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]] | ||
= | = General applications = | ||
== Generate a POTCAR file == | |||
Script to generate pseudopotentials automatically: [[potcar.sh]] | Script to generate pseudopotentials automatically: [[potcar.sh]] | ||
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*/home/oldhome/nlopez/PPS/pot_for_vasp5.2/pot_paw_PBE | */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]] | 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 [[Tekla]] ''' [[run-vasp-tekla.s]] | ||
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''' Automatic generation of job scripts (3)''', [[rungen]] (''by Rodrigo''): Works in tekla, tekla2 and MareNostrum. | ''' Automatic generation of job scripts (3)''', [[rungen]] (''by Rodrigo''): Works in tekla, tekla2 and MareNostrum. | ||
= Specific applications = | |||
== Molecular dynamics == | |||
'''Extracting useful information''' [[Image:vaspmd.tgz]] (''modified version of Luca'') | '''Extracting useful information''' [[Image:vaspmd.tgz]] (''modified version of Luca'') | ||
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'''Preparing the videos for VMD''': [[KeSoL.tgz]] (''by Luca'') | '''Preparing the videos for VMD''': [[KeSoL.tgz]] (''by Luca'') | ||
== CI-NEB == | |||
See /home/iciq08/iciq08897/tools (''by Uberuaga'') | See /home/iciq08/iciq08897/tools (''by Uberuaga'') | ||
== IDM & IRC == | |||
'''Improved Dimer Method''': [[IDM]] (''by Rodrigo'') | '''Improved Dimer Method''': [[IDM]] (''by Rodrigo'') | ||
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'''Get IRC trajectory (VASP 5.2_IDM only)''': [[get-irc-path.sh]] (''by David'') | '''Get IRC trajectory (VASP 5.2_IDM only)''': [[get-irc-path.sh]] (''by David'') | ||
== Radial Distribution Function == | |||
'''Computing BI- and TRI-dimensional RDF for an optimization/dynamics''': [[RDF]] (''by Luca'') | '''Computing BI- and TRI-dimensional RDF for an optimization/dynamics''': [[RDF]] (''by Luca'') | ||
= Auxiliar applications = | |||
'''General script for handling inputs''': [[coco.sh]] (''by Luca'') | '''General script for handling inputs''': [[coco.sh]] (''by Luca'') | ||
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'''Calculate intensities (VASP 5.2 only)''': [[intensities.sh]] (''by David'') | '''Calculate intensities (VASP 5.2 only)''': [[intensities.sh]] (''by David'') | ||
== Format conversion == | |||
Conversion between different formats: [http://openbabel.org/wiki/Main_Page Open Babel] | Conversion between different formats: [http://openbabel.org/wiki/Main_Page Open Babel] | ||
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'''.com to POSCAR/CONTCAR''' : [[gv_vasp.sh]] Interface between GaussView and VASP (''by Luca'') | '''.com to POSCAR/CONTCAR''' : [[gv_vasp.sh]] Interface between GaussView and VASP (''by Luca'') | ||
== Visual tools == | |||
'''Visualizing vibrations with MOLDEN''': [[nfreq.sh]] (''by Luca'') | '''Visualizing vibrations with MOLDEN''': [[nfreq.sh]] (''by Luca'') | ||
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'''Generating a large number of figures with xcrysden''': [[generate_figures]] (''by Rodrigo'') | '''Generating a large number of figures with xcrysden''': [[generate_figures]] (''by Rodrigo'') | ||
== Queue management == | |||
'''Removing files from queues''': [[annihilator.s]] | '''Removing files from queues''': [[annihilator.s]] | ||
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'''Checking elapsed/remaining time of a queue''': [[bcheck]] (''by Luca'') | '''Checking elapsed/remaining time of a queue''': [[bcheck]] (''by Luca'') | ||
== Old applications == | |||
'''Starting a Database''' : [[setandsubmit.s]] | '''Starting a Database''' : [[setandsubmit.s]] | ||
Revision as of 11:16, 18 November 2014
go back to Main Page, Computational Resources, Scripts, VASP, Núria López and Group
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)
Preparing the videos for VMD: KeSoL.tgz (by Luca)
CI-NEB
See /home/iciq08/iciq08897/tools (by Uberuaga)
IDM & IRC
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)
Radial Distribution Function
Computing BI- and TRI-dimensional RDF for an optimization/dynamics: RDF (by Luca)
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
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 :
.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)
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