run_from_python.sh

#!/bin/bash

#!/bin/bash #-f 

# the -f option disables filename expansion (globbing), preventing characters like *, ?, and [ ] from being interpreted as wildcards.

# this script works similarly to to run_auto but takes the x, y and z 
# coordinate of the molecule from the script arguments $1, $2 and $3. 
export RASPA_DIR=${HOME}/RASPA/simulations/
export DYLD_LIBRARY_PATH=${RASPA_DIR}/lib
export LD_LIBRARY_PATH=${RASPA_DIR}/lib

# remove calculation folders
rm -rf RestartInitial                                                                                    
rm -rf CrashRestart
rm -rf Movies
rm -rf Output
rm -rf VTK
rm -rf Restart

# Check if exactly four arguments are provided
if [ "$#" -ne 4 ]; then
    echo "Usage: $0 -- <number1> <number2> <number3>" >&2 # to stderr
    exit 1
fi

# check if $1, $2 and $3 are numbers
if ! [[ $2 =~ ^[+-]?[0-9]+\.?[0-9]*$ ]]; then
    echo "Error: $1 is not a number" >&2 # to stderr
    exit 1
fi

x=$2
y=$3
z=$4

# run initial simulation
awk '!found && /^RestartFile/ {print "#" $0; found=1; next} {print}' simulation.input > temp && mv temp simulation.input 
awk '!found && /^#CreateNumberOfMolecules/ {sub(/^#/, ""); found=1} {print}' simulation.input > temp && mv temp simulation.input    
$RASPA_DIR/bin/simulate $1 > /dev/null 2>&1

# remove output files so they dont get interpreted as results if the 2nd simulation (restart) fails
#rm -r Output/System_0/* # (the output of this initial simulation is random as the adsorbate is placed randomly)
rm -rf Output
# copy restart file
cp -r Restart RestartInitial/

# delete (random) position of adsorbate created in initial simulation

sed -i '' '/^Adsorbate-atom/d' RestartInitial/System_0/*

###sed -i '' '/^Adsorbate-atom/d' RestartInitial/System_0/*
# add desired adsorbate position to restart file
echo "Adsorbate-atom-position: 0 0    $x $y $z" >> RestartInitial/System_0/*
#echo "Adsorbate-atom-position: 0 0    -1.54928252, 17.45034191, 12.71675087" >> RestartInitial/System_0/*

# restart simulation
awk '!found && /^#RestartFile/ {sub(/^#/, ""); found=1} {print}' simulation.input > temp && mv temp simulation.input    
awk '!found && /^CreateNumberOfMolecules/ {print "#" $0; found=1; next} {print}' simulation.input > temp && mv temp simulation.input    
$RASPA_DIR/bin/simulate $1 > /dev/null 2>&1

# check if Output dir exists:
if [ ! -d "Output/System_0" ]; then
    echo "Error: Output directory not found. maybe simulations (restart) failed" >&2 # to stderr
    exit 1
fi

# print energy results:
#grep -m1 -A4 "Host/Adsorbate energy:" Output/System_0/* #outputs the total energy (Host/Adsorbent), the LJ part, the Coulomb part, the 
#real part of the Coulomb and the fourier part of the Coulomb as text in seperate lines.
grep -m1 -A4 "Host/Adsorbate energy:" Output/System_0/* | awk '{print $NF}' # prints just the numerical values of the above mentioned energies

grep -m1 "Alpha convergence parameter" Output/System_0/* | awk '{print $NF}' # prints the alpha/kappa/smearing cooefficient RASPA used for the calculation

grep -m1 "Tail-correction energy" Output/System_0/* | awk '{print $NF}' # prints the tail correction energy

grep -m1 "kvec (x,y,z)" Output/System_0/* | awk '{print $(NF-2) ";" $(NF-1) ";" $NF}' # prints the kvec (x,y,z) as kx;ky;kz