mirror of https://github.com/phonopy/phono3py.git
Updated document toward v2 release
This commit is contained in:
Atsushi Togo
parent
ffff9e61f1
commit
7561c4c878
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@ -35,6 +35,7 @@ nosetests.xml
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.mr.developer.cfg
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.project
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.pydevproject
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.vscode
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# Doc
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.buildinfo
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@ -40,14 +40,16 @@ How to use ``phono3py-kaccum``
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Let's computer lattice thermal conductivity of Si using the ``Si-PBEsol``
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example found in the example directory.
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::
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.. code-block:: shell
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% phono3py --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" -c POSCAR-unitcell --mesh="11 11 11" --sym-fc --br
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% phono3py --dim="2 2 2" --pa="F" -c POSCAR-unitcell --mesh="11 11 11" --sym-fc --br
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Then using the output file, ``kappa-m111111.hdf5``, run
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``phono3py-kaccum`` as follows::
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``phono3py-kaccum`` as follows:
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% 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
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.. code-block:: shell
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% phono3py-kaccum --pa="F" -c POSCAR-unitcell kappa-m111111.hdf5 |tee kaccum.dat
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Here ``--pa`` is optional. The definition of ``--pa`` option is same
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as :ref:`pa_option`. ``POSCAR-unitcell`` is the unit cell filename
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@ -66,7 +68,7 @@ temperatures calculated.
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To plot the output by gnuplot at temperature index 30 that may
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correspond to 300 K,
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::
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.. code-block:: shell
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% gnuplot
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...
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@ -106,9 +108,11 @@ POSCAR-unitcell``.
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^^^^^^^^
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Let ``phono3py-kaccum`` read a QE (pw) unit cell file with ``-c``
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option, for example::
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option, for example:
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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
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.. code-block:: bash
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phono3py-kaccum --qe --pa="F" -c Si.in kappa-m191919.hdf5
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.. |ipwscf| image:: Si-kaccum-pwscf.png
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:width: 25%
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@ -201,25 +205,25 @@ convergence.
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``--gv``
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^^^^^^^^^
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^^^^^^^^
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Outer product of group velocities :math:`\mathbf{v}_\lambda \otimes
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\mathbf{v}_\lambda` divided by primitive cell volume (in :math:`\text{THz}^2 /
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\text{Angstrom}`)
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``--average``
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^^^^^^^^^^^^^^
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^^^^^^^^^^^^^
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Output the traces of the tensors divided by 3 rather than the unique
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elements.
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``--trace``
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^^^^^^^^^^^^
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^^^^^^^^^^^
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Output the traces of the tensors rather than the unique elements.
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Options for scalar properties
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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For the following properties, those values are normalized by the
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number of full grid points. This is understood as normalized for one
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@ -230,31 +234,36 @@ frequency, cumulative property, and derivative of cumulative property
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such like DOS.
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``--gamma``
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^^^^^^^^^^^^
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^^^^^^^^^^^
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:math:`\Gamma_\lambda(\omega_\lambda)` (in THz)
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``--tau``
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^^^^^^^^^^^
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^^^^^^^^^
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Lifetime :math:`\tau_\lambda = \frac{1}{2\Gamma_\lambda(\omega_\lambda)}` (in ps)
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``--cv``
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^^^^^^^^^
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^^^^^^^^
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Modal heat capacity :math:`C_\lambda` (in eV/K)
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``--gv-norm``
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^^^^^^^^^^^^^^
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^^^^^^^^^^^^^
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Absolute value of group velocity :math:`|\mathbf{v}_\lambda|` (in
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:math:`\text{THz}\cdot\text{Angstrom}`)
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``--pqj``
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^^^^^^^^^^^^^^
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^^^^^^^^^
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Averaged phonon-phonon interaction :math:`P_{\mathbf{q}j}` (in :math:`\text{eV}^2`)
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``--dos``
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^^^^^^^^^
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Constant value of 1. This results in phonon DOS.
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.. _auxiliary_tools_kdeplot:
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``phono3py-kdeplot``
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@ -271,7 +280,9 @@ Then (frequency, lifetime)-data points are superimposed on the density
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plot.
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``phono3py-kdeplot`` reads a result of the thermal conductivity
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calculation as the first argument::
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calculation as the first argument:
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.. code-block:: shell
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% phono3py-kdeplot kappa-m111111.hdf5
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@ -318,7 +329,7 @@ This option controls the resolution of the density plot. The default
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value is 100. With larger nbins, the resolution of the plot becomes
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better, but the computation will take more time.
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::
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.. code-block:: shell
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% phono3py-kdeplot --nbins=200 kappa-m111111.hdf5
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@ -342,7 +353,7 @@ respectively.
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of drawing region along y-axis, therefore as a side effect, the
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computation will be roughly twice faster.
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::
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.. code-block:: shell
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% phono3py-kdeplot --ymax=60 kappa-m111111.hdf5
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@ -363,7 +374,7 @@ maximum density. Normally smaller value results in larger drawing
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region. The default value is 0.1. When ``--ymax`` is specified
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together, this option is ignored.
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::
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.. code-block:: shell
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% phono3py-kdeplot --dr=0.01 kappa-m111111.hdf5
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@ -375,7 +386,7 @@ presented at the matplotlib documentation,
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https://matplotlib.org/users/colormaps.html. The default colormap
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depends on your matplotlib environment.
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::
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.. code-block:: shell
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% phono3py-kdeplot --cmap="OrRd" kappa-m111111.hdf5
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@ -13,7 +13,9 @@ instead of and together with the command options. The setting tags are
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mostly equivalent to the respective most command options, but when
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both are set simultaneously, the command options are preferred. An
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example of configuration (e.g., saved in a file ``setting.conf``) is
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as follow::
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as follow:
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.. code-block:: bash
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DIM = 2 2 2
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DIM_FC2 = 4 4 4
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@ -27,13 +29,13 @@ as follow::
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where the setting tag names are case insensitive. This is run by
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::
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.. code-block:: bash
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% phono3py setting.conf [comannd options]
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or
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::
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.. code-block:: bash
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% phono3py [comannd options] -- setting.conf
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@ -50,7 +52,7 @@ Input cell file name
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This specifies input unit cell filename.
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::
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.. code-block:: bash
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% phono3py -c POSCAR-unitcell ... (many options)
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@ -83,18 +85,18 @@ These options have no respective configuration file tags.
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``--cf3`` (command option only)
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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This is used to create ``FORCES_FC3`` from ``disp_fc3.yaml`` and
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force calculator outputs containing forces in supercells. ``disp_fc3.yaml``
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This is used to create ``FORCES_FC3`` from ``phono3py_disp.yaml`` and
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force calculator outputs containing forces in supercells. ``phono3py_disp.yaml``
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has to be located at the current directory. Calculator interface has
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to be specified except for VASP (default) case.
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::
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.. code-block:: bash
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% phono3py --cf3 disp-{00001..00755}/vasprun.xml
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::
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.. code-block:: bash
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% phono3py --qe --cf3 supercell_out/disp-{00001..00111}/Si.out
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% phono3py --cf3 supercell_out/disp-{00001..00111}/Si.out
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.. _cf3_file_option:
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@ -102,16 +104,18 @@ to be specified except for VASP (default) case.
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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This is used to create ``FORCES_FC3`` from a text file containing a
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list of calculator output file names. ``disp_fc3.yaml`` has to be
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list of calculator output file names. ``phono3py_disp.yaml`` has to be
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located at the current directory. Calculator interface has to be
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specified except for VASP (default) case.
