def s2n(N, tmpdir='/tmp', Sg=1, Sv=1):
"""
S[2]*N linear transformation:
<[q,k]> = <[E(Sg)_{ij}, k_{kl}, E(Sv)_{kl}]> =
= k_{kl} [E_{il}d(kj) - E(kj)d(il)]
= k(jl)E(SgSv)(il) - k(ki)E(SgSv)(kj)
= D(SgSv)k.T(ij) - k.TD(SgSv)(ij)
= [D(SgSv), k.T](ij)
"""
SIRIFC = os.path.join(tmpdir, 'SIRIFC')
AOONEINT = os.path.join(tmpdir, 'AOONEINT')
AOTWOINT = os.path.join(tmpdir, 'AOTWOINT')
LUINDF = os.path.join(tmpdir, 'LUINDF')
ifc = sirifc.sirifc(SIRIFC)
cmo = ifc.cmo.unblock()
S = one.read('OVERLAP', filename=AOONEINT).unblock().unpack()
da, db = dens.Dab(SIRIFC)
kN = rspvec.tomat(N, ifc, tmpdir=tmpdir).T
kn = cmo*kN*cmo.T
dak = (kn.T*S*da - da*S*kn.T)
dbk = (kn.T*S*db - db*S*kn.T)*Sv
gv = -rspvec.tovec(cmo.T*S*(dak+Sg*dbk)*S*cmo, ifc)
return gv
def count_electrons(bas_file, quad_file):
from daltools import dens
nel = 0
cfunc = set_cfunc(bas_file)
Da, Db = dens.Dab()
D = Da + Db
for x, y, z, w in quaditer(quad_file):
f = eval_cfunc(cfunc, (x, y, z))
n = f & (D * f)
nel += w * n
return nel
def integrator(*args, **kwargs):
"Integrate list of args, defined as functionals of density"
from daltools import dens
bf = kwargs['bf']
qf = kwargs['qf']
cfunc = set_cfunc(bf)
Da, Db = dens.Dab()
res = [0 for a in args]
for x, y, z, w in quaditer(qf):
cx = eval_cfunc(cfunc, (x, y, z))
rhoax = cx & (Da * cx)
rhobx = cx & (Db * cx)
for i, a in enumerate(args):
res[i] += w * a(rhoax, rhobx)
return res
def main(*args, **kwargs):
labs = args
tmpdir = kwargs.get("tmpdir", ".")
ranks = kwargs.get('rank', (0, 0, 0))
pars = [ (-1)**r for r in ranks]
ifc = sirifc.sirifc(os.path.join(tmpdir, "SIRIFC"))
cmo = ifc.cmo.unblock()
AOONEINT = os.path.join(tmpdir, "AOONEINT")
AOPROPER = os.path.join(tmpdir, "AOPROPER")
RSPVEC = os.path.join(tmpdir, "RSPVEC")
vecs = rspvec.read(*labs, propfile=RSPVEC)[0]
kappa = [rspvec.tomat(vec, ifc).T for vec in vecs]
kappa[0] = kappa[0].T
a, b, c = [cmo.T*x*cmo for x in prop.read(*labs, filename=AOPROPER)]
NA = vecs[0]
kA, kB, kC = kappa
pA, pB, pC = [{ "lab":lab, "rank":rank, 'kappa':k} for lab, rank, k in zip(labs, ranks, kappa)]
da, db = dens.Dab(ifc_=ifc)
d = da + db
S = one.read(label = "OVERLAP", filename = AOONEINT).unblock().unpack()
D = cmo.T*S*d*S*cmo
E3BC = E3(pB, pC, ifc, tmpdir=tmpdir)
AE3BC = -NA&E3BC
B2C = (-(kA^(kC^b))&D)
C2B = (-(kA^(kB^c))&D)
A2B = (.5*(kC^(kB^a))&D)
A2C = (.5*(kB^(kC^a))&D)
#print "E3BC",E3BC
val = AE3BC
print("E3 %14.8f %14.8f" % (AE3BC, val))
val += B2C
print("B2C %14.8f %14.8f" % (B2C, val))
val += C2B
print("C2B %14.8f %14.8f" % (C2B, val))
val += A2B
print("A2B %14.8f %14.8f" % (A2B, val))
val += A2C
print("A2C %14.8f %14.8f" % (A2C, val))
return val
def A2B(*args, **kwargs):
pA, pB, ifc = args
tmpdir = kwargs.get("tmpdir", ".")
