mirror of https://github.com/phonopy/phono3py.git
Update doc
This commit is contained in:
Atsushi Togo
parent
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648aceac10
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@ -39,7 +39,7 @@ Let's compute lattice thermal conductivity of Si using the `Si-PBEsol` example
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found in the example directory.
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```bash
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% phono3py --mesh="11 11 11" --sym-fc --br
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% phono3py --mesh="11 11 11" --fc-symmetry --br
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```
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Then using the output file, `kappa-m111111.hdf5`, run `phono3py-kaccum` as
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@ -2,6 +2,10 @@
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# Command options / Setting tags
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(use_config_with_option)=
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## Use of configuration file
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Phono3py is operated with command options or with a configuration file that
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contains setting tags. In this page, the command options are explained. Most of
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command options have their respective setting tags.
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@ -27,13 +31,19 @@ CELL_FILENAME = POSCAR-unitcell
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where the setting tag names are case insensitive. This is run by
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```bash
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% phono3py setting.conf [command options]
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% phono3py setting.conf [OPTIONS]
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```
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or
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```bash
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% phono3py [command options] -- setting.conf
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% phono3py [OPTIONS] -- setting.conf
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```
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When using `phono3py-load` (see also {ref}`phono3py_load_command`)
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```bash
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% phono3py-load --config setting.conf [OPTIONS]
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```
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```{contents}
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@ -201,15 +211,32 @@ When using with `--cf2`, `--cf3` has to be specified simultaneously as below,
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### `--dim` (`DIM`)
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**`phono3py-load` doesn't have this option.**
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Supercell dimension is specified. See the detail at
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<http://phonopy.github.io/phonopy/setting-tags.html#dim>. When a proper
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`phono3py_disp.yaml` exists in the current directory, this is unnecessary to be
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specified.
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<http://phonopy.github.io/phonopy/setting-tags.html#dim>. When
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`phono3py_disp.yaml` is found in the current directory, it is read
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automatically. Since supercell dimension is written in this file, `--dim` is
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unnecessary to specify. For example, just
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```bash
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% phono3py --fc-symmetry
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```
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or
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```bash
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% phono3py --symfc
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```
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can be used to calculate force constants.
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(dim_fc2_option)=
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### `--dim-fc2` (`DIM_FC2`)
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**`phono3py-load` doesn't have this option.**
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Supercell dimension for 2nd order force constants (for harmonic phonons) is
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specified. This is optional. When a proper `phono3py_disp.yaml` exists in the
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current directory, this is unnecessary to be specified.
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@ -228,7 +255,7 @@ supercell size and these force calculations have to be done in addition to the
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usual force calculations for 3rd order force constants.
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```bash
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% phono3py -d --dim="2 2 2" --dim-fc2="4 4 4" -c POSCAR-unitcell
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% phono3py -d --dim 2 2 2 --dim-fc2 4 4 4 --pa auto -c POSCAR-unitcell
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```
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After the force calculations, `--cf2` option is used to create `FORCES_FC2`.
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@ -253,10 +280,11 @@ that created in the usual phono3py run without `--dim-fc2` option.
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### `--pa`, `--primitive-axes` (`PRIMITIVE_AXES`)
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Transformation matrix from a non-primitive cell to the primitive cell. See
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phonopy `PRIMITIVE_AXES` tag (`--pa` option) at
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<http://phonopy.github.io/phonopy/setting-tags.html#primitive-axis>. When a proper
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`phono3py_disp.yaml` exists in the current directory, this is unnecessary to be
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specified.
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phonopy `PRIMITIVE_AXES` tag (`--pa` option) at [primitive-axis
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(phonopy)](https://phonopy.github.io/phonopy/setting-tags.html#primitive-axes-or-primitive-axis).
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When `phono3py_disp.yaml` contains this information and `phono3py_disp.yaml` is
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read when running `phono3py` or `phono3py-load` command, this is unnecessary to
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be specified.
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### `--mass` (`MASS`)
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@ -273,24 +301,45 @@ web page](https://phonopy.github.io/phonopy/setting-tags.html#magmom).
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(create_displacements_option)=
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### `-d` (`CREATE_DISPLACEMENTS = .TRUE.`)
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Supercell with displacements are created. Using with `--amplitude` option,
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atomic displacement distances are controlled. With this option, files for
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supercells with displacements and `phono3py_disp.yaml` file are created. `--pa`
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should be specified if the input unit cell structure is not a primitive cell,
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e.g., `--pa="F"` if the input unit cell has F-centring.
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**`phono3py-load` doesn't have this option.**
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Supercells with displacements and `phono3py_disp.yaml` are created. Using with
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`--amplitude` option, atomic displacement distances are controlled. With this
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option, files for supercells with displacements and `phono3py_disp.yaml` file
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are created.