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::
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.. code-block:: bash
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% phono3py --cf3-file file_list.dat
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where ``file_list.dat`` contains file names that can be recognized
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from the current directory and is expected to be like::
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from the current directory and is expected to be like:
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.. code-block:: bash
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disp-00001/vasprun.xml
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disp-00002/vasprun.xml
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@ -128,12 +132,12 @@ to be used together with ``--cutoff-pair`` option.
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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This is used to create ``FORCES_FC2`` similarly to ``--cf3``
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option. ``disp_fc2.yaml`` has to be located at the current
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option. ``phono3py_disp.yaml`` has to be located at the current
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directory. This is optional. Calculator interface has to be specified
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except for VASP (default) case. ``FORCES_FC2`` is necessary to run
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with ``--dim-fc2`` option.
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::
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.. code-block:: bash
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% phono3py --cf2 disp_fc2-{00001..00002}/vasprun.xml
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@ -153,7 +157,7 @@ the forces of the perfect supercells. In ideal case, these forces are
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zero, but often they are not. Here, this is called "residual
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forces". Sometimes quality of force constants is improved in this way.
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::
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.. code-block:: bash
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% phono3py --cf3 disp3-{00001..01254}/vasprun.xml --cfz disp3-00000/vasprun.xml
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% phono3py --cf2 disp2-{00001..00006}/vasprun.xml --cfz disp2-00000/vasprun.xml
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@ -163,10 +167,10 @@ forces". Sometimes quality of force constants is improved in this way.
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``--fs2f2`` or ``--force-sets-to-forces-fc2`` (command option only)
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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``FORCES_FC2`` and ``disp_fc2.yaml`` are created
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from phonopy's ``FORCE_SETS`` file.
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``FORCES_FC2`` is created from phonopy's ``FORCE_SETS`` file.
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Necessary yaml lines for ``phono3py_disp.yaml`` is displayed as text.
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::
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.. code-block:: bash
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% phono3py --fs2f2
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@ -176,17 +180,17 @@ from phonopy's ``FORCE_SETS`` file.
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Phonopy's ``FORCE_SETS`` is created from
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``FORCES_FC3`` and ``disp_fc3.yaml``.
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``FORCES_FC3`` and ``phono3py_disp.yaml``.
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::
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.. code-block:: bash
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% phono3py --cfs
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In conjunction with :ref:`--dim-fc2 <dim_fc2_option>`, phonopy's
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``FORCE_SETS`` is created from ``FORCES_FC2`` and ``disp_fc2.yaml``
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instead of ``FORCES_FC3`` and ``disp_fc3.yaml``.
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``FORCE_SETS`` is created from ``FORCES_FC2`` and ``phono3py_disp.yaml``
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instead of ``FORCES_FC3`` and ``phono3py_disp.yaml``.
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::
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.. code-block:: bash
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% phono3py --cfs --dim-fc2="x x x"
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@ -199,7 +203,9 @@ Supercell and primitive cell
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~~~~~~~~~~~~~~~~~~~
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Supercell dimension is specified. See the
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detail at http://phonopy.github.io/phonopy/setting-tags.html#dim .
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detail at http://phonopy.github.io/phonopy/setting-tags.html#dim.
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When a proper ``phono3py_disp.yaml`` exists in the current directory,
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this is unnecessary to be specified.
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.. _dim_fc2_option:
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@ -208,6 +214,8 @@ detail at http://phonopy.github.io/phonopy/setting-tags.html#dim .
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Supercell dimension for 2nd order force constants (for harmonic
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phonons) is specified. This is optional.
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When a proper ``phono3py_disp.yaml`` exists in the current directory,
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this is unnecessary to be specified.
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A larger and different supercell size for 2nd order force constants
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than that for 3rd order force constants can be specified with this
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@ -218,31 +226,31 @@ order force constants may be a good idea.
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Using this option with ``-d`` option, the structure files
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(e.g. ``POSCAR_FC2-xxxxx`` or equivalent files for the other
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interfaces) and ``disp_fc2.yaml`` are created. These are used to
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interfaces) and ``phono3py_disp.yaml`` are created. These are used to
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calculate 2nd order force constants for the larger supercell size and
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these force calculations have to be done in addition to the usual
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force calculations for 3rd order force constants.
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::
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.. code-block:: bash
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phono3py -d --dim="2 2 2" --dim-fc2="4 4 4" -c POSCAR-unitcell
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After the force calculations, ``--cf2`` option is used to create
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``FORCES_FC2``.
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::
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.. code-block:: bash
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phono3py --cf2 disp-{001,002}/vasprun.xml
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To calculate 2nd order force constants for the larger supercell size,
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``FORCES_FC2`` and ``disp_fc2.yaml`` are necessary. Whenever running
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``FORCES_FC2`` and ``phono3py_disp.yaml`` are necessary. Whenever running
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phono3py for the larger 2nd order force constants, ``--dim-fc2``
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option has to be specified. ``fc2.hdf5`` created as a result of
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running phono3py contains the 2nd order force constants with
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larger supercell size. The filename is the same as that created in the
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usual phono3py run without ``--dim-fc2`` option.
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::
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.. code-block:: bash
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phono3py --dim="2 2 2" --dim_fc2="4 4 4" -c POSCAR-unitcell ... (many options)
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@ -253,7 +261,9 @@ usual phono3py run without ``--dim-fc2`` option.
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Transformation matrix from a non-primitive cell to the primitive
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cell. See phonopy ``PRIMITIVE_AXES`` tag (``--pa`` option) at
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http://phonopy.github.io/phonopy/setting-tags.html#primitive-axis
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http://phonopy.github.io/phonopy/setting-tags.html#primitive-axis.
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When a proper ``phono3py_disp.yaml`` exists in the current directory,
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this is unnecessary to be specified.
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Displacement creation
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---------------------
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@ -265,8 +275,10 @@ Displacement creation
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Supercell with displacements are created. Using with ``--amplitude``
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option, atomic displacement distances are controlled. With this
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option, files for supercells with displacements and ``disp_fc3.yaml``
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file are created.
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option, files for supercells with displacements and ``phono3py_disp.yaml``
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file are created. ``--pa`` should be specified if the input unit cell
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structure is not a primitive cell, e.g., ``--pa="F"`` if the input
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unit cell has F-centring.
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.. _amplitude_option:
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@ -304,9 +316,9 @@ using with ``--sym-fc``, the calculated results will become slightly
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different due to imperfect symmetrization scheme that phono3py
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employs.
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::
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.. code-block:: bash
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% 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
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% phono3py --dim="2 2 2" --cfc --pa="F" -c POSCAR-unitcell
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.. _symmetrization_option:
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@ -398,9 +410,9 @@ Indices of grid points are specified by space or comma (``,``)
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separated numbers. The mapping table between grid points to its
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indices is obtained by running with ``--loglevel=2`` option.
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::
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.. code-block:: bash
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% phono3py --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" -c POSCAR-unitcell --mesh="19 19 19" --fc3 --fc2 --br --write-gamma --gp="0 1 2 3 4 5"
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% 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"
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where ``--gp="0 1 2 3 4 5"`` can be also written
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``--gp="0,1,2,3,4,5"``. ``--ga`` option below can be used similarly
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@ -432,7 +444,7 @@ indices used to be averaged. The calculated values at indices
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separated by space are averaged, and those separated by comma are
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separately calculated.
