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go back to [[Main Page]], [[Computational Resources]], [[Scripts]] or [[VASP]]
go back to [[Main Page]], [[Computational Resources]], [[Scripts]], [[VASP_beginners]], [[Núria López and Group]]


== GENERAL INFOS AND EXAMPLES ==
= General applications =


        '''Pseudopotentials Location''':           /home/oldhome/nlopez/potpaw_GGA
* '''Generate pseudopotentials''' automatically: In bash: [[potgen]]; in python: [[potgenpbe5.3]] and [[pos2pot.py]] (''by David, Rodrigo, Qiang, and Konstantin).
                                              /home/oldhome/nlopez/potpaw_PBE


        '''Starting CI-NEB and other scripts''':   /home/iciq08/iciq08897/tools
* '''Generate KPOINTS file''' containing a Gamma-centered Monkhorst-Pack grid: [[kpoints]] (''by Rodrigo'').
                ''(by Uberuaga)''


        '''Running VASP calcul. on [[Tekla]] ''' :  ==>  [[run-vasp-tekla.s]] <==
* '''Automatic generation of job scripts''' (1), [[rungen]] (''by Rodrigo''): Works in tekla, tekla2 and MareNostrum4. Use along [[savecalc]].  
        '''Running VASP calcul. on [[Tekla2]] ''':  ==>  [[http://aliga.iciq.es/wiki/index.php/SENDING_CALCULATIONS tekla2_scripts]] <==


== SCRIPTS: GENERAL CALCULATIONS AND FILE MANAGEMENT ==
* '''Automatic generation of job scripts''' (2), [[vasp.sh]] (''by Max''): Works in tekla and tekla2.


        '''Calculation of the Cell Parameter''' :  ==>      [[loop.s]]     <==  (''by David'')
* '''Automatic generation of job scripts''' (3), [[adjust.sh]] (''by Luca''): Works in tekla and tekla2.


        '''Starting a Database''' :                ==>  [[setandsubmit.s]] <==
* '''Running VASP on [[Tekla2]]''' [[http://aliga.iciq.es/wiki/index.php/SENDING_CALCULATIONS]]


        '''Removing files from queues''' :          ==>  [[annihilator.s]]   <==
* '''Running VASP on [http://www.bsc.es/marenostrum-support-services/res MareNostrum]''' [[vasp-mn.s]]


        '''Preparing job files''' :                ==>    [[adjust.sh]]    <== Preparation of the .sub file  (''by Luca'')
= Specific applications =


        '''General script for handling inputs''':  ==>      [[coco.sh]]    <==  
== Molecular dynamics ==
          (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'')


== SCRIPTS: FORMAT CONVERSION ==
'''Extracting useful information''' [[Image:vaspmd.tgz]] (''modified version of Luca'')


        '''From CONTCAR/POSCAR to .xcrysden''':     ==>  [[poscar2xcrysden.pl]]  <== (ASKS FOR ATOM LABELS)
'''Running iteratively on MareNostrum (1)''': [[scylla&charybdis.tgz]] (''by Luca'')
                                              ==>      [[pos2xcry.pl]]     <== (NO QUESTIONS ABOUT ATOM LABELS) (''by Luca'')
                                              ==>      [[xcrysden.tgz]] (By Jens Kunstmann, posted by Rodrigo García)


        '''From XYZ to POSCAR''' :                 ==>  [[xyz_poscar.pl]] <==
'''Running iteratively on MareNostrum (2)''': [[resurrection_script]] (''by Rodrigo'')
        ''(Courtesy from Ata)''


        '''From PDB to POSCAR''' :                 ==>  [[pdb_poscar.pl]] <==    '''FALTA!!!!!'''
'''Computing BI- and TRI-dimensional RDF for an optimization/dynamics''': [[RDF]] (''by Luca'')


        '''Translating POSCAR/CONTCAR to .com for gaussview''' : ==>  [[xcr_gv.sh]] <== Interface between xcrysden and gv  (''by Luca'')
'''Measuring distance between two atoms during MD run ''': [[curls]] (''by Federico & Edvin'')


