def __init__(self, atoms,
temperature=100 * kB,
optimizer=FIRE,
fmax=0.1,
dr=.1,
logfile='-',
trajectory='lowest.traj',
optimizer_logfile='-',
local_minima_trajectory='local_minima.traj',
adjust_cm=True):
Dynamics.__init__(self, atoms, logfile, trajectory)
self.kT = temperature
self.optimizer = optimizer
self.fmax = fmax
self.dr = dr
if adjust_cm:
self.cm = atoms.get_center_of_mass()
else:
self.cm = None
self.optimizer_logfile = optimizer_logfile
self.lm_trajectory = local_minima_trajectory
if isinstance(local_minima_trajectory, str):
self.lm_trajectory = PickleTrajectory(local_minima_trajectory,
'w', atoms)
self.initialize()
def write_mode(self, n, kT=units.kB * 300, nimages=30):
"""Write mode to trajectory file."""
mode = self.get_mode(n) * sqrt(kT / abs(self.hnu[n]))
p = self.atoms.positions.copy()
n %= 3 * len(self.indices)
traj = PickleTrajectory('%s.%d.traj' % (self.name, n), 'w')
calc = self.atoms.get_calculator()
self.atoms.set_calculator()
for x in np.linspace(0, 2 * pi, nimages, endpoint=False):
self.atoms.set_positions(p + sin(x) * mode)
traj.write(self.atoms)
self.atoms.set_positions(p)
self.atoms.set_calculator(calc)
traj.close()
def replay_trajectory(self, traj):
"""Initialize hessian from old trajectory."""
self.replay = True
if isinstance(traj, str):
from ase_ext.io.trajectory import PickleTrajectory
traj = PickleTrajectory(traj, 'r')
atoms = traj[0]
r0 = None
g0 = None
for i in range(0, len(traj) - 1):
r = traj[i].get_positions().ravel()
g = -traj[i].get_forces().ravel() / self.alpha
self.update(r, g, r0, g0, self.p)
self.p = -np.dot(self.H, g)
r0 = r.copy()
g0 = g.copy()
self.r0 = r0
self.g0 = g0
def replay_trajectory(self, traj):
"""Initialize history from old trajectory."""
if isinstance(traj, str):
from ase_ext.io.trajectory import PickleTrajectory
traj = PickleTrajectory(traj, 'r')
r0 = None
f0 = None
# The last element is not added, as we get that for free when taking
# the first qn-step after the replay
for i in range(0, len(traj) - 1):
r = traj[i].get_positions()
f = traj[i].get_forces()
self.update(r, f, r0, f0)
r0 = r.copy()
f0 = f.copy()
self.iteration += 1
self.r0 = r0
self.f0 = f0
def replay_trajectory(self, traj):
"""Initialize hessian from old trajectory."""
if isinstance(traj, str):
from ase_ext.io.trajectory import PickleTrajectory
traj = PickleTrajectory(traj, 'r')
self.H = None
atoms = traj[0]
r0 = atoms.get_positions().ravel()
f0 = atoms.get_forces().ravel()
for atoms in traj:
r = atoms.get_positions().ravel()
f = atoms.get_forces().ravel()
self.update(r, f, r0, f0)
r0 = r
f0 = f
self.r0 = r0
self.f0 = f0
def __init__(self, atoms, logfile, trajectory):
self.atoms = atoms
if rank != 0:
logfile = None
elif isinstance(logfile, str):
if logfile == '-':
logfile = sys.stdout
else:
logfile = open(logfile, 'a')
self.logfile = logfile
self.observers = []
self.nsteps = 0
if trajectory is not None:
if isinstance(trajectory, str):
trajectory = PickleTrajectory(trajectory, 'w', atoms)
self.attach(trajectory)
def write(self, filename):
from ase_ext.io.trajectory import PickleTrajectory
traj = PickleTrajectory(filename, 'w', self)
traj.write()
traj.close()