class Dynamics(Motion):
"""self (path integral) molecular dynamics class.
Gives the standard methods and attributes needed in all the
dynamics classes.
Attributes:
beads: A beads object giving the atoms positions.
cell: A cell object giving the system box.
forces: A forces object giving the virial and the forces acting on
each bead.
prng: A random number generator object.
nm: An object which does the normal modes transformation.
Depend objects:
econs: The conserved energy quantity appropriate to the given
ensemble. Depends on the various energy terms which make it up,
which are different depending on the ensemble.he
temp: The system temperature.
dt: The timestep for the algorithms.
ntemp: The simulation temperature. Will be nbeads times higher than
the system temperature as PIMD calculations are done at this
effective classical temperature.
"""
def __init__(self, timestep, mode="nve", splitting="obabo", thermostat=None, barostat=None, fixcom=False, fixatoms=None, nmts=None):
"""Initialises a "dynamics" motion object.
Args:
dt: The timestep of the simulation algorithms.
fixcom: An optional boolean which decides whether the centre of mass
motion will be constrained or not. Defaults to False.
"""
super(Dynamics, self).__init__(fixcom=fixcom, fixatoms=fixatoms)
dself = dd(self)
# initialize time step. this is the master time step that covers a full time step
dd(self).dt = depend_value(name='dt', value=timestep)
if thermostat is None:
self.thermostat = Thermostat()
else:
self.thermostat = thermostat
if nmts is None or len(nmts) == 0:
dd(self).nmts = depend_array(name="nmts", value=np.asarray([1], int))
else:
dd(self).nmts = depend_array(name="nmts", value=np.asarray(nmts, int))
if barostat is None:
self.barostat = Barostat()
else:
self.barostat = barostat
self.enstype = mode
if self.enstype == "nve":
self.integrator = NVEIntegrator()
elif self.enstype == "nvt":
self.integrator = NVTIntegrator()
elif self.enstype == "npt":
self.integrator = NPTIntegrator()
elif self.enstype == "nst":
self.integrator = NSTIntegrator()
elif self.enstype == "sc":
self.integrator = SCIntegrator()
elif self.enstype == "scnpt":
self.integrator = SCNPTIntegrator()
else:
self.integrator = DummyIntegrator()
# splitting mode for the integrators
dd(self).splitting = depend_value(name='splitting', value=splitting)
# constraints
self.fixcom = fixcom
if fixatoms is None:
self.fixatoms = np.zeros(0, int)
else:
self.fixatoms = fixatoms
def bind(self, ens, beads, nm, cell, bforce, prng):
"""Binds ensemble beads, cell, bforce, and prng to the dynamics.
This takes a beads object, a cell object, a forcefield object and a
random number generator object and makes them members of the ensemble.
It also then creates the objects that will hold the data needed in the
ensemble algorithms and the dependency network. Note that the conserved
quantity is defined in the init, but as each ensemble has a different
conserved quantity the dependencies are defined in bind.
Args:
beads: The beads object from whcih the bead positions are taken.
nm: A normal modes object used to do the normal modes transformation.
cell: The cell object from which the system box is taken.
bforce: The forcefield object from which the force and virial are
taken.
prng: The random number generator object which controls random number
generation.
"""
super(Dynamics, self).bind(ens, beads, nm, cell, bforce, prng)
# Checks if the number of mts levels is equal to the dimensionality of the mts weights.
if (len(self.nmts) != self.forces.nmtslevels):
raise ValueError("The number of mts levels for the integrator does not agree with the mts_weights of the force components.")
