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]], [[VASP_beginners]], [[Núria López and Group]] | ||
= | = 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]]''' [[http://aliga.iciq.es/wiki/index.php/SENDING_CALCULATIONS]] | |||
* '''Running VASP on [http://www.bsc.es/marenostrum-support-services/res MareNostrum]''' [[vasp-mn.s]] | |||
= Specific applications = | |||
== Molecular dynamics == | |||
''' | '''Extracting useful information''' [[Image: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: [http://openbabel.org/wiki/Main_Page 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''' ( | '''POSCAR/CONTCAR to .xcrysden''' (3): [[Image:Xcrysden.tgz]] ('''v2xsf''', ''by Jens Kunstmann''[https://nano.tu-dresden.de/~jkunstmann/software.html], ''posted by Rodrigo'') | ||
''' | '''POSCAR/CONTCAR to .com''': [[xcr_gv.sh]] Interface between xcrysden and GaussView (''by Luca'') | ||
'''POSCAR/CONTCAR to . | '''POSCAR/CONTCAR to .xyz''' : [[vasp2xyz.sh]] (''by Luca'') | ||
'''POSCAR/CONTCAR to . | '''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'') | '''.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 == | == Visual tools == | ||
'''Visualizing vibrations with MOLDEN''': | '''Visualizing vibrations with MOLDEN''': [[nfreq]] | ||
old versions: [[freq.s]] [[freq_2.s]] [[nfreq46.sh]] | 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'') | '''Visualizing optimizations with MOLDEN''': [[ngeom.sh]] (''by Luca'') | ||
old versions: [[geom.s]] [[geom_2.s]] | 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'') | |||
go back to [[Main Page]], [[Computational Resources]], [[Scripts]], [[VASP]], [[Núria López and Group]] | |||
Latest revision as of 15:54, 13 September 2021
go back to Main Page, Computational Resources, Scripts, VASP_beginners, Núria López and Group
General applications[edit]
- 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 MareNostrum vasp-mn.s
Specific applications[edit]
Molecular dynamics[edit]
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[edit]
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[edit]
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[edit]
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[edit]
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[edit]
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[edit]
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[edit]
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)
go back to Main Page, Computational Resources, Scripts, VASP, Núria López and Group