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166 lines
18 KiB
Plaintext
166 lines
18 KiB
Plaintext
# cp how_to_set_environment_variables ~/.vaspkit and modify the ~/.vaspkit file based on the settings in your supercomputer!
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# All environment variables are case sensitive.
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VASP5 = .TRUE. # .TRUE. or .FALSE.; Set .FALSE. if you are using vasp.4.x
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LDA_PATH = /data/gpfs01/jykang/linwei/chn/software/vaspkit-1.4.1/POTCAR/PAW_LDA
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PBE_PATH = /data/gpfs01/jykang/linwei/chn/software/vaspkit-1.4.1/POTCAR/PAW_PBE
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GGA_PATH = /data/gpfs01/jykang/linwei/chn/software/vaspkit-1.4.1/POTCAR/PAW_PW91
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VASPKIT_UTILITIES_PATH = /data/gpfs01/jykang/linwei/chn/software/vaspkit-1.4.1/utilities
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PYTHON_BIN = /data/gpfs01/jykang/linwei/chn/software/scripts/chn_python3.sh
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POTCAR_TYPE = PBE # PBE, PW91 or LDA; Set PBE if you want to make PBE-POTCAR file
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GW_POTCAR = .FALSE. # .TRUE. or .FALSE.; For example, H_GW, O_GW will be chose when POTCAR_GW set to .TRUE.
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RECOMMENDED_POTCAR = .TRUE. # .TRUE. or .FALSE.; The recommended PAW potential will be chose when RECOMMENDED_POTCAR set to .TRUE.
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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.
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SET_MINI_INCAR = .FALSE. # .TRUE. or .FALSE.; A simplified INCAR will be written when MINI_INCAR set to .TRUE.
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USER_DEFINED_INCAR = .FALSE. # .TRUE. or .FALSE.; whether to use embedded INCAR templates or user defined INCAR templates
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WRITE_SELECTIVE_DYNAMICS = .FALSE. # .TRUE. or .FALSE.; the selective dymanics set will be forced to write when SET_SELECTIVE_DYNAMICS_MODE set to .TRUE.
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GET_DOS_FROM_HYBRID_BAND = .FASLE. # .TRUE. or .FALSE.; whether to calculate DOS using optimized tetrahedron method in the hybrid band strucutre calculations
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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.
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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
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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)
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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
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NORMALIZE_ORBITAL_WEIGHTS = .FALSE. # .TRUE. or .FALSE.; whether to normalize orbital-projected weights in each state (default: .FALSE.)
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REORIENTATE_LATTICE_VECTORS = .FALSE. # .TRUE. or .FALSE.; reorientate lattice vectors when build supercell or heterojunction or not (default: .FALSE.)
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GET_IRREDUCIBLE_KPOINTS = .TRUE. # .TRUE. or .FALSE.; Control whether to generate k-points in the symmetry-irreducible wedge of the Brillouin Zone (default: .TRUE.)
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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”.
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SYMMETRY_TOLERANCE = 1E-5 # Tolerance in Cartesian coordinates to find crystal symmetry, compatibility with SYMPREC (default: 1E-5)
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LATTICE_TOLERANCE = 0.2 # Float lattice tolerance for the lattice vectors (default: 0.2 angstrom)
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ANGLE_TOLERANCE = 0.2 # Float angle tolerance for the lattice vectors in degrees (default: 0.2 degree)
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EMIN = -20.0 # Minimum energy for evaluation of DOS (default: -20.0 eV)
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EMAX = 20.0 # Maximum energy for evaluation of DOS (default: 20.0 eV)
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SIGMA = 0.2 # The width of the smearing to calculate DOS from eigenvalue (default: 0.2 eV)
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NEDOS = 2001 # Number of grid points in DOS (default: 2001)
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GAMMA_CENTERED = .TRUE. # .TRUE. or .FALSE. (default: .TRUE.).
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VACUUM_THICKNESS = 15.0 # The thickness of vacuum to build slab or 2D materials (default: 10 angstrom)
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CENTER_SLAB = .TRUE. # Center the slab in the z direction; (default: .TRUE.)
