# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under the Lesser GNU Public Licence, v2.1 or any higher version
#
# Please cite your use of MDAnalysis in published work:
#
# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
# doi: 10.25080/majora-629e541a-00e
#
# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
#
#
"""Fast distance array computation --- :mod:`MDAnalysis.lib.distances`
===================================================================
Fast C-routines to calculate arrays of distances or angles from coordinate
arrays. Distance functions can accept a NumPy :class:`np.ndarray` or an
:class:`~MDAnalysis.core.groups.AtomGroup`. Many of the functions also exist
in parallel versions, which typically provide higher performance than the
serial code. The boolean attribute `MDAnalysis.lib.distances.USED_OPENMP` can
be checked to see if OpenMP was used in the compilation of MDAnalysis.
Selection of acceleration ("backend")
-------------------------------------
All functions take the optional keyword `backend`, which determines the type of
acceleration. Currently, the following choices are implemented (`backend` is
case-insensitive):
.. Table:: Available *backends* for accelerated distance functions.
========== ========================= ======================================
*backend* module description
========== ========================= ======================================
"serial" :mod:`c_distances` serial implementation in C/Cython
"OpenMP" :mod:`c_distances_openmp` parallel implementation in C/Cython
with OpenMP
"distopia" `_distopia` SIMD-accelerated implementation
with the `distopia`_ library
========== ========================= ======================================
Use of the distopia library
---------------------------
MDAnalysis has developed a standalone library, `distopia`_ for accelerating
the distance functions in this module using explicit SIMD vectorisation.
This can provide many-fold speedups in calculating distances. Distopia is
under active development and as such only a selection of functions in this
module are covered. Consult the following table to see if the function
you wish to use is covered by distopia. For more information see the
`distopia documentation`_.
.. table:: Functions available using the `distopia`_ backend.
:align: center
+-------------------------------------------------------+
| Functions |
+=======================================================+
| :func:`MDAnalysis.lib.distances.calc_bonds` |
+-------------------------------------------------------+
| :func:`MDAnalysis.lib.distances.calc_angles` |
+-------------------------------------------------------+
| :func:`MDAnalysis.lib.distances.calc_dihedrals` |
+-------------------------------------------------------+
| :func:`MDAnalysis.lib.distances.distance_array` |
+-------------------------------------------------------+
| :func:`MDAnalysis.lib.distances.self_distance_array` |
+-------------------------------------------------------+
If `distopia`_ is installed, the functions in this table will accept the key
'distopia' for the `backend` keyword argument. The variable
:data:`HAS_DISTOPIA` is set to ``True`` if distopia is available.
If the distopia backend is selected the `distopia` library will be used to
calculate the distances. Note that for functions listed in this table
**distopia is not the default backend and must be explicitly selected.**
.. Note::
Due to the use of Instruction Set Architecture (`ISA`_) specific SIMD
intrinsics in distopia via `HWY`_, the precision of your results may
depend on the ISA available on your machine. However, in all tested cases
distopia satisfied the accuracy thresholds used to the functions in this
module. Please document any issues you encounter with distopia's accuracy
in the `relevant distopia issue`_ on the MDAnalysis GitHub repository.
.. _distopia: https://github.com/MDAnalysis/distopia
.. _distopia documentation: https://www.mdanalysis.org/distopia
.. _ISA: https://en.wikipedia.org/wiki/Instruction_set_architecture
.. _HWY: https://github.com/google/highway
.. _relevant distopia issue: https://github.com/MDAnalysis/mdanalysis/issues/3915
.. versionadded:: 0.13.0
.. versionchanged:: 2.3.0
Distance functions can now accept an
:class:`~MDAnalysis.core.groups.AtomGroup` or an :class:`np.ndarray`
.. versionchanged:: 2.5.0
Interface to the `distopia`_ package added.
.. versionchanged:: 2.9.0
Distopia support greatly expanded (with distopia ≥ 0.4.0).
Constants
---------
.. data:: HAS_DISTOPIA
This variable is ``True`` if the :mod:`distopia` package has been
installed and is available as a `backend`. Otherwise it is
``False``.
Functions
---------
.. autofunction:: distance_array
.. autofunction:: self_distance_array
.. autofunction:: capped_distance
.. autofunction:: self_capped_distance
.. autofunction:: calc_bonds
.. autofunction:: calc_angles
.. autofunction:: calc_dihedrals
.. autofunction:: apply_PBC
.. autofunction:: transform_RtoS
.. autofunction:: transform_StoR
.. autofunction:: augment_coordinates(coordinates, box, r)
.. autofunction:: undo_augment(results, translation, nreal)
.. autofunction:: minimize_vectors(vectors, box)
"""
import numpy as np
import numpy.typing as npt
from typing import Union, Optional, Callable
from typing import TYPE_CHECKING
if TYPE_CHECKING: # pragma: no cover
from ..core.groups import AtomGroup
from .util import check_coords, check_box
from .mdamath import triclinic_vectors
from ._augment import augment_coordinates, undo_augment
from .nsgrid import FastNS
from .c_distances import _minimize_vectors_ortho, _minimize_vectors_triclinic
from ._distopia import HAS_DISTOPIA
# hack to select backend with backend=<backend> kwarg. Note that
# the cython parallel code (prange) in parallel.distances is
# independent from the OpenMP code
import importlib
_distances = {}
_distances["serial"] = importlib.import_module(
".c_distances", package="MDAnalysis.lib"
)
try:
_distances["openmp"] = importlib.import_module(
".c_distances_openmp", package="MDAnalysis.lib"
)
except ImportError:
pass
if HAS_DISTOPIA:
_distances["distopia"] = importlib.import_module(
"._distopia", package="MDAnalysis.lib"
)
del importlib
def _run(
funcname: str,
args: Optional[tuple] = None,
kwargs: Optional[dict] = None,
backend: str = "serial",
) -> Callable:
"""Helper function to select a backend function `funcname`."""
args = args if args is not None else tuple()
kwargs = kwargs if kwargs is not None else dict()
backend = backend.lower()
try:
func = getattr(_distances[backend], funcname)
except KeyError:
errmsg = (
f"Function {funcname} not available with backend {backend} "
f"try one of: {_distances.keys()}"
)
raise ValueError(errmsg) from None
return func(*args, **kwargs)
# serial versions are always available (and are typically used within
# the core and topology modules)
from .c_distances import (
_UINT64_MAX,
calc_distance_array,
calc_distance_array_ortho,
calc_distance_array_triclinic,
calc_self_distance_array,
calc_self_distance_array_ortho,
calc_self_distance_array_triclinic,
coord_transform,
calc_bond_distance,
calc_bond_distance_ortho,
calc_bond_distance_triclinic,
calc_angle,
calc_angle_ortho,
calc_angle_triclinic,
calc_dihedral,
calc_dihedral_ortho,
calc_dihedral_triclinic,
ortho_pbc,
triclinic_pbc,
)
from .c_distances_openmp import OPENMP_ENABLED as USED_OPENMP
def _check_result_array(
result: Optional[npt.NDArray], shape: tuple
) -> npt.NDArray:
"""Check if the result array is ok to use.
The `result` array must meet the following requirements:
* Must have a shape equal to `shape`.
* Its dtype must be ``numpy.float64``.
Paramaters
----------
result : numpy.ndarray or None
The result array to check. If `result` is `None``, a newly created
array of correct shape and dtype ``numpy.float64`` will be returned.
shape : tuple
The shape expected for the `result` array.
Returns
-------
result : numpy.ndarray (``dtype=numpy.float64``, ``shape=shape``)
The input array or a newly created array if the input was ``None``.
Raises
------
ValueError
If `result` is of incorrect shape.
TypeError
If the dtype of `result` is not ``numpy.float64``.
"""
if result is None:
return np.zeros(shape, dtype=np.float64)
if result.shape != shape:
raise ValueError(
"Result array has incorrect shape, should be {0}, got "
"{1}.".format(shape, result.shape)
)
if result.dtype != np.float64:
raise TypeError(
"Result array must be of type numpy.float64, got {}."
"".format(result.dtype)
)
# The following two lines would break a lot of tests. WHY?!
# if not coords.flags['C_CONTIGUOUS']:
# raise ValueError("{0} is not C-contiguous.".format(desc))
return result
[docs]
@check_coords(
"reference",
"configuration",
reduce_result_if_single=False,
check_lengths_match=False,
allow_atomgroup=True,
)
def distance_array(
reference: Union[npt.NDArray, "AtomGroup"],
configuration: Union[npt.NDArray, "AtomGroup"],
box: Optional[npt.NDArray] = None,
result: Optional[npt.NDArray] = None,
backend: str = "serial",
) -> npt.NDArray:
"""Calculate all possible distances between a reference set and another
configuration.
If there are ``n`` positions in `reference` and ``m`` positions in
`configuration`, a distance array of shape ``(n, m)`` will be computed.
If the optional argument `box` is supplied, the minimum image convention is
applied when calculating distances. Either orthogonal or triclinic boxes are
supported.
If a 2D numpy array of dtype ``numpy.float64`` with the shape ``(n, m)``
is provided in `result`, then this preallocated array is filled. This can
speed up calculations.
