LAttice DYnamic tools
The set of helpful tools for ab initio calculation software packages like ABINIT VASP CRYSTAL etc.
- scan_alnog_mode_vasp.py - the program to distort geometry along selected normal mode eigenvector. VASP POSCAR format.
1a. make_scan_dirs.sh - script to copy geometry and other VASP files in new directories
1b. To plot table Energy vs shift one may use bash command:
VASP:
for i in SCAN*; do cd
$i; echo -n "$ {i##SCAN-} "; grep TOTEN OUTCAR | tail -n1 | awk '{print ($5)}'; cd ..; done ABINIT: for i in displ*; do cd$i; echo -n "$ {i##displ-} "; grep etotal displ.out | tail -n1 | awk '{print ($2)}'; cd ..; done - abi_fc_extract.py -- Simple script to extract FORCE_CONSTANTS from abinit output file in PHONOPY software format.
- Two utilites make_repr.py and make_irreps_table.py to plot characters table and Irreps using ABINIT anaddb utility.
- abinit-patterns.tar.bz2 -- is a set of patterns for ABINIT.
- extract_raman_abinit.py -- Extract raman tensor and rotational invariants (Long's notation) from ABINIT anaddb output
- plot_ramanspectrum.py -- Plot raman spectrum with given intensities and line halfwidths.
- bond_shortcut_by_atom.py -- Add atoms into the file with xyz format to shortcut open bonds.
- extract_dipole_geom.py -- Exctract from Gaussian output dipole oriented geometry and save file in xyz format (the rotation option could be activated)
- seekpath_poscar.py -- seek path in reciprocal space for a given crystallographic unitcell (obsolete)
- seekpath_calc.py -- seek path in reciprocal space for a given crystallographic unitcell and diferent calculators (vasp, abinit, castep)
- xsf2cube.py -- convert grid Data from xsf format to the CUBE one, which is supported by Jmol
- cube2jvxl.sh -- convert isosurface in CUBE file format into JVXL format one and put crystallographic and isosurface data in zip
- vec_decompose_on_eigvecs.py -- Decomposition of the vector (For example LO) given in xyz format (see below how to generate it) on the basis of eigenvectors (mass weighted) of the Dynamical matrix stored in qpoints.yaml file (PHONOPY format).
- eigvec2xyz_vasp_singlemode.py -- Extract atomic displacements for a given mode from Dynamical matrix stored in qpoints.yaml file (PHONOPY format).
- reciprocal_distance.py -- Get distance in reciprocal space and generate k-points
- fc2xyz.py -- create file with atomic displacements for each phonon mode using force contants in PHONOPY format.
- plot_band_dos_phonopy.py -- tool to plot nice bandstructure and phonon density of states using results obtained with phonopy.
- plot_phbands_and_dos.py -- tool to plot nice bandstructure and phonon density of states using results obtained with ABINIT.
- BORNCP2K -- calculate BORN charges using finite difference method within CP2K
- decompose_lo_on_to.py -- decompose LO eigenvectors on TO basis in order to establish the "nature" of LO modes.