def make_Td(names, sizes):
#work out the expansion factor
factor = sum(sizes)
#factor = 3.0
Td = Atoms()
Td.append(Atom('F', position=(0, 0, 0)))
Td.append(Atom('N', position=(0, 0, factor)))
#Atom 3
Td.append(Atom('N', position=(1.0, 0, 0.0)))
Td.set_angle([1, 0, 2], 1.91062939)
Td.set_distance(0, 2, factor, fix=0)
#Atom 4
Td.append(Atom('N', position=(1.0, 0, 0.0)))
Td.set_distance(0, 3, factor, fix=0)
Td.set_angle([1, 0, 3], 1.91062939, mask=None)
Td.set_dihedral([2, 1, 0, 3], 2.0943951, mask=None)
#print Td.get_angle([1,0,2])
#Atom 5
Td.append(Atom('N', position=(1.0, 0, 0)))
Td.set_angle([1, 0, 4], 1.91062939)
Td.set_dihedral([2, 1, 0, 4], -2.0943951)
Td.set_distance(0, 4, factor, fix=0)
#find side centroids
tmp1 = Td[1:4]
coside = tmp1.get_center_of_mass()
Td.append(Atom('C', position=coside))
#
tmp1 = Td[2:5]
coside = tmp1.get_center_of_mass()
Td.append(Atom('C', position=coside))
#
tmp1 = Td[3:5]
tmp1.append(Td[1])
coside = tmp1.get_center_of_mass()
Td.append(Atom('C', position=coside))
#
tmp1 = Td[1:3]
tmp1.append(Td[4])
coside = tmp1.get_center_of_mass()
Td.append(Atom('C', position=coside))
write('td.xyz', Td)
# Now we make tags etc
## C -> triangles (faces), N => triangle caps
eps = 0.05
model_molecule = {}
n_obj = -1 #initialise to -1 such that it can be indexed at start of add
n_tags = 0
#First detect global bonding
cov_rad = []
for atom in Td:
#cov_rad.append(covalent_radii[atom.number])
cov_rad.append(factor / 2)
nlist = NeighborList(cov_rad,
skin=0.1,
self_interaction=False,
bothways=True)
nlist.build(Td)
nbond = 1
bond_matrix = np.zeros((len(Td), len(Td)))
pbc_bond_matrix = np.zeros((len(Td), len(Td)))
bond_dict = {}
for atom in Td:
print "---------------------"
indices, offsets = nlist.get_neighbors(atom.index)
for index, offset in zip(indices, offsets):
print atom.index, index, atom.symbol, Td[
index].symbol, offset, Td.get_distance(atom.index,
index,
mic=True)
if atom.index < index:
this_bond = [atom.index, index]
for o in offset:
this_bond.append(o)
bond = tuple(this_bond)
print bond
bond_dict[bond] = nbond
#Now we need to find the same bond the other direction to get the offsets right
indices2, offsets2 = nlist.get_neighbors(index)
for i2, o2 in zip(indices2, offsets2):
if i2 == atom.index:
#print "sum of offsets = ", offset, o2, sum(offset + o2)
if sum(offset + o2) == 0: #same bond
this_bond = [index, atom.index]
for o in o2:
this_bond.append(o)
bond = tuple(this_bond)
print bond
bond_dict[bond] = nbond
nbond += 1
print nbond
for k, v in bond_dict.items():
print k, v
#Now we look for all the things with unit*factor bondlengths
#Start with N (rectangles)
for atom in Td:
if atom.symbol == 'N':
print '======================================='
print 'N Atom ', atom.index
n_obj += 1
model_molecule[n_obj] = Atoms()
model_molecule[n_obj] += atom
model_molecule[n_obj][0].original_index = atom.index
model_molecule[n_obj][0].symbol = 'F'
indices, offsets = nlist.get_neighbors(atom.index)
#Just checking the symbols here
print indices
print offsets
symbols = ([Td[index].symbol for index in indices])
symbol_string = ''.join(
sorted([Td[index].symbol for index in indices]))
#print symbol_string
#for i,o in zip(indices, offsets):
# print i,o
for index, offset in zip(indices, offsets):
print atom.index, index, offset
this_bond = [atom.index, index]
for o in offset:
this_bond.append(o)
