mirror of https://github.com/phonopy/phono3py.git
Made supercell_matrix have explicitly int_ dtype and made supercell_matrix in __init__ method as a kwarg.
This commit is contained in:
Atsushi Togo
parent
e42c8e2a15
commit
1cf0487724
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@ -1,132 +0,0 @@
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(output_files)=
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# Output files
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```{contents}
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:depth: 3
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:local:
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```
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The calculation results are written into files. Mostly the data are
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stored in HDF5 format, therefore how to read the data
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from HDF5 files is also shown.
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## Intermediate text files
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The following files are not compatible with phonopy. But phonopy's
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`FORCE_SETS` file can be created using phono3py command options from
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the following files. See the detail at {ref}`file_format_compatibility`.
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### `phono3py_disp.yaml`
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This is created with `-d` option. See {ref}`create_displacements_option`.
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### `FORCES_FC3`
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This is created with `--cf3` option. See {ref}`cf3_option`.
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### `FORCES_FC2`
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This is created with `--cf2` option. See {ref}`cf2_option` and
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{ref}`dim_fc2_option`.
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## HDF5 files
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### `kappa-*.hdf5`
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See the detail at {ref}`kappa_hdf5_file`.
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(fc3_hdf5_file)=
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### `fc3.hdf5`
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Third order force constants (in real space) are stored in
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$\mathrm{eV}/\text{Angstrom}^3$.
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In phono3py, this is stored in the numpy array `dtype='double'` and
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`order='C'` in the shape of:
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```
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(num_atom, num_atom, num_atom, 3, 3, 3)
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```
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against $\Phi_{\alpha\beta\gamma}(l\kappa, l'\kappa',
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l''\kappa'')$. The first three `num_atom` are the atom indices in supercell
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corresponding to $l\kappa$, $l'\kappa'$,
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$l''\kappa''$, respectively. The last three elements are the Cartesian
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coordinates corresponding to $\alpha$, $\beta$,
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$\gamma$, respectively.
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If you want to import a supercell structure and its fc3, you may
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suffer from matching its atom index between the supercell and an
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expected unit cell. This may be easily dealt with by letting phono3py
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see your supercell as the unit cell (e.g., `POSCAR`,
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`unitcell.in`, etc) and find the unit (primitive) cell using
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{ref}`--pa option <pa_option>`. For example, let us assume your
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supercell is the 2x2x2 multiples of your unit cell that has no
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centring, then your `--pa` setting will be `1/2 0 0 0 1/2 0 0 1/2
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0`. If your unit cell is a conventional unit cell and has a centring,
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e.g., the face centring,
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$$
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(\mathbf{a}_\text{p}, \mathbf{b}_\text{p}, \mathbf{c}_\text{p}) =
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(\mathbf{a}_\text{s}, \mathbf{b}_\text{s}, \mathbf{c}_\text{s})
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\begin{pmatrix}
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\frac{{1}}{2} & 0 & 0 \\
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0 & \frac{{1}}{2} & 0 \\
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0 & 0 & \frac{{1}}{2}
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\end{pmatrix}
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\begin{pmatrix}
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0 & \frac{{1}}{2} & \frac{{1}}{2} \\
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\frac{{1}}{2} & 0 & \frac{{1}}{2} \\
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\frac{{1}}{2} & \frac{{1}}{2} & 0
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\end{pmatrix} =
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(\mathbf{a}_\text{s}, \mathbf{b}_\text{s}, \mathbf{c}_\text{s})
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\begin{pmatrix}
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0 & \frac{{1}}{4} & \frac{{1}}{4} \\
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\frac{{1}}{4} & 0 & \frac{{1}}{4} \\
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\frac{{1}}{4} & \frac{{1}}{4} & 0
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\end{pmatrix}.
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$$
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So what you have to set is `--pa="0 1/4 1/4 1/4 0 1/4 1/4 1/4 0"`.
