def init_amps(self, eris):
time0 = time.clock(), time.time()
nocc = self.nocc()
nvir = self.nmo() - nocc
nkpts = self.nkpts
t1 = numpy.zeros((nkpts,nocc,nvir), dtype=numpy.complex128)
t2 = numpy.zeros((nkpts,nkpts,nkpts,nocc,nocc,nvir,nvir), dtype=numpy.complex128)
self.emp2 = 0
foo = eris.fock[:,:nocc,:nocc].copy()
fvv = eris.fock[:,nocc:,nocc:].copy()
eris_oovv = eris.oovv.copy()
eia = numpy.zeros((nocc,nvir))
eijab = numpy.zeros((nocc,nocc,nvir,nvir))
kconserv = tools.get_kconserv(self._scf.cell,self.kpts)
for ki in range(nkpts):
for kj in range(nkpts):
for ka in range(nkpts):
kb = kconserv[ki,ka,kj]
for i in range(nocc):
for a in range(nvir):
eia[i,a] = foo[ki,i,i] - fvv[ka,a,a]
for j in range(nocc):
for b in range(nvir):
eijab[i,j,a,b] = ( foo[ki,i,i] + foo[kj,j,j]
- fvv[ka,a,a] - fvv[kb,b,b] )
t2[ki,kj,ka,i,j,a,b] = eris_oovv[ki,kj,ka,i,j,a,b]/eijab[i,j,a,b]
t2 = numpy.conj(t2)
self.emp2 = 0.25*numpy.einsum('pqrijab,pqrijab',t2,eris_oovv).real
self.emp2 /= nkpts
logger.info(self, 'Init t2, MP2 energy = %.15g', self.emp2.real)
logger.timer(self, 'init mp2', *time0)
print "MP2 energy =", self.emp2
return self.emp2, t1, t2
def __init__(self, mf, frozen=0, mo_coeff=None, mo_occ=None):
if mo_coeff is None: mo_coeff = mf.mo_coeff
if mo_occ is None: mo_occ = mf.mo_occ
self.mol = mf.mol
self._scf = mf
self.verbose = self.mol.verbose
self.stdout = self.mol.stdout
self.max_memory = mf.max_memory
self.frozen = frozen
##################################################
# don't modify the following attributes, they are not input options
self.kpts = mf.kpts
self.mo_energy = mf.mo_energy
self.nkpts = len(self.kpts)
self.kconserv = tools.get_kconserv(mf.cell, mf.kpts)
self.mo_energy = mf.mo_energy
self.mo_coeff = mo_coeff
self.mo_occ = mo_occ
self._nocc = None
self._nmo = None
self.emp2 = None
self.e_corr = None
self.t2 = None
self._keys = set(self.__dict__.keys())
def cc_Wovvo(cc,t1,t2,eris):
nkpts, nocc, nvir = t1.shape
kconserv = tools.get_kconserv(cc._scf.cell, cc.kpts)
eris_ovvo = numpy.zeros(shape=(nkpts,nkpts,nkpts,nocc,nvir,nvir,nocc),dtype=t2.dtype)
eris_oovo = numpy.zeros(shape=(nkpts,nkpts,nkpts,nocc,nocc,nvir,nocc),dtype=t2.dtype)
for km in range(nkpts):
for kb in range(nkpts):
for ke in range(nkpts):
kj = kconserv[km,ke,kb]
# <mb||je> -> -<mb||ej>
eris_ovvo[km,kb,ke] = -eris.ovov[km,kb,kj].transpose(0,1,3,2)
# <mn||je> -> -<mn||ej>
# let kb = kn as a dummy variable
eris_oovo[km,kb,ke] = -eris.ooov[km,kb,kj].transpose(0,1,3,2)
Wmbej = eris_ovvo.copy()
for km in range(nkpts):
for kb in range(nkpts):
for ke in range(nkpts):
kj = kconserv[km,ke,kb]
Wmbej[km,kb,ke] += einsum('jf,mbef->mbej',t1[kj,:,:],eris.ovvv[km,kb,ke])
Wmbej[km,kb,ke] += -einsum('nb,mnej->mbej',t1[kb,:,:],eris_oovo[km,kb,ke])
for kn in range(nkpts):
kf = kconserv[km,ke,kn]
Wmbej[km,kb,ke] += -0.5*einsum('jnfb,mnef->mbej',t2[kj,kn,kf],
eris.oovv[km,kn,ke])
if kn == kb and kf == kj:
Wmbej[km,kb,ke] += -einsum('jf,nb,mnef->mbej',t1[kj],t1[kn],
eris.oovv[km,kn,ke])
return Wmbej
def init_amps(self, eris):
time0 = time.clock(), time.time()
nocc = self.nocc()
nvir = self.nmo() - nocc
nkpts = self.nkpts
t1 = numpy.zeros((nkpts,nocc,nvir), dtype=numpy.complex128)
t2 = numpy.zeros((nkpts,nkpts,nkpts,nocc,nocc,nvir,nvir), dtype=numpy.complex128)
self.emp2 = 0
foo = eris.fock[:,:nocc,:nocc].copy()
fvv = eris.fock[:,nocc:,nocc:].copy()
eris_oovv = eris.oovv.copy()
eia = numpy.zeros((nocc,nvir))
eijab = numpy.zeros((nocc,nocc,nvir,nvir))
kconserv = tools.get_kconserv(self._scf.cell,self.kpts)
for ki in range(nkpts):
for kj in range(nkpts):
for ka in range(nkpts):
kb = kconserv[ki,ka,kj]
for i in range(nocc):
for a in range(nvir):
eia[i,a] = foo[ki,i,i] - fvv[ka,a,a]
for j in range(nocc):
for b in range(nvir):
eijab[i,j,a,b] = ( foo[ki,i,i] + foo[kj,j,j]
- fvv[ka,a,a] - fvv[kb,b,b] )
t2[ki,kj,ka,i,j,a,b] = eris_oovv[ki,kj,ka,i,j,a,b]/eijab[i,j,a,b]
t2 = numpy.conj(t2)
self.emp2 = 0.25*numpy.einsum('pqrijab,pqrijab',t2,eris_oovv).real
