mirror of https://github.com/phonopy/phono3py.git
Update document for v1.12.3
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Atsushi Togo
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6ddfd90502
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@ -229,7 +229,7 @@ Lifetime :math:`\tau_\lambda = \frac{1}{2\Gamma_\lambda(\omega_\lambda)}` (in ps
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Modal heat capacity :math:`C_\lambda` (in eV/K)
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``--gv_norm``
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``--gv-norm``
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^^^^^^^^^^^^^^
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Absolute value of group velocity :math:`|\mathbf{v}_\lambda|` (in
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@ -340,7 +340,7 @@ of density in the data.
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.. _kdeplot_density_ratio:
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``--dr``, ``--density_ratio``
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``--dr``, ``--density-ratio``
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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The density threshold is specified by the ratio with respect to
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@ -13,7 +13,7 @@ Here the detail of the command option :ref:`--cutoff_pair
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What is cutff pair-distance in phono3py?
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----------------------------------------
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Using ``--cutoff_pair`` option, number of supercells with
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Using ``--cutoff-pair`` option, number of supercells with
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displacements to be calculated is reduced. But of course this
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sacrifices the accuracy of third-order force constants (fc3).
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@ -29,7 +29,7 @@ be huge and beyond our computational resource.
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Sometimes we may expect that interaction range of fc3 among triplets
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of atoms is shorter than chosen supercell size. If it is the case, we
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may be allowed to omit computing some elements of supercell-fc3. This
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is what achieved by ``--cutoff_pair`` option.
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is what achieved by ``--cutoff-pair`` option.
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A supercell-fc3 element is specified by three atomic
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displacements. Two of three are finitely displaced
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@ -50,11 +50,11 @@ Usage
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Creating supercells with displacements
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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``-cutoff_pair`` option is employed when creating supercells with
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``--cutoff-pair`` option is employed when creating supercells with
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displacements, therefore this option must be used with ``-d`` option
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when running phono3py, for example for the Si example::
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% phono3py --cutoff_pair=5 -d --dim="2 2 2" -c POSCAR-unitcell
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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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@ -62,9 +62,9 @@ when running phono3py, for example for the Si example::
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| .__/|_| |_|\___/|_| |_|\___/____/| .__/ \__, |
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|_| |_| |___/
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1.11.11
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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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@ -91,10 +91,10 @@ when running phono3py, for example for the Si example::
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51
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``Number of displacements: 111`` shows the number of supercells with
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displacements when this is run without ``--cutoff_pair``
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displacements when this is run without ``--cutoff-pair``
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option. ``Number of displacement supercell files created: 51`` gives
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the contracted number of supercells with displacements by
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``--cutoff_pair`` option. There number of ``POSCAR-0xxxx`` files is found
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``--cutoff-pair`` option. There number of ``POSCAR-0xxxx`` files is found
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51. At this step, a special ``disp_fc3.yaml`` is created. This
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contains information on this contraction and used in the other
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calculation step, therefore this file must be kept carefully.
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@ -115,19 +115,19 @@ changing the cutoff-pair-distance.
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Special ``disp_fc3.yaml``
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^^^^^^^^^^^^^^^^^^^^^^^^^^
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Using ``-cutoff_pair`` option together with ``-d`` option, a special
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Using ``--cutoff-pair`` option together with ``-d`` option, a special
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``disp_fc3.yaml`` is created. This contains information on distances
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between displaced atomic-pairs and whether those pairs are to be
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computed or not. This special ``disp_fc3.yaml`` is necessary to create
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fc3, therefore be careful not to overwrite it by running the option
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``-d`` without ``-cutoff_pair`` or with different ``-cutoff_pair``
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``-d`` without ``--cutoff-pair`` or with different ``--cutoff-pair``
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with different value.
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Making ``FORCES_FC3``
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~~~~~~~~~~~~~~~~~~~~~~
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To create ``FORCES_FC3``, only output files of the supercells created
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using ``--cutoff_pair`` option are passed to ``phono3py`` as the
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using ``--cutoff-pair`` option are passed to ``phono3py`` as the
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arguments. The special ``disp_fc3.yaml`` file is necessary to be
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located at current directory.
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@ -147,7 +147,7 @@ output file containing forces in each directory (for VASP
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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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@ -188,14 +188,14 @@ script:
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Running phonon-phonon interaction calculation
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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To create fc3, ``--cutoff_pair`` option is not necessary but the
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To create fc3, ``--cutoff-pair`` option is not necessary but the
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special ``disp_fc3.yaml`` is required.
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::
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% phono3py --dim="2 2 2" -c POSCAR-unitcell
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...
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Displacement dataset is read from disp_fc3.yaml.
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Sets of supercell forces are read from FORCES_FC3.
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Solving fc3[ 1, x, x ] with a displacement:
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@ -214,9 +214,9 @@ special ``disp_fc3.yaml`` is required.
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___ _ __ __| |
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/ _ \ '_ \ / _` |
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| __/ | | | (_| |
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\___|_| |_|\__,_|
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\___|_| |_|\__,_|
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Once ``fc3.hdf5`` and ``fc2.hdf5`` are created, ``--cutoff_pair``
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Once ``fc3.hdf5`` and ``fc2.hdf5`` are created, ``--cutoff-pair``
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option and the special ``disp_fc3.yaml`` are not needed anymore.
