def calculate(self, filename):
"""Run calculation and write results to file."""
self.log('Calculating', self.name, '...')
config = self.atoms.copy()
self.set_calculator(config, filename)
traj = PickleTrajectory(filename, 'w', backup=False)
cell = config.get_cell()
self.energies = []
if self.fmax is not None:
if (not config.constraints and
not config.positions.any(axis=1).all()):
# one atom is at (0,0,0) - fix it:
mask = np.logical_not(config.positions.any(axis=1))
config.constraints = FixAtoms(mask=mask)
dyn = LBFGS(config)
dyn.attach(traj, 1, config)
dyn.run(fmax=self.fmax)
e = config.get_potential_energy()
self.post_process(config)
self.energies.append(e)
elif not config.pbc.any() and len(config) == 2:
# This is a dimer.
self.bondlengths = []
d0 = config.get_distance(0, 1)
for strain in self.strains:
d = d0 * strain
config.set_distance(0, 1, d)
self.bondlengths.append(d)
e = config.get_potential_energy()
self.energies.append(e)
self.post_process(config)
traj.write(config)
else:
self.volumes = []
for strain in self.strains:
config.set_cell(strain * cell, scale_atoms=True)
self.volumes.append(config.get_volume())
e = config.get_potential_energy()
self.energies.append(e)
self.post_process(config)
traj.write(config)
return config
from ase.io import PickleTrajectory
from ase.optimize.lbfgs import LBFGS
from ase.optimize.mdmin import MDMin
try:
from asap3 import EMT
except ImportError:
pass
else:
a = 3.6
b = a / 2
cu = Atoms('Cu', cell=[(0, b, b), (b, 0, b), (b, b, 0)], pbc=1) * (6, 6, 6)
cu.set_calculator(EMT())
f = UnitCellFilter(cu, [1, 1, 1, 0, 0, 0])
opt = LBFGS(f)
t = PickleTrajectory('Cu-fcc.traj', 'w', cu)
opt.attach(t)
opt.run(5.0)
# HCP:
from ase.lattice.surface import hcp0001
cu = hcp0001('Cu', (1, 1, 2), a=a / sqrt(2))
cu.cell[1, 0] += 0.05
cu *= (6, 6, 3)
cu.set_calculator(EMT())
print cu.get_forces()
print cu.get_stress()
f = UnitCellFilter(cu)
opt = MDMin(f, dt=0.01)
t = PickleTrajectory('Cu-hcp.traj', 'w', cu)
opt.attach(t)
opt.run(0.2)
from ase.io import Trajectory
from ase.optimize.lbfgs import LBFGS
from ase.optimize.mdmin import MDMin
try:
from asap3 import EMT
except ImportError:
pass
else:
a = 3.6
b = a / 2
cu = Atoms('Cu', cell=[(0,b,b),(b,0,b),(b,b,0)], pbc=1) * (6, 6, 6)
cu.set_calculator(EMT())
f = UnitCellFilter(cu, [1, 1, 1, 0, 0, 0])
opt = LBFGS(f)
t = Trajectory('Cu-fcc.traj', 'w', cu)
opt.attach(t)
opt.run(5.0)
# HCP:
from ase.lattice.surface import hcp0001
cu = hcp0001('Cu', (1, 1, 2), a=a / sqrt(2))
cu.cell[1,0] += 0.05
cu *= (6, 6, 3)
cu.set_calculator(EMT())
print(cu.get_forces())
print(cu.get_stress())
f = UnitCellFilter(cu)
opt = MDMin(f,dt=0.01)
t = Trajectory('Cu-hcp.traj', 'w', cu)
opt.attach(t)
opt.run(0.2)
