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
def absorber_sphere(atoms, absorber, radius):
box = atoms.get_cell()
ibox = numpy.linalg.inv(box)
pos = atoms.get_positions()
elements = atoms.get_chemical_symbols()
atoms_sphere = [Atom(elements[absorber], (0.,0.,0.))]
for i in xrange(len(atoms)):
if i == absorber: continue
r = pbc(pos[i] - pos[absorber], box, ibox)
d = numpy.linalg.norm(r)
if d <= radius:
atoms_sphere.append(Atom(elements[i], r))
return Atoms(atoms_sphere)
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 load_feff_dat(filename):
xk = []
cdelta = []
afeff = []
phfeff = []
redfac = []
xlam = []
rep = []
atoms = Atoms()
atoms.set_pbc((False,False,False))
path_section = False
atoms_section = False
data_section = False
f = open(filename)
for line in f:
line = line.strip()
fields = line.split()
if "genfmt" in line:
path_section = True
continue
if fields[0] == "x" and fields[1] == "y" and fields[2] == "z":
atoms_section = True
path_section = False
continue
if fields[0] == "k" and fields[1] == "real[2*phc]":
data_section = True
atoms_section = False
continue
if path_section:
if "---------------" in line:
continue
reff = float(fields[2])
path_section = False
if atoms_section:
x = float(fields[0])
y = float(fields[1])
z = float(fields[2])
pot = int(fields[3])
atomic_number = int(fields[4])
atoms.append(Atom(symbol=atomic_number, position=(x,y,z),
tag=pot))
if data_section:
fields = [ float(f) for f in fields ]
xk.append(fields[0])
cdelta.append(fields[1])
afeff.append(fields[2])
phfeff.append(fields[3])
redfac.append(fields[4])
xlam.append(fields[5])
rep.append(fields[6])
xk = numpy.array(xk)
cdelta = numpy.array(cdelta)
afeff = numpy.array(afeff)
phfeff = numpy.array(phfeff)
redfac = numpy.array(redfac)
xlam = numpy.array(xlam)
rep = numpy.array(rep)
return {
"atoms":atoms,
"reff":reff,
"xk":xk,
"cdelta":cdelta,
"afeff":afeff,
"phfeff":phfeff,
"redfac":redfac,
"xlam":xlam,
"rep":rep,
}
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 load_feff_dat(filename):
xk = []
cdelta = []
afeff = []
phfeff = []
redfac = []
xlam = []
rep = []
atoms = Atoms()
atoms.set_pbc((False,False,False))
path_section = False
atoms_section = False
data_section = False
f = open(filename)
for line in f:
line = line.strip()
fields = line.split()
if "genfmt" in line:
path_section = True
continue
if fields[0] == "x" and fields[1] == "y" and fields[2] == "z":
atoms_section = True
path_section = False
continue
if fields[0] == "k" and fields[1] == "real[2*phc]":
data_section = True
atoms_section = False
continue
if path_section:
if "---------------" in line:
continue
reff = float(fields[2])
path_section = False
if atoms_section:
x = float(fields[0])
y = float(fields[1])
z = float(fields[2])
pot = int(fields[3])
atomic_number = int(fields[4])
atoms.append(Atom(symbol=atomic_number, position=(x,y,z),
tag=pot))
if data_section:
fields = [ float(f) for f in fields ]
xk.append(fields[0])
cdelta.append(fields[1])
afeff.append(fields[2])
phfeff.append(fields[3])
redfac.append(fields[4])
xlam.append(fields[5])
rep.append(fields[6])
xk = numpy.array(xk)
cdelta = numpy.array(cdelta)
afeff = numpy.array(afeff)
phfeff = numpy.array(phfeff)
redfac = numpy.array(redfac)
xlam = numpy.array(xlam)
rep = numpy.array(rep)
return {
"atoms":atoms,
"reff":reff,
"xk":xk,
"cdelta":cdelta,
"afeff":afeff,
"phfeff":phfeff,
"redfac":redfac,
"xlam":xlam,
"rep":rep,
}
