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Commit ba2d16f3 authored by Matthieu Schaller's avatar Matthieu Schaller
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Also allow for type 2 background particles in the serial MPI i/o code.

parent e2115b2a
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examples/main.c
View file @ ba2d16f3
......@@ -867,19 +867,19 @@ int main(int argc, char *argv[]) {
#if defined(HAVE_HDF5)
#if defined(WITH_MPI)
#if defined(HAVE_PARALLEL_HDF5)
read_ic_parallel(ICfileName, &us, dim, &parts, &gparts, &sparts, &bparts,
&Ngas, &Ngpart, &Nspart, &Nbpart, &flag_entropy_ICs,
with_hydro, (with_external_gravity || with_self_gravity),
with_stars, with_black_holes, cleanup_h, cleanup_sqrt_a,
cosmo.h, cosmo.a, myrank, nr_nodes, MPI_COMM_WORLD,
MPI_INFO_NULL, nr_threads, dry_run);
read_ic_parallel(
ICfileName, &us, dim, &parts, &gparts, &sparts, &bparts, &Ngas, &Ngpart,
&Ngpart_background, &Nspart, &Nbpart, &flag_entropy_ICs, with_hydro,
(with_external_gravity || with_self_gravity), with_stars,
with_black_holes, cleanup_h, cleanup_sqrt_a, cosmo.h, cosmo.a, myrank,
nr_nodes, MPI_COMM_WORLD, MPI_INFO_NULL, nr_threads, dry_run);
#else
read_ic_serial(ICfileName, &us, dim, &parts, &gparts, &sparts, &bparts,
&Ngas, &Ngpart, &Nspart, &Nbpart, &flag_entropy_ICs,
with_hydro, (with_external_gravity || with_self_gravity),
with_stars, with_black_holes, cleanup_h, cleanup_sqrt_a,
cosmo.h, cosmo.a, myrank, nr_nodes, MPI_COMM_WORLD,
MPI_INFO_NULL, nr_threads, dry_run);
read_ic_serial(
ICfileName, &us, dim, &parts, &gparts, &sparts, &bparts, &Ngas, &Ngpart,
&Ngpart_background, &Nspart, &Nbpart, &flag_entropy_ICs, with_hydro,
(with_external_gravity || with_self_gravity), with_stars,
with_black_holes, cleanup_h, cleanup_sqrt_a, cosmo.h, cosmo.a, myrank,
nr_nodes, MPI_COMM_WORLD, MPI_INFO_NULL, nr_threads, dry_run);
#endif
#else
read_ic_single(ICfileName, &us, dim, &parts, &gparts, &sparts, &bparts,
......
src/serial_io.c
View file @ ba2d16f3
......@@ -492,12 +492,12 @@ void writeArray(const struct engine* e, hid_t grp, char* fileName,
void read_ic_serial(char* fileName, const struct unit_system* internal_units,
double dim[3], struct part** parts, struct gpart** gparts,
struct spart** sparts, struct bpart** bparts, size_t* Ngas,
size_t* Ngparts, size_t* Nstars, size_t* Nblackholes,
int* flag_entropy, int with_hydro, int with_gravity,
int with_stars, int with_black_holes, int cleanup_h,
int cleanup_sqrt_a, double h, double a, int mpi_rank,
int mpi_size, MPI_Comm comm, MPI_Info info, int n_threads,
int dry_run) {
size_t* Ngparts, size_t* Ngparts_background, size_t* Nstars,
size_t* Nblackholes, int* flag_entropy, int with_hydro,
int with_gravity, int with_stars, int with_black_holes,
int cleanup_h, int cleanup_sqrt_a, double h, double a,
int mpi_rank, int mpi_size, MPI_Comm comm, MPI_Info info,
int n_threads, int dry_run) {
hid_t h_file = 0, h_grp = 0;
/* GADGET has only cubic boxes (in cosmological mode) */
......@@ -510,11 +510,13 @@ void read_ic_serial(char* fileName, const struct unit_system* internal_units,
long long offset[swift_type_count] = {0};
int dimension = 3; /* Assume 3D if nothing is specified */
size_t Ndm = 0;
size_t Ndm_background = 0;
struct unit_system* ic_units =
(struct unit_system*)malloc(sizeof(struct unit_system));
/* Initialise counters */
