1.. _command_options: 2 3Command options / Setting tags 4================================= 5 6Phono3py is operated with command options or with a configuration file 7that contains setting tags. In this page, the command options are 8explained. Most of command options have their respective setting 9tags. 10 11A configuration file with setting tags like phonopy can be used 12instead of and together with the command options. The setting tags are 13mostly equivalent to the respective most command options, but when 14both are set simultaneously, the command options are preferred. An 15example of configuration (e.g., saved in a file ``setting.conf``) is 16as follow:: 17 18 DIM = 2 2 2 19 DIM_FC2 = 4 4 4 20 PRIMITIVE_AXES = 0 1/2 1/2 1/2 0 1/2 1/2 1/2 0 21 MESH = 11 11 11 22 BTERTA = .TRUE. 23 NAC = .TRUE. 24 READ_FC2 = .TRUE. 25 READ_FC3 = .TRUE. 26 CELL_FILENAME = POSCAR-unitcell 27 28where the setting tag names are case insensitive. This is run by 29 30:: 31 32 % phono3py setting.conf [comannd options] 33 34or 35 36:: 37 38 % phono3py [comannd options] -- setting.conf 39 40 41.. contents:: 42 :depth: 2 43 :local: 44 45Input cell file name 46-------------------- 47 48``-c`` (``CELL_FILENAME``) 49~~~~~~~~~~~~~~~~~~~~~~~~~~ 50 51This specifies input unit cell filename. 52 53:: 54 55 % phono3py -c POSCAR-unitcell ... (many options) 56 57Calculator interface 58--------------------- 59 60``--qe`` (``CALCULATOR = QE``) 61~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 62 63Quantum espresso (pw) interface is invoked. 64See the detail at :ref:`qe_interface`. 65 66``--crystal`` (``CALCULATOR = CRYSTAL``) 67~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 69CRYSTAL interface is invoked. 70See the detail at :ref:`crystal_interface`. 71 72``--turbomole`` (``CALCULATOR = TURBOMOLE``) 73~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 74 75TURBOMOLE interface is invoked. 76See the details at :ref:`turbomole_interface`. 77 78Utilities to create default input files 79---------------------------------------- 80 81These options have no respective configuration file tags. 82 83``--cf3`` (command option only) 84~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 86This is used to create ``FORCES_FC3`` from ``disp_fc3.yaml`` and 87force calculator outputs containing forces in supercells. ``disp_fc3.yaml`` 88has to be located at the current directory. Calculator interface has 89to be specified except for VASP (default) case. 90 91:: 92 93 % phono3py --cf3 disp-{00001..00755}/vasprun.xml 94 95:: 96 97 % phono3py --qe --cf3 supercell_out/disp-{00001..00111}/Si.out 98 99.. _cf3_file_option: 100 101``--cf3-file`` (command option only) 102~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 103 104This is used to create ``FORCES_FC3`` from a text file containing a 105list of calculator output file names. ``disp_fc3.yaml`` has to be 106located at the current directory. Calculator interface has to be 107specified except for VASP (default) case. 108 109:: 110 111 % phono3py --cf3-file file_list.dat 112 113where ``file_list.dat`` contains file names that can be recognized 114from the current directory and is expected to be like:: 115 116 disp-00001/vasprun.xml 117 disp-00002/vasprun.xml 118 disp-00003/vasprun.xml 119 disp-00004/vasprun.xml 120 ... 121 122The order of the file names is important. This option may be useful 123to be used together with ``--cutoff-pair`` option. 124 125.. _cf2_option: 126 127``--cf2`` (command option only) 128~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 129 130This is used to create ``FORCES_FC2`` similarly to ``--cf3`` 131option. ``disp_fc2.yaml`` has to be located at the current 132directory. This is optional. Calculator interface has to be specified 133except for VASP (default) case. ``FORCES_FC2`` is necessary to run 134with ``--dim-fc2`` option. 135 136:: 137 138 % phono3py --cf2 disp_fc2-{00001..00002}/vasprun.xml 139 140.. _cfz_option: 141 142``--cfz`` (command option only) 143~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 144 145This is used to create ``FORCES_FC3`` and ``FORCES_FC2`` subtracting 146residual forces combined with ``--cf3`` and ``--cf2``, 147respectively. Calculator interface has to be specified except for VASP 148(default) case. 149 150In the following example, it is supposed that 151``disp3-00000/vasprun.xml`` and ``disp2-00000/vasprun.xml`` contain 152the forces of the perfect supercells. In ideal case, these forces are 153zero, but often they are not. Here, this is called "residual 154forces". Sometimes quality of force constants is improved in this way. 155 156:: 157 158 % phono3py --cf3 disp3-{00001..01254}/vasprun.xml --cfz disp3-00000/vasprun.xml 159 % phono3py --cf2 disp2-{00001..00006}/vasprun.xml --cfz disp2-00000/vasprun.xml 160 161.. _fs2f2_option: 162 163``--fs2f2`` or ``--force-sets-to-forces-fc2`` (command option only) 164~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 165 166``FORCES_FC2`` and ``disp_fc2.yaml`` are created 167from phonopy's ``FORCE_SETS`` file. 168 169:: 170 171 % phono3py --fs2f2 172 173.. _cfs_option: 174 175``--cfs`` or ``--create-force-sets`` (command option only) 176~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 178Phonopy's ``FORCE_SETS`` is created from 179``FORCES_FC3`` and ``disp_fc3.yaml``. 180 181:: 182 183 % phono3py --cfs 184 185In conjunction with :ref:`--dim-fc2 <dim_fc2_option>`, phonopy's 186``FORCE_SETS`` is created from ``FORCES_FC2`` and ``disp_fc2.yaml`` 187instead of ``FORCES_FC3`` and ``disp_fc3.yaml``. 