mirror of https://github.com/phonopy/phono3py.git
Update document for v1.10.4
This commit is contained in:
Atsushi Togo
parent
e75f29ff5d
commit
10cde4ef34
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@ -3,33 +3,38 @@
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Command options
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===============
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.. _create_displacements_option:
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``-d``
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~~~~~~
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Supercell with displacements are created. Using with ``--amplitude``
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option, atomic displacement distances are controlled.
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option, atomic displacement distances are controlled. With this
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option, files for supercells with displacements and ``disp_fc3.yaml``
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file are created.
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``--amplitude``
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~~~~~~~~~~~~~~~
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Displacement distance. The default value is 0.03.
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Displacement distance. The default value depends on calculator. See
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:ref:`default_displacement_distance_for_calculator`.
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``--pa``, ``--primitive_axis``
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Transformation matrix from a non-primitive cell to the primitive
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cell. See phonopy ``PRIMITIVE_AXIS`` tag (``--pa`` option) at
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http://phonopy.sourceforge.net/setting-tags.html#primitive-axis
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http://atztogo.github.io/phonopy/setting-tags.html#primitive-axis
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``--fc2``
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~~~~~~~~~
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Read ``fc2.hdf5``.
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Read 2nd order force constants from ``fc2.hdf5``.
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``--fc3``
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~~~~~~~~~
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Read ``fc3.hdf5``.
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Read 3rd order force constants from ``fc3.hdf5``.
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``--sym_fc2``, ``--sym_fc3r``, ``--tsym``
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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@ -51,7 +56,9 @@ files.
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~~~~~~~~~
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Supercell size is specified. See the
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detail at http://phonopy.sourceforge.net/setting-tags.html#dim .
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detail at http://atztogo.github.io/phonopy/setting-tags.html#dim .
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.. _dim_fc2_option:
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``--dim_fc2``
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~~~~~~~~~~~~~
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@ -107,7 +114,9 @@ numerical values. This is used when we want to test several
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~~~~~~~~~
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Tetrahedron method is used for calculation of imaginary part of self
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energy.
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energy. This is the default option. Therefore it is not necessary to
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specify this unless both results by tetrahedron method and
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smearing method in one time execution are expected.
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``--tmax``, ``--tmin``, ``--tstep``, ``--ts``
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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@ -115,7 +124,7 @@ energy.
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Temperatures at equal interval are specified by ``--tmax``,
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``--tmin``, ``--tstep``. See phonopy ``TMAX``, ``TMIN``, ``TSTEP``
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tags (``--tmax``, ``--tmin``, ``--tstep`` options) at
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http://phonopy.sourceforge.net/setting-tags.html#tprop-tmin-tmax-tstep .
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http://atztogo.github.io/phonopy/setting-tags.html#tprop-tmin-tmax-tstep .
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::
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@ -177,14 +186,16 @@ points are shown by using with ``--gp`` or ``--ga`` option.
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~~~~~~~~~
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Non-analytical term correction for harmonic phonons. Like as phonopy,
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``BORN`` file has to be put on the same directory.
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``BORN`` file has to be put on the same directory. Always the default
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value of unit conversion factor is used even if it is written in the
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first line of ``BORN`` file.
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``--q_direction``
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~~~~~~~~~~~~~~~~~
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This is used with ``--nac`` to specify the direction to polarize in
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reciprocal space. See the detail at
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http://phonopy.sourceforge.net/setting-tags.html#q-direction .
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http://atztogo.github.io/phonopy/setting-tags.html#q-direction .
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``--isotope``
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~~~~~~~~~~~~~
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@ -230,6 +241,8 @@ free path. The value is given in micrometre. The default value, 1
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metre, is just used to avoid divergence of phonon lifetime and the
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contribution to the thermal conducitivity is considered negligible.
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.. _cf3_option:
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``--cf3``
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~~~~~~~~~
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@ -240,6 +253,8 @@ located at the current directory.
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% phono3py --cf3 disp-{00001..00755}/vasprun.xml
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.. _cf2_option:
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``--cf2``
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~~~~~~~~~
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@ -288,6 +303,8 @@ After running VASP calculations,
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``disp_fc3.yaml`` may be readable and helpful to understand this procedure.
