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Documentation for random displacement
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atztogo committed Aug 4, 2024
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59 changes: 49 additions & 10 deletions doc/command-options.md
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Expand Up @@ -27,13 +27,13 @@ CELL_FILENAME = POSCAR-unitcell
where the setting tag names are case insensitive. This is run by

```bash
% phono3py setting.conf [comannd options]
% phono3py setting.conf [command options]
```

or

```bash
% phono3py [comannd options] -- setting.conf
% phono3py [command options] -- setting.conf
```

```{contents}
Expand All @@ -48,7 +48,7 @@ or
This specifies input unit cell filename.

```bash
% phono3py -c POSCAR-unitcell ... (many options)
% phono3py -c POSCAR-unitcell ... (options)
```

## Calculator interface
Expand Down Expand Up @@ -250,7 +250,6 @@ web page](https://phonopy.github.io/phonopy/setting-tags.html#magmom).
## Displacement creation

(create_displacements_option)=

### `-d` (`CREATE_DISPLACEMENTS = .TRUE.`)

Supercell with displacements are created. Using with `--amplitude` option,
Expand All @@ -259,15 +258,16 @@ supercells with displacements and `phono3py_disp.yaml` file are created. `--pa`
should be specified if the input unit cell structure is not a primitive cell,
e.g., `--pa="F"` if the input unit cell has F-centring.

(amplitude_option)=

(random_displacements_option)=
### `--rd` (`RANDOM_DISPLACEMENTS`), `--rd-fc2` (`RANDOM_DISPLACEMENTS_FC2`) and `--random-seed` (`RANDOM_SEED`)

Random directional displacements are generated for fc3 and fc2 supercells by
`--rd` and `--rd-fc2`, respectively. `--amplitude` and `--random-seed` options
may be used together. These are used in the equivalent way to [`--rd` of
phonopy](https://phonopy.github.io/phonopy/setting-tags.html#random-displacements).

(amplitude_option)=
### `--amplitude` (`DISPLACEMENT_DISTANCE`)

Atomic displacement distance is specified. This value may be increased for the
Expand All @@ -277,6 +277,43 @@ very accurate.
The default value depends on calculator. See
{ref}`default_displacement_distance_for_calculator`.

(fc_calculator_options_option)=
### `--fc-calc`, `--fc-calculator` (`FC_CALCULATOR`)

Choice of force constants calculator.

```
% phono3py --fc-calc symfc ...
```

To use different force constants calculators for fc2 and fc3
```
% phono3py --fc-calc "symfc|" ...
```
Those for fc2 and fc3 are seprated by `|` such as `symfc|` . Blank means to
employ the finite difference method for systematic displacements generated by
the option `-d`.

### `--fc-calc-opt`, `--fc-calculator-options` (`FC_CALCULATOR_OPTIONS`)

Special options for force constants calculators.

```
% phono3py --fc-calc-opt "cutoff=8" ...
```

Similarly to `--fc-calc`, `|` can be used to separated those for fc2 and fc3.

#### Options for symfc

* cutoff : cutoff pair distance beyond that third-order force constants are zero
(fc3 only).
* use_mkl : sparse_dot_mkl is employed when it is available.

### `--symfc` and `--alm`

These are shortcuts of `--fc-calc symfc` and `--fc-calc alm`, respectively.

## Force constants

(compact_fc_option)=
Expand Down Expand Up @@ -331,14 +368,16 @@ supercell size and the second choice is using `--cutoff-pair` option.

### `--cutoff-pair` or `--cutoff-pair-distance` (`CUTOFF_PAIR_DISTANCE`)

This option is only used together with `-d` option.
This option works differently for the `-d` and `--rd` options.

A cutoff pair-distance in a supercell is used to reduce the number of necessary
supercells with displacements to obtain third order force constants. As the
drawback, a certain number of third-order-force-constants elements are abandoned
or computed with less numerical accuracy. More details are found at
For `-d`, A cutoff pair-distance in a supercell is used to reduce the number of
necessary supercells with displacements to obtain third order force constants.
As the 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`.

For `--rd`, `--cutoff-pair VAL` is equivalent to `--fc-calc-opt "cutoff=VAL"`.

### `--alm`

This invokes ALM as the force constants calculator for fc2 and fc3. See the
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1 change: 1 addition & 0 deletions doc/index.md
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Expand Up @@ -58,6 +58,7 @@ auxiliary-tools
direct-solution
wigner-solution
workload-distribution
random-displacements
cutoff-pair
external-tools
phono3py-api
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27 changes: 27 additions & 0 deletions doc/random-displacements.md
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(random-displacements)=
# Randan displacements

Random displacements and corresponding forces in supercells can be employed as a
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

- {ref}`random_displacements_option` (`--rd`, `--random-seed`)
- {ref}`fc_calculator_option` (`--fc-calc`)
- {ref}`fc_calculator_options_option` (`--fc-calc-opt`)

## Generation of random directional displacements

The option `--rd NUM` is used instead of `-d` in generating displacements as follows:

