void construct_galaxies(int halonr, int tree)
{
static int halosdone = 0;
int prog, fofhalo, ngal;
HaloAux[halonr].DoneFlag = 1;
halosdone++;
prog = Halo[halonr].FirstProgenitor;
while(prog >= 0)
{
if(HaloAux[prog].DoneFlag == 0)
construct_galaxies(prog, tree);
prog = Halo[prog].NextProgenitor;
}
fofhalo = Halo[halonr].FirstHaloInFOFgroup;
if(HaloAux[fofhalo].HaloFlag == 0)
{
HaloAux[fofhalo].HaloFlag = 1;
while(fofhalo >= 0)
{
prog = Halo[fofhalo].FirstProgenitor;
while(prog >= 0)
{
if(HaloAux[prog].DoneFlag == 0)
construct_galaxies(prog, tree);
prog = Halo[prog].NextProgenitor;
}
fofhalo = Halo[fofhalo].NextHaloInFOFgroup;
}
}
// At this point, the galaxies for all progenitors of this halo have been
// properly constructed. Also, the galaxies of the progenitors of all other
// halos in the same FOF group have been constructed as well. We can hence go
// ahead and construct all galaxies for the subhalos in this FOF halo, and
// evolve them in time.
fofhalo = Halo[halonr].FirstHaloInFOFgroup;
if(HaloAux[fofhalo].HaloFlag == 1)
{
ngal = 0;
HaloAux[fofhalo].HaloFlag = 2;
while(fofhalo >= 0)
{
ngal = join_galaxies_of_progenitors(fofhalo, ngal);
fofhalo = Halo[fofhalo].NextHaloInFOFgroup;
}
evolve_galaxies(Halo[halonr].FirstHaloInFOFgroup, ngal, tree);
}
}
/**@brief Main routine of L-Galaxies*/
int main(int argc, char **argv)
{
int filenr, *FileToProcess, *TaskToProcess, nfiles;
char buf[1000];
time_t start, current;
#ifdef PARALLEL
MPI_Init(&argc, &argv);
MPI_Comm_rank(MPI_COMM_WORLD, &ThisTask);
MPI_Comm_size(MPI_COMM_WORLD, &NTask);
#else
NTask = 1;
ThisTask = 0;
#endif //PARALLEL
#ifdef MCMC
time(&global_starting_time);
#endif
if(ThisTask==0)
{
printf("\n\n\n");
printf("**************************************************************************\n");
printf("* *\n");
printf("* Copyright (C) <2016> <L-Galaxies> *\n");
printf("* *\n");
printf("* This program is free software: you can redistribute it and/or modify *\n");
printf("* it under the terms of the GNU General Public License as published by *\n");
printf("* the Free Software Foundation, either version 3 of the License, or *\n");
printf("* (at your option) any later version. *\n");
printf("* *\n");
printf("* This program is distributed in the hope that it will be useful, *\n");
printf("* but WITHOUT ANY WARRANTY; without even the implied warranty of *\n");
printf("* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *\n");
printf("* GNU General Public License for more details. *\n");
printf("* *\n");
printf("* You should have received a copy of the GNU General Public License *\n");
printf("* along with this program. If not, see <http://www.gnu.org/licenses/> *\n");
printf("* *\n");
printf("**************************************************************************\n\n\n");
}
if(argc > 3 || argc<2)
{
printf("\n Wrong number of runtime arguments\n\n");
printf("\n usage: ./L-Galaxies <parameterfile>\n\n");
