def main():
# sys.argv[1] should be the modelfile in the xyz format
# sys.argv[2] should be the cutoff desired
modelfile = sys.argv[1]
cutoff = float(sys.argv[2])
ag = AtomGraph(modelfile, cutoff)
clusters = ag.get_clusters("Icosahedra-like", "Mixed")
## Let's just get the biggest one for now.
## Comment this section to get them all.
# l = 0
# for cluster in clusters:
# if(len(cluster) > l):
# l = len(cluster)
# i = clusters.index(cluster)
# clusters = [clusters[i]]
orig_clusters = clusters[:]
# Print orig clusters
j = 0
for i, cluster in enumerate(clusters):
print("Orig cluster {0} contains {1} atoms.".format(i, len(cluster)))
# for atom in cluster:
# if atom not in orig_clusters[i]:
# #print("{0} {1}".format(atom.vesta(),atom.vp))
# print(atom.vesta())
# j += 1
# else:
# print(atom.vesta())
# Save cluster files
cluster_model = Model(
"Orig cluster {0} contains {1} atoms.".format(i, len(cluster)),
ag.model.lx,
ag.model.ly,
ag.model.lz,
cluster,
)
cluster_model.write_cif("cluster{0}.cif".format(i))
# Expand the clusters
for i, cluster in enumerate(clusters):
new_clust = [
atom for atom in ag.model.atoms if atom in clusters[i] or (nnnic(atom, ag.model, clusters[i]) >= 4)
]
new_clust = list(set(new_clust))
clusters[i] = new_clust[:]
j = 0
for i, cluster in enumerate(clusters):
print("New, bigger cluster {0} contains {1} atoms.".format(i, len(cluster)))
# for atom in cluster:
# if atom not in orig_clusters[i]:
# #print("{0} {1}".format(atom.vesta(),atom.vp))
# print(atom.vesta())
# j += 1
# else:
# print(atom.vesta())
# Save cluster files
cluster_model = Model(
"New, bigger cluster {0} contains {1} atoms.".format(i, len(cluster)),
ag.model.lx,
ag.model.ly,
ag.model.lz,
cluster,
)
cluster_model.write_cif("cluster{0}.big.cif".format(i))
