def test_nsgrid_PBC_rect():
"""Check that nsgrid works with rect boxes and PBC"""
ref_id = 191
results = np.array(
[191, 192, 672, 682, 683, 684, 995, 996, 2060, 2808, 3300, 3791, 3792]
) - 1 # Atomid are from gmx select so there start from 1 and not 0. hence -1!
universe = mda.Universe(Martini_membrane_gro)
cutoff = 7
# FastNS is called differently to max coverage
searcher = nsgrid.FastNS(cutoff,
universe.atoms.positions,
box=universe.dimensions)
results_grid = searcher.search(
universe.atoms.positions[ref_id][None, :]).get_indices()[0]
results_grid2 = searcher.search(universe.atoms.positions).get_indices(
) # call without specifying any ids, should do NS for all beads
assert_equal(np.sort(results), np.sort(results_grid))
assert_equal(len(universe.atoms), len(results_grid2))
assert searcher.cutoff == 7
assert_equal(np.sort(results_grid), np.sort(results_grid2[ref_id]))
def run_grid_search(u, ref_id, cutoff=3):
coords = u.atoms.positions
searchcoords = u.atoms.positions[ref_id]
if searchcoords.shape == (3, ):
searchcoords = searchcoords[None, :]
# Run grid search
searcher = nsgrid.FastNS(cutoff, coords, box=u.dimensions)
return searcher.search(searchcoords)
def test_fastns_warning(universe):
"""
Tests for warning on the use of FastNS.
TODO: remove when nsgrid is fixed.
"""
wmsg = ("The current nsgrid code can return incorrect values and should "
"not be used for production work.")
with pytest.warns(UserWarning, match=wmsg):
searcher = nsgrid.FastNS(3, universe.atoms.positions,
universe.dimensions)
def test_nsgrid_selfsearch(box, result):
np.random.seed(90003)
points = (np.random.uniform(low=0, high=1.0,
size=(100, 3))*(10.)).astype(np.float32)
cutoff = 1.0
if box is None or np.allclose(box[:3], 0):
# 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 = points.max(axis=0)
lmin = points.min(axis=0)
pseudobox[:3] = 1.1*(lmax - lmin)
pseudobox[3:] = 90.
shiftref = points.copy()
shiftref -= lmin
searcher = nsgrid.FastNS(cutoff, shiftref, box=pseudobox, pbc=False)
searchresults = searcher.self_search()
else:
searcher = nsgrid.FastNS(cutoff, points, box=box)
searchresults = searcher.self_search()
pairs = searchresults.get_pairs()
assert_equal(len(pairs), result)
def test_nsgrid_search(box, results):
np.random.seed(90003)
points = (np.random.uniform(low=0, high=1.0,
size=(100, 3))*(10.)).astype(np.float32)
cutoff = 2.0
query = np.array([1., 1., 1.], dtype=np.float32).reshape((1, 3))
if box is None:
pseudobox = np.zeros(6, dtype=np.float32)
all_coords = np.concatenate([points, query])
lmax = all_coords.max(axis=0)
lmin = all_coords.min(axis=0)
pseudobox[:3] = 1.1*(lmax - lmin)
pseudobox[3:] = 90.
shiftpoints, shiftquery = points.copy(), query.copy()
shiftpoints -= lmin
shiftquery -= lmin
searcher = nsgrid.FastNS(cutoff, shiftpoints, box=pseudobox, pbc=False)
searchresults = searcher.search(shiftquery)
else:
searcher = nsgrid.FastNS(cutoff, points, box)
searchresults = searcher.search(query)
indices = searchresults.get_pairs()[:, 1]
assert_equal(np.sort(indices), results)
def test_nsgrid_probe_close_to_box_boundary():
# FastNS.search used to segfault with this box, cutoff and reference
# coordinate prior to PR #2136, so we ensure that this remains fixed.
# See Issue #2132 for further information.
ref = np.array([[55.783722, 44.190044, -54.16671]], dtype=np.float32)
box = np.array([53.785854, 43.951054, 57.17597, 90., 90., 90.], dtype=np.float32)
cutoff = 3.0
# search within a configuration where we know the expected outcome:
conf = np.ones((1, 3), dtype=np.float32)
searcher = nsgrid.FastNS(cutoff, conf, box)
results = searcher.search(ref)
# check if results are as expected:
expected_pairs = np.zeros((1, 2), dtype=np.int64)
expected_dists = np.array([2.3689647], dtype=np.float64)
assert_equal(results.get_pairs(), expected_pairs)
assert_allclose(results.get_pair_distances(), expected_dists, rtol=1.e-6)
def test_nsgrid_PBC_rect():
"""Check that nsgrid works with rect boxes and PBC"""
ref_id = 191
# Atomid are from gmx select so there start from 1 and not 0. hence -1!
results = np.array([191, 192, 672, 682, 683, 684, 995, 996, 2060, 2808, 3300, 3791,
3792]) - 1
universe = mda.Universe(Martini_membrane_gro)
cutoff = 7
# FastNS is called differently to max coverage
searcher = nsgrid.FastNS(cutoff, universe.atoms.positions, box=universe.dimensions)
results_grid = searcher.search(universe.atoms.positions[ref_id][None, :]).get_pairs()
other_ix = sorted(i for (_, i) in results_grid)
assert len(results) == len(results_grid)
assert other_ix == sorted(results)
def test_pbc_box(box):
"""Check that PBC box accepts only well-formated boxes"""
coords = np.array([[1.0, 1.0, 1.0]], dtype=np.float32)
with pytest.raises(ValueError):
nsgrid.FastNS(4.0, coords, box=box)
