int main(int argc, char *argv[]) {
int n_search;
int i_halo;
char filename_in[SID_MAX_FILENAME_LENGTH];
char group_text_prefix[4];
int n_files;
int k_read;
int max_n_groups;
int l_read;
int n_groups;
int * n_particles_i;
int * n_particles_j;
int j_read;
int mode;
int n_groups_i;
int n_groups_j;
int j_halo;
int i_read;
int i_read_start;
int i_read_stop;
SID_fp fp_in;
SID_Init(&argc, &argv, NULL);
// Fetch user inputs
char filename_root_in[SID_MAX_FILENAME_LENGTH];
char filename_catalog_root[SID_MAX_FILENAME_LENGTH];
char filename_halo_version[SID_MAX_FILENAME_LENGTH];
strcpy(filename_root_in, argv[1]);
strcpy(filename_halo_version, argv[2]);
if(!strcmp(argv[3], "groups") || !strcmp(argv[3], "group"))
mode = MATCH_GROUPS;
else if(!strcmp(argv[3], "subgroups") || !strcmp(argv[3], "subgroup"))
mode = MATCH_SUBGROUPS;
else {
SID_exit_error("Invalid mode selection {%s}. Should be 'group' or 'subgroup'.", SID_ERROR_SYNTAX, argv[3]);
}
i_read = atoi(argv[4]);
j_read = atoi(argv[5]);
int flag_SSimPL_base = GBP_TRUE;
if(argc == 7) {
flag_SSimPL_base = GBP_FALSE;
strcpy(filename_catalog_root, argv[6]);
sprintf(filename_catalog_root, "%s/halos/%s", argv[6], filename_halo_version);
} else
sprintf(filename_catalog_root, "%s/halos/%s", filename_root_in, filename_halo_version);
SID_log("Searching match information for halo #%d in file #%d of {%s}...", SID_LOG_OPEN | SID_LOG_TIMER, i_halo, i_read, filename_root_in);
// Convert filename_root to filename
switch(mode) {
case MATCH_SUBGROUPS:
sprintf(group_text_prefix, "sub");
break;
case MATCH_GROUPS:
sprintf(group_text_prefix, "");
break;
}
// Set the standard SSiMPL match file path
char filename_root[SID_MAX_FILENAME_LENGTH];
if(flag_SSimPL_base)
sprintf(filename_root, "%s/trees/matches/%03d/", filename_root_in, i_read);
else
sprintf(filename_root, "%s_", filename_root_in);
// Read header information
int i_read_in;
int j_read_in;
int n_groups_1;
int n_groups_2;
float score_rank_index;
sprintf(filename_in, "%s%sgroup_matches_%03d_%03d.dat", filename_root, group_text_prefix, i_read, j_read);
SID_fopen(filename_in, "r", &fp_in);
SID_fread(&i_read_in, sizeof(int), 1, &fp_in);
SID_log("i_read =%d", SID_LOG_COMMENT, i_read_in);
SID_fread(&j_read_in, sizeof(int), 1, &fp_in);
SID_log("j_read =%d", SID_LOG_COMMENT, j_read_in);
SID_fread(&n_groups_i, sizeof(int), 1, &fp_in);
SID_log("n_groups_i=%d", SID_LOG_COMMENT, n_groups_i);
SID_fread(&n_groups_j, sizeof(int), 1, &fp_in);
SID_log("n_groups_j=%d", SID_LOG_COMMENT, n_groups_j);
SID_fread(&score_rank_index, sizeof(int), 1, &fp_in);
SID_log("score_idx =%f", SID_LOG_COMMENT, score_rank_index);
// Allocate RAM
int * match = (int *)SID_malloc(sizeof(int) * n_groups_i);
float *score = (float *)SID_malloc(sizeof(float) * n_groups_i);
int * count = (int *)SID_malloc(sizeof(int) * n_groups_i);
// Read arrays
SID_fread(match, sizeof(int), n_groups_i, &fp_in);
SID_fread(score, sizeof(float), n_groups_i, &fp_in);
SID_fread(count, sizeof(int), n_groups_i, &fp_in);
// Close file
SID_fclose(&fp_in);
// Read halo sizes from header file
SID_log("Reading halo sizes...", SID_LOG_OPEN);
int *n_p_i = (int *)SID_malloc(sizeof(int) * n_groups_i);
sprintf(filename_in, "%s_%03d.catalog_%sgroups", filename_catalog_root, i_read, group_text_prefix);
SID_fopen(filename_in, "r", &fp_in);
int n_cat_i;
int offset_size_i;
SID_fread(&n_cat_i, sizeof(int), 1, &fp_in);
SID_fread(&offset_size_i, sizeof(int), 1, &fp_in);
if(n_cat_i != n_groups_i)
SID_exit_error("Catalog 'i' halo counts don't match (ie %d!=%d)", SID_ERROR_LOGIC, n_cat_i, n_groups_i);
SID_fread(n_p_i, sizeof(int), n_cat_i, &fp_in);
SID_fclose(&fp_in);
int *n_p_j = (int *)SID_malloc(sizeof(int) * n_groups_j);
sprintf(filename_in, "%s_%03d.catalog_%sgroups", filename_catalog_root, j_read, group_text_prefix);
SID_fopen(filename_in, "r", &fp_in);
int n_cat_j;
int offset_size_j;
SID_fread(&n_cat_j, sizeof(int), 1, &fp_in);
SID_fread(&offset_size_j, sizeof(int), 1, &fp_in);
if(n_cat_j != n_groups_j)
SID_exit_error("Catalog 'i' halo counts don't match (ie %d!=%d)", SID_ERROR_LOGIC, n_cat_j, n_groups_j);
SID_fread(n_p_j, sizeof(int), n_cat_j, &fp_in);
SID_fclose(&fp_in);
SID_log("Done.", SID_LOG_CLOSE);
// Print results
for(k_read = 0; k_read < n_groups_i; k_read++) {
if(match[k_read] >= 0)
printf("%7d %7d %7d %7d %7d %le %le %le\n",
k_read,
match[k_read],
n_p_i[k_read],
n_p_j[match[k_read]],
count[k_read],
score[k_read],
maximum_match_score(n_p_i[k_read]),
match_score_f_goodness(score[k_read], n_p_i[k_read]));
}
// Clean-up
SID_free(SID_FARG match);
SID_free(SID_FARG score);
SID_free(SID_FARG count);
SID_free(SID_FARG n_p_i);
SID_free(SID_FARG n_p_j);
SID_log("Done.", SID_LOG_CLOSE);
SID_Finalize();
}
void SID_init(int *argc,
char **argv[],
SID_args args[],
void *mpi_comm_as_void){
int status;
int i_level;
int i_char;
int flag_continue;
int flag_passed_comm;
// MPI-specific things
#if USE_MPI
int n_keys;
int i_key;
char key[256];
char key_value[256];
int key_exists;
char nodes_string[256];
SID_fp fp_tmp;
FILE *fp_hack;
int node_name_length;
MPI_Comm mpi_comm;
#if USE_MPI_IO
MPI_Info info_disp;
#endif
if (mpi_comm_as_void == NULL)
{
flag_passed_comm = 0;
MPI_Init(argc,argv);
MPI_Comm_dup(MPI_COMM_WORLD, &mpi_comm);
}
else
{
mpi_comm = *((MPI_Comm *) mpi_comm_as_void);
flag_passed_comm = 1;
}
MPI_Comm_size(mpi_comm, &(SID.n_proc));
MPI_Comm_rank(mpi_comm, &(SID.My_rank));
SID.My_node =(char *)SID_malloc(SID_MAXLENGTH_PROCESSOR_NAME * sizeof(char));
#if USE_MPI
MPI_Get_processor_name(SID.My_node, &node_name_length);
#else
sprintf(SID.My_node,"localhost");
node_name_length=strlen(SID.My_node);
#endif
if (node_name_length >= SID_MAXLENGTH_PROCESSOR_NAME-1)
SID_trap_error("SID_MAXLENGTH_PROCESSOR_NAME needs to be increased",ERROR_LOGIC);
// Make my_rank=MASTER_RANK the master
if(SID.My_rank==MASTER_RANK)
SID.I_am_Master=TRUE;
else
SID.I_am_Master=FALSE;
// Identify the last rank
if(SID.My_rank==SID.n_proc-1)
SID.I_am_last_rank=TRUE;
else
SID.I_am_last_rank=FALSE;
#if USE_MPI_IO
// Fetch collective buffering defaults
MPI_Info_create(&(SID.file_info));
if(SID.I_am_Master){
fp_hack=fopen(".tmp.SID","w+");
fclose(fp_hack);
}
MPI_Barrier(mpi_comm);
MPI_File_open(mpi_comm,
".tmp.SID",
MPI_MODE_WRONLY,
MPI_INFO_NULL,
&(fp_tmp.fp));
MPI_File_get_info(fp_tmp.fp,&info_disp);
MPI_Info_get_nkeys(info_disp,&n_keys);
for(i_key=0;i_key<n_keys;i_key++){
MPI_Info_get_nthkey(info_disp,i_key,key);
MPI_Info_get(info_disp,key,MPI_MAX_INFO_VAL,key_value,&key_exists);
if(key_exists)
MPI_Info_set((SID.file_info),key,key_value);
}
MPI_File_close(&(fp_tmp.fp));
if(SID.I_am_Master)
remove(".tmp.SID");
// Set user-defined colective buffering optimizations
sprintf(nodes_string,"%d",MIN(SID.n_proc,N_IO_FILES_MAX));
MPI_Info_set((SID.file_info),"cb_nodes", nodes_string);
MPI_Info_set((SID.file_info),"cb_config_list", "*:1");
#endif
#else
SID.My_rank=MASTER_RANK;
SID.n_proc =1;
#endif
/*
#if !USE_MPI_IO
SID.n_groups=SID.n_proc/N_IO_FILES_MAX;
if(SID.n_proc%N_IO_FILES_MAX) SID.n_groups++;
SID.My_group=SID.My_rank/N_IO_FILES_MAX;
#endif
*/
// Set ranks to the left and right
SID.rank_to_right =(SID.My_rank+1)%SID.n_proc;
SID.rank_to_left = SID.My_rank-1;
if(SID.rank_to_left<0)
