def init_direct_scf(self, mol=None):
if mol is None: mol = self.mol
def set_vkscreen(opt, name):
opt._this.contents.r_vkscreen = _vhf._fpointer(name)
opt_llll = _vhf.VHFOpt(mol, 'int2e_spinor', 'CVHFrkbllll_prescreen',
'CVHFrkbllll_direct_scf',
'CVHFrkbllll_direct_scf_dm')
opt_llll.direct_scf_tol = self.direct_scf_tol
set_vkscreen(opt_llll, 'CVHFrkbllll_vkscreen')
opt_ssss = _vhf.VHFOpt(mol, 'int2e_spsp1spsp2_spinor',
'CVHFrkbllll_prescreen',
'CVHFrkbssss_direct_scf',
'CVHFrkbssss_direct_scf_dm')
opt_ssss.direct_scf_tol = self.direct_scf_tol
set_vkscreen(opt_ssss, 'CVHFrkbllll_vkscreen')
opt_ssll = _vhf.VHFOpt(mol, 'int2e_spsp1_spinor',
'CVHFrkbssll_prescreen',
'CVHFrkbssll_direct_scf',
'CVHFrkbssll_direct_scf_dm')
opt_ssll.direct_scf_tol = self.direct_scf_tol
set_vkscreen(opt_ssll, 'CVHFrkbssll_vkscreen')
#TODO: prescreen for gaunt
opt_gaunt = None
return opt_llll, opt_ssll, opt_ssss, opt_gaunt
def init_direct_scf(self, mol=None):
if mol is None: mol = self.mol
def set_vkscreen(opt, name):
opt._this.contents.r_vkscreen = \
ctypes.c_void_p(_ctypes.dlsym(_vhf.libcvhf._handle, name))
opt_llll = _vhf.VHFOpt(mol, 'cint2e', 'CVHFrkbllll_prescreen',
'CVHFrkbllll_direct_scf',
'CVHFrkbllll_direct_scf_dm')
opt_llll.direct_scf_tol = self.direct_scf_tol
set_vkscreen(opt_llll, 'CVHFrkbllll_vkscreen')
opt_ssss = _vhf.VHFOpt(mol, 'cint2e_spsp1spsp2',
'CVHFrkbllll_prescreen',
'CVHFrkbssss_direct_scf',
'CVHFrkbssss_direct_scf_dm')
opt_ssss.direct_scf_tol = self.direct_scf_tol
set_vkscreen(opt_ssss, 'CVHFrkbllll_vkscreen')
opt_ssll = _vhf.VHFOpt(mol, 'cint2e_spsp1', 'CVHFrkbssll_prescreen',
'CVHFrkbssll_direct_scf',
'CVHFrkbssll_direct_scf_dm')
opt_ssll.direct_scf_tol = self.direct_scf_tol
set_vkscreen(opt_ssll, 'CVHFrkbssll_vkscreen')
#TODO: prescreen for gaunt
opt_gaunt = None
return opt_llll, opt_ssll, opt_ssss, opt_gaunt
def init_direct_scf(self, mol=None):
if mol is None: mol = self.mol
def set_vkscreen(opt, name):
opt._this.contents.r_vkscreen = _vhf._fpointer(name)
with mol.with_integral_screen(self.direct_scf_tol**2):
opt_llll = _vhf.VHFOpt(mol, 'int2e_spinor', 'CVHFrkbllll_prescreen',
'CVHFrkbllll_direct_scf',
'CVHFrkbllll_direct_scf_dm')
opt_llll.direct_scf_tol = self.direct_scf_tol
set_vkscreen(opt_llll, 'CVHFrkbllll_vkscreen')
opt_ssss = _vhf.VHFOpt(mol, 'int2e_spsp1spsp2_spinor',
'CVHFrkbllll_prescreen',
'CVHFrkbssss_direct_scf',
'CVHFrkbssss_direct_scf_dm')
c1 = .5 / lib.param.LIGHT_SPEED
q_cond = opt_ssss.get_q_cond()
q_cond *= c1**2
opt_ssss.direct_scf_tol = self.direct_scf_tol
