int main(int argc, char *argv[]){
plist_info plist;
char filename_in_root[256];
char filename_out_root[256];
char filename_in[256];
char filename_out[256];
int subsample_factor;
int i_snap,i_file,j_file;
int n_files;
unsigned int n_local[N_GADGET_TYPE];
int i_type;
size_t i_particle,j_particle;
FILE *fp;
FILE *fp_out;
int record_length_in;
int record_length_out;
GBPREAL position[3];
GBPREAL velocity[3];
int ID_int;
RNG_info RNG;
int seed_init=10463743;
int seed;
GBPREAL RNG_max;
long long n_all_keep[N_GADGET_TYPE];
long long n_all_init[N_GADGET_TYPE];
unsigned int n_all_high_word[N_GADGET_TYPE];
unsigned int n_all[N_GADGET_TYPE];
double mass_array[N_GADGET_TYPE];
int n_keep_total;
int n_init_total;
int record_length;
int flag_long_ids;
int id_in_int;
long long id_in_long;
int n_groups;
SID_init(&argc,&argv,NULL,NULL);
// Parse command line
if(argc!=4){
fprintf(stderr,"\n syntax: %s filename_in_root snapshot_number subsample_factor\n",argv[0]);
fprintf(stderr," ------\n\n");
return(ERROR_SYNTAX);
}
else{
strcpy(filename_in_root, argv[1]);
i_snap =atoi(argv[2]);
subsample_factor=atoi(argv[3]);
}
sprintf(filename_out_root,"%s_subsample",filename_in_root);
RNG_max=1./(GBPREAL)(subsample_factor);
SID_log("Subsampling GADGET file by a factor of %d...",SID_LOG_OPEN,subsample_factor);
// Grab info from first header
// Read the header and determine the input file-format
gadget_read_info fp_gadget;
int flag_filefound=init_gadget_read(filename_in_root,i_snap,&fp_gadget);
int flag_multifile=fp_gadget.flag_multifile;
int flag_file_type=fp_gadget.flag_file_type;
gadget_header_info header =fp_gadget.header;
if(!flag_filefound)
SID_trap_error("File not found.",ERROR_LOGIC);
if(flag_filefound)
n_files =header.n_files;
else
n_files=0;
if(n_files>0){
init_seed_from_clock(&seed_init);
SID_log("Seed=%d",SID_LOG_COMMENT,seed_init);
SID_log("Counting particles in %d files...",SID_LOG_OPEN|SID_LOG_TIMER,n_files);
for(i_type=0;i_type<N_GADGET_TYPE;i_type++)
n_all_keep[i_type]=0;
for(i_file=SID.My_rank,j_file=0;j_file<n_files;i_file+=SID.n_proc,j_file+=SID.n_proc){
if(n_files>1)
SID_log("Processing file(s) %d->%d...",SID_LOG_OPEN,j_file,MIN(j_file+SID.n_proc-1,n_files-1));
if(i_file<n_files){
set_gadget_filename(&fp_gadget,i_file,filename_in);
fp=fopen(filename_in,"r");
fread_verify(&record_length_in,sizeof(int),1,fp);
fread_verify(&header,sizeof(gadget_header_info),1,fp);
fread_verify(&record_length_out,sizeof(int),1,fp);
seed=seed_init+1387*i_file;
init_RNG(&seed,&RNG,RNG_DEFAULT);
for(i_type=0;i_type<N_GADGET_TYPE;i_type++){
for(j_particle=0;j_particle<header.n_file[i_type];j_particle++){
if(random_number(&RNG)<=RNG_max)
n_all_keep[i_type]++;
}
}
free_RNG(&RNG);
fclose(fp);
}
if(n_files>1)
SID_log("Done.",SID_LOG_CLOSE);
}
SID_Allreduce(SID_IN_PLACE,n_all_keep,N_GADGET_TYPE,SID_LONG_LONG,SID_SUM,SID.COMM_WORLD);
SID_log("Done.",SID_LOG_CLOSE);
SID_log("Header properties will be...",SID_LOG_OPEN);
for(i_type=0;i_type<N_GADGET_TYPE;i_type++){
n_all_high_word[i_type]=(unsigned int)(((long long)n_all_keep[i_type])>>32);
n_all[i_type] =(unsigned int)(((long long)n_all_keep[i_type])-(((long long)(n_all_high_word[i_type]))<<32));
n_all_init[i_type] =((long long)(header.n_all_lo_word[i_type]))+(((long long)(header.n_all_hi_word[i_type]))<<32);
if(n_all_keep[i_type]>0)
mass_array[i_type]=header.mass_array[i_type]*((double)n_all_init[i_type]/(double)n_all_keep[i_type]);
else
mass_array[i_type]=0.;
}
for(i_type=0;i_type<N_GADGET_TYPE;i_type++)
SID_log("mass_array[%d]=%le (was %le)", SID_LOG_COMMENT,i_type,mass_array[i_type],header.mass_array[i_type]);
for(i_type=0;i_type<N_GADGET_TYPE;i_type++)
SID_log("n_all[%d] =%d (was %d)",SID_LOG_COMMENT,i_type,n_all[i_type],header.n_all_lo_word[i_type]);
for(i_type=0;i_type<N_GADGET_TYPE;i_type++)
SID_log("high_word[%d] =%d (was %d)",SID_LOG_COMMENT,i_type,n_all_high_word[i_type],header.n_all_hi_word[i_type]);
SID_log("Done.",SID_LOG_CLOSE);
SID_log("Writing subsampled snapshot...",SID_LOG_OPEN|SID_LOG_TIMER);
for(i_file=SID.My_rank,j_file=0;j_file<n_files;i_file+=SID.n_proc,j_file+=SID.n_proc){
if(n_files>1)
SID_log("Processing file(s) %d->%d...",SID_LOG_OPEN,j_file,MIN(j_file+SID.n_proc-1,n_files-1));
if(i_file<n_files){
set_gadget_filename(&fp_gadget,i_file,filename_in);
change_gadget_filename(filename_in_root,"snapshot_subsample",i_snap,i_file,flag_multifile,flag_file_type,filename_out);
