -465.770185 -465.769517 -465.769517 0.023829 -2.632443 0.051459 3556 scf: 6 -465.769763 -465.769654 -465.769654 0.001677 -2.627348 0.032581 3557 scf: 7 -465.769727 -465.769693 -465.769693 0.001027 -2.627075 0.017074 3558 scf: 8 -465.769713 -465.769704 -465.769704 0.000590 -2.629402 0.011344 3559 scf: 9 -465.769708 -465.769706 -465.769706 0.000518 -2.633348 0.004456 3560 scf: 10 -465.769706 -465.769706 -465.769706 0.000094 -2.635292 0.002214 3561 scf: 11 -465.769707 -465.769706 -465.769706 0.000023 -2.636738 0.001692 3562 scf: 12 -465.769707 -465.769706 -465.769706 0.000020 -2.637047 0.000980 3563 3564SCF Convergence by DM+H criterion 3565max |DM_out - DM_in| : 0.0000198530 3566max |H_out - H_in| (eV) : 0.0009803347 3567SCF cycle converged after 12 iterations 3568 3569Using DM_out to compute the final energy and forces 3570No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 3571 3572siesta: E_KS(eV) = -465.7697 3573 3574siesta: E_KS - E_eggbox = -465.7697 3575 3576siesta: Atomic forces (eV/Ang): 3577 1 0.085359 1.939331 -0.333528 3578 2 -0.205938 -1.068491 0.081347 3579 3 0.095667 -0.831304 0.088205 3580---------------------------------------- 3581 Tot -0.024911 0.039535 -0.163976 3582---------------------------------------- 3583 Max 1.939331 3584 Res 0.801265 sqrt( Sum f_i^2 / 3N ) 3585---------------------------------------- 3586 Max 1.939331 constrained 3587 3588Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 0.50 4.48 -1.01 -0.49 -0.16 0.45 3589(Free)E + p*V (eV/cell) -466.1080 3590Target enthalpy (eV/cell) -465.7697 3591 3592siesta: Stress tensor (static) (eV/Ang**3): 3593 0.000434 0.000216 0.000019 3594 0.000216 0.002919 -0.000259 3595 0.000019 -0.000259 -0.000379 3596 3597siesta: Pressure (static): -1.58880755 kBar 3598 3599siesta: Stress tensor (total) (eV/Ang**3): 3600 0.000310 0.000280 -0.000100 3601 0.000280 0.002795 -0.000308 3602 -0.000100 -0.000308 -0.000628 3603 3604siesta: Pressure (total): -1.32322336 kBar 3605 3606siesta: Temp_ion = 396.830 K 3607 3608 ==================================== 3609 Begin MD step = 2 3610 ==================================== 3611 3612outcoor: Atomic coordinates (Ang): 3613 0.00559273 -0.00786435 0.00746058 1 1 O 3614 0.69346884 0.71536274 -0.00048103 2 2 H 3615 -0.78302323 0.58093758 -0.12250409 2 3 H 3616 3617outcell: Unit cell vectors (Ang): 3618 8.000000 0.000000 0.000000 3619 0.000000 8.000000 0.000000 3620 0.000000 0.000000 6.400000 3621 3622outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 3623outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 3624outcell: Cell volume (Ang**3) : 409.6000 3625<dSpData1D:S at geom step 2 3626 <sparsity:sparsity for geom step 2 3627 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 3628 <dData1D:(new from dSpData1D) n=69, refcount: 1> 3629refcount: 1> 3630new_DM -- step: 2 3631Re-using DM from previous geometries... 3632Number of DMs in history: 1 3633 DM extrapolation coefficients: 36341 1.00000 3635New DM after history re-use: 3636<dSpData2D:SpM extrapolated using coords 3637 <sparsity:sparsity for geom step 2 3638 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 3639 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 3640refcount: 1> 3641No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 3642New grid distribution: 1 3643 1 1: 25 1: 13 1: 5 3644 2 1: 25 1: 13 6: 10 3645 3 1: 25 1: 13 11: 15 3646 4 1: 25 1: 13 16: 20 3647 5 1: 25 14: 25 1: 5 3648 6 1: 25 14: 25 6: 10 3649 7 1: 25 14: 25 11: 15 3650 8 1: 25 14: 25 16: 20 3651 3652InitMesh: MESH = 50 x 50 x 40 = 100000 3653InitMesh: (bp) = 25 x 25 x 20 = 12500 3654InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 3655ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 3656New grid distribution: 2 3657 1 7: 25 6: 25 1: 6 3658 2 7: 25 1: 5 1: 6 3659 3 7: 25 1: 5 7: 20 3660 4 1: 6 1: 5 7: 20 3661 5 1: 6 6: 25 1: 6 3662 6 1: 6 1: 5 1: 6 3663 7 7: 25 6: 25 7: 20 3664 8 1: 6 6: 25 7: 20 3665New grid distribution: 3 3666 1 1: 9 7: 25 1: 7 3667 2 11: 25 1: 6 1: 12 3668 3 11: 25 1: 6 13: 20 3669 4 10: 25 7: 25 13: 20 3670 5 10: 25 7: 25 1: 12 3671 6 1: 10 1: 6 9: 20 3672 7 1: 9 7: 25 8: 20 3673 8 1: 10 1: 6 1: 8 3674Setting up quadratic distribution... 3675ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 3676PhiOnMesh: Number of (b)points on node 0 = 2280 3677PhiOnMesh: nlist on node 0 = 5134 3678 3679 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 3680 scf: 1 -465.780804 -465.765983 -465.765983 0.005855 -2.641986 0.037703 3681 scf: 2 -465.765704 -465.765920 -465.765920 0.001429 -2.664523 0.066994 3682 scf: 3 -465.766051 -465.766017 -465.766017 0.000922 -2.650051 0.002585 3683 scf: 4 -465.766018 -465.766018 -465.766018 0.000053 -2.650149 0.001774 3684 scf: 5 -465.766019 -465.766018 -465.766018 0.000098 -2.650379 0.000383 3685 3686SCF Convergence by DM+H criterion 3687max |DM_out - DM_in| : 0.0000983573 3688max |H_out - H_in| (eV) : 0.0003832012 3689SCF cycle converged after 5 iterations 3690 3691Using DM_out to compute the final energy and forces 3692No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 3693 3694siesta: E_KS(eV) = -465.7660 3695 3696siesta: Atomic forces (eV/Ang): 3697 1 0.002634 2.022374 -0.363266 3698 2 -0.207316 -1.085304 0.086256 3699 3 0.178986 -0.897309 0.105279 3700---------------------------------------- 3701 Tot -0.025697 0.039761 -0.171730 3702---------------------------------------- 3703 Max 2.022374 3704 Res 0.836564 sqrt( Sum f_i^2 / 3N ) 3705---------------------------------------- 3706 Max 2.022374 constrained 3707 3708Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 0.77 4.69 -0.99 -0.55 -0.12 0.27 3709(Free)E + p*V (eV/cell) -466.1465 3710Target enthalpy (eV/cell) -465.7660 3711 3712siesta: Stress tensor (static) (eV/Ang**3): 3713 0.000602 0.000103 0.000047 3714 0.000102 0.003052 -0.000293 3715 0.000046 -0.000293 -0.000370 3716 3717siesta: Pressure (static): -1.75381269 kBar 3718 3719siesta: Stress tensor (total) (eV/Ang**3): 3720 0.000478 0.000166 -0.000073 3721 0.000166 0.002928 -0.000342 3722 -0.000074 -0.000342 -0.000619 3723 3724siesta: Pressure (total): -1.48822850 kBar 3725 3726siesta: Temp_ion = 382.582 K 3727 3728 ==================================== 3729 Begin MD step = 3 3730 ==================================== 3731 3732outcoor: Atomic coordinates (Ang): 3733 0.00595803 -0.00796664 0.00778406 1 1 O 3734 0.69028804 0.71889520 -0.00028922 2 2 H 3735 -0.78575790 0.57912556 -0.12854505 2 3 H 3736 3737outcell: Unit cell vectors (Ang): 3738 8.000000 0.000000 0.000000 3739 0.000000 8.000000 0.000000 3740 0.000000 0.000000 6.400000 3741 3742outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 3743outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 3744outcell: Cell volume (Ang**3) : 409.6000 3745<dSpData1D:S at geom step 3 3746 <sparsity:sparsity for geom step 3 3747 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 3748 <dData1D:(new from dSpData1D) n=69, refcount: 1> 3749refcount: 1> 3750new_DM -- step: 3 3751Re-using DM from previous geometries... 3752Number of DMs in history: 1 3753 DM extrapolation coefficients: 37541 1.00000 3755New DM after history re-use: 3756<dSpData2D:SpM extrapolated using coords 3757 <sparsity:sparsity for geom step 3 3758 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 3759 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 3760refcount: 1> 3761No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 3762New grid distribution: 1 3763 1 1: 25 1: 13 1: 5 3764 2 1: 25 1: 13 6: 10 3765 3 1: 25 1: 13 11: 15 3766 4 1: 25 1: 13 16: 20 3767 5 1: 25 14: 25 1: 5 3768 6 1: 25 14: 25 6: 10 3769 7 1: 25 14: 25 11: 15 3770 8 1: 25 14: 25 16: 20 3771 3772InitMesh: MESH = 50 x 50 x 40 = 100000 3773InitMesh: (bp) = 25 x 25 x 20 = 12500 3774InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 3775ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 3776New grid distribution: 2 3777 1 7: 25 6: 25 1: 6 3778 2 7: 25 1: 5 1: 6 3779 3 7: 25 1: 5 7: 20 3780 4 1: 6 1: 5 7: 20 3781 5 1: 6 6: 25 1: 6 3782 6 1: 6 1: 5 1: 6 3783 7 7: 25 6: 25 7: 20 3784 8 1: 6 6: 25 7: 20 3785New grid distribution: 3 3786 1 1: 9 7: 25 1: 7 3787 2 11: 25 1: 6 1: 12 3788 3 11: 25 1: 6 13: 20 3789 4 10: 25 7: 25 13: 20 3790 5 10: 25 7: 25 1: 12 3791 6 1: 10 1: 6 9: 20 3792 7 1: 9 7: 25 8: 20 3793 8 1: 10 1: 6 1: 8 3794Setting up quadratic distribution... 3795ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 3796PhiOnMesh: Number of (b)points on node 0 = 2280 3797PhiOnMesh: nlist on node 0 = 5135 3798 3799 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 3800 scf: 1 -465.774824 -465.762869 -465.762869 0.005807 -2.654538 0.030291 3801 scf: 2 -465.762691 -465.762830 -465.762830 0.001129 -2.672812 0.054010 3802 scf: 3 -465.762916 -465.762894 -465.762894 0.000729 -2.661122 0.002538 3803 scf: 4 -465.762895 -465.762894 -465.762894 0.000053 -2.661197 0.001733 3804 scf: 5 -465.762895 -465.762895 -465.762895 0.000096 -2.661379 0.000380 3805 3806SCF Convergence by DM+H criterion 3807max |DM_out - DM_in| : 0.0000963897 3808max |H_out - H_in| (eV) : 0.0003802018 3809SCF cycle converged after 5 iterations 3810 3811Using DM_out to compute the final energy and forces 3812No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 3813 3814siesta: E_KS(eV) = -465.7629 3815 3816siesta: Atomic forces (eV/Ang): 3817 1 -0.081429 2.085796 -0.392353 3818 2 -0.199878 -1.091016 0.090576 3819 3 0.254160 -0.955127 0.122050 3820---------------------------------------- 3821 Tot -0.027147 0.039653 -0.179726 3822---------------------------------------- 3823 Max 2.085796 3824 Res 0.865470 sqrt( Sum f_i^2 / 3N ) 3825---------------------------------------- 3826 Max 2.085796 constrained 3827 3828Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 0.98 4.87 -0.97 -0.62 -0.07 0.06 3829(Free)E + p*V (eV/cell) -466.1791 3830Target enthalpy (eV/cell) -465.7629 3831 3832siesta: Stress tensor (static) (eV/Ang**3): 3833 0.000737 -0.000016 0.000075 3834 -0.000016 0.003151 -0.000326 3835 0.000074 -0.000326 -0.000360 3836 3837siesta: Pressure (static): -1.88404385 kBar 3838 3839siesta: Stress tensor (total) (eV/Ang**3): 3840 0.000611 0.000035 -0.000041 3841 0.000035 0.003043 -0.000389 3842 -0.000042 -0.000389 -0.000606 3843 3844siesta: Pressure (total): -1.62799507 kBar 3845 3846siesta: Temp_ion = 370.519 K 3847 3848 ==================================== 3849 Begin MD step = 4 3850 ==================================== 3851 3852outcoor: Atomic coordinates (Ang): 3853 0.00632138 -0.00801898 0.00809814 1 1 O 3854 0.68703142 0.72201377 -0.00006305 2 2 H 3855 -0.78839614 0.57695119 -0.13453970 2 3 H 3856 3857outcell: Unit cell vectors (Ang): 3858 8.000000 0.000000 0.000000 3859 0.000000 8.000000 0.000000 3860 0.000000 0.000000 6.400000 3861 3862outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 3863outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 3864outcell: Cell volume (Ang**3) : 409.6000 3865<dSpData1D:S at geom step 4 3866 <sparsity:sparsity for geom step 4 3867 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 3868 <dData1D:(new from dSpData1D) n=69, refcount: 1> 3869refcount: 1> 3870new_DM -- step: 4 3871Re-using DM from previous geometries... 3872Number of DMs in history: 1 3873 DM extrapolation coefficients: 38741 1.00000 3875New DM after history re-use: 3876<dSpData2D:SpM extrapolated using coords 3877 <sparsity:sparsity for geom step 4 3878 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 3879 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 3880refcount: 1> 3881No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 3882New grid distribution: 1 3883 1 1: 25 1: 13 1: 5 3884 2 1: 25 1: 13 6: 10 3885 3 1: 25 1: 13 11: 15 3886 4 1: 25 1: 13 16: 20 3887 5 1: 25 14: 25 1: 5 3888 6 1: 25 14: 25 6: 10 3889 7 1: 25 14: 25 11: 15 3890 8 1: 25 14: 25 16: 20 3891 3892InitMesh: MESH = 50 x 50 x 40 = 100000 3893InitMesh: (bp) = 25 x 25 x 20 = 12500 3894InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 3895ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 3896New grid distribution: 2 3897 1 7: 25 6: 25 1: 6 3898 2 7: 25 1: 5 1: 6 3899 3 7: 25 1: 5 7: 20 3900 4 1: 6 1: 5 7: 20 3901 5 1: 6 6: 25 1: 6 3902 6 1: 6 1: 5 1: 6 3903 7 7: 25 6: 25 7: 20 3904 8 1: 6 6: 25 7: 20 3905New grid distribution: 3 3906 1 1: 9 7: 25 1: 7 3907 2 11: 25 1: 6 1: 12 3908 3 1: 9 7: 25 8: 20 3909 4 11: 25 1: 6 13: 20 3910 5 10: 25 7: 25 1: 13 3911 6 1: 10 1: 6 9: 20 3912 7 1: 10 1: 6 1: 8 3913 8 10: 25 7: 25 14: 20 3914Setting up quadratic distribution... 3915ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 3916PhiOnMesh: Number of (b)points on node 0 = 2280 3917PhiOnMesh: nlist on node 0 = 5136 3918 3919 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 3920 scf: 1 -465.769327 -465.760436 -465.760436 0.005777 -2.664480 0.022417 3921 scf: 2 -465.760340 -465.760417 -465.760417 0.000831 -2.678021 0.040226 3922 scf: 3 -465.760465 -465.760453 -465.760453 0.000534 -2.669398 0.002392 3923 scf: 4 -465.760454 -465.760453 -465.760453 0.000052 -2.669429 0.001680 3924 scf: 5 -465.760454 -465.760454 -465.760454 0.000093 -2.669534 0.000377 3925 3926SCF Convergence by DM+H criterion 3927max |DM_out - DM_in| : 0.0000927473 3928max |H_out - H_in| (eV) : 0.0003766835 3929SCF cycle converged after 5 iterations 3930 3931Using DM_out to compute the final energy and forces 3932No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 3933 3934siesta: E_KS(eV) = -465.7605 3935 3936siesta: Atomic forces (eV/Ang): 3937 1 -0.165410 2.129459 -0.420043 3938 2 -0.184118 -1.085775 0.094632 3939 3 0.321210 -1.004325 0.138049 3940---------------------------------------- 3941 Tot -0.028318 0.039359 -0.187362 3942---------------------------------------- 3943 Max 2.129459 3944 Res 0.887635 sqrt( Sum f_i^2 / 3N ) 3945---------------------------------------- 3946 Max 2.129459 constrained 3947 3948Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 1.15 5.00 -0.95 -0.70 -0.01 -0.16 3949(Free)E + p*V (eV/cell) -466.2038 3950Target enthalpy (eV/cell) -465.7605 3951 3952siesta: Stress tensor (static) (eV/Ang**3): 3953 0.000845 -0.000136 0.000103 3954 -0.000136 0.003216 -0.000357 3955 0.000101 -0.000357 -0.000350 3956 3957siesta: Pressure (static): -1.98208068 kBar 3958 3959siesta: Stress tensor (total) (eV/Ang**3): 3960 0.000720 -0.000099 -0.000008 3961 -0.000099 0.003119 -0.000436 3962 -0.000009 -0.000436 -0.000592 3963 3964siesta: Pressure (total): -1.73410538 kBar 3965 3966siesta: Temp_ion = 361.109 K 3967 3968 ==================================== 3969 Begin MD step = 5 3970 ==================================== 3971 3972outcoor: Atomic coordinates (Ang): 3973 0.00668077 -0.00802032 0.00840216 1 1 O 3974 0.68370495 0.72472043 0.00019902 2 2 H 3975 -0.79091253 0.57439581 -0.14048198 2 3 H 3976 3977outcell: Unit cell vectors (Ang): 3978 8.000000 0.000000 0.000000 3979 0.000000 8.000000 0.000000 3980 0.000000 0.000000 6.400000 3981 3982outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 3983outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 3984outcell: Cell volume (Ang**3) : 409.6000 3985<dSpData1D:S at geom step 5 3986 <sparsity:sparsity for geom step 5 3987 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 3988 <dData1D:(new from dSpData1D) n=69, refcount: 1> 3989refcount: 1> 3990new_DM -- step: 5 3991Re-using DM from previous geometries... 3992Number of DMs in history: 1 3993 DM extrapolation coefficients: 39941 1.00000 3995New DM after history re-use: 3996<dSpData2D:SpM extrapolated using coords 3997 <sparsity:sparsity for geom step 5 3998 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 3999 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 4000refcount: 1> 4001No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 4002New grid distribution: 1 4003 1 1: 25 1: 13 1: 5 4004 2 1: 25 1: 13 6: 10 4005 3 1: 25 1: 13 11: 15 4006 4 1: 25 1: 13 16: 20 4007 5 1: 25 14: 25 1: 5 4008 6 1: 25 14: 25 6: 10 4009 7 1: 25 14: 25 11: 15 4010 8 1: 25 14: 25 16: 20 4011 4012InitMesh: MESH = 50 x 50 x 40 = 100000 4013InitMesh: (bp) = 25 x 25 x 20 = 12500 4014InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 4015ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 4016New grid distribution: 2 4017 1 7: 25 6: 25 1: 6 4018 2 8: 25 1: 5 1: 6 4019 3 8: 25 1: 5 7: 20 4020 4 1: 7 1: 5 7: 20 4021 5 1: 6 6: 25 1: 6 4022 6 1: 7 1: 5 1: 6 4023 7 7: 25 6: 25 7: 20 4024 8 1: 6 6: 25 7: 20 4025New grid distribution: 3 4026 1 1: 9 7: 25 1: 7 4027 2 11: 25 1: 6 1: 12 4028 3 1: 9 7: 25 8: 20 4029 4 11: 25 1: 6 13: 20 4030 5 10: 25 7: 25 1: 13 4031 6 1: 10 1: 6 9: 20 4032 7 1: 10 1: 6 1: 8 4033 8 10: 25 7: 25 14: 20 4034Setting up quadratic distribution... 4035ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 4036PhiOnMesh: Number of (b)points on node 0 = 2280 4037PhiOnMesh: nlist on node 0 = 5131 4038 4039 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 4040 scf: 1 -465.764464 -465.758782 -465.758782 0.005745 -2.671563 0.014858 4041 scf: 2 -465.758748 -465.758778 -465.758778 0.000579 -2.680189 0.025802 4042 scf: 3 -465.758799 -465.758794 -465.758794 0.000331 -2.674774 0.002213 4043 scf: 4 -465.758794 -465.758794 -465.758794 0.000049 -2.674749 0.001550 4044 scf: 5 -465.758795 -465.758794 -465.758794 0.000083 -2.674766 0.000371 4045 4046SCF Convergence by DM+H criterion 4047max |DM_out - DM_in| : 0.0000827890 4048max |H_out - H_in| (eV) : 0.0003710915 4049SCF cycle converged after 5 iterations 4050 4051Using DM_out to compute the final energy and forces 4052No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 4053 4054siesta: E_KS(eV) = -465.7588 4055 4056siesta: Atomic forces (eV/Ang): 4057 1 -0.248805 2.153510 -0.446209 4058 2 -0.159365 -1.069405 0.098435 4059 3 0.379227 -1.044491 0.152970 4060---------------------------------------- 4061 Tot -0.028943 0.039614 -0.194804 4062---------------------------------------- 4063 Max 2.153510 4064 Res 0.902804 sqrt( Sum f_i^2 / 3N ) 4065---------------------------------------- 4066 Max 2.153510 constrained 4067 4068Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 1.28 5.06 -0.92 -0.77 0.04 -0.38 4069(Free)E + p*V (eV/cell) -466.2198 4070Target enthalpy (eV/cell) -465.7588 4071 4072siesta: Stress tensor (static) (eV/Ang**3): 4073 0.000921 -0.000259 0.000129 4074 -0.000259 0.003247 -0.000386 4075 0.000128 -0.000386 -0.000340 4076 4077siesta: Pressure (static): -2.04494868 kBar 4078 4079siesta: Stress tensor (total) (eV/Ang**3): 4080 0.000796 -0.000236 0.000025 4081 -0.000236 0.003157 -0.000480 4082 0.000024 -0.000480 -0.000577 4083 4084siesta: Pressure (total): -1.80327115 kBar 4085 4086siesta: Temp_ion = 354.716 K 4087 4088 ==================================== 4089 Begin MD step = 6 4090 ==================================== 4091 4092outcoor: Atomic coordinates (Ang): 4093 0.00703420 -0.00797009 0.00869550 1 1 O 4094 0.68031802 0.72702139 0.00049843 2 2 H 4095 -0.79328506 0.57144419 -0.14636624 2 3 H 4096 4097outcell: Unit cell vectors (Ang): 4098 8.000000 0.000000 0.000000 4099 0.000000 8.000000 0.000000 4100 0.000000 0.000000 6.400000 4101 4102outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 4103outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 4104outcell: Cell volume (Ang**3) : 409.6000 4105<dSpData1D:S at geom step 6 4106 <sparsity:sparsity for geom step 6 4107 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 4108 <dData1D:(new from dSpData1D) n=69, refcount: 1> 4109refcount: 1> 4110new_DM -- step: 6 4111Re-using DM from previous geometries... 4112Number of DMs in history: 1 4113 DM extrapolation coefficients: 41141 1.00000 4115New DM after history re-use: 4116<dSpData2D:SpM extrapolated using coords 4117 <sparsity:sparsity for geom step 6 4118 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 4119 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 4120refcount: 1> 4121No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 4122New grid distribution: 1 4123 1 1: 25 1: 13 1: 5 4124 2 1: 25 1: 13 6: 10 4125 3 1: 25 1: 13 11: 15 4126 4 1: 25 1: 13 16: 20 4127 5 1: 25 14: 25 1: 5 4128 6 1: 25 14: 25 6: 10 4129 7 1: 25 14: 25 11: 15 4130 8 1: 25 14: 25 16: 20 4131 4132InitMesh: MESH = 50 x 50 x 40 = 100000 4133InitMesh: (bp) = 25 x 25 x 20 = 12500 4134InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 4135ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 4136New grid distribution: 2 4137 1 7: 25 6: 25 1: 6 4138 2 8: 25 1: 5 1: 6 4139 3 8: 25 1: 5 7: 20 4140 4 1: 7 1: 5 7: 20 4141 5 1: 6 6: 25 1: 6 4142 6 1: 7 1: 5 1: 6 4143 7 7: 25 6: 25 7: 20 4144 8 1: 6 6: 25 7: 20 4145New grid distribution: 3 4146 1 1: 9 7: 25 1: 7 4147 2 11: 25 1: 6 1: 12 4148 3 1: 9 7: 25 8: 20 4149 4 11: 25 1: 6 13: 20 4150 5 10: 25 7: 25 1: 13 4151 6 1: 10 1: 6 9: 20 4152 7 1: 10 1: 6 1: 8 4153 8 10: 25 7: 25 14: 20 4154Setting up quadratic distribution... 4155ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 4156PhiOnMesh: Number of (b)points on node 0 = 2280 4157PhiOnMesh: nlist on node 0 = 5122 4158 4159 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 4160 scf: 1 -465.760349 -465.757967 -465.757967 0.005712 -2.675708 0.010053 4161 scf: 2 -465.757972 -465.757977 -465.757977 0.000562 -2.679296 0.010948 4162 scf: 3 -465.757983 -465.757981 -465.757981 0.000218 -2.677167 0.001650 4163 scf: 4 -465.757981 -465.757981 -465.757981 0.000035 -2.677074 0.001138 4164 scf: 5 -465.757981 -465.757981 -465.757981 0.000052 -2.677020 0.000341 4165 4166SCF Convergence by DM+H criterion 4167max |DM_out - DM_in| : 0.0000515139 4168max |H_out - H_in| (eV) : 0.0003408861 4169SCF cycle converged after 5 iterations 4170 4171Using DM_out to compute the final energy and forces 4172No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 4173 4174siesta: E_KS(eV) = -465.7580 4175 4176siesta: Atomic forces (eV/Ang): 4177 1 -0.331172 2.156705 -0.470740 4178 2 -0.126950 -1.042201 0.101920 4179 3 0.427411 -1.075341 0.166664 4180---------------------------------------- 4181 Tot -0.030711 0.039163 -0.202155 4182---------------------------------------- 4183 Max 2.156705 4184 Res 0.910564 sqrt( Sum f_i^2 / 3N ) 4185---------------------------------------- 4186 Max 2.156705 constrained 4187 4188Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 1.35 5.05 -0.90 -0.84 0.09 -0.60 4189(Free)E + p*V (eV/cell) -466.2271 4190Target enthalpy (eV/cell) -465.7580 4191 4192siesta: Stress tensor (static) (eV/Ang**3): 4193 0.000969 -0.000382 0.000154 4194 -0.000382 0.003241 -0.000413 4195 0.000153 -0.000413 -0.000329 4196 4197siesta: Pressure (static): -2.07224449 kBar 4198 4199siesta: Stress tensor (total) (eV/Ang**3): 4200 0.000846 -0.000372 0.000057 4201 -0.000373 0.003152 -0.000522 4202 0.000056 -0.000522 -0.000562 4203 4204siesta: Pressure (total): -1.83484591 kBar 4205 4206siesta: Temp_ion = 351.583 K 4207 4208 ==================================== 4209 Begin MD step = 7 4210 ==================================== 4211 4212outcoor: Atomic coordinates (Ang): 4213 0.00737969 -0.00786822 0.00897757 1 1 O 4214 0.67688293 0.72892697 0.00083651 2 2 H 4215 -0.79549544 0.56808461 -0.15218726 2 3 H 4216 4217outcell: Unit cell vectors (Ang): 4218 8.000000 0.000000 0.000000 4219 0.000000 8.000000 0.000000 4220 0.000000 0.000000 6.400000 4221 4222outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 4223outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 4224outcell: Cell volume (Ang**3) : 409.6000 4225<dSpData1D:S at geom step 7 4226 <sparsity:sparsity for geom step 7 4227 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 4228 <dData1D:(new from dSpData1D) n=69, refcount: 1> 4229refcount: 1> 4230new_DM -- step: 7 4231Re-using DM from previous geometries... 4232Number of DMs in history: 1 4233 DM extrapolation coefficients: 42341 1.00000 4235New DM after history re-use: 4236<dSpData2D:SpM extrapolated using coords 4237 <sparsity:sparsity for geom step 7 4238 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 4239 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 4240refcount: 1> 4241No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 4242New grid distribution: 1 4243 1 1: 25 1: 13 1: 5 4244 2 1: 25 1: 13 6: 10 4245 3 1: 25 1: 13 11: 15 4246 4 1: 25 1: 13 16: 20 4247 5 1: 25 14: 25 1: 5 4248 6 1: 25 14: 25 6: 10 4249 7 1: 25 14: 25 11: 15 4250 8 1: 25 14: 25 16: 20 4251 4252InitMesh: MESH = 50 x 50 x 40 = 100000 4253InitMesh: (bp) = 25 x 25 x 20 = 12500 4254InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 4255ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 4256New grid distribution: 2 4257 1 7: 25 6: 25 1: 6 4258 2 8: 25 1: 5 1: 6 4259 3 8: 25 1: 5 7: 20 4260 4 1: 7 1: 5 7: 20 4261 5 1: 6 6: 25 1: 6 4262 6 1: 7 1: 5 1: 6 4263 7 7: 25 6: 25 7: 20 4264 8 1: 6 6: 25 7: 20 4265New grid distribution: 3 4266 1 1: 9 7: 25 1: 7 4267 2 11: 25 1: 6 1: 12 4268 3 1: 9 7: 25 8: 20 4269 4 11: 25 1: 6 13: 20 4270 5 10: 25 7: 25 1: 13 4271 6 1: 10 1: 6 9: 20 4272 7 1: 10 1: 6 1: 8 4273 8 10: 25 7: 25 14: 20 4274Setting up quadratic distribution... 4275ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 4276PhiOnMesh: Number of (b)points on node 0 = 2280 4277PhiOnMesh: nlist on node 0 = 5107 4278 4279 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 4280 scf: 1 -465.757083 -465.758033 -465.758033 0.005681 -2.676866 0.010052 4281 scf: 2 -465.758039 -465.758039 -465.758039 0.000542 -2.675360 0.006013 4282 scf: 3 -465.758042 -465.758041 -465.758041 0.000169 -2.676196 0.001181 4283 scf: 4 -465.758041 -465.758041 -465.758041 0.000021 -2.676268 0.000841 4284 4285SCF Convergence by DM+H criterion 4286max |DM_out - DM_in| : 0.0000205560 4287max |H_out - H_in| (eV) : 0.0008407716 4288SCF cycle converged after 4 iterations 4289 4290Using DM_out to compute the final energy and forces 4291No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 4292 4293siesta: E_KS(eV) = -465.7580 4294 4295siesta: Atomic forces (eV/Ang): 4296 1 -0.409533 2.138843 -0.492447 4297 2 -0.086969 -1.004243 0.105501 4298 3 0.466050 -1.096827 0.178280 4299---------------------------------------- 4300 Tot -0.030452 0.037773 -0.208666 4301---------------------------------------- 4302 Max 2.138843 4303 Res 0.910682 sqrt( Sum f_i^2 / 3N ) 4304---------------------------------------- 4305 Max 2.138843 constrained 4306 4307Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 1.38 4.97 -0.88 -0.90 0.13 -0.81 4308(Free)E + p*V (eV/cell) -466.2248 4309Target enthalpy (eV/cell) -465.7580 4310 4311siesta: Stress tensor (static) (eV/Ang**3): 4312 0.000981 -0.000502 0.000176 4313 -0.000503 0.003198 -0.000436 4314 0.000173 -0.000435 -0.000320 4315 4316siesta: Pressure (static): -2.06096253 kBar 4317 4318siesta: Stress tensor (total) (eV/Ang**3): 4319 0.000861 -0.000505 0.000087 4320 -0.000506 0.003105 -0.000560 4321 0.000084 -0.000560 -0.000548 4322 4323siesta: Pressure (total): -1.82566041 kBar 4324 4325siesta: Temp_ion = 351.835 K 4326 4327 ==================================== 4328 Begin MD step = 8 4329 ==================================== 4330 4331outcoor: Atomic coordinates (Ang): 4332 0.00771538 -0.00771512 0.00924784 1 1 O 4333 0.67341485 0.73045158 0.00121461 2 2 H 4334 -0.79752901 0.56430894 -0.15794065 2 3 H 4335 4336outcell: Unit cell vectors (Ang): 4337 8.000000 0.000000 0.000000 4338 0.000000 8.000000 0.000000 4339 0.000000 0.000000 6.400000 4340 4341outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 4342outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 4343outcell: Cell volume (Ang**3) : 409.6000 4344<dSpData1D:S at geom step 8 4345 <sparsity:sparsity for geom step 8 4346 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 4347 <dData1D:(new from dSpData1D) n=69, refcount: 1> 4348refcount: 1> 4349new_DM -- step: 8 4350Re-using DM from previous geometries... 4351Number of DMs in history: 1 4352 DM extrapolation coefficients: 43531 1.00000 4354New DM after history re-use: 4355<dSpData2D:SpM extrapolated using coords 4356 <sparsity:sparsity for geom step 8 4357 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 4358 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 4359refcount: 1> 4360No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 4361New grid distribution: 1 4362 1 1: 25 1: 13 1: 5 4363 2 1: 25 1: 13 6: 10 4364 3 1: 25 1: 13 11: 15 4365 4 1: 25 1: 13 16: 20 4366 5 1: 25 14: 25 1: 5 4367 6 1: 25 14: 25 6: 10 4368 7 1: 25 14: 25 11: 15 4369 8 1: 25 14: 25 16: 20 4370 4371InitMesh: MESH = 50 x 50 x 40 = 100000 4372InitMesh: (bp) = 25 x 25 x 20 = 12500 4373InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 4374ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 4375New grid distribution: 2 4376 1 7: 25 6: 25 1: 6 4377 2 8: 25 1: 5 1: 6 4378 3 8: 25 1: 5 7: 20 4379 4 1: 7 1: 5 7: 20 4380 5 1: 6 6: 25 1: 6 4381 6 1: 7 1: 5 1: 6 4382 7 7: 25 6: 25 7: 20 4383 8 1: 6 6: 25 7: 20 4384New grid distribution: 3 4385 1 1: 9 7: 25 1: 7 4386 2 11: 25 1: 6 1: 12 4387 3 1: 9 7: 25 8: 20 4388 4 11: 25 1: 6 13: 20 4389 5 10: 25 7: 25 1: 13 4390 6 1: 10 1: 6 9: 20 4391 7 1: 10 1: 6 1: 8 4392 8 10: 25 7: 25 14: 20 4393Setting up quadratic distribution... 4394ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 4395PhiOnMesh: Number of (b)points on node 0 = 2280 4396PhiOnMesh: nlist on node 0 = 5099 4397 4398 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 4399 scf: 1 -465.754697 -465.758960 -465.758960 0.005614 -2.675017 0.011672 4400 scf: 2 -465.758943 -465.758960 -465.758960 0.000641 -2.668420 0.019340 4401 scf: 3 -465.758973 -465.758970 -465.758970 0.000360 -2.672491 0.002014 4402 scf: 4 -465.758970 -465.758970 -465.758970 0.000045 -2.672540 0.001401 4403 scf: 5 -465.758970 -465.758970 -465.758970 0.000073 -2.672556 0.000353 4404 4405SCF Convergence by DM+H criterion 4406max |DM_out - DM_in| : 0.0000734859 4407max |H_out - H_in| (eV) : 0.0003526076 4408SCF cycle converged after 5 iterations 4409 4410Using DM_out to compute the final energy and forces 4411No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 4412 4413siesta: E_KS(eV) = -465.7590 4414 4415siesta: Atomic forces (eV/Ang): 4416 1 -0.485248 2.100666 -0.512272 4417 2 -0.039845 -0.956079 0.108094 4418 3 0.494085 -1.108416 0.189496 4419---------------------------------------- 4420 Tot -0.031007 0.036171 -0.214682 4421---------------------------------------- 4422 Max 2.100666 4423 Res 0.903491 sqrt( Sum f_i^2 / 3N ) 4424---------------------------------------- 4425 Max 2.100666 constrained 4426 4427Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 1.36 4.83 -0.85 -0.95 0.18 -1.02 4428(Free)E + p*V (eV/cell) -466.2141 4429Target enthalpy (eV/cell) -465.7590 4430 4431siesta: Stress tensor (static) (eV/Ang**3): 4432 0.000965 -0.000619 0.000195 4433 -0.000619 0.003119 -0.000455 4434 0.000194 -0.000455 -0.000310 4435 4436siesta: Pressure (static): -2.01595119 kBar 4437 4438siesta: Stress tensor (total) (eV/Ang**3): 4439 0.000849 -0.000634 0.000115 4440 -0.000634 0.003018 -0.000594 4441 0.000114 -0.000594 -0.000533 4442 4443siesta: Pressure (total): -1.78048075 kBar 4444 4445siesta: Temp_ion = 355.436 K 4446 4447 ==================================== 4448 Begin MD step = 9 4449 ==================================== 4450 4451outcoor: Atomic coordinates (Ang): 4452 0.00803945 -0.00751172 0.00950584 1 1 O 4453 0.66993165 0.73161348 0.00163372 2 2 H 4454 -0.79937514 0.56011276 -0.16362215 2 3 H 4455 4456outcell: Unit cell vectors (Ang): 4457 8.000000 0.000000 0.000000 4458 0.000000 8.000000 0.000000 4459 0.000000 0.000000 6.400000 4460 4461outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 4462outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 4463outcell: Cell volume (Ang**3) : 409.6000 4464<dSpData1D:S at geom step 9 4465 <sparsity:sparsity for geom step 9 4466 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 4467 <dData1D:(new from dSpData1D) n=69, refcount: 1> 4468refcount: 1> 4469new_DM -- step: 9 4470Re-using DM from previous geometries... 4471Number of DMs in history: 1 4472 DM extrapolation coefficients: 44731 1.00000 4474New DM after history re-use: 4475<dSpData2D:SpM extrapolated using coords 4476 <sparsity:sparsity for geom step 9 4477 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 4478 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 4479refcount: 1> 4480No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 4481New grid distribution: 1 4482 1 1: 25 1: 13 1: 5 4483 2 1: 25 1: 13 6: 10 4484 3 1: 25 1: 13 11: 15 4485 4 1: 25 1: 13 16: 20 4486 5 1: 25 14: 25 1: 5 4487 6 1: 25 14: 25 6: 10 4488 7 1: 25 14: 25 11: 15 4489 8 1: 25 14: 25 16: 20 4490 4491InitMesh: MESH = 50 x 50 x 40 = 100000 4492InitMesh: (bp) = 25 x 25 x 20 = 12500 4493InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 4494ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 4495New grid distribution: 2 4496 1 7: 25 6: 25 1: 6 4497 2 8: 25 1: 5 1: 6 4498 3 8: 25 1: 5 7: 20 4499 4 1: 7 1: 5 7: 20 4500 5 1: 6 6: 25 1: 6 4501 6 1: 7 1: 5 1: 6 4502 7 7: 25 6: 25 7: 20 4503 8 1: 6 6: 25 7: 20 4504New grid distribution: 3 4505 1 1: 9 7: 25 1: 7 4506 2 11: 25 1: 6 1: 12 4507 3 1: 9 7: 25 8: 20 4508 4 11: 25 1: 6 13: 20 4509 5 10: 25 7: 25 1: 13 4510 6 1: 10 1: 6 9: 20 4511 7 1: 10 1: 6 1: 8 4512 8 10: 25 7: 25 14: 20 4513Setting up quadratic distribution... 4514ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 4515PhiOnMesh: Number of (b)points on node 0 = 2280 4516PhiOnMesh: nlist on node 0 = 5093 4517 4518 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 4519 scf: 1 -465.753205 -465.760706 -465.760706 0.005610 -2.670056 0.018970 4520 scf: 2 -465.760644 -465.760695 -465.760695 0.000972 -2.658784 0.032965 4521 scf: 3 -465.760728 -465.760720 -465.760720 0.000579 -2.665911 0.002247 4522 scf: 4 -465.760721 -465.760720 -465.760720 0.000050 -2.665896 0.001584 4523 scf: 5 -465.760721 -465.760721 -465.760721 0.000088 -2.665823 0.000358 4524 4525SCF Convergence by DM+H criterion 4526max |DM_out - DM_in| : 0.0000879326 4527max |H_out - H_in| (eV) : 0.0003575688 4528SCF cycle converged after 5 iterations 4529 4530Using DM_out to compute the final energy and forces 4531No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 4532 4533siesta: E_KS(eV) = -465.7607 4534 4535siesta: Atomic forces (eV/Ang): 4536 1 -0.556615 2.043030 -0.529167 4537 2 0.013924 -0.897853 0.110719 4538 3 0.511365 -1.110715 0.198123 4539---------------------------------------- 4540 Tot -0.031326 0.034461 -0.220325 4541---------------------------------------- 4542 Max 2.043030 4543 Res 0.889247 sqrt( Sum f_i^2 / 3N ) 4544---------------------------------------- 4545 Max 2.043030 constrained 4546 4547Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 1.29 4.63 -0.83 -1.00 0.22 -1.21 4548(Free)E + p*V (eV/cell) -466.1949 4549Target enthalpy (eV/cell) -465.7607 4550 4551siesta: Stress tensor (static) (eV/Ang**3): 4552 0.000919 -0.000732 0.000210 4553 -0.000732 0.003008 -0.000470 4554 0.000209 -0.000470 -0.000301 4555 4556siesta: Pressure (static): -1.93632173 kBar 4557 4558siesta: Stress tensor (total) (eV/Ang**3): 4559 0.000807 -0.000758 0.000139 4560 -0.000758 0.002891 -0.000624 4561 0.000138 -0.000624 -0.000518 4562 4563siesta: Pressure (total): -1.69844067 kBar 4564 4565siesta: Temp_ion = 362.224 K 4566 4567 ==================================== 4568 Begin MD step = 10 4569 ==================================== 4570 4571outcoor: Atomic coordinates (Ang): 4572 0.00835019 -0.00725939 0.00975117 1 1 O 4573 0.66645374 0.73243476 0.00209483 2 2 H 4574 -0.80102728 0.55549522 -0.16922850 2 3 H 4575 4576outcell: Unit cell vectors (Ang): 4577 8.000000 0.000000 0.000000 4578 0.000000 8.000000 0.000000 4579 0.000000 0.000000 6.400000 4580 4581outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 4582outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 4583outcell: Cell volume (Ang**3) : 409.6000 4584<dSpData1D:S at geom step 10 4585 <sparsity:sparsity for geom step 10 4586 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 4587 <dData1D:(new from dSpData1D) n=69, refcount: 1> 4588refcount: 1> 4589new_DM -- step: 10 4590Re-using DM from previous geometries... 4591Number of DMs in history: 1 4592 DM extrapolation coefficients: 45931 1.00000 4594New DM after history re-use: 4595<dSpData2D:SpM extrapolated using coords 4596 <sparsity:sparsity for geom step 10 4597 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 4598 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 4599refcount: 1> 4600No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 4601New grid distribution: 1 4602 1 1: 25 1: 13 1: 5 4603 2 1: 25 1: 13 6: 10 4604 3 1: 25 1: 13 11: 15 4605 4 1: 25 1: 13 16: 20 4606 5 1: 25 14: 25 1: 5 4607 6 1: 25 14: 25 6: 10 4608 7 1: 25 14: 25 11: 15 4609 8 1: 25 14: 25 16: 20 4610 4611InitMesh: MESH = 50 x 50 x 40 = 100000 4612InitMesh: (bp) = 25 x 25 x 20 = 12500 4613InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 4614ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 4615New grid distribution: 2 4616 1 7: 25 6: 25 1: 6 4617 2 8: 25 1: 5 1: 6 4618 3 8: 25 1: 5 7: 20 4619 4 1: 7 1: 5 7: 20 4620 5 1: 6 6: 25 1: 6 4621 6 1: 7 1: 5 1: 6 4622 7 7: 25 6: 25 7: 20 4623 8 1: 6 6: 25 7: 20 4624New grid distribution: 3 4625 1 1: 9 7: 25 1: 7 4626 2 11: 25 1: 6 1: 12 4627 3 1: 9 7: 25 8: 20 4628 4 11: 25 1: 6 13: 20 4629 5 10: 25 7: 25 1: 13 4630 6 1: 10 1: 6 9: 20 4631 7 1: 10 1: 6 1: 8 4632 8 10: 25 7: 25 14: 20 4633Setting up quadratic distribution... 