def energygrad(self):
"""
# N = <0|0>
# dN = 2<d0|0>
# E = <0|H|0>/<0|0>
# dE = 2<d0|H-E|0>/<0|0>
"""
h_struct_grad = full.matrix(len(self.structs))
h_orb_grad = full.matrix(Nod.C.shape)
for s1, (str1, cstr1) in enumerate(zip(self.structs, self.coef)):
for str2, cstr2 in zip(self.structs, self.coef):
for det1, cdet1 in zip(str1.nods, str1.coef):
for det2, cdet2 in zip(str2.nods, str2.coef):
det12 = BraKet(det1, det2)
h_struct_grad[s1] += \
2*(cdet1*cstr2*cdet2)*\
det12.overlap()*\
det12.energy((self.h, self.h))
h_orb_grad += \
cstr1*cdet1*cstr2*cdet2*\
det12.energy_gradient((self.h, self.h))
N = self.norm()
E = self.energy()
n_struct_grad, n_orb_grad = self.normgrad()
structgrad = (1/N)*(h_struct_grad - E*n_struct_grad)
orbgrad = (1/N)*(h_orb_grad - E*n_orb_grad)
return (structgrad, orbgrad[:, :])
def normhess(self):
"""
Numerical norm Hessian
# N = <0|0>
# d2<0|0> = <d20|0> + <0|d20> + 2<d0|d0> = 2<0|d20> + 2<d0|d0>
"""
n_struct_hess = full.matrix(self.coef.shape*2)
n_orb_structhess = full.matrix(Nod.C.shape + self.coef.shape)
n_orb_hess = full.matrix(Nod.C.shape*2)
#
for s1, (str1, cstr1) in enumerate(zip(self.structs, self.coef)):
for s2, (str2, cstr2) in enumerate(zip(self.structs, self.coef)):
for det1, cdet1 in zip(str1.nods, str1.coef):
for det2, cdet2 in zip(str2.nods, str2.coef):
#
bk12 = BraKet(det1, det2)
#
n_struct_hess[s1, s2] += (cdet1*cdet2)*bk12.overlap()
n_orb_structhess[:, :, s1] += \
cdet1*cstr2*cdet2*bk12.overlap_gradient()
n_orb_hess += \
cstr1*cdet1*cstr2*cdet2*bk12.overlap_hessian()
n_struct_hess *= 2
n_orb_structhess *= 2
#n_orb_hess
return n_struct_hess, n_orb_structhess, n_orb_hess
def constraint(x, self):
self.x = x
mo = self.C[:, i]
sg = full.matrix(self.coef.shape)
og = full.matrix(self.C.shape)
og[:, i] = 2*vb.Nod.S*mo
return self.so2x(sg, og)
def numgrad(self, func, delta=1e-3):
"""
# Numerical gradient
"""
deltah = delta/2
#
# structure coefficients
#
structgrad = full.matrix(len(self.structs))
#
#
for s in range(structgrad.shape[0]):
self.coef[s] += deltah
ep = func()
self.coef[s] -= delta
em = func()
self.coef[s] += deltah
structgrad[s] = (ep - em)/delta
#
# orbital gradient
#
r, c = Nod.C.shape
orbgrad = full.matrix((r, c))
for m in range(c):
for t in range(r):
Nod.C[t, m] += deltah
ep = func()
Nod.C[t, m] -= delta
em = func()
orbgrad[t, m] = (ep - em)/delta
Nod.C[t, m] += deltah
return (structgrad, orbgrad[:, :])
def test_quadrupole_total(self, molfrag):
rRab = full.matrix((6, molfrag.noa, molfrag.noa))
RRab = full.matrix((6, molfrag.noa, molfrag.noa))
Rabc = 1.0 * molfrag.Rab
for a in range(molfrag.noa):
for b in range(molfrag.noa):
Rabc[a, b, :] -= molfrag.Rc
for a in range(molfrag.noa):
for b in range(molfrag.noa):
ij = 0
for i in range(3):
for j in range(i, 3):
rRab[ij, a, b] = (
molfrag.Dab[i, a, b] * Rabc[a, b, j]
+ molfrag.Dab[j, a, b] * Rabc[a, b, i]
)
RRab[ij, a, b] = (
molfrag.Qab[a, b]
* (molfrag.R[a, i] - molfrag.Rc[i])
* (molfrag.R[b, j] - molfrag.Rc[j])
)
ij += 1
QUcab = molfrag.QUab + rRab + RRab
QUc = QUcab.sum(axis=2).sum(axis=1).view(full.matrix)
self.assert_allclose(QUc, ref.QUc)
def contravariant_transition_density_ao_mo(self):
"""Return contravariant density matrix in mix ao,mo basis"""
d_am = (full.matrix(Nod.C.shape), full.matrix(Nod.C.shape))
CK = self.K.orbitals()
for s in (0, 1):
if self.K(s) and self.L(s):
d_am[s][:, self.L(s)] = CK[s]*self.transition_density[s]
return d_am
def contravariant_transition_density_mo_ao(self):
"""Return contravariant density matrix in mix mo,ao basis"""
d_ma = (full.matrix(Nod.C.shape[::-1]), full.matrix(Nod.C.shape[::-1]))
CL = self.L.orbitals()
for s in (0, 1):
if self.K(s) and self.L(s):
d_ma[s][self.K(s), :] = self.transition_density[s]*CL[s].T
return d_ma
def fun(coef, wf):
grad = full.matrix(coef.size)
VBTestH2C.update_wf(coef, wf)
mo = wf.C[:, i]
dc2 = 2*vb.Nod.S*mo
tmp = full.matrix(wf.C.shape)
tmp[:, i] = dc2
grad[wf.coef.size:] = tmp.block(*wf.blockdims).ravel(order='F')
return grad
def QUab(self):
"""Quadrupole moment"""
if self._QUab is not None: return self._QUab
D = self.D
