def fetch(self):
"""Creates a motion calculator object.
Returns:
An ensemble object of the appropriate mode and with the appropriate
objects given the attributes of the InputEnsemble object.
"""
super(InputMotionBase, self).fetch()
if self.mode.fetch() == "replay":
sc = Replay(fixcom=self.fixcom.fetch(), fixatoms=self.fixatoms.fetch(), intraj=self.file.fetch())
elif self.mode.fetch() == "minimize":
sc = GeopMotion(fixcom=self.fixcom.fetch(), fixatoms=self.fixatoms.fetch(), **self.optimizer.fetch())
elif self.mode.fetch() == "neb":
sc = NEBMover(fixcom=self.fixcom.fetch(), fixatoms=self.fixatoms.fetch(), **self.neb_optimizer.fetch())
elif self.mode.fetch() == "dynamics":
sc = Dynamics(fixcom=self.fixcom.fetch(), fixatoms=self.fixatoms.fetch(), **self.dynamics.fetch())
elif self.mode.fetch() == "vibrations":
sc = DynMatrixMover(fixcom=self.fixcom.fetch(), fixatoms=self.fixatoms.fetch(), **self.vibrations.fetch())
elif self.mode.fetch() == "alchemy":
sc = AlchemyMC(fixcom=self.fixcom.fetch(), fixatoms=self.fixatoms.fetch(), **self.alchemy.fetch())
elif self.mode.fetch() == "instanton":
sc = InstantonMotion(fixcom=self.fixcom.fetch(), fixatoms=self.fixatoms.fetch(), **self.instanton.fetch())
elif self.mode.fetch() == "t_ramp":
sc = TemperatureRamp(**self.t_ramp.fetch())
elif self.mode.fetch() == "p_ramp":
sc = PressureRamp(**self.p_ramp.fetch())
else:
sc = Motion()
# raise ValueError("'" + self.mode.fetch() + "' is not a supported motion calculation mode.")
return sc
def fetch(self):
"""Creates a motion calculator object.
Returns:
An ensemble object of the appropriate mode and with the appropriate
objects given the attributes of the InputEnsemble object.
"""
super(InputMotion, self).fetch()
if self.mode.fetch() == "replay":
sc = Replay(fixcom=False, fixatoms=None, intraj=self.file.fetch())
elif self.mode.fetch() == "minimize":
sc = GeopMover(fixcom=False,
fixatoms=None,
**self.optimizer.fetch())
elif self.mode.fetch() == "neb":
sc = NEBMover(fixcom=False,
fixatoms=None,
**self.neb_optimizer.fetch())
elif self.mode.fetch() == "dynamics":
sc = Dynamics(fixcom=self.fixcom.fetch(),
fixatoms=self.fixatoms.fetch(),
**self.dynamics.fetch())
else:
sc = Motion()
#raise ValueError("'" + self.mode.fetch() + "' is not a supported motion calculation mode.")
return sc
def init_stage1(self, simul):
"""Initializes the simulation -- first stage.
Takes a simulation object, and uses all the data in the initialization
queue to fill up the beads and cell data needed to run the simulation.
Args:
simul: A simulation object to be initialized.
Raises:
ValueError: Raised if there is a problem with the initialization,
if something that should have been has not been, or if the objects
that have been specified are not compatible with each other.
"""
if simul.beads.nbeads == 0:
fpos = fmom = fmass = flab = fcell = False # we don't have an explicitly defined beads object yet
else:
fpos = fmom = fmass = flab = fcell = True
for (k, v) in self.queue:
info(" # Initializer (stage 1) parsing " + str(k) + " object.",
verbosity.high)
if k == "cell":
if v.mode == "manual":
rh = v.value.reshape(
(3, 3)) * unit_to_internal("length", v.units, 1.0)
elif v.mode == "chk":
rh = init_chk(v.value)[1].h
elif init_file(v.mode, v.value)[1].h.trace() == -3:
