bash_scripts/geometry_optimisation_cubic_profess_serial at master · PascalSalzbrenner/bash_scripts · GitHub

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#!/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 *.inpt`
fileroot=`python3 -c "print('$name'.split('.')[0])"`

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

counter=0

while [ `python3 -c "print(int($lattice_param <= $max))"` -eq 1 ]; do

	if [ ! -d lattice_parameter_$lattice_param ]; then

		mkdir lattice_parameter_$lattice_param

		cp ${fileroot}.inpt lattice_parameter_$lattice_param
		cp *.usp* lattice_parameter_$lattice_param
        	cp *pot* lattice_parameter_$lattice_param

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

		cd lattice_parameter_$lattice_param

		echo "Now running PROFESS 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

		PROFESS $fileroot > profess.run &

        	cd ..

        	counter=$((counter+1))

	fi

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

	if [ $counter -eq $NCORES ]; then
		wait
               	# all jobs are done; next num_cores jobs can be started
               	counter=0

       	fi

done

running_jobs=`jobs -r | tail -1`
# as long as this is not empty, there are running jobs
while [ `python3 -c "print(int(not '$running_jobs'))"` -eq 0 ]; do
        # OFDFT jobs are quite fast, so it makes sense to check frequently
        running_jobs=`jobs -r | tail -1`
done

# do the same loop again to read output data

lattice_param=$1 # reset to initial lattice parameter

while [ `python3 -c "print(int($lattice_param <= $max))"` -eq 1 ]; do

	cd lattice_parameter_$lattice_param

	energy=`awk '{IGNORECASE=1} /total energy/ {print $5}' ${fileroot}.out`
	volume=`awk '/Cell Volume/ {print $4}' ${fileroot}.out`
	echo $lattice_param $volume $energy >> ../energy.txt

	cd ..

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

done

c2x --int lattice_parameter_${1}/${fileroot}.ion
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