Merge branch 'main' into feature-CMake_CI_1

.github/workflows/mattermost_issue.yml

@@ -44,20 +44,26 @@ jobs:
       - name: debug_before_build
         run: echo ${{ env.message_build}}
       # build the message depending on different types of events and event actions. Message is written into mattermost.json
+      - name: dispatch_run
+        if: github.event_name == 'workflow_dispatch'
+        run: |
+          echo message_build=1 >> $GITHUB_ENV &&
+          echo message_content='User ${{github.actor}} triggered the workflow_dispatch' >> $GITHUB_ENV
       - name: closed_message
         if: github.event.action == 'closed'
         run: |
           echo message_build=1 >> $GITHUB_ENV &&
-          echo message_content='Issue ${{ github.event.issue.number }} has been closed. See ${{ github.event.issue.html_url }} for more details.' >> $GITHUB_ENV
-# Would like to have this message read "User X closed issue ...".
-# How can we get the user name? Tried ${{ github.event.issue.user.name }} and others, did not work.
+          echo message_content='User ${{ github.actor }} closed issue ${{ github.event.issue.number }}. See ${{ github.event.issue.html_url }} for more details.' >> $GITHUB_ENV
       - name: opened_message
-        if: github.event.action == 'opened' || github.event.action == 'reopened'
+        if: github.event.action == 'opened'
+        run: |
+          echo message_build=1 >> $GITHUB_ENV &&
+          echo message_content='User ${{ github.actor }} opened issue ${{ github.event.issue.number }}. See ${{ github.event.issue.html_url }} for more details.' >> $GITHUB_ENV
+      - name: reopened_message
+        if: github.event.action == 'reopened'
         run: |
           echo message_build=1 >> $GITHUB_ENV &&
-          echo message_content='Issue ${{ github.event.issue.number }} was (re-)opened. See ${{ github.event.issue.html_url }} for more details.' >> $GITHUB_ENV
-# Would like to have this message read "User X (re-)opened issue ...".
-# How can we get the user name? Tried ${{ github.event.issue.user.name }} and others, did not work.
+          echo message_content='User ${{ github.actor }} reopened issue ${{ github.event.issue.number }}. See ${{ github.event.issue.html_url }} for more details.' >> $GITHUB_ENV
       - name: debug_after_build
         run: echo ${{ env.message_build }}
       # if a message has been written send the message to the mattermost-channel described in the secrets

CMakeLists.txt

@@ -57,7 +57,10 @@ if( T8CODE_ENABLE_MPI )
 endif()
 
 if( T8CODE_ENABLE_VTK )
-    find_package( VTK REQUIRED )
+    find_package( VTK REQUIRED COMPONENTS
+        IOXML CommonExecutionModel CommonDataModel
+        IOGeometry IOXMLParser IOParallelXML IOPLY
+        ParallelMPI FiltersCore vtksys CommonCore zlib IOLegacy)
     if(VTK_FOUND)
         message("Found VTK")
     endif (VTK_FOUND)

benchmarks/ExtremeScaling/bunny.cxx

@@ -24,7 +24,8 @@
 #include <t8.h>
 #include <t8_cmesh.h>
 #include <t8_cmesh_tetgen.h>
-#include <t8_cmesh_vtk_writer.h>
+#include <t8_vtk/t8_vtk_writer.h>
+
 #include <t8_cmesh/t8_cmesh_examples.h>
 #include <t8_forest/t8_forest_general.h>
 #include <t8_schemes/t8_default/t8_default.hxx>

benchmarks/time_forest_partition.cxx

@@ -28,7 +28,8 @@
 #include <p4est_connectivity.h>
 #include <t8_cmesh.h>
 #include <t8_cmesh/t8_cmesh_examples.h>
-#include <t8_cmesh_vtk_writer.h>
+#include <t8_vtk/t8_vtk_writer.h>
+
 #include <t8_cmesh/t8_cmesh_partition.h>
 #include <t8_cmesh/t8_cmesh_cad.hxx>
 #include <t8_cmesh_readmshfile.h>

