# 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.
# ============================================================================
"""
Barostat
"""
from typing import Union, Tuple, List
from numpy import ndarray
import mindspore as ms
import mindspore.numpy as msnp
from mindspore import Tensor, Parameter
from mindspore.ops import functional as F
from .. import Controller
from ...system import Molecule
from ...function import get_ms_array, get_arguments
_BAROSTAT_BY_KEY = dict()
def _barostat_register(*aliases):
"""Return the alias register."""
def alias_reg(cls):
name = cls.__name__
name = name.lower()
if name not in _BAROSTAT_BY_KEY:
_BAROSTAT_BY_KEY[name] = cls
for alias in aliases:
if alias not in _BAROSTAT_BY_KEY:
_BAROSTAT_BY_KEY[alias] = cls
return cls
return alias_reg
[文档]class Barostat(Controller):
r"""
Base class for barostat module in MindSPONGE,
which is a subclass of :class:`sponge.control.Controller`.
The :class:`sponge.control.Barostat` module is used for pressure coupling.
It controls the atomic coordinates and the size of the PBC box of
the system during the simulation process.
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: ``1.0``.
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: ``1.0``.
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 Barostat
>>> system = Molecule(template='water.tip3p.yaml')
>>> controller = Barostat(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,
control_step=control_step,
)
self._kwargs = get_arguments(locals(), kwargs)
self.anisotropic = anisotropic
self.sens = Tensor(1e8, ms.float32)
self.inv_sens = msnp.reciprocal(self.sens)
self.size_error_info = f'The size of pressure must be equal to 1 or ' \
f'the number of multiple walker ({self.num_walker}) but got '
pressure = self._get_mw_tensor(pressure, 'pressure')
self.ref_press = Parameter(pressure, name='ref_press', requires_grad=False)
# isothermal compressibility
self.beta = get_ms_array(compressibility, ms.float32)
# \tau_t
self.time_constant = self._get_mw_tensor(time_constant, 'time_constant')
self.shape = (self.num_walker, self.dimension)
self.change_accumulation = Parameter(msnp.zeros(self.shape), name='change_accumulation', requires_grad=False)
self.critical_change = 1e-6
@property
def pressure(self) -> Tensor:
r"""
Reference pressure.
Returns:
Tensor, reference pressure.
"""
return self.identity(self.ref_press)
@property
def compressibility(self) -> Tensor:
r"""
Isothermal compressibility.
Returns:
Tensor, isothermal compressibility."""
return self.beta
[文档] def set_pressure(self, pressure: Union[float, ndarray, Tensor, List[float]]) -> Tensor:
r"""
Set the value of reference pressure.
The size of the pressure array must be equal to current pressure.
Args:
pressure (Union[float, ndarray, Tensor, List[float]]): pressure.
Returns:
Tensor, reference pressure.
"""
return F.assign(self.ref_press, self._get_mw_tensor(pressure, 'pressure'))
[文档] def reconstruct_pressure(self, pressure: Union[float, ndarray, Tensor, List[float]]):
r"""
Reset the reference pressure.
Args:
pressure (Union[float, ndarray, Tensor, List[float]]): pressure.
Returns:
:class:`sponge.control.Barostat`, current object of barostat.
"""
pressure = self._get_mw_tensor(pressure, 'pressure')
self.ref_press = Parameter(pressure, name='ref_press', requires_grad=False)
return self
[文档] def pressure_scale(self, sim_press: Tensor, ref_press: Tensor, ratio: float = 1) -> Tensor:
r"""
Calculate the coordinate scale factor for pressure coupling.
Args:
sim_press (Tensor): Current pressure.
ref_press (Tensor): Reference pressure.
ratio (float, optional): Ratio of pressure coupling. Default: ``1.0``
Returns:
Tensor, scale factor for pressure coupling.
"""
delta_p = ref_press - sim_press
change = - ratio * self.beta * delta_p
# If the change is too small, the float32 data will not be able to represent the scale.
# Therefore, the small changes will be accumulated:
# (1 + x) ^ n \approx 1 + nx, when x << 1
# When the total change accumulates to a critical value, then the coordinate and PBC box will be scaled.
change += self.change_accumulation
mask = msnp.abs(change) > self.critical_change
scale = msnp.where(mask, 1+change, 1.)
change = msnp.where(mask, 0., change)
scale = F.depend(scale, F.assign(self.change_accumulation, change))
return scale
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.
"""
raise NotImplementedError