set_vkscreen(opt_ssss, 'CVHFrkbllll_vkscreen')
opt_ssll = _vhf.VHFOpt(mol, 'int2e_spsp1_spinor',
'CVHFrkbssll_prescreen',
'CVHFrkbssll_direct_scf',
'CVHFrkbssll_direct_scf_dm')
opt_ssll.direct_scf_tol = self.direct_scf_tol
set_vkscreen(opt_ssll, 'CVHFrkbssll_vkscreen')
nbas = mol.nbas
# The second parts of q_cond corresponds to ssss integrals. They
# need to be scaled by the factor (1/2c)^2
q_cond = opt_ssll.get_q_cond(shape=(2, nbas, nbas))
q_cond[1] *= c1**2
#TODO: prescreen for gaunt
opt_gaunt = None
return opt_llll, opt_ssll, opt_ssss, opt_gaunt
def get_jk(mol, dm):
'''J = ((-nabla i) j| kl) D_lk
K = ((-nabla i) j| kl) D_jk
'''
vhfopt = _vhf.VHFOpt(mol, 'int2e_ip1ip2', 'CVHFgrad_jk_prescreen',
'CVHFgrad_jk_direct_scf')
dm = numpy.asarray(dm, order='C')
if dm.ndim == 3:
n_dm = dm.shape[0]
else:
n_dm = 1
ao_loc = mol.ao_loc_nr()
fsetdm = getattr(_vhf.libcvhf, 'CVHFgrad_jk_direct_scf_dm')
fsetdm(vhfopt._this,
dm.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(n_dm),
ao_loc.ctypes.data_as(ctypes.c_void_p),
mol._atm.ctypes.data_as(ctypes.c_void_p), mol.natm,
mol._bas.ctypes.data_as(ctypes.c_void_p), mol.nbas,
mol._env.ctypes.data_as(ctypes.c_void_p))
# Update the vhfopt's attributes intor. Function direct_mapdm needs
# vhfopt._intor and vhfopt._cintopt to compute J/K. intor was initialized
# as int2e_ip1ip2. It should be int2e_ip1
vhfopt._intor = intor = mol._add_suffix('int2e_ip1')
vhfopt._cintopt = None
vj, vk = _vhf.direct_mapdm(intor, # (nabla i,j|k,l)
's2kl', # ip1_sph has k>=l,
('lk->s1ij', 'jk->s1il'),
dm, 3, # xyz, 3 components
mol._atm, mol._bas, mol._env, vhfopt=vhfopt)
return -vj, -vk
def init_direct_scf(self, mol=None):
if mol is None: mol = self.mol
opt = _vhf.VHFOpt(mol, 'cint2e_sph', 'CVHFnrs8_prescreen',
'CVHFsetnr_direct_scf',
'CVHFsetnr_direct_scf_dm')
opt.direct_scf_tol = self.direct_scf_tol
return opt
def _make_vhfopt(mol, dms, key, vhf_intor):
if not hasattr(_vhf.libcvhf, vhf_intor):
return None
vhfopt = _vhf.VHFOpt(mol, vhf_intor, 'CVHF' + key + '_prescreen',
'CVHF' + key + '_direct_scf')
dms = numpy.asarray(dms, order='C')
if dms.ndim == 3:
n_dm = dms.shape[0]
else:
n_dm = 1
ao_loc = mol.ao_loc_nr()
fsetdm = getattr(_vhf.libcvhf, 'CVHF' + key + '_direct_scf_dm')
fsetdm(vhfopt._this, dms.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(n_dm), ao_loc.ctypes.data_as(ctypes.c_void_p),
mol._atm.ctypes.data_as(ctypes.c_void_p), mol.natm,
mol._bas.ctypes.data_as(ctypes.c_void_p), mol.nbas,
mol._env.ctypes.data_as(ctypes.c_void_p))