4634ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 4635PhiOnMesh: Number of (b)points on node 0 = 2280 4636PhiOnMesh: nlist on node 0 = 5101 4637 4638 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 4639 scf: 1 -465.752595 -465.763205 -465.763205 0.005574 -2.662237 0.026902 4640 scf: 2 -465.763070 -465.763176 -465.763176 0.001307 -2.646130 0.047025 4641 scf: 3 -465.763242 -465.763225 -465.763225 0.000795 -2.656398 0.002435 4642 scf: 4 -465.763226 -465.763226 -465.763226 0.000051 -2.656333 0.001638 4643 scf: 5 -465.763226 -465.763226 -465.763226 0.000092 -2.656178 0.000357 4644 4645SCF Convergence by DM+H criterion 4646max |DM_out - DM_in| : 0.0000923641 4647max |H_out - H_in| (eV) : 0.0003566734 4648SCF cycle converged after 5 iterations 4649 4650Using DM_out to compute the final energy and forces 4651No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 4652 4653siesta: E_KS(eV) = -465.7632 4654 4655siesta: Atomic forces (eV/Ang): 4656 1 -0.623931 1.965534 -0.542832 4657 2 0.073970 -0.830063 0.113077 4658 3 0.517897 -1.103604 0.204606 4659---------------------------------------- 4660 Tot -0.032064 0.031867 -0.225150 4661---------------------------------------- 4662 Max 1.965534 4663 Res 0.868112 sqrt( Sum f_i^2 / 3N ) 4664---------------------------------------- 4665 Max 1.965534 constrained 4666 4667Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 1.17 4.37 -0.81 -1.04 0.25 -1.41 4668(Free)E + p*V (eV/cell) -466.1665 4669Target enthalpy (eV/cell) -465.7632 4670 4671siesta: Stress tensor (static) (eV/Ang**3): 4672 0.000839 -0.000842 0.000221 4673 -0.000842 0.002862 -0.000481 4674 0.000220 -0.000481 -0.000294 4675 4676siesta: Pressure (static): -1.81973287 kBar 4677 4678siesta: Stress tensor (total) (eV/Ang**3): 4679 0.000732 -0.000877 0.000160 4680 -0.000877 0.002726 -0.000648 4681 0.000158 -0.000649 -0.000505 4682 4683siesta: Pressure (total): -1.57730944 kBar 4684 4685siesta: Temp_ion = 371.921 K 4686 4687 ==================================== 4688 Begin MD step = 11 4689 ==================================== 4690 4691outcoor: Atomic coordinates (Ang): 4692 0.00864599 -0.00696000 0.00998350 1 1 O 4693 0.66300388 0.73294114 0.00259884 2 2 H 4694 -0.80248295 0.55045901 -0.17475722 2 3 H 4695 4696outcell: Unit cell vectors (Ang): 4697 8.000000 0.000000 0.000000 4698 0.000000 8.000000 0.000000 4699 0.000000 0.000000 6.400000 4700 4701outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 4702outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 4703outcell: Cell volume (Ang**3) : 409.6000 4704<dSpData1D:S at geom step 11 4705 <sparsity:sparsity for geom step 11 4706 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 4707 <dData1D:(new from dSpData1D) n=69, refcount: 1> 4708refcount: 1> 4709new_DM -- step: 11 4710Re-using DM from previous geometries... 4711Number of DMs in history: 1 4712 DM extrapolation coefficients: 47131 1.00000 4714New DM after history re-use: 4715<dSpData2D:SpM extrapolated using coords 4716 <sparsity:sparsity for geom step 11 4717 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 4718 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 4719refcount: 1> 4720No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 4721New grid distribution: 1 4722 1 1: 25 1: 13 1: 5 4723 2 1: 25 1: 13 6: 10 4724 3 1: 25 1: 13 11: 15 4725 4 1: 25 1: 13 16: 20 4726 5 1: 25 14: 25 1: 5 4727 6 1: 25 14: 25 6: 10 4728 7 1: 25 14: 25 11: 15 4729 8 1: 25 14: 25 16: 20 4730 4731InitMesh: MESH = 50 x 50 x 40 = 100000 4732InitMesh: (bp) = 25 x 25 x 20 = 12500 4733InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 4734ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 4735New grid distribution: 2 4736 1 7: 25 6: 25 1: 6 4737 2 8: 25 1: 5 1: 6 4738 3 8: 25 1: 5 7: 20 4739 4 1: 7 1: 5 7: 20 4740 5 1: 6 6: 25 1: 6 4741 6 1: 7 1: 5 1: 6 4742 7 7: 25 6: 25 7: 20 4743 8 1: 6 6: 25 7: 20 4744New grid distribution: 3 4745 1 1: 9 7: 25 1: 7 4746 2 11: 25 1: 6 1: 12 4747 3 1: 9 7: 25 8: 20 4748 4 11: 25 1: 6 13: 20 4749 5 10: 25 7: 25 1: 13 4750 6 1: 10 1: 6 9: 20 4751 7 1: 10 1: 6 1: 8 4752 8 10: 25 7: 25 14: 20 4753Setting up quadratic distribution... 4754ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 4755PhiOnMesh: Number of (b)points on node 0 = 2280 4756PhiOnMesh: nlist on node 0 = 5094 4757 4758 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 4759 scf: 1 -465.752825 -465.766359 -465.766359 0.005537 -2.651523 0.034507 4760 scf: 2 -465.766133 -465.766309 -465.766309 0.001623 -2.630803 0.060277 4761 scf: 3 -465.766416 -465.766389 -465.766389 0.000996 -2.644045 0.002529 4762 scf: 4 -465.766390 -465.766389 -465.766389 0.000050 -2.643939 0.001652 4763 scf: 5 -465.766390 -465.766390 -465.766390 0.000093 -2.643710 0.000358 4764 4765SCF Convergence by DM+H criterion 4766max |DM_out - DM_in| : 0.0000932700 4767max |H_out - H_in| (eV) : 0.0003581336 4768SCF cycle converged after 5 iterations 4769 4770Using DM_out to compute the final energy and forces 4771No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 4772 4773siesta: E_KS(eV) = -465.7664 4774 4775siesta: Atomic forces (eV/Ang): 4776 1 -0.685280 1.870618 -0.553041 4777 2 0.139091 -0.753585 0.115098 4778 3 0.513484 -1.087257 0.208667 4779---------------------------------------- 4780 Tot -0.032705 0.029775 -0.229276 4781---------------------------------------- 4782 Max 1.870618 4783 Res 0.840932 sqrt( Sum f_i^2 / 3N ) 4784---------------------------------------- 4785 Max 1.870618 constrained 4786 4787Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 1.01 4.05 -0.79 -1.07 0.28 -1.58 4788(Free)E + p*V (eV/cell) -466.1306 4789Target enthalpy (eV/cell) -465.7664 4790 4791siesta: Stress tensor (static) (eV/Ang**3): 4792 0.000731 -0.000945 0.000227 4793 -0.000946 0.002689 -0.000487 4794 0.000226 -0.000487 -0.000286 4795 4796siesta: Pressure (static): -1.67353522 kBar 4797 4798siesta: Stress tensor (total) (eV/Ang**3): 4799 0.000630 -0.000987 0.000175 4800 -0.000987 0.002529 -0.000667 4801 0.000174 -0.000667 -0.000492 4802 4803siesta: Pressure (total): -1.42462137 kBar 4804 4805siesta: Temp_ion = 384.139 K 4806 4807 ==================================== 4808 Begin MD step = 12 4809 ==================================== 4810 4811outcoor: Atomic coordinates (Ang): 4812 0.00892538 -0.00661580 0.01020259 1 1 O 4813 0.65960680 0.73316164 0.00314652 2 2 H 4814 -0.80374381 0.54501032 -0.18020678 2 3 H 4815 4816outcell: Unit cell vectors (Ang): 4817 8.000000 0.000000 0.000000 4818 0.000000 8.000000 0.000000 4819 0.000000 0.000000 6.400000 4820 4821outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 4822outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 4823outcell: Cell volume (Ang**3) : 409.6000 4824<dSpData1D:S at geom step 12 4825 <sparsity:sparsity for geom step 12 4826 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 4827 <dData1D:(new from dSpData1D) n=69, refcount: 1> 4828refcount: 1> 4829new_DM -- step: 12 4830Re-using DM from previous geometries... 4831Number of DMs in history: 1 4832 DM extrapolation coefficients: 48331 1.00000 4834New DM after history re-use: 4835<dSpData2D:SpM extrapolated using coords 4836 <sparsity:sparsity for geom step 12 4837 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 4838 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 4839refcount: 1> 4840No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 4841New grid distribution: 1 4842 1 1: 25 1: 13 1: 5 4843 2 1: 25 1: 13 6: 10 4844 3 1: 25 1: 13 11: 15 4845 4 1: 25 1: 13 16: 20 4846 5 1: 25 14: 25 1: 5 4847 6 1: 25 14: 25 6: 10 4848 7 1: 25 14: 25 11: 15 4849 8 1: 25 14: 25 16: 20 4850 4851InitMesh: MESH = 50 x 50 x 40 = 100000 4852InitMesh: (bp) = 25 x 25 x 20 = 12500 4853InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 4854ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 4855New grid distribution: 2 4856 1 7: 25 6: 25 1: 6 4857 2 8: 25 1: 5 1: 6 4858 3 8: 25 1: 5 7: 20 4859 4 1: 7 1: 5 7: 20 4860 5 1: 6 6: 25 1: 6 4861 6 1: 7 1: 5 1: 6 4862 7 7: 25 6: 25 7: 20 4863 8 1: 6 6: 25 7: 20 4864New grid distribution: 3 4865 1 1: 9 7: 25 1: 7 4866 2 11: 25 1: 6 1: 12 4867 3 1: 9 7: 25 8: 20 4868 4 11: 25 1: 6 13: 20 4869 5 10: 25 7: 25 1: 13 4870 6 1: 10 1: 6 9: 20 4871 7 1: 10 1: 6 1: 8 4872 8 10: 25 7: 25 14: 20 4873Setting up quadratic distribution... 4874ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 4875PhiOnMesh: Number of (b)points on node 0 = 2280 4876PhiOnMesh: nlist on node 0 = 5088 4877 4878 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 4879 scf: 1 -465.753811 -465.770036 -465.770036 0.005500 -2.638003 0.041618 4880 scf: 2 -465.769706 -465.769960 -465.769960 0.001915 -2.612949 0.072547 4881 scf: 3 -465.770115 -465.770075 -465.770075 0.001180 -2.628967 0.002590 4882 scf: 4 -465.770076 -465.770076 -465.770076 0.000050 -2.628825 0.001650 4883 scf: 5 -465.770077 -465.770076 -465.770076 0.000093 -2.628528 0.000411 4884 4885SCF Convergence by DM+H criterion 4886max |DM_out - DM_in| : 0.0000926868 4887max |H_out - H_in| (eV) : 0.0004112516 4888SCF cycle converged after 5 iterations 4889 4890Using DM_out to compute the final energy and forces 4891No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 4892 4893siesta: E_KS(eV) = -465.7701 4894 4895siesta: Atomic forces (eV/Ang): 4896 1 -0.740025 1.758480 -0.559487 4897 2 0.208613 -0.668991 0.116822 4898 3 0.498431 -1.061770 0.210123 4899---------------------------------------- 4900 Tot -0.032981 0.027719 -0.232543 4901---------------------------------------- 4902 Max 1.758480 4903 Res 0.808123 sqrt( Sum f_i^2 / 3N ) 4904---------------------------------------- 4905 Max 1.758480 constrained 4906 4907Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 0.80 3.68 -0.77 -1.09 0.30 -1.74 4908(Free)E + p*V (eV/cell) -466.0870 4909Target enthalpy (eV/cell) -465.7701 4910 4911siesta: Stress tensor (static) (eV/Ang**3): 4912 0.000596 -0.001041 0.000229 4913 -0.001042 0.002487 -0.000487 4914 0.000228 -0.000488 -0.000280 4915 4916siesta: Pressure (static): -1.49658939 kBar 4917 4918siesta: Stress tensor (total) (eV/Ang**3): 4919 0.000501 -0.001088 0.000186 4920 -0.001089 0.002300 -0.000680 4921 0.000185 -0.000680 -0.000480 4922 4923siesta: Pressure (total): -1.23949878 kBar 4924 4925siesta: Temp_ion = 398.399 K 4926 4927 ==================================== 4928 Begin MD step = 13 4929 ==================================== 4930 4931outcoor: Atomic coordinates (Ang): 4932 0.00918705 -0.00622950 0.01040828 1 1 O 4933 0.65628885 0.73312834 0.00373851 2 2 H 4934 -0.80481559 0.53915884 -0.18557662 2 3 H 4935 4936outcell: Unit cell vectors (Ang): 4937 8.000000 0.000000 0.000000 4938 0.000000 8.000000 0.000000 4939 0.000000 0.000000 6.400000 4940 4941outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 4942outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 4943outcell: Cell volume (Ang**3) : 409.6000 4944<dSpData1D:S at geom step 13 4945 <sparsity:sparsity for geom step 13 4946 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 4947 <dData1D:(new from dSpData1D) n=69, refcount: 1> 4948refcount: 1> 4949new_DM -- step: 13 4950Re-using DM from previous geometries... 4951Number of DMs in history: 1 4952 DM extrapolation coefficients: 49531 1.00000 4954New DM after history re-use: 4955<dSpData2D:SpM extrapolated using coords 4956 <sparsity:sparsity for geom step 13 4957 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 4958 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 4959refcount: 1> 4960No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 4961New grid distribution: 1 4962 1 1: 25 1: 13 1: 5 4963 2 1: 25 1: 13 6: 10 4964 3 1: 25 1: 13 11: 15 4965 4 1: 25 1: 13 16: 20 4966 5 1: 25 14: 25 1: 5 4967 6 1: 25 14: 25 6: 10 4968 7 1: 25 14: 25 11: 15 4969 8 1: 25 14: 25 16: 20 4970 4971InitMesh: MESH = 50 x 50 x 40 = 100000 4972InitMesh: (bp) = 25 x 25 x 20 = 12500 4973InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 4974ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 4975New grid distribution: 2 4976 1 7: 25 6: 25 1: 6 4977 2 8: 25 1: 5 1: 6 4978 3 8: 25 1: 5 7: 20 4979 4 1: 7 1: 5 7: 20 4980 5 1: 6 6: 25 1: 6 4981 6 1: 7 1: 5 1: 6 4982 7 7: 25 6: 25 7: 20 4983 8 1: 6 6: 25 7: 20 4984New grid distribution: 3 4985 1 1: 10 7: 25 1: 7 4986 2 11: 25 1: 6 1: 12 4987 3 1: 10 7: 25 8: 20 4988 4 11: 25 1: 6 13: 20 4989 5 11: 25 7: 25 1: 13 4990 6 1: 10 1: 6 9: 20 4991 7 1: 10 1: 6 1: 8 4992 8 11: 25 7: 25 14: 20 4993Setting up quadratic distribution... 4994ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 4995PhiOnMesh: Number of (b)points on node 0 = 2280 4996PhiOnMesh: nlist on node 0 = 5091 4997 4998 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 4999 scf: 1 -465.755476 -465.774106 -465.774106 0.005539 -2.621797 0.048150 5000 scf: 2 -465.773666 -465.774005 -465.774005 0.002180 -2.592735 0.083670 5001 scf: 3 -465.774210 -465.774157 -465.774157 0.001345 -2.611302 0.002637 5002 scf: 4 -465.774158 -465.774158 -465.774158 0.000049 -2.611126 0.001641 5003 scf: 5 -465.774158 -465.774158 -465.774158 0.000091 -2.610770 0.000465 5004 5005SCF Convergence by DM+H criterion 5006max |DM_out - DM_in| : 0.0000912736 5007max |H_out - H_in| (eV) : 0.0004652322 5008SCF cycle converged after 5 iterations 5009 5010Using DM_out to compute the final energy and forces 5011No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 5012 5013siesta: E_KS(eV) = -465.7742 5014 5015siesta: Atomic forces (eV/Ang): 5016 1 -0.787740 1.629352 -0.562264 5017 2 0.281093 -0.577686 0.118204 5018 3 0.472696 -1.027533 0.208741 5019---------------------------------------- 5020 Tot -0.033952 0.024134 -0.235319 5021---------------------------------------- 5022 Max 1.629352 5023 Res 0.770354 sqrt( Sum f_i^2 / 3N ) 5024---------------------------------------- 5025 Max 1.629352 constrained 5026 5027Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 0.56 3.27 -0.75 -1.10 0.30 -1.89 5028(Free)E + p*V (eV/cell) -466.0359 5029Target enthalpy (eV/cell) -465.7742 5030 5031siesta: Stress tensor (static) (eV/Ang**3): 5032 0.000436 -0.001129 0.000225 5033 -0.001129 0.002257 -0.000484 5034 0.000223 -0.000484 -0.000276 5035 5036siesta: Pressure (static): -1.29064200 kBar 5037 5038siesta: Stress tensor (total) (eV/Ang**3): 5039 0.000348 -0.001179 0.000191 5040 -0.001180 0.002040 -0.000687 5041 0.000189 -0.000687 -0.000470 5042 5043siesta: Pressure (total): -1.02400730 kBar 5044 5045siesta: Temp_ion = 414.164 K 5046 5047 ==================================== 5048 Begin MD step = 14 5049 ==================================== 5050 5051outcoor: Atomic coordinates (Ang): 5052 0.00942985 -0.00580418 0.01060050 1 1 O 5053 0.65307754 0.73287589 0.00437535 2 2 H 5054 -0.80570804 0.53291754 -0.19086728 2 3 H 5055 5056outcell: Unit cell vectors (Ang): 5057 8.000000 0.000000 0.000000 5058 0.000000 8.000000 0.000000 5059 0.000000 0.000000 6.400000 5060 5061outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 5062outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 5063outcell: Cell volume (Ang**3) : 409.6000 5064<dSpData1D:S at geom step 14 5065 <sparsity:sparsity for geom step 14 5066 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 5067 <dData1D:(new from dSpData1D) n=69, refcount: 1> 5068refcount: 1> 5069new_DM -- step: 14 5070Re-using DM from previous geometries... 5071Number of DMs in history: 1 5072 DM extrapolation coefficients: 50731 1.00000 5074New DM after history re-use: 5075<dSpData2D:SpM extrapolated using coords 5076 <sparsity:sparsity for geom step 14 5077 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 5078 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 5079refcount: 1> 5080No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 5081New grid distribution: 1 5082 1 1: 25 1: 13 1: 5 5083 2 1: 25 1: 13 6: 10 5084 3 1: 25 1: 13 11: 15 5085 4 1: 25 1: 13 16: 20 5086 5 1: 25 14: 25 1: 5 5087 6 1: 25 14: 25 6: 10 5088 7 1: 25 14: 25 11: 15 5089 8 1: 25 14: 25 16: 20 5090 5091InitMesh: MESH = 50 x 50 x 40 = 100000 5092InitMesh: (bp) = 25 x 25 x 20 = 12500 5093InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 5094ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 5095New grid distribution: 2 5096 1 7: 25 6: 25 1: 6 5097 2 8: 25 1: 5 1: 6 5098 3 8: 25 1: 5 7: 20 5099 4 1: 7 1: 5 7: 20 5100 5 1: 6 6: 25 1: 6 5101 6 1: 7 1: 5 1: 6 5102 7 7: 25 6: 25 7: 20 5103 8 1: 6 6: 25 7: 20 5104New grid distribution: 3 5105 1 1: 10 7: 25 1: 7 5106 2 12: 25 1: 6 1: 12 5107 3 1: 10 7: 25 8: 20 5108 4 12: 25 1: 6 13: 20 5109 5 11: 25 7: 25 1: 13 5110 6 1: 11 1: 6 9: 20 5111 7 1: 11 1: 6 1: 8 5112 8 11: 25 7: 25 14: 20 5113Setting up quadratic distribution... 5114ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 5115PhiOnMesh: Number of (b)points on node 0 = 2280 5116PhiOnMesh: nlist on node 0 = 5083 5117 5118 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 5119 scf: 1 -465.757697 -465.778401 -465.778401 0.006016 -2.603030 0.054013 5120 scf: 2 -465.777852 -465.778274 -465.778274 0.002414 -2.570343 0.093494 5121 scf: 3 -465.778530 -465.778463 -465.778463 0.001490 -2.591198 0.002679 5122 scf: 4 -465.778465 -465.778464 -465.778464 0.000048 -2.590992 0.001629 5123 scf: 5 -465.778465 -465.778465 -465.778465 0.000090 -2.590584 0.000519 5124 5125SCF Convergence by DM+H criterion 5126max |DM_out - DM_in| : 0.0000901545 5127max |H_out - H_in| (eV) : 0.0005189689 5128SCF cycle converged after 5 iterations 5129 5130Using DM_out to compute the final energy and forces 5131No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 5132 5133siesta: E_KS(eV) = -465.7785 5134 5135siesta: Atomic forces (eV/Ang): 5136 1 -0.827155 1.485565 -0.561191 5137 2 0.355579 -0.480705 0.119253 5138 3 0.436559 -0.984928 0.204190 5139---------------------------------------- 5140 Tot -0.035017 0.019932 -0.237747 5141---------------------------------------- 5142 Max 1.485565 5143 Res 0.728783 sqrt( Sum f_i^2 / 3N ) 5144---------------------------------------- 5145 Max 1.485565 constrained 5146 5147Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 0.27 2.81 -0.74 -1.10 0.30 -2.02 5148(Free)E + p*V (eV/cell) -465.9783 5149Target enthalpy (eV/cell) -465.7785 5150 5151siesta: Stress tensor (static) (eV/Ang**3): 5152 0.000252 -0.001208 0.000214 5153 -0.001208 0.002005 -0.000475 5154 0.000212 -0.000475 -0.000274 5155 5156siesta: Pressure (static): -1.05880929 kBar 5157 5158siesta: Stress tensor (total) (eV/Ang**3): 5159 0.000171 -0.001259 0.000188 5160 -0.001259 0.001755 -0.000688 5161 0.000186 -0.000688 -0.000462 5162 5163siesta: Pressure (total): -0.78162372 kBar 5164 5165siesta: Temp_ion = 430.868 K 5166 5167 ==================================== 5168 Begin MD step = 15 5169 ==================================== 5170 5171outcoor: Atomic coordinates (Ang): 5172 0.00965284 -0.00534328 0.01077929 1 1 O 5173 0.65000113 0.73244108 0.00505743 2 2 H 5174 -0.80643488 0.52630259 -0.19608047 2 3 H 5175 5176outcell: Unit cell vectors (Ang): 5177 8.000000 0.000000 0.000000 5178 0.000000 8.000000 0.000000 5179 0.000000 0.000000 6.400000 5180 5181outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 5182outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 5183outcell: Cell volume (Ang**3) : 409.6000 5184<dSpData1D:S at geom step 15 5185 <sparsity:sparsity for geom step 15 5186 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 5187 <dData1D:(new from dSpData1D) n=69, refcount: 1> 5188refcount: 1> 5189new_DM -- step: 15 5190Re-using DM from previous geometries... 5191Number of DMs in history: 1 5192 DM extrapolation coefficients: 51931 1.00000 5194New DM after history re-use: 5195<dSpData2D:SpM extrapolated using coords 5196 <sparsity:sparsity for geom step 15 5197 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 5198 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 5199refcount: 1> 5200No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 5201New grid distribution: 1 5202 1 1: 25 1: 13 1: 5 5203 2 1: 25 1: 13 6: 10 5204 3 1: 25 1: 13 11: 15 5205 4 1: 25 1: 13 16: 20 5206 5 1: 25 14: 25 1: 5 5207 6 1: 25 14: 25 6: 10 5208 7 1: 25 14: 25 11: 15 5209 8 1: 25 14: 25 16: 20 5210 5211InitMesh: MESH = 50 x 50 x 40 = 100000 5212InitMesh: (bp) = 25 x 25 x 20 = 12500 5213InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 5214ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 5215New grid distribution: 2 5216 1 7: 25 6: 25 1: 6 5217 2 8: 25 1: 5 1: 6 5218 3 8: 25 1: 5 7: 20 5219 4 1: 7 1: 5 7: 20 5220 5 1: 6 6: 25 1: 6 5221 6 1: 7 1: 5 1: 6 5222 7 7: 25 6: 25 7: 20 5223 8 1: 6 6: 25 7: 20 5224New grid distribution: 3 5225 1 1: 10 7: 25 1: 7 5226 2 1: 14 1: 6 1: 8 5227 3 1: 10 7: 25 8: 20 5228 4 1: 14 1: 6 9: 20 5229 5 11: 25 7: 25 1: 13 5230 6 15: 25 1: 6 1: 12 5231 7 15: 25 1: 6 13: 20 5232 8 11: 25 7: 25 14: 20 5233Setting up quadratic distribution... 5234ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 5235PhiOnMesh: Number of (b)points on node 0 = 2280 5236PhiOnMesh: nlist on node 0 = 5075 5237 5238 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 5239 scf: 1 -465.760392 -465.782798 -465.782798 0.006435 -2.581865 0.059135 5240 scf: 2 -465.782152 -465.782652 -465.782652 0.002615 -2.545973 0.101923 5241 scf: 3 -465.782956 -465.782877 -465.782877 0.001612 -2.568832 0.002718 5242 scf: 4 -465.782878 -465.782878 -465.782878 0.000052 -2.568598 0.001616 5243 scf: 5 -465.782879 -465.782878 -465.782878 0.000096 -2.568144 0.000571 5244 5245SCF Convergence by DM+H criterion 5246max |DM_out - DM_in| : 0.0000959361 5247max |H_out - H_in| (eV) : 0.0005709931 5248SCF cycle converged after 5 iterations 5249 5250Using DM_out to compute the final energy and forces 5251No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 5252 5253siesta: E_KS(eV) = -465.7829 5254 5255siesta: Atomic forces (eV/Ang): 5256 1 -0.857230 1.329066 -0.555941 5257 2 0.430659 -0.379421 0.119955 5258 3 0.390456 -0.934322 0.196379 5259---------------------------------------- 5260 Tot -0.036115 0.015323 -0.239607 5261---------------------------------------- 5262 Max 1.329066 5263 Res 0.684602 sqrt( Sum f_i^2 / 3N ) 5264---------------------------------------- 5265 Max 1.329066 constrained 5266 5267Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -0.04 2.32 -0.73 -1.09 0.28 -2.12 5268(Free)E + p*V (eV/cell) -465.9150 5269Target enthalpy (eV/cell) -465.7829 5270 5271siesta: Stress tensor (static) (eV/Ang**3): 5272 0.000047 -0.001274 0.000196 5273 -0.001274 0.001735 -0.000460 5274 0.000195 -0.000460 -0.000274 5275 5276siesta: Pressure (static): -0.80530745 kBar 5277 5278siesta: Stress tensor (total) (eV/Ang**3): 5279 -0.000026 -0.001324 0.000178 5280 -0.001325 0.001450 -0.000683 5281 0.000177 -0.000683 -0.000456 5282 5283siesta: Pressure (total): -0.51694296 kBar 5284 5285siesta: Temp_ion = 447.943 K 5286 5287 ==================================== 5288 Begin MD step = 16 5289 ==================================== 5290 5291outcoor: Atomic coordinates (Ang): 5292 0.00985531 -0.00485055 0.01094476 1 1 O 5293 0.64708810 0.73186232 0.00578501 2 2 H 5294 -0.80701358 0.51933319 -0.20121916 2 3 H 5295 5296outcell: Unit cell vectors (Ang): 5297 8.000000 0.000000 0.000000 5298 0.000000 8.000000 0.000000 5299 0.000000 0.000000 6.400000 5300 5301outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 5302outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 5303outcell: Cell volume (Ang**3) : 409.6000 5304<dSpData1D:S at geom step 16 5305 <sparsity:sparsity for geom step 16 5306 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 5307 <dData1D:(new from dSpData1D) n=69, refcount: 1> 5308refcount: 1> 5309new_DM -- step: 16 5310Re-using DM from previous geometries... 5311Number of DMs in history: 1 5312 DM extrapolation coefficients: 53131 1.00000 5314New DM after history re-use: 5315<dSpData2D:SpM extrapolated using coords 5316 <sparsity:sparsity for geom step 16 5317 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 5318 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 5319refcount: 1> 5320No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 5321New grid distribution: 1 5322 1 1: 25 1: 13 1: 5 5323 2 1: 25 1: 13 6: 10 5324 3 1: 25 1: 13 11: 15 5325 4 1: 25 1: 13 16: 20 5326 5 1: 25 14: 25 1: 5 5327 6 1: 25 14: 25 6: 10 5328 7 1: 25 14: 25 11: 15 5329 8 1: 25 14: 25 16: 20 5330 5331InitMesh: MESH = 50 x 50 x 40 = 100000 5332InitMesh: (bp) = 25 x 25 x 20 = 12500 5333InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 5334ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 5335New grid distribution: 2 5336 1 7: 25 6: 25 1: 6 5337 2 8: 25 1: 5 1: 6 5338 3 8: 25 1: 5 7: 20 5339 4 1: 7 1: 5 7: 20 5340 5 1: 6 6: 25 1: 6 5341 6 1: 7 1: 5 1: 6 5342 7 7: 25 6: 25 7: 20 5343 8 1: 6 6: 25 7: 20 5344New grid distribution: 3 5345 1 1: 10 7: 25 1: 7 5346 2 1: 14 1: 6 1: 8 5347 3 1: 10 7: 25 8: 20 5348 4 1: 14 1: 6 9: 20 5349 5 11: 25 7: 25 1: 13 5350 6 15: 25 1: 6 1: 12 5351 7 15: 25 1: 6 13: 20 5352 8 11: 25 7: 25 14: 20 5353Setting up quadratic distribution... 5354ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 5355PhiOnMesh: Number of (b)points on node 0 = 2280 5356PhiOnMesh: nlist on node 0 = 5082 5357 5358 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 5359 scf: 1 -465.763468 -465.787164 -465.787164 0.006792 -2.558459 0.063454 5360 scf: 2 -465.786423 -465.786993 -465.786993 0.002781 -2.519827 0.108829 5361 scf: 3 -465.787338 -465.787248 -465.787248 0.001711 -2.544377 0.002754 5362 scf: 4 -465.787250 -465.787249 -465.787249 0.000055 -2.544118 0.001603 5363 scf: 5 -465.787250 -465.787249 -465.787249 0.000100 -2.543627 0.000620 5364 scf: 6 -465.787249 -465.787249 -465.787249 0.000010 -2.543563 0.000376 5365 5366SCF Convergence by DM+H criterion 5367max |DM_out - DM_in| : 0.0000101023 5368max |H_out - H_in| (eV) : 0.0003762859 5369SCF cycle converged after 6 iterations 5370 5371Using DM_out to compute the final energy and forces 5372No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 5373 5374siesta: E_KS(eV) = -465.7872 5375 5376siesta: Atomic forces (eV/Ang): 5377 1 -0.877478 1.162683 -0.546609 5378 2 0.505008 -0.275313 0.120104 5379 3 0.334784 -0.876204 0.185205 5380---------------------------------------- 5381 Tot -0.037686 0.011166 -0.241300 5382---------------------------------------- 5383 Max 1.162683 5384 Res 0.639440 sqrt( Sum f_i^2 / 3N ) 5385---------------------------------------- 5386 Max 1.162683 constrained 5387 5388Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -0.39 1.82 -0.73 -1.08 0.26 -2.21 5389(Free)E + p*V (eV/cell) -465.8474 5390Target enthalpy (eV/cell) -465.7872 5391 5392siesta: Stress tensor (static) (eV/Ang**3): 5393 -0.000176 -0.001329 0.000173 5394 -0.001329 0.001454 -0.000441 5395 0.000172 -0.000441 -0.000276 5396 5397siesta: Pressure (static): -0.53524507 kBar 5398 5399siesta: Stress tensor (total) (eV/Ang**3): 5400 -0.000241 -0.001377 0.000161 5401 -0.001377 0.001135 -0.000671 5402 0.000160 -0.000671 -0.000453 5403 5404siesta: Pressure (total): -0.23545233 kBar 5405 5406siesta: Temp_ion = 464.855 K 5407 5408 ==================================== 5409 Begin MD step = 17 5410 ==================================== 5411 5412outcoor: Atomic coordinates (Ang): 5413 0.01003676 -0.00432998 0.01109714 1 1 O 5414 0.64436664 0.73117912 0.00655816 2 2 H 5415 -0.80746529 0.51203138 -0.20628759 2 3 H 5416 5417outcell: Unit cell vectors (Ang): 5418 8.000000 0.000000 0.000000 5419 0.000000 8.000000 0.000000 5420 0.000000 0.000000 6.400000 5421 5422outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 5423outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 5424outcell: Cell volume (Ang**3) : 409.6000 5425<dSpData1D:S at geom step 17 5426 <sparsity:sparsity for geom step 17 5427 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 5428 <dData1D:(new from dSpData1D) n=69, refcount: 1> 5429refcount: 1> 5430new_DM -- step: 17 5431Re-using DM from previous geometries... 5432Number of DMs in history: 1 5433 DM extrapolation coefficients: 54341 1.00000 5435New DM after history re-use: 5436<dSpData2D:SpM extrapolated using coords 5437 <sparsity:sparsity for geom step 17 5438 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 5439 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 5440refcount: 1> 5441No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 5442New grid distribution: 1 5443 1 1: 25 1: 13 1: 5 5444 2 1: 25 1: 13 6: 10 5445 3 1: 25 1: 13 11: 15 5446 4 1: 25 1: 13 16: 20 5447 5 1: 25 14: 25 1: 5 5448 6 1: 25 14: 25 6: 10 5449 7 1: 25 14: 25 11: 15 5450 8 1: 25 14: 25 16: 20 5451 5452InitMesh: MESH = 50 x 50 x 40 = 100000 5453InitMesh: (bp) = 25 x 25 x 20 = 12500 5454InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 5455ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 5456New grid distribution: 2 5457 1 7: 25 6: 25 1: 6 5458 2 8: 25 1: 5 1: 6 5459 3 8: 25 1: 5 7: 20 5460 4 1: 7 1: 5 8: 20 5461 5 1: 6 6: 25 1: 6 5462 6 1: 7 1: 5 1: 7 5463 7 7: 25 6: 25 7: 20 5464 8 1: 6 6: 25 7: 20 5465New grid distribution: 3 5466 1 1: 10 7: 25 1: 7 5467 2 1: 15 1: 6 1: 8 5468 3 1: 10 7: 25 8: 20 5469 4 1: 15 1: 6 9: 20 5470 5 11: 25 7: 25 1: 13 5471 6 16: 25 1: 6 1: 12 5472 7 16: 25 1: 6 13: 20 5473 8 11: 25 7: 25 14: 20 5474Setting up quadratic distribution... 5475ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 5476PhiOnMesh: Number of (b)points on node 0 = 2280 5477PhiOnMesh: nlist on node 0 = 5072 5478 5479 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 5480 scf: 1 -465.766816 -465.791360 -465.791360 0.007092 -2.532993 0.066918 5481 scf: 2 -465.790548 -465.791173 -465.791173 0.002910 -2.492123 0.114104 5482 scf: 3 -465.791552 -465.791453 -465.791453 0.001787 -2.518029 0.002785 5483 scf: 4 -465.791454 -465.791454 -465.791454 0.000057 -2.517749 0.001604 5484 scf: 5 -465.791455 -465.791454 -465.791454 0.000104 -2.517225 0.000662 5485 scf: 6 -465.791454 -465.791454 -465.791454 0.000011 -2.517158 0.000404 5486 5487SCF Convergence by DM+H criterion 5488max |DM_out - DM_in| : 0.0000108125 5489max |H_out - H_in| (eV) : 0.0004040267 5490SCF cycle converged after 6 iterations 5491 5492Using DM_out to compute the final energy and forces 5493No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 5494 5495siesta: E_KS(eV) = -465.7915 5496 5497siesta: Atomic forces (eV/Ang): 5498 1 -0.886508 0.988341 -0.532947 5499 2 0.576942 -0.170251 0.120007 5500 3 0.270849 -0.811550 0.170356 5501---------------------------------------- 5502 Tot -0.038716 0.006540 -0.242585 5503---------------------------------------- 5504 Max 0.988341 5505 Res 0.594791 sqrt( Sum f_i^2 / 3N ) 5506---------------------------------------- 5507 Max 0.988341 constrained 5508 5509Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -0.75 1.30 -0.72 -1.05 0.22 -2.27 5510(Free)E + p*V (eV/cell) -465.7766 5511Target enthalpy (eV/cell) -465.7915 5512 5513siesta: Stress tensor (static) (eV/Ang**3): 5514 -0.000411 -0.001370 0.000143 5515 -0.001370 0.001164 -0.000416 5516 0.000142 -0.000416 -0.000280 5517 5518siesta: Pressure (static): -0.25295775 kBar 5519 5520siesta: Stress tensor (total) (eV/Ang**3): 5521 -0.000467 -0.001415 0.000136 5522 -0.001415 0.000810 -0.000654 5523 0.000135 -0.000654 -0.000452 5524 5525siesta: Pressure (total): 0.05815301 kBar 5526 5527siesta: Temp_ion = 481.130 K 5528 5529 ==================================== 5530 Begin MD step = 18 5531 ==================================== 5532 5533outcoor: Atomic coordinates (Ang): 5534 0.01019698 -0.00378574 0.01123676 1 1 O 5535 0.64186407 0.73043133 0.00737683 2 2 H 5536 -0.80781424 0.50442170 -0.21129140 2 3 H 5537 5538outcell: Unit cell vectors (Ang): 5539 8.000000 0.000000 0.000000 5540 0.000000 8.000000 0.000000 5541 0.000000 0.000000 6.400000 5542 5543outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 5544outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 5545outcell: Cell volume (Ang**3) : 409.6000 5546<dSpData1D:S at geom step 18 5547 <sparsity:sparsity for geom step 18 5548 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 5549 <dData1D:(new from dSpData1D) n=69, refcount: 1> 5550refcount: 1> 5551new_DM -- step: 18 5552Re-using DM from previous geometries... 5553Number of DMs in history: 1 5554 DM extrapolation coefficients: 55551 1.00000 5556New DM after history re-use: 5557<dSpData2D:SpM extrapolated using coords 5558 <sparsity:sparsity for geom step 18 5559 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 5560 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 5561refcount: 1> 5562No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 5563New grid distribution: 1 5564 1 1: 25 1: 13 1: 5 5565 2 1: 25 1: 13 6: 10 5566 3 1: 25 1: 13 11: 15 5567 4 1: 25 1: 13 16: 20 5568 5 1: 25 14: 25 1: 5 5569 6 1: 25 14: 25 6: 10 5570 7 1: 25 14: 25 11: 15 5571 8 1: 25 14: 25 16: 20 5572 5573InitMesh: MESH = 50 x 50 x 40 = 100000 5574InitMesh: (bp) = 25 x 25 x 20 = 12500 5575InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 5576ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 5577New grid distribution: 2 5578 1 7: 25 6: 25 1: 6 5579 2 8: 25 1: 5 1: 6 5580 3 8: 25 1: 5 7: 20 5581 4 1: 7 1: 5 8: 20 5582 5 1: 6 6: 25 1: 6 5583 6 1: 7 1: 5 1: 7 5584 7 7: 25 6: 25 7: 20 5585 8 1: 6 6: 25 7: 20 5586New grid distribution: 3 5587 1 1: 10 7: 25 1: 7 5588 2 1: 15 1: 6 1: 8 5589 3 1: 10 7: 25 8: 20 5590 4 1: 15 1: 6 9: 20 5591 5 11: 25 7: 25 1: 13 5592 6 16: 25 1: 6 1: 12 5593 7 16: 25 1: 6 13: 20 5594 8 11: 25 7: 25 14: 20 5595Setting up quadratic distribution... 5596ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 5597PhiOnMesh: Number of (b)points on node 0 = 2280 5598PhiOnMesh: nlist on node 0 = 5077 5599 5600 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 5601 scf: 1 -465.770371 -465.795295 -465.795295 0.007309 -2.505645 0.069492 5602 scf: 2 -465.794433 -465.795097 -465.795097 0.003001 -2.463057 0.117795 5603 scf: 3 -465.795500 -465.795395 -465.795395 0.001838 -2.489979 0.002818 5604 scf: 4 -465.795397 -465.795396 -465.795396 0.000059 -2.489682 0.001623 5605 scf: 5 -465.795397 -465.795396 -465.795396 0.000106 -2.489137 0.000700 5606 scf: 6 -465.795396 -465.795396 -465.795396 0.000011 -2.489067 0.000430 5607 5608SCF Convergence by DM+H criterion 5609max |DM_out - DM_in| : 0.0000114006 5610max |H_out - H_in| (eV) : 0.0004296090 5611SCF cycle converged after 6 iterations 5612 5613Using DM_out to compute the final energy and forces 5614No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 5615 5616siesta: E_KS(eV) = -465.7954 5617 5618siesta: Atomic forces (eV/Ang): 5619 1 -0.883531 0.809407 -0.515391 5620 2 0.644696 -0.066204 0.119423 5621 3 0.199077 -0.741155 0.151826 5622---------------------------------------- 5623 Tot -0.039757 0.002048 -0.244142 5624---------------------------------------- 5625 Max 0.883531 5626 Res 0.552536 sqrt( Sum f_i^2 / 3N ) 5627---------------------------------------- 5628 Max 0.883531 constrained 5629 5630Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -1.12 0.78 -0.73 -1.01 0.17 -2.30 5631(Free)E + p*V (eV/cell) -465.7041 5632Target enthalpy (eV/cell) -465.7954 5633 5634siesta: Stress tensor (static) (eV/Ang**3): 5635 -0.000654 -0.001396 0.000106 5636 -0.001396 0.000874 -0.000388 5637 0.000105 -0.000388 -0.000285 5638 5639siesta: Pressure (static): 0.03516456 kBar 5640 5641siesta: Stress tensor (total) (eV/Ang**3): 5642 -0.000702 -0.001436 0.000104 5643 -0.001436 0.000486 -0.000632 5644 0.000103 -0.000632 -0.000453 5645 5646siesta: Pressure (total): 0.35716809 kBar 5647 5648siesta: Temp_ion = 496.396 K 5649 5650 ==================================== 5651 Begin MD step = 19 5652 ==================================== 5653 5654outcoor: Atomic coordinates (Ang): 5655 0.01033604 -0.00322212 0.01136404 1 1 O 5656 0.63960607 0.72965843 0.00824081 2 2 H 5657 -0.80808767 0.49653085 -0.21623760 2 3 H 5658 5659outcell: Unit cell vectors (Ang): 5660 8.000000 0.000000 0.000000 5661 0.000000 8.000000 0.000000 5662 0.000000 0.000000 6.400000 5663 5664outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 5665outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 5666outcell: Cell volume (Ang**3) : 409.6000 5667<dSpData1D:S at geom step 19 5668 <sparsity:sparsity for geom step 19 5669 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 5670 <dData1D:(new from dSpData1D) n=69, refcount: 1> 5671refcount: 1> 5672new_DM -- step: 19 5673Re-using DM from previous geometries... 