int
SolveStep::solve(double timestep,
double time,
std::string name,
std::string method,
std::string dimension)
{
/* Solves given system with given parametres using
* given method
* timestep: size of timestep
* time: total simulation time
* name: name of files where the position of the
* particles are saved at some timesteps
* method: verlet or RK4
* dimension: ly or AU
*
* Ditterent timers have not been used at the
* same time.*/
clock_t start, finish;
Distance d;
//declaration and intialisation
omp_set_num_threads(8); //parallelisation
double limit = 60; //definition of bound system
arma::Col<double> center(3), position(3);
center.zeros();
double t = 0.;
System newsystem = mysolarsystem_;
int n = time/timestep;
//file to store energy of the system
std::ofstream energy("energy.m");
energy << "A = [";
//file to store energy of the bound system
std::ofstream bound("BoundEnergy.m");
bound << "A = [";
//update the objects initial acceleration
for (int i = 0 ; i < size() ; ++i)
{
Object &mainbody = newsystem.objectlist[i];
newsystem.acceleration(mainbody, i, 0.0,dimension);
}
// start = clock(); //start timer
//start simulation
for (int k = 0 ; k < n ; ++k)
{
t += timestep;
//file to store position of particles
name.append("t");
std::string filename = name;
filename.append(".m");
std::ofstream fout(filename.c_str());
fout << "t = " << t << "\n A = [";
//variable needed for calculating intermediate steps
double addtime = 0.0;
//simulate all particles for one timestep
#pragma omp parallel for private(i)
for (int i = 0 ; i < size() ; ++i)
{
Object &mainbody = newsystem.objectlist[i];
System tempSystem = mysolarsystem_;
double dt = timestep;
int j = 0;
double maxTimestep;
//chose the smallest timestep
if (mainbody.maxTimestep() < tempSystem.maxTimestep(i))
{
maxTimestep = mainbody.maxTimestep();
}
else
{
maxTimestep = tempSystem.maxTimestep(i);
}
//make sure to use small endough timesteps
while(dt > maxTimestep)
{
dt = dt/2.0;
j += 1;
}
//simulate timesteps
for (int kk = 0 ; kk < std::pow(2,j); ++kk)
{
if (method == "rk4")
{
start = clock(); //start timer
rk4Step(dt, i, mainbody, tempSystem, addtime, dimension);
finish = clock(); //stop timer
std::cout << "time one rk4 step: " <<
static_cast<double>(finish - start)/
static_cast<double>(CLOCKS_PER_SEC ) << " s" << std::endl;
// mainbody.addToFile(name);
addtime += dt;
}
else if(method == "verlet")
{
start = clock(); //start timer
verlet(dt, i, mainbody, tempSystem, addtime, dimension);
finish = clock(); //stop timer
std::cout << "time one verlet step: " <<
static_cast<double>(finish - start)/
static_cast<double>(CLOCKS_PER_SEC ) << " s" << std::endl;
// mainbody.addToFile(name);
addtime += dt;
}
else
{
std::cout << "method must be 'verlet' or 'rk4'" << std::endl;
}
}
mysolarsystem_ = newsystem;
//save position to file
for (int i = 0 ; i < size() ; ++i)
{
Object &mainbody = mysolarsystem_.objectlist[i];
position = mainbody.getPosition();
double dist = d.twoObjects(position,center) ;
if(dist < limit)
{
fout << mainbody.getPosition()(0) << "\t\t" << mainbody.getPosition()(1)
<< "\t\t" << mainbody.getPosition()(2) << "\n";
}
// else
// {
// mysolarsystem_.removeObject(i);
// i-=1;
// }
}
fout << "]; \n";
fout << "plot3(A(:,1), A(:,2),A(:,3), 'o')\n";
fout << "t = " << t ;
fout.close();
}
//write energy of the system to file
bound << t << "\t\t" << mysolarsystem_.boundPotentialEnergy(limit) << "\t\t"
<< mysolarsystem_.boundKineticEnergi(limit) << "\n";
energy << t << "\t\t" << mysolarsystem_.potentialEnergy() << "\t\t"
<< mysolarsystem_.kineticEnergi() << "\n";
if (k % 100 == 0)
{
std::cout << t << std::endl;
}
}
// finish = clock(); //stop timer
// std::cout << "time: " <<
// static_cast<double>(finish - start)/
// static_cast<double>(CLOCKS_PER_SEC ) << " s" << std::endl;
energy << "]; \n";
energy.close();
bound << "]; \n";
bound.close();
for (int i = 0 ; i < size() ; ++i)
{
Object &mainbody = mysolarsystem_.objectlist[i];
mysolarsystem_.acceleration(mainbody, i, 0.0,dimension);
}
//write final postition to file
std::ofstream fout("end.m");
fout << "A = [";
for (int i = 0 ; i < size() ; ++i)
{
Object &mainbody = mysolarsystem_.objectlist[i];
fout << mainbody.getPosition()(0) << "\t\t" << mainbody.getPosition()(1)
<< "\t\t" << mainbody.getPosition()(2) << "\n";
}
fout << "] \n";
fout.close();
return 0;
}
/**
* Name: main
*
* Description:
* See usage statement (run program with '-h' flag).
