Editing 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]]''' [[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''' (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 .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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