From f68206d687ff7160930ed32c794711cdd1613d59 Mon Sep 17 00:00:00 2001
From: Sandro Elsweijer <sandro.elsweijer@dlr.de>
Date: Mon, 16 Sep 2024 17:03:19 +0200
Subject: [PATCH 01/24] move binary soearch to forest_private

---
 src/CMakeLists.txt                            |  2 +-
 src/t8_forest/t8_forest.cxx                   | 46 -------------------
 ...forest_private.c => t8_forest_private.cxx} | 46 +++++++++++++++++++
 src/t8_forest/t8_forest_private.h             | 11 +++++
 4 files changed, 58 insertions(+), 47 deletions(-)
 rename src/t8_forest/{t8_forest_private.c => t8_forest_private.cxx} (60%)

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index b562792f1d..35ab90de74 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -105,7 +105,7 @@ target_sources( T8 PRIVATE
     t8_forest/t8_forest_adapt.cxx 
     t8_forest/t8_forest_partition.cxx 
     t8_forest/t8_forest.cxx 
-    t8_forest/t8_forest_private.c 
+    t8_forest/t8_forest_private.cxx
     t8_forest/t8_forest_vtk.cxx 
     t8_forest/t8_forest_ghost.cxx 
     t8_forest/t8_forest_iterate.cxx 
diff --git a/src/t8_forest/t8_forest.cxx b/src/t8_forest/t8_forest.cxx
index 23a718fee4..1a3a2aa910 100644
--- a/src/t8_forest/t8_forest.cxx
+++ b/src/t8_forest/t8_forest.cxx
@@ -1441,52 +1441,6 @@ t8_forest_copy_trees (t8_forest_t forest, t8_forest_t from, int copy_elements)
   }
 }
 
-/* Search for a linear element id (at forest->maxlevel) in a sorted array of
- * elements. If the element does not exist, return the largest index i
- * such that the element at position i has a smaller id than the given one.
- * If no such i exists, return -1.
- */
-/* TODO: should return t8_locidx_t */
-static t8_locidx_t
-t8_forest_bin_search_lower (const t8_element_array_t *elements, const t8_linearidx_t element_id, const int maxlevel)
-{
-  t8_linearidx_t query_id;
-  t8_locidx_t low, high, guess;
-
-  const t8_eclass_scheme_c *ts = t8_element_array_get_scheme (elements);
-  /* At first, we check whether any element has smaller id than the
-   * given one. */
-  const t8_element_t *query = t8_element_array_index_int (elements, 0);
-  query_id = ts->t8_element_get_linear_id (query, maxlevel);
-  if (query_id > element_id) {
-    /* No element has id smaller than the given one */
-    return -1;
-  }
-
-  /* We now perform the binary search */
-  low = 0;
-  high = t8_element_array_get_count (elements) - 1;
-  while (low < high) {
-    guess = (low + high + 1) / 2;
-    query = t8_element_array_index_int (elements, guess);
-    query_id = ts->t8_element_get_linear_id (query, maxlevel);
-    if (query_id == element_id) {
-      /* we are done */
-      return guess;
-    }
-    else if (query_id > element_id) {
-      /* look further left */
-      high = guess - 1;
-    }
-    else {
-      /* look further right, but keep guess in the search range */
-      low = guess;
-    }
-  }
-  T8_ASSERT (low == high);
-  return low;
-}
-
 t8_eclass_t
 t8_forest_element_neighbor_eclass (t8_forest_t forest, t8_locidx_t ltreeid, const t8_element_t *elem, int face)
 {
diff --git a/src/t8_forest/t8_forest_private.c b/src/t8_forest/t8_forest_private.cxx
similarity index 60%
rename from src/t8_forest/t8_forest_private.c
rename to src/t8_forest/t8_forest_private.cxx
index 6febf22cc1..85a536b918 100644
--- a/src/t8_forest/t8_forest_private.c
+++ b/src/t8_forest/t8_forest_private.cxx
@@ -23,6 +23,9 @@
 #include <t8_forest/t8_forest_types.h>
 #include <t8_forest/t8_forest_private.h>
 #include <t8_forest/t8_forest_general.h>
+#include <t8_element.hxx>
+
+T8_EXTERN_C_BEGIN ();
 
 const t8_element_t*
 t8_forest_get_tree_element (t8_tree_t tree, t8_locidx_t elem_in_tree)
@@ -52,3 +55,46 @@ t8_forest_get_tree_element_array_mutable (const t8_forest_t forest, t8_locidx_t
 {
   return (t8_element_array_t*) t8_forest_get_tree_element_array (forest, ltreeid);
 }
+
+/* TODO: should return t8_locidx_t */
+t8_locidx_t
+t8_forest_bin_search_lower (const t8_element_array_t* elements, const t8_linearidx_t element_id, const int maxlevel)
+{
+  t8_linearidx_t query_id;
+  t8_locidx_t low, high, guess;
+
+  const t8_eclass_scheme_c* ts = t8_element_array_get_scheme (elements);
+  /* At first, we check whether any element has smaller id than the
+   * given one. */
+  const t8_element_t* query = t8_element_array_index_int (elements, 0);
+  query_id = ts->t8_element_get_linear_id (query, maxlevel);
+  if (query_id > element_id) {
+    /* No element has id smaller than the given one */
+    return -1;
+  }
+
+  /* We now perform the binary search */
+  low = 0;
+  high = t8_element_array_get_count (elements) - 1;
+  while (low < high) {
+    guess = (low + high + 1) / 2;
+    query = t8_element_array_index_int (elements, guess);
+    query_id = ts->t8_element_get_linear_id (query, maxlevel);
+    if (query_id == element_id) {
+      /* we are done */
+      return guess;
+    }
+    else if (query_id > element_id) {
+      /* look further left */
+      high = guess - 1;
+    }
+    else {
+      /* look further right, but keep guess in the search range */
+      low = guess;
+    }
+  }
+  T8_ASSERT (low == high);
+  return low;
+}
+
+T8_EXTERN_C_END ();
diff --git a/src/t8_forest/t8_forest_private.h b/src/t8_forest/t8_forest_private.h
index f43e244631..f4197c3409 100644
--- a/src/t8_forest/t8_forest_private.h
+++ b/src/t8_forest/t8_forest_private.h
@@ -195,6 +195,17 @@ t8_forest_get_tree_element_array (t8_forest_t forest, t8_locidx_t ltreeid);
 t8_element_array_t *
 t8_forest_get_tree_element_array_mutable (const t8_forest_t forest, t8_locidx_t ltreeid);
 
+/** Search for a linear element id (at forest->maxlevel) in a sorted array of
+ * elements. If the element does not exist, return the largest index i
+ * such that the element at position i has a smaller id than the given one.
+ * If no such i exists, return -1.
+ * \param [in]     elements    The array of elements.
+ * \param [in]     element_id  The linear id of the element to search for.
+ * \param [in]     maxlevel    The maximum level of the elements.
+ */
+t8_locidx_t
+t8_forest_bin_search_lower (const t8_element_array_t *elements, const t8_linearidx_t element_id, const int maxlevel);
+
 /** Find the owner process of a given element, deprecated version.
  * Use t8_forest_element_find_owner instead.
  * \param [in]     forest  The forest.

From 933ac8810ba457a96d2c70b4f6ec76aa1d662d5a Mon Sep 17 00:00:00 2001
From: Sandro Elsweijer <sandro.elsweijer@dlr.de>
Date: Mon, 16 Sep 2024 17:03:47 +0200
Subject: [PATCH 02/24] consting

---
 src/t8_forest/t8_forest.cxx | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/t8_forest/t8_forest.cxx b/src/t8_forest/t8_forest.cxx
index 1a3a2aa910..4b4eaf16a0 100644
--- a/src/t8_forest/t8_forest.cxx
+++ b/src/t8_forest/t8_forest.cxx
@@ -3643,11 +3643,10 @@ t8_forest_get_element (t8_forest_t forest, t8_locidx_t lelement_id, t8_locidx_t
 const t8_element_t *
 t8_forest_get_element_in_tree (t8_forest_t forest, t8_locidx_t ltreeid, t8_locidx_t leid_in_tree)
 {
-  t8_tree_t tree;
   T8_ASSERT (t8_forest_is_committed (forest));
   T8_ASSERT (0 <= ltreeid && ltreeid < t8_forest_get_num_local_trees (forest));
 
-  tree = t8_forest_get_tree (forest, ltreeid);
+  const t8_tree_t tree = t8_forest_get_tree (forest, ltreeid);
   const t8_element_t *element = t8_forest_get_tree_element (tree, leid_in_tree);
   T8_ASSERT (t8_forest_element_is_leaf (forest, element, ltreeid));
   return element;

From 1e0ef3711fbc67e499da70d544b4d72b1e65512b Mon Sep 17 00:00:00 2001
From: Sandro Elsweijer <sandro.elsweijer@dlr.de>
Date: Mon, 16 Sep 2024 17:05:44 +0200
Subject: [PATCH 03/24] add ghost retrieval functions

