mirror of https://github.com/phonopy/phono3py.git
Update phono3py document
This commit is contained in:
Atsushi Togo
parent
44eec6bfdf
commit
0f4ba0b3b1
|
|
@ -3,41 +3,84 @@
|
|||
Command options
|
||||
===============
|
||||
|
||||
.. contents::
|
||||
:depth: 2
|
||||
:local:
|
||||
|
||||
Force constants
|
||||
----------------
|
||||
|
||||
.. _create_displacements_option:
|
||||
|
||||
``-d``
|
||||
~~~~~~
|
||||
``-d``: Create displacements
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
Supercell with displacements are created. Using with ``--amplitude``
|
||||
option, atomic displacement distances are controlled. With this
|
||||
option, files for supercells with displacements and ``disp_fc3.yaml``
|
||||
file are created.
|
||||
|
||||
``--amplitude``
|
||||
~~~~~~~~~~~~~~~
|
||||
``--amplitude``: Amplitude of displacements
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
Displacement distance. The default value depends on calculator. See
|
||||
:ref:`default_displacement_distance_for_calculator`.
|
||||
|
||||
``--pa``, ``--primitive_axis``
|
||||
``--dim``: Supercell dimension
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
Supercell size is specified. See the
|
||||
detail at http://atztogo.github.io/phonopy/setting-tags.html#dim .
|
||||
|
||||
.. _dim_fc2_option:
|
||||
|
||||
``--dim_fc2``: Supercell dimension 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
|
||||
option. Often interaction between a pair of atoms has longer range in
|
||||
real space than interaction among three atoms. Therefore to reduce
|
||||
computational demand, choosing larger supercell size only for 2nd
|
||||
order force constants may be a good idea.
|
||||
|
||||
Using this option with ``-d`` option, the structure files
|
||||
(e.g. ``POSCAR_FC2-xxxxx`` or equivalent files for the other
|
||||
interfaces) and ``disp_fc2.yaml`` are created. These are used to
|
||||
calculate 2nd order force constants for the larger supercell size and
|
||||
these force calculations have to be done in addition to the usual
|
||||
force calculations for 3rd order force constants.
|
||||
|
||||
After the force calculations, ``--cf2`` option is used to create
|
||||
``FORCES_FC2``.
|
||||
|
||||
To calculate 2nd order force constants for the larger supercell size,
|
||||
``FORCES_FC2`` and ``disp_fc2.yaml`` are necessary. Whenever running
|
||||
phono3py for the larger 2nd order force constants, ``--dim_fc2``
|
||||
option has to be specified. ``fc2.hdf5`` created as a result of
|
||||
running phono3py contains the 2nd order force constants with
|
||||
larger supercell size. The filename is the same as that created in the
|
||||
usual phono3py run without ``--dim_fc2`` option.
|
||||
|
||||
``--pa``, ``--primitive_axis``: Transformation matrix to primitive cell
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
Transformation matrix from a non-primitive cell to the primitive
|
||||
cell. See phonopy ``PRIMITIVE_AXIS`` tag (``--pa`` option) at
|
||||
http://atztogo.github.io/phonopy/setting-tags.html#primitive-axis
|
||||
|
||||
``--fc2``
|
||||
~~~~~~~~~
|
||||
``--fc2``: Read 2nd order force constants
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
Read 2nd order force constants from ``fc2.hdf5``.
|
||||
|
||||
``--fc3``
|
||||
~~~~~~~~~
|
||||
``--fc3``: Read 3nd order force constants
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
Read 3rd order force constants from ``fc3.hdf5``.
|
||||
|
||||
``--sym_fc2``, ``--sym_fc3r``, ``--tsym``
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
``--sym_fc2``, ``--sym_fc3r``, ``--tsym``: Symmetries force constants
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
These are used to symmetrize second- and third-order force
|
||||
constants. ``--sym_fc2`` and ``--sym_fc3r`` symmetrize those in real
|
||||
|
|
@ -52,199 +95,8 @@ When those force constants are not read from the hdf5 files,
|
|||
symmetrized force constants in real space are written into those hdf5
|
||||
files.
|
||||
|
||||
``--dim``
|
||||
~~~~~~~~~
|
||||
|
||||
Supercell size is specified. See the
|
||||
detail at http://atztogo.github.io/phonopy/setting-tags.html#dim .