# Update the vhfopt's attributes intor. Function direct_mapdm needs
# vhfopt._intor and vhfopt._cintopt to compute J/K.
if vhf_intor != 'int2e_' + key:
vhfopt._intor = mol._add_suffix('int2e_' + key)
vhfopt._cintopt = None
return vhfopt
def init_direct_scf(self, mol=None):
if mol is None: mol = self.mol
def set_vkscreen(opt, name):
opt._this.contents.r_vkscreen = _vhf._fpointer(name)
opt = _vhf.VHFOpt(mol, 'int2e_spinor', 'CVHFrkbllll_prescreen',
'CVHFrkbllll_direct_scf',
'CVHFrkbllll_direct_scf_dm')
opt.direct_scf_tol = self.direct_scf_tol
set_vkscreen(opt, 'CVHFrkbllll_vkscreen')
return opt
def init_direct_scf(self, mol=None):
if mol is None: mol = self.mol
if mol.cart:
intor = 'int2e_cart'
else:
intor = 'int2e_sph'
opt = _vhf.VHFOpt(mol, intor, 'CVHFnrs8_prescreen',
'CVHFsetnr_direct_scf', 'CVHFsetnr_direct_scf_dm')
opt.direct_scf_tol = self.direct_scf_tol
return opt
def _make_opt(mol):
'''Optimizer to genrate 3-center 2-electron integrals'''
intor = mol._add_suffix('int3c2e')
cintopt = gto.moleintor.make_cintopt(mol._atm, mol._bas, mol._env, intor)
# intor 'int1e_ovlp' is used by the prescreen method
# 'SGXnr_ovlp_prescreen' only. Not used again in other places.
# It can be released early
vhfopt = _vhf.VHFOpt(mol, 'int1e_ovlp', 'SGXnr_ovlp_prescreen',
'SGXsetnr_direct_scf')
vhfopt._intor = intor
vhfopt._cintopt = cintopt
return vhfopt
def test_direct_bindm1(self):
numpy.random.seed(1)
nao = mol.nao_nr(cart=True)
dm = numpy.random.random((nao,nao))
vhfopt = _vhf.VHFOpt(mol, 'int2e_cart', 'CVHFnrs8_prescreen',
'CVHFsetnr_direct_scf',
'CVHFsetnr_direct_scf_dm')
vj0, vk0 = _vhf.direct(dm, mol._atm, mol._bas, mol._env,
vhfopt=vhfopt, hermi=0, cart=True)
vj = _vhf.direct_bindm('int2e_cart', 's1', 'kl->s1ij', dm, 1,
mol._atm, mol._bas, mol._env, vhfopt)
self.assertTrue(numpy.allclose(vj0,vj))
def init_direct_scf(self, mol=None):
if mol is None: mol = self.mol
def set_vkscreen(opt, name):
opt._this.contents.r_vkscreen = \
ctypes.c_void_p(_ctypes.dlsym(_vhf.libcvhf._handle, name))
opt = _vhf.VHFOpt(mol, 'cint2e', 'CVHFrkbllll_prescreen',
'CVHFrkbllll_direct_scf',
'CVHFrkbllll_direct_scf_dm')
opt.direct_scf_tol = self.direct_scf_tol
set_vkscreen(opt, 'CVHFrkbllll_vkscreen')
return opt
def jk_ints(molA, molB, dm_ia, dm_jb):
from pyscf.scf import jk, _vhf
naoA = molA.nao
naoB = molB.nao
assert (dm_ia.shape == (naoA, naoA))
assert (dm_jb.shape == (naoB, naoB))
molAB = molA + molB
vhfopt = _vhf.VHFOpt(molAB, 'int2e', 'CVHFnrs8_prescreen',
'CVHFsetnr_direct_scf', 'CVHFsetnr_direct_scf_dm')
dmAB = scipy.linalg.block_diag(dm_ia, dm_jb)