---
 src/t8_forest/t8_forest_ghost.cxx | 49 +++++++++++++++++++++++++++++++
 src/t8_forest/t8_forest_ghost.h   | 24 +++++++++++++++
 2 files changed, 73 insertions(+)

diff --git a/src/t8_forest/t8_forest_ghost.cxx b/src/t8_forest/t8_forest_ghost.cxx
index b537cb0ed3..be01f6c74e 100644
--- a/src/t8_forest/t8_forest_ghost.cxx
+++ b/src/t8_forest/t8_forest_ghost.cxx
@@ -303,6 +303,55 @@ t8_forest_ghost_tree_num_elements (t8_forest_t forest, t8_locidx_t lghost_tree)
   return t8_element_array_get_count (&ghost_tree->elements);
 }
 
+const t8_element_t *
+t8_ghost_get_ghost_in_tree (t8_forest_t forest, t8_locidx_t lghost_tree, t8_linearidx_t linear_id, int element_level,
+                            t8_locidx_t *loc_ghost_id)
+{
+  T8_ASSERT (t8_forest_is_committed (forest));
+  const t8_element_array_t *ghost_elements = t8_forest_ghost_get_tree_elements (forest, lghost_tree);
+  T8_ASSERT (ghost_elements != NULL);
+  /* Search for the element.
+   * The search returns the largest index i,
+   * such that the element at position i has a smaller id than the given one.
+   * If no such i exists, it returns -1. */
+  *loc_ghost_id = t8_forest_bin_search_lower (ghost_elements, linear_id, element_level);
+  if (*loc_ghost_id >= 0) {
+    /* The element was found */
+    return (const t8_element_t *) t8_sc_array_index_locidx (&(ghost_elements->array), *loc_ghost_id);
+  }
+  return nullptr;
+}
+
+t8_locidx_t
+t8_ghost_get_ghost_id_in_tree (t8_forest_t forest, t8_locidx_t lghost_tree, t8_element_t *ghost_element)
+{
+  T8_ASSERT (t8_forest_is_committed (forest));
+  const t8_element_array_t *ghost_elements = t8_forest_ghost_get_tree_elements (forest, lghost_tree);
+  T8_ASSERT (ghost_elements != NULL);
+  /* In order to find the element, we need to compute its linear id.
+   * To do so, we need the scheme and the level of the element. */
+  const t8_eclass_scheme_c *scheme = t8_element_array_get_scheme (ghost_elements);
+  const int ghost_level = scheme->t8_element_level (ghost_element);
+  /* Compute the linear id. */
+  const t8_linearidx_t element_id = scheme->t8_element_get_linear_id (ghost_element, ghost_level);
+  /* Search for the element */
+  int loc_ghost_id;
+  const t8_element_t *found_ghost
+    = t8_ghost_get_ghost_in_tree (forest, lghost_tree, element_id, ghost_level, &loc_ghost_id);
+  if (loc_ghost_id < 0) {
+    /* The element was not found */
+    return -1;
+  }
+  /* An element was found but it may not be the candidate element. 
+   * To identify whether the element was found, we compare these two. */
+  if (scheme->t8_element_equal (ghost_element, found_ghost)) {
+    return loc_ghost_id;
+  }
+  else {
+    return -1;
+  }
+}
+
 t8_element_array_t *
 t8_forest_ghost_get_tree_elements (const t8_forest_t forest, const t8_locidx_t lghost_tree)
 {
diff --git a/src/t8_forest/t8_forest_ghost.h b/src/t8_forest/t8_forest_ghost.h
index 9236f54312..140f363b78 100644
--- a/src/t8_forest/t8_forest_ghost.h
+++ b/src/t8_forest/t8_forest_ghost.h
@@ -69,6 +69,30 @@ t8_forest_ghost_get_tree_element_offset (t8_forest_t forest, t8_locidx_t lghost_
 t8_locidx_t
 t8_forest_ghost_tree_num_elements (t8_forest_t forest, t8_locidx_t lghost_tree);
 
+/** Retrieves the ghost index of an element in a specific ghost tree.
+ *
+ * \param [in] forest The forest object.
+ * \param [in] lghost_tree The local index of the ghost tree.
+ * \param [in] linear_id The local index of the element.
+ * \param [in] element_level The level of the element.
+ * \param [out] loc_ghost_id The local id of the ghost. -1 if no ghost was found.
+ * \return The ghost element. nullptr if no ghost was found.
+ */
+const t8_element_t *
+t8_ghost_get_ghost_in_tree (t8_forest_t forest, t8_locidx_t lghost_tree, t8_linearidx_t linear_id, int element_level,
+                            t8_locidx_t *loc_ghost_id);
+
+/** Retrieves the ghost index of an element in a specific ghost tree.
+ *
+ * \param [in] forest The forest object.
+ * \param [in] lghost_tree The local index of the ghost tree.
+ * \param [in] ghost_element The ghost element.
+ * \return The local index of the element in the ghost element array of the ghost tree.
+ *         -1 if no ghost element was found.
+ */
+t8_locidx_t
+t8_ghost_get_ghost_id_in_tree (t8_forest_t forest, t8_locidx_t lghost_tree, t8_element_t *ghost_element);
+
 /** Get a pointer to the ghost element array of a ghost tree.
  * \param [in]  forest    The forest. Ghost layer must exist.
  * \param [in]  lghost_tree The ghost tree id of a ghost tree.

From 3fee901469f7bccccdacf69a79c0cff440531d7b Mon Sep 17 00:00:00 2001
From: Johannes Holke <johannes.holke@dlr.de>
Date: Wed, 18 Sep 2024 12:17:00 +0200
Subject: [PATCH 04/24] Typos

---
 src/t8_forest/t8_forest_ghost.cxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/t8_forest/t8_forest_ghost.cxx b/src/t8_forest/t8_forest_ghost.cxx
index be01f6c74e..394a33c45c 100644
--- a/src/t8_forest/t8_forest_ghost.cxx
+++ b/src/t8_forest/t8_forest_ghost.cxx
@@ -1938,9 +1938,9 @@ t8_forest_ghost_destroy (t8_forest_ghost_t *pghost)
 
 /**
  * Implementation of the ghost-interface
- * Wrapper for the abstracte base classe
+ * Wrapper for the abstracte base class
  * Implementation of the comunication steps
- * and implementation of the dreived classe search
+ * and implementation of the dreived class search
 */
 
 t8_ghost_type_t 

From 8c171a8b65a0381cf69dfd63b72736dceb76585f Mon Sep 17 00:00:00 2001
From: Johannes Holke <johannes.holke@dlr.de>
Date: Tue, 24 Sep 2024 16:27:56 +0200
Subject: [PATCH 05/24] Update src/t8_forest/t8_forest_ghost.cxx

---
 src/t8_forest/t8_forest_ghost.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/t8_forest/t8_forest_ghost.cxx b/src/t8_forest/t8_forest_ghost.cxx
index 394a33c45c..af47985b47 100644
--- a/src/t8_forest/t8_forest_ghost.cxx
+++ b/src/t8_forest/t8_forest_ghost.cxx
@@ -317,7 +317,7 @@ t8_ghost_get_ghost_in_tree (t8_forest_t forest, t8_locidx_t lghost_tree, t8_line
   *loc_ghost_id = t8_forest_bin_search_lower (ghost_elements, linear_id, element_level);
   if (*loc_ghost_id >= 0) {
     /* The element was found */
-    return (const t8_element_t *) t8_sc_array_index_locidx (&(ghost_elements->array), *loc_ghost_id);
+    return t8_element_array_index_locidx (ghost_elements, *loc_ghost_id);
   }
   return nullptr;
 }

From 5616096041297d6c21b418ba020e5b198c2959fb Mon Sep 17 00:00:00 2001
From: Johannes Holke <johannes.holke@dlr.de>
Date: Tue, 24 Sep 2024 16:28:05 +0200
Subject: [PATCH 06/24] Update src/t8_forest/t8_forest_ghost.h

---
 src/t8_forest/t8_forest_ghost.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/t8_forest/t8_forest_ghost.h b/src/t8_forest/t8_forest_ghost.h
index 140f363b78..e67048be6a 100644
--- a/src/t8_forest/t8_forest_ghost.h
+++ b/src/t8_forest/t8_forest_ghost.h
@@ -73,7 +73,7 @@ t8_forest_ghost_tree_num_elements (t8_forest_t forest, t8_locidx_t lghost_tree);
  *
  * \param [in] forest The forest object.
  * \param [in] lghost_tree The local index of the ghost tree.
- * \param [in] linear_id The local index of the element.
+ * \param [in] linear_id The linear id of the element.
  * \param [in] element_level The level of the element.
  * \param [out] loc_ghost_id The local id of the ghost. -1 if no ghost was found.
  * \return The ghost element. nullptr if no ghost was found.

