def vppnl_by_k(kpt):
Gk = Gv + kpt
G_rad = lib.norm(Gk, axis=1)
aokG = ft_ao.ft_ao(cell, Gv, kpt=kpt) * (ngs / cell.vol)
vppnl = 0
for ia in range(cell.natm):
symb = cell.atom_symbol(ia)
if symb not in cell._pseudo:
continue
pp = cell._pseudo[symb]
for l, proj in enumerate(pp[5:]):
rl, nl, hl = proj
if nl > 0:
hl = numpy.asarray(hl)
fakemol._bas[0, gto.ANG_OF] = l
fakemol._env[ptr + 3] = 0.5 * rl ** 2
fakemol._env[ptr + 4] = rl ** (l + 1.5) * numpy.pi ** 1.25
pYlm_part = dft.numint.eval_ao(fakemol, Gk, deriv=0)
pYlm = numpy.empty((nl, l * 2 + 1, ngs))
for k in range(nl):
qkl = pseudo.pp._qli(G_rad * rl, l, k)
pYlm[k] = pYlm_part.T * qkl
# pYlm is real
SPG_lmi = numpy.einsum("g,nmg->nmg", SI[ia].conj(), pYlm)
SPG_lm_aoG = numpy.einsum("nmg,gp->nmp", SPG_lmi, aokG)
tmp = numpy.einsum("ij,jmp->imp", hl, SPG_lm_aoG)
vppnl += numpy.einsum("imp,imq->pq", SPG_lm_aoG.conj(), tmp)
return vppnl * (1.0 / ngs ** 2)
def get_nuc_less_accurate(mydf, kpts=None):
log = logger.Logger(mydf.stdout, mydf.verbose)
t1 = t0 = (time.clock(), time.time())
if kpts is None:
kpts_lst = numpy.zeros((1, 3))
else:
kpts_lst = numpy.reshape(kpts, (-1, 3))
nkpts = len(kpts_lst)
if mydf._cderi is None:
mydf.build()
cell = mydf.cell
fused_cell, fuse = fuse_auxcell_(mydf, mydf.auxcell)
nao = cell.nao_nr()
charge = -cell.atom_charges()
j2c = pgto.intor_cross("cint2c2e_sph", fused_cell, _fake_nuc(cell))
jaux = j2c.dot(charge)
jaux -= charge.sum() * mydf.auxbar(fused_cell)
Gv = cell.get_Gv(mydf.gs)
SI = cell.get_SI(Gv)
# The normal nuclues have been considered in function get_gth_vlocG_part1
# The result vG is the potential in G-space for erf part of the pp nuclues and
# "numpy.dot(charge, SI) * coulG" for normal nuclues.
vpplocG = pgto.pseudo.pp_int.get_gth_vlocG_part1(cell, Gv)
vG = -1.0 / cell.vol * numpy.einsum("ij,ij->j", SI, vpplocG)
kpt_allow = numpy.zeros(3)
if is_zero(kpts_lst):
vj = numpy.zeros((nkpts, nao ** 2))
else:
vj = numpy.zeros((nkpts, nao ** 2), dtype=numpy.complex128)
max_memory = max(2000, mydf.max_memory - lib.current_memory()[0])
for k, pqkR, pqkI, p0, p1 in mydf.ft_loop(cell, mydf.gs, kpt_allow, kpts_lst, max_memory=max_memory):
if not gamma_point(kpts_lst[k]):
vj[k] += numpy.einsum("k,xk->x", vG.real, pqkI) * 1j
vj[k] += numpy.einsum("k,xk->x", vG.imag, pqkR) * -1j
vj[k] += numpy.einsum("k,xk->x", vG.real, pqkR)
vj[k] += numpy.einsum("k,xk->x", vG.imag, pqkI)
pqkR = pqkI = None
Gv = cell.get_Gv(mydf.gs)
aoaux = ft_ao.ft_ao(fused_cell, Gv)
jaux -= numpy.einsum("x,xj->j", vG.real, aoaux.real)
jaux -= numpy.einsum("x,xj->j", vG.imag, aoaux.imag)
jaux = fuse(jaux)
vj = vj.reshape(-1, nao, nao)
for k, kpt in enumerate(kpts_lst):
with mydf.load_Lpq((kpt, kpt)) as Lpq:
v = 0
for p0, p1 in lib.prange(0, jaux.size, mydf.blockdim):
v += numpy.dot(jaux[p0:p1], numpy.asarray(Lpq[p0:p1]))
if gamma_point(kpt):
vj[k] += lib.unpack_tril(numpy.asarray(v.real, order="C"))
else:
vj[k] += lib.unpack_tril(v)
if kpts is None or numpy.shape(kpts) == (3,):
vj = vj[0]
return vj
def test_ft_ao(self):
coords = pdft.gen_grid.gen_uniform_grids(cell)
aoR = pdft.numint.eval_ao(cell, coords)
ngs, nao = aoR.shape
ref = numpy.asarray([tools.fft(aoR[:,i], cell.gs) for i in range(nao)])
ref = ref.T * (cell.vol/ngs)
dat = ft_ao.ft_ao(cell, cell.Gv)
self.assertAlmostEqual(numpy.linalg.norm(ref[:,0]-dat[:,0]) , 8.4358614794095722e-11, 9)
self.assertAlmostEqual(numpy.linalg.norm(ref[:,1]-dat[:,1]) , 0.0041669297531642616 , 4)
self.assertAlmostEqual(numpy.linalg.norm(ref[:,2:]-dat[:,2:]), 5.8677286005879366e-14, 9)
def pw_contract(istep, sh_range, j3cR, j3cI):
bstart, bend, ncol = sh_range
if aosym == 's2':
shls_slice = (bstart, bend, 0, bend)
else:
shls_slice = (bstart, bend, 0, cell.nbas)
for p0, p1 in lib.prange(0, ngrids, Gblksize):
dat = ft_ao._ft_aopair_kpts(cell, Gv[p0:p1], shls_slice, aosym,
b, gxyz[p0:p1], Gvbase, kpt,
adapted_kptjs, out=buf)
if (cell.dimension == 1 or cell.dimension == 2) and is_zero(kpt):
G0idx, SI_on_z = pbcgto.cell._SI_for_uniform_model_charge(cell, Gv[p0:p1])
if SI_on_z.size > 0:
for k, aoao in enumerate(dat):
aoao[G0idx] -= numpy.einsum('g,i->gi', SI_on_z, ovlp[k])
aux = fuse(ft_ao.ft_ao(fused_cell, Gv[p0:p1][G0idx]).T)
vG_mod = numpy.einsum('ig,g,g->i', aux.conj(),
wcoulG[p0:p1][G0idx], SI_on_z)
if gamma_point(adapted_kptjs[k]):
j3cR[k][:naux] -= vG_mod[:,None].real * ovlp[k]
else:
tmp = vG_mod[:,None] * ovlp[k]
j3cR[k][:naux] -= tmp.real
j3cI[k][:naux] -= tmp.imag
tmp = aux = vG_mod
nG = p1 - p0
for k, ji in enumerate(adapted_ji_idx):
aoao = dat[k].reshape(nG,ncol)
pqkR = numpy.ndarray((ncol,nG), buffer=pqkRbuf)
pqkI = numpy.ndarray((ncol,nG), buffer=pqkIbuf)
pqkR[:] = aoao.real.T
pqkI[:] = aoao.imag.T
lib.dot(kLR[p0:p1].T, pqkR.T, -1, j3cR[k][naux:], 1)
lib.dot(kLI[p0:p1].T, pqkI.T, -1, j3cR[k][naux:], 1)
if not (is_zero(kpt) and gamma_point(adapted_kptjs[k])):
lib.dot(kLR[p0:p1].T, pqkI.T, -1, j3cI[k][naux:], 1)
lib.dot(kLI[p0:p1].T, pqkR.T, 1, j3cI[k][naux:], 1)
for k, ji in enumerate(adapted_ji_idx):
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
v = fuse(j3cR[k])
else:
v = fuse(j3cR[k] + j3cI[k] * 1j)
if j2ctag == 'CD':
v = scipy.linalg.solve_triangular(j2c, v, lower=True, overwrite_b=True)
else:
v = lib.dot(j2c, v)
feri['j3c/%d/%d'%(ji,istep)] = v
def test_ft_ao_with_kpts(self):
numpy.random.seed(1)
kpt = numpy.random.random(3)
coords = pdft.gen_grid.gen_uniform_grids(cell)
aoR = pdft.numint.eval_ao(cell, coords, kpt=kpt)
ngs, nao = aoR.shape
expmikr = numpy.exp(-1j*numpy.dot(coords,kpt))
ref = numpy.asarray([tools.fftk(aoR[:,i], cell.gs, expmikr) for i in range(nao)])
ref = ref.T * (cell.vol/ngs)
dat = ft_ao.ft_ao(cell, cell.Gv, kpt=kpt)
self.assertAlmostEqual(numpy.linalg.norm(ref[:,0]-dat[:,0]) , 1.3359899490499813e-10, 9)
self.assertAlmostEqual(numpy.linalg.norm(ref[:,1]-dat[:,1]) , 0.0042404556036939756 , 4)
self.assertAlmostEqual(numpy.linalg.norm(ref[:,2:]-dat[:,2:]), 4.8856357999633564e-14, 9)
def vppnl_by_k(kpt):
Gk = Gv + kpt
G_rad = lib.norm(Gk, axis=1)
aokG = ft_ao.ft_ao(cell, Gv, kpt=kpt) * (ngs / cell.vol)
vppnl = 0
for ia in range(cell.natm):
symb = cell.atom_symbol(ia)
if symb not in cell._pseudo:
continue
pp = cell._pseudo[symb]
p1 = 0
for l, proj in enumerate(pp[5:]):
rl, nl, hl = proj
if nl > 0:
fakemol._bas[0, gto.ANG_OF] = l
fakemol._env[ptr + 3] = .5 * rl**2
fakemol._env[ptr + 4] = rl**(l + 1.5) * numpy.pi**1.25
pYlm_part = dft.numint.eval_ao(fakemol, Gk, deriv=0)
p0, p1 = p1, p1 + nl * (l * 2 + 1)
# pYlm is real, SI[ia] is complex
pYlm = numpy.ndarray((nl, l * 2 + 1, ngs),
dtype=numpy.complex128,
buffer=buf[p0:p1])
for k in range(nl):
qkl = pseudo.pp._qli(G_rad * rl, l, k)
pYlm[k] = pYlm_part.T * qkl
#:SPG_lmi = numpy.einsum('g,nmg->nmg', SI[ia].conj(), pYlm)
#:SPG_lm_aoG = numpy.einsum('nmg,gp->nmp', SPG_lmi, aokG)
#:tmp = numpy.einsum('ij,jmp->imp', hl, SPG_lm_aoG)
#:vppnl += numpy.einsum('imp,imq->pq', SPG_lm_aoG.conj(), tmp)
if p1 > 0:
SPG_lmi = buf[:p1]
SPG_lmi *= SI[ia].conj()
SPG_lm_aoGs = lib.zdot(SPG_lmi, aokG)
p1 = 0
for l, proj in enumerate(pp[5:]):
rl, nl, hl = proj
if nl > 0:
p0, p1 = p1, p1 + nl * (l * 2 + 1)
hl = numpy.asarray(hl)
SPG_lm_aoG = SPG_lm_aoGs[p0:p1].reshape(
nl, l * 2 + 1, -1)
tmp = numpy.einsum('ij,jmp->imp', hl, SPG_lm_aoG)
vppnl += numpy.einsum('imp,imq->pq', SPG_lm_aoG.conj(),
tmp)
return vppnl * (1. / ngs**2)
def get_pnucp(mydf, kpts=None):
cell = mydf.cell
if kpts is None:
kpts_lst = numpy.zeros((1,3))
else:
kpts_lst = numpy.reshape(kpts, (-1,3))
log = logger.Logger(mydf.stdout, mydf.verbose)
t1 = t0 = (time.clock(), time.time())
nkpts = len(kpts_lst)
nao = cell.nao_nr()
nao_pair = nao * (nao+1) // 2
Gv, Gvbase, kws = cell.get_Gv_weights(mydf.mesh)
charge = -cell.atom_charges()
kpt_allow = numpy.zeros(3)
coulG = tools.get_coulG(cell, kpt_allow, mesh=mydf.mesh, Gv=Gv)
coulG *= kws
if mydf.eta == 0:
wj = numpy.zeros((nkpts,nao_pair), dtype=numpy.complex128)
SI = cell.get_SI(Gv)
vG = numpy.einsum('i,ix->x', charge, SI) * coulG
wj = numpy.zeros((nkpts,nao_pair), dtype=numpy.complex128)
else:
nuccell = copy.copy(cell)
half_sph_norm = .5/numpy.sqrt(numpy.pi)
norm = half_sph_norm/mole.gaussian_int(2, mydf.eta)
chg_env = [mydf.eta, norm]
ptr_eta = cell._env.size
ptr_norm = ptr_eta + 1
chg_bas = [[ia, 0, 1, 1, 0, ptr_eta, ptr_norm, 0] for ia in range(cell.natm)]
nuccell._atm = cell._atm
nuccell._bas = numpy.asarray(chg_bas, dtype=numpy.int32)
nuccell._env = numpy.hstack((cell._env, chg_env))
wj = lib.asarray(mydf._int_nuc_vloc(nuccell, kpts_lst, 'int3c2e_pvp1'))
t1 = log.timer_debug1('pnucp pass1: analytic int', *t1)
aoaux = ft_ao.ft_ao(nuccell, Gv)
vG = numpy.einsum('i,xi->x', charge, aoaux) * coulG
if cell.dimension == 3:
nucbar = sum([z/nuccell.bas_exp(i)[0] for i,z in enumerate(charge)])
nucbar *= numpy.pi/cell.vol
ovlp = cell.pbc_intor('int1e_kin', 1, lib.HERMITIAN, kpts_lst)
for k in range(nkpts):
s = lib.pack_tril(ovlp[k])
# *2 due to the factor 1/2 in T
wj[k] -= nucbar*2 * s
max_memory = max(2000, mydf.max_memory-lib.current_memory()[0])
for aoaoks, p0, p1 in mydf.ft_loop(mydf.mesh, kpt_allow, kpts_lst,
max_memory=max_memory, aosym='s2',
intor='GTO_ft_pdotp'):
for k, aoao in enumerate(aoaoks):
if aft_jk.gamma_point(kpts_lst[k]):
wj[k] += numpy.einsum('k,kx->x', vG[p0:p1].real, aoao.real)
wj[k] += numpy.einsum('k,kx->x', vG[p0:p1].imag, aoao.imag)
else:
wj[k] += numpy.einsum('k,kx->x', vG[p0:p1].conj(), aoao)
t1 = log.timer_debug1('contracting pnucp', *t1)
wj_kpts = []
for k, kpt in enumerate(kpts_lst):
if aft_jk.gamma_point(kpt):
wj_kpts.append(lib.unpack_tril(wj[k].real.copy()))
else:
wj_kpts.append(lib.unpack_tril(wj[k]))
if kpts is None or numpy.shape(kpts) == (3,):
wj_kpts = wj_kpts[0]
return numpy.asarray(wj_kpts)
def get_pp_loc_part1(mydf, kpts=None):
cell = mydf.cell
if kpts is None:
kpts_lst = numpy.zeros((1, 3))
else:
kpts_lst = numpy.reshape(kpts, (-1, 3))
log = logger.Logger(mydf.stdout, mydf.verbose)
t0 = t1 = (time.clock(), time.time())
mesh = numpy.asarray(mydf.mesh)
nkpts = len(kpts_lst)
nao = cell.nao_nr()
nao_pair = nao * (nao + 1) // 2
charges = cell.atom_charges()
kpt_allow = numpy.zeros(3)
if mydf.eta == 0:
if cell.dimension > 0:
ke_guess = estimate_ke_cutoff(cell, cell.precision)
mesh_guess = tools.cutoff_to_mesh(cell.lattice_vectors(), ke_guess)
if numpy.any(
mesh[:cell.dimension] < mesh_guess[:cell.dimension] * .8):
logger.warn(
mydf, 'mesh %s is not enough for AFTDF.get_nuc function '
'to get integral accuracy %g.\nRecommended mesh is %s.',
mesh, cell.precision, mesh_guess)
Gv, Gvbase, kws = cell.get_Gv_weights(mesh)
vpplocG = pseudo.pp_int.get_gth_vlocG_part1(cell, Gv)
vpplocG = -numpy.einsum('ij,ij->j', cell.get_SI(Gv), vpplocG)
vpplocG *= kws
vG = vpplocG
vj = numpy.zeros((nkpts, nao_pair), dtype=numpy.complex128)
else:
if cell.dimension > 0:
ke_guess = estimate_ke_cutoff_for_eta(cell, mydf.eta,
cell.precision)
mesh_guess = tools.cutoff_to_mesh(cell.lattice_vectors(), ke_guess)
if numpy.any(mesh < mesh_guess * .8):
logger.warn(
mydf, 'mesh %s is not enough for AFTDF.get_nuc function '
'to get integral accuracy %g.\nRecommended mesh is %s.',
mesh, cell.precision, mesh_guess)
mesh_min = numpy.min((mesh_guess, mesh), axis=0)
if cell.dimension < 2 or cell.low_dim_ft_type == 'inf_vacuum':
mesh[:cell.dimension] = mesh_min[:cell.dimension]
else:
mesh = mesh_min
Gv, Gvbase, kws = cell.get_Gv_weights(mesh)
nuccell = _compensate_nuccell(mydf)
# PP-loc part1 is handled by fakenuc in _int_nuc_vloc
vj = lib.asarray(mydf._int_nuc_vloc(nuccell, kpts_lst))
t0 = t1 = log.timer_debug1('vnuc pass1: analytic int', *t0)
coulG = tools.get_coulG(cell, kpt_allow, mesh=mesh, Gv=Gv) * kws
aoaux = ft_ao.ft_ao(nuccell, Gv)
vG = numpy.einsum('i,xi->x', -charges, aoaux) * coulG
max_memory = max(2000, mydf.max_memory - lib.current_memory()[0])
for aoaoks, p0, p1 in mydf.ft_loop(mesh,
kpt_allow,
kpts_lst,
max_memory=max_memory,
aosym='s2'):
for k, aoao in enumerate(aoaoks):
# rho_ij(G) nuc(-G) / G^2
# = [Re(rho_ij(G)) + Im(rho_ij(G))*1j] [Re(nuc(G)) - Im(nuc(G))*1j] / G^2
if gamma_point(kpts_lst[k]):
vj[k] += numpy.einsum('k,kx->x', vG[p0:p1].real, aoao.real)
vj[k] += numpy.einsum('k,kx->x', vG[p0:p1].imag, aoao.imag)
else:
vj[k] += numpy.einsum('k,kx->x', vG[p0:p1].conj(), aoao)
t1 = log.timer_debug1('contracting Vnuc [%s:%s]' % (p0, p1), *t1)
log.timer_debug1('contracting Vnuc', *t0)
vj_kpts = []
for k, kpt in enumerate(kpts_lst):
if gamma_point(kpt):
vj_kpts.append(lib.unpack_tril(vj[k].real.copy()))
else:
vj_kpts.append(lib.unpack_tril(vj[k]))
if kpts is None or numpy.shape(kpts) == (3, ):
vj_kpts = vj_kpts[0]
return numpy.asarray(vj_kpts)
def _make_j3c(mydf, cell, auxcell, kptij_lst):
t1 = (time.clock(), time.time())
log = logger.Logger(mydf.stdout, mydf.verbose)
max_memory = max(2000, mydf.max_memory-lib.current_memory()[0])
fused_cell, fuse = fuse_auxcell(mydf, mydf.auxcell)
if mydf.metric.upper() != 'J':
outcore.aux_e2(cell, fused_cell, mydf._cderi, 'cint3c2e_sph',
kptij_lst=kptij_lst, dataname='j3c', max_memory=max_memory)
t1 = log.timer_debug1('3c2e', *t1)
nao = cell.nao_nr()
naux = auxcell.nao_nr()
gs = mydf.gs
Gv, Gvbase, kws = cell.get_Gv_weights(gs)
b = cell.reciprocal_vectors()
gxyz = lib.cartesian_prod([numpy.arange(len(x)) for x in Gvbase])
ngs = gxyz.shape[0]
kptis = kptij_lst[:,0]
kptjs = kptij_lst[:,1]
kpt_ji = kptjs - kptis
uniq_kpts, uniq_index, uniq_inverse = unique(kpt_ji)
# j2c ~ (-kpt_ji | kpt_ji)
j2c = fused_cell.pbc_intor('cint2c2e_sph', hermi=1, kpts=uniq_kpts)
kLRs = []
kLIs = []
for k, kpt in enumerate(uniq_kpts):
aoaux = ft_ao.ft_ao(fused_cell, Gv, None, b, gxyz, Gvbase, kpt).T
aoaux = fuse(aoaux)
coulG = numpy.sqrt(mydf.weighted_coulG(kpt, False, gs))
kLR = (aoaux.real * coulG).T
kLI = (aoaux.imag * coulG).T
if not kLR.flags.c_contiguous: kLR = lib.transpose(kLR.T)
if not kLI.flags.c_contiguous: kLI = lib.transpose(kLI.T)
j2c[k] = fuse(fuse(j2c[k]).T).T.copy()
if is_zero(kpt): # kpti == kptj
j2c[k] -= lib.dot(kLR.T, kLR)
j2c[k] -= lib.dot(kLI.T, kLI)
else:
# aoaux ~ kpt_ij, aoaux.conj() ~ kpt_kl
j2cR, j2cI = zdotCN(kLR.T, kLI.T, kLR, kLI)
j2c[k] -= j2cR + j2cI * 1j
kLR *= coulG.reshape(-1,1)
kLI *= coulG.reshape(-1,1)
kLRs.append(kLR)
kLIs.append(kLI)
aoaux = kLR = kLI = j2cR = j2cI = coulG = None
feri = h5py.File(mydf._cderi)
log.debug2('memory = %s', lib.current_memory()[0])
# Expand approx Lpq for aosym='s1'. The approx Lpq are all in aosym='s2' mode
if mydf.approx_sr_level > 0 and len(kptij_lst) > 1:
Lpq_fake = _fake_Lpq_kpts(mydf, feri, naux, nao)
def save(label, dat, col0, col1):
nrow = dat.shape[0]
feri[label][:nrow,col0:col1] = dat
def make_kpt(uniq_kptji_id): # kpt = kptj - kpti
kpt = uniq_kpts[uniq_kptji_id]
log.debug1('kpt = %s', kpt)
adapted_ji_idx = numpy.where(uniq_inverse == uniq_kptji_id)[0]
adapted_kptjs = kptjs[adapted_ji_idx]
nkptj = len(adapted_kptjs)
log.debug1('adapted_ji_idx = %s', adapted_ji_idx)
kLR = kLRs[uniq_kptji_id]
kLI = kLIs[uniq_kptji_id]
if is_zero(kpt): # kpti == kptj
aosym = 's2'
nao_pair = nao*(nao+1)//2
vbar = fuse(mydf.auxbar(fused_cell))
ovlp = cell.pbc_intor('cint1e_ovlp_sph', hermi=1, kpts=adapted_kptjs)
for k, ji in enumerate(adapted_ji_idx):
ovlp[k] = lib.pack_tril(ovlp[k])
else:
aosym = 's1'
nao_pair = nao**2
mem_now = lib.current_memory()[0]
log.debug2('memory = %s', mem_now)
max_memory = max(2000, mydf.max_memory-mem_now)
# nkptj for 3c-coulomb arrays plus 1 Lpq array
buflen = min(max(int(max_memory*.6*1e6/16/naux/(nkptj+1)), 1), nao_pair)
shranges = pyscf.df.outcore._guess_shell_ranges(cell, buflen, aosym)
buflen = max([x[2] for x in shranges])
# +1 for a pqkbuf
if aosym == 's2':
Gblksize = max(16, int(max_memory*.2*1e6/16/buflen/(nkptj+1)))
else:
Gblksize = max(16, int(max_memory*.4*1e6/16/buflen/(nkptj+1)))
Gblksize = min(Gblksize, ngs, 16384)
pqkRbuf = numpy.empty(buflen*Gblksize)
pqkIbuf = numpy.empty(buflen*Gblksize)
# buf for ft_aopair
buf = numpy.zeros((nkptj,buflen*Gblksize), dtype=numpy.complex128)
col1 = 0
for istep, sh_range in enumerate(shranges):
log.debug1('int3c2e [%d/%d], AO [%d:%d], ncol = %d', \
istep+1, len(shranges), *sh_range)
bstart, bend, ncol = sh_range
col0, col1 = col1, col1+ncol
j3cR = []
j3cI = []
for k, idx in enumerate(adapted_ji_idx):
v = fuse(numpy.asarray(feri['j3c/%d'%idx][:,col0:col1]))
if mydf.approx_sr_level == 0:
Lpq = numpy.asarray(feri['Lpq/%d'%idx][:,col0:col1])
elif aosym == 's2':
Lpq = numpy.asarray(feri['Lpq/0'][:,col0:col1])
else:
Lpq = numpy.asarray(Lpq_fake[:,col0:col1])
lib.dot(j2c[uniq_kptji_id], Lpq, -.5, v, 1)
if is_zero(kpt):
for i, c in enumerate(vbar):
if c != 0:
v[i] -= c * ovlp[k][col0:col1]
j3cR.append(numpy.asarray(v.real, order='C'))
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
j3cI.append(None)
else:
j3cI.append(numpy.asarray(v.imag, order='C'))
v = Lpq = None
log.debug3(' istep, k = %d %d memory = %s',
istep, k, lib.current_memory()[0])
if aosym == 's2':
shls_slice = (bstart, bend, 0, bend)
for p0, p1 in lib.prange(0, ngs, Gblksize):
ft_ao._ft_aopair_kpts(cell, Gv[p0:p1], shls_slice, aosym,
b, gxyz[p0:p1], Gvbase, kpt,
adapted_kptjs, out=buf)
nG = p1 - p0
for k, ji in enumerate(adapted_ji_idx):
aoao = numpy.ndarray((nG,ncol), dtype=numpy.complex128,
order='F', buffer=buf[k])
pqkR = numpy.ndarray((ncol,nG), buffer=pqkRbuf)
pqkI = numpy.ndarray((ncol,nG), buffer=pqkIbuf)
pqkR[:] = aoao.real.T
pqkI[:] = aoao.imag.T
aoao[:] = 0
lib.dot(kLR[p0:p1].T, pqkR.T, -1, j3cR[k], 1)
lib.dot(kLI[p0:p1].T, pqkI.T, -1, j3cR[k], 1)
if not (is_zero(kpt) and gamma_point(adapted_kptjs[k])):
lib.dot(kLR[p0:p1].T, pqkI.T, -1, j3cI[k], 1)
lib.dot(kLI[p0:p1].T, pqkR.T, 1, j3cI[k], 1)
log.debug3(' p0:p1 = %d:%d memory = %s',
p0, p1, lib.current_memory()[0])
else:
shls_slice = (bstart, bend, 0, cell.nbas)
ni = ncol // nao
for p0, p1 in lib.prange(0, ngs, Gblksize):
ft_ao._ft_aopair_kpts(cell, Gv[p0:p1], shls_slice, aosym,
b, gxyz[p0:p1], Gvbase, kpt,
adapted_kptjs, out=buf)
nG = p1 - p0
for k, ji in enumerate(adapted_ji_idx):
aoao = numpy.ndarray((nG,ni,nao), dtype=numpy.complex128,
order='F', buffer=buf[k])
pqkR = numpy.ndarray((ni,nao,nG), buffer=pqkRbuf)
pqkI = numpy.ndarray((ni,nao,nG), buffer=pqkIbuf)
pqkR[:] = aoao.real.transpose(1,2,0)
pqkI[:] = aoao.imag.transpose(1,2,0)
aoao[:] = 0
pqkR = pqkR.reshape(-1,nG)
pqkI = pqkI.reshape(-1,nG)
zdotCN(kLR[p0:p1].T, kLI[p0:p1].T, pqkR.T, pqkI.T,
-1, j3cR[k], j3cI[k], 1)
log.debug3(' p0:p1 = %d:%d memory = %s',
p0, p1, lib.current_memory()[0])
for k, ji in enumerate(adapted_ji_idx):
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
save('j3c/%d'%ji, j3cR[k], col0, col1)
else:
save('j3c/%d'%ji, j3cR[k]+j3cI[k]*1j, col0, col1)
for k, kpt in enumerate(uniq_kpts):
make_kpt(k)
feri.close()
def get_nuc(mydf, kpts=None):
cell = mydf.cell
if kpts is None:
kpts_lst = numpy.zeros((1,3))
else:
kpts_lst = numpy.reshape(kpts, (-1,3))
log = logger.Logger(mydf.stdout, mydf.verbose)
t1 = t0 = (time.clock(), time.time())
nkpts = len(kpts_lst)
nao = cell.nao_nr()
nao_pair = nao * (nao+1) // 2
Gv, Gvbase, kws = cell.get_Gv_weights(mydf.gs)
kpt_allow = numpy.zeros(3)
if mydf.eta == 0:
vpplocG = pseudo.pp_int.get_gth_vlocG_part1(cell, Gv)
vpplocG = -numpy.einsum('ij,ij->j', cell.get_SI(Gv), vpplocG)
vpplocG *= kws
vGR = vpplocG.real
vGI = vpplocG.imag
vjR = numpy.zeros((nkpts,nao_pair))
vjI = numpy.zeros((nkpts,nao_pair))
else:
nuccell = copy.copy(cell)
half_sph_norm = .5/numpy.sqrt(numpy.pi)
norm = half_sph_norm/gto.mole._gaussian_int(2, mydf.eta)
chg_env = [mydf.eta, norm]
ptr_eta = cell._env.size
ptr_norm = ptr_eta + 1
chg_bas = [[ia, 0, 1, 1, 0, ptr_eta, ptr_norm, 0] for ia in range(cell.natm)]
nuccell._atm = cell._atm
nuccell._bas = numpy.asarray(chg_bas, dtype=numpy.int32)
nuccell._env = numpy.hstack((cell._env, chg_env))
# PP-loc part1 is handled by fakenuc in _int_nuc_vloc
vj = lib.asarray(mydf._int_nuc_vloc(nuccell, kpts_lst))
vjR = vj.real
vjI = vj.imag
t1 = log.timer_debug1('vnuc pass1: analytic int', *t1)
charge = -cell.atom_charges()
coulG = tools.get_coulG(cell, kpt_allow, gs=mydf.gs, Gv=Gv)
coulG *= kws
aoaux = ft_ao.ft_ao(nuccell, Gv)
vGR = numpy.einsum('i,xi->x', charge, aoaux.real) * coulG
vGI = numpy.einsum('i,xi->x', charge, aoaux.imag) * coulG
max_memory = max(2000, mydf.max_memory-lib.current_memory()[0])
for k, pqkR, pqkI, p0, p1 \
in mydf.ft_loop(mydf.gs, kpt_allow, kpts_lst,
max_memory=max_memory, aosym='s2'):
# rho_ij(G) nuc(-G) / G^2
# = [Re(rho_ij(G)) + Im(rho_ij(G))*1j] [Re(nuc(G)) - Im(nuc(G))*1j] / G^2
if not gamma_point(kpts_lst[k]):
vjI[k] += numpy.einsum('k,xk->x', vGR[p0:p1], pqkI)
vjI[k] -= numpy.einsum('k,xk->x', vGI[p0:p1], pqkR)
vjR[k] += numpy.einsum('k,xk->x', vGR[p0:p1], pqkR)
vjR[k] += numpy.einsum('k,xk->x', vGI[p0:p1], pqkI)
t1 = log.timer_debug1('contracting Vnuc', *t1)
if mydf.eta != 0 and cell.dimension == 3:
nucbar = sum([z/nuccell.bas_exp(i)[0] for i,z in enumerate(charge)])
nucbar *= numpy.pi/cell.vol
ovlp = cell.pbc_intor('cint1e_ovlp_sph', 1, lib.HERMITIAN, kpts_lst)
for k in range(nkpts):
s = lib.pack_tril(ovlp[k])
vjR[k] -= nucbar * s.real
vjI[k] -= nucbar * s.imag
vj = []
for k, kpt in enumerate(kpts_lst):
if gamma_point(kpt):
vj.append(lib.unpack_tril(vjR[k]))
else:
vj.append(lib.unpack_tril(vjR[k]+vjI[k]*1j))
if kpts is None or numpy.shape(kpts) == (3,):
vj = vj[0]
return vj
def get_nuc(mydf, kpts=None):
cell = mydf.cell
if kpts is None:
kpts_lst = numpy.zeros((1, 3))
else:
kpts_lst = numpy.reshape(kpts, (-1, 3))
log = logger.Logger(mydf.stdout, mydf.verbose)
t1 = (time.clock(), time.time())
nkpts = len(kpts_lst)
nao = cell.nao_nr()
nao_pair = nao * (nao + 1) // 2
Gv, Gvbase, kws = cell.get_Gv_weights(mydf.gs)
kpt_allow = numpy.zeros(3)
if mydf.eta == 0:
vpplocG = pseudo.pp_int.get_gth_vlocG_part1(cell, Gv)
vpplocG = -numpy.einsum('ij,ij->j', cell.get_SI(Gv), vpplocG)
vpplocG *= kws
vG = vpplocG
vj = numpy.zeros((nkpts, nao_pair), dtype=numpy.complex128)
else:
nuccell = copy.copy(cell)
half_sph_norm = .5 / numpy.sqrt(numpy.pi)
norm = half_sph_norm / gto.mole._gaussian_int(2, mydf.eta)
chg_env = [mydf.eta, norm]
ptr_eta = cell._env.size
ptr_norm = ptr_eta + 1
chg_bas = [[ia, 0, 1, 1, 0, ptr_eta, ptr_norm, 0]
for ia in range(cell.natm)]
nuccell._atm = cell._atm
nuccell._bas = numpy.asarray(chg_bas, dtype=numpy.int32)
nuccell._env = numpy.hstack((cell._env, chg_env))
# PP-loc part1 is handled by fakenuc in _int_nuc_vloc
vj = lib.asarray(mydf._int_nuc_vloc(nuccell, kpts_lst))
t1 = log.timer_debug1('vnuc pass1: analytic int', *t1)
charge = -cell.atom_charges()
coulG = tools.get_coulG(cell, kpt_allow, gs=mydf.gs, Gv=Gv)
coulG *= kws
aoaux = ft_ao.ft_ao(nuccell, Gv)
vG = numpy.einsum('i,xi->x', charge, aoaux) * coulG
max_memory = max(2000, mydf.max_memory - lib.current_memory()[0])
for aoaoks, p0, p1 in mydf.ft_loop(mydf.gs,
kpt_allow,
kpts_lst,
max_memory=max_memory,
aosym='s2'):
for k, aoao in enumerate(aoaoks):
# rho_ij(G) nuc(-G) / G^2
# = [Re(rho_ij(G)) + Im(rho_ij(G))*1j] [Re(nuc(G)) - Im(nuc(G))*1j] / G^2
if gamma_point(kpts_lst[k]):
vj[k] += numpy.einsum('k,kx->x', vG[p0:p1].real, aoao.real)
vj[k] += numpy.einsum('k,kx->x', vG[p0:p1].imag, aoao.imag)
else:
vj[k] += numpy.einsum('k,kx->x', vG[p0:p1].conj(), aoao)
t1 = log.timer_debug1('contracting Vnuc', *t1)
vj_kpts = []
for k, kpt in enumerate(kpts_lst):
if gamma_point(kpt):
vj_kpts.append(lib.unpack_tril(vj[k].real.copy()))
else:
vj_kpts.append(lib.unpack_tril(vj[k]))
if kpts is None or numpy.shape(kpts) == (3, ):
vj_kpts = vj_kpts[0]
return numpy.asarray(vj_kpts)
def _make_j3c(mydf, cell, auxcell, kptij_lst, cderi_file):
t1 = (time.clock(), time.time())
log = logger.Logger(mydf.stdout, mydf.verbose)
max_memory = max(2000, mydf.max_memory-lib.current_memory()[0])
fused_cell, fuse = fuse_auxcell(mydf, auxcell)
# Create swap file to avoid huge cderi_file. see also function
# pyscf.pbc.df.df._make_j3c
swapfile = tempfile.NamedTemporaryFile(dir=os.path.dirname(cderi_file))
fswap = lib.H5TmpFile(swapfile.name)
# Unlink swapfile to avoid trash
swapfile = None
outcore._aux_e2(cell, fused_cell, fswap, 'int3c2e', aosym='s2',
kptij_lst=kptij_lst, dataname='j3c-junk', max_memory=max_memory)
t1 = log.timer_debug1('3c2e', *t1)
nao = cell.nao_nr()
naux = auxcell.nao_nr()
mesh = mydf.mesh
Gv, Gvbase, kws = cell.get_Gv_weights(mesh)
b = cell.reciprocal_vectors()
gxyz = lib.cartesian_prod([numpy.arange(len(x)) for x in Gvbase])
ngrids = gxyz.shape[0]
kptis = kptij_lst[:,0]
kptjs = kptij_lst[:,1]
kpt_ji = kptjs - kptis
uniq_kpts, uniq_index, uniq_inverse = unique(kpt_ji)
log.debug('Num uniq kpts %d', len(uniq_kpts))
log.debug2('uniq_kpts %s', uniq_kpts)
# j2c ~ (-kpt_ji | kpt_ji)
j2c = fused_cell.pbc_intor('int2c2e', hermi=1, kpts=uniq_kpts)
for k, kpt in enumerate(uniq_kpts):
aoaux = ft_ao.ft_ao(fused_cell, Gv, None, b, gxyz, Gvbase, kpt).T
aoaux = fuse(aoaux)
coulG = mydf.weighted_coulG(kpt, False, mesh)
LkR = numpy.asarray(aoaux.real, order='C')
LkI = numpy.asarray(aoaux.imag, order='C')
j2c_k = fuse(fuse(j2c[k]).T).T.copy()
if is_zero(kpt): # kpti == kptj
j2c_k -= lib.dot(LkR*coulG, LkR.T)
j2c_k -= lib.dot(LkI*coulG, LkI.T)
else:
# aoaux ~ kpt_ij, aoaux.conj() ~ kpt_kl
j2cR, j2cI = zdotCN(LkR*coulG, LkI*coulG, LkR.T, LkI.T)
j2c_k -= j2cR + j2cI * 1j
fswap['j2c/%d'%k] = j2c_k
aoaux = LkR = LkI = j2cR = j2cI = coulG = None
j2c = None
def cholesky_decomposed_metric(uniq_kptji_id):
j2c = numpy.asarray(fswap['j2c/%d'%uniq_kptji_id])
