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Updated document toward v2 release

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Atsushi Togo 2021-07-21 10:39:47 +09:00
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.gitignore vendored
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@ -35,6 +35,7 @@ nosetests.xml
.mr.developer.cfg .mr.developer.cfg
.project .project
.pydevproject .pydevproject
.vscode
# Doc # Doc
.buildinfo .buildinfo

53
doc/auxiliary-tools.rst
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@ -40,14 +40,16 @@ How to use ``phono3py-kaccum``
Let's computer lattice thermal conductivity of Si using the ``Si-PBEsol`` Let's computer lattice thermal conductivity of Si using the ``Si-PBEsol``
example found in the example directory. example found in the example directory.
:: .. code-block:: shell
% 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 % phono3py --dim="2 2 2" --pa="F" -c POSCAR-unitcell --mesh="11 11 11" --sym-fc --br
Then using the output file, ``kappa-m111111.hdf5``, run Then using the output file, ``kappa-m111111.hdf5``, run
``phono3py-kaccum`` as follows:: ``phono3py-kaccum`` as follows:
% phono3py-kaccum --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" -c POSCAR-unitcell kappa-m111111.hdf5 |tee kaccum.dat .. code-block:: shell
% phono3py-kaccum --pa="F" -c POSCAR-unitcell kappa-m111111.hdf5 |tee kaccum.dat
Here ``--pa`` is optional. The definition of ``--pa`` option is same Here ``--pa`` is optional. The definition of ``--pa`` option is same
as :ref:`pa_option`. ``POSCAR-unitcell`` is the unit cell filename as :ref:`pa_option`. ``POSCAR-unitcell`` is the unit cell filename
@ -66,7 +68,7 @@ temperatures calculated.
To plot the output by gnuplot at temperature index 30 that may To plot the output by gnuplot at temperature index 30 that may
correspond to 300 K, correspond to 300 K,
:: .. code-block:: shell
% gnuplot % gnuplot
... ...
@ -106,9 +108,11 @@ POSCAR-unitcell``.
^^^^^^^^ ^^^^^^^^
Let ``phono3py-kaccum`` read a QE (pw) unit cell file with ``-c`` Let ``phono3py-kaccum`` read a QE (pw) unit cell file with ``-c``
option, for example:: option, for example:
phono3py-kaccum --qe --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" -c Si.in kappa-m191919.hdf5 .. code-block:: bash
phono3py-kaccum --qe --pa="F" -c Si.in kappa-m191919.hdf5
.. |ipwscf| image:: Si-kaccum-pwscf.png .. |ipwscf| image:: Si-kaccum-pwscf.png
:width: 25% :width: 25%
@ -201,25 +205,25 @@ convergence.
``--gv`` ``--gv``
^^^^^^^^^ ^^^^^^^^
Outer product of group velocities :math:`\mathbf{v}_\lambda \otimes Outer product of group velocities :math:`\mathbf{v}_\lambda \otimes
\mathbf{v}_\lambda` divided by primitive cell volume (in :math:`\text{THz}^2 / \mathbf{v}_\lambda` divided by primitive cell volume (in :math:`\text{THz}^2 /
\text{Angstrom}`) \text{Angstrom}`)
``--average`` ``--average``
^^^^^^^^^^^^^^ ^^^^^^^^^^^^^
Output the traces of the tensors divided by 3 rather than the unique Output the traces of the tensors divided by 3 rather than the unique
elements. elements.
``--trace`` ``--trace``
^^^^^^^^^^^^ ^^^^^^^^^^^
Output the traces of the tensors rather than the unique elements. Output the traces of the tensors rather than the unique elements.
Options for scalar properties Options for scalar properties
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
For the following properties, those values are normalized by the For the following properties, those values are normalized by the
number of full grid points. This is understood as normalized for one number of full grid points. This is understood as normalized for one
@ -230,31 +234,36 @@ frequency, cumulative property, and derivative of cumulative property
such like DOS. such like DOS.
``--gamma`` ``--gamma``
^^^^^^^^^^^^ ^^^^^^^^^^^
:math:`\Gamma_\lambda(\omega_\lambda)` (in THz) :math:`\Gamma_\lambda(\omega_\lambda)` (in THz)
``--tau`` ``--tau``
^^^^^^^^^^^ ^^^^^^^^^
Lifetime :math:`\tau_\lambda = \frac{1}{2\Gamma_\lambda(\omega_\lambda)}` (in ps) Lifetime :math:`\tau_\lambda = \frac{1}{2\Gamma_\lambda(\omega_\lambda)}` (in ps)
``--cv`` ``--cv``
^^^^^^^^^ ^^^^^^^^
Modal heat capacity :math:`C_\lambda` (in eV/K) Modal heat capacity :math:`C_\lambda` (in eV/K)
``--gv-norm`` ``--gv-norm``
^^^^^^^^^^^^^^ ^^^^^^^^^^^^^
Absolute value of group velocity :math:`|\mathbf{v}_\lambda|` (in Absolute value of group velocity :math:`|\mathbf{v}_\lambda|` (in
:math:`\text{THz}\cdot\text{Angstrom}`) :math:`\text{THz}\cdot\text{Angstrom}`)
``--pqj`` ``--pqj``
^^^^^^^^^^^^^^ ^^^^^^^^^
Averaged phonon-phonon interaction :math:`P_{\mathbf{q}j}` (in :math:`\text{eV}^2`) Averaged phonon-phonon interaction :math:`P_{\mathbf{q}j}` (in :math:`\text{eV}^2`)
``--dos``
^^^^^^^^^
Constant value of 1. This results in phonon DOS.
.. _auxiliary_tools_kdeplot: .. _auxiliary_tools_kdeplot:
``phono3py-kdeplot`` ``phono3py-kdeplot``
@ -271,7 +280,9 @@ Then (frequency, lifetime)-data points are superimposed on the density
plot. plot.
``phono3py-kdeplot`` reads a result of the thermal conductivity ``phono3py-kdeplot`` reads a result of the thermal conductivity
calculation as the first argument:: calculation as the first argument:
.. code-block:: shell
% phono3py-kdeplot kappa-m111111.hdf5 % phono3py-kdeplot kappa-m111111.hdf5
@ -318,7 +329,7 @@ This option controls the resolution of the density plot. The default
value is 100. With larger nbins, the resolution of the plot becomes value is 100. With larger nbins, the resolution of the plot becomes
better, but the computation will take more time. better, but the computation will take more time.
:: .. code-block:: shell
% phono3py-kdeplot --nbins=200 kappa-m111111.hdf5 % phono3py-kdeplot --nbins=200 kappa-m111111.hdf5
@ -342,7 +353,7 @@ respectively.
of drawing region along y-axis, therefore as a side effect, the of drawing region along y-axis, therefore as a side effect, the
computation will be roughly twice faster. computation will be roughly twice faster.
:: .. code-block:: shell
% phono3py-kdeplot --ymax=60 kappa-m111111.hdf5 % phono3py-kdeplot --ymax=60 kappa-m111111.hdf5
@ -363,7 +374,7 @@ maximum density. Normally smaller value results in larger drawing
region. The default value is 0.1. When ``--ymax`` is specified region. The default value is 0.1. When ``--ymax`` is specified
together, this option is ignored. together, this option is ignored.
:: .. code-block:: shell
% phono3py-kdeplot --dr=0.01 kappa-m111111.hdf5 % phono3py-kdeplot --dr=0.01 kappa-m111111.hdf5
@ -375,7 +386,7 @@ presented at the matplotlib documentation,
https://matplotlib.org/users/colormaps.html. The default colormap https://matplotlib.org/users/colormaps.html. The default colormap
depends on your matplotlib environment. depends on your matplotlib environment.
:: .. code-block:: shell
% phono3py-kdeplot --cmap="OrRd" kappa-m111111.hdf5 % phono3py-kdeplot --cmap="OrRd" kappa-m111111.hdf5

158
doc/command-options.rst
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@ -13,7 +13,9 @@ instead of and together with the command options. The setting tags are
mostly equivalent to the respective most command options, but when mostly equivalent to the respective most command options, but when
both are set simultaneously, the command options are preferred. An both are set simultaneously, the command options are preferred. An
example of configuration (e.g., saved in a file ``setting.conf``) is example of configuration (e.g., saved in a file ``setting.conf``) is
as follow:: as follow:
.. code-block:: bash
DIM = 2 2 2 DIM = 2 2 2
DIM_FC2 = 4 4 4 DIM_FC2 = 4 4 4
@ -27,13 +29,13 @@ as follow::
where the setting tag names are case insensitive. This is run by where the setting tag names are case insensitive. This is run by
:: .. code-block:: bash
% phono3py setting.conf [comannd options] % phono3py setting.conf [comannd options]
or or
:: .. code-block:: bash
% phono3py [comannd options] -- setting.conf % phono3py [comannd options] -- setting.conf
@ -50,7 +52,7 @@ Input cell file name
This specifies input unit cell filename. This specifies input unit cell filename.
:: .. code-block:: bash
% phono3py -c POSCAR-unitcell ... (many options) % phono3py -c POSCAR-unitcell ... (many options)
@ -83,18 +85,18 @@ These options have no respective configuration file tags.
``--cf3`` (command option only) ``--cf3`` (command option only)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
This is used to create ``FORCES_FC3`` from ``disp_fc3.yaml`` and This is used to create ``FORCES_FC3`` from ``phono3py_disp.yaml`` and
force calculator outputs containing forces in supercells. ``disp_fc3.yaml`` force calculator outputs containing forces in supercells. ``phono3py_disp.yaml``
has to be located at the current directory. Calculator interface has has to be located at the current directory. Calculator interface has
to be specified except for VASP (default) case. to be specified except for VASP (default) case.
:: .. code-block:: bash
% phono3py --cf3 disp-{00001..00755}/vasprun.xml % phono3py --cf3 disp-{00001..00755}/vasprun.xml
:: .. code-block:: bash
% phono3py --qe --cf3 supercell_out/disp-{00001..00111}/Si.out % phono3py --cf3 supercell_out/disp-{00001..00111}/Si.out
.. _cf3_file_option: .. _cf3_file_option:
@ -102,16 +104,18 @@ to be specified except for VASP (default) case.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
This is used to create ``FORCES_FC3`` from a text file containing a This is used to create ``FORCES_FC3`` from a text file containing a
list of calculator output file names. ``disp_fc3.yaml`` has to be list of calculator output file names. ``phono3py_disp.yaml`` has to be
located at the current directory. Calculator interface has to be located at the current directory. Calculator interface has to be
specified except for VASP (default) case. specified except for VASP (default) case.
:: .. code-block:: bash
% phono3py --cf3-file file_list.dat % phono3py --cf3-file file_list.dat
where ``file_list.dat`` contains file names that can be recognized where ``file_list.dat`` contains file names that can be recognized
from the current directory and is expected to be like:: from the current directory and is expected to be like:
.. code-block:: bash
disp-00001/vasprun.xml disp-00001/vasprun.xml
disp-00002/vasprun.xml disp-00002/vasprun.xml
@ -128,12 +132,12 @@ to be used together with ``--cutoff-pair`` option.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
This is used to create ``FORCES_FC2`` similarly to ``--cf3`` This is used to create ``FORCES_FC2`` similarly to ``--cf3``
option. ``disp_fc2.yaml`` has to be located at the current option. ``phono3py_disp.yaml`` has to be located at the current
directory. This is optional. Calculator interface has to be specified directory. This is optional. Calculator interface has to be specified
except for VASP (default) case. ``FORCES_FC2`` is necessary to run except for VASP (default) case. ``FORCES_FC2`` is necessary to run
with ``--dim-fc2`` option. with ``--dim-fc2`` option.
:: .. code-block:: bash
% phono3py --cf2 disp_fc2-{00001..00002}/vasprun.xml % phono3py --cf2 disp_fc2-{00001..00002}/vasprun.xml
@ -153,7 +157,7 @@ the forces of the perfect supercells. In ideal case, these forces are
zero, but often they are not. Here, this is called "residual zero, but often they are not. Here, this is called "residual
forces". Sometimes quality of force constants is improved in this way. forces". Sometimes quality of force constants is improved in this way.
:: .. code-block:: bash
% phono3py --cf3 disp3-{00001..01254}/vasprun.xml --cfz disp3-00000/vasprun.xml % phono3py --cf3 disp3-{00001..01254}/vasprun.xml --cfz disp3-00000/vasprun.xml
% phono3py --cf2 disp2-{00001..00006}/vasprun.xml --cfz disp2-00000/vasprun.xml % phono3py --cf2 disp2-{00001..00006}/vasprun.xml --cfz disp2-00000/vasprun.xml
@ -163,10 +167,10 @@ forces". Sometimes quality of force constants is improved in this way.
