03_vaspkit快速安装 - Yiwei666/13_vasp GitHub Wiki
安装步骤
1. 使用wget下载vaspkit的安装包到自定义的目录
wget -O vaspkit.1.4.1.linux.x64.tar.gz https://sourceforge.net/projects/vaspkit/files/Binaries/vaspkit.1.4.1.linux.x64.tar.gz/download
2. 对安装包进行解压缩
tar -zxvf vaspkit.1.4.1.linux.x64.tar.gz
解压缩后的目录如下所示
.
├── acknowledgement
├── bin
├── changelog
├── citations
├── contributors
├── crystals
├── docs
├── examples
├── how_to_cite
├── how_to_install
├── how_to_set_auto_plot
├── how_to_set_environment_variables
├── license
├── matplotlib
├── setup.sh
├── utilities
└── vaspkit_logo.pdf
3. 将解压缩目录中的配置文件how_to_set_environment_variable复制到当前用户的家目录下~/.vaspkit，如果当前用户为root，则家目录位于/root。使用cd命令可以直接进入家目录
cp -f how_to_set_environment_variable ~/.vaspkit
注意：~/.vaspkit 是隐藏文件，需要使用如下命令才能列出
ls -a
4. 编辑配置文件，指定赝势路径、python路径等
vi ~/.vaspkit
将PBE_PATH，PYTHON_BIN替换成实际的路径
# cp how_to_set_environment_variables ~/.vaspkit and modify the ~/.vaspkit file based on the settings in your supercomputer!
# All environment variables are case sensitive.
VASP5 = .TRUE. # .TRUE. or .FALSE.; Set .FALSE. if you are using vasp.4.x
LDA_PATH = ~/POTCAR/LDA # Path of LDA potential
PBE_PATH = /home/01_html/29_paw_pbe54 # Path of PBE potential
GGA_PATH = ~/POTCAR/GGA # Path of PW91 potential
VASPKIT_UTILITIES_PATH = ~/vaspkit/utilities # Path of VASPKIT
PYTHON_BIN = /home/anaconda/anaconda3_installation/bin/ # Python executable program with its installation path. Recommend Anaconda package
POTCAR_TYPE = PBE # PBE, PW91 or LDA; Set PBE if you want to make PBE-POTCAR file
GW_POTCAR = .FALSE. # .TRUE. or .FALSE.; For example, H_GW, O_GW will be chose when POTCAR_GW set to .TRUE.
RECOMMENDED_POTCAR = .TRUE. # .TRUE. or .FALSE.; The recommended PAW potential will be chose when RECOMMENDED_POTCAR set to .TRUE.
SET_FERMI_ENERGY_ZERO = .TRUE. # .TRUE. or .FALSE.; The Fermi Energy will be set to zero eV when SET_FERMI_ENERGY_ZERO set to .TRUE.
SET_MINI_INCAR = .FALSE. # .TRUE. or .FALSE.; A simplified INCAR will be written when MINI_INCAR set to .TRUE.
USER_DEFINED_INCAR = .FALSE. # .TRUE. or .FALSE.; whether to use embedded INCAR templates or user defined INCAR templates
WRITE_SELECTIVE_DYNAMICS = .FALSE. # .TRUE. or .FALSE.; the selective dymanics set will be forced to write when SET_SELECTIVE_DYNAMICS_MODE set to .TRUE.
GET_DOS_FROM_HYBRID_BAND = .FASLE. # .TRUE. or .FALSE.; whether to calculate DOS using optimized tetrahedron method in the hybrid band strucutre calculations
ADVANCED_USER = .TRUE. # .TRUE. or .FALSE.; Please fill in your settings in the block 'USER_DEFINED' if you want vaspkit to integrate your own scripts in the 'UTILITIES' file.
SET_INCAR_WRITE_MODE = OVERRIDE # OVERRIDE, APPEND, BACK-UP-OLD,BACK-UP-NEW; "Customize INCAR File" whether to override existing or appending existing INCAR/backup existing INCAR to INCAR.old && write into INCAR/write into INCAR.new
APPLY_SCISSOR_CORRECTION = .FALSE. # .TRUE. or .FALSE.; whether to rigidly shift of the conduction band with respect to the valence band of nonmagnetic semiconductors to matches with that of the experimental, HSE or GW value (default: .FALSE)
APPLY_PHS_CORRECTION = .FALSE. # .TRUE. or .FALSE.; whether to make PHS correction during linear optical calculations. More details are given in Comput. Mater. Sci. 172 (2020) 109315
NORMALIZE_ORBITAL_WEIGHTS = .FALSE. # .TRUE. or .FALSE.; whether to normalize orbital-projected weights in each state (default: .FALSE.)