R = self.R
Rc = self.Rc
dRab = self.dRab
Qab = self.Qab
Dab = self.Dab
lab = ("XXSECMOM", "XYSECMOM", "XZSECMOM",
"YYSECMOM", "YZSECMOM",
"ZZSECMOM")
xy = self.getprop(*lab)
noa = self.noa
QUab = full.matrix((6, noa, noa))
rrab = full.matrix((6, noa, noa))
rRab = full.matrix((6, noa, noa))
RRab = full.matrix((6, noa, noa))
Rab = self.Rab
for a in range(noa):
for b in range(noa):
ij = 0
for i in range(3):
for j in range(i, 3):
rrab[ij, a, b] = -(
xy[ij].subblock[a][b]&D.subblock[a][b]
)
rRab[ij, a, b] = Dab[i, a, b]*Rab[a,b,j]+Dab[j, a, b]*Rab[a,b,i]
RRab[ij, a, b] = Rab[a,b,i]*Rab[a,b,j]*Qab[a, b]
ij += 1
QUab = rrab-rRab-RRab
self._QUab = QUab
#
# Addition term - gauge correction summing up bonds
#
dQUab = full.matrix(self.QUab.shape)
for a in range(noa):
for b in range(noa):
ij = 0
for i in range(3):
for j in range(i, 3):
dQUab[ij, a, b] = dRab[a, b, i]*Dab[j, a, b] \
+dRab[a, b, j]*Dab[i, a, b]
ij += 1
self.dQUab = - dQUab
return self._QUab
def project_virtual_occupied(self, h1):
"""Rhs derivative <K|h|dL/dC(mu, m)>"""
D_mo = self.transition_density
delta = self.co_contravariant_transition_delta()
K_h_dL = (full.matrix(Nod.C.shape), full.matrix(Nod.C.shape))
CK = self.K.orbitals()
for s in (0, 1):
if self.K(s) and self.L(s):
K_h_dL[s][:, self.L(s)] += \
delta[s]*h1[s].T*CK[s]*D_mo[s]*self.overlap()
return K_h_dL
def full_mo_transition_density(self):
"""
Return mo transition density matrix in full mo basis
"""
if self._ftd is None:
_, mo = Nod.C.shape
D_KL = self.transition_density
self._ftd = (full.matrix((mo, mo)), full.matrix((mo, mo)))
for s in (0, 1):
if self.K(s) and self.L(s):
D_KL[s].scatter(
self._ftd[s], rows=self.K(s), columns=self.L(s)
)
return self._ftd
def fock(D, component, **kwargs):
""" Generate two-electron spin-orbit Fock matrix
from integral file AO2SOINT
"""
hfc = kwargs.get('hfc', 1.0)
hfx = kwargs.get('hfx', 1.0)
#
left = 1
right = 2
nbast, _ = D.shape
J = matrix((nbast, nbast))
JL = matrix((nbast, nbast))
JR = matrix((nbast, nbast))
K = matrix((nbast, nbast))
for buf, ibuf in two.list_buffers(label='AO2SOINT', **kwargs):
for g, ig in zip(buf, ibuf):
if ig[0] == 0:
comp = "*xyz"[ig[1]]
else:
#print comp, ig, g, component
if comp != component:
continue
p, q, r, s = ig
s, r, q, p = (p - 1, q - 1, r - 1, s - 1)
if (p == q): g *= 0.5
x = 1.5 * g
JL[r, s] += g * (D[p, q] + D[q, p])
JL[s, r] -= g * (D[p, q] + D[q, p])
JR[p, q] += 2 * g * (D[r, s] - D[s, r])
JR[q, p] += 2 * g * (D[r, s] - D[s, r])
K[p, s] -= x * D[r, q]
K[s, p] += x * D[q, r]
K[p, r] += x * D[s, q]
K[r, p] -= x * D[q, s]
K[q, s] -= x * D[r, p]
K[s, q] += x * D[p, r]
K[q, r] += x * D[s, p]
K[r, q] -= x * D[p, s]
J = JR + JL
F = hfc * J + hfx * K
return F
def Dao(K, L):
"""
# Return intermediate normalized ao transition density matrix given
# determinants K and L
# as [Dalpha, Dbeta]
"""
if abs(K*L) < SINGULAR_OVERLAP_THRESHOLD:
raise SingularOverlapError
CK = K.orbitals()
CL = L.orbitals()
#
D = []
for s in range(2):
if CK[s] is None or CL[s] is None:
#
# if None orbitals set atomic density to zero matrix
#
D.append(full.matrix(Nod.S.shape))
else:
SLK = CL[s].T*Nod.S*CK[s]
try:
D.append(CK[s]*(CL[s].T/SLK))
except LinAlgError:
raise SingularOverlapError
return D
def vb_transform2(Dma, Dam, Delta1, Delta2, **kwargs):
filename = kwargs.get('filename', '/tmp/AOTWOINT')
H_umvn = matrix(Dam[0].shape + Dam[0].shape)
for ig, g in list_integrals(filename):
p, q, r, s = ig
s, r, q, p = p-1, q-1, r-1, s-1
if p == q: g *= 0.5
if r == s: g *= 0.5
if (p, q) == (r, s): g *= 0.5
for d1a, d2a, D1a, D2a in zip(Dma, Dam, Delta1, Delta2):
for d1b, d2b, D1b, D2b in zip(Dma, Dam, Delta1, Delta2):
H_umvn += D1a[p,:].x(d1a[:, q].x(D2b[:, s].x(d2b[r, :]*g)))
H_umvn += D1a[q,:].x(d1a[:, p].x(D2b[:, s].x(d2b[r, :]*g)))
H_umvn += D1a[p,:].x(d1a[:, q].x(D2b[:, r].x(d2b[s, :]*g)))
H_umvn += D1a[q,:].x(d1a[:, p].x(D2b[:, r].x(d2b[s, :]*g)))
H_umvn += D1a[r,:].x(d1a[:, s].x(D2b[:, q].x(d2b[p, :]*g)))
H_umvn += D1a[r,:].x(d1a[:, s].x(D2b[:, p].x(d2b[q, :]*g)))
H_umvn += D1a[s,:].x(d1a[:, r].x(D2b[:, q].x(d2b[p, :]*g)))