*
* Parameters:
* @param argc number of command line arguments
* @param argv command line arguments
*/
int main( int argc, char **argv )
{
CmdArgs cmd_args; // Command line arguments.
int num_comps, num_dendrs; // Simulation parameters.
int i, j, t_ms, step, dendrite; // Various indexing variables.
struct timeval start, stop, diff; // Values used to measure time.
double exec_time; // How long we take.
// Accumulators used during dendrite simulation.
// NOTE: We depend on the compiler to handle the use of double[] variables as
// double*.
double current, **dendr_volt;
double res[COMPTIME], y[NUMVAR], y0[NUMVAR], dydt[NUMVAR], soma_params[3];
// Strings used to store filenames for the graph and data files.
char time_str[14];
char graph_fname[ FNAME_LEN ];
char data_fname[ FNAME_LEN ];
FILE *data_file; // The output file where we store the soma potential values.
FILE *graph_file; // File where graph will be saved.
PlotInfo pinfo; // Info passed to the plotting functions.
//////////////////////////////////////////////////////////////////////////////
// Parse command line arguments.
//////////////////////////////////////////////////////////////////////////////
if (!parseArgs( &cmd_args, argc, argv )) {
// Something was wrong.
exit(1);
}
// Pull out the parameters so we don't need to type 'cmd_args.' all the time.
num_dendrs = cmd_args.num_dendrs;
num_comps = cmd_args.num_comps;
printf( "Simulating %d dendrites with %d compartments per dendrite.\n",
num_dendrs, num_comps );
//////////////////////////////////////////////////////////////////////////////
// Create files where results will be stored.
//////////////////////////////////////////////////////////////////////////////
// Generate the graph and data file names.
time_t t = time(NULL);
struct tm *tmp = localtime( &t );
strftime( time_str, 14, "%m%d%y_%H%M%S", tmp );
// The resulting filenames will resemble
// pWWdXXcYY_MoDaYe_HoMiSe.xxx
// where 'WW' is the number of processes, 'XX' is the number of dendrites,
// 'YY' the number of compartments, and 'MoDaYe...' the time at which this
// simulation was run.
sprintf( graph_fname, "graphs/p1d%dc%d_%s.png",
num_dendrs, num_comps, time_str );
sprintf( data_fname, "data/p1d%dc%d_%s.dat",
num_dendrs, num_comps, time_str );
// Verify that the graphs/ and data/ directories exist. Create them if they
// don't.
struct stat stat_buf;
stat( "graphs", &stat_buf );
if ((!S_ISDIR(stat_buf.st_mode)) && (mkdir( "graphs", 0700 ) != 0)) {
fprintf( stderr, "Could not create 'graphs' directory!\n" );
exit(1);
}
stat( "data", &stat_buf );
if ((!S_ISDIR(stat_buf.st_mode)) && (mkdir( "data", 0700 ) != 0)) {
fprintf( stderr, "Could not create 'data' directory!\n" );
exit(1);
}
// Verify that we can open files where results will be stored.
if ((data_file = fopen(data_fname, "wb")) == NULL) {
fprintf(stderr, "Can't open %s file!\n", data_fname);
exit(1);
} else {
printf( "\nData will be stored in %s\n", data_fname );
}
if (ISDEF_PLOT_PNG && (graph_file = fopen(graph_fname, "wb")) == NULL) {
fprintf(stderr, "Can't open %s file!\n", graph_fname);
exit(1);
} else {
printf( "Graph will be stored in %s\n", graph_fname );
fclose(graph_file);
}
//////////////////////////////////////////////////////////////////////////////
// Initialize simulation parameters.