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It is recommended to use this option with `--pa auto` option to store
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information about primitive cell (`primitive_matrix` key) in
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`phono3py_disp.yaml`, e.g.,
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```bash
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% phono3py -c POSCAR-unitcell -d --dim 2 2 2 --dim-fc2 4 4 4 --pa auto
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```
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(random_displacements_option)=
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### `--rd` (`RANDOM_DISPLACEMENTS`), `--rd-fc2` (`RANDOM_DISPLACEMENTS_FC2`) and `--random-seed` (`RANDOM_SEED`)
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**`phono3py-load` doesn't have this option.**
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See also {ref}`random-displacements`.
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Random directional displacements are generated for fc3 and fc2 supercells by
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`--rd` and `--rd-fc2`, respectively. `--amplitude` and `--random-seed` options
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may be used together. These are used in the equivalent way to [`--rd` of
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phonopy](https://phonopy.github.io/phonopy/setting-tags.html#random-displacements).
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Like `-d` option, it is recommended to specify `--pa auto` together with `--rd`
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and/or `--rd-fc2`,
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```bash
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% phono3py -c POSCAR-unitcell --dim 2 2 2 --dim-fc2 4 4 4 --rd 100 --rd-fc2 2 --pa auto
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```
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(amplitude_option)=
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### `--amplitude` (`DISPLACEMENT_DISTANCE`)
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**`phono3py-load` doesn't have this option.**
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Atomic displacement distance is specified. This value may be increased for the
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weak interaction systems and decreased when the force calculator is numerically
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very accurate.
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@ -303,13 +352,13 @@ The default value depends on calculator. See
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Choice of force constants calculator.
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```
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% phono3py --fc-calc symfc ...
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```bash
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% phono3py-load --fc-calc symfc ...
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```
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To use different force constants calculators for fc2 and fc3
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```
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% phono3py --fc-calc "symfc|" ...
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```bash
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% phono3py-load --fc-calc "symfc|" ...
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```
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Those for fc2 and fc3 are seprated by `|` such as `symfc|` . Blank means to
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employ the finite difference method for systematic displacements generated by
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@ -320,8 +369,8 @@ the option `-d`.
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Special options for force constants calculators.
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```
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% phono3py --fc-calc-opt "cutoff=8" ...
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```bash
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% phono3py-load --fc-calc-opt "cutoff=8" ...
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```
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Similarly to `--fc-calc`, `|` can be used to separated those for fc2 and fc3.
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@ -336,6 +385,9 @@ Similarly to `--fc-calc`, `|` can be used to separated those for fc2 and fc3.
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These are shortcuts of `--fc-calc symfc` and `--fc-calc alm`, respectively.
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Please be careful that `--symfc` and `--sym-fc` (deprecated) are similar, but
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different.
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## Force constants
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(compact_fc_option)=
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@ -352,16 +404,16 @@ data size becomes large. If the input crystal structure has centring
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{ref}`--pa <pa_option>` is necessary to have smallest data size. In this case,
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`--pa` option has to be specified on reading. Otherwise phono3py can recognize
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if `fc2.hdf5` and `fc3.hdf5` are compact or full automatically. When using with
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`--sym-fc`, the calculated results will become slightly different due to
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`--fc-symmetry`, the calculated results will become slightly different due to
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imperfect symmetrization scheme that phono3py employs.
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```bash
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% phono3py --dim="2 2 2" --cfc --pa="F" -c POSCAR-unitcell
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% phono3py-load --compact-fc
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```
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(symmetrization_option)=
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### `--sym-fc` (`FC_SYMMETRY = .TRUE.`)
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### `--fc-symmetry` (`FC_SYMMETRY = .TRUE.`)
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Second- and third-order force constants are symmetrized. The index exchange of
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real space force constants and translational invariance symmetry are applied in a
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@ -390,15 +442,16 @@ supercell size and the second choice is using `--cutoff-pair` option.
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### `--cutoff-pair` or `--cutoff-pair-distance` (`CUTOFF_PAIR_DISTANCE`)
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This option works differently for the `-d` and `--rd` options.
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This option works in two ways.
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For `-d`, A cutoff pair-distance in a supercell is used to reduce the number of
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necessary supercells with displacements to obtain third order force constants.
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As the drawback, a certain number of third-order-force-constants elements are
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abandoned or computed with less numerical accuracy. More details are found at
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{ref}`command_cutoff_pair`.
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When using with `-d` options, a cutoff pair-distance in a supercell is used to
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reduce the number of necessary supercells with displacements to obtain third
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order force constants. As the drawback, a certain number of
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third-order-force-constants elements are abandoned or computed with less
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numerical accuracy. More details are found at {ref}`command_cutoff_pair`.
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For `--rd`, `--cutoff-pair VAL` is equivalent to `--fc-calc-opt "cutoff=VAL"`.
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When using with an external force constants calculator, `--cutoff-pair VAL` works
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equivalent to `--fc-calc-opt "cutoff=VAL"`.