H_umvn += D1a[s,:].x(d1a[:, r].x(D2b[:, p].x(d2b[q, :]*g)))
H_umvn -= D1a[p, :].x(d1a[:, s].x(D2a[:, q].x(d2a[r, :]*g)))
H_umvn -= D1a[q, :].x(d1a[:, s].x(D2a[:, p].x(d2a[r, :]*g)))
H_umvn -= D1a[p, :].x(d1a[:, r].x(D2a[:, q].x(d2a[s, :]*g)))
H_umvn -= D1a[q, :].x(d1a[:, r].x(D2a[:, p].x(d2a[s, :]*g)))
H_umvn -= D1a[r, :].x(d1a[:, q].x(D2a[:, s].x(d2a[p, :]*g)))
H_umvn -= D1a[r, :].x(d1a[:, p].x(D2a[:, s].x(d2a[q, :]*g)))
H_umvn -= D1a[s, :].x(d1a[:, q].x(D2a[:, r].x(d2a[p, :]*g)))
H_umvn -= D1a[s, :].x(d1a[:, p].x(D2a[:, r].x(d2a[q, :]*g)))
return H_umvn
def vb_transform(dens, delta, **kwargs):
filename = kwargs.get('filename', '/tmp/AOTWOINT')
a, m = dens[0].shape
H_uvmn = matrix((a, a, m, m))
for ig, g in list_integrals(filename):
p, q, r, s = ig
s, r, q, p = p-1, q-1, r-1, s-1
if p == q: g *= 0.5
if r == s: g *= 0.5
if (p, q) == (r, s): g *= 0.5
for d1, D1 in zip(dens, delta):
for d2, D2 in zip(dens, delta):
H_uvmn += D1[:, q].x(D2[:, s].x(d1[p, :].x(d2[r, :]*g)))
H_uvmn += D1[:, p].x(D2[:, s].x(d1[q, :].x(d2[r, :]*g)))
H_uvmn += D1[:, q].x(D2[:, r].x(d1[p, :].x(d2[s, :]*g)))
H_uvmn += D1[:, p].x(D2[:, r].x(d1[q, :].x(d2[s, :]*g)))
H_uvmn += D1[:, s].x(D2[:, q].x(d1[r, :].x(d2[p, :]*g)))
H_uvmn += D1[:, r].x(D2[:, q].x(d1[s, :].x(d2[p, :]*g)))
H_uvmn += D1[:, s].x(D2[:, p].x(d1[r, :].x(d2[q, :]*g)))
H_uvmn += D1[:, r].x(D2[:, p].x(d1[s, :].x(d2[q, :]*g)))
H_uvmn -= D1[:, s].x(D1[:, q].x(d1[p, :].x(d1[r, :]*g)))
H_uvmn -= D1[:, s].x(D1[:, p].x(d1[q, :].x(d1[r, :]*g)))
H_uvmn -= D1[:, r].x(D1[:, q].x(d1[p, :].x(d1[s, :]*g)))
H_uvmn -= D1[:, r].x(D1[:, p].x(d1[q, :].x(d1[s, :]*g)))
H_uvmn -= D1[:, q].x(D1[:, s].x(d1[r, :].x(d1[p, :]*g)))
H_uvmn -= D1[:, q].x(D1[:, r].x(d1[s, :].x(d1[p, :]*g)))
H_uvmn -= D1[:, p].x(D1[:, s].x(d1[r, :].x(d1[q, :]*g)))
H_uvmn -= D1[:, p].x(D1[:, r].x(d1[s, :].x(d1[q, :]*g)))
return H_uvmn.transpose(0, 2, 1, 3)
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 Bab(self):
"""Localized hyperpolariziabilities"""
if self._Bab is not None: return self._Bab
D2k = self.D2k
Rab = self.Rab
d2Qa = self.d2Qa
x = self.x
labs = ('XDIPLEN ', 'YDIPLEN ', 'ZDIPLEN ')
qlabs = [labs[i] + labs[j] for i in range(3) for j in range(i,3)]
Bab = full.matrix( (self.nfreqs, 3, 6, self.noa, self.noa) )
#correction term for shifting origin from O to Rab
for i, li in enumerate(labs):
for jk,ljk in enumerate(qlabs):
for a in range(self.noa):
for b in range(self.noa):
for iw, w in enumerate(self.freqs):
Bab[iw, i, jk, a, b] = (
-x[i].subblock[a][b] & D2k [(ljk, w, w)].subblock[a][b]
)
for iw in self.rfreqs:
Bab[iw, i, jk, a, a] -= d2Qa[iw, a, jk]*Rab[a, a, i]
self._Bab = Bab
return self._Bab
def ifc(filename="SIRIFC", ifc_=None):
"""
Return inactive/active densities from orbitals on interface file SIRIFC
"""
if ifc_ is None:
ifc_ = sirifc.sirifc(filename)
Di = blocked.BlockDiagonalMatrix(ifc_.nbas, ifc_.nbas)
for isym in range(ifc_.nsym):
if ifc_.nish[isym]:
Ci = ifc_.cmo.subblock[isym]
Cocci = Ci[:, : ifc_.nish[isym]]
Di.subblock[isym] = 2 * Cocci @ Cocci.T
Di = Di.unblock()
if ifc_.nasht:
cmoa = blocked.BlockDiagonalMatrix(ifc_.nbas, ifc_.nash)
for isym in range(ifc_.nsym):
if ifc_.nash[isym]:
nishi = ifc_.nish[isym]
nocci = ifc_.nish[isym] + ifc_.nash[isym]
cmoa.subblock[isym] = ifc_.cmo.subblock[isym][:, nishi:nocci]
cmoa = cmoa.unblock()
Dv = cmoa @ ifc_.dv.unpack() @ cmoa.T
else:
Dv = full.matrix((ifc_.nbast, ifc_.nbast))
return Di, Dv
def constraint_norm_grad(coef, wf):
grad = full.matrix(coef.size)
VBTestH2C.update_wf(coef, wf)
sg, og = wf.normgrad()
grad[:wf.coef.size] = sg
grad[wf.coef.size:] = og.block(*wf.blockdims).ravel(order='F')
return grad
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 wf_gradient(coef, wf):
grad = full.matrix(coef.size)
VBTestH2C.update_wf(coef, wf)
sg, og = wf.energygrad()
grad[:wf.coef.size] = sg
grad[wf.coef.size:] = og.block(*wf.blockdims).ravel(order='F')
return grad
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_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 mkB2(vecs):
B = full.matrix(len(vecs) + 1, len(vecs) + 1)
