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 information and examples == | ||
'''Pseudopotentials Location''': /home/oldhome/nlopez/potpaw_GGA | '''Pseudopotentials Location''': /home/oldhome/nlopez/potpaw_GGA | ||
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'''Running VASP calcul. on [[Tekla2]] ''': ==> [[http://aliga.iciq.es/wiki/index.php/SENDING_CALCULATIONS tekla2_scripts]] <== | '''Running VASP calcul. on [[Tekla2]] ''': ==> [[http://aliga.iciq.es/wiki/index.php/SENDING_CALCULATIONS tekla2_scripts]] <== | ||
== | == General calculations and file management == | ||
'''Generating a POTCAR file''' ==> [[potcar.sh]] <== | '''Generating a POTCAR file''' ==> [[potcar.sh]] <== | ||
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the job (with ''adjust.sh'')). (''by Luca'') | the job (with ''adjust.sh'')). (''by Luca'') | ||
== | == Format conversion == | ||
'''From CONTCAR/POSCAR to .xcrysden''': ==> [[poscar2xcrysden.pl]] <== (ASKS FOR ATOM LABELS) | '''From CONTCAR/POSCAR to .xcrysden''': ==> [[poscar2xcrysden.pl]] <== (ASKS FOR ATOM LABELS) | ||
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'''Changing the dimension and the size of the cell''' : ==> [[ShapeChange.tgz]] <== ''by Luca'' | '''Changing the dimension and the size of the cell''' : ==> [[ShapeChange.tgz]] <== ''by Luca'' | ||
== | == Files visualization == | ||
'''Visualizing vibrations with MOLDEN''': ==> [[freq.s]] <== ''Outdated'' | '''Visualizing vibrations with MOLDEN''': ==> [[freq.s]] <== ''Outdated'' | ||
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'''Generating a large number of figures ''': ==> [[generate figures]] | '''Generating a large number of figures ''': ==> [[generate figures]] | ||
== | == Molecular Dynamics == | ||
'''Extracting useful information''': ==> [[Image:vaspmd.tgz]] <== (modified version, ''by Luca'') | '''Extracting useful information''': ==> [[Image:vaspmd.tgz]] <== (modified version, ''by Luca'') | ||
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'''Running iteratively''': ==> [[scylla&charybdis.tgz]] <== (''by Luca'') | '''Running iteratively''': ==> [[scylla&charybdis.tgz]] <== (''by Luca'') | ||
== | == Queue management and check == | ||
'''Checking elapsed/remaining time of a queue''': ==> [[bcheck]] <== (''by Luca'') | '''Checking elapsed/remaining time of a queue''': ==> [[bcheck]] <== (''by Luca'') | ||
== | == Vibrational modes == | ||
'''Calculate intensities (VASP 5.2 only)''': ==> [[intensities.sh]] <== (''by David'') | '''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 dimer direction (VASP 5.2_IDM only)''': ==> [[get-dimer-dir.sh]] <== (''by David'') | ||
Revision as of 15:59, 30 April 2013
go back to Main Page, Computational Resources, Scripts, VASP, Núria López and Group
General information and examples
Pseudopotentials Location: /home/oldhome/nlopez/potpaw_GGA
/home/oldhome/nlopez/potpaw_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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