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Atsushi Togo
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@ -220,29 +220,96 @@ reduce the supercell size and the second choice is using
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This option is only used together with ``-d`` option. Using this
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option, number of supercells with displacements is reduced and a
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special ``disp_fc3.yaml`` is created.
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special ``disp_fc3.yaml`` is created. This special ``disp_fc3.yaml``
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contains the information of the distance and which configurations of
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pair-displacements are included or not included.
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Cut-off pair distance is used to cut-off configurations of pairs of
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displacements. ``POSCAR-xxxxx`` are not created if distance between a
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pair of atoms to be displaced is larger than the specified cut-off
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pair distance. The indexing of ``POSCAR-xxxxx`` files is same as the
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usual case, i.e., without this option. But using this option, a lot of
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indices are missing, which are not necessary to be put for creating
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``FORCES_THIRD``. Only ``vasprun.xml``'s calculated for these reduced
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number of ``POSCAR-xxxxx`` have to be given at ``phono3py --cf3 ...``.
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Cut-off pair distance is used to cut-off the number of configurations
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of pair-displacements. ``POSCAR-xxxxx`` (in the other calculator
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interface, the prefix of the filename is different) are not generated
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if distance between a pair of atoms to be displaced is larger than the
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specified cut-off pair distance. The indexing number (``xxxxx``)
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corresponds to that of the case without setting this option, i.e., the
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same ``POSCAR-xxxxx`` files are created for the same configurations of
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pairs of displacements but ``POSCAR-xxxxx`` files not being included
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are not generated. The reason of this indexing is that it can be
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useful when changing the cutoff-pair-distance.
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To create ``FORCES_FC3``, only the respective output files containing
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forces are necessary to be given to ``phono3py`` command as the
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arguments.
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An example is shown below using the Si example.
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::
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phono3py -d --cutpair=4
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% phono3py --cutoff_pair=5 -d --dim="2 2 2" -c POSCAR-unitcell
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_ _____
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_ __ | |__ ___ _ __ ___|___ / _ __ _ _
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| '_ \| '_ \ / _ \| '_ \ / _ \ |_ \| '_ \| | | |
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| |_) | | | | (_) | | | | (_) |__) | |_) | |_| |
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| .__/|_| |_|\___/|_| |_|\___/____/| .__/ \__, |
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|_| |_| |___/
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1.11.7
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Run mode: displacements
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Displacement distance: 0.03
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Number of displacements: 111
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Cutoff distance for displacements: 5.0
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Number of displacement supercell files created: 51
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_
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___ _ __ __| |
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/ _ \ '_ \ / _` |
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| __/ | | | (_| |
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\___|_| |_|\__,_|
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After running VASP calculations,
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% ls POSCAR-0*
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POSCAR-00001 POSCAR-00032 POSCAR-00043 POSCAR-00080 POSCAR-00097
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POSCAR-00002 POSCAR-00033 POSCAR-00070 POSCAR-00081 POSCAR-00098
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POSCAR-00003 POSCAR-00034 POSCAR-00071 POSCAR-00082 POSCAR-00099
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POSCAR-00016 POSCAR-00035 POSCAR-00072 POSCAR-00083 POSCAR-00100
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POSCAR-00017 POSCAR-00036 POSCAR-00073 POSCAR-00084 POSCAR-00101
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POSCAR-00018 POSCAR-00037 POSCAR-00074 POSCAR-00085 POSCAR-00102
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POSCAR-00019 POSCAR-00038 POSCAR-00075 POSCAR-00086 POSCAR-00103
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POSCAR-00024 POSCAR-00039 POSCAR-00076 POSCAR-00087
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POSCAR-00025 POSCAR-00040 POSCAR-00077 POSCAR-00088
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POSCAR-00026 POSCAR-00041 POSCAR-00078 POSCAR-00089
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POSCAR-00027 POSCAR-00042 POSCAR-00079 POSCAR-00096
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::
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phono3py --cf3 all_calculated_vasprun_xmls
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For example, supporse forces are calculated using VASP in
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``disp-xxxxx`` directories, after running force calculations,
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``FORCES_FC3`` is created as follows::
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% phono3py --cf3 disp-{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}/vasprun.xml
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_ _____
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_ __ | |__ ___ _ __ ___|___ / _ __ _ _
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| '_ \| '_ \ / _ \| '_ \ / _ \ |_ \| '_ \| | | |
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| |_) | | | | (_) | | | | (_) |__) | |_) | |_| |
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| .__/|_| |_|\___/|_| |_|\___/____/| .__/ \__, |
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|_| |_| |___/
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1.11.7
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Displacement dataset is read from disp_fc3.yaml.
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counter (file index): 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51
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FORCES_FC3 has been created.
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_
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___ _ __ __| |
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/ _ \ '_ \ / _` |
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| __/ | | | (_| |
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\___|_| |_|\__,_|
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Here one must mind that since the special ``disp_fc3.yaml`` is read in
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creating ``FORCES_FC3``, it has to be located on the current directory.
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Although it depends on computer systems, to obtain the list of file
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indices, a small shell one-liner may be used::
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% for i in `ls POSCAR-0*|sed s/POSCAR-//`;do echo -n $i,;done
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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,
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``disp_fc3.yaml`` may be readable and helpful to understand this
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procedure.
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Reciprocal space sampling mesh and grid points
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-----------------------------------------------
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@ -365,10 +432,11 @@ points are written into ``kappa-mxxx-gx(-sx).hdf5``.
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(Setting tag: ``ISOTOPE``, ``.TRUE.`` or ``.FALSE.``)
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Phonon-isotope scattering is calculated.. Mass variance parameters are
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read from database of the natural abundance data for elements, which
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refers Laeter *et al.*, Pure Appl. Chem., **75**, 683
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(2003)
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Phonon-isotope scattering is calculated based on the formula by
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Shin-ichiro Tamura, Phys. Rev. B, **27**, 858 (1983). Mass variance
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parameters are read from database of the natural abundance data for
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elements, which refers Laeter *et al.*, Pure Appl. Chem., **75**, 683
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(2003).
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::
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