Class Avogadro::Core::GaussianSet

class GaussianSet : public BasisSet

A container for Gaussian type outputs from QM codes.

The GaussianSet class has a transparent data structure for storing the basis sets output by many quantum mechanical codes. It has a certain hierarchy where shells are built up from n primitives, in this case Gaussian Type Orbitals (GTOs). Each shell has a type (S, P, D, F, etc) and is composed of one or more GTOs. Each GTO has a contraction coefficient, c, and an exponent, a.

Author

Marcus D. Hanwell

When calculating Molecular Orbitals (MOs) each orthogonal shell has an independent coefficient. That is the S type orbitals have one coefficient, the P type orbitals have three coefficients (Px, Py and Pz), the D type orbitals have five (or six if cartesian types) coefficients, and so on.

Public Types

enum orbital

Enumeration of the Gaussian type orbitals.

Values:

enumerator S

enumerator SP

enumerator P

enumerator D

enumerator D5

enumerator F

enumerator F7

enumerator G

enumerator G9

enumerator H

enumerator H11

enumerator I

enumerator I13

enumerator UU

Public Functions

GaussianSet()

Constructor.

~GaussianSet() override

Destructor.

inline virtual GaussianSet *clone() const override

Clone.

unsigned int addBasis(unsigned int atom, orbital type)

Add a basis to the basis set.

Parameters:

• atom – Index of the atom to add the Basis to.

• type – The type of the Basis being added.

Returns:

The index of the added Basis.

unsigned int addGto(unsigned int basis, double c, double a)

Add a GTO to the supplied basis.

Parameters:

• basis – The index of the Basis to add the GTO to.

• c – The contraction coefficient of the GTO.

• a – The exponent of the GTO.

Returns:

The index of the added GTO.

void setMolecularOrbitals(const std::vector<double> &MOs, ElectronType type = Paired)

Set the molecular orbital (MO) coefficients to the GaussianSet.

Parameters:

• MOs – Vector containing the MO coefficients for the GaussianSet.

• type – The type of the MOs (Paired, Alpha, Beta).

void setMolecularOrbitals(const std::vector<double> &MOs, ElectronType type, Index index)

Set the molecular orbital (MO) coefficients for a given index. Note that this must be used with coordinate sets to work correctly.

Parameters:

• MOs – Vector containing the MO coefficients for the GaussianSet.

• type – The type of the MOs (Paired, Alpha, Beta).

• index – The index of the MO in the sequence.

inline int setCount()

Get the number of elements in the set.

bool setActiveSetStep(int index)

Set the active element in the set, this expects a corresponding coordinate set element, and will change the active MO matrix.

void setMolecularOrbitalEnergy(const std::vector<double> &energies, ElectronType type = Paired)

Set the molecular orbital energies, expected in Hartrees.

Parameters:

• energies – The vector containing energies for the MOs of type

• type – The type of the electrons being set.

void setMolecularOrbitalOccupancy(const std::vector<unsigned char> &occ, ElectronType type = Paired)

Set the molecular orbital occupancies.

Parameters:

• occ – The occupancies for the MOs of type.

• type – The type of the electrons being set.

void setMolecularOrbitalNumber(const std::vector<unsigned int> &nums, ElectronType type = Paired)

This enables support of sparse orbital sets, and provides a mapping from the index in memory to the actual molecular orbital number.

Parameters:

• nums – The MO numbers (starting with an index of 1 for the first one).

• type – The MO type (Paired, Alpha, Beta).

bool setDensityMatrix(const MatrixX &m)

Set the SCF density matrix for the GaussianSet.

bool setSpinDensityMatrix(const MatrixX &m)

Set the spin density matrix for the GaussianSet.

bool generateDensityMatrix()

Generate the density matrix if we have the required information.

Returns:

True on success, false on failure.

bool generateSpinDensityMatrix()

Generate the spin density matrix if we have the required information.

Returns:

True on success, false on failure.

virtual unsigned int molecularOrbitalCount(ElectronType type = Paired) override

Returns:

The number of molecular orbitals in the GaussianSet.

void outputAll(ElectronType type = Paired)

Debug routine, outputs all of the data in the GaussianSet.

Parameters:

type – The electrons to output the information for.

virtual bool isValid() override

Returns:

True of the basis set is valid, false otherwise. Default is true, if false then the basis set is likely unusable.

inline void setScfType(ScfType type)

Set the SCF type for the object.

inline ScfType scfType() const

Get the SCF type for the object.

inline void setFunctionalName(const std::string &name)

Set the functional name (if applicable).

inline std::string functionalName() const

Get the functional name (empty if none used).

void initCalculation()

Initialize the calculation, this must normally be done before anything.

inline std::vector<int> &symmetry()

Accessors for the various properties of the GaussianSet.

inline std::vector<int> symmetry() const

inline std::vector<unsigned int> &atomIndices()

inline std::vector<unsigned int> atomIndices() const

inline std::vector<unsigned int> &moIndices()

inline std::vector<unsigned int> moIndices() const

inline std::vector<unsigned int> &gtoIndices()

inline std::vector<unsigned int> gtoIndices() const

inline std::vector<unsigned int> &cIndices()

inline std::vector<unsigned int> cIndices() const

inline std::vector<double> &gtoA()

inline std::vector<double> gtoA() const

inline std::vector<double> &gtoC()

inline std::vector<double> gtoC() const

inline std::vector<double> &gtoCN()

inline MatrixX &moMatrix(ElectronType type = Paired)

inline MatrixX moMatrix(ElectronType type = Paired) const

inline std::vector<double> &moEnergy(ElectronType type = Paired)

inline std::vector<double> moEnergy(ElectronType type = Paired) const

inline std::vector<unsigned char> &moOccupancy(ElectronType type = Paired)

inline std::vector<unsigned char> moOccupancy(ElectronType type = Paired) const

inline std::vector<unsigned int> &moNumber(ElectronType type = Paired)

inline std::vector<unsigned int> moNumber(ElectronType type = Paired) const

inline MatrixX &densityMatrix()

inline MatrixX &spinDensityMatrix()