text: /******************************************************************************
  
    This source file is part of the Avogadro project.
  
    Copyright 2008-2009 Marcus D. Hanwell
    Copyright 2008 Albert De Fusco
    Copyright 2010-2013 Kitware, Inc.
  
    This source code is released under the New BSD License, (the "License").
  
    Unless required by applicable law or agreed to in writing, software
    distributed under the License is distributed on an "AS IS" BASIS,
    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
    See the License for the specific language governing permissions and
    limitations under the License.
  
  ******************************************************************************/
  
  #ifndef AVOGADRO_CORE_GAUSSIANSET_H
  #define AVOGADRO_CORE_GAUSSIANSET_H
  
  #include "basisset.h"
  
  #include <avogadro/core/matrix.h>
  #include <avogadro/core/vector.h>
  
  #include <vector>
  
  namespace Avogadro {
  namespace Core {
  
  /**
   * Enumeration of the SCF type.
   */
  enum ScfType
  {
    Rhf,
    Uhf,
    Rohf,
    Unknown
  };
  
  /**
   * @class GaussianSet gaussianset.h <avogadro/core/gaussianset.h>
   * @brief A container for Gaussian type outputs from QM codes.
   * @author Marcus D. Hanwell
   *
   * 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.
   *
   * 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.
   */
  
  class AVOGADROCORE_EXPORT GaussianSet : public BasisSet
  {
  public:
    /**
     * Constructor.
     */
    GaussianSet();
  
    /**
     * Destructor.
     */
    ~GaussianSet() override;
  
    /**
     * Clone.
     */
    GaussianSet* clone() const override { return new GaussianSet(*this); }
  
    /**
     * Enumeration of the Gaussian type orbitals.
     */
    enum orbital
    {
      S,
      SP,
      P,
      D,
      D5,
      F,
      F7,
      G,
      G9,
      H,
      H11,
      I,
      I13,
      UU
    };
  
    /**
     * Add a basis to the basis set.
     * @param atom Index of the atom to add the Basis to.
     * @param type The type of the Basis being added.
     * @return The index of the added Basis.
     */
    unsigned int addBasis(unsigned int atom, orbital type);
  
    /**
     * Add a GTO to the supplied basis.
     * @param basis The index of the Basis to add the GTO to.
     * @param c The contraction coefficient of the GTO.
     * @param a The exponent of the GTO.
     * @return The index of the added GTO.
     */
    unsigned int addGto(unsigned int basis, double c, double a);
  
    /**
     * Set the molecular orbital (MO) coefficients to the GaussianSet.
     * @param MOs Vector containing the MO coefficients for the GaussianSet.
     * @param type The type of the MOs (Paired, Alpha, Beta).
     */
    void setMolecularOrbitals(const std::vector<double>& MOs,
                              ElectronType type = Paired);
  
    /**
     * Set the molecular orbital (MO) coefficients for a given index. Note
     * that this must be used with coordinate sets to work correctly.
     * @param MOs Vector containing the MO coefficients for the GaussianSet.
     * @param type The type of the MOs (Paired, Alpha, Beta).
     * @param index The index of the MO in the sequence.
     */
    void setMolecularOrbitals(const std::vector<double>& MOs, ElectronType type,
                              Index index);
  
    /**
     * Get the number of elements in the set.
     */
    int setCount() { return static_cast<int>(m_moMatrixSet[0].size()); }
  
    /**
     * Set the active element in the set, this expects a corresponding
     * coordinate set element, and will change the active MO matrix.
     */
    bool setActiveSetStep(int index);
  
    /**
     * @brief Set the molecular orbital energies, expected in Hartrees.
     * @param energies The vector containing energies for the MOs of type
     * @param type The type of the electrons being set.
     */
    void setMolecularOrbitalEnergy(const std::vector<double>& energies,
                                   ElectronType type = Paired);
  
    /**
     * @brief Set the molecular orbital occupancies.
     * @param occ The occupancies for the MOs of type.
     * @param type The type of the electrons being set.
     */
    void setMolecularOrbitalOccupancy(const std::vector<unsigned char>& occ,
                                      ElectronType type = Paired);
  
    /**
     * @brief This enables support of sparse orbital sets, and provides a mapping
     * from the index in memory to the actual molecular orbital number.
     * @param nums The MO numbers (starting with an index of 1 for the first one).
     * @param type The MO type (Paired, Alpha, Beta).
     */
    void setMolecularOrbitalNumber(const std::vector<unsigned int>& nums,
                                   ElectronType type = Paired);
  
    /**
     * Set the SCF density matrix for the GaussianSet.
     */
    bool setDensityMatrix(const MatrixX& m);
  
    /**
     * Set the spin density matrix for the GaussianSet.
     */
    bool setSpinDensityMatrix(const MatrixX& m);
  
    /**
     * @brief Generate the density matrix if we have the required information.
     * @return True on success, false on failure.
     */
    bool generateDensityMatrix();
  
    /**
     * @return The number of molecular orbitals in the GaussianSet.
     */
    unsigned int molecularOrbitalCount(ElectronType type = Paired) override;
  
    /**
     * Debug routine, outputs all of the data in the GaussianSet.
     * @param The electrons to output the information for.
     */
    void outputAll(ElectronType type = Paired);
  
    /**
     * @return True of the basis set is valid, false otherwise.
     * Default is true, if false then the basis set is likely unusable.
     */
    bool isValid() override;
  
    /**
     * Set the SCF type for the object.
     */
    void setScfType(ScfType type) { m_scfType = type; }
  
    /**
     * Get the SCF type for the object.
     */
    ScfType scfType() const { return m_scfType; }
  
