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Update document for --cf3_file

This commit is contained in:
Atsushi Togo 2017-04-02 13:27:20 +09:00
parent 30ef5b3b23
commit 916160b905
1 changed files with 50 additions and 2 deletions
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doc/command-options.rst
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@ -187,14 +187,36 @@ located at the current directory.
% phono3py --cf3 disp-{00001..00755}/vasprun.xml
``--cf3_file``: Create ``FORCES_FC3`` from file name list
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
This is used to create ``FORCES_FC3`` from a file name
list. ``disp_fc3.yaml`` has to be located at the current directory.
::
% phono3py --cf3 phono3py --cf3_file file_list.dat
where ``file_list.dat`` contains file names that can be recognized
from the current directory and is expected to be like::
disp-00001/vasprun.xml
disp-00002/vasprun.xml
disp-00003/vasprun.xml
disp-00004/vasprun.xml
...
The order of the file names is important. This option may be useful
to be used together with ``--cutoff_pair`` option.
.. _cf2_option:
``--cf2``: Create ``FORCES_FC2``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
This is used to create ``FORCES_FC2``. ``disp_fc2.yaml`` has to be
located at the current directory. This is
optional. ``FORCES_FC2`` is necessary to run with ``--dim_fc2``.
located at the current directory. This is optional. ``FORCES_FC2`` is
necessary to run with ``--dim_fc2`` option.
::
@ -312,6 +334,32 @@ indices, a small shell one-liner may be used::
% for i in `ls POSCAR-0*|sed s/POSCAR-//`;do echo -n $i,;done
00001,00002,00003,00016,00017,00018,00019,00024,00025,00026,00027,00032,00033,00034,00035,00036,00037,00038,00039,00040,00041,00042,00043,00070,00071,00072,00073,00074,00075,00076,00077,00078,00079,00080,00081,00082,00083,00084,00085,00086,00087,00088,00089,00096,00097,00098,00099,00100,00101,00102,00103,
When the number of force files is large, using ``--cf3_file`` option
may be better::
% for i in `ls POSCAR-0*|sed s/POSCAR-//`;do echo disp-$i/vasprun.xml;done > file_list.dat
% phono3py --cf3_file file_list.dat
Using a python script, ``disp_fc3.yaml`` is easily parsed. So it is also
easy to create the file list by a python script such as
::
#!/usr/bin/env python
import yaml
file_name_tmpl = "disp-%05d/vasprun.xml"
dds = yaml.load(open("disp_fc3.yaml"))
count = 1
for d1 in dds['first_atoms']:
print(file_name_tmpl % count)
count += 1
for d1 in dds['first_atoms']:
for d2 in d1['second_atoms']:
for d in d2['displacements']:
if d2['included']:
print(file_name_tmpl % count)
count += 1
Reciprocal space sampling mesh and grid points
-----------------------------------------------