qm-scripts/cry2cif.py at main · tzyii/qm-scripts · GitHub

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#!/usr/bin/env python3

from sys import argv
import numpy as np

def SkipLines(fd, nline):
	for i in range(nline):
		fd.readline()

def WriteCif(param, atomsymbol, factcoor, filename = 'naphthalene'):
	outp = []
	atomamount = {}
	atomformat = '   {0:<8s}1.0{1[0]:15.10f}{1[1]:15.10f}{1[2]:15.10f}   Biso{2:15.10f} {3:2s}\n'.format
	outp.append('#' * 70 + '\n')
	outp.append('#' + ' ' * 68 + '#\n')
	outp.append('#' + ' ' * 23 + 'Optimized Crystal Data' + ' ' * 23 + '#\n')
	outp.append('#' + ' ' * 68 + '#\n')
	outp.append('#' + ' ' * 68 + '#\n')
	outp.append('#' * 70 + '\n')
	outp.append('\ndata_%s\n\n' % filename)
	outp.append('%-38s%-15s\n' % ('_cell_length_a', param[0]))
	outp.append('%-38s%-15s\n' % ('_cell_length_b', param[1]))
	outp.append('%-38s%-15s\n' % ('_cell_length_c', param[2]))
	outp.append('%-38s%-15s\n' % ('_cell_angle_alpha', param[3]))
	outp.append('%-38s%-15s\n' % ('_cell_angle_beta', param[4]))
	outp.append('%-38s%-15s\n' % ('_cell_angle_gamma', param[5]))
	outp.append('%-38s%-15s\n' % ('_symmetry_space_group_name_H-M', "'P 1'"))
	outp.append('%-38s%-15s\n\n' % ('_symmetry_Int_Tables_number', '1'))
	outp.append("loop_\n_symmetry_equiv_pos_as_xyz\n   'x, y, z'\n\nloop_\n")
	outp.append('   _atom_site_label\n   _atom_site_occupancy\n')
	outp.append('   _atom_site_fract_x\n   _atom_site_fract_y\n   _atom_site_fract_z\n')
	outp.append('   _atom_site_adp_type\n   _atom_site_B_iso_or_equiv\n   _atom_site_type_symbol\n')
	for symbol, coor in zip(atomsymbol, factcoor):
		atomamount[symbol] = atomamount.get(symbol, 0) + 1
		atomname = symbol + str(atomamount[symbol])
		outp.append(atomformat(atomname, coor, 1.0, symbol))
	with open(filename + '.cif', 'w') as f:
		f.write(''.join(outp))

factcoor = []                  # Fractional coordinates
lattice = []                   # Lattice vectors of supercell

if len(argv) != 2:
	print("Usage: cry2cif.py xx.out")
elif argv[1][-4 :] == '.out':
	readf = False
	f = open(argv[1], 'r')
	print('Reading ' + argv[1] + '...')
	while True:
		try:
			line = f.readline()
		except UnicodeDecodeError:
			continue
		if line[: 25] == ' FINAL OPTIMIZED GEOMETRY':
			atomsymbol, factcoor = [], []
			SkipLines(f, 5)
			param = f.readline().split()       #lattice parameters
			SkipLines(f, 4)
			while True:
				line = f.readline()
				if line == '\n': break
				sline = line.split()
				atomsymbol.append(sline[3])
				factcoor.append(sline[4 :])
			readf = True
			break
	if not readf:
		raise IOError('Final optimized geometry not found!')
	f.close()
	factcoor = np.array(factcoor, dtype = 'double')
	WriteCif(param, atomsymbol, factcoor, argv[1].split('.')[0])     # Write cif for visualization
else:
    raise ValueError('Only output file of CRYSTAL17 named "xx.out" is supported!')