def calculate(self,
atoms=None,
properties=['energy', 'forces', 'dipole'],
system_changes=[
'positions', 'numbers', 'cell', 'pbc', 'charges',
'magmoms'
]):
Calculator.calculate(self, atoms, properties, system_changes)
mol = neo.Mole()
atoms = self.atoms.get_chemical_symbols()
positions = self.atoms.get_positions()
atom_pyscf = []
for i in range(len(atoms)):
if atoms[i] == 'Mu':
atom_pyscf.append(['H@0', tuple(positions[i])])
elif atoms[i] == 'D':
atom_pyscf.append(['H@2', tuple(positions[i])])
else:
atom_pyscf.append(
['%s%i' % (atoms[i], i),
tuple(positions[i])])
mol.build(quantum_nuc=self.parameters.quantum_nuc,
atom=atom_pyscf,
basis=self.parameters.basis,
charge=self.parameters.charge,
spin=self.parameters.spin)
if self.parameters.spin == 0:
mf = neo.CDFT(mol)
else:
mf = neo.CDFT(mol, unrestricted=True)
mf.mf_elec.xc = self.parameters.xc
self.results['energy'] = mf.scf() * Hartree
g = mf.Gradients()
self.results['forces'] = -g.grad() * Hartree / Bohr
dip_elec = dip_moment(
mol.elec,
mf.mf_elec.make_rdm1()) # dipole of electrons and classical nuclei
dip_nuc = 0
for i in range(len(mf.mf_nuc)):
ia = mf.mf_nuc[i].mol.atom_index
dip_nuc += mol.atom_charge(
ia) * mf.mf_nuc[i].nuclei_expect_position * nist.AU2DEBYE
self.results['dipole'] = dip_elec + dip_nuc
def test_grad_cdft(self):
mol = neo.Mole()
mol.build(atom='''H 0 0 0; F 0 0 0.94''',
basis='ccpvdz',
quantum_nuc=[0])
mf = neo.CDFT(mol)
mf.scf()
g = neo.Gradients(mf)
grad = g.kernel()
self.assertAlmostEqual(grad[0, -1], 0.0051324194, 6)
def test_scf_epc17_2(self):
mf = neo.CDFT(mol, epc='17-2')
mf.max_cycle = 1000
self.assertAlmostEqual(mf.scf(), -93.3661447224845, 6)
def test_scf_epc17_1(self):
mf = neo.CDFT(mol, epc='17-1')
pass
def test_scf_noepc(self):
mf = neo.CDFT(mol, epc=None)
self.assertAlmostEqual(mf.scf(), -93.3384022881535, 6)
self.assertAlmostEqual(mf.f[0][-1], -4.03031884e-02, 5)