# Strips off depend machinery for easier referencing.
dself = dd(self)
dthrm = dd(self.thermostat)
dbaro = dd(self.barostat)
dnm = dd(self.nm)
dens = dd(self.ensemble)
# n times the temperature (for path integral partition function)
dself.ntemp = depend_value(name='ntemp', func=self.get_ntemp, dependencies=[dens.temp])
# fixed degrees of freedom count
fixdof = len(self.fixatoms) * 3 * self.beads.nbeads
if self.fixcom:
fixdof += 3
# first makes sure that the thermostat has the correct temperature and timestep, then proceeds with binding it.
dpipe(dself.ntemp, dthrm.temp)
# depending on the kind, the thermostat might work in the normal mode or the bead representation.
self.thermostat.bind(beads=self.beads, nm=self.nm, prng=prng, fixdof=fixdof)
# first makes sure that the barostat has the correct stress andf timestep, then proceeds with binding it.
dpipe(dself.ntemp, dbaro.temp)
dpipe(dens.pext, dbaro.pext)
dpipe(dens.stressext, dbaro.stressext)
self.barostat.bind(beads, nm, cell, bforce, prng=prng, fixdof=fixdof, nmts=len(self.nmts))
# now that the timesteps are decided, we proceed to bind the integrator.
self.integrator.bind(self)
self.ensemble.add_econs(dthrm.ethermo)
self.ensemble.add_econs(dbaro.ebaro)
# adds the potential, kinetic enrgy and the cell jacobian to the ensemble
self.ensemble.add_xlpot(dbaro.pot)
self.ensemble.add_xlpot(dbaro.cell_jacobian)
self.ensemble.add_xlkin(dbaro.kin)
# applies constraints immediately after initialization.
self.integrator.pconstraints()
#!TODO THOROUGH CLEAN-UP AND CHECK
if self.enstype == "nvt" or self.enstype == "npt" or self.enstype == "nst":
if self.ensemble.temp < 0:
raise ValueError("Negative or unspecified temperature for a constant-T integrator")
if self.enstype == "npt":
if type(self.barostat) is Barostat:
raise ValueError("The barostat and its mode have to be specified for constant-p integrators")
if self.ensemble.pext < 0:
raise ValueError("Negative or unspecified pressure for a constant-p integrator")
elif self.enstype == "nst":
if np.trace(self.ensemble.stressext) < 0:
raise ValueError("Negative or unspecified stress for a constant-s integrator")
def get_ntemp(self):
"""Returns the PI simulation temperature (P times the physical T)."""
return self.ensemble.temp * self.beads.nbeads
def step(self, step=None):
self.integrator.step(step)
class Dynamics(Motion):
"""self (path integral) molecular dynamics class.
Gives the standard methods and attributes needed in all the
dynamics classes.
Attributes:
beads: A beads object giving the atoms positions.
cell: A cell object giving the system box.
forces: A forces object giving the virial and the forces acting on
each bead.
prng: A random number generator object.
nm: An object which does the normal modes transformation.
Depend objects:
econs: The conserved energy quantity appropriate to the given
ensemble. Depends on the various energy terms which make it up,
which are different depending on the ensemble.he
temp: The system temperature.
dt: The timestep for the algorithms.
ntemp: The simulation temperature. Will be nbeads times higher than
the system temperature as PIMD calculations are done at this
effective classical temperature.
"""
def __init__(self, timestep, mode="nve", thermostat=None, barostat=None, fixcom=False, fixatoms=None, nmts=None):
"""Initialises a "dynamics" motion object.
Args:
dt: The timestep of the simulation algorithms.
fixcom: An optional boolean which decides whether the centre of mass
motion will be constrained or not. Defaults to False.
