mirror of https://github.com/phonopy/phono3py.git
CRYSTAL interface for Phono3py
This commit is contained in:
Antti Karttunen
parent
4ee5251add
commit
7e5276a592
|
|
@ -103,6 +103,10 @@ Let ``kaccum`` read a Pwscf unit cell file with ``-c`` option, for example::
|
|||
|
||||
|ipwscf|
|
||||
|
||||
``--crystal``
|
||||
^^^^^^^^^^^^^
|
||||
|
||||
Analogous to ``--pwscf``, but to be used with the CRYSTAL interface.
|
||||
|
||||
``--temperature``
|
||||
^^^^^^^^^^^^^^^^^^
|
||||
|
|
|
|||
|
|
@ -0,0 +1,92 @@
|
|||
.. _crystal_interface:
|
||||
|
||||
CRYSTAL & phono3py calculation
|
||||
=============================
|
||||
|
||||
CRYSTAL program package has a robust built-in phonon calculation
|
||||
workflow for harmonic phonon properties. However, combining CRYSTAL
|
||||
with Phono3py enables convenient access to anharmonic phonon properties.
|
||||
|
||||
An example for CRYSTAL is found in the ``example/Si-CRYSTAL`` directory.
|
||||
|
||||
To invoke the CRYSTAL interface, ``--crystal`` option has to be always
|
||||
specified::
|
||||
|
||||
% phono3py --crystal [options] [arguments]
|
||||
|
||||
When the file name of the unit cell is different from the default one
|
||||
(see :ref:`default_unit_cell_file_name_for_calculator`), ``-c`` option
|
||||
is used to specify the file name. CRYSTAL unit cell file parser used in
|
||||
phono3py is the same as that in phonopy. It can read
|
||||
only limited number of keywords that are shown in the phonopy web site
|
||||
(http://atztogo.github.io/phonopy/crystal.html#crystal-interface).
|
||||
|
||||
.. _crystal_workflow:
|
||||
|
||||
Workflow
|
||||
---------
|
||||
|
||||
In this example (Si-CRYSTAL), the CRYSTAL output file is crystal.o.
|
||||
This is the default file name for the CRYSTAL interface,
|
||||
so the -c crystal.o parameter is not needed.
|
||||
|
||||
1) Create supercells with displacements
|
||||
(4x4x4 for 2nd order FC, 2x2x2 for 3rd order FC)
|
||||
|
||||
::
|
||||
|
||||
% phono3py --crystal --dim="2 2 2" --dim_fc2="4 4 4" -d
|
||||
|
||||
57 supercell files (``supercell-xxx.d12/.ext``) for the third order
|
||||
force constants are created. In addition, one supercell file
|
||||
(``supercell_fc2-00001.d12/.ext``) is created for the second order
|
||||
force constants.
|
||||
|
||||
2) To make valid CRYSTAL input files, there are two possible options:
|
||||
|
||||
a) Manually: modify the generated supercell-xxx.d12 and supercell_fc2-xxxxx.d12
|
||||
files by replacing the line ``Insert basis sets and parameters here`` with the
|
||||
basis set and computational parameters.
|
||||
|
||||
b) Recommended option: before generating the supercells, include files named
|
||||
``TEMPLATE`` and ``TEMPLATE3`` in the current directory. These files should
|
||||
contain the basis sets and computational parameters for CRYSTAL (see the example).
|
||||
When phono3py finds these files it automatically generates complete
|
||||
CRYSTAL input files in the step 1.
|
||||
|
||||
Note that supercells with displacements must not be relaxed in the
|
||||
force calculations, because atomic forces induced by a small atomic
|
||||
displacement are what we need for phonon calculation. To get accurate
|
||||
forces, TOLDEE parameter should be 10 or higher. Phonopy includes this
|
||||
parameter and the necessary GRADCAL keyword automatically in the inputs.
