Modify the i/o routines to make sure we do not write out particles that do not exist.

src/common_io.c

@@ -811,7 +811,8 @@ void io_collect_parts_to_write(const struct part* restrict 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) {
+    if (parts[i].time_bin != time_bin_inhibited &&
+        parts[i].time_bin != time_bin_not_created) {
 
       parts_written[count] = parts[i];
       xparts_written[count] = xparts[i];
@@ -845,7 +846,8 @@ void io_collect_sparts_to_write(const struct spart* restrict sparts,
   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) {
+    if (sparts[i].time_bin != time_bin_inhibited &&
+        sparts[i].time_bin != time_bin_not_created) {
 
       sparts_written[count] = sparts[i];
       count++;
@@ -879,6 +881,7 @@ void io_collect_gparts_to_write(const struct gpart* restrict gparts,
 
     /* And collect the ones that have not been removed */
     if ((gparts[i].time_bin != time_bin_inhibited) &&
+        (gparts[i].time_bin != time_bin_not_created) &&
         (gparts[i].type == swift_type_dark_matter)) {
 
       gparts_written[count] = gparts[i];

src/parallel_io.c

@@ -1204,9 +1204,12 @@ void write_output_parallel(struct engine* e, const char* baseName,
   // 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 Ntot_written =
+      e->s->nr_gparts - e->s->nr_inhibited_gparts - e->s->nr_extra_gparts;
+  const size_t Ngas_written =
+      e->s->nr_parts - e->s->nr_inhibited_parts - e->s->nr_extra_parts;
+  const size_t Nstars_written =
+      e->s->nr_sparts - e->s->nr_inhibited_sparts - e->s->nr_extra_sparts;
   const size_t Nbaryons_written = Ngas_written + Nstars_written;
   const size_t Ndm_written =
       Ntot_written > 0 ? Ntot_written - Nbaryons_written : 0;

src/serial_io.c

@@ -775,9 +775,12 @@ void write_output_serial(struct engine* e, const char* baseName,
   // 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 Ntot_written =
+      e->s->nr_gparts - e->s->nr_inhibited_gparts - e->s->nr_extra_gparts;
+  const size_t Ngas_written =
+      e->s->nr_parts - e->s->nr_inhibited_parts - e->s->nr_extra_parts;
+  const size_t Nstars_written =
+      e->s->nr_sparts - e->s->nr_inhibited_sparts - e->s->nr_extra_sparts;
   const size_t Nbaryons_written = Ngas_written + Nstars_written;
   const size_t Ndm_written =
       Ntot_written > 0 ? Ntot_written - Nbaryons_written : 0;

src/single_io.c

@@ -639,9 +639,12 @@ void write_output_single(struct engine* e, const char* baseName,
   // 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 Ntot_written =
+      e->s->nr_gparts - e->s->nr_inhibited_gparts - e->s->nr_extra_gparts;
+  const size_t Ngas_written =
+      e->s->nr_parts - e->s->nr_inhibited_parts - e->s->nr_extra_parts;
+  const size_t Nstars_written =
+      e->s->nr_sparts - e->s->nr_inhibited_sparts - e->s->nr_extra_sparts;
   const size_t Nbaryons_written = Ngas_written + Nstars_written;
   const size_t Ndm_written =
       Ntot_written > 0 ? Ntot_written - Nbaryons_written : 0;