VASP-Structural_Descriptors

Simple description:

Pymatgen-based Python script to extract structural descriptors from vasprun.xml or POSCAR file(s)

How to use:

python Structural_descriptor.py [filenames or entries]

• [filename]: name of vasprun.xml file or POSCAR file (wildcard (*,?) is usable!) if you use xml file, you can extract band gap despite longer execution time
• [entries]: Descriptors of user choice
  • atom1-atom2: the distance between two atoms is called with one dash (-)
    • atoms can be designated as VESTA format (Sr1, Sr2, etc.)
    • Or, index number starting from 1 (This feature will be useful to compare a set of structures with different chemistries)
    • Ex) In SrTiO3, Sr --> Sr1 or 1, Fe --> Fe1 or 2, O1 --> O1 or 3
  • atom1-atom2-atom3: bond angle is callable with two dashes joining three atoms
    • This feature is intended to calculate angles for neighboring atoms
    • If the distance between atoms is comparable to the lattice parameters, I recommend double-checking the value using VESTA.
  • SG, #SG: Space group with symbol or space group number
  • Eg: Band gap (xml file is needed for this)
  • a, b, c, alpha, beta, gamma: lattice parameters and interaxial angles
  • V: unit cell volume
  • natom: number of atoms in the structure
  • Ewald: Ewald summation of the given structure (nominal charge states will be automatically assigned)
  • GII: Global Instability Index (GII) captures instability of deviation from the ideal coordination environment. Parameters will be taken from 'Bond_Valcne2016.csv' file as reference.
  • atom1.BV: bond valence of the atom1, calculated based on the same parameters used for GII.
    • Ex) Sr1.BV
  • Mathematical operation of descriptors:
    • If you format a descriptor or column with brackets ([ and ]), you can execute simple operations.
    • Ex) [Fe5-O1]+[Fe5-O2]: sum of bond length of Fe5-O1 and Fe5-O2
    • Ex) [11-O1]+[Fe5-O2]: sum of bond length of (11th atom)-O1 and Fe5-O2
    • Ex) [Fe5-O1]/[Fe5-O2]: ratio of bond length between Fe5-O1 and Fe5-O2
    • Ex) [1]/[2]: ratio between 1th column value and 2nd column value (Note that 0th column is the filename column).
    • Note: If you want to use parentheses for complicated forms, you may want to enclose the expression with quotation marks (') to avoid a syntax error coming from parentheses. For example, the average of two values can be printed by addting ([1]+[2])/2.