        '''Translating .com to POSCAR/CONTCAR''' :              ==>  [[gv_vasp.sh]]  <== Interface between gv and xcrysden  (''by Luca'')
== Reactions: NEB, IDM & IRC, Network==


        '''Translating POSCAR/CONTCAR to XYZ''' :               ==>  [[vasp2xyz.sh]] <== ''by Luca''
'''Improved Dimer Method''': [[IDM]] (''by Rodrigo'')


== SCRIPTS: FILES VISUALIZATION ==
'''Get dimer direction (VASP 5.2_IDM only)''': [[get-dimer-dir.sh]] (''by David'')


        '''Visualizing vibrations with MOLDEN''':     ==>  [[freq.s]]  <==  ''Outdated''
'''Get IRC trajectory (VASP 5.2_IDM only)''': [[get-irc-path.sh]] (''by David'')
                                                ==>  [[freq_2.s]]  <==  ''Outdated''
                                                ==> [[nfreq46.sh]] <==  ''Outdated''
                                                ==>  [[nfreq.sh]] <==  ''by Luca'' (improved version of older versions)


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


        '''Visualizing optimizations  with MOLDEN''': ==>  [[geom.s]]   <==  ''Outdated''
'''Calculate entropy from vibrations''': [[entropy.py]] (''by Qiang'')
                                                ==>  [[geom_2.s]]  <==  ''Outdated''
                                                ==>  [[ngeom.sh]]  <==  Improved and quicker version of geom_2.s  (''by Luca'')


        '''Generating figures massively    ''': ==>  [[generate_massive_figures]]
'''Get complete reaction network of Glycerol decomposition''': [[version-6.py]] (''By Qiang'')


== SCRIPTS: MOLECULAR DYNAMICS ANALYSIS ==
== Format conversion ==


        '''Extracting useful information''':           ==>  [[Image:vaspmd.tgz]] <== (modified version, ''by Luca'')
Conversion between different formats: [http://openbabel.org/wiki/Main_Page Open Babel]


== SCRIPTS: VIBRATIONAL MODES' INTENSITIES ==
''' ''From VASP'' ''':


        '''Calculate intensities (VASP 5.2 only)''':   ==>  [[intensities.sh]]  <== (''by David'')
'''POSCAR/CONTCAR to .xcrysden''' (1): [[poscar2xcrysden.pl]]  (asks for atom labels) (''by Luca'')


== SCRIPTS: IDM & IRC ==
'''POSCAR/CONTCAR to .xcrysden''' (2): [[pos2xcry.pl]] (does not ask for atom labels) (''by Luca'')


        '''Get dimer direction (VASP 5.2_IDM only)''':     ==>  [[get-dimer-dir.sh]] <== (''by David'')
'''POSCAR/CONTCAR to .xcrysden''' (3): [[Image:Xcrysden.tgz]] ('''v2xsf''', ''by Jens Kunstmann''[https://nano.tu-dresden.de/~jkunstmann/software.html], ''posted by Rodrigo'')


        '''Get IRC trajectory (VASP 5.2_IDM only)''':     ==>  [[get-irc-path.sh]] <== (''by David'')
'''POSCAR/CONTCAR to .com''': [[xcr_gv.sh]] Interface between xcrysden and GaussView (''by Luca'')


== TRICKS: VDW forces ==
'''POSCAR/CONTCAR to .xyz''' : [[vasp2xyz.sh]]  (''by Luca'')


To include vdW interactions in a calculation with VASP, simply add this tag to your INCAR file:
'''POSCAR/CONTCAR to .cif''' : [[vasp2cif.sh]]  (''by Marcos'')
       
        '''LVDW = .TRUE.'''


The vdW's contribution to the energy is easy to identify in the OUTCAR file (if you open the file with vi you can find it with /vdW).
''' ''To VASP'' ''':
Up to now the best results were obtained using the RPBE pseudopotential; to use it, insert this tag in your INCAR file:


        '''GGA = RP'''
'''.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'')
 
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.

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

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