[转载] 科学无国界:关于VASP常用代码分享

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VASP代码讨论论坛
http://theory.cm.utexas.edu/forum/
VASP有用的代码分享:
http://theory.cm.utexas.edu/vtsttools/index.html
https://notendur.hi.is//~hj/indexE.html
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Graeme Henkelman
Research
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Hannes Jónsson: Research area
More general description of the research area.
A. Methods for calculating rates and long time scale dynamics
The group has developed several methods for calculating rates of
slow transitions, such as chemical reactions and diffusion. The
methods are based on transition state theory (TST), with or without
the harmonic approximation.
B. Density functional theory calculations The group mainly uses
plane wave based DFT to calculate the interaction between atoms in
condensed systems. While a parallel DFT program was developed in the group in
the early 90s, the rapid development of the methodology and
maturity of the field has made it more practical to adopt some of
the sophisticated packages now available such as the
代码下载页面:
http://theory.cm.utexas.edu/vtsttools/download.html
Transition State Tools for VASP¶
This is not the official VASP web page. Designed to simulate the properties of systems at the atomic scale, VASP (Vienna Ab-initio Simulation Package) is a software package created, distributed, and maintained by the Hafner Research Group at the University of Vienna.
This page contains source code and scripts for finding saddle points and evaluating transition state theory (TST) rate constants with VASP.
Three saddle point finding methods and a couple other tools have been implemented to work with the VASP code. These methods are the
-
Nudged Elastic Band: method for finding reaction pathways between two stable states.
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Dimer: method for finding reaction pathways when only one state is known.
-
Lanczos: provides an alternative way to find the lowest mode and find saddle points.
-
Optimizers: provides an alternative way to find the lowest mode and find saddle points.
-
Dynamical Matrix: uses finite difference to find normal modes and reaction prefactors.
The code on this site was written
by several people who were in or associated with
the
We have a discussion forum to address issues related to the code and scripts
Scripts简介页面:
http://theory.cm.utexas.edu/vtsttools/scripts.html#id2
The following are a set of scripts to perform common tasks to help with VASP calculations, and particularly with transition state finding. The included Vasp.pm perl module contains several simple routines that are used by many of the scripts.
Download the scripts: `vtstscripts.tgz`_
Install by uncompressing this file, and adding the vtstscripts directory to your path.
The scripts are organized into the following categories (portals to them are on the left):
-
general
-
file conversion
-
nudged elastic band
-
dynamical matrix
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dimer
-
charge density
-
density of states
Notes:
-
We recommend that the first line in the POSCAR file contain the element symbols, in the same order as they appear in the POTCAR. This will allow for proper visualization when files are converted to xyz files.
-
For NEB scripts, there needs to be OUTCAR files for the initial and final states placed in the 00 and NI+1, respectively. Please direct questions about these scripts to the discussion `forum`_.
Scripts | Usage/Description |
---|---|
Vasp.pm | Perl module that contains various common commands that one might want when deal with VASP POSCAR files. These include reading and writing a POSCAR 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 |
Scripts | Usage/Description |
---|---|
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 |
Scripts | Usage/Description |
---|---|
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 are written 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 input argument is given then the dimer is formed by interpolation around the highest point in the exts.dat file. Otherwise it is formed around the input 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 input argument 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 the input 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 is used 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 to the 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 MEP path. | |
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 and nebconverge.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 that atom 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 the old saved as POSCAR_orig. | |
Warning: this script does not give a set of equally spaced images. |
Scripts | Usage/Description |
---|---|
gavg.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 charge density 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. |
Scripts | Usage/Description |
---|---|
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. |
Scripts | Usage/Description |
---|---|
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 freedom that were calculated in their corresponding OUTCARs (see dymcmpdisp.pl). The scripts now handles the diagonalization itself via package from CPAN. (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 largest displacement between the two POSCAR files. 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 dynamical matrix routine. | |
dymselsph.pl | 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 the chosen 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 one DISPLACECAR but not the other. Thus, if you use dymseldsp.pl to create a DISPLACECAR with 24 degrees of freedom, and then you want to calculate then 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’t included in the first DISPLACECAR. You can then run the dynamical matrix calculation on this new file, getting the forces for these 12 new displacements, 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. It outputs 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 how the quantity converges versus degrees of freedom, use this to create the smaller matrix. You need the DISPLACECAR for the matrix you have and the 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, one you 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 ordering of 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: informationontheagreementbetweenthe |
|
Intended to help analyze the convergence of the dynamical matrices and compare the differences both between different displacements as well as different 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 constants change 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 for any 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 of each 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 mode movie 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 this script (i.e., cat those DISPLACECAR files in the same order as they were used in dymmatrix.pl). |
Scripts | Usage/Description |
---|---|
split_dos | usage:
|
output: DOS0,DOS1,DOS2,..,DOSN | |
Split the DOSCAR file into atomic
DOS files, (DOS1, DOS2,..,DOSN). |
|
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 weighted average. The default is set to calcualted the center for the whole band. However, it can also consider DOS within a user specified range by using 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 a weighted average within the limits of that many half widths at half height from the center. In this manner, a band center may be found by weighted 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, the center 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 of atoms 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). |
|
Note: Only LORBIT=11 and up to s,p,d bands can be handled with this script. |
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