mirror of https://github.com/phonopy/phono3py.git
Update document for removal of --tsym
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Atsushi Togo
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@ -42,7 +42,7 @@ example found in the example directory.
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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="11 11 11" --sym_fc3r --sym_fc2 --tsym --br
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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="11 11 11" --sym-fc --br
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Then using the output file, ``kappa-m111111.hdf5``, run
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``phono3py-kaccum`` as follows::
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@ -168,17 +168,18 @@ Read 3rd order force constants from ``fc3.hdf5``.
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.. _symmetrization_option:
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``--sym-fc2``, ``--sym-fc3r``, ``--tsym``: Symmetries force constants
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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``--sym-fc2``, ``--sym-fc3r``, ``--sym-fc``: Symmetries force constants
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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(Setting tags: ``SYMMETRIZE_FC2``, ``.TRUE.`` or ``.FALSE.``)
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(Setting tags: ``SYMMETRIZE_FC3``, ``.TRUE.`` or ``.FALSE.``)
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(Setting tags: ``TRANSLATION``, ``.TRUE.`` or ``.FALSE.``)
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(Setting tags: ``FC_SYMMETRY``, ``.TRUE.`` or ``.FALSE.``)
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These are used to symmetrize second- and third-order force
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constants. ``--sym-fc2`` and ``--sym-fc3r`` symmetrize those in real
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space by the index exchange, respectively, and ``--tsym`` symmetrizes
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by the translational invariance, respectively.
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constants. With ``--sym-fc2`` and ``--sym-fc3r``,
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the index exchange of real space force constantsand translational
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invariance symmetry are applied, respectively. ``--sym-fc`` is an
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alias to set both of ``--sym-fc2`` and ``--sym-fc3r``.
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..
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``--sym-fc3q`` symmetrizes third-order force constants in normal
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@ -50,9 +50,9 @@ copyright = u'2015, Atsushi Togo'
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# built documents.
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#
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# The short X.Y version.
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version = '1.12.5'
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version = '1.12.7'
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# The full version, including alpha/beta/rc tags.
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release = '1.12.5'
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release = '1.12.7'
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# The language for content autogenerated by Sphinx. Refer to documentation
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# for a list of supported languages.
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@ -3,10 +3,10 @@
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CRYSTAL & phono3py calculation
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==============================
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CRYSTAL program package has a robust built-in phonon calculation
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CRYSTAL program package has a robust built-in phonon calculation
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workflow for harmonic phonon properties. However, combining CRYSTAL
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with Phono3py enables convenient access to anharmonic phonon properties.
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An example for CRYSTAL is found in the ``example/Si-CRYSTAL`` directory.
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To invoke the CRYSTAL interface, ``--crystal`` option has to be always
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@ -26,8 +26,8 @@ only limited number of keywords that are shown in the phonopy web site
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Workflow
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---------
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In this example (Si-CRYSTAL), the CRYSTAL output file is crystal.o.
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This is the default file name for the CRYSTAL interface,
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In this example (Si-CRYSTAL), the CRYSTAL output file is crystal.o.
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This is the default file name for the CRYSTAL interface,
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so the -c crystal.o parameter is not needed.
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1) Create supercells with displacements
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@ -35,25 +35,25 @@ so the -c crystal.o parameter is not needed.
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::
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% phono3py --crystal --dim="2 2 2" --dim_fc2="4 4 4" -d
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% phono3py --crystal --dim="2 2 2" --dim_fc2="4 4 4" -d
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57 supercell files (``supercell-xxx.d12/.ext``) for the third order
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force constants are created. In addition, one supercell file
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force constants are created. In addition, one supercell file
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(``supercell_fc2-00001.d12/.ext``) is created for the second order
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force constants.
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2) To make valid CRYSTAL input files, there are two possible options:
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a) Manually: modify the generated supercell-xxx.d12 and supercell_fc2-xxxxx.d12
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files by replacing the line ``Insert basis sets and parameters here`` with the
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files by replacing the line ``Insert basis sets and parameters here`` with the
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basis set and computational parameters.
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b) Recommended option: before generating the supercells, include files named
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``TEMPLATE`` and ``TEMPLATE3`` in the current directory. These files should
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contain the basis sets and computational parameters for CRYSTAL (see the example).
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When phono3py finds these files it automatically generates complete
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CRYSTAL input files in the step 1.
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CRYSTAL input files in the step 1.
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Note that supercells with displacements must not be relaxed in the
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force calculations, because atomic forces induced by a small atomic
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displacement are what we need for phonon calculation. To get accurate
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@ -76,10 +76,10 @@ so the -c crystal.o parameter is not needed.
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4) Calculate 3rd and 2nd order force constants in files ``fc3.hdf5`` and ``fc2.hdf5``::
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% phono3py --crystal --dim="2 2 2" --dim_fc2="4 4 4" --sym_fc3r --sym_fc2 --tsym
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% phono3py --crystal --dim="2 2 2" --dim_fc2="4 4 4" --sym-fc
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``--sym_fc2``, ``--sym_fc3r``, and ``--tsym`` are used to symmetrize second- and third-order
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force constants.
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``--sym-fc`` is used to symmetrize second- and third-order force
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constants.
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5) Thermal conductivity calculation::
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@ -89,4 +89,3 @@ so the -c crystal.o parameter is not needed.
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Add ``--isotope`` for isotope scattering.
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Check the effect of ``--nac`` for polar systems.
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Carefully test the convergence with respect to ``--mesh``!
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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-fc --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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@ -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-fc --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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@ -14,5 +14,3 @@ https://pypi.python.org/pypi/phono3py .
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Examples of silicon with VASP and Pwscf as calculators are given in
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the ``example`` directory. An example using phono3py API is found in
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the ``example/Si-PBEsol/Si.py`` but the API document has not yet written.
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@ -64,7 +64,7 @@ Workflow
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``fc3.hdf5`` and ``fc2.hdf5`` files are created by::
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% phono3py --pwscf --dim="2 2 2" -c Si.in --sym_fc3r --sym_fc2 --tsym
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% phono3py --pwscf --dim="2 2 2" -c Si.in --sym-fc
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5) Calculate lattice thermal conductivity, e.g., by::
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@ -25,7 +25,7 @@ Workflow
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In this case, ``disp_fc2.yaml`` and ``POSCAR_FC2-xxxxx`` files are
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also created.
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2. Run VASP for supercell force calculations
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2. Run VASP for supercell force calculations
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To calculate forces on atoms in supercells, ``POSCAR-xxxxx`` (and
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``POSCAR_FC2-xxxxx`` if they exist) are used as VASP (or any force
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@ -54,7 +54,7 @@ Workflow
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``disp_fc2.yaml`` is necessary in this case and ``FORCES_FC2`` is
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created.
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4. Create fc2.hdf and fc3.hdf
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::
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@ -66,7 +66,7 @@ Workflow
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calculating fc2 and fc3 at every run time.
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When you use larger supercell for fc2 calculation::
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% phono3py --dim_fc2="4 4 4" --dim="2 2 2" -c POSCAR-unitcell
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Similarly ``fc2.hdf5`` and ``fc3.hdf5`` are created from ``FORCES_FC3``,
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@ -115,4 +115,3 @@ Workflow
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Once this calculation runs without problem, separately calculated
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hdf5 files on grid points are no more necessary and may be deleted.
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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-fc -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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