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https://github.com/june976/vibration-plot-mode-in-vesta-2

Automatically generates visualizations of vibrational modes from vasp calcualtion results or Phonopy calculation results.
https://github.com/june976/vibration-plot-mode-in-vesta-2

Last synced: 9 months ago
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Automatically generates visualizations of vibrational modes from vasp calcualtion results or Phonopy calculation results.

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README 

          
# vibration-plot-mode-in-vesta-2



## Abstract



This is an updated version of [vibration-plot-mode-in-vesta](https://github.com/faradaymahe/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](https://www.vasp.at/wiki/index.php/Phonons_from_finite_differences).For [finite differences](https://www.vasp.at/wiki/index.php/Phonons_from_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](https://www.vasp.at/wiki/index.php/Phonons_from_density-functional-perturbation_theory), For [density-functional-perturbation theory](https://www.vasp.at/wiki/index.php/Phonons_from_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 

```bash

python vasp_modes_to_vesta.py

```

and you can get the result.



The dependent libraries for running the python script are:

- [numpy](https://numpy.org/)

- [pandas](https://pandas.pydata.org/)

- [pymatgen](https://pymatgen.org/)

- sys, os, re



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

```python

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

```



---



### **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](https://phonopy.github.io/phonopy/vasp.html#vasp-interface)

- qe: [https://phonopy.github.io/phonopy/qe.html](https://phonopy.github.io/phonopy/qe.html)

- cp2k: [https://phonopy.github.io/phonopy/cp2k.html](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 

```bash

python phonopy_modes_to_vesta.py

```

and you can get the result.



The dependent libraries for running the python script are:

- [numpy](https://numpy.org/)

- [pandas](https://pandas.pydata.org/)

- [pymatgen](https://pymatgen.org/)

- [phonopy](https://phonopy.github.io/phonopy/#)

- sys, os



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

```python

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



![outcar](./figs/outcar.png)



> [https://www.vasp.at/wiki/index.php/Phonons_from_finite_differences](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](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](https://github.com/June976/vibration-plot-mode-in-vesta-2/tree/main/Si) for more details.



Some related repositories in Github:

- [vibration-plot-mode-in-vesta](https://github.com/faradaymahe/vibration-plot-mode-in-vesta)

- [Phonopy_VESTA](https://github.com/AdityaRoy-1996/Phonopy_VESTA)

- [VASP-plot-modes](https://github.com/Stanford-MCTG/VASP-plot-modes)