Scripts for VASP

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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 [tekla2_scripts]

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)

Queue management

Removing files from queues: annihilator.s

Checking elapsed/remaining time of a queue: bcheck (by Luca)

Format conversion

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 (By Jens Kunstmann, 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: generate_figures

Old applications

Starting a Database : setandsubmit.s

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 :  ==>  [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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