Engine Addition: NuSQUIDS

CMakeLists.txt

@@ -55,14 +55,16 @@ DefineEnabledRequiredSwitch(UseCUDAProb3Linear 0)
 DefineEnabledRequiredSwitch(UseProb3ppLinear 0)
 DefineEnabledRequiredSwitch(UseProbGPULinear 0)
 DefineEnabledRequiredSwitch(UseNuFASTLinear 0)
+DefineEnabledRequiredSwitch(UseNuSQUIDSLinear 0)
 
 # KS: NuFastLinear by default
-if(UseCUDAProb3       EQUAL 0 AND
-   UseCUDAProb3Linear EQUAL 0 AND
-   UseProb3ppLinear   EQUAL 0 AND
-   UseProbGPULinear   EQUAL 0 AND
-   UseNuFASTLinear    EQUAL 0)
-    set(UseNuFASTLinear 1)
+if(UseCUDAProb3        EQUAL 0 AND
+    UseCUDAProb3Linear EQUAL 0 AND
+    UseProb3ppLinear   EQUAL 0 AND
+    UseProbGPULinear   EQUAL 0 AND
+    UseNuFASTLinear    EQUAL 0 AND
+    UseNuSQUIDSLinear  EQUAL 0)
+  set(UseNuFASTLinear 1)
 endif()
 
 LIST(APPEND ALL_Engines
@@ -71,6 +73,7 @@ LIST(APPEND ALL_Engines
   Prob3ppLinear
   ProbGPULinear
   NuFASTLinear
+  NuSQUIDSLinear
   )
 cmessage(STATUS "NuOscillator Features: ")
 foreach(f ${ALL_Engines})
@@ -252,6 +255,48 @@ if(${UseNuFASTLinear} EQUAL 1)
       target_compile_definitions(NuOscillatorCompilerOptions INTERFACE UseNuFASTLinear=1)
 endif()
 
+if(${UseNuSQUIDSLinear} EQUAL 1)
+  find_package(GSL REQUIRED)
+  find_package(HDF5 REQUIRED)
+
+  include(ExternalProject)
+
+  ExternalProject_Add(SQUIDS
+    GIT_REPOSITORY https://github.com/jsalvado/SQuIDS.git
+    GIT_TAG master
+    BINARY_DIR = <SOURCE_DIR> 
+    CONFIGURE_HANDLED_BY_BUILD true
+    CONFIGURE_COMMAND <SOURCE_DIR>/configure --with-gsl=${GSL_ROOT_DIR} --prefix=<INSTALL_DIR>
+    BUILD_COMMAND make
+    INSTALL_COMMAND make install
+  )
+
+  SET(SQUIDS_INC_DIR ${CMAKE_CURRENT_BINARY_DIR}/SQUIDS-prefix/include)
+  SET(SQUIDS_LIB_DIR ${CMAKE_CURRENT_BINARY_DIR}/SQUIDS-prefix/lib)
+
+  add_library(SQUIDS::SQUIDS SHARED IMPORTED)
+  set_target_properties(SQUIDS::SQUIDS PROPERTIES IMPORTED_LOCATION ${SQUIDS_LIB_DIR}/libSQuIDS.so)
+
+  ExternalProject_Add(NUSQUIDS
+    GIT_REPOSITORY https://github.com/arguelles/nuSQuIDS.git
+    GIT_TAG master
+    BINARY_DIR = <SOURCE_DIR>
+    CONFIGURE_HANDLED_BY_BUILD true
+    CONFIGURE_COMMAND <SOURCE_DIR>/configure --with-gsl=${GSL_ROOT_DIR} --with-hdf5=${HDF5_INCLUDE_DIRS}/../ --with-squids=${CMAKE_CURRENT_BINARY_DIR}/SQUIDS-prefix --prefix=<INSTALL_DIR>
+    BUILD_COMMAND make examples
+    INSTALL_COMMAND make install
+  )
+
+  SET(NUSQUIDS_SRC_DIR ${CMAKE_CURRENT_BINARY_DIR}/NUSQUIDS-prefix/src/NUSQUIDS/)
+  SET(NUSQUIDS_INC_DIR ${CMAKE_CURRENT_BINARY_DIR}/NUSQUIDS-prefix/include/)
+  SET(NUSQUIDS_LIB_DIR ${CMAKE_CURRENT_BINARY_DIR}/NUSQUIDS-prefix/lib/)
+
+  add_library(NUSQUIDS::NUSQUIDS SHARED IMPORTED)
+  set_target_properties(NUSQUIDS::NUSQUIDS PROPERTIES IMPORTED_LOCATION ${NUSQUIDS_LIB_DIR}/libnuSQuIDS.so)
+
+  target_compile_definitions(NuOscillatorCompilerOptions INTERFACE UseNuSQUIDSLinear=1)
+endif()    
+
 if(${UseGPU} EQUAL 1)
     target_compile_definitions(NuOscillatorCompilerOptions INTERFACE UseGPU=1)
 else()