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.. _write_gamma_option:
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``--write_gamma``
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~~~~~~~~~~~~~~~~~
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@ -310,6 +327,8 @@ found, it tries to read ``kappa`` file for each grid point,
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``kappa-mxxx-dx-gx(-sx).hdf5`` not found,
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``kappa-mxxx-dx-gx-bx(-sx).hdf5`` files for band indices are searched.
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.. _write_detailed_gamma_option:
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``--write_detailed_gamma``
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~~~~~~~~~~~~~~~~~~~~~~~~~~
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@ -368,35 +387,43 @@ following script::
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format. This file can be huge and usually it is not recommended to
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write it out.
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.. _ise_option:
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``--ise``
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~~~~~~~~~~
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Imaginary part of self energy :math:`\Gamma_\lambda(\omega)` is
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calculated with respect to :math:`\omega`. The output is written to ``gammas-mxxxx-gx-sx-tx-bx.dat``.
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calculated with respect to :math:`\omega`. The output is written to
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``gammas-mxxxx-gx-sx-tx-bx.dat`` in THz (without :math:`2\pi`).
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::
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% phono3py --fc3 --fc2 --dim="2 2 2" --mesh="16 16 16" -c POSCAR-unitcell \
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--nac --q_direction="1 0 0" --gp=0 --ise --bi="4 5, 6"
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.. _lw_option:
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``--lw``
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~~~~~~~~
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Linewidth :math:`2\Gamma_\lambda(\omega_\lambda)` is calculated with
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respect to temperature. The output is written to
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``linewidth-mxxxx-gx-sx-bx.dat``.
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``linewidth-mxxxx-gx-sx-bx.dat`` in THz (without :math:`2\pi`).
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::
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% phono3py --fc3 --fc2 --dim="2 2 2" --mesh="16 16 16" -c POSCAR-unitcell \
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--nac --q_direction="1 0 0" --gp=0 --lw --bi="4 5, 6"
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.. _jdos_option:
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``--jdos``
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~~~~~~~~~~
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Two classes of joint density of states (JDOS) are calculated. The
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result is written into ``jdos-mxxxxxx-gx.dat``. The first column is
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the frequency, and the second and third columns are the values given
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as follows, respectively,
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result is written into ``jdos-mxxxxxx-gx.dat`` in THz (without
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:math:`2\pi`). The first column is the frequency, and the second and
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third columns are the values given as follows, respectively,
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.. math::
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@ -49,9 +49,9 @@ 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 = '0.9.14'
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version = '1.10.3'
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# The full version, including alpha/beta/rc tags.
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release = '0.9.14'
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release = '1.10.3'
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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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@ -10,7 +10,8 @@ This software calculates phonon-phonon interaction related properties:
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- Joint density of states (JDOS) and weighted-JDOS
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The theoretical background is summarized in the paper found at
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http://dx.doi.org/10.1103/PhysRevB.91.094306 .
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http://dx.doi.org/10.1103/PhysRevB.91.094306 or the draft in arxiv at
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http://arxiv.org/abs/1501.00691 .
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Examples are found in ``example-phono3py`` directory.
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@ -24,6 +25,7 @@ Documentation
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install
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output-files
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command-options
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interfaces
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auxiliary-tools
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citation
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changelog
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@ -20,14 +20,15 @@ ubuntu linux, these are installed using the package manager::
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% sudo apt-get install python-dev python-numpy python-matplotlib \
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python-yaml python-h5py libgomp1 liblapacke-dev
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After the versions of Ubuntu-12.10, lapacke
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In the versions of Ubuntu-12.10 or later, lapacke
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(http://www.netlib.org/lapack/lapacke.html) can be installed from the
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package manager (``liblapacke`` and ``liblapacke-dev``), but in older
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versions of ubuntu, or in other environments, you may have to compile
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lapacke by yourself. The compilation procedure is found at the lapacke
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web site. After creating the lapacke library, ``liblapacke.a`` (or the
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dynamic link library) ``setup3.py`` must be properly modified to link
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it. As an example, the procedure of compiling lapacke is shown below.