REORIENTATE_LATTICE_VECTORS = .FALSE. # .TRUE. or .FALSE.; reorientate lattice vectors when build supercell or heterojunction or not (default: .FALSE.)
GET_IRREDUCIBLE_KPOINTS = .TRUE. # .TRUE. or .FALSE.; Control whether to generate k-points in the symmetry-irreducible wedge of the Brillouin Zone (default: .TRUE.)
FACTOR_ENCUT2NPWS = 0.262465831d0 # Adjust the final decimal place (or one beyond that) of this parameter if you encounter an error message saying that “Error: the calculated NPWS is not equal to the read NPWS”.
SYMMETRY_TOLERANCE = 1E-5 # Tolerance in Cartesian coordinates to find crystal symmetry, compatibility with SYMPREC (default: 1E-5)
LATTICE_TOLERANCE = 0.2 # Float lattice tolerance for the lattice vectors (default: 0.2 angstrom)
ANGLE_TOLERANCE = 0.2 # Float angle tolerance for the lattice vectors in degrees (default: 0.2 degree)
EMIN = -20.0 # Minimum energy for evaluation of DOS (default: -20.0 eV)
EMAX = 20.0 # Maximum energy for evaluation of DOS (default: 20.0 eV)
SIGMA = 0.2 # The width of the smearing to calculate DOS from eigenvalue (default: 0.2 eV)
NEDOS = 2001 # Number of grid points in DOS (default: 2001)
GAMMA_CENTERED = .TRUE. # .TRUE. or .FALSE. (default: .TRUE.).
VACUUM_THICKNESS = 15.0 # The thickness of vacuum to build slab or 2D materials (default: 10 angstrom)
CENTER_SLAB = .TRUE. # Center the slab in the z direction; (default: .TRUE.)
# New added in Version 1.3.0
MAX_ATOM_NUMBER = 10000 # The maximum number of atoms to screen heterostructures (default: 10000)
MIN_ATOM_NUMBER = 1 # The minimum number of atoms to screen heterostructures (default: 1)
MIN_LATTICE_ANGLE = 0.0 # The minimum lattice angle to screen heterostructures (default: 0.0)
MAX_LATTICE_ANGLE = 180.0 # The maximum lattice angle to screen heterostructures (default: 180.0)
GET_INTERPOLATED_DATA = .FALSE. # .TRUE. or .FALSE.; Whether to interpolate the grid data of charge/spin density, potential, band structure, etc. (default: .FALSE.)
INTERPOLATION_SPACING = 0.04 # Determines the number of interpolation grids, in unit of A in real-space or 1/A in reciprocal space (default: 0.04)
INTERPOLATION_METHOD = 'cubic' # 'linear', 'cubic' (3rd order-spline interpolation), quartic (4th order-spline interpolation), or FFT available only for 2D and 3D grids (default method: 'cubic')
AUTO_SUBMIT_JOB = .FALSE. # .TRUE. or .FALSE. (default: .FASLE.). Whether to auto-submit vaspkit or vasp job or not.
SUBMIT_JOB_COMMAND = 'qsub job.sh' # The command line to submit job
AUTO_PLOT = .FALSE. # TRUE. or .FALSE. (default: .FASLE.). Whether to auto-plot data graphs in the post-processing.
# New added in Version 1.4.1
REDUCE_FERMISURFACE_FILE = .FALSE. # TRUE. or .FALSE. (default: .FASLE.). Whether to write only the bands which cross the Fermi energy.
WEIGHT_THRESHOLD = 0.00 # Threshold value of spectra weight in the band structure unfolding.
#USER_DEFINED
#Synopsis:The first parameter is the command-id,starting with 'u'; the second is the interpreter, like 'python/bash/perl'(Please left it blank if you are using an executive binary); the third is the name of a script or an executive binary; the fourth one is a switch, if any extra argv is needed, please set if .TRUE. ; the last on is the description, MUST use '_' as delimiter.
