def aux_e2(mol, auxmol, intor='cint3c2e_spinor', aosym='s1', comp=1, hermi=0):
atm, bas, env = \
pyscf.gto.mole.conc_env(mol._atm, mol._bas, mol._env,
auxmol._atm, auxmol._bas, auxmol._env)
c_atm = numpy.asarray(atm, dtype=numpy.int32, order='C')
c_bas = numpy.asarray(bas, dtype=numpy.int32, order='C')
c_env = numpy.asarray(env, dtype=numpy.double, order='C')
natm = ctypes.c_int(mol.natm + auxmol.natm)
nbas = ctypes.c_int(mol.nbas)
nao = mol.nao_2c()
naoaux = auxmol.nao_nr()
if aosym == 's1':
eri = numpy.empty((nao * nao, naoaux), dtype=numpy.complex)
fill = _fpointer('RIfill_r_s1_auxe2')
else:
eri = numpy.empty((nao * (nao + 1) // 2, naoaux), dtype=numpy.complex)
fill = _fpointer('RIfill_r_s2ij_auxe2')
fintor = _fpointer(intor)
cintopt = _vhf.make_cintopt(c_atm, c_bas, c_env, intor)
libri.RIr_3c2e_auxe2_drv(fintor, fill, eri.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(0), ctypes.c_int(mol.nbas),
ctypes.c_int(mol.nbas), ctypes.c_int(auxmol.nbas),
ctypes.c_int(1), cintopt,
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))
return eri
def __init__(self, mol, intor, prescreen='CVHFnoscreen', qcondname=None):
self._this = ctypes.POINTER(_vhf._CVHFOpt)()
#print self._this.contents, expect ValueError: NULL pointer access
self._intor = _fpointer(intor)
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])
self._cintopt = _vhf.make_cintopt(c_atm, c_bas, c_env, intor)
libao2mo.CVHFinit_optimizer(ctypes.byref(self._this),
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))
self._this.contents.fprescreen = _fpointer(prescreen)
if prescreen != 'CVHFnoscreen':
# for cint2e_sph, qcondname is 'CVHFsetnr_direct_scf'
fsetqcond = getattr(libao2mo, qcondname)
fsetqcond(self._this, 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))
def run3c(fill, kpts, shls_slice=None):
intor = 'int3c2e_sph'
nao = cell.nao_nr()
nkpts = len(kpts)
if fill == 'PBCnr3c_fill_gs2':
out = numpy.empty((nao * (nao + 1) // 2, nao))
kptij_idx = numpy.arange(nkpts).astype(numpy.int32)
elif fill == 'PBCnr3c_fill_gs1':
out = numpy.empty((nao, nao, nao))
kptij_idx = numpy.arange(nkpts).astype(numpy.int32)
elif fill in ('PBCnr3c_fill_kks1', 'PBCnr3c_fill_kks2'):
kptij_idx = numpy.asarray(
[i * nkpts + j for i in range(nkpts) for j in range(i + 1)],
dtype=numpy.int32)
out = numpy.empty((len(kptij_idx), nao, nao, nao),
dtype=numpy.complex128)
elif fill == 'PBCnr3c_fill_ks1':
kptij_idx = numpy.arange(nkpts).astype(numpy.int32)
out = numpy.empty((nkpts, nao, nao, nao), dtype=numpy.complex128)
elif fill == 'PBCnr3c_fill_ks2':
out = numpy.empty((nkpts, nao * (nao + 1) // 2, nao),
dtype=numpy.complex128)
kptij_idx = numpy.arange(nkpts).astype(numpy.int32)
else:
raise RuntimeError
nkpts_ij = len(kptij_idx)
Ls = cell.get_lattice_Ls()
nimgs = len(Ls)
expkL = numpy.exp(1j * numpy.dot(kpts, Ls.T))
comp = 1
if shls_slice is None:
