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pair.py
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pair.py
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# 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.
"""HOOMD plugin for a variety of pair interactions."""
import copy
import warnings
from hoomd import _hoomd
from hoomd.logging import log
from hoomd.md import _md, force
from hoomd.pair_plugin import _pair_plugin
import hoomd
from hoomd.md.nlist import NeighborList
from hoomd.data.parameterdicts import ParameterDict, TypeParameterDict
from hoomd.data.typeparam import TypeParameter
from hoomd.data.typeconverter import (OnlyFrom, OnlyTypes, nonnegative_real)
import hoomd.md.pair as _pair
validate_nlist = OnlyTypes(NeighborList)
class ModLJ(_pair.Pair):
r"""Modified Lennard-Jones pair potential to showcase an example of a pair plugin.
Args:
nlist (`hoomd.md.nlist.NeighborList`): Neighbor list.
default_r_cut (float): Default cutoff radius :math:`[\mathrm{length}]`.
default_r_on (float): Default turn-on radius :math:`[\mathrm{length}]`.
mode (str): Energy shifting/smoothing mode.
`ExampleLJ` specifies that a modified Lennard-Jones pair potential should be
applied between every non-excluded particle pair in the simulation.
.. math::
:nowrap:
\begin{eqnarray*}
V_{\mathrm{LJ}}(r) = & 4 \varepsilon \left[ \left(
\frac{\sigma}{r-\Delta} \right)^{12} - \left( \frac{\sigma}{r-\Delta}
\right)^{6} \right]; & r < r_{\mathrm{cut}} \\
= & 0; & r \ge r_{\mathrm{cut}} \\
\end{eqnarray*}
See `Pair` for details on how forces are calculated and the available
energy shifting and smoothing modes.
.. py:attribute:: params
The example potential parameters. The dictionary has the following keys:
* ``epsilon`` (`float`, **required**) -
energy parameter :math:`\varepsilon` :math:`[\mathrm{energy}]`
* ``sigma`` (`float`, **required**) -
particle size :math:`\sigma` :math:`[\mathrm{length}]`
* ``delta`` (`float`, **required**) -
particle size :math:`\sigma` :math:`[\mathrm{length}]`
Type: `TypeParameter` [`tuple` [``particle_type``, ``particle_type``],
`dict`]
Example::
nl = nlist.Cell()
lj = pair.ExamplePair(nl, default_r_cut=2.5)
lj.params[('A', 'A')] = {'sigma': 1.0, 'epsilon': 1.0, 'delta': 0.25}
lj.r_cut[('A', 'A')] = 2.5
"""
# Name of the potential we want to reference on the C++ side
_cpp_class_name = "PotentialPairMLJ"
_ext_module = _pair_plugin
def __init__(self,
nlist,
default_r_cut=None,
default_r_on=0.,
mode='none'):
super().__init__(nlist, default_r_cut, default_r_on, mode)
params = TypeParameter(
'params', 'particle_types',
TypeParameterDict(epsilon=float,
sigma=float,
delta=0.0,
len_keys=2))
self._add_typeparam(params)
class LJLow(_pair.Pair):
r"""
"""
# Name of the potential we want to reference on the C++ side
_cpp_class_name = "PotentialPairLJLow"
_ext_module = _pair_plugin
def __init__(self,
nlist,
default_r_cut=None,
default_r_on=0.,
mode='none'):
super().__init__(nlist, default_r_cut, default_r_on, mode)
params = TypeParameter(
'params', 'particle_types',
TypeParameterDict(epsilon=float,
sigma=float,
len_keys=2))
self._add_typeparam(params)
class MLJ(ModLJ):
pass
class WLJ(_pair.Pair):
r"""Modified Lennard-Jones pair potential to showcase an example of a pair plugin.
Args:
nlist (`hoomd.md.nlist.NeighborList`): Neighbor list.
default_r_cut (float): Default cutoff radius :math:`[\mathrm{length}]`.
default_r_on (float): Default turn-on radius :math:`[\mathrm{length}]`.
mode (str): Energy shifting/smoothing mode.
`WLJ` specifies that a modified Lennard-Jones pair potential should be
applied between every non-excluded particle pair in the simulation.
