mirror of https://github.com/phonopy/phono3py.git
Update document for --write-phonon and --write-gamma-details
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Atsushi Togo
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9a4b00303d
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@ -438,8 +438,7 @@ separately calculated.
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::
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% phono3py --fc3 --fc2 --dim="2 2 2" --mesh="16 16 16" \
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-c POSCAR-unitcell --nac --gp="34" --bi="4 5, 6"
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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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Brillouin zone integration
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---------------------------
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@ -573,8 +572,7 @@ without isotope calculation::
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Then running with isotope calculation::
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% phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br \
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--read-gamma --mv="1.97e-4 1.97e-4 0 0"
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% 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"
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In the result hdf5 file, currently isotope scattering strength is not
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written out, i.e., ``gamma`` is still imaginary part of self energy of
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@ -621,6 +619,8 @@ Specific temperatures are specified by ``--ts``.
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% phono3py --fc3 --fc2 --dim="2 2 2" -v --mesh="11 11 11" -c POSCAR-unitcell --br --ts="200 300 400"
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.. _nac_option:
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``--nac``: Non-analytical term correction
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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@ -708,24 +708,7 @@ triplet (symmetry reduced set of triplets at a gr
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weight (symmetry reduced set of triplets at a grid point,), Weight of each triplet to imaginary part of self energy
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====================================== =============================================================================================================================================
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Q-points corresponding to grid point indices are calculated from
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grid addresses and sampling mesh numbers given in
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``grid_address-mxxx.hdf5`` that is obtained by ``--wgp`` option. A
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python script to obtain q-point triplets is shown below.
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.. code-block:: python
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import h5py
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import numpy as np
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f = h5py.File("gamma_detail-mxxx-gx.hdf5")
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g = h5py.File("grid_address-mxxx.hdf5")
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grid_address = f['grid_address'][:]
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triplets = g['triplet'][:]
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mesh = f['mesh'][:]
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q = grid_address[triplets] / np.array(mesh, dtype='double')
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Imaginary part of self energy or linewidth/2 is recovered by the
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Imaginary part of self energy (linewidth/2) is recovered by the
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following script:
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.. code-block:: python
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@ -733,11 +716,12 @@ following script:
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import h5py
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import numpy as np
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f = h5py.File("gamma_detail-mxxx-gx.hdf5")
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temp = 30 # index of temperature
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gamma_tp = f['gamma_detail'][:].sum(axis=-1).sum(axis=-1)
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weight = f['weight'][:]
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gamma = np.dot(weight, gamma_tp[temp])
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gd = h5py.File("gamma_detail-mxxx-gx.hdf5")
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temp_index = 30 # index of temperature
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temperature = gd['temperature'][temp_index]
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gamma_tp = gd['gamma_detail'][:].sum(axis=-1).sum(axis=-1)
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weight = gd['weight'][:]
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gamma = np.dot(weight, gamma_tp[temp_index])
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For example, for ``--lw`` or ``--br``, this ``gamma`` gives
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:math:`\Gamma_\lambda(\omega_\lambda)` of the band indices at the grid
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@ -748,6 +732,29 @@ type file are averaged, but the ``gamma`` obtained here in this way
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are not symmetrized. Apart from this symmetrization, the values must
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be equivalent between them.