188 189:: 190 191 % phono3py --cfs --dim-fc2="x x x" 192 193Supercell and primitive cell 194---------------------------- 195 196.. _dim_option: 197 198``--dim`` (``DIM``) 199~~~~~~~~~~~~~~~~~~~ 200 201Supercell dimension is specified. See the 202detail at http://phonopy.github.io/phonopy/setting-tags.html#dim . 203 204.. _dim_fc2_option: 205 206``--dim-fc2`` (``DIM_FC2``) 207~~~~~~~~~~~~~~~~~~~~~~~~~~~ 208 209Supercell dimension for 2nd order force constants (for harmonic 210phonons) is specified. This is optional. 211 212A larger and different supercell size for 2nd order force constants 213than that for 3rd order force constants can be specified with this 214option. Often interaction between a pair of atoms has longer range in 215real space than interaction among three atoms. Therefore to reduce 216computational demand, choosing larger supercell size only for 2nd 217order force constants may be a good idea. 218 219Using this option with ``-d`` option, the structure files 220(e.g. ``POSCAR_FC2-xxxxx`` or equivalent files for the other 221interfaces) and ``disp_fc2.yaml`` are created. These are used to 222calculate 2nd order force constants for the larger supercell size and 223these force calculations have to be done in addition to the usual 224force calculations for 3rd order force constants. 225 226:: 227 228 phono3py -d --dim="2 2 2" --dim-fc2="4 4 4" -c POSCAR-unitcell 229 230After the force calculations, ``--cf2`` option is used to create 231``FORCES_FC2``. 232 233:: 234 235 phono3py --cf2 disp-{001,002}/vasprun.xml 236 237To calculate 2nd order force constants for the larger supercell size, 238``FORCES_FC2`` and ``disp_fc2.yaml`` are necessary. Whenever running 239phono3py for the larger 2nd order force constants, ``--dim-fc2`` 240option has to be specified. ``fc2.hdf5`` created as a result of 241running phono3py contains the 2nd order force constants with 242larger supercell size. The filename is the same as that created in the 243usual phono3py run without ``--dim-fc2`` option. 244 245:: 246 247 phono3py --dim="2 2 2" --dim_fc2="4 4 4" -c POSCAR-unitcell ... (many options) 248 249.. _pa_option: 250 251``--pa``, ``--primitive-axes`` (``PRIMITIVE_AXES``) 252~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 253 254Transformation matrix from a non-primitive cell to the primitive 255cell. See phonopy ``PRIMITIVE_AXES`` tag (``--pa`` option) at 256http://phonopy.github.io/phonopy/setting-tags.html#primitive-axis 257 258Displacement creation 259--------------------- 260 261.. _create_displacements_option: 262 263``-d`` (``CREATE_DISPLACEMENTS = .TRUE.``) 264~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 265 266Supercell with displacements are created. Using with ``--amplitude`` 267option, atomic displacement distances are controlled. With this 268option, files for supercells with displacements and ``disp_fc3.yaml`` 269file are created. 270 271.. _amplitude_option: 272 273``--amplitude`` (``DISPLACEMENT_DISTANCE``) 274~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 275 276Atomic displacement distance is specified. This 277value may be increased for the weak interaction systems and descreased 278when the force calculator is numerically very accurate. 279 280The default value depends on calculator. See 281:ref:`default_displacement_distance_for_calculator`. 282 283Force constants 284---------------- 285 286.. _compact_fc_option: 287 288``--cfc`` or ``--compact-fc`` (``COMPACT_FC = .TRUE.``) 289~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 290 291When creating force constants from ``FORCES_FC3`` and/or 292``FORCES_FC2``, force constants that use smaller data size are 293created. The shape of the data array is ``(num_patom, num_satom)`` for 294fc2 and ``(num_patom, num_satom, num_satom)`` for fc3, where 295``num_patom`` and ``num_satom`` are the numbers of atoms in primtive 296cell and supercell. In the full size force constants case, 297``num_patom`` is replaced by ``num_satom``. Therefore if the supercell 298dimension is large, this reduction of data size becomes large. If the 299input crystal structure has centring :ref:`--pa <pa_option>` is 300necessary to have smallest data size. In this case, ``--pa`` option 301has to be specified on reading. Otherwise phono3py can recognize if 302``fc2.hdf5`` and ``fc3.hdf5`` are compact or full automatically. When 303using with ``--sym-fc``, the calculated results will become slightly 304different due to imperfect symmetrization scheme that phono3py 305employs. 306 307:: 308 309 % phono3py --dim="2 2 2" --cfc --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" -c POSCAR-unitcell 310 311.. _symmetrization_option: 312 313``--sym-fc`` (``FC_SYMMETRY = .TRUE.``) 314~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 315 316Second- and third-order force constants are symmetrized. The index 317exchange of real space force constantsand translational invariance 318symmetry are applied in a simple way. This symmetrization just removes 319drift force constants evenly from all elements and then applies 320averaging index-exchange equivalent elements. Therefore the different 321symmetries are not simultaneously enforced. For better symmetrization, 322it is recommended to use an external force constants calculator like ALM. 323 324The symmetrizations for the second and third orders can be 325independently applied by ``--sym-fc2`` (``SYMMETRIZE_FC2 = .TRUE.