def main():
modelfile = sys.argv[1]
paramfile = sys.argv[2]
m = Model(modelfile)
m.generate_neighbors(3.45)
cutoff = {}
cutoff[(40,40)] = 3.6
cutoff[(13,29)] = 3.6
cutoff[(29,13)] = 3.6
cutoff[(40,13)] = 3.6
cutoff[(13,40)] = 3.6
cutoff[(29,40)] = 3.6
cutoff[(40,29)] = 3.6
cutoff[(13,13)] = 3.6
cutoff[(29,29)] = 3.6
cutoff[(41,41)] = 3.7
cutoff[(28,28)] = 3.7
cutoff[(41,28)] = 3.7
cutoff[(28,41)] = 3.7
cutoff[(46,46)] = 3.45
cutoff[(14,14)] = 3.45
cutoff[(46,14)] = 3.45
cutoff[(14,46)] = 3.45
m.generate_neighbors(cutoff)
voronoi_3d(m,cutoff)
vp_dict = load_param_file(paramfile)
set_atom_vp_types(m,vp_dict)
#vor_stats(m) # Prints what you probably want
#index_stats(m)
count = 0
for atom in m.atoms:
#print(atom.vp.index[:4])
if(atom.vp.index[:4] == (0,1,10,2)):
atoms = [a for a in atom.neighs]+[atom]
for atom in atoms[1:]:
#if( abs(atom.coord[0]-atoms[0].coord[0]) > 10 ):
fix_atom(m, atoms[0], atom)
vp = Model('0,1,10,2 vp',100,100,100,atoms)
recenter_model(vp)
vp.write('vp_data/vp{0}.xyz'.format(count))
convert(vp,'polyhedron','vp_data/vp{0}.txt'.format(count))
count += 1
def normalize_bond_distances(m):
""" Rescales a cluster so that the average bond length is 1.0 """
center = find_center_atom(m)
for atom in m.atoms:
atom.coord = (atom.coord[0]-center.coord[0], atom.coord[1]-center.coord[1], atom.coord[2]-center.coord[2])
avg = 0.
for atom in m.atoms:
if atom.id != center.id:
avg += m.dist(center, atom)
avg /= (m.natoms-1)
for atom in m.atoms:
if atom.id != center.id:
atom.coord = (atom.coord[0]/avg, atom.coord[1]/avg, atom.coord[2]/avg)
recenter_model(m)
return avg
def fix_cluster_pbcs(m):
# First recenter to first octant
recenter_model(m)
meanx, meany, meanz = m.lx/4.0, m.ly/4.0, m.lz/4.0
for atom in m.atoms[1:]:
atom.coord = (atom.coord[0]+meanx-m.atoms[0].coord[0], atom.coord[1]+meany-m.atoms[0].coord[1], atom.coord[2]+meanz-m.atoms[0].coord[2])
m.atoms[0].coord = (m.atoms[0].coord[0]+meanx-m.atoms[0].coord[0], m.atoms[0].coord[1]+meany-m.atoms[0].coord[1], m.atoms[0].coord[2]+meanz-m.atoms[0].coord[2])
# See if we need to fix
fix = False
for atom in m.atoms[1:]:
if round(m.dist(m.atoms[0], atom)) != round(dist(m.atoms[0], atom)):
fix = True
break
else:
recenter_model(m)
return m
# If so, fix
for atom in m.atoms:
new = []
if round(m.dist(m.atoms[0], atom)) != round(dist(m.atoms[0], atom)):
for c in atom.coord:
if c < 0:
new.append(c+m.lx)
elif c > m.lx:
new.append(c-m.lx)
else:
new.append(c)
atom.coord = copy.copy(new)
recenter_model(m)
return m