5674Number of DMs in history: 1 5675 DM extrapolation coefficients: 56761 1.00000 5677New DM after history re-use: 5678<dSpData2D:SpM extrapolated using coords 5679 <sparsity:sparsity for geom step 19 5680 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 5681 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 5682refcount: 1> 5683No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 5684New grid distribution: 1 5685 1 1: 25 1: 13 1: 5 5686 2 1: 25 1: 13 6: 10 5687 3 1: 25 1: 13 11: 15 5688 4 1: 25 1: 13 16: 20 5689 5 1: 25 14: 25 1: 5 5690 6 1: 25 14: 25 6: 10 5691 7 1: 25 14: 25 11: 15 5692 8 1: 25 14: 25 16: 20 5693 5694InitMesh: MESH = 50 x 50 x 40 = 100000 5695InitMesh: (bp) = 25 x 25 x 20 = 12500 5696InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 5697ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 5698New grid distribution: 2 5699 1 7: 25 6: 25 1: 6 5700 2 8: 25 1: 5 1: 6 5701 3 8: 25 1: 5 7: 20 5702 4 1: 7 1: 5 8: 20 5703 5 1: 6 6: 25 1: 6 5704 6 1: 7 1: 5 1: 7 5705 7 7: 25 6: 25 7: 20 5706 8 1: 6 6: 25 7: 20 5707New grid distribution: 3 5708 1 1: 10 7: 25 1: 7 5709 2 1: 15 1: 6 1: 8 5710 3 1: 10 7: 25 8: 20 5711 4 1: 15 1: 6 9: 20 5712 5 11: 25 7: 25 1: 13 5713 6 16: 25 1: 6 1: 12 5714 7 16: 25 1: 6 13: 20 5715 8 11: 25 7: 25 14: 20 5716Setting up quadratic distribution... 5717ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 5718PhiOnMesh: Number of (b)points on node 0 = 2280 5719PhiOnMesh: nlist on node 0 = 5066 5720 5721 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 5722 scf: 1 -465.774085 -465.798906 -465.798906 0.007449 -2.476615 0.071155 5723 scf: 2 -465.798019 -465.798704 -465.798704 0.003054 -2.432852 0.119856 5724 scf: 3 -465.799121 -465.799012 -465.799012 0.001865 -2.460436 0.003028 5725 scf: 4 -465.799014 -465.799013 -465.799013 0.000060 -2.460127 0.001715 5726 scf: 5 -465.799014 -465.799013 -465.799013 0.000107 -2.459570 0.000730 5727 scf: 6 -465.799013 -465.799013 -465.799013 0.000012 -2.459499 0.000451 5728 5729SCF Convergence by DM+H criterion 5730max |DM_out - DM_in| : 0.0000118276 5731max |H_out - H_in| (eV) : 0.0004507566 5732SCF cycle converged after 6 iterations 5733 5734Using DM_out to compute the final energy and forces 5735No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 5736 5737siesta: E_KS(eV) = -465.7990 5738 5739siesta: Atomic forces (eV/Ang): 5740 1 -0.867705 0.629342 -0.493670 5741 2 0.706410 0.034763 0.118302 5742 3 0.120983 -0.666262 0.129897 5743---------------------------------------- 5744 Tot -0.040312 -0.002156 -0.245472 5745---------------------------------------- 5746 Max 0.867705 5747 Res 0.514493 sqrt( Sum f_i^2 / 3N ) 5748---------------------------------------- 5749 Max 0.867705 constrained 5750 5751Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -1.51 0.27 -0.73 -0.97 0.10 -2.31 5752(Free)E + p*V (eV/cell) -465.6315 5753Target enthalpy (eV/cell) -465.7990 5754 5755siesta: Stress tensor (static) (eV/Ang**3): 5756 -0.000901 -0.001404 0.000065 5757 -0.001404 0.000589 -0.000355 5758 0.000064 -0.000355 -0.000294 5759 5760siesta: Pressure (static): 0.32307975 kBar 5761 5762siesta: Stress tensor (total) (eV/Ang**3): 5763 -0.000940 -0.001439 0.000066 5764 -0.001439 0.000171 -0.000604 5765 0.000065 -0.000604 -0.000458 5766 5767siesta: Pressure (total): 0.65530025 kBar 5768 5769siesta: Temp_ion = 510.391 K 5770 5771 ==================================== 5772 Begin MD step = 20 5773 ==================================== 5774 5775outcoor: Atomic coordinates (Ang): 5776 0.01045433 -0.00264342 0.01147949 1 1 O 5777 0.63761606 0.72889872 0.00914967 2 2 H 5778 -0.80831520 0.48838724 -0.22113453 2 3 H 5779 5780outcell: Unit cell vectors (Ang): 5781 8.000000 0.000000 0.000000 5782 0.000000 8.000000 0.000000 5783 0.000000 0.000000 6.400000 5784 5785outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 5786outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 5787outcell: Cell volume (Ang**3) : 409.6000 5788<dSpData1D:S at geom step 20 5789 <sparsity:sparsity for geom step 20 5790 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 5791 <dData1D:(new from dSpData1D) n=69, refcount: 1> 5792refcount: 1> 5793new_DM -- step: 20 5794Re-using DM from previous geometries... 5795Number of DMs in history: 1 5796 DM extrapolation coefficients: 57971 1.00000 5798New DM after history re-use: 5799<dSpData2D:SpM extrapolated using coords 5800 <sparsity:sparsity for geom step 20 5801 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 5802 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 5803refcount: 1> 5804No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 5805New grid distribution: 1 5806 1 1: 25 1: 13 1: 5 5807 2 1: 25 1: 13 6: 10 5808 3 1: 25 1: 13 11: 15 5809 4 1: 25 1: 13 16: 20 5810 5 1: 25 14: 25 1: 5 5811 6 1: 25 14: 25 6: 10 5812 7 1: 25 14: 25 11: 15 5813 8 1: 25 14: 25 16: 20 5814 5815InitMesh: MESH = 50 x 50 x 40 = 100000 5816InitMesh: (bp) = 25 x 25 x 20 = 12500 5817InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 5818ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 5819New grid distribution: 2 5820 1 7: 25 6: 25 1: 6 5821 2 8: 25 1: 5 1: 6 5822 3 8: 25 1: 5 7: 20 5823 4 1: 7 1: 5 8: 20 5824 5 1: 6 6: 25 1: 6 5825 6 1: 7 1: 5 1: 7 5826 7 7: 25 6: 25 7: 20 5827 8 1: 6 6: 25 7: 20 5828New grid distribution: 3 5829 1 1: 10 7: 25 1: 7 5830 2 1: 15 1: 6 1: 8 5831 3 1: 10 7: 25 8: 20 5832 4 1: 15 1: 6 9: 20 5833 5 11: 25 7: 25 1: 13 5834 6 16: 25 1: 6 1: 12 5835 7 16: 25 1: 6 13: 20 5836 8 11: 25 7: 25 14: 20 5837Setting up quadratic distribution... 5838ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 5839PhiOnMesh: Number of (b)points on node 0 = 2280 5840PhiOnMesh: nlist on node 0 = 5058 5841 5842 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 5843 scf: 1 -465.777915 -465.802147 -465.802147 0.007511 -2.446110 0.071911 5844 scf: 2 -465.801252 -465.801940 -465.801940 0.003071 -2.401716 0.120324 5845 scf: 3 -465.802366 -465.802255 -465.802255 0.001869 -2.429610 0.003243 5846 scf: 4 -465.802258 -465.802257 -465.802257 0.000061 -2.429294 0.001834 5847 scf: 5 -465.802258 -465.802257 -465.802257 0.000107 -2.428733 0.000752 5848 scf: 6 -465.802257 -465.802257 -465.802257 0.000012 -2.428662 0.000467 5849 5850SCF Convergence by DM+H criterion 5851max |DM_out - DM_in| : 0.0000120733 5852max |H_out - H_in| (eV) : 0.0004665857 5853SCF cycle converged after 6 iterations 5854 5855Using DM_out to compute the final energy and forces 5856No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 5857 5858siesta: E_KS(eV) = -465.8023 5859 5860siesta: Atomic forces (eV/Ang): 5861 1 -0.839479 0.449243 -0.467943 5862 2 0.760536 0.130640 0.116668 5863 3 0.037601 -0.588004 0.104776 5864---------------------------------------- 5865 Tot -0.041341 -0.008121 -0.246499 5866---------------------------------------- 5867 Max 0.839479 5868 Res 0.482211 sqrt( Sum f_i^2 / 3N ) 5869---------------------------------------- 5870 Max 0.839479 constrained 5871 5872Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -1.89 -0.22 -0.75 -0.92 0.03 -2.29 5873(Free)E + p*V (eV/cell) -465.5590 5874Target enthalpy (eV/cell) -465.8023 5875 5876siesta: Stress tensor (static) (eV/Ang**3): 5877 -0.001148 -0.001397 0.000017 5878 -0.001397 0.000310 -0.000317 5879 0.000016 -0.000317 -0.000304 5880 5881siesta: Pressure (static): 0.60974711 kBar 5882 5883siesta: Stress tensor (total) (eV/Ang**3): 5884 -0.001178 -0.001427 0.000020 5885 -0.001428 -0.000138 -0.000572 5886 0.000019 -0.000572 -0.000465 5887 5888siesta: Pressure (total): 0.95133354 kBar 5889 5890siesta: Temp_ion = 522.973 K 5891 5892siesta: Program's energy decomposition (eV): 5893siesta: Ebs = -103.597105 5894siesta: Eions = 815.854478 5895siesta: Ena = 175.020443 5896siesta: Ekin = 351.850237 5897siesta: Enl = -62.028573 5898siesta: Eso = 0.000000 5899siesta: Edftu = 0.000000 5900siesta: DEna = -2.686492 5901siesta: DUscf = 0.738051 5902siesta: DUext = 0.000000 5903siesta: Exc = -112.841446 5904siesta: eta*DQ = 0.000000 5905siesta: Emadel = 0.000000 5906siesta: Emeta = 0.000000 5907siesta: Emolmec = 0.000000 5908siesta: Ekinion = 0.135194 5909siesta: Eharris = -465.667064 5910siesta: Etot = -465.667064 5911siesta: FreeEng = -465.667064 5912 5913siesta: Final energy (eV): 5914siesta: Band Struct. = -103.597105 5915siesta: Kinetic = 351.850237 5916siesta: Hartree = 414.775787 5917siesta: Edftu = 0.000000 5918siesta: Eso = 0.000000 5919siesta: Ext. field = 0.000000 5920siesta: Exch.-corr. = -112.841446 5921siesta: Ion-electron = -1137.151829 5922siesta: Ion-ion = 17.564994 5923siesta: Ekinion = 0.135194 5924siesta: Total = -465.667064 5925siesta: Fermi = -2.428662 5926 5927siesta: Atomic forces (eV/Ang): 5928siesta: 1 -0.839479 0.449243 -0.467943 5929siesta: 2 0.760536 0.130640 0.116668 5930siesta: 3 0.037601 -0.588004 0.104776 5931siesta: ---------------------------------------- 5932siesta: Tot -0.041341 -0.008121 -0.246499 5933 5934siesta: Stress tensor (static) (eV/Ang**3): 5935siesta: -0.001148 -0.001397 0.000017 5936siesta: -0.001397 0.000310 -0.000317 5937siesta: 0.000016 -0.000317 -0.000304 5938 5939siesta: Cell volume = 409.600000 Ang**3 5940 5941siesta: Pressure (static): 5942siesta: Solid Molecule Units 5943siesta: 0.00000414 0.00000229 Ry/Bohr**3 5944siesta: 0.00038057 0.00020987 eV/Ang**3 5945siesta: 0.60974711 0.33625591 kBar 5946(Free)E+ p_basis*V_orbitals = -465.217090 5947(Free)Eharris+ p_basis*V_orbitals = -465.217090 5948 5949siesta: Electric dipole (a.u.) = -0.088042 0.562278 -0.109158 5950siesta: Electric dipole (Debye) = -0.223780 1.429170 -0.277451 5951 5952cite: Please see "h2o.bib" for an exhaustive BiBTeX file. 5953cite: Please clearly indicate Siesta version in published work: v4.1-b4-351 5954cite: This calculation has made use of the following articles 5955cite: which are encouraged to be cited in a published work. 5956 Primary SIESTA paper 5957 DOI: www.doi.org/10.1088/0953-8984/14/11/302 5958 5959>> End of run: 22-JAN-2021 23:12:50 5960Job completed 5961Siesta Version : v4.1-b4-351 5962Architecture : x86_64-linux-n-62-26-19 5963Compiler version: GNU Fortran (GCC) 9.3.0 5964Compiler flags : mpifort -m64 -fPIC -O3 -march=native -ftree-vectorize -fexpensive-optimizatioons -funroll-loops -fprefetch-loop-arrays -fno-second-underscore -flto 5965PP flags : -I/dtu/sw/dcc/SL73/2020-aug/generic/build-tools/1.0/include -I/dtu/sw/dcc/SL773/2020-aug/generic/gcc/9.3.0/include -I/dtu/sw/dcc/SL73/2020-aug/generic/gcc/9.3.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/zlib/1.2.11/include -I/dtu/sw/dcc/SL73/2020-aug/generic/numactl/2.0.12/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/libxml2/2.9.10/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/hwloc/2.2.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/knem/1.1.4/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/ucx/1.8.1/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/openmpi/4.0.4/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/szip/2.1.1/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/hdf5/1.12.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/pnetcdf/1.12.1/include -I/dtu/sw/dcc/SL73/2020-aug/generic/gen-zlib/1.2.11/include -I/dtu/sw/dcc/SL73/2020-aug/generic/openssl/1.1.1/include -I/dtu/sw/dcc/SL73/2020-aug/generic/libssh2/1.8.2/include -I/dtu/sw/dcc/SL73/2020-aug/generic/curl/7.65.1/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/netcdf/4.7.4/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/flook/0.8.1/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/fftw/3.3.8/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/parmetis/4.0.3/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/scalapack/2.1.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/lapack/3.9.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/blis/0.7.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/scotch/6.0.9/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/mumps/5.3.3/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/elpa/2020.05.001/include -DSIESTA__ELPA -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DCDF -DCDF4 -DSIESTA__FLOOK -DNCDF -DNCDF_4 -DNCDF_PARALLEL -DTS_NOCHECKS -DSIESTA__METIS -DSIESTA__MUMPS -DSIESTA__MRRR -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/elpa/2020.05.001/include/elpa 5966Libraries : libncdf.a libfdict.a -lnetcdff -lnetcdf -lpnetcdf -lhdf5_hl -lhdf5 -lz -lzmuumps -lmumps_common -lesmumps -lscotch -lscotcherr -lpord -lparmetis -lmetis -lelpa -lscalapack -llapack -lblis -L/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/flook/0.8.1/lib -Wl,-rpath=/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/flook/0.8.1/lib -lflookall -ldl -flto -fuse-linker-plugin -lmetis 5967PARALLEL version 5968NetCDF support 5969NetCDF-4 support 5970NetCDF-4 MPI-IO support 5971METIS ordering support 5972Lua support 5973 5974* Running on 8 nodes in parallel 5975>> Start of run: 22-JAN-2021 23:12:51 5976 5977 *********************** 5978 * WELCOME TO SIESTA * 5979 *********************** 5980 5981reinit: Reading from standard input 5982reinit: Dumped input in INPUT_TMP.03479 5983************************** Dump of input data file **************************** 5984SystemName Water molecule -- md verlet 5985SystemLabel h2o 5986NumberOfAtoms 3 5987NumberOfSpecies 2 5988MeshCutoff 100 Ry 5989%block ChemicalSpeciesLabel 5990 1 8 O # Species index, atomic number, species label 5991 2 1 H 5992%endblock ChemicalSpeciesLabel 5993LatticeConstant 8.0 Ang 5994%block LatticeVectors 59951.0 0.0 0.0 59960.0 1.0 0.0 59970.0 0.0 0.8 5998%endblock LatticeVectors 5999AtomicCoordinatesFormat Ang 6000%block AtomicCoordinatesAndAtomicSpecies 6001 0.000 0.000 0.000 1 6002 0.757 0.586 0.000 2 6003-0.757 0.586 0.000 2 6004%endblock AtomicCoordinatesAndAtomicSpecies 6005Solution.Method diagon 6006MeshCutoff 100 Ry 6007WriteCoorStep .true. 6008WriteForces .true. 6009WriteMDHistory .true. 6010MD.UseSaveXV T 6011MD.TypeOfRun Verlet 6012MD.InitialTemperature 600 K 6013MD.Initial.Time.Step 1 6014MD.Final.Time.Step 20 6015MD.Length.Time.Step 0.2 fs 6016************************** End of input data file ***************************** 6017 6018reinit: ----------------------------------------------------------------------- 6019reinit: System Name: Water molecule -- md verlet 6020reinit: ----------------------------------------------------------------------- 6021reinit: System Label: h2o 6022reinit: ----------------------------------------------------------------------- 6023 6024initatom: Reading input for the pseudopotentials and atomic orbitals ---------- 6025Species number: 1 Atomic number: 8 Label: O 6026Species number: 2 Atomic number: 1 Label: H 6027 6028Ground state valence configuration: 2s02 2p04 6029Reading pseudopotential information in formatted form from O.psf 6030 6031Valence configuration for pseudopotential generation: 60322s( 2.00) rc: 1.14 60332p( 4.00) rc: 1.14 60343d( 0.00) rc: 1.14 60354f( 0.00) rc: 1.14 6036Ground state valence configuration: 1s01 6037Reading pseudopotential information in formatted form from H.psf 6038 6039Valence configuration for pseudopotential generation: 60401s( 1.00) rc: 1.25 60412p( 0.00) rc: 1.25 60423d( 0.00) rc: 1.25 60434f( 0.00) rc: 1.25 6044For O, standard SIESTA heuristics set lmxkb to 3 6045 (one more than the basis l, including polarization orbitals). 6046Use PS.lmax or PS.KBprojectors blocks to override. 6047For H, standard SIESTA heuristics set lmxkb to 2 6048 (one more than the basis l, including polarization orbitals). 6049Use PS.lmax or PS.KBprojectors blocks to override. 6050 6051<basis_specs> 6052=============================================================================== 6053O Z= 8 Mass= 16.000 Charge= 0.17977+309 6054Lmxo=1 Lmxkb= 3 BasisType=split Semic=F 6055L=0 Nsemic=0 Cnfigmx=2 6056 i=1 nzeta=2 polorb=0 (2s) 6057 splnorm: 0.15000 6058 vcte: 0.0000 6059 rinn: 0.0000 6060 qcoe: 0.0000 6061 qyuk: 0.0000 6062 qwid: 0.10000E-01 6063 rcs: 0.0000 0.0000 6064 lambdas: 1.0000 1.0000 6065L=1 Nsemic=0 Cnfigmx=2 6066 i=1 nzeta=2 polorb=1 (2p) 6067 splnorm: 0.15000 6068 vcte: 0.0000 6069 rinn: 0.0000 6070 qcoe: 0.0000 6071 qyuk: 0.0000 6072 qwid: 0.10000E-01 6073 rcs: 0.0000 0.0000 6074 lambdas: 1.0000 1.0000 6075------------------------------------------------------------------------------- 6076L=0 Nkbl=1 erefs: 0.17977+309 6077L=1 Nkbl=1 erefs: 0.17977+309 6078L=2 Nkbl=1 erefs: 0.17977+309 6079L=3 Nkbl=1 erefs: 0.17977+309 6080=============================================================================== 6081</basis_specs> 6082 6083atom: Called for O (Z = 8) 6084 6085read_vps: Pseudopotential generation method: 6086read_vps: ATM3 Troullier-Martins 6087Valence charge for ps generation: 6.00000 6088 6089xc_check: Exchange-correlation functional: 6090xc_check: Ceperley-Alder 6091V l=0 = -2*Zval/r beyond r= 1.1278 6092V l=1 = -2*Zval/r beyond r= 1.1278 6093V l=2 = -2*Zval/r beyond r= 1.1278 6094V l=3 = -2*Zval/r beyond r= 1.1138 6095All V_l potentials equal beyond r= 1.1278 6096This should be close to max(r_c) in ps generation 6097All pots = -2*Zval/r beyond r= 1.1278 6098 6099VLOCAL1: 99.0% of the norm of Vloc inside 34.126 Ry 6100VLOCAL1: 99.9% of the norm of Vloc inside 77.774 Ry 6101atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.37759 6102atom: Maximum radius for r*vlocal+2*Zval: 1.18566 6103GHOST: No ghost state for L = 0 6104GHOST: No ghost state for L = 1 6105GHOST: No ghost state for L = 2 6106GHOST: No ghost state for L = 3 6107 6108KBgen: Kleinman-Bylander projectors: 6109 l= 0 rc= 1.294105 el= -1.742414 Ekb= 9.135903 kbcos= 0.326910 6110 l= 1 rc= 1.294105 el= -0.676589 Ekb= -8.124878 kbcos= -0.395047 6111 l= 2 rc= 1.448233 el= 0.002386 Ekb= -2.039267 kbcos= -0.003484 6112 l= 3 rc= 1.561052 el= 0.003508 Ekb= -0.799141 kbcos= -0.000344 6113 6114KBgen: Total number of Kleinman-Bylander projectors: 16 6115atom: ------------------------------------------------------------------------- 6116 6117atom: SANKEY-TYPE ORBITALS: 6118atom: Selected multiple-zeta basis: split 6119 6120SPLIT: Orbitals with angular momentum L= 0 6121 6122SPLIT: Basis orbitals for state 2s 6123 6124SPLIT: PAO cut-off radius determined from an 6125SPLIT: energy shift= 0.020000 Ry 6126 6127 izeta = 1 6128 lambda = 1.000000 6129 rc = 3.305093 6130 energy = -1.723766 6131 kinetic = 1.614911 6132 potential(screened) = -3.338677 6133 potential(ionic) = -11.304675 6134 6135 izeta = 2 6136 rmatch = 2.510382 6137 splitnorm = 0.150000 6138 energy = -1.471299 6139 kinetic = 2.446434 6140 potential(screened) = -3.917732 6141 potential(ionic) = -12.476133 6142 6143SPLIT: Orbitals with angular momentum L= 1 6144 6145SPLIT: Basis orbitals for state 2p 6146 6147SPLIT: PAO cut-off radius determined from an 6148SPLIT: energy shift= 0.020000 Ry 6149 6150 izeta = 1 6151 lambda = 1.000000 6152 rc = 3.937239 6153 energy = -0.658841 6154 kinetic = 5.005986 6155 potential(screened) = -5.664827 6156 potential(ionic) = -13.452360 6157 6158 izeta = 2 6159 rmatch = 2.541963 6160 splitnorm = 0.150000 6161 energy = -0.367441 6162 kinetic = 7.530509 6163 potential(screened) = -7.897949 6164 potential(ionic) = -16.611953 6165 6166POLgen: Perturbative polarization orbital with L= 2 6167 6168POLgen: Polarization orbital for state 2p 6169 6170 izeta = 1 6171 rc = 3.937239 6172 energy = 2.398520 6173 kinetic = 4.716729 6174 potential(screened) = -2.318209 6175 potential(ionic) = -8.603170 6176atom: Total number of Sankey-type orbitals: 13 6177 6178atm_pop: Valence configuration (for local Pseudopot. screening): 6179 2s( 2.00) 6180 2p( 4.00) 6181Vna: chval, zval: 6.00000 6.00000 6182 6183Vna: Cut-off radius for the neutral-atom potential: 3.937239 6184 6185atom: _________________________________________________________________________ 6186 6187<basis_specs> 6188=============================================================================== 6189H Z= 1 Mass= 1.0100 Charge= 0.17977+309 6190Lmxo=0 Lmxkb= 2 BasisType=split Semic=F 6191L=0 Nsemic=0 Cnfigmx=1 6192 i=1 nzeta=2 polorb=1 (1s) 6193 splnorm: 0.15000 6194 vcte: 0.0000 6195 rinn: 0.0000 6196 qcoe: 0.0000 6197 qyuk: 0.0000 6198 qwid: 0.10000E-01 6199 rcs: 0.0000 0.0000 6200 lambdas: 1.0000 1.0000 6201------------------------------------------------------------------------------- 6202L=0 Nkbl=1 erefs: 0.17977+309 6203L=1 Nkbl=1 erefs: 0.17977+309 6204L=2 Nkbl=1 erefs: 0.17977+309 6205=============================================================================== 6206</basis_specs> 6207 6208atom: Called for H (Z = 1) 6209 6210read_vps: Pseudopotential generation method: 6211read_vps: ATM3 Troullier-Martins 6212Valence charge for ps generation: 1.00000 6213 6214xc_check: Exchange-correlation functional: 6215xc_check: Ceperley-Alder 6216V l=0 = -2*Zval/r beyond r= 1.2343 6217V l=1 = -2*Zval/r beyond r= 1.2189 6218V l=2 = -2*Zval/r beyond r= 1.2189 6219All V_l potentials equal beyond r= 1.2343 6220This should be close to max(r_c) in ps generation 6221All pots = -2*Zval/r beyond r= 1.2343 6222 6223VLOCAL1: 99.0% of the norm of Vloc inside 28.493 Ry 6224VLOCAL1: 99.9% of the norm of Vloc inside 64.935 Ry 6225atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.45251 6226atom: Maximum radius for r*vlocal+2*Zval: 1.21892 6227GHOST: No ghost state for L = 0 6228GHOST: No ghost state for L = 1 6229GHOST: No ghost state for L = 2 6230 6231KBgen: Kleinman-Bylander projectors: 6232 l= 0 rc= 1.364359 el= -0.467325 Ekb= -2.005361 kbcos= -0.336422 6233 l= 1 rc= 1.434438 el= 0.001430 Ekb= -0.501708 kbcos= -0.021697 6234 l= 2 rc= 1.470814 el= 0.002365 Ekb= -0.190555 kbcos= -0.002281 6235 6236KBgen: Total number of Kleinman-Bylander projectors: 9 6237atom: ------------------------------------------------------------------------- 6238 6239atom: SANKEY-TYPE ORBITALS: 6240atom: Selected multiple-zeta basis: split 6241 6242SPLIT: Orbitals with angular momentum L= 0 6243 6244SPLIT: Basis orbitals for state 1s 6245 6246SPLIT: PAO cut-off radius determined from an 6247SPLIT: energy shift= 0.020000 Ry 6248 6249 izeta = 1 6250 lambda = 1.000000 6251 rc = 4.828263 6252 energy = -0.449375 6253 kinetic = 0.929372 6254 potential(screened) = -1.378747 6255 potential(ionic) = -1.915047 6256 6257 izeta = 2 6258 rmatch = 3.854947 6259 splitnorm = 0.150000 6260 energy = -0.336153 6261 kinetic = 1.505294 6262 potential(screened) = -1.841447 6263 potential(ionic) = -2.413582 6264 6265POLgen: Perturbative polarization orbital with L= 1 6266 6267POLgen: Polarization orbital for state 1s 6268 6269 izeta = 1 6270 rc = 4.828263 6271 energy = 0.706972 6272 kinetic = 1.396397 6273 potential(screened) = -0.689424 6274 potential(ionic) = -1.169792 6275atom: Total number of Sankey-type orbitals: 5 6276 6277atm_pop: Valence configuration (for local Pseudopot. screening): 6278 1s( 1.00) 6279Vna: chval, zval: 1.00000 1.00000 6280 6281Vna: Cut-off radius for the neutral-atom potential: 4.828263 6282 6283atom: _________________________________________________________________________ 6284 6285prinput: Basis input ---------------------------------------------------------- 6286 6287PAO.BasisType split 6288 6289%block ChemicalSpeciesLabel 6290 1 8 O # Species index, atomic number, species label 6291 2 1 H # Species index, atomic number, species label 6292%endblock ChemicalSpeciesLabel 6293 6294%block PAO.Basis # Define Basis set 6295O 2 # Species label, number of l-shells 6296 n=2 0 2 # n, l, Nzeta 6297 3.305 2.510 6298 1.000 1.000 6299 n=2 1 2 P 1 # n, l, Nzeta, Polarization, NzetaPol 6300 3.937 2.542 6301 1.000 1.000 6302H 1 # Species label, number of l-shells 6303 n=1 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol 6304 4.828 3.855 6305 1.000 1.000 6306%endblock PAO.Basis 6307 6308prinput: ---------------------------------------------------------------------- 6309 6310Dumping basis to NetCDF file O.ion.nc 6311Dumping basis to NetCDF file H.ion.nc 6312coor: Atomic-coordinates input format = Cartesian coordinates 6313coor: (in Angstroms) 6314 6315ioxv: Reading coordinates and velocities from file 6316! Info in XV file prevails over previous structure input 6317WARNING: h2o.VERLET_RESTART not found--reading only XV file and moving back 1 time step using Euler 6318 6319siesta: Atomic coordinates (Bohr) and species 6320siesta: 0.01974 -0.00499 0.02168 1 1 6321siesta: 1.20519 1.37747 0.01733 2 2 6322siesta: -1.52748 0.92271 -0.41785 2 3 6323 6324siesta: System type = molecule 6325 6326initatomlists: Number of atoms, orbitals, and projectors: 3 23 34 6327 6328siesta: ******************** Simulation parameters **************************** 6329siesta: 6330siesta: The following are some of the parameters of the simulation. 6331siesta: A complete list of the parameters used, including default values, 6332siesta: can be found in file out.fdf 6333siesta: 6334redata: Spin configuration = none 6335redata: Number of spin components = 1 6336redata: Time-Reversal Symmetry = T 6337redata: Spin spiral = F 6338redata: Long output = F 6339redata: Number of Atomic Species = 2 6340redata: Charge density info will appear in .RHO file 6341redata: Write Mulliken Pop. = NO 6342redata: Matel table size (NRTAB) = 1024 6343redata: Mesh Cutoff = 100.0000 Ry 6344redata: Net charge of the system = 0.0000 |e| 6345redata: Min. number of SCF Iter = 0 6346redata: Max. number of SCF Iter = 1000 6347redata: SCF convergence failure will abort job 6348redata: SCF mix quantity = Hamiltonian 6349redata: Mix DM or H after convergence = F 6350redata: Recompute H after scf cycle = F 6351redata: Mix DM in first SCF step = T 6352redata: Write Pulay info on disk = F 6353redata: New DM Occupancy tolerance = 0.000000000001 6354redata: No kicks to SCF 6355redata: DM Mixing Weight for Kicks = 0.5000 6356redata: Require Harris convergence for SCF = F 6357redata: Harris energy tolerance for SCF = 0.000100 eV 6358redata: Require DM convergence for SCF = T 6359redata: DM tolerance for SCF = 0.000100 6360redata: Require EDM convergence for SCF = F 6361redata: EDM tolerance for SCF = 0.001000 eV 6362redata: Require H convergence for SCF = T 6363redata: Hamiltonian tolerance for SCF = 0.001000 eV 6364redata: Require (free) Energy convergence for SCF = F 6365redata: (free) Energy tolerance for SCF = 0.000100 eV 6366redata: Using Saved Data (generic) = F 6367redata: Use continuation files for DM = F 6368redata: Neglect nonoverlap interactions = F 6369redata: Method of Calculation = Diagonalization 6370redata: Electronic Temperature = 299.9869 K 6371redata: Fix the spin of the system = F 6372redata: Dynamics option = Verlet MD run 6373redata: Initial MD time step = 1 6374redata: Final MD time step = 20 6375redata: Length of MD time step = 0.2000 fs 6376redata: Initial Temperature of MD run = 600.0000 K 6377redata: Perform a MD quench = F 6378mix.SCF: Pulay mixing = Pulay 6379mix.SCF: Variant = stable 6380mix.SCF: History steps = 2 6381mix.SCF: Linear mixing weight = 0.250000 6382mix.SCF: Mixing weight = 0.250000 6383mix.SCF: SVD condition = 0.1000E-07 6384redata: Save all siesta data in one NC = F 6385redata: *********************************************************************** 6386 6387%block SCF.Mixers 6388 Pulay 6389%endblock SCF.Mixers 6390 6391%block SCF.Mixer.Pulay 6392 # Mixing method 6393 method pulay 6394 variant stable 6395 6396 # Mixing options 6397 weight 0.2500 6398 weight.linear 0.2500 6399 history 2 6400%endblock SCF.Mixer.Pulay 6401 6402Size of DM history Fstack: 1 6403Total number of electrons: 8.000000 6404Total ionic charge: 8.000000 6405 6406* ProcessorY, Blocksize: 2 3 6407 6408 6409* Orbital distribution balance (max,min): 3 2 6410 6411 Kpoints in: 1 . Kpoints trimmed: 1 6412 6413siesta: k-grid: Number of k-points = 1 6414siesta: k-grid: Cutoff (effective) = 3.200 Ang 6415siesta: k-grid: Supercell and displacements 6416siesta: k-grid: 1 0 0 0.000 6417siesta: k-grid: 0 1 0 0.000 6418siesta: k-grid: 0 0 1 0.000 6419 6420diag: Algorithm = D&C 6421diag: Parallel over k = F 6422diag: Use parallel 2D distribution = T 6423diag: Parallel block-size = 3 6424diag: Parallel distribution = 2 x 4 6425diag: Used triangular part = Lower 6426diag: Absolute tolerance = 0.100E-15 6427diag: Orthogonalization factor = 0.100E-05 6428diag: Memory factor = 1.0000 6429 6430 6431ts: ************************************************************** 6432ts: Save H and S matrices = F 6433ts: Save DM and EDM matrices = F 6434ts: Only save the overlap matrix S = F 6435ts: ************************************************************** 6436 6437************************ Begin: TS CHECKS AND WARNINGS ************************ 6438************************ End: TS CHECKS AND WARNINGS ************************** 6439 6440 6441 ==================================== 6442 Begin MD step = 1 6443 ==================================== 6444 6445outcoor: Atomic coordinates (Ang): 6446 0.01044428 -0.00263804 0.01147389 1 1 O 6447 0.63776032 0.72892350 0.00917180 2 2 H 6448 -0.80830806 0.48827571 -0.22111466 2 3 H 6449 6450outcell: Unit cell vectors (Ang): 6451 8.000000 0.000000 0.000000 6452 0.000000 8.000000 0.000000 6453 0.000000 0.000000 6.400000 6454 6455outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 6456outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 6457outcell: Cell volume (Ang**3) : 409.6000 6458<dSpData1D:S at geom step 1 6459 <sparsity:sparsity for geom step 1 6460 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 6461 <dData1D:(new from dSpData1D) n=69, refcount: 1> 6462refcount: 1> 6463new_DM -- step: 1 6464Initializing Density Matrix... 6465DM filled with atomic data: 6466<dSpData2D:DM initialized from atoms 6467 <sparsity:sparsity for geom step 1 6468 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 8> 6469 <dData2D:DM n=69 m=1, refcount: 1> 6470refcount: 1> 6471No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 6472New grid distribution: 1 6473 1 1: 25 1: 13 1: 5 6474 2 1: 25 1: 13 6: 10 6475 3 1: 25 1: 13 11: 15 6476 4 1: 25 1: 13 16: 20 6477 5 1: 25 14: 25 1: 5 6478 6 1: 25 14: 25 6: 10 6479 7 1: 25 14: 25 11: 15 6480 8 1: 25 14: 25 16: 20 6481 6482InitMesh: MESH = 50 x 50 x 40 = 100000 6483InitMesh: (bp) = 25 x 25 x 20 = 12500 6484InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 6485ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 6486New grid distribution: 2 6487 1 7: 25 6: 25 1: 6 6488 2 8: 25 1: 5 1: 6 6489 3 8: 25 1: 5 7: 20 6490 4 1: 7 1: 5 8: 20 6491 5 1: 6 6: 25 1: 6 6492 6 1: 7 1: 5 1: 7 6493 7 7: 25 6: 25 7: 20 6494 8 1: 6 6: 25 7: 20 6495New grid distribution: 3 6496 1 1: 10 7: 25 1: 7 6497 2 1: 15 1: 6 1: 8 6498 3 1: 10 7: 25 8: 20 6499 4 1: 15 1: 6 9: 20 6500 5 11: 25 7: 25 1: 13 6501 6 16: 25 1: 6 1: 12 6502 7 16: 25 1: 6 13: 20 6503 8 11: 25 7: 25 14: 20 6504Setting up quadratic distribution... 6505ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 6506PhiOnMesh: Number of (b)points on node 0 = 2280 6507PhiOnMesh: nlist on node 0 = 5058 6508 6509stepf: Fermi-Dirac step function 6510 6511siesta: Program's energy decomposition (eV): 6512siesta: Ebs = -82.376595 6513siesta: Eions = 815.854478 6514siesta: Ena = 175.020263 6515siesta: Ekin = 374.722329 6516siesta: Enl = -68.070849 6517siesta: Eso = 0.000000 6518siesta: Edftu = 0.000000 6519siesta: DEna = -16.250328 6520siesta: DUscf = 2.005479 6521siesta: DUext = 0.000000 6522siesta: Exc = -116.590183 6523siesta: eta*DQ = 0.000000 6524siesta: Emadel = 0.000000 6525siesta: Emeta = 0.000000 6526siesta: Emolmec = 0.000000 6527siesta: Ekinion = 0.000000 6528siesta: Eharris = -467.090534 6529siesta: Etot = -465.017768 6530siesta: FreeEng = -465.017768 6531 6532 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 6533 scf: 1 -467.090534 -465.017768 -465.017768 1.395154 -4.640241 7.085923 6534timer: Routine,Calls,Time,% = IterSCF 1 0.020 1.52 6535 scf: 2 -466.182135 -465.712932 -465.712932 0.055425 -3.483389 2.692412 6536 scf: 3 -465.812595 -465.797866 -465.797866 0.025484 -2.732741 0.355489 6537 scf: 4 -465.803388 -465.800803 -465.800803 0.010180 -2.653238 0.269178 6538 scf: 5 -465.802922 -465.802288 -465.802288 0.021748 -2.427259 0.054044 6539 scf: 6 -465.802494 -465.802405 -465.802405 0.000936 -2.414545 0.028503 6540 scf: 7 -465.802462 -465.802435 -465.802435 0.000734 -2.414720 0.020220 6541 scf: 8 -465.802460 -465.802448 -465.802448 0.000575 -2.417268 0.015366 6542 scf: 9 -465.802456 -465.802453 -465.802453 0.000699 -2.423133 0.006370 6543 scf: 10 -465.802453 -465.802453 -465.802453 0.000167 -2.426319 0.002887 6544 scf: 11 -465.802453 -465.802453 -465.802453 0.000018 -2.427633 0.002170 6545 scf: 12 -465.802454 -465.802453 -465.802453 0.000026 -2.428060 0.001203 6546 scf: 13 -465.802454 -465.802453 -465.802453 0.000024 -2.428116 0.000684 6547 6548SCF Convergence by DM+H criterion 6549max |DM_out - DM_in| : 0.0000243222 6550max |H_out - H_in| (eV) : 0.0006838238 6551SCF cycle converged after 13 iterations 6552 6553Using DM_out to compute the final energy and forces 6554No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 6555 6556siesta: E_KS(eV) = -465.8025 6557 6558siesta: E_KS - E_eggbox = -465.8025 6559 6560siesta: Atomic forces (eV/Ang): 6561 1 -0.832186 0.450317 -0.466715 6562 2 0.755644 0.126677 0.116118 6563 3 0.035264 -0.585172 0.104218 6564---------------------------------------- 6565 Tot -0.041278 -0.008178 -0.246379 6566---------------------------------------- 6567 Max 0.832186 6568 Res 0.479375 sqrt( Sum f_i^2 / 3N ) 6569---------------------------------------- 6570 Max 0.832186 constrained 6571 6572Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -1.87 -0.26 -0.74 -0.92 0.03 -2.26 6573(Free)E + p*V (eV/cell) -465.5579 6574Target enthalpy (eV/cell) -465.8025 6575 6576siesta: Stress tensor (static) (eV/Ang**3): 6577 -0.001145 -0.001385 0.000016 6578 -0.001385 0.000313 -0.000316 6579 0.000016 -0.000316 -0.000304 6580 6581siesta: Pressure (static): 0.60673177 kBar 6582 6583siesta: Stress tensor (total) (eV/Ang**3): 6584 -0.001168 -0.001412 0.000019 6585 -0.001412 -0.000160 -0.000575 6586 0.000019 -0.000575 -0.000463 6587 6588siesta: Pressure (total): 0.95673889 kBar 6589 6590siesta: Temp_ion = 522.973 K 6591 6592 ==================================== 6593 Begin MD step = 2 6594 ==================================== 6595 6596outcoor: Atomic coordinates (Ang): 6597 0.01054254 -0.00204858 0.01157815 1 1 O 6598 0.63605790 0.72821259 0.01012482 2 2 H 6599 -0.80852177 0.47990957 -0.22597194 2 3 H 6600 6601outcell: Unit cell vectors (Ang): 6602 8.000000 0.000000 0.000000 6603 0.000000 8.000000 0.000000 6604 0.000000 0.000000 6.400000 6605 6606outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 6607outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 6608outcell: Cell volume (Ang**3) : 409.6000 6609<dSpData1D:S at geom step 2 6610 <sparsity:sparsity for geom step 2 6611 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 6612 <dData1D:(new from dSpData1D) n=69, refcount: 1> 6613refcount: 1> 6614new_DM -- step: 2 6615Re-using DM from previous geometries... 6616Number of DMs in history: 1 6617 DM extrapolation coefficients: 66181 1.00000 6619New DM after history re-use: 6620<dSpData2D:SpM extrapolated using coords 6621 <sparsity:sparsity for geom step 2 6622 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 6623 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 6624refcount: 1> 6625No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 6626New grid distribution: 1 6627 1 1: 25 1: 13 1: 5 6628 2 1: 25 1: 13 6: 10 6629 3 1: 25 1: 13 11: 15 6630 4 1: 25 1: 13 16: 20 6631 5 1: 25 14: 25 1: 5 6632 6 1: 25 14: 25 6: 10 6633 7 1: 25 14: 25 11: 15 6634 8 1: 25 14: 25 16: 20 6635 6636InitMesh: MESH = 50 x 50 x 40 = 100000 6637InitMesh: (bp) = 25 x 25 x 20 = 12500 6638InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 6639ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 6640New grid distribution: 2 6641 1 7: 25 6: 25 1: 6 6642 2 8: 25 1: 5 1: 6 6643 3 8: 25 1: 5 7: 20 6644 4 1: 7 1: 5 8: 20 6645 5 1: 6 6: 25 1: 6 6646 6 1: 7 1: 5 1: 7 6647 7 7: 25 6: 25 7: 20 6648 8 1: 6 6: 25 7: 20 6649New grid distribution: 3 6650 1 1: 10 7: 25 1: 7 6651 2 1: 15 1: 6 1: 8 6652 3 1: 10 7: 25 8: 20 6653 4 1: 15 1: 6 9: 20 6654 5 11: 25 7: 25 1: 13 6655 6 16: 25 1: 6 1: 12 6656 7 16: 25 1: 6 13: 20 6657 8 11: 25 7: 25 14: 20 6658Setting up quadratic distribution... 