class FittingStructureFunction(ForceFieldFittingFunction):
def __init__(self):
self.mols = []
self.ny = 0
self.optjob = OptimizeJob()
def get_y0(self):
return [0] * self.ny
def calc_y(self):
result = []
for model, bonds, angles, efunc, y0 in self.mols:
coords = model.coords
model.coords = 2 * self.noise * rand(len(coords)) - self.noise
model.coords += coords
self.optjob.fmin_ncg(model, efunc)
y1 = FittingStructureFunction.__calc_ab(model, bonds,angles)
assert len(y0) == len(y1)
for i in range(len(y0)):
result.append((y0[i]-y1[i])/y0[i])
model.coords = coords # restore old coords
raise NotImplementedError()
@staticmethod
def __calc_ab(model, bonds, angles):
y0 = []
for i1 in range(0, len(bonds), 2):
i2 = i1 + 1
x = model.coords[i1*3] - model.coords[i2*3]
y = model.coords[i1*3+1] - model.coords[i2*3+1]
z = model.coords[i1*3+2] - model.coords[i2*3+2]
y0.append(sqrt(x*x+y*y+z*z))
for i1 in range(0, len(angles), 3):
i2 = i1 + 1
i3 = i2 + 2
v1 = XYZ(model.coords[i1*3], model.coords[i1*3+1], model.coords[i1*3+2])
v2 = XYZ(model.coords[i2*3], model.coords[i2*3+1], model.coords[i2*3+2])
v3 = XYZ(model.coords[i3*3], model.coords[i3*3+1], model.coords[i3*3+2])
y0.append(angle(v1, v2, v3))
return y0
def add_mol(self, mol):
bonds = list_bond_atoms(mol)
bonds = [mol.index(i) for i in bonds]
angles = list_angle_atoms(mol)
bonds = [mol.index(i) for i in bonds]
efunc = make_efunc(mol, self.index)
model = setup_model(mol, self.index, self.par)
y0 = FittingStructureFunction.__calc_ab(model, bonds, angles)
self.mols.append((model, bonds, angles, efunc, y0))
self.ny += len(bonds) / 2 + len(angles) / 3
def __init__(self):
self.mols = []
self.ny = 0
self.optjob = OptimizeJob()
