species.h

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namespace Species {
        extern int nspecies;
        class Specie {
                char id[WORDLENGTH];
                REAL mass,size,//molecular characteristics
                        cp,//heat capacity
//-                     dof,// =2*c_v/R=2*(c_p/R-1) http://en.wikipedia.org/wiki/Heat_capacity#Heat_capacity
                        inertia[DIM];//tensor of inertia (geometrical param).
                public:
                Specie() {
                        id[0]='\0';
                        mass=size=cp=0.0;
                        for(int i=0;i<DIM;i++) inertia[i]=0.0;
                }
//-             inline void DOF(REAL f) {dof=f;}
//-             inline REAL DOF() {return dof;}
                inline void Cp(REAL c) {cp=c;}
                inline REAL Cp() {return cp;}
                inline char* Id() {return id;}
                inline void Mass(REAL m) { mass=m; }
                inline REAL Mass() { return mass; }
                inline REAL Size() { return size; }
                inline void Size(REAL s) { size=s; }
        };
        struct Gas {
                REAL density; 
                Specie *specie;
                Gas(Specie *s) {specie=s;}
        };
        struct Reaction {
                struct Outcome {
                        int product[2];
                        REAL activationEnergy,probability,enthalpy,
                                time; 


                        Outcome *next;
                        Outcome() {
                                for(int j=0;j<2;j++) product[j]=VOIDSPECIE;//VOID reaction
                                probability=enthalpy=time=0.0;
                                next=NULL;
                        }
                        Outcome(
                                int ip0,
                                int ip1,
                                REAL a, 
                                REAL p, 
                                REAL h  
                        ) {
                                if(ip0<0||ip0>nspecies) {
                                        cout<<"ERROR: Invalid first product specie index "<<ip0<<" of maximum "<<nspecies<<endl;
                                        exit(1);
                                }
                                product[0]=ip0;
                                if(ip1<0||ip1>nspecies) {
                                        cout<<"ERROR: Invalid second product specie index "<<ip1<<" of maximum "<<nspecies<<endl;
                                        exit(1);
                                }
                                product[1]=ip1;
                                activationEnergy=a;
                                probability=p;
                                enthalpy=h;
                                time=0.0;
                                next=NULL;
                        }
#ifdef ADSORPTION
                        Outcome(
                                int ip0, 
                                int ip1, 
                                REAL a, 
                                REAL p, 
                                REAL h, 
                                REAL t  
                        ) {
                                if(ip0<0||ip0>nspecies) {
                                        cout<<"ERROR: Invalid first product specie index "<<ip0<<" of maximum "<<nspecies<<endl;
                                        exit(1);
                                }
                                product[0]=ip0;
                                if(ip1<0||ip1>nspecies) {
                                        cout<<"ERROR: Invalid second product specie index "<<ip1<<" of maximum "<<nspecies<<endl;
                                        exit(1);
                                }
                                product[1]=ip1;
                                activationEnergy=a;
                                probability=p;
                                enthalpy=h;
                                time=t;
                                next=NULL;
                        }
#endif
                        void Products(int ip0, int ip1) {
                                if(ip0<0||ip0>=nspecies) {
                                        cout<<"Product index "<<ip0<<" outside of species index\n";
                                        exit(1);
                                }
                                product[0]=ip0;
                                if(ip1<0||ip1>=nspecies) {
                                        cout<<"Product index "<<ip1<<" outside of species index\n";
                                        exit(1);
                                }
                                product[1]=ip1;
                        }
                        int Product(int i) {
                                if(i<0||i>1) {
                                        cout<<"ERROR: product index "<<i<<" outside of bounds\n";
                                        exit(1);
                                }
                                return product[i];
                        }
                        inline void Time(REAL t) {time=t;}
                        inline REAL Time() {return time;}
                        inline void ActivationEnergy(REAL a) { activationEnergy=a; }
                        inline REAL ActivationEnergy() { return activationEnergy; }
                        inline void Probability(REAL r) { probability=r; }
                        inline REAL Probability() { return probability; }
                        inline void Enthalpy(REAL h) { enthalpy=h; }
                        inline REAL Enthalpy() { return enthalpy; }
                }       *outcomes,*current;
                Reaction() {current=outcomes=NULL;}
                ~Reaction() {
                        Erase(outcomes);
                        outcomes=NULL;
                }
                void Erase(Outcome *outcome) {
                        if(outcome->next!=NULL) Erase(outcome->next);
                        delete outcome;
                }
                void Add(int ip0, int ip1, REAL a, REAL p, REAL h) {
                        if(outcomes==NULL) {
                                outcomes=new Outcome(ip0,ip1,a,p,h);
                                return;
                        }
                        Outcome *outcome=outcomes;
                        for(;outcome->next!=NULL;outcome=outcome->next);
                        outcome->next=new Outcome(ip0,ip1,a,p,h);
                }
#ifdef ADSORPTION
                void Add(int ip0, int ip1, REAL a, REAL p, REAL h, REAL t) {
                        if(outcomes==NULL) {
                                outcomes=new Outcome(ip0,ip1,a,p,h,t);
                                return;
                        }
                        Outcome *outcome=outcomes;
                        for(;outcome->next!=NULL;outcome=outcome->next);
                        outcome->next=new Outcome(ip0,ip1,a,p,h,t);
                }
#endif
                Outcome *First() { current=outcomes; return current; } 
                Outcome *Next() { 
                        current=current->next; 
                        if(current!=NULL) return current; 
                        current=outcomes; return NULL;
                } 
        };
        enum Interaction {
                missed=0,
                collided,
                reacted, 
                annihalated  
        };
        extern Specie *species;
        extern Reaction *reactions;
}

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