def test_scf(self):
mol = neo.Mole()
mol.build(atom='''H 0 0 0; C 0 0 1.064; N 0 0 2.220''',
basis='ccpvdz',
quantum_nuc=[0])
mf = neo.HF(mol)
energy = mf.scf()
self.assertAlmostEqual(energy, -92.8437063572664, 8)
def test_scf3(self):
mol = neo.Mole()
mol.build(atom='''H 0 0 0; C 0 0 1.064; N 0 0 2.220''',
basis='ccpvdz',
quantum_nuc=[0, 1, 2])
mf = neo.HF(mol)
energy = mf.scf()
self.assertAlmostEqual(energy, -91.6090279376862, 8)
def test_scf2(self):
mol = neo.Mole()
mol.build(atom='''H 0 0 0; C 0 0 1.064; N 0 0 2.220''',
basis='ccpvdz',
quantum_nuc=[0, 1])
mf = neo.HF(mol)
energy = mf.scf()
self.assertAlmostEqual(energy, -92.3015848917516, 8)
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 init_guess_nuc_by_calculation(mf_nuc, mol):
"""Generate initial dm"""
dm_nuc = [None] * mol.nuc_num
for i in range(mol.nuc_num):
ia = mol.nuc[i].atom_index
mol_tmp = neo.Mole()
mol_tmp.build(atom=mol.atom,
charge=mol.charge,
spin=mol.spin,
quantum_nuc=[ia])
dm_nuc[i] = get_init_guess_nuc(mf_nuc[i], mol_tmp.nuc[0])
return dm_nuc
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
#!/usr/bin/env python
import unittest
from pyscf import neo
mol = neo.Mole()
mol.build(atom='''H 0 0 0; C 0 0 1.064; N 0 0 2.220''',
basis='ccpvdz',
quantum_nuc=[0])
class KnownValues(unittest.TestCase):
def test_scf_noepc(self):
mf = neo.KS(mol, epc=None)
self.assertAlmostEqual(mf.scf(), -93.3393561862119, 8)
def test_scf_epc17_1(self):
mf = neo.KS(mol, epc='17-1')
mf.max_cycle = 2000
self.assertAlmostEqual(mf.scf(), -93.3963856345767, 5)
def test_scf_epc17_2(self):
mf = neo.KS(mol, epc='17-2')
mf.max_cycle = 1000
self.assertAlmostEqual(mf.scf(), -93.3670499235643, 5)
if __name__ == "__main__":
print("Full Tests for neo.ks")
unittest.main()