6659ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 6660PhiOnMesh: Number of (b)points on node 0 = 2280 6661PhiOnMesh: nlist on node 0 = 5059 6662 6663 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 6664 scf: 1 -465.782042 -465.805202 -465.805202 0.007552 -2.413549 0.071837 6665 scf: 2 -465.804335 -465.805008 -465.805008 0.003062 -2.368945 0.119240 6666 scf: 3 -465.805420 -465.805312 -465.805312 0.001856 -2.396861 0.003393 6667 scf: 4 -465.805314 -465.805313 -465.805313 0.000061 -2.396535 0.001917 6668 scf: 5 -465.805314 -465.805314 -465.805314 0.000107 -2.395965 0.000757 6669 scf: 6 -465.805314 -465.805314 -465.805314 0.000012 -2.395897 0.000470 6670 6671SCF Convergence by DM+H criterion 6672max |DM_out - DM_in| : 0.0000120979 6673max |H_out - H_in| (eV) : 0.0004699475 6674SCF cycle converged after 6 iterations 6675 6676Using DM_out to compute the final energy and forces 6677No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 6678 6679siesta: E_KS(eV) = -465.8053 6680 6681siesta: Atomic forces (eV/Ang): 6682 1 -0.790493 0.274698 -0.437709 6683 2 0.800346 0.215122 0.114158 6684 3 -0.051357 -0.505073 0.076149 6685---------------------------------------- 6686 Tot -0.041504 -0.015253 -0.247402 6687---------------------------------------- 6688 Max 0.800346 6689 Res 0.454035 sqrt( Sum f_i^2 / 3N ) 6690---------------------------------------- 6691 Max 0.800346 constrained 6692 6693Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -2.25 -0.68 -0.76 -0.86 -0.05 -2.22 6694(Free)E + p*V (eV/cell) -465.4900 6695Target enthalpy (eV/cell) -465.8053 6696 6697siesta: Stress tensor (static) (eV/Ang**3): 6698 -0.001383 -0.001360 -0.000035 6699 -0.001360 0.000046 -0.000277 6700 -0.000036 -0.000277 -0.000317 6701 6702siesta: Pressure (static): 0.88346206 kBar 6703 6704siesta: Stress tensor (total) (eV/Ang**3): 6705 -0.001406 -0.001386 -0.000032 6706 -0.001387 -0.000427 -0.000536 6707 -0.000034 -0.000536 -0.000476 6708 6709siesta: Pressure (total): 1.23346918 kBar 6710 6711siesta: Temp_ion = 534.092 K 6712 6713 ==================================== 6714 Begin MD step = 3 6715 ==================================== 6716 6717outcoor: Atomic coordinates (Ang): 6718 0.01062188 -0.00145253 0.01167193 1 1 O 6719 0.63465911 0.72758329 0.01112114 2 2 H 6720 -0.80875496 0.47135182 -0.23080034 2 3 H 6721 6722outcell: Unit cell vectors (Ang): 6723 8.000000 0.000000 0.000000 6724 0.000000 8.000000 0.000000 6725 0.000000 0.000000 6.400000 6726 6727outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 6728outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 6729outcell: Cell volume (Ang**3) : 409.6000 6730<dSpData1D:S at geom step 3 6731 <sparsity:sparsity for geom step 3 6732 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 6733 <dData1D:(new from dSpData1D) n=69, refcount: 1> 6734refcount: 1> 6735new_DM -- step: 3 6736Re-using DM from previous geometries... 6737Number of DMs in history: 1 6738 DM extrapolation coefficients: 67391 1.00000 6740New DM after history re-use: 6741<dSpData2D:SpM extrapolated using coords 6742 <sparsity:sparsity for geom step 3 6743 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 6744 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 6745refcount: 1> 6746No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 6747New grid distribution: 1 6748 1 1: 25 1: 13 1: 5 6749 2 1: 25 1: 13 6: 10 6750 3 1: 25 1: 13 11: 15 6751 4 1: 25 1: 13 16: 20 6752 5 1: 25 14: 25 1: 5 6753 6 1: 25 14: 25 6: 10 6754 7 1: 25 14: 25 11: 15 6755 8 1: 25 14: 25 16: 20 6756 6757InitMesh: MESH = 50 x 50 x 40 = 100000 6758InitMesh: (bp) = 25 x 25 x 20 = 12500 6759InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 6760ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 6761New grid distribution: 2 6762 1 8: 25 6: 25 1: 6 6763 2 8: 25 1: 5 1: 6 6764 3 8: 25 1: 5 7: 20 6765 4 1: 7 1: 5 8: 20 6766 5 1: 7 6: 25 1: 6 6767 6 1: 7 1: 5 1: 7 6768 7 8: 25 6: 25 7: 20 6769 8 1: 7 6: 25 7: 20 6770New grid distribution: 3 6771 1 1: 10 7: 25 1: 7 6772 2 1: 15 1: 6 1: 8 6773 3 1: 10 7: 25 8: 20 6774 4 1: 15 1: 6 9: 20 6775 5 11: 25 7: 25 1: 13 6776 6 16: 25 1: 6 1: 12 6777 7 16: 25 1: 6 13: 20 6778 8 11: 25 7: 25 14: 20 6779Setting up quadratic distribution... 6780ExtMesh (bp) on 0 = 50 x 52 x 38 = 98800 6781PhiOnMesh: Number of (b)points on node 0 = 2160 6782PhiOnMesh: nlist on node 0 = 4789 6783 6784 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 6785 scf: 1 -465.786090 -465.807720 -465.807720 0.007400 -2.380661 0.070749 6786 scf: 2 -465.806894 -465.807538 -465.807538 0.002998 -2.336633 0.116685 6787 scf: 3 -465.807933 -465.807828 -465.807828 0.001812 -2.364106 0.003585 6788 scf: 4 -465.807831 -465.807830 -465.807830 0.000060 -2.363792 0.002022 6789 scf: 5 -465.807831 -465.807830 -465.807830 0.000102 -2.363249 0.000766 6790 scf: 6 -465.807831 -465.807830 -465.807830 0.000012 -2.363182 0.000479 6791 6792SCF Convergence by DM+H criterion 6793max |DM_out - DM_in| : 0.0000119887 6794max |H_out - H_in| (eV) : 0.0004791759 6795SCF cycle converged after 6 iterations 6796 6797Using DM_out to compute the final energy and forces 6798No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 6799 6800siesta: E_KS(eV) = -465.8078 6801 6802siesta: Atomic forces (eV/Ang): 6803 1 -0.735503 0.106082 -0.405779 6804 2 0.834401 0.295038 0.111141 6805 3 -0.139871 -0.423626 0.046220 6806---------------------------------------- 6807 Tot -0.040972 -0.022506 -0.248417 6808---------------------------------------- 6809 Max 0.834401 6810 Res 0.436356 sqrt( Sum f_i^2 / 3N ) 6811---------------------------------------- 6812 Max 0.834401 constrained 6813 6814Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -2.61 -1.12 -0.78 -0.80 -0.14 -2.15 6815(Free)E + p*V (eV/cell) -465.4238 6816Target enthalpy (eV/cell) -465.8078 6817 6818siesta: Stress tensor (static) (eV/Ang**3): 6819 -0.001610 -0.001315 -0.000091 6820 -0.001315 -0.000201 -0.000235 6821 -0.000092 -0.000235 -0.000332 6822 6823siesta: Pressure (static): 1.14482937 kBar 6824 6825siesta: Stress tensor (total) (eV/Ang**3): 6826 -0.001627 -0.001339 -0.000089 6827 -0.001339 -0.000697 -0.000499 6828 -0.000090 -0.000499 -0.000489 6829 6830siesta: Pressure (total): 1.50227851 kBar 6831 6832siesta: Temp_ion = 543.854 K 6833 6834 ==================================== 6835 Begin MD step = 4 6836 ==================================== 6837 6838outcoor: Atomic coordinates (Ang): 6839 0.01068360 -0.00085395 0.01175600 1 1 O 6840 0.63357686 0.72706592 0.01215963 2 2 H 6841 -0.80904122 0.46263336 -0.23561120 2 3 H 6842 6843outcell: Unit cell vectors (Ang): 6844 8.000000 0.000000 0.000000 6845 0.000000 8.000000 0.000000 6846 0.000000 0.000000 6.400000 6847 6848outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 6849outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 6850outcell: Cell volume (Ang**3) : 409.6000 6851<dSpData1D:S at geom step 4 6852 <sparsity:sparsity for geom step 4 6853 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 6854 <dData1D:(new from dSpData1D) n=69, refcount: 1> 6855refcount: 1> 6856new_DM -- step: 4 6857Re-using DM from previous geometries... 6858Number of DMs in history: 1 6859 DM extrapolation coefficients: 68601 1.00000 6861New DM after history re-use: 6862<dSpData2D:SpM extrapolated using coords 6863 <sparsity:sparsity for geom step 4 6864 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 6865 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 6866refcount: 1> 6867No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 6868New grid distribution: 1 6869 1 1: 25 1: 13 1: 5 6870 2 1: 25 1: 13 6: 10 6871 3 1: 25 1: 13 11: 15 6872 4 1: 25 1: 13 16: 20 6873 5 1: 25 14: 25 1: 5 6874 6 1: 25 14: 25 6: 10 6875 7 1: 25 14: 25 11: 15 6876 8 1: 25 14: 25 16: 20 6877 6878InitMesh: MESH = 50 x 50 x 40 = 100000 6879InitMesh: (bp) = 25 x 25 x 20 = 12500 6880InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 6881ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 6882New grid distribution: 2 6883 1 8: 25 6: 25 1: 6 6884 2 8: 25 1: 5 1: 6 6885 3 8: 25 1: 5 7: 20 6886 4 1: 7 1: 5 8: 20 6887 5 1: 7 6: 25 1: 6 6888 6 1: 7 1: 5 1: 7 6889 7 8: 25 6: 25 7: 20 6890 8 1: 7 6: 25 7: 20 6891New grid distribution: 3 6892 1 1: 11 7: 25 1: 7 6893 2 1: 15 1: 6 1: 8 6894 3 1: 11 7: 25 8: 20 6895 4 1: 15 1: 6 9: 20 6896 5 12: 25 7: 25 1: 14 6897 6 16: 25 1: 6 1: 12 6898 7 16: 25 1: 6 13: 20 6899 8 12: 25 7: 25 15: 20 6900Setting up quadratic distribution... 6901ExtMesh (bp) on 0 = 50 x 52 x 38 = 98800 6902PhiOnMesh: Number of (b)points on node 0 = 2160 6903PhiOnMesh: nlist on node 0 = 4776 6904 6905 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 6906 scf: 1 -465.790275 -465.809934 -465.809934 0.007227 -2.347015 0.068905 6907 scf: 2 -465.809169 -465.809768 -465.809768 0.002913 -2.303953 0.112764 6908 scf: 3 -465.810138 -465.810040 -465.810040 0.001753 -2.330721 0.003704 6909 scf: 4 -465.810042 -465.810041 -465.810041 0.000058 -2.330417 0.002084 6910 scf: 5 -465.810042 -465.810042 -465.810042 0.000098 -2.329896 0.000759 6911 6912SCF Convergence by DM+H criterion 6913max |DM_out - DM_in| : 0.0000984379 6914max |H_out - H_in| (eV) : 0.0007586657 6915SCF cycle converged after 5 iterations 6916 6917Using DM_out to compute the final energy and forces 6918No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 6919 6920siesta: E_KS(eV) = -465.8100 6921 6922siesta: Atomic forces (eV/Ang): 6923 1 -0.669505 -0.052839 -0.370949 6924 2 0.856184 0.364253 0.107508 6925 3 -0.228022 -0.342421 0.014463 6926---------------------------------------- 6927 Tot -0.041342 -0.031007 -0.248978 6928---------------------------------------- 6929 Max 0.856184 6930 Res 0.426273 sqrt( Sum f_i^2 / 3N ) 6931---------------------------------------- 6932 Max 0.856184 constrained 6933 6934Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -2.93 -1.51 -0.81 -0.73 -0.24 -2.05 6935(Free)E + p*V (eV/cell) -465.3628 6936Target enthalpy (eV/cell) -465.8100 6937 6938siesta: Stress tensor (static) (eV/Ang**3): 6939 -0.001818 -0.001255 -0.000148 6940 -0.001256 -0.000427 -0.000191 6941 -0.000150 -0.000191 -0.000349 6942 6943siesta: Pressure (static): 1.38543320 kBar 6944 6945siesta: Stress tensor (total) (eV/Ang**3): 6946 -0.001829 -0.001278 -0.000149 6947 -0.001279 -0.000942 -0.000459 6948 -0.000150 -0.000459 -0.000505 6949 6950siesta: Pressure (total): 1.74941550 kBar 6951 6952siesta: Temp_ion = 552.427 K 6953 6954 ==================================== 6955 Begin MD step = 5 6956 ==================================== 6957 6958outcoor: Atomic coordinates (Ang): 6959 0.01072929 -0.00025663 0.01183118 1 1 O 6960 0.63281943 0.72668674 0.01323890 2 2 H 6961 -0.80941398 0.45378499 -0.24041658 2 3 H 6962 6963outcell: Unit cell vectors (Ang): 6964 8.000000 0.000000 0.000000 6965 0.000000 8.000000 0.000000 6966 0.000000 0.000000 6.400000 6967 6968outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 6969outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 6970outcell: Cell volume (Ang**3) : 409.6000 6971<dSpData1D:S at geom step 5 6972 <sparsity:sparsity for geom step 5 6973 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 6974 <dData1D:(new from dSpData1D) n=69, refcount: 1> 6975refcount: 1> 6976new_DM -- step: 5 6977Re-using DM from previous geometries... 6978Number of DMs in history: 1 6979 DM extrapolation coefficients: 69801 1.00000 6981New DM after history re-use: 6982<dSpData2D:SpM extrapolated using coords 6983 <sparsity:sparsity for geom step 5 6984 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 6985 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 6986refcount: 1> 6987No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 6988New grid distribution: 1 6989 1 1: 25 1: 13 1: 5 6990 2 1: 25 1: 13 6: 10 6991 3 1: 25 1: 13 11: 15 6992 4 1: 25 1: 13 16: 20 6993 5 1: 25 14: 25 1: 5 6994 6 1: 25 14: 25 6: 10 6995 7 1: 25 14: 25 11: 15 6996 8 1: 25 14: 25 16: 20 6997 6998InitMesh: MESH = 50 x 50 x 40 = 100000 6999InitMesh: (bp) = 25 x 25 x 20 = 12500 7000InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 7001ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 7002New grid distribution: 2 7003 1 8: 25 6: 25 1: 6 7004 2 8: 25 1: 5 1: 6 7005 3 8: 25 1: 5 7: 20 7006 4 1: 7 1: 5 8: 20 7007 5 1: 7 6: 25 1: 6 7008 6 1: 7 1: 5 1: 7 7009 7 8: 25 6: 25 7: 20 7010 8 1: 7 6: 25 7: 20 7011New grid distribution: 3 7012 1 14: 25 7: 25 1: 14 7013 2 1: 15 1: 6 1: 8 7014 3 1: 15 1: 6 9: 20 7015 4 14: 25 7: 25 15: 20 7016 5 1: 13 7: 25 1: 7 7017 6 16: 25 1: 6 1: 12 7018 7 1: 13 7: 25 8: 20 7019 8 16: 25 1: 6 13: 20 7020Setting up quadratic distribution... 7021ExtMesh (bp) on 0 = 50 x 52 x 38 = 98800 7022PhiOnMesh: Number of (b)points on node 0 = 2160 7023PhiOnMesh: nlist on node 0 = 4788 7024 7025 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 7026 scf: 1 -465.794602 -465.811891 -465.811891 0.006967 -2.312735 0.066254 7027 scf: 2 -465.811201 -465.811745 -465.811745 0.002796 -2.271142 0.107583 7028 scf: 3 -465.812082 -465.811992 -465.811992 0.001675 -2.296891 0.003782 7029 scf: 4 -465.811995 -465.811994 -465.811994 0.000055 -2.296605 0.002123 7030 scf: 5 -465.811995 -465.811995 -465.811995 0.000093 -2.296116 0.000741 7031 7032SCF Convergence by DM+H criterion 7033max |DM_out - DM_in| : 0.0000929810 7034max |H_out - H_in| (eV) : 0.0007405902 7035SCF cycle converged after 5 iterations 7036 7037Using DM_out to compute the final energy and forces 7038No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 7039 7040siesta: E_KS(eV) = -465.8120 7041 7042siesta: Atomic forces (eV/Ang): 7043 1 -0.591481 -0.197774 -0.333876 7044 2 0.864589 0.421390 0.102842 7045 3 -0.313630 -0.262236 -0.017983 7046---------------------------------------- 7047 Tot -0.040521 -0.038620 -0.249017 7048---------------------------------------- 7049 Max 0.864589 7050 Res 0.422105 sqrt( Sum f_i^2 / 3N ) 7051---------------------------------------- 7052 Max 0.864589 constrained 7053 7054Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -3.22 -1.85 -0.84 -0.67 -0.34 -1.92 7055(Free)E + p*V (eV/cell) -465.3093 7056Target enthalpy (eV/cell) -465.8120 7057 7058siesta: Stress tensor (static) (eV/Ang**3): 7059 -0.002000 -0.001176 -0.000206 7060 -0.001176 -0.000623 -0.000145 7061 -0.000208 -0.000145 -0.000366 7062 7063siesta: Pressure (static): 1.59650352 kBar 7064 7065siesta: Stress tensor (total) (eV/Ang**3): 7066 -0.002007 -0.001200 -0.000210 7067 -0.001201 -0.001153 -0.000417 7068 -0.000212 -0.000417 -0.000522 7069 7070siesta: Pressure (total): 1.96622328 kBar 7071 7072siesta: Temp_ion = 560.046 K 7073 7074 ==================================== 7075 Begin MD step = 6 7076 ==================================== 7077 7078outcoor: Atomic coordinates (Ang): 7079 0.01076082 0.00033595 0.01189836 1 1 O 7080 0.63238999 0.72646742 0.01435719 2 2 H 7081 -0.80990572 0.44483715 -0.24522877 2 3 H 7082 7083outcell: Unit cell vectors (Ang): 7084 8.000000 0.000000 0.000000 7085 0.000000 8.000000 0.000000 7086 0.000000 0.000000 6.400000 7087 7088outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 7089outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 7090outcell: Cell volume (Ang**3) : 409.6000 7091<dSpData1D:S at geom step 6 7092 <sparsity:sparsity for geom step 6 7093 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 7094 <dData1D:(new from dSpData1D) n=69, refcount: 1> 7095refcount: 1> 7096new_DM -- step: 6 7097Re-using DM from previous geometries... 7098Number of DMs in history: 1 7099 DM extrapolation coefficients: 71001 1.00000 7101New DM after history re-use: 7102<dSpData2D:SpM extrapolated using coords 7103 <sparsity:sparsity for geom step 6 7104 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 7105 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 7106refcount: 1> 7107No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 7108New grid distribution: 1 7109 1 1: 25 1: 13 1: 5 7110 2 1: 25 1: 13 6: 10 7111 3 1: 25 1: 13 11: 15 7112 4 1: 25 1: 13 16: 20 7113 5 1: 25 14: 25 1: 5 7114 6 1: 25 14: 25 6: 10 7115 7 1: 25 14: 25 11: 15 7116 8 1: 25 14: 25 16: 20 7117 7118InitMesh: MESH = 50 x 50 x 40 = 100000 7119InitMesh: (bp) = 25 x 25 x 20 = 12500 7120InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 7121ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 7122New grid distribution: 2 7123 1 8: 25 6: 25 1: 6 7124 2 8: 25 1: 5 1: 6 7125 3 8: 25 1: 5 7: 20 7126 4 1: 7 1: 5 8: 20 7127 5 1: 7 6: 25 1: 6 7128 6 1: 7 1: 5 1: 7 7129 7 8: 25 6: 25 7: 20 7130 8 1: 7 6: 25 7: 20 7131New grid distribution: 3 7132 1 14: 25 7: 25 1: 14 7133 2 1: 15 1: 6 1: 8 7134 3 1: 15 1: 6 9: 20 7135 4 14: 25 7: 25 15: 20 7136 5 1: 13 7: 25 1: 7 7137 6 16: 25 1: 6 1: 12 7138 7 1: 13 7: 25 8: 20 7139 8 16: 25 1: 6 13: 20 7140Setting up quadratic distribution... 7141ExtMesh (bp) on 0 = 50 x 52 x 38 = 98800 7142PhiOnMesh: Number of (b)points on node 0 = 2160 7143PhiOnMesh: nlist on node 0 = 4782 7144 7145 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 7146 scf: 1 -465.799108 -465.813675 -465.813675 0.006655 -2.278061 0.062918 7147 scf: 2 -465.813069 -465.813550 -465.813550 0.002655 -2.238381 0.101272 7148 scf: 3 -465.813850 -465.813770 -465.813770 0.001583 -2.262834 0.003808 7149 scf: 4 -465.813772 -465.813771 -465.813771 0.000052 -2.262570 0.002131 7150 scf: 5 -465.813773 -465.813772 -465.813772 0.000087 -2.262121 0.000714 7151 7152SCF Convergence by DM+H criterion 7153max |DM_out - DM_in| : 0.0000869943 7154max |H_out - H_in| (eV) : 0.0007138576 7155SCF cycle converged after 5 iterations 7156 7157Using DM_out to compute the final energy and forces 7158No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 7159 7160siesta: E_KS(eV) = -465.8138 7161 7162siesta: Atomic forces (eV/Ang): 7163 1 -0.504964 -0.329041 -0.295609 7164 2 0.858696 0.465253 0.097221 7165 3 -0.394532 -0.184402 -0.050708 7166---------------------------------------- 7167 Tot -0.040800 -0.048191 -0.249096 7168---------------------------------------- 7169 Max 0.858696 7170 Res 0.422446 sqrt( Sum f_i^2 / 3N ) 7171---------------------------------------- 7172 Max 0.858696 constrained 7173 7174Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -3.46 -2.14 -0.87 -0.60 -0.44 -1.78 7175(Free)E + p*V (eV/cell) -465.2626 7176Target enthalpy (eV/cell) -465.8138 7177 7178siesta: Stress tensor (static) (eV/Ang**3): 7179 -0.002155 -0.001083 -0.000263 7180 -0.001084 -0.000794 -0.000099 7181 -0.000265 -0.000099 -0.000386 7182 7183siesta: Pressure (static): 1.78098040 kBar 7184 7185siesta: Stress tensor (total) (eV/Ang**3): 7186 -0.002158 -0.001111 -0.000272 7187 -0.001112 -0.001337 -0.000375 7188 -0.000274 -0.000375 -0.000541 7189 7190siesta: Pressure (total): 2.15579946 kBar 7191 7192siesta: Temp_ion = 566.971 K 7193 7194 ==================================== 7195 Begin MD step = 7 7196 ==================================== 7197 7198outcoor: Atomic coordinates (Ang): 7199 0.01078025 0.00092065 0.01195847 1 1 O 7200 0.63228631 0.72642460 0.01551236 2 2 H 7201 -0.81054713 0.43581934 -0.25006021 2 3 H 7202 7203outcell: Unit cell vectors (Ang): 7204 8.000000 0.000000 0.000000 7205 0.000000 8.000000 0.000000 7206 0.000000 0.000000 6.400000 7207 7208outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 7209outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 7210outcell: Cell volume (Ang**3) : 409.6000 7211<dSpData1D:S at geom step 7 7212 <sparsity:sparsity for geom step 7 7213 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 7214 <dData1D:(new from dSpData1D) n=69, refcount: 1> 7215refcount: 1> 7216new_DM -- step: 7 7217Re-using DM from previous geometries... 7218Number of DMs in history: 1 7219 DM extrapolation coefficients: 72201 1.00000 7221New DM after history re-use: 7222<dSpData2D:SpM extrapolated using coords 7223 <sparsity:sparsity for geom step 7 7224 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 7225 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 7226refcount: 1> 7227No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 7228New grid distribution: 1 7229 1 1: 25 1: 13 1: 5 7230 2 1: 25 1: 13 6: 10 7231 3 1: 25 1: 13 11: 15 7232 4 1: 25 1: 13 16: 20 7233 5 1: 25 14: 25 1: 5 7234 6 1: 25 14: 25 6: 10 7235 7 1: 25 14: 25 11: 15 7236 8 1: 25 14: 25 16: 20 7237 7238InitMesh: MESH = 50 x 50 x 40 = 100000 7239InitMesh: (bp) = 25 x 25 x 20 = 12500 7240InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 7241ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 7242New grid distribution: 2 7243 1 8: 25 6: 25 1: 6 7244 2 8: 25 1: 5 1: 6 7245 3 8: 25 1: 5 7: 20 7246 4 1: 7 1: 5 8: 20 7247 5 1: 7 6: 25 1: 6 7248 6 1: 7 1: 5 1: 7 7249 7 8: 25 6: 25 7: 20 7250 8 1: 7 6: 25 7: 20 7251New grid distribution: 3 7252 1 16: 25 7: 25 1: 14 7253 2 1: 15 1: 6 1: 8 7254 3 1: 15 1: 6 9: 20 7255 4 16: 25 7: 25 15: 20 7256 5 1: 15 7: 25 1: 7 7257 6 16: 25 1: 6 1: 12 7258 7 1: 15 7: 25 8: 20 7259 8 16: 25 1: 6 13: 20 7260Setting up quadratic distribution... 7261ExtMesh (bp) on 0 = 50 x 52 x 38 = 98800 7262PhiOnMesh: Number of (b)points on node 0 = 2160 7263PhiOnMesh: nlist on node 0 = 4795 7264 7265 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 7266 scf: 1 -465.803801 -465.815353 -465.815353 0.006286 -2.243205 0.058957 7267 scf: 2 -465.814837 -465.815251 -465.815251 0.002492 -2.205844 0.094019 7268 scf: 3 -465.815511 -465.815441 -465.815441 0.001477 -2.228751 0.003780 7269 scf: 4 -465.815444 -465.815443 -465.815443 0.000048 -2.228515 0.002108 7270 scf: 5 -465.815444 -465.815443 -465.815443 0.000080 -2.228114 0.000678 7271 7272SCF Convergence by DM+H criterion 7273max |DM_out - DM_in| : 0.0000800792 7274max |H_out - H_in| (eV) : 0.0006782753 7275SCF cycle converged after 5 iterations 7276 7277Using DM_out to compute the final energy and forces 7278No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 7279 7280siesta: E_KS(eV) = -465.8154 7281 7282siesta: Atomic forces (eV/Ang): 7283 1 -0.411081 -0.442575 -0.256968 7284 2 0.838103 0.495115 0.090562 7285 3 -0.468119 -0.109904 -0.082908 7286---------------------------------------- 7287 Tot -0.041097 -0.057363 -0.249314 7288---------------------------------------- 7289 Max 0.838103 7290 Res 0.424884 sqrt( Sum f_i^2 / 3N ) 7291---------------------------------------- 7292 Max 0.838103 constrained 7293 7294Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -3.64 -2.38 -0.90 -0.54 -0.54 -1.62 7295(Free)E + p*V (eV/cell) -465.2256 7296Target enthalpy (eV/cell) -465.8154 7297 7298siesta: Stress tensor (static) (eV/Ang**3): 7299 -0.002271 -0.000978 -0.000317 7300 -0.000978 -0.000933 -0.000055 7301 -0.000319 -0.000055 -0.000405 7302 7303siesta: Pressure (static): 1.92759023 kBar 7304 7305siesta: Stress tensor (total) (eV/Ang**3): 7306 -0.002274 -0.001012 -0.000333 7307 -0.001012 -0.001484 -0.000334 7308 -0.000335 -0.000334 -0.000562 7309 7310siesta: Pressure (total): 2.30704361 kBar 7311 7312siesta: Temp_ion = 573.458 K 7313 7314 ==================================== 7315 Begin MD step = 8 7316 ==================================== 7317 7318outcoor: Atomic coordinates (Ang): 7319 0.01078984 0.00149476 0.01201242 1 1 O 7320 0.63250058 0.72656962 0.01670189 2 2 H 7321 -0.81136613 0.42675984 -0.25492309 2 3 H 7322 7323outcell: Unit cell vectors (Ang): 7324 8.000000 0.000000 0.000000 7325 0.000000 8.000000 0.000000 7326 0.000000 0.000000 6.400000 7327 7328outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 7329outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 7330outcell: Cell volume (Ang**3) : 409.6000 7331<dSpData1D:S at geom step 8 7332 <sparsity:sparsity for geom step 8 7333 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 7334 <dData1D:(new from dSpData1D) n=69, refcount: 1> 7335refcount: 1> 7336new_DM -- step: 8 7337Re-using DM from previous geometries... 7338Number of DMs in history: 1 7339 DM extrapolation coefficients: 73401 1.00000 7341New DM after history re-use: 7342<dSpData2D:SpM extrapolated using coords 7343 <sparsity:sparsity for geom step 8 7344 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 7345 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 7346refcount: 1> 7347No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 7348New grid distribution: 1 7349 1 1: 25 1: 13 1: 5 7350 2 1: 25 1: 13 6: 10 7351 3 1: 25 1: 13 11: 15 7352 4 1: 25 1: 13 16: 20 7353 5 1: 25 14: 25 1: 5 7354 6 1: 25 14: 25 6: 10 7355 7 1: 25 14: 25 11: 15 7356 8 1: 25 14: 25 16: 20 7357 7358InitMesh: MESH = 50 x 50 x 40 = 100000 7359InitMesh: (bp) = 25 x 25 x 20 = 12500 7360InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 7361ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 7362New grid distribution: 2 7363 1 8: 25 6: 25 1: 6 7364 2 8: 25 1: 5 1: 6 7365 3 8: 25 1: 5 7: 20 7366 4 1: 7 1: 5 8: 20 7367 5 1: 7 6: 25 1: 6 7368 6 1: 7 1: 5 1: 7 7369 7 8: 25 6: 25 7: 20 7370 8 1: 7 6: 25 7: 20 7371New grid distribution: 3 7372 1 16: 25 7: 25 1: 14 7373 2 1: 15 1: 6 1: 8 7374 3 1: 15 1: 6 9: 20 7375 4 16: 25 7: 25 15: 20 7376 5 1: 15 7: 25 1: 7 7377 6 16: 25 1: 6 1: 12 7378 7 1: 15 7: 25 8: 20 7379 8 16: 25 1: 6 13: 20 7380Setting up quadratic distribution... 7381ExtMesh (bp) on 0 = 50 x 52 x 38 = 98800 7382PhiOnMesh: Number of (b)points on node 0 = 2160 7383PhiOnMesh: nlist on node 0 = 4785 7384 7385 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 7386 scf: 1 -465.808660 -465.816970 -465.816970 0.005866 -2.208394 0.054464 7387 scf: 2 -465.816545 -465.816891 -465.816891 0.002309 -2.173705 0.085976 7388 scf: 3 -465.817109 -465.817051 -465.817051 0.001360 -2.194849 0.003693 7389 scf: 4 -465.817053 -465.817052 -465.817052 0.000044 -2.194648 0.002104 7390 scf: 5 -465.817054 -465.817053 -465.817053 0.000072 -2.194302 0.000634 7391 7392SCF Convergence by DM+H criterion 7393max |DM_out - DM_in| : 0.0000722752 7394max |H_out - H_in| (eV) : 0.0006342515 7395SCF cycle converged after 5 iterations 7396 7397Using DM_out to compute the final energy and forces 7398No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 7399 7400siesta: E_KS(eV) = -465.8171 7401 7402siesta: Atomic forces (eV/Ang): 7403 1 -0.311252 -0.537192 -0.218841 7404 2 0.802759 0.510695 0.082794 7405 3 -0.532378 -0.039750 -0.113778 7406---------------------------------------- 7407 Tot -0.040870 -0.066247 -0.249825 7408---------------------------------------- 7409 Max 0.802759 7410 Res 0.427315 sqrt( Sum f_i^2 / 3N ) 7411---------------------------------------- 7412 Max 0.802759 constrained 7413 7414Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -3.77 -2.55 -0.93 -0.47 -0.63 -1.44 7415(Free)E + p*V (eV/cell) -465.1986 7416Target enthalpy (eV/cell) -465.8171 7417 7418siesta: Stress tensor (static) (eV/Ang**3): 7419 -0.002349 -0.000858 -0.000367 7420 -0.000858 -0.001038 -0.000011 7421 -0.000369 -0.000011 -0.000424 7422 7423siesta: Pressure (static): 2.03530453 kBar 7424 7425siesta: Stress tensor (total) (eV/Ang**3): 7426 -0.002352 -0.000901 -0.000390 7427 -0.000901 -0.001594 -0.000295 7428 -0.000392 -0.000295 -0.000584 7429 7430siesta: Pressure (total): 2.41909964 kBar 7431 7432siesta: Temp_ion = 579.728 K 7433 7434 ==================================== 7435 Begin MD step = 9 7436 ==================================== 7437 7438outcoor: Atomic coordinates (Ang): 7439 0.01079198 0.00205600 0.01206113 1 1 O 7440 0.63301939 0.72690837 0.01792282 2 2 H 7441 -0.81238710 0.41768526 -0.25982915 2 3 H 7442 7443outcell: Unit cell vectors (Ang): 7444 8.000000 0.000000 0.000000 7445 0.000000 8.000000 0.000000 7446 0.000000 0.000000 6.400000 7447 7448outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 7449outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 7450outcell: Cell volume (Ang**3) : 409.6000 7451<dSpData1D:S at geom step 9 7452 <sparsity:sparsity for geom step 9 7453 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 7454 <dData1D:(new from dSpData1D) n=69, refcount: 1> 7455refcount: 1> 7456new_DM -- step: 9 7457Re-using DM from previous geometries... 7458Number of DMs in history: 1 7459 DM extrapolation coefficients: 74601 1.00000 7461New DM after history re-use: 7462<dSpData2D:SpM extrapolated using coords 7463 <sparsity:sparsity for geom step 9 7464 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 7465 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 7466refcount: 1> 7467No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 7468New grid distribution: 1 7469 1 1: 25 1: 13 1: 5 7470 2 1: 25 1: 13 6: 10 7471 3 1: 25 1: 13 11: 15 7472 4 1: 25 1: 13 16: 20 7473 5 1: 25 14: 25 1: 5 7474 6 1: 25 14: 25 6: 10 7475 7 1: 25 14: 25 11: 15 7476 8 1: 25 14: 25 16: 20 7477 7478InitMesh: MESH = 50 x 50 x 40 = 100000 7479InitMesh: (bp) = 25 x 25 x 20 = 12500 7480InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 7481ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 7482New grid distribution: 2 7483 1 8: 25 6: 25 1: 6 7484 2 8: 25 1: 5 1: 6 7485 3 8: 25 1: 5 7: 20 7486 4 1: 7 1: 5 8: 20 7487 5 1: 7 6: 25 1: 6 7488 6 1: 7 1: 5 1: 7 7489 7 8: 25 6: 25 7: 20 7490 8 1: 7 6: 25 7: 20 7491New grid distribution: 3 7492 1 16: 25 7: 25 1: 14 7493 2 1: 15 1: 6 1: 8 7494 3 1: 15 1: 6 9: 20 7495 4 16: 25 7: 25 15: 20 7496 5 1: 15 7: 25 1: 7 7497 6 16: 25 1: 6 1: 12 7498 7 1: 15 7: 25 8: 20 7499 8 16: 25 1: 6 13: 20 7500Setting up quadratic distribution... 7501ExtMesh (bp) on 0 = 50 x 52 x 38 = 98800 7502PhiOnMesh: Number of (b)points on node 0 = 2160 7503PhiOnMesh: nlist on node 0 = 4784 7504 7505 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 7506 scf: 1 -465.813653 -465.818566 -465.818566 0.005696 -2.173858 0.049540 7507 scf: 2 -465.818229 -465.818508 -465.818508 0.002111 -2.142132 0.077307 7508 scf: 3 -465.818687 -465.818639 -465.818639 0.001233 -2.161334 0.003540 7509 scf: 4 -465.818642 -465.818640 -465.818640 0.000043 -2.161175 0.002129 7510 scf: 5 -465.818642 -465.818641 -465.818641 0.000070 -2.160892 0.000617 7511 7512SCF Convergence by DM+H criterion 7513max |DM_out - DM_in| : 0.0000695000 7514max |H_out - H_in| (eV) : 0.0006165140 7515SCF cycle converged after 5 iterations 7516 7517Using DM_out to compute the final energy and forces 7518No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 7519 7520siesta: E_KS(eV) = -465.8186 7521 7522siesta: Atomic forces (eV/Ang): 7523 1 -0.208954 -0.611822 -0.181604 7524 2 0.752982 0.512119 0.073839 7525 3 -0.584800 0.025257 -0.142331 7526---------------------------------------- 7527 Tot -0.040773 -0.074446 -0.250096 7528---------------------------------------- 7529 Max 0.752982 7530 Res 0.427987 sqrt( Sum f_i^2 / 3N ) 7531---------------------------------------- 7532 Max 0.752982 constrained 7533 7534Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -3.83 -2.67 -0.97 -0.41 -0.71 -1.26 7535(Free)E + p*V (eV/cell) -465.1825 7536Target enthalpy (eV/cell) -465.8186 7537 7538siesta: Stress tensor (static) (eV/Ang**3): 7539 -0.002383 -0.000729 -0.000411 7540 -0.000729 -0.001108 0.000031 7541 -0.000413 0.000031 -0.000442 7542 7543siesta: Pressure (static): 2.10053430 kBar 7544 7545siesta: Stress tensor (total) (eV/Ang**3): 7546 -0.002389 -0.000783 -0.000442 7547 -0.000784 -0.001666 -0.000257 7548 -0.000444 -0.000257 -0.000604 7549 7550siesta: Pressure (total): 2.48852579 kBar 7551 7552siesta: Temp_ion = 585.931 K 7553 7554 ==================================== 7555 Begin MD step = 10 7556 ==================================== 7557 7558outcoor: Atomic coordinates (Ang): 7559 0.01078911 0.00260258 0.01210549 1 1 O 7560 0.63382386 0.72744140 0.01917177 2 2 H 7561 -0.81362992 0.40862027 -0.26478919 2 3 H 7562 7563outcell: Unit cell vectors (Ang): 7564 8.000000 0.000000 0.000000 7565 0.000000 8.000000 0.000000 7566 0.000000 0.000000 6.400000 7567 7568outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 7569outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 7570outcell: Cell volume (Ang**3) : 409.6000 7571<dSpData1D:S at geom step 10 7572 <sparsity:sparsity for geom step 10 7573 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 7574 <dData1D:(new from dSpData1D) n=69, refcount: 1> 7575refcount: 1> 7576new_DM -- step: 10 7577Re-using DM from previous geometries... 7578Number of DMs in history: 1 7579 DM extrapolation coefficients: 75801 1.00000 7581New DM after history re-use: 7582<dSpData2D:SpM extrapolated using coords 7583 <sparsity:sparsity for geom step 10 7584 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 7585 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 7586refcount: 1> 7587No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 7588New grid distribution: 1 7589 1 1: 25 1: 13 1: 5 7590 2 1: 25 1: 13 6: 10 7591 3 1: 25 1: 13 11: 15 7592 4 1: 25 1: 13 16: 20 7593 5 1: 25 14: 25 1: 5 7594 6 1: 25 14: 25 6: 10 7595 7 1: 25 14: 25 11: 15 7596 8 1: 25 14: 25 16: 20 7597 7598InitMesh: MESH = 50 x 50 x 40 = 100000 7599InitMesh: (bp) = 25 x 25 x 20 = 12500 7600InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 7601ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 7602New grid distribution: 2 7603 1 8: 25 6: 25 1: 6 7604 2 8: 25 1: 5 1: 6 7605 3 8: 25 1: 5 7: 20 7606 4 1: 7 1: 5 8: 20 7607 5 1: 7 6: 25 1: 6 7608 6 1: 7 1: 5 1: 7 7609 7 8: 25 6: 25 7: 20 7610 8 1: 7 6: 25 7: 20 7611New grid distribution: 3 7612 1 16: 25 7: 25 1: 14 7613 2 1: 15 1: 6 1: 8 7614 3 1: 15 1: 6 9: 20 7615 4 16: 25 7: 25 15: 20 7616 5 1: 15 7: 25 1: 7 7617 6 16: 25 1: 6 1: 12 7618 7 1: 15 7: 25 8: 20 7619 8 16: 25 1: 6 13: 20 7620Setting up quadratic distribution... 7621ExtMesh (bp) on 0 = 50 x 52 x 38 = 98800 7622PhiOnMesh: Number of (b)points on node 0 = 2160 7623PhiOnMesh: nlist on node 0 = 4778 7624 7625 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 7626 scf: 1 -465.818726 -465.820165 -465.820165 0.005797 -2.139839 0.044288 7627 scf: 2 -465.819910 -465.820127 -465.820127 0.001902 -2.111303 0.068182 7628 scf: 3 -465.820269 -465.820230 -465.820230 0.001100 -2.128425 0.003367 7629 scf: 4 -465.820233 -465.820232 -465.820232 0.000042 -2.128314 0.002128 7630 scf: 5 -465.820233 -465.820233 -465.820233 0.000068 -2.128102 0.000665 7631 7632SCF Convergence by DM+H criterion 7633max |DM_out - DM_in| : 0.0000676877 7634max |H_out - H_in| (eV) : 0.0006654102 7635SCF cycle converged after 5 iterations 7636 7637Using DM_out to compute the final energy and forces 7638No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 7639 7640siesta: E_KS(eV) = -465.8202 7641 7642siesta: Atomic forces (eV/Ang): 7643 1 -0.106819 -0.666521 -0.146575 7644 2 0.689437 0.499940 0.063678 7645 3 -0.623453 0.084330 -0.167656 7646---------------------------------------- 7647 Tot -0.040835 -0.082251 -0.250553 7648---------------------------------------- 7649 Max 0.689437 7650 Res 0.425621 sqrt( Sum f_i^2 / 3N ) 7651---------------------------------------- 7652 Max 0.689437 constrained 7653 7654Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -3.81 -2.73 -1.00 -0.36 -0.78 -1.06 7655(Free)E + p*V (eV/cell) -465.1776 7656Target enthalpy (eV/cell) -465.8202 7657 7658siesta: Stress tensor (static) (eV/Ang**3): 7659 -0.002368 -0.000591 -0.000445 7660 -0.000592 -0.001146 0.000070 7661 -0.000447 0.000070 -0.000459 7662 7663siesta: Pressure (static): 2.12172738 kBar 7664 7665siesta: Stress tensor (total) (eV/Ang**3): 7666 -0.002379 -0.000659 -0.000486 7667 -0.000659 -0.001704 -0.000222 7668 -0.000488 -0.000222 -0.000624 7669 7670siesta: Pressure (total): 2.51387010 kBar 7671 7672siesta: Temp_ion = 592.122 K 7673 7674 ==================================== 7675 Begin MD step = 11 7676 ==================================== 7677 7678outcoor: Atomic coordinates (Ang): 7679 0.01078368 0.00313321 0.01214634 1 1 O 7680 0.63488988 0.72816410 0.02044487 2 2 H 7681 -0.81510926 0.39958726 -0.26981284 2 3 H 7682 7683outcell: Unit cell vectors (Ang): 7684 8.000000 0.000000 0.000000 7685 0.000000 8.000000 0.000000 7686 0.000000 0.000000 6.400000 7687 7688outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 7689outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 7690outcell: Cell volume (Ang**3) : 409.6000 7691<dSpData1D:S at geom step 11 7692 <sparsity:sparsity for geom step 11 7693 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 7694 <dData1D:(new from dSpData1D) n=69, refcount: 1> 7695refcount: 1> 7696new_DM -- step: 11 7697Re-using DM from previous geometries... 7698Number of DMs in history: 1 7699 DM extrapolation coefficients: 77001 1.00000 7701New DM after history re-use: 7702<dSpData2D:SpM extrapolated using coords 7703 <sparsity:sparsity for geom step 11 7704 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 7705 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 7706refcount: 1> 7707No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 7708New grid distribution: 1 7709 1 1: 25 1: 13 1: 5 7710 2 1: 25 1: 13 6: 10 7711 3 1: 25 1: 13 11: 15 7712 4 1: 25 1: 13 16: 20 7713 5 1: 25 14: 25 1: 5 7714 6 1: 25 14: 25 6: 10 7715 7 1: 25 14: 25 11: 15 7716 8 1: 25 14: 25 16: 20 7717 7718InitMesh: MESH = 50 x 50 x 40 = 100000 7719InitMesh: (bp) = 25 x 25 x 20 = 12500 7720InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 7721ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 7722New grid distribution: 2 7723 1 8: 25 6: 25 1: 6 7724 2 8: 25 1: 5 1: 6 7725 3 8: 25 1: 5 7: 20 7726 4 1: 7 1: 5 8: 20 7727 5 1: 7 6: 25 1: 6 7728 6 1: 7 1: 5 1: 7 7729 7 8: 25 6: 25 7: 20 7730 8 1: 7 6: 25 7: 20 7731New grid distribution: 3 7732 1 16: 25 7: 25 1: 14 7733 2 1: 14 1: 6 1: 8 7734 3 1: 14 1: 6 9: 20 7735 4 16: 25 7: 25 15: 20 7736 5 1: 15 7: 25 1: 7 7737 6 15: 25 1: 6 1: 12 7738 7 1: 15 7: 25 8: 20 7739 8 15: 25 1: 6 13: 20 7740Setting up quadratic distribution... 