# id interpreter script argv description
#Example1 'u1 python get_entropy.py .TRUE. get_entropy'
#Example2 'u2 hello.exe .FALSE. ls '
u1 python get_entropy.py .TRUE. get_entropy_for_adsorbate
u2 python bader2pqr.py .FALSE. bader2pqr
#END_USER_DEFINED
#+------------------------------------------------------------------------------------------------------------------+
#| Customize VASP job script |
#| Must copy the block from #BEGIN_CUSTOMIZE_JOB_SCRIPT to #END_CUSTOMIZE_JOB_SCRIPT |
#+------------------------------------------------------------------------------------------------------------------+
#BEGIN_CUSTOMIZE_JOB_SCRIPT
#PBS -N name
#PBS -o out
#PBS -e err
#PBS -l nodes=2:ppn=4
#PBS -r y
cd $PBS_O_WORKDIR
mpirun -np 8 vasp_std > vasp-out
#END_CUSTOMIZE_JOB_SCRIPT
#+------------------------------------------------------------------------------------------------------------------+
#BEGIN_CUSTOMIZE_PLOT
#+------------------------------------------------------------------------------------------------------------------+
#| WARNNING! The character-type values of plot variables are case sensitive and must be enclosed in single quotes. |
#+------------------------------------------------------------------------------------------------------------------+
# https://matplotlib.org/3.3.3/tutorials/introductory/customizing.html
# https://matplotlib.org/tutorials/text/text_props.html
# https://github.com/rougier/matplotlib-cheatsheet
# Advanced Features of VASPKIT Pro version
figure_format = 'pdf' # string type (default: 'jpg'). Options: 'png', 'pdf', 'eps', 'jpg', etc.
figure_height = 4.0 # float type (default: 4.0). The height of the figure.
figure_width = 5.0 # float type (default: 5.0). The width of the figure.
dpi = 400 # integer type (default: 400). The resolution of the figure in dots-per-inch.
# Global settings =
figure_style = 'default' # string type (default: 'default'). Options: 'default', 'classic', 'grayscale', 'seaborn', 'bmh', 'seaborn-notebook', etc.
font_family = 'arial' # string type (default: 'arial'). Options: 'fantasy','arial','sans-serif', 'monospace', 'cursive', 'serif', etc.
global_fontsize = 12.0 # float type (default: 15.0).
label_fontsize = 12.0 # float type (default: 15.0).
number_format = '%.3f' # string type (default: 15.0).
# Legend-related settings =
show_legend = .TRUE. # .TRUE. or .FALSE (default: .TRUE.).
legend_location = 'best' # string type (default: 'best'). Options: 'best', 'upper right', 'upper left', 'lower left', 'lower right', 'right', 'center left', 'center right', 'lower center', 'upper center', 'center', etc.
legend_fontsize = 12.0 # float type (default: 14.0).
=
# Line-related settings =
line_colors = ['b', 'g', 'r', 'm'] # string type (default: 'blue'). Options: 'red', 'green', 'cyan', '#4c005c', etc.
line_styles = ['-', '-', '-', '-'] # string type (default: '-'). Options: '-' or solid, '--' or 'dashed', '-.' or 'dashdot', etc.
line_widths = [1.5, 1.5, 1.5] # float type (default: 1.5).
line_alpha = [1.0, 1.0, 1.0] # float type (default: 1.0). 0.0< alpha <=1.0, adjust the transparency of each line (by default, alpha=1.0)
fill_areas = .FALSE. # .TRUE. or .FALSE (default: .FLASE.). Fill the area between two horizontal curves.
# Marker-related settings =
#marker_colors = ['blue', 'cyan', 'red', 'magenta', 'orange', 'lawngreen', 'deeppink', 'brown', 'dodgerblue']
marker_symbols = ['o','o','o'] # string type (default: 'o'). Options: 'o': Circle, 'x': Cross, '+': Plus sign, 'D': Filled diamond, 's': Square, '^': Triangle, etc.
marker_colors = ['#0db14b', '#4c005c', '#d93b2b','#0075dc', '#740aff', '#993f00', '#4c005c', '#426600']
marker_sizes = [60, 60.0, 60.0] # float type (default: 10.0).
marker_scale = 1.0 # float type (default: 1.0). marker_sizes = marker_sizes * marker_scale
marker_alpha = [0.8, 0.7, 0.6, 0.5, 0.4] # float type (default: 1.0). 0.0< alpha <=1.0), adjust the transparency of markers (by default, alpha=1.0)
# Tick-related settings =
#x_label = 'Wave vector' # string type (No default value).
