Merge branch 'master' into milkyway

Author: JulienDoerner

.github/workflows/testing_OSX.yml

@@ -13,14 +13,18 @@ jobs:
             cc: "clang"
             fc: "gfortran-14"
             swig_builtin: "On" #uses swig 4.0.2
-            py: "/usr/bin/python3"
+            py: "/usr/bin/python3" # python 3.14
     steps:
      - name: Checkout repository 
        uses: actions/checkout@v4 
      - name: Preinstall 
        run: | 
-         brew install hdf5 fftw cfitsio muparser libomp swig
-         pip install numpy==1.26
+         brew install hdf5 fftw cfitsio muparser libomp swig 
+         python3 -m venv venv
+         source venv/bin/activate
+         python -m pip install --upgrade pip
+         pip install numpy cmake
+         pip show numpy # cross-check numpy version for Python_NumPy_INCLUDE_DIR
      - name: Set up the build
        env:
          CXX: ${{ matrix.config.cxx }}
@@ -30,7 +34,17 @@ jobs:
        run: |
         mkdir build
         cd build
-        cmake .. -DENABLE_PYTHON=True  -DENABLE_TESTING=On  -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS="none"
+      
+        cmake .. \
+          -DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/venv \
+          -DENABLE_PYTHON=True \
+          -DPython_EXECUTABLE=$GITHUB_WORKSPACE/venv/bin/python \
+          -DCMAKE_CXX_STANDARD=17 \
+          -DCMAKE_CXX_FLAGS="-std=c++17 -stdlib=libc++" \
+          -DENABLE_TESTING=On \
+          -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} \
+          -DPython_INSTALL_PACKAGE_DIR=$GITHUB_WORKSPACE/venv/lib/python3.14/site-packages
+
      - name: Build CRPropa
        run: |
          cd build

.github/workflows/testing_ubuntu20.yml

@@ -21,7 +21,10 @@ jobs:
       - name: Preinstall
         run: |
           sudo apt-get update
-          sudo apt-get install libmuparser-dev python3 python3-numpy python3-setuptools libhdf5-serial-dev libomp5 libomp-dev libfftw3-dev libcfitsio-dev lcov
+          sudo apt-get install libmuparser-dev python3 python3-setuptools libhdf5-serial-dev libomp5 libomp-dev libfftw3-dev libcfitsio-dev lcov
+          pip install --upgrade pip
+          pip install numpy 
+          pip show numpy
       - name: Set up the build
         env:
           CXX: ${{ matrix.config.cxx }}

.github/workflows/testing_ubuntu22.yml

@@ -0,0 +1,93 @@
+name: crpropa-testing_ubuntu24
+on: [push, pull_request]
+
+jobs:
+  x64:
+    runs-on: ${{ matrix.config.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - name: "ubuntu-24"
+            os: ubuntu-24.04
+            cxx: "g++-14"
+            cc: "gcc-14"
+            fc: "gfortran-14"
+            swig_builtin: "On" 
+            py: "/usr/bin/python3" 
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Preinstall
+        run: |
+          sudo apt-get update
+          sudo apt-get install libmuparser-dev python-dev-is-python3 libhdf5-serial-dev libomp5 libomp-dev libfftw3-dev libcfitsio-dev lcov
+          pip install numpy
+      - name: Set up the build
+        env:
+          CXX: ${{ matrix.config.cxx }}
+          CC: ${{ matrix.config.cc }}
+          FC: ${{ matrix.config.fc }}
+        run: |
+          mkdir build
+          cd build
+          cmake .. -DENABLE_PYTHON=True -DENABLE_TESTING=On  -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS="none" 
+      - name: Build CRPropa
+        run: |
+          cd build
+          make
+      - name: Run tests
+        run: |
+          cd build
+          make test
+      - name: Archive test results
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: "test-report_${{matrix.config.os}}"
+          path: build/Testing/Temporary/LastTest.log
+  arm:
+    runs-on: ${{ matrix.config.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - name: "ubuntu-24"
+            os: ubuntu-24.04-arm
+            cxx: "g++-14"
+            cc: "gcc-14"
+            fc: "gfortran-14"
+            swig_builtin: "On" 
+            py: "/usr/bin/python3" 
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Preinstall
+        run: |
+          sudo apt-get update
+          sudo apt-get install libmuparser-dev python-dev-is-python3 libhdf5-serial-dev libomp5 libomp-dev libfftw3-dev libcfitsio-dev lcov
+          pip install numpy
+          pip show numpy
+      - name: Set up the build
+        env:
+          CXX: ${{ matrix.config.cxx }}
+          CC: ${{ matrix.config.cc }}
+          FC: ${{ matrix.config.fc }}
+        run: |
+          mkdir build
+          cd build
+          cmake .. -DENABLE_PYTHON=True -DENABLE_TESTING=On  -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS="none" 
+      - name: Build CRPropa
+        run: |
+          cd build
+          make
+      - name: Run tests
+        run: |
+          cd build
+          make test 
+      - name: Archive test results
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: "test-report_${{matrix.config.os}}"
+          path: build/Testing/Temporary/LastTest.log