"""
super(Dynamics, self).__init__(fixcom=fixcom, fixatoms=fixatoms)
dself = dd(self)
dself.dt = depend_value(name='dt', value=timestep)
if thermostat is None:
self.thermostat = Thermostat()
else:
self.thermostat = thermostat
if barostat is None:
self.barostat = Barostat()
else:
self.barostat = barostat
if nmts is np.zeros(0, int):
self.nmts = np.asarray([1], int)
elif nmts is None or len(nmts) == 0:
self.nmts = np.asarray([1], int)
else:
self.nmts = np.asarray(nmts)
self.enstype = mode
if self.enstype == "nve":
self.integrator = NVEIntegrator()
elif self.enstype == "nvt":
self.integrator = NVTIntegrator()
elif self.enstype == "npt":
self.integrator = NPTIntegrator()
elif self.enstype == "nst":
self.integrator = NSTIntegrator()
elif self.enstype == "mts":
self.integrator = MTSIntegrator()
elif self.enstype == "sc":
self.integrator = SCIntegrator()
else:
self.integrator = DummyIntegrator()
self.fixcom = fixcom
if fixatoms is None:
self.fixatoms = np.zeros(0, int)
else:
self.fixatoms = fixatoms
def bind(self, ens, beads, nm, cell, bforce, prng):
"""Binds ensemble beads, cell, bforce, and prng to the dynamics.
This takes a beads object, a cell object, a forcefield object and a
random number generator object and makes them members of the ensemble.
It also then creates the objects that will hold the data needed in the
ensemble algorithms and the dependency network. Note that the conserved
quantity is defined in the init, but as each ensemble has a different
conserved quantity the dependencies are defined in bind.
Args:
beads: The beads object from whcih the bead positions are taken.
nm: A normal modes object used to do the normal modes transformation.
cell: The cell object from which the system box is taken.
bforce: The forcefield object from which the force and virial are
taken.
prng: The random number generator object which controls random number
generation.
"""
super(Dynamics, self).bind(ens, beads, nm, cell, bforce, prng)
dself = dd(self)
# Checks if the number of mts levels is equal to the dimensionality of the mts weights.
if (len(self.nmts) != self.forces.nmtslevels):
raise ValueError("The number of mts levels for the integrator does not agree with the mts_weights of the force components.")
# Binds integrators
self.integrator.bind(self)
dself = dd(self)
# n times the temperature (for path integral partition function)
dself.ntemp = depend_value(name='ntemp', func=self.get_ntemp,
dependencies=[dd(self.ensemble).temp])
self.integrator.pconstraints()
fixdof = len(self.fixatoms) * 3 * self.beads.nbeads
if self.fixcom:
fixdof += 3
# first makes sure that the thermostat has the correct temperature, then proceed with binding it.
dpipe(dself.ntemp, dd(self.thermostat).temp)
dpipe(dself.dt, dd(self.thermostat).dt)
# the free ring polymer propagator is called in the inner loop, so propagation time should be redefined accordingly.
self.inmts = 1
for mk in self.nmts: self.inmts *= mk
dself.deltat = depend_value(name="deltat", func=(lambda: self.dt / self.inmts), dependencies=[dself.dt])
dpipe(dself.deltat, dd(self.nm).dt)
# depending on the kind, the thermostat might work in the normal mode or the bead representation.
self.thermostat.bind(beads=self.beads, nm=self.nm, prng=prng, fixdof=fixdof)
dbarostat = dd(self.barostat)
dpipe(dself.ntemp, dbarostat.temp)
dpipe(dself.dt, dbarostat.dt)
dpipe(dd(self.ensemble).pext, dbarostat.pext)
dpipe(dd(self.ensemble).stressext, dbarostat.stressext)
#!TODO the barostat should also be connected to the bias stress
self.barostat.bind(beads, nm, cell, bforce, prng=prng, fixdof=fixdof, bias=ens.bias)
self.ensemble.add_econs(dd(self.thermostat).ethermo)
self.ensemble.add_econs(dd(self.barostat).ebaro)
# adds potential and kinetic energy for the barostat to the ensemble
self.ensemble.add_xlpot(dd(self.barostat).pot)
self.ensemble.add_xlkin(dd(self.barostat).kin)
#!TODO THOROUGH CLEAN-UP AND CHECK
# if self.enstype in ["nvt", "npt", "nst"]:
if self.enstype == "nvt" or self.enstype == "npt" or self.enstype == "nst":
if self.ensemble.temp < 0:
raise ValueError("Negative or unspecified temperature for a constant-T integrator")
if self.enstype == "npt":
if type(self.barostat) is Barostat:
raise ValueError("The barostat and its mode have to be specified for constant-p integrators")
if self.ensemble.pext < 0:
raise ValueError("Negative or unspecified pressure for a constant-p integrator")
elif self.enstype == "nst":
if np.trace(self.ensemble.stressext) < 0:
raise ValueError("Negative or unspecified stress for a constant-s integrator")
def get_ntemp(self):
"""Returns the PI simulation temperature (P times the physical T)."""