Parameters
----------
reference :numpy.ndarray or :class:`~MDAnalysis.core.groups.AtomGroup`
Reference coordinate array of shape ``(3,)`` or ``(n, 3)`` (dtype is
arbitrary, will be converted to ``numpy.float32`` internally). Also
accepts an :class:`~MDAnalysis.core.groups.AtomGroup`.
configuration : numpy.ndarray or :class:`~MDAnalysis.core.groups.AtomGroup`
Configuration coordinate array of shape ``(3,)`` or ``(m, 3)`` (dtype is
arbitrary, will be converted to ``numpy.float32`` internally). Also
accepts an :class:`~MDAnalysis.core.groups.AtomGroup`.
box : array_like, optional
The unitcell dimensions of the system, which can be orthogonal or
triclinic and must be provided in the same format as returned by
:attr:`MDAnalysis.coordinates.timestep.Timestep.dimensions`:
``[lx, ly, lz, alpha, beta, gamma]``.
result : numpy.ndarray, optional
Preallocated result array which must have the shape ``(n, m)`` and dtype
``numpy.float64``.
Avoids creating the array which saves time when the function
is called repeatedly.
backend : {'serial', 'OpenMP', 'distopia'}, optional
Keyword selecting the type of acceleration.
Returns
-------
d : numpy.ndarray (``dtype=numpy.float64``, ``shape=(n, m)``)
Array containing the distances ``d[i,j]`` between reference coordinates
``i`` and configuration coordinates ``j``.
.. versionchanged:: 0.13.0
Added *backend* keyword.
.. versionchanged:: 0.19.0
Internal dtype conversion of input coordinates to ``numpy.float32``.
Now also accepts single coordinates as input.
.. versionchanged:: 2.3.0
Can now accept an :class:`~MDAnalysis.core.groups.AtomGroup` as an
argument in any position and checks inputs using type hinting.
.. versionchanged:: 2.9.0
Added support for the `distopia` backend.
"""
confnum = configuration.shape[0]
refnum = reference.shape[0]
# check resulting array will not overflow UINT64_MAX
if refnum * confnum > _UINT64_MAX:
raise ValueError(
f"Size of resulting array {refnum * confnum} elements"
" larger than size of maximum integer"
)
distances = _check_result_array(result, (refnum, confnum))
if len(distances) == 0:
return distances
if backend == "distopia":
# distopia requires that all the input arrays are the same type,
# while MDAnalysis allows for mixed types, this should be changed
# pre 3.0.0 release see issue #3707
distances = distances.astype(np.float32)
box = np.asarray(box).astype(np.float32) if box is not None else None
if box is not None:
boxtype, box = check_box(box)
if boxtype == "ortho":
_run(
"calc_distance_array_ortho",
args=(reference, configuration, box, distances),
backend=backend,
)
else:
_run(
"calc_distance_array_triclinic",
args=(reference, configuration, box, distances),
backend=backend,
)
else:
_run(
"calc_distance_array",
args=(reference, configuration, distances),
backend=backend,
)
if backend == "distopia":
# mda expects the result to be in float64, so we need to convert it back
# to float64, change for 3.0, see #3707
distances = distances.astype(np.float64)
if result is not None:
result[:] = distances
return distances
[docs]
@check_coords("reference", reduce_result_if_single=False, allow_atomgroup=True)
def self_distance_array(
reference: Union[npt.NDArray, "AtomGroup"],
box: Optional[npt.NDArray] = None,
result: Optional[npt.NDArray] = None,
backend: str = "serial",
) -> npt.NDArray:
"""Calculate all possible distances within a configuration `reference`.
If the optional argument `box` is supplied, the minimum image convention is
applied when calculating distances. Either orthogonal or triclinic boxes are
supported.
If a 1D numpy array of dtype ``numpy.float64`` with the shape
``(n*(n-1)/2,)`` is provided in `result`, then this preallocated array is
filled. This can speed up calculations.
Parameters
----------
reference : numpy.ndarray or :class:`~MDAnalysis.core.groups.AtomGroup`
Reference coordinate array of shape ``(3,)`` or ``(n, 3)`` (dtype is
arbitrary, will be converted to ``numpy.float32`` internally). Also
accepts an :class:`~MDAnalysis.core.groups.AtomGroup`.
box : array_like, optional
The unitcell dimensions of the system, which can be orthogonal or
triclinic and must be provided in the same format as returned by
:attr:`MDAnalysis.coordinates.timestep.Timestep.dimensions`:
``[lx, ly, lz, alpha, beta, gamma]``.
result : numpy.ndarray, optional
Preallocated result array which must have the shape ``(n*(n-1)/2,)`` and
dtype ``numpy.float64``. Avoids creating the array which saves time when
the function is called repeatedly.
backend : {'serial', 'OpenMP', 'distopia'}, optional
Keyword selecting the type of acceleration.
Returns
-------
d : numpy.ndarray (``dtype=numpy.float64``, ``shape=(n*(n-1)/2,)``)
Array containing the distances ``dist[i,j]`` between reference
coordinates ``i`` and ``j`` at position ``d[k]``. Loop through ``d``:
.. code-block:: python
for i in range(n):
for j in range(i + 1, n):
dist[i, j] = dist[j, i] = d[k]
k += 1
.. versionchanged:: 0.13.0
Added *backend* keyword.
.. versionchanged:: 0.19.0
Internal dtype conversion of input coordinates to ``numpy.float32``.
.. versionchanged:: 2.3.0
Can now accept an :class:`~MDAnalysis.core.groups.AtomGroup` as an
argument in any position and checks inputs using type hinting.
.. versionchanged:: 2.9.0
Added support for the `distopia` backend.
"""
refnum = reference.shape[0]
distnum = refnum * (refnum - 1) // 2
# check resulting array will not overflow UINT64_MAX
if distnum > _UINT64_MAX:
raise ValueError(
f"Size of resulting array {distnum} elements larger"
" than size of maximum integer"
)
distances = _check_result_array(result, (distnum,))
if len(distances) == 0:
return distances
if backend == "distopia":
# distopia requires that all the input arrays are the same type,
# while MDAnalysis allows for mixed types, this should be changed
# pre 3.0.0 release see issue #3707
distances = distances.astype(np.float32)
box = np.asarray(box).astype(np.float32) if box is not None else None
if box is not None:
boxtype, box = check_box(box)
if boxtype == "ortho":
_run(
"calc_self_distance_array_ortho",
args=(reference, box, distances),
backend=backend,
)
else:
_run(
"calc_self_distance_array_triclinic",
args=(reference, box, distances),
backend=backend,
)
else:
_run(
"calc_self_distance_array",
args=(reference, distances),
backend=backend,
)
if backend == "distopia":
# mda expects the result to be in float64, so we need to convert it back
# to float64, change for 3.0, see #3707
distances = distances.astype(np.float64)
if result is not None:
result[:] = distances
return distances
[docs]
@check_coords(
"reference",
"configuration",
enforce_copy=False,
reduce_result_if_single=False,
check_lengths_match=False,
allow_atomgroup=True,
)
def capped_distance(
reference: Union[npt.NDArray, "AtomGroup"],
configuration: Union[npt.NDArray, "AtomGroup"],
max_cutoff: float,
min_cutoff: Optional[float] = None,
box: Optional[npt.NDArray] = None,
method: Optional[str] = None,
return_distances: Optional[bool] = True,
backend: Optional[str] = "serial",
):
"""Calculates pairs of indices corresponding to entries in the `reference`
and `configuration` arrays which are separated by a distance lying within
the specified cutoff(s). Optionally, these distances can be returned as
well.
If the optional argument `box` is supplied, the minimum image convention is
applied when calculating distances. Either orthogonal or triclinic boxes are
supported.
An automatic guessing of the optimal method to calculate the distances is
included in the function. An optional keyword for the method is also
provided. Users can enforce a particular method with this functionality.
Currently brute force, grid search, and periodic KDtree methods are
implemented.
Parameters
-----------
reference : numpy.ndarray or :class:`~MDAnalysis.core.groups.AtomGroup`
Reference coordinate array with shape ``(3,)`` or ``(n, 3)``. Also
accepts an :class:`~MDAnalysis.core.groups.AtomGroup`.
configuration : numpy.ndarray or :class:`~MDAnalysis.core.groups.AtomGroup`
Configuration coordinate array with shape ``(3,)`` or ``(m, 3)``. Also
accepts an :class:`~MDAnalysis.core.groups.AtomGroup`.
max_cutoff : float
Maximum cutoff distance between the reference and configuration.
min_cutoff : float, optional
Minimum cutoff distance between reference and configuration.
box : array_like, optional
The unitcell dimensions of the system, which can be orthogonal or
triclinic and must be provided in the same format as returned by
:attr:`MDAnalysis.coordinates.timestep.Timestep.dimensions`:
``[lx, ly, lz, alpha, beta, gamma]``.
method : {'bruteforce', 'nsgrid', 'pkdtree'}, optional
Keyword to override the automatic guessing of the employed search
method.
return_distances : bool, optional
If set to ``True``, distances will also be returned.
backend : {'serial', 'OpenMP', 'distopia'}, optional
Keyword selecting the type of acceleration.
