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Added own scripts: getPOTCAR.sh, plotHOMA_withPBC.py and xyz2POSCAR.py #15

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Added own scripts: getPOTCAR.sh, plotHOMA_withPBC.py and xyz2POSCAR.py #15

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Added own scripts: getPOTCAR.sh, plotHOMA_withPBC.py and xyz2POSCAR.py
JakobSchramm Mar 26, 2026
40a8fa3
Fix Python linting
JakobSchramm Mar 26, 2026
480c6d2
Fix shellcheck warnings
JakobSchramm Mar 26, 2026
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3 changes: 3 additions & 0 deletions README.md
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Expand Up @@ -127,10 +127,12 @@ plotIRC --reactant_dir irc_r/ --product_dir irc_p/ \
|------|-------------|---------|
| `add-MODECAR` | Add MODECAR displacements to a POSCAR, output xyz animation. | `add-MODECAR --poscar POSCAR --modecar MODECAR` |
| `freq2mode` | Generate MODECAR and mass-weighted MODECAR from a frequency calculation. | `freq2mode -i 0` |
| `getPOTCAR` | Generate POTCAR with same order of elements as specified in POSCAR. | `getPOTCAR -r` |
| `kgrid2kspacing` | Get KSPACING equivalent for the current POSCAR+KPOINTS. | `kgrid2kspacing` |
| `kspacing2kgrid` | Get k-point grid for a given KSPACING and the current POSCAR. | `kspacing2kgrid 0.15` |
| `mixed_interpolate` | Geodesic interpolation for the molecule + IDPP for the surface. | `mixed_interpolate` |
| `poscar2nbands` | Compute the recommended NBANDS for LOBSTER from POSCAR/INCAR/POTCAR. | `poscar2nbands` |
| `xyz2POSCAR` | Insert molecule from .xyz file into a cell from a POSCAR. | `xyz2POSCAR mol.xyz POSCAR_with_cell` |

## Post-processing tools

Expand All @@ -141,6 +143,7 @@ plotIRC --reactant_dir irc_r/ --product_dir irc_p/ \
| `elf2cube` | Convert ELFCAR files to cube files. | `elf2cube ELFCAR --output elf` |
| `freq2jmol` | Write JMol-compatible xyz files for all vibrational modes. | `freq2jmol --directory ./` |
| `neb2movie` | Convert VASP NEB images to an ASE ext-xyz movie (like `nebmovie.pl`). | `neb2movie --output neb.xyz` |
| `plotHOMA_withPBC` | Calculate and plot HOMA from coordinates, including pbc. | `plotHOMA_withPBC POSCAR` |
| `plotIRC` | Plot VASP IRC calculations in both directions, shift-compatible. | `plotIRC -r irc_r/ -p irc_p/ -t ts/` |
| `plotNEB` | Plot VASP+VTST NEB results (reads `spline.dat` + `neb.dat`). | `plotNEB --unit eV --file neb.png` |
| `plot_neb_movie` | Create presentation images for NEB using VMD and plotNEB. | `plot_neb_movie` |
Expand Down
134 changes: 134 additions & 0 deletions src/tools4vasp/bash_scripts/getPOTCAR.sh
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#!/bin/bash

# The only thing you need to change: The path to the POTCARs!
POTDIR='/PUT/PATH/TO/POTCARS/HERE/'

# Some general variables
myPWD=$(pwd)
decision='0'

# Function for how to use the script
function usage
{
echo " "
echo "* DESCRIPTION : This scripts reads the POSCAR file and creats the POTCAR file of corresponding elements in order."
echo " "
echo "* USAGE: $(basename "$0") [-h|--help|-rnspdbcSHgG]"
echo " -h | --help : For help."
echo " -r : If you want the recommended default potentials (see IMPORTANT)"
echo " -n : If you want no extension of the POTCAR (minimal valence)"
echo " -s : If you want the _sv extension of the POTCAR (semicore p and s states in valence)"
echo " -p : If you want the _pv extension of the POTCAR (semicore p states in valence)"
echo " -d : If you want the _d extension of the POTCAR (semicore d states in valence)"
echo " -b : If you want the _2 extension of the POTCAR (some 4f electrons of Lanthanides are frozen)"
echo " -c : If you want the _3 extension of the POTCAR (some 4f electrons of Lanthanides are frozen)"
echo " -S : If you want the _s extension of the POTCAR (soft potential)"
echo " -H : If you want the _h extension of the POTCAR (hard potential)"
echo " -g : If you want the _GW extension of the POTCAR (opt. for unoccupied states)"
echo " -G : If you want the _sv_GW extension of the POTCAR (see _sv & _GW)"
echo " "
echo "* IMPORTANT : It uses the following extensions as the recommended default potentials (-r):"
echo " None : H, He, Be, B, C, N, O, F, Ne, Mg, Al, Si, P, S, Cl, Ar, Fr, Co,"
echo " Ni, Cu, Zn, As, Se, Br, Kr, Pd, Ag, Cd, Sb, Te, I, Xe, La, Ce,"
echo " Re, Os, Ir, Pt, Au, Hg, At, Rn, Ac, Th, Pa, U, Np, Pu, Am, Cm"
echo " sv : Li, K, Ca, Sc, Ti, V, Rb, Sr, Y, Zr, Nb, Mo, Cs, Ba, W, Fr, Ra"
echo " pv : Na, Cr, Mn, Tc, Ru, Rh, Hf, Ta"
echo " d : Ga, Ge, In, Sn, Tl, Pb, Bi, Po"
echo " 2 : Eu, Yb"
echo " 3 : Pr, Nd, Pm, Sm, Gd, Tb, Dy, Ho, Er, Tm, Lu"
echo " "
echo "* NOTE : To create the POTCAR you must need the POSCAR file. You first have to move to"
echo " the folder that contains the POSCAR. It can't create POTCAR from external path."
echo " "
echo "--------------- Enjoy. Have a good day. ---------------"
echo " "
exit 0
}

