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# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# 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
#
import pytest
import numpy as np
from numpy.testing import assert_equal
from MDAnalysis.lib.pkdtree import PeriodicKDTree
from MDAnalysis.lib.distances import transform_StoR
# fractional coordinates for data points
f_dataset = np.array(
[
[0.2, 0.2, 0.2], # center of the box
[0.5, 0.5, 0.5],
[0.11, 0.11, 0.11],
[1.1, -1.1, 1.1], # wrapped to [1, 9, 1]
[2.1, 2.1, 0.3], # wrapped to [1, 1, 3]
],
dtype=np.float32,
)
@pytest.mark.parametrize(
"b, cut, result",
(
(
None,
1.0,
"Donot provide cutoff distance" " for non PBC aware calculations",
),
(
[10, 10, 10, 90, 90, 90],
None,
"Provide a cutoff distance with" " tree.set_coords(...)",
),
),
)
def test_setcoords(b, cut, result):
coords = np.array([[1, 1, 1], [2, 2, 2]], dtype=np.float32)
if b is not None:
b = np.array(b, dtype=np.float32)
tree = PeriodicKDTree(box=b)
print(b, tree.box, cut, result)
with pytest.raises(RuntimeError, match=result):
tree.set_coords(coords, cutoff=cut)
def test_searchfail():
coords = np.array([[1, 1, 1], [2, 2, 2]], dtype=np.float32)
b = np.array([10, 10, 10, 90, 90, 90], dtype=np.float32)
cutoff = 1.0
search_radius = 2.0
query = np.array([1, 1, 1], dtype=np.float32)
tree = PeriodicKDTree(box=b)
tree.set_coords(coords, cutoff=cutoff)
match = "Set cutoff greater or equal to the radius."
with pytest.raises(RuntimeError, match=match):
tree.search(query, search_radius)
@pytest.mark.parametrize(
"b, q, result",
(
([10, 10, 10, 90, 90, 90], [0.5, -0.1, 1.1], []),
([10, 10, 10, 90, 90, 90], [2.1, -3.1, 0.1], [2, 3, 4]),
([10, 10, 10, 45, 60, 90], [2.1, -3.1, 0.1], [2, 3]),
),
)
def test_search(b, q, result):
b = np.array(b, dtype=np.float32)
q = transform_StoR(np.array(q, dtype=np.float32), b)
cutoff = 3.0
coords = transform_StoR(f_dataset, b)
tree = PeriodicKDTree(box=b)
tree.set_coords(coords, cutoff=cutoff)
indices = tree.search(q, cutoff)
assert_equal(indices, result)
def test_nopbc():
cutoff = 0.3
q = np.array([0.2, 0.3, 0.1])
coords = f_dataset.copy()
tree = PeriodicKDTree(box=None)
tree.set_coords(coords)
indices = tree.search(q, cutoff)
assert_equal(indices, [0, 2])
@pytest.mark.parametrize(
"b, radius, result",
(
([10, 10, 10, 90, 90, 90], 2.0, [[0, 2], [0, 4], [2, 4]]),
([10, 10, 10, 45, 60, 90], 2.0, [[0, 4], [2, 4]]),
(
[10, 10, 10, 45, 60, 90],
4.5,
"Set cutoff greater or equal to the radius.",
),
([10, 10, 10, 45, 60, 90], 0.1, []),
),
)
def test_searchpairs(b, radius, result):
b = np.array(b, dtype=np.float32)
cutoff = 2.0
coords = transform_StoR(f_dataset, b)
tree = PeriodicKDTree(box=b)
tree.set_coords(coords, cutoff=cutoff)
if cutoff < radius:
with pytest.raises(RuntimeError, match=result):
indices = tree.search_pairs(radius)
else:
indices = tree.search_pairs(radius)
assert_equal(len(indices), len(result))
@pytest.mark.parametrize("radius, result", ((0.1, []), (0.3, [[0, 2]])))
def test_ckd_searchpairs_nopbc(radius, result):
coords = f_dataset.copy()
tree = PeriodicKDTree()
tree.set_coords(coords)
indices = tree.search_pairs(radius)
assert_equal(indices, result)
# fmt: off
@pytest.mark.parametrize('b, q, result', (
([10, 10, 10, 90, 90, 90], [0.5, -0.1, 1.1], []),
([10, 10, 10, 90, 90, 90], [2.1, -3.1, 0.1], [[0, 2],
[0, 3],
[0, 4]]),
([10, 10, 10, 90, 90, 90], [[2.1, -3.1, 0.1],
[0.5, 0.5, 0.5]], [[0, 2],
[0, 3],
[0, 4],
[1, 1]]),
([10, 10, 10, 45, 60, 90], [2.1, -3.1, 0.1], [[0, 2],
[0, 3]])
))
# fmt: on
def test_searchtree(b, q, result):
b = np.array(b, dtype=np.float32)
cutoff = 3.0
coords = transform_StoR(f_dataset, b)
q = transform_StoR(np.array(q, dtype=np.float32), b)
tree = PeriodicKDTree(box=b)
tree.set_coords(coords, cutoff=cutoff)
pairs = tree.search_tree(q, cutoff)
assert_equal(pairs, result)
|