From 574b4152e7992ce1797e9f1bfaa9dc317dfedf5b Mon Sep 17 00:00:00 2001
From: Johannes Holke <johannes.holke@dlr.de>
Date: Tue, 24 Sep 2024 16:28:14 +0200
Subject: [PATCH 07/24] Update src/t8_forest/t8_forest_private.cxx

---
 src/t8_forest/t8_forest_private.cxx | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/t8_forest/t8_forest_private.cxx b/src/t8_forest/t8_forest_private.cxx
index 85a536b918..6e09489e26 100644
--- a/src/t8_forest/t8_forest_private.cxx
+++ b/src/t8_forest/t8_forest_private.cxx
@@ -56,7 +56,6 @@ t8_forest_get_tree_element_array_mutable (const t8_forest_t forest, t8_locidx_t
   return (t8_element_array_t*) t8_forest_get_tree_element_array (forest, ltreeid);
 }
 
-/* TODO: should return t8_locidx_t */
 t8_locidx_t
 t8_forest_bin_search_lower (const t8_element_array_t* elements, const t8_linearidx_t element_id, const int maxlevel)
 {

From 5909a16c87d7c0086bb206ce2ba598f5631cbee4 Mon Sep 17 00:00:00 2001
From: Johannes Holke <johannes.holke@dlr.de>
Date: Tue, 24 Sep 2024 16:28:26 +0200
Subject: [PATCH 08/24] Update src/t8_forest/t8_forest_private.h

---
 src/t8_forest/t8_forest_private.h | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/t8_forest/t8_forest_private.h b/src/t8_forest/t8_forest_private.h
index f4197c3409..4d03aeffaa 100644
--- a/src/t8_forest/t8_forest_private.h
+++ b/src/t8_forest/t8_forest_private.h
@@ -199,6 +199,7 @@ t8_forest_get_tree_element_array_mutable (const t8_forest_t forest, t8_locidx_t
  * elements. If the element does not exist, return the largest index i
  * such that the element at position i has a smaller id than the given one.
  * If no such i exists, return -1.
+ * \note This search does not work for subelements.
  * \param [in]     elements    The array of elements.
  * \param [in]     element_id  The linear id of the element to search for.
  * \param [in]     maxlevel    The maximum level of the elements.

From 31e9d928b3442969e123b01efdeacb03f2cd8193 Mon Sep 17 00:00:00 2001
From: Johannes Holke <johannes.holke@dlr.de>
Date: Fri, 18 Oct 2024 13:11:38 +0200
Subject: [PATCH 09/24] indent example

---
 benchmarks/time_forest_partition.cxx | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/benchmarks/time_forest_partition.cxx b/benchmarks/time_forest_partition.cxx
index fc280e2e62..674ee56734 100644
--- a/benchmarks/time_forest_partition.cxx
+++ b/benchmarks/time_forest_partition.cxx
@@ -421,11 +421,12 @@ main (int argc, char *argv[])
   /* check for wrong usage of arguments */
   if (first_argc < 0 || first_argc != argc || dim < 2 || dim > 3
       || (cmeshfileprefix == NULL && mshfileprefix == NULL && test_tet == 0 && test_cad_cylinder == 0
-          && test_linear_cylinder == 0 && test_hybrid_cube == 0 && test_hex_cube == 0 )
+          && test_linear_cylinder == 0 && test_hybrid_cube == 0 && test_hex_cube == 0)
       || stride <= 0 || (num_files - 1) * stride >= mpisize || cfl < 0 || T <= 0
       || test_tet + test_linear_cylinder + test_cad_cylinder + test_hybrid_cube + test_hex_cube > 1
       || (cmesh_level >= 0 && (!test_linear_cylinder && !test_cad_cylinder && !test_hybrid_cube && !test_hex_cube))
-      || ((mshfileprefix != NULL || cmeshfileprefix != NULL) && (test_linear_cylinder || test_cad_cylinder || test_tet || test_hybrid_cube || test_hex_cube))
+      || ((mshfileprefix != NULL || cmeshfileprefix != NULL)
+          && (test_linear_cylinder || test_cad_cylinder || test_tet || test_hybrid_cube || test_hex_cube))
       || (mshfileprefix == NULL && use_cad)) {
     sc_options_print_usage (t8_get_package_id (), SC_LP_ERROR, opt, NULL);
     return 1;
@@ -460,12 +461,12 @@ main (int argc, char *argv[])
                                             sc_intpow (2, cmesh_level), sc_intpow (2, cmesh_level), test_cad_cylinder);
       test_linear_cylinder ? vtu_prefix = "test_linear_cylinder" : vtu_prefix = "test_cad_cylinder";
     }
-    else if (test_hybrid_cube){
+    else if (test_hybrid_cube) {
       cmesh = t8_cmesh_new_hypercube_hybrid (sc_MPI_COMM_WORLD, 0, 0);
       vtu_prefix = "test_hypercube_hybrid";
     }
-    else if (test_hex_cube){
-      cmesh = t8_cmesh_new_hypercube(T8_ECLASS_HEX, sc_MPI_COMM_WORLD, 0, 0, 0);
+    else if (test_hex_cube) {
+      cmesh = t8_cmesh_new_hypercube (T8_ECLASS_HEX, sc_MPI_COMM_WORLD, 0, 0, 0);
       vtu_prefix = "test_hypercube_hex";
     }
     else {

From e718252fa5177275d0f09bc5506da34f7081b563 Mon Sep 17 00:00:00 2001
From: Johannes Holke <johannes.holke@dlr.de>
Date: Tue, 29 Oct 2024 11:34:14 +0100
Subject: [PATCH 10/24] Fix Makefile line wrap

---
 src/Makefile.am | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Makefile.am b/src/Makefile.am
index e2bc6ba6e7..ac4b843944 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -59,7 +59,7 @@ libt8_installed_headers_forest = \
   src/t8_forest/t8_forest_ghost_interface_wrapper.h \
   src/t8_forest/t8_forest_ghost_interface.h \
   src/t8_forest/t8_forest_ghost_interface.hxx \
-  src/t8_forest/t8_forest_ghost_search.hxx
+  src/t8_forest/t8_forest_ghost_search.hxx \
   src/t8_forest/t8_forest_ghost_stencil.hxx
 libt8_installed_headers_geometry = \
   src/t8_geometry/t8_geometry.h \

From 8d929a8d7b4a1d64a116f6f1161f9083a02b61ac Mon Sep 17 00:00:00 2001
From: Johannes Holke <johannes.holke@dlr.de>
Date: Tue, 29 Oct 2024 11:48:08 +0100
Subject: [PATCH 11/24] Add new bin search to private and remove from static

---
 src/t8_forest/t8_forest.cxx         | 33 ------------------
 src/t8_forest/t8_forest_private.cxx | 53 +++++++++++++----------------
 2 files changed, 23 insertions(+), 63 deletions(-)

diff --git a/src/t8_forest/t8_forest.cxx b/src/t8_forest/t8_forest.cxx
index a434708ef1..d0893292b6 100644
--- a/src/t8_forest/t8_forest.cxx
+++ b/src/t8_forest/t8_forest.cxx
@@ -1444,39 +1444,6 @@ t8_forest_copy_trees (t8_forest_t forest, t8_forest_t from, int copy_elements)
   }
 }
 
-/** \brief Search for a linear element id (at forest->maxlevel) in a sorted array of
- * elements. If the element does not exist, return the largest index i
- * such that the element at position i has a smaller id than the given one.
- * If no such i exists, return -1.
- */
-static t8_locidx_t
-t8_forest_bin_search_lower (const t8_element_array_t *elements, const t8_linearidx_t element_id, const int maxlevel)
-{
-  const t8_eclass_scheme_c *ts = t8_element_array_get_scheme (elements);
-  /* At first, we check whether any element has smaller id than the
-   * given one. */
-  const t8_element_t *query = t8_element_array_index_int (elements, 0);
-  const t8_linearidx_t query_id = ts->t8_element_get_linear_id (query, maxlevel);
-  if (query_id > element_id) {
-    /* No element has id smaller than the given one. */
-    return -1;
-  }
-
-  /* We search for the first element in the array that is greater than the given element id. */
-  auto elem_iter = std::upper_bound (
-    t8_element_array_begin (elements), t8_element_array_end (elements), element_id,
-    [&maxlevel, &ts] (const t8_linearidx_t element_id_, const t8_element_array_iterator::value_type &elem_ptr) {
-      return (element_id_ < ts->t8_element_get_linear_id (elem_ptr, maxlevel));
-    });
-
-  /* After we found the element with an id greater than the given one, we are able to jump one index back.
-   * This guarantees us that the element at (index - 1) is smaller or equal to the given element id.
-   * In case we do not find an element that is greater than the given element_id, the binary search returns
-   * the end-iterator of the element array. In that case, we want to return the last index from the element
-   * array. */
-  return elem_iter.GetCurrentIndex () - 1;
-}
-
 t8_eclass_t
 t8_forest_element_neighbor_eclass (t8_forest_t forest, t8_locidx_t ltreeid, const t8_element_t *elem, int face)
 {
diff --git a/src/t8_forest/t8_forest_private.cxx b/src/t8_forest/t8_forest_private.cxx
index 6e09489e26..426585fb89 100644
--- a/src/t8_forest/t8_forest_private.cxx
+++ b/src/t8_forest/t8_forest_private.cxx
@@ -56,44 +56,37 @@ t8_forest_get_tree_element_array_mutable (const t8_forest_t forest, t8_locidx_t
   return (t8_element_array_t*) t8_forest_get_tree_element_array (forest, ltreeid);
 }
 
