moved to pi git

README.md

@@ -0,0 +1,113 @@
+This is based on code from Mirco Deckenhoff and modified by Blake Leverington, Peter Stromberger, _et al_.
+### Based on https://gitlab.cern.ch/lhcb-scifi/SciFiSimG4, but now expanded to a fibre mat, rather than a single fibre, with SiPM readout.
+
+
+## How to get SciFiSim running
+ _Installation of GEANT4 help is at the bottom of this readme. Check the cmake options for compatibility._
+
+
+ > $ git clone https://$USER@gitlab.cern.ch/lhcb-scifi/SciFiMatG4_v2
+ 
+ > $ cd SciFiMatG4_v2
+ 
+Edit the environment script setup.sh to point to your Geant and ROOT installation and `source` it to add it to your environment:
+
+ > $ source setup.sh //(required before running the software too if you open a new terminal.)
+
+Now to cun cmake in the build folder:
+
+ >  mkdir -p SciFiSim-build //it is safe to delete this folder if you have problems during compilation
+
+ >  cd SciFiSim-build
+
+ >  cmake ../SciFiSim
+ 
+ >  cmake --build . // or make clean; make
+
+
+To run the Geant4 simulation in batch mode:
+ 
+ >  cd ../SimulationData
+ 
+ >  ../SciFiSim-build/scifiSim muongun.mac
+
+
+To run the simulation from within the GUI (for visualization only) very slow if optical photon physics are enabled:
+ > $ ../SciFiSim-build/scifiSim //opens the gui
+ > /control/execute/ vis.mac
+
+
+
+## The Geometry file
+../SciFiSim/src/DetectorConstruction.cc&
+
+ - a multi-layer ribbon of fibres with LHCb style SiPM array at the end (no 64ch gap)
+
+ *if you make changes to the code, run `make` again in the build folder to recompile with the changes. Sometimes you might need `make clean; make`.*
+
+## Input Parameters
+Various parameters of the simulation are read in from a parameters file in /SimulationData/parameterFiles/ .
+The description is in SciFiSi 
+
+## PhysicsList.cc
+The optical photon physics can be turned off by commenting out the OpticalPhyics section with `/*  */`  in /src/PhysicsList.cc
+if you are only interested in energy deposit in the fibres from the primary track, for example. 
+
+
+## The root output
+
+There are 5 different TTrees created.
+
+ - DetectedPhotons (information about photons detected at SiPM, each photon is an entry)
+ - Trigger(information about trigger)
+ - PrimaryParticleTrack
+ - InitialParticle(Not sure what the difference is)
+ - EnergyTrack (track length in fibres and energy deposited)
+ 
+## SciFiSimG4_v2 requires installation of Geant4 first
+ 
+ > $ wget http://geant4.web.cern.ch/geant4/support/source/geant4.10.07.p01.tar.gz
+ 
+ > $ tar -xzvf geant4.10.07.p01.tar.gz 
+ 
+ > $ mkdir geant4.10.07.p01-build
+ 
+ > $ mkdir geant4.10.07.p01-install
+ 
+ > $ cd geant4.10.07.p01-build/
+ 
+
+
+ > https://geant4-userdoc.web.cern.ch/UsersGuides/InstallationGuide/html/gettingstarted.html#softwarerequirements
+ 
+ > sudo apt-get install libxerces-c-dev qt4-dev-tools freeglut3-dev libmotif-dev tk-dev cmake libxpm-dev libxmu-dev libxi-dev
+ > libqt5opengl5-dev
+ >libqt4-dev
+ >cmake libx11-dev xorg-dev libglu1-mesa-dev freeglut3-dev libglew1.5 libglew1.5-dev libglu1-mesa libglu1-mesa-dev libgl1-mesa-glx libgl1-mesa-dev
+ >libfontconfig1-dev libfreetype6-dev libx11-dev libxcursor-dev libxext-dev libxfixes-dev libxft-dev libxi-dev libxrandr-dev libxrender-dev
+ >libxmu-dev expat
+ >freeglut3 freeglut3-dev mesa-utils
+
+### add your favourite options. the Granular libraries are required by the code, for some reason.
+
+ > cmake -DCMAKE_INSTALL_PREFIX=/home/leverington/software/geant4.10.07.p01-install -DGEANT4_INSTALL_DATA=ON -DGEANT4_BUILD_MULTITHREADED=ON -DGEANT4_USE_OPENGL_X11=ON -DGEANT4_USE_QT=ON -DGEANT4_BUILD_CXXSTD=17 -DGEANT4_USE_FREETYPE=ON -DGEANT4_USE_SYSTEM_CLHEP_GRANULAR=ON ../geant4.10.07.p01
+
+ > fix any missing software that is might complain is missing
+
+ > $ make
+ 
+ > $ make install
+
+
+## Cern ROOT must also be installed. Compiled with CXX17
+currently works with ROOT Version: 6.23/01
+
+> $ root-config --features
+
+ > cxx17 asimage builtin_afterimage builtin_clang builtin_gl2ps builtin_llvm builtin_lz4 builtin_nlohmannjson builtin_openui5 builtin_tbb builtin_vdt builtin_xrootd builtin_xxhash builtin_zstd clad dataframe exceptions fftw3 fitsio gdml http imt mathmore mlp mysql opengl pyroot roofit webgui root7 runtime_cxxmodules shared ssl tmva tmva-cpu tmva-pymva spectrum vdt x11 xml xrootd
+
+ > cmake -Dpython=ON -Droofit=ON -DCMAKE_INSTALL_PREFIX:PATH=/home/leverington/software/root-install-cxx17 -DCMAKE_CXX_STANDARD=17 ../root
+
+ > make
+
+ > make install

SciFiSim/CMakeFiles/2.8.12.2/CMakeCCompiler.cmake

@@ -0,0 +1,56 @@
+set(CMAKE_C_COMPILER "/usr/bin/cc")
+set(CMAKE_C_COMPILER_ARG1 "")
+set(CMAKE_C_COMPILER_ID "GNU")
+set(CMAKE_C_COMPILER_VERSION "4.4.7")
+set(CMAKE_C_PLATFORM_ID "Linux")
+
+set(CMAKE_AR "/usr/bin/ar")
+set(CMAKE_RANLIB "/usr/bin/ranlib")
+set(CMAKE_LINKER "/usr/bin/ld")
+set(CMAKE_COMPILER_IS_GNUCC 1)
+set(CMAKE_C_COMPILER_LOADED 1)
+set(CMAKE_C_COMPILER_WORKS TRUE)
+set(CMAKE_C_ABI_COMPILED TRUE)
+set(CMAKE_COMPILER_IS_MINGW )
+set(CMAKE_COMPILER_IS_CYGWIN )
+if(CMAKE_COMPILER_IS_CYGWIN)
+  set(CYGWIN 1)
+  set(UNIX 1)
+endif()
+
+set(CMAKE_C_COMPILER_ENV_VAR "CC")
+
+if(CMAKE_COMPILER_IS_MINGW)
+  set(MINGW 1)
+endif()
+set(CMAKE_C_COMPILER_ID_RUN 1)
+set(CMAKE_C_SOURCE_FILE_EXTENSIONS c)
+set(CMAKE_C_IGNORE_EXTENSIONS h;H;o;O;obj;OBJ;def;DEF;rc;RC)
+set(CMAKE_C_LINKER_PREFERENCE 10)
+
+# Save compiler ABI information.
+set(CMAKE_C_SIZEOF_DATA_PTR "8")
+set(CMAKE_C_COMPILER_ABI "ELF")
+set(CMAKE_C_LIBRARY_ARCHITECTURE "")
+
+if(CMAKE_C_SIZEOF_DATA_PTR)
+  set(CMAKE_SIZEOF_VOID_P "${CMAKE_C_SIZEOF_DATA_PTR}")
+endif()
+
+if(CMAKE_C_COMPILER_ABI)
+  set(CMAKE_INTERNAL_PLATFORM_ABI "${CMAKE_C_COMPILER_ABI}")
+endif()
+
+if(CMAKE_C_LIBRARY_ARCHITECTURE)
+  set(CMAKE_LIBRARY_ARCHITECTURE "")
+endif()
+
+
+
+
+set(CMAKE_C_IMPLICIT_LINK_LIBRARIES "c")
+set(CMAKE_C_IMPLICIT_LINK_DIRECTORIES "/usr/lib/gcc/x86_64-redhat-linux/4.4.7;/usr/lib64;/lib64;/usr/lib")
+set(CMAKE_C_IMPLICIT_LINK_FRAMEWORK_DIRECTORIES "")
+
+
+

SciFiSim/CMakeFiles/2.8.12.2/CMakeCXXCompiler.cmake

@@ -0,0 +1,57 @@
+set(CMAKE_CXX_COMPILER "/usr/bin/c++")
+set(CMAKE_CXX_COMPILER_ARG1 "")
+set(CMAKE_CXX_COMPILER_ID "GNU")
+set(CMAKE_CXX_COMPILER_VERSION "4.4.7")
+set(CMAKE_CXX_PLATFORM_ID "Linux")
+
+set(CMAKE_AR "/usr/bin/ar")
+set(CMAKE_RANLIB "/usr/bin/ranlib")
+set(CMAKE_LINKER "/usr/bin/ld")
+set(CMAKE_COMPILER_IS_GNUCXX 1)
+set(CMAKE_CXX_COMPILER_LOADED 1)
+set(CMAKE_CXX_COMPILER_WORKS TRUE)
+set(CMAKE_CXX_ABI_COMPILED TRUE)
+set(CMAKE_COMPILER_IS_MINGW )
+set(CMAKE_COMPILER_IS_CYGWIN )
+if(CMAKE_COMPILER_IS_CYGWIN)
+  set(CYGWIN 1)
+  set(UNIX 1)
+endif()
+
+set(CMAKE_CXX_COMPILER_ENV_VAR "CXX")
+
+if(CMAKE_COMPILER_IS_MINGW)
+  set(MINGW 1)
+endif()
+set(CMAKE_CXX_COMPILER_ID_RUN 1)
+set(CMAKE_CXX_IGNORE_EXTENSIONS inl;h;hpp;HPP;H;o;O;obj;OBJ;def;DEF;rc;RC)
+set(CMAKE_CXX_SOURCE_FILE_EXTENSIONS C;M;c++;cc;cpp;cxx;m;mm;CPP)
+set(CMAKE_CXX_LINKER_PREFERENCE 30)
+set(CMAKE_CXX_LINKER_PREFERENCE_PROPAGATES 1)
+
+# Save compiler ABI information.
+set(CMAKE_CXX_SIZEOF_DATA_PTR "8")
+set(CMAKE_CXX_COMPILER_ABI "ELF")
+set(CMAKE_CXX_LIBRARY_ARCHITECTURE "")
+
+if(CMAKE_CXX_SIZEOF_DATA_PTR)
+  set(CMAKE_SIZEOF_VOID_P "${CMAKE_CXX_SIZEOF_DATA_PTR}")
+endif()
+
+if(CMAKE_CXX_COMPILER_ABI)
+  set(CMAKE_INTERNAL_PLATFORM_ABI "${CMAKE_CXX_COMPILER_ABI}")
+endif()
+
+if(CMAKE_CXX_LIBRARY_ARCHITECTURE)
+  set(CMAKE_LIBRARY_ARCHITECTURE "")
+endif()
+
+
+
+
+set(CMAKE_CXX_IMPLICIT_LINK_LIBRARIES "stdc++;m;c")
+set(CMAKE_CXX_IMPLICIT_LINK_DIRECTORIES "/usr/lib/gcc/x86_64-redhat-linux/4.4.7;/usr/lib64;/lib64;/usr/lib")
+set(CMAKE_CXX_IMPLICIT_LINK_FRAMEWORK_DIRECTORIES "")
+
+
+