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To understand each contribution of triptle to imaginary part of self
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energy, reading ``phonon-mxxx.hdf5`` is useful (see
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:ref:`write_phonon_option`). For example,
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phonon triplets of three phonon scatterings are obtained by
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.. code-block:: python
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import h5py
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import numpy as np
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gd = h5py.File("gamma_detail-mxxx-gx.hdf5", 'r')
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ph = h5py.File("phonon-mxxx.hdf5", 'r')
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gp1 = gd['grid_point'][()]
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triplets = gd['triplet'][:] # Sets of (gp1, gp2, gp3) where gp1 is fixed
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mesh = gd['mesh'][:]
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grid_address = ph['grid_address'][:]
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q_triplets = grid_address[triplets] / mesh.astype('double')
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# Phonons of triplets[2]
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phonon_tp = [(ph['frequency'][i], ph['eigenvector'][i]) for i in triplets[2]]
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# Fractions of contributions of tripltes at this grid point and temperture index 30
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gamma_sum_over_bands = np.dot(weight, gd['gamma_detail'][30].sum(axis=-1).sum(axis=-1).sum(axis=-1))
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contrib_tp = [gd['gamma_detail'][30, i].sum() / gamma_sum_over_bands for i in range(len(weight))]
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np.dot(weight, contrib_tp) # is one
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..
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``--write-amplitude``
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~~~~~~~~~~~~~~~~~~~~~~
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@ -763,12 +770,45 @@ be equivalent between them.
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Phonon frequencies, eigenvectors, and grid point addresses are stored
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in ``phonon-mxxx.hdf5`` file. After writing phonons, phono3py stops
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without going to calculation.
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without going to calculation. :ref:`--pa <pa_option>` and :ref:`--nac
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<nac_option>` may be required depending on calculation setting.
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::
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% phono3py --fc2 --dim="2 2 2" --mesh="16 16 16" -c POSCAR-unitcell \
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--nac --write-phoonon
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% 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
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Contents of ``phonon-mxxx.hdf5`` are watched by::
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In [1]: import h5py
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In [2]: ph = h5py.File("phonon-m111111.hdf5", 'r')
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In [3]: list(ph)
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Out[3]: ['eigenvector', 'frequency', 'grid_address', 'mesh']
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In [4]: ph['mesh'][:]
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Out[4]: array([11, 11, 11], dtype=int32)
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In [5]: ph['grid_address'].shape
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Out[5]: (1367, 3)
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In [6]: ph['frequency'].shape
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Out[6]: (1367, 6)
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In [7]: ph['eigenvector'].shape
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Out[7]: (1367, 6, 6)
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The first axis of ``ph['grid_address']``, ``ph['frequency']``, and
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``ph['eigenvector']`` corresponds to the number of q-points where
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phonons are calculated. Here the number of phonons may not be equal to
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product of mesh numbers (:math:`1367 \neq 11^3`). This is because all
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q-points on Brillouin zone boundary are included, i.e., even if
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multiple q-points are translationally equivalent, those phonons are
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stored separately though these phonons are physically equivalent
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within the equations employed in phono3py. Here Brillouin zone is
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defined by Wigner–Seitz cell of reciprocal primitive basis
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vectors. This is convenient to categorize phonon triplets into Umklapp
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and Normal scatterings based on the Brillouin zone.
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.. _read_phonon_option:
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@ -779,12 +819,13 @@ Phonon frequencies, eigenvectors, and grid point addresses are read
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from ``phonon-mxxx.hdf5`` file and the calculation is continued using
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these phonon values. This is useful when we want to use fixed phonon
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eigenvectors that can be different for degenerate bands when using
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different eigenvalue solvers or different CPU architectures.
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different eigenvalue solvers or different CPU
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architectures. :ref:`--pa <pa_option>` and :ref:`--nac <nac_option>`
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may be required depending on calculation setting.
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::
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% phono3py --fc2 --fc3 --dim="2 2 2" --mesh="16 16 16" -c POSCAR-unitcell \
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--nac --read-phoonon --br
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% 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
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.. _ise_option:
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@ -800,8 +841,7 @@ with respect to frequency in THz (without :math:`2\pi`).