# The prescreen function CVHFnrs8_prescreen indexes q_cond and dm_cond
# over the entire basis. "set_dm" in function jk.get_jk/direct_bindm only
# creates a subblock of dm_cond which is not compatible with
# CVHFnrs8_prescreen.
vhfopt.set_dm(dmAB, molAB._atm, molAB._bas, molAB._env)
# Then skip the "set_dm" initialization in function jk.get_jk/direct_bindm.
vhfopt._dmcondname = None
with lib.temporary_env(vhfopt._this.contents,
fprescreen=_vhf._fpointer('CVHFnrs8_vj_prescreen')):
shls_slice = (0, molA.nbas, 0, molA.nbas, molA.nbas, molAB.nbas,
molA.nbas, molAB.nbas) # AABB
vJ = jk.get_jk(molAB,
dm_jb,
'ijkl,lk->s2ij',
shls_slice=shls_slice,
vhfopt=vhfopt,
aosym='s4',
hermi=1)
cJ = np.einsum('ia,ia->', vJ, dm_ia)
with lib.temporary_env(vhfopt._this.contents,
fprescreen=_vhf._fpointer('CVHFnrs8_vk_prescreen')):
shls_slice = (0, molA.nbas, molA.nbas, molAB.nbas, molA.nbas,
molAB.nbas, 0, molA.nbas) # ABBA
vK = jk.get_jk(molAB,
dm_jb,
'ijkl,jk->il',
shls_slice=shls_slice,
vhfopt=vhfopt,
aosym='s1',
hermi=0)
cK = np.einsum('ia,ia->', vK, dm_ia)
return cJ, cK
def test_rdirect_bindm(self):
n2c = nao * 2
numpy.random.seed(1)
dm = (numpy.random.random((n2c, n2c)) + numpy.random.random(
(n2c, n2c)) * 1j)
dm = dm + dm.conj().T
eri0 = mol.intor('int2e_spsp1_spinor').reshape(n2c, n2c, n2c, n2c)
vk0 = numpy.einsum('ijkl,jk->il', eri0, dm)
vk1 = _vhf.rdirect_bindm('int2e_spsp1_spinor', 's4', 'jk->s1il', dm, 1,
mol._atm, mol._bas, mol._env)
self.assertTrue(numpy.allclose(vk0, vk1))
opt_llll = _vhf.VHFOpt(mol, 'int2e_spinor', 'CVHFrkbllll_prescreen',
'CVHFrkbllll_direct_scf',
'CVHFrkbllll_direct_scf_dm')
opt_llll._this.contents.r_vkscreen = _vhf._fpointer(
'CVHFrkbllll_vkscreen')
eri0 = mol.intor('int2e_spinor').reshape(n2c, n2c, n2c, n2c)
vk0 = numpy.einsum('ijkl,jk->il', eri0, dm)
vk1 = _vhf.rdirect_bindm('int2e_spinor', 's1', 'jk->s1il', dm, 1,
mol._atm, mol._bas, mol._env, opt_llll)
self.assertTrue(numpy.allclose(vk0, vk1))
def get_j(dfobj, dm, hermi=1, direct_scf_tol=1e-13):
from pyscf.scf import _vhf
from pyscf.scf import jk
from pyscf.df import addons
t0 = t1 = (time.clock(), time.time())
mol = dfobj.mol
if dfobj._vjopt is None:
dfobj.auxmol = auxmol = addons.make_auxmol(mol, dfobj.auxbasis)
opt = _vhf.VHFOpt(mol, 'int3c2e', 'CVHFnr3c2e_schwarz_cond')
opt.direct_scf_tol = direct_scf_tol
# q_cond part 1: the regular int2e (ij|ij) for mol's basis
opt.init_cvhf_direct(mol, 'int2e', 'CVHFsetnr_direct_scf')
mol_q_cond = lib.frompointer(opt._this.contents.q_cond, mol.nbas**2)
# Update q_cond to include the 2e-integrals (auxmol|auxmol)
j2c = auxmol.intor('int2c2e', hermi=1)
j2c_diag = numpy.sqrt(abs(j2c.diagonal()))
aux_loc = auxmol.ao_loc
aux_q_cond = [
j2c_diag[i0:i1].max() for i0, i1 in zip(aux_loc[:-1], aux_loc[1:])
]
q_cond = numpy.hstack((mol_q_cond, aux_q_cond))
fsetqcond = _vhf.libcvhf.CVHFset_q_cond
fsetqcond(opt._this, q_cond.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(q_cond.size))
try:
opt.j2c = j2c = scipy.linalg.cho_factor(j2c, lower=True)
opt.j2c_type = 'cd'
except scipy.linalg.LinAlgError:
opt.j2c = j2c
opt.j2c_type = 'regular'
