Merge remote-tracking branch 'origin/main' into scheme-tutorial

.github/workflows/build_cmake_tarball.yml

@@ -41,7 +41,7 @@ jobs:
   build:
 
     if: (github.event_name == 'schedule' && github.repository == 'DLR-AMR/t8code') || (github.event_name != 'schedule')
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     container: dlramr/t8code-ubuntu:t8-dependencies
     timeout-minutes: 90
     steps:
@@ -59,8 +59,6 @@ jobs:
       uses: nikeee/setup-pandoc@v1
     - name: Test pandoc
       run: pandoc --version
-    # On the github Ubuntu 20.04, sudo is not available by default
-    # we need it, however, to update/upgrade our packages.    
     - name: Update packages
       run: sudo apt-get update && sudo apt-get upgrade -y
     # This step is necessary to get the newest package data
@@ -99,14 +97,12 @@ jobs:
 
   test-tarball:
     needs: build
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     container: dlramr/t8code-ubuntu:t8-dependencies
     timeout-minutes: 90
     steps:
     - name: install sudo
       run: apt update && apt install sudo
-    # On the github Ubuntu 20.04, sudo is not available by default
-    # we need it, however, to update/upgrade our packages.       
     - name: Update packages
       run: sudo apt-get update && sudo apt-get upgrade -y
     # This step is necessary to get the newest package data

.github/workflows/check_indentation.yml

@@ -31,15 +31,11 @@ name: t8code indentation check
 # The output is uploaded as an artifact to the github page.
 
 on:
+  merge_group:
   push:
     branches:
       - main
-      - develop
-      - feature-*CI* # for testing this script, all feature branches with "CI" in their name
   pull_request:
-    branches:
-      - main
-      - develop
   workflow_dispatch: # Be able to trigger this manually on github.com
   # Run every night at 1:05
   schedule:
@@ -48,7 +44,7 @@ on:
 jobs:
   indent:
     if: (github.event_name == 'schedule' && github.repository == 'DLR-AMR/t8code') || (github.event_name != 'schedule')
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     timeout-minutes: 10
     steps:
     - uses: actions/checkout@v4
@@ -58,8 +54,6 @@ jobs:
     # Deactivated the install sudo because it failed.
     #- name: install sudo
     #  run: apt update && apt install sudo
-    # On the github Ubuntu 20.04, sudo is not available by default
-    # we need it, however, to update/upgrade our packages.
     - name: Update packages
       run: sudo apt-get update && sudo apt-get upgrade -y
     # This step is necessary to get the newest package data

.github/workflows/mattermost_issue.yml

@@ -39,7 +39,7 @@ env:
 jobs:
   send_mm_message_issue:
     if: github.repository == 'DLR-AMR/t8code'
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
       - name: debug_before_build
         run: echo ${{ env.message_build}}

.github/workflows/mattermost_pull_request.yml

@@ -28,7 +28,7 @@ name: Mattermost_message_pull_request
 on:
   # Triggers the workflow on pull request events on the feature-CI_mattermost_messages, develop or main branch
   pull_request:
-    branches: [ feature-CI_mattermost_messages, develop, main ]
+    branches:
     types: [ opened, synchronize, reopened, closed]
 
   # Allows you to run this workflow manually from the Actions tab
@@ -39,7 +39,7 @@ env:
 jobs:
   send_mm_message_pr:
     if: github.repository == 'DLR-AMR/t8code'
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
       - name: debug_before_build
         run: echo ${{ env.message_build}}

.github/workflows/spell_check.yml

@@ -1,10 +1,10 @@
 name: spell_check
 
 on:
+  merge_group:
   push:
     branches:
       - main
-      - feature-*CI* # for testing this script, all feature branches with "CI" in their name
   pull_request:
   workflow_dispatch: # Be able to trigger this manually on github.com
 

.github/workflows/tests_cmake_testsuite.yml

@@ -31,15 +31,11 @@ name: t8code CMake testsuite
 #       IGNORE_CACHE to true in the respective steps.
 
 on:
+  merge_group:
   push:
     branches:
       - main
-      - develop
-      - feature-*CI* # for testing this script, all feature branches with "CI" in their name
   pull_request:
-    branches:
-      - main
-      - develop
   workflow_dispatch: # Be able to trigger this manually on github.com
   # Run every night at 1:10
   schedule:

AUTHORS

@@ -26,5 +26,5 @@ Contributors:
   Andrew Kirby <[email protected]>
   Hendrik Ranocha <[email protected]>
   Michael Schlottke-Lakemper <[email protected]>
-  Kathrin Schoenlein <kathrin[email protected]>
+  Katrin Schoenlein <katrin[email protected]>
 

CITATION.cff

@@ -113,9 +113,9 @@ authors:
     family-names: Schlottke-Lakemper
     email: [email protected]
     affiliation: "RWTH Aachen"
-  - given-names: Kathrin
+  - given-names: Katrin
     family-names: Schoenlein
-    email: kathrin[email protected]
+    email: katrin[email protected]
     affiliation: "German Aerospace Center (DLR)"
   - given-names: Tabea
     family-names: Leistikow 

README.md

@@ -134,6 +134,9 @@ to install the package on your system.
   [6] **Geometry controlled refinement for hexahedra**:
   Elsweijer, Sandro and Holke, Johannes and Kleinert, Jan and Reith, Dirk  (2022) *Constructing a Volume Geometry Map for Hexahedra with Curved Boundary Geometries*.   In: SIAM International Meshing Roundtable Workshop 2022.  SIAM International Meshing Roundtable Workshop 2022, 22. - 25. Feb. 2022, [Full text available](https://elib.dlr.de/186570/1/ConstructingAVolumeGeometryMapForHexahedraWithCurvedBoundaryGeometries.pdf) 
 
+  [7] **JOSS entry**:
+  Holke, Johannes and Markert, Johannes, et. al. (2025) *t8code - modular adaptive mesh refinement in the exascale era*. In: Journal of Open Source Software, [Full text available](https://www.theoj.org/joss-papers/joss.06887/10.21105.joss.06887.pdf)
+
 ### Theses with t8code relations
 
   An (incomplete) list of theses written with or about t8code:

api/t8_fortran_interface/CMakeLists.txt

@@ -8,11 +8,11 @@ target_include_directories( T8 PRIVATE ${CMAKE_CURRENT_LIST_DIR} )
 # Install header files.
 install(
     FILES ${CMAKE_CURRENT_LIST_DIR}/t8_fortran_interface.h
-    DESTINATION ${CMAKE_INSTALL_PREFIX}/include/t8_fortran_interface
+    DESTINATION include/t8_fortran_interface
 )
 
 # Install module files.
 install(
     FILES ${CMAKE_BINARY_DIR}/src/t8_fortran_interface_mod.mod
-    DESTINATION ${CMAKE_INSTALL_PREFIX}/include/t8_fortran_interface
+    DESTINATION include/t8_fortran_interface
 )

api/t8_fortran_interface/t8_fortran_interface.c

@@ -3,7 +3,7 @@
   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) 2024 the developers
+  Copyright (C) 2025 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

api/t8_fortran_interface/t8_fortran_interface.h

@@ -3,7 +3,7 @@
   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) 2024 the developers
+  Copyright (C) 2025 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

benchmarks/CMakeLists.txt

@@ -25,7 +25,7 @@ function( add_t8_benchmark )
         set_target_properties( ${ADD_T8_BENCHMARK_NAME} PROPERTIES EXPORT_COMPILE_COMMANDS ON )
     endif( T8CODE_EXPORT_COMPILE_COMMANDS )
 
-    install( TARGETS ${ADD_T8_BENCHMARK_NAME} DESTINATION ${CMAKE_INSTALL_PREFIX}/bin )
+    install( TARGETS ${ADD_T8_BENCHMARK_NAME} DESTINATION bin )
 endfunction()
 
 add_t8_benchmark( NAME t8_time_partition SOURCES t8_time_partition.cxx )

doc/Doxyfile.in

@@ -457,7 +457,7 @@ LOOKUP_CACHE_SIZE      = 0
 # than 0 to get more control over the balance between CPU load and processing
 # speed. At this moment only the input processing can be done using multiple
 # threads. Since this is still an experimental feature the default is set to 1,
-# which efficively disables parallel processing. Please report any issues you
+# which effectively disables parallel processing. Please report any issues you
 # encounter. Generating dot graphs in parallel is controlled by the
 # DOT_NUM_THREADS setting.
 # Minimum value: 0, maximum value: 32, default value: 1.