# In case the file do not contain any
# + cell parameters, the diagonal elements of the cell will be
# +set to -1 from the io_units and nothing is read here.
continue
else:
rh = init_file(v.mode, v.value, cell_units=v.units)[1].h
if fcell:
warning("Overwriting previous cell parameters",
verbosity.low)
simul.cell.h = rh
if simul.cell.V == 0.0:
ValueError("Cell provided has zero volume")
fcell = True
elif k == "masses":
if simul.beads.nbeads == 0:
raise ValueError(
"Cannot initialize the masses before the size of the system is known"
)
if fmass:
warning("Overwriting previous atomic masses",
verbosity.medium)
if v.mode == "manual":
rm = v.value * unit_to_internal("mass", v.units, 1.0)
else:
rm = init_beads(v, self.nbeads).m
if v.bead < 0: # we are initializing the path
if (fmom and fmass):
warning(
"Rescaling momenta to make up for changed mass",
verbosity.medium)
simul.beads.p /= simul.beads.sm3 # go to mass-scaled momenta, that are mass-invariant
if v.index < 0:
simul.beads.m = rm
else: # we are initializing a specific atom
simul.beads.m[v.index:v.index + 1] = rm
if (fmom and fmass): # finishes correcting the momenta
simul.beads.p *= simul.beads.sm3 # back to normal momenta
else:
raise ValueError("Cannot change the mass of a single bead")
fmass = True
elif k == "labels":
if simul.beads.nbeads == 0:
raise ValueError(
"Cannot initialize the labels before the size of the system is known"
)
if flab:
warning("Overwriting previous atomic labels",
verbosity.medium)
if v.mode == "manual":
rn = v.value
else:
rn = init_beads(v, self.nbeads).names
if v.bead < 0: # we are initializing the path
if v.index < 0:
simul.beads.names = rn
else: # we are initializing a specific atom
simul.beads.names[v.index:v.index + 1] = rn
else:
raise ValueError(
"Cannot change the label of a single bead")
flab = True
elif k == "positions":
if fpos:
warning("Overwriting previous atomic positions",
verbosity.medium)
# read the atomic positions as a vector
rq = init_vector(v,
self.nbeads,
dimension="length",
units=v.units)
nbeads, natoms = rq.shape
natoms //= 3
# check if we must initialize the simulation beads
if simul.beads.nbeads == 0:
if v.index >= 0:
raise ValueError(
"Cannot initialize single atoms before the size of the system is known"
)
simul.beads.resize(natoms, self.nbeads)
set_vector(v, simul.beads.q, rq)
fpos = True
elif (
k == "velocities" or k == "momenta"
) and v.mode == "thermal": # intercept here thermal initialization, so we don't need to check further down
if fmom:
warning("Overwriting previous atomic momenta",
verbosity.medium)
if simul.beads.natoms == 0:
raise ValueError(
"Cannot initialize momenta before the size of the system is known."
)
if not fmass:
raise ValueError(
"Trying to resample velocities before having masses.")
rtemp = v.value * unit_to_internal("temperature", v.units, 1.0)
if rtemp <= 0:
warning(
"Using the simulation temperature to resample velocities",
verbosity.low)
rtemp = simul.ensemble.temp
else:
info(
" # Resampling velocities at temperature %s %s" %
(v.value, v.units), verbosity.low)
# pull together a mock initialization to get NM masses right
# without too much code duplication
if v.bead >= 0:
raise ValueError("Cannot thermalize a single bead")
if v.index >= 0:
rnatoms = 1
else:
rnatoms = simul.beads.natoms
rbeads = Beads(rnatoms, simul.beads.nbeads)
if v.index < 0:
rbeads.m[:] = simul.beads.m
else:
rbeads.m[:] = simul.beads.m[v.index]
rnm = NormalModes(mode=simul.nm.mode,
transform_method=simul.nm.transform_method,
freqs=simul.nm.nm_freqs)
rens = Ensemble(temp=simul.ensemble.temp)
rmv = Motion()
rnm.bind(rens, rmv, rbeads)
# then we exploit the sync magic to do a complicated initialization
# in the NM representation
# with (possibly) shifted-frequencies NM
rnm.pnm = simul.prng.gvec(
(rbeads.nbeads, 3 * rbeads.natoms)) * np.sqrt(
rnm.dynm3) * np.sqrt(
rbeads.nbeads * rtemp * Constants.kb)
if v.index < 0:
simul.beads.p = rbeads.p
else:
simul.beads.p[:, 3 * v.index:3 * (v.index + 1)] = rbeads.p
fmom = True
elif k == "momenta":
if fmom:
warning("Overwriting previous atomic momenta",
verbosity.medium)
# read the atomic momenta as a vector
rp = init_vector(v,
self.nbeads,
momenta=True,
dimension="momentum",
units=v.units)
nbeads, natoms = rp.shape
natoms //= 3
# checks if we must initialize the simulation beads
if simul.beads.nbeads == 0:
if v.index >= 0:
raise ValueError(
"Cannot initialize single atoms before the size of the system is known"
)
simul.beads.resize(natoms, self.nbeads)
rp *= np.sqrt(self.nbeads / nbeads)
set_vector(v, simul.beads.p, rp)
fmom = True
elif k == "velocities":
if fmom:
warning("Overwriting previous atomic momenta",
verbosity.medium)
# read the atomic velocities as a vector
rv = init_vector(v,
self.nbeads,
dimension="velocity",
units=v.units)
nbeads, natoms = rv.shape
natoms //= 3
# checks if we must initialize the simulation beads
if simul.beads.nbeads == 0 or not fmass:
ValueError(
"Cannot initialize velocities before the masses of the atoms are known"
)
simul.beads.resize(natoms, self.nbeads)
warning(
"Initializing from velocities uses the previously defined masses -- not the masses inferred from the file -- to build momenta",
verbosity.low)
if v.index >= 0:
rv *= simul.beads.m[v.index]
else:
for ev in rv:
ev *= simul.beads.m3[0]
rv *= np.sqrt(self.nbeads / nbeads)
set_vector(v, simul.beads.p, rv)
fmom = True
elif k == "gle":
pass # thermostats must be initialised in a second stage
if simul.beads.natoms == 0:
raise ValueError(
"Initializer could not initialize the atomic positions")
if simul.cell.V == 0:
raise ValueError("Initializer could not initialize the cell")
for i in range(simul.beads.natoms):
if simul.beads.m[i] <= 0:
raise ValueError("Initializer could not initialize the masses")
if simul.beads.names[i] == "":
raise ValueError(
"Initializer could not initialize the atom labels")
if not fmom:
warning(
"Momenta not specified in initialize. Will start with zero velocity if they are not specified in beads.",
verbosity.low)
def fetch(self):
"""Creates a motion calculator object.
