Storage class for relevant information of a dimer (pair) of Molecule objects. More...

#include <dimer.h>

Public Types
enum class	MoleculeOrder : bool { AB = true , BA = false }
	An enum to clarify the order of information presented when for merged arrays e.g. More...

Public Member Functions
	Dimer ()=default

	Dimer (const Molecule &mol_A, const Molecule &mol_B)
	Constructor from two Molecule objects.

	Dimer (const std::vector< occ::core::Atom > &atoms_A, const std::vector< occ::core::Atom > &atoms_B)
	Constructor from two std::vector<Atom> objects.

Vec3	centroid () const

const Molecule &	a () const
	Convenience wrapper to access the Molecule instance for Molecule A.

const Molecule &	b () const
	Convenience wrapper to access the Molecule instance for Molecule B.

double	centroid_distance () const
	Calculate the centroid - centroid distance between A & B.

double	center_of_mass_distance () const
	Calculate the distance between centre of mass of Molecules A & B.

double	nearest_distance () const
	Calculate the distance between closest pair of Atoms in Molecules A & B.

std::optional< occ::Mat4 >	symmetry_relation () const
	The symmetry operation to transform from Molecule A to Molecule B, if there is one.

Vec3	v_ab () const
	The vector from centroid of Molecule A to the centroid of Molecule B.

Vec	vdw_radii (MoleculeOrder order=MoleculeOrder::AB) const
	Vector of van der Waals radii for the atoms in this Dimer.

IVec	atomic_numbers (MoleculeOrder order=MoleculeOrder::AB) const
	Vector of atomic numbers for the atoms in this Dimer.

Mat3N	positions (MoleculeOrder order=MoleculeOrder::AB) const
	The positions of all atoms in this Dimer.

int	num_electrons () const
	The total number of electrons in this Dimer.

int	charge () const
	The net charge of this Dimer.

int	multiplicity () const
	The net spin multiplicity of this Dimer.

void	set_interaction_id (size_t i)
	Set the index or identifier for which interaction this Dimer represents.

size_t	interaction_id () const
	Get the index or identifier for which interaction this Dimer represents.

void	set_interaction_energy (double e, const std::string &key="Total")
	Set the value of the interaction energy for this Dimer.

double	interaction_energy (const std::string &key="Total") const
	Get the stored interaction energy for this Dimer.

void	set_interaction_energies (const ankerl::unordered_dense::map< std::string, double > &e)

const auto &	interaction_energies () const
	Get the stored interaction energy components for this Dimer.

bool	same_asymmetric_molecule_idxs (const Dimer &rhs) const
	Check if two dimers have the same asymmetric molecul indexes.

bool	operator== (const Dimer &rhs) const
	Check if two dimers are identical under some transformation.

bool	operator!= (const Dimer &rhs) const
	Check if two dimers are not identical under some transformation.

bool	equivalent_in_opposite_frame (const Dimer &b, const Mat3 &rot=Mat3::Identity()) const
	Check if two dimers are identical in the opposite reference frame.

bool	equivalent (const Dimer &b, const Mat3 &rot=Mat3::Identity()) const
	Check if two dimers are identical in the same reference frame.

const auto &	name () const

void	set_name (const std::string &name)

std::string	xyz_string () const

void	set_property (const std::string &key, const std::string &value)
	Set the value of a property for this Dimer.

const auto &	properties () const

void	set_properties (const ankerl::unordered_dense::map< std::string, std::string > &p)

Detailed Description

Storage class for relevant information of a dimer (pair) of Molecule objects.

The role of the Dimer class is to store information about a pair of molecules which represents a dimer, and to calculate relevant properties.

Member Enumeration Documentation

◆ MoleculeOrder

enum class occ::core::Dimer::MoleculeOrder : bool

strong

An enum to clarify the order of information presented when for merged arrays e.g.

atomic_numbers(), positions() etc.

Enumerator
AB	The A molecule data is first, then B.
BA	The B molecule data is first, then A.

Constructor & Destructor Documentation

◆ Dimer() [1/3]

occ::core::Dimer::Dimer ( )

default

◆ Dimer() [2/3]

occ::core::Dimer::Dimer	(	const Molecule &	mol_A,
		const Molecule &	mol_B
	)

Constructor from two Molecule objects.

Parameters

mol_A	Molecule A
mol_B	Molecule B

A copy of these two molecules is kept internally, so they need not exist outside this Dimer. Further, any changes to those Molecule objects after Dimer construction will not appear here.

◆ Dimer() [3/3]

occ::core::Dimer::Dimer	(	const std::vector< occ::core::Atom > &	atoms_A,
		const std::vector< occ::core::Atom > &	atoms_B
	)

Constructor from two std::vector<Atom> objects.

