Data *
QpGenSparseSeq::makeData( double c_[],
int krowQ[], int jcolQ[], double dQ[],
double xlow_[], char ixlow_[],
double xupp_[], char ixupp_[],
int krowA[],
int jcolA[], double dA[],
double b_[],
int krowC[],
int jcolC[], double dC[],
double clow_[], char iclow_[],
double cupp_[], char icupp_[] )
{
// Objective funcition
SimpleVectorHandle c( new SimpleVector( c_, nx ) );
nnzQ = krowQ[nx];
SparseSymMatrixHandle Q( new SparseSymMatrix( nx, nnzQ,
krowQ, jcolQ, dQ ) );
// Bounds on variables
SimpleVectorHandle xlow( new SimpleVector( xlow_, nx ) );
SimpleVectorHandle ixlow( new SimpleVector( nx ) );
ixlow->copyFromArray( ixlow_ );
SimpleVectorHandle xupp( new SimpleVector( xupp_, nx ) );
SimpleVectorHandle ixupp( new SimpleVector( nx ) );
ixupp->copyFromArray( ixupp_ );
// Equality constraints
nnzA = 0;
if( my > 0 ) nnzA = krowA[my];
SparseGenMatrixHandle A( new SparseGenMatrix( my, nx,
nnzA, krowA, jcolA, dA ) );
SimpleVectorHandle b( new SimpleVector( b_, my ) );
// Inequality constraints
nnzC = 0;
if( mz > 0 ) nnzC = krowC[mz];
SparseGenMatrixHandle C( new SparseGenMatrix( mz, nx,
nnzC, krowC, jcolC, dC ) );
SimpleVectorHandle clow( new SimpleVector( clow_, mz ) );
SimpleVectorHandle iclow( new SimpleVector( mz ) );
iclow->copyFromArray( iclow_ );
SimpleVectorHandle cupp( new SimpleVector( cupp_, mz ) );
SimpleVectorHandle icupp( new SimpleVector( mz ) );
icupp->copyFromArray( icupp_ );
QpGenData *
data = new QpGenData( SparseLinearAlgebraPackage::soleInstance(),
c, Q, xlow, ixlow, xupp, ixupp,
A, b,
C, clow, iclow, cupp, icupp );
return data;
}
int main(int argc, char* argv[]) {
if (argc < 2) {
std::cout << "Usage: simpleBD h" << std::endl;
exit(-1);
}
const unsigned int num_particles = 1;
const double h_in = atof(argv[1]);
const double end_time = 1.0;
//const double dt = 0.0001;
const double dt = h_in*h_in/PI;
/*
* Create Compartments (a structured grid from r = (0,0,0) to r = (1,0.1,0.1). resolution = h = h_in for all dimensions)
*/
StructuredGrid grid(Vect3d(0.25-h_in,0,0), Vect3d(0.75+h_in,1,1), Vect3d(h_in,h_in,h_in));
/*
* Create "red" species with D=1. Fill with a uniform distribution of particles
*/
Species red(1, grid);
/*
* create diffusion operator and apply to red species
*/
Diffusion bd; bd.add_species(red);
/*
* Create simulation boundary planes
*/
xplane xlow(0,1),xhigh(1,-1);
yplane ylow(0,1),yhigh(1,-1);
zplane zlow(0,1),zhigh(1,-1);
xplane couple_C_to_M_1(0.25,-1);
xplane couple_C_to_M_2(0.75,1);
xplane first_line_of_compartments(0.25-0.5*h_in,1);
xplane second_line_of_compartments(0.25+0.5*h_in,1);
xplane second_last_line_of_compartments(0.75-0.5*h_in,1);
xplane last_line_of_compartments(0.75+0.5*h_in,1);
/*
* Create jump (periodic) boundaries
*/
JumpBoundaryWithCorrection<xplane> jb1(xlow,xhigh-xlow); jb1.add_species(red);
JumpBoundary<yplane> jb2(ylow,yhigh-ylow); jb2.add_species(red);
JumpBoundary<zplane> jb3(zlow,zhigh-zlow); jb3.add_species(red);
JumpBoundary<yplane> jb4(yhigh,ylow-yhigh); jb4.add_species(red);
JumpBoundary<zplane> jb5(zhigh,zlow-zhigh); jb5.add_species(red);
/*
* Create reflective boundary
*/
ReflectiveBoundary<xplane> rb(xhigh); rb.add_species(red);
/*
* create Next Subvolume Method operator. The constructor takes the compartment grid as input
*/
NextSubvolumeMethod nsm(red.grid);
// add diffusion equations to nsm
//nsm.add_diffusion(red);
nsm.add_diffusion(red, red.D/pow(h_in,2));
/*
* Setup reactions for coupling
*/
// nsm.remove_diffusion_between(red, second_line_of_compartments, first_line_of_compartments);
// nsm.remove_diffusion_between(red, second_last_line_of_compartments, last_line_of_compartments);
