def to_mol(self):
'''Return a Mole object using the same atoms and basis functions as
the Cell object.
'''
mol = mole.Mole()
cell_dic = [(key, getattr(self, key)) for key in mol.__dict__.keys()]
mol.__dict__.update(cell_dic)
return mol
def _make_fakemol():
fakemol = mole.Mole()
fakemol._atm = np.zeros((1,mole.ATM_SLOTS), dtype=np.int32)
fakemol._bas = np.zeros((1,mole.BAS_SLOTS), dtype=np.int32)
ptr = mole.PTR_ENV_START
fakemol._env = np.zeros(ptr+10)
fakemol._bas[0,mole.NPRIM_OF ] = 1
fakemol._bas[0,mole.NCTR_OF ] = 1
fakemol._bas[0,mole.PTR_EXP ] = ptr+3
fakemol._bas[0,mole.PTR_COEFF] = ptr+4
return fakemol
def get_pp(cell, kpt=np.zeros(3)):
'''Get the periodic pseudotential nuc-el AO matrix
'''
from pyscf.pbc import tools
coords = cell.get_uniform_grids()
aoR = cell.pbc_eval_gto('GTOval', coords, kpt=kpt)
nao = cell.nao_nr()
SI = cell.get_SI()
vlocG = get_vlocG(cell)
vpplocG = -np.sum(SI * vlocG, axis=0)
vpplocG[0] = np.sum(get_alphas(cell)) # from get_jvloc_G0 function
# vpploc evaluated in real-space
vpplocR = tools.ifft(vpplocG, cell.mesh).real
vpploc = np.dot(aoR.T.conj(), vpplocR.reshape(-1, 1) * aoR)
# vppnonloc evaluated in reciprocal space
aokG = tools.fftk(np.asarray(aoR.T, order='C'), cell.mesh,
np.exp(-1j * np.dot(coords, kpt))).T
ngrids = len(aokG)
fakemol = mole.Mole()
fakemol._atm = np.zeros((1, mole.ATM_SLOTS), dtype=np.int32)
fakemol._bas = np.zeros((1, mole.BAS_SLOTS), dtype=np.int32)
ptr = mole.PTR_ENV_START
fakemol._env = np.zeros(ptr + 10)
fakemol._bas[0, mole.NPRIM_OF] = 1
fakemol._bas[0, mole.NCTR_OF] = 1
fakemol._bas[0, mole.PTR_EXP] = ptr + 3
fakemol._bas[0, mole.PTR_COEFF] = ptr + 4
Gv = np.asarray(cell.Gv + kpt)
G_rad = lib.norm(Gv, axis=1)
vppnl = np.zeros((nao, nao), dtype=np.complex128)
for ia in range(cell.natm):
symb = cell.atom_symbol(ia)
if symb not in cell._pseudo:
continue
pp = cell._pseudo[symb]
for l, proj in enumerate(pp[5:]):
rl, nl, hl = proj
if nl > 0:
hl = np.asarray(hl)
fakemol._bas[0, mole.ANG_OF] = l
fakemol._env[ptr + 3] = .5 * rl**2
fakemol._env[ptr + 4] = rl**(l + 1.5) * np.pi**1.25
pYlm_part = fakemol.eval_gto('GTOval', Gv)
pYlm = np.empty((nl, l * 2 + 1, ngrids))
for k in range(nl):
qkl = _qli(G_rad * rl, l, k)
pYlm[k] = pYlm_part.T * qkl
# pYlm is real
SPG_lmi = np.einsum('g,nmg->nmg', SI[ia].conj(), pYlm)
SPG_lm_aoG = np.einsum('nmg,gp->nmp', SPG_lmi, aokG)
tmp = np.einsum('ij,jmp->imp', hl, SPG_lm_aoG)
vppnl += np.einsum('imp,imq->pq', SPG_lm_aoG.conj(), tmp)
vppnl *= (1. / ngrids**2)
if aoR.dtype == np.double:
return vpploc.real + vppnl.real
else:
return vpploc + vppnl
def _proj_dmll(mol_nr, dm_nr, mol):
from pyscf.scf import addons
proj = addons.project_mo_nr2r(mol_nr, numpy.eye(mol_nr.nao_nr()), mol)
# *.5 because alpha and beta are summed in project_mo_nr2r
dm_ll = reduce(numpy.dot, (proj, dm_nr * .5, proj.T.conj()))
dm_ll = (dm_ll + dhf.time_reversal_matrix(mol, dm_ll)) * .5
return dm_ll
# A tag to label the derived SCF class
class _X2C_SCF:
pass
if __name__ == '__main__':
mol = mole.Mole()
mol.build(
verbose=0,
atom=[["O", (0., 0., 0.)], [1, (0., -0.757, 0.587)],
[1, (0., 0.757, 0.587)]],
basis='ccpvdz-dk',
)
method = hf.RHF(mol)
enr = method.kernel()
print('E(NR) = %.12g' % enr)
method = UHF(mol)
ex2c = method.kernel()
print('E(X2C1E) = %.12g' % ex2c)
method.with_x2c.basis = {'O': 'unc-ccpvqz', 'H': 'unc-ccpvdz'}
add_so('E%dy' % m, identity(idy0))
ip += nc * degen
so = []
irrep_ids = []
irrep_names = list(sodic.keys())
for irname in irrep_names:
irrep_ids.append(linearmole_irrep_symb2id(gpname, irname))
idx = numpy.argsort(irrep_ids)
for i in idx:
so.append(numpy.vstack(sodic[irrep_names[i]]).T)
irrep_ids = [irrep_ids[i] for i in idx]
return so, irrep_ids
if __name__ == "__main__":
h2o = mole.Mole()
h2o.verbose = 0
h2o.output = None
h2o.atom = [['O', (
1.,
0.,
0.,
)], [1, (
0.,
-.757,
0.587,
)], [1, (
0.,
0.757,
0.587,
)]]
