Commit 05cacf92 authored by Matthieu Schaller's avatar Matthieu Schaller
Browse files

When dumping a snapshot, fish out the particles that have not been inhibited.

parent 33c9cc37
......@@ -787,36 +787,102 @@ void io_duplicate_stars_gparts(struct threadpool* tp,
}
/**
* @brief Copy every DM #gpart into the dmparts array.
* @brief Copy every non-inhibited #part into the parts_written array.
*
* @param parts The array of #part containing all particles.
* @param xparts The array of #xpart containing all particles.
* @param parts_written The array of #part to fill with particles we want to write.
* @param xparts_written The array of #xpart to fill with particles we want to write.
* @param Nparts The total number of #part.
* @param Nparts_written The total number of #part to write.
*/
void io_collect_parts_to_write(const struct part* restrict parts,
const struct xpart* restrict xparts,
struct part* restrict parts_written,
struct xpart* restrict xparts_written,
const size_t Nparts, const size_t Nparts_written) {
size_t count = 0;
/* Loop over all parts */
for (size_t i = 0; i < Nparts; ++i) {
/* And collect the ones that have not been removed */
if(parts[i].time_bin != time_bin_inhibited) {
parts_written[count] = parts[i];
xparts_written[count] = xparts[i];
count++;
}
}
/* Check that everything is fine */
if (count != Nparts_written)
error("Collected the wrong number of particles (%zu vs. %zu expected)",
count, Nparts_written);
}
/**
* @brief Copy every non-inhibited #spart into the sparts_written array.
*
* @param sparts The array of #spart containing all particles.
* @param sparts_written The array of #spart to fill with particles we want to write.
* @param Nsparts The total number of #part.
* @param Nsparts_written The total number of #part to write.
*/
void io_collect_sparts_to_write(const struct spart* restrict sparts,
struct spart* restrict sparts_written,
const size_t Nsparts, const size_t Nsparts_written) {
size_t count = 0;
/* Loop over all parts */
for (size_t i = 0; i < Nsparts; ++i) {
/* And collect the ones that have not been removed */
if(sparts[i].time_bin != time_bin_inhibited) {
sparts_written[count] = sparts[i];
count++;
}
}
/* Check that everything is fine */
if (count != Nsparts_written)
error("Collected the wrong number of s-particles (%zu vs. %zu expected)",
count, Nsparts_written);
}
/**
* @brief Copy every non-inhibited DM #gpart into the gparts_written array.
*
* @param gparts The array of #gpart containing all particles.
* @param Ntot The number of #gpart.
* @param dmparts The array of #gpart containg DM particles to be filled.
* @param Ndm The number of DM particles.
* @param gparts_written The array of #gpart to fill with particles we want to write.
* @param Ngparts The total number of #part.
* @param Ngparts_written The total number of #part to write.
*/
void io_collect_dm_gparts(const struct gpart* const gparts, size_t Ntot,
struct gpart* const dmparts, size_t Ndm) {
void io_collect_gparts_to_write(const struct gpart* restrict gparts,
struct gpart* restrict gparts_written,
const size_t Ngparts, const size_t Ngparts_written) {
size_t count = 0;
/* Loop over all gparts */
for (size_t i = 0; i < Ntot; ++i) {
/* Loop over all parts */
for (size_t i = 0; i < Ngparts; ++i) {
/* message("i=%zd count=%zd id=%lld part=%p", i, count, gparts[i].id,
* gparts[i].part); */
/* And collect the ones that have not been removed */
if((gparts[i].time_bin != time_bin_inhibited) &&
(gparts[i].type == swift_type_dark_matter)) {
/* And collect the DM ones that have not been removed */
if (gparts[i].type == swift_type_dark_matter &&
gparts[i].time_bin != time_bin_inhibited) {
dmparts[count] = gparts[i];
gparts_written[count] = gparts[i];
count++;
}
}
/* Check that everything is fine */
if (count != Ndm)
error("Collected the wrong number of dm particles (%zu vs. %zu expected)",
count, Ndm);
if (count != Ngparts_written)
error("Collected the wrong number of s-particles (%zu vs. %zu expected)",
count, Ngparts_written);
}
/**
......
