mirror of https://github.com/phonopy/phono3py.git
Update document for distributing thermal cond. calc.
This commit is contained in:
Atsushi Togo
parent
8a7cefc506
commit
cf6a3b5186
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@ -280,18 +280,37 @@ axes and is always Gamma-centered.
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calculation of phonon lifetimes when it is specified, e.g.,
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``--mesh="11 11 11" --md="2 2 2"``.
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.. _gp_option:
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``--gp``: Grid points by their ID
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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(Setting tag: ``GRID_POINTS``)
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Grid points where imaginary part of self energy is calculated. Indices
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of grid points are specified by space separated numbers. The mapping
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table between grid points to its indices is obtained by running with
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``--loglevel=2`` option.
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Grid points where imaginary part of self energy is calculated are
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specified. Indices of grid points are specified by space or comma
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(``,``) separated numbers. The mapping table between grid points to its
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indices is obtained by running with ``--loglevel=2`` option.
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``--ga`` option can be used instead of ``--gp`` option. See ``--gp``
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section.
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::
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% 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"
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where ``--gp="0 1 2 3 4 5"`` can be also written
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``--gp="0,1,2,3,4,5"``. There is a similar option as this option,
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:ref:`--ga option <ga_option>`.
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``--ga`` option may be also useful when a workload of thermal
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conductivity calculation is expected to be distributed into different
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computer nodes.
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.. toctree::
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:maxdepth: 1
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workload-distribution
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.. _ga_option:
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``--ga``: Grid points by address with three integer values
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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@ -307,17 +326,19 @@ grid point. The grid points given by ``--ga`` option are translated to
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grid point indices as given by ``--gp`` option, and the values given
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by ``--ga`` option will not be shown in log files.
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.. _wgp_option:
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``--wgp``: Write grid point information
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Irreducible grid point indices are written into
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``ir_grid_points.yaml``. This information may be used when we want to
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calculate imaginary part of self energy at each grid point in
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conjunction with ``--gp`` option. ``grid_address-mxxx.hdf5`` is also
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written. This file contains all the grid points and their grid
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addresses in integers. Q-points corresponding to grid points are
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calculated divided these integers by sampling mesh numbers for
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respective reciprocal axes.
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conjunction with :ref:`--gp option <gp_option>`.
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``grid_address-mxxx.hdf5`` is also written. This file contains all the
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grid points and their grid addresses in integers. Q-points
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corresponding to grid points are calculated divided these integers by
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sampling mesh numbers for respective reciprocal axes.
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``--stp``: Show number of triplets to be calculated for each grid point
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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@ -485,6 +506,8 @@ into file in hdf5 format. The result is written into
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``--bi`` option. With ``--sigma`` option, ``-sx`` is inserted in front
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of ``.hdf5``.
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.. _read_gamma_option:
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``--read_gamma``
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~~~~~~~~~~~~~~~~
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@ -528,7 +551,7 @@ grid addresses and sampling mesh numbers given in
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``grid_address-mxxx.hdf5`` that is obtained by ``--wgp`` option. A
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python script to obtain q-point triplets is shown below.
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::
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.. code-block:: python
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import h5py
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import numpy as np
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@ -541,7 +564,9 @@ python script to obtain q-point triplets is shown below.
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q = grid_address[triplets] / np.array(mesh, dtype='double')
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Imaginary part of self energy or linewidth/2 is recovered by the
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following script::
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following script:
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.. code-block:: python
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import h5py
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import numpy as np
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@ -665,6 +690,8 @@ For spectrum like calculations of imaginary part of self energy and
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JDOS, number of sampling frequency points is controlled by
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``--num_freq_points`` or ``--freq_pitch``.
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.. _bi_option:
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``--bi``: Specific band index
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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@ -163,7 +163,9 @@ when the number of force files is large. ::
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Using a python script, ``disp_fc3.yaml`` is easily parsed. So
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it is also easy to create the file list by a python
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script::
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script:
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.. code-block:: python
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#!/usr/bin/env python
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import yaml
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@ -0,0 +1,131 @@
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.. _workload_distribution:
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Workload distribution
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======================
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Workload of thermal conductivity calculation can be distributed into
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computer nodes. The distribution over q-point grid points (:ref:`--gp
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option <gp_option>`) and phonon bands (:ref:`--bi option <bi_option>`)
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are supported. Distribution over bands has some overhead in
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calculation of Fourier transformation of force constants. Below
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distribution over only grid points is explained. For each computer
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node, selected irreducible grid points needed for completing thermal
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conductivity are calculated. Te resulting data for each grid point are
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stored in its ``kappa-mxxx-gx.hdf5`` file on each node by setting
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:ref:`--write_gamma option <write_gamma_option>`. Once all data are
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obtained, those data are collected by :ref:`--read_gamma option
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<read_gamma_option>`.
