Random displacements#
Phonopy supports generating two types of random displacements.
Random directions with constant displacement distance
Random sampling of harmonic oscillator probability densities of phonon modes
In both cases, phonopy generates dataset of displacements of supercells in
phonopy_disp.yaml, supercells with displacements, and a perfect supercell. The
number of the supercells with displacements are specified by
RANDOM_DISPLACEMENTS tag (or --rd option) in either case.
Forces on atoms in supercells with displacements are calculated by a force calculator and force constants are computed by a force constants calculator. As the force constants calculators, currently SYMFC and ALM are supported.
Random directions with constant displacement distance#
See also RANDOM_DISPLACEMENTS.
Example#
An example to generate the random direction diplacements with distance of 0.03
Angstrom in example/NaCl-rd directory is as shown below,
% phonopy --rd 10 --dim 2 2 2 --pa auto --amplitude 0.03 -c POSCAR-unitcell
_
_ __ | |__ ___ _ __ ___ _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
| |_) | | | | (_) | | | | (_) || |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
|_| |_| |___/
2.20.0
Compiled with OpenMP support (max 10 threads).
Python version 3.11.4
Spglib version 2.1.0
Crystal structure was read from "POSCAR-unitcell".
Unit of length: angstrom
Displacements creation mode
Number of supercells with random displacements: 10
Displacement distance: 0.03
Settings:
Supercell: [2 2 2]
Spacegroup: Fm-3m (225)
Use -v option to watch primitive cell, unit cell, and supercell structures.
"phonopy_disp.yaml" and supercells have been created.
Summary of calculation was written in "phonopy_disp.yaml".
_
___ _ __ __| |
/ _ \ '_ \ / _` |
| __/ | | | (_| |
\___|_| |_|\__,_|
In the generated phonopy_disp.yaml, dataset of displacements is stored as follows:
% cat phonopy_disp.yaml
...
displacements:
- # 1
- displacement: # 1
[ -0.0201336051051884, 0.0137526506253330, 0.0174786311319239 ]
- displacement: # 2
[ -0.0176810186962932, 0.0037245664471804, -0.0239480517504424 ]
- displacement: # 3
[ -0.0028626950563326, -0.0032145292137935, 0.0296895904139501 ]
- displacement: # 4
[ 0.0251664434224757, 0.0149681266628547, 0.0065272742908559 ]
- displacement: # 5
[ -0.0136393731379345, -0.0226372187886819, -0.0141959087739228 ]
- displacement: # 6
[ 0.0299122348895043, -0.0003839832933863, -0.0022606991718315 ]
- displacement: # 7
[ -0.0265153637733336, -0.0030921513486749, -0.0136884653633881 ]
- displacement: # 8
[ 0.0284712562630672, -0.0049105574746481, -0.0080792321473599 ]
...
where the displacements are given in the Cartesian coordinates. The supercell with displacements in the VASP interface is found as
% cat POSCAR-001
generated by phonopy
1.0
11.3806029523513423 0.0000000000000000 0.0000000000000000
0.0000000000000000 11.3806029523513423 0.0000000000000000
0.0000000000000000 0.0000000000000000 11.3806029523513423
Na Cl
32 32
Direct
0.9982308841465181 0.0012084289982625 0.0015358264588532
0.4984463899873917 0.0003272732088778 0.9978957132718971
0.9997484584016929 0.4997175431541499 0.0026087888786082
0.5022113453503161 0.5013152314271505 0.0005735438023965
0.9988015245593718 0.9980108945999205 0.4987526224371979
0.5026283523829750 0.9999662598462494 0.4998013550616521
0.9976701266282333 0.4997282963511142 0.4987972108841070
0.5025017353107100 0.4995685151748806 0.4992900875128334
...