SciFiSim/CMakeFiles/2.8.12.2/CMakeSystem.cmake

@@ -0,0 +1,15 @@
+set(CMAKE_HOST_SYSTEM "Linux-3.2.0-40-generic")
+set(CMAKE_HOST_SYSTEM_NAME "Linux")
+set(CMAKE_HOST_SYSTEM_VERSION "3.2.0-40-generic")
+set(CMAKE_HOST_SYSTEM_PROCESSOR "x86_64")
+
+
+
+set(CMAKE_SYSTEM "Linux-3.2.0-40-generic")
+set(CMAKE_SYSTEM_NAME "Linux")
+set(CMAKE_SYSTEM_VERSION "3.2.0-40-generic")
+set(CMAKE_SYSTEM_PROCESSOR "x86_64")
+
+set(CMAKE_CROSSCOMPILING "FALSE")
+
+set(CMAKE_SYSTEM_LOADED 1)

SciFiSim/CMakeFiles/2.8.12.2/CompilerIdC/CMakeCCompilerId.c

@@ -0,0 +1,389 @@
+#ifdef __cplusplus
+# error "A C++ compiler has been selected for C."
+#endif
+
+/* Version number components: V=Version, R=Revision, P=Patch
+   Version date components:   YYYY=Year, MM=Month,   DD=Day  */
+
+#if defined(__18CXX)
+# define ID_VOID_MAIN
+#endif
+
+#if defined(__INTEL_COMPILER) || defined(__ICC)
+# define COMPILER_ID "Intel"
+  /* __INTEL_COMPILER = VRP */
+# define COMPILER_VERSION_MAJOR DEC(__INTEL_COMPILER/100)
+# define COMPILER_VERSION_MINOR DEC(__INTEL_COMPILER/10 % 10)
+# define COMPILER_VERSION_PATCH DEC(__INTEL_COMPILER    % 10)
+# if defined(__INTEL_COMPILER_BUILD_DATE)
+  /* __INTEL_COMPILER_BUILD_DATE = YYYYMMDD */
+#  define COMPILER_VERSION_TWEAK DEC(__INTEL_COMPILER_BUILD_DATE)
+# endif
+
+#elif defined(__PATHCC__)
+# define COMPILER_ID "PathScale"
+# define COMPILER_VERSION_MAJOR DEC(__PATHCC__)
+# define COMPILER_VERSION_MINOR DEC(__PATHCC_MINOR__)
+# if defined(__PATHCC_PATCHLEVEL__)
+#  define COMPILER_VERSION_PATCH DEC(__PATHCC_PATCHLEVEL__)
+# endif
+
+#elif defined(__clang__)
+# define COMPILER_ID "Clang"
+# define COMPILER_VERSION_MAJOR DEC(__clang_major__)
+# define COMPILER_VERSION_MINOR DEC(__clang_minor__)
+# define COMPILER_VERSION_PATCH DEC(__clang_patchlevel__)
+
+#elif defined(__BORLANDC__) && defined(__CODEGEARC_VERSION__)
+# define COMPILER_ID "Embarcadero"
+# define COMPILER_VERSION_MAJOR HEX(__CODEGEARC_VERSION__>>24 & 0x00FF)
+# define COMPILER_VERSION_MINOR HEX(__CODEGEARC_VERSION__>>16 & 0x00FF)
+# define COMPILER_VERSION_PATCH HEX(__CODEGEARC_VERSION__     & 0xFFFF)
+
+#elif defined(__BORLANDC__)
+# define COMPILER_ID "Borland"
+  /* __BORLANDC__ = 0xVRR */
+# define COMPILER_VERSION_MAJOR HEX(__BORLANDC__>>8)
+# define COMPILER_VERSION_MINOR HEX(__BORLANDC__ & 0xFF)
+
+#elif defined(__WATCOMC__)
+# define COMPILER_ID "Watcom"
+  /* __WATCOMC__ = VVRR */
+# define COMPILER_VERSION_MAJOR DEC(__WATCOMC__ / 100)
+# define COMPILER_VERSION_MINOR DEC(__WATCOMC__ % 100)
+
+#elif defined(__SUNPRO_C)
+# define COMPILER_ID "SunPro"
+# if __SUNPRO_C >= 0x5100
+   /* __SUNPRO_C = 0xVRRP */
+#  define COMPILER_VERSION_MAJOR HEX(__SUNPRO_C>>12)
+#  define COMPILER_VERSION_MINOR HEX(__SUNPRO_C>>4 & 0xFF)
+#  define COMPILER_VERSION_PATCH HEX(__SUNPRO_C    & 0xF)
+# else
+   /* __SUNPRO_C = 0xVRP */
+#  define COMPILER_VERSION_MAJOR HEX(__SUNPRO_C>>8)
+#  define COMPILER_VERSION_MINOR HEX(__SUNPRO_C>>4 & 0xF)
+#  define COMPILER_VERSION_PATCH HEX(__SUNPRO_C    & 0xF)
+# endif
+
+#elif defined(__HP_cc)
+# define COMPILER_ID "HP"
+  /* __HP_cc = VVRRPP */
+# define COMPILER_VERSION_MAJOR DEC(__HP_cc/10000)
+# define COMPILER_VERSION_MINOR DEC(__HP_cc/100 % 100)
+# define COMPILER_VERSION_PATCH DEC(__HP_cc     % 100)
+
+#elif defined(__DECC)
+# define COMPILER_ID "Compaq"
+  /* __DECC_VER = VVRRTPPPP */
+# define COMPILER_VERSION_MAJOR DEC(__DECC_VER/10000000)
+# define COMPILER_VERSION_MINOR DEC(__DECC_VER/100000  % 100)
+# define COMPILER_VERSION_PATCH DEC(__DECC_VER         % 10000)
+
+#elif defined(__IBMC__)
+# if defined(__COMPILER_VER__)
+#  define COMPILER_ID "zOS"
+# else
+#  if __IBMC__ >= 800
+#   define COMPILER_ID "XL"
+#  else
+#   define COMPILER_ID "VisualAge"
+#  endif
+   /* __IBMC__ = VRP */
+#  define COMPILER_VERSION_MAJOR DEC(__IBMC__/100)
+#  define COMPILER_VERSION_MINOR DEC(__IBMC__/10 % 10)
+#  define COMPILER_VERSION_PATCH DEC(__IBMC__    % 10)
+# endif
+
+#elif defined(__PGI)
+# define COMPILER_ID "PGI"
+# define COMPILER_VERSION_MAJOR DEC(__PGIC__)
+# define COMPILER_VERSION_MINOR DEC(__PGIC_MINOR__)
+# if defined(__PGIC_PATCHLEVEL__)
+#  define COMPILER_VERSION_PATCH DEC(__PGIC_PATCHLEVEL__)
+# endif
+
+#elif defined(_CRAYC)
+# define COMPILER_ID "Cray"
+# define COMPILER_VERSION_MAJOR DEC(_RELEASE)
+# define COMPILER_VERSION_MINOR DEC(_RELEASE_MINOR)
+
+#elif defined(__TI_COMPILER_VERSION__)
+# define COMPILER_ID "TI"
+  /* __TI_COMPILER_VERSION__ = VVVRRRPPP */
+# define COMPILER_VERSION_MAJOR DEC(__TI_COMPILER_VERSION__/1000000)
+# define COMPILER_VERSION_MINOR DEC(__TI_COMPILER_VERSION__/1000   % 1000)
+# define COMPILER_VERSION_PATCH DEC(__TI_COMPILER_VERSION__        % 1000)
+
+#elif defined(__TINYC__)
+# define COMPILER_ID "TinyCC"
+
+#elif defined(__SCO_VERSION__)
+# define COMPILER_ID "SCO"
+
+#elif defined(__GNUC__)
+# define COMPILER_ID "GNU"
+# define COMPILER_VERSION_MAJOR DEC(__GNUC__)
+# define COMPILER_VERSION_MINOR DEC(__GNUC_MINOR__)
+# if defined(__GNUC_PATCHLEVEL__)
+#  define COMPILER_VERSION_PATCH DEC(__GNUC_PATCHLEVEL__)
+# endif
+
+#elif defined(_MSC_VER)
+# define COMPILER_ID "MSVC"
+  /* _MSC_VER = VVRR */
+# define COMPILER_VERSION_MAJOR DEC(_MSC_VER / 100)
+# define COMPILER_VERSION_MINOR DEC(_MSC_VER % 100)
+# if defined(_MSC_FULL_VER)
+#  if _MSC_VER >= 1400
+    /* _MSC_FULL_VER = VVRRPPPPP */
+#   define COMPILER_VERSION_PATCH DEC(_MSC_FULL_VER % 100000)
+#  else
+    /* _MSC_FULL_VER = VVRRPPPP */
+#   define COMPILER_VERSION_PATCH DEC(_MSC_FULL_VER % 10000)
+#  endif
+# endif
+# if defined(_MSC_BUILD)
+#  define COMPILER_VERSION_TWEAK DEC(_MSC_BUILD)
+# endif
+
+/* Analog VisualDSP++ >= 4.5.6 */
+#elif defined(__VISUALDSPVERSION__)
+# define COMPILER_ID "ADSP"
+  /* __VISUALDSPVERSION__ = 0xVVRRPP00 */
+# define COMPILER_VERSION_MAJOR HEX(__VISUALDSPVERSION__>>24)
+# define COMPILER_VERSION_MINOR HEX(__VISUALDSPVERSION__>>16 & 0xFF)
+# define COMPILER_VERSION_PATCH HEX(__VISUALDSPVERSION__>>8  & 0xFF)
+
+/* Analog VisualDSP++ < 4.5.6 */
+#elif defined(__ADSPBLACKFIN__) || defined(__ADSPTS__) || defined(__ADSP21000__)
+# define COMPILER_ID "ADSP"
+
+/* IAR Systems compiler for embedded systems.
+   http://www.iar.com */
+#elif defined(__IAR_SYSTEMS_ICC__ ) || defined(__IAR_SYSTEMS_ICC)
+# define COMPILER_ID "IAR"
+
+/* sdcc, the small devices C compiler for embedded systems,
+   http://sdcc.sourceforge.net  */
+#elif defined(SDCC)
+# define COMPILER_ID "SDCC"
+  /* SDCC = VRP */