``--fs2f2`` or ``--force-sets-to-forces-fc2`` (command option only) ``--fs2f2`` or ``--force-sets-to-forces-fc2`` (command option only)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``FORCES_FC2`` and ``disp_fc2.yaml`` are created ``FORCES_FC2`` is created from phonopy's ``FORCE_SETS`` file.
from phonopy's ``FORCE_SETS`` file. Necessary yaml lines for ``phono3py_disp.yaml`` is displayed as text.
:: .. code-block:: bash
% phono3py --fs2f2 % phono3py --fs2f2
@ -176,17 +180,17 @@ from phonopy's ``FORCE_SETS`` file.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Phonopy's ``FORCE_SETS`` is created from Phonopy's ``FORCE_SETS`` is created from
``FORCES_FC3`` and ``disp_fc3.yaml``. ``FORCES_FC3`` and ``phono3py_disp.yaml``.
:: .. code-block:: bash
% phono3py --cfs % phono3py --cfs
In conjunction with :ref:`--dim-fc2 <dim_fc2_option>`, phonopy's In conjunction with :ref:`--dim-fc2 <dim_fc2_option>`, phonopy's
``FORCE_SETS`` is created from ``FORCES_FC2`` and ``disp_fc2.yaml`` ``FORCE_SETS`` is created from ``FORCES_FC2`` and ``phono3py_disp.yaml``
instead of ``FORCES_FC3`` and ``disp_fc3.yaml``. instead of ``FORCES_FC3`` and ``phono3py_disp.yaml``.
:: .. code-block:: bash
% phono3py --cfs --dim-fc2="x x x" % phono3py --cfs --dim-fc2="x x x"
@ -199,7 +203,9 @@ Supercell and primitive cell
~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~
Supercell dimension is specified. See the Supercell dimension is specified. See the
detail at http://phonopy.github.io/phonopy/setting-tags.html#dim . detail at http://phonopy.github.io/phonopy/setting-tags.html#dim.
When a proper ``phono3py_disp.yaml`` exists in the current directory,
this is unnecessary to be specified.
.. _dim_fc2_option: .. _dim_fc2_option:
@ -208,6 +214,8 @@ detail at http://phonopy.github.io/phonopy/setting-tags.html#dim .
Supercell dimension for 2nd order force constants (for harmonic Supercell dimension for 2nd order force constants (for harmonic
phonons) is specified. This is optional. phonons) is specified. This is optional.
When a proper ``phono3py_disp.yaml`` exists in the current directory,
this is unnecessary to be specified.
A larger and different supercell size for 2nd order force constants A larger and different supercell size for 2nd order force constants
than that for 3rd order force constants can be specified with this than that for 3rd order force constants can be specified with this
@ -218,31 +226,31 @@ order force constants may be a good idea.
Using this option with ``-d`` option, the structure files Using this option with ``-d`` option, the structure files
(e.g. ``POSCAR_FC2-xxxxx`` or equivalent files for the other (e.g. ``POSCAR_FC2-xxxxx`` or equivalent files for the other
interfaces) and ``disp_fc2.yaml`` are created. These are used to interfaces) and ``phono3py_disp.yaml`` are created. These are used to
calculate 2nd order force constants for the larger supercell size and calculate 2nd order force constants for the larger supercell size and
these force calculations have to be done in addition to the usual these force calculations have to be done in addition to the usual
force calculations for 3rd order force constants. force calculations for 3rd order force constants.
:: .. code-block:: bash
phono3py -d --dim="2 2 2" --dim-fc2="4 4 4" -c POSCAR-unitcell phono3py -d --dim="2 2 2" --dim-fc2="4 4 4" -c POSCAR-unitcell
After the force calculations, ``--cf2`` option is used to create After the force calculations, ``--cf2`` option is used to create
``FORCES_FC2``. ``FORCES_FC2``.
:: .. code-block:: bash
phono3py --cf2 disp-{001,002}/vasprun.xml phono3py --cf2 disp-{001,002}/vasprun.xml
To calculate 2nd order force constants for the larger supercell size, To calculate 2nd order force constants for the larger supercell size,
``FORCES_FC2`` and ``disp_fc2.yaml`` are necessary. Whenever running ``FORCES_FC2`` and ``phono3py_disp.yaml`` are necessary. Whenever running
phono3py for the larger 2nd order force constants, ``--dim-fc2`` phono3py for the larger 2nd order force constants, ``--dim-fc2``
option has to be specified. ``fc2.hdf5`` created as a result of option has to be specified. ``fc2.hdf5`` created as a result of
running phono3py contains the 2nd order force constants with running phono3py contains the 2nd order force constants with
larger supercell size. The filename is the same as that created in the larger supercell size. The filename is the same as that created in the
usual phono3py run without ``--dim-fc2`` option. usual phono3py run without ``--dim-fc2`` option.
:: .. code-block:: bash
phono3py --dim="2 2 2" --dim_fc2="4 4 4" -c POSCAR-unitcell ... (many options) phono3py --dim="2 2 2" --dim_fc2="4 4 4" -c POSCAR-unitcell ... (many options)
@ -253,7 +261,9 @@ usual phono3py run without ``--dim-fc2`` option.
Transformation matrix from a non-primitive cell to the primitive Transformation matrix from a non-primitive cell to the primitive
cell. See phonopy ``PRIMITIVE_AXES`` tag (``--pa`` option) at cell. See phonopy ``PRIMITIVE_AXES`` tag (``--pa`` option) at
http://phonopy.github.io/phonopy/setting-tags.html#primitive-axis http://phonopy.github.io/phonopy/setting-tags.html#primitive-axis.
When a proper ``phono3py_disp.yaml`` exists in the current directory,
this is unnecessary to be specified.
Displacement creation Displacement creation
--------------------- ---------------------
@ -265,8 +275,10 @@ Displacement creation
Supercell with displacements are created. Using with ``--amplitude`` Supercell with displacements are created. Using with ``--amplitude``
option, atomic displacement distances are controlled. With this option, atomic displacement distances are controlled. With this
option, files for supercells with displacements and ``disp_fc3.yaml`` option, files for supercells with displacements and ``phono3py_disp.yaml``
file are created. file are created. ``--pa`` should be specified if the input unit cell
structure is not a primitive cell, e.g., ``--pa="F"`` if the input
unit cell has F-centring.
.. _amplitude_option: .. _amplitude_option:
@ -304,9 +316,9 @@ using with ``--sym-fc``, the calculated results will become slightly
different due to imperfect symmetrization scheme that phono3py different due to imperfect symmetrization scheme that phono3py
employs. employs.
:: .. code-block:: bash
% phono3py --dim="2 2 2" --cfc --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" -c POSCAR-unitcell % phono3py --dim="2 2 2" --cfc --pa="F" -c POSCAR-unitcell
.. _symmetrization_option: .. _symmetrization_option:
@ -398,9 +410,9 @@ Indices of grid points are specified by space or comma (``,``)
separated numbers. The mapping table between grid points to its separated numbers. The mapping table between grid points to its
indices is obtained by running with ``--loglevel=2`` option. indices is obtained by running with ``--loglevel=2`` option.
:: .. code-block:: bash
% 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" % phono3py --dim="2 2 2" --pa="F" -c POSCAR-unitcell --mesh="19 19 19" --fc3 --fc2 --br --write-gamma --gp="0 1 2 3 4 5"
where ``--gp="0 1 2 3 4 5"`` can be also written where ``--gp="0 1 2 3 4 5"`` can be also written
``--gp="0,1,2,3,4,5"``. ``--ga`` option below can be used similarly ``--gp="0,1,2,3,4,5"``. ``--ga`` option below can be used similarly
@ -432,7 +444,7 @@ indices used to be averaged. The calculated values at indices
separated by space are averaged, and those separated by comma are separated by space are averaged, and those separated by comma are
separately calculated. separately calculated.
:: .. code-block:: bash
% phono3py --fc3 --fc2 --dim="2 2 2" --mesh="16 16 16" -c POSCAR-unitcell --nac --gp="34" --bi="4 5, 6" % phono3py --fc3 --fc2 --dim="2 2 2" --mesh="16 16 16" -c POSCAR-unitcell --nac --gp="34" --bi="4 5, 6"
@ -457,9 +469,9 @@ grid points and their grid addresses in integers. Q-points
corresponding to grid points are calculated divided these integers by corresponding to grid points are calculated divided these integers by
sampling mesh numbers for respective reciprocal axes. sampling mesh numbers for respective reciprocal axes.
:: .. code-block:: bash
% 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" --wgp % phono3py --dim="2 2 2" --pa="F" -c POSCAR-unitcell --mesh="19 19 19" --wgp
.. _stp_option: .. _stp_option:
@ -471,9 +483,9 @@ points for specified sampling mesh numbers are shown. This can be used
to estimate how large a calculation is. Only those for specific grid to estimate how large a calculation is. Only those for specific grid
points are shown by using with ``--gp`` or ``--ga`` option. points are shown by using with ``--gp`` or ``--ga`` option.
:: .. code-block:: bash
% 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" --stp --gp 20 % phono3py --dim="2 2 2" --pa="F" -c POSCAR-unitcell --mesh="19 19 19" --stp --gp 20
Brillouin zone integration Brillouin zone integration
--------------------------- ---------------------------
@ -585,7 +597,7 @@ parameters are read from database of the natural abundance data for
elements, which refers Laeter *et al.*, Pure Appl. Chem., **75**, 683 elements, which refers Laeter *et al.*, Pure Appl. Chem., **75**, 683
(2003). (2003).
:: .. code-block:: bash
% phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br --isotope % phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br --isotope
@ -599,11 +611,15 @@ option. For example of GaN, this may be set like ``--mv="1.97e-4
of atoms in the primitive cell. of atoms in the primitive cell.
Isotope effect to thermal conductivity may be checked first running Isotope effect to thermal conductivity may be checked first running
without isotope calculation:: without isotope calculation:
.. code-block:: bash
% phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br % phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br
Then running with isotope calculation:: Then running with isotope calculation:
.. code-block:: bash
% phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br --read-gamma --mv="1.97e-4 1.97e-4 0 0" % phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br --read-gamma --mv="1.97e-4 1.97e-4 0 0"
@ -660,13 +676,13 @@ together with ``-o`` option is strongly recommended.
First, run full conductivity calculation, First, run full conductivity calculation,
:: .. code-block:: bash
% phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br % phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br
Then Then
:: .. code-block:: bash
% phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br --read-gamma --ave-pp -o ave_pp % phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br --read-gamma --ave-pp -o ave_pp
@ -680,7 +696,7 @@ conductivity calculation. This option works only when ``--br`` options
are activated. Therefore third-order force constants are not necessary are activated. Therefore third-order force constants are not necessary
to input. The physical unit of the value is :math:`\text{eV}^2`. to input. The physical unit of the value is :math:`\text{eV}^2`.
:: .. code-block:: bash
% phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br --const-ave-pp=1e-10 % phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br --const-ave-pp=1e-10
@ -702,9 +718,9 @@ accessed by ``gamma_N`` and ``gamma_U`` keys. The shape of the arrays
is the same as that of ``gamma`` (see is the same as that of ``gamma`` (see
:ref:`kappa_hdf5_file_gamma`). An example (Si-PBEsol) is shown below: :ref:`kappa_hdf5_file_gamma`). An example (Si-PBEsol) is shown below:
:: .. code-block:: bash
% 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" --fc3 --fc2 --br --nu % phono3py --dim="2 2 2" --pa="F" -c POSCAR-unitcell --mesh="11 11 11" --fc3 --fc2 --br --nu
... ...
% ipython % ipython
@ -748,7 +764,7 @@ Temperature
Specific temperatures are specified by ``--ts``. Specific temperatures are specified by ``--ts``.
:: .. code-block:: bash
% phono3py --fc3 --fc2 --dim="2 2 2" -v --mesh="11 11 11" -c POSCAR-unitcell --br --ts="200 300 400" % phono3py --fc3 --fc2 --dim="2 2 2" -v --mesh="11 11 11" -c POSCAR-unitcell --br --ts="200 300 400"
@ -760,7 +776,7 @@ Temperatures at equal interval are specified by ``--tmax``,
http://phonopy.github.io/phonopy/setting-tags.html#tprop-tmin-tmax-tstep http://phonopy.github.io/phonopy/setting-tags.html#tprop-tmin-tmax-tstep
. .