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### `--alm`
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@ -436,10 +489,10 @@ The mapping table between grid points to its indices is obtained by running with
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`--loglevel=2` option.
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```bash
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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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% phono3py-load --mesh 19 19 19 --br --write-gamma --gp 0 1 2 3 4 5
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```
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where `--gp="0 1 2 3 4 5"` can be also written `--gp="0,1,2,3,4,5"`. `--ga`
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where `--gp 0 1 2 3 4 5` can be also written `--gp="0,1,2,3,4,5"`. `--ga`
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option below can be used similarly for the same purpose.
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(ga_option)=
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@ -447,10 +500,10 @@ option below can be used similarly for the same purpose.
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### `--ga` (`GRID_ADDRESSES`)
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This is used to specify grid points like `--gp` option but in their addresses
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represented by integer numbers. For example with `--mesh="16 16 16"`, a q-point
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of (0.5, 0.5, 0.5) is given by `--ga="8 8 8"`. The values have to be integers.
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represented by integer numbers. For example with `--mesh 16 16 16`, a q-point
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of (0.5, 0.5, 0.5) is given by `--ga 8 8 8`. The values have to be integers.
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If you want to specify the point on a path,
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`--ga="0 0 0 1 1 1 2 2 2 3 3 3 ..."`, where each three values are recognized as
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`--ga 0 0 0 1 1 1 2 2 2 3 3 3 ...`, where each three values are recognized as
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a grid point. The grid points given by `--ga` option are translated to grid
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point indices as given by `--gp` option, and the values given by `--ga` option
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will not be shown in log files.
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@ -466,7 +519,7 @@ band indices where the values are calculated and summed and averaged over those
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bands.
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```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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% phono3py-load --mesh 16 16 16 --nac --gp 34 --bi "4 5, 6"
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```
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This option may be also useful to distribute the computational demand such like
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@ -489,7 +542,7 @@ calculated divided these integers by sampling mesh numbers for respective
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reciprocal axes.
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```bash
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% phono3py --dim="2 2 2" --pa="F" -c POSCAR-unitcell --mesh="19 19 19" --wgp
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% phono3py-load --mesh 19 19 19 --wgp
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```
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(stp_option)=
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@ -502,7 +555,7 @@ large a calculation is. Only those for specific grid points are shown by using
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with `--gp` or `--ga` option.
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```bash
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% phono3py --dim="2 2 2" --pa="F" -c POSCAR-unitcell --mesh="19 19 19" --stp --gp 20
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% phono3py-load --mesh 19 19 19 --stp --gp 20
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```
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## Brillouin zone integration
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@ -533,7 +586,7 @@ This is used when we want to test several $\sigma$ values simultaneously.
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The tails of the Gaussian functions that are used to replace delta functions in
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the equation shown at {ref}`--full-pp <full_pp_option>` are cut with this
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option. The value is specified in number of standard deviation.
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`--sigma-cutoff=5` gives the Gaussian functions to be cut at $5\sigma$. Using
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`--sigma-cutoff 5` gives the Gaussian functions to be cut at $5\sigma$. Using
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this option scarifies the numerical accuracy. So the number has to be carefully
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tested. But computation of phonon-phonon interaction strength becomes much
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faster in exchange for it.
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@ -614,27 +667,27 @@ database of the natural abundance data for elements, which refers Laeter _et
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al._, Pure Appl. Chem., **75**, 683 (2003).
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```bash
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% phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br --isotope
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% phono3py-load -v --mesh 32 32 20 --br --isotope
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```
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### `--mass-variances` or `--mv` (`MASS_VARIANCES`)
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Mass variance parameters are specified by this option to include phonon-isotope
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scattering effect in the same way as `--isotope` option. For example of GaN,
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this may be set like `--mv="1.97e-4 1.97e-4 0 0"`. The number of elements has to
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this may be set like `--mv 1.97e-4 1.97e-4 0 0`. The number of elements has to
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correspond to the number of atoms in the primitive cell.
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Isotope effect to thermal conductivity may be checked first running without
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isotope calculation:
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```bash
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% phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br
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% phono3py-load -v --mesh 32 32 20 --br
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```
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Then running with isotope calculation:
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```bash
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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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% phono3py -v --mesh 32 32 20 --br --read-gamma --mv 1.97e-4 1.97e-4 0 0
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```
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In the result hdf5 file, currently isotope scattering strength is not written
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@ -648,7 +701,7 @@ A most simple phonon boundary scattering treatment is included. $v_g/L$ is just
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used as the scattering rate, where $v_g$ is the group velocity and $L$ is the
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boundary mean free path. The value is given in micrometre. The default value, 1
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metre, is just used to avoid divergence of phonon lifetime and the contribution
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to the thermal conducitivity is considered negligible.
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to the thermal conductivity is considered negligible.
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(ave_pp_option)=
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@ -691,13 +744,13 @@ option is strongly recommended.
