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)
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)
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)
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 = lib.c_null_ptr()
pbcopt = _pbcintor.PBCOpt(pcell).init_rcut_cond(pcell, 1e-9)
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,
lib.c_null_ptr(), 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),
ctypes.c_int(env.size))
return out
def __init__(self, mol, intor=None,
prescreen='CVHFnoscreen', qcondname=None, dmcondname=None):
'''If function "qcondname" is presented, the qcond (sqrt(integrals))
and will be initialized in __init__.
prescreen, qcondname, dmcondname can be either function pointers or
names of C functions defined in libcvhf module
'''
self._this = ctypes.POINTER(_CVHFOpt)()
#print self._this.contents, expect ValueError: NULL pointer access
if intor is None:
self._intor = intor
self._cintopt = lib.c_null_ptr()
else:
self._intor = mol._add_suffix(intor)
self._cintopt = make_cintopt(mol._atm, mol._bas, mol._env, intor)
self._dmcondname = dmcondname
natm = ctypes.c_int(mol.natm)
nbas = ctypes.c_int(mol.nbas)
libcvhf.CVHFinit_optimizer(ctypes.byref(self._this),
mol._atm.ctypes.data_as(ctypes.c_void_p), natm,
mol._bas.ctypes.data_as(ctypes.c_void_p), nbas,
mol._env.ctypes.data_as(ctypes.c_void_p))
self.prescreen = prescreen
if qcondname is not None and intor is not None:
self.init_cvhf_direct(mol, intor, qcondname)
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
def run(intor, comp=1, suffix='_sph', thr=1e-7):
if suffix == '_spinor':
intor = intor = 'c%s'%intor
else:
intor = intor = 'c%s%s'%(intor,suffix)
print intor
fn1 = getattr(_cint3, intor)
fn2 = getattr(_cint2, intor)
cintopt = make_cintopt(mol._atm, mol._bas, mol._env, intor)
args = (mol._atm.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(mol.natm),
mol._bas.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(mol.nbas),
mol._env.ctypes.data_as(ctypes.c_void_p), cintopt)
for i in range(mol.nbas):
for j in range(mol.nbas):
for k in range(mol.nbas):
for l in range(mol.nbas):
ref = mol.intor_by_shell(intor, [i,j,k,l], comp=comp)
#fn2(ref.ctypes.data_as(ctypes.c_void_p),
# (ctypes.c_int*4)(i,j,k,l),
# mol._atm.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(mol.natm),
# mol._bas.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(mol.nbas),
# mol._env.ctypes.data_as(ctypes.c_void_p), lib.c_null_ptr())
buf = numpy.empty_like(ref)
fn1(buf.ctypes.data_as(ctypes.c_void_p),
(ctypes.c_int*4)(i,j,k,l),
mol._atm.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(mol.natm),
mol._bas.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(mol.nbas),
mol._env.ctypes.data_as(ctypes.c_void_p), lib.c_null_ptr())
if numpy.linalg.norm(ref-buf) > thr:
print intor, '| nopt', i, j, k, l, numpy.linalg.norm(ref-buf)#, ref, buf
#exit()
fn1(buf.ctypes.data_as(ctypes.c_void_p),
(ctypes.c_int*4)(i,j,k,l), *args)
if numpy.linalg.norm(ref-buf) > thr:
print intor, '|', i, j, k, l, numpy.linalg.norm(ref-buf)
def get_ovlp(mf, cell=None, kpts=None):
'''Get the overlap AO matrices at sampled k-points.
Args:
kpts : (nkpts, 3) ndarray
Returns:
ovlp_kpts : (nkpts, nao, nao) ndarray
'''
if cell is None: cell = mf.cell
if kpts is None: kpts = mf.kpts
# Avoid pbcopt's prescreening in the lattice sum, for better accuracy
s = cell.pbc_intor('int1e_ovlp',
hermi=1,
kpts=kpts,
pbcopt=lib.c_null_ptr())
cond = np.max(lib.cond(s))
if cond * cell.precision > 1e2:
prec = 1e2 / cond
rmin = max([cell.bas_rcut(ib, prec) for ib in range(cell.nbas)])
if cell.rcut < rmin:
logger.warn(
cell, 'Singularity detected in overlap matrix. '
'Integral accuracy may be not enough.\n '
'You can adjust cell.precision or cell.rcut to '
'improve accuracy. Recommended values are\n '
'cell.precision = %.2g or smaller.\n '
'cell.rcut = %.4g or larger.', prec, rmin)
return lib.asarray(s)
def type2_by_shell(mol, shls, cart=False):
li = mol.bas_angular(shls[0])
lj = mol.bas_angular(shls[1])
if cart:
fn = libecp.ECPtype2_cart
di = (li + 1) * (li + 2) // 2 * mol.bas_nctr(shls[0])
dj = (lj + 1) * (lj + 2) // 2 * mol.bas_nctr(shls[1])
else:
fn = libecp.ECPtype2_sph
di = (li * 2 + 1) * mol.bas_nctr(shls[0])
dj = (lj * 2 + 1) * mol.bas_nctr(shls[1])
cache_size = libecp.ECPscalar_cache_size(
ctypes.c_int(1), (ctypes.c_int * 2)(*shls),
mol._atm.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(mol.natm),
mol._bas.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(mol.nbas),
mol._env.ctypes.data_as(ctypes.c_void_p))
cache = numpy.empty(cache_size)
buf = numpy.empty((di, dj), order='F')
fn(buf.ctypes.data_as(ctypes.c_void_p), (ctypes.c_int * 2)(*shls),
mol._ecpbas.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(len(mol._ecpbas)),
mol._atm.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(mol.natm),
mol._bas.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(mol.nbas),
mol._env.ctypes.data_as(ctypes.c_void_p), lib.c_null_ptr(),
cache.ctypes.data_as(ctypes.c_void_p))
return buf
def get_ovlp(cell, kpt=np.zeros(3)):
'''Get the overlap AO matrix.
'''
# Avoid pbcopt's prescreening in the lattice sum, for better accuracy
s = cell.pbc_intor('int1e_ovlp',
hermi=0,
kpts=kpt,
pbcopt=lib.c_null_ptr())
s = lib.asarray(s)
hermi_error = abs(s - np.rollaxis(s.conj(), -1, -2)).max()
if hermi_error > cell.precision and hermi_error > 1e-12:
logger.warn(
cell, '%.4g error found in overlap integrals. '
'cell.precision or cell.rcut can be adjusted to '
'improve accuracy.')
cond = np.max(lib.cond(s))
if cond * cell.precision > 1e2:
prec = 1e2 / cond
rmin = max([cell.bas_rcut(ib, prec) for ib in range(cell.nbas)])
if cell.rcut < rmin:
logger.warn(
cell, 'Singularity detected in overlap matrix. '
'Integral accuracy may be not enough.\n '
'You can adjust cell.precision or cell.rcut to '
'improve accuracy. Recommended values are\n '
'cell.precision = %.2g or smaller.\n '
'cell.rcut = %.4g or larger.', prec, rmin)
return s
def _get_jk(_rdm1, _eri):
j = np.zeros((nphys * (nphys + 1) // 2), dtype=types.float64)
k = np.zeros((nphys, nphys), dtype=types.float64)
_rdm1_tril = lib.pack_tril(_rdm1 + np.tril(_rdm1, k=-1))
c_int = ctypes.c_int
args = (c_int(nphys), (c_int * 4)(0, nphys, 0, nphys),
lib.c_null_ptr(), c_int(0))
buf = np.empty((2, maxblk, nphys, nphys))
for p0 in range(0, naux, maxblk):
s = slice(p0, min(p0 + maxblk, naux))
eri1 = _eri[s]
naux_block = eri1.shape[0]
rho = np.dot(eri1, _rdm1_tril)
j += np.dot(rho, eri1)
buf1 = buf[0, :naux_block]
_fdrv(to_ptr(buf1), to_ptr(eri1), to_ptr(_rdm1),
c_int(naux_block), *args)
buf2 = lib.unpack_tril(eri1, out=buf[1])
k = util.dgemm(buf1.reshape((-1, nphys)).T,
buf2.reshape((-1, nphys)),
c=k,
beta=1)
j = lib.unpack_tril(j).reshape(_rdm1.shape)
k = k.reshape(_rdm1.shape)
return j, k
def get_A_mat(self):
'''
Construct the projection matrix: A_{m,n}^{\mathbf{k}}
Equation (62) in MV, Phys. Rev. B 56, 12847 or equation (22) in SMV, Phys. Rev. B 65, 035109
'''
A_matrix_loc = np.empty(
[self.num_kpts_loc, self.num_wann_loc, self.num_bands_loc],
dtype=np.complex128)
if self.use_bloch_phases == True:
Amn = np.zeros([self.num_wann_loc, self.num_bands_loc])
np.fill_diagonal(Amn, 1)
A_matrix_loc[:, :, :] = Amn
else:
from pyscf.dft import numint, gen_grid
grids = gen_grid.Grids(self.cell).build()
coords = grids.coords
weights = grids.weights
for ith_wann in range(self.num_wann_loc):
frac_site = self.proj_site[ith_wann]
abs_site = frac_site.dot(self.real_lattice_loc) / param.BOHR
l = self.proj_l[ith_wann]
mr = self.proj_m[ith_wann]
r = self.proj_radial[ith_wann]
zona = self.proj_zona[ith_wann]
x_axis = self.proj_x[ith_wann]
z_axis = self.proj_z[ith_wann]
gr = g_r(coords,
abs_site,
l,
mr,
r,
zona,
x_axis,
z_axis,
unit='B')
ao_L0 = numint.eval_ao(self.cell, coords)
s_aoL0_g = np.einsum('i,i,iv->v',
weights,
gr,
ao_L0,
optimize=True)
for k_id in range(self.num_kpts_loc):
kpt = self.cell.get_abs_kpts(self.kpt_latt_loc[k_id])
mo_included = self.mo_coeff_kpts[k_id][:, self.