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# New added in Version 1.3.0
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MAX_ATOM_NUMBER = 10000 # The maximum number of atoms to screen heterostructures (default: 10000)
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MIN_ATOM_NUMBER = 1 # The minimum number of atoms to screen heterostructures (default: 1)
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MIN_LATTICE_ANGLE = 0.0 # The minimum lattice angle to screen heterostructures (default: 0.0)
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MAX_LATTICE_ANGLE = 180.0 # The maximum lattice angle to screen heterostructures (default: 180.0)
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GET_INTERPOLATED_DATA = .FALSE. # .TRUE. or .FALSE.; Whether to interpolate the grid data of charge/spin density, potential, band structure, etc. (default: .FALSE.)
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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)
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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')
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AUTO_SUBMIT_JOB = .FALSE. # .TRUE. or .FALSE. (default: .FASLE.). Whether to auto-submit vaspkit or vasp job or not.
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SUBMIT_JOB_COMMAND = 'qsub job.sh' # The command line to submit job
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AUTO_PLOT = .TRUE. # TRUE. or .FALSE. (default: .FASLE.). Whether to auto-plot data graphs in the post-processing.
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# New added in Version 1.4.1
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REDUCE_FERMISURFACE_FILE = .FALSE. # TRUE. or .FALSE. (default: .FASLE.). Whether to write only the bands which cross the Fermi energy.
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WEIGHT_THRESHOLD = 0.00 # Threshold value of spectra weight in the band structure unfolding.
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# New added in Version 1.5.0
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CENTER_DEFECT_POSITION = .TRUE. # Move the position of defect to the center of the supercell; (default value: .TRUE.)
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VACUUM_THICKNES = 10 # Vacuum thickness (default value: 10 Angstrom).
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UNWRAP_TRAJECTORIES = .TRUE. # Unwrap MD trajectories or not; (default value: .TRUE.)
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#USER_DEFINED
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#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.
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# id interpreter script argv description
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#Example1 'u1 python get_entropy.py .TRUE. get_entropy'
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#Example2 'u2 hello.exe .FALSE. ls '
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u1 python get_entropy.py .TRUE. get_entropy_for_adsorbate
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u2 python bader2pqr.py .FALSE. bader2pqr
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#END_USER_DEFINED
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#+------------------------------------------------------------------------------------------------------------------+
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#| Customize VASP job script |
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#| Must copy the block from #BEGIN_CUSTOMIZE_JOB_SCRIPT to #END_CUSTOMIZE_JOB_SCRIPT |
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#+------------------------------------------------------------------------------------------------------------------+
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#BEGIN_CUSTOMIZE_JOB_SCRIPT
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#PBS -N name
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#PBS -o out
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#PBS -e err
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#PBS -l nodes=2:ppn=4
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#PBS -r y
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cd $PBS_O_WORKDIR
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mpirun -np 8 vasp_std > vasp-out
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#END_CUSTOMIZE_JOB_SCRIPT
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#+------------------------------------------------------------------------------------------------------------------+
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#BEGIN_CUSTOMIZE_PLOT
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#+------------------------------------------------------------------------------------------------------------------+
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#| WARNNING! The character-type values of plot variables are case sensitive and must be enclosed in single quotes. |
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#+------------------------------------------------------------------------------------------------------------------+
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# https://matplotlib.org/3.3.3/tutorials/introductory/customizing.html
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# https://matplotlib.org/tutorials/text/text_props.html
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# https://github.com/rougier/matplotlib-cheatsheet
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# Advanced Features of VASPKIT Pro version
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figure_format = 'pdf' # string type (default: 'jpg'). Options: 'png', 'pdf', 'eps', 'jpg', etc.
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figure_height = 4.0 # float type (default: 4.0). The height of the figure.
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figure_width = 5.0 # float type (default: 5.0). The width of the figure.
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dpi = 400 # integer type (default: 400). The resolution of the figure in dots-per-inch.
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set_tight_layout = .FALSE. # .TRUE. or .FALSE (default: .FALSE.). Automatically adjust the padding between and around subplots.
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# Global settings =
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figure_style = 'default' # string type (default: 'default'). Options: 'default', 'classic', 'grayscale', 'seaborn', 'bmh', 'seaborn-notebook', etc.
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font_family = 'arial' # string type (default: 'arial'). Options: 'fantasy','arial','sans-serif', 'monospace', 'cursive', 'serif', etc.
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global_fontsize = 12.0 # float type (default: 15.0).
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label_fontsize = 12.0 # float type (default: 15.0).
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number_format = '%.3f' # string type (default: 15.0).
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# Legend-related settings =
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show_legend = .TRUE. # .TRUE. or .FALSE (default: .TRUE.).