``) 326and ``--sym-fc3r`` (``SYMMETRIZE_FC3 = .TRUE.``), , respectively. 327 328.. 329 ``--sym-fc3q`` symmetrizes third-order force constants in normal 330 coordinates by the index exchange. 331 332.. _cf3_option: 333 334``--cutoff-fc3`` or ``--cutoff-fc3-distance`` (``CUTOFF_FC3_DISTANCE``) 335~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 337This option is **not** used to reduce number of supercells with 338displacements, but this option is used to set zero in elements of 339given third-order force constants. The zero elements are selected by 340the condition that any pair-distance of atoms in each atom triplet is 341larger than the specified cut-off distance. 342 343If one wants to reduce number of supercells, the first choice is to 344reduce the supercell size and the second choice is using 345``--cutoff-pair`` option. 346 347.. _cutoff_pair_option: 348 349``--cutoff-pair`` or ``--cutoff-pair-distance`` (``CUTOFF_PAIR_DISTANCE``) 350~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 351 352This option is only used together with ``-d`` option. 353 354A cutoff pair-distance in a supercell is used to reduce the number of 355necessary supercells with displacements to obtain third order force 356constants. As the drawback, a certain number of 357third-order-force-constants elements are abandoned or computed with 358less numerical accuracy. More details are found in the following link: 359 360.. toctree:: 361 :maxdepth: 1 362 363 cutoff-pair 364 365Reciprocal space sampling mesh and grid points, and band indices 366----------------------------------------------------------------- 367 368``--mesh`` (``MESH`` or ``MESH_NUMBERS``) 369~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 370 371Mesh sampling grids in reciprocal space are generated with the 372specified numbers. This mesh is made along reciprocal axes and 373is always Gamma-centered. Except for that this mesh is always 374Gamma-centered, this works in the same way as written here, 375https://phonopy.github.io/phonopy/setting-tags.html#mesh-mp-or-mesh-numbers. 376 377.. 378 ``--md`` 379 ~~~~~~~~~ 380 381 Divisors of mesh numbers. Another sampling mesh is used to calculate 382 phonon lifetimes. :math:`8\times 8\times 8` mesh is used for the 383 calculation of phonon lifetimes when it is specified, e.g., 384 ``--mesh="11 11 11" --md="2 2 2"``. 385 386.. _gp_option: 387 388``--gp`` (``GRID_POINTS``) 389~~~~~~~~~~~~~~~~~~~~~~~~~~ 390 391Grid points are specified by their unique indices, e.g., for selecting 392the q-points where imaginary parts of self energees are 393calculated. For thermal conductivity calculation, this can be 394used to distribute its calculation over q-points (see 395:ref:`workload_distribution`). 396 397Indices of grid points are specified by space or comma (``,``) 398separated numbers. The mapping table between grid points to its 399indices is obtained by running with ``--loglevel=2`` option. 400 401:: 402 403 % phono3py --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" -c POSCAR-unitcell --mesh="19 19 19" --fc3 --fc2 --br --write-gamma --gp="0 1 2 3 4 5" 404 405where ``--gp="0 1 2 3 4 5"`` can be also written 406``--gp="0,1,2,3,4,5"``. ``--ga`` option below can be used similarly 407for the same purpose. 408 409.. _ga_option: 410 411``--ga`` (``GRID_ADDRESSES``) 412~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 413 414This is used to specify grid points like ``--gp`` option but in their 415addresses represented by integer numbers. For example with 416``--mesh="16 16 16"``, a q-point of (0.5, 0.5, 0.5) is given by 417``--ga="8 8 8"``. The values have to be integers. If you want to 418specify the point on a path, ``--ga="0 0 0 1 1 1 2 2 2 3 3 3 ..."``, 419where each three values are recogninzed as a grid point. The grid 420points given by ``--ga`` option are translated to grid point indices 421as given by ``--gp`` option, and the values given by ``--ga`` option 422will not be shown in log files. 423 424.. _bi_option: 425 426``--bi`` (``BAND_INDICES``) 427~~~~~~~~~~~~~~~~~~~~~~~~~~~ 428 429Band indices are specified. The output file name will be, e.g., 430``gammas-mxxx-gxx(-sx)-bx.dat`` where ``bxbx...`` shows the band 431indices used to be averaged. The calculated values at indices 432separated by space are averaged, and those separated by comma are 433separately calculated. 434 435:: 436 437 % phono3py --fc3 --fc2 --dim="2 2 2" --mesh="16 16 16" -c POSCAR-unitcell --nac --gp="34" --bi="4 5, 6" 438 439This may be also useful to distribute the computational demand 440such like that the unit cell is large and the calculation of 441phonon-phonon interaction is heavy. 442 443.. _wgp_option: 444 445``--wgp`` (command option only) 446~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 447 448Irreducible grid point indices and related information are written 449into ``ir_grid_points.yaml``. This information may be used when we 450want to distribute thermal conductivity calculation into small pieces 451or to find specific grid points to calculate imaginary part of self 452energy, for which :ref:`--gp option <gp_option>` can be used to 453specify the grid point indices. 