+/** \brief Search for a linear element id (at forest->maxlevel) in a sorted array of
+ * elements. If the element does not exist, return the largest index i
+ * such that the element at position i has a smaller id than the given one.
+ * If no such i exists, return -1.
+ */
 t8_locidx_t
-t8_forest_bin_search_lower (const t8_element_array_t* elements, const t8_linearidx_t element_id, const int maxlevel)
+t8_forest_bin_search_lower (const t8_element_array_t *elements, const t8_linearidx_t element_id, const int maxlevel)
 {
-  t8_linearidx_t query_id;
-  t8_locidx_t low, high, guess;
-
-  const t8_eclass_scheme_c* ts = t8_element_array_get_scheme (elements);
+  const t8_eclass_scheme_c *ts = t8_element_array_get_scheme (elements);
   /* At first, we check whether any element has smaller id than the
    * given one. */
-  const t8_element_t* query = t8_element_array_index_int (elements, 0);
-  query_id = ts->t8_element_get_linear_id (query, maxlevel);
+  const t8_element_t *query = t8_element_array_index_int (elements, 0);
+  const t8_linearidx_t query_id = ts->t8_element_get_linear_id (query, maxlevel);
   if (query_id > element_id) {
-    /* No element has id smaller than the given one */
+    /* No element has id smaller than the given one. */
     return -1;
   }
 
-  /* We now perform the binary search */
-  low = 0;
-  high = t8_element_array_get_count (elements) - 1;
-  while (low < high) {
-    guess = (low + high + 1) / 2;
-    query = t8_element_array_index_int (elements, guess);
-    query_id = ts->t8_element_get_linear_id (query, maxlevel);
-    if (query_id == element_id) {
-      /* we are done */
-      return guess;
-    }
-    else if (query_id > element_id) {
-      /* look further left */
-      high = guess - 1;
-    }
-    else {
-      /* look further right, but keep guess in the search range */
-      low = guess;
-    }
-  }
-  T8_ASSERT (low == high);
-  return low;
+  /* We search for the first element in the array that is greater than the given element id. */
+  auto elem_iter = std::upper_bound (
+    t8_element_array_begin (elements), t8_element_array_end (elements), element_id,
+    [&maxlevel, &ts] (const t8_linearidx_t element_id_, const t8_element_array_iterator::value_type &elem_ptr) {
+      return (element_id_ < ts->t8_element_get_linear_id (elem_ptr, maxlevel));
+    });
+
+  /* After we found the element with an id greater than the given one, we are able to jump one index back.
+   * This guarantees us that the element at (index - 1) is smaller or equal to the given element id.
+   * In case we do not find an element that is greater than the given element_id, the binary search returns
+   * the end-iterator of the element array. In that case, we want to return the last index from the element
+   * array. */
+  return elem_iter.GetCurrentIndex () - 1;
 }
 
 T8_EXTERN_C_END ();

From 2d977da9d228620f78872a7eebec7fd2e68448c3 Mon Sep 17 00:00:00 2001
From: Johannes Holke <johannes.holke@dlr.de>
Date: Tue, 29 Oct 2024 11:48:50 +0100
Subject: [PATCH 12/24] rename get ghost function to better match parameters

---
 src/t8_forest/t8_forest_ghost.cxx | 9 +++++----
 src/t8_forest/t8_forest_ghost.h   | 4 ++--
 2 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/src/t8_forest/t8_forest_ghost.cxx b/src/t8_forest/t8_forest_ghost.cxx
index fd34e260bb..07c9543df5 100644
--- a/src/t8_forest/t8_forest_ghost.cxx
+++ b/src/t8_forest/t8_forest_ghost.cxx
@@ -304,12 +304,13 @@ t8_forest_ghost_tree_num_elements (t8_forest_t forest, t8_locidx_t lghost_tree)
 }
 
 const t8_element_t *
-t8_ghost_get_ghost_in_tree (t8_forest_t forest, t8_locidx_t lghost_tree, t8_linearidx_t linear_id, int element_level,
-                            t8_locidx_t *loc_ghost_id)
+t8_ghost_get_ghost_in_tree_from_linear_id (t8_forest_t forest, t8_locidx_t lghost_tree, t8_linearidx_t linear_id,
+                                           int element_level, t8_locidx_t *loc_ghost_id)
 {
   T8_ASSERT (t8_forest_is_committed (forest));
   const t8_element_array_t *ghost_elements = t8_forest_ghost_get_tree_elements (forest, lghost_tree);
   T8_ASSERT (ghost_elements != NULL);
+  T8_ASSERT (forest->incomplete_trees);  // This function will not word properlt with incomplete trees.
   /* Search for the element.
    * The search returns the largest index i,
    * such that the element at position i has a smaller id than the given one.
@@ -335,9 +336,9 @@ t8_ghost_get_ghost_id_in_tree (t8_forest_t forest, t8_locidx_t lghost_tree, t8_e
   /* Compute the linear id. */
   const t8_linearidx_t element_id = scheme->t8_element_get_linear_id (ghost_element, ghost_level);
   /* Search for the element */
-  int loc_ghost_id;
+  t8_locidx_t loc_ghost_id;
   const t8_element_t *found_ghost
-    = t8_ghost_get_ghost_in_tree (forest, lghost_tree, element_id, ghost_level, &loc_ghost_id);
+    = t8_ghost_get_ghost_in_tree_from_linear_id (forest, lghost_tree, element_id, ghost_level, &loc_ghost_id);
   if (loc_ghost_id < 0) {
     /* The element was not found */
     return -1;
diff --git a/src/t8_forest/t8_forest_ghost.h b/src/t8_forest/t8_forest_ghost.h
index e7703da12f..a6c4eba608 100644
--- a/src/t8_forest/t8_forest_ghost.h
+++ b/src/t8_forest/t8_forest_ghost.h
@@ -79,8 +79,8 @@ t8_forest_ghost_tree_num_elements (t8_forest_t forest, t8_locidx_t lghost_tree);
  * \return The ghost element. nullptr if no ghost was found.
  */
 const t8_element_t *
-t8_ghost_get_ghost_in_tree (t8_forest_t forest, t8_locidx_t lghost_tree, t8_linearidx_t linear_id, int element_level,
-                            t8_locidx_t *loc_ghost_id);
+t8_ghost_get_ghost_in_tree_from_linear_id (t8_forest_t forest, t8_locidx_t lghost_tree, t8_linearidx_t linear_id,
+                                           int element_level, t8_locidx_t *loc_ghost_id);
 
 /** Retrieves the ghost index of an element in a specific ghost tree.
  *

From 4581fe0d29b7a187dfc4ace38ed5b5b9dc89e08b Mon Sep 17 00:00:00 2001
From: Johannes Holke <johannes.holke@dlr.de>
Date: Tue, 29 Oct 2024 11:49:00 +0100
Subject: [PATCH 13/24] indent

---
 src/t8_forest/t8_forest_private.cxx | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/t8_forest/t8_forest_private.cxx b/src/t8_forest/t8_forest_private.cxx
index 426585fb89..71770198ea 100644
--- a/src/t8_forest/t8_forest_private.cxx
+++ b/src/t8_forest/t8_forest_private.cxx
@@ -27,7 +27,7 @@
 
 T8_EXTERN_C_BEGIN ();
 
-const t8_element_t*
+const t8_element_t *
 t8_forest_get_tree_element (t8_tree_t tree, t8_locidx_t elem_in_tree)
 {
   T8_ASSERT (tree != NULL);
@@ -35,13 +35,13 @@ t8_forest_get_tree_element (t8_tree_t tree, t8_locidx_t elem_in_tree)
   return t8_element_array_index_locidx (&tree->elements, elem_in_tree);
 }
 
-t8_element_t*
+t8_element_t *
 t8_forest_get_tree_element_mutable (t8_tree_t tree, t8_locidx_t elem_in_tree)
 {
-  return (t8_element_t*) t8_forest_get_tree_element (tree, elem_in_tree);
+  return (t8_element_t *) t8_forest_get_tree_element (tree, elem_in_tree);
 }
 
-const t8_element_array_t*
+const t8_element_array_t *
 t8_forest_get_tree_element_array (const t8_forest_t forest, t8_locidx_t ltreeid)
 {
   T8_ASSERT (t8_forest_is_committed (forest));
@@ -50,10 +50,10 @@ t8_forest_get_tree_element_array (const t8_forest_t forest, t8_locidx_t ltreeid)
   return &t8_forest_get_tree (forest, ltreeid)->elements;
 }
 
