bash_scripts/geometry_optimisation_cubic_qe at master · PascalSalzbrenner/bash_scripts · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
#!/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

ry_to_ev=13.605698066
bohr_to_angstrom=0.52917721067

if [ ! -f energy.txt ]; then
	echo "# Lattice Parameter [Bohr]; 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

		sed "s/lattice_parameter/$lattice_param/g" pw.in > lattice_parameter_$lattice_param/pw.in
		cp *upf lattice_parameter_$lattice_param
		cp *UPF lattice_parameter_$lattice_param

		cd lattice_parameter_$lattice_param

		echo "Now running Quantum Espresso pw.x 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 -np $NCORES pw.x -i pw.in > pw.out

		energy=`awk '/total energy/ {print $5}' pw.out | tail -2 | head -1`
		energy=`python3 -c "print(float('$energy')*float('$ry_to_ev'))"`

		volume=`awk '/unit-cell volume/ {print $4}' pw.out`
		volume=`python3 -c "print(float('$volume')*float('$bohr_to_angstrom')**3)"`

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

		rm -r *.save

		cd ..

	fi

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

done

c2x --int lattice_parameter_${1}/pw.in
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