benchmarks/time_partition.cxx

@@ -26,7 +26,8 @@
 #include <sc_options.h>
 #include <p4est_connectivity.h>
 #include <t8_cmesh.h>
-#include <t8_cmesh_vtk_writer.h>
+#include <t8_vtk/t8_vtk_writer.h>
+
 #include <t8_cmesh/t8_cmesh_partition.h>
 #include "t8_cmesh/t8_cmesh_types.h"
 #include <t8_cmesh/t8_cmesh_examples.h>

example/IO/cmesh/gmsh/t8_read_msh_file.cxx

@@ -22,7 +22,7 @@
 
 #include <sc_options.h>
 #include <t8.h>
-#include <t8_cmesh_vtk_writer.h>
+#include <t8_vtk/t8_vtk_writer.h>
 #include <t8_cmesh/t8_cmesh_partition.h>
 #include <t8_cmesh_readmshfile.h>
 #include <t8_schemes/t8_default/t8_default.hxx>

example/IO/cmesh/t8_cmesh_load_save.cxx

@@ -22,9 +22,9 @@
 
 #include <sc_options.h>
 #include <t8_cmesh.h>
-#include <t8_cmesh_vtk_writer.h>
-#include <t8_cmesh_readmshfile.h>
+#include <t8_vtk/t8_vtk_writer.h>
 #include <t8_cmesh/t8_cmesh_examples.h>
+#include <t8_cmesh_readmshfile.h>
 #include <t8_schemes/t8_default/t8_default.hxx>
 
 static void

example/IO/cmesh/tetgen/t8_forest_from_tetgen.cxx

@@ -25,7 +25,7 @@
 #include <t8_cmesh.h>
 #include <t8_cmesh/t8_cmesh_partition.h>
 #include <t8_cmesh_tetgen.h>
-#include <t8_cmesh_vtk_writer.h>
+#include <t8_vtk/t8_vtk_writer.h>
 #include <t8_schemes/t8_default/t8_default.hxx>
 #include <t8_forest/t8_forest_general.h>
 #include <t8_forest/t8_forest_io.h>

example/IO/cmesh/tetgen/t8_read_tetgen_file.cxx

@@ -25,7 +25,7 @@
 #include <t8_cmesh.h>
 #include <t8_cmesh/t8_cmesh_partition.h>
 #include <t8_cmesh_tetgen.h>
-#include <t8_cmesh_vtk_writer.h>
+#include <t8_vtk/t8_vtk_writer.h>
 
 void
 t8_read_tetgen_file_build_cmesh (const char *prefix, int do_dup, int do_partition)

example/IO/cmesh/triangle/t8_read_triangle_file.cxx

@@ -24,7 +24,8 @@
 #include <t8.h>
 #include <t8_cmesh.h>
 #include <t8_cmesh_triangle.h>
-#include <t8_cmesh_vtk_writer.h>
+#include <t8_vtk/t8_vtk_writer.h>
+
 #include <t8_schemes/t8_default/t8_default.hxx>
 
 void

example/IO/cmesh/vtk/t8_cmesh_read_from_vtk.cxx

@@ -17,7 +17,7 @@ along with t8code; if not, write to the Free Software Foundation, Inc.,
 */
 
 #include <t8_cmesh_vtk_reader.hxx>
-#include <t8_cmesh_vtk_writer.h>
+#include <t8_vtk/t8_vtk_writer.h>
 #include <t8_cmesh.h>
 #include <sc_options.h>
 #include <t8.h>

example/advect/t8_advection.cxx

@@ -33,7 +33,7 @@
 #include <example/common/t8_example_common.h>
 #include <t8_cmesh.h>
 #include <t8_cmesh_readmshfile.h>
-#include <t8_cmesh_vtk_writer.h>
+#include <t8_vtk/t8_vtk_writer.h>
 #include <t8_cmesh/t8_cmesh_examples.h>
 #include <t8_vec.h>
 

example/cmesh/t8_cmesh_create_partitioned.cxx

@@ -20,7 +20,7 @@
   51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
 */
 
-#include <t8_cmesh_vtk_writer.h>
+#include <t8_vtk/t8_vtk_writer.h>
 
 /* Create a coarse mesh that is partitioned across two processes
  * (if mpisize >= 2).