shls_slice = (0, cell.nbas, cell.nbas, cell.nbas * 2, cell.nbas * 2,
cell.nbas * 3)
atm, bas, env = gto.conc_env(cell._atm, cell._bas, cell._env, cell._atm,
cell._bas, cell._env)
atm, bas, env = gto.conc_env(atm, bas, env, cell._atm, cell._bas,
cell._env)
ao_loc = gto.moleintor.make_loc(bas, 'int3c2e_sph')
cintopt = _vhf.make_cintopt(atm, bas, env, intor)
libpbc.PBCnr3c_drv(getattr(libpbc, intor), getattr(libpbc, fill),
out.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(nkpts_ij), ctypes.c_int(nkpts),
ctypes.c_int(comp), ctypes.c_int(len(Ls)),
Ls.ctypes.data_as(ctypes.c_void_p),
expkL.ctypes.data_as(ctypes.c_void_p),
kptij_idx.ctypes.data_as(ctypes.c_void_p),
(ctypes.c_int * 6)(*shls_slice),
ao_loc.ctypes.data_as(ctypes.c_void_p), cintopt,
atm.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(cell.natm),
bas.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(cell.nbas),
env.ctypes.data_as(ctypes.c_void_p))
return out
def _wrap_int3c(cell, auxcell, intor, comp, Ls, out_lst):
atm, bas, env = pyscf.gto.conc_env(cell._atm, cell._bas, cell._env,
cell._atm, cell._bas, cell._env)
atm, bas, env = pyscf.gto.conc_env(atm, bas, env, auxcell._atm,
auxcell._bas, auxcell._env)
atm = numpy.asarray(atm, dtype=numpy.int32)
bas = numpy.asarray(bas, dtype=numpy.int32)
env = numpy.asarray(env, dtype=numpy.double)
natm = len(atm)
nbas = len(bas)
if 'ssc' in intor:
ao_loc = cell.ao_loc_nr()
ao_loc = numpy.hstack((ao_loc[:-1], ao_loc[-1] + ao_loc))
ao_loc = numpy.hstack(
(ao_loc[:-1], ao_loc[-1] + auxcell.ao_loc_nr(cart=True)))
ao_loc = numpy.asarray(ao_loc, dtype=numpy.int32)
else:
ao_loc = pyscf.gto.moleintor.make_loc(bas, intor)
cintopt = _vhf.make_cintopt(atm, bas, env, intor)
fintor = getattr(pyscf.gto.moleintor.libcgto, intor)
fill = getattr(libpbc, 'PBCnr3c_fill_s1')
drv = libpbc.PBCnr3c_drv
outs = (ctypes.c_void_p * len(out_lst))(
*[out.ctypes.data_as(ctypes.c_void_p) for out in out_lst])
xyz = numpy.asarray(cell.atom_coords(), order='C')
ptr_coords = numpy.asarray(atm[cell.natm:cell.natm * 2,
pyscf.gto.PTR_COORD],
dtype=numpy.int32,
order='C')
c_ptr_coords = ptr_coords.ctypes.data_as(ctypes.c_void_p)
c_xyz = xyz.ctypes.data_as(ctypes.c_void_p)
c_nxyz = ctypes.c_int(len(xyz))
Ls = numpy.asarray(Ls, order='C')
c_Ls = Ls.ctypes.data_as(ctypes.c_void_p)
c_comp = ctypes.c_int(comp)
c_ao_loc = ao_loc.ctypes.data_as(ctypes.c_void_p)
c_atm = atm.ctypes.data_as(ctypes.c_void_p)
c_bas = bas.ctypes.data_as(ctypes.c_void_p)
c_env = env.ctypes.data_as(ctypes.c_void_p)
c_natm = ctypes.c_int(natm)
c_nbas = ctypes.c_int(nbas)
def ints(facs, c_shls_slice):
nimgs, nkpts = facs.shape
drv(fintor, fill, outs, c_xyz, c_ptr_coords, c_nxyz, c_Ls,
ctypes.c_int(nimgs), facs.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(nkpts), c_comp, c_shls_slice, c_ao_loc, cintopt,
c_atm, c_natm, c_bas, c_nbas, c_env)