band_included_list]
s_kpt = self.cell.pbc_intor('int1e_ovlp',
hermi=1,
kpts=kpt,
pbcopt=lib.c_null_ptr())
s_ao = np.einsum('uv,v->u', s_kpt, s_aoL0_g, optimize=True)
A_matrix_loc[k_id, ith_wann, :] = np.einsum(
'v,vu,um->m',
s_aoL0_g,
s_kpt,
mo_included,
optimize=True).conj()
return A_matrix_loc
def run2c(intor, fill, kpts, shls_slice=None):
nkpts = len(kpts)
atm, bas, env = gto.conc_env(cell._atm, cell._bas, cell._env, cell._atm,
cell._bas, cell._env)
if shls_slice is None:
shls_slice = (0, cell.nbas, cell.nbas, cell.nbas * 2)
ao_loc = gto.moleintor.make_loc(bas, intor)
ni = ao_loc[shls_slice[1]] - ao_loc[shls_slice[0]]
nj = ao_loc[shls_slice[3]] - ao_loc[shls_slice[2]]
comp = 1
out = numpy.empty((nkpts, comp, ni, nj), dtype=numpy.complex128)
fintor = getattr(gto.moleintor.libcgto, intor)
fill = getattr(libpbc, fill)
intopt = lib.c_null_ptr()
Ls = cell.get_lattice_Ls()
expkL = numpy.asarray(numpy.exp(1j * numpy.dot(kpts, Ls.T)), order='C')
drv = libpbc.PBCnr2c_drv
drv(fintor, fill, out.ctypes.data_as(ctypes.c_void_p), 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),
(ctypes.c_int * 4)(*(shls_slice[:4])),
ao_loc.ctypes.data_as(ctypes.c_void_p), intopt,
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 run2c(intor, fill, kpts, shls_slice=None):
nkpts = len(kpts)
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)
if shls_slice is None:
shls_slice = (0, cell.nbas, cell.nbas, cell.nbas*2)
ao_loc = gto.moleintor.make_loc(bas, intor)
ni = ao_loc[shls_slice[1]] - ao_loc[shls_slice[0]]
nj = ao_loc[shls_slice[3]] - ao_loc[shls_slice[2]]
comp = 1
out = numpy.empty((nkpts,comp,ni,nj), dtype=numpy.complex128)
fintor = getattr(gto.moleintor.libcgto, intor)
fill = getattr(libpbc, fill)
intopt = lib.c_null_ptr()
pbcopt = _pbcintor.PBCOpt(pcell).init_rcut_cond(pcell, 1e-9)
expkL = numpy.asarray(numpy.exp(1j*numpy.dot(kpts, Ls.T)), order='C')
drv = libpbc.PBCnr2c_drv
drv(fintor, fill, out.ctypes.data_as(ctypes.c_void_p),
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),
(ctypes.c_int*4)(*(shls_slice[:4])),
ao_loc.ctypes.data_as(ctypes.c_void_p), intopt, pbcopt._this,
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 ft_ao(mol,
Gv,
shls_slice=None,
b=numpy.eye(3),
gxyz=None,
Gvbase=None,
verbose=None):
''' FT transform AO
'''
if shls_slice is None:
shls_slice = (0, mol.nbas)
nGv = Gv.shape[0]
if (gxyz is None or b is None or Gvbase is None
# backward compatibility for pyscf-1.2, in which the argument Gvbase is gs
or (Gvbase is not None and isinstance(Gvbase[0],
(int, numpy.integer)))):
GvT = numpy.asarray(Gv.T, order='C')
p_gxyzT = lib.c_null_ptr()
p_gs = (ctypes.c_int * 3)(0, 0, 0)
p_b = (ctypes.c_double * 1)(0)
eval_gz = 'GTO_Gv_general'
else:
if abs(b - numpy.diag(b.diagonal())).sum() < 1e-8:
eval_gz = 'GTO_Gv_orth'
else:
eval_gz = 'GTO_Gv_nonorth'
GvT = numpy.asarray(Gv.T, order='C')
gxyzT = numpy.asarray(gxyz.T, order='C', dtype=numpy.int32)
p_gxyzT = gxyzT.ctypes.data_as(ctypes.c_void_p)
b = numpy.hstack((b.ravel(), numpy.zeros(3)) + Gvbase)
p_b = b.ctypes.data_as(ctypes.c_void_p)
p_gs = (ctypes.c_int * 3)(*[len(x) for x in Gvbase])
fn = libcgto.GTO_ft_ovlp_mat
intor = getattr(libcgto, 'GTO_ft_ovlp_sph')
eval_gz = getattr(libcgto, eval_gz)
fill = getattr(libcgto, 'GTO_ft_fill_s1')
ghost_atm = numpy.array([[0, 0, 0, 0, 0, 0]], dtype=numpy.int32)
ghost_bas = numpy.array([[0, 0, 1, 1, 0, 0, 3, 0]], dtype=numpy.int32)
ghost_env = numpy.zeros(4)
ghost_env[3] = numpy.sqrt(4 * numpy.pi) # s function spherical norm
atm, bas, env = gto.conc_env(mol._atm, mol._bas, mol._env, ghost_atm,
ghost_bas, ghost_env)
ao_loc = mol.ao_loc_nr()
nao = ao_loc[mol.nbas]
ao_loc = numpy.asarray(numpy.hstack((ao_loc, [nao + 1])),
dtype=numpy.int32)
ni = ao_loc[shls_slice[1]] - ao_loc[shls_slice[0]]
mat = numpy.zeros((nGv, ni), order='F', dtype=numpy.complex)
shls_slice = shls_slice + (mol.nbas, mol.nbas + 1)
fn(intor, eval_gz, fill,
mat.ctypes.data_as(ctypes.c_void_p), (ctypes.c_int * 4)(*shls_slice),
ao_loc.ctypes.data_as(ctypes.c_void_p), ctypes.c_double(0),
GvT.ctypes.data_as(ctypes.c_void_p), p_b, p_gxyzT, p_gs,
ctypes.c_int(nGv), atm.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(len(atm)), bas.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(len(bas)), env.ctypes.data_as(ctypes.c_void_p))
return mat
def int_ket(_bas, intor):
if len(_bas) == 0:
return []
intor = cell._add_suffix(intor)
atm, bas, env = gto.conc_env(cell._atm, cell._bas, cell._env,
fakecell._atm, _bas, fakecell._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)
shls_slice = (cell.nbas, nbas, 0, cell.nbas)
ao_loc = gto.moleintor.make_loc(bas, intor)
ni = ao_loc[shls_slice[1]] - ao_loc[shls_slice[0]]
nj = ao_loc[shls_slice[3]] - ao_loc[shls_slice[2]]
out = numpy.empty((nkpts, ni, nj), dtype=numpy.complex128)
comp = 1
fintor = getattr(gto.moleintor.libcgto, intor)
drv = libpbc.PBCnr2c_drv
drv(fintor, fill, out.ctypes.data_as(ctypes.c_void_p),
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),
(ctypes.c_int * 4)(*(shls_slice[:4])),
ao_loc.ctypes.data_as(ctypes.c_void_p), intopt, lib.c_null_ptr(),
atm.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(natm),
bas.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(nbas),
env.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(env.size))
return out
def int_ket(_bas, intor):
if len(_bas) == 0:
return []
intor = cell._add_suffix(intor)
atm, bas, env = gto.conc_env(cell._atm, cell._bas, cell._env,
fakecell._atm, _bas, fakecell._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)
shls_slice = (cell.nbas, nbas, 0, cell.nbas)
ao_loc = gto.moleintor.make_loc(bas, intor)
ni = ao_loc[shls_slice[1]] - ao_loc[shls_slice[0]]
nj = ao_loc[shls_slice[3]] - ao_loc[shls_slice[2]]
out = numpy.empty((nkpts,ni,nj), dtype=numpy.complex128)
comp = 1
fintor = getattr(gto.moleintor.libcgto, intor)
drv = libpbc.PBCnr2c_drv
drv(fintor, fill, out.ctypes.data_as(ctypes.c_void_p),
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),
(ctypes.c_int*4)(*(shls_slice[:4])),
ao_loc.ctypes.data_as(ctypes.c_void_p), intopt, lib.c_null_ptr(),
atm.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(natm),
bas.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(nbas),
env.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(env.size))
return out
def run(intor, comp=1, suffix='_sph', thr=1e-9):
if suffix == '_spinor':
intor = intor = 'c%s' % intor
else:
intor = intor = 'c%s%s' % (intor, suffix)
print intor
fn1 = getattr(_cint3, intor)
#fn2 = getattr(_cint2, intor)
#cintopt = make_cintopt(mol._atm, mol._bas, mol._env, intor)
cintopt = lib.c_null_ptr()
args = (mol._atm.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(mol.natm),
mol._bas.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(mol.nbas),
mol._env.ctypes.data_as(ctypes.c_void_p), cintopt)
for i in range(mol.nbas):
for j in range(mol.nbas):
ref = mol.intor_by_shell(intor, [i, j], comp=comp)
#fn2(ref.ctypes.data_as(ctypes.c_void_p),
# (ctypes.c_int*2)(i,j),
# mol._atm.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(mol.natm),
# mol._bas.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(mol.nbas),
# mol._env.ctypes.data_as(ctypes.c_void_p), lib.c_null_ptr())
buf = numpy.empty_like(ref)
fn1(buf.ctypes.data_as(ctypes.c_void_p), (ctypes.c_int * 2)(i, j),
mol._atm.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(mol.natm),
mol._bas.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(mol.nbas),
mol._env.ctypes.data_as(ctypes.c_void_p))
if numpy.linalg.norm(ref - buf) > thr:
print intor, '| nopt', i, j, numpy.linalg.norm(
ref - buf) #, ref, buf
exit()
def gen_type1(shls):
di = (mol.bas_angular(shls[0]) * 2 + 1) * mol.bas_nctr(shls[0])
dj = (mol.bas_angular(shls[1]) * 2 + 1) * mol.bas_nctr(shls[1])
mat0 = numpy.zeros((di, dj))
for ia in range(mol.natm):
ecpbas = mol._ecpbas[mol._ecpbas[:, ATOM_OF] == ia]
if len(ecpbas) == 0:
continue
ecpbas0 = ecpbas[ecpbas[:, ANG_OF] < 0]
if len(ecpbas0) == 0:
continue
mat0 += type1_by_shell(mol, shls, ia, ecpbas0)
mat1 = numpy.empty(mat0.shape, order='F')
cache = numpy.empty(100000)
libecp.ECPtype1_sph(mat1.ctypes.data_as(ctypes.c_void_p),
(ctypes.c_int * 2)(*shls),
mol._ecpbas.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(len(mol._ecpbas)),
mol._atm.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(mol.natm),
mol._bas.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(mol.nbas),
mol._env.ctypes.data_as(ctypes.c_void_p),
lib.c_null_ptr(),
cache.ctypes.data_as(ctypes.c_void_p))
if not numpy.allclose(mat0, mat1, atol=1e-8):
print(i, j, numpy.linalg.norm(mat0 - mat1))
self.assertTrue(numpy.allclose(mat0, mat1, atol=1e-6))
mat2 = gto.ecp.type1_by_shell(mol, shls)
self.assertTrue(numpy.allclose(mat0, mat2, atol=1e-6))
def gen_type1(shls):
di = (mol.bas_angular(shls[0])*2+1) * mol.bas_nctr(shls[0])
dj = (mol.bas_angular(shls[1])*2+1) * mol.bas_nctr(shls[1])
mat0 = numpy.zeros((di,dj))
for ia in range(mol.natm):
ecpbas = mol._ecpbas[mol._ecpbas[:,ATOM_OF] == ia]
if len(ecpbas) == 0:
continue
ecpbas0 = ecpbas[ecpbas[:,ANG_OF] < 0]
if len(ecpbas0) == 0:
continue
mat0 += type1_by_shell(mol, shls, ia, ecpbas0)
mat1 = numpy.empty(mat0.shape, order='F')
cache = numpy.empty(100000)
libecp.ECPtype1_sph(mat1.ctypes.data_as(ctypes.c_void_p),
(ctypes.c_int*2)(*shls),
mol._ecpbas.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(len(mol._ecpbas)),
mol._atm.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(mol.natm),
mol._bas.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(mol.nbas),
mol._env.ctypes.data_as(ctypes.c_void_p),
lib.c_null_ptr(), cache.ctypes.data_as(ctypes.c_void_p))
if not numpy.allclose(mat0, mat1, atol=1e-8):
print(i, j, numpy.linalg.norm(mat0-mat1))
self.assertTrue(numpy.allclose(mat0, mat1, atol=1e-6))
mat2 = gto.ecp.type1_by_shell(mol, shls)
self.assertTrue(numpy.allclose(mat0, mat2, atol=1e-6))
def ft_aopair(mol, Gv, shls_slice=None, aosym='s1', b=numpy.eye(3),
gxyz=None, Gvbase=None, buf=None, verbose=None):
r''' FT transform AO pair
\int i(r) j(r) exp(-ikr) dr^3
'''
if shls_slice is None:
shls_slice = (0, mol.nbas, 0, mol.nbas)
nGv = Gv.shape[0]
if (gxyz is None or b is None or Gvbase is None
# backward compatibility for pyscf-1.2, in which the argument Gvbase is gs
or (Gvbase is not None and isinstance(Gvbase[0], (int, numpy.integer)))):
GvT = numpy.asarray(Gv.T, order='C')
p_gxyzT = lib.c_null_ptr()
p_gs = (ctypes.c_int*3)(0,0,0)
p_b = (ctypes.c_double*1)(0)
eval_gz = 'GTO_Gv_general'
else:
if abs(b-numpy.diag(b.diagonal())).sum() < 1e-8:
eval_gz = 'GTO_Gv_orth'
else:
eval_gz = 'GTO_Gv_nonorth'
GvT = numpy.asarray(Gv.T, order='C')
gxyzT = numpy.asarray(gxyz.T, order='C', dtype=numpy.int32)
p_gxyzT = gxyzT.ctypes.data_as(ctypes.c_void_p)
b = numpy.hstack((b.ravel(), numpy.zeros(3)) + Gvbase)
p_b = b.ctypes.data_as(ctypes.c_void_p)
p_gs = (ctypes.c_int*3)(*[len(x) for x in Gvbase])
fn = libcgto.GTO_ft_ovlp_mat
intor = getattr(libcgto, 'GTO_ft_ovlp_sph')
eval_gz = getattr(libcgto, eval_gz)
ao_loc = numpy.asarray(mol.ao_loc_nr(), dtype=numpy.int32)
ni = ao_loc[shls_slice[1]] - ao_loc[shls_slice[0]]
nj = ao_loc[shls_slice[3]] - ao_loc[shls_slice[2]]
if aosym == 's1':
if shls_slice[:2] == shls_slice[2:4]:
fill = getattr(libcgto, 'GTO_ft_fill_s1hermi')
else:
fill = getattr(libcgto, 'GTO_ft_fill_s1')
shape = (nGv,ni,nj)
else:
fill = getattr(libcgto, 'GTO_ft_fill_s2')
i0 = ao_loc[shls_slice[0]]
i1 = ao_loc[shls_slice[1]]
nij = i1*(i1+1)//2 - i0*(i0+1)//2
shape = (nGv,nij)
mat = numpy.ndarray(shape, order='F', dtype=numpy.complex128, buffer=buf)
fn(intor, eval_gz, fill, mat.ctypes.data_as(ctypes.c_void_p),
(ctypes.c_int*4)(*shls_slice),
ao_loc.ctypes.data_as(ctypes.c_void_p), ctypes.c_double(0),
GvT.ctypes.data_as(ctypes.c_void_p),
p_b, p_gxyzT, p_gs, ctypes.c_int(nGv),
mol._atm.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(mol.natm),
mol._bas.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(mol.nbas),
mol._env.ctypes.data_as(ctypes.c_void_p))
return mat
def fill_2c2e(cell, auxcell, intor='int2c2e', hermi=0, kpt=numpy.zeros(3)):
'''2-center 2-electron AO integrals (L|ij), where L is the auxiliary basis.