......@@ -35,6 +35,7 @@
struct part;
struct gpart;
struct spart;
struct xpart;
struct io_props;
struct engine;
struct threadpool;
......@@ -91,8 +92,17 @@ void io_copy_temp_buffer(void* temp, const struct engine* e,
size_t io_sizeof_type(enum IO_DATA_TYPE type);
int io_is_double_precision(enum IO_DATA_TYPE type);
void io_collect_dm_gparts(const struct gpart* const gparts, size_t Ntot,
struct gpart* const dmparts, size_t Ndm);
void io_collect_parts_to_write(const struct part* restrict parts,
const struct xpart* restrict xparts,
struct part* restrict parts_written,
struct xpart* restrict xparts_written,
const size_t Nparts, const size_t Nparts_written);
void io_collect_sparts_to_write(const struct spart* restrict sparts,
struct spart* restrict sparts_written,
const size_t Nsparts, const size_t Nsparts_written);
void io_collect_gparts_to_write(const struct gpart* restrict gparts,
struct gpart* restrict gparts_written,
const size_t Ngparts, const size_t Ngparts_written);
void io_prepare_dm_gparts(struct threadpool* tp, struct gpart* const gparts,
size_t Ndm);
void io_duplicate_hydro_gparts(struct threadpool* tp, struct part* const parts,
......
......@@ -603,9 +603,6 @@ void write_output_single(struct engine* e, const char* baseName,
const struct unit_system* snapshot_units) {
hid_t h_file = 0, h_grp = 0;
const size_t Ngas = e->total_nr_parts - e->nr_inhibited_parts;
const size_t Nstars = e->total_nr_sparts - e->nr_inhibited_sparts;
const size_t Ntot = e->total_nr_gparts - e->nr_inhibited_gparts;
int periodic = e->s->periodic;
int numFiles = 1;
const struct part* parts = e->s->parts;
......@@ -614,12 +611,24 @@ void write_output_single(struct engine* e, const char* baseName,
const struct spart* sparts = e->s->sparts;
const struct cooling_function_data* cooling = e->cooling_func;
struct swift_params* params = e->parameter_file;
/* Number of unassociated gparts */
const size_t Ndm = Ntot > 0 ? Ntot - (Ngas + Nstars) : 0;
/* Number of particles currently in the arrays */
const size_t Ntot = e->s->nr_gparts;
const size_t Ngas = e->s->nr_parts;
const size_t Nstars = e->s->nr_sparts;
//const size_t Nbaryons = Ngas + Nstars;
//const size_t Ndm = Ntot > 0 ? Ntot - Nbaryons : 0;
/* Number of particles that we will write */
const size_t Ntot_written = e->s->nr_gparts - e->s->nr_inhibited_sparts;
const size_t Ngas_written = e->s->nr_parts - e->s->nr_inhibited_parts;
const size_t Nstars_written = e->s->nr_sparts - e->s->nr_inhibited_gparts;
const size_t Nbaryons_written = Ngas_written + Nstars_written;
const size_t Ndm_written = Ntot_written > 0 ? Ntot_written - Nbaryons_written : 0;
/* Format things in a Gadget-friendly array */
long long N_total[swift_type_count] = {
(long long)Ngas, (long long)Ndm, 0, 0, (long long)Nstars, 0};
(long long)Ngas_written, (long long)Ndm_written, 0, 0, (long long)Nstars_written, 0};
/* File name */
char fileName[FILENAME_BUFFER_SIZE];
......@@ -827,38 +836,97 @@ void write_output_single(struct engine* e, const char* baseName,
struct io_props list[100];
size_t N = 0;
struct gpart* dmparts = NULL;
struct part* parts_written = NULL;
struct xpart* xparts_written = NULL;
struct gpart* gparts_written = NULL;
struct spart* sparts_written = NULL;
/* Write particle fields from the particle structure */
switch (ptype) {
case swift_type_gas:
N = Ngas;
hydro_write_particles(parts, xparts, list, &num_fields);
num_fields += chemistry_write_particles(parts, list + num_fields);
num_fields +=
cooling_write_particles(xparts, list + num_fields, cooling);
