vibration plot mode in vesta-2

vibration-plot-mode-in-vesta-2

Abstract

This is an updated version of vibration-plot-mode-in-vesta code. The main function is the same as older version, which is to automatically convert the vibration modes at Γ point calculated by other software to Vesta format file to visualize it. The improvements include:

• Simplify operating procedures and make it more automated: No more manual generation of initial Vesta files.
• More complete information: Beside the vibration modes in vesta file, other information such as vibration frequency, atoms cartesian coordinate etc is also exported to a csv file.
• Supports converting results from more calculation software: Not only the results of vasp calculation, the calculation results of phonopy are also supported.

Usage

1. Generate VESTA mode files from VASP calculation

a. Perform phonons calculation in vasp

There are two methods to calculate phonons at Γ point in vasp. The first is finite differences.For finite differences calculation, IBRION should be set 5 or 6, NSW=1, and ISIF, POTIM, NFREE should be set carefully.

The second method is density-functional-perturbation theory, For density-functional-perturbation theory calculation, IBRION should be set 7 or 8, NSW=1.

After this step, you can get the OUTCAR from the calculation. Also, the input file POSCAR is needed for next step.

b. Run python script

With POSCAR file and OUTCAR file from previous step, now run command

python vasp_modes_to_vesta.py

and you can get the result.

The dependent libraries for running the python script are:

• numpy
• pandas
• pymatgen
• sys, os, re

The parameters that need to be set in the python script are:

dir_out_file = 'out'                                        # The directory for saving result file   
scaling_factor = 3                                          # The scale factor of the length of vector in VESTA file     
poscar_filename = './POSCAR'                                # The full path of POSCAR for VASP frequency calculation
outcar_filename = './OUTCAR'                                # The full path of OUTCAR generated in VASP frequency calculation
cmd_vesta_path = 'D:\VESTA-win64\VESTA-win64\VESTA.exe'     # The full path of VESTA command

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2. Generate VESTA mode files from Phonopy calculation

a. Perform force sets calculation in phonopy

Since phonopy itself cannot perform DFT calculation, this step requires the use of DFT software. vasp, quantum-espresso, abinit, etc. are all ok. Here is the referencce:

• vasp: https://phonopy.github.io/phonopy/vasp.html#vasp-interface
• qe: https://phonopy.github.io/phonopy/qe.html
• cp2k: https://phonopy.github.io/phonopy/cp2k.html
• …

Before calculating force sets, the input parameters of supercell_matrix and initial unitcell are also needed for next step, together with the force sets file generated in this step.

b. Run python script

With unitcell file , force sets file and supercell_matrix from previous step, now run command

python phonopy_modes_to_vesta.py

and you can get the result.

The dependent libraries for running the python script are:

• numpy
• pandas
• pymatgen
• phonopy
• sys, os

The parameters that need to be set in the python script are:

dir_out_file = 'out'                                        # The directory for saving result file  
scaling_factor = 3                                          # The scale factor of the length of vector in VESTA file             
supercell_matrix = [4, 4, 1]                                # The supercell matrix used for force sets calculation
unitcell_filename = './CONTCAR'                             # The unit cell used for force sets calculation
force_sets_filename = './FORCE_SETS'                        # The force sets file path calculated by Phonopy
cmd_vesta_path = 'D:\VESTA-win64\VESTA-win64\VESTA.exe'     # The full path of VESTA command

Tips

1. How to read phonons calculation results from OUTCAR file

https://www.vasp.at/wiki/index.php/Phonons_from_finite_differences

2. How to read eigenvectors from phonopy calculation

General#

Key	Description
nqpoint	Number of q-points calculated.
natom	Number of atoms in the primitive cell.
phonon	Key name of list for q-points.
q-position	Position of q-vector in reduced coordinates.
band	Key name of list for bands.
frequency	Phonon frequency in a specified unit at each phonon mode
eigenvector	Eigenvector at each phonon mode. Each eigenvector :math:\mathbf{e} of dynamical matrix is shown as sets of three complex values of each atom along the Cartesian axes in the primitive cell. The real and imaginary values correspond to the left and right, respectively. A set of eigenvectors comprising all bands at a q-point forms a unitary matrix obtained as the result of numpy.linalg.eigh, i.e., LAPACK of routine _heevd. Therefore eigenvectors correspond to the column vectors of the unitary matrix.
group_velocity	Group velocity at each phonon mode in the Cartesian coordinates defined in the unit cell.

https://phonopy.github.io/phonopy/output-files.html#general

The form of eigenvector output by phonopy

	Band #1	Band #2	…	Band #3N
Atom #1	Eig_X	Eig_X	…	Eig_X
Atom #1	Eig_Y	Eig_Y	…	Eig_Y
Atom #1	Eig_Z	Eig_Z	…	Eig_Z
…	…	…	…	…
Atom #N	Eig_X	Eig_X	…	Eig_X
Atom #N	Eig_Y	Eig_Y	…	Eig_Y
Atom #N	Eig_Z	Eig_Z	…	Eig_Z

References

Refers to the examples of Si for more details.

Some related repositories in Github:

• vibration-plot-mode-in-vesta
• Phonopy_VESTA
• VASP-plot-modes