void save(std::ofstream& ofs, const boost::shared_ptr<Space>& space)
{
ofs << std::setprecision(17);
if (header.size() > 0)
{
ofs << header << std::endl;
}
if (species.size() == 0)
{
const particle_container_type particles(space->list_particles());
write_particles(ofs, space->t(), particles);
}
else
{
for (std::vector<std::string>::const_iterator i(species.begin());
i != species.end(); ++i)
{
const Species sp(*i);
const particle_container_type particles(space->list_particles(sp));
write_particles(ofs, space->t(), particles, *i);
}
}
}
particle* read_particles(const char* file) {
char postfix[10];
srand((unsigned)time(NULL));
rand_string(postfix, 10);
sprintf(dir_name, "out_%s_%s", basename((char*)file), postfix);
mkdir(dir_name, 0777);
ps = NULL;
char* line = NULL;
FILE* fp = fopen(file, "r");
size_t len = 0;
if (!fp) {
printf("Invalid input: %s\nCould not open file.\n", file);
exit(EXIT_FAILURE);
}
if (getline(&line, &len, fp) != -1) {
char* end;
particle_count = strtol(line, &end, 10);
if (*end == 0) {
printf("Invalid input: %s\nExpected number of particles.\n", line);
exit(EXIT_FAILURE);
}
ps = _mm_malloc(particle_count * sizeof(particle), 64);
} else {
printf("Invalid input: Empty file.\n");
exit(EXIT_FAILURE);
}
// m x y z vx vy vz
for (long i = 0; i < particle_count; i++) {
getline(&line, &len, fp);
sscanf(line, "%lf %lf %lf %lf %lf %lf %lf", &ps[i].mass,
&ps[i].position[X], &ps[i].position[Y], &ps[i].position[Z],
&ps[i].velocity[X], &ps[i].velocity[Y], &ps[i].velocity[Z]);
if (ps[i].mass == 0) {
printf("Invalid input: Invald particle at line %ld.\n", i + 1);
exit(EXIT_FAILURE);
}
ps[i].force[X] = 0.0;
ps[i].force[Y] = 0.0;
ps[i].force[Z] = 0.0;
update_minmax(ps[i].position);
}
calculate_cube();
fclose(fp);
if (line) {
free(line);
}
write_plot_limits();
write_particles(-1); // Initial state of particles.
return ps;
}
int main(int argn, char** args){
if (argn !=2 ) {
printf("When running the simulation, please give a valid geometry file name!\n");
return 1;
}
//set the geometry file
char *filename = NULL;
filename = args[1];
//initialize variables
double t = 0; /*time start*/
int it, n = 0; /*iteration and time step counter*/
double res; /*residual for SOR*/
/*arrays*/
double ***U, ***V, ***W, ***P;
double ***RS, ***F, ***G, ***H;
int ***Flag; //additional data structure for arbitrary geometry
int ***S; //additional data structure for arbitrary geometry
int matrix_output = 0;
/*those to be read in from the input file*/
double Re, UI, VI, WI, PI, GX, GY, GZ, t_end, xlength, ylength, zlength, dt, dx, dy, dz, alpha, omg, tau, eps, dt_value;
int imax, jmax, kmax, itermax;
//double presLeft, presRight, presDelta; //for pressure stuff ...TODO: not allowed for now
int wl, wr, wt, wb, wf, wh;
char problemGeometry[200];
//in case of a given inflow or wall velocity TODO: will we have this? needs to be a vector?