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::
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.. code-block:: bash
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% phono3py --fc3 --fc2 --dim="2 2 2" --mesh="16 16 16" -c POSCAR-unitcell --nac --gp="34" --bi="4 5, 6"
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@ -457,9 +469,9 @@ grid points and their grid addresses in integers. Q-points
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corresponding to grid points are calculated divided these integers by
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sampling mesh numbers for respective reciprocal axes.
|
||||
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||||
::
|
||||
.. code-block:: bash
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||||
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% phono3py --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" -c POSCAR-unitcell --mesh="19 19 19" --wgp
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% phono3py --dim="2 2 2" --pa="F" -c POSCAR-unitcell --mesh="19 19 19" --wgp
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||||
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.. _stp_option:
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||||
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||||
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@ -471,9 +483,9 @@ points for specified sampling mesh numbers are shown. This can be used
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to estimate how large a calculation is. Only those for specific grid
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points are shown by using with ``--gp`` or ``--ga`` option.
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||||
::
|
||||
.. 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
|
||||
---------------------------
|
||||
|
|
@ -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
|
||||
(2003).
|
||||
|
||||
::
|
||||
.. code-block:: bash
|
||||
|
||||
% 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.
|
||||
|
||||
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
|
||||
|
||||
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"
|
||||
|
||||
|
|
@ -660,13 +676,13 @@ together with ``-o`` option is strongly recommended.
|
|||
|
||||
First, run full conductivity calculation,
|
||||
|
||||
::
|
||||
.. code-block:: bash
|
||||
|
||||
% phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br
|
||||
|
||||
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
|
||||
|
||||
|
|
@ -680,7 +696,7 @@ 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`.
|
||||
|
||||
::
|
||||
.. code-block:: bash
|
||||
|
||||
% 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
|
||||
: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
|
||||
|
||||
|
|
@ -748,7 +764,7 @@ Temperature
|
|||
|
||||
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"
|
||||
|
||||
|
|
@ -760,7 +776,7 @@ Temperatures at equal interval are specified by ``--tmax``,
|
|||
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
|
||||
|
||||
|
|
@ -782,7 +798,7 @@ first line of ``BORN`` file.
|
|||
|
||||
This is used with ``--nac`` to specify reciprocal-space direction
|
||||
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:
|
||||
|
||||
|
|
@ -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
|
||||
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"
|
||||
|
||||
|
|
@ -832,9 +848,9 @@ are the values given as follows, respectively,
|
|||
\Delta(-\mathbf{q}+\mathbf{q}'+\mathbf{q}'') \delta(\omega-\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
|
||||
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'} -
|
||||
\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``.
|
||||
|
||||
|
|
@ -891,11 +907,15 @@ Mode-Gruneisen parameter from 3rd order force constants
|
|||
|
||||
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
|
||||
|
||||
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"
|
||||
|
||||
|
|
@ -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
|
||||
<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::
|
||||
|
||||
|
|
@ -1065,9 +1085,9 @@ different eigenvalue solvers or different CPU
|
|||
architectures. :ref:`--pa <pa_option>` and :ref:`--nac <nac_option>`
|
||||
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:
|
||||
|
||||
|
|
@ -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
|
||||
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:
|
||||
|
|
@ -1125,8 +1145,6 @@ This rule is applied to
|
|||
- ``kappa-xxx.hdf5``
|
||||
- ``phonon-xxx.hdf5``
|
||||
- ``pp-xxx.hdf5``
|
||||
- ``disp_fc3.yaml``
|
||||
- ``disp_fc2.yaml``
|
||||
- ``gamma_detail-xxx.hdf5`` (write only)
|
||||
|
||||
.. _input_filename_option:
|
||||
|
|
@ -1147,8 +1165,6 @@ This rule is applied to
|
|||
- ``kappa-xxx.hdf5``
|
||||
- ``phonon-xxx.hdf5``
|
||||
- ``pp-xxx.hdf5``
|
||||
- ``disp_fc3.yaml``
|
||||
- ``disp_fc2.yaml``
|
||||
|
||||
``--io`` (command option only)
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
|
|
|||
204
doc/conf.py
204
doc/conf.py
|
|
@ -1,9 +1,10 @@
|
|||
# -*- coding: utf-8 -*-
|
||||
"""Sphinx phono3py configuration file."""
|
||||
#
|
||||
# phono3py documentation build configuration file, created by
|
||||
# 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
|
||||
# autogenerated file.
|
||||
|
|
@ -11,22 +12,23 @@
|
|||
# All configuration values have a default; values that are commented out
|
||||
# serve to show the default.
|
||||
|
||||
import sys, os
|
||||
import sys
|
||||
import os
|
||||
|
||||
# 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
|
||||
# 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.
|
||||
#needs_sphinx = '1.0'
|
||||
# needs_sphinx = '1.0'
|
||||
|
||||
# Add any Sphinx extension module names here, as strings. They can be extensions
|
||||
# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
|
||||
#extensions = ['sphinx.ext.imgmath']
|
||||
extensions = ['sphinx.ext.mathjax']
|
||||
# Add any Sphinx extension module names here, as strings. They can be
|
||||
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
|
||||
# extensions = ['sphinx.ext.imgmath']
|
||||
extensions = ['sphinx.ext.mathjax', 'myst_parser']
|
||||
|
||||
# Add any paths that contain templates here, relative to this directory.
|
||||
templates_path = ['_templates']
|
||||
|
|
@ -35,7 +37,7 @@ templates_path = ['_templates']
|
|||
source_suffix = '.rst'
|
||||
|
||||
# The encoding of source files.
|
||||
#source_encoding = 'utf-8-sig'
|
||||
# source_encoding = 'utf-8-sig'
|
||||
|
||||
# The master toctree document.
|
||||
master_doc = 'index'
|
||||
|
|
@ -49,52 +51,53 @@ copyright = u'2015, Atsushi Togo'
|
|||
# built documents.
|
||||
#
|
||||
# The short X.Y version.
|
||||
version = '1.22'
|
||||
version = '2.0'
|
||||
# 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
|
||||
# for a list of supported languages.
|
||||
#language = None
|
||||
# language = None
|
||||
|
||||
# There are two options for replacing |today|: either, you set today to some
|
||||
# non-false value, then it is used:
|
||||
#today = ''
|
||||
# today = ''
|
||||
# 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
|
||||
# directories to ignore when looking for source files.
|
||||
exclude_patterns = ['_build']
|
||||
|
||||
# The reST default role (used for this markup: `text`) to use for all documents.
|
||||
#default_role = None
|
||||
# The reST default role (used for this markup: `text`) to use for all
|
||||
# documents.
|
||||
# default_role = None
|
||||
|
||||
# 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
|
||||
# unit titles (such as .. function::).
|
||||
#add_module_names = True
|
||||
# add_module_names = True
|
||||
|
||||
# If true, sectionauthor and moduleauthor directives will be shown in the
|
||||
# output. They are ignored by default.
|
||||
#show_authors = False
|
||||
# show_authors = False
|
||||
|
||||
# The name of the Pygments (syntax highlighting) style to use.
|
||||
pygments_style = 'sphinx'
|
||||
|
||||
# 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
|
||||
# a list of builtin themes.
|
||||
# html_theme = 'default'
|
||||
# Add any paths that contain custom themes here, relative to this directory.
|
||||
#html_theme_path = []
|
||||
# html_theme_path = []
|
||||
|
||||
################
|
||||
# guzzle theme #
|
||||
|
|
@ -145,102 +148,24 @@ pygments_style = 'sphinx'
|
|||
# # "globaltoc_includehidden": False,
|
||||
# }
|
||||
|
||||
###################
|
||||
# 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",
|
||||
}
|
||||
html_theme = 'sphinx_book_theme'