Returns
-------
pairs : numpy.ndarray (``dtype=numpy.int64``, ``shape=(n_pairs, 2)``)
Pairs of indices, corresponding to coordinates in the `reference` and
`configuration` arrays such that the distance between them lies within
the interval (`min_cutoff`, `max_cutoff`].
Each row in `pairs` is an index pair ``[i, j]`` corresponding to the
``i``-th coordinate in `reference` and the ``j``-th coordinate in
`configuration`.
distances : numpy.ndarray (``dtype=numpy.float64``, ``shape=(n_pairs,)``), optional
Distances corresponding to each pair of indices. Only returned if
`return_distances` is ``True``. ``distances[k]`` corresponds to the
``k``-th pair returned in `pairs` and gives the distance between the
coordinates ``reference[pairs[k, 0]]`` and
``configuration[pairs[k, 1]]``.
.. code-block:: python
pairs, distances = capped_distances(reference, configuration,
max_cutoff, return_distances=True)
for k, [i, j] in enumerate(pairs):
coord1 = reference[i]
coord2 = configuration[j]
distance = distances[k]
See Also
--------
distance_array
MDAnalysis.lib.pkdtree.PeriodicKDTree.search
MDAnalysis.lib.nsgrid.FastNS.search
.. versionchanged:: 1.0.1
nsgrid was temporarily removed and replaced with pkdtree due to issues
relating to its reliability and accuracy (Issues #2919, #2229, #2345,
#2670, #2930)
.. versionchanged:: 1.0.2
nsgrid enabled again
.. versionchanged:: 2.3.0
Can now accept an :class:`~MDAnalysis.core.groups.AtomGroup` as an
argument in any position and checks inputs using type hinting.
.. versionchanged:: 2.10.0
Added the "backend" argument to select the type of acceleration of
the distance calculations.
"""
if box is not None:
box = np.asarray(box, dtype=np.float32)
if box.shape[0] != 6:
raise ValueError(
"Box Argument is of incompatible type. The "
"dimension should be either None or of the form "
"[lx, ly, lz, alpha, beta, gamma]"
)
# The check_coords decorator made sure that reference and configuration
# are arrays of positions. Mypy does not know about that so we have to
# tell it.
reference_positions: npt.NDArray = reference # type: ignore
configuration_positions: npt.NDArray = configuration # type: ignore
function = _determine_method(
reference_positions,
configuration_positions,
max_cutoff,
min_cutoff=min_cutoff,
box=box,
method=method,
)
if function.__name__ == "_nsgrid_capped":
return function(
reference,
configuration,
max_cutoff,
min_cutoff=min_cutoff,
box=box,
return_distances=return_distances,
)
else:
return function(
reference,
configuration,
max_cutoff,
min_cutoff=min_cutoff,
box=box,
return_distances=return_distances,
backend=backend,
)
def _determine_method(
reference: npt.NDArray,
configuration: npt.NDArray,
max_cutoff: float,
min_cutoff: Optional[float] = None,
box: Optional[npt.NDArray] = None,
method: Optional[str] = None,
) -> Callable:
"""Guesses the fastest method for capped distance calculations based on the
size of the coordinate sets and the relative size of the target volume.
Parameters
----------
reference : numpy.ndarray
Reference coordinate array with shape ``(3,)`` or ``(n, 3)``.
configuration : numpy.ndarray
Configuration coordinate array with shape ``(3,)`` or ``(m, 3)``.
max_cutoff : float
Maximum cutoff distance between `reference` and `configuration`
coordinates.
min_cutoff : float, optional
Minimum cutoff distance between `reference` and `configuration`
coordinates.
box : numpy.ndarray
The unitcell dimensions of the system, which can be orthogonal or
triclinic and must be provided in the same format as returned by
:attr:`MDAnalysis.coordinates.timestep.Timestep.dimensions`:
``[lx, ly, lz, alpha, beta, gamma]``.
method : {'bruteforce', 'nsgrid', 'pkdtree'}, optional
Keyword to override the automatic guessing of the employed search
method.
Returns
-------
function : callable
The function implementing the guessed (or deliberatly chosen) method.
.. versionchanged:: 1.0.1
nsgrid was temporarily removed and replaced with pkdtree due to issues
relating to its reliability and accuracy (Issues #2919, #2229, #2345,
#2670, #2930)
.. versionchanged:: 1.1.0
enabled nsgrid again
"""
methods = {
"bruteforce": _bruteforce_capped,
"pkdtree": _pkdtree_capped,
"nsgrid": _nsgrid_capped,
}
if method is not None:
return methods[method.lower()]
if len(reference) < 10 or len(configuration) < 10:
return methods["bruteforce"]
elif len(reference) * len(configuration) >= 1e8:
# CAUTION : for large datasets, shouldnt go into 'bruteforce'
# in any case. Arbitrary number, but can be characterized
return methods["nsgrid"]
else:
if box is None:
min_dim = np.array(
[reference.min(axis=0), configuration.min(axis=0)]
)
max_dim = np.array(
[reference.max(axis=0), configuration.max(axis=0)]
)
size = max_dim.max(axis=0) - min_dim.min(axis=0)
elif np.all(box[3:] == 90.0):
size = box[:3]
else:
tribox = triclinic_vectors(box)
size = tribox.max(axis=0) - tribox.min(axis=0)
if np.any(max_cutoff > 0.3 * size):
return methods["bruteforce"]
else:
return methods["nsgrid"]
@check_coords(
"reference",
"configuration",
enforce_copy=False,
reduce_result_if_single=False,
check_lengths_match=False,
allow_atomgroup=True,
)
def _bruteforce_capped(
reference: Union[npt.NDArray, "AtomGroup"],
configuration: Union[npt.NDArray, "AtomGroup"],
max_cutoff: float,
min_cutoff: Optional[float] = None,
box: Optional[npt.NDArray] = None,
return_distances: Optional[bool] = True,
backend: Optional[str] = "serial",
):
"""Capped distance evaluations using a brute force method.
Computes and returns an array containing pairs of indices corresponding to
entries in the `reference` and `configuration` arrays which are separated by
a distance lying within the specified cutoff(s). Employs naive distance
computations (brute force) to find relevant distances.
Optionally, these distances can be returned as well.
If the optional argument `box` is supplied, the minimum image convention is
applied when calculating distances. Either orthogonal or triclinic boxes are
supported.
Parameters
----------
reference : numpy.ndarray or :class:`~MDAnalysis.core.groups.AtomGroup`
Reference coordinate array with shape ``(3,)`` or ``(n, 3)`` (dtype will
be converted to ``numpy.float32`` internally). Also
accepts an :class:`~MDAnalysis.core.groups.AtomGroup`.
configuration : array or :class:`~MDAnalysis.core.groups.AtomGroup`
Configuration coordinate array with shape ``(3,)`` or ``(m, 3)`` (dtype
will be converted to ``numpy.float32`` internally). Also
accepts an :class:`~MDAnalysis.core.groups.AtomGroup`.
max_cutoff : float
Maximum cutoff distance between `reference` and `configuration`
coordinates.
min_cutoff : float, optional
Minimum cutoff distance between `reference` and `configuration`
coordinates.
box : numpy.ndarray, optional
The unitcell dimensions of the system, which can be orthogonal or
triclinic and must be provided in the same format as returned by
:attr:`MDAnalysis.coordinates.timestep.Timestep.dimensions`:
``[lx, ly, lz, alpha, beta, gamma]``.
return_distances : bool, optional
If set to ``True``, distances will also be returned.
backend : {'serial', 'OpenMP', 'distopia'}, optional
Keyword selecting the type of acceleration.
Returns
-------
pairs : numpy.ndarray (``dtype=numpy.int64``, ``shape=(n_pairs, 2)``)
Pairs of indices, corresponding to coordinates in the `reference` and
`configuration` arrays such that the distance between them lies within
the interval (`min_cutoff`, `max_cutoff`].
Each row in `pairs` is an index pair ``[i, j]`` corresponding to the
``i``-th coordinate in `reference` and the ``j``-th coordinate in
`configuration`.
distances : numpy.ndarray (``dtype=numpy.float64``, ``shape=(n_pairs,)``), optional
Distances corresponding to each pair of indices. Only returned if
`return_distances` is ``True``. ``distances[k]`` corresponds to the
``k``-th pair returned in `pairs` and gives the distance between the
coordinates ``reference[pairs[k, 0]]`` and
``configuration[pairs[k, 1]]``.
.. versionchanged:: 2.3.0
Can now accept an :class:`~MDAnalysis.core.groups.AtomGroup` as an
argument in any position and checks inputs using type hinting.
.. versionchanged:: 2.10.0
Added the "backend" argument to select the type of acceleration of
the distance calculations.
"""
# Default return values (will be overwritten only if pairs are found):
pairs = np.empty((0, 2), dtype=np.intp)
distances = np.empty((0,), dtype=np.float64)
if len(reference) > 0 and len(configuration) > 0:
_distances = distance_array(
reference, configuration, box=box, backend=backend
)
if min_cutoff is not None:
mask = np.where(
(_distances <= max_cutoff) & (_distances > min_cutoff)
)
else:
mask = np.where((_distances <= max_cutoff))
if mask[0].size > 0:
pairs = np.c_[mask[0], mask[1]]
if return_distances:
distances = _distances[mask]
if return_distances:
return pairs, distances
else:
return pairs
@check_coords(
"reference",
"configuration",
enforce_copy=False,
reduce_result_if_single=False,
check_lengths_match=False,
allow_atomgroup=True,
)
def _pkdtree_capped(
reference: Union[npt.NDArray, "AtomGroup"],
configuration: Union[npt.NDArray, "AtomGroup"],
max_cutoff: float,
min_cutoff: Optional[float] = None,
box: Optional[npt.NDArray] = None,
return_distances: Optional[bool] = True,
backend: Optional[str] = "serial",
):
"""Capped distance evaluations using a KDtree method.