for i in range(len(vecs)):
for j in range(len(vecs)):
B[i, j] = -(vecs[i] * vecs[j]).tr()
B[i, len(vecs)] = -1
B[len(vecs), i] = -1
return B
def grad(x, self):
_x = self.x
self.x = x
p = self.p
dL = full.matrix(len(x))
dL[:len(p)] = self.gp(p) - sum(l*c['jac'](p) for l, c in zip(self.l, self.cp))
dL[len(p):] = [-c['fun'](p) for c in self.cp]
self.x = _x
return dL
def project_occupied_virtual(self, h1):
"""Lhs derivative <dK/dC(mu,m)|h|L>"""
D_mo = self.transition_density
delta = self.contra_covariant_transition_delta()
dK_h_La = full.matrix(Nod.C.shape[::-1])
dK_h_Lb = full.matrix(Nod.C.shape[::-1])
CL = self.L.orbitals()
if self.L(0):
dK_h_La[self.K(0), :] += \
D_mo[0]*CL[0].T*h1[0].T*delta[0]*self.overlap()
if self.L(1):
dK_h_Lb[self.K(1), :] += \
D_mo[1]*CL[1].T*h1[1].T*delta[1]*self.overlap()
return dK_h_La.T, dK_h_Lb.T
def tovec(mat, ifc, tmpdir="/tmp"):
"""Vector to matrix"""
lwop = ifc.nisht * ifc.nasht + ifc.nocct * (ifc.norbt - ifc.nocct)
N = full.matrix((2 * lwop, ))
for ij, (i, j) in enumerate(jwop(ifc)):
N[ij] = mat[i, j]
N[ij + lwop] = mat[j, i]
return N
def test_quadrupole_total(self):
rrab=full.matrix((6, self.m.noa, self.m.noa))
rRab=full.matrix((6, self.m.noa, self.m.noa))
RRab=full.matrix((6, self.m.noa, self.m.noa))
Rabc = 1.0*self.m.Rab
for a in range(self.m.noa):
for b in range(self.m.noa):
Rabc[a,b,:] -= self.m.Rc
for a in range(self.m.noa):
for b in range(self.m.noa):
ij = 0
for i in range(3):
for j in range(i,3):
rRab[ij, a, b] = self.m.Dab[i, a, b]*Rabc[a, b, j]\
+ self.m.Dab[j, a, b]*Rabc[a, b, i]
RRab[ij, a, b] = self.m.Qab[a, b]*(self.m.R[a, i] - self.m.Rc[i])*(self.m.R[b, j] - self.m.Rc[j])
ij += 1
QUcab = self.m.QUab + rRab + RRab
QUc = QUcab.sum(axis=2).sum(axis=1).view(full.matrix)
self.assert_allclose(QUc, ref.QUc)
def ao_density(self):
"""Electron number check"""
D_ao = full.matrix(Nod.S.shape)
for S, CS in zip(self.structs, self.coef):
for T, CT in zip(self.structs, self.coef):
for K, CK in zip(S.nods, S.coef):
for L, CL in zip(T.nods, T.coef):
KL = BraKet(K, L)
DKL = KL.transition_ao_density
D_ao += sum(DKL)*CS*CT*CK*CL*KL.overlap()
return D_ao/self.norm()
def hess(x, self):
_x = self.x
self.x = x
p = self.p
d2L = full.matrix((len(x), len(x)))
d2L[:len(p), :len(p)] = self.hp(p) - sum(l*c['hes'](p) for l, c in zip(self.l, self.cp))
for i, c in enumerate(self.cp):
d2L[:len(p), len(p) + i] = -c['jac'](p)
d2L[len(p):, :len(p)] = d2L[:len(p), len(p):].T
d2L[len(p):, len(p):] = 0.0
self.x = _x
return d2L
def tovec(mat, ifc, tmpdir='/tmp'):
"""Vector to matrix"""
import os
from util import full
lwop = ifc.nisht*ifc.nasht + ifc.nocct*(ifc.norbt-ifc.nocct)
N = full.matrix((2*lwop,))
ij = 0
for i, j in jwop(ifc):
N[ij] = mat[i, j]
N[ij+lwop] = mat[j, i]
ij += 1
return N
def tomat(N, ifc, tmpdir="/tmp"):
"""Vector to matrix"""
norbt = ifc.norbt
new = full.matrix((norbt, norbt))
lwop = len(N) // 2
for ij, (i, j) in enumerate(jwop(ifc)):
new[i, j] = N[ij]
new[j, i] = N[ij + lwop]
return new
def get_dens(self, ndim, idim, nocc=None):
if nocc is None:
nocc_ = [1]*len(ndim)
else:
nocc_ = nocc
dens = matrix((self.nbast, self.nbast))
for ni, no, offset in zip(ndim, nocc_, idim):
if ni > 0:
cmoi = self.cmo[:, offset: offset + ni]
dens += no*cmoi*cmoi.T
return dens
def test_polarizability_nobonds(self, molfrag):
Aab = molfrag.Aab[0] + molfrag.dAab[0] / 2
noa = molfrag.noa
Acmp = full.matrix((6, noa))
Aa = Aab.sum(axis=3).view(full.matrix)
for a in range(noa):
Acmp[:, a] = Aa[:, :, a].pack()
# atoms
self.assert_allclose(Acmp, ref.Aa, atol=0.07)
def get_dens(self, ndim, idim, nocc=None):
if nocc is None:
nocc_ = [1] * len(ndim)
else:
nocc_ = nocc
dens = matrix((self.nbast, self.nbast))
for ni, no, offset in zip(ndim, nocc_, idim):
if ni > 0:
cmoi = self.cmo[:, offset:offset + ni]
dens += no * cmoi * cmoi.T
return dens
def test_bond_charge_shift(self, molfrag):
dQab = molfrag.dQab[0]
noa = molfrag.noa
dQabref = (ref.dQab[:, 1:7:2] - ref.dQab[:, 2:7:2]) / (2 * ref.ff)
dQabcmp = full.matrix((3, 3))
ab = 0
for a in range(noa):
for b in range(a):