7741ExtMesh (bp) on 0 = 50 x 52 x 38 = 98800 7742PhiOnMesh: Number of (b)points on node 0 = 2160 7743PhiOnMesh: nlist on node 0 = 4774 7744 7745 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 7746 scf: 1 -465.823785 -465.821750 -465.821750 0.005898 -2.106581 0.038829 7747 scf: 2 -465.821568 -465.821729 -465.821729 0.001685 -2.081386 0.058799 7748 scf: 3 -465.821838 -465.821808 -465.821808 0.000963 -2.096335 0.003325 7749 scf: 4 -465.821811 -465.821809 -465.821809 0.000040 -2.096279 0.002093 7750 scf: 5 -465.821811 -465.821810 -465.821810 0.000065 -2.096144 0.000706 7751 7752SCF Convergence by DM+H criterion 7753max |DM_out - DM_in| : 0.0000651193 7754max |H_out - H_in| (eV) : 0.0007060195 7755SCF cycle converged after 5 iterations 7756 7757Using DM_out to compute the final energy and forces 7758No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 7759 7760siesta: E_KS(eV) = -465.8218 7761 7762siesta: Atomic forces (eV/Ang): 7763 1 -0.008113 -0.701184 -0.114951 7764 2 0.613268 0.475154 0.052240 7765 3 -0.646536 0.136775 -0.188833 7766---------------------------------------- 7767 Tot -0.041380 -0.089254 -0.251543 7768---------------------------------------- 7769 Max 0.701184 7770 Res 0.419247 sqrt( Sum f_i^2 / 3N ) 7771---------------------------------------- 7772 Max 0.701184 constrained 7773 7774Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -3.72 -2.73 -1.03 -0.31 -0.84 -0.85 7775(Free)E + p*V (eV/cell) -465.1843 7776Target enthalpy (eV/cell) -465.8218 7777 7778siesta: Stress tensor (static) (eV/Ang**3): 7779 -0.002303 -0.000450 -0.000469 7780 -0.000451 -0.001152 0.000105 7781 -0.000471 0.000105 -0.000473 7782 7783siesta: Pressure (static): 2.09746629 kBar 7784 7785siesta: Stress tensor (total) (eV/Ang**3): 7786 -0.002320 -0.000532 -0.000520 7787 -0.000533 -0.001707 -0.000191 7788 -0.000522 -0.000191 -0.000643 7789 7790siesta: Pressure (total): 2.49375255 kBar 7791 7792siesta: Temp_ion = 598.254 K 7793 7794 ==================================== 7795 Begin MD step = 12 7796 ==================================== 7797 7798outcoor: Atomic coordinates (Ang): 7799 0.01077806 0.00364704 0.01218444 1 1 O 7800 0.63618856 0.72906706 0.02173780 2 2 H 7801 -0.81683388 0.39060615 -0.27490813 2 3 H 7802 7803outcell: Unit cell vectors (Ang): 7804 8.000000 0.000000 0.000000 7805 0.000000 8.000000 0.000000 7806 0.000000 0.000000 6.400000 7807 7808outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 7809outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 7810outcell: Cell volume (Ang**3) : 409.6000 7811<dSpData1D:S at geom step 12 7812 <sparsity:sparsity for geom step 12 7813 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 7814 <dData1D:(new from dSpData1D) n=69, refcount: 1> 7815refcount: 1> 7816new_DM -- step: 12 7817Re-using DM from previous geometries... 7818Number of DMs in history: 1 7819 DM extrapolation coefficients: 78201 1.00000 7821New DM after history re-use: 7822<dSpData2D:SpM extrapolated using coords 7823 <sparsity:sparsity for geom step 12 7824 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 7825 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 7826refcount: 1> 7827No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 7828New grid distribution: 1 7829 1 1: 25 1: 13 1: 5 7830 2 1: 25 1: 13 6: 10 7831 3 1: 25 1: 13 11: 15 7832 4 1: 25 1: 13 16: 20 7833 5 1: 25 14: 25 1: 5 7834 6 1: 25 14: 25 6: 10 7835 7 1: 25 14: 25 11: 15 7836 8 1: 25 14: 25 16: 20 7837 7838InitMesh: MESH = 50 x 50 x 40 = 100000 7839InitMesh: (bp) = 25 x 25 x 20 = 12500 7840InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 7841ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 7842New grid distribution: 2 7843 1 8: 25 6: 25 1: 6 7844 2 8: 25 1: 5 1: 6 7845 3 8: 25 1: 5 7: 20 7846 4 1: 7 1: 5 8: 20 7847 5 1: 7 6: 25 1: 6 7848 6 1: 7 1: 5 1: 7 7849 7 8: 25 6: 25 7: 20 7850 8 1: 7 6: 25 7: 20 7851New grid distribution: 3 7852 1 16: 25 7: 25 1: 14 7853 2 1: 14 1: 6 1: 8 7854 3 1: 14 1: 6 9: 20 7855 4 16: 25 7: 25 15: 20 7856 5 1: 15 7: 25 1: 7 7857 6 15: 25 1: 6 1: 12 7858 7 1: 15 7: 25 8: 20 7859 8 15: 25 1: 6 13: 20 7860Setting up quadratic distribution... 7861ExtMesh (bp) on 0 = 50 x 52 x 38 = 98800 7862PhiOnMesh: Number of (b)points on node 0 = 2160 7863PhiOnMesh: nlist on node 0 = 4765 7864 7865 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 7866 scf: 1 -465.828716 -465.823283 -465.823283 0.005994 -2.074326 0.033277 7867 scf: 2 -465.823163 -465.823277 -465.823277 0.001467 -2.052552 0.049336 7868 scf: 3 -465.823358 -465.823335 -465.823335 0.000823 -2.065280 0.003217 7869 scf: 4 -465.823337 -465.823336 -465.823336 0.000040 -2.065284 0.002020 7870 scf: 5 -465.823338 -465.823337 -465.823337 0.000062 -2.065233 0.000733 7871 7872SCF Convergence by DM+H criterion 7873max |DM_out - DM_in| : 0.0000616151 7874max |H_out - H_in| (eV) : 0.0007334626 7875SCF cycle converged after 5 iterations 7876 7877Using DM_out to compute the final energy and forces 7878No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 7879 7880siesta: E_KS(eV) = -465.8233 7881 7882siesta: Atomic forces (eV/Ang): 7883 1 0.084619 -0.717414 -0.086730 7884 2 0.525933 0.439030 0.039570 7885 3 -0.652934 0.182009 -0.205123 7886---------------------------------------- 7887 Tot -0.042381 -0.096375 -0.252283 7888---------------------------------------- 7889 Max 0.717414 7890 Res 0.408495 sqrt( Sum f_i^2 / 3N ) 7891---------------------------------------- 7892 Max 0.717414 constrained 7893 7894Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -3.55 -2.69 -1.06 -0.26 -0.87 -0.65 7895(Free)E + p*V (eV/cell) -465.2018 7896Target enthalpy (eV/cell) -465.8233 7897 7898siesta: Stress tensor (static) (eV/Ang**3): 7899 -0.002188 -0.000307 -0.000483 7900 -0.000307 -0.001129 0.000137 7901 -0.000484 0.000137 -0.000485 7902 7903siesta: Pressure (static): 2.03078758 kBar 7904 7905siesta: Stress tensor (total) (eV/Ang**3): 7906 -0.002214 -0.000405 -0.000544 7907 -0.000405 -0.001679 -0.000163 7908 -0.000546 -0.000163 -0.000659 7909 7910siesta: Pressure (total): 2.43117794 kBar 7911 7912siesta: Temp_ion = 604.177 K 7913 7914 ==================================== 7915 Begin MD step = 13 7916 ==================================== 7917 7918outcoor: Atomic coordinates (Ang): 7919 0.01077447 0.00414370 0.01222047 1 1 O 7920 0.63768675 0.73013656 0.02304573 2 2 H 7921 -0.81880620 0.38169408 -0.28008124 2 3 H 7922 7923outcell: Unit cell vectors (Ang): 7924 8.000000 0.000000 0.000000 7925 0.000000 8.000000 0.000000 7926 0.000000 0.000000 6.400000 7927 7928outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 7929outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 7930outcell: Cell volume (Ang**3) : 409.6000 7931<dSpData1D:S at geom step 13 7932 <sparsity:sparsity for geom step 13 7933 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 7934 <dData1D:(new from dSpData1D) n=69, refcount: 1> 7935refcount: 1> 7936new_DM -- step: 13 7937Re-using DM from previous geometries... 7938Number of DMs in history: 1 7939 DM extrapolation coefficients: 79401 1.00000 7941New DM after history re-use: 7942<dSpData2D:SpM extrapolated using coords 7943 <sparsity:sparsity for geom step 13 7944 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 7945 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 7946refcount: 1> 7947No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 7948New grid distribution: 1 7949 1 1: 25 1: 13 1: 5 7950 2 1: 25 1: 13 6: 10 7951 3 1: 25 1: 13 11: 15 7952 4 1: 25 1: 13 16: 20 7953 5 1: 25 14: 25 1: 5 7954 6 1: 25 14: 25 6: 10 7955 7 1: 25 14: 25 11: 15 7956 8 1: 25 14: 25 16: 20 7957 7958InitMesh: MESH = 50 x 50 x 40 = 100000 7959InitMesh: (bp) = 25 x 25 x 20 = 12500 7960InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 7961ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 7962New grid distribution: 2 7963 1 8: 25 6: 25 1: 6 7964 2 8: 25 1: 5 1: 6 7965 3 8: 25 1: 5 7: 20 7966 4 1: 7 1: 5 8: 20 7967 5 1: 7 6: 25 1: 6 7968 6 1: 7 1: 5 1: 7 7969 7 8: 25 6: 25 7: 20 7970 8 1: 7 6: 25 7: 20 7971New grid distribution: 3 7972 1 16: 25 7: 25 1: 14 7973 2 1: 13 1: 6 1: 8 7974 3 1: 13 1: 6 9: 20 7975 4 16: 25 7: 25 15: 20 7976 5 1: 15 7: 25 1: 7 7977 6 14: 25 1: 6 1: 12 7978 7 1: 15 7: 25 8: 20 7979 8 14: 25 1: 6 13: 20 7980Setting up quadratic distribution... 7981ExtMesh (bp) on 0 = 50 x 52 x 38 = 98800 7982PhiOnMesh: Number of (b)points on node 0 = 2160 7983PhiOnMesh: nlist on node 0 = 4776 7984 7985 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 7986 scf: 1 -465.833367 -465.824691 -465.824691 0.006085 -2.043330 0.027742 7987 scf: 2 -465.824620 -465.824696 -465.824696 0.001249 -2.024982 0.039972 7988 scf: 3 -465.824754 -465.824738 -465.824738 0.000684 -2.035487 0.003022 7989 scf: 4 -465.824740 -465.824739 -465.824739 0.000039 -2.035558 0.001902 7990 scf: 5 -465.824740 -465.824739 -465.824739 0.000057 -2.035592 0.000741 7991 7992SCF Convergence by DM+H criterion 7993max |DM_out - DM_in| : 0.0000569961 7994max |H_out - H_in| (eV) : 0.0007407038 7995SCF cycle converged after 5 iterations 7996 7997Using DM_out to compute the final energy and forces 7998No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 7999 8000siesta: E_KS(eV) = -465.8247 8001 8002siesta: Atomic forces (eV/Ang): 8003 1 0.169232 -0.715752 -0.062969 8004 2 0.429213 0.393252 0.025706 8005 3 -0.641418 0.219803 -0.215794 8006---------------------------------------- 8007 Tot -0.042973 -0.102697 -0.253058 8008---------------------------------------- 8009 Max 0.715752 8010 Res 0.393098 sqrt( Sum f_i^2 / 3N ) 8011---------------------------------------- 8012 Max 0.715752 constrained 8013 8014Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -3.30 -2.60 -1.08 -0.22 -0.89 -0.44 8015(Free)E + p*V (eV/cell) -465.2306 8016Target enthalpy (eV/cell) -465.8247 8017 8018siesta: Stress tensor (static) (eV/Ang**3): 8019 -0.002023 -0.000162 -0.000482 8020 -0.000163 -0.001079 0.000166 8021 -0.000484 0.000166 -0.000493 8022 8023siesta: Pressure (static): 1.91970226 kBar 8024 8025siesta: Stress tensor (total) (eV/Ang**3): 8026 -0.002057 -0.000276 -0.000554 8027 -0.000277 -0.001623 -0.000137 8028 -0.000556 -0.000138 -0.000672 8029 8030siesta: Pressure (total): 2.32405650 kBar 8031 8032siesta: Temp_ion = 609.642 K 8033 8034 ==================================== 8035 Begin MD step = 14 8036 ==================================== 8037 8038outcoor: Atomic coordinates (Ang): 8039 0.01077492 0.00462321 0.01225498 1 1 O 8040 0.63934778 0.73135526 0.02436342 2 2 H 8041 -0.82102185 0.37286540 -0.28533621 2 3 H 8042 8043outcell: Unit cell vectors (Ang): 8044 8.000000 0.000000 0.000000 8045 0.000000 8.000000 0.000000 8046 0.000000 0.000000 6.400000 8047 8048outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 8049outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 8050outcell: Cell volume (Ang**3) : 409.6000 8051<dSpData1D:S at geom step 14 8052 <sparsity:sparsity for geom step 14 8053 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 8054 <dData1D:(new from dSpData1D) n=69, refcount: 1> 8055refcount: 1> 8056new_DM -- step: 14 8057Re-using DM from previous geometries... 8058Number of DMs in history: 1 8059 DM extrapolation coefficients: 80601 1.00000 8061New DM after history re-use: 8062<dSpData2D:SpM extrapolated using coords 8063 <sparsity:sparsity for geom step 14 8064 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 8065 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 8066refcount: 1> 8067No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 8068New grid distribution: 1 8069 1 1: 25 1: 13 1: 5 8070 2 1: 25 1: 13 6: 10 8071 3 1: 25 1: 13 11: 15 8072 4 1: 25 1: 13 16: 20 8073 5 1: 25 14: 25 1: 5 8074 6 1: 25 14: 25 6: 10 8075 7 1: 25 14: 25 11: 15 8076 8 1: 25 14: 25 16: 20 8077 8078InitMesh: MESH = 50 x 50 x 40 = 100000 8079InitMesh: (bp) = 25 x 25 x 20 = 12500 8080InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 8081ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 8082New grid distribution: 2 8083 1 7: 25 6: 25 1: 6 8084 2 8: 25 1: 5 1: 6 8085 3 8: 25 1: 5 7: 20 8086 4 1: 7 1: 5 8: 20 8087 5 1: 6 6: 25 1: 6 8088 6 1: 7 1: 5 1: 7 8089 7 7: 25 6: 25 7: 20 8090 8 1: 6 6: 25 7: 20 8091New grid distribution: 3 8092 1 16: 25 7: 25 1: 14 8093 2 1: 13 1: 6 1: 8 8094 3 1: 13 1: 6 9: 20 8095 4 16: 25 7: 25 15: 20 8096 5 1: 15 7: 25 1: 7 8097 6 14: 25 1: 6 1: 12 8098 7 1: 15 7: 25 8: 20 8099 8 14: 25 1: 6 13: 20 8100Setting up quadratic distribution... 8101ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 8102PhiOnMesh: Number of (b)points on node 0 = 2280 8103PhiOnMesh: nlist on node 0 = 5054 8104 8105 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 8106 scf: 1 -465.837598 -465.825903 -465.825903 0.006167 -2.013832 0.022343 8107 scf: 2 -465.825870 -465.825916 -465.825916 0.001038 -1.998839 0.030890 8108 scf: 3 -465.825957 -465.825945 -465.825945 0.000549 -2.007174 0.002720 8109 scf: 4 -465.825947 -465.825946 -465.825946 0.000036 -2.007313 0.001749 8110 scf: 5 -465.825947 -465.825946 -465.825946 0.000056 -2.007434 0.000716 8111 8112SCF Convergence by DM+H criterion 8113max |DM_out - DM_in| : 0.0000555895 8114max |H_out - H_in| (eV) : 0.0007155612 8115SCF cycle converged after 5 iterations 8116 8117Using DM_out to compute the final energy and forces 8118No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 8119 8120siesta: E_KS(eV) = -465.8259 8121 8122siesta: Atomic forces (eV/Ang): 8123 1 0.242968 -0.698503 -0.044341 8124 2 0.325142 0.339673 0.010671 8125 3 -0.611658 0.250116 -0.220433 8126---------------------------------------- 8127 Tot -0.043548 -0.108714 -0.254102 8128---------------------------------------- 8129 Max 0.698503 8130 Res 0.373480 sqrt( Sum f_i^2 / 3N ) 8131---------------------------------------- 8132 Max 0.698503 constrained 8133 8134Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -2.97 -2.47 -1.09 -0.19 -0.88 -0.24 8135(Free)E + p*V (eV/cell) -465.2693 8136Target enthalpy (eV/cell) -465.8259 8137 8138siesta: Stress tensor (static) (eV/Ang**3): 8139 -0.001809 -0.000020 -0.000467 8140 -0.000021 -0.001008 0.000191 8141 -0.000469 0.000191 -0.000496 8142 8143siesta: Pressure (static): 1.76922027 kBar 8144 8145siesta: Stress tensor (total) (eV/Ang**3): 8146 -0.001853 -0.000150 -0.000550 8147 -0.000151 -0.001543 -0.000116 8148 -0.000552 -0.000116 -0.000681 8149 8150siesta: Pressure (total): 2.17723247 kBar 8151 8152siesta: Temp_ion = 614.322 K 8153 8154 ==================================== 8155 Begin MD step = 15 8156 ==================================== 8157 8158outcoor: Atomic coordinates (Ang): 8159 0.01078120 0.00508600 0.01228843 1 1 O 8160 0.64113215 0.73270282 0.02568515 2 2 H 8161 -0.82346954 0.36413160 -0.29067480 2 3 H 8162 8163outcell: Unit cell vectors (Ang): 8164 8.000000 0.000000 0.000000 8165 0.000000 8.000000 0.000000 8166 0.000000 0.000000 6.400000 8167 8168outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 8169outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 8170outcell: Cell volume (Ang**3) : 409.6000 8171<dSpData1D:S at geom step 15 8172 <sparsity:sparsity for geom step 15 8173 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 8174 <dData1D:(new from dSpData1D) n=69, refcount: 1> 8175refcount: 1> 8176new_DM -- step: 15 8177Re-using DM from previous geometries... 8178Number of DMs in history: 1 8179 DM extrapolation coefficients: 81801 1.00000 8181New DM after history re-use: 8182<dSpData2D:SpM extrapolated using coords 8183 <sparsity:sparsity for geom step 15 8184 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 8185 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 8186refcount: 1> 8187No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 8188New grid distribution: 1 8189 1 1: 25 1: 13 1: 5 8190 2 1: 25 1: 13 6: 10 8191 3 1: 25 1: 13 11: 15 8192 4 1: 25 1: 13 16: 20 8193 5 1: 25 14: 25 1: 5 8194 6 1: 25 14: 25 6: 10 8195 7 1: 25 14: 25 11: 15 8196 8 1: 25 14: 25 16: 20 8197 8198InitMesh: MESH = 50 x 50 x 40 = 100000 8199InitMesh: (bp) = 25 x 25 x 20 = 12500 8200InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 8201ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 8202New grid distribution: 2 8203 1 7: 25 6: 25 1: 6 8204 2 8: 25 1: 5 1: 6 8205 3 8: 25 1: 5 7: 20 8206 4 1: 7 1: 5 8: 20 8207 5 1: 6 6: 25 1: 6 8208 6 1: 7 1: 5 1: 7 8209 7 7: 25 6: 25 7: 20 8210 8 1: 6 6: 25 7: 20 8211New grid distribution: 3 8212 1 16: 25 7: 25 1: 14 8213 2 1: 14 1: 6 1: 8 8214 3 1: 14 1: 6 9: 20 8215 4 16: 25 7: 25 15: 20 8216 5 1: 15 7: 25 1: 7 8217 6 15: 25 1: 6 1: 12 8218 7 1: 15 7: 25 8: 20 8219 8 15: 25 1: 6 13: 20 8220Setting up quadratic distribution... 8221ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 8222PhiOnMesh: Number of (b)points on node 0 = 2280 8223PhiOnMesh: nlist on node 0 = 5052 8224 8225 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 8226 scf: 1 -465.841237 -465.826810 -465.826810 0.006237 -1.986072 0.017184 8227 scf: 2 -465.826804 -465.826829 -465.826829 0.000836 -1.974295 0.022256 8228 scf: 3 -465.826858 -465.826849 -465.826849 0.000421 -1.980569 0.002325 8229 scf: 4 -465.826850 -465.826849 -465.826849 0.000032 -1.980768 0.001601 8230 scf: 5 -465.826850 -465.826850 -465.826850 0.000059 -1.980971 0.000633 8231 8232SCF Convergence by DM+H criterion 8233max |DM_out - DM_in| : 0.0000589885 8234max |H_out - H_in| (eV) : 0.0006327504 8235SCF cycle converged after 5 iterations 8236 8237Using DM_out to compute the final energy and forces 8238No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 8239 8240siesta: E_KS(eV) = -465.8268 8241 8242siesta: Atomic forces (eV/Ang): 8243 1 0.304117 -0.667010 -0.031479 8244 2 0.215452 0.280127 -0.005444 8245 3 -0.563201 0.273301 -0.218581 8246---------------------------------------- 8247 Tot -0.043632 -0.113582 -0.255505 8248---------------------------------------- 8249 Max 0.667010 8250 Res 0.350074 sqrt( Sum f_i^2 / 3N ) 8251---------------------------------------- 8252 Max 0.667010 constrained 8253 8254Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -2.56 -2.31 -1.10 -0.16 -0.85 -0.04 8255(Free)E + p*V (eV/cell) -465.3184 8256Target enthalpy (eV/cell) -465.8268 8257 8258siesta: Stress tensor (static) (eV/Ang**3): 8259 -0.001546 0.000119 -0.000436 8260 0.000118 -0.000914 0.000211 8261 -0.000438 0.000211 -0.000494 8262 8263siesta: Pressure (static): 1.57765995 kBar 8264 8265siesta: Stress tensor (total) (eV/Ang**3): 8266 -0.001600 -0.000026 -0.000530 8267 -0.000027 -0.001440 -0.000098 8268 -0.000531 -0.000098 -0.000685 8269 8270siesta: Pressure (total): 1.98880380 kBar 8271 8272siesta: Temp_ion = 617.823 K 8273 8274 ==================================== 8275 Begin MD step = 16 8276 ==================================== 8277 8278outcoor: Atomic coordinates (Ang): 8279 0.01079476 0.00553281 0.01232113 1 1 O 8280 0.64299827 0.73415664 0.02700482 2 2 H 8281 -0.82613090 0.35550149 -0.29609632 2 3 H 8282 8283outcell: Unit cell vectors (Ang): 8284 8.000000 0.000000 0.000000 8285 0.000000 8.000000 0.000000 8286 0.000000 0.000000 6.400000 8287 8288outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 8289outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 8290outcell: Cell volume (Ang**3) : 409.6000 8291<dSpData1D:S at geom step 16 8292 <sparsity:sparsity for geom step 16 8293 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 8294 <dData1D:(new from dSpData1D) n=69, refcount: 1> 8295refcount: 1> 8296new_DM -- step: 16 8297Re-using DM from previous geometries... 8298Number of DMs in history: 1 8299 DM extrapolation coefficients: 83001 1.00000 8301New DM after history re-use: 8302<dSpData2D:SpM extrapolated using coords 8303 <sparsity:sparsity for geom step 16 8304 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 8305 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 8306refcount: 1> 8307No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 8308New grid distribution: 1 8309 1 1: 25 1: 13 1: 5 8310 2 1: 25 1: 13 6: 10 8311 3 1: 25 1: 13 11: 15 8312 4 1: 25 1: 13 16: 20 8313 5 1: 25 14: 25 1: 5 8314 6 1: 25 14: 25 6: 10 8315 7 1: 25 14: 25 11: 15 8316 8 1: 25 14: 25 16: 20 8317 8318InitMesh: MESH = 50 x 50 x 40 = 100000 8319InitMesh: (bp) = 25 x 25 x 20 = 12500 8320InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 8321ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 8322New grid distribution: 2 8323 1 7: 25 6: 25 1: 6 8324 2 8: 25 1: 5 1: 6 8325 3 8: 25 1: 5 7: 20 8326 4 1: 7 1: 5 8: 20 8327 5 1: 6 6: 25 1: 7 8328 6 1: 7 1: 5 1: 7 8329 7 7: 25 6: 25 7: 20 8330 8 1: 6 6: 25 8: 20 8331New grid distribution: 3 8332 1 16: 25 7: 25 1: 14 8333 2 11: 25 1: 6 1: 13 8334 3 1: 10 1: 6 9: 20 8335 4 11: 25 1: 6 14: 20 8336 5 1: 15 7: 25 1: 7 8337 6 1: 10 1: 6 1: 8 8338 7 1: 15 7: 25 8: 20 8339 8 16: 25 7: 25 15: 20 8340Setting up quadratic distribution... 8341ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 8342PhiOnMesh: Number of (b)points on node 0 = 2280 8343PhiOnMesh: nlist on node 0 = 5042 8344 8345 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 8346 scf: 1 -465.844124 -465.827311 -465.827311 0.006292 -1.960265 0.016630 8347 scf: 2 -465.827321 -465.827334 -465.827334 0.000733 -1.951499 0.014241 8348 scf: 3 -465.827354 -465.827347 -465.827347 0.000304 -1.955893 0.002141 8349 scf: 4 -465.827348 -465.827348 -465.827348 0.000034 -1.956124 0.001537 8350 scf: 5 -465.827348 -465.827348 -465.827348 0.000064 -1.956404 0.000434 8351 8352SCF Convergence by DM+H criterion 8353max |DM_out - DM_in| : 0.0000638905 8354max |H_out - H_in| (eV) : 0.0004342194 8355SCF cycle converged after 5 iterations 8356 8357Using DM_out to compute the final energy and forces 8358No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 8359 8360siesta: E_KS(eV) = -465.8273 8361 8362siesta: Atomic forces (eV/Ang): 8363 1 0.350923 -0.625263 -0.024160 8364 2 0.102587 0.216661 -0.022457 8365 3 -0.497173 0.289684 -0.210267 8366---------------------------------------- 8367 Tot -0.043663 -0.118918 -0.256884 8368---------------------------------------- 8369 Max 0.625263 8370 Res 0.324545 sqrt( Sum f_i^2 / 3N ) 8371---------------------------------------- 8372 Max 0.625263 constrained 8373 8374Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -2.09 -2.12 -1.10 -0.13 -0.79 0.14 8375(Free)E + p*V (eV/cell) -465.3748 8376Target enthalpy (eV/cell) -465.8273 8377 8378siesta: Stress tensor (static) (eV/Ang**3): 8379 -0.001244 0.000249 -0.000391 8380 0.000249 -0.000809 0.000228 8381 -0.000392 0.000228 -0.000488 8382 8383siesta: Pressure (static): 1.35660445 kBar 8384 8385siesta: Stress tensor (total) (eV/Ang**3): 8386 -0.001307 0.000091 -0.000495 8387 0.000090 -0.001324 -0.000084 8388 -0.000496 -0.000084 -0.000684 8389 8390siesta: Pressure (total): 1.77009150 kBar 8391 8392siesta: Temp_ion = 619.727 K 8393 8394 ==================================== 8395 Begin MD step = 17 8396 ==================================== 8397 8398outcoor: Atomic coordinates (Ang): 8399 0.01081672 0.00596465 0.01235325 1 1 O 8400 0.64490329 0.73569266 0.02831597 2 2 H 8401 -0.82898087 0.34698127 -0.30159760 2 3 H 8402 8403outcell: Unit cell vectors (Ang): 8404 8.000000 0.000000 0.000000 8405 0.000000 8.000000 0.000000 8406 0.000000 0.000000 6.400000 8407 8408outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 8409outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 8410outcell: Cell volume (Ang**3) : 409.6000 8411<dSpData1D:S at geom step 17 8412 <sparsity:sparsity for geom step 17 8413 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 8414 <dData1D:(new from dSpData1D) n=69, refcount: 1> 8415refcount: 1> 8416new_DM -- step: 17 8417Re-using DM from previous geometries... 8418Number of DMs in history: 1 8419 DM extrapolation coefficients: 84201 1.00000 8421New DM after history re-use: 8422<dSpData2D:SpM extrapolated using coords 8423 <sparsity:sparsity for geom step 17 8424 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 8425 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 8426refcount: 1> 8427No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 8428New grid distribution: 1 8429 1 1: 25 1: 13 1: 5 8430 2 1: 25 1: 13 6: 10 8431 3 1: 25 1: 13 11: 15 8432 4 1: 25 1: 13 16: 20 8433 5 1: 25 14: 25 1: 5 8434 6 1: 25 14: 25 6: 10 8435 7 1: 25 14: 25 11: 15 8436 8 1: 25 14: 25 16: 20 8437 8438InitMesh: MESH = 50 x 50 x 40 = 100000 8439InitMesh: (bp) = 25 x 25 x 20 = 12500 8440InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 8441ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 8442New grid distribution: 2 8443 1 7: 25 6: 25 1: 6 8444 2 8: 25 1: 5 1: 6 8445 3 8: 25 1: 5 7: 20 8446 4 1: 7 1: 5 8: 20 8447 5 1: 6 6: 25 1: 7 8448 6 1: 7 1: 5 1: 7 8449 7 7: 25 6: 25 7: 20 8450 8 1: 6 6: 25 8: 20 8451New grid distribution: 3 8452 1 16: 25 7: 25 1: 14 8453 2 11: 25 1: 6 1: 13 8454 3 1: 10 1: 6 9: 20 8455 4 11: 25 1: 6 14: 20 8456 5 1: 15 7: 25 1: 7 8457 6 1: 10 1: 6 1: 8 8458 7 1: 15 7: 25 8: 20 8459 8 16: 25 7: 25 15: 20 8460Setting up quadratic distribution... 8461ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 8462PhiOnMesh: Number of (b)points on node 0 = 2280 8463PhiOnMesh: nlist on node 0 = 5016 8464 8465 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 8466 scf: 1 -465.846085 -465.827280 -465.827280 0.006331 -1.936594 0.017059 8467 scf: 2 -465.827299 -465.827304 -465.827304 0.000644 -1.930565 0.012305 8468 scf: 3 -465.827320 -465.827314 -465.827314 0.000232 -1.933331 0.002532 8469 scf: 4 -465.827315 -465.827314 -465.827314 0.000034 -1.933540 0.001696 8470 scf: 5 -465.827315 -465.827315 -465.827315 0.000072 -1.933888 0.000244 8471 8472SCF Convergence by DM+H criterion 8473max |DM_out - DM_in| : 0.0000723844 8474max |H_out - H_in| (eV) : 0.0002441246 8475SCF cycle converged after 5 iterations 8476 8477Using DM_out to compute the final energy and forces 8478No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 8479 8480siesta: E_KS(eV) = -465.8273 8481 8482siesta: Atomic forces (eV/Ang): 8483 1 0.383005 -0.575405 -0.022361 8484 2 -0.011816 0.151067 -0.040367 8485 3 -0.413761 0.300392 -0.195161 8486---------------------------------------- 8487 Tot -0.042571 -0.123946 -0.257888 8488---------------------------------------- 8489 Max 0.575405 8490 Res 0.298589 sqrt( Sum f_i^2 / 3N ) 8491---------------------------------------- 8492 Max 0.575405 constrained 8493 8494Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -1.56 -1.92 -1.08 -0.11 -0.71 0.33 8495(Free)E + p*V (eV/cell) -465.4386 8496Target enthalpy (eV/cell) -465.8273 8497 8498siesta: Stress tensor (static) (eV/Ang**3): 8499 -0.000901 0.000374 -0.000331 8500 0.000373 -0.000694 0.000242 8501 -0.000331 0.000242 -0.000475 8502 8503siesta: Pressure (static): 1.10576037 kBar 8504 8505siesta: Stress tensor (total) (eV/Ang**3): 8506 -0.000973 0.000204 -0.000443 8507 0.000204 -0.001197 -0.000071 8508 -0.000443 -0.000071 -0.000677 8509 8510siesta: Pressure (total): 1.52052170 kBar 8511 8512siesta: Temp_ion = 619.611 K 8513 8514 ==================================== 8515 Begin MD step = 18 8516 ==================================== 8517 8518outcoor: Atomic coordinates (Ang): 8519 0.01084786 0.00638271 0.01238483 1 1 O 8520 0.64680384 0.73728600 0.02961181 2 2 H 8521 -0.83198780 0.33857501 -0.30717293 2 3 H 8522 8523outcell: Unit cell vectors (Ang): 8524 8.000000 0.000000 0.000000 8525 0.000000 8.000000 0.000000 8526 0.000000 0.000000 6.400000 8527 8528outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 8529outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 8530outcell: Cell volume (Ang**3) : 409.6000 8531<dSpData1D:S at geom step 18 8532 <sparsity:sparsity for geom step 18 8533 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 8534 <dData1D:(new from dSpData1D) n=69, refcount: 1> 8535refcount: 1> 8536new_DM -- step: 18 8537Re-using DM from previous geometries... 8538Number of DMs in history: 1 8539 DM extrapolation coefficients: 85401 1.00000 8541New DM after history re-use: 8542<dSpData2D:SpM extrapolated using coords 8543 <sparsity:sparsity for geom step 18 8544 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 8545 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 8546refcount: 1> 8547No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 8548New grid distribution: 1 8549 1 1: 25 1: 13 1: 5 8550 2 1: 25 1: 13 6: 10 8551 3 1: 25 1: 13 11: 15 8552 4 1: 25 1: 13 16: 20 8553 5 1: 25 14: 25 1: 5 8554 6 1: 25 14: 25 6: 10 8555 7 1: 25 14: 25 11: 15 8556 8 1: 25 14: 25 16: 20 8557 8558InitMesh: MESH = 50 x 50 x 40 = 100000 8559InitMesh: (bp) = 25 x 25 x 20 = 12500 8560InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 8561ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 8562New grid distribution: 2 8563 1 7: 25 6: 25 1: 6 8564 2 8: 25 1: 5 1: 6 8565 3 8: 25 1: 5 7: 20 8566 4 1: 7 1: 5 8: 20 8567 5 1: 6 6: 25 1: 7 8568 6 1: 7 1: 5 1: 7 8569 7 7: 25 6: 25 7: 20 8570 8 1: 6 6: 25 8: 20 8571New grid distribution: 3 8572 1 16: 25 7: 25 1: 14 8573 2 11: 25 1: 6 1: 13 8574 3 1: 10 1: 6 9: 20 8575 4 11: 25 1: 6 14: 20 8576 5 1: 15 7: 25 1: 7 8577 6 1: 10 1: 6 1: 8 8578 7 1: 15 7: 25 8: 20 8579 8 16: 25 7: 25 15: 20 8580Setting up quadratic distribution... 8581ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 8582PhiOnMesh: Number of (b)points on node 0 = 2280 8583PhiOnMesh: nlist on node 0 = 5012 8584 8585 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 8586 scf: 1 -465.846995 -465.826630 -465.826630 0.006349 -1.915218 0.017264 8587 scf: 2 -465.826650 -465.826652 -465.826652 0.000570 -1.911529 0.010773 8588 scf: 3 -465.826667 -465.826661 -465.826661 0.000221 -1.912993 0.002633 8589 scf: 4 -465.826662 -465.826662 -465.826662 0.000034 -1.913126 0.001755 8590 scf: 5 -465.826662 -465.826662 -465.826662 0.000076 -1.913465 0.000247 8591 8592SCF Convergence by DM+H criterion 8593max |DM_out - DM_in| : 0.0000764012 8594max |H_out - H_in| (eV) : 0.0002474815 8595SCF cycle converged after 5 iterations 8596 8597Using DM_out to compute the final energy and forces 8598No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 8599 8600siesta: E_KS(eV) = -465.8267 8601 8602siesta: Atomic forces (eV/Ang): 8603 1 0.400136 -0.519994 -0.026241 8604 2 -0.125422 0.085150 -0.058824 8605 3 -0.315154 0.306493 -0.173320 8606---------------------------------------- 8607 Tot -0.040440 -0.128351 -0.258385 8608---------------------------------------- 8609 Max 0.519994 8610 Res 0.275062 sqrt( Sum f_i^2 / 3N ) 8611---------------------------------------- 8612 Max 0.519994 constrained 8613 8614Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -0.97 -1.71 -1.07 -0.10 -0.60 0.50 8615(Free)E + p*V (eV/cell) -465.5073 8616Target enthalpy (eV/cell) -465.8267 8617 8618siesta: Stress tensor (static) (eV/Ang**3): 8619 -0.000530 0.000490 -0.000257 8620 0.000489 -0.000574 0.000252 8621 -0.000257 0.000252 -0.000458 8622 8623siesta: Pressure (static): 0.83439447 kBar 8624 8625siesta: Stress tensor (total) (eV/Ang**3): 8626 -0.000608 0.000311 -0.000376 8627 0.000311 -0.001065 -0.000062 8628 -0.000377 -0.000062 -0.000665 8629 8630siesta: Pressure (total): 1.24907795 kBar 8631 8632siesta: Temp_ion = 617.075 K 8633 8634 ==================================== 8635 Begin MD step = 19 8636 ==================================== 8637 8638outcoor: Atomic coordinates (Ang): 8639 0.01088858 0.00678832 0.01241579 1 1 O 8640 0.64865680 0.73891163 0.03088533 2 2 H 8641 -0.83511429 0.33028503 -0.31281400 2 3 H 8642 8643outcell: Unit cell vectors (Ang): 8644 8.000000 0.000000 0.000000 8645 0.000000 8.000000 0.000000 8646 0.000000 0.000000 6.400000 8647 8648outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 8649outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 8650outcell: Cell volume (Ang**3) : 409.6000 8651<dSpData1D:S at geom step 19 8652 <sparsity:sparsity for geom step 19 8653 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 8654 <dData1D:(new from dSpData1D) n=69, refcount: 1> 8655refcount: 1> 8656new_DM -- step: 19 8657Re-using DM from previous geometries... 8658Number of DMs in history: 1 8659 DM extrapolation coefficients: 86601 1.00000 8661New DM after history re-use: 8662<dSpData2D:SpM extrapolated using coords 8663 <sparsity:sparsity for geom step 19 8664 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 8665 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 8666refcount: 1> 8667No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 8668New grid distribution: 1 8669 1 1: 25 1: 13 1: 5 8670 2 1: 25 1: 13 6: 10 8671 3 1: 25 1: 13 11: 15 8672 4 1: 25 1: 13 16: 20 8673 5 1: 25 14: 25 1: 5 8674 6 1: 25 14: 25 6: 10 8675 7 1: 25 14: 25 11: 15 8676 8 1: 25 14: 25 16: 20 8677 8678InitMesh: MESH = 50 x 50 x 40 = 100000 8679InitMesh: (bp) = 25 x 25 x 20 = 12500 8680InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 8681ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 8682New grid distribution: 2 8683 1 7: 25 6: 25 1: 6 8684 2 8: 25 1: 5 1: 6 8685 3 8: 25 1: 5 7: 20 8686 4 1: 7 1: 5 8: 20 8687 5 1: 6 6: 25 1: 7 8688 6 1: 7 1: 5 1: 7 8689 7 7: 25 6: 25 7: 20 8690 8 1: 6 6: 25 8: 20 8691New grid distribution: 3 8692 1 16: 25 7: 25 1: 14 8693 2 11: 25 1: 6 1: 13 8694 3 1: 10 1: 6 9: 20 8695 4 11: 25 1: 6 14: 20 8696 5 1: 15 7: 25 1: 7 8697 6 1: 10 1: 6 1: 8 8698 7 1: 15 7: 25 8: 20 8699 8 16: 25 7: 25 15: 20 8700Setting up quadratic distribution... 8701ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 8702PhiOnMesh: Number of (b)points on node 0 = 2280 8703PhiOnMesh: nlist on node 0 = 5004 8704 8705 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 8706 scf: 1 -465.846731 -465.825265 -465.825265 0.006357 -1.896262 0.017292 8707 scf: 2 -465.825284 -465.825287 -465.825287 0.000553 -1.894372 0.010917 8708 scf: 3 -465.825301 -465.825296 -465.825296 0.000217 -1.894889 0.002528 8709 scf: 4 -465.825296 -465.825296 -465.825296 0.000035 -1.894937 0.001749 8710 scf: 5 -465.825296 -465.825296 -465.825296 0.000069 -1.895181 0.000339 8711 8712SCF Convergence by DM+H criterion 8713max |DM_out - DM_in| : 0.0000685594 8714max |H_out - H_in| (eV) : 0.0003387599 8715SCF cycle converged after 5 iterations 8716 8717Using DM_out to compute the final energy and forces 8718No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 8719 8720siesta: E_KS(eV) = -465.8253 8721 8722siesta: Atomic forces (eV/Ang): 8723 1 0.401690 -0.461465 -0.035129 8724 2 -0.236458 0.020504 -0.077641 8725 3 -0.203646 0.309543 -0.144731 8726---------------------------------------- 8727 Tot -0.038414 -0.131419 -0.257501 8728---------------------------------------- 8729 Max 0.461465 8730 Res 0.257366 sqrt( Sum f_i^2 / 3N ) 8731---------------------------------------- 8732 Max 0.461465 constrained 8733 8734Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -0.35 -1.49 -1.04 -0.09 -0.47 0.66 8735(Free)E + p*V (eV/cell) -465.5804 8736Target enthalpy (eV/cell) -465.8253 8737 8738siesta: Stress tensor (static) (eV/Ang**3): 8739 -0.000133 0.000595 -0.000170 8740 0.000595 -0.000451 0.000260 8741 -0.000170 0.000260 -0.000436 8742 8743siesta: Pressure (static): 0.54509316 kBar 8744 8745siesta: Stress tensor (total) (eV/Ang**3): 8746 -0.000216 0.000411 -0.000295 8747 0.000410 -0.000930 -0.000054 8748 -0.000296 -0.000054 -0.000648 8749 8750siesta: Pressure (total): 0.95807977 kBar 8751 8752siesta: Temp_ion = 611.788 K 8753 8754 ==================================== 8755 Begin MD step = 20 8756 ==================================== 8757 8758outcoor: Atomic coordinates (Ang): 8759 0.01093891 0.00718287 0.01244591 1 1 O 8760 0.65042006 0.74054504 0.03212940 2 2 H 8761 -0.83831804 0.32211247 -0.31850999 2 3 H 8762 8763outcell: Unit cell vectors (Ang): 8764 8.000000 0.000000 0.000000 8765 0.000000 8.000000 0.000000 8766 0.000000 0.000000 6.400000 8767 8768outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 8769outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 8770outcell: Cell volume (Ang**3) : 409.6000 8771<dSpData1D:S at geom step 20 8772 <sparsity:sparsity for geom step 20 8773 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 8774 <dData1D:(new from dSpData1D) n=69, refcount: 1> 8775refcount: 1> 8776new_DM -- step: 20 8777Re-using DM from previous geometries... 8778Number of DMs in history: 1 8779 DM extrapolation coefficients: 87801 1.00000 8781New DM after history re-use: 8782<dSpData2D:SpM extrapolated using coords 8783 <sparsity:sparsity for geom step 20 8784 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 8785 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 8786refcount: 1> 8787No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 8788New grid distribution: 1 8789 1 1: 25 1: 13 1: 5 8790 2 1: 25 1: 13 6: 10 8791 3 1: 25 1: 13 11: 15 8792 4 1: 25 1: 13 16: 20 8793 5 1: 25 14: 25 1: 5 8794 6 1: 25 14: 25 6: 10 8795 7 1: 25 14: 25 11: 15 8796 8 1: 25 14: 25 16: 20 8797 8798InitMesh: MESH = 50 x 50 x 40 = 100000 8799InitMesh: (bp) = 25 x 25 x 20 = 12500 8800InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 8801ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 8802New grid distribution: 2 8803 1 7: 25 6: 25 1: 6 8804 2 8: 25 1: 5 1: 6 8805 3 8: 25 1: 5 7: 20 8806 4 1: 7 1: 5 8: 20 8807 5 1: 6 6: 25 1: 7 8808 6 1: 7 1: 5 1: 7 8809 7 7: 25 6: 25 7: 20 8810 8 1: 6 6: 25 8: 20 8811New grid distribution: 3 8812 1 16: 25 7: 25 1: 14 8813 2 11: 25 1: 6 1: 13 8814 3 1: 10 1: 6 9: 20 8815 4 11: 25 1: 6 14: 20 8816 5 1: 15 7: 25 1: 7 8817 6 1: 10 1: 6 1: 8 8818 7 1: 15 7: 25 8: 20 8819 8 16: 25 7: 25 15: 20 8820Setting up quadratic distribution... 