454 455``grid_address-mxxx.hdf5`` is also written. This file contains all the 456grid points and their grid addresses in integers. Q-points 457corresponding to grid points are calculated divided these integers by 458sampling mesh numbers for respective reciprocal axes. 459 460:: 461 462 % phono3py --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" -c POSCAR-unitcell --mesh="19 19 19" --wgp 463 464.. _stp_option: 465 466``--stp`` (command option only) 467~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 468 469Numbers of q-point triplets to be calculated for irreducible grid 470points for specified sampling mesh numbers are shown. This can be used 471to estimate how large a calculation is. Only those for specific grid 472points are shown by using with ``--gp`` or ``--ga`` option. 473 474:: 475 476 % phono3py --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" -c POSCAR-unitcell --mesh="19 19 19" --stp --gp 20 477 478Brillouin zone integration 479--------------------------- 480 481.. _thm_option: 482 483``--thm`` (``TETRAHEDRON = .TRUE.``) 484~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 485 486Tetrahedron method is used for calculation of imaginary part of self 487energy. This is the default option. Therefore it is not necessary to 488specify this unless both results by tetrahedron method and 489smearing method in one time execution are expected. 490 491.. _sigma_option: 492 493``--sigma`` (``SIGMA``) 494~~~~~~~~~~~~~~~~~~~~~~~ 495 496:math:`\sigma` value of Gaussian function for smearing when 497calculating imaginary part of self energy. See the detail at 498:ref:`brillouinzone_sum`. 499 500Multiple :math:`\sigma` values are also specified by space separated 501numerical values. This is used when we want to test several 502:math:`\sigma` values simultaneously. 503 504.. _sigma_cutoff_option: 505 506``--sigma-cutoff`` (``SIGMA_CUTOFF_WIDTH``) 507~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 508 509The tails of the Gaussian functions that are used to replace delta 510functions in the equation shown at :ref:`--full-pp <full_pp_option>` 511are cut with this option. The value is specified in number of standard 512deviation. ``--sigma-cutoff=5`` gives the Gaussian functions to be cut 513at :math:`5\sigma`. Using this option scarifies the numerical 514accuracy. So the number has to be carefully tested. But computation of 515phonon-phonon interaction strength becomes much faster in exchange for 516it. 517 518.. _full_pp_option: 519 520``--full-pp`` (``FULL_PP = .TRUE.``) 521~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 522 523For thermal conductivity calculation using the linear tetrahedron 524method (from version 1.10.5) and smearing method with 525``--simga-cutoff`` (from version 1.12.3), only necessary elements 526(i.e., that have non-zero delta functions) of phonon-phonon interaction strength, 527:math:`\bigl|\Phi_{-\lambda\lambda'\lambda''}\bigl|^2`, is calculated 528due to delta functions in calculation of 529:math:`\Gamma_\lambda(\omega)`, 530 531.. math:: 532 533 \Gamma_\lambda(\omega) = \frac{18\pi}{\hbar^2} 534 \sum_{\lambda' \lambda''} 535 \bigl|\Phi_{-\lambda\lambda'\lambda''}\bigl|^2 536 \left\{(n_{\lambda'}+ n_{\lambda''}+1) 537 \delta(\omega-\omega_{\lambda'}-\omega_{\lambda''}) \right. 538 + (n_{\lambda'}-n_{\lambda''}) 539 \left[\delta(\omega+\omega_{\lambda'}-\omega_{\lambda''}) 540 - \left. \delta(\omega-\omega_{\lambda'}+\omega_{\lambda''}) 541 \right]\right\}. 542 543But using this option, full elements of phonon-phonon interaction 544strength are calculated and averaged phonon-phonon interaction 545strength (:math:`P_{\mathbf{q}j}`, see :ref:`--ave-pp 546<ave_pp_option>`) is also given and stored. 547 548Method to solve BTE 549------------------- 550 551``--br`` (``BTERTA = .TRUE.``) 552~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 553 554Run calculation of lattice thermal conductivity tensor with the single 555mode relaxation time approximation (RTA) and linearized phonon 556Boltzmann equation. Without specifying ``--gp`` (or ``--ga``) option, 557all necessary phonon lifetime calculations for grid points are 558sequentially executed and then thermal conductivity is calculated 559under RTA. The thermal conductivity and many related properties are 560written into ``kappa-mxxx.hdf5``. 561 562With ``--gp`` (or ``--ga``) option, 563phonon lifetimes on the specified grid points are calculated. To save 564the results, ``--write-gamma`` option has to be specified and the 565physical properties belonging to the grid 566points are written into ``kappa-mxxx-gx(-sx).hdf5``. 567 568``--lbte`` (``LBTE = .TRUE.``) 569~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 570 571Run calculation of lattice thermal conductivity tensor with a direct 572solution of linearized phonon Boltzmann equation. The basis usage of 573this option is equivalent to that of ``--br``. More detail is 574documented at :ref:`direct_solution`. 575 576Scattering 577---------- 578 579``--isotope`` (``ISOTOPE =.TRUE.``) 580~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 581 582Phonon-isotope scattering is calculated based on the formula by 583Shin-ichiro Tamura, Phys. Rev. B, **27**, 858 (1983). Mass variance 584parameters are read from database of the natural abundance data for 585elements, which refers Laeter *et al.*, Pure Appl. Chem., **75**, 683 586(2003). 