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> > &,
75 std::vector<double> &concs,
76 std::vector<double> &constant_vec);
80 void setReactants(std::vector< std::pair<int,double> > &products );
82 void setProducts(std::vector< std::pair<int,double> > &products );
84 double getRate(std::vector<double> &concentrations,
85 std::vector<double> &constants);
86 void getDdt(std::vector<double> &concentrations,
87 std::vector<double> &constants,
88 std::vector<double> &ddt);
89 void getDRateDC(std::vector<double> &concentrations,
90 std::vector<double> &constants,
91 std::vector<double> &dratedc);
93 std::vector<double> &concentrations,
94 std::vector<double> &constants,
96 void getJac(std::vector<double> &concentrations,
97 std::vector<double> &constants,
98 std::vector<std::vector<double> > &jac);
100 std::vector<double> &concentrations,
101 std::vector<double> &constants,
102 std::vector<double> &dFdConst);
104 void output (
const std::vector<Specie> & species,
105 std::ostream & os )
const;
111 double Energy,
double C0,
double t0,
114 std::vector<Specie> &ConstantSpecies,
115 double C0,
double t0,
double x0);
117 std::vector<Specie> &ConstantSpecies,
118 double bindingEnergy,
119 double gammaAB,
double gammaA,
double gammaB,
121 double C0,
double t0,
double x0);
124 std::vector<Specie> &ConstantSpecies,
125 double sigma,
double C0,
double t0,
double x0);