|
||||
|
||||
# The name for this set of Sphinx documents. If None, it defaults to
|
||||
# "<project> v<release> documentation".
|
||||
#html_title = None
|
||||
# html_title = None
|
||||
html_title = 'Phono3py v.%s' % release
|
||||
|
||||
# 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
|
||||
# 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
|
||||
# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
|
||||
# pixels large.
|
||||
#html_favicon = None
|
||||
# html_favicon = None
|
||||
|
||||
# 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,
|
||||
|
|
@ -249,64 +174,65 @@ html_static_path = ['_static']
|
|||
|
||||
# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
|
||||
# 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
|
||||
# typographically correct entities.
|
||||
#html_use_smartypants = True
|
||||
# html_use_smartypants = True
|
||||
|
||||
# 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
|
||||
# template names.
|
||||
#html_additional_pages = {}
|
||||
# html_additional_pages = {}
|
||||
|
||||
# If false, no module index is generated.
|
||||
#html_domain_indices = True
|
||||
# html_domain_indices = True
|
||||
|
||||
# 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.
|
||||
#html_split_index = False
|
||||
# html_split_index = False
|
||||
|
||||
# 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.
|
||||
#html_show_sphinx = True
|
||||
# html_show_sphinx = 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
|
||||
# contain a <link> tag referring to it. The value of this option must be the
|
||||
# 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").
|
||||
#html_file_suffix = None
|
||||
# html_file_suffix = None
|
||||
|
||||
# Output file base name for HTML help builder.
|
||||
htmlhelp_basename = 'phono3pydoc'
|
||||
|
||||
|
||||
# -- Options for LaTeX output --------------------------------------------------
|
||||
# -- Options for LaTeX output -------------------------------------------------
|
||||
|
||||
latex_elements = {
|
||||
# The paper size ('letterpaper' or 'a4paper').
|
||||
#'papersize': 'letterpaper',
|
||||
# The paper size ('letterpaper' or 'a4paper').
|
||||
# 'papersize': 'letterpaper',
|
||||
|
||||
# The font size ('10pt', '11pt' or '12pt').
|
||||
#'pointsize': '10pt',
|
||||
# The font size ('10pt', '11pt' or '12pt').
|
||||
# 'pointsize': '10pt',
|
||||
|
||||
# Additional stuff for the LaTeX preamble.
|
||||
#'preamble': '',
|
||||
# Additional stuff for the LaTeX preamble.
|
||||
'preamble': '',
|
||||
}
|
||||
|
||||
# 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 = [
|
||||
('index', 'phono3py.tex', u'phono3py 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 title page.
|
||||
#latex_logo = None
|
||||
# latex_logo = None
|
||||
|
||||
# For "manual" documents, if this is true, then toplevel headings are parts,
|
||||
# not chapters.
|
||||
#latex_use_parts = False
|
||||
# latex_use_parts = False
|
||||
|
||||
# If true, show page references after internal links.
|
||||
#latex_show_pagerefs = False
|
||||
# latex_show_pagerefs = False
|
||||
|
||||
# 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.
|
||||
#latex_appendices = []
|
||||
# latex_appendices = []
|
||||
|
||||
# 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
|
||||
# (source start file, name, description, authors, manual section).
|
||||
|
|
@ -343,10 +269,10 @@ man_pages = [
|
|||
]
|
||||
|
||||
# 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
|
||||
# (source start file, target name, title, author,
|
||||
|
|
@ -358,10 +284,10 @@ texinfo_documents = [
|
|||
]
|
||||
|
||||
# Documents to append as an appendix to all manuals.
|
||||
#texinfo_appendices = []
|
||||
# texinfo_appendices = []
|
||||
|
||||
# If false, no module index is generated.
|
||||
#texinfo_domain_indices = True
|
||||
# texinfo_domain_indices = True
|
||||
|
||||
# How to display URL addresses: 'footnote', 'no', or 'inline'.
|
||||
#texinfo_show_urls = 'footnote'
|
||||
# texinfo_show_urls = 'footnote'
|
||||
|
|
|
|||
|
|
@ -52,28 +52,21 @@ Creating supercells with displacements
|
|||
|
||||
``--cutoff-pair`` option is employed when creating supercells with
|
||||
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
|
||||
_ _____
|
||||
_ __ | |__ ___ _ __ ___|___ / _ __ _ _
|
||||
| '_ \| '_ \ / _ \| '_ \ / _ \ |_ \| '_ \| | | |
|
||||
| |_) | | | | (_) | | | | (_) |__) | |_) | |_| |
|
||||
| .__/|_| |_|\___/|_| |_|\___/____/| .__/ \__, |
|
||||
|_| |_| |___/
|
||||
1.11.11
|
||||
|
||||
Run mode: displacements
|
||||
...
|
||||
|
||||
Unit cell was read from "POSCAR-unitcell".
|
||||
Displacement distance: 0.03
|
||||
Number of displacements: 111
|
||||
Cutoff distance for displacements: 5.0
|
||||
Number of displacement supercell files created: 51
|
||||
_
|
||||
___ _ __ __| |
|
||||
/ _ \ '_ \ / _` |
|
||||
| __/ | | | (_| |
|
||||
\___|_| |_|\__,_|
|
||||
|
||||
Displacement dataset was written in "phono3py_disp.yaml".
|
||||
...
|
||||
|
||||
% ls POSCAR-0*
|
||||
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
|
||||
the contracted number of supercells with displacements by
|
||||
``--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
|
||||
calculation step, therefore this file must be kept carefully.
|
||||
|
||||
Supercell files
|
||||
^^^^^^^^^^^^^^^^
|
||||
^^^^^^^^^^^^^^^
|
||||
|
||||
``POSCAR-xxxxx`` (in the other calculator interface, the prefix of the
|
||||
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
|
||||
changing the cutoff-pair-distance.
|
||||
|
||||
Special ``disp_fc3.yaml``
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
Special ``phono3py_disp.yaml``
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
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
|
||||
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
|
||||
``-d`` without ``--cutoff-pair`` or with different ``--cutoff-pair``
|
||||
with different value.
|
||||
|
|
@ -128,7 +121,7 @@ Making ``FORCES_FC3``
|
|||
|
||||
To create ``FORCES_FC3``, only output files of the supercells created
|
||||
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.
|
||||
|
||||
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
|
||||
``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
|
||||
_ _____
|
||||
_ __ | |__ ___ _ __ ___|___ / _ __ _ _
|
||||
| '_ \| '_ \ / _ \| '_ \ / _ \ |_ \| '_ \| | | |
|
||||
| |_) | | | | (_) | | | | (_) |__) | |_) | |_| |
|
||||
| .__/|_| |_|\___/|_| |_|\___/____/| .__/ \__, |
|
||||
|_| |_| |___/
|
||||
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
|
||||
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
|
||||
% 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
|
||||
script:
|
||||
|
||||
.. code-block:: 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"
|
||||
dds = yaml.load(open("disp_fc3.yaml"))
|
||||
count = 1
|
||||
for d1 in dds['first_atoms']:
|
||||
print(file_name_tmpl % count)
|
||||
count += 1
|
||||
for d1 in dds['first_atoms']:
|
||||
for d2 in d1['second_atoms']:
|
||||
for d in d2['displacements']:
|
||||
if d2['included']:
|
||||
print(file_name_tmpl % count)
|
||||
count += 1
|
||||
if d2['included']:
|
||||
print(file_name_tmpl % count)
|
||||
count += 1
|
||||
|
||||
Running phonon-phonon interaction calculation
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
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.