:: .. code-block:: bash
% phono3py --fc3 --fc2 --dim="2 2 2" -v --mesh="11 11 11" -c POSCAR-unitcell --br --tmin=100 --tmax=1000 --tstep=50 % phono3py --fc3 --fc2 --dim="2 2 2" -v --mesh="11 11 11" -c POSCAR-unitcell --br --tmin=100 --tmax=1000 --tstep=50
@ -782,7 +798,7 @@ first line of ``BORN`` file.
This is used with ``--nac`` to specify reciprocal-space direction This is used with ``--nac`` to specify reciprocal-space direction
at :math:`\mathbf{q}\rightarrow \mathbf{0}`. See the detail at :math:`\mathbf{q}\rightarrow \mathbf{0}`. See the detail
at http://phonopy.github.io/phonopy/setting-tags.html#q-direction . at http://phonopy.github.io/phonopy/setting-tags.html#q-direction.
.. _write_gamma_option: .. _write_gamma_option:
@ -800,7 +816,7 @@ calculated with respect to :math:`\omega`. The output is written to
with respect to frequency in THz (without :math:`2\pi`). Frequency sampling with respect to frequency in THz (without :math:`2\pi`). Frequency sampling
points can be specified by :ref:`freq_sampling_option`. points can be specified by :ref:`freq_sampling_option`.
:: .. code-block:: bash
% phono3py --fc3 --fc2 --dim="2 2 2" --mesh="16 16 16" -c POSCAR-unitcell --nac --q-direction="1 0 0" --gp=0 --ise --bi="4 5, 6" % phono3py --fc3 --fc2 --dim="2 2 2" --mesh="16 16 16" -c POSCAR-unitcell --nac --q-direction="1 0 0" --gp=0 --ise --bi="4 5, 6"
@ -832,9 +848,9 @@ are the values given as follows, respectively,
\Delta(-\mathbf{q}+\mathbf{q}'+\mathbf{q}'') \delta(\omega-\omega_{\lambda'} \Delta(-\mathbf{q}+\mathbf{q}'+\mathbf{q}'') \delta(\omega-\omega_{\lambda'}
-\omega_{\lambda''}). -\omega_{\lambda''}).
:: .. code-block:: bash
% phono3py --fc2 --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" -c POSCAR-unitcell --mesh="16 16 16" --jdos --ga="0 0 0 8 8 8" % phono3py --fc2 --dim="2 2 2" --pa="F" -c POSCAR-unitcell --mesh="16 16 16" --jdos --ga="0 0 0 8 8 8"
When temperatures are specified, two classes of weighted JDOS are When temperatures are specified, two classes of weighted JDOS are
calculated. The result is written into calculated. The result is written into
@ -856,9 +872,9 @@ the values given as follows, respectively,
(n_{\lambda'}+ n_{\lambda''}+1) \delta( \omega - \omega_{\lambda'} - (n_{\lambda'}+ n_{\lambda''}+1) \delta( \omega - \omega_{\lambda'} -
\omega_{\lambda''}). \omega_{\lambda''}).
:: .. code-block:: bash
% phono3py --fc2 --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" -c POSCAR-unitcell --mesh="16 16 16" --jdos --ga="0 0 0 8 8 8" --ts=300 % phono3py --fc2 --dim="2 2 2" --pa="F" -c POSCAR-unitcell --mesh="16 16 16" --jdos --ga="0 0 0 8 8 8" --ts=300
This is an example of ``Si-PBEsol``. This is an example of ``Si-PBEsol``.
@ -891,11 +907,15 @@ Mode-Gruneisen parameter from 3rd order force constants
Mode-Gruneisen-parameters are calculated from fc3. Mode-Gruneisen-parameters are calculated from fc3.
Mesh sampling mode:: Mesh sampling mode:
.. code-block:: bash
% phono3py --fc3 --fc2 --dim="2 2 2" -v --mesh="16 16 16" -c POSCAR-unitcell --nac --gruneisen % phono3py --fc3 --fc2 --dim="2 2 2" -v --mesh="16 16 16" -c POSCAR-unitcell --nac --gruneisen
Band path mode:: Band path mode:
.. code-block:: bash
% phono3py --fc3 --fc2 --dim="2 2 2" -v -c POSCAR-unitcell --nac --gruneisen --band="0 0 0 0 0 1/2" % phono3py --fc3 --fc2 --dim="2 2 2" -v -c POSCAR-unitcell --nac --gruneisen --band="0 0 0 0 0 1/2"
@ -1015,9 +1035,9 @@ Phonon frequencies, eigenvectors, and grid point addresses are stored
in ``phonon-mxxx.hdf5`` file. :ref:`--pa <pa_option>` and :ref:`--nac in ``phonon-mxxx.hdf5`` file. :ref:`--pa <pa_option>` and :ref:`--nac
<nac_option>` may be required depending on calculation setting. <nac_option>` may be required depending on calculation setting.
:: .. code-block:: bash
% phono3py --fc2 --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" --mesh="11 11 11" -c POSCAR-unitcell --nac --write-phoonon % phono3py --fc2 --dim="2 2 2" --pa="F" --mesh="11 11 11" -c POSCAR-unitcell --nac --write-phoonon
Contents of ``phonon-mxxx.hdf5`` are watched by:: Contents of ``phonon-mxxx.hdf5`` are watched by::
@ -1065,9 +1085,9 @@ different eigenvalue solvers or different CPU
architectures. :ref:`--pa <pa_option>` and :ref:`--nac <nac_option>` architectures. :ref:`--pa <pa_option>` and :ref:`--nac <nac_option>`
may be required depending on calculation setting. may be required depending on calculation setting.
:: .. code-block:: bash
% phono3py --fc2 --fc3 --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" --mesh="11 11 11" -c POSCAR-unitcell --nac --read-phoonon --br % phono3py --fc2 --fc3 --dim="2 2 2" --pa="F" --mesh="11 11 11" -c POSCAR-unitcell --nac --read-phoonon --br
.. _write_read_pp_option: .. _write_read_pp_option:
@ -1086,13 +1106,13 @@ conductivity calculation, in writing and reading, ph-ph interaction
strength has to be stored in memory, so there is overhead in memory strength has to be stored in memory, so there is overhead in memory
than usual RTA calculation. than usual RTA calculation.
:: .. code-block:: bash
% phono3py --fc2 --fc3 --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" --mesh="11 11 11" -c POSCAR-unitcell --nac --write-pp --br --gp=1 % phono3py --fc2 --fc3 --dim="2 2 2" --pa="F" --mesh="11 11 11" -c POSCAR-unitcell --nac --write-pp --br --gp=1
:: .. code-block:: bash
% phono3py --fc2 --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" --mesh="11 11 11" -c POSCAR-unitcell --nac --read-pp --br --gp=1 % phono3py --fc2 --dim="2 2 2" --pa="F" --mesh="11 11 11" -c POSCAR-unitcell --nac --read-pp --br --gp=1
.. _hdf5_compression_option: .. _hdf5_compression_option:
@ -1125,8 +1145,6 @@ This rule is applied to
- ``kappa-xxx.hdf5`` - ``kappa-xxx.hdf5``
- ``phonon-xxx.hdf5`` - ``phonon-xxx.hdf5``
- ``pp-xxx.hdf5`` - ``pp-xxx.hdf5``
- ``disp_fc3.yaml``
- ``disp_fc2.yaml``
- ``gamma_detail-xxx.hdf5`` (write only) - ``gamma_detail-xxx.hdf5`` (write only)
.. _input_filename_option: .. _input_filename_option:
@ -1147,8 +1165,6 @@ This rule is applied to
- ``kappa-xxx.hdf5`` - ``kappa-xxx.hdf5``
- ``phonon-xxx.hdf5`` - ``phonon-xxx.hdf5``
- ``pp-xxx.hdf5`` - ``pp-xxx.hdf5``
- ``disp_fc3.yaml``
- ``disp_fc2.yaml``
``--io`` (command option only) ``--io`` (command option only)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

204
doc/conf.py
View File

@ -1,9 +1,10 @@
# -*- coding: utf-8 -*- """Sphinx phono3py configuration file."""
# #
# phono3py documentation build configuration file, created by # phono3py documentation build configuration file, created by
# sphinx-quickstart on Wed Jun 26 13:13:14 2013. # sphinx-quickstart on Wed Jun 26 13:13:14 2013.
# #
# This file is execfile()d with the current directory set to its containing dir. # This file is execfile()d with the current directory set to its containing
# dir.
# #
# Note that not all possible configuration values are present in this # Note that not all possible configuration values are present in this
# autogenerated file. # autogenerated file.
@ -11,22 +12,23 @@
# All configuration values have a default; values that are commented out # All configuration values have a default; values that are commented out
# serve to show the default. # serve to show the default.
import sys, os import sys
import os
# If extensions (or modules to document with autodoc) are in another directory, # If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the # add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here. # documentation root, use os.path.abspath to make it absolute, like shown here.
#sys.path.insert(0, os.path.abspath('.')) # sys.path.insert(0, os.path.abspath('.'))
# -- General configuration ----------------------------------------------------- # -- General configuration ----------------------------------------------------
# If your documentation needs a minimal Sphinx version, state it here. # If your documentation needs a minimal Sphinx version, state it here.
#needs_sphinx = '1.0' # needs_sphinx = '1.0'
# Add any Sphinx extension module names here, as strings. They can be extensions # Add any Sphinx extension module names here, as strings. They can be
# coming with Sphinx (named 'sphinx.ext.*') or your custom ones. # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
#extensions = ['sphinx.ext.imgmath'] # extensions = ['sphinx.ext.imgmath']
extensions = ['sphinx.ext.mathjax'] extensions = ['sphinx.ext.mathjax', 'myst_parser']
# Add any paths that contain templates here, relative to this directory. # Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates'] templates_path = ['_templates']
@ -35,7 +37,7 @@ templates_path = ['_templates']
source_suffix = '.rst' source_suffix = '.rst'
# The encoding of source files. # The encoding of source files.
#source_encoding = 'utf-8-sig' # source_encoding = 'utf-8-sig'
# The master toctree document. # The master toctree document.
master_doc = 'index' master_doc = 'index'
@ -49,52 +51,53 @@ copyright = u'2015, Atsushi Togo'
# built documents. # built documents.
# #
# The short X.Y version. # The short X.Y version.
version = '1.22' version = '2.0'
# The full version, including alpha/beta/rc tags. # The full version, including alpha/beta/rc tags.
release = '1.22.3' release = '2.0.0'
# The language for content autogenerated by Sphinx. Refer to documentation # The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages. # for a list of supported languages.
#language = None # language = None
# There are two options for replacing |today|: either, you set today to some # There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used: # non-false value, then it is used:
#today = '' # today = ''
# Else, today_fmt is used as the format for a strftime call. # Else, today_fmt is used as the format for a strftime call.
#today_fmt = '%B %d, %Y' # today_fmt = '%B %d, %Y'
# List of patterns, relative to source directory, that match files and # List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files. # directories to ignore when looking for source files.
exclude_patterns = ['_build'] exclude_patterns = ['_build']
# The reST default role (used for this markup: `text`) to use for all documents. # The reST default role (used for this markup: `text`) to use for all
#default_role = None # documents.
# default_role = None
# If true, '()' will be appended to :func: etc. cross-reference text. # If true, '()' will be appended to :func: etc. cross-reference text.
#add_function_parentheses = True # add_function_parentheses = True
# If true, the current module name will be prepended to all description # If true, the current module name will be prepended to all description
# unit titles (such as .. function::). # unit titles (such as .. function::).
#add_module_names = True # add_module_names = True
# If true, sectionauthor and moduleauthor directives will be shown in the # If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default. # output. They are ignored by default.
#show_authors = False # show_authors = False
# The name of the Pygments (syntax highlighting) style to use. # The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx' pygments_style = 'sphinx'
# A list of ignored prefixes for module index sorting. # A list of ignored prefixes for module index sorting.
#modindex_common_prefix = [] # modindex_common_prefix = []
# -- Options for HTML output --------------------------------------------------- # -- Options for HTML output --------------------------------------------------
# The theme to use for HTML and HTML Help pages. See the documentation for # The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes. # a list of builtin themes.
# html_theme = 'default' # html_theme = 'default'
# Add any paths that contain custom themes here, relative to this directory. # Add any paths that contain custom themes here, relative to this directory.