if(i_file==0){
FILE *fp_test;
char filename_out_directory[MAX_FILENAME_LENGTH];
strcpy(filename_out_directory,filename_out);
strip_file_root(filename_out_directory);
if((fp_test=fopen(filename_out_directory,"r"))==NULL)
mkdir(filename_out_directory,02755);
else
fclose(fp_test);
}
fp =fopen(filename_in, "r");
fp_out=fopen(filename_out,"w");
// Header
fread_verify(&record_length_in,sizeof(int),1,fp);
fread_verify(&header,sizeof(gadget_header_info),1,fp);
fread_verify(&record_length_out,sizeof(int),1,fp);
for(i_type=0;i_type<N_GADGET_TYPE;i_type++){
n_local[i_type] =header.n_file[i_type];
header.n_file[i_type] =0;
header.mass_array[i_type] =mass_array[i_type];
header.n_all_lo_word[i_type] =n_all[i_type];
header.n_all_hi_word[i_type] =n_all_high_word[i_type];
}
seed=seed_init+1387*i_file;
init_RNG(&seed,&RNG,RNG_DEFAULT);
for(i_type=0,n_keep_total=0,n_init_total=0;i_type<N_GADGET_TYPE;i_type++){
for(j_particle=0;j_particle<n_local[i_type];j_particle++,i_particle++){
if(random_number(&RNG)<=RNG_max){
header.n_file[i_type]++;
n_keep_total++;
}
n_init_total++;
}
}
free_RNG(&RNG);
record_length=record_length_in;
fwrite(&record_length,sizeof(int),1,fp_out);
fwrite(&header,sizeof(gadget_header_info),1,fp_out);
fwrite(&record_length,sizeof(int),1,fp_out);
// Positions
record_length=3*sizeof(GBPREAL)*n_keep_total;
seed=seed_init+1387*i_file;
init_RNG(&seed,&RNG,RNG_DEFAULT);
fread_verify(&record_length_in,sizeof(int),1,fp);
fwrite(&record_length,sizeof(int),1,fp_out);
for(i_type=0;i_type<N_GADGET_TYPE;i_type++){
for(j_particle=0;j_particle<n_local[i_type];j_particle++){
fread_verify(position,sizeof(GBPREAL),3,fp);
if(random_number(&RNG)<=RNG_max)
fwrite(position,sizeof(GBPREAL),3,fp_out);
}
}
fread_verify(&record_length_out,sizeof(int),1,fp);
fwrite(&record_length,sizeof(int),1,fp_out);
free_RNG(&RNG);
// Velocities
record_length=3*sizeof(GBPREAL)*n_keep_total;
seed=seed_init+1387*i_file;
init_RNG(&seed,&RNG,RNG_DEFAULT);
fread_verify(&record_length_in,sizeof(int),1,fp);
fwrite(&record_length,sizeof(int),1,fp_out);
for(i_type=0;i_type<N_GADGET_TYPE;i_type++){
for(j_particle=0;j_particle<n_local[i_type];j_particle++){
fread_verify(velocity,sizeof(GBPREAL),3,fp);
if(random_number(&RNG)<=RNG_max)
fwrite(velocity,sizeof(GBPREAL),3,fp_out);
}
}
fread_verify(&record_length_out,sizeof(int),1,fp);
fwrite(&record_length,sizeof(int),1,fp_out);
free_RNG(&RNG);
// IDs
seed=seed_init+1387*i_file;
init_RNG(&seed,&RNG,RNG_DEFAULT);
fread_verify(&record_length_in,sizeof(int),1,fp);
if(record_length_in/sizeof(int)==n_init_total){
flag_long_ids=FALSE;
record_length=n_keep_total*sizeof(int);
}
else{
flag_long_ids=TRUE;
record_length=n_keep_total*sizeof(long long);
}
fwrite(&record_length,sizeof(int),1,fp_out);
if(flag_long_ids){
for(i_type=0;i_type<N_GADGET_TYPE;i_type++){
for(j_particle=0;j_particle<n_local[i_type];j_particle++){
fread_verify(&id_in_long,sizeof(long long),1,fp);
if(random_number(&RNG)<=RNG_max)
fwrite(&id_in_long,sizeof(long long),1,fp_out);
}
}
}
else{
for(i_type=0;i_type<N_GADGET_TYPE;i_type++){
for(j_particle=0;j_particle<n_local[i_type];j_particle++){
fread_verify(&id_in_int,sizeof(int),1,fp);
if(random_number(&RNG)<=RNG_max)
fwrite(&id_in_int,sizeof(int),1,fp_out);
}
}
}
fread_verify(&record_length_out,sizeof(int),1,fp);
fwrite(&record_length,sizeof(int),1,fp_out);
free_RNG(&RNG);
fclose(fp);
fclose(fp_out);
}
if(n_files>1)
SID_log("Done.",SID_LOG_CLOSE);
}
SID_log("Done.",SID_LOG_CLOSE);
}
int main(int argc, char *argv[]){
int n_species;
int n_load;
int n_used;
int flag_used[N_GADGET_TYPE];
char species_name[256];
double h_Hubble;
double n_spec;
double redshift;
int i_species;
char n_string[64];
int n[3];
double L[3];
FILE *fp_1D;
FILE *fp_2D;
cosmo_info *cosmo;
field_info *field[N_GADGET_TYPE];
field_info *field_norm[N_GADGET_TYPE];
plist_info plist_header;
plist_info plist;
FILE *fp;
int i_temp;
int n_temp;
double *k_temp;
double *kmin_temp;
double *kmax_temp;
double *P_temp;
size_t *n_mode_temp;
double *sigma_P_temp;
double *shot_noise_temp;
double *dP_temp;
int snapshot_number;
int i_compute;
int distribution_scheme;
double k_min_1D;
double k_max_1D;
double k_min_2D;
double k_max_2D;
int n_k_1D;
int n_k_2D;
double *k_1D;
double *P_k_1D;
double *dP_k_1D;
int *n_modes_1D;
double *P_k_2D;
double *dP_k_2D;
int *n_modes_2D;
int n_groups=1;
double dk_1D;
double dk_2D;
char *grid_identifier;
// Initialization -- MPI etc.
