def load(self):
"Rewrite load method"
PosCar.load(self)
with open(self.filename, 'r') as f:
for i in range(self.totline):
f.readline()
#get dimension of 3d array
grid = f.readline().strip(whitespace)
empty = not grid # empty row
while empty:
grid = f.readline().strip(whitespace)
empty = not grid
x, y, z = line2list(grid, dtype=int)
#read electron localization function data
elf_data = []
for line in f:
datalist = line2list(line)
elf_data.extend(datalist)
#########################################
# #
# !!! Notice !!! #
# NGX is the length of the **0th** axis #
# NGY is the length of the **1st** axis #
# NGZ is the length of the **2nd** axis #
# #
#########################################
#reshape to 3d array
elf_data = np.array(elf_data).reshape((x, y, z), order='F')
#set attrs
self.grid = x, y, z
self.elf_data = elf_data
return
def load(self):
"Rewrite load method"
PosCar.load(self)
with open(self.filename, 'r') as f:
for i in range(self.totline):
f.readline()
#get dimension of 3d array
grid = f.readline().strip(whitespace)
empty = not grid # empty row
while empty:
grid = f.readline().strip(whitespace)
empty = not grid
x, y, z = line2list(grid, dtype=int)
#read electron localization function data
elf_data = []
for line in f:
datalist = line2list(line)
elf_data.extend(datalist)
#########################################
# #
# !!! Notice !!! #
# NGX is the length of the **0th** axis #
# NGY is the length of the **1st** axis #
# NGZ is the length of the **2nd** axis #
# #
#########################################
#reshape to 3d array
elf_data = np.array(elf_data).reshape((x, y, z), order='F')
#set attrs
self.grid = x, y, z
self.elf_data = elf_data
return
def freq_iterator(self):
"""
返回频率信息字典的迭代器。
Return frequency iterator to generating frequency related data.
"""
with open(self.filename, "r") as f:
collecting = False
for line in f:
freq = self.freq_regex.match(line)
title = self.title_regex.match(line)
empty_line = (line.strip(whitespace) == "")
if freq:
freq_data = list(freq.groups())
# Collect start.
if title and not collecting:
collecting = True
coords, deltas = [], []
# Collect stop.
elif empty_line and collecting:
collecting = False
freq_data.append(coords)
freq_data.append(deltas)
freq_dict = dict(zip(self.freq_info, freq_data))
yield freq_dict
# Collect data.
elif collecting:
x, y, z, dx, dy, dz = line2list(line)
coord = (x, y, z)
delta = (dx, dy, dz)
coords.append(coord)
deltas.append(delta)
def force_iterator(self):
"""
返回每个离子步迭代的步数，坐标和每个原子受力信息。
Return a generator yield ionic_step, coordinates, forces on atoms.
NOTE: ionic step starts from 1 **NOT 0**.
"""
with open(self.filename, "r") as f:
ion_step = 0
# Force data collection flags.
collect_begin = False
collecting = False
# Collect force data for each ionic step and yield.
for line in f:
if not collect_begin:
if self.force_regex.match(line):
collect_begin = True
ion_step += 1
elif not collecting:
if "-"*6 in line:
collecting = True
coordinates = []
forces = []
else:
if "-"*6 in line:
collecting = False
collect_begin = False
yield ion_step, coordinates, forces
else:
x, y, z, fx, fy, fz = line2list(line)
coordinates.append([x, y, z])
forces.append([fx, fy, fz])
def freq_iterator(self):
"""
返回频率信息字典的迭代器。
Return frequency iterator to generating frequency related data.
"""
with open(self.filename, "r") as f:
collecting = False
for line in f:
freq = self.freq_regex.match(line)
title = self.title_regex.match(line)
empty_line = (line.strip(whitespace) == "")
if freq:
freq_data = list(freq.groups())
# Collect start.
if title and not collecting:
collecting = True
coords, deltas = [], []
# Collect stop.
elif empty_line and collecting:
collecting = False
freq_data.append(coords)
freq_data.append(deltas)
freq_dict = dict(zip(self.freq_info, freq_data))
yield freq_dict
# Collect data.
elif collecting:
x, y, z, dx, dy, dz = line2list(line)
coord = (x, y, z)
delta = (dx, dy, dz)
coords.append(coord)
deltas.append(delta)
def force_iterator(self):
"""
返回每个离子步迭代的步数，坐标和每个原子受力信息。
Return a generator yield ionic_step, coordinates, forces on atoms.