//////////////////////////////////////////////////////////////////////////////
// The first compartment is a dummy and the last is connected to the soma.
num_comps = num_comps + 2;
// Initialize 'y' with precomputed values from the HH model.
y[0] = VREST;
y[1] = 0.037;
y[2] = 0.0148;
y[3] = 0.9959;
// Setup parameters for the soma.
soma_params[0] = 1.0 / (double) STEPS; // dt
soma_params[1] = 0.0; // Direct current injection into soma is always zero.
soma_params[2] = 0.0; // Dendritic current injected into soma. This is the
// value that our simulation will update at each step.
printf( "\nIntegration step dt = %f\n", soma_params[0]);
// Start the clock.
gettimeofday( &start, NULL );
// Initialize the potential of each dendrite compartment to the rest voltage.
dendr_volt = (double**) malloc( num_dendrs * sizeof(double*) );
for (i = 0; i < num_dendrs; i++) {
dendr_volt[i] = (double*) malloc( num_comps * sizeof(double) );
for (j = 0; j < num_comps; j++) {
dendr_volt[i][j] = VREST;
}
}
//////////////////////////////////////////////////////////////////////////////
// Main computation.
//////////////////////////////////////////////////////////////////////////////
// Record the initial potential value in our results array.
res[0] = y[0];
// Loop over milliseconds.
for (t_ms = 1; t_ms < COMPTIME; t_ms++) {
// Loop over integration time steps in each millisecond.
for (step = 0; step < STEPS; step++) {
soma_params[2] = 0.0;
// Loop over all the dendrites.
for (dendrite = 0; dendrite < num_dendrs; dendrite++) {
// This will update Vm in all compartments and will give a new injected
// current value from last compartment into the soma.
current = dendriteStep( dendr_volt[ dendrite ],
step + dendrite + 1,
num_comps,
soma_params[0],
y[0] );
// Accumulate the current generated by the dendrite.
soma_params[2] += current;
}
// Store previous HH model parameters.
y0[0] = y[0]; y0[1] = y[1]; y0[2] = y[2]; y0[3] = y[3];
// This is the main HH computation. It updates the potential, Vm, of the
// soma, injects current, and calculates action potential. Good stuff.
soma(dydt, y, soma_params);
rk4Step(y, y0, dydt, NUMVAR, soma_params, 1, soma);
}
// Record the membrane potential of the soma at this simulation step.
// Let's show where we are in terms of computation.
printf("\r%02d ms",t_ms); fflush(stdout);
res[t_ms] = y[0];
}
//////////////////////////////////////////////////////////////////////////////
// Report results of computation.
//////////////////////////////////////////////////////////////////////////////
// Stop the clock, compute how long the program was running and report that
// time.
gettimeofday( &stop, NULL );
timersub( &stop, &start, &diff );
exec_time = (double) (diff.tv_sec) + (double) (diff.tv_usec) * 0.000001;
printf("\n\nExecution time: %f seconds.\n", exec_time);
// Record the parameters for this simulation as well as data for gnuplot.
fprintf( data_file,
"# Vm for HH model. "
"Simulation time: %d ms, Integration step: %f ms, "
"Compartments: %d, Dendrites: %d, Execution time: %f s, "
"Slave processes: %d\n",
COMPTIME, soma_params[0], num_comps - 2, num_dendrs, exec_time,
0 );
fprintf( data_file, "# X Y\n");
for (t_ms = 0; t_ms < COMPTIME; t_ms++) {
fprintf(data_file, "%d %f\n", t_ms, res[t_ms]);
}
fflush(data_file); // Flush and close the data file so that gnuplot will
fclose(data_file); // see it.
//////////////////////////////////////////////////////////////////////////////
// Plot results if approriate macro was defined.
//////////////////////////////////////////////////////////////////////////////
if (ISDEF_PLOT_PNG || ISDEF_PLOT_SCREEN) {
pinfo.sim_time = COMPTIME;
pinfo.int_step = soma_params[0];
pinfo.num_comps = num_comps - 2;
pinfo.num_dendrs = num_dendrs;
pinfo.exec_time = exec_time;
pinfo.slaves = 0;
}
if (ISDEF_PLOT_PNG) { plotData( &pinfo, data_fname, graph_fname ); }
if (ISDEF_PLOT_SCREEN) { plotData( &pinfo, data_fname, NULL ); }
//////////////////////////////////////////////////////////////////////////////
// Free up allocated memory.
//////////////////////////////////////////////////////////////////////////////
for(i = 0; i < num_dendrs; i++) {
free(dendr_volt[i]);
}
free(dendr_volt);
return 0;
}
