void run_output() {
int i, j;
int ipart;
char filename[128];
double pos[nDim];
double phi;
double x_rms, x_norm;
double v_rms, v_norm;
double x_rms_total, v_rms_total;
double x_norm_total, v_norm_total;
double x_z, v_z;
double q, q_i;
int num_level_cells;
int *level_cells;
sprintf(filename, "dumps/zeldovich_[%5.4f]_%03d.dat", abox[min_level], local_proc_id );
output = fopen(filename, "w");
#ifdef PARTICLES
sprintf(filename, "dumps/zeldovich_particles_[%5.4f]_%03d.dat", abox[min_level], local_proc_id );
particles = fopen(filename, "w");
#endif
dgrowth0 = growth(auni_init);
dgrowth = growth(abox[min_level]);
ddgrowthdt = dgrowthdt(abox[min_level]);
c1 = 6.0/abox[min_level];
c2 = 1.0 / (ak*ak);
c3 = dgrowth*ampl*ak;
#ifdef GRAVITY
pos[1] = pos[2] = (double)num_grid / 2.0 - 0.5*cell_size[max_level];
pos[0] = 0.0;
i = cell_find_position(pos);
if ( i != -1 ) {
phi = cell_potential(i);
} else {
phi = 0.0;
}
#endif
MPI_Allreduce( &phi, &phi0, 1, MPI_DOUBLE, MPI_MAX, mpi.comm.run );
/* uncommment to print all cells */
/*
for ( i = min_level; i <= max_level; i++ ) {
select_level( i, CELL_TYPE_LOCAL, &num_level_cells, &level_cells );
for ( j = 0; j < num_level_cells; j++ ) {
output_cell( level_cells[j], i );
}
cart_free(level_cells);
}
*/
for ( pos[0] = 0.0; pos[0] < num_grid; pos[0] += 0.5*cell_size[max_level] ) {
i=cell_find_position(pos);
if ( i != -1 ) {
output_cell( i, cell_level(i) );
}
}
fclose(output);
/* compute rms fluctuations */
x_rms = x_norm = 0.0;
v_rms = v_norm = 0.0;
ddgrowthdt = dgrowthdt( abox_from_tcode( tl[min_level] - 0.5*dtl[min_level] ) );
#ifdef PARTICLES
for ( i = 0; i < num_particles; i++ ) {
if ( particle_level[i] != FREE_PARTICLE_LEVEL ) {
ipart = i;
x0 = particle_x[i][0];
q = root_finder( qsolve, 0.0, num_grid, 1e-9, 1e-9 );
q_i = particle_q_init( particle_id[i] );
x_z = q_i + dgrowth*ampl*sin(ak*q_i);
v_z = ddgrowthdt*ampl*sin(ak*q_i);
x_rms += (x0-x_z)*(x0-x_z);
x_norm += (x_z-q_i)*(x_z-q_i);
v_rms += (particle_v[i][0]-v_z)*(particle_v[i][0]-v_z);
v_norm += v_z*v_z;
fprintf(particles, "%lu %e %e %e %e %e \n",
particle_id[i],
particle_x[i][0],
particle_v[i][0],
particle_pot[i],
x_z,v_z );
}
}
fclose(particles);
MPI_Reduce( &x_rms, &x_rms_total, 1, MPI_DOUBLE, MPI_SUM, MASTER_NODE, mpi.comm.run );
MPI_Reduce( &v_rms, &v_rms_total, 1, MPI_DOUBLE, MPI_SUM, MASTER_NODE, mpi.comm.run );
MPI_Reduce( &x_norm, &x_norm_total, 1, MPI_DOUBLE, MPI_SUM, MASTER_NODE, mpi.comm.run );
MPI_Reduce( &v_norm, &v_norm_total, 1, MPI_DOUBLE, MPI_SUM, MASTER_NODE, mpi.comm.run );
if ( local_proc_id == MASTER_NODE ) {
x_rms_total /= x_norm_total;
v_rms_total /= v_norm_total;
x_rms_total = sqrt(x_rms_total);
v_rms_total = sqrt(v_rms_total);
particles = fopen("dumps/particle_rms.dat", "a");
fprintf(particles, "%e %e %e %e %e\n", abox[min_level], x_rms_total, v_rms_total, x_norm_total, v_norm_total );
fclose(particles);
}
#endif /* PARTICLES */
}
void init_run() {
int i, j, k;
int index;
double a_th;
int ipart;
int icell;
double qi, qj, qk;
double xcons, vcons;
double dx, dvx;