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First, run full conductivity calculation,
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```bash
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% phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br
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% phono3py-load -v --mesh 32 32 20 --br
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```
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Then
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```bash
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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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% phono3py-load -v --mesh 32 32 20 --br --read-gamma --ave-pp -o ave_pp
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```
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### `--const-ave-pp` (`CONST_AVE_PP = .TRUE.`)
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@ -715,7 +768,7 @@ $\text{eV}^2$.
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See also {ref}`reference papers <ave_pp_reference>`.
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```bash
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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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% phono3py-load -v --mesh 32 32 20 --br --const-ave-pp 1e-10
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```
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(normal_umklapp_option)=
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@ -739,7 +792,7 @@ The data are stored in `kappa-mxxx(-gx-sx-sdx).hdf5` file and accessed by
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below:
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```bash
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% phono3py --dim="2 2 2" --pa="F" -c POSCAR-unitcell --mesh="11 11 11" --fc3 --fc2 --br --nu
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% phono3py-load --mesh 11 11 11 --fc3 --fc2 --br --nu
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...
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% ipython
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@ -820,7 +873,7 @@ $$
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Specific temperatures are specified by `--ts`.
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```bash
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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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% phono3py-load -v --mesh 11 11 11 -c POSCAR-unitcell --br --ts 200 300 400
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```
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### `--tmax`, `--tmin`, `--tstep` (`TMAX`, `TMIN`, `TSTEP`)
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|
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@ -830,7 +883,7 @@ See phonopy's document for the same tags at
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<http://phonopy.github.io/phonopy/setting-tags.html#tprop-tmin-tmax-tstep>.
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```bash
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% phono3py --fc3 --fc2 --dim="2 2 2" -v --mesh="11 11 11" -c POSCAR-unitcell --br --tmin=100 --tmax=1000 --tstep=50
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% phono3py-load -v --mesh 11 11 11 --br --tmin 100 --tmax 1000 --tstep 50
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```
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## Non-analytical term correction
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|
|
@ -918,7 +971,7 @@ to `gammas-mxxx-gx(-sx)-tx-bx.dat` in THz (without $2\pi$) with respect to
|
|||
samplied frequency points of $\omega$ in THz (without $2\pi$).
|
||||
|
||||
```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"
|
||||
% phono3py-load --mesh 16 16 16 --nac --q-direction 1 0 0 --gp 0 --ise --bi "4 5, 6"
|
||||
```
|
||||
|
||||
(rse_option)=
|
||||
|
|
@ -945,7 +998,7 @@ $\Delta_\lambda(\omega)$ is written to `deltas-mxxx-gx-sx-tx-bx.dat` in THz
|
|||
(without $2\pi$).
|
||||
|
||||
```bash
|
||||
% phono3py --fc3 --fc2 --dim="2 2 2" --mesh="16 16 16" -c POSCAR-unitcell --nac --q-direction="1 0 0" --gp=0 --rse --sigma="0.1" --bi="4 5, 6"
|
||||
% phono3py-load --mesh 16 16 16 --nac --q-direction 1 0 0 --gp 0 --rse --sigma 0.1 --bi "4 5, 6"
|
||||
```
|
||||
|
||||
(spectral_function_option)=
|
||||
|
|
@ -982,7 +1035,7 @@ THz (without $2\pi$) with respect to samplied frequency points of $\omega$ in
|
|||
THz (without $2\pi$), and `spectral-mxxx-gx.hdf5`.
|
||||
|
||||
```bash
|
||||
% phono3py --fc3 --fc2 --dim="2 2 2" --mesh="16 16 16" -c POSCAR-unitcell --nac --q-direction="1 0 0" --gp=0 --spf
|
||||
% phono3py-load --mesh 16 16 16 --nac --q-direction 1 0 0 --gp 0 --spf
|
||||
```
|
||||
|
||||
```{note}
|
||||
|
|
@ -1026,7 +1079,7 @@ $$
|
|||
See also {ref}`reference papers <spectral_function_reference>`.
|
||||
|
||||
```bash
|
||||
% phono3py --fc2 --dim="2 2 2" --pa="F" -c POSCAR-unitcell --mesh="16 16 16" --jdos --ga="0 0 0 8 8 8"
|
||||
% phono3py-load --mesh 16 16 16 --jdos --ga 0 0 0 8 8 8
|
||||
```
|
||||
|
||||
When temperatures are specified, two classes of weighted JDOS are calculated.
|
||||
|
|
@ -1052,7 +1105,7 @@ $$
|
|||
See also {ref}`reference papers <spectral_function_reference>`.
|
||||
|
||||
```bash
|
||||
% 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
|
||||
% phono3py-load --mesh 16 16 16 --jdos --ga 0 0 0 8 8 8 --ts 300
|
||||
```
|
||||
|
||||
This is an example of `Si-PBEsol`.