# jk.get_jk function supports 4-index integrals. Use bas_placeholder
# (l=0, nctr=1, 1 function) to hold the last index.
bas_placeholder = numpy.array([0, 0, 1, 1, 0, 0, 0, 0],
dtype=numpy.int32)
fakemol = mol + auxmol
fakemol._bas = numpy.vstack((fakemol._bas, bas_placeholder))
opt.fakemol = fakemol
dfobj._vjopt = opt
t1 = logger.timer_debug1(dfobj, 'df-vj init_direct_scf', *t1)
opt = dfobj._vjopt
fakemol = opt.fakemol
dm = numpy.asarray(dm, order='C')
dm_shape = dm.shape
nao = dm_shape[-1]
dm = dm.reshape(-1, nao, nao)
n_dm = dm.shape[0]
# First compute the density in auxiliary basis
# j3c = fauxe2(mol, auxmol)
# jaux = numpy.einsum('ijk,ji->k', j3c, dm)
# rho = numpy.linalg.solve(auxmol.intor('int2c2e'), jaux)
nbas = mol.nbas
nbas1 = mol.nbas + dfobj.auxmol.nbas
shls_slice = (0, nbas, 0, nbas, nbas, nbas1, nbas1, nbas1 + 1)
with lib.temporary_env(opt,
prescreen='CVHFnr3c2e_vj_pass1_prescreen',
_dmcondname='CVHFsetnr_direct_scf_dm'):
jaux = jk.get_jk(fakemol,
dm, ['ijkl,ji->kl'] * n_dm,
'int3c2e',
aosym='s2ij',
hermi=0,
shls_slice=shls_slice,
vhfopt=opt)
# remove the index corresponding to bas_placeholder
jaux = numpy.array(jaux)[:, :, 0]
t1 = logger.timer_debug1(dfobj, 'df-vj pass 1', *t1)
if opt.j2c_type == 'cd':
rho = scipy.linalg.cho_solve(opt.j2c, jaux.T)
else:
rho = scipy.linalg.solve(opt.j2c, jaux.T)
# transform rho to shape (:,1,naux), to adapt to 3c2e integrals (ij|k)
rho = rho.T[:, numpy.newaxis, :]
t1 = logger.timer_debug1(dfobj, 'df-vj solve ', *t1)
# Next compute the Coulomb matrix
# j3c = fauxe2(mol, auxmol)
# vj = numpy.einsum('ijk,k->ij', j3c, rho)
with lib.temporary_env(opt,
prescreen='CVHFnr3c2e_vj_pass2_prescreen',
_dmcondname=None):
# CVHFnr3c2e_vj_pass2_prescreen requires custom dm_cond
aux_loc = dfobj.auxmol.ao_loc
dm_cond = [
abs(rho[:, :, i0:i1]).max()
for i0, i1 in zip(aux_loc[:-1], aux_loc[1:])
]
dm_cond = numpy.array(dm_cond)
fsetcond = _vhf.libcvhf.CVHFset_dm_cond
fsetcond(opt._this, dm_cond.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(dm_cond.size))
vj = jk.get_jk(fakemol,
rho, ['ijkl,lk->ij'] * n_dm,
'int3c2e',
aosym='s2ij',
hermi=1,
shls_slice=shls_slice,
vhfopt=opt)
t1 = logger.timer_debug1(dfobj, 'df-vj pass 2', *t1)
logger.timer(dfobj, 'df-vj', *t0)
return numpy.asarray(vj).reshape(dm_shape)
def build(self, omega=None, direct_scf_tol=None):
cpu0 = (time.clock(), time.time())
cell = self.cell
kpts = self.kpts
k_scaled = cell.get_scaled_kpts(kpts).sum(axis=0)
k_mod_to_half = k_scaled * 2 - (k_scaled * 2).round(0)
if abs(k_mod_to_half).sum() > 1e-5:
raise NotImplementedError('k-points must be symmetryic')
if omega is not None:
self.omega = omega
if self.omega is None:
# Search a proper range-separation parameter omega that can balance the
# computational cost between the real space integrals and moment space
# integrals
self.omega, self.mesh, self.ke_cutoff = _guess_omega(
cell, kpts, self.mesh)
else:
self.ke_cutoff = aft.estimate_ke_cutoff_for_omega(cell, self.omega)
self.mesh = pbctools.cutoff_to_mesh(cell.lattice_vectors(),
self.ke_cutoff)
logger.info(self, 'omega = %.15g ke_cutoff = %s mesh = %s',
self.omega, self.ke_cutoff, self.mesh)
if direct_scf_tol is None:
direct_scf_tol = cell.precision**1.5
logger.debug(self, 'Set direct_scf_tol %g', direct_scf_tol)
self.cell_rs = cell_rs = _re_contract_cell(cell, self.ke_cutoff)
self.bvk_kmesh = kmesh = k2gamma.kpts_to_kmesh(cell_rs, kpts)
bvkcell, phase = k2gamma.get_phase(cell_rs, kpts, kmesh)
self.bvkmesh_Ls = Ks = k2gamma.translation_vectors_for_kmesh(
cell_rs, kmesh)
self.bvkcell = bvkcell
self.phase = phase
# Given ke_cutoff, eta corresponds to the most steep Gaussian basis
# of which the Coulomb integrals can be accurately computed in moment
# space.
eta = aft.estimate_eta_for_ke_cutoff(cell,
self.ke_cutoff,
precision=cell.precision)
