def apply(self, compound, orientation='', compound_port=''):
"""Arrange copies of a Compound as specified by the Pattern.
Parameters
----------
compound
orientation
Returns
-------
"""
compounds = list()
if self.orientations.get(orientation):
for port in self.orientations[orientation]:
new_compound = clone(compound)
new_port = new_compound.labels[compound_port]
(new_compound, new_port['up'], port['up'])
compounds.append(new_compound)
else:
for point in self.points:
new_compound = clone(compound)
translate(new_compound, point)
compounds.append(new_compound)
return compounds
def apply(self, compound, orientation='', compound_port=''):
"""Arrange copies of a Compound as specified by the Pattern.
Parameters
----------
compound
orientation
Returns
-------
"""
compounds = list()
if self.orientations.get(orientation):
for port in self.orientations[orientation]:
new_compound = clone(compound)
new_port = new_compound.labels[compound_port]
equivalence_transform(new_compound, new_port['up'], port['up'])
compounds.append(new_compound)
else:
for point in self.points:
new_compound = clone(compound)
translate(new_compound, point)
compounds.append(new_compound)
return compounds
def __init__(self, tile, n_tiles, name=None):
super(TiledCompound, self).__init__()
n_tiles = np.asarray(n_tiles)
if not np.all(n_tiles > 0):
raise ValueError('Number of tiles must be positive.')
# Check that the tile is periodic in the requested dimensions.
if np.any(np.logical_and(n_tiles != 1, tile.periodicity == 0)):
raise ValueError('Tile not periodic in at least one of the '
'specified dimensions.')
if name is None:
name = tile.name + '-'.join(str(d) for d in n_tiles)
self.name = name
self.periodicity = np.array(tile.periodicity * n_tiles)
if all(n_tiles == 1):
self._add_tile(tile, [(0, 0, 0)])
self._hoist_ports(tile)
return # Don't waste time copying and checking bonds.
# For every tile, assign temporary ID's to particles which are internal
# to that tile. E.g., when replicating a tile with 1800 particles, every
# tile will contain particles with ID's from 0-1799. These ID's are used
# below to fix bonds crossing periodic boundary conditions where a new
# tile has been placed.
for idx, particle in enumerate(tile.particles(include_ports=True)):
particle.index = idx
# Replicate and place periodic tiles.
# -----------------------------------
for ijk in it.product(range(n_tiles[0]),
range(n_tiles[1]),
range(n_tiles[2])):
new_tile = clone(tile)
translate(new_tile, np.array(ijk * tile.periodicity))
self._add_tile(new_tile, ijk)
self._hoist_ports(new_tile)
# Fix bonds across periodic boundaries.
# -------------------------------------
# Cutoff for long bonds is half the shortest periodic distance.
bond_dist_thres = min(tile.periodicity[tile.periodicity > 0]) / 2
# Bonds that were periodic in the original tile.
indices_of_periodic_bonds = set()
for particle1, particle2 in tile.bonds():
if np.linalg.norm(particle1.pos - particle2.pos) > bond_dist_thres:
indices_of_periodic_bonds.add((particle1.index,
particle2.index))
# Build a periodic kdtree of all particle positions.
self.particle_kdtree = PeriodicCKDTree(data=self.xyz, bounds=self.periodicity)
all_particles = np.asarray(list(self.particles(include_ports=False)))
# Store bonds to remove/add since we'll be iterating over all bonds.
bonds_to_remove = set()
bonds_to_add = set()
for particle1, particle2 in self.bonds():
if (particle1.index, particle2.index) not in indices_of_periodic_bonds \
and (particle2.index, particle1.index) not in indices_of_periodic_bonds:
continue
if self.min_periodic_distance(particle1.pos, particle2.pos) > bond_dist_thres:
bonds_to_remove.add((particle1, particle2))
image2 = self._find_particle_image(particle1, particle2,
all_particles)
image1 = self._find_particle_image(particle2, particle1,
all_particles)
if (image2, particle1) not in bonds_to_add:
bonds_to_add.add((particle1, image2))
if (image1, particle2) not in bonds_to_add:
bonds_to_add.add((particle2, image1))
for bond in bonds_to_remove:
self.remove_bond(bond)
for bond in bonds_to_add:
self.add_bond(bond)