|
||||
|
||||
.. _dim_fc2_option:
|
||||
|
||||
``--dim_fc2``
|
||||
~~~~~~~~~~~~~
|
||||
|
||||
Larger supercell size to calculate harmonic force constants can be
|
||||
used with these options. The larger supercell size is specified by
|
||||
``--dim_fc2``. When running with ``--dim_fc2`` option, a pair of
|
||||
``FORCES_fC2`` and ``disp_fc2.yaml`` or ``fc2.hdf5`` has to be
|
||||
prepared.
|
||||
|
||||
The larger supercells for fc2 in ``POSCAR`` format are created
|
||||
specifying this option with ``-d`` option as
|
||||
``POSCAR_FC2-xxxxx``. Simultaneously ``disp_fc2.yaml`` is created,
|
||||
which is necessary to generate fc2 from ``FORCES_FC2``.
|
||||
|
||||
``--mesh``
|
||||
~~~~~~~~~~
|
||||
|
||||
Phonon triples are chosen on the grid points on the sampling mesh
|
||||
specified by this option. This mesh is made along reciprocal
|
||||
axes and is always Gamma-centered.
|
||||
|
||||
..
|
||||
``--md``
|
||||
~~~~~~~~~
|
||||
|
||||
Divisors of mesh numbers. Another sampling mesh is used to calculate
|
||||
phonon lifetimes. :math:`8\times 8\times 8` mesh is used for the
|
||||
calculation of phonon lifetimes when it is specified, e.g.,
|
||||
``--mesh="11 11 11" --md="2 2 2"``.
|
||||
|
||||
``--br``
|
||||
~~~~~~~~
|
||||
|
||||
Run calculation of lattice thermal conductivity tensor with the single
|
||||
mode relaxation time approximation and linearized phonon Boltzmann
|
||||
equation. Without specifying ``--gp`` option, thermal conductivity is
|
||||
written into ``kappa-mxxx.hdf5``.
|
||||
|
||||
``--sigma``
|
||||
~~~~~~~~~~~
|
||||
|
||||
:math:`\sigma` value of Gaussian function for smearing when
|
||||
calculating imaginary part of self energy. See the detail at
|
||||
:ref:`brillouinzone_sum`.
|
||||
|
||||
Multiple :math:`\sigma` values are also specified by space separated
|
||||
numerical values. This is used when we want to test several
|
||||
:math:`\sigma` values simultaneously.
|
||||
|
||||
|
||||
``--thm``
|
||||
~~~~~~~~~
|
||||
|
||||
Tetrahedron method is used for calculation of imaginary part of self
|
||||
energy. This is the default option. Therefore it is not necessary to
|
||||
specify this unless both results by tetrahedron method and
|
||||
smearing method in one time execution are expected.
|
||||
|
||||
``--tmax``, ``--tmin``, ``--tstep``, ``--ts``
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
Temperatures at equal interval are specified by ``--tmax``,
|
||||
``--tmin``, ``--tstep``. See phonopy ``TMAX``, ``TMIN``, ``TSTEP``
|
||||
tags (``--tmax``, ``--tmin``, ``--tstep`` options) at
|
||||
http://atztogo.github.io/phonopy/setting-tags.html#tprop-tmin-tmax-tstep .
|
||||
|
||||
::
|
||||
|
||||
% phono3py --fc3 --fc2 --dim="2 2 2" -v --mesh="11 11 11" \
|
||||
-c POSCAR-unitcell --br --tmin=100 --tmax=1000 --tstep=50
|
||||
|
||||
|
||||
Specific temperatures are given by ``--ts``.
|
||||
|
||||
::
|
||||
|
||||
% phono3py --fc3 --fc2 --dim="2 2 2" -v --mesh="11 11 11" \
|
||||
-c POSCAR-unitcell --br --ts="200 300 400"
|
||||
|
||||
``--gp``
|
||||
~~~~~~~~
|
||||
|
||||
Grid points where imaginary part of self energy is calculated. Indices
|
||||
of grid points are specified by space separated numbers. The mapping
|
||||
table between grid points to its indices is obtained by running with
|
||||
``--loglevel=2`` option.
|
||||
|
||||
``--ga`` option can be used instead of ``--gp`` option. See ``--gp``
|
||||
section.