bond = tuple(this_bond)
print bond_dict[bond]
if Td[index].symbol == 'C':
#By definition, we can't be going over a periodic boundary (no pbc)
model_molecule[n_obj] += Td[index]
model_molecule[n_obj][-1].tag = bond_dict[bond]
model_molecule[n_obj].positions[-1] = Td.positions[index]
n_centers = n_obj
##Now we do the C (triangles)
for atom in Td:
if atom.symbol == 'C':
#print'======================================='
#print 'N Atom ',atom.index, " finding squares1"
n_obj += 1
model_molecule[n_obj] = Atoms()
model_molecule[n_obj] += atom
indices, offsets = nlist.get_neighbors(atom.index)
for index, offset in zip(indices, offsets):
print index, offset, Td[index].symbol
this_bond = [atom.index, index]
for o in offset:
this_bond.append(o)
bond = tuple(this_bond)
#if not bond_dict.has_key(bond):
#Then
if Td[index].symbol == 'N':
#By definition, we can't be going over a periodic boundary (no pbc)
model_molecule[n_obj] += Td[index]
model_molecule[n_obj][-1].tag = bond_dict[bond]
model_molecule[n_obj].positions[-1] = Td.positions[index]
f = open('Td.model', 'w')
g = open('control-mofgen.txt', 'w')
#Just for checking, now lets gather everything in the model_molecule dict into one big thing and print it
test_mol = Atoms()
for obj in model_molecule:
test_mol += model_molecule[obj]
write('test_model.xyz', test_mol)
#print n_centers, n_model, n_obj
#Headers and cell
f.write('%-20s %-3d\n' % ('Number of objects =', n_obj + 1))
f.write('%-20s\n' % ('build = systre'))
f.write('%5s\n' % ('Cell:'))
f.write('%8.3f %8.3f %8.3f \n' % (0.0, 0.0, 0.0))
f.write('%8.3f %8.3f %8.3f \n' % (0.0, 0.0, 0.0))
f.write('%8.3f %8.3f %8.3f \n' % (0.0, 0.0, 0.0))
g.write('%-20s\n' % ('model = Td'))
for obj in xrange(n_centers + 1):
f.write('\n%-8s %-3d\n' % ('Center: ', obj + 1))
f.write('%-3d\n' % (len(model_molecule[obj])))
f.write('%-20s\n' % ('type = triangle'))
#process positions to make it a bit more ideal
for atom in model_molecule[obj]:
#if atom.symbol == 'C':
if atom.index != 0:
model_molecule[obj].set_distance(atom.index, 0, 1.0, fix=1)
for atom in model_molecule[obj]:
(x, y, z) = atom.position
#print atom.symbol, atom.position, atom.tag
if atom.tag:
f.write('%-2s %15.8f %15.8f %15.8f %-4s\n' %
('X', x, y, z, atom.tag))
#f.write('%-2s %15.8f %15.8f %15.8f %-4s\n' % (atom.symbol, x, y, z, atom.tag))
else:
f.write('%-2s %15.8f %15.8f %15.8f\n' % ('Q', x, y, z))
#f.write('%-2s %15.8f %15.8f %15.8f\n' % (atom.symbol, x, y, z))
g.write('%-9s %-50s\n' % ('center =', names[0]))
for obj in xrange(n_centers + 1, n_obj + 1):
f.write('\n%-8s %-3d\n' % ('Linker: ', obj - n_centers))
f.write('%-3d\n' % (len(model_molecule[obj])))
f.write('%-20s\n' % ('type = triangle'))
#process positions to make it a bit more ideal
for atom in model_molecule[obj]:
#if atom.symbol == 'C':
if atom.index != 0:
model_molecule[obj].set_distance(atom.index, 0, 1.0, fix=1)
for atom in model_molecule[obj]:
(x, y, z) = atom.position
#print atom.symbol, atom.position, atom.tag
if atom.tag:
f.write('%-2s %15.8f %15.8f %15.8f %-4s\n' %
('X', x, y, z, atom.tag))
#f.write('%-2s %15.8f %15.8f %15.8f %-4s\n' % (atom.symbol, x, y, z, atom.tag))
else:
f.write('%-2s %15.8f %15.8f %15.8f\n' % ('Q', x, y, z))
#f.write('%-2s %15.8f %15.8f %15.8f\n' % (atom.symbol, x, y, z))
g.write('%-9s %-50s\n' % ('linker =', names[1]))
test_mol = Atoms()
for obj in model_molecule:
test_mol += model_molecule[obj]
