# 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.
# ============================================================================
"""
Thermostat
"""
from typing import Union, Tuple, List
from numpy import ndarray
from mindspore import Tensor, Parameter
from mindspore.ops import functional as F
from .. import Controller
from ...system import Molecule
from ...function import get_arguments
_THERMOSTAT_BY_KEY = dict()
def _thermostat_register(*aliases):
"""Return the alias register."""
def alias_reg(cls):
name = cls.__name__
name = name.lower()
if name not in _THERMOSTAT_BY_KEY:
_THERMOSTAT_BY_KEY[name] = cls
for alias in aliases:
if alias not in _THERMOSTAT_BY_KEY:
_THERMOSTAT_BY_KEY[alias] = cls
return cls
return alias_reg
[文档]class Thermostat(Controller):
r"""
Base class for thermostat module in MindSPONGE, which is a subclass of :class:`sponge.control.Controller`.
The :class:`sponge.control.thermostat.Thermostat` module is used for
temperature coupling. It controls the atomic velocities and the kinetics
of the system during the simulation process.
Args:
system ( :class:`sponge.system.Molecule`): Simulation system.
temperature (Union[float, ndarray, Tensor], optional): Reference temperature :math:`T_{ref}`
in unit Kelvin for temperature coupling.
Default: ``300.0``.
control_step (int, optional): Step interval for controller execution.
Default: ``1``.
time_constant (float, optional): Time constant :math:`\tau_T`
in unit picosecond for temperature coupling.
Default: ``0.5``.
Inputs:
- **coordinate** (Tensor) - Coordinate. Tensor of shape :math:`(B, A, D)`.
Data type is float.
Here :math:`B` is the number of walkers in simulation,
:math:`A` is the number of atoms and
:math:`D` is the spatial dimension of the simulation system, which is usually 3.
- **velocity** (Tensor) - Velocity. Tensor of shape :math:`(B, A, D)`. Data type is float.
- **force** (Tensor) - Force. Tensor of shape :math:`(B, A, D)`. Data type is float.
- **energy** (Tensor) - Energy. Tensor of shape :math:`(B, 1)`. Data type is float.
- **kinetics** (Tensor) - Kinetics. Tensor of shape :math:`(B, D)`. Data type is float.
- **virial** (Tensor) - Virial. Tensor of shape :math:`(B, D)`. Data type is float.
- **pbc_box** (Tensor) - Pressure boundary condition box. Tensor of shape :math:`(B, D)`.
Data type is float.
- **step** (int) - Simulation step. Default: ``0``.
Outputs:
- coordinate, Tensor of shape :math:`(B, A, D)`. Coordinate. Data type is float.
- velocity, Tensor of shape :math:`(B, A, D)`. Velocity. Data type is float.
- force, Tensor of shape :math:`(B, A, D)`. Force. Data type is float.
- energy, Tensor of shape :math:`(B, 1)`. Energy. Data type is float.
- kinetics, Tensor of shape :math:`(B, D)`. Kinetics. Data type is float.
- virial, Tensor of shape :math:`(B, D)`. Virial. Data type is float.
- pbc_box, Tensor of shape :math:`(B, D)`. Periodic boundary condition box.
Data type is float.
Supported Platforms:
``Ascend`` ``GPU``
Examples:
>>> from sponge import Molecule
>>> from sponge.control import Thermostat
>>> system = Molecule(template='water.tip3p.yaml')
>>> controller = Thermostat(system)
"""
def __init__(self,
system: Molecule,
temperature: Union[float, ndarray, Tensor, List[float]] = 300,
control_step: int = 1,
time_constant: float = 0.5,
**kwargs,
):
super().__init__(
system=system,
control_step=control_step,
)
self._kwargs = get_arguments(locals(), kwargs)
temperature = self._get_mw_tensor(temperature, 'temperature')
self.ref_temp = Parameter(temperature, name='ref_temp', requires_grad=False)
# \tau_t
self.time_constant = self._get_mw_tensor(time_constant, 'time_constant')
@property
def temperature(self) -> Tensor:
r"""
Reference temperature.
Returns:
Tensor, reference temperature.