Configs/Binned_NuSQUIDSLinear.yaml

@@ -0,0 +1,22 @@
+General:
+  Verbosity: "NONE"
+  CosineZIgnored: false
+  CalculationType: "Binned"
+
+Binned:
+  FileName: "./Inputs/ExampleAtmosphericBinning.root"
+  EnergyAxisHistName: "EnergyAxisBinning"
+  CosineZAxisHistName: "CosineZAxisBinning"
+
+OscProbCalcerSetup:
+  ImplementationName: "NuSQUIDSLinear"
+  OscChannelMapping:
+    - Entry: "Electron:Electron"
+    - Entry: "Electron:Muon"
+    - Entry: "Electron:Tau"
+    - Entry: "Muon:Electron"
+    - Entry: "Muon:Muon"
+    - Entry: "Muon:Tau"
+    - Entry: "Tau:Electron"
+    - Entry: "Tau:Muon"
+    - Entry: "Tau:Tau"

Configs/OscProbCalcerConfigs/NuSQUIDSLinear.yaml

@@ -0,0 +1,15 @@
+General:
+  Verbosity: "NONE"
+
+OscProbCalcerSetup:
+  ImplementationName: "NuSQUIDSLinear"
+  OscChannelMapping:
+    - Entry: "Electron:Electron"
+    - Entry: "Electron:Muon"
+    - Entry: "Electron:Tau"
+    - Entry: "Muon:Electron"
+    - Entry: "Muon:Muon"
+    - Entry: "Muon:Tau"
+    - Entry: "Tau:Electron"
+    - Entry: "Tau:Muon"
+    - Entry: "Tau:Tau"

Configs/Unbinned_NuSQUIDSLinear.yaml

@@ -0,0 +1,17 @@
+General:
+  Verbosity: "NONE"
+  CosineZIgnored: false
+  CalculationType: "Unbinned"
+
+OscProbCalcerSetup:
+  ImplementationName: "NuSQUIDSLinear"
+  OscChannelMapping:
+    - Entry: "Electron:Electron"
+    - Entry: "Electron:Muon"
+    - Entry: "Electron:Tau"
+    - Entry: "Muon:Electron"
+    - Entry: "Muon:Muon"
+    - Entry: "Muon:Tau"
+    - Entry: "Tau:Electron"
+    - Entry: "Tau:Muon"
+    - Entry: "Tau:Tau"

Constants/OscillatorConstants.h

@@ -100,6 +100,10 @@ inline std::vector<std::string> ReturnKnownConfigs() {
 
 #if UseNuFASTLinear == 1
   ConfigNames.push_back("./Configs/Binned_NuFASTLinear.yaml");
+#endif
+
+#if UseNuSQUIDSLinear == 1
+  ConfigNames.push_back("./Configs/Binned_NuSQUIDSLinear.yaml");
 #endif  
 
   return ConfigNames;

Docs/DockerFiles/Alma9/Dockerfile

@@ -24,7 +24,7 @@ RUN git checkout ${NUOSCILLATOR_VERSION}
 
 RUN mkdir -p ${NuOscillator_INSTALL_DIR}
 WORKDIR ${NuOscillator_INSTALL_DIR}
-RUN cmake -DUseGPU=0 -DUseMultithreading=1 -DUseDoubles=1 -DUseCUDAProb3=0 -DUseCUDAProb3Linear=1 -DUseProb3ppLinear=1 -DUseNuFASTLinear=1 -DUseProbGPULinear=0 ${NuOscillator_WORK_DIR}
+RUN cmake -DUseGPU=0 -DUseMultithreading=1 -DUseDoubles=1 -DUseCUDAProb3=0 -DUseCUDAProb3Linear=1 -DUseProb3ppLinear=1 -DUseNuFASTLinear=1 -DUseProbGPULinear=0 -DUseNuSQUIDSLinear=1 ${NuOscillator_WORK_DIR}
 RUN make VERBOSE=1 && make install
 