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package manager (``liblapacke`` and ``liblapacke-dev``). But in the
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older versions of Ubuntu or in the other environments, e.g., Mac, you
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may have to compile lapacke by yourself. The compilation procedure is
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found at the lapacke web site. After creating the lapacke library,
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``liblapacke.a`` (or the dynamic link library), ``setup3.py`` must be
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properly modified to link it. As an example, the procedure of
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compiling lapacke is shown below.
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::
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@ -40,10 +41,11 @@ Multithreading support
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------------------------
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Phono3py supports OpenMP multithreading and most users will need it,
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otherwise the calculation may take long time. However, without special
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OpenMP environment variables (``-lgomp`` and ``-fopenmp`` in
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``setup3.py``), phono3py will be compiled without the OpenMP
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multithreding support.
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otherwise the calculation may take long time. The library options used
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for GCC, ``-lgomp`` and ``-fopenmp``, are written in ``setup3.py``,
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but for the other compilers, you may have to change them. If you need
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to compile without the OpenMP support, you can remove these options in
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``setup3.py``.
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Installation procedure
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------------------------
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@ -70,10 +72,10 @@ sourceforge.net will be removed from the list of the ``PYTHONPATH``.
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The ``PYTHONPATH`` setting depends on shells that you use. For example
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in bash or zsh::
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export PYTHONPATH=~/phonopy-0.9.9/lib/python
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export PYTHONPATH=~/phonopy-1.10.3/lib/python
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or::
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export PYTHONPATH=$PYTHONPATH:~/phonopy-0.9.9/lib/python
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export PYTHONPATH=$PYTHONPATH:~/phonopy-1.10.3/lib/python
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@ -0,0 +1,120 @@
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Interfaces to calculators
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==========================
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Currently the built-in interfaces for VASP and Pwscf are
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prepared. VASP is the default interface and no special option is
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necessary to invoke it, but for the other interfaces, each special
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option has to be specified, e.g. ``--pwscf``.
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.. _calculator_interfaces:
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Calculator specific behaviors
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------------------------------
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Physical unit
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^^^^^^^^^^^^^^
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The interfaces for VASP and Pwscf are built in to the phono3py command.
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For each calculator, each physical unit system is used. The physical
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unit systems used for the calculators are summarized below.
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::
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| unit-cell FORCES_FC3 disp_fc3.yaml
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-----------------------------------------------
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VASP | Angstrom eV/Angstrom Angstrom
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Pwscf | au (bohr) Ry/au au
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``FORCES_FC2`` and ``disp_fc2.yaml`` have the same physical units as
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``FORCES_FC3`` and ``disp_fc3.yaml``, respectively.
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.. _default_unit_cell_file_name_for_calculator:
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Default unit cell file name
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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Default unit cell file names are also changed according to the calculators::
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VASP | POSCAR
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Pwscf | unitcell.in
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.. _default_displacement_distance_for_calculator:
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Default displacement distance created
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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Default displacement distances created by ``-d`` option without
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``--amplitude`` option are respectively as follows::
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VASP | 0.03 Angstrom
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Pwscf | 0.06 au (bohr)
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Usage of VASP interface
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-------------------------
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The VASP interface is the default one. Therefore how to use is found
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in :ref:`workflow`.
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Usage of Pwscf interface
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-------------------------
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To invoke the Pwscf interface, ``--pwscf`` option has to be always
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specified::
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% phono3py --pwscf [options] [arguments]
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The usage of the Pwscf interface is almost the same as that of the
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default case shown in :ref:`workflow`.
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When the file name of the unit cell is different from the default one
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(see :ref:`default_unit_cell_file_name_for_calculator`), ``-c`` option
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is used to specify the file name. Pwscf unit cell file parser used in
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phono3py is the same as that in phonopy. It can read
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only limited number of keywords that are shown in the phonopy web site
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(http://atztogo.github.io/phonopy/pwscf.html#pwscf-interface).
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1. Create supercells with displacements
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::
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% phono3py --pwscf -d --dim="2 2 2" -c Si.in
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In this example, probably 111 different supercells with
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displacements are created. Supercell files (``supercell-xxx.in``)
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are created but they contain only the crystal
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structures. Calculation setting has to be added before running the
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calculation.