|
||||
|
||||
``--ga``
|
||||
~~~~~~~~
|
||||
|
||||
This option is used to specify grid points like ``--gp`` option but in
|
||||
the different way. For example with ``--mesh="16 16 16"``, a q-point
|
||||
of (0.5, 0.5, 0.5) is given by ``--ga="8 8 8"``. The values have to be
|
||||
integers. If you want to specify the point on a path, ``--ga="0 0 0 1
|
||||
1 1 2 2 2 3 3 3 ..."``, where each three values are recogninzed as a
|
||||
grid point. The grid points given by ``--ga`` option are translated to
|
||||
grid point indices as given by ``--gp`` option, and the values given
|
||||
by ``--ga`` option will not be shown in log files.
|
||||
|
||||
``--wgp``
|
||||
~~~~~~~~~
|
||||
|
||||
Irreducible grid point indices are written into
|
||||
``ir_grid_points.yaml``. This information may be used when we want to
|
||||
calculate imaginary part of self energy at each grid point in
|
||||
conjunction with ``--gp`` option. ``grid_address-mxxx.hdf5`` is also
|
||||
written. This file contains all the grid points and their grid
|
||||
addresses in integers. Q-points corresponding to grid points are
|
||||
calculated divided these integers by sampling mesh numbers for
|
||||
respective reciprocal axes.
|
||||
|
||||
``--stp``
|
||||
~~~~~~~~~~
|
||||
|
||||
Numbers of q-point triplets to be calculated for irreducible grid
|
||||
points for specified sampling mesh numbers are shown. This can be used
|
||||
to estimate how large a calculation is. Only those for specific grid
|
||||
points are shown by using with ``--gp`` or ``--ga`` option.
|
||||
|
||||
``--nac``
|
||||
~~~~~~~~~
|
||||
|
||||
Non-analytical term correction for harmonic phonons. Like as phonopy,
|
||||
``BORN`` file has to be put on the same directory. Always the default
|
||||
value of unit conversion factor is used even if it is written in the
|
||||
first line of ``BORN`` file.
|
||||
|
||||
``--q_direction``
|
||||
~~~~~~~~~~~~~~~~~
|
||||
|
||||
This is used with ``--nac`` to specify the direction to polarize in
|
||||
reciprocal space. See the detail at
|
||||
http://atztogo.github.io/phonopy/setting-tags.html#q-direction .
|
||||
|
||||
``--isotope``
|
||||
~~~~~~~~~~~~~
|
||||
|
||||
Phonon-isotope scattering is calculated.. Mass variance parameters are
|
||||
read from database of the natural abundance data for elements, which
|
||||
refers Laeter *et al.*, Pure Appl. Chem., **75**, 683
|
||||
(2003)
|
||||
|
||||
::
|
||||
|
||||
% phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br --isotope
|
||||
|
||||
``--mass_variances`` or ``--mv``
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
This option is used to include isotope effect by reading specified
|
||||
mass variance parameters. For example of GaN, this may be set like
|
||||
``--mv="1.97e-4 1.97e-4 0 0"``. The number of elements has to
|
||||
correspond to the number of atoms in the primitive cell.
|
||||
|
||||
Isotope effect to thermal conductivity may be checked first running
|
||||
without isotope calculation::
|
||||
|
||||
% phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br
|
||||
|
||||
Then running with isotope calculation::
|
||||
|
||||
% 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"
|
||||
|
||||
In the result hdf5 file, currently isotope scattering strength is not
|
||||
written out, i.e., ``gamma`` is still imaginary part of self energy of
|
||||
ph-ph scattering.
|
||||
|
||||
``--boundary_mfp``, ``--bmfp``
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
A most simple boundary scattering treatment is
|
||||
implemented. :math:`v_g/L` is just used as the scattering rate, where
|
||||
:math:`v_g` is the group velocity and :math:`L` is the boundary mean
|
||||
free path. The value is given in micrometre. The default value, 1
|
||||
metre, is just used to avoid divergence of phonon lifetime and the
|
||||
contribution to the thermal conducitivity is considered negligible.
|
||||
|
||||
.. _cf3_option:
|
||||
|
||||
``--cf3``
|
||||
~~~~~~~~~
|
||||
``--cf3``: Create ``FORCES_FC3``
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
This is used to create ``FORCES_FC3``. ``disp_fc3.yaml`` has to be
|
||||
located at the current directory.