587 588:: 589 590 % phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br --isotope 591 592``--mass-variances`` or ``--mv`` (``MASS_VARIANCES``) 593~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 594 595Mass variance parameters are specified by this option to include 596phonon-isotope scattering effect in the same way as ``--isotope`` 597option. For example of GaN, this may be set like ``--mv="1.97e-4 5981.97e-4 0 0"``. The number of elements has to correspond to the number 599of atoms in the primitive cell. 600 601Isotope effect to thermal conductivity may be checked first running 602without isotope calculation:: 603 604 % phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br 605 606Then running with isotope calculation:: 607 608 % phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br --read-gamma --mv="1.97e-4 1.97e-4 0 0" 609 610In the result hdf5 file, currently isotope scattering strength is not 611written out, i.e., ``gamma`` is still imaginary part of self energy of 612ph-ph scattering. 613 614``--boundary-mfp``, ``--bmfp`` (``BOUNDARY_MFP``) 615~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 616 617A most simple phonon boundary scattering treatment is 618included. :math:`v_g/L` is just used as the scattering rate, where 619:math:`v_g` is the group velocity and :math:`L` is the boundary mean 620free path. The value is given in micrometre. The default value, 1 621metre, is just used to avoid divergence of phonon lifetime and the 622contribution to the thermal conducitivity is considered negligible. 623 624.. _normal_umklapp_option: 625 626``--ave-pp`` (``USE_AVE_PP = .TRUE.``) 627~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 628 629Averaged phonon-phonon interaction strength (:math:`P_{\mathbf{q}j}=P_\lambda`) 630is used to calculate imaginary part of self energy in thermal 631conductivity calculation. :math:`P_\lambda` is defined as 632 633.. math:: 634 635 P_\lambda = \frac{1}{(3n_\text{a})^2}\sum_{\lambda' 636 \lambda''}|\Phi_{\lambda \lambda' \lambda''}|^2, 637 638where :math:`n_\text{a}` is the number of atoms in unit cell. This is 639roughly constant with respect to the sampling mesh density for 640converged :math:`|\Phi_{\lambda \lambda' \lambda''}|^2`. Then for all 641:math:`\mathbf{q}',j',j''`, 642 643.. math:: 644 645 |\Phi_{\mathbf{q}j,\mathbf{q}'j',\mathbf{G-q-q'}j''}|^2 := 646 P_{\mathbf{q}j} / N, 647 648where :math:`N` is the number of grid points on the sampling 649mesh. :math:`\Phi_{\lambda \lambda' \lambda''} \equiv 0` unless 650:math:`\mathbf{q} + \mathbf{q}' + \mathbf{q}'' = \mathbf{G}`. 651 652This option works only when ``--read-gamma`` 653and ``--br`` options are activated where the averaged phonon-phonon 654interaction that is read from ``kappa-mxxx(-sx-sdx).hdf5`` file is 655used if it exists in the file. Therefore the averaged phonon-phonon 656interaction has to be stored before using this option (see 657:ref:`--full-pp <full_pp_option>`). The calculation result **overwrites** 658``kappa-mxxx(-sx-sdx).hdf5`` file. Therefore to use this option 659together with ``-o`` option is strongly recommended. 660 661First, run full conductivity calculation, 662 663:: 664 665 % phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br 666 667Then 668 669:: 670 671 % phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br --read-gamma --ave-pp -o ave_pp 672 673``--const-ave-pp`` (``CONST_AVE_PP = .TRUE.``) 674~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 675 676Averaged phonon-phonon interaction (:math:`P_{\mathbf{q}j}`) is 677replaced by this constant value and :math:`|\Phi_{\lambda \lambda' 678\lambda''}|^2` are set as written in :ref:`--ave-pp <ave_pp_option>` for thermal 679conductivity calculation. This option works only when ``--br`` options 680are activated. Therefore third-order force constants are not necessary 681to input. The physical unit of the value is :math:`\text{eV}^2`. 682 683:: 684 685 % phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br --const-ave-pp=1e-10 686 687``--nu`` (``N_U = .TRUE.``) 688~~~~~~~~~~~~~~~~~~~~~~~~~~~ 689 690Integration over q-point triplets for the calculation of 691:math:`\Gamma_\lambda(\omega_\lambda)` is made separately for normal 692:math:`\Gamma^\text{N}_\lambda(\omega_\lambda)` and Umklapp 693:math:`\Gamma^\text{U}_\lambda(\omega_\lambda)` processes. The sum of 694them is usual :math:`\Gamma_\lambda(\omega_\lambda) = 695\Gamma^\text{N}_\lambda(\omega_\lambda) + 696\Gamma^\text{U}_\lambda(\omega_\lambda)` and this is used to calcualte 697thermal conductivity in single-mode RTA. The separation, i.e., the 698choice of G-vector, is made based on the first Brillouin zone. 699 700The data are stored in ``kappa-mxxx(-gx-sx-sdx).hdf5`` file and 701accessed by ``gamma_N`` and ``gamma_U`` keys. The shape of the arrays 702is the same as that of ``gamma`` (see 703:ref:`kappa_hdf5_file_gamma`). An example (Si-PBEsol) is shown below: 704 705:: 706 707 % phono3py --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" -c POSCAR-unitcell --mesh="11 11 11" --fc3 --fc2 --br --nu 708 ... 709 % ipython 710 711 In [1]: import h5py 712 713 In [2]: f = h5py.File("kappa-m111111.hdf5", 'r') 714 715 In [3]: list(f) 716 Out[3]: 717 ['frequency', 718 'gamma', 719 'gamma_N', 720 'gamma_U', 721 'group_velocity', 722 'gv_by_gv', 723 'heat_capacity', 724 'kappa', 725 'kappa_unit_conversion', 726 'mesh', 727 'mode_kappa', 728 'qpoint', 729 'temperature', 730 'weight'] 731 732 In [4]: f['gamma'].shape 733 Out[4]: (101, 56, 6) 734 735 In [5]: f['gamma_N'].shape 736 Out[5]: (101, 56, 6) 737 738 In [6]: f['gamma_U'].shape 739 Out[6]: (101, 56, 6) 740 741Temperature 742----------- 743 744.. _ts_option: 745 746``--ts`` (``TEMPERATURES``): Temperatures 747~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 748 749Specific temperatures are specified by ``--ts``. 