+#  define COMPILER_VERSION_MAJOR DEC(SDCC/100)
+#  define COMPILER_VERSION_MINOR DEC(SDCC/10 % 10)
+#  define COMPILER_VERSION_PATCH DEC(SDCC    % 10)
+
+#elif defined(_SGI_COMPILER_VERSION) || defined(_COMPILER_VERSION)
+# define COMPILER_ID "MIPSpro"
+# if defined(_SGI_COMPILER_VERSION)
+  /* _SGI_COMPILER_VERSION = VRP */
+#  define COMPILER_VERSION_MAJOR DEC(_SGI_COMPILER_VERSION/100)
+#  define COMPILER_VERSION_MINOR DEC(_SGI_COMPILER_VERSION/10 % 10)
+#  define COMPILER_VERSION_PATCH DEC(_SGI_COMPILER_VERSION    % 10)
+# else
+  /* _COMPILER_VERSION = VRP */
+#  define COMPILER_VERSION_MAJOR DEC(_COMPILER_VERSION/100)
+#  define COMPILER_VERSION_MINOR DEC(_COMPILER_VERSION/10 % 10)
+#  define COMPILER_VERSION_PATCH DEC(_COMPILER_VERSION    % 10)
+# endif
+
+/* This compiler is either not known or is too old to define an
+   identification macro.  Try to identify the platform and guess that
+   it is the native compiler.  */
+#elif defined(__sgi)
+# define COMPILER_ID "MIPSpro"
+
+#elif defined(__hpux) || defined(__hpua)
+# define COMPILER_ID "HP"
+
+#else /* unknown compiler */
+# define COMPILER_ID ""
+
+#endif
+
+/* Construct the string literal in pieces to prevent the source from
+   getting matched.  Store it in a pointer rather than an array
+   because some compilers will just produce instructions to fill the
+   array rather than assigning a pointer to a static array.  */
+char const* info_compiler = "INFO" ":" "compiler[" COMPILER_ID "]";
+
+/* Identify known platforms by name.  */
+#if defined(__linux) || defined(__linux__) || defined(linux)
+# define PLATFORM_ID "Linux"
+
+#elif defined(__CYGWIN__)
+# define PLATFORM_ID "Cygwin"
+
+#elif defined(__MINGW32__)
+# define PLATFORM_ID "MinGW"
+
+#elif defined(__APPLE__)
+# define PLATFORM_ID "Darwin"
+
+#elif defined(_WIN32) || defined(__WIN32__) || defined(WIN32)
+# define PLATFORM_ID "Windows"
+
+#elif defined(__FreeBSD__) || defined(__FreeBSD)
+# define PLATFORM_ID "FreeBSD"
+
+#elif defined(__NetBSD__) || defined(__NetBSD)
+# define PLATFORM_ID "NetBSD"
+
+#elif defined(__OpenBSD__) || defined(__OPENBSD)
+# define PLATFORM_ID "OpenBSD"
+
+#elif defined(__sun) || defined(sun)
+# define PLATFORM_ID "SunOS"
+
+#elif defined(_AIX) || defined(__AIX) || defined(__AIX__) || defined(__aix) || defined(__aix__)
+# define PLATFORM_ID "AIX"
+
+#elif defined(__sgi) || defined(__sgi__) || defined(_SGI)
+# define PLATFORM_ID "IRIX"
+
+#elif defined(__hpux) || defined(__hpux__)
+# define PLATFORM_ID "HP-UX"
+
+#elif defined(__HAIKU__)
+# define PLATFORM_ID "Haiku"
+
+#elif defined(__BeOS) || defined(__BEOS__) || defined(_BEOS)
+# define PLATFORM_ID "BeOS"
+
+#elif defined(__QNX__) || defined(__QNXNTO__)
+# define PLATFORM_ID "QNX"
+
+#elif defined(__tru64) || defined(_tru64) || defined(__TRU64__)
+# define PLATFORM_ID "Tru64"
+
+#elif defined(__riscos) || defined(__riscos__)
+# define PLATFORM_ID "RISCos"
+
+#elif defined(__sinix) || defined(__sinix__) || defined(__SINIX__)
+# define PLATFORM_ID "SINIX"
+
+#elif defined(__UNIX_SV__)
+# define PLATFORM_ID "UNIX_SV"
+
+#elif defined(__bsdos__)
+# define PLATFORM_ID "BSDOS"
+
+#elif defined(_MPRAS) || defined(MPRAS)
+# define PLATFORM_ID "MP-RAS"
+
+#elif defined(__osf) || defined(__osf__)
+# define PLATFORM_ID "OSF1"
+
+#elif defined(_SCO_SV) || defined(SCO_SV) || defined(sco_sv)
+# define PLATFORM_ID "SCO_SV"
+
+#elif defined(__ultrix) || defined(__ultrix__) || defined(_ULTRIX)
+# define PLATFORM_ID "ULTRIX"
+
+#elif defined(__XENIX__) || defined(_XENIX) || defined(XENIX)
+# define PLATFORM_ID "Xenix"
+
+#else /* unknown platform */
+# define PLATFORM_ID ""
+
+#endif
+
+/* For windows compilers MSVC and Intel we can determine
+   the architecture of the compiler being used.  This is because
+   the compilers do not have flags that can change the architecture,
+   but rather depend on which compiler is being used
+*/
+#if defined(_WIN32) && defined(_MSC_VER)
+# if defined(_M_IA64)
+#  define ARCHITECTURE_ID "IA64"
+
+# elif defined(_M_X64) || defined(_M_AMD64)
+#  define ARCHITECTURE_ID "x64"
+
+# elif defined(_M_IX86)
+#  define ARCHITECTURE_ID "X86"
+
+# elif defined(_M_ARM)
+#  define ARCHITECTURE_ID "ARM"
+
+# elif defined(_M_MIPS)
+#  define ARCHITECTURE_ID "MIPS"
+
+# elif defined(_M_SH)
+#  define ARCHITECTURE_ID "SHx"
+
+# else /* unknown architecture */
+#  define ARCHITECTURE_ID ""
+# endif
+
+#else
+#  define ARCHITECTURE_ID ""
+#endif
+
+/* Convert integer to decimal digit literals.  */
+#define DEC(n)                   \
+  ('0' + (((n) / 10000000)%10)), \
+  ('0' + (((n) / 1000000)%10)),  \
+  ('0' + (((n) / 100000)%10)),   \
+  ('0' + (((n) / 10000)%10)),    \
+  ('0' + (((n) / 1000)%10)),     \
+  ('0' + (((n) / 100)%10)),      \
+  ('0' + (((n) / 10)%10)),       \
+  ('0' +  ((n) % 10))
+
+/* Convert integer to hex digit literals.  */
+#define HEX(n)             \
+  ('0' + ((n)>>28 & 0xF)), \
+  ('0' + ((n)>>24 & 0xF)), \
+  ('0' + ((n)>>20 & 0xF)), \
+  ('0' + ((n)>>16 & 0xF)), \
+  ('0' + ((n)>>12 & 0xF)), \
+  ('0' + ((n)>>8  & 0xF)), \
+  ('0' + ((n)>>4  & 0xF)), \
+  ('0' + ((n)     & 0xF))
+
+/* Construct a string literal encoding the version number components. */
+#ifdef COMPILER_VERSION_MAJOR
+char const info_version[] = {
+  'I', 'N', 'F', 'O', ':',
+  'c','o','m','p','i','l','e','r','_','v','e','r','s','i','o','n','[',
+  COMPILER_VERSION_MAJOR,
+# ifdef COMPILER_VERSION_MINOR
+  '.', COMPILER_VERSION_MINOR,
+#  ifdef COMPILER_VERSION_PATCH
+   '.', COMPILER_VERSION_PATCH,
+#   ifdef COMPILER_VERSION_TWEAK
+    '.', COMPILER_VERSION_TWEAK,
+#   endif
+#  endif
+# endif
+  ']','\0'};
+#endif
+
+/* Construct the string literal in pieces to prevent the source from
+   getting matched.  Store it in a pointer rather than an array
+   because some compilers will just produce instructions to fill the
+   array rather than assigning a pointer to a static array.  */
+char const* info_platform = "INFO" ":" "platform[" PLATFORM_ID "]";
+char const* info_arch = "INFO" ":" "arch[" ARCHITECTURE_ID "]";
+
+
+
+/*--------------------------------------------------------------------------*/
+
+#ifdef ID_VOID_MAIN
+void main() {}
+#else
+int main(int argc, char* argv[])
+{
+  int require = 0;
+  require += info_compiler[argc];
+  require += info_platform[argc];
+  require += info_arch[argc];
+#ifdef COMPILER_VERSION_MAJOR
+  require += info_version[argc];
+#endif
+  (void)argv;
+  return require;
+}
+#endif