example/cmesh/t8_cmesh_geometry_examples.cxx

@@ -27,7 +27,8 @@
 #include <t8_forest/t8_forest_general.h>        /* Forest definition and basic interface. */
 #include <t8_forest/t8_forest_geometrical.h>    /* Forest-related geometry operations. */
 #include <t8_schemes/t8_default/t8_default.hxx> /* Default refinement scheme. */
-#include <t8_cmesh_vtk_writer.h>                /* Write file in vtu file */
+#include <t8_vtk/t8_vtk_writer.h>
+/* Write file in vtu file */
 #include <t8_forest/t8_forest_io.h>
 #include <t8_cmesh/t8_cmesh_examples.h>
 
@@ -114,17 +115,17 @@ main (int argc, char **argv)
     const char *prefix_forest = "t8_quadrangulated_disk_forest";
 
     const int uniform_level = 5;
-    const double radius = 1.0;
+    const double radius = 5.0;
 
     t8_cmesh_t cmesh = t8_cmesh_new_quadrangulated_disk (radius, comm);
 
     t8_forest_t forest = t8_forest_new_uniform (cmesh, t8_scheme_new_default_cxx (), uniform_level, 0, comm);
 
     t8_cmesh_vtk_write_file (cmesh, prefix_cmesh);
-    t8_global_productionf ("Wrote %s.\n", prefix_cmesh);
+    t8_global_productionf ("Wrote %s.pvtu\n", prefix_cmesh);
 
     t8_write_forest_to_vtu (forest, prefix_forest);
-    t8_global_productionf ("Wrote %s.\n\n", prefix_forest);
+    t8_global_productionf ("Wrote %s.pvtu\n\n", prefix_forest);
 
     t8_forest_unref (&forest);
   }
@@ -141,10 +142,10 @@ main (int argc, char **argv)
     t8_forest_t forest = t8_forest_new_uniform (cmesh, t8_scheme_new_default_cxx (), uniform_level, 0, comm);
 
     t8_cmesh_vtk_write_file (cmesh, prefix_cmesh);
-    t8_global_productionf ("Wrote %s.\n", prefix_cmesh);
+    t8_global_productionf ("Wrote %s.pvtu\n", prefix_cmesh);
 
     t8_write_forest_to_vtu (forest, prefix_forest);
-    t8_global_productionf ("Wrote %s.\n\n", prefix_forest);
+    t8_global_productionf ("Wrote %s.pvtu\n\n", prefix_forest);
 
     t8_forest_unref (&forest);
   }
@@ -161,10 +162,30 @@ main (int argc, char **argv)
     t8_forest_t forest = t8_forest_new_uniform (cmesh, t8_scheme_new_default_cxx (), uniform_level, 0, comm);
 
     t8_cmesh_vtk_write_file (cmesh, prefix_cmesh);
-    t8_global_productionf ("Wrote %s.\n", prefix_cmesh);
+    t8_global_productionf ("Wrote %s.pvtu\n", prefix_cmesh);
 
     t8_write_forest_to_vtu (forest, prefix_forest);
-    t8_global_productionf ("Wrote %s.\n\n", prefix_forest);
+    t8_global_productionf ("Wrote %s.pvtu\n\n", prefix_forest);
+
+    t8_forest_unref (&forest);
+  }
+
+  {
+    const char *prefix_cmesh = "t8_triangulated_spherical_surface_cube_cmesh";
+    const char *prefix_forest = "t8_triangulated_spherical_surface_cube_forest";
+
+    const int uniform_level = 4;
+    const double radius = 42.0;
+
+    t8_cmesh_t cmesh = t8_cmesh_new_triangulated_spherical_surface_cube (radius, comm);
+
+    t8_forest_t forest = t8_forest_new_uniform (cmesh, t8_scheme_new_default_cxx (), uniform_level, 0, comm);
+
+    t8_cmesh_vtk_write_file (cmesh, prefix_cmesh);
+    t8_global_productionf ("Wrote %s.pvtu\n", prefix_cmesh);
+
+    t8_write_forest_to_vtu (forest, prefix_forest);
+    t8_global_productionf ("Wrote %s.pvtu\n\n", prefix_forest);
 