8821ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 8822PhiOnMesh: Number of (b)points on node 0 = 2280 8823PhiOnMesh: nlist on node 0 = 5008 8824 8825 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 8826 scf: 1 -465.845218 -465.823129 -465.823129 0.006364 -1.879680 0.017263 8827 scf: 2 -465.823144 -465.823148 -465.823148 0.000541 -1.879275 0.010996 8828 scf: 3 -465.823163 -465.823158 -465.823158 0.000217 -1.879019 0.002336 8829 scf: 4 -465.823158 -465.823158 -465.823158 0.000035 -1.878992 0.001702 8830 scf: 5 -465.823158 -465.823158 -465.823158 0.000059 -1.879144 0.000499 8831 8832SCF Convergence by DM+H criterion 8833max |DM_out - DM_in| : 0.0000591572 8834max |H_out - H_in| (eV) : 0.0004987894 8835SCF cycle converged after 5 iterations 8836 8837Using DM_out to compute the final energy and forces 8838No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 8839 8840siesta: E_KS(eV) = -465.8232 8841 8842siesta: Atomic forces (eV/Ang): 8843 1 0.390093 -0.403259 -0.048481 8844 2 -0.343009 -0.041021 -0.096604 8845 3 -0.082914 0.310139 -0.110030 8846---------------------------------------- 8847 Tot -0.035830 -0.134141 -0.255115 8848---------------------------------------- 8849 Max 0.403259 8850 Res 0.249662 sqrt( Sum f_i^2 / 3N ) 8851---------------------------------------- 8852 Max 0.403259 constrained 8853 8854Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 0.31 -1.28 -1.00 -0.07 -0.32 0.81 8855(Free)E + p*V (eV/cell) -465.6550 8856Target enthalpy (eV/cell) -465.8232 8857 8858siesta: Stress tensor (static) (eV/Ang**3): 8859 0.000276 0.000691 -0.000071 8860 0.000691 -0.000332 0.000266 8861 -0.000072 0.000266 -0.000409 8862 8863siesta: Pressure (static): 0.24824066 kBar 8864 8865siesta: Stress tensor (total) (eV/Ang**3): 8866 0.000191 0.000504 -0.000200 8867 0.000504 -0.000798 -0.000046 8868 -0.000201 -0.000046 -0.000624 8869 8870siesta: Pressure (total): 0.65768849 kBar 8871 8872siesta: Temp_ion = 603.530 K 8873 8874siesta: Program's energy decomposition (eV): 8875siesta: Ebs = -103.241556 8876siesta: Eions = 815.854478 8877siesta: Ena = 175.088041 8878siesta: Ekin = 352.894003 8879siesta: Enl = -62.841393 8880siesta: Eso = 0.000000 8881siesta: Edftu = 0.000000 8882siesta: DEna = -2.947026 8883siesta: DUscf = 0.766537 8884siesta: DUext = 0.000000 8885siesta: Exc = -112.928841 8886siesta: eta*DQ = 0.000000 8887siesta: Emadel = 0.000000 8888siesta: Emeta = 0.000000 8889siesta: Emolmec = 0.000000 8890siesta: Ekinion = 0.156019 8891siesta: Eharris = -465.667140 8892siesta: Etot = -465.667139 8893siesta: FreeEng = -465.667139 8894 8895siesta: Final energy (eV): 8896siesta: Band Struct. = -103.241556 8897siesta: Kinetic = 352.894003 8898siesta: Hartree = 415.380290 8899siesta: Edftu = 0.000000 8900siesta: Eso = 0.000000 8901siesta: Ext. field = 0.000000 8902siesta: Exch.-corr. = -112.928841 8903siesta: Ion-electron = -1138.933270 8904siesta: Ion-ion = 17.764660 8905siesta: Ekinion = 0.156019 8906siesta: Total = -465.667139 8907siesta: Fermi = -1.879144 8908 8909siesta: Atomic forces (eV/Ang): 8910siesta: 1 0.390093 -0.403259 -0.048481 8911siesta: 2 -0.343009 -0.041021 -0.096604 8912siesta: 3 -0.082914 0.310139 -0.110030 8913siesta: ---------------------------------------- 8914siesta: Tot -0.035830 -0.134141 -0.255115 8915 8916siesta: Stress tensor (static) (eV/Ang**3): 8917siesta: 0.000276 0.000691 -0.000071 8918siesta: 0.000691 -0.000332 0.000266 8919siesta: -0.000072 0.000266 -0.000409 8920 8921siesta: Cell volume = 409.600000 Ang**3 8922 8923siesta: Pressure (static): 8924siesta: Solid Molecule Units 8925siesta: 0.00000169 0.00000194 Ry/Bohr**3 8926siesta: 0.00015494 0.00017848 eV/Ang**3 8927siesta: 0.24824066 0.28596547 kBar 8928(Free)E+ p_basis*V_orbitals = -465.237991 8929(Free)Eharris+ p_basis*V_orbitals = -465.237991 8930 8931siesta: Electric dipole (a.u.) = -0.098717 0.493917 -0.147951 8932siesta: Electric dipole (Debye) = -0.250913 1.255413 -0.376055 8933 8934cite: Please see "h2o.bib" for an exhaustive BiBTeX file. 8935cite: Please clearly indicate Siesta version in published work: v4.1-b4-351 8936cite: This calculation has made use of the following articles 8937cite: which are encouraged to be cited in a published work. 8938 Primary SIESTA paper 8939 DOI: www.doi.org/10.1088/0953-8984/14/11/302 8940 8941>> End of run: 22-JAN-2021 23:12:56 8942Job completed 8943Siesta Version : v4.1-b4-351 8944Architecture : x86_64-linux-n-62-26-19 8945Compiler version: GNU Fortran (GCC) 9.3.0 8946Compiler flags : mpifort -m64 -fPIC -O3 -march=native -ftree-vectorize -fexpensive-optimizatioons -funroll-loops -fprefetch-loop-arrays -fno-second-underscore -flto 8947PP flags : -I/dtu/sw/dcc/SL73/2020-aug/generic/build-tools/1.0/include -I/dtu/sw/dcc/SL773/2020-aug/generic/gcc/9.3.0/include -I/dtu/sw/dcc/SL73/2020-aug/generic/gcc/9.3.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/zlib/1.2.11/include -I/dtu/sw/dcc/SL73/2020-aug/generic/numactl/2.0.12/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/libxml2/2.9.10/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/hwloc/2.2.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/knem/1.1.4/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/ucx/1.8.1/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/openmpi/4.0.4/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/szip/2.1.1/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/hdf5/1.12.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/pnetcdf/1.12.1/include -I/dtu/sw/dcc/SL73/2020-aug/generic/gen-zlib/1.2.11/include -I/dtu/sw/dcc/SL73/2020-aug/generic/openssl/1.1.1/include -I/dtu/sw/dcc/SL73/2020-aug/generic/libssh2/1.8.2/include -I/dtu/sw/dcc/SL73/2020-aug/generic/curl/7.65.1/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/netcdf/4.7.4/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/flook/0.8.1/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/fftw/3.3.8/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/parmetis/4.0.3/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/scalapack/2.1.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/lapack/3.9.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/blis/0.7.0/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/scotch/6.0.9/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/mumps/5.3.3/include -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/elpa/2020.05.001/include -DSIESTA__ELPA -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DCDF -DCDF4 -DSIESTA__FLOOK -DNCDF -DNCDF_4 -DNCDF_PARALLEL -DTS_NOCHECKS -DSIESTA__METIS -DSIESTA__MUMPS -DSIESTA__MRRR -I/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/elpa/2020.05.001/include/elpa 8948Libraries : libncdf.a libfdict.a -lnetcdff -lnetcdf -lpnetcdf -lhdf5_hl -lhdf5 -lz -lzmuumps -lmumps_common -lesmumps -lscotch -lscotcherr -lpord -lparmetis -lmetis -lelpa -lscalapack -llapack -lblis -L/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/flook/0.8.1/lib -Wl,-rpath=/dtu/sw/dcc/SL73/2020-aug/XeonE5-2660v3/gnu/9.3.0/flook/0.8.1/lib -lflookall -ldl -flto -fuse-linker-plugin -lmetis 8949PARALLEL version 8950NetCDF support 8951NetCDF-4 support 8952NetCDF-4 MPI-IO support 8953METIS ordering support 8954Lua support 8955 8956* Running on 8 nodes in parallel 8957>> Start of run: 22-JAN-2021 23:12:57 8958 8959 *********************** 8960 * WELCOME TO SIESTA * 8961 *********************** 8962 8963reinit: Reading from standard input 8964reinit: Dumped input in INPUT_TMP.08870 8965************************** Dump of input data file **************************** 8966SystemName Water molecule -- md verlet 8967SystemLabel h2o 8968NumberOfAtoms 3 8969NumberOfSpecies 2 8970MeshCutoff 100 Ry 8971%block ChemicalSpeciesLabel 8972 1 8 O # Species index, atomic number, species label 8973 2 1 H 8974%endblock ChemicalSpeciesLabel 8975LatticeConstant 8.0 Ang 8976%block LatticeVectors 89771.0 0.0 0.0 89780.0 1.0 0.0 89790.0 0.0 0.8 8980%endblock LatticeVectors 8981AtomicCoordinatesFormat Ang 8982%block AtomicCoordinatesAndAtomicSpecies 8983 0.000 0.000 0.000 1 8984 0.757 0.586 0.000 2 8985-0.757 0.586 0.000 2 8986%endblock AtomicCoordinatesAndAtomicSpecies 8987Solution.Method diagon 8988MeshCutoff 100 Ry 8989WriteCoorStep .true. 8990WriteForces .true. 8991WriteMDHistory .true. 8992MD.UseSaveXV T 8993MD.TypeOfRun Verlet 8994MD.InitialTemperature 600 K 8995MD.Initial.Time.Step 1 8996MD.Final.Time.Step 20 8997MD.Length.Time.Step 0.2 fs 8998************************** End of input data file ***************************** 8999 9000reinit: ----------------------------------------------------------------------- 9001reinit: System Name: Water molecule -- md verlet 9002reinit: ----------------------------------------------------------------------- 9003reinit: System Label: h2o 9004reinit: ----------------------------------------------------------------------- 9005 9006initatom: Reading input for the pseudopotentials and atomic orbitals ---------- 9007Species number: 1 Atomic number: 8 Label: O 9008Species number: 2 Atomic number: 1 Label: H 9009 9010Ground state valence configuration: 2s02 2p04 9011Reading pseudopotential information in formatted form from O.psf 9012 9013Valence configuration for pseudopotential generation: 90142s( 2.00) rc: 1.14 90152p( 4.00) rc: 1.14 90163d( 0.00) rc: 1.14 90174f( 0.00) rc: 1.14 9018Ground state valence configuration: 1s01 9019Reading pseudopotential information in formatted form from H.psf 9020 9021Valence configuration for pseudopotential generation: 90221s( 1.00) rc: 1.25 90232p( 0.00) rc: 1.25 90243d( 0.00) rc: 1.25 90254f( 0.00) rc: 1.25 9026For O, standard SIESTA heuristics set lmxkb to 3 9027 (one more than the basis l, including polarization orbitals). 9028Use PS.lmax or PS.KBprojectors blocks to override. 9029For H, standard SIESTA heuristics set lmxkb to 2 9030 (one more than the basis l, including polarization orbitals). 9031Use PS.lmax or PS.KBprojectors blocks to override. 9032 9033<basis_specs> 9034=============================================================================== 9035O Z= 8 Mass= 16.000 Charge= 0.17977+309 9036Lmxo=1 Lmxkb= 3 BasisType=split Semic=F 9037L=0 Nsemic=0 Cnfigmx=2 9038 i=1 nzeta=2 polorb=0 (2s) 9039 splnorm: 0.15000 9040 vcte: 0.0000 9041 rinn: 0.0000 9042 qcoe: 0.0000 9043 qyuk: 0.0000 9044 qwid: 0.10000E-01 9045 rcs: 0.0000 0.0000 9046 lambdas: 1.0000 1.0000 9047L=1 Nsemic=0 Cnfigmx=2 9048 i=1 nzeta=2 polorb=1 (2p) 9049 splnorm: 0.15000 9050 vcte: 0.0000 9051 rinn: 0.0000 9052 qcoe: 0.0000 9053 qyuk: 0.0000 9054 qwid: 0.10000E-01 9055 rcs: 0.0000 0.0000 9056 lambdas: 1.0000 1.0000 9057------------------------------------------------------------------------------- 9058L=0 Nkbl=1 erefs: 0.17977+309 9059L=1 Nkbl=1 erefs: 0.17977+309 9060L=2 Nkbl=1 erefs: 0.17977+309 9061L=3 Nkbl=1 erefs: 0.17977+309 9062=============================================================================== 9063</basis_specs> 9064 9065atom: Called for O (Z = 8) 9066 9067read_vps: Pseudopotential generation method: 9068read_vps: ATM3 Troullier-Martins 9069Valence charge for ps generation: 6.00000 9070 9071xc_check: Exchange-correlation functional: 9072xc_check: Ceperley-Alder 9073V l=0 = -2*Zval/r beyond r= 1.1278 9074V l=1 = -2*Zval/r beyond r= 1.1278 9075V l=2 = -2*Zval/r beyond r= 1.1278 9076V l=3 = -2*Zval/r beyond r= 1.1138 9077All V_l potentials equal beyond r= 1.1278 9078This should be close to max(r_c) in ps generation 9079All pots = -2*Zval/r beyond r= 1.1278 9080 9081VLOCAL1: 99.0% of the norm of Vloc inside 34.126 Ry 9082VLOCAL1: 99.9% of the norm of Vloc inside 77.774 Ry 9083atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.37759 9084atom: Maximum radius for r*vlocal+2*Zval: 1.18566 9085GHOST: No ghost state for L = 0 9086GHOST: No ghost state for L = 1 9087GHOST: No ghost state for L = 2 9088GHOST: No ghost state for L = 3 9089 9090KBgen: Kleinman-Bylander projectors: 9091 l= 0 rc= 1.294105 el= -1.742414 Ekb= 9.135903 kbcos= 0.326910 9092 l= 1 rc= 1.294105 el= -0.676589 Ekb= -8.124878 kbcos= -0.395047 9093 l= 2 rc= 1.448233 el= 0.002386 Ekb= -2.039267 kbcos= -0.003484 9094 l= 3 rc= 1.561052 el= 0.003508 Ekb= -0.799141 kbcos= -0.000344 9095 9096KBgen: Total number of Kleinman-Bylander projectors: 16 9097atom: ------------------------------------------------------------------------- 9098 9099atom: SANKEY-TYPE ORBITALS: 9100atom: Selected multiple-zeta basis: split 9101 9102SPLIT: Orbitals with angular momentum L= 0 9103 9104SPLIT: Basis orbitals for state 2s 9105 9106SPLIT: PAO cut-off radius determined from an 9107SPLIT: energy shift= 0.020000 Ry 9108 9109 izeta = 1 9110 lambda = 1.000000 9111 rc = 3.305093 9112 energy = -1.723766 9113 kinetic = 1.614911 9114 potential(screened) = -3.338677 9115 potential(ionic) = -11.304675 9116 9117 izeta = 2 9118 rmatch = 2.510382 9119 splitnorm = 0.150000 9120 energy = -1.471299 9121 kinetic = 2.446434 9122 potential(screened) = -3.917732 9123 potential(ionic) = -12.476133 9124 9125SPLIT: Orbitals with angular momentum L= 1 9126 9127SPLIT: Basis orbitals for state 2p 9128 9129SPLIT: PAO cut-off radius determined from an 9130SPLIT: energy shift= 0.020000 Ry 9131 9132 izeta = 1 9133 lambda = 1.000000 9134 rc = 3.937239 9135 energy = -0.658841 9136 kinetic = 5.005986 9137 potential(screened) = -5.664827 9138 potential(ionic) = -13.452360 9139 9140 izeta = 2 9141 rmatch = 2.541963 9142 splitnorm = 0.150000 9143 energy = -0.367441 9144 kinetic = 7.530509 9145 potential(screened) = -7.897949 9146 potential(ionic) = -16.611953 9147 9148POLgen: Perturbative polarization orbital with L= 2 9149 9150POLgen: Polarization orbital for state 2p 9151 9152 izeta = 1 9153 rc = 3.937239 9154 energy = 2.398520 9155 kinetic = 4.716729 9156 potential(screened) = -2.318209 9157 potential(ionic) = -8.603170 9158atom: Total number of Sankey-type orbitals: 13 9159 9160atm_pop: Valence configuration (for local Pseudopot. screening): 9161 2s( 2.00) 9162 2p( 4.00) 9163Vna: chval, zval: 6.00000 6.00000 9164 9165Vna: Cut-off radius for the neutral-atom potential: 3.937239 9166 9167atom: _________________________________________________________________________ 9168 9169<basis_specs> 9170=============================================================================== 9171H Z= 1 Mass= 1.0100 Charge= 0.17977+309 9172Lmxo=0 Lmxkb= 2 BasisType=split Semic=F 9173L=0 Nsemic=0 Cnfigmx=1 9174 i=1 nzeta=2 polorb=1 (1s) 9175 splnorm: 0.15000 9176 vcte: 0.0000 9177 rinn: 0.0000 9178 qcoe: 0.0000 9179 qyuk: 0.0000 9180 qwid: 0.10000E-01 9181 rcs: 0.0000 0.0000 9182 lambdas: 1.0000 1.0000 9183------------------------------------------------------------------------------- 9184L=0 Nkbl=1 erefs: 0.17977+309 9185L=1 Nkbl=1 erefs: 0.17977+309 9186L=2 Nkbl=1 erefs: 0.17977+309 9187=============================================================================== 9188</basis_specs> 9189 9190atom: Called for H (Z = 1) 9191 9192read_vps: Pseudopotential generation method: 9193read_vps: ATM3 Troullier-Martins 9194Valence charge for ps generation: 1.00000 9195 9196xc_check: Exchange-correlation functional: 9197xc_check: Ceperley-Alder 9198V l=0 = -2*Zval/r beyond r= 1.2343 9199V l=1 = -2*Zval/r beyond r= 1.2189 9200V l=2 = -2*Zval/r beyond r= 1.2189 9201All V_l potentials equal beyond r= 1.2343 9202This should be close to max(r_c) in ps generation 9203All pots = -2*Zval/r beyond r= 1.2343 9204 9205VLOCAL1: 99.0% of the norm of Vloc inside 28.493 Ry 9206VLOCAL1: 99.9% of the norm of Vloc inside 64.935 Ry 9207atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.45251 9208atom: Maximum radius for r*vlocal+2*Zval: 1.21892 9209GHOST: No ghost state for L = 0 9210GHOST: No ghost state for L = 1 9211GHOST: No ghost state for L = 2 9212 9213KBgen: Kleinman-Bylander projectors: 9214 l= 0 rc= 1.364359 el= -0.467325 Ekb= -2.005361 kbcos= -0.336422 9215 l= 1 rc= 1.434438 el= 0.001430 Ekb= -0.501708 kbcos= -0.021697 9216 l= 2 rc= 1.470814 el= 0.002365 Ekb= -0.190555 kbcos= -0.002281 9217 9218KBgen: Total number of Kleinman-Bylander projectors: 9 9219atom: ------------------------------------------------------------------------- 9220 9221atom: SANKEY-TYPE ORBITALS: 9222atom: Selected multiple-zeta basis: split 9223 9224SPLIT: Orbitals with angular momentum L= 0 9225 9226SPLIT: Basis orbitals for state 1s 9227 9228SPLIT: PAO cut-off radius determined from an 9229SPLIT: energy shift= 0.020000 Ry 9230 9231 izeta = 1 9232 lambda = 1.000000 9233 rc = 4.828263 9234 energy = -0.449375 9235 kinetic = 0.929372 9236 potential(screened) = -1.378747 9237 potential(ionic) = -1.915047 9238 9239 izeta = 2 9240 rmatch = 3.854947 9241 splitnorm = 0.150000 9242 energy = -0.336153 9243 kinetic = 1.505294 9244 potential(screened) = -1.841447 9245 potential(ionic) = -2.413582 9246 9247POLgen: Perturbative polarization orbital with L= 1 9248 9249POLgen: Polarization orbital for state 1s 9250 9251 izeta = 1 9252 rc = 4.828263 9253 energy = 0.706972 9254 kinetic = 1.396397 9255 potential(screened) = -0.689424 9256 potential(ionic) = -1.169792 9257atom: Total number of Sankey-type orbitals: 5 9258 9259atm_pop: Valence configuration (for local Pseudopot. screening): 9260 1s( 1.00) 9261Vna: chval, zval: 1.00000 1.00000 9262 9263Vna: Cut-off radius for the neutral-atom potential: 4.828263 9264 9265atom: _________________________________________________________________________ 9266 9267prinput: Basis input ---------------------------------------------------------- 9268 9269PAO.BasisType split 9270 9271%block ChemicalSpeciesLabel 9272 1 8 O # Species index, atomic number, species label 9273 2 1 H # Species index, atomic number, species label 9274%endblock ChemicalSpeciesLabel 9275 9276%block PAO.Basis # Define Basis set 9277O 2 # Species label, number of l-shells 9278 n=2 0 2 # n, l, Nzeta 9279 3.305 2.510 9280 1.000 1.000 9281 n=2 1 2 P 1 # n, l, Nzeta, Polarization, NzetaPol 9282 3.937 2.542 9283 1.000 1.000 9284H 1 # Species label, number of l-shells 9285 n=1 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol 9286 4.828 3.855 9287 1.000 1.000 9288%endblock PAO.Basis 9289 9290prinput: ---------------------------------------------------------------------- 9291 9292Dumping basis to NetCDF file O.ion.nc 9293Dumping basis to NetCDF file H.ion.nc 9294coor: Atomic-coordinates input format = Cartesian coordinates 9295coor: (in Angstroms) 9296 9297ioxv: Reading coordinates and velocities from file 9298! Info in XV file prevails over previous structure input 9299WARNING: h2o.VERLET_RESTART not found--reading only XV file and moving back 1 time step using Euler 9300 9301siesta: Atomic coordinates (Bohr) and species 9302siesta: 0.02068 0.01356 0.02352 1 1 9303siesta: 1.22899 1.39941 0.06068 2 2 9304siesta: -1.58422 0.60882 -0.60194 2 3 9305 9306siesta: System type = molecule 9307 9308initatomlists: Number of atoms, orbitals, and projectors: 3 23 34 9309 9310siesta: ******************** Simulation parameters **************************** 9311siesta: 9312siesta: The following are some of the parameters of the simulation. 9313siesta: A complete list of the parameters used, including default values, 9314siesta: can be found in file out.fdf 9315siesta: 9316redata: Spin configuration = none 9317redata: Number of spin components = 1 9318redata: Time-Reversal Symmetry = T 9319redata: Spin spiral = F 9320redata: Long output = F 9321redata: Number of Atomic Species = 2 9322redata: Charge density info will appear in .RHO file 9323redata: Write Mulliken Pop. = NO 9324redata: Matel table size (NRTAB) = 1024 9325redata: Mesh Cutoff = 100.0000 Ry 9326redata: Net charge of the system = 0.0000 |e| 9327redata: Min. number of SCF Iter = 0 9328redata: Max. number of SCF Iter = 1000 9329redata: SCF convergence failure will abort job 9330redata: SCF mix quantity = Hamiltonian 9331redata: Mix DM or H after convergence = F 9332redata: Recompute H after scf cycle = F 9333redata: Mix DM in first SCF step = T 9334redata: Write Pulay info on disk = F 9335redata: New DM Occupancy tolerance = 0.000000000001 9336redata: No kicks to SCF 9337redata: DM Mixing Weight for Kicks = 0.5000 9338redata: Require Harris convergence for SCF = F 9339redata: Harris energy tolerance for SCF = 0.000100 eV 9340redata: Require DM convergence for SCF = T 9341redata: DM tolerance for SCF = 0.000100 9342redata: Require EDM convergence for SCF = F 9343redata: EDM tolerance for SCF = 0.001000 eV 9344redata: Require H convergence for SCF = T 9345redata: Hamiltonian tolerance for SCF = 0.001000 eV 9346redata: Require (free) Energy convergence for SCF = F 9347redata: (free) Energy tolerance for SCF = 0.000100 eV 9348redata: Using Saved Data (generic) = F 9349redata: Use continuation files for DM = F 9350redata: Neglect nonoverlap interactions = F 9351redata: Method of Calculation = Diagonalization 9352redata: Electronic Temperature = 299.9869 K 9353redata: Fix the spin of the system = F 9354redata: Dynamics option = Verlet MD run 9355redata: Initial MD time step = 1 9356redata: Final MD time step = 20 9357redata: Length of MD time step = 0.2000 fs 9358redata: Initial Temperature of MD run = 600.0000 K 9359redata: Perform a MD quench = F 9360mix.SCF: Pulay mixing = Pulay 9361mix.SCF: Variant = stable 9362mix.SCF: History steps = 2 9363mix.SCF: Linear mixing weight = 0.250000 9364mix.SCF: Mixing weight = 0.250000 9365mix.SCF: SVD condition = 0.1000E-07 9366redata: Save all siesta data in one NC = F 9367redata: *********************************************************************** 9368 9369%block SCF.Mixers 9370 Pulay 9371%endblock SCF.Mixers 9372 9373%block SCF.Mixer.Pulay 9374 # Mixing method 9375 method pulay 9376 variant stable 9377 9378 # Mixing options 9379 weight 0.2500 9380 weight.linear 0.2500 9381 history 2 9382%endblock SCF.Mixer.Pulay 9383 9384Size of DM history Fstack: 1 9385Total number of electrons: 8.000000 9386Total ionic charge: 8.000000 9387 9388* ProcessorY, Blocksize: 2 3 9389 9390 9391* Orbital distribution balance (max,min): 3 2 9392 9393 Kpoints in: 1 . Kpoints trimmed: 1 9394 9395siesta: k-grid: Number of k-points = 1 9396siesta: k-grid: Cutoff (effective) = 3.200 Ang 9397siesta: k-grid: Supercell and displacements 9398siesta: k-grid: 1 0 0 0.000 9399siesta: k-grid: 0 1 0 0.000 9400siesta: k-grid: 0 0 1 0.000 9401 9402diag: Algorithm = D&C 9403diag: Parallel over k = F 9404diag: Use parallel 2D distribution = T 9405diag: Parallel block-size = 3 9406diag: Parallel distribution = 2 x 4 9407diag: Used triangular part = Lower 9408diag: Absolute tolerance = 0.100E-15 9409diag: Orthogonalization factor = 0.100E-05 9410diag: Memory factor = 1.0000 9411 9412 9413ts: ************************************************************** 9414ts: Save H and S matrices = F 9415ts: Save DM and EDM matrices = F 9416ts: Only save the overlap matrix S = F 9417ts: ************************************************************** 9418 9419************************ Begin: TS CHECKS AND WARNINGS ************************ 9420************************ End: TS CHECKS AND WARNINGS ************************** 9421 9422 9423 ==================================== 9424 Begin MD step = 1 9425 ==================================== 9426 9427outcoor: Atomic coordinates (Ang): 9428 0.01094358 0.00717805 0.01244532 1 1 O 9429 0.65035500 0.74053726 0.03211107 2 2 H 9430 -0.83833377 0.32217130 -0.31853086 2 3 H 9431 9432outcell: Unit cell vectors (Ang): 9433 8.000000 0.000000 0.000000 9434 0.000000 8.000000 0.000000 9435 0.000000 0.000000 6.400000 9436 9437outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 9438outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 9439outcell: Cell volume (Ang**3) : 409.6000 9440<dSpData1D:S at geom step 1 9441 <sparsity:sparsity for geom step 1 9442 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 9443 <dData1D:(new from dSpData1D) n=69, refcount: 1> 9444refcount: 1> 9445new_DM -- step: 1 9446Initializing Density Matrix... 9447DM filled with atomic data: 9448<dSpData2D:DM initialized from atoms 9449 <sparsity:sparsity for geom step 1 9450 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 8> 9451 <dData2D:DM n=69 m=1, refcount: 1> 9452refcount: 1> 9453No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 9454New grid distribution: 1 9455 1 1: 25 1: 13 1: 5 9456 2 1: 25 1: 13 6: 10 9457 3 1: 25 1: 13 11: 15 9458 4 1: 25 1: 13 16: 20 9459 5 1: 25 14: 25 1: 5 9460 6 1: 25 14: 25 6: 10 9461 7 1: 25 14: 25 11: 15 9462 8 1: 25 14: 25 16: 20 9463 9464InitMesh: MESH = 50 x 50 x 40 = 100000 9465InitMesh: (bp) = 25 x 25 x 20 = 12500 9466InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 9467ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 9468New grid distribution: 2 9469 1 7: 25 6: 25 1: 6 9470 2 8: 25 1: 5 1: 6 9471 3 8: 25 1: 5 7: 20 9472 4 1: 7 1: 5 8: 20 9473 5 1: 6 6: 25 1: 7 9474 6 1: 7 1: 5 1: 7 9475 7 7: 25 6: 25 7: 20 9476 8 1: 6 6: 25 8: 20 9477New grid distribution: 3 9478 1 16: 25 7: 25 1: 14 9479 2 11: 25 1: 6 1: 13 9480 3 1: 10 1: 6 9: 20 9481 4 11: 25 1: 6 14: 20 9482 5 1: 15 7: 25 1: 7 9483 6 1: 10 1: 6 1: 8 9484 7 1: 15 7: 25 8: 20 9485 8 16: 25 7: 25 15: 20 9486Setting up quadratic distribution... 9487ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 9488PhiOnMesh: Number of (b)points on node 0 = 2280 9489PhiOnMesh: nlist on node 0 = 5008 9490 9491stepf: Fermi-Dirac step function 9492 9493siesta: Program's energy decomposition (eV): 9494siesta: Ebs = -81.381907 9495siesta: Eions = 815.854478 9496siesta: Ena = 175.088001 9497siesta: Ekin = 376.395689 9498siesta: Enl = -68.955909 9499siesta: Eso = 0.000000 9500siesta: Edftu = 0.000000 9501siesta: DEna = -16.972909 9502siesta: DUscf = 2.091072 9503siesta: DUext = 0.000000 9504siesta: Exc = -116.798708 9505siesta: eta*DQ = 0.000000 9506siesta: Emadel = 0.000000 9507siesta: Emeta = 0.000000 9508siesta: Emolmec = 0.000000 9509siesta: Ekinion = 0.000000 9510siesta: Eharris = -467.075475 9511siesta: Etot = -465.007242 9512siesta: FreeEng = -465.007242 9513 9514 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 9515 scf: 1 -467.075475 -465.007242 -465.007242 1.455125 -4.169504 7.243025 9516timer: Routine,Calls,Time,% = IterSCF 1 0.021 1.55 9517 scf: 2 -466.215583 -465.723676 -465.723676 0.055936 -2.969817 2.796687 9518 scf: 3 -465.836758 -465.818463 -465.818463 0.026979 -2.172878 0.339013 9519 scf: 4 -465.824200 -465.821519 -465.821519 0.009712 -2.100462 0.261222 9520 scf: 5 -465.823786 -465.823073 -465.823073 0.019398 -1.903769 0.064105 9521 scf: 6 -465.823188 -465.823137 -465.823137 0.000942 -1.867747 0.034743 9522 scf: 7 -465.823223 -465.823183 -465.823183 0.000825 -1.867782 0.022292 9523 scf: 8 -465.823220 -465.823203 -465.823203 0.000704 -1.870317 0.013852 9524 scf: 9 -465.823211 -465.823208 -465.823208 0.000504 -1.874663 0.006731 9525 scf: 10 -465.823207 -465.823207 -465.823207 0.000198 -1.877969 0.002483 9526 scf: 11 -465.823208 -465.823208 -465.823208 0.000012 -1.879156 0.001992 9527 scf: 12 -465.823208 -465.823208 -465.823208 0.000014 -1.879747 0.001087 9528 scf: 13 -465.823208 -465.823208 -465.823208 0.000015 -1.879834 0.000547 9529 9530SCF Convergence by DM+H criterion 9531max |DM_out - DM_in| : 0.0000154296 9532max |H_out - H_in| (eV) : 0.0005471635 9533SCF cycle converged after 13 iterations 9534 9535Using DM_out to compute the final energy and forces 9536No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 9537 9538siesta: E_KS(eV) = -465.8232 9539 9540siesta: E_KS - E_eggbox = -465.8232 9541 9542siesta: Atomic forces (eV/Ang): 9543 1 0.386384 -0.404584 -0.049337 9544 2 -0.340970 -0.039044 -0.096727 9545 3 -0.081249 0.309517 -0.109022 9546---------------------------------------- 9547 Tot -0.035835 -0.134111 -0.255086 9548---------------------------------------- 9549 Max 0.404584 9550 Res 0.248740 sqrt( Sum f_i^2 / 3N ) 9551---------------------------------------- 9552 Max 0.404584 constrained 9553 9554Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 0.31 -1.26 -1.00 -0.07 -0.32 0.80 9555(Free)E + p*V (eV/cell) -465.6562 9556Target enthalpy (eV/cell) -465.8232 9557 9558siesta: Stress tensor (static) (eV/Ang**3): 9559 0.000276 0.000687 -0.000070 9560 0.000687 -0.000335 0.000266 9561 -0.000070 0.000266 -0.000408 9562 9563siesta: Pressure (static): 0.24937643 kBar 9564 9565siesta: Stress tensor (total) (eV/Ang**3): 9566 0.000192 0.000500 -0.000201 9567 0.000500 -0.000788 -0.000045 9568 -0.000201 -0.000045 -0.000627 9569 9570siesta: Pressure (total): 0.65329788 kBar 9571 9572siesta: Temp_ion = 603.530 K 9573 9574 ==================================== 9575 Begin MD step = 2 9576 ==================================== 9577 9578outcoor: Atomic coordinates (Ang): 9579 0.01100322 0.00756293 0.01247427 1 1 O 9580 0.65198852 0.74215549 0.03331847 2 2 H 9581 -0.84156866 0.31411629 -0.32426839 2 3 H 9582 9583outcell: Unit cell vectors (Ang): 9584 8.000000 0.000000 0.000000 9585 0.000000 8.000000 0.000000 9586 0.000000 0.000000 6.400000 9587 9588outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 9589outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 9590outcell: Cell volume (Ang**3) : 409.6000 9591<dSpData1D:S at geom step 2 9592 <sparsity:sparsity for geom step 2 9593 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 9594 <dData1D:(new from dSpData1D) n=69, refcount: 1> 9595refcount: 1> 9596new_DM -- step: 2 9597Re-using DM from previous geometries... 9598Number of DMs in history: 1 9599 DM extrapolation coefficients: 96001 1.00000 9601New DM after history re-use: 9602<dSpData2D:SpM extrapolated using coords 9603 <sparsity:sparsity for geom step 2 9604 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 9605 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 9606refcount: 1> 9607No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 9608New grid distribution: 1 9609 1 1: 25 1: 13 1: 5 9610 2 1: 25 1: 13 6: 10 9611 3 1: 25 1: 13 11: 15 9612 4 1: 25 1: 13 16: 20 9613 5 1: 25 14: 25 1: 5 9614 6 1: 25 14: 25 6: 10 9615 7 1: 25 14: 25 11: 15 9616 8 1: 25 14: 25 16: 20 9617 9618InitMesh: MESH = 50 x 50 x 40 = 100000 9619InitMesh: (bp) = 25 x 25 x 20 = 12500 9620InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 9621ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 9622New grid distribution: 2 9623 1 7: 25 6: 25 1: 6 9624 2 8: 25 1: 5 1: 6 9625 3 8: 25 1: 5 7: 20 9626 4 1: 7 1: 5 8: 20 9627 5 1: 6 6: 25 1: 7 9628 6 1: 7 1: 5 1: 7 9629 7 7: 25 6: 25 7: 20 9630 8 1: 6 6: 25 8: 20 9631New grid distribution: 3 9632 1 16: 25 7: 25 1: 14 9633 2 11: 25 1: 6 1: 13 9634 3 1: 10 1: 6 9: 20 9635 4 11: 25 1: 6 14: 20 9636 5 1: 15 7: 25 1: 7 9637 6 1: 10 1: 6 1: 8 9638 7 1: 15 7: 25 8: 20 9639 8 16: 25 7: 25 15: 20 9640Setting up quadratic distribution... 9641ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 9642PhiOnMesh: Number of (b)points on node 0 = 2280 9643PhiOnMesh: nlist on node 0 = 5002 9644 9645 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 9646 scf: 1 -465.842499 -465.820263 -465.820263 0.006362 -1.865504 0.017321 9647 scf: 2 -465.820273 -465.820281 -465.820281 0.000546 -1.866573 0.011691 9648 scf: 3 -465.820297 -465.820291 -465.820291 0.000221 -1.865524 0.002103 9649 scf: 4 -465.820292 -465.820291 -465.820291 0.000037 -1.865429 0.001632 9650 scf: 5 -465.820292 -465.820292 -465.820292 0.000055 -1.865509 0.000702 9651 9652SCF Convergence by DM+H criterion 9653max |DM_out - DM_in| : 0.0000545059 9654max |H_out - H_in| (eV) : 0.0007019773 9655SCF cycle converged after 5 iterations 9656 9657Using DM_out to compute the final energy and forces 9658No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 9659 9660siesta: E_KS(eV) = -465.8203 9661 9662siesta: Atomic forces (eV/Ang): 9663 1 0.362047 -0.347728 -0.067031 9664 2 -0.441616 -0.096418 -0.115472 9665 3 0.045485 0.307194 -0.070202 9666---------------------------------------- 9667 Tot -0.034084 -0.136952 -0.252706 9668---------------------------------------- 9669 Max 0.441616 9670 Res 0.252874 sqrt( Sum f_i^2 / 3N ) 9671---------------------------------------- 9672 Max 0.441616 constrained 9673 9674Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 0.97 -1.08 -0.95 -0.07 -0.15 0.94 9675(Free)E + p*V (eV/cell) -465.7300 9676Target enthalpy (eV/cell) -465.8203 9677 9678siesta: Stress tensor (static) (eV/Ang**3): 9679 0.000693 0.000772 0.000037 9680 0.000772 -0.000221 0.000269 9681 0.000036 0.000269 -0.000377 9682 9683siesta: Pressure (static): -0.05081471 kBar 9684 9685siesta: Stress tensor (total) (eV/Ang**3): 9686 0.000608 0.000586 -0.000094 9687 0.000585 -0.000674 -0.000041 9688 -0.000095 -0.000041 -0.000595 9689 9690siesta: Pressure (total): 0.35310675 kBar 9691 9692siesta: Temp_ion = 592.276 K 9693 9694 ==================================== 9695 Begin MD step = 3 9696 ==================================== 9697 9698outcoor: Atomic coordinates (Ang): 9699 0.01107152 0.00793949 0.01250161 1 1 O 9700 0.65345451 0.74373714 0.03448205 2 2 H 9701 -0.84478630 0.30617781 -0.33003255 2 3 H 9702 9703outcell: Unit cell vectors (Ang): 9704 8.000000 0.000000 0.000000 9705 0.000000 8.000000 0.000000 9706 0.000000 0.000000 6.400000 9707 9708outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 9709outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 9710outcell: Cell volume (Ang**3) : 409.6000 9711<dSpData1D:S at geom step 3 9712 <sparsity:sparsity for geom step 3 9713 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 9714 <dData1D:(new from dSpData1D) n=69, refcount: 1> 9715refcount: 1> 9716new_DM -- step: 3 9717Re-using DM from previous geometries... 9718Number of DMs in history: 1 9719 DM extrapolation coefficients: 97201 1.00000 9721New DM after history re-use: 9722<dSpData2D:SpM extrapolated using coords 9723 <sparsity:sparsity for geom step 3 9724 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 9725 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 9726refcount: 1> 9727No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 9728New grid distribution: 1 9729 1 1: 25 1: 13 1: 5 9730 2 1: 25 1: 13 6: 10 9731 3 1: 25 1: 13 11: 15 9732 4 1: 25 1: 13 16: 20 9733 5 1: 25 14: 25 1: 5 9734 6 1: 25 14: 25 6: 10 9735 7 1: 25 14: 25 11: 15 9736 8 1: 25 14: 25 16: 20 9737 9738InitMesh: MESH = 50 x 50 x 40 = 100000 9739InitMesh: (bp) = 25 x 25 x 20 = 12500 9740InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 9741ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 9742New grid distribution: 2 9743 1 7: 25 6: 25 1: 6 9744 2 8: 25 1: 5 1: 6 9745 3 8: 25 1: 5 7: 20 9746 4 1: 7 1: 5 8: 20 9747 5 1: 6 6: 25 1: 7 9748 6 1: 7 1: 5 1: 7 9749 7 7: 25 6: 25 7: 20 9750 8 1: 6 6: 25 8: 20 9751New grid distribution: 3 9752 1 16: 25 7: 25 1: 14 9753 2 11: 25 1: 6 1: 13 9754 3 1: 10 1: 6 9: 20 9755 4 11: 25 1: 6 14: 20 9756 5 1: 15 7: 25 1: 7 9757 6 1: 10 1: 6 1: 8 9758 7 1: 15 7: 25 8: 20 9759 8 16: 25 7: 25 15: 20 9760Setting up quadratic distribution... 9761ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 9762PhiOnMesh: Number of (b)points on node 0 = 2280 9763PhiOnMesh: nlist on node 0 = 4997 9764 9765 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 9766 scf: 1 -465.838524 -465.816610 -465.816610 0.006340 -1.853636 0.016751 9767 scf: 2 -465.816617 -465.816626 -465.816626 0.000592 -1.855394 0.013035 9768 scf: 3 -465.816641 -465.816636 -465.816636 0.000229 -1.853999 0.001967 9769 scf: 4 -465.816637 -465.816636 -465.816636 0.000037 -1.853888 0.001560 9770 scf: 5 -465.816637 -465.816636 -465.816636 0.000053 -1.853948 0.000719 9771 9772SCF Convergence by DM+H criterion 9773max |DM_out - DM_in| : 0.0000530949 9774max |H_out - H_in| (eV) : 0.0007191727 9775SCF cycle converged after 5 iterations 9776 9777Using DM_out to compute the final energy and forces 9778No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 9779 9780siesta: E_KS(eV) = -465.8166 9781 9782siesta: Atomic forces (eV/Ang): 9783 1 0.326271 -0.296594 -0.087647 9784 2 -0.535300 -0.148109 -0.134590 9785 3 0.175303 0.303412 -0.028311 9786---------------------------------------- 9787 Tot -0.033726 -0.141291 -0.250549 9788---------------------------------------- 9789 Max 0.535300 9790 Res 0.269215 sqrt( Sum f_i^2 / 3N ) 9791---------------------------------------- 9792 Max 0.535300 constrained 9793 9794Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 1.64 -0.89 -0.90 -0.05 0.03 1.06 9795(Free)E + p*V (eV/cell) -465.8040 9796Target enthalpy (eV/cell) -465.8166 9797 9798siesta: Stress tensor (static) (eV/Ang**3): 9799 0.001109 0.000848 0.000151 9800 0.000847 -0.000118 0.000273 9801 0.000150 0.000273 -0.000342 9802 9803siesta: Pressure (static): -0.34678193 kBar 9804 9805siesta: Stress tensor (total) (eV/Ang**3): 9806 0.001026 0.000665 0.000021 9807 0.000664 -0.000557 -0.000034 9808 0.000020 -0.000034 -0.000562 9809 9810siesta: Pressure (total): 0.04960744 kBar 9811 9812siesta: Temp_ion = 578.181 K 9813 9814 ==================================== 9815 Begin MD step = 4 9816 ==================================== 9817 9818outcoor: Atomic coordinates (Ang): 9819 0.01114764 0.00830894 0.01252685 1 1 O 9820 0.65471741 0.74526260 0.03559458 2 2 H 9821 -0.84793742 0.29835444 -0.33580746 2 3 H 9822 9823outcell: Unit cell vectors (Ang): 9824 8.000000 0.000000 0.000000 9825 0.000000 8.000000 0.000000 9826 0.000000 0.000000 6.400000 9827 9828outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 9829outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 9830outcell: Cell volume (Ang**3) : 409.6000 9831<dSpData1D:S at geom step 4 9832 <sparsity:sparsity for geom step 4 9833 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 9834 <dData1D:(new from dSpData1D) n=69, refcount: 1> 9835refcount: 1> 9836new_DM -- step: 4 9837Re-using DM from previous geometries... 