Parameters

atoms_A	atoms representing/constituting Molecule A
atoms_B	atoms representing/constituting Molecule B

The data from these two vectors is copied internally, so they need not exist outside this Dimer. Further, any changes to those Atom objects after Dimer construction will not appear here.

Member Function Documentation

◆ a()

const Molecule & occ::core::Dimer::a ( ) const

inline

Convenience wrapper to access the Molecule instance for Molecule A.

Returns: Molecule A

◆ atomic_numbers()

IVec occ::core::Dimer::atomic_numbers ( MoleculeOrder order = MoleculeOrder::AB ) const

Vector of atomic numbers for the atoms in this Dimer.

Parameters

order specify whether the atomic numbers of the atoms in Molecule A should be first, or those in Molecule B.

Returns: an IVec object representing the atomic numbers of atoms in the Dimer in the specified (AB or BA) order.

◆ b()

const Molecule & occ::core::Dimer::b ( ) const

inline

Convenience wrapper to access the Molecule instance for Molecule B.

Returns: Molecule A

◆ center_of_mass_distance()

double occ::core::Dimer::center_of_mass_distance ( ) const

Calculate the distance between centre of mass of Molecules A & B.

Returns: a double representing the distance (in Angstroms) between the centre of mass of Molecule A and centre of mass of Molecule B.

◆ centroid()

Vec3 occ::core::Dimer::centroid ( ) const

◆ centroid_distance()

double occ::core::Dimer::centroid_distance ( ) const

Calculate the centroid - centroid distance between A & B.

Returns: a double representing the distance (in Angstroms) between the centroid of Molecule A and Molecule B. The centroid is the geometric average positions (it is not the centre of mass).

◆ charge()

int occ::core::Dimer::charge ( ) const

inline

The net charge of this Dimer.

Returns: an integer with value equal to the sum of the net charge of Molecule A and the net charge of Molecule B.

◆ equivalent()

bool occ::core::Dimer::equivalent	(	const Dimer &	b,
		const Mat3 &	rot = `Mat3::Identity()`
	)		const

Check if two dimers are identical in the same reference frame.

Parameters

b	another Dimer object
rot	a Matrix representing a rotation, applied to A.

Returns: True if the Dimer objects are found to be equivalent.

This is defined such that that Dimer b will be equivalent if Molecule B from the reference frame of Molecule A is equivalent to Molecule rhs.B in the reference frame of rhs.A

◆ equivalent_in_opposite_frame()

bool occ::core::Dimer::equivalent_in_opposite_frame	(	const Dimer &	b,
		const Mat3 &	rot = `Mat3::Identity()`
	)		const

Check if two dimers are identical in the opposite reference frame.

Parameters

b	another Dimer object
rot	a Matrix representing a rotation, applied to A.

Returns: True if the Dimer objects are found to be equivalent.

The opposite reference frame here is that Dimer b will be equivalent if Molecule B from the reference frame of Molecule A is equivalent to Molecule rhs.A in the reference frame of rhs.B

◆ interaction_energies()

const auto & occ::core::Dimer::interaction_energies ( ) const

inline

Get the stored interaction energy components for this Dimer.

Returns: a map representing the interaction energies, index by string identifiers

◆ interaction_energy()

double occ::core::Dimer::interaction_energy ( const std::string & key = "Total" ) const

Get the stored interaction energy for this Dimer.

Parameters

key	a string labelling the component of the interaction energy.

Returns: a double representing the interaction energy (default = 0.0)

◆ interaction_id()

size_t occ::core::Dimer::interaction_id ( ) const

inline

Get the index or identifier for which interaction this Dimer represents.

Returns: a size_t representing the interaction index (default = 0)

◆ multiplicity()

int occ::core::Dimer::multiplicity ( ) const

inline

The net spin multiplicity of this Dimer.

Returns: an integer with value equal to net spin multiplicity when combining Molecule A and Molecule B.

◆ name()

const auto & occ::core::Dimer::name ( ) const

inline

◆ nearest_distance()

double occ::core::Dimer::nearest_distance ( ) const

Calculate the distance between closest pair of Atoms in Molecules A & B.

Returns: a double representing the distance (in Angstroms) between the nearest pair of Atoms (one from Molecule A & one from Molecule B).

Note: This will be significantly more expensive and scale as O(Na * Nb) for the number of atoms Na in Molecule A and Nb for the number of atoms in Molecule B

◆ num_electrons()

int occ::core::Dimer::num_electrons ( ) const

inline

The total number of electrons in this Dimer.

Returns: an integer with value equal to the sum of the number of electrons in Molecule A and the number of electrons in Molecule B.

◆ operator!=()

bool occ::core::Dimer::operator!= ( const Dimer & rhs ) const

inline

Check if two dimers are not identical under some transformation.

Parameters

rhs	another Dimer object

Returns: True if the dimers are not found to be identical.

Uses Dimer::operator== to find the result.