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.. contents::
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:depth: 2
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:local:
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How to do it
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------------
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The following example is executed in the ``Si-PBE`` example.
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To avoid re-calculating fc3 and fc2, ``fc3.hdf5`` and ``fc2.hdf5`` are
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created on a single node::
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% phono3py --dim="2 2 2" --sym_fc3r --sym_fc2 --tsym -c POSCAR-unitcell
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The indices of the irreducible grid points neccesarry for ``--ga``
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option are found by :ref:`--wgp option <wgp_option>`
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::
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% 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 --wgp
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and they are stored in ``ir_grid_points.yaml``.
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::
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% egrep '^- grid_point:' ir_grid_points.yaml|awk '{printf("%d,",$3)}'
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0,1,2,3,4,5,6,7,8,9,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,60,61,62,63,64,65,66,67,68,69,70,71,72,73,80,81,82,83,84,85,86,87,88,89,90,91,100,101,102,103,104,105,106,107,108,109,120,121,122,123,124,125,126,127,140,141,142,143,144,145,160,161,162,163,180,181,402,403,404,405,406,407,408,409,422,423,424,425,426,427,428,429,430,431,432,433,434,435,442,443,444,445,446,447,448,449,450,451,452,453,462,463,464,465,466,467,468,469,470,471,482,483,484,485,486,487,488,489,502,503,504,505,506,507,522,523,524,525,542,543,804,805,806,807,808,809,824,825,826,827,828,829,830,831,832,833,844,845,846,847,848,849,850,851,864,865,866,867,868,869,884,885,886,887,904,905,1206,1207,1208,1209,1226,1227,1228,1229,1230,1231,1246,1247,1248,1249,1266,1267,1608,1609,1628,1629,
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Some of all the indices are specified and executed as follows::
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% 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 --gp="0,1,2,3,4,5,6,7,8,9,20,21,22,23,24,25" --write_gamma
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After finishing calculations on all nodes, the RTA thermal
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conductivity is computed in a short time from the stored data by
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::
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% 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 --read_gamma
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A convenient script
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--------------------
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The following short script may be used to splitting all irreducible
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grid point indices into some number (first argument) of sets of grid
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point indices for workload distribution.
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.. code-block:: python
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#!/usr/bin/env python
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import sys
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import yaml
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if len(sys.argv) > 1:
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num = int(sys.argv[1])
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else:
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num = 1
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with open("ir_grid_points.yaml") as f:
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data = yaml.load(f)
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gps = [gp['grid_point'] for gp in data['ir_grid_points']]
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gp_lists = [[] for i in range(num)]
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for i, gp in enumerate(gps):
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gp_lists[i % num].append(gp)
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for gp_set in gp_lists:
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print(",".join(["%d" % gp for gp in gp_set]))
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Supposed that this script is saved as ``divide_gps.py``,
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::
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% python divide_gps.py 20
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0,30,52,82,120,402,434,468,524,844,1206
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1,31,53,83,121,403,435,469,525,845,1207
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2,32,54,84,122,404,442,470,542,846,1208
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3,33,55,85,123,405,443,471,543,847,1209
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4,34,60,86,124,406,444,482,804,848,1226
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5,35,61,87,125,407,445,483,805,849,1227
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6,36,62,88,126,408,446,484,806,850,1228
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7,37,63,89,127,409,447,485,807,851,1229
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8,40,64,90,140,422,448,486,808,864,1230
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9,41,65,91,141,423,449,487,809,865,1231
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20,42,66,100,142,424,450,488,824,866,1246
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21,43,67,101,143,425,451,489,825,867,1247
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22,44,68,102,144,426,452,502,826,868,1248
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23,45,69,103,145,427,453,503,827,869,1249
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24,46,70,104,160,428,462,504,828,884,1266
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25,47,71,105,161,429,463,505,829,885,1267
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26,48,72,106,162,430,464,506,830,886,1608
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27,49,73,107,163,431,465,507,831,887,1609
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28,50,80,108,180,432,466,522,832,904,1628
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29,51,81,109,181,433,467,523,833,905,1629
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For example distributing into 20 computer nodes using a queueing
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system,
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.. code-block:: shell
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% j=1; for i in `python divide_gps.py 20`;do echo $i; sed -e s/gps/$i/g -e s/num/$j/g job.sh|qsub; j=$((j+1)); done
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with ``job.sh`` (here for grid-engine):
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.. code-block:: shell
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#$ -S /bin/zsh
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#$ -cwd
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#$ -N phono3py-num
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#$ -pe mpi* 16
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#$ -e err-phono3py-num.log
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#$ -o std-phono3py-num.log
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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 --gp="gps" --write_gamma
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