def get_atoms():
srf = Atoms('Cu64', [(1.2763, 1.2763, 4.0000), (3.8290, 1.2763, 4.0000),
(6.3816, 1.2763, 4.0000), (8.9343, 1.2763, 4.0000),
(1.2763, 3.8290, 4.0000), (3.8290, 3.8290, 4.0000),
(6.3816, 3.8290, 4.0000), (8.9343, 3.8290, 4.0000),
(1.2763, 6.3816, 4.0000), (3.8290, 6.3816, 4.0000),
(6.3816, 6.3816, 4.0000), (8.9343, 6.3816, 4.0000),
(1.2763, 8.9343, 4.0000), (3.8290, 8.9343, 4.0000),
(6.3816, 8.9343, 4.0000), (8.9343, 8.9343, 4.0000),
(0.0000, 0.0000, 5.8050), (2.5527, 0.0000, 5.8050),
(5.1053, 0.0000, 5.8050), (7.6580, 0.0000, 5.8050),
(0.0000, 2.5527, 5.8050), (2.5527, 2.5527, 5.8050),
(5.1053, 2.5527, 5.8050), (7.6580, 2.5527, 5.8050),
(0.0000, 5.1053, 5.8050), (2.5527, 5.1053, 5.8050),
(5.1053, 5.1053, 5.8050), (7.6580, 5.1053, 5.8050),
(0.0000, 7.6580, 5.8050), (2.5527, 7.6580, 5.8050),
(5.1053, 7.6580, 5.8050), (7.6580, 7.6580, 5.8050),
(1.2409, 1.2409, 7.6081), (3.7731, 1.2803, 7.6603),
(6.3219, 1.3241, 7.6442), (8.8935, 1.2669, 7.6189),
(1.2803, 3.7731, 7.6603), (3.8188, 3.8188, 7.5870),
(6.3457, 3.8718, 7.6649), (8.9174, 3.8340, 7.5976),
(1.3241, 6.3219, 7.6442), (3.8718, 6.3457, 7.6649),
(6.3945, 6.3945, 7.6495), (8.9576, 6.3976, 7.6213),
(1.2669, 8.8935, 7.6189), (3.8340, 8.9174, 7.5976),
(6.3976, 8.9576, 7.6213), (8.9367, 8.9367, 7.6539),
(0.0582, 0.0582, 9.4227), (2.5965, -0.2051, 9.4199),
(5.1282, 0.0663, 9.4037), (7.6808, -0.0157, 9.4235),
(-0.2051, 2.5965, 9.4199), (2.1913, 2.1913, 9.6123),
(5.0046, 2.5955, 9.4873), (7.5409, 2.5336, 9.4126),
(0.0663, 5.1282, 9.4037), (2.5955, 5.0046, 9.4873),
(5.3381, 5.3381, 9.6106), (7.8015, 5.0682, 9.4237),
(-0.0157, 7.6808, 9.4235), (2.5336, 7.5409, 9.4126),
(5.0682, 7.8015, 9.4237), (7.6155, 7.6155, 9.4317)])
c2 = Atoms('C2', [(3.2897, 3.2897, 10.6627), (4.2113, 4.2113, 10.6493)])
srf.extend(c2)
srf.pbc = (1, 1, 0)
srf.set_cell([10.2106, 10.2106, 20.6572], scale_atoms=False)
mask = [a.index < 32 for a in srf]
c1 = FixedPlane(-1, (1 / np.sqrt(2), 1 / np.sqrt(2), 1))
c2 = FixedPlane(-2, (1 / np.sqrt(2), 1 / np.sqrt(2), 1))
constraint = FixAtoms(mask=mask)
srf.set_constraint([constraint, c1, c2])
return srf
def read_aims_output(filename, index=-1):
""" Import FHI-aims output files with all data available, i.e. relaxations,
MD information, force information etc etc etc. """
from ase_ext import Atoms, Atom
from ase_ext.calculators.singlepoint import SinglePointCalculator
from ase_ext.units import Ang, fs
molecular_dynamics = False
fd = open(filename, 'r')
cell = []
images = []
n_periodic = -1
f = None
pbc = False
found_aims_calculator = False
v_unit = Ang / (1000.0 * fs)
while True:
line = fd.readline()
if not line:
break
if "List of parameters used to initialize the calculator:" in line:
fd.readline()
calc = read_aims_calculator(fd)
calc.out = filename
found_aims_calculator = True
if "Number of atoms" in line:
inp = line.split()
n_atoms = int(inp[5])
if "| Unit cell:" in line:
if not pbc:
pbc = True
for i in range(3):
inp = fd.readline().split()
cell.append([inp[1], inp[2], inp[3]])
if "Atomic structure:" in line and not molecular_dynamics:
fd.readline()
atoms = Atoms()
for i in range(n_atoms):
inp = fd.readline().split()
atoms.append(Atom(inp[3], (inp[4], inp[5], inp[6])))
if "Complete information for previous time-step:" in line:
molecular_dynamics = True
if "Updated atomic structure:" in line and not molecular_dynamics:
fd.readline()
atoms = Atoms()
velocities = []
for i in range(n_atoms):
inp = fd.readline().split()
atoms.append(Atom(inp[4], (inp[1], inp[2], inp[3])))
if molecular_dynamics:
inp = fd.readline().split()
if "Atomic structure (and velocities)" in line:
fd.readline()
atoms = Atoms()
velocities = []
for i in range(n_atoms):
inp = fd.readline().split()
atoms.append(Atom(inp[4], (inp[1], inp[2], inp[3])))
inp = fd.readline().split()
velocities += [[
float(inp[1]) * v_unit,
float(inp[2]) * v_unit,
float(inp[3]) * v_unit
]]
atoms.set_velocities(velocities)
images.append(atoms)
if "Total atomic forces" in line:
f = []
for i in range(n_atoms):
inp = fd.readline().split()
f.append([float(inp[2]), float(inp[3]), float(inp[4])])
if not found_aims_calculator:
e = images[-1].get_potential_energy()
images[-1].set_calculator(
SinglePointCalculator(e, f, None, None, atoms))
e = None
f = None
if "Total energy corrected" in line:
e = float(line.split()[5])
if pbc:
atoms.set_cell(cell)
atoms.pbc = True
if not found_aims_calculator:
atoms.set_calculator(
SinglePointCalculator(e, None, None, None, atoms))
if not molecular_dynamics:
images.append(atoms)
e = None
if found_aims_calculator:
calc.set_results(images[-1])
images[-1].set_calculator(calc)
fd.close()
if molecular_dynamics:
images = images[1:]
# return requested images, code borrowed from ase_ext.io/trajectory.py
if isinstance(index, int):
return images[index]
else:
step = index.step or 1
if step > 0:
start = index.start or 0
if start < 0:
start += len(images)
stop = index.stop or len(images)
if stop < 0:
stop += len(images)
else:
if index.start is None:
start = len(images) - 1
else:
start = index.start
if start < 0:
start += len(images)
if index.stop is None:
stop = -1
else:
stop = index.stop
if stop < 0:
stop += len(images)
return [images[i] for i in range(start, stop, step)]
from ase_ext import Atoms
a = Atoms('H2', positions=[(0, 0, 0), (0, 0, 1.1)])
a.pbc[0] = 1
assert a.pbc.any()
assert not a.pbc.all()
a.pbc = 1
assert a.pbc.all()
a.cell = (1, 2, 3)
a.cell *= 2
a.cell[0, 0] = 3
assert not (a.cell.diagonal() - (3, 4, 6)).any()
