def test_altint(self, molfrag):
R = molfrag.R
rMP = ref.rMP
diff = [(1, 2), (3, 4), (5, 6)]
bonds = (1, 3, 4)
ablab = ("O", "H1O", "H1", "H2O", "H2H1", "H2")
ijlab = ("xx", "yx", "yy", "zx", "zy", "zz")
pol = np.zeros((6, molfrag.noa * (molfrag.noa + 1) // 2))
for ab, a, b in pairs(molfrag.noa):
for ij, i, j in pairs(3):
i1, i2 = diff[i]
j1, j2 = diff[j]
pol[ij, ab] += (
rMP[i + 1, j1, ab]
- rMP[i + 1, j2, ab]
+ rMP[j + 1, i1, ab]
- rMP[j + 1, i2, ab]
) / (4 * ref.ff)
if ab in bonds:
pol[ij, ab] -= (
(R[a][i] - R[b][i])
* (rMP[0, j1, ab] - rMP[0, j2, ab])
/ (2 * ref.ff)
)
self.assert_allclose(
ref.Aab[ij, ab], pol[ij, ab], text="%s%s" % (ablab[ab], ijlab[ij])
)
def test_quadrupole_allbonds(self):
QU = full.matrix(ref.QU.shape)
QUab = self.m.QUab
for ab, a, b in pairs(self.m.noa):
QU[:, ab] += QUab[:, a, b ]
if a != b: QU[:, ab] += QUab[:, b, a]
self.assert_allclose(QU, ref.QU)
def test_dipole_allbonds(self):
D = full.matrix(ref.D.shape)
Dab = self.m.Dab
for ab, a, b in pairs(self.m.noa):
D[:, ab] += Dab[:, a, b ]
if a != b: D[:, ab] += Dab[:, b, a]
self.assert_allclose(D, ref.D)
def test_dipole_allbonds(self, molfrag):
D = full.matrix(ref.D.shape)
Dab = molfrag.Dab
for ab, a, b in pairs(molfrag.noa):
D[:, ab] += Dab[:, a, b]
if a != b:
D[:, ab] += Dab[:, b, a]
self.assert_allclose(D, ref.D)
def test_quadrupole_allbonds(self, molfrag):
QU = full.matrix(ref.QU.shape)
QUab = molfrag.QUab
for ab, a, b in pairs(molfrag.noa):
QU[:, ab] += QUab[:, a, b]
if a != b:
QU[:, ab] += QUab[:, b, a]
self.assert_allclose(QU, ref.QU)
def test_altint(self):
R = self.m.R
rMP = ref.rMP
diff = [(1, 2), (3, 4), (5, 6)]
atoms = (0, 2, 5)
bonds = (1, 3, 4)
ablab = ("O", "H1O", "H1", "H2O", "H2H1", "H2")
ijlab = ("xx", "yx", "yy", "zx", "zy", "zz")
pol = np.zeros((6, self.m.noa*(self.m.noa+1)//2))
for ab, a, b in pairs(self.m.noa):
for ij, i, j in pairs(3):
#from pdb import set_trace; set_trace(self)
i1, i2 = diff[i]
j1, j2 = diff[j]
pol[ij, ab] += (rMP[i+1, j1, ab] - rMP[i+1, j2, ab]
+ rMP[j+1, i1, ab] - rMP[j+1, i2, ab])/(4*ref.ff)
if ab in bonds:
pol[ij, ab] -= (R[a][i]-R[b][i])*(rMP[0, j1, ab] - rMP[0, j2, ab])/(2*ref.ff)
self.assert_allclose(ref.Aab[ij, ab], pol[ij, ab], text="%s%s"%(ablab[ab], ijlab[ij]))