double pw;
double a_vel;
double qfact;
int num_level_cells;
int *level_cells;
cosmology_set(OmegaM,OmM0);
cosmology_set(OmegaB,OmB0);
cosmology_set(OmegaL,OmL0);
cosmology_set(h,h0);
cosmology_set(DeltaDC,dDC);
box_size = Lbox0;
units_set_art(cosmology->OmegaM,cosmology->h,box_size);
units_init();
build_cell_buffer();
repair_neighbors();
auni[min_level] = auni_init;
tl[min_level] = tcode_from_auni( auni_init );
for ( i = min_level; i <= max_level; i++ ) { tl[i] = tl[min_level]; }
abox[min_level] = auni_init;
for(i=min_level+1; i<=max_level; i++)
{
tl[i] = tl[min_level];
auni[i] = auni[min_level];
abox[i] = abox[min_level];
}
units_update(min_level);
cart_debug("tl[min_level] = %f", tl[min_level] );
cart_debug("au[min_level] = %f", auni[min_level] );
cart_debug("ab[min_level] = %f", abox[min_level] );
cart_debug("DC mode = %f", cosmology->DeltaDC );
cosmology_set_fixed();
rhogas0 = cosmology->OmegaB/cosmology->OmegaM;
cart_debug("rhogas0 = %e", rhogas0 );
Tinit = TinitK/units->temperature;
ak = 2.0*M_PI / lambda;
dgrowth = growth(abox[min_level]);
ddgrowthdt = dgrowthdt(abox[min_level]);
ampl = 1.0 / ( growth(a_cross) * ak );
cart_debug("Tinit,TinitK = %e %e", Tinit,TinitK );
#ifdef HYDRO
for ( i = min_level; i <= max_level; i++ ) {
cart_debug("generating initial conditions on level %u", i );
select_level( i, CELL_TYPE_LOCAL, &num_level_cells, &level_cells );
for ( j = 0; j < num_level_cells; j++ ) {
// cart_debug("%d %d",level_cells[j],num_cells);
initial_conditions( level_cells[j], i );
}
cart_free( level_cells );
}
for ( i = min_level; i <= max_level; i++ ) {
update_buffer_level( i, all_hydro_vars, num_hydro_vars );
}
#endif /* HYDRO */
cart_debug("choose timestep and set velocity on the half step");
dtl[min_level] = 0.0;
set_timestepping_scheme();
dtl[min_level]=.125;
cart_debug("=======================%e",dtl[min_level]);
dtl_old[min_level] = dtl[min_level];
tl_old[min_level] = tl[min_level]-dtl[min_level];
abox_old[min_level] = abox_from_tcode(tl_old[min_level]);
dtl_old[min_level] = dtl[min_level];
for ( i = min_level+1; i <= max_level; i++ ) {
tl_old[i] = tl[i]-dtl[i];
abox_old[i] = abox_from_tcode(tl_old[i]);
dtl_old[i] = dtl[i];
}
#ifdef GRAVITY
#ifdef HYDRO
for ( i = min_level; i <= max_level; i++ ) {
cart_debug("generating gravity on level %u", i );
// cart_assert(dtl[i]==0);
select_level( i, CELL_TYPE_LOCAL, &num_level_cells, &level_cells );
for ( j = 0; j < num_level_cells; j++ ) {
initial_gravity( level_cells[j], i );
}
cart_free( level_cells );
}
for ( i = min_level; i <= max_level; i++ ) {
update_buffer_level( i, all_hydro_vars, num_hydro_vars );
}
#endif /* GRAVITY */
#endif /* HYDRO */
#ifdef PARTICLES
qfact = (double)num_grid / (double)num_grid;
pw = (1.0-rhogas0)*qfact*qfact*qfact;
cart_debug("particle weight = %e", pw );
xcons = dgrowth*ampl;
a_vel = abox_from_tcode( tl[min_level] - 0.5*dtl[min_level] );
vcons = ampl * dgrowthdt( a_vel);
ipart = 0;
for ( i = 0; i < num_grid; i++ ) {
qi = qfact*((double)i + 0.5);
dx = xcons * sin( ak * qi );
