def __init__(self,
filter,
flow_target,
slab_direction,
flow_direction,
n_slabs,
max_slab=-1,
min_slab=-1):
params = ParameterDict(
filter=hoomd.filter.ParticleFilter,
flow_target=hoomd.variant.Variant,
slab_direction=OnlyTypes(str,
strict=True,
postprocess=self._to_lowercase),
flow_direction=OnlyTypes(str,
strict=True,
postprocess=self._to_lowercase),
n_slabs=OnlyTypes(int, preprocess=self._preprocess_n_slabs),
max_slab=OnlyTypes(int, preprocess=self._preprocess_max_slab),
min_slab=OnlyTypes(int, preprocess=self._preprocess_min_slab),
flow_epsilon=float(1e-2))
params.update(
dict(filter=filter,
flow_target=flow_target,
slab_direction=slab_direction,
flow_direction=flow_direction,
n_slabs=n_slabs))
self._param_dict.update(params)
self._param_dict.update(dict(max_slab=max_slab))
self._param_dict.update(dict(min_slab=min_slab))
# This updater has to be applied every timestep
super().__init__(hoomd.trigger.Periodic(1))
def __init__(self, target, solver, max_chain_time=None):
# A flag for knowing when to update the maximum move sizes
self._update_chain_time = False
# A counter when tuned reaches 1 it means that the tuner has reported
# being tuned one time in a row. However, as the first run of the tuner
# is likely at timestep 0 which means that the counters are (0, 0) and
# _ChainTimeTuneDefinition returns y == target for that case, we need
# two rounds of tuning to be sure that we have converged. Since, in
# general, solvers do not do much if any work on already tuned tunables,
# this is not a performance problem.
self._tuned = 0
self._is_attached = False
self._chain_time_def = _ChainTimeTuneDefinition(
target, (self._min_chain_time, max_chain_time))
param_dict = ParameterDict(
target=OnlyTypes(float,
postprocess=self._process_chain_time_target),
solver=SolverStep,
max_chain_time=OnlyTypes(
float,
allow_none=True,
postprocess=self._process_chain_time_range),
min_chain_time=OnlyTypes(
float, postprocess=self._process_chain_time_range))
self._param_dict.update(param_dict)
self.target = target
self.solver = solver
self.max_chain_time = max_chain_time
self.min_chain_time = self._min_chain_time
def __init__(self):
self._compute = list()
self._scheduled = False
self._updaters = SyncedList(OnlyTypes(Updater),
_triggered_op_conversion)
self._writers = SyncedList(OnlyTypes(Writer), _triggered_op_conversion)
self._tuners = SyncedList(OnlyTypes(Tuner), lambda x: x._cpp_obj)
self._computes = SyncedList(OnlyTypes(Compute), lambda x: x._cpp_obj)
self._integrator = None
self._tuners.append(ParticleSorter())
def __init__(self, filter, limit=None):
# store metadata
param_dict = ParameterDict(
filter=ParticleFilter,
limit=OnlyTypes(float, allow_none=True),
zero_force=OnlyTypes(bool, allow_none=False),
)
param_dict.update(dict(filter=filter, limit=limit, zero_force=False))
# set defaults
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,
moves,
target,
solver,
types=None,
max_translation_move=None,
max_rotation_move=None):
super().__init__(target, solver)
# A flag for knowing when to update the maximum move sizes
self._should_update_move_sizes = False
# set up maximum trial move sizes
t_moves = TypeParameter(
'max_translation_move', 'particle_type',
TypeParameterDict(OnlyTypes(
float,
postprocess=self._flag_move_size_update,
allow_none=True),
len_keys=1))
r_moves = TypeParameter(
'max_rotation_move', 'particle_type',
TypeParameterDict(OnlyTypes(
float,
postprocess=self._flag_move_size_update,
allow_none=True),
len_keys=1))