.. math::
:nowrap:
\begin{eqnarray*}
V_{\mathrm{LJ}}(r) = & 4 \varepsilon \left[ \left(
\frac{\sigma}{r-\Delta} \right)^{12} - \left( \frac{\sigma}{r-\Delta}
\right)^{6} \right]; & r < r_{\mathrm{cut}} \\
= & 0; & r \ge r_{\mathrm{cut}} \\
\end{eqnarray*}
See `Pair` for details on how forces are calculated and the available
energy shifting and smoothing modes.
.. py:attribute:: params
The example potential parameters. The dictionary has the following keys:
* ``epsilon`` (`float`, **required**) -
energy parameter :math:`\varepsilon` :math:`[\mathrm{energy}]`
* ``sigma`` (`float`, **required**) -
particle size :math:`\sigma` :math:`[\mathrm{length}]`
* ``delta`` (`float`, **required**) -
particle size :math:`\sigma` :math:`[\mathrm{length}]`
Type: `TypeParameter` [`tuple` [``particle_type``, ``particle_type``],
`dict`]
Example::
nl = nlist.Cell()
lj = pair.ExamplePair(nl, default_r_cut=2.5)
lj.params[('A', 'A')] = {'sigma': 1.0, 'epsilon': 1.0, 'delta': 0.25}
lj.r_cut[('A', 'A')] = 2.5
"""
# Name of the potential we want to reference on the C++ side
_cpp_class_name = "PotentialPairWLJ"
_ext_module = _pair_plugin
def __init__(self,
nlist,
default_r_cut=None,
default_r_on=0.,
mode='none'):
super().__init__(nlist, default_r_cut, default_r_on, mode)
params = TypeParameter(
'params', 'particle_types',
TypeParameterDict(epsilon=float,
sigma=float,
delta=0.0,
epsilon_a=float,
delta_a=0.0,
len_keys=2))
self._add_typeparam(params)
class Hertzian(_pair.Pair):
r"""Hertzian pair potential.
Args:
nlist (`hoomd.md.nlist.NeighborList`): Neighbor list.
default_r_cut (float): Default cutoff radius :math:`[\mathrm{length}]`.
default_r_on (float): Default turn-on radius :math:`[\mathrm{length}]`.
mode (str): Energy shifting/smoothing mode.
See `Pair` for details on how forces are calculated and the available
energy shifting and smoothing modes.
.. py:attribute:: params
The example potential parameters. The dictionary has the following keys:
* ``epsilon`` (`float`, **required**) -
energy parameter :math:`\varepsilon` :math:`[\mathrm{energy}]`
* ``sigma`` (`float`, **required**) -
particle size :math:`\sigma` :math:`[\mathrm{length}]`
* ``delta`` (`float`, **required**) -
particle size :math:`\sigma` :math:`[\mathrm{length}]`
Type: `TypeParameter` [`tuple` [``particle_type``, ``particle_type``],
`dict`]
Example::
nl = nlist.Cell()
lj = pair.ExamplePair(nl, default_r_cut=1.0)
lj.params[('A', 'A')] = {'sigma': 1.0, 'epsilon': 1.0}
lj.r_cut[('A', 'A')] = 1.0
"""
# Name of the potential we want to reference on the C++ side
_cpp_class_name = "PotentialPairHertzian"
_ext_module = _pair_plugin
def __init__(self,
nlist,
default_r_cut=None,
default_r_on=0.,
mode='none'):
super().__init__(nlist, default_r_cut, default_r_on, mode)
params = TypeParameter(
'params', 'particle_types',
TypeParameterDict(epsilon=float, sigma=float, len_keys=2))
self._add_typeparam(params)
class DipoleDipole(_pair.Pair):
# Name of the potential we want to reference on the C++ side
_cpp_class_name = "PotentialPairDipoleDipole"
_ext_module = _pair_plugin
def __init__(self,
nlist,
default_r_cut=None,
default_r_on=0.,
mode='none'):
super().__init__(nlist, default_r_cut, default_r_on, mode)
params = TypeParameter(
'params', 'particle_types',
TypeParameterDict(epsilon=float, len_keys=2))
self._add_typeparam(params)
class HPFPair(force.Force):
r"""Base class hard-particle frictional forces.