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::
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@ -225,7 +225,7 @@ option and the special ``disp_fc3.yaml`` are not needed anymore.
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...
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300.0 118.778 118.778 118.778 -0.000 -0.000 0.000
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...
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@ -235,7 +235,7 @@ The Test
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Si-PBE
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~~~~~~
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For testing, thermal conductivities with respect to ``--cutoff_pair``
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For testing, thermal conductivities with respect to ``--cutoff-pair``
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values are calculated as follows. Note that if ``FORCES_FC3`` for full
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fc3 elements exists, the same ``FORCES_FC3`` file can be used for
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generating contracted fc3 for each special ``disp_fc3.yaml``.
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@ -253,7 +253,7 @@ generating contracted fc3 for each special ``disp_fc3.yaml``.
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7.100884
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7.730463
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9.467845
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% for i in {2..10};do d=`grep distance disp_fc3.yaml|awk '{print $2}'|sort|uniq|sed "${i}q;d"`; d=$((d+0.1)); phono3py --cutoff_pair=$d -o $i -d --dim="2 2 2" -c POSCAR-unitcell ;done
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% for i in {2..10};do d=`grep distance disp_fc3.yaml|awk '{print $2}'|sort|uniq|sed "${i}q;d"`; d=$((d+0.1)); phono3py --cutoff-pair=$d -o $i -d --dim="2 2 2" -c POSCAR-unitcell ;done
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% ls disp_fc3.*.yaml
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disp_fc3.10.yaml disp_fc3.4.yaml disp_fc3.7.yaml
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disp_fc3.2.yaml disp_fc3.5.yaml disp_fc3.8.yaml
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@ -279,7 +279,7 @@ generating contracted fc3 for each special ``disp_fc3.yaml``.
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300.0 119.466 119.466 119.466 -0.000 -0.000 0.000
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300.0 119.447 119.447 119.447 -0.000 -0.000 0.000
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300.0 119.445 119.445 119.445 -0.000 -0.000 0.000
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% for i in {2..10};do 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" --sym_fc3r --sym_fc2 --tsym --br -i $i -o sym-$i|tee std.sym-$i.out;done
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% for i in {2..10};do 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" --sym-fc3r --sym-fc2 --tsym --br -i $i -o sym-$i|tee std.sym-$i.out;done
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% for i in {2..10};do egrep '^\s+300' std.sym-$i.out;done
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300.0 124.626 124.626 124.626 -0.000 0.000 0.000
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300.0 119.721 119.721 119.721 -0.000 0.000 0.000
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@ -319,7 +319,7 @@ AlN-LDA
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6.205027
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6.469591
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7.335901
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% for i in {2..22};do d=`egrep '^\s+distance' disp_fc3.yaml|awk '{print $2}'|sort|uniq|sed "${i}q;d"`; d=$((d+0.0001)); phono3py --cutoff_pair=$d -o $i -d --dim="3 3 2" -c POSCAR-unitcell ;done
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% for i in {2..22};do d=`egrep '^\s+distance' disp_fc3.yaml|awk '{print $2}'|sort|uniq|sed "${i}q;d"`; d=$((d+0.0001)); phono3py --cutoff-pair=$d -o $i -d --dim="3 3 2" -c POSCAR-unitcell ;done
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% for i in {2..22};do grep num_displacements_created disp_fc3.$i.yaml;done
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num_displacements_created: 78
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num_displacements_created: 98
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@ -365,7 +365,7 @@ AlN-LDA
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300.0 224.645 224.645 215.260 -0.000 -0.000 -0.000
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300.0 224.769 224.769 215.220 -0.000 -0.000 -0.000
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300.0 224.650 224.650 215.090 -0.000 -0.000 -0.000
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% for i in {2..22};do phono3py --dim="3 3 2" -c POSCAR-unitcell --mesh="13 13 9" --sym_fc3r --sym_fc2 --tsym --br --nac -i $i -o sym-$i|tee std.sym-$i.out; done
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% for i in {2..22};do phono3py --dim="3 3 2" -c POSCAR-unitcell --mesh="13 13 9" --sym-fc3r --sym-fc2 --tsym --br --nac -i $i -o sym-$i|tee std.sym-$i.out; done
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% for i in {2..22};do egrep '^\s+300\.0' std.sym-$i.out;done
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300.0 224.122 224.122 213.086 0.000 -0.000 0.000
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300.0 225.394 225.394 215.683 0.000 -0.000 0.000
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@ -32,7 +32,7 @@ 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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% 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 to specify
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``--ga`` option are found by :ref:`--wgp option <wgp_option>`
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@ -53,7 +53,7 @@ necessary to obtain lattice thermal conductivity. To distribute
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computational demands into computer nodes, a set of the grid-point
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indices are chosen 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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% 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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Then many ``kappa-m191919-gx.hdf5`` files are generated. These file
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names should not be altered because in reading the data by phono3py,
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@ -66,7 +66,7 @@ short time from the stored data:
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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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% 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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@ -78,15 +78,15 @@ 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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@ -141,6 +141,5 @@ with ``job.sh`` (here for grid-engine):
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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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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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