feat: integrate the FortFEM backend

CMakeLists.txt

@@ -4,9 +4,11 @@ set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_SOURCE_DIR}/cmake)
 
 ### Define the project
 project(MEPHIT LANGUAGES C CXX Fortran)
+include(CTest)
 
 ### Define options
 option(WITH_MFEM "Compile with MFEM" FALSE)
+option(WITH_FORTFEM "Use FortFEM for supported finite-element operations" FALSE)
 
 ### Specify paths
 set(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/bin)
@@ -58,11 +60,18 @@ find_package(FFTW REQUIRED COMPONENTS DOUBLE_LIB)
 
 include(ExternalProject)
 include(SetupCODE)
-include(SetupTriangle)
+if(WITH_FORTFEM)
+  include(SetupFortfem)
+else()
+  include(SetupTriangle)
+endif()
 if(WITH_MFEM)
   include(SetupMFEM)
   add_definitions(-DUSE_MFEM)
 endif()
+if(WITH_FORTFEM)
+  add_definitions(-DUSE_FORTFEM)
+endif()
 include(Util)
 find_or_fetch(libneo)
 
@@ -108,6 +117,9 @@ set(MEPHIT_C_SRC_FILES
   src/mephit_fem.c
   src/hyper1F1.c
 )
+if(WITH_FORTFEM)
+  list(APPEND MEPHIT_C_SRC_FILES src/mephit_fortfem.c)
+endif()
 set(MEPHIT_CPP_SRC_FILES
   src/mephit_fem.cpp
 )
@@ -117,8 +129,15 @@ if(WITH_MFEM)
     src/miscellaneous.cpp
   )
 endif()
-set_source_files_properties(src/mephit_run.c ${MEPHIT_C_SRC_FILES} ${MEPHIT_CPP_SRC_FILES}
-	PROPERTIES COMPILE_FLAGS "${CMAKE_C_FLAGS} -DREAL=double -I${TRIANGLE_INCLUDE_DIR} -I${SUITESPARSE_INCLUDE_DIRS} -L${TRIANGLE_LIB_DIR}")
+set(MEPHIT_C_DEPENDENCY_FLAGS "-I${SUITESPARSE_INCLUDE_DIRS}")
+if(NOT WITH_FORTFEM)
+  string(APPEND MEPHIT_C_DEPENDENCY_FLAGS
+    " -I${TRIANGLE_INCLUDE_DIR} -L${TRIANGLE_LIB_DIR}")
+endif()
+set_source_files_properties(
+  src/mephit_run.c ${MEPHIT_C_SRC_FILES} ${MEPHIT_CPP_SRC_FILES}
+  PROPERTIES COMPILE_FLAGS
+    "${CMAKE_C_FLAGS} -DREAL=double ${MEPHIT_C_DEPENDENCY_FLAGS}")
 
 
 ### Define library
@@ -129,28 +148,37 @@ add_library(mephit SHARED
   ${MEPHIT_C_SRC_FILES}
   ${MEPHIT_CPP_SRC_FILES}
 )
-add_dependencies(mephit TRIANGLE)
+if(NOT WITH_FORTFEM)
+  add_dependencies(mephit TRIANGLE)
+endif()
 target_include_directories(mephit PUBLIC
   ${magfie_include_dir}
-  ${TRIANGLE_INCLUDE_DIR}
   ${FFTW_INCLUDE_DIRS}
 )
+if(NOT WITH_FORTFEM)
+  target_include_directories(mephit PUBLIC ${TRIANGLE_INCLUDE_DIR})
+endif()
 set(MEPHIT_LIBS
   GSL::gsl
   BLAS::BLAS
   LAPACK::LAPACK
   ${FFTW_LIBRARIES}
-  ${triangle_lib}
   LIBNEO::magfie
   LIBNEO::odeint
   LIBNEO::hdf5_tools
 )
+if(NOT WITH_FORTFEM)
+  list(APPEND MEPHIT_LIBS ${triangle_lib})
+endif()
 target_link_libraries(mephit ${MEPHIT_LIBS})
 if(LEGACY_SUITESPARSE)
   target_link_libraries(mephit ${SUITESPARSE_LIBRARIES})
 else()
   target_link_libraries(mephit SuiteSparse::umfpack)
 endif()
+if(WITH_FORTFEM)
+  target_link_libraries(mephit fortfem::capi)
+endif()
 if(WITH_MFEM)
   add_dependencies(mephit MFEM)
   target_include_directories(mephit PUBLIC ${MFEM_INCLUDE_DIRS})
@@ -165,11 +193,56 @@ target_link_libraries(mephit_run.x mephit)
 target_link_libraries(mephit_test.x mephit)
 target_link_libraries(mephit_post.x mephit)
 