# Save the numpy arrays in envs because ctypes does not increase their
# reference counting.
ints._envs = (atm, bas, env, ao_loc, xyz, ptr_coords, Ls)
return ints
def nr_e1fill(intor,
sh_range,
atm,
bas,
env,
aosym='s1',
comp=1,
ao2mopt=None,
out=None):
assert (aosym in ('s4', 's2ij', 's2kl', 's1'))
c_atm = numpy.asarray(atm, dtype=numpy.int32, order='C')
c_bas = numpy.asarray(bas, dtype=numpy.int32, order='C')
c_env = numpy.asarray(env, order='C')
natm = ctypes.c_int(c_atm.shape[0])
nbas = ctypes.c_int(c_bas.shape[0])
ao_loc = moleintor.make_loc(bas, intor)
nao = ao_loc[-1]
klsh0, klsh1, nkl = sh_range
if aosym in ('s4', 's2ij'):
nao_pair = nao * (nao + 1) // 2
else:
nao_pair = nao * nao
if out is None:
out = numpy.empty((comp, nkl, nao_pair))
else:
out = numpy.ndarray((comp, nkl, nao_pair), buffer=out)
if out.size == 0:
return out
if ao2mopt is not None:
cao2mopt = ao2mopt._this
cintopt = ao2mopt._cintopt
cintor = ao2mopt._intor
else:
cao2mopt = lib.c_null_ptr()
cintor = _fpointer(intor)
cintopt = _vhf.make_cintopt(c_atm, c_bas, c_env, intor)
fdrv = getattr(libao2mo, 'AO2MOnr_e1fill_drv')
fill = _fpointer('AO2MOfill_nr_' + aosym)
fdrv(cintor, fill,
out.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(klsh0),
ctypes.c_int(klsh1 - klsh0), ctypes.c_int(nkl), ctypes.c_int(comp),
ao_loc.ctypes.data_as(ctypes.c_void_p), cintopt, cao2mopt,
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))
return out
def getints2e(intor_name, atm, bas, env, shls_slice=None, comp=1,
aosym='s1', ao_loc=None, cintopt=None, out=None):
aosym = _stand_sym_code(aosym)
atm = numpy.asarray(atm, dtype=numpy.int32, order='C')
bas = numpy.asarray(bas, dtype=numpy.int32, order='C')
env = numpy.asarray(env, dtype=numpy.double, order='C')
c_atm = atm.ctypes.data_as(pyscf.lib.c_int_p)
c_bas = bas.ctypes.data_as(pyscf.lib.c_int_p)
c_env = env.ctypes.data_as(pyscf.lib.c_double_p)
natm = atm.shape[0]
nbas = bas.shape[0]
if '_cart' in intor_name:
libcgto.CINTtot_cgto_cart.restype = ctypes.c_int
nao = libcgto.CINTtot_cgto_cart(c_bas, ctypes.c_int(nbas))
cgto_in_shell = 'CINTcgto_cart'
elif '_sph' in intor_name:
libcgto.CINTtot_cgto_spheric.restype = ctypes.c_int
nao = libcgto.CINTtot_cgto_spheric(c_bas, ctypes.c_int(nbas))
cgto_in_shell = 'CINTcgto_spheric'
else:
raise NotImplementedError('cint2e spinor AO integrals')
if intor_name in ('cint2e_sph', 'cint2e_cart') and aosym == 's8':
assert(shls_slice is None)
nao_pair = nao*(nao+1)//2
if out is None:
out = numpy.empty((nao_pair*(nao_pair+1)//2))
else:
out = numpy.ndarray((nao_pair*(nao_pair+1)//2), buffer=out)
drv = libcvhf.GTO2e_cart_or_sph
drv(_fpointer(intor_name), _fpointer(cgto_in_shell),
out.ctypes.data_as(ctypes.c_void_p),
c_atm, ctypes.c_int(natm), c_bas, ctypes.c_int(nbas), c_env)
return out
else:
from pyscf.scf import _vhf
if shls_slice is None:
shls_slice = (0, nbas, 0, nbas)
else:
assert(shls_slice[1] <= nbas and shls_slice[3] <= nbas)
bralst = numpy.arange(shls_slice[0], shls_slice[1], dtype=numpy.int32)
ketlst = numpy.arange(shls_slice[2], shls_slice[3], dtype=numpy.int32)
num_cgto_of = getattr(libcgto, cgto_in_shell)
naoi = sum([num_cgto_of(ctypes.c_int(i), c_bas) for i in bralst])
naoj = sum([num_cgto_of(ctypes.c_int(i), c_bas) for i in ketlst])
if aosym in ('s4', 's2ij'):
nij = naoi * (naoi + 1) // 2
assert(numpy.alltrue(bralst == ketlst))
else:
nij = naoi * naoj
if aosym in ('s4', 's2kl'):
nkl = nao * (nao + 1) // 2
else:
nkl = nao * nao
if comp == 1:
if out is None:
out = numpy.empty((nij,nkl))
else:
out = numpy.ndarray((nij,nkl), buffer=out)
else:
if out is None:
out = numpy.empty((comp,nij,nkl))
else:
out = numpy.ndarray((comp,nij,nkl), buffer=out)
cintopt = _vhf.make_cintopt(atm, bas, env, intor_name)
prescreen = pyscf.lib.c_null_ptr()