SciFiSim/CMakeFiles/2.8.12.2/CompilerIdCXX/CMakeCXXCompilerId.cpp

@@ -0,0 +1,377 @@
+/* This source file must have a .cpp extension so that all C++ compilers
+   recognize the extension without flags.  Borland does not know .cxx for
+   example.  */
+#ifndef __cplusplus
+# error "A C compiler has been selected for C++."
+#endif
+
+/* Version number components: V=Version, R=Revision, P=Patch
+   Version date components:   YYYY=Year, MM=Month,   DD=Day  */
+
+#if defined(__COMO__)
+# define COMPILER_ID "Comeau"
+  /* __COMO_VERSION__ = VRR */
+# define COMPILER_VERSION_MAJOR DEC(__COMO_VERSION__ / 100)
+# define COMPILER_VERSION_MINOR DEC(__COMO_VERSION__ % 100)
+
+#elif defined(__INTEL_COMPILER) || defined(__ICC)
+# define COMPILER_ID "Intel"
+  /* __INTEL_COMPILER = VRP */
+# define COMPILER_VERSION_MAJOR DEC(__INTEL_COMPILER/100)
+# define COMPILER_VERSION_MINOR DEC(__INTEL_COMPILER/10 % 10)
+# define COMPILER_VERSION_PATCH DEC(__INTEL_COMPILER    % 10)
+# if defined(__INTEL_COMPILER_BUILD_DATE)
+  /* __INTEL_COMPILER_BUILD_DATE = YYYYMMDD */
+#  define COMPILER_VERSION_TWEAK DEC(__INTEL_COMPILER_BUILD_DATE)
+# endif
+
+#elif defined(__PATHCC__)
+# define COMPILER_ID "PathScale"
+# define COMPILER_VERSION_MAJOR DEC(__PATHCC__)
+# define COMPILER_VERSION_MINOR DEC(__PATHCC_MINOR__)
+# if defined(__PATHCC_PATCHLEVEL__)
+#  define COMPILER_VERSION_PATCH DEC(__PATHCC_PATCHLEVEL__)
+# endif
+
+#elif defined(__clang__)
+# define COMPILER_ID "Clang"
+# define COMPILER_VERSION_MAJOR DEC(__clang_major__)
+# define COMPILER_VERSION_MINOR DEC(__clang_minor__)
+# define COMPILER_VERSION_PATCH DEC(__clang_patchlevel__)
+
+#elif defined(__BORLANDC__) && defined(__CODEGEARC_VERSION__)
+# define COMPILER_ID "Embarcadero"
+# define COMPILER_VERSION_MAJOR HEX(__CODEGEARC_VERSION__>>24 & 0x00FF)
+# define COMPILER_VERSION_MINOR HEX(__CODEGEARC_VERSION__>>16 & 0x00FF)
+# define COMPILER_VERSION_PATCH HEX(__CODEGEARC_VERSION__     & 0xFFFF)
+
+#elif defined(__BORLANDC__)
+# define COMPILER_ID "Borland"
+  /* __BORLANDC__ = 0xVRR */
+# define COMPILER_VERSION_MAJOR HEX(__BORLANDC__>>8)
+# define COMPILER_VERSION_MINOR HEX(__BORLANDC__ & 0xFF)
+
+#elif defined(__WATCOMC__)
+# define COMPILER_ID "Watcom"
+  /* __WATCOMC__ = VVRR */
+# define COMPILER_VERSION_MAJOR DEC(__WATCOMC__ / 100)
+# define COMPILER_VERSION_MINOR DEC(__WATCOMC__ % 100)
+
+#elif defined(__SUNPRO_CC)
+# define COMPILER_ID "SunPro"
+# if __SUNPRO_CC >= 0x5100
+   /* __SUNPRO_CC = 0xVRRP */
+#  define COMPILER_VERSION_MAJOR HEX(__SUNPRO_CC>>12)
+#  define COMPILER_VERSION_MINOR HEX(__SUNPRO_CC>>4 & 0xFF)
+#  define COMPILER_VERSION_PATCH HEX(__SUNPRO_CC    & 0xF)
+# else
+   /* __SUNPRO_CC = 0xVRP */
+#  define COMPILER_VERSION_MAJOR HEX(__SUNPRO_CC>>8)
+#  define COMPILER_VERSION_MINOR HEX(__SUNPRO_CC>>4 & 0xF)
+#  define COMPILER_VERSION_PATCH HEX(__SUNPRO_CC    & 0xF)
+# endif
+
+#elif defined(__HP_aCC)
+# define COMPILER_ID "HP"
+  /* __HP_aCC = VVRRPP */
+# define COMPILER_VERSION_MAJOR DEC(__HP_aCC/10000)
+# define COMPILER_VERSION_MINOR DEC(__HP_aCC/100 % 100)
+# define COMPILER_VERSION_PATCH DEC(__HP_aCC     % 100)
+
+#elif defined(__DECCXX)
+# define COMPILER_ID "Compaq"
+  /* __DECCXX_VER = VVRRTPPPP */
+# define COMPILER_VERSION_MAJOR DEC(__DECCXX_VER/10000000)
+# define COMPILER_VERSION_MINOR DEC(__DECCXX_VER/100000  % 100)
+# define COMPILER_VERSION_PATCH DEC(__DECCXX_VER         % 10000)
+
+#elif defined(__IBMCPP__)
+# if defined(__COMPILER_VER__)
+#  define COMPILER_ID "zOS"
+# else
+#  if __IBMCPP__ >= 800
+#   define COMPILER_ID "XL"
+#  else
+#   define COMPILER_ID "VisualAge"
+#  endif
+   /* __IBMCPP__ = VRP */
+#  define COMPILER_VERSION_MAJOR DEC(__IBMCPP__/100)
+#  define COMPILER_VERSION_MINOR DEC(__IBMCPP__/10 % 10)
+#  define COMPILER_VERSION_PATCH DEC(__IBMCPP__    % 10)
+# endif
+
+#elif defined(__PGI)
+# define COMPILER_ID "PGI"
+# define COMPILER_VERSION_MAJOR DEC(__PGIC__)
+# define COMPILER_VERSION_MINOR DEC(__PGIC_MINOR__)
+# if defined(__PGIC_PATCHLEVEL__)
+#  define COMPILER_VERSION_PATCH DEC(__PGIC_PATCHLEVEL__)
+# endif
+
+#elif defined(_CRAYC)
+# define COMPILER_ID "Cray"
+# define COMPILER_VERSION_MAJOR DEC(_RELEASE)
+# define COMPILER_VERSION_MINOR DEC(_RELEASE_MINOR)
+
+#elif defined(__TI_COMPILER_VERSION__)
+# define COMPILER_ID "TI"
+  /* __TI_COMPILER_VERSION__ = VVVRRRPPP */
+# define COMPILER_VERSION_MAJOR DEC(__TI_COMPILER_VERSION__/1000000)
+# define COMPILER_VERSION_MINOR DEC(__TI_COMPILER_VERSION__/1000   % 1000)
+# define COMPILER_VERSION_PATCH DEC(__TI_COMPILER_VERSION__        % 1000)
+
+#elif defined(__SCO_VERSION__)
+# define COMPILER_ID "SCO"
+
+#elif defined(__GNUC__)
+# define COMPILER_ID "GNU"
+# define COMPILER_VERSION_MAJOR DEC(__GNUC__)
+# define COMPILER_VERSION_MINOR DEC(__GNUC_MINOR__)
+# if defined(__GNUC_PATCHLEVEL__)
+#  define COMPILER_VERSION_PATCH DEC(__GNUC_PATCHLEVEL__)
+# endif
+
+#elif defined(_MSC_VER)
+# define COMPILER_ID "MSVC"
+  /* _MSC_VER = VVRR */
+# define COMPILER_VERSION_MAJOR DEC(_MSC_VER / 100)
+# define COMPILER_VERSION_MINOR DEC(_MSC_VER % 100)
+# if defined(_MSC_FULL_VER)
+#  if _MSC_VER >= 1400
+    /* _MSC_FULL_VER = VVRRPPPPP */
+#   define COMPILER_VERSION_PATCH DEC(_MSC_FULL_VER % 100000)
+#  else
+    /* _MSC_FULL_VER = VVRRPPPP */
+#   define COMPILER_VERSION_PATCH DEC(_MSC_FULL_VER % 10000)
+#  endif
+# endif
+# if defined(_MSC_BUILD)
+#  define COMPILER_VERSION_TWEAK DEC(_MSC_BUILD)
+# endif
+
+/* Analog VisualDSP++ >= 4.5.6 */
+#elif defined(__VISUALDSPVERSION__)
+# define COMPILER_ID "ADSP"
+  /* __VISUALDSPVERSION__ = 0xVVRRPP00 */
+# define COMPILER_VERSION_MAJOR HEX(__VISUALDSPVERSION__>>24)
+# define COMPILER_VERSION_MINOR HEX(__VISUALDSPVERSION__>>16 & 0xFF)
+# define COMPILER_VERSION_PATCH HEX(__VISUALDSPVERSION__>>8  & 0xFF)
+
+/* Analog VisualDSP++ < 4.5.6 */
+#elif defined(__ADSPBLACKFIN__) || defined(__ADSPTS__) || defined(__ADSP21000__)
+# define COMPILER_ID "ADSP"
+
+/* IAR Systems compiler for embedded systems.
+   http://www.iar.com */
+#elif defined(__IAR_SYSTEMS_ICC__ ) || defined(__IAR_SYSTEMS_ICC)
+# define COMPILER_ID "IAR"
+
+#elif defined(_SGI_COMPILER_VERSION) || defined(_COMPILER_VERSION)
+# define COMPILER_ID "MIPSpro"
+# if defined(_SGI_COMPILER_VERSION)
+  /* _SGI_COMPILER_VERSION = VRP */
+#  define COMPILER_VERSION_MAJOR DEC(_SGI_COMPILER_VERSION/100)
+#  define COMPILER_VERSION_MINOR DEC(_SGI_COMPILER_VERSION/10 % 10)
+#  define COMPILER_VERSION_PATCH DEC(_SGI_COMPILER_VERSION    % 10)
+# else
+  /* _COMPILER_VERSION = VRP */
+#  define COMPILER_VERSION_MAJOR DEC(_COMPILER_VERSION/100)
+#  define COMPILER_VERSION_MINOR DEC(_COMPILER_VERSION/10 % 10)
+#  define COMPILER_VERSION_PATCH DEC(_COMPILER_VERSION    % 10)
+# endif
+
+/* This compiler is either not known or is too old to define an
+   identification macro.  Try to identify the platform and guess that
+   it is the native compiler.  */
+#elif defined(__sgi)
+# define COMPILER_ID "MIPSpro"
+
+#elif defined(__hpux) || defined(__hpua)
+# define COMPILER_ID "HP"
+
+#else /* unknown compiler */
+# define COMPILER_ID ""
+
+#endif
+
+/* Construct the string literal in pieces to prevent the source from
+   getting matched.  Store it in a pointer rather than an array
+   because some compilers will just produce instructions to fill the
+   array rather than assigning a pointer to a static array.  */
+char const* info_compiler = "INFO" ":" "compiler[" COMPILER_ID "]";
+
+/* Identify known platforms by name.  */
+#if defined(__linux) || defined(__linux__) || defined(linux)
+# define PLATFORM_ID "Linux"
+
+#elif defined(__CYGWIN__)
+# define PLATFORM_ID "Cygwin"
+
+#elif defined(__MINGW32__)
+# define PLATFORM_ID "MinGW"
+
+#elif defined(__APPLE__)
+# define PLATFORM_ID "Darwin"
+
+#elif defined(_WIN32) || defined(__WIN32__) || defined(WIN32)
+# define PLATFORM_ID "Windows"
+
+#elif defined(__FreeBSD__) || defined(__FreeBSD)
+# define PLATFORM_ID "FreeBSD"
+
+#elif defined(__NetBSD__) || defined(__NetBSD)
+# define PLATFORM_ID "NetBSD"
+
+#elif defined(__OpenBSD__) || defined(__OPENBSD)
+# define PLATFORM_ID "OpenBSD"
+
+#elif defined(__sun) || defined(sun)
+# define PLATFORM_ID "SunOS"
+
+#elif defined(_AIX) || defined(__AIX) || defined(__AIX__) || defined(__aix) || defined(__aix__)
+# define PLATFORM_ID "AIX"
+
+#elif defined(__sgi) || defined(__sgi__) || defined(_SGI)
+# define PLATFORM_ID "IRIX"
+
+#elif defined(__hpux) || defined(__hpux__)
+# define PLATFORM_ID "HP-UX"
+
+#elif defined(__HAIKU__)
+# define PLATFORM_ID "Haiku"
+
+#elif defined(__BeOS) || defined(__BEOS__) || defined(_BEOS)
+# define PLATFORM_ID "BeOS"
+
+#elif defined(__QNX__) || defined(__QNXNTO__)
+# define PLATFORM_ID "QNX"
+
+#elif defined(__tru64) || defined(_tru64) || defined(__TRU64__)
+# define PLATFORM_ID "Tru64"
+
+#elif defined(__riscos) || defined(__riscos__)
+# define PLATFORM_ID "RISCos"
+
+#elif defined(__sinix) || defined(__sinix__) || defined(__SINIX__)
+# define PLATFORM_ID "SINIX"
+
+#elif defined(__UNIX_SV__)
+# define PLATFORM_ID "UNIX_SV"
+
+#elif defined(__bsdos__)
+# define PLATFORM_ID "BSDOS"
+
+#elif defined(_MPRAS) || defined(MPRAS)
+# define PLATFORM_ID "MP-RAS"
+
+#elif defined(__osf) || defined(__osf__)
+# define PLATFORM_ID "OSF1"
+
+#elif defined(_SCO_SV) || defined(SCO_SV) || defined(sco_sv)
+# define PLATFORM_ID "SCO_SV"
+
+#elif defined(__ultrix) || defined(__ultrix__) || defined(_ULTRIX)
+# define PLATFORM_ID "ULTRIX"
+
+#elif defined(__XENIX__) || defined(_XENIX) || defined(XENIX)
+# define PLATFORM_ID "Xenix"
+
+#else /* unknown platform */
+# define PLATFORM_ID ""
+
+#endif
+
+/* For windows compilers MSVC and Intel we can determine
+   the architecture of the compiler being used.  This is because
+   the compilers do not have flags that can change the architecture,
+   but rather depend on which compiler is being used
+*/
+#if defined(_WIN32) && defined(_MSC_VER)
+# if defined(_M_IA64)
+#  define ARCHITECTURE_ID "IA64"
+
+# elif defined(_M_X64) || defined(_M_AMD64)
+#  define ARCHITECTURE_ID "x64"
+
+# elif defined(_M_IX86)
+#  define ARCHITECTURE_ID "X86"
+
+# elif defined(_M_ARM)
+#  define ARCHITECTURE_ID "ARM"
+
+# elif defined(_M_MIPS)
+#  define ARCHITECTURE_ID "MIPS"
+
+# elif defined(_M_SH)
+#  define ARCHITECTURE_ID "SHx"
+
+# else /* unknown architecture */
+#  define ARCHITECTURE_ID ""
+# endif
+
+#else
+#  define ARCHITECTURE_ID ""
+#endif
+
+/* Convert integer to decimal digit literals.  */
+#define DEC(n)                   \
+  ('0' + (((n) / 10000000)%10)), \
+  ('0' + (((n) / 1000000)%10)),  \
+  ('0' + (((n) / 100000)%10)),   \
+  ('0' + (((n) / 10000)%10)),    \
+  ('0' + (((n) / 1000)%10)),     \
+  ('0' + (((n) / 100)%10)),      \
+  ('0' + (((n) / 10)%10)),       \
+  ('0' +  ((n) % 10))
+
+/* Convert integer to hex digit literals.  */
+#define HEX(n)             \
+  ('0' + ((n)>>28 & 0xF)), \
+  ('0' + ((n)>>24 & 0xF)), \
+  ('0' + ((n)>>20 & 0xF)), \
+  ('0' + ((n)>>16 & 0xF)), \
+  ('0' + ((n)>>12 & 0xF)), \
+  ('0' + ((n)>>8  & 0xF)), \
+  ('0' + ((n)>>4  & 0xF)), \
+  ('0' + ((n)     & 0xF))
+
+/* Construct a string literal encoding the version number components. */
+#ifdef COMPILER_VERSION_MAJOR
+char const info_version[] = {
+  'I', 'N', 'F', 'O', ':',
+  'c','o','m','p','i','l','e','r','_','v','e','r','s','i','o','n','[',
+  COMPILER_VERSION_MAJOR,
+# ifdef COMPILER_VERSION_MINOR
+  '.', COMPILER_VERSION_MINOR,
+#  ifdef COMPILER_VERSION_PATCH
+   '.', COMPILER_VERSION_PATCH,
+#   ifdef COMPILER_VERSION_TWEAK
+    '.', COMPILER_VERSION_TWEAK,
+#   endif
+#  endif
+# endif
+  ']','\0'};
+#endif
+
+/* Construct the string literal in pieces to prevent the source from
+   getting matched.  Store it in a pointer rather than an array
+   because some compilers will just produce instructions to fill the
+   array rather than assigning a pointer to a static array.  */
+char const* info_platform = "INFO" ":" "platform[" PLATFORM_ID "]";
+char const* info_arch = "INFO" ":" "arch[" ARCHITECTURE_ID "]";
+
+
+
+/*--------------------------------------------------------------------------*/
+
+int main(int argc, char* argv[])
+{
+  int require = 0;
+  require += info_compiler[argc];
+  require += info_platform[argc];
+#ifdef COMPILER_VERSION_MAJOR
+  require += info_version[argc];
+#endif
+  (void)argv;
+  return require;
+}

