pydft_qmmm.interfaces.interface.MMInterface¶

class pydft_qmmm.interfaces.interface.MMInterface(system)[source]¶

The abstract MM interface base class.

Parameters:: system (System) – The system that will inform the interface to the external software.

theory_level¶: The level of theory that the software applies in energy and force calculations.

Methods

`add_non_elst`(atoms[, inclusion])	Add a non-electrostatic interaction for the specified atoms.
`add_real_elst`(atoms[, const, inclusion])	Add Coulomb interaction for the specified atoms.
`get_pme_parameters`()	Get the parameters used for PME summation.
`zero_charges`(atoms)	Remove charges from the specified atoms.
`zero_forces`(atoms)	Zero forces on the specified atoms.
`zero_intermolecular`(atoms)	Remove inter-molecular interactions for the specified atoms.
`zero_intramolecular`(atoms)	Remove intra-molecular interactions for the specified atoms.

abstractmethod add_non_elst(atoms, inclusion=None)[source]¶

Add a non-electrostatic interaction for the specified atoms.

Parameters:

atoms (frozenset[int]) – The indices of atoms for which to add non-electrostatic, non-bonded interactions.
inclusion (ndarray[tuple[Any, ...], dtype[float64]] | None, default: None) – An Nx3 array with values that will be applied to the forces of the non-electrostatic interaction through element-wise multiplication.

Return type:

None

abstractmethod add_real_elst(atoms, const=1, inclusion=None)[source]¶

Add Coulomb interaction for the specified atoms.

Parameters:

atoms (frozenset[int]) – The indices of atoms for which to add a Coulomb interaction.
const (float | int, default: 1) – A constant to multiply at the beginning of the coulomb expression.
inclusion (ndarray[tuple[Any, ...], dtype[float64]] | None, default: None) – An Nx3 array with values that will be applied to the forces of the Coulomb interaction through element-wise multiplication.

Return type:

None

abstractmethod get_pme_parameters()[source]¶

Get the parameters used for PME summation.

Return type:: tuple[float, tuple[int, int, int], int]
Returns:: The Gaussian width parameter in Ewald summation (\(\mathrm{\mathring(A)^{-1}}\)), the number of grid points to include along each lattice edge, and the order of splines used on the FFT grid.

abstractmethod zero_charges(atoms)[source]¶

Remove charges from the specified atoms.

Parameters:: atoms (frozenset[int]) – The indices of atoms from which to remove charges.
Return type:: None

abstractmethod zero_forces(atoms)[source]¶

Zero forces on the specified atoms.

Parameters:: atoms (frozenset[int]) – The indices of atoms for which to zero forces.
Return type:: None

abstractmethod zero_intermolecular(atoms)[source]¶

Remove inter-molecular interactions for the specified atoms.

Parameters:: atoms (frozenset[int]) – The indices of atoms from which to remove inter-molecular interactions.
Return type:: None

abstractmethod zero_intramolecular(atoms)[source]¶

Remove intra-molecular interactions for the specified atoms.

Parameters:: atoms (frozenset[int]) – The indices of atoms to from which to remove intra-molecular interactions.
Return type:: None