self.emp2 /= nkpts
logger.info(self, 'Init t2, MP2 energy = %.15g', self.emp2.real)
logger.timer(self, 'init mp2', *time0)
print "MP2 energy =", self.emp2
return self.emp2, t1, t2
def __init__(self, mf, frozen=[], mo_energy=None, mo_coeff=None, mo_occ=None):
pyscf.cc.ccsd.CCSD.__init__(self, mf, frozen, mo_energy, mo_coeff, mo_occ)
self.kpts = mf.kpts
self.nkpts = len(self.kpts)
self.kconserv = tools.get_kconserv(mf.cell, mf.kpts)
self.khelper = kpoint_helper.unique_pqr_list(mf.cell, mf.kpts)
self.made_ee_imds = False
self.made_ip_imds = False
self.made_ea_imds = False
def __init__(self, mf, frozen=0, mo_coeff=None, mo_occ=None):
assert (isinstance(mf, scf.khf.KSCF))
pyscf.cc.ccsd.CCSD.__init__(self, mf, frozen, mo_coeff, mo_occ)
self.max_space = 20
self._keys = self._keys.union(['max_space'])
self.kpts = mf.kpts
self.mo_energy = mf.mo_energy
self.nkpts = len(self.kpts)
self.kconserv = tools.get_kconserv(mf.cell, mf.kpts)
self.khelper = kpoint_helper.unique_pqr_list(mf.cell, mf.kpts)
self.made_ee_imds = False
self.made_ip_imds = False
self.made_ea_imds = False
self.diis = None
def __init__(self, kmf, frozen=0, mo_coeff=None, mo_occ=None):
if frozen != 0:
raise NotImplementedError
self._scf = kmf
self.kpts = kmf.kpts
self.nkpts = len(kmf.kpts)
self.kconserv = tools.get_kconserv(kmf.cell, kmf.kpts)
self.diis = None
self.khelper = kpts_helper.KptsHelper(kmf.cell, kmf.kpts)
self.verbose = kmf.verbose
if mo_coeff is None: mo_coeff = kmf.mo_coeff
if mo_occ is None: mo_occ = kmf.mo_occ
self.mo_coeff = mo_coeff
self.mo_occ = mo_occ
self.mo_energy = kmf.mo_energy
self.max_cycle = kmf.max_cycle
self.conv_tol = kmf.conv_tol
def check_antisymm_34(cc, kpts, integrals):
kconserv = tools.get_kconserv(cc._scf.cell, cc.kpts)
nkpts = len(kpts)
diff = 0.0
for kp in range(nkpts):
for kq in range(nkpts):
for kr in range(nkpts):
ks = kconserv[kp, kr, kq]
for p in range(integrals.shape[3]):
for q in range(integrals.shape[4]):
for r in range(integrals.shape[5]):
for s in range(integrals.shape[6]):
pqrs = integrals[kp, kq, kr, p, q, r, s]
pqsr = integrals[kp, kq, ks, p, q, s, r]
cdiff = numpy.linalg.norm(pqrs + pqsr).real
print "AS diff = %.15g" % cdiff, pqrs, pqsr, kp, kq, kr, ks, p, q, r, s
diff = max(diff, cdiff)
print "antisymmetrization : max diff = %.15g" % diff
def check_antisymm_34( cc, kpts, integrals ):
kconserv = tools.get_kconserv(cc._scf.cell,cc.kpts)
nkpts = len(kpts)
diff = 0.0
for kp in range(nkpts):
for kq in range(nkpts):
for kr in range(nkpts):
ks = kconserv[kp,kr,kq]
for p in range(integrals.shape[3]):
for q in range(integrals.shape[4]):
for r in range(integrals.shape[5]):
for s in range(integrals.shape[6]):
pqrs = integrals[kp,kq,kr,p,q,r,s]
pqsr = integrals[kp,kq,ks,p,q,s,r]
cdiff = numpy.linalg.norm(pqrs+pqsr).real
print "AS diff = %.15g" % cdiff, pqrs, pqsr, kp, kq, kr, ks, p, q, r, s
diff = max(diff,cdiff)
print "antisymmetrization : max diff = %.15g" % diff
def get_TEI(self, ao2eo):
'''Get embedding TEI without density fitting'''
kconserv = pbctools.get_kconserv(self.cell, self.kpts)
Nkpts, nao, neo = ao2eo.shape
TEI = 0.0
for i in range(Nkpts):
for j in range(Nkpts):
for k in range(Nkpts):
l = kconserv[i, j, k]
ki, COi = self.kpts[i], ao2eo[i]
kj, COj = self.kpts[j], ao2eo[j]
kk, C*k = self.kpts[k], ao2eo[k]
kl, COl = self.kpts[l], ao2eo[l]
TEI += self.kmf.with_df.ao2mo([COi, COj, C*k, COl],
[ki, kj, kk, kl],
compact=False)
return TEI.reshape(neo, neo, neo, neo).real / Nkpts
def make_tau(cc, t2, t1a, t1b, fac=1., out=None):
nkpts, nocc, nvir = t1a.shape
tau1 = t2.copy()
kconserv = tools.get_kconserv(cc._scf.cell, cc.kpts)
for ki in range(nkpts):
for ka in range(nkpts):
for kj in range(nkpts):
kb = kconserv[ki,ka,kj]
tmp = numpy.zeros((nocc,nocc,nvir,nvir),dtype=t2.dtype)
if ki == ka and kj == kb:
tmp += einsum('ia,jb->ijab',t1a[ki],t1b[kj])
if ki == kb and kj == ka:
tmp -= einsum('ib,ja->ijab',t1a[ki],t1b[kj])
if kj == ka and ki == kb:
