Class Avogadro::Core::GaussianSet#
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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
Public Functions
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GaussianSet()#
Constructor.
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~GaussianSet() override#
Destructor.
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inline virtual GaussianSet *clone() const override#
Clone.
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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.
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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.
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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).
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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.
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inline int setCount()#
Get the number of elements in the set.
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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.
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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.
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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.
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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).
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bool setDensityMatrix(const MatrixX &m)#
Set the SCF density matrix for the GaussianSet.
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bool setSpinDensityMatrix(const MatrixX &m)#
Set the spin density matrix for the GaussianSet.
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bool generateDensityMatrix()#
Generate the density matrix if we have the required information.
- Returns:
True on success, false on failure.
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bool generateSpinDensityMatrix()#
Generate the spin density matrix if we have the required information.
- Returns:
True on success, false on failure.
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virtual unsigned int molecularOrbitalCount(ElectronType type = Paired) override#
- Returns:
The number of molecular orbitals in the GaussianSet.
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void outputAll(ElectronType type = Paired)#
Debug routine, outputs all of the data in the GaussianSet.
- Parameters:
type – The electrons to output the information for.
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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.
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inline void setScfType(ScfType type)#
Set the SCF type for the object.
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inline ScfType scfType() const#
Get the SCF type for the object.
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inline void setFunctionalName(const std::string &name)#
Set the functional name (if applicable).
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inline std::string functionalName() const#
Get the functional name (empty if none used).
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void initCalculation()#
Initialize the calculation, this must normally be done before anything.
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inline std::vector<int> &symmetry()#
Accessors for the various properties of the GaussianSet.
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inline std::vector<int> symmetry() const#
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inline std::vector<unsigned int> &atomIndices()#
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inline std::vector<unsigned int> atomIndices() const#
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inline std::vector<unsigned int> &moIndices()#
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inline std::vector<unsigned int> moIndices() const#
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inline std::vector<unsigned int> >oIndices()#
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inline std::vector<unsigned int> gtoIndices() const#
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inline std::vector<unsigned int> &cIndices()#
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inline std::vector<unsigned int> cIndices() const#
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inline std::vector<double> >oA()#
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inline std::vector<double> gtoA() const#
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inline std::vector<double> >oC()#
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inline std::vector<double> gtoC() const#
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inline std::vector<double> >oCN()#
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inline MatrixX &moMatrix(ElectronType type = Paired)#
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inline MatrixX moMatrix(ElectronType type = Paired) const#
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inline std::vector<double> &moEnergy(ElectronType type = Paired)#
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inline std::vector<double> moEnergy(ElectronType type = Paired) const#
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inline std::vector<unsigned char> &moOccupancy(ElectronType type = Paired)#
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inline std::vector<unsigned char> moOccupancy(ElectronType type = Paired) const#
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inline std::vector<unsigned int> &moNumber(ElectronType type = Paired)#
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inline std::vector<unsigned int> moNumber(ElectronType type = Paired) const#
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inline MatrixX &densityMatrix()#
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inline MatrixX &spinDensityMatrix()#