int main(int argc, char* argv[]) {
assert(argc>1 && argc < 7);
int nx = argc>2 ? std::atoi(argv[2]) : 2;
int ny = argc>3 ? std::atoi(argv[3]) : 2;
int nz = argc>4 ? std::atoi(argv[4]) : 2;
std::ifstream in(argv[1]);
Nef_polyhedron Nin;
in >> Nin;
Nin.transform(Aff_transformation_3(CGAL::SCALING,2,1));
std::ostringstream out1;
ggen g(out1, Nin);
g.print(nx,ny,nz);
std::istringstream in1(out1.str());
Nef_polyhedron N1;
in1 >> N1;
RT s = g.size_x();
N1.transform(Aff_transformation_3(CGAL::TRANSLATION,Vector_3(s,s,s,2)));
CGAL_assertion(N1.is_valid());
std::ostringstream out2;
CGAL::Random r;
if(argc>5) {
tgen t2(out2,s,std::atoi(argv[5]));
t2.create_tetrahedra(nx+1,ny+1,nz+1);
} else {
tgen t2(out2,s);
t2.create_tetrahedra(nx+1,ny+1,nz+1);
}
std::istringstream in2(out2.str());
Nef_polyhedron N2;
in2 >> N2;
CGAL_assertion(N2.is_valid());
char* dir="nef3/";
char* tetrahedra="tetrahedra";
char* grid="grid";
char* suffix=".nef3";
char* us="_";
char* full_suffix = new char[strlen(argv[2])+strlen(argv[3])+strlen(argv[4])+strlen(argv[5])+strlen(suffix)+5];
strcpy(full_suffix, us);
strcat(full_suffix, argv[2]);
strcat(full_suffix, us);
strcat(full_suffix, argv[3]);
strcat(full_suffix, us);
strcat(full_suffix, argv[4]);
strcat(full_suffix, us);
strcat(full_suffix, argv[5]);
strcat(full_suffix, suffix);
char* full_tetrahedra = new char[strlen(dir)+strlen(tetrahedra)+strlen(full_suffix)+1];
strcpy(full_tetrahedra, dir);
strcat(full_tetrahedra, tetrahedra);
strcat(full_tetrahedra, full_suffix);
std::ofstream out_tetrahedra(full_tetrahedra);
out_tetrahedra << N2;
char* full_grid = new char[strlen(dir)+strlen(grid)+strlen(full_suffix)+1];
strcpy(full_grid, dir);
strcat(full_grid, grid);
strcat(full_grid, full_suffix);
std::ofstream out_grid(full_grid);
out_grid << N1;
}
int main(int argc, char* argv[]) {
if (argc < 2) {
std::cout << "Usage: simpleReact num_particles" << std::endl;
exit(-1);
}
const unsigned int num_particles = atoi(argv[1]);
std::ofstream tf;
tf.open(("output/time_simpleReact_"+std::string(argv[1])+".dat").c_str());
boost::progress_timer t(tf);
const double end_time = 5.0;
const double dt = 0.001;
/*
* Create "red" species with D=1
*/
Species red(0.1);
//red.fill_uniform(0.0,1.0,1);
/*
* create diffusion operator and apply to red species
*/
Diffusion bd; bd.add_species(red);
/*
* Create simulation boundary planes
*/
AxisAlignedPlane<0> xlow(0,1);
AxisAlignedPlane<0> xhigh(1,-1);
AxisAlignedPlane<1> ylow(0,1),yhigh(1,-1);
AxisAlignedPlane<2> zlow(0,1),zhigh(1,-1);
/*
* Create input flux boundary
*/
FluxBoundary fb(Vect3d(1,0,0),Vect3d(0,1,0),Vect3d(0,0,1),num_particles); fb.add_species(red);
/*
* Create jump (periodic) boundaries
*/
//JumpBoundary<AxisAlignedPlane<0> > jb1(xlow,Vect3d(1,0,0)); jb1.add_species(red);
JumpBoundary<AxisAlignedPlane<1> > jb2(ylow,Vect3d(0,1,0)); jb2.add_species(red);
JumpBoundary<AxisAlignedPlane<2> > jb3(zlow,Vect3d(0,0,1)); jb3.add_species(red);
JumpBoundary<AxisAlignedPlane<1> > jb4(yhigh,Vect3d(0,-1,0)); jb4.add_species(red);
JumpBoundary<AxisAlignedPlane<2> > jb5(zhigh,Vect3d(0,0,-1)); jb5.add_species(red);
/*
* Create reflective boundary
*/
ReflectiveBoundary<AxisAlignedPlane<0> > rb(xhigh); rb.add_species(red);
/*
* Create unimolecular reaction operator (red -> 0)
*/
UniMolecularReaction dr(1,red >> 0);
const double h_in = 0.1;
StructuredGrid out_grid(Vect3d(0,0,0), Vect3d(1,1,1), Vect3d(h_in,1.0,1.0));
OutputConcentrations out_concen_1d("output/simpleReact_",end_time/100.0, out_grid);out_concen_1d.add_species(red);
OutputCompareWithFunction<rmsError<MyFunction> > out_compare("output/simpleReact_error",end_time/100.0,0,1,out_grid,
rmsError<MyFunction>(MyFunction(num_particles,red.D))); out_compare.add_species(red);
Plot2d plot(0,out_concen_1d.get_data("x"),out_concen_1d.get_data("Concentration"),"x","Concentration","My first plot");
Visualisation vis(0);vis.add_species(red);
vis.add_geometry(xlow);
vis.add_geometry(xhigh);
vis.add_geometry(ylow);
vis.add_geometry(yhigh);
vis.add_geometry(zlow);
vis.add_geometry(zhigh);
/*
* Run simulation until end_time with timestep dt
*/
run(red, end_time, dt, bd, fb, jb2, jb3, jb4, jb5, rb, dr, out_concen_1d, out_compare, vis,plot);
std::vector<int> bins;
make_histogram(bins,red,100, 0,1);
std::ofstream f;
f.open(("output/simpleReact_"+std::string(argv[1])+".dat").c_str());
f << end_time << ' ';
BOOST_FOREACH(int x,bins) {
f << x <<' ';
}
f << std::endl;
f.close();
return EXIT_SUCCESS;
}
