def __init__(self,
mode,
syslist,
fflist,
outputs,
prng,
paratemp,
step=0,
tsteps=1000,
ttime=0):
"""Initialises Simulation class.
Args:
mode: What kind of simulation is this
syslist: A list of system objects
fflist: A list of forcefield objects
prng: A random number object.
paratemp: A parallel tempering helper class.
outputs: A list of output objects.
step: An optional integer giving the current simulation time step.
Defaults to 0.
tsteps: An optional integer giving the total number of steps. Defaults
to 1000.
ttime: The simulation running time. Used on restart, to keep a
cumulative total.
"""
info(" # Initializing simulation object ", verbosity.low)
self.prng = prng
self.mode = mode
self.syslist = syslist
for s in syslist:
s.prng = self.prng # bind the system's prng to self prng
s.init.init_stage1(s)
if self.mode == "md" and len(syslist) > 1:
warning("Multiple systems will evolve independently in a '" +
self.mode + "' simulation.")
self.fflist = {}
for f in fflist:
self.fflist[f.name] = f
self.outtemplate = outputs
dset(self, "step", depend_value(name="step", value=step))
self.tsteps = tsteps
self.ttime = ttime
self.paratemp = paratemp
self.chk = None
self.rollback = True
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)
dset(self, "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 None:
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()
else:
self.integrator = DummyIntegrator()
self.fixcom = fixcom
if fixatoms is None:
self.fixatoms = np.zeros(0, int)
else:
self.fixatoms = fixatoms
def bind(self, motion):
""" Reference all the variables for simpler access."""
self.beads = motion.beads
self.bias = motion.bias
self.ensemble = motion.ensemble
self.forces = motion.forces
self.prng = motion.prng
self.nm = motion.nm
self.thermostat = motion.thermostat
self.barostat = motion.barostat
self.fixcom = motion.fixcom
self.fixatoms = motion.fixatoms
dset(self, "dt", dget(motion, "dt"))
if motion.enstype == "mts": self.nmts = motion.nmts
def __init__(self, fixcom=False, fixatoms=None):
"""Initialises Motion object.
Args:
fixcom: An optional boolean which decides whether the centre of mass
motion will be constrained or not. Defaults to False.
fixatoms: A list of atoms that should be held fixed to their
initial positions.
"""
dset(self, "dt", depend_value(name="dt", value=0.0))
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)
# Binds integrators
self.integrator.bind(self)
# n times the temperature (for path integral partition function)
dset(
self, "ntemp",
depend_value(name='ntemp',
func=self.get_ntemp,
dependencies=[dget(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.
deppipe(self, "ntemp", self.thermostat, "temp")
deppipe(self, "dt", self.thermostat, "dt")
# the free ring polymer propagator is called in the inner loop, so propagation time should be redefined accordingly.
if self.enstype == "mts":
self.inmts = 1
for mk in self.nmts:
self.inmts *= mk
dset(
self, "deltat",
depend_value(name="deltat",
func=(lambda: self.dt / self.inmts),
dependencies=[dget(self, "dt")]))
deppipe(self, "deltat", 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)
deppipe(self, "ntemp", self.barostat, "temp")
deppipe(self, "dt", self.barostat, "dt")
deppipe(self.ensemble, "pext", self.barostat, "pext")
deppipe(self.ensemble, "stressext", self.barostat, "stressext")
self.barostat.bind(beads, nm, cell, bforce, prng=prng, fixdof=fixdof)
self.ensemble.add_econs(dget(self.thermostat, "ethermo"))
self.ensemble.add_econs(dget(self.barostat, "ebaro"))
#!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":
print "STRESS:", np.trace(self.ensemble.stressext)
if np.trace(self.ensemble.stressext) < 0:
raise ValueError(
"Negative or unspecified stress for a constant-s integrator"
)