tmp -= einsum('ja,ib->ijab',t1a[kj],t1b[ki])
if kj == kb and ki == ka:
tmp += einsum('jb,ia->ijab',t1a[kj],t1b[ki])
tau1[ki,kj,ka] += fac*0.5*tmp
return tau1
def cc_Woooo(cc,t1,t2,eris):
nkpts, nocc, nvir = t1.shape
tau = make_tau(cc,t2,t1,t1)
Wmnij = eris.oooo.copy()
kconserv = tools.get_kconserv(cc._scf.cell, cc.kpts)
for km in range(nkpts):
for kn in range(nkpts):
# Since it's not enough just to switch i and j and need to create the k_i and k_j
# so that P(ij) switches both i,j and k_i,k_j
# t1[ k_j, j, e ] * v[ k_m, k_n, k_i, m, n, i, e ] -> tmp[ k_i, k_j, m, n, i, j ]
# Here, x = k_j and y = k_i
tmp = einsum('xje,ymnie->yxmnij',t1,eris.ooov[km,kn])
tmp = tmp - tmp.transpose(1,0,2,3,5,4)
for ki in range(nkpts):
kj = kconserv[km,ki,kn]
Wmnij[km,kn,ki] += tmp[ki,kj]
# Here, x = k_e
Wmnij[km,kn,ki] += 0.25*einsum('xijef,xmnef->mnij',
tau[ki,kj],eris.oovv[km,kn])
return Wmnij
def cc_Wvvvv(cc,t1,t2,eris):
nkpts, nocc, nvir = t1.shape
eris_vovv = - eris.ovvv.transpose(1,0,2,4,3,5,6)
tau = make_tau(cc,t2,t1,t1)
Wabef = eris.vvvv.copy()
kconserv = tools.get_kconserv(cc._scf.cell, cc.kpts)
for ka in range(nkpts):
for kb in range(nkpts):
for ke in range(nkpts):
km = kb
tmp = einsum('mb,amef->abef',t1[kb],eris_vovv[ka,km,ke])
km = ka
tmp -= einsum('ma,bmef->abef',t1[ka],eris_vovv[kb,km,ke])
Wabef[ka,kb,ke] += -tmp
# km + kn - ka = kb
# => kn = ka - km + kb
for km in range(nkpts):
kn = kconserv[ka,km,kb]
Wabef[ka,kb,ke] += 0.25*einsum('mnab,mnef->abef',tau[km,kn,ka],
eris.oovv[km,kn,ke])
return Wabef
def get_loc_TEI(self, ao2lo=None):
'''Get local TEI in R-space without density fitting'''
kconserv = pbctools.get_kconserv(self.cell, self.kpts)
if ao2lo is None: ao2lo = self.ao2lo
Nkpts, nao, nlo = ao2lo.shape
size = Nkpts * nlo
mo_phase = lib.einsum('kui,Rk->kuRi', ao2lo,
self.phase.conj()).reshape(Nkpts, nao, size)
TEI = 0.0
for i in range(Nkpts):
for j in range(Nkpts):
for k in range(Nkpts):
l = kconserv[i, j, k]
ki, COi = self.kpts[i], mo_phase[i]
kj, COj = self.kpts[j], mo_phase[j]
kk, C*k = self.kpts[k], mo_phase[k]
kl, COl = self.kpts[l], mo_phase[l]
TEI += self.kmf.with_df.ao2mo([COi, COj, C*k, COl],
[ki, kj, kk, kl],
compact=False)
self.is_real(TEI)
return TEI.reshape(size, size, size, size).real / Nkpts
def update_amps(cc, t1, t2, eris, max_memory=2000):
time0 = time.clock(), time.time()
log = logger.Logger(cc.stdout, cc.verbose)
nkpts, nocc, nvir = t1.shape
fock = eris.fock
fov = fock[:, :nocc, nocc:].copy()
foo = fock[:, :nocc, :nocc].copy()
fvv = fock[:, nocc:, nocc:].copy()
#mo_e = eris.fock.diagonal()
#eia = mo_e[:nocc,None] - mo_e[None,nocc:]
#eijab = lib.direct_sum('ia,jb->ijab',eia,eia)
tau = imdk.make_tau(cc, t2, t1, t1)
Fvv = imdk.cc_Fvv(cc, t1, t2, eris)
Foo = imdk.cc_Foo(cc, t1, t2, eris)
Fov = imdk.cc_Fov(cc, t1, t2, eris)
Woooo = imdk.cc_Woooo(cc, t1, t2, eris)
Wvvvv = imdk.cc_Wvvvv(cc, t1, t2, eris)
Wovvo = imdk.cc_Wovvo(cc, t1, t2, eris)
# Move energy terms to the other side
for k in range(nkpts):
Fvv[k] -= numpy.diag(numpy.diag(fvv[k]))
Foo[k] -= numpy.diag(numpy.diag(foo[k]))
# Get the momentum conservation array
# Note: chemist's notation for momentum conserving t2(ki,kj,ka,kb), even though
# integrals are in physics notation
kconserv = tools.get_kconserv(cc._scf.cell, cc.kpts)
eris_ovvo = numpy.zeros(shape=(nkpts, nkpts, nkpts, nocc, nvir, nvir,
nocc),
dtype=t2.dtype)
eris_oovo = numpy.zeros(shape=(nkpts, nkpts, nkpts, nocc, nocc, nvir,
nocc),
dtype=t2.dtype)
eris_vvvo = numpy.zeros(shape=(nkpts, nkpts, nkpts, nvir, nvir, nvir,
nocc),
dtype=t2.dtype)
for km in range(nkpts):
for kb in range(nkpts):
for ke in range(nkpts):
kj = kconserv[km, ke, kb]
# <mb||je> -> -<mb||ej>
eris_ovvo[km, kb,
ke] = -eris.ovov[km, kb, kj].transpose(0, 1, 3, 2)
# <mn||je> -> -<mn||ej>
# let kb = kn as a dummy variable
eris_oovo[km, kb,
ke] = -eris.ooov[km, kb, kj].transpose(0, 1, 3, 2)
# <ma||be> -> - <be||am>*
# let kj = ka as a dummy variable
kj = kconserv[km, ke, kb]
