def read_xdatcar(filename, skip=0, every=1):
f = open(filename, 'r')
lines = f.readlines()
f.close()
lattice_constant = float(lines[1].strip())
cell = numpy.array([[float(x) * lattice_constant for x in lines[2].split()],
[float(x) * lattice_constant for x in lines[3].split()],
[float(x) * lattice_constant for x in lines[4].split()]])
elements = lines[5].split()
natoms = [int(x) for x in lines[6].split()]
nframes = (len(lines)-7)/(sum(natoms) + 1)
trajectory = []
for i in range(skip, nframes, every):
a = Atoms('H'*sum(natoms))
a.masses = [1.0] * len(a)
a.set_chemical_symbols(''.join([n*e for (n, e) in zip(natoms, elements)]))
a.cell = cell.copy()
j = 0
for N, e in zip(natoms, elements):
for k in range(N):
split = lines[8 + i * (sum(natoms) + 1) + j].split()
a[j].position = [float(l) for l in split[0:3]]
j += 1
a.positions = numpy.dot(a.positions, cell)
trajectory.append(a)
return trajectory
def read_xdatcar(filename, skip=0, every=1):
f = open(filename, 'r')
lines = f.readlines()
f.close()
lattice_constant = float(lines[1].strip())
cell = numpy.array(
[[float(x) * lattice_constant for x in lines[2].split()],
[float(x) * lattice_constant for x in lines[3].split()],
[float(x) * lattice_constant for x in lines[4].split()]])
elements = lines[5].split()
natoms = [int(x) for x in lines[6].split()]
nframes = (len(lines) - 7) / (sum(natoms) + 1)
trajectory = []
for i in range(skip, nframes, every):
a = Atoms('H' * sum(natoms))
a.masses = [1.0] * len(a)
a.set_chemical_symbols(''.join(
[n * e for (n, e) in zip(natoms, elements)]))
a.cell = cell.copy()
j = 0
for N, e in zip(natoms, elements):
for k in range(N):
split = lines[8 + i * (sum(natoms) + 1) + j].split()
a[j].position = [float(l) for l in split[0:3]]
j += 1
a.positions = numpy.dot(a.positions, cell)
trajectory.append(a)
return trajectory