9838Number of DMs in history: 1 9839 DM extrapolation coefficients: 98401 1.00000 9841New DM after history re-use: 9842<dSpData2D:SpM extrapolated using coords 9843 <sparsity:sparsity for geom step 4 9844 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 9845 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 9846refcount: 1> 9847No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 9848New grid distribution: 1 9849 1 1: 25 1: 13 1: 5 9850 2 1: 25 1: 13 6: 10 9851 3 1: 25 1: 13 11: 15 9852 4 1: 25 1: 13 16: 20 9853 5 1: 25 14: 25 1: 5 9854 6 1: 25 14: 25 6: 10 9855 7 1: 25 14: 25 11: 15 9856 8 1: 25 14: 25 16: 20 9857 9858InitMesh: MESH = 50 x 50 x 40 = 100000 9859InitMesh: (bp) = 25 x 25 x 20 = 12500 9860InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 9861ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 9862New grid distribution: 2 9863 1 7: 25 6: 25 1: 6 9864 2 8: 25 1: 5 1: 6 9865 3 8: 25 1: 5 7: 20 9866 4 1: 7 1: 5 8: 20 9867 5 1: 6 6: 25 1: 7 9868 6 1: 7 1: 5 1: 7 9869 7 7: 25 6: 25 7: 20 9870 8 1: 6 6: 25 8: 20 9871New grid distribution: 3 9872 1 16: 25 7: 25 1: 14 9873 2 11: 25 1: 6 1: 13 9874 3 1: 10 1: 6 9: 20 9875 4 11: 25 1: 6 14: 20 9876 5 1: 15 7: 25 1: 7 9877 6 1: 10 1: 6 1: 8 9878 7 1: 15 7: 25 8: 20 9879 8 16: 25 7: 25 15: 20 9880Setting up quadratic distribution... 9881ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 9882PhiOnMesh: Number of (b)points on node 0 = 2280 9883PhiOnMesh: nlist on node 0 = 4999 9884 9885 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 9886 scf: 1 -465.833446 -465.812303 -465.812303 0.006300 -1.844005 0.016242 9887 scf: 2 -465.812308 -465.812317 -465.812317 0.000628 -1.846228 0.013957 9888 scf: 3 -465.812333 -465.812328 -465.812328 0.000250 -1.844594 0.001863 9889 scf: 4 -465.812328 -465.812328 -465.812328 0.000037 -1.844474 0.001496 9890 scf: 5 -465.812328 -465.812328 -465.812328 0.000052 -1.844521 0.000713 9891 9892SCF Convergence by DM+H criterion 9893max |DM_out - DM_in| : 0.0000520274 9894max |H_out - H_in| (eV) : 0.0007134945 9895SCF cycle converged after 5 iterations 9896 9897Using DM_out to compute the final energy and forces 9898No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 9899 9900siesta: E_KS(eV) = -465.8123 9901 9902siesta: Atomic forces (eV/Ang): 9903 1 0.281016 -0.251517 -0.110640 9904 2 -0.620589 -0.193302 -0.153422 9905 3 0.306461 0.298658 0.015471 9906---------------------------------------- 9907 Tot -0.033112 -0.146161 -0.248591 9908---------------------------------------- 9909 Max 0.620589 9910 Res 0.295120 sqrt( Sum f_i^2 / 3N ) 9911---------------------------------------- 9912 Max 0.620589 constrained 9913 9914Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 2.31 -0.72 -0.84 -0.04 0.23 1.18 9915(Free)E + p*V (eV/cell) -465.8760 9916Target enthalpy (eV/cell) -465.8123 9917 9918siesta: Stress tensor (static) (eV/Ang**3): 9919 0.001519 0.000914 0.000271 9920 0.000913 -0.000026 0.000277 9921 0.000270 0.000277 -0.000303 9922 9923siesta: Pressure (static): -0.63613230 kBar 9924 9925siesta: Stress tensor (total) (eV/Ang**3): 9926 0.001442 0.000737 0.000144 9927 0.000736 -0.000452 -0.000026 9928 0.000142 -0.000026 -0.000524 9929 9930siesta: Pressure (total): -0.24917627 kBar 9931 9932siesta: Temp_ion = 561.548 K 9933 9934 ==================================== 9935 Begin MD step = 5 9936 ==================================== 9937 9938outcoor: Atomic coordinates (Ang): 9939 0.01123049 0.00867237 0.01254944 1 1 O 9940 0.65574489 0.74671473 0.03664891 2 2 H 9941 -0.85097229 0.29064437 -0.34157650 2 3 H 9942 9943outcell: Unit cell vectors (Ang): 9944 8.000000 0.000000 0.000000 9945 0.000000 8.000000 0.000000 9946 0.000000 0.000000 6.400000 9947 9948outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 9949outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 9950outcell: Cell volume (Ang**3) : 409.6000 9951<dSpData1D:S at geom step 5 9952 <sparsity:sparsity for geom step 5 9953 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 9954 <dData1D:(new from dSpData1D) n=69, refcount: 1> 9955refcount: 1> 9956new_DM -- step: 5 9957Re-using DM from previous geometries... 9958Number of DMs in history: 1 9959 DM extrapolation coefficients: 99601 1.00000 9961New DM after history re-use: 9962<dSpData2D:SpM extrapolated using coords 9963 <sparsity:sparsity for geom step 5 9964 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 9965 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 9966refcount: 1> 9967No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 9968New grid distribution: 1 9969 1 1: 25 1: 13 1: 5 9970 2 1: 25 1: 13 6: 10 9971 3 1: 25 1: 13 11: 15 9972 4 1: 25 1: 13 16: 20 9973 5 1: 25 14: 25 1: 5 9974 6 1: 25 14: 25 6: 10 9975 7 1: 25 14: 25 11: 15 9976 8 1: 25 14: 25 16: 20 9977 9978InitMesh: MESH = 50 x 50 x 40 = 100000 9979InitMesh: (bp) = 25 x 25 x 20 = 12500 9980InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 9981ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 9982New grid distribution: 2 9983 1 7: 25 6: 25 1: 6 9984 2 8: 25 1: 5 1: 6 9985 3 8: 25 1: 5 7: 20 9986 4 1: 7 1: 5 8: 20 9987 5 1: 6 6: 25 1: 7 9988 6 1: 7 1: 5 1: 7 9989 7 7: 25 6: 25 7: 20 9990 8 1: 6 6: 25 8: 20 9991New grid distribution: 3 9992 1 16: 25 7: 25 1: 14 9993 2 11: 25 1: 6 1: 13 9994 3 1: 10 1: 6 9: 20 9995 4 11: 25 1: 6 14: 20 9996 5 1: 15 7: 25 1: 7 9997 6 1: 10 1: 6 1: 8 9998 7 1: 15 7: 25 8: 20 9999 8 16: 25 7: 25 15: 20 10000Setting up quadratic distribution... 10001ExtMesh (bp) on 0 = 51 x 52 x 38 = 100776 10002PhiOnMesh: Number of (b)points on node 0 = 2280 10003PhiOnMesh: nlist on node 0 = 5003 10004 10005 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 10006 scf: 1 -465.827396 -465.807450 -465.807450 0.006241 -1.836546 0.015603 10007 scf: 2 -465.807454 -465.807463 -465.807463 0.000641 -1.838816 0.013727 10008 scf: 3 -465.807477 -465.807472 -465.807472 0.000256 -1.837177 0.001814 10009 scf: 4 -465.807473 -465.807473 -465.807473 0.000035 -1.837061 0.001431 10010 scf: 5 -465.807473 -465.807473 -465.807473 0.000050 -1.837106 0.000679 10011 10012SCF Convergence by DM+H criterion 10013max |DM_out - DM_in| : 0.0000498483 10014max |H_out - H_in| (eV) : 0.0006792670 10015SCF cycle converged after 5 iterations 10016 10017Using DM_out to compute the final energy and forces 10018No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 10019 10020siesta: E_KS(eV) = -465.8075 10021 10022siesta: Atomic forces (eV/Ang): 10023 1 0.227727 -0.214215 -0.135201 10024 2 -0.696566 -0.231212 -0.171773 10025 3 0.435994 0.293935 0.060143 10026---------------------------------------- 10027 Tot -0.032845 -0.151491 -0.246830 10028---------------------------------------- 10029 Max 0.696566 10030 Res 0.327329 sqrt( Sum f_i^2 / 3N ) 10031---------------------------------------- 10032 Max 0.696566 constrained 10033 10034Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 2.95 -0.58 -0.77 -0.03 0.43 1.28 10035(Free)E + p*V (eV/cell) -465.9443 10036Target enthalpy (eV/cell) -465.8075 10037 10038siesta: Stress tensor (static) (eV/Ang**3): 10039 0.001914 0.000969 0.000393 10040 0.000968 0.000053 0.000280 10041 0.000392 0.000280 -0.000261 10042 10043siesta: Pressure (static): -0.91101141 kBar 10044 10045siesta: Stress tensor (total) (eV/Ang**3): 10046 0.001844 0.000801 0.000271 10047 0.000801 -0.000360 -0.000017 10048 0.000270 -0.000017 -0.000482 10049 10050siesta: Pressure (total): -0.53518746 kBar 10051 10052siesta: Temp_ion = 542.819 K 10053 10054 ==================================== 10055 Begin MD step = 6 10056 ==================================== 10057 10058outcoor: Atomic coordinates (Ang): 10059 0.01131879 0.00903067 0.01256879 1 1 O 10060 0.65650812 0.74807914 0.03763807 2 2 H 10061 -0.85384176 0.28304581 -0.34732272 2 3 H 10062 10063outcell: Unit cell vectors (Ang): 10064 8.000000 0.000000 0.000000 10065 0.000000 8.000000 0.000000 10066 0.000000 0.000000 6.400000 10067 10068outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 10069outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 10070outcell: Cell volume (Ang**3) : 409.6000 10071<dSpData1D:S at geom step 6 10072 <sparsity:sparsity for geom step 6 10073 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 10074 <dData1D:(new from dSpData1D) n=69, refcount: 1> 10075refcount: 1> 10076new_DM -- step: 6 10077Re-using DM from previous geometries... 10078Number of DMs in history: 1 10079 DM extrapolation coefficients: 100801 1.00000 10081New DM after history re-use: 10082<dSpData2D:SpM extrapolated using coords 10083 <sparsity:sparsity for geom step 6 10084 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 10085 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 10086refcount: 1> 10087No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 10088New grid distribution: 1 10089 1 1: 25 1: 13 1: 5 10090 2 1: 25 1: 13 6: 10 10091 3 1: 25 1: 13 11: 15 10092 4 1: 25 1: 13 16: 20 10093 5 1: 25 14: 25 1: 5 10094 6 1: 25 14: 25 6: 10 10095 7 1: 25 14: 25 11: 15 10096 8 1: 25 14: 25 16: 20 10097 10098InitMesh: MESH = 50 x 50 x 40 = 100000 10099InitMesh: (bp) = 25 x 25 x 20 = 12500 10100InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 10101ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 10102New grid distribution: 2 10103 1 8: 25 6: 25 1: 6 10104 2 8: 25 1: 5 1: 6 10105 3 8: 25 1: 5 7: 20 10106 4 1: 7 1: 5 8: 20 10107 5 1: 7 6: 25 1: 7 10108 6 1: 7 1: 5 1: 7 10109 7 8: 25 6: 25 7: 20 10110 8 1: 7 6: 25 8: 20 10111New grid distribution: 3 10112 1 17: 25 7: 25 1: 14 10113 2 11: 25 1: 6 1: 13 10114 3 1: 10 1: 6 9: 20 10115 4 11: 25 1: 6 14: 20 10116 5 1: 16 7: 25 1: 7 10117 6 1: 10 1: 6 1: 8 10118 7 1: 16 7: 25 8: 20 10119 8 17: 25 7: 25 15: 20 10120Setting up quadratic distribution... 10121ExtMesh (bp) on 0 = 50 x 52 x 38 = 98800 10122PhiOnMesh: Number of (b)points on node 0 = 2160 10123PhiOnMesh: nlist on node 0 = 4721 10124 10125 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 10126 scf: 1 -465.820552 -465.802195 -465.802195 0.006164 -1.831091 0.014853 10127 scf: 2 -465.802201 -465.802208 -465.802208 0.000630 -1.833008 0.012387 10128 scf: 3 -465.802220 -465.802216 -465.802216 0.000247 -1.831590 0.001726 10129 scf: 4 -465.802216 -465.802216 -465.802216 0.000033 -1.831489 0.001356 10130 scf: 5 -465.802216 -465.802216 -465.802216 0.000046 -1.831543 0.000624 10131 10132SCF Convergence by DM+H criterion 10133max |DM_out - DM_in| : 0.0000461621 10134max |H_out - H_in| (eV) : 0.0006237034 10135SCF cycle converged after 5 iterations 10136 10137Using DM_out to compute the final energy and forces 10138No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 10139 10140siesta: E_KS(eV) = -465.8022 10141 10142siesta: Atomic forces (eV/Ang): 10143 1 0.167753 -0.185814 -0.160421 10144 2 -0.762731 -0.261349 -0.189595 10145 3 0.561420 0.290115 0.104724 10146---------------------------------------- 10147 Tot -0.033558 -0.157048 -0.245292 10148---------------------------------------- 10149 Max 0.762731 10150 Res 0.362819 sqrt( Sum f_i^2 / 3N ) 10151---------------------------------------- 10152 Max 0.762731 constrained 10153 10154Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 3.56 -0.45 -0.70 -0.01 0.64 1.37 10155(Free)E + p*V (eV/cell) -466.0077 10156Target enthalpy (eV/cell) -465.8022 10157 10158siesta: Stress tensor (static) (eV/Ang**3): 10159 0.002286 0.001013 0.000515 10160 0.001012 0.000117 0.000285 10161 0.000514 0.000285 -0.000218 10162 10163siesta: Pressure (static): -1.16703114 kBar 10164 10165siesta: Stress tensor (total) (eV/Ang**3): 10166 0.002225 0.000857 0.000401 10167 0.000857 -0.000283 -0.000007 10168 0.000399 -0.000007 -0.000437 10169 10170siesta: Pressure (total): -0.80374177 kBar 10171 10172siesta: Temp_ion = 522.546 K 10173 10174 ==================================== 10175 Begin MD step = 7 10176 ==================================== 10177 10178outcoor: Atomic coordinates (Ang): 10179 0.01141111 0.00938452 0.01258430 1 1 O 10180 0.65698198 0.74934441 0.03855530 2 2 H 10181 -0.85649824 0.27555731 -0.35302921 2 3 H 10182 10183outcell: Unit cell vectors (Ang): 10184 8.000000 0.000000 0.000000 10185 0.000000 8.000000 0.000000 10186 0.000000 0.000000 6.400000 10187 10188outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 10189outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 10190outcell: Cell volume (Ang**3) : 409.6000 10191<dSpData1D:S at geom step 7 10192 <sparsity:sparsity for geom step 7 10193 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 10194 <dData1D:(new from dSpData1D) n=69, refcount: 1> 10195refcount: 1> 10196new_DM -- step: 7 10197Re-using DM from previous geometries... 10198Number of DMs in history: 1 10199 DM extrapolation coefficients: 102001 1.00000 10201New DM after history re-use: 10202<dSpData2D:SpM extrapolated using coords 10203 <sparsity:sparsity for geom step 7 10204 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 10205 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 10206refcount: 1> 10207No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 10208New grid distribution: 1 10209 1 1: 25 1: 13 1: 5 10210 2 1: 25 1: 13 6: 10 10211 3 1: 25 1: 13 11: 15 10212 4 1: 25 1: 13 16: 20 10213 5 1: 25 14: 25 1: 5 10214 6 1: 25 14: 25 6: 10 10215 7 1: 25 14: 25 11: 15 10216 8 1: 25 14: 25 16: 20 10217 10218InitMesh: MESH = 50 x 50 x 40 = 100000 10219InitMesh: (bp) = 25 x 25 x 20 = 12500 10220InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 10221ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 10222New grid distribution: 2 10223 1 8: 25 6: 25 1: 7 10224 2 8: 25 1: 5 1: 6 10225 3 8: 25 1: 5 7: 20 10226 4 1: 7 1: 5 8: 20 10227 5 1: 7 6: 25 1: 7 10228 6 1: 7 1: 5 1: 7 10229 7 8: 25 6: 25 8: 20 10230 8 1: 7 6: 25 8: 20 10231New grid distribution: 3 10232 1 17: 25 7: 25 1: 14 10233 2 11: 25 1: 6 1: 13 10234 3 1: 10 1: 6 9: 20 10235 4 11: 25 1: 6 14: 20 10236 5 1: 16 7: 25 1: 7 10237 6 1: 10 1: 6 1: 8 10238 7 1: 16 7: 25 8: 20 10239 8 17: 25 7: 25 15: 20 10240Setting up quadratic distribution... 10241ExtMesh (bp) on 0 = 50 x 52 x 39 = 101400 10242PhiOnMesh: Number of (b)points on node 0 = 2520 10243PhiOnMesh: nlist on node 0 = 4852 10244 10245 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 10246 scf: 1 -465.813121 -465.796710 -465.796710 0.006070 -1.827426 0.014004 10247 scf: 2 -465.796724 -465.796728 -465.796728 0.000597 -1.828619 0.010012 10248 scf: 3 -465.796732 -465.796729 -465.796729 0.000224 -1.827628 0.001654 10249 scf: 4 -465.796729 -465.796729 -465.796729 0.000029 -1.827555 0.001265 10250 scf: 5 -465.796729 -465.796729 -465.796729 0.000041 -1.827631 0.000540 10251 10252SCF Convergence by DM+H criterion 10253max |DM_out - DM_in| : 0.0000414555 10254max |H_out - H_in| (eV) : 0.0005402997 10255SCF cycle converged after 5 iterations 10256 10257Using DM_out to compute the final energy and forces 10258No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 10259 10260siesta: E_KS(eV) = -465.7967 10261 10262siesta: Atomic forces (eV/Ang): 10263 1 0.103477 -0.167290 -0.185712 10264 2 -0.818399 -0.283118 -0.206627 10265 3 0.681031 0.287994 0.148540 10266---------------------------------------- 10267 Tot -0.033891 -0.162414 -0.243799 10268---------------------------------------- 10269 Max 0.818399 10270 Res 0.399252 sqrt( Sum f_i^2 / 3N ) 10271---------------------------------------- 10272 Max 0.818399 constrained 10273 10274Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 4.14 -0.36 -0.63 0.01 0.85 1.45 10275(Free)E + p*V (eV/cell) -466.0655 10276Target enthalpy (eV/cell) -465.7967 10277 10278siesta: Stress tensor (static) (eV/Ang**3): 10279 0.002634 0.001048 0.000635 10280 0.001048 0.000165 0.000290 10281 0.000634 0.000290 -0.000175 10282 10283siesta: Pressure (static): -1.40106957 kBar 10284 10285siesta: Stress tensor (total) (eV/Ang**3): 10286 0.002582 0.000907 0.000530 10287 0.000906 -0.000223 0.000005 10288 0.000529 0.000005 -0.000390 10289 10290siesta: Pressure (total): -1.05134801 kBar 10291 10292siesta: Temp_ion = 501.354 K 10293 10294 ==================================== 10295 Begin MD step = 8 10296 ==================================== 10297 10298outcoor: Atomic coordinates (Ang): 10299 0.01150590 0.00973436 0.01259536 1 1 O 10300 0.65714538 0.75050227 0.03939414 2 2 H 10301 -0.85889636 0.26817807 -0.35867935 2 3 H 10302 10303outcell: Unit cell vectors (Ang): 10304 8.000000 0.000000 0.000000 10305 0.000000 8.000000 0.000000 10306 0.000000 0.000000 6.400000 10307 10308outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 10309outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 10310outcell: Cell volume (Ang**3) : 409.6000 10311<dSpData1D:S at geom step 8 10312 <sparsity:sparsity for geom step 8 10313 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 10314 <dData1D:(new from dSpData1D) n=69, refcount: 1> 10315refcount: 1> 10316new_DM -- step: 8 10317Re-using DM from previous geometries... 10318Number of DMs in history: 1 10319 DM extrapolation coefficients: 103201 1.00000 10321New DM after history re-use: 10322<dSpData2D:SpM extrapolated using coords 10323 <sparsity:sparsity for geom step 8 10324 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 10325 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 10326refcount: 1> 10327No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 10328New grid distribution: 1 10329 1 1: 25 1: 13 1: 5 10330 2 1: 25 1: 13 6: 10 10331 3 1: 25 1: 13 11: 15 10332 4 1: 25 1: 13 16: 20 10333 5 1: 25 14: 25 1: 5 10334 6 1: 25 14: 25 6: 10 10335 7 1: 25 14: 25 11: 15 10336 8 1: 25 14: 25 16: 20 10337 10338InitMesh: MESH = 50 x 50 x 40 = 100000 10339InitMesh: (bp) = 25 x 25 x 20 = 12500 10340InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 10341ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 10342New grid distribution: 2 10343 1 8: 25 6: 25 1: 7 10344 2 8: 25 1: 5 1: 6 10345 3 8: 25 1: 5 7: 20 10346 4 1: 7 1: 5 8: 20 10347 5 1: 7 6: 25 1: 7 10348 6 1: 7 1: 5 1: 7 10349 7 8: 25 6: 25 8: 20 10350 8 1: 7 6: 25 8: 20 10351New grid distribution: 3 10352 1 17: 25 7: 25 1: 14 10353 2 11: 25 1: 6 1: 13 10354 3 1: 10 1: 6 9: 20 10355 4 11: 25 1: 6 14: 20 10356 5 1: 16 7: 25 1: 7 10357 6 1: 10 1: 6 1: 8 10358 7 1: 16 7: 25 8: 20 10359 8 17: 25 7: 25 15: 20 10360Setting up quadratic distribution... 10361ExtMesh (bp) on 0 = 50 x 52 x 39 = 101400 10362PhiOnMesh: Number of (b)points on node 0 = 2520 10363PhiOnMesh: nlist on node 0 = 4857 10364 10365 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 10366 scf: 1 -465.805324 -465.791171 -465.791171 0.005964 -1.825306 0.013076 10367 scf: 2 -465.791177 -465.791178 -465.791178 0.000542 -1.825438 0.008238 10368 scf: 3 -465.791186 -465.791183 -465.791183 0.000187 -1.825047 0.001569 10369 scf: 4 -465.791183 -465.791183 -465.791183 0.000024 -1.825028 0.001156 10370 scf: 5 -465.791178 -465.791178 -465.791178 0.000038 -1.825152 0.000384 10371 10372SCF Convergence by DM+H criterion 10373max |DM_out - DM_in| : 0.0000381248 10374max |H_out - H_in| (eV) : 0.0003840590 10375SCF cycle converged after 5 iterations 10376 10377Using DM_out to compute the final energy and forces 10378No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 10379 10380siesta: E_KS(eV) = -465.7912 10381 10382siesta: Atomic forces (eV/Ang): 10383 1 0.036129 -0.159352 -0.209978 10384 2 -0.862877 -0.296079 -0.222750 10385 3 0.791800 0.287704 0.190440 10386---------------------------------------- 10387 Tot -0.034948 -0.167726 -0.242288 10388---------------------------------------- 10389 Max 0.862877 10390 Res 0.434436 sqrt( Sum f_i^2 / 3N ) 10391---------------------------------------- 10392 Max 0.862877 constrained 10393 10394Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 4.65 -0.29 -0.55 0.03 1.05 1.51 10395(Free)E + p*V (eV/cell) -466.1155 10396Target enthalpy (eV/cell) -465.7912 10397 10398siesta: Stress tensor (static) (eV/Ang**3): 10399 0.002942 0.001072 0.000749 10400 0.001071 0.000194 0.000296 10401 0.000748 0.000296 -0.000133 10402 10403siesta: Pressure (static): -1.60424565 kBar 10404 10405siesta: Stress tensor (total) (eV/Ang**3): 10406 0.002900 0.000946 0.000655 10407 0.000945 -0.000181 0.000019 10408 0.000654 0.000019 -0.000344 10409 10410siesta: Pressure (total): -1.26870723 kBar 10411 10412siesta: Temp_ion = 479.921 K 10413 10414 ==================================== 10415 Begin MD step = 9 10416 ==================================== 10417 10418outcoor: Atomic coordinates (Ang): 10419 0.01160157 0.01008039 0.01260140 1 1 O 10420 0.65698142 0.75154780 0.04014849 2 2 H 10421 -0.86099410 0.26090797 -0.36425724 2 3 H 10422 10423outcell: Unit cell vectors (Ang): 10424 8.000000 0.000000 0.000000 10425 0.000000 8.000000 0.000000 10426 0.000000 0.000000 6.400000 10427 10428outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 10429outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 10430outcell: Cell volume (Ang**3) : 409.6000 10431<dSpData1D:S at geom step 9 10432 <sparsity:sparsity for geom step 9 10433 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 10434 <dData1D:(new from dSpData1D) n=69, refcount: 1> 10435refcount: 1> 10436new_DM -- step: 9 10437Re-using DM from previous geometries... 10438Number of DMs in history: 1 10439 DM extrapolation coefficients: 104401 1.00000 10441New DM after history re-use: 10442<dSpData2D:SpM extrapolated using coords 10443 <sparsity:sparsity for geom step 9 10444 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 10445 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 10446refcount: 1> 10447No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 10448New grid distribution: 1 10449 1 1: 25 1: 13 1: 5 10450 2 1: 25 1: 13 6: 10 10451 3 1: 25 1: 13 11: 15 10452 4 1: 25 1: 13 16: 20 10453 5 1: 25 14: 25 1: 5 10454 6 1: 25 14: 25 6: 10 10455 7 1: 25 14: 25 11: 15 10456 8 1: 25 14: 25 16: 20 10457 10458InitMesh: MESH = 50 x 50 x 40 = 100000 10459InitMesh: (bp) = 25 x 25 x 20 = 12500 10460InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 10461ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 10462New grid distribution: 2 10463 1 8: 25 6: 25 1: 7 10464 2 8: 25 1: 5 1: 6 10465 3 8: 25 1: 5 7: 20 10466 4 1: 7 1: 5 8: 20 10467 5 1: 7 6: 25 1: 7 10468 6 1: 7 1: 5 1: 7 10469 7 8: 25 6: 25 8: 20 10470 8 1: 7 6: 25 8: 20 10471New grid distribution: 3 10472 1 17: 25 7: 25 1: 14 10473 2 11: 25 1: 6 1: 13 10474 3 1: 10 1: 6 9: 20 10475 4 11: 25 1: 6 14: 20 10476 5 1: 16 7: 25 1: 7 10477 6 1: 10 1: 6 1: 8 10478 7 1: 16 7: 25 8: 20 10479 8 17: 25 7: 25 15: 20 10480Setting up quadratic distribution... 10481ExtMesh (bp) on 0 = 50 x 52 x 39 = 101400 10482PhiOnMesh: Number of (b)points on node 0 = 2520 10483PhiOnMesh: nlist on node 0 = 4853 10484 10485 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 10486 scf: 1 -465.797365 -465.785737 -465.785737 0.005844 -1.824466 0.012076 10487 scf: 2 -465.785750 -465.785749 -465.785749 0.000526 -1.823227 0.007496 10488 scf: 3 -465.785755 -465.785753 -465.785753 0.000160 -1.823592 0.001483 10489 scf: 4 -465.785753 -465.785753 -465.785753 0.000019 -1.823662 0.001043 10490 scf: 5 -465.785753 -465.785753 -465.785753 0.000043 -1.823903 0.000226 10491 10492SCF Convergence by DM+H criterion 10493max |DM_out - DM_in| : 0.0000428280 10494max |H_out - H_in| (eV) : 0.0002264373 10495SCF cycle converged after 5 iterations 10496 10497Using DM_out to compute the final energy and forces 10498No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 10499 10500siesta: E_KS(eV) = -465.7858 10501 10502siesta: Atomic forces (eV/Ang): 10503 1 -0.032643 -0.162575 -0.232650 10504 2 -0.896063 -0.300094 -0.237944 10505 3 0.893073 0.289723 0.229940 10506---------------------------------------- 10507 Tot -0.035633 -0.172946 -0.240654 10508---------------------------------------- 10509 Max 0.896063 10510 Res 0.467335 sqrt( Sum f_i^2 / 3N ) 10511---------------------------------------- 10512 Max 0.896063 constrained 10513 10514Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 5.10 -0.25 -0.48 0.06 1.24 1.56 10515(Free)E + p*V (eV/cell) -466.1581 10516Target enthalpy (eV/cell) -465.7858 10517 10518siesta: Stress tensor (static) (eV/Ang**3): 10519 0.003214 0.001085 0.000856 10520 0.001085 0.000206 0.000303 10521 0.000855 0.000303 -0.000092 10522 10523siesta: Pressure (static): -1.77779049 kBar 10524 10525siesta: Stress tensor (total) (eV/Ang**3): 10526 0.003181 0.000976 0.000775 10527 0.000976 -0.000157 0.000035 10528 0.000775 0.000035 -0.000297 10529 10530siesta: Pressure (total): -1.45659632 kBar 10531 10532siesta: Temp_ion = 458.937 K 10533 10534 ==================================== 10535 Begin MD step = 10 10536 ==================================== 10537 10538outcoor: Atomic coordinates (Ang): 10539 0.01169645 0.01042253 0.01260186 1 1 O 10540 0.65647753 0.75247950 0.04081256 2 2 H 10541 -0.86275303 0.25374778 -0.36974790 2 3 H 10542 10543outcell: Unit cell vectors (Ang): 10544 8.000000 0.000000 0.000000 10545 0.000000 8.000000 0.000000 10546 0.000000 0.000000 6.400000 10547 10548outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 10549outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 10550outcell: Cell volume (Ang**3) : 409.6000 10551<dSpData1D:S at geom step 10 10552 <sparsity:sparsity for geom step 10 10553 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 10554 <dData1D:(new from dSpData1D) n=69, refcount: 1> 10555refcount: 1> 10556new_DM -- step: 10 10557Re-using DM from previous geometries... 10558Number of DMs in history: 1 10559 DM extrapolation coefficients: 105601 1.00000 10561New DM after history re-use: 10562<dSpData2D:SpM extrapolated using coords 10563 <sparsity:sparsity for geom step 10 10564 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 10565 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 10566refcount: 1> 10567No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 10568New grid distribution: 1 10569 1 1: 25 1: 13 1: 5 10570 2 1: 25 1: 13 6: 10 10571 3 1: 25 1: 13 11: 15 10572 4 1: 25 1: 13 16: 20 10573 5 1: 25 14: 25 1: 5 10574 6 1: 25 14: 25 6: 10 10575 7 1: 25 14: 25 11: 15 10576 8 1: 25 14: 25 16: 20 10577 10578InitMesh: MESH = 50 x 50 x 40 = 100000 10579InitMesh: (bp) = 25 x 25 x 20 = 12500 10580InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 10581ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 10582New grid distribution: 2 10583 1 8: 25 6: 25 1: 7 10584 2 8: 25 1: 5 1: 6 10585 3 8: 25 1: 5 7: 20 10586 4 1: 7 1: 5 8: 20 10587 5 1: 7 6: 25 1: 7 10588 6 1: 7 1: 5 1: 7 10589 7 8: 25 6: 25 8: 20 10590 8 1: 7 6: 25 8: 20 10591New grid distribution: 3 10592 1 17: 25 7: 25 1: 14 10593 2 11: 25 1: 6 1: 13 10594 3 1: 10 1: 6 9: 20 10595 4 11: 25 1: 6 14: 20 10596 5 1: 16 7: 25 1: 7 10597 6 1: 10 1: 6 1: 8 10598 7 1: 16 7: 25 8: 20 10599 8 17: 25 7: 25 15: 20 10600Setting up quadratic distribution... 10601ExtMesh (bp) on 0 = 50 x 52 x 39 = 101400 10602PhiOnMesh: Number of (b)points on node 0 = 2520 10603PhiOnMesh: nlist on node 0 = 4858 10604 10605 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 10606 scf: 1 -465.789475 -465.780590 -465.780590 0.005712 -1.824612 0.010963 10607 scf: 2 -465.780603 -465.780601 -465.780601 0.000511 -1.821810 0.006681 10608 scf: 3 -465.780607 -465.780604 -465.780604 0.000159 -1.823059 0.001418 10609 scf: 4 -465.780605 -465.780605 -465.780605 0.000018 -1.823223 0.000963 10610 10611SCF Convergence by DM+H criterion 10612max |DM_out - DM_in| : 0.0000180429 10613max |H_out - H_in| (eV) : 0.0009631713 10614SCF cycle converged after 4 iterations 10615 10616Using DM_out to compute the final energy and forces 10617No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 10618 10619siesta: E_KS(eV) = -465.7806 10620 10621siesta: Atomic forces (eV/Ang): 10622 1 -0.102003 -0.176953 -0.253473 10623 2 -0.917819 -0.294852 -0.251097 10624 3 0.983028 0.293261 0.265488 10625---------------------------------------- 10626 Tot -0.036794 -0.178543 -0.239081 10627---------------------------------------- 10628 Max 0.983028 10629 Res 0.496787 sqrt( Sum f_i^2 / 3N ) 10630---------------------------------------- 10631 Max 0.983028 constrained 10632 10633Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 5.47 -0.24 -0.40 0.08 1.42 1.59 10634(Free)E + p*V (eV/cell) -466.1918 10635Target enthalpy (eV/cell) -465.7806 10636 10637siesta: Stress tensor (static) (eV/Ang**3): 10638 0.003442 0.001086 0.000953 10639 0.001085 0.000198 0.000310 10640 0.000950 0.000310 -0.000054 10641 10642siesta: Pressure (static): -1.91551572 kBar 10643 10644siesta: Stress tensor (total) (eV/Ang**3): 10645 0.003417 0.000996 0.000887 10646 0.000994 -0.000153 0.000050 10647 0.000884 0.000050 -0.000252 10648 10649siesta: Pressure (total): -1.60836526 kBar 10650 10651siesta: Temp_ion = 439.080 K 10652 10653 ==================================== 10654 Begin MD step = 11 10655 ==================================== 10656 10657outcoor: Atomic coordinates (Ang): 10658 0.01178888 0.01076042 0.01259625 1 1 O 10659 0.65562545 0.75329933 0.04138138 2 2 H 10660 -0.86413904 0.24669885 -0.37513784 2 3 H 10661 10662outcell: Unit cell vectors (Ang): 10663 8.000000 0.000000 0.000000 10664 0.000000 8.000000 0.000000 10665 0.000000 0.000000 6.400000 10666 10667outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 10668outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 10669outcell: Cell volume (Ang**3) : 409.6000 10670<dSpData1D:S at geom step 11 10671 <sparsity:sparsity for geom step 11 10672 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 10673 <dData1D:(new from dSpData1D) n=69, refcount: 1> 10674refcount: 1> 10675new_DM -- step: 11 10676Re-using DM from previous geometries... 10677Number of DMs in history: 1 10678 DM extrapolation coefficients: 106791 1.00000 10680New DM after history re-use: 10681<dSpData2D:SpM extrapolated using coords 10682 <sparsity:sparsity for geom step 11 10683 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 10684 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 10685refcount: 1> 10686No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 10687New grid distribution: 1 10688 1 1: 25 1: 13 1: 5 10689 2 1: 25 1: 13 6: 10 10690 3 1: 25 1: 13 11: 15 10691 4 1: 25 1: 13 16: 20 10692 5 1: 25 14: 25 1: 5 10693 6 1: 25 14: 25 6: 10 10694 7 1: 25 14: 25 11: 15 10695 8 1: 25 14: 25 16: 20 10696 10697InitMesh: MESH = 50 x 50 x 40 = 100000 10698InitMesh: (bp) = 25 x 25 x 20 = 12500 10699InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 10700ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 10701New grid distribution: 2 10702 1 8: 25 6: 25 1: 7 10703 2 8: 25 1: 5 1: 6 10704 3 8: 25 1: 5 7: 20 10705 4 1: 7 1: 5 8: 20 10706 5 1: 7 6: 25 1: 7 10707 6 1: 7 1: 5 1: 7 10708 7 8: 25 6: 25 8: 20 10709 8 1: 7 6: 25 8: 20 10710New grid distribution: 3 10711 1 17: 25 7: 25 1: 14 10712 2 11: 25 1: 6 1: 13 10713 3 1: 10 1: 6 9: 20 10714 4 11: 25 1: 6 14: 20 10715 5 1: 16 7: 25 1: 7 10716 6 1: 10 1: 6 1: 8 10717 7 1: 16 7: 25 8: 20 10718 8 17: 25 7: 25 15: 20 10719Setting up quadratic distribution... 10720ExtMesh (bp) on 0 = 50 x 52 x 39 = 101400 10721PhiOnMesh: Number of (b)points on node 0 = 2520 10722PhiOnMesh: nlist on node 0 = 4855 10723 10724 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 10725 scf: 1 -465.781856 -465.775881 -465.775881 0.005573 -1.825563 0.010035 10726 scf: 2 -465.775890 -465.775891 -465.775891 0.000571 -1.820992 0.008022 10727 scf: 3 -465.775897 -465.775895 -465.775895 0.000242 -1.823302 0.001700 10728 scf: 4 -465.775895 -465.775895 -465.775895 0.000021 -1.823489 0.000930 10729 10730SCF Convergence by DM+H criterion 10731max |DM_out - DM_in| : 0.0000210684 10732max |H_out - H_in| (eV) : 0.0009295151 10733SCF cycle converged after 4 iterations 10734 10735Using DM_out to compute the final energy and forces 10736No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 10737 10738siesta: E_KS(eV) = -465.7759 10739 10740siesta: Atomic forces (eV/Ang): 10741 1 -0.169490 -0.201778 -0.271016 10742 2 -0.928229 -0.280612 -0.263657 10743 3 1.060463 0.299564 0.297498 10744---------------------------------------- 10745 Tot -0.037257 -0.182826 -0.237175 10746---------------------------------------- 10747 Max 1.060463 10748 Res 0.522343 sqrt( Sum f_i^2 / 3N ) 10749---------------------------------------- 10750 Max 1.060463 constrained 10751 10752Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 5.78 -0.26 -0.33 0.11 1.58 1.61 10753(Free)E + p*V (eV/cell) -466.2175 10754Target enthalpy (eV/cell) -465.7759 10755 10756siesta: Stress tensor (static) (eV/Ang**3): 10757 0.003626 0.001079 0.001041 10758 0.001077 0.000175 0.000319 10759 0.001038 0.000319 -0.000017 10760 10761siesta: Pressure (static): -2.02116046 kBar 10762 10763siesta: Stress tensor (total) (eV/Ang**3): 10764 0.003607 0.001009 0.000989 10765 0.001006 -0.000164 0.000068 10766 0.000986 0.000069 -0.000209 10767 10768siesta: Pressure (total): -1.72729976 kBar 10769 10770siesta: Temp_ion = 420.960 K 10771 10772 ==================================== 10773 Begin MD step = 12 10774 ==================================== 10775 10776outcoor: Atomic coordinates (Ang): 10777 0.01187726 0.01109349 0.01258415 1 1 O 10778 0.65442122 0.75401271 0.04185017 2 2 H 10779 -0.86512273 0.23976356 -0.38041492 2 3 H 10780 10781outcell: Unit cell vectors (Ang): 10782 8.000000 0.000000 0.000000 10783 0.000000 8.000000 0.000000 10784 0.000000 0.000000 6.400000 10785 10786outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 10787outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 10788outcell: Cell volume (Ang**3) : 409.6000 10789<dSpData1D:S at geom step 12 10790 <sparsity:sparsity for geom step 12 10791 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 10792 <dData1D:(new from dSpData1D) n=69, refcount: 1> 10793refcount: 1> 10794new_DM -- step: 12 10795Re-using DM from previous geometries... 10796Number of DMs in history: 1 10797 DM extrapolation coefficients: 107981 1.00000 10799New DM after history re-use: 10800<dSpData2D:SpM extrapolated using coords 10801 <sparsity:sparsity for geom step 12 10802 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 10803 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 10804refcount: 1> 10805No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 10806New grid distribution: 1 10807 1 1: 25 1: 13 1: 5 10808 2 1: 25 1: 13 6: 10 10809 3 1: 25 1: 13 11: 15 10810 4 1: 25 1: 13 16: 20 10811 5 1: 25 14: 25 1: 5 10812 6 1: 25 14: 25 6: 10 10813 7 1: 25 14: 25 11: 15 10814 8 1: 25 14: 25 16: 20 10815 10816InitMesh: MESH = 50 x 50 x 40 = 100000 10817InitMesh: (bp) = 25 x 25 x 20 = 12500 10818InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 10819ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 10820New grid distribution: 2 10821 1 8: 25 6: 25 1: 7 10822 2 8: 25 1: 5 1: 6 10823 3 8: 25 1: 5 7: 20 10824 4 1: 7 1: 5 8: 20 10825 5 1: 7 6: 25 1: 7 10826 6 1: 7 1: 5 1: 7 10827 7 8: 25 6: 25 8: 20 10828 8 1: 7 6: 25 8: 20 10829New grid distribution: 3 10830 1 17: 25 7: 25 1: 14 10831 2 11: 25 1: 6 1: 13 10832 3 1: 10 1: 6 9: 20 10833 4 11: 25 1: 6 14: 20 10834 5 1: 16 7: 25 1: 7 10835 6 1: 10 1: 6 1: 8 10836 7 1: 16 7: 25 8: 20 10837 8 17: 25 7: 25 15: 20 10838Setting up quadratic distribution... 10839ExtMesh (bp) on 0 = 50 x 52 x 39 = 101400 10840PhiOnMesh: Number of (b)points on node 0 = 2520 10841PhiOnMesh: nlist on node 0 = 4860 10842 10843 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 10844 scf: 1 -465.774707 -465.771758 -465.771758 0.005418 -1.827050 0.010076 10845 scf: 2 -465.771758 -465.771765 -465.771765 0.000725 -1.820356 0.014448 10846 scf: 3 -465.771773 -465.771771 -465.771771 0.000352 -1.824087 0.002087 10847 scf: 4 -465.771771 -465.771771 -465.771771 0.000031 -1.824230 0.001143 10848 scf: 5 -465.771771 -465.771771 -465.771771 0.000049 -1.824388 0.000295 10849 10850SCF Convergence by DM+H criterion 10851max |DM_out - DM_in| : 0.0000485203 10852max |H_out - H_in| (eV) : 0.0002953515 10853SCF cycle converged after 5 iterations 10854 10855Using DM_out to compute the final energy and forces 10856No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 10857 10858siesta: E_KS(eV) = -465.7718 10859 10860siesta: Atomic forces (eV/Ang): 10861 1 -0.233629 -0.237778 -0.285542 10862 2 -0.927601 -0.257577 -0.275362 10863 3 1.124376 0.309081 0.325703 10864---------------------------------------- 10865 Tot -0.036853 -0.186275 -0.235202 10866---------------------------------------- 10867 Max 1.124376 10868 Res 0.543763 sqrt( Sum f_i^2 / 3N ) 10869---------------------------------------- 10870 Max 1.124376 constrained 10871 10872Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 6.00 -0.31 -0.27 0.14 1.73 1.62 10873(Free)E + p*V (eV/cell) -466.2345 10874Target enthalpy (eV/cell) -465.7718 10875 10876siesta: Stress tensor (static) (eV/Ang**3): 10877 0.003764 0.001064 0.001115 10878 0.001063 0.000136 0.000329 10879 0.001114 0.000329 0.000016 10880 10881siesta: Pressure (static): -2.09182896 kBar 10882 10883siesta: Stress tensor (total) (eV/Ang**3): 10884 0.003748 0.001013 0.001079 10885 0.001012 -0.000191 0.000089 10886 0.001077 0.000089 -0.000167 10887 10888siesta: Pressure (total): -1.81009522 kBar 10889 10890siesta: Temp_ion = 405.059 K 10891 10892 ==================================== 10893 Begin MD step = 13 10894 ==================================== 10895 10896outcoor: Atomic coordinates (Ang): 10897 0.01196005 0.01142086 0.01256522 1 1 O 10898 0.65286510 0.75462837 0.04221450 2 2 H 10899 -0.86567988 0.23294553 -0.38556844 2 3 H 10900 10901outcell: Unit cell vectors (Ang): 10902 8.000000 0.000000 0.000000 10903 0.000000 8.000000 0.000000 10904 0.000000 0.000000 6.400000 10905 10906outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 10907outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 10908outcell: Cell volume (Ang**3) : 409.6000 10909<dSpData1D:S at geom step 13 10910 <sparsity:sparsity for geom step 13 10911 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 10912 <dData1D:(new from dSpData1D) n=69, refcount: 1> 10913refcount: 1> 10914new_DM -- step: 13 10915Re-using DM from previous geometries... 