◆ operator==()

bool occ::core::Dimer::operator== ( const Dimer & rhs ) const

Check if two dimers are identical under some transformation.

Parameters

rhs	another Dimer object

Returns: True if the dimers are found to be identical.

The working definition of equality here is such that all the following must be true:

The asymmetric molecule indices must be the same i.e. calling same_asymmetric_molecule_idxs yields true.
Both Dimers have the same centroid_distance, center_of_mass_distance and nearest_atom_distance
Either this.a is equivalent to rhs.a and this.b is equivalent to rhs.b, or this.a is equivalent to rhs.b and rhs.a is equivalent to this.b. See Molecule::equivalent_to

◆ positions()

Mat3N occ::core::Dimer::positions ( MoleculeOrder order = MoleculeOrder::AB ) const

The positions of all atoms in this Dimer.

Parameters

order specify whether the positions of the atoms in Molecule A should be first, or those in Molecule B.

Returns: A (3, N) matrix of atomic positions for the atoms in this dimer, in Angstroms

◆ properties()

const auto & occ::core::Dimer::properties ( ) const

inline

◆ same_asymmetric_molecule_idxs()

bool occ::core::Dimer::same_asymmetric_molecule_idxs ( const Dimer & rhs ) const

Check if two dimers have the same asymmetric molecul indexes.

Parameters

rhs	another Dimer object

Returns: True if all the asymmetric Molecule indices of all Molecules have been set, and they are equal (ignoring ordering of AB in either Dimer).

◆ set_interaction_energies()

void occ::core::Dimer::set_interaction_energies ( const ankerl::unordered_dense::map< std::string, double > & e )

inline

◆ set_interaction_energy()

void occ::core::Dimer::set_interaction_energy	(	double	e,
		const std::string &	key = `"Total"`
	)

Set the value of the interaction energy for this Dimer.

Parameters

e	a double representing the interaction energy.
key	a string labelling the component of the interaction energy.

◆ set_interaction_id()

void occ::core::Dimer::set_interaction_id ( size_t i )

inline

Set the index or identifier for which interaction this Dimer represents.

Parameters

i	the interaction index.

◆ set_name()

void occ::core::Dimer::set_name ( const std::string & name )

inline

◆ set_properties()

void occ::core::Dimer::set_properties ( const ankerl::unordered_dense::map< std::string, std::string > & p )

inline

◆ set_property()

void occ::core::Dimer::set_property	(	const std::string &	key,
		const std::string &	value
	)

inline

Set the value of a property for this Dimer.

Parameters

key	a string labelling the property.
value	a string containing the value of the property

◆ symmetry_relation()

std::optional< occ::Mat4 > occ::core::Dimer::symmetry_relation ( ) const

The symmetry operation to transform from Molecule A to Molecule B, if there is one.

Returns: either std::nullopt if Molecule A and Molecule B are not symmetry related, or a Mat4 object containing the rotation and translation to transform Molecule A to Molecule B.

Under the hood, this uses the Kabsch algorithm

◆ v_ab()

Vec3 occ::core::Dimer::v_ab ( ) const

The vector from centroid of Molecule A to the centroid of Molecule B.

Returns: a Vec3 representing the vector between the centroid of A and the centroid of B.

◆ vdw_radii()

Vec occ::core::Dimer::vdw_radii ( MoleculeOrder order = MoleculeOrder::AB ) const

Vector of van der Waals radii for the atoms in this Dimer.

Parameters

order specify whether the radii of the atoms in Molecule A should be first, or those in Molecule B.

Returns: a Vec object representing the van der Waals radii of atoms in the Dimer in the specified (AB or BA) order, in Angstroms.

◆ xyz_string()

std::string occ::core::Dimer::xyz_string ( ) const

The documentation for this class was generated from the following file:

/home/runner/work/occ/occ/include/occ/core/dimer.h

Public Types

Public Member Functions

Detailed Description

Member Enumeration Documentation

◆ MoleculeOrder

Constructor & Destructor Documentation

◆ Dimer() [1/3]

◆ Dimer() [2/3]

◆ Dimer() [3/3]

Member Function Documentation

◆ a()

◆ atomic_numbers()

◆ b()

◆ center_of_mass_distance()

◆ centroid()

◆ centroid_distance()

◆ charge()

◆ equivalent()

◆ equivalent_in_opposite_frame()

◆ interaction_energies()

◆ interaction_energy()

◆ interaction_id()

◆ multiplicity()

◆ name()

◆ nearest_distance()

◆ num_electrons()

◆ operator!=()

◆ operator==()

◆ positions()

◆ properties()

◆ same_asymmetric_molecule_idxs()

◆ set_interaction_energies()

◆ set_interaction_energy()

◆ set_interaction_id()

◆ set_name()

◆ set_properties()

◆ set_property()

◆ symmetry_relation()

◆ v_ab()

◆ vdw_radii()

◆ xyz_string()