j2c_negative = None
# Note large difference may be found in results between the CD/eig treatments.
# In some systems, small integral errors can lead to different treatments of
# linear dependency which can be observed in the total energy/orbital energy
# around 4th decimal place.
# try:
# j2c = scipy.linalg.cholesky(j2c, lower=True)
# j2ctag = 'CD'
# except scipy.linalg.LinAlgError as e:
#
# Abandon CD treatment for better numerical stability
w, v = scipy.linalg.eigh(j2c)
log.debug('MDF metric for kpt %s cond = %.4g, drop %d bfns',
uniq_kptji_id, w[-1]/w[0], numpy.count_nonzero(w<mydf.linear_dep_threshold))
v1 = v[:,w>mydf.linear_dep_threshold].T.conj()
v1 /= numpy.sqrt(w[w>mydf.linear_dep_threshold]).reshape(-1,1)
j2c = v1
if cell.dimension == 2 and cell.low_dim_ft_type != 'inf_vacuum':
idx = numpy.where(w < -mydf.linear_dep_threshold)[0]
if len(idx) > 0:
j2c_negative = (v[:,idx]/numpy.sqrt(-w[idx])).conj().T
j2ctag = 'eig'
return j2c, j2c_negative, j2ctag
feri = h5py.File(cderi_file, 'w')
feri['j3c-kptij'] = kptij_lst
nsegs = len(fswap['j3c-junk/0'])
def make_kpt(uniq_kptji_id, cholesky_j2c): # kpt = kptj - kpti
kpt = uniq_kpts[uniq_kptji_id]
log.debug1('kpt = %s', kpt)
adapted_ji_idx = numpy.where(uniq_inverse == uniq_kptji_id)[0]
adapted_kptjs = kptjs[adapted_ji_idx]
nkptj = len(adapted_kptjs)
log.debug1('adapted_ji_idx = %s', adapted_ji_idx)
j2c, j2c_negative, j2ctag = cholesky_j2c
Gaux = ft_ao.ft_ao(fused_cell, Gv, None, b, gxyz, Gvbase, kpt).T
Gaux = fuse(Gaux)
Gaux *= mydf.weighted_coulG(kpt, False, mesh)
kLR = Gaux.T.real.copy('C')
kLI = Gaux.T.imag.copy('C')
if is_zero(kpt): # kpti == kptj
aosym = 's2'
nao_pair = nao*(nao+1)//2
if cell.dimension == 3:
vbar = fuse(mydf.auxbar(fused_cell))
ovlp = cell.pbc_intor('int1e_ovlp', hermi=1, kpts=adapted_kptjs)
ovlp = [lib.pack_tril(s) for s in ovlp]
else:
aosym = 's1'
nao_pair = nao**2
mem_now = lib.current_memory()[0]
log.debug2('memory = %s', mem_now)
max_memory = max(2000, mydf.max_memory-mem_now)
# nkptj for 3c-coulomb arrays plus 1 Lpq array
buflen = min(max(int(max_memory*.38e6/16/naux/(nkptj+1)), 1), nao_pair)
shranges = _guess_shell_ranges(cell, buflen, aosym)
buflen = max([x[2] for x in shranges])
# +1 for a pqkbuf
if aosym == 's2':
Gblksize = max(16, int(max_memory*.1e6/16/buflen/(nkptj+1)))
else:
Gblksize = max(16, int(max_memory*.2e6/16/buflen/(nkptj+1)))
Gblksize = min(Gblksize, ngrids, 16384)
pqkRbuf = numpy.empty(buflen*Gblksize)
pqkIbuf = numpy.empty(buflen*Gblksize)
# buf for ft_aopair
buf = numpy.empty((nkptj,buflen*Gblksize), dtype=numpy.complex128)
def pw_contract(istep, sh_range, j3cR, j3cI):
bstart, bend, ncol = sh_range
if aosym == 's2':
shls_slice = (bstart, bend, 0, bend)
else:
shls_slice = (bstart, bend, 0, cell.nbas)
for p0, p1 in lib.prange(0, ngrids, Gblksize):
dat = ft_ao._ft_aopair_kpts(cell, Gv[p0:p1], shls_slice, aosym,
b, gxyz[p0:p1], Gvbase, kpt,
adapted_kptjs, out=buf)
nG = p1 - p0
for k, ji in enumerate(adapted_ji_idx):
aoao = dat[k].reshape(nG,ncol)
pqkR = numpy.ndarray((ncol,nG), buffer=pqkRbuf)
pqkI = numpy.ndarray((ncol,nG), buffer=pqkIbuf)
pqkR[:] = aoao.real.T
pqkI[:] = aoao.imag.T
lib.dot(kLR[p0:p1].T, pqkR.T, -1, j3cR[k], 1)
lib.dot(kLI[p0:p1].T, pqkI.T, -1, j3cR[k], 1)
if not (is_zero(kpt) and gamma_point(adapted_kptjs[k])):
lib.dot(kLR[p0:p1].T, pqkI.T, -1, j3cI[k], 1)
lib.dot(kLI[p0:p1].T, pqkR.T, 1, j3cI[k], 1)
for k, ji in enumerate(adapted_ji_idx):
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
v = j3cR[k]
else:
v = j3cR[k] + j3cI[k] * 1j
if j2ctag == 'CD':
v = scipy.linalg.solve_triangular(j2c, v, lower=True, overwrite_b=True)
feri['j3c/%d/%d'%(ji,istep)] = v
else:
feri['j3c/%d/%d'%(ji,istep)] = lib.dot(j2c, v)
# low-dimension systems
if j2c_negative is not None:
feri['j3c-/%d/%d'%(ji,istep)] = lib.dot(j2c_negative, v)
with lib.call_in_background(pw_contract) as compute:
col1 = 0
for istep, sh_range in enumerate(shranges):
log.debug1('int3c2e [%d/%d], AO [%d:%d], ncol = %d', \
istep+1, len(shranges), *sh_range)
bstart, bend, ncol = sh_range
col0, col1 = col1, col1+ncol
j3cR = []
j3cI = []
for k, idx in enumerate(adapted_ji_idx):
v = [fswap['j3c-junk/%d/%d'%(idx,i)][0,col0:col1].T for i in range(nsegs)]
v = fuse(numpy.vstack(v))
if is_zero(kpt) and cell.dimension == 3:
for i in numpy.where(vbar != 0)[0]:
v[i] -= vbar[i] * ovlp[k][col0:col1]
j3cR.append(numpy.asarray(v.real, order='C'))
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
j3cI.append(None)
else:
j3cI.append(numpy.asarray(v.imag, order='C'))
v = None
compute(istep, sh_range, j3cR, j3cI)
for ji in adapted_ji_idx:
del(fswap['j3c-junk/%d'%ji])
# Wrapped around boundary and symmetry between k and -k can be used
# explicitly for the metric integrals. We consider this symmetry
# because it is used in the df_ao2mo module when contracting two 3-index
# integral tensors to the 4-index 2e integral tensor. If the symmetry
# related k-points are treated separately, the resultant 3-index tensors
# may have inconsistent dimension due to the numerial noise when handling
# linear dependency of j2c.
def conj_j2c(cholesky_j2c):
j2c, j2c_negative, j2ctag = cholesky_j2c
if j2c_negative is None:
return j2c.conj(), None, j2ctag
else:
return j2c.conj(), j2c_negative.conj(), j2ctag
a = cell.lattice_vectors() / (2*numpy.pi)
def kconserve_indices(kpt):
'''search which (kpts+kpt) satisfies momentum conservation'''
kdif = numpy.einsum('wx,ix->wi', a, uniq_kpts + kpt)
kdif_int = numpy.rint(kdif)
mask = numpy.einsum('wi->i', abs(kdif - kdif_int)) < KPT_DIFF_TOL
uniq_kptji_ids = numpy.where(mask)[0]
return uniq_kptji_ids
done = numpy.zeros(len(uniq_kpts), dtype=bool)
for k, kpt in enumerate(uniq_kpts):
if done[k]:
continue
log.debug1('Cholesky decomposition for j2c at kpt %s', k)
cholesky_j2c = cholesky_decomposed_metric(k)
# The k-point k' which has (k - k') * a = 2n pi. Metric integrals have the
# symmetry S = S
uniq_kptji_ids = kconserve_indices(-kpt)
log.debug1("Symmetry pattern (k - %s)*a= 2n pi", kpt)
log.debug1(" make_kpt for uniq_kptji_ids %s", uniq_kptji_ids)
for uniq_kptji_id in uniq_kptji_ids:
if not done[uniq_kptji_id]:
make_kpt(uniq_kptji_id, cholesky_j2c)
done[uniq_kptji_ids] = True
# The k-point k' which has (k + k') * a = 2n pi. Metric integrals have the
# symmetry S = S*
uniq_kptji_ids = kconserve_indices(kpt)
log.debug1("Symmetry pattern (k + %s)*a= 2n pi", kpt)
log.debug1(" make_kpt for %s", uniq_kptji_ids)
cholesky_j2c = conj_j2c(cholesky_j2c)
for uniq_kptji_id in uniq_kptji_ids:
if not done[uniq_kptji_id]:
make_kpt(uniq_kptji_id, cholesky_j2c)
done[uniq_kptji_ids] = True
feri.close()
def _make_j3c(mydf, cell, auxcell, kptij_lst, cderi_file):
log = logger.Logger(mydf.stdout, mydf.verbose)
t1 = t0 = (time.clock(), time.time())
fused_cell, fuse = fuse_auxcell(mydf, mydf.auxcell)
ao_loc = cell.ao_loc_nr()
nao = ao_loc[-1]
naux = auxcell.nao_nr()
nkptij = len(kptij_lst)
mesh = mydf.mesh
Gv, Gvbase, kws = cell.get_Gv_weights(mesh)
b = cell.reciprocal_vectors()
gxyz = lib.cartesian_prod([numpy.arange(len(x)) for x in Gvbase])
ngrids = gxyz.shape[0]
kptis = kptij_lst[:,0]
kptjs = kptij_lst[:,1]
kpt_ji = kptjs - kptis
uniq_kpts, uniq_index, uniq_inverse = unique(kpt_ji)
log.debug('Num uniq kpts %d', len(uniq_kpts))
log.debug2('uniq_kpts %s', uniq_kpts)
# j2c ~ (-kpt_ji | kpt_ji)
j2c = fused_cell.pbc_intor('int2c2e', hermi=1, kpts=uniq_kpts)
j2ctags = []
t1 = log.timer_debug1('2c2e', *t1)
swapfile = tempfile.NamedTemporaryFile(dir=os.path.dirname(cderi_file))
fswap = lib.H5TmpFile(swapfile.name)
# Unlink swapfile to avoid trash
swapfile = None
for k, kpt in enumerate(uniq_kpts):
coulG = mydf.weighted_coulG(kpt, False, mesh)
j2c[k] = fuse(fuse(j2c[k]).T).T.copy()
j2c_k = numpy.zeros_like(j2c[k])
for p0, p1 in mydf.mpi_prange(0, ngrids):
aoaux = ft_ao.ft_ao(fused_cell, Gv[p0:p1], None, b, gxyz[p0:p1], Gvbase, kpt).T
aoaux = fuse(aoaux)
LkR = numpy.asarray(aoaux.real, order='C')
LkI = numpy.asarray(aoaux.imag, order='C')
aoaux = None
if is_zero(kpt): # kpti == kptj
j2cR = lib.dot(LkR*coulG[p0:p1], LkR.T)
j2c_k += lib.dot(LkI*coulG[p0:p1], LkI.T, 1, j2cR, 1)
else:
# aoaux ~ kpt_ij, aoaux.conj() ~ kpt_kl
j2cR, j2cI = zdotCN(LkR*coulG[p0:p1], LkI*coulG[p0:p1], LkR.T, LkI.T)
j2c_k += j2cR + j2cI * 1j
LkR = LkI = None
j2c[k] -= mpi.allreduce(j2c_k)
try:
fswap['j2c/%d'%k] = scipy.linalg.cholesky(j2c[k], lower=True)
j2ctags.append('CD')
except scipy.linalg.LinAlgError:
w, v = scipy.linalg.eigh(j2c[k])
log.debug2('metric linear dependency for kpt %s', k)
log.debug2('cond = %.4g, drop %d bfns',
w[0]/w[-1], numpy.count_nonzero(w<mydf.linear_dep_threshold))
v1 = v[:,w>mydf.linear_dep_threshold].T.conj()
v1 /= numpy.sqrt(w[w>mydf.linear_dep_threshold]).reshape(-1,1)
fswap['j2c/%d'%k] = v1
if cell.dimension == 2 and cell.low_dim_ft_type != 'inf_vacuum':
idx = numpy.where(w < -mydf.linear_dep_threshold)[0]
if len(idx) > 0:
fswap['j2c-/%d'%k] = (v[:,idx]/numpy.sqrt(-w[idx])).conj().T
w = v = v1 = v2 = None
j2ctags.append('eig')
aoaux = kLR = kLI = j2cR = j2cI = coulG = None
j2c = None
aosym_s2 = numpy.einsum('ix->i', abs(kptis-kptjs)) < 1e-9
j_only = numpy.all(aosym_s2)
if gamma_point(kptij_lst):
dtype = 'f8'
else:
dtype = 'c16'
t1 = log.timer_debug1('aoaux and int2c', *t1)
# Estimates the buffer size based on the last contraction in G-space.
# This contraction requires to hold nkptj copies of (naux,?) array
# simultaneously in memory.
mem_now = max(comm.allgather(lib.current_memory()[0]))
max_memory = max(2000, mydf.max_memory - mem_now)
nkptj_max = max((uniq_inverse==x).sum() for x in set(uniq_inverse))
buflen = max(int(min(max_memory*.5e6/16/naux/(nkptj_max+2)/nao,
nao/3/mpi.pool.size)), 1)
chunks = (buflen, nao)
j3c_jobs = mpi_df.grids2d_int3c_jobs(cell, auxcell, kptij_lst, chunks, j_only)
log.debug1('max_memory = %d MB (%d in use) chunks %s',
max_memory, mem_now, chunks)
log.debug2('j3c_jobs %s', j3c_jobs)
if j_only:
int3c = wrap_int3c(cell, fused_cell, 'int3c2e', 's2', 1, kptij_lst)
else:
int3c = wrap_int3c(cell, fused_cell, 'int3c2e', 's1', 1, kptij_lst)
idxb = numpy.tril_indices(nao)
idxb = (idxb[0] * nao + idxb[1]).astype('i')
aux_loc = fused_cell.ao_loc_nr(fused_cell.cart)
def gen_int3c(job_id, ish0, ish1):
dataname = 'j3c-chunks/%d' % job_id
i0 = ao_loc[ish0]
i1 = ao_loc[ish1]
dii = i1*(i1+1)//2 - i0*(i0+1)//2
dij = (i1 - i0) * nao
if j_only:
buflen = max(8, int(max_memory*1e6/16/(nkptij*dii+dii)))
else:
buflen = max(8, int(max_memory*1e6/16/(nkptij*dij+dij)))
auxranges = balance_segs(aux_loc[1:]-aux_loc[:-1], buflen)
buflen = max([x[2] for x in auxranges])
buf = numpy.empty(nkptij*dij*buflen, dtype=dtype)
buf1 = numpy.empty(dij*buflen, dtype=dtype)
naux = aux_loc[-1]
for kpt_id, kptij in enumerate(kptij_lst):
key = '%s/%d' % (dataname, kpt_id)
if aosym_s2[kpt_id]:
shape = (naux, dii)
else:
shape = (naux, dij)
if gamma_point(kptij):
fswap.create_dataset(key, shape, 'f8')
else:
fswap.create_dataset(key, shape, 'c16')
naux0 = 0
for istep, auxrange in enumerate(auxranges):
log.alldebug2("aux_e1 job_id %d step %d", job_id, istep)
sh0, sh1, nrow = auxrange
sub_slice = (ish0, ish1, 0, cell.nbas, sh0, sh1)
if j_only:
mat = numpy.ndarray((nkptij,dii,nrow), dtype=dtype, buffer=buf)
else:
mat = numpy.ndarray((nkptij,dij,nrow), dtype=dtype, buffer=buf)
mat = int3c(sub_slice, mat)
for k, kptij in enumerate(kptij_lst):
h5dat = fswap['%s/%d'%(dataname,k)]
v = lib.transpose(mat[k], out=buf1)
if not j_only and aosym_s2[k]:
idy = idxb[i0*(i0+1)//2:i1*(i1+1)//2] - i0 * nao
out = numpy.ndarray((nrow,dii), dtype=v.dtype, buffer=mat[k])
v = numpy.take(v, idy, axis=1, out=out)
if gamma_point(kptij):
h5dat[naux0:naux0+nrow] = v.real
else:
h5dat[naux0:naux0+nrow] = v
naux0 += nrow
def ft_fuse(job_id, uniq_kptji_id, sh0, sh1):
kpt = uniq_kpts[uniq_kptji_id] # kpt = kptj - kpti
adapted_ji_idx = numpy.where(uniq_inverse == uniq_kptji_id)[0]
adapted_kptjs = kptjs[adapted_ji_idx]
nkptj = len(adapted_kptjs)
Gaux = ft_ao.ft_ao(fused_cell, Gv, None, b, gxyz, Gvbase, kpt).T
Gaux = fuse(Gaux)
Gaux *= mydf.weighted_coulG(kpt, False, mesh)
kLR = lib.transpose(numpy.asarray(Gaux.real, order='C'))
kLI = lib.transpose(numpy.asarray(Gaux.imag, order='C'))
j2c = numpy.asarray(fswap['j2c/%d'%uniq_kptji_id])
j2ctag = j2ctags[uniq_kptji_id]
naux0 = j2c.shape[0]
if ('j2c-/%d' % uniq_kptji_id) in fswap:
j2c_negative = numpy.asarray(fswap['j2c-/%d'%uniq_kptji_id])
else:
j2c_negative = None
if is_zero(kpt):
aosym = 's2'
else:
aosym = 's1'
if aosym == 's2' and cell.dimension == 3:
vbar = fuse(mydf.auxbar(fused_cell))
ovlp = cell.pbc_intor('int1e_ovlp', hermi=1, kpts=adapted_kptjs)
ovlp = [lib.pack_tril(s) for s in ovlp]
j3cR = [None] * nkptj
j3cI = [None] * nkptj
i0 = ao_loc[sh0]
i1 = ao_loc[sh1]
for k, idx in enumerate(adapted_ji_idx):
key = 'j3c-chunks/%d/%d' % (job_id, idx)
v = fuse(numpy.asarray(fswap[key]))
if aosym == 's2' and cell.dimension == 3:
for i in numpy.where(vbar != 0)[0]:
v[i] -= vbar[i] * ovlp[k][i0*(i0+1)//2:i1*(i1+1)//2].ravel()
j3cR[k] = numpy.asarray(v.real, order='C')
if v.dtype == numpy.complex128:
j3cI[k] = numpy.asarray(v.imag, order='C')
v = None
ncol = j3cR[0].shape[1]
Gblksize = max(16, int(max_memory*1e6/16/ncol/(nkptj+1))) # +1 for pqkRbuf/pqkIbuf
Gblksize = min(Gblksize, ngrids, 16384)
pqkRbuf = numpy.empty(ncol*Gblksize)
pqkIbuf = numpy.empty(ncol*Gblksize)
buf = numpy.empty(nkptj*ncol*Gblksize, dtype=numpy.complex128)
log.alldebug2(' blksize (%d,%d)', Gblksize, ncol)
if aosym == 's2':
shls_slice = (sh0, sh1, 0, sh1)
else:
shls_slice = (sh0, sh1, 0, cell.nbas)
for p0, p1 in lib.prange(0, ngrids, Gblksize):
dat = ft_ao._ft_aopair_kpts(cell, Gv[p0:p1], shls_slice, aosym, b,
gxyz[p0:p1], Gvbase, kpt,
adapted_kptjs, out=buf)
nG = p1 - p0
for k, ji in enumerate(adapted_ji_idx):
aoao = dat[k].reshape(nG,ncol)
pqkR = numpy.ndarray((ncol,nG), buffer=pqkRbuf)
pqkI = numpy.ndarray((ncol,nG), buffer=pqkIbuf)
pqkR[:] = aoao.real.T
pqkI[:] = aoao.imag.T
lib.dot(kLR[p0:p1].T, pqkR.T, -1, j3cR[k], 1)
lib.dot(kLI[p0:p1].T, pqkI.T, -1, j3cR[k], 1)
if not (is_zero(kpt) and gamma_point(adapted_kptjs[k])):
lib.dot(kLR[p0:p1].T, pqkI.T, -1, j3cI[k], 1)
lib.dot(kLI[p0:p1].T, pqkR.T, 1, j3cI[k], 1)
for k, idx in enumerate(adapted_ji_idx):
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
v = j3cR[k]
else:
v = j3cR[k] + j3cI[k] * 1j
if j2ctag == 'CD':
v = scipy.linalg.solve_triangular(j2c, v, lower=True, overwrite_b=True)
fswap['j3c-chunks/%d/%d'%(job_id,idx)][:naux0] = v
else:
fswap['j3c-chunks/%d/%d'%(job_id,idx)][:naux0] = lib.dot(j2c, v)
# low-dimension systems
if j2c_negative is not None:
fswap['j3c-/%d/%d'%(job_id,idx)] = lib.dot(j2c_negative, v)
mpi_df._assemble(mydf, kptij_lst, j3c_jobs, gen_int3c, ft_fuse, cderi_file, fswap, log)
def make_kpt(uniq_kptji_id): # kpt = kptj - kpti
kpt = uniq_kpts[uniq_kptji_id]
log.debug1('kpt = %s', kpt)
adapted_ji_idx = numpy.where(uniq_inverse == uniq_kptji_id)[0]
adapted_kptjs = kptjs[adapted_ji_idx]
nkptj = len(adapted_kptjs)
log.debug1('adapted_ji_idx = %s', adapted_ji_idx)
Gaux = ft_ao.ft_ao(fused_cell, Gv, None, b, gxyz, Gvbase, kpt).T
Gaux = fuse(Gaux)
Gaux *= mydf.weighted_coulG(kpt, False, gs)
kLR = Gaux.T.real.copy('C')
kLI = Gaux.T.imag.copy('C')
j2c = numpy.asarray(feri['j2c/%d' % uniq_kptji_id])
