bash_scripts/castep_pseudopotential_convergence_test_postprocessing 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
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
#!/bin/bash

# script to postprocess a castep_pseudopotential_convergence_test
# requires at the very least a number of r_cutoff_* directories
# currently supports postprocessing of bond length (grabs the first bond length in ${fileroot}.castep) & relative energies
# relative energies need to have been calculated in advance if that task is requested
# might add others in a modular fashion as and when I need them

# the radius in the pseudopotential string (and hence the directory names) is given in Bohr - conversion factor to Angstrom used for output
bohr_to_angstrom=0.529177249

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

echo "Which task would you like to carry out? (currently supported: bond_length, relative_enthalpy)"
read task

if [ $task == "bond_length" ]; then

	echo "# cutoff_radius [Bohr]; cutoff_radius [Ang]; bond length [Ang]" > bond_length.txt

	for d in r_cutoff_*; do
		radius_bohr=`python3 -c "print('$d'.split('_')[-1])"`
		radius_ang=`python3 -c "print(float('$radius_bohr')*float('$bohr_to_angstrom'))"`

		length_line=`awk '/Bond/ {print NR}' $d/geometry_optimisation/${fileroot}.castep`
		length=`awk -v awk_length_line=$length_line 'NR==(awk_length_line+2) {print $7}' $d/geometry_optimisation/${fileroot}.castep`

		echo $radius_bohr $radius_ang $length >> bond_length.txt
	done

	# define task-dependent variables to be used in plotting output
	y_label="Bond length [A]"
	columns="2:3"

elif [ $task == "relative_enthalpy" ]; then
	# read the two names of the directories containing the two structures which are compared - note that the script must be run in the directory containing the relative_enthalpy_*.txt file
	echo "What are the names of the two directories containing the calculations to be compared?"
	read material_1 material_2

	# strip any pontential slashes
	material_1=`python3 -c "print('$material_1'.rstrip('/'))"`
	material_2=`python3 -c "print('$material_2'.rstrip('/'))"`

	# reassign the task variable such that it gives the correct name (root) for the file which contains the relative energies
	# allow either order of materials
	if [ -f ${task}_${material_1}_${material_2}.txt ]; then
		task=${task}_${material_1}_${material_2}
	else
		task=${task}_${material_2}_${material_1}
	fi

	# define task-dependent variables to be used in plotting output
	y_label="Relative enthalpy [eV]"
	columns="2:5"

else
	echo "The task you requested ($task) is not supported. Please request one of the supported tasks (bond_length, relative_energies), or write your own utility."
	exit 1
fi

# generate gnuplot file to plot output

echo "set terminal postscript eps colour" >> ${task}.gnu
echo "set style data points" >> ${task}.gnu
echo "set output '| epstopdf --filter --outfile=${task}.pdf'" >> ${task}.gnu
echo "set xlabel 'Cutoff radius [A]'" >> ${task}.gnu
echo "set ylabel '${y_label}'" >> ${task}.gnu
echo "plot '${task}.txt' u ${columns} w points pt 7 ps 1.2 lc rgb '#DC143C' notitle" >> ${task}.gnu

gnuplot ${task}.gnu