.github/workflows/testing_ubuntu24.yml

@@ -1,14 +1,20 @@
 ## CRPropa vNext
 
 ### Bug fixes:
- * Fixed sign for exponential decay of magn. field strength with Galactic height in LogarithmicSpiralField
- * Fixed r term in source distribution for SNR and Pulsar
- * Fixed wrong mass inheritance for secondaries other than nuclei or electron/positron
+* Fixed sign for exponential decay of magn. field strength with Galactic height in LogarithmicSpiralField
+* Fixed r term in source distribution for SNR and Pulsar
+* Fixed wrong mass inheritance for secondaries other than nuclei or electron/positron
+* Fixed wrong generation of interval ranges in ObserverTimeEvolution
 
 ### New features:
+
  * Added new backwards-compatible function particleMass that returns particle mass also for non-nuclei
  * Added the new Galactic magnetic field models from Unger&Farrar arXiv:2311.12120
  * Added EBL model from Finke et al. 2022
+ * Added ReflectiveShell boundary condition
+ * Added overridable getTime function to ObserverTimeEvolution which is called instead of detList. 
+  Old functionalities are preserved by adding old functions and setter/getter functions.
+
 
 ### Interface changes:
 

CHANGELOG.md

@@ -70,7 +70,7 @@ if(ENABLE_GIT)
   get_git_head_revision(GIT_REFSPEC GIT_SHA1)
   git_describe(GIT_DESC --tags)
 endif(ENABLE_GIT)
-IF(NOT ENABLE_GIT OR (${GIT_SHA1} STREQUAL "GITDIR-NOTFOUND"))
+IF(NOT ENABLE_GIT OR ("${GIT_SHA1}" STREQUAL "GITDIR-NOTFOUND"))
   set(GIT_REFSPEC "")
   set(GIT_SHA1 "")
   set(GIT_DESC "${CRPROPA_RELEASE_VERSION}-no-git")
@@ -157,7 +157,7 @@ list(APPEND CRPROPA_EXTRA_LIBRARIES sophia gfortran)
 list(APPEND CRPROPA_EXTRA_INCLUDES libs/sophia)
 
 # Galactic magnetic lenses
-option(ENABLE_GALACTICMAGNETICLENS "Galactic Magnetic Lens" ON)
+option(ENABLE_GALACTICMAGNETICLENS "Galactic Magnetic Lens" OFF)
 option(INSTALL_EIGEN "Install provided EIGEN headers" OFF)
 SET(EIGEN_PATH  "" CACHE STRING "Use EIGEN from this path instead of the version shipped with CRPropa")
 SET(WITH_GALACTIC_LENSES FALSE)
@@ -407,8 +407,10 @@ add_library(crpropa SHARED
   src/magneticField/turbulentField/SimpleGridTurbulence.cpp
   src/magneticField/TF17Field.cpp
   src/magneticField/UF23Field.cpp
+  src/magneticField/KST24Field.cpp
   src/magneticField/CMZField.cpp
   src/advectionField/AdvectionField.cpp
+  src/advectionField/TimeDependentAdvectionField.cpp
   src/massDistribution/ConstantDensity.cpp
   src/massDistribution/Cordes.cpp
   src/massDistribution/Ferriere.cpp
@@ -456,6 +458,8 @@ find_package(Python 3.0 REQUIRED COMPONENTS Interpreter Development NumPy)
 if(ENABLE_PYTHON AND Python_FOUND)
   find_package(SWIG 3.0 REQUIRED)
   include_directories(${Python_INCLUDE_DIRS})
+  add_definitions(-DCRPROPA_HAVE_PYTHON)
+  list(APPEND CRPROPA_SWIG_DEFINES -DCRPROPA_HAVE_PYTHON)
 
   # print Python info in detail
   message(STATUS "Python: Found!")
@@ -470,23 +474,29 @@ if(ENABLE_PYTHON AND Python_FOUND)
     message(STATUS "  development libraries: NOT found!")
   endif(Python_Development_FOUND)
 