# Note large difference may be found in results between the CD/eig treatments.
# In some systems, small integral errors can lead to different treatments of
# linear dependency which can be observed in the total energy/orbital energy
# around 4th decimal place.
# try:
# j2c = scipy.linalg.cholesky(j2c, lower=True)
# j2ctag = 'CD'
# except scipy.linalg.LinAlgError as e:
#
# Abandon CD treatment for better numerical stablity
w, v = scipy.linalg.eigh(j2c)
log.debug('MDF metric for kpt %s cond = %.4g, drop %d bfns',
uniq_kptji_id, w[-1] / w[0],
numpy.count_nonzero(w < mydf.linear_dep_threshold))
v = v[:, w > mydf.linear_dep_threshold].T.conj()
v /= numpy.sqrt(w[w > mydf.linear_dep_threshold]).reshape(-1, 1)
j2c = v
j2ctag = 'eig'
naux0 = j2c.shape[0]
if is_zero(kpt): # kpti == kptj
aosym = 's2'
nao_pair = nao * (nao + 1) // 2
vbar = fuse(mydf.auxbar(fused_cell))
ovlp = cell.pbc_intor('int1e_ovlp_sph',
hermi=1,
kpts=adapted_kptjs)
for k, ji in enumerate(adapted_ji_idx):
ovlp[k] = lib.pack_tril(ovlp[k])
else:
aosym = 's1'
nao_pair = nao**2
mem_now = lib.current_memory()[0]
log.debug2('memory = %s', mem_now)
max_memory = max(2000, mydf.max_memory - mem_now)
# nkptj for 3c-coulomb arrays plus 1 Lpq array
buflen = min(
max(int(max_memory * .6 * 1e6 / 16 / naux / (nkptj + 1)), 1),
nao_pair)
shranges = _guess_shell_ranges(cell, buflen, aosym)
buflen = max([x[2] for x in shranges])
# +1 for a pqkbuf
if aosym == 's2':
Gblksize = max(
16, int(max_memory * .2 * 1e6 / 16 / buflen / (nkptj + 1)))
else:
Gblksize = max(
16, int(max_memory * .4 * 1e6 / 16 / buflen / (nkptj + 1)))
Gblksize = min(Gblksize, ngs, 16384)
pqkRbuf = numpy.empty(buflen * Gblksize)
pqkIbuf = numpy.empty(buflen * Gblksize)
# buf for ft_aopair
buf = numpy.empty((nkptj, buflen * Gblksize), dtype=numpy.complex128)
col1 = 0
for istep, sh_range in enumerate(shranges):
log.debug1('int3c2e [%d/%d], AO [%d:%d], ncol = %d', \
istep+1, len(shranges), *sh_range)
bstart, bend, ncol = sh_range
col0, col1 = col1, col1 + ncol
j3cR = []
j3cI = []
for k, idx in enumerate(adapted_ji_idx):
v = fuse(numpy.asarray(feri['j3c/%d' % idx][:, col0:col1]))
if is_zero(kpt):
for i, c in enumerate(vbar):
if c != 0:
v[i] -= c * ovlp[k][col0:col1]
j3cR.append(numpy.asarray(v.real, order='C'))
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
j3cI.append(None)
else:
j3cI.append(numpy.asarray(v.imag, order='C'))
v = None
if aosym == 's2':
shls_slice = (bstart, bend, 0, bend)
else:
shls_slice = (bstart, bend, 0, cell.nbas)
for p0, p1 in lib.prange(0, ngs, Gblksize):
dat = ft_ao._ft_aopair_kpts(cell,
Gv[p0:p1],
shls_slice,
aosym,
b,
gxyz[p0:p1],
Gvbase,
kpt,
adapted_kptjs,
out=buf)
nG = p1 - p0
for k, ji in enumerate(adapted_ji_idx):
aoao = dat[k].reshape(nG, ncol)
pqkR = numpy.ndarray((ncol, nG), buffer=pqkRbuf)
pqkI = numpy.ndarray((ncol, nG), buffer=pqkIbuf)
pqkR[:] = aoao.real.T
pqkI[:] = aoao.imag.T
lib.dot(kLR[p0:p1].T, pqkR.T, -1, j3cR[k], 1)
lib.dot(kLI[p0:p1].T, pqkI.T, -1, j3cR[k], 1)
if not (is_zero(kpt) and gamma_point(adapted_kptjs[k])):
lib.dot(kLR[p0:p1].T, pqkI.T, -1, j3cI[k], 1)
lib.dot(kLI[p0:p1].T, pqkR.T, 1, j3cI[k], 1)
for k, ji in enumerate(adapted_ji_idx):
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
v = j3cR[k]
else:
v = j3cR[k] + j3cI[k] * 1j
if j2ctag == 'CD':
v = scipy.linalg.solve_triangular(j2c,
v,
lower=True,
overwrite_b=True)
else:
v = lib.dot(j2c, v)
feri['j3c/%d' % ji][:naux0, col0:col1] = v
del (feri['j2c/%d' % uniq_kptji_id])
for k, ji in enumerate(adapted_ji_idx):
v = feri['j3c/%d' % ji][:naux0]
del (feri['j3c/%d' % ji])
feri['j3c/%d' % ji] = v
def ft_fuse(job_id, uniq_kptji_id, sh0, sh1):
kpt = uniq_kpts[uniq_kptji_id] # kpt = kptj - kpti
adapted_ji_idx = numpy.where(uniq_inverse == uniq_kptji_id)[0]
adapted_kptjs = kptjs[adapted_ji_idx]
nkptj = len(adapted_kptjs)
j2c = numpy.asarray(fswap['j2c/%d' % uniq_kptji_id])
j2ctag = j2ctags[uniq_kptji_id]
naux0 = j2c.shape[0]
if ('j2c-/%d' % uniq_kptji_id) in fswap:
j2c_negative = numpy.asarray(fswap['j2c-/%d' % uniq_kptji_id])
else:
j2c_negative = None
if is_zero(kpt):
aosym = 's2'
else:
aosym = 's1'
if aosym == 's2' and cell.dimension == 3:
vbar = fuse(mydf.auxbar(fused_cell))
ovlp = cell.pbc_intor('int1e_ovlp', hermi=1, kpts=adapted_kptjs)
ovlp = [lib.pack_tril(s) for s in ovlp]
j3cR = [None] * nkptj
j3cI = [None] * nkptj
i0 = ao_loc[sh0]
i1 = ao_loc[sh1]
for k, idx in enumerate(adapted_ji_idx):
key = 'j3c-chunks/%d/%d' % (job_id, idx)
v = numpy.asarray(fswap[key])
if aosym == 's2' and cell.dimension == 3:
for i in numpy.where(vbar != 0)[0]:
v[i] -= vbar[i] * ovlp[k][i0 * (i0 + 1) // 2:i1 *
(i1 + 1) // 2].ravel()
j3cR[k] = numpy.asarray(v.real, order='C')
if v.dtype == numpy.complex128:
j3cI[k] = numpy.asarray(v.imag, order='C')
v = None
ncol = j3cR[0].shape[1]
Gblksize = max(16, int(max_memory * 1e6 / 16 / ncol /
(nkptj + 1))) # +1 for pqkRbuf/pqkIbuf
Gblksize = min(Gblksize, ngrids, 16384)
pqkRbuf = numpy.empty(ncol * Gblksize)
pqkIbuf = numpy.empty(ncol * Gblksize)
buf = numpy.empty(nkptj * ncol * Gblksize, dtype=numpy.complex128)
log.alldebug2('job_id %d blksize (%d,%d)', job_id, Gblksize, ncol)
wcoulG = mydf.weighted_coulG(kpt, False, mesh)
fused_cell_slice = (auxcell.nbas, fused_cell.nbas)
if aosym == 's2':
shls_slice = (sh0, sh1, 0, sh1)
else:
shls_slice = (sh0, sh1, 0, cell.nbas)
for p0, p1 in lib.prange(0, ngrids, Gblksize):
Gaux = ft_ao.ft_ao(fused_cell, Gv[p0:p1], fused_cell_slice, b,
gxyz[p0:p1], Gvbase, kpt)
Gaux *= wcoulG[p0:p1, None]
kLR = Gaux.real.copy('C')
kLI = Gaux.imag.copy('C')
Gaux = None
dat = ft_ao._ft_aopair_kpts(cell,
Gv[p0:p1],
shls_slice,
aosym,
b,
gxyz[p0:p1],
Gvbase,
kpt,
adapted_kptjs,
out=buf)
nG = p1 - p0
for k, ji in enumerate(adapted_ji_idx):
aoao = dat[k].reshape(nG, ncol)
pqkR = numpy.ndarray((ncol, nG), buffer=pqkRbuf)
pqkI = numpy.ndarray((ncol, nG), buffer=pqkIbuf)
pqkR[:] = aoao.real.T
pqkI[:] = aoao.imag.T
lib.dot(kLR.T, pqkR.T, -1, j3cR[k][naux:], 1)
lib.dot(kLI.T, pqkI.T, -1, j3cR[k][naux:], 1)
if not (is_zero(kpt) and gamma_point(adapted_kptjs[k])):
lib.dot(kLR.T, pqkI.T, -1, j3cI[k][naux:], 1)
lib.dot(kLI.T, pqkR.T, 1, j3cI[k][naux:], 1)
kLR = kLI = None
for k, idx in enumerate(adapted_ji_idx):
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
v = fuse(j3cR[k])
else:
v = fuse(j3cR[k] + j3cI[k] * 1j)
if j2ctag == 'CD':
v = scipy.linalg.solve_triangular(j2c,
v,
lower=True,
overwrite_b=True)
fswap['j3c-chunks/%d/%d' % (job_id, idx)][:naux0] = v
else:
fswap['j3c-chunks/%d/%d' % (job_id, idx)][:naux0] = lib.dot(
j2c, v)
# low-dimension systems
if j2c_negative is not None:
fswap['j3c-/%d/%d' % (job_id, idx)] = lib.dot(j2c_negative, v)
def get_pnucp(mydf, kpts=None):
cell = mydf.cell
if kpts is None:
kpts_lst = numpy.zeros((1,3))
else:
kpts_lst = numpy.reshape(kpts, (-1,3))
log = logger.Logger(mydf.stdout, mydf.verbose)
t1 = t0 = (time.clock(), time.time())
nkpts = len(kpts_lst)
nao = cell.nao_nr()
nao_pair = nao * (nao+1) // 2
Gv, Gvbase, kws = cell.get_Gv_weights(mydf.gs)
kpt_allow = numpy.zeros(3)
if mydf.eta == 0:
charge = -cell.atom_charges()
#coulG=4*numpy.pi/G^2 is cancelled with (sigma dot p i, sigma dot p j)
SI = cell.get_SI(Gv)
vGR = numpy.einsum('i,ix->x', 4*numpy.pi*charge, SI.real) * kws
vGI = numpy.einsum('i,ix->x', 4*numpy.pi*charge, SI.imag) * kws
wjR = numpy.zeros((nkpts,nao_pair))
wjI = numpy.zeros((nkpts,nao_pair))
else:
nuccell = copy.copy(cell)
half_sph_norm = .5/numpy.sqrt(numpy.pi)
norm = half_sph_norm/mole._gaussian_int(2, mydf.eta)
chg_env = [mydf.eta, norm]
ptr_eta = cell._env.size
ptr_norm = ptr_eta + 1
chg_bas = [[ia, 0, 1, 1, 0, ptr_eta, ptr_norm, 0] for ia in range(cell.natm)]
nuccell._atm = cell._atm
nuccell._bas = numpy.asarray(chg_bas, dtype=numpy.int32)
nuccell._env = numpy.hstack((cell._env, chg_env))
wj = lib.asarray(mydf._int_nuc_vloc(nuccell, kpts_lst, 'cint3c2e_pvp1_sph'))
wjR = wj.real
wjI = wj.imag
t1 = log.timer_debug1('pnucp pass1: analytic int', *t1)
charge = -cell.atom_charges()
#coulG=4*numpy.pi/G^2 is cancelled with (sigma dot p i, sigma dot p j)
aoaux = ft_ao.ft_ao(nuccell, Gv)
vGR = numpy.einsum('i,xi->x', 4*numpy.pi*charge, aoaux.real) * kws
vGI = numpy.einsum('i,xi->x', 4*numpy.pi*charge, aoaux.imag) * kws
max_memory = max(2000, mydf.max_memory-lib.current_memory()[0])
for k, pqkR, pqkI, p0, p1 \
in mydf.ft_loop(mydf.gs, kpt_allow, kpts_lst,
max_memory=max_memory, aosym='s2'):
# rho_ij(G) nuc(-G) / G^2
# = [Re(rho_ij(G)) + Im(rho_ij(G))*1j] [Re(nuc(G)) - Im(nuc(G))*1j] / G^2
if not pwdf_jk.gamma_point(kpts_lst[k]):
wjI[k] += numpy.einsum('k,xk->x', vGR[p0:p1], pqkI)
wjI[k] -= numpy.einsum('k,xk->x', vGI[p0:p1], pqkR)
wjR[k] += numpy.einsum('k,xk->x', vGR[p0:p1], pqkR)
wjR[k] += numpy.einsum('k,xk->x', vGI[p0:p1], pqkI)
t1 = log.timer_debug1('contracting Vnuc', *t1)
if mydf.eta != 0 and cell.dimension == 3:
nucbar = sum([z/nuccell.bas_exp(i)[0] for i,z in enumerate(charge)])
nucbar *= numpy.pi/cell.vol * 2
ovlp = cell.pbc_intor('cint1e_kin_sph', 1, lib.HERMITIAN, kpts_lst)
for k in range(nkpts):
s = lib.pack_tril(ovlp[k])
wjR[k] -= nucbar * s.real
wjI[k] -= nucbar * s.imag
wj = []
for k, kpt in enumerate(kpts_lst):
if pwdf_jk.gamma_point(kpt):
wj.append(lib.unpack_tril(wjR[k]))
else:
wj.append(lib.unpack_tril(wjR[k]+wjI[k]*1j))
if kpts is None or numpy.shape(kpts) == (3,):
wj = wj[0]
return wj
def get_nuc(mydf, kpts=None):
cell = mydf.cell
if kpts is None:
kpts_lst = numpy.zeros((1, 3))
else:
kpts_lst = numpy.reshape(kpts, (-1, 3))
log = logger.Logger(mydf.stdout, mydf.verbose)
t0 = t1 = (time.clock(), time.time())
mesh = numpy.asarray(mydf.mesh)
nkpts = len(kpts_lst)
nao = cell.nao_nr()
nao_pair = nao * (nao + 1) // 2
charges = cell.atom_charges()
kpt_allow = numpy.zeros(3)
if mydf.eta == 0:
if cell.dimension > 0:
ke_guess = estimate_ke_cutoff(cell, cell.precision)
mesh_guess = tools.cutoff_to_mesh(cell.lattice_vectors(), ke_guess)
if numpy.any(mesh < mesh_guess * .8):
logger.warn(
mydf, 'mesh %s is not enough for AFTDF.get_nuc function '
'to get integral accuracy %g.\nRecommended mesh is %s.',
mesh, cell.precision, mesh_guess)
Gv, Gvbase, kws = cell.get_Gv_weights(mesh)
vpplocG = pseudo.pp_int.get_gth_vlocG_part1(cell, Gv)
vpplocG = -numpy.einsum('ij,ij->j', cell.get_SI(Gv), vpplocG)
v1 = -vpplocG.copy()
if cell.dimension == 1 or cell.dimension == 2:
G0idx, SI_on_z = pbcgto.cell._SI_for_uniform_model_charge(cell, Gv)
coulG = 4 * numpy.pi / numpy.linalg.norm(Gv[G0idx], axis=1)**2
vpplocG[G0idx] += charges.sum() * SI_on_z * coulG
vpplocG *= kws
vG = vpplocG
vj = numpy.zeros((nkpts, nao_pair), dtype=numpy.complex128)
else:
if cell.dimension > 0:
ke_guess = estimate_ke_cutoff_for_eta(cell, mydf.eta,
cell.precision)
mesh_guess = tools.cutoff_to_mesh(cell.lattice_vectors(), ke_guess)
if numpy.any(mesh < mesh_guess * .8):
logger.warn(
mydf, 'mesh %s is not enough for AFTDF.get_nuc function '
'to get integral accuracy %g.\nRecommended mesh is %s.',
mesh, cell.precision, mesh_guess)
mesh_min = numpy.min(
(mesh_guess[:cell.dimension], mesh[:cell.dimension]), axis=0)
mesh[:cell.dimension] = mesh_min.astype(int)
Gv, Gvbase, kws = cell.get_Gv_weights(mesh)
nuccell = copy.copy(cell)
half_sph_norm = .5 / numpy.sqrt(numpy.pi)
norm = half_sph_norm / gto.gaussian_int(2, mydf.eta)
chg_env = [mydf.eta, norm]
ptr_eta = cell._env.size
ptr_norm = ptr_eta + 1
chg_bas = [[ia, 0, 1, 1, 0, ptr_eta, ptr_norm, 0]
for ia in range(cell.natm)]
nuccell._atm = cell._atm
nuccell._bas = numpy.asarray(chg_bas, dtype=numpy.int32)
nuccell._env = numpy.hstack((cell._env, chg_env))
# PP-loc part1 is handled by fakenuc in _int_nuc_vloc
vj = lib.asarray(mydf._int_nuc_vloc(nuccell, kpts_lst))
t0 = t1 = log.timer_debug1('vnuc pass1: analytic int', *t0)
coulG = tools.get_coulG(cell, kpt_allow, mesh=mesh, Gv=Gv) * kws
aoaux = ft_ao.ft_ao(nuccell, Gv)
vG = numpy.einsum('i,xi->x', -charges, aoaux) * coulG
if cell.dimension == 1 or cell.dimension == 2:
G0idx, SI_on_z = pbcgto.cell._SI_for_uniform_model_charge(cell, Gv)
vG[G0idx] += charges.sum() * SI_on_z * coulG[G0idx]
max_memory = max(2000, mydf.max_memory - lib.current_memory()[0])
for aoaoks, p0, p1 in mydf.ft_loop(mesh,
kpt_allow,
kpts_lst,
max_memory=max_memory,
aosym='s2'):
for k, aoao in enumerate(aoaoks):
# rho_ij(G) nuc(-G) / G^2
# = [Re(rho_ij(G)) + Im(rho_ij(G))*1j] [Re(nuc(G)) - Im(nuc(G))*1j] / G^2
if gamma_point(kpts_lst[k]):
vj[k] += numpy.einsum('k,kx->x', vG[p0:p1].real, aoao.real)
vj[k] += numpy.einsum('k,kx->x', vG[p0:p1].imag, aoao.imag)
else:
vj[k] += numpy.einsum('k,kx->x', vG[p0:p1].conj(), aoao)
t1 = log.timer_debug1('contracting Vnuc [%s:%s]' % (p0, p1), *t1)
log.timer_debug1('contracting Vnuc', *t0)
vj_kpts = []
for k, kpt in enumerate(kpts_lst):
if gamma_point(kpt):
vj_kpts.append(lib.unpack_tril(vj[k].real.copy()))
else:
vj_kpts.append(lib.unpack_tril(vj[k]))
if kpts is None or numpy.shape(kpts) == (3, ):
vj_kpts = vj_kpts[0]
return numpy.asarray(vj_kpts)
def _int_nuc_vloc(mydf, nuccell, kpts, intor='int3c2e', aosym='s2', comp=1):
'''Vnuc - Vloc'''
cell = mydf.cell
nkpts = len(kpts)
# Use the 3c2e code with steep s gaussians to mimic nuclear density
fakenuc = _fake_nuc(cell)
fakenuc._atm, fakenuc._bas, fakenuc._env = \
gto.conc_env(nuccell._atm, nuccell._bas, nuccell._env,
fakenuc._atm, fakenuc._bas, fakenuc._env)
kptij_lst = numpy.hstack((kpts, kpts)).reshape(-1, 2, 3)
buf = incore.aux_e2(cell,
fakenuc,
intor,
aosym=aosym,
comp=comp,
kptij_lst=kptij_lst)
charge = cell.atom_charges()
charge = numpy.append(charge,
-charge) # (charge-of-nuccell, charge-of-fakenuc)
nao = cell.nao_nr()
nchg = len(charge)
if aosym == 's1':
nao_pair = nao**2
else:
nao_pair = nao * (nao + 1) // 2
if comp == 1:
buf = buf.reshape(nkpts, nao_pair, nchg)
mat = numpy.einsum('kxz,z->kx', buf, charge)
else:
buf = buf.reshape(nkpts, comp, nao_pair, nchg)
mat = numpy.einsum('kcxz,z->kcx', buf, charge)
if cell.dimension != 0 and intor in ('int3c2e', 'int3c2e_sph',
'int3c2e_cart'):
assert (comp == 1)
charge = -cell.atom_charges()
if cell.dimension == 1 or cell.dimension == 2:
Gv, Gvbase, kws = cell.get_Gv_weights(mydf.mesh)
G0idx, SI_on_z = pbcgto.cell._SI_for_uniform_model_charge(cell, Gv)
ZSI = numpy.einsum("i,ix->x", charge, cell.get_SI(Gv[G0idx]))
ZSI -= numpy.einsum('i,xi->x', charge,
ft_ao.ft_ao(nuccell, Gv[G0idx]))
coulG = 4 * numpy.pi / numpy.linalg.norm(Gv[G0idx], axis=1)**2
nucbar = numpy.einsum('i,i,i,i', ZSI.conj(), coulG, kws[G0idx],
SI_on_z)
if abs(kpts).sum() < 1e-9:
nucbar = nucbar.real
else: # cell.dimension == 3
nucbar = sum(
[z / nuccell.bas_exp(i)[0] for i, z in enumerate(charge)])
nucbar *= numpy.pi / cell.vol
ovlp = cell.pbc_intor('int1e_ovlp', 1, lib.HERMITIAN, kpts)
for k in range(nkpts):
if aosym == 's1':
mat[k] -= nucbar * ovlp[k].reshape(nao_pair)
else:
mat[k] -= nucbar * lib.pack_tril(ovlp[k])
return mat
def _make_j3c(mydf, cell, auxcell, kptij_lst):
t1 = (time.clock(), time.time())
log = logger.Logger(mydf.stdout, mydf.verbose)
max_memory = max(2000, mydf.max_memory-lib.current_memory()[0])
fused_cell, fuse = fuse_auxcell(mydf, auxcell)
outcore.aux_e2(cell, fused_cell, mydf._cderi, 'cint3c2e_sph',
kptij_lst=kptij_lst, dataname='j3c', max_memory=max_memory)
t1 = log.timer_debug1('3c2e', *t1)
nao = cell.nao_nr()
naux = auxcell.nao_nr()
gs = mydf.gs
Gv, Gvbase, kws = cell.get_Gv_weights(gs)
b = cell.reciprocal_vectors()
gxyz = lib.cartesian_prod([numpy.arange(len(x)) for x in Gvbase])
ngs = gxyz.shape[0]
kptis = kptij_lst[:,0]
kptjs = kptij_lst[:,1]
kpt_ji = kptjs - kptis
uniq_kpts, uniq_index, uniq_inverse = unique(kpt_ji)
# j2c ~ (-kpt_ji | kpt_ji)
j2c = fused_cell.pbc_intor('cint2c2e_sph', hermi=1, kpts=uniq_kpts)
kLRs = []
kLIs = []
# chgcell = make_modchg_basis(auxcell, mydf.eta)
# for k, kpt in enumerate(uniq_kpts):
# aoaux = ft_ao.ft_ao(chgcell, Gv, None, b, gxyz, Gvbase, kpt).T
# coulG = numpy.sqrt(mydf.weighted_coulG(kpt, False, gs))
# LkR = aoaux.real * coulG
# LkI = aoaux.imag * coulG
# j2caux = numpy.zeros_like(j2c[k])
# j2caux[naux:,naux:] = j2c[naux:,naux:]
# if is_zero(kpt): # kpti == kptj
# j2caux[naux:,naux:] -= lib.ddot(LkR, LkR.T)
# j2caux[naux:,naux:] -= lib.ddot(LkI, LkI.T)
# j2c[k] = j2c[k][:naux,:naux] - fuse(fuse(j2caux.T).T)
# vbar = fuse(mydf.auxbar(fused_cell))
# s = (vbar != 0).astype(numpy.double)
# j2c[k] -= numpy.einsum('i,j->ij', vbar, s)
# j2c[k] -= numpy.einsum('i,j->ij', s, vbar)
# else:
# j2cR, j2cI = zdotCN(LkR, LkI, LkR.T, LkI.T)
# j2caux[naux:,naux:] -= j2cR + j2cI * 1j
# j2c[k] = j2c[k][:naux,:naux] - fuse(fuse(j2caux.T).T)
# #j2c[k] = fuse(fuse(j2c[k]).T).T.copy()
# try:
# j2c[k] = scipy.linalg.cholesky(fuse(fuse(j2c[k]).T).T, lower=True)
# except scipy.linalg.LinAlgError as e:
# msg =('===================================\n'
# 'J-metric not positive definite.\n'
# 'It is likely that gs is not enough.\n'
# '===================================')
# log.error(msg)
# raise scipy.linalg.LinAlgError('\n'.join([e.message, msg]))
# kLR = LkR.T
# kLI = LkI.T
# if not kLR.flags.c_contiguous: kLR = lib.transpose(LkR)
# if not kLI.flags.c_contiguous: kLI = lib.transpose(LkI)
# kLR *= coulG.reshape(-1,1)
# kLI *= coulG.reshape(-1,1)
# kLRs.append(kLR)
# kLIs.append(kLI)
# aoaux = LkR = LkI = kLR = kLI = coulG = None
for k, kpt in enumerate(uniq_kpts):
aoaux = ft_ao.ft_ao(fused_cell, Gv, None, b, gxyz, Gvbase, kpt).T
coulG = numpy.sqrt(mydf.weighted_coulG(kpt, False, gs))
LkR = aoaux.real * coulG
LkI = aoaux.imag * coulG
if is_zero(kpt): # kpti == kptj
j2c[k][naux:] -= lib.ddot(LkR[naux:], LkR.T)
j2c[k][naux:] -= lib.ddot(LkI[naux:], LkI.T)
j2c[k][:naux,naux:] = j2c[k][naux:,:naux].T
else:
j2cR, j2cI = zdotCN(LkR[naux:], LkI[naux:], LkR.T, LkI.T)
j2c[k][naux:] -= j2cR + j2cI * 1j
j2c[k][:naux,naux:] = j2c[k][naux:,:naux].T.conj()
#j2c[k] = fuse(fuse(j2c[k]).T).T.copy()
try:
j2c[k] = scipy.linalg.cholesky(fuse(fuse(j2c[k]).T).T, lower=True)
except scipy.linalg.LinAlgError as e:
msg =('===================================\n'
'J-metric not positive definite.\n'
'It is likely that gs is not enough.\n'
'===================================')
log.error(msg)
raise scipy.linalg.LinAlgError('\n'.join([e.message, msg]))
kLR = LkR[naux:].T
kLI = LkI[naux:].T
if not kLR.flags.c_contiguous: kLR = lib.transpose(LkR[naux:])
if not kLI.flags.c_contiguous: kLI = lib.transpose(LkI[naux:])
kLR *= coulG.reshape(-1,1)
kLI *= coulG.reshape(-1,1)
kLRs.append(kLR)
kLIs.append(kLI)
aoaux = LkR = LkI = kLR = kLI = coulG = None
feri = h5py.File(mydf._cderi)
def make_kpt(uniq_kptji_id): # kpt = kptj - kpti
kpt = uniq_kpts[uniq_kptji_id]
log.debug1('kpt = %s', kpt)
adapted_ji_idx = numpy.where(uniq_inverse == uniq_kptji_id)[0]
adapted_kptjs = kptjs[adapted_ji_idx]
nkptj = len(adapted_kptjs)
log.debug1('adapted_ji_idx = %s', adapted_ji_idx)
kLR = kLRs[uniq_kptji_id]
kLI = kLIs[uniq_kptji_id]
if is_zero(kpt): # kpti == kptj
aosym = 's2'
nao_pair = nao*(nao+1)//2
vbar = fuse(mydf.auxbar(fused_cell))
ovlp = cell.pbc_intor('cint1e_ovlp_sph', hermi=1, kpts=adapted_kptjs)
for k, ji in enumerate(adapted_ji_idx):
ovlp[k] = lib.pack_tril(ovlp[k])
else:
aosym = 's1'
nao_pair = nao**2
max_memory = max(2000, mydf.max_memory-lib.current_memory()[0])
# nkptj for 3c-coulomb arrays plus 1 Lpq array
buflen = min(max(int(max_memory*.6*1e6/16/naux/(nkptj+1)), 1), nao_pair)
shranges = _guess_shell_ranges(cell, buflen, aosym)
buflen = max([x[2] for x in shranges])
# +1 for a pqkbuf
if aosym == 's2':
Gblksize = max(16, int(max_memory*.2*1e6/16/buflen/(nkptj+1)))
else:
Gblksize = max(16, int(max_memory*.4*1e6/16/buflen/(nkptj+1)))
Gblksize = min(Gblksize, ngs, 16384)
pqkRbuf = numpy.empty(buflen*Gblksize)
pqkIbuf = numpy.empty(buflen*Gblksize)
# buf for ft_aopair
buf = numpy.zeros((nkptj,buflen*Gblksize), dtype=numpy.complex128)
col1 = 0
for istep, sh_range in enumerate(shranges):
log.debug1('int3c2e [%d/%d], AO [%d:%d], ncol = %d', \
istep+1, len(shranges), *sh_range)
bstart, bend, ncol = sh_range
col0, col1 = col1, col1+ncol
j3cR = []
j3cI = []
for k, idx in enumerate(adapted_ji_idx):
v = numpy.asarray(feri['j3c/%d'%idx][:,col0:col1])
if is_zero(kpt):
for i, c in enumerate(vbar):
if c != 0:
v[i] -= c * ovlp[k][col0:col1]
j3cR.append(numpy.asarray(v.real, order='C'))
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
j3cI.append(None)
else:
j3cI.append(numpy.asarray(v.imag, order='C'))
if aosym == 's2':
shls_slice = (bstart, bend, 0, bend)
for p0, p1 in lib.prange(0, ngs, Gblksize):
ft_ao._ft_aopair_kpts(cell, Gv[p0:p1], shls_slice, aosym,
b, gxyz[p0:p1], Gvbase, kpt,
adapted_kptjs, out=buf)
nG = p1 - p0
for k, ji in enumerate(adapted_ji_idx):
aoao = numpy.ndarray((nG,ncol), dtype=numpy.complex128,
order='F', buffer=buf[k])
pqkR = numpy.ndarray((ncol,nG), buffer=pqkRbuf)
pqkI = numpy.ndarray((ncol,nG), buffer=pqkIbuf)
pqkR[:] = aoao.real.T
pqkI[:] = aoao.imag.T
aoao[:] = 0
lib.dot(kLR[p0:p1].T, pqkR.T, -1, j3cR[k][naux:], 1)
lib.dot(kLI[p0:p1].T, pqkI.T, -1, j3cR[k][naux:], 1)
if not (is_zero(kpt) and gamma_point(adapted_kptjs[k])):
lib.dot(kLR[p0:p1].T, pqkI.T, -1, j3cI[k][naux:], 1)
lib.dot(kLI[p0:p1].T, pqkR.T, 1, j3cI[k][naux:], 1)
else:
shls_slice = (bstart, bend, 0, cell.nbas)
ni = ncol // nao
for p0, p1 in lib.prange(0, ngs, Gblksize):
ft_ao._ft_aopair_kpts(cell, Gv[p0:p1], shls_slice, aosym,
b, gxyz[p0:p1], Gvbase, kpt,
adapted_kptjs, out=buf)
nG = p1 - p0
for k, ji in enumerate(adapted_ji_idx):
aoao = numpy.ndarray((nG,ni,nao), dtype=numpy.complex128,
order='F', buffer=buf[k])
pqkR = numpy.ndarray((ni,nao,nG), buffer=pqkRbuf)
pqkI = numpy.ndarray((ni,nao,nG), buffer=pqkIbuf)
pqkR[:] = aoao.real.transpose(1,2,0)
pqkI[:] = aoao.imag.transpose(1,2,0)
aoao[:] = 0
pqkR = pqkR.reshape(-1,nG)
pqkI = pqkI.reshape(-1,nG)
zdotCN(kLR[p0:p1].T, kLI[p0:p1].T, pqkR.T, pqkI.T,
-1, j3cR[k][naux:], j3cI[k][naux:], 1)
for k, ji in enumerate(adapted_ji_idx):
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
v = fuse(j3cR[k])
else:
v = fuse(j3cR[k] + j3cI[k] * 1j)
v = scipy.linalg.solve_triangular(j2c[uniq_kptji_id], v,
lower=True, overwrite_b=True)
feri['j3c/%d'%ji][:naux,col0:col1] = v
for k, kpt in enumerate(uniq_kpts):
make_kpt(k)
for k, kptij in enumerate(kptij_lst):
v = feri['j3c/%d'%k][:naux]
del(feri['j3c/%d'%k])
feri['j3c/%d'%k] = v
feri.close()
def get_pp_loc_part1(mydf, kpts=None):
cell = mydf.cell
if kpts is None:
kpts_lst = numpy.zeros((1,3))
else:
kpts_lst = numpy.reshape(kpts, (-1,3))
log = logger.Logger(mydf.stdout, mydf.verbose)
t0 = t1 = (time.clock(), time.time())
mesh = numpy.asarray(mydf.mesh)
nkpts = len(kpts_lst)
nao = cell.nao_nr()
nao_pair = nao * (nao+1) // 2
charges = cell.atom_charges()
kpt_allow = numpy.zeros(3)
if mydf.eta == 0:
if cell.dimension > 0:
ke_guess = estimate_ke_cutoff(cell, cell.precision)
mesh_guess = tools.cutoff_to_mesh(cell.lattice_vectors(), ke_guess)
if numpy.any(mesh[:cell.dimension] < mesh_guess[:cell.dimension]*.8):
logger.warn(mydf, 'mesh %s is not enough for AFTDF.get_nuc function '
'to get integral accuracy %g.\nRecommended mesh is %s.',
mesh, cell.precision, mesh_guess)
Gv, Gvbase, kws = cell.get_Gv_weights(mesh)
vpplocG = pseudo.pp_int.get_gth_vlocG_part1(cell, Gv)
vpplocG = -numpy.einsum('ij,ij->j', cell.get_SI(Gv), vpplocG)
vpplocG *= kws
vG = vpplocG
vj = numpy.zeros((nkpts,nao_pair), dtype=numpy.complex128)
else:
if cell.dimension > 0:
ke_guess = estimate_ke_cutoff_for_eta(cell, mydf.eta, cell.precision)
mesh_guess = tools.cutoff_to_mesh(cell.lattice_vectors(), ke_guess)
if numpy.any(mesh < mesh_guess*.8):
logger.warn(mydf, 'mesh %s is not enough for AFTDF.get_nuc function '
'to get integral accuracy %g.\nRecommended mesh is %s.',
mesh, cell.precision, mesh_guess)
mesh_min = numpy.min((mesh_guess, mesh), axis=0)
if cell.dimension < 2 or cell.low_dim_ft_type == 'inf_vacuum':
mesh[:cell.dimension] = mesh_min[:cell.dimension]
else:
mesh = mesh_min
Gv, Gvbase, kws = cell.get_Gv_weights(mesh)
nuccell = _compensate_nuccell(mydf)
# PP-loc part1 is handled by fakenuc in _int_nuc_vloc
vj = lib.asarray(mydf._int_nuc_vloc(nuccell, kpts_lst))
t0 = t1 = log.timer_debug1('vnuc pass1: analytic int', *t0)
coulG = tools.get_coulG(cell, kpt_allow, mesh=mesh, Gv=Gv) * kws
aoaux = ft_ao.ft_ao(nuccell, Gv)
vG = numpy.einsum('i,xi->x', -charges, aoaux) * coulG
max_memory = max(2000, mydf.max_memory-lib.current_memory()[0])
for aoaoks, p0, p1 in mydf.ft_loop(mesh, kpt_allow, kpts_lst,
max_memory=max_memory, aosym='s2'):
for k, aoao in enumerate(aoaoks):
# rho_ij(G) nuc(-G) / G^2
# = [Re(rho_ij(G)) + Im(rho_ij(G))*1j] [Re(nuc(G)) - Im(nuc(G))*1j] / G^2
if gamma_point(kpts_lst[k]):
vj[k] += numpy.einsum('k,kx->x', vG[p0:p1].real, aoao.real)
vj[k] += numpy.einsum('k,kx->x', vG[p0:p1].imag, aoao.imag)
else:
vj[k] += numpy.einsum('k,kx->x', vG[p0:p1].conj(), aoao)
t1 = log.timer_debug1('contracting Vnuc [%s:%s]'%(p0, p1), *t1)
log.timer_debug1('contracting Vnuc', *t0)
vj_kpts = []
for k, kpt in enumerate(kpts_lst):
if gamma_point(kpt):
vj_kpts.append(lib.unpack_tril(vj[k].real.copy()))
else:
vj_kpts.append(lib.unpack_tril(vj[k]))
if kpts is None or numpy.shape(kpts) == (3,):
vj_kpts = vj_kpts[0]
return numpy.asarray(vj_kpts)
def _make_j3c(mydf, cell, auxcell, kptij_lst, cderi_file):
t1 = (time.clock(), time.time())
log = logger.Logger(mydf.stdout, mydf.verbose)
max_memory = max(2000, mydf.max_memory - lib.current_memory()[0])
fused_cell, fuse = fuse_auxcell(mydf, auxcell)
# The ideal way to hold the temporary integrals is to store them in the
# cderi_file and overwrite them inplace in the second pass. The current
# HDF5 library does not have an efficient way to manage free space in
# overwriting. It often leads to the cderi_file ~2 times larger than the
# necessary size. For now, dumping the DF integral intermediates to a
# separated temporary file can avoid this issue. The DF intermediates may
# be terribly huge. The temporary file should be placed in the same disk
# as cderi_file.
swapfile = tempfile.NamedTemporaryFile(dir=os.path.dirname(cderi_file))
fswap = lib.H5TmpFile(swapfile.name)
# Unlink swapfile to avoid trash
swapfile = None
outcore._aux_e2(cell,
fused_cell,
fswap,
'int3c2e',
aosym='s2',
kptij_lst=kptij_lst,
dataname='j3c-junk',
max_memory=max_memory)
t1 = log.timer_debug1('3c2e', *t1)
nao = cell.nao_nr()
naux = auxcell.nao_nr()
mesh = mydf.mesh
Gv, Gvbase, kws = cell.get_Gv_weights(mesh)
b = cell.reciprocal_vectors()
gxyz = lib.cartesian_prod([numpy.arange(len(x)) for x in Gvbase])
ngrids = gxyz.shape[0]
kptis = kptij_lst[:, 0]
kptjs = kptij_lst[:, 1]
kpt_ji = kptjs - kptis
uniq_kpts, uniq_index, uniq_inverse = unique(kpt_ji)
log.debug('Num uniq kpts %d', len(uniq_kpts))
log.debug2('uniq_kpts %s', uniq_kpts)
# j2c ~ (-kpt_ji | kpt_ji)
j2c = fused_cell.pbc_intor('int2c2e', hermi=1, kpts=uniq_kpts)
max_memory = max(2000, mydf.max_memory - lib.current_memory()[0])
blksize = max(2048, int(max_memory * .5e6 / 16 / fused_cell.nao_nr()))
log.debug2('max_memory %s (MB) blocksize %s', max_memory, blksize)
for k, kpt in enumerate(uniq_kpts):
coulG = mydf.weighted_coulG(kpt, False, mesh)
for p0, p1 in lib.prange(0, ngrids, blksize):
aoaux = ft_ao.ft_ao(fused_cell, Gv[p0:p1], None, b, gxyz[p0:p1],
Gvbase, kpt).T
LkR = numpy.asarray(aoaux.real, order='C')
LkI = numpy.asarray(aoaux.imag, order='C')
aoaux = None
if is_zero(kpt): # kpti == kptj
j2c[k][naux:] -= lib.ddot(LkR[naux:] * coulG[p0:p1], LkR.T)
j2c[k][naux:] -= lib.ddot(LkI[naux:] * coulG[p0:p1], LkI.T)
j2c[k][:naux, naux:] = j2c[k][naux:, :naux].T
else:
j2cR, j2cI = zdotCN(LkR[naux:] * coulG[p0:p1],
LkI[naux:] * coulG[p0:p1], LkR.T, LkI.T)
j2c[k][naux:] -= j2cR + j2cI * 1j
j2c[k][:naux, naux:] = j2c[k][naux:, :naux].T.conj()
LkR = LkI = None
fswap['j2c/%d' % k] = fuse(fuse(j2c[k]).T).T
j2c = coulG = None
def cholesky_decomposed_metric(uniq_kptji_id):
j2c = numpy.asarray(fswap['j2c/%d' % uniq_kptji_id])
j2c_negative = None
try:
j2c = scipy.linalg.cholesky(j2c, lower=True)
j2ctag = 'CD'
except scipy.linalg.LinAlgError:
#msg =('===================================\n'
# 'J-metric not positive definite.\n'
# 'It is likely that mesh is not enough.\n'
# '===================================')
#log.error(msg)
#raise scipy.linalg.LinAlgError('\n'.join([str(e), msg]))
w, v = scipy.linalg.eigh(j2c)
log.debug('DF metric linear dependency for kpt %s', uniq_kptji_id)
log.debug('cond = %.4g, drop %d bfns', w[-1] / w[0],
numpy.count_nonzero(w < mydf.linear_dep_threshold))
v1 = v[:, w > mydf.linear_dep_threshold].conj().T
v1 /= numpy.sqrt(w[w > mydf.linear_dep_threshold]).reshape(-1, 1)
j2c = v1
if cell.dimension == 2 and cell.low_dim_ft_type != 'inf_vacuum':
idx = numpy.where(w < -mydf.linear_dep_threshold)[0]
if len(idx) > 0:
j2c_negative = (v[:, idx] / numpy.sqrt(-w[idx])).conj().T
w = v = None
j2ctag = 'eig'
return j2c, j2c_negative, j2ctag
feri = h5py.File(cderi_file, 'w')
feri['j3c-kptij'] = kptij_lst
nsegs = len(fswap['j3c-junk/0'])
def make_kpt(uniq_kptji_id, cholesky_j2c):
kpt = uniq_kpts[uniq_kptji_id] # kpt = kptj - kpti
log.debug1('kpt = %s', kpt)
adapted_ji_idx = numpy.where(uniq_inverse == uniq_kptji_id)[0]
adapted_kptjs = kptjs[adapted_ji_idx]
nkptj = len(adapted_kptjs)
log.debug1('adapted_ji_idx = %s', adapted_ji_idx)
j2c, j2c_negative, j2ctag = cholesky_j2c
shls_slice = (auxcell.nbas, fused_cell.nbas)
Gaux = ft_ao.ft_ao(fused_cell, Gv, shls_slice, b, gxyz, Gvbase, kpt)
wcoulG = mydf.weighted_coulG(kpt, False, mesh)
Gaux *= wcoulG.reshape(-1, 1)
kLR = Gaux.real.copy('C')
kLI = Gaux.imag.copy('C')
Gaux = None
if is_zero(kpt): # kpti == kptj
aosym = 's2'
nao_pair = nao * (nao + 1) // 2
if cell.dimension == 3:
vbar = fuse(mydf.auxbar(fused_cell))
ovlp = cell.pbc_intor('int1e_ovlp',
hermi=1,
kpts=adapted_kptjs)
ovlp = [lib.pack_tril(s) for s in ovlp]
else:
aosym = 's1'
nao_pair = nao**2
mem_now = lib.current_memory()[0]
log.debug2('memory = %s', mem_now)
max_memory = max(2000, mydf.max_memory - mem_now)
# nkptj for 3c-coulomb arrays plus 1 Lpq array
buflen = min(max(int(max_memory * .38e6 / 16 / naux / (nkptj + 1)), 1),
nao_pair)
shranges = _guess_shell_ranges(cell, buflen, aosym)
buflen = max([x[2] for x in shranges])
# +1 for a pqkbuf
if aosym == 's2':
Gblksize = max(16,
int(max_memory * .1e6 / 16 / buflen / (nkptj + 1)))
else:
Gblksize = max(16,
int(max_memory * .2e6 / 16 / buflen / (nkptj + 1)))
Gblksize = min(Gblksize, ngrids, 16384)
def load(aux_slice):
col0, col1 = aux_slice
j3cR = []
j3cI = []
for k, idx in enumerate(adapted_ji_idx):
v = numpy.vstack([
fswap['j3c-junk/%d/%d' % (idx, i)][0, col0:col1].T
for i in range(nsegs)
])
