class Polycrystal(OrthoBox):
def __init__(self, boxsize, numcrystallites, crystallitenames,
crystallitecenters):
super().__init__(boxsize)
self.numcrystallites = numcrystallites
self.crystaltype = crystallitenames
self.crystallitecenters = crystallitecenters
self.crystallites = [Atoms() for n in range(numcrystallites)]
self.crystalliteids = [[i] for i in range(numcrystallites)]
def setgraintypes(self, typemap):
self.graintypes = typemap
def embedatoms(self, maskcrystal, grainid, keepatoms, compress=True):
crystal = maskcrystal.copy()
slicecrystal = crystal[keepatoms]
natoms = slicecrystal.get_global_number_of_atoms()
self.crystalliteids[grainid] = [grainid for i in range(natoms)]
self.crystallites[grainid] = slicecrystal
def compress(self):
polycrystalbox = self.sidelens + self.angles
self.polycrystal = Atoms(cell=polycrystalbox, pbc=True)
for i, c in enumerate(self.crystallites):
cids = self.crystalliteids[i]
c.set_tags(cids)
self.polycrystal += c
self.natoms = self.polycrystal.get_global_number_of_atoms()
chemsym = set(self.polycrystal.get_chemical_symbols())
self.chemmap = {c: i + 1 for i, c in enumerate(chemsym)}
self.nspecies = len(chemsym)
def pruneoverlap(self, criteria=0.5, verbose=False):
''' TODO: remove atoms overlapping assume PBC conditions'''
print(
"NOTICE: The pruning routine does not accoutn for stoichiometry restrictions."
)
cutoff = neighborlist.natural_cutoffs(self.polycrystal)
neighbors = neighborlist.NeighborList(cutoff,
self_interaction=False,
bothways=False)
neighbors.update(self.polycrystal)
isremoved = []
for a in self.polycrystal:
ineigh = neighbors.get_neighbors(a.index)
for j in ineigh[0]:
r = self.polycrystal.get_distance(a.index, j, mic=True)
if r < criteria and j not in isremoved:
isremoved.append(j)
if verbose:
print("Atom ID %i removed due to overlap!" % (j))
del self.polycrystal[isremoved]
self.natoms = self.polycrystal.get_global_number_of_atoms()
