52 #ifndef N_DEV_REACTION_H
53 #define N_DEV_REACTION_H
67 Reaction(std::vector< std::pair<int,double> > & ,
68 std::vector< std::pair<int,double> > &,
77 void setReactants(std::vector< std::pair<int,double> > &products );
79 void setProducts(std::vector< std::pair<int,double> > &products );
81 double getRate(std::vector<double> &concentrations,
82 std::vector<double> &constants);
83 void getDdt(std::vector<double> &concentrations,
84 std::vector<double> &constants,
85 std::vector<double> &ddt);
86 void getDRateDC(std::vector<double> &concentrations,
87 std::vector<double> &constants,
88 std::vector<double> &dratedc);
90 std::vector<double> &concentrations,
91 std::vector<double> &constants,
93 void getJac(std::vector<double> &concentrations,
94 std::vector<double> &constants,
95 std::vector<std::vector<double> > &jac);
97 std::vector<double> &concentrations,
98 std::vector<double> &constants,
99 std::vector<double> &dFdConst);
101 void output (
const std::vector<Specie> & species,
102 std::ostream & os )
const;
108 double Energy,
double C0,
double t0,
111 std::vector<Specie> &ConstantSpecies,
112 double C0,
double t0,
double x0);
114 std::vector<Specie> &ConstantSpecies,
115 double bindingEnergy,
116 double gammaAB,
double gammaA,
double gammaB,
118 double C0,
double t0,
double x0);