Vasp.pm

Perl module that contains various common commands that one might want when deal with VASP POSCAR files. These include reading and writing aPOSCAR file, reading and writing a generic vector file, doing dot products and finding magnitudes of vectors and other similar functions

vef.pl

usage: vef.pl

Prints the force and energy at each iteration of a vasp run.

vfin.pl

usage: vfin.pl(outputdirectory)

This script finds the ICHAIN tag from the OUTCAR and cleans up the run directory accordingly. All relevant files (POSCAR, CONTCAR,OUTCAR (zipped), INCAR, KPOINTS, XDATCAR (zipped), CHGCAR and WAVECAR if the are non-empty) are copied to the output directory.In the run directory CONTCARs are moved over POSCARs in preparation for a new run.

boxset.pl

usage: boxset.pl(POSCAR)(latticeconstant)

output: POSCARwithspecifiedlatticeconstant

posinterp.pl

usage: posinterp.pl(POSCAR1)(POSCAR2)(fraction)

output: POSCAR.outfile,toSTDOUT

pos2rdf.pl

usage: pos2rdf.pl(POSCAR)(atom)(binsize)

output: radialdistributionaroundspecifiedatom,toSTDOUT

neighbors.pl

usage: neighbors.pl(confile)(atom)

output: neighbordistancesfromaspecifiedatom,toSTDOUT

diffcon.pl

usage: diffcon.pl(POSCAR1)(POSCAR2)

output: distancebetweenatoms,scalarandvectorsum,toSTDOUT

dist.pl

usage: dist.pl(POSCAR1)(POSCAR2)

output: rootsumsquareddistancebetweenconfigurationfiles

modemake.pl

usage: modemake.pl(POSCAR1)(POSCAR2)

output: unitvectorbetweenPOSCARfiles,toMODECARfile

pos2con.pl

usage: pos2con.pl(POSCARorconfile)

output: conorPOSCARfile(respectively)

xdat2pos.pl

usage: xdat2pos.pl(StepnumberinXDATCARtobeturnedintoPOSCAR)

output: POSCARfile

xdat2xyz.pl

usage: xdat2xyz.pl(XDATCARfile)

output: xyzmoviefile(playableinjmol)

con2xyz.pl

usage: con2xyz.pl(confile)

output: xyzfile

xdat2vdat.pl

usage: xdat2vdat.pl(XDATCARandOUTCAR)VASP5.2ONLY

output: velocityusingforwarddifferencemethodtoVDATCARfile

nebmake.pl

usage: nebmake.pl(POSCAR1)(POSCAR2)(numberofimages,NI)

output: directories[00,NI+1]containinginitialNEBPOSCARfiles

Takes initial and final POSCAR files, and linearly interpolates the specified number of images between them. The interpolated files arewritten to the directories 00 to NI+1, where NI is the number of specified images.

neb2dim.pl

usage: neb2dim.plorneb2dim.pl(numberofanimage)

output: directorysaddle_dimercontainingfilesfordimerrun

Sets up a dimer run from a NEB run. It is assumed that the configuration is contained in POSCARs, i.e. vfin.pl has been run. If no inputargument is given then the dimer is formed by interpolation around the highest point in the exts.dat file. Otherwise it is formed around theinput image. Curvature data from the MEP is used for the initial orientation of the DIMER.

neb2lan.pl

usage: neb2lan.plorneb2lan.pl(numberofanimage)

output: directorysaddle_lanczoscontainingfilesforlanczosrun

Sets up a lanczos run from a NEB run. It is assumed that the configuration is contained in POSCARs, i.e. vfin.pl has been run. If no inputargument is given then the run is set up by interpolation around the highest point in the exts.dat file. Otherwise it is set up around theinput image. Curvature data from the MEP is used for the initial MODECAR.

nebef.pl

usage: nebef.pl

output: energyandforceofimagesintheneb

nebbarrier.pl

usage: nebbarrier.pl

output: energy,distance,andforcesalongtheneb

Generates the file neb.dat which contains the distance between images, the energy of each image, and the force along the band. This data isused by nebspline.pl to generate a force-based cubic spline along the band.