# * Assuming the most steep function in smooth basis has exponent eta,
# with attenuation parameter omega, rcut_sr is the distance of which
# the value of attenuated Coulomb integrals of four shells |eta> is
# smaller than the required precision.
# * The attenuated coulomb integrals between four s-type Gaussians
# (2*a/pi)^{3/4}exp(-a*r^2) is
# (erfc(omega*a^0.5/(omega^2+a)^0.5*R) - erfc(a^0.5*R)) / R
# if two Gaussians on one center and the other two on another center
# and the distance between the two centers are R.
# * The attenuated coulomb integrals between two spherical charge
# distributions is
# ~(pi/eta)^3/2 (erfc(tau*(eta/2)^0.5*R) - erfc((eta/2)^0.5*R)) / R
# tau = omega/sqrt(omega^2 + eta/2)
# if the spherical charge distribution is the product of above s-type
# Gaussian with exponent eta and a very smooth function.
# When R is large, the attenuated Coulomb integral is
# ~= (pi/eta)^3/2 erfc(tau*(eta/2)^0.5*R) / R
# ~= pi/(tau*eta^2*R^2) exp(-tau^2*eta*R^2/2)
tau = self.omega / (self.omega**2 + eta / 2)**.5
rcut_sr = 10 # initial guess
rcut_sr = (-np.log(direct_scf_tol * tau * (eta * rcut_sr)**2 / np.pi) /
(tau**2 * eta / 2))**.5
logger.debug(self, 'eta = %g rcut_sr = %g', eta, rcut_sr)
# Ls is the translation vectors to mimic periodicity of a cell
Ls = bvkcell.get_lattice_Ls(rcut=cell.rcut + rcut_sr)
self.supmol_Ls = Ls = Ls[np.linalg.norm(Ls, axis=1).argsort()]
supmol = _make_extended_mole(cell_rs, Ls, Ks, self.omega,
direct_scf_tol)
self.supmol = supmol
nkpts = len(self.bvkmesh_Ls)
nbas = cell_rs.nbas
n_steep, n_local, n_diffused = cell_rs._nbas_each_set
n_compact = n_steep + n_local
bas_mask = supmol._bas_mask
self.bvk_bas_mask = bvk_bas_mask = bas_mask.any(axis=2)
# Some basis in bvk-cell are not presented in the supmol. They can be
# skipped when computing SR integrals
self.bvkcell._bas = bvkcell._bas[bvk_bas_mask.ravel()]
# Record the mapping between the dense bvkcell basis and the
# original sparse bvkcell basis
bvk_cell_idx = np.repeat(np.arange(nkpts)[:, None], nbas, axis=1)
self.bvk_cell_id = bvk_cell_idx[bvk_bas_mask].astype(np.int32)
cell0_shl_idx = np.repeat(np.arange(nbas)[None, :], nkpts, axis=0)
self.cell0_shl_id = cell0_shl_idx[bvk_bas_mask].astype(np.int32)