-t8_element_array_t*
+t8_element_array_t *
 t8_forest_get_tree_element_array_mutable (const t8_forest_t forest, t8_locidx_t ltreeid)
 {
-  return (t8_element_array_t*) t8_forest_get_tree_element_array (forest, ltreeid);
+  return (t8_element_array_t *) t8_forest_get_tree_element_array (forest, ltreeid);
 }
 
 /** \brief Search for a linear element id (at forest->maxlevel) in a sorted array of

From 49b2dc37ef09c15cda3c766b8664caa6da6d73f2 Mon Sep 17 00:00:00 2001
From: Johannes Holke <johannes.holke@dlr.de>
Date: Tue, 29 Oct 2024 11:58:53 +0100
Subject: [PATCH 14/24] remove vtk file from build list

---
 src/CMakeLists.txt | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index c5a4c823b5..4b94e9a294 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -109,7 +109,6 @@ target_sources( T8 PRIVATE
     t8_forest/t8_forest_partition.cxx 
     t8_forest/t8_forest.cxx 
     t8_forest/t8_forest_private.cxx
-    t8_forest/t8_forest_vtk.cxx 
     t8_forest/t8_forest_ghost.cxx 
     t8_forest/t8_forest_iterate.cxx 
     t8_forest/t8_forest_balance.cxx 

From 38deaa6ed6fca2be1cbed5699e778213ad81fea9 Mon Sep 17 00:00:00 2001
From: Johannes Holke <johannes.holke@dlr.de>
Date: Tue, 29 Oct 2024 12:07:44 +0100
Subject: [PATCH 15/24] finish moving bin search - move includes

---
 src/t8_forest/t8_forest.cxx         | 3 ---
 src/t8_forest/t8_forest_private.cxx | 2 ++
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/t8_forest/t8_forest.cxx b/src/t8_forest/t8_forest.cxx
index d0893292b6..0fd3f5a12f 100644
--- a/src/t8_forest/t8_forest.cxx
+++ b/src/t8_forest/t8_forest.cxx
@@ -46,9 +46,6 @@
 #include <t8_geometry/t8_geometry_implementations/t8_geometry_linear.h>
 #include <t8_geometry/t8_geometry_implementations/t8_geometry_linear_axis_aligned.h>
 #endif
-#include <t8_data/t8_element_array_iterator.hxx>
-
-#include <algorithm>
 
 /* We want to export the whole implementation to be callable from "C" */
 T8_EXTERN_C_BEGIN ();
diff --git a/src/t8_forest/t8_forest_private.cxx b/src/t8_forest/t8_forest_private.cxx
index 71770198ea..ce9c31bacf 100644
--- a/src/t8_forest/t8_forest_private.cxx
+++ b/src/t8_forest/t8_forest_private.cxx
@@ -24,6 +24,8 @@
 #include <t8_forest/t8_forest_private.h>
 #include <t8_forest/t8_forest_general.h>
 #include <t8_element.hxx>
+#include <t8_data/t8_element_array_iterator.hxx>
+#include <algorithm>
 
 T8_EXTERN_C_BEGIN ();
 

From 975e66bbd590a221d923eed3bdcb2e923c10ebef Mon Sep 17 00:00:00 2001
From: Johannes Holke <johannes.holke@dlr.de>
Date: Tue, 29 Oct 2024 12:16:08 +0100
Subject: [PATCH 16/24] improve documentation

---
 src/t8_forest/t8_forest_ghost.h | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/t8_forest/t8_forest_ghost.h b/src/t8_forest/t8_forest_ghost.h
index a6c4eba608..f68c66f7ac 100644
--- a/src/t8_forest/t8_forest_ghost.h
+++ b/src/t8_forest/t8_forest_ghost.h
@@ -69,7 +69,7 @@ t8_forest_ghost_get_tree_element_offset (t8_forest_t forest, t8_locidx_t lghost_
 t8_locidx_t
 t8_forest_ghost_tree_num_elements (t8_forest_t forest, t8_locidx_t lghost_tree);
 
-/** Retrieves the ghost index of an element in a specific ghost tree.
+/** Retrieves a ghost element from its ghost tree given the element's linear id.
  *
  * \param [in] forest The forest object.
  * \param [in] lghost_tree The local index of the ghost tree.
@@ -82,7 +82,7 @@ const t8_element_t *
 t8_ghost_get_ghost_in_tree_from_linear_id (t8_forest_t forest, t8_locidx_t lghost_tree, t8_linearidx_t linear_id,
                                            int element_level, t8_locidx_t *loc_ghost_id);
 
-/** Retrieves the ghost index of an element in a specific ghost tree.
+/** Retrieves the local index of a ghost element in its specific ghost tree.
  *
  * \param [in] forest The forest object.
  * \param [in] lghost_tree The local index of the ghost tree.

From c79445b8a421ce3f6a57db99ddc6e7a09eb2cad8 Mon Sep 17 00:00:00 2001
From: Johannes Holke <johannes.holke@dlr.de>
Date: Tue, 29 Oct 2024 12:42:30 +0100
Subject: [PATCH 17/24] Add test for ghost in tree getters

---
 test/CMakeLists.txt                       |   1 +
 test/t8_forest/t8_gtest_ghost_in_tree.cxx | 149 ++++++++++++++++++++++
 2 files changed, 150 insertions(+)
 create mode 100644 test/t8_forest/t8_gtest_ghost_in_tree.cxx

diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
index ef9f9ba71a..cc738e695a 100644
--- a/test/CMakeLists.txt
+++ b/test/CMakeLists.txt
@@ -96,6 +96,7 @@ add_t8_test( NAME t8_gtest_find_owner_parallel          SOURCES t8_gtest_main.cx
 add_t8_test( NAME t8_gtest_user_data_parallel           SOURCES t8_gtest_main.cxx t8_forest/t8_gtest_user_data.cxx )
 add_t8_test( NAME t8_gtest_transform_serial             SOURCES t8_gtest_main.cxx t8_forest/t8_gtest_transform.cxx )
 add_t8_test( NAME t8_gtest_ghost_exchange_parallel      SOURCES t8_gtest_main.cxx t8_forest/t8_gtest_ghost_exchange.cxx )
+add_t8_test( NAME t8_gtest_ghost_in_tree                SOURCES t8_gtest_main.cxx t8_forest/t8_gtest_ghost_in_tree.cxx )
 add_t8_test( NAME t8_gtest_ghost_delete_parallel        SOURCES t8_gtest_main.cxx t8_forest/t8_gtest_ghost_delete.cxx )
 add_t8_test( NAME t8_gtest_ghost_and_owner_parallel     SOURCES t8_gtest_main.cxx t8_forest/t8_gtest_ghost_and_owner.cxx )
 add_t8_test( NAME t8_gtest_balance_parallel             SOURCES t8_gtest_main.cxx t8_forest/t8_gtest_balance.cxx )
diff --git a/test/t8_forest/t8_gtest_ghost_in_tree.cxx b/test/t8_forest/t8_gtest_ghost_in_tree.cxx
new file mode 100644
index 0000000000..ab152e8f3b
--- /dev/null
+++ b/test/t8_forest/t8_gtest_ghost_in_tree.cxx
@@ -0,0 +1,149 @@
+/*
+  This file is part of t8code.
+  t8code is a C library to manage a collection (a forest) of multiple
+  connected adaptive space-trees of general element classes in parallel.
+
+  Copyright (C) 2015 the developers
+
+  t8code is free software; you can redistribute it and/or modify
+  it under the terms of the GNU General Public License as published by
+  the Free Software Foundation; either version 2 of the License, or
+  (at your option) any later version.
+
+  t8code is distributed in the hope that it will be useful,
+  but WITHOUT ANY WARRANTY; without even the implied warranty of
+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+  GNU General Public License for more details.
+
+  You should have received a copy of the GNU General Public License
+  along with t8code; if not, write to the Free Software Foundation, Inc.,
+  51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+*/
+
+#include <gtest/gtest.h>
+#include <t8_eclass.h>
+#include <t8_schemes/t8_default/t8_default.hxx>
+#include <t8_forest/t8_forest_general.h>
+#include <t8_forest/t8_forest_ghost.h>
+#include <t8_forest/t8_forest_private.h>
+#include <t8_cmesh.h>
+#include "test/t8_cmesh_generator/t8_cmesh_example_sets.hxx"
+#include <test/t8_gtest_macros.hxx>
+
+/* This test program tests the t8_ghost_get_ghost_in_tree_from_linear_id
+ * and t8_ghost_get_ghost_id_in_tree function of the Ghost interface.
+ * We adapt a forest and create its ghost layer. Afterwards, we
+ * parse through all ghost elements and perform checks.
+  */
+
+static int
+t8_test_adapt_second_element (t8_forest_t forest, t8_forest_t forest_from, t8_locidx_t which_tree,
+                              t8_locidx_t lelement_id, t8_eclass_scheme_c *ts, const int is_family,
+                              const int num_elements, t8_element_t *elements[])
+{
+  /* refine every second element up to the provided maximum level */
+  int level = ts->t8_element_level (elements[0]);
+  t8_linearidx_t eid = ts->t8_element_get_linear_id (elements[0], level);
+  int maxlevel = *(int *) t8_forest_get_user_data (forest);
+
+  if (eid % 2 && level < maxlevel) {
+    return 1;
+  }
+  return 0;
+}
+
+class forest_ghost_in_tree: public testing::TestWithParam<cmesh_example_base *> {
+ protected:
+  void
+  SetUp () override
+  {
+
+    scheme = t8_scheme_new_default_cxx ();
+    /* Construct a cmesh */
+    cmesh = GetParam ()->cmesh_create ();
+    if (t8_cmesh_is_empty (cmesh)) {
+      /* empty cmeshes do not have ghosts and are skipped */
+      GTEST_SKIP ();
+    }
+
+    /* Create a uniformly refined forest */
+    t8_forest_t forest_uniform = t8_forest_new_uniform (cmesh, scheme, level, 1, sc_MPI_COMM_WORLD);
+    /* Adapt the forest */
+    int maxlevel = level + 2;
+    forest_adapt = t8_forest_new_adapt (forest, t8_test_gao_adapt, 1, 1, &maxlevel);
+  }
+  void
+  TearDown () override
+  {
+    t8_cmesh_destroy (&cmesh);
+    t8_scheme_cxx_unref (&scheme);
+  }
+  t8_cmesh_t cmesh;
+  t8_scheme_cxx_t *scheme;
+  t8_forest_t forest_adapt;
+  int level =  // initial uniform refinement level
+#if T8_ENABLE_LESS_TESTS
+    5;  // less-tests, shorter runtime
+#else
+    7;  // more tests, longer runtime
+#endif
+};
+
+// For reference:
+// t8_ghost_get_ghost_id_in_tree
+// Retrieves the local index of a ghost element in its specific ghost tree.
+//
+// t8_ghost_get_ghost_in_tree_from_linear_id
+// Retrieves a ghost element from its ghost tree given the element's linear id.
+
+TEST_P (forest_ghost_in_tree, test_get_ghost_id_in_tree)
+{
+  const t8_locidx_t num_ghost_trees = t8_forest_get_num_ghost_trees (forest_adapt);
+  const t8_locidx_t num_local_trees = t8_forest_get_num_local_trees (forest_adapt);
+
+  for (t8_locidx_t ighost_tree = 0; ighost_tree < num_ghost_trees; ++ighost_tree) {
+    // iterate over all Ghost trees
+    // Get the ghost elements of that tree
+    const t8_element_array_t *ghosts = t8_forest_ghost_get_tree_elements (forest_adapt, ighost_tree);
+    t8_locidx_t ghost_index_in_tree = 0;
+    for (const t8_element_t &ighost : ghosts) {  // loop over all ghost elements
+      // Compute the index in the tree of the current ghost
+      const t8_locidx_t check_ghost_index_in_tree = t8_ghost_get_ghost_id_in_tree (forest_adapt, ighost_tree, ighost);
+      ASSERT_GE (check_ghost_index_in_tree, 0) << "Ghost element was not found.";  // The ghost must have been found.
+      // Check that the index is correct
+      EXPECT_EQ (check_ghost_index_in_tree, ghost_index_in_tree) << "Wrong index returned for ghost element.";
+      ++ghost_index_in_tree;
+    }
+  }
+}
+
+TEST_P (forest_ghost_in_tree, test_get_ghost_in_tree_from_linear_id)
+{
+  const t8_locidx_t num_ghost_trees = t8_forest_get_num_ghost_trees (forest_adapt);
+  const t8_locidx_t num_local_trees = t8_forest_get_num_local_trees (forest_adapt);
+
+  for (t8_locidx_t ighost_tree = 0; ighost_tree < num_ghost_trees; ++ighost_tree) {
+    // iterate over all Ghost trees
+    // Get the ghost elements of that tree
+    const t8_element_array_t *ghosts = t8_forest_ghost_get_tree_elements (forest_adapt, ighost_tree);
+    t8_locidx_t ghost_index_in_tree = 0;
+    for (const t8_element_t &ighost : ghosts) {  // loop over all ghost elements
+      // Now checking t8_ghost_get_ghost_in_tree_from_linear_id
+      const t8_eclass_t eclass = t8_forest_get_tree_class (forest_adapt, num_local_trees + ighost_tree);
+      const t8_eclass_scheme_c *scheme = t8_forest_get_eclass_scheme (forest_adapt, eclass);
+      const int ghost_level = scheme->t8_element_level (ghost);
+      const t8_linearidx_t ghost_id = scheme->t8_element_get_linear_id (ghost, ghost_level);
+      t8_locidx_t check_ghost_index;
+      const t8_element_t *check_ghost = t8_ghost_get_ghost_in_tree_from_linear_id (forest_adapt, ighost_tree, ghost_id,
+                                                                                   ghost_level, &check_ghost_index);
+
+      EXPECT_TRUE (scheme->t8_element_equal (ighost, check_ghost)) << "Returned wrong ghost element.";
+      EXPECT_EQ (check_ghost_index, ghost_index_in_tree) << "Returned wrong ghost index.";
+
+      ++ghost_index_in_tree;
+    }
+  }
+}
+
+INSTANTIATE_TEST_SUITE_P (t8_gtest_forest_ghost_in_tree, forest_ghost_in_tree, AllCmeshsParam,
+                          pretty_print_base_example);

From a05f39ad5b35ca9342e9647f9ccf9e437727321f Mon Sep 17 00:00:00 2001
From: Johannes Holke <johannes.holke@dlr.de>
Date: Tue, 29 Oct 2024 13:04:47 +0100
Subject: [PATCH 18/24] fix assertion logic

---
 src/t8_forest/t8_forest_ghost.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/t8_forest/t8_forest_ghost.cxx b/src/t8_forest/t8_forest_ghost.cxx
index 07c9543df5..a9ad8c7a91 100644
--- a/src/t8_forest/t8_forest_ghost.cxx
+++ b/src/t8_forest/t8_forest_ghost.cxx
@@ -310,7 +310,7 @@ t8_ghost_get_ghost_in_tree_from_linear_id (t8_forest_t forest, t8_locidx_t lghos
   T8_ASSERT (t8_forest_is_committed (forest));
   const t8_element_array_t *ghost_elements = t8_forest_ghost_get_tree_elements (forest, lghost_tree);
   T8_ASSERT (ghost_elements != NULL);
-  T8_ASSERT (forest->incomplete_trees);  // This function will not word properlt with incomplete trees.
+  T8_ASSERT (!forest->incomplete_trees);  // This function will not word properlt with incomplete trees.
   /* Search for the element.
    * The search returns the largest index i,
    * such that the element at position i has a smaller id than the given one.

From 039efd7079d738ad774c786b3b94f2d63d4a4a10 Mon Sep 17 00:00:00 2001
From: Johannes Holke <johannes.holke@dlr.de>
Date: Tue, 29 Oct 2024 13:05:13 +0100
Subject: [PATCH 19/24] more const

---
 src/t8_forest/t8_forest_ghost.cxx | 2 +-
 src/t8_forest/t8_forest_ghost.h   | 7 ++++---
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/t8_forest/t8_forest_ghost.cxx b/src/t8_forest/t8_forest_ghost.cxx
index a9ad8c7a91..4cc515052d 100644
--- a/src/t8_forest/t8_forest_ghost.cxx
+++ b/src/t8_forest/t8_forest_ghost.cxx
@@ -324,7 +324,7 @@ t8_ghost_get_ghost_in_tree_from_linear_id (t8_forest_t forest, t8_locidx_t lghos
 }
 
 t8_locidx_t
-t8_ghost_get_ghost_id_in_tree (t8_forest_t forest, t8_locidx_t lghost_tree, t8_element_t *ghost_element)
+t8_ghost_get_ghost_id_in_tree (t8_forest_t forest, t8_locidx_t lghost_tree, const t8_element_t *ghost_element)
 {
   T8_ASSERT (t8_forest_is_committed (forest));
   const t8_element_array_t *ghost_elements = t8_forest_ghost_get_tree_elements (forest, lghost_tree);
diff --git a/src/t8_forest/t8_forest_ghost.h b/src/t8_forest/t8_forest_ghost.h
index f68c66f7ac..1edee32ddf 100644
--- a/src/t8_forest/t8_forest_ghost.h
+++ b/src/t8_forest/t8_forest_ghost.h
@@ -79,8 +79,9 @@ t8_forest_ghost_tree_num_elements (t8_forest_t forest, t8_locidx_t lghost_tree);
  * \return The ghost element. nullptr if no ghost was found.
  */
 const t8_element_t *
-t8_ghost_get_ghost_in_tree_from_linear_id (t8_forest_t forest, t8_locidx_t lghost_tree, t8_linearidx_t linear_id,
-                                           int element_level, t8_locidx_t *loc_ghost_id);
+t8_ghost_get_ghost_in_tree_from_linear_id (t8_forest_t forest, const t8_locidx_t lghost_tree,
+                                           const t8_linearidx_t linear_id, const int element_level,
+                                           t8_locidx_t *loc_ghost_id);
 
 /** Retrieves the local index of a ghost element in its specific ghost tree.
  *
@@ -91,7 +92,7 @@ t8_ghost_get_ghost_in_tree_from_linear_id (t8_forest_t forest, t8_locidx_t lghos
  *         -1 if no ghost element was found.
  */
 t8_locidx_t
-t8_ghost_get_ghost_id_in_tree (t8_forest_t forest, t8_locidx_t lghost_tree, t8_element_t *ghost_element);
+t8_ghost_get_ghost_id_in_tree (t8_forest_t forest, const t8_locidx_t lghost_tree, const t8_element_t *ghost_element);
 
 /** Get a pointer to the ghost element array of a ghost tree.
  * \param [in]  forest    The forest. Ghost layer must exist.