return self.ensemble.temp * self.beads.nbeads
def step(self, step=None):
self.integrator.step(step)
class Dynamics(Motion):
"""self (path integral) molecular dynamics class.
Gives the standard methods and attributes needed in all the
dynamics classes.
Attributes:
beads: A beads object giving the atoms positions.
cell: A cell object giving the system box.
forces: A forces object giving the virial and the forces acting on
each bead.
prng: A random number generator object.
nm: An object which does the normal modes transformation.
Depend objects:
econs: The conserved energy quantity appropriate to the given
ensemble. Depends on the various energy terms which make it up,
which are different depending on the ensemble.he
temp: The system temperature.
dt: The timestep for the algorithms.
ntemp: The simulation temperature. Will be nbeads times higher than
the system temperature as PIMD calculations are done at this
effective classical temperature.
"""
def __init__(
self,
timestep,
mode="nve",
splitting="obabo",
thermostat=None,
barostat=None,
fixcom=False,
fixatoms=None,
nmts=None,
):
"""Initialises a "dynamics" motion object.
Args:
dt: The timestep of the simulation algorithms.
fixcom: An optional boolean which decides whether the centre of mass
motion will be constrained or not. Defaults to False.
"""
super(Dynamics, self).__init__(fixcom=fixcom, fixatoms=fixatoms)
dself = dd(self) # noqa
# initialize time step. this is the master time step that covers a full time step
dd(self).dt = depend_value(name="dt", value=timestep)
if thermostat is None:
self.thermostat = Thermostat()
else:
if (
thermostat.__class__.__name__ is ("ThermoPILE_G" or "ThermoNMGLEG ")
) and (len(fixatoms) > 0):
softexit.trigger(
"!! Sorry, fixed atoms and global thermostat on the centroid not supported. Use a local thermostat. !!"
)
self.thermostat = thermostat
if nmts is None or len(nmts) == 0:
dd(self).nmts = depend_array(name="nmts", value=np.asarray([1], int))
else:
dd(self).nmts = depend_array(name="nmts", value=np.asarray(nmts, int))
if barostat is None:
self.barostat = Barostat()
else:
self.barostat = barostat
self.enstype = mode
if self.enstype == "nve":
self.integrator = NVEIntegrator()
elif self.enstype == "nvt":
self.integrator = NVTIntegrator()
elif self.enstype == "nvt-cc":
self.integrator = NVTCCIntegrator()
elif self.enstype == "npt":
self.integrator = NPTIntegrator()
elif self.enstype == "nst":
self.integrator = NSTIntegrator()
elif self.enstype == "sc":
self.integrator = SCIntegrator()
elif self.enstype == "scnpt":
self.integrator = SCNPTIntegrator()
else:
self.integrator = DummyIntegrator()
# splitting mode for the integrators
dd(self).splitting = depend_value(name="splitting", value=splitting)
# constraints
self.fixcom = fixcom
if fixatoms is None:
self.fixatoms = np.zeros(0, int)
else:
self.fixatoms = fixatoms
def get_fixdof(self):
"""Calculate the number of fixed degrees of freedom, required for
temperature and pressure calculations.
