3.2 借助辅助工具vaspkit生成输入文件#

在这里我们安装VASP的辅助工具vaspkit,在后续生成INCAR和数据后处理中会用到该软件。

(1)官网下载并安装vaspkit

网上直接搜索“Vaspkit”,进入官网,找到左侧的Installation(安装)

vaspkit-input 配图 image43.png

按照里面的操作下载-解压-配置环境(第一次做这个都会摸不着头脑,这是正常现象,需要耐心看官网慢慢习惯)。在vim ~/.vaspkit这一步时,需要我们提供我们自己的赝势库路径(自己找组里的师兄师姐要到VASP的POTCAR压缩包,并自行上传到服务器的自己的目录下),比如我这里的路径如下(注意要用绝对路径,用pwd命令可以显示当前的绝对路径):

VASP5          .TRUE.
LDA_PATH       ~/POTCAR/LDA
PBE_PATH       /public/home/zpwu/VASP/PBE-pesudopotential
GGA_PATH       ~/POTCAR/GGA
POTCAR_TYPE    PBE
GW_POTCAR      .FALSE.

后面我们会使用Vaspkit帮我们从这个路径中复制POTCAR到计算目录下。

另外说明一下最后一步“配置环境”,下图是vaspkit官网给的操作步骤

 3. Add the absolute path of the vaspkit to the environment variable.
4.The ~/.vaspkit file might need to be manually updated if some new environment variables are introduced in the newest version of vaspkit
 echo'export PATH=/home/vaspkit.1.00/bin/:$PATH'>> /.bashrc
 source~/.bashrc
Replace the absolutepath of the/home/vaspkit.1.oo/bin/ directory by user's ownVASPKlT executablepath.

最后一句replace the absolute path……意思是要我们对/home/vaspkit.1.00/bin这部分内容替换成自己服务器下安转的vaspkit路径。可以通过cd命令进入vaspkit的文件夹,用pwd命令显示当前(vaspkit)的绝对路径。最后记得要source,让~/.bashrc文件生效。

当你跟着官网的安装以及配置步骤走完,输入vim ~/.bashrc并回车会看到里面有一条这样的信息:

export PATH=/public/home/zpwu/software/vaspkit.1.3.3/bin:$PATH

接下来我们学习使用vaspkit来基于POSCAR文件,辅助生成INCAR,KPOINTS和POTCAR. 首先建立一个工作目录,并准备一个POSCAR文件,用前面的金刚石单质Si即可。

(2)vaspkit生成INCAR:输入vaspkit并回车

[zpwu@node1 new] vaspkit
           11V//
                         Hey, you must know what you are doing.
        (l (o)(o) I)     Otherwise you might get wrong results.
       .0000--()--0000.
          VASPKIT Standard Edition 1.3.3 (24 Feb. 2022)
          Core Developer: Vei WANG (wangvei@icloud.com)
      Main Contributors: Nan XU, Jin-Cheng LIU & Gang TANG
   Online Tutorials Available on Website: https://vaspkit.com
       .0000-
              0oo0.                       VASPKIT Made Simple
                   : Structural Utilities
 1) VASP Input-Files Kit       2)  Mechanical Properties
 3) K-Path for Band-Structure  4) Structure Editor
 5) Catalysis-ElectroChem Kit  6) Symmetry Analysis
 (8 Advanced Structure Models
                ==== Electronic Utilities
 11) Density-of-States         21) DFT Band-Structure
 23) 3D Band-Structure         25) Hybrid-DFT Band-Structure
 26) Fermi-Surface             28) Band-Structure Unfolding
 31) Charge & Spin Density     42) Potential Analysis
 51) Wave-Function Analysis    62) Magnetic Properties
 65) Spin-Texture              68) Transport Properties
                       Misc Utilities =
 71) Optical Properties        72) Molecular-Dynamics Kit
 73) VASP2other Interface      74) User Interface
 91) Semiconductor Kit         92) 2D-Material Kit
 (0 Quit
           >>

大致浏览一下这些内容,我们输入1并回车,显示如下

                    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
105) Generate PoSCAR R File from cif (no fractional occupations)
106) Generate POsCAR File from Material Studio xsd (retain fixes)
107) Reformat PoSCAR File in Specified Order of Elements
108) Successive Procedure to Generate VAsP Files and Check
109) Submit Job Queue
(0   Quit
(6   Back

输入101

101
                         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) Gwo 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
 (6  Back
 Input Key-Parameters (STH6D3 means HSE06-D3 Static-Calcualtion)

输入ST并回车(大写)