dQabcmp[ab, :] = dQab[a, b, :]
ab += 1
# The sign difference is because mocas sets up rhs with opposite sign
self.assert_allclose(-dQabref, dQabcmp, atol=0.006)
def test_bond_charge_shift(self):
dQab = self.m.dQab[0]
noa = self.m.noa
dQabref = (ref.dQab[:, 1:7:2] - ref.dQab[:, 2:7:2])/(2*ref.ff)
dQabcmp = full.matrix((3, 3))
ab = 0
for a in range(noa):
for b in range(a):
dQabcmp[ab, :] = dQab[a, b, :]
ab += 1
# The sign difference is because mocas sets up rhs with opposite sign
self.assert_allclose(-dQabref, dQabcmp, atol=0.006)
def QUc(self):
if self._QUc is not None: return self._QUc
rrab=full.matrix((6, self.noa, self.noa))
rRab=full.matrix((6, self.noa, self.noa))
RRab=full.matrix((6, self.noa, self.noa))
Rabc = 1.0*self.Rab
for a in range(self.noa):
for b in range(self.noa):
Rabc[a,b,:] -= self.Rc
for a in range(self.noa):
for b in range(self.noa):
ij = 0
for i in range(3):
for j in range(i,3):
rRab[ij, a, b] = self.Dab[i, a, b]*Rabc[a, b, j]\
+ self.Dab[j, a, b]*Rabc[a, b, i]
RRab[ij, a, b] = self.Qab[a, b]*(self.R[a, i] - self.Rc[i])*(self.R[b, j] - self.Rc[j])
ij += 1
QUcab = self.QUab + rRab + RRab
self._QUc = QUcab.sum(axis=2).sum(axis=1).view(full.matrix)
return self._QUc
def tomat(N, ifc, tmpdir='/tmp'):
"""Vector to matrix"""
import os
from util import full
norbt = ifc.norbt
new = full.matrix((norbt, norbt))
lwop = len(N)/2
ij = 0
for i, j in jwop(ifc):
new[i, j] = N[ij]
new[j, i] = N[ij+lwop]
ij += 1
return new
def setUp(self):
self.tmp = os.path.join(os.path.dirname(__file__), 'test_h2_c')
def tmp(fil):
return os.path.join(self.tmp, fil)
self.qcifc = QuantumChemistry.get_factory('Dalton', tmpdir=self.tmp)
vb.Nod.tmpdir = self.tmp
vb.Nod.C = full.matrix((10, 2))
vb.Nod.C[0, 0] = 1.0
vb.Nod.C[5, 1] = 1.0
vb.Nod.S = self.qcifc.get_overlap()
self.blockdims = ((5, 5), (1, 1))
self.wf = vb.WaveFunction(
[vb.Structure(
[vb.Nod([0], [1]), vb.Nod([1], [0])],
[1.0, 1.0]
),
vb.Structure([vb.Nod([0], [0])], [1.0]),
vb.Structure([vb.Nod([1], [1])], [1.0]),
],
[1.0, 0.0, 0.0],
tmpdir = self.tmp,
blockdims=self.blockdims
)
# In this setup we have local expansions of mos, leading to a block diagonal C
self.final = full.matrix(13)
self.final_coef =[0.83675, 0.09850, 0.09850]
self.final[:3] = self.final_coef
self.final_C = full.init([
[0.7633862173, 0.3075441467, 0.0, 0.0, 0.0328947818,0,0,0,0,0],
[0,0,0,0,0, 0.7633862173, 0.3075441467, 0.0, 0.0, -0.0328947818]
])
self.final[3:8] = self.final_C[:5, 0]
self.final[8:13] = self.final_C[5:, 1]
self.wf.normalize_structures()
self.xfg = VBMinimizer(self.wf)
def test_polarizability_nobonds(self):
Aab = self.m.Aab[0] + self.m.dAab[0]/2
noa = self.m.noa
Acmp = full.matrix((6, noa ))
Aa = Aab.sum(axis=3).view(full.matrix)
ab = 0
for a in range(noa):
Acmp[:, a,] = Aa[:, :, a].pack()
# atoms
self.assert_allclose(Acmp, ref.Aa, atol=0.07)
def get_molecule_info(self):
"""
` Get overlap, nuclear charges and coordinates from AOONEINT
"""
#
# Data from the ISORDK section in AOONEINT
#
isordk = one.readisordk(filename=self.aooneint)
#
# Number of nuclei
#
N = isordk["nucdep"]
#
# MXCENT , Fix dimension defined in nuclei.h
#
mxcent = len(isordk["chrn"])
#
# Nuclear charges
#
self.Z = full.matrix((N, ))
self.Z[:] = isordk["chrn"][:N]
#
# Nuclear coordinates
#
R = full.matrix((mxcent * 3, ))
R[:] = isordk["cooo"][:]
self.R = R.reshape((mxcent, 3), order="F")[:N, :]
#
# Bond center matrix and half bond vector
#
noa = self.noa
self.Rab = full.matrix((noa, noa, 3))
self.dRab = full.matrix((noa, noa, 3))
for a in range(noa):
for b in range(noa):
self.Rab[a, b, :] = (self.R[a, :] + self.R[b, :]) / 2
self.dRab[a, b, :] = (self.R[a, :] - self.R[b, :]) / 2
def mkB3(avecs, bvecs, unrest):
dim = len(avecs)
B = full.matrix((dim + 1, dim + 1))
for i in range(dim):
for j in range(dim):
if unrest:
B[i, j] = -(avecs[i] @ avecs[j]).tr() - (
bvecs[i] @ bvecs[j]).tr()
else:
vecsi = avecs[i] + bvecs[i]
vecsj = avecs[j] + bvecs[j]
B[i, j] = (vecsi @ vecsj.T).tr()
B[i, dim] = -1
B[dim, i] = -1
return B
def pv(self):
"""Get two-electron density"""
if self._pv is None:
with FortranBinary(self.name) as fb:
fb.find(self.ifclabel)
for i in range(7):
fb.next()
m2ashy = max(self.nnashx**2, 4)
dbl = fb.readbuf(m2ashy, self.FLOAT)
self._pv = full.matrix((self.nnashx, self.nnashx))
n = 0
for i in range(self.nnashx):
for j in range(self.nnashx):
self._pv[j, i] = dbl[n]
n += 1
assert n == self.nnashx**2
return self._pv
def test_polarizability_allbonds_atoms(self, molfrag):
Aab = molfrag.Aab[0] # + molfrag.dAab[0]
noa = molfrag.noa
Acmp = full.matrix(ref.Aab.shape)
ab = 0
for a in range(noa):
for b in range(a):
Acmp[:, ab] = (Aab[:, :, a, b] + Aab[:, :, b, a]).pack()
ab += 1
Acmp[:, ab] = Aab[:, :, a, a].pack()
ab += 1
# atoms
self.assert_allclose(ref.Aab[:, 0], Acmp[:, 0], atol=0.005)
self.assert_allclose(ref.Aab[:, 2], Acmp[:, 2], atol=0.005)
self.assert_allclose(ref.Aab[:, 5], Acmp[:, 5], atol=0.005)
def test_polarizability_allbonds_bonds(self, molfrag):
Aab = molfrag.Aab[0] + molfrag.dAab[0] / 2
noa = molfrag.noa
Acmp = full.matrix(ref.Aab.shape)
ab = 0
for a in range(noa):
for b in range(a):
Acmp[:, ab] = (Aab[:, :, a, b] + Aab[:, :, b, a]).pack()
ab += 1
Acmp[:, ab] = Aab[:, :, a, a].pack()
ab += 1
# atoms
self.assert_allclose(ref.Aab[:, 1], Acmp[:, 1], atol=0.150, err_msg="H1O")
self.assert_allclose(ref.Aab[:, 3], Acmp[:, 3], atol=0.150, err_msg="H2O")
self.assert_allclose(ref.Aab[:, 4], Acmp[:, 4], atol=0.005, err_msg="H2H1")
def read(label="OVERLAP", filename="AOONEINT"):
"""Read integral for label"""
lbuf = 600
#
# Initialize
#
unlabeled = readhead(filename)
nsym = unlabeled["nsym"]
nbas = unlabeled["naos"]
INT = unlabeled["int_fmt"]
FLOAT = unlabeled["float_fmt"]
nnbast = 0
for nbasi in nbas:
nnbast += nbasi * (nbasi + 1) // 2
s = full.matrix((nnbast, ))
#
# Open file, locate label
#
aooneint = FortranBinary(filename)
aooneint.find(label)
#
# Loop over records
#
for rec in aooneint:
buf = rec.read(lbuf, FLOAT)
ibuf = rec.read(lbuf, INT)
length, = rec.read(1, INT)
if length < 0:
break
for i, b in zip(ibuf[:length], buf[:length]):
s[i - 1] = b
_S = blocked.triangular(nbas)
off = 0
for isym in range(nsym):
nbasi = nbas[isym] * (nbas[isym] + 1) // 2
_S.subblock[isym] = np.array(s[off:off + nbasi]).view(full.triangular)
off += nbasi
# aooneint.close()
return _S
def cmo(F, S, filename="AOONEINT"):
"""
Return MO coefficients from diagonalization of a provided Fock matrix F, an
optional overlap matrix S. The returned MOs are normalized and ordered with
respect to eigenvalue
"""
nbast = F.shape[0]
e, V = F.eigvec(S)
C = full.matrix((nbast, nbast))
N2 = (V.T @ S @ V).diagonal()
for i in range(nbast):
Ni = 1.0 / sqrt(N2[i])
C[:, i] = V[:, i] * Ni
rephase_columns(C, inplace=True)
#
# Finish off with Gram Schmidt because degenerate orbitals are not
# properly orthonormalized
#
C = C.GS(S)
#
#
return C
import numpy
from util.full import matrix
d = matrix((24, 24))
f = matrix((24, 24))
d[:11, :5] = numpy.array([
[ 2.00160706, -0.01036708, -0.00181429, 0.00677187, -0.00241386],
[-0.01036708, 1.69869523, -0.09633899, -0.27114604, -0.10920586],
[-0.00181429, -0.09633899, 0.08874347, -0.30570693, 0.01352778],
[ 0.00677187, -0.27114604, -0.30570693, 1.28122865, -0.01084007],
[-0.00241386, -0.10920586, 0.01352778, -0.01084007, 0.00767067],
[ 0.00006681, -0.00823265, -0.00653547, 0.02831209, -0.00008716],
[-0.00018734, -0.00235146, 0.00228316, -0.00791291, 0.00034070],
[-0.00389444, 0.35145795, -0.19737922, 0.62805954, -0.03821221],
[ 0.00283175, -0.18331099, 0.08114304, -0.24351160, 0.01800991],
[ 0.00146798, -0.04495921, 0.01951429, -0.05823360, 0.00438197],
[ 0.00123945, -0.03923112, 0.00210759, 0.00671245, 0.00251033]
])
d[:11, 5:10] = numpy.array([
[ 0.00006681, -0.00018734, -0.00389444, 0.00283175, 0.00146798],
[-0.00823265, -0.00235146, 0.35145795, -0.18331099, -0.04495921],
[-0.00653547, 0.00228316, -0.19737922, 0.08114304, 0.01951429],
[ 0.02831209, -0.00791291, 0.62805954, -0.24351160, -0.05823360],
[-0.00008716, 0.00034070, -0.03821221, 0.01800991, 0.00438197],
[ 0.00062869, -0.00016935, 0.01321749, -0.00506051, -0.00120868],
[-0.00016935, 0.00005876, -0.00506668, 0.00207976, 0.00050004],