endrun(0);
}
if (ThisTask == 0)
printf("%s\n",COMPILETIMESETTINGS);
/* check compatibility of some Makefile Options*/
check_options();
/*Reads the parameter file, given as an argument at run time. */
read_parameter_file(argv[1]);
#ifdef MR_PLUS_MRII
//Start with MR files and later change to MRII
LastDarkMatterSnapShot=LastDarkMatterSnapShot_MR;
sprintf(FileWithZList, "%s", FileWithZList_MR);
sprintf(FileWithZList_OriginalCosm, "%s", FileWithZList_OriginalCosm_MR);
#endif
mymalloc_init();
sprintf(FinalOutputDir, "%s", OutputDir);
#ifndef MCMC
if(argc == 3)
sprintf(OutputDir, "%s", argv[2]);
#else
FirstChainNumber=0;
if(argc == 3)
FirstChainNumber=atoi(argv[2]);
#endif
//time(&start);
#ifdef COMPUTE_SPECPHOT_PROPERTIES
//for dust_model
mu_seed = -150;
#endif
init();
#ifdef STAR_FORMATION_HISTORY
#ifdef PARALLEL
if(ThisTask == 0)
#endif
write_sfh_bins();
#endif
#ifndef MCMC
nfiles=get_nr_files_to_process(ThisTask);
FileToProcess=mymalloc("FileToProcess", sizeof(int) * nfiles);
TaskToProcess=mymalloc("TaskToProcess", sizeof(int) * nfiles);
assign_files_to_tasks(FileToProcess, TaskToProcess, ThisTask, NTask, nfiles);
int file;
for(file = 0; file < nfiles; file++)
{
if(ThisTask==TaskToProcess[file])
filenr=FileToProcess[file];
else
continue;
#else //MCMC
/* In MCMC mode only one file is loaded into memory
* and the sampling for all the steps is done on it */
sprintf(SimulationDir, "%s/", SimulationDir);
for(filenr = MCMCTreeSampleFile; filenr <= MCMCTreeSampleFile; filenr++)
{
#endif //MCMC
time(&start);
#ifdef PARALLEL
#ifndef MCMC
time_t current;
do
time(¤t);
//while(difftime(current, start) < 5.0 * ThisTask);
while(difftime(current, start) < 1.0 * ThisTask);
#endif
#endif
load_tree_table(filenr);
#ifdef MCMC
Senna(); // run the model in MCMC MODE
#else
SAM(filenr); // run the model in NORMAL MODE
#endif
#ifdef MCMC
break; //break loop on files since the MCMC is done on a single file
#else
time(¤t);
printf("\ndone tree file %d in %ldmin and %lds\n\n", filenr, (current - start)/60, (current - start)%60);
#endif //MCMC
free_tree_table();
//if temporary directory given as argument
if(argc == 3)
{
#ifdef GALAXYTREE
sprintf(buf, "mv %s/%s_galtree_%d %s", OutputDir,FileNameGalaxies, filenr, FinalOutputDir);
#else
sprintf(buf, "mv %s/%s_z*_%d %s", OutputDir,FileNameGalaxies, filenr, FinalOutputDir);
#endif
system(buf);
}
}
#ifndef MCMC
myfree(TaskToProcess);
myfree(FileToProcess);
#endif
#ifdef PARALLEL
MPI_Finalize();
#endif
return 0;
}
/**@brief SAM() loops on trees and calls construct_galaxies.*/
#ifdef MCMC
double SAM(int filenr)
#else
void SAM(int filenr)
#endif
{
int treenr, halonr;
#ifdef MCMC
int ii;
MCMC_GAL = mymalloc("MCMC_Gal", sizeof(struct MCMC_GALAXY) * MCMCAllocFactor);
for(ii=0;ii<NOUT;ii++)
TotMCMCGals[ii] = 0;
#ifdef MR_PLUS_MRII
change_dark_matter_sim("MR");
#else
if(CurrentMCMCStep==1)
read_sample_info();
#ifdef HALOMODEL
else