*Ngas = 0, *Ngparts = 0, *Nstars = 0, *Nblackholes = 0;
*Ngas = 0, *Ngparts = 0, *Ngparts_background = 0, *Nstars = 0,
*Nblackholes = 0;
/* First read some information about the content */
if (mpi_rank == 0) {
......@@ -676,10 +678,13 @@ void read_ic_serial(char* fileName, const struct unit_system* internal_units,
/* Allocate memory to store all gravity particles */
if (with_gravity) {
Ndm = N[1];
Ndm_background = N[swift_type_dark_matter_background];
*Ngparts = (with_hydro ? N[swift_type_gas] : 0) +
N[swift_type_dark_matter] +
N[swift_type_dark_matter_background] +
(with_stars ? N[swift_type_stars] : 0) +
(with_black_holes ? N[swift_type_black_hole] : 0);
*Ngparts_background = Ndm_background;
if (swift_memalign("gparts", (void**)gparts, gpart_align,
*Ngparts * sizeof(struct gpart)) != 0)
error("Error while allocating memory for gravity particles");
......@@ -740,6 +745,13 @@ void read_ic_serial(char* fileName, const struct unit_system* internal_units,
}
break;
case swift_type_dark_matter_background:
if (with_gravity) {
Nparticles = Ndm_background;
darkmatter_read_particles(*gparts + Ndm, list, &num_fields);
}
break;
case swift_type_stars:
if (with_stars) {
Nparticles = *Nstars;
......@@ -789,17 +801,23 @@ void read_ic_serial(char* fileName, const struct unit_system* internal_units,
/* Prepare the DM particles */
io_prepare_dm_gparts(&tp, *gparts, Ndm);
/* Prepare the DM background particles */
io_prepare_dm_background_gparts(&tp, *gparts + Ndm, Ndm_background);
/* Duplicate the hydro particles into gparts */
if (with_hydro) io_duplicate_hydro_gparts(&tp, *parts, *gparts, *Ngas, Ndm);
if (with_hydro)
io_duplicate_hydro_gparts(&tp, *parts, *gparts, *Ngas,
Ndm + Ndm_background);
/* Duplicate the stars particles into gparts */
if (with_stars)
io_duplicate_stars_gparts(&tp, *sparts, *gparts, *Nstars, Ndm + *Ngas);
io_duplicate_stars_gparts(&tp, *sparts, *gparts, *Nstars,
Ndm + Ndm_background + *Ngas);
/* Duplicate the black holes particles into gparts */
if (with_black_holes)
io_duplicate_black_holes_gparts(&tp, *bparts, *gparts, *Nblackholes,
Ndm + *Ngas + *Nstars);
Ndm + Ndm_background + *Ngas + *Nstars);
threadpool_clean(&tp);
}
......@@ -847,6 +865,7 @@ void write_output_serial(struct engine* e, const char* baseName,
const int with_cooling = e->policy & engine_policy_cooling;
const int with_temperature = e->policy & engine_policy_temperature;
const int with_fof = e->policy & engine_policy_fof;
const int with_DM_background = e->s->with_DM_background;
#ifdef HAVE_VELOCIRAPTOR
const int with_stf = (e->policy & engine_policy_structure_finding) &&
(e->s->gpart_group_data != NULL);
......@@ -864,7 +883,13 @@ void write_output_serial(struct engine* e, const char* baseName,
// const size_t Nbaryons = Ngas + Nstars;
// const size_t Ndm = Ntot > 0 ? Ntot - Nbaryons : 0;
/* Number of particles that we will write */
size_t Ndm_background = 0;
if (with_DM_background) {
Ndm_background = io_count_dm_background_gparts(gparts, Ntot);
}
/* Number of particles that we will write
* Recall that background particles are never inhibited and have no extras */
const size_t Ntot_written =
e->s->nr_gparts - e->s->nr_inhibited_gparts - e->s->nr_extra_gparts;
const size_t Ngas_written =
......@@ -876,7 +901,7 @@ void write_output_serial(struct engine* e, const char* baseName,
const size_t Nbaryons_written =
Ngas_written + Nstars_written + Nblackholes_written;
const size_t Ndm_written =
Ntot_written > 0 ? Ntot_written - Nbaryons_written : 0;
Ntot_written > 0 ? Ntot_written - Nbaryons_written - Ndm_background : 0;
/* File name */
char fileName[FILENAME_BUFFER_SIZE];
......@@ -888,7 +913,8 @@ void write_output_serial(struct engine* e, const char* baseName,
e->snapshot_output_count);
/* Compute offset in the file and total number of particles */
size_t N[swift_type_count] = {Ngas_written, Ndm_written, 0, 0,
size_t N[swift_type_count] = {Ngas_written, Ndm_written,
Ndm_background, 0,
Nstars_written, Nblackholes_written};
long long N_total[swift_type_count] = {0};
long long offset[swift_type_count] = {0};
......@@ -1242,7 +1268,8 @@ void write_output_serial(struct engine* e, const char* baseName,
case swift_type_dark_matter: {
if (Ntot == Ndm_written) {
/* This is a DM-only run without inhibited particles */
/* This is a DM-only run without background or inhibited particles
*/
Nparticles = Ntot;
darkmatter_write_particles(gparts, list, &num_fields);
if (with_fof) {
......@@ -1293,6 +1320,46 @@ void write_output_serial(struct engine* e, const char* baseName,
}
} break;
case swift_type_dark_matter_background: {
/* Ok, we need to fish out the particles we want */
Nparticles = Ndm_background;
/* Allocate temporary array */
if (swift_memalign("gparts_written", (void**)&gparts_written,
gpart_align,
Ndm_background * sizeof(struct gpart)) != 0)
error("Error while allocating temporart memory for gparts");
if (with_stf) {
if (swift_memalign("gpart_group_written",
(void**)&gpart_group_data_written, gpart_align,
Ndm_background *
sizeof(struct velociraptor_gpart_data)) !=
0)
error(
"Error while allocating temporart memory for gparts STF "
"data");
}
/* Collect the non-inhibited DM particles from gpart */
io_collect_gparts_background_to_write(
gparts, e->s->gpart_group_data, gparts_written,
gpart_group_data_written, Ntot, Ndm_background, with_stf);
/* Select the fields to write */
darkmatter_write_particles(gparts_written, list, &num_fields);
if (with_fof) {
num_fields +=
fof_write_gparts(gparts_written, list + num_fields);
}
if (with_stf) {
num_fields += velociraptor_write_gparts(gpart_group_data_written,
list + num_fields);
}
} break;
case swift_type_stars: {
if (Nstars == Nstars_written) {
......
src/serial_io.h
View file @ ba2d16f3
......@@ -38,12 +38,12 @@
void read_ic_serial(char* fileName, const struct unit_system* internal_units,
double dim[3], struct part** parts, struct gpart** gparts,
struct spart** sparts, struct bpart** bparts, size_t* Ngas,
size_t* Ngparts, size_t* Nstars, size_t* Nblackholes,
int* flag_entropy, int with_hydro, int with_gravity,
int with_stars, int with_black_holes, int cleanup_h,
int cleanup_sqrt_a, double h, double a, int mpi_rank,
int mpi_size, MPI_Comm comm, MPI_Info info, int n_threads,
int dry_run);
size_t* Ngparts, size_t* Ngparts_background, size_t* Nstars,
size_t* Nblackholes, int* flag_entropy, int with_hydro,
int with_gravity, int with_stars, int with_black_holes,
int cleanup_h, int cleanup_sqrt_a, double h, double a,
int mpi_rank, int mpi_size, MPI_Comm comm, MPI_Info info,
int n_threads, int dry_run);
void write_output_serial(struct engine* e, const char* baseName,
const struct unit_system* internal_units,
......
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