AOONEINT = os.path.join(tmpdir, "AOONEINT")
S = one.read(label = "OVERLAP", filename = AOONEINT).unblock().unpack()
cmo = ifc.cmo.unblock()
mA = pA["matrix"]
kB = cmo*pB["kappa"]*cmo.T
BA = S*kB*mA - mA*kB*S
da, db = dens.Dab(ifc_=ifc)
G = cmo.T*(S*(da*BA.T + db*BA.T) - (BA.T*da + BA.T*db)*S)*cmo
Gv = rspvec.tovec(G, ifc)
return Gv
def B2C(*args, **kwargs):
pB, pC, ifc = args
tmpdir = kwargs.get("tmpdir", ".")
AOONEINT = os.path.join(tmpdir, "AOONEINT")
S = one.read(label = "OVERLAP", filename = AOONEINT).unblock().unpack()
cmo = ifc.cmo.unblock()
mB = pB["matrix"]
mC = pC["matrix"]
kB = cmo*pB["kappa"]*cmo.T
kC = cmo*pC["kappa"]*cmo.T
kBmC = S*kB*mC - mC*kB*S
kCmB = S*kC*mB - mB*kC*S
BC = kBmC + kCmB
da, db = dens.Dab(ifc_=ifc)
G = cmo.T*(S*(da*BC.T + db*BC.T) - (BC.T*da + BC.T*db)*S)*cmo
Gv = rspvec.tovec(G, ifc)
return Gv
def setUp(self):
n, e = os.path.splitext(__file__)
self.suppdir = n + ".d"
self.A = "XDIPLEN"
self.B = "YDIPLEN"
self.C = "XDIPLEN"
AOONEINT = os.path.join(self.suppdir, 'AOONEINT')
S = one.read(label="OVERLAP", filename=AOONEINT).unblock().unpack()
SIRIFC = os.path.join(self.suppdir, 'SIRIFC')
self.ifc = sirifc.sirifc(SIRIFC)
cmo = self.ifc.cmo.unblock()
da, db = dens.Dab(ifc_=self.ifc)
self.D = cmo.T * S * (da + db) * S * cmo
RSPVEC = os.path.join(self.suppdir, 'RSPVEC')
rspvecs = rspvec.read(self.A, self.B, self.C, propfile=RSPVEC)
self.NA = rspvecs[(self.A, 0)]
self.NB = rspvecs[(self.B, 0)]
self.NC = rspvecs[(self.C, 0)]
self.kA = rspvec.tomat(self.NA, self.ifc, tmpdir=self.suppdir)
self.kB = rspvec.tomat(self.NB, self.ifc, tmpdir=self.suppdir).T
self.kC = rspvec.tomat(self.NC, self.ifc, tmpdir=self.suppdir).T
AOPROPER = os.path.join(self.suppdir, 'AOPROPER')
#a, b, c = [cmo.T*x*cmo for x in prop.read(A, B, C, filename=AOPROPER, unpack=True)]
global pmat
pmat = prop.read(self.A,
self.B,
self.C,
filename=AOPROPER,
unpack=True)
self.a, self.b, self.c = [cmo.T * x * cmo for x in pmat]
def get_densities(SIRIFC):
da, db = [d.view(util.full.matrix) for d in dens.Dab(SIRIFC)]
return da, db
def get_density_matrix(self):
D = sum(dens.Dab(filename=self.sirifc))
return D
def E3(pB, pC, ifc, **kwargs):
""" Emulate the so called E3 contribution to a quadratic response function