doc/author_brandt.txt

@@ -0,0 +1 @@
+I place my contributions to t8code under the FreeBSD license. Hannes Brandt ([email protected])

doc/author_nguyenxuan.txt

@@ -0,0 +1,2 @@
+I place my contributions to t8code under the FreeBSD license.
+Tu Nguyen Xuan ([email protected])

doc/author_ploetzke.txt

@@ -0,0 +1 @@
+I place my contributions to t8code under the FreeBSD license. Lena Plötzke ([email protected])

doc/author_spenke.txt

@@ -0,0 +1 @@
+I place my contributions to t8code under the FreeBSD license. Thomas Spenke ([email protected])

example/CMakeLists.txt

@@ -7,7 +7,7 @@ endif()
 target_sources( t8example PRIVATE common/t8_example_common.cxx common/t8_example_common_functions.cxx )
 target_include_directories( t8example PRIVATE ${CMAKE_CURRENT_LIST_DIR}/.. ${SC_INCLUDE_DIR} )
 target_link_libraries( t8example PRIVATE T8 ${SC_LIBRARIES} m )
-install( TARGETS t8example DESTINATION ${CMAKE_INSTALL_PREFIX}/lib )
+install( TARGETS t8example DESTINATION lib )
 
 function( add_t8_example )
     set( options "" )
@@ -36,7 +36,7 @@ function( add_t8_example )
         set_target_properties( ${ADD_T8_EXAMPLE_NAME} PROPERTIES EXPORT_COMPILE_COMMANDS ON )
     endif( T8CODE_EXPORT_COMPILE_COMMANDS )
 
-    install( TARGETS ${ADD_T8_EXAMPLE_NAME} DESTINATION ${CMAKE_INSTALL_PREFIX}/bin )
+    install( TARGETS ${ADD_T8_EXAMPLE_NAME} DESTINATION bin )
 endfunction()
 
 add_t8_example( NAME t8_advection                       SOURCES advect/t8_advection.cxx )

example/IO/cmesh/vtk/t8_cmesh_read_from_vtk.cxx

@@ -131,7 +131,7 @@ main (int argc, char **argv)
   snprintf (usage, BUFSIZ, "Usage:\t%s <OPTIONS> <ARGUMENTS>\n\t%s -h\t for a brief overview of all options.",
             basename (argv[0]), basename (argv[0]));
   sreturn = snprintf (help, BUFSIZ,
-                      "This program reads a .vtk-file and constructs a mesh representing the given Data."
+                      "This program reads a .vtk-file and constructs a mesh representing the given Data.\n"
                       "Arguments can be passed via:\n%s\n\n",
                       usage);
   if (sreturn >= BUFSIZ) {
@@ -151,7 +151,7 @@ main (int argc, char **argv)
   sc_options_add_string (opt, 'f', "vtk-file", &vtk_file, "", "The prefix of the .vtk file.");
   sc_options_add_string (opt, 'o', "output", &out_file, "output", "The prefix of the output-file.");
   sc_options_add_int (opt, 'c', "num_cell_values", &num_keys, 0, "Number of values per cell stored in the vtk-file.");
-  sc_options_add_bool (opt, 'p', "partition", &partition, 0, "If set, partition the cmesh uniformly.");
+  sc_options_add_switch (opt, 'p', "partition", &partition, "If set, partition the cmesh uniformly.");
   sc_options_add_int (opt, 't', "type_of_file", &vtk_file_type_int, -1,
                       "Set the type of the data in the file.\n"
                       "\t\t\t\t\t0 for vtkUnstructuredGrid,\n"

src/CMakeLists.txt

@@ -60,7 +60,7 @@ endif()
 
 if( T8CODE_ENABLE_OCC )
     target_compile_definitions( T8 PUBLIC T8_WITH_OCC=1 )
-    target_include_directories( T8 PUBLIC ${OpenCASCADE_INCLUDE_DIR} )
+    target_include_directories( T8 SYSTEM PUBLIC ${OpenCASCADE_INCLUDE_DIR} )
     target_link_libraries( T8 PUBLIC ${OpenCASCADE_LIBRARIES} )
 endif()
 