"""
return self.identity(self.ref_temp)
@property
def ref_kinetics(self) -> Tensor:
r"""
Reference kinetics.
Returns:
Tensor, reference kinetics.
"""
return self.get_ref_kinetics()
[文档] def get_ref_kinetics(self) -> Tensor:
r"""
Get reference kinetics.
Returns:
Tensor, reference kinetics.
"""
return 0.5 * self.degrees_of_freedom * self.boltzmann * self.ref_temp
[文档] def set_temperature(self, temperature: Union[float, ndarray, Tensor, List[float]]) -> Tensor:
r"""
Set the value of reference temperature.
The size of the temperature array must be equal to current temperature.
Args:
temperature (Union[float, ndarray, Tensor, List[float]]): temperature.
"""
return F.assign(self.ref_temp, self._get_mw_tensor(temperature, 'temperature'))
[文档] def reconstruct_temperature(self, temperature: Union[float, ndarray, Tensor, List[float]]):
r"""
Reset the reference temperature.
Args:
temperature (Union[float, ndarray, Tensor, List[float]]): temperature.
"""
temperature = self._get_mw_tensor(temperature, 'temperature')
self.ref_temp = Parameter(temperature, name='ref_temp', requires_grad=False)
return self
[文档] def set_degrees_of_freedom(self, dofs: int):
r"""
Set degrees of freedom (DOFs).
Args:
dofs (int): degrees of freedom.
"""
self.degrees_of_freedom = dofs
return self
[文档] def velocity_scale(self, sim_kinetics: Tensor, ref_kinetics: Tensor, ratio: float = 1) -> Tensor:
r"""
Calculate the velocity scale factor for temperature coupling.
Args:
sim_kinetics (Tensor): Simulation kinetics. Tensor of shape :math:`(B, D)`.
Data type is float.
ref_kinetics (Tensor): Reference kinetics. Tensor of shape :math:`(B, D)`.
Data type is float.
ratio (float, optional): Ratio of temperature coupling. Default: ``1``.
Returns:
Tensor, velocity scale factor.
"""
sim_kinetics = self.keepdims_sum(sim_kinetics, -1)
lambda_ = 1. + ratio * (ref_kinetics / sim_kinetics - 1)
return F.sqrt(lambda_)
def construct(self,
coordinate: Tensor,
velocity: Tensor,
force: Tensor,
energy: Tensor,
kinetics: Tensor,
virial: Tensor = None,
pbc_box: Tensor = None,
step: int = 0,
) -> Tuple[Tensor, Tensor, Tensor, Tensor, Tensor, Tensor, Tensor]:
r"""
Control the temperature of the simulation system
Args:
coordinate (Tensor): Tensor of shape :math:`(B, A, D)`. Data type is float.
velocity (Tensor): Tensor of shape :math:`(B, A, D)`. Data type is float.
force (Tensor): Tensor of shape :math:`(B, A, D)`. Data type is float.
energy (Tensor): Tensor of shape :math:`(B, 1)`. Data type is float.
kinetics (Tensor): Tensor of shape :math:`(B, D)`. Data type is float.
virial (Tensor): Tensor of shape :math:`(B, D)`. Data type is float.
pbc_box (Tensor): Tensor of shape :math:`(B, D)`. Data type is float.
step (int): Simulation step. Default: ``0``.
Returns:
- **coordinate** (Tensor) - Tensor of shape :math:`(B, A, D)`. Data type is float.
- **velocity** (Tensor) - Tensor of shape :math:`(B, A, D)`. Data type is float.
- **force** (Tensor) - Tensor of shape :math:`(B, A, D)`. Data type is float.
- **energy** (Tensor) - Tensor of shape :math:`(B, 1)`. Data type is float.
- **kinetics** (Tensor) - Tensor of shape :math:`(B, D)`. Data type is float.
- **virial** (Tensor) - Tensor of shape :math:`(B, D)`. Data type is float.
- **pbc_box** (Tensor) - Tensor of shape :math:`(B, D)`. Data type is float.
Note:
:math:`B` is the number of walkers in simulation.
:math:`A` is the number of atoms.
:math:`D` is the spatial dimension of the simulation system. Usually is 3.
"""
raise NotImplementedError