def pairNonbondCreator(name, model, key2index, filter):
result = NonbondEnergyProxy()
result.name = name
result.filter = filter
if ':columnb-constant:' in key2index and hasattr(model, 'charges'):
result.columnb_constant = key2index[':columnb-constant:']
result.par0 = key2index[':start:']
return result
def pairCreator(name, model, key2index, filter):
result = NonbondEnergyProxy()
result.name = name
type = name.split('/')[0]
rank = 0
if type == 'pair-14':
fffunc = FunctionPair14()
rank = 2
elif type == 'pair-13':
fffunc = FunctionPair13()
rank = 2
else:
assert False
lists = []
start = 0
for mol, n in model.mols:
data = fffunc.setup(mol, key2index)
for atom, _, _ in data:
for i in range(len(atom)):
atom[i] = mol.index(atom[i])
natoms = len(mol.atoms)
for _ in range(n):
for atom, _, index in data:
for j in atom:
lists.append(j+start)
lists.append(index)
start += natoms
if lists:
result.lists = lists
if ':columnb-constant:' in key2index and hasattr(model, 'charges'):
result.columnb_constant = key2index[':columnb-constant:']
if rank != 0:
screenPairList(filter, result, rank)
return result
else:
return None