# 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.
# ============================================================================
"""Berendsen barostat"""
from typing import Tuple
import mindspore as ms
import mindspore.numpy as msnp
from mindspore import Tensor
from mindspore.ops import functional as F
from .barostat import Barostat, _barostat_register
from ...system import Molecule
from ...function import get_arguments
[docs]@_barostat_register('berendsen')
class BerendsenBarostat(Barostat):
r"""
A Berendsen (weak coupling) barostat module,
which is a subclass of :class:`sponge.control.Barostat`.
Reference Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R.
Molecular Dynamics with Coupling to an External Bath [J].
The Journal of Chemical Physics, 1984, 81(8).
Args:
system (:class:`sponge.system.Molecule`): Simulation system.
pressure (float, optional): Reference pressure :math:`P_{ref}`
in unit :math:`bar` for pressure coupling.
Default: ``1.0``.
anisotropic (bool, optional): Whether to perform anisotropic pressure control.
Default: ``False``.
control_step (int, optional): Step interval for controller execution. Default: ``1``.
compressibility (float, optional): Isothermal compressibility :math:`\beta`
in unit :math:`bar^{-1}`.
Default: ``4.6e-5``.
time_constant (float, optional): Time constant :math:`\tau_p` in
unit picosecond for pressure coupling.
Default: ``1``.
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 BerendsenBarostat
>>> system = Molecule(template='water.tip3p.yaml')
>>> controller = BerendsenBarostat(system)
"""
def __init__(self,
system: Molecule,
pressure: float = 1,
anisotropic: bool = False,
control_step: int = 1,
compressibility: float = 4.6e-5,
time_constant: float = 1.,
**kwargs
):
super().__init__(
system=system,
pressure=pressure,
anisotropic=anisotropic,
control_step=control_step,
compressibility=compressibility,
time_constant=time_constant,
)
self._kwargs = get_arguments(locals(), kwargs)
self.ratio = self.control_step * self.time_step / self.time_constant / 3.
[docs] def set_time_step(self, dt: float):
r"""
Set simulation time step.
Args:
dt (float): Simulation time step.
Returns:
:class:`sponge.control.BerendsenBarostat`, current object of :class:`sponge.control.BerendsenBarostat`.
"""
self.time_step = Tensor(dt, ms.float32)
self.ratio = self.control_step * self.time_step / self.time_constant / 3.
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 the pressure 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.
"""
if self.control_step == 1 or step % self.control_step == 0:
# (B, D)
pressure = self.get_pressure(kinetics, virial, pbc_box)
if not self.anisotropic:
# (B, 1) <- (B, D)
pressure = msnp.mean(pressure, axis=-1, keepdims=True)
# (B, D) <- (B, 1)
pressure = msnp.broadcast_to(pressure, self.shape)
# (B, D)
scale = self.pressure_scale(pressure, self.ref_press, self.ratio)
# (B, A, D) * (B, 1, D)
coordinate *= F.expand_dims(scale, -2)
# (B, D)
pbc_box *= scale
return coordinate, velocity, force, energy, kinetics, virial, pbc_box