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ionz_main.c
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ionz_main.c
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#include<stdio.h>
#include<math.h>
#include<stdlib.h>
#include<string.h>
#include<fftw3.h>
#include<omp.h>
#include"nbody.h"
/*------------------------------GLOBAL VARIABLES-------------------------------*/
//-----------------------------------------------------------------------------//
// from N-body code
//-----------------------------------------------------------------------------//
float vhh, // Hubble parameter in units of 100 km/s/Mpc
vomegam, // Omega_matter, total matter density (baryons+CDM) parameter
vomegalam, // Cosmological Constant
vomegab, //Omega_baryon
sigma_8_present, // Last updated value of sigma_8 (Presently PLANCK+WMAP)
vnn; //Spectral index of primordial Power spectrum
long N1, N2, N3; // box dimension (grid)
int NF, // Fill every NF grid point
Nbin; // Number of bins to calculate final P(k) (output)
float LL; // grid spacing in Mpc
long MM; // Number of particles
int zel_flag=1, // memory allocation for zel is 3 times that for nbody
fourier_flag; //for fourier transfrom
float DM_m, // Darm matter mass of simulation particle in (10^10 M_sun h^-1) unit
norm, // normalize Pk
pi=M_PI;
io_header header1;
//-----------------------------------------------------------------------------//
// from N-body code done
//-----------------------------------------------------------------------------//
//-----------------------------------------------------------------------------//
// needed for N-bdy funcs
//-----------------------------------------------------------------------------//
float ***ro; // for density
fftwf_plan p_ro; // for FFT
fftwf_plan q_ro; // for FFT
//-----------------------------------------------------------------------------//
// needed for N-bdy funcs done
//-----------------------------------------------------------------------------//
//----------------------arrays for storing ionization data---------------------//
float ***nh, // stores neutral hydrogen on grid points
***nhs, // stores smoothed neutral hydrogen on grid point
***ngamma, // stores photon number on grid points
***ngammas, // stores smoothed photon number on grid points
***nxion; // stores ionization fractions for different nions on grid points
/*----------------------------GLOBAL VARIABLES DONE----------------------------*/
void main()
{
long int seed;
FILE *inp,*outpp;
int i;
long ii,jj, kk,ll, tmp;
int sfac;
float vaa; // final scale factor
//-----------------done variables for non-uniform recombination------------//
double *power_P0, *power_P2, *power_P4, *kmode; // arrays for power spectrum
double *no;
float dr,r_min,r_max; // radious for smoothing
char file[100], file1[100], file2[100], num[8], num1[8], num2[8];
float nion,xh1; // to store ionization fraction and neutral hydrogen fraction
double vion, roion; // to store vol. avg. and mass avg. ionization fraction
int output_flag,in_flag;
long totcluster; // total no. of haloes in halo_catalogue
float robar,Radii;
double robarhalo; //no. of dark matter paricle density per (grid)^3
float vfac; //coefficient for redshift space distortion
float **rra,**vva,**data, //to store particle positions and velocities
**halo;
double t,T=omp_get_wtime(); // for timing
int Noutput;
float *nz;
/*---------------------------------------------------------------------------*/
/* Read input parameters for the simulation from the file "input.nbody_comp" */
/*---------------------------------------------------------------------------*/
inp=fopen("input.nbody_comp","r");
fscanf(inp,"%ld%*d",&tmp);
fscanf(inp,"%*f%*f%*f%*f");
fscanf(inp,"%*f%*f");
fscanf(inp,"%ld%ld%ld%*d%*f",&tmp,&tmp,&tmp);
fscanf(inp,"%*d%*d");
fscanf(inp,"%*f%*f"); /* time step, final scale factor*/
fscanf(inp,"%d",&Noutput);
nz=(float*)calloc(Noutput,sizeof(float)); // array to store Noutput
for(i=0;i<Noutput;i++)
fscanf(inp,"%f",&nz[i]);
fclose(inp);
/*-----------------------------------------------------------*/
//---------------------------------------------------------------------------//