[ 0.01321749, -0.00506668, 0.45083132, -0.18868220, -0.04545457],
[-0.00506051, 0.00207976, -0.18868220, 0.07988865, 0.01926631],
[-0.00120868, 0.00050004, -0.04545457, 0.01926631, 0.00464710],
def udiis(
Ca,
Cb,
na,
nb,
iters=10,
fock=jensen,
hfx=1,
threshold=1e-6,
maxerr=2,
unrest=False,
wrkdir="/tmp",
):
print(Ca, Cb)
saveD = 1
saveC = 0
E = 0
aooneint = os.path.join(wrkdir, "AOONEINT")
aotwoint = os.path.join(wrkdir, "AOTWOINT")
potnuc = one.readhead(aooneint)["potnuc"]
vecs = []
vecsa = []
vecsb = []
evecsa = []
evecsb = []
Eit = []
S = one.read("OVERLAP", aooneint).unpack().unblock()
h = S.I @ one.read("ONEHAMIL", aooneint).unpack().unblock()
Da = dens.C1D(Ca, na) @ S
Db = dens.C1D(Cb, nb) @ S
try:
for i in range(iters):
Da = dens.C1D(Ca, na) @ S
Db = dens.C1D(Cb, nb) @ S
print("D", (Da + Db) @ S.I)
(Fa, Fb), = two.fockab((Da, Db), hfx=hfx, filename=aotwoint)
Fa = h + S.I @ Fa
Fb = h + S.I @ Fb
E0 = E
E = ((Da @ (h + Fa)) + (Db @ (h + Fb))).tr() / 2 + potnuc
D = Da + Db
print("hd", (h @ D).tr(), h & D, h & D.T)
print("FD", Fa & Da)
Eit.append(E)
ga = Da @ Fa - Fa @ Da
gb = Db @ Fb - Fb @ Db
if unrest:
g2 = -(ga @ ga + gb @ gb)
else:
g2 = -(ga + gb) @ (ga + gb)
gn = math.sqrt(g2.tr())
print("%2d:E = %16.12f %16.5e %16.2e" % (i + 1, E, gn, E - E0))
if gn < threshold:
raise Converged(gn)
# if E > E0:
# raise Exception("Energy increase")
if unrest:
Ca = dens.cmo(Fa)
Cb = dens.cmo(Fb)
# Ca = Ca*Ua
# Cb = Cb*Ub
else:
Ca = dens.cmo(Feff(Da, Db, Fa, Fb), S)
Cb = Ca[:, :]
Da = dens.C1D(Ca, na) @ S
Db = dens.C1D(Cb, nb) @ S
if saveD:
vecsa.append(Da)
vecsb.append(Db)
evecsa.append(ga @ Da - Da @ ga)
evecsb.append(gb @ Db - Db @ gb)
elif saveC:
vecsa.append(Ca)
vecsb.append(Cb)
evecsa.append(ga)
evecsb.append(gb)
else:
vecsa.append(Fa)
vecsb.append(Fb)
evecsa.append(ga)
evecsb.append(gb)
edim = min(len(evecsa), maxerr)
eva = evecsa[-edim:]
evb = evecsb[-edim:]
fva = vecsa[-edim:]
fvb = vecsb[-edim:]
B = mkB3(eva, evb, unrest)
rhs = full.matrix((edim + 1, 1))
rhs[-1, 0] = -1
c = rhs / B
subvecsa = full.matrix(Fa.shape)
subvecsb = full.matrix(Fb.shape)
for j in range(edim):
subvecsa += c[j, 0] * fva[j]
subvecsb += c[j, 0] * fvb[j]
if saveD:
Da = subvecsa
Db = subvecsb
(Fa, Fb), = two.fockab((Da, Db), hfx=hfx, filename=aotwoint)
Fa = h + S.I @ Fa
Fb = h + S.I @ Fb
vecsa[i] = Da
vecsb[i] = Db
elif saveC:
Ca = subvecsa
Cb = subvecsb
Da = dens.C1D(Ca, na) @ S
Db = dens.C1D(Cb, nb) @ S
else:
Fa = subvecsa
Fb = subvecsb
Da = dens.C1D(Ca, na) @ S
Db = dens.C1D(Cb, nb) @ S
except Converged:
print("Converged after %d iterations\n" % (i + 1, ))
except Increase:
print("Ca Cb", Ca, Cb)
print("Da Db", Da, Db)
print("Na Nb", Da.tr(), Db.tr())
print("Fa Fb", Fa, Fb)
print("E1", (h * (Da + Db)).tr())
print("E2", (Fa * Da + Fb * Db).tr() / 2 - (h * (Da + Db)).tr() / 2)
print("E", E - potnuc)
def diis(
C,
nisht,
nasht,
iters=10,
fock=jensen,
hfx=1,
threshold=1e-6,
maxerr=2,
wrkdir="/tmp",
):
C1 = C
E = 0
aooneint = pathlib.Path(wrkdir) / "AOONEINT"
aotwoint = pathlib.Path(wrkdir) / "AOTWOINT"
potnuc = one.readhead(aooneint)["potnuc"]
vecs = []
evecs = []
h = one.read("ONEHAMIL", aooneint).unpack().unblock()
S = one.read("OVERLAP", aooneint).unpack().unblock()
try:
for i in range(iters):
Di, Da = dens.C2D(C, nisht, nasht)
D = Di + Da
Fc = h + two.fock(D, filename=aotwoint, hfx=hfx)
Fo = two.fock(Da, hfc=0, filename=aotwoint) + Fc
F = fock(S, Di, Da, Fc, Fo, C, h)
E0 = E
E = ((h + Fc) & D) / 2 + ((Fo - Fc) & Da) / 2 + potnuc
g = grad(S, C1, Di, Da, Fc, Fo)
# gao = gradao(S, C, Di, Da, Fc, Fo)
gn = gradvec(S, C, Di, Da, Fc, Fo, nisht, nasht).norm2()
gn /= math.sqrt(2)
print("%2d:E = %16.12f %16.5e %16.2e" % (i + 1, E, gn, E - E0))
if gn < threshold:
raise Converged(gn)
vecs.append(F)
evecs.append(g)
edim = min(len(evecs), maxerr)
ev = evecs[-edim:]
fv = vecs[-edim:]
B = mkB(ev)
rhs = full.matrix((edim + 1, 1))
rhs[-1, 0] = 1
c = rhs / B
subevecs = full.matrix(g.shape)
subvecs = full.matrix(F.shape)
for i in range(edim):
subevecs += c[i, 0] * ev[i]
subvecs += c[i, 0] * fv[i]