'''
if hermi != 0:
hermi = pyscf.lib.HERMITIAN
# pbcopt use the value of AO-pair to prescreening PBC integrals in the lattice
# summation. Pass NULL pointer to pbcopt to prevent the prescreening
return auxcell.pbc_intor(intor, 1, hermi, kpt, pbcopt=lib.c_null_ptr())
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'))
intor = ascint3(intor)
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 = make_cintopt(c_atm, c_bas, c_env, intor)
tao = numpy.asarray(tao, dtype=numpy.int32)
ao_loc = 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 ft_ao(mol, Gv, shls_slice=None, b=numpy.eye(3),
gxyz=None, Gvbase=None, verbose=None):
''' FT transform AO
'''
if shls_slice is None:
shls_slice = (0, mol.nbas)
nGv = Gv.shape[0]
if (gxyz is None or b is None or Gvbase is None
# backward compatibility for pyscf-1.2, in which the argument Gvbase is gs
or (Gvbase is not None and isinstance(Gvbase[0], (int, numpy.integer)))):
GvT = numpy.asarray(Gv.T, order='C')
p_gxyzT = lib.c_null_ptr()
p_gs = (ctypes.c_int*3)(0,0,0)
p_b = (ctypes.c_double*1)(0)
eval_gz = 'GTO_Gv_general'
else:
if abs(b-numpy.diag(b.diagonal())).sum() < 1e-8:
eval_gz = 'GTO_Gv_orth'
else:
eval_gz = 'GTO_Gv_nonorth'
GvT = numpy.asarray(Gv.T, order='C')
gxyzT = numpy.asarray(gxyz.T, order='C', dtype=numpy.int32)
p_gxyzT = gxyzT.ctypes.data_as(ctypes.c_void_p)
b = numpy.hstack((b.ravel(), numpy.zeros(3)) + Gvbase)
p_b = b.ctypes.data_as(ctypes.c_void_p)
p_gs = (ctypes.c_int*3)(*[len(x) for x in Gvbase])
fn = libcgto.GTO_ft_fill_drv
if mol.cart:
intor = getattr(libcgto, 'GTO_ft_ovlp_cart')
else:
intor = getattr(libcgto, 'GTO_ft_ovlp_sph')
eval_gz = getattr(libcgto, eval_gz)
fill = getattr(libcgto, 'GTO_ft_fill_s1')
ghost_atm = numpy.array([[0,0,0,0,0,0]], dtype=numpy.int32)
ghost_bas = numpy.array([[0,0,1,1,0,0,3,0]], dtype=numpy.int32)
ghost_env = numpy.zeros(4)
ghost_env[3] = numpy.sqrt(4*numpy.pi) # s function spherical norm
atm, bas, env = gto.conc_env(mol._atm, mol._bas, mol._env,
ghost_atm, ghost_bas, ghost_env)
ao_loc = mol.ao_loc_nr()
nao = ao_loc[mol.nbas]
ao_loc = numpy.asarray(numpy.hstack((ao_loc, [nao+1])), dtype=numpy.int32)
ni = ao_loc[shls_slice[1]] - ao_loc[shls_slice[0]]
mat = numpy.zeros((nGv,ni), order='F', dtype=numpy.complex)
shls_slice = shls_slice + (mol.nbas, mol.nbas+1)
fn(intor, eval_gz, fill, mat.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(1), (ctypes.c_int*4)(*shls_slice),
ao_loc.ctypes.data_as(ctypes.c_void_p),
ctypes.c_double(0),
GvT.ctypes.data_as(ctypes.c_void_p),
p_b, p_gxyzT, p_gs, ctypes.c_int(nGv),
atm.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(len(atm)),
bas.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(len(bas)),
env.ctypes.data_as(ctypes.c_void_p))
return mat
def ft_ao(mol, Gv, shls_slice=None,
invh=None, gxyz=None, gs=None, verbose=None):
''' FT transform AO
'''
if shls_slice is None:
shls_slice = (0, mol.nbas)
nGv = Gv.shape[0]
if gxyz is None or invh is None or gs is None:
GvT = numpy.asarray(Gv.T, order='C')
p_gxyzT = lib.c_null_ptr()
p_gs = (ctypes.c_int*3)(0,0,0)
p_invh = (ctypes.c_double*1)(0)
eval_gz = 'GTO_Gv_general'
else:
GvT = numpy.asarray(Gv.T, order='C')
gxyzT = numpy.asarray(gxyz.T, order='C', dtype=numpy.int32)
p_gxyzT = gxyzT.ctypes.data_as(ctypes.c_void_p)
p_gs = (ctypes.c_int*3)(*gs)
# Guess what type of eval_gz to use
if isinstance(invh, numpy.ndarray) and invh.shape == (3,3):
p_invh = invh.ctypes.data_as(ctypes.c_void_p)
if numpy.allclose(invh-numpy.diag(invh.diagonal()), 0):
eval_gz = 'GTO_Gv_uniform_orth'
else:
eval_gz = 'GTO_Gv_uniform_nonorth'
else:
invh = numpy.hstack(invh)
p_invh = invh.ctypes.data_as(ctypes.c_void_p)
eval_gz = 'GTO_Gv_nonuniform_orth'
fn = libcgto.GTO_ft_ovlp_mat
intor = getattr(libcgto, 'GTO_ft_ovlp_sph')
eval_gz = getattr(libcgto, eval_gz)
fill = getattr(libcgto, 'GTO_ft_fill_s1')
ghost_atm = numpy.array([[0,0,0,0,0,0]], dtype=numpy.int32)
ghost_bas = numpy.array([[0,0,1,1,0,0,3,0]], dtype=numpy.int32)
ghost_env = numpy.zeros(4)
ghost_env[3] = numpy.sqrt(4*numpy.pi) # s function spheric norm
atm, bas, env = gto.conc_env(mol._atm, mol._bas, mol._env,
ghost_atm, ghost_bas, ghost_env)
ao_loc = mol.ao_loc_nr()
nao = ao_loc[mol.nbas]
ao_loc = numpy.asarray(numpy.hstack((ao_loc, [nao+1])), dtype=numpy.int32)
ni = ao_loc[shls_slice[1]] - ao_loc[shls_slice[0]]
mat = numpy.zeros((nGv,ni), order='F', dtype=numpy.complex)
shls_slice = shls_slice + (mol.nbas, mol.nbas+1)
fn(intor, eval_gz, fill, mat.ctypes.data_as(ctypes.c_void_p),
(ctypes.c_int*4)(*shls_slice),
ao_loc.ctypes.data_as(ctypes.c_void_p),
ctypes.c_double(0),
GvT.ctypes.data_as(ctypes.c_void_p),
p_invh, p_gxyzT, p_gs, ctypes.c_int(nGv),
atm.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(len(atm)),
bas.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(len(bas)),
env.ctypes.data_as(ctypes.c_void_p))
return mat
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 __init__(self, mol, intor,
prescreen='CVHFnoscreen', qcondname=None, dmcondname=None):
intor = mol._add_suffix(intor)
self._this = ctypes.POINTER(_CVHFOpt)()
#print self._this.contents, expect ValueError: NULL pointer access
self._intor = intor
self._cintopt = lib.c_null_ptr()
self._dmcondname = dmcondname
self.init_cvhf_direct(mol, intor, prescreen, qcondname)
def _int_vnl(cell, fakecell, hl_blocks, kpts):
'''Vnuc - Vloc'''
nimgs = numpy.max((cell.nimgs, fakecell.nimgs), axis=0)
Ls = numpy.asarray(cell.get_lattice_Ls(nimgs), order='C')
expLk = numpy.asarray(numpy.exp(1j * numpy.dot(Ls, kpts.T)), order='C')
nkpts = len(kpts)
xyz = numpy.asarray(cell.atom_coords(), order='C')
fill = getattr(libpbc, 'PBCnr2c_fill_s1')
intopt = lib.c_null_ptr()
def int_ket(_bas, intor):
if len(_bas) == 0:
return []
atm, bas, env = gto.conc_env(cell._atm, cell._bas, cell._env,
fakecell._atm, _bas, fakecell._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)
shls_slice = (cell.nbas, nbas, 0, cell.nbas)
ao_loc = gto.moleintor.make_loc(bas, intor)
ni = ao_loc[shls_slice[1]] - ao_loc[shls_slice[0]]
nj = ao_loc[shls_slice[3]] - ao_loc[shls_slice[2]]
out = [
numpy.zeros((ni, nj), order='F', dtype=numpy.complex128)
for k in range(nkpts)
]
out_ptrs = (ctypes.c_void_p *
nkpts)(*[x.ctypes.data_as(ctypes.c_void_p) for x in out])
comp = 1
fintor = getattr(gto.moleintor.libcgto, intor)
ptr_coords = numpy.asarray(atm[:cell.natm, gto.PTR_COORD],
dtype=numpy.int32,
order='C')
drv = libpbc.PBCnr2c_drv
drv(fintor, fill, out_ptrs, xyz.ctypes.data_as(ctypes.c_void_p),
ptr_coords.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(cell.natm), Ls.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(len(Ls)), expLk.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(nkpts), ctypes.c_int(comp),
(ctypes.c_int * 4)(*(shls_slice[:4])),
ao_loc.ctypes.data_as(ctypes.c_void_p), intopt,
atm.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(natm),
bas.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(nbas),
env.ctypes.data_as(ctypes.c_void_p))
return out
hl_dims = numpy.asarray([len(hl) for hl in hl_blocks])
out = (int_ket(fakecell._bas[hl_dims > 0], 'cint1e_ovlp_sph'),
int_ket(fakecell._bas[hl_dims > 1], 'cint1e_pbc_r2_origi_sph'),
int_ket(fakecell._bas[hl_dims > 2], 'cint1e_pbc_r4_origi_sph'))
return out
def ft_aopair(mol, Gv, shls_slice=None, aosym='s1', b=numpy.eye(3),
gxyz=None, Gvbase=None, buf=None, verbose=None):
''' FT transform AO pair
\int i(r) j(r) exp(-ikr) dr^3
'''
if shls_slice is None:
shls_slice = (0, mol.nbas, 0, mol.nbas)
nGv = Gv.shape[0]
if (gxyz is None or b is None or Gvbase is None
# backward compatibility for pyscf-1.2, in which the argument Gvbase is gs
or (Gvbase is not None and isinstance(Gvbase[0], (int, numpy.integer)))):
GvT = numpy.asarray(Gv.T, order='C')
p_gxyzT = lib.c_null_ptr()
p_gs = (ctypes.c_int*3)(0,0,0)
p_b = (ctypes.c_double*1)(0)
eval_gz = 'GTO_Gv_general'
else:
GvT = numpy.asarray(Gv.T, order='C')
gxyzT = numpy.asarray(gxyz.T, order='C', dtype=numpy.int32)
p_gxyzT = gxyzT.ctypes.data_as(ctypes.c_void_p)
b = numpy.hstack((b.ravel(), numpy.zeros(3)) + Gvbase)
p_b = b.ctypes.data_as(ctypes.c_void_p)
p_gs = (ctypes.c_int*3)(*[len(x) for x in Gvbase])
eval_gz = 'GTO_Gv_cubic'
fn = libcgto.GTO_ft_ovlp_mat
intor = getattr(libcgto, 'GTO_ft_ovlp_sph')
eval_gz = getattr(libcgto, eval_gz)
ao_loc = numpy.asarray(mol.ao_loc_nr(), dtype=numpy.int32)
ni = ao_loc[shls_slice[1]] - ao_loc[shls_slice[0]]
nj = ao_loc[shls_slice[3]] - ao_loc[shls_slice[2]]
if aosym == 's1':
if shls_slice[:2] == shls_slice[2:4]:
fill = getattr(libcgto, 'GTO_ft_fill_s1hermi')
else:
fill = getattr(libcgto, 'GTO_ft_fill_s1')
shape = (nGv,ni,nj)
else:
fill = getattr(libcgto, 'GTO_ft_fill_s2')
i0 = ao_loc[shls_slice[0]]
i1 = ao_loc[shls_slice[1]]
nij = i1*(i1+1)//2 - i0*(i0+1)//2
shape = (nGv,nij)
mat = numpy.ndarray(shape, order='F', dtype=numpy.complex128, buffer=buf)
fn(intor, eval_gz, fill, mat.ctypes.data_as(ctypes.c_void_p),
(ctypes.c_int*4)(*shls_slice),
ao_loc.ctypes.data_as(ctypes.c_void_p), ctypes.c_double(0),
GvT.ctypes.data_as(ctypes.c_void_p),
p_b, p_gxyzT, p_gs, ctypes.c_int(nGv),
mol._atm.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(mol.natm),
mol._bas.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(mol.nbas),
mol._env.ctypes.data_as(ctypes.c_void_p))
return mat
def make_cintopt(atm, bas, env, intor):
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 = c_atm.shape[0]
nbas = c_bas.shape[0]
cintopt = lib.c_null_ptr()
foptinit = getattr(_cint3, intor + '_optimizer')
foptinit(ctypes.byref(cintopt), c_atm.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(natm), c_bas.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(nbas), c_env.ctypes.data_as(ctypes.c_void_p))
return cintopt
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)
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)
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)
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 = lib.c_null_ptr()
pbcopt = _pbcintor.PBCOpt(pcell).init_rcut_cond(pcell, 1e-9)
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, pbcopt._this,
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 _int_vnl(cell, fakecell, hl_blocks, kpts):
'''Vnuc - Vloc'''
rcut = max(cell.rcut, fakecell.rcut)
Ls = cell.get_lattice_Ls(rcut=rcut)
expLk = numpy.asarray(numpy.exp(1j*numpy.dot(Ls, kpts.T)), order='C')
nkpts = len(kpts)
xyz = numpy.asarray(cell.atom_coords(), order='C')
fill = getattr(libpbc, 'PBCnr2c_fill_s1')
intopt = lib.c_null_ptr()
def int_ket(_bas, intor):
if len(_bas) == 0:
return []
atm, bas, env = gto.conc_env(cell._atm, cell._bas, cell._env,
fakecell._atm, _bas, fakecell._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)
shls_slice = (cell.nbas, nbas, 0, cell.nbas)
ao_loc = gto.moleintor.make_loc(bas, intor)
ni = ao_loc[shls_slice[1]] - ao_loc[shls_slice[0]]
nj = ao_loc[shls_slice[3]] - ao_loc[shls_slice[2]]
out = [numpy.zeros((ni,nj), order='F', dtype=numpy.complex128)
for k in range(nkpts)]
out_ptrs = (ctypes.c_void_p*nkpts)(
*[x.ctypes.data_as(ctypes.c_void_p) for x in out])
comp = 1
fintor = getattr(gto.moleintor.libcgto, intor)
ptr_coords = numpy.asarray(atm[:cell.natm,gto.PTR_COORD],
dtype=numpy.int32, order='C')
drv = libpbc.PBCnr2c_drv
drv(fintor, fill, out_ptrs, xyz.ctypes.data_as(ctypes.c_void_p),
ptr_coords.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(cell.natm),
Ls.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(len(Ls)),
expLk.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(nkpts),
ctypes.c_int(comp), (ctypes.c_int*4)(*(shls_slice[:4])),
ao_loc.ctypes.data_as(ctypes.c_void_p), intopt,
atm.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(natm),
bas.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(nbas),
env.ctypes.data_as(ctypes.c_void_p))
return out
hl_dims = numpy.asarray([len(hl) for hl in hl_blocks])
out = (int_ket(fakecell._bas[hl_dims>0], 'cint1e_ovlp_sph'),
int_ket(fakecell._bas[hl_dims>1], 'cint1e_pbc_r2_origi_sph'),
int_ket(fakecell._bas[hl_dims>2], 'cint1e_pbc_r4_origi_sph'))
return out
def make_cintopt(atm, bas, env, intor):
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 = c_atm.shape[0]
nbas = c_bas.shape[0]
cintopt = lib.c_null_ptr()
foptinit = getattr(_cint3, intor+'_optimizer')
foptinit(ctypes.byref(cintopt),
c_atm.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(natm),
c_bas.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(nbas),
c_env.ctypes.data_as(ctypes.c_void_p))
return cintopt
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 test_rad_part(self):
rs, ws = radi.gauss_chebyshev(99)
ur0 = rad_part(mol, mol._ecpbas, rs)
ur1 = numpy.empty_like(ur0)
libecp.ECPrad_part(ur1.ctypes.data_as(ctypes.c_void_p),
rs.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(0), ctypes.c_int(len(rs)), ctypes.c_int(1),
(ctypes.c_int*2)(0, len(mol._ecpbas)),
mol._ecpbas.ctypes.data_as(ctypes.c_void_p),
mol._atm.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(mol.natm),
mol._bas.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(mol.nbas),
mol._env.ctypes.data_as(ctypes.c_void_p),
lib.c_null_ptr())
self.assertTrue(numpy.allclose(ur0, ur1))
def make_cintopt(atm, bas, env, intor):
intor = intor.replace('_sph', '').replace('_cart',
'').replace('_spinor', '')
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 = c_atm.shape[0]
nbas = c_bas.shape[0]
cintopt = lib.c_null_ptr()
foptinit = getattr(libcgto, intor + '_optimizer')
foptinit(ctypes.byref(cintopt), c_atm.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(natm), c_bas.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(nbas), c_env.ctypes.data_as(ctypes.c_void_p))
return ctypes.cast(cintopt, _cintoptHandler)
def init_cvhf_direct(self, mol, intor, qcondname):
intor = mol._add_suffix(intor)
if intor == self._intor:
cintopt = self._cintopt
else:
cintopt = lib.c_null_ptr()
ao_loc = make_loc(mol._bas, intor)
fsetqcond = getattr(libcvhf, qcondname)
natm = ctypes.c_int(mol.natm)
nbas = ctypes.c_int(mol.nbas)
fsetqcond(self._this, getattr(libcvhf, intor), cintopt,
ao_loc.ctypes.data_as(ctypes.c_void_p),
mol._atm.ctypes.data_as(ctypes.c_void_p), natm,
mol._bas.ctypes.data_as(ctypes.c_void_p), nbas,
mol._env.ctypes.data_as(ctypes.c_void_p))
def _int_vnl(cell, fakecell, hl_blocks, kpts):
'''Vnuc - Vloc'''
rcut = max(cell.rcut, fakecell.rcut)
Ls = cell.get_lattice_Ls(rcut=rcut)
nimgs = len(Ls)
expkL = numpy.asarray(numpy.exp(1j * numpy.dot(kpts, Ls.T)), order='C')
nkpts = len(kpts)
fill = getattr(libpbc, 'PBCnr2c_fill_ks1')
intopt = lib.c_null_ptr()
def int_ket(_bas, intor):
if len(_bas) == 0:
return []
intor = cell._add_suffix(intor)
atm, bas, env = gto.conc_env(cell._atm, cell._bas, cell._env,
fakecell._atm, _bas, fakecell._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)
shls_slice = (cell.nbas, nbas, 0, cell.nbas)
ao_loc = gto.moleintor.make_loc(bas, intor)
ni = ao_loc[shls_slice[1]] - ao_loc[shls_slice[0]]
nj = ao_loc[shls_slice[3]] - ao_loc[shls_slice[2]]
out = numpy.empty((nkpts, ni, nj), dtype=numpy.complex128)
comp = 1
fintor = getattr(gto.moleintor.libcgto, intor)
drv = libpbc.PBCnr2c_drv
drv(fintor, fill, out.ctypes.data_as(ctypes.c_void_p),
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),
(ctypes.c_int * 4)(*(shls_slice[:4])),
ao_loc.ctypes.data_as(ctypes.c_void_p), intopt, lib.c_null_ptr(),
atm.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(natm),
bas.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(nbas),
env.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(env.size))
return out
hl_dims = numpy.asarray([len(hl) for hl in hl_blocks])
out = (int_ket(fakecell._bas[hl_dims > 0], 'int1e_ovlp'),
int_ket(fakecell._bas[hl_dims > 1], 'int1e_r2_origi'),
int_ket(fakecell._bas[hl_dims > 2], 'int1e_r4_origi'))
return out
def _int_vnl(cell, fakecell, hl_blocks, kpts):
'''Vnuc - Vloc'''
rcut = max(cell.rcut, fakecell.rcut)
Ls = cell.get_lattice_Ls(rcut=rcut)
nimgs = len(Ls)
expkL = numpy.asarray(numpy.exp(1j*numpy.dot(kpts, Ls.T)), order='C')
nkpts = len(kpts)
fill = getattr(libpbc, 'PBCnr2c_fill_ks1')
intopt = lib.c_null_ptr()
def int_ket(_bas, intor):
if len(_bas) == 0:
return []
intor = cell._add_suffix(intor)
atm, bas, env = gto.conc_env(cell._atm, cell._bas, cell._env,
fakecell._atm, _bas, fakecell._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)
shls_slice = (cell.nbas, nbas, 0, cell.nbas)
ao_loc = gto.moleintor.make_loc(bas, intor)
ni = ao_loc[shls_slice[1]] - ao_loc[shls_slice[0]]
nj = ao_loc[shls_slice[3]] - ao_loc[shls_slice[2]]
out = numpy.empty((nkpts,ni,nj), dtype=numpy.complex128)
comp = 1
fintor = getattr(gto.moleintor.libcgto, intor)
drv = libpbc.PBCnr2c_drv
drv(fintor, fill, out.ctypes.data_as(ctypes.c_void_p),
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),
(ctypes.c_int*4)(*(shls_slice[:4])),
ao_loc.ctypes.data_as(ctypes.c_void_p), intopt, lib.c_null_ptr(),
atm.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(natm),
bas.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(nbas),
env.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(env.size))
return out
hl_dims = numpy.asarray([len(hl) for hl in hl_blocks])
out = (int_ket(fakecell._bas[hl_dims>0], 'int1e_ovlp'),
int_ket(fakecell._bas[hl_dims>1], 'int1e_r2_origi'),
int_ket(fakecell._bas[hl_dims>2], 'int1e_r4_origi'))
return out
def test_rad_part(self):
rs, ws = radi.gauss_chebyshev(99)
ur0 = rad_part(mol, mol._ecpbas, rs)
ur1 = numpy.empty_like(ur0)
libecp.ECPrad_part(ur1.ctypes.data_as(ctypes.c_void_p),
rs.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(0),
ctypes.c_int(len(rs)), ctypes.c_int(1),
(ctypes.c_int * 2)(0, len(mol._ecpbas)),
mol._ecpbas.ctypes.data_as(ctypes.c_void_p),
mol._atm.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(mol.natm),
mol._bas.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(mol.nbas),
mol._env.ctypes.data_as(ctypes.c_void_p),
lib.c_null_ptr())
self.assertTrue(numpy.allclose(ur0, ur1))
def _dot_ao_mo(mol,
ao,
mo,
non0tab=None,
shls_slice=None,
ao_loc=None,
hermi=0):
if hermi:
#print ("_dot_ao_mo punting to numint._dot_ao_ao")
return numint._dot_ao_ao(mol,
ao,
mo,
non0tab=non0tab,
shls_slice=shls_slice,
ao_loc=ao_loc,
hermi=hermi)
ngrids, nao = ao.shape
nmo = mo.shape[-1]
if nao < SWITCH_SIZE:
#print ("_dot_ao_mo punting to lib.dot")
return lib.dot(ao.T.conj(), mo)
#print ("_dot_ao_mo doing my own thing")
if not ao.flags.f_contiguous:
ao = lib.transpose(ao)
if not mo.flags.f_contiguous:
mo = lib.transpose(mo)
if ao.dtype == mo.dtype == np.double:
fn = libpdft.VOTdot_ao_mo
else:
raise NotImplementedError("Complex-orbital PDFT")
if non0tab is None or shls_slice is None or ao_loc is None:
pnon0tab = pshls_slice = pao_loc = lib.c_null_ptr()
else:
pnon0tab = non0tab.ctypes.data_as(ctypes.c_void_p)
pshls_slice = (ctypes.c_int * 2)(*shls_slice)
pao_loc = ao_loc.ctypes.data_as(ctypes.c_void_p)
vv = np.empty((nao, nmo), dtype=ao.dtype)
fn(vv.ctypes.data_as(ctypes.c_void_p), ao.ctypes.data_as(ctypes.c_void_p),
mo.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(nao), ctypes.c_int(nmo), ctypes.c_int(ngrids),
ctypes.c_int(mol.nbas), pnon0tab, pshls_slice, pao_loc)
return vv
def get_fock(self, rdm1=None):
''' Returns the Fock matrix resulting from the current, or
provided, density.
'''
if rdm1 is None:
rdm1 = self.rdm1
nphys = self.nphys
naux = self.eri.shape[0]
maxblk = self.options['maxblk']
j = np.zeros((nphys * (nphys + 1) // 2), dtype=types.float64)
k = np.zeros((nphys, nphys), dtype=types.float64)
rdm1_tril = lib.pack_tril(rdm1 + np.tril(rdm1, k=-1))
c_int = ctypes.c_int
args = (c_int(nphys), (c_int * 4)(0, nphys, 0,
nphys), lib.c_null_ptr(), c_int(0))
buf = np.empty((2, maxblk, nphys, nphys))
for p0 in range(0, naux, maxblk):
s = slice(p0, min(p0 + maxblk, naux))
eri1 = self.eri[s]
naux_block = eri1.shape[0]
rho = np.dot(eri1, rdm1_tril)
j += np.dot(rho, eri1)
buf1 = buf[0, :naux_block]
_fdrv(to_ptr(buf1), to_ptr(eri1), to_ptr(rdm1), c_int(naux_block),
*args)
buf2 = lib.unpack_tril(eri1, out=buf[1])
k = util.dgemm(buf1.reshape((-1, nphys)).T,
buf2.reshape((-1, nphys)),
c=k,
beta=1)
j = lib.unpack_tril(j).reshape(rdm1.shape)
k = k.reshape(rdm1.shape)
f = self.h1e + j - 0.5 * k
return f
def get_ovlp(cell, kpt=np.zeros(3)):
'''Get the overlap AO matrix.
'''
# Avoid pbcopt's prescreening in the lattice sum, for better accuracy
s = cell.pbc_intor('int1e_ovlp', hermi=1, kpts=kpt,
pbcopt=lib.c_null_ptr())
cond = np.max(lib.cond(s))
if cond * cell.precision > 1e2:
prec = 1e2 / cond
rmin = max([cell.bas_rcut(ib, prec) for ib in range(cell.nbas)])
if cell.rcut < rmin:
logger.warn(cell, 'Singularity detected in overlap matrix. '
'Integral accuracy may be not enough.\n '
'You can adjust cell.precision or cell.rcut to '
'improve accuracy. Recommended values are\n '
'cell.precision = %.2g or smaller.\n '
'cell.rcut = %.4g or larger.', prec, rmin)
return s
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 so_by_shell(mol, shls):
'''Spin-orbit coupling ECP in spinor basis
i/2 <Pauli_matrix dot l U(r)>
'''
li = mol.bas_angular(shls[0])
lj = mol.bas_angular(shls[1])
di = (li * 4 + 2) * mol.bas_nctr(shls[0])
dj = (lj * 4 + 2) * mol.bas_nctr(shls[1])
bas = numpy.vstack((mol._bas, mol._ecpbas))
mol._env[AS_ECPBAS_OFFSET] = len(mol._bas)
mol._env[AS_NECPBAS] = len(mol._ecpbas)
buf = numpy.empty((di, dj), order='F', dtype=numpy.complex128)
cache = numpy.empty(buf.size * 48 + 100000)
fn = libecp.ECPso_spinor
fn(buf.ctypes.data_as(ctypes.c_void_p), (ctypes.c_int * 2)(di, dj),
(ctypes.c_int * 2)(*shls), mol._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), mol._env.ctypes.data_as(ctypes.c_void_p),
lib.c_null_ptr(), cache.ctypes.data_as(ctypes.c_void_p))
return buf
def get_fock(rdm1, h1e, eri, maxblk=DF_MAXBLK):
# Gets the Fock matrix (MO basis)
# Transforms to AO basis and then back to appease pyscf
nphys = rdm1.shape[-1]
naux = eri.shape[0]
j = np.zeros((nphys * (nphys + 1) // 2))
k = np.zeros((nphys, nphys))
rdm1tril = lib.pack_tril(rdm1 + np.tril(rdm1, k=-1))
rargs = (ctypes.c_int(nphys), (ctypes.c_int * 4)(0, nphys, 0, nphys),
lib.c_null_ptr(), ctypes.c_int(0))
buf = np.empty((2, maxblk, nphys, nphys))
for s in _get_df_blocks(eri, maxblk):
eri1 = eri[s]
naux_block = eri1.shape[0]
rho = dot(eri1, rdm1tril)
j += dot(rho, eri1)
buf1 = buf[0, :naux_block]
_fdrv(_ftrans, _fmmm, to_ptr(buf1), to_ptr(eri1), to_ptr(rdm1),
ctypes.c_int(naux_block), *rargs)
buf2 = lib.unpack_tril(eri1, out=buf[1])
k = dgemm(buf1.reshape(-1, nphys).T,
buf2.reshape(-1, nphys),
c=k,
beta=1)
j = mpi_reduce(j)
k = mpi_reduce(k)
j = lib.unpack_tril(j).reshape(rdm1.shape)
k = k.reshape(rdm1.shape)
f = h1e + j - 0.5 * k
return f
def init_cvhf_direct(self, mol, intor, qcondname):
'''qcondname can be the function pointer or the name of a C function
defined in libcvhf module
'''
intor = mol._add_suffix(intor)
if intor == self._intor:
cintopt = self._cintopt
else:
cintopt = lib.c_null_ptr()
ao_loc = make_loc(mol._bas, intor)
if isinstance(qcondname, ctypes._CFuncPtr):
fsetqcond = qcondname
else:
fsetqcond = getattr(libcvhf, qcondname)
natm = ctypes.c_int(mol.natm)
nbas = ctypes.c_int(mol.nbas)
fsetqcond(self._this, getattr(libcvhf, intor), cintopt,
ao_loc.ctypes.data_as(ctypes.c_void_p),
mol._atm.ctypes.data_as(ctypes.c_void_p), natm,
mol._bas.ctypes.data_as(ctypes.c_void_p), nbas,
mol._env.ctypes.data_as(ctypes.c_void_p))
def make_cintopt(atm, bas, env, intor):
intor = intor.replace('_sph', '').replace('_cart',
'').replace('_spinor', '')
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 = c_atm.shape[0]
nbas = c_bas.shape[0]
cintopt = lib.c_null_ptr()
# TODO: call specific ECP optimizers for each intor.
if intor[:3] == 'ECP':
foptinit = libcgto.ECPscalar_optimizer
foptinit(ctypes.byref(cintopt), c_atm.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(natm), c_bas.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(nbas), c_env.ctypes.data_as(ctypes.c_void_p))
return ctypes.cast(cintopt, _ecpoptHandler)
else:
foptinit = getattr(libcgto, intor + '_optimizer')
foptinit(ctypes.byref(cintopt), c_atm.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(natm), c_bas.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(nbas), c_env.ctypes.data_as(ctypes.c_void_p))
return ctypes.cast(cintopt, _cintoptHandler)
def make_cintopt(atm, bas, env, intor):
intor = intor.replace('_sph','').replace('_cart','').replace('_spinor','')
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 = c_atm.shape[0]
nbas = c_bas.shape[0]
cintopt = lib.c_null_ptr()
# TODO: call specific ECP optimizers for each intor.
if intor[:3] == 'ECP':
foptinit = libcgto.ECPscalar_optimizer
foptinit(ctypes.byref(cintopt),
c_atm.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(natm),
c_bas.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(nbas),
c_env.ctypes.data_as(ctypes.c_void_p))
return ctypes.cast(cintopt, _ecpoptHandler)
else:
foptinit = getattr(libcgto, intor+'_optimizer')
foptinit(ctypes.byref(cintopt),
c_atm.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(natm),
c_bas.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(nbas),
c_env.ctypes.data_as(ctypes.c_void_p))
return ctypes.cast(cintopt, _cintoptHandler)
def ft_aopair(mol, Gv, shls_slice=None, aosym='s1', b=numpy.eye(3),
gxyz=None, Gvbase=None, buf=None, intor='GTO_ft_ovlp',
comp=1, verbose=None):
r''' FT transform AO pair
\int i(r) j(r) exp(-ikr) dr^3
'''
intor = mol._add_suffix(intor)
if shls_slice is None:
shls_slice = (0, mol.nbas, 0, mol.nbas)
nGv = Gv.shape[0]
if (gxyz is None or b is None or Gvbase is None
# backward compatibility for pyscf-1.2, in which the argument Gvbase is gs
or (Gvbase is not None and isinstance(Gvbase[0], (int, numpy.integer)))):
GvT = numpy.asarray(Gv.T, order='C')
p_gxyzT = lib.c_null_ptr()
p_gs = (ctypes.c_int*3)(0,0,0)
p_b = (ctypes.c_double*1)(0)
eval_gz = 'GTO_Gv_general'
else:
if abs(b-numpy.diag(b.diagonal())).sum() < 1e-8:
eval_gz = 'GTO_Gv_orth'
else:
eval_gz = 'GTO_Gv_nonorth'
GvT = numpy.asarray(Gv.T, order='C')
gxyzT = numpy.asarray(gxyz.T, order='C', dtype=numpy.int32)
p_gxyzT = gxyzT.ctypes.data_as(ctypes.c_void_p)
b = numpy.hstack((b.ravel(), numpy.zeros(3)) + Gvbase)
p_b = b.ctypes.data_as(ctypes.c_void_p)
p_gs = (ctypes.c_int*3)(*[len(x) for x in Gvbase])
ao_loc = gto.moleintor.make_loc(mol._bas, intor)
ni = ao_loc[shls_slice[1]] - ao_loc[shls_slice[0]]
nj = ao_loc[shls_slice[3]] - ao_loc[shls_slice[2]]
if aosym == 's1':
if (shls_slice[:2] == shls_slice[2:4] and
intor.startswith('GTO_ft_ovlp')):
fill = getattr(libcgto, 'GTO_ft_fill_s1hermi')
else:
fill = getattr(libcgto, 'GTO_ft_fill_s1')
shape = (nGv,ni,nj,comp)
else:
fill = getattr(libcgto, 'GTO_ft_fill_s2')
i0 = ao_loc[shls_slice[0]]
i1 = ao_loc[shls_slice[1]]
nij = i1*(i1+1)//2 - i0*(i0+1)//2
shape = (nGv,nij,comp)
mat = numpy.ndarray(shape, order='F', dtype=numpy.complex128, buffer=buf)
fn = libcgto.GTO_ft_fill_drv
intor = getattr(libcgto, intor)
eval_gz = getattr(libcgto, eval_gz)
fn(intor, eval_gz, fill, mat.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(comp), (ctypes.c_int*4)(*shls_slice),
ao_loc.ctypes.data_as(ctypes.c_void_p), ctypes.c_double(0),
GvT.ctypes.data_as(ctypes.c_void_p),
p_b, p_gxyzT, p_gs, ctypes.c_int(nGv),
mol._atm.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(mol.natm),
mol._bas.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(mol.nbas),
mol._env.ctypes.data_as(ctypes.c_void_p))
mat = numpy.rollaxis(mat, -1, 0)
if comp == 1:
mat = mat[0]
return mat
def direct_bindm(intor, aosym, jkdescript,
dms, ncomp, atm, bas, env, vhfopt=None, cintopt=None,
shls_slice=None):
assert(aosym in ('s8', 's4', 's2ij', 's2kl', 's1',
'aa4', 'a4ij', 'a4kl', 'a2ij', 'a2kl'))
intor = ascint3(intor)
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(c_atm.shape[0])
nbas = ctypes.c_int(c_bas.shape[0])
if isinstance(dms, numpy.ndarray) and dms.ndim == 2:
dms = dms[numpy.newaxis,:,:]
n_dm = len(dms)
nao = dms[0].shape[0]
dms = [numpy.asarray(dm, order='C') for dm in dms]
if isinstance(jkdescript, str):
jkdescripts = (jkdescript,)
else:
jkdescripts = jkdescript
njk = len(jkdescripts)
assert(njk == n_dm)
if vhfopt is None:
cintor = _fpointer(intor)
cvhfopt = lib.c_null_ptr()
else:
vhfopt.set_dm(dms, atm, bas, env)
cvhfopt = vhfopt._this
cintopt = vhfopt._cintopt
cintor = getattr(libcvhf, vhfopt._intor)
if cintopt is None:
cintopt = make_cintopt(c_atm, c_bas, c_env, intor)
fdrv = getattr(libcvhf, 'CVHFnr_direct_drv')
dotsym = _INTSYMAP[aosym]
fdot = _fpointer('CVHFdot_nr'+dotsym)
if shls_slice is None:
shls_slice = (0, c_bas.shape[0])*4
ao_loc = make_loc(bas, intor)
vjk = []
descr_sym = [x.split('->') for x in jkdescripts]
fjk = (ctypes.c_void_p*(n_dm))()
dmsptr = (ctypes.c_void_p*(n_dm))()
vjkptr = (ctypes.c_void_p*(n_dm))()
for i, (dmsym, vsym) in enumerate(descr_sym):
f1 = _fpointer('CVHFnr%s_%s_%s'%(aosym, dmsym, vsym))
assert(dms[i].shape == get_dims(dmsym, shls_slice, ao_loc))
vshape = (ncomp,) + get_dims(vsym[-2:], shls_slice, ao_loc)
vjk.append(numpy.empty(vshape))
dmsptr[i] = dms[i].ctypes.data_as(ctypes.c_void_p)
vjkptr[i] = vjk[i].ctypes.data_as(ctypes.c_void_p)
fjk[i] = f1
shls_slice = (ctypes.c_int*8)(*shls_slice)
fdrv(cintor, fdot, fjk, dmsptr, vjkptr,
ctypes.c_int(n_dm), ctypes.c_int(ncomp),
shls_slice, ao_loc.ctypes.data_as(ctypes.c_void_p), cintopt, cvhfopt,
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))
if ncomp == 1:
vjk = [v.reshape(v.shape[1:]) for v in vjk]
if isinstance(jkdescript, str):
vjk = vjk[0]
return vjk
def gen_partition(mol, atom_grids_tab,
radii_adjust=None, atomic_radii=radi.BRAGG_RADII,
becke_scheme=original_becke):
'''Generate the mesh grid coordinates and weights for DFT numerical integration.
We can change radii_adjust, becke_scheme functions to generate different meshgrid.
Returns:
grid_coord and grid_weight arrays. grid_coord array has shape (N,3);
weight 1D array has N elements.
'''
if callable(radii_adjust) and atomic_radii is not None:
f_radii_adjust = radii_adjust(mol, atomic_radii)
else:
f_radii_adjust = None
atm_coords = numpy.asarray(mol.atom_coords() , order='C')
atm_dist = gto.inter_distance(mol)
if (becke_scheme is original_becke and
(radii_adjust is radi.treutler_atomic_radii_adjust or
radii_adjust is radi.becke_atomic_radii_adjust or
f_radii_adjust is None)):
if f_radii_adjust is None:
p_radii_table = lib.c_null_ptr()
else:
f_radii_table = numpy.asarray([f_radii_adjust(i, j, 0)
for i in range(mol.natm)
for j in range(mol.natm)])
p_radii_table = f_radii_table.ctypes.data_as(ctypes.c_void_p)
def gen_grid_partition(coords):
coords = numpy.asarray(coords, order='F')
ngrids = coords.shape[0]
pbecke = numpy.empty((mol.natm,ngrids))
libdft.VXCgen_grid(pbecke.ctypes.data_as(ctypes.c_void_p),
coords.ctypes.data_as(ctypes.c_void_p),
atm_coords.ctypes.data_as(ctypes.c_void_p),
p_radii_table,
ctypes.c_int(mol.natm), ctypes.c_int(ngrids))
return pbecke
else:
def gen_grid_partition(coords):
ngrids = coords.shape[0]
grid_dist = numpy.empty((mol.natm,ngrids))
for ia in range(mol.natm):
dc = coords - atm_coords[ia]
grid_dist[ia] = numpy.sqrt(numpy.einsum('ij,ij->i',dc,dc))
pbecke = numpy.ones((mol.natm,ngrids))
for i in range(mol.natm):
for j in range(i):
g = 1/atm_dist[i,j] * (grid_dist[i]-grid_dist[j])
if f_radii_adjust is not None:
g = f_radii_adjust(i, j, g)
g = becke_scheme(g)
pbecke[i] *= .5 * (1-g)
pbecke[j] *= .5 * (1+g)
return pbecke
coords_all = []
weights_all = []
for ia in range(mol.natm):
coords, vol = atom_grids_tab[mol.atom_symbol(ia)]
coords = coords + atm_coords[ia]
pbecke = gen_grid_partition(coords)
weights = vol * pbecke[ia] * (1./pbecke.sum(axis=0))
coords_all.append(coords)
weights_all.append(weights)
return numpy.vstack(coords_all), numpy.hstack(weights_all)
def intor_cross(intor, cell1, cell2, comp=1, hermi=0, kpts=None, kpt=None):
r'''1-electron integrals from two cells like
.. math::
\langle \mu | intor | \nu \rangle, \mu \in cell1, \nu \in cell2
'''
if kpts is None:
if kpt is not None:
kpts_lst = np.reshape(kpt, (1,3))
else:
kpts_lst = np.zeros((1,3))
else:
kpts_lst = np.reshape(kpts, (-1,3))
nkpts = len(kpts_lst)
atm, bas, env = conc_env(cell1._atm, cell1._bas, cell1._env,
cell2._atm, cell2._bas, cell2._env)
atm = np.asarray(atm, dtype=np.int32)
bas = np.asarray(bas, dtype=np.int32)
env = np.asarray(env, dtype=np.double)
natm = len(atm)
nbas = len(bas)
shls_slice = (0, cell1.nbas, cell1.nbas, nbas)
ao_loc = moleintor.make_loc(bas, intor)
ni = ao_loc[shls_slice[1]] - ao_loc[shls_slice[0]]
nj = ao_loc[shls_slice[3]] - ao_loc[shls_slice[2]]
out = [np.zeros((ni,nj,comp), order='F', dtype=np.complex128)
for k in range(nkpts)]
out_ptrs = (ctypes.c_void_p*nkpts)(
*[x.ctypes.data_as(ctypes.c_void_p) for x in out])
if hermi == 0:
aosym = 's1'
else:
aosym = 's2'
if '2c2e' in intor:
fill = getattr(libpbc, 'PBCnr2c2e_fill_'+aosym)
else:
assert('2e' not in intor)
fill = getattr(libpbc, 'PBCnr2c_fill_'+aosym)
fintor = moleintor._fpointer(intor)
intopt = lib.c_null_ptr()
nimgs = np.max((cell1.nimgs, cell2.nimgs), axis=0)
Ls = np.asarray(cell1.get_lattice_Ls(nimgs), order='C')
expLk = np.asarray(np.exp(1j*np.dot(Ls, kpts_lst.T)), order='C')
xyz = np.asarray(cell2.atom_coords(), order='C')
ptr_coords = np.asarray(atm[cell1.natm:,mole.PTR_COORD],
dtype=np.int32, order='C')
drv = libpbc.PBCnr2c_drv
drv(fintor, fill, out_ptrs, xyz.ctypes.data_as(ctypes.c_void_p),
ptr_coords.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(cell2.natm),
Ls.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(len(Ls)),
expLk.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(nkpts),
ctypes.c_int(comp), (ctypes.c_int*4)(*(shls_slice[:4])),
ao_loc.ctypes.data_as(ctypes.c_void_p), intopt,
atm.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(natm),
bas.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(nbas),
env.ctypes.data_as(ctypes.c_void_p))
def trans(out):
out = out.transpose(2,0,1)
if hermi == lib.HERMITIAN:
# GTOint2c fills the upper triangular of the F-order array.
idx = np.triu_indices(ni)
for i in range(comp):
out[i,idx[1],idx[0]] = out[i,idx[0],idx[1]].conj()
elif hermi == lib.ANTIHERMI:
idx = np.triu_indices(ni)
for i in range(comp):
out[i,idx[1],idx[0]] = -out[i,idx[0],idx[1]].conj()
elif hermi == lib.SYMMETRIC:
idx = np.triu_indices(ni)
for i in range(comp):
out[i,idx[1],idx[0]] = out[i,idx[0],idx[1]]
if comp == 1:
out = out.reshape(ni,nj)
return out
for k, kpt in enumerate(kpts_lst):
if abs(kpt).sum() < 1e-9: # gamma_point
out[k] = np.asarray(trans(out[k].real), order='C')
else:
out[k] = np.asarray(trans(out[k]), order='C')
if kpts is None or np.shape(kpts) == (3,):
# A single k-point
out = out[0]
return out
def _ft_aopair_kpts(cell, Gv, shls_slice=None, aosym='s1',
b=None, gxyz=None, Gvbase=None, q=numpy.zeros(3),
kptjs=numpy.zeros((1,3)), intor='GTO_ft_ovlp', comp=1,
out=None):
r'''
FT transform AO pair
\sum_T exp(-i k_j * T) \int exp(-i(G+q)r) i(r) j(r-T) dr^3
The return array holds the AO pair
corresponding to the kpoints given by kptjs
'''
intor = cell._add_suffix(intor)
q = numpy.reshape(q, 3)
kptjs = numpy.asarray(kptjs, order='C').reshape(-1,3)
Gv = numpy.asarray(Gv, order='C').reshape(-1,3)
nGv = Gv.shape[0]
GvT = numpy.asarray(Gv.T, order='C')
GvT += q.reshape(-1,1)
if (gxyz is None or b is None or Gvbase is None or (abs(q).sum() > 1e-9)
# backward compatibility for pyscf-1.2, in which the argument Gvbase is gs
or (Gvbase is not None and isinstance(Gvbase[0], (int, numpy.integer)))):
p_gxyzT = lib.c_null_ptr()
p_mesh = (ctypes.c_int*3)(0,0,0)
p_b = (ctypes.c_double*1)(0)
eval_gz = 'GTO_Gv_general'
else:
if abs(b-numpy.diag(b.diagonal())).sum() < 1e-8:
eval_gz = 'GTO_Gv_orth'
else:
eval_gz = 'GTO_Gv_nonorth'
gxyzT = numpy.asarray(gxyz.T, order='C', dtype=numpy.int32)
p_gxyzT = gxyzT.ctypes.data_as(ctypes.c_void_p)
b = numpy.hstack((b.ravel(), q) + Gvbase)
p_b = b.ctypes.data_as(ctypes.c_void_p)
p_mesh = (ctypes.c_int*3)(*[len(x) for x in Gvbase])
Ls = cell.get_lattice_Ls()
expkL = numpy.exp(1j * numpy.dot(kptjs, Ls.T))
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)
if shls_slice is None:
shls_slice = (0, cell.nbas, cell.nbas, cell.nbas*2)
else:
shls_slice = (shls_slice[0], shls_slice[1],
cell.nbas+shls_slice[2], cell.nbas+shls_slice[3])
ni = ao_loc[shls_slice[1]] - ao_loc[shls_slice[0]]
nj = ao_loc[shls_slice[3]] - ao_loc[shls_slice[2]]
nkpts = len(kptjs)
nimgs = len(Ls)
shape = (nkpts, comp, ni, nj, nGv)
# Theoretically, hermitian symmetry can be also found for kpti == kptj:
# f_ji(G) = \int f_ji exp(-iGr) = \int f_ij^* exp(-iGr) = [f_ij(-G)]^*
# hermi operation needs reordering the axis-0. It is inefficient.
if aosym == 's1hermi': # Symmetry for Gamma point
assert(is_zero(q) and is_zero(kptjs) and ni == nj)
elif aosym == 's2':
i0 = ao_loc[shls_slice[0]]
i1 = ao_loc[shls_slice[1]]
nij = i1*(i1+1)//2 - i0*(i0+1)//2
shape = (nkpts, comp, nij, nGv)
drv = libpbc.PBC_ft_latsum_drv
cintor = getattr(libpbc, intor)
eval_gz = getattr(libpbc, eval_gz)
if nkpts == 1:
fill = getattr(libpbc, 'PBC_ft_fill_nk1'+aosym)
else:
fill = getattr(libpbc, 'PBC_ft_fill_k'+aosym)
out = numpy.ndarray(shape, dtype=numpy.complex128, buffer=out)
drv(cintor, eval_gz, fill, out.ctypes.data_as(ctypes.c_void_p),
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),
(ctypes.c_int*4)(*shls_slice), ao_loc.ctypes.data_as(ctypes.c_void_p),
GvT.ctypes.data_as(ctypes.c_void_p), p_b, p_gxyzT, p_mesh, ctypes.c_int(nGv),
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))
if aosym == 's1hermi':
for i in range(1,ni):
out[:,:,:i,i] = out[:,:,i,:i]
out = numpy.rollaxis(out, -1, 2)
if comp == 1:
out = out[:,0]
return out
def _ft_aopair_kpts(cell, Gv, shls_slice=None, aosym='s1',
invh=None, gxyz=None, gs=None,
kpt=numpy.zeros(3), kptjs=numpy.zeros((2,3)), out=None):
''' FT transform AO pair
\int i(r) j(r) exp(-ikr) dr^3
for all kpt = kptj - kpti. The return list holds the AO pair array
corresponding to the kpoints given by kptjs
'''
kpt = numpy.reshape(kpt, 3)
kptjs = numpy.asarray(kptjs, order='C').reshape(-1,3)
nGv = Gv.shape[0]
Gv = Gv + kpt # kptis = kptjs - kpt
if (gxyz is None or invh is None or gs is None or (abs(kpt).sum() > 1e-9)):
GvT = numpy.asarray(Gv.T, order='C')
p_gxyzT = lib.c_null_ptr()
p_gs = (ctypes.c_int*3)(0,0,0)
p_invh = (ctypes.c_double*1)(0)
eval_gz = 'GTO_Gv_general'
else:
GvT = numpy.asarray(Gv.T, order='C')
gxyzT = numpy.asarray(gxyz.T, order='C', dtype=numpy.int32)
p_gxyzT = gxyzT.ctypes.data_as(ctypes.c_void_p)
p_gs = (ctypes.c_int*3)(*gs)
# Guess what type of eval_gz to use
if isinstance(invh, numpy.ndarray) and invh.shape == (3,3):
p_invh = invh.ctypes.data_as(ctypes.c_void_p)
if abs(invh-numpy.diag(invh.diagonal())).sum() < 1e-8:
eval_gz = 'GTO_Gv_uniform_orth'
else:
eval_gz = 'GTO_Gv_uniform_nonorth'
else:
invh = numpy.hstack(invh)
p_invh = invh.ctypes.data_as(ctypes.c_void_p)
eval_gz = 'GTO_Gv_nonuniform_orth'
drv = libpbc.PBC_ft_latsum_kpts
intor = getattr(libpbc, 'GTO_ft_ovlp_sph')
eval_gz = getattr(libpbc, eval_gz)
# make copy of atm,bas,env because they are modified in the lattice sum
atm, bas, env = gto.conc_env(cell._atm, cell._bas, cell._env,
cell._atm, cell._bas, cell._env)
ao_loc = cell.ao_loc_nr()
nao = ao_loc[cell.nbas]
ao_loc = numpy.asarray(numpy.hstack((ao_loc[:-1], ao_loc+nao)),
dtype=numpy.int32)
if shls_slice is None:
shls_slice = (0, cell.nbas, cell.nbas, cell.nbas*2)
else:
shls_slice = (shls_slice[0], shls_slice[1],
cell.nbas+shls_slice[2], cell.nbas+shls_slice[3])
ni = ao_loc[shls_slice[1]] - ao_loc[shls_slice[0]]
nj = ao_loc[shls_slice[3]] - ao_loc[shls_slice[2]]
shape = (nGv, ni, nj)
fill = getattr(libpbc, 'PBC_ft_fill_'+aosym)
if aosym == 's1hermi': # Symmetry for Gamma point
assert(abs(kpt).sum() < 1e-9 and abs(kptjs).sum() < 1e-9)
elif aosym == 's2':
i0 = ao_loc[shls_slice[0]]
i1 = ao_loc[shls_slice[1]]
nij = i1*(i1+1)//2 - i0*(i0+1)//2
shape = (nGv, nij)
if out is None:
out = [numpy.zeros(shape, order='F', dtype=numpy.complex128)
for k in range(len(kptjs))]
else:
out = [numpy.ndarray(shape, order='F', dtype=numpy.complex128,
buffer=out[k]) for k in range(len(kptjs))]
out_ptrs = (ctypes.c_void_p*len(out))(
*[x.ctypes.data_as(ctypes.c_void_p) for x in out])
xyz = numpy.asarray(cell.atom_coords(), order='C')
ptr_coord = numpy.asarray(atm[cell.natm:,gto.PTR_COORD],
dtype=numpy.int32, order='C')
Ls = numpy.asarray(cell.get_lattice_Ls(cell.nimgs), order='C')
exp_Lk = numpy.einsum('ik,jk->ij', Ls, kptjs)
exp_Lk = numpy.exp(1j * numpy.asarray(exp_Lk, order='C'))
drv(intor, eval_gz, fill, out_ptrs, xyz.ctypes.data_as(ctypes.c_void_p),
ptr_coord.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(len(xyz)),
Ls.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(len(Ls)),
exp_Lk.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(len(kptjs)),
(ctypes.c_int*4)(*shls_slice),
ao_loc.ctypes.data_as(ctypes.c_void_p),
GvT.ctypes.data_as(ctypes.c_void_p),
p_invh, p_gxyzT, p_gs, ctypes.c_int(nGv),
atm.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(cell.natm*2),
bas.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(cell.nbas*2),
env.ctypes.data_as(ctypes.c_void_p))
if aosym == 's1hermi':
for mat in out:
for i in range(1,ni):
mat[:,:i,i] = mat[:,i,:i]
return out
mol.basis = "cc-pvdz"
mol.build()
rhf = scf.RHF(mol)
rhf.scf()
nao = mol.nao_nr()
npair = nao * (nao + 1) // 2
c_atm = numpy.array(mol._atm, dtype=numpy.int32)
c_bas = numpy.array(mol._bas, dtype=numpy.int32)
c_env = numpy.array(mol._env)
natm = ctypes.c_int(c_atm.shape[0])
nbas = ctypes.c_int(c_bas.shape[0])
cvhfopt = lib.c_null_ptr()
cintopt = lib.c_null_ptr()
ao_loc = numpy.asarray(mol.ao_loc_nr(), dtype=numpy.int32)
# for each dm1, call namejk
def runjk(dm1, ncomp, intorname, filldot, *namejk):
fdrv = getattr(libcvhf2, "CVHFnr_direct_drv")
intor = getattr(libcvhf2, intorname)
fdot = getattr(libcvhf2._handle, filldot)
njk = len(namejk)
if dm1.ndim == 2:
n_dm = 1
dm1 = (dm1,)
else:
n_dm = dm1.shape[0]
def get_jk(dfobj, dm, hermi=1, vhfopt=None, with_j=True, with_k=True):
t0 = t1 = (time.clock(), time.time())
log = logger.Logger(dfobj.stdout, dfobj.verbose)
assert(with_j or with_k)
fmmm = _ao2mo.libao2mo.AO2MOmmm_bra_nr_s2
fdrv = _ao2mo.libao2mo.AO2MOnr_e2_drv
ftrans = _ao2mo.libao2mo.AO2MOtranse2_nr_s2
null = lib.c_null_ptr()
dms = numpy.asarray(dm)
dm_shape = dms.shape
nao = dm_shape[-1]
dms = dms.reshape(-1,nao,nao)
nset = dms.shape[0]
vj = [0] * nset
vk = [0] * nset
if not with_k:
dmtril = []
idx = numpy.arange(nao)
for k in range(nset):
dm = lib.pack_tril(dms[k]+dms[k].T)
dm[idx*(idx+1)//2+idx] *= .5
dmtril.append(dm)
for eri1 in dfobj.loop():
naux, nao_pair = eri1.shape
for k in range(nset):
rho = numpy.einsum('px,x->p', eri1, dmtril[k])
vj[k] += numpy.einsum('p,px->x', rho, eri1)
elif getattr(dm, 'mo_coeff', None) is not None:
#TODO: test whether dm.mo_coeff matching dm
mo_coeff = numpy.asarray(dm.mo_coeff, order='F')
mo_occ = numpy.asarray(dm.mo_occ)
nmo = mo_occ.shape[-1]
mo_coeff = mo_coeff.reshape(-1,nao,nmo)
mo_occ = mo_occ.reshape(-1,nmo)
if mo_occ.shape[0] * 2 == nset: # handle ROHF DM
mo_coeff = numpy.vstack((mo_coeff, mo_coeff))
mo_occa = numpy.array(mo_occ> 0, dtype=numpy.double)
mo_occb = numpy.array(mo_occ==2, dtype=numpy.double)
assert(mo_occa.sum() + mo_occb.sum() == mo_occ.sum())
mo_occ = numpy.vstack((mo_occa, mo_occb))
dmtril = []
orbo = []
for k in range(nset):
if with_j:
dmtril.append(lib.pack_tril(dms[k]+dms[k].T))
i = numpy.arange(nao)
dmtril[k][i*(i+1)//2+i] *= .5
c = numpy.einsum('pi,i->pi', mo_coeff[k][:,mo_occ[k]>0],
numpy.sqrt(mo_occ[k][mo_occ[k]>0]))
orbo.append(numpy.asarray(c, order='F'))
buf = numpy.empty((dfobj.blockdim*nao,nao))
for eri1 in dfobj.loop():
naux, nao_pair = eri1.shape
assert(nao_pair == nao*(nao+1)//2)
for k in range(nset):
if with_j:
rho = numpy.einsum('px,x->p', eri1, dmtril[k])
vj[k] += numpy.einsum('p,px->x', rho, eri1)
nocc = orbo[k].shape[1]
if nocc > 0:
buf1 = buf[:naux*nocc]
fdrv(ftrans, fmmm,
buf1.ctypes.data_as(ctypes.c_void_p),
eri1.ctypes.data_as(ctypes.c_void_p),
orbo[k].ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(naux), ctypes.c_int(nao),
(ctypes.c_int*4)(0, nocc, 0, nao),
null, ctypes.c_int(0))
vk[k] += lib.dot(buf1.T, buf1)
t1 = log.timer_debug1('jk', *t1)
else:
#:vk = numpy.einsum('pij,jk->pki', cderi, dm)
#:vk = numpy.einsum('pki,pkj->ij', cderi, vk)
rargs = (ctypes.c_int(nao), (ctypes.c_int*4)(0, nao, 0, nao),
null, ctypes.c_int(0))
dms = [numpy.asarray(x, order='F') for x in dms]
buf = numpy.empty((2,dfobj.blockdim,nao,nao))
for eri1 in dfobj.loop():
naux, nao_pair = eri1.shape
for k in range(nset):
buf1 = buf[0,:naux]
fdrv(ftrans, fmmm,
buf1.ctypes.data_as(ctypes.c_void_p),
eri1.ctypes.data_as(ctypes.c_void_p),
dms[k].ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(naux), *rargs)
if with_j:
rho = numpy.einsum('kii->k', buf1)
vj[k] += numpy.einsum('p,px->x', rho, eri1)
buf2 = lib.unpack_tril(eri1, out=buf[1])
vk[k] += lib.dot(buf1.reshape(-1,nao).T, buf2.reshape(-1,nao))
t1 = log.timer_debug1('jk', *t1)
if with_j: vj = lib.unpack_tril(vj, 1).reshape(dm_shape)
if with_k: vk = numpy.asarray(vk).reshape(dm_shape)
logger.timer(dfobj, 'vj and vk', *t0)
return vj, vk
def _ft_aopair_kpts(cell, Gv, shls_slice=None, aosym='s1',
b=None, gxyz=None, Gvbase=None,
kpt=numpy.zeros(3), kptjs=numpy.zeros((2,3)), out=None):
''' FT transform AO pair
\int i(r) j(r) exp(-ikr) dr^3
for all kpt = kptj - kpti. The return list holds the AO pair array
corresponding to the kpoints given by kptjs
'''
kpt = numpy.reshape(kpt, 3) # kptis = kptjs - kpt
kptjs = numpy.asarray(kptjs, order='C').reshape(-1,3)
nGv = Gv.shape[0]
GvT = numpy.asarray(Gv.T, order='C')
GvT += kpt.reshape(-1,1)
if (gxyz is None or b is None or Gvbase is None or (abs(kpt).sum() > 1e-9)
# backward compatibility for pyscf-1.2, in which the argument Gvbase is gs
or (Gvbase is not None and isinstance(Gvbase[0], (int, numpy.integer)))):
p_gxyzT = lib.c_null_ptr()
p_gs = (ctypes.c_int*3)(0,0,0)
p_b = (ctypes.c_double*1)(0)
eval_gz = 'GTO_Gv_general'
else:
gxyzT = numpy.asarray(gxyz.T, order='C', dtype=numpy.int32)
p_gxyzT = gxyzT.ctypes.data_as(ctypes.c_void_p)
b = numpy.hstack((b.ravel(), kpt) + Gvbase)
p_b = b.ctypes.data_as(ctypes.c_void_p)
p_gs = (ctypes.c_int*3)(*[len(x) for x in Gvbase])
eval_gz = 'GTO_Gv_cubic'
drv = libpbc.PBC_ft_latsum_kpts
intor = getattr(libpbc, 'GTO_ft_ovlp_sph')
eval_gz = getattr(libpbc, eval_gz)
# make copy of atm,bas,env because they are modified in the lattice sum
atm, bas, env = gto.conc_env(cell._atm, cell._bas, cell._env,
cell._atm, cell._bas, cell._env)
ao_loc = cell.ao_loc_nr()
nao = ao_loc[cell.nbas]
ao_loc = numpy.asarray(numpy.hstack((ao_loc[:-1], ao_loc+nao)),
dtype=numpy.int32)
if shls_slice is None:
shls_slice = (0, cell.nbas, cell.nbas, cell.nbas*2)
else:
shls_slice = (shls_slice[0], shls_slice[1],
cell.nbas+shls_slice[2], cell.nbas+shls_slice[3])
ni = ao_loc[shls_slice[1]] - ao_loc[shls_slice[0]]
nj = ao_loc[shls_slice[3]] - ao_loc[shls_slice[2]]
shape = (nGv, ni, nj)
fill = getattr(libpbc, 'PBC_ft_fill_'+aosym)