double velIN;
double velMW[3]; // the moving wall velocity is a vector
struct particleline *Partlines = (struct particleline *)malloc((unsigned)(1 * sizeof(struct particleline)));
//char szFileName[80];
//read the parameters, using problem.dat, including wl, wr, wt, wb
read_parameters(filename, &Re, &UI, &VI, &WI, &PI, &GX, &GY, &GZ, &t_end, &xlength, &ylength, &zlength, &dt, &dx, &dy, &dz, &imax,
&jmax, &kmax, &alpha, &omg, &tau, &itermax, &eps, &dt_value, &wl, &wr, &wf, &wh, &wt, &wb, problemGeometry, &velIN, &velMW[0]); //&presLeft, &presRight, &presDelta, &vel);
//printf("d: %f, %f, %f\n", dx,dy,dz);
//int pics = dt_value/dt; //just a helping variable for outputing vtk
double last_output_t = -dt_value;
//double every = t_end/10; //helping variable. Can be used for displaying info every tenth of the progress during simulation
//allocate memory, including Flag
U = matrix2(0, imax+1, 0, jmax+1, 0, kmax+1);
V = matrix2(0, imax+1, 0, jmax+1, 0, kmax+1);
W = matrix2(0, imax+1, 0, jmax+1, 0, kmax+1);
P = matrix2(0, imax+1, 0, jmax+1, 0, kmax+1);
RS = matrix2(1, imax, 1, jmax, 1, kmax);
F = matrix2(0, imax, 1, jmax, 1, kmax);
G = matrix2(1, imax, 0, jmax, 1, kmax);
H = matrix2(1, imax, 1, jmax, 0, kmax);
Flag = imatrix2(0, imax+1, 0, jmax+1, 0, kmax+1); // or Flag = imatrix(1, imax, 1, jmax);
S = imatrix2(0, imax+1, 0, jmax+1, 0, kmax+1);
//S = Flag -> adjust C_x Flags in helper.h
//initialisation, including **Flag
init_flag(problemGeometry, imax, jmax, kmax, Flag, wl, wr, wf, wh, wt, wb); //presDelta, Flag);
init_particles(Flag,dx,dy,dz,imax,jmax,kmax,3,Partlines);
printf("!!!!!!!!%d\n",binMatch(B_NO,B_N));
init_uvwp(UI, VI, WI, PI, Flag,imax, jmax, kmax, U, V, W, P, problemGeometry);
write_particles("particles_init",0, 1, Partlines);
write_imatrix2("Flag_start.txt",t,Flag, 0, imax, 1, jmax, 1, kmax);
//write_flag_imatrix("Flag.txt",t,Flag, 0, imax+1, 0, jmax+1, 0, kmax+1);
write_vtkFile(filename, -1, xlength, ylength, zlength, imax, jmax, kmax, dx, dy, dz, U, V, W, P,Flag);
//write_vtkFile("init", n, xlength, ylength, zlength, imax, jmax, kmax, dx, dy, dz, U, V, W, P);
//going through all time steps
/*
write_matrix2("P_start.txt",t,P, 0, imax+1, 0, jmax+1, 0, kmax+1);
write_matrix2("U_start.txt",t,U, 0, imax+1, 0, jmax+1, 0, kmax+1);
write_matrix2("V_start.txt",t,V, 0, imax+1, 0, jmax+1, 0, kmax+1);
write_matrix2("W_start.txt",t,W, 0, imax+1, 0, jmax+1, 0, kmax+1);
*/
//setting bound.values
boundaryvalues(imax, jmax, kmax, U, V, W, P, F, G, H, problemGeometry, Flag, velIN, velMW); //including P, wl, wr, wt, wb, F, G, problem
// printf("calc bc \n");
while(t < t_end){
/*if(t - every >= 0){
printf("Calculating time %f ... \n", t);
every += t;
}*/
//adaptive time stepping
calculate_dt(Re, tau, &dt, dx, dy, dz, imax, jmax, kmax, U, V, W);
// printf("calc dt \n");
/*
mark_cells(Flag,dx,dy,dz,imax,jmax,kmax,1,Partlines);
set_uvwp_surface(U,V,W,P,Flag,dx,dy,dz,imax,jmax,kmax,GX,GY,GZ,dt,Re);
*/
//computing F, G, H and right hand side of pressue eq.
