def learn_pes_by_tempering(atoms,
gp,
cutoff,
ttime,
calculator=None,
model=None,
dt=2.,
ediff=0.01,
volatile=None,
target_temperature=1000.,
stages=1,
equilibration=5,
rescale_velocities=1.05,
pressure=None,
stress_equilibration=5,
rescale_cell=1.01,
eps='random',
algorithm='fastfast',
name='model',
overwrite=True,
traj='tempering.traj',
logfile='leapfrog.log'):
"""
pressure (hydrostatic):
defined in units of Pascal and is equal to -(trace of stress tensor)/3
eps:
if 'random', strain *= a random number [0, 1)
if a positive float, strain *= 1-e^(-|dp/p|/eps) i.e. eps ~ relative p fluctuations
else, no action
"""
assert rescale_velocities > 1 and rescale_cell > 1
if pressure is not None:
warnings.warn('rescaling cell is not robust!')
if model is not None:
if type(model) == str:
model = PosteriorPotentialFromFolder(model)
if gp is None:
gp = model.gp
if atoms.get_velocities() is None:
t = target_temperature
MaxwellBoltzmannDistribution(atoms, t * units.kB)
Stationary(atoms)
ZeroRotation(atoms)
dyn = VelocityVerlet(atoms, dt * units.fs, trajectory=traj)
dyn = Leapfrog(dyn,
gp,
cutoff,
calculator=calculator,
model=model,
ediff=ediff,
volatile=volatile,
algorithm=algorithm,
logfile=logfile)
t = 0
T = '{} (instant)'.format(atoms.get_temperature())
checkpoints = np.linspace(0, ttime, stages + 1)[1:]
for k, target_t in enumerate(checkpoints):
print('stage: {}, time: {}, target time: {}, (temperature={})'.format(
k, t, target_t, T))
while t < target_t:
spu, e, T, s = dyn.run_updates(equilibration)
t += spu * equilibration * dt
dyn.rescale_velocities(
rescale_velocities if T < target_temperature else 1. /
rescale_velocities)
if pressure is not None:
spu, e, T, s = dyn.run_updates(stress_equilibration)
t += spu * stress_equilibration * dt
p = -s[:3].mean() / units.Pascal
# figure out strain
dp = p - pressure
strain = (rescale_cell if dp > 0 else 1. / rescale_cell) - 1
if eps is 'random':
strain *= np.random.uniform()
elif type(eps) == float and eps > 0 and abs(p) > 0:
strain *= 1 - np.exp(-np.abs(dp / p) / eps)
# apply strain
dyn.strain_atoms(np.eye(3) * strain)
if k == stages - 1:
dyn.model.to_folder(name,
info='temperature: {}'.format(T),
overwrite=overwrite)
else:
dyn.model.to_folder('{}_{}'.format(name, k),
info='temperature: {}'.format(T),
overwrite=overwrite)
return dyn.get_atoms(), dyn.model
def learn_pes_by_anealing(atoms,
gp,
cutoff,
calculator=None,
model=None,
dt=2.,
ediff=0.01,
volatile=None,
target_temperature=1000.,
stages=1,
equilibration=5,
rescale_velocities=1.05,
algorithm='fastfast',
name='model',
overwrite=True,
traj='anealing.traj',
logfile='leapfrog.log'):
assert rescale_velocities > 1
if model is not None:
if type(model) == str:
model = PosteriorPotentialFromFolder(model)
if gp is None:
gp = model.gp
if atoms.get_velocities() is None:
t = target_temperature / stages
MaxwellBoltzmannDistribution(atoms, t * units.kB)
Stationary(atoms)
ZeroRotation(atoms)
dyn = VelocityVerlet(atoms, dt * units.fs, trajectory=traj)
dyn = Leapfrog(dyn,
gp,
cutoff,
calculator=calculator,
model=model,
ediff=ediff,
volatile=volatile,
algorithm=algorithm,
logfile=logfile)
# initial equilibration
while dyn.volatile():
_, e, t, s = dyn.run_updates(1)
_, e, t, s = dyn.run_updates(equilibration)
temperatures = np.linspace(t, target_temperature, stages + 1)[1:]
heating = t < target_temperature
cooling = not heating
for k, target_t in enumerate(temperatures):
print(
'stage: {}, temperature: {}, target temperature: {}, ({})'.format(
k, t, target_t, 'heating' if heating else 'cooling'))
while (heating and t < target_t) or (cooling and t > target_t):
dyn.rescale_velocities(rescale_velocities if heating else 1. /
rescale_velocities)
_, e, t, s = dyn.run_updates(equilibration)
if k == stages - 1:
dyn.model.to_folder(name,
info='temperature: {}'.format(t),
overwrite=overwrite)
else:
dyn.model.to_folder('{}_{}'.format(name, k),
info='temperature: {}'.format(t),
overwrite=overwrite)
return dyn.get_atoms(), dyn.model
def train_pes_by_tempering(atoms,
gp,
cutoff,
ttime,
calculator=None,
model=None,
dt=2.,
ediff=0.01,
volatile=None,
target_temperature=1000.,
stages=1,
equilibration=5,
rescale_velocities=1.05,
pressure=None,
stress_equilibration=5,
rescale_cell=1.01,
randomize=True,
algorithm='fastfast',
name='model',
overwrite=True,
traj='tempering.traj',
logfile='leapfrog.log'):
assert rescale_velocities > 1 and rescale_cell > 1
if model is not None:
if type(model) == str:
model = PosteriorPotentialFromFolder(model)
if gp is None:
gp = model.gp
if atoms.get_velocities() is None:
t = target_temperature
MaxwellBoltzmannDistribution(atoms, t * units.kB)
Stationary(atoms)
ZeroRotation(atoms)
dyn = VelocityVerlet(atoms, dt * units.fs, trajectory=traj)
dyn = Leapfrog(dyn,
gp,
cutoff,
calculator=calculator,
model=model,
ediff=ediff,
volatile=volatile,
algorithm=algorithm,
logfile=logfile)
t = 0
T = '{} (instant)'.format(atoms.get_temperature())
checkpoints = np.linspace(0, ttime, stages + 1)[1:]
for k, target_t in enumerate(checkpoints):
print('stage: {}, time: {}, target time: {}, (temperature={})'.format(
k, t, target_t, T))
while t < target_t:
spu, e, T, s = dyn.run_updates(equilibration)
t += spu * equilibration * dt
dyn.rescale_velocities(
rescale_velocities if T < target_temperature else 1. /
rescale_velocities)
if pressure is not None:
spu, e, T, s = dyn.run_updates(stress_equilibration)
t += spu * stress_equilibration * dt
p = -s[:3].mean() / units.Pascal
# figure out factor
dp = p - pressure
factor = (rescale_cell if dp > 0 else 1. / rescale_cell)
if randomize:
factor = 1 + np.random.uniform(0, 1) * (factor - 1)
# apply rescaling
dyn.rescale_cell(factor)
if k == stages - 1:
dyn.model.to_folder(name,
info='temperature: {}'.format(T),
overwrite=overwrite)
else:
dyn.model.to_folder('{}_{}'.format(name, k),
info='temperature: {}'.format(T),
overwrite=overwrite)
return dyn.get_atoms(), dyn.model