num_structures = 0
coordinates = []
# 0→1
for i in range(0, frames + 1):
num_structures += 1
coordinates.append(freq_pos + vibration * dframe * i * scale)
# 1→0
for i in range(frames, -1, -1):
num_structures += 1
coordinates.append(freq_pos + vibration * dframe * i * scale)
# 0→-1
for i in range(-1, -frames - 1, -1):
num_structures += 1
coordinates.append(freq_pos + vibration * dframe * i * scale)
# -1→0
for i in range(-frames, 0):
num_structures += 1
coordinates.append(freq_pos + vibration * dframe * i * scale)
coordinates = np.concatenate(coordinates)
writeXYZ('%s.xyz' % freq_file, num_structures, elements, num_atoms, coordinates)
print('')
print(' ------------------ Done ------------------')
import re
from VASP import readGjf, writeXYZ
import sys
space = re.compile(r'\s+')
if len(sys.argv) == 1:
print("")
print("Usage: %s line1,line2,.... T/F vaspfile" %
sys.argv[0].split('/')[-1])
print("the format of line1,line2,... can be either x or x-x")
print("try again")
print("")
exit(1)
print('')
print('############ This script converts gjf to xyz ############')
print(' ############ gjf -> xyz ############')
print('')
for gjf_file in sys.argv[1:]:
print(' processing %s' % gjf_file)
elements, num_atoms, coordinates = readGjf(gjf_file)
if gjf_file.endswith('.gjf'):
gjf_file = '%s.xyz' % gjf_file[:-4]
else:
gjf_file = '%s.xyz' % gjf_file
writeXYZ(gjf_file, 1, elements, num_atoms, coordinates)
print('')
print(' ---------- Done ----------')