# vbar is the interaction between the background charge
# and the auxiliary basis. 0D, 1D, 2D do not have vbar.
if is_zero(kpt) and cell.dimension == 3:
for i in numpy.where(vbar != 0)[0]:
v[i] -= vbar[i] * ovlp[k][col0:col1]
j3cR.append(numpy.asarray(v.real, order='C'))
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
j3cI.append(None)
else:
j3cI.append(numpy.asarray(v.imag, order='C'))
v = None
return j3cR, j3cI
pqkRbuf = numpy.empty(buflen * Gblksize)
pqkIbuf = numpy.empty(buflen * Gblksize)
# buf for ft_aopair
buf = numpy.empty(nkptj * buflen * Gblksize, dtype=numpy.complex128)
cols = [sh_range[2] for sh_range in shranges]
locs = numpy.append(0, numpy.cumsum(cols))
tasks = zip(locs[:-1], locs[1:])
for istep, (j3cR,
j3cI) in enumerate(lib.map_with_prefetch(load, tasks)):
bstart, bend, ncol = shranges[istep]
log.debug1('int3c2e [%d/%d], AO [%d:%d], ncol = %d', istep + 1,
len(shranges), bstart, bend, ncol)
if aosym == 's2':
shls_slice = (bstart, bend, 0, bend)
else:
shls_slice = (bstart, bend, 0, cell.nbas)
for p0, p1 in lib.prange(0, ngrids, Gblksize):
dat = ft_ao._ft_aopair_kpts(cell,
Gv[p0:p1],
shls_slice,
aosym,
b,
gxyz[p0:p1],
Gvbase,
kpt,
adapted_kptjs,
out=buf)
nG = p1 - p0
for k, ji in enumerate(adapted_ji_idx):
aoao = dat[k].reshape(nG, ncol)
pqkR = numpy.ndarray((ncol, nG), buffer=pqkRbuf)
pqkI = numpy.ndarray((ncol, nG), buffer=pqkIbuf)
pqkR[:] = aoao.real.T
pqkI[:] = aoao.imag.T
lib.dot(kLR[p0:p1].T, pqkR.T, -1, j3cR[k][naux:], 1)
lib.dot(kLI[p0:p1].T, pqkI.T, -1, j3cR[k][naux:], 1)
if not (is_zero(kpt) and gamma_point(adapted_kptjs[k])):
lib.dot(kLR[p0:p1].T, pqkI.T, -1, j3cI[k][naux:], 1)
lib.dot(kLI[p0:p1].T, pqkR.T, 1, j3cI[k][naux:], 1)
for k, ji in enumerate(adapted_ji_idx):
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
v = fuse(j3cR[k])
else:
v = fuse(j3cR[k] + j3cI[k] * 1j)
if j2ctag == 'CD':
v = scipy.linalg.solve_triangular(j2c,
v,
lower=True,
overwrite_b=True)
feri['j3c/%d/%d' % (ji, istep)] = v
else:
feri['j3c/%d/%d' % (ji, istep)] = lib.dot(j2c, v)
# low-dimension systems
if j2c_negative is not None:
feri['j3c-/%d/%d' % (ji, istep)] = lib.dot(j2c_negative, v)
j3cR = j3cI = None
for ji in adapted_ji_idx:
del (fswap['j3c-junk/%d' % ji])
# Wrapped around boundary and symmetry between k and -k can be used
# explicitly for the metric integrals. We consider this symmetry
# because it is used in the df_ao2mo module when contracting two 3-index
# integral tensors to the 4-index 2e integral tensor. If the symmetry
# related k-points are treated separately, the resultant 3-index tensors
# may have inconsistent dimension due to the numerial noise when handling
# linear dependency of j2c.
def conj_j2c(cholesky_j2c):
j2c, j2c_negative, j2ctag = cholesky_j2c
if j2c_negative is None:
return j2c.conj(), None, j2ctag
else:
return j2c.conj(), j2c_negative.conj(), j2ctag
a = cell.lattice_vectors() / (2 * numpy.pi)
def kconserve_indices(kpt):
'''search which (kpts+kpt) satisfies momentum conservation'''
kdif = numpy.einsum('wx,ix->wi', a, uniq_kpts + kpt)
kdif_int = numpy.rint(kdif)
mask = numpy.einsum('wi->i', abs(kdif - kdif_int)) < KPT_DIFF_TOL
uniq_kptji_ids = numpy.where(mask)[0]
return uniq_kptji_ids
done = numpy.zeros(len(uniq_kpts), dtype=bool)
for k, kpt in enumerate(uniq_kpts):
if done[k]:
continue
log.debug1('Cholesky decomposition for j2c at kpt %s', k)
cholesky_j2c = cholesky_decomposed_metric(k)
# The k-point k' which has (k - k') * a = 2n pi. Metric integrals have the
# symmetry S = S
uniq_kptji_ids = kconserve_indices(-kpt)
log.debug1("Symmetry pattern (k - %s)*a= 2n pi", kpt)
log.debug1(" make_kpt for uniq_kptji_ids %s", uniq_kptji_ids)
for uniq_kptji_id in uniq_kptji_ids:
if not done[uniq_kptji_id]:
make_kpt(uniq_kptji_id, cholesky_j2c)
done[uniq_kptji_ids] = True
# The k-point k' which has (k + k') * a = 2n pi. Metric integrals have the
# symmetry S = S*
uniq_kptji_ids = kconserve_indices(kpt)
log.debug1("Symmetry pattern (k + %s)*a= 2n pi", kpt)
log.debug1(" make_kpt for %s", uniq_kptji_ids)
cholesky_j2c = conj_j2c(cholesky_j2c)
for uniq_kptji_id in uniq_kptji_ids:
if not done[uniq_kptji_id]:
make_kpt(uniq_kptji_id, cholesky_j2c)
done[uniq_kptji_ids] = True
feri.close()
def get_nuc_less_accurate(mydf, kpts=None):
log = logger.Logger(mydf.stdout, mydf.verbose)
t1 = t0 = (time.clock(), time.time())
if kpts is None:
kpts_lst = numpy.zeros((1, 3))
else:
kpts_lst = numpy.reshape(kpts, (-1, 3))
nkpts = len(kpts_lst)
if mydf._cderi is None:
mydf.build()
cell = mydf.cell
fused_cell, fuse = fuse_auxcell_(mydf, mydf.auxcell)
nao = cell.nao_nr()
charge = -cell.atom_charges()
j2c = pgto.intor_cross('cint2c2e_sph', fused_cell, _fake_nuc(cell))
jaux = j2c.dot(charge)
jaux -= charge.sum() * mydf.auxbar(fused_cell)
Gv = cell.get_Gv(mydf.gs)
SI = cell.get_SI(Gv)
# The normal nuclues have been considered in function get_gth_vlocG_part1
# The result vG is the potential in G-space for erf part of the pp nuclues and
# "numpy.dot(charge, SI) * coulG" for normal nuclues.
vpplocG = pgto.pseudo.pp_int.get_gth_vlocG_part1(cell, Gv)
vG = -1. / cell.vol * numpy.einsum('ij,ij->j', SI, vpplocG)
kpt_allow = numpy.zeros(3)
if is_zero(kpts_lst):
vj = numpy.zeros((nkpts, nao**2))
else:
vj = numpy.zeros((nkpts, nao**2), dtype=numpy.complex128)
max_memory = max(2000, mydf.max_memory - lib.current_memory()[0])
for k, pqkR, pqkI, p0, p1 \
in mydf.ft_loop(cell, mydf.gs, kpt_allow, kpts_lst, max_memory=max_memory):
if not gamma_point(kpts_lst[k]):
vj[k] += numpy.einsum('k,xk->x', vG.real, pqkI) * 1j
vj[k] += numpy.einsum('k,xk->x', vG.imag, pqkR) * -1j
vj[k] += numpy.einsum('k,xk->x', vG.real, pqkR)
vj[k] += numpy.einsum('k,xk->x', vG.imag, pqkI)
pqkR = pqkI = None
Gv = cell.get_Gv(mydf.gs)
aoaux = ft_ao.ft_ao(fused_cell, Gv)
jaux -= numpy.einsum('x,xj->j', vG.real, aoaux.real)
jaux -= numpy.einsum('x,xj->j', vG.imag, aoaux.imag)
jaux = fuse(jaux)
vj = vj.reshape(-1, nao, nao)
for k, kpt in enumerate(kpts_lst):
with mydf.load_Lpq((kpt, kpt)) as Lpq:
v = 0
for p0, p1 in lib.prange(0, jaux.size, mydf.blockdim):
v += numpy.dot(jaux[p0:p1], numpy.asarray(Lpq[p0:p1]))
if gamma_point(kpt):
vj[k] += lib.unpack_tril(numpy.asarray(v.real, order='C'))
else:
vj[k] += lib.unpack_tril(v)
if kpts is None or numpy.shape(kpts) == (3, ):
vj = vj[0]
return vj
def get_nuc(mydf, kpts=None):
cell = mydf.cell
if kpts is None:
kpts_lst = numpy.zeros((1,3))
else:
kpts_lst = numpy.reshape(kpts, (-1,3))
if mydf._cderi is None:
mydf.build()
log = logger.Logger(mydf.stdout, mydf.verbose)
t1 = t0 = (time.clock(), time.time())
auxcell = mydf.auxcell
nuccell = make_modchg_basis(cell, mydf.eta, 0)
nuccell._bas = numpy.asarray(nuccell._bas[nuccell._bas[:,gto.ANG_OF]==0],
dtype=numpy.int32, order='C')
charge = -cell.atom_charges()
nucbar = sum([z/nuccell.bas_exp(i)[0] for i,z in enumerate(charge)])
nucbar *= numpy.pi/cell.vol
vj = [v.ravel() for v in _int_nuc_vloc(cell, nuccell, kpts_lst)]
t1 = log.timer_debug1('vnuc pass1: analytic int', *t1)
j2c = pgto.intor_cross('cint2c2e_sph', auxcell, nuccell)
jaux = j2c.dot(charge)
kpt_allow = numpy.zeros(3)
coulG = tools.get_coulG(cell, kpt_allow, gs=mydf.gs) / cell.vol
Gv = cell.get_Gv(mydf.gs)
aoaux = ft_ao.ft_ao(nuccell, Gv)
vGR = numpy.einsum('i,xi->x', charge, aoaux.real) * coulG
vGI = numpy.einsum('i,xi->x', charge, aoaux.imag) * coulG
max_memory = mydf.max_memory - lib.current_memory()[0]
for k, pqkR, pqkI, p0, p1 \
in mydf.ft_loop(cell, mydf.gs, kpt_allow, kpts_lst, max_memory=max_memory):
# rho_ij(G) nuc(-G) / G^2
# = [Re(rho_ij(G)) + Im(rho_ij(G))*1j] [Re(nuc(G)) - Im(nuc(G))*1j] / G^2
if not gamma_point(kpts_lst[k]):
vj[k] += numpy.einsum('k,xk->x', vGR[p0:p1], pqkI) * 1j
vj[k] += numpy.einsum('k,xk->x', vGI[p0:p1], pqkR) *-1j
vj[k] += numpy.einsum('k,xk->x', vGR[p0:p1], pqkR)
vj[k] += numpy.einsum('k,xk->x', vGI[p0:p1], pqkI)
t1 = log.timer_debug1('contracting Vnuc', *t1)
# Append nuccell to auxcell, so that they can be FT together in pw_loop
# the first [:naux] of ft_ao are aux fitting functions.
nuccell._atm, nuccell._bas, nuccell._env = \
gto.conc_env(auxcell._atm, auxcell._bas, auxcell._env,
nuccell._atm, nuccell._bas, nuccell._env)
naux = auxcell.nao_nr()
aoaux = ft_ao.ft_ao(nuccell, Gv)
vG = numpy.einsum('i,xi,x->x', charge, aoaux[:,naux:], coulG)
jaux -= numpy.einsum('x,xj->j', vG.real, aoaux[:,:naux].real)
jaux -= numpy.einsum('x,xj->j', vG.imag, aoaux[:,:naux].imag)
jaux -= charge.sum() * mydf.auxbar(auxcell)
ovlp = cell.pbc_intor('cint1e_ovlp_sph', 1, lib.HERMITIAN, kpts_lst)
nao = cell.nao_nr()
nao_pair = nao * (nao+1) // 2
max_memory = max(2000, mydf.max_memory-lib.current_memory()[0])
blksize = max(16, min(int(max_memory*1e6/16/nao_pair), mydf.blockdim))
for k, kpt in enumerate(kpts_lst):
with mydf.load_Lpq((kpt,kpt)) as Lpq:
v = 0
for p0, p1 in lib.prange(0, jaux.size, blksize):
v += numpy.dot(jaux[p0:p1], numpy.asarray(Lpq[p0:p1]))
vj[k] = vj[k].reshape(nao,nao) - nucbar * ovlp[k]
if gamma_point(kpt):
vj[k] += lib.unpack_tril(numpy.asarray(v.real,order='C'))
else:
vj[k] += lib.unpack_tril(v)
if kpts is None or numpy.shape(kpts) == (3,):
vj = vj[0]
return vj
def get_nuc(mydf, kpts=None):
cell = mydf.cell
if kpts is None:
kpts_lst = numpy.zeros((1, 3))
else:
kpts_lst = numpy.reshape(kpts, (-1, 3))
if mydf._cderi is None:
mydf.build()
log = logger.Logger(mydf.stdout, mydf.verbose)
t1 = t0 = (time.clock(), time.time())
fused_cell, fuse = fuse_auxcell_(mydf, mydf.auxcell)
nuccell = make_modchg_basis(cell, mydf.eta, 0)
nuccell._bas = numpy.asarray(nuccell._bas[nuccell._bas[:,
gto.ANG_OF] == 0],
dtype=numpy.int32,
order='C')
charge = -cell.atom_charges()
nucbar = sum([z / nuccell.bas_exp(i)[0] for i, z in enumerate(charge)])
nucbar *= numpy.pi / cell.vol
vj = [v.ravel() for v in _int_nuc_vloc(cell, nuccell, kpts_lst)]
t1 = log.timer_debug1('vnuc pass1: analytic int', *t1)
j2c = pgto.intor_cross('cint2c2e_sph', fused_cell, nuccell)
jaux = j2c.dot(charge)
kpt_allow = numpy.zeros(3)
coulG = tools.get_coulG(cell, kpt_allow, gs=mydf.gs) / cell.vol
Gv = cell.get_Gv(mydf.gs)
aoaux = ft_ao.ft_ao(nuccell, Gv)
vGR = numpy.einsum('i,xi->x', charge, aoaux.real) * coulG
vGI = numpy.einsum('i,xi->x', charge, aoaux.imag) * coulG
max_memory = mydf.max_memory - lib.current_memory()[0]
for k, pqkR, pqkI, p0, p1 \
in mydf.ft_loop(cell, mydf.gs, kpt_allow, kpts_lst, max_memory=max_memory):
# rho_ij(G) nuc(-G) / G^2
# = [Re(rho_ij(G)) + Im(rho_ij(G))*1j] [Re(nuc(G)) - Im(nuc(G))*1j] / G^2
if not gamma_point(kpts_lst[k]):
vj[k] += numpy.einsum('k,xk->x', vGR[p0:p1], pqkI) * 1j
vj[k] += numpy.einsum('k,xk->x', vGI[p0:p1], pqkR) * -1j
vj[k] += numpy.einsum('k,xk->x', vGR[p0:p1], pqkR)
vj[k] += numpy.einsum('k,xk->x', vGI[p0:p1], pqkI)
pqkR = pqkI = None
t1 = log.timer_debug1('contracting Vnuc', *t1)
vG = numpy.einsum('i,xi,x->x', charge, ft_ao.ft_ao(nuccell, Gv), coulG)
aoaux = ft_ao.ft_ao(fused_cell, Gv)
jaux -= numpy.einsum('x,xj->j', vG.real, aoaux.real)
jaux -= numpy.einsum('x,xj->j', vG.imag, aoaux.imag)
jaux -= charge.sum() * mydf.auxbar(fused_cell)
jaux = fuse(jaux)
aoaux = None
ovlp = cell.pbc_intor('cint1e_ovlp_sph', 1, lib.HERMITIAN, kpts_lst)
nao = cell.nao_nr()
nao_pair = nao * (nao + 1) // 2
max_memory = max(2000, mydf.max_memory - lib.current_memory()[0])
blksize = max(16, min(int(max_memory * 1e6 / 16 / nao_pair),
mydf.blockdim))
for k, kpt in enumerate(kpts_lst):
with mydf.load_Lpq((kpt, kpt)) as Lpq:
v = 0
for p0, p1 in lib.prange(0, jaux.size, blksize):
v += numpy.dot(jaux[p0:p1], numpy.asarray(Lpq[p0:p1]))
vj[k] = vj[k].reshape(nao, nao) - nucbar * ovlp[k]
if gamma_point(kpt):
vj[k] += lib.unpack_tril(numpy.asarray(v.real, order='C'))
else:
vj[k] += lib.unpack_tril(v)
if kpts is None or numpy.shape(kpts) == (3, ):
vj = vj[0]
return vj
def ft_fuse(job_id, uniq_kptji_id, sh0, sh1):
kpt = uniq_kpts[uniq_kptji_id] # kpt = kptj - kpti
adapted_ji_idx = numpy.where(uniq_inverse == uniq_kptji_id)[0]
adapted_kptjs = kptjs[adapted_ji_idx]
nkptj = len(adapted_kptjs)
Gaux = ft_ao.ft_ao(fused_cell, Gv, None, b, gxyz, Gvbase, kpt).T
Gaux = fuse(Gaux)
Gaux *= mydf.weighted_coulG(kpt, False, mesh)
kLR = lib.transpose(numpy.asarray(Gaux.real, order='C'))
kLI = lib.transpose(numpy.asarray(Gaux.imag, order='C'))
j2c = numpy.asarray(fswap['j2c/%d'%uniq_kptji_id])
j2ctag = j2ctags[uniq_kptji_id]
naux0 = j2c.shape[0]
if ('j2c-/%d' % uniq_kptji_id) in fswap:
j2c_negative = numpy.asarray(fswap['j2c-/%d'%uniq_kptji_id])
else:
j2c_negative = None
if is_zero(kpt):
aosym = 's2'
else:
aosym = 's1'
if aosym == 's2' and cell.dimension == 3:
vbar = fuse(mydf.auxbar(fused_cell))
ovlp = cell.pbc_intor('int1e_ovlp', hermi=1, kpts=adapted_kptjs)
ovlp = [lib.pack_tril(s) for s in ovlp]
j3cR = [None] * nkptj
j3cI = [None] * nkptj
i0 = ao_loc[sh0]
i1 = ao_loc[sh1]
for k, idx in enumerate(adapted_ji_idx):
key = 'j3c-chunks/%d/%d' % (job_id, idx)
v = fuse(numpy.asarray(fswap[key]))
if aosym == 's2' and cell.dimension == 3:
for i in numpy.where(vbar != 0)[0]:
v[i] -= vbar[i] * ovlp[k][i0*(i0+1)//2:i1*(i1+1)//2].ravel()
j3cR[k] = numpy.asarray(v.real, order='C')
if v.dtype == numpy.complex128:
j3cI[k] = numpy.asarray(v.imag, order='C')
v = None
ncol = j3cR[0].shape[1]
Gblksize = max(16, int(max_memory*1e6/16/ncol/(nkptj+1))) # +1 for pqkRbuf/pqkIbuf
Gblksize = min(Gblksize, ngrids, 16384)
pqkRbuf = numpy.empty(ncol*Gblksize)
pqkIbuf = numpy.empty(ncol*Gblksize)
buf = numpy.empty(nkptj*ncol*Gblksize, dtype=numpy.complex128)
log.alldebug2(' blksize (%d,%d)', Gblksize, ncol)
if aosym == 's2':
shls_slice = (sh0, sh1, 0, sh1)
else:
shls_slice = (sh0, sh1, 0, cell.nbas)
for p0, p1 in lib.prange(0, ngrids, Gblksize):
dat = ft_ao._ft_aopair_kpts(cell, Gv[p0:p1], shls_slice, aosym, b,
gxyz[p0:p1], Gvbase, kpt,
adapted_kptjs, out=buf)
nG = p1 - p0
for k, ji in enumerate(adapted_ji_idx):
aoao = dat[k].reshape(nG,ncol)
pqkR = numpy.ndarray((ncol,nG), buffer=pqkRbuf)
pqkI = numpy.ndarray((ncol,nG), buffer=pqkIbuf)
pqkR[:] = aoao.real.T
pqkI[:] = aoao.imag.T
lib.dot(kLR[p0:p1].T, pqkR.T, -1, j3cR[k], 1)
lib.dot(kLI[p0:p1].T, pqkI.T, -1, j3cR[k], 1)
if not (is_zero(kpt) and gamma_point(adapted_kptjs[k])):
lib.dot(kLR[p0:p1].T, pqkI.T, -1, j3cI[k], 1)
lib.dot(kLI[p0:p1].T, pqkR.T, 1, j3cI[k], 1)
for k, idx in enumerate(adapted_ji_idx):
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
v = j3cR[k]
else:
v = j3cR[k] + j3cI[k] * 1j
if j2ctag == 'CD':
v = scipy.linalg.solve_triangular(j2c, v, lower=True, overwrite_b=True)
fswap['j3c-chunks/%d/%d'%(job_id,idx)][:naux0] = v
else:
fswap['j3c-chunks/%d/%d'%(job_id,idx)][:naux0] = lib.dot(j2c, v)
# low-dimension systems
if j2c_negative is not None:
fswap['j3c-/%d/%d'%(job_id,idx)] = lib.dot(j2c_negative, v)
def _make_j3c(mydf, cell, auxcell, kptij_lst):
t1 = (time.clock(), time.time())
log = logger.Logger(mydf.stdout, mydf.verbose)
max_memory = max(2000, mydf.max_memory - lib.current_memory()[0])
fused_cell, fuse = fuse_auxcell_(mydf, mydf.auxcell)
outcore.aux_e2(cell,
fused_cell,
mydf._cderi,
'cint3c2e_sph',
kptij_lst=kptij_lst,
dataname='j3c',
max_memory=max_memory)
t1 = log.timer_debug1('3c2e', *t1)
nao = cell.nao_nr()
naux = auxcell.nao_nr()
gs = mydf.gs
gxyz = lib.cartesian_prod(
(numpy.append(range(gs[0] + 1), range(-gs[0], 0)),
numpy.append(range(gs[1] + 1), range(-gs[1], 0)),
numpy.append(range(gs[2] + 1), range(-gs[2], 0))))
invh = numpy.linalg.inv(cell._h)
Gv = 2 * numpy.pi * numpy.dot(gxyz, invh)
ngs = gxyz.shape[0]
kptis = kptij_lst[:, 0]
kptjs = kptij_lst[:, 1]
kpt_ji = kptjs - kptis
uniq_kpts, uniq_index, uniq_inverse = unique(kpt_ji)
# j2c ~ (-kpt_ji | kpt_ji)
j2c = fused_cell.pbc_intor('cint2c2e_sph', hermi=1, kpts=uniq_kpts)
kLRs = []
kLIs = []
for k, kpt in enumerate(uniq_kpts):
aoaux = ft_ao.ft_ao(fused_cell, Gv, None, invh, gxyz, gs, kpt).T
aoaux = fuse(aoaux)
coulG = numpy.sqrt(tools.get_coulG(cell, kpt, gs=gs) / cell.vol)
kLR = (aoaux.real * coulG).T
kLI = (aoaux.imag * coulG).T
if not kLR.flags.c_contiguous: kLR = lib.transpose(kLR.T)
if not kLI.flags.c_contiguous: kLI = lib.transpose(kLI.T)
j2c[k] = fuse(fuse(j2c[k]).T).T.copy()
if is_zero(kpt): # kpti == kptj
j2c[k] -= lib.dot(kLR.T, kLR)
j2c[k] -= lib.dot(kLI.T, kLI)
else:
# aoaux ~ kpt_ij, aoaux.conj() ~ kpt_kl
j2cR, j2cI = zdotCN(kLR.T, kLI.T, kLR, kLI)
j2c[k] -= j2cR + j2cI * 1j
kLR *= coulG.reshape(-1, 1)
kLI *= coulG.reshape(-1, 1)
kLRs.append(kLR)
kLIs.append(kLI)
aoaux = kLR = kLI = j2cR = j2cI = coulG = None
feri = h5py.File(mydf._cderi)
# Expand approx Lpq for aosym='s1'. The approx Lpq are all in aosym='s2' mode
if mydf.approx_sr_level > 0 and len(kptij_lst) > 1:
Lpq_fake = _fake_Lpq_kpts(mydf, feri, naux, nao)
def save(label, dat, col0, col1):
nrow = dat.shape[0]
feri[label][:nrow, col0:col1] = dat
def make_kpt(uniq_kptji_id): # kpt = kptj - kpti
kpt = uniq_kpts[uniq_kptji_id]
log.debug1('kpt = %s', kpt)
adapted_ji_idx = numpy.where(uniq_inverse == uniq_kptji_id)[0]
adapted_kptjs = kptjs[adapted_ji_idx]
nkptj = len(adapted_kptjs)
log.debug1('adapted_ji_idx = %s', adapted_ji_idx)
kLR = kLRs[uniq_kptji_id]
kLI = kLIs[uniq_kptji_id]
if is_zero(kpt): # kpti == kptj
aosym = 's2'
nao_pair = nao * (nao + 1) // 2
vbar = fuse(mydf.auxbar(fused_cell))
ovlp = cell.pbc_intor('cint1e_ovlp_sph',
hermi=1,
kpts=adapted_kptjs)
for k, ji in enumerate(adapted_ji_idx):
ovlp[k] = lib.pack_tril(ovlp[k])
else:
aosym = 's1'
nao_pair = nao**2
max_memory = max(2000, mydf.max_memory - lib.current_memory()[0])
# nkptj for 3c-coulomb arrays plus 1 Lpq array
buflen = min(
max(int(max_memory * .6 * 1e6 / 16 / naux / (nkptj + 1)), 1),
nao_pair)
shranges = pyscf.df.outcore._guess_shell_ranges(cell, buflen, aosym)
buflen = max([x[2] for x in shranges])
# +1 for a pqkbuf
if aosym == 's2':
Gblksize = max(
16, int(max_memory * .2 * 1e6 / 16 / buflen / (nkptj + 1)))
else:
Gblksize = max(
16, int(max_memory * .4 * 1e6 / 16 / buflen / (nkptj + 1)))
Gblksize = min(Gblksize, ngs)
pqkRbuf = numpy.empty(buflen * Gblksize)
pqkIbuf = numpy.empty(buflen * Gblksize)
# buf for ft_aopair
buf = numpy.zeros((nkptj, buflen * Gblksize), dtype=numpy.complex128)
col1 = 0
for istep, sh_range in enumerate(shranges):
log.debug1('int3c2e [%d/%d], AO [%d:%d], ncol = %d', \
istep+1, len(shranges), *sh_range)
bstart, bend, ncol = sh_range
col0, col1 = col1, col1 + ncol
j3cR = []
j3cI = []
for k, idx in enumerate(adapted_ji_idx):
v = fuse(numpy.asarray(feri['j3c/%d' % idx][:, col0:col1]))
if mydf.approx_sr_level == 0:
Lpq = numpy.asarray(feri['Lpq/%d' % idx][:, col0:col1])
elif aosym == 's2':
Lpq = numpy.asarray(feri['Lpq/0'][:, col0:col1])
else:
Lpq = numpy.asarray(Lpq_fake[:, col0:col1])
lib.dot(j2c[uniq_kptji_id], Lpq, -.5, v, 1)
if is_zero(kpt):
for i, c in enumerate(vbar):
if c != 0:
v[i] -= c * ovlp[k][col0:col1]
j3cR.append(numpy.asarray(v.real, order='C'))
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
j3cI.append(None)
else:
j3cI.append(numpy.asarray(v.imag, order='C'))
v = Lpq = None
if aosym == 's2':
shls_slice = (bstart, bend, 0, bend)
for p0, p1 in lib.prange(0, ngs, Gblksize):
ft_ao._ft_aopair_kpts(cell,
Gv[p0:p1],
shls_slice,
aosym,
invh,
gxyz[p0:p1],
gs,
kpt,
adapted_kptjs,
out=buf)
nG = p1 - p0
for k, ji in enumerate(adapted_ji_idx):
aoao = numpy.ndarray((nG, ncol),
dtype=numpy.complex128,
order='F',
buffer=buf[k])
pqkR = numpy.ndarray((ncol, nG), buffer=pqkRbuf)
pqkI = numpy.ndarray((ncol, nG), buffer=pqkIbuf)
pqkR[:] = aoao.real.T
pqkI[:] = aoao.imag.T
aoao[:] = 0
lib.dot(kLR[p0:p1].T, pqkR.T, -1, j3cR[k], 1)
lib.dot(kLI[p0:p1].T, pqkI.T, -1, j3cR[k], 1)
if not (is_zero(kpt)
and gamma_point(adapted_kptjs[k])):
lib.dot(kLR[p0:p1].T, pqkI.T, -1, j3cI[k], 1)
lib.dot(kLI[p0:p1].T, pqkR.T, 1, j3cI[k], 1)
else:
shls_slice = (bstart, bend, 0, cell.nbas)
ni = ncol // nao
for p0, p1 in lib.prange(0, ngs, Gblksize):
ft_ao._ft_aopair_kpts(cell,
Gv[p0:p1],
shls_slice,
aosym,
invh,
gxyz[p0:p1],
gs,
kpt,
adapted_kptjs,
out=buf)
nG = p1 - p0
for k, ji in enumerate(adapted_ji_idx):
aoao = numpy.ndarray((nG, ni, nao),
dtype=numpy.complex128,
order='F',
buffer=buf[k])
pqkR = numpy.ndarray((ni, nao, nG), buffer=pqkRbuf)
pqkI = numpy.ndarray((ni, nao, nG), buffer=pqkIbuf)
pqkR[:] = aoao.real.transpose(1, 2, 0)
pqkI[:] = aoao.imag.transpose(1, 2, 0)
aoao[:] = 0
pqkR = pqkR.reshape(-1, nG)
pqkI = pqkI.reshape(-1, nG)
zdotCN(kLR[p0:p1].T, kLI[p0:p1].T, pqkR.T, pqkI.T, -1,
j3cR[k], j3cI[k], 1)
for k, ji in enumerate(adapted_ji_idx):
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
save('j3c/%d' % ji, j3cR[k], col0, col1)
else:
save('j3c/%d' % ji, j3cR[k] + j3cI[k] * 1j, col0, col1)
for k, kpt in enumerate(uniq_kpts):
make_kpt(k)
feri.close()
def _make_j3c(mydf, cell, auxcell, kptij_lst):
max_memory = max(2000, mydf.max_memory-pyscflib.current_memory()[0])
fused_cell, fuse = df.df.fuse_auxcell(mydf, auxcell)
log = Logger(mydf.stdout, mydf.verbose)
nao, nfao = cell.nao_nr(), fused_cell.nao_nr()
jobs = np.arange(fused_cell.nbas)
tasks = list(static_partition(jobs))
ntasks = max(comm.allgather(len(tasks)))
j3c_junk = ctf.zeros([len(kptij_lst), nao**2, nfao], dtype=np.complex128)
t1 = t0 = (time.clock(), time.time())
idx_full = np.arange(j3c_junk.size).reshape(j3c_junk.shape)
if len(tasks) > 0:
q0, q1 = tasks[0], tasks[-1] + 1
shls_slice = (0, cell.nbas, 0, cell.nbas, q0, q1)
bstart, bend = fused_cell.ao_loc_nr()[q0], fused_cell.ao_loc_nr()[q1]
idx = idx_full[:,:,bstart:bend].ravel()
tmp = df.incore.aux_e2(cell, fused_cell, intor='int3c2e', aosym='s2', kptij_lst=kptij_lst, shls_slice=shls_slice)
nao_pair = nao**2
if tmp.shape[-2] != nao_pair and tmp.ndim == 2:
tmp = pyscflib.unpack_tril(tmp, axis=0).reshape(nao_pair,-1)
j3c_junk.write(idx, tmp.ravel())
else:
j3c_junk.write([],[])
t1 = log.timer('j3c_junk', *t1)
naux = auxcell.nao_nr()
mesh = mydf.mesh
Gv, Gvbase, kws = cell.get_Gv_weights(mesh)
b = cell.reciprocal_vectors()
gxyz = pyscflib.cartesian_prod([np.arange(len(x)) for x in Gvbase])
ngrids = gxyz.shape[0]
kptis = kptij_lst[:,0]
kptjs = kptij_lst[:,1]
kpt_ji = kptjs - kptis
mydf.kptij_lst = kptij_lst
uniq_kpts, uniq_index, uniq_inverse = unique(kpt_ji)
jobs = np.arange(len(uniq_kpts))
tasks = list(static_partition(jobs))
ntasks = max(comm.allgather(len(tasks)))
blksize = max(2048, int(max_memory*.5e6/16/fused_cell.nao_nr()))
log.debug2('max_memory %s (MB) blocksize %s', max_memory, blksize)
j2c = ctf.zeros([len(uniq_kpts),naux,naux], dtype=np.complex128)
a = cell.lattice_vectors() / (2*np.pi)
def kconserve_indices(kpt):
'''search which (kpts+kpt) satisfies momentum conservation'''
kdif = np.einsum('wx,ix->wi', a, uniq_kpts + kpt)
kdif_int = np.rint(kdif)
mask = np.einsum('wi->i', abs(kdif - kdif_int)) < KPT_DIFF_TOL
uniq_kptji_ids = np.where(mask)[0]
return uniq_kptji_ids
def cholesky_decomposed_metric(j2c_kptij):
j2c_negative = None
try:
j2c_kptij = scipy.linalg.cholesky(j2c_kptij, lower=True)
j2ctag = 'CD'
except scipy.linalg.LinAlgError as e:
w, v = scipy.linalg.eigh(j2c_kptij)
log.debug('cond = %.4g, drop %d bfns',
w[-1]/w[0], np.count_nonzero(w<mydf.linear_dep_threshold))
v1 = np.zeros(v.T.shape, dtype=v.dtype)
v1[w>mydf.linear_dep_threshold,:] = v[:,w>mydf.linear_dep_threshold].conj().T
v1[w>mydf.linear_dep_threshold,:] /= np.sqrt(w[w>mydf.linear_dep_threshold]).reshape(-1,1)
j2c_kptij = v1
if cell.dimension == 2 and cell.low_dim_ft_type != 'inf_vacuum':
idx = np.where(w < -mydf.linear_dep_threshold)[0]
if len(idx) > 0:
j2c_negative = np.zeros(v1.shape, dtype=v1.dtype)
j2c_negative[idx,:] = (v[:,idx]/np.sqrt(-w[idx])).conj().T
w = v = None
j2ctag = 'eig'
return j2c_kptij, j2c_negative, j2ctag
for itask in range(ntasks):
if itask >= len(tasks):
j2c.write([],[])
continue
k = tasks[itask]
kpt = uniq_kpts[k]
j2ctmp = np.asarray(fused_cell.pbc_intor('int2c2e', hermi=1, kpts=kpt))
coulG = mydf.weighted_coulG(kpt, False, mesh)
for p0, p1 in pyscflib.prange(0, ngrids, blksize):
aoaux = ft_ao.ft_ao(fused_cell, Gv[p0:p1], None, b, gxyz[p0:p1], Gvbase, kpt).T
if is_zero(kpt):
j2ctmp[naux:] -= np.dot(aoaux[naux:].conj()*coulG[p0:p1].conj(), aoaux.T).real
j2ctmp[:naux,naux:] = j2ctmp[naux:,:naux].T
else:
j2ctmp[naux:] -= np.dot(aoaux[naux:].conj()*coulG[p0:p1].conj(), aoaux.T)
j2ctmp[:naux,naux:] = j2ctmp[naux:,:naux].T.conj()
tmp = fuse(fuse(j2ctmp).T).T
idx = k * naux**2 + np.arange(naux**2)
j2c.write(idx, tmp.ravel())
j2ctmp = tmp = None
coulG = None
t1 = log.timer('j2c', *t1)
j3c = ctf.zeros([len(kpt_ji),nao,nao,naux], dtype=np.complex128)
jobs = np.arange(len(kpt_ji))
tasks = list(static_partition(jobs))
ntasks = max(comm.allgather(len(tasks)))
for itask in range(ntasks):
if itask >= len(tasks):
j2c_ji = j2c.read([])
j3ctmp = j3c_junk.read([])
j3c.write([],[])
continue
idx_ji = tasks[itask]
kpti, kptj = kptij_lst[idx_ji]
idxi, idxj = member(kpti, mydf.kpts), member(kptj, mydf.kpts)
uniq_idx = uniq_inverse[idx_ji]
kpt = uniq_kpts[uniq_idx]
id_eq = kconserve_indices(-kpt)
id_conj = kconserve_indices(kpt)
id_conj = np.asarray([i for i in id_conj if i not in id_eq], dtype=int)
id_full = np.hstack((id_eq, id_conj))
map_id, conj = min(id_full), np.argmin(id_full) >=len(id_eq)
j2cidx = map_id * naux**2 + np.arange(naux**2)
j2c_ji = j2c.read(j2cidx).reshape(naux, naux) # read to be added
j2c_ji, j2c_negative, j2ctag = cholesky_decomposed_metric(j2c_ji)
if conj: j2c_ji = j2c_ji.conj()
shls_slice= (auxcell.nbas, fused_cell.nbas)
Gaux = ft_ao.ft_ao(fused_cell, Gv, shls_slice, b, gxyz, Gvbase, kpt)
wcoulG = mydf.weighted_coulG(kpt, False, mesh)
Gaux *= wcoulG.reshape(-1,1)
j3c_id = idx_ji * nao**2*nfao + np.arange(nao**2*nfao)
j3ctmp = j3c_junk.read(j3c_id).reshape(nao**2, fused_cell.nao_nr()).T
if is_zero(kpt): # kpti == kptj
if cell.dimension == 3:
vbar = fuse(mydf.auxbar(fused_cell))
ovlp = cell.pbc_intor('int1e_ovlp', hermi=1, kpts=kptj)
for i in np.where(vbar != 0)[0]:
j3ctmp[i] -= vbar[i] * ovlp.reshape(-1)
aoao = ft_ao._ft_aopair_kpts(cell, Gv, None, 's1', b, gxyz, Gvbase, kpt, kptj)[0].reshape(len(Gv),-1)
j3ctmp[naux:] -= np.dot(Gaux.T.conj(), aoao)
j3ctmp = fuse(j3ctmp)
if j2ctag == 'CD':
v = scipy.linalg.solve_triangular(j2c_ji, j3ctmp, lower=True, overwrite_b=True)
else:
v = np.dot(j2c_ji, j3ctmp)
v = v.T.reshape(nao,nao,naux)
j3c_id = idx_ji * nao**2*naux + np.arange(nao**2*naux)
j3c.write(j3c_id, v.ravel())
mydf.j3c = j3c
return None
def get_nuc(mydf, kpts=None):
cell = mydf.cell
if kpts is None:
kpts_lst = numpy.zeros((1,3))
else:
kpts_lst = numpy.reshape(kpts, (-1,3))
log = logger.Logger(mydf.stdout, mydf.verbose)
t1 = t0 = (time.clock(), time.time())
nkpts = len(kpts_lst)
nao = cell.nao_nr()
nao_pair = nao * (nao+1) // 2
Gv, Gvbase, kws = cell.get_Gv_weights(mydf.gs)
kpt_allow = numpy.zeros(3)
if mydf.eta == 0:
vpplocG = pseudo.pp_int.get_gth_vlocG_part1(cell, Gv)
vpplocG = -numpy.einsum('ij,ij->j', cell.get_SI(Gv), vpplocG)
vpplocG *= kws
vGR = vpplocG.real
vGI = vpplocG.imag
vjR = numpy.zeros((nkpts,nao_pair))
vjI = numpy.zeros((nkpts,nao_pair))
else:
nuccell = copy.copy(cell)
half_sph_norm = .5/numpy.sqrt(numpy.pi)
norm = half_sph_norm/gto.mole._gaussian_int(2, mydf.eta)
chg_env = [mydf.eta, norm]
ptr_eta = cell._env.size
ptr_norm = ptr_eta + 1
chg_bas = [[ia, 0, 1, 1, 0, ptr_eta, ptr_norm, 0] for ia in range(cell.natm)]
nuccell._atm = cell._atm
nuccell._bas = numpy.asarray(chg_bas, dtype=numpy.int32)
nuccell._env = numpy.hstack((cell._env, chg_env))
# PP-loc part1 is handled by fakenuc in _int_nuc_vloc
vj = lib.asarray(mydf._int_nuc_vloc(nuccell, kpts_lst))
vjR = vj.real
vjI = vj.imag
t1 = log.timer_debug1('vnuc pass1: analytic int', *t1)
charge = -cell.atom_charges()
coulG = tools.get_coulG(cell, kpt_allow, gs=mydf.gs, Gv=Gv)
coulG *= kws
aoaux = ft_ao.ft_ao(nuccell, Gv)
vGR = numpy.einsum('i,xi->x', charge, aoaux.real) * coulG
vGI = numpy.einsum('i,xi->x', charge, aoaux.imag) * coulG
max_memory = max(2000, mydf.max_memory-lib.current_memory()[0])
for k, pqkR, pqkI, p0, p1 \
in mydf.ft_loop(mydf.gs, kpt_allow, kpts_lst,
max_memory=max_memory, aosym='s2'):
# rho_ij(G) nuc(-G) / G^2
# = [Re(rho_ij(G)) + Im(rho_ij(G))*1j] [Re(nuc(G)) - Im(nuc(G))*1j] / G^2
if not gamma_point(kpts_lst[k]):
vjI[k] += numpy.einsum('k,xk->x', vGR[p0:p1], pqkI)
vjI[k] -= numpy.einsum('k,xk->x', vGI[p0:p1], pqkR)
vjR[k] += numpy.einsum('k,xk->x', vGR[p0:p1], pqkR)
vjR[k] += numpy.einsum('k,xk->x', vGI[p0:p1], pqkI)
t1 = log.timer_debug1('contracting Vnuc', *t1)
if mydf.eta != 0 and cell.dimension == 3:
nucbar = sum([z/nuccell.bas_exp(i)[0] for i,z in enumerate(charge)])
nucbar *= numpy.pi/cell.vol
ovlp = cell.pbc_intor('cint1e_ovlp_sph', 1, lib.HERMITIAN, kpts_lst)
for k in range(nkpts):
s = lib.pack_tril(ovlp[k])
vjR[k] -= nucbar * s.real
vjI[k] -= nucbar * s.imag
vj = []
for k, kpt in enumerate(kpts_lst):
if gamma_point(kpt):
vj.append(lib.unpack_tril(vjR[k]))
else:
vj.append(lib.unpack_tril(vjR[k]+vjI[k]*1j))
if kpts is None or numpy.shape(kpts) == (3,):
vj = vj[0]
return vj
def _make_j3c(mydf, cell, auxcell, kptij_lst, cderi_file):
t1 = (time.clock(), time.time())
log = logger.Logger(mydf.stdout, mydf.verbose)
max_memory = max(2000, mydf.max_memory-lib.current_memory()[0])
fused_cell, fuse = fuse_auxcell(mydf, auxcell)