|
||||
Sets of supercell forces are read from FORCES_FC3.
|
||||
Solving fc3[ 1, x, x ] with a displacement:
|
||||
----------------------------- General settings -----------------------------
|
||||
Run mode: None
|
||||
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]
|
||||
Expanding fc3
|
||||
Expanding fc3.
|
||||
Cutting-off fc3 (cut-off distance: 5.000000)
|
||||
Building atom mapping table...
|
||||
Creating contracted fc3...
|
||||
Writing fc3 to fc3.hdf5
|
||||
max drift of fc3: 0.043921 (zyx) 0.043921 (yzx) 0.043921 (yxz)
|
||||
Solving fc2
|
||||
Writing fc2 to fc2.hdf5
|
||||
max drift of fc2: -0.000001 (xx) -0.000001 (xx)
|
||||
*************** None of ph-ph interaction was calculated. ****************
|
||||
_
|
||||
___ _ __ __| |
|
||||
/ _ \ '_ \ / _` |
|
||||
| __/ | | | (_| |
|
||||
\___|_| |_|\__,_|
|
||||
Writing fc3 to "fc3.hdf5".
|
||||
Max drift of fc3: 0.047748 (yxz) 0.047748 (xyz) 0.047748 (xzy)
|
||||
Displacement dataset for fc2 was read from "phono3py_disp.yaml".
|
||||
Sets of supercell forces were read from "FORCES_FC3".
|
||||
Writing fc2 to "fc2.hdf5".
|
||||
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``
|
||||
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 ``disp_fc3.yaml``
|
||||
-----------------------------------------------------
|
||||
A script extract supercell IDs from ``phono3py_disp.yaml``
|
||||
----------------------------------------------------------
|
||||
|
||||
The following script is an example to collect supercell IDs
|
||||
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
|
||||
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
|
||||
to consider.
|
||||
|
||||
::
|
||||
.. code-block:: python
|
||||
|
||||
#!/usr/bin/env python
|
||||
|
||||
import yaml
|
||||
try:
|
||||
from yaml import CLoader as Loader
|
||||
except ImportError:
|
||||
from yaml import Loader
|
||||
from phono3py.interface.phono3py_yaml import Phono3pyYaml
|
||||
|
||||
with open("disp_fc3.yaml", 'r') as f:
|
||||
data = yaml.load(f, Loader=Loader)
|
||||
p3yaml = Phono3pyYaml()
|
||||
p3yaml.read("phono3py_disp.yaml")
|
||||
data = p3yaml.dataset
|
||||
|
||||
disp_ids = []
|
||||
for data1 in data['first_atoms']:
|
||||
disp_ids.append(data1['displacement_id'])
|
||||
disp_ids.append(data1['id'])
|
||||
|
||||
for data1 in data['first_atoms']:
|
||||
for data2 in data1['second_atoms']:
|
||||
if data2['included']:
|
||||
disp_ids += data2['displacement_ids']
|
||||
disp_ids.append(data2['id'])
|
||||
|
||||
# # To remove duplicates
|
||||
# duplicates = data['duplicates']
|
||||
# print(len(duplicates))
|
||||
# To remove duplicates
|
||||
# duplicates = dict(data['duplicates'])
|
||||
# disp_ids_nodup = [i for i in disp_ids if i not in duplicates]
|
||||
|
||||
print(" ".join(["%05d" % i for i in disp_ids]))
|
||||
|
||||
Even for the case that ``disp_fc3.yaml`` was created without
|
||||
``--cutoff-pair`` option, if we replace the line in the above script::
|
||||
Even for the case that ``phono3py_disp.yaml`` was created without
|
||||
``--cutoff-pair`` option, if we replace the line in the above script:
|
||||
|
||||
.. code-block:: python
|
||||
|
||||
if data2['included']:
|
||||
|
||||
by
|
||||
|
||||
::
|
||||
.. code-block:: python
|
||||
|
||||
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``
|
||||
values are calculated as follows. Note that if ``FORCES_FC3`` for full
|
||||
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
|
||||
2.366961
|
||||
3.865232
|
||||
|
|
@ -308,50 +305,53 @@ generating contracted fc3 for each special ``disp_fc3.yaml``.
|
|||
7.100884
|
||||
7.730463
|
||||
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 $i -d --dim="2 2 2" -c POSCAR-unitcell ;done
|
||||
% ls disp_fc3.*.yaml
|
||||
disp_fc3.10.yaml disp_fc3.4.yaml disp_fc3.7.yaml
|
||||
disp_fc3.2.yaml disp_fc3.5.yaml disp_fc3.8.yaml
|
||||
disp_fc3.3.yaml disp_fc3.6.yaml disp_fc3.9.yaml
|
||||
% for i in {2..10};do grep num_displacements_created disp_fc3.$i.yaml;done
|
||||
num_displacements_created: 11
|
||||
num_displacements_created: 31
|
||||
num_displacements_created: 51
|
||||
num_displacements_created: 56
|
||||
num_displacements_created: 76
|
||||
num_displacements_created: 96
|
||||
num_displacements_created: 104
|
||||
num_displacements_created: 109
|
||||
num_displacements_created: 111
|
||||
% 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
|
||||
% cp phono3py_disp.yaml phono3py_disp.orig.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
|
||||
% ls phono3py_disp.*.yaml
|
||||
% ls phono3py_disp.*.yaml
|
||||
phono3py_disp.10.yaml phono3py_disp.5.yaml phono3py_disp.9.yaml
|
||||
phono3py_disp.2.yaml phono3py_disp.6.yaml phono3py_disp.orig.yaml
|
||||
phono3py_disp.3.yaml phono3py_disp.7.yaml
|
||||
phono3py_disp.4.yaml phono3py_disp.8.yaml
|
||||
% for i in {2..10};do grep number_of_pairs_in_cutoff phono3py_disp.$i.yaml;done
|
||||
number_of_pairs_in_cutoff: 10
|
||||
number_of_pairs_in_cutoff: 30
|
||||
number_of_pairs_in_cutoff: 50
|
||||
number_of_pairs_in_cutoff: 55
|
||||
number_of_pairs_in_cutoff: 75
|
||||
number_of_pairs_in_cutoff: 95
|
||||
number_of_pairs_in_cutoff: 103
|
||||
number_of_pairs_in_cutoff: 108
|
||||
number_of_pairs_in_cutoff: 110
|
||||
% for i in {2..10};do cp phono3py_disp.$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
|
||||
300.0 123.559 123.559 123.559 -0.000 -0.000 0.000
|
||||
300.0 118.586 118.586 118.586 -0.000 -0.000 0.000
|
||||
300.0 118.778 118.778 118.778 -0.000 -0.000 0.000
|
||||
300.0 118.839 118.839 118.839 -0.000 -0.000 0.000
|
||||
300.0 119.433 119.433 119.433 -0.000 -0.000 0.000
|
||||
300.0 119.453 119.453 119.453 -0.000 -0.000 0.000
|
||||
300.0 119.466 119.466 119.466 -0.000 -0.000 0.000
|
||||
300.0 119.447 119.447 119.447 -0.000 -0.000 0.000
|
||||
300.0 119.445 119.445 119.445 -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-$i.out;done
|
||||
300.0 123.606 123.606 123.606 -0.000 -0.000 0.000