//-------------parameters read from input file. Check this ------------------//
sfac=2;
Nbin=10;
nion=23.21;
vion=0.0;
roion=0.0;
//---------------------------------------------------------------------------//
system("mkdir ionz_out");
/*-----------------------------read nbody output-----------------------------*/
for(i=0;i<Noutput;i++)
{
strcpy(file,"output.nbody_");
sprintf(num,"%3.3f",nz[i]);
strcat(file,num);
read_output(file,1,&seed,&output_flag,&in_flag,rra,vva,&vaa); // only read header
if(i==0)
{
rra = allocate_float_2d(MM,3);
vva = allocate_float_2d(MM,3);
data = allocate_float_2d(MM,5);
}
read_output(file,2,&seed,&output_flag,&in_flag,rra,vva,&vaa); // read data
printf("ok read nbody output = %e\n",omp_get_wtime()-t);
//---------------------------------------------------------------------------//
//-------------------------reading the halo catalogue------------------------//
t=omp_get_wtime();
strcpy(file1,"halo_catalogue_");
sprintf(num1,"%3.3f",nz[i]);
strcat(file1,num1);
read_fof(file1,1,&output_flag,&totcluster,halo,&vaa);
halo = allocate_float_2d(totcluster,7);
read_fof(file1,2,&output_flag,&totcluster,halo,&vaa);
printf("ok read halo catalogue = %e\n",omp_get_wtime()-t);
//---------------------------------------------------------------------------//
//-----------------------------Redefine grid---------------------------------//
N1=N1/sfac; N2=N2/sfac; N3=N3/sfac;// new grid dimensions
LL=LL*sfac;
robar=MM/(1.*N1*N2*N3); // mean numbder density (grid)^{-3}
vfac=1./(Hf(vaa)*vaa*vaa); // for redshift space distortion
//---------------------------------------------------------------------------//
for(ii=0;ii<MM;ii++)
{
data[ii][0] = rra[ii][0]/(1.*sfac);
data[ii][1] = rra[ii][1]/(1.*sfac);
data[ii][2] = rra[ii][2]/(1.*sfac);
data[ii][3] = (rra[ii][2] + vfac*vva[ii][2])/(1.*sfac); // redshift space distortion applied
data[ii][3] += N3*1.;
data[ii][3] = data[ii][3]-1.0*N3*(int)(floor(data[ii][3])/(1.*N3));
data[ii][4] = 1.; // same mass for all particles
}
/*----------------------------------------------------------------*/
for(ii=0;ii<totcluster;ii++)
{
halo[ii][1] /= (1.*sfac);
halo[ii][2] /= (1.*sfac);
halo[ii][3] /= (1.*sfac);
}
/*----------------------------------------------------------------*/
if(i==0)
{
Setting_Up_Memory_For_ionz();
/*---------allocate memory for power spectrum and k modes--------*/
kmode=calloc((size_t)Nbin,sizeof(double));
power_P0=calloc((size_t)Nbin,sizeof(double));
power_P2=calloc((size_t)Nbin,sizeof(double));
power_P4=calloc((size_t)Nbin,sizeof(double));
no=calloc((size_t)Nbin,sizeof(double));
}
/*----------------------------------------------------------------*/
t=omp_get_wtime();
/* calculating the halo mass density at each grid point */
MM=totcluster;
cic_vmass(ngamma, halo, 1, 2, 3, 0);
/*----------------------------------------------------------------*/
MM=header1.npart[1];
cic_vmass(nh, data, 0, 1, 2, 4);
printf("ok cic_vmass= %e\n",omp_get_wtime()-t);
/*----------------------------------------------------------------*/
t=omp_get_wtime();
//---------------------subgrid re-ionization----------------------//
t=omp_get_wtime();
for(ii=0;ii<N1;ii++)
for(jj=0;jj<N2;jj++)
for(kk=0;kk<N3;kk++)
{
if(nh[ii][jj][kk]>nion*ngamma[ii][jj][kk]) // checking ionization condition
{
nxion[ii][jj][kk]=nion*ngamma[ii][jj][kk]/nh[ii][jj][kk];
}
else
{
nxion[ii][jj][kk]=1.;
}
}
//printf("ok sub grid re-ionization = %e\n",omp_get_wtime()-t);
/*----------------------------------------------------------------*/
//-------------calculating avg. ionization fraction---------------//
/*----------------------------------------------------------------*/
/*----------------------------------------------------------------*/
//calculating max and min radius for smoothing in units of grid size
r_min=1.;
r_max=20.0/LL; // Mpc/LL in grid unit
//r_max=pow((1.*N1*N2*N3),(1./3.))/2.;
/*----------------------------------------------------------------*/
/* smoothing */
/*----------------------------------------------------------------*/
t=omp_get_wtime();
Radii=r_min;
while(Radii < r_max)
{
for(ii=0;ii<N1;ii++)
for(jj=0;jj<N2;jj++)
for(kk=0;kk<N3;kk++)
{
nhs[ii][jj][kk]=nh[ii][jj][kk];
ngammas[ii][jj][kk]=ngamma[ii][jj][kk];
}
//printf("starting smoothing for radius of size %e\n",Radii);
smooth(nhs,Radii);
smooth(ngammas,Radii);
for(ii=0;ii<N1;ii++)
for(jj=0;jj<N2;jj++)
for(kk=0;kk<N3;kk++)
{
if(nhs[ii][jj][kk]<=nion*ngammas[ii][jj][kk]) // checking ionization condition
nxion[ii][jj][kk]=1.;
}
dr=(Radii*0.1) < 2.0 ? (Radii*0.1) : 2.0; //increment of the smoothing radius
Radii += dr;
}
printf("ok smoothing = %e\n",omp_get_wtime()-t);
/*----------------------------------------------------------------*/
/*----------------------------------------------------------------*/
t=omp_get_wtime();
//---------------calculating avg. neutral fraction-------------*/
vion =0.0;
roion=0.0;
/*----------------------------------------------------------------*/
strcpy(file2,"ionz_out/HI_map_");
sprintf(num2,"%3.3f",nz[i]);
strcat(file2,num2);
outpp=fopen(file2,"w");
fwrite(&N1,sizeof(int),1,outpp);
fwrite(&N2,sizeof(int),1,outpp);
fwrite(&N3,sizeof(int),1,outpp);
for(ii=0;ii<N1;ii++)
for(jj=0;jj<N2;jj++)
for(kk=0;kk<N3;kk++)
{
xh1=(1.-nxion[ii][jj][kk]);
xh1=(xh1 >0.0)? xh1: 0.0;
nxion[ii][jj][kk]=xh1; // store x_HI instead of x_ion
nhs[ii][jj][kk]=xh1*nh[ii][jj][kk]; // ro_HI on grid
vion+=(double)xh1;
roion+=(double)nhs[ii][jj][kk];
fwrite(&nhs[ii][jj][kk],sizeof(float),1,outpp);
}
fclose(outpp);
/*----------------------------------------------------------------*/
roion/=(1.*N1*N2*N3); // mean HI density
/*----------------------------------------------------------------*/
calpow_mom(nhs,Nbin,power_P0,kmode,power_P2,power_P4,no); // calculates moments of redshift space power spectrum
strcpy(file2,"ionz_out/pk.ionz");
sprintf(num2,"%4.3f",roion/robar);
strcat(file2,num2);
strcat(file2,"_");
sprintf(num2,"%3.3f",nz[i]);
strcat(file2,num2);
outpp=fopen(file2,"w");
for(ii=0;ii<Nbin;++ii)
{
power_P0[ii]/=(roion*roion);
power_P2[ii]/=(roion*roion);
power_P4[ii]/=(roion*roion);
fprintf(outpp,"%e %e %e %e %ld\n",kmode[ii],power_P0[ii],power_P2[ii],power_P4[ii],(long)no[ii]);
}
fclose(outpp);
/*----------------------------------------------------------------*/
vion/=(1.*N1*N2*N3); // volume avg xHI
roion/=robar; // divide by H density to get mass avg. xHI
printf("vol. avg. x_HI=%e, mass avg. x_HI=%e\n",vion,roion);
/*----------------------------------------------------------------*/
/* Do the same for redshift space */
/*----------------------------------------------------------------*/
density_2_mass(nxion, data, 0, 1, 2, 4); // get particles HI masses from HI density
cic_vmass(nhs, data, 0, 1, 3, 4); // convert particles HI masses to HI density
//------------calculating avg. ionization fraction----------------//
roion=0.0;
strcpy(file2,"ionz_out/HI_maprs_");
sprintf(num2,"%3.3f",nz[i]);
strcat(file2,num2);
outpp=fopen(file2,"w");
fwrite(&N1,sizeof(int),1,outpp);
fwrite(&N2,sizeof(int),1,outpp);
fwrite(&N3,sizeof(int),1,outpp);
for(ii=0;ii<N1;ii++)
for(jj=0;jj<N2;jj++)
for(kk=0;kk<N3;kk++)
{
roion+=(double)nhs[ii][jj][kk];
fwrite(&nhs[ii][jj][kk],sizeof(float),1,outpp);
}
fclose(outpp);
roion/=(1.*N1*N2*N3); // mean HI density
/*----------------------------------------------------------------*/
calpow_mom(nhs,Nbin,power_P0,kmode,power_P2,power_P4,no); // calculates moments of redshift space power spectrum
strcpy(file2,"ionz_out/pk.ionzs");
sprintf(num2,"%4.3f",roion/robar);
strcat(file2,num2);
strcat(file2,"_");
sprintf(num2,"%3.3f",nz[i]);
strcat(file2,num2);
outpp=fopen(file2,"w");
for(ii=0;ii<Nbin;++ii)
{
power_P0[ii]/=(roion*roion);
power_P2[ii]/=(roion*roion);
power_P4[ii]/=(roion*roion);
fprintf(outpp,"%e %e %e %e %ld\n",kmode[ii],power_P0[ii],power_P2[ii],power_P4[ii],(long)no[ii]);
}
fclose(outpp);
/*----------------------------------------------------------------*/
roion/=robar; // divide by H density to get mass avg. xHI
printf("mass avg. x_HI=%e\n",roion);
printf("ok time taken= %e\n\n",omp_get_wtime()-t);
free(halo);
}
free(rra);
free(vva);
free(data);
free(ro);
free(nh);
free(nhs);
free(ngamma);
free(ngammas);
free(nxion);
printf("done. Total time taken = %dhr %dmin %dsec\n",(int)((omp_get_wtime()-T)/3600), (int)((omp_get_wtime()-T)/60)%60, (int)(omp_get_wtime()-T)%60);
}