# Copyright 2022 Multiscale Modeling of Fluid Materials, TU Munich
#
# 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
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# distributed under the License is distributed on an "AS IS" BASIS,
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"""Custom functions simplifying the handling of fractional coordinates."""
from typing import Union, Tuple, Callable
from jax_md import space, util
import jax.numpy as jnp
Box = Union[float, util.Array]
def _rectangular_boxtensor(box: Box) -> Box:
"""Transforms a 1-dimensional box to a 2D box tensor."""
spatial_dim = box.shape[0]
return jnp.eye(spatial_dim).at[jnp.diag_indices(spatial_dim)].set(box)
[docs]def init_fractional_coordinates(box: Box) -> Tuple[Box, Callable]:
"""Returns a 2D box tensor and a scale function that projects positions
within a box in real space to the unit-hypercube as required by fractional
coordinates.
Args:
box: A 1 or 2-dimensional box
Returns:
A tuple (box, scale_fn) of a 2D box tensor and a scale_fn that scales
positions in real-space to the unit hypercube.
"""
if box.ndim != 2: # we need to transform to box tensor
box_tensor = _rectangular_boxtensor(box)
else:
box_tensor = box
inv_box_tensor = space.inverse(box_tensor)
scale_fn = lambda positions: jnp.dot(positions, inv_box_tensor)
return box_tensor, scale_fn