SID_init(&argc,&argv,NULL,NULL);
// Parse arguments
int grid_size;
char filename_in_root[MAX_FILENAME_LENGTH];
char filename_out_root[MAX_FILENAME_LENGTH];
strcpy(filename_in_root, argv[1]);
snapshot_number=(int)atoi(argv[2]);
strcpy(filename_out_root, argv[3]);
grid_size =(int)atoi(argv[4]);
if(!strcmp(argv[5],"ngp") || !strcmp(argv[5],"NGP"))
distribution_scheme=MAP2GRID_DIST_NGP;
else if(!strcmp(argv[5],"cic") || !strcmp(argv[5],"CIC"))
distribution_scheme=MAP2GRID_DIST_CIC;
else if(!strcmp(argv[5],"tsc") || !strcmp(argv[5],"TSC"))
distribution_scheme=MAP2GRID_DIST_TSC;
else if(!strcmp(argv[5],"d12") || !strcmp(argv[5],"D12"))
distribution_scheme=MAP2GRID_DIST_DWT12;
else if(!strcmp(argv[5],"d20") || !strcmp(argv[5],"D20"))
distribution_scheme=MAP2GRID_DIST_DWT20;
else
SID_trap_error("Invalid distribution scheme {%s} specified.",ERROR_SYNTAX,argv[5]);
SID_log("Smoothing Gadget file {%s;snapshot=#%d} to a %dx%dx%d grid with %s kernel...",SID_LOG_OPEN|SID_LOG_TIMER,
filename_in_root,snapshot_number,grid_size,grid_size,grid_size,argv[5]);
// Initialization -- fetch header info
SID_log("Reading Gadget header...",SID_LOG_OPEN);
gadget_read_info fp_gadget;
int flag_filefound=init_gadget_read(filename_in_root,snapshot_number,&fp_gadget);
int flag_multifile=fp_gadget.flag_multifile;
int flag_file_type=fp_gadget.flag_file_type;
gadget_header_info header =fp_gadget.header;
double box_size =(double)(header.box_size);
size_t *n_all =(size_t *)SID_calloc(sizeof(size_t)*N_GADGET_TYPE);
size_t n_total;
if(flag_filefound){
if(SID.I_am_Master){
FILE *fp_in;
char filename[MAX_FILENAME_LENGTH];
int block_length_open;
int block_length_close;
set_gadget_filename(&fp_gadget,0,filename);
fp_in=fopen(filename,"r");
fread_verify(&block_length_open, sizeof(int),1,fp_in);
fread_verify(&header, sizeof(gadget_header_info),1,fp_in);
fread_verify(&block_length_close,sizeof(int),1,fp_in);
fclose(fp_in);
if(block_length_open!=block_length_close)
SID_trap_error("Block lengths don't match (ie. %d!=%d).",ERROR_LOGIC,block_length_open,block_length_close);
}
SID_Bcast(&header,sizeof(gadget_header_info),MASTER_RANK,SID.COMM_WORLD);
redshift=header.redshift;
h_Hubble=header.h_Hubble;
box_size=header.box_size;
if(SID.n_proc>1)
n_load=1;
else
n_load=header.n_files;
for(i_species=0,n_total=0,n_used=0;i_species<N_GADGET_TYPE;i_species++){
n_all[i_species]=(size_t)header.n_all_lo_word[i_species]+((size_t)header.n_all_hi_word[i_species])<<32;
n_total+=n_all[i_species];
if(n_all[i_species]>0){
n_used++;
flag_used[i_species]=TRUE;
}
else
flag_used[i_species]=FALSE;
}
// Initialize cosmology
double box_size =((double *)ADaPS_fetch(plist.data,"box_size"))[0];
double h_Hubble =((double *)ADaPS_fetch(plist.data,"h_Hubble"))[0];
double redshift =((double *)ADaPS_fetch(plist.data,"redshift"))[0];
double expansion_factor=((double *)ADaPS_fetch(plist.data,"expansion_factor"))[0];
double Omega_M =((double *)ADaPS_fetch(plist.data,"Omega_M"))[0];
double Omega_Lambda =((double *)ADaPS_fetch(plist.data,"Omega_Lambda"))[0];
double Omega_k =1.-Omega_Lambda-Omega_M;
double Omega_b=0.; // not needed, so doesn't matter
double f_gas =Omega_b/Omega_M;
double sigma_8=0.; // not needed, so doesn't matter
double n_spec =0.; // not needed, so doesn't matter
char cosmo_name[16];
sprintf(cosmo_name,"Gadget file's");
init_cosmo(&cosmo,
cosmo_name,
Omega_Lambda,
Omega_M,
Omega_k,
Omega_b,
f_gas,
h_Hubble,
sigma_8,
n_spec);
}
SID_log("Done.",SID_LOG_CLOSE);
grid_identifier=(char *)SID_calloc(GRID_IDENTIFIER_SIZE*sizeof(char));
// Only process if there are >0 particles present
if(n_used>0){
// Loop over ithe real-space and 3 redshift-space frames
int i_write;
int i_run;
int n_run;
int n_grids_total;
n_grids_total=4; // For now, hard-wire real-space density and velocity grids only
n_run=1; // For now, hard-wire real-space calculation only
for(i_run=0,i_write=0;i_run<n_run;i_run++){
// Read catalog
int n_grid;
char i_run_identifier[8];
switch(i_run){
case 0:
SID_log("Processing real-space ...",SID_LOG_OPEN|SID_LOG_TIMER);
sprintf(i_run_identifier,"r");
n_grid=4;
break;
case 1:
SID_log("Processing v_x redshift space...",SID_LOG_OPEN|SID_LOG_TIMER);
sprintf(i_run_identifier,"x");
n_grid=1;
break;
case 2:
SID_log("Processing v_y redshift space...",SID_LOG_OPEN|SID_LOG_TIMER);
sprintf(i_run_identifier,"y");
n_grid=1;
break;
case 3:
SID_log("Processing v_z redsift space...",SID_LOG_OPEN|SID_LOG_TIMER);
sprintf(i_run_identifier,"z");
n_grid=1;
break;
}
// For each i_run case, loop over the fields we want to produce
int i_grid;
for(i_grid=0;i_grid<n_grid;i_grid++){
char i_grid_identifier[8];
switch(i_grid){
case 0:
SID_log("Processing density grid ...",SID_LOG_OPEN|SID_LOG_TIMER);
sprintf(i_grid_identifier,"rho");