750 751:: 752 753 % phono3py --fc3 --fc2 --dim="2 2 2" -v --mesh="11 11 11" -c POSCAR-unitcell --br --ts="200 300 400" 754 755``--tmax``, ``--tmin``, ``--tstep`` (``TMAX``, ``TMIN``, ``TSTEP``) 756~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 757 758Temperatures at equal interval are specified by ``--tmax``, 759``--tmin``, ``--tstep``. See phonopy's document for the same tags at 760http://phonopy.github.io/phonopy/setting-tags.html#tprop-tmin-tmax-tstep 761. 762 763:: 764 765 % phono3py --fc3 --fc2 --dim="2 2 2" -v --mesh="11 11 11" -c POSCAR-unitcell --br --tmin=100 --tmax=1000 --tstep=50 766 767Non-analytical term correction 768------------------------------ 769 770.. _nac_option: 771 772``--nac`` (``NAC = .TRUE.``) 773~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 774 775Non-analytical term correction for harmonic phonons. Like as phonopy, 776``BORN`` file has to be put on the same directory. Always the default 777value of unit conversion factor is used even if it is written in the 778first line of ``BORN`` file. 779 780``--q-direction`` (``Q_DIRECTION``) 781~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 782 783This is used with ``--nac`` to specify reciprocal-space direction 784at :math:`\mathbf{q}\rightarrow \mathbf{0}`. See the detail 785at http://phonopy.github.io/phonopy/setting-tags.html#q-direction . 786 787.. _write_gamma_option: 788 789Imaginary part of self energy 790----------------------------- 791 792.. _ise_option: 793 794``--ise`` (``IMAG_SELF_ENERGY = .TRUE.``) 795~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 796 797Imaginary part of self energy :math:`\Gamma_\lambda(\omega)` is 798calculated with respect to :math:`\omega`. The output is written to 799``gammas-mxxx-gx(-sx)-tx-bx.dat`` in THz (without :math:`2\pi`) 800with respect to frequency in THz (without :math:`2\pi`). Frequency sampling 801points can be specified by :ref:`freq_sampling_option`. 802 803:: 804 805 % phono3py --fc3 --fc2 --dim="2 2 2" --mesh="16 16 16" -c POSCAR-unitcell --nac --q-direction="1 0 0" --gp=0 --ise --bi="4 5, 6" 806 807Joint density of states 808----------------------- 809 810.. _jdos_option: 811 812``--jdos`` (``JOINT_DOS = .TRUE.``) 813~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 814 815Two classes of joint density of states (JDOS) are calculated. The 816result is written into ``jdos-mxxx-gx(-sx-sdx).dat`` in 817:math:`\text{THz}^{-1}` (without :math:`(2\pi)^{-1}`) with 818respect to frequency in THz (without :math:`2\pi`). Frequency sampling 819points can be specified by :ref:`freq_sampling_option`. 820 821The first column is the frequency, and the second and third columns 822are the values given as follows, respectively, 823 824.. math:: 825 826 &D_2^{(1)}(\mathbf{q}, \omega) = \frac{1}{N} 827 \sum_{\lambda',\lambda''} \Delta(-\mathbf{q}+\mathbf{q}'+\mathbf{q}'') 828 \left[\delta(\omega+\omega_{\lambda'}-\omega_{\lambda''}) + 829 \delta(\omega-\omega_{\lambda'}+\omega_{\lambda''}) \right], \\ 830 &D_2^{(2)}(\mathbf{q}, \omega) = \frac{1}{N} 831 \sum_{\lambda',\lambda''} 832 \Delta(-\mathbf{q}+\mathbf{q}'+\mathbf{q}'') \delta(\omega-\omega_{\lambda'} 833 -\omega_{\lambda''}). 834 835:: 836 837 % phono3py --fc2 --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" -c POSCAR-unitcell --mesh="16 16 16" --jdos --ga="0 0 0 8 8 8" 838 839When temperatures are specified, two classes of weighted JDOS are 840calculated. The result is written into 841``jdos-mxxx-gx(-sx)-txxx.dat`` in :math:`\text{THz}^{-1}` (without 842:math:`(2\pi)^{-1}`) with respect to frequency in THz (without 843:math:`2\pi`). In the file name, ``txxx`` shows the temperature. The 844first column is the frequency, and the second and third columns are 845the values given as follows, respectively, 846 847.. math:: 848 849 &N_2^{(1)}(\mathbf{q}, \omega) = \frac{1}{N} 850 \sum_{\lambda'\lambda''} \Delta(-\mathbf{q}+\mathbf{q}'+\mathbf{q}'') 851 (n_{\lambda'} - n_{\lambda''}) [ \delta( \omega + \omega_{\lambda'} - 852 \omega_{\lambda''}) - \delta( \omega - \omega_{\lambda'} + 853 \omega_{\lambda''})], \\ 854 &N_2^{(2)}(\mathbf{q}, \omega) = \frac{1}{N} 855 \sum_{\lambda'\lambda''} \Delta(-\mathbf{q}+\mathbf{q}'+\mathbf{q}'') 856 (n_{\lambda'}+ n_{\lambda''}+1) \delta( \omega - \omega_{\lambda'} - 857 \omega_{\lambda''}). 858 859:: 860 861 % phono3py --fc2 --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" -c POSCAR-unitcell --mesh="16 16 16" --jdos --ga="0 0 0 8 8 8" --ts=300 862 863This is an example of ``Si-PBEsol``. 864 865.. |Si-JDOS| image:: Si-JDOS.png 866 :width: 50% 867 868|Si-JDOS| 869 870 871Sampling frequency for distribution functions 872--------------------------------------------- 873 874.. _freq_sampling_option: 875 876``--num-freq-points``, ``--freq-pitch`` (``NUM_FREQUENCY_POINTS``) 877~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 878 879For spectrum like calculations of imaginary part of self energy and 880JDOS, number of sampling frequency points is controlled by 881``--num-freq-points`` or ``--freq-pitch``. 882 883.. _ave_pp_option: 884 885 886Mode-Gruneisen parameter from 3rd order force constants 887------------------------------------------------------- 888 889``--gruneisen`` (``GRUNEISEN = .TRUE.``) 890~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 891 892Mode-Gruneisen-parameters are calculated from fc3. 893 894Mesh sampling mode:: 895 896 % phono3py --fc3 --fc2 --dim="2 2 2" -v --mesh="16 16 16" -c POSCAR-unitcell --nac --gruneisen 897 898Band path mode:: 899 900 % phono3py --fc3 --fc2 --dim="2 2 2" -v -c POSCAR-unitcell --nac --gruneisen --band="0 0 0 0 0 1/2" 901 902File I/O 903-------- 904 905``--fc2`` (``READ_FC2 = .TRUE.