Returns:
An ensemble object of the appropriate mode and with the appropriate
objects given the attributes of the InputEnsemble object.
"""
super(InputMotionBase, self).fetch()
if self.mode.fetch() == "replay":
sc = Replay(
fixcom=self.fixcom.fetch(),
fixatoms=self.fixatoms.fetch(),
intraj=self.file.fetch(),
)
elif self.mode.fetch() == "minimize":
sc = GeopMotion(fixcom=self.fixcom.fetch(),
fixatoms=self.fixatoms.fetch(),
**self.optimizer.fetch())
elif self.mode.fetch() == "neb":
raise ValueError(
"The nudged elastic band calculation has been temporarily disabled until further bug-fixes."
)
# sc = NEBMover(
# fixcom=self.fixcom.fetch(),
# fixatoms=self.fixatoms.fetch(),
# **self.neb_optimizer.fetch()
# )
elif self.mode.fetch() == "dynamics":
sc = Dynamics(fixcom=self.fixcom.fetch(),
fixatoms=self.fixatoms.fetch(),
**self.dynamics.fetch())
elif self.mode.fetch() == "constrained_dynamics":
sc = ConstrainedDynamics(fixcom=self.fixcom.fetch(),
fixatoms=self.fixatoms.fetch(),
**self.constrained_dynamics.fetch())
elif self.mode.fetch() == "vibrations":
sc = DynMatrixMover(fixcom=self.fixcom.fetch(),
fixatoms=self.fixatoms.fetch(),
**self.vibrations.fetch())
elif self.mode.fetch() == "normalmodes":
sc = NormalModeMover(fixcom=self.fixcom.fetch(),
fixatoms=self.fixatoms.fetch(),
**self.normalmodes.fetch())
elif self.mode.fetch() == "scp":
sc = SCPhononsMover(fixcom=self.fixcom.fetch(),
fixatoms=self.fixatoms.fetch(),
**self.scp.fetch())
elif self.mode.fetch() == "alchemy":
sc = AlchemyMC(fixcom=self.fixcom.fetch(),
fixatoms=self.fixatoms.fetch(),
**self.alchemy.fetch())
elif self.mode.fetch() == "atomswap":
sc = AtomSwap(fixcom=self.fixcom.fetch(),
fixatoms=self.fixatoms.fetch(),
**self.atomswap.fetch())
elif self.mode.fetch() == "instanton":
sc = InstantonMotion(fixcom=self.fixcom.fetch(),
fixatoms=self.fixatoms.fetch(),
**self.instanton.fetch())
elif self.mode.fetch() == "planetary":
sc = Planetary(fixcom=self.fixcom.fetch(),
fixatoms=self.fixatoms.fetch(),
**self.planetary.fetch())
elif self.mode.fetch() == "t_ramp":
sc = TemperatureRamp(**self.t_ramp.fetch())
elif self.mode.fetch() == "p_ramp":
sc = PressureRamp(**self.p_ramp.fetch())
elif self.mode.fetch() == "al-kmc":
sc = AlKMC(fixcom=self.fixcom.fetch(),
fixatoms=self.fixatoms.fetch(),
**self.al6xxx_kmc.fetch())
else:
sc = Motion()
# raise ValueError("'" + self.mode.fetch() + "' is not a supported motion calculation mode.")
return sc