logger.timer_debug1(self, 'initializing supmol', *cpu0)
logger.info(self, 'sup-mol nbas = %d cGTO = %d pGTO = %d', supmol.nbas,
supmol.nao, supmol.npgto_nr())
supmol.omega = -self.omega # Set short range coulomb
with supmol.with_integral_screen(direct_scf_tol**2):
vhfopt = _vhf.VHFOpt(supmol,
'int2e_sph',
qcondname=libpbc.PBCVHFsetnr_direct_scf)
vhfopt.direct_scf_tol = direct_scf_tol
self.vhfopt = vhfopt
logger.timer(self, 'initializing vhfopt', *cpu0)
q_cond = vhfopt.get_q_cond((supmol.nbas, supmol.nbas))
idx = supmol._images_loc
bvk_q_cond = lib.condense('NP_absmax', q_cond, idx, idx)
ovlp_mask = bvk_q_cond > direct_scf_tol
# Remove diffused-diffused block
if n_diffused > 0:
diffused_mask = np.zeros_like(bvk_bas_mask)
diffused_mask[:, n_compact:] = True
diffused_mask = diffused_mask[bvk_bas_mask]
ovlp_mask[diffused_mask[:, None] & diffused_mask] = False
self.ovlp_mask = ovlp_mask.astype(np.int8)
# mute rcut_threshold, divide basis into two sets only
cell_lr_aft = _re_contract_cell(cell, self.ke_cutoff, -1, verbose=0)
self.lr_aft = lr_aft = _LongRangeAFT(cell_lr_aft, kpts, self.omega,
self.bvk_kmesh)
lr_aft.ke_cutoff = self.ke_cutoff
lr_aft.mesh = self.mesh
lr_aft.eta = eta
return self
def _gen_jk_direct(mol, aosym, with_j, with_k, direct_scf_tol):
'''Contraction between sgX Coulomb integrals and density matrices
J: einsum('guv,xg->xuv', gbn, dms) if dms == rho at grid
einsum('gij,xij->xg', gbn, dms) if dms are density matrices
K: einsum('gtv,xgt->xgv', gbn, fg)
'''
intor = mol._add_suffix('int3c2e')
cintopt = gto.moleintor.make_cintopt(mol._atm, mol._bas, mol._env, intor)
ncomp = 1
nao = mol.nao
vhfopt = _vhf.VHFOpt(mol, 'int1e_ovlp', 'SGXnr_ovlp_prescreen',
'SGXsetnr_direct_scf')
vhfopt.direct_scf_tol = direct_scf_tol
cintor = _vhf._fpointer(intor)
fdot = _vhf._fpointer('SGXdot_nr' + aosym)
drv = _vhf.libcvhf.SGXnr_direct_drv
# for linsgx, from _vhf.VHFOpt
libcvhf = lib.load_library('libcvhf')
intor = mol._add_suffix('int1e_ovlp')
c_atm = numpy.asarray(mol._atm, dtype=numpy.int32, order='C')
c_bas = numpy.asarray(mol._bas, dtype=numpy.int32, order='C')
c_env = numpy.asarray(mol._env, dtype=numpy.double, order='C')
natm = ctypes.c_int(c_atm.shape[0])
nbas = ctypes.c_int(c_bas.shape[0])
@profile