# Theoretically, hermitian symmetry can be also found for kpti == kptj:
# f_ji(G) = \int f_ji exp(-iGr) = \int f_ij^* exp(-iGr) = [f_ij(-G)]^*
# The hermi operation needs reordering the axis-0. It is inefficient.
if aosym == 's1hermi': # Symmetry for Gamma point
assert(abs(kpt).sum() < 1e-9 and abs(kptjs).sum() < 1e-9)
elif aosym == 's2':
i0 = ao_loc[shls_slice[0]]
i1 = ao_loc[shls_slice[1]]
nij = i1*(i1+1)//2 - i0*(i0+1)//2
shape = (nGv, nij)
if out is None:
out = [numpy.zeros(shape, order='F', dtype=numpy.complex128)
for k in range(len(kptjs))]
else:
out = [numpy.ndarray(shape, order='F', dtype=numpy.complex128,
buffer=out[k]) for k in range(len(kptjs))]
out_ptrs = (ctypes.c_void_p*len(out))(
*[x.ctypes.data_as(ctypes.c_void_p) for x in out])
xyz = numpy.asarray(cell.atom_coords(), order='C')
ptr_coord = numpy.asarray(atm[cell.natm:,gto.PTR_COORD],
dtype=numpy.int32, order='C')
Ls = cell.get_lattice_Ls()
exp_Lk = numpy.einsum('ik,jk->ij', Ls, kptjs)
exp_Lk = numpy.exp(1j * numpy.asarray(exp_Lk, order='C'))
drv(intor, eval_gz, fill, out_ptrs, xyz.ctypes.data_as(ctypes.c_void_p),
ptr_coord.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(len(xyz)),
Ls.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(len(Ls)),
exp_Lk.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(len(kptjs)),
(ctypes.c_int*4)(*shls_slice),
ao_loc.ctypes.data_as(ctypes.c_void_p),
GvT.ctypes.data_as(ctypes.c_void_p),
p_b, p_gxyzT, p_gs, ctypes.c_int(nGv),
atm.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(cell.natm*2),
bas.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(cell.nbas*2),
env.ctypes.data_as(ctypes.c_void_p))
if aosym == 's1hermi':
for mat in out:
for i in range(1,ni):
mat[:,:i,i] = mat[:,i,:i]
return out
def direct(dms, atm, bas, env, vhfopt=None, hermi=0, cart=False):
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(c_atm.shape[0])
nbas = ctypes.c_int(c_bas.shape[0])
if isinstance(dms, numpy.ndarray) and dms.ndim == 2:
dms = dms[numpy.newaxis,:,:]
n_dm = len(dms)
nao = dms[0].shape[0]
dms = numpy.asarray(dms, order='C')
if vhfopt is None:
if cart:
intor = 'int2e_cart'
else:
intor = 'int2e_sph'
cintopt = make_cintopt(c_atm, c_bas, c_env, intor)
cvhfopt = lib.c_null_ptr()
else:
vhfopt.set_dm(dms, atm, bas, env)
cvhfopt = vhfopt._this
cintopt = vhfopt._cintopt
intor = vhfopt._intor
cintor = _fpointer(intor)
fdrv = getattr(libcvhf, 'CVHFnr_direct_drv')
fdot = _fpointer('CVHFdot_nrs8')
fvj = _fpointer('CVHFnrs8_ji_s2kl')
if hermi == 1:
fvk = _fpointer('CVHFnrs8_li_s2kj')
else:
fvk = _fpointer('CVHFnrs8_li_s1kj')
vjk = numpy.empty((2,n_dm,nao,nao))
fjk = (ctypes.c_void_p*(2*n_dm))()
dmsptr = (ctypes.c_void_p*(2*n_dm))()
vjkptr = (ctypes.c_void_p*(2*n_dm))()
for i in range(n_dm):
dmsptr[i] = dms[i].ctypes.data_as(ctypes.c_void_p)
vjkptr[i] = vjk[0,i].ctypes.data_as(ctypes.c_void_p)
fjk[i] = fvj
for i in range(n_dm):
dmsptr[n_dm+i] = dms[i].ctypes.data_as(ctypes.c_void_p)
vjkptr[n_dm+i] = vjk[1,i].ctypes.data_as(ctypes.c_void_p)
fjk[n_dm+i] = fvk
shls_slice = (ctypes.c_int*8)(*([0, c_bas.shape[0]]*4))
ao_loc = make_loc(bas, intor)
fdrv(cintor, fdot, fjk, dmsptr, vjkptr,
ctypes.c_int(n_dm*2), ctypes.c_int(1),
shls_slice, ao_loc.ctypes.data_as(ctypes.c_void_p), cintopt, cvhfopt,
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))
# vj must be symmetric
for idm in range(n_dm):
vjk[0,idm] = lib.hermi_triu(vjk[0,idm], 1)
if hermi != 0: # vk depends
for idm in range(n_dm):
vjk[1,idm] = lib.hermi_triu(vjk[1,idm], hermi)
if n_dm == 1:
vjk = vjk.reshape(2,nao,nao)
return vjk
def rdirect_bindm(intor, aosym, jkdescript,
dms, ncomp, atm, bas, env, vhfopt=None, cintopt=None,
shls_slice=None):
assert(aosym in ('s8', 's4', 's2ij', 's2kl', 's1',
'a4ij', 'a4kl', 'a2ij', 'a2kl'))
intor = ascint3(intor)
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(c_atm.shape[0])
nbas = ctypes.c_int(c_bas.shape[0])
if isinstance(dms, numpy.ndarray) and dms.ndim == 2:
dms = dms[numpy.newaxis,:,:]
n_dm = len(dms)
nao = dms[0].shape[0]
dms = numpy.asarray(dms, order='C', dtype=numpy.complex128)
if isinstance(jkdescript, str):
jkdescript = (jkdescript,)
njk = len(jkdescript)
assert(njk == n_dm)
if vhfopt is None:
cintor = _fpointer(intor)
cvhfopt = lib.c_null_ptr()
else:
vhfopt.set_dm(dms, atm, bas, env)
cvhfopt = vhfopt._this
cintopt = vhfopt._cintopt
cintor = getattr(libcvhf, vhfopt._intor)
if cintopt is None:
cintopt = make_cintopt(c_atm, c_bas, c_env, intor)
fdrv = getattr(libcvhf, 'CVHFr_direct_drv')
dotsym = _INTSYMAP[aosym]
fdot = _fpointer('CVHFdot_r'+dotsym)
if shls_slice is None:
shls_slice = (0, c_bas.shape[0])*4
else:
raise NotImplementedError
ao_loc = make_loc(bas, intor)
unpackas = _INTUNPACKMAP_R[aosym]
descr_sym = [x.split('->') for x in jkdescript]
fjk = (ctypes.c_void_p*(n_dm))()
dm1 = (ctypes.c_void_p*(n_dm))()
for i, (dmsym, vsym) in enumerate(descr_sym):
f1 = _fpointer('CVHFr%s_%s_%s'%(unpackas, dmsym, vsym))
dm1[i] = dms[i].ctypes.data_as(ctypes.c_void_p)
fjk[i] = f1
vjk = numpy.empty((njk,ncomp,nao,nao), dtype=numpy.complex)
fdrv(cintor, fdot, fjk, dm1,
vjk.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(n_dm), ctypes.c_int(ncomp),
(ctypes.c_int*8)(*shls_slice),
ao_loc.ctypes.data_as(ctypes.c_void_p), cintopt, cvhfopt,
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))
if ncomp == 1:
vjk = vjk.reshape(njk,nao,nao)
if njk == 1:
vjk = vjk.reshape(vjk.shape[1:])
return vjk
def get_becke_grids(cell, atom_grid={}, radi_method=dft.radi.gauss_chebyshev,
level=3, prune=nwchem_prune):
'''real-space grids using Becke scheme
Args:
cell : instance of :class:`Cell`
Returns:
coords : (N, 3) ndarray
The real-space grid point coordinates.
weights : (N) ndarray
'''
# When low_dim_ft_type is set, pbc_eval_gto treats the 2D system as a 3D system.
# To get the correct particle number in numint module, the atomic grids needs to
# be consistent with the treatment in pbc_eval_gto (see issue 164).
if cell.dimension < 2 or cell.low_dim_ft_type == 'inf_vacuum':
dimension = cell.dimension
else:
dimension = 3
Ls = cell.get_lattice_Ls(dimension=dimension)
atm_coords = Ls.reshape(-1,1,3) + cell.atom_coords()
atom_grids_tab = gen_atomic_grids(cell, atom_grid, radi_method, level, prune)
coords_all = []
weights_all = []
b = cell.reciprocal_vectors(norm_to=1)
supatm_idx = []
k = 0
for iL, L in enumerate(Ls):
for ia in range(cell.natm):
coords, vol = atom_grids_tab[cell.atom_symbol(ia)]
coords = coords + atm_coords[iL,ia]
# search for grids in unit cell
c = b.dot(coords.T).round(8)
mask = np.ones(c.shape[1], dtype=bool)
if dimension >= 1:
mask &= (c[0]>=0) & (c[0]<=1)
if dimension >= 2:
mask &= (c[1]>=0) & (c[1]<=1)
if dimension == 3:
mask &= (c[2]>=0) & (c[2]<=1)
vol = vol[mask]
if vol.size > 8:
c = c[:,mask]
if dimension >= 1:
vol[c[0]==0] *= .5
vol[c[0]==1] *= .5
if dimension >= 2:
vol[c[1]==0] *= .5
vol[c[1]==1] *= .5
if dimension == 3:
vol[c[2]==0] *= .5
vol[c[2]==1] *= .5
coords = coords[mask]
coords_all.append(coords)
weights_all.append(vol)
supatm_idx.append(k)
k += 1
offs = np.append(0, np.cumsum([w.size for w in weights_all]))
coords_all = np.vstack(coords_all)
weights_all = np.hstack(weights_all)
atm_coords = np.asarray(atm_coords.reshape(-1,3)[supatm_idx], order='C')
sup_natm = len(atm_coords)
p_radii_table = lib.c_null_ptr()
fn = dft.gen_grid.libdft.VXCgen_grid
ngrids = weights_all.size
max_memory = cell.max_memory - lib.current_memory()[0]
blocksize = min(ngrids, max(2000, int(max_memory*1e6/8 / sup_natm)))
displs = lib.misc._blocksize_partition(offs, blocksize)
for n0, n1 in zip(displs[:-1], displs[1:]):
p0, p1 = offs[n0], offs[n1]
pbecke = np.empty((sup_natm,p1-p0))
coords = np.asarray(coords_all[p0:p1], order='F')
fn(pbecke.ctypes.data_as(ctypes.c_void_p),
coords.ctypes.data_as(ctypes.c_void_p),
atm_coords.ctypes.data_as(ctypes.c_void_p),
p_radii_table, ctypes.c_int(sup_natm), ctypes.c_int(p1-p0))
weights_all[p0:p1] /= pbecke.sum(axis=0)
for ia in range(n0, n1):
i0, i1 = offs[ia], offs[ia+1]
weights_all[i0:i1] *= pbecke[ia,i0-p0:i1-p0]
return coords_all, weights_all
def get_jk(dfobj, dms, hermi=1, vhfopt=None, with_j=True, with_k=True):
t0 = t1 = (time.clock(), time.time())
log = logger.Logger(dfobj.stdout, dfobj.verbose)
if len(dms) == 0:
return [], []
elif isinstance(dms, numpy.ndarray) and dms.ndim == 2:
nset = 1
dms = [dms]
is_single_dm = True
else:
nset = len(dms)
is_single_dm = False
nao = dms[0].shape[0]
fmmm = _ao2mo.libao2mo.AO2MOmmm_bra_nr_s2
fdrv = _ao2mo.libao2mo.AO2MOnr_e2_drv
ftrans = _ao2mo.libao2mo.AO2MOtranse2_nr_s2
vj = numpy.zeros((nset,nao,nao))
vk = numpy.zeros((nset,nao,nao))
null = lib.c_null_ptr()
#:vj = reduce(numpy.dot, (cderi.reshape(-1,nao*nao), dm.reshape(-1),
#: cderi.reshape(-1,nao*nao))).reshape(nao,nao)
if hermi == 1: # and numpy.einsum('ij,ij->', dm, ovlp) > 0.1
# I cannot assume dm is positive definite because it might be the density
# matrix difference when the mf.direct_scf flag is set.
dmtril = []
cpos = []
cneg = []
for k, dm in enumerate(dms):
if with_j:
dmtril.append(lib.pack_tril(dm+dm.T))
i = numpy.arange(nao)
dmtril[k][i*(i+1)//2+i] *= .5
if with_k:
e, c = scipy.linalg.eigh(dm)
pos = e > OCCDROP
neg = e < -OCCDROP
#:vk = numpy.einsum('pij,jk->kpi', cderi, c[:,abs(e)>OCCDROP])
#:vk = numpy.einsum('kpi,kpj->ij', vk, vk)
tmp = numpy.einsum('ij,j->ij', c[:,pos], numpy.sqrt(e[pos]))
cpos.append(numpy.asarray(tmp, order='F'))
tmp = numpy.einsum('ij,j->ij', c[:,neg], numpy.sqrt(-e[neg]))
cneg.append(numpy.asarray(tmp, order='F'))
buf = numpy.empty((dfobj.blockdim*nao,nao))
for eri1 in dfobj.loop():
naux, nao_pair = eri1.shape
assert(nao_pair == nao*(nao+1)//2)
for k in range(nset):
if with_j:
buf1 = reduce(numpy.dot, (eri1, dmtril[k], eri1))
vj[k] += lib.unpack_tril(buf1, hermi)
if with_k and cpos[k].shape[1] > 0:
buf1 = buf[:naux*cpos[k].shape[1]]
fdrv(ftrans, fmmm,
buf1.ctypes.data_as(ctypes.c_void_p),
eri1.ctypes.data_as(ctypes.c_void_p),
cpos[k].ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(naux), ctypes.c_int(nao),
(ctypes.c_int*4)(0, cpos[k].shape[1], 0, 0),
null, ctypes.c_int(0))
vk[k] += lib.dot(buf1.T, buf1)
if with_k and cneg[k].shape[1] > 0:
buf1 = buf[:naux*cneg[k].shape[1]]
fdrv(ftrans, fmmm,
buf1.ctypes.data_as(ctypes.c_void_p),
eri1.ctypes.data_as(ctypes.c_void_p),
cneg[k].ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(naux), ctypes.c_int(nao),
(ctypes.c_int*4)(0, cneg[k].shape[1], 0, 0),
null, ctypes.c_int(0))
vk[k] -= lib.dot(buf1.T, buf1)
t1 = log.timer_debug1('jk', *t1)
else:
#:vk = numpy.einsum('pij,jk->pki', cderi, dm)
#:vk = numpy.einsum('pki,pkj->ij', cderi, vk)
rargs = (ctypes.c_int(nao), (ctypes.c_int*4)(0, nao, 0, 0),
null, ctypes.c_int(0))
dms = [numpy.asarray(dm, order='F') for dm in dms]
buf = numpy.empty((2,dfobj.blockdim,nao,nao))
for eri1 in dfobj.loop():
naux, nao_pair = eri1.shape
for k in range(nset):
buf1 = buf[0,:naux]
fdrv(ftrans, fmmm,
buf1.ctypes.data_as(ctypes.c_void_p),
eri1.ctypes.data_as(ctypes.c_void_p),
dms[k].ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(naux), *rargs)
rho = numpy.einsum('kii->k', buf1)
vj[k] += lib.unpack_tril(numpy.dot(rho, eri1), 1)
if with_k:
buf2 = lib.unpack_tril(eri1, out=buf[1])
vk[k] += lib.dot(buf1.reshape(-1,nao).T,
buf2.reshape(-1,nao))
t1 = log.timer_debug1('jk', *t1)
if is_single_dm:
vj = vj[0]
vk = vk[0]
logger.timer(dfobj, 'vj and vk', *t0)
return vj, vk