``) 906~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 907 908Read 2nd order force constants from ``fc2.hdf5``. 909 910``--fc3`` (``READ_FC3 = .TRUE.``) 911~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 912 913Read 3rd order force constants from ``fc3.hdf5``. 914 915``--write-gamma`` (``WRITE_GAMMA = .TRUE.``) 916~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 917 918Imaginary parts of self energy at harmonic phonon frequencies 919:math:`\Gamma_\lambda(\omega_\lambda)` are written into file in hdf5 920format. The result is written into ``kappa-mxxx-gx(-sx-sdx).hdf5`` or 921``kappa-mxxx-gx-bx(-sx-sdx).hdf5`` with ``--bi`` option. With 922``--sigma`` and ``--sigma-cutoff`` options, ``-sx`` and ``--sdx`` are 923inserted, respectively, in front of ``.hdf5``. 924 925.. _read_gamma_option: 926 927``--read-gamma`` (``READ_GAMMA = .TRUE.``) 928~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 929 930Imaginary parts of self energy at harmonic phonon frequencies 931:math:`\Gamma_\lambda(\omega_\lambda)` 932are read from ``kappa`` file in hdf5 format. Initially the usual 933result file of ``kappa-mxxx(-sx-sdx).hdf5`` is searched. Unless it is 934found, it tries to read ``kappa`` file for each grid point, 935``kappa-mxxx-gx(-sx-sdx).hdf5``. Then, similarly, 936``kappa-mxxx-gx(-sx-sdx).hdf5`` not found, 937``kappa-mxxx-gx-bx(-sx-sdx).hdf5`` files for band indices are searched. 938 939.. _write_detailed_gamma_option: 940 941``--write-gamma-detail`` (``WRITE_GAMMA_DETAIL = .TRUE.``) 942~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 943 944Each q-point triplet contribution to imaginary part of self energy is 945written into ``gamma_detail-mxxx-gx(-sx-sdx).hdf5`` file. Be careful 946that this is large data. 947 948In the output file in hdf5, following keys are used to extract the 949detailed information. 950 951====================================== ============================================================================================================================================= 952gamma_detail for ``--ise`` (temperature, sampling frequency point, symmetry reduced set of triplets at a grid point, band1, band2, band3) in THz (without :math:`2\pi`) 953gamma_detail for ``--br`` (temperature, symmetry reduced set of triplets at a grid point, band1, band2, band3) in THz (without :math:`2\pi`) 954mesh Numbers of sampling mesh along reciprocal axes. 955frequency_point for ``--ise`` Sampling frequency points in THz (without :math:`2\pi`), i.e., :math:`\omega` in :math:`\Gamma_\lambda(\omega)` 956temperature (temperature,), Temperatures in K 957triplet (symmetry reduced set of triplets at a grid point, 3), Triplets are given by the grid point indices (see below). 958weight (symmetry reduced set of triplets at a grid point,), Weight of each triplet to imaginary part of self energy 959====================================== ============================================================================================================================================= 960 961Imaginary part of self energy (linewidth/2) is recovered by the 962following script: 963 964.. code-block:: python 965 966 import h5py 967 import numpy as np 968 969 gd = h5py.File("gamma_detail-mxxx-gx.hdf5") 970 temp_index = 30 # index of temperature 971 temperature = gd['temperature'][temp_index] 972 gamma_tp = gd['gamma_detail'][:].sum(axis=-1).sum(axis=-1) 973 weight = gd['weight'][:] 974 gamma = np.dot(weight, gamma_tp[temp_index]) 975 976For example, for ``--br``, this ``gamma`` gives 977:math:`\Gamma_\lambda(\omega_\lambda)` of the band indices at the grid 978point indicated by :math:`\lambda` at the temperature of index 30. If 979any bands are degenerated, those ``gamma`` in 980``kappa-mxxx-gx(-sx-sdx).hdf5`` or ``gamma-mxxx-gx(-sx-sdx).hdf5`` 981type file are averaged, but the ``gamma`` obtained here in this way 982are not symmetrized. Apart from this symmetrization, the values must 983be equivalent between them. 984 985To understand each contribution of triptle to imaginary part of self 986energy, reading ``phonon-mxxx.hdf5`` is useful (see 987:ref:`write_phonon_option`). For example, 988phonon triplets of three phonon scatterings are obtained by 989 990.. code-block:: python 991 992 import h5py 993 import numpy as np 994 995 gd = h5py.File("gamma_detail-mxxx-gx.hdf5", 'r') 996 ph = h5py.File("phonon-mxxx.hdf5", 'r') 997 gp1 = gd['grid_point'][()] 998 triplets = gd['triplet'][:] # Sets of (gp1, gp2, gp3) where gp1 is fixed 999 mesh = gd['mesh'][:] 1000 grid_address = ph['grid_address'][:] 1001 q_triplets = grid_address[triplets] / mesh.astype('double') 1002 # Phonons of triplets[2] 1003 phonon_tp = [(ph['frequency'][i], ph['eigenvector'][i]) for i in triplets[2]] 1004 # Fractions of contributions of tripltes at this grid point and temperture index 30 1005 gamma_sum_over_bands = np.dot(weight, gd['gamma_detail'][30].sum(axis=-1).sum(axis=-1).sum(axis=-1)) 1006 contrib_tp = [gd['gamma_detail'][30, i].sum() / gamma_sum_over_bands for i in range(len(weight))] 1007 np.dot(weight, contrib_tp) # is one 1008 1009.. _write_phonon_option: 1010 1011``--write-phonon`` (``WRITE_PHONON = .TRUE.``) 1012~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1013 1014Phonon frequencies, eigenvectors, and grid point addresses are stored 1015in ``phonon-mxxx.hdf5`` file. :ref:`--pa <pa_option>` and :ref:`--nac 1016<nac_option>` may be required depending on calculation setting. 