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2. Run Pwscf for supercell force calculations
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Let's assume that the calculations have been made in ``disp-xxx``
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directories with the file names of ``Si-supercell.in``. Then after
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finishing those calculations, ``Si-supercell.out`` may be created
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in each directory.
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3. Collect forces
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``FORCES_FC3`` is obtained with ``--cf3`` options collecting the
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forces on atoms in Pwscf calculation results::
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% phono3py --pwscf --cf3 disp-00001/Si-supercell.out disp-00002/Si-supercell.out ...
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or in recent bash or zsh::
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% phono3py --pwscf --cf3 disp-{00001..00111}/Si-supercell.out
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``disp_fc3.yaml`` is used to create ``FORCES_FC3``, therefore it
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must exist in current directory.
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4) Calculate 3rd and 2nd order force constants
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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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5) Calculate lattice thermal conductivity, e.g., by::
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% phono3py --pwscf --dim="2 2 2" -c Si.in --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" \
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--mesh="11 11 11" --fc3 --fc2 --br
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@ -3,6 +3,89 @@
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Output files
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============
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The calculation results are written into files. Mostly the data are
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stored in HDF5 format. In the following sections, how to read the data
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from HDF5 files is shown.
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Intermediate text files
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------------------------
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``disp_fc3.yaml``
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^^^^^^^^^^^^^^^^^^
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This is created with ``-d`` option. See :ref:`create_displacements_option`.
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``disp_fc2.yaml``
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^^^^^^^^^^^^^^^^^^
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This is created with ``-d`` option with ``--dim_fc2`` option. See
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:ref:`dim_fc2_option`.
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``FORCES_FC3``
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^^^^^^^^^^^^^^^
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This is created with ``--cf3`` option. See :ref:`cf3_option`.
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``FORCES_FC2``
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^^^^^^^^^^^^^^^
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This is created with ``--cf2`` option. See :ref:`cf2_option` and
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:ref:`dim_fc2_option`.
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HDF5 files
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-------------
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``kappa-*.hdf5``
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^^^^^^^^^^^^^^^^^
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See the detail at :ref:`kappa_hdf5_file`.
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``fc3.hdf5``
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^^^^^^^^^^^^^
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Third order force constants are stored in :math:`\mathrm{eV}/\mathrm{\AA}^3`.
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``fc2.hdf5``
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^^^^^^^^^^^^^
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Second order force constants are stored in
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:math:`\mathrm{eV}/\mathrm{\AA}^3`.
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``gamma-*.hdf5``
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^^^^^^^^^^^^^^^^^
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Imaginary parts of self energies at harmonic phonon frequencies
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(:math:`\Gamma_\lambda(\omega_\lambda)` = half linewidths) are stored in
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THz. See :ref:`write_gamma_option`.
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``gamma_detail-*.hdf5``
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^^^^^^^^^^^^^^^^^^^^^^^^
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Q-point triplet contributions to imaginary parts of self energies at
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phonon frequencies (half linewidths) are stored in THz. See
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:ref:`write_detailed_gamma_option`.
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Simple text file
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-----------------
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``gammas-*.dat``
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^^^^^^^^^^^^^^^^^
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Imaginary parts of self energies with respect to frequency
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:math:`\Gamma_\lambda(\omega)` are stored in THz. See :ref:`ise_option`.
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``jdos-*.dat``
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^^^^^^^^^^^^^^^
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Joint densities of states are stored in Thz. See :ref:`jdos_option`.
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``linewidth-*.dat``
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^^^^^^^^^^^^^^^^^^^^
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Linewidths (FWHM) at temperatures are stored in THz. See :ref:`lw_option`.