|
||||
300.0 118.617 118.617 118.617 -0.000 -0.000 0.000
|
||||
300.0 118.818 118.818 118.818 -0.000 -0.000 0.000
|
||||
300.0 118.879 118.879 118.879 -0.000 -0.000 0.000
|
||||
300.0 119.468 119.468 119.468 -0.000 -0.000 0.000
|
||||
300.0 119.489 119.489 119.489 -0.000 -0.000 0.000
|
||||
300.0 119.501 119.501 119.501 -0.000 -0.000 0.000
|
||||
300.0 119.483 119.483 119.483 -0.000 -0.000 0.000
|
||||
300.0 119.481 119.481 119.481 -0.000 -0.000 0.000
|
||||
% for i in {2..10};do cp phono3py_disp.$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
|
||||
300.0 124.626 124.626 124.626 -0.000 0.000 0.000
|
||||
300.0 119.721 119.721 119.721 -0.000 0.000 0.000
|
||||
300.0 118.806 118.806 118.806 -0.000 0.000 0.000
|
||||
300.0 118.741 118.741 118.741 -0.000 0.000 0.000
|
||||
300.0 119.446 119.446 119.446 -0.000 0.000 0.000
|
||||
300.0 119.339 119.339 119.339 -0.000 0.000 0.000
|
||||
300.0 119.323 119.323 119.323 -0.000 0.000 0.000
|
||||
300.0 119.313 119.313 119.313 -0.000 0.000 0.000
|
||||
300.0 119.311 119.311 119.311 -0.000 0.000 0.000
|
||||
300.0 124.650 124.650 124.650 -0.000 -0.000 0.000
|
||||
300.0 119.765 119.765 119.765 -0.000 -0.000 0.000
|
||||
300.0 118.847 118.847 118.847 -0.000 -0.000 0.000
|
||||
300.0 118.782 118.782 118.782 -0.000 -0.000 0.000
|
||||
300.0 119.471 119.471 119.471 -0.000 -0.000 0.000
|
||||
300.0 119.366 119.366 119.366 -0.000 -0.000 0.000
|
||||
300.0 119.350 119.350 119.350 -0.000 -0.000 0.000
|
||||
300.0 119.339 119.339 119.339 -0.000 -0.000 0.000
|
||||
300.0 119.337 119.337 119.337 -0.000 -0.000 0.000
|
||||
|
||||
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
|
||||
1.889907
|
||||
1.901086
|
||||
|
|
@ -374,72 +374,70 @@ AlN-LDA
|
|||
6.205027
|
||||
6.469591
|
||||
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 $i -d --dim="3 3 2" -c POSCAR-unitcell ;done
|
||||
% for i in {2..22};do grep num_displacements_created disp_fc3.$i.yaml;done
|
||||
num_displacements_created: 78
|
||||
num_displacements_created: 98
|
||||
num_displacements_created: 202
|
||||
num_displacements_created: 222
|
||||
num_displacements_created: 318
|
||||
num_displacements_created: 370
|
||||
num_displacements_created: 466
|
||||
num_displacements_created: 570
|
||||
num_displacements_created: 666
|
||||
num_displacements_created: 718
|
||||
num_displacements_created: 718
|
||||
num_displacements_created: 770
|
||||
num_displacements_created: 790
|
||||
num_displacements_created: 894
|
||||
num_displacements_created: 934
|
||||
num_displacements_created: 986
|
||||
num_displacements_created: 1026
|
||||
num_displacements_created: 1122
|
||||
num_displacements_created: 1162
|
||||
num_displacements_created: 1214
|
||||
num_displacements_created: 1254
|
||||
% 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..22};do egrep '^\s+300\.0' std.$i.out;done
|
||||
300.0 201.530 201.530 192.685 -0.000 -0.000 -0.000
|
||||
300.0 212.963 212.963 204.362 -0.000 -0.000 -0.000
|
||||
300.0 208.005 208.005 196.684 -0.000 -0.000 -0.000
|
||||
300.0 212.213 212.213 200.778 -0.000 -0.000 -0.000
|
||||
300.0 223.019 223.019 214.702 -0.000 -0.000 -0.000
|
||||
300.0 223.181 223.181 214.351 -0.000 -0.000 -0.000
|
||||
300.0 222.360 222.360 213.924 -0.000 -0.000 -0.000
|
||||
300.0 223.245 223.245 214.561 -0.000 -0.000 -0.000
|
||||
300.0 223.812 223.812 215.359 -0.000 -0.000 -0.000
|
||||
300.0 223.959 223.959 215.701 -0.000 -0.000 -0.000
|
||||
300.0 223.959 223.959 215.701 -0.000 -0.000 -0.000
|
||||
300.0 224.507 224.507 215.384 -0.000 -0.000 -0.000
|
||||
300.0 224.278 224.278 215.396 -0.000 -0.000 -0.000
|
||||
300.0 223.551 223.551 212.671 -0.000 -0.000 -0.000
|
||||
300.0 224.732 224.732 214.463 -0.000 -0.000 -0.000
|
||||
300.0 224.291 224.291 213.270 -0.000 -0.000 -0.000
|
||||
300.0 224.805 224.805 214.771 -0.000 -0.000 -0.000
|
||||
300.0 224.834 224.834 215.025 -0.000 -0.000 -0.000
|
||||
300.0 224.645 224.645 215.260 -0.000 -0.000 -0.000
|
||||
300.0 224.769 224.769 215.220 -0.000 -0.000 -0.000
|
||||
300.0 224.650 224.650 215.090 -0.000 -0.000 -0.000
|
||||
% 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-$i.out; done
|
||||
% for i in {2..22};do egrep '^\s+300\.0' std.sym-$i.out;done
|
||||
300.0 224.122 224.122 213.086 0.000 -0.000 0.000
|
||||
300.0 225.394 225.394 215.683 0.000 -0.000 0.000
|
||||
300.0 223.748 223.748 213.682 0.000 -0.000 0.000
|
||||
300.0 223.973 223.973 213.543 0.000 -0.000 0.000
|
||||
300.0 224.876 224.876 216.489 0.000 -0.000 0.000
|
||||
300.0 224.603 224.603 216.204 0.000 -0.000 0.000
|
||||
300.0 223.773 223.773 214.657 0.000 -0.000 0.000
|
||||
300.0 224.173 224.173 215.517 0.000 -0.000 0.000
|
||||
300.0 224.596 224.596 215.896 0.000 -0.000 0.000
|
||||
300.0 224.401 224.401 215.955 0.000 -0.000 0.000
|
||||
300.0 224.401 224.401 215.955 0.000 -0.000 0.000
|
||||
300.0 224.077 224.077 215.565 0.000 -0.000 0.000
|
||||
300.0 224.285 224.285 215.654 0.000 -0.000 0.000
|
||||
300.0 224.136 224.136 215.053 0.000 -0.000 0.000
|
||||
300.0 224.469 224.469 215.462 0.000 -0.000 0.000
|
||||
300.0 224.109 224.109 215.011 0.000 -0.000 0.000
|
||||
300.0 224.108 224.108 215.447 0.000 -0.000 0.000
|
||||
300.0 224.592 224.592 215.046 0.000 -0.000 0.000
|
||||
300.0 224.640 224.640 215.113 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
|
||||
% cp phono3py_disp.yaml phono3py_disp.orig.yaml
|
||||
% 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
|
||||
% for i in {2..21};do grep number_of_pairs_in_cutoff phono3py_disp.$i.yaml;done
|
||||
number_of_pairs_in_cutoff: 72
|
||||
number_of_pairs_in_cutoff: 92
|
||||
number_of_pairs_in_cutoff: 196
|
||||
number_of_pairs_in_cutoff: 216
|
||||
number_of_pairs_in_cutoff: 312
|
||||
number_of_pairs_in_cutoff: 364
|
||||
number_of_pairs_in_cutoff: 460
|
||||
number_of_pairs_in_cutoff: 564
|
||||
number_of_pairs_in_cutoff: 660
|
||||
number_of_pairs_in_cutoff: 712
|
||||
number_of_pairs_in_cutoff: 764
