# 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.
# ============================================================================
"""
Atom group
"""
from typing import Union
from numpy import ndarray
import mindspore as ms
import mindspore.numpy as msnp
from mindspore import ops
from mindspore.ops import functional as F
from mindspore import Tensor, Parameter
from .atoms import AtomsBase
from ...function import get_ms_array
__all__ = ['Position', 'BatchedPosition']
[文档]class Position(AtomsBase):
r"""
Virtual atom(s) in fixed position(s).
Args:
coordinate (Union[Tensor, Parameter, ndarray]):
Array of th position coordinate(s) of specific virtual atom(s).
The shape of Tensor is (a_1, a_2, ..., a_n, D), and the data type is float.
`a_{i}` means dimension of specific atoms.
`D` means dimension of the simulation system. Usually is 3.
batched (bool): Whether the first dimension of coordinate is the batch size.
Default: ``False``.
keep_in_box (bool): Whether to displace the coordinate in PBC box.
Default: ``False``.
dimension (int): Space dimension of system. Default: 3.
name (str): Name of the Colvar. Default: 'position'.
Supported Platforms:
``Ascend`` ``GPU``
"""
def __init__(self,
coordinate: Union[Tensor, Parameter, ndarray],
batched: bool = False,
keep_in_box: bool = False,
name: str = 'position',
):
super().__init__(
keep_in_box=keep_in_box,
name=name,
)
self.coordinate = get_ms_array(coordinate, ms.float32)
if batched:
if self.coordinate.ndim < 2:
raise ValueError('The rank of coordinate must be larger than 1 '
'when using batched coordinate.')
else:
self.coordinate = F.expand_dims(self.coordinate, 0)
if self.coordinate.ndim == 2:
self.coordinate = F.expand_dims(self.coordinate, -2)
self._set_shape(self.coordinate.shape[1:])
self.identity = ops.Identity()
def update(self, coordinate: Tensor):
self.coordinate = coordinate
return self
[文档] def reshape(self, input_shape: tuple):
"""rearranges the shape of atoms"""
shape = self.coordinate.shape[0] + input_shape
self.coordinate = F.reshape(self.coordinate, shape)
self._ndim = self.coordinate.ndim - 1
self._shape = self.coordinate.shape[1:]
self._periodic = msnp.full(self._shape, False)
return self
def construct(self, coordinate: Tensor, pbc_box: Tensor = None):
r"""get position coordinate(s) of virtual atom(s)
Args:
coordinate (Tensor): Tensor of shape (B, A, D). Data type is float.
Position coordinate of atoms in system.
`B` means batchsize, i.e. number of walkers in simulation.
`A` means number of atoms in system.
pbc_box (Tensor): Tensor of shape (B, D). Data type is float.
Tensor of PBC box. Default: ``None``.
Returns:
position (Tensor): Tensor of shape (B, a_1, a_2, ..., a_n, D). Data type is float.
"""
if coordinate.shape[0] > 1:
shape = (coordinate.shape[0],) + self.coordinate.shape[1:]
position = msnp.broadcast_to(self.coordinate, shape)
else:
position = self.identity(self.coordinate)
if self.keep_in_box:
return self.coordinate_in_pbc(position, pbc_box)
return position
[文档]class BatchedPosition(Position):
r"""
Virtual atom(s) in fixed position(s) with batched coordinate
Args:
coordinate (Tensor): Tensor of shape (B, a_1, a_2, ..., a_n, D). Data type is float.
Position coordinate(s) of virtual atom(s).
keep_in_box (bool): Whether to displace the coordinate in PBC box.
Default: ``False``.
dimension (int): Space dimension of system. Default: 3
name (str): Name of the Colvar. Default: 'position'
Supported Platforms:
``Ascend`` ``GPU``
"""
def __init__(self,
coordinate: Union[Tensor, Parameter, ndarray],
keep_in_box: bool = False,
dimension: int = 3,
name: str = 'position',
):
super().__init__(
coordinate=coordinate,
batched=True,
keep_in_box=keep_in_box,
dimension=dimension,
name=name,
)