break;
case 1:
SID_log("Processing v_x velocity grid...",SID_LOG_OPEN|SID_LOG_TIMER);
sprintf(i_grid_identifier,"v_x");
break;
case 2:
SID_log("Processing v_y velocity grid...",SID_LOG_OPEN|SID_LOG_TIMER);
sprintf(i_grid_identifier,"v_y");
break;
case 3:
SID_log("Processing v_z velocity grid...",SID_LOG_OPEN|SID_LOG_TIMER);
sprintf(i_grid_identifier,"v_z");
break;
}
// Initialize the field that will hold the grid
int n[]={grid_size,grid_size,grid_size};
double L[]={box_size, box_size, box_size};
int i_init;
for(i_species=0;i_species<N_GADGET_TYPE;i_species++){
if(flag_used[i_species]){
field[i_species] =(field_info *)SID_malloc(sizeof(field_info));
field_norm[i_species]=(field_info *)SID_malloc(sizeof(field_info));
init_field(3,n,L,field[i_species]);
init_field(3,n,L,field_norm[i_species]);
i_init=i_species;
}
else{
field[i_species] =NULL;
field_norm[i_species]=NULL;
}
}
// Loop over all the files that this rank will read
int i_load;
for(i_load=0;i_load<n_load;i_load++){
if(n_load>1)
SID_log("Processing file No. %d of %d...",SID_LOG_OPEN|SID_LOG_TIMER,i_load+1,n_load);
// Initialization -- read gadget file
GBPREAL mass_array[N_GADGET_TYPE];
init_plist(&plist,&((field[i_init])->slab),GADGET_LENGTH,GADGET_MASS,GADGET_VELOCITY);
char filename_root[MAX_FILENAME_LENGTH];
read_gadget_binary_local(filename_in_root,
snapshot_number,
i_run,
i_load,
n_load,
mass_array,
&(field[i_init]->slab),
cosmo,
&plist);
// Generate power spectra
for(i_species=0;i_species<plist.n_species;i_species++){
// Determine how many particles of species i_species there are
if(n_all[i_species]>0){
// Fetch the needed information
size_t n_particles;
size_t n_particles_local;
int flag_alloc_m;
GBPREAL *x_particles_local;
GBPREAL *y_particles_local;
GBPREAL *z_particles_local;
GBPREAL *vx_particles_local;
GBPREAL *vy_particles_local;
GBPREAL *vz_particles_local;
GBPREAL *m_particles_local;
GBPREAL *v_particles_local;
GBPREAL *w_particles_local;
n_particles =((size_t *)ADaPS_fetch(plist.data,"n_all_%s",plist.species[i_species]))[0];
n_particles_local=((size_t *)ADaPS_fetch(plist.data,"n_%s", plist.species[i_species]))[0];
x_particles_local= (GBPREAL *)ADaPS_fetch(plist.data,"x_%s", plist.species[i_species]);
y_particles_local= (GBPREAL *)ADaPS_fetch(plist.data,"y_%s", plist.species[i_species]);
z_particles_local= (GBPREAL *)ADaPS_fetch(plist.data,"z_%s", plist.species[i_species]);
vx_particles_local=(GBPREAL *)ADaPS_fetch(plist.data,"vx_%s", plist.species[i_species]);
vy_particles_local=(GBPREAL *)ADaPS_fetch(plist.data,"vy_%s", plist.species[i_species]);
vz_particles_local=(GBPREAL *)ADaPS_fetch(plist.data,"vz_%s", plist.species[i_species]);
if(ADaPS_exist(plist.data,"M_%s",plist.species[i_species])){
flag_alloc_m=FALSE;
m_particles_local=(GBPREAL *)ADaPS_fetch(plist.data,"M_%s",plist.species[i_species]);
}
else{
flag_alloc_m=TRUE;
m_particles_local=(GBPREAL *)SID_malloc(n_particles_local*sizeof(GBPREAL));
int i_particle;
for(i_particle=0;i_particle<n_particles_local;i_particle++)
m_particles_local[i_particle]=mass_array[i_species];
}
// Decide the map_to_grid() mode
int mode;
if(n_load==1)
mode=MAP2GRID_MODE_DEFAULT;
else if(i_load==0 || n_load==1)
mode=MAP2GRID_MODE_DEFAULT|MAP2GRID_MODE_NONORM;
else if(i_load==(n_load-1))
mode=MAP2GRID_MODE_NOCLEAN;
else
mode=MAP2GRID_MODE_NOCLEAN|MAP2GRID_MODE_NONORM;
// Set the array that will weight the grid
field_info *field_i;
field_info *field_norm_i;
double factor;
switch(i_grid){
case 0:
v_particles_local=m_particles_local;
w_particles_local=NULL;
field_i =field[i_species];
field_norm_i =NULL;
mode|=MAP2GRID_MODE_APPLYFACTOR;
factor=pow((double)grid_size/box_size,3.);
break;
case 1:
v_particles_local=vx_particles_local;
w_particles_local=m_particles_local;
field_i =field[i_species];
field_norm_i =field_norm[i_species];
factor=1.;
break;
case 2:
v_particles_local=vy_particles_local;
w_particles_local=m_particles_local;
field_i =field[i_species];
field_norm_i =field_norm[i_species];
factor=1.;
break;
case 3:
v_particles_local=vz_particles_local;
w_particles_local=m_particles_local;
field_i =field[i_species];
field_norm_i =field_norm[i_species];
factor=1.;
break;
}
// Generate grid
map_to_grid(n_particles_local,
x_particles_local,
y_particles_local,
z_particles_local,
v_particles_local,
w_particles_local,
cosmo,
redshift,
distribution_scheme,
factor,
field_i,
field_norm_i,
mode);
if(flag_alloc_m)
SID_free(SID_FARG m_particles_local);
}
}
// Clean-up
free_plist(&plist);
if(n_load>1)
SID_log("Done.",SID_LOG_CLOSE);
} // loop over i_load
// Write results to disk
char filename_out_species[MAX_FILENAME_LENGTH];
init_plist(&plist,NULL,GADGET_LENGTH,GADGET_MASS,GADGET_VELOCITY);
for(i_species=0;i_species<plist.n_species;i_species++){
