Merge branch 'CRPropa:master' into cringe_reproduction

CHANGELOG.md

@@ -1,25 +1,51 @@
-# CRPropa vNext
+## CRPropa vNext
+
+### Bug fixes:
+
+### New features:
+
+### Interface changes:
+
+### Features that are deprecated and will be removed after this release
+
+### Removed features 
+
+### New plugins and resources linked on the webpages
+
+
+## CRPropa 3.2.1
 
 ### Bug fixes:
 * Re-added ToroidalHaloField and LogarithmicSpiralField models. Note, that the class name was also corrected in spelling: TorroidalHaloField --> ToroidalHaloField
 * Synchronized signature of ParticleSplitting constructor
 
 ### New features:
-* new candidate property tagOrigin to trace back which source or which interaction created the candidate
-* new interace for massdistributions given on a Grid1f
-* grids can be restricted to the volume without repetition
-* sourceFeature to sample the source position from a given massdistribution
+* New candidate property tagOrigin to trace back which source or which interaction created the candidate
+* New interface for massdistributions given on a Grid1f
+* Grids can be restricted to the volume without repetition (clipVolume parameter)
+* SourceFeature to sample the source position from a given massdistribution
+* EBL model from Saldana-Lopez et al. 2021
+* New module CandidateSplitting for better statistics at high energies for e.g. diffusive shock acceleration
+* New advection fields for modeling diffusive shock acceleration at 1D planar, oblique and spherical shocks
 
 ### Interface changes:
 * Weight column in hdf-Output is now called "W", which is the same as for TextOutput.
 
 ### Features that are deprecated and will be removed after this release
 * ObserverPoint will be renamed into Observer1D.
-* AMRMagenticField - underlying library (saga) is no longer supported.
-
-### New plugins and resources linked on the webpages:
+* AMRMagneticField - underlying library (saga) is no longer supported.
 
+### Removed features 
+* External extensions DINT and Eleca, which can be replaced with the 
+  EM*-modules combined with the thinning option for reasonable computation
+  times.
 
+### New plugins and resources linked on the webpages:
+* FieldlineIntegrator
+* grplinst
+* monopole
+* ROOTOutputPlugin
+
 
 ## CRPropa 3.2
 

CITATION.bib

@@ -0,0 +1,12 @@
+@ARTICLE{crpropa3.2,
+  author = {{Alves Batista}, Rafael and {Becker Tjus}, Julia and {D{\"o}rner}, Julien and {Dundovic}, Andrej and {Eichmann}, Bj{\"o}rn and {Frie}, Antonius and {Heiter}, Christopher and {Hoerbe}, Mario R. and {Kampert}, Karl-Heinz and {Merten}, Lukas and {M{\"u}ller}, Gero and {Reichherzer}, Patrick and {Saveliev}, Andrey and {Schlegel}, Leander and {Sigl}, G{\"u}nter and {van Vliet}, Arjen and {Winchen}, Tobias},
+  title = "{CRPropa 3.2 - an advanced framework for high-energy particle propagation in extragalactic and galactic spaces}",
+  journal = {Journal of Cosmology and Astroparticle Physics},
+  year = 2022,
+  volume = {9},
+  eid = {035},
+  pages = {035},
+  doi = {10.1088/1475-7516/2022/09/035},
+  eprint = {2208.00107}
+}
+

CMakeLists.txt

@@ -8,7 +8,7 @@ else(APPLE)
 endif(APPLE)
 
 project(CRPropa Fortran C CXX)
-set(CRPROPA_RELEASE_VERSION 3.2+)  # Update for new release
+set(CRPROPA_RELEASE_VERSION 3.2.1+)  # Update for new release
 
 set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})
 
@@ -164,16 +164,6 @@ add_subdirectory(libs/sophia)
 list(APPEND CRPROPA_EXTRA_LIBRARIES sophia gfortran)
 list(APPEND CRPROPA_EXTRA_INCLUDES libs/sophia)
 
-# DINT (provided)
-add_subdirectory(libs/dint)
-list(APPEND CRPROPA_EXTRA_LIBRARIES dint)
-list(APPEND CRPROPA_EXTRA_INCLUDES libs/dint/include)
-
-# EleCa (provided)
-add_subdirectory(libs/EleCa)
-list(APPEND CRPROPA_EXTRA_LIBRARIES eleca)
-list(APPEND CRPROPA_EXTRA_INCLUDES libs/EleCa/include)
-
 # GlacticMagneticLenses
 option(ENABLE_GALACTICMAGETICLENS "Galactic Magnetic Lens" ON)
 option(INSTALL_EIGEN "Install provided EIGEN headers" OFF)
@@ -242,7 +232,7 @@ if(FFTW3F_FOUND)
 endif(FFTW3F_FOUND)
 
