Source code for jax_md_mod.custom_space

# Copyright 2023 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

import jax
from jax_md import space, util
import jax.numpy as jnp
from jax import vmap

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)




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:
        box = _rectangular_boxtensor(box)

    def scale_fn(positions, **kwargs):
        _box = kwargs.get('box', box)
        if _box.ndim != 2:
            _box = _rectangular_boxtensor(_box)
        inv_box = jnp.linalg.inv(_box)
        return jnp.dot(inv_box, positions.T).T

    return box, scale_fn



def general_space(box: Box,
                  periodic: jax.Array,
                  wrapped: bool = True,
                  fractional: bool = False) -> space.Space:
    """TODO
    """

    def displacement_fn(Ra: jax.Array, Rb: jax.Array, **kwargs):
        _periodic = kwargs.get('periodic', periodic)
        _box = kwargs.get('box', box)

        if not fractional:
            _inv_box = jnp.linalg.inv(_box)
            Ra = space.transform(_inv_box, Ra)
            Rb = space.transform(_inv_box, Rb)

        dR = space.pairwise_displacement(Ra, Rb)
        dR = jnp.where(_periodic, space.periodic_displacement(1.0, dR), dR)
        dR = space.transform(_box, dR)

        return dR

    if wrapped:
        def shift_fn(R: jax.Array, dR: jax.Array, **kwargs):
            _periodic = kwargs.get('periodic', periodic)
            _box = kwargs.get('box', box)
            
            if not fractional:
                _inv_box = jnp.linalg.inv(_box)
                R = space.transform(_inv_box, R)
                dR = space.transform(_inv_box, dR)

            R = jnp.where(_periodic, space.periodic_shift(1.0, R, dR), R + dR)
            
            if not fractional:
                R = space.transform(_box, R)
            
            return R
    else:
        def shift_fn(R: jax.Array, dR: jax.Array, **kwargs):
            del kwargs
            return R + dR

    return displacement_fn, shift_fn