SID.rank_to_left = SID.n_proc-1;
// Intitialize log timing information
SID.time_start_level=(time_t *)SID_malloc(sizeof(time_t)*SID_LOG_MAX_LEVELS);
SID.time_stop_level =(time_t *)SID_malloc(sizeof(time_t)*SID_LOG_MAX_LEVELS);
SID.time_total_level=(int *)SID_malloc(sizeof(int) *SID_LOG_MAX_LEVELS);
SID.IO_size =(double *)SID_malloc(sizeof(double)*SID_LOG_MAX_LEVELS);
SID.flag_use_timer =(int *)SID_malloc(sizeof(int) *SID_LOG_MAX_LEVELS);
for(i_level=0;i_level<SID_LOG_MAX_LEVELS;i_level++){
SID.time_start_level[i_level]=0;
SID.time_stop_level[i_level] =0;
SID.time_total_level[i_level]=0;
SID.IO_size[i_level] =0.;
SID.flag_use_timer[i_level] =FALSE;
}
// Initialize other log information
#if USE_MPI
if(*argc>1)
SID.fp_in =fopen((*argv)[1],"r");
else
SID.fp_in =NULL;
#else
SID.fp_in =stdin;
#endif
if (flag_passed_comm)
SID.fp_log = NULL;
else
SID.fp_log = stderr;
SID.level =0;
SID.indent =TRUE;
SID.awake =TRUE;
SID.flag_results_on=FALSE;
SID.verbosity =SID_LOG_MAX_LEVELS;
// Store the name of the binary executable that brought us here
strcpy(SID.My_binary,(*argv)[0]);
strip_path(SID.My_binary);
// Initialize argument information
if(args!=NULL){
if((status=SID_parse_args(*argc,*argv,args))>0){
SID_print_syntax(*argc,*argv,args);
SID_exit(status);
}
}
else
SID.args=NULL;
#if USE_MPI_IO
if(SID.I_am_Master){
fp_hack=fopen(".tmp.SID","w+");
fclose(fp_hack);
}
MPI_Barrier(mpi_comm);
SID_fopen(".tmp.SID","w",&fp_tmp);
MPI_File_get_info(fp_tmp.fp,&info_disp);
if(SID.I_am_Master){
fprintf(stdout,"\n");
fprintf(stdout,"MPI-I/O Configuration:\n");
fprintf(stdout,"---------------------\n");
MPI_Info_get_nkeys(info_disp,&n_keys);
for(i_key=0;i_key<n_keys;i_key++){
MPI_Info_get_nthkey(info_disp,i_key,key);
MPI_Info_get(info_disp,key,MPI_MAX_INFO_VAL,key_value,&key_exists);
if(key_exists)
fprintf(stdout,"key %2d of %d: {%s}={%s}\n",i_key+1,n_keys,key,key_value);
}
fprintf(stdout,"\n");
}
SID_fclose(&fp_tmp);
if(SID.I_am_Master)
remove(".tmp.SID");
#else
#if USE_MPI
if(SID.I_am_Master)
fprintf(stdout,"MPI-I/O switched off.\n\n");
#endif
#endif
// Create private COMM_WORLD
SID_Comm_init(&(SID.COMM_WORLD));
#if USE_MPI
MPI_Comm_dup(mpi_comm, &((SID.COMM_WORLD)->comm));
MPI_Comm_group((SID.COMM_WORLD)->comm,&((SID.COMM_WORLD)->group));
MPI_Comm_size(SID.COMM_WORLD->comm, &((SID.COMM_WORLD)->n_proc));
MPI_Comm_rank(SID.COMM_WORLD->comm, &((SID.COMM_WORLD)->My_rank));
// We have duplicated our duplicate mpi communicator - now we can free the
// original duplicate
MPI_Comm_free(&mpi_comm);
#else
SID.COMM_WORLD->comm =NULL;
SID.COMM_WORLD->group =NULL;
SID.COMM_WORLD->n_proc =1;
SID.COMM_WORLD->My_rank=MASTER_RANK;
#endif
// Start total-run-ime timer
(void)time(&(SID.time_start));
// Default max wallclock
SID.max_wallclock=DEFAULT_MAX_WALLCLOCK_TIME;
}
int main(int argc, char *argv[]) {
int n_search;
int i_halo;
char filename_in[SID_MAX_FILENAME_LENGTH];
char group_text_prefix[4];
int n_files;
int k_read;
int l_read;
int * n_particles_i;
int * n_particles_j;
int j_read;
int mode;
int j_halo;
int i_read;
int i_read_start;
int i_read_stop;
SID_fp fp_in;
SID_Init(&argc, &argv, NULL);
// Fetch user inputs
char filename_SSimPL_root[SID_MAX_FILENAME_LENGTH];
strcpy(filename_SSimPL_root, argv[1]);
SID_log("Checking the integrity of the match files for {%s}...", SID_LOG_OPEN | SID_LOG_TIMER, filename_SSimPL_root);
int *n_groups = NULL;
int *n_subgroups = NULL;
for(int i_type = 0; i_type < 2; i_type++) {
// Convert filename_root to filename
switch(i_type) {
case 0:
mode = MATCH_SUBGROUPS;
sprintf(group_text_prefix, "sub");
break;
case 1:
mode = MATCH_GROUPS;
sprintf(group_text_prefix, "");
break;
}
SID_log("Processing %sgroups...", SID_LOG_OPEN | SID_LOG_TIMER, group_text_prefix);
// Set the standard SSiMPL match file path
char filename_root_in[SID_MAX_FILENAME_LENGTH];
sprintf(filename_root_in, "%s/trees/matches/", filename_SSimPL_root);
// Read halo sizes from header file
SID_log("Processing header file...", SID_LOG_OPEN | SID_LOG_TIMER);
sprintf(filename_in, "%s/%sgroup_matches_header.dat", filename_root_in, group_text_prefix);
SID_fopen(filename_in, "r", &fp_in);
SID_fread(&i_read_start, sizeof(int), 1, &fp_in);
SID_fread(&i_read_stop, sizeof(int), 1, &fp_in);
SID_fread(&n_search, sizeof(int), 1, &fp_in);
SID_fread(&n_files, sizeof(int), 1, &fp_in);
int *n_halos = NULL;
switch(mode) {
case MATCH_SUBGROUPS:
n_subgroups = (int *)SID_malloc(sizeof(int) * n_files);
n_halos = n_subgroups;
break;
case MATCH_GROUPS:
n_groups = (int *)SID_malloc(sizeof(int) * n_files);
n_halos = n_groups;
break;
}
if(mode == MATCH_GROUPS)
SID_log("Halo counts (snap/No. groups/No. subgroups):", SID_LOG_OPEN);
for(k_read = 0; k_read < n_files; k_read++) {
SID_fread(&l_read, sizeof(int), 1, &fp_in);
SID_fread(&(n_halos[k_read]), sizeof(int), 1, &fp_in);
SID_fskip(sizeof(int), n_halos[k_read], &fp_in);
if(mode == MATCH_GROUPS) {
int *n_subgroups_group = (int *)SID_malloc(sizeof(int) * n_halos[k_read]);
SID_fread(n_subgroups_group, sizeof(int), n_halos[k_read], &fp_in);
int n_subgroups_test = 0;
for(int i_test = 0; i_test < n_halos[k_read]; i_test++)
n_subgroups_test += n_subgroups_group[i_test];
if(n_subgroups[k_read] != n_subgroups_test)
SID_log("Error in %s header: l_read=%3d k_read=%3d n_subgroups: %d!=%d\n",
SID_LOG_COMMENT,
l_read,
k_read,
n_subgroups[k_read],
n_subgroups_test);
SID_free(SID_FARG n_subgroups_group);
}
if(mode == MATCH_GROUPS)
SID_log("%03d %d %d", SID_LOG_COMMENT, k_read, n_groups[k_read], n_subgroups[k_read]);
}
if(mode == MATCH_GROUPS)
SID_log("", SID_LOG_CLOSE | SID_LOG_NOPRINT);
SID_fclose(&fp_in);
SID_log("Done.", SID_LOG_CLOSE);
SID_log("Processing match files...", SID_LOG_OPEN | SID_LOG_TIMER);
for(int i_read = i_read_start; i_read < i_read_stop; i_read++) {
for(int j_read = GBP_MAX(0, i_read - n_search); j_read < GBP_MIN(i_read_stop, i_read + n_search); j_read++) {
if(i_read != j_read) {
sprintf(filename_in, "%s/%03d/%sgroup_matches_%03d_%03d.dat", filename_root_in, i_read, group_text_prefix, i_read, j_read);
SID_log("Processing {%s}...", SID_LOG_OPEN, filename_in);
// Read header information
int i_read_in;
int j_read_in;
int n_groups_i;
int n_groups_j;
SID_fopen(filename_in, "r", &fp_in);
SID_fread(&i_read_in, sizeof(int), 1, &fp_in);
SID_fread(&j_read_in, sizeof(int), 1, &fp_in);
SID_fread(&n_groups_i, sizeof(int), 1, &fp_in);
SID_fread(&n_groups_j, sizeof(int), 1, &fp_in);
if(i_read_in != i_read || j_read_in != j_read || n_groups_i != n_halos[n_files - i_read_in - 1] ||
n_groups_j != n_halos[n_files - j_read_in - 1])
SID_log("Error in matching file: i_read=%3d j_read=%3d n_i_in=%d n_i=%d n_j_in=%d n_j=%d\n",
SID_LOG_COMMENT,
i_read,
j_read,
n_groups_i,
n_halos[n_files - i_read_in - 1],
n_groups_j,
n_halos[n_files - j_read_in - 1]);
// Read matches
int match;
for(k_read = 0; k_read < n_groups_i; k_read++)
SID_fread(&match, sizeof(int), 1, &fp_in);
// Read indices
size_t indices;
for(k_read = 0; k_read < n_groups_i; k_read++)
SID_fread(&indices, sizeof(size_t), 1, &fp_in);
// Read scores
float score;
for(k_read = 0; k_read < n_groups_i; k_read++)
SID_fread(&score, sizeof(float), 1, &fp_in);
// Close file
SID_fclose(&fp_in);
SID_log("Done.", SID_LOG_CLOSE);
}
}
}
SID_log("Done.", SID_LOG_CLOSE);
