# 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.
# ============================================================================
"""
Brownian integrator
"""
from typing import Tuple
import mindspore as ms
import mindspore.numpy as msnp
from mindspore import Tensor
from mindspore import ops
from mindspore.ops import functional as F
from .integrator import Integrator, _integrator_register
from ...system import Molecule
from ...function import get_arguments
[docs]@_integrator_register('brownian')
class Brownian(Integrator):
r"""
A Brownian integrator module, which is a subclass of :class:`sponge.control.Integrator`.
Args:
system (:class:`sponge.system.Molecule`): Simulation system
temperature (float, optional): Simulation temperature T (K). Default: ``300.0``.
friction_coefficient (float, optional): Friction coefficient g (amu/ps). Default: ``1e3``.
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 Brownian
>>> system = Molecule(template='water.tip3p.yaml')
>>> controller = Brownian(system)
"""
def __init__(self,
system: Molecule,
temperature: float = 300,
friction_coefficient: float = 1e3,
**kwargs,
):
super().__init__(
system=system,
thermostat=None,
barostat=None,
constraint=None,
)
self._kwargs = get_arguments(locals(), kwargs)
self.ref_temp = Tensor(temperature, ms.float32)
self.inv_sqrt_mass = F.sqrt(self._inv_mass)
self.friction_coefficient = Tensor(friction_coefficient, ms.float32)
# \gamma = 1.0 / \tau_t
self.inv_gamma = msnp.reciprocal(self.friction_coefficient) * self._inv_mass
# k = \sqrt(2 * k_B * T * dt / \gamma)
self.random_scale = F.sqrt(2 * self.boltzmann * self.ref_temp * self.time_step
* self.inv_gamma / self.kinetic_unit_scale)
self.normal = ops.StandardNormal()
@property
def temperature(self) -> Tensor:
return self.ref_temp
[docs] def set_thermostat(self, thermostat: None = None):
r"""
Set thermostat algorithm for integrator.
Args:
thermostat (None): Thermostat algorithm,
which needs to be ``None`` for Brownian integrator. Default: ``None``.
"""
if thermostat is not None:
raise ValueError('The Brownian integrator cannot accept thermostat')
return self
[docs] def set_barostat(self, barostat: None = None):
r"""
Set barostat algorithm for integrator.
Args:
barostat (None): Barostat algorithm,
which needs to be ``None`` for Brownian integrator. Default: ``None``.
"""
if barostat is not None:
raise ValueError('The Brownian integrator cannot accept barostat')
return self
[docs] def set_constraint(self, constraint: None = None, num_constraints: int = 0):
r"""
Set constraint algorithm for integrator.
Args:
constraint (None): Constraint algorithm,
which needs to be ``None`` for Brownian integrator. Default: ``None``.
num_constraints (int, optional): Number of constraints. Default: ``0.0``.
"""
if constraint is not None:
raise ValueError('The Brownian integrator cannot accept constraint')
return self
[docs] def set_time_step(self, dt: float):
r"""
Set simulation time step.
Args:
dt (float): Simulation time step.
"""
self.time_step = Tensor(dt, ms.float32)
self.random_scale = F.sqrt(2 * self.boltzmann * self.ref_temp * self.time_step * self.inv_gamma)
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"""
Update simulation step.
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.
"""
coordinate += self.acc_unit_scale * force * self.inv_gamma * self.time_step
coordinate += self.normal(coordinate.shape) * self.random_scale
return coordinate, velocity, force, energy, kinetics, virial, pbc_box