eris_vvvo[ke, kj, kb] = -eris.ovvv[km, kb, ke].transpose(
2, 3, 1, 0).conj()
# T1 equation
t1new = numpy.zeros(shape=t1.shape, dtype=t1.dtype)
for ka in range(nkpts):
ki = ka
t1new[ka] += numpy.array(fov[ka, :, :]).conj()
t1new[ka] += einsum('ie,ae->ia', t1[ka], Fvv[ka])
t1new[ka] += -einsum('ma,mi->ia', t1[ka], Foo[ka])
for km in range(nkpts):
t1new[ka] += einsum('imae,me->ia', t2[ka, km, ka], Fov[km])
t1new[ka] += -einsum('nf,naif->ia', t1[km], eris.ovov[km, ka, ki])
for kn in range(nkpts):
ke = kconserv[km, ki, kn]
t1new[ka] += -0.5 * einsum('imef,maef->ia', t2[ki, km, ke],
eris.ovvv[km, ka, ke])
t1new[ka] += -0.5 * einsum('mnae,nmei->ia', t2[km, kn, ka],
eris_oovo[kn, km, ke])
# T2 equation
t2new = numpy.array(eris.oovv).conj()
for ki in range(nkpts):
for kj in range(nkpts):
for ka in range(nkpts):
# Chemist's notation for momentum conserving t2(ki,kj,ka,kb)
kb = kconserv[ki, ka, kj]
Ftmp = Fvv[kb] - 0.5 * einsum('mb,me->be', t1[kb], Fov[kb])
tmp = einsum('ijae,be->ijab', t2[ki, kj, ka], Ftmp)
t2new[ki, kj, ka] += tmp
#t2new[ki,kj,kb] -= tmp.transpose(0,1,3,2)
Ftmp = Fvv[ka] - 0.5 * einsum('ma,me->ae', t1[ka], Fov[ka])
tmp = einsum('ijbe,ae->ijab', t2[ki, kj, kb], Ftmp)
t2new[ki, kj, ka] -= tmp
Ftmp = Foo[kj] + 0.5 * einsum('je,me->mj', t1[kj], Fov[kj])
tmp = einsum('imab,mj->ijab', t2[ki, kj, ka], Ftmp)
t2new[ki, kj, ka] -= tmp
#t2new[kj,ki,ka] += tmp.transpose(1,0,2,3)
Ftmp = Foo[ki] + 0.5 * einsum('ie,me->mi', t1[ki], Fov[ki])
tmp = einsum('jmab,mi->ijab', t2[kj, ki, ka], Ftmp)
t2new[ki, kj, ka] += tmp
for km in range(nkpts):
# Wminj
# - km - kn + ka + kb = 0
# => kn = ka - km + kb
kn = kconserv[ka, km, kb]
t2new[ki, kj, ka] += 0.5 * einsum(
'mnab,mnij->ijab', tau[km, kn, ka], Woooo[km, kn, ki])
ke = km
t2new[ki, kj, ka] += 0.5 * einsum(
'ijef,abef->ijab', tau[ki, kj, ke], Wvvvv[ka, kb, ke])
# Wmbej
# - km - kb + ke + kj = 0
# => ke = km - kj + kb
ke = kconserv[km, kj, kb]
tmp = einsum('imae,mbej->ijab', t2[ki, km, ka],
Wovvo[km, kb, ke])
# - km - kb + ke + kj = 0
# => ke = km - kj + kb
#
# t[i,e] => ki = ke
# t[m,a] => km = ka
if km == ka and ke == ki:
tmp -= einsum('ie,ma,mbej->ijab', t1[ki], t1[km],
eris_ovvo[km, kb, ke])
t2new[ki, kj, ka] += tmp
t2new[ki, kj, kb] -= tmp.transpose(0, 1, 3, 2)
t2new[kj, ki, ka] -= tmp.transpose(1, 0, 2, 3)
t2new[kj, ki, kb] += tmp.transpose(1, 0, 3, 2)
ke = ki
tmp = einsum('ie,abej->ijab', t1[ki], eris_vvvo[ka, kb, ke])
t2new[ki, kj, ka] += tmp
# P(ij) term
ke = kj
tmp = einsum('je,abei->ijab', t1[kj], eris_vvvo[ka, kb, ke])
t2new[ki, kj, ka] -= tmp
km = ka
tmp = einsum('ma,mbij->ijab', t1[ka], eris.ovoo[km, kb, ki])
t2new[ki, kj, ka] -= tmp
# P(ab) term
km = kb
tmp = einsum('mb,maij->ijab', t1[kb], eris.ovoo[km, ka, ki])
t2new[ki, kj, ka] += tmp
eia = numpy.zeros(shape=t1new.shape, dtype=t1new.dtype)
for ki in range(nkpts):
for i in range(nocc):
for a in range(nvir):
eia[ki, i, a] = foo[ki, i, i] - fvv[ki, a, a]
t1new[ki] /= eia[ki]
eijab = numpy.zeros(shape=t2new.shape, dtype=t2new.dtype)
kconserv = tools.get_kconserv(cc._scf.cell, cc.kpts)
for ki in range(nkpts):
for kj in range(nkpts):
for ka in range(nkpts):
kb = kconserv[ki, ka, kj]
for i in range(nocc):
for a in range(nvir):
for j in range(nocc):
for b in range(nvir):
eijab[ki, kj, ka, i, j, a,
b] = (foo[ki, i, i] + foo[kj, j, j] -
fvv[ka, a, a] - fvv[kb, b, b])
t2new[ki, kj, ka] /= eijab[ki, kj, ka]
time0 = log.timer_debug1('update t1 t2', *time0)
return t1new, t2new
def __init__(self, cell, kpts):
kconserv = tools.get_kconserv(cell, kpts)
nkpts = len(kpts)
temp = range(0, nkpts)
klist = pyscf.lib.cartesian_prod((temp, temp, temp))
completed = numpy.zeros((nkpts, nkpts, nkpts), dtype=int)
self.operations = numpy.zeros((nkpts, nkpts, nkpts), dtype=int)
self.equivalentList = numpy.zeros((nkpts, nkpts, nkpts, 3), dtype=int)
self.nUnique = 0
self.uniqueList = numpy.array([])
ivec = 0
not_done = True
while (not_done):
current_kvec = klist[ivec]