# The ideal way to hold the temporary integrals is to store them in the
# cderi_file and overwrite them inplace in the second pass. The current
# HDF5 library does not have an efficient way to manage free space in
# overwriting. It often leads to the cderi_file ~2 times larger than the
# necessary size. For now, dumping the DF integral intermediates to a
# separated temporary file can avoid this issue. The DF intermediates may
# be terribly huge. The temporary file should be placed in the same disk
# as cderi_file.
swapfile = tempfile.NamedTemporaryFile(dir=os.path.dirname(cderi_file))
fswap = lib.H5TmpFile(swapfile.name)
# Unlink swapfile to avoid trash
swapfile = None
outcore._aux_e2(cell, fused_cell, fswap, 'int3c2e', aosym='s2',
kptij_lst=kptij_lst, dataname='j3c-junk', max_memory=max_memory)
t1 = log.timer_debug1('3c2e', *t1)
nao = cell.nao_nr()
naux = auxcell.nao_nr()
mesh = mydf.mesh
Gv, Gvbase, kws = cell.get_Gv_weights(mesh)
b = cell.reciprocal_vectors()
gxyz = lib.cartesian_prod([numpy.arange(len(x)) for x in Gvbase])
ngrids = gxyz.shape[0]
kptis = kptij_lst[:,0]
kptjs = kptij_lst[:,1]
kpt_ji = kptjs - kptis
uniq_kpts, uniq_index, uniq_inverse = unique(kpt_ji)
log.debug('Num uniq kpts %d', len(uniq_kpts))
log.debug2('uniq_kpts %s', uniq_kpts)
# j2c ~ (-kpt_ji | kpt_ji)
j2c = fused_cell.pbc_intor('int2c2e', hermi=1, kpts=uniq_kpts)
max_memory = max(2000, mydf.max_memory - lib.current_memory()[0])
blksize = max(2048, int(max_memory*.5e6/16/fused_cell.nao_nr()))
log.debug2('max_memory %s (MB) blocksize %s', max_memory, blksize)
for k, kpt in enumerate(uniq_kpts):
coulG = mydf.weighted_coulG(kpt, False, mesh)
for p0, p1 in lib.prange(0, ngrids, blksize):
aoaux = ft_ao.ft_ao(fused_cell, Gv[p0:p1], None, b, gxyz[p0:p1], Gvbase, kpt).T
LkR = numpy.asarray(aoaux.real, order='C')
LkI = numpy.asarray(aoaux.imag, order='C')
aoaux = None
if is_zero(kpt): # kpti == kptj
j2c[k][naux:] -= lib.ddot(LkR[naux:]*coulG[p0:p1], LkR.T)
j2c[k][naux:] -= lib.ddot(LkI[naux:]*coulG[p0:p1], LkI.T)
j2c[k][:naux,naux:] = j2c[k][naux:,:naux].T
else:
j2cR, j2cI = zdotCN(LkR[naux:]*coulG[p0:p1],
LkI[naux:]*coulG[p0:p1], LkR.T, LkI.T)
j2c[k][naux:] -= j2cR + j2cI * 1j
j2c[k][:naux,naux:] = j2c[k][naux:,:naux].T.conj()
LkR = LkI = None
fswap['j2c/%d'%k] = fuse(fuse(j2c[k]).T).T
j2c = coulG = None
def cholesky_decomposed_metric(uniq_kptji_id):
j2c = numpy.asarray(fswap['j2c/%d'%uniq_kptji_id])
j2c_negative = None
try:
j2c = scipy.linalg.cholesky(j2c, lower=True)
j2ctag = 'CD'
except scipy.linalg.LinAlgError as e:
#msg =('===================================\n'
# 'J-metric not positive definite.\n'
# 'It is likely that mesh is not enough.\n'
# '===================================')
#log.error(msg)
#raise scipy.linalg.LinAlgError('\n'.join([str(e), msg]))
w, v = scipy.linalg.eigh(j2c)
log.debug('DF metric linear dependency for kpt %s', uniq_kptji_id)
log.debug('cond = %.4g, drop %d bfns',
w[-1]/w[0], numpy.count_nonzero(w<mydf.linear_dep_threshold))
v1 = v[:,w>mydf.linear_dep_threshold].conj().T
v1 /= numpy.sqrt(w[w>mydf.linear_dep_threshold]).reshape(-1,1)
j2c = v1
if cell.dimension == 2 and cell.low_dim_ft_type != 'inf_vacuum':
idx = numpy.where(w < -mydf.linear_dep_threshold)[0]
if len(idx) > 0:
j2c_negative = (v[:,idx]/numpy.sqrt(-w[idx])).conj().T
w = v = None
j2ctag = 'eig'
return j2c, j2c_negative, j2ctag
feri = h5py.File(cderi_file, 'w')
feri['j3c-kptij'] = kptij_lst
nsegs = len(fswap['j3c-junk/0'])
def make_kpt(uniq_kptji_id, cholesky_j2c):
kpt = uniq_kpts[uniq_kptji_id] # kpt = kptj - kpti
log.debug1('kpt = %s', kpt)
adapted_ji_idx = numpy.where(uniq_inverse == uniq_kptji_id)[0]
adapted_kptjs = kptjs[adapted_ji_idx]
nkptj = len(adapted_kptjs)
log.debug1('adapted_ji_idx = %s', adapted_ji_idx)
j2c, j2c_negative, j2ctag = cholesky_j2c
shls_slice = (auxcell.nbas, fused_cell.nbas)
Gaux = ft_ao.ft_ao(fused_cell, Gv, shls_slice, b, gxyz, Gvbase, kpt)
wcoulG = mydf.weighted_coulG(kpt, False, mesh)
Gaux *= wcoulG.reshape(-1,1)
kLR = Gaux.real.copy('C')
kLI = Gaux.imag.copy('C')
Gaux = None
if is_zero(kpt): # kpti == kptj
aosym = 's2'
nao_pair = nao*(nao+1)//2
if cell.dimension == 3:
vbar = fuse(mydf.auxbar(fused_cell))
ovlp = cell.pbc_intor('int1e_ovlp', hermi=1, kpts=adapted_kptjs)
ovlp = [lib.pack_tril(s) for s in ovlp]
else:
aosym = 's1'
nao_pair = nao**2
mem_now = lib.current_memory()[0]
log.debug2('memory = %s', mem_now)
max_memory = max(2000, mydf.max_memory-mem_now)
# nkptj for 3c-coulomb arrays plus 1 Lpq array
buflen = min(max(int(max_memory*.38e6/16/naux/(nkptj+1)), 1), nao_pair)
shranges = _guess_shell_ranges(cell, buflen, aosym)
buflen = max([x[2] for x in shranges])
# +1 for a pqkbuf
if aosym == 's2':
Gblksize = max(16, int(max_memory*.1e6/16/buflen/(nkptj+1)))
else:
Gblksize = max(16, int(max_memory*.2e6/16/buflen/(nkptj+1)))
Gblksize = min(Gblksize, ngrids, 16384)
pqkRbuf = numpy.empty(buflen*Gblksize)
pqkIbuf = numpy.empty(buflen*Gblksize)
# buf for ft_aopair
buf = numpy.empty(nkptj*buflen*Gblksize, dtype=numpy.complex128)
def pw_contract(istep, sh_range, j3cR, j3cI):
bstart, bend, ncol = sh_range
if aosym == 's2':
shls_slice = (bstart, bend, 0, bend)
else:
shls_slice = (bstart, bend, 0, cell.nbas)
for p0, p1 in lib.prange(0, ngrids, Gblksize):
dat = ft_ao._ft_aopair_kpts(cell, Gv[p0:p1], shls_slice, aosym,
b, gxyz[p0:p1], Gvbase, kpt,
adapted_kptjs, out=buf)
nG = p1 - p0
for k, ji in enumerate(adapted_ji_idx):
aoao = dat[k].reshape(nG,ncol)
pqkR = numpy.ndarray((ncol,nG), buffer=pqkRbuf)
pqkI = numpy.ndarray((ncol,nG), buffer=pqkIbuf)
pqkR[:] = aoao.real.T
pqkI[:] = aoao.imag.T
lib.dot(kLR[p0:p1].T, pqkR.T, -1, j3cR[k][naux:], 1)
lib.dot(kLI[p0:p1].T, pqkI.T, -1, j3cR[k][naux:], 1)
if not (is_zero(kpt) and gamma_point(adapted_kptjs[k])):
lib.dot(kLR[p0:p1].T, pqkI.T, -1, j3cI[k][naux:], 1)
lib.dot(kLI[p0:p1].T, pqkR.T, 1, j3cI[k][naux:], 1)
for k, ji in enumerate(adapted_ji_idx):
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
v = fuse(j3cR[k])
else:
v = fuse(j3cR[k] + j3cI[k] * 1j)
if j2ctag == 'CD':
v = scipy.linalg.solve_triangular(j2c, v, lower=True, overwrite_b=True)
feri['j3c/%d/%d'%(ji,istep)] = v
else:
feri['j3c/%d/%d'%(ji,istep)] = lib.dot(j2c, v)
# low-dimension systems
if j2c_negative is not None:
feri['j3c-/%d/%d'%(ji,istep)] = lib.dot(j2c_negative, v)
with lib.call_in_background(pw_contract) as compute:
col1 = 0
for istep, sh_range in enumerate(shranges):
log.debug1('int3c2e [%d/%d], AO [%d:%d], ncol = %d', \
istep+1, len(shranges), *sh_range)
bstart, bend, ncol = sh_range
col0, col1 = col1, col1+ncol
j3cR = []
j3cI = []
for k, idx in enumerate(adapted_ji_idx):
v = numpy.vstack([fswap['j3c-junk/%d/%d'%(idx,i)][0,col0:col1].T
for i in range(nsegs)])
# vbar is the interaction between the background charge
# and the auxiliary basis. 0D, 1D, 2D do not have vbar.
if is_zero(kpt) and cell.dimension == 3:
for i in numpy.where(vbar != 0)[0]:
v[i] -= vbar[i] * ovlp[k][col0:col1]
j3cR.append(numpy.asarray(v.real, order='C'))
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
j3cI.append(None)
else:
j3cI.append(numpy.asarray(v.imag, order='C'))
v = None
compute(istep, sh_range, j3cR, j3cI)
for ji in adapted_ji_idx:
del(fswap['j3c-junk/%d'%ji])
# Wrapped around boundary and symmetry between k and -k can be used
# explicitly for the metric integrals. We consider this symmetry
# because it is used in the df_ao2mo module when contracting two 3-index
# integral tensors to the 4-index 2e integral tensor. If the symmetry
# related k-points are treated separately, the resultant 3-index tensors
# may have inconsistent dimension due to the numerial noise when handling
# linear dependency of j2c.
def conj_j2c(cholesky_j2c):
j2c, j2c_negative, j2ctag = cholesky_j2c
if j2c_negative is None:
return j2c.conj(), None, j2ctag
else:
return j2c.conj(), j2c_negative.conj(), j2ctag
a = cell.lattice_vectors() / (2*numpy.pi)
def kconserve_indices(kpt):
'''search which (kpts+kpt) satisfies momentum conservation'''
kdif = numpy.einsum('wx,ix->wi', a, uniq_kpts + kpt)
kdif_int = numpy.rint(kdif)
mask = numpy.einsum('wi->i', abs(kdif - kdif_int)) < KPT_DIFF_TOL
uniq_kptji_ids = numpy.where(mask)[0]
return uniq_kptji_ids
done = numpy.zeros(len(uniq_kpts), dtype=bool)
for k, kpt in enumerate(uniq_kpts):
if done[k]:
continue
log.debug1('Cholesky decomposition for j2c at kpt %s', k)
cholesky_j2c = cholesky_decomposed_metric(k)
# The k-point k' which has (k - k') * a = 2n pi. Metric integrals have the
# symmetry S = S
uniq_kptji_ids = kconserve_indices(-kpt)
log.debug1("Symmetry pattern (k - %s)*a= 2n pi", kpt)
log.debug1(" make_kpt for uniq_kptji_ids %s", uniq_kptji_ids)
for uniq_kptji_id in uniq_kptji_ids:
if not done[uniq_kptji_id]:
make_kpt(uniq_kptji_id, cholesky_j2c)
done[uniq_kptji_ids] = True
# The k-point k' which has (k + k') * a = 2n pi. Metric integrals have the
# symmetry S = S*
uniq_kptji_ids = kconserve_indices(kpt)
log.debug1("Symmetry pattern (k + %s)*a= 2n pi", kpt)
log.debug1(" make_kpt for %s", uniq_kptji_ids)
cholesky_j2c = conj_j2c(cholesky_j2c)
for uniq_kptji_id in uniq_kptji_ids:
if not done[uniq_kptji_id]:
make_kpt(uniq_kptji_id, cholesky_j2c)
done[uniq_kptji_ids] = True
feri.close()
def get_pnucp(mydf, kpts=None):
cell = mydf.cell
if kpts is None:
kpts_lst = numpy.zeros((1, 3))
else:
kpts_lst = numpy.reshape(kpts, (-1, 3))
log = logger.Logger(mydf.stdout, mydf.verbose)
t1 = t0 = (time.clock(), time.time())
nkpts = len(kpts_lst)
nao = cell.nao_nr()
nao_pair = nao * (nao + 1) // 2
Gv, Gvbase, kws = cell.get_Gv_weights(mydf.gs)
kpt_allow = numpy.zeros(3)
if mydf.eta == 0:
charge = -cell.atom_charges()
#coulG=4*numpy.pi/G^2 is cancelled with (sigma dot p i, sigma dot p j)
SI = cell.get_SI(Gv)
vGR = numpy.einsum('i,ix->x', 4 * numpy.pi * charge, SI.real) * kws
vGI = numpy.einsum('i,ix->x', 4 * numpy.pi * charge, SI.imag) * kws
wjR = numpy.zeros((nkpts, nao_pair))
wjI = numpy.zeros((nkpts, nao_pair))
else:
nuccell = copy.copy(cell)
half_sph_norm = .5 / numpy.sqrt(numpy.pi)
norm = half_sph_norm / mole._gaussian_int(2, mydf.eta)
chg_env = [mydf.eta, norm]
ptr_eta = cell._env.size
ptr_norm = ptr_eta + 1
chg_bas = [[ia, 0, 1, 1, 0, ptr_eta, ptr_norm, 0]
for ia in range(cell.natm)]
nuccell._atm = cell._atm
nuccell._bas = numpy.asarray(chg_bas, dtype=numpy.int32)
nuccell._env = numpy.hstack((cell._env, chg_env))
wj = lib.asarray(
mydf._int_nuc_vloc(nuccell, kpts_lst, 'int3c2e_pvp1_sph'))
wjR = wj.real
wjI = wj.imag
t1 = log.timer_debug1('pnucp pass1: analytic int', *t1)
charge = -cell.atom_charges()
#coulG=4*numpy.pi/G^2 is cancelled with (sigma dot p i, sigma dot p j)
aoaux = ft_ao.ft_ao(nuccell, Gv)
vGR = numpy.einsum('i,xi->x', 4 * numpy.pi * charge, aoaux.real) * kws
vGI = numpy.einsum('i,xi->x', 4 * numpy.pi * charge, aoaux.imag) * kws
max_memory = max(2000, mydf.max_memory - lib.current_memory()[0])
for k, pqkR, pqkI, p0, p1 \
in mydf.ft_loop(mydf.gs, kpt_allow, kpts_lst,
max_memory=max_memory, aosym='s2'):
# rho_ij(G) nuc(-G) / G^2
# = [Re(rho_ij(G)) + Im(rho_ij(G))*1j] [Re(nuc(G)) - Im(nuc(G))*1j] / G^2
if not aft_jk.gamma_point(kpts_lst[k]):
wjI[k] += numpy.einsum('k,xk->x', vGR[p0:p1], pqkI)
wjI[k] -= numpy.einsum('k,xk->x', vGI[p0:p1], pqkR)
wjR[k] += numpy.einsum('k,xk->x', vGR[p0:p1], pqkR)
wjR[k] += numpy.einsum('k,xk->x', vGI[p0:p1], pqkI)
t1 = log.timer_debug1('contracting Vnuc', *t1)
if mydf.eta != 0 and cell.dimension == 3:
nucbar = sum([z / nuccell.bas_exp(i)[0] for i, z in enumerate(charge)])
nucbar *= numpy.pi / cell.vol * 2
ovlp = cell.pbc_intor('int1e_kin_sph', 1, lib.HERMITIAN, kpts_lst)
for k in range(nkpts):
s = lib.pack_tril(ovlp[k])
wjR[k] -= nucbar * s.real
wjI[k] -= nucbar * s.imag
wj = []
for k, kpt in enumerate(kpts_lst):
if aft_jk.gamma_point(kpt):
wj.append(lib.unpack_tril(wjR[k]))
else:
wj.append(lib.unpack_tril(wjR[k] + wjI[k] * 1j))
if kpts is None or numpy.shape(kpts) == (3, ):
wj = wj[0]
return wj
def _make_j3c(mydf, cell, auxcell, kptij_lst):
t1 = (time.clock(), time.time())
log = logger.Logger(mydf.stdout, mydf.verbose)
max_memory = max(2000, mydf.max_memory - lib.current_memory()[0])
fused_cell, fuse = fuse_auxcell(mydf, auxcell)
outcore.aux_e2(cell,
fused_cell,
mydf._cderi,
'cint3c2e_sph',
kptij_lst=kptij_lst,
dataname='j3c',
max_memory=max_memory)
t1 = log.timer_debug1('3c2e', *t1)
nao = cell.nao_nr()
naux = auxcell.nao_nr()
gs = mydf.gs
Gv, Gvbase, kws = cell.get_Gv_weights(gs)
b = cell.reciprocal_vectors()
gxyz = lib.cartesian_prod([numpy.arange(len(x)) for x in Gvbase])
ngs = gxyz.shape[0]
kptis = kptij_lst[:, 0]
kptjs = kptij_lst[:, 1]
kpt_ji = kptjs - kptis
uniq_kpts, uniq_index, uniq_inverse = unique(kpt_ji)
# j2c ~ (-kpt_ji | kpt_ji)
j2c = fused_cell.pbc_intor('cint2c2e_sph', hermi=1, kpts=uniq_kpts)
kLRs = []
kLIs = []