|
||||
|
|
@ -1081,13 +1134,13 @@ Mode-Gruneisen-parameters are calculated from fc3.
|
|||
Mesh sampling mode:
|
||||
|
||||
```bash
|
||||
% phono3py --fc3 --fc2 --dim="2 2 2" -v --mesh="16 16 16" -c POSCAR-unitcell --nac --gruneisen
|
||||
% phono3py-load -v --mesh 16 16 16 --nac --gruneisen
|
||||
```
|
||||
|
||||
Band path mode:
|
||||
|
||||
```bash
|
||||
% phono3py --fc3 --fc2 --dim="2 2 2" -v -c POSCAR-unitcell --nac --gruneisen --band="0 0 0 0 0 1/2"
|
||||
% phono3py-load -v --nac --gruneisen --band "0 0 0 0 0 1/2"
|
||||
```
|
||||
|
||||
## File I/O
|
||||
|
|
@ -1199,7 +1252,7 @@ Phonon frequencies, eigenvectors, and grid point addresses are stored in
|
|||
may be required depending on calculation setting.
|
||||
|
||||
```bash
|
||||
% phono3py --fc2 --dim="2 2 2" --pa="F" --mesh="11 11 11" -c POSCAR-unitcell --nac --write-phoonon
|
||||
% phono3py-load --mesh 11 11 11 --nac --write-phoonon
|
||||
```
|
||||
|
||||
Contents of `phonon-mxxx.hdf5` are watched by:
|
||||
|
|
@ -1248,7 +1301,7 @@ different CPU architectures. {ref}`--pa <pa_option>` and
|
|||
{ref}`--nac <nac_option>` may be required depending on calculation setting.
|
||||
|
||||
```bash
|
||||
% phono3py --fc2 --fc3 --dim="2 2 2" --pa="F" --mesh="11 11 11" -c POSCAR-unitcell --nac --read-phoonon --br
|
||||
% phono3py-load --mesh 11 11 11 --nac --read-phoonon --br
|
||||
```
|
||||
|
||||
(write_read_pp_option)=
|
||||
|
|
@ -1266,11 +1319,11 @@ 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.
|
||||
|
||||
```bash
|
||||
% phono3py --fc2 --fc3 --dim="2 2 2" --pa="F" --mesh="11 11 11" -c POSCAR-unitcell --nac --write-pp --br --gp=1
|
||||
% phono3py-load --mesh 11 11 11 --nac --write-pp --br --gp 1
|
||||
```
|
||||
|
||||
```bash
|
||||
% phono3py --fc2 --dim="2 2 2" --pa="F" --mesh="11 11 11" -c POSCAR-unitcell --nac --read-pp --br --gp=1
|
||||
% phono3py-load --mesh 11 11 11 --nac --read-pp --br --gp 1
|
||||
```
|
||||
|
||||
(hdf5_compression_option)=
|
||||
|
|
|
|||
|
|
@ -78,10 +78,10 @@ so the -c crystal.o parameter is not needed.
|
|||
4) Calculate 3rd and 2nd order force constants in files `fc3.hdf5` and `fc2.hdf5`:
|
||||
|
||||
```bash
|
||||
% phono3py --crystal --dim="2 2 2" --dim-fc2="4 4 4" --sym-fc
|
||||
% phono3py --crystal --dim="2 2 2" --dim-fc2="4 4 4" --fc-symmetry
|
||||
```
|
||||
|
||||
`--sym-fc` is used to symmetrize second- and third-order force constants.
|
||||
`--fc-symmetry` is used to symmetrize second- and third-order force constants.
|
||||
|
||||
5) Thermal conductivity calculation:
|
||||
|
||||
|
|
|
|||
|
|
@ -1,17 +1,14 @@
|
|||
(command_cutoff_pair)=
|
||||
|
||||
# Force constants calculation with cutoff pair-distance
|
||||
|
||||
Since this calculation is a little bit tricky. It may be recommended to try
|
||||
```{note}
|
||||
Since usage of this calculation is complicated. It is recommended to try
|
||||
{ref}`random-displacements` with `--fc-calc-opt "cutoff = VAL"` before trying
|
||||
this option.
|
||||
```
|
||||
|
||||
Here the detail of the command option {ref}`--cutoff-pair <cutoff_pair_option>`
|
||||
is explained.
|
||||
|
||||
<!-- See also reference {cite}`Mizokami-PRB-2018`. -->
|
||||
|
||||
See also {ref}`a reference paper <cutoff_pair_reference>`.
|
||||
is explained. See also {ref}`a reference paper <cutoff_pair_reference>`.