# check to see if it's been done...
kp = current_kvec[0]
kq = current_kvec[1]
kr = current_kvec[2]
#print "computing ",kp,kq,kr
if completed[kp, kq, kr] == 0:
self.nUnique += 1
self.uniqueList = numpy.append(self.uniqueList, current_kvec)
ks = kconserv[kp, kq, kr]
# Now find all equivalent kvectors by permuting it all possible ways...
# and then storing how its related by symmetry
completed[kp, kq, kr] = 1
self.operations[kp, kq, kr] = 0
self.equivalentList[kp, kq, kr] = current_kvec.copy()
completed[kr, ks, kp] = 1
self.operations[kr, ks, kp] = 1 #.transpose(2,3,0,1)
self.equivalentList[kr, ks, kp] = current_kvec.copy()
completed[kq, kp, ks] = 1
self.operations[kq, kp,
ks] = 2 #numpy.conj(.transpose(1,0,3,2))
self.equivalentList[kq, kp, ks] = current_kvec.copy()
completed[ks, kr, kq] = 1
self.operations[ks, kr,
kq] = 3 #numpy.conj(.transpose(3,2,1,0))
self.equivalentList[ks, kr, kq] = current_kvec.copy()
ivec += 1
if ivec == len(klist):
not_done = False
self.uniqueList = self.uniqueList.reshape(self.nUnique, -1)
if DEBUG == 1:
print "::: kpoint helper :::"
print "kvector list (in)"
print " shape = ", klist.shape
print "kvector list (out)"
print " shape = ", self.uniqueList.shape
print " unique list ="
print self.uniqueList
print "transformation ="
for i in range(klist.shape[0]):
pqr = klist[i]
irr_pqr = self.equivalentList[pqr[0], pqr[1], pqr[2]]
print "%3d %3d %3d -> %3d %3d %3d" % (
pqr[0], pqr[1], pqr[2], irr_pqr[0], irr_pqr[1], irr_pqr[2])
def update_amps(cc, t1, t2, eris, max_memory=2000):
time0 = time.clock(), time.time()
log = logger.Logger(cc.stdout, cc.verbose)
nkpts, nocc, nvir = t1.shape
#nov = nocc*nvir
fock = eris.fock
#t1new = numpy.zeros_like(t1)
#t2new = numpy.zeros_like(t2)
fov = fock[:,:nocc,nocc:].copy()
foo = fock[:,:nocc,:nocc].copy()
fvv = fock[:,nocc:,nocc:].copy()
#mo_e = eris.fock.diagonal()
#eia = mo_e[:nocc,None] - mo_e[None,nocc:]
#eijab = lib.direct_sum('ia,jb->ijab',eia,eia)
tau = imdk.make_tau(cc,t2,t1,t1)
### From eom-cc hackathon code ###
Fvv = imdk.cc_Fvv(cc,t1,t2,eris)
Foo = imdk.cc_Foo(cc,t1,t2,eris)
Fov = imdk.cc_Fov(cc,t1,t2,eris)
Woooo = imdk.cc_Woooo(cc,t1,t2,eris)
Wvvvv = imdk.cc_Wvvvv(cc,t1,t2,eris)
Wovvo = imdk.cc_Wovvo(cc,t1,t2,eris)
# Move energy terms to the other side
Fvv -= fvv
Foo -= foo
# Get the momentum conservation array
# Note: chemist's notation for momentum conserving t2(ki,kj,ka,kb), even though
# integrals are in physics notation
kconserv = tools.get_kconserv(cc._scf.cell, cc.kpts)
eris_ovvo = numpy.zeros(shape=(nkpts,nkpts,nkpts,nocc,nvir,nvir,nocc), dtype=t2.dtype)
eris_oovo = numpy.zeros(shape=(nkpts,nkpts,nkpts,nocc,nocc,nvir,nocc), dtype=t2.dtype)
eris_vvvo = numpy.zeros(shape=(nkpts,nkpts,nkpts,nvir,nvir,nvir,nocc), dtype=t2.dtype)
for km in range(nkpts):
for kb in range(nkpts):
for ke in range(nkpts):
kj = kconserv[km,ke,kb]
# <mb||je> -> -<mb||ej>
eris_ovvo[km,kb,ke] = -eris.ovov[km,kb,kj].transpose(0,1,3,2)
# <mn||je> -> -<mn||ej>
# let kb = kn as a dummy variable
eris_oovo[km,kb,ke] = -eris.ooov[km,kb,kj].transpose(0,1,3,2)
# <ma||be> -> - <be||am>*
# let kj = ka as a dummy variable
kj = kconserv[km,ke,kb]
eris_vvvo[ke,kj,kb] = -eris.ovvv[km,kb,ke].transpose(2,3,1,0).conj()
# T1 equation
t1new = numpy.zeros(shape=t1.shape, dtype=t1.dtype)
for ka in range(nkpts):
