def test_diff_bond(self):
for a1, a2 in yield_bonds():
d = numpy.random.normal(0,eps,6) # random displacements
b1 = a1+d[:3] # displaced
b2 = a2+d[3:] # displaced
qa, ga, ha = ic.bond_length(a1,a2,2)
qb, gb, hb = ic.bond_length(b1,b2,2)
delta1 = qb - qa
delta2 = numpy.dot(0.5*(ga+gb).ravel(), d)
error = abs(delta1-delta2)
oom = abs(delta1)
self.assert_(error*1e5 < oom)
delta1 = (gb - ga).ravel()
delta2 = numpy.dot(0.5*(ha+hb).reshape((6,6)), d)
error = ((delta1-delta2)**2).mean()
oom = (delta1**2).mean()
self.assert_(error*1e5 < oom)
def get_bonds_angles(geometries, atoms):
"""
This functions takes an array with the geometries, and a list with a group of atoms
and returns the bond or angle evolution during the simulation
"""
number_of_steps, number_of_atoms, _ = geometries.shape
colvar = np.empty(number_of_steps)
if len(atoms) == 2:
for frame in range(number_of_steps):
colvar[frame] = bond_length(geometries[frame, atoms])[0]
elif len(atoms) == 3:
for frame in range(number_of_steps):
colvar[frame] = bend_angle(geometries[frame, atoms])[0]
return colvar
def bond_length(mol, i0, i1):
c = mol.coordinates
return ic.bond_length(c[i0], c[i1])[0]
def bond_length(mol, i0, i1):
c = mol.coordinates
return ic.bond_length(c[i0], c[i1])[0]