|
||||
|
||||
Then, CRYSTAL supercell calculations are executed to obtain forces on
|
||||
atoms, e.g., as follows::
|
||||
|
||||
% runcry14 supercell-001.d12
|
||||
|
||||
3) Collect forces in ``FORCES_FC3`` and ``FORCES_FC2``::
|
||||
|
||||
% phono3py --crystal --cf3 supercell-*o
|
||||
|
||||
% phono3py --crystal --cf2 supercell_fc2-*o
|
||||
|
||||
``disp_fc3.yaml`` and ``disp_fc2.yaml`` are used to create ``FORCES_FC3`` and
|
||||
``FORCES_FC2``, therefore they must exist in current directory.
|
||||
|
||||
4) Calculate 3rd and 2nd order force constants in files ``fc3.hdf5`` and ``fc2.hdf5``::
|
||||
|
||||
% phono3py --crystal --dim="2 2 2" --dim_fc2="4 4 4" --sym_fc3r --sym_fc2 --tsym
|
||||
|
||||
``--sym_fc2``, ``--sym_fc3r``, and ``--tsym`` are used to symmetrize second- and third-order
|
||||
force constants.
|
||||
|
||||
5) Thermal conductivity calculation::
|
||||
|
||||
% phono3py --crystal --fc3 --fc2 --dim="2 2 2" --dim_fc2="4 4 4" --mesh="20 20 20" --br
|
||||
|
||||
``--br`` invokes the Relaxation Time Approximation.
|
||||
Add ``--isotope`` for isotope scattering.
|
||||
Check the effect of ``--nac`` for polar systems.
|
||||
Carefully test the convergence with respect to ``--mesh``!
|
||||
|
||||
|
|
@ -15,8 +15,8 @@ The theoretical background is summarized in the paper found at
|
|||
http://dx.doi.org/10.1103/PhysRevB.91.094306 or the draft in arxiv at
|
||||
http://arxiv.org/abs/1501.00691 .
|
||||
|
||||
:ref:`Interfaces to calculators <calculator_interfaces>` for VASP and
|
||||
pwscf are built-in.
|
||||
:ref:`Interfaces to calculators <calculator_interfaces>` for VASP,
|
||||
pwscf, and CRYSTAL are built-in.
|
||||
|
||||
|
||||
Documentation
|
||||
|
|
@ -30,6 +30,7 @@ Documentation
|
|||
interfaces
|
||||
vasp
|
||||
pwscf
|
||||
crystal
|
||||
command-options
|
||||
output-files
|
||||
tips
|
||||
|
|
|
|||
|
|
@ -3,16 +3,17 @@
|
|||
Interfaces to calculators
|
||||
==========================
|
||||
|
||||
Currently the built-in interfaces for VASP and Pwscf are
|
||||
Currently the built-in interfaces for VASP, Pwscf, and CRYSTAL are
|
||||
prepared. VASP is the default interface and no special option is
|
||||
necessary to invoke it, but for the other interfaces, each special
|
||||
option has to be specified, e.g. ``--pwscf``.
|
||||
option has to be specified, e.g. ``--pwscf`` or ``--crystal``.
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 1
|
||||
|
||||
vasp
|
||||
pwscf
|
||||
crystal
|
||||
|
||||
Calculator specific behaviors
|
||||
------------------------------
|
||||
|
|
@ -20,7 +21,7 @@ Calculator specific behaviors
|
|||
Physical unit
|
||||
^^^^^^^^^^^^^^
|
||||
|
||||
The interfaces for VASP and Pwscf are built in to the phono3py command.
|
||||
The interfaces for VASP, Pwscf, and CRYSTAL are built in to the phono3py command.
|
||||
|
||||
For each calculator, each physical unit system is used. The physical
|
||||
unit systems used for the calculators are summarized below.
|
||||
|
|
@ -31,6 +32,7 @@ unit systems used for the calculators are summarized below.
|
|||
-----------------------------------------------
|
||||
VASP | Angstrom eV/Angstrom Angstrom
|
||||
Pwscf | au (bohr) Ry/au au
|
||||
CRYSTAL | Angstrom eV/Angstrom Angstrom
|
||||
|
||||
``FORCES_FC2`` and ``disp_fc2.yaml`` have the same physical units as
|
||||
``FORCES_FC3`` and ``disp_fc3.yaml``, respectively.
