/* 
 *            Copyright 2009-2018 The VOTCA Development Team
 *                       (http://www.votca.org)
 *
 *      Licensed under the Apache License, Version 2.0 (the "License")
 *
 * You may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *              http://www.apache.org/licenses/LICENSE-2.0
 *
 * 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 VOTCA_XTP_AOBASIS_H
#define	VOTCA_XTP_AOBASIS_H


#include <boost/math/constants/constants.hpp>
#include <votca/xtp/basisset.h>
#include <votca/xtp/qmmolecule.h>
#include <votca/xtp/eigen.h>
#include <votca/xtp/aoshell.h>


namespace votca { namespace xtp {

/**
 * \brief Container to hold Basisfunctions for all atoms 
 * 
 * It is constructed from a vector of QMAtoms and a BasisSet.
 */
class AOBasis 
{   
public:
    
    void ReorderMOs(Eigen::MatrixXd &v,const std::string& start, const std::string& target ); 
       
    void ReorderMatrix(Eigen::MatrixXd &v,const std::string& start,const std::string& target );

    void AOBasisFill( const BasisSet& bs , const QMMolecule& atoms, int fragbreak = -1);
    
//returns element names for which no ecp was found
    std::vector<std::string> ECPFill( const BasisSet& bs , QMMolecule& atoms);
    
    int AOBasisSize() const {return _AOBasisSize; }
    
    typedef std::vector< AOShell >::const_iterator AOShellIterator;
    AOShellIterator begin() const{ return _aoshells.begin(); }
    AOShellIterator end() const{ return _aoshells.end(); }

    Eigen::MatrixXd getTransformationCartToSpherical(const std::string& package);
    
    const AOShell& getShell( int idx )const{ return _aoshells[idx] ;}
    
    const std::vector<const AOShell*> getShellsofAtom(int AtomId)const;
    
    int getNumofShells() const{return _aoshells.size();}
   
    int getAOBasisFragA() const{return _AOBasisFragA;}
    
   int getAOBasisFragB() const{return _AOBasisFragB;}
   
   int getFuncOfAtom(int AtomIndex)const{return _FuncperAtom[AtomIndex];}
   
   const std::vector<int>& getFuncPerAtom()const {return _FuncperAtom;}

   const AOShell& back()const{return _aoshells.back();}

private:
    
  AOShell& addShell( const Shell& shell, const QMAtom& atom, int startIndex );
  
  AOShell& addECPShell( const Shell& shell, const QMAtom& atom, int startIndex,bool nonlocal);
    
  void MultiplyMOs(Eigen::MatrixXd &v, std::vector<int> const &multiplier );
   


    std::vector<int> invertOrder(const std::vector<int>& order );
    
    std::vector<int> getReorderVector(const std::string& start,const std::string& target );
   
    void addReorderShell(const std::string& start,const std::string& target,const std::string& shell, std::vector<int>& neworder );
  
    std::vector<int> getMultiplierVector(const std::string& start,const std::string& target );
    
    void addMultiplierShell(const std::string& start,const std::string& target,const std::string& shell, std::vector<int>& multiplier );  
  
    void addTrafoCartShell( const AOShell& shell , Eigen::Block<Eigen::MatrixXd>& submatrix );
    std::vector<AOShell> _aoshells;
    
    std::vector<int> _FuncperAtom;
    
    int _AOBasisFragA;
    int _AOBasisFragB;
    int _AOBasisSize;
    
};


 
}}

#endif	// VOTCA_XTP_AOBASIS_H