update = -subevecs
upd = update.lower()
upd.anti = 0
update = upd.unpack()
F = subvecs # +update
C = dens.cmo(F, S)
except Converged:
print("-Converged-")
except Stop:
print("-STOP-")
import numpy
from util.full import matrix
cmo = matrix((24, 24))
cmo[:11, :11] = numpy.array(
[[
1.00037005644774, 0.00213928142197, -0.00139645162733,
0.00250320614892, -0.00168365551156, 0.00000417179213,
-0.00010568751627, -0.00027311036476, 0.00056204660778,
0.00052477299313, 0.00045051613113
],
[
-0.00764995676695, 0.87372007927195, -0.11446369166089,
0.11081294767437, -0.06188049075196, 0.00122390477237,
-0.00288482651200, 0.31909593297047, -0.14943668512171,
-0.03635107656087, -0.02008905901125
],
[
0.00218188411380, -0.29318297900759, -0.17682717408706,
0.79267177820451, 0.00181832874368, 0.01768753372185,
-0.00458766924852, 0.35155848740093, -0.13271279540296,
-0.03165237343243, 0.00704103155682
],
[
0.05189274589511, -0.14332375175701, -0.90584515407463,
-0.28547304713507, -0.21170912054705, -0.00753222886420,
0.00920238615519, 0.10575589422514, 0.76987725358803,
-0.01621298099706, -0.01563551317394
],
[
0.06833791423126, 0.50854763250820, -0.61069110991343,
def setup_class(cls):
numpy.random.seed(0)
cls.beta = full.matrix((3, 6)).random()
cls.dipole = full.matrix(3).random()
def fockab(Da, Db, component, **kwargs):
""" Generate two-electron spin-orbit Fock(alpha,beta) matrix from
integral file AO2SOINT
Input: component 'x', 'y', or 'z'
Density matrices, tuple (Da, Db)
AO integral file, FortranBinary object, positioned
Output Fock matrics, tuple(Fa, Fb)
"""
hfc = kwargs.get('hfc', 1.0)
hfx = kwargs.get('hfx', 1.0)
Fa = matrix(Da.shape)
Fb = matrix(Db.shape)
for buf, ibuf in two.list_buffers(label='AO2SOINT', **kwargs):
for g, ig in zip(buf, ibuf):
if ig[0] == 0:
comp = "*xyz"[ig[1]]
else:
#print comp, ig, g, component
if comp != component:
continue
p, q, r, s = ig
s, r, q, p = (p - 1, q - 1, r - 1, s - 1)
if (p == q): g *= 0.5
j = hfc * g
x = 3 * hfx * g
#Fa[p,q]=(pq|rs)(2D+(r,s) + D-(r,s))
Fapq = j * (3 * (Da[r, s] - Da[s, r]) + Db[r, s] - Db[s, r])
Fa[p, q] += Fapq
Fa[q, p] += Fapq
#Fb[p,q]=(pq|rs)(-2D+(r,s) + D-(r,s))
Fbpq = j * (-(Da[r, s] - Da[s, r]) - 3 * (Db[r, s] - Db[s, r]))
Fb[p, q] += Fbpq
Fb[q, p] += Fbpq
#Fa[r,s]=(pq|rs)(2D-(p,p) + D+(p,q))
Fars = j * (3 * (Da[p, q] + Da[q, p]) - Db[p, q] - Db[q, p])
Fa[r, s] += Fars
Fa[s, r] -= Fars
#Fb[r,s]=(pq|rs)(2D+(p,q) - D-(p,q))
Fbrs = j * (Da[p, q] + Da[q, p] - 3 * (Db[p, q] + Db[q, p]))
Fb[r, s] += Fbrs
Fb[s, r] -= Fbrs
Fa[p, s] -= x * Da[r, q]
Fa[q, s] -= x * Da[r, p]
Fa[p, r] += x * Da[s, q]
Fa[q, r] += x * Da[s, p]
Fb[p, s] += x * Db[r, q]
Fb[q, s] += x * Db[r, p]
Fb[p, r] -= x * Db[s, q]
Fb[q, r] -= x * Db[s, p]
Fa[r, q] -= x * Da[p, s]
Fa[r, p] -= x * Da[q, s]
Fa[s, q] += x * Da[p, r]
Fa[s, p] += x * Da[q, r]
Fb[r, q] += x * Db[p, s]
Fb[r, p] += x * Db[q, s]
Fb[s, q] -= x * Db[p, r]
Fb[s, p] -= x * Db[q, r]
return (Fa, Fb)
1 1.481 0.000 -0.349 0.352 -0.153 0.000 0.127 -0.132 -0.000 -0.250 -0.445 0.000 -0.261 """ PA21 = """AU 3 2 1 1 1 0.000 0.000 0.698 -0.703 -0.000 0.000 -0.284 -3.293 0.000 -0.000 -4.543 -0.000 -4.005 3.466 1 -1.481 0.000 -0.349 0.352 0.153 0.000 0.127 -0.132 0.000 0.250 -0.445 0.000 -0.261 1.576 1 1.481 0.000 -0.349 0.352 -0.153 0.000 0.127 -0.132 -0.000 -0.250 -0.445 0.000 -0.261 1.576 """ PA22 = """AU 3 2 2 1 1 0.000 0.000 0.698 -0.703 -0.000 0.000 -0.284 -3.293 0.000 -0.000 -4.543 -0.000 -4.005 3.875 -0.000 -0.000 3.000 -0.000 3.524 1 -1.481 0.000 -0.349 0.352 0.153 0.000 0.127 -0.132 0.000 0.250 -0.445 0.000 -0.261 2.156 -0.000 1.106 1.051 -0.000 1.520 1 1.481 0.000 -0.349 0.352 -0.153 0.000 0.127 -0.132 -0.000 -0.250 -0.445 0.000 -0.261 2.156 -0.000 -1.106 1.051 -0.000 1.520 """ Bm = matrix((3, 6)) # matrix components (x, y, z)(T) * (xx xy xz yy yz zz) # xxz, zxx Bm[0, 2] = Bm[2, 0] = 14.74097586 # yyz, zyy Bm[1, 4] = Bm[2, 3] = 3.28345383 # zzz Bm[2, 5] = 9.20782221 OUTPUT_BY_ATOM_n0 = """\ --------------- Atomic domain 1 --------------- Domain center: 0.00000 0.00000 0.69801 Nuclear charge: 8.00000