Merge branch 'geodynamics:main' into main

.github/workflows/linux.yml

@@ -38,7 +38,7 @@ jobs:
       run: |
         mkdir build-no-unity
         cd build-no-unity
-        cmake -D CMAKE_BUILD_TYPE=Debug -D ASPECT_PRECOMPILE_HEADERS=OFF -D ASPECT_UNITY_BUILD=OFF -D CMAKE_CXX_FLAGS='-Werror' ..
+        cmake -D CMAKE_BUILD_TYPE=Debug -D ASPECT_PRECOMPILE_HEADERS=OFF -D ASPECT_UNITY_BUILD=OFF -D CMAKE_CXX_FLAGS='-Werror' -D ASPECT_ADDITIONAL_CXX_FLAGS='-Wdeprecated-declarations' ..
         make -j 4
         ./aspect --test
 
@@ -130,7 +130,7 @@ jobs:
         -D CMAKE_BUILD_TYPE=Debug \
         -G 'Ninja' \
         -D CMAKE_CXX_FLAGS='-Werror' \
-        -D ASPECT_ADDITIONAL_CXX_FLAGS='-O3' \
+        -D ASPECT_ADDITIONAL_CXX_FLAGS='-O3 -Wdeprecated-declarations' \
         -D ASPECT_TEST_GENERATOR='Ninja' \
         -D ASPECT_PRECOMPILE_HEADERS=ON \
         -D ASPECT_UNITY_BUILD=ON \

.gitignore

@@ -21,6 +21,8 @@
 /benchmarks/**/cmake_install.cmake
 /benchmarks/**/lib*.so
 /benchmarks/**/aspect
+/benchmarks/**/aspect-debug
+/benchmarks/**/aspect-release
 /benchmarks/**/temp.prm
 /benchmarks/tangurnis/*/*csv
 /benchmarks/tangurnis/*/solution*
@@ -30,6 +32,8 @@
 /cookbooks/**/lib*.so
 /cookbooks/**/Makefile
 /cookbooks/**/aspect
+/cookbooks/**/aspect-debug
+/cookbooks/**/aspect-release
 /detailed.log
 /doc/aspect.dox
 /doc/aspect.tag

AUTHORS.md

@@ -1,33 +1,41 @@
+(sec:authors)=
+# Authors
+
 ASPECT is being developed by a large, collaborative, and inclusive
 community. The code and its community are currently maintained by the
 following *Maintainers*:
 
 * Wolfgang Bangerth (Colorado State University, USA)
-* Juliane Dannberg (University of Florida, USA)
+* Juliane Dannberg (GEOMAR Helmholtz Centre for Ocean Research, Germany)
 * Menno Fraters (University of California, Davis, USA)
-* Rene Gassmoeller (University of Florida, USA)
+* Rene Gassmoeller (GEOMAR Helmholtz Centre for Ocean Research, Germany)
 * Anne Glerum (Geoforschungszentrum Potsdam, Germany)
 * Timo Heister (Clemson University, USA)
 * Bob Myhill (University of Bristol, UK)
 * John Naliboff (New Mexico Tech, USA)
 
+## Principal developers
+
 The following people currently serve as *Principal Developers* -- people
 who have and are providing substantial technical contributions to ASPECT:
 
 * Jacky Austermann (Columbia University and Lamont-Doherty Earth Observatory, USA)
 * Wolfgang Bangerth (Colorado State University, USA)
-* Juliane Dannberg (University of Florida, USA)
+* Juliane Dannberg (GEOMAR Helmholtz Centre for Ocean Research, Germany)
 * Menno Fraters (University of California, Davis, USA)
-* Rene Gassmoeller (University of Florida, USA)
+* Rene Gassmoeller (GEOMAR Helmholtz Centre for Ocean Research, Germany)
 * Anne Glerum (Geoforschungszentrum Potsdam, Germany)
 * Timo Heister (Clemson University, USA)
 * Bob Myhill (University of Bristol, UK)
 * John Naliboff (New Mexico Tech, USA)
 * Cedric Thieulot (Utrecht University, Netherlands)
 
+## Community
+
+A complete and growing list of the many authors that have contributed to ASPECT
+can be found [in our Github repository](https://github.com/geodynamics/aspect/graphs/contributors).
 
-A complete and growing list of the many authors that have contributed
-over the years can be found at [here](https://github.com/geodynamics/aspect/graphs/contributors).
+**With special contributions to the manual by:** Jacqueline Austermann, Magali Billen, Markus Bürg, Thomas Clevenger, Samuel Cox, William Durkin, Grant Euen, Thomas Geenen, Ryan Grove, Eric Heien, Ludovic Jeanniot, Louise Kellogg, Scott King, Martin Kronbichler, Marine Lasbleis, Haoyuan Li, Shangxin Liu, Hannah Mark, Elvira Mulyukova, Bart Niday, Jonathan Perry-Houts, Elbridge Gerry Puckett, Tahiry Rajaonarison, Fred Richards, Jonathan Robey, Ian Rose, Max Rudolph, Stephanie Sparks, D. Sarah Stamps, Cedric Thieulot, Wanying Wang, Iris van Zelst, Siqi Zhang.
 
-We are grateful for the contributions of all of these people, and
-their participation in our community!
+We are grateful for all contributions to ASPECT and its documentation, and
+your participation in our community!

CMakeLists.txt

@@ -1,4 +1,4 @@
-# Copyright (C) 2013 - 2023 by the authors of the ASPECT code.
+# Copyright (C) 2013 - 2024 by the authors of the ASPECT code.
 #
 # This file is part of ASPECT.
 #
@@ -91,6 +91,8 @@ else()
   set(ASPECT_BUILD_RELEASE "OFF")
 endif()
 
+# Some other ASPECT configuration options:
+set(ASPECT_MAX_NUM_PARTICLE_SYSTEMS 2 CACHE STRING "The maximum number of particle systems supported at runtime.")
 
 
 
@@ -290,7 +292,8 @@ if(ASPECT_WITH_WORLD_BUILDER)
 
       set(WB_TARGET "WorldBuilderDebug")
       add_subdirectory("${WORLD_BUILDER_SOURCE_DIR}" ${CMAKE_BINARY_DIR}/world_builder/)
-      target_compile_options(WorldBuilderDebug PRIVATE "-g" "${ASPECT_ADDITIONAL_CXX_FLAGS}")
+      separate_arguments(SEPARATED_FLAGS NATIVE_COMMAND ${ASPECT_ADDITIONAL_CXX_FLAGS})
+      target_compile_options(WorldBuilderDebug PRIVATE "-g" "${SEPARATED_FLAGS}")
 
       set(CMAKE_BUILD_TYPE ${_build_type})
     endif()
@@ -306,7 +309,9 @@ if(ASPECT_WITH_WORLD_BUILDER)
       set(WB_TARGET "WorldBuilderRelease")
       add_subdirectory("${WORLD_BUILDER_SOURCE_DIR}" ${CMAKE_BINARY_DIR}/world_builder_release/)
       target_compile_definitions(WorldBuilderRelease PUBLIC "NDEBUG")
-      target_compile_options(WorldBuilderRelease PRIVATE "-O3" "${ASPECT_ADDITIONAL_CXX_FLAGS}")
+
+      separate_arguments(SEPARATED_FLAGS NATIVE_COMMAND ${ASPECT_ADDITIONAL_CXX_FLAGS})
+      target_compile_options(WorldBuilderRelease PRIVATE "-O3" "${SEPARATED_FLAGS}")
 
       set(CMAKE_BUILD_TYPE ${_build_type})
     endif()
@@ -769,12 +774,17 @@ if (${FORCE_COLORED_OUTPUT})
   endif()
 endif()
 
+# deal.II versions >=9.5 disable deprecation warnings in user code. Enable
+# the warnings again by removing the flag that disables them.
+string(REPLACE "-Wno-deprecated-declarations" "" DEAL_II_WARNING_FLAGS "${DEAL_II_WARNING_FLAGS}")
+
 set(ASPECT_ADDITIONAL_CXX_FLAGS "" CACHE STRING "Additional CMAKE_CXX_FLAGS applied after the deal.II options.")
 
 if(NOT ASPECT_ADDITIONAL_CXX_FLAGS STREQUAL "")
   message(STATUS "Appending ASPECT_ADDITIONAL_CXX_FLAGS: '${ASPECT_ADDITIONAL_CXX_FLAGS}':")
   string(APPEND DEAL_II_CXX_FLAGS_DEBUG " ${ASPECT_ADDITIONAL_CXX_FLAGS}")
   string(APPEND DEAL_II_CXX_FLAGS_RELEASE " ${ASPECT_ADDITIONAL_CXX_FLAGS}")
+  message(STATUS "  DEAL_II_WARNING_FLAGS: ${DEAL_II_WARNING_FLAGS}")
   message(STATUS "  DEAL_II_CXX_FLAGS_DEBUG: ${DEAL_II_CXX_FLAGS_DEBUG}")
   message(STATUS "  DEAL_II_CXX_FLAGS_RELEASE: ${DEAL_II_CXX_FLAGS_RELEASE}")
 endif()
@@ -827,6 +837,11 @@ if(${ASPECT_BUILD_RELEASE} STREQUAL "ON")
   endif()
 endif()
 
+# turn on debug checks like invalid element access in c++ standard library:
+if(${ASPECT_BUILD_DEBUG} STREQUAL "ON")
+  target_compile_definitions(${TARGET_EXE_DEBUG} PUBLIC "_GLIBCXX_ASSERTIONS")
+endif()
+
 
 # ##############################################################################
 # Make sure we correctly link with external libraries
@@ -999,51 +1014,6 @@ MESSAGE(STATUS "===== Configuring ASPECT documentation =============")
 
 add_subdirectory(doc)
 
-
-# Find the deal.II parameter GUI and install helper script
-find_program(PARAMETER_GUI_EXECUTABLE
-        parameter_gui
-        HINTS $ENV{PARAMETER_GUI_DIR} $ENV{PARAMETER_GUI_DIR}/bin ${PARAMETER_GUI_DIR} ${PARAMETER_GUI_DIR}/bin
-        PATH bin)
-mark_as_advanced(CLEAR PARAMETER_GUI_EXECUTABLE)
-
-# Did the user specify something that doesn't exist?
-if(PARAMETER_GUI_EXECUTABLE
-        AND
-    (NOT EXISTS ${PARAMETER_GUI_EXECUTABLE} OR IS_DIRECTORY ${PARAMETER_GUI_EXECUTABLE}))
-  message(STATUS "Warning: PARAMETER_GUI_EXECUTABLE '${PARAMETER_GUI_EXECUTABLE}' does not exist")
-  set(PARAMETER_GUI_EXECUTABLE "PARAMETER_GUI_EXECUTABLE-NOTFOUND" CACHE FILEPATH "" FORCE)
-endif()
-
-if(NOT PARAMETER_GUI_EXECUTABLE)
-  message(STATUS "Parameter GUI not found: install and provide a hint using -D PARAMETER_GUI_DIR or set -D PARAMETER_GUI_EXECUTABLE directly.")
-else()
-  message(STATUS "Found parameter GUI at: ${PARAMETER_GUI_EXECUTABLE}")
-  configure_file(
-    ${CMAKE_SOURCE_DIR}/doc/aspect-gui
-    ${CMAKE_BINARY_DIR}/aspect-gui
-    @ONLY
-  )
-install(FILES ${CMAKE_BINARY_DIR}/aspect-gui
-        DESTINATION bin
-        PERMISSIONS OWNER_EXECUTE OWNER_WRITE OWNER_READ
-                GROUP_READ GROUP_EXECUTE
-                WORLD_READ WORLD_EXECUTE)
-endif()
-
-
-
-# A target to create parameters.json after building the ASPECT binary.
-
-add_custom_command(TARGET ${TARGET_EXE} POST_BUILD
-  COMMAND sh -c 'echo "" | ./$<TARGET_PROPERTY:${TARGET_EXE},OUTPUT_NAME> --output-json -- > parameters.json'
-  WORKING_DIRECTORY ${CMAKE_BINARY_DIR})
-
-
-
-message(STATUS "")
-message(STATUS "===== Writing final configuration ==================")
-
 include(cmake/write_config)
 
 # print "info" if run for the first time:

VERSION

@@ -1 +1 @@
-2.6.0-pre
+3.1.0-pre

benchmarks/CMakeLists.txt

@@ -1,4 +1,4 @@
-# Copyright (C) 2023 by the authors of the ASPECT code.
+# Copyright (C) 2023 - 2024 by the authors of the ASPECT code.
 #
 # This file is part of ASPECT.
 #

benchmarks/advection_in_annulus/CMakeLists.txt

@@ -1,4 +1,4 @@
-# Copyright (C) 2015 - 2021 by the authors of the ASPECT code.
+# Copyright (C) 2015 - 2024 by the authors of the ASPECT code.
 #
 # This file is part of ASPECT.
 #

benchmarks/advection_in_annulus/advection_in_annulus.cc

@@ -1,5 +1,5 @@
 /*
-  Copyright (C) 2011 - 2023 by the authors of the ASPECT code.
+  Copyright (C) 2011 - 2024 by the authors of the ASPECT code.
 
   This file is part of ASPECT.
 
@@ -64,10 +64,10 @@ namespace aspect
         const double theta = std::atan2(y,x);
         const double f_r = A*r + B/r;
         const double g_r = A*r/2 + B*std::log(r)/r + C/r;
-        const double v_r = g_r*k*sin(k*theta);
-        const double v_theta = f_r*cos(k*theta);
-        const double v_x = cos(theta)*v_r - sin(theta)*v_theta;
-        const double v_y = sin(theta)*v_r + cos(theta)*v_theta;
+        const double v_r = g_r*k*std::sin(k*theta);
+        const double v_theta = f_r*std::cos(k*theta);
+        const double v_x = std::cos(theta)*v_r - std::sin(theta)*v_theta;
+        const double v_y = std::sin(theta)*v_r + std::cos(theta)*v_theta;
         return Point<2> (v_x,v_y);
       }
 
@@ -82,7 +82,7 @@ namespace aspect
         const double f_r = 2*r + B/r;
         const double g_r = A*r/2 + B*std::log(r)/r + C/r;
         const double h_r=(2*g_r-f_r)/r;
-        return k*h_r*sin(k*theta)+rho_0*gravity*(outer_radius-r);
+        return k*h_r*std::sin(k*theta)+rho_0*gravity*(outer_radius-r);
       }
 
       template <int dim>

benchmarks/annulus/instantaneous/annulus.prm

@@ -76,8 +76,12 @@ subsection Postprocess
   end
 
   subsection Visualization
-    set List of output variables = density, viscosity, strain rate, dynamic topography, AnnulusVisualizationPostprocessor
+    set List of output variables = material properties, strain rate, dynamic topography, AnnulusVisualizationPostprocessor
     set Time between graphical output = 0
+
+    subsection Material properties
+      set List of material properties = density, viscosity
+    end
   end
 end
 

benchmarks/annulus/plugin/CMakeLists.txt

@@ -1,4 +1,4 @@
-# Copyright (C) 2015 - 2022 by the authors of the ASPECT code.
+# Copyright (C) 2015 - 2024 by the authors of the ASPECT code.
 #
 # This file is part of ASPECT.
 #

benchmarks/annulus/plugin/annulus.cc

@@ -1,5 +1,5 @@
 /*
-  Copyright (C) 2011 - 2023 by the authors of the ASPECT code.
+  Copyright (C) 2011 - 2024 by the authors of the ASPECT code.
 
   This file is part of ASPECT.
 
@@ -219,7 +219,7 @@ namespace aspect
             const double r = spherical_position[0];
             const double theta = spherical_position[1];
 
-            const double forcing_term = m(r,k)*k*sin(k*(theta-phase(t))) + rho_0;
+            const double forcing_term = m(r,k)*k*std::sin(k*(theta-phase(t))) + rho_0;
             gravity_magnitude = forcing_term / Annulus_density(pos,k,t, transient);
           }
 
@@ -615,7 +615,7 @@ namespace aspect
         compute_dynamic_topography_error() const
         {
           const Postprocess::DynamicTopography<dim> &dynamic_topography =
-            this->get_postprocess_manager().template get_matching_postprocessor<Postprocess::DynamicTopography<dim>>();
+            this->get_postprocess_manager().template get_matching_active_plugin<Postprocess::DynamicTopography<dim>>();
 
           const AnnulusMaterial<dim> &material_model
             = Plugins::get_plugin_as_type<const AnnulusMaterial<dim>>(this->get_material_model());

benchmarks/annulus/transient/transient_annulus.prm

@@ -53,8 +53,12 @@ subsection Postprocess
   end
 
   subsection Visualization
-    set List of output variables = density, gravity, AnnulusVisualizationPostprocessor
+    set List of output variables = material properties, gravity, AnnulusVisualizationPostprocessor
     set Time between graphical output = 0.1
+
+    subsection Material properties
+      set List of material properties = density
+    end
   end
 
   subsection Particles
@@ -76,13 +80,12 @@ subsection Particles
   set Integration scheme = rk2
   set Interpolation scheme = bilinear least squares
   set List of particle properties = particle density
-  set Update ghost particles = true
   set Particle generator name = random uniform
   set Load balancing strategy = add particles
   set Minimum particles per cell = 12
 
   subsection Generator
-    subsection Probability density function
+    subsection Random uniform
       set Number of particles = 49152
     end
   end

benchmarks/blankenbach/base_case1a.prm

@@ -97,7 +97,11 @@ subsection Postprocess
 
   subsection Visualization
     set Time between graphical output = 0.05
-    set List of output variables      = material properties, adiabat, thermal conductivity, heating, artificial viscosity
+    set List of output variables      = material properties, adiabat, heating, artificial viscosity
+
+    subsection Material properties
+      set List of material properties = density, thermal expansivity, specific heat, viscosity, thermal conductivity
+    end
   end
 end
 

benchmarks/blankenbach/base_case2a.prm

@@ -97,7 +97,11 @@ subsection Postprocess
 
   subsection Visualization
     set Time between graphical output = 0.05
-    set List of output variables      = material properties, adiabat, thermal conductivity, heating, artificial viscosity
+    set List of output variables      = material properties, adiabat, heating, artificial viscosity
+
+    subsection Material properties
+      set List of material properties = density, thermal expansivity, specific heat, viscosity, thermal conductivity
+    end
   end
 end
 

benchmarks/blankenbach/base_case2b.prm

@@ -99,7 +99,11 @@ subsection Postprocess
 
   subsection Visualization
     set Time between graphical output = 0.002
-    set List of output variables      = material properties, adiabat, thermal conductivity, heating, artificial viscosity
+    set List of output variables      = material properties, adiabat, heating, artificial viscosity
+
+    subsection Material properties
+      set List of material properties = density, thermal expansivity, specific heat, viscosity, thermal conductivity
+    end
   end
 end
 

benchmarks/blankenbach/plugin/CMakeLists.txt

@@ -1,4 +1,4 @@
-# Copyright (C) 2011 - 2021 by the authors of the ASPECT code.
+# Copyright (C) 2011 - 2024 by the authors of the ASPECT code.
 #
 # This file is part of ASPECT.
 #

benchmarks/buiter_et_al_2008_jgr/figure_6_1e20.prm

@@ -172,8 +172,12 @@ subsection Postprocess
   set List of postprocessors = velocity statistics, basic statistics, temperature statistics, visualization
 
   subsection Visualization
-    set List of output variables = density, viscosity, strain rate, error indicator, partition
+    set List of output variables = material properties, strain rate, error indicator, partition
     set Time between graphical output = 1e5
     set Interpolate output = false
+
+    subsection Material properties
+      set List of material properties = density, viscosity
+    end
   end
 end

benchmarks/buiter_et_al_2016_jsg/exp_1.prm

@@ -167,10 +167,14 @@ subsection Postprocess
   set List of postprocessors = velocity statistics, basic statistics, visualization
 
   subsection Visualization
-    set List of output variables      = density, viscosity, strain rate, named additional outputs
+    set List of output variables      = material properties, strain rate, named additional outputs
     set Output format                 = vtu
     set Time between graphical output = 144
     set Interpolate output            = false
+
+    subsection Material properties
+      set List of material properties = density, viscosity
+    end
   end
 end