1017 1018:: 1019 1020 % phono3py --fc2 --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" --mesh="11 11 11" -c POSCAR-unitcell --nac --write-phoonon 1021 1022Contents of ``phonon-mxxx.hdf5`` are watched by:: 1023 1024 In [1]: import h5py 1025 1026 In [2]: ph = h5py.File("phonon-m111111.hdf5", 'r') 1027 1028 In [3]: list(ph) 1029 Out[3]: ['eigenvector', 'frequency', 'grid_address', 'mesh'] 1030 1031 In [4]: ph['mesh'][:] 1032 Out[4]: array([11, 11, 11], dtype=int32) 1033 1034 In [5]: ph['grid_address'].shape 1035 Out[5]: (1367, 3) 1036 1037 In [6]: ph['frequency'].shape 1038 Out[6]: (1367, 6) 1039 1040 In [7]: ph['eigenvector'].shape 1041 Out[7]: (1367, 6, 6) 1042 1043The first axis of ``ph['grid_address']``, ``ph['frequency']``, and 1044``ph['eigenvector']`` corresponds to the number of q-points where 1045phonons are calculated. Here the number of phonons may not be equal to 1046product of mesh numbers (:math:`1367 \neq 11^3`). This is because all 1047q-points on Brillouin zone boundary are included, i.e., even if 1048multiple q-points are translationally equivalent, those phonons are 1049stored separately though these phonons are physically equivalent 1050within the equations employed in phono3py. Here Brillouin zone is 1051defined by Wigner–Seitz cell of reciprocal primitive basis 1052vectors. This is convenient to categorize phonon triplets into Umklapp 1053and Normal scatterings based on the Brillouin zone. 1054 1055.. _read_phonon_option: 1056 1057``--read-phonon`` (``READ_PHONON = .TRUE.``) 1058~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1059 1060Phonon frequencies, eigenvectors, and grid point addresses are read 1061from ``phonon-mxxx.hdf5`` file and the calculation is continued using 1062these phonon values. This is useful when we want to use fixed phonon 1063eigenvectors that can be different for degenerate bands when using 1064different eigenvalue solvers or different CPU 1065architectures. :ref:`--pa <pa_option>` and :ref:`--nac <nac_option>` 1066may be required depending on calculation setting. 1067 1068:: 1069 1070 % phono3py --fc2 --fc3 --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" --mesh="11 11 11" -c POSCAR-unitcell --nac --read-phoonon --br 1071 1072.. _write_read_pp_option: 1073 1074``--write-pp`` (``WRITE_PP = .TRUE.``) and ``--read-pp`` (``READ_PP = .TRUE.``) 1075~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1076 1077Phonon-phonon (ph-ph) intraction strengths are written to and read 1078from ``pp-mxxx-gx.hdf5``. This works only in the calculation of 1079lattice thermal conductivity, i.e., usable only with ``--br`` or 1080``--lbte``. The stored data are different with and without specifying 1081``--full-pp`` option. In the former case, all the ph-ph interaction 1082strengths among considered phonon triplets are stored in a simple 1083manner, but in the later case, only necessary elements to calculate 1084collisions are stored in a complicated way. In the case of RTA 1085conductivity calculation, in writing and reading, ph-ph interaction 1086strength has to be stored in memory, so there is overhead in memory 1087than usual RTA calculation. 1088 1089:: 1090 1091 % phono3py --fc2 --fc3 --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" --mesh="11 11 11" -c POSCAR-unitcell --nac --write-pp --br --gp=1 1092 1093:: 1094 1095 % phono3py --fc2 --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" --mesh="11 11 11" -c POSCAR-unitcell --nac --read-pp --br --gp=1 1096 1097 1098.. _hdf5_compression_option: 1099 1100``--hdf5-compression`` (command option only) 1101~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1102 1103Most of phono3py HDF5 output file is compressed by default with the 1104``gzip`` compression filter. To avoid compression, 1105``--hdf5-compression=None`` has to be set. Other filters (``lzf`` or 1106integer values of 0 to 9) may be used, see h5py 1107documentation 1108(http://docs.h5py.org/en/stable/high/dataset.html#filter-pipeline). 1109 1110.. _output_filename_option: 1111 1112``-o`` (command option only) 1113~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1114 1115This modifies default output file names to write. 1116 1117Using this option, output file names are slightly modified. For example, 1118with ``-o iso``, a file name ``kappa-m191919.hdf5`` is changed 1119to ``kappa-m191919.iso.hdf5``. 1120 1121This rule is applied to 1122 1123- ``fc3.hdf5`` 1124- ``fc2.hdf5`` 1125- ``kappa-xxx.hdf5`` 1126- ``phonon-xxx.hdf5`` 1127- ``pp-xxx.hdf5`` 1128- ``disp_fc3.yaml`` 1129- ``disp_fc2.yaml`` 1130- ``gamma_detail-xxx.hdf5`` (write only) 1131 1132.. _input_filename_option: 1133 1134``-i`` (command option only) 1135~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1136 1137This modifies default input file names to read. 1138 1139Using this option, input file names are slightly modified. For example, 1140specifying ``-i iso --fc3``, a file name ``fc3.iso.hdf5`` is read 1141instead of ``fc3.hdf5``. 1142 1143This rule is applied to 1144 1145- ``fc3.hdf5`` 1146- ``fc2.hdf5`` 1147- ``kappa-xxx.hdf5`` 1148- ``phonon-xxx.hdf5`` 1149- ``pp-xxx.hdf5`` 1150- ``disp_fc3.yaml`` 1151- ``disp_fc2.yaml`` 1152 1153``--io`` (command option only) 1154~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1155 1156This modifies default input and output file names. 1157 1158This is equivalent to setting ``-i`` and ``-o`` simultaneously. 1159