SciFiSim/CMakeFiles/3.3.2/CMakeCCompiler.cmake

@@ -0,0 +1,63 @@
+set(CMAKE_C_COMPILER "/usr/bin/cc")
+set(CMAKE_C_COMPILER_ARG1 "")
+set(CMAKE_C_COMPILER_ID "GNU")
+set(CMAKE_C_COMPILER_VERSION "4.8.1")
+set(CMAKE_C_COMPILE_FEATURES "c_function_prototypes;c_restrict;c_variadic_macros;c_static_assert")
+set(CMAKE_C90_COMPILE_FEATURES "c_function_prototypes")
+set(CMAKE_C99_COMPILE_FEATURES "c_restrict;c_variadic_macros")
+set(CMAKE_C11_COMPILE_FEATURES "c_static_assert")
+
+set(CMAKE_C_PLATFORM_ID "Linux")
+set(CMAKE_C_SIMULATE_ID "")
+set(CMAKE_C_SIMULATE_VERSION "")
+
+set(CMAKE_AR "/usr/bin/ar")
+set(CMAKE_RANLIB "/usr/bin/ranlib")
+set(CMAKE_LINKER "/usr/bin/ld")
+set(CMAKE_COMPILER_IS_GNUCC 1)
+set(CMAKE_C_COMPILER_LOADED 1)
+set(CMAKE_C_COMPILER_WORKS TRUE)
+set(CMAKE_C_ABI_COMPILED TRUE)
+set(CMAKE_COMPILER_IS_MINGW )
+set(CMAKE_COMPILER_IS_CYGWIN )
+if(CMAKE_COMPILER_IS_CYGWIN)
+  set(CYGWIN 1)
+  set(UNIX 1)
+endif()
+
+set(CMAKE_C_COMPILER_ENV_VAR "CC")
+
+if(CMAKE_COMPILER_IS_MINGW)
+  set(MINGW 1)
+endif()
+set(CMAKE_C_COMPILER_ID_RUN 1)
+set(CMAKE_C_SOURCE_FILE_EXTENSIONS c;m)
+set(CMAKE_C_IGNORE_EXTENSIONS h;H;o;O;obj;OBJ;def;DEF;rc;RC)
+set(CMAKE_C_LINKER_PREFERENCE 10)
+
+# Save compiler ABI information.
+set(CMAKE_C_SIZEOF_DATA_PTR "8")
+set(CMAKE_C_COMPILER_ABI "ELF")
+set(CMAKE_C_LIBRARY_ARCHITECTURE "x86_64-linux-gnu")
+
+if(CMAKE_C_SIZEOF_DATA_PTR)
+  set(CMAKE_SIZEOF_VOID_P "${CMAKE_C_SIZEOF_DATA_PTR}")
+endif()
+
+if(CMAKE_C_COMPILER_ABI)
+  set(CMAKE_INTERNAL_PLATFORM_ABI "${CMAKE_C_COMPILER_ABI}")
+endif()
+
+if(CMAKE_C_LIBRARY_ARCHITECTURE)
+  set(CMAKE_LIBRARY_ARCHITECTURE "x86_64-linux-gnu")
+endif()
+
+
+
+
+set(CMAKE_C_IMPLICIT_LINK_LIBRARIES "c")
+set(CMAKE_C_IMPLICIT_LINK_DIRECTORIES "/usr/lib/gcc/x86_64-linux-gnu/4.8;/usr/lib/x86_64-linux-gnu;/usr/lib;/lib/x86_64-linux-gnu;/lib")
+set(CMAKE_C_IMPLICIT_LINK_FRAMEWORK_DIRECTORIES "")
+
+
+

SciFiSim/CMakeFiles/3.3.2/CMakeCXXCompiler.cmake

@@ -0,0 +1,64 @@
+set(CMAKE_CXX_COMPILER "/usr/bin/c++")
+set(CMAKE_CXX_COMPILER_ARG1 "")
+set(CMAKE_CXX_COMPILER_ID "GNU")
+set(CMAKE_CXX_COMPILER_VERSION "4.8.1")
+set(CMAKE_CXX_COMPILE_FEATURES "cxx_template_template_parameters;cxx_alias_templates;cxx_alignas;cxx_alignof;cxx_attributes;cxx_auto_type;cxx_constexpr;cxx_decltype;cxx_decltype_incomplete_return_types;cxx_default_function_template_args;cxx_defaulted_functions;cxx_defaulted_move_initializers;cxx_delegating_constructors;cxx_deleted_functions;cxx_enum_forward_declarations;cxx_explicit_conversions;cxx_extended_friend_declarations;cxx_extern_templates;cxx_final;cxx_func_identifier;cxx_generalized_initializers;cxx_inheriting_constructors;cxx_inline_namespaces;cxx_lambdas;cxx_local_type_template_args;cxx_long_long_type;cxx_noexcept;cxx_nonstatic_member_init;cxx_nullptr;cxx_override;cxx_range_for;cxx_raw_string_literals;cxx_reference_qualified_functions;cxx_right_angle_brackets;cxx_rvalue_references;cxx_sizeof_member;cxx_static_assert;cxx_strong_enums;cxx_thread_local;cxx_trailing_return_types;cxx_unicode_literals;cxx_uniform_initialization;cxx_unrestricted_unions;cxx_user_literals;cxx_variadic_macros;cxx_variadic_templates")
+set(CMAKE_CXX98_COMPILE_FEATURES "cxx_template_template_parameters")
+set(CMAKE_CXX11_COMPILE_FEATURES "cxx_alias_templates;cxx_alignas;cxx_alignof;cxx_attributes;cxx_auto_type;cxx_constexpr;cxx_decltype;cxx_decltype_incomplete_return_types;cxx_default_function_template_args;cxx_defaulted_functions;cxx_defaulted_move_initializers;cxx_delegating_constructors;cxx_deleted_functions;cxx_enum_forward_declarations;cxx_explicit_conversions;cxx_extended_friend_declarations;cxx_extern_templates;cxx_final;cxx_func_identifier;cxx_generalized_initializers;cxx_inheriting_constructors;cxx_inline_namespaces;cxx_lambdas;cxx_local_type_template_args;cxx_long_long_type;cxx_noexcept;cxx_nonstatic_member_init;cxx_nullptr;cxx_override;cxx_range_for;cxx_raw_string_literals;cxx_reference_qualified_functions;cxx_right_angle_brackets;cxx_rvalue_references;cxx_sizeof_member;cxx_static_assert;cxx_strong_enums;cxx_thread_local;cxx_trailing_return_types;cxx_unicode_literals;cxx_uniform_initialization;cxx_unrestricted_unions;cxx_user_literals;cxx_variadic_macros;cxx_variadic_templates")
+set(CMAKE_CXX14_COMPILE_FEATURES "")
+
+set(CMAKE_CXX_PLATFORM_ID "Linux")
+set(CMAKE_CXX_SIMULATE_ID "")
+set(CMAKE_CXX_SIMULATE_VERSION "")
+
+set(CMAKE_AR "/usr/bin/ar")
+set(CMAKE_RANLIB "/usr/bin/ranlib")
+set(CMAKE_LINKER "/usr/bin/ld")
+set(CMAKE_COMPILER_IS_GNUCXX 1)
+set(CMAKE_CXX_COMPILER_LOADED 1)
+set(CMAKE_CXX_COMPILER_WORKS TRUE)
+set(CMAKE_CXX_ABI_COMPILED TRUE)
+set(CMAKE_COMPILER_IS_MINGW )
+set(CMAKE_COMPILER_IS_CYGWIN )
+if(CMAKE_COMPILER_IS_CYGWIN)
+  set(CYGWIN 1)
+  set(UNIX 1)
+endif()
+
+set(CMAKE_CXX_COMPILER_ENV_VAR "CXX")
+
+if(CMAKE_COMPILER_IS_MINGW)
+  set(MINGW 1)
+endif()
+set(CMAKE_CXX_COMPILER_ID_RUN 1)
+set(CMAKE_CXX_IGNORE_EXTENSIONS inl;h;hpp;HPP;H;o;O;obj;OBJ;def;DEF;rc;RC)
+set(CMAKE_CXX_SOURCE_FILE_EXTENSIONS C;M;c++;cc;cpp;cxx;mm;CPP)
+set(CMAKE_CXX_LINKER_PREFERENCE 30)
+set(CMAKE_CXX_LINKER_PREFERENCE_PROPAGATES 1)
+
+# Save compiler ABI information.
+set(CMAKE_CXX_SIZEOF_DATA_PTR "8")
+set(CMAKE_CXX_COMPILER_ABI "ELF")
+set(CMAKE_CXX_LIBRARY_ARCHITECTURE "x86_64-linux-gnu")
+
+if(CMAKE_CXX_SIZEOF_DATA_PTR)
+  set(CMAKE_SIZEOF_VOID_P "${CMAKE_CXX_SIZEOF_DATA_PTR}")
+endif()
+
+if(CMAKE_CXX_COMPILER_ABI)
+  set(CMAKE_INTERNAL_PLATFORM_ABI "${CMAKE_CXX_COMPILER_ABI}")
+endif()
+
+if(CMAKE_CXX_LIBRARY_ARCHITECTURE)
+  set(CMAKE_LIBRARY_ARCHITECTURE "x86_64-linux-gnu")
+endif()
+
+
+
+
+set(CMAKE_CXX_IMPLICIT_LINK_LIBRARIES "stdc++;m;c")
+set(CMAKE_CXX_IMPLICIT_LINK_DIRECTORIES "/usr/lib/gcc/x86_64-linux-gnu/4.8;/usr/lib/x86_64-linux-gnu;/usr/lib;/lib/x86_64-linux-gnu;/lib")
+set(CMAKE_CXX_IMPLICIT_LINK_FRAMEWORK_DIRECTORIES "")
+
+
+

SciFiSim/CMakeFiles/3.3.2/CMakeSystem.cmake

@@ -0,0 +1,15 @@
+set(CMAKE_HOST_SYSTEM "Linux-3.2.0-96-generic")
+set(CMAKE_HOST_SYSTEM_NAME "Linux")
+set(CMAKE_HOST_SYSTEM_VERSION "3.2.0-96-generic")
+set(CMAKE_HOST_SYSTEM_PROCESSOR "x86_64")
+
+
+
+set(CMAKE_SYSTEM "Linux-3.2.0-96-generic")
+set(CMAKE_SYSTEM_NAME "Linux")
+set(CMAKE_SYSTEM_VERSION "3.2.0-96-generic")
+set(CMAKE_SYSTEM_PROCESSOR "x86_64")
+
+set(CMAKE_CROSSCOMPILING "FALSE")
+
+set(CMAKE_SYSTEM_LOADED 1)