dvx = vcons * sin( ak * qi );
for ( j = 0; j < num_grid; j++ ) {
qj = qfact*((double)j + 0.5);
for ( k = 0; k < num_grid; k++ ) {
qk = qfact*((double)k + 0.5);
particle_x[ipart][0] = qi + dx;
particle_x[ipart][1] = qj;
particle_x[ipart][2] = qk;
if ( particle_x[ipart][0] >= (double)num_grid ) {
particle_x[ipart][0] -= num_grid;
}
if ( particle_x[ipart][1] >= (double)num_grid ) {
particle_x[ipart][1] -= num_grid;
}
if ( particle_x[ipart][2] >= (double)num_grid ) {
particle_x[ipart][2] -= num_grid;
}
icell = cell_find_position( particle_x[ipart] );
if ( icell != -1 && cell_is_local(icell) ) {
particle_v[ipart][0] = dvx;
particle_v[ipart][1] = 0.0;
particle_v[ipart][2] = 0.0;
particle_id[ipart] = (particleid_t)num_grid*(num_grid*i + j) + k;
particle_mass[ipart] = pw;
cart_assert( qi == particle_q_init( particle_id[ipart] ) );
particle_t[ipart] = tl[min_level];
particle_dt[ipart] = dtl[min_level];
ipart++;
}
}
}
}
cart_debug("created %u particles", ipart );
num_local_particles = ipart;
num_particles_total = (particleid_t)num_grid*(particleid_t)num_grid*(particleid_t)num_grid;
num_particle_species = 1;
particle_species_mass[0] = pw;
particle_species_num[0] = num_particles_total;
particle_species_indices[0] = 0;
particle_species_indices[1] = num_particles_total;
build_particle_list();
/* assign_density( min_level, min_level ); */ //for refinement
/* modify( min_level, 0 ); */
assign_density( min_level, min_level ); //for refinement
modify( min_level, 0 );
if ( local_proc_id == MASTER_NODE ) {
particles = fopen("dumps/particle_rms.dat", "w");
fclose(particles);
}
#endif
check_map();
cart_debug("done with initialization");
}
int main(int argc, char * argv[]) {
fftw_plan pc2r;
fftw_plan pr2c;
fftw_complex *dvdk;
DIR* dir;
float *temp;
char fname[256];
FILE *fid,*fidtxt, *fidtxt2;
double *t21, *dvdr;
long int i,j,p,indi,indj;
int nmaxcut,nmincut;
double aver,Tcmb,kk,growth,dgdt,Hubz,TS,xtot;
double zmin,zmax,dz,z;
/* Check for correct number of parameters*/
if(argc != 2) {
printf("Usage : t21 base_dir\n");
exit(1);
}
get_Simfast21_params(argv[1]);
if(global_use_Lya_xrays==0) printf("Lya and xray use set to false - assuming TS>>TCMB in t21 calculation.\n");
zmin=global_Zminsim;
zmax=global_Zmaxsim;
dz=global_Dzsim;
#ifdef _OMPTHREAD_
omp_set_num_threads(global_nthreads);
fftw_init_threads();
fftw_plan_with_nthreads(global_nthreads);
printf("Using %d threads\n",global_nthreads);
#endif
/* Create directory deltaTb */
sprintf(fname,"%s/deltaTb",argv[1]);
if((dir=opendir(fname))==NULL) {
printf("Creating t21 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/t21_av_N%ld_L%.1f.dat",argv[1],global_N_smooth,global_L/global_hubble);
if((fidtxt=fopen(fname,"a"))==NULL){
printf("\nError opening output %s file...\n",fname);
exit(1);
}
sprintf(fname,"%s/Output_text_files/TS_av_N%ld_L%.1f.dat",argv[1],global_N_smooth,global_L/global_hubble);
if((fidtxt2=fopen(fname,"a"))==NULL){
printf("\nError opening output %s file...\n",fname);
exit(1);
}
if(!(temp=(float *) malloc(global_N3_smooth*sizeof(float)))) {