 # Quimby (optional for SPH magnetic fields)
-option(ENABLE_QUIMBY "Quimby Support" ON)
+option(ENABLE_QUIMBY "Quimby Support" OFF)
 if(ENABLE_QUIMBY)
   find_package(Quimby)
   if(QUIMBY_FOUND)
@@ -336,16 +326,18 @@ endif(APPLE)
 # Download data files (interaction data, masses, decay data ...)
 # ----------------------------------------------------------------------------
 OPTION(DOWNLOAD_DATA "Download CRPropa data files" ON)
-set(CRPROPA_DATAFILE_VER "2022-07-06")
+set(CRPROPA_DATAFILE_VER "2023-10-20")
 if(DOWNLOAD_DATA)
-  message("-- Downloading data file from crpropa.desy.de ~ 65 MB")
+  message("-- Downloading data files from sciebo ~ 73 MB")
   file(DOWNLOAD
-    https://www.desy.de/~crpropa/data/interaction_data/data-${CRPROPA_DATAFILE_VER}.tar.gz-CHECKSUM
-    ${CMAKE_BINARY_DIR}/data-${CRPROPA_DATAFILE_VER}.tar.gz-CHECKSUM)
+  https://ruhr-uni-bochum.sciebo.de/public.php/webdav/data-${CRPROPA_DATAFILE_VER}.tar.gz-CHECKSUM
+    ${CMAKE_BINARY_DIR}/data-${CRPROPA_DATAFILE_VER}.tar.gz-CHECKSUM 
+    USERPWD "3juW9sntQX2IWBS")
   file(STRINGS ${CMAKE_BINARY_DIR}/data-${CRPROPA_DATAFILE_VER}.tar.gz-CHECKSUM DATA_CHECKSUM LIMIT_COUNT 1 LENGTH_MINIMUM 32 LENGTH_MAXIMUM 32)
   file(DOWNLOAD
-    https://www.desy.de/~crpropa/data/interaction_data/data-${CRPROPA_DATAFILE_VER}.tar.gz
+  https://ruhr-uni-bochum.sciebo.de/public.php/webdav/data-${CRPROPA_DATAFILE_VER}.tar.gz
     ${CMAKE_BINARY_DIR}/data-${CRPROPA_DATAFILE_VER}.tar.gz
+    USERPWD "3juW9sntQX2IWBS"
     EXPECTED_MD5 "${DATA_CHECKSUM}")
   message("-- Extracting data file")
 else()
@@ -381,7 +373,6 @@ add_library(crpropa SHARED
   src/ParticleMass.cpp
   src/ParticleState.cpp
   src/PhotonBackground.cpp
-  src/PhotonPropagation.cpp
   src/ProgressBar.cpp
   src/Random.cpp
   src/Source.cpp
@@ -391,23 +382,23 @@ add_library(crpropa SHARED
   src/module/Acceleration.cpp
   src/module/Boundary.cpp
   src/module/BreakCondition.cpp
+  src/module/CandidateSplitting.cpp
   src/module/DiffusionSDE.cpp
-  src/module/EMCascade.cpp
   src/module/EMDoublePairProduction.cpp
   src/module/EMInverseComptonScattering.cpp
   src/module/EMPairProduction.cpp
   src/module/EMTripletPairProduction.cpp
   src/module/ElasticScattering.cpp
   src/module/ElectronPairProduction.cpp
   src/module/HDF5Output.cpp
+  src/module/MomentumDiffusion.cpp
   src/module/NuclearDecay.cpp
   src/module/Observer.cpp
   src/module/Output.cpp
   src/module/OutputShell.cpp
   src/module/ParticleCollector.cpp
   src/module/PhotoDisintegration.cpp
   src/module/PhotoPionProduction.cpp
-  src/module/PhotonEleCa.cpp
   src/module/PhotonOutput1D.cpp
   src/module/PropagationBP.cpp
   src/module/PropagationCK.cpp
@@ -625,10 +616,6 @@ if(ENABLE_TESTING)
   target_link_libraries(testDensity crpropa gtest gtest_main pthread ${COVERAGE_LIBS})
   add_test(testDensity testDensity)
 
-  add_executable(testDINT test/testDINT.cpp)
-  target_link_libraries(testDINT crpropa gtest gtest_main pthread ${COVERAGE_LIBS})
-  add_test(testDINT testDINT)
-
   add_executable(testPropagation test/testPropagation.cpp)
   target_link_libraries(testPropagation crpropa gtest gtest_main pthread ${COVERAGE_LIBS})
   add_test(testPropagation testPropagation)
@@ -657,6 +644,9 @@ if(ENABLE_TESTING)
   target_link_libraries(testAdiabaticCooling crpropa gtest gtest_main pthread ${COVERAGE_LIBS})
   add_test(testAdiabaticCooling testAdiabaticCooling)
 