self._typeparam_dict = {
'max_translation_move': t_moves,
'max_rotation_move': r_moves
}
# This is a bit complicated because we are having to ensure that we keep
# the list of tunables and the solver updated with the changes to
# attributes. However, these are simply forwarding a change along.
param_dict = ParameterDict(
moves=OnlyIf(to_type_converter([OnlyFrom(['a', 'd'])]),
postprocess=self._update_moves),
types=OnlyIf(to_type_converter([str]),
postprocess=self._update_types,
allow_none=True),
)
self._param_dict.update(param_dict)
self.target = target
self.solver = solver
self.moves = moves
self.types = types
self.max_rotation_move.default = max_rotation_move
self.max_translation_move.default = max_translation_move
if types is not None:
self._update_tunables(new_moves=moves, new_types=types)
def __init__(self, filter, limit=None, manifold_constraint=None, tolerance=0.000001):
# store metadata
param_dict = ParameterDict(
filter=ParticleFilter,
limit=OnlyTypes(float, allow_none=True),
zero_force=OnlyTypes(bool, allow_none=False),
)
param_dict.update(dict(filter=filter, limit=limit, zero_force=False))
# set defaults
self._param_dict.update(param_dict)
super().__init__(manifold_constraint,tolerance)
def __init__(self, box1, box2, variant, trigger, filter=All()):
params = ParameterDict(box1=OnlyTypes(Box,
preprocess=box_preprocessing),
box2=OnlyTypes(Box,
preprocess=box_preprocessing),
variant=Variant,
filter=ParticleFilter)
params['box1'] = box1
params['box2'] = box2
params['variant'] = variant
params['trigger'] = trigger
params['filter'] = filter
self._param_dict.update(params)
super().__init__(trigger)
def __init__(self, filter, manifold_constraint):
# store metadata
super().__init__(filter)
param_dict = ParameterDict(
manifold_constraint=OnlyTypes(Manifold, allow_none=False))
param_dict["manifold_constraint"] = manifold_constraint
self._param_dict.update(param_dict)
def __init__(self, filter, rotation_diff=0.1):
# store metadata
param_dict = ParameterDict(
filter=ParticleFilter,
rotation_diff=float(rotation_diff),
constraint=OnlyTypes(
ConstraintForce, allow_none=True, preprocess=ellip_preprocessing
),
)
param_dict.update(
dict(
constraint=None,
rotation_diff=rotation_diff,
filter=filter,
)
)
# set defaults
self._param_dict.update(param_dict)
active_force = TypeParameter(
"active_force",
type_kind="particle_types",
param_dict=TypeParameterDict((1.0, 0.0, 0.0), len_keys=1),
)
active_torque = TypeParameter(
"active_torque",
type_kind="particle_types",
param_dict=TypeParameterDict((0.0, 0.0, 0.0), len_keys=1),
)
self._extend_typeparam([active_force, active_torque])
def __init__(self,
filter,
manifold_constraint,
tolerance=0.000001,
alpha=None):
# store metadata
param_dict = ParameterDict(
filter=ParticleFilter,
alpha=OnlyTypes(float, allow_none=True),
)
param_dict.update(dict(alpha=alpha, filter=filter))
# set defaults
self._param_dict.update(param_dict)
gamma = TypeParameter('gamma',
type_kind='particle_types',
param_dict=TypeParameterDict(1., len_keys=1))
gamma_r = TypeParameter('gamma_r',
type_kind='particle_types',
param_dict=TypeParameterDict((1., 1., 1.),
len_keys=1))
self._extend_typeparam([gamma, gamma_r])
super().__init__(manifold_constraint, tolerance)
def __setstate__(self, state):
if state['_param_dict']['output'] is None:
del state['_param_dict']['output']
state['_param_dict']['output'] = stdout
state['_param_dict']._type_converter['output'] = OnlyTypes(
_OutputWriter, postprocess=_ensure_writable),
self.__dict__ = state
def __init__(self, manifold_constraint, tolerance):
param_dict = ParameterDict(manifold_constraint=OnlyTypes(
Manifold, allow_none=False),
tolerance=float(tolerance))
param_dict['manifold_constraint'] = manifold_constraint
# set defaults
self._param_dict.update(param_dict)
def __init__(self,
logger,
output=stdout,
header_sep='.',
delimiter=' ',
pretty=True,
max_precision=10,
max_header_len=None):
def writable(fh):
if not fh.writable():
raise ValueError("file-like object must be writable.")
return fh
param_dict = ParameterDict(header_sep=str,
delimiter=str,
min_column_width=int,
max_header_len=OnlyTypes(int,
allow_none=True),
pretty=bool,
max_precision=int,
output=OnlyTypes(_OutputWriter,
postprocess=writable),
logger=Logger)
param_dict.update(
dict(header_sep=header_sep,
delimiter=delimiter,
min_column_width=max(10, max_precision + 6),
max_header_len=max_header_len,
max_precision=max_precision,
pretty=pretty,
output=output,
logger=logger))
self._param_dict = param_dict
# internal variables that are not part of the state.
# Ensure that only scalar and potentially string are set for the logger
if (LoggerCategories.scalar not in logger.categories
or logger.categories & self._invalid_logger_categories !=
LoggerCategories.NONE):
raise ValueError(
"Given Logger must have the scalar categories set.")
