content = freq_file.readlines()
index = 2
while index < len(content):
line = content[index].strip()
if line == '':
break
line = list(map(float, space.split(line)))
coordinates.append(np.array([line[0], line[1], line[2]]))
dcoordinates.append(np.array([line[3], line[4], line[5]]))
index += 1
return np.stack(coordinates), np.stack(dcoordinates)
_, _, elements, num_atoms, _, _, _, _ = readVasp(sys.argv[1])
frames = int(sys.argv[-2])
dframe = 1 / float(frames)
scale = float(sys.argv[-1])
print('')
print('################ This script makes animation of vibration ################')
print('')
for freq_file in sys.argv[2:-2]:
print(' Processing %s' % freq_file)
freq_pos, vibration = readFreq(freq_file)
num_structures = 0
coordinates = []
# 0→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)
flag = sys.argv[-2]
if flag != 'T' and flag != 'F':
print('')
print("error: unidentified flag %s" % flag)
print('')
exit(1)
lattice, basis, elements, num_atoms, selectiveflag, coordinate_type, coordinates, selective = readVasp(
sys.argv[-1])
edit_line_number = []
pattern = re.compile(r'-')
if len(sys.argv) == 4:
line_number = re.split(',', sys.argv[1])
for num in line_number:
if pattern.search(num):
num_list = pattern.split(num)
num_list[0] = int(num_list[0]) - 1
num_list[1] = int(num_list[1])
for i in range(num_list[0], num_list[1]):
edit_line_number.append(i)
else:
edit_line_number.append(int(num) - 1)
#!/bin/env python3
import sys
from VASP import readVasp
threshold = 0.001
if len(sys.argv) == 4:
threshold = float(sys.argv[3])
elif len(sys.argv) != 3:
print('')
print("usage: poscar.py POSCAR1 POSCAR2 threshold")
print("try again!")
print('')
exit(1)
lattice1, basis1, elements1, num_atoms1, selectiveflag1, coordinate_type1, coordinates1, selective1 = readVasp(sys.argv[1])
lattice2, basis2, elements2, num_atoms2, selectiveflag2, coordinate_type2, coordinates2, selective2 = readVasp(sys.argv[2])
if abs(lattice1 - lattice2) > threshold:
print('')
print("Lattices are different:")
print("%s: %10.5f" % (sys.argv[1], lattice1))
print("%s: %10.5f" % (sys.argv[2], lattice2))
print('')
basis_diff = []
for i in range(0, 3):
for j in range(0, 3):
if abs(basis1[i][j] - basis2[i][j]) > threshold:
basis_diff.append([i, j, basis1[i][j] - basis2[i][j]])
#!/bin/env python3
import sys
from VASP import readVasp
from VASP import writeVasp
if len(sys.argv) == 1:
print('')
print('Usage: %s vasp_file1 vasp_file2 ...' % sys.argv[0].split('/')[-1])
print('')
exit(1)
print('')
print('############ This script converts direct to cartesian ############')
print(' ############ direct -> cartesian ############')
print('')
for vasp_file in sys.argv[1:]:
print(' processing %s' % vasp_file)
lattice, basis, elements, num_atoms, selectiveflag, coordinate_type, coordinates, selective = readVasp(vasp_file)
if vasp_file.endswith('.vasp'):
vasp_file = '%s-C.vasp' % vasp_file[:-5]
else:
vasp_file = '%s-C.vasp' % vasp_file
writeVasp(vasp_file, lattice, basis, elements, num_atoms, selectiveflag, coordinate_type, coordinates, selective)
print('')
print(' ---------- Done ----------')
print('')
import sys
from VASP import readGjf, readVasp, writeVasp
if len(sys.argv) == 1:
print('')
print('Usage: %s POSCAR gjf_file1 gjf_file2 ...' %
sys.argv[0].split('/')[-1])
print('')
exit(1)
print('')
print(
'############### This script converts vasp file into gview file ###############'
)
print('')
lattice, basis, _, _, selectiveflag, coordinate_type, _, selective = readVasp(
sys.argv[1])
for gjf_file in sys.argv[2:]:
print(' Processing %s' % gjf_file)
elements, num_atoms, coordinates = readGjf(gjf_file)
if gjf_file.endswith('.gjf'):
gjf_file = '%s.vasp' % gjf_file[:-4]
else:
gjf_file = '%s.vasp' % gjf_file
writeVasp(gjf_file, lattice, basis, elements, num_atoms, selectiveflag,
coordinate_type, coordinates, selective)
print('')
print(' -------------------- DONE --------------------')
print('')
