def eval_ao(mol, coords, isgga=False, relativity=0, bastart=0, bascount=None,
non0tab=None, verbose=None):
assert(coords.flags.c_contiguous)
natm = ctypes.c_int(mol._atm.shape[0])
nbas = ctypes.c_int(mol.nbas)
nao = mol.nao_nr()
ngrids = len(coords)
if bascount is None:
bascount = mol.nbas - bastart
if isgga:
ao = numpy.empty((4, ngrids,nao)) # plain, dx, dy, dz
feval = _ctypes.dlsym(libdft._handle, 'VXCeval_nr_gto_grad')
else:
ao = numpy.empty((ngrids,nao))
feval = _ctypes.dlsym(libdft._handle, 'VXCeval_nr_gto')
if non0tab is None:
non0tab = numpy.ones(((ngrids+BLKSIZE-1)//BLKSIZE,mol.nbas),
dtype=numpy.int8)
libdft.VXCeval_ao_drv(ctypes.c_void_p(feval),
ctypes.c_int(nao), ctypes.c_int(ngrids),
ctypes.c_int(bastart), ctypes.c_int(bascount),
ctypes.c_int(BLKSIZE),
ao.ctypes.data_as(ctypes.c_void_p),
coords.ctypes.data_as(ctypes.c_void_p),
non0tab.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))
return ao
def runjk(dm1, ncomp, intorname, filldot, *namejk):
fdrv = getattr(libcvhf2, 'CVHFnr_direct_drv')
intor = ctypes.c_void_p(_ctypes.dlsym(libcvhf2._handle,
intorname))
fdot = ctypes.c_void_p(_ctypes.dlsym(libcvhf2._handle, filldot))
njk = len(namejk)
if dm1.ndim == 2:
n_dm = 1
dm1 = (dm1,)
else:
n_dm = dm1.shape[0]
vjk = numpy.zeros((njk,n_dm*ncomp,nao,nao))
fjk = (ctypes.c_void_p*(njk*n_dm))()
dmsptr = (ctypes.c_void_p*(njk*n_dm))()
vjkptr = (ctypes.c_void_p*(njk*n_dm))()
for i, symb in enumerate(namejk):
f1 = ctypes.c_void_p(_ctypes.dlsym(libcvhf2._handle, symb))
for j in range(n_dm):
dmsptr[i*n_dm+j] = dm1[j].ctypes.data_as(ctypes.c_void_p)
vjkptr[i*n_dm+j] = vjk[i,j*ncomp].ctypes.data_as(ctypes.c_void_p)
fjk[i*n_dm+j] = f1
shls_slice = (ctypes.c_int*8)(*([0, mol.nbas]*4))
fdrv(intor, fdot, fjk, dmsptr, vjkptr,
ctypes.c_int(njk*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 n_dm * ncomp == 1:
vjk = vjk.reshape(njk,nao,nao)
return vjk
def _trans(vin, i0, icount, j0, jcount, out=None):
nrow = vin.shape[0]
fdrv = getattr(_ccsd.libcc, 'AO2MOnr_e2_drv')
pao_loc = ctypes.POINTER(ctypes.c_void_p)()
ftrans = ctypes.c_void_p(_ctypes.dlsym(_ccsd.libcc._handle, 'AO2MOtranse2_nr_s1'))
fmmm = ctypes.c_void_p(_ctypes.dlsym(_ccsd.libcc._handle, 'CCmmm_transpose_sum'))
fdrv(ftrans, fmmm,
out.ctypes.data_as(ctypes.c_void_p),
vin.ctypes.data_as(ctypes.c_void_p),
mo_coeff.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(nrow), ctypes.c_int(nao),
ctypes.c_int(i0), ctypes.c_int(icount),
ctypes.c_int(j0), ctypes.c_int(jcount),
pao_loc, ctypes.c_int(0))
return out
def _trans(vin, i0, icount, j0, jcount, out=None):
nrow = vin.shape[0]
fdrv = getattr(_ccsd.libcc, 'AO2MOnr_e2_drv')
pao_loc = ctypes.POINTER(ctypes.c_void_p)()
ftrans = ctypes.c_void_p(_ctypes.dlsym(_ccsd.libcc._handle, 'AO2MOtranse2_nr_s1'))
fmmm = ctypes.c_void_p(_ctypes.dlsym(_ccsd.libcc._handle, 'CCmmm_transpose_sum'))
fdrv(ftrans, fmmm,
out.ctypes.data_as(ctypes.c_void_p),
vin.ctypes.data_as(ctypes.c_void_p),
mo_coeff.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(nrow), ctypes.c_int(nao),
ctypes.c_int(i0), ctypes.c_int(icount),
ctypes.c_int(j0), ctypes.c_int(jcount),
pao_loc, ctypes.c_int(0))
return out
def make_dm123(fname, cibra, ciket, norb, nelec):
r'''Spin traced 1, 2 and 3-particle density matrices.
.. note::
The 2pdm is :math:`\langle p^\dagger q^\dagger s r\rangle` but is
stored as [p,r,q,s];
The 3pdm is :math:`\langle p^\dagger q^\dagger r^\dagger u t s\rangle`,
stored as [p,s,q,t,r,u].