|
||||
|
|
@ -255,8 +107,8 @@ located at the current directory.
|
|||
|
||||
.. _cf2_option:
|
||||
|
||||
``--cf2``
|
||||
~~~~~~~~~
|
||||
``--cf2``: Create ``FORCES_FC2``
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
This is used to create ``FORCES_FC2``. ``disp_fc2.yaml`` has to be
|
||||
located at the current directory. This is
|
||||
|
|
@ -301,7 +153,194 @@ After running VASP calculations,
|
|||
|
||||
phono3py --cf3 all_calculated_vasprun_xmls
|
||||
|
||||
``disp_fc3.yaml`` may be readable and helpful to understand this procedure.
|
||||
``disp_fc3.yaml`` may be readable and helpful to understand this
|
||||
procedure.
|
||||
|
||||
Reciprocal space sampling mesh and grid points
|
||||
-----------------------------------------------
|
||||
|
||||
``--mesh``: Sampling mesh
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
Phonon triples are chosen on the grid points on the sampling mesh
|
||||
specified by this option. This mesh is made along reciprocal
|
||||
axes and is always Gamma-centered.
|
||||
|
||||
..
|
||||
``--md``
|
||||
~~~~~~~~~
|
||||
|
||||
Divisors of mesh numbers. Another sampling mesh is used to calculate
|
||||
phonon lifetimes. :math:`8\times 8\times 8` mesh is used for the
|
||||
calculation of phonon lifetimes when it is specified, e.g.,
|
||||
``--mesh="11 11 11" --md="2 2 2"``.
|
||||
|
||||
``--gp``: Specific grid point by indices
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
Grid points where imaginary part of self energy is calculated. Indices
|
||||
of grid points are specified by space separated numbers. The mapping
|
||||
table between grid points to its indices is obtained by running with
|
||||
``--loglevel=2`` option.
|
||||
|
||||
``--ga`` option can be used instead of ``--gp`` option. See ``--gp``
|
||||
section.
|
||||
|
||||
``--ga``: Specific grid point by address with three integer values
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
This option is used to specify grid points like ``--gp`` option but in
|
||||
the different way. For example with ``--mesh="16 16 16"``, a q-point
|
||||
of (0.5, 0.5, 0.5) is given by ``--ga="8 8 8"``. The values have to be
|
||||
integers. If you want to specify the point on a path, ``--ga="0 0 0 1
|
||||
1 1 2 2 2 3 3 3 ..."``, where each three values are recogninzed as a
|
||||
grid point. The grid points given by ``--ga`` option are translated to
|
||||
grid point indices as given by ``--gp`` option, and the values given
|
||||
by ``--ga`` option will not be shown in log files.
|
||||
|
||||
``--wgp``: Write grid point information
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
Irreducible grid point indices are written into
|
||||
``ir_grid_points.yaml``. This information may be used when we want to
|
||||
calculate imaginary part of self energy at each grid point in
|
||||
conjunction with ``--gp`` option. ``grid_address-mxxx.hdf5`` is also
|
||||
written. This file contains all the grid points and their grid
|
||||
addresses in integers. Q-points corresponding to grid points are
|
||||
calculated divided these integers by sampling mesh numbers for
|
||||
respective reciprocal axes.
|
||||
|
||||
``--stp``: Show number of triplets to be calculated for each grid point
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
Numbers of q-point triplets to be calculated for irreducible grid
|
||||
points for specified sampling mesh numbers are shown. This can be used
|
||||
to estimate how large a calculation is. Only those for specific grid
|
||||
points are shown by using with ``--gp`` or ``--ga`` option.
|
||||
|
||||
Brillouin zone integration
|
||||
---------------------------
|
||||
|
||||
``--thm``: Tetrahedron method (default choice)
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
Tetrahedron method is used for calculation of imaginary part of self
|
||||
energy. This is the default option. Therefore it is not necessary to
|
||||
specify this unless both results by tetrahedron method and
|
||||
smearing method in one time execution are expected.
|
||||
|
||||
``--sigma``: Smearing method
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
:math:`\sigma` value of Gaussian function for smearing when
|
||||
calculating imaginary part of self energy. See the detail at
|
||||
:ref:`brillouinzone_sum`.