self._cur_headers_with_width = dict()
self._fmt = _Formatter(pretty, max_precision)
self._comm = None
def __init__(self, trigger=200, grid=None):
super().__init__(trigger)
sorter_params = ParameterDict(
grid=OnlyTypes(int,
postprocess=ParticleSorter._to_power_of_two,
preprocess=ParticleSorter._natural_number,
allow_none=True))
self._param_dict.update(sorter_params)
self.grid = grid
def __init__(self, trigger=200, grid=None):
self._param_dict = ParameterDict(
trigger=Trigger,
grid=OnlyTypes(int,
postprocess=ParticleSorter._to_power_of_two,
preprocess=ParticleSorter._natural_number,
allow_none=True))
self.trigger = trigger
self.grid = grid
def __init__(self, nlist, default_r_cut=None, mode="none"):
self._nlist = OnlyTypes(md.nlist.NList, strict=True)(nlist)
tp_r_cut = TypeParameter('r_cut', 'particle_types',
TypeParameterDict(positive_real, len_keys=2))
if default_r_cut is not None:
tp_r_cut.default = default_r_cut
self._param_dict.update(ParameterDict(mode=OnlyFrom(['none', 'shift'])))
self.mode = mode
self._add_typeparam(tp_r_cut)
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,
default_d=0.1,
default_a=0.1,
chain_probability=0.5,
chain_time=0.5,
update_fraction=0.5,
nselect=1):
# initialize base class
super().__init__(default_d, default_a, 0.5, nselect)
# Set base parameter dict for hpmc chain integrators
param_dict = ParameterDict(
chain_probability=OnlyTypes(
float, postprocess=self._process_chain_probability),
chain_time=OnlyTypes(float, postprocess=self._process_chain_time),
update_fraction=OnlyTypes(
float, postprocess=self._process_update_fraction))
self._param_dict.update(param_dict)
self.chain_probability = chain_probability
self.chain_time = chain_time
self.update_fraction = update_fraction
def __init__(self, manifold_constraint, tolerance):
if manifold_constraint == None and tolerance != 1e-6:
raise TypeError("The tolerance for RATTLE integration has been changed but "
"manifold_constraint is not specified!")
param_dict = ParameterDict(
manifold_constraint = OnlyTypes(Manifold, allow_none=True),
tolerance=float(tolerance)
)
param_dict['manifold_constraint'] = manifold_constraint
# set defaults
self._param_dict.update(param_dict)
def __init__(self, buffer, exclusions, rebuild_check_delay, check_dist,
mesh):
validate_exclusions = OnlyFrom([
'bond', 'angle', 'constraint', 'dihedral', 'special_pair', 'body',
'1-3', '1-4', 'meshbond'
])
validate_mesh = OnlyTypes(Mesh, allow_none=True)
# default exclusions
params = ParameterDict(exclusions=[validate_exclusions],
buffer=float(buffer),
rebuild_check_delay=int(rebuild_check_delay),
check_dist=bool(check_dist))
params["exclusions"] = exclusions
self._param_dict.update(params)
self._mesh = validate_mesh(mesh)
def __init__(
self,
boxmc,
moves,
target,
solver,
max_move_size=None,
):
super().__init__(target, solver)
# Flags for knowing when to update classes attributes
self._update_move_sizes = False
self._should_update_tunables = False
# This is a bit complicated because we are having to ensure that we keep
# the list of tunables and the solver updated with the changes to
# attributes. However, these are simply forwarding a change along.
params = ParameterDict(
boxmc=hoomd.hpmc.update.BoxMC,
moves=[
OnlyFrom(_MoveSizeTuneDefinition.acceptable_attrs,
postprocess=self._flag_new_tunables)
],
max_move_size=OnlyIf(
to_type_converter({
attr: OnlyTypes(float,
allow_none=True,
postprocess=self._flag_move_size_update)
for attr in _MoveSizeTuneDefinition.acceptable_attrs
}),))
params["boxmc"] = boxmc
params["moves"] = moves
if max_move_size is None:
max_move_size = {
attr: None for attr in _MoveSizeTuneDefinition.acceptable_attrs
}
params["max_move_size"] = max_move_size
self._param_dict.update(params)
self._update_tunables()
def __init__(self, target, solver):
self._tunables = []