# Clean up temporary data.
for particle in self._particles(include_ports=True):
particle.index = None
del self.particle_kdtree
def _adjust_ports(self):
for orientation, ports in self.orientations.items():
for port, point in zip(ports, self.points):
translate(port, point)
def test_translate(self, methane):
methane_atoms = list(methane.particles())
translate(methane, -methane_atoms[0].pos)
assert (methane_atoms[0].pos == np.array([0, 0, 0])).all()
def _adjust_ports(self):
for orientation, ports in self.orientations.items():
for port, point in zip(ports, self.points):
translate(port, point)
def test_translate(self, methane):
methane_atoms = list(methane.particles())
translate(methane, -methane_atoms[0].pos)
assert (methane_atoms[0].pos == np.array([0, 0, 0])).all()
def __init__(self, tile, n_tiles, name=None):
super(TiledCompound, self).__init__()
n_tiles = np.asarray(n_tiles)
if not np.all(n_tiles > 0):
raise ValueError('Number of tiles must be positive.')
# Check that the tile is periodic in the requested dimensions.
if np.any(np.logical_and(n_tiles != 1, tile.periodicity == 0)):
raise ValueError('Tile not periodic in at least one of the '
'specified dimensions.')
if name is None:
name = tile.name + '-'.join(str(d) for d in n_tiles)
self.name = name
self.periodicity = np.array(tile.periodicity * n_tiles)
if all(n_tiles == 1):
self._add_tile(tile, [(0, 0, 0)])
self._hoist_ports(tile)
return # Don't waste time copying and checking bonds.
# For every tile, assign temporary ID's to particles which are internal
# to that tile. E.g., when replicating a tile with 1800 particles, every
# tile will contain particles with ID's from 0-1799. These ID's are used
# below to fix bonds crossing periodic boundary conditions where a new
# tile has been placed.
for idx, particle in enumerate(tile.particles(include_ports=True)):
particle.index = idx
# Replicate and place periodic tiles.
# -----------------------------------
for ijk in it.product(range(n_tiles[0]), range(n_tiles[1]),
range(n_tiles[2])):
new_tile = clone(tile)
translate(new_tile, np.array(ijk * tile.periodicity))
self._add_tile(new_tile, ijk)
self._hoist_ports(new_tile)
# Fix bonds across periodic boundaries.
# -------------------------------------
# Cutoff for long bonds is half the shortest periodic distance.
bond_dist_thres = min(tile.periodicity[tile.periodicity > 0]) / 2
# Bonds that were periodic in the original tile.
indices_of_periodic_bonds = set()
for particle1, particle2 in tile.bonds():
if np.linalg.norm(particle1.pos - particle2.pos) > bond_dist_thres:
indices_of_periodic_bonds.add(
(particle1.index, particle2.index))
# Build a periodic kdtree of all particle positions.
self.particle_kdtree = PeriodicCKDTree(data=self.xyz,
bounds=self.periodicity)
all_particles = np.asarray(list(self.particles(include_ports=False)))
# Store bonds to remove/add since we'll be iterating over all bonds.
bonds_to_remove = set()
bonds_to_add = set()
for particle1, particle2 in self.bonds():
if (particle1.index, particle2.index) not in indices_of_periodic_bonds \
and (particle2.index, particle1.index) not in indices_of_periodic_bonds:
continue
if self.min_periodic_distance(particle1.pos,
particle2.pos) > bond_dist_thres:
bonds_to_remove.add((particle1, particle2))
image2 = self._find_particle_image(particle1, particle2,
all_particles)
image1 = self._find_particle_image(particle2, particle1,
all_particles)
if (image2, particle1) not in bonds_to_add:
bonds_to_add.add((particle1, image2))
if (image1, particle2) not in bonds_to_add:
bonds_to_add.add((particle2, image1))
for bond in bonds_to_remove:
self.remove_bond(bond)
for bond in bonds_to_add:
self.add_bond(bond)
# Clean up temporary data.
for particle in self._particles(include_ports=True):
particle.index = None
del self.particle_kdtree