# An alternative method to evalute j2c. This method might have larger numerical error?
# chgcell = make_modchg_basis(auxcell, mydf.eta)
# for k, kpt in enumerate(uniq_kpts):
# aoaux = ft_ao.ft_ao(chgcell, Gv, None, b, gxyz, Gvbase, kpt).T
# coulG = numpy.sqrt(mydf.weighted_coulG(kpt, False, gs))
# LkR = aoaux.real * coulG
# LkI = aoaux.imag * coulG
# j2caux = numpy.zeros_like(j2c[k])
# j2caux[naux:,naux:] = j2c[k][naux:,naux:]
# if is_zero(kpt): # kpti == kptj
# j2caux[naux:,naux:] -= lib.ddot(LkR, LkR.T)
# j2caux[naux:,naux:] -= lib.ddot(LkI, LkI.T)
# j2c[k] = j2c[k][:naux,:naux] - fuse(fuse(j2caux.T).T)
# vbar = fuse(mydf.auxbar(fused_cell))
# s = (vbar != 0).astype(numpy.double)
# j2c[k] -= numpy.einsum('i,j->ij', vbar, s)
# j2c[k] -= numpy.einsum('i,j->ij', s, vbar)
# else:
# j2cR, j2cI = zdotCN(LkR, LkI, LkR.T, LkI.T)
# j2caux[naux:,naux:] -= j2cR + j2cI * 1j
# j2c[k] = j2c[k][:naux,:naux] - fuse(fuse(j2caux.T).T)
#
# try:
# j2c[k] = scipy.linalg.cholesky(j2c[k], lower=True)
# except scipy.linalg.LinAlgError as e:
# msg =('===================================\n'
# 'J-metric not positive definite.\n'
# 'It is likely that gs is not enough.\n'
# '===================================')
# log.error(msg)
# raise scipy.linalg.LinAlgError('\n'.join([e.message, msg]))
# kLR = LkR.T
# kLI = LkI.T
# if not kLR.flags.c_contiguous: kLR = lib.transpose(LkR)
# if not kLI.flags.c_contiguous: kLI = lib.transpose(LkI)
# kLR *= coulG.reshape(-1,1)
# kLI *= coulG.reshape(-1,1)
# kLRs.append(kLR)
# kLIs.append(kLI)
# aoaux = LkR = LkI = kLR = kLI = coulG = None
for k, kpt in enumerate(uniq_kpts):
aoaux = ft_ao.ft_ao(fused_cell, Gv, None, b, gxyz, Gvbase, kpt).T
coulG = numpy.sqrt(mydf.weighted_coulG(kpt, False, gs))
LkR = aoaux.real * coulG
LkI = aoaux.imag * coulG
if is_zero(kpt): # kpti == kptj
j2c[k][naux:] -= lib.ddot(LkR[naux:], LkR.T)
j2c[k][naux:] -= lib.ddot(LkI[naux:], LkI.T)
j2c[k][:naux, naux:] = j2c[k][naux:, :naux].T
else:
j2cR, j2cI = zdotCN(LkR[naux:], LkI[naux:], LkR.T, LkI.T)
j2c[k][naux:] -= j2cR + j2cI * 1j
j2c[k][:naux, naux:] = j2c[k][naux:, :naux].T.conj()
j2c[k] = fuse(fuse(j2c[k]).T).T
try:
j2c[k] = ('CD', scipy.linalg.cholesky(j2c[k], lower=True))
except scipy.linalg.LinAlgError as e:
#msg =('===================================\n'
# 'J-metric not positive definite.\n'
# 'It is likely that gs is not enough.\n'
# '===================================')
#log.error(msg)
#raise scipy.linalg.LinAlgError('\n'.join([e.message, msg]))
w, v = scipy.linalg.eigh(j2c[k])
log.debug2('metric linear dependency for kpt %s', k)
log.debug2('cond = %.4g, drop %d bfns', w[0] / w[-1],
numpy.count_nonzero(w < LINEAR_DEP_THR))
v = v[:, w > LINEAR_DEP_THR].T.conj()
v /= numpy.sqrt(w[w > LINEAR_DEP_THR]).reshape(-1, 1)
j2c[k] = ('eig', v)
kLR = LkR[naux:].T
kLI = LkI[naux:].T
if not kLR.flags.c_contiguous: kLR = lib.transpose(LkR[naux:])
if not kLI.flags.c_contiguous: kLI = lib.transpose(LkI[naux:])
kLR *= coulG.reshape(-1, 1)
kLI *= coulG.reshape(-1, 1)
kLRs.append(kLR)
kLIs.append(kLI)
aoaux = LkR = LkI = kLR = kLI = coulG = None
nauxs = [v[1].shape[0] for v in j2c]
feri = h5py.File(mydf._cderi)
def make_kpt(uniq_kptji_id): # kpt = kptj - kpti
kpt = uniq_kpts[uniq_kptji_id]
log.debug1('kpt = %s', kpt)
adapted_ji_idx = numpy.where(uniq_inverse == uniq_kptji_id)[0]
adapted_kptjs = kptjs[adapted_ji_idx]
nkptj = len(adapted_kptjs)
log.debug1('adapted_ji_idx = %s', adapted_ji_idx)
kLR = kLRs[uniq_kptji_id]
kLI = kLIs[uniq_kptji_id]
if is_zero(kpt): # kpti == kptj
aosym = 's2'
nao_pair = nao * (nao + 1) // 2
vbar = fuse(mydf.auxbar(fused_cell))
ovlp = cell.pbc_intor('cint1e_ovlp_sph',
hermi=1,
kpts=adapted_kptjs)
for k, ji in enumerate(adapted_ji_idx):
ovlp[k] = lib.pack_tril(ovlp[k])
else:
aosym = 's1'
nao_pair = nao**2
mem_now = lib.current_memory()[0]
log.debug2('memory = %s', mem_now)
max_memory = max(2000, mydf.max_memory - mem_now)
# nkptj for 3c-coulomb arrays plus 1 Lpq array
buflen = min(
max(int(max_memory * .6 * 1e6 / 16 / naux / (nkptj + 1)), 1),
nao_pair)
shranges = _guess_shell_ranges(cell, buflen, aosym)
buflen = max([x[2] for x in shranges])
# +1 for a pqkbuf
if aosym == 's2':
Gblksize = max(
16, int(max_memory * .2 * 1e6 / 16 / buflen / (nkptj + 1)))
else:
Gblksize = max(
16, int(max_memory * .4 * 1e6 / 16 / buflen / (nkptj + 1)))
Gblksize = min(Gblksize, ngs, 16384)
pqkRbuf = numpy.empty(buflen * Gblksize)
pqkIbuf = numpy.empty(buflen * Gblksize)
# buf for ft_aopair
buf = numpy.zeros((nkptj, buflen * Gblksize), dtype=numpy.complex128)
col1 = 0
for istep, sh_range in enumerate(shranges):
log.debug1('int3c2e [%d/%d], AO [%d:%d], ncol = %d', \
istep+1, len(shranges), *sh_range)
bstart, bend, ncol = sh_range
col0, col1 = col1, col1 + ncol
j3cR = []
j3cI = []
for k, idx in enumerate(adapted_ji_idx):
v = numpy.asarray(feri['j3c/%d' % idx][:, col0:col1])
if is_zero(kpt):
for i, c in enumerate(vbar):
if c != 0:
v[i] -= c * ovlp[k][col0:col1]
j3cR.append(numpy.asarray(v.real, order='C'))
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
j3cI.append(None)
else:
j3cI.append(numpy.asarray(v.imag, order='C'))
v = None
if aosym == 's2':
shls_slice = (bstart, bend, 0, bend)
for p0, p1 in lib.prange(0, ngs, Gblksize):
ft_ao._ft_aopair_kpts(cell,
Gv[p0:p1],
shls_slice,
aosym,
b,
gxyz[p0:p1],
Gvbase,
kpt,
adapted_kptjs,
out=buf)
nG = p1 - p0
for k, ji in enumerate(adapted_ji_idx):
aoao = numpy.ndarray((nG, ncol),
dtype=numpy.complex128,
order='F',
buffer=buf[k])
pqkR = numpy.ndarray((ncol, nG), buffer=pqkRbuf)
pqkI = numpy.ndarray((ncol, nG), buffer=pqkIbuf)
pqkR[:] = aoao.real.T
pqkI[:] = aoao.imag.T
aoao[:] = 0
lib.dot(kLR[p0:p1].T, pqkR.T, -1, j3cR[k][naux:], 1)
lib.dot(kLI[p0:p1].T, pqkI.T, -1, j3cR[k][naux:], 1)
if not (is_zero(kpt)
and gamma_point(adapted_kptjs[k])):
lib.dot(kLR[p0:p1].T, pqkI.T, -1, j3cI[k][naux:],
1)
lib.dot(kLI[p0:p1].T, pqkR.T, 1, j3cI[k][naux:], 1)
else:
shls_slice = (bstart, bend, 0, cell.nbas)
ni = ncol // nao
for p0, p1 in lib.prange(0, ngs, Gblksize):
ft_ao._ft_aopair_kpts(cell,
Gv[p0:p1],
shls_slice,
aosym,
b,
gxyz[p0:p1],
Gvbase,
kpt,
adapted_kptjs,
out=buf)
nG = p1 - p0
for k, ji in enumerate(adapted_ji_idx):
aoao = numpy.ndarray((nG, ni, nao),
dtype=numpy.complex128,
order='F',
buffer=buf[k])
pqkR = numpy.ndarray((ni, nao, nG), buffer=pqkRbuf)
pqkI = numpy.ndarray((ni, nao, nG), buffer=pqkIbuf)
pqkR[:] = aoao.real.transpose(1, 2, 0)
pqkI[:] = aoao.imag.transpose(1, 2, 0)
aoao[:] = 0
pqkR = pqkR.reshape(-1, nG)
pqkI = pqkI.reshape(-1, nG)
zdotCN(kLR[p0:p1].T, kLI[p0:p1].T, pqkR.T, pqkI.T, -1,
j3cR[k][naux:], j3cI[k][naux:], 1)
naux0 = nauxs[uniq_kptji_id]
for k, ji in enumerate(adapted_ji_idx):
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
v = fuse(j3cR[k])
else:
v = fuse(j3cR[k] + j3cI[k] * 1j)
if j2c[uniq_kptji_id][0] == 'CD':
v = scipy.linalg.solve_triangular(j2c[uniq_kptji_id][1],
v,
lower=True,
overwrite_b=True)
else:
v = lib.dot(j2c[uniq_kptji_id][1], v)
feri['j3c/%d' % ji][:naux0, col0:col1] = v
naux0 = nauxs[uniq_kptji_id]
for k, ji in enumerate(adapted_ji_idx):
v = feri['j3c/%d' % ji][:naux0]
del (feri['j3c/%d' % ji])
feri['j3c/%d' % ji] = v
for k, kpt in enumerate(uniq_kpts):
make_kpt(k)
feri.close()
def ft_fuse(job_id, uniq_kptji_id, sh0, sh1):
kpt = uniq_kpts[uniq_kptji_id] # kpt = kptj - kpti
adapted_ji_idx = numpy.where(uniq_inverse == uniq_kptji_id)[0]
adapted_kptjs = kptjs[adapted_ji_idx]
nkptj = len(adapted_kptjs)
shls_slice = (auxcell.nbas, fused_cell.nbas)
Gaux = ft_ao.ft_ao(fused_cell, Gv, shls_slice, b, gxyz, Gvbase, kpt)
Gaux *= mydf.weighted_coulG(kpt, False, gs).reshape(-1, 1)
kLR = Gaux.real.copy('C')
kLI = Gaux.imag.copy('C')
j2c = numpy.asarray(feri['j2c/%d' % uniq_kptji_id])
j2ctag = j2ctags[uniq_kptji_id]
naux0 = j2c.shape[0]
if is_zero(kpt):
aosym = 's2'
else:
aosym = 's1'
j3cR = [None] * nkptj
j3cI = [None] * nkptj
i0 = ao_loc[sh0]
i1 = ao_loc[sh1]
for k, idx in enumerate(adapted_ji_idx):
key = 'j3c-chunks/%d/%d' % (job_id, idx)
v = numpy.asarray(feri[key])
if is_zero(kpt):
for i, c in enumerate(vbar):
if c != 0:
v[i] -= c * ovlp[k][i0 * (i0 + 1) // 2:i1 *
(i1 + 1) // 2].ravel()
j3cR[k] = numpy.asarray(v.real, order='C')
if v.dtype == numpy.complex128:
j3cI[k] = numpy.asarray(v.imag, order='C')
v = None
ncol = j3cR[0].shape[1]
Gblksize = max(16, int(max_memory * 1e6 / 16 / ncol /
(nkptj + 1))) # +1 for pqkRbuf/pqkIbuf
Gblksize = min(Gblksize, ngs, 16384)
pqkRbuf = numpy.empty(ncol * Gblksize)
pqkIbuf = numpy.empty(ncol * Gblksize)
buf = numpy.empty(nkptj * ncol * Gblksize, dtype=numpy.complex128)
log.alldebug2(' blksize (%d,%d)', Gblksize, ncol)
shls_slice = (sh0, sh1, 0, cell.nbas)
for p0, p1 in lib.prange(0, ngs, Gblksize):
dat = ft_ao._ft_aopair_kpts(cell,
Gv[p0:p1],
shls_slice,
aosym,
b,
gxyz[p0:p1],
Gvbase,
kpt,
adapted_kptjs,
out=buf)
nG = p1 - p0
for k, ji in enumerate(adapted_ji_idx):
aoao = dat[k].reshape(nG, ncol)
pqkR = numpy.ndarray((ncol, nG), buffer=pqkRbuf)
pqkI = numpy.ndarray((ncol, nG), buffer=pqkIbuf)
pqkR[:] = aoao.real.T
pqkI[:] = aoao.imag.T
lib.dot(kLR[p0:p1].T, pqkR.T, -1, j3cR[k][naux:], 1)
lib.dot(kLI[p0:p1].T, pqkI.T, -1, j3cR[k][naux:], 1)
if not (is_zero(kpt) and gamma_point(adapted_kptjs[k])):
lib.dot(kLR[p0:p1].T, pqkI.T, -1, j3cI[k][naux:], 1)
lib.dot(kLI[p0:p1].T, pqkR.T, 1, j3cI[k][naux:], 1)
for k, idx in enumerate(adapted_ji_idx):
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
v = fuse(j3cR[k])
else:
v = fuse(j3cR[k] + j3cI[k] * 1j)
if j2ctag == 'CD':
v = scipy.linalg.solve_triangular(j2c,
v,
lower=True,
overwrite_b=True)
else:
v = lib.dot(j2c, v)
feri['j3c-chunks/%d/%d' % (job_id, idx)][:naux0] = v
def make_kpt(uniq_kptji_id, cholesky_j2c):
kpt = uniq_kpts[uniq_kptji_id] # kpt = kptj - kpti
log.debug1('kpt = %s', kpt)
adapted_ji_idx = numpy.where(uniq_inverse == uniq_kptji_id)[0]
adapted_kptjs = kptjs[adapted_ji_idx]
nkptj = len(adapted_kptjs)
log.debug1('adapted_ji_idx = %s', adapted_ji_idx)
j2c, j2c_negative, j2ctag = cholesky_j2c
shls_slice = (auxcell.nbas, fused_cell.nbas)
Gaux = ft_ao.ft_ao(fused_cell, Gv, shls_slice, b, gxyz, Gvbase, kpt)
wcoulG = mydf.weighted_coulG(kpt, False, mesh)
Gaux *= wcoulG.reshape(-1,1)
kLR = Gaux.real.copy('C')
kLI = Gaux.imag.copy('C')
Gaux = None
if is_zero(kpt): # kpti == kptj
aosym = 's2'
nao_pair = nao*(nao+1)//2
if cell.dimension == 3:
vbar = fuse(mydf.auxbar(fused_cell))
ovlp = cell.pbc_intor('int1e_ovlp', hermi=1, kpts=adapted_kptjs)
ovlp = [lib.pack_tril(s) for s in ovlp]
else:
aosym = 's1'
nao_pair = nao**2
mem_now = lib.current_memory()[0]
log.debug2('memory = %s', mem_now)
max_memory = max(2000, mydf.max_memory-mem_now)
# nkptj for 3c-coulomb arrays plus 1 Lpq array
buflen = min(max(int(max_memory*.38e6/16/naux/(nkptj+1)), 1), nao_pair)
shranges = _guess_shell_ranges(cell, buflen, aosym)
buflen = max([x[2] for x in shranges])
# +1 for a pqkbuf
if aosym == 's2':
Gblksize = max(16, int(max_memory*.1e6/16/buflen/(nkptj+1)))
else:
Gblksize = max(16, int(max_memory*.2e6/16/buflen/(nkptj+1)))
Gblksize = min(Gblksize, ngrids, 16384)
pqkRbuf = numpy.empty(buflen*Gblksize)
pqkIbuf = numpy.empty(buflen*Gblksize)
# buf for ft_aopair
buf = numpy.empty(nkptj*buflen*Gblksize, dtype=numpy.complex128)
def pw_contract(istep, sh_range, j3cR, j3cI):
bstart, bend, ncol = sh_range
if aosym == 's2':
shls_slice = (bstart, bend, 0, bend)
else:
shls_slice = (bstart, bend, 0, cell.nbas)
for p0, p1 in lib.prange(0, ngrids, Gblksize):
dat = ft_ao._ft_aopair_kpts(cell, Gv[p0:p1], shls_slice, aosym,
b, gxyz[p0:p1], Gvbase, kpt,
adapted_kptjs, out=buf)
nG = p1 - p0
for k, ji in enumerate(adapted_ji_idx):
aoao = dat[k].reshape(nG,ncol)
pqkR = numpy.ndarray((ncol,nG), buffer=pqkRbuf)
pqkI = numpy.ndarray((ncol,nG), buffer=pqkIbuf)
pqkR[:] = aoao.real.T
pqkI[:] = aoao.imag.T
lib.dot(kLR[p0:p1].T, pqkR.T, -1, j3cR[k][naux:], 1)
lib.dot(kLI[p0:p1].T, pqkI.T, -1, j3cR[k][naux:], 1)
if not (is_zero(kpt) and gamma_point(adapted_kptjs[k])):
lib.dot(kLR[p0:p1].T, pqkI.T, -1, j3cI[k][naux:], 1)
lib.dot(kLI[p0:p1].T, pqkR.T, 1, j3cI[k][naux:], 1)
for k, ji in enumerate(adapted_ji_idx):
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
v = fuse(j3cR[k])
else:
v = fuse(j3cR[k] + j3cI[k] * 1j)
if j2ctag == 'CD':
v = scipy.linalg.solve_triangular(j2c, v, lower=True, overwrite_b=True)
feri['j3c/%d/%d'%(ji,istep)] = v
else:
feri['j3c/%d/%d'%(ji,istep)] = lib.dot(j2c, v)
# low-dimension systems
if j2c_negative is not None:
feri['j3c-/%d/%d'%(ji,istep)] = lib.dot(j2c_negative, v)
with lib.call_in_background(pw_contract) as compute:
col1 = 0
for istep, sh_range in enumerate(shranges):
log.debug1('int3c2e [%d/%d], AO [%d:%d], ncol = %d', \
istep+1, len(shranges), *sh_range)
bstart, bend, ncol = sh_range
col0, col1 = col1, col1+ncol
j3cR = []
j3cI = []
for k, idx in enumerate(adapted_ji_idx):
v = numpy.vstack([fswap['j3c-junk/%d/%d'%(idx,i)][0,col0:col1].T
for i in range(nsegs)])
# vbar is the interaction between the background charge
# and the auxiliary basis. 0D, 1D, 2D do not have vbar.
if is_zero(kpt) and cell.dimension == 3:
for i in numpy.where(vbar != 0)[0]:
v[i] -= vbar[i] * ovlp[k][col0:col1]
j3cR.append(numpy.asarray(v.real, order='C'))
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
j3cI.append(None)
else:
j3cI.append(numpy.asarray(v.imag, order='C'))
v = None
compute(istep, sh_range, j3cR, j3cI)
for ji in adapted_ji_idx:
del(fswap['j3c-junk/%d'%ji])
def _make_j3c(mydf, cell, auxcell, chgcell, kptij_lst):
t1 = (time.clock(), time.time())
log = logger.Logger(mydf.stdout, mydf.verbose)
max_memory = max(2000, mydf.max_memory-lib.current_memory()[0])
auxcell = copy.copy(auxcell)
auxcell._atm, auxcell._bas, auxcell._env = \
gto.conc_env(auxcell._atm, auxcell._bas, auxcell._env,
chgcell._atm, chgcell._bas, chgcell._env)
outcore.aux_e2(cell, auxcell, mydf._cderi, 'cint3c2e_sph',
kptij_lst=kptij_lst, dataname='j3c', max_memory=max_memory)
t1 = log.timer_debug1('3c2e', *t1)
nao = cell.nao_nr()
naux = auxcell.nao_nr()
gs = mydf.gs
gxyz = lib.cartesian_prod((numpy.append(range(gs[0]+1), range(-gs[0],0)),
numpy.append(range(gs[1]+1), range(-gs[1],0)),
numpy.append(range(gs[2]+1), range(-gs[2],0))))
invh = numpy.linalg.inv(cell._h)
Gv = 2*numpy.pi * numpy.dot(gxyz, invh)
ngs = gxyz.shape[0]
kptis = kptij_lst[:,0]
kptjs = kptij_lst[:,1]
kpt_ji = kptjs - kptis
uniq_kpts, uniq_index, uniq_inverse = unique(kpt_ji)
# j2c ~ (-kpt_ji | kpt_ji)
j2c = auxcell.pbc_intor('cint2c2e_sph', hermi=1, kpts=uniq_kpts)
kLRs = []
kLIs = []
for k, kpt in enumerate(uniq_kpts):
aoaux = ft_ao.ft_ao(auxcell, Gv, None, invh, gxyz, gs, kpt)
coulG = tools.get_coulG(cell, kpt, gs=gs) / cell.vol
aoauxG = aoaux * coulG.reshape(-1,1)
kLRs.append(numpy.asarray(aoauxG.real, order='C'))
kLIs.append(numpy.asarray(aoauxG.imag, order='C'))
if is_zero(kpt): # kpti == kptj
j2c[k] -= lib.dot(kLRs[-1].T, numpy.asarray(aoaux.real,order='C'))
j2c[k] -= lib.dot(kLIs[-1].T, numpy.asarray(aoaux.imag,order='C'))
else:
# aoaux ~ kpt_ij, aoaux.conj() ~ kpt_kl
j2c[k] -= lib.dot(aoauxG.conj().T, aoaux)
aoaux = coulG = None
feri = h5py.File(mydf._cderi)
# Expand approx Lpq for aosym='s1'. The approx Lpq are all in aosym='s2' mode
if mydf.approx_sr_level > 0 and len(kptij_lst) > 1:
Lpq_fake = _fake_Lpq_kpts(mydf, feri, naux, nao)
def save(label, dat, col0, col1):
feri[label][:,col0:col1] = dat
def make_kpt(uniq_kptji_id): # kpt = kptj - kpti
kpt = uniq_kpts[uniq_kptji_id]
log.debug1('kpt = %s', kpt)
adapted_ji_idx = numpy.where(uniq_inverse == uniq_kptji_id)[0]
adapted_kptjs = kptjs[adapted_ji_idx]
nkptj = len(adapted_kptjs)
log.debug1('adapted_ji_idx = %s', adapted_ji_idx)
kLR = kLRs[uniq_kptji_id]
kLI = kLIs[uniq_kptji_id]
if is_zero(kpt): # kpti == kptj
aosym = 's2'
nao_pair = nao*(nao+1)//2
vbar = mydf.auxbar(auxcell)
ovlp = cell.pbc_intor('cint1e_ovlp_sph', hermi=1, kpts=adapted_kptjs)
for k, ji in enumerate(adapted_ji_idx):
ovlp[k] = lib.pack_tril(ovlp[k])
else:
aosym = 's1'
nao_pair = nao**2
max_memory = max(2000, mydf.max_memory-lib.current_memory()[0])
# nkptj for 3c-coulomb arrays plus 1 Lpq array
buflen = min(max(int(max_memory*.6*1e6/16/naux/(nkptj+1)), 1), nao_pair)
shranges = pyscf.df.outcore._guess_shell_ranges(cell, buflen, aosym)
buflen = max([x[2] for x in shranges])
# +1 for a pqkbuf
if aosym == 's2':
Gblksize = max(16, int(max_memory*.2*1e6/16/buflen/(nkptj+1)))
else:
Gblksize = max(16, int(max_memory*.4*1e6/16/buflen/(nkptj+1)))
Gblksize = min(Gblksize, ngs)
pqkRbuf = numpy.empty(buflen*Gblksize)
pqkIbuf = numpy.empty(buflen*Gblksize)
# buf for ft_aopair
buf = numpy.zeros((nkptj,buflen*Gblksize), dtype=numpy.complex128)
col1 = 0
for istep, sh_range in enumerate(shranges):
log.debug1('int3c2e [%d/%d], AO [%d:%d], ncol = %d', \
istep+1, len(shranges), *sh_range)
bstart, bend, ncol = sh_range
col0, col1 = col1, col1+ncol
j3cR = []
j3cI = []
for k, idx in enumerate(adapted_ji_idx):
v = numpy.asarray(feri['j3c/%d'%idx][:,col0:col1])
if mydf.approx_sr_level == 0:
Lpq = numpy.asarray(feri['Lpq/%d'%idx][:,col0:col1])
elif aosym == 's2':
Lpq = numpy.asarray(feri['Lpq/0'][:,col0:col1])
else:
Lpq = numpy.asarray(Lpq_fake[:,col0:col1])
lib.dot(j2c[uniq_kptji_id], Lpq, -.5, v, 1)
j3cR.append(numpy.asarray(v.real, order='C'))
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
j3cI.append(None)
else:
j3cI.append(numpy.asarray(v.imag, order='C'))
v = Lpq = None
if aosym == 's2':
shls_slice = (bstart, bend, 0, bend)
for p0, p1 in lib.prange(0, ngs, Gblksize):
ft_ao._ft_aopair_kpts(cell, Gv[p0:p1], shls_slice, aosym, invh,
gxyz[p0:p1], gs, kpt, adapted_kptjs, out=buf)
nG = p1 - p0
for k, ji in enumerate(adapted_ji_idx):
aoao = numpy.ndarray((nG,ncol), dtype=numpy.complex128,
order='F', buffer=buf[k])
pqkR = numpy.ndarray((ncol,nG), buffer=pqkRbuf)
pqkI = numpy.ndarray((ncol,nG), buffer=pqkIbuf)
pqkR[:] = aoao.real.T
pqkI[:] = aoao.imag.T
aoao[:] = 0
lib.dot(kLR[p0:p1].T, pqkR.T, -1, j3cR[k], 1)
lib.dot(kLI[p0:p1].T, pqkI.T, -1, j3cR[k], 1)
if not (is_zero(kpt) and gamma_point(adapted_kptjs[k])):
lib.dot(kLR[p0:p1].T, pqkI.T, -1, j3cI[k], 1)
lib.dot(kLI[p0:p1].T, pqkR.T, 1, j3cI[k], 1)
else:
shls_slice = (bstart, bend, 0, cell.nbas)
ni = ncol // nao
for p0, p1 in lib.prange(0, ngs, Gblksize):
ft_ao._ft_aopair_kpts(cell, Gv[p0:p1], shls_slice, aosym, invh,
gxyz[p0:p1], gs, kpt, adapted_kptjs, out=buf)
nG = p1 - p0
for k, ji in enumerate(adapted_ji_idx):
aoao = numpy.ndarray((nG,ni,nao), dtype=numpy.complex128,
order='F', buffer=buf[k])
pqkR = numpy.ndarray((ni,nao,nG), buffer=pqkRbuf)
pqkI = numpy.ndarray((ni,nao,nG), buffer=pqkIbuf)
pqkR[:] = aoao.real.transpose(1,2,0)
pqkI[:] = aoao.imag.transpose(1,2,0)
aoao[:] = 0
pqkR = pqkR.reshape(-1,nG)
pqkI = pqkI.reshape(-1,nG)
zdotCN(kLR[p0:p1].T, kLI[p0:p1].T, pqkR.T, pqkI.T,
-1, j3cR[k], j3cI[k], 1)
if is_zero(kpt):
for k, ji in enumerate(adapted_ji_idx):
if gamma_point(adapted_kptjs[k]):
for i, c in enumerate(vbar):
if c != 0:
j3cR[k][i] -= c * ovlp[k][col0:col1].real
else:
for i, c in enumerate(vbar):
if c != 0:
j3cR[k][i] -= c * ovlp[k][col0:col1].real
j3cI[k][i] -= c * ovlp[k][col0:col1].imag
for k, ji in enumerate(adapted_ji_idx):
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
save('j3c/%d'%ji, j3cR[k], col0, col1)
else:
save('j3c/%d'%ji, j3cR[k]+j3cI[k]*1j, col0, col1)
for k, kpt in enumerate(uniq_kpts):
make_kpt(k)
feri.close()
def get_pnucp(mydf, kpts=None):
cell = mydf.cell
if kpts is None:
kpts_lst = numpy.zeros((1, 3))
else:
kpts_lst = numpy.reshape(kpts, (-1, 3))
log = logger.Logger(mydf.stdout, mydf.verbose)
t1 = (logger.process_clock(), logger.perf_counter())
nkpts = len(kpts_lst)
nao = cell.nao_nr()
nao_pair = nao * (nao + 1) // 2
Gv, Gvbase, kws = cell.get_Gv_weights(mydf.mesh)
charge = -cell.atom_charges()
kpt_allow = numpy.zeros(3)
coulG = tools.get_coulG(cell, kpt_allow, mesh=mydf.mesh, Gv=Gv)
coulG *= kws
if mydf.eta == 0:
wj = numpy.zeros((nkpts, nao_pair), dtype=numpy.complex128)
SI = cell.get_SI(Gv)
vG = numpy.einsum('i,ix->x', charge, SI) * coulG
wj = numpy.zeros((nkpts, nao_pair), dtype=numpy.complex128)
else:
nuccell = copy.copy(cell)
half_sph_norm = .5 / numpy.sqrt(numpy.pi)
norm = half_sph_norm / mole.gaussian_int(2, mydf.eta)
chg_env = [mydf.eta, norm]
ptr_eta = cell._env.size
ptr_norm = ptr_eta + 1
chg_bas = [[ia, 0, 1, 1, 0, ptr_eta, ptr_norm, 0]
for ia in range(cell.natm)]
nuccell._atm = cell._atm
nuccell._bas = numpy.asarray(chg_bas, dtype=numpy.int32)
nuccell._env = numpy.hstack((cell._env, chg_env))
wj = lib.asarray(mydf._int_nuc_vloc(nuccell, kpts_lst, 'int3c2e_pvp1'))
t1 = log.timer_debug1('pnucp pass1: analytic int', *t1)
aoaux = ft_ao.ft_ao(nuccell, Gv)
vG = numpy.einsum('i,xi->x', charge, aoaux) * coulG
if cell.dimension == 3:
nucbar = sum(
[z / nuccell.bas_exp(i)[0] for i, z in enumerate(charge)])
nucbar *= numpy.pi / cell.vol
ovlp = cell.pbc_intor('int1e_kin', 1, lib.HERMITIAN, kpts_lst)
for k in range(nkpts):
s = lib.pack_tril(ovlp[k])
# *2 due to the factor 1/2 in T
wj[k] -= nucbar * 2 * s
max_memory = max(2000, mydf.max_memory - lib.current_memory()[0])
for aoaoks, p0, p1 in mydf.ft_loop(mydf.mesh,
kpt_allow,
kpts_lst,
max_memory=max_memory,
aosym='s2',
intor='GTO_ft_pdotp'):
for k, aoao in enumerate(aoaoks):
if aft_jk.gamma_point(kpts_lst[k]):
wj[k] += numpy.einsum('k,kx->x', vG[p0:p1].real, aoao.real)
wj[k] += numpy.einsum('k,kx->x', vG[p0:p1].imag, aoao.imag)
else:
wj[k] += numpy.einsum('k,kx->x', vG[p0:p1].conj(), aoao)
t1 = log.timer_debug1('contracting pnucp', *t1)
wj_kpts = []
for k, kpt in enumerate(kpts_lst):
if aft_jk.gamma_point(kpt):
wj_kpts.append(lib.unpack_tril(wj[k].real.copy()))
else:
wj_kpts.append(lib.unpack_tril(wj[k]))
if kpts is None or numpy.shape(kpts) == (3, ):
wj_kpts = wj_kpts[0]
return numpy.asarray(wj_kpts)
def _gaussian_int(cell):
r'''Regular gaussian integral \int g(r) dr^3'''
return ft_ao.ft_ao(cell, numpy.zeros((1,3)))[0].real
def _make_j3c(mydf, cell, auxcell, kptij_lst, cderi_file):
log = logger.Logger(mydf.stdout, mydf.verbose)
t1 = t0 = (time.clock(), time.time())
fused_cell, fuse = fuse_auxcell(mydf, mydf.auxcell)
ao_loc = cell.ao_loc_nr()
nao = ao_loc[-1]
naux = auxcell.nao_nr()
nkptij = len(kptij_lst)
gs = mydf.gs
Gv, Gvbase, kws = cell.get_Gv_weights(gs)
b = cell.reciprocal_vectors()
gxyz = lib.cartesian_prod([numpy.arange(len(x)) for x in Gvbase])
ngs = gxyz.shape[0]
kptis = kptij_lst[:, 0]
kptjs = kptij_lst[:, 1]
kpt_ji = kptjs - kptis
uniq_kpts, uniq_index, uniq_inverse = unique(kpt_ji)
log.debug('Num uniq kpts %d', len(uniq_kpts))
log.debug2('uniq_kpts %s', uniq_kpts)
# j2c ~ (-kpt_ji | kpt_ji)
j2c = fused_cell.pbc_intor('int2c2e_sph', hermi=1, kpts=uniq_kpts)
j2ctags = []
nauxs = []
t1 = log.timer_debug1('2c2e', *t1)
if h5py.is_hdf5(cderi_file):
feri = h5py.File(cderi_file)
else:
feri = h5py.File(cderi_file, 'w')
for k, kpt in enumerate(uniq_kpts):
aoaux = ft_ao.ft_ao(fused_cell, Gv, None, b, gxyz, Gvbase, kpt).T
coulG = numpy.sqrt(mydf.weighted_coulG(kpt, False, gs))
kLR = (aoaux.real * coulG).T
kLI = (aoaux.imag * coulG).T
if not kLR.flags.c_contiguous: kLR = lib.transpose(kLR.T)
if not kLI.flags.c_contiguous: kLI = lib.transpose(kLI.T)
aoaux = None
kLR1 = numpy.asarray(kLR[:, naux:], order='C')
kLI1 = numpy.asarray(kLI[:, naux:], order='C')
if is_zero(kpt): # kpti == kptj
for p0, p1 in mydf.mpi_prange(0, ngs):
j2cR = lib.ddot(kLR1[p0:p1].T, kLR[p0:p1])
j2cR = lib.ddot(kLI1[p0:p1].T, kLI[p0:p1], 1, j2cR, 1)
j2c[k][naux:] -= mpi.allreduce(j2cR)
j2c[k][:naux, naux:] = j2c[k][naux:, :naux].T
else:
for p0, p1 in mydf.mpi_prange(0, ngs):
j2cR, j2cI = zdotCN(kLR1[p0:p1].T, kLI1[p0:p1].T, kLR[p0:p1],
kLI[p0:p1])
j2cR = mpi.allreduce(j2cR)
j2cI = mpi.allreduce(j2cI)
j2c[k][naux:] -= j2cR + j2cI * 1j
j2c[k][:naux, naux:] = j2c[k][naux:, :naux].T.conj()
j2c[k] = fuse(fuse(j2c[k]).T).T
try:
feri['j2c/%d' % k] = scipy.linalg.cholesky(j2c[k], lower=True)
j2ctags.append('CD')
nauxs.append(naux)
except scipy.linalg.LinAlgError as e:
#msg =('===================================\n'
# 'J-metric not positive definite.\n'
# 'It is likely that gs is not enough.\n'
# '===================================')
#log.error(msg)
#raise scipy.linalg.LinAlgError('\n'.join([e.message, msg]))
w, v = scipy.linalg.eigh(j2c)
log.debug2('metric linear dependency for kpt %s', uniq_kptji_id)
log.debug2('cond = %.4g, drop %d bfns', w[0] / w[-1],
numpy.count_nonzero(w < LINEAR_DEP_THR))
v = v[:, w > LINEAR_DEP_THR].T.conj()
v /= numpy.sqrt(w[w > LINEAR_DEP_THR]).reshape(-1, 1)
feri['j2c/%d' % k] = v
j2ctags.append('eig')
nauxs.append(v.shape[0])
kLR = kLI = kLR1 = kLI1 = coulG = None
j2c = None
aosym_s2 = numpy.einsum('ix->i', abs(kptis - kptjs)) < 1e-9
j_only = numpy.all(aosym_s2)
if gamma_point(kptij_lst):
dtype = 'f8'
else:
dtype = 'c16'
vbar = mydf.auxbar(fused_cell)
vbar = fuse(vbar)
ovlp = cell.pbc_intor('int1e_ovlp_sph', hermi=1, kpts=kptjs[aosym_s2])
ovlp = [lib.pack_tril(s) for s in ovlp]
t1 = log.timer_debug1('aoaux and int2c', *t1)
