MESMER Code

#ifndef GUARD_Molecule_h
#define GUARD_Molecule_h

//-------------------------------------------------------------------------------------------
//
// Molecule.h
//
// Author: Struan Robertson
// Date:   5/Jan/2003
//
// This header file contains the declaration of the Molecule class.
//
//-------------------------------------------------------------------------------------------

#include "MolecularComponents.h"

namespace mesmer
{
  class MoleculeManager ;

  // Because many Molecule properties are not needed in all molecules, they are
  // handled in the following classes, which are derived from MolecularComponent.
	class gWellProperties ;
  class gBathProperties ;
  class gTransitionState;
  class gDensityOfStates;
  class gPopulation;
  class gStructure;

  //**************************************************
  /// Basic molecule: has name and some collision parameters.
  /// Used for bath gases and unmodelled product molecules.
  class Molecule
  {

    //-------------------------------------------------------------------------------------------------
    // Basic information of a molecule
    //-------------------------------------------------------------------------------------------------

  private:

    const MesmerEnv& m_Env;
    MesmerFlags&     m_Flags;
    unsigned int     m_atomNumber;         // If (m_atomNumber == 0), the atomArray element is missing.

    PersistPtr       m_ppPersist;          // Conduit for I/O
    std::string      m_Name ;              // Molecule name.
    std::string      m_Description;        // Longer description for the structure
	MoleculeManager *m_pMoleculeManager;   // Pointer molecule manager for navigation purposes.
    std::map<std::string, bool> m_molTypes;

	// Component pointers
    friend class MolecularComponent; // Provide access privalage of MolecularComponent to private members of Molecule.
    gBathProperties*        g_bath;  // Component pointer for bath gas properties
    gDensityOfStates*       g_dos;   // Component pointer for cell density of state properties
    gTransitionState*       g_ts;    // Component pointer for transition state properties
    gPopulation*            g_pop;   // Component pointer for population and equilibrium fraction
    gWellProperties*        g_coll;  // Component pointer for collision down model properties
    gStructure*             g_struc; // Component pointer for chemical structural properties

  public:

    //
    // Constructor
    //
    Molecule(const MesmerEnv& Env, MesmerFlags& m_Flags, const string& molType, MoleculeManager *pMoleculeManager) ;
    virtual ~Molecule();

    // Initialize Molecule. Returns false if no id attribute
    // or if no description attribute and <molecule> has no child elements. Probably just a placeholder.
    virtual bool InitializeMolecule(PersistPtr pp);

    PersistPtr  get_PersistentPointer() const { return m_ppPersist; } ;

    std::string getDescription() const { return m_Description ; } ;

    const MesmerEnv& getEnv() const { return m_Env; } ;

    std::string getName() const { return m_Name ; } ;

    const MesmerFlags& getFlags() const { return m_Flags;} ;

	MoleculeManager* getMoleculeManager() const { return m_pMoleculeManager; } ;

    bool checkDegOfFreedom();

    //-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
    // Manipulators of component pointers
    gBathProperties&  getBath();
    gDensityOfStates& getDOS();
    gTransitionState& getTS();
    gPopulation&      getPop();
    gWellProperties&  getColl();
    gStructure&       getStruc();

    bool activateRole(string molType);
    bool hasDOSProperties(){return g_dos!=NULL;}
    bool isMolType(const string& molType){
      return m_molTypes[molType];
    }
    //-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
  };

}//namespace

// CHECK FOR INPUTFILE PARAMETERS
// for these check values, initially the values are given -1. If not provided by user the value will remain as -1.
// If provided by the user the value will be increased to 0.
// During calcualtion, every inputfile parameter if called by any function, the class will check if the parameter
// is provided. If it is provided, the chk value will increase by 1. So if a chk value is 9, it is asked for 9 times.
// However, if the user did not provide the value and the values is asked. The program will stop and report error.
// Values with obvious default values are also accounted in this check but the program will not exit; only
// warning message will be given.

#endif // GUARD_Molecule_h