SID_log("Done.", SID_LOG_CLOSE);
}
SID_free(SID_FARG n_groups);
SID_free(SID_FARG n_subgroups);
SID_log("Done.", SID_LOG_CLOSE);
SID_Finalize();
}
int main(int argc, char *argv[]){
int n_search;
int i_halo;
char filename_SSimPL_root[MAX_FILENAME_LENGTH];
char filename_in[MAX_FILENAME_LENGTH];
char group_text_prefix[4];
int n_files;
int k_read;
int max_n_groups;
int l_read;
int n_groups;
int j_read;
int mode;
int n_groups_i;
int n_groups_j;
int j_halo;
int match;
int i_read;
int i_read_start;
int i_read_stop;
SID_fp fp_in;
SID_init(&argc,&argv,NULL,NULL);
// Fetch user inputs
strcpy(filename_SSimPL_root,argv[1]);
if(!strcmp(argv[2],"groups") || !strcmp(argv[2],"group"))
mode=MATCH_GROUPS;
else if(!strcmp(argv[2],"subgroups") || !strcmp(argv[2],"subgroup"))
mode=MATCH_SUBGROUPS;
else{
SID_log("Invalid mode selection {%s}. Should be 'group' or 'subgroup'.",SID_LOG_COMMENT,argv[2]);
SID_exit(ERROR_SYNTAX);
}
i_read=atoi(argv[3]);
j_read=atoi(argv[4]);
SID_log("Searching match information for halo #%d in file #%d of {%s}...",SID_LOG_OPEN|SID_LOG_TIMER,i_halo,i_read,filename_SSimPL_root);
// Convert filename_root to filename
switch(mode){
case MATCH_SUBGROUPS:
sprintf(group_text_prefix,"sub");
break;
case MATCH_GROUPS:
sprintf(group_text_prefix,"");
break;
}
// Set the standard SSiMPL match file path
char filename_root_in[MAX_FILENAME_LENGTH];
sprintf(filename_root_in,"%s/trees/matches/",filename_SSimPL_root);
// Set the output file
char filename_base[MAX_FILENAME_LENGTH];
char filename_out[MAX_FILENAME_LENGTH];
sprintf(filename_base,filename_SSimPL_root);
if(!strcmp(&(filename_base[strlen(filename_base)-1]),"/"))
strcpy(&(filename_base[strlen(filename_base)-1]),"\0");
strip_path(filename_base);
sprintf(filename_out,"%s_%d_%d_2way_matches.txt",filename_base,i_read,j_read);
// Read header information
SID_log("Reading header information...",SID_LOG_OPEN);
sprintf(filename_in,"%s/%sgroup_matches_header.dat",filename_root_in,group_text_prefix);
SID_fopen(filename_in,"r",&fp_in);
SID_fread(&i_read_start,sizeof(int),1,&fp_in);SID_log("snap start =%d",SID_LOG_COMMENT,i_read_start);
SID_fread(&i_read_stop, sizeof(int),1,&fp_in);SID_log("snap stop =%d",SID_LOG_COMMENT,i_read_stop);
SID_fread(&n_search, sizeof(int),1,&fp_in);SID_log("search range=%d",SID_LOG_COMMENT,n_search);
SID_fread(&n_files, sizeof(int),1,&fp_in);SID_log("# of files =%d",SID_LOG_COMMENT,n_files);
for(k_read=0,max_n_groups=0;k_read<n_files;k_read++){
SID_fread(&l_read, sizeof(int),1,&fp_in);
SID_fread(&n_groups,sizeof(int),1,&fp_in);
SID_fseek(&fp_in, sizeof(int),n_groups,SID_SEEK_CUR);
if(mode==MATCH_GROUPS)
SID_fseek(&fp_in, sizeof(int),n_groups,SID_SEEK_CUR);
max_n_groups=MAX(max_n_groups,n_groups);
}
SID_log("Max # groups=%d",SID_LOG_COMMENT,max_n_groups);
SID_fclose(&fp_in);
SID_log("Done.",SID_LOG_CLOSE);
// Initialize some arrays
int *n_particles_i =(int *)SID_malloc(sizeof(int) *max_n_groups);
int *n_particles_j =(int *)SID_malloc(sizeof(int) *max_n_groups);
int *match_forward_ids =(int *)SID_malloc(sizeof(int) *max_n_groups);
size_t *match_forward_index =(size_t *)SID_malloc(sizeof(size_t)*max_n_groups);
float *match_forward_score =(float *)SID_malloc(sizeof(float) *max_n_groups);
char *match_forward_2way =(char *)SID_malloc(sizeof(char) *max_n_groups);
int *match_backward_ids =(int *)SID_malloc(sizeof(int) *max_n_groups);
size_t *match_backward_index=(size_t *)SID_malloc(sizeof(size_t)*max_n_groups);
float *match_backward_score=(float *)SID_malloc(sizeof(float) *max_n_groups);
char *match_backward_2way =(char *)SID_malloc(sizeof(char) *max_n_groups);
// Loop over all matching combinations
SID_log("Reading forward matches...",SID_LOG_OPEN|SID_LOG_TIMER);
SID_set_verbosity(SID_SET_VERBOSITY_DEFAULT);
read_matches(filename_root_in,
i_read,
j_read,
max_n_groups,
mode,
&n_groups_i,
&n_groups_j,
n_particles_i,
n_particles_j,
NULL,
NULL,
match_forward_ids,
match_forward_score,
match_forward_index,
match_forward_2way,
FALSE);
SID_log("Done.",SID_LOG_CLOSE);
SID_log("Processing backwards matches...",SID_LOG_OPEN|SID_LOG_TIMER);
read_matches(filename_root_in,
j_read,
i_read,
max_n_groups,
mode,
&n_groups_j,
&n_groups_i,
n_particles_j,
n_particles_i,
NULL,
NULL,
match_backward_ids,
match_backward_score,
match_backward_index,
match_backward_2way,
FALSE);
SID_log("Done.",SID_LOG_CLOSE);
// Open output file
FILE *fp_out;
fp_out=fopen(filename_out,"w");
int i_column=1;
fprintf(fp_out,"# Column (%02d): Halo index for snapshot %d\n", i_column++,i_read);
fprintf(fp_out,"# (%02d): Halo index for snapshot %d\n", i_column++,j_read);
fprintf(fp_out,"# (%02d): No. particles in snapshot %d\n", i_column++,i_read);
fprintf(fp_out,"# (%02d): No. particles in snapshot %d\n", i_column++,j_read);
fprintf(fp_out,"# (%02d): Forward match score\n", i_column++);
fprintf(fp_out,"# (%02d): Forward match score/min match score\n",i_column++);
fprintf(fp_out,"# (%02d): Backward match score\n", i_column++);
fprintf(fp_out,"# (%02d): Backward match score/min match score\n",i_column++);
for(int i_halo=0;i_halo<n_groups_i;i_halo++){
int j_halo=match_forward_ids[i_halo];
if(match_forward_2way[i_halo]){
if(j_halo<0 || j_halo>n_groups_j)
SID_trap_error("There's an invalid match id (ie. %d<0 || %d>%d) attached to a 2-way match!",ERROR_LOGIC,j_halo,j_halo,n_groups_j);
fprintf(fp_out,"%7d %7d %6d %6d %10.3le %10.3le %10.3le %10.3le\n",
i_halo,
j_halo,
n_particles_i[i_halo],
n_particles_j[j_halo],
match_forward_score[i_halo],
match_forward_score[i_halo]/minimum_match_score((double)n_particles_i[i_halo]),
match_backward_score[j_halo],
match_backward_score[j_halo]/minimum_match_score((double)n_particles_j[j_halo]));
}
}
fclose(fp_out);
// Clean-up
SID_free(SID_FARG n_particles_i);
SID_free(SID_FARG n_particles_j);
SID_free(SID_FARG match_forward_ids);
SID_free(SID_FARG match_forward_index);
SID_free(SID_FARG match_forward_score);
SID_free(SID_FARG match_forward_2way);
SID_free(SID_FARG match_backward_ids);
SID_free(SID_FARG match_backward_index);
SID_free(SID_FARG match_backward_score);
SID_free(SID_FARG match_backward_2way);
SID_log("Done.",SID_LOG_CLOSE);
SID_exit(ERROR_NONE);
}
void read_matches(char *filename_in_dir,
int i_read_in,
int j_read_in,
int n_halos_max,
int mode,
int *n_groups_i,
int *n_groups_j,
int *n_particles_i_in,
int *n_particles_j_in,
int *n_sub_group_i_in,
int *n_sub_group_j_in,
int *match_ids,
float *match_score,
size_t *match_index,
char *match_flag_two_way,
int flag_reject_bad_matches){
char group_text_prefix[5];
char filename_in[MAX_FILENAME_LENGTH];
SID_fp fp_in;
int k_read;
int l_read;
int n_search;
int n_matches;
size_t offset;
int flag_continue;
int i_read_file;
int j_read_file;
int n_groups_file;
int n_groups_file_1;
int n_groups_file_2;
int n_groups;
int n_groups_i_file;
int n_groups_j_file;
int *n_sub_group_i;
int *n_sub_group_j;
int flag_alloc_n_sub_i=FALSE;
int flag_alloc_n_sub_j=FALSE;
if(i_read_in==j_read_in)
SID_trap_error("i_read=j_read in read_matches",ERROR_LOGIC);
switch(mode){
case MATCH_SUBGROUPS:
sprintf(group_text_prefix,"sub");
break;
case MATCH_GROUPS:
sprintf(group_text_prefix,"");
// We need n_subgroups arrays for removal of bad groups
// if they have not been passed to us.
