Scripts for VASP
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General applications
Generate a POTCAR file
Script to generate pseudopotentials automatically: potcar.sh
Pseudopotentials Location:
- /home/oldhome/nlopez/PPS/pot_for_vasp5.3/PBE
- /home/oldhome/nlopez/PPS/pot_for_vasp5.3/LDA
- /home/oldhome/nlopez/PPS/pot_for_vasp5.3/PW91
Generate a KPOINTS file
This script generates automatically a KPOINTS file containing a Gamma-centered Monkhorst-Pack grid kpoints.sh
Generate a run file
Automatic generation of job scripts (1), rungen (by Rodrigo): Works in tekla, tekla2 and MareNostrum4. Use along savecalc.
Automatic generation of job scripts (2), vasp.sh (by Max): Works in tekla and tekla2.
Automatic generation of job scripts (3), adjust.sh (by Luca): Works in tekla and tekla2.
Running VASP on Tekla run-vasp-tekla.s
Running VASP on MareNostrum vasp-mn.s
Specific applications
Molecular dynamics
Extracting useful information File:Vaspmd.tgz (modified version of Luca)
Running iteratively on MareNostrum (1): scylla&charybdis.tgz (by Luca)
Running iteratively on MareNostrum (2): resurrection_script (by Rodrigo)
Preparing the videos for VMD: KeSoL.tgz (by Luca)
Computing BI- and TRI-dimensional RDF for an optimization/dynamics: RDF (by Luca)
Reactions: NEB, IDM & IRC, Network
Improved Dimer Method: IDM (by Rodrigo)
Get dimer direction (VASP 5.2_IDM only): get-dimer-dir.sh (by David)
Get IRC trajectory (VASP 5.2_IDM only): get-irc-path.sh (by David)
CI-NEB: see /home/iciq08/iciq08897/tools (by Uberuaga)
Get complete reaction network of Glycerol decomposition: version-6.py (By Qiang)
Format conversion
Conversion between different formats: Open Babel
From VASP :
POSCAR/CONTCAR to .xcrysden (1): poscar2xcrysden.pl (asks for atom labels) (by Luca)
POSCAR/CONTCAR to .xcrysden (2): pos2xcry.pl (does not ask for atom labels) (by Luca)
POSCAR/CONTCAR to .xcrysden (3): File:Xcrysden.tgz (v2xsf, by Jens Kunstmann[2], posted by Rodrigo)
POSCAR/CONTCAR to .com: xcr_gv.sh Interface between xcrysden and GaussView (by Luca)
POSCAR/CONTCAR to .xyz : vasp2xyz.sh (by Luca)
POSCAR/CONTCAR to .cif : vasp2cif.sh (by Marcos)
To VASP :
.cif to POSCAR/CONTCAR : cif2vasp.py (by Rodrigo)
.xyz to POSCAR/CONTCAR : xyz_poscar.pl (by Atahualpa)
.com to POSCAR/CONTCAR : gv_vasp.sh Interface between GaussView and VASP (by Luca)
Direct coordinates to Cartesian for POSCAR/CONTCAR : dire2cart.py (by Qiang) or posutil_d2c (by Rodrigo)
Visual tools
Visualizing vibrations with MOLDEN: nfreq.sh (by Luca) old versions: freq.s, freq_2.s, nfreq46.sh
Visualizing optimizations with MOLDEN: ngeom.sh (by Luca) old versions: geom.s, geom_2.s
Generating a large number of figures with xcrysden: generate_figures (by Rodrigo)
Generating a LOCPOT_Z from LOCPOT for Work Function Visualization : vtotav.py (by Qiang)
Extract the DOS data from DOSCAR : dos_extract.py (by Qiang)
Queue management
Removing files from queues: annihilator.s
Checking elapsed/remaining time of a queue: bcheck (by Luca)
Quickly get into the calculation directory: enter (by Qiang)
Band and DOS Calculations
Get Kpoints coordinations connecting specific points in the Brillouin zone: pbekpoints.py(by Qiang)
Get PBE band data for visulization: pbeband.py(by Qiang)
Get KPOINTS for HSE band calculation: hsekpoints.py(by Qiang)
Get HSE band data for visulization: hseband.py(by Qiang)
Get Specific DOS information: dos_extract_v4.py(by Qiang)
Get d band center: dcenter.py(by Qiang)
Compare two dos data and visulize them: ddos_compare.py(by Qiang)
Other applications
General script for handling inputs: coco.sh (by Luca)
All in one script: translation from VASP format to Gaussian with pos2xcry.pl and xcr_gv.sh, running GaussView to prepare the input, and translation back to VASP format with gv_vasp.sh and preparation of the job with adjust.sh
Changing the dimension and the size of the cell : ShapeChange.tgz (by Luca)
Extracting specific orbitals from one atom in the DOSCAR: pdos.py (by Nathan)
Sorting the coordinates in a POSCAR file: sortcolumn.py (by Nathan)
Starting a Database : setandsubmit.s
Calculation of the Cell Parameter : loop.s (by David)
Calculate intensities: intensities.sh (by David)
Breaking bonds in batch mode: batch_dehydrogenation (by Rodrigo)
(Un)Mount Marenostrum to your Computer: alias (by Qiang)
Get the specific atoms' magnetization from OUTCAR: get_mag.sh (by Qiang)
Get entropy from vibration calculation: entropy.py (by Qiang)
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