#y_label = 'Energy (eV)' # string type (No default value).
#z_label = 'k$_x$ ($\\mathrm{\\AA}$)' # string type (No default value).
#x_limits = [-8.0, 8.0] # float type [xmin, xmax] (No default value).
#y_limits = [-8.0, 8.0] # float type [ymin, ymax] (No default value).
#z_limits = [-8.0, 8.0] # float type [zmin, zmax] (No default value).
#x_major_locator = 2.0 # float type (No default value).
#y_major_locator = 2.0 # float type (No default value).
#z_major_locator = 2.0 # float type (No default value).
#x_minor_locator = 1.0 # float type (No default value).
#y_minor_locator = 1.0 # float type (No default value).
#z_minor_locator = 1.0 # float type (No default value).
# contour-related settings
colormap = 'RdBu' # string typ (default: 'jet'). Options: 'jet', 'hsv', 'viridis', 'gray', etc.
contour_levels = 5 # integer type (default: 5).
contour_limits = [0.0, 0.5] # float type (No default value).
display_colorbar = .FLASE. # .TRUE. or .FALSE (default: .FLASE.).
display_level_value = .FLASE. # .TRUE. or .FALSE (default: .FLASE.).
display_contour = .FLASE. # .TRUE. or .FALSE (default: .FLASE.).
colorbar_shrink = 0.5 # float type (default: 0.4).
colorbar_orientation = 'vertical' # 'horizontal' or 'vertical' (default: 'horizontal')
# 3D-plot related settings
elevation = 12.0 # float type (default: 12).
azimuth = 24.0 # float type (default: 23).
display_coordinate_axes = .TRUE. # .TRUE. or .FALSE (default: .TRUE.).
# XKCD sketch-style related settings
xkcd_style = .FALSE. # .TRUE. or .FALSE (default: .FLASE.). Turn on xkcd sketch-style drawing mode or not.
xkcd_scale = 1 # float type (default: 1.0). The amplitude of the wiggle perpendicular to the source line (default: 1).
xkcd_length = 100 # float type (default: 100.0). The length of the wiggle along the line (default: 100).
xkcd_randomness = 2 # float type (default: 2.0). The scale factor by which the length is shrunken or expanded (default: 2).
#END_CUSTOMIZE_PLOT
5. 将vaspkit添加到环境变量中
vi ~/.bashrc
添加vaspkit的bin路径
export PATH="/home/01_html/31_vaspkit/vaspkit.1.4.1/bin/:$PATH"
然后更新
source ~/.bashrc
6. 启动vaspkit
在终端中输入vaspkit命令即可启动
\\\///
/ _ _ \ Hey, you must know what you are doing.
(| (o)(o) |) Otherwise you might get wrong results.
o-----.OOOo--()--oOOO.------------------------------------------o
| VASPKIT Standard Edition 1.4.1 (26 Apr. 2023) |
| Core Developer: Vei WANG ([email protected]) |
| Main Contributors: Gang TANG, Nan XU & Jin-Cheng LIU |
| Online Tutorials Available on Website: https://vaspkit.com |
o-----.oooO-----------------------------------------------------o
( ) Oooo. VASPKIT Made Simple
\ ( ( )
\_) ) /
(_/
===================== Structural Utilities ======================
1) VASP Input-Files Generator 2) Mechanical Properties
3) K-Path for Band-Structure 4) Structure Editor
5) Catalysis-ElectroChem Kit 6) Symmetry Analysis
7) Materials Databases 8) Advanced Structure Models
===================== Electronic Utilities ======================
11) Density-of-States 21) Band-Structure
23) 3D Band-Structure 25) Hybrid-DFT Band-Structure
26) Fermi-Surface 28) Band-Structure Unfolding
31) Charge-Density Analysis 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
74) User Interface 78) VASP2other Interface
91) Semiconductor Kit 92) 2D-Material Kit
0) Quit
------------>>
参考资料
- vaspkit官网：https://vaspkit.com/installation.html