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'''Calculation of the Cell Parameter''' : [[loop.s]] (''by David'')
'''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]] ''':  ==>  [[http://aliga.iciq.es/wiki/index.php/SENDING_CALCULATIONS 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'')
                                              ==>      [[Image: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''':          ==>  [[Image: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'')


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]]

Revision as of 10:15, 13 June 2013

go back to Main Page, Computational Resources, Scripts, VASP, Núria López and Group

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 Tekla2 [[1]]

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

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)

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)

go back to Main Page, Computational Resources, Scripts, VASP, Núria López and Group

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