# Estimates the buffer size based on the last contraction in G-space.
# This contraction requires to hold nkptj copies of (naux,?) array
# simultaneously in memory.
mem_now = max(comm.allgather(lib.current_memory()[0]))
max_memory = max(2000, mydf.max_memory - mem_now)
nkptj_max = max((uniq_inverse == x).sum() for x in set(uniq_inverse))
buflen = max(
int(
min(max_memory * .5e6 / 16 / naux / (nkptj_max + 2) / nao,
nao / 3 / mpi.pool.size)), 1)
chunks = (buflen, nao)
j3c_jobs = grids2d_int3c_jobs(cell, auxcell, kptij_lst, chunks, j_only)
log.debug1('max_memory = %d MB (%d in use) chunks %s', max_memory,
mem_now, chunks)
log.debug2('j3c_jobs %s', j3c_jobs)
if j_only:
int3c = wrap_int3c(cell, fused_cell, 'int3c2e_sph', 's2', 1, kptij_lst)
else:
int3c = wrap_int3c(cell, fused_cell, 'int3c2e_sph', 's1', 1, kptij_lst)
idxb = numpy.tril_indices(nao)
idxb = (idxb[0] * nao + idxb[1]).astype('i')
aux_loc = fused_cell.ao_loc_nr('ssc' in 'int3c2e_sph')
def gen_int3c(auxcell, job_id, ish0, ish1):
dataname = 'j3c-chunks/%d' % job_id
if dataname in feri:
del (feri[dataname])
i0 = ao_loc[ish0]
i1 = ao_loc[ish1]
dii = i1 * (i1 + 1) // 2 - i0 * (i0 + 1) // 2
dij = (i1 - i0) * nao
if j_only:
buflen = max(8, int(max_memory * 1e6 / 16 / (nkptij * dii + dii)))
else:
buflen = max(8, int(max_memory * 1e6 / 16 / (nkptij * dij + dij)))
auxranges = balance_segs(aux_loc[1:] - aux_loc[:-1], buflen)
buflen = max([x[2] for x in auxranges])
buf = numpy.empty(nkptij * dij * buflen, dtype=dtype)
buf1 = numpy.empty(dij * buflen, dtype=dtype)
naux = aux_loc[-1]
for kpt_id, kptij in enumerate(kptij_lst):
key = '%s/%d' % (dataname, kpt_id)
if aosym_s2[kpt_id]:
shape = (naux, dii)
else:
shape = (naux, dij)
if gamma_point(kptij):
feri.create_dataset(key, shape, 'f8')
else:
feri.create_dataset(key, shape, 'c16')
naux0 = 0
for istep, auxrange in enumerate(auxranges):
log.alldebug2("aux_e2 job_id %d step %d", job_id, istep)
sh0, sh1, nrow = auxrange
sub_slice = (ish0, ish1, 0, cell.nbas, sh0, sh1)
if j_only:
mat = numpy.ndarray((nkptij, dii, nrow),
dtype=dtype,
buffer=buf)
else:
mat = numpy.ndarray((nkptij, dij, nrow),
dtype=dtype,
buffer=buf)
mat = int3c(sub_slice, mat)
for k, kptij in enumerate(kptij_lst):
h5dat = feri['%s/%d' % (dataname, k)]
v = lib.transpose(mat[k], out=buf1)
if not j_only and aosym_s2[k]:
idy = idxb[i0 * (i0 + 1) // 2:i1 *
(i1 + 1) // 2] - i0 * nao
out = numpy.ndarray((nrow, dii),
dtype=v.dtype,
buffer=mat[k])
v = numpy.take(v, idy, axis=1, out=out)
if gamma_point(kptij):
h5dat[naux0:naux0 + nrow] = v.real
else:
h5dat[naux0:naux0 + nrow] = v
naux0 += nrow
def ft_fuse(job_id, uniq_kptji_id, sh0, sh1):
kpt = uniq_kpts[uniq_kptji_id] # kpt = kptj - kpti
adapted_ji_idx = numpy.where(uniq_inverse == uniq_kptji_id)[0]
adapted_kptjs = kptjs[adapted_ji_idx]
nkptj = len(adapted_kptjs)
shls_slice = (auxcell.nbas, fused_cell.nbas)
Gaux = ft_ao.ft_ao(fused_cell, Gv, shls_slice, b, gxyz, Gvbase, kpt)
Gaux *= mydf.weighted_coulG(kpt, False, gs).reshape(-1, 1)
kLR = Gaux.real.copy('C')
kLI = Gaux.imag.copy('C')
j2c = numpy.asarray(feri['j2c/%d' % uniq_kptji_id])
j2ctag = j2ctags[uniq_kptji_id]
naux0 = j2c.shape[0]
if is_zero(kpt):
aosym = 's2'
else:
aosym = 's1'
j3cR = [None] * nkptj
j3cI = [None] * nkptj
i0 = ao_loc[sh0]
i1 = ao_loc[sh1]
for k, idx in enumerate(adapted_ji_idx):
key = 'j3c-chunks/%d/%d' % (job_id, idx)
v = numpy.asarray(feri[key])
if is_zero(kpt):
for i, c in enumerate(vbar):
if c != 0:
v[i] -= c * ovlp[k][i0 * (i0 + 1) // 2:i1 *
(i1 + 1) // 2].ravel()
j3cR[k] = numpy.asarray(v.real, order='C')
if v.dtype == numpy.complex128:
j3cI[k] = numpy.asarray(v.imag, order='C')
v = None
ncol = j3cR[0].shape[1]
Gblksize = max(16, int(max_memory * 1e6 / 16 / ncol /
(nkptj + 1))) # +1 for pqkRbuf/pqkIbuf
Gblksize = min(Gblksize, ngs, 16384)
pqkRbuf = numpy.empty(ncol * Gblksize)
pqkIbuf = numpy.empty(ncol * Gblksize)
buf = numpy.empty(nkptj * ncol * Gblksize, dtype=numpy.complex128)
log.alldebug2(' blksize (%d,%d)', Gblksize, ncol)
shls_slice = (sh0, sh1, 0, cell.nbas)
for p0, p1 in lib.prange(0, ngs, Gblksize):
dat = ft_ao._ft_aopair_kpts(cell,
Gv[p0:p1],
shls_slice,
aosym,
b,
gxyz[p0:p1],
Gvbase,
kpt,
adapted_kptjs,
out=buf)
nG = p1 - p0
for k, ji in enumerate(adapted_ji_idx):
aoao = dat[k].reshape(nG, ncol)
pqkR = numpy.ndarray((ncol, nG), buffer=pqkRbuf)
pqkI = numpy.ndarray((ncol, nG), buffer=pqkIbuf)
pqkR[:] = aoao.real.T
pqkI[:] = aoao.imag.T
lib.dot(kLR[p0:p1].T, pqkR.T, -1, j3cR[k][naux:], 1)
lib.dot(kLI[p0:p1].T, pqkI.T, -1, j3cR[k][naux:], 1)
if not (is_zero(kpt) and gamma_point(adapted_kptjs[k])):
lib.dot(kLR[p0:p1].T, pqkI.T, -1, j3cI[k][naux:], 1)
lib.dot(kLI[p0:p1].T, pqkR.T, 1, j3cI[k][naux:], 1)
for k, idx in enumerate(adapted_ji_idx):
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
v = fuse(j3cR[k])
else:
v = fuse(j3cR[k] + j3cI[k] * 1j)
if j2ctag == 'CD':
v = scipy.linalg.solve_triangular(j2c,
v,
lower=True,
overwrite_b=True)
else:
v = lib.dot(j2c, v)
feri['j3c-chunks/%d/%d' % (job_id, idx)][:naux0] = v
t2 = t1
j3c_workers = numpy.zeros(len(j3c_jobs), dtype=int)
#for job_id, ish0, ish1 in mpi.work_share_partition(j3c_jobs):
for job_id, ish0, ish1 in mpi.work_stealing_partition(j3c_jobs):
gen_int3c(fused_cell, job_id, ish0, ish1)
t2 = log.alltimer_debug2('int j3c %d' % job_id, *t2)
for k, kpt in enumerate(uniq_kpts):
ft_fuse(job_id, k, ish0, ish1)
t2 = log.alltimer_debug2('ft-fuse %d k %d' % (job_id, k), *t2)
j3c_workers[job_id] = rank
j3c_workers = mpi.allreduce(j3c_workers)
log.debug2('j3c_workers %s', j3c_workers)
j2c = kLRs = kLIs = ovlp = vbar = fuse = gen_int3c = ft_fuse = None
t1 = log.timer_debug1('int3c and fuse', *t1)
def get_segs_loc(aosym):
off0 = numpy.asarray([ao_loc[i0] for x, i0, i1 in j3c_jobs])
off1 = numpy.asarray([ao_loc[i1] for x, i0, i1 in j3c_jobs])
if aosym: # s2
dims = off1 * (off1 + 1) // 2 - off0 * (off0 + 1) // 2
else:
dims = (off1 - off0) * nao
#dims = numpy.asarray([ao_loc[i1]-ao_loc[i0] for x,i0,i1 in j3c_jobs])
dims = numpy.hstack(
[dims[j3c_workers == w] for w in range(mpi.pool.size)])
job_idx = numpy.hstack(
[numpy.where(j3c_workers == w)[0] for w in range(mpi.pool.size)])
segs_loc = numpy.append(0, numpy.cumsum(dims))
segs_loc = [(segs_loc[j], segs_loc[j + 1])
for j in numpy.argsort(job_idx)]
return segs_loc
segs_loc_s1 = get_segs_loc(False)
segs_loc_s2 = get_segs_loc(True)
if 'j3c' in feri: del (feri['j3c'])
segsize = (max(nauxs) + mpi.pool.size - 1) // mpi.pool.size
naux0 = rank * segsize
for k, kptij in enumerate(kptij_lst):
naux1 = min(nauxs[uniq_inverse[k]], naux0 + segsize)
nrow = max(0, naux1 - naux0)
if gamma_point(kptij):
dtype = 'f8'
else:
dtype = 'c16'
if aosym_s2[k]:
nao_pair = nao * (nao + 1) // 2
else:
nao_pair = nao * nao
feri.create_dataset('j3c/%d' % k, (nrow, nao_pair),
dtype,
maxshape=(None, nao_pair))
def load(k, p0, p1):
naux1 = nauxs[uniq_inverse[k]]
slices = [(min(i * segsize + p0, naux1), min(i * segsize + p1, naux1))
for i in range(mpi.pool.size)]
segs = []
for p0, p1 in slices:
val = []
for job_id, worker in enumerate(j3c_workers):
if rank == worker:
key = 'j3c-chunks/%d/%d' % (job_id, k)
val.append(feri[key][p0:p1].ravel())
if val:
segs.append(numpy.hstack(val))
else:
segs.append(numpy.zeros(0))
return segs
def save(k, p0, p1, segs):
segs = mpi.alltoall(segs)
naux1 = nauxs[uniq_inverse[k]]
loc0, loc1 = min(p0, naux1 - naux0), min(p1, naux1 - naux0)
nL = loc1 - loc0
if nL > 0:
if aosym_s2[k]:
segs = numpy.hstack([
segs[i0 * nL:i1 * nL].reshape(nL, -1)
for i0, i1 in segs_loc_s2
])
else:
segs = numpy.hstack([
segs[i0 * nL:i1 * nL].reshape(nL, -1)
for i0, i1 in segs_loc_s1
])
feri['j3c/%d' % k][loc0:loc1] = segs
mem_now = max(comm.allgather(lib.current_memory()[0]))
max_memory = max(2000, min(8000, mydf.max_memory - mem_now))
if numpy.all(aosym_s2):
if gamma_point(kptij_lst):
blksize = max(16, int(max_memory * .5e6 / 8 / nao**2))
else:
blksize = max(16, int(max_memory * .5e6 / 16 / nao**2))
else:
blksize = max(16, int(max_memory * .5e6 / 16 / nao**2 / 2))
log.debug1('max_momory %d MB (%d in use), blksize %d', max_memory, mem_now,
blksize)
t2 = t1
with lib.call_in_background(save) as async_write:
for k, kptji in enumerate(kptij_lst):
for p0, p1 in lib.prange(0, segsize, blksize):
segs = load(k, p0, p1)
async_write(k, p0, p1, segs)
t2 = log.timer_debug1(
'assemble k=%d %d:%d (in %d)' % (k, p0, p1, segsize), *t2)
if 'j3c-chunks' in feri: del (feri['j3c-chunks'])
if 'j3c-kptij' in feri: del (feri['j3c-kptij'])
feri['j3c-kptij'] = kptij_lst
t1 = log.alltimer_debug1('assembling j3c', *t1)
feri.close()
def get_pbc_pvxp(cell, kpts=None):
import numpy
import copy
import time
from pyscf import lib
from pyscf.lib import logger
from pyscf.pbc import tools
from pyscf.gto import mole
from pyscf.pbc.df import ft_ao
from pyscf.pbc.df import aft_jk
from pyscf.pbc.df import aft
if kpts is None:
kpts_lst = numpy.zeros((1,3))
else:
kpts_lst = numpy.reshape(kpts, (-1,3))
log = logger.Logger(cell.stdout, cell.verbose)
t1 = t0 = (time.clock(), time.time())
mydf = aft.AFTDF(cell, kpts)
mydf.eta = 0.2
ke_guess = aft.estimate_ke_cutoff_for_eta(cell, mydf.eta, cell.precision)
mydf.mesh = tools.cutoff_to_mesh(cell.lattice_vectors(), ke_guess)
log.debug('mydf.mesh %s', mydf.mesh)
nkpts = len(kpts_lst)
nao = cell.nao_nr()
nao_pair = nao * (nao+1) // 2
Gv, Gvbase, kws = cell.get_Gv_weights(mydf.mesh)
charge = -cell.atom_charges() # Apply Koseki effective charge?
kpt_allow = numpy.zeros(3)
coulG = tools.get_coulG(cell, kpt_allow, mesh=mydf.mesh, Gv=Gv)
coulG *= kws
if mydf.eta == 0:
soc_mat = numpy.zeros((nkpts,3,nao*nao), dtype=numpy.complex128)
SI = cell.get_SI(Gv)
vG = numpy.einsum('i,ix->x', charge, SI) * coulG
else:
nuccell = copy.copy(cell)
half_sph_norm = .5/numpy.sqrt(numpy.pi)
norm = half_sph_norm/mole.gaussian_int(2, mydf.eta)
chg_env = [mydf.eta, norm]
ptr_eta = cell._env.size
ptr_norm = ptr_eta + 1
chg_bas = [[ia, 0, 1, 1, 0, ptr_eta, ptr_norm, 0] for ia in range(cell.natm)]
nuccell._atm = cell._atm
nuccell._bas = numpy.asarray(chg_bas, dtype=numpy.int32)
nuccell._env = numpy.hstack((cell._env, chg_env))
soc_mat = mydf._int_nuc_vloc(nuccell, kpts_lst, 'int3c2e_pvxp1_sph',
aosym='s1', comp=3)
soc_mat = numpy.asarray(soc_mat).reshape(nkpts,3,nao**2)
t1 = log.timer_debug1('pnucp pass1: analytic int', *t1)
aoaux = ft_ao.ft_ao(nuccell, Gv)
vG = numpy.einsum('i,xi->x', charge, aoaux) * coulG
max_memory = max(2000, mydf.max_memory-lib.current_memory()[0])
for aoaoks, p0, p1 in mydf.ft_loop(mydf.mesh, kpt_allow, kpts_lst,
max_memory=max_memory, aosym='s1',
intor='GTO_ft_pxp_sph', comp=3):
for k, aoao in enumerate(aoaoks):
aoao = aoao.reshape(3,-1,nao**2)
if aft_jk.gamma_point(kpts_lst[k]):
soc_mat[k] += numpy.einsum('k,ckx->cx', vG[p0:p1].real, aoao.real)
soc_mat[k] += numpy.einsum('k,ckx->cx', vG[p0:p1].imag, aoao.imag)
else:
soc_mat[k] += numpy.einsum('k,ckx->cx', vG[p0:p1].conj(), aoao)
t1 = log.timer_debug1('contracting pnucp', *t1)
soc_mat_kpts = []
for k, kpt in enumerate(kpts_lst):
if aft_jk.gamma_point(kpt):
soc_mat_kpts.append(soc_mat[k].real.reshape(3,nao,nao))
else:
soc_mat_kpts.append(soc_mat[k].reshape(3,nao,nao))
if kpts is None or numpy.shape(kpts) == (3,):
soc_mat_kpts = soc_mat_kpts[0]
return numpy.asarray(soc_mat_kpts)
def _make_j3c(mydf, cell, auxcell, kptij_lst, cderi_file):
t1 = (time.clock(), time.time())
log = logger.Logger(mydf.stdout, mydf.verbose)
max_memory = max(2000, mydf.max_memory - lib.current_memory()[0])
fused_cell, fuse = fuse_auxcell(mydf, auxcell)
outcore.aux_e2(cell,
fused_cell,
cderi_file,
'int3c2e_sph',
aosym='s2',
kptij_lst=kptij_lst,
dataname='j3c',
max_memory=max_memory)
t1 = log.timer_debug1('3c2e', *t1)
nao = cell.nao_nr()
naux = auxcell.nao_nr()
gs = mydf.gs
Gv, Gvbase, kws = cell.get_Gv_weights(gs)
b = cell.reciprocal_vectors()
gxyz = lib.cartesian_prod([numpy.arange(len(x)) for x in Gvbase])
ngs = gxyz.shape[0]
kptis = kptij_lst[:, 0]
kptjs = kptij_lst[:, 1]
kpt_ji = kptjs - kptis
uniq_kpts, uniq_index, uniq_inverse = unique(kpt_ji)
log.debug('Num uniq kpts %d', len(uniq_kpts))
log.debug2('uniq_kpts %s', uniq_kpts)
# j2c ~ (-kpt_ji | kpt_ji)
j2c = fused_cell.pbc_intor('int2c2e_sph', hermi=1, kpts=uniq_kpts)
feri = h5py.File(cderi_file)
for k, kpt in enumerate(uniq_kpts):
aoaux = ft_ao.ft_ao(fused_cell, Gv, None, b, gxyz, Gvbase, kpt).T
aoaux = fuse(aoaux)
coulG = numpy.sqrt(mydf.weighted_coulG(kpt, False, gs))
kLR = (aoaux.real * coulG).T
kLI = (aoaux.imag * coulG).T
if not kLR.flags.c_contiguous: kLR = lib.transpose(kLR.T)
if not kLI.flags.c_contiguous: kLI = lib.transpose(kLI.T)
j2c_k = fuse(fuse(j2c[k]).T).T.copy()
if is_zero(kpt): # kpti == kptj
j2c_k -= lib.dot(kLR.T, kLR)
j2c_k -= lib.dot(kLI.T, kLI)
else:
# aoaux ~ kpt_ij, aoaux.conj() ~ kpt_kl
j2cR, j2cI = zdotCN(kLR.T, kLI.T, kLR, kLI)
j2c_k -= j2cR + j2cI * 1j
feri['j2c/%d' % k] = j2c_k
aoaux = kLR = kLI = j2cR = j2cI = coulG = None
j2c = None
def make_kpt(uniq_kptji_id): # kpt = kptj - kpti
kpt = uniq_kpts[uniq_kptji_id]
log.debug1('kpt = %s', kpt)
adapted_ji_idx = numpy.where(uniq_inverse == uniq_kptji_id)[0]
adapted_kptjs = kptjs[adapted_ji_idx]
nkptj = len(adapted_kptjs)
log.debug1('adapted_ji_idx = %s', adapted_ji_idx)
Gaux = ft_ao.ft_ao(fused_cell, Gv, None, b, gxyz, Gvbase, kpt).T
Gaux = fuse(Gaux)
Gaux *= mydf.weighted_coulG(kpt, False, gs)
kLR = Gaux.T.real.copy('C')
kLI = Gaux.T.imag.copy('C')
j2c = numpy.asarray(feri['j2c/%d' % uniq_kptji_id])
# Note large difference may be found in results between the CD/eig treatments.
# In some systems, small integral errors can lead to different treatments of
# linear dependency which can be observed in the total energy/orbital energy
# around 4th decimal place.
# try:
# j2c = scipy.linalg.cholesky(j2c, lower=True)
# j2ctag = 'CD'
# except scipy.linalg.LinAlgError as e:
#
# Abandon CD treatment for better numerical stablity
w, v = scipy.linalg.eigh(j2c)
log.debug('MDF metric for kpt %s cond = %.4g, drop %d bfns',
uniq_kptji_id, w[-1] / w[0],
numpy.count_nonzero(w < mydf.linear_dep_threshold))
v = v[:, w > mydf.linear_dep_threshold].T.conj()
v /= numpy.sqrt(w[w > mydf.linear_dep_threshold]).reshape(-1, 1)
j2c = v
j2ctag = 'eig'
naux0 = j2c.shape[0]
if is_zero(kpt): # kpti == kptj
aosym = 's2'
nao_pair = nao * (nao + 1) // 2
vbar = fuse(mydf.auxbar(fused_cell))
ovlp = cell.pbc_intor('int1e_ovlp_sph',
hermi=1,
kpts=adapted_kptjs)
for k, ji in enumerate(adapted_ji_idx):
ovlp[k] = lib.pack_tril(ovlp[k])
else:
aosym = 's1'
nao_pair = nao**2
mem_now = lib.current_memory()[0]
log.debug2('memory = %s', mem_now)
max_memory = max(2000, mydf.max_memory - mem_now)
# nkptj for 3c-coulomb arrays plus 1 Lpq array
buflen = min(
max(int(max_memory * .6 * 1e6 / 16 / naux / (nkptj + 1)), 1),
nao_pair)
shranges = _guess_shell_ranges(cell, buflen, aosym)
buflen = max([x[2] for x in shranges])
# +1 for a pqkbuf
if aosym == 's2':
Gblksize = max(
16, int(max_memory * .2 * 1e6 / 16 / buflen / (nkptj + 1)))
else:
Gblksize = max(
16, int(max_memory * .4 * 1e6 / 16 / buflen / (nkptj + 1)))
Gblksize = min(Gblksize, ngs, 16384)
pqkRbuf = numpy.empty(buflen * Gblksize)
pqkIbuf = numpy.empty(buflen * Gblksize)
# buf for ft_aopair
buf = numpy.empty((nkptj, buflen * Gblksize), dtype=numpy.complex128)
col1 = 0
for istep, sh_range in enumerate(shranges):
log.debug1('int3c2e [%d/%d], AO [%d:%d], ncol = %d', \
istep+1, len(shranges), *sh_range)
bstart, bend, ncol = sh_range
col0, col1 = col1, col1 + ncol
j3cR = []
j3cI = []
for k, idx in enumerate(adapted_ji_idx):
v = fuse(numpy.asarray(feri['j3c/%d' % idx][:, col0:col1]))
if is_zero(kpt):
for i, c in enumerate(vbar):
if c != 0:
v[i] -= c * ovlp[k][col0:col1]
j3cR.append(numpy.asarray(v.real, order='C'))
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
j3cI.append(None)
else:
j3cI.append(numpy.asarray(v.imag, order='C'))
v = None
if aosym == 's2':
shls_slice = (bstart, bend, 0, bend)
else:
shls_slice = (bstart, bend, 0, cell.nbas)
for p0, p1 in lib.prange(0, ngs, Gblksize):
dat = ft_ao._ft_aopair_kpts(cell,
Gv[p0:p1],
shls_slice,
aosym,
b,
gxyz[p0:p1],
Gvbase,
kpt,
adapted_kptjs,
out=buf)
nG = p1 - p0
for k, ji in enumerate(adapted_ji_idx):
aoao = dat[k].reshape(nG, ncol)
pqkR = numpy.ndarray((ncol, nG), buffer=pqkRbuf)
pqkI = numpy.ndarray((ncol, nG), buffer=pqkIbuf)
pqkR[:] = aoao.real.T
pqkI[:] = aoao.imag.T
lib.dot(kLR[p0:p1].T, pqkR.T, -1, j3cR[k], 1)
lib.dot(kLI[p0:p1].T, pqkI.T, -1, j3cR[k], 1)
if not (is_zero(kpt) and gamma_point(adapted_kptjs[k])):
lib.dot(kLR[p0:p1].T, pqkI.T, -1, j3cI[k], 1)
lib.dot(kLI[p0:p1].T, pqkR.T, 1, j3cI[k], 1)
for k, ji in enumerate(adapted_ji_idx):
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
v = j3cR[k]
else:
v = j3cR[k] + j3cI[k] * 1j
if j2ctag == 'CD':
v = scipy.linalg.solve_triangular(j2c,
v,
lower=True,
overwrite_b=True)
else:
v = lib.dot(j2c, v)
feri['j3c/%d' % ji][:naux0, col0:col1] = v
del (feri['j2c/%d' % uniq_kptji_id])
for k, ji in enumerate(adapted_ji_idx):
v = feri['j3c/%d' % ji][:naux0]
del (feri['j3c/%d' % ji])
feri['j3c/%d' % ji] = v
for k, kpt in enumerate(uniq_kpts):
make_kpt(k)
feri.close()
def _make_j3c(mydf, cell, auxcell, kptij_lst, cderi_file):
t1 = (time.clock(), time.time())
log = logger.Logger(mydf.stdout, mydf.verbose)
max_memory = max(2000, mydf.max_memory-lib.current_memory()[0])
fused_cell, fuse = fuse_auxcell(mydf, auxcell)
# The ideal way to hold the temporary integrals is to store them in the
# cderi_file and overwrite them inplace in the second pass. The current
# HDF5 library does not have an efficient way to manage free space in
# overwriting. It often leads to the cderi_file ~2 times larger than the
# necessary size. For now, dumping the DF integral intermediates to a
# separated temporary file can avoid this issue. The DF intermediates may
# be terribly huge. The temporary file should be placed in the same disk
# as cderi_file.
swapfile = tempfile.NamedTemporaryFile(dir=os.path.dirname(cderi_file))
fswap = lib.H5TmpFile(swapfile.name)
# Unlink swapfile to avoid trash
swapfile = None
outcore._aux_e2(cell, fused_cell, fswap, 'int3c2e', aosym='s2',
kptij_lst=kptij_lst, dataname='j3c-junk', max_memory=max_memory)
t1 = log.timer_debug1('3c2e', *t1)
nao = cell.nao_nr()
naux = auxcell.nao_nr()
mesh = mydf.mesh
Gv, Gvbase, kws = cell.get_Gv_weights(mesh)
b = cell.reciprocal_vectors()
gxyz = lib.cartesian_prod([numpy.arange(len(x)) for x in Gvbase])
ngrids = gxyz.shape[0]
kptis = kptij_lst[:,0]
kptjs = kptij_lst[:,1]
kpt_ji = kptjs - kptis
uniq_kpts, uniq_index, uniq_inverse = unique(kpt_ji)
log.debug('Num uniq kpts %d', len(uniq_kpts))
log.debug2('uniq_kpts %s', uniq_kpts)
# j2c ~ (-kpt_ji | kpt_ji)
j2c = fused_cell.pbc_intor('int2c2e', hermi=1, kpts=uniq_kpts)
# An alternative method to evalute j2c. This method might have larger numerical error?
# chgcell = make_modchg_basis(auxcell, mydf.eta)
# for k, kpt in enumerate(uniq_kpts):
# aoaux = ft_ao.ft_ao(chgcell, Gv, None, b, gxyz, Gvbase, kpt).T
# coulG = numpy.sqrt(mydf.weighted_coulG(kpt, False, mesh))
# LkR = aoaux.real * coulG
# LkI = aoaux.imag * coulG
# j2caux = numpy.zeros_like(j2c[k])
# j2caux[naux:,naux:] = j2c[k][naux:,naux:]
# if is_zero(kpt): # kpti == kptj
# j2caux[naux:,naux:] -= lib.ddot(LkR, LkR.T)
# j2caux[naux:,naux:] -= lib.ddot(LkI, LkI.T)
# j2c[k] = j2c[k][:naux,:naux] - fuse(fuse(j2caux.T).T)
# vbar = fuse(mydf.auxbar(fused_cell))
# s = (vbar != 0).astype(numpy.double)
# j2c[k] -= numpy.einsum('i,j->ij', vbar, s)
# j2c[k] -= numpy.einsum('i,j->ij', s, vbar)
# else:
# j2cR, j2cI = zdotCN(LkR, LkI, LkR.T, LkI.T)
# j2caux[naux:,naux:] -= j2cR + j2cI * 1j
# j2c[k] = j2c[k][:naux,:naux] - fuse(fuse(j2caux.T).T)
# fswap['j2c/%d'%k] = fuse(fuse(j2c[k]).T).T
# aoaux = LkR = LkI = coulG = None
if cell.dimension == 1 or cell.dimension == 2:
plain_ints = _gaussian_int(fused_cell)
max_memory = max(2000, mydf.max_memory - lib.current_memory()[0])
blksize = max(2048, int(max_memory*.5e6/16/fused_cell.nao_nr()))
log.debug2('max_memory %s (MB) blocksize %s', max_memory, blksize)
for k, kpt in enumerate(uniq_kpts):
coulG = numpy.sqrt(mydf.weighted_coulG(kpt, False, mesh))
for p0, p1 in lib.prange(0, ngrids, blksize):
aoaux = ft_ao.ft_ao(fused_cell, Gv[p0:p1], None, b, gxyz[p0:p1], Gvbase, kpt)
if (cell.dimension == 1 or cell.dimension == 2) and is_zero(kpt):
G0idx, SI_on_z = pbcgto.cell._SI_for_uniform_model_charge(cell, Gv[p0:p1])
aoaux[G0idx] -= numpy.einsum('g,i->gi', SI_on_z, plain_ints)
aoaux = aoaux.T
LkR = aoaux.real * coulG[p0:p1]
LkI = aoaux.imag * coulG[p0:p1]
aoaux = None
if is_zero(kpt): # kpti == kptj
j2c[k][naux:] -= lib.ddot(LkR[naux:], LkR.T)
j2c[k][naux:] -= lib.ddot(LkI[naux:], LkI.T)
j2c[k][:naux,naux:] = j2c[k][naux:,:naux].T
else:
j2cR, j2cI = zdotCN(LkR[naux:], LkI[naux:], LkR.T, LkI.T)
j2c[k][naux:] -= j2cR + j2cI * 1j
j2c[k][:naux,naux:] = j2c[k][naux:,:naux].T.conj()
LkR = LkI = None
fswap['j2c/%d'%k] = fuse(fuse(j2c[k]).T).T
j2c = coulG = None
feri = h5py.File(cderi_file, 'w')
feri['j3c-kptij'] = kptij_lst
nsegs = len(fswap['j3c-junk/0'])
def make_kpt(uniq_kptji_id): # kpt = kptj - kpti
kpt = uniq_kpts[uniq_kptji_id]
log.debug1('kpt = %s', kpt)
adapted_ji_idx = numpy.where(uniq_inverse == uniq_kptji_id)[0]
adapted_kptjs = kptjs[adapted_ji_idx]
nkptj = len(adapted_kptjs)
log.debug1('adapted_ji_idx = %s', adapted_ji_idx)
shls_slice = (auxcell.nbas, fused_cell.nbas)
Gaux = ft_ao.ft_ao(fused_cell, Gv, shls_slice, b, gxyz, Gvbase, kpt)
if (cell.dimension == 1 or cell.dimension == 2) and is_zero(kpt):
G0idx, SI_on_z = pbcgto.cell._SI_for_uniform_model_charge(cell, Gv)
s = plain_ints[-Gaux.shape[1]:] # Only compensated Gaussians
Gaux[G0idx] -= numpy.einsum('g,i->gi', SI_on_z, s)
wcoulG = mydf.weighted_coulG(kpt, False, mesh)
Gaux *= wcoulG.reshape(-1,1)
kLR = Gaux.real.copy('C')
kLI = Gaux.imag.copy('C')
Gaux = None
j2c = numpy.asarray(fswap['j2c/%d'%uniq_kptji_id])
try:
j2c = scipy.linalg.cholesky(j2c, lower=True)
j2ctag = 'CD'
except scipy.linalg.LinAlgError as e:
#msg =('===================================\n'
# 'J-metric not positive definite.\n'
# 'It is likely that mesh is not enough.\n'
# '===================================')
#log.error(msg)
#raise scipy.linalg.LinAlgError('\n'.join([e.message, msg]))
w, v = scipy.linalg.eigh(j2c)
log.debug('DF metric linear dependency for kpt %s', uniq_kptji_id)
log.debug('cond = %.4g, drop %d bfns',
w[-1]/w[0], numpy.count_nonzero(w<mydf.linear_dep_threshold))
v = v[:,w>mydf.linear_dep_threshold].T.conj()
v /= numpy.sqrt(w[w>mydf.linear_dep_threshold]).reshape(-1,1)
j2c = v
j2ctag = 'eig'
naux0 = j2c.shape[0]
if is_zero(kpt): # kpti == kptj
aosym = 's2'
nao_pair = nao*(nao+1)//2
vbar = mydf.auxbar(fused_cell)
ovlp = cell.pbc_intor('int1e_ovlp', hermi=1, kpts=adapted_kptjs)
ovlp = [lib.pack_tril(s) for s in ovlp]
else:
aosym = 's1'
nao_pair = nao**2
mem_now = lib.current_memory()[0]
log.debug2('memory = %s', mem_now)
max_memory = max(2000, mydf.max_memory-mem_now)
# nkptj for 3c-coulomb arrays plus 1 Lpq array
buflen = min(max(int(max_memory*.38e6/16/naux/(nkptj+1)), 1), nao_pair)
shranges = _guess_shell_ranges(cell, buflen, aosym)
buflen = max([x[2] for x in shranges])
# +1 for a pqkbuf
if aosym == 's2':
Gblksize = max(16, int(max_memory*.1e6/16/buflen/(nkptj+1)))
else:
Gblksize = max(16, int(max_memory*.2e6/16/buflen/(nkptj+1)))
Gblksize = min(Gblksize, ngrids, 16384)
pqkRbuf = numpy.empty(buflen*Gblksize)
pqkIbuf = numpy.empty(buflen*Gblksize)
# buf for ft_aopair
buf = numpy.empty(nkptj*buflen*Gblksize, dtype=numpy.complex128)
def pw_contract(istep, sh_range, j3cR, j3cI):
bstart, bend, ncol = sh_range
if aosym == 's2':
shls_slice = (bstart, bend, 0, bend)
else:
shls_slice = (bstart, bend, 0, cell.nbas)
for p0, p1 in lib.prange(0, ngrids, Gblksize):
dat = ft_ao._ft_aopair_kpts(cell, Gv[p0:p1], shls_slice, aosym,
b, gxyz[p0:p1], Gvbase, kpt,
adapted_kptjs, out=buf)
if (cell.dimension == 1 or cell.dimension == 2) and is_zero(kpt):
G0idx, SI_on_z = pbcgto.cell._SI_for_uniform_model_charge(cell, Gv[p0:p1])
if SI_on_z.size > 0:
for k, aoao in enumerate(dat):
aoao[G0idx] -= numpy.einsum('g,i->gi', SI_on_z, ovlp[k])
aux = fuse(ft_ao.ft_ao(fused_cell, Gv[p0:p1][G0idx]).T)
vG_mod = numpy.einsum('ig,g,g->i', aux.conj(),
wcoulG[p0:p1][G0idx], SI_on_z)
if gamma_point(adapted_kptjs[k]):
j3cR[k][:naux] -= vG_mod[:,None].real * ovlp[k]
else:
tmp = vG_mod[:,None] * ovlp[k]
j3cR[k][:naux] -= tmp.real
j3cI[k][:naux] -= tmp.imag
tmp = aux = vG_mod
nG = p1 - p0
for k, ji in enumerate(adapted_ji_idx):
aoao = dat[k].reshape(nG,ncol)
pqkR = numpy.ndarray((ncol,nG), buffer=pqkRbuf)
pqkI = numpy.ndarray((ncol,nG), buffer=pqkIbuf)
pqkR[:] = aoao.real.T
pqkI[:] = aoao.imag.T
lib.dot(kLR[p0:p1].T, pqkR.T, -1, j3cR[k][naux:], 1)
lib.dot(kLI[p0:p1].T, pqkI.T, -1, j3cR[k][naux:], 1)
if not (is_zero(kpt) and gamma_point(adapted_kptjs[k])):
lib.dot(kLR[p0:p1].T, pqkI.T, -1, j3cI[k][naux:], 1)
lib.dot(kLI[p0:p1].T, pqkR.T, 1, j3cI[k][naux:], 1)
for k, ji in enumerate(adapted_ji_idx):
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
v = fuse(j3cR[k])
else:
v = fuse(j3cR[k] + j3cI[k] * 1j)
if j2ctag == 'CD':
v = scipy.linalg.solve_triangular(j2c, v, lower=True, overwrite_b=True)
else:
v = lib.dot(j2c, v)
feri['j3c/%d/%d'%(ji,istep)] = v
with lib.call_in_background(pw_contract) as compute:
col1 = 0
for istep, sh_range in enumerate(shranges):
log.debug1('int3c2e [%d/%d], AO [%d:%d], ncol = %d', \
istep+1, len(shranges), *sh_range)
bstart, bend, ncol = sh_range
col0, col1 = col1, col1+ncol
j3cR = []
j3cI = []
for k, idx in enumerate(adapted_ji_idx):
v = numpy.vstack([fswap['j3c-junk/%d/%d'%(idx,i)][0,col0:col1].T
for i in range(nsegs)])
if is_zero(kpt) and cell.dimension == 3:
for i in numpy.where(vbar != 0)[0]:
v[i] -= vbar[i] * ovlp[k][col0:col1]
j3cR.append(numpy.asarray(v.real, order='C'))
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
j3cI.append(None)
else:
j3cI.append(numpy.asarray(v.imag, order='C'))
v = None
compute(istep, sh_range, j3cR, j3cI)
for ji in adapted_ji_idx:
del(fswap['j3c-junk/%d'%ji])
for k, kpt in enumerate(uniq_kpts):
make_kpt(k)
feri.close()
def _gaussian_int(cell):
r'''Regular gaussian integral \int g(r) dr^3'''
return ft_ao.ft_ao(cell, numpy.zeros((1, 3)))[0].real
def make_kpt(uniq_kptji_id): # kpt = kptj - kpti
kpt = uniq_kpts[uniq_kptji_id]
log.debug1('kpt = %s', kpt)
adapted_ji_idx = numpy.where(uniq_inverse == uniq_kptji_id)[0]
adapted_kptjs = kptjs[adapted_ji_idx]
nkptj = len(adapted_kptjs)
log.debug1('adapted_ji_idx = %s', adapted_ji_idx)
shls_slice = (auxcell.nbas, fused_cell.nbas)
Gaux = ft_ao.ft_ao(fused_cell, Gv, shls_slice, b, gxyz, Gvbase, kpt)
if (cell.dimension == 1 or cell.dimension == 2) and is_zero(kpt):
G0idx, SI_on_z = pbcgto.cell._SI_for_uniform_model_charge(cell, Gv)
s = plain_ints[-Gaux.shape[1]:] # Only compensated Gaussians
Gaux[G0idx] -= numpy.einsum('g,i->gi', SI_on_z, s)
wcoulG = mydf.weighted_coulG(kpt, False, mesh)
Gaux *= wcoulG.reshape(-1,1)
kLR = Gaux.real.copy('C')
kLI = Gaux.imag.copy('C')
Gaux = None
j2c = numpy.asarray(fswap['j2c/%d'%uniq_kptji_id])
try:
j2c = scipy.linalg.cholesky(j2c, lower=True)
j2ctag = 'CD'
except scipy.linalg.LinAlgError as e:
#msg =('===================================\n'
# 'J-metric not positive definite.\n'
# 'It is likely that mesh is not enough.\n'
# '===================================')
#log.error(msg)
#raise scipy.linalg.LinAlgError('\n'.join([e.message, msg]))
w, v = scipy.linalg.eigh(j2c)
log.debug('DF metric linear dependency for kpt %s', uniq_kptji_id)
log.debug('cond = %.4g, drop %d bfns',
w[-1]/w[0], numpy.count_nonzero(w<mydf.linear_dep_threshold))
v = v[:,w>mydf.linear_dep_threshold].T.conj()
v /= numpy.sqrt(w[w>mydf.linear_dep_threshold]).reshape(-1,1)
j2c = v
j2ctag = 'eig'
naux0 = j2c.shape[0]
if is_zero(kpt): # kpti == kptj
aosym = 's2'
nao_pair = nao*(nao+1)//2
vbar = mydf.auxbar(fused_cell)
ovlp = cell.pbc_intor('int1e_ovlp', hermi=1, kpts=adapted_kptjs)
ovlp = [lib.pack_tril(s) for s in ovlp]
else:
aosym = 's1'
nao_pair = nao**2
mem_now = lib.current_memory()[0]
log.debug2('memory = %s', mem_now)
max_memory = max(2000, mydf.max_memory-mem_now)
# nkptj for 3c-coulomb arrays plus 1 Lpq array
buflen = min(max(int(max_memory*.38e6/16/naux/(nkptj+1)), 1), nao_pair)
shranges = _guess_shell_ranges(cell, buflen, aosym)
buflen = max([x[2] for x in shranges])
# +1 for a pqkbuf
if aosym == 's2':
Gblksize = max(16, int(max_memory*.1e6/16/buflen/(nkptj+1)))
else:
Gblksize = max(16, int(max_memory*.2e6/16/buflen/(nkptj+1)))
Gblksize = min(Gblksize, ngrids, 16384)
pqkRbuf = numpy.empty(buflen*Gblksize)
pqkIbuf = numpy.empty(buflen*Gblksize)
# buf for ft_aopair
buf = numpy.empty(nkptj*buflen*Gblksize, dtype=numpy.complex128)
def pw_contract(istep, sh_range, j3cR, j3cI):
bstart, bend, ncol = sh_range
if aosym == 's2':
shls_slice = (bstart, bend, 0, bend)
else:
shls_slice = (bstart, bend, 0, cell.nbas)
for p0, p1 in lib.prange(0, ngrids, Gblksize):
dat = ft_ao._ft_aopair_kpts(cell, Gv[p0:p1], shls_slice, aosym,
b, gxyz[p0:p1], Gvbase, kpt,
adapted_kptjs, out=buf)
if (cell.dimension == 1 or cell.dimension == 2) and is_zero(kpt):
G0idx, SI_on_z = pbcgto.cell._SI_for_uniform_model_charge(cell, Gv[p0:p1])
if SI_on_z.size > 0:
for k, aoao in enumerate(dat):
aoao[G0idx] -= numpy.einsum('g,i->gi', SI_on_z, ovlp[k])
aux = fuse(ft_ao.ft_ao(fused_cell, Gv[p0:p1][G0idx]).T)
vG_mod = numpy.einsum('ig,g,g->i', aux.conj(),
wcoulG[p0:p1][G0idx], SI_on_z)
if gamma_point(adapted_kptjs[k]):
j3cR[k][:naux] -= vG_mod[:,None].real * ovlp[k]
else:
tmp = vG_mod[:,None] * ovlp[k]
j3cR[k][:naux] -= tmp.real
j3cI[k][:naux] -= tmp.imag
tmp = aux = vG_mod
nG = p1 - p0
for k, ji in enumerate(adapted_ji_idx):
aoao = dat[k].reshape(nG,ncol)
pqkR = numpy.ndarray((ncol,nG), buffer=pqkRbuf)
pqkI = numpy.ndarray((ncol,nG), buffer=pqkIbuf)
pqkR[:] = aoao.real.T
pqkI[:] = aoao.imag.T
lib.dot(kLR[p0:p1].T, pqkR.T, -1, j3cR[k][naux:], 1)
lib.dot(kLI[p0:p1].T, pqkI.T, -1, j3cR[k][naux:], 1)
if not (is_zero(kpt) and gamma_point(adapted_kptjs[k])):
lib.dot(kLR[p0:p1].T, pqkI.T, -1, j3cI[k][naux:], 1)
lib.dot(kLI[p0:p1].T, pqkR.T, 1, j3cI[k][naux:], 1)
for k, ji in enumerate(adapted_ji_idx):
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
v = fuse(j3cR[k])
else:
v = fuse(j3cR[k] + j3cI[k] * 1j)
if j2ctag == 'CD':
v = scipy.linalg.solve_triangular(j2c, v, lower=True, overwrite_b=True)
else:
v = lib.dot(j2c, v)
feri['j3c/%d/%d'%(ji,istep)] = v
with lib.call_in_background(pw_contract) as compute:
col1 = 0
for istep, sh_range in enumerate(shranges):
log.debug1('int3c2e [%d/%d], AO [%d:%d], ncol = %d', \
istep+1, len(shranges), *sh_range)
bstart, bend, ncol = sh_range
col0, col1 = col1, col1+ncol
j3cR = []
j3cI = []
for k, idx in enumerate(adapted_ji_idx):
v = numpy.vstack([fswap['j3c-junk/%d/%d'%(idx,i)][0,col0:col1].T
for i in range(nsegs)])
if is_zero(kpt) and cell.dimension == 3:
for i in numpy.where(vbar != 0)[0]:
v[i] -= vbar[i] * ovlp[k][col0:col1]
j3cR.append(numpy.asarray(v.real, order='C'))
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
j3cI.append(None)
else:
j3cI.append(numpy.asarray(v.imag, order='C'))
v = None
compute(istep, sh_range, j3cR, j3cI)
for ji in adapted_ji_idx:
del(fswap['j3c-junk/%d'%ji])
def make_kpt(uniq_kptji_id, cholesky_j2c):
kpt = uniq_kpts[uniq_kptji_id] # kpt = kptj - kpti
log.debug1('kpt = %s', kpt)
adapted_ji_idx = numpy.where(uniq_inverse == uniq_kptji_id)[0]
adapted_kptjs = kptjs[adapted_ji_idx]
nkptj = len(adapted_kptjs)
log.debug1('adapted_ji_idx = %s', adapted_ji_idx)
j2c, j2c_negative, j2ctag = cholesky_j2c
shls_slice = (auxcell.nbas, fused_cell.nbas)
Gaux = ft_ao.ft_ao(fused_cell, Gv, shls_slice, b, gxyz, Gvbase, kpt)
wcoulG = mydf.weighted_coulG(kpt, False, mesh)
Gaux *= wcoulG.reshape(-1, 1)
kLR = Gaux.real.copy('C')
kLI = Gaux.imag.copy('C')
Gaux = None
if is_zero(kpt): # kpti == kptj
aosym = 's2'
nao_pair = nao * (nao + 1) // 2
if cell.dimension == 3:
vbar = fuse(mydf.auxbar(fused_cell))
ovlp = cell.pbc_intor('int1e_ovlp',
hermi=1,
kpts=adapted_kptjs)
ovlp = [lib.pack_tril(s) for s in ovlp]
else:
aosym = 's1'
nao_pair = nao**2
mem_now = lib.current_memory()[0]
log.debug2('memory = %s', mem_now)
max_memory = max(2000, mydf.max_memory - mem_now)
# nkptj for 3c-coulomb arrays plus 1 Lpq array
buflen = min(max(int(max_memory * .38e6 / 16 / naux / (nkptj + 1)), 1),
nao_pair)
shranges = _guess_shell_ranges(cell, buflen, aosym)
buflen = max([x[2] for x in shranges])
# +1 for a pqkbuf
if aosym == 's2':
Gblksize = max(16,
int(max_memory * .1e6 / 16 / buflen / (nkptj + 1)))
else:
Gblksize = max(16,
int(max_memory * .2e6 / 16 / buflen / (nkptj + 1)))
Gblksize = min(Gblksize, ngrids, 16384)
def load(aux_slice):
col0, col1 = aux_slice
j3cR = []
j3cI = []
for k, idx in enumerate(adapted_ji_idx):
v = numpy.vstack([
fswap['j3c-junk/%d/%d' % (idx, i)][0, col0:col1].T
for i in range(nsegs)
])
