int dtf_createmap(t_dtf *map, char ***raw)
{
if (get_crtreturn(NULL))
return (0);
if (map == NULL || raw == NULL)
return (dbgerr("Error: dtf_createmap: NULL parameter"));
if ((map->width = get_mapwidth(raw[0])) <= 0 ||
(map->height = get_mapheight(raw)) <= 0 || !check_maprect(map, raw) ||
!convert_rawtomap(map, raw) || !check_borders(map))
return (dbgerr("Error: dtf_createmap: invalid parameters"));
return (1);
}
void Cell:: dispatch_all( )
{
MPI.Printf0( stderr, "\t---> check_and_dispatch bubbles\n");
bubbles.check_and_dispatch_all(MPI,rescaler);
MPI.Printf0( stderr, "\t---> compute bubbles properties\n");
bubbles.check_geometries_within(Y[Y.lower], Y[Y.upper]);
MPI.Printf0( stderr, "\t---> segmentation: process\n");
segmenter.process( bubbles );
MPI.Printf0( stderr, "\t---> segmentation: check_borders\n");
check_borders();
MPI.Printf0( stderr, "\t---> segmentation: assign\n");
segmenter.assign_markers();
MPI.Printf0( stderr, "\t---> segmentation: fill B\n");
bubbles.fill(B);
}
int main(int argc, char * argv[])
{
PV::PV_Init* initObj = new PV::PV_Init(&argc, &argv);
int err = 0;
PVLayerLoc loc;
PV::Communicator * comm = new PV::Communicator(argc, argv);
int nxProc = comm->numCommColumns();
int nyProc = comm->numCommRows();
int commRow = comm->commRow();
int commCol = comm->commColumn();
printf("[%d]: nxProc==%d nyProc==%d commRow==%d commCol==%d numNeighbors==%d\n", comm->commRank(), nxProc, nyProc, commRow, commCol, comm->numberOfNeighbors()); fflush(stdout);
loc.nx = 128;
loc.ny = 128;
loc.nxGlobal = nxProc * loc.nx;
loc.nyGlobal = nyProc * loc.ny;
// this info not used for send/recv
loc.kx0 = 0; loc.ky0 = 0;
const int nxBorder = 16;
const int nyBorder = 16;
int numItems = (2*nxBorder + loc.nx) * (2*nyBorder + loc.ny);
MPI_Datatype * datatypes = comm->newDatatypes(&loc);
// create a local portion of the "image"
float * image = new float [numItems];
int k0 = commCol * loc.nx + commRow * loc.ny * loc.nxGlobal;
int sy = 2 * nxBorder + loc.nx;
for (int ky = 0; ky < loc.ny; ky++) {
int k = k0 + ky * loc.nxGlobal;
float * buf = image + nxBorder + (ky + nyBorder) * sy;
for (int kx = 0; kx < loc.nx; kx++) {
buf[kx] = (float) k++;
}
}
// send and recv the "image"
comm->exchange(image, datatypes, &loc);
err = check_borders(image, comm, loc);
if (err != 0) {
printf("[%d]: check_borders failed\n", comm->commRank());
}
else {
printf("[%d]: check_borders succeeded\n", comm->commRank());
}
delete datatypes;
delete comm;
delete initObj;
return 0;
}
int main(int argc, char *argv[]) {
char fname[300];
FILE *fid;
DIR* dir;
size_t elem;
long int ii,ij,ik, ii_c, ij_c, ik_c, a, b, c;
long int ncells_1D;
long int i,j,p,indi,indj,ind;
int flag_bub,iz;
double redshift,tmp;
double kk;
double bfactor; /* value by which to divide bubble size R */
double neutral,*xHI;
float *halo_map, *top_hat_r, *density_map,*bubblef, *bubble;
fftwf_complex *halo_map_c, *top_hat_c, *collapsed_mass_c, *density_map_c, *total_mass_c, *bubble_c;