{
int snap, ii;
for(snap=0;snap<NOUT;snap++)
for(ii=0;ii<NFofsInSample[snap];ii++)
MCMC_FOF[ii].NGalsInFoF[snap]=0;
}
#endif //HALOMODEL
#endif //MR_PLUS_MRII
#endif //MCMC
//to be used when we have tables for the scaling in any cosmology
//read_scaling_parameters();
#ifndef MCMC
#ifdef GALAXYTREE
create_galaxy_tree_file(filenr);
#else
create_galaxy_files(filenr);
#endif
#endif
#ifdef GALAXYTREE
FILE *fdg = fopen("treengal.dat", "w");
#endif
//***************************************************************************************
//***************************************************************************************
//for(treenr = 0; treenr < NTrees_Switch_MR_MRII; treenr++)
for(treenr = 0; treenr < Ntrees; treenr++)
{
//printf("doing tree %d of %d\n", treenr, Ntrees);
#ifdef MR_PLUS_MRII
if(treenr == NTrees_Switch_MR_MRII)
change_dark_matter_sim("MRII");
#endif
load_tree(treenr);
#ifdef MCMC
#ifdef PRELOAD_TREES
if(CurrentMCMCStep==1)
#endif
#endif
scale_cosmology(TreeNHalos[treenr]);
gsl_rng_set(random_generator, filenr * 100000 + treenr);
NumMergers = 0;
NHaloGal = 0;
#ifdef GALAXYTREE
NGalTree = 0;
IndexStored = 0;
#endif
int snapnum;
//LastSnapShotNr is the highest output snapshot
/* we process the snapshots now in temporal order
* (as a means to reduce peak memory usage) */
for(snapnum = 0; snapnum <= LastSnapShotNr; snapnum++)
{
#ifdef MCMC
/* read the appropriate parameter list for current snapnum
* into the parameter variables to be used in construct_galaxies */
read_mcmc_par(snapnum);
#ifdef HALOMODEL
//because we need halo masses even for FOFs
//with no galaxies it needs to be done here
assign_FOF_masses(snapnum, treenr);
#endif
#endif
for(halonr = 0; halonr < TreeNHalos[treenr]; halonr++)
if(HaloAux[halonr].DoneFlag == 0 && Halo[halonr].SnapNum == snapnum)
construct_galaxies(filenr, treenr, halonr);
}
/* output remaining galaxies as needed */
while(NHaloGal)
output_galaxy(treenr, 0);
#ifndef MCMC
#ifdef GALAXYTREE
save_galaxy_tree_finalize(filenr, treenr);
#ifndef PARALLEL
if((treenr/100)*100==treenr) printf("treenr=%d TotGalCount=%d\n", treenr, TotGalCount);
#endif
fflush(stdout);
fprintf(fdg, "%d\n", NGalTree);
#endif
#else//ifdef MCMC
#endif
free_galaxies_and_tree();
}//loop on trees
#ifdef MCMC
double lhood = get_likelihood();
#ifdef MR_PLUS_MRII
free(MCMC_FOF);
#else
if(CurrentMCMCStep==ChainLength)
free(MCMC_FOF);
#endif
myfree(MCMC_GAL);
return lhood;
#else //MCMC
#ifdef GALAXYTREE
close_galaxy_tree_file();
#else
close_galaxy_files();
#endif
return;
#endif
}
/**@brief construct_galaxies() recursively runs the semi-analytic model.
* For each halo it checks if its main progenitor has been done, then
* if all the halos in the FOF of its main progenitor have been
* done and then runs the SAM in the current halo. This means that
* for the first time its called it will walk up the tree into the
* haloes in the earliest snapshot.
*
* When it finds a halo that needs to be done it calls
* join_galaxies_of_progenitors and evolve_galaxies. */
void construct_galaxies(int filenr, int treenr, int halonr)
{
static int halosdone = 0;
int prog, fofhalo, ngal, cenngal, p;
HaloAux[halonr].DoneFlag = 1;
halosdone++;
prog = Halo[halonr].FirstProgenitor;
while(prog >= 0) //If halo has a progenitor
{
if(HaloAux[prog].DoneFlag == 0) //If progenitor hasn't been done yet
construct_galaxies(filenr, treenr, prog);
prog = Halo[prog].NextProgenitor; //Jump to next halo in progenitors FOF
}
//Now check for the progenitors of all the halos in the current FOF group
fofhalo = Halo[halonr].FirstHaloInFOFgroup; //Starting at the first halo in current FOF
if(HaloAux[fofhalo].HaloFlag == 0) //If it hasn't been done
{
HaloAux[fofhalo].HaloFlag = 1; //mark as to do
while(fofhalo >= 0) //go through all the halos in current FOF
{
prog = Halo[fofhalo].FirstProgenitor;
while(prog >= 0) //build its progenitors
{
if(HaloAux[prog].DoneFlag == 0)
construct_galaxies(filenr, treenr, prog);
prog = Halo[prog].NextProgenitor;
}
fofhalo = Halo[fofhalo].NextHaloInFOFgroup; //Jump to next halo in FOF
}
}
/* At this point, the galaxies for all progenitors of this halo have been
* properly constructed. Also, the galaxies of the progenitors of all other
* halos in the same FOF-group have been constructed as well. We can hence go
* ahead and construct all galaxies for the subhalos in this FOF halo, and
* evolve them in time. */
fofhalo = Halo[halonr].FirstHaloInFOFgroup;
if(HaloAux[fofhalo].HaloFlag == 1) //If it is marked as an halo to do
{
ngal = 0;
HaloAux[fofhalo].HaloFlag = 2;
cenngal = set_merger_center(fofhalo); //Find type 0 for type 1 to merge into
/*For all the halos in the current FOF join all the progenitor galaxies together
* ngals will be the total number of galaxies in the current FOF*/
while(fofhalo >= 0)
{
ngal = join_galaxies_of_progenitors(fofhalo, ngal, &cenngal);
fofhalo = Halo[fofhalo].NextHaloInFOFgroup;
}
/*Evolve the Galaxies -> SAM! */
evolve_galaxies(Halo[halonr].FirstHaloInFOFgroup, ngal, treenr, cenngal);
for (p =0;p<ngal;p++)
mass_checks("Construct_galaxies #1",p);
}
}
/**@brief Main routine of L-Galaxies*/
int main(int argc, char **argv)
{
int filenr, *FileToProcess, *TaskToProcess, nfiles;
char buf[1000];
time_t start, current;
//Catch floating point exceptions
#ifdef DEBUG
#endif
#ifdef PARALLEL
MPI_Init(&argc, &argv);
MPI_Comm_rank(MPI_COMM_WORLD, &ThisTask);
MPI_Comm_size(MPI_COMM_WORLD, &NTask);
#else
NTask = 1;
ThisTask = 0;
#endif //PARALLEL
#ifdef MCMC
time(&global_starting_time);
#endif
if(argc > 3)
{
printf("\n usage: L-Galaxies <parameterfile>\n\n");
endrun(0);
}
if (ThisTask == 0)
printf("%s\n",COMPILETIMESETTINGS);
/*Reads the parameter file, given as an argument at run time. */
read_parameter_file(argv[1]);
#ifdef MR_PLUS_MRII
//Start with MR files and later change to MRII
LastDarkMatterSnapShot=LastDarkMatterSnapShot_MR;
sprintf(FileWithZList, "%s", FileWithZList_MR);
sprintf(FileWithZList_OriginalCosm, "%s", FileWithZList_OriginalCosm_MR);
#endif
mymalloc_init();
sprintf(FinalOutputDir, "%s", OutputDir);
if(argc == 3)
sprintf(OutputDir, "%s", argv[2]);
//time(&start);
/* check compatibility of some Makefile Options*/
check_options();
#ifdef COMPUTE_SPECPHOT_PROPERTIES
//for dust_model
mu_seed = -150;
#endif
init();
#ifdef STAR_FORMATION_HISTORY
#ifdef PARALLEL
if(ThisTask == 0)
#endif
write_sfh_bins();
#endif
#ifdef MCMC
#ifdef PARALLEL
/* a small delay to avoid all processors reading trees at the same time*/
time(&start);
do
time(¤t);
while(difftime(current, start) < 10.0 * ThisTask);
#endif
#endif
#ifndef MCMC
nfiles=get_nr_files_to_process(ThisTask);
FileToProcess=mymalloc("FileToProcess", sizeof(int) * nfiles);
TaskToProcess=mymalloc("TaskToProcess", sizeof(int) * nfiles);
assign_files_to_tasks(FileToProcess, TaskToProcess, ThisTask, NTask, nfiles);
int file;
for(file = 0; file < nfiles; file++)
{
if(ThisTask==TaskToProcess[file])
filenr=FileToProcess[file];
else
continue;
#else //MCMC
/* In MCMC mode only one file is loaded into memory
* and the sampling for all the steps is done on it */
sprintf(SimulationDir, "%s/MergerTrees_%d/", SimulationDir, ThisTask);
for(filenr = MCMCTreeSampleFile; filenr <= MCMCTreeSampleFile; filenr++)
{
#endif //MCMC
time(&start);
#ifdef READXFRAC
get_xfrac_mesh();
#endif
load_tree_table(filenr);
/* Read in mesh dimensions */
#ifdef MCMC
#ifdef PARALLEL
time_t start, start2;
/* a small delay to reset processors to the same time*/
time(&start2);
do
time(¤t);
while(difftime(current, start2) < 10.0 * (NTask-ThisTask));
#endif
Senna(); // run the model in MCMC MODE
#else
SAM(filenr); // run the model in NORMAL MODE
#endif
#ifdef MCMC
break; //break loop on files since the MCMC is done on a single file
#else
time(¤t);
printf("\ndone tree file %d in %ldmin and %lds\n\n", filenr, (current - start)/60, (current - start)%60);
#endif //MCMC
free_tree_table();
//if temporary directory given as argument
if(argc == 3)
{
#ifdef GALAXYTREE
sprintf(buf, "mv %s/%s_galtree_%d %s", OutputDir,FileNameGalaxies, filenr, FinalOutputDir);
#else
sprintf(buf, "mv %s/%s_z*_%d %s", OutputDir,FileNameGalaxies, filenr, FinalOutputDir);
#endif
system(buf);
}
}
#ifndef MCMC
myfree(TaskToProcess);
myfree(FileToProcess);
#endif
#ifdef PARALLEL
MPI_Barrier(MPI_COMM_WORLD);
MPI_Finalize();
#endif
return 0;
}
/**@brief SAM() loops on trees and calls construct_galaxies.*/
#ifdef MCMC
double SAM(int filenr)
#else
void SAM(int filenr)
#endif
{
int treenr, halonr;
time_t t_mark_a, t_mark_b;
#ifdef MCMC
int ii;
MCMC_GAL = mymalloc("MCMC_Gal", sizeof(struct MCMC_GALAXY) * MCMCAllocFactor);
for(ii=0;ii<NOUT;ii++)
TotMCMCGals[ii] = 0;
if(Sample_Cosmological_Parameters==1)
{
reset_cosmology ();
#ifdef HALOMODEL
initialize_halomodel();
#endif
}
#ifdef MR_PLUS_MRII
change_dark_matter_sim("MR");
#else
if(Sample_Cosmological_Parameters==1 || CurrentMCMCStep==1)
read_sample_info();
else
{
int snap, ii;
for(snap=0;snap<NOUT;snap++)
for(ii=0;ii<NFofsInSample[snap];ii++)
MCMC_FOF[ii].NGalsInFoF[snap]=0;
}
#endif
#endif
//to be used when we have tables for the scaling in any cosmology
//read_scaling_parameters();
#ifndef MCMC
#ifdef GALAXYTREE
create_galaxy_tree_file(filenr);
#else
create_galaxy_files(filenr);
#endif
#ifdef ALL_SKY_LIGHTCONE
int nr;
for ( nr = 0; nr < NCONES; nr++)
create_galaxy_lightcone_files(filenr, nr);
#endif
#endif
#ifdef GALAXYTREE
FILE *fdg = fopen("treengal.dat", "w");
#endif
//***************************************************************************************
//***************************************************************************************
//for(treenr = 0; treenr < NTrees_Switch_MR_MRII; treenr++)
//for(treenr = NTrees_Switch_MR_MRII; treenr < Ntrees; treenr++)
/* Scan through all trees snapshot by snapshot */
int snapnum;
//for(treenr = 0; treenr < NTrees_Switch_MR_MRII; treenr++)
//for(treenr = NTrees_Switch_MR_MRII; treenr < Ntrees; treenr++)
for(treenr = 0; treenr < Ntrees; treenr++)
//for(treenr = 0; treenr < 1;treenr++)
{
//printf("doing tree %d of %d\n", treenr, Ntrees);
#ifdef MR_PLUS_MRII
if(treenr == NTrees_Switch_MR_MRII)
change_dark_matter_sim("MRII");
#endif
load_tree(treenr);
#ifdef MCMC
#ifdef PRELOAD_TREES
if(Sample_Cosmological_Parameters==1 || CurrentMCMCStep==0)
#endif
#endif
scale_cosmology(TreeNHalos[treenr]);
gsl_rng_set(random_generator, filenr * 100000 + treenr);
NumMergers = 0;
NHaloGal = 0;
#ifdef GALAXYTREE
NGalTree = 0;
IndexStored = 0;
#endif
//LastSnapShotNr is the highest output snapshot
/* we process the snapshots now in temporal order
* (as a means to reduce peak memory usage) */
for(snapnum = 0; snapnum <= LastSnapShotNr; snapnum++)
//for(snapnum = 0; snapnum <= 30; snapnum++)
{
#ifdef MCMC
/* read the appropriate parameter list for current snapnum
* into the parameter variables to be used in construct_galaxies */
read_mcmc_par(snapnum);
#else
//used to allow parameter values to vary with redshift
//re_set_parameters(snapnum);
#endif
//printf("doing snap=%d\n",snapnum);
for(halonr = 0; halonr < TreeNHalos[treenr]; halonr++)
if(HaloAux[halonr].DoneFlag == 0 && Halo[halonr].SnapNum == snapnum)
construct_galaxies(filenr, treenr, halonr);
}
/* output remaining galaxies as needed */
while(NHaloGal)
output_galaxy(treenr, 0);
#ifndef MCMC
#ifdef GALAXYTREE
save_galaxy_tree_finalize(filenr, treenr);
#ifndef PARALLEL
if((treenr/100)*100==treenr) printf("treenr=%d TotGalCount=%d\n", treenr, TotGalCount);
#endif
fflush(stdout);
fprintf(fdg, "%d\n", NGalTree);
#endif
#else//ifdef MCMC
#ifdef PRELOAD_TREES
if(Sample_Cosmological_Parameters==1)
un_scale_cosmology(TreeNHalos[treenr]);
#endif
#endif
free_galaxies_and_tree();
}
#ifdef MCMC
double lhood = get_likelihood();
#ifdef MR_PLUS_MRII
free(MCMC_FOF);
#else
if(Sample_Cosmological_Parameters==1 || CurrentMCMCStep==ChainLength)
free(MCMC_FOF);
#endif
#ifdef HALOMODEL
if (Sample_Cosmological_Parameters==1) {
gsl_spline_free(FofSpline);
gsl_interp_accel_free(FofAcc);
gsl_spline_free(SigmaSpline);
gsl_interp_accel_free(SigmaAcc);
gsl_spline_free(ellipSpline);
gsl_interp_accel_free(ellipAcc);
gsl_spline_free(PowSpline);
} //if
#endif
myfree(MCMC_GAL);
return lhood;
#else //MCMC
#ifdef GALAXYTREE
close_galaxy_tree_file();
#else
close_galaxy_files();
#endif
#ifdef ALL_SKY_LIGHTCONE
for (nr = 0; nr < NCONES; nr++)
close_galaxy_lightcone_files(nr);
#endif
return;
#endif
}