def capped_distance_array(a, b, cellsize, box=None):
"""Calculate all pairwise distances between *a* and *b* up to *max_dist*
If given, *box* defines the unit cell size for periodic boundaries
"""
cga = CellGrid(box, cellsize, a)
cgb = CellGrid(box, cellsize, b)
return cellgrid_distance_array(cga, cgb)
def test_placement(self):
points = np.array([[0.1, 0.1, 0.1], [0.9, 0.9, 0.9]])
cg = CellGrid(box=np.ones(3), cellsize=0.25)
cg.coordinates = points
assert all(cg._cell_addresses[0] == np.array([0, 0, 0]))
assert all(cg._cell_addresses[1] == np.array([3, 3, 3]))
assert cg._cell_indices[0] == 0
assert cg._cell_indices[1] == 63
def test_placement(self):
points = np.array([[0.1, 0.1, 0.1],
[0.9, 0.9, 0.9]])
cg = CellGrid(box=np.ones(3), max_dist=0.25)
cg.coordinates = points
assert all(cg._cell_addresses[0] == np.array([0, 0, 0]))
assert all(cg._cell_addresses[1] == np.array([3, 3, 3]))
assert cg._cell_indices[0] == 0
assert cg._cell_indices[1] == 63
def test_change_max_dist(self):
"""Redefine max dist"""
cg = CellGrid(box=np.ones(3), cellsize=0.25)
assert all(cg._cell_size == np.array([0.25, 0.25, 0.25]))
assert all(cg._ncells == np.array([4, 4, 4]))
assert cg._total_cells == 64
assert len(cg) == 64
cg.cellsize = 0.50
assert all(cg._cell_size == np.array([0.50, 0.50, 0.50]))
assert all(cg._ncells == np.array([2, 2, 2]))
assert cg._total_cells == 8
assert len(cg) == 8
def test_change_box(self):
"""Redefine box"""
cg = CellGrid(box=np.ones(3), cellsize=0.25)
assert all(cg._cell_size == np.array([0.25, 0.25, 0.25]))
assert all(cg._ncells == np.array([4, 4, 4]))
assert cg._total_cells == 64
assert len(cg) == 64
cg.box = np.ones(3) * 2
assert all(cg._cell_size == np.array([0.25, 0.25, 0.25]))
assert all(cg._ncells == np.array([8, 8, 8]))
assert cg._total_cells == 512
assert len(cg) == 512
def test_change_max_dist(self):
"""Redefine max dist"""
cg = CellGrid(box=np.ones(3), max_dist=0.25)
assert all(cg._cell_size == np.array([0.25, 0.25, 0.25]))
assert all(cg._ncells == np.array([4, 4, 4]))
assert cg._total_cells == 64
assert len(cg) == 64
cg.max_dist = 0.50
assert all(cg._cell_size == np.array([0.50, 0.50, 0.50]))
assert all(cg._ncells == np.array([2, 2, 2]))
assert cg._total_cells == 8
assert len(cg) == 8
def test_change_box(self):
"""Redefine box"""
cg = CellGrid(box=np.ones(3), max_dist=0.25)
assert all(cg._cell_size == np.array([0.25, 0.25, 0.25]))
assert all(cg._ncells == np.array([4, 4, 4]))
assert cg._total_cells == 64
assert len(cg) == 64
cg.box = np.ones(3) * 2
assert all(cg._cell_size == np.array([0.25, 0.25, 0.25]))
assert all(cg._ncells == np.array([8, 8, 8]))
assert cg._total_cells == 512
assert len(cg) == 512
def test_creation_2(self):
"""Box split into 4, 0.22 needs to round up to 0.25"""
cg = CellGrid(box=np.ones(3), cellsize=0.22)
assert all(cg._cell_size == np.array([0.25, 0.25, 0.25]))
assert all(cg._ncells == np.array([4, 4, 4]))
assert cg._total_cells == 64
def test_creation(self):
"""Box split directly into 4 cells"""
cg = CellGrid(box=np.ones(3), cellsize=0.25)
assert all(cg._cell_size == np.array([0.25, 0.25, 0.25]))
assert all(cg._ncells == np.array([4, 4, 4]))
assert cg._total_cells == 64
assert len(cg) == 64
def test_create_cg_views(self):
for prec in self.precs:
points = np.array(
[[0.8, 0.8, 0.8], [0.1, 0.1, 0.1], [0.9, 0.9, 0.9]],
dtype=prec)
cg = CellGrid(box=np.ones(3), cellsize=0.25, coordinates=points)
views = cg._views
assert len(views) == cg._total_cells
assert all(views[0][0][0] == points[1])
assert all(views[26][0] == points[0, 2])
def test_create_cg_views_2(self):
# 8 cells
# 1 coordinate in cell 0 (first)
# 2 coordinates in cell 7 (last)
for prec in self.precs:
points = np.array(
[[0.8, 0.8, 0.8], [0.1, 0.1, 0.1], [0.9, 0.9, 0.9]],
dtype=prec)
cg = CellGrid(box=np.ones(3), cellsize=0.50, coordinates=points)
for cell, exp in zip(cg, [1, 0, 0, 0, 0, 0, 0, 2]):
assert len(cell) == exp
def capped_self_distance_array(a, cellsize, box, particles_per_cell=30):
"""
Optimized to identify pair contacts within a distance
Cellsize is changed based on the maximum of number of
particles per cell and provided cellsize
"""
if particles_per_cell is not None:
cellsize = min(
max(cellsize, _per_cell(a.shape[0], box, particles_per_cell)),
0.33 * min(box))
cga = CellGrid(box, cellsize, a)
return cellgrid_self_distance_array(cga)
def test_sorting(self):
points = np.array([[0.8, 0.8, 0.8], [0.1, 0.1, 0.1], [0.9, 0.9, 0.9]])
cg = CellGrid(box=np.ones(3), cellsize=0.25, coordinates=points)
assert all(cg._original_indices == np.array([1, 0, 2]))
assert all(cg._order == np.array([1, 0, 2]))
for val, ref in zip(
cg._sorted_coords,
np.array([[0.1, 0.1, 0.1], [0.8, 0.8, 0.8], [0.9, 0.9, 0.9]])):
assert all(val == ref)
# Check that sorted coordinates are continuous C
# important for later work
assert cg._sorted_coords.flags['C'] == True
def test_creation_3(self):
cg = CellGrid(box=np.array([1.0, 1.0, 2.0]), cellsize=0.25)
assert all(cg._cell_size == np.array([0.25, 0.25, 0.25]))
assert all(cg._ncells == np.array([4, 4, 8]))
assert cg._total_cells == 128
def test_nocoords(self):
cg = CellGrid(box=np.ones(3), cellsize=0.25)
cg.coordinates = None
assert cg.coordinates is None
def test_nocoords(self):
cg = CellGrid(box=np.ones(3), max_dist=0.25)
cg.coordinates = None
assert cg.coordinates is None
