Component.h

#ifndef COMPONENT_H_
#define COMPONENT_H_
 
#include <vector>
#include <string>
 
#include "molecules/Site.h"
 
class Component {
public:
    Component(unsigned int id = 0);
 
    void readXML(XMLfileUnits& xmlconfig);
 
    void setID(unsigned int id) { _id = id; }
    unsigned int ID() const { return _id; }
 
    unsigned int numSites() const {
        return this->numLJcenters() + this->numCharges()
                                    + this->numDipoles()
                                    + this->numQuadrupoles();
    }
    unsigned int numOrientedSites() const { return numDipoles() + numQuadrupoles(); }
    unsigned int numLJcenters() const { return _ljcenters.size(); }
    unsigned int numCharges() const { return _charges.size(); }
    unsigned int numDipoles() const { return _dipoles.size(); }
    unsigned int numQuadrupoles() const { return _quadrupoles.size(); }
 
    double m() const { return _m; }
    double I11() const { return _Ipa[0]; }
    double I22() const { return _Ipa[1]; }
    double I33() const { return _Ipa[2]; }
    void setI11(double I) { _Ipa[0]=I; }
    void setI22(double I) { _Ipa[1]=I; }
    void setI33(double I) { _Ipa[2]=I; }
 
    unsigned int getRotationalDegreesOfFreedom() const { return _rot_dof; }
 
    const std::vector<LJcenter>& ljcenters() const { return _ljcenters; }
    LJcenter& ljcenter(unsigned int i) { return _ljcenters[i]; }
    const LJcenter& ljcenter(unsigned int i) const { return _ljcenters[i]; }
    const std::vector<Charge>& charges() const { return _charges; }
    Charge& charge(unsigned i) { return _charges[i]; }
    const Charge& charge(unsigned i) const { return _charges[i]; }
    const std::vector<Dipole>& dipoles() const { return _dipoles; }
    Dipole& dipole(unsigned int i) { return _dipoles[i]; }
    const Dipole& dipole(unsigned int i) const { return _dipoles[i]; }
    const std::vector<Quadrupole>& quadrupoles() const { return _quadrupoles; }
    Quadrupole& quadrupole(unsigned int i) { return _quadrupoles[i]; }
    const Quadrupole& quadrupole(unsigned int i) const { return _quadrupoles[i]; }
 
    void setNumMolecules(unsigned long num) { _numMolecules = num; }  
    void incNumMolecules() { ++_numMolecules; }  
    void incNumMolecules(int N) { _numMolecules += N; }  
    unsigned long getNumMolecules() const { return _numMolecules; }  
    void addLJcenter(LJcenter& ljsite);
    void addLJcenter(
            double x, double y, double z, double m, double eps,
            double sigma, double rc = 0, bool TRUNCATED_SHIFTED = 0
    );
    void addCharge(Charge& chargesite);
    void addCharge(double x, double y, double z, double m, double q);
    void addDipole(Dipole& dipolesite);
    void addDipole(double x, double y, double z,
                   double eMyx, double eMyy, double eMyz, double eMyabs);
    void addQuadrupole(Quadrupole& quadrupolesite);
    void addQuadrupole(double x, double y, double z,
                       double eQx, double eQy, double eQz, double eQabs);
 
    void deleteLJCenter() { _ljcenters.pop_back() ;}
    void deleteCharge() { _charges.pop_back() ;}
    void deleteDipole() { _dipoles.pop_back() ;}
    void deleteQuadrupole() { _quadrupoles.pop_back() ;}
 
 
    void updateMassInertia();
 
    void write(std::ostream& ostrm) const;
 
    void writeVIM(std::ostream& ostrm);
 
    void setE_trans(double E) { _E_trans = E; }
    void setE_rot(double E) { _E_rot = E; }
    void setT(double T) { _T = T; }
    double E_trans() const { return _E_trans; }
    double E_rot() const { return _E_rot; }
    double E() const { return _E_trans + _E_rot; }
    double T() const { return _T; }
    void setName(std::string name) { _name = name; }
    std::string getName() const { return _name; }
 
    double getEps(unsigned int i) const {return _ljcenters[i].eps();}
    double getSigma(unsigned int i) const {return _ljcenters[i].sigma();}
 
    unsigned getLookUpId() const {
        return _lookUpID;
    }
 
    void setLookUpId(unsigned lookUpId) {
        _lookUpID = lookUpId;
    }
 
private:
 
    void updateMassInertia(Site& site);
 
    unsigned int _id; 
    // LJcenter,Dipole,Quadrupole have different size -> not suitable to store in a _Site_-array
    //std::vector<Site> _sites;
    // use separate vectors instead...
    std::vector<LJcenter> _ljcenters;
    std::vector<Charge> _charges;
    std::vector<Dipole> _dipoles;
    std::vector<Quadrupole> _quadrupoles;
    /* for performance reasons better(?) omit Site-class indirection and use cached values */
    double _m; 
    double _I[6];
    double _Ipa[3]; 
    unsigned long _rot_dof; 
    /* cached values, set by ensemble class! */
    unsigned long _numMolecules; // number of molecules for this molecule type
    double _E_trans; // translational energy
    double _E_rot; // rotational energy
    double _T; // temperature
    
    bool _isStockmayer; //Checks whether component is a Stockmayer fluid to determine moments of inertia
    
    std::string _name; 
    unsigned _lookUpID;
};
 
std::ostream& operator<<(std::ostream& stream, const Component& component);
 
#endif /* COMPONENT_H_ */