Update documentation

This commit is contained in:
Atsushi Togo 2022-03-21 11:55:36 +09:00
parent ea9c11ed4a
commit 85d455214f
3 changed files with 30 additions and 12 deletions

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@ -322,6 +322,18 @@ drawback, a certain number of third-order-force-constants elements are abandoned
or computed with less numerical accuracy. More details are found at
{ref}`command_cutoff_pair`.
### `--alm`
This invokes ALM as the force constants calculator for fc2 and fc3. See the
detail at
[phonopy documentaton](https://phonopy.github.io/phonopy/setting-tags.html#alm).
This option is useful for fitting random displacement dataset or MD data to
force constants. Phono3py doesn't provide command-line interface to generate
random displacements. Instead simply
[phonopy can be used for this purpose](https://phonopy.github.io/phonopy/setting-tags.html#random-displacements),
because `FORCE_SETS` in the type-II format obtained using phonopy can be used as
`FORCES_FC3` and `FORCES_FC2` just renaming the file name.
## Reciprocal space sampling mesh and grid points, and band indices
### `--mesh` (`MESH` or `MESH_NUMBERS`)
@ -329,8 +341,8 @@ or computed with less numerical accuracy. More details are found at
Mesh sampling grids in reciprocal space are generated with the specified
numbers. This mesh is made along reciprocal axes and is always Gamma-centered.
Except for that this mesh is always Gamma-centered, this works in the same way
as written here,
https://phonopy.github.io/phonopy/setting-tags.html#mesh-mp-or-mesh-numbers.
as written
[here](https://phonopy.github.io/phonopy/setting-tags.html#mesh-mp-or-mesh-numbers).
(gp_option)=

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@ -28,7 +28,8 @@ This file contains displacement dataset and crystal structure information.
This is created with `--cf3` option. See {ref}`cf3_option`.
This file has a simple format like
There are two formats of `FORCES_FC3`. The type-I format is like that shown
below
```
# File: 1
@ -74,12 +75,16 @@ numpy as follows:
np.savetxt("FORCES_FC3", forces.reshape(-1, 3))
```
The type-II format is the same as
[phonopy's type-II format](https://phonopy.github.io/phonopy/input-files.html#type-2)
of `FORCE_SETS`.
### `FORCES_FC2`
This is created with `--cf2` option. See {ref}`cf2_option` and
{ref}`dim_fc2_option`.
The file format of this file is similar to that of `FORCES_FC3`.
The file formats (type-I and type-II) are same as those of `FORCES_FC3`.
## HDF5 files

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@ -142,13 +142,14 @@ In [8]: ph3.save("phono3py_disp.yaml")
Forces of the generated supercells with displacements are calculated by some
external force calculator such as first-principles calculation code.
Calculated supercell forces will be stored in `Phono3py` class instance through
`Phono3py.forces` attribute by setting an array_like variable with the shape of
`(num_supercells, num_atoms_in_supercell, 3)`. In the above example, the array
shape is `(1254, 72, 3)`.
Calculated supercell forces will be stored in a `Phono3py` class instance
through `Phono3py.forces` attribute by setting an array_like variable with the
shape of `(num_supercells, num_atoms_in_supercell, 3)`. In the above example,
the array shape is `(1254, 72, 3)`.
If calculated force sets are stored in the {ref}`input-output_files_FORCES_FC3`
format, the numpy array of `forces` is obtained by
If the calculated force sets are stored in the
{ref}`input-output_files_FORCES_FC3` file, the numpy array of `forces` is
obtained by
```python
forces = np.loadtxt("FORCES_FC3").reshape(-1, num_atoms_in_supercell, 3)
@ -200,8 +201,6 @@ Now it is ready to compute force constants.
In [12]: ph3.produce_fc3()
```
(api-phono3py-load)=
## Non-analytical term correction parameters
Users collects Born effective charges and dielectric constant tensor from
@ -424,6 +423,8 @@ Phono3py.phonon_supercells_with_displacements
The meanings of them are found in their docstrings though they may be guessed
easily.
(api-phono3py-load)=
## `phono3py.load`
The purpose of `phono3py.load` is to create a `Phono3py` class instance with