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 fcell:
warning("Overwriting previous cell parameters",
verbosity.medium)
if v.mode == "pdb":
rh = init_pdb(v.value)[1].h
elif v.mode == "chk":
rh = init_chk(v.value)[1].h
else:
rh = v.value.reshape((3, 3))
rh *= unit_to_internal("length", v.units, 1.0)
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
else:
rm = init_beads(v, self.nbeads).m
rm *= unit_to_internal("mass", v.units, 1.0)
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)
rq *= unit_to_internal("length", v.units, 1.0)
(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(dt=simul.ensemble.dt, temp=simul.ensemble.temp)
rnm.bind(rbeads, rens)
# 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)
rp *= unit_to_internal("momentum", v.units, 1.0)
(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)
rv *= unit_to_internal("velocity", v.units, 1.0)
(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]
elif v.bead >= 0:
rv *= simul.beads.m3[0]
else:
rv *= simul.beads.m3
rv *= np.sqrt(self.nbeads / nbeads)
set_vector(v, simul.beads.p, rv)
fmom = True
elif k == "thermostat":
pass # thermostats must be initialized 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 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)