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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.
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legend_fontsize = 12.0 # float type (default: 14.0).
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=
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# Line-related settings =
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line_colors = ['b', 'g', 'r', 'm'] # string type (default: 'blue'). Options: 'red', 'green', 'cyan', '#4c005c', etc.
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line_styles = ['-', '-', '-', '-'] # string type (default: '-'). Options: '-' or solid, '--' or 'dashed', '-.' or 'dashdot', etc.
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line_widths = [1.5, 1.5, 1.5] # float type (default: 1.5).
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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)
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fill_areas = .FALSE. # .TRUE. or .FALSE (default: .FLASE.). Fill the area between two horizontal curves.
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# Marker-related settings =
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#marker_colors = ['blue', 'cyan', 'red', 'magenta', 'orange', 'lawngreen', 'deeppink', 'brown', 'dodgerblue']
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marker_symbols = ['o','o','o'] # string type (default: 'o'). Options: 'o': Circle, 'x': Cross, '+': Plus sign, 'D': Filled diamond, 's': Square, '^': Triangle, etc.
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marker_colors = ['#0db14b', '#4c005c', '#d93b2b','#0075dc', '#740aff', '#993f00', '#4c005c', '#426600']
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marker_sizes = [60, 60.0, 60.0] # float type (default: 10.0).
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marker_scale = 1.0 # float type (default: 1.0). marker_sizes = marker_sizes * marker_scale
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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)
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# Tick-related settings =
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#x_label = 'Wave vector' # string type (No default value).
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#y_label = 'Energy (eV)' # string type (No default value).
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#z_label = 'k$_x$ ($\\mathrm{\\AA}$)' # string type (No default value).
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#x_limits = [-8.0, 8.0] # float type [xmin, xmax] (No default value).
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#y_limits = [-8.0, 8.0] # float type [ymin, ymax] (No default value).
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#z_limits = [-8.0, 8.0] # float type [zmin, zmax] (No default value).
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#x_major_locator = 2.0 # float type (No default value).
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#y_major_locator = 2.0 # float type (No default value).
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#z_major_locator = 2.0 # float type (No default value).
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#x_minor_locator = 1.0 # float type (No default value).
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#y_minor_locator = 1.0 # float type (No default value).
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#z_minor_locator = 1.0 # float type (No default value).
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# contour-related settings
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colormap = 'RdBu' # string typ (default: 'jet'). Options: 'jet', 'hsv', 'viridis', 'gray', etc.
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contour_levels = 5 # integer type (default: 5).
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contour_limits = [0.0, 0.5] # float type (No default value).
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display_colorbar = .FLASE. # .TRUE. or .FALSE (default: .FLASE.).
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display_level_value = .FLASE. # .TRUE. or .FALSE (default: .FLASE.).
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display_contour = .FLASE. # .TRUE. or .FALSE (default: .FLASE.).
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colorbar_shrink = 0.5 # float type (default: 0.4).
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colorbar_orientation = 'vertical' # 'horizontal' or 'vertical' (default: 'horizontal')
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# 3D-plot related settings
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elevation = 12.0 # float type (default: 12).
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azimuth = 24.0 # float type (default: 23).
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display_coordinate_axes = .TRUE. # .TRUE. or .FALSE (default: .TRUE.).
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display_brillouin_zone = .TRUE. # .TRUE. or .FALSE (default: .TRUE.).
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axis_length = [1.0, 1.0, 1.0] # Determine the length of each axis
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box_linewidth = 1.0 # Specify the transparency level for the lines of the box or Brillouin zone
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box_linealpha = 1.0 # Evaluate the line width of the box or Brillouin zone
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# XKCD sketch-style related settings
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xkcd_style = .FALSE. # .TRUE. or .FALSE (default: .FLASE.). Turn on xkcd sketch-style drawing mode or not.
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xkcd_scale = 1 # float type (default: 1.0). The amplitude of the wiggle perpendicular to the source line (default: 1).
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xkcd_length = 100 # float type (default: 100.0). The length of the wiggle along the line (default: 100).
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xkcd_randomness = 2 # float type (default: 2.0). The scale factor by which the length is shrunken or expanded (default: 2).
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# band structure related settings
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disconnecte_band_paths = .TRUE. # .TRUE. or .FALSE (default: .TRUE.). Turn on disconnected band paths drawing mode or not.
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#END_CUSTOMIZE_PLOT
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