Computes and returns an array containing pairs of indices corresponding to
entries in the `reference` and `configuration` arrays which are separated by
a distance lying within the specified cutoff(s). Employs a (periodic) KDtree
algorithm to find relevant distances.
Optionally, these distances can be returned as well.
If the optional argument `box` is supplied, the minimum image convention is
applied when calculating distances. Either orthogonal or triclinic boxes are
supported.
Parameters
----------
reference : numpy.ndarray or :class:`~MDAnalysis.core.groups.AtomGroup`
Reference coordinate array with shape ``(3,)`` or ``(n, 3)`` (dtype will
be converted to ``numpy.float32`` internally). Also
accepts an :class:`~MDAnalysis.core.groups.AtomGroup`.
configuration : numpy.ndarray or :class:`~MDAnalysis.core.groups.AtomGroup`
Configuration coordinate array with shape ``(3,)`` or ``(m, 3)`` (dtype
will be converted to ``numpy.float32`` internally). Also
accepts an :class:`~MDAnalysis.core.groups.AtomGroup`.
max_cutoff : float
Maximum cutoff distance between `reference` and `configuration`
coordinates.
min_cutoff : float, optional
Minimum cutoff distance between `reference` and `configuration`
coordinates.
box : numpy.ndarray, optional
The unitcell dimensions of the system, which can be orthogonal or
triclinic and must be provided in the same format as returned by
:attr:`MDAnalysis.coordinates.timestep.Timestep.dimensions`:
``[lx, ly, lz, alpha, beta, gamma]``.
return_distances : bool, optional
If set to ``True``, distances will also be returned.
backend : {'serial', 'OpenMP', 'distopia'}, optional
Keyword selecting the type of acceleration.
Returns
-------
pairs : numpy.ndarray (``dtype=numpy.int64``, ``shape=(n_pairs, 2)``)
Pairs of indices, corresponding to coordinates in the `reference` and
`configuration` arrays such that the distance between them lies within
the interval (`min_cutoff`, `max_cutoff`].
Each row in `pairs` is an index pair ``[i, j]`` corresponding to the
``i``-th coordinate in `reference` and the ``j``-th coordinate in
`configuration`.
distances : numpy.ndarray (``dtype=numpy.float64``, ``shape=(n_pairs,)``), optional
Distances corresponding to each pair of indices. Only returned if
`return_distances` is ``True``. ``distances[k]`` corresponds to the
``k``-th pair returned in `pairs` and gives the distance between the
coordinates ``reference[pairs[k, 0]]`` and
``configuration[pairs[k, 1]]``.
.. versionchanged:: 2.3.0
Can now accept an :class:`~MDAnalysis.core.groups.AtomGroup` as an
argument in any position and checks inputs using type hinting.
.. versionchanged:: 2.10.0
Added the "backend" argument to select the type of acceleration of
the distance calculations.
"""
from .pkdtree import (
PeriodicKDTree,
) # must be here to avoid circular import
# Default return values (will be overwritten only if pairs are found):
pairs = np.empty((0, 2), dtype=np.intp)
distances = np.empty((0,), dtype=np.float64)
if len(reference) > 0 and len(configuration) > 0:
kdtree = PeriodicKDTree(box=box)
cut = max_cutoff if box is not None else None
kdtree.set_coords(configuration, cutoff=cut)
_pairs = kdtree.search_tree(reference, max_cutoff)
if _pairs.size > 0:
pairs = _pairs
if return_distances or (min_cutoff is not None):
refA, refB = pairs[:, 0], pairs[:, 1]
distances = calc_bonds(
reference[refA],
configuration[refB],
box=box,
backend=backend,
)
if min_cutoff is not None:
mask = np.where(distances > min_cutoff)
pairs, distances = pairs[mask], distances[mask]
if return_distances:
return pairs, distances
else:
return pairs
@check_coords(
"reference",
"configuration",
enforce_copy=False,
reduce_result_if_single=False,
check_lengths_match=False,
allow_atomgroup=True,
)
def _nsgrid_capped(
reference: Union[npt.NDArray, "AtomGroup"],
configuration: Union[npt.NDArray, "AtomGroup"],
max_cutoff: float,
min_cutoff: Optional[float] = None,
box: Optional[npt.NDArray] = None,
return_distances: Optional[bool] = True,
):
"""Capped distance evaluations using a grid-based search method.
Computes and returns an array containing pairs of indices corresponding to
entries in the `reference` and `configuration` arrays which are separated by
a distance lying within the specified cutoff(s). Employs a grid-based search
algorithm to find relevant distances.
Optionally, these distances can be returned as well.
If the optional argument `box` is supplied, the minimum image convention is
applied when calculating distances. Either orthogonal or triclinic boxes are
supported.
Parameters
----------
reference : numpy.ndarray or :class:`~MDAnalysis.core.groups.AtomGroup`
Reference coordinate array with shape ``(3,)`` or ``(n, 3)`` (dtype will
be converted to ``numpy.float32`` internally). Also
accepts an :class:`~MDAnalysis.core.groups.AtomGroup`.
configuration : numpy.ndarray or :class:`~MDAnalysis.core.groups.AtomGroup`
Configuration coordinate array with shape ``(3,)`` or ``(m, 3)`` (dtype
will be converted to ``numpy.float32`` internally). Also
accepts an :class:`~MDAnalysis.core.groups.AtomGroup`.
max_cutoff : float
Maximum cutoff distance between `reference` and `configuration`
coordinates.
min_cutoff : float, optional
Minimum cutoff distance between `reference` and `configuration`
coordinates.
box : numpy.ndarray (``dtype=numpy.float64``, ``shape=(n_pairs,)``), optional
The unitcell dimensions of the system, which can be orthogonal or
triclinic and must be provided in the same format as returned by
:attr:`MDAnalysis.coordinates.timestep.Timestep.dimensions`:
``[lx, ly, lz, alpha, beta, gamma]``.
return_distances : bool, optional
If set to ``True``, distances will also be returned.
Returns
-------
pairs : numpy.ndarray (``dtype=numpy.int64``, ``shape=(n_pairs, 2)``)
Pairs of indices, corresponding to coordinates in the `reference` and
`configuration` arrays such that the distance between them lies within
the interval (`min_cutoff`, `max_cutoff`].
Each row in `pairs` is an index pair ``[i, j]`` corresponding to the
``i``-th coordinate in `reference` and the ``j``-th coordinate in
`configuration`.
distances : numpy.ndarray, optional
Distances corresponding to each pair of indices. Only returned if
`return_distances` is ``True``. ``distances[k]`` corresponds to the
``k``-th pair returned in `pairs` and gives the distance between the
coordinates ``reference[pairs[k, 0]]`` and
``configuration[pairs[k, 1]]``.
.. versionchanged:: 2.3.0
Can now accept an :class:`~MDAnalysis.core.groups.AtomGroup` as an
argument in any position and checks inputs using type hinting.
"""
# Default return values (will be overwritten only if pairs are found):
pairs = np.empty((0, 2), dtype=np.intp)
distances = np.empty((0,), dtype=np.float64)
if len(reference) > 0 and len(configuration) > 0:
if box is None:
# create a pseudobox
# define the max range
# and supply the pseudobox
# along with only one set of coordinates
pseudobox = np.zeros(6, dtype=np.float32)
all_coords = np.concatenate([reference, configuration])
lmax = all_coords.max(axis=0)
lmin = all_coords.min(axis=0)
# Using maximum dimension as the box size
boxsize = (lmax - lmin).max()
# to avoid failures for very close particles but with
# larger cutoff
boxsize = np.maximum(boxsize, 2 * max_cutoff)
pseudobox[:3] = boxsize + 2.2 * max_cutoff
pseudobox[3:] = 90.0
shiftref, shiftconf = reference.copy(), configuration.copy()
# Extra padding near the origin
shiftref -= lmin - 0.1 * max_cutoff
shiftconf -= lmin - 0.1 * max_cutoff
gridsearch = FastNS(
max_cutoff, shiftconf, box=pseudobox, pbc=False
)
results = gridsearch.search(shiftref)
else:
gridsearch = FastNS(max_cutoff, configuration, box=box)
results = gridsearch.search(reference)
pairs = results.get_pairs()
if return_distances or (min_cutoff is not None):
distances = results.get_pair_distances()
if min_cutoff is not None:
idx = distances > min_cutoff
pairs, distances = pairs[idx], distances[idx]
if return_distances:
return pairs, distances
else:
return pairs
[docs]
@check_coords(
"reference",
enforce_copy=False,
reduce_result_if_single=False,
check_lengths_match=False,
allow_atomgroup=True,
)
def self_capped_distance(
reference: Union[npt.NDArray, "AtomGroup"],
max_cutoff: float,
min_cutoff: Optional[float] = None,
box: Optional[npt.NDArray] = None,
method: Optional[str] = None,
return_distances: Optional[bool] = True,
backend: Optional[str] = "serial",
):
"""Calculates pairs of indices corresponding to entries in the `reference`
array which are separated by a distance lying within the specified
cutoff(s). Optionally, these distances can be returned as well.
