1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
|
# Si example using LAMMPS interface
The `pair_style` of
`polymlp` is a LAMMPS module of the polynomial machine learning potentials
provided at https://sekocha.github.io/lammps/index-e.html. For the silicon
calculation found in the [example
directory](https://github.com/phonopy/phonopy/tree/develop/example), `mlp.lammp`
of gtinv-289 was obtained from [Polynomial Machine Learning Potential Repository
at Kyoto
University](http://cms.mtl.kyoto-u.ac.jp/seko/mlp-repository/index.html).
This example shows how to generate supercells from non-LAMMPS structure but the
structure defined in yaml style format. This is not supported by usual phonopy
command line interface. So a python script that runs this task using phonopy-API
is provided in this example directory. See also the documentation of the phonopy
LAMMPS interface.
1. Generate supercells using a python script
```
% python generate_displacements.py
```
The `supercell-001` LAMMPS structure file follows the LAMMPS structure input
format. The basis vectors are rotated from that defined in
`phonopy_disp.yaml`. Therefore forces as obtained LAMMPS calculation have to
be rotated back to the original coordinate system, which is performed
automatically in the step 3.
2. Run LAMMPS
```bash
% lmp_serial -in in.polymlp
```
Suppose that the LAMMPS output file name is removed to `lammps_forces_Si.0`
after the LAMMPS calculation.
3. Make `FORCE_SETS`
```
% phonopy -f lammps_forces_Si.0
_
_ __ | |__ ___ _ __ ___ _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
| |_) | | | | (_) | | | | (_) || |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
|_| |_| |___/
2.18.0
Compiled with OpenMP support (max 10 threads).
Python version 3.11.0
Spglib version 2.0.2
Calculator interface: lammps
Displacements were read from "phonopy_disp.yaml".
1. Drift force of "lammps_forces_Si.0" to be subtracted
-0.00000000 -0.00000000 -0.00000000
Forces parsed from LAMMPS output were rotated by F=R.F(lammps) with R:
0.00000 0.57735 0.57735
0.70711 0.57735 0.57735
0.70711 -0.57735 -0.57735
"FORCE_SETS" has been created.
_
___ _ __ __| |
/ _ \ '_ \ / _` |
| __/ | | | (_| |
\___|_| |_|\__,_|
```
The rotation of forces is performed and the rotation matrix is found in last
lines of the output.
|
