Scripts for VASP
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TEST VERSION
General applications
Generate a POTCAR file
Script to generate pseudopotentials automatically: potcar.sh
Pseudopotentials Location:
- /home/oldhome/nlopez/PPS/pot_for_vasp5.2/pot_paw_LDA
- /home/oldhome/nlopez/PPS/pot_for_vasp5.2/pot_paw_PBE
Generate a KPOINTS file
This script generates automatically a KPOINTS file containing a Gamma-centered Monkhorst-Pack grid kpoints.sh
Generate a run file
Running VASP on Tekla run-vasp-tekla.s
Running VASP on MareNostrum vasp-mn.s
Automatic generation of job scripts (1), adjust.sh (by Luca): Works in tekla and tekla2.
Automatic generation of job scripts (2), vasp.sh (by Max): Works in tekla and tekla2.
Automatic generation of job scripts (3), rungen (by Rodrigo): Works in tekla, tekla2 and MareNostrum.
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)
CI-NEB
See /home/iciq08/iciq08897/tools (by Uberuaga)
IDM & IRC
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)
Auxiliar 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)
Calculate intensities (VASP 5.2 only): intensities.sh (by David)
Format conversion
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 .xys : vasp2xyz.sh (by Luca)
To VASP :
.xyz to POSCAR/CONTCAR : xyz_poscar.pl (By Atahualpa)
.pdb to POSCAR/CONTCAR : pdb_poscar.pl FALTA!!!!!
.com to POSCAR/CONTCAR : gv_vasp.sh Interface between GaussView and VASP (by Luca)
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)
Queue management
Removing files from queues: annihilator.s
Checking elapsed/remaining time of a queue: bcheck (by Luca)
Old applications
Starting a Database : setandsubmit.s
Calculation of the Cell Parameter : loop.s (by David)
# # # # # # # # # # # # # OLD PAGE # # # # # # # # # # # # # # #
General information and examples
Pseudopotentials Location: /home/oldhome/nlopez/PPS/pot_for_vasp5.2/pot_paw_LDA
/home/oldhome/nlopez/PPS/pot_for_vasp5.2/pot_paw_PBE
Starting CI-NEB and other scripts: /home/iciq08/iciq08897/tools
(by Uberuaga)
Running VASP calcul. on Tekla : ==> run-vasp-tekla.s <== Running VASP calcul. on Tekla2 : ==> [tekla2_scripts] <==
General calculations and file management
Generating a POTCAR file ==> potcar.sh <==
Calculation of the Cell Parameter : ==> loop.s <== (by David)
Starting a Database : ==> setandsubmit.s <==
Removing files from queues : ==> annihilator.s <==
Preparing job files : ==> adjust.sh <== Preparation of the .sub file (by Luca)
Preparing and submitting job files : ==> vasp.sh <== Preparation and submission of the .sub file (by Max)
General script for handling inputs: ==> coco.sh <== (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)). (by Luca)
Format conversion
From CONTCAR/POSCAR to .xcrysden: ==> poscar2xcrysden.pl <== (ASKS FOR ATOM LABELS) ==> pos2xcry.pl <== (NO QUESTIONS ABOUT ATOM LABELS) (by Luca) ==> File:Xcrysden.tgz (By Jens Kunstmann, posted by Rodrigo García)
From XYZ to POSCAR : ==> xyz_poscar.pl <== (Courtesy from Ata)
From PDB to POSCAR : ==> pdb_poscar.pl <== FALTA!!!!!
Translating POSCAR/CONTCAR to .com for gaussview : ==> xcr_gv.sh <== Interface between xcrysden and gv (by Luca)
Translating .com to POSCAR/CONTCAR : ==> gv_vasp.sh <== Interface between gv and xcrysden (by Luca)
Translating POSCAR/CONTCAR to XYZ : ==> vasp2xyz.sh <== by Luca
Changing the dimension and the size of the cell : ==> ShapeChange.tgz <== by Luca
Files visualization
Visualizing vibrations with MOLDEN: ==> freq.s <== Outdated ==> freq_2.s <== Outdated ==> nfreq46.sh <== Outdated ==> nfreq.sh <== by Luca (improved version of older versions)
Visualizing optimizations with MOLDEN: ==> geom.s <== Outdated ==> geom_2.s <== Outdated ==> ngeom.sh <== Improved and quicker version of geom_2.s (by Luca)
Generating a large number of figures : ==> generate figures
Molecular Dynamics
Extracting useful information: ==> File:Vaspmd.tgz <== (modified version, by Luca)
Running iteratively: ==> scylla&charybdis.tgz <== (by Luca)
Queue management and check
Checking elapsed/remaining time of a queue: ==> bcheck <== (by Luca)
Vibrational modes
Calculate intensities (VASP 5.2 only): ==> intensities.sh <== (by David)
IDM & IRC
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)
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