# 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
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# ============================================================================
"""Berendsen barostat"""
from typing import Tuple
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('andersen')
class AndersenBarostat(Barostat):
r"""
An Andersen barostat module, which is a subclass of `Barostat`.
Reference Andersen, Hans Christian.
Molecular dynamics simulations at constant pressure and/or temperature [J].
Journal of Chemical Physics, 1980, 72.
Args:
system (:class:`sponge.system.Molecule`): Simulation system.
pressure (float, optional): Reference pressure :math:`P_{ref}` in unit 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 bar^-1.
Default: ``4.6e-5``.
time_constant (float, optional): Time constant :math:`\tau_p` in unit picosecond
for pressure coupling.
Default: ``1.0``.
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 AndersenBarostat
>>> system = Molecule(template='water.tip3p.yaml')
>>> controller = AndersenBarostat(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.h_mass_inverse_0 = F.square(self.time_constant) / self.compressibility
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 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:
crd_scale_factor = 0
# (B, D)
pressure = self.get_pressure(kinetics, virial, pbc_box)
volume0 = self.get_volume(pbc_box)
dv_dt = F.reduce_sum(pressure - self.ref_press) / self.h_mass_inverse_0 * volume0
volume = volume0 + dv_dt * self.time_step
crd_scale_factor = msnp.cbrt(volume / volume0)
coordinate *= crd_scale_factor
pbc_box *= crd_scale_factor
velocity *= msnp.reciprocal(crd_scale_factor)
return coordinate, velocity, force, energy, kinetics, virial, pbc_box