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(fc2_hdf5_file)=
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### `fc2.hdf5`
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Second order force constants are stored in
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$\mathrm{eV}/\text{Angstrom}^2$.
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In phono3py, this is stored in the numpy array `dtype='double'` and
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`order='C'` in the shape of:
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```
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(num_atom, num_atom, 3, 3)
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```
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against $\Phi_{\alpha\beta}(l\kappa, l'\kappa')$. More detail is
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similar to the case for {ref}`fc3_hdf5_file`.
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### `gamma-*.hdf5`
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Imaginary parts of self energies at harmonic phonon frequencies
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($\Gamma_\lambda(\omega_\lambda)$ = half linewidths) are stored in
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THz. See {ref}`write_gamma_option`.
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### `gamma_detail-*.hdf5`
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Q-point triplet contributions to imaginary parts of self energies at
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phonon frequencies (half linewidths) are stored in THz. See
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{ref}`write_detailed_gamma_option`.
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## Simple text file
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### `gammas-*.dat`
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Imaginary parts of self energies with respect to frequency
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$\Gamma_\lambda(\omega)$ are stored in THz. See {ref}`ise_option`.
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### `jdos-*.dat`
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Joint densities of states are stored in Thz. See {ref}`jdos_option`.
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### `linewidth-*.dat`
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@ -135,7 +135,7 @@ class Phono3py:
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def __init__(
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self,
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unitcell: PhonopyAtoms,
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supercell_matrix,
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supercell_matrix=None,
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primitive_matrix=None,
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phonon_supercell_matrix=None,
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masses=None,
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@ -162,10 +162,12 @@ class Phono3py:
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----------
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unitcell : PhonopyAtoms, optional
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Input unit cell.
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supercell_matrix : array_like
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supercell_matrix : array_like, optional
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Supercell matrix multiplied to input cell basis vectors.
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shape=(3, ) or (3, 3), where the former is considered a diagonal
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matrix. The elements have to be given by integers.
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Although the default is None, which results in identity
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matrix, it is recommended to give `supercell_matrix` explicitly.
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primitive_matrix : array_like or str, optional
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Primitive matrix multiplied to input cell basis vectors. Default is
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the identity matrix.
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@ -242,13 +244,15 @@ class Phono3py:
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# Create supercell and primitive cell
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self._unitcell = unitcell
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self._supercell_matrix = shape_supercell_matrix(supercell_matrix)
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self._supercell_matrix = np.array(
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shape_supercell_matrix(supercell_matrix), dtype="int_", order="C"
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)
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pmat = self._determine_primitive_matrix(primitive_matrix)
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self._primitive_matrix = pmat
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self._nac_params = None
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if phonon_supercell_matrix is not None:
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self._phonon_supercell_matrix = shape_supercell_matrix(
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phonon_supercell_matrix
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self._phonon_supercell_matrix = np.array(
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shape_supercell_matrix(phonon_supercell_matrix), dtype="int_", order="C"
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)
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else:
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self._phonon_supercell_matrix = None
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@ -721,7 +725,7 @@ class Phono3py:
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ndarray
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Supercell matrix with respect to unit cell.
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shape=(3, 3), dtype='intc', order='C'
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shape=(3, 3), dtype='int_', order='C'
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"""
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return self._supercell_matrix
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@ -741,7 +745,7 @@ class Phono3py:
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ndarray
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Supercell matrix with respect to unit cell.
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shape=(3, 3), dtype='intc', order='C'
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shape=(3, 3), dtype='int_', order='C'
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"""
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return self._phonon_supercell_matrix
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@ -1426,7 +1430,7 @@ class Phono3py:
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prod(mesh) because it includes Brillouin zone boundary. The detail
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is found in the docstring of
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phono3py.phonon3.triplets.get_triplets_at_q.
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shape=(num_grid_points, 3), dtype='intc', order='C'
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shape=(num_grid_points, 3), dtype=int
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"""
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if self._interaction is not None:
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