def add_mm_charges(scf_method, atoms_or_coords, charges, unit=None):
'''Embedding the one-electron (non-relativistic) potential generated by MM
point charges into QM Hamiltonian.
The total energy includes the regular QM energy, the interaction between
the nuclei in QM region and the MM charges, and the static Coulomb
interaction between the electron density and the MM charges. It does not
include the static Coulomb interactions of the MM point charges, the MM
energy, the vdw interaction or other bonding/non-bonding effects between
QM region and MM particles.
Args:
scf_method : a HF or DFT object
atoms_or_coords : 2D array, shape (N,3)
MM particle coordinates
charges : 1D array
MM particle charges
Kwargs:
unit : str
Bohr, AU, Ang (case insensitive). Default is the same to mol.unit
Returns:
Same method object as the input scf_method with modified 1e Hamiltonian
Note:
1. if MM charge and X2C correction are used together, function mm_charge
needs to be applied after X2C decoration (.x2c method), eg
mf = mm_charge(scf.RHF(mol).x2c()), [(0.5,0.6,0.8)], [-0.5]).
2. Once mm_charge function is applied on the SCF object, it
affects all the post-HF calculations eg MP2, CCSD, MCSCF etc
Examples:
>>> mol = gto.M(atom='H 0 0 0; F 0 0 1', basis='ccpvdz', verbose=0)
>>> mf = mm_charge(dft.RKS(mol), [(0.5,0.6,0.8)], [-0.3])
>>> mf.kernel()
-101.940495711284
'''
mol = scf_method.mol
if unit is None:
unit = mol.unit
mm_mol = mm_mole.create_mm_mol(atoms_or_coords, charges, unit)
return qmmm_for_scf(scf_method, mm_mol)
def add_mm_charges_grad(scf_grad, atoms_or_coords, charges, unit=None):
'''Apply the MM charges in the QM gradients' method. It affects both the
electronic and nuclear parts of the QM fragment.
Args:
scf_grad : a HF or DFT gradient object (grad.HF or grad.RKS etc)
Once the add_mm_charges_grad was applied, it affects all post-HF
calculations eg MP2, CCSD, MCSCF etc
coords : 2D array, shape (N,3)
MM particle coordinates
charges : 1D array
MM particle charges
Kwargs:
unit : str
Bohr, AU, Ang (case insensitive). Default is the same to mol.unit
Returns:
Same gradeints method object as the input scf_grad method
Examples:
>>> from pyscf import gto, scf, grad
>>> mol = gto.M(atom='H 0 0 0; F 0 0 1', basis='ccpvdz', verbose=0)
>>> mf = mm_charge(scf.RHF(mol), [(0.5,0.6,0.8)], [-0.3])
>>> mf.kernel()
-101.940495711284
>>> hfg = mm_charge_grad(grad.hf.RHF(mf), coords, charges)
>>> hfg.kernel()
[[-0.25912357 -0.29235976 -0.38245077]
[-1.70497052 -1.89423883 1.2794798 ]]
'''
assert (isinstance(scf_grad, grad.rhf.Gradients))
mol = scf_grad.mol
if unit is None:
unit = mol.unit
mm_mol = mm_mole.create_mm_mol(atoms_or_coords, charges, unit)
mm_grad = qmmm_grad_for_scf(scf_grad)
mm_grad.base.mm_mol = mm_mol
return mm_grad