def free_end_dist(mols, shs):
filler, filler_cm = {}, []
matrix = {}
shell, rdf = [0] * shs, [0] * shs
box, isomer_hash, mol_list = mols.box, mols.isomer_hash, mols.molecular_list
molecular_bodies_list = mols.molecular_bodies_list
mol_type_list = mols.molecular_types_list
pos = mols.nodes['position']
masses = mols.masses
boxmin = min(box.x, box.y, box.z)
check = boxmin/ 2 / shs
for key in isomer_hash.keys():
if MoleCules.is_filler_p(molecular_bodies_list, key) == 1:
filler[key] = isomer_hash[key]
continue
matrix[key] = isomer_hash[key]
fillerlen = 0
for molecules in filler.values():
for molecule in molecules:
#print(molecule)
#print(mol_list[molecule])
fillerlen += len(mol_list[molecule])
filler_cm.append(cm_no_image(mol_list[molecule], mol_type_list[molecule], pos, masses, box))
rhom = (mols.natoms - fillerlen) / box.x / box.y / box.z
m = 0
for cm in filler_cm:
for molecules in matrix.values():
for molecule in iter(molecules):
m += 2
mol = mol_list[molecule]
ends = mol[0]
ende = mol[-1]
poss = pos[ends]
pose = pos[ende]
diste = pbc_pos(pose - cm, box).mod
dists = pbc_pos(poss - cm, box).mod
if diste < boxmin / 2:
shell[int(diste/check)] += 1
if dists < boxmin / 2:
shell[int(dists/check)] += 1
for mdx in mol_list[molecule]:
p = pos[mdx]
dist = pbc_pos(p - cm, box).mod
if dist < boxmin / 2:
rdf[int(dist/check)]+=1
rho = m / box.x / box.y / box.z
for i in range(shs):
dv = 4/3 * math.pi * (((i+1)*check)**3 - (i*check)**3)
shell[i] /= dv * len(filler_cm) * rho
rdf[i] /= dv * len(filler_cm) * rhom
return shell, rdf, check
def chaindist(ranges, shs):
from sys import argv
analyzed = 0
for filename in argv[1:]:
res = {}
rhodict = {}
matrix = {}
filler = {}
filler_cm = []
mols = MoleCules(filename, no_graph_tool, analyzed=analyzed)
if analyzed == 0:
masses = mols.masses
mol_list = mols.molecular_list
mol_type_list = mols.molecular_types_list
isomer_hash = mols.isomer_hash
molecular_bodies_list = mols.molecular_bodies_list
analyzed += 1
for ran in ranges:
res["%s" % (ran,)] = [0] * shs
rhodict["%s" % (ran,)] = 0
box = mols.box
boxmin = min(box.x, box.y, box.z)
check = boxmin / 2 / shs
pos = mols.nodes['position']
moldict = {}
for key in isomer_hash.keys():
if MoleCules.is_filler_p(molecular_bodies_list, key) == 1:
filler[key] = isomer_hash[key]
continue
matrix[key] = isomer_hash[key]
moldict[len(mol_list[key])] = [0] * shs
for molecules in filler.values():
for molecule in molecules:
# print(molecule)
# print(mol_list[molecule])
filler_cm.append(cm_no_image(mol_list[molecule], mol_type_list[molecule], pos, masses, box))
for cm in filler_cm:
for molecules in matrix.values():
for molecule in iter(molecules):
mollen = len(mol_list[molecule])
# cmmol = cm_no_image(mol_list[molecule], mol_type_list[molecule], pos, masses, box)
for ran in ranges:
s = ran[0]
e = ran[1]
if s <= mollen < e:
rhodict["%s" % (ran,)] += mollen
for mdx in iter(mol_list[molecule]):
dist = pbc_pos(pos[mdx] - cm, box).mod
if dist < boxmin / 2:
# moldict[mollen][int(dist/check)] += 1
idx = int(dist/check)
for ran in ranges:
s = ran[0]
e = ran[1]
if s <= mollen < e:
res["%s" % (ran,)][idx] += 1
for k in rhodict:
rhodict[k]/=box.x * box.y * box.z
for i in range(shs):
dv = 4 / 3 * math.pi * (((i + 1) * check) ** 3 - (i * check) ** 3)
for k in res:
res[k][i] /= dv # * rhodict[k]
# for key in moldict.keys():
# moldict[key][i] /= dv * rhodict[key]
o = open(filename + '.chd', 'w')
p = open(filename + '.rho', 'w')
# o.write("#r %s\n" % ' '.join([str(key) for key in moldict.keys()]))
kl = [ str(x) for x in ranges ]
o.write("#r %s\n" % (' '.join(kl)))
p.write("#r %s\n" % (' '.join(kl)))
s = ''
for k in kl:
s += ' '+ str(rhodict[k])
p.write(s+'\n')
p.close()
for i in range(shs):
s = ''
for k in kl:
# o.write("%s %s\n" % ((i+0.5)*check, ' '.join([str(moldict[key][i]) for key in moldict.keys()])))
s += ' '+ str(res[k][i])
o.write("%s %s\n" % ((i + 0.5) * check, s))
o.close()