If the optional argument `box` is supplied, the minimum image convention is
applied when calculating distances. Either orthogonal or triclinic boxes are
supported.
An automatic guessing of the optimal method to calculate the distances is
included in the function. An optional keyword for the method is also
provided. Users can enforce a particular method with this functionality.
Currently brute force, grid search, and periodic KDtree methods are
implemented.
Parameters
-----------
reference : numpy.ndarray or :class:`~MDAnalysis.core.groups.AtomGroup`
Reference coordinate array with shape ``(3,)`` or ``(n, 3)``. Also
accepts an :class:`~MDAnalysis.core.groups.AtomGroup`.
max_cutoff : float
Maximum cutoff distance between `reference` coordinates.
min_cutoff : float, optional
Minimum cutoff distance between `reference` coordinates.
box : array_like, optional
The unitcell dimensions of the system, which can be orthogonal or
triclinic and must be provided in the same format as returned by
:attr:`MDAnalysis.coordinates.timestep.Timestep.dimensions`:
``[lx, ly, lz, alpha, beta, gamma]``.
method : {'bruteforce', 'nsgrid', 'pkdtree'}, optional
Keyword to override the automatic guessing of the employed search
method.
return_distances : bool, optional
If set to ``True``, distances will also be returned.
backend : {'serial', 'OpenMP', 'distopia'}, optional
Keyword selecting the type of acceleration.
Returns
-------
pairs : numpy.ndarray (``dtype=numpy.int64``, ``shape=(n_pairs, 2)``)
Pairs of indices, corresponding to coordinates in the `reference` array
such that the distance between them lies within the interval
(`min_cutoff`, `max_cutoff`].
Each row in `pairs` is an index pair ``[i, j]`` corresponding to the
``i``-th and the ``j``-th coordinate in `reference`.
distances : numpy.ndarray (``dtype=numpy.float64``, ``shape=(n_pairs,)``)
Distances corresponding to each pair of indices. Only returned if
`return_distances` is ``True``. ``distances[k]`` corresponds to the
``k``-th pair returned in `pairs` and gives the distance between the
coordinates ``reference[pairs[k, 0]]`` and ``reference[pairs[k, 1]]``.
.. code-block:: python
pairs, distances = self_capped_distances(reference, max_cutoff,
return_distances=True)
for k, [i, j] in enumerate(pairs):
coord1 = reference[i]
coord2 = reference[j]
distance = distances[k]
Note
-----
Currently supports brute force, grid-based, and periodic KDtree search
methods.
See Also
--------
self_distance_array
MDAnalysis.lib.pkdtree.PeriodicKDTree.search
MDAnalysis.lib.nsgrid.FastNS.self_search
.. versionchanged:: 0.20.0
Added `return_distances` keyword.
.. versionchanged:: 1.0.1
nsgrid was temporarily removed and replaced with pkdtree due to issues
relating to its reliability and accuracy (Issues #2919, #2229, #2345,
#2670, #2930)
.. versionchanged:: 1.0.2
enabled nsgrid again
.. versionchanged:: 2.3.0
Can now accept an :class:`~MDAnalysis.core.groups.AtomGroup` as an
argument in any position and checks inputs using type hinting.
.. versionchanged:: 2.10.0
Added the "backend" argument to select the type of acceleration of
the distance calculations.
"""
if box is not None:
box = np.asarray(box, dtype=np.float32)
if box.shape[0] != 6:
raise ValueError(
"Box Argument is of incompatible type. The "
"dimension should be either None or of the form "
"[lx, ly, lz, alpha, beta, gamma]"
)
# The check_coords decorator made sure that reference is an
# array of positions. Mypy does not know about that so we have to
# tell it.
reference_positions: npt.NDArray = reference # type: ignore
function = _determine_method_self(
reference_positions,
max_cutoff,
min_cutoff=min_cutoff,
box=box,
method=method,
)
if function.__name__ == "_nsgrid_capped_self":
return function(
reference,
max_cutoff,
min_cutoff=min_cutoff,
box=box,
return_distances=return_distances,
)
else:
return function(
reference,
max_cutoff,
min_cutoff=min_cutoff,
box=box,
return_distances=return_distances,
backend=backend,
)
def _determine_method_self(
reference: npt.NDArray,
max_cutoff: float,
min_cutoff: Optional[float] = None,
box: Optional[npt.NDArray] = None,
method: Optional[str] = None,
):
"""Guesses the fastest method for capped distance calculations based on the
size of the `reference` coordinate set and the relative size of the target
volume.
Parameters
----------
reference : numpy.ndarray
Reference coordinate array with shape ``(3,)`` or ``(n, 3)``.
max_cutoff : float
Maximum cutoff distance between `reference` coordinates.
min_cutoff : float, optional
Minimum cutoff distance between `reference` coordinates.
box : numpy.ndarray
The unitcell dimensions of the system, which can be orthogonal or
triclinic and must be provided in the same format as returned by
:attr:`MDAnalysis.coordinates.timestep.Timestep.dimensions`:
``[lx, ly, lz, alpha, beta, gamma]``.
method : {'bruteforce', 'nsgrid', 'pkdtree'}, optional
Keyword to override the automatic guessing of the employed search
method.
Returns
-------
function : callable
The function implementing the guessed (or deliberatly chosen) method.
.. versionchanged:: 1.0.1
nsgrid was temporarily removed and replaced with pkdtree due to issues
relating to its reliability and accuracy (Issues #2919, #2229, #2345,
#2670, #2930)
.. versionchanged:: 1.0.2
enabled nsgrid again
"""
methods = {
"bruteforce": _bruteforce_capped_self,
"pkdtree": _pkdtree_capped_self,
"nsgrid": _nsgrid_capped_self,
}
if method is not None:
return methods[method.lower()]
if len(reference) < 100:
return methods["bruteforce"]
if box is None:
min_dim = np.array([reference.min(axis=0)])
max_dim = np.array([reference.max(axis=0)])
size = max_dim.max(axis=0) - min_dim.min(axis=0)
elif np.all(box[3:] == 90.0):
size = box[:3]
else:
tribox = triclinic_vectors(box)
size = tribox.max(axis=0) - tribox.min(axis=0)
if max_cutoff < 0.03 * size.min():
return methods["pkdtree"]
else:
return methods["nsgrid"]
@check_coords(
"reference",
enforce_copy=False,
reduce_result_if_single=False,
allow_atomgroup=True,
)
def _bruteforce_capped_self(
reference: Union[npt.NDArray, "AtomGroup"],
max_cutoff: float,
min_cutoff: Optional[float] = None,
box: Optional[npt.NDArray] = None,
return_distances: Optional[bool] = True,
backend: Optional[str] = "serial",
):
"""Capped distance evaluations using a brute force method.
Computes and returns an array containing pairs of indices corresponding to
entries in the `reference` array which are separated by a distance lying
within the specified cutoff(s). Employs naive distance computations (brute
force) to find relevant distances. Optionally, these distances can be
returned as well.
If the optional argument `box` is supplied, the minimum image convention is
applied when calculating distances. Either orthogonal or triclinic boxes are
supported.
Parameters
----------
reference : numpy.ndarray or :class:`~MDAnalysis.core.groups.AtomGroup`
Reference coordinate array with shape ``(3,)`` or ``(n, 3)`` (dtype will
be converted to ``numpy.float32`` internally). Also accepts an
:class:`~MDAnalysis.core.groups.AtomGroup`.
max_cutoff : float
Maximum cutoff distance between `reference` coordinates.
min_cutoff : float, optional
Minimum cutoff distance between `reference` coordinates.
box : numpy.ndarray, optional
The unitcell dimensions of the system, which can be orthogonal or
triclinic and must be provided in the same format as returned by
:attr:`MDAnalysis.coordinates.timestep.Timestep.dimensions`:
``[lx, ly, lz, alpha, beta, gamma]``.
return_distances : bool, optional
If set to ``True``, distances will also be returned.
backend : {'serial', 'OpenMP', 'distopia'}, optional
Keyword selecting the type of acceleration.
Returns
-------
pairs : numpy.ndarray (``dtype=numpy.int64``, ``shape=(n_pairs, 2)``)
Pairs of indices, corresponding to coordinates in the `reference` array
such that the distance between them lies within the interval
(`min_cutoff`, `max_cutoff`].
Each row in `pairs` is an index pair ``[i, j]`` corresponding to the
``i``-th and the ``j``-th coordinate in `reference`.
distances : numpy.ndarray (``dtype=numpy.float64``, ``shape=(n_pairs,)``), optional
Distances corresponding to each pair of indices. Only returned if
`return_distances` is ``True``. ``distances[k]`` corresponds to the
``k``-th pair returned in `pairs` and gives the distance between the
coordinates ``reference[pairs[k, 0]]`` and
``configuration[pairs[k, 1]]``.
.. versionchanged:: 0.20.0
Added `return_distances` keyword.