+if(WITH_FORTFEM AND BUILD_TESTING)
+  add_executable(test_fortfem_adapter
+    test/test_fortfem_adapter.c
+    src/mephit_fortfem.c)
+  target_include_directories(test_fortfem_adapter PRIVATE src)
+  target_link_libraries(test_fortfem_adapter PRIVATE fortfem::capi m)
+  add_test(NAME fortfem_adapter COMMAND test_fortfem_adapter)
+
+  add_executable(test_fortfem_production_mesh
+    test/test_fortfem_production_mesh.c
+    src/mephit_fortfem.c)
+  target_include_directories(test_fortfem_production_mesh PRIVATE src)
+  target_link_libraries(test_fortfem_production_mesh PRIVATE fortfem::capi m)
+  add_test(
+    NAME fortfem_production_mesh
+    COMMAND test_fortfem_production_mesh)
+
+  add_executable(test_fortfem_dispatch
+    test/test_fortfem_dispatch.c)
+  target_include_directories(test_fortfem_dispatch PRIVATE src)
+  target_link_libraries(test_fortfem_dispatch PRIVATE mephit)
+  add_test(NAME fortfem_dispatch COMMAND test_fortfem_dispatch)
+
+  add_test(
+    NAME fortfem_no_daemon
+    COMMAND
+      ${CMAKE_COMMAND}
+      -DMEPHIT_RUN=$<TARGET_FILE:mephit_run.x>
+      -DTEST_TEMP=${PROJECT_BINARY_DIR}
+      -P ${CMAKE_CURRENT_SOURCE_DIR}/test/test_fortfem_no_daemon.cmake)
+
+  add_test(
+    NAME fortfem_no_triangle
+    COMMAND
+      ${CMAKE_COMMAND}
+      -DC_COMPILER=${CMAKE_C_COMPILER}
+      -DMEPHIT_INCLUDE=${CMAKE_CURRENT_SOURCE_DIR}/src
+      -DFORTFEM_INCLUDE=$<TARGET_PROPERTY:fortfem::capi,INTERFACE_INCLUDE_DIRECTORIES>
+      -DMEPHIT_FEM_SOURCE=${CMAKE_CURRENT_SOURCE_DIR}/src/mephit_fem.c
+      -DTEST_OBJECT=${PROJECT_BINARY_DIR}/test_fortfem_no_triangle.o
+      -P ${CMAKE_CURRENT_SOURCE_DIR}/test/test_fortfem_no_triangle.cmake)
+endif()
+
 ### Add helper script to binaries
 configure_file(scripts/mephit.bash ${PROJECT_BINARY_DIR}/scripts/mephit.bash @ONLY)
-configure_file(scripts/ff-mephit.bash ${PROJECT_BINARY_DIR}/scripts/ff-mephit.bash COPYONLY)
-configure_file(scripts/maxwell_daemon.edp ${PROJECT_BINARY_DIR}/scripts/maxwell_daemon.edp COPYONLY)
-configure_file(scripts/extmesh.edp ${PROJECT_BINARY_DIR}/scripts/extmesh.edp COPYONLY)
+if(NOT WITH_FORTFEM)
+  configure_file(scripts/ff-mephit.bash ${PROJECT_BINARY_DIR}/scripts/ff-mephit.bash COPYONLY)
+  configure_file(scripts/maxwell_daemon.edp ${PROJECT_BINARY_DIR}/scripts/maxwell_daemon.edp COPYONLY)
+  configure_file(scripts/extmesh.edp ${PROJECT_BINARY_DIR}/scripts/extmesh.edp COPYONLY)
+endif()
 configure_file(scripts/mephit.gdb ${PROJECT_BINARY_DIR}/scripts/mephit.gdb COPYONLY)
 configure_file(data/convexwall_asdex.dat ${PROJECT_BINARY_DIR}/data/convexwall_asdex.dat COPYONLY)
 configure_file(data/convexwall_kilca.dat ${PROJECT_BINARY_DIR}/data/convexwall_kilca.dat COPYONLY)