write('test_model2.xyz', test_mol)
def make_Td(names,sizes):
#work out the expansion factor
factor = sum(sizes)
#factor = 3.0
Td = Atoms()
Td.append(Atom('F', position=(0,0,0)))
Td.append(Atom('N', position=(0,0,factor)))
#Atom 3
Td.append(Atom('N', position=(1.0,0,0.0)))
Td.set_angle([1,0,2],1.91062939)
Td.set_distance(0,2, factor, fix=0)
#Atom 4
Td.append(Atom('N', position=(1.0,0,0.0)))
Td.set_distance(0,3, factor, fix=0)
Td.set_angle([1,0,3],1.91062939, mask=None)
Td.set_dihedral([2,1,0,3],2.0943951, mask=None)
#print Td.get_angle([1,0,2])
#Atom 5
Td.append(Atom('N', position=(1.0,0,0)))
Td.set_angle([1,0,4],1.91062939)
Td.set_dihedral([2,1,0,4],-2.0943951)
Td.set_distance(0,4, factor, fix=0)
#find side centroids
tmp1 = Td[1:4]
coside = tmp1.get_center_of_mass()
Td.append(Atom('C', position = coside))
#
tmp1 = Td[2:5]
coside = tmp1.get_center_of_mass()
Td.append(Atom('C', position = coside))
#
tmp1 = Td[3:5]
tmp1.append(Td[1])
coside = tmp1.get_center_of_mass()
Td.append(Atom('C', position = coside))
#
tmp1 = Td[1:3]
tmp1.append(Td[4])
coside = tmp1.get_center_of_mass()
Td.append(Atom('C', position = coside))
write('td.xyz',Td)
# Now we make tags etc
## C -> triangles (faces), N => triangle caps
eps = 0.05
model_molecule={}
n_obj = -1 #initialise to -1 such that it can be indexed at start of add
n_tags = 0
#First detect global bonding
cov_rad=[]
for atom in Td:
#cov_rad.append(covalent_radii[atom.number])
cov_rad.append(factor / 2)
nlist = NeighborList(cov_rad,skin=0.1,self_interaction=False,bothways=True)
nlist.build(Td)
nbond = 1
bond_matrix = np.zeros( (len(Td),len(Td)) )
pbc_bond_matrix = np.zeros( (len(Td),len(Td)) )
bond_dict = {}
for atom in Td:
print "---------------------"
indices, offsets = nlist.get_neighbors(atom.index)
for index,offset in zip(indices,offsets):
print atom.index, index, atom.symbol, Td[index].symbol, offset, Td.get_distance(atom.index,index,mic=True)
if atom.index < index:
this_bond = [atom.index, index]
for o in offset:
this_bond.append(o)
bond = tuple(this_bond)
print bond
bond_dict[bond] = nbond
#Now we need to find the same bond the other direction to get the offsets right
indices2,offsets2 = nlist.get_neighbors(index)
for i2,o2 in zip(indices2,offsets2):
if i2 == atom.index:
#print "sum of offsets = ", offset, o2, sum(offset + o2)
if sum(offset + o2) == 0: #same bond
this_bond = [index, atom.index]
for o in o2:
this_bond.append(o)
bond = tuple(this_bond)
print bond
bond_dict[bond] = nbond
nbond +=1
print nbond
for k,v in bond_dict.items():
print k,v
#Now we look for all the things with unit*factor bondlengths
#Start with N (rectangles)
for atom in Td:
if atom.symbol == 'N':
print'======================================='
print 'N Atom ',atom.index
n_obj+=1
model_molecule[n_obj] = Atoms()
model_molecule[n_obj] += atom
model_molecule[n_obj][0].original_index = atom.index
model_molecule[n_obj][0].symbol = 'F'
indices, offsets = nlist.get_neighbors(atom.index)
#Just checking the symbols here
print indices
print offsets
symbols = ([Td[index].symbol for index in indices])
symbol_string = ''.join(sorted([Td[index].symbol for index in indices]))
#print symbol_string
#for i,o in zip(indices, offsets):
# print i,o
for index,offset in zip(indices,offsets):
print atom.index, index, offset
this_bond = [atom.index, index]
for o in offset:
this_bond.append(o)