-
+  
   #  use Python_INSTALL_PACKAGE_DIR if provided; otherwise, install in Python_SITELIB
   set(Python_INSTALL_PACKAGE_DIR "${Python_SITELIB}" CACHE PATH "folder in which the python package is installed")
   message(STATUS "  package install directory: ${Python_INSTALL_PACKAGE_DIR}")
-
-
+  
   # look for NumPy
   if(Python_NumPy_FOUND)
-    set(CMAKE_SWIG_FLAGS -DWITHNUMPY ${CRP})
-    list(APPEND CRPROPA_SWIG_DEFINES -DWITHNUMPY)
-    include_directories(${Python_NumPy_INCLUDE_DIRS})
-    message(STATUS "NumPy: Found!")
-    message(STATUS "  headers: ${Python_NumPy_INCLUDE_DIRS} (version ${Python_NumPy_VERSION})")
+  set(CMAKE_SWIG_FLAGS -DWITHNUMPY ${CRP})
+  list(APPEND CRPROPA_SWIG_DEFINES -DWITHNUMPY)
+  include_directories(${Python_NumPy_INCLUDE_DIRS})
+  message(STATUS "NumPy: Found!")
+  message(STATUS "  headers: ${Python_NumPy_INCLUDE_DIRS} (version ${Python_NumPy_VERSION})")
   elseif(Python_NumPy_FOUND)
-    message(STATUS "NumPy: NOT found!")
-    message(STATUS "  CRPropa might work just fine with Python, but features like Galactic lenses will not be available.")
+  message(STATUS "NumPy: NOT found!")
+  message(STATUS "  CRPropa might work just fine with Python, but features like Galactic lenses will not be available.")
   endif(Python_NumPy_FOUND)
+  
+  # deactivate lenses if NumPy version is >= 2.0
+  if(Python_NumPy_VERSION VERSION_GREATER_EQUAL 2.0 AND WITH_GALACTIC_LENSES)
+    set(WITH_GALACTIC_LENSES FALSE CACHE BOOL "" FORCE)
+    set(ENABLE_GALACTICMAGNETICLENS OFF CACHE BOOL "" FORCE)
+    message(WARNING "NumPy version >= 2.0 detected, disabling Galactic lenses support")
+  endif()
 
   if(SWIG_VERSION VERSION_GREATER 4.0)
     # Use swig 4 builtin doxygen instead of external program

CMakeLists.txt

@@ -41,7 +41,7 @@ General interactions/processes
 Conditional modules implement certain conditions for stopping propagation.
 They provide interfaces to act onReject or onAccept of a cosmic ray.
 Boundary modules can be used to limit the simulation volume.
-Periodic- and ReflectiveBox implement boundary conditions for the particles. They are useful for a 3D setup where an initial volume is to be repeated (periodically or reflectively). When using them, a couple of things need to be considered. Observers will shadow the volume behind if they are set to inactivate particles. Also Observers should be placed at a distance to the boundaries that is larger than the maximum step size of the propagator, since step size limitation does not work beyond periodic/reflective boundaries.
+Periodic-/ReflectiveBox and ReflectiveShell implement boundary conditions for the particles. They are useful for a 3D setup where an initial volume is to be repeated (periodically or reflectively). When using them, a couple of things need to be considered. Observers will shadow the volume behind if they are set to inactivate particles. Also Observers should be placed at a distance to the boundaries that is larger than the maximum step size of the propagator, since step size limitation does not work beyond periodic/reflective boundaries.
 
 * **MaximumTrajectoryLength** - Stop after reaching maximum trajectory length
 * **MinimumEnergy** - Stop after reaching a minimum energy
@@ -53,6 +53,7 @@ Periodic- and ReflectiveBox implement boundary conditions for the particles. The
 * **CylindricalBoundary** - Cylindric simulation volume
 * **PeriodicBox** - Periodic boundary conditions for the particle: If a particle leaves the box it will enter from the opposite side and the initial position will be changed as if it had come from that side.
 * **ReflectiveBox** - Reflective boundary conditions for the particle: If a particle leaves the box it will be reflected (mirrored) and the initial position will be changed as if it had come from that side.
+* **ReflectiveShell** - Reflective spherical boundary condition for the particle; If a particle crosses the shell during the current step it will be reflected back at the boundary according to the law of reflection. Particles coming from the outside are only reflected if the current step ends inside the shell.
 * **DetectionLength** - Detects the candidate at a given trajectory length.
 
 ### Observers

doc/pages/Simulation-Modules.md

@@ -30,7 +30,12 @@ The exact nature of the dependency is subject of ongoing research. Here,
 so far only quasi-linear theory, a simplistic approach to diffusion of charged
 particles in magnetic fields is implemented in the corresponding modifier :cpp:class:`crpropa::QuasiLinearTheory`.
 
+In the diffusive picture, the diffusive picture as an interplay between diffusion, 
+advection and adiabatic cooling. Simple shock configurations are shown in the following 
+example notebook using the DiffusionSDE module:
 
+.. toctree::
+   example_notebooks/acceleration/diffusive_shock_acceleration.ipynb