/VASP-DOS_extractor

Pymatgen-based python script to extract density of states (DOS) and projected DOS from vasprun.xml file

Primary LanguagePython

VASP_DOS_extractor

Simple description:

Pymatgen-based python script to extract density of states (DOS) and projected DOS from vasprun.xml file

What does this do:

This script replaces one of the most common use of p4vasp: extracting DOS data from VASP output, which is a density functional theory (DFT) calculation program. Though p4vasp is with intuitive GUI, extracting DOS data can easily take time especially when the number of atom, band, and energy grid are larger. Note that you should install pymatgen (http://pymatgen.org/) before using this script.

The process with p4vasp usually happens as follows:

  • Download xml file to local computer (often over 100 MB)
  • Open p4vasp and open xml file
  • Plot element or individual atom of interest to plot the local projection of DOS (PDOS). (This process takes most of the time)
  • Export data to designated filename (This file is usually less than 1MB)

With DOS_extractor.py, these four process can be done with one command line:

 $ python DOS_extractor.py [xml_filename] [out_filename] [entries_or_options]
  • [xml_filename]: name of vasprun.xml file.
  • [out_filename]: name of DOS data file. By default it follows the printing format of p4vasp. For spin polarized system, spin up/down
    • p4vasp format: This format is collection of data arrays. Each data array represents each entry, including total DOS, which are composed of two columns; column1 for energy and column2 for DOS of entry. line1 is header starting with #, which shows the Band gap, and list of data in the output file.
    • block format: This format is intuitive structured data with row of energy grid and column of each entry. The line1 contains labels.
  • [entries]: Entry can be element or specific atom. Atom label follows the VESTA, for example atoms in BaTiO3 unit cell would be Ba1, Ti1, O1, O2, O3. The script also supports orbital projection by specifiying orbital after dash (-). Examples and nomenclatures are as follows.
    • Ex) Fe: DOS of all Fe atoms
    • Ex) Fe-d: d-orbitals of Fe
    • Ex) Fe-dxy: dxy-orbital of Fe
    • Ex) Fe1: DOS of Fe1 atom
    • Ex) Fe1-dxy: dxy-orbital of Fe1 atom
    • Ex) O-px: px-orbital of O
    • Note that these nomenclatures are basically the order in which the orbitals are reported in VASP and has no special meaning.
      • p-orbitals: px, py, pz
      • d-orbitals: dxy, dyz, dz2, dxz, dx2
      • f-orbitals: f_3, f_2, f_1, f0, f1, f2, f3
  • [options]: option can be stated with --. At this moment there are three options.
    • --elements: Include all elements in the system to the entries.
    • --atoms: Include all individual atoms in the system to the entries.
    • --block: Change printing option to block data. Otherwise the printing option will follow p4vasp.

Example case

For example, if you want to extract PDOS of all elements in Sr2Fe2O5, and Fe1 atom, you might do the command as follows.

$ python DOS_extractor.py vasprun.xml Sr2Fe2O5.dat Sr Fe O Fe1-d

Corresponding output file is as follows (basically same with p4vasp format)
alt text

$ python DOS_extractor.py vasprun.xml Sr2Fe2O5_block.dat --elements Fe1-d --block

Output file will contain same data as above, but with block data format (Note that '--elements' substitutes Sr Fe O command in this case)
alt text