SciFiSim/CMakeFiles/3.3.2/CompilerIdC/CMakeCCompilerId.c

@@ -0,0 +1,508 @@
+#ifdef __cplusplus
+# error "A C++ compiler has been selected for C."
+#endif
+
+#if defined(__18CXX)
+# define ID_VOID_MAIN
+#endif
+
+
+/* Version number components: V=Version, R=Revision, P=Patch
+   Version date components:   YYYY=Year, MM=Month,   DD=Day  */
+
+#if defined(__INTEL_COMPILER) || defined(__ICC)
+# define COMPILER_ID "Intel"
+# if defined(_MSC_VER)
+#  define SIMULATE_ID "MSVC"
+# endif
+  /* __INTEL_COMPILER = VRP */
+# define COMPILER_VERSION_MAJOR DEC(__INTEL_COMPILER/100)
+# define COMPILER_VERSION_MINOR DEC(__INTEL_COMPILER/10 % 10)
+# if defined(__INTEL_COMPILER_UPDATE)
+#  define COMPILER_VERSION_PATCH DEC(__INTEL_COMPILER_UPDATE)
+# else
+#  define COMPILER_VERSION_PATCH DEC(__INTEL_COMPILER   % 10)
+# endif
+# if defined(__INTEL_COMPILER_BUILD_DATE)
+  /* __INTEL_COMPILER_BUILD_DATE = YYYYMMDD */
+#  define COMPILER_VERSION_TWEAK DEC(__INTEL_COMPILER_BUILD_DATE)
+# endif
+# if defined(_MSC_VER)
+   /* _MSC_VER = VVRR */
+#  define SIMULATE_VERSION_MAJOR DEC(_MSC_VER / 100)
+#  define SIMULATE_VERSION_MINOR DEC(_MSC_VER % 100)
+# endif
+
+#elif defined(__PATHCC__)
+# define COMPILER_ID "PathScale"
+# define COMPILER_VERSION_MAJOR DEC(__PATHCC__)
+# define COMPILER_VERSION_MINOR DEC(__PATHCC_MINOR__)
+# if defined(__PATHCC_PATCHLEVEL__)
+#  define COMPILER_VERSION_PATCH DEC(__PATHCC_PATCHLEVEL__)
+# endif
+
+#elif defined(__BORLANDC__) && defined(__CODEGEARC_VERSION__)
+# define COMPILER_ID "Embarcadero"
+# define COMPILER_VERSION_MAJOR HEX(__CODEGEARC_VERSION__>>24 & 0x00FF)
+# define COMPILER_VERSION_MINOR HEX(__CODEGEARC_VERSION__>>16 & 0x00FF)
+# define COMPILER_VERSION_PATCH HEX(__CODEGEARC_VERSION__     & 0xFFFF)
+
+#elif defined(__BORLANDC__)
+# define COMPILER_ID "Borland"
+  /* __BORLANDC__ = 0xVRR */
+# define COMPILER_VERSION_MAJOR HEX(__BORLANDC__>>8)
+# define COMPILER_VERSION_MINOR HEX(__BORLANDC__ & 0xFF)
+
+#elif defined(__WATCOMC__) && __WATCOMC__ < 1200
+# define COMPILER_ID "Watcom"
+   /* __WATCOMC__ = VVRR */
+# define COMPILER_VERSION_MAJOR DEC(__WATCOMC__ / 100)
+# define COMPILER_VERSION_MINOR DEC((__WATCOMC__ / 10) % 10)
+# if (__WATCOMC__ % 10) > 0
+#  define COMPILER_VERSION_PATCH DEC(__WATCOMC__ % 10)
+# endif
+
+#elif defined(__WATCOMC__)
+# define COMPILER_ID "OpenWatcom"
+   /* __WATCOMC__ = VVRP + 1100 */
+# define COMPILER_VERSION_MAJOR DEC((__WATCOMC__ - 1100) / 100)
+# define COMPILER_VERSION_MINOR DEC((__WATCOMC__ / 10) % 10)
+# if (__WATCOMC__ % 10) > 0
+#  define COMPILER_VERSION_PATCH DEC(__WATCOMC__ % 10)
+# endif
+
+#elif defined(__SUNPRO_C)
+# define COMPILER_ID "SunPro"
+# if __SUNPRO_C >= 0x5100
+   /* __SUNPRO_C = 0xVRRP */
+#  define COMPILER_VERSION_MAJOR HEX(__SUNPRO_C>>12)
+#  define COMPILER_VERSION_MINOR HEX(__SUNPRO_C>>4 & 0xFF)
+#  define COMPILER_VERSION_PATCH HEX(__SUNPRO_C    & 0xF)
+# else
+   /* __SUNPRO_CC = 0xVRP */
+#  define COMPILER_VERSION_MAJOR HEX(__SUNPRO_C>>8)
+#  define COMPILER_VERSION_MINOR HEX(__SUNPRO_C>>4 & 0xF)
+#  define COMPILER_VERSION_PATCH HEX(__SUNPRO_C    & 0xF)
+# endif
+
+#elif defined(__HP_cc)
+# define COMPILER_ID "HP"
+  /* __HP_cc = VVRRPP */
+# define COMPILER_VERSION_MAJOR DEC(__HP_cc/10000)
+# define COMPILER_VERSION_MINOR DEC(__HP_cc/100 % 100)
+# define COMPILER_VERSION_PATCH DEC(__HP_cc     % 100)
+
+#elif defined(__DECC)
+# define COMPILER_ID "Compaq"
+  /* __DECC_VER = VVRRTPPPP */
+# define COMPILER_VERSION_MAJOR DEC(__DECC_VER/10000000)
+# define COMPILER_VERSION_MINOR DEC(__DECC_VER/100000  % 100)
+# define COMPILER_VERSION_PATCH DEC(__DECC_VER         % 10000)
+
+#elif defined(__IBMC__) && defined(__COMPILER_VER__)
+# define COMPILER_ID "zOS"
+  /* __IBMC__ = VRP */
+# define COMPILER_VERSION_MAJOR DEC(__IBMC__/100)
+# define COMPILER_VERSION_MINOR DEC(__IBMC__/10 % 10)
+# define COMPILER_VERSION_PATCH DEC(__IBMC__    % 10)
+
+#elif defined(__IBMC__) && !defined(__COMPILER_VER__) && __IBMC__ >= 800
+# define COMPILER_ID "XL"
+  /* __IBMC__ = VRP */
+# define COMPILER_VERSION_MAJOR DEC(__IBMC__/100)
+# define COMPILER_VERSION_MINOR DEC(__IBMC__/10 % 10)
+# define COMPILER_VERSION_PATCH DEC(__IBMC__    % 10)
+
+#elif defined(__IBMC__) && !defined(__COMPILER_VER__) && __IBMC__ < 800
+# define COMPILER_ID "VisualAge"
+  /* __IBMC__ = VRP */
+# define COMPILER_VERSION_MAJOR DEC(__IBMC__/100)
+# define COMPILER_VERSION_MINOR DEC(__IBMC__/10 % 10)
+# define COMPILER_VERSION_PATCH DEC(__IBMC__    % 10)
+
+#elif defined(__PGI)
+# define COMPILER_ID "PGI"
+# define COMPILER_VERSION_MAJOR DEC(__PGIC__)
+# define COMPILER_VERSION_MINOR DEC(__PGIC_MINOR__)
+# if defined(__PGIC_PATCHLEVEL__)
+#  define COMPILER_VERSION_PATCH DEC(__PGIC_PATCHLEVEL__)
+# endif
+
+#elif defined(_CRAYC)
+# define COMPILER_ID "Cray"
+# define COMPILER_VERSION_MAJOR DEC(_RELEASE)
+# define COMPILER_VERSION_MINOR DEC(_RELEASE_MINOR)
+
+#elif defined(__TI_COMPILER_VERSION__)
+# define COMPILER_ID "TI"
+  /* __TI_COMPILER_VERSION__ = VVVRRRPPP */
+# define COMPILER_VERSION_MAJOR DEC(__TI_COMPILER_VERSION__/1000000)
+# define COMPILER_VERSION_MINOR DEC(__TI_COMPILER_VERSION__/1000   % 1000)
+# define COMPILER_VERSION_PATCH DEC(__TI_COMPILER_VERSION__        % 1000)
+
+#elif defined(__FUJITSU) || defined(__FCC_VERSION) || defined(__fcc_version)
+# define COMPILER_ID "Fujitsu"
+
+#elif defined(__TINYC__)
+# define COMPILER_ID "TinyCC"
+
+#elif defined(__SCO_VERSION__)
+# define COMPILER_ID "SCO"
+
+#elif defined(__clang__) && defined(__apple_build_version__)
+# define COMPILER_ID "AppleClang"
+# if defined(_MSC_VER)
+#  define SIMULATE_ID "MSVC"
+# endif
+# define COMPILER_VERSION_MAJOR DEC(__clang_major__)
+# define COMPILER_VERSION_MINOR DEC(__clang_minor__)
+# define COMPILER_VERSION_PATCH DEC(__clang_patchlevel__)
+# if defined(_MSC_VER)
+   /* _MSC_VER = VVRR */
+#  define SIMULATE_VERSION_MAJOR DEC(_MSC_VER / 100)
+#  define SIMULATE_VERSION_MINOR DEC(_MSC_VER % 100)
+# endif
+# define COMPILER_VERSION_TWEAK DEC(__apple_build_version__)
+
+#elif defined(__clang__)
+# define COMPILER_ID "Clang"
+# if defined(_MSC_VER)
+#  define SIMULATE_ID "MSVC"
+# endif
+# define COMPILER_VERSION_MAJOR DEC(__clang_major__)
+# define COMPILER_VERSION_MINOR DEC(__clang_minor__)
+# define COMPILER_VERSION_PATCH DEC(__clang_patchlevel__)
+# if defined(_MSC_VER)
+   /* _MSC_VER = VVRR */
+#  define SIMULATE_VERSION_MAJOR DEC(_MSC_VER / 100)
+#  define SIMULATE_VERSION_MINOR DEC(_MSC_VER % 100)
+# endif
+
+#elif defined(__GNUC__)
+# define COMPILER_ID "GNU"
+# define COMPILER_VERSION_MAJOR DEC(__GNUC__)
+# define COMPILER_VERSION_MINOR DEC(__GNUC_MINOR__)
+# if defined(__GNUC_PATCHLEVEL__)
+#  define COMPILER_VERSION_PATCH DEC(__GNUC_PATCHLEVEL__)
+# endif
+
+#elif defined(_MSC_VER)
+# define COMPILER_ID "MSVC"
+  /* _MSC_VER = VVRR */
+# define COMPILER_VERSION_MAJOR DEC(_MSC_VER / 100)
+# define COMPILER_VERSION_MINOR DEC(_MSC_VER % 100)
+# if defined(_MSC_FULL_VER)
+#  if _MSC_VER >= 1400
+    /* _MSC_FULL_VER = VVRRPPPPP */
+#   define COMPILER_VERSION_PATCH DEC(_MSC_FULL_VER % 100000)
+#  else
+    /* _MSC_FULL_VER = VVRRPPPP */
+#   define COMPILER_VERSION_PATCH DEC(_MSC_FULL_VER % 10000)
+#  endif
+# endif
+# if defined(_MSC_BUILD)
+#  define COMPILER_VERSION_TWEAK DEC(_MSC_BUILD)
+# endif
+
+#elif defined(__VISUALDSPVERSION__) || defined(__ADSPBLACKFIN__) || defined(__ADSPTS__) || defined(__ADSP21000__)
+# define COMPILER_ID "ADSP"
+#if defined(__VISUALDSPVERSION__)
+  /* __VISUALDSPVERSION__ = 0xVVRRPP00 */
+# define COMPILER_VERSION_MAJOR HEX(__VISUALDSPVERSION__>>24)
+# define COMPILER_VERSION_MINOR HEX(__VISUALDSPVERSION__>>16 & 0xFF)
+# define COMPILER_VERSION_PATCH HEX(__VISUALDSPVERSION__>>8  & 0xFF)
+#endif
+
+#elif defined(__IAR_SYSTEMS_ICC__ ) || defined(__IAR_SYSTEMS_ICC)
+# define COMPILER_ID "IAR"
+
+#elif defined(SDCC)
+# define COMPILER_ID "SDCC"
+  /* SDCC = VRP */
+#  define COMPILER_VERSION_MAJOR DEC(SDCC/100)
+#  define COMPILER_VERSION_MINOR DEC(SDCC/10 % 10)