if(n_sub_group_i_in==NULL){
flag_alloc_n_sub_i=TRUE;
n_sub_group_i =(int *)SID_malloc(sizeof(int)*n_halos_max);
}
else
n_sub_group_i=n_sub_group_i_in;
if(n_sub_group_j_in==NULL){
flag_alloc_n_sub_j=TRUE;
n_sub_group_j =(int *)SID_malloc(sizeof(int)*n_halos_max);
}
else
n_sub_group_j=n_sub_group_j_in;
break;
}
// Since we need the particle counts for the goodness of match criterion,
// create temporary arrays in case we weren't passed an array for them.
int *n_particles_i=n_particles_i_in;
int *n_particles_j=n_particles_j_in;
// 1) We always need n_particles_i
int flag_alloc_n_particles_i=FALSE;
int flag_alloc_n_particles_j=FALSE;
if(n_particles_i==NULL)
flag_alloc_n_particles_i=TRUE;
if(n_particles_j==NULL)
flag_alloc_n_particles_j=TRUE;
// 2) We need n_particles_j if doing 2-way checks
if(match_flag_two_way!=NULL && n_particles_j==NULL)
flag_alloc_n_particles_j=TRUE;
// Read the needed info from the header file
int i_read;
int i_read_start;
int i_read_stop;
int n_search_total;
int n_files;
int n_groups_in;
int counter=0;
char filename_in_name[256];
strcpy(filename_in_name,filename_in_dir);
strip_path(filename_in_name);
sprintf(filename_in,"%s/%sgroup_matches_header.dat",filename_in_dir,group_text_prefix);
SID_fopen(filename_in,"r",&fp_in);
SID_fread(&i_read_start, sizeof(int),1,&fp_in);
SID_fread(&i_read_stop, sizeof(int),1,&fp_in);
SID_fread(&n_search_total,sizeof(int),1,&fp_in);
SID_fread(&n_files, sizeof(int),1,&fp_in);
for(i_read=i_read_stop;i_read>=i_read_start && counter<2;i_read--){
SID_fread(&i_read_file, sizeof(int),1,&fp_in);
if(i_read_file==i_read_in){
SID_fread(n_groups_i,sizeof(int),1,&fp_in);
if((*n_groups_i)>0){
// Create a temporary array for n_particles_i if we were not passed one
if(flag_alloc_n_particles_i)
n_particles_i=(int *)SID_malloc(sizeof(int)*(*n_groups_i));
if(n_particles_i!=NULL)
SID_fread_ordered(n_particles_i,sizeof(int),(size_t)(*n_groups_i),&fp_in);
else
SID_fskip(sizeof(int),(*n_groups_i),&fp_in);
if(mode==MATCH_GROUPS){
if(n_sub_group_i!=NULL)
SID_fread_ordered(n_sub_group_i,sizeof(int),(size_t)(*n_groups_i),&fp_in);
else
SID_fskip(sizeof(int),(*n_groups_i),&fp_in);
}
}
counter++;
}
else if(i_read_file==j_read_in){
SID_fread(n_groups_j,sizeof(int),1,&fp_in);
if((*n_groups_j)>0){
if(flag_alloc_n_particles_j)
n_particles_j=(int *)SID_malloc(sizeof(int)*(*n_groups_j));
if(n_particles_j!=NULL)
SID_fread_ordered(n_particles_j,sizeof(int),(size_t)(*n_groups_j),&fp_in);
else
SID_fskip(sizeof(int),(*n_groups_j),&fp_in);
if(mode==MATCH_GROUPS){
if(n_sub_group_j!=NULL)
SID_fread_ordered(n_sub_group_j,sizeof(int),(size_t)(*n_groups_j),&fp_in);
else
SID_fskip(sizeof(int),(*n_groups_j),&fp_in);
}
}
counter++;
}
else{
SID_fread(&n_groups_in,sizeof(int),1,&fp_in);
if(n_groups_in>0){
SID_fskip(sizeof(int),n_groups_in,&fp_in);
if(mode==MATCH_GROUPS)
SID_fskip(sizeof(int),n_groups_in,&fp_in);
}
}
}
SID_fclose(&fp_in);
// Read the matching file
char filename_cat1[256];
char filename_cat2[256];
char filename_in_dir_snap[256];
sprintf(filename_cat1,"%03d",i_read_in);
sprintf(filename_cat2,"%03d",j_read_in);
sprintf(filename_in_dir_snap,"%s/%s",filename_in_dir,filename_cat1);
if(filename_in_dir!=NULL)
sprintf(filename_in,"%s/%sgroup_matches_%s_%s.dat",filename_in_dir_snap,group_text_prefix,filename_cat1,filename_cat2);
else
sprintf(filename_in,"%s_%sgroup_matches_%s_%s.dat",filename_in_name, group_text_prefix,filename_cat1,filename_cat2);
SID_fopen(filename_in,"r",&fp_in);
SID_fread(&i_read_file,sizeof(int),1,&fp_in);
SID_fread(&j_read_file,sizeof(int),1,&fp_in);
SID_fread(n_groups_i, sizeof(int),1,&fp_in);
SID_fread(n_groups_j, sizeof(int),1,&fp_in);
// Read matching data
SID_fread(match_ids, sizeof(int), (*n_groups_i),&fp_in);
SID_fread(match_index,sizeof(size_t),(*n_groups_i),&fp_in);
SID_fread(match_score,sizeof(float), (*n_groups_i),&fp_in);
SID_fclose(&fp_in);
// If one of the catalogs is empty, set to no-match defaults
if((*n_groups_i)<=0 || (*n_groups_j)<=0){
for(int i_halo=0;i_halo<(*n_groups_i);i_halo++){
match_ids[i_halo] =-1;
match_score[i_halo]= 0.;
}
if(match_flag_two_way!=NULL){
for(int i_halo=0;i_halo<(*n_groups_i);i_halo++)
match_flag_two_way[i_halo]=FALSE;
}
}
else{
// If we are reading groups, nullify all matches
// between halos with no substructures.
int i_halo;
if(mode==MATCH_GROUPS){
size_t *match_index_temp;
for(i_halo=0;i_halo<(*n_groups_i);i_halo++){
if(n_sub_group_i[i_halo]<=0){
match_ids[i_halo] =-1;
match_score[i_halo]= 0.;
}
else if(match_ids[i_halo]>=0 && (*n_groups_j)>0){
if(n_sub_group_j[match_ids[i_halo]]<=0){
match_ids[i_halo] =-1;
match_score[i_halo]= 0.;
}
}
}
merge_sort(match_ids,(size_t)(*n_groups_i),&match_index_temp,SID_INT,SORT_COMPUTE_INDEX,SORT_COMPUTE_NOT_INPLACE);
memcpy(match_index,match_index_temp,(*n_groups_i)*sizeof(size_t));
SID_free(SID_FARG match_index_temp);
}
// Apply a goodness-of-fit criterion and check that the maximum allowed score has not been exceeded
for(i_halo=0;i_halo<(*n_groups_i);i_halo++){
if(match_ids[i_halo]>=0){
if(flag_reject_bad_matches && !check_validity_of_match(n_particles_i[i_halo],match_score[i_halo]))
match_ids[i_halo]=-1;
}
}
// Since we may have changed some matches with the goodness
// of fit criterion, we need to re-perform the sort
size_t *match_index_temp=NULL;
merge_sort(match_ids,(size_t)(*n_groups_i),&match_index_temp,SID_INT,SORT_COMPUTE_INDEX,SORT_COMPUTE_NOT_INPLACE);
memcpy(match_index,match_index_temp,(*n_groups_i)*sizeof(size_t));
SID_free(SID_FARG match_index_temp);
// Determine if the matches are two-way if we have been asked to check this
if(match_flag_two_way!=NULL && (*n_groups_i)>0){
// We're going to need the particle counts in the target catalog for checking the goodness of return matches. Make sure we have them.
if(n_particles_j==NULL)
SID_trap_error("Target catalog halo sizes are not defined in read_matches() but are needed for checking two-way match flags.",ERROR_LOGIC);
// Flip the file names for reading the return matches
sprintf(filename_in_dir_snap,"%s/%s",filename_in_dir,filename_cat2);
if(filename_in_dir!=NULL)
sprintf(filename_in,"%s/%sgroup_matches_%s_%s.dat",filename_in_dir_snap,group_text_prefix,filename_cat2,filename_cat1);
else
sprintf(filename_in,"%s_%sgroup_matches_%s_%s.dat",filename_in_name, group_text_prefix,filename_cat2,filename_cat1);
// Open two files, one for reading the IDs and one for matching the scores of the matching file
int i_read_file_check;
int j_read_file_check;
int n_groups_i_check;
int n_groups_j_check;
SID_fp fp_check_ids;
SID_fp fp_check_score;
SID_fopen(filename_in,"r",&fp_check_ids);
SID_fopen(filename_in,"r",&fp_check_score);
SID_fread(&j_read_file_check,sizeof(int),1,&fp_check_ids);
SID_fread(&i_read_file_check,sizeof(int),1,&fp_check_ids);
SID_fread(&n_groups_j_check, sizeof(int),1,&fp_check_ids);
SID_fread(&n_groups_i_check, sizeof(int),1,&fp_check_ids);
// Check that we have the right files
if(n_groups_i_check!=(*n_groups_i))
SID_trap_error("Source halo counts don't match (ie. %d!=%d) in two-way check in read_matches().",ERROR_LOGIC,n_groups_i_check,(*n_groups_i));
if(n_groups_j_check!=(*n_groups_j))
SID_trap_error("Target halo counts don't match (ie. %d!=%d) in two-way check in read_matches().",ERROR_LOGIC,n_groups_j_check,(*n_groups_j));
if(i_read_file_check!=i_read_file)
SID_trap_error("Source file numbers don't match (ie. %d!=%d) in two-way check in read_matches().",ERROR_LOGIC,i_read_file_check,i_read_file);
if(j_read_file_check!=j_read_file)
SID_trap_error("Target file numbers don't match (ie. %d!=%d) in two-way check in read_matches().",ERROR_LOGIC,j_read_file_check,j_read_file);
// Skip to the beginning of the relevant block for the score-reading file pointer
SID_fskip(sizeof(int), 4, &fp_check_score); // header
SID_fskip(sizeof(int), (*n_groups_j),&fp_check_score); // ids
SID_fskip(sizeof(size_t),(*n_groups_j),&fp_check_score); // indices
// Set everything to being a one-way match unless subsequently changed
for(i_halo=0;i_halo<(*n_groups_i);i_halo++)
match_flag_two_way[i_halo]=FALSE;
// Read matching data in buffered chunks
int n_good =0;
int n_2way =0;
int n_buffer =1024*1024;
int n_chunk =0;
int n_remaining =(*n_groups_j);
int *buffer_ids =(int *)SID_malloc(sizeof(int) *n_buffer);
float *buffer_score=(float *)SID_malloc(sizeof(float)*n_buffer);
for(int j_halo=0;n_remaining>0;n_remaining-=n_chunk){
n_chunk=MIN(n_remaining,n_buffer);
SID_fread(buffer_ids, sizeof(int), n_chunk,&fp_check_ids);
SID_fread(buffer_score,sizeof(float),n_chunk,&fp_check_score);
for(int k_halo=0;k_halo<n_chunk;k_halo++,j_halo++){
int id_i=buffer_ids[k_halo];
if(id_i>=0){
if(id_i>=(*n_groups_i))
SID_trap_error("Allowed matching index has been exceeded i(ie %d>=%d) while determining two-way match flags.",
ERROR_LOGIC,id_i,(*n_groups_i));
// Do this check first to avoid having to check if both needed n_particles_* references are defined
int id_j=match_ids[id_i];
if(id_j==j_halo){
if(!flag_reject_bad_matches || check_validity_of_match(n_particles_j[j_halo],buffer_score[k_halo])){
match_flag_two_way[id_i]=TRUE;
n_2way++;
}
n_good++;
}
}
}
}
//SID_log("n_good=%d n_2way=%d",SID_LOG_COMMENT,n_good,n_2way);
SID_fclose(&fp_check_ids);
SID_fclose(&fp_check_score);
SID_free(SID_FARG buffer_ids);
SID_free(SID_FARG buffer_score);
}
}
// If any of these arrays are temporary, free them.