ki = ka
# TODO: Does this fov need a conj()? Usually zero w/ canonical HF.
t1new[ka] += fov[ka,:,:]
t1new[ka] += einsum('ie,ae->ia',t1[ka],Fvv[ka])
t1new[ka] += -einsum('ma,mi->ia',t1[ka],Foo[ka])
for km in range(nkpts):
t1new[ka] += einsum('imae,me->ia',t2[ka,km,ka],Fov[km])
t1new[ka] += -einsum('nf,naif->ia',t1[km],eris.ovov[km,ka,ki])
for kn in range(nkpts):
ke = kconserv[km,ki,kn]
t1new[ka] += -0.5*einsum('imef,maef->ia',t2[ki,km,ke],eris.ovvv[km,ka,ke])
t1new[ka] += -0.5*einsum('mnae,nmei->ia',t2[km,kn,ka],eris_oovo[kn,km,ke])
# T2 equation
# For conj(), see Hirata and Bartlett, Eq. (36)
t2new = eris.oovv.copy().conj()
for ki in range(nkpts):
for kj in range(nkpts):
for ka in range(nkpts):
# Chemist's notation for momentum conserving t2(ki,kj,ka,kb)
kb = kconserv[ki,ka,kj]
Ftmp = Fvv[kb] - 0.5*einsum('mb,me->be',t1[kb],Fov[kb])
tmp = einsum('ijae,be->ijab',t2[ki,kj,ka],Ftmp)
t2new[ki,kj,ka] += tmp
Ftmp = Fvv[ka] - 0.5*einsum('ma,me->ae',t1[ka],Fov[ka])
tmp = einsum('ijbe,ae->ijab',t2[ki,kj,kb],Ftmp)
t2new[ki,kj,ka] -= tmp
#t2new[ki,kj,kb] -= tmp.transpose(0,1,3,2)
Ftmp = Foo[kj] + 0.5*einsum('je,me->mj',t1[kj],Fov[kj])
tmp = einsum('imab,mj->ijab',t2[ki,kj,ka],Ftmp)
t2new[ki,kj,ka] -= tmp
Ftmp = Foo[ki] + 0.5*einsum('ie,me->mi',t1[ki],Fov[ki])
tmp = einsum('jmab,mi->ijab',t2[kj,ki,ka],Ftmp)
t2new[ki,kj,ka] += tmp
#t2new[kj,ki,ka] += tmp.transpose(1,0,2,3)
for km in range(nkpts):
# Wminj
# - km - kn + ka + kb = 0
# => kn = ka - km + kb
kn = kconserv[ka,km,kb]
t2new[ki,kj,ka] += 0.5*einsum('mnab,mnij->ijab',tau[km,kn,ka],Woooo[km,kn,ki])
ke = km
t2new[ki,kj,ka] += 0.5*einsum('ijef,abef->ijab',tau[ki,kj,ke],Wvvvv[ka,kb,ke])
# Wmbej
# - km - kb + ke + kj = 0
# => ke = km - kj + kb
ke = kconserv[km,kj,kb]
tmp = einsum('imae,mbej->ijab',t2[ki,km,ka],Wovvo[km,kb,ke])
# - km - kb + ke + kj = 0
# => ke = km - kj + kb
#
# t[i,e] => ki = ke
# t[m,a] => km = ka
if km == ka and ke == ki:
tmp -= einsum('ie,ma,mbej->ijab',t1[ki],t1[km],eris_ovvo[km,kb,ke])
t2new[ki,kj,ka] += tmp
t2new[ki,kj,kb] -= tmp.transpose(0,1,3,2)
t2new[kj,ki,ka] -= tmp.transpose(1,0,2,3)
t2new[kj,ki,kb] += tmp.transpose(1,0,3,2)
ke = ki
tmp = einsum('ie,abej->ijab',t1[ki],eris_vvvo[ka,kb,ke])
t2new[ki,kj,ka] += tmp
# P(ij) term
ke = kj
tmp = einsum('je,abei->ijab',t1[kj],eris_vvvo[ka,kb,ke])
t2new[ki,kj,ka] -= tmp
km = ka
tmp = einsum('ma,mbij->ijab',t1[ka],eris.ovoo[km,kb,ki])
t2new[ki,kj,ka] -= tmp
# P(ab) term
km = kb
tmp = einsum('mb,maij->ijab',t1[kb],eris.ovoo[km,ka,ki])
t2new[ki,kj,ka] += tmp
eia = numpy.zeros(shape=t1new.shape, dtype=t1new.dtype)
for ki in range(nkpts):
for i in range(nocc):
for a in range(nvir):
eia[ki,i,a] = foo[ki,i,i] - fvv[ki,a,a]
t1new[ki] /= eia[ki]
eijab = numpy.zeros(shape=t2new.shape, dtype=t2new.dtype)
kconserv = tools.get_kconserv(cc._scf.cell, cc.kpts)
for ki in range(nkpts):
for kj in range(nkpts):
for ka in range(nkpts):
kb = kconserv[ki,ka,kj]
for i in range(nocc):
for a in range(nvir):
for j in range(nocc):
for b in range(nvir):
eijab[ki,kj,ka,i,j,a,b] = ( foo[ki,i,i] + foo[kj,j,j]
- fvv[ka,a,a] - fvv[kb,b,b] )
t2new[ki,kj,ka] /= eijab[ki,kj,ka]
time0 = log.timer_debug1('update t1 t2', *time0)
return t1new, t2new
def __init__(self, cc, mo_coeff=None, method='incore'):
cput0 = (time.clock(), time.time())
moidx = numpy.ones(shape=cc.mo_energy.shape, dtype=numpy.bool)
nkpts = cc.nkpts
nmo = cc.nmo()
# TODO change this for k-points ... seems like it should work
if isinstance(cc.frozen, (int, numpy.integer)):
for k in range(nkpts):
moidx[k, :cc.frozen] = False
elif len(cc.frozen) > 0:
for k in range(nkpts):
moidx[k, numpy.asarray(cc.frozen)] = False
assert (numpy.count_nonzero(moidx) % 2 == 0
) # works for restricted CCSD only
if mo_coeff is None:
# TODO make this work for frozen maybe... seems like it should work
nao = cc._scf.cell.nao_nr()
self.mo_coeff = numpy.zeros((nkpts, nao * 2, nmo),
dtype=numpy.complex128)
for k in range(nkpts):
self.mo_coeff[k] = cc.mo_coeff[k][:, moidx[k]]
mo_coeff = self.mo_coeff
self.fock = numpy.zeros((nkpts, nmo, nmo))
for k in range(nkpts):
self.fock[k] = numpy.diag(cc.mo_energy[k][moidx[k]])