'''
if isinstance(nelec, (int, numpy.integer)):
neleca = nelecb = nelec//2
else:
neleca, nelecb = nelec
link_indexa = cistring.gen_linkstr_index(range(norb), neleca)
link_indexb = cistring.gen_linkstr_index(range(norb), nelecb)
na,nlinka = link_indexa.shape[:2]
nb,nlinkb = link_indexb.shape[:2]
rdm1 = numpy.empty((norb,)*2)
rdm2 = numpy.empty((norb,)*4)
rdm3 = numpy.empty((norb,)*6)
kernel = _ctypes.dlsym(librdm._handle, fname)
librdm.FCIrdm3_drv(ctypes.c_void_p(kernel),
rdm1.ctypes.data_as(ctypes.c_void_p),
rdm2.ctypes.data_as(ctypes.c_void_p),
rdm3.ctypes.data_as(ctypes.c_void_p),
cibra.ctypes.data_as(ctypes.c_void_p),
ciket.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(norb),
ctypes.c_int(na), ctypes.c_int(nb),
ctypes.c_int(nlinka), ctypes.c_int(nlinkb),
link_indexa.ctypes.data_as(ctypes.c_void_p),
link_indexb.ctypes.data_as(ctypes.c_void_p))
rdm3 = _complete_dm3_(rdm2, rdm3)
return rdm1, rdm2, rdm3
def make_dm123(fname, cibra, ciket, norb, nelec):
r'''Spin traced 1, 2 and 3-particle density matrices.
.. note::
The 2pdm is :math:`\langle p^\dagger q^\dagger r s\rangle` but is
stored as [p,s,q,r];
The 3pdm is :math:`\langle p^\dagger q^\dagger r^\dagger s t u\rangle`,
stored as [p,u,q,t,r,s].
'''
cibra = numpy.asarray(cibra, order='C')
ciket = numpy.asarray(ciket, order='C')
if isinstance(nelec, (int, numpy.number)):
neleca = nelecb = nelec // 2
else:
neleca, nelecb = nelec
link_indexa = cistring.gen_linkstr_index(range(norb), neleca)
link_indexb = cistring.gen_linkstr_index(range(norb), nelecb)
na, nlinka = link_indexa.shape[:2]
nb, nlinkb = link_indexb.shape[:2]
rdm1 = numpy.empty((norb, ) * 2)
rdm2 = numpy.empty((norb, ) * 4)
rdm3 = numpy.empty((norb, ) * 6)
kernel = _ctypes.dlsym(librdm._handle, fname)
librdm.FCIrdm3_drv(ctypes.c_void_p(kernel),
rdm1.ctypes.data_as(ctypes.c_void_p),
rdm2.ctypes.data_as(ctypes.c_void_p),
rdm3.ctypes.data_as(ctypes.c_void_p),
cibra.ctypes.data_as(ctypes.c_void_p),
ciket.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(norb), ctypes.c_int(na), ctypes.c_int(nb),
ctypes.c_int(nlinka), ctypes.c_int(nlinkb),
link_indexa.ctypes.data_as(ctypes.c_void_p),
link_indexb.ctypes.data_as(ctypes.c_void_p))
rdm3 = _complete_dm3_(rdm2, rdm3)
return rdm1, rdm2, rdm3
def make_rdm12_spin1(fname,
cibra,
ciket,
norb,
nelec,
link_index=None,
symm=0):
cibra = numpy.asarray(cibra, order='C')
ciket = numpy.asarray(ciket, order='C')
if link_index is None:
if isinstance(nelec, (int, numpy.number)):
nelecb = nelec // 2
neleca = nelec - nelecb
else:
neleca, nelecb = nelec
link_indexa = cistring.gen_linkstr_index(range(norb), neleca)
link_indexb = cistring.gen_linkstr_index(range(norb), nelecb)
else:
link_indexa, link_indexb = link_index
na, nlinka = link_indexa.shape[:2]
nb, nlinkb = link_indexb.shape[:2]
rdm1 = numpy.empty((norb, norb))
rdm2 = numpy.empty((norb, norb, norb, norb))
fn = _ctypes.dlsym(librdm._handle, fname)
librdm.FCIrdm12_drv(ctypes.c_void_p(fn),
rdm1.ctypes.data_as(ctypes.c_void_p),
rdm2.ctypes.data_as(ctypes.c_void_p),
cibra.ctypes.data_as(ctypes.c_void_p),
ciket.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(norb), ctypes.c_int(na), ctypes.c_int(nb),
ctypes.c_int(nlinka), ctypes.c_int(nlinkb),
link_indexa.ctypes.data_as(ctypes.c_void_p),
link_indexb.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(symm))
return rdm1, rdm2
def condense(opname, a, locs):
'''
.. code-block:: python
nd = loc[-1]
out = numpy.empty((nd,nd))
for i,i0 in enumerate(loc):
i1 = loc[i+1]
for j,j0 in enumerate(loc):
j1 = loc[j+1]
out[i,j] = op(a[i0:i1,j0:j1])
return out
'''
assert (a.flags.c_contiguous)
assert (a.dtype == numpy.double)
if not opname.startswith('NP_'):
opname = 'NP_' + opname
op = ctypes.c_void_p(_ctypes.dlsym(_np_helper._handle, opname))
locs = numpy.asarray(locs, numpy.int32)
nloc = locs.size - 1
out = numpy.empty((nloc, nloc))
_np_helper.NPcondense(op, out.ctypes.data_as(ctypes.c_void_p),