|
||||
|
|
@ -44,6 +46,7 @@ Default unit cell file names are also changed according to the calculators::
|
|||
|
||||
VASP | POSCAR
|
||||
Pwscf | unitcell.in
|
||||
CRYSTAL | crystal.o
|
||||
|
||||
|
||||
.. _default_displacement_distance_for_calculator:
|
||||
|
|
@ -56,5 +59,6 @@ Default displacement distances created by ``-d`` option without
|
|||
|
||||
VASP | 0.03 Angstrom
|
||||
Pwscf | 0.06 au (bohr)
|
||||
CRYSTAL | 0.03 Angstrom
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,130 @@
|
|||
# File: 1
|
||||
# 1 0.0000000000000000 0.0212132034355964 0.0212132034355964
|
||||
0.0150976605 -0.3163819396 -0.3163819277
|
||||
-0.0054602591 0.0087171452 0.0087171442
|
||||
-0.0000437632 0.0008860815 0.0008860764
|
||||
0.0054065797 0.0084647803 0.0084647870
|
||||
0.0072700323 -0.0134898680 0.0067130300
|
||||
-0.0003425048 0.0005255843 0.0002913698
|
||||
0.0001092286 0.0002141440 0.0007133425
|
||||
-0.0072386504 0.0068925342 -0.0135907834
|
||||
0.0007938985 -0.0037625558 0.0001684110
|
||||
-0.0000019785 0.0008487945 0.0008448124
|
||||
-0.0007262144 0.0000923840 -0.0037863325
|
||||
-0.0000744613 0.0008682887 0.0008075646
|
||||
0.0019126545 -0.0081228720 0.0013522477
|
||||
-0.0017805163 0.0014261364 -0.0080896560
|
||||
0.0003798291 0.0003711173 0.0004988628
|
||||
-0.0002242597 0.0005713680 0.0005128868
|
||||
0.0072700223 0.0067130253 -0.0134898717
|
||||
-0.0003425079 0.0002913515 0.0005255850
|
||||
0.0001092128 0.0007133426 0.0002141419
|
||||
-0.0072386408 -0.0135907884 0.0068925378
|
||||
0.0005934919 -0.0005295764 -0.0005295749
|
||||
0.0001049676 0.0002369483 0.0002369366
|
||||
-0.0005117262 -0.0003186875 -0.0003187059
|
||||
0.0000840176 0.0004934495 0.0004934474
|
||||
0.0010350740 -0.0002178299 -0.0002995492
|
||||
-0.0010624196 -0.0003010124 -0.0001827984
|
||||
0.0000354204 0.0002497281 0.0002187150
|
||||
-0.0000141969 0.0002453053 0.0002632214
|
||||
0.0000450642 -0.0004972834 -0.0004029749
|
||||
-0.0000524363 0.0002264256 0.0005114953
|
||||
0.0000289109 0.0002329099 0.0002180236
|
||||
0.0000021968 0.0005288888 0.0000998905
|
||||
0.0007939085 0.0001684174 -0.0037625284
|
||||
-0.0000019764 0.0008448116 0.0008487883
|
||||
-0.0007261914 -0.0037863172 0.0000923906
|
||||
-0.0000744374 0.0008075691 0.0008682961
|
||||
0.0010350876 -0.0002995289 -0.0002178050
|
||||
-0.0010624364 -0.0001828011 -0.0003010229
|
||||
0.0000354084 0.0002187104 0.0002497348
|
||||
-0.0000141760 0.0002632292 0.0002453116
|
||||
0.0000000994 -0.0006325457 -0.0006325633
|
||||
-0.0000454780 0.0002348777 0.0002348755
|
||||
-0.0000009003 0.0001879496 0.0001879511
|
||||
0.0000413368 0.0002230884 0.0002230796
|
||||
0.0008636117 -0.0004790172 0.0000087743
|
||||
0.0000370405 0.0002134394 0.0002881943
|
||||
-0.0000284279 0.0002670895 0.0001800384
|
||||
-0.0008616020 -0.0000621134 -0.0004043397
|
||||
0.0019126494 0.0013522302 -0.0081228984
