Scripts for VASP: Difference between revisions
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go back to [[Main Page]], [[Computational Resources]], [[Scripts]] | go back to [[Main Page]], [[Computational Resources]], [[Scripts]] | ||
== GENERAL INFOS AND EXAMPLES == | == GENERAL INFOS AND EXAMPLES == | ||
'''Pseudopotentials Location''': /home/oldhome/nlopez/potpaw_GGA | '''Pseudopotentials Location''': /home/oldhome/nlopez/potpaw_GGA | ||
/home/oldhome/nlopez/potpaw_PBE | /home/oldhome/nlopez/potpaw_PBE | ||
'''Starting CI-NEB and other scripts''': /home/iciq08/iciq08897/tools | '''Starting CI-NEB and other scripts''': /home/iciq08/iciq08897/tools | ||
''(by Uberuaga)'' | ''(by Uberuaga)'' | ||
'''Running VASP calcul. on [[Tekla]] ''' : ==> [[run-vasp-tekla.s]] <== | '''Running VASP calcul. on [[Tekla]] ''' : ==> [[run-vasp-tekla.s]] <== | ||
'''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]] <== | ||
== SCRIPTS: GENERAL CALCULATIONS AND FILE MANAGEMENT == | == SCRIPTS: GENERAL CALCULATIONS AND FILE MANAGEMENT == | ||
'''Calculation of the Cell Parameter''' : ==> [[loop.s]] <== (''by David'') | |||
'''Calculation of the Cell Parameter''' : ==> [[loop.s]] <== | |||
'''Starting a Database''' : ==> [[setandsubmit.s]] <== | '''Starting a Database''' : ==> [[setandsubmit.s]] <== | ||
| Line 31: | Line 21: | ||
'''Removing files from queues''' : ==> [[annihilator.s]] <== | '''Removing files from queues''' : ==> [[annihilator.s]] <== | ||
'''Preparing job files''' : ==> [[adjust.sh]] <== Preparation of the .sub file | '''Preparing job files''' : ==> [[adjust.sh]] <== Preparation of the .sub file (''by Luca'') | ||
'''General script for handling inputs''': ==> [[coco.sh]] <== | '''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 | (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 | gaussview to prepare the input, and translation back to vasp format (with ''gv_vasp.sh'') and preparation of | ||
the job (with ''adjust.sh'')). | the job (with ''adjust.sh'')). (''by Luca'') | ||
== SCRIPTS: FORMAT CONVERSION == | == SCRIPTS: FORMAT CONVERSION == | ||
'''From CONTCAR/POSCAR to .xcrysden''': ==> [[poscar2xcrysden.pl]] <== (ASKS FOR ATOM LABELS) | '''From CONTCAR/POSCAR to .xcrysden''': ==> [[poscar2xcrysden.pl]] <== (ASKS FOR ATOM LABELS) | ||
==> [[pos2xcry.pl]] <== (NO QUESTIONS ABOUT ATOM LABELS) (''by Luca'') | ==> [[pos2xcry.pl]] <== (NO QUESTIONS ABOUT ATOM LABELS) (''by Luca'') | ||
'''From XYZ to POSCAR''' : ==> [[xyz_poscar.pl]] <== | '''From XYZ to POSCAR''' : ==> [[xyz_poscar.pl]] <== | ||
''(Courtesy from Ata)'' | ''(Courtesy from Ata)'' | ||
'''From PDB to POSCAR''' : ==> [[pdb_poscar.pl]] <== '''FALTA!!!!!''' | '''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 .com to POSCAR/CONTCAR''' : ==> [[gv_vasp.sh]] <== Interface between gv and xcrysden | |||
'''Translating POSCAR/CONTCAR to XYZ''' : ==> [[vasp2xyz.sh]] <== ''by Luca'' | '''Translating POSCAR/CONTCAR to XYZ''' : ==> [[vasp2xyz.sh]] <== ''by Luca'' | ||
== SCRIPTS: FILES VISUALIZATION == | == SCRIPTS: FILES VISUALIZATION == | ||
'''Visualizing vibrations with MOLDEN''': ==> [[freq.s]] <== | '''Visualizing vibrations with MOLDEN''': ==> [[freq.s]] <== | ||
==> [[freq_2.s]] <== | ==> [[freq_2.s]] <== | ||
==> [[nfreq46.sh]] <== ''by Luca'' (improved version of older versions) | ==> [[nfreq46.sh]] <== ''by Luca'' (improved version of older versions) | ||
'''Visualizing optimizations with MOLDEN''': ==> [[geom.s]] <== ''Old Version'' | '''Visualizing optimizations with MOLDEN''': ==> [[geom.s]] <== ''Old Version'' | ||
==> [[geom_2.s]] <== | ==> [[geom_2.s]] <== | ||
==> [[ngeom.sh]] <== Improved and quicker version of geom_2.s (''by Luca'') | |||
==> [[ngeom.sh]] <== Improved and quicker version of geom_2.s | |||
== SCRIPTS: MOLECULAR DYNAMICS ANALYSIS == | == SCRIPTS: MOLECULAR DYNAMICS ANALYSIS == | ||
'''Extracting useful information''': ==> [[Image:vaspmd.tgz]] <== (modified version, by Luca) | '''Extracting useful information''': ==> [[Image:vaspmd.tgz]] <== (modified version, by Luca) | ||
Revision as of 13:12, 21 September 2010
go back to Main Page, Computational Resources, Scripts
GENERAL INFOS 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] <==
SCRIPTS: GENERAL CALCULATIONS AND FILE MANAGEMENT
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)
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)
SCRIPTS: FORMAT CONVERSION
From CONTCAR/POSCAR to .xcrysden: ==> poscar2xcrysden.pl <== (ASKS FOR ATOM LABELS) ==> pos2xcry.pl <== (NO QUESTIONS ABOUT ATOM LABELS) (by Luca)
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
SCRIPTS: FILES VISUALIZATION
Visualizing vibrations with MOLDEN: ==> freq.s <== ==> freq_2.s <== ==> nfreq46.sh <== by Luca (improved version of older versions)
Visualizing optimizations with MOLDEN: ==> geom.s <== Old Version ==> geom_2.s <== ==> ngeom.sh <== Improved and quicker version of geom_2.s (by Luca)
SCRIPTS: MOLECULAR DYNAMICS ANALYSIS
Extracting useful information: ==> File:Vaspmd.tgz <== (modified version, by Luca)