|
||||
number_of_pairs_in_cutoff: 784
|
||||
number_of_pairs_in_cutoff: 888
|
||||
number_of_pairs_in_cutoff: 928
|
||||
number_of_pairs_in_cutoff: 980
|
||||
number_of_pairs_in_cutoff: 1020
|
||||
number_of_pairs_in_cutoff: 1116
|
||||
number_of_pairs_in_cutoff: 1156
|
||||
number_of_pairs_in_cutoff: 1208
|
||||
number_of_pairs_in_cutoff: 1248
|
||||
% for i in {2..21};do cp phono3py_disp.$i.yaml phono3py_disp.yaml; phono3py --mesh="13 13 9" --br --nac --io $i|tee std.$i.out; done
|
||||
% for i in {2..21};do egrep '^\s+300\.0' std.$i.out;done
|
||||
300.0 205.550 205.550 193.665 -0.000 -0.000 -0.000
|
||||
300.0 218.963 218.963 204.942 -0.000 -0.000 -0.000
|
||||
300.0 213.624 213.624 193.863 -0.000 -0.000 -0.000
|
||||
300.0 219.932 219.932 199.819 -0.000 -0.000 -0.000
|
||||
300.0 235.516 235.516 218.843 -0.000 -0.000 -0.000
|
||||
300.0 234.750 234.750 217.384 -0.000 -0.000 -0.000
|
||||
300.0 234.355 234.355 218.030 -0.000 -0.000 -0.000
|
||||
300.0 235.381 235.381 218.609 -0.000 -0.000 -0.000
|
||||
300.0 235.996 235.996 219.785 -0.000 -0.000 -0.000
|
||||
300.0 236.220 236.220 219.867 -0.000 -0.000 -0.000
|
||||
300.0 236.161 236.161 219.298 -0.000 -0.000 -0.000
|
||||
300.0 236.096 236.096 219.313 -0.000 -0.000 -0.000
|
||||
300.0 234.602 234.602 217.064 -0.000 -0.000 -0.000
|
||||
300.0 235.914 235.914 218.689 -0.000 -0.000 -0.000
|
||||
300.0 235.049 235.049 217.935 -0.000 -0.000 -0.000
|
||||
300.0 235.877 235.877 219.065 -0.000 -0.000 -0.000
|
||||
300.0 236.133 236.133 219.364 -0.000 -0.000 -0.000
|
||||
300.0 236.207 236.207 219.595 -0.000 -0.000 -0.000
|
||||
300.0 236.035 236.035 219.463 -0.000 -0.000 -0.000
|
||||
300.0 236.104 236.104 219.348 -0.000 -0.000 -0.000
|
||||
% for i in {2..21};do cp phono3py_disp.$i.yaml phono3py_disp.yaml; phono3py --mesh="13 13 9" --br --nac --io $i|tee std.$i.out; done|tee std.sym-$i.out; done
|
||||
% for i in {2..21};do egrep '^\s+300\.0' std.sym-$i.out;done
|
||||
300.0 232.964 232.964 216.333 0.000 -0.000 -0.000
|
||||
300.0 235.442 235.442 219.602 0.000 -0.000 -0.000
|
||||
300.0 235.521 235.521 217.767 0.000 -0.000 -0.000
|
||||
300.0 235.581 235.581 217.687 0.000 -0.000 -0.000
|
||||
300.0 236.837 236.837 219.933 0.000 -0.000 -0.000
|
||||
300.0 236.020 236.020 219.324 0.000 -0.000 -0.000
|
||||
300.0 235.482 235.482 218.633 0.000 -0.000 -0.000
|
||||
300.0 236.313 236.313 219.677 0.000 -0.000 -0.000
|
||||
300.0 236.308 236.308 219.955 0.000 -0.000 -0.000
|
||||
300.0 236.074 236.074 219.882 0.000 -0.000 -0.000
|
||||
300.0 235.520 235.520 219.450 0.000 -0.000 -0.000
|
||||
300.0 235.769 235.769 219.562 0.000 -0.000 -0.000
|
||||
300.0 235.441 235.441 219.168 0.000 -0.000 -0.000
|
||||
300.0 235.892 235.892 219.590 0.000 -0.000 -0.000
|
||||
300.0 235.509 235.509 219.167 0.000 -0.000 -0.000
|
||||
300.0 235.646 235.646 219.521 0.000 -0.000 -0.000
|
||||
300.0 235.783 235.783 219.311 0.000 -0.000 -0.000
|
||||
300.0 235.887 235.887 219.301 0.000 -0.000 -0.000
|
||||
300.0 235.642 235.642 219.348 0.000 -0.000 -0.000
|
||||
300.0 235.728 235.728 219.102 0.000 -0.000 -0.000
|
||||
|
|
|
|||
|
|
@ -19,12 +19,14 @@ memory space. When running multiple temperature points, simply the
|
|||
memory space needed is multiplied by the number of the temperature
|
||||
points. Therefore it is normally recommended to specify :ref:`--ts
|
||||
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" --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 ===================
|
||||
|
|
@ -41,11 +43,8 @@ LBTE for ``example/Si-PBEsol`` is as follows::
|
|||
Thermal conductivity and related properties were written into
|
||||
"kappa-m111111.hdf5".
|
||||
Eigenvalues of collision matrix were written into "coleigs-m111111.hdf5"
|
||||
_
|
||||
___ _ __ __| |
|
||||
/ _ \ '_ \ / _` |
|
||||
| __/ | | | (_| |
|
||||
\___|_| |_|\__,_|
|
||||
|
||||
...
|
||||
|
||||
Memory usage
|
||||
-------------
|
||||
|
|
@ -69,9 +68,11 @@ memory space is consumed in total.
|
|||
|
||||
When phono3py runs with :ref:`--wgp option <wgp_option>` together with
|
||||
``--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:
|
||||
|
|
@ -149,19 +150,26 @@ The summary of the procedure is as follows:
|
|||
file names of the results at different temperatures.
|
||||
|
||||
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
|
||||
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
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
|
|
@ -203,20 +211,26 @@ The summary of the procedure is as follows:
|
|||
temperatures.
|
||||
|
||||
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
|
||||
``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
|
||||
: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
|
||||
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
|
||||
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
|
||||
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
|
||||
created. This contains the eigenvalues of the collision matrix (either
|
||||
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
|
||||
|
||||
|
|
|
|||
|
|
@ -325,18 +325,33 @@ For example, :math:`\kappa_{\lambda,{xx}}` is calculated by::
|
|||
array([ 1.02050201e+03, 1.02050201e+03, 1.02050201e+03,
|
||||
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
|
||||
with grid point numbers such as ``kappa-m202020-g4200.hdf5``. You may
|
||||
want to know the grid point number with given grid address. This is
|
||||
done using ``get_grid_point_from_address`` as follows::
|
||||
Runngin with ``--write-gamma``, hdf5 files are written out with file names
|
||||
such as ``kappa-m202020-g4448.hdf5``. You may want to know the grid point
|
||||
index number with given grid address. This is done 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])
|
||||
Out[2]: 4200
|
||||
In [1]: import phono3py
|
||||
|
||||
Here the first argument of this method is the grid address and the
|
||||
second argument is the mesh numbers.