calculate_fgh(Re, GX, GY, GZ, alpha, dt, dx, dy, dz, imax, jmax, kmax, U, V, W, F, G, H, Flag);
// printf("calc fgh \n");
calculate_rs(dt, dx, dy, dz, imax, jmax, kmax, F, G, H, RS,Flag);
// printf("calc rs \n");
//iteration counter
it = 0;
//write_matrix2("RS.txt",t,RS, 1, imax, 1, jmax, 1, kmax);
//write_matrix2("F.txt",t,F, 0, imax, 1, jmax, 1, kmax);
//write_matrix2("G.txt",t,G, 1, imax, 0, jmax, 1, kmax);
//write_matrix2("H.txt",t,H, 1, imax, 1, jmax, 0, kmax);
do{
// sprintf( szFileName, "P_%d.txt",it );
//write_matrix2(szFileName,1000+t,P, 0, imax+1, 0, jmax+1, 0, kmax+1);
//perform SOR iteration, at same time set bound.values for P and new residual value
sor(omg, dx, dy, dz, imax, jmax, kmax, P, RS, &res, Flag); //, presLeft, presRight);
it++;
}while(it<itermax && res>eps);
/*if (it == itermax) {
printf("Warning: sor while loop exits because it reaches the itermax. res = %f, time =%f\n", res, t);
} */
//write_matrix2("P.txt",t,P, 0, imax+1, 0, jmax+1, 0, kmax+1);
//calculate U, V and W of this time step
calculate_uvw(dt, dx, dy, dz, imax, jmax, kmax, U, V, W, F, G, H, P, Flag);
//write_matrix2("U.txt",t,U, 0, imax+1, 0, jmax+1, 0, kmax+1);
//write_matrix2("V.txt",t,V, 0, imax+1, 0, jmax+1, 0, kmax+1);
//write_matrix2("W.txt",t,W, 0, imax+1, 0, jmax+1, 0, kmax+1);
// printf("calc uvw \n");
//sprintf( szFileName, "simulation/%s.%i_debug.vtk", szProblem, timeStepNumber );
//setting bound.values
boundaryvalues(imax, jmax, kmax, U, V, W, P, F, G, H, problemGeometry, Flag, velIN, velMW); //including P, wl, wr, wt, wb, F, G, problem
/*
set_uvwp_surface(U,V,W,P,Flag,dx,dy,dz,imax,jmax,kmax,GX,GY,GZ,dt,Re);
printf("advance_particles!\n");
advance_particles(dx,dy, dz,imax,jmax,kmax, dt,U,V,W,1,Partlines);
*/
//indent time and number of time steps
printf("timer\n");
n++;
t += dt;
//output of pics for animation
if ( t-last_output_t >= dt_value ){ //n%pics==0 ){
printf("output\n!");
write_particles(filename,n, 1, Partlines);
write_vtkFile(filename, n, xlength, ylength, zlength, imax, jmax, kmax, dx, dy, dz, U, V, W, P,Flag);
printf("output vtk (%d)\n",n);
last_output_t = t;
matrix_output++;
}
printf("timestep: %f - next output: %f (dt: %f) \n",t,dt_value- (t-last_output_t),dt);
}
//output of U, V, P at the end for visualization
//write_vtkFile("DrivenCavity", n, xlength, ylength, imax, jmax, dx, dy, U, V, P);
//free memory
free_matrix2(U, 0, imax+1, 0, jmax+1, 0, kmax+1);
free_matrix2(V, 0, imax+1, 0, jmax+1, 0, kmax+1);
free_matrix2(W, 0, imax+1, 0, jmax+1, 0, kmax+1);
free_matrix2(P, 0, imax+1, 0, jmax+1, 0, kmax+1);
free_matrix2(RS, 1, imax, 1, jmax, 1, kmax);
free_matrix2(F, 0, imax, 1, jmax, 1, kmax);
free_matrix2(G, 1, imax, 0, jmax, 1, kmax);
free_matrix2(H, 1, imax, 1, jmax, 0, kmax);
free_imatrix2(Flag, 0, imax+1, 0, jmax+1, 0, kmax+1);
free_imatrix2(S, 0, imax+1, 0, jmax+1, 0, kmax+1);
//printf("\n-\n");
return -1;
}
