Source code for

"""mBuild monolayer recipe."""

from copy import deepcopy
from warnings import warn

import numpy as np

import mbuild as mb

__all__ = ["Monolayer"]

[docs] class Monolayer(mb.Compound): """A general monolayer recipe. Parameters ---------- surface : mb.Compound Surface on which the monolayer will be built. chains : list of mb.Compounds The chains to be replicated and attached to the surface. fractions : list of floats The fractions of the pattern to be allocated to each chain. backfill : list of mb.Compound, optional, default=None If there are fewer chains than there are ports on the surface, copies of `backfill` will be used to fill the remaining ports. pattern : mb.Pattern, optional, default=mb.Random2DPattern An array of planar binding locations. If not provided, the entire surface will be filled with `chain`. tile_x : int, optional, default=1 Number of times to replicate substrate in x-direction. tile_y : int, optional, default=1 Number of times to replicate substrate in y-direction. """ def __init__( self, surface, chains, fractions=None, backfill=None, pattern=None, tile_x=1, tile_y=1, **kwargs ): from import TiledCompound super(Monolayer, self).__init__() # Replicate the surface. tiled_compound = TiledCompound(surface, n_tiles=(tile_x, tile_y, 1)) self.add(tiled_compound, label="tiled_surface") if pattern is None: # Fill the surface. pattern = mb.Random2DPattern(len(tiled_compound.referenced_ports())) if isinstance(chains, mb.Compound): chains = [chains] if fractions: fractions = list(fractions) if len(chains) != len(fractions): raise ValueError( "Number of fractions does not match the number" " of chain types provided" ) n_chains = len(pattern.points) # Attach chains of each type to binding sites based on # respective fractions. for chain, fraction in zip(chains[:-1], fractions[:-1]): # Create sub-pattern for this chain type subpattern = deepcopy(pattern) n_points = int(round(fraction * n_chains)) warn("\n Adding {} of chain {}".format(n_points, chain)) pick = np.random.choice( subpattern.points.shape[0], n_points, replace=False ) points = subpattern.points[pick] subpattern.points = points # Remove now-occupied points from overall pattern pattern.points = np.array( [ point for point in pattern.points.tolist() if point not in subpattern.points.tolist() ] ) # Attach chains to the surface attached_chains, _ = subpattern.apply_to_compound( guest=chain, host=self["tiled_surface"], backfill=None, **kwargs ) self.add(attached_chains) else: warn("\n No fractions provided. Assuming a single chain type.") # Attach final chain type. Remaining sites get a backfill. warn("\n Adding {} of chain {}".format(len(pattern), chains[-1])) attached_chains, backfills = pattern.apply_to_compound( guest=chains[-1], host=self["tiled_surface"], backfill=backfill, **kwargs ) self.add(attached_chains) self.add(backfills)