+#  define COMPILER_VERSION_PATCH DEC(SDCC    % 10)
+
+#elif defined(_SGI_COMPILER_VERSION) || defined(_COMPILER_VERSION)
+# define COMPILER_ID "MIPSpro"
+# if defined(_SGI_COMPILER_VERSION)
+  /* _SGI_COMPILER_VERSION = VRP */
+#  define COMPILER_VERSION_MAJOR DEC(_SGI_COMPILER_VERSION/100)
+#  define COMPILER_VERSION_MINOR DEC(_SGI_COMPILER_VERSION/10 % 10)
+#  define COMPILER_VERSION_PATCH DEC(_SGI_COMPILER_VERSION    % 10)
+# else
+  /* _COMPILER_VERSION = VRP */
+#  define COMPILER_VERSION_MAJOR DEC(_COMPILER_VERSION/100)
+#  define COMPILER_VERSION_MINOR DEC(_COMPILER_VERSION/10 % 10)
+#  define COMPILER_VERSION_PATCH DEC(_COMPILER_VERSION    % 10)
+# endif
+
+
+/* These compilers are either not known or too old to define an
+  identification macro.  Try to identify the platform and guess that
+  it is the native compiler.  */
+#elif defined(__sgi)
+# define COMPILER_ID "MIPSpro"
+
+#elif defined(__hpux) || defined(__hpua)
+# define COMPILER_ID "HP"
+
+#else /* unknown compiler */
+# define COMPILER_ID ""
+#endif
+
+/* Construct the string literal in pieces to prevent the source from
+   getting matched.  Store it in a pointer rather than an array
+   because some compilers will just produce instructions to fill the
+   array rather than assigning a pointer to a static array.  */
+char const* info_compiler = "INFO" ":" "compiler[" COMPILER_ID "]";
+#ifdef SIMULATE_ID
+char const* info_simulate = "INFO" ":" "simulate[" SIMULATE_ID "]";
+#endif
+
+#ifdef __QNXNTO__
+char const* qnxnto = "INFO" ":" "qnxnto[]";
+#endif
+
+#define STRINGIFY_HELPER(X) #X
+#define STRINGIFY(X) STRINGIFY_HELPER(X)
+
+/* Identify known platforms by name.  */
+#if defined(__linux) || defined(__linux__) || defined(linux)
+# define PLATFORM_ID "Linux"
+
+#elif defined(__CYGWIN__)
+# define PLATFORM_ID "Cygwin"
+
+#elif defined(__MINGW32__)
+# define PLATFORM_ID "MinGW"
+
+#elif defined(__APPLE__)
+# define PLATFORM_ID "Darwin"
+
+#elif defined(_WIN32) || defined(__WIN32__) || defined(WIN32)
+# define PLATFORM_ID "Windows"
+
+#elif defined(__FreeBSD__) || defined(__FreeBSD)
+# define PLATFORM_ID "FreeBSD"
+
+#elif defined(__NetBSD__) || defined(__NetBSD)
+# define PLATFORM_ID "NetBSD"
+
+#elif defined(__OpenBSD__) || defined(__OPENBSD)
+# define PLATFORM_ID "OpenBSD"
+
+#elif defined(__sun) || defined(sun)
+# define PLATFORM_ID "SunOS"
+
+#elif defined(_AIX) || defined(__AIX) || defined(__AIX__) || defined(__aix) || defined(__aix__)
+# define PLATFORM_ID "AIX"
+
+#elif defined(__sgi) || defined(__sgi__) || defined(_SGI)
+# define PLATFORM_ID "IRIX"
+
+#elif defined(__hpux) || defined(__hpux__)
+# define PLATFORM_ID "HP-UX"
+
+#elif defined(__HAIKU__)
+# define PLATFORM_ID "Haiku"
+
+#elif defined(__BeOS) || defined(__BEOS__) || defined(_BEOS)
+# define PLATFORM_ID "BeOS"
+
+#elif defined(__QNX__) || defined(__QNXNTO__)
+# define PLATFORM_ID "QNX"
+
+#elif defined(__tru64) || defined(_tru64) || defined(__TRU64__)
+# define PLATFORM_ID "Tru64"
+
+#elif defined(__riscos) || defined(__riscos__)
+# define PLATFORM_ID "RISCos"
+
+#elif defined(__sinix) || defined(__sinix__) || defined(__SINIX__)
+# define PLATFORM_ID "SINIX"
+
+#elif defined(__UNIX_SV__)
+# define PLATFORM_ID "UNIX_SV"
+
+#elif defined(__bsdos__)
+# define PLATFORM_ID "BSDOS"
+
+#elif defined(_MPRAS) || defined(MPRAS)
+# define PLATFORM_ID "MP-RAS"
+
+#elif defined(__osf) || defined(__osf__)
+# define PLATFORM_ID "OSF1"
+
+#elif defined(_SCO_SV) || defined(SCO_SV) || defined(sco_sv)
+# define PLATFORM_ID "SCO_SV"
+
+#elif defined(__ultrix) || defined(__ultrix__) || defined(_ULTRIX)
+# define PLATFORM_ID "ULTRIX"
+
+#elif defined(__XENIX__) || defined(_XENIX) || defined(XENIX)
+# define PLATFORM_ID "Xenix"
+
+#elif defined(__WATCOMC__)
+# if defined(__LINUX__)
+#  define PLATFORM_ID "Linux"
+
+# elif defined(__DOS__)
+#  define PLATFORM_ID "DOS"
+
+# elif defined(__OS2__)
+#  define PLATFORM_ID "OS2"
+
+# elif defined(__WINDOWS__)
+#  define PLATFORM_ID "Windows3x"
+
+# else /* unknown platform */
+#  define PLATFORM_ID ""
+# endif
+
+#else /* unknown platform */
+# define PLATFORM_ID ""
+
+#endif
+
+/* For windows compilers MSVC and Intel we can determine
+   the architecture of the compiler being used.  This is because
+   the compilers do not have flags that can change the architecture,
+   but rather depend on which compiler is being used
+*/
+#if defined(_WIN32) && defined(_MSC_VER)
+# if defined(_M_IA64)
+#  define ARCHITECTURE_ID "IA64"
+
+# elif defined(_M_X64) || defined(_M_AMD64)
+#  define ARCHITECTURE_ID "x64"
+
+# elif defined(_M_IX86)
+#  define ARCHITECTURE_ID "X86"
+
+# elif defined(_M_ARM)
+#  if _M_ARM == 4
+#   define ARCHITECTURE_ID "ARMV4I"
+#  elif _M_ARM == 5
+#   define ARCHITECTURE_ID "ARMV5I"
+#  else
+#   define ARCHITECTURE_ID "ARMV" STRINGIFY(_M_ARM)
+#  endif
+
+# elif defined(_M_MIPS)
+#  define ARCHITECTURE_ID "MIPS"
+
+# elif defined(_M_SH)
+#  define ARCHITECTURE_ID "SHx"
+
+# else /* unknown architecture */
+#  define ARCHITECTURE_ID ""
+# endif
+
+#elif defined(__WATCOMC__)
+# if defined(_M_I86)
+#  define ARCHITECTURE_ID "I86"
+
+# elif defined(_M_IX86)
+#  define ARCHITECTURE_ID "X86"
+
+# else /* unknown architecture */
+#  define ARCHITECTURE_ID ""
+# endif
+
+#else
+#  define ARCHITECTURE_ID ""
+#endif
+
+/* Convert integer to decimal digit literals.  */
+#define DEC(n)                   \
+  ('0' + (((n) / 10000000)%10)), \
+  ('0' + (((n) / 1000000)%10)),  \
+  ('0' + (((n) / 100000)%10)),   \
+  ('0' + (((n) / 10000)%10)),    \
+  ('0' + (((n) / 1000)%10)),     \
+  ('0' + (((n) / 100)%10)),      \
+  ('0' + (((n) / 10)%10)),       \
+  ('0' +  ((n) % 10))
+
+/* Convert integer to hex digit literals.  */
+#define HEX(n)             \
+  ('0' + ((n)>>28 & 0xF)), \
+  ('0' + ((n)>>24 & 0xF)), \
+  ('0' + ((n)>>20 & 0xF)), \
+  ('0' + ((n)>>16 & 0xF)), \
+  ('0' + ((n)>>12 & 0xF)), \
+  ('0' + ((n)>>8  & 0xF)), \
+  ('0' + ((n)>>4  & 0xF)), \
+  ('0' + ((n)     & 0xF))
+
+/* Construct a string literal encoding the version number components. */
+#ifdef COMPILER_VERSION_MAJOR
+char const info_version[] = {
+  'I', 'N', 'F', 'O', ':',
+  'c','o','m','p','i','l','e','r','_','v','e','r','s','i','o','n','[',
+  COMPILER_VERSION_MAJOR,
+# ifdef COMPILER_VERSION_MINOR
+  '.', COMPILER_VERSION_MINOR,
+#  ifdef COMPILER_VERSION_PATCH
+   '.', COMPILER_VERSION_PATCH,
+#   ifdef COMPILER_VERSION_TWEAK
+    '.', COMPILER_VERSION_TWEAK,
+#   endif
+#  endif
+# endif
+  ']','\0'};
+#endif
+
+/* Construct a string literal encoding the version number components. */
+#ifdef SIMULATE_VERSION_MAJOR
+char const info_simulate_version[] = {
+  'I', 'N', 'F', 'O', ':',
+  's','i','m','u','l','a','t','e','_','v','e','r','s','i','o','n','[',
+  SIMULATE_VERSION_MAJOR,
+# ifdef SIMULATE_VERSION_MINOR
+  '.', SIMULATE_VERSION_MINOR,
+#  ifdef SIMULATE_VERSION_PATCH
+   '.', SIMULATE_VERSION_PATCH,
+#   ifdef SIMULATE_VERSION_TWEAK
+    '.', SIMULATE_VERSION_TWEAK,
+#   endif
+#  endif
+# endif
+  ']','\0'};
+#endif
+
+/* Construct the string literal in pieces to prevent the source from
+   getting matched.  Store it in a pointer rather than an array
+   because some compilers will just produce instructions to fill the
+   array rather than assigning a pointer to a static array.  */
+char const* info_platform = "INFO" ":" "platform[" PLATFORM_ID "]";
+char const* info_arch = "INFO" ":" "arch[" ARCHITECTURE_ID "]";
+
+
+
+
+/*--------------------------------------------------------------------------*/
+
+#ifdef ID_VOID_MAIN
+void main() {}
+#else
+int main(int argc, char* argv[])
+{
+  int require = 0;
+  require += info_compiler[argc];
+  require += info_platform[argc];
+  require += info_arch[argc];
+#ifdef COMPILER_VERSION_MAJOR
+  require += info_version[argc];
+#endif
+#ifdef SIMULATE_ID
+  require += info_simulate[argc];
+#endif
+#ifdef SIMULATE_VERSION_MAJOR
+  require += info_simulate_version[argc];
+#endif
+  (void)argv;
+  return require;
+}
+#endif

