diff --git a/src/parallel_io.c b/src/parallel_io.c
index cb02d1806c6ede5edfeaeb13d61cbecb09ac57e6..600eee21cece8692f839b94a53f8de819b450ab4 100644
--- a/src/parallel_io.c
+++ b/src/parallel_io.c
@@ -1171,22 +1171,28 @@ void write_output_parallel(struct engine* e, const char* baseName,
int mpi_rank, int mpi_size, MPI_Comm comm,
MPI_Info info) {
- const size_t Ngas = e->s->nr_parts;
- const size_t Nstars = e->s->nr_sparts;
- const size_t Ntot = e->s->nr_gparts;
const struct part* parts = e->s->parts;
const struct xpart* xparts = e->s->xparts;
const struct gpart* gparts = e->s->gparts;
- struct gpart* dmparts = NULL;
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;
/* Compute offset in the file and total number of particles */
- size_t N[swift_type_count] = {Ngas, Ndm, 0, 0, Nstars, 0};
+ size_t N[swift_type_count] = {Ngas_written, Ndm_written, 0, 0, Nstars_written, 0};
long long N_total[swift_type_count] = {0};
long long offset[swift_type_count] = {0};
MPI_Exscan(&N, &offset, swift_type_count, MPI_LONG_LONG_INT, MPI_SUM, comm);
@@ -1337,37 +1343,96 @@ void write_output_parallel(struct engine* e, const char* baseName,
struct io_props list[100];
size_t Nparticles = 0;
+ 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:
- Nparticles = 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 */
+ Nparticles = 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, e->cooling_func);
+ }
+ else {
+
+ /* Ok, we need to fish out the particles we want */
+ Nparticles = 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, e->cooling_func);
+ }
+ }
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 DM particles from gpart */
- io_collect_dm_gparts(gparts, Ntot, dmparts, Ndm);
-
- /* Write DM particles */
- Nparticles = Ndm;
- darkmatter_write_particles(dmparts, list, &num_fields);
+ {
+ if(Ntot == Ndm_written) {
+
+ /* This is a DM-only run without inhibited particles */
+ Nparticles = Ntot;
+ darkmatter_write_particles(gparts, list, &num_fields);
+ }
+ else {
+
+ /* Ok, we need to fish out the particles we want */
+ Nparticles = 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:
- Nparticles = Nstars;
- stars_write_particles(sparts, list, &num_fields);
+ {
+ if(Nstars == Nstars_written) {
+
+ /* No inhibted particles: easy case */
+ Nparticles = Nstars;
+ stars_write_particles(sparts, list, &num_fields);
+ }
+ else {
+
+ /* Ok, we need to fish out the particles we want */
+ Nparticles = 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:
@@ -1390,10 +1455,10 @@ void write_output_parallel(struct engine* e, const char* baseName,
}
/* Free temporary array */
- if (dmparts) {
- free(dmparts);
- dmparts = 0;
- }
+ if(parts_written) free(parts_written);
+ if(xparts_written) free(xparts_written);
+ if(gparts_written) free(gparts_written);
+ if(sparts_written) free(sparts_written);
#ifdef IO_SPEED_MEASUREMENT
MPI_Barrier(MPI_COMM_WORLD);
diff --git a/src/serial_io.c b/src/serial_io.c
index 32329a296f98687f4a44ad806b52eb259e65207c..5ae2062482a2ed0be62de006031e4ec135d329b3 100644
--- a/src/serial_io.c
+++ b/src/serial_io.c
@@ -739,22 +739,28 @@ void write_output_serial(struct engine* e, const char* baseName,
int mpi_size, MPI_Comm comm, MPI_Info info) {
hid_t h_file = 0, h_grp = 0;
- const size_t Ngas = e->s->nr_parts;
- const size_t Nstars = e->s->nr_sparts;
- const size_t Ntot = e->s->nr_gparts;
int periodic = e->s->periodic;
int numFiles = 1;
const struct part* parts = e->s->parts;
const struct xpart* xparts = e->s->xparts;
const struct gpart* gparts = e->s->gparts;
- struct gpart* dmparts = NULL;
const struct spart* sparts = e->s->sparts;
- const struct cooling_function_data* cooling = e->cooling_func;
struct swift_params* params = e->parameter_file;
FILE* xmfFile = 0;
- /* 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;
/* File name */
char fileName[FILENAME_BUFFER_SIZE];
@@ -766,7 +772,7 @@ 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, Ndm, 0, 0, Nstars, 0};
+ size_t N[swift_type_count] = {Ngas_written, Ndm_written, 0, 0, Nstars_written, 0};
long long N_total[swift_type_count] = {0};
long long offset[swift_type_count] = {0};
MPI_Exscan(&N, &offset, swift_type_count, MPI_LONG_LONG_INT, MPI_SUM, comm);
@@ -1012,35 +1018,96 @@ void write_output_serial(struct engine* e, const char* baseName,
struct io_props list[100];
size_t Nparticles = 0;
+ 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:
- Nparticles = 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);
- break;
+ {
+ if (Ngas == Ngas_written) {
+
+ /* No inhibted particles: easy case */
+ Nparticles = 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, e->cooling_func);
+ }
+ else {
+
+ /* Ok, we need to fish out the particles we want */
+ Nparticles = 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, e->cooling_func);
+ }
+ }
+ 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 DM particles from gpart */
- io_collect_dm_gparts(gparts, Ntot, dmparts, Ndm);
-
- /* Write DM particles */
- Nparticles = Ndm;
- darkmatter_write_particles(dmparts, list, &num_fields);
+ {
+ if(Ntot == Ndm_written) {
+
+ /* This is a DM-only run without inhibited particles */
+ Nparticles = Ntot;
+ darkmatter_write_particles(gparts, list, &num_fields);
+ }
+ else {
+
+ /* Ok, we need to fish out the particles we want */
+ Nparticles = 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:
- Nparticles = Nstars;
- stars_write_particles(sparts, list, &num_fields);
+ {
+ if(Nstars == Nstars_written) {
+
+ /* No inhibted particles: easy case */
+ Nparticles = Nstars;
+ stars_write_particles(sparts, list, &num_fields);
+ }
+ else {
+
+ /* Ok, we need to fish out the particles we want */
+ Nparticles = 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:
@@ -1063,10 +1130,10 @@ void write_output_serial(struct engine* e, const char* baseName,
}
/* Free temporary array */
- if (dmparts) {
- free(dmparts);
- dmparts = 0;
- }
+ 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);
diff --git a/src/single_io.c b/src/single_io.c
index 4a8e9ed25e7ede2432baffeeb38d38cdb52471cc..2586b2909a7c6df8d21c2e9ddbcb3c5dd29e6833 100644
--- a/src/single_io.c
+++ b/src/single_io.c
@@ -609,7 +609,6 @@ void write_output_single(struct engine* e, const char* baseName,
const struct xpart* xparts = e->s->xparts;
const struct gpart* gparts = e->s->gparts;
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 particles currently in the arrays */
@@ -852,7 +851,7 @@ void write_output_single(struct engine* e, const char* baseName,
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);
+ num_fields += cooling_write_particles(xparts, list + num_fields, e->cooling_func);
}
else {
@@ -871,7 +870,7 @@ void write_output_single(struct engine* e, const char* baseName,
/* 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);
+ num_fields += cooling_write_particles(xparts_written, list + num_fields, e->cooling_func);
}
}
break;