NOTE: ionic step starts from 1 **NOT 0**.
"""
with open(self.filename, "r") as f:
ion_step = 0
# Force data collection flags.
collect_begin = False
collecting = False
# Collect force data for each ionic step and yield.
for line in f:
if not collect_begin:
if self.force_regex.match(line):
collect_begin = True
ion_step += 1
elif not collecting:
if "-" * 6 in line:
collecting = True
coordinates = []
forces = []
else:
if "-" * 6 in line:
collecting = False
collect_begin = False
yield ion_step, coordinates, forces
else:
x, y, z, fx, fy, fz = line2list(line)
coordinates.append([x, y, z])
forces.append([fx, fy, fz])
def __read_info(info):
'''
read lattice info
'''
# read lattice info
info['bases_const'] = float(f.readline().strip())
# lattice basis
info['bases'] = []
for i in range(3):
vector = line2list(f.readline())
info['bases'].append(vector)
def load(self):
"Load all data in file into array."
data = []
with open(self.filename, 'r') as f:
for line in f:
line = line.strip()
if not line: # blank line
continue
if not line[0].isdigit(): # comment line or not
if not line.startswith('-'):
continue
elif not line[1].isdigit() and line[1] != '.':
continue
linedata = line2list(line, field=self.field, dtype=self.dtype)
data.append(linedata)
self.data = np.array(data)
return data
def iforces(self):
"""
返回每个离子步迭代的步数，坐标和每个原子受力信息。
Return a generator yield ionic_step, coordinates, forces on atoms.
NOTE: ionic step starts from 1 **NOT 0**.
"""
# Define namedtuple for item in force iteration.
ForceItem = namedtuple('ForceItem', ['step', 'coordinates', 'forces'])
with open(self.filename, "r") as f:
ion_step = 0
# Force data collection flags.
collect_begin = False
collecting = False
# Collect force data for each ionic step and yield.
for line in f:
if not collect_begin:
if self.force_regex.match(line):
collect_begin = True
ion_step += 1
elif not collecting:
if "-" * 6 in line:
collecting = True
coordinates = []
forces = []
else:
if "-" * 6 in line:
collecting = False
collect_begin = False
yield ForceItem._make([ion_step, coordinates, forces])
else:
x, y, z, fx, fy, fz = line2list(line)
coordinates.append([x, y, z])
forces.append([fx, fy, fz])
def iforces(self):
"""
返回每个离子步迭代的步数，坐标和每个原子受力信息。
Return a generator yield ionic_step, coordinates, forces on atoms.
NOTE: ionic step starts from 1 **NOT 0**.
"""
# Define namedtuple for item in force iteration.
ForceItem = namedtuple('ForceItem', ['step', 'coordinates', 'forces'])
with open(self.filename, "r") as f:
ion_step = 0
# Force data collection flags.
collect_begin = False
collecting = False
# Collect force data for each ionic step and yield.
for line in f:
if not collect_begin:
if self.force_regex.match(line):
collect_begin = True
ion_step += 1
elif not collecting:
if "-"*6 in line:
collecting = True
coordinates = []
forces = []
else:
if "-"*6 in line:
collecting = False
collect_begin = False
yield ForceItem._make([ion_step, coordinates, forces])
else:
x, y, z, fx, fy, fz = line2list(line)
coordinates.append([x, y, z])
forces.append([fx, fy, fz])
flush = f.readline().strip()
if flush == system:
__read_info(info) # update info
# skip atom info
f.readline()
f.readline()
step = f.readline().strip().split()[-1]
else:
step = flush.split()[-1]
content += ' ' + str(info['natom']) + '\n'
content += 'STEP = ' + str(step) + '\n'
for i in range(info['natom']):
content += '%2s' % info['atom_names'][i]
relative_coord = np.array(line2list(f.readline()),
dtype='float64')
direct_coord = np.dot(info['bases'],
relative_coord) * info['bases_const']
content += '%16.9f%16.9f%16.9f\n' %\
(direct_coord[0], direct_coord[1], direct_coord[2])
out_name = 'xdatcar' + str(step) + '.xyz'
with open(out_name, 'w') as f1:
f1.write(content)
with open('xdatcar.xyz', 'a') as f2:
f2.write(content)
f2.close()
except IndexError:
break
