# Copyright 2021-2023 @ Shenzhen Bay Laboratory &
# Peking University &
# Huawei Technologies Co., Ltd
#
# This code is a part of MindSPONGE:
# MindSpore Simulation Package tOwards Next Generation molecular modelling.
#
# MindSPONGE is open-source software based on the AI-framework:
# MindSpore (https://www.mindspore.cn/)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# ============================================================================
"""
Simulation Cell
"""
from ...partition import NeighbourList
from ...system import Molecule
from ...potential import PotentialCell
from ...potential.bias import Bias
from ...sampling.wrapper import EnergyWrapper
from .energy import WithEnergyCell
[docs]class SimulationCell(WithEnergyCell):
r"""
Cell for simulation, equivalent to :class:`sponge.core.WithEnergyCell`.
Note:
This Cell will be removed a future release.
Please use :class:`sponge.core.WithEnergyCell` instead.
Args:
system (:class:`sponge.system.Molecule`): Simulation system.
potential (:class:`sponge.potential.PotentialCell`): Potential energy function cell.
bias (`sponge.potential.Bias`, optional): Bias potential function cell.
Default: ``None``.
cutoff (float, optional): Cut-off distance for neighbour list.
If ``None`` is given, it will be assigned as
the cutoff value of the of potential energy.
Default: ``None``.
neighbour_list (:class:`sponge.partition.NeighbourList`, optional): Neighbour list.
Default: ``None``.
wrapper (`sponge.sampling.wrapper.EnergyWrapper`, optional): Network to wrap
and process potential and bias.
Default: ``None``.
Supported Platforms:
``Ascend`` ``GPU``
Examples:
>>> # You can find case2.pdb file under MindSPONGE/tutorials/basic/case2.pdb
>>> from sponge import Protein
>>> from sponge.potential.forcefield import ForceField
>>> from sponge.partition import NeighbourList
>>> from sponge.core.simulation import SimulationCell
>>> system = Protein(pdb='case2.pdb', rebuild_hydrogen=True)
>>> potential = ForceField(system, 'AMBER.FF99SB')
>>> neighbour_list = NeighbourList(system, cutoff=None, cast_fp16=True)
>>> simulation_cell = SimulationCell(
... system=system,
... potential=potential,
... neighbour_list=neighbour_list,
... )
"""
def __init__(self,
system: Molecule,
potential: PotentialCell,
bias: Bias = None,
cutoff: float = None,
neighbour_list: NeighbourList = None,
wrapper: EnergyWrapper = None,
):
super().__init__(
system=system,
potential=potential,
cutoff=cutoff,
neighbour_list=neighbour_list,
wrapper=wrapper,
bias=bias,
)
print('[WARNING] `SimulationCell` will be removed a future release. '
'Please use "WithEnergyCell" instead.')