def jk_part(mol, grid_coords, dms, fg):
# transfer bvv to SGXsetnr_direct_scf_blk. from _vhf.VHFOpt
# need add mol._bvv in scf.mole.py
c_bvv = numpy.asarray(mol._bvv, dtype=numpy.int32, order='C')
nbvv = ctypes.c_int(c_bvv.shape[0])
ao_loc = make_loc(c_bas, intor)
fsetqcond = getattr(libcvhf, 'SGXsetnr_direct_scf_blk')
fsetqcond(vhfopt._this, getattr(libcvhf, intor), lib.c_null_ptr(),
ao_loc.ctypes.data_as(ctypes.c_void_p),
c_atm.ctypes.data_as(ctypes.c_void_p), natm,
c_bas.ctypes.data_as(ctypes.c_void_p), nbas,
c_env.ctypes.data_as(ctypes.c_void_p),
c_bvv.ctypes.data_as(ctypes.c_void_p), nbvv)
fakemol = gto.fakemol_for_charges(grid_coords)
atm, bas, env = gto.mole.conc_env(mol._atm, mol._bas, mol._env,
fakemol._atm, fakemol._bas,
fakemol._env)
ao_loc = moleintor.make_loc(bas, intor)
shls_slice = (0, mol.nbas, 0, mol.nbas, mol.nbas, len(bas))
ngrids = grid_coords.shape[0]
vj = vk = None
fjk = []
dmsptr = []
vjkptr = []
if with_j:
if dms[0].ndim == 1: # the value of density at each grid
vj = numpy.zeros((len(dms), ncomp, nao, nao))[:, 0]
for i, dm in enumerate(dms):
dmsptr.append(dm.ctypes.data_as(ctypes.c_void_p))
vjkptr.append(vj[i].ctypes.data_as(ctypes.c_void_p))
fjk.append(_vhf._fpointer('SGXnr' + aosym + '_ijg_g_ij'))
else:
vj = numpy.zeros((len(dms), ncomp, ngrids))[:, 0]
for i, dm in enumerate(dms):
dmsptr.append(dm.ctypes.data_as(ctypes.c_void_p))
vjkptr.append(vj[i].ctypes.data_as(ctypes.c_void_p))
fjk.append(_vhf._fpointer('SGXnr' + aosym + '_ijg_ji_g'))
if with_k:
vk = numpy.zeros((len(fg), ncomp, ngrids, nao))[:, 0]
for i, dm in enumerate(fg):
dmsptr.append(dm.ctypes.data_as(ctypes.c_void_p))
vjkptr.append(vk[i].ctypes.data_as(ctypes.c_void_p))
fjk.append(_vhf._fpointer('SGXnr' + aosym + '_ijg_gj_gi'))
n_dm = len(fjk)
fjk = (ctypes.c_void_p * (n_dm))(*fjk)
dmsptr = (ctypes.c_void_p * (n_dm))(*dmsptr)
vjkptr = (ctypes.c_void_p * (n_dm))(*vjkptr)
drv(cintor, fdot, fjk, dmsptr, vjkptr, n_dm, ncomp,
(ctypes.c_int * 6)(*shls_slice),
ao_loc.ctypes.data_as(ctypes.c_void_p), cintopt, vhfopt._this,
atm.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(mol.natm),
bas.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(mol.nbas),
env.ctypes.data_as(ctypes.c_void_p))
return vj, vk
return jk_part