|
||||
|
||||
```{contents}
|
||||
:depth: 2
|
||||
|
|
@ -329,7 +326,7 @@ number_of_pairs_in_cutoff: 110
|
|||
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 cp phono3py_disp.$i.yaml phono3py_disp.yaml; phono3py --fc-symmetry --mesh="11 11 11" --br|tee std.sym-$i.out;done
|
||||
% for i in {2..10};do egrep '^\s+300' std.sym-$i.out;done
|
||||
300.0 124.650 124.650 124.650 -0.000 -0.000 0.000
|
||||
300.0 119.765 119.765 119.765 -0.000 -0.000 0.000
|
||||
|
|
|
|||
22
doc/index.md
22
doc/index.md
|
|
@ -20,28 +20,16 @@ the Wigner transport equation <LTC_options>`
|
|||
Papers that may introduce phono3py:
|
||||
|
||||
- Theoretical background is summarized in this paper:
|
||||
<http://dx.doi.org/10.1103/PhysRevB.91.094306> (arxiv
|
||||
<http://arxiv.org/abs/1501.00691>).
|
||||
[PRB.91.094306](http://dx.doi.org/10.1103/PhysRevB.91.094306) (arxiv
|
||||
[1501.00691](http://arxiv.org/abs/1501.00691>)).
|
||||
- Introduction to phono3py application:
|
||||
<https://journals.jps.jp/doi/10.7566/JPSJ.92.012001> (open access),
|
||||
[JPSJ.92.012001](https://journals.jps.jp/doi/10.7566/JPSJ.92.012001) (open access),
|
||||
and phono3py inputs for 103 compounds found in Fig.17
|
||||
<https://github.com/atztogo/phonondb/blob/main/mdr/phono3py_103compounds_fd/README.md>
|
||||
- Implementation of phono3py:
|
||||
<https://iopscience.iop.org/article/10.1088/1361-648X/acd831> (open access)
|
||||
[JPCM.35.353001](https://iopscience.iop.org/article/10.1088/1361-648X/acd831)
|
||||
(open access)
|
||||
|
||||
A set of pre-calculated data for phono3py in
|
||||
|
||||
```{image} Si-kaccum.png
|
||||
:width: 20%
|
||||
```
|
||||
|
||||
```{image} Si-kaccum-MFP.png
|
||||
:width: 20%
|
||||
```
|
||||
|
||||
```{image} Si-kdeplot.png
|
||||
:width: 22%
|
||||
```
|
||||
|
||||
## Documentation
|
||||
|
||||
|
|
|
|||
|
|
@ -8,31 +8,42 @@ module. The main aim of introducing this command is to provide uniform usage
|
|||
over many different force calculators. Once `phono3py_disp.yaml` is created, the
|
||||
following operations will be the same using this command.
|
||||
|
||||
The following default behaviours are different from that of those of `phono3py`
|
||||
command:
|
||||
This is used almost in the same way as `phono3py` command, e.g., but there are
|
||||
some differences. The following default behaviours are different from that of
|
||||
those of `phono3py` command:
|
||||
|
||||
1. `phono3py_xxx.yaml` type file is always necessary in either of two ways:
|
||||
|
||||
- `phono3py_xxx.yaml` type file is given as the first argument of the
|
||||
command.
|
||||
- `phono3py_xxx.yaml` type file is put in the current directory with one of
|
||||
the default filenames of `phono3py_params.yaml`, `phono3py_disp.yaml`,
|
||||
`phono3py.yaml`. The searching preference order is `phono3py_params.yaml` >
|
||||
`phono3py_disp.yaml` > `phono3py.yaml`.
|
||||
command, e.g.,
|
||||
|
||||
```bash
|
||||
% phono3py-load phono3py_xxx.yaml --br --ts 300 --mesh 50
|
||||
```
|
||||
|
||||
- With first argument unspecified, `phono3py_disp.yaml` or `phono3py.yaml`
|
||||
file is read if it is found in the current directory. If both found,
|
||||
`phono3py_disp.yaml` is read. For example, having `phono3py_disp.yaml`
|
||||
under the current directory,
|
||||
|
||||
```bash
|
||||
% phono3py-load --br --ts 300 --mesh 50
|
||||
```
|
||||
|
||||
2. `-c` option (read crystal structure) does not exist.
|
||||
|
||||
3. `-d` option (create displacements) does not exist.
|
||||
3. `-d` option (create displacements) does not exist. Please use `phono3py`
|
||||
command.
|
||||
|
||||
4. Use of command options is recommended, but phono3py configuration file can be
|
||||
read through `--config` option.
|
||||
4. Phono3py configuration file can be read through `--config` option. See
|
||||
{ref}`use_config_with_option`.
|
||||
|
||||
5. If parameters for non-analytical term correction (NAC) are found, NAC is
|
||||
automatically enabled. This can be disabled by `--nonac` option.
|
||||
|
||||
6. When force constants are calculated from displacements and forces dataset,
|
||||
force constants are automatically symmetrized. To disable this, `--no-sym-fc`
|
||||
option is used.
|
||||
option can be used.