fftwf_plan pr2c1,pr2c2,pr2c3,pr2c4,pc2r1,pc2r2,pc2r3;
double zmin,zmax,dz;
double R;
if(argc != 2) {
printf("Generates boxes with ionization fraction for a range of redshifts\n");
printf("usage: get_HIIbubbles base_dir\n");
printf("base_dir contains simfast21.ini and directory structure\n");
exit(1);
}
get_Simfast21_params(argv[1]);
zmin=global_Zminsim;
zmax=global_Zmaxsim;
dz=global_Dzsim;
bfactor=pow(10.0,log10(global_bubble_Rmax/global_dx_smooth)/global_bubble_Nbins);
printf("Bubble radius ratio (bfactor): %f\n", bfactor); fflush(0);
#ifdef _OMPTHREAD_
omp_set_num_threads(global_nthreads);
fftwf_init_threads();
fftwf_plan_with_nthreads(global_nthreads);
printf("Using %d threads\n",global_nthreads);fflush(0);
#endif
/* Create directory Ionization */
sprintf(fname,"%s/Ionization",argv[1]);
if((dir=opendir(fname))==NULL) {
printf("Creating Ionization directory\n");
if(mkdir(fname,(S_IRWXU | S_IRGRP | S_IXGRP | S_IROTH | S_IXOTH))!=0) {
printf("Error creating directory!\n");
exit(1);
}
}
sprintf(fname,"%s/Output_text_files",argv[1]);
if((dir=opendir(fname))==NULL) {
printf("Creating Output_text_files directory\n");
if(mkdir(fname,(S_IRWXU | S_IRGRP | S_IXGRP | S_IROTH | S_IXOTH))!=0) {
printf("Error creating directory!\n");
exit(1);
}
}
/* Memory allocation - we could do some of the FFTs inline... */
/*************************************************************/
/* density_map mass */
if(!(density_map=(float *) fftwf_malloc(global_N3_smooth*sizeof(float)))) {
printf("Problem1...\n");
exit(1);
}
if(!(density_map_c=(fftwf_complex *) fftwf_malloc(global_N_smooth*global_N_smooth*(global_N_smooth/2+1)*sizeof(fftwf_complex)))) {
printf("Problem2...\n");
exit(1);
}
if(!(pr2c1=fftwf_plan_dft_r2c_3d(global_N_smooth, global_N_smooth, global_N_smooth, density_map, density_map_c, FFTWflag))) {
printf("Problem3...\n");
exit(1);
}
/* halo_map mass */
if(!(halo_map=(float *) fftwf_malloc(global_N3_smooth*sizeof(float)))) {
printf("Problem4...\n");
exit(1);
}
if(!(halo_map_c=(fftwf_complex *) fftwf_malloc(global_N_smooth*global_N_smooth*(global_N_smooth/2+1)*sizeof(fftwf_complex)))) {
printf("Problem5...\n");
exit(1);
}
if(!(pr2c2=fftwf_plan_dft_r2c_3d(global_N_smooth, global_N_smooth, global_N_smooth, halo_map, halo_map_c, FFTWflag))) {
printf("Problem6...\n");
exit(1);
}
/* total mass */
if(!(total_mass_c=(fftwf_complex *) fftwf_malloc(global_N_smooth*global_N_smooth*(global_N_smooth/2+1)*sizeof(fftwf_complex)))) {
printf("Problem7...\n");
exit(1);
}
if(!(pc2r1=fftwf_plan_dft_c2r_3d(global_N_smooth, global_N_smooth, global_N_smooth, total_mass_c, density_map, FFTWflag))) {
printf("Problem8...\n");
exit(1);
}
/* collapsed mass */
if(!(collapsed_mass_c=(fftwf_complex *) fftwf_malloc(global_N_smooth*global_N_smooth*(global_N_smooth/2+1)*sizeof(fftwf_complex)))) {
printf("Problem9...\n");
exit(1);
}
if(!(pc2r2=fftwf_plan_dft_c2r_3d(global_N_smooth, global_N_smooth, global_N_smooth, collapsed_mass_c, halo_map, FFTWflag))) {
