def co_contravariant_transition_delta(self):
"""
Return mixed covariant-contravariant ao delta matrix
"""
S = Nod.S
I = full.unit(S.shape[0])
delta_aa = (I - S*d for d in self.transition_ao_density)
return tuple(delta_aa)
def Feff(Da, Db, Fa, Fb):
I_n = full.unit(len(Da))
D = Da + Db
Ds = Da - Db
ID = I_n - D
Fs = Fa - Fb
F = ((Fa + Fb) + Ds * Fs * ID + ID * Fs * Ds) / 2
return F
def test_Dab(self):
na = 2
nb = 1
C = full.unit(3)
da, db = dens.C2Dab(C, na, nb)
daref = full.init([[1.0, 0.0, 0], [0.0, 1.0, 0.0], [0.0, 0.0, 0.0]])
dbref = full.init([[1.0, 0.0, 0], [0.0, 0.0, 0.0], [0.0, 0.0, 0.0]])
np.testing.assert_almost_equal(da, daref)
np.testing.assert_almost_equal(db, dbref)
def project_occupied_from_virtual(self, S2):
#
# Project occupied out of virtual
#
vpa = [c - len(o) for c, o in zip(self.cpa, self.opa)]
nocc = sum(len(occ) for occ in self.opa)
occdim = (nocc, sum(vpa))
S2sb = S2.subblocked(occdim, occdim)
nbf = S2.shape[0]
T3sb = full.unit(nbf).subblocked(occdim, occdim)
T3sb.subblock[0][1] = -S2sb.subblock[0][1]
T3 = T3sb.unblock()
return T3
def P2(self):
vpa = []
adim = []
for at in range(self.noa):
vpa.append(self.cpa[at]-len(self.opa[at]))
adim.append(len(self.opa[at]))
adim.append(vpa[at])
#
# dimensions for permuted basis
#
pdim = []
for at in range(self.noa):
pdim.append(len(self.opa[at]))
for at in range(self.noa):
pdim.append(vpa[at])
P2 = subblocked.matrix(adim, pdim)
for i in range(0, len(adim), 2):
P2.subblock[i][i//2] = full.unit(adim[i])
for i in range(1, len(adim), 2):
P2.subblock[i][self.noa+(i-1)//2] = full.unit(adim[i])
P2 = P2.unblock()
return P2
def setUp(self):
self.tmp = os.path.join(os.path.dirname(__file__), 'test_h2_ab')
self.qc = QuantumChemistry.get_factory('Dalton', tmpdir=self.tmp)
def tmp(fil):
return os.path.join(self.tmp, fil)
vb.Nod.tmpdir = self.tmp
vb.Nod.C = full.unit(2)
vb.Nod.S = self.qc.get_overlap()
self.wf = vb.WaveFunction(
[vb.Structure(
[vb.Nod([0], [0]), vb.Nod([1], [1])],
[1.0, 1.0]
),
vb.Structure(
[vb.Nod([0], [1]), vb.Nod([1], [0])],
[1.0, 1.0]
)
],
[1.0, 1.0],
tmpdir = self.tmp
)
def setUp(self):
"""
Model the fci result as a wb wave function
WF = cg(1sg|1sg) + cu(1su|1su)
1sg=Ng(a+b) norm Ng=1/sqrt(2(1+Sab))
1su=Nu(a-b) norm Nu=1/sqrt(2(1-Sab))
WF = cg*Ng**2(a+b|a+b) + cu*Nu**2(a-b|a-b)
= (cg*Ng**2+cu*Nu**2)[(a|a) + (b|b)]
+ (cg*Ng**2-cu*Nu**2)[(a|b) + (b|a)]
"""
VBTest.setUp(self, 'test_h2_ab')
#
# Setup VB wave function
#
Nod.C=full.unit(2)
ion_a = Structure([Nod([0],[0])], [1.0], normalize=False)
ion_b = Structure([Nod([1],[1])], [1.0], normalize=False)
import math
N = math.sqrt(0.5)
cov=Structure([Nod([0],[1]),Nod([1],[0])], [N, N], normalize=False)
cg = 0.99364675
cu = -0.11254389
Sab = 0.65987313
Ng2=1/(2*(1+Sab))
Nu2=1/(2*(1-Sab))
cion = cg*Ng2 + cu*Nu2
ccov = (cg*Ng2 - cu*Nu2)/N
self.WF=WaveFunctionND(
[cov, ion_a, ion_b],[ccov, cion, cion],
tmpdir=self.tmpdir
)
def gram_schmidt_atomic_blocks(self, S):
cpa = self.cpa
opa = self.opa
#
# 1. orthogonalize in each atomic block
#
nbf = sum(cpa)
#
# obtain atomic blocking
#
noa = len(cpa)
nocc = 0
for at in range(noa):
nocc += len(opa[at])
Satom = S.block(cpa, cpa)
Ubl = full.unit(nbf).subblocked((nbf,), cpa)
#
# Diagonalize atom-wise
#
T1 = blocked.BlockDiagonalMatrix(cpa, cpa)
for at in range(noa):
T1.subblock[at] = Ubl.subblock[0][at].GST(S)
T1 = T1.unblock()
return T1
def test_S4(self):
T = self.T.T
S4 = T.T*self.S*T
self.assert_allclose(S4, full.unit(58))
def test_s2n_S():
refs2 = matrix.diag([2., -2.])
s2 = [oli.s2n(n, tmpdir=suppdir) for n in unit(2)]
assert_(s2, refs2)
def test_unit2(self):
identity = init([[2, 0, 0], [0, 2, 0], [0, 0, 2]])
np.testing.assert_almost_equal(unit(3, factor=2), identity)
def test_unit(self):
identity = init([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
np.testing.assert_almost_equal(unit(3), identity)
def test_S4(self, transformer):
T = transformer.T
S4 = T.T * transformer.S * T
self.assert_allclose(S4, full.unit(58))
def test_e2n_S():
refe2 = init([[0.91587038, -0.00000000], [0.00000000, 0.91587038]])
e2 = init([oli.e2n(n, tmpdir=suppdir) for n in unit(2)])
assert_(e2, refe2)
def test_e2n_S():
refe2 = init([[0.78643356, -0.50624296], [-0.50624296, 0.78643356]])
e2 = [oli.e2n(n, tmpdir=suppdir) for n in unit(2)]
assert_(e2, refe2)
def test_s2n_S():
refs2 = matrix.diag([1, -1])
s2 = init([oli.s2n(n, tmpdir=suppdir) for n in unit(2)])
assert_(s2, refs2)
def test_e2n_S():
refe2 = init([[-0.22605236, 0.50624296], [0.50624296, -0.22605236]])
e2 = init([oli.e2n(n, tmpdir=suppdir, Sg=-1, Sv=-1) for n in unit(2)])
assert_(e2, refe2)