# Function for what changes when the options are read in
function readoptions
{
OPTIND=1
while getopts :rnspdbcSHgG options; do
case $options in
r) decision='1' ;;
n) extension='' ;;
s) extension='_sv' ;;
p) extension='_pv' ;;
d) extension='_d' ;;
b) extension='_2' ;;
c) extension='_3' ;;
S) extension='_s' ;;
H) extension='_h' ;;
g) extension='_GW' ;;
G) extension='_sv_GW' ;;
\?) printf "\n\e[38;5;1m* Error: Invalid option %s. Use -h for help. \e[0m\n\n" "$1"; exit 1 ;;
esac
done
}

# Check if help is needed, if there are no or too many options given, and change variables according to options
if [ -n "$2" ]; then
printf "\n\e[38;5;1m* Error: Only one option allowed at a time! Use -h for help. \e[0m\n\n"
exit 1
elif [ -n "$1" ]; then
if [ "$1" == "-h" ] || [ "$1" == "--help" ]; then
usage
elif [ "$1" == "-" ]; then
printf "\n\e[38;5;1m* Error: Invalid option '-'. Use -h for help. \e[0m\n\n"
exit 1
elif [[ "$1" == -* ]]; then
if [[ ${#1} -gt 2 ]]; then
printf "\n\e[38;5;1m* Error: Only one option allowed at a time! You passed combined options %s. Use -h for help. \e[0m\n\n" "$1"
exit 1
else
readoptions "$@"
fi
else
printf "\n\e[38;5;1m* Error: Invalid option %s. Use -h for help. \e[0m\n\n" "$1"
exit 1
fi
else
printf "\n\e[38;5;1m* Error: You must specify one option! Use -h for help. \e[0m\n\n"
exit 1
fi

# Definition of recommended default options
declare -A element_group=(
[H]="" [He]="" [Be]="" [B]="" [C]="" [N]="" [O]="" [F]="" [Ne]="" [Mg]="" [Al]="" [Si]="" [P]="" [S]="" [Cl]="" [Ar]="" [Fr]="" [Co]="" [Ni]="" [Cu]="" [Zn]="" [As]="" [Se]="" [Br]="" [Kr]=""
[Pd]="" [Ag]="" [Cd]="" [Sb]="" [Te]="" [I]="" [Xe]="" [La]="" [Ce]="" [Re]="" [Os]="" [Ir]="" [Pt]="" [Au]="" [Hg]="" [At]="" [Rn]="" [Ac]="" [Th]="" [Pa]="" [U]="" [Np]="" [Pu]="" [Am]="" [Cm]=""
[Li]="_sv" [K]="_sv" [Ca]="_sv" [Sc]="_sv" [Ti]="_sv" [V]="_sv" [Rb]="_sv" [Sr]="_sv" [Y]="_sv" [Zr]="_sv" [Nb]="_sv" [Mo]="_sv" [Cs]="_sv" [Ba]="_sv" [W]="_sv" [Fr]="_sv" [Ra]="_sv"
[Na]="_pv" [Cr]="_pv" [Mn]="_pv" [Tc]="_pv" [Ru]="_pv" [Rh]="_pv" [Hf]="_pv" [Ta]="_pv"
[Ga]="_d" [Ge]="_d" [In]="_d" [Sn]="_d" [Tl]="_d" [Pb]="_d" [Bi]="_d" [Po]="_d"
[Eu]="_2" [Yb]="_2"
[Pr]="_3" [Nd]="_3" [Pm]="_3" [Sm]="_3" [Gd]="_3" [Tb]="_3" [Dy]="_3" [Ho]="_3" [Er]="_3" [Tm]="_3" [Lu]="_3"
)

# Execution of creating the POTCAR
if [ -f POSCAR ]; then # Check if POSCAR exists
if [ -s POTCAR ]; then # Check if old POTCAR already exists
printf "\n\e[38;5;9;4m* Warning:\e[0m Hi %s, you already have an old POTCAR. I am deleting it and creating the new one.\n\n" "$(whoami)"
rm POTCAR
fi
ATOMS=$(sed -n '6p' POSCAR) && nA=$(wc -w <<< "$ATOMS") # Get elements
NUMBERS=$(sed -n '7p' POSCAR) && nN=$(wc -w <<< "$NUMBERS") # Get number of atoms
if [ "$nA" -ne "$nN" ]; then # Check if number of elements in line 6 and 7 match
printf "\n\e[38;5;1m* Error: Number of elements in line 6 (elements) and line 7 (count) do not match: %s vs. %s \e[0m \n\n" "$nA" "$nN"
exit 1
fi
echo "POTCAR for these elements will be created (in order): $ATOMS"
for element in $ATOMS
do
if [ "$decision" == "1" ]; then # Check if recommended default potentials should be used
extension="${element_group[$element]}" # Assign extension for each element
fi
if [ ! -d "$POTDIR$element$extension" ]; then # Check if element with extension actually exists
printf "\n\e[38;5;1m* Error: %s does not exist.\e[0m \n\n" "$(printf '%q' "$POTDIR$element$extension")"
exit 1
fi
cat "$POTDIR$element$extension/POTCAR" >> "$myPWD/POTCAR" # Important part: attach the POTCARs to each other in order
done
else
printf "\n\e[38;5;1m* Error: No POSCAR file here! POSCAR file is mandatory. Please move to the file containing the POSCAR. \e[0m\n\n"
fi

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