# 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.
# ============================================================================
"""Langevin thermostat"""
from typing import Tuple
import mindspore.numpy as msnp
from mindspore import Tensor
from mindspore import ops
from mindspore.ops import functional as F
from .thermostat import Thermostat, _thermostat_register
from ...system import Molecule
from ...function import get_arguments
[文档]@_thermostat_register('langevin')
class Langevin(Thermostat):
r"""
A Langevin thermostat module, which is a subclass of :class:`sponge.control.Thermostat`.
Reference Goga, N.; Rzepiela, A. J.; de Vries, A. H.; Marrink, S. J.; Berendsen, H. J. C..,
Efficient Algorithms for Langevin and DPD Dynamics [J].
Journal of Chemical Theory and Computation, 2012.
Args:
system ( :class:`sponge.system.Molecule`): Simulation system
temperature (float, 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: ``0.2``.
seed (int, optional): Random seed for standard normal. Default: ``0``.
seed2 (int, optional): Random seed2 for standard normal. Default: ``0``.
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 Langevin
>>> system = Molecule(template='water.tip3p.yaml')
>>> controller = Langevin(system)
"""
def __init__(self,
system: Molecule,
temperature: float = 300,
control_step: int = 1,
time_constant: float = 0.5,
seed: int = 0,
seed2: int = 0,
**kwargs,
):
super().__init__(
system=system,
temperature=temperature,
control_step=control_step,
time_constant=time_constant,
)
self._kwargs = get_arguments(locals(), kwargs)
# (B,A,1)
self._inv_sqrt_mass = F.sqrt(self._inv_mass)
# (B,1,1)
# \gamma = 1.0 / \tau_t
self.effective_friction_rate = msnp.reciprocal(self.time_constant)
# \f = 1 - exp(-\gamma * dt)
self.friction = 1.0 - \
msnp.exp(-self.effective_friction_rate*self.time_step)
# k = \sqrt(f * (2 - f) * k_B * T)
self.random_const = self.friction * (2 - self.friction) * self.boltzmann / self.kinetic_unit_scale
self.standard_normal = ops.StandardNormal(seed, seed2)
[文档] def set_time_step(self, dt):
"""set simulation time step"""
self.time_step = dt
# \f = 1 - exp(-\gamma * dt)
self.friction = 1.0 - \
msnp.exp(-self.effective_friction_rate*self.time_step)
# k = f * (2 - f) * k_B
self.random_const = self.friction * (2 - self.friction) * self.boltzmann / self.kinetic_unit_scale
return self
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 temperature.
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.
"""
if self.control_step == 1 or step % self.control_step == 0:
velocity += -self.friction * velocity + F.sqrt(self.random_const * self.ref_temp) * \
self._inv_sqrt_mass * self.standard_normal(velocity.shape)
return coordinate, velocity, force, energy, kinetics, virial, pbc_box