    /**
     * Set the functional name (if applicable).
     */
    void setFunctionalName(const std::string& name) { m_functionalName = name; }
  
    /**
     * Get the functional name (empty if none used).
     */
    std::string functionalName() const { return m_functionalName; }
  
    /**
     * Initialize the calculation, this must normally be done before anything.
     */
    void initCalculation();
  
    /**
     * Accessors for the various properties of the GaussianSet.
     */
    std::vector<int>& symmetry() { return m_symmetry; }
    std::vector<int> symmetry() const { return m_symmetry; }
    std::vector<unsigned int>& atomIndices() { return m_atomIndices; }
    std::vector<unsigned int> atomIndices() const { return m_atomIndices; }
    std::vector<unsigned int>& moIndices() { return m_moIndices; }
    std::vector<unsigned int> moIndices() const { return m_moIndices; }
    std::vector<unsigned int>& gtoIndices() { return m_gtoIndices; }
    std::vector<unsigned int> gtoIndices() const { return m_gtoIndices; }
    std::vector<unsigned int>& cIndices() { return m_cIndices; }
    std::vector<unsigned int> cIndices() const { return m_cIndices; }
    std::vector<double>& gtoA() { return m_gtoA; }
    std::vector<double> gtoA() const { return m_gtoA; }
    std::vector<double>& gtoC() { return m_gtoC; }
    std::vector<double> gtoC() const { return m_gtoC; }
    std::vector<double>& gtoCN()
    {
      initCalculation();
      return m_gtoCN;
    }
  
    MatrixX& moMatrix(ElectronType type = Paired)
    {
      if (type == Paired || type == Alpha)
        return m_moMatrix[0];
      else
        return m_moMatrix[1];
    }
  
    MatrixX moMatrix(ElectronType type = Paired) const
    {
      if (type == Paired || type == Alpha)
        return m_moMatrix[0];
      else
        return m_moMatrix[1];
    }
  
    std::vector<double>& moEnergy(ElectronType type = Paired)
    {
      if (type == Paired || type == Alpha)
        return m_moEnergy[0];
      else
        return m_moEnergy[1];
    }
  
    std::vector<double> moEnergy(ElectronType type = Paired) const
    {
      if (type == Paired || type == Alpha)
        return m_moEnergy[0];
      else
        return m_moEnergy[1];
    }
  
    std::vector<unsigned char>& moOccupancy(ElectronType type = Paired)
    {
      if (type == Paired || type == Alpha)
        return m_moOccupancy[0];
      else
        return m_moOccupancy[1];
    }
  
    std::vector<unsigned char> moOccupancy(ElectronType type = Paired) const
    {
      if (type == Paired || type == Alpha)
        return m_moOccupancy[0];
      else
        return m_moOccupancy[1];
    }
  
    std::vector<unsigned int>& moNumber(ElectronType type = Paired)
    {
      if (type == Paired || type == Alpha)
        return m_moNumber[0];
      else
        return m_moNumber[1];
    }
  
    std::vector<unsigned int> moNumber(ElectronType type = Paired) const
    {
      if (type == Paired || type == Alpha)
        return m_moNumber[0];
      else
        return m_moNumber[1];
    }
  
    MatrixX& densityMatrix() { return m_density; }
    MatrixX& spinDensityMatrix() { return m_spinDensity; }
  
  private:
    /**
     * @brief This group is used once, and refers to the entire molecule.
     */
    std::vector<int> m_symmetry;             //! Symmetry of the basis, S, P...
    std::vector<unsigned int> m_atomIndices; //! Indices into the atomPos vector
    std::vector<unsigned int> m_moIndices;  //! Indices into the MO/density matrix
    std::vector<unsigned int> m_gtoIndices; //! Indices into the GTO vector
    std::vector<unsigned int> m_cIndices;   //! Indices into m_gtoCN
    std::vector<double> m_gtoA;             //! The GTO exponent
    std::vector<double> m_gtoC;             //! The GTO contraction coefficient
    std::vector<double> m_gtoCN; //! The GTO contraction coefficient (normalized)
  
    /**
     * @brief This block can be once (doubly) or in two parts (alpha and beta) for
     * open shell calculations.
     */
    MatrixX m_moMatrix[2]; //! MO coefficient matrix
  
    /**
     * @brief If there are a sequence of related MOs, they are stored here, and
     * set as the active MOs upon demand. Alpha will store Paired or the Alpha,
     * Beta will store Beta coefficients for the appropriate calculation types.
     */
    std::vector<MatrixX> m_moMatrixSet[2];
  
    /**
     * @brief This block stores energies for the molecular orbitals (same
     * convention as the molecular orbital coefficients).
     */
    std::vector<double> m_moEnergy[2];
  
    /**
     * @brief The occupancy of the molecular orbitals.
     */
    std::vector<unsigned char> m_moOccupancy[2];
  
    /**
     * @brief This stores the molecular orbital number (when they are sparse). It
     * is used to lookup the actual index of the molecular orbital data.
     */
    std::vector<unsigned int> m_moNumber[2];
  
    MatrixX m_density;     //! Density matrix
    MatrixX m_spinDensity; //! Spin Density matrix
  
    unsigned int m_numMOs; //! The number of GTOs (not always!)
    bool m_init;           //! Has the calculation been initialised?
  
    ScfType m_scfType;
  
    std::string m_functionalName;
  
    /**
     * @brief Generate the density matrix if we have the required information.
     * @return True on success, false on failure.
     */
    bool generateDensity();
  
    /**
     * @brief Generate the spin density matrix if we have the required
     * information.
     * @return True on success, false on failure.
     */
    bool generateSpinDensity();
  };
  
  } // End Core namespace
  } // End Avogadro namespace
  
  #endif
  