def get_tsites(code):
from zse.collections import get_tsites
z = framework(code)
tsites, tmult = get_tsites(code)
tinds = [atom.index for atom in z if atom.symbol != 'O']
index = 0
first_ts = []
for i, m in enumerate(tmult):
first_ts.append(tinds[index])
index += m
return tsites, tmult, first_ts
def get_unique_trings(code, ring_size):
z = framework(code)
pr = get_fwrings(code)
tsites, tmult = get_tsites(code)
tinds = [atom.index for atom in z if atom.symbol != 'O']
index = 0
firstts = []
for i, m in enumerate(tmult):
firstts.append(tinds[index])
index += m
allrings = []
for f in firstts:
c, r, ringatoms, repeat = tring_driver(z, f, pr, delete=False)
for ring in r:
allrings.append(ring)
tinds = [atom.index for atom in ringatoms if atom.symbol != 'O']
rp = np.prod(repeat)
Dict = {}
j = 0
for i in range(rp):
for s, t in enumerate(tsites):
for q in range(tmult[s]):
Dict[tinds[j]] = t
j += 1
ring_tsites = []
for ring in allrings:
tmp = []
for i in ring:
if ringatoms[i].symbol != 'O':
tmp.append(Dict[i])
ring_tsites.append(tmp)
desired_rings_tsites = []
desired_rings_full = []
for i, r in enumerate(ring_tsites):
if len(r) == ring_size:
desired_rings_tsites.append(r)
desired_rings_full.append(allrings[i])
unique_tsites = []
unique_full = []
d = []
for i in range(len(desired_rings_tsites)):
for j in range((i + 1), len(desired_rings_tsites)):
if i != j:
st1 = ' '.join(map(str, desired_rings_tsites[i]))
st2 = ' '.join(map(str, desired_rings_tsites[j]))
st2_2 = ' '.join(map(str, reversed(desired_rings_tsites[j])))
# st1 = set(desired_rings_tsites[i])
# st2 = set(desired_rings_tsites[j])
# if st1 == st2:
if st2 in st1 + ' ' + st1 or st2_2 in st1 + ' ' + st1:
d.append(int(j))
for i in range(len(desired_rings_tsites)):
if i not in d:
unique_tsites.append(desired_rings_tsites[i])
unique_full.append(desired_rings_full[i])
traj = []
com = ringatoms.get_center_of_mass()
for ring in unique_full:
keepers = []
atoms = ringatoms.copy()
for i in ring:
if i not in keepers:
keepers.append(i)
d = [atom.index for atom in atoms if atom.index not in keepers]
del atoms[d]
position = atoms[0].position
trans = com - position
atoms.translate(trans)
atoms.wrap()
traj += [atoms]
return traj, unique_tsites
def get_all_rings(code):
'''
For developmental testing only.
'''
z = framework(code)
pr = get_fwrings(code)
tsites, tmult, first = get_tsites(code)
tinds = [atom.index for atom in z if atom.symbol != 'O']
index = 0
firstts = []
for i, m in enumerate(tmult):
firstts.append(tinds[index])
index += m
allrings = []
for f in firstts:
c, r, ringatoms, repeat = all_trings(z, f, pr, delete=False)
for ring in r:
allrings.append(ring)
tinds = [atom.index for atom in ringatoms if atom.symbol != 'O']
rp = np.prod(repeat)
Dict = {}
j = 0
for i in range(rp):
for s, t in enumerate(tsites):
for q in range(tmult[s]):
Dict[tinds[j]] = t
j += 1
ring_tsites = []
for ring in allrings:
tmp = []
for i in ring:
if ringatoms[i].symbol != 'O':
tmp.append(Dict[i])
ring_tsites.append(tmp)
unique_tsites = {}
unique_full = {}
for i, r in enumerate(ring_tsites):
length = len(r)
if length not in unique_tsites:
unique_tsites[length] = [r]
unique_full[length] = [allrings[i]]
else:
unique_tsites[length].append(r)
unique_full[length].append(allrings[i])
trajectories = {}
com = ringatoms.get_center_of_mass()
for length in pr:
ring_tlist = unique_tsites[length]
ring_full = unique_full[length]
d = []
for i in range(len(ring_tlist)):
for j in range((i + 1), len(ring_tlist)):
st1 = ' '.join(map(str, ring_tlist[i]))
st2 = ' '.join(map(str, ring_tlist[j]))
st2_2 = ' '.join(map(str, reversed(ring_tlist[j])))
if st2 in st1 + ' ' + st1 or st2_2 in st1 + ' ' + st1:
d.append(int(j))
tmp1 = []
tmp2 = []
for i in range(len(ring_tlist)):
if i not in d:
tmp1.append(ring_tlist[i])
tmp2.append(ring_full[i])
unique_tsites[length] = tmp1
unique_full[length] = tmp2
traj = []
for ring in tmp2:
keepers = []
atoms = ringatoms.copy()
for i in ring:
if i not in keepers:
keepers.append(i)
d = [atom.index for atom in atoms if atom.index not in keepers]
del atoms[d]
position = atoms[0].position
trans = com - position
atoms.translate(trans)
atoms.wrap()
traj += [atoms]
trajectories[length] = traj
return unique_tsites, unique_full, trajectories