printf("Problem10...\n");
exit(1);
}
/* top hat window */
if(!(top_hat_r=(float *) fftwf_malloc(global_N3_smooth*sizeof(float)))) {
printf("Problem11...\n");
exit(1);
}
if(!(top_hat_c=(fftwf_complex *) fftwf_malloc(global_N_smooth*global_N_smooth*(global_N_smooth/2+1)*sizeof(fftwf_complex)))) {
printf("Problem12...\n");
exit(1);
}
if(!(pr2c3=fftwf_plan_dft_r2c_3d(global_N_smooth, global_N_smooth, global_N_smooth, top_hat_r, top_hat_c, FFTWflag))) {
printf("Problem13...\n");
exit(1);
}
/* bubble boxes */
if(!(bubble=(float *) fftwf_malloc(global_N3_smooth*sizeof(float)))) {
printf("Problem14...\n");
exit(1);
}
if(!(bubble_c=(fftwf_complex *) fftwf_malloc(global_N_smooth*global_N_smooth*(global_N_smooth/2+1)*sizeof(fftwf_complex)))) {
printf("Problem15...\n");
exit(1);
}
if(!(bubblef=(float *) malloc(global_N3_smooth*sizeof(float)))) {
printf("Problem16...\n");
exit(1);
}
if(!(pr2c4=fftwf_plan_dft_r2c_3d(global_N_smooth, global_N_smooth, global_N_smooth, bubble, bubble_c, FFTWflag))) {
printf("Problem17...\n");
exit(1);
}
if(!(pc2r3=fftwf_plan_dft_c2r_3d(global_N_smooth, global_N_smooth, global_N_smooth, bubble_c, bubble, FFTWflag))) {
printf("Problem18...\n");
exit(1);
}
if(!(xHI=(double *) malloc((int)((zmax-zmin)/dz+2)*sizeof(double)))) {
printf("Problem19...\n");
exit(1);
}
/****************************************************/
/***************** Redshift cycle *******************/
printf("Number of bubble sizes: %d\n",(int)((log(global_bubble_Rmax)-log(2.*global_dx_smooth))/log(bfactor)));
printf("Redshift cycle...\n");fflush(0);
iz=0;
neutral=0.;
for(redshift=zmin;redshift<(zmax+dz/10) && (neutral < xHlim);redshift+=dz){
printf("z = %f\n",redshift);fflush(0);
sprintf(fname, "%s/delta/deltanl_z%.3f_N%ld_L%.1f.dat",argv[1],redshift,global_N_smooth,global_L/global_hubble);
fid=fopen(fname,"rb");
if (fid==NULL) {printf("\nError reading deltanl file... Check path or if the file exists..."); exit (1);}
elem=fread(density_map,sizeof(float),global_N3_smooth,fid);
fclose(fid);
#ifdef _OMPTHREAD_
#pragma omp parallel for shared(global_N3_smooth, density_map,global_rho_m, global_dx_smooth,bubblef) private(i)
#endif
for(i=0;i<(global_N3_smooth);i++){
density_map[i]=(1.0+density_map[i])*global_rho_m*global_dx_smooth*global_dx_smooth*global_dx_smooth; /* total mass in 1 cell */
bubblef[i]=0.0;
}
sprintf(fname, "%s/Halos/masscoll_z%.3f_N%ld_L%.1f.dat",argv[1],redshift,global_N_smooth,global_L/global_hubble);
fid=fopen(fname,"rb");
if (fid==NULL) {printf("\nError reading %s file... Check path or if the file exists...",fname); exit (1);}
elem=fread(halo_map,sizeof(float),global_N3_smooth,fid);
fclose(fid);
/* Quick fill of single cells before going to bubble cycle */
#ifdef _OMPTHREAD_
#pragma omp parallel for shared(global_N3_smooth,halo_map,density_map,global_eff,bubblef) private(i,tmp)
#endif
for(i=0;i<global_N3_smooth;i++) {
if(halo_map[i]>0.) {
if(density_map[i]>0.)
