#!/bin/bash ################################################################# # Copyright 2016-2024, Johns Hopkins University # # # # Permission is hereby granted, free of charge, # # to any person obtaining a copy of this software # # and associated documentation files (the "Software"), # # to deal in the Software without restriction, including # # without limitation the rights to use, copy, modify, # # merge, publish, distribute, sublicense, and/or sell # # copies of the Software, and to permit persons to # # whom the Software is furnished to do so, # # subject to the following conditions: # # # # The above copyright notice and this permission # # notice shall be included in all copies or # # substantial portions of the Software. # # # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY # # OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING # # BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. # # IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT # # HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES # # OR OTHER LIABILITY, WHETHER IN AN ACTION # # OF CONTRACT, TORT OR OTHERWISE, ARISING # # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE # # OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. # ################################################################# ################################################################# # Generate a k-point grid by calling the servlet # # This script is assumes that the user is calling # # it from the directory containing the necessary files. # # (although the script can be placed some place else) # # # # Questions, comments, feedback, saw some bad coding? # # Email us at kpoints@jhu.edu # # by Pandu Wisesa # ################################################################# version="C2023.04.28" echo "Running getKPoints script version" $version"."; # This switch controls the information regarding grid generation output file. # The default is "TRUE", replacing it with "FALSE" or any other values will turn it off. list_message="TRUE" # These format the messages accordingly warning_message() { echo "*** WARNING: $1 ***" } error_message() { echo "*** ERROR: $1 ***" } # Check for early kill signals. killed() { error_message "Command was terminated by user." } trap 'killed' 1 2 3 failed_to_connect() { error_message "There is a problem connecting to the database." } trap 'failed_to_connect' 6 7 10 27 # Check for format of the software package, right now only VASP is supported. found_input_files="FALSE" determine_input_format() { input="$1" if [ "$input" == "POSCAR" ]; then echo "-vasp" fi } # Generate a KPOINTS file for VASP. # Due to how VASP filenames are, the files can be fetched directly by their names. generate_grid_for_vasp() { found_input_files="TRUE" if [ -f INCAR ]; then KPTS=$(curl -s https://muellergroup.jhu.edu/kpts/PreCalcServer/PreCalcServlet?format=vasp\&messagelist="$list_message"\&clientversion=$version --form "fileupload=@PRECALC" --form "fileupload=@POSCAR" --form "fileupload=@INCAR") else warning_message "No INCAR file detected. Using only symmetry information from structure file." KPTS=$(curl -s https://muellergroup.jhu.edu/kpts/PreCalcServer/PreCalcServlet?format=vasp\&messagelist="$list_message"\&clientversion=$version --form "fileupload=@PRECALC" --form "fileupload=@POSCAR") fi STAT=$(echo $?) if [ "$STAT" -ne 0 ]; then error_message "Can't connect to the database." exit 7 else if [ "$list_message" == "TRUE" ]; then HEAD=$(echo "$KPTS" | sed '/+++SEPARATE_HERE+++/,$d') GRID=$(echo "$KPTS" | sed '/+++SEPARATE_HERE+++/,$!d' | sed 1d) OUT_OK="TRUE" if echo "$HEAD" | grep --quiet "ERROR"; then OUT_OK="FALSE" fi echo "$HEAD" if [ "$OUT_OK" == "TRUE" ]; then echo "$GRID" > KPOINTS fi else echo "$KPTS" > KPOINTS fi fi # Do a quick check of the integrity of the KPOINTS file. if [ -f KPOINTS ]; then if grep --quiet "HTTP Status" KPOINTS; then rm KPOINTS error_message "Invalid KPOINTS file was generated. Please check your input files and re-submit the request." fi if grep "ERROR" KPOINTS; then # Useful when "list_message=FALSE" rm KPOINTS fi fi } # Check if PRECALC file exists precalc_default="FALSE" check_precalc() { if [ -f PRECALC ]; then echo "Generating grids..." precalc_default="FALSE" else # In the case PRECALC does not exists, create an empty file to feed in warning_message "No PRECALC file detected. Using default values." touch PRECALC # If you want to edit your own default PRECALC settings, you can uncomment and edit these lines. #echo "MINDISTANCE=28.1" >> PRECALC #echo "INCLUDEGAMMA=FALSE" >> PRECALC echo "Generating grids..." precalc_default="TRUE" fi } # Write output to screen output_to_stdout() { if [ -e KPOINTS ]; then echo "=============== CONTENT OF KPOINTS ===============" cat KPOINTS fi } ################################## main() ##################################### # These lines below are the "main method" of this script. check_precalc # Check if the first argument is the format or filename. if [ "$1" == -* ]; then format="$1" file1="$2" else format="" file1="$1" fi # If no format is specified, scour through the files in this directories for input structure(s). # In addition, generate the grids for every structures found. if [ "$format" == "" ]; then for files in *; do format=$(determine_input_format $files) if [ "$format" == "-vasp" ]; then generate_grid_for_vasp fi done # Otherwise generate the grid for that input file. elif [ "$format" == "-vasp" ]; then generate_grid_for_vasp fi # Final cleanup if [ "$precalc_default" == "TRUE" ]; then rm PRECALC fi if [ "$OUT_OK" == "FALSE" ] && [ -e KPOINTS ]; then rm KPOINTS fi if [ "$found_input_files" == "FALSE" ]; then error_message "Found no input files for grid generation! Exit." echo "Finished." exit 1 fi echo "Finished" # If write generating vectors, write output to screen. if [ "$precalc_default" == "FALSE" ] && [ -e PRECALC ]; then write_vectors=$( grep -iE "^[ ]*WRITE_LATTICE_VECTORS" ./PRECALC 2> /dev/null | \ awk -F "[=#]" '{ print tolower($2) }' | tr -d [:space:] 2> /dev/null ) if [ ! -z $write_vectors ] && [ $write_vectors == "true" ]; then output_to_stdout fi fi