#html_theme_path = [] # html_theme_path = []
################ ################
# guzzle theme # # guzzle theme #
@ -145,102 +148,24 @@ pygments_style = 'sphinx'
# # "globaltoc_includehidden": False, # # "globaltoc_includehidden": False,
# } # }
################### html_theme = 'sphinx_book_theme'
# bootstrap theme #
###################
import sphinx_bootstrap_theme
html_theme = 'bootstrap'
html_theme_path = sphinx_bootstrap_theme.get_html_theme_path()
# Theme options are theme-specific and customize the look and feel of a theme
# further. For a list of options available for each theme, see the
# documentation.
#html_theme_options = {}
html_theme_options = {
# Navigation bar title. (Default: ``project`` value)
'navbar_title': "Phono3py",
# Tab name for entire site. (Default: "Site")
'navbar_site_name': "Site",
# A list of tuples containing pages or urls to link to.
# Valid tuples should be in the following forms:
# (name, page) # a link to a page
# (name, "/aa/bb", 1) # a link to an arbitrary relative url
# (name, "http://example.com", True) # arbitrary absolute url
# Note the "1" or "True" value above as the third argument to indicate
# an arbitrary url.
# 'navbar_links': [
# ("Examples", "examples"),
# ("Link", "http://example.com", True),
# ],
# 'navbar_links': [
# ("Options", "command-options"),
# ],
# Render the next and previous page links in navbar. (Default: true)
'navbar_sidebarrel': True,
# Render the current pages TOC in the navbar. (Default: true)
'navbar_pagenav': True,
# Global TOC depth for "site" navbar tab. (Default: 1)
# Switching to -1 shows all levels.
'globaltoc_depth': 2,
# Include hidden TOCs in Site navbar?
#
# Note: If this is "false", you cannot have mixed ``:hidden:`` and
# non-hidden ``toctree`` directives in the same page, or else the build
# will break.
#
# Values: "true" (default) or "false"
'globaltoc_includehidden': "true",
# HTML navbar class (Default: "navbar") to attach to <div> element.
# For black navbar, do "navbar navbar-inverse"
# 'navbar_class': "navbar navbar-inverse",
'navbar_class': "navbar",
# Fix navigation bar to top of page?
# Values: "true" (default) or "false"
'navbar_fixed_top': "true",
# Location of link to source.
# Options are "nav" (default), "footer" or anything else to exclude.
# 'source_link_position': "nav",
'source_link_position': "footer",
# Bootswatch (http://bootswatch.com/) theme.
#
# Options are nothing with "" (default) or the name of a valid theme
# such as "amelia" or "cosmo".
# 'bootswatch_theme': "united",
'bootswatch_theme': "cerulean",
# Choose Bootstrap version.
# Values: "3" (default) or "2" (in quotes)
'bootstrap_version': "3",
'nosidebar': "true",
}
# The name for this set of Sphinx documents. If None, it defaults to # The name for this set of Sphinx documents. If None, it defaults to
# "<project> v<release> documentation". # "<project> v<release> documentation".
#html_title = None # html_title = None
html_title = 'Phono3py v.%s' % release html_title = 'Phono3py v.%s' % release
# A shorter title for the navigation bar. Default is the same as html_title. # A shorter title for the navigation bar. Default is the same as html_title.
#html_short_title = None # html_short_title = None
# The name of an image file (relative to this directory) to place at the top # The name of an image file (relative to this directory) to place at the top
# of the sidebar. # of the sidebar.
#html_logo = None # html_logo = None
# The name of an image file (within the static path) to use as favicon of the # The name of an image file (within the static path) to use as favicon of the
# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
# pixels large. # pixels large.
#html_favicon = None # html_favicon = None
# Add any paths that contain custom static files (such as style sheets) here, # Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files, # relative to this directory. They are copied after the builtin static files,
@ -249,64 +174,65 @@ html_static_path = ['_static']
# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
# using the given strftime format. # using the given strftime format.
#html_last_updated_fmt = '%b %d, %Y' # html_last_updated_fmt = '%b %d, %Y'
# If true, SmartyPants will be used to convert quotes and dashes to # If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities. # typographically correct entities.
#html_use_smartypants = True # html_use_smartypants = True
# Custom sidebar templates, maps document names to template names. # Custom sidebar templates, maps document names to template names.
#html_sidebars = {} # html_sidebars = {}
# Additional templates that should be rendered to pages, maps page names to # Additional templates that should be rendered to pages, maps page names to
# template names. # template names.
#html_additional_pages = {} # html_additional_pages = {}
# If false, no module index is generated. # If false, no module index is generated.
#html_domain_indices = True # html_domain_indices = True
# If false, no index is generated. # If false, no index is generated.
#html_use_index = True # html_use_index = True
# If true, the index is split into individual pages for each letter. # If true, the index is split into individual pages for each letter.
#html_split_index = False # html_split_index = False
# If true, links to the reST sources are added to the pages. # If true, links to the reST sources are added to the pages.
#html_show_sourcelink = True # html_show_sourcelink = True
# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. # If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
#html_show_sphinx = True # html_show_sphinx = True
# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
#html_show_copyright = True # html_show_copyright = True
# If true, an OpenSearch description file will be output, and all pages will # If true, an OpenSearch description file will be output, and all pages will
# contain a <link> tag referring to it. The value of this option must be the # contain a <link> tag referring to it. The value of this option must be the
# base URL from which the finished HTML is served. # base URL from which the finished HTML is served.
#html_use_opensearch = '' # html_use_opensearch = ''
# This is the file name suffix for HTML files (e.g. ".xhtml"). # This is the file name suffix for HTML files (e.g. ".xhtml").
#html_file_suffix = None # html_file_suffix = None
# Output file base name for HTML help builder. # Output file base name for HTML help builder.
htmlhelp_basename = 'phono3pydoc' htmlhelp_basename = 'phono3pydoc'
# -- Options for LaTeX output -------------------------------------------------- # -- Options for LaTeX output -------------------------------------------------
latex_elements = { latex_elements = {
# The paper size ('letterpaper' or 'a4paper'). # The paper size ('letterpaper' or 'a4paper').
#'papersize': 'letterpaper', # 'papersize': 'letterpaper',
# The font size ('10pt', '11pt' or '12pt'). # The font size ('10pt', '11pt' or '12pt').
#'pointsize': '10pt', # 'pointsize': '10pt',
# Additional stuff for the LaTeX preamble. # Additional stuff for the LaTeX preamble.
#'preamble': '', 'preamble': '',
} }
# Grouping the document tree into LaTeX files. List of tuples # Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, documentclass [howto/manual]). # (source start file, target name, title, author, documentclass [howto/manual])
# .
latex_documents = [ latex_documents = [
('index', 'phono3py.tex', u'phono3py manual', ('index', 'phono3py.tex', u'phono3py manual',
u'Atsushi Togo', 'manual'), u'Atsushi Togo', 'manual'),
@ -314,26 +240,26 @@ latex_documents = [
# The name of an image file (relative to this directory) to place at the top of # The name of an image file (relative to this directory) to place at the top of
# the title page. # the title page.
#latex_logo = None # latex_logo = None
# For "manual" documents, if this is true, then toplevel headings are parts, # For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters. # not chapters.
#latex_use_parts = False # latex_use_parts = False
# If true, show page references after internal links. # If true, show page references after internal links.
#latex_show_pagerefs = False # latex_show_pagerefs = False
# If true, show URL addresses after external links. # If true, show URL addresses after external links.
#latex_show_urls = False # latex_show_urls = False
# Documents to append as an appendix to all manuals. # Documents to append as an appendix to all manuals.
#latex_appendices = [] # latex_appendices = []
# If false, no module index is generated. # If false, no module index is generated.
#latex_domain_indices = True # latex_domain_indices = True
# -- Options for manual page output -------------------------------------------- # -- Options for manual page output -------------------------------------------
# One entry per manual page. List of tuples # One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section). # (source start file, name, description, authors, manual section).
@ -343,10 +269,10 @@ man_pages = [
] ]
# If true, show URL addresses after external links. # If true, show URL addresses after external links.
#man_show_urls = False # man_show_urls = False
# -- Options for Texinfo output ------------------------------------------------ # -- Options for Texinfo output -----------------------------------------------
# Grouping the document tree into Texinfo files. List of tuples # Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author, # (source start file, target name, title, author,
@ -358,10 +284,10 @@ texinfo_documents = [
] ]
# Documents to append as an appendix to all manuals. # Documents to append as an appendix to all manuals.
#texinfo_appendices = [] # texinfo_appendices = []
# If false, no module index is generated. # If false, no module index is generated.
#texinfo_domain_indices = True # texinfo_domain_indices = True
# How to display URL addresses: 'footnote', 'no', or 'inline'. # How to display URL addresses: 'footnote', 'no', or 'inline'.
#texinfo_show_urls = 'footnote' # texinfo_show_urls = 'footnote'

394
doc/cutoff-pair.rst
View File

@ -52,28 +52,21 @@ Creating supercells with displacements
``--cutoff-pair`` option is employed when creating supercells with ``--cutoff-pair`` option is employed when creating supercells with
displacements, therefore this option must be used with ``-d`` option displacements, therefore this option must be used with ``-d`` option
when running phono3py, for example for the Si example:: when running phono3py, for the Si-PBEsol example:
.. code-block:: bash
% phono3py --cutoff-pair=5 -d --dim="2 2 2" -c POSCAR-unitcell % phono3py --cutoff-pair=5 -d --dim="2 2 2" -c POSCAR-unitcell
_ _____ ...
_ __ | |__ ___ _ __ ___|___ / _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ |_ \| '_ \| | | |
| |_) | | | | (_) | | | | (_) |__) | |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___/____/| .__/ \__, |
|_| |_| |___/
1.11.11
Run mode: displacements
Unit cell was read from "POSCAR-unitcell".
Displacement distance: 0.03 Displacement distance: 0.03
Number of displacements: 111 Number of displacements: 111
Cutoff distance for displacements: 5.0 Cutoff distance for displacements: 5.0
Number of displacement supercell files created: 51 Number of displacement supercell files created: 51
_
___ _ __ __| | Displacement dataset was written in "phono3py_disp.yaml".
/ _ \ '_ \ / _` | ...
| __/ | | | (_| |
\___|_| |_|\__,_|
% ls POSCAR-0* % ls POSCAR-0*
POSCAR-00001 POSCAR-00032 POSCAR-00043 POSCAR-00080 POSCAR-00097 POSCAR-00001 POSCAR-00032 POSCAR-00043 POSCAR-00080 POSCAR-00097
@ -95,12 +88,12 @@ displacements when this is run without ``--cutoff-pair``
option. ``Number of displacement supercell files created: 51`` gives option. ``Number of displacement supercell files created: 51`` gives
the contracted number of supercells with displacements by the contracted number of supercells with displacements by
``--cutoff-pair`` option. There number of ``POSCAR-0xxxx`` files is found ``--cutoff-pair`` option. There number of ``POSCAR-0xxxx`` files is found
51. At this step, a special ``disp_fc3.yaml`` is created. This 1. At this step, a special ``phono3py_disp.yaml`` is created. This
contains information on this contraction and used in the other contains information on this contraction and used in the other
calculation step, therefore this file must be kept carefully. calculation step, therefore this file must be kept carefully.
Supercell files Supercell files
^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^
``POSCAR-xxxxx`` (in the other calculator interface, the prefix of the ``POSCAR-xxxxx`` (in the other calculator interface, the prefix of the
filename is different) are not generated if distance between a pair of filename is different) are not generated if distance between a pair of
@ -112,13 +105,13 @@ displacements but ``POSCAR-xxxxx`` files not being included are not
generated. The reason of this indexing is that it can be useful when generated. The reason of this indexing is that it can be useful when
changing the cutoff-pair-distance. changing the cutoff-pair-distance.
Special ``disp_fc3.yaml`` Special ``phono3py_disp.yaml``
^^^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Using ``--cutoff-pair`` option together with ``-d`` option, a special Using ``--cutoff-pair`` option together with ``-d`` option, a special
``disp_fc3.yaml`` is created. This contains information on distances ``phono3py_disp.yaml`` is created. This contains information on distances
between displaced atomic-pairs and whether those pairs are to be between displaced atomic-pairs and whether those pairs are to be
computed or not. This special ``disp_fc3.yaml`` is necessary to create computed or not. This special ``phono3py_disp.yaml`` is necessary to create
fc3, therefore be careful not to overwrite it by running the option fc3, therefore be careful not to overwrite it by running the option
``-d`` without ``--cutoff-pair`` or with different ``--cutoff-pair`` ``-d`` without ``--cutoff-pair`` or with different ``--cutoff-pair``
with different value. with different value.
@ -128,7 +121,7 @@ Making ``FORCES_FC3``
To create ``FORCES_FC3``, only output files of the supercells created To create ``FORCES_FC3``, only output files of the supercells created
using ``--cutoff-pair`` option are passed to ``phono3py`` as the using ``--cutoff-pair`` option are passed to ``phono3py`` as the
arguments. The special ``disp_fc3.yaml`` file is necessary to be arguments. The special ``phono3py_disp.yaml`` file is necessary to be
located at current directory. located at current directory.
