def dip_moment(mol, dm, unit_symbol='Debye', verbose=logger.NOTE):
r''' Dipole moment calculation
.. math::
\mu_x = -\sum_{\mu}\sum_{\nu} P_{\mu\nu}(\nu|x|\mu) + \sum_A Q_A X_A\\
\mu_y = -\sum_{\mu}\sum_{\nu} P_{\mu\nu}(\nu|y|\mu) + \sum_A Q_A Y_A\\
\mu_z = -\sum_{\mu}\sum_{\nu} P_{\mu\nu}(\nu|z|\mu) + \sum_A Q_A Z_A
where :math:`\mu_x, \mu_y, \mu_z` are the x, y and z components of dipole
moment
Args:
mol: an instance of :class:`Mole`
dm : a list of 2D ndarrays
a list of density matrices
Return:
A list: the dipole moment on x, y and z component
'''
if isinstance(dm, numpy.ndarray) and dm.ndim == 2:
return hf.dip_moment(mol, dm, unit_symbol, verbose)
else:
return hf.dip_moment(mol, dm[0] + dm[1], unit_symbol, verbose)
def dip_moment(mol, dm, unit_symbol='Debye', verbose=logger.NOTE):
r''' Dipole moment calculation
.. math::
\mu_x = -\sum_{\mu}\sum_{\nu} P_{\mu\nu}(\nu|x|\mu) + \sum_A Q_A X_A\\
\mu_y = -\sum_{\mu}\sum_{\nu} P_{\mu\nu}(\nu|y|\mu) + \sum_A Q_A Y_A\\
\mu_z = -\sum_{\mu}\sum_{\nu} P_{\mu\nu}(\nu|z|\mu) + \sum_A Q_A Z_A
where :math:`\mu_x, \mu_y, \mu_z` are the x, y and z components of dipole
moment
Args:
mol: an instance of :class:`Mole`
dm : a list of 2D ndarrays
a list of density matrices
Return:
A list: the dipole moment on x, y and z component
'''
if isinstance(dm, numpy.ndarray) and dm.ndim == 2:
return hf.dip_moment(mol, dm, unit_symbol, verbose)
else:
return hf.dip_moment(mol, dm[0]+dm[1], unit_symbol, verbose)
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 = gto.Mole()
atoms = self.atoms.get_chemical_symbols()
positions = self.atoms.get_positions()
atom_pyscf = []
for i in range(len(atoms)):
if atoms[i] == 'D':
atom_pyscf.append(['H@2', tuple(positions[i])])
else:
atom_pyscf.append(['%s' % (atoms[i]), tuple(positions[i])])
mol.build(atom=atom_pyscf,
basis=self.parameters.basis,
charge=self.parameters.charge,
spin=self.parameters.spin)
if self.parameters.spin != 0:
mf = dft.UKS(mol)
else:
mf = dft.RKS(mol)
mf.xc = self.parameters.xc
self.results['energy'] = mf.scf() * Hartree
g = mf.Gradients()
self.results['forces'] = -g.grad() * Hartree / Bohr
self.results['dipole'] = dip_moment(mol, mf.make_rdm1())
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 dip_moment(mol, dm, unit_symbol='Debye', verbose=logger.NOTE):
nao = mol.nao_nr()
dma = dm[:nao, :nao]
dmb = dm[nao:, nao:]
return hf.dip_moment(mol, dma + dmb, unit_symbol, verbose)
