def bind(self,
beads=None,
atoms=None,
pm=None,
nm=None,
prng=None,
fixdof=None):
"""Binds the appropriate degrees of freedom to the thermostat.
This takes an object with degrees of freedom, and makes their momentum
and mass vectors members of the thermostat. It also then creates the
objects that will hold the data needed in the thermostat algorithms
and the dependency network.
Args:
beads: An optional beads object to take the mass and momentum vectors
from.
atoms: An optional atoms object to take the mass and momentum vectors
from.
pm: An optional tuple containing a single momentum value and its
conjugate mass.
prng: An optional pseudo random number generator object. Defaults to
Random().
fixdof: An optional integer which can specify the number of constraints
applied to the system. Defaults to zero.
Raises:
TypeError: Raised if no appropriate degree of freedom or object
containing a momentum vector is specified for
the thermostat to couple to.
"""
super(ThermoGLE, self).bind(beads=beads,
atoms=atoms,
pm=pm,
prng=prng,
fixdof=fixdof)
dself = dd(self)
# allocates, initializes or restarts an array of s's
if self.s.shape != (self.ns + 1, len(dself.m)):
if len(self.s) > 0:
warning(
"Mismatch in GLE s array size on restart, will reinitialise to free particle.",
verbosity.low,
)
self.s = np.zeros((self.ns + 1, len(dself.m)))
# Initializes the s vector in the free-particle limit
info(
" GLE additional DOFs initialised to the free-particle limit.",
verbosity.low,
)
SC = stab_cholesky(self.C * Constants.kb)
self.s[:] = np.dot(SC, self.prng.gvec(self.s.shape))
else:
info("GLE additional DOFs initialised from input.",
verbosity.medium)
def bind(self, beads=None, atoms=None, pm=None, nm=None, prng=None, fixdof=None):
"""Binds the appropriate degrees of freedom to the thermostat.
This takes an object with degrees of freedom, and makes their momentum
and mass vectors members of the thermostat. It also then creates the
objects that will hold the data needed in the thermostat algorithms
and the dependency network.
Args:
beads: An optional beads object to take the mass and momentum vectors
from.
atoms: An optional atoms object to take the mass and momentum vectors
from.
pm: An optional tuple containing a single momentum value and its
conjugate mass.
prng: An optional pseudo random number generator object. Defaults to
Random().
fixdof: An optional integer which can specify the number of constraints
applied to the system. Defaults to zero.
Raises:
TypeError: Raised if no appropriate degree of freedom or object
containing a momentum vector is specified for
the thermostat to couple to.
"""
super(ThermoGLE, self).bind(beads=beads, atoms=atoms, pm=pm, prng=prng, fixdof=fixdof)
dself = dd(self)
# allocates, initializes or restarts an array of s's
if self.s.shape != (self.ns + 1, len(dself.m)):
if len(self.s) > 0:
warning("Mismatch in GLE s array size on restart, will reinitialise to free particle.", verbosity.low)
self.s = np.zeros((self.ns + 1, len(dself.m)))
# Initializes the s vector in the free-particle limit
info(" GLE additional DOFs initialised to the free-particle limit.", verbosity.low)
SC = stab_cholesky(self.C * Constants.kb)
self.s[:] = np.dot(SC, self.prng.gvec(self.s.shape))
else:
info("GLE additional DOFs initialised from input.", verbosity.medium)
def bind(self,
beads=None,
atoms=None,
pm=None,
nm=None,
prng=None,
fixdof=None):
"""Binds the appropriate degrees of freedom to the thermostat.
This takes an object with degrees of freedom, and makes their momentum
and mass vectors members of the thermostat. It also then creates the
objects that will hold the data needed in the thermostat algorithms
and the dependency network. Actually, this specific thermostat requires
being called on a beads object.
Args:
nm: An optional normal modes object to take the mass and momentum
vectors from.
prng: An optional pseudo random number generator object. Defaults to
Random().
fixdof: An optional integer which can specify the number of constraints
applied to the system. Defaults to zero.
Raises:
TypeError: Raised if no beads object is specified for
the thermostat to couple to.