"""
fixdof = len(self.fixatoms) * 3 * self.beads.nbeads
if self.fixcom:
fixdof += 3
return fixdof
def bind(self, ens, beads, nm, cell, bforce, prng, omaker):
"""Binds ensemble beads, cell, bforce, and prng to the dynamics.
This takes a beads object, a cell object, a forcefield object and a
random number generator object and makes them members of the ensemble.
It also then creates the objects that will hold the data needed in the
ensemble algorithms and the dependency network. Note that the conserved
quantity is defined in the init, but as each ensemble has a different
conserved quantity the dependencies are defined in bind.
Args:
beads: The beads object from which the bead positions are taken.
nm: A normal modes object used to do the normal modes transformation.
cell: The cell object from which the system box is taken.
bforce: The forcefield object from which the force and virial are
taken.
prng: The random number generator object which controls random number
generation.
"""
super(Dynamics, self).bind(ens, beads, nm, cell, bforce, prng, omaker)
# Checks if the number of mts levels is equal to the dimensionality of the mts weights.
if len(self.nmts) != self.forces.nmtslevels:
raise ValueError(
"The number of mts levels for the integrator does not agree with the mts_weights of the force components."
)
# Strips off depend machinery for easier referencing.
dself = dd(self)
dthrm = dd(self.thermostat)
dbaro = dd(self.barostat)
dnm = dd(self.nm) # noqa
dens = dd(self.ensemble)
# n times the temperature (for path integral partition function)
dself.ntemp = depend_value(
name="ntemp", func=self.get_ntemp, dependencies=[dens.temp]
)
# fixed degrees of freedom count
fixdof = self.get_fixdof()
# first makes sure that the thermostat has the correct temperature and timestep, then proceeds with binding it.
dpipe(dself.ntemp, dthrm.temp)
# depending on the kind, the thermostat might work in the normal mode or the bead representation.
self.thermostat.bind(beads=self.beads, nm=self.nm, prng=prng, fixdof=fixdof)
# first makes sure that the barostat has the correct stress and timestep, then proceeds with binding it.
dpipe(dself.ntemp, dbaro.temp)
dpipe(dens.pext, dbaro.pext)
dpipe(dens.stressext, dbaro.stressext)
self.barostat.bind(
beads,
nm,
cell,
bforce,
bias=self.ensemble.bias,
prng=prng,
fixdof=fixdof,
nmts=len(self.nmts),
)
# now that the timesteps are decided, we proceed to bind the integrator.
self.integrator.bind(self)
self.ensemble.add_econs(dthrm.ethermo)
self.ensemble.add_econs(dbaro.ebaro)
# adds the potential, kinetic energy and the cell Jacobian to the ensemble
self.ensemble.add_xlpot(dbaro.pot)
self.ensemble.add_xlpot(dbaro.cell_jacobian)
self.ensemble.add_xlkin(dbaro.kin)
# applies constraints immediately after initialization.
self.integrator.pconstraints()
# TODO THOROUGH CLEAN-UP AND CHECK
if (
self.enstype == "nvt"
or self.enstype == "nvt-cc"
or self.enstype == "npt"
or self.enstype == "nst"
):
if self.ensemble.temp < 0:
raise ValueError(
"Negative or unspecified temperature for a constant-T integrator"
)
if self.enstype == "npt":
if type(self.barostat) is Barostat:
raise ValueError(
"The barostat and its mode have to be specified for constant-p integrators"
)
if np.allclose(self.ensemble.pext, -12345):
raise ValueError("Unspecified pressure for a constant-p integrator")
elif self.enstype == "nst":
if np.allclose(self.ensemble.stressext.diagonal(), -12345):
raise ValueError("Unspecified stress for a constant-s integrator")
def get_ntemp(self):
"""Returns the PI simulation temperature (P times the physical T)."""
return self.ensemble.temp * self.beads.nbeads
def step(self, step=None):
"""Advances the dynamics by one time step"""
self.integrator.step(step)
self.ensemble.time += self.dt # increments internal time