Update public_mirror

A very naive approach following what git says:
> To add an exception for this directory, call:
	git config --global --add safe.directory /builds/gysela-developpers/gyselalibxx/.git

See merge request gysela-developpers/gyselalibxx!504

--------------------------------------------

bin/public_mirror

@@ -14,6 +14,7 @@ cp "${GITHUB_MIRROR_PRIVKEY}" "${SSH_DIR}/id_rsa"
 chmod -R go-rwx "${SSH_DIR}"
 
 git config --global --add safe.directory "${SRC_DIR}"
+git config --global --add safe.directory "${SRC_DIR}/.git"
 
 cd "$(mktemp --tmpdir -d)"
 WK_DIR="$PWD"

ci_tools/check_readme_presence.py

@@ -15,10 +15,12 @@
 
 missing_readme = False
 
-for diff_file in diff:
-    if 'src' not in diff_file.parts:
+modified_folders = set(diff_file.parents[0] for diff_file in diff)
+
+for folder in modified_folders:
+    if 'src' not in folder.parts:
         continue
-    expected_readme = diff_file.parents[0].joinpath('README.md')
+    expected_readme = folder.joinpath('README.md')
     if not os.path.exists(expected_readme):
         missing_readme = True
         print("Cannot find README.md file : ", expected_readme)

simulations/geometryXVx/CMakeLists.txt

@@ -2,4 +2,5 @@
 
 add_subdirectory(landau)
 add_subdirectory(bump_on_tail)
+add_subdirectory(neutrals)
 add_subdirectory(sheath)

simulations/geometryXVx/neutrals/CMakeLists.txt

@@ -0,0 +1,30 @@
+# SPDX-License-Identifier: MIT
+
+foreach(GEOMETRY_VARIANT IN LISTS GEOMETRY_XVx_VARIANTS_LIST)
+
+add_executable(neutrals_${GEOMETRY_VARIANT} neutrals.cpp)
+target_compile_features(neutrals_${GEOMETRY_VARIANT} PUBLIC cxx_std_17)
+target_link_libraries(neutrals_${GEOMETRY_VARIANT}
+    PUBLIC
+        DDC::DDC
+        DDC::PDI_Wrapper
+        gslx::advection
+        gslx::boltzmann_${GEOMETRY_VARIANT}
+        gslx::fluidinitialization_${GEOMETRY_VARIANT}
+        gslx::fluidsolver_${GEOMETRY_VARIANT}
+        gslx::moments
+        gslx::initialization_${GEOMETRY_VARIANT}
+        gslx::interpolation
+        gslx::paraconfpp
+        gslx::poisson_${GEOMETRY_VARIANT}
+        gslx::reactionrates_${GEOMETRY_VARIANT}
+        gslx::rhs_${GEOMETRY_VARIANT}
+        gslx::speciesinfo
+        gslx::time_integration_hybrid_${GEOMETRY_VARIANT}
+        paraconf::paraconf
+        PDI::pdi
+)
+
+install(TARGETS neutrals_${GEOMETRY_VARIANT})
+
+endforeach()

simulations/geometryXVx/neutrals/README.md

@@ -0,0 +1,9 @@
+# Neutral simulations
+
+## Description 
+The `neutral` executable allows the study of plasma-neutral interactions on a single magnetic field line. The magnetic field line is connected at both of its ends to a solid wall. A Boltzmann-Poisson system is solved for the electric field and the distribution function for both electrons and ions species. The model is one dimensional in space and velocity (1D1V).   
+
+The wall region is treated using immersed boundary condition (or penalization). Electrons and ions are absorbed inside this region. The inertia difference between the two species drives the appearance of a positively charged layer (the sheath) at the plasma boundary. The neutrals are treated using a simple fluid model (advective, pressure-diffusion, etc.)
+
+## Usage
+After building the code, run the executable located in `build/simulations/neutral/`. To use the default simulation parameters the user can provide the `--dump-config` option when launching the executable.