.. versionchanged:: 2.3.0
Can now accept an :class:`~MDAnalysis.core.groups.AtomGroup` as an
argument in any position and checks inputs using type hinting.
.. versionchanged:: 2.10.0
Added the "backend" argument to select the type of acceleration of
the distance calculations.
"""
# Default return values (will be overwritten only if pairs are found):
pairs = np.empty((0, 2), dtype=np.intp)
distances = np.empty((0,), dtype=np.float64)
N = len(reference)
# We're searching within a single coordinate set, so we need at least two
# coordinates to find distances between them.
if N > 1:
distvec = self_distance_array(reference, box=box, backend=backend)
dist = np.full((N, N), np.finfo(np.float64).max, dtype=np.float64)
dist[np.triu_indices(N, 1)] = distvec
if min_cutoff is not None:
mask = np.where((dist <= max_cutoff) & (dist > min_cutoff))
else:
mask = np.where((dist <= max_cutoff))
if mask[0].size > 0:
pairs = np.c_[mask[0], mask[1]]
distances = dist[mask]
if return_distances:
return pairs, distances
return pairs
@check_coords(
"reference",
enforce_copy=False,
reduce_result_if_single=False,
allow_atomgroup=True,
)
def _pkdtree_capped_self(
reference: Union[npt.NDArray, "AtomGroup"],
max_cutoff: float,
min_cutoff: Optional[float] = None,
box: Optional[npt.NDArray] = None,
return_distances: Optional[bool] = True,
backend: Optional[str] = "serial",
):
"""Capped distance evaluations using a KDtree method.
Computes and returns an array containing pairs of indices corresponding to
entries in the `reference` array which are separated by a distance lying
within the specified cutoff(s). Employs a (periodic) KDtree algorithm to
find relevant distances. Optionally, these distances can be returned as
well.
If the optional argument `box` is supplied, the minimum image convention is
applied when calculating distances. Either orthogonal or triclinic boxes are
supported.
Parameters
----------
reference : numpy.ndarray or :class:`~MDAnalysis.core.groups.AtomGroup`
Reference coordinate array with shape ``(3,)`` or ``(n, 3)`` (dtype will
be converted to ``numpy.float32`` internally). Also accepts an
:class:`~MDAnalysis.core.groups.AtomGroup`.
max_cutoff : float
Maximum cutoff distance between `reference` coordinates.
min_cutoff : float, optional
Minimum cutoff distance between `reference` coordinates.
box : numpy.ndarray, optional
The unitcell dimensions of the system, which can be orthogonal or
triclinic and must be provided in the same format as returned by
:attr:`MDAnalysis.coordinates.timestep.Timestep.dimensions`:
``[lx, ly, lz, alpha, beta, gamma]``.
return_distances : bool, optional
If set to ``True``, distances will also be returned.
backend : {'serial', 'OpenMP', 'distopia'}, optional
Keyword selecting the type of acceleration.
Returns
-------
pairs : numpy.ndarray (``dtype=numpy.int64``, ``shape=(n_pairs, 2)``)
Pairs of indices, corresponding to coordinates in the `reference` array
such that the distance between them lies within the interval
(`min_cutoff`, `max_cutoff`].
Each row in `pairs` is an index pair ``[i, j]`` corresponding to the
``i``-th and the ``j``-th coordinate in `reference`.
distances : numpy.ndarray (``dtype=numpy.float64``, ``shape=(n_pairs,)``)
Distances corresponding to each pair of indices. Only returned if
`return_distances` is ``True``. ``distances[k]`` corresponds to the
``k``-th pair returned in `pairs` and gives the distance between
the coordinates ``reference[pairs[k, 0]]`` and
``reference[pairs[k, 1]]``.
.. versionchanged:: 0.20.0
Added `return_distances` keyword.
.. versionchanged:: 2.3.0
Can now accept an :class:`~MDAnalysis.core.groups.AtomGroup` as an
argument in any position and checks inputs using type hinting.
.. versionchanged:: 2.10.0
Added the "backend" argument to select the type of acceleration of
the distance calculations.
"""
from .pkdtree import (
PeriodicKDTree,
) # must be here to avoid circular import
# Default return values (will be overwritten only if pairs are found):
pairs = np.empty((0, 2), dtype=np.intp)
distances = np.empty((0,), dtype=np.float64)
# We're searching within a single coordinate set, so we need at least two
# coordinates to find distances between them.
if len(reference) > 1:
kdtree = PeriodicKDTree(box=box)
cut = max_cutoff if box is not None else None
kdtree.set_coords(reference, cutoff=cut)
_pairs = kdtree.search_pairs(max_cutoff)
if _pairs.size > 0:
pairs = _pairs
if return_distances or (min_cutoff is not None):
refA, refB = pairs[:, 0], pairs[:, 1]
distances = calc_bonds(
reference[refA], reference[refB], box=box, backend=backend
)
if min_cutoff is not None:
idx = distances > min_cutoff
pairs, distances = pairs[idx], distances[idx]
if return_distances:
return pairs, distances
return pairs
@check_coords(
"reference",
enforce_copy=False,
reduce_result_if_single=False,
allow_atomgroup=True,
)
def _nsgrid_capped_self(
reference: Union[npt.NDArray, "AtomGroup"],
max_cutoff: float,
min_cutoff: Optional[float] = None,
box: Optional[npt.NDArray] = None,
return_distances: Optional[bool] = True,
):
"""Capped distance evaluations using a grid-based search method.
Computes and returns an array containing pairs of indices corresponding to
entries in the `reference` array which are separated by a distance lying
within the specified cutoff(s). Employs a grid-based search algorithm to
find relevant distances. Optionally, these distances can be returned as
well.
If the optional argument `box` is supplied, the minimum image convention is
applied when calculating distances. Either orthogonal or triclinic boxes are
supported.
Parameters
----------
reference : numpy.ndarray or :class:`~MDAnalysis.core.groups.AtomGroup`
Reference coordinate array with shape ``(3,)`` or ``(n, 3)`` (dtype will
be converted to ``numpy.float32`` internally). Also accepts an
:class:`~MDAnalysis.core.groups.AtomGroup`.
max_cutoff : float
Maximum cutoff distance between `reference` coordinates.
min_cutoff : float, optional
Minimum cutoff distance between `reference` coordinates.
box : numpy.ndarray, optional
The unitcell dimensions of the system, which can be orthogonal or
triclinic and must be provided in the same format as returned by
:attr:`MDAnalysis.coordinates.timestep.Timestep.dimensions`:
``[lx, ly, lz, alpha, beta, gamma]``.
Returns
-------
pairs : numpy.ndarray (``dtype=numpy.int64``, ``shape=(n_pairs, 2)``)
Pairs of indices, corresponding to coordinates in the `reference` array
such that the distance between them lies within the interval
(`min_cutoff`, `max_cutoff`].
Each row in `pairs` is an index pair ``[i, j]`` corresponding to the
``i``-th and the ``j``-th coordinate in `reference`.
distances : numpy.ndarray, optional
Distances corresponding to each pair of indices. Only returned if
`return_distances` is ``True``. ``distances[k]`` corresponds to the
``k``-th pair returned in `pairs` and gives the distance between the
coordinates ``reference[pairs[k, 0]]`` and
``configuration[pairs[k, 1]]``.
.. versionchanged:: 0.20.0
Added `return_distances` keyword.
.. versionchanged:: 2.3.0
Can now accept an :class:`~MDAnalysis.core.groups.AtomGroup` as an
argument in any position and checks inputs using type hinting.
"""
# Default return values (will be overwritten only if pairs are found):
pairs = np.empty((0, 2), dtype=np.intp)
distances = np.empty((0,), dtype=np.float64)
# We're searching within a single coordinate set, so we need at least two
# coordinates to find distances between them.
if len(reference) > 1:
if box is None:
# create a pseudobox
# define the max range
# and supply the pseudobox
# along with only one set of coordinates
pseudobox = np.zeros(6, dtype=np.float32)
lmax = reference.max(axis=0)
lmin = reference.min(axis=0)
# Using maximum dimension as the box size
boxsize = (lmax - lmin).max()
# to avoid failures of very close particles
# but with larger cutoff
if boxsize < 2 * max_cutoff:
# just enough box size so that NSGrid doesnot fails
sizefactor = 2.2 * max_cutoff / boxsize
else:
sizefactor = 1.2
pseudobox[:3] = sizefactor * boxsize
pseudobox[3:] = 90.0
shiftref = reference.copy()
# Extra padding near the origin
shiftref -= lmin - 0.1 * boxsize
gridsearch = FastNS(max_cutoff, shiftref, box=pseudobox, pbc=False)
results = gridsearch.self_search()
else:
gridsearch = FastNS(max_cutoff, reference, box=box)
results = gridsearch.self_search()
pairs = results.get_pairs()
if return_distances or (min_cutoff is not None):
distances = results.get_pair_distances()
if min_cutoff is not None:
idx = distances > min_cutoff
pairs, distances = pairs[idx], distances[idx]
if return_distances:
return pairs, distances
return pairs
[docs]
@check_coords("coords1", "coords2", allow_atomgroup=True)
def calc_bonds(
coords1: Union[npt.NDArray, "AtomGroup"],
coords2: Union[npt.NDArray, "AtomGroup"],
box: Optional[npt.NDArray] = None,
result: Optional[npt.NDArray] = None,
backend: str = "serial",
) -> npt.NDArray:
"""Calculates the bond lengths between pairs of atom positions from the two
coordinate arrays `coords1` and `coords2`, which must contain the same
number of coordinates. ``coords1[i]`` and ``coords2[i]`` represent the
positions of atoms connected by the ``i``-th bond. If single coordinates are
supplied, a single distance will be returned.