if(flag_used[i_species]){
sprintf(grid_identifier,"%s_%s_%s",i_grid_identifier,i_run_identifier,plist.species[i_species]);
sprintf(filename_out_species,"%s_%s",filename_out_root,plist.species[i_species]);
write_grid(field[i_species],
filename_out_species,
i_write,
n_grids_total,
distribution_scheme,
grid_identifier,
header.box_size);
free_field(field[i_species]);
free_field(field_norm[i_species]);
SID_free(SID_FARG field[i_species]);
SID_free(SID_FARG field_norm[i_species]);
i_write++;
}
}
// Clean-up
free_plist(&plist);
SID_log("Done.",SID_LOG_CLOSE);
} // loop over i_grid
SID_log("Done.",SID_LOG_CLOSE);
} // loop over i_run
} // if n_used>0
// Clean-up
free_cosmo(&cosmo);
SID_free(SID_FARG grid_identifier);
SID_free(SID_FARG n_all);
SID_log("Done.",SID_LOG_CLOSE);
SID_exit(ERROR_NONE);
}
int main(int argc, char *argv[]) {
SID_Init(&argc, &argv, NULL);
// Parse command line
select_gadget_volume_params_info select_gadget_volume_params;
int snapshot;
int n_files_out;
int select_mode;
char filename_in_root[SID_MAX_FILENAME_LENGTH];
char filename_out_root[SID_MAX_FILENAME_LENGTH];
GBPREAL cen_select[3];
GBPREAL select_size;
strcpy(filename_in_root, argv[1]);
snapshot = atoi(argv[2]);
select_gadget_volume_params.cen[0] = (GBPREAL)atof(argv[3]);
select_gadget_volume_params.cen[1] = (GBPREAL)atof(argv[4]);
select_gadget_volume_params.cen[2] = (GBPREAL)atof(argv[5]);
select_gadget_volume_params.size = (GBPREAL)atof(argv[6]);
strcpy(filename_out_root, argv[7]);
n_files_out = atoi(argv[8]);
select_mode = atoi(argv[9]);
// Check that the selection mode is valid and set function pointer
int (*select_function)(
gadget_read_info * fp_gadget, void *params, size_t i_particle, size_t i_particle_type, int i_type, GBPREAL *pos, GBPREAL *vel, size_t ID_i);
if(select_mode == 1)
select_function = select_gadget_cube;
else if(select_mode == 2) {
select_function = select_gadget_sphere;
select_gadget_volume_params.size2 = pow(select_gadget_volume_params.size, 2.);
} else
SID_exit_error("Invalid selection mode (%d) given.", SID_ERROR_SYNTAX, select_mode);
SID_log("Excising volume from Gadget binary file {%s;snapshot=%d}...", SID_LOG_OPEN | SID_LOG_TIMER, filename_in_root, snapshot);
// Initialize the plist data structure
plist_info plist;
select_gadget_volume_params.plist = &plist;
init_plist(&plist, NULL, GADGET_LENGTH, GADGET_MASS, GADGET_VELOCITY);
// Read the header and determine the input file-format
gadget_read_info fp_gadget;
int flag_filefound = init_gadget_read(filename_in_root, snapshot, &fp_gadget);
int flag_multifile = fp_gadget.flag_multifile;
int flag_file_type = fp_gadget.flag_file_type;
gadget_header_info header = fp_gadget.header;
if(!flag_filefound)
SID_exit_error("File not found.", SID_ERROR_LOGIC);
select_gadget_volume_params.box_size = fp_gadget.header.box_size;
// Count the particles
size_t n_particles_type_local[N_GADGET_TYPE];
size_t n_particles_type[N_GADGET_TYPE];
int flag_long_IDs;
process_gadget_file("Counting particles in selection...",
filename_in_root,
snapshot,
select_function,
process_gadget_file_fctn_null,
&select_gadget_volume_params,
n_particles_type_local,
n_particles_type,
&flag_long_IDs,
PROCESS_GADGET_BINARY_DEFAULT);
// Allocate RAM for the particles
allocate_gadget_particles(&plist, n_particles_type_local, n_particles_type, flag_long_IDs);
// Read the particles
process_gadget_file("Performing read/select/write...",
filename_in_root,
snapshot,
select_function,
store_gadget_particles,
&select_gadget_volume_params,
NULL,
NULL,
&flag_long_IDs,
PROCESS_GADGET_BINARY_DEFAULT);
// Write the snapshot
char filename_out[SID_MAX_FILENAME_LENGTH];
sprintf(filename_out, "%s_%03d", filename_out_root, snapshot);
write_gadget_binary_new(&plist, filename_out, n_files_out, WRITE_GADGET_BINARY_DEFAULT);
// Clean-up
free_plist(&plist);
SID_log("Done.", SID_LOG_CLOSE);
SID_Finalize();
}
void read_gadget_binary_local(char *filename_root_in,
int snapshot_number,
int i_coord,
int i_load,
int n_load,
GBPREAL mass_array[N_GADGET_TYPE],
slab_info *slab,
cosmo_info *cosmo,
plist_info *plist){
size_t n_of_type_local[N_GADGET_TYPE];
size_t n_of_type[N_GADGET_TYPE];
size_t type_counter[N_GADGET_TYPE];
GBPREAL *x_array[N_GADGET_TYPE];
GBPREAL *y_array[N_GADGET_TYPE];
GBPREAL *z_array[N_GADGET_TYPE];
GBPREAL *vx_array[N_GADGET_TYPE];
GBPREAL *vy_array[N_GADGET_TYPE];
GBPREAL *vz_array[N_GADGET_TYPE];
int i_type;
// Determine file format and read the header
gadget_read_info fp_gadget;
int flag_filefound=init_gadget_read(filename_root_in,snapshot_number,&fp_gadget);
int flag_multifile=fp_gadget.flag_multifile;
int flag_file_type=fp_gadget.flag_file_type;
gadget_header_info header =fp_gadget.header;
// A file was found ...