nebspline.pl

usage: nebspline.pl

output: spline.dat,exts.dat,mep.eps

Reads the file neb.dat and creates the files spline.dat,exts.dat and mep.eps. spline.dat is a set of points that describe the spline fitted tothe data in the neb.dat while exts.dat contains the location and energy of all extrema found along the curve and mep.eps is a plot of the MEPpath.

nebmovie.pl

usage: nebmovie.pl(flag)

output: movie.xyz

Can be used to generate a movie from standard xyz files, generated either by POSCARs (flag=0) or CONTCARs (flag=1) in every directory.

nebconverge.pl

usage: nebconverge.pl

output: directory(vaspgr)withplotsofenergyandforces

Can be used to monitor convergence for each image while the job is still running.

nebresults.pl

usage: nebresults.pl

output: spline.dat,neb.dat,exts.dat,mep.eps,movie.xyz,vaspgr

After a run has finished and wrapped up with vfin.pl, the nebresults.pl can be used to run nebef.pl, nebspline.pl, nebmovie.pl andnebconverge.pl automatically.

nebfreeze.pl

usage: nebfreeze.pl(atom)(listofPOSCARfiles)

output: POSCARfiles,tooriginalfiles

Takes an atom number and a list of POSCAR files and then freezes that atom, as well as shifting the contents of each POSCAR file so that thatatom has the same position in each cell. This is useful if you need to give all POSCARs in a NEB calculation the same frozen point.

nebavoid.pl

usage: nebavoid.pldistance

output: POSCARfiles,tooriginalfiles

If atoms are closer than the specified distance, the script pushes these atoms apart. The new geometry is written in the POSCAR file, and theold saved as POSCAR_orig.

Warning: this script does not give a set of equally spaced images.

chgavg.pl

usage: chgavg.plCHGCAR1CHGCAR2

output: CHGCAR_avg

Generates an average CHGCAR.

chgsum.pl

usage: chgsum.pl(CHGCAR1)(CHGCAR2)(fact1)(fact2)

output: CHGCAR_sum

The values in CHGCAR_sum are (CHGCAR1*fact1+CHGCAR2+fact2). By default, fact1=fact2=1.0, so that the output is the sum of the input chargedensity files

chgdiff.pl

usage: chgdiff.pl(CHGCAR1)(CHGCAR2)

output: CHGCAR_diff

Generates a CHGCAR difference.

chgparavg.pl

usage: chgparavg.plPARCHG1PARCHG2

output: PARCHG_avg

Generates an average PARCHG.

chg2cube.pl

usage: chg2cube.plCHGCAR

output: CHGCAR.cube

Converts a CHGCAR file to the CUBE format.

dimplot.pl

usage: dimplot.pl

output: force.eps,energy.eps,curvature.eps

Generates simple figures from the out.dat file to monitor the behavior of a dimer run.

diminit.pl

usage: diminit.pl(DIRornumber)usage: diminit.pl(DisplaceAlgo)(DisplaceRange)(Rcut)usage: diminit.pl(MaxCord)(POSCAR)(DISPLACECAR_sp)

output: DIRorprXXXXcontainingfilesfordimerruns

Generates an initialized dimer run in DIR or the numbered directories prXXXX, from a POSCAR and DISPLACECAR

dimmins.pl

usage: dimmins.pl(POSCAR1)(POSCAR2)(displacement)

output: mins/min1/POSCARmins/min2/POSCAR(andrelatedfiles)

Generates initial configurations which can be minimized from a converged dimer run.

dimmode.pl

usage: dimmmode.pl(CENTCAR)(NEWMODECAR)(numimages)(dist)

output: dimmode.xyz

Generates a movie along the dimer mode.

dymmatrix.pl

usage: dymmatrix.pl(DISPLACECAR)(OUTCAR)

or : dymmatrix.pl(#DISPLACECAR)(DISPLACECAR1)(DISPLACECAR2)..

