Update document for version 1.10.5

doc/changelog.rst

@@ -3,6 +3,20 @@
 Change Log
 ==========
 
+Mar-15-2016: version 1.10.5
+------------------------------
+
+- Numbering way of phono3py version was just changed (No big updates
+  were made against previous version.) The number is given based on
+  the phonopy version. For example, the harmonic part of
+  phono3py-1.10.5 is based on the code close to phonopy-1.10.4.
+- Python3 support
+- For the RTA thermal conductivity calculation mode with using the
+  linear tetrahedron method, only necessary part of phonon-phonon
+  interaction strengh among phonons. This improves lifetime
+  calculation performance, but as the drawback, averaged ph-ph
+  interaction strength can not be given. See :ref:`full_pp_option`.
+
 Oct-10-2015: version 0.9.14
 ------------------------------
 

doc/command-options.rst

@@ -308,19 +308,19 @@ After running VASP calculations,
 ``--write_gamma``
 ~~~~~~~~~~~~~~~~~
 
-Imaginary part of self energy at harmonic phonon frequency
-:math:`\Gamma_\lambda(\omega_\lambda)` (or twice of inverse phonon
-lifetime) is written into file in hdf5 format.  The result is written
-into ``kappa-mxxx-dx-gx.hdf5`` or ``kappa-mxxx-dx-gx-bx.hdf5`` with
+Imaginary parts of self energy at harmonic phonon frequencies
+:math:`\Gamma_\lambda(\omega_\lambda) = 1/2\tau_\lambda` are written
+into file in hdf5 format.  The result is written into
+``kappa-mxxx-dx-gx.hdf5`` or ``kappa-mxxx-dx-gx-bx.hdf5`` with
 ``--bi`` option. With ``--sigma`` option, ``-sx`` is inserted in front
 of ``.hdf5``.
 
 ``--read_gamma``
 ~~~~~~~~~~~~~~~~
 
-Imaginary part of self energy at harmonic phonon frequency
-:math:`\Gamma_\lambda(\omega_\lambda)` (or twice of inverse phonon lifetime)
-is read from ``kappa`` file in hdf5 format.  Initially the usual
+Imaginary parts of self energy at harmonic phonon frequencies
+:math:`\Gamma_\lambda(\omega_\lambda) = 1/2\tau_\lambda`
+are read from ``kappa`` file in hdf5 format.  Initially the usual
 result file of ``kappa-mxxx-dx(-sx).hdf5`` is searched. Unless it is
 found, it tries to read ``kappa`` file for each grid point,
 ``kappa-mxxx-dx-gx(-sx).hdf5``. Then, similarly,
@@ -473,8 +473,7 @@ JDOS, number of sampling frequency points is controlled by
 ``--bi``
 ~~~~~~~~
 
-Specify band indices. Imaginary part of self energy is calculated when
-``--lw`` is not specified. The output file name is like
+Specify band indices. The output file name will be, e.g.,
 ``gammas-mxxxxxx-gxx-bx.dat`` where ``bxbx...`` shows the band indices
 used to be averaged. The calculated values at indices separated by
 space are averaged, and those separated by comma are separately
@@ -485,6 +484,34 @@ calculated.
    % phono3py --fc3 --fc2 --dim="2 2 2" --mesh="16 16 16" \
      -c POSCAR-unitcell --nac --gp="34" --bi="4 5, 6"
 
+.. _full_pp_option:
+
+``--full_pp``
+~~~~~~~~~~~~~~
+
+After version 1.10.5, for RTA thermal conductivity calculation with
+using the linear tetrahedron method, only necessary part of
+phonon-phonon interaction strengh among phonons,
+:math:`\bigl|\Phi_{-\lambda\lambda'\lambda''}\bigl|^2`, is
+calculated due to delta functions in calculation of
+:math:`\Gamma_\lambda(\omega)`,
+
+.. math::
+
+   \Gamma_\lambda(\omega) = \frac{18\pi}{\hbar^2}
+    \sum_{\lambda' \lambda''}
+    \bigl|\Phi_{-\lambda\lambda'\lambda''}\bigl|^2 
+    \left\{(n_{\lambda'}+ n_{\lambda''}+1) 
+     \delta(\omega-\omega_{\lambda'}-\omega_{\lambda''}) \right.
+     + (n_{\lambda'}-n_{\lambda''})
+    \left[\delta(\omega+\omega_{\lambda'}-\omega_{\lambda''})
+   - \left. \delta(\omega-\omega_{\lambda'}+\omega_{\lambda''})
+   \right]\right\}.
+
+But specifying this option, full elements of phonon-phonon interaction
+strengh among phonons are calculated and averaged phonon-phonon
+interaction strength (:math:`P_{\mathbf{q}j}`) is also given.
+
 ``--ave_pp``
 ~~~~~~~~~~~~
 
@@ -492,11 +519,11 @@ Averaged phonon-phonon interaction strength (:math:`P_{\mathbf{q}j}`)
 is used to calculate imaginary part of self energy. This option works
 only when ``--read_gamma`` and ``--br`` options are activated where
 the averaged phonon-phonon interaction that is read from
-``kappa-mxxxxx.hdf5`` file is used. Therefore the averaged
-phonon-phonon interaction has to be stored before using this
-option. The calculation result **overwrites** ``kappa-mxxxxx.hdf5``
-file. Therefore to use this option together with ``-o`` option is
-strongly recommended.
+``kappa-mxxxxx.hdf5`` file is used if it exists in the file. Therefore the
+averaged phonon-phonon interaction has to be stored before using this
+option (see :ref:`full_pp_option`). The calculation result
+**overwrites** ``kappa-mxxxxx.hdf5`` file. Therefore to use this
+option together with ``-o`` option is strongly recommended.
 
 First, run full conductivity calculation,
 

doc/conf.py

@@ -49,9 +49,9 @@ copyright = u'2015, Atsushi Togo'
 # built documents.
 #
 # The short X.Y version.
-version = '1.10.3'
+version = '1.10.5'
 # The full version, including alpha/beta/rc tags.
-release = '1.10.3'
+release = '1.10.5'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/output-files.rst

@@ -115,7 +115,6 @@ conductivity calculation is loaded and thermal conductivity tensor at
     u'heat_capacity',
     u'kappa',
     u'mode_kappa',
-    u'ave_pp',
     u'qpoint',
     u'temperature',
     u'weight']
@@ -281,3 +280,7 @@ Averaged phonon-phonon interaction in :math:`\text{eV}^2`,
 
    P_{\mathbf{q}j} = \frac{1}{(3n_\mathrm{a})^2} \sum_{\lambda'\lambda''}
    |\Phi_{\lambda\lambda'\lambda''}|^2.
+
+This is not going to be calculated in the RTA thermal coductivity
+calculation mode by default. To calculate this, ``--full_pp`` option
+has to be specified (see :ref:`full_pp_option`).