```
% phono3py --rd 100 --dim 2 2 2 --pa auto -c POSCAR-unitcell
```

`NUM` means the number of supercells with random directional displacements. This
must be specified, and the initial guess may be from around the number of
supecells generated for the systematic displacements by `-d`. In the case of the
`NaCl-rd` example, 146 supercells are generated with `-d`, so similar
number `--rd 100` was chosen here.
66 changes: 66 additions & 0 deletions example/NaCl-rd/README.md
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# Example of using random directional displacements

## How to use symfc

This example utilizes an NaCl calculation result from A. Togo and A. Seko, J.
Chem. Phys. 160, 211001 (2024). Supercells of 2x2x2 and 4x4x4 conventional unit
cells are chosen for the third-order force constants (fc3) and second-order
force constants (fc2), respectively. Displacement-force datasets consisting of
100 supercells for fc3 and 4 supercells for fc2 are extracted and stored in
`phono3py_params_NaCl.yaml.xz`. Random directional displacements of a constant
0.03 Angstrom are used.

To calculate force constants, an external force constants calculator is
necessary. Here, the symfc tool (available at https://github.com/symfc/symfc) is
used, which can be easily installed via pip or conda.

The `fc3.hdf5` and `fc2.hdf5` are computed using the command:

```
% phono3py-load phono3py_params_NaCl.yaml.xz --symfc -v
```

Lattice thermal conductivity (LTC) is calculated with the following command:

```
% phono3py-load phono3py_params_NaCl.yaml.xz --br --ts 300 --mesh 50
```

By this, LTC is obtained around 7.8 W/m-k.


## How to use pypolymlp

The polynomial machine learning potential (poly-MLP) by pypolymlp can be used to
calculate fc3 by the following command:

```
% phono3py-load phono3py_params_NaCl.yaml.xz --pypolymlp --symfc --rd 400 -v
```

the procedure below is performed:

1. Poly-MLPs are computed from the displacement-force dataset for fc3. This is
activated by the `--pypolymlp` option.
2. 800=400+400 supercells for random directional displacements are generated,
where 400+400 means 400 supercells with random displacements (u) and 400
supercells with opposite displacement vectors (-u). This is activated by the
`--rd 400` option. The default displacement distance is 0.001 Angstrom in the
`--pypolymlp` mode. Since random displacements are generated `--symfc` has to
be specified for fc3. In this example, random displacements are used for fc2,
too, `--symfc` is applied to both of fc3 and fc2. Without the `--rd` option,
systematic displacements are generated, for which the option `--fc-calc "symfc|"`
has to be specified instead of `--symfc` (equivalent to `--fc-calc "symfc|symfc")`).
3. Forces on atoms in these 800 supercells are calculated using poly-MLP.
4. Force constants are calculated.


The `fc3.hdf5` and `fc2.hdf5` are obtained. Using these force constants, LTC is
calculated by

```
% phono3py-load phono3py_params_NaCl.yaml.xz --br --ts 300 --mesh 50
```

and the LTC value of around 7.8 W/m-k is obtained. This LTC value is equivalent
to above, but of course, it can be different.
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