 # KS: Need to set them here, otherwise container using this container will not be able to find NuOscillator

OscProbCalcer/CMakeLists.txt

@@ -5,72 +5,88 @@ add_library(OscProbCalcer SHARED OscProbCalcerBase.cpp OscProbCalcerFactory.cpp)
 target_link_libraries(OscProbCalcer yaml-cpp NuOscillatorCompilerOptions)
 
 target_include_directories(OscProbCalcer PUBLIC
-    $<BUILD_INTERFACE:${CMAKE_CURRENT_LIST_DIR}/../>
-    $<INSTALL_INTERFACE:include>
+  $<BUILD_INTERFACE:${CMAKE_CURRENT_LIST_DIR}/../>
+  $<INSTALL_INTERFACE:include>
 )
 
 install(TARGETS yaml-cpp
-        EXPORT NuOscillator-targets
-        LIBRARY DESTINATION lib/
-        PUBLIC_HEADER DESTINATION include/yaml-cpp
-        )
+  EXPORT NuOscillator-targets
+  LIBRARY DESTINATION lib/
+  PUBLIC_HEADER DESTINATION include/yaml-cpp
+)
 
 install(DIRECTORY ${yaml-cpp_SOURCE_DIR}/include/
-    DESTINATION include/
+  DESTINATION include/
 )
 
 if(${UseCUDAProb3} EQUAL 1)
-	   target_sources(OscProbCalcer PRIVATE OscProbCalcer_CUDAProb3.cpp)
-	   if(${UseGPU} EQUAL 1)
-	     set_source_files_properties(OscProbCalcer_CUDAProb3.cpp PROPERTIES LANGUAGE CUDA)
-	   endif()
-	   target_include_directories(OscProbCalcer PRIVATE ${CUDAProb3_SOURCE_DIR})
-	   list(APPEND HEADERS OscProbCalcer_CUDAProb3.h)
+  target_sources(OscProbCalcer PRIVATE OscProbCalcer_CUDAProb3.cpp)
+  if(${UseGPU} EQUAL 1)
+    set_source_files_properties(OscProbCalcer_CUDAProb3.cpp PROPERTIES LANGUAGE CUDA)
+  endif()
+  target_include_directories(OscProbCalcer PRIVATE ${CUDAProb3_SOURCE_DIR})
+  list(APPEND HEADERS OscProbCalcer_CUDAProb3.h)
 endif()
 
 if(${UseCUDAProb3Linear} EQUAL 1)
-	   target_link_libraries(OscProbCalcer CUDAProb3Beam)
-	   target_sources(OscProbCalcer PRIVATE OscProbCalcer_CUDAProb3Linear.cpp)
-	   if(${UseGPU} EQUAL 1)
-            set_source_files_properties(OscProbCalcer_CUDAProb3Linear.cpp PROPERTIES LANGUAGE CUDA)
-            target_include_directories(OscProbCalcer PRIVATE ${CUDAProb3_SOURCE_DIR})
-	   endif()
-	   list(APPEND HEADERS OscProbCalcer_CUDAProb3Linear.h)
+  target_link_libraries(OscProbCalcer CUDAProb3Beam)
+  target_sources(OscProbCalcer PRIVATE OscProbCalcer_CUDAProb3Linear.cpp)
+  if(${UseGPU} EQUAL 1)
+    set_source_files_properties(OscProbCalcer_CUDAProb3Linear.cpp PROPERTIES LANGUAGE CUDA)
+    target_include_directories(OscProbCalcer PRIVATE ${CUDAProb3_SOURCE_DIR})
+  endif()
+  list(APPEND HEADERS OscProbCalcer_CUDAProb3Linear.h)
 endif()
 
 if(${UseProbGPULinear} EQUAL 1)
-	   target_link_libraries(OscProbCalcer ProbGPU)
-	   set_property(TARGET ProbGPU PROPERTY CUDA_ARCHITECTURES ${CMAKE_CUDA_ARCHITECTURES})
-	   target_sources(OscProbCalcer PRIVATE OscProbCalcer_ProbGPULinear.cpp)
-	   list(APPEND HEADERS OscProbCalcer_ProbGPULinear.h)
+  target_link_libraries(OscProbCalcer ProbGPU)
+  set_property(TARGET ProbGPU PROPERTY CUDA_ARCHITECTURES ${CMAKE_CUDA_ARCHITECTURES})
+  target_sources(OscProbCalcer PRIVATE OscProbCalcer_ProbGPULinear.cpp)
+  list(APPEND HEADERS OscProbCalcer_ProbGPULinear.h)
 endif()
 
 if(${UseProb3ppLinear} EQUAL 1)
-	   target_link_libraries(OscProbCalcer Prob3plusplus)
-	   target_sources(OscProbCalcer PRIVATE OscProbCalcer_Prob3ppLinear.cpp)
-	   list(APPEND HEADERS OscProbCalcer_Prob3ppLinear.h)
+  target_link_libraries(OscProbCalcer Prob3plusplus)
+  target_sources(OscProbCalcer PRIVATE OscProbCalcer_Prob3ppLinear.cpp)
+  list(APPEND HEADERS OscProbCalcer_Prob3ppLinear.h)
 endif()
 