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::
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% phono3py --fc3 --fc2 --dim="2 2 2" --mesh="16 16 16" -c POSCAR-unitcell \
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--nac --q-direction="1 0 0" --gp=0 --ise --bi="4 5, 6"
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% 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"
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.. _lw_option:
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@ -816,8 +856,7 @@ respect to temperature. The output is written to
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::
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% phono3py --fc3 --fc2 --dim="2 2 2" --mesh="16 16 16" -c POSCAR-unitcell \
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--nac --q-direction="1 0 0" --gp=0 --lw --bi="4 5, 6"
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% phono3py --fc3 --fc2 --dim="2 2 2" --mesh="16 16 16" -c POSCAR-unitcell --nac --q-direction="1 0 0" --gp=0 --lw --bi="4 5, 6"
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.. _jdos_option:
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@ -846,8 +885,7 @@ values given as follows, respectively,
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::
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% phono3py --fc2 --dim="2 2 2" -c POSCAR-unitcell --mesh="16 16 16" \
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--nac --jdos --ga="0 0 0 8 8 8"
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% phono3py --fc2 --dim="2 2 2" -c POSCAR-unitcell --mesh="16 16 16" --nac --jdos --ga="0 0 0 8 8 8"
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When temperatures are specified, two classes of weighted JDOS are
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calculated. The result is written into
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@ -871,8 +909,7 @@ the values given as follows, respectively,
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::
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% phono3py --fc2 --dim="2 2 2" -c POSCAR-unitcell --mesh="16 16 16" \
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--nac --jdos --ga="0 0 0 8 8 8" --ts=300
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% phono3py --fc2 --dim="2 2 2" -c POSCAR-unitcell --mesh="16 16 16" --nac --jdos --ga="0 0 0 8 8 8" --ts=300
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``--num-freq-points``, ``--freq-pitch``: Sampling frequency for distribution functions
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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@ -932,8 +969,7 @@ Then
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::
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% phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br \
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--read-gamma --ave-pp -o ave_pp
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% phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br --read-gamma --ave-pp -o ave_pp
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``--const-ave-pp``: Use constant phonon-phonon interaction strength
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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@ -949,8 +985,7 @@ to input. The physical unit of the value is :math:`\text{eV}^2`.
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::
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% phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br \
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--const-ave-pp=1e-10
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% phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br --const-ave-pp=1e-10
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``--gruneisen``: Mode-Gruneisen parameter from 3rd order force constants
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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@ -961,13 +996,11 @@ Mode-Gruneisen-parameters are calculated from fc3.
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Mesh sampling mode::
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% phono3py --fc3 --fc2 --dim="2 2 2" -v --mesh="16 16 16"
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-c POSCAR-unitcell --nac --gruneisen
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% phono3py --fc3 --fc2 --dim="2 2 2" -v --mesh="16 16 16" -c POSCAR-unitcell --nac --gruneisen
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Band path mode::
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% phono3py --fc3 --fc2 --dim="2 2 2" -v \
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-c POSCAR-unitcell --nac --gruneisen --band="0 0 0 0 0 1/2"
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% phono3py --fc3 --fc2 --dim="2 2 2" -v -c POSCAR-unitcell --nac --gruneisen --band="0 0 0 0 0 1/2"
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Input and output file names
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----------------------------
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@ -105,15 +105,14 @@ for the symmetrized collision matrix.
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collision matrix.
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These collision matrices contain real values and are supposed to be
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64bit float symmetric matrices. During the diagonalization, depending
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on the choice of the solver, around 2 to 3 times more memory space
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than that of the collision matrix is required.
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64bit float symmetric matrices. During the diagonalization with LAPACK
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``dsyev`` solver, around 1.2 times more memory space of that needed
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for the collision matrix is required.
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When phono3py runs with :ref:`--wgp option <wgp_option>` together with
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``--write-collision`` option, estimated memory space needed for
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storing collision matrix is presented. With :ref:`--stp option <stp_option>`,
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estimated memory space needed for ph-ph interaction strengths is
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shown.
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``--lbte`` option, estimated memory space needed for storing collision
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matrix is presented. With :ref:`--stp option <stp_option>`, estimated
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memory space needed for ph-ph interaction strengths is shown.
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Work load distribution
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-----------------------
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