{
if (Ngas == Ngas_written) {
/* No inhibted particles: easy case */
N = Ngas;
hydro_write_particles(parts, xparts, list, &num_fields);
num_fields += chemistry_write_particles(parts, list + num_fields);
num_fields += cooling_write_particles(xparts, list + num_fields, cooling);
}
else {
/* Ok, we need to fish out the particles we want */
N = Ngas_written;
/* Allocate temporary arrays */
if (posix_memalign((void**)&parts_written, part_align, Ngas_written * sizeof(struct part)) != 0)
error("Error while allocating temporart memory for parts");
if (posix_memalign((void**)&xparts_written, xpart_align, Ngas_written * sizeof(struct xpart)) != 0)
error("Error while allocating temporart memory for xparts");
/* Collect the particles we want to write */
io_collect_parts_to_write(parts, xparts, parts_written, xparts_written, Ngas, Ngas_written);
/* Select the fields to write */
hydro_write_particles(parts_written, xparts_written, list, &num_fields);
num_fields += chemistry_write_particles(parts_written, list + num_fields);
num_fields += cooling_write_particles(xparts_written, list + num_fields, cooling);
}
}
break;
case swift_type_dark_matter:
/* Allocate temporary array */
if (posix_memalign((void**)&dmparts, gpart_align,
Ndm * sizeof(struct gpart)) != 0)
error("Error while allocating temporart memory for DM particles");
bzero(dmparts, Ndm * sizeof(struct gpart));
/* Collect the non-inhibited DM particles from gpart */
io_collect_dm_gparts(gparts, Ntot, dmparts, Ndm);
/* Write DM particles */
N = Ndm;
darkmatter_write_particles(dmparts, list, &num_fields);
{
if(Ntot == Ndm_written) {
/* This is a DM-only run without inhibited particles */
N = Ntot;
darkmatter_write_particles(gparts, list, &num_fields);
}
else {
/* Ok, we need to fish out the particles we want */
N = Ndm_written;
/* Allocate temporary array */
if (posix_memalign((void**)&gparts_written, gpart_align, Ndm_written * sizeof(struct gpart)) != 0)
error("Error while allocating temporart memory for gparts");
/* Collect the non-inhibited DM particles from gpart */
io_collect_gparts_to_write(gparts, gparts_written, Ntot, Ndm_written);
/* Write DM particles */
darkmatter_write_particles(gparts_written, list, &num_fields);
}
}
break;
case swift_type_stars:
N = Nstars;
stars_write_particles(sparts, list, &num_fields);
break;
{
if(Nstars == Nstars_written) {
/* No inhibted particles: easy case */
N = Nstars;
stars_write_particles(sparts, list, &num_fields);
}
else {
/* Ok, we need to fish out the particles we want */
N = Nstars_written;
/* Allocate temporary arrays */
if (posix_memalign((void**)&sparts_written, spart_align, Nstars_written * sizeof(struct spart)) != 0)
error("Error while allocating temporart memory for sparts");
/* Collect the particles we want to write */
io_collect_sparts_to_write(sparts, sparts_written, Nstars, Nstars_written);
/* Select the fields to write */
stars_write_particles(sparts, list, &num_fields);
}
}
break;
default:
error("Particle Type %d not yet supported. Aborting", ptype);
......@@ -878,12 +946,12 @@ void write_output_single(struct engine* e, const char* baseName,
internal_units, snapshot_units);
}
/* Free temporary array */
if (dmparts) {
free(dmparts);
dmparts = NULL;
}
/* Free temporary arrays */
if(parts_written) free(parts_written);
if(xparts_written) free(xparts_written);
if(gparts_written) free(gparts_written);
if(sparts_written) free(sparts_written);
/* Close particle group */
H5Gclose(h_grp);
......
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