"""
dself = dd(self)
if nm is None or not type(nm) is NormalModes:
raise TypeError(
"ThermoNMGLE.bind expects a NormalModes argument to bind to")
if prng is None:
self.prng = Random()
else:
self.prng = prng
if nm.nbeads != self.nb:
raise IndexError(
"The parameters in nm_gle options correspond to a bead number "
+ str(self.nb) +
" which does not match the number of beads in the path" +
str(nm.nbeads))
# allocates, initializes or restarts an array of s's
if self.s.shape != (self.nb, self.ns + 1, nm.natoms * 3):
if len(self.s) > 0:
warning(
"Mismatch in GLE s array size on restart, will reinitialise to free particle.",
verbosity.low,
)
self.s = np.zeros((self.nb, self.ns + 1, nm.natoms * 3))
# Initializes the s vector in the free-particle limit
info(
" GLE additional DOFs initialised to the free-particle limit.",
verbosity.low,
)
for b in range(self.nb):
SC = stab_cholesky(self.C[b] * Constants.kb)
self.s[b] = np.dot(SC, self.prng.gvec(self.s[b].shape))
else:
info("GLE additional DOFs initialised from input.",
verbosity.medium)
prev_ethermo = self.ethermo
# creates a set of thermostats to be applied to individual normal modes
self._thermos = [
ThermoGLE(temp=1, dt=1, A=self.A[b], C=self.C[b])
for b in range(self.nb)
]
# must pipe all the dependencies in such a way that values for the nm
# thermostats are automatically updated based on the "master" thermostat
def make_Agetter(k):
return lambda: self.A[k]
def make_Cgetter(k):
return lambda: self.C[k]
it = 0
for t in self._thermos:
t.s = self.s[it] # gets the s's as a slice of self.s
t.bind(
pm=(nm.pnm[it, :], nm.dynm3[it, :]),
prng=self.prng) # bind thermostat t to the it-th normal mode
# pipes temp and dt
dpipe(dself.temp, dd(t).temp)
dpipe(dself.dt, dd(t).dt)
# here we pipe the A and C of individual NM to the "master" arrays
dd(t).A.add_dependency(dself.A)
dd(t).A._func = make_Agetter(it)
dd(t).C.add_dependency(dself.C)
dd(t).C._func = make_Cgetter(it)
dself.ethermo.add_dependency(dd(t).ethermo)
it += 1
# since the ethermo will be "delegated" to the normal modes thermostats,
# one has to split
# any previously-stored value between the sub-thermostats
for t in self._thermos:
t.ethermo = prev_ethermo / self.nb
dself.ethermo._func = self.get_ethermo
def bind(self, nm=None, prng=None, fixdof=None):
"""Binds the appropriate degrees of freedom to the thermostat.
This takes an object with degrees of freedom, and makes their momentum
and mass vectors members of the thermostat. It also then creates the
objects that will hold the data needed in the thermostat algorithms
and the dependency network. Actually, this specific thermostat requires
being called on a beads object.
Args:
nm: An optional normal modes object to take the mass and momentum
vectors from.
prng: An optional pseudo random number generator object. Defaults to
Random().
fixdof: An optional integer which can specify the number of constraints
applied to the system. Defaults to zero.
Raises:
TypeError: Raised if no beads object is specified for
the thermostat to couple to.
"""
if nm is None or not type(nm) is NormalModes:
raise TypeError("ThermoNMGLE.bind expects a NormalModes argument to bind to")
if prng is None:
self.prng = Random()
else:
self.prng = prng
if (nm.nbeads != self.nb):
raise IndexError("The parameters in nm_gle options correspond to a bead number "+str(self.nb)+ " which does not match the number of beads in the path" + str(nm.nbeads) )
# allocates, initializes or restarts an array of s's
if self.s.shape != (self.nb, self.ns + 1, nm.natoms *3) :
if len(self.s) > 0:
warning("Mismatch in GLE s array size on restart, will reinitialise to free particle.", verbosity.low)
self.s = np.zeros((self.nb, self.ns + 1, nm.natoms*3))
# Initializes the s vector in the free-particle limit
info(" GLE additional DOFs initialised to the free-particle limit.", verbosity.low)
for b in range(self.nb):
SC = stab_cholesky(self.C[b]*Constants.kb)
self.s[b] = np.dot(SC, self.prng.gvec(self.s[b].shape))
else:
info("GLE additional DOFs initialised from input.", verbosity.medium)
prev_ethermo = self.ethermo
# creates a set of thermostats to be applied to individual normal modes
self._thermos = [ThermoGLE(temp=1, dt=1, A=self.A[b], C=self.C[b]) for b in range(self.nb)]
# must pipe all the dependencies in such a way that values for the nm
# thermostats are automatically updated based on the "master" thermostat
def make_Agetter(k):
return lambda: self.A[k]
def make_Cgetter(k):
return lambda: self.C[k]
it = 0
for t in self._thermos:
t.s = self.s[it] # gets the s's as a slice of self.s
t.bind(pm=(nm.pnm[it,:],nm.dynm3[it,:]), prng=self.prng) # bind thermostat t to the it-th normal mode
# pipes temp and dt
deppipe(self,"temp", t, "temp")
deppipe(self,"dt", t, "dt")
# here we pipe the A and C of individual NM to the "master" arrays
dget(t,"A").add_dependency(dget(self,"A"))
dget(t,"A")._func = make_Agetter(it)
dget(t,"C").add_dependency(dget(self,"C"))
dget(t,"C")._func = make_Cgetter(it)
dget(self,"ethermo").add_dependency(dget(t,"ethermo"))
it += 1
# since the ethermo will be "delegated" to the normal modes thermostats,
# one has to split
# any previously-stored value between the sub-thermostats
for t in self._thermos:
t.ethermo = prev_ethermo/self.nb
dget(self,"ethermo")._func = self.get_ethermo;