a.ctypes.data_as(ctypes.c_void_p),
locs.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(nloc))
return out
def make_rdm12_spin1(fname, cibra, ciket, norb, nelec, link_index=None, symm=0):
assert(cibra.flags.c_contiguous)
assert(ciket.flags.c_contiguous)
if isinstance(nelec, (int, numpy.integer)):
neleca = nelecb = nelec//2
else:
neleca, nelecb = nelec
if link_index is None:
link_indexa = cistring.gen_linkstr_index(range(norb), neleca)
link_indexb = cistring.gen_linkstr_index(range(norb), nelecb)
else:
link_indexa, link_indexb = link_index
na,nlinka = link_indexa.shape[:2]
nb,nlinkb = link_indexb.shape[:2]
rdm1 = numpy.empty((norb,norb))
rdm2 = numpy.empty((norb,norb,norb,norb))
fn = _ctypes.dlsym(librdm._handle, fname)
librdm.FCIrdm12_drv(ctypes.c_void_p(fn),
rdm1.ctypes.data_as(ctypes.c_void_p),
rdm2.ctypes.data_as(ctypes.c_void_p),
cibra.ctypes.data_as(ctypes.c_void_p),
ciket.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(norb),
ctypes.c_int(na), ctypes.c_int(nb),
ctypes.c_int(nlinka), ctypes.c_int(nlinkb),
link_indexa.ctypes.data_as(ctypes.c_void_p),
link_indexb.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(symm))
return rdm1, rdm2
def make_rdm12_spin1(fname, cibra, ciket, norb, nelec, link_index=None, symm=0):
cibra = numpy.asarray(cibra, order='C')
ciket = numpy.asarray(ciket, order='C')
if link_index is None:
if isinstance(nelec, (int, numpy.number)):
nelecb = nelec//2
neleca = nelec - nelecb
else:
neleca, nelecb = nelec
link_indexa = cistring.gen_linkstr_index(range(norb), neleca)
link_indexb = cistring.gen_linkstr_index(range(norb), nelecb)
else:
link_indexa, link_indexb = link_index
na,nlinka = link_indexa.shape[:2]
nb,nlinkb = link_indexb.shape[:2]
rdm1 = numpy.empty((norb,norb))
rdm2 = numpy.empty((norb,norb,norb,norb))
fn = _ctypes.dlsym(librdm._handle, fname)
librdm.FCIrdm12_drv(ctypes.c_void_p(fn),
rdm1.ctypes.data_as(ctypes.c_void_p),
rdm2.ctypes.data_as(ctypes.c_void_p),
cibra.ctypes.data_as(ctypes.c_void_p),
ciket.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(norb),
ctypes.c_int(na), ctypes.c_int(nb),
ctypes.c_int(nlinka), ctypes.c_int(nlinkb),
link_indexa.ctypes.data_as(ctypes.c_void_p),
link_indexb.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(symm))
return rdm1, rdm2
def make_dm1234(fname, cibra, ciket, norb, nelec):
if isinstance(nelec, (int, numpy.integer)):
neleca = nelecb = nelec//2
else:
neleca, nelecb = nelec
link_indexa = cistring.gen_linkstr_index(range(norb), neleca)
link_indexb = cistring.gen_linkstr_index(range(norb), nelecb)
na,nlinka = link_indexa.shape[:2]
nb,nlinkb = link_indexb.shape[:2]
rdm1 = numpy.empty((norb,)*2)
rdm2 = numpy.empty((norb,)*4)
rdm3 = numpy.empty((norb,)*6)
rdm4 = numpy.empty((norb,)*8)
librdm.FCIrdm4_drv(ctypes.c_void_p(_ctypes.dlsym(librdm._handle, fname)),
rdm1.ctypes.data_as(ctypes.c_void_p),
rdm2.ctypes.data_as(ctypes.c_void_p),
rdm3.ctypes.data_as(ctypes.c_void_p),
rdm4.ctypes.data_as(ctypes.c_void_p),
cibra.ctypes.data_as(ctypes.c_void_p),
ciket.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(norb),
ctypes.c_int(na), ctypes.c_int(nb),
ctypes.c_int(nlinka), ctypes.c_int(nlinkb),
link_indexa.ctypes.data_as(ctypes.c_void_p),
link_indexb.ctypes.data_as(ctypes.c_void_p))
rdm3 = _complete_dm3_(rdm2, rdm3)
rdm4 = _complete_dm4_(rdm3, rdm4)
return rdm1, rdm2, rdm3, rdm4
def _make_rdm2_abba(fcivec, norb, nelec):
if isinstance(nelec, (int, numpy.integer)):
neleca = nelecb = nelec // 2
else:
neleca, nelecb = nelec
if nelecb == norb or neleca == 0: # no intermediate determinants
return numpy.zeros((norb,norb,norb,norb))
acre_index = cistring.gen_cre_str_index(range(norb), neleca-1)
bdes_index = cistring.gen_des_str_index(range(norb), nelecb+1)
instra = cistring.num_strings(norb, neleca-1)
nb = cistring.num_strings(norb, nelecb)
dm1 = numpy.empty((norb,norb))
dm2 = numpy.empty((norb,norb,norb,norb))
fn = _ctypes.dlsym(librdm._handle, 'FCIdm2_abba_kern')
librdm.FCIspindm12_drv(ctypes.c_void_p(fn),
dm1.ctypes.data_as(ctypes.c_void_p),
dm2.ctypes.data_as(ctypes.c_void_p),
fcivec.ctypes.data_as(ctypes.c_void_p),
fcivec.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(norb),
ctypes.c_int(instra), ctypes.c_int(nb),
ctypes.c_int(neleca), ctypes.c_int(nelecb),
acre_index.ctypes.data_as(ctypes.c_void_p),
bdes_index.ctypes.data_as(ctypes.c_void_p))
return dm2
def _contract4pdm(kern, eri, civec, norb, nelec, link_index=None):
if isinstance(nelec, (int, numpy.integer)):
neleca = nelecb = nelec//2
else:
neleca, nelecb = nelec
if link_index is None:
link_indexa = fci.cistring.gen_linkstr_index(range(norb), neleca)
link_indexb = fci.cistring.gen_linkstr_index(range(norb), nelecb)
else:
link_indexa, link_indexb = link_index
na,nlinka = link_indexa.shape[:2]
nb,nlinkb = link_indexb.shape[:2]
fdm2 = numpy.empty((norb,norb,norb,norb))
fdm3 = numpy.empty((norb,norb,norb,norb,norb,norb))
eri = numpy.ascontiguousarray(eri)
libmc.NEVPTcontract(ctypes.c_void_p(_ctypes.dlsym(libmc._handle, kern)),
fdm2.ctypes.data_as(ctypes.c_void_p),
fdm3.ctypes.data_as(ctypes.c_void_p),
eri.ctypes.data_as(ctypes.c_void_p),
civec.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(norb),
ctypes.c_int(na), ctypes.c_int(nb),
ctypes.c_int(nlinka), ctypes.c_int(nlinkb),
link_indexa.ctypes.data_as(ctypes.c_void_p),
link_indexb.ctypes.data_as(ctypes.c_void_p))
for i in range(norb):
for j in range(i):
fdm3[j,:,i] = fdm3[i,:,j].transpose(1,0,2,3)
fdm3[j,i,i,:] += fdm2[j,:]
fdm3[j,:,i,j] -= fdm2[i,:]
return fdm3
def _contract4pdm(kern, eri, civec, norb, nelec, link_index=None):
if isinstance(nelec, (int, numpy.integer)):
neleca = nelecb = nelec//2
else:
neleca, nelecb = nelec
if link_index is None:
link_indexa = fci.cistring.gen_linkstr_index(range(norb), neleca)
link_indexb = fci.cistring.gen_linkstr_index(range(norb), nelecb)
else:
link_indexa, link_indexb = link_index
na,nlinka = link_indexa.shape[:2]
nb,nlinkb = link_indexb.shape[:2]
fdm2 = numpy.empty((norb,norb,norb,norb))
fdm3 = numpy.empty((norb,norb,norb,norb,norb,norb))
eri = numpy.ascontiguousarray(eri)
libmc.NEVPTcontract(ctypes.c_void_p(_ctypes.dlsym(libmc._handle, kern)),
fdm2.ctypes.data_as(ctypes.c_void_p),
fdm3.ctypes.data_as(ctypes.c_void_p),
eri.ctypes.data_as(ctypes.c_void_p),
civec.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(norb),
ctypes.c_int(na), ctypes.c_int(nb),
ctypes.c_int(nlinka), ctypes.c_int(nlinkb),
link_indexa.ctypes.data_as(ctypes.c_void_p),
link_indexb.ctypes.data_as(ctypes.c_void_p))
for i in range(norb):
for j in range(i):
fdm3[j,:,i] = fdm3[i,:,j].transpose(1,0,2,3)
fdm3[j,i,i,:] += fdm2[j,:]
fdm3[j,:,i,j] -= fdm2[i,:]
return fdm3
def condense(opname, a, locs):
'''
.. code-block:: python
nd = loc[-1]
out = numpy.empty((nd,nd))
for i,i0 in enumerate(loc):
i1 = loc[i+1]
for j,j0 in enumerate(loc):
j1 = loc[j+1]
out[i,j] = op(a[i0:i1,j0:j1])
return out
'''
assert(a.flags.c_contiguous)
assert(a.dtype == numpy.double)
if not opname.startswith('NP_'):
opname = 'NP_' + opname
op = ctypes.c_void_p(_ctypes.dlsym(_np_helper._handle, opname))
locs = numpy.asarray(locs, numpy.int32)
nloc = locs.size - 1
out = numpy.empty((nloc,nloc))
_np_helper.NPcondense(op, out.ctypes.data_as(ctypes.c_void_p),
a.ctypes.data_as(ctypes.c_void_p),
locs.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(nloc))
return out
def getints1e(intor_name, atm, bas, env, bras=None, kets=None, comp=1, hermi=0):
if bras is None:
bralst = numpy.arange(len(bas), dtype=numpy.int32)
else:
bralst = numpy.asarray(bras, dtype=numpy.int32)
assert(bralst.max() < len(bas))
if kets is None:
ketlst = numpy.arange(len(bas), dtype=numpy.int32)
else:
ketlst = numpy.asarray(kets, dtype=numpy.int32)
assert(ketlst.max() < len(bas))
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)
c_natm = ctypes.c_int(atm.shape[0])
c_nbas = ctypes.c_int(bas.shape[0])
nbra = len(bralst)
nket = len(ketlst)
if '_cart' in intor_name:
dtype = numpy.double
num_cgto_of = libcgto.CINTcgto_cart
drv = libcgto.GTO1eintor_cart
elif '_sph' in intor_name:
dtype = numpy.double
num_cgto_of = libcgto.CINTcgto_spheric
drv = libcgto.GTO1eintor_sph
else:
dtype = numpy.complex
num_cgto_of = libcgto.CINTcgto_spinor
drv = libcgto.GTO1eintor_spinor
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])
mat = numpy.empty((comp,naoi,naoj), dtype)
fnaddr = ctypes.c_void_p(_ctypes.dlsym(libcgto._handle, intor_name))
drv(fnaddr, mat.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(comp),
ctypes.c_int(hermi),
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),
c_atm, c_natm, c_bas, c_nbas, c_env)
if comp == 1:
mat = mat.reshape(naoi,naoj)
if hermi == 0:
return mat
else:
if comp == 1:
pyscf.lib.hermi_triu_(mat, hermi=hermi)
else:
for i in range(comp):
pyscf.lib.hermi_triu_(mat[i], hermi=hermi)
return mat
def call_with_fpointer(fdistname, coord, charge):
import _ctypes
coord = numpy.ascontiguousarray(coord)
charge = numpy.ascontiguousarray(charge)
cenergy = ctypes.CDLL('libcenergy.so')
fn = getattr(cenergy, 'runcallback')
fn.restype = ctypes.c_double
fptr = ctypes.c_void_p(_ctypes.dlsym(cenergy._handle, fdistname))
nc = len(charge)
e = 0
for i in range(nc):
for j in range(i):
e += fn(coord[i].ctypes.data_as(ctypes.c_void_p),
coord[j].ctypes.data_as(ctypes.c_void_p),
ctypes.c_double(charge[i]), ctypes.c_double(charge[j]),
fptr)
return e
def make_dm1234(fname, cibra, ciket, norb, nelec):
r'''Spin traced 1, 2, 3 and 4-particle density matrices.
.. note::
The 2pdm is :math:`\langle p^\dagger q^\dagger s r\rangle` but is
stored as [p,r,q,s];
The 3pdm is :math:`\langle p^\dagger q^\dagger r^\dagger u t s\rangle`,
stored as [p,s,q,t,r,u];
The 4pdm is :math:`\langle p^\dagger q^\dagger r^\dagger s^dagger w v u t\rangle`,
stored as [p,w,q,v,r,u,s,t].
'''
cibra = numpy.asarray(cibra, order='C')
ciket = numpy.asarray(ciket, order='C')
if isinstance(nelec, (int, numpy.number)):
neleca = nelecb = nelec//2
else:
neleca, nelecb = nelec
link_indexa = cistring.gen_linkstr_index(range(norb), neleca)
link_indexb = cistring.gen_linkstr_index(range(norb), nelecb)
na,nlinka = link_indexa.shape[:2]
nb,nlinkb = link_indexb.shape[:2]
rdm1 = numpy.empty((norb,)*2)
rdm2 = numpy.empty((norb,)*4)
rdm3 = numpy.empty((norb,)*6)
rdm4 = numpy.empty((norb,)*8)
librdm.FCIrdm4_drv(ctypes.c_void_p(_ctypes.dlsym(librdm._handle, fname)),
rdm1.ctypes.data_as(ctypes.c_void_p),
rdm2.ctypes.data_as(ctypes.c_void_p),
rdm3.ctypes.data_as(ctypes.c_void_p),
rdm4.ctypes.data_as(ctypes.c_void_p),
cibra.ctypes.data_as(ctypes.c_void_p),
ciket.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(norb),
ctypes.c_int(na), ctypes.c_int(nb),
ctypes.c_int(nlinka), ctypes.c_int(nlinkb),
link_indexa.ctypes.data_as(ctypes.c_void_p),
link_indexb.ctypes.data_as(ctypes.c_void_p))
rdm3 = _complete_dm3_(rdm2, rdm3)
rdm4 = _complete_dm4_(rdm3, rdm4)
return rdm1, rdm2, rdm3, rdm4
def _make_rdm2_baab(fcivec, norb, nelec):
fcivec = numpy.asarray(fcivec, order='C')
neleca, nelecb = _unpack(nelec)
if neleca == norb or nelecb == 0: # no intermediate determinants
return numpy.zeros((norb,norb,norb,norb))
ades_index = cistring.gen_des_str_index(range(norb), neleca+1)
bcre_index = cistring.gen_cre_str_index(range(norb), nelecb-1)
instra = cistring.num_strings(norb, neleca+1)
nb = cistring.num_strings(norb, nelecb)
dm1 = numpy.empty((norb,norb))
dm2 = numpy.empty((norb,norb,norb,norb))
fn = _ctypes.dlsym(librdm._handle, 'FCIdm2_baab_kern')
librdm.FCIspindm12_drv(ctypes.c_void_p(fn),
dm1.ctypes.data_as(ctypes.c_void_p),
dm2.ctypes.data_as(ctypes.c_void_p),
fcivec.ctypes.data_as(ctypes.c_void_p),
fcivec.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(norb),
ctypes.c_int(instra), ctypes.c_int(nb),
ctypes.c_int(neleca), ctypes.c_int(nelecb),
ades_index.ctypes.data_as(ctypes.c_void_p),
bcre_index.ctypes.data_as(ctypes.c_void_p))
return dm2
def _make_rdm2_abba(fcivec, norb, nelec):
fcivec = numpy.asarray(fcivec, order='C')
neleca, nelecb = _unpack(nelec)
if nelecb == norb or neleca == 0: # no intermediate determinants
return numpy.zeros((norb,norb,norb,norb))
acre_index = cistring.gen_cre_str_index(range(norb), neleca-1)
bdes_index = cistring.gen_des_str_index(range(norb), nelecb+1)
instra = cistring.num_strings(norb, neleca-1)
nb = cistring.num_strings(norb, nelecb)
dm1 = numpy.empty((norb,norb))
dm2 = numpy.empty((norb,norb,norb,norb))
fn = _ctypes.dlsym(librdm._handle, 'FCIdm2_abba_kern')
librdm.FCIspindm12_drv(ctypes.c_void_p(fn),
dm1.ctypes.data_as(ctypes.c_void_p),
dm2.ctypes.data_as(ctypes.c_void_p),
fcivec.ctypes.data_as(ctypes.c_void_p),
fcivec.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(norb),
ctypes.c_int(instra), ctypes.c_int(nb),
ctypes.c_int(neleca), ctypes.c_int(nelecb),
acre_index.ctypes.data_as(ctypes.c_void_p),
bdes_index.ctypes.data_as(ctypes.c_void_p))
return dm2
def eval_ao(mol, coords, isgga=False, relativity=0, bastart=0, bascount=None,
non0tab=None, verbose=None):
'''Evaluate AO function value on the given grids, for LDA and GGA functional.
Args:
mol : an instance of :class:`Mole`
coords : 2D array, shape (N,3)
The coordinates of the grids.
Kwargs:
isgga : bool
Whether to evalute the AO gradients for GGA functional. It affects
the shape of the return array. If isgga=False, the returned AO
values are stored in a (N,nao) array. Otherwise the AO values are
stored in an array of shape (4,N,nao). Here N is the number of
grids, nao is the number of AO functions.
relativity : bool
No effects.
bastart, bascount : int
If given, only part of AOs (bastart <= shell_id < bastart+bascount) are evaluated.
non0tab : 2D bool array
mask array to indicate whether the AO values are zero. The mask
array can be obtained by calling :func:`make_mask`
verbose : int or object of :class:`Logger`
No effects.
Returns:
2D array of shape (N,nao) for AO values if isgga is False.
Or 3D array of shape (4,N,nao) for AO values and AO gradients if isgga is True.
In the 3D array, the first (N,nao) elements are the AO values. The
following (3,N,nao) are the AO gradients for x,y,z compoents.
Examples:
>>> mol = gto.M(atom='O 0 0 0; H 0 0 1; H 0 1 0', basis='ccpvdz')
>>> coords = numpy.random.random((100,3)) # 100 random points
>>> ao_value = eval_ao(mol, coords)
>>> print(ao_value.shape)
(100, 24)
>>> ao_value = eval_ao(mol, coords, isgga=True, bastart=1, bascount=3)
>>> print(ao_value.shape)
(4, 100, 7)
'''
assert(coords.flags.c_contiguous)
natm = ctypes.c_int(mol._atm.shape[0])
nbas = ctypes.c_int(mol.nbas)
ngrids = len(coords)
if bascount is None:
bascount = mol.nbas - bastart
nao = mol.nao_nr()
else:
nao_bound = mol.nao_nr_range(bastart, bastart+bascount)
nao = nao_bound[1] - nao_bound[0]
if isgga:
ao = numpy.empty((4, ngrids,nao)) # plain, dx, dy, dz
feval = _ctypes.dlsym(libdft._handle, 'VXCeval_nr_gto_grad')
else:
ao = numpy.empty((ngrids,nao))
feval = _ctypes.dlsym(libdft._handle, 'VXCeval_nr_gto')
if non0tab is None:
non0tab = numpy.ones(((ngrids+BLKSIZE-1)//BLKSIZE,mol.nbas),
dtype=numpy.int8)
libdft.VXCeval_ao_drv(ctypes.c_void_p(feval),
ctypes.c_int(nao), ctypes.c_int(ngrids),
ctypes.c_int(bastart), ctypes.c_int(bascount),
ctypes.c_int(BLKSIZE),
ao.ctypes.data_as(ctypes.c_void_p),
coords.ctypes.data_as(ctypes.c_void_p),
non0tab.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))
return ao
def func_address(adll, name):
if 'dlsym' in dir(_ctypes):
return _ctypes.dlsym(adll._handle, name)
else:
return _ctypes.GetProcAddress(adll._handle, name)
def set_vkscreen(opt, name):
opt._this.contents.r_vkscreen = \
ctypes.c_void_p(_ctypes.dlsym(_vhf.libcvhf._handle, name))
def getints(intor_name, atm, bas, env, bras=None, kets=None, comp=1, hermi=0):
r'''One electron integral generator.
Args:
intor_name : str
Name of the 1-electron integral. The list of 1e integrals in
current version of libcint (v2.5.1)
========================== ========= =============
Function type Expression
========================== ========= =============
"cint1e_ovlp_sph" spheric ( \| \)
"cint1e_nuc_sph" spheric ( \| nuc \| \)
"cint1e_kin_sph" spheric (.5 \| p dot p\)
"cint1e_ia01p_sph" spheric (#C(0 1) \| nabla-rinv \| cross p\)
"cint1e_giao_irjxp_sph" spheric (#C(0 1) \| r cross p\)
"cint1e_cg_irxp_sph" spheric (#C(0 1) \| rc cross p\)
"cint1e_giao_a11part_sph" spheric (-.5 \| nabla-rinv \| r\)
"cint1e_cg_a11part_sph" spheric (-.5 \| nabla-rinv \| rc\)
"cint1e_a01gp_sph" spheric (g \| nabla-rinv cross p \|\)
"cint1e_igkin_sph" spheric (#C(0 .5) g \| p dot p\)
"cint1e_igovlp_sph" spheric (#C(0 1) g \|\)
"cint1e_ignuc_sph" spheric (#C(0 1) g \| nuc \|\)
"cint1e_z_sph" spheric ( \| zc \| \)
"cint1e_zz_sph" spheric ( \| zc zc \| \)
"cint1e_r_sph" spheric ( \| rc \| \)
"cint1e_r2_sph" spheric ( \| rc dot rc \| \)
"cint1e_rr_sph" spheric ( \| rc rc \| \)
"cint1e_pnucp_sph" spheric (p* \| nuc dot p \| \)
"cint1e_prinvxp_sph" spheric (p* \| rinv cross p \| \)
"cint1e_ovlp" spinor ( \| \)
"cint1e_nuc" spinor ( \| nuc \|\)
"cint1e_srsr" spinor (sigma dot r \| sigma dot r\)
"cint1e_sr" spinor (sigma dot r \|\)
"cint1e_srsp" spinor (sigma dot r \| sigma dot p\)
"cint1e_spsp" spinor (sigma dot p \| sigma dot p\)
"cint1e_sp" spinor (sigma dot p \|\)
"cint1e_spnucsp" spinor (sigma dot p \| nuc \| sigma dot p\)
"cint1e_srnucsr" spinor (sigma dot r \| nuc \| sigma dot r\)
"cint1e_govlp" spinor (g \|\)
"cint1e_gnuc" spinor (g \| nuc \|\)
"cint1e_cg_sa10sa01" spinor (.5 sigma cross rc \| sigma cross nabla-rinv \|\)
"cint1e_cg_sa10sp" spinor (.5 rc cross sigma \| sigma dot p\)
"cint1e_cg_sa10nucsp" spinor (.5 rc cross sigma \| nuc \| sigma dot p\)
"cint1e_giao_sa10sa01" spinor (.5 sigma cross r \| sigma cross nabla-rinv \|\)
"cint1e_giao_sa10sp" spinor (.5 r cross sigma \| sigma dot p\)
"cint1e_giao_sa10nucsp" spinor (.5 r cross sigma \| nuc \| sigma dot p\)
"cint1e_sa01sp" spinor (\| nabla-rinv cross sigma \| sigma dot p\)
"cint1e_spgsp" spinor (g sigma dot p \| sigma dot p\)
"cint1e_spgnucsp" spinor (g sigma dot p \| nuc \| sigma dot p\)
"cint1e_spgsa01" spinor (g sigma dot p \| nabla-rinv cross sigma \|\)
"cint1e_spspsp" spinor (sigma dot p \| sigma dot p sigma dot p\)
"cint1e_spnuc" spinor (sigma dot p \| nuc \|\)
"cint1e_ovlp_cart" cartesian ( \| \)
"cint1e_nuc_cart" cartesian ( \| nuc \| \)
"cint1e_kin_cart" cartesian (.5 \| p dot p\)
"cint1e_ia01p_cart" cartesian (#C(0 1) \| nabla-rinv \| cross p\)
"cint1e_giao_irjxp_cart" cartesian (#C(0 1) \| r cross p\)
"cint1e_cg_irxp_cart" cartesian (#C(0 1) \| rc cross p\)
"cint1e_giao_a11part_cart" cartesian (-.5 \| nabla-rinv \| r\)
"cint1e_cg_a11part_cart" cartesian (-.5 \| nabla-rinv \| rc\)
"cint1e_a01gp_cart" cartesian (g \| nabla-rinv cross p \|\)
"cint1e_igkin_cart" cartesian (#C(0 .5) g \| p dot p\)
"cint1e_igovlp_cart" cartesian (#C(0 1) g \|\)
"cint1e_ignuc_cart" cartesian (#C(0 1) g \| nuc \|\)
"cint1e_ipovlp_sph" spheric (nabla \|\)
"cint1e_ipkin_sph" spheric (.5 nabla \| p dot p\)
"cint1e_ipnuc_sph" spheric (nabla \| nuc \|\)
"cint1e_iprinv_sph" spheric (nabla \| rinv \|\)
"cint1e_rinv_sph" spheric (\| rinv \|\)
"cint1e_ipovlp" spinor (nabla \|\)
"cint1e_ipkin" spinor (.5 nabla \| p dot p\)
"cint1e_ipnuc" spinor (nabla \| nuc \|\)