     t8_forest_unref (&forest);
   }
@@ -181,10 +202,10 @@ main (int argc, char **argv)
     t8_forest_t forest = t8_forest_new_uniform (cmesh, t8_scheme_new_default_cxx (), uniform_level, 0, comm);
 
     t8_cmesh_vtk_write_file (cmesh, prefix_cmesh);
-    t8_global_productionf ("Wrote %s.\n", prefix_cmesh);
+    t8_global_productionf ("Wrote %s.pvtu\n", prefix_cmesh);
 
     t8_write_forest_to_vtu (forest, prefix_forest);
-    t8_global_productionf ("Wrote %s.\n\n", prefix_forest);
+    t8_global_productionf ("Wrote %s.pvtu\n\n", prefix_forest);
 
     t8_forest_unref (&forest);
   }
@@ -206,10 +227,10 @@ main (int argc, char **argv)
     t8_forest_t forest = t8_forest_new_uniform (cmesh, t8_scheme_new_default_cxx (), uniform_level, 0, comm);
 
     t8_cmesh_vtk_write_file (cmesh, prefix_cmesh);
-    t8_global_productionf ("Wrote %s.\n", prefix_cmesh);
+    t8_global_productionf ("Wrote %s.pvtu\n", prefix_cmesh);
 
     t8_write_forest_to_vtu (forest, prefix_forest);
-    t8_global_productionf ("Wrote %s.\n\n", prefix_forest);
+    t8_global_productionf ("Wrote %s.pvtu\n\n", prefix_forest);
 
     t8_forest_unref (&forest);
   }
@@ -218,7 +239,7 @@ main (int argc, char **argv)
     const char *prefix_cmesh = "t8_prismed_spherical_shell_octahedron_cmesh";
     const char *prefix_forest = "t8_prismed_spherical_shell_octahedron_forest";
 
-    const int uniform_level = 3;
+    const int uniform_level = 2;
     const double inner_radius = 42.0;
     const double shell_thickness = 5.0;
     const int num_levels = 2;
@@ -230,10 +251,10 @@ main (int argc, char **argv)
     t8_forest_t forest = t8_forest_new_uniform (cmesh, t8_scheme_new_default_cxx (), uniform_level, 0, comm);
 
     t8_cmesh_vtk_write_file (cmesh, prefix_cmesh);
-    t8_global_productionf ("Wrote %s.\n", prefix_cmesh);
+    t8_global_productionf ("Wrote %s.pvtu\n", prefix_cmesh);
 
     t8_write_forest_to_vtu (forest, prefix_forest);
-    t8_global_productionf ("Wrote %s.\n\n", prefix_forest);
+    t8_global_productionf ("Wrote %s.pvtu\n\n", prefix_forest);
 
     t8_forest_unref (&forest);
   }
@@ -242,7 +263,7 @@ main (int argc, char **argv)
     const char *prefix_cmesh = "t8_prismed_spherical_shell_icosahedron_cmesh";
     const char *prefix_forest = "t8_prismed_spherical_shell_icosahedron_forest";
 
-    const int uniform_level = 3;
+    const int uniform_level = 2;
     const double inner_radius = 42.0;
     const double shell_thickness = 5.0;
     const int num_levels = 2;
@@ -254,10 +275,10 @@ main (int argc, char **argv)
     t8_forest_t forest = t8_forest_new_uniform (cmesh, t8_scheme_new_default_cxx (), uniform_level, 0, comm);
 
     t8_cmesh_vtk_write_file (cmesh, prefix_cmesh);
-    t8_global_productionf ("Wrote %s.\n", prefix_cmesh);
+    t8_global_productionf ("Wrote %s.pvtu\n", prefix_cmesh);
 
     t8_write_forest_to_vtu (forest, prefix_forest);
-    t8_global_productionf ("Wrote %s.\n\n", prefix_forest);
+    t8_global_productionf ("Wrote %s.pvtu\n\n", prefix_forest);
 