It is easy to verify consistency between them, e.g.,
np.dot(ph.displacements[0], np.linalg.inv(ph.supercell.cell)) + ph.supercell.scaled_positions
Once forces on atoms in these supercells with displacements, FORCE_SETS can be generated by the usual manner. For the NaCl-rd example,
% phonopy -f force-calcs/disp-{001..010}/vasprun.xml
where phonopy_disp.yaml has to be located in the current directory when the
above command is executed. The FORCE_SETS file is written in the
Type 2 format. To compute force constants for the type-2
displacements-forces dataset, an external force constants calculator is
necessary, e.g., symfc(symfc/symfc) or ALM
(ttadano/ALM) by
% phonopy-load --symfc [OPTIONS]
Random sampling of harmonic oscillator probability densities of phonon modes#
Random displacements corresponding to a specific temperature are generated with
the combination of the RANDOM_DISPLACEMENTS (--rd) and
RANDOM_DISPLACEMENT_TEMPERATURE tags. This is based on the harmonic
phonon approximation. Since each phonon follows the probability density function
of the harmonic oscillator, the random displacements are generated by randomly
sampling the probability density functions of phonons at the commensurate
points. More details are found in the paper “Implementation
strategies in phonopy and phono3py” (see Citation of phonopy).
Example#
To generate the random displacements in this approach, phonon information is
required. At the first step, phonons at the commensurate points are calculated.
Then, the random displacements are generated in the next step. Since
phonopy_disp.yaml is generated by the following command, it is necessary to
rename original phonopy_disp.yaml file (e.g., phonopy_disp_orig.yaml).
Assuming FORCE_SETS for phonopy_disp_orig.yaml exists in the current
directory:
% phonopy-load phonopy_disp_orig.yaml --rd 1000 --temperature 300
will generate 1000 supercells with displacements at 300K.
Visualization of displacement distance distribution#
Distribution of displacement distances may be visualized and checked by a python script shown below.
Note that if FORCE_SETS or FORCE_CONSTANTS file exists in
the current directory, those are automatically read by phonopy.load function
even if phonopy_disp.yaml file contains displacements. So the following script
is recommended to run in an isolated directory, e.g.,
% mkdir rd && cd rd
% cp ../phonopy_disp.yaml
Then opening ipython (or jupiter),
import matplotlib.pyplot as plt
import numpy as np
import phonopy
ph = phonopy.load("phonopy_disp.yaml")
plt.hist(np.linalg.norm(ph.displacements.reshape(-1, 3), axis=1), 100)
plt.show()
Another example#
In the below, a step-by-step example is presented.
Compute supercell force sets in the usual manner with small displacements. Generate
FORCE_SETSin the current directory.Create new directory and copy
FORCE_SETSand input crystal structure, orphonopy_disp.yamlto the new directory, then change to the new directory.Using
FORCE_SETS, generate supercells with random displacements at finite temperature using this tag.phonopy_disp.yamlis generated at this step. Therefore, ifphonopy_disp.yamlalready exists in this directory, it is overwritten. The required number of supercells depends on your system and also the purpose. It can be 10, or can be 1000.Using those supercells with random displacements, calculate supercell forces with some force calculator with VASP, QE, etc.
Generate
FORCE_SETSin this directory, which overwrites previousFORCE_SETS.Run the force constants calculation, e.g., with symfc. Symfc fits the displacement-force dataset stored in
FORCE_SETSto symmetry adapted force constants. Run also phonon calculation. This is done for example,phonopy-load -v --symfc --mesh 10 10 10 -p
or
phonopy-load -v --symfc --writefc phonopy-load --readfc --mesh 10 10 10 -p
Force constants calculated as above contain a part of temperature effect from atomic displacements. To even better include the temperature effect, this calculation has to be done self-consistently, i.e., it is required to repeat the loop over the steps 2-5 until the phonon structure is converged. The solution corresponds to a stochastic self-consistent harmonic approximation (SSCHA) approach.
It is also possible to perform the same calculation as above using the phonopy API.