|
||||
|
||||
Multiple :math:`\sigma` values are also specified by space separated
|
||||
numerical values. This is used when we want to test several
|
||||
:math:`\sigma` values simultaneously.
|
||||
|
||||
Physical properties
|
||||
--------------------
|
||||
|
||||
``--br``: Thermal conductivity with relaxation time approximation
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
Run calculation of lattice thermal conductivity tensor with the single
|
||||
mode relaxation time approximation (RTA) and linearized phonon
|
||||
Boltzmann equation. Without specifying ``--gp`` (or ``--ga``) option,
|
||||
all necessary phonon lifetime calculations for grid points are
|
||||
sequentially executed and then thermal conductivity is calculated
|
||||
under RTA. The thermal conductivity and many related properties are
|
||||
written into ``kappa-mxxx.hdf5``.
|
||||
|
||||
With ``--gp`` (or ``--ga``) option,
|
||||
phonon lifetimes on the specified grid points are calculated. To save
|
||||
the results, ``--write_gamma`` option has to be specified and the
|
||||
physical properties belonging to the grid
|
||||
points are written into ``kappa-mxxx-gx.hdf5``.
|
||||
|
||||
``--isotope``: Phonon-isotope scattering
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
Phonon-isotope scattering is calculated.. Mass variance parameters are
|
||||
read from database of the natural abundance data for elements, which
|
||||
refers Laeter *et al.*, Pure Appl. Chem., **75**, 683
|
||||
(2003)
|
||||
|
||||
::
|
||||
|
||||
% phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br --isotope
|
||||
|
||||
``--mass_variances`` or ``--mv``: Parameter for phonon-isotope scattering
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
This option is used to include isotope effect by reading specified
|
||||
mass variance parameters. For example of GaN, this may be set like
|
||||
``--mv="1.97e-4 1.97e-4 0 0"``. The number of elements has to
|
||||
correspond to the number of atoms in the primitive cell.
|
||||
|
||||
Isotope effect to thermal conductivity may be checked first running
|
||||
without isotope calculation::
|
||||
|
||||
% phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br
|
||||
|
||||
Then running with isotope calculation::
|
||||
|
||||
% 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"
|
||||
|
||||
In the result hdf5 file, currently isotope scattering strength is not
|
||||
written out, i.e., ``gamma`` is still imaginary part of self energy of
|
||||
ph-ph scattering.
|
||||
|
||||
``--boundary_mfp``, ``--bmfp``: Very simple phonon-boundary scattering model
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
A most simple boundary scattering treatment is
|
||||
implemented. :math:`v_g/L` is just used as the scattering rate, where
|
||||
:math:`v_g` is the group velocity and :math:`L` is the boundary mean
|
||||
free path. The value is given in micrometre. The default value, 1
|
||||
metre, is just used to avoid divergence of phonon lifetime and the
|
||||
contribution to the thermal conducitivity is considered negligible.
|
||||
|
||||
.. _cf3_option:
|
||||
|
||||
``--tmax``, ``--tmin``, ``--tstep``, ``--ts``: Temperatures
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
Temperatures at equal interval are specified by ``--tmax``,
|
||||
``--tmin``, ``--tstep``. See phonopy ``TMAX``, ``TMIN``, ``TSTEP``
|
||||
tags (``--tmax``, ``--tmin``, ``--tstep`` options) at
|
||||
http://atztogo.github.io/phonopy/setting-tags.html#tprop-tmin-tmax-tstep .
|
||||
|
||||
::
|
||||
|
||||
% phono3py --fc3 --fc2 --dim="2 2 2" -v --mesh="11 11 11" \
|
||||
-c POSCAR-unitcell --br --tmin=100 --tmax=1000 --tstep=50
|
||||
|
||||
|
||||
Specific temperatures are given by ``--ts``.
|
||||
|
||||
::
|
||||
|
||||
% phono3py --fc3 --fc2 --dim="2 2 2" -v --mesh="11 11 11" \
|
||||
-c POSCAR-unitcell --br --ts="200 300 400"
|
||||
|
||||
``--nac``: Non-analytical term correction
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
Non-analytical term correction for harmonic phonons. Like as phonopy,
|
||||
``BORN`` file has to be put on the same directory. Always the default
|
||||
value of unit conversion factor is used even if it is written in the
|
||||
first line of ``BORN`` file.
