Scripts for VASP

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General applications

• Generate pseudopotentials automatically: In bash: potgen; in python: potgenpbe5.3 and pos2pot.py (by David, Rodrigo, Qiang, and Konstantin).

• Generate KPOINTS file containing a Gamma-centered Monkhorst-Pack grid: kpoints (by Rodrigo).

• Automatic generation of job scripts (1), rungen (by Rodrigo): Works in tekla, tekla2 and MareNostrum4. Use along savecalc.

• Automatic generation of job scripts (2), vasp.sh (by Max): Works in tekla and tekla2.

• Automatic generation of job scripts (3), adjust.sh (by Luca): Works in tekla and tekla2.

• Running VASP on Tekla2 [[1]]

• Running VASP on MareNostrum vasp-mn.s

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)

Computing BI- and TRI-dimensional RDF for an optimization/dynamics: RDF (by Luca)

Measuring distance between two atoms during MD run : curls (by Federico & Edvin)

Reactions: NEB, IDM & IRC, Network

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)

CI-NEB: see /home/iciq08/iciq08897/tools (by Uberuaga)

Calculate entropy from vibrations: entropy.py (by Qiang)

Get complete reaction network of Glycerol decomposition: version-6.py (By Qiang)

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 :

.cif to POSCAR/CONTCAR : cif2vasp.py (by Rodrigo)

.xyz to POSCAR/CONTCAR : xyz_poscar.pl (by Atahualpa)

.com to POSCAR/CONTCAR : gv_vasp.sh Interface between GaussView and VASP (by Luca)

Direct coordinates to Cartesian for POSCAR/CONTCAR : dire2cart.py (by Qiang) or posutil_d2c (by Rodrigo)

Visual tools

Visualizing vibrations with MOLDEN: nfreq old versions: nfreq-luca, freq.s, freq_2.s, nfreq46.sh

Visualizing vibrations with Jmol: Simply draw the OUTCAR file to the Jmol window.

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)

Generating a LOCPOT_Z from LOCPOT for Work Function Visualization : vtotav.py (by Qiang)

Visualizing Vibrations with Jmol: Jmol.sh (by Qiang)

Queue and Job management

Removing files from queues: annihilator.s

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

Quickly get into the calculation directory: enter (by Qiang)

Band, DOS, and XPS Calculations

Get Kpoints coordinations connecting specific points in the Brillouin zone: pbekpoints.py(by Qiang)

Get PBE band data for visulization: pbeband.py(by Qiang)

Get KPOINTS for HSE band calculation: hsekpoints.py(by Qiang)

Get HSE band data for visulization: hseband.py(by Qiang)

HSE-band calculation example: Si: Example_hse_band.tgz(by Qiang)

Get Specific DOS information: dos_extract_v5.py(by Qiang)

Extracting specific orbitals from one atom in the DOSCAR: pdos.py (by Nathan)

Get d band center: dcenter.py(by Qiang)

Compare two dos data and visualize them: dos_compare.py(by Qiang)

Prepare POSCAR for XPS calculations (version-1): xps.py(by Qiang)

Prepare POSCAR for XPS calculations (version-2: Recommend): xps_2.py(by Qiang)

Assign Gaussian bells to computed XPS shift and sum the bells generating a spectra: curlz (by Javier & Edvin)

Get the specific atoms' magnetization from OUTCAR: get_mag.sh (by Qiang)

Geometry Manipulations

Direct coordinates to Cartesian for POSCAR/CONTCAR and fix layers : dire2cart.py (by Qiang)

Sorting the coordinates in a POSCAR file: sortcolumn.py (by Nathan)

Sorting the coordinates in a POSCAR file: sortcar.py (by Qiang)

Move species from one POSCAR to another : move_atoms_v1.py (by Qiang)

Species translations on the Surface : translate.py (by Qiang)

Species rotations : rotation.py (by Qiang)

Move a molecule over a surface: putontop (by Sergio Pablo)

Breaking bonds in batch mode: batch_dehydrogenation (by Rodrigo)

Other 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)

Starting a Database : setandsubmit.s

Calculation of the Cell Parameter : loop.s (by David)

Calculate intensities: intensities.sh (by David)

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