From 74322410e7a08533d1572dfcc879b2dcfa0c2a08 Mon Sep 17 00:00:00 2001
From: Johannes Holke <johannes.holke@dlr.de>
Date: Tue, 29 Oct 2024 13:05:48 +0100
Subject: [PATCH 20/24] minor test changes

---
 test/t8_forest/t8_gtest_ghost_in_tree.cxx | 19 +++++++++++++------
 1 file changed, 13 insertions(+), 6 deletions(-)

diff --git a/test/t8_forest/t8_gtest_ghost_in_tree.cxx b/test/t8_forest/t8_gtest_ghost_in_tree.cxx
index ab152e8f3b..0cbc5dc268 100644
--- a/test/t8_forest/t8_gtest_ghost_in_tree.cxx
+++ b/test/t8_forest/t8_gtest_ghost_in_tree.cxx
@@ -29,6 +29,7 @@
 #include <t8_cmesh.h>
 #include "test/t8_cmesh_generator/t8_cmesh_example_sets.hxx"
 #include <test/t8_gtest_macros.hxx>
+#include <t8_data/t8_element_array_iterator.hxx>
 
 /* This test program tests the t8_ghost_get_ghost_in_tree_from_linear_id
  * and t8_ghost_get_ghost_id_in_tree function of the Ghost interface.
@@ -58,7 +59,6 @@ class forest_ghost_in_tree: public testing::TestWithParam<cmesh_example_base *>
   SetUp () override
   {
 
-    scheme = t8_scheme_new_default_cxx ();
     /* Construct a cmesh */
     cmesh = GetParam ()->cmesh_create ();
     if (t8_cmesh_is_empty (cmesh)) {
@@ -66,26 +66,33 @@ class forest_ghost_in_tree: public testing::TestWithParam<cmesh_example_base *>
       GTEST_SKIP ();
     }
 
+    scheme = t8_scheme_new_default_cxx ();
     /* Create a uniformly refined forest */
     t8_forest_t forest_uniform = t8_forest_new_uniform (cmesh, scheme, level, 1, sc_MPI_COMM_WORLD);
     /* Adapt the forest */
     int maxlevel = level + 2;
-    forest_adapt = t8_forest_new_adapt (forest, t8_test_gao_adapt, 1, 1, &maxlevel);
+    forest_adapt = t8_forest_new_adapt (forest_uniform, t8_test_adapt_second_element, 1, 1, &maxlevel);
+    // We need to update the cmesh since it changes with adapt.
+    cmesh = t8_forest_get_cmesh (forest_adapt);
   }
   void
   TearDown () override
   {
-    t8_cmesh_destroy (&cmesh);
-    t8_scheme_cxx_unref (&scheme);
+    if (t8_cmesh_is_empty (cmesh)) {
+      t8_cmesh_destroy (&cmesh);
+    }
+    else {
+      t8_forest_unref (&forest_adapt);
+    }
   }
   t8_cmesh_t cmesh;
   t8_scheme_cxx_t *scheme;
   t8_forest_t forest_adapt;
   int level =  // initial uniform refinement level
 #if T8_ENABLE_LESS_TESTS
-    5;  // less-tests, shorter runtime
+    3;  // less-tests, shorter runtime
 #else
-    7;  // more tests, longer runtime
+    5;  // more tests, longer runtime
 #endif
 };
 

From 183b117b8e48761ad1c49959346ca860963a82a1 Mon Sep 17 00:00:00 2001
From: Johannes Holke <johannes.holke@dlr.de>
Date: Tue, 29 Oct 2024 13:06:04 +0100
Subject: [PATCH 21/24] temporarily remove foreach loop over ghosts

---
 test/t8_forest/t8_gtest_ghost_in_tree.cxx | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)

diff --git a/test/t8_forest/t8_gtest_ghost_in_tree.cxx b/test/t8_forest/t8_gtest_ghost_in_tree.cxx
index 0cbc5dc268..97d02ce5fb 100644
--- a/test/t8_forest/t8_gtest_ghost_in_tree.cxx
+++ b/test/t8_forest/t8_gtest_ghost_in_tree.cxx
@@ -113,13 +113,16 @@ TEST_P (forest_ghost_in_tree, test_get_ghost_id_in_tree)
     // Get the ghost elements of that tree
     const t8_element_array_t *ghosts = t8_forest_ghost_get_tree_elements (forest_adapt, ighost_tree);
     t8_locidx_t ghost_index_in_tree = 0;
-    for (const t8_element_t &ighost : ghosts) {  // loop over all ghost elements
+    //for (const t8_element_t &ighost : ghosts) {  // loop over all ghost elements
+
+    for (; ghost_index_in_tree < t8_element_array_get_count (ghosts); ++ghost_index_in_tree) {
+      const t8_element_t *ighost = t8_element_array_index_locidx (ghosts, ghost_index_in_tree);
       // Compute the index in the tree of the current ghost
       const t8_locidx_t check_ghost_index_in_tree = t8_ghost_get_ghost_id_in_tree (forest_adapt, ighost_tree, ighost);
       ASSERT_GE (check_ghost_index_in_tree, 0) << "Ghost element was not found.";  // The ghost must have been found.
       // Check that the index is correct
       EXPECT_EQ (check_ghost_index_in_tree, ghost_index_in_tree) << "Wrong index returned for ghost element.";
-      ++ghost_index_in_tree;
+      // ++ghost_index_in_tree;
     }
   }
 }
@@ -134,12 +137,15 @@ TEST_P (forest_ghost_in_tree, test_get_ghost_in_tree_from_linear_id)
     // Get the ghost elements of that tree
     const t8_element_array_t *ghosts = t8_forest_ghost_get_tree_elements (forest_adapt, ighost_tree);
     t8_locidx_t ghost_index_in_tree = 0;
-    for (const t8_element_t &ighost : ghosts) {  // loop over all ghost elements
+    //for (const t8_element_t &ighost : ghosts) {  // loop over all ghost elements
+    for (; ghost_index_in_tree < t8_element_array_get_count (ghosts); ++ghost_index_in_tree) {
+
+      const t8_element_t *ighost = t8_element_array_index_locidx (ghosts, ghost_index_in_tree);
       // Now checking t8_ghost_get_ghost_in_tree_from_linear_id
       const t8_eclass_t eclass = t8_forest_get_tree_class (forest_adapt, num_local_trees + ighost_tree);
       const t8_eclass_scheme_c *scheme = t8_forest_get_eclass_scheme (forest_adapt, eclass);
-      const int ghost_level = scheme->t8_element_level (ghost);
-      const t8_linearidx_t ghost_id = scheme->t8_element_get_linear_id (ghost, ghost_level);
+      const int ghost_level = scheme->t8_element_level (ighost);
+      const t8_linearidx_t ghost_id = scheme->t8_element_get_linear_id (ighost, ghost_level);
       t8_locidx_t check_ghost_index;
       const t8_element_t *check_ghost = t8_ghost_get_ghost_in_tree_from_linear_id (forest_adapt, ighost_tree, ghost_id,
                                                                                    ghost_level, &check_ghost_index);
@@ -147,7 +153,7 @@ TEST_P (forest_ghost_in_tree, test_get_ghost_in_tree_from_linear_id)
       EXPECT_TRUE (scheme->t8_element_equal (ighost, check_ghost)) << "Returned wrong ghost element.";
       EXPECT_EQ (check_ghost_index, ghost_index_in_tree) << "Returned wrong ghost index.";
 
-      ++ghost_index_in_tree;
+      // ++ghost_index_in_tree;
     }
   }
 }

From e1ee81f463eac4d1f983f75b9294ede4125a0c0b Mon Sep 17 00:00:00 2001
From: Johannes Holke <johannes.holke@dlr.de>
Date: Mon, 4 Nov 2024 12:10:07 +0100
Subject: [PATCH 22/24] Add negative result tests

---
 src/t8_forest/t8_forest_ghost.cxx         |  1 +
 test/t8_forest/t8_gtest_ghost_in_tree.cxx | 63 ++++++++++++++++++++---
 2 files changed, 56 insertions(+), 8 deletions(-)

diff --git a/src/t8_forest/t8_forest_ghost.cxx b/src/t8_forest/t8_forest_ghost.cxx
index 4cc515052d..9abaad318c 100644
--- a/src/t8_forest/t8_forest_ghost.cxx
+++ b/src/t8_forest/t8_forest_ghost.cxx
@@ -320,6 +320,7 @@ t8_ghost_get_ghost_in_tree_from_linear_id (t8_forest_t forest, t8_locidx_t lghos
     /* The element was found */
     return t8_element_array_index_locidx (ghost_elements, *loc_ghost_id);
   }
+  *loc_ghost_id = -1;
   return nullptr;
 }
 
diff --git a/test/t8_forest/t8_gtest_ghost_in_tree.cxx b/test/t8_forest/t8_gtest_ghost_in_tree.cxx
index 97d02ce5fb..16487fb849 100644
--- a/test/t8_forest/t8_gtest_ghost_in_tree.cxx
+++ b/test/t8_forest/t8_gtest_ghost_in_tree.cxx
@@ -112,10 +112,9 @@ TEST_P (forest_ghost_in_tree, test_get_ghost_id_in_tree)
     // iterate over all Ghost trees
     // Get the ghost elements of that tree
     const t8_element_array_t *ghosts = t8_forest_ghost_get_tree_elements (forest_adapt, ighost_tree);
-    t8_locidx_t ghost_index_in_tree = 0;
-    //for (const t8_element_t &ighost : ghosts) {  // loop over all ghost elements
-
-    for (; ghost_index_in_tree < t8_element_array_get_count (ghosts); ++ghost_index_in_tree) {
+    // loop over all ghosts in that tree
+    const size_t num_ghosts_of_tree = t8_element_array_get_count (ghosts);
+    for (t8_locidx_t ghost_index_in_tree = 0; ghost_index_in_tree < num_ghosts_of_tree; ++ghost_index_in_tree) {
       const t8_element_t *ighost = t8_element_array_index_locidx (ghosts, ghost_index_in_tree);
       // Compute the index in the tree of the current ghost
       const t8_locidx_t check_ghost_index_in_tree = t8_ghost_get_ghost_id_in_tree (forest_adapt, ighost_tree, ighost);
@@ -127,6 +126,24 @@ TEST_P (forest_ghost_in_tree, test_get_ghost_id_in_tree)
   }
 }
 
+TEST_P (forest_ghost_in_tree, test_get_ghost_id_in_tree_negative)
+{
+  // Get a not ghost element and try to query it.
+  // We check for the correct return value.
+  if (t8_forest_get_local_num_elements (forest_adapt) > 0) {
+    // Get the first element of the forest.
+    // This will not be a ghost.
+    const t8_element_t *element = t8_forest_get_element_in_tree (forest_adapt, 0, 0);
+    // Loop over all ghost trees
+    const t8_locidx_t num_ghost_trees = t8_forest_get_num_ghost_trees (forest_adapt);
+    for (t8_locidx_t ighost_tree = 0; ighost_tree < num_ghost_trees; ++ighost_tree) {
+      t8_locidx_t check_ghost_id = t8_ghost_get_ghost_id_in_tree (forest_adapt, ighost_tree, element);
+      /* Since the element is not a ghost, we expect -1 as return value. */
+      EXPECT_EQ (check_ghost_id, -1) << "Element was wrongly recognized as ghost.";
+    }
+  }
+}
+
 TEST_P (forest_ghost_in_tree, test_get_ghost_in_tree_from_linear_id)
 {
   const t8_locidx_t num_ghost_trees = t8_forest_get_num_ghost_trees (forest_adapt);
@@ -136,10 +153,9 @@ TEST_P (forest_ghost_in_tree, test_get_ghost_in_tree_from_linear_id)
     // iterate over all Ghost trees
     // Get the ghost elements of that tree
     const t8_element_array_t *ghosts = t8_forest_ghost_get_tree_elements (forest_adapt, ighost_tree);
-    t8_locidx_t ghost_index_in_tree = 0;
-    //for (const t8_element_t &ighost : ghosts) {  // loop over all ghost elements
-    for (; ghost_index_in_tree < t8_element_array_get_count (ghosts); ++ghost_index_in_tree) {
-
+    // Loop over all ghost elements of that tree
+    const size_t num_ghosts_of_tree = t8_element_array_get_count (ghosts);
+    for (t8_locidx_t ghost_index_in_tree = 0; ghost_index_in_tree < num_ghosts_of_tree; ++ghost_index_in_tree) {
       const t8_element_t *ighost = t8_element_array_index_locidx (ghosts, ghost_index_in_tree);
       // Now checking t8_ghost_get_ghost_in_tree_from_linear_id
       const t8_eclass_t eclass = t8_forest_get_tree_class (forest_adapt, num_local_trees + ighost_tree);
@@ -158,5 +174,36 @@ TEST_P (forest_ghost_in_tree, test_get_ghost_in_tree_from_linear_id)
   }
 }
 
+TEST_P (forest_ghost_in_tree, test_get_ghost_in_tree_from_linear_id_negative)
+{
+  // Get a not ghost element and try to query it.
+  // We check for the correct return value.
+  const t8_locidx_t tree_id = 0;  // We check the first element of the first tree
+  const t8_locidx_t element_id = 0;
+  if (t8_forest_get_local_num_elements (forest_adapt) > 0) {
+    // Get the first element of the forest.
+    // This will not be a ghost.
+    const t8_element_t *element = t8_forest_get_element_in_tree (forest_adapt, tree_id, element_id);
+    // Loop over all ghost trees
+    const t8_locidx_t num_ghost_trees = t8_forest_get_num_ghost_trees (forest_adapt);
+    for (t8_locidx_t ighost_tree = 0; ighost_tree < num_ghost_trees; ++ighost_tree) {
+      // Now checking t8_ghost_get_ghost_in_tree_from_linear_id
+      // Get the scheme
+      const t8_eclass_t eclass = t8_forest_get_tree_class (forest_adapt, tree_id);
+      const t8_eclass_scheme_c *scheme = t8_forest_get_eclass_scheme (forest_adapt, eclass);
+      // Get the element's level and linear id
+      const int element_level = scheme->t8_element_level (element);
+      const t8_linearidx_t element_id = scheme->t8_element_get_linear_id (element, element_level);
+      // Query t8_ghost_get_ghost_in_tree_from_linear_id
+      t8_locidx_t check_ghost_index;
+      const t8_element_t *check_ghost = t8_ghost_get_ghost_in_tree_from_linear_id (
+        forest_adapt, ighost_tree, element_id, element_level, &check_ghost_index);
+      // The element should not have been found - we check for the error return values.
+      EXPECT_EQ (check_ghost_index, -1) << "Wrongly found ghost index for non-existing ghost.";
+      EXPECT_EQ (check_ghost, nullptr) << "Wrongly found ghost element for non-existing ghost.";
+    }
+  }
+}
+
 INSTANTIATE_TEST_SUITE_P (t8_gtest_forest_ghost_in_tree, forest_ghost_in_tree, AllCmeshsParam,
                           pretty_print_base_example);

From 3dd4d2cd6b2fd5f93bc7782f37f720d99bccef22 Mon Sep 17 00:00:00 2001
From: Johannes Holke <johannes.holke@dlr.de>
Date: Fri, 8 Nov 2024 09:56:22 +0100
Subject: [PATCH 23/24] fix private.c rename in Makefile

---
 src/Makefile.am | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Makefile.am b/src/Makefile.am
index ac4b843944..95a7ee8995 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -144,7 +144,7 @@ libt8_compiled_sources = \
   src/t8_geometry/t8_geometry_implementations/t8_geometry_zero.cxx \
   src/t8_geometry/t8_geometry_implementations/t8_geometry_examples.cxx \
   src/t8_forest/t8_forest_partition.cxx src/t8_forest/t8_forest.cxx \
-  src/t8_forest/t8_forest_private.c \
+  src/t8_forest/t8_forest_private.cxx \
   src/t8_forest/t8_forest_ghost.cxx src/t8_forest/t8_forest_iterate.cxx \
   src/t8_version.c \
   src/t8_vtk.c src/t8_forest/t8_forest_balance.cxx \

From 6c699d2821e05af5eaa1b4c34afbd1ed4bd18adf Mon Sep 17 00:00:00 2001
From: Johannes Holke <johannes.holke@dlr.de>
Date: Tue, 12 Nov 2024 10:27:09 +0100
Subject: [PATCH 24/24] remove old files from Makefile

---
 src/Makefile.am | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/Makefile.am b/src/Makefile.am
index 95a7ee8995..3bc8c1058e 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -53,8 +53,6 @@ libt8_installed_headers_forest = \
   src/t8_forest/t8_forest_profiling.h \
   src/t8_forest/t8_forest_io.h \
   src/t8_forest/t8_forest_adapt.h \
-  src/t8_forest/t8_forest_vtk.h \
-  src/t8_forest/t8_forest_to_vtkUnstructured.hxx \
   src/t8_forest/t8_forest_iterate.h src/t8_forest/t8_forest_partition.h \
   src/t8_forest/t8_forest_ghost_interface_wrapper.h \
   src/t8_forest/t8_forest_ghost_interface.h \