|
||||
|
||||
7. `-o` option works differently from `phono3py` command. This option requires
|
||||
one argument of string. The string is used as the output yaml filename that
|
||||
|
|
|
|||
|
|
@ -67,10 +67,10 @@ only limited number of keywords that are shown in the phonopy web site
|
|||
`fc3.hdf5` and `fc2.hdf5` files are created by:
|
||||
|
||||
```bash
|
||||
% phono3py --sym-fc
|
||||
% phono3py --fc-symmetry
|
||||
```
|
||||
|
||||
where `--sym-fc` symmetrizes fc3 and fc2.
|
||||
where `--fc-symmetry` symmetrizes fc3 and fc2.
|
||||
|
||||
5) Calculate lattice thermal conductivity, e.g., by:
|
||||
|
||||
|
|
|
|||
|
|
@ -6,7 +6,7 @@ displacement-force dataset for computing force constants. This requires an
|
|||
external force constants calculator, e.g., symfc or ALM. Here, examples are
|
||||
presented with using symfc that can be installed via pip or conda easily.
|
||||
|
||||
## Related setting tags
|
||||
## Related command options
|
||||
|
||||
- {ref}`random_displacements_option` (`--rd`, `--random-seed`)
|
||||
- {ref}`fc_calculator_option` (`--fc-calc`)
|
||||
|
|
@ -81,6 +81,18 @@ If `phono3py_disp.yaml` is located in current directory, force constants are
|
|||
calculated from `FORCES_FC3` (and optionally `FORCES_FC2`) and
|
||||
`phono3py_disp.yaml` by
|
||||
|
||||
```bash
|
||||
% phono3py-load --symfc -v
|
||||
```
|
||||
|
||||
or
|
||||
|
||||
```bash
|
||||
% phono3py-load phono3py_params.yaml --symfc -v
|
||||
```
|
||||
|
||||
Similarly, it is performed by also using `phono3py` command,
|
||||
|
||||
```bash
|
||||
% phono3py --symfc -v
|
||||
```
|
||||
|
|
@ -91,17 +103,6 @@ or with `phono3py_params.yaml`
|
|||
% phono3py -c phono3py_params.yaml --symfc -v
|
||||
```
|
||||
|
||||
Similarly, it is performed by also using `phono3py-load` command,
|
||||
|
||||
```bash
|
||||
% phono3py-load --symfc -v
|
||||
```
|
||||
|
||||
or
|
||||
|
||||
```bash
|
||||
% phono3py-load phono3py_params.yaml --symfc -v
|
||||
```
|
||||
|
||||
## Cutoff pair-distance for fc3 calculation
|
||||
|
||||
|
|
@ -113,7 +114,7 @@ introducing cutoff distance for pairs of atoms. It is performed by
|
|||
`--fc-calc-opt` option as
|
||||
|
||||
```bash
|
||||
% phono3py --symfc -v --fc-calc-opt "cutoff=8"
|
||||
% phono3py-load --symfc -v --fc-calc-opt "cutoff=8"
|
||||
```
|
||||
|
||||
The shortcut of `--fc-calc-opt "cutoff=8"` is `--cutoff-pair 8`.
|
||||
|
|
|
|||
|
|
@ -69,7 +69,7 @@ so the `-c control` parameter is not needed.
|
|||
4) Calculate 3rd and 2nd order force constants in files `fc3.hdf5` and `fc2.hdf5`:
|
||||
|
||||
```bash
|
||||
% phono3py --turbomole --dim="2 2 2" --dim-fc2="3 3 3" --sym-fc
|
||||
% phono3py --turbomole --dim="2 2 2" --dim-fc2="3 3 3" --fc-symmetry
|
||||
```
|
||||
|
||||
`--sym-fc` is used to symmetrize second- and third-order force constants.
|
||||
|
|
|
|||
|
|
@ -61,10 +61,10 @@
|
|||
4. Create `fc2.hdf` and `fc3.hdf`
|
||||
|
||||
```bash
|
||||
% phono3py --sym-fc
|
||||
% phono3py --fc-symmetry
|
||||
```
|
||||
|
||||
`--sym-fc` symmetrizes fc3 and fc2. `fc2.hdf5` and `fc3.hdf5`
|
||||
`--fc-symmetry` 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
|
||||
|
|
|
|||
|
|
@ -38,7 +38,7 @@ As discussed in the references above, the term $\kappa_{\rm P}^{\alpha \beta}$ c
|
|||
To compute the Wigner conductivity with scattering in the RTA approximation, specify `--br` and `--wigner`. For `example/Wigner_La2Zr2O7`, the command is:
|
||||
|
||||
```bash
|
||||
phono3py --nac --cell POSCAR --fc2 --dim="2 2 2" --dim-fc2="4 4 4" --mesh="19 19 19" --tmin=300 --tmax=1000 --tstep=700 --sym-fc --isotope --br --wigner --read-gamma > tc_La2Zr2O7.out
|
||||
phono3py --nac --cell POSCAR --fc2 --dim="2 2 2" --dim-fc2="4 4 4" --mesh="19 19 19" --tmin=300 --tmax=1000 --tstep=700 --fc-symmetry --isotope --br --wigner --read-gamma > tc_La2Zr2O7.out
|
||||
```
|
||||
The example above uses the `--read-gamma` option to read the phonon linewidths stored in the file `kappa-m191919.hdf5`. The calculation of these linewidths is computationally expensive, more details are reported in the {ref}`paper on the Wigner formulation <citation_wigner_formulation>`, and in this example the linewidths are provided.