|
||||
In [2]: ph3 = phono3py.load("phono3py_disp.yaml")
|
||||
|
||||
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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
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`.
|
||||
|
||||
``disp_fc2.yaml``
|
||||
^^^^^^^^^^^^^^^^^^
|
||||
|
||||
This is created with ``-d`` option with ``--dim_fc2`` option. See
|
||||
:ref:`dim_fc2_option`.
|
||||
|
||||
``FORCES_FC3``
|
||||
^^^^^^^^^^^^^^^
|
||||
|
||||
|
|
|
|||
41
doc/qe.rst
41
doc/qe.rst
|
|
@ -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.
|
||||
|
||||
To invoke the QE (pw) interface, ``--qe`` option has to be always
|
||||
specified::
|
||||
Unless a proper ``phono3py_disp.yaml`` containing calculator information,
|
||||
to invoke the QE (pw) interface, ``--qe`` option has to be specified,
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
% phono3py --qe [options] [arguments]
|
||||
|
||||
|
|
@ -29,15 +31,15 @@ Workflow
|
|||
|
||||
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
|
||||
displacements are created. Supercell files (``supercell-xxx.in``)
|
||||
are created but they contain only the crystal
|
||||
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
|
||||
|
||||
|
|
@ -49,24 +51,33 @@ Workflow
|
|||
3. Collect forces
|
||||
|
||||
``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.
|
||||
|
||||
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" \
|
||||
--mesh="11 11 11" --fc3 --fc2 --br
|
||||
where ``--sym-fc`` symmetrizes fc3 and fc2.
|
||||
|
||||
5) Calculate lattice thermal conductivity, e.g., by:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
% phono3py --mesh="11 11 11" --fc3 --fc2 --br
|
||||
|
|
|
|||
|
|
@ -112,14 +112,12 @@ higher order anharmonicity is involved (renormalized) into fc3 and fc2.
|
|||
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
|
||||
compatible with phonopy's ``FORCE_SETS``.
|
||||
- ``FORCE_SETS`` can be created using :ref:`--cfs <cfs_option>` from
|
||||
``FORCES_FC3`` and ``disp_fc3.yaml`` or ``FORCES_FC2`` and
|
||||
``disp_fc2.yaml`` (needs to specify ``--dim-fc2``).
|
||||
- ``FORCES_FC2`` and ``disp_fc2.yaml`` can be created using :ref:`--fs2f2
|
||||
``FORCES_FC3`` and ``phono3py_disp.yaml`` or ``FORCES_FC2`` and
|
||||
``phono3py_disp.yaml`` (needs to specify ``--dim-fc2``).
|
||||
- ``FORCES_FC2`` can be created using :ref:`--fs2f2
|
||||
<fs2f2_option>` from ``FORCE_SETS``.
|
||||
- ``fc2.hdf5`` can be used in phonopy in the ``hdf5`` mode when it is
|
||||
renamed to ``force_constants.hdf5``. In the previous combinations of
|
||||
|
|
|
|||
86
doc/vasp.rst
86
doc/vasp.rst
|
|
@ -10,22 +10,25 @@ Workflow
|
|||
|
||||
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
|
||||
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
|
||||
also created.
|
||||
% phono3py -d --dim-fc2="4 4 4" --dim="2 2 2" --pa="F" -c POSCAR-unitcell
|
||||
|
||||
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
|
||||
``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
|
||||
``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
|
||||
fc3 and fc2 are created as follows.
|
||||
|
||||
::
|
||||
.. code-block:: bash
|
||||
|
||||
% phono3py --cf3 disp-{00001..00755}/vasprun.xml
|
||||
|
||||
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.
|
||||
|
||||
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
|
||||
|
||||
``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.
|
||||
|
||||
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
|
||||
``disp_fc3.yaml``. This step is not mandatory, but you can avoid
|
||||
calculating fc2 and fc3 at every run time.
|
||||
``--sym-fc`` symmetrizes fc3 and fc2. ``fc2.hdf5`` and ``fc3.hdf5``
|
||||
are created from ``FORCES_FC3`` (and
|
||||
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``,
|
||||
``FORCES_FC2``, ``disp_fc3.yaml``, and ``disp_fc2.yaml``.
|
||||
.. code-block:: bash
|
||||
|
||||
5. Thermal conductivity calculation
|
||||
|
||||
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
|
||||
% phono3py --mesh="11 11 11" --br
|
||||
|
||||
This calculation may take very long time. ``--thm`` invokes a
|
||||
tetrahedron method for Brillouin zone integration for phonon
|
||||
|
|
@ -95,23 +92,26 @@ Workflow
|
|||
are independent and no communication is necessary at the
|
||||
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" \
|
||||
-c POSCAR-unitcell --br --wgp
|
||||
.. code-block:: bash
|
||||
|
||||
% phono3py --fc3 --fc2 --mesh="11 11 11" --br --wgp
|
||||
|
||||
``ir_grid_points.yaml`` is obtained. In this file, irreducible
|
||||
q-points are shown. Then distribute calculations of phonon
|
||||
lifetimes on grid points with ``--write_gamma`` option by::
|
||||
lifetimes on grid points with ``--write-gamma`` option by:
|
||||
|
||||
% phono3py --fc3 --fc2 --dim="2 2 2" --mesh="11 11 11" \
|
||||
-c POSCAR-unitcell --br --write_gamma --gp="[grid ponit(s)]"
|
||||
.. code-block:: bash
|
||||
|
||||
% phono3py --mesh="11 11 11" --br --write-gamma --gp="[grid ponit(s)]"
|
||||
|
||||
After finishing all distributed calculations, run with
|
||||
``--read_gamma`` option::
|
||||
``--read-gamma`` option:
|
||||
|
||||
% phono3py --fc3 --fc2 --dim="2 2 2" --mesh="11 11 11" \
|
||||
-c POSCAR-unitcell --br --read_gamma
|
||||
.. code-block:: bash
|
||||
|
||||
% phono3py --fc3 --fc2 --mesh="11 11 11" --br --read-gamma
|
||||
|
||||
Once this calculation runs without problem, separately calculated
|
||||
hdf5 files on grid points are no more necessary and may be deleted.
|
||||
|
|
|
|||
|
|
@ -30,20 +30,22 @@ How to do it
|
|||
The following example is executed in the ``Si-PBE`` example.
|
||||
|
||||
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
|
||||
|
||||
The indices of the irreducible grid-points neccesarry to specify
|
||||
``--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``.
|
||||
|
||||
::
|
||||
.. code-block:: bash
|
||||
|
||||
% 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,
|
||||
|
|
@ -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
|
||||
necessary to obtain lattice thermal conductivity. To distribute
|
||||
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
|
||||
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
|
||||
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
|
||||
--------------------
|
||||
|
|
@ -98,9 +102,9 @@ indices for workload distribution.
|
|||
|
||||
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
|
||||
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
|
||||
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
|
||||
|
||||
with ``job.sh`` (here for grid-engine):
|
||||
|
||||
.. code-block:: shell
|
||||
.. code-block:: bash
|
||||
|
||||
#$ -S /bin/zsh
|
||||
#$ -cwd
|
||||
|
|
@ -142,4 +146,4 @@ with ``job.sh`` (here for grid-engine):
|
|||
#$ -e err-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
|
||||
|
|
|
|||
Loading…
Reference in New Issue