|
||||
-0.0017805242 -0.0080896598 0.0014261211
|
||||
0.0003798274 0.0004988624 0.0003711110
|
||||
-0.0002242478 0.0005129134 0.0005713888
|
||||
0.0000450575 -0.0004029829 -0.0004972923
|
||||
-0.0000524277 0.0005115123 0.0002264515
|
||||
0.0000289057 0.0002180064 0.0002329146
|
||||
0.0000021909 0.0000998951 0.0005288889
|
||||
0.0008636298 0.0000087886 -0.0004790212
|
||||
0.0000370343 0.0002881816 0.0002134153
|
||||
-0.0000284308 0.0001800532 0.0002670926
|
||||
-0.0008615816 -0.0004043475 -0.0000621283
|
||||
0.0009096140 -0.0002923207 -0.0002923132
|
||||
-0.0000546316 0.0005483269 0.0005483302
|
||||
-0.0008528723 -0.0003736493 -0.0003736575
|
||||
-0.0000135065 0.0001383702 0.0001383687
|
||||
0.0940259460 0.1237610724 0.1237610697
|
||||
-0.1074750502 0.1335935647 0.1335935642
|
||||
0.0020945508 0.0009774950 0.0009774937
|
||||
-0.0020997064 0.0008164474 0.0008164484
|
||||
-0.0010921579 0.0287655206 0.0273879080
|
||||
-0.0000522363 -0.0011793956 -0.0011964612
|
||||
0.0000208779 -0.0000333893 -0.0000131292
|
||||
0.0001807783 -0.0009937077 -0.0013565717
|
||||
0.0014352883 0.0055844176 0.0015188572
|
||||
0.0002133943 -0.0005027673 -0.0001882659
|
||||
-0.0001833857 -0.0002482003 -0.0005296154
|
||||
-0.0013943858 0.0015136065 0.0056748094
|
||||
-0.0006869295 0.0034637249 -0.0006008870
|
||||
0.0000668131 -0.0012068723 -0.0011016380
|
||||
0.0005802701 -0.0004550163 0.0036036305
|
||||
-0.0000749226 -0.0011125598 -0.0010105746
|
||||
-0.0010921532 0.0273879145 0.0287655199
|
||||
-0.0000522324 -0.0011964548 -0.0011793946
|
||||
0.0000208783 -0.0000131238 -0.0000333828
|
||||
0.0001807778 -0.0013565643 -0.0009937115
|
||||
-0.0017853483 0.0002405606 0.0002405642
|
||||
-0.0000697686 -0.0002833354 -0.0002833353
|
||||
-0.0000605993 -0.0001692702 -0.0001692786
|
||||
0.0016146737 0.0000616185 0.0000616178
|
||||
-0.0004760496 0.0002192043 0.0005034363
|
||||
-0.0000114179 -0.0002176520 -0.0002235621
|
||||
0.0005429647 0.0004721528 0.0001815748
|
||||
0.0000080300 -0.0003476301 -0.0003363376
|
||||
-0.0014247595 0.0002591475 0.0006096810
|
||||
0.0014241416 0.0005866693 0.0002821379
|
||||
-0.0000007649 -0.0001211218 -0.0003392563
|
||||
0.0000239044 -0.0003227733 -0.0000958257
|
||||
0.0014352846 0.0015188592 0.0055844268
|
||||
0.0002133920 -0.0001882723 -0.0005027777
|
||||
-0.0001833792 -0.0005295925 -0.0002481861
|
||||
-0.0013943904 0.0056747942 0.0015135890
|
||||
-0.0004760461 0.0005034376 0.0002192074
|
||||
-0.0000114126 -0.0002235620 -0.0002176541
|
||||
0.0005429525 0.0001815609 0.0004721516
|
||||
0.0000080328 -0.0003363289 -0.0003476229
|
||||
-0.0007153041 0.0002881965 0.0002881946
|
||||
0.0007123602 0.0002895198 0.0002895263
|
||||
0.0000322988 -0.0002152397 -0.0002152371
|
||||
-0.0000439948 -0.0002241525 -0.0002241513
|
||||
0.0000140268 0.0001155596 0.0000947410
|
||||
0.0000503583 -0.0001306265 -0.0003834122