// nsm.add_diffusion_between(red, (2.0*h_in/sqrt(PI*red.D*dt))*(red.D/pow(h_in,2)), second_line_of_compartments, first_line_of_compartments);
// nsm.add_diffusion_between(red, (2.0*h_in/sqrt(PI*red.D*dt))*(red.D/pow(h_in,2)), second_last_line_of_compartments, last_line_of_compartments);
nsm.add_diffusion_between(red,red.D/pow(h_in,2),ylow, yhigh);
nsm.add_diffusion_between(red,red.D/pow(h_in,2),yhigh, ylow);
nsm.add_diffusion_between(red,red.D/pow(h_in,2),zlow, zhigh);
nsm.add_diffusion_between(red,red.D/pow(h_in,2),zhigh, zlow);
// nsm.clear_reactions(first_line_of_compartments);
// nsm.clear_reactions(last_line_of_compartments);
nsm.list_reactions();
/*
* Create coupling boundaries between compartments and free-space
*/
Intersection<xplane,xplane> compartment_volume(couple_C_to_M_1, couple_C_to_M_2);
CouplingBoundary_C_to_M<Intersection<xplane,xplane> > c_to_m(compartment_volume, nsm); c_to_m.add_species(red, dt);
CouplingBoundary_M_to_C<Intersection<xplane,xplane> > m_to_c(compartment_volume, nsm); m_to_c.add_species(red);
std::vector<int> bins_m, bins_c;
const int num_bins = 100;
bins_m.assign(num_bins,0);
bins_c.assign(red.grid.get_cells_along_axes()[0],0);
for (int i = 0; i < 50000; ++i) {
std::cout << "doing iteration " << i << std::endl;
red.fill_uniform(Vect3d(0,0,0),Vect3d(1.0,1,1),num_particles);
// calculate next reaction times for all compartments
nsm.reset_all_priorities();
/*
* Run simulation until end_time with timestep dt
*/
run(red, end_time, dt, nsm, bd, jb1, jb2, jb3, jb4, jb5, rb, m_to_c, c_to_m);
if (red.mols.size() > 0) {
const double scaled_position = (red.mols.r[0][0])*num_bins;
if ((scaled_position < 0) || (scaled_position > num_bins)) {
printf("outside area: position = (%f %f %f)\n",red.mols.r[0][0],red.mols.r[0][1],red.mols.r[0][2]);
}
const int index = int(scaled_position);
bins_m[index]++;
red.mols.delete_molecule(0);
}
const int nc = red.grid.size();
for(int i = 0; i < nc; i++) {
Vect3i cell_indices = red.grid.get_cell_indicies(i);
bins_c[cell_indices[0]] += red.copy_numbers[i];
red.copy_numbers[i] = 0;
}
}
std::ofstream f;
f.open(("output/simpleBD_couple_single_mols_"+std::string(argv[1])+".dat").c_str());
f << end_time << ' ';
int count = 0;
BOOST_FOREACH(int x,bins_m) {
f << x <<' ';
count += x;
}
int main(int argc, char* argv[]) {
if (argc < 2) {
std::cout << "Usage: simpleReactWithJumpCorrection num_particles" << std::endl;
exit(-1);
}
const unsigned int num_particles = atoi(argv[1]);
std::ofstream tf;
tf.open(("time_simpleReactWithJumpCorrection_"+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(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 (0 -> red) 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
*/
JumpBoundaryWithCorrection<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 iterations = end_time/dt;
const double num_out = 100;
const int it_per_out = int(iterations/num_out);
/*
* Run simulation until end_time with timestep dt
*/
run(red, end_time, dt, bd, fb, jb1, jb2, jb3, jb4, jb5, rb, dr);
std::vector<int> bins;
make_histogram(bins,red,100, 0,1);
std::ofstream f;
f.open(("simpleReactWithJumpCorrection_"+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;
}
int main(int argc, char* argv[]) {
if (argc < 3) {
std::cout << "Usage: simpleBD num_particles h" << std::endl;
exit(-1);
}
const unsigned int num_particles = atoi(argv[1]);
const double h_in = atof(argv[2]);
std::ofstream tf;
tf.open(("output/time_simpleBD_couple_"+std::string(argv[1])+"_"+std::string(argv[2])+".dat").c_str());
boost::progress_timer t(tf);
const double end_time = 1.0;
//const double dt = 0.0001;
const double dt = h_in*h_in/PI;
/*
