From 969b89e49de43af4e6392bf68d08b5a67153bbc8 Mon Sep 17 00:00:00 2001 From: chn Date: Tue, 23 Apr 2024 18:40:02 +0800 Subject: [PATCH] init --- jykang/.bash_profile | 15 ++++ jykang/.bashrc | 5 ++ jykang/.vaspkit | 165 +++++++++++++++++++++++++++++++++++++++++++ wlin/.bash_profile | 12 ++++ wlin/.bashrc | 43 +++++++++++ 5 files changed, 240 insertions(+) create mode 100644 jykang/.bash_profile create mode 100644 jykang/.bashrc create mode 100644 jykang/.vaspkit create mode 100644 wlin/.bash_profile create mode 100644 wlin/.bashrc diff --git a/jykang/.bash_profile b/jykang/.bash_profile new file mode 100644 index 0000000..6abf491 --- /dev/null +++ b/jykang/.bash_profile @@ -0,0 +1,15 @@ +if [[ $TERM == chn_unset_ls_colors* ]]; then + export TERM=${TERM#*:} + export CHN_LS_USE_COLOR=1 +fi +if [[ $TERM == chn_cd* ]]; then + export TERM=${TERM#*:} + cd ~/${TERM%%:*} + export TERM=${TERM#*:} +fi + +if [ -f ~/.bashrc ]; then + . ~/.bashrc +fi + +export PATH=$PATH:$HOME/bin:$HOME/linwei/chn/software/scripts diff --git a/jykang/.bashrc b/jykang/.bashrc new file mode 100644 index 0000000..d0ef57a --- /dev/null +++ b/jykang/.bashrc @@ -0,0 +1,5 @@ +if [ -f /etc/bashrc ]; then + . /etc/bashrc +fi + +[ -n "$CHN_LS_USE_COLOR" ] && alias ls="ls --color=auto" diff --git a/jykang/.vaspkit b/jykang/.vaspkit new file mode 100644 index 0000000..8be3f9f --- /dev/null +++ b/jykang/.vaspkit @@ -0,0 +1,165 @@ +# 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 = /data/gpfs01/jykang/linwei/chn/software/vaspkit-1.4.1/POTCAR/PAW_LDA +PBE_PATH = /data/gpfs01/jykang/linwei/chn/software/vaspkit-1.4.1/POTCAR/PAW_PBE +GGA_PATH = /data/gpfs01/jykang/linwei/chn/software/vaspkit-1.4.1/POTCAR/PAW_PW91 +VASPKIT_UTILITIES_PATH = /data/gpfs01/jykang/linwei/chn/software/vaspkit-1.4.1/utilities +PYTHON_BIN = /data/gpfs01/jykang/linwei/chn/software/scripts/chn_python3.sh +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 = .TRUE. # 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. + +# New added in Version 1.5.0 +CENTER_DEFECT_POSITION = .TRUE. # Move the position of defect to the center of the supercell; (default value: .TRUE.) +VACUUM_THICKNES = 10 # Vacuum thickness (default value: 10 Angstrom). +UNWRAP_TRAJECTORIES = .TRUE. # Unwrap MD trajectories or not; (default value: .TRUE.) + +#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. +set_tight_layout = .FALSE. # .TRUE. or .FALSE (default: .FALSE.). Automatically adjust the padding between and around subplots. + +# 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.). +display_brillouin_zone = .TRUE. # .TRUE. or .FALSE (default: .TRUE.). +axis_length = [1.0, 1.0, 1.0] # Determine the length of each axis +box_linewidth = 1.0 # Specify the transparency level for the lines of the box or Brillouin zone +box_linealpha = 1.0 # Evaluate the line width of the box or Brillouin zone + +# 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). + +# band structure related settings +disconnecte_band_paths = .TRUE. # .TRUE. or .FALSE (default: .TRUE.). Turn on disconnected band paths drawing mode or not. + +#END_CUSTOMIZE_PLOT diff --git a/wlin/.bash_profile b/wlin/.bash_profile new file mode 100644 index 0000000..3dc099a --- /dev/null +++ b/wlin/.bash_profile @@ -0,0 +1,12 @@ +# .bash_profile + +# Get the aliases and functions +if [ -f ~/.bashrc ]; then + . ~/.bashrc +fi + +# User specific environment and startup programs + +PATH=$PATH:$HOME/bin + +export PATH diff --git a/wlin/.bashrc b/wlin/.bashrc new file mode 100644 index 0000000..c19f52c --- /dev/null +++ b/wlin/.bashrc @@ -0,0 +1,43 @@ +# .bashrc + +# Source global definitions +if [ -f /etc/bashrc ]; then + . /etc/bashrc +fi + +export PATH=$PATH:/data/gpfs01/wlin/bin + +# User specific aliases and functions +export PATH=/data/gpfs01/wlin/bin/vaspkit.1.4.1/bin:${PATH} +#export PATH=~/bin:/data/gpfs01/wlin/opt/mpich_ifort/bin:$PATH +#export LD_LIBRARY_PATH=/data/gpfs01/wlin/opt/mpich_ifort/lib:$LD_LIBRARY_PATH +#export PATH=~/bin:/data/gpfs01/wlin/opt/mpich/bin:$PATH +#export LD_LIBRARY_PATH=/data/gpfs01/wlin/opt/mpich/lib:$LD_LIBRARY_PATH +export P4_RSHCOMMAND=ssh + shopt -s cdspell + export HISTCONTROL=ignoredups +#shopt -s histappend + PROMPT_COMMAND='history -a' + export C3_RSH="ssh -x" +export OMP_NUM_THREADS=1 +export MKL_NUM_THREADS=1 +alias grep='grep --color' +USER_IP=`who -u am i 2>/dev/null| awk '{print $NF}'|sed -e 's/[()]//g'` + +export HISTTIMEFORMAT="%Y-%m-%d %H:%M:%S `whoami`@${USER_IP}: " +export HISTFILESIZE=1000000 +export PROMPT_COMMAND="history -a; history -r; $PROMPT_COMMAND" +shopt -s histappend +# Auto add env parameter $PROMPT_COMMAND when use non-Linux tty login by ssh. +if [ "$SSH_CONNECTION" != '' -a "$TERM" != 'linux' ]; then +declare -a HOSTIP +HOSTIP=`echo $SSH_CONNECTION |awk '{print $3}'` +export PROMPT_COMMAND='echo -ne "\033]0;${USER}@$HOSTIP:[${HOSTNAME%%.*}]:${PWD/#$HOME/~} \007"' +fi +ulimit -s unlimited +export PYTHONPATH=/data/gpfs01/wlin/bin/VaspBandUnfolding-master:${PYTHONPATH} + +# vsts, see https://theory.cm.utexas.edu/vtsttools/scripts.html +export PATH=$PATH:/data/gpfs01/wlin/yjj/vtstscripts-1022 +export PERL5LIB=/data/gpfs01/wlin/yjj/vtstscripts-1022 +