|
||||
0.0000068092 -0.0002562272 -0.0002560770
|
||||
-0.0000269462 -0.0003764980 -0.0001375593
|
||||
-0.0006869303 -0.0006008874 0.0034637282
|
||||
0.0000668006 -0.0011016604 -0.0012068846
|
||||
0.0005802619 0.0036036250 -0.0004550103
|
||||
-0.0000749057 -0.0010105654 -0.0011125428
|
||||
-0.0014247567 0.0006096877 0.0002591561
|
||||
0.0014241380 0.0002821414 0.0005866699
|
||||
-0.0000007783 -0.0003392669 -0.0001211442
|
||||
0.0000238925 -0.0000958317 -0.0003227683
|
||||
0.0000140314 0.0000947461 0.0001155809
|
||||
0.0000503497 -0.0003834264 -0.0001306401
|
||||
0.0000068086 -0.0002560744 -0.0002562210
|
||||
-0.0000269567 -0.0001375724 -0.0003764931
|
||||
-0.0013902779 0.0003019739 0.0003019710
|
||||
0.0000320540 -0.0003584461 -0.0003584451
|
||||
-0.0000157402 -0.0003775628 -0.0003775495
|
||||
0.0013912666 0.0003560504 0.0003560465
|
||||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,29 @@
|
|||
Si lattice thermal conductivity
|
||||
|
||||
CRYSTAL output file is crystal.o. This is the default file name
|
||||
for the CRYSTAL interface, so the -c crystal.o parameter is not needed
|
||||
|
||||
1) Create displaced supercells:
|
||||
(4x4x4 for 2nd order FC, 2x2x2 for 3rd order FC)
|
||||
phono3py --crystal --dim="2 2 2" --dim_fc2="4 4 4" -d
|
||||
Complete CRYSTAL inputs can be prepared manually
|
||||
or with the help of a template
|
||||
(TEMPLATE for FC2-supercells, TEMPLATE3 for FC3-supercells)
|
||||
|
||||
2) Run the supercell input with CRYSTAL
|
||||
Here the supercells have been pre-calculated (outputs.tar.gz).
|
||||
|
||||
3) Collect forces:
|
||||
phono3py --crystal --cf3 supercell-*o
|
||||
phono3py --crystal --cf2 supercell_fc2-*o
|
||||
(Here the pre-calculated forces are available as FORCES_FC2 and FORCES_FC3)
|
||||
|
||||
4) Create force constant files fc2.hdf5 and fc3.hdf5:
|
||||
phono3py --crystal --dim="2 2 2" --dim_fc2="4 4 4" --sym_fc3r --sym_fc2 --tsym
|
||||
|
||||
5) Thermal conductivity calculation:
|
||||
phono3py --crystal --fc3 --fc2 --dim="2 2 2" --dim_fc2="4 4 4" --mesh="20 20 20" --br
|
||||
--br -> Relaxation time approximation
|
||||
Add --isotope for isotope scattering
|
||||
Check the effect of --nac for polar systems
|
||||
|
||||
|
|
@ -0,0 +1,45 @@
|
|||
14 7
|
||||
0 0 5 2.0 1.0
|
||||
6903.7118686 0.13373962995E-02
|
||||
1038.4346419 0.99966546241E-02
|
||||
235.87581480 0.44910165101E-01
|
||||
66.069385169 0.11463638540
|
||||
20.247945761 0.10280063858
|
||||
0 0 3 2.0 1.0
|
||||
34.353481730 0.70837285010E-01
|
||||
3.6370788192 -0.43028836252
|
||||
1.4002048599 -0.41382774969
|
||||
0 0 1 2.0 1.0
|
||||
0.25943211957 1.0000000000
|
||||
0 1 1 0.0 1.0
|
||||
0.12000000000 1.0 1.0
|
||||
0 2 5 6.0 1.0
|
||||
179.83907373 0.61916656462E-02
|
||||
41.907258846 0.43399431982E-01
|
||||
12.955294367 0.15632019351
|
||||
4.4383267393 0.29419996982
|
||||