bond = tuple(this_bond)
print bond_dict[bond]
if Td[index].symbol == 'C':
#By definition, we can't be going over a periodic boundary (no pbc)
model_molecule[n_obj] += Td[index]
model_molecule[n_obj][-1].tag = bond_dict[bond]
model_molecule[n_obj].positions[-1] = Td.positions[index]
n_centers = n_obj
##Now we do the C (triangles)
for atom in Td:
if atom.symbol == 'C':
#print'======================================='
#print 'N Atom ',atom.index, " finding squares1"
n_obj+=1
model_molecule[n_obj] = Atoms()
model_molecule[n_obj] += atom
indices, offsets = nlist.get_neighbors(atom.index)
for index,offset in zip(indices,offsets):
print index, offset, Td[index].symbol
this_bond = [atom.index, index]
for o in offset:
this_bond.append(o)
bond = tuple(this_bond)
#if not bond_dict.has_key(bond):
#Then
if Td[index].symbol == 'N':
#By definition, we can't be going over a periodic boundary (no pbc)
model_molecule[n_obj] += Td[index]
model_molecule[n_obj][-1].tag = bond_dict[bond]
model_molecule[n_obj].positions[-1] = Td.positions[index]
f = open('Td.model','w')
g = open('control-mofgen.txt','w')
#Just for checking, now lets gather everything in the model_molecule dict into one big thing and print it
test_mol = Atoms()
for obj in model_molecule:
test_mol += model_molecule[obj]
write('test_model.xyz',test_mol)
#print n_centers, n_model, n_obj
#Headers and cell
f.write('%-20s %-3d\n' %('Number of objects =',n_obj+1))
f.write('%-20s\n' %('build = systre'))
f.write('%5s\n' %('Cell:'))
f.write('%8.3f %8.3f %8.3f \n' % (0.0, 0.0, 0.0))
f.write('%8.3f %8.3f %8.3f \n' % (0.0, 0.0, 0.0))
f.write('%8.3f %8.3f %8.3f \n' % (0.0, 0.0, 0.0))
g.write('%-20s\n' %('model = Td'))
for obj in xrange(n_centers+1):
f.write('\n%-8s %-3d\n' %('Center: ', obj+1))
f.write('%-3d\n' %(len(model_molecule[obj])))
f.write('%-20s\n' %('type = triangle'))
#process positions to make it a bit more ideal
for atom in model_molecule[obj]:
#if atom.symbol == 'C':
if atom.index != 0:
model_molecule[obj].set_distance(atom.index,0,1.0,fix=1)
for atom in model_molecule[obj]:
(x,y,z) = atom.position
#print atom.symbol, atom.position, atom.tag
if atom.tag:
f.write('%-2s %15.8f %15.8f %15.8f %-4s\n' % ('X', x, y, z, atom.tag))
#f.write('%-2s %15.8f %15.8f %15.8f %-4s\n' % (atom.symbol, x, y, z, atom.tag))
else:
f.write('%-2s %15.8f %15.8f %15.8f\n' % ('Q', x, y, z))
#f.write('%-2s %15.8f %15.8f %15.8f\n' % (atom.symbol, x, y, z))
g.write('%-9s %-50s\n' %('center =', names[0]))
for obj in xrange(n_centers+1,n_obj+1):
f.write('\n%-8s %-3d\n' %('Linker: ', obj-n_centers))
f.write('%-3d\n' %(len(model_molecule[obj])))
f.write('%-20s\n' %('type = triangle'))
#process positions to make it a bit more ideal
for atom in model_molecule[obj]:
#if atom.symbol == 'C':
if atom.index != 0:
model_molecule[obj].set_distance(atom.index,0,1.0,fix=1)
for atom in model_molecule[obj]:
(x,y,z) = atom.position
#print atom.symbol, atom.position, atom.tag
if atom.tag:
f.write('%-2s %15.8f %15.8f %15.8f %-4s\n' % ('X', x, y, z, atom.tag))
#f.write('%-2s %15.8f %15.8f %15.8f %-4s\n' % (atom.symbol, x, y, z, atom.tag))
else:
f.write('%-2s %15.8f %15.8f %15.8f\n' % ('Q', x, y, z))
#f.write('%-2s %15.8f %15.8f %15.8f\n' % (atom.symbol, x, y, z))
g.write('%-9s %-50s\n' %('linker =', names[1]))
test_mol = Atoms()
for obj in model_molecule:
test_mol += model_molecule[obj]
write('test_model2.xyz',test_mol)