|
||||
|
||||
``--q_direction``: Direction for non-analytical term correction at :math:`\mathbf{q}\rightarrow \mathbf{0}`
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
This is used with ``--nac`` to specify the direction to polarize in
|
||||
reciprocal space. See the detail at
|
||||
http://atztogo.github.io/phonopy/setting-tags.html#q-direction .
|
||||
|
||||
.. _write_gamma_option:
|
||||
|
||||
|
|
@ -389,8 +428,8 @@ following script::
|
|||
|
||||
.. _ise_option:
|
||||
|
||||
``--ise``
|
||||
~~~~~~~~~~
|
||||
``--ise``: Imaginary part of self energy
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
Imaginary part of self energy :math:`\Gamma_\lambda(\omega)` is
|
||||
calculated with respect to :math:`\omega`. The output is written to
|
||||
``gammas-mxxxx-gx-sx-tx-bx.dat`` in THz (without :math:`2\pi`).
|
||||
|
|
@ -402,8 +441,8 @@ calculated with respect to :math:`\omega`. The output is written to
|
|||
|
||||
.. _lw_option:
|
||||
|
||||
``--lw``
|
||||
~~~~~~~~
|
||||
``--lw``: Line width
|
||||
~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
Linewidth :math:`2\Gamma_\lambda(\omega_\lambda)` is calculated with
|
||||
respect to temperature. The output is written to
|
||||
|
|
@ -417,8 +456,8 @@ respect to temperature. The output is written to
|
|||
|
||||
.. _jdos_option:
|
||||
|
||||
``--jdos``
|
||||
~~~~~~~~~~
|
||||
``--jdos``: Joint density of states
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
Two classes of joint density of states (JDOS) are calculated. The
|
||||
result is written into ``jdos-mxxxxxx-gx.dat`` in THz (without
|
||||
|
|
@ -463,15 +502,15 @@ follows, respectively,
|
|||
% phono3py --fc2 --dim="2 2 2" -c POSCAR-unitcell --mesh="16 16 16" \
|
||||
--nac --jdos --ga="0 0 0 8 8 8" --ts=300
|
||||
|
||||
``--num_freq_points``, ``--freq_pitch``
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
``--num_freq_points``, ``--freq_pitch``: Sampling frequency for distribution functions
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
For spectrum like calculations of imaginary part of self energy and
|
||||
JDOS, number of sampling frequency points is controlled by
|
||||
``--num_freq_points`` or ``--freq_pitch``.
|
||||
|
||||
``--bi``
|
||||
~~~~~~~~
|
||||
``--bi``: Specific band index
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
Specify band indices. The output file name will be, e.g.,
|
||||
``gammas-mxxxxxx-gxx-bx.dat`` where ``bxbx...`` shows the band indices
|
||||
|
|
@ -486,8 +525,8 @@ calculated.
|
|||
|
||||
.. _full_pp_option:
|
||||
|
||||
``--full_pp``
|
||||
~~~~~~~~~~~~~~
|
||||
``--full_pp``: Calculate all elements of phonon-phonon interaction strength
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
After version 1.10.5, for RTA thermal conductivity calculation with
|
||||
using the linear tetrahedron method, only necessary part of
|
||||
|
|
@ -512,11 +551,12 @@ But specifying this option, full elements of phonon-phonon interaction
|
|||
strengh among phonons are calculated and averaged phonon-phonon
|
||||
interaction strength (:math:`P_{\mathbf{q}j}`) is also given.
|
||||
|
||||
``--ave_pp``
|
||||
~~~~~~~~~~~~
|
||||
``--ave_pp``: Use averaged phonon-phonon interaction strength
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
Averaged phonon-phonon interaction strength (:math:`P_{\mathbf{q}j}`)
|
||||
is used to calculate imaginary part of self energy. This option works
|
||||
is used to calculate imaginary part of self energy in thermal
|
||||
conductivity calculation. This option works
|
||||
only when ``--read_gamma`` and ``--br`` options are activated where
|
||||
the averaged phonon-phonon interaction that is read from
|
||||
``kappa-mxxxxx.hdf5`` file is used if it exists in the file. Therefore the
|
||||
|
|
@ -538,21 +578,22 @@ Then
|
|||
% phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br \
|
||||
--read_gamma --ave_pp -o ave_pp
|
||||
|
||||
``--const_ave_pp``
|
||||
~~~~~~~~~~~~~~~~~~
|
||||
``--const_ave_pp``: Use constant phonon-phonon interaction strength
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
Averaged phonon-phonon interaction (:math:`P_{\mathbf{q}j}`) is
|
||||
replaced by this constant value. Therefore third-order force constants
|
||||
are not necessary to input. The physical unit of the value is
|
||||
:math:`\text{eV}^2`.