or : dymmatrix.pl(OUTCAR1)(OUTCAR2)(OUTCAR3)..

output: mass-scaleddynamicalmatrix(freq.mat)

normalmodefrequencies(freq.dat)

eigenvalues(eigs.dat)

andeigenvectors(modes.dat)

Takes the output from the dynamical matrix calculation and creates the matrix. The DISPLACECARs should only contain those degrees of freedomthat were calculated in their corresponding OUTCARs (see dymcmpdisp.pl). The scripts now handles the diagonalization itself via package fromCPAN. (It could be a bit slow for large matrices).

dymeffbar.pl

usage: dymeffbar.pl(initialtemperature)(finaltemperature)

(saddlepointenergy)(filewithinitialstatefrequencies)

(filewithsaddlepointfrequencies)

output: eff_ea.dat,afilecontaining:

(temperature)(1000/temperature)

(classicalenergybarrier)

(zeropointenergycorrectedenergybarrier)

(quantumbarrierwithzeropointandtunneling)

dymzpbar.pl

usage: dymzpbar.pl(omegasquaredfile[eigs.dat])

output: thezeropointenergyineVtotheSTDOUT

This script sums up the zero point energy contribution from the stable modes.

dymseldsp.pl

usage: dymseldsp.pl(POSCAR1)(POSCAR2)(atomstoinclude)(displacement)

output: DISPLACECARfile,toSTDOUT

Takes as input two POSCAR files, n, the number of atoms to include, and the displacement. It then finds the n atoms that have the largestdisplacement between the two POSCAR files. Ncr personal scanner driver for mac. The file DISPLACECAR is created, which contains the displacements of each degree of freedom (zero,unless the atom is one of the n atoms, in which case it is the entered displacement). This file is ready to use, then, with the dynamicalmatrix routine.

dymselsph.pl

Medieval total war mac download. usage: dymselsph.pl(POSCAR)(Centralatom)(radius)(displacement)

output: DISPLACECARfile,toSTDOUT

Similar to dymseldsp.pl, except it only takes one POSCAR and also needs an atom number as input. It then finds the n atoms closest to thechosen atom and these are the atoms given non-zero displacements in the DISPLACECAR file.

dymcmpdisp.pl

usage: dymcmpdisp.pl(DISPLACECAR1)(DISPLACECAR2)

output: DISPLACECARfile,toSTDOUT

Takes as input two DISPLACECAR files, compares them, and outputs a DISPLACECAR file in which those degrees of freedom that are set in oneDISPLACECAR but not the other. Thus, if you use dymseldsp.pl to create a DISPLACECAR with 24 degrees of freedom, and then you want to calculatethen next 12 degrees of freedom, you would dymseldsp.pl for 36 degrees of freedom and use compare_disp.pl to extract those 12 which aren’tincluded in the first DISPLACECAR. You can then run the dynamical matrix calculation on this new file, getting the forces for these 12 newdisplacements, and then use dymmatrix.pl to combine the OUTCARs from both calculations into one matrix.

dymfit.pl

usage: dymfit.pl(orderoffit)(displacement1)(matrix1)(displacement2)(matrix2)..

output: dynamicalmatrix,toSTDOUT

Used to fit between two or more matrices together. It takes as input the order of the fit, and then pairs of displacements and matrices. Itoutputs a matrix of the same order. It requires the Perl modules Math::Matrix and Math::Approx.

dymextract.pl

usage: dymextract.pl(DISPLACECARofmatrixyouhave)(DISPLACECARofmatrixyouwant)(matrixyouhave)

output: dynamicalmatrix,toSTDOUT

Used to create a smaller dynamical matrix from a larger one. If you calculated many degrees of freedom the first time and want to check howthe quantity converges versus degrees of freedom, use this to create the smaller matrix. You need the DISPLACECAR for the matrix you have andthe DISPLACECAR for the matrix you want.