1.5462247904 0.23536823814
|
||||
0 2 1 2.0 1.0
|
||||
0.40981363585 1.0000000000
|
||||
0 3 1 0.0 1.0
|
||||
0.35000000000 1.0000000000
|
||||
99 0
|
||||
ENDBAS
|
||||
DFT
|
||||
PBE0
|
||||
END
|
||||
SHRINK
|
||||
1 1
|
||||
TOLINTEG
|
||||
8 8 8 8 16
|
||||
MAXCYCLE
|
||||
60
|
||||
FMIXING
|
||||
80
|
||||
BROYDEN
|
||||
0.01 50 4
|
||||
NOSHIFT
|
||||
EXCHSIZE
|
||||
30000000
|
||||
BIPOSIZE
|
||||
30000000
|
||||
|
|
@ -0,0 +1,45 @@
|
|||
14 7
|
||||
0 0 5 2.0 1.0
|
||||
6903.7118686 0.13373962995E-02
|
||||
1038.4346419 0.99966546241E-02
|
||||
235.87581480 0.44910165101E-01
|
||||
66.069385169 0.11463638540
|
||||
20.247945761 0.10280063858
|
||||
0 0 3 2.0 1.0
|
||||
34.353481730 0.70837285010E-01
|
||||
3.6370788192 -0.43028836252
|
||||
1.4002048599 -0.41382774969
|
||||
0 0 1 2.0 1.0
|
||||
0.25943211957 1.0000000000
|
||||
0 1 1 0.0 1.0
|
||||
0.12000000000 1.0 1.0
|
||||
0 2 5 6.0 1.0
|
||||
179.83907373 0.61916656462E-02
|
||||
41.907258846 0.43399431982E-01
|
||||
12.955294367 0.15632019351
|
||||
4.4383267393 0.29419996982
|
||||
1.5462247904 0.23536823814
|
||||
0 2 1 2.0 1.0
|
||||
0.40981363585 1.0000000000
|
||||
0 3 1 0.0 1.0
|
||||
0.35000000000 1.0000000000
|
||||
99 0
|
||||
ENDBAS
|
||||
DFT
|
||||
PBE0
|
||||
END
|
||||
SHRINK
|
||||
4 4
|
||||
TOLINTEG
|
||||
8 8 8 8 16
|
||||
MAXCYCLE
|
||||
60
|
||||
FMIXING
|
||||
80
|
||||
BROYDEN
|
||||
0.01 50 4
|
||||
NOSHIFT
|
||||
EXCHSIZE
|
||||
30000000
|
||||
BIPOSIZE
|
||||
30000000
|
||||
Binary file not shown.
Binary file not shown.
|
|
@ -52,6 +52,8 @@ def create_phono3py_supercells(unitcell,
|
|||
if displacement_distance is None:
|
||||
if interface_mode == 'pwscf':
|
||||
distance = 0.06
|
||||
elif interface_mode == 'crystal':
|
||||
distance = 0.03
|
||||
else:
|
||||
distance = 0.03
|
||||
else:
|
||||
|
|
@ -88,6 +90,14 @@ def create_phono3py_supercells(unitcell,
|
|||
cells_with_disps,
|
||||
pp_filenames,
|
||||
width=5)
|
||||
elif interface_mode == 'crystal':
|
||||
conv_numbers = optional_structure_file_information[1]
|
||||
write_supercells_with_displacements(supercell,
|
||||
cells_with_disps,
|
||||
conv_numbers,
|
||||
supercell_matrix,
|
||||
width=5,
|
||||
template_file="TEMPLATE3")
|
||||
else:
|
||||
write_supercells_with_displacements(supercell,
|
||||
cells_with_disps,
|
||||
|
|
@ -120,6 +130,15 @@ def create_phono3py_supercells(unitcell,
|
|||
pp_filenames,
|
||||
pre_filename="supercell_fc2",
|
||||
width=5)
|
||||
elif interface_mode == 'crystal':
|
||||
conv_numbers = optional_structure_file_information[1]
|
||||
write_supercells_with_displacements(phonon_supercell,
|
||||
cells_with_disps,
|
||||
conv_numbers,
|
||||
phonon_supercell_matrix,
|
||||
pre_filename="supercell_fc2",
|
||||
width=5,
|
||||
template_file="TEMPLATE")
|
||||
else:
|
||||
write_supercells_with_displacements(phonon_supercell,
|
||||
cells_with_disps,
|
