testNotchDiffusion.cpp
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testNotchDiffusion.cpp
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			#include "deltaNotch3.hpp"


			typedef runge_kutta_dopri5< double , double , double , double , vector_space_algebra > stepper_type;

			typedef runge_kutta_cash_karp54< state_type , double > error_stepper_type;

			int main(int argc, char *argv[]){
			//Lattice lat(TWO_CELLS);
			Lattice lat(SEVEN_CELLS);
			DeltaNotch3 dn;
			dn.setLattice(&lat);
			dn.initState();
			dn.deltaUp(0);
			vector<state_type> x_vec;
			vector<double> times;
			for(int i=1;i<argc;i++){
			char *p;
			p=strtok(argv[i],"=");
			if(!strcmp(p,"bn")){
			dn.setNotchProduction(atof(strtok(NULL,"=")));
			}
			if(!strcmp(p,"bd")){
			dn.setDeltaProduction(atof(strtok(NULL,"=")));
			}
			if(!strcmp(p,"ktp")){
			dn.setTransBindingRate(atof(strtok(NULL,"=")));
			}
			if(!strcmp(p,"kcp")){
			dn.setCisBindingRate(atof(strtok(NULL,"=")));
			}
			if(!strcmp(p,"ks")){
			dn.setNotchCleavageRate(atof(strtok(NULL,"=")));
			}
			if(!strcmp(p,"diff")){
			dn.setDiffusion(atof(strtok(NULL,"=")));
			}
			if(!strcmp(p,"kcs")){
			dn.setCisNotchCleavageRate(atof(strtok(NULL,"=")));
			}
			if(!strcmp(p,"gd")){
			dn.setNotchDegradation(atof(strtok(NULL,"=")));
			}
			}
			state_type& y0 = dn.getState();
			// cout<<"dimension "<<dn.getStateDimension()<<endl;
			uint steps = integrate_adaptive(make_controlled<error_stepper_type>(0.001,0.01),dn,y0,0.0,600.0,2.0, push_back_state_and_time(x_vec,times));
			// cout<<"done"<<endl;
			for(uint i=0; i<=steps; i++ ){
			cout << times[i] <<" ";
			for(uint j=0;j<x_vec[i].size();j++){
			cout<< x_vec[i][j]<<" ";
			}
			cout<<endl;
			}
			return 0;
			}