printf("Problem...\n");
exit(1);
}
if(!(t21=(double *) malloc(global_N3_smooth*sizeof(double)))) {
printf("Problem...\n");
exit(1);
}
if(!(dvdk = (fftw_complex*) fftw_malloc(sizeof(fftw_complex)*global_N_smooth*global_N_smooth*(global_N_smooth/2+1)))) {
printf("Problem...\n");
exit(1);
}
if(!(dvdr=(double *) fftw_malloc(global_N3_smooth*sizeof(double)))) {
printf("Problem...\n");
exit(1);
}
if(!(pr2c=fftw_plan_dft_r2c_3d(global_N_smooth, global_N_smooth, global_N_smooth, dvdr , dvdk, FFTW_MEASURE))) {
printf("Problem...\n");
exit(1);
}
if(!(pc2r=fftw_plan_dft_c2r_3d(global_N_smooth, global_N_smooth, global_N_smooth, dvdk, dvdr, FFTW_MEASURE))) {
printf("Problem...\n");
exit(1);
}
/**************************************************/
/************** redshift cycle ********************/
/**************************************************/
for(z=zmax;z>(zmin-dz/10);z-=dz){
printf("z = %f\n",z);fflush(0);
sprintf(fname,"%s/deltaTb/deltaTb_z%.3lf_N%ld_L%.1f.dat",argv[1],z,global_N_smooth,global_L/global_hubble);
if((fid = fopen(fname,"rb"))!=NULL) {
printf("File:%s already exists - skipping this redshift...\n",fname);
fclose(fid);
}else {
if(z>(global_Zminsfr-global_Dzsim/10) && global_use_Lya_xrays==1) {
Tcmb=Tcmb0*(1.+z);
sprintf(fname,"%s/x_c/xc_z%.3lf_N%ld_L%.1f.dat",argv[1],z,global_N_smooth,global_L/global_hubble);
if((fid = fopen(fname,"rb"))==NULL) {
printf("Error opening file:%s\n",fname);
exit(1);
}
fread(temp,sizeof(float),global_N3_smooth,fid);
fclose(fid);
for(i=0;i<global_N3_smooth;i++) t21[i]=(double)temp[i];
sprintf(fname,"%s/Lya/xalpha_z%.3lf_N%ld_L%.1f.dat",argv[1],z,global_N_smooth,global_L/global_hubble);
if((fid = fopen(fname,"rb"))==NULL) {
printf("Error opening file:%s\n",fname);
exit(1);
}
fread(temp,sizeof(float),global_N3_smooth,fid);
fclose(fid);
aver=0.;
for(i=0;i<global_N3_smooth;i++) {
xtot=(double)temp[i]+t21[i];
t21[i]=xtot/(1.+xtot);
}
sprintf(fname,"%s/xrays/TempX_z%.3lf_N%ld_L%.1f.dat",argv[1],z,global_N_smooth,global_L/global_hubble);
if((fid = fopen(fname,"rb"))==NULL) {
printf("Error opening file:%s\n",fname);
exit(1);
}
fread(temp,sizeof(float),global_N3_smooth,fid);
fclose(fid);
TS=0.;
for(i=0;i<global_N3_smooth;i++) {
t21[i]=t21[i]*(1.-Tcmb/(double)temp[i]); // Temperature correction for high redshifts
TS+=Tcmb/(1.-t21[i]);
}
}else {
for(i=0;i<global_N3_smooth;i++) t21[i]=1.0;
}
sprintf(fname, "%s/delta/deltanl_z%.3f_N%ld_L%.1f.dat",argv[1],z,global_N_smooth,global_L/global_hubble);
fid=fopen(fname,"rb");
if (fid==NULL) {printf("Error reading deltanl file... Check path or if the file exists..."); exit (1);}
fread(temp,sizeof(float),global_N3_smooth,fid);
fclose(fid);
for(i=0;i<global_N3_smooth;i++) dvdr[i]=(double)temp[i];
/* Executes FFT */
fftw_execute(pr2c);
/********************************************************************/
printf("Computing v field...\n");
#ifdef _OMPTHREAD_
#pragma omp parallel for shared(dvdk,global_dk) private(i,indi,j,indj,p,kk)
#endif
for(i=0;i<global_N_smooth;i++) {
