geometry_optimisation_cubic_castep

#!/bin/bash

# calculation must be set up to carry out a simple SCF cycle

lattice_param=$1 #the initial lattice parameter
max=$2 #the final lattice parameter
step=$3 #by how much the lattice parameter is incremented

# auto-determine fileroot
name=`ls *.param`
fileroot=${name%.param}

if [ ! -f energy.txt ]; then
        echo "# Lattice Parameter [A]; Volume [A^3]; Energy [eV]" > energy.txt
fi

while [ `python3 -c "print(int($lattice_param <= $max))"` -eq 1 ]; do
	
	if [ ! -d lattice_parameter_$lattice_param ]; then	
		
		mkdir lattice_parameter_$lattice_param
	
		cp ${fileroot}.param lattice_parameter_$lattice_param
		cp *.usp* lattice_parameter_$lattice_param
        	cp *pot* lattice_parameter_$lattice_param

		sed "s/lattice_parameter/$lattice_param/g" ${fileroot}.cell > lattice_parameter_$lattice_param/${fileroot}.cell

		cd lattice_parameter_$lattice_param
		
		echo "Now running CASTEP at lattice parameter $lattice_param" # I think since "all output is appended to nohup.out", this should write it into the same file as all the other output
			
		mpirun -n $NCORES castep.mpi $fileroot

		# the output format for the energy is different between SOC and not SOC calculations, so here we determine which it is
        	is_soc=`awk '/spin-orbit coupling/ {print $4}' ${fileroot}.castep`

		# the same goes for non-metallic (fix_occupancy=true) and metallic calculations
        	is_non_metallic=`awk '/non-metallic/ {print}' ${fileroot}.castep`
        	# this will be empty if the calculations is metallic

        	if [ $is_soc == "off" ] && [ `python3 -c "print(int(not '$is_non_metallic'))"` -eq 1 ] || [ $is_soc == "on" ]; then
                	# calculation is metallic and not spin-orbit coupled
                	energy=`awk '/Final energy/ {print $5}' ${fileroot}.castep`
       	 	else
                	energy=`awk '/Final energy/ {print $4}' ${fileroot}.castep`
        	fi

		volume=`awk '/Current cell volume/ {print $5}' ${fileroot}.castep`

		echo $lattice_param $volume $energy >> ../energy.txt

		rm ${fileroot}.check ${fileroot}.castep_bin ${fileroot}.bands

		cd ..
	
	fi

	lattice_param=`echo $lattice_param + $step | bc`

done

c2x --int lattice_parameter_${1}/${fileroot}.cell
space_group=`cat nohup.out | tail -1 | awk '{print $NF}'`

cp ~/bin/python_scripts/birch_murnaghan_eos_fit.py .
python3 birch_murnaghan_eos_fit.py $space_group

gnuplot energy_volume.gnu