||||
|
|
|
|||
|
|
@ -41,6 +41,7 @@ def get_parser():
|
|||
band_points=None,
|
||||
cell_filename=None,
|
||||
constant_averaged_pp_interaction=None,
|
||||
crystal_mode=False,
|
||||
cutoff_fc3_distance=None,
|
||||
cutoff_frequency=None,
|
||||
boundary_mfp=None,
|
||||
|
|
@ -173,6 +174,11 @@ def get_parser():
|
|||
dest="constant_averaged_pp_interaction",
|
||||
type="float",
|
||||
help="Set constant averaged ph-ph interaction (Pqj)")
|
||||
parser.add_option(
|
||||
"--crystal",
|
||||
dest="crystal_mode",
|
||||
action="store_true",
|
||||
help="Invoke CRYSTAL mode")
|
||||
parser.add_option(
|
||||
"--cutoff_fc3", "--cutoff_fc3_distance",
|
||||
dest="cutoff_fc3_distance", type="float",
|
||||
|
|
|
|||
|
|
@ -265,11 +265,12 @@ class Phono3pyYaml(object):
|
|||
# Abinit | au (bohr) AMU eV/Angstrom eV/Angstrom.au
|
||||
# Siesta | au (bohr) AMU eV/Angstrom eV/Angstrom.au
|
||||
# elk | au (bohr) AMU hartree/au hartree/au^2
|
||||
# CRYSTAL | Angstrom AMU eV/Angstrom eV/Angstrom^2
|
||||
|
||||
lines = []
|
||||
if self._calculator in ['wien2k', 'abinit', 'elk', 'pwscf', 'siesta']:
|
||||
lines.append(" length: au")
|
||||
elif self._calculator == 'vasp':
|
||||
elif self._calculator in ['vasp', 'crystal']:
|
||||
lines.append(" length: Angstrom")
|
||||
|
||||
if len(lines) > 0:
|
||||
|
|
|
|||
|
|
@ -350,12 +350,16 @@ if __name__ == '__main__':
|
|||
help='Use smearing method (only for scalar density)')
|
||||
parser.add_argument('--pwscf', dest="pwscf_mode",
|
||||
action="store_true", help="Invoke Pwscf mode")
|
||||
parser.add_argument('--crystal', dest="crystal_mode",
|
||||
action="store_true", help="Invoke CRYSTAL mode")
|
||||
parser.add_argument('filenames', nargs='*')
|
||||
args = parser.parse_args()
|
||||
|
||||
interface_mode = None
|
||||
if args.pwscf_mode:
|
||||
interface_mode = 'pwscf'
|
||||
elif args.crystal_mode:
|
||||
interface_mode = 'crystal'
|
||||
if len(args.filenames) > 1:
|
||||
cell, _ = read_crystal_structure(args.filenames[0],
|
||||
interface_mode=interface_mode)
|
||||
|
|
|
|||
|
|
@ -94,12 +94,18 @@ if options.log_level is not None:
|
|||
# Physical units: energy, distance, atomic mass, force
|
||||
# vasp : eV, Angstrom, AMU, eV/Angstrom
|
||||
# pwscf : Ry, au, AMU, Ry/au
|
||||
# CRYSTAL : eV, Angstrom, AMU, eV/Angstrom
|
||||
#
|
||||
if options.pwscf_mode:
|
||||
interface_mode = 'pwscf'
|
||||
from phonopy.interface.pwscf import write_supercells_with_displacements
|
||||
energy_to_eV = Rydberg
|
||||
distance_to_A = Bohr
|
||||
if options.crystal_mode:
|
||||
interface_mode = 'crystal'
|
||||
from phonopy.interface.crystal import write_supercells_with_displacements
|
||||
energy_to_eV = None
|
||||
distance_to_A = None
|
||||
else:
|
||||
interface_mode = 'vasp'
|
||||
from phonopy.interface.vasp import write_supercells_with_displacements
|
||||
|
|
|
|||
Loading…
Reference in New Issue