An example is shown below for the Si example. Here, it is supposed An example is shown below for the Si example. Here, it is supposed
@ -137,146 +130,150 @@ directories. After running force calculations, there should be the
output file containing forces in each directory (for VASP output file containing forces in each directory (for VASP
``vasprun.xml``). ``vasprun.xml``).
:: .. code-block:: bash
% 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 % 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
_ _____ ...
_ __ | |__ ___ _ __ ___|___ / _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ |_ \| '_ \| | | |
| |_) | | | | (_) | | | | (_) |__) | |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___/____/| .__/ \__, |
|_| |_| |___/
1.11.7
Displacement dataset is read from disp_fc3.yaml. Displacement dataset is read from phono3py_disp.yaml.
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 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
FORCES_FC3 has been created. FORCES_FC3 has been created.
_
___ _ __ __| |
/ _ \ '_ \ / _` |
| __/ | | | (_| |
\___|_| |_|\__,_|
Using :ref:`--cf3_file option <cf3_file_option>` may be recommended
when the number of force files is large. :: Using :ref:`--cf3-file option <cf3_file_option>` may be recommended
when the number of force files is large.
.. code-block:: bash
% for i in `ls POSCAR-0*|sed s/POSCAR-//`;do echo disp-$i/vasprun.xml;done > file_list.dat % for i in `ls POSCAR-0*|sed s/POSCAR-//`;do echo disp-$i/vasprun.xml;done > file_list.dat
% phono3py --cf3_file file_list.dat % phono3py --cf3-file file_list.dat
Using a python script, ``disp_fc3.yaml`` is easily parsed. So Using a python script, ``phono3py_disp.yaml`` is easily parsed. So
it is also easy to create the file list by a python it is also easy to create the file list by a python
script: script:
.. code-block:: python .. code-block:: python
#!/usr/bin/env python #!/usr/bin/env python
import yaml
from phono3py.interface.phono3py_yaml import Phono3pyYaml
p3yaml = Phono3pyYaml()
p3yaml.read("phono3py_disp.yaml")
dds = p3yaml.dataset
file_name_tmpl = "disp-%05d/vasprun.xml" file_name_tmpl = "disp-%05d/vasprun.xml"
dds = yaml.load(open("disp_fc3.yaml"))
count = 1 count = 1
for d1 in dds['first_atoms']: for d1 in dds['first_atoms']:
print(file_name_tmpl % count) print(file_name_tmpl % count)
count += 1 count += 1
for d1 in dds['first_atoms']: for d1 in dds['first_atoms']:
for d2 in d1['second_atoms']: for d2 in d1['second_atoms']:
for d in d2['displacements']: if d2['included']:
if d2['included']: print(file_name_tmpl % count)
print(file_name_tmpl % count) count += 1
count += 1
Running phonon-phonon interaction calculation Running phonon-phonon interaction calculation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
To create fc3, ``--cutoff-pair`` option is not necessary but the To create fc3, ``--cutoff-pair`` option is not necessary but the
special ``disp_fc3.yaml`` is required. special ``phono3py_disp.yaml`` is required.
:: .. code-block:: bash
% phono3py --dim="2 2 2" -c POSCAR-unitcell % phono3py
... ...
Displacement dataset is read from disp_fc3.yaml. ----------------------------- General settings -----------------------------
Sets of supercell forces are read from FORCES_FC3. Run mode: None
Solving fc3[ 1, x, x ] with a displacement: HDF5 data compression filter: gzip
Crystal structure was read from "phono3py_disp.yaml".
Supercell (dim): [2 2 2]
Primitive matrix:
[0. 0.5 0.5]
[0.5 0. 0.5]
[0.5 0.5 0. ]
Spacegroup: Fd-3m (227)
Use -v option to watch primitive cell, unit cell, and supercell structures.
----------------------------- Force constants ------------------------------
Imposing translational and index exchange symmetry to fc2: False
Imposing translational and index exchange symmetry to fc3: False
Imposing symmetry of index exchange to fc3 in reciprocal space: False
Displacement dataset for fc3 was read from "phono3py_disp.yaml".
Sets of supercell forces were read from "FORCES_FC3".
Computing fc3[ 1, x, x ] using numpy.linalg.pinv with a displacement:
[ 0.0300 0.0000 0.0000] [ 0.0300 0.0000 0.0000]
Expanding fc3 Expanding fc3.
Cutting-off fc3 (cut-off distance: 5.000000) Cutting-off fc3 (cut-off distance: 5.000000)
Building atom mapping table... Building atom mapping table...
Creating contracted fc3... Creating contracted fc3...
Writing fc3 to fc3.hdf5 Writing fc3 to "fc3.hdf5".
max drift of fc3: 0.043921 (zyx) 0.043921 (yzx) 0.043921 (yxz) Max drift of fc3: 0.047748 (yxz) 0.047748 (xyz) 0.047748 (xzy)
Solving fc2 Displacement dataset for fc2 was read from "phono3py_disp.yaml".
Writing fc2 to fc2.hdf5 Sets of supercell forces were read from "FORCES_FC3".
max drift of fc2: -0.000001 (xx) -0.000001 (xx) Writing fc2 to "fc2.hdf5".
*************** None of ph-ph interaction was calculated. **************** Max drift of fc2: -0.000001 (zz) -0.000001 (zz)
_ ----------- None of ph-ph interaction calculation was performed. -----------
___ _ __ __| |
/ _ \ '_ \ / _` | Summary of calculation was written in "phono3py.yaml".
| __/ | | | (_| | ...
\___|_| |_|\__,_|
Once ``fc3.hdf5`` and ``fc2.hdf5`` are created, ``--cutoff-pair`` Once ``fc3.hdf5`` and ``fc2.hdf5`` are created, ``--cutoff-pair``
option and the special ``disp_fc3.yaml`` are not needed anymore. option and the special ``phono3py_disp.yaml`` are not needed anymore.
:: .. code-block:: bash
% 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" --fc3 --fc2 --br % phono3py --mesh="11 11 11" --fc3 --fc2 --br
... ...
300.0 118.778 118.778 118.778 -0.000 -0.000 0.000 300.0 108.051 108.051 108.051 0.000 0.000 -0.000
... ...
A script extract supercell IDs from ``phono3py_disp.yaml``
A script extract supercell IDs from ``disp_fc3.yaml`` ----------------------------------------------------------
-----------------------------------------------------
The following script is an example to collect supercell IDs The following script is an example to collect supercell IDs
with the cutoff-pair distance, for which ``included: true`` is used with the cutoff-pair distance, for which ``included: true`` is used
to hook. ``duplicates`` in ``disp_fc3.yaml`` gives the pairs of to hook them. ``duplicates`` in ``phono3py_disp.yaml`` gives the pairs of
exactly same supercells having different IDs. Therefore one of each exactly same supercells having different IDs. Therefore one of each
pair is necessary to calculate. As a ratio, the number is not many, pair is necessary to calculate. As a ratio, the number is not many,
but if we want to save very much the computational demand, it is good but if we want to save very much the computational demand, it is good
to consider. to consider.
:: .. code-block:: python
#!/usr/bin/env python #!/usr/bin/env python
import yaml from phono3py.interface.phono3py_yaml import Phono3pyYaml
try:
from yaml import CLoader as Loader
except ImportError:
from yaml import Loader
with open("disp_fc3.yaml", 'r') as f: p3yaml = Phono3pyYaml()
data = yaml.load(f, Loader=Loader) p3yaml.read("phono3py_disp.yaml")
data = p3yaml.dataset
disp_ids = [] disp_ids = []
for data1 in data['first_atoms']: for data1 in data['first_atoms']:
disp_ids.append(data1['displacement_id']) disp_ids.append(data1['id'])
for data1 in data['first_atoms']: for data1 in data['first_atoms']:
for data2 in data1['second_atoms']: for data2 in data1['second_atoms']:
if data2['included']: if data2['included']:
disp_ids += data2['displacement_ids'] disp_ids.append(data2['id'])
# # To remove duplicates # To remove duplicates
# duplicates = data['duplicates'] # duplicates = dict(data['duplicates'])
# print(len(duplicates))
# disp_ids_nodup = [i for i in disp_ids if i not in duplicates] # disp_ids_nodup = [i for i in disp_ids if i not in duplicates]
print(" ".join(["%05d" % i for i in disp_ids])) print(" ".join(["%05d" % i for i in disp_ids]))
Even for the case that ``disp_fc3.yaml`` was created without Even for the case that ``phono3py_disp.yaml`` was created without
``--cutoff-pair`` option, if we replace the line in the above script:: ``--cutoff-pair`` option, if we replace the line in the above script:
.. code-block:: python
if data2['included']: if data2['included']:
by by
:: .. code-block:: python
if data2['distance'] < 5.0: # 5.0 is cutoff-pair distance if data2['distance'] < 5.0: # 5.0 is cutoff-pair distance
@ -293,11 +290,11 @@ Si-PBE
For testing, thermal conductivities with respect to ``--cutoff-pair`` For testing, thermal conductivities with respect to ``--cutoff-pair``
values are calculated as follows. Note that if ``FORCES_FC3`` for full values are calculated as follows. Note that if ``FORCES_FC3`` for full
fc3 elements exists, the same ``FORCES_FC3`` file can be used for fc3 elements exists, the same ``FORCES_FC3`` file can be used for
generating contracted fc3 for each special ``disp_fc3.yaml``. generating contracted fc3 for each special ``phono3py_disp.yaml``.
:: .. code-block:: bash
% egrep '^\s+distance' disp_fc3.yaml|awk '{print $2}'|sort|uniq % egrep '^\s+pair_distance' phono3py_disp.yaml|awk '{print $2}'|sort|uniq
0.000000 0.000000
2.366961 2.366961
3.865232 3.865232
@ -308,50 +305,53 @@ generating contracted fc3 for each special ``disp_fc3.yaml``.
