Updated the cell sanitization tool to give more sensible values to the extreme h outliers.

examples/main.c

@@ -418,6 +418,8 @@ int main(int argc, char *argv[]) {
   parser_get_param_string(params, "InitialConditions:file_name", ICfileName);
   const int replicate =
       parser_get_opt_param_int(params, "InitialConditions:replicate", 1);
+  const int clean_h_values =
+      parser_get_opt_param_int(params, "InitialConditions:cleanup_h", 0);
   if (myrank == 0) message("Reading ICs from file '%s'", ICfileName);
   fflush(stdout);
 
@@ -619,7 +621,7 @@ int main(int argc, char *argv[]) {
 #endif
 
   /* Initialise the particles */
-  engine_init_particles(&e, flag_entropy_ICs);
+  engine_init_particles(&e, flag_entropy_ICs, clean_h_values);
 
   /* Write the state of the system before starting time integration. */
   engine_dump_snapshot(&e);

examples/parameter_example.yml

@@ -60,6 +60,7 @@ Gravity:
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  SedovBlast/sedov.hdf5 # The file to read
+  cleanup_h:   0                    # (Optional) Clean the values of h that are read in. Set to 1 to activate.
   h_scaling:  1.                    # (Optional) A scaling factor to apply to all smoothing lengths in the ICs.
   shift_x:    0.                    # (Optional) A shift to apply to all particles read from the ICs (in internal units).
   shift_y:    0.

src/cell.c

@@ -941,53 +941,52 @@ void cell_split(struct cell *c, ptrdiff_t parts_offset, ptrdiff_t sparts_offset,
  * @brief Sanitizes the smoothing length values of cells by setting large
  * outliers to more sensible values.
  *
- * We compute the mean and standard deviation of the smoothing lengths in
- * logarithmic space and limit values to mean + 4 sigma.
+ * Each cell with <1000 part will be processed. We limit h to be the size of
+ * the cell and replace 0s with a good estimate.
  *
  * @param c The cell.
+ * @param treated Has the cell already been sanitized at this level ?
  */
-void cell_sanitize(struct cell *c) {
+void cell_sanitize(struct cell *c, int treated) {
 
   const int count = c->count;
   struct part *parts = c->parts;
+  float h_max = 0.f;
 
-  /* First collect some statistics */
-  float h_mean = 0.f, h_mean2 = 0.f;
-  float h_min = FLT_MAX, h_max = 0.f;
-  for (int i = 0; i < count; ++i) {
+  /* Treat cells will <1000 particles */
+  if (count < 1000 && !treated) {
 
-    const float h = logf(parts[i].h);
-    h_mean += h;
-    h_mean2 += h * h;
-    h_max = max(h_max, h);
-    h_min = min(h_min, h);
-  }
-  h_mean /= count;
-  h_mean2 /= count;
-  const float h_var = h_mean2 - h_mean * h_mean;
-  const float h_std = (h_var > 0.f) ? sqrtf(h_var) : 0.1f * h_mean;
-
-  /* Choose a cut */
-  const float h_limit = expf(h_mean + 4.f * h_std);
-
-  /* Be verbose this is not innocuous */
-  message("Cell properties: h_min= %f h_max= %f geometric mean= %f.",
-          expf(h_min), expf(h_max), expf(h_mean));
+    /* Get an upper bound on h */
+    const float upper_h_max = c->dmin / (1.2f * kernel_gamma);
 
-  if (c->h_max > h_limit) {
+    /* Apply it */
+    for (int i = 0; i < count; ++i) {
+      if (parts[i].h == 0.f || parts[i].h > upper_h_max)
+        parts[i].h = upper_h_max;
+    }
+  }
 
-    message("Smoothing lengths will be limited to (mean + 4sigma)= %f.",
-            h_limit);
+  /* Recurse and gather the new h_max values */
+  if (c->split) {
 
-    /* Apply the cut */
-    for (int i = 0; i < count; ++i) parts->h = min(parts[i].h, h_limit);
+    for (int k = 0; k < 8; ++k) {
+      if (c->progeny[k] != NULL) {
 
-    c->h_max = h_limit;
+        /* Recurse */
+        cell_sanitize(c->progeny[k], (count < 1000));
 
+        /* And collect */
+        h_max = max(h_max, c->progeny[k]->h_max);
+      }
+    }
   } else {
 
-    message("Smoothing lengths will not be limited.");
+    /* Get the new value of h_max */
+    for (int i = 0; i < count; ++i) h_max = max(h_max, parts[i].h);
   }
+
+  /* Record the change */
+  c->h_max = h_max;
 }
 
 /**

src/cell.h

@@ -344,7 +344,7 @@ struct cell {
 void cell_split(struct cell *c, ptrdiff_t parts_offset, ptrdiff_t sparts_offset,
                 struct cell_buff *buff, struct cell_buff *sbuff,
                 struct cell_buff *gbuff);
-void cell_sanitize(struct cell *c);
+void cell_sanitize(struct cell *c, int treated);
 int cell_locktree(struct cell *c);
 void cell_unlocktree(struct cell *c);
 int cell_glocktree(struct cell *c);

src/engine.c

@@ -2790,8 +2790,10 @@ void engine_print_task_counts(struct engine *e) {
  * @brief Rebuild the space and tasks.
  *
  * @param e The #engine.
+ * @param clean_h_values Are we cleaning up the values of h before building
+ * the tasks ?
  */
-void engine_rebuild(struct engine *e) {
+void engine_rebuild(struct engine *e, int clean_h_values) {
 
   const ticks tic = getticks();
 
@@ -2802,7 +2804,7 @@ void engine_rebuild(struct engine *e) {
   space_rebuild(e->s, e->verbose);
 
   /* Initial cleaning up session ? */
-  if (e->s->sanitized == 0) space_sanitize(e->s);
+  if (clean_h_values) space_sanitize(e->s);
 
 /* If in parallel, exchange the cell structure. */
 #ifdef WITH_MPI
@@ -2856,7 +2858,7 @@ void engine_prepare(struct engine *e) {
   if (e->forcerepart) engine_repartition(e);
 
   /* Do we need rebuilding ? */
-  if (e->forcerebuild) engine_rebuild(e);
+  if (e->forcerebuild) engine_rebuild(e, 0);
 
   /* Unskip active tasks and check for rebuild */
   engine_unskip(e);
@@ -3218,9 +3220,12 @@ void engine_launch(struct engine *e, int nr_runners) {
  *
  * @param e The #engine
  * @param flag_entropy_ICs Did the 'Internal Energy' of the particles actually
- *contain entropy ?
+ * contain entropy ?
+ * @param clean_h_values Are we cleaning up the values of h before building
+ * the tasks ?
  */
-void engine_init_particles(struct engine *e, int flag_entropy_ICs) {
+void engine_init_particles(struct engine *e, int flag_entropy_ICs,
+                           int clean_h_values) {
 
   struct space *s = e->s;
 
@@ -3237,7 +3242,7 @@ void engine_init_particles(struct engine *e, int flag_entropy_ICs) {
   }
 
   /* Construct all cells and tasks to start everything */
-  engine_rebuild(e);
+  engine_rebuild(e, clean_h_values);
 
   /* No time integration. We just want the density and ghosts */
   engine_skip_force_and_kick(e);

src/engine.h

@@ -272,7 +272,8 @@ void engine_init(struct engine *e, struct space *s,
                  struct sourceterms *sourceterms);
 void engine_launch(struct engine *e, int nr_runners);
 void engine_prepare(struct engine *e);
-void engine_init_particles(struct engine *e, int flag_entropy_ICs);
+void engine_init_particles(struct engine *e, int flag_entropy_ICs,
+                           int clean_h_values);
 void engine_step(struct engine *e);
 void engine_maketasks(struct engine *e);
 void engine_split(struct engine *e, struct partition *initial_partition);
@@ -281,7 +282,7 @@ void engine_exchange_strays(struct engine *e, size_t offset_parts,
                             int *ind_gpart, size_t *Ngpart,
                             size_t offset_sparts, int *ind_spart,
                             size_t *Nspart);
-void engine_rebuild(struct engine *e);
+void engine_rebuild(struct engine *e, int clean_h_values);
 void engine_repartition(struct engine *e);
 void engine_repartition_trigger(struct engine *e);
 void engine_makeproxies(struct engine *e);

src/space.c

@@ -962,28 +962,33 @@ void space_split(struct space *s, struct cell *cells, int nr_cells,
 }
 
 /**
- * @brief Runs through the top-level cells and checks whether tasks associated
- * with them can be split. If not, try to sanitize the cells.
+ * @brief #threadpool mapper function to sanitize the cells
  *
- * @param s The #space to act upon.
+ * @param map_data Pointers towards the top-level cells.
+ * @param num_cells The number of top-level cells.
+ * @param extra_data Unused parameters.
  */
-void space_sanitize(struct space *s) {
-
-  s->sanitized = 1;
+void space_sanitize_mapper(void *map_data, int num_cells, void *extra_data) {
+  /* Unpack the inputs. */
+  struct cell *cells_top = (struct cell *)map_data;
 
-  for (int k = 0; k < s->nr_cells; k++) {
+  for (int ind = 0; ind < num_cells; ind++) {
+    struct cell *c = &cells_top[ind];
+    cell_sanitize(c, 0);
+  }
+}
 
-    struct cell *c = &s->cells_top[k];
-    const double min_width = c->dmin;
+/**
+ * @brief Runs through the top-level cells and sanitize their h values
+ *
+ * @param s The #space to act upon.
+ */
+void space_sanitize(struct space *s) {
 
-    /* Do we have a problem ? */
-    if (c->h_max * kernel_gamma * space_stretch > min_width * 0.5 &&
-        c->count > space_maxcount) {
+  if (s->e->nodeID == 0) message("Cleaning up unreasonable values of h");
 
-      /* Ok, clean-up the mess */
-      cell_sanitize(c);
-    }
-  }
+  threadpool_map(&s->e->threadpool, space_sanitize_mapper, s->cells_top,
+                 s->nr_cells, sizeof(struct cell), 1, NULL);
 }
 
 /**
@@ -2630,7 +2635,6 @@ void space_init(struct space *s, const struct swift_params *params,
   s->dim[0] = dim[0];
   s->dim[1] = dim[1];
   s->dim[2] = dim[2];
-  s->sanitized = 0;
   s->periodic = periodic;
   s->gravity = gravity;
   s->nr_parts = Npart;

src/space.h

@@ -139,9 +139,6 @@ struct space {
   /*! Number of queues in the system. */
   int nr_queues;
 
-  /*! Has this space already been sanitized ? */
-  int sanitized;
-
   /*! The associated engine. */
   struct engine *e;