# A counter when tuned reaches 1 it means that the tuner has reported
# being tuned one time in a row. However, as the first run of the tuner
# is likely at timestep 0 which means that the counters are (0, 0) and
# _MoveSizeTuneDefinition returns y == target for that case, we need two
# rounds of tuning to be sure that we have converged. Since, in general,
# solvers do not do much if any work on already tuned tunables, this is
# not a performance problem.
self._tuned = 0
self._is_attached = False
# This is a bit complicated because we are having to ensure that we keep
# the list of tunables and the solver updated with the changes to
# attributes. However, these are simply forwarding a change along.
param_dict = ParameterDict(target=OnlyTypes(
float, postprocess=self._target_postprocess),
solver=SolverStep)
self._param_dict.update(param_dict)
self.target = target
self.solver = solver
def __init__(self, filter, kT, alpha=None):
# store metadata
param_dict = ParameterDict(
filter=ParticleFilter,
kT=Variant,
alpha=OnlyTypes(float, allow_none=True),
)
param_dict.update(dict(kT=kT, alpha=alpha, filter=filter))
# set defaults
self._param_dict.update(param_dict)
gamma = TypeParameter('gamma',
type_kind='particle_types',
param_dict=TypeParameterDict(1., len_keys=1))
gamma_r = TypeParameter('gamma_r',
type_kind='particle_types',
param_dict=TypeParameterDict((1., 1., 1.),
len_keys=1))
self._extend_typeparam([gamma, gamma_r])
def __init__(self,
moves,
target,
solver,
types=None,
max_translation_move=None,
max_rotation_move=None):
def target_postprocess(target):
def check_fraction(value):
if 0 <= value <= 1:
return value
raise ValueError(
"Value {} should be between 0 and 1.".format(value))
self._update_tunables_attr('target', check_fraction(target))
self._tuned = 0
return target
def update_moves(value):
self._update_tunables(new_moves=value)
self._tuned = 0
return value
def update_types(value):
self._update_tunables(new_types=value)
self._tuned = 0
return value
# A flag for knowing when to update the maximum move sizes
self._update_move_sizes = False
self._tunables = []
# A counter when tuned reaches 1 it means that the tuner has reported
# being tuned one time in a row. However, as the first run of the tuner
# is likely at timestep 0 which means that the counters are (0, 0) and
# _MoveSizeTuneDefinition returns y == target for that case, we need two
# rounds of tuning to be sure that we have converged. Since, in general,
# solvers do not do much if any work on already tuned tunables, this is
# not a performance problem.
self._tuned = 0
self._is_attached = False
# set up maximum trial move sizes
def flag_move_size_update(value):
self._update_move_sizes = True
return value
t_moves = TypeParameter(
'max_translation_move', 'particle_type',
TypeParameterDict(OnlyTypes(float,
postprocess=flag_move_size_update,
allow_none=True),
len_keys=1))
r_moves = TypeParameter(
'max_rotation_move', 'particle_type',
TypeParameterDict(OnlyTypes(float,
postprocess=flag_move_size_update,
allow_none=True),
len_keys=1))
self._typeparam_dict = {
'max_translation_move': t_moves,
'max_rotation_move': r_moves
}
# This is a bit complicated because we are having to ensure that we keep
# the list of tunables and the solver updated with the changes to
# attributes. However, these are simply forwarding a change along.
param_dict = ParameterDict(
moves=OnlyIf(to_type_converter([OnlyFrom(['a', 'd'])]),
postprocess=update_moves),
types=OnlyIf(to_type_converter([str]),
postprocess=update_types,
allow_none=True),
target=OnlyTypes(float, postprocess=target_postprocess),
solver=SolverStep)
self._param_dict.update(param_dict)
self.target = target
self.solver = solver
self.moves = moves
self.types = types
self.max_rotation_move.default = max_rotation_move
self.max_translation_move.default = max_translation_move
if types is not None:
self._update_tunables(new_moves=moves, new_types=types)
# Copyright (c) 2009-2021 The Regents of the University of Michigan
# This file is part of the HOOMD-blue project, released under the BSD 3-Clause
# License.
"""Implement many body potentials."""
import hoomd
from hoomd.data.parameterdicts import TypeParameterDict
from hoomd.data.typeconverter import OnlyTypes, positive_real
from hoomd.data.typeparam import TypeParameter
from hoomd.md import _md
from hoomd.md.force import Force
from hoomd.md.nlist import NList
validate_nlist = OnlyTypes(NList)
class Triplet(Force):
r"""Common three body potential documentation.
Users should not invoke :py:class:`Triplet` directly. It is a base class
that provides common features to all standard triplet forces. Common
documentation for all three-body potentials is documented here.
All triplet force commands specify that a given force be computed on all
particles which have at least two other particles within a short range
cutoff distance :math:`r_{\mathrm{cut}}`.
The force :math:`\vec{F}` applied to each particle :math:`i` is:
.. math::
:nowrap:
# Copyright (c) 2009-2022 The Regents of the University of Michigan.
# Part of HOOMD-blue, released under the BSD 3-Clause License.
"""Mesh potential base class."""
from hoomd.md import _md
from hoomd.mesh import Mesh
from hoomd.md.force import Force
from hoomd.data.typeconverter import OnlyTypes
import hoomd
import warnings
import copy
validate_mesh = OnlyTypes(Mesh)
class MeshPotential(Force):
"""Constructs the bond potential applied to a mesh.
`MeshPotential` is the base class for all bond potentials applied to meshes.
Warning:
This class should not be instantiated by users. The class can be used
for `isinstance` or `issubclass` checks.
"""
def __init__(self, mesh):
self._mesh = validate_mesh(mesh)
def _add(self, simulation):
# if mesh was associated with multiple pair forces and is still
# attached, we need to deepcopy existing mesh.
mesh = self._mesh