* Create Compartments (a structured grid from r = (0,0,0) to r = (1,0.1,0.1). resolution = h = h_in for all dimensions)
*/
StructuredGrid grid(Vect3d(0.25-h_in,0,0), Vect3d(0.75+h_in,1,1), Vect3d(h_in,h_in,h_in));
/*
* Create "red" species with D=1. Fill with a uniform distribution of particles
*/
Species red(1, grid);
red.fill_uniform(Vect3d(0,0,0),Vect3d(0.25,1,1),num_particles/4.0);
red.fill_uniform(Vect3d(0.75,0,0),Vect3d(1.0,1,1),num_particles/4.0);
//red.fill_uniform(Vect3d(0.75,0,0),Vect3d(1.0,0.1,0.1),1);
red.fill_uniform(num_particles/2.0);
/*
* create diffusion operator and apply to red species
*/
Diffusion bd; bd.add_species(red);
/*
* Create simulation boundary planes
*/
xplane xlow(0,1),xhigh(1,-1);
yplane ylow(0,1),yhigh(1,-1);
zplane zlow(0,1),zhigh(1,-1);
xplane couple_C_to_M_1(0.25,-1);
xplane couple_C_to_M_2(0.75,1);
xplane first_line_of_compartments(0.25-0.5*h_in,1);
xplane second_line_of_compartments(0.25+0.5*h_in,1);
xplane second_last_line_of_compartments(0.75-0.5*h_in,1);
xplane last_line_of_compartments(0.75+0.5*h_in,1);
/*
* Create jump (periodic) boundaries
*/
JumpBoundaryWithCorrection<xplane> jb1(xlow,xhigh-xlow); jb1.add_species(red);
JumpBoundary<yplane> jb2(ylow,yhigh-ylow); jb2.add_species(red);
JumpBoundary<zplane> jb3(zlow,zhigh-zlow); jb3.add_species(red);
JumpBoundary<yplane> jb4(yhigh,ylow-yhigh); jb4.add_species(red);
JumpBoundary<zplane> jb5(zhigh,zlow-zhigh); jb5.add_species(red);
/*
* Create reflective boundary
*/
ReflectiveBoundary<xplane> rb(xhigh); rb.add_species(red);
/*
* create Next Subvolume Method operator. The constructor takes the compartment grid as input
*/
NextSubvolumeMethod nsm(red.grid);
// add diffusion equations to nsm
//nsm.add_diffusion(red);
nsm.add_diffusion(red, red.D/pow(h_in,2));
/*
* Setup reactions for coupling
*/
// nsm.remove_diffusion_between(red, second_line_of_compartments, first_line_of_compartments);
// nsm.remove_diffusion_between(red, second_last_line_of_compartments, last_line_of_compartments);
// nsm.add_diffusion_between(red, (2.0*h_in/sqrt(PI*red.D*dt))*(red.D/pow(h_in,2)), second_line_of_compartments, first_line_of_compartments);
// nsm.add_diffusion_between(red, (2.0*h_in/sqrt(PI*red.D*dt))*(red.D/pow(h_in,2)), second_last_line_of_compartments, last_line_of_compartments);
nsm.add_diffusion_between(red,red.D/pow(h_in,2),ylow, yhigh);
nsm.add_diffusion_between(red,red.D/pow(h_in,2),yhigh, ylow);
nsm.add_diffusion_between(red,red.D/pow(h_in,2),zlow, zhigh);
nsm.add_diffusion_between(red,red.D/pow(h_in,2),zhigh, zlow);
// nsm.clear_reactions(first_line_of_compartments);
// nsm.clear_reactions(last_line_of_compartments);
nsm.list_reactions();
// calculate next reaction times for all compartments
nsm.reset_all_priorities();
/*
* Create coupling boundaries between compartments and free-space
*/
Intersection<xplane,xplane> compartment_volume(couple_C_to_M_1, couple_C_to_M_2);
CouplingBoundary_C_to_M<Intersection<xplane,xplane> > c_to_m(compartment_volume, nsm); c_to_m.add_species(red, dt);
CouplingBoundary_M_to_C<Intersection<xplane,xplane> > m_to_c(compartment_volume, nsm); m_to_c.add_species(red);
/*
* Run simulation until end_time with timestep dt
*/
run(red, end_time, dt, nsm, bd, jb1, jb2, jb3, jb4, jb5, rb, m_to_c, c_to_m);
//nsm(dt/2);
//run(red, end_time, dt, nsm, c_to_m, bd, jb1, jb2, jb3, jb4, jb5, rb, m_to_c, output);
std::vector<int> bins;
make_histogram(bins,red,100, 0,1);
std::ofstream f;
f.open(("output/simpleBD_couple_mols_"+std::string(argv[1])+"_"+std::string(argv[2])+".dat").c_str());
f << end_time << ' ';
int count = 0;
BOOST_FOREACH(int x,bins) {
f << x <<' ';
count += x;
}
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;
}