@@ -122,7 +122,8 @@ target_sources( T8 PRIVATE
     t8_forest/t8_forest_ghost.cxx 
     t8_forest/t8_forest_iterate.cxx 
     t8_forest/t8_forest_balance.cxx 
-    t8_forest/t8_forest_netcdf.cxx 
+    t8_forest/t8_forest_netcdf.cxx
+    t8_forest/t8_forest_search/t8_forest_search.cxx 
     t8_geometry/t8_geometry.cxx 
     t8_geometry/t8_geometry_helpers.c 
     t8_geometry/t8_geometry_base.cxx 
@@ -155,7 +156,6 @@ target_sources( T8 PRIVATE
     t8_schemes/t8_default/t8_default_tri/t8_dtri_bits.c
     t8_schemes/t8_default/t8_default_tri/t8_dtri_connectivity.c
     t8_schemes/t8_default/t8_default_vertex/t8_default_vertex.cxx
-    t8_schemes/t8_default/t8_default_vertex/t8_dvertex_bits.c
     t8_schemes/t8_standalone/t8_standalone.cxx
     t8_vtk/t8_vtk_polydata.cxx 
     t8_vtk/t8_vtk_unstructured.cxx 
@@ -204,26 +204,27 @@ install( FILES
     t8_vec.h
     t8_version.h
     t8_vtk.h
-    t8_windows.h DESTINATION ${CMAKE_INSTALL_PREFIX}/include
+    t8_windows.h DESTINATION include
 )
 
-install( DIRECTORY t8_cmesh DESTINATION ${CMAKE_INSTALL_PREFIX}/include FILES_MATCHING PATTERN "*.h" )
-install( DIRECTORY t8_data DESTINATION ${CMAKE_INSTALL_PREFIX}/include FILES_MATCHING PATTERN "*.h" )
-install( DIRECTORY t8_forest DESTINATION ${CMAKE_INSTALL_PREFIX}/include FILES_MATCHING
+install( DIRECTORY t8_cmesh DESTINATION include FILES_MATCHING PATTERN "*.h" )
+install( DIRECTORY t8_data DESTINATION include FILES_MATCHING PATTERN "*.h" )
+install( DIRECTORY t8_forest DESTINATION include FILES_MATCHING
   PATTERN "*.h"
   PATTERN "*private.h" EXCLUDE )
-install( DIRECTORY t8_geometry DESTINATION ${CMAKE_INSTALL_PREFIX}/include FILES_MATCHING PATTERN "*.h" )
-install( DIRECTORY t8_schemes DESTINATION ${CMAKE_INSTALL_PREFIX}/include FILES_MATCHING PATTERN "*.h" )
-install( DIRECTORY t8_vtk DESTINATION ${CMAKE_INSTALL_PREFIX}/include FILES_MATCHING PATTERN "*.h" )
-
-install( DIRECTORY t8_cmesh DESTINATION ${CMAKE_INSTALL_PREFIX}/include FILES_MATCHING PATTERN "*.hxx" )
-install( DIRECTORY t8_data DESTINATION ${CMAKE_INSTALL_PREFIX}/include FILES_MATCHING PATTERN "*.hxx" )
-install( DIRECTORY t8_forest DESTINATION ${CMAKE_INSTALL_PREFIX}/include FILES_MATCHING PATTERN "*.hxx" )
-install( DIRECTORY t8_geometry DESTINATION ${CMAKE_INSTALL_PREFIX}/include FILES_MATCHING PATTERN "*.hxx" )
-install( DIRECTORY t8_schemes DESTINATION ${CMAKE_INSTALL_PREFIX}/include FILES_MATCHING PATTERN "*.hxx" )
-install( DIRECTORY t8_vtk DESTINATION ${CMAKE_INSTALL_PREFIX}/include FILES_MATCHING PATTERN "*.hxx" )
-
-install( TARGETS T8 DESTINATION ${CMAKE_INSTALL_PREFIX}/lib )
+install( DIRECTORY t8_geometry DESTINATION include FILES_MATCHING PATTERN "*.h" )
+install( DIRECTORY t8_schemes DESTINATION include FILES_MATCHING PATTERN "*.h" )
+install( DIRECTORY t8_vtk DESTINATION include FILES_MATCHING PATTERN "*.h" )
+
+install( DIRECTORY t8_cmesh DESTINATION include FILES_MATCHING PATTERN "*.hxx" )
+install( DIRECTORY t8_data DESTINATION include FILES_MATCHING PATTERN "*.hxx" )
+install( DIRECTORY t8_forest DESTINATION include FILES_MATCHING PATTERN "*.hxx" )
+install( DIRECTORY t8_geometry DESTINATION include FILES_MATCHING PATTERN "*.hxx" )
+install( DIRECTORY t8_schemes DESTINATION include FILES_MATCHING PATTERN "*.hxx" )
+install( DIRECTORY t8_vtk DESTINATION include FILES_MATCHING PATTERN "*.hxx" )
+install( DIRECTORY t8_types DESTINATION include FILES_MATCHING PATTERN "*.hxx" )
+
+install( TARGETS T8 DESTINATION lib )
 install( TARGETS T8 EXPORT ${PROJECT_NAME}-targets )
 
 include( CMakePackageConfigHelpers )

src/Makefile.am

@@ -53,7 +53,9 @@ 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_iterate.h src/t8_forest/t8_forest_partition.h
+  src/t8_forest/t8_forest_iterate.h \
+  src/t8_forest/t8_forest_partition.h \
+  src/t8_forest/t8_forest_search/t8_forest_search.hxx
 libt8_installed_headers_geometry = \
   src/t8_geometry/t8_geometry.h \
   src/t8_geometry/t8_geometry_handler.hxx \
@@ -139,6 +141,7 @@ libt8_compiled_sources = \
   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_ghost.cxx src/t8_forest/t8_forest_iterate.cxx \
+  src/t8_forest/t8_forest_search/t8_forest_search.cxx \
   src/t8_version.c \
   src/t8_vtk.c src/t8_forest/t8_forest_balance.cxx \
   src/t8_forest/t8_forest_netcdf.cxx \

src/t8_cmesh.h

@@ -769,11 +769,6 @@ t8_cmesh_unref (t8_cmesh_t *pcmesh);
 void
 t8_cmesh_destroy (t8_cmesh_t *pcmesh);
 
-/* Functions for constructing complete and committed cmeshes */
-
-t8_cmesh_t
-t8_cmesh_new_testhybrid (sc_MPI_Comm comm);
-
 /** Compute y = ax + b on an array of doubles, interpreting
  * each 3 as one vector x 
  * \param[in]   coords_in         The incoming coordinates of the vectors

src/t8_cmesh.hxx

@@ -24,7 +24,8 @@
  * We define the coarse mesh of trees in this file.
  */
 
-#pragma once
+#ifndef T8_CMESH_HXX
+#define T8_CMESH_HXX
 
 #include <t8_cmesh.h>
 #include <t8_cmesh/t8_cmesh_types.h>
@@ -48,3 +49,5 @@ t8_cmesh_register_geometry (t8_cmesh_t cmesh, _args &&...args)
   }
   return cmesh->geometry_handler->register_geometry<geometry_type> (std::forward<_args> (args)...);
 }
+
+#endif /* T8_CMESH_HXX */

src/t8_cmesh/t8_cmesh_examples.cxx

@@ -680,12 +680,6 @@ t8_cmesh_new_hypercube (t8_eclass_t eclass, sc_MPI_Comm comm, int do_bcast, int
 
   SC_CHECK_ABORT (eclass != T8_ECLASS_PYRAMID || !periodic, "The pyramid cube mesh cannot be periodic.\n");
 
-  if (do_partition) {
-    t8_global_errorf (
-      "WARNING: Partitioning the hypercube cmesh is currently not supported.\n"
-      "Using this cmesh will crash when vertices are used. See also https://github.com/DLR-AMR/t8code/issues/79\n");
-  }
-
   mpiret = sc_MPI_Comm_rank (comm, &mpirank);
   SC_CHECK_MPI (mpiret);
   if (!do_bcast || mpirank == 0) {

src/t8_forest/t8_forest.cxx

@@ -3685,7 +3685,6 @@ t8_eclass_t
 t8_forest_get_tree_class (const t8_forest_t forest, const t8_locidx_t ltreeid)
 {
   t8_locidx_t num_local_trees = t8_forest_get_num_local_trees (forest);
-
   T8_ASSERT (0 <= ltreeid && ltreeid < num_local_trees + t8_forest_get_num_ghost_trees (forest));
   if (ltreeid < num_local_trees) {
     /* The id belongs to a local tree */