     t8_forest_unref (&forest);
   }
@@ -267,17 +288,17 @@ main (int argc, char **argv)
     const char *prefix_forest = "t8_cubed_sphere_forest";
 
     const int uniform_level = 2;
-    const double radius = 1.0;
+    const double radius = 5.0;
 
     t8_cmesh_t cmesh = t8_cmesh_new_cubed_sphere (radius, comm);
 
     t8_forest_t forest = t8_forest_new_uniform (cmesh, t8_scheme_new_default_cxx (), uniform_level, 0, comm);
 
     t8_cmesh_vtk_write_file (cmesh, prefix_cmesh);
-    t8_global_productionf ("Wrote %s.\n", prefix_cmesh);
+    t8_global_productionf ("Wrote %s.pvtu\n", prefix_cmesh);
 
     t8_write_forest_to_vtu (forest, prefix_forest);
-    t8_global_productionf ("Wrote %s.\n\n", prefix_forest);
+    t8_global_productionf ("Wrote %s.pvtu\n\n", prefix_forest);
 
     t8_forest_unref (&forest);
   }

example/cmesh/t8_cmesh_hypercube_pad.cxx

@@ -22,11 +22,11 @@
 
 #include <t8.h>
 #include <t8_cmesh.h>
-#include <t8_cmesh_vtk_writer.h>
+#include <t8_vtk/t8_vtk_writer.h>
+
 #include <t8_cmesh/t8_cmesh_examples.h>
 #include <t8_schemes/t8_default/t8_default.hxx>
 #include <t8_forest/t8_forest_general.h>
-#include <t8_forest/t8_forest_vtk.h>
 int
 main (int argc, char **argv)
 {

example/cmesh/t8_cmesh_partition.cxx

@@ -23,7 +23,8 @@
 #include <sc_refcount.h>
 #include <t8_forest/t8_forest_adapt.h>
 #include <t8_forest/t8_forest_general.h>
-#include <t8_cmesh_vtk_writer.h>
+#include <t8_vtk/t8_vtk_writer.h>
+
 #include <t8_cmesh/t8_cmesh_partition.h>
 #include <t8_cmesh/t8_cmesh_examples.h>
 #include <p4est_connectivity.h>

example/forest/t8_test_face_iterate.cxx

@@ -31,9 +31,9 @@
 #include <t8_forest/t8_forest_geometrical.h>
 #include <t8_cmesh.h>
 #include <t8_cmesh_readmshfile.h>
-#include <t8_cmesh_vtk_writer.h>
 #include <t8_cmesh/t8_cmesh_examples.h>
 #include <t8_data/t8_containers.h>
+#include <t8_vtk/t8_vtk_writer.h>
 
 typedef struct
 {

example/forest/t8_test_ghost.cxx

@@ -30,7 +30,7 @@
 #include <t8_forest/t8_forest_profiling.h>
 #include <t8_cmesh.h>
 #include <t8_cmesh_readmshfile.h>
-#include <t8_cmesh_vtk_writer.h>
+#include <t8_vtk/t8_vtk_writer.h>
 #include <t8_cmesh/t8_cmesh_examples.h>
 #include <example/common/t8_example_common.h>
 

example/forest/t8_test_ghost_large_level_diff.cxx

@@ -37,7 +37,7 @@
 #include <sc_statistics.h>
 #include <sc_options.h>
 #include <t8_cmesh_readmshfile.h>
-#include <t8_cmesh_vtk_writer.h>
+#include <t8_vtk/t8_vtk_writer.h>
 #include <t8_cmesh/t8_cmesh_examples.h>
 #include <t8_schemes/t8_default/t8_default_prism/t8_dprism.h>
 #include <t8_schemes/t8_default/t8_default_tet/t8_dtet.h>

scripts/indent_all_files.scp

@@ -55,6 +55,7 @@ echo	$PWD/../example/
 echo	$PWD/../test/
 echo	$PWD/../tutorials/
 echo	$PWD/../benchmarks/
+echo	$PWD/../api/
 echo
 read -p "Are you sure? ('Y' or 'y' to continue)" -n 1 -r
 echo