 if(${UseNuFASTLinear} EQUAL 1)
-	   include_directories(${NuFAST_SOURCE_DIR})
-	   target_sources(OscProbCalcer PRIVATE OscProbCalcer_NuFASTLinear.cpp)
-	   list(APPEND HEADERS OscProbCalcer_NuFASTLinear.h)
+  include_directories(${NuFAST_SOURCE_DIR})
+  target_sources(OscProbCalcer PRIVATE OscProbCalcer_NuFASTLinear.cpp)
+  list(APPEND HEADERS OscProbCalcer_NuFASTLinear.h)
+endif()
+
+if(${UseNuSQUIDSLinear} EQUAL 1)
+  include_directories(${SQUIDS_INC_DIR})
+  include_directories(${NUSQUIDS_INC_DIR})
+  include_directories(${NUSQUIDS_SRC_DIR})
+
+  set(NUSQUIDSEXAMPLES nuSQUIDSDecoh.o)
+
+  target_link_libraries(OscProbCalcer GSL::gsl GSL::gslcblas HDF5::HDF5 SQUIDS::SQUIDS NUSQUIDS::NUSQUIDS)
+  foreach(VAR ${NUSQUIDSEXAMPLES})
+    target_link_libraries(OscProbCalcer ${NUSQUIDS_SRC_DIR}/build/${VAR})
+  endforeach(VAR)
+  target_sources(OscProbCalcer PRIVATE OscProbCalcer_NuSQUIDSLinear.cpp)
+  list(APPEND HEADERS OscProbCalcer_NuSQUIDSLinear.h)
+
 endif()
 
 if (${UseGPU} EQUAL 1)
-   set_target_properties(OscProbCalcer PROPERTIES
-				    CUDA_SEPARABLE_COMPILATION ON
-				    LINKER_LANGUAGE CUDA
-				    EXPORT_NAME OscProbCalcer)
+  set_target_properties(OscProbCalcer PROPERTIES
+    CUDA_SEPARABLE_COMPILATION ON
+    LINKER_LANGUAGE CUDA
+    EXPORT_NAME OscProbCalcer)
 endif()
 
 set_target_properties(OscProbCalcer PROPERTIES
-    PUBLIC_HEADER "${HEADERS}"
-    EXPORT_NAME OscProbCalcer)
+  PUBLIC_HEADER "${HEADERS}"
+  EXPORT_NAME OscProbCalcer)
 
 install(TARGETS OscProbCalcer
-        EXPORT NuOscillator-targets
-        LIBRARY DESTINATION lib/
-        PUBLIC_HEADER DESTINATION include/OscProbCalcer)
+  EXPORT NuOscillator-targets
+  LIBRARY DESTINATION lib/
+  PUBLIC_HEADER DESTINATION include/OscProbCalcer)
 
 add_library(OscProbCalcer::OscProbCalcer ALIAS OscProbCalcer)

OscProbCalcer/OscProbCalcerFactory.cpp

@@ -20,6 +20,10 @@
 #include "OscProbCalcer/OscProbCalcer_NuFASTLinear.h"
 #endif
 
+#if UseNuSQUIDSLinear==1
+#include "OscProbCalcer/OscProbCalcer_NuSQUIDSLinear.h"
+#endif
+
 #include <iostream>
 
 OscProbCalcerFactory::OscProbCalcerFactory() {
@@ -94,6 +98,17 @@ OscProbCalcerBase* OscProbCalcerFactory::CreateOscProbCalcer(YAML::Node OscProbC
     throw;
 #endif
   }
+
+  else if (OscProbCalcerImplementationToCreate == "NuSQUIDSLinear") {
+#if UseNuSQUIDSLinear==1
+    OscProbCalcerNuSQUIDSLinear* NuSQUIDSLinear = new OscProbCalcerNuSQUIDSLinear(OscProbCalcerConfig);
+    Calcer = (OscProbCalcerBase*)NuSQUIDSLinear;
+    if (Verbose >= NuOscillator::INFO) {std::cout << "Initalised OscProbCalcer Implementation:" << Calcer->ReturnImplementationName() << " in OscProbCalcerFactory object" << std::endl;}
+#else
+    std::cerr << "OscProbCalcerFactory was requsted to create " << OscProbCalcerImplementationToCreate << " OscProbCalcer but Use" << OscProbCalcerImplementationToCreate << " is undefined. Indicates problem in setup" << std::endl;
+    throw;
+#endif
+  }
 
   else {
     std::cerr << "OscProbCalcerFactory was requsted to create " << OscProbCalcerImplementationToCreate << " OscProbCalcer but this is not implemented within " << __FILE__ << std::endl;