|
||||
To learn how to compute the linewidths, the reader is referred to the documentation of the `--write-gamma` option.
|
||||
|
|
|
|||
|
|
@ -28,14 +28,14 @@ To avoid re-calculating fc3 and fc2, `fc3.hdf5` and `fc2.hdf5` are
|
|||
created on a single node:
|
||||
|
||||
```bash
|
||||
% phono3py --dim="2 2 2" --sym-fc -c POSCAR-unitcell
|
||||
% phono3py-load
|
||||
```
|
||||
|
||||
The indices of the irreducible grid-points neccesarry to specify
|
||||
`--ga` option are found by {ref}`--wgp option <wgp_option>`
|
||||
|
||||
```bash
|
||||
% phono3py --dim="2 2 2" --pa="F" -c POSCAR-unitcell --mesh="19 19 19" --fc3 --fc2 --br --wgp
|
||||
% phono3py-load --mesh 19 19 19 --br --wgp
|
||||
```
|
||||
|
||||
and they are stored in `ir_grid_points.yaml`.
|
||||
|
|
@ -51,7 +51,7 @@ computational demands into computer nodes, a set of the grid-point
|
|||
indices are chosen and executed as follows:
|
||||
|
||||
```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
|
||||
% phono3py-load --mesh 19 19 19 --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
|
||||
|
|
@ -63,7 +63,7 @@ indices, the RTA thermal conductivity is computed by another run in a
|
|||
short time from the stored data:
|
||||
|
||||
```bash
|
||||
% phono3py --dim="2 2 2" --pa="F" -c POSCAR-unitcell --mesh="19 19 19" --fc3 --fc2 --br --read-gamma
|
||||
% phono3py-load --mesh 19 19 19 --br --read-gamma
|
||||
```
|
||||
|
||||
## A convenient script
|
||||
|
|
@ -96,7 +96,7 @@ with open("ir_grid_points.yaml") as f:
|
|||
Supposed that this script is saved as `divide_gps.py`,
|
||||
|
||||
```bash
|
||||
% phono3py --dim="2 2 2" --pa="F" -c POSCAR-unitcell --mesh="19 19 19" --wgp
|
||||
% phono3py-load --mesh 19 19 19 --wgp
|
||||
...
|
||||
% python divide_gps.py 20
|
||||
0,30,52,82,120,402,434,468,524,844,1206
|
||||
|
|
@ -138,5 +138,5 @@ with `job.sh` (here for grid-engine):
|
|||
#$ -e err-phono3py-num.log
|
||||
#$ -o std-phono3py-num.log
|
||||
|
||||
phono3py --dim="2 2 2" --pa="F" -c POSCAR-unitcell --mesh="19 19 19" --fc3 --fc2 --br --gp="gps" --write-gamma
|
||||
phono3py-load --mesh 19 19 19 --br --gp "gps" --write-gamma
|
||||
```
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ for the CRYSTAL interface, so the -c crystal.o parameter is not needed
|
|||
|
||||
4) Create force constant files fc2.hdf5 and fc3.hdf5:
|
||||
|
||||
phono3py --crystal --dim="2 2 2" --dim-fc2="4 4 4" --sym-fc
|
||||
phono3py --crystal --dim="2 2 2" --dim-fc2="4 4 4" --fc-symmetry
|
||||
|
||||
5) Thermal conductivity calculation:
|
||||
|
||||
|
|
|
|||
|
|
@ -59,13 +59,14 @@ def get_parser(fc_symmetry=False, is_nac=False, load_phono3py_yaml=False):
|
|||
default=False,
|
||||
help=("Use ALM for generating 2nd and 3rd force constants " "in one fitting"),
|
||||
)
|
||||
parser.add_argument(
|
||||
"--amplitude",
|
||||
dest="displacement_distance",
|
||||
type=float,
|
||||
default=None,
|
||||
help="Distance of displacements",
|
||||
)
|
||||
if not load_phono3py_yaml:
|
||||
parser.add_argument(
|
||||
"--amplitude",
|
||||
dest="displacement_distance",
|
||||
type=float,
|
||||
default=None,
|
||||
help="Distance of displacements",
|
||||
)
|
||||
parser.add_argument(
|
||||
"--ave-pp",
|
||||
dest="use_ave_pp",
|
||||
|
|
|
|||
Loading…
Reference in New Issue