7.100884 7.100884
7.730463 7.730463
9.467845 9.467845
% 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 % cp phono3py_disp.yaml phono3py_disp.orig.yaml
% ls disp_fc3.*.yaml % for i in {2..10};do d=`grep pair_distance phono3py_disp.orig.yaml|awk '{print $2}'|sort|uniq|sed "${i}q;d"`; d=$((d+0.1)); phono3py --cutoff-pair=$d -o $i -d --pa="F" --dim="2 2 2" -c POSCAR-unitcell; mv phono3py_disp.yaml phono3py_disp.$i.yaml; done
disp_fc3.10.yaml disp_fc3.4.yaml disp_fc3.7.yaml % ls phono3py_disp.*.yaml
disp_fc3.2.yaml disp_fc3.5.yaml disp_fc3.8.yaml % ls phono3py_disp.*.yaml
disp_fc3.3.yaml disp_fc3.6.yaml disp_fc3.9.yaml phono3py_disp.10.yaml phono3py_disp.5.yaml phono3py_disp.9.yaml
% for i in {2..10};do grep num_displacements_created disp_fc3.$i.yaml;done phono3py_disp.2.yaml phono3py_disp.6.yaml phono3py_disp.orig.yaml
num_displacements_created: 11 phono3py_disp.3.yaml phono3py_disp.7.yaml
num_displacements_created: 31 phono3py_disp.4.yaml phono3py_disp.8.yaml
num_displacements_created: 51 % for i in {2..10};do grep number_of_pairs_in_cutoff phono3py_disp.$i.yaml;done
num_displacements_created: 56 number_of_pairs_in_cutoff: 10
num_displacements_created: 76 number_of_pairs_in_cutoff: 30
num_displacements_created: 96 number_of_pairs_in_cutoff: 50
num_displacements_created: 104 number_of_pairs_in_cutoff: 55
num_displacements_created: 109 number_of_pairs_in_cutoff: 75
num_displacements_created: 111 number_of_pairs_in_cutoff: 95
% 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" --br --io=$i|tee std.$i.out;done number_of_pairs_in_cutoff: 103
number_of_pairs_in_cutoff: 108
number_of_pairs_in_cutoff: 110
% for i in {2..10};do cp phono3py_disp.$i.yaml phono3py_disp.yaml; phono3py --mesh="11 11 11" --br|tee std.$i.out;done
% for i in {2..10};do egrep '^\s+300' std.$i.out;done % for i in {2..10};do egrep '^\s+300' std.$i.out;done
300.0 123.559 123.559 123.559 -0.000 -0.000 0.000 300.0 123.606 123.606 123.606 -0.000 -0.000 0.000
300.0 118.586 118.586 118.586 -0.000 -0.000 0.000 300.0 118.617 118.617 118.617 -0.000 -0.000 0.000
300.0 118.778 118.778 118.778 -0.000 -0.000 0.000 300.0 118.818 118.818 118.818 -0.000 -0.000 0.000
300.0 118.839 118.839 118.839 -0.000 -0.000 0.000 300.0 118.879 118.879 118.879 -0.000 -0.000 0.000
300.0 119.433 119.433 119.433 -0.000 -0.000 0.000 300.0 119.468 119.468 119.468 -0.000 -0.000 0.000
300.0 119.453 119.453 119.453 -0.000 -0.000 0.000 300.0 119.489 119.489 119.489 -0.000 -0.000 0.000
300.0 119.466 119.466 119.466 -0.000 -0.000 0.000 300.0 119.501 119.501 119.501 -0.000 -0.000 0.000
300.0 119.447 119.447 119.447 -0.000 -0.000 0.000 300.0 119.483 119.483 119.483 -0.000 -0.000 0.000
300.0 119.445 119.445 119.445 -0.000 -0.000 0.000 300.0 119.481 119.481 119.481 -0.000 -0.000 0.000
% 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-$i.out;done % for i in {2..10};do cp phono3py_disp.$i.yaml phono3py_disp.yaml; phono3py --sym-fc --mesh="11 11 11" --br|tee std.sym-$i.out;done
% for i in {2..10};do egrep '^\s+300' std.sym-$i.out;done % for i in {2..10};do egrep '^\s+300' std.sym-$i.out;done
300.0 124.626 124.626 124.626 -0.000 0.000 0.000 300.0 124.650 124.650 124.650 -0.000 -0.000 0.000
300.0 119.721 119.721 119.721 -0.000 0.000 0.000 300.0 119.765 119.765 119.765 -0.000 -0.000 0.000
300.0 118.806 118.806 118.806 -0.000 0.000 0.000 300.0 118.847 118.847 118.847 -0.000 -0.000 0.000
300.0 118.741 118.741 118.741 -0.000 0.000 0.000 300.0 118.782 118.782 118.782 -0.000 -0.000 0.000
300.0 119.446 119.446 119.446 -0.000 0.000 0.000 300.0 119.471 119.471 119.471 -0.000 -0.000 0.000
300.0 119.339 119.339 119.339 -0.000 0.000 0.000 300.0 119.366 119.366 119.366 -0.000 -0.000 0.000
300.0 119.323 119.323 119.323 -0.000 0.000 0.000 300.0 119.350 119.350 119.350 -0.000 -0.000 0.000
300.0 119.313 119.313 119.313 -0.000 0.000 0.000 300.0 119.339 119.339 119.339 -0.000 -0.000 0.000
300.0 119.311 119.311 119.311 -0.000 0.000 0.000 300.0 119.337 119.337 119.337 -0.000 -0.000 0.000
AlN-LDA AlN-LDA
~~~~~~~ ~~~~~~~
:: .. code-block:: bash
% egrep '^\s+distance' disp_fc3.yaml|awk '{print $2}'|sort|uniq % egrep '^\s+pair_distance' phono3py_disp.yaml|awk '{print $2}'|sort|uniq
0.000000 0.000000
1.889907 1.889907
1.901086 1.901086
@ -374,72 +374,70 @@ AlN-LDA
6.205027 6.205027
6.469591 6.469591
7.335901 7.335901
% 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 $i -d --dim="3 3 2" -c POSCAR-unitcell ;done % cp phono3py_disp.yaml phono3py_disp.orig.yaml
% for i in {2..22};do grep num_displacements_created disp_fc3.$i.yaml;done % for i in {2..21};do d=`grep pair_distance phono3py_disp.orig.yaml|awk '{print $2}'|sort|uniq|sed "${i}q;d"`; d=$((d+0.0001)); phono3py --cutoff-pair=$d -o $i -d --dim="3 3 2" -c POSCAR-unitcell; mv phono3py_disp.yaml phono3py_disp.$i.yaml; done
num_displacements_created: 78 % for i in {2..21};do grep number_of_pairs_in_cutoff phono3py_disp.$i.yaml;done
num_displacements_created: 98 number_of_pairs_in_cutoff: 72
num_displacements_created: 202 number_of_pairs_in_cutoff: 92
num_displacements_created: 222 number_of_pairs_in_cutoff: 196
num_displacements_created: 318 number_of_pairs_in_cutoff: 216
num_displacements_created: 370 number_of_pairs_in_cutoff: 312
num_displacements_created: 466 number_of_pairs_in_cutoff: 364
num_displacements_created: 570 number_of_pairs_in_cutoff: 460
num_displacements_created: 666 number_of_pairs_in_cutoff: 564
num_displacements_created: 718 number_of_pairs_in_cutoff: 660
num_displacements_created: 718 number_of_pairs_in_cutoff: 712
num_displacements_created: 770 number_of_pairs_in_cutoff: 764
num_displacements_created: 790 number_of_pairs_in_cutoff: 784
num_displacements_created: 894 number_of_pairs_in_cutoff: 888
num_displacements_created: 934 number_of_pairs_in_cutoff: 928
num_displacements_created: 986 number_of_pairs_in_cutoff: 980
num_displacements_created: 1026 number_of_pairs_in_cutoff: 1020
num_displacements_created: 1122 number_of_pairs_in_cutoff: 1116
num_displacements_created: 1162 number_of_pairs_in_cutoff: 1156
num_displacements_created: 1214 number_of_pairs_in_cutoff: 1208
num_displacements_created: 1254 number_of_pairs_in_cutoff: 1248
% for i in {2..22};do phono3py --dim="3 3 2" -c POSCAR-unitcell --mesh="13 13 9" --br --nac --io $i|tee std.$i.out; done % for i in {2..21};do cp phono3py_disp.$i.yaml phono3py_disp.yaml; phono3py --mesh="13 13 9" --br --nac --io $i|tee std.$i.out; done
% for i in {2..22};do egrep '^\s+300\.0' std.$i.out;done % for i in {2..21};do egrep '^\s+300\.0' std.$i.out;done
300.0 201.530 201.530 192.685 -0.000 -0.000 -0.000 300.0 205.550 205.550 193.665 -0.000 -0.000 -0.000
300.0 212.963 212.963 204.362 -0.000 -0.000 -0.000 300.0 218.963 218.963 204.942 -0.000 -0.000 -0.000
300.0 208.005 208.005 196.684 -0.000 -0.000 -0.000 300.0 213.624 213.624 193.863 -0.000 -0.000 -0.000
300.0 212.213 212.213 200.778 -0.000 -0.000 -0.000 300.0 219.932 219.932 199.819 -0.000 -0.000 -0.000
300.0 223.019 223.019 214.702 -0.000 -0.000 -0.000 300.0 235.516 235.516 218.843 -0.000 -0.000 -0.000
300.0 223.181 223.181 214.351 -0.000 -0.000 -0.000 300.0 234.750 234.750 217.384 -0.000 -0.000 -0.000
300.0 222.360 222.360 213.924 -0.000 -0.000 -0.000 300.0 234.355 234.355 218.030 -0.000 -0.000 -0.000
300.0 223.245 223.245 214.561 -0.000 -0.000 -0.000 300.0 235.381 235.381 218.609 -0.000 -0.000 -0.000
300.0 223.812 223.812 215.359 -0.000 -0.000 -0.000 300.0 235.996 235.996 219.785 -0.000 -0.000 -0.000
300.0 223.959 223.959 215.701 -0.000 -0.000 -0.000 300.0 236.220 236.220 219.867 -0.000 -0.000 -0.000
300.0 223.959 223.959 215.701 -0.000 -0.000 -0.000 300.0 236.161 236.161 219.298 -0.000 -0.000 -0.000
300.0 224.507 224.507 215.384 -0.000 -0.000 -0.000 300.0 236.096 236.096 219.313 -0.000 -0.000 -0.000
300.0 224.278 224.278 215.396 -0.000 -0.000 -0.000 300.0 234.602 234.602 217.064 -0.000 -0.000 -0.000
300.0 223.551 223.551 212.671 -0.000 -0.000 -0.000 300.0 235.914 235.914 218.689 -0.000 -0.000 -0.000
300.0 224.732 224.732 214.463 -0.000 -0.000 -0.000 300.0 235.049 235.049 217.935 -0.000 -0.000 -0.000
300.0 224.291 224.291 213.270 -0.000 -0.000 -0.000 300.0 235.877 235.877 219.065 -0.000 -0.000 -0.000
300.0 224.805 224.805 214.771 -0.000 -0.000 -0.000 300.0 236.133 236.133 219.364 -0.000 -0.000 -0.000
300.0 224.834 224.834 215.025 -0.000 -0.000 -0.000 300.0 236.207 236.207 219.595 -0.000 -0.000 -0.000
300.0 224.645 224.645 215.260 -0.000 -0.000 -0.000 300.0 236.035 236.035 219.463 -0.000 -0.000 -0.000
300.0 224.769 224.769 215.220 -0.000 -0.000 -0.000 300.0 236.104 236.104 219.348 -0.000 -0.000 -0.000
300.0 224.650 224.650 215.090 -0.000 -0.000 -0.000 % for i in {2..21};do cp phono3py_disp.$i.yaml phono3py_disp.yaml; phono3py --mesh="13 13 9" --br --nac --io $i|tee std.$i.out; done|tee std.sym-$i.out; done
% 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-$i.out; done % for i in {2..21};do egrep '^\s+300\.0' std.sym-$i.out;done
% for i in {2..22};do egrep '^\s+300\.0' std.sym-$i.out;done 300.0 232.964 232.964 216.333 0.000 -0.000 -0.000
300.0 224.122 224.122 213.086 0.000 -0.000 0.000 300.0 235.442 235.442 219.602 0.000 -0.000 -0.000
300.0 225.394 225.394 215.683 0.000 -0.000 0.000 300.0 235.521 235.521 217.767 0.000 -0.000 -0.000
300.0 223.748 223.748 213.682 0.000 -0.000 0.000 300.0 235.581 235.581 217.687 0.000 -0.000 -0.000
300.0 223.973 223.973 213.543 0.000 -0.000 0.000 300.0 236.837 236.837 219.933 0.000 -0.000 -0.000
300.0 224.876 224.876 216.489 0.000 -0.000 0.000 300.0 236.020 236.020 219.324 0.000 -0.000 -0.000
300.0 224.603 224.603 216.204 0.000 -0.000 0.000 300.0 235.482 235.482 218.633 0.000 -0.000 -0.000
300.0 223.773 223.773 214.657 0.000 -0.000 0.000 300.0 236.313 236.313 219.677 0.000 -0.000 -0.000
300.0 224.173 224.173 215.517 0.000 -0.000 0.000 300.0 236.308 236.308 219.955 0.000 -0.000 -0.000
300.0 224.596 224.596 215.896 0.000 -0.000 0.000 300.0 236.074 236.074 219.882 0.000 -0.000 -0.000
300.0 224.401 224.401 215.955 0.000 -0.000 0.000 300.0 235.520 235.520 219.450 0.000 -0.000 -0.000
300.0 224.401 224.401 215.955 0.000 -0.000 0.000 300.0 235.769 235.769 219.562 0.000 -0.000 -0.000
300.0 224.077 224.077 215.565 0.000 -0.000 0.000 300.0 235.441 235.441 219.168 0.000 -0.000 -0.000
300.0 224.285 224.285 215.654 0.000 -0.000 0.000 300.0 235.892 235.892 219.590 0.000 -0.000 -0.000
300.0 224.136 224.136 215.053 0.000 -0.000 0.000 300.0 235.509 235.509 219.167 0.000 -0.000 -0.000
300.0 224.469 224.469 215.462 0.000 -0.000 0.000 300.0 235.646 235.646 219.521 0.000 -0.000 -0.000
300.0 224.109 224.109 215.011 0.000 -0.000 0.000 300.0 235.783 235.783 219.311 0.000 -0.000 -0.000
300.0 224.108 224.108 215.447 0.000 -0.000 0.000 300.0 235.887 235.887 219.301 0.000 -0.000 -0.000
300.0 224.592 224.592 215.046 0.000 -0.000 0.000 300.0 235.642 235.642 219.348 0.000 -0.000 -0.000
300.0 224.640 224.640 215.113 0.000 -0.000 0.000 300.0 235.728 235.728 219.102 0.000 -0.000 -0.000
300.0 224.344 224.344 215.203 0.000 -0.000 0.000
300.0 224.481 224.481 214.936 0.000 -0.000 0.000

64
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@ -19,12 +19,14 @@ memory space. When running multiple temperature points, simply the
memory space needed is multiplied by the number of the temperature memory space needed is multiplied by the number of the temperature
points. Therefore it is normally recommended to specify :ref:`--ts points. Therefore it is normally recommended to specify :ref:`--ts
option <ts_option>`. An example to run with the direct solution of option <ts_option>`. An example to run with the direct solution of
LBTE for ``example/Si-PBEsol`` is as follows:: LBTE for ``example/Si-PBEsol`` is as follows:
.. code-block:: bash
% phono3py --dim="2 2 2" --sym-fc -c POSCAR-unitcell % phono3py --dim="2 2 2" --sym-fc -c POSCAR-unitcell
... ...