tmp=(double)halo_map[i]*global_eff/density_map[i];
else tmp=1.0;
}else tmp=0.;
if(tmp>=1.0) bubblef[i]=1.0; else bubblef[i]=tmp;
}
/* FFT density and halos */
fftwf_execute(pr2c1);
fftwf_execute(pr2c2);
/************** going over the bubble sizes ****************/
R=global_bubble_Rmax; /* Maximum bubble size...*/
while(R>=2*global_dx_smooth){
printf("bubble radius R= %lf\n", R);fflush(0);
// printf("Filtering halo and density boxes...\n");fflush(0);
#ifdef _OMPTHREAD_
#pragma omp parallel for shared(collapsed_mass_c,halo_map_c,total_mass_c,density_map_c,global_N_smooth,global_dk,R) private(i,j,p,indi,indj,kk)
#endif
for(i=0;i<global_N_smooth;i++) {
if(i>global_N_smooth/2) {
indi=-(global_N_smooth-i);
}else indi=i;
for(j=0;j<global_N_smooth;j++) {
if(j>global_N_smooth/2) {
indj=-(global_N_smooth-j);
}else indj=j;
for(p=0;p<=global_N_smooth/2;p++) {
kk=global_dk*sqrt(indi*indi+indj*indj+p*p);
total_mass_c[i*global_N_smooth*(global_N_smooth/2+1)+j*(global_N_smooth/2+1)+p]=density_map_c[i*global_N_smooth*(global_N_smooth/2+1)+j*(global_N_smooth/2+1)+p]*W_filter(kk*R);
collapsed_mass_c[i*global_N_smooth*(global_N_smooth/2+1)+j*(global_N_smooth/2+1)+p]=halo_map_c[i*global_N_smooth*(global_N_smooth/2+1)+j*(global_N_smooth/2+1)+p]*W_filter(kk*R);
}
}
}
fftwf_execute(pc2r1);
fftwf_execute(pc2r2);
flag_bub=0;
// printf("Starting to find and fill bubbles...\n");fflush(0);
/* signal center of bubbles */
#ifdef _OMPTHREAD_
#pragma omp parallel for shared(halo_map,density_map,bubble,global_N_smooth,global_eff,flag_bub) private(ii,ij,ik,ind)
#endif
for(ii=0;ii<global_N_smooth;ii++){
for(ij=0;ij<global_N_smooth;ij++){
for(ik=0;ik<global_N_smooth;ik++){
ind=ii*global_N_smooth*global_N_smooth+ij*global_N_smooth+ik;
if(halo_map[ind]>0.) {
if(density_map[ind]>0.) {
if((double)halo_map[ind]/density_map[ind]>=1.0/global_eff) {
flag_bub=1;
bubble[ind]=1.0;
}else bubble[ind]=0;
}else {
flag_bub=1;
bubble[ind]=1.0;
}
}else bubble[ind]=0;
}
}
}
/* generate spherical window in real space for a given R */
if(flag_bub>0){
printf("Found bubble...\n");fflush(0);
#ifdef _OMPTHREAD_
#pragma omp parallel for shared(top_hat_r,R,global_dx_smooth,global_N_smooth) private(i,j,p)
#endif
for(i=0;i<global_N_smooth;i++){
for(j=0;j<global_N_smooth;j++){
for(p=0;p<global_N_smooth;p++){
if(sqrt(i*i+j*j+p*p)*global_dx_smooth<=R || sqrt(i*i+(j-global_N_smooth)*(j-global_N_smooth)+p*p)*global_dx_smooth<=R || sqrt(i*i+(j-global_N_smooth)*(j-global_N_smooth)+(p-global_N_smooth)*(p-global_N_smooth))*global_dx_smooth <=R || sqrt(i*i+(p-global_N_smooth)*(p-global_N_smooth)+j*j)*global_dx_smooth<=R || sqrt((i-global_N_smooth)*(i-global_N_smooth)+j*j+p*p)*global_dx_smooth<=R || sqrt((i-global_N_smooth)*(i-global_N_smooth)+(j-global_N_smooth)*(j-global_N_smooth)+p*p)*global_dx_smooth<=R || sqrt((i-global_N_smooth)*(i-global_N_smooth)+(j-global_N_smooth)*(j-global_N_smooth)+(p-global_N_smooth)*(p-global_N_smooth))*global_dx_smooth<=R || sqrt((i-global_N_smooth)*(i-global_N_smooth)+j*j+(p-global_N_smooth)*(p-global_N_smooth))*global_dx_smooth<=R ) {