In comparison to :meth:`distance_array` and :meth:`self_distance_array`,
which calculate distances between all possible combinations of coordinates,
:meth:`calc_bonds` only calculates distances between pairs of coordinates,
similar to::
numpy.linalg.norm(a - b) for a, b in zip(coords1, coords2)
If the optional argument `box` is supplied, the minimum image convention is
applied when calculating distances. Either orthogonal or triclinic boxes are
supported.
If a numpy array of dtype ``numpy.float64`` with shape ``(n,)`` (for ``n``
coordinate pairs) is provided in `result`, then this preallocated array is
filled. This can speed up calculations.
Parameters
----------
coords1 : numpy.ndarray or :class:`~MDAnalysis.core.groups.AtomGroup`
Coordinate array of shape ``(3,)`` or ``(n, 3)`` for one half of a
single or ``n`` bonds, respectively (dtype is arbitrary, will be
converted to ``numpy.float32`` internally). Also accepts an
:class:`~MDAnalysis.core.groups.AtomGroup`.
coords2 : numpy.ndarray or :class:`~MDAnalysis.core.groups.AtomGroup`
Coordinate array of shape ``(3,)`` or ``(n, 3)`` for the other half of
a single or ``n`` bonds, respectively (dtype is arbitrary, will be
converted to ``numpy.float32`` internally). Also accepts an
:class:`~MDAnalysis.core.groups.AtomGroup`.
box : numpy.ndarray, optional
The unitcell dimensions of the system, which can be orthogonal or
triclinic and must be provided in the same format as returned by
:attr:`MDAnalysis.coordinates.timestep.Timestep.dimensions`:
``[lx, ly, lz, alpha, beta, gamma]``.
result : numpy.ndarray, optional
Preallocated result array of dtype ``numpy.float64`` and shape ``(n,)``
(for ``n`` coordinate pairs). Avoids recreating the array in repeated
function calls.
backend : {'serial', 'OpenMP', 'distopia'}, optional
Keyword selecting the type of acceleration. Defaults to 'serial'.
Returns
-------
bondlengths : numpy.ndarray (``dtype=numpy.float64``, ``shape=(n,)``) or
numpy.float64 Array containing the bond lengths between each pair of
coordinates. If two single coordinates were supplied, their distance is
returned as a single number instead of an array.
.. versionadded:: 0.8
.. versionchanged:: 0.13.0
Added *backend* keyword.
.. versionchanged:: 0.19.0
Internal dtype conversion of input coordinates to ``numpy.float32``.
Now also accepts single coordinates as input.
.. versionchanged:: 2.3.0
Can now accept an :class:`~MDAnalysis.core.groups.AtomGroup` as an
argument in any position and checks inputs using type hinting.
.. versionchanged:: 2.5.0
Can now optionally use the fast distance functions from distopia
"""
numatom = coords1.shape[0]
bondlengths = _check_result_array(result, (numatom,))
if backend == "distopia":
# distopia requires that all the input arrays are the same type,
# while MDAnalysis allows for mixed types, this should be changed
# pre 3.0.0 release see issue #3707
bondlengths = bondlengths.astype(np.float32)
box = np.asarray(box).astype(np.float32) if box is not None else None
if numatom > 0:
if box is not None:
boxtype, box = check_box(box)
if boxtype == "ortho":
_run(
"calc_bond_distance_ortho",
args=(coords1, coords2, box, bondlengths),
backend=backend,
)
else:
_run(
"calc_bond_distance_triclinic",
args=(coords1, coords2, box, bondlengths),
backend=backend,
)
else:
_run(
"calc_bond_distance",
args=(coords1, coords2, bondlengths),
backend=backend,
)
if backend == "distopia":
# mda expects the result to be in float64, so we need to convert it back
# to float64, change for 3.0, see #3707
bondlengths = bondlengths.astype(np.float64)
if result is not None:
result[:] = bondlengths
return bondlengths
[docs]
@check_coords("coords1", "coords2", "coords3", allow_atomgroup=True)
def calc_angles(
coords1: Union[npt.NDArray, "AtomGroup"],
coords2: Union[npt.NDArray, "AtomGroup"],
coords3: Union[npt.NDArray, "AtomGroup"],
box: Optional[npt.NDArray] = None,
result: Optional[npt.NDArray] = None,
backend: str = "serial",
) -> npt.NDArray:
"""Calculates the angles formed between triplets of atom positions from the
three coordinate arrays `coords1`, `coords2`, and `coords3`. All coordinate
arrays must contain the same number of coordinates.
The coordinates in `coords2` represent the apices of the angles::
2---3
/
1
Configurations where the angle is undefined (e.g., when coordinates 1 or 3
of a triplet coincide with coordinate 2) result in a value of **zero** for
that angle.
If the optional argument `box` is supplied, periodic boundaries are taken
into account when constructing the connecting vectors between coordinates,
i.e., the minimum image convention is applied for the vectors forming the
angles. Either orthogonal or triclinic boxes are supported.
If a numpy array of dtype ``numpy.float64`` with shape ``(n,)`` (for ``n``
coordinate triplets) is provided in `result`, then this preallocated array
is filled. This can speed up calculations.
Parameters
----------
coords1 : numpy.ndarray or :class:`~MDAnalysis.core.groups.AtomGroup`
Array of shape ``(3,)`` or ``(n, 3)`` containing the coordinates of one
side of a single or ``n`` angles, respectively (dtype is arbitrary, will
be converted to ``numpy.float32`` internally). Also accepts an
:class:`~MDAnalysis.core.groups.AtomGroup`.
coords2 : numpy.ndarray or :class:`~MDAnalysis.core.groups.AtomGroup`
Array of shape ``(3,)`` or ``(n, 3)`` containing the coordinates of the
apices of a single or ``n`` angles, respectively (dtype is arbitrary,
will be converted to ``numpy.float32`` internally). Also accepts an
:class:`~MDAnalysis.core.groups.AtomGroup`.
coords3 : numpy.ndarray or :class:`~MDAnalysis.core.groups.AtomGroup`
Array of shape ``(3,)`` or ``(n, 3)`` containing the coordinates of the
other side of a single or ``n`` angles, respectively (dtype is
arbitrary, will be converted to ``numpy.float32`` internally).
Also accepts an :class:`~MDAnalysis.core.groups.AtomGroup`.
box : numpy.ndarray, optional
The unitcell dimensions of the system, which can be orthogonal or
triclinic and must be provided in the same format as returned by
:attr:`MDAnalysis.coordinates.timestep.Timestep.dimensions`:
``[lx, ly, lz, alpha, beta, gamma]``.
result : numpy.ndarray, optional
Preallocated result array of dtype ``numpy.float64`` and shape ``(n,)``
(for ``n`` coordinate triplets). Avoids recreating the array in repeated
function calls.
backend : {'serial', 'OpenMP', 'distopia'}, optional
Keyword selecting the type of acceleration.
Returns
-------
angles : numpy.ndarray (``dtype=numpy.float64``, ``shape=(n,)``) or numpy.float64
Array containing the angles between each triplet of coordinates. Values
are returned in radians (rad). If three single coordinates were
supplied, the angle is returned as a single number instead of an array.
.. versionadded:: 0.8
.. versionchanged:: 0.9.0
Added optional box argument to account for periodic boundaries in
calculation
.. versionchanged:: 0.13.0
Added *backend* keyword.
.. versionchanged:: 0.19.0
Internal dtype conversion of input coordinates to ``numpy.float32``.
Now also accepts single coordinates as input.
.. versionchanged:: 2.3.0
Can now accept an :class:`~MDAnalysis.core.groups.AtomGroup` as an
argument in any position and checks inputs using type hinting.
"""
numatom = coords1.shape[0]
angles = _check_result_array(result, (numatom,))
if backend == "distopia":
# distopia requires that all the input arrays are the same type,
# while MDAnalysis allows for mixed types, this should be changed
# pre 3.0.0 release see issue #3707
angles = angles.astype(np.float32)
box = np.asarray(box).astype(np.float32) if box is not None else None
if numatom > 0:
if box is not None:
boxtype, box = check_box(box)
if boxtype == "ortho":
_run(
"calc_angle_ortho",
args=(coords1, coords2, coords3, box, angles),
backend=backend,
)
else:
_run(
"calc_angle_triclinic",
args=(coords1, coords2, coords3, box, angles),
backend=backend,
)
else:
_run(
"calc_angle",
args=(coords1, coords2, coords3, angles),
backend=backend,
)
if backend == "distopia":
# mda expects the result to be in float64, so we need to convert it back
# to float64, change for 3.0, see #3707
angles = angles.astype(np.float64)
if result is not None:
result[:] = angles
return angles
[docs]
@check_coords("coords1", "coords2", "coords3", "coords4", allow_atomgroup=True)
def calc_dihedrals(
coords1: Union[npt.NDArray, "AtomGroup"],
coords2: Union[npt.NDArray, "AtomGroup"],
coords3: Union[npt.NDArray, "AtomGroup"],
coords4: Union[npt.NDArray, "AtomGroup"],
box: Optional[npt.NDArray] = None,
result: Optional[npt.NDArray] = None,
backend: str = "serial",
) -> npt.NDArray:
r"""Calculates the dihedral angles formed between quadruplets of positions
from the four coordinate arrays `coords1`, `coords2`, `coords3`, and
`coords4`, which must contain the same number of coordinates.