else: # If mo_coeff is not canonical orbital
# TODO does this work for k-points? changed to conjugate.
self.mo_coeff = mo_coeff = mo_coeff[:, moidx]
dm = cc._scf.make_rdm1(cc.mo_coeff, cc.mo_occ)
fockao = cc._scf.get_hcore() + cc._scf.get_veff(cc.mol, dm)
self.fock = reduce(numpy.dot,
(numpy.conj(mo_coeff.T), fockao, mo_coeff))
nocc = cc.nocc()
nmo = cc.nmo()
nvir = nmo - nocc
mem_incore, mem_outcore, mem_basic = pyscf.cc.ccsd._mem_usage(
nocc, nvir)
mem_now = lib.current_memory()[0]
# Convert to spin-orbitals and anti-symmetrize
nao = cc._scf.cell.nao_nr()
so_coeff = numpy.zeros((nkpts, nao, nmo), dtype=numpy.complex128)
so_coeff[:, :, ::2] = so_coeff[:, :, 1::2] = mo_coeff[:, :nao, ::2]
log = logger.Logger(cc.stdout, cc.verbose)
if (method == 'incore' and cc._scf._eri is None and
(mem_incore + mem_now < cc.max_memory) or cc.mol.incore_anyway):
kconserv = tools.get_kconserv(cc._scf.cell, cc.kpts)
eri = numpy.zeros((nkpts, nkpts, nkpts, nmo, nmo, nmo, nmo),
dtype=numpy.complex128)
fao2mo = cc._scf.with_df.ao2mo
for kp in range(nkpts):
for kq in range(nkpts):
for kr in range(nkpts):
ks = kconserv[kp, kq, kr]
eri_kpt = fao2mo((so_coeff[kp], so_coeff[kq],
so_coeff[kr], so_coeff[ks]),
(cc.kpts[kp], cc.kpts[kq],
cc.kpts[kr], cc.kpts[ks]),
compact=False)
eri_kpt = eri_kpt.reshape(nmo, nmo, nmo, nmo)
eri[kp, kq, kr] = eri_kpt.copy()
eri[:, :, :, ::2,
1::2] = eri[:, :, :,
1::2, ::2] = eri[:, :, :, :, :, ::2,
1::2] = eri[:, :, :, :, :,
1::2, ::2] = 0.
# Checking some things...
maxdiff = 0.0
for kp in range(nkpts):
for kq in range(nkpts):
for kr in range(nkpts):
ks = kconserv[kp, kq, kr]
for p in range(nmo):
for q in range(nmo):
for r in range(nmo):
for s in range(nmo):
pqrs = eri[kp, kq, kr, p, q, r, s]
rspq = eri[kr, ks, kp, r, s, p, q]
diff = numpy.linalg.norm(pqrs -
rspq).real
if diff > 1e-5:
print "** Warning: ERI diff at ",
print "kp,kq,kr,ks,p,q,r,s =", kp, kq, kr, ks, p, q, r, s
maxdiff = max(maxdiff, diff)
print "Max difference in (pq|rs) - (rs|pq) = %.15g" % maxdiff
#print "ERI ="
#print eri
# Antisymmetrizing (pq|rs)-(ps|rq), where the latter integral is equal to
# (rq|ps); done since we aren't tracking the kpoint of orbital 's'
eri1 = eri - eri.transpose(2, 1, 0, 5, 4, 3, 6)
# Chemist -> physics notation
eri1 = eri1.transpose(0, 2, 1, 3, 5, 4, 6)
self.dtype = eri1.dtype
self.oooo = eri1[:, :, :, :nocc, :nocc, :nocc, :nocc].copy(
) / nkpts
self.ooov = eri1[:, :, :, :nocc, :nocc, :nocc,
nocc:].copy() / nkpts
self.ovoo = eri1[:, :, :, :nocc,
nocc:, :nocc, :nocc].copy() / nkpts
self.oovv = eri1[:, :, :, :nocc, :nocc, nocc:,
nocc:].copy() / nkpts
self.ovov = eri1[:, :, :, :nocc, nocc:, :nocc,
nocc:].copy() / nkpts
self.ovvv = eri1[:, :, :, :nocc, nocc:, nocc:,
nocc:].copy() / nkpts
self.vvvv = eri1[:, :, :, nocc:, nocc:, nocc:,
nocc:].copy() / nkpts
#ovvv = eri1[:nocc,nocc:,nocc:,nocc:].copy()
#self.ovvv = numpy.empty((nocc,nvir,nvir*(nvir+1)//2))
#for i in range(nocc):
# for j in range(nvir):
# self.ovvv[i,j] = lib.pack_tril(ovvv[i,j])
#self.vvvv = pyscf.ao2mo.restore(4, eri1[nocc:,nocc:,nocc:,nocc:], nvir)
log.timer('CCSD integral transformation', *cput0)
def __init__(self, cc, mo_coeff=None, method='incore'):
cput0 = (time.clock(), time.time())
moidx = numpy.ones(shape=cc.mo_energy.shape, dtype=numpy.bool)
nkpts = cc.nkpts
nmo = cc.nmo()
# TODO change this for k-points ... seems like it should work
if isinstance(cc.frozen, (int, numpy.integer)):
for k in range(nkpts):
moidx[k,:cc.frozen] = False
elif len(cc.frozen) > 0:
for k in range(nkpts):
moidx[k,numpy.asarray(cc.frozen)] = False
if mo_coeff is None:
# TODO make this work for frozen maybe... seems like it should work
self.mo_coeff = numpy.zeros((nkpts,nmo,nmo),dtype=numpy.complex128)
for k in range(nkpts):
self.mo_coeff[k] = cc.mo_coeff[k][:,moidx[k]]
mo_coeff = self.mo_coeff
self.fock = numpy.zeros((nkpts,nmo,nmo))
for k in range(nkpts):
self.fock[k] = numpy.diag(cc.mo_energy[k][moidx[k]])
