static void runForever(const uavcan_linux::NodePtr& node)
{
/*
* Subscribing to the UAVCAN logging topic
*/
auto log_handler = [](const uavcan::ReceivedDataStructure<uavcan::protocol::debug::LogMessage>& msg)
{
std::cout << msg << std::endl;
};
auto log_sub = node->makeSubscriber<uavcan::protocol::debug::LogMessage>(log_handler);
/*
* Printing when other nodes enter the network or change status
*/
struct NodeStatusMonitor : public uavcan::NodeStatusMonitor
{
explicit NodeStatusMonitor(uavcan::INode& node) : uavcan::NodeStatusMonitor(node) { }
void handleNodeStatusChange(const NodeStatusChangeEvent& event) override
{
std::cout << "Remote node NID " << int(event.node_id.get()) << " changed status: "
<< int(event.old_status.status_code) << " --> "
<< int(event.status.status_code) << std::endl;
}
};
NodeStatusMonitor nsm(*node);
ENFORCE(0 == nsm.start());
/*
* Adding a stupid timer that does nothing once a minute
*/
auto do_nothing_once_a_minute = [&node](const uavcan::TimerEvent&)
{
node->logInfo("timer", "Another minute passed...");
// coverity[dont_call]
node->setVendorSpecificStatusCode(static_cast<std::uint16_t>(std::rand())); // Setting to an arbitrary value
};
auto timer = node->makeTimer(uavcan::MonotonicDuration::fromMSec(60000), do_nothing_once_a_minute);
/*
* Spinning forever
*/
while (true)
{
const int res = node->spin(uavcan::MonotonicDuration::getInfinite());
if (res < 0)
{
node->logError("spin", "Error %*", res);
}
}
}
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;
}
static void runSubNode(const uavcan_linux::SubNodePtr& node)
{
std::cout << "Running sub node" << std::endl;
/*
* Log subscriber
*/
auto log_sub = node->makeSubscriber<uavcan::protocol::debug::LogMessage>(
[](const uavcan::ReceivedDataStructure<uavcan::protocol::debug::LogMessage>& msg)
{
std::cout << msg << std::endl;
});
/*
* Node status monitor
*/
struct NodeStatusMonitor : public uavcan::NodeStatusMonitor
{
explicit NodeStatusMonitor(uavcan::INode& node) : uavcan::NodeStatusMonitor(node) { }
virtual void handleNodeStatusChange(const NodeStatusChangeEvent& event) override
{
std::cout << "Remote node NID " << int(event.node_id.get()) << " changed status: "
<< int(event.old_status.status_code) << " --> " << int(event.status.status_code) << std::endl;
}
};
NodeStatusMonitor nsm(*node);
ENFORCE(0 == nsm.start());
/*
* KV subscriber
*/
auto kv_sub = node->makeSubscriber<uavcan::protocol::debug::KeyValue>(
[](const uavcan::ReceivedDataStructure<uavcan::protocol::debug::KeyValue>& msg)
{
std::cout << msg << std::endl;
});
/*
* KV publisher
*/
unsigned kv_value = 0;
auto kv_pub = node->makePublisher<uavcan::protocol::debug::KeyValue>();
auto timer = node->makeTimer(uavcan::MonotonicDuration::fromMSec(5000), [&](const uavcan::TimerEvent&)
{
uavcan::protocol::debug::KeyValue kv;
kv.key = "five_seconds";
kv.value = kv_value++;
const int res = kv_pub->broadcast(kv);
if (res < 0)
{
std::cerr << "Sub KV pub err " << res << std::endl;
}
});
while (true)
{
const int res = node->spin(uavcan::MonotonicDuration::fromMSec(1000));
if (res < 0)
{
std::cerr << "SubNode spin error: " << res << std::endl;
}
}
}
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;
}
