Scripts for VASP: Difference between revisions
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go back to [[Main Page]], [[Computational Resources]], [[Scripts]], [[VASP]], [[Núria López and Group]] | go back to [[Main Page]], [[Computational Resources]], [[Scripts]], [[VASP]], [[Núria López and Group]] | ||
= TEST VERSION = | |||
== General applications == | |||
=== Generate a POTCAR file === | |||
[[potcar.sh]] | |||
=== 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 [[Tekla2]] ''' [[http://aliga.iciq.es/wiki/index.php/SENDING_CALCULATIONS tekla2_scripts]] | |||
''' Running VASP on [[MareNostrum]] ''' [[vasp-mn.s]] | |||
''' Automatic generation of job scripts, by Luca: ''' [[adjust.sh]] | |||
''' Automatic generation of job scripts, by Max: ''' [[vasp.sh]] | |||
''' Automatic generation of job scripts, by Rodrigo: ''' [[rungen]] (Works in tekla, tekla2 and MareNostrum) | |||
== Specific applications == | |||
=== Molecular dynamics === | |||
'''Extracting useful information''' [[Image: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 | |||
/home/iciq08/iciq08897/tools (by Uberuaga) | |||
== Auxiliar applications == | |||
=== Queue management === | |||
'''Removing files from queues''' : ==> [[annihilator.s]] <== | |||
= Old = | |||
== General information and examples == | == General information and examples == | ||
| Line 73: | Line 126: | ||
== Queue management and check == | == Queue management and check == | ||
''' | ''' | ||
Revision as of 15:01, 21 May 2013
go back to Main Page, Computational Resources, Scripts, VASP, Núria López and Group
TEST VERSION
General applications
Generate a POTCAR file
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 onTekla run-vasp-tekla.s
Running VASP on Tekla2 [tekla2_scripts]
Running VASP on MareNostrum vasp-mn.s
Automatic generation of job scripts, by Luca: adjust.sh
Automatic generation of job scripts, by Max: vasp.sh
Automatic generation of job scripts, by Rodrigo: rungen (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
/home/iciq08/iciq08897/tools (by Uberuaga)
Auxiliar applications
Queue management
Removing files from queues : ==> annihilator.s <==
Old
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)