As the first step of easing and generalizing access to Gemini3D from other libraries and programs, make a C CLI to complement the Fortran CLI. It's possible that the Fortran CLI will go away to be replaced by C CLI. From user's perspective little would change.

More FindHDF5 fixes based on user experiences

More MSIS 2.0 fixes--require /msis_version in HDF5 input instead of CLI argument for MSIS version. The CLI seemed to give intermittent all-zero output from MSIS 2.0. Added more MSIS 2.0 unit tests

Add requirements.json that's human readable. Using cmake -P scripts/requirements.cmake will print how to install the requirements on the user's particular computer.

MSIS 2.0 has a known bug causing all-zero output acknowledged by the authors along with our patch applied in Gemini3D.

HDF5 is more easily found on MacOS, particularly with MacPorts and Homebrew, despite the presence of Anaconda Python.

Grid and Neutral enhancements by @mattzett

Minor Rearchitect gemini.bin to make amenable for libgemini future work

fix segfault on large e.g. 600x600x600 simulations by fixing MatGemini to write proper scalar datasets, and h5fortran to verify scalar is read into scalar as array into scalar segfaults.

Also switched allocatable actual args to have intent(inout) dummy args, as forced reallocation results otherwise, which is unintended but Fortran standard 2003 behavior.

• Added our own FindMPI as the vendor FindMPI is frequently a source of trouble as like vendor FindHDF5, it covers a large range of rare/old systems, and fails to work on our more up to date systems
• ci: added JUnit dash demo
• Find*.cmake: works better with CentOS packages
• numerous magcalc improvements, and add magcalc.run frontend
• remove Apple Silicon M1 workaround in anticipation of HWLOC 2.6, which we contributed to handling this and future Apple Silicon properly.

As before, Gemini3D works with GCC 8, 9, 10, 11. Gemini3D also now works with GCC 7.5.0.
GCC older than 7.5.0 is unlikely to work. For example GCC 7.4.0 is known to be broken.

Updated h5fortran,nc4fortran interfaces to auto-close files on leaving scope--still recommended to use %close() to be clear.

Fixed/updates Matlab self-tests, although Python is recommended as more complete as faster as before.

abstract interface based grid, allowing more general grid types.
MPI has been deembedded from the grid, allowing external program to interface with the grid more easily.

Numerous bug fixes and optimizations.

improve quality of .run frontends with functionalization and reuse

• gemini3d.run
• magcalc.run

• patched Zlib 2.0.3 (will be included in next Zlib-ng release) to work with GCC mpicc
• make h5fortran internals TKR interface procedure instead of select type for robustness and runtime improvements

• Option to disable TLS verification (discourage unless your computer has broken certificates, just for debugging) -DCMAKE_TLS_VERIFY=off. Default is TLS verify on
• Option to fall back to unmaintained Zlib 1.x. Zlib 2.x works on most systems and is significantly faster for compressed HDF5 operations. -Dzlib_legacy=on. Default is to use Zlib 2.x
• check that TLS working from CMake before downloading to avoid confusing errors when user's CMake doesn't have SSL or TLS certificates are broken.

gemini3d.run: correct behavior on Windows. Also in general allow running from same directory or other directory.

HDF5 is crucial to Gemini3D functionality. We overhauled how HDF5 is found and linked via h5fortran. To help make Gemini3D more robust build overall, we now require CMake >= 3.19 to build Gemini3D.

To run the full Gemini3D self-tests required CMake >= 3.20 as before. Intel compilers also require CMake >= 3.20 in general.

A recent CMake release (usually the latest) is available almost instantly by:

cmake -P gemini3d/scripts/install_cmake.cmake