<<A; B, C>> = NA E3 (NB NC + NC NB) + A2 (NB NC + NC NB) + NA (B2 NC + C2 NB)
Emulation of current Dalton implementation in terms of high spin fock matrices
Closed and open shell matrices
Dc = inactive
Do = -active
Fc = Fa+Q
Fo = ? CHECK
Formulas
1/2*[qa, [kb, [kc, H]]] + P(b,c)
[kc, H] = (p~q|rs)H(Sc, 0) + (pq|r~s) H(0, Sc)
[kb, [kc, H]]
= (p~~q|rs)H(SbSc, 0) + (p~q|r~s) H(Sb, Sc)
+ (p~q|r~s)H(Sc, Sb) + (pq|r~~s) H(0, SbSc)
and for
H(S1, S2) generates Fock from (D(S1) g D(S2) - Da g Da - Db g Db
F(S1, S2) = E(S1) g D(S2) - D(S1) g E(S2) - Ea g Da - Da g Ea - Eb g Db - Db g Eb
= Ea [ g D(S2) - D(S1) g - g Da - Da g ]
+ Eb [ S1 g D(S2) - D(S1) g S2 - g Db - Db g ]
"""
tmpdir = kwargs.get('tmpdir', '/tmp')
AOONEINT = os.path.join(tmpdir, "AOONEINT")
h = one.read(label='ONEHAMIL', filename=AOONEINT).unpack().unblock()
S = one.read(label='OVERLAP', filename=AOONEINT).unblock().unpack()
AOTWOINT = os.path.join(tmpdir, "AOTWOINT")
kwargs['filename'] = AOTWOINT
cmo = ifc.cmo.unblock()
kB = cmo*pB["kappa"]*cmo.T
kC = cmo*pC["kappa"]*cmo.T
kB_ = kB*S
_kB = S*kB
kC_ = kC*S
_kC = S*kC
sB = pB.get("spin", 1)
sC = pC.get("spin", 1)
#
# Fock matrices
#
da, db = dens.Dab(ifc_=ifc)
(fa, fb), = two.fockab((da, db), **kwargs)
fa += h
fb += h
Bfa, Bfb = [_kB*f - f*kB_ for f in (fa, sB*fb)]
Cfa, Cfb = [_kC*f - f*kC_ for f in (fa, sC*fb)]
BCfa, BCfb = [_kB*Cf - Cf*kB_ for Cf in (Cfa, sB*Cfb)]
CBfa, CBfb = [_kC*Bf - Bf*kC_ for Bf in (Bfa, sC*Bfb)]
daB, dbB = [_kB.T*d - d*kB_.T for d in (da, sB*db)]
(faB, fbB), = two.fockab((daB, dbB), **kwargs)
CfaB, CfbB = [_kC*fB - fB*kC_ for fB in (faB, sC*fbB)]
daC, dbC = [_kC.T*d - d*kC_.T for d in (da, sC*db)]
(faC, fbC), = two.fockab((daC, dbC), **kwargs)
BfaC, BfbC = [_kB*fC - fC*kB_ for fC in (faC, sB*fbC)]
daBC, dbBC = (_kB.T*dC - dC*kB_.T for dC in (daC, sB*dbC))
daCB, dbCB = (_kC.T*dB - dB*kC_.T for dB in (daB, sC*dbB))
daBC = 0.5*(daBC + daCB)
dbBC = 0.5*(dbBC + dbCB)
(faBC, fbBC), = two.fockab((daBC, dbBC), **kwargs)
#
# Add all focks
#
fa = faBC + BfaC + CfaB + .5*(BCfa + CBfa)
fb = fbBC + BfbC + CfbB + .5*(BCfb + CBfb)
G = cmo.T*(S*(da*fa.T + db*fb.T) - (fa.T*da + fb.T*db)*S)*cmo
#G = cmo.T*(S*da*fa.T - fa.T*da *S)*cmo + \
# cmo.T*(S*db*fb.T - fb.T*db *S)*cmo
Gv = rspvec.tovec(G, ifc)
#print Gv
return Gv