if(i>global_N_smooth/2) { /* Large frequencies are equivalent to smaller negative ones */
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++) {
if(i==0 && j==0 && p==0) {
dvdk[i*global_N_smooth*(global_N_smooth/2+1)+j*(global_N_smooth/2+1)+p]=0.;
}else {
kk=global_dk*sqrt(indi*indi+indj*indj+p*p);
if(global_vi==1) {
dvdk[i*global_N_smooth*(global_N_smooth/2+1)+j*(global_N_smooth/2+1)+p]=(global_dk*indi)*(global_dk*indi)/(kk*kk)*dvdk[i*global_N_smooth*(global_N_smooth/2+1)+j*(global_N_smooth/2+1)+p];
}else if(global_vi==2) {
dvdk[i*global_N_smooth*(global_N_smooth/2+1)+j*(global_N_smooth/2+1)+p]=(global_dk*indj)*(global_dk*indj)/(kk*kk)*dvdk[i*global_N_smooth*(global_N_smooth/2+1)+j*(global_N_smooth/2+1)+p];
}else {
dvdk[i*global_N_smooth*(global_N_smooth/2+1)+j*(global_N_smooth/2+1)+p]=(global_dk*p)*(global_dk*p)/(kk*kk)*dvdk[i*global_N_smooth*(global_N_smooth/2+1)+j*(global_N_smooth/2+1)+p];
}
}
}
}
}
/* Executes FFT */
fftw_execute(pc2r);
nmaxcut=0;
nmincut=0;
growth=getGrowth(z);
dgdt=dgrowthdt(z);
Hubz=Hz(z);
#ifdef _OMPTHREAD_
#pragma omp parallel for shared(dvdr,global_L,global_dx_smooth,global_N3_smooth) private(i)
#endif
for(i=0;i<global_N3_smooth;i++) {
dvdr[i]=-dgdt*dvdr[i]/global_L/global_L/global_L/Hubz*global_dx_smooth*global_dx_smooth*global_dx_smooth/growth; /* FT normalization + divide by H(z). Divide by growth to get deltanl back to z=0 */
}
for(i=0;i<global_N3_smooth;i++) {
if(dvdr[i] > maxcut) {dvdr[i]=maxcut; nmaxcut++;}
else if(dvdr[i] < mincut) {dvdr[i]=mincut; nmincut++;}
}
printf("nmaxcut: %d (%f %%), nmincut: %d (%f %%)\n\n",nmaxcut,100.*nmaxcut/global_N3_smooth,nmincut,100.*nmincut/global_N3_smooth);fflush(0);
#ifdef _OMPTHREAD_
#pragma omp parallel for shared(t21,temp,dvdr,global_hubble,global_omega_b,global_omega_m,global_N3_smooth,z) private(i)
#endif
for(i=0;i<global_N3_smooth;i++) {
/* output in K */
t21[i]=23.0/1000.*(1.+(double)temp[i])*t21[i]/(1.+1.*dvdr[i])*(0.7/global_hubble)*(global_omega_b*global_hubble*global_hubble/0.02)*sqrt((0.15/global_omega_m/global_hubble/global_hubble)*(1.+z)/10.); /*Units in Kelvin */
}
sprintf(fname,"%s/Ionization/xHII_z%.3f_eff%.2lf_N%ld_L%.1f.dat",argv[1],z,global_eff,global_N_smooth,global_L/global_hubble);
if((fid = fopen(fname,"rb"))==NULL) {
printf("Error opening file:%s\n",fname);
exit(1);
}
fread(temp,sizeof(float),global_N3_smooth,fid);
fclose(fid);
for(i=0;i<global_N3_smooth;i++) {
t21[i]=t21[i]*(1.-(double)temp[i]); // neutral fraction...
}
sprintf(fname,"%s/deltaTb/deltaTb_z%.3lf_N%ld_L%.1f.dat",argv[1],z,global_N_smooth,global_L/global_hubble);
if((fid = fopen(fname,"wb"))==NULL) {
printf("Cannot open file:%s...\n",fname);
exit(1);
}
for(i=0;i<global_N3_smooth;i++) temp[i]=(float)t21[i];
fwrite(temp,sizeof(float),global_N3_smooth,fid);
fclose(fid);
aver=0.;
for(i=0; i<global_N3_smooth; i++) aver+=t21[i];
fprintf(fidtxt,"%f %.8E\n",z,aver/global_N3_smooth);
if(z>(global_Zminsfr-global_Dzsim/10) && global_use_Lya_xrays==1) fprintf(fidtxt2,"%f %.8E\n",z,TS/global_N3_smooth);
}
} /* ends z cycle */
fclose(fidtxt);
exit(0);
}