10916Number of DMs in history: 1 10917 DM extrapolation coefficients: 109181 1.00000 10919New DM after history re-use: 10920<dSpData2D:SpM extrapolated using coords 10921 <sparsity:sparsity for geom step 13 10922 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 10923 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 10924refcount: 1> 10925No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 10926New grid distribution: 1 10927 1 1: 25 1: 13 1: 5 10928 2 1: 25 1: 13 6: 10 10929 3 1: 25 1: 13 11: 15 10930 4 1: 25 1: 13 16: 20 10931 5 1: 25 14: 25 1: 5 10932 6 1: 25 14: 25 6: 10 10933 7 1: 25 14: 25 11: 15 10934 8 1: 25 14: 25 16: 20 10935 10936InitMesh: MESH = 50 x 50 x 40 = 100000 10937InitMesh: (bp) = 25 x 25 x 20 = 12500 10938InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 10939ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 10940New grid distribution: 2 10941 1 8: 25 6: 25 1: 7 10942 2 8: 25 1: 5 1: 6 10943 3 8: 25 1: 5 7: 20 10944 4 1: 7 1: 5 8: 20 10945 5 1: 7 6: 25 1: 7 10946 6 1: 7 1: 5 1: 7 10947 7 8: 25 6: 25 8: 20 10948 8 1: 7 6: 25 8: 20 10949New grid distribution: 3 10950 1 17: 25 7: 25 1: 14 10951 2 11: 25 1: 6 1: 13 10952 3 1: 10 1: 6 9: 20 10953 4 11: 25 1: 6 14: 20 10954 5 1: 16 7: 25 1: 7 10955 6 1: 10 1: 6 1: 8 10956 7 1: 16 7: 25 8: 20 10957 8 17: 25 7: 25 15: 20 10958Setting up quadratic distribution... 10959ExtMesh (bp) on 0 = 50 x 52 x 39 = 101400 10960PhiOnMesh: Number of (b)points on node 0 = 2520 10961PhiOnMesh: nlist on node 0 = 4850 10962 10963 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 10964 scf: 1 -465.768175 -465.768317 -465.768317 0.005277 -1.828634 0.013258 10965 scf: 2 -465.768307 -465.768321 -465.768321 0.000855 -1.820330 0.019148 10966 scf: 3 -465.768333 -465.768330 -465.768330 0.000440 -1.825142 0.002191 10967 scf: 4 -465.768331 -465.768330 -465.768330 0.000036 -1.825237 0.001258 10968 scf: 5 -465.768331 -465.768331 -465.768331 0.000057 -1.825335 0.000298 10969 10970SCF Convergence by DM+H criterion 10971max |DM_out - DM_in| : 0.0000573807 10972max |H_out - H_in| (eV) : 0.0002978704 10973SCF cycle converged after 5 iterations 10974 10975Using DM_out to compute the final energy and forces 10976No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 10977 10978siesta: E_KS(eV) = -465.7683 10979 10980siesta: Atomic forces (eV/Ang): 10981 1 -0.295366 -0.284477 -0.295837 10982 2 -0.915768 -0.225565 -0.285161 10983 3 1.173743 0.319755 0.348129 10984---------------------------------------- 10985 Tot -0.037391 -0.190287 -0.232869 10986---------------------------------------- 10987 Max 1.173743 10988 Res 0.560518 sqrt( Sum f_i^2 / 3N ) 10989---------------------------------------- 10990 Max 1.173743 constrained 10991 10992Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 6.14 -0.38 -0.21 0.18 1.85 1.61 10993(Free)E + p*V (eV/cell) -466.2414 10994Target enthalpy (eV/cell) -465.7683 10995 10996siesta: Stress tensor (static) (eV/Ang**3): 10997 0.003850 0.001035 0.001178 10998 0.001034 0.000078 0.000341 10999 0.001177 0.000341 0.000045 11000 11001siesta: Pressure (static): -2.12169710 kBar 11002 11003siesta: Stress tensor (total) (eV/Ang**3): 11004 0.003833 0.001004 0.001156 11005 0.001004 -0.000238 0.000110 11006 0.001155 0.000110 -0.000130 11007 11008siesta: Pressure (total): -1.85060522 kBar 11009 11010siesta: Temp_ion = 391.777 K 11011 11012 ==================================== 11013 Begin MD step = 14 11014 ==================================== 11015 11016outcoor: Atomic coordinates (Ang): 11017 0.01203576 0.01174142 0.01253920 1 1 O 11018 0.65096156 0.75515846 0.04247065 2 2 H 11019 -0.86579175 0.22624880 -0.39058990 2 3 H 11020 11021outcell: Unit cell vectors (Ang): 11022 8.000000 0.000000 0.000000 11023 0.000000 8.000000 0.000000 11024 0.000000 0.000000 6.400000 11025 11026outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 11027outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 11028outcell: Cell volume (Ang**3) : 409.6000 11029<dSpData1D:S at geom step 14 11030 <sparsity:sparsity for geom step 14 11031 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 11032 <dData1D:(new from dSpData1D) n=69, refcount: 1> 11033refcount: 1> 11034new_DM -- step: 14 11035Re-using DM from previous geometries... 11036Number of DMs in history: 1 11037 DM extrapolation coefficients: 110381 1.00000 11039New DM after history re-use: 11040<dSpData2D:SpM extrapolated using coords 11041 <sparsity:sparsity for geom step 14 11042 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 11043 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 11044refcount: 1> 11045No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 11046New grid distribution: 1 11047 1 1: 25 1: 13 1: 5 11048 2 1: 25 1: 13 6: 10 11049 3 1: 25 1: 13 11: 15 11050 4 1: 25 1: 13 16: 20 11051 5 1: 25 14: 25 1: 5 11052 6 1: 25 14: 25 6: 10 11053 7 1: 25 14: 25 11: 15 11054 8 1: 25 14: 25 16: 20 11055 11056InitMesh: MESH = 50 x 50 x 40 = 100000 11057InitMesh: (bp) = 25 x 25 x 20 = 12500 11058InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 11059ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 11060New grid distribution: 2 11061 1 8: 25 6: 25 1: 7 11062 2 8: 25 1: 5 1: 6 11063 3 8: 25 1: 5 7: 20 11064 4 1: 7 1: 5 8: 20 11065 5 1: 7 6: 25 1: 7 11066 6 1: 7 1: 5 1: 7 11067 7 8: 25 6: 25 8: 20 11068 8 1: 7 6: 25 8: 20 11069New grid distribution: 3 11070 1 17: 25 7: 25 1: 14 11071 2 11: 25 1: 6 1: 13 11072 3 1: 10 1: 6 9: 20 11073 4 11: 25 1: 6 14: 20 11074 5 1: 16 7: 25 1: 7 11075 6 1: 10 1: 6 1: 8 11076 7 1: 16 7: 25 8: 20 11077 8 17: 25 7: 25 15: 20 11078Setting up quadratic distribution... 11079ExtMesh (bp) on 0 = 50 x 52 x 39 = 101400 11080PhiOnMesh: Number of (b)points on node 0 = 2520 11081PhiOnMesh: nlist on node 0 = 4841 11082 11083 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 11084 scf: 1 -465.762395 -465.765639 -465.765639 0.005117 -1.830502 0.017279 11085 scf: 2 -465.765612 -465.765639 -465.765639 0.001012 -1.820062 0.025381 11086 scf: 3 -465.765659 -465.765654 -465.765654 0.000547 -1.826309 0.002193 11087 scf: 4 -465.765655 -465.765654 -465.765654 0.000039 -1.826352 0.001324 11088 scf: 5 -465.765655 -465.765654 -465.765654 0.000065 -1.826380 0.000290 11089 11090SCF Convergence by DM+H criterion 11091max |DM_out - DM_in| : 0.0000649752 11092max |H_out - H_in| (eV) : 0.0002901622 11093SCF cycle converged after 5 iterations 11094 11095Using DM_out to compute the final energy and forces 11096No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 11097 11098siesta: E_KS(eV) = -465.7657 11099 11100siesta: Atomic forces (eV/Ang): 11101 1 -0.352313 -0.341628 -0.301461 11102 2 -0.893558 -0.185132 -0.293545 11103 3 1.207537 0.332135 0.364578 11104---------------------------------------- 11105 Tot -0.038334 -0.194625 -0.230428 11106---------------------------------------- 11107 Max 1.207537 11108 Res 0.572711 sqrt( Sum f_i^2 / 3N ) 11109---------------------------------------- 11110 Max 1.207537 constrained 11111 11112Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 6.19 -0.48 -0.16 0.21 1.95 1.58 11113(Free)E + p*V (eV/cell) -466.2383 11114Target enthalpy (eV/cell) -465.7657 11115 11116siesta: Stress tensor (static) (eV/Ang**3): 11117 0.003882 0.000997 0.001224 11118 0.000997 0.000003 0.000354 11119 0.001223 0.000354 0.000067 11120 11121siesta: Pressure (static): -2.11086986 kBar 11122 11123siesta: Stress tensor (total) (eV/Ang**3): 11124 0.003862 0.000987 0.001217 11125 0.000986 -0.000301 0.000134 11126 0.001215 0.000134 -0.000099 11127 11128siesta: Pressure (total): -1.84866725 kBar 11129 11130siesta: Temp_ion = 381.407 K 11131 11132 ==================================== 11133 Begin MD step = 15 11134 ==================================== 11135 11136outcoor: Atomic coordinates (Ang): 11137 0.01210303 0.01205379 0.01250596 1 1 O 11138 0.64871904 0.75561832 0.04261543 2 2 H 11139 -0.86544551 0.21967808 -0.39547304 2 3 H 11140 11141outcell: Unit cell vectors (Ang): 11142 8.000000 0.000000 0.000000 11143 0.000000 8.000000 0.000000 11144 0.000000 0.000000 6.400000 11145 11146outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 11147outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 11148outcell: Cell volume (Ang**3) : 409.6000 11149<dSpData1D:S at geom step 15 11150 <sparsity:sparsity for geom step 15 11151 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 11152 <dData1D:(new from dSpData1D) n=69, refcount: 1> 11153refcount: 1> 11154new_DM -- step: 15 11155Re-using DM from previous geometries... 11156Number of DMs in history: 1 11157 DM extrapolation coefficients: 111581 1.00000 11159New DM after history re-use: 11160<dSpData2D:SpM extrapolated using coords 11161 <sparsity:sparsity for geom step 15 11162 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 11163 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 11164refcount: 1> 11165No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 11166New grid distribution: 1 11167 1 1: 25 1: 13 1: 5 11168 2 1: 25 1: 13 6: 10 11169 3 1: 25 1: 13 11: 15 11170 4 1: 25 1: 13 16: 20 11171 5 1: 25 14: 25 1: 5 11172 6 1: 25 14: 25 6: 10 11173 7 1: 25 14: 25 11: 15 11174 8 1: 25 14: 25 16: 20 11175 11176InitMesh: MESH = 50 x 50 x 40 = 100000 11177InitMesh: (bp) = 25 x 25 x 20 = 12500 11178InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 11179ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 11180New grid distribution: 2 11181 1 8: 25 6: 25 1: 7 11182 2 8: 25 1: 5 1: 6 11183 3 8: 25 1: 5 7: 20 11184 4 1: 7 1: 5 8: 20 11185 5 1: 7 6: 25 1: 7 11186 6 1: 7 1: 5 1: 7 11187 7 8: 25 6: 25 8: 20 11188 8 1: 7 6: 25 8: 20 11189New grid distribution: 3 11190 1 17: 25 7: 25 1: 14 11191 2 11: 25 1: 6 1: 13 11192 3 1: 10 1: 6 9: 20 11193 4 11: 25 1: 6 14: 20 11194 5 1: 16 7: 25 1: 7 11195 6 1: 10 1: 6 1: 8 11196 7 1: 16 7: 25 8: 20 11197 8 17: 25 7: 25 15: 20 11198Setting up quadratic distribution... 11199ExtMesh (bp) on 0 = 50 x 52 x 39 = 101400 11200PhiOnMesh: Number of (b)points on node 0 = 2520 11201PhiOnMesh: nlist on node 0 = 4840 11202 11203 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 11204 scf: 1 -465.757434 -465.763742 -465.763742 0.004956 -1.832327 0.021300 11205 scf: 2 -465.763693 -465.763736 -465.763736 0.001166 -1.819753 0.031593 11206 scf: 3 -465.763765 -465.763757 -465.763757 0.000649 -1.827416 0.002166 11207 scf: 4 -465.763758 -465.763758 -465.763758 0.000040 -1.827418 0.001355 11208 scf: 5 -465.763759 -465.763758 -465.763758 0.000069 -1.827386 0.000296 11209 11210SCF Convergence by DM+H criterion 11211max |DM_out - DM_in| : 0.0000686979 11212max |H_out - H_in| (eV) : 0.0002961707 11213SCF cycle converged after 5 iterations 11214 11215Using DM_out to compute the final energy and forces 11216No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 11217 11218siesta: E_KS(eV) = -465.7638 11219 11220siesta: Atomic forces (eV/Ang): 11221 1 -0.403704 -0.408070 -0.302188 11222 2 -0.861250 -0.136581 -0.300394 11223 3 1.225609 0.345992 0.374761 11224---------------------------------------- 11225 Tot -0.039344 -0.198659 -0.227821 11226---------------------------------------- 11227 Max 1.225609 11228 Res 0.580587 sqrt( Sum f_i^2 / 3N ) 11229---------------------------------------- 11230 Max 1.225609 constrained 11231 11232Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 6.15 -0.61 -0.12 0.25 2.02 1.53 11233(Free)E + p*V (eV/cell) -466.2256 11234Target enthalpy (eV/cell) -465.7638 11235 11236siesta: Stress tensor (static) (eV/Ang**3): 11237 0.003864 0.000949 0.001253 11238 0.000949 -0.000087 0.000368 11239 0.001252 0.000368 0.000083 11240 11241siesta: Pressure (static): -2.06167916 kBar 11242 11243siesta: Stress tensor (total) (eV/Ang**3): 11244 0.003836 0.000959 0.001260 11245 0.000958 -0.000380 0.000158 11246 0.001259 0.000158 -0.000074 11247 11248siesta: Pressure (total): -1.80641711 kBar 11249 11250siesta: Temp_ion = 374.081 K 11251 11252 ==================================== 11253 Begin MD step = 16 11254 ==================================== 11255 11256outcoor: Atomic coordinates (Ang): 11257 0.01216063 0.01235640 0.01246548 1 1 O 11258 0.64614978 0.75602636 0.04264626 2 2 H 11259 -0.86463432 0.21323861 -0.40021401 2 3 H 11260 11261outcell: Unit cell vectors (Ang): 11262 8.000000 0.000000 0.000000 11263 0.000000 8.000000 0.000000 11264 0.000000 0.000000 6.400000 11265 11266outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 11267outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 11268outcell: Cell volume (Ang**3) : 409.6000 11269<dSpData1D:S at geom step 16 11270 <sparsity:sparsity for geom step 16 11271 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 11272 <dData1D:(new from dSpData1D) n=69, refcount: 1> 11273refcount: 1> 11274new_DM -- step: 16 11275Re-using DM from previous geometries... 11276Number of DMs in history: 1 11277 DM extrapolation coefficients: 112781 1.00000 11279New DM after history re-use: 11280<dSpData2D:SpM extrapolated using coords 11281 <sparsity:sparsity for geom step 16 11282 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 11283 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 11284refcount: 1> 11285No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 11286New grid distribution: 1 11287 1 1: 25 1: 13 1: 5 11288 2 1: 25 1: 13 6: 10 11289 3 1: 25 1: 13 11: 15 11290 4 1: 25 1: 13 16: 20 11291 5 1: 25 14: 25 1: 5 11292 6 1: 25 14: 25 6: 10 11293 7 1: 25 14: 25 11: 15 11294 8 1: 25 14: 25 16: 20 11295 11296InitMesh: MESH = 50 x 50 x 40 = 100000 11297InitMesh: (bp) = 25 x 25 x 20 = 12500 11298InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 11299ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 11300New grid distribution: 2 11301 1 8: 25 6: 25 1: 7 11302 2 8: 25 1: 5 1: 6 11303 3 8: 25 1: 5 7: 20 11304 4 1: 7 1: 5 8: 20 11305 5 1: 7 6: 25 1: 7 11306 6 1: 7 1: 5 1: 7 11307 7 8: 25 6: 25 8: 20 11308 8 1: 7 6: 25 8: 20 11309New grid distribution: 3 11310 1 17: 25 7: 25 1: 14 11311 2 11: 25 1: 6 1: 13 11312 3 1: 10 1: 6 9: 20 11313 4 11: 25 1: 6 14: 20 11314 5 1: 16 7: 25 1: 7 11315 6 1: 10 1: 6 1: 8 11316 7 1: 16 7: 25 8: 20 11317 8 17: 25 7: 25 15: 20 11318Setting up quadratic distribution... 11319ExtMesh (bp) on 0 = 50 x 52 x 39 = 101400 11320PhiOnMesh: Number of (b)points on node 0 = 2520 11321PhiOnMesh: nlist on node 0 = 4836 11322 11323 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 11324 scf: 1 -465.753351 -465.762628 -465.762628 0.005156 -1.833995 0.025200 11325 scf: 2 -465.762554 -465.762617 -465.762617 0.001313 -1.819361 0.037586 11326 scf: 3 -465.762657 -465.762646 -465.762646 0.000743 -1.828371 0.002288 11327 scf: 4 -465.762647 -465.762647 -465.762647 0.000042 -1.828345 0.001372 11328 scf: 5 -465.762648 -465.762647 -465.762647 0.000077 -1.828261 0.000326 11329 11330SCF Convergence by DM+H criterion 11331max |DM_out - DM_in| : 0.0000772452 11332max |H_out - H_in| (eV) : 0.0003264774 11333SCF cycle converged after 5 iterations 11334 11335Using DM_out to compute the final energy and forces 11336No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 11337 11338siesta: E_KS(eV) = -465.7626 11339 11340siesta: Atomic forces (eV/Ang): 11341 1 -0.448499 -0.483207 -0.297621 11342 2 -0.819836 -0.080575 -0.305849 11343 3 1.227575 0.361168 0.378236 11344---------------------------------------- 11345 Tot -0.040760 -0.202614 -0.225234 11346---------------------------------------- 11347 Max 1.227575 11348 Res 0.584601 sqrt( Sum f_i^2 / 3N ) 11349---------------------------------------- 11350 Max 1.227575 constrained 11351 11352Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 6.02 -0.76 -0.09 0.29 2.06 1.48 11353(Free)E + p*V (eV/cell) -466.2036 11354Target enthalpy (eV/cell) -465.7626 11355 11356siesta: Stress tensor (static) (eV/Ang**3): 11357 0.003796 0.000893 0.001266 11358 0.000892 -0.000190 0.000383 11359 0.001265 0.000382 0.000093 11360 11361siesta: Pressure (static): -1.97530740 kBar 11362 11363siesta: Stress tensor (total) (eV/Ang**3): 11364 0.003757 0.000922 0.001286 11365 0.000921 -0.000471 0.000184 11366 0.001284 0.000183 -0.000055 11367 11368siesta: Pressure (total): -1.72494818 kBar 11369 11370siesta: Temp_ion = 369.784 K 11371 11372 ==================================== 11373 Begin MD step = 17 11374 ==================================== 11375 11376outcoor: Atomic coordinates (Ang): 11377 0.01220750 0.01264743 0.01241788 1 1 O 11378 0.64326951 0.75640384 0.04256106 2 2 H 11379 -0.86335743 0.20693615 -0.40481149 2 3 H 11380 11381outcell: Unit cell vectors (Ang): 11382 8.000000 0.000000 0.000000 11383 0.000000 8.000000 0.000000 11384 0.000000 0.000000 6.400000 11385 11386outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 11387outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 11388outcell: Cell volume (Ang**3) : 409.6000 11389<dSpData1D:S at geom step 17 11390 <sparsity:sparsity for geom step 17 11391 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 11392 <dData1D:(new from dSpData1D) n=69, refcount: 1> 11393refcount: 1> 11394new_DM -- step: 17 11395Re-using DM from previous geometries... 11396Number of DMs in history: 1 11397 DM extrapolation coefficients: 113981 1.00000 11399New DM after history re-use: 11400<dSpData2D:SpM extrapolated using coords 11401 <sparsity:sparsity for geom step 17 11402 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 11403 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 11404refcount: 1> 11405No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 11406New grid distribution: 1 11407 1 1: 25 1: 13 1: 5 11408 2 1: 25 1: 13 6: 10 11409 3 1: 25 1: 13 11: 15 11410 4 1: 25 1: 13 16: 20 11411 5 1: 25 14: 25 1: 5 11412 6 1: 25 14: 25 6: 10 11413 7 1: 25 14: 25 11: 15 11414 8 1: 25 14: 25 16: 20 11415 11416InitMesh: MESH = 50 x 50 x 40 = 100000 11417InitMesh: (bp) = 25 x 25 x 20 = 12500 11418InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 11419ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 11420New grid distribution: 2 11421 1 8: 25 6: 25 1: 7 11422 2 8: 25 1: 5 1: 6 11423 3 8: 25 1: 5 7: 20 11424 4 1: 7 1: 5 8: 20 11425 5 1: 7 6: 25 1: 7 11426 6 1: 7 1: 5 1: 7 11427 7 8: 25 6: 25 8: 20 11428 8 1: 7 6: 25 8: 20 11429New grid distribution: 3 11430 1 17: 25 7: 25 1: 14 11431 2 11: 25 1: 6 1: 13 11432 3 1: 10 1: 6 9: 20 11433 4 11: 25 1: 6 14: 20 11434 5 1: 16 7: 25 1: 7 11435 6 1: 10 1: 6 1: 8 11436 7 1: 16 7: 25 8: 20 11437 8 17: 25 7: 25 15: 20 11438Setting up quadratic distribution... 11439ExtMesh (bp) on 0 = 50 x 52 x 39 = 101400 11440PhiOnMesh: Number of (b)points on node 0 = 2520 11441PhiOnMesh: nlist on node 0 = 4824 11442 11443 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 11444 scf: 1 -465.750153 -465.762259 -465.762259 0.005622 -1.835431 0.028890 11445 scf: 2 -465.762157 -465.762241 -465.762241 0.001448 -1.818866 0.043178 11446 scf: 3 -465.762294 -465.762280 -465.762280 0.000827 -1.829125 0.002481 11447 scf: 4 -465.762281 -465.762280 -465.762280 0.000048 -1.829076 0.001389 11448 scf: 5 -465.762281 -465.762281 -465.762281 0.000087 -1.828951 0.000362 11449 11450SCF Convergence by DM+H criterion 11451max |DM_out - DM_in| : 0.0000874903 11452max |H_out - H_in| (eV) : 0.0003621526 11453SCF cycle converged after 5 iterations 11454 11455Using DM_out to compute the final energy and forces 11456No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 11457 11458siesta: E_KS(eV) = -465.7623 11459 11460siesta: Atomic forces (eV/Ang): 11461 1 -0.486440 -0.565442 -0.288130 11462 2 -0.769852 -0.017640 -0.309804 11463 3 1.213697 0.377438 0.374871 11464---------------------------------------- 11465 Tot -0.042595 -0.205644 -0.223063 11466---------------------------------------- 11467 Max 1.213697 11468 Res 0.585413 sqrt( Sum f_i^2 / 3N ) 11469---------------------------------------- 11470 Max 1.213697 constrained 11471 11472Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 5.81 -0.92 -0.07 0.33 2.07 1.40 11473(Free)E + p*V (eV/cell) -466.1733 11474Target enthalpy (eV/cell) -465.7623 11475 11476siesta: Stress tensor (static) (eV/Ang**3): 11477 0.003682 0.000827 0.001264 11478 0.000826 -0.000305 0.000398 11479 0.001263 0.000397 0.000097 11480 11481siesta: Pressure (static): -1.85530577 kBar 11482 11483siesta: Stress tensor (total) (eV/Ang**3): 11484 0.003628 0.000875 0.001295 11485 0.000874 -0.000574 0.000209 11486 0.001294 0.000209 -0.000043 11487 11488siesta: Pressure (total): -1.60782215 kBar 11489 11490siesta: Temp_ion = 368.359 K 11491 11492 ==================================== 11493 Begin MD step = 18 11494 ==================================== 11495 11496outcoor: Atomic coordinates (Ang): 11497 0.01224271 0.01292492 0.01236338 1 1 O 11498 0.64009717 0.75677462 0.04235832 2 2 H 11499 -0.86162010 0.20077689 -0.40926675 2 3 H 11500 11501outcell: Unit cell vectors (Ang): 11502 8.000000 0.000000 0.000000 11503 0.000000 8.000000 0.000000 11504 0.000000 0.000000 6.400000 11505 11506outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 11507outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 11508outcell: Cell volume (Ang**3) : 409.6000 11509<dSpData1D:S at geom step 18 11510 <sparsity:sparsity for geom step 18 11511 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 11512 <dData1D:(new from dSpData1D) n=69, refcount: 1> 11513refcount: 1> 11514new_DM -- step: 18 11515Re-using DM from previous geometries... 11516Number of DMs in history: 1 11517 DM extrapolation coefficients: 115181 1.00000 11519New DM after history re-use: 11520<dSpData2D:SpM extrapolated using coords 11521 <sparsity:sparsity for geom step 18 11522 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 11523 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 11524refcount: 1> 11525No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 11526New grid distribution: 1 11527 1 1: 25 1: 13 1: 5 11528 2 1: 25 1: 13 6: 10 11529 3 1: 25 1: 13 11: 15 11530 4 1: 25 1: 13 16: 20 11531 5 1: 25 14: 25 1: 5 11532 6 1: 25 14: 25 6: 10 11533 7 1: 25 14: 25 11: 15 11534 8 1: 25 14: 25 16: 20 11535 11536InitMesh: MESH = 50 x 50 x 40 = 100000 11537InitMesh: (bp) = 25 x 25 x 20 = 12500 11538InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 11539ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 11540New grid distribution: 2 11541 1 8: 25 6: 25 1: 7 11542 2 8: 25 1: 5 1: 6 11543 3 8: 25 1: 5 7: 20 11544 4 1: 7 1: 5 8: 20 11545 5 1: 7 6: 25 1: 7 11546 6 1: 7 1: 5 1: 7 11547 7 8: 25 6: 25 8: 20 11548 8 1: 7 6: 25 8: 20 11549New grid distribution: 3 11550 1 17: 25 7: 25 1: 14 11551 2 11: 25 1: 6 1: 13 11552 3 1: 10 1: 6 9: 20 11553 4 11: 25 1: 6 14: 20 11554 5 1: 16 7: 25 1: 7 11555 6 1: 10 1: 6 1: 8 11556 7 1: 16 7: 25 8: 20 11557 8 17: 25 7: 25 15: 20 11558Setting up quadratic distribution... 11559ExtMesh (bp) on 0 = 50 x 52 x 39 = 101400 11560PhiOnMesh: Number of (b)points on node 0 = 2520 11561PhiOnMesh: nlist on node 0 = 4821 11562 11563 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 11564 scf: 1 -465.747816 -465.762559 -465.762559 0.006064 -1.836596 0.032283 11565 scf: 2 -465.762430 -465.762535 -465.762535 0.001569 -1.818281 0.048222 11566 scf: 3 -465.762601 -465.762584 -465.762584 0.000901 -1.829661 0.002649 11567 scf: 4 -465.762585 -465.762584 -465.762584 0.000052 -1.829595 0.001488 11568 scf: 5 -465.762585 -465.762585 -465.762585 0.000096 -1.829436 0.000403 11569 11570SCF Convergence by DM+H criterion 11571max |DM_out - DM_in| : 0.0000960678 11572max |H_out - H_in| (eV) : 0.0004030267 11573SCF cycle converged after 5 iterations 11574 11575Using DM_out to compute the final energy and forces 11576No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 11577 11578siesta: E_KS(eV) = -465.7626 11579 11580siesta: Atomic forces (eV/Ang): 11581 1 -0.515028 -0.654836 -0.272064 11582 2 -0.712294 0.051322 -0.312315 11583 3 1.183324 0.394356 0.364067 11584---------------------------------------- 11585 Tot -0.043998 -0.209157 -0.220312 11586---------------------------------------- 11587 Max 1.183324 11588 Res 0.583470 sqrt( Sum f_i^2 / 3N ) 11589---------------------------------------- 11590 Max 1.183324 constrained 11591 11592Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 5.52 -1.10 -0.06 0.38 2.05 1.31 11593(Free)E + p*V (eV/cell) -466.1335 11594Target enthalpy (eV/cell) -465.7626 11595 11596siesta: Stress tensor (static) (eV/Ang**3): 11597 0.003518 0.000755 0.001241 11598 0.000754 -0.000432 0.000414 11599 0.001240 0.000413 0.000092 11600 11601siesta: Pressure (static): -1.69729394 kBar 11602 11603siesta: Stress tensor (total) (eV/Ang**3): 11604 0.003445 0.000821 0.001282 11605 0.000820 -0.000689 0.000235 11606 0.001281 0.000235 -0.000039 11607 11608siesta: Pressure (total): -1.45076394 kBar 11609 11610siesta: Temp_ion = 369.524 K 11611 11612 ==================================== 11613 Begin MD step = 19 11614 ==================================== 11615 11616outcoor: Atomic coordinates (Ang): 11617 0.01226560 0.01318673 0.01230236 1 1 O 11618 0.63665462 0.75716488 0.04203711 2 2 H 11619 -0.85943385 0.19476723 -0.41358391 2 3 H 11620 11621outcell: Unit cell vectors (Ang): 11622 8.000000 0.000000 0.000000 11623 0.000000 8.000000 0.000000 11624 0.000000 0.000000 6.400000 11625 11626outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 11627outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 11628outcell: Cell volume (Ang**3) : 409.6000 11629<dSpData1D:S at geom step 19 11630 <sparsity:sparsity for geom step 19 11631 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 11632 <dData1D:(new from dSpData1D) n=69, refcount: 1> 11633refcount: 1> 11634new_DM -- step: 19 11635Re-using DM from previous geometries... 11636Number of DMs in history: 1 11637 DM extrapolation coefficients: 116381 1.00000 11639New DM after history re-use: 11640<dSpData2D:SpM extrapolated using coords 11641 <sparsity:sparsity for geom step 19 11642 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 11643 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 11644refcount: 1> 11645No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 11646New grid distribution: 1 11647 1 1: 25 1: 13 1: 5 11648 2 1: 25 1: 13 6: 10 11649 3 1: 25 1: 13 11: 15 11650 4 1: 25 1: 13 16: 20 11651 5 1: 25 14: 25 1: 5 11652 6 1: 25 14: 25 6: 10 11653 7 1: 25 14: 25 11: 15 11654 8 1: 25 14: 25 16: 20 11655 11656InitMesh: MESH = 50 x 50 x 40 = 100000 11657InitMesh: (bp) = 25 x 25 x 20 = 12500 11658InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 11659ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 11660New grid distribution: 2 11661 1 8: 25 6: 25 1: 7 11662 2 8: 25 1: 5 1: 6 11663 3 8: 25 1: 5 7: 20 11664 4 1: 7 1: 5 8: 20 11665 5 1: 7 6: 25 1: 7 11666 6 1: 7 1: 5 1: 7 11667 7 8: 25 6: 25 8: 20 11668 8 1: 7 6: 25 8: 20 11669New grid distribution: 3 11670 1 17: 25 7: 25 1: 14 11671 2 11: 25 1: 6 1: 13 11672 3 1: 10 1: 6 9: 20 11673 4 11: 25 1: 6 14: 20 11674 5 1: 16 7: 25 1: 7 11675 6 1: 10 1: 6 1: 8 11676 7 1: 16 7: 25 8: 20 11677 8 17: 25 7: 25 15: 20 11678Setting up quadratic distribution... 11679ExtMesh (bp) on 0 = 50 x 52 x 39 = 101400 11680PhiOnMesh: Number of (b)points on node 0 = 2520 11681PhiOnMesh: nlist on node 0 = 4819 11682 11683 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 11684 scf: 1 -465.746287 -465.763431 -465.763431 0.006468 -1.837478 0.035294 11685 scf: 2 -465.763276 -465.763401 -465.763401 0.001672 -1.817645 0.052578 11686 scf: 3 -465.763480 -465.763459 -465.763459 0.000963 -1.829986 0.002799 11687 scf: 4 -465.763460 -465.763460 -465.763460 0.000056 -1.829909 0.001575 11688 scf: 5 -465.763460 -465.763460 -465.763460 0.000103 -1.829724 0.000449 11689 scf: 6 -465.763460 -465.763460 -465.763460 0.000010 -1.829685 0.000260 11690 11691SCF Convergence by DM+H criterion 11692max |DM_out - DM_in| : 0.0000097427 11693max |H_out - H_in| (eV) : 0.0002600409 11694SCF cycle converged after 6 iterations 11695 11696Using DM_out to compute the final energy and forces 11697No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 11698 11699siesta: E_KS(eV) = -465.7635 11700 11701siesta: Atomic forces (eV/Ang): 11702 1 -0.533882 -0.749521 -0.249730 11703 2 -0.648530 0.125114 -0.313686 11704 3 1.136501 0.411796 0.345643 11705---------------------------------------- 11706 Tot -0.045911 -0.212610 -0.217773 11707---------------------------------------- 11708 Max 1.136501 11709 Res 0.579703 sqrt( Sum f_i^2 / 3N ) 11710---------------------------------------- 11711 Max 1.136501 constrained 11712 11713Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 5.15 -1.30 -0.07 0.42 2.00 1.22 11714(Free)E + p*V (eV/cell) -466.0852 11715Target enthalpy (eV/cell) -465.7635 11716 11717siesta: Stress tensor (static) (eV/Ang**3): 11718 0.003309 0.000678 0.001200 11719 0.000677 -0.000568 0.000430 11720 0.001199 0.000430 0.000078 11721 11722siesta: Pressure (static): -1.50592267 kBar 11723 11724siesta: Stress tensor (total) (eV/Ang**3): 11725 0.003215 0.000761 0.001250 11726 0.000761 -0.000812 0.000262 11727 0.001249 0.000262 -0.000045 11728 11729siesta: Pressure (total): -1.25861299 kBar 11730 11731siesta: Temp_ion = 372.893 K 11732 11733 ==================================== 11734 Begin MD step = 20 11735 ==================================== 11736 11737outcoor: Atomic coordinates (Ang): 11738 0.01227569 0.01343060 0.01223536 1 1 O 11739 0.63296603 0.75760260 0.04159689 2 2 H 11740 -0.85681646 0.18891379 -0.41776993 2 3 H 11741 11742outcell: Unit cell vectors (Ang): 11743 8.000000 0.000000 0.000000 11744 0.000000 8.000000 0.000000 11745 0.000000 0.000000 6.400000 11746 11747outcell: Cell vector modules (Ang) : 8.000000 8.000000 6.400000 11748outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 11749outcell: Cell volume (Ang**3) : 409.6000 11750<dSpData1D:S at geom step 20 11751 <sparsity:sparsity for geom step 20 11752 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 7> 11753 <dData1D:(new from dSpData1D) n=69, refcount: 1> 11754refcount: 1> 11755new_DM -- step: 20 11756Re-using DM from previous geometries... 11757Number of DMs in history: 1 11758 DM extrapolation coefficients: 117591 1.00000 11760New DM after history re-use: 11761<dSpData2D:SpM extrapolated using coords 11762 <sparsity:sparsity for geom step 20 11763 nrows_g=23 nrows=3 sparsity=.1304 nnzs=69, refcount: 9> 11764 <dData2D:(temp array for extrapolation) n=69 m=1, refcount: 1> 11765refcount: 1> 11766No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 11767New grid distribution: 1 11768 1 1: 25 1: 13 1: 5 11769 2 1: 25 1: 13 6: 10 11770 3 1: 25 1: 13 11: 15 11771 4 1: 25 1: 13 16: 20 11772 5 1: 25 14: 25 1: 5 11773 6 1: 25 14: 25 6: 10 11774 7 1: 25 14: 25 11: 15 11775 8 1: 25 14: 25 16: 20 11776 11777InitMesh: MESH = 50 x 50 x 40 = 100000 11778InitMesh: (bp) = 25 x 25 x 20 = 12500 11779InitMesh: Mesh cutoff (required, used) = 100.000 107.960 Ry 11780ExtMesh (bp) on 0 = 57 x 45 x 37 = 94905 11781New grid distribution: 2 11782 1 8: 25 6: 25 1: 7 11783 2 8: 25 1: 5 1: 6 11784 3 8: 25 1: 5 7: 20 11785 4 1: 7 1: 5 8: 20 11786 5 1: 7 6: 25 1: 7 11787 6 1: 7 1: 5 1: 7 11788 7 8: 25 6: 25 8: 20 11789 8 1: 7 6: 25 8: 20 11790New grid distribution: 3 11791 1 17: 25 7: 25 1: 14 11792 2 11: 25 1: 6 1: 13 11793 3 1: 10 1: 6 9: 20 11794 4 11: 25 1: 6 14: 20 11795 5 1: 16 7: 25 1: 7 11796 6 1: 10 1: 6 1: 8 11797 7 1: 16 7: 25 8: 20 11798 8 17: 25 7: 25 15: 20 11799Setting up quadratic distribution... 11800ExtMesh (bp) on 0 = 50 x 52 x 39 = 101400 11801PhiOnMesh: Number of (b)points on node 0 = 2520 11802PhiOnMesh: nlist on node 0 = 4816 11803 11804 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) 11805 scf: 1 -465.745492 -465.764754 -465.764754 0.006843 -1.838097 0.037910 11806 scf: 2 -465.764575 -465.764719 -465.764719 0.001756 -1.816996 0.056202 11807 scf: 3 -465.764809 -465.764785 -465.764785 0.001012 -1.830131 0.002930 11808 scf: 4 -465.764787 -465.764786 -465.764786 0.000059 -1.830046 0.001649 11809 scf: 5 -465.764787 -465.764786 -465.764786 0.000109 -1.829840 0.000518 11810 scf: 6 -465.764786 -465.764786 -465.764786 0.000011 -1.829793 0.000309 11811 11812SCF Convergence by DM+H criterion 11813max |DM_out - DM_in| : 0.0000110611 11814max |H_out - H_in| (eV) : 0.0003089775 11815SCF cycle converged after 6 iterations 11816 11817Using DM_out to compute the final energy and forces 11818No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23 11819 11820siesta: E_KS(eV) = -465.7648 11821 11822siesta: Atomic forces (eV/Ang): 11823 1 -0.542424 -0.847938 -0.220926 11824 2 -0.579369 0.203037 -0.313582 11825 3 1.073763 0.429257 0.319370 11826---------------------------------------- 11827 Tot -0.048029 -0.215644 -0.215138 11828---------------------------------------- 11829 Max 1.073763 11830 Res 0.575083 sqrt( Sum f_i^2 / 3N ) 11831---------------------------------------- 11832 Max 1.073763 constrained 11833 11834Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 4.71 -1.51 -0.10 0.46 1.92 1.11 11835(Free)E + p*V (eV/cell) -466.0290 11836Target enthalpy (eV/cell) -465.7648 11837 11838siesta: Stress tensor (static) (eV/Ang**3): 11839 0.003057 0.000594 0.001140 11840 0.000593 -0.000711 0.000447 11841 0.001140 0.000447 0.000056 11842 11843siesta: Pressure (static): -1.28307235 kBar 11844 11845siesta: Stress tensor (total) (eV/Ang**3): 11846 0.002939 0.000694 0.001197 11847 0.000693 -0.000943 0.000289 11848 0.001196 0.000289 -0.000061 11849 11850siesta: Pressure (total): -1.03350821 kBar 11851 11852siesta: Temp_ion = 378.000 K 11853 11854siesta: Program's energy decomposition (eV): 11855siesta: Ebs = -102.377839 11856siesta: Eions = 815.854478 11857siesta: Ena = 175.055262 11858siesta: Ekin = 352.539931 11859siesta: Enl = -62.869075 11860siesta: Eso = 0.000000 11861siesta: Edftu = 0.000000 11862siesta: DEna = -2.691593 11863siesta: DUscf = 0.782208 11864siesta: DUext = 0.000000 11865siesta: Exc = -112.727041 11866siesta: eta*DQ = 0.000000 11867siesta: Emadel = 0.000000 11868siesta: Emeta = 0.000000 11869siesta: Emolmec = 0.000000 11870siesta: Ekinion = 0.097717 11871siesta: Eharris = -465.667070 11872siesta: Etot = -465.667070 11873siesta: FreeEng = -465.667070 11874 11875siesta: Final energy (eV): 11876siesta: Band Struct. = -102.377839 11877siesta: Kinetic = 352.539931 11878siesta: Hartree = 414.202777 11879siesta: Edftu = 0.000000 11880siesta: Eso = 0.000000 11881siesta: Ext. field = 0.000000 11882siesta: Exch.-corr. = -112.727041 11883siesta: Ion-electron = -1135.626479 11884siesta: Ion-ion = 15.846026 11885siesta: Ekinion = 0.097717 11886siesta: Total = -465.667070 11887siesta: Fermi = -1.829793 11888 11889siesta: Atomic forces (eV/Ang): 11890siesta: 1 -0.542424 -0.847938 -0.220926 11891siesta: 2 -0.579369 0.203037 -0.313582 11892siesta: 3 1.073763 0.429257 0.319370 11893siesta: ---------------------------------------- 11894siesta: Tot -0.048029 -0.215644 -0.215138 11895 11896siesta: Stress tensor (static) (eV/Ang**3): 11897siesta: 0.003057 0.000594 0.001140 11898siesta: 0.000593 -0.000711 0.000447 11899siesta: 0.001140 0.000447 0.000056 11900 11901siesta: Cell volume = 409.600000 Ang**3 11902 11903siesta: Pressure (static): 11904siesta: Solid Molecule Units 11905siesta: -0.00000872 0.00000173 Ry/Bohr**3 11906siesta: -0.00080082 0.00015908 eV/Ang**3 11907siesta: -1.28307235 0.25487437 kBar 11908(Free)E+ p_basis*V_orbitals = -465.179619 11909(Free)Eharris+ p_basis*V_orbitals = -465.179619 11910 11911siesta: Electric dipole (a.u.) = -0.119974 0.436779 -0.192833 11912siesta: Electric dipole (Debye) = -0.304943 1.110183 -0.490133 11913 11914cite: Please see "h2o.bib" for an exhaustive BiBTeX file. 11915cite: Please clearly indicate Siesta version in published work: v4.1-b4-351 11916cite: This calculation has made use of the following articles 11917cite: which are encouraged to be cited in a published work. 11918 Primary SIESTA paper 11919 DOI: www.doi.org/10.1088/0953-8984/14/11/302 11920 11921>> End of run: 22-JAN-2021 23:13:01 11922Job completed 11923