drv = libcgto.GTOnr2e_fill_drv
drv(_fpointer(intor_name), _fpointer(cgto_in_shell),
_fpointer('GTOnr2e_fill_'+aosym), prescreen,
out.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(comp),
bralst.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(bralst.size),
ketlst.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(ketlst.size),
cintopt, c_atm, ctypes.c_int(natm), c_bas, ctypes.c_int(nbas), c_env)
cintopt = None
return out
def r_e1(intor,
mo_coeff,
orbs_slice,
sh_range,
atm,
bas,
env,
tao,
aosym='s1',
comp=1,
ao2mopt=None,
out=None):
assert (aosym in ('s4', 's2ij', 's2kl', 's1', 'a2ij', 'a2kl', 'a4ij',
'a4kl', 'a4'))
mo_coeff = numpy.asfortranarray(mo_coeff)
i0, i1, j0, j1 = orbs_slice
icount = i1 - i0
jcount = j1 - j0
ij_count = icount * jcount
c_atm = numpy.asarray(atm, dtype=numpy.int32)
c_bas = numpy.asarray(bas, dtype=numpy.int32)
c_env = numpy.asarray(env)
natm = ctypes.c_int(c_atm.shape[0])
nbas = ctypes.c_int(c_bas.shape[0])
klsh0, klsh1, nkl = sh_range
if icount <= jcount:
fmmm = _fpointer('AO2MOmmm_r_iltj')
else:
fmmm = _fpointer('AO2MOmmm_r_igtj')
if out is None:
out = numpy.empty((comp, nkl, ij_count), dtype=numpy.complex)
else:
out = numpy.ndarray((comp, nkl, nao_pair),
dtype=numpy.complex,
buffer=out)
if out.size == 0:
return out
if ao2mopt is not None:
cao2mopt = ao2mopt._this
cintopt = ao2mopt._cintopt
cintor = ao2mopt._intor
else:
cao2mopt = lib.c_null_ptr()
cintor = _fpointer(intor)
cintopt = _vhf.make_cintopt(c_atm, c_bas, c_env, intor)
tao = numpy.asarray(tao, dtype=numpy.int32)
ao_loc = moleintor.make_loc(bas, 'spinor')
fdrv = getattr(libao2mo, 'AO2MOr_e1_drv')
fill = _fpointer('AO2MOfill_r_' + aosym)
ftrans = _fpointer('AO2MOtranse1_r_' + aosym)
fdrv(cintor, fill, ftrans, fmmm, out.ctypes.data_as(ctypes.c_void_p),
mo_coeff.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(klsh0),
ctypes.c_int(klsh1 - klsh0), ctypes.c_int(nkl), ctypes.c_int(comp),
(ctypes.c_int * 4)(*orbs_slice), tao.ctypes.data_as(ctypes.c_void_p),
ao_loc.ctypes.data_as(ctypes.c_void_p), cintopt, cao2mopt,
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))
return out
def wrap_int3c(cell,
auxcell,
intor='int3c2e',
aosym='s1',
comp=1,
kptij_lst=numpy.zeros((1, 2, 3)),
cintopt=None,
pbcopt=None):
intor = cell._add_suffix(intor)
pcell = copy.copy(cell)
pcell._atm, pcell._bas, pcell._env = \
atm, bas, env = gto.conc_env(cell._atm, cell._bas, cell._env,
cell._atm, cell._bas, cell._env)
ao_loc = gto.moleintor.make_loc(bas, intor)
aux_loc = auxcell.ao_loc_nr(auxcell.cart or 'ssc' in intor)
ao_loc = numpy.asarray(numpy.hstack([ao_loc, ao_loc[-1] + aux_loc[1:]]),
dtype=numpy.int32)
atm, bas, env = gto.conc_env(atm, bas, env, auxcell._atm, auxcell._bas,
auxcell._env)
Ls = cell.get_lattice_Ls()
nimgs = len(Ls)
kpti = kptij_lst[:, 0]
kptj = kptij_lst[:, 1]
if gamma_point(kptij_lst):
kk_type = 'g'
dtype = numpy.double
nkpts = nkptij = 1
kptij_idx = numpy.array([0], dtype=numpy.int32)
expkL = numpy.ones(1)
elif is_zero(kpti - kptj): # j_only
kk_type = 'k'
dtype = numpy.complex128
kpts = kptij_idx = numpy.asarray(kpti, order='C')
expkL = numpy.exp(1j * numpy.dot(kpts, Ls.T))
nkpts = nkptij = len(kpts)
else:
kk_type = 'kk'
dtype = numpy.complex128
kpts = unique(numpy.vstack([kpti, kptj]))[0]
expkL = numpy.exp(1j * numpy.dot(kpts, Ls.T))
wherei = numpy.where(
abs(kpti.reshape(-1, 1, 3) - kpts).sum(axis=2) < KPT_DIFF_TOL)[1]
wherej = numpy.where(
abs(kptj.reshape(-1, 1, 3) - kpts).sum(axis=2) < KPT_DIFF_TOL)[1]
nkpts = len(kpts)
kptij_idx = numpy.asarray(wherei * nkpts + wherej, dtype=numpy.int32)
nkptij = len(kptij_lst)
fill = 'PBCnr3c_fill_%s%s' % (kk_type, aosym[:2])
drv = libpbc.PBCnr3c_drv
if cintopt is None:
cintopt = _vhf.make_cintopt(atm, bas, env, intor)