"cint1e_iprinv" spinor (nabla \| rinv \|\)
"cint1e_ipspnucsp" spinor (nabla sigma dot p \| nuc \| sigma dot p\)
"cint1e_ipsprinvsp" spinor (nabla sigma dot p \| rinv \| sigma dot p\)
"cint1e_ipovlp_cart" cartesian (nabla \|\)
"cint1e_ipkin_cart" cartesian (.5 nabla \| p dot p\)
"cint1e_ipnuc_cart" cartesian (nabla \| nuc \|\)
"cint1e_iprinv_cart" cartesian (nabla \| rinv \|\)
"cint1e_rinv_cart" cartesian (\| rinv \|\)
========================== ========= =============
atm : int32 ndarray
libcint integral function argument
bas : int32 ndarray
libcint integral function argument
env : float64 ndarray
libcint integral function argument
Kwargs:
bras : list of int
shell ids for bra. Default is all shells given by bas
kets : list of int
shell ids for ket. Default is all shells given by bas
comp : int
Components of the integrals, e.g. cint1e_ipovlp has 3 components.
hermi : int
Symmetry of the integrals
| 0 : no symmetry assumed (default)
| 1 : hermitian
| 2 : anti-hermitian
Returns:
ndarray of 1-electron integrals, can be either 2-dim or 3-dim, depending on comp
Examples:
>>> mol.build(atom='H 0 0 0; H 0 0 1.1', basis='sto-3g')
>>> gto.moleintor('cint1e_ipnuc_sph', mol._atm, mol._bas, mol._env, comp=3) # <nabla i | V_nuc | j>
[[[ 0. 0. ]
[ 0. 0. ]]
[[ 0. 0. ]
[ 0. 0. ]]
[[ 0.10289944 0.48176097]
[-0.48176097 -0.10289944]]]
'''
nbas = len(bas)
if bras is None:
bras = range(nbas)
else:
assert(max(bras) < len(bas))
if kets is None:
kets = range(nbas)
else:
assert(max(kets) < len(bas))
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)
c_natm = ctypes.c_int(atm.shape[0])
c_nbas = ctypes.c_int(bas.shape[0])
nbra = len(bras)
nket = len(kets)
if '_cart' in intor_name:
dtype = numpy.double
num_cgto_of = _cint.CINTcgto_cart
c_intor = _cint.GTO1eintor_cart
elif '_sph' in intor_name:
dtype = numpy.double
num_cgto_of = _cint.CINTcgto_spheric
c_intor = _cint.GTO1eintor_sph
else:
dtype = numpy.complex
num_cgto_of = _cint.CINTcgto_spinor
c_intor = _cint.GTO1eintor_spinor
naoi = sum([num_cgto_of(ctypes.c_int(i), c_bas) for i in bras])
naoj = sum([num_cgto_of(ctypes.c_int(i), c_bas) for i in kets])
bralst = numpy.array(bras, dtype=numpy.int32)
ketlst = numpy.array(kets, dtype=numpy.int32)
mat = numpy.empty((comp,naoi,naoj), dtype)
fnaddr = ctypes.c_void_p(_ctypes.dlsym(_cint._handle, intor_name))
c_intor(fnaddr, mat.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(comp), \
ctypes.c_int(hermi), \
bralst.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(nbra),
ketlst.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(nket),
c_atm, c_natm, c_bas, c_nbas, c_env)
if comp == 1:
mat = mat.reshape(naoi,naoj)
if hermi == 0:
return mat
else:
if comp == 1:
pyscf.lib.hermi_triu(mat, hermi=hermi)
else:
for i in range(comp):
pyscf.lib.hermi_triu(mat[i], hermi=hermi)
return mat
def set_vkscreen(opt, name):
opt._this.contents.r_vkscreen = \
ctypes.c_void_p(_ctypes.dlsym(_vhf.libcvhf._handle, name))
def func_address(adll, name):
if 'dlsym' in dir(_ctypes):
return _ctypes.dlsym(adll._handle, name)
else:
return _ctypes.GetProcAddress(adll._handle, name)
def f1pointer(name):
return ctypes.c_void_p(_ctypes.dlsym(libri1._handle, name))
def __getitem__(self, name):
return Address(dlsym(self.dll._handle, name))
def _fpointer(name):
return ctypes.c_void_p(_ctypes.dlsym(libcgto._handle, name))
def f1pointer(name):
return ctypes.c_void_p(_ctypes.dlsym(libri1._handle, name))
