def test_rhf_0d(self):
from pyscf.df import mdf_jk
from pyscf.scf import hf
L = 4
cell = pbcgto.Cell()
cell.build(unit = 'B',
a = numpy.eye(3)*L*5,
gs = [10]*3,
atom = '''He 2 2 2; He 2 2 3''',
dimension = 0,
verbose = 0,
basis = { 'He': [[0, (0.8, 1.0)],
[0, (1.0, 1.0)],
[0, (1.2, 1.0)]]})
mol = cell.to_mol()
mf = mdf_jk.density_fit(hf.RHF(mol))
mf.with_df.gs = [10]*3
mf.with_df.auxbasis = {'He':[[0, (1e6, 1)]]}
mf.with_df.charge_constraint = False
mf.with_df.metric = 'S'
eref = mf.kernel()
mf = pbchf.RHF(cell)
mf.with_df = pdf.PWDF(cell)
mf.get_hcore = lambda *args: hf.get_hcore(mol)
mf.energy_nuc = lambda *args: mol.energy_nuc()
e1 = mf.kernel()
self.assertAlmostEqual(e1, eref, 8)
def test_rhf_0d(self):
from pyscf.df import mdf_jk
from pyscf.scf import hf
L = 4
cell = pbcgto.Cell()
cell.build(
unit='B',
a=numpy.eye(3) * L * 5,
gs=[10] * 3,
atom='''He 2 2 2; He 2 2 3''',
dimension=0,
verbose=0,
basis={'He': [[0, (0.8, 1.0)], [0, (1.0, 1.0)], [0, (1.2, 1.0)]]})
mol = cell.to_mol()
mf = mdf_jk.density_fit(hf.RHF(mol))
mf.with_df.gs = [10] * 3
mf.with_df.auxbasis = {'He': [[0, (1e6, 1)]]}
mf.with_df.charge_constraint = False
mf.with_df.metric = 'S'
eref = mf.kernel()
mf = pbchf.RHF(cell)
mf.with_df = pdf.PWDF(cell)
mf.exxdiv = None
mf.get_hcore = lambda *args: hf.get_hcore(mol)
mf.energy_nuc = lambda *args: mol.energy_nuc()
e1 = mf.kernel()
self.assertAlmostEqual(e1, eref, 8)
def init_guess_by_wolfsberg_helmholtz(mol):
"""Diagonal will be taken from core hamiltonian, the off diagonal elements
are interpolated by wolfsberg helmholtz scheme.
H_ji = k_ji (H_ii + H_ij) S_ij / 2, with k_ij =1.75
(Generalized Wolfsberg Helmholtz GWH). See here:
http://www.q-chem.com/qchem-website/manual/qchem50_manual/sect-initialguess.html
M. Wolfsberg and L. Helmholz, J. Chem. Phys. 20, 837 (1952).
"""
from pyscf.scf.hf import eig, get_hcore, get_ovlp, get_occ, make_rdm1, SCF
import numpy
H = numpy.diag(get_hcore(mol))
k = numpy.ones((len(H), len(H))) * 1.75 - \
numpy.diag(numpy.ones(H.shape)) * 0.75
S = get_ovlp(mol)
H = k * numpy.add.outer(H, H) * S / 2
mo_energy, mo_coeff = eig(H, S)
mo_occ = get_occ(SCF(mol), mo_energy, mo_coeff)
return make_rdm1(mo_coeff, mo_occ)
def get_hcore(ks,mol=None):
if mol is None: mol = ks.mol
h = hf.get_hcore(mol)
if ks.vext_1e is not None:
h = h + ks.vext_1e
return h
def get_hcore(self, mol=None):
if mol is None: mol = self.mol
hcore = hf.get_hcore(mol)
hcore = scipy.linalg.block_diag(hcore, hcore)
if self.with_soc and mol.has_ecp_soc():
# The ECP SOC contribution = <|1j * s * U_SOC|>
s = .5 * lib.PauliMatrices
ecpso = numpy.einsum('sxy,spq->xpyq', -1j * s, mol.intor('ECPso'))
hcore = hcore + ecpso.reshape(hcore.shape)
return hcore
def get_hcore(mf, mol=None):
if mol is None: mol = mf.mol
h = 0.0
if (mf.oei is not None):
h = mf.oei
else:
h = hf.get_hcore(mol)
if mf.vext_1e is not None:
h = h + mf.vext_1e
return h
def test_gwh_by_density(self):
from SCFInitialGuess.construction.fock import gwh_scheme
mol = self.molecule
h = hf.get_hcore(mol)
s = hf.get_ovlp(mol)
f_gwh = gwh_scheme(np.diag(h), s)
p_gwh = density_from_fock(f_gwh, s, mol)
#TODO: use pyscf method
p_ref = init_guess_by_wolfsberg_helmholtz(mol)
np.testing.assert_allclose(p_gwh, p_ref)
def energy_elec(ks, dm=None, h1e=None, vhf=None):
tot_e,e_hxc = rks.energy_elec(ks, dm=dm, h1e=h1e, vhf=vhf)
if(ks.smear_sigma > 1e-8 ):
#add entropy contribution
tot_e += entropy_corr(ks.mo_occ, ks.smear_sigma)
#add frozen density hcore energy
if(isinstance(ks.coredm, numpy.ndarray) and ks.coredm.ndim == 2):
h = hf.get_hcore(ks.mol)
if(ks.add_coredm_ext_energy == True):
h = h + ks.vext_1e
e1 = numpy.einsum('ij,ji', h, ks.coredm).real
tot_e += e1
return tot_e, e_hxc
def get_hcore(self, mol=None):
if mol is None: mol = self.mol
hcore = hf.get_hcore(mol)
return scipy.linalg.block_diag(hcore, hcore)