dymreorder.pl

usage: dymreorder.pl(numberofDISPLACECARswithdesiredorder)(listofDISPLACECARs)(numberofDISPLACECARsofcurrentorder)(listofDISPLACECARs)(currentmatrix)

output: dynamical matrix, to STDOUT

Reorders a dynamical matrix. You might want to use this if you plan on fitting matrices, but you got at them different ways (for example, oneyou had by doing all of the degrees of freedom at once and the second you created by doing degrees of freedom a bit at a time… the orderingof the displacements in each matrix will be different). You need the series of DISPLACECARs that were used to create each matrix.

dymprefactor.pl

usage: dymprefactor.pl(freq.datofminimum)(freq.datoftransitionstate)

output: prefactorinunitsofinversecm

dymanalyze.pl

usage: dymanalyze.pl(flag)(modevalue)(displacement1)(matrix1)(displacement2)(matrix2)..

output: informationontheagreementbetweenthefitsandtheoriginalmatrices Convert dae to software for mac.

Intended to help analyze the convergence of the dynamical matrices and compare the differences both between different displacements as well asdifferent orders of fits. It takes as input pairs of displacements and their corresponding matrix. The first argument is a flag. If it is zero,then a fit is done with each successive matrix added to the points used to determine the fit. The output tells how much the force constantschange as each point is added to the fit. If the flag is greater than zero, then a fit is done with the first n, where flag equals n, matrices,and the difference between the force constants calculated for the other matrices and the fitted matrices is printed. The analysis is done forany modes which have a frequency larger than modevalue.

dymmodes2xyz.pl

usage: dymmodes2xyz.plPOSCARDISPLACECARmodes.dat(moviefolder)(freq.dat)(numimages)(dist)

output: moviesforeachnormalmode

Takes the configuration file (POSCAR), displacement file (DISPLACECAR) and modes file (modes.dat), which is created by running dymmatrix.pl,and creates a movie for each mode. These xyz movies are saved in the moviefolder (if designated) or the current directory. The frequency ofeach mode will be written to the xyz files if the freq.dat file is provided. The numimages variable sets the number of frames in each modemovie and the dist variable sets the vibrational amplitude.

Note: if the modes.dat is created by using serveral DISPLACECARs as indicated in dymmatrix.pl, use the concatenated DISPLACECAR file in thisscript (i.e., cat those DISPLACECAR files in the same order as they were used in dymmatrix.pl).

split_dos

usage: split_dos

output: DOS0,DOS1,DOS2,.,DOSN

Split the DOSCAR file into atomic DOS files, (DOS1, DOS2,.,DOSN). The DOSCAR and OUTCAR in the working directory will be used.This bash script was written for LORBIT =10 and = 11 calculations as well as spin (un)restricted. The energy will be referenced to the fermienergy specified in the OUTCAR, (E-Ef).

dosanalyze.pl

usage: dosanalyze.pl[w=numwidthatquarter-height][e=emin,emax]

output: centerofthespecifiedbandforselectedatomsbasedonaweightedaverage,toSTDOUT

This script sums up the atomic projected DOS over some group of atoms, and then calculates the center of the specific band using a weightedaverage. The default is set to calcualted the center for the whole band. However, it can also consider DOS within a user specified range byusing the optional “w=” or “e=” flag.

By using “e=emin,emax” flag, only the states in ranger [emin,emax] are considered.

By using “w=” flag, the script finds a half width for the band at half the max height and, based on the number following w= , calculates aweighted average within the limits of that many half widths at half height from the center. In this manner, a band center may be found byweighted average without including noncontributing states.

If no orbital flag is specified, the script analyzes the d-band. If no atom is selected, it analyzes all of them. If no w= tag specified, thecenter is calculated between 2.5 half widths at half height

Note: the split_dos script should be run first to get the resulting new files labeled as DOS1, DOS2, …, DOSN,where N is the number ofatoms in the unit cell.

doslplot.pl

usage: doslplot.pl

output: ldosplot.eps

The eps file has DOS plot for each of selected atoms (blue lines), and the DOS plot for the all system (red line). If no orbital flag, plotthe d-band.If no atom is selected, plot all of them.

Note: Only LORBIT=11 and up to s,p,d bands can be handled with this script.