README.md

Mview

Mview is a 3D visulization script written in python to view the molecular structures contained in files like VASP POSCAR. The script utilizes ASE to read the structural information from input files, therefore, the input file formats are not limited to VASP POSCAR. In principle, any file format that can be recognized by ASE can be used as input. For 3D visulization, it utilizes mayavi to do the plotting work.

In addition, the script can also plot the vibration mode with arrows if the vibrational modes are provided.

Prerequisites

The following python library must be installed to run the script

• numpy
• ase
• mayavi

Examples

For a compliete list of functions, please refer to the help message by mview -h. The following line shows the possible usage of the script:

1. designate the input files by -i POSCAR
2. make a 2x2x1 supercell by -r 2 2 1
3. set the background color to black by -bg 0 0 0, where 0 0 0 is the RGB triplet, each with value in [0,255]
4. save the figure -o out.png. The output image format is determined by the suffix of the output file name. use -s width height to change the size of the output image.
5. show the second vibration mode with arrows -n 2. The OUTCAR containing the normal mode should be designated by -outcar /path/to/OUTCAR.
6. set the azimuth and elevation view angle by -phi and -theta.
7. do not show the mayavi UI -q

mview -i POSCAR -r 2 2 1 -bg 0 0 0 -o out.png -n 2 -phi 0 -theta 90 -q

The resulting image looks like this: