VASPKIT-VASP Software pre-Post-

processing tools introduced

Introduction 1. VASPKIT
VASP Full name Vienna Ab initio Simulation Package, Is the University of ViennaHafnerPanel
developed electronic structure calculations and quantum mechanics-Molecular dynamics
simulation software package. It is one of the materials simulation and computational materials
science in popular commercial software. versus
Material Studio Software package CASTEP Similar functions, but VASP The accuracy is relatively
higher. Different from CASTEP Graphical interface, VASP No interface is a calculation software,
modeling, visualization, data analysis tools such as the need to rely on third parties P4VASP,
ASE, Pymatgen, VESTA Software. VESTA, P4VASP. It is mainly used for modeling, visualization and
analysis of partial data. And ASE, Pymatgen These software specializes in data processing, but the
installation is too much trouble, while relatively high barriers to entry, the user needs to have a
certain level of programming. VASPA wide distribution of subjects the user has to do catalysis,
optics had done, the material has to do, the data is handled very different fields. Many users to
develop and contribute their own areas where the use of scripts or applets, himself developed a
structure to handle files POSCAR tookit script. But for new users to find and successfully used these
scripts are not easy. So a easy to use, powerful pre Data Post-Processing Software vaspkit It came
into being.
The new version ofvaspkit Wang Wei teacher, Xu Nan, Liu Jincheng, Tang Gang, Li Qiang and
Leping joint effort. vaspkit 0.71Recent
Done a lot of menu adjustment, similar to the function are classified, optimizing some existing
features and adds a number of functions related to the catalytic
can. VASPKIT release Is a version with FORTRAN Written in the LINUX Binary software running
environment. It almost does not depend on other libraries, software volume only4.5MNo
installation needed to use, at the same time EXAMPLES Here are the main examples directory test
function, user-friendly learning to use.

The main features are:[Link] generatedVASPCalculate the required necessary

documents, includingINCAR,POTCAR,POSCAREtc., and check its format [Link] structural
symmetry [Link] tool, according to the number of layers or the height of a fixed interval
atom. [Link] a band path crystals (including functional hybrid), and data processing
can take [Link] DensityDOSAnd a projection density of statesPDOS [Link] charge
density, electrostatic potential, rendering the wave function is a space [Link] features, such
as thermodynamic correction amount (the adsorbate molecules and vapor molecules), optics,
molecular dynamics, the conductivity of semiconductors, and small tools.

0.71Version fixesBUGs

Fixed a bug in finding the suggested KPath for 2D oblique Bravais lattice thanks to iGo;

Fixed a bug in generating [Link] file thanks to [Link]@THU

2. VASPKIT configuration and usage
vaspkit It is a runLINUXSoftware in an environment, in order to ensure that the use of vaspkit. The
full functionality. Users can configure vaspkit. The environment directory, to take effect the next
run time. By bash Terminal run the following command to copy the file to the user environment
variable directory.

\ Cp -f how_to_set_environment_variable ~ / .vaspkit

And edit .vaspkit file

vi ~ / .vaspkit

The configuration file is used to setv aspkit Environment variables, Include VASP Version
information, directory pseudopotential library, functional method of selection, and choose
whether to follow VASP The official recommendation generation elements pseudopotential files,
settings generated INCAR Templates are covered, additional or backup of the original
INCAR.

# Cp how_to_set_environment_variable ~ / .vaspkit and modify the ~ / .vaspkit file based on your

settings!

[Link]. #.TRUE. or .FALSE.; [Link]. if you are using vasp.4.x

GGA_PATH '~ / POTCAR / GGA' # Path of GGA potential.

PBE_PATH '~ / POTCAR / PBE' # Path of PBE potential.
LDA_PATH '~ / POTCAR / LDA' # Path of LDA potential.
POTCAR_TYPE PBE # PBE, GGA or LDA; GW_POTCAR.FALSE. #.TRUE. or .FALSE.;

RECOMMENDED_POTCAR.TRUE. #.TRUE. or .FALSE.;

SET_FERMI_ENERGY_ZERO.TRUE. #.TRUE. or .FALSE.;
SET_INCAR_WRITE_MODE OVERRIDE # OVERRIDE, APPEND, BACK-UP-OLD, BAC K-UP-NEW;

Set up POTCAR After completion of the catalog and some other settings, you can start vaspkit A.
For convenience, you can vaspkit The absolute path is added to the environment variable, if it is
LINUX The user can do this:

echo 'Export PATH = $ PATH: /home/vaspkit.0.71/bin/' >> ~ / .bashrc source ~ /

.Bashrc

among them/home/vaspkit.0.71/bin/With their own vaspkit Executable file bin Absolute path to the
directory instead.
Directly input terminal vaspkit or/home/vaspkit.0.71/bin/vaspkit start operation vaspkit program. Not
surprisingly,
You will get a show with my consistent interface:
 + ------------------------------------------------- -------------- + | VASPKIT Version:

0.71 (16 Nov. 2018) | | Developed by Vei WANG (wangvei@[Link]) |

| Contributor: Nan XU (tamas@[Link]) |

| A Pre- and Post-Processing Program for VASP Code |
| Official Website: [Link] |
+ ------------------------------------------------- -------------- + =====================

Structural Options ========================

1) VASP Input Files Generator 2) Elastic-Properties Toolkit

3) K-Path Generator 4) Structure Toolkit
5) Catalysis-ElectroChem Kit6) Symmetry Toolkit

===================== Electronic Options ========================

11) Total Density-of-States 12) Projected Density-of-States
twenty one) Band-Structure twenty two) Projected Band-Structure
twenty three) 3D Band-Structure 25) Hybrid-DFT Band-Structure
26) Fermi-Surface Calculator

=========== Charge & Potential & Wavefunction Options ===========

31) Charge Density 32) Spin Density
33) Spin-Up & -Down Density 34) Charge-Density Difference
41) Planar-Average Charge-Density 42) Planar-Average Potential
51) Real-Space WaveFunction Plot
====================== Misc Utilities ========================== =
71) Linear Optics 72) Molecular-Dynamics Toolkit73) VASP2BoltzTraP

Interface

91) Semiconductor Calculator 92) 2D-Materials Toolkit

0) Quit
------------ >>

If the following problems, Explain your LINUX Run dependent library version is too low, you need
to upgrade (not recommended), you can contact the developer in a low version LINUX Under the
compiled version of the environment.

vaspkit: /lib64/[Link].6: version `GLIBC_2.14'Not found (required by vaspkit)

If the-bash: line 7: ./vaspkit: Permission denied Permissions problem, simply giving vaspkit Execute
permissions to:

chmod u + x /home/vaspkit.0.71/bin/vaspkit

vaspkit Currently only supports command line batch operations, by vaspkit –h Get help.
3. VASPKIT child Features
This tutorial covers the use of vaspki generate VASP The input file, usePBE with HSE06 Band
calculation, the correction thermodynamic quantities, and generates a differential charge density,
band calculation includes two common examples of the use of a hybrid functional and functional,
while the main thermodynamic correction amount calculating zero-point vibrational energy and
thermal energy and enthalpy contribution to the free .

3.1 VASP generation and checking input files

In order to successfully runVASPComputing tasks, we need at least 4
Files: INCAR, POSCAR, POTCAR and KPOINTS,
INCAR I am told VASP What kind of task, how to count the control file; POSCAR Lattice containing
information, the information and the atomic coordinates of atoms speed information (MDA)
documents;POTCARIs pseudopotential file, which is expressed in the inner electron potential
function; KPOINTS (Can be included in
INCAR Inside, not recommended omitted) contains reciprocal space KPoint information, the wave
function obtained by integrating the charge density at these points.
vaspkit 0.71Version will KPoint generation, POTCAR Generation and INCAR Generating integrated

into the function1: VASP Input Files

Generator in.

==================== VASP Input Files Options ===================

101) Customize INCAR File

102) Generate KPOINTS File for SCF Calculation

103) Generate POTCAR File with Default Setting
104) Generate POTCAR File with User Specified Potential
107) Reformat POSCAR File by Specified Order of Elements
108) Successive Procedure to Generate VASP Files and Check 109) Check All VASP Files

The following shows how to use vaspkit Conducted a VASP Computing tasks.
POSCAR Or generated by the software are generally obtained from the database, the system can
simply build their own. In the present embodiment from the database
([Link] Obtained wurtzite ZnO of POSCAR File (you can also download CIF
File, and then VTST script [Link] VESTA Converted to POSCAR File, only a matter of atomic
positions occupied by scores of note). In catalysthub Retrieves ZnO, As shown in the search result.
Wurtzite ZnO The hexagonal system, space groupP63mc. So next
The second line of the carrier POSCAR Download the file named [Link]. Place
vaspkit.0.71 / examples / ZnO_optimization Under contents.

The following shows the results (4) for: ZnO

Full formula Space group HM HALL Lattice system Band gap Structure f ile

Zn1O1 216 F-43m F -4 2 3 Cubic 0.63110 eV CIF | POSCAR | LAMMPS

Zn2O2 186 P63mc P 6c -2c Hexagonal 0.73170 eV CIF | POSCAR | LAMMPS

Zn1O1 225 Fm-3m -F 4 2 3 Cubic 0.71940 eV CIF | POSCAR | LAMMPS Zn1O1 221 Pm-
3m -P 4 2 3 Cubic 0.00000 eV CIF | POSCAR | LAMMPS
Next reasonably be optimized lattice structure. Will be renamedPOSCARfile.

\ Cp -f [Link] POSCAR

We use vaspkit default INCARc ombination Generate the required INCAR file. In There POSCAR The
directory run vaspkit, Entry 1 Select function VASP Input Files Generator And then enter 101 select
Customize INCAR File You will get to
Display information under:
+ -------------------------- Warm Tips --------------------- ----- +
You MUST Know What You Are Doing
Some Parameters in INCAR File Neet To Be Set/ Adjusted Manually
+ ------------------------------------------------- -------------- +
======================== INCAR Options ======================== ==
ST) Static-Calculation SR) Standard Relaxation MG) Magnetic Properties SO)

Spin-Orbit Coupling

D3) DFT-D3 no-damping Correction H6) HSE06 Calculation

PU) DFT + U Calculation MD) Molecular Dynamics GW) GW0 Calculation

BS) BSE Calculation

DC) Elastic Constant EL) ELF Calculation

BD) Bader Charge Analysis OP) Optical Properties
EC) Static Dielectric Constant PC) Decomposed Charge Density
FD) Phonon-Finite-Displacement DT) Phonon-DFPT
NE) Nudged Elastic Band (NEB) DM) The Dimer Method
FQ) Frequence Calculations LR) Lattice Relaxation

0) Quit
9) Back
------------ >>
Input Key-Parameters (STH6D2 means HSE06-D2 Static-Calcualtion) LR
Entry LR, You'll get a good pre-lattice relaxation for doing the task INCAR(Some templates need to
manually modify. such as DFT + U of U Value is set, NEB of IMAGES Number, etc.). If you already
have INCAR File, the original INCAR The file will be overwritten. You can edit~ / .Vaspkit change
INCAR The write settings. Just after row SET_INCAR_WRITE_MODE From the default OVERRIDE change
to APPEND, BACK-UP-OLD, BACK-UP-NEW One, corresponding to a new content added to the initial
INCAR Later, the original backup INCAR And then write the new INCAR And written to the new
INCAR .new inside. The next generation KPOINTS file. For non-band calculation mode, simply
sprinkle automatically, but requires the user to select the point spread mode and
KDot density. Li Qiang, the specific content can refer to the tutorial Learn VASP The Hard Way(Ex1):
VASP Prepare basic input file. start up vaspkit,Entry 1 Select function VASP Input Files Generator And

then enter 102 Select function Generate KPOINTS File for SCF Calculation, Then enter 2 select Gamma
Scheme Sprinkle way (safe choice), will
Get the following information is displayed:
 ->> (1) Reading Lattices & Atomic-Positions from POSCAR File ...
+ -------------------------- Warm Tips --------------------- ----- +
* Accuracy Levels: (1) Low: 0.06 ~ 0.04;
(2) Medium: 0.04 ~ 0.03;
(3) Fine: 0.02-0.01.
(4) Gamma-Only: 0. * 0.04 is Generally Precise Enough!

+ ------------------------------------------------- -------------- +
Input KP-Resolved Value (unit: 2 * PI / Angstrom):
------------>>

Follow the prompts0.04Accurate enough, so input0.04, You will have to get in the current directory
KPOINTS with POTCAR (Automatic generated)file.

->> (2) Written KPOINTS File!

->> (3) Written POTCAR File with the Recommended Potential!

KPOINTS It reads as follows:

K-Mesh Generated with KP-Resolved Value : 0.040 0

Gamma

995

0.0 0.0 0.0

Learn VASP The Hard Way Ex19 Who stole my time machine is? (three)He referred to a simpleKThe
number of point criterion, the semiconductorkDot number corresponding to the real space vector
is larger than the grain20Å(Refer to the diagram), the present embodimentka = 29.62ÅIt has been
in line with empirical laws. Liu Jincheng mentioned for non-orthogonal system , And the length of
reciprocal lattice vectors crystal constant inverse relationship is not satisfied, so the use
ofka≈kb≈kcThe rule of thumb does not guarantee Kpoint
Density of equal length in all Strict calculated the proportion fell lattice vector Depending on the
KDot density
directions. is automatically
and [Link], so use selected will be
generated in all directions

generateKPOINTSAt the same time, based onPOSCARThe pseudopotential element type extracted from
the library and combined to generatePOTCAR, Provided that you~ / .VaspkitIt was set up
correctlyPBE_PATHPath, and in accordance withPOTCAR_TYPESelect is generatedGGAPW91,LDAstill
isPBEPseudopotential. It is noteworthy that messageWritten POTCAR File with the Recommended
Potential!,meanvaspkitaccording toVASPRecommendations from official websitePBEThe pseudopotential

library select
Pseudopotentials[Link]
g_vasp_5_2.html.
PBEThe pseudopotential divided into several, no suffix,_pv, _sv, _dAnd numeric suffix,_pv, _sv,
_dThat issemicoreofp, sordAlso be used as the valence process. Because in some cases, once the
outer electrons are also involved in bonding. Liu Jincheng be mentionedBaderAnalysis of charge,
with a need
_pv, _svPseudopotential. Special mention official websiteImportant Note: If dimers with short bonds
are present in the compound (O2, CO, N2, F2, P2, S2, Cl2), we recommend to use the _h potentials
Specifically, C_h, O_h, N_h, F_h, P_h, S_h. , Cl_h.Common practice is to: measure in two pseudopotential
Try influence the situation on the issues they care. Under little effect, the free choice of suffix
pseudopotential, containing more valence electrons after truncation can rise much, the amount of
calculation is increased significantly.

If you need to manually generatePOTCAR, For example, the passivationHSelectionH.5The

pseudo-potential, can function104Pseudopotential manually select the type of each element.
This example demonstrates aZnselectZn_pvofPBEPseudopotential. Select function104In turn
enter the required set of pseudo-potential typeOwithZn_pv.

- >> Reading Structural Parameters from POSCAR File (1) ...

Auto detected POTCAR_TYPE is O, please type the one you want!

Auto detected POTCAR_TYPE is Zn, please type the one you want!

Zn_pv

- >> (2) Written POTCAR File with user specified Potential!

By commandgrep TIT POTCARcan be seenPOTCARThe pseudopotential isOwithZn_pvTo meet our

needs. In order to achieve meaningful results, we need to meetINCARmiddleENCUTmore than
thePOTCARAll the elementsENMAX. You can view all the elements with the following
commandENMAX:

grep ENMAX POTCAR

You can see the default INCAR Parameters ENCUT = 400eVCommented out, but retained PREC =
Normal, The program will automatically ENCUT Set max (ENMAX). Of course be provided on their
own ENCUT Parameters, as long as all elements of the parameter is larger than ENMAX, This time
to set their own ENCUT Parameters prevail. Note that in the optimization unit cell constants,
needed higher ENCUT (Learn VASP The Hard
Way (Ex36): Direct optimal lattice constant), therefore LR Task (optimized lattice constant)
generated template INCAR The default settings
PREC = High, VASP The program will automatically ENCUT Set max (ENMAX) * 1.3. Leping teacher

mentioned, in order to ensure that the same system

ENCUT Consistent, VASP The new official manual has been deprecated PREC = High, And it is

recommended to PREC = Accurate And manually set ENCUT Value.

Submit VASP Computing task, the task can be found quickly failed. Error log is as follows:

running on 16 total cores

distrk: each k-point on 16 cores, 1 groups distr: one

band on 1 cores, 16 groups using from now: INCAR

vasp.5.4.4.18Apr17-6-g9f103f2a35 (build Apr 07 2018 [Link]) Complex

POSCAR found type information on POSCAR O

ERROR: the type information is not consistent with the number of types

The analysis revealed that, VASPA read-only O Elements and pseudopotential, Zn Not from
POSCAR Read out, and therefore error. The reason is that downloading from a database
POSCAR The spaces in the separator is a tab\ T, VASP Can not be read out correctly \ T It
is a string delimiter. The same problem also inINCARAppear. Also in WINDOWS System-
generated POSCAR or INCAR in VASP It may be very strange errors. The most deadly VASP
Does not automatically check POSCAR Whether the element type POTCAR Element types
are the same, that is, you count graphene can also be used H The pseudo-potential, and
does not complain, but the results must be wrong! Therefore vaspkit 0.71 He joined the
correct format and function elements pseudopotential check 109. Entry 109 , vaspkit 0.71
Will automatically INCAR with POSCAR The correct format, and check pseudo-potential
elements consistent.

- >> (1) Reading Structural Parameters from POSCAR File ...

All Files Needed Exist.

Element type in POSCAR may be not corresponding to POTCAR POTCAR: Zn_pv POSCAR: Zn

After performing the examination, submit the job again. At this time, the task has been to run
correctly.

For your convenience, on the advice of Leping teachers, we set the function 108:Successive
procedure to

generate VASP files and check. First set INCAR Before setting KDot density, generating KPOINTS

with
POTCAR, Then call the function 109 Automatically check all files problems. our target is, VASP
Before first KIT a bit.

3.2 Calculation of Energy Band

Band calculation of KPOINTS And general computing KPOINTS Not the same, typically requires
one or several of the first Brillouin zone of high symmetry Point Road
Diameter calculated band nature. The traditional approach is through See KPath
website([Link]
By Material Studio Software to obtain crystals of high pour point symmetry reciprocal space of the
first Brillouin zone, then the script by generating an interpolation point of the path on the high
symmetryKPoint, satisfied requirements of theKPOINTS. The good news is the new version of
vaspkit Integration with See Kpath Consistent high symmetry point algorithm analysis crystal can
easily generatePBEFunctional andHSE06Hybrid functional requiredKPOINTS, Does not currently
support triclinic.
In vaspkit.0.71 / examples / hybrid_DFT_band There is a directory useHSE06Examples of Functional
calculated band structure of the hybrid gallium phosphide. The same can also be used PBE
Functional calculated band structure of gallium phosphide, just plainPBEFunctional
underestimates the band gap. In order to calculate one or several bands, you must first obtain a
crystal of the first Brillouin zone of high symmetry point path. In TherePOSCARThe directory
transport
Row vaspkit, Entry 3 Select function Band-Path Generator Next input interface 3 select 3D bulk
structure (Experimental) You will get the following message:

+-------------------------- Warm Tips ---------------------- ---- +

See An Example in vaspkit / examples / seek_kpath.

This Feature Is Experimental & Check Your System using SeeK-Path.

For More details See [[Link]/work/ Tools / seekpath]. +-----------------------------------

--------------- ------------- +

- >> Reading Structural Parameters from POSCAR File (1) ...

+-------------------------- Summary ----------------------- ----- +

Prototype: AB

Total Atoms in Input Cell: 2

Lattice Constants in Input Cell: 3.854 3.854 3.854 Lattice Angles in Input Cell: 60.000 60.000
60.000

Total Atoms in Primitive Cell: 2

Lattice Constants in Primitive Cell: 3.854 3.854 3.854

Lattice Angles in Primitive Cell: 60.000 60.000 60.000

 Crystal System: Cubic
Crystal Class: -43m
Bravais Lattice: cF
Extended Bravais Lattice: cF2 Space

Group: 216

Point Group: 31 [Td]

International: F-43m
Symmetry Operations: twenty four
Suggested K-Path: (Shown in the next line) [GAMMA-XU | K-

GAMMA-LWX]

+-------------------------------------------------- ------------- +
- >> (2) Written [Link] file.
- >> (3) Written [Link] File for Band-Structure Calculation.
- >> (4) Written HIGH_SYMMETRY_POINTS File for Reference.
- >> (5) Written POTCAR File with the Recommended Potential!
+-------------------------------------------------- ------------- +
| * DISCLAIMER * | | CHECK Your Results for Consistency if Necessary | | Bug

Reports and Suggestions for Improvements Are Welcome | | Citation of VASPKIT Is

Not Mandatory BUT Would Be Appreciated | | (. ^ ^) GOOD LUCK (^ ^.) |

+-------------------------------------------------- ------------- +
Vaspkit Analysis of the crystal symmetry and will be suggested to give two band path [GAMMA-XU |

K-GAMMA-LWX], While generating a

Unit cell of the crystal structure of [Link] And generate [Link] band structure
calculation. [Link] The second line shows the number of each interpolation path
subparagraphKThe number of points,If the default values are considered not move, then it may
be considered provided the small. Only in the band for the path primitive cell, The following
command needs to be performed, with the resulting primitive cell As the file structure calculations.

\ Cp -f [Link] POSCAR

The following figure shows the gallium phosphide primitive cell High symmetry and a first position
of the Brillouin zone, the See Kpath Web Site Builder.
PBE functional computing band
PBEFunctional calculated to bring in two steps, the first step in the use of ordinary KPoint Grid
(function102) Self-consistent calculation, start up vaspkit, Entry1select VASP Input Files Generator
And then select108selectSuccessive Procedure to Generate VASP
Files and Check Function, input ST, Generate static self-consistent INCAR And follow the prompts
generated by the self-consistent Kpoint. In the present embodiment
ISMEAR = 0, which is Gaussian Smearing The method, the system may be selected if it is replaced by
a metal ISMEAR = 1. Then callVASPCalculation. Step two:[Link] the high-symmetry points
as the new informationKPOINTSThen reads the chargeCHGCARBand for non-self-consistent
calculation, namely:

\ Cp -f [Link] KPOINTSecho
"ICHARG = 11" >> INCAR

That is, read on further generated CHGCAR And remain unchanged, call VASP Calculation.
After completion of the second step, by the function twenty one From the energy eigenvalues
document read in the band structure. It is worth mentioning that the Fermi level in a self-
consistent calculation should prevail, so if you want to get an accurate Fermi level, the following
command to extract self-consistent operation may be performed after the first stepDOSCARThe
Fermi level to the second step of processing the band data:

echo -e "\ N" $ (Sed -n 6p DOSCAR | awk '{Print $ 4}')> FERMI_LEVEL.in

HSE06 Functional calculated to hybridization with Compared to hybrid functional PBE

Functional and DFT + U Method, in calculating the bandgap great advantage, but HSE06 Hybrid

functional needs

KPOINTS Where weight is not only the right to 0 of KPoint self-consistent calculation, and
demanded the right weight 0 High symmetry points calculated band nature. Thus the process is
quite complicated operation. Restart vaspkit Input 25 Select function Hybrid-DFT Band-Structure
Next input interface 251 select
Generate KPOINTS File for Hybrid Band-Structure Calculation. Then enter 1 select Monkhorst-
Pack Scheme use MP The method of generating a self-consistent with KPoints of the grid and on
the recommendation of input0.04Select denser KPoint density (weight not 0 of K Point) to
generate HSE06 Calculate the required KPOINTS.
Because HSE06 Calculation is very time-consuming, two-step process used in this example to
accelerate the convergence, of course, may skip the first step directlyHSE06Self-consistent. The
first step: Use PBE Functional wave function and the electron density is generated, the second
step: maintain KPOINTS Unchanged, read the wave function get on HSE06
Calculation. Use function Customize INCAR FileThe first step in generating PBE Self-consistent need
INCR. Restart vaspkit, Entry1 select VASP Input Files Generator And then select 101 select Customize
INCAR File Function, input ST, Generate static self-consistent INCAR. In the present embodiment t
ISMEAR = 0, which is Gaussian Smearing The method, the system may be selected if it is replaced by
a metal ISMEAR = 1. transferVASPCalculated to be consistent since the completion of the second
stepHSE06Calculation. Restart vaspkit ,Select function101 Customize INCAR File Function, input STH6
,generate HSE06 Calculate the required INCAR. Call againVASPAfter the calculation, is
completeHSE06The self-consistent calculation. Then use vaspkit Extracting energy band data, and
outputs the coordinate information of the high symmetry points of the energy band diagram. Entry
25 Select function Hybrid-DFT Band-Structure Next input interface 252 select Read Band-Structure for
Hybrid-DFT
Calculation Data processing band. The processing results are shown below
->> (1) Reading Input Parameters From INCAR File ... ->> (2) Reading

Fermi-Level From DOSCAR File ...

->> (3) Reading Energy-Levels From EIGENVAL File ...

->> (4) Reading Lattices & Atomic-Positions from POSCAR File ...
->> (5) Reading K-Paths From [Link] File ...
->> (6) Written [Link] File!
->> (7) Written [Link] File!
->> (8) Written [Link] File!
->> (9) Written KLABELS File!
[Link] It is modified to generate an energy band information (0.70Generation
version of a problem, Band. Datnormal !0.71 Version has been fixed. ), Format is shown below, the
first column is KPATH Adjacent point distance is the distance down the high symmetry space,
second column, third row and so is the required energy with different lines. If the spin open, the
second and third row as the band1ofspin up with spin down And so on. Will dat File into Origin The
software, can obtain an energy band diagram.

# Kpath Energy-Level (in eV)

0.00000 -14.54063 -0.82009 -0.82009

0.12809 -14.48597 -1.24459 -0.97903 0.25617 -14.32291 -

2.13627 -1.37615 0.38426 -14.05442 -3.15793 -1.87258
0.51234 -13.68641 -4.20790 -2.37100 0.64043 -13.22973 -
5.24586 -2.81765 0.76851 -12.70500 -6.23748 -3.18362
0.89660 -12.15541 -7.12954 -3.45312

KLABELS It is generated by the reading sub-band identification module. By reading [Link] (PBE
Energy is calculated withKPOINTS) After high symmetry point identification, writing KLABELS file.
[Link] Document reads as follows:
 Generated by VASPKIT based on Hinuma et al.'S Paper, Comp. Mat. Sci. 128, 140
(2017), DOI: 10.1016/[Link].2016.10.015.
10
Line-Mode
Reciprocal
0.0000000000 0.0000000000 0.0000000000 GAMMA
0.5000000000 0.0000000000 0.5000000000 X

0.5000000000 0.0000000000 0.5000000000 X

0.6250000000 0.2500000000 0.6250000000 U

0.3750000000 0.3750000000 0.7500000000 K

0.0000000000 0.0000000000 0.0000000000 GAMMA

0.0000000000 0.0000000000 0.0000000000 GAMMA

0.5000000000 0.5000000000 0.5000000000 L

0.5000000000 0.5000000000 0.5000000000 L

0.5000000000 0.2500000000 0.7500000000 W

0.5000000000 0.2500000000 0.7500000000 W

0.5000000000 0.0000000000 0.5000000000 X

KLABELS File as follows:

K-Label K-Coordinate in band-structure plots

GAMMA 0.000

X 1.153

U|K 1.560

GAMMA 2.783

L 3.781

W 4.597

X 5.173

* Give the label for each high symmetry point in KPOINTS ([Link]) file. Other wise, they will be
identified as 'Undefined' in KLABELS file

Since the path of the two points, it is possible to identify with a second drawing position is high
symmetry U | K.
Users in Origin Software for processing the [Link] After, we need to follow
KLABELS The file location identified in the high energy band diagram symmetrical position. The
next version of the version will be added to generate an energy band diagram of the drawing
python Function scripts, users need to install
Matplotlib Library. The next version of eggs: There is an example of a band_plot.py Script, as long as
the implementation of thispython Script, on the next FIG.
Can be generated in a ,After the program is the energy band diagram
[Link]),Such
folder of the automatic drawing (repair as

Thermodynamic correction amount 3.3

As we all know,VASPIt is calculated in the system 0 K Under the electron energy, without
considering the contribution of temperature. The electrochemical reaction was calculated to make
analog or
When the rate needs to be calculated free energy, In order to obtain the heat necessary to
calculate the enthalpy of the reaction, in order to achieve 0 K To calculate the energy in the
system under ZPE. Learn
VASP The Hard Way (Ex69) Adsorption entropy calculation species Describes the gas phase molecules
and different adsorbate molecules entropy calculation method, This series of tutorials in the
group 217 821 116 To download PDF version.

For a system, the enthalpy and entropy of the partition function can be calculated by
statistical thermodynamics molecules to obtain: the main consideration ideal gas translation,
rotation, vibration, electronic contribution. Molecule is, for example, a non-linear triatomic
molecule, a total of 3N Degrees of freedom. Gas which is: 3A translation,3 And a rotation 3N
6A vibration. But when it is adsorbed onto the surface, since the translation and rotation is
locked, and this 6 Degrees of freedom will be converted to vibrational degrees of freedom,
i.e. on the surface of the molecule 3N A vibration mode. If the result of molecules adsorbed
on the calculated frequency you visualize the surface, will find that the last6Is a
corresponding translation and rotation, but they are not the translation and rotation of the
gas phase, we call: frustrated translation, frustrated rotation.
Thermodynamics of gas phase molecules correction
Li Qiang tutorialLearn VASP The Hard Way(Ex68) Frequency, zero-point energy, Gibbs free energy
calculationsMentionVASPFor temperature correction do really bad, he suggested that by querying
the database (NISTEtc.) thermodynamic quantities obtained by the method of gas phase
molecules.
andGaussianCorrection for thermodynamic and molecular clusters more
[Link] a practical sense, also have significant
teachingShermoprogram([Link] The output of the Gaussian analysis calculated
translational, rotational, vibrational and electronic contribution, to obtain a given temperature,
internal energy, enthalpy, entropy of the system under pressure, free energy, heat capacity. I
suggest that you look at the text of the program
[Link] program integrated in, the user can directly according to theVASPThe results are
given gas phase molecular vibration of the internal energy, enthalpy, entropy, free energy
correction.
Below ethanol (/ Examples / thermo_correction / ethanol), For example
contrastVASPwithGaussianThermodynamic calibration results. After completion of the calculation
of vibration, startVASPKIT,Entry5Select functionCatalysis-ElectroChem Kit, The next input interface
Enter502selectThermal corrections for Gas. Then prompted for temperature298.15K,pressure1atmAnd
spin multiplicity
1. Spin multiplicity is defined as2S + 1,among themSIs the spin angular momentum, the number of
single-electron system within it(N)Related.S = N / 2, The simple method of determining the final
analysis: single electron spin multiplicity is equal to the number of+1. Ethanol is not a single
electron, so as spin multiplicity1. (Spin multiplicity of oxygen3.) The module requires all atoms are
released, i.e. there can not be secured atoms.
+ -------------------------- Warm Tips --------------------- ----- +
This Feature Was Contributed by Nan XU, Sobereva.
See An Example in vaspkit / examples / thermo_correction / ethanol.
Vibrations, Translation, Rotation, Electron contribitions are considered.
GAS molecules should not be with any fix.
- >> (1) Reading Structural Parameters from CONTCAR File...
- >> (2) Analyze Molecular symmetry information ...
Molecular symmetry is: Cs
+ ------------------------------------------------- -------------- +
Please input Temperature (K)!
298.15
Please input Pressure (Atm)!
1
Please input Spin multiplicity -! (Number of Unpaired electron + 1) 1

------------ >>

VASPKITCalculates callShermoModule calculates the thermodynamic contribution.

->> (3) Extracting frequencies from OUTCAR...

->> (4) Reading OUTCAR File...

->> (5) Calculate Thermal Corrections...

 Zero-point 能源 E_ZPE : 48.501 kcal/mol 2.103130 eV

Thermal correction to U(T):51.486 kcal/mol 2.232567 eV

Thermal correction to H(T):52.078 kcal/mol 2.258259 eV Thermal correction to G(T):

31.891 kcal/mol 1.382881 eV

Thanks to Sobereva! (Sobereva@[Link])

GossG09RevD.01The calculation resultsU (T) 51.94 kcal / mol, H (T) 52.53 kcal / mol, G (T) 33.67 kcal /
molTheoretical levelB3LYP / CC-pVDZ, You can see the use ofVASPKITThermodynamic calculation

of the correction amount is close to the molecularGaussianThe calculation results.

Adsorption thermodynamics calibrate the mass of molecules

For the adsorbate molecules,Learn VASP The Hard Way(Ex69) Adsorption entropy calculation
speciesRecommendations ignoredfrustratedThe translation and rotation and electronic
contribution, consider only3N6The vibrating portion. This module is based on the principles of this
tutorial,Contributed by Xu Nan, Li Qiang and Liu Jincheng. Note: The module does not calculate
the thermodynamic contribution of the gas phase molecules.
With/vaspkit.0.71/examples/thermo_correction/ORRExample. The following figure shows the oxygen
in the solution to the phosphorus doped graphene dissociative adsorption of transition state
(Carbon, 2016, 105: 214223.), With picturesVESTAVisualization software. In order to obtain the
contribution of temperature, vibration analysis is required(IBRION = 5 ),In order to save computing
resources onlyP,OAtomic release, andCHold the atoms in the calculationEnergy Profile
When, vibration analysis needs to be done to other systems, maintaining a consistent release of
atoms. It is worth noting that the contribution of this module only consider vibration, and
Ignoring the contribution of electrons, the wave number less than50cm1 of frustrated
translation,frustrated rotationThe restricted oscillation portion was adjusted to50cm1 The vibration
included contributions to the entropy.
start ,Entry Select Next input interface selec
up function . Then Tips , Enter
t room
298.15KThe screen will output the temperature
following information:
+-------------------------- Warm Tips ---------------------- ---- + This Feature Was

Contributed by Nan XU, Qiang LI and Jincheng LIU.

See An Example in vaspkit / examples / thermo_correction / ORR.

Only vibrations! No Translation & Rotation & Electron contribitions.
+-------------------------------------------------- ------------- +

Please Enter The Temperature (K):

------------ >>
298.15
- >> (1) Reading OUTCAR File ...
+-------------------------- Summary ----------------------- ----- + H = E_DFT + E_ZPE

+ E_H

G = H - TS = E_DFT + E_ZPE + E_H - T * S

Temperature (K): 298.1

Entropy (eV / K): 0.0005
Entropy contribution T * S (eV): .1541
Enthalpy contribution E_H (eV): 0.0858
Zero-point energy E_ZPE (eV): .1944
Thermal correction to G (T) (eV): 0.1261
Total energy at Zero K (eV): -159.3511
Gibbs free energy at 298.1 K (eV): -159.2250
298.15KGibbs free energy of the system under given by the following equation:

H = E_DFT + E_ZPE + E_H

G = H TS = E_DFT + E_ZPE + E_H T * S
 E_DFTFor the system in0KStatic electronic energy under. In the present embodiment, the
system298.15Under the free energy of159.2250 eV. To remember isDFTAbsolutely no sense
energy calculation, only the relative energy onlymake sense. It should be noted that,0.70Read
versionTotal energy at Zero K (eV)There is abug,0.71Version has been fixed.

FIG draw charge density difference of 3.4

See for charge density difference before and after the key to redistribute charge. Here with a
worm on a small woodenCOFor example differential charge
([Link]

Document conventional differential charge density in the secondary differential charge

density graph in FIG.(Difference charge density), Differential charge density different from
FIG.(Deformation charge density). Differential charge is defined as the difference between
atomic charges into the charge density and density after the point corresponding to the key.
By calculating and analyzing the differential charge density, it can be clearly obtained in the
charge-transfer properties and bonding process of bonding the electronic coupling and
bonding the direction of polarization and the like. "Secondary"Referring to the same chemical
component or system to redistribute charge after the geometric configuration change.
Deformation charge densityThe formula is defined as
Difference charge densityThe formula is defined as

ComputeDeformation charge densityWhen, by the self-consistent calculation

ofCHGorCHGCARget,The required CHG orCHGCAR Obtained by the following non-self-consistent
calculation:Still using four self-consistent calculation of the input file, butINCARNeed to setICHARG
= 12with
NELM = 0, That is,CHGCARIs made of a simple superposition of the isolated atomic

charges.([Link]
[Link])
andDifference charge densityThe method is commonly used in the literature, the need for three
different structures(A, B, AB)Do self-consistent calculation. Proceed as follows:

The structure optimized to do static self-consistent calculation

To be careful of,AB,AwithBTo put the size of the space lattice, respectively, and the same
guaranteeAwithBversusABThe corresponding coordinates unchanged, but also to ensure
the three self-consistent calculation used when calculating theFFT mesh Agreement (NGXF,
NGYF, NGZF).
INCARNote that several parameters:
IBRION = -1; NSW = 0; NGXF, NGYF, NGZF

usevaspkitThree structuresCHGCARMake the difference

According to the formula We need toCOofCHGCARminusO, MinusC, You can get a
secondary charge density difference you want. Start in the parent
directoryvaspkitInput34Select functionCharge-Density
Difference, The next screen prompts forCO / CHGCAR C / CHGCAR O / CHGCAR, Displays the

following information:
 ======================= File Options ========================= ===
Input the Names of Charge / Potential Files with Space:
(Tip: To get AB-AB, type: ~ / AB / CHGCAR ./A/CHGCAR ../B/CHGCAR)

------------>>
CO / CHGCAR C / CHGCAR O / CHGCAR

->> (1) Reading Structural Parameters from CO / CHGCAR File ...

->> (2) Reading Charge Density From CO / CHGCAR File ...
->> (3) Reading Structural Parameters from C / CHGCAR File ... ->> (4) Reading

Charge Density From C / CHGCAR File ...

->> (5) Reading Structural Parameters from O / CHGCAR File ...

->> (6) Reading Charge Density From O / CHGCAR File ...
->> (7) Written CHGDIFF_1.vasp File!
This version of the route without quotation marks. After the operation, it will generate in the
current [Link], That isCOThe difference in charge density. use
VESTAVisualization software follows, yellow indicates an increase portion of the charge density,
charge density indicates a decrease blue:

4. Small features
vaspkitNear also added a few more are also distinctive features, several of which were related to
catalysis. Features5It contains several have been developed
Catalytic related gadgets. as follows:

==================== Chemistry-Related Toolkits ====================

501) Thermal corrections for Adsorbate

502) Thermal corrections for Gas

503) d-Band Center (experimental)

504) Convert NEB / POSCAR to PDB for Animation

Which features501with502It has been introduced,503The catalyst is used to calculatedWith the

[Link] can be viewed with a center of research into what reason
Zhengda article"DBand Center-Successful descriptor"([Link]
Features504
willNudged Elastic Band(A transition state search method)imagesCombined into multiframesPDBFile,
you can view the file by visualizingVTSTInterpolation script generated path is our path instead of
the expected energy
( [Link]
willimagesCombined into multiframesxyzFile structure, but becausexyzFile does not contain lattice
information, you can not view the image periodically, if the molecule is in the edge of the box, it
may be unable to view the full energy path. To catalogORRreaction(/ Examples / neb_animation)
Function as an example504Usage. start upVASPKIT ,Entry5Select functionCatalysis-ElectroChem
KitNext input interface504selectTheConvert NEB-Path to PDB Format for [Link] will be
from00 to 07Directory readPOSCARCombinersNEB _ *. Pdb.

Before submitting the task, I want to check it again envisaged right, run it504Get
aNEB_initial.pdbfile. submit
After the task, for example, forget30Step, I want to look at how to count, and it needs to
run504To give a
MoreNEB_30.pdbfile,Meanwhile prompt youNEB is still runing, NOW 30 step!. If the task is
considered finished, I run504,getNEB_final.pdb file,Meanwhile prompt youNEB has finished. in
caseNSWSet100,Ran100Step no convergence, running504The same will be
obtainedNEB_100_end.pdbFiles, but you will be prompted toNEB has
stopped, but has reached NSW step, NOT converged!.`

start upVMD,[Link] intoVMDSwitch the display mode, theVMDThe main window

select the menuDisplay,selectOrthographicOrthogonal display mode. ThenVMDThe main window
select the menuGraphicsAnd then selectRepresentations,Drawing MethodsselectCPK. The default is not
to display a box border, inVMDThe main window select the menuExtensions,selectTk Console,inVMD
TkConsoleWindow, enterpbc box -color whiteIt can display a complete system, as follows
If the molecule is in the border, in order to see the complete vibration, can beSelection
, Select x, in
opened periodically. y, zWhether the periodic panel
direction.

The bottom bar of the main window can be animated feature bar, click on the small arrow in the lower right co
Judg
play multi-frameLinear interpolation
animation. point
By looking is vibration direction,
at the
e reasonable.
Li Qiang can be made in real time
Imageby
Into the bond length between atoms determines VMDthe
Main
Port Mouse
displaying each -> Label -> 2 , Then on to the model NEB The most relevant
interpolation points is reasonable. in 2Atoms, can be
wind
To seeNEBPath, as the distance between
Selection IMAGEChanges
interface, point in the route
atoms structure.
Main 4Gadgets structure contains several
featuresoperations.

=================== Structure Operations ========================

401) Build Supercell

 402) Fix atoms (FFF) by Layers

403) Fix atoms (FFF) by Heights

404) Apply Random-Displacement on Atomic-Positions

405) Converte XDATCARto PDB Format for Animation

409) Remove Spurious Lattice-Distortion after Optimization

Features401Expansion for cellular structure, the new version has been improved, the cells can
remain after expansion of the original structureSelective Information, I.e. the position of atoms
restriction information. With wurtziteZnOof0001Surface structure as an example. Fixing the
bottom three layers in the optimization process (ZnOBilayer) and hydrogen passivated, and the
surface of the three-layer release (ZnOBilayer) simulated surface relaxation. When the expanded
cell, inx, yThe position of atoms in the same layer information will be fixed in the same direction.
ZnO-1811117\ (0\0\1)
1.00000000000000
3.2890999317000000 .0000000000000000 .0000000000000000 -1.6445499659000000

2.8484440965000002 .0000000000000000 .0000000000000000 .0000000000000000

31.0000000000000000

O Zn H
6 6 1 Selective dynamics

Direct
.6666700244773196 .3333300053761477 .1505069039677451 FFF .6666716924670117

.3333278011868069 .3220708624919105 TTT .6666726846730975 .3333236596434402

.4952603515620634 TTT .3333300053138402 .6666700242891679 .0649169839032240 FFF

.3333300053138402 .6666700242891679 .2361085000000003 FFF .3333199694428693

.6666773648761363 .4080366153030212 TTT .6666700244773196 .3333300053761477

.0855899113548375 FFF .6666700244773196 .3333300053761477 .2567814361612903 FFF

.6666745852439349 .3333222632901633 .4277261402910583 TTT .3333300053138402

.6666700242891679 .1711915073870998 FFF .3333495480118175 .6666503610072737

.3422927302063438 TTT .3333226658022473 .6666735134936482 .5114804524358304 TTT

.3353480398005857 .6659931540629387 .0310253291612881 FFF

Features402 ,403The surface is very useful in the simulation. Features402The automatically
atomsZOrientation coordinates stratified, prompts the user requires a fixed bottom layers of
atoms, is output fixing at the bottom surface of the release configuration file.
Also to wurtziteZnOof0001Surface, for example, we want to fix the bottom4Floor(ZnODouble),
release only the surface layers. start upVASPKIT,Entry4Select functionStructure ManipulatorNext
input interface402selectFix atoms (FFF) by Layers.

+-------------------------------------------------- ------------- + | Selective Dynamics

is Activated |! +-------------------------------------------------- ------------- + Found 7
layers, choose how many layers to be fixed

promptCONTCARinZDirection7Atomic layer, we choose5Layer (the passivation layer comprising

hydrogen), is generatedCONTCAR_fix. We can see already met our needs.
 1.6445664829999989 0.9494718860000013 4.6657140230000982 F F F 1.6445755940842863

0.9494656074898858 9.9841967372492260 F F F 1.6445856685242579 0.9494538105351326

15.3530708984239652 T T T -0.0000164679999908 1.8989722949999921 2.0124265009999438 F F F

-0.0000164679999908 1.8989722949999921 7.3193635000000095 F F F -0.0000615489445641

1.8989932042516069 12.6491350743936568 T T T

1.6445664829999989 0.9494718860000013 2.6532872519999624 F F F 1.6445664829999989

0.9494718860000013 7.9602245209999989 F F F 1.6445942160644029 0.9494498331008844

13.2595103490228077 T T T -0.0000164679999908 1.8989722949999921 5.3069367290000935 F F F

0.0000801471361600 1.8989162852407626 10.6110746363966584 F F F -0.0000463465581788

1.8989822338038955 15.8558940255107430 T T T

0.0077341959999959 1.8970442679999928 0.9617852039999312 F F F

Sometimes for a complex system, it is difficult to achieve our objective by selecting the layer, in
Liu Jincheng proposal to develop a functional403, By selecting the height atoms fixed interval. By
determining the need to be fixed in other visualization software layer in which the atomic height
interval, inVASPKITAtoms selected height fixed [Link].0.71 / utilities /It has extended the
functionality of the script directoryPOSCARtoolkit, May fulfill the functions of the fixed portion
atom or relaxation.
Features405 ,Converte XDATCAR to PDB for AnimationAnd function504Similarly, it is possible to
molecular dynamics, normal optimization,Lattice optimization processinXDATCARIon is converted
into a recording step of a plurality of frames can be [Link],OVITOOther
visualization software can only be visualized by Molecular Dynamics, ordinary ion optimization
step for optimizing the crystal lattice (ISIF = 3)ofXDATCARYou can only see the first frame
structure. [Link] same can be madeVMDView optimization
process ion step.

5. VASPKIT and reference manuals

At the present stagevaspkitThe manual is not too perfect, developers are trying to develop.
However, at the followingQQThe group
(331 895 604 ,364 586 948 , 217 821 116) Find developers exchanges are welcome to usevaspkitAnd
timely feedbackBUG. group331 895 604YesvaspkitSpecial discussion groups.
vaspkitThe Download:[Link] The new version will be released in all

three groups
In myGithub Repository ([Link] Quote Reference: V. Wang, N. Xu,

VASPKIT: A Pre- and Post-Processing Program for the VASP Code.

[Link] This document by theZhejiang UniversityofXu NanStudents write, e-mail

address istamas@[Link] is not easy, your reward is to

encourage the fight against developers.