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||||
How to read the results stored in hdf5 files
|
||||
-----------------------------------------------
|
||||
|
||||
|
|
@ -78,6 +161,8 @@ conductivity calculation is loaded and thermal conductivity tensor at
|
|||
5.84389577e-18, 0.00000000e+00, -7.63278476e-18])
|
||||
|
||||
|
||||
.. _kappa_hdf5_file:
|
||||
|
||||
Details of ``kappa-*.hdf5`` file
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
|
|
|
|||
|
|
@ -74,18 +74,18 @@ Calculation procedure
|
|||
|
||||
An example of thermal conductivity calculation is::
|
||||
|
||||
% phono3py --fc3 --fc2 --dim="2 2 2" -v --mesh="11 11 11" \
|
||||
-c POSCAR-unitcell --br --thm
|
||||
% phono3py --fc3 --fc2 --dim="2 2 2" --mesh="11 11 11" \
|
||||
-c POSCAR-unitcell --br
|
||||
|
||||
or with larger supercell for fc2::
|
||||
|
||||
% phono3py --fc3 --fc2 --dim_fc2="4 4 4" --dim="2 2 2" -v --mesh="11 11 11" \
|
||||
-c POSCAR-unitcell --br --thm
|
||||
% phono3py --fc3 --fc2 --dim_fc2="4 4 4" --dim="2 2 2" --mesh="11 11 11" \
|
||||
-c POSCAR-unitcell --br
|
||||
|
||||
This calculation may take very long time. ``--thm`` invokes a
|
||||
tetrahedron method for Brillouin zone integration for phonon
|
||||
lifetime calculation. Instead, ``--sigma`` option can be used with
|
||||
the smearing widths.
|
||||
lifetime calculation, which is the default option. Instead,
|
||||
``--sigma`` option can be used with the smearing widths.
|
||||
|
||||
In this command, phonon lifetimes at many grid points are
|
||||
calculated in series. The phonon lifetime calculation at each grid
|
||||
|
|
@ -95,21 +95,21 @@ Calculation procedure
|
|||
|
||||
First run the same command with the addition option of ``--wgp``::
|
||||
|
||||
% phono3py --fc3 --fc2 --dim="2 2 2" -v --mesh="11 11 11" \
|
||||
-c POSCAR-unitcell --br --thm --wgp
|
||||
% phono3py --fc3 --fc2 --dim="2 2 2" --mesh="11 11 11" \
|
||||
-c POSCAR-unitcell --br --wgp
|
||||
|
||||
``ir_grid_points.yaml`` is obtained. In this file, irreducible
|
||||
q-points are shown. Then distribute calculations of phonon
|
||||
lifetimes on grid points with ``--write_gamma`` option by::
|
||||
|
||||
% phono3py --fc3 --fc2 --dim="2 2 2" -v --mesh="11 11 11" \
|
||||
-c POSCAR-unitcell --br --thm --write_gamma --gp="[grid ponit(s)]"
|
||||
% phono3py --fc3 --fc2 --dim="2 2 2" --mesh="11 11 11" \
|
||||
-c POSCAR-unitcell --br --write_gamma --gp="[grid ponit(s)]"
|
||||
|
||||
After finishing all distributed calculations, run with
|
||||
``--read_gamma`` option::
|
||||
|
||||
% phono3py --fc3 --fc2 --dim="2 2 2" -v --mesh="11 11 11" \
|
||||
-c POSCAR-unitcell --br --thm --read_gamma
|
||||
% phono3py --fc3 --fc2 --dim="2 2 2" --mesh="11 11 11" \
|
||||
-c POSCAR-unitcell --br --read_gamma
|
||||
|
||||
Once this calculation runs without problem, separately calculated
|
||||
hdf5 files on grid points are no more necessary and may be deleted.
|
||||
|
|
@ -132,9 +132,9 @@ to use denser meshes. But the denser mesh requires more
|
|||
computationally demanding.
|
||||
|
||||
The second Brillouin zone sum contains delta functions. In phono3py
|
||||
calculation, a linear tetrahedron method (``--thm``) and a smearing
|
||||
method (``--sigma``) can be used for this Brillouin zone
|
||||
integration. Smearing parameter is used to approximate delta
|
||||
calculation, a linear tetrahedron method (``--thm``, default option)
|
||||
and a smearing method (``--sigma``) can be used for this Brillouin
|
||||
zone integration. Smearing parameter is used to approximate delta
|
||||
functions. Small ``sigma`` value is better to describe the detailed
|
||||
structure of three-phonon-space, but it requires a denser mesh to
|
||||
converge.
|
||||
|
|
|
|||
Loading…
Reference in New Issue