Note:
:py:class:`HPFPair` is the base class for all frictional pair forces. Users should
not instantiate this class directly.
.. py:attribute:: r_cut
Cuttoff radius beyond which the energy and force are 0
:math:`[\mathrm{length}]`. *Optional*: defaults to the value
``default_r_cut`` specified on construction.
Type: `TypeParameter` [`tuple` [``particle_type``, ``particle_type``],
`float`])
.. py:attribute:: mode
*mode*, *optional*: defaults to ``"none"``.
Possible values: ``"none"``, ``"shift"``
Type: `str`
.. py:attribute:: nlist
Neighbor list used to compute the pair force.
Type: `hoomd.md.nlist.NeighborList`
"""
# The accepted modes for the potential. Should be reset by subclasses with
# restricted modes.
_accepted_modes = ("none", )
_ext_module = _pair_plugin
@log(category="pair", requires_run=True)
def nlist_pairs(self):
pass
@log(category="pair", requires_run=True)
def pair_conserv_forces(self):
pass
@log(category="pair", requires_run=True)
def pair_friction_forces(self):
pass
@log(category="pair", requires_run=True)
def pair_torques(self):
pass
def __init__(self,
nlist,
default_r_cut=None,
mode='none',
mus=0.0,
mur=0.0,
ks=0.0,
kr=0.0):
super().__init__()
tp_r_cut = TypeParameter(
'r_cut', 'particle_types',
TypeParameterDict(nonnegative_real, len_keys=2))
if default_r_cut is not None:
tp_r_cut.default = default_r_cut
type_params = [tp_r_cut]
self._extend_typeparam(type_params)
self._param_dict.update(
ParameterDict(mode=OnlyFrom(self._accepted_modes),
nlist=hoomd.md.nlist.NeighborList))
self.mode = mode
self.nlist = nlist
self.mus = mus
self.mur = mur
self.ks = ks
self.kr = kr
def _add(self, simulation):
super()._add(simulation)
self._add_nlist()
def _add_nlist(self):
nlist = self.nlist
deepcopy = False
if not isinstance(self._simulation, hoomd.Simulation):
if nlist._added:
deepcopy = True
else:
return
# We need to check if the force is added since if it is not then this is
# being called by a SyncedList object and a disagreement between the
# simulation and nlist._simulation is an error. If the force is added
# then the nlist is compatible. We cannot just check the nlist's _added
# property because _add is also called when the SyncedList is synced.
if deepcopy or nlist._added and nlist._simulation != self._simulation:
warnings.warn(
f"{self} object is creating a new equivalent neighbor list."
f" This is happending since the force is moving to a new "
f"simulation. Set a new nlist to suppress this warning.",
RuntimeWarning)
self.nlist = copy.deepcopy(nlist)
self.nlist._add(self._simulation)
# This is ideopotent, but we need to ensure that if we change
# neighbor list when not attached we handle correctly.
self._add_dependency(self.nlist)
def _setattr_param(self, attr, value):
if attr == "nlist":
self._nlist_setter(value)
return
super()._setattr_param(attr, value)
def _nlist_setter(self, new_nlist):
if new_nlist is self.nlist:
return
if self._attached:
raise RuntimeError("nlist cannot be set after scheduling.")
old_nlist = self.nlist
self._param_dict._dict["nlist"] = new_nlist
if self._added:
self._add_nlist()
old_nlist._remove_dependent(self)
class HarmHPF(HPFPair):
"""Harmonic hard-particle interaction with frictional force"""
_cpp_class_name = "PotentialPairHPF"
_ext_module = _pair_plugin
def __init__(self,
nlist,
default_r_cut=None,
mode='none',
mus=0.0,
mur=0.0,
ks=0.0,
kr=0.0):
super().__init__(nlist, default_r_cut, mode, mus, mur, ks, kr)
params = TypeParameter(
'params', 'particle_types',
TypeParameterDict(k=float, rcut=float, len_keys=2))
self._add_typeparam(params)