% 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" --fc3 --fc2 --lbte --ts=300 % phono3py --dim="2 2 2" --pa="F" -c POSCAR-unitcell --mesh="11 11 11" --fc3 --fc2 --lbte --ts=300
... ...
=================== End of collection of collisions =================== =================== End of collection of collisions ===================
@ -41,11 +43,8 @@ LBTE for ``example/Si-PBEsol`` is as follows::
Thermal conductivity and related properties were written into Thermal conductivity and related properties were written into
"kappa-m111111.hdf5". "kappa-m111111.hdf5".
Eigenvalues of collision matrix were written into "coleigs-m111111.hdf5" Eigenvalues of collision matrix were written into "coleigs-m111111.hdf5"
_
___ _ __ __| | ...
/ _ \ '_ \ / _` |
| __/ | | | (_| |
\___|_| |_|\__,_|
Memory usage Memory usage
------------- -------------
@ -69,9 +68,11 @@ memory space is consumed in total.
When phono3py runs with :ref:`--wgp option <wgp_option>` together with When phono3py runs with :ref:`--wgp option <wgp_option>` together with
``--lbte`` option, estimated memory space needed for storing collision ``--lbte`` option, estimated memory space needed for storing collision
matrix is presented. An example for ``example/Si-PBEsol`` is as follows:: matrix is presented. An example for ``example/Si-PBEsol`` is as follows:
% 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="40 40 40" --wgp --lbte .. code-block:: bash
% phono3py --dim="2 2 2" --pa="F" -c POSCAR-unitcell --mesh="40 40 40" --wgp --lbte
... ...
Memory requirements: Memory requirements:
@ -149,19 +150,26 @@ The summary of the procedure is as follows:
file names of the results at different temperatures. file names of the results at different temperatures.
Examples of command options are shown below using ``Si-PBE`` example. Examples of command options are shown below using ``Si-PBE`` example.
Irreducible grid point indices are obtained by :ref:`--wgp option<wgp_option>`:: Irreducible grid point indices are obtained by :ref:`--wgp option<wgp_option>`:
% 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" --lbte --wgp .. code-block:: bash
% phono3py --dim="2 2 2" --pa="F" -c POSCAR-unitcell --mesh="19 19 19" --lbte --wgp
and the information is given in ``ir_grid_points.yaml``. For and the information is given in ``ir_grid_points.yaml``. For
distribution of collision matrix calculation (see also :ref:`workload_distribution`):: distribution of collision matrix calculation
(see also :ref:`workload_distribution`):
% 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 --lbte --ts=300 --write-collision --gp="grid_point_numbers..." .. code-block:: bash
% phono3py --dim="2 2 2" --pa="F" -c POSCAR-unitcell --mesh="19 19 19" --fc3 --fc2 --lbte --ts=300 --write-collision --gp="grid_point_numbers..."
To collect distributed pieces of the collision matrix:: To collect distributed pieces of the collision matrix:
% 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 --lbte --ts=300 --read-collision=0 .. code-block:: bash
% phono3py --dim="2 2 2" --pa="F" -c POSCAR-unitcell --mesh="19 19 19" --fc3 --fc2 --lbte --ts=300 --read-collision=0
Distribution of phonon-phonon interaction strengths Distribution of phonon-phonon interaction strengths
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@ -203,20 +211,26 @@ The summary of the procedure is as follows:
temperatures. temperatures.
Examples of command options are shown below using ``Si-PBE`` example. Examples of command options are shown below using ``Si-PBE`` example.
Irreducible grid point indices are obtained by :ref:`--wgp option<wgp_option>`:: Irreducible grid point indices are obtained by :ref:`--wgp option<wgp_option>`
% 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" --lbte --wgp .. code-block:: bash
% phono3py --dim="2 2 2" --pa="F" -c POSCAR-unitcell --mesh="19 19 19" --lbte --wgp
and the grid point information is provided in and the grid point information is provided in
``ir_grid_points.yaml``. All phonons on mesh grid points are saved ``ir_grid_points.yaml``. All phonons on mesh grid points are saved
by:: by
% 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" --fc2 --write-phonon .. code-block:: bash
% phono3py --dim="2 2 2" --pa="F" -c POSCAR-unitcell --mesh="19 19 19" --fc2 --write-phonon
For distribution of ph-ph interaction strength calculation (see also For distribution of ph-ph interaction strength calculation (see also
:ref:`workload_distribution`):: :ref:`workload_distribution`)
% 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 --lbte --ts=300 --write-pp --gp="grid_point_numbers..." --read-phonon .. code-block:: bash
% phono3py --dim="2 2 2" --pa="F" -c POSCAR-unitcell --mesh="19 19 19" --fc3 --fc2 --lbte --ts=300 --write-pp --gp="grid_point_numbers..." --read-phonon
Here one temperature has to be specified but any one of temperatures Here one temperature has to be specified but any one of temperatures
is OK since ph-ph interaction strength computed here is assumed to be is OK since ph-ph interaction strength computed here is assumed to be
@ -224,9 +238,9 @@ temperature independent. Then the computed ph-ph interaction strengths
are read and used to compute collision matrix and lattice thermal are read and used to compute collision matrix and lattice thermal
conductivity at a temperature by conductivity at a temperature by
:: .. code-block:: bash
% 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 --lbte --ts=300 --read-pp --read-phonon % phono3py --dim="2 2 2" --pa="F" -c POSCAR-unitcell --mesh="19 19 19" --fc3 --fc2 --lbte --ts=300 --read-pp --read-phonon
This last command is repeated at different temperatures to obtain the This last command is repeated at different temperatures to obtain the
properties at multiple temperatures. properties at multiple temperatures.
@ -246,7 +260,9 @@ is clear gap between non-zero eigenvalue and nearly-zero eigenvalues.
After running the direct solution of LBTE, ``coleigs-mxxx.hdf5`` is After running the direct solution of LBTE, ``coleigs-mxxx.hdf5`` is
created. This contains the eigenvalues of the collision matrix (either created. This contains the eigenvalues of the collision matrix (either
symmetrized or non-symmetrized). The eigenvalues are plotted using symmetrized or non-symmetrized). The eigenvalues are plotted using
``phono3py-coleigplot`` in the phono3py package:: ``phono3py-coleigplot`` in the phono3py package:
.. code-block:: bash
phono3py-coleigplot coleigs-mxxx.hdf5 phono3py-coleigplot coleigs-mxxx.hdf5

37
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@ -325,18 +325,33 @@ For example, :math:`\kappa_{\lambda,{xx}}` is calculated by::
array([ 1.02050201e+03, 1.02050201e+03, 1.02050201e+03, array([ 1.02050201e+03, 1.02050201e+03, 1.02050201e+03,
4.40486209e-15, 0.00000000e+00, -4.40486209e-15]) 4.40486209e-15, 0.00000000e+00, -4.40486209e-15])
How to know grid point number corresponding to grid address How to know grid point index number corresponding to grid address
------------------------------------------------------------ -----------------------------------------------------------------
Runngin with ``--write-gamma``, hdf5 files are written out file names Runngin with ``--write-gamma``, hdf5 files are written out with file names
with grid point numbers such as ``kappa-m202020-g4200.hdf5``. You may such as ``kappa-m202020-g4448.hdf5``. You may want to know the grid point
want to know the grid point number with given grid address. This is index number with given grid address. This is done as follows:
done using ``get_grid_point_from_address`` as follows::
In [1]: from phono3py.phonon3.triplets import get_grid_point_from_address .. code-block:: python
In [2]: get_grid_point_from_address([0, 10, 10], [20, 20, 20]) In [1]: import phono3py
Out[2]: 4200
Here the first argument of this method is the grid address and the In [2]: ph3 = phono3py.load("phono3py_disp.yaml")
second argument is the mesh numbers.
In [3]: ph3.mesh_numbers = [20, 20, 20]
In [4]: ph3.grid.get_indices_from_addresses([0, 10, 10])
Out[4]: 4448
This index number is different between phono3py version 1.x and 2.x.
To get the number corresponding to the phono3py version 1.x,
``store_dense_gp_map=False`` should be specified in ``phono3py.load``,
.. code-block:: python
In [5]: ph3 = phono3py.load("phono3py_disp.yaml", store_dense_gp_map=False)
In [6]: ph3.mesh_numbers = [20, 20, 20]
In [7]: ph3.grid.get_indices_from_addresses([0, 10, 10])
Out[7]: 4200

10
doc/output-files.rst
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@ -18,17 +18,11 @@ The following files are not compatible with phonopy. But phonopy's
``FORCE_SETS`` file can be created using phono3py command options from ``FORCE_SETS`` file can be created using phono3py command options from
the following files. See the detail at :ref:`file_format_compatibility`. the following files. See the detail at :ref:`file_format_compatibility`.
``disp_fc3.yaml`` ``phono3py_disp.yaml``
^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^
This is created with ``-d`` option. See :ref:`create_displacements_option`. This is created with ``-d`` option. See :ref:`create_displacements_option`.
``disp_fc2.yaml``
^^^^^^^^^^^^^^^^^^
This is created with ``-d`` option with ``--dim_fc2`` option. See
:ref:`dim_fc2_option`.
``FORCES_FC3`` ``FORCES_FC3``
^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^

41
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@ -10,8 +10,10 @@ phono3py, i.e., using the finite displacement and supercell approach.
An example for QE (pw) is found in the ``example-phono3py/Si-QE`` directory. An example for QE (pw) is found in the ``example-phono3py/Si-QE`` directory.
To invoke the QE (pw) interface, ``--qe`` option has to be always Unless a proper ``phono3py_disp.yaml`` containing calculator information,
specified:: to invoke the QE (pw) interface, ``--qe`` option has to be specified,
.. code-block:: bash
% phono3py --qe [options] [arguments] % phono3py --qe [options] [arguments]
@ -29,15 +31,15 @@ Workflow
1. Create supercells with displacements 1. Create supercells with displacements
:: .. code-block:: bash
% phono3py --qe -d --dim="2 2 2" -c Si.in % phono3py --qe -d --dim="2 2 2" --pa="F" -c Si.in
In this example, probably 111 different supercells with In this example, probably 111 different supercells with
displacements are created. Supercell files (``supercell-xxx.in``) displacements are created. Supercell files (``supercell-xxx.in``)
are created but they contain only the crystal are created but they contain only the crystal
structures. Calculation setting has to be added before running the structures. Calculation setting has to be added before running the
calculation. calculation. In this step, the option ``--qe`` is necessary.
2. Run QE (pw) for supercell force calculations 2. Run QE (pw) for supercell force calculations
@ -49,24 +51,33 @@ Workflow
3. Collect forces 3. Collect forces
``FORCES_FC3`` is obtained with ``--cf3`` options collecting the ``FORCES_FC3`` is obtained with ``--cf3`` options collecting the
forces on atoms in QE (pw) calculation results:: forces on atoms in QE (pw) calculation results:
% phono3py --qe --cf3 disp-00001/Si-supercell.out disp-00002/Si-supercell.out ... .. code-block:: bash
or in recent bash or zsh:: % phono3py --cf3 disp-00001/Si-supercell.out disp-00002/Si-supercell.out ...
% phono3py --qe --cf3 disp-{00001..00111}/Si-supercell.out or in recent bash or zsh:
``disp_fc3.yaml`` is used to create ``FORCES_FC3``, therefore it .. code-block:: bash
% phono3py --cf3 disp-{00001..00111}/Si-supercell.out
``phono3py_disp.yaml`` is used to create ``FORCES_FC3``, therefore it
must exist in current directory. must exist in current directory.
4) Calculate 3rd and 2nd order force constants 4) Calculate 3rd and 2nd order force constants
``fc3.hdf5`` and ``fc2.hdf5`` files are created by:: ``fc3.hdf5`` and ``fc2.hdf5`` files are created by:
% phono3py --qe --dim="2 2 2" -c Si.in --sym-fc .. code-block:: bash
5) Calculate lattice thermal conductivity, e.g., by:: % phono3py --sym-fc
% phono3py --qe --dim="2 2 2" -c Si.in --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" \ where ``--sym-fc`` symmetrizes fc3 and fc2.
