def read_con(filename):
f = open(filename, 'r')
lines = f.readlines()
f.close()
trajectory = []
line_index = 0
while True:
try:
boxlengths = numpy.array([
float(length) for length in lines[line_index + 2].split()[0:3]
])
boxangles = numpy.array(
[float(angle) for angle in lines[line_index + 3].split()[0:3]])
cell = length_angle_to_box(boxlengths, boxangles)
num_types = int(lines[line_index + 6].split()[0])
num_each_type = [
int(n) for n in lines[line_index + 7].split()[0:num_types]
]
mass_each_type = [
float(n) for n in lines[line_index + 8].split()[0:num_types]
]
a = Atoms('H' * sum(num_each_type))
a.cell = cell
a.set_pbc((True, True, True))
frozen = []
positions = []
symbols = []
masses = []
line_index += 9
atom_index = 0
for i in range(num_types):
symbol = lines[line_index].strip()
mass = mass_each_type[i]
line_index += 2
for j in range(num_each_type[i]):
split = lines[line_index].split()
positions.append([float(s) for s in split[0:3]])
symbols.append(symbol)
masses.append(mass)
if split[3] != '0':
frozen.append(atom_index)
atom_index += 1
line_index += 1
a.set_chemical_symbols(symbols)
a.set_positions(positions)
a.set_masses(masses)
a.set_constraint(FixAtoms(frozen))
except:
if len(trajectory) == 1:
return trajectory[0]
if len(trajectory) == 0:
raise IOError, "Could not read con file."
return trajectory
trajectory.append(a)
def read_con(filename):
f = open(filename, 'r')
lines = f.readlines()
f.close()
trajectory = []
line_index = 0
while True:
try:
boxlengths = numpy.array([float(length) for length in lines[line_index+2].split()[0:3]])
boxangles = numpy.array([float(angle) for angle in lines[line_index+3].split()[0:3]])
cell = length_angle_to_box(boxlengths, boxangles)
num_types = int(lines[line_index+6].split()[0])
num_each_type = [int(n) for n in lines[line_index+7].split()[0:num_types]]
mass_each_type = [float(n) for n in lines[line_index+8].split()[0:num_types]]
a = Atoms('H'*sum(num_each_type))
a.cell = cell
a.set_pbc((True, True, True))
frozen = []
positions = []
symbols = []
masses = []
line_index += 9
atom_index = 0
for i in range(num_types):
symbol = lines[line_index].strip()
mass = mass_each_type[i]
line_index += 2
for j in range(num_each_type[i]):
split = lines[line_index].split()
positions.append([float(s) for s in split[0:3]])
symbols.append(symbol)
masses.append(mass)
if split[3] != '0':
frozen.append(atom_index)
atom_index += 1
line_index += 1
a.set_chemical_symbols(symbols)
a.set_positions(positions)
a.set_masses(masses)
a.set_constraint(FixAtoms(frozen))
except:
if len(trajectory) == 1:
return trajectory[0]
if len(trajectory) == 0:
raise IOError, "Could not read con file."
return trajectory
trajectory.append(a)