if(flag_filefound){
char **pname;
SID_log("Reading GADGET binary file...",SID_LOG_OPEN|SID_LOG_TIMER);
pname=plist->species;
// Expansion factor (or time)
ADaPS_store(&(plist->data),(void *)(&(header.time)),"expansion_factor",ADaPS_SCALAR_DOUBLE);
ADaPS_store(&(plist->data),(void *)(&(header.time)),"time", ADaPS_SCALAR_DOUBLE);
// Redshift
double d_value;
d_value=(double)header.redshift;
ADaPS_store(&(plist->data),(void *)(&d_value),"redshift",ADaPS_SCALAR_DOUBLE);
// Number of particles and masses for each species in all files
size_t n_all[N_GADGET_TYPE];
for(i_type=0;i_type<N_GADGET_TYPE;i_type++){
n_all[i_type] =(size_t)header.n_all_lo_word[i_type]+((size_t)header.n_all_hi_word[i_type])<<32;
mass_array[i_type]=(GBPREAL)header.mass_array[i_type];
}
// Number of files in this snapshot
int n_files;
ADaPS_store(&(plist->data),(void *)(&(header.n_files)),"n_files",ADaPS_SCALAR_INT);
n_files=header.n_files;
// Cosmology
// Omega_o
d_value=(double)header.Omega_M;
ADaPS_store(&(plist->data),(void *)(&d_value),"Omega_M",ADaPS_SCALAR_DOUBLE);
// Omega_Lambda
d_value=(double)header.Omega_Lambda;
ADaPS_store(&(plist->data),(void *)(&d_value),"Omega_Lambda",ADaPS_SCALAR_DOUBLE);
// Hubble parameter
double h_Hubble;
double redshift;
h_Hubble=(double)header.h_Hubble;
if(h_Hubble<1e-10) h_Hubble=1.;
ADaPS_store(&(plist->data),(void *)(&h_Hubble),"h_Hubble",ADaPS_SCALAR_DOUBLE);
redshift=header.redshift;
ADaPS_store(&(plist->data),(void *)(&redshift),"redshift",ADaPS_SCALAR_DOUBLE);
// Count and report the total number of particles
size_t n_particles_all;
int n_non_zero;
n_particles_all=0;
for(i_type=0,n_non_zero=0;i_type<N_GADGET_TYPE;i_type++){
if(n_all[i_type]>0){
n_particles_all+=n_all[i_type];
n_non_zero++;
}
}
SID_log("%zd",SID_LOG_CONTINUE,n_particles_all);
if(n_non_zero>0)
SID_log(" (",SID_LOG_CONTINUE,n_particles_all);
for(i_type=0;i_type<N_GADGET_TYPE;i_type++){
if(n_all[i_type]>0){
if(i_type==n_non_zero-1){
if(n_non_zero>1)
SID_log("and %lld %s",SID_LOG_CONTINUE,n_all[i_type],pname[i_type]);
else
SID_log("%lld %s",SID_LOG_CONTINUE,n_all[i_type],pname[i_type]);
}
else{
if(n_non_zero>1)
SID_log("%lld %s, ",SID_LOG_CONTINUE,n_all[i_type],pname[i_type]);
else
SID_log("%lld %s",SID_LOG_CONTINUE,n_all[i_type],pname[i_type]);
}
}
}
if(n_non_zero>0)
SID_log(") particles...",SID_LOG_CONTINUE);
else
SID_log(" particles...",SID_LOG_CONTINUE);
// Count the number of particles that will be scattered to each rank
char filename[MAX_FILENAME_LENGTH];
size_t k_particle;
int i_file;
int record_length_open;
int record_length_close;
size_t i_particle;
size_t i_buffer;
size_t i_step;
int i_type;
size_t index;
GBPREAL *pos_buffer;
GBPREAL *vel_buffer;
double pos_test;
// Initialize some arrays
pos_buffer=(GBPREAL *)SID_malloc(sizeof(GBPREAL)*READ_BUFFER_ALLOC_LOCAL);
vel_buffer=(GBPREAL *)SID_malloc(sizeof(GBPREAL)*READ_BUFFER_ALLOC_LOCAL);
for(i_type=0;i_type<N_GADGET_TYPE;i_type++){
n_of_type_local[i_type]=0;
n_of_type[i_type] =0;
type_counter[i_type] =0;
}
// Determine how many particles of each type will end-up on each core
SID_log("Performing domain decomposition...",SID_LOG_OPEN|SID_LOG_TIMER);
int n_read;
if(n_load<n_files)
n_read=n_files;
else
n_read=1;
for(i_file=i_load;i_file<(i_load+n_read);i_file++){
set_gadget_filename(&fp_gadget,i_file,filename);
// Read header and move to the positions
FILE *fp_pos;
FILE *fp_vel;
fp_pos=fopen(filename,"r");
fread_verify(&record_length_open,4,1,fp_pos);
fread_verify(&header,sizeof(gadget_header_info),1,fp_pos);
fread_verify(&record_length_close,4,1,fp_pos);
if(record_length_open!=record_length_close)
SID_log_warning("Problem with GADGET record size (close of header)",ERROR_LOGIC);
fread_verify(&record_length_open,4,1,fp_pos);
// Create a file pointer to the velocities
fp_vel=fopen(filename,"r");
fread_verify(&record_length_open,4,1,fp_vel);
fseeko(fp_vel,(off_t)(record_length_open),SEEK_CUR);
fread_verify(&record_length_close,4,1,fp_vel);
fread_verify(&record_length_open,4,1,fp_vel);
fseeko(fp_vel,(off_t)(record_length_open),SEEK_CUR);
fread_verify(&record_length_close,4,1,fp_vel);
if(record_length_open!=record_length_close)
SID_log_warning("Problem with GADGET record size (close of positons)",ERROR_LOGIC);
fread_verify(&record_length_open,4,1,fp_vel);
// We only have to worry about z-space effects for domain decomposition in this one case.
if(i_coord==1){
for(i_type=0;i_type<N_GADGET_TYPE;i_type++){
for(i_particle=0;i_particle<header.n_file[i_type];i_particle+=i_step){
i_step=MIN(READ_BUFFER_SIZE_LOCAL,header.n_file[i_type]-i_particle);
if(SID.I_am_Master){
fread_verify(pos_buffer,sizeof(GBPREAL),3*i_step,fp_pos);
fread_verify(vel_buffer,sizeof(GBPREAL),3*i_step,fp_vel);
}
SID_Bcast(pos_buffer,sizeof(GBPREAL)*3*i_step,MASTER_RANK,SID.COMM_WORLD);
SID_Bcast(vel_buffer,sizeof(GBPREAL)*3*i_step,MASTER_RANK,SID.COMM_WORLD);
for(i_buffer=0;i_buffer<i_step;i_buffer++){
index=3*i_buffer;
pos_test =(double)(pos_buffer[index]);
pos_test+=(double)(1e3*h_Hubble*((double)vel_buffer[index])/(a_of_z(redshift)*M_PER_MPC*H_convert(H_z(redshift,cosmo))));
if(pos_test<0) pos_test+=header.box_size;
if(pos_test>=header.box_size) pos_test-=header.box_size;
if(pos_test>=slab->x_min_local && pos_test<slab->x_max_local)
n_of_type_local[i_type]++;
}
}
}
}
else{
for(i_type=0;i_type<N_GADGET_TYPE;i_type++){
for(i_particle=0;i_particle<header.n_file[i_type];i_particle+=i_step){
i_step=MIN(READ_BUFFER_SIZE_LOCAL,header.n_file[i_type]-i_particle);
if(SID.I_am_Master){
fread_verify(pos_buffer,sizeof(GBPREAL),3*i_step,fp_pos);
fread_verify(vel_buffer,sizeof(GBPREAL),3*i_step,fp_vel);
}
SID_Bcast(pos_buffer,sizeof(GBPREAL)*3*i_step,MASTER_RANK,SID.COMM_WORLD);
SID_Bcast(vel_buffer,sizeof(GBPREAL)*3*i_step,MASTER_RANK,SID.COMM_WORLD);
for(i_buffer=0;i_buffer<i_step;i_buffer++){
pos_test=pos_buffer[3*i_buffer];
if(pos_test>=slab->x_min_local && pos_test<slab->x_max_local)
n_of_type_local[i_type]++;
}
}
i_step=MIN(READ_BUFFER_SIZE_LOCAL,header.n_file[i_type]-i_particle);
}
}
fclose(fp_pos);
fclose(fp_vel);
}
SID_log("Done.",SID_LOG_CLOSE);
// Allocate arrays
for(i_type=0;i_type<N_GADGET_TYPE;i_type++){
if(n_all[i_type]>0){
x_array[i_type] =(GBPREAL *)SID_malloc(sizeof(GBPREAL)*n_of_type_local[i_type]);
y_array[i_type] =(GBPREAL *)SID_malloc(sizeof(GBPREAL)*n_of_type_local[i_type]);
z_array[i_type] =(GBPREAL *)SID_malloc(sizeof(GBPREAL)*n_of_type_local[i_type]);
vx_array[i_type]=(GBPREAL *)SID_malloc(sizeof(GBPREAL)*n_of_type_local[i_type]);
vy_array[i_type]=(GBPREAL *)SID_malloc(sizeof(GBPREAL)*n_of_type_local[i_type]);
vz_array[i_type]=(GBPREAL *)SID_malloc(sizeof(GBPREAL)*n_of_type_local[i_type]);
}
}
// Perform read
SID_log("Performing read...",SID_LOG_OPEN|SID_LOG_TIMER);
for(i_file=i_load;i_file<(i_load+n_read);i_file++){
set_gadget_filename(&fp_gadget,i_file,filename);
// Read header and move to the positions
FILE *fp_pos;
FILE *fp_vel;
fp_pos=fopen(filename,"r");
fread_verify(&record_length_open,4,1,fp_pos);
fread_verify(&header,sizeof(gadget_header_info),1,fp_pos);
fread_verify(&record_length_close,4,1,fp_pos);
if(record_length_open!=record_length_close)
SID_log_warning("Problem with GADGET record size (close of header)",ERROR_LOGIC);
fread_verify(&record_length_open,4,1,fp_pos);
// Create a file pointer to the velocities
fp_vel=fopen(filename,"r");
fread_verify(&record_length_open,4,1,fp_vel);
fseeko(fp_vel,(off_t)(record_length_open),SEEK_CUR);
fread_verify(&record_length_close,4,1,fp_vel);
fread_verify(&record_length_open,4,1,fp_vel);
fseeko(fp_vel,(off_t)(record_length_open),SEEK_CUR);
fread_verify(&record_length_close,4,1,fp_vel);
if(record_length_open!=record_length_close)
SID_log_warning("Problem with GADGET record size (close of positions)",ERROR_LOGIC);
fread_verify(&record_length_open,4,1,fp_vel);
// Perform the read and populate the local position arrays
size_t i_particle;
size_t i_step;
int i_type;
for(i_type=0;i_type<N_GADGET_TYPE;i_type++){
for(i_particle=0;i_particle<header.n_file[i_type];i_particle+=i_step){
i_step=MIN(READ_BUFFER_SIZE_LOCAL,header.n_file[i_type]-i_particle);
if(SID.I_am_Master){
fread_verify(pos_buffer,sizeof(GBPREAL),3*i_step,fp_pos);
fread_verify(vel_buffer,sizeof(GBPREAL),3*i_step,fp_vel);
}
SID_Bcast(pos_buffer,sizeof(GBPREAL)*3*i_step,MASTER_RANK,SID.COMM_WORLD);
SID_Bcast(vel_buffer,sizeof(GBPREAL)*3*i_step,MASTER_RANK,SID.COMM_WORLD);
for(i_buffer=0;i_buffer<i_step;i_buffer++){
double x_test;
double y_test;
double z_test;
double vx_test;
double vy_test;
double vz_test;
index=3*i_buffer;
x_test =(double)pos_buffer[index+0];
y_test =(double)pos_buffer[index+1];
z_test =(double)pos_buffer[index+2];
vx_test=(double)vel_buffer[index+0];
vy_test=(double)vel_buffer[index+1];
vz_test=(double)vel_buffer[index+2];
switch(i_coord){
case 1:
x_test+=(1e3*h_Hubble*vx_test/(a_of_z(redshift)*M_PER_MPC*H_convert(H_z(redshift,cosmo))));
if(x_test<0) x_test+=header.box_size;
if(x_test>=header.box_size) x_test-=header.box_size;
break;
case 2:
y_test+=(1e3*h_Hubble*vy_test/(a_of_z(redshift)*M_PER_MPC*H_convert(H_z(redshift,cosmo))));
if(y_test<0) y_test+=header.box_size;
if(y_test>=header.box_size) y_test-=header.box_size;
break;
case 3:
z_test+=(1e3*h_Hubble*vz_test/(a_of_z(redshift)*M_PER_MPC*H_convert(H_z(redshift,cosmo))));
if(z_test<0) z_test+=header.box_size;
if(z_test>=header.box_size) z_test-=header.box_size;
break;
}
if(x_test>=slab->x_min_local && x_test<slab->x_max_local){
x_array[i_type][type_counter[i_type]] =x_test;
y_array[i_type][type_counter[i_type]] =y_test;
z_array[i_type][type_counter[i_type]] =z_test;
vx_array[i_type][type_counter[i_type]]=vx_test;
vy_array[i_type][type_counter[i_type]]=vy_test;
vz_array[i_type][type_counter[i_type]]=vz_test;
type_counter[i_type]++;
}
}
}
}
// Close file pointers
fclose(fp_pos);
fclose(fp_vel);
}
SID_free(SID_FARG pos_buffer);
SID_free(SID_FARG vel_buffer);
SID_log("Done.",SID_LOG_CLOSE);
// Sanity checks
size_t n_particles_local;
size_t n_particles_read;
size_t n_particles_test;
for(i_type=0,n_particles_local=0,n_particles_test=0;i_type<N_GADGET_TYPE;i_type++){
n_particles_local+=n_of_type_local[i_type];
n_particles_test +=n_all[i_type];
}
SID_Allreduce(&n_particles_local,&n_particles_read,1,SID_SIZE_T,SID_SUM,SID.COMM_WORLD);
if(n_particles_read!=n_particles_test && n_load==1)
SID_trap_error("Total particle counts don't make sense after read_gadget (ie. %zd!=%zd).",ERROR_LOGIC,n_particles_read,n_particles_test);
for(i_type=0;i_type<N_GADGET_TYPE;i_type++){
SID_Allreduce(&(n_of_type_local[i_type]),&(n_of_type[i_type]),1,SID_SIZE_T,SID_SUM,SID.COMM_WORLD);
if(n_of_type[i_type]!=n_all[i_type] && n_load==1)
SID_trap_error("Particle counts don't make sense after read_gadget (ie. %zd!=%zd).",ERROR_LOGIC,n_of_type[i_type],n_all[i_type]);
}
// Store results
for(i_type=0;i_type<N_GADGET_TYPE;i_type++){
if(n_of_type[i_type]>0){
ADaPS_store(&(plist->data),(void *)(&(n_of_type_local[i_type])),"n_%s", ADaPS_SCALAR_SIZE_T,pname[i_type]);
ADaPS_store(&(plist->data),(void *)(&(n_of_type[i_type])), "n_all_%s", ADaPS_SCALAR_SIZE_T,pname[i_type]);
}
}
ADaPS_store(&(plist->data),(void *)(&n_particles_all),"n_particles_all",ADaPS_SCALAR_SIZE_T);
for(i_type=0;i_type<N_GADGET_TYPE;i_type++){
if(n_of_type_local[i_type]>0){
ADaPS_store(&(plist->data),(void *)x_array[i_type], "x_%s", ADaPS_DEFAULT, pname[i_type]);
ADaPS_store(&(plist->data),(void *)y_array[i_type], "y_%s", ADaPS_DEFAULT, pname[i_type]);
ADaPS_store(&(plist->data),(void *)z_array[i_type], "z_%s", ADaPS_DEFAULT, pname[i_type]);
ADaPS_store(&(plist->data),(void *)vx_array[i_type],"vx_%s",ADaPS_DEFAULT,pname[i_type]);
ADaPS_store(&(plist->data),(void *)vy_array[i_type],"vy_%s",ADaPS_DEFAULT,pname[i_type]);
ADaPS_store(&(plist->data),(void *)vz_array[i_type],"vz_%s",ADaPS_DEFAULT,pname[i_type]);
}
}
SID_log("Done.",SID_LOG_CLOSE);
}
}