--mesh="11 11 11" --fc3 --fc2 --br
5) Calculate lattice thermal conductivity, e.g., by:
.. code-block:: bash
% phono3py --mesh="11 11 11" --fc3 --fc2 --br

8
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@ -112,14 +112,12 @@ higher order anharmonicity is involved (renormalized) into fc3 and fc2.
File format compatibility with phonopy File format compatibility with phonopy
--------------------------------------- ---------------------------------------
- ``disp_fc3.yaml`` and ``disp_fc2.yaml`` are not compatible with
phonopy's ``phonopy_disp.yaml``.
- ``FORCES_FC3`` and ``FORCES_FC2`` are not - ``FORCES_FC3`` and ``FORCES_FC2`` are not
compatible with phonopy's ``FORCE_SETS``. compatible with phonopy's ``FORCE_SETS``.
- ``FORCE_SETS`` can be created using :ref:`--cfs <cfs_option>` from - ``FORCE_SETS`` can be created using :ref:`--cfs <cfs_option>` from
``FORCES_FC3`` and ``disp_fc3.yaml`` or ``FORCES_FC2`` and ``FORCES_FC3`` and ``phono3py_disp.yaml`` or ``FORCES_FC2`` and
``disp_fc2.yaml`` (needs to specify ``--dim-fc2``). ``phono3py_disp.yaml`` (needs to specify ``--dim-fc2``).
- ``FORCES_FC2`` and ``disp_fc2.yaml`` can be created using :ref:`--fs2f2 - ``FORCES_FC2`` can be created using :ref:`--fs2f2
<fs2f2_option>` from ``FORCE_SETS``. <fs2f2_option>` from ``FORCE_SETS``.
- ``fc2.hdf5`` can be used in phonopy in the ``hdf5`` mode when it is - ``fc2.hdf5`` can be used in phonopy in the ``hdf5`` mode when it is
renamed to ``force_constants.hdf5``. In the previous combinations of renamed to ``force_constants.hdf5``. In the previous combinations of

86
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@ -10,22 +10,25 @@ Workflow
1. Create POSCARs with displacements 1. Create POSCARs with displacements
This is the same way as usual phonopy:: This is the same way as usual phonopy:
% phono3py -d --dim="2 2 2" -c POSCAR-unitcell .. code-block:: bash
``disp_fc3.yaml`` and ``POSCAR-xxxxx`` files are created. % phono3py -d --dim="2 2 2" --pa="F" -c POSCAR-unitcell
``phono3py_disp.yaml`` and ``POSCAR-xxxxx`` files are created.
If you want to use larger supercell size for If you want to use larger supercell size for
second-order force constants (fc2) calculation than that second-order force constants (fc2) calculation than that
for third-order force constants (fc3) calculation:: for third-order force constants (fc3) calculation:
% phono3py -d --dim_fc2="4 4 4" --dim="2 2 2" -c POSCAR-unitcell .. code-block:: bash
In this case, ``disp_fc2.yaml`` and ``POSCAR_FC2-xxxxx`` files are % phono3py -d --dim-fc2="4 4 4" --dim="2 2 2" --pa="F" -c POSCAR-unitcell
also created.
2. Run VASP for supercell force calculations In this case, ``POSCAR_FC2-xxxxx`` files are also created.
1. Run VASP for supercell force calculations
To calculate forces on atoms in supercells, ``POSCAR-xxxxx`` (and To calculate forces on atoms in supercells, ``POSCAR-xxxxx`` (and
``POSCAR_FC2-xxxxx`` if they exist) are used as VASP (or any force ``POSCAR_FC2-xxxxx`` if they exist) are used as VASP (or any force
@ -35,54 +38,48 @@ Workflow
directory named ``disp-xxxxx`` (and ``disp_fc2-xxxxx``), where directory named ``disp-xxxxx`` (and ``disp_fc2-xxxxx``), where
``xxxxx`` is sequential number. ``xxxxx`` is sequential number.
3. Collect ``vasprun.xml``'s 2. Collect ``vasprun.xml``'s
When VASP is used as the force calculator, force sets to calculate When VASP is used as the force calculator, force sets to calculate
fc3 and fc2 are created as follows. fc3 and fc2 are created as follows.
:: .. code-block:: bash
% phono3py --cf3 disp-{00001..00755}/vasprun.xml % phono3py --cf3 disp-{00001..00755}/vasprun.xml
where 0755 is an example of the index of the last displacement where 0755 is an example of the index of the last displacement
supercell. To perform this collection, ``disp_fc3.yaml`` created at supercell. To perform this collection, ``phono3py_disp.yaml`` created at
step 1 is required. Then ``FORCES_FC3`` is created. step 1 is required. Then ``FORCES_FC3`` is created.
When you use larger supercell for fc2 calculation:: When you use larger supercell for fc2 calculation:
.. code-block:: bash
% phono3py --cf2 disp_fc2-{00001..00002}/vasprun.xml % phono3py --cf2 disp_fc2-{00001..00002}/vasprun.xml
``disp_fc2.yaml`` is necessary in this case and ``FORCES_FC2`` is ``phono3py_displ.yaml`` is necessary in this case and ``FORCES_FC2`` is
created. created.
4. Create fc2.hdf and fc3.hdf 3. Create fc2.hdf and fc3.hdf
:: .. code-block:: bash
% phono3py --dim="2 2 2" -c POSCAR-unitcell % phono3py --sym-fc
``fc2.hdf5`` and ``fc3.hdf5`` are created from ``FORCES_FC3`` and ``--sym-fc`` symmetrizes fc3 and fc2. ``fc2.hdf5`` and ``fc3.hdf5``
``disp_fc3.yaml``. This step is not mandatory, but you can avoid are created from ``FORCES_FC3`` (and
calculating fc2 and fc3 at every run time. optionally ``FORCES_FC2``) and ``phono3py_disp.yaml``. This step is
not mandatory, but you can avoid calculating fc2 and fc3 at every
run time when reading force constants from these files with
``--fc3`` and ``--fc2`` options.
When you use larger supercell for fc2 calculation:: 4. Thermal conductivity calculation
% phono3py --dim_fc2="4 4 4" --dim="2 2 2" -c POSCAR-unitcell An example of thermal conductivity calculation is:
Similarly ``fc2.hdf5`` and ``fc3.hdf5`` are created from ``FORCES_FC3``, .. code-block:: bash
``FORCES_FC2``, ``disp_fc3.yaml``, and ``disp_fc2.yaml``.
5. Thermal conductivity calculation % phono3py --mesh="11 11 11" --br
An example of thermal conductivity calculation is::
% 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" --mesh="11 11 11" \
-c POSCAR-unitcell --br
This calculation may take very long time. ``--thm`` invokes a This calculation may take very long time. ``--thm`` invokes a
tetrahedron method for Brillouin zone integration for phonon tetrahedron method for Brillouin zone integration for phonon
@ -95,23 +92,26 @@ Workflow
are independent and no communication is necessary at the are independent and no communication is necessary at the
computation. The procedure is as follows: computation. The procedure is as follows:
First run the same command with the addition option of ``--wgp``:: First run the same command with the addition option of ``--wgp``:
% phono3py --fc3 --fc2 --dim="2 2 2" --mesh="11 11 11" \ .. code-block:: bash
-c POSCAR-unitcell --br --wgp
% phono3py --fc3 --fc2 --mesh="11 11 11" --br --wgp
``ir_grid_points.yaml`` is obtained. In this file, irreducible ``ir_grid_points.yaml`` is obtained. In this file, irreducible
q-points are shown. Then distribute calculations of phonon q-points are shown. Then distribute calculations of phonon
lifetimes on grid points with ``--write_gamma`` option by:: lifetimes on grid points with ``--write-gamma`` option by:
% phono3py --fc3 --fc2 --dim="2 2 2" --mesh="11 11 11" \ .. code-block:: bash
-c POSCAR-unitcell --br --write_gamma --gp="[grid ponit(s)]"
% phono3py --mesh="11 11 11" --br --write-gamma --gp="[grid ponit(s)]"
After finishing all distributed calculations, run with After finishing all distributed calculations, run with
``--read_gamma`` option:: ``--read-gamma`` option:
% phono3py --fc3 --fc2 --dim="2 2 2" --mesh="11 11 11" \ .. code-block:: bash
-c POSCAR-unitcell --br --read_gamma
% phono3py --fc3 --fc2 --mesh="11 11 11" --br --read-gamma
Once this calculation runs without problem, separately calculated Once this calculation runs without problem, separately calculated
hdf5 files on grid points are no more necessary and may be deleted. hdf5 files on grid points are no more necessary and may be deleted.

30
doc/workload-distribution.rst
View File

@ -30,20 +30,22 @@ How to do it
The following example is executed in the ``Si-PBE`` example. The following example is executed in the ``Si-PBE`` example.
To avoid re-calculating fc3 and fc2, ``fc3.hdf5`` and ``fc2.hdf5`` are To avoid re-calculating fc3 and fc2, ``fc3.hdf5`` and ``fc2.hdf5`` are
created on a single node:: created on a single node:
.. code-block:: bash
% phono3py --dim="2 2 2" --sym-fc -c POSCAR-unitcell % phono3py --dim="2 2 2" --sym-fc -c POSCAR-unitcell
The indices of the irreducible grid-points neccesarry to specify The indices of the irreducible grid-points neccesarry to specify
``--ga`` option are found by :ref:`--wgp option <wgp_option>` ``--ga`` option are found by :ref:`--wgp option <wgp_option>`
:: .. code-block:: bash
% 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 % phono3py --dim="2 2 2" --pa="F" -c POSCAR-unitcell --mesh="19 19 19" --fc3 --fc2 --br --wgp
and they are stored in ``ir_grid_points.yaml``. and they are stored in ``ir_grid_points.yaml``.
:: .. code-block:: bash
% egrep '^- grid_point:' ir_grid_points.yaml|awk '{printf("%d,",$3)}' % egrep '^- grid_point:' ir_grid_points.yaml|awk '{printf("%d,",$3)}'
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, 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,
@ -51,9 +53,11 @@ and they are stored in ``ir_grid_points.yaml``.
The calculated data on all the grid points shown above as indices are The calculated data on all the grid points shown above as indices are
necessary to obtain lattice thermal conductivity. To distribute necessary to obtain lattice thermal conductivity. To distribute
computational demands into computer nodes, a set of the grid-point computational demands into computer nodes, a set of the grid-point
indices are chosen and executed as follows:: indices are chosen and executed as follows:
% 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 .. code-block:: bash
% phono3py --dim="2 2 2" --pa="F" -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
Then many ``kappa-m191919-gx.hdf5`` files are generated. These file Then many ``kappa-m191919-gx.hdf5`` files are generated. These file
names should not be altered because in reading the data by phono3py, names should not be altered because in reading the data by phono3py,
@ -64,9 +68,9 @@ options. After completing calculations for all irreducible grid-point
indices, the RTA thermal conductivity is computed by another run in a indices, the RTA thermal conductivity is computed by another run in a
short time from the stored data: short time from the stored data:
:: .. code-block:: bash
% 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 % phono3py --dim="2 2 2" --pa="F" -c POSCAR-unitcell --mesh="19 19 19" --fc3 --fc2 --br --read-gamma
A convenient script A convenient script
-------------------- --------------------
@ -98,9 +102,9 @@ indices for workload distribution.
Supposed that this script is saved as ``divide_gps.py``, Supposed that this script is saved as ``divide_gps.py``,
:: .. code-block:: bash
% 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" --wgp % phono3py --dim="2 2 2" --pa="F" -c POSCAR-unitcell --mesh="19 19 19" --wgp
... ...
% python divide_gps.py 20 % python divide_gps.py 20
0,30,52,82,120,402,434,468,524,844,1206 0,30,52,82,120,402,434,468,524,844,1206
@ -127,13 +131,13 @@ Supposed that this script is saved as ``divide_gps.py``,
For example distributing into 20 computer nodes using a queueing For example distributing into 20 computer nodes using a queueing
system, system,
.. code-block:: shell .. code-block:: bash
% 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 % 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
with ``job.sh`` (here for grid-engine): with ``job.sh`` (here for grid-engine):
.. code-block:: shell .. code-block:: bash
#$ -S /bin/zsh #$ -S /bin/zsh
#$ -cwd #$ -cwd
@ -142,4 +146,4 @@ with ``job.sh`` (here for grid-engine):
#$ -e err-phono3py-num.log #$ -e err-phono3py-num.log
#$ -o std-phono3py-num.log #$ -o std-phono3py-num.log
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 phono3py --dim="2 2 2" --pa="F" -c POSCAR-unitcell --mesh="19 19 19" --fc3 --fc2 --br --gp="gps" --write-gamma