ST
       (01) Written TNCAR file!
                           ACKNOWLEDGMENTS
   Other Contributors (in  no particular order): Peng-Fei LIU,

说明vaspkit帮我们生成了INCAR,用cat命令查看INCAR

# Global Parameters
ISTART = 1
ISPIN = 1
# ICHARG = 11
LREAL = .FALSE.
# ENCUT = 400
# PREC = Accurate
LWAVE = .TRUE.
LCHARG = .TRUE.
ADDGRID = .TRUE.
# LVTOT = .TRUE.
# LVHAR = .TRUE.
# NELECT =
# LPLANE = .TRUE.
# NWRITE = 2
# KPAR = 2
# NGXF = 300
# NGYF = 300
# NGZF = 300

# Static Calculation
ISMEAR = 0
SIGMA = 0.05
LORBIT = 11
NEDOS = 2001
NELM = 60
EDIFF = 1E-08

这里有很多参数,注意,vaspkit生成的INCAR默认把ENCUT注释掉了,意味着VASP计算时会默认取POTCAR中的ENMAX的最大值,这通常是不太够的。所以我们需要对这份INCAR文件手动修改,并且参照下面的内容,使用dd命令把Vaspkit生成的INCAR中多余的行删除(请自行搜索vim编辑器下dd命令的使用),最后得到一个干净的INCAR:

# Global Parameters
ISTART = 1
ISPIN = 1
# ICHARG = 11
LREAL = .FALSE.
ENCUT = 400
# PREC = Accurate
LWAVE = .TRUE.
LCHARG = .TRUE.
ADDGRID = .TRUE.

# Static Calculation
ISMEAR = 0
SIGMA = 0.05
LORBIT = 11
NEDOS = 2001
NELM = 60
EDIFF = 1E-06

NCORE = 4
KPAR = 2

必须非常强调的一点是,vaspkit自动生成的INCAR不一定足够合理,尤其是ENCUT,你必须明确知道vaspkit帮你生成的INCAR中的每一个参数代表的含义(查VASP的wiki网页)。

(3)vaspkit生成KPOINTS和POTCAR

类似前面生成INCAR步骤,运行vaspkit,输入1并回车,再输入102并回车

102
                         K-Mesh Scheme
 1) Monkhorst-PackScheme
 2) Gamma Scheme
 3) Irreducible K-Points with Gamma Scheme
 (0   Quit
 (6   Back

有三种Kmesh方案可以选择,我们选择第一种,输入1并回车

1
 ->>  (01)F Reading Structure from PoscAR File..
                            Warm Tips
     Accuracy Levels: Gamma-0nly: 0;
                     Low:0.06~0.04;
                     Medium:0.04~0.03;
                     Fine: 0.02-0.01.
     0.03-0.04 is Genera1ly Precise Enough!

在这里我们输入的是0.03(0.03意思就是前面提到的2π×0.03Å−1密度)。

Reciprocal Lattice Constants:   1.1489   1.1489   1.1489
Real-Space Lattice Constants:   5.4687   5.4687   5.4687
K-Mesh Size:    6    6    6
      (02) Written KPOINTS File!
                            Summary
POTCAR Type: PBE
Number of Elements: 1
POTCAR File No.1: [ POTCAR_Si ],Valence Electron: 4.0
Total Atoms: 8
Total Valence Electrons: 32.0
0-
 ->> (03) Written PoTCAR File vlith the Recommended Potential!

我们可以看到此时Vaspkit输出了倒空间第一布里渊区的b1b2b3基矢长度,并给出了MP下的Kmesh 6 6 6,生成了KPOINTS文件和POTCAR文件,且给出了体系的总价电子数32。

我们在生成KPOINTS时,vaspkit也自动生成了POTCAR文件。这是因为当前目录并没有POTCAR文件,所以尽管我们没有给出“让vaspkit生成POTCAR的指令”,但vaspkit识别到当前路径下没有POTCAR文件时,会自动在生成KPOINTS时帮我们从赝势路径中把POTCAR复制到当前目录。注意,vaspkit生成POTCAR的逻辑是自动读取我们给定的POTCAR路径,然后自动把那里的POTCAR文件复制到当前路径。如果多元素时,会自动把两个POTCAR按照POSCAR的元素顺序进行拼接。这是因为前面我们在安装Vaspkit时,在vim ~/.vaspkit那一步实际上把我们自己服务器下VASP的赝势库的路径写进去了,所以vaspkit能自动在这些路径里面找到POTCAR

你也可以直接使用vaspkit-103功能来生成POTCAR