if(flag_alloc_n_sub_i)
SID_free(SID_FARG n_sub_group_i);
if(flag_alloc_n_sub_j)
SID_free(SID_FARG n_sub_group_j);
if(flag_alloc_n_particles_i)
SID_free(SID_FARG n_particles_i);
if(flag_alloc_n_particles_j)
SID_free(SID_FARG n_particles_j);
}
int main(int argc, char *argv[]) {
int n_search;
int n_files;
int k_read;
int max_n_groups;
int l_read;
int * n_particles_i;
int * n_particles_j;
int n_groups_i;
int n_groups_j;
int * match_ids;
float * match_score;
size_t *match_index;
int j_halo;
int match;
int i_read;
int i_read_start;
int i_read_stop;
SID_fp fp_in;
SID_Init(&argc, &argv, NULL);
// Fetch user inputs
if(argc != 12)
SID_exit_error("Invalid Syntax.", SID_ERROR_SYNTAX);
char filename_SSimPL_root[SID_MAX_FILENAME_LENGTH];
char filename_halos_root[SID_MAX_FILENAME_LENGTH];
char filename_trees_root[SID_MAX_FILENAME_LENGTH];
char filename_out_root[SID_MAX_FILENAME_LENGTH];
strcpy(filename_SSimPL_root, argv[1]);
strcpy(filename_halos_root, argv[2]);
strcpy(filename_trees_root, argv[3]);
double x_cen = (double)atof(argv[4]);
double y_cen = (double)atof(argv[5]);
double z_cen = (double)atof(argv[6]);
double radius = (double)atof(argv[7]);
double z_min_in = (double)atof(argv[8]);
double z_max_in = (double)atof(argv[9]);
double M_min = (double)atof(argv[10]);
strcpy(filename_out_root, argv[11]);
double radius2 = radius * radius;
SID_log("Query trees for sphere (x,y,z,r)=(%.2lf,%.2lf,%.2lf,%.2lf) between z=%.2lf and z=%.2lf...",
SID_LOG_OPEN,
x_cen,
y_cen,
z_cen,
radius,
z_min_in,
z_max_in);
char filename_catalog_root[SID_MAX_FILENAME_LENGTH];
sprintf(filename_catalog_root, "%s/catalogs/%s", filename_SSimPL_root, filename_halos_root);
// Read tree header information
tree_info *trees;
char filename_file_root[SID_MAX_FILENAME_LENGTH];
sprintf(filename_file_root, "%s/trees/%s", filename_SSimPL_root, filename_trees_root);
SID_set_verbosity(SID_SET_VERBOSITY_RELATIVE, 0);
init_trees_read(filename_SSimPL_root, filename_halos_root, filename_trees_root, TREE_READ_HEADER_ONLY, &trees);
SID_set_verbosity(SID_SET_VERBOSITY_DEFAULT);
// Turn given redshift range into snapshot range
int i_snap_min_z = find_treesnap_z(trees, z_max_in);
int i_snap_max_z = find_treesnap_z(trees, z_min_in);
SID_log("z=%.2lf -> snapshot=%d", SID_LOG_COMMENT, z_min_in, trees->snap_list[i_snap_max_z]);
SID_log("z=%.2lf -> snapshot=%d", SID_LOG_COMMENT, z_max_in, trees->snap_list[i_snap_min_z]);
// Perform query
int n_groups_list = 0;
int n_subgroups_list = 0;
int *group_list = NULL;
int *subgroup_list = NULL;
for(int i_pass = 0; i_pass < 3; i_pass++) {
if(i_pass == 0)
SID_log("Counting halos to be queried...", SID_LOG_OPEN | SID_LOG_TIMER);
else if(i_pass == 1)
SID_log("Identifying halos to be queried...", SID_LOG_OPEN | SID_LOG_TIMER);
else if(i_pass == 2)
SID_log("Performing query...", SID_LOG_OPEN | SID_LOG_TIMER);
// Write headers
if(i_pass == 2) {
for(int i_type = 0; i_type < 2; i_type++) {
int n_list = 0;
int *halo_list = NULL;
if(i_type == 0) {
n_list = n_groups_list;
halo_list = group_list;
} else {
n_list = n_subgroups_list;
halo_list = subgroup_list;
}
for(int i_list = 0; i_list < n_list; i_list++) {
int i_column = 1;
char filename_out[SID_MAX_FILENAME_LENGTH];
if(i_type == 0)
sprintf(filename_out, "%s_group_%09d.txt", filename_out_root, halo_list[i_list]);
else
sprintf(filename_out, "%s_subgroup_%09d.txt", filename_out_root, halo_list[i_list]);
FILE *fp_out = fopen(filename_out, "w");
fprintf(fp_out, "# Column (%02d): Halo expansion factor\n", i_column++);
fprintf(fp_out, "# (%02d): Halo redshift\n", i_column++);
fprintf(fp_out, "# (%02d): Halo snapshot\n", i_column++);
fprintf(fp_out, "# (%02d): Halo index\n", i_column++);
fprintf(fp_out, "# (%02d): Halo ID\n", i_column++);
fprintf(fp_out, "# (%02d): Halo log10(M_vir [M_sol/h])\n", i_column++);
fprintf(fp_out, "# (%02d): Halo n_particles\n", i_column++);
fprintf(fp_out, "# (%02d): Halo n_particles_peak\n", i_column++);
fprintf(fp_out, "# (%02d): Halo x [Mpc/h])\n", i_column++);
fprintf(fp_out, "# (%02d): Halo y [Mpc/h])\n", i_column++);
fprintf(fp_out, "# (%02d): Halo z [Mpc/h])\n", i_column++);
fprintf(fp_out, "# (%02d): Halo radius [Mpc/h])\n", i_column++);
fprintf(fp_out, "# (%02d): Halo tree ID\n", i_column++);
fprintf(fp_out, "# (%02d): Descendant file offset\n", i_column++);
fprintf(fp_out, "# (%02d): Descendant snapshot\n", i_column++);
fprintf(fp_out, "# (%02d): Descendant index\n", i_column++);
fprintf(fp_out, "# (%02d): Descendant ID\n", i_column++);
fprintf(fp_out, "# (%02d): Bridge forematch snapshot\n", i_column++);
fprintf(fp_out, "# (%02d): Bridge forematch index\n", i_column++);
fprintf(fp_out, "# (%02d): Bridge backmatch snapshot\n", i_column++);
fprintf(fp_out, "# (%02d): Bridge backmatch index\n", i_column++);
fprintf(fp_out, "# (%02d): Halo type\n", i_column++);
fprintf(fp_out, "# (%02d): Halo type string\n", i_column++);
if(i_type == 1) {
fprintf(fp_out, "# (%02d): Group index\n", i_column++);
fprintf(fp_out, "# (%02d): Group ID\n", i_column++);
fprintf(fp_out, "# (%02d): Subgroup index\n", i_column++);
fprintf(fp_out, "# (%02d): FoF Centre dx [Mpc/h])\n", i_column++);
fprintf(fp_out, "# (%02d): FoF Centre dy [Mpc/h])\n", i_column++);
fprintf(fp_out, "# (%02d): FoF Centre dz [Mpc/h])\n", i_column++);
}
fclose(fp_out);
}
}
}
// Set the snapshot range we need to scan
int i_snap_start;
int i_snap_stop;
if(i_pass < 2) {
i_snap_start = i_snap_min_z;
i_snap_stop = i_snap_max_z;
} else {
i_snap_start = 0;
i_snap_stop = trees->n_snaps - 1;
}
// Loop over the range of snapshots
int i_list = 0;
for(int i_snap = i_snap_start; i_snap <= i_snap_stop; i_snap++) {
// Get the snapshot
int snapshot = trees->snap_list[i_snap];
if(i_pass == 2)
SID_log("Processing snapshot %03d...", SID_LOG_OPEN, snapshot);
// Open properties for this snapshot
fp_catalog_info fp_properties_groups;
fp_catalog_info fp_properties_subgroups;
halo_properties_info properties_groups;
halo_properties_info properties_subgroups;
fopen_catalog(filename_catalog_root, snapshot, READ_CATALOG_GROUPS | READ_CATALOG_PROPERTIES, &fp_properties_groups);
fopen_catalog(filename_catalog_root, snapshot, READ_CATALOG_SUBGROUPS | READ_CATALOG_PROPERTIES, &fp_properties_subgroups);
// Open horizontal trees for this snapshot
SID_fp fp_in_trees;
SID_fp fp_in_bridge_forematch;
SID_fp fp_in_bridge_backmatch;
char filename_in[SID_MAX_FILENAME_LENGTH];
sprintf(filename_in, "%s/trees/%s/horizontal/trees/horizontal_trees_%03d.dat", filename_SSimPL_root, filename_trees_root, snapshot);
SID_fopen(filename_in, "r", &fp_in_trees);
sprintf(filename_in,
"%s/trees/%s/horizontal/trees/horizontal_trees_forematch_pointers_%03d.dat",
filename_SSimPL_root,
filename_trees_root,
snapshot);
SID_fopen(filename_in, "r", &fp_in_bridge_forematch);
sprintf(filename_in,
"%s/trees/%s/horizontal/trees/horizontal_trees_backmatch_pointers_%03d.dat",
filename_SSimPL_root,
filename_trees_root,
snapshot);
SID_fopen(filename_in, "r", &fp_in_bridge_backmatch);
// Read trees header
int n_step_in;
int n_search_in;
int n_groups;
int n_subgroups;
int n_groups_max_in;
int n_subgroups_max_in;
int n_trees_subgroup_in;
int n_trees_group_in;
SID_fread_all(&n_step_in, sizeof(int), 1, &fp_in_trees);
SID_fread_all(&n_search_in, sizeof(int), 1, &fp_in_trees);
SID_fread_all(&n_groups, sizeof(int), 1, &fp_in_trees);
SID_fread_all(&n_subgroups, sizeof(int), 1, &fp_in_trees);
SID_fread_all(&n_groups_max_in, sizeof(int), 1, &fp_in_trees);
SID_fread_all(&n_subgroups_max_in, sizeof(int), 1, &fp_in_trees);
SID_fread_all(&n_trees_subgroup_in, sizeof(int), 1, &fp_in_trees);
SID_fread_all(&n_trees_group_in, sizeof(int), 1, &fp_in_trees);
SID_fskip(sizeof(int), 8, &fp_in_bridge_forematch);
SID_fskip(sizeof(int), 8, &fp_in_bridge_backmatch);
// Scan through the trees
int i_subgroup = 0;
for(int i_group = 0; i_group < n_groups; i_group++) {
// Read group
int group_id;
int group_type;
int group_descendant_id;
int group_tree_id;
int group_file_offset;
int group_index;
int group_n_particles_peak;
int n_subgroups_group;
int group_forematch_id;
int group_forematch_first_file;
int group_forematch_first_index;
float group_forematch_first_score;
int group_forematch_default_file;
int group_forematch_default_index;
float group_forematch_default_score;
int group_forematch_best_file;
int group_forematch_best_index;
float group_forematch_best_score;
float group_forematch_score_prog;
int group_backmatch_id;
int group_backmatch_file;
int group_backmatch_index;
float group_backmatch_score;
float group_backmatch_score_prog;
SID_fread_all(&group_id, sizeof(int), 1, &fp_in_trees);
SID_fread_all(&group_type, sizeof(int), 1, &fp_in_trees);
SID_fread_all(&group_descendant_id, sizeof(int), 1, &fp_in_trees);
SID_fread_all(&group_tree_id, sizeof(int), 1, &fp_in_trees);
SID_fread_all(&group_file_offset, sizeof(int), 1, &fp_in_trees);
SID_fread_all(&group_index, sizeof(int), 1, &fp_in_trees);
SID_fread_all(&group_n_particles_peak, sizeof(int), 1, &fp_in_trees);
SID_fread_all(&n_subgroups_group, sizeof(int), 1, &fp_in_trees);
SID_fread_all(&group_forematch_id, sizeof(int), 1, &fp_in_bridge_forematch);
SID_fread_all(&group_forematch_first_file, sizeof(int), 1, &fp_in_bridge_forematch);
SID_fread_all(&group_forematch_first_index, sizeof(int), 1, &fp_in_bridge_forematch);
SID_fread_all(&group_forematch_first_score, sizeof(float), 1, &fp_in_bridge_forematch);
SID_fread_all(&group_forematch_default_file, sizeof(int), 1, &fp_in_bridge_forematch);
SID_fread_all(&group_forematch_default_index, sizeof(int), 1, &fp_in_bridge_forematch);
SID_fread_all(&group_forematch_default_score, sizeof(float), 1, &fp_in_bridge_forematch);
SID_fread_all(&group_forematch_best_file, sizeof(int), 1, &fp_in_bridge_forematch);
SID_fread_all(&group_forematch_best_index, sizeof(int), 1, &fp_in_bridge_forematch);
SID_fread_all(&group_forematch_best_score, sizeof(float), 1, &fp_in_bridge_forematch);
SID_fread_all(&group_forematch_score_prog, sizeof(float), 1, &fp_in_bridge_forematch);
SID_fread_all(&group_backmatch_id, sizeof(int), 1, &fp_in_bridge_backmatch);
SID_fread_all(&group_backmatch_file, sizeof(int), 1, &fp_in_bridge_backmatch);
SID_fread_all(&group_backmatch_index, sizeof(int), 1, &fp_in_bridge_backmatch);
SID_fread_all(&group_backmatch_score, sizeof(float), 1, &fp_in_bridge_backmatch);
SID_fread_all(&group_backmatch_score_prog, sizeof(float), 1, &fp_in_bridge_backmatch);
SID_fskip(sizeof(int), 1, &fp_in_bridge_forematch); // skip subhalo count
SID_fskip(sizeof(int), 1, &fp_in_bridge_backmatch); // skip subhalo count
fread_catalog_file(&fp_properties_groups, NULL, NULL, &properties_groups, NULL, i_group);
// Process group
process_local(trees,
i_pass,
filename_out_root,
radius2,
M_min,
i_snap,
i_group,
0,
i_group,
group_id,
group_file_offset,
group_type,
group_n_particles_peak,
group_tree_id,
group_index,
group_descendant_id,
group_forematch_first_index,
group_forematch_first_file,
group_backmatch_index,
group_backmatch_file,
group_id,
&properties_groups,
NULL,
&n_groups_list,
group_list,
x_cen,
y_cen,
z_cen);
for(int j_subgroup = 0; j_subgroup < n_subgroups_group; i_subgroup++, j_subgroup++) {
// Read subgroup
int subgroup_id;
int subgroup_type;
int subgroup_descendant_id;
int subgroup_tree_id;
int subgroup_file_offset;
int subgroup_index;
int subgroup_n_particles_peak;
int subgroup_forematch_id;
int subgroup_forematch_first_file;
int subgroup_forematch_first_index;
float subgroup_forematch_first_score;
int subgroup_forematch_default_file;
int subgroup_forematch_default_index;
float subgroup_forematch_default_score;
int subgroup_forematch_best_file;
int subgroup_forematch_best_index;
float subgroup_forematch_best_score;
float subgroup_forematch_score_prog;
int subgroup_backmatch_id;
int subgroup_backmatch_file;
int subgroup_backmatch_index;
float subgroup_backmatch_score;
float subgroup_backmatch_score_prog;
SID_fread_all(&subgroup_id, sizeof(int), 1, &fp_in_trees);
SID_fread_all(&subgroup_type, sizeof(int), 1, &fp_in_trees);
SID_fread_all(&subgroup_descendant_id, sizeof(int), 1, &fp_in_trees);
SID_fread_all(&subgroup_tree_id, sizeof(int), 1, &fp_in_trees);
SID_fread_all(&subgroup_file_offset, sizeof(int), 1, &fp_in_trees);
SID_fread_all(&subgroup_index, sizeof(int), 1, &fp_in_trees);
SID_fread_all(&subgroup_n_particles_peak, sizeof(int), 1, &fp_in_trees);
SID_fread_all(&subgroup_forematch_id, sizeof(int), 1, &fp_in_bridge_forematch);
SID_fread_all(&subgroup_forematch_first_file, sizeof(int), 1, &fp_in_bridge_forematch);
SID_fread_all(&subgroup_forematch_first_index, sizeof(int), 1, &fp_in_bridge_forematch);
SID_fread_all(&subgroup_forematch_first_score, sizeof(float), 1, &fp_in_bridge_forematch);
SID_fread_all(&subgroup_forematch_default_file, sizeof(int), 1, &fp_in_bridge_forematch);
SID_fread_all(&subgroup_forematch_default_index, sizeof(int), 1, &fp_in_bridge_forematch);
SID_fread_all(&subgroup_forematch_default_score, sizeof(float), 1, &fp_in_bridge_forematch);
SID_fread_all(&subgroup_forematch_best_file, sizeof(int), 1, &fp_in_bridge_forematch);
SID_fread_all(&subgroup_forematch_best_index, sizeof(int), 1, &fp_in_bridge_forematch);
SID_fread_all(&subgroup_forematch_best_score, sizeof(float), 1, &fp_in_bridge_forematch);
SID_fread_all(&subgroup_forematch_score_prog, sizeof(float), 1, &fp_in_bridge_forematch);
SID_fread_all(&subgroup_backmatch_id, sizeof(int), 1, &fp_in_bridge_backmatch);
SID_fread_all(&subgroup_backmatch_file, sizeof(int), 1, &fp_in_bridge_backmatch);
SID_fread_all(&subgroup_backmatch_index, sizeof(int), 1, &fp_in_bridge_backmatch);
SID_fread_all(&subgroup_backmatch_score, sizeof(float), 1, &fp_in_bridge_backmatch);
SID_fread_all(&subgroup_backmatch_score_prog, sizeof(float), 1, &fp_in_bridge_backmatch);
fread_catalog_file(&fp_properties_subgroups, NULL, NULL, &properties_subgroups, NULL, i_subgroup);
// Process subgroup
process_local(trees,
i_pass,
filename_out_root,
radius2,
M_min,
i_snap,
i_subgroup,
j_subgroup,
i_group,
subgroup_id,
subgroup_file_offset,
subgroup_type,
subgroup_n_particles_peak,
subgroup_tree_id,
subgroup_index,
subgroup_descendant_id,
subgroup_forematch_first_index,
subgroup_forematch_first_file,
subgroup_backmatch_index,
subgroup_backmatch_file,
group_id,
&properties_subgroups,
&properties_groups,
&n_subgroups_list,
subgroup_list,
x_cen,
y_cen,
z_cen);
}
}
fclose_catalog(&fp_properties_groups);
fclose_catalog(&fp_properties_subgroups);
SID_fclose(&fp_in_trees);
SID_fclose(&fp_in_bridge_forematch);
SID_fclose(&fp_in_bridge_backmatch);
if(i_pass == 2)
SID_log("Done.", SID_LOG_CLOSE);
} // i_snap
if(i_pass == 0) {
group_list = (int *)SID_malloc(sizeof(int) * n_groups_list);
subgroup_list = (int *)SID_malloc(sizeof(int) * n_subgroups_list);
n_groups_list = 0;
n_subgroups_list = 0;
} else if(i_pass == 1) {
SID_log("(%d groups and %d subgroups found)...", SID_LOG_CONTINUE, n_groups_list, n_subgroups_list);
// Write list files
for(int i_type = 0; i_type < 2; i_type++) {
char filename_out[SID_MAX_FILENAME_LENGTH];
int n_list = 0;
int *halo_list = NULL;
if(i_type == 0) {
sprintf(filename_out, "%s_group_list.txt", filename_out_root);
n_list = n_groups_list;
halo_list = group_list;
} else {
sprintf(filename_out, "%s_subgroup_list.txt", filename_out_root);
n_list = n_subgroups_list;
halo_list = subgroup_list;
}
FILE *fp_out = fopen(filename_out, "w");
fprintf(fp_out, "# Halo IDs in list of tree tracks with base {%s}\n", filename_out_root);
for(int i_list = 0; i_list < n_list; i_list++)
fprintf(fp_out, "%d\n", halo_list[i_list]);
fclose(fp_out);
}
}
SID_log("Done.", SID_LOG_CLOSE);
}
// Clean-up
SID_free(SID_FARG group_list);
SID_free(SID_FARG subgroup_list);
free_trees(&trees);
SID_log("Done.", SID_LOG_CLOSE);
SID_Finalize();
}
size_t SID_fread_chunked_ordered(void *buffer,
size_t n_x_read_local,
SID_fp *fp){
int i_chunk;
int i_group;
int i_rank;
size_t i_x_offset_local;
size_t n_x_read_local_bcast;
size_t i_x_read_chunk;
size_t i_x_offset_global;
size_t i_x_chunk;
size_t n_skip;
size_t n_x_chunk;
size_t n_x_chunk_max;
size_t header_size;
size_t r_val=0;
char filename_chunk[256];
// Operates the same way as SID_fread_chunked() except i_x_offset_local is
// computed here under the assumption that reads are done in order by rank
i_x_offset_local=0;
#if USE_MPI
for(i_rank=0;i_rank<SID.n_proc;i_rank++){
n_x_read_local_bcast=n_x_read_local;
SID_Bcast(&n_x_read_local_bcast,sizeof(size_t),i_rank,SID.COMM_WORLD);
if(i_rank<SID.My_rank)
i_x_offset_local+=n_x_read_local_bcast;
}
#endif
i_x_offset_global=fp->last_item;
for(i_chunk=0,i_x_read_chunk=0,i_x_chunk=i_x_offset_local+i_x_offset_global;
i_chunk<fp->chunked_header.n_chunk;
i_chunk++){
if(fp->i_x_start_chunk[i_chunk]<=i_x_chunk && fp->i_x_last_chunk[i_chunk]>=i_x_chunk){
n_skip =i_x_chunk-fp->i_x_start_chunk[i_chunk];
n_x_chunk=MIN(n_x_read_local-i_x_read_chunk,fp->i_x_step_chunk[i_chunk]-n_skip);
}
else{
n_x_chunk=0;
n_skip =0;
}
SID_Allreduce(&n_x_chunk,&n_x_chunk_max,1,SID_SIZE_T,SID_MAX,SID.COMM_WORLD);
if(n_x_chunk_max>0){
sprintf(filename_chunk,"%s.%d",fp->filename_root,i_chunk);
#if !USE_MPI_IO
for(i_group=0;i_group<SID.n_proc;i_group++){
if(SID.My_group==i_group && n_x_chunk>0){
#endif
SID_fopen(filename_chunk,"r",fp);
if(n_x_chunk>0){
SID_fseek(fp,
1,
fp->header_offset[i_chunk]+n_skip*fp->chunked_header.item_size,
SID_SEEK_SET);
SID_fread((char *)buffer+i_x_read_chunk*fp->chunked_header.item_size,
fp->chunked_header.item_size,
n_x_chunk,
fp);
i_x_chunk +=n_x_chunk;
i_x_read_chunk+=n_x_chunk;
}
SID_fclose(fp);
#if !USE_MPI_IO
}
SID_Barrier(SID.COMM_WORLD);
}
#endif
}
}
SID_Allreduce(&i_x_chunk,&(fp->last_item),1,SID_SIZE_T,SID_MAX,SID.COMM_WORLD);
//fp->last_item--;
return(r_val);
}
void read_trees_horizontal(void **groups_in,
int * n_groups_in,
void **subgroups_in,
int * n_subgroups_in,
int * n_subgroups_group,
int * n_trees_subgroup_in,
int * n_trees_group_in,
int i_file, // tree snapshot index
int i_read, // actual snapshot index
int j_file,
int n_wrap,
char * filename_output_dir,
int mode) {
char filename_output_dir_horizontal[SID_MAX_FILENAME_LENGTH];
char filename_output_dir_horizontal_trees[SID_MAX_FILENAME_LENGTH];
char filename_in[SID_MAX_FILENAME_LENGTH];
char filename_output_file_root[SID_MAX_FILENAME_LENGTH];
SID_fp fp_in;
SID_log("Reading horizontal trees for snapshot #%03d...", SID_LOG_OPEN, i_read);
// Parse the mode and set things up accordingly
if(SID_CHECK_BITFIELD_SWITCH(mode, TREE_HORIZONTAL_STORE_EXTENDED) &&
SID_CHECK_BITFIELD_SWITCH(mode, TREE_HORIZONTAL_STORE_GHOSTS))
SID_exit_error("Too many storage modes chosen in read_trees_horizontal.", SID_ERROR_LOGIC);
int flag_read_extended = SID_CHECK_BITFIELD_SWITCH(mode, TREE_HORIZONTAL_READ_EXTENDED);
int flag_store_extended = SID_CHECK_BITFIELD_SWITCH(mode, TREE_HORIZONTAL_STORE_EXTENDED);
int flag_store_ghosts = SID_CHECK_BITFIELD_SWITCH(mode, TREE_HORIZONTAL_STORE_GHOSTS);
if(flag_store_ghosts)
SID_exit_error("Ghost processing not supported in read_trees_horizontal().", SID_ERROR_LOGIC);
if(!flag_read_extended)
SID_exit_error("Reading of non-extended horizontal trees not yet implemented in read_trees_horizontal().",
SID_ERROR_LOGIC);
// Set filename and open file
strcpy(filename_output_file_root, filename_output_dir);
strip_path(filename_output_file_root);
sprintf(filename_output_dir_horizontal, "%s/horizontal", filename_output_dir);
sprintf(filename_output_dir_horizontal_trees, "%s/trees", filename_output_dir_horizontal);
if(flag_read_extended)
sprintf(filename_in, "%s/horizontal_trees_tmp_%03d.dat", filename_output_dir_horizontal_trees, i_read);
else
sprintf(filename_in, "%s/horizontal_trees_%03d.dat", filename_output_dir_horizontal_trees, i_read);
SID_fopen(filename_in, "r", &fp_in);
// Read header
int n_step_in;
int n_search_in;
int n_groups_max_in;
int n_subgroups_max_in;
SID_fread_all(&n_step_in, sizeof(int), 1, &fp_in);
SID_fread_all(&n_search_in, sizeof(int), 1, &fp_in);
SID_fread_all(n_groups_in, sizeof(int), 1, &fp_in);
SID_fread_all(n_subgroups_in, sizeof(int), 1, &fp_in);
SID_fread_all(&n_groups_max_in, sizeof(int), 1, &fp_in);
SID_fread_all(&n_subgroups_max_in, sizeof(int), 1, &fp_in);
SID_fread_all(n_trees_subgroup_in, sizeof(int), 1, &fp_in);
SID_fread_all(n_trees_group_in, sizeof(int), 1, &fp_in);
tree_horizontal_extended_info *groups_extended = NULL;
tree_horizontal_extended_info *subgroups_extended = NULL;
if(flag_store_extended) {
groups_extended = (tree_horizontal_extended_info *)groups_in[i_file % n_wrap];
subgroups_extended = (tree_horizontal_extended_info *)subgroups_in[i_file % n_wrap];
}
// Perform read
int i_group;
int i_subgroup;
for(i_group = 0, i_subgroup = 0; i_group < (*n_groups_in); i_group++) {
// Read groups
int group_id;
int group_type;
int group_descendant_id;
int group_tree_id;
int group_file_offset;
int group_index;
int group_n_particles_peak = 0; // default when reading extended format files
SID_fread_all(&group_id, sizeof(int), 1, &fp_in);
SID_fread_all(&group_type, sizeof(int), 1, &fp_in);
SID_fread_all(&group_descendant_id, sizeof(int), 1, &fp_in);
SID_fread_all(&group_tree_id, sizeof(int), 1, &fp_in);
SID_fread_all(&group_file_offset, sizeof(int), 1, &fp_in);
SID_fread_all(&group_index, sizeof(int), 1, &fp_in);
if(!flag_read_extended)
SID_fread_all(&group_n_particles_peak, sizeof(int), 1, &fp_in);
if(!check_validity_of_tree_case_flag(group_type))
SID_exit_error("Invalid match type (%d) for i_group=%d", SID_ERROR_LOGIC, group_type, i_group);
if(flag_store_extended) {
groups_extended[i_group].id = group_id;
groups_extended[i_group].type = group_type;
groups_extended[i_group].descendant_id = group_descendant_id;
groups_extended[i_group].tree_id = group_tree_id;
groups_extended[i_group].descendant_file_offset = group_file_offset;
groups_extended[i_group].descendant_index = group_index;
}
if(flag_read_extended) {
int group_file_root;
int group_n_particles;
int group_n_particles_parent;
int group_n_particles_desc;
int group_n_particles_proj;
float group_score_desc;
float group_score_prog;
int group_snap_bridge;
int group_file_bridge;
int group_index_bridge;
int group_id_bridge;
int group_first_progenitor_file;
int group_first_progenitor_index;
int group_next_progenitor_file;
int group_next_progenitor_index;
SID_fread(&group_file_root, sizeof(int), 1, &fp_in);
SID_fread(&group_n_particles, sizeof(int), 1, &fp_in);
SID_fread(&group_n_particles_parent, sizeof(int), 1, &fp_in);
SID_fread(&group_n_particles_desc, sizeof(int), 1, &fp_in);
SID_fread(&group_n_particles_proj, sizeof(int), 1, &fp_in);
SID_fread(&group_score_desc, sizeof(float), 1, &fp_in);
SID_fread(&group_score_prog, sizeof(float), 1, &fp_in);
SID_fread(&group_snap_bridge, sizeof(int), 1, &fp_in);
SID_fread(&group_file_bridge, sizeof(int), 1, &fp_in);
SID_fread(&group_index_bridge, sizeof(int), 1, &fp_in);
SID_fread(&group_id_bridge, sizeof(int), 1, &fp_in);
SID_fread(&group_first_progenitor_file, sizeof(int), 1, &fp_in);
SID_fread(&group_first_progenitor_index, sizeof(int), 1, &fp_in);
SID_fread(&group_next_progenitor_file, sizeof(int), 1, &fp_in);
SID_fread(&group_next_progenitor_index, sizeof(int), 1, &fp_in);
if(flag_store_extended) {
groups_extended[i_group].file_root = group_file_root;
groups_extended[i_group].n_particles_peak = 0;
groups_extended[i_group].parent_id = group_id;
groups_extended[i_group].substructure_index = 0;
groups_extended[i_group].n_particles = group_n_particles;
groups_extended[i_group].n_particles_parent = group_n_particles_parent;
groups_extended[i_group].n_particles_desc = group_n_particles_desc;
groups_extended[i_group].n_particles_proj = group_n_particles_proj;
groups_extended[i_group].score_desc = group_score_desc;
groups_extended[i_group].score_prog = group_score_prog;
// Only read the bridge information if the halo is marked
// TREE_CASE_FRAGMENTED_NEW. This prevents us from overwriting
// the bridge info we need to propagate in order to check for
// when a fragmented halo returns to its bridge.
if(SID_CHECK_BITFIELD_SWITCH(group_type, TREE_CASE_FRAGMENTED_NEW)) {
groups_extended[i_group].snap_bridge = group_snap_bridge;
groups_extended[i_group].file_bridge = group_file_bridge;
groups_extended[i_group].index_bridge = group_index_bridge;
groups_extended[i_group].id_bridge = group_id_bridge;
} else {
groups_extended[i_group].snap_bridge = -1;
groups_extended[i_group].file_bridge = -1;
groups_extended[i_group].index_bridge = -1;
groups_extended[i_group].id_bridge = -1;
}
groups_extended[i_group].first_progenitor_file = group_first_progenitor_file;
groups_extended[i_group].first_progenitor_index = group_first_progenitor_index;
groups_extended[i_group].next_progenitor_file = group_next_progenitor_file;
groups_extended[i_group].next_progenitor_index = group_next_progenitor_index;
}
}
SID_fread_all(&(n_subgroups_group[i_group]), sizeof(int), 1, &fp_in);
int j_subgroup;
for(j_subgroup = 0; j_subgroup < n_subgroups_group[i_group]; i_subgroup++, j_subgroup++) {
// Read subgroups
int subgroup_id;
int subgroup_type;
int subgroup_descendant_id;
int subgroup_tree_id;
int subgroup_file_offset;
int subgroup_index;
int subgroup_n_particles_peak = 0; // default when reading extended format files
SID_fread_all(&subgroup_id, sizeof(int), 1, &fp_in);
SID_fread_all(&subgroup_type, sizeof(int), 1, &fp_in);
SID_fread_all(&subgroup_descendant_id, sizeof(int), 1, &fp_in);
SID_fread_all(&subgroup_tree_id, sizeof(int), 1, &fp_in);
SID_fread_all(&subgroup_file_offset, sizeof(int), 1, &fp_in);
SID_fread_all(&subgroup_index, sizeof(int), 1, &fp_in);
if(!flag_read_extended)
SID_fread_all(&subgroup_n_particles_peak, sizeof(int), 1, &fp_in);
if(!check_validity_of_tree_case_flag(subgroup_type))
SID_exit_error("Invalid match type (%d) for i_group,j_subgroup,i_subgroup=%d,%d,%d", SID_ERROR_LOGIC,
subgroup_type, i_group, j_subgroup, i_subgroup);
if(flag_store_extended) {
subgroups_extended[i_subgroup].id = subgroup_id;
subgroups_extended[i_subgroup].type = subgroup_type;
subgroups_extended[i_subgroup].descendant_id = subgroup_descendant_id;
subgroups_extended[i_subgroup].tree_id = subgroup_tree_id;
subgroups_extended[i_subgroup].descendant_file_offset = subgroup_file_offset;
subgroups_extended[i_subgroup].descendant_index = subgroup_index;
}
if(flag_read_extended) {
int subgroup_file_root;
int subgroup_n_particles;
int subgroup_n_particles_parent;
int subgroup_n_particles_desc;
int subgroup_n_particles_proj;
float subgroup_score_desc;
float subgroup_score_prog;
int subgroup_snap_bridge;
int subgroup_file_bridge;
int subgroup_index_bridge;
int subgroup_id_bridge;
int subgroup_first_progenitor_file;
int subgroup_first_progenitor_index;
int subgroup_next_progenitor_file;
int subgroup_next_progenitor_index;
SID_fread(&subgroup_file_root, sizeof(int), 1, &fp_in);
SID_fread(&subgroup_n_particles, sizeof(int), 1, &fp_in);
SID_fread(&subgroup_n_particles_parent, sizeof(int), 1, &fp_in);
SID_fread(&subgroup_n_particles_desc, sizeof(int), 1, &fp_in);
SID_fread(&subgroup_n_particles_proj, sizeof(int), 1, &fp_in);
SID_fread(&subgroup_score_desc, sizeof(float), 1, &fp_in);
SID_fread(&subgroup_score_prog, sizeof(float), 1, &fp_in);
SID_fread(&subgroup_snap_bridge, sizeof(int), 1, &fp_in);
SID_fread(&subgroup_file_bridge, sizeof(int), 1, &fp_in);
SID_fread(&subgroup_index_bridge, sizeof(int), 1, &fp_in);
SID_fread(&subgroup_id_bridge, sizeof(int), 1, &fp_in);
SID_fread(&subgroup_first_progenitor_file, sizeof(int), 1, &fp_in);
SID_fread(&subgroup_first_progenitor_index, sizeof(int), 1, &fp_in);
SID_fread(&subgroup_next_progenitor_file, sizeof(int), 1, &fp_in);
SID_fread(&subgroup_next_progenitor_index, sizeof(int), 1, &fp_in);
if(flag_store_extended) {
subgroups_extended[i_subgroup].file_root = subgroup_file_root;
subgroups_extended[i_subgroup].n_particles_peak = 0;
subgroups_extended[i_subgroup].parent_id = group_id;
subgroups_extended[i_subgroup].substructure_index = i_subgroup;
subgroups_extended[i_subgroup].n_particles = subgroup_n_particles;
subgroups_extended[i_subgroup].n_particles_parent = subgroup_n_particles_parent;
subgroups_extended[i_subgroup].n_particles_desc = subgroup_n_particles_desc;
subgroups_extended[i_subgroup].n_particles_proj = subgroup_n_particles_proj;
subgroups_extended[i_subgroup].score_desc = subgroup_score_desc;
subgroups_extended[i_subgroup].score_prog = subgroup_score_prog;
// Only read the bridge information if the halo is marked
// TREE_CASE_FRAGMENTED_NEW. This prevents us from overwriting
// the bridge info we need to propagate in order to check for
// when a fragmented halo returns to its bridge.
if(SID_CHECK_BITFIELD_SWITCH(subgroup_type, TREE_CASE_FRAGMENTED_NEW)) {
subgroups_extended[i_subgroup].snap_bridge = subgroup_snap_bridge;
subgroups_extended[i_subgroup].file_bridge = subgroup_file_bridge;
subgroups_extended[i_subgroup].index_bridge = subgroup_index_bridge;
subgroups_extended[i_subgroup].id_bridge = subgroup_id_bridge;
} else {
subgroups_extended[i_subgroup].snap_bridge = -1;
subgroups_extended[i_subgroup].file_bridge = -1;
subgroups_extended[i_subgroup].index_bridge = -1;
subgroups_extended[i_subgroup].id_bridge = -1;
}
subgroups_extended[i_subgroup].first_progenitor_file = subgroup_first_progenitor_file;
subgroups_extended[i_subgroup].first_progenitor_index = subgroup_first_progenitor_index;
subgroups_extended[i_subgroup].next_progenitor_file = subgroup_next_progenitor_file;
subgroups_extended[i_subgroup].next_progenitor_index = subgroup_next_progenitor_index;
}
}
}
}
if(flag_store_extended) {
for(; i_group < n_groups_max_in; i_group++)
groups_extended[i_group].type = TREE_CASE_INVALID;
for(; i_subgroup < n_subgroups_max_in; i_subgroup++)
subgroups_extended[i_subgroup].type = TREE_CASE_INVALID;
}
SID_fclose(&fp_in);
SID_log("Done.", SID_LOG_CLOSE);
}