Source code for

"""Module for creating TiledCompounds."""
__all__ = ["TiledCompound"]

import itertools as it

import numpy as np

from mbuild import Box, Compound, Port, clone
from mbuild.exceptions import MBuildError
from mbuild.periodic_kdtree import PeriodicCKDTree

[docs]class TiledCompound(Compound): """Replicates a Compound in any cartesian direction(s). Correctly updates connectivity while respecting periodic boundary conditions. Parameters ---------- tile : mb.Compound The Compound to be replicated. n_tiles : array-like, shape=(3,), dtype=int, optional, default=(1, 1, 1) Number of times to replicate tile in the x, y and z-directions. name : str, optional, Descriptive string for the compound. """ def __init__(self, tile, n_tiles, name=None): super(TiledCompound, self).__init__() n_tiles = np.asarray(n_tiles) periodicity = np.asarray(tile.periodicity) if not np.all(n_tiles > 0): raise ValueError("Number of tiles must be positive.") if is None: = tile.get_boundingbox() # Check that the tile is periodic in the requested dimensions. if not np.all(np.logical_or((n_tiles == 1), periodicity)): raise ValueError( "Tile not periodic in at least one of the specified dimensions." ) if name is None: name = + "-".join(str(d) for d in n_tiles) = name self.periodicity = tile.periodicity = Box( np.array( * 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(i) for i in n_tiles]): new_tile = clone(tile) new_tile.translate(np.multiply(ijk, np.asarray( 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. threshold_calc = [np.inf, np.inf, np.inf] for i, truthy in enumerate(tile.periodicity): if truthy: threshold_calc[i] =[i] else: continue dist_thresh = np.min(threshold_calc) / 2 # Create the bounds for the periodicKDtree, non-periodic dimensions are 0 bounds = [0, 0, 0] length_array = np.asarray( for i, dim in enumerate(bounds): if tile.periodicity[i]: bounds[i] =[i] else: continue # Bonds that were periodic in the original tile. periodic_bonds = set() for particle1, particle2 in tile.bonds(): if np.linalg.norm(particle1.pos - particle2.pos) > dist_thresh: periodic_bonds.add((particle1.index, particle2.index)) # Build a periodic kdtree of all particle positions. self.particle_kdtree = PeriodicCKDTree(, bounds=bounds) 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 periodic_bonds and ( particle2.index, particle1.index, ) not in periodic_bonds: continue dist = self.min_periodic_distance(particle1.pos, particle2.pos) if dist > dist_thresh: 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 _add_tile(self, new_tile, ijk): """Add a tile with a label indicating its tiling position.""" i, j, k = ijk tile_label = f"{}_{i}-{j}-{k}" self.add(new_tile, label=tile_label, inherit_periodicity=False) def _hoist_ports(self, new_tile): """Add labels for all the ports to the parent (TiledCompound).""" for port in new_tile.children: if isinstance(port, Port): self.add(port, containment=False) def _find_particle_image(self, query, match, all_particles): """Find particle with the same index as match in a neighboring tile.""" _, idxs = self.particle_kdtree.query(query.pos, k=10) neighbors = all_particles[idxs] for particle in neighbors: if particle.index == match.index: return particle raise MBuildError( "Unable to find matching particle image while stitching bonds." )