top_hat_r[i*global_N_smooth*global_N_smooth+j*global_N_smooth+p]=1.0;
}else top_hat_r[i*global_N_smooth*global_N_smooth+j*global_N_smooth+p]=0.0;
}
}
}
/* FFT bubble centers and window */
fftwf_execute(pr2c3);
fftwf_execute(pr2c4);
/* Make convolution */
#ifdef _OMPTHREAD_
#pragma omp parallel for shared(bubble_c,top_hat_c,global_N_smooth) private(i)
#endif
for(i=0;i<global_N_smooth*global_N_smooth*(global_N_smooth/2+1);i++) {
bubble_c[i]*=top_hat_c[i];
}
fftwf_execute(pc2r3);
/* after dividing by global_N3_smooth, values in bubble are between 0 (neutral)and global_N3_smooth */
#ifdef _OMPTHREAD_
#pragma omp parallel for shared(bubble,bubblef,global_N3_smooth) private(i)
#endif
for (i=0; i<global_N3_smooth; i++){
bubble[i]/=global_N3_smooth;
if (bubble[i]>0.2) bubblef[i]=1.0; /* neutral should be zero */
}
} /* ends filling out bubbles in box for R */
R/=bfactor;
} /* ends R cycle */
/* just to check smallest bubbles through older method */
printf("Going to smaller R cycle...\n"); fflush(0);
while(R>=global_dx_smooth){
printf("bubble radius R= %lf\n", R);fflush(0);
flag_bub=0;
#ifdef _OMPTHREAD_
#pragma omp parallel for shared(collapsed_mass_c,halo_map_c,total_mass_c,density_map_c,global_N_smooth,global_dx_smooth,global_dk,R) private(i,j,p,indi,indj,kk)
#endif
for(i=0;i<global_N_smooth;i++) {
if(i>global_N_smooth/2) {
indi=-(global_N_smooth-i);
}else indi=i;
for(j=0;j<global_N_smooth;j++) {
if(j>global_N_smooth/2) {
indj=-(global_N_smooth-j);
}else indj=j;
for(p=0;p<=global_N_smooth/2;p++) {
kk=global_dk*sqrt(indi*indi+indj*indj+p*p);
total_mass_c[i*global_N_smooth*(global_N_smooth/2+1)+j*(global_N_smooth/2+1)+p]=density_map_c[i*global_N_smooth*(global_N_smooth/2+1)+j*(global_N_smooth/2+1)+p]*W_filter(kk*R);
collapsed_mass_c[i*global_N_smooth*(global_N_smooth/2+1)+j*(global_N_smooth/2+1)+p]=halo_map_c[i*global_N_smooth*(global_N_smooth/2+1)+j*(global_N_smooth/2+1)+p]*W_filter(kk*R);
}
}
}
fftwf_execute(pc2r1);
fftwf_execute(pc2r2);
/* fill smaller bubbles in box */
ncells_1D=(long int)(R/global_dx_smooth);
// printf("Starting to find and fill bubbles...\n");fflush(0);
#ifdef _OMPTHREAD_
#pragma omp parallel for shared(halo_map,density_map,global_eff,global_N_smooth,global_dx_smooth,R,ncells_1D,bubblef,flag_bub) private(ii_c,ij_c,ik_c,ii,ij,ik,a,b,c,ind)
#endif
for(ii_c=0;ii_c<global_N_smooth;ii_c++){
for(ij_c=0;ij_c<global_N_smooth;ij_c++){
for(ik_c=0;ik_c<global_N_smooth;ik_c++){
