def project_mo_r2r(mol1, mo1, mol2):
nbas1 = len(mol1._bas)
nbas2 = len(mol2._bas)
atm, bas, env = mole.conc_env(mol2._atm, mol2._bas, mol2._env,
mol1._atm, mol1._bas, mol1._env)
bras = kets = range(nbas2)
s22 = moleintor.getints('cint1e_ovlp', atm, bas, env,
bras, kets, comp=1, hermi=1)
t22 = moleintor.getints('cint1e_spsp', atm, bas, env,
bras, kets, comp=1, hermi=1)
bras = range(nbas2)
kets = range(nbas2, nbas1+nbas2)
s21 = moleintor.getints('cint1e_ovlp', atm, bas, env,
bras, kets, comp=1, hermi=0)
t21 = moleintor.getints('cint1e_spsp', atm, bas, env,
bras, kets, comp=1, hermi=0)
n2c = s21.shape[1]
pl = numpy.linalg.solve(s22, s21)
ps = numpy.linalg.solve(t22, t21)
return numpy.vstack((numpy.dot(pl, mo1[:n2c]),
numpy.dot(ps, mo1[n2c:])))
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 = getattr(moleintor.libcgto, intor)
intopt = lib.c_null_ptr()
Ls = cell1.get_lattice_Ls(rcut=max(cell1.rcut, cell2.rcut))
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 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 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
'''
intor = moleintor.ascint3(intor)
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.empty((nkpts, comp, ni, nj), dtype=np.complex128)
if hermi == 0:
aosym = 's1'
else:
aosym = 's2'
fill = getattr(libpbc, 'PBCnr2c_fill_k' + aosym)
fintor = getattr(moleintor.libcgto, intor)
intopt = lib.c_null_ptr()
Ls = cell1.get_lattice_Ls(rcut=max(cell1.rcut, cell2.rcut))
expkL = np.asarray(np.exp(1j * np.dot(kpts_lst, 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(natm),
bas.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(nbas),
env.ctypes.data_as(ctypes.c_void_p))
mat = []
for k, kpt in enumerate(kpts_lst):
v = out[k]
if hermi != 0:
for ic in range(comp):
lib.hermi_triu(v[ic], hermi=hermi, inplace=True)
if comp == 1:
v = v[0]
if abs(kpt).sum() < 1e-9: # gamma_point
v = v.real
mat.append(v)
if kpts is None or np.shape(kpts) == (3, ): # A single k-point
mat = mat[0]
return mat