# vbar is the interaction between the background charge
# and the auxiliary basis. 0D, 1D, 2D do not have vbar.
if is_zero(kpt) and cell.dimension == 3:
for i in numpy.where(vbar != 0)[0]:
v[i] -= vbar[i] * ovlp[k][col0:col1]
j3cR.append(numpy.asarray(v.real, order='C'))
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
j3cI.append(None)
else:
j3cI.append(numpy.asarray(v.imag, order='C'))
v = None
return j3cR, j3cI
pqkRbuf = numpy.empty(buflen * Gblksize)
pqkIbuf = numpy.empty(buflen * Gblksize)
# buf for ft_aopair
buf = numpy.empty(nkptj * buflen * Gblksize, dtype=numpy.complex128)
cols = [sh_range[2] for sh_range in shranges]
locs = numpy.append(0, numpy.cumsum(cols))
tasks = zip(locs[:-1], locs[1:])
for istep, (j3cR,
j3cI) in enumerate(lib.map_with_prefetch(load, tasks)):
bstart, bend, ncol = shranges[istep]
log.debug1('int3c2e [%d/%d], AO [%d:%d], ncol = %d', istep + 1,
len(shranges), bstart, bend, ncol)
if aosym == 's2':
shls_slice = (bstart, bend, 0, bend)
else:
shls_slice = (bstart, bend, 0, cell.nbas)
for p0, p1 in lib.prange(0, ngrids, Gblksize):
dat = ft_ao._ft_aopair_kpts(cell,
Gv[p0:p1],
shls_slice,
aosym,
b,
gxyz[p0:p1],
Gvbase,
kpt,
adapted_kptjs,
out=buf)
nG = p1 - p0
for k, ji in enumerate(adapted_ji_idx):
aoao = dat[k].reshape(nG, ncol)
pqkR = numpy.ndarray((ncol, nG), buffer=pqkRbuf)
pqkI = numpy.ndarray((ncol, nG), buffer=pqkIbuf)
pqkR[:] = aoao.real.T
pqkI[:] = aoao.imag.T
lib.dot(kLR[p0:p1].T, pqkR.T, -1, j3cR[k][naux:], 1)
lib.dot(kLI[p0:p1].T, pqkI.T, -1, j3cR[k][naux:], 1)
if not (is_zero(kpt) and gamma_point(adapted_kptjs[k])):
lib.dot(kLR[p0:p1].T, pqkI.T, -1, j3cI[k][naux:], 1)
lib.dot(kLI[p0:p1].T, pqkR.T, 1, j3cI[k][naux:], 1)
for k, ji in enumerate(adapted_ji_idx):
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
v = fuse(j3cR[k])
else:
v = fuse(j3cR[k] + j3cI[k] * 1j)
if j2ctag == 'CD':
v = scipy.linalg.solve_triangular(j2c,
v,
lower=True,
overwrite_b=True)
feri['j3c/%d/%d' % (ji, istep)] = v
else:
feri['j3c/%d/%d' % (ji, istep)] = lib.dot(j2c, v)
# low-dimension systems
if j2c_negative is not None:
feri['j3c-/%d/%d' % (ji, istep)] = lib.dot(j2c_negative, v)
j3cR = j3cI = None
for ji in adapted_ji_idx:
del (fswap['j3c-junk/%d' % ji])
def make_kpt(uniq_kptji_id): # kpt = kptj - kpti
kpt = uniq_kpts[uniq_kptji_id]
log.debug1('kpt = %s', kpt)
adapted_ji_idx = numpy.where(uniq_inverse == uniq_kptji_id)[0]
adapted_kptjs = kptjs[adapted_ji_idx]
nkptj = len(adapted_kptjs)
log.debug1('adapted_ji_idx = %s', adapted_ji_idx)
shls_slice = (auxcell.nbas, fused_cell.nbas)
Gaux = ft_ao.ft_ao(fused_cell, Gv, shls_slice, b, gxyz, Gvbase, kpt)
Gaux *= mydf.weighted_coulG(kpt, False, gs).reshape(-1, 1)
kLR = Gaux.real.copy('C')
kLI = Gaux.imag.copy('C')
j2c = numpy.asarray(feri['j2c/%d' % uniq_kptji_id])
try:
j2c = scipy.linalg.cholesky(j2c, lower=True)
j2ctag = 'CD'
except scipy.linalg.LinAlgError as e:
#msg =('===================================\n'
# 'J-metric not positive definite.\n'
# 'It is likely that gs is not enough.\n'
# '===================================')
#log.error(msg)
#raise scipy.linalg.LinAlgError('\n'.join([e.message, msg]))
w, v = scipy.linalg.eigh(j2c)
log.debug('DF metric linear dependency for kpt %s', uniq_kptji_id)
log.debug('cond = %.4g, drop %d bfns', w[-1] / w[0],
numpy.count_nonzero(w < mydf.linear_dep_threshold))
v = v[:, w > mydf.linear_dep_threshold].T.conj()
v /= numpy.sqrt(w[w > mydf.linear_dep_threshold]).reshape(-1, 1)
j2c = v
j2ctag = 'eig'
naux0 = j2c.shape[0]
if is_zero(kpt): # kpti == kptj
aosym = 's2'
nao_pair = nao * (nao + 1) // 2
vbar = fuse(mydf.auxbar(fused_cell))
ovlp = cell.pbc_intor('int1e_ovlp_sph',
hermi=1,
kpts=adapted_kptjs)
for k, ji in enumerate(adapted_ji_idx):
ovlp[k] = lib.pack_tril(ovlp[k])
else:
aosym = 's1'
nao_pair = nao**2
mem_now = lib.current_memory()[0]
log.debug2('memory = %s', mem_now)
max_memory = max(2000, mydf.max_memory - mem_now)
# nkptj for 3c-coulomb arrays plus 1 Lpq array
buflen = min(
max(int(max_memory * .6 * 1e6 / 16 / naux / (nkptj + 1)), 1),
nao_pair)
shranges = _guess_shell_ranges(cell, buflen, aosym)
buflen = max([x[2] for x in shranges])
# +1 for a pqkbuf
if aosym == 's2':
Gblksize = max(
16, int(max_memory * .2 * 1e6 / 16 / buflen / (nkptj + 1)))
else:
Gblksize = max(
16, int(max_memory * .4 * 1e6 / 16 / buflen / (nkptj + 1)))
Gblksize = min(Gblksize, ngs, 16384)
pqkRbuf = numpy.empty(buflen * Gblksize)
pqkIbuf = numpy.empty(buflen * Gblksize)
# buf for ft_aopair
buf = numpy.empty(nkptj * buflen * Gblksize, dtype=numpy.complex128)
col1 = 0
for istep, sh_range in enumerate(shranges):
log.debug1('int3c2e [%d/%d], AO [%d:%d], ncol = %d', \
istep+1, len(shranges), *sh_range)
bstart, bend, ncol = sh_range
col0, col1 = col1, col1 + ncol
j3cR = []
j3cI = []
for k, idx in enumerate(adapted_ji_idx):
v = numpy.asarray(feri['j3c/%d' % idx][:, col0:col1])
if is_zero(kpt):
for i, c in enumerate(vbar):
if c != 0:
v[i] -= c * ovlp[k][col0:col1]
j3cR.append(numpy.asarray(v.real, order='C'))
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
j3cI.append(None)
else:
j3cI.append(numpy.asarray(v.imag, order='C'))
v = None
if aosym == 's2':
shls_slice = (bstart, bend, 0, bend)
else:
shls_slice = (bstart, bend, 0, cell.nbas)
for p0, p1 in lib.prange(0, ngs, Gblksize):
dat = ft_ao._ft_aopair_kpts(cell,
Gv[p0:p1],
shls_slice,
aosym,
b,
gxyz[p0:p1],
Gvbase,
kpt,
adapted_kptjs,
out=buf)
nG = p1 - p0
for k, ji in enumerate(adapted_ji_idx):
aoao = dat[k].reshape(nG, ncol)
pqkR = numpy.ndarray((ncol, nG), buffer=pqkRbuf)
pqkI = numpy.ndarray((ncol, nG), buffer=pqkIbuf)
pqkR[:] = aoao.real.T
pqkI[:] = aoao.imag.T
lib.dot(kLR[p0:p1].T, pqkR.T, -1, j3cR[k][naux:], 1)
lib.dot(kLI[p0:p1].T, pqkI.T, -1, j3cR[k][naux:], 1)
if not (is_zero(kpt) and gamma_point(adapted_kptjs[k])):
lib.dot(kLR[p0:p1].T, pqkI.T, -1, j3cI[k][naux:], 1)
lib.dot(kLI[p0:p1].T, pqkR.T, 1, j3cI[k][naux:], 1)
for k, ji in enumerate(adapted_ji_idx):
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
v = fuse(j3cR[k])
else:
v = fuse(j3cR[k] + j3cI[k] * 1j)
if j2ctag == 'CD':
v = scipy.linalg.solve_triangular(j2c,
v,
lower=True,
overwrite_b=True)
else:
v = lib.dot(j2c, v)
feri['j3c/%d' % ji][:naux0, col0:col1] = v
del (feri['j2c/%d' % uniq_kptji_id])
for k, ji in enumerate(adapted_ji_idx):
v = feri['j3c/%d' % ji][:naux0]
del (feri['j3c/%d' % ji])
feri['j3c/%d' % ji] = v
def _make_j3c(mydf, cell, auxcell, kptij_lst, cderi_file):
log = logger.Logger(mydf.stdout, mydf.verbose)
t1 = t0 = (time.clock(), time.time())
fused_cell, fuse = fuse_auxcell(mydf, mydf.auxcell)
ao_loc = cell.ao_loc_nr()
nao = ao_loc[-1]
naux = auxcell.nao_nr()
nkptij = len(kptij_lst)
mesh = mydf.mesh
Gv, Gvbase, kws = cell.get_Gv_weights(mesh)
b = cell.reciprocal_vectors()
gxyz = lib.cartesian_prod([numpy.arange(len(x)) for x in Gvbase])
ngrids = gxyz.shape[0]
kptis = kptij_lst[:, 0]
kptjs = kptij_lst[:, 1]
kpt_ji = kptjs - kptis
uniq_kpts, uniq_index, uniq_inverse = unique(kpt_ji)
log.debug('Num uniq kpts %d', len(uniq_kpts))
log.debug2('uniq_kpts %s', uniq_kpts)
# j2c ~ (-kpt_ji | kpt_ji)
j2c = fused_cell.pbc_intor('int2c2e', hermi=1, kpts=uniq_kpts)
j2ctags = []
t1 = log.timer_debug1('2c2e', *t1)
swapfile = tempfile.NamedTemporaryFile(dir=os.path.dirname(cderi_file))
fswap = lib.H5TmpFile(swapfile.name)
# Unlink swapfile to avoid trash
swapfile = None
mem_now = max(comm.allgather(lib.current_memory()[0]))
max_memory = max(2000, mydf.max_memory - mem_now)
blksize = max(2048, int(max_memory * .5e6 / 16 / fused_cell.nao_nr()))
log.debug2('max_memory %s (MB) blocksize %s', max_memory, blksize)
for k, kpt in enumerate(uniq_kpts):
coulG = mydf.weighted_coulG(kpt, False, mesh)
j2c_k = numpy.zeros_like(j2c[k])
for p0, p1 in mydf.prange(0, ngrids, blksize):
aoaux = ft_ao.ft_ao(fused_cell, Gv[p0:p1], None, b, gxyz[p0:p1],
Gvbase, kpt).T
LkR = numpy.asarray(aoaux.real, order='C')
LkI = numpy.asarray(aoaux.imag, order='C')
aoaux = None
if is_zero(kpt): # kpti == kptj
j2c_k[naux:] += lib.ddot(LkR[naux:] * coulG[p0:p1], LkR.T)
j2c_k[naux:] += lib.ddot(LkI[naux:] * coulG[p0:p1], LkI.T)
else:
j2cR, j2cI = zdotCN(LkR[naux:] * coulG[p0:p1],
LkI[naux:] * coulG[p0:p1], LkR.T, LkI.T)
j2c_k[naux:] += j2cR + j2cI * 1j
kLR = kLI = None
j2c_k[:naux, naux:] = j2c_k[naux:, :naux].conj().T
j2c[k] -= mpi.allreduce(j2c_k)
j2c[k] = fuse(fuse(j2c[k]).T).T
try:
fswap['j2c/%d' % k] = scipy.linalg.cholesky(j2c[k], lower=True)
j2ctags.append('CD')
except scipy.linalg.LinAlgError as e:
#msg =('===================================\n'
# 'J-metric not positive definite.\n'
# 'It is likely that mesh is not enough.\n'
# '===================================')
#log.error(msg)
#raise scipy.linalg.LinAlgError('\n'.join([str(e), msg]))
w, v = scipy.linalg.eigh(j2c[k])
log.debug2('metric linear dependency for kpt %s', k)
log.debug2('cond = %.4g, drop %d bfns', w[0] / w[-1],
numpy.count_nonzero(w < mydf.linear_dep_threshold))
v1 = v[:, w > mydf.linear_dep_threshold].T.conj()
v1 /= numpy.sqrt(w[w > mydf.linear_dep_threshold]).reshape(-1, 1)
fswap['j2c/%d' % k] = v1
if cell.dimension == 2 and cell.low_dim_ft_type != 'inf_vacuum':
idx = numpy.where(w < -mydf.linear_dep_threshold)[0]
if len(idx) > 0:
fswap['j2c-/%d' % k] = (v[:, idx] /
numpy.sqrt(-w[idx])).conj().T
w = v = v1 = None
j2ctags.append('eig')
j2c = coulG = None
aosym_s2 = numpy.einsum('ix->i', abs(kptis - kptjs)) < 1e-9
j_only = numpy.all(aosym_s2)
if gamma_point(kptij_lst):
dtype = 'f8'
else:
dtype = 'c16'
t1 = log.timer_debug1('aoaux and int2c', *t1)
# Estimates the buffer size based on the last contraction in G-space.
# This contraction requires to hold nkptj copies of (naux,?) array
# simultaneously in memory.
mem_now = max(comm.allgather(lib.current_memory()[0]))
max_memory = max(2000, mydf.max_memory - mem_now)
nkptj_max = max((uniq_inverse == x).sum() for x in set(uniq_inverse))
buflen = max(
int(
min(max_memory * .5e6 / 16 / naux / (nkptj_max + 2) / nao,
nao / 3 / mpi.pool.size)), 1)
chunks = (buflen, nao)
j3c_jobs = grids2d_int3c_jobs(cell, auxcell, kptij_lst, chunks, j_only)
log.debug1('max_memory = %d MB (%d in use) chunks %s', max_memory,
mem_now, chunks)
log.debug2('j3c_jobs %s', j3c_jobs)
if j_only:
int3c = wrap_int3c(cell, fused_cell, 'int3c2e', 's2', 1, kptij_lst)
else:
int3c = wrap_int3c(cell, fused_cell, 'int3c2e', 's1', 1, kptij_lst)
idxb = numpy.tril_indices(nao)
idxb = (idxb[0] * nao + idxb[1]).astype('i')
aux_loc = fused_cell.ao_loc_nr('ssc' in 'int3c2e')
def gen_int3c(job_id, ish0, ish1):
dataname = 'j3c-chunks/%d' % job_id
i0 = ao_loc[ish0]
i1 = ao_loc[ish1]
dii = i1 * (i1 + 1) // 2 - i0 * (i0 + 1) // 2
if j_only:
dij = dii
buflen = max(8, int(max_memory * 1e6 / 16 / (nkptij * dii + dii)))
else:
dij = (i1 - i0) * nao
buflen = max(8, int(max_memory * 1e6 / 16 / (nkptij * dij + dij)))
auxranges = balance_segs(aux_loc[1:] - aux_loc[:-1], buflen)
buflen = max([x[2] for x in auxranges])
buf = numpy.empty(nkptij * dij * buflen, dtype=dtype)
buf1 = numpy.empty(dij * buflen, dtype=dtype)
naux = aux_loc[-1]
for kpt_id, kptij in enumerate(kptij_lst):
key = '%s/%d' % (dataname, kpt_id)
if aosym_s2[kpt_id]:
shape = (naux, dii)
else:
shape = (naux, dij)
if gamma_point(kptij):
fswap.create_dataset(key, shape, 'f8')
else:
fswap.create_dataset(key, shape, 'c16')
naux0 = 0
for istep, auxrange in enumerate(auxranges):
log.alldebug2("aux_e1 job_id %d step %d", job_id, istep)
sh0, sh1, nrow = auxrange
sub_slice = (ish0, ish1, 0, cell.nbas, sh0, sh1)
mat = numpy.ndarray((nkptij, dij, nrow), dtype=dtype, buffer=buf)
mat = int3c(sub_slice, mat)
for k, kptij in enumerate(kptij_lst):
h5dat = fswap['%s/%d' % (dataname, k)]
v = lib.transpose(mat[k], out=buf1)
if not j_only and aosym_s2[k]:
idy = idxb[i0 * (i0 + 1) // 2:i1 *
(i1 + 1) // 2] - i0 * nao
out = numpy.ndarray((nrow, dii),
dtype=v.dtype,
buffer=mat[k])
v = numpy.take(v, idy, axis=1, out=out)
if gamma_point(kptij):
h5dat[naux0:naux0 + nrow] = v.real
else:
h5dat[naux0:naux0 + nrow] = v
naux0 += nrow
def ft_fuse(job_id, uniq_kptji_id, sh0, sh1):
kpt = uniq_kpts[uniq_kptji_id] # kpt = kptj - kpti
adapted_ji_idx = numpy.where(uniq_inverse == uniq_kptji_id)[0]
adapted_kptjs = kptjs[adapted_ji_idx]
nkptj = len(adapted_kptjs)
j2c = numpy.asarray(fswap['j2c/%d' % uniq_kptji_id])
j2ctag = j2ctags[uniq_kptji_id]
naux0 = j2c.shape[0]
if ('j2c-/%d' % uniq_kptji_id) in fswap:
j2c_negative = numpy.asarray(fswap['j2c-/%d' % uniq_kptji_id])
else:
j2c_negative = None
if is_zero(kpt):
aosym = 's2'
else:
aosym = 's1'
if aosym == 's2' and cell.dimension == 3:
vbar = fuse(mydf.auxbar(fused_cell))
ovlp = cell.pbc_intor('int1e_ovlp', hermi=1, kpts=adapted_kptjs)
ovlp = [lib.pack_tril(s) for s in ovlp]
j3cR = [None] * nkptj
j3cI = [None] * nkptj
i0 = ao_loc[sh0]
i1 = ao_loc[sh1]
for k, idx in enumerate(adapted_ji_idx):
key = 'j3c-chunks/%d/%d' % (job_id, idx)
v = numpy.asarray(fswap[key])
if aosym == 's2' and cell.dimension == 3:
for i in numpy.where(vbar != 0)[0]:
v[i] -= vbar[i] * ovlp[k][i0 * (i0 + 1) // 2:i1 *
(i1 + 1) // 2].ravel()
j3cR[k] = numpy.asarray(v.real, order='C')
if v.dtype == numpy.complex128:
j3cI[k] = numpy.asarray(v.imag, order='C')
v = None
ncol = j3cR[0].shape[1]
Gblksize = max(16, int(max_memory * 1e6 / 16 / ncol /
(nkptj + 1))) # +1 for pqkRbuf/pqkIbuf
Gblksize = min(Gblksize, ngrids, 16384)
pqkRbuf = numpy.empty(ncol * Gblksize)
pqkIbuf = numpy.empty(ncol * Gblksize)
buf = numpy.empty(nkptj * ncol * Gblksize, dtype=numpy.complex128)
log.alldebug2('job_id %d blksize (%d,%d)', job_id, Gblksize, ncol)
wcoulG = mydf.weighted_coulG(kpt, False, mesh)
fused_cell_slice = (auxcell.nbas, fused_cell.nbas)
if aosym == 's2':
shls_slice = (sh0, sh1, 0, sh1)
else:
shls_slice = (sh0, sh1, 0, cell.nbas)
for p0, p1 in lib.prange(0, ngrids, Gblksize):
Gaux = ft_ao.ft_ao(fused_cell, Gv[p0:p1], fused_cell_slice, b,
gxyz[p0:p1], Gvbase, kpt)
Gaux *= wcoulG[p0:p1, None]
kLR = Gaux.real.copy('C')
kLI = Gaux.imag.copy('C')
Gaux = None
dat = ft_ao._ft_aopair_kpts(cell,
Gv[p0:p1],
shls_slice,
aosym,
b,
gxyz[p0:p1],
Gvbase,
kpt,
adapted_kptjs,
out=buf)
nG = p1 - p0
for k, ji in enumerate(adapted_ji_idx):
aoao = dat[k].reshape(nG, ncol)
pqkR = numpy.ndarray((ncol, nG), buffer=pqkRbuf)
pqkI = numpy.ndarray((ncol, nG), buffer=pqkIbuf)
pqkR[:] = aoao.real.T
pqkI[:] = aoao.imag.T
lib.dot(kLR.T, pqkR.T, -1, j3cR[k][naux:], 1)
lib.dot(kLI.T, pqkI.T, -1, j3cR[k][naux:], 1)
if not (is_zero(kpt) and gamma_point(adapted_kptjs[k])):
lib.dot(kLR.T, pqkI.T, -1, j3cI[k][naux:], 1)
lib.dot(kLI.T, pqkR.T, 1, j3cI[k][naux:], 1)
kLR = kLI = None
for k, idx in enumerate(adapted_ji_idx):
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
v = fuse(j3cR[k])
else:
v = fuse(j3cR[k] + j3cI[k] * 1j)
if j2ctag == 'CD':
v = scipy.linalg.solve_triangular(j2c,
v,
lower=True,
overwrite_b=True)
fswap['j3c-chunks/%d/%d' % (job_id, idx)][:naux0] = v
else:
fswap['j3c-chunks/%d/%d' % (job_id, idx)][:naux0] = lib.dot(
j2c, v)
# low-dimension systems
if j2c_negative is not None:
fswap['j3c-/%d/%d' % (job_id, idx)] = lib.dot(j2c_negative, v)
_assemble(mydf, kptij_lst, j3c_jobs, gen_int3c, ft_fuse, cderi_file, fswap,
log)
def make_kpt(uniq_kptji_id, cholesky_j2c): # kpt = kptj - kpti
kpt = uniq_kpts[uniq_kptji_id]
log.debug1('kpt = %s', kpt)
adapted_ji_idx = numpy.where(uniq_inverse == uniq_kptji_id)[0]
adapted_kptjs = kptjs[adapted_ji_idx]
nkptj = len(adapted_kptjs)
log.debug1('adapted_ji_idx = %s', adapted_ji_idx)
j2c, j2c_negative, j2ctag = cholesky_j2c
Gaux = ft_ao.ft_ao(fused_cell, Gv, None, b, gxyz, Gvbase, kpt).T
Gaux = fuse(Gaux)
Gaux *= mydf.weighted_coulG(kpt, False, mesh)
kLR = Gaux.T.real.copy('C')
kLI = Gaux.T.imag.copy('C')
if is_zero(kpt): # kpti == kptj
aosym = 's2'
nao_pair = nao*(nao+1)//2
if cell.dimension == 3:
vbar = fuse(mydf.auxbar(fused_cell))
ovlp = cell.pbc_intor('int1e_ovlp', hermi=1, kpts=adapted_kptjs)
ovlp = [lib.pack_tril(s) for s in ovlp]
else:
aosym = 's1'
nao_pair = nao**2
mem_now = lib.current_memory()[0]
log.debug2('memory = %s', mem_now)
max_memory = max(2000, mydf.max_memory-mem_now)
# nkptj for 3c-coulomb arrays plus 1 Lpq array
buflen = min(max(int(max_memory*.38e6/16/naux/(nkptj+1)), 1), nao_pair)
shranges = _guess_shell_ranges(cell, buflen, aosym)
buflen = max([x[2] for x in shranges])
# +1 for a pqkbuf
if aosym == 's2':
Gblksize = max(16, int(max_memory*.1e6/16/buflen/(nkptj+1)))
else:
Gblksize = max(16, int(max_memory*.2e6/16/buflen/(nkptj+1)))
Gblksize = min(Gblksize, ngrids, 16384)
pqkRbuf = numpy.empty(buflen*Gblksize)
pqkIbuf = numpy.empty(buflen*Gblksize)
# buf for ft_aopair
buf = numpy.empty((nkptj,buflen*Gblksize), dtype=numpy.complex128)
def pw_contract(istep, sh_range, j3cR, j3cI):
bstart, bend, ncol = sh_range
if aosym == 's2':
shls_slice = (bstart, bend, 0, bend)
else:
shls_slice = (bstart, bend, 0, cell.nbas)
for p0, p1 in lib.prange(0, ngrids, Gblksize):
dat = ft_ao._ft_aopair_kpts(cell, Gv[p0:p1], shls_slice, aosym,
b, gxyz[p0:p1], Gvbase, kpt,
adapted_kptjs, out=buf)
nG = p1 - p0
for k, ji in enumerate(adapted_ji_idx):
aoao = dat[k].reshape(nG,ncol)
pqkR = numpy.ndarray((ncol,nG), buffer=pqkRbuf)
pqkI = numpy.ndarray((ncol,nG), buffer=pqkIbuf)
pqkR[:] = aoao.real.T
pqkI[:] = aoao.imag.T
lib.dot(kLR[p0:p1].T, pqkR.T, -1, j3cR[k], 1)
lib.dot(kLI[p0:p1].T, pqkI.T, -1, j3cR[k], 1)
if not (is_zero(kpt) and gamma_point(adapted_kptjs[k])):
lib.dot(kLR[p0:p1].T, pqkI.T, -1, j3cI[k], 1)
lib.dot(kLI[p0:p1].T, pqkR.T, 1, j3cI[k], 1)
for k, ji in enumerate(adapted_ji_idx):
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
v = j3cR[k]
else:
v = j3cR[k] + j3cI[k] * 1j
if j2ctag == 'CD':
v = scipy.linalg.solve_triangular(j2c, v, lower=True, overwrite_b=True)
feri['j3c/%d/%d'%(ji,istep)] = v
else:
feri['j3c/%d/%d'%(ji,istep)] = lib.dot(j2c, v)
# low-dimension systems
if j2c_negative is not None:
feri['j3c-/%d/%d'%(ji,istep)] = lib.dot(j2c_negative, v)
with lib.call_in_background(pw_contract) as compute:
col1 = 0
for istep, sh_range in enumerate(shranges):
log.debug1('int3c2e [%d/%d], AO [%d:%d], ncol = %d', \
istep+1, len(shranges), *sh_range)
bstart, bend, ncol = sh_range
col0, col1 = col1, col1+ncol
j3cR = []
j3cI = []
for k, idx in enumerate(adapted_ji_idx):
v = [fswap['j3c-junk/%d/%d'%(idx,i)][0,col0:col1].T for i in range(nsegs)]
v = fuse(numpy.vstack(v))
if is_zero(kpt) and cell.dimension == 3:
for i in numpy.where(vbar != 0)[0]:
v[i] -= vbar[i] * ovlp[k][col0:col1]
j3cR.append(numpy.asarray(v.real, order='C'))
if is_zero(kpt) and gamma_point(adapted_kptjs[k]):
j3cI.append(None)
else:
j3cI.append(numpy.asarray(v.imag, order='C'))
v = None
compute(istep, sh_range, j3cR, j3cI)
for ji in adapted_ji_idx:
del(fswap['j3c-junk/%d'%ji])