else: # If mo_coeff is not canonical orbital
# TODO does this work for k-points? changed to conjugate.
self.mo_coeff = mo_coeff = mo_coeff[:,moidx]
dm = cc._scf.make_rdm1(cc.mo_coeff, cc.mo_occ)
fockao = cc._scf.get_hcore() + cc._scf.get_veff(cc.mol, dm)
self.fock = reduce(numpy.dot, (numpy.conj(mo_coeff.T), fockao, mo_coeff))
nocc = cc.nocc()
nmo = cc.nmo()
nvir = nmo - nocc
mem_incore, mem_outcore, mem_basic = pyscf.cc.ccsd._mem_usage(nocc, nvir)
mem_now = lib.current_memory()[0]
# Convert to spin-orbitals and anti-symmetrize
so_coeff = numpy.zeros((nkpts,nmo/2,nmo),dtype=numpy.complex128)
so_coeff[:,:,::2] = so_coeff[:,:,1::2] = mo_coeff[:,:nmo/2,::2]
log = logger.Logger(cc.stdout, cc.verbose)
if (method == 'incore' and cc._scf._eri is None and
(mem_incore+mem_now < cc.max_memory) or cc.mol.incore_anyway):
kconserv = tools.get_kconserv(cc._scf.cell,cc.kpts)
eri = numpy.zeros((nkpts,nkpts,nkpts,nmo,nmo,nmo,nmo), dtype=numpy.complex128)
for kp in range(nkpts):
for kq in range(nkpts):
for kr in range(nkpts):
ks = kconserv[kp,kq,kr]
eri_kpt = pyscf.pbc.ao2mo.general(cc._scf.cell,
(so_coeff[kp,:,:],so_coeff[kq,:,:],so_coeff[kr,:,:],so_coeff[ks,:,:]),
(cc.kpts[kp],cc.kpts[kq],cc.kpts[kr],cc.kpts[ks]))
eri_kpt = eri_kpt.reshape(nmo,nmo,nmo,nmo)
eri[kp,kq,kr] = eri_kpt.copy()
eri[:,:,:,::2,1::2] = eri[:,:,:,1::2,::2] = eri[:,:,:,:,:,::2,1::2] = eri[:,:,:,:,:,1::2,::2] = 0.
# Checking some things...
maxdiff = 0.0
for kp in range(nkpts):
for kq in range(nkpts):
for kr in range(nkpts):
ks = kconserv[kp,kq,kr]
for p in range(nmo):
for q in range(nmo):
for r in range(nmo):
for s in range(nmo):
pqrs = eri[kp,kq,kr,p,q,r,s]
rspq = eri[kr,ks,kp,r,s,p,q]
diff = numpy.linalg.norm(pqrs - rspq).real
if diff > 1e-5:
print "** Warning: ERI diff at ",
print "kp,kq,kr,ks,p,q,r,s =", kp, kq, kr, ks, p, q, r, s
maxdiff = max(maxdiff,diff)
print "Max difference in (pq|rs) - (rs|pq) = %.15g" % maxdiff
#print "ERI ="
#print eri
# Antisymmetrizing (pq|rs)-(ps|rq), where the latter integral is equal to
# (rq|ps); done since we aren't tracking the kpoint of orbital 's'
eri1 = eri - eri.transpose(2,1,0,5,4,3,6)
# Chemist -> physics notation
eri1 = eri1.transpose(0,2,1,3,5,4,6)
self.dtype = eri1.dtype
self.oooo = eri1[:,:,:,:nocc,:nocc,:nocc,:nocc].copy() / nkpts
self.ooov = eri1[:,:,:,:nocc,:nocc,:nocc,nocc:].copy() / nkpts
self.ovoo = eri1[:,:,:,:nocc,nocc:,:nocc,:nocc].copy() / nkpts
self.oovv = eri1[:,:,:,:nocc,:nocc,nocc:,nocc:].copy() / nkpts
self.ovov = eri1[:,:,:,:nocc,nocc:,:nocc,nocc:].copy() / nkpts
self.ovvv = eri1[:,:,:,:nocc,nocc:,nocc:,nocc:].copy() / nkpts
self.vvvv = eri1[:,:,:,nocc:,nocc:,nocc:,nocc:].copy() / nkpts
#ovvv = eri1[:nocc,nocc:,nocc:,nocc:].copy()
#self.ovvv = numpy.empty((nocc,nvir,nvir*(nvir+1)//2))
#for i in range(nocc):
# for j in range(nvir):
# self.ovvv[i,j] = lib.pack_tril(ovvv[i,j])
#self.vvvv = pyscf.ao2mo.restore(4, eri1[nocc:,nocc:,nocc:,nocc:], nvir)
log.timer('CCSD integral transformation', *cput0)