README.md

@@ -12,9 +12,12 @@ Prerequisites from external sources for running MEPHIT are as follows.
 - [SuiteSparse](https://github.com/DrTimothyAldenDavis/SuiteSparse)
 - [GSL](https://www.gnu.org/software/gsl/)
 - [FFTW3](http://fftw.org/)
-- [Triangle](https://www.cs.cmu.edu/~quake/triangle.html)
 - [Boost](https://www.boost.org/)
-- [FreeFem++](https://github.com/FreeFem/FreeFem-sources)
+- [FortFEM](https://github.com/lazy-fortran/fortfem) for the native
+  finite-element backend
+- [Triangle](https://www.cs.cmu.edu/~quake/triangle.html) and
+  [FreeFem++](https://github.com/FreeFem/FreeFem-sources) only for the legacy
+  finite-element backend
 - [MFEM](https://mfem.org/) is optional
 - [zlib](https://zlib.net/) for Fortio's compressed NetCDF-4/HDF5 subset;
   Fortio itself is fetched transitively through libneo
@@ -38,6 +41,21 @@ export MEPHIT_DIR="$(git rev-parse --show-toplevel)/build"
 export MEPHIT_RUN_DIR="$(git rev-parse --show-toplevel)/run"
 ```
 
+To use the native FortFEM backend, configure MEPHIT with:
+
+```bash
+cmake -S . -B build \
+    -DWITH_FORTFEM=ON
+cmake --build build
+```
+
+The build fetches FortFEM at the pinned revision in
+[`cmake/SetupFortfem.cmake`](cmake/SetupFortfem.cmake). For local development,
+pass `-DFORTFEM_PATH=/path/to/fortfem`; to use an installed package instead,
+pass `-DFORTFEM_FETCH=OFF -DCMAKE_PREFIX_PATH=/path/to/fortfem/install`.
+This configuration does not fetch or link Triangle and does not launch
+FreeFem++. Omitting `WITH_FORTFEM` retains the legacy backend.
+
 ### Coil geometry
 
 In order to use the default configuration in `mephit.in` (see below) for pre-computed Fourier modes for the vacuum field, i.e., `config%vac_src = 2`, you need to generate a coil file once to be used for `config%coil_file`. **Create a namelist file for `coil_field`, like [libneo](https://github.com/itpplasma/libneo)'s `tools/vacfield_AUG.in`**, and run `vacfield.x`. The build fetches and builds libneo from source, so `vacfield.x` is at `$MEPHIT_DIR/libneo/vacfield.x`; set `LIBNEO_DIR` to that directory. To generate the coil file for ASDEX Upgrade at ITPcp, run:
@@ -101,7 +119,8 @@ Simulations consist of three phases:
 
 Each phase can be run separately by specifying the corresponding command line switch; if none are given, all phases are run by default. For testing and debugging, there are additionally three mutually exclusive flags:
 
-- `--debug` starts a [GDB](https://www.gnu.org/software/gdb) session, using [a script](scripts/mephit.gdb) to navigate to the entry point of the main Fortran subroutine,
+- `--debug` starts a [GDB](https://www.gnu.org/software/gdb) session, using
+  [a script](scripts/mephit.gdb) that stops at the main Fortran subroutine,
 - `--memcheck` runs [Valgrind's Memcheck](https://valgrind.org/info/tools.html#memcheck),
 - `--test` runs internal tests (expensive, ignores phases).
 
@@ -111,9 +130,9 @@ The following files are generated for `mephit*.in`, with `*` a possible suffix:
 
 - `mephit*.h5` contains all relevant numerical results,
 - `mephit*.log` contains the text output also displayed on the screen,
-- `core_plasma*.msh`, `outer*.msh`, and `maxwell*.msh` contain the meshes for the core plasma, the surrounding elliptical boundary for imposition of boundary conditions, and the union of the two, for use with FreeFem++,
-- `edgemap*.dat` contains the mapping of edge degrees of freedom between MEPHIT and FreeFem++,
-- `fglut_dump*` contains graphics generated by FreeFem++ which can be viewed with the command `ffglut`.
+- legacy-backend runs also produce `core_plasma*.msh`, `outer*.msh`, and
+  `maxwell*.msh` for FreeFem++, `edgemap*.dat` for edge-degree-of-freedom
+  transfer, and `fglut_dump*` graphics viewable with `ffglut`.
 
 ### Plotting results
 

cmake/SetupCODE.cmake