|
||||
replaced by this constant value in thermal conductivity
|
||||
calculation. This option works only when ``--br`` options are
|
||||
activated. Therefore third-order force constants are not necessary to
|
||||
input. The physical unit of the value is :math:`\text{eV}^2`.
|
||||
|
||||
::
|
||||
|
||||
% phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br \
|
||||
--const_ave_pp=1e-10
|
||||
|
||||
``--gruneisen``
|
||||
~~~~~~~~~~~~~~~
|
||||
``--gruneisen``: Mode-Gruneisen parameter from 3rd order force constants
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
Mode-Gruneisen-parameters are calculated from fc3.
|
||||
|
||||
|
|
|
|||
|
|
@ -49,9 +49,9 @@ copyright = u'2015, Atsushi Togo'
|
|||
# built documents.
|
||||
#
|
||||
# The short X.Y version.
|
||||
version = '1.10.11'
|
||||
version = '1.11.1'
|
||||
# The full version, including alpha/beta/rc tags.
|
||||
release = '1.10.11'
|
||||
release = '1.11.1'
|
||||
|
||||
# The language for content autogenerated by Sphinx. Refer to documentation
|
||||
# for a list of supported languages.
|
||||
|
|
|
|||
|
|
@ -2,11 +2,13 @@
|
|||
Welcome to phono3py
|
||||
=======================================================
|
||||
|
||||
This software calculates phonon-phonon interaction related properties:
|
||||
This software calculates phonon-phonon interaction and related
|
||||
properties using the supercell approach. For example, the following
|
||||
physical properties are obtained:
|
||||
|
||||
- Lattice thermal conductivity
|
||||
- Phonon lifetime/linewidth
|
||||
- Imaginary part of self energy at the lowest order
|
||||
- Imaginary part of self energy
|
||||
- Joint density of states (JDOS) and weighted-JDOS
|
||||
|
||||
The theoretical background is summarized in the paper found at
|
||||
|
|
@ -17,6 +19,10 @@ Examples are found in ``example-phono3py`` directory. Phono3py API
|
|||
example ``Si.py`` is found in ``example-phono3py/Si`` directory, but
|
||||
the API document has not yet written.
|
||||
|
||||
:ref:`Interfaces to calculators <calculator_interfaces>` for VASP and
|
||||
pwscf are built-in.
|
||||
|
||||
|
||||
Documentation
|
||||
=============
|
||||
|
||||
|
|
|
|||
|
|
@ -1,3 +1,5 @@
|
|||
.. _calculator_interfaces:
|
||||
|
||||
Interfaces to calculators
|
||||
==========================
|
||||
|
||||
|
|
@ -6,8 +8,6 @@ prepared. VASP is the default interface and no special option is
|
|||
necessary to invoke it, but for the other interfaces, each special
|
||||
option has to be specified, e.g. ``--pwscf``.
|
||||
|
||||
.. _calculator_interfaces:
|
||||
|
||||
Calculator specific behaviors
|
||||
------------------------------
|
||||
|
||||
|
|
@ -60,6 +60,13 @@ in :ref:`workflow`.
|
|||
Usage of Pwscf interface
|
||||
-------------------------
|
||||
|
||||
Quantum espresso package itself has a set of the force constants
|
||||
calculation environment based on DFPT. But the document here explains how
|
||||
to calculate phonon-phonon interaction and related properties using
|
||||
phono3py, i.e., using the finite displacement and supercell approach.
|
||||
|
||||
An example for pwscf is found in the ``example-phono3py/Si-pwscf`` directory.
|
||||
|
||||
To invoke the Pwscf interface, ``--pwscf`` option has to be always
|
||||
specified::
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue