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Commit 1ac1d920 authored by Matthieu Schaller's avatar Matthieu Schaller
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Initialise the output_options also in the stand-alone FoF code

parent c577fae8
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doc/RTD/source/FriendsOfFriends/stand_alone_fof.rst
View file @ 1ac1d920
......@@ -21,7 +21,12 @@ command line:
* ``--hydro``: Read and process the gas particles,
* ``--stars``: Read and process the star particles,
* ``--black-holes``: Read and process the black hole particles.
* ``--black-holes``: Read and process the black hole particles,
* ``--cosmology``: Consider cosmological terms.
Running with cosmology is necessary when using a linking length based
on the mean inter-particle separation. For analysis where an absolute
linking length is used this is not necessary.
The group catalogues contain a unique identifier for each group as
well as the number of particles in each group and their total mass (in
......
examples/main.c
View file @ 1ac1d920
......@@ -991,7 +991,8 @@ int main(int argc, char *argv[]) {
/* Initialise the FOF properties */
bzero(&fof_properties, sizeof(struct fof_props));
#ifdef WITH_FOF
if (with_fof) fof_init(&fof_properties, params, &prog_const, &us);
if (with_fof)
fof_init(&fof_properties, params, &prog_const, &us, /*stand-alone=*/0);
#endif
/* Be verbose about what happens next */
......
examples/main_fof.c
View file @ 1ac1d920
......@@ -139,8 +139,8 @@ int main(int argc, char *argv[]) {
int with_aff = 0;
int dump_tasks = 0;
int dump_threadpool = 0;
int with_fof = 1;
int with_fp_exceptions = 0;
int with_cosmology = 0;
int with_stars = 0;
int with_black_holes = 0;
int with_hydro = 0;
......@@ -160,6 +160,8 @@ int main(int argc, char *argv[]) {
OPT_HELP(),
OPT_GROUP(" Friends-of-Friends options:\n"),
OPT_BOOLEAN('c', "cosmology", &with_cosmology,
"Run with cosmological information.", NULL, 0, 0),
OPT_BOOLEAN(0, "hydro", &with_hydro, "Read gas particles from the ICs.",
NULL, 0, 0),
OPT_BOOLEAN(0, "stars", &with_stars, "Read stars from the ICs.", NULL, 0,
......@@ -257,8 +259,7 @@ int main(int argc, char *argv[]) {
/* Write output parameter file */
if (myrank == 0 && output_parameters_filename != NULL) {
io_write_output_field_parameter(output_parameters_filename,
/*with_cosmology=*/1);
io_write_output_field_parameter(output_parameters_filename, with_cosmology);
printf("End of run.\n");
return 0;
}
......@@ -389,6 +390,10 @@ int main(int argc, char *argv[]) {
}
#endif
/* Prepare and verify the selection of outputs */
io_prepare_output_fields(output_options, with_cosmology, /*with_fof=*/1,
/*with_structure_finding=*/0);
/* Initialize unit system and constants */
units_init_from_params(&us, params, "InternalUnitSystem");
phys_const_init(&us, params, &prog_const);
......@@ -414,12 +419,23 @@ int main(int argc, char *argv[]) {
params, "InitialConditions:cleanup_h_factors", 0);
const int cleanup_sqrt_a = parser_get_opt_param_int(
params, "InitialConditions:cleanup_velocity_factors", 0);
/* Initialise the cosmology */
cosmology_init(params, &us, &prog_const, &cosmo);
if (with_cosmology)
cosmology_init(params, &us, &prog_const, &cosmo);
else
cosmology_init_no_cosmo(&cosmo);
if (myrank == 0 && with_cosmology) cosmology_print(&cosmo);
/* Initialise the equation of state */
if (with_hydro)
eos_init(&eos, &prog_const, &us, params);
else
bzero(&eos, sizeof(struct eos_parameters));
/* Initialise the FOF properties */
bzero(&fof_properties, sizeof(struct fof_props));
if (with_fof) fof_init(&fof_properties, params, &prog_const, &us);
fof_init(&fof_properties, params, &prog_const, &us, /*stand-alone=*/1);
/* Be verbose about what happens next */
if (myrank == 0) message("Reading ICs from file '%s'", ICfileName);
......@@ -438,27 +454,27 @@ 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,
&Ngpart_background, &Nspart, &Nbpart, &flag_entropy_ICs, with_hydro,
/*with_grav=*/1, with_stars, with_black_holes, /*with_cosmology=*/1,
cleanup_h, cleanup_sqrt_a, cosmo.h, cosmo.a, myrank, nr_nodes,
MPI_COMM_WORLD, MPI_INFO_NULL, nr_threads,
/*dry_run=*/0);
read_ic_parallel(ICfileName, &us, dim, &parts, &gparts, &sparts, &bparts,
&Ngas, &Ngpart, &Ngpart_background, &Nspart, &Nbpart,
&flag_entropy_ICs, with_hydro,
/*with_grav=*/1, with_stars, with_black_holes,
with_cosmology, cleanup_h, cleanup_sqrt_a, cosmo.h, cosmo.a,
myrank, nr_nodes, MPI_COMM_WORLD, MPI_INFO_NULL, nr_threads,
/*dry_run=*/0);
#else
read_ic_serial(
ICfileName, &us, dim, &parts, &gparts, &sparts, &bparts, &Ngas, &Ngpart,
&Ngpart_background, &Nspart, &Nbpart, &flag_entropy_ICs, with_hydro,
/*with_grav=*/1, with_stars, with_black_holes, /*with_cosmology=*/1,
cleanup_h, cleanup_sqrt_a, cosmo.h, cosmo.a, myrank, nr_nodes,
MPI_COMM_WORLD, MPI_INFO_NULL, nr_threads, /*dry_run=*/0);
read_ic_serial(ICfileName, &us, dim, &parts, &gparts, &sparts, &bparts, &Ngas,
&Ngpart, &Ngpart_background, &Nspart, &Nbpart,
&flag_entropy_ICs, with_hydro,
/*with_grav=*/1, with_stars, with_black_holes, with_cosmology,
cleanup_h, cleanup_sqrt_a, cosmo.h, cosmo.a, myrank, nr_nodes,
MPI_COMM_WORLD, MPI_INFO_NULL, nr_threads, /*dry_run=*/0);
#endif
#else
read_ic_single(
ICfileName, &us, dim, &parts, &gparts, &sparts, &bparts, &Ngas, &Ngpart,
&Ngpart_background, &Nspart, &Nbpart, &flag_entropy_ICs, with_hydro,
/*with_grav=*/1, with_stars, with_black_holes, /*with_cosmology=*/1,
cleanup_h, cleanup_sqrt_a, cosmo.h, cosmo.a, nr_threads, /*dry_run=*/0);
/*with_grav=*/1, with_stars, with_black_holes, with_cosmology, cleanup_h,
cleanup_sqrt_a, cosmo.h, cosmo.a, nr_threads, /*dry_run=*/0);
#endif
#endif
if (myrank == 0) {
......@@ -532,7 +548,7 @@ int main(int argc, char *argv[]) {
/* Initialise the gravity scheme */
bzero(&gravity_properties, sizeof(struct gravity_props));
gravity_props_init(&gravity_properties, params, &prog_const, &cosmo,
/*with_cosmology=*/1, /*with_external_gravity=*/0,
with_cosmology, /*with_external_gravity=*/0,
with_baryon_particles, with_DM_particles,
with_DM_background_particles, periodic, s.dim);
......@@ -583,8 +599,8 @@ int main(int argc, char *argv[]) {
/* Construct the engine policy */
int engine_policies = ENGINE_POLICY | engine_policy_steal;
engine_policies |= engine_policy_self_gravity;
engine_policies |= engine_policy_cosmology;
engine_policies |= engine_policy_fof;
if (with_cosmology) engine_policies |= engine_policy_cosmology;
/* Initialize the engine with the space and policies. */
if (myrank == 0) clocks_gettime(&tic);
......
src/common_io.c
View file @ 1ac1d920
......@@ -206,11 +206,13 @@ void io_assert_valid_header_cosmology(hid_t h_grp, double a) {
&redshift_from_snapshot);
/* If the Header/Redshift value is not present, then we skip this check */
if (redshift_from_snapshot == -1.0) {
return;
}
if (redshift_from_snapshot == -1.0) return;
const double current_redshift = 1.0 / a - 1.0;
/* Escape if non-cosmological */
if (current_redshift == 0.) return;
const double redshift_fractional_difference =
fabs(redshift_from_snapshot - current_redshift) / current_redshift;
......
src/fof.c
View file @ 1ac1d920
......@@ -88,10 +88,12 @@ static integertime_t ti_current;
* @param params the parameter file parser.
* @param phys_const The physical constants in internal units.
* @param us The internal unit system.
* @param stand_alone_fof Are we initialising for stand-alone? (1) or
* on-the-fly? (0)
*/
void fof_init(struct fof_props *props, struct swift_params *params,
const struct phys_const *phys_const,
const struct unit_system *us) {
const struct phys_const *phys_const, const struct unit_system *us,
const int stand_alone_fof) {
/* Base name for the FOF output file */
parser_get_param_string(params, "FOF:basename", props->base_name);
......@@ -118,24 +120,27 @@ void fof_init(struct fof_props *props, struct swift_params *params,
/* Read the linking length ratio to the mean inter-particle separation. */
props->l_x_ratio =
parser_get_param_double(params, "FOF:linking_length_ratio");
if (props->l_x_ratio <= 0.)
error("The FOF linking length can't be negative!");
parser_get_opt_param_double(params, "FOF:linking_length_ratio", -1.);
/* Read value of absolute linking length aksed by the user */
props->l_x_absolute =
parser_get_opt_param_double(params, "FOF:absolute_linking_length", -1.);
if (props->l_x_ratio <= 0. && props->l_x_ratio != -1.)
if (props->l_x_ratio == -1. && props->l_x_absolute <= 0.)
error("The FOF linking length can't be negative!");
/* Read the minimal halo mass for black hole seeding */
props->seed_halo_mass =
parser_get_param_double(params, "FOF:black_hole_seed_halo_mass_Msun");
if (props->l_x_ratio <= 0. && props->l_x_absolute == -1.)
error("The FOF linking length ratio can't be negative!");
/* Convert to internal units */
props->seed_halo_mass *= phys_const->const_solar_mass;
if (!stand_alone_fof) {
/* Read the minimal halo mass for black hole seeding */
props->seed_halo_mass =
parser_get_param_double(params, "FOF:black_hole_seed_halo_mass_Msun");
/* Convert to internal units */
props->seed_halo_mass *= phys_const->const_solar_mass;
}
#if defined(WITH_MPI) && defined(UNION_BY_SIZE_OVER_MPI)
if (engine_rank == 0)
......@@ -262,26 +267,6 @@ void fof_allocate(const struct space *s, const long long total_nr_DM_particles,
}
}
/* Calculate the mean inter-particle separation as if we were in
a scenario where the entire box was filled with high-resolution
particles */
const double Omega_m = s->e->cosmology->Omega_m;
const double Omega_b = s->e->cosmology->Omega_b;
const double critical_density_0 = s->e->cosmology->critical_density_0;
double mean_matter_density;
if (s->with_hydro)
mean_matter_density = (Omega_m - Omega_b) * critical_density_0;
else
mean_matter_density = Omega_m * critical_density_0;
/* Mean inter-particle separation of the DM particles */
const double mean_inter_particle_sep =
cbrt(high_res_DM_mass / mean_matter_density);
/* Calculate the particle linking length based upon the mean inter-particle
* spacing of the DM particles. */
const double l_x = props->l_x_ratio * mean_inter_particle_sep;
/* Are we using the aboslute value or the one derived from the mean
inter-particle sepration? */
if (props->l_x_absolute != -1.) {
......@@ -292,6 +277,33 @@ void fof_allocate(const struct space *s, const long long total_nr_DM_particles,
props->l_x_absolute);
}
} else {
/* Safety check */
if (!(s->e->policy | engine_policy_cosmology))
error(
"Attempting to run FoF on a simulation using cosmological "
"information but cosmology was not initialised");
/* Calculate the mean inter-particle separation as if we were in
a scenario where the entire box was filled with high-resolution
particles */
const double Omega_m = s->e->cosmology->Omega_m;
const double Omega_b = s->e->cosmology->Omega_b;
const double critical_density_0 = s->e->cosmology->critical_density_0;
double mean_matter_density;
if (s->with_hydro)
mean_matter_density = (Omega_m - Omega_b) * critical_density_0;
else
mean_matter_density = Omega_m * critical_density_0;
/* Mean inter-particle separation of the DM particles */
const double mean_inter_particle_sep =
cbrt(high_res_DM_mass / mean_matter_density);
/* Calculate the particle linking length based upon the mean inter-particle
* spacing of the DM particles. */
const double l_x = props->l_x_ratio * mean_inter_particle_sep;
props->l_x2 = l_x * l_x;
if (s->e->nodeID == 0) {
......
src/fof.h
View file @ 1ac1d920
......@@ -159,8 +159,8 @@ struct cell_pair_indices {
/* Function prototypes. */
void fof_init(struct fof_props *props, struct swift_params *params,
const struct phys_const *phys_const,
const struct unit_system *us);
const struct phys_const *phys_const, const struct unit_system *us,
const int stand_alone_fof);
void fof_create_mpi_types(void);
void fof_allocate(const struct space *s, const long long total_nr_DM_particles,
struct fof_props *props);
......
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