@@ -5,6 +5,6 @@
 #   -DLIBNEO_PATH=<dir>  local libneo source directory (empty = fetch from git)
 #   -DTRIANGLE_DIR=<dir>  prebuilt Triangle directory (see SetupTriangle)
 #   -DMFEM_DIR=<dir>      prebuilt MFEM directory (see SetupMFEM)
-set(LIBNEO_REF "f3f241dea2c7dc25cf29731bb0a1328ff98f48c8" CACHE STRING
+set(LIBNEO_REF "f05e4f20ce32dbb0b9e4b5e3c433fe6a2b8ce770" CACHE STRING
     "libneo branch, tag, or SHA to fetch")
 set(LIBNEO_PATH "" CACHE PATH "local libneo source directory (empty = fetch from git)")

cmake/SetupFortfem.cmake

@@ -0,0 +1,44 @@
+# Configure the native FortFEM backend from a reproducible source revision.
+# A local source tree is useful for development; disabling the fetch keeps the
+# installed-package workflow available for downstream builds.
+include(FetchContent)
+
+set(FORTFEM_REF "605dc7f056aa9b15cf8e0673eaa13b13ce12a273" CACHE STRING
+    "fortfem commit to fetch")
+set(FORTFEM_PATH "" CACHE PATH
+    "local fortfem source directory (empty = fetch or find package)")
+option(FORTFEM_FETCH "Fetch the pinned FortFEM source when no local path is set" ON)
+
+if(FORTFEM_PATH)
+    add_subdirectory(${FORTFEM_PATH} ${CMAKE_CURRENT_BINARY_DIR}/fortfem EXCLUDE_FROM_ALL)
+elseif(FORTFEM_FETCH)
+    if(CMAKE_VERSION VERSION_LESS 3.22)
+        message(FATAL_ERROR
+            "WITH_FORTFEM=ON with source fetching requires CMake 3.22 or newer")
+    endif()
+    FetchContent_Declare(fortfem
+        GIT_REPOSITORY https://github.com/lazy-fortran/fortfem.git
+        GIT_TAG ${FORTFEM_REF}
+        GIT_SHALLOW FALSE)
+    FetchContent_MakeAvailable(fortfem)
+else()
+    find_package(fortfem CONFIG REQUIRED)
+endif()
+
+if(NOT TARGET fortfem::capi)
+    message(FATAL_ERROR "FortFEM was configured without the fortfem::capi target")
+endif()
+
+# MEPHIT uses -fno-realloc-lhs for its legacy Fortran sources.  FortFEM and
+# its in-tree FortSparse dependency use standard allocatable assignment, so
+# restore the standard GNU behavior for those targets only.
+if(CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
+    if(TARGET fortfem_capi)
+        target_compile_options(fortfem_capi PRIVATE
+            "$<$<COMPILE_LANGUAGE:Fortran>:-frealloc-lhs>")
+    endif()
+    if(TARGET fortsparse)
+        target_compile_options(fortsparse PRIVATE
+            "$<$<COMPILE_LANGUAGE:Fortran>:-frealloc-lhs>")
+    endif()
+endif()

scripts/mephit.bash

@@ -225,7 +225,7 @@ mephit_run() {
                              "$config" \
                              "$suffix" \
                              "$tmpdir" \
-                             "$scriptdir/ff-mephit.bash" \
+                             "${fem_backend_args[@]}" \
                              2>&1 | tee -a "$log"
                     lasterr=$?
                     ;;
@@ -236,7 +236,7 @@ mephit_run() {
                         "$config" \
                         "$suffix" \
                         "$tmpdir" \
-                        "$scriptdir/ff-mephit.bash"
+                        "${fem_backend_args[@]}"
                     lasterr=$?
                     ;;
                 *)
@@ -245,7 +245,7 @@ mephit_run() {
                         "$config" \
                         "$suffix" \
                         "$tmpdir" \
-                        "$scriptdir/ff-mephit.bash" \
+                        "${fem_backend_args[@]}" \
                         2>&1 | tee -a "$log"
                     lasterr=$?
                     ;;
@@ -269,6 +269,10 @@ scriptdir=$(dirname "$0")
 scriptdir=$(realpath "$scriptdir")
 bindir=$(realpath -m "$scriptdir/../bin")
 datadir=$(realpath -m "$scriptdir/../data")
+fem_backend_args=()
+if [ "@WITH_FORTFEM@" != "ON" ]; then
+    fem_backend_args=( "$scriptdir/ff-mephit.bash" )
+fi
 if [ -d "@tmpdir@" ]; then
     tmpdir=@tmpdir@
 else