+  add_executable(testCandidateSplitting test/testCandidateSplitting.cpp)
+  target_link_libraries(testCandidateSplitting crpropa gtest gtest_main pthread ${COVERAGE_LIBS})
+  add_test(testCandidateSplitting testCandidateSplitting)
 
   if(WITH_GALACTIC_LENSES)
     add_executable(testGalacticMagneticLens test/testMagneticLens.cpp)
@@ -677,6 +667,9 @@ if(ENABLE_TESTING)
     CONFIGURE_FILE(test/testDiffusionSDE.py testDiffusionSDE.py COPYONLY)
     add_test(testDiffusionSDE ${PYTHON_EXECUTABLE} testDiffusionSDE.py)
 
+    CONFIGURE_FILE(test/testMomentumDiffusion.py testMomentumDiffusion.py COPYONLY)
+    add_test(testMomentumDiffusion ${PYTHON_EXECUTABLE} testMomentumDiffusion.py)
+
     CONFIGURE_FILE(test/testPythonExtension.py testPythonExtension.py COPYONLY)
     add_test(testPythonExtension ${PYTHON_EXECUTABLE} testPythonExtension.py)
   endif(ENABLE_PYTHON AND PYTHONLIBS_FOUND)

README.md

@@ -1,10 +1,15 @@
-CRPropa3
+CRPropa
 ========
 
+![stable release](https://img.shields.io/badge/stable\_release-3.2.0-darkblue)
 [![Build status](https://github.com/crpropa/crpropa3/actions/workflows/testing.yml/badge.svg)](https://github.com/crpropa/crpropa3/actions/)
 [![Average time to resolve an issue](https://isitmaintained.com/badge/resolution/CRPropa/CRPropa3.svg)](https://isitmaintained.com/project/CRPropa/CRPropa3)
 [![Percentage of issues still open](https://isitmaintained.com/badge/open/CRPropa/CRPropa3.svg)](https://isitmaintained.com/project/CRPropa/CRPropa3)
 
+[![DOI:10.1088/1475-7516/2022/09/035](http://img.shields.io/badge/DOI-10.1088/1475-7516/2022/09/035.svg)](<https://doi.org/10.1088/1475-7516/2022/09/035>)
+[![arXiv](https://img.shields.io/badge/arXiv-2208.00107-b31b1b.svg)](https://arxiv.org/abs/2208.00107)
+[![ascl:2208.016](https://img.shields.io/badge/ascl-2208.016-blue.svg?colorB=262255)](https://ascl.net/2208.016)
+
 CRPropa is a publicly available simulation framework to study the propagation
 of ultra-high-energy nuclei up to iron on their voyage through an
 (extra)galactic environment. It takes into account: pion production,
@@ -61,3 +66,15 @@ as well as [additional publications](https://crpropa.github.io/CRPropa3/pages/ho
 An extensive list of publications using CRPropa can be found via
 [inSPIRE](https://inspirehep.net/search?ln=en&ln=en&p=refersto%3Arecid%3A1322902+or+refersto%3Arecid%3A1432676+or+refersto%3Arecid%3A1242078&of=hb&action_search=Search&sf=earliestdate&so=d&rm=&rg=25&sc=0).
 
+
+## Plugins
+Plugins are extensions of the core CRPropa framework, but they are not maintained by the CRPropa developer team. Instructions to install plugins can be found in the [documentation](https://crpropa.github.io/CRPropa3/pages/example_notebooks/extending-CRPropa/extending-CRPropa.html#Plugins:-Integrate-Custom-C++-Code-to-CRPropa%E2%80%99s-Python-Steering).
+
+Make sure to correctly cite the plugins when using them.
+
+| Name | Purpose | Link |
+| ---- | ------- | ---- |
+| FieldlineIntegrator | Magnetic Field Analysis | <https://github.com/lukasmerten/CRPropa_FieldLineIntegrator> |
+| grplinst | Plasma Instabilities | <https://github.com/rafaelab/grplinst> |
+| monopole | Magnetic Monopole Studies | https://github.com/chchristie/monopole/tree/main |
+| ROOTOutputPlugin | Output into root file format | https://github.com/CRPropa/ROOTOutputPlugin |

doc/pages/AdditionalResources.rst

@@ -20,6 +20,8 @@ Additional Resources
 -  Data for the strong extragalactic magnetic fields by `Alves Batista  et al. 
    <https://arxiv.org/abs/1704.05869>`__ can be downloaded
    `here <https://syncandshare.desy.de/index.php/s/Fo5xceXtwtk5Exo>`__.
+-  Data for the Galactic mass distribution by `Mertsch et al. (2020) <https://arxiv.org/abs/2012.15770>`__ can be found 
+   `here <https://syncandshare.desy.de/index.php/s/aR8wkqYYkDyfWgs>`__. 
 
 
 Note that these resources are completely external to CRPropa. We cannot supply any kind of additional information nor can we offer support on how to use them.