ind=ii_c*global_N_smooth*global_N_smooth+ij_c*global_N_smooth+ik_c;
if(halo_map[ind]>0.) {
if(!(density_map[ind]>0.) || ((double)halo_map[ind]/density_map[ind]>=1.0/global_eff)) {
flag_bub=1;
for(ii=-(ncells_1D+1);ii<=ncells_1D+1;ii++){
a=check_borders(ii_c+ii,global_N_smooth);
for(ij=-(ncells_1D+1);ij<=ncells_1D+1;ij++){
if(sqrt(ii*ii+ij*ij)*global_dx_smooth <= R){
b=check_borders(ij_c+ij,global_N_smooth);
for(ik=-(ncells_1D+1);ik<=ncells_1D+1;ik++){
c=check_borders(ik_c+ik,global_N_smooth);
if(sqrt(ii*ii+ij*ij+ik*ik)*global_dx_smooth <= R){
bubblef[a*global_N_smooth*global_N_smooth+b*global_N_smooth+c]=1.0;
}
}
}
}
}
}
}
}
}
}
if(flag_bub>0){printf("Found bubble...\n");fflush(0);}
R/=bfactor;
} /* ends small bubbles R cycle */
neutral=0.;
for (i=0; i<global_N3_smooth; i++){
neutral+=1.0-bubblef[i];
}
neutral/=global_N3_smooth;
printf("neutral fraction=%lf\n",neutral);fflush(0);
xHI[iz]=neutral;
sprintf(fname, "%s/Ionization/xHII_z%.3f_eff%.2lf_N%ld_L%.1f.dat",argv[1],redshift,global_eff,global_N_smooth,global_L/global_hubble);
if((fid = fopen(fname,"wb"))==NULL) {
printf("Error opening file:%s\n",fname);
exit(1);
}
elem=fwrite(bubblef,sizeof(float),global_N3_smooth,fid);
fclose(fid);
iz++;
} /* ends redshift cycle */
/* z cycle for neutral>=xHlim */
while(redshift<(zmax+dz/10)) {
printf("z(>%f) = %f\n",xHlim,redshift);fflush(0);
xHI[iz]=1.0;
sprintf(fname, "%s/Ionization/xHII_z%.3f_eff%.2lf_N%ld_L%.1f.dat",argv[1],redshift,global_eff,global_N_smooth,global_L/global_hubble);
if((fid = fopen(fname,"wb"))==NULL) {
printf("Error opening file:%s\n",fname);
exit(1);
}
#ifdef _OMPTHREAD_
#pragma omp parallel for shared(bubblef,global_N3_smooth) private(i)
#endif
for(i=0;i<global_N3_smooth;i++) bubblef[i]=0.0;
elem=fwrite(bubblef,sizeof(float),global_N3_smooth,fid);
fclose(fid);
iz++;
redshift+=dz;
}
sprintf(fname, "%s/Output_text_files/zsim.txt",argv[1]);
if((fid = fopen(fname,"a"))==NULL) {
printf("Error opening file:%s\n",fname);
exit(1);
}
for(redshift=zmax;redshift>(zmin-dz/10);redshift-=dz) fprintf(fid,"%f\n",redshift); /* first line should be highest redshift */
fclose(fid);
sprintf(fname, "%s/Output_text_files/x_HI_eff%.2lf_N%ld_L%.1f.dat",argv[1],global_eff,global_N_smooth,global_L/global_hubble);
if((fid = fopen(fname,"a"))==NULL) {
printf("Error opening file:%s\n",fname);
exit(1);
}
for(i=iz-1;i>=0;i--) fprintf(fid,"%lf\n",xHI[i]); /* first line should be highest redshift */
fclose(fid);
free(xHI);
free(bubblef);
fftwf_free(top_hat_r);
fftwf_free(top_hat_c);
fftwf_free(collapsed_mass_c);
fftwf_free(density_map);
fftwf_free(density_map_c);
fftwf_free(halo_map);
fftwf_free(halo_map_c);
fftwf_free(total_mass_c);
fftwf_free(bubble);
fftwf_free(bubble_c);
exit(0);
}