def __init__(self):
self._scheduled = False
self._simulation = None
self._updaters = syncedlist.SyncedList(Updater,
_triggered_op_conversion)
self._writers = syncedlist.SyncedList(Writer, _triggered_op_conversion)
self._tuners = syncedlist.SyncedList(
Tuner, syncedlist._PartialGetAttr('_cpp_obj'))
self._computes = syncedlist.SyncedList(
Compute, syncedlist._PartialGetAttr('_cpp_obj'))
self._integrator = None
self._tuners.append(ParticleSorter())
def __init__(self, forces, constraints, methods):
forces = [] if forces is None else forces
constraints = [] if constraints is None else constraints
methods = [] if methods is None else methods
self._forces = syncedlist.SyncedList(
Force, syncedlist._PartialGetAttr('_cpp_obj'), iterable=forces)
self._constraints = syncedlist.SyncedList(
ConstraintForce,
syncedlist._PartialGetAttr('_cpp_obj'),
iterable=constraints)
self._methods = syncedlist.SyncedList(
Method, syncedlist._PartialGetAttr('_cpp_obj'), iterable=methods)
def __init__(self, forces, constraints, methods, rigid):
forces = [] if forces is None else forces
constraints = [] if constraints is None else constraints
methods = [] if methods is None else methods
self._forces = syncedlist.SyncedList(
Force, syncedlist._PartialGetAttr('_cpp_obj'), iterable=forces)
self._constraints = syncedlist.SyncedList(
OnlyTypes(Constraint, disallow_types=(Rigid,)),
syncedlist._PartialGetAttr('_cpp_obj'),
iterable=constraints)
self._methods = syncedlist.SyncedList(
Method, syncedlist._PartialGetAttr('_cpp_obj'), iterable=methods)
param_dict = ParameterDict(rigid=OnlyTypes(Rigid, allow_none=True))
if rigid is not None and rigid._added:
raise ValueError("Rigid object can only belong to one integrator.")
param_dict["rigid"] = rigid
self._param_dict.update(param_dict)
def __init__(self,
dt,
force_tol,
angmom_tol,
energy_tol,
integrate_rotational_dof=False,
forces=None,
constraints=None,
methods=None,
rigid=None,
min_steps_adapt=5,
finc_dt=1.1,
fdec_dt=0.5,
alpha_start=0.1,
fdec_alpha=0.99,
min_steps_conv=10):
super().__init__(forces, constraints, methods, rigid)
pdict = ParameterDict(
dt=float(dt),
integrate_rotational_dof=bool(integrate_rotational_dof),
min_steps_adapt=OnlyTypes(int, preprocess=positive_real),
finc_dt=float(finc_dt),
fdec_dt=float(fdec_dt),
alpha_start=float(alpha_start),
fdec_alpha=float(fdec_alpha),
force_tol=float(force_tol),
angmom_tol=float(angmom_tol),
energy_tol=float(energy_tol),
min_steps_conv=OnlyTypes(int, preprocess=positive_real),
_defaults={
'min_steps_adapt': 5,
'min_steps_conv': 10
})
self._param_dict.update(pdict)
# set these values explicitly so they can be validated
self.min_steps_adapt = min_steps_adapt
self.min_steps_conv = min_steps_conv
# have to remove methods from old syncedlist so new syncedlist doesn't
# think members are attached to multiple syncedlists
self._methods.clear()
methods_list = syncedlist.SyncedList(
OnlyTypes((hoomd.md.methods.NVE, hoomd.md.methods.NPH,
hoomd.md.methods.rattle.NVE)),
syncedlist._PartialGetAttr("_cpp_obj"),
iterable=methods)
self._methods = methods_list
def __init__(self, alchemical_dof):
self._alchemical_dof = syncedlist.SyncedList(
AlchemicalDOF, syncedlist._PartialGetAttr("_cpp_obj"))
if alchemical_dof is not None:
self._alchemical_dof.extend(alchemical_dof)