# Remove the precomputed pair data because the pair data corresponds to the
# integral of cell #0 while the lattice sum moves shls to all repeated images.
if intor[:3] != 'ECP':
libpbc.CINTdel_pairdata_optimizer(cintopt)
if pbcopt is None:
pbcopt = _pbcintor.PBCOpt(pcell).init_rcut_cond(pcell)
if isinstance(pbcopt, _pbcintor.PBCOpt):
cpbcopt = pbcopt._this
else:
cpbcopt = lib.c_null_ptr()
nbas = cell.nbas
def int3c(shls_slice, out):
shls_slice = (shls_slice[0], shls_slice[1], nbas + shls_slice[2],
nbas + shls_slice[3], nbas * 2 + shls_slice[4],
nbas * 2 + shls_slice[5])
drv(
getattr(libpbc, intor),
getattr(libpbc, fill),
out.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(nkptij),
ctypes.c_int(nkpts),
ctypes.c_int(comp),
ctypes.c_int(nimgs),
Ls.ctypes.data_as(ctypes.c_void_p),
expkL.ctypes.data_as(ctypes.c_void_p),
kptij_idx.ctypes.data_as(ctypes.c_void_p),
(ctypes.c_int * 6)(*shls_slice),
ao_loc.ctypes.data_as(ctypes.c_void_p),
cintopt,
cpbcopt,
atm.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(cell.natm),
bas.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(nbas), # need to pass cell.nbas to libpbc.PBCnr3c_drv
env.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(env.size))
return out
return int3c
def nr_e1fill(intor,
sh_range,
atm,
bas,
env,
aosym='s1',
comp=1,
ao2mopt=None,
out=None):
assert (aosym in ('s4', 's2ij', 's2kl', 's1'))
c_atm = numpy.asarray(atm, dtype=numpy.int32, order='C')
c_bas = numpy.asarray(bas, dtype=numpy.int32, order='C')
c_env = numpy.asarray(env, order='C')
natm = ctypes.c_int(c_atm.shape[0])
nbas = ctypes.c_int(c_bas.shape[0])
klsh0, klsh1, nkl = sh_range
if '_cart' in intor:
libao2mo.CINTtot_cgto_cart.restype = ctypes.c_int
nao = libao2mo.CINTtot_cgto_cart(c_bas.ctypes.data_as(ctypes.c_void_p),
nbas)
cgto_in_shell = _fpointer('CINTcgto_cart')
elif '_sph' in intor:
libao2mo.CINTtot_cgto_spheric.restype = ctypes.c_int
nao = libao2mo.CINTtot_cgto_spheric(
c_bas.ctypes.data_as(ctypes.c_void_p), nbas)
cgto_in_shell = _fpointer('CINTcgto_spheric')
else:
raise NotImplementedError('cint2e spinor AO integrals')
if aosym in ('s4', 's2ij'):
nao_pair = nao * (nao + 1) // 2
else:
nao_pair = nao * nao
if out is None:
out = numpy.empty((comp, nkl, nao_pair))
else:
out = numpy.ndarray((comp, nkl, nao_pair), buffer=out)
if out.size == 0:
return out
if ao2mopt is not None:
cao2mopt = ao2mopt._this
cintopt = ao2mopt._cintopt
cintor = ao2mopt._intor
else:
cao2mopt = pyscf.lib.c_null_ptr()
cintor = _fpointer(intor)
cintopt = _vhf.make_cintopt(c_atm, c_bas, c_env, intor)
fdrv = getattr(libao2mo, 'AO2MOnr_e1fill_drv')
fill = _fpointer('AO2MOfill_nr_' + aosym)
fdrv(cintor, cgto_in_shell, fill, out.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(klsh0), ctypes.c_int(klsh1 - klsh0), ctypes.c_int(nkl),
ctypes.c_int(comp), cintopt, cao2mopt,
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))
return out