The dihedral angle formed by a quadruplet of positions (1,2,3,4) is
calculated around the axis connecting positions 2 and 3 (i.e., the angle
between the planes spanned by positions (1,2,3) and (2,3,4))::
4
|
2-----3
/
1
If all coordinates lie in the same plane, the cis configuration corresponds
to a dihedral angle of zero, and the trans configuration to :math:`\pi`
radians (180 degrees). Configurations where the dihedral angle is undefined
(e.g., when all coordinates lie on the same straight line) result in a value
of ``nan`` (not a number) for that dihedral.
If the optional argument `box` is supplied, periodic boundaries are taken
into account when constructing the connecting vectors between coordinates,
i.e., the minimum image convention is applied for the vectors forming the
dihedral angles. Either orthogonal or triclinic boxes are supported.
If a numpy array of dtype ``numpy.float64`` with shape ``(n,)`` (for ``n``
coordinate quadruplets) is provided in `result` then this preallocated array
is filled. This can speed up calculations.
Parameters
----------
coords1 : numpy.ndarray or :class:`~MDAnalysis.core.groups.AtomGroup`
Coordinate array of shape ``(3,)`` or ``(n, 3)`` containing the 1st
positions in dihedrals (dtype is arbitrary, will be converted to
``numpy.float32`` internally). Also accepts an
:class:`~MDAnalysis.core.groups.AtomGroup`.
coords2 : numpy.ndarray or :class:`~MDAnalysis.core.groups.AtomGroup`
Coordinate array of shape ``(3,)`` or ``(n, 3)`` containing the 2nd
positions in dihedrals (dtype is arbitrary, will be converted to
``numpy.float32`` internally). Also accepts an
:class:`~MDAnalysis.core.groups.AtomGroup`.
coords3 : numpy.ndarray or :class:`~MDAnalysis.core.groups.AtomGroup`
Coordinate array of shape ``(3,)`` or ``(n, 3)`` containing the 3rd
positions in dihedrals (dtype is arbitrary, will be converted to
``numpy.float32`` internally). Also accepts an
:class:`~MDAnalysis.core.groups.AtomGroup`.
coords4 : numpy.ndarray or :class:`~MDAnalysis.core.groups.AtomGroup`
Coordinate array of shape ``(3,)`` or ``(n, 3)`` containing the 4th
positions in dihedrals (dtype is arbitrary, will be converted to
``numpy.float32`` internally). Also accepts an
:class:`~MDAnalysis.core.groups.AtomGroup`.
box : numpy.ndarray, optional
The unitcell dimensions of the system, which can be orthogonal or
triclinic and must be provided in the same format as returned by
:attr:`MDAnalysis.coordinates.timestep.Timestep.dimensions`:
``[lx, ly, lz, alpha, beta, gamma]``.
result : numpy.ndarray, optional
Preallocated result array of dtype ``numpy.float64`` and shape ``(n,)``
(for ``n`` coordinate quadruplets). Avoids recreating the array in
repeated function calls.
backend : {'serial', 'OpenMP', 'distopia'}, optional
Keyword selecting the type of acceleration.
Returns
-------
dihedrals : numpy.ndarray (``dtype=numpy.float64``, ``shape=(n,)``) or numpy.float64
Array containing the dihedral angles formed by each quadruplet of
coordinates. Values are returned in radians (rad). If four single
coordinates were supplied, the dihedral angle is returned as a single
number instead of an array. The range of dihedral angle is
:math:`(-\pi, \pi)`.
.. versionadded:: 0.8
.. versionchanged:: 0.9.0
Added optional box argument to account for periodic boundaries in
calculation
.. versionchanged:: 0.11.0
Renamed from calc_torsions to calc_dihedrals
.. versionchanged:: 0.13.0
Added *backend* keyword.
.. versionchanged:: 0.19.0
Internal dtype conversion of input coordinates to ``numpy.float32``.
Now also accepts single coordinates as input.
.. versionchanged:: 2.3.0
Can now accept an :class:`~MDAnalysis.core.groups.AtomGroup` as an
argument in any position and checks inputs using type hinting.
"""
numatom = coords1.shape[0]
dihedrals = _check_result_array(result, (numatom,))
if backend == "distopia":
# distopia requires that all the input arrays are the same type,
# while MDAnalysis allows for mixed types, this should be changed
# pre 3.0.0 release see issue #3707
dihedrals = dihedrals.astype(np.float32)
box = np.asarray(box).astype(np.float32) if box is not None else None
if numatom > 0:
if box is not None:
boxtype, box = check_box(box)
if boxtype == "ortho":
_run(
"calc_dihedral_ortho",
args=(coords1, coords2, coords3, coords4, box, dihedrals),
backend=backend,
)
else:
_run(
"calc_dihedral_triclinic",
args=(coords1, coords2, coords3, coords4, box, dihedrals),
backend=backend,
)
else:
_run(
"calc_dihedral",
args=(coords1, coords2, coords3, coords4, dihedrals),
backend=backend,
)
if backend == "distopia":
# mda expects the result to be in float64, so we need to convert it back
# to float64, change for 3.0, see #3707
dihedrals = dihedrals.astype(np.float64)
if result is not None:
result[:] = dihedrals
return dihedrals
[docs]
@check_coords("coords", allow_atomgroup=True)
def apply_PBC(
coords: Union[npt.NDArray, "AtomGroup"],
box: Optional[npt.NDArray] = None,
backend: str = "serial",
) -> npt.NDArray:
"""Moves coordinates into the primary unit cell.
Parameters
----------
coords : numpy.ndarray or :class:`~MDAnalysis.core.groups.AtomGroup`
Coordinate array of shape ``(3,)`` or ``(n, 3)`` (dtype is arbitrary,
will be converted to ``numpy.float32`` internally). Also accepts an
:class:`~MDAnalysis.core.groups.AtomGroup`.
box : numpy.ndarray
The unitcell dimensions of the system, which can be orthogonal or
triclinic and must be provided in the same format as returned by
:attr:`MDAnalysis.coordinates.timestep.Timestep.dimensions`:
``[lx, ly, lz, alpha, beta, gamma]``.
backend : {'serial', 'OpenMP'}, optional
Keyword selecting the type of acceleration.
Returns
-------
newcoords : numpy.ndarray (``dtype=numpy.float32``, ``shape=coords.shape``)
Array containing coordinates that all lie within the primary unit cell
as defined by `box`.
.. versionadded:: 0.8
.. versionchanged:: 0.13.0
Added *backend* keyword.
.. versionchanged:: 0.19.0
Internal dtype conversion of input coordinates to ``numpy.float32``.
Now also accepts (and, likewise, returns) single coordinates.
.. versionchanged:: 2.3.0
Can now accept an :class:`~MDAnalysis.core.groups.AtomGroup` as an
argument in any position and checks inputs using type hinting.
"""
# coords is an array, the check_coords decorator made sure of that.
# Mypy, however, is not aware of that so we have to tell it explicitly.
coords_array: npt.NDArray = coords # type: ignore
if len(coords_array) == 0:
return coords_array
boxtype, box = check_box(box)
if boxtype == "ortho":
_run("ortho_pbc", args=(coords_array, box), backend=backend)
else:
_run("triclinic_pbc", args=(coords_array, box), backend=backend)
return coords_array
[docs]
@check_coords("vectors", enforce_copy=False, enforce_dtype=False)
def minimize_vectors(vectors: npt.NDArray, box: npt.NDArray) -> npt.NDArray:
"""Apply minimum image convention to an array of vectors
This function is required for calculating the correct vectors between two
points. A naive approach of ``ag1.positions - ag2.positions`` will not
provide the minimum vectors between particles, even if all particles are
within the primary unit cell (box).
Parameters
----------
vectors : numpy.ndarray
Vector array of shape ``(n, 3)``, either float32 or float64. These
represent many vectors (such as between two particles).
box : numpy.ndarray
The unitcell dimensions of the system, which can be orthogonal or
triclinic and must be provided in the same format as returned by
:attr:`MDAnalysis.coordinates.timestep.Timestep.dimensions`:
``[lx, ly, lz, alpha, beta, gamma]``.
Returns
-------
minimized_vectors : numpy.ndarray
Same shape and dtype as input. The vectors from the input, but
minimized according to the size of the box.
.. versionadded:: 2.1.0
"""
boxtype, box = check_box(box)
output = np.empty_like(vectors)
# use box which is same precision as input vectors
box = box.astype(vectors.dtype)
if boxtype == "ortho":
_minimize_vectors_ortho(vectors, box, output)
else:
_minimize_vectors_triclinic(vectors, box.ravel(), output)
return output