SciFiSim/CMakeFiles/3.3.2/CompilerIdCXX/CMakeCXXCompilerId.cpp

@@ -0,0 +1,498 @@
+/* This source file must have a .cpp extension so that all C++ compilers
+   recognize the extension without flags.  Borland does not know .cxx for
+   example.  */
+#ifndef __cplusplus
+# error "A C compiler has been selected for C++."
+#endif
+
+
+/* Version number components: V=Version, R=Revision, P=Patch
+   Version date components:   YYYY=Year, MM=Month,   DD=Day  */
+
+#if defined(__COMO__)
+# define COMPILER_ID "Comeau"
+  /* __COMO_VERSION__ = VRR */
+# define COMPILER_VERSION_MAJOR DEC(__COMO_VERSION__ / 100)
+# define COMPILER_VERSION_MINOR DEC(__COMO_VERSION__ % 100)
+
+#elif defined(__INTEL_COMPILER) || defined(__ICC)
+# define COMPILER_ID "Intel"
+# if defined(_MSC_VER)
+#  define SIMULATE_ID "MSVC"
+# endif
+  /* __INTEL_COMPILER = VRP */
+# define COMPILER_VERSION_MAJOR DEC(__INTEL_COMPILER/100)
+# define COMPILER_VERSION_MINOR DEC(__INTEL_COMPILER/10 % 10)
+# if defined(__INTEL_COMPILER_UPDATE)
+#  define COMPILER_VERSION_PATCH DEC(__INTEL_COMPILER_UPDATE)
+# else
+#  define COMPILER_VERSION_PATCH DEC(__INTEL_COMPILER   % 10)
+# endif
+# if defined(__INTEL_COMPILER_BUILD_DATE)
+  /* __INTEL_COMPILER_BUILD_DATE = YYYYMMDD */
+#  define COMPILER_VERSION_TWEAK DEC(__INTEL_COMPILER_BUILD_DATE)
+# endif
+# if defined(_MSC_VER)
+   /* _MSC_VER = VVRR */
+#  define SIMULATE_VERSION_MAJOR DEC(_MSC_VER / 100)
+#  define SIMULATE_VERSION_MINOR DEC(_MSC_VER % 100)
+# endif
+
+#elif defined(__PATHCC__)
+# define COMPILER_ID "PathScale"
+# define COMPILER_VERSION_MAJOR DEC(__PATHCC__)
+# define COMPILER_VERSION_MINOR DEC(__PATHCC_MINOR__)
+# if defined(__PATHCC_PATCHLEVEL__)
+#  define COMPILER_VERSION_PATCH DEC(__PATHCC_PATCHLEVEL__)
+# endif
+
+#elif defined(__BORLANDC__) && defined(__CODEGEARC_VERSION__)
+# define COMPILER_ID "Embarcadero"
+# define COMPILER_VERSION_MAJOR HEX(__CODEGEARC_VERSION__>>24 & 0x00FF)
+# define COMPILER_VERSION_MINOR HEX(__CODEGEARC_VERSION__>>16 & 0x00FF)
+# define COMPILER_VERSION_PATCH HEX(__CODEGEARC_VERSION__     & 0xFFFF)
+
+#elif defined(__BORLANDC__)
+# define COMPILER_ID "Borland"
+  /* __BORLANDC__ = 0xVRR */
+# define COMPILER_VERSION_MAJOR HEX(__BORLANDC__>>8)
+# define COMPILER_VERSION_MINOR HEX(__BORLANDC__ & 0xFF)
+
+#elif defined(__WATCOMC__) && __WATCOMC__ < 1200
+# define COMPILER_ID "Watcom"
+   /* __WATCOMC__ = VVRR */
+# define COMPILER_VERSION_MAJOR DEC(__WATCOMC__ / 100)
+# define COMPILER_VERSION_MINOR DEC((__WATCOMC__ / 10) % 10)
+# if (__WATCOMC__ % 10) > 0
+#  define COMPILER_VERSION_PATCH DEC(__WATCOMC__ % 10)
+# endif
+
+#elif defined(__WATCOMC__)
+# define COMPILER_ID "OpenWatcom"
+   /* __WATCOMC__ = VVRP + 1100 */
+# define COMPILER_VERSION_MAJOR DEC((__WATCOMC__ - 1100) / 100)
+# define COMPILER_VERSION_MINOR DEC((__WATCOMC__ / 10) % 10)
+# if (__WATCOMC__ % 10) > 0
+#  define COMPILER_VERSION_PATCH DEC(__WATCOMC__ % 10)
+# endif
+
+#elif defined(__SUNPRO_CC)
+# define COMPILER_ID "SunPro"
+# if __SUNPRO_CC >= 0x5100
+   /* __SUNPRO_CC = 0xVRRP */
+#  define COMPILER_VERSION_MAJOR HEX(__SUNPRO_CC>>12)
+#  define COMPILER_VERSION_MINOR HEX(__SUNPRO_CC>>4 & 0xFF)
+#  define COMPILER_VERSION_PATCH HEX(__SUNPRO_CC    & 0xF)
+# else
+   /* __SUNPRO_CC = 0xVRP */
+#  define COMPILER_VERSION_MAJOR HEX(__SUNPRO_CC>>8)
+#  define COMPILER_VERSION_MINOR HEX(__SUNPRO_CC>>4 & 0xF)
+#  define COMPILER_VERSION_PATCH HEX(__SUNPRO_CC    & 0xF)
+# endif
+
+#elif defined(__HP_aCC)
+# define COMPILER_ID "HP"
+  /* __HP_aCC = VVRRPP */
+# define COMPILER_VERSION_MAJOR DEC(__HP_aCC/10000)
+# define COMPILER_VERSION_MINOR DEC(__HP_aCC/100 % 100)
+# define COMPILER_VERSION_PATCH DEC(__HP_aCC     % 100)
+
+#elif defined(__DECCXX)
+# define COMPILER_ID "Compaq"
+  /* __DECCXX_VER = VVRRTPPPP */
+# define COMPILER_VERSION_MAJOR DEC(__DECCXX_VER/10000000)
+# define COMPILER_VERSION_MINOR DEC(__DECCXX_VER/100000  % 100)
+# define COMPILER_VERSION_PATCH DEC(__DECCXX_VER         % 10000)
+
+#elif defined(__IBMCPP__) && defined(__COMPILER_VER__)
+# define COMPILER_ID "zOS"
+  /* __IBMCPP__ = VRP */
+# define COMPILER_VERSION_MAJOR DEC(__IBMCPP__/100)
+# define COMPILER_VERSION_MINOR DEC(__IBMCPP__/10 % 10)
+# define COMPILER_VERSION_PATCH DEC(__IBMCPP__    % 10)
+
+#elif defined(__IBMCPP__) && !defined(__COMPILER_VER__) && __IBMCPP__ >= 800
+# define COMPILER_ID "XL"
+  /* __IBMCPP__ = VRP */
+# define COMPILER_VERSION_MAJOR DEC(__IBMCPP__/100)
+# define COMPILER_VERSION_MINOR DEC(__IBMCPP__/10 % 10)
+# define COMPILER_VERSION_PATCH DEC(__IBMCPP__    % 10)
+
+#elif defined(__IBMCPP__) && !defined(__COMPILER_VER__) && __IBMCPP__ < 800
+# define COMPILER_ID "VisualAge"
+  /* __IBMCPP__ = VRP */
+# define COMPILER_VERSION_MAJOR DEC(__IBMCPP__/100)
+# define COMPILER_VERSION_MINOR DEC(__IBMCPP__/10 % 10)
+# define COMPILER_VERSION_PATCH DEC(__IBMCPP__    % 10)
+
+#elif defined(__PGI)
+# define COMPILER_ID "PGI"
+# define COMPILER_VERSION_MAJOR DEC(__PGIC__)
+# define COMPILER_VERSION_MINOR DEC(__PGIC_MINOR__)
+# if defined(__PGIC_PATCHLEVEL__)
+#  define COMPILER_VERSION_PATCH DEC(__PGIC_PATCHLEVEL__)
+# endif
+
+#elif defined(_CRAYC)
+# define COMPILER_ID "Cray"
+# define COMPILER_VERSION_MAJOR DEC(_RELEASE)
+# define COMPILER_VERSION_MINOR DEC(_RELEASE_MINOR)
+
+#elif defined(__TI_COMPILER_VERSION__)
+# define COMPILER_ID "TI"
+  /* __TI_COMPILER_VERSION__ = VVVRRRPPP */
+# define COMPILER_VERSION_MAJOR DEC(__TI_COMPILER_VERSION__/1000000)
+# define COMPILER_VERSION_MINOR DEC(__TI_COMPILER_VERSION__/1000   % 1000)
+# define COMPILER_VERSION_PATCH DEC(__TI_COMPILER_VERSION__        % 1000)
+
+#elif defined(__FUJITSU) || defined(__FCC_VERSION) || defined(__fcc_version)
+# define COMPILER_ID "Fujitsu"
+
+#elif defined(__SCO_VERSION__)
+# define COMPILER_ID "SCO"
+
+#elif defined(__clang__) && defined(__apple_build_version__)
+# define COMPILER_ID "AppleClang"
+# if defined(_MSC_VER)
+#  define SIMULATE_ID "MSVC"
+# endif
+# define COMPILER_VERSION_MAJOR DEC(__clang_major__)
+# define COMPILER_VERSION_MINOR DEC(__clang_minor__)
+# define COMPILER_VERSION_PATCH DEC(__clang_patchlevel__)
+# if defined(_MSC_VER)
+   /* _MSC_VER = VVRR */
+#  define SIMULATE_VERSION_MAJOR DEC(_MSC_VER / 100)
+#  define SIMULATE_VERSION_MINOR DEC(_MSC_VER % 100)
+# endif
+# define COMPILER_VERSION_TWEAK DEC(__apple_build_version__)
+
+#elif defined(__clang__)
+# define COMPILER_ID "Clang"
+# if defined(_MSC_VER)
+#  define SIMULATE_ID "MSVC"
+# endif
+# define COMPILER_VERSION_MAJOR DEC(__clang_major__)
+# define COMPILER_VERSION_MINOR DEC(__clang_minor__)
+# define COMPILER_VERSION_PATCH DEC(__clang_patchlevel__)
+# if defined(_MSC_VER)
+   /* _MSC_VER = VVRR */
+#  define SIMULATE_VERSION_MAJOR DEC(_MSC_VER / 100)
+#  define SIMULATE_VERSION_MINOR DEC(_MSC_VER % 100)
+# endif
+
+#elif defined(__GNUC__)
+# define COMPILER_ID "GNU"
+# define COMPILER_VERSION_MAJOR DEC(__GNUC__)
+# define COMPILER_VERSION_MINOR DEC(__GNUC_MINOR__)
+# if defined(__GNUC_PATCHLEVEL__)
+#  define COMPILER_VERSION_PATCH DEC(__GNUC_PATCHLEVEL__)
+# endif
+
+#elif defined(_MSC_VER)
+# define COMPILER_ID "MSVC"
+  /* _MSC_VER = VVRR */
+# define COMPILER_VERSION_MAJOR DEC(_MSC_VER / 100)
+# define COMPILER_VERSION_MINOR DEC(_MSC_VER % 100)
+# if defined(_MSC_FULL_VER)
+#  if _MSC_VER >= 1400
+    /* _MSC_FULL_VER = VVRRPPPPP */
+#   define COMPILER_VERSION_PATCH DEC(_MSC_FULL_VER % 100000)
+#  else
+    /* _MSC_FULL_VER = VVRRPPPP */
+#   define COMPILER_VERSION_PATCH DEC(_MSC_FULL_VER % 10000)
+#  endif
+# endif
+# if defined(_MSC_BUILD)
+#  define COMPILER_VERSION_TWEAK DEC(_MSC_BUILD)
+# endif
+
+#elif defined(__VISUALDSPVERSION__) || defined(__ADSPBLACKFIN__) || defined(__ADSPTS__) || defined(__ADSP21000__)
+# define COMPILER_ID "ADSP"
+#if defined(__VISUALDSPVERSION__)
+  /* __VISUALDSPVERSION__ = 0xVVRRPP00 */
+# define COMPILER_VERSION_MAJOR HEX(__VISUALDSPVERSION__>>24)
+# define COMPILER_VERSION_MINOR HEX(__VISUALDSPVERSION__>>16 & 0xFF)
+# define COMPILER_VERSION_PATCH HEX(__VISUALDSPVERSION__>>8  & 0xFF)
+#endif
+
+#elif defined(__IAR_SYSTEMS_ICC__ ) || defined(__IAR_SYSTEMS_ICC)
+# define COMPILER_ID "IAR"
+
+#elif defined(_SGI_COMPILER_VERSION) || defined(_COMPILER_VERSION)
+# define COMPILER_ID "MIPSpro"
+# if defined(_SGI_COMPILER_VERSION)
+  /* _SGI_COMPILER_VERSION = VRP */
+#  define COMPILER_VERSION_MAJOR DEC(_SGI_COMPILER_VERSION/100)
+#  define COMPILER_VERSION_MINOR DEC(_SGI_COMPILER_VERSION/10 % 10)
+#  define COMPILER_VERSION_PATCH DEC(_SGI_COMPILER_VERSION    % 10)
+# else
+  /* _COMPILER_VERSION = VRP */
+#  define COMPILER_VERSION_MAJOR DEC(_COMPILER_VERSION/100)
+#  define COMPILER_VERSION_MINOR DEC(_COMPILER_VERSION/10 % 10)
+#  define COMPILER_VERSION_PATCH DEC(_COMPILER_VERSION    % 10)
+# endif
+
+
+/* These compilers are either not known or too old to define an
+  identification macro.  Try to identify the platform and guess that
+  it is the native compiler.  */
+#elif defined(__sgi)
+# define COMPILER_ID "MIPSpro"
+
+#elif defined(__hpux) || defined(__hpua)
+# define COMPILER_ID "HP"
+
+#else /* unknown compiler */
+# define COMPILER_ID ""
+#endif
+
+/* Construct the string literal in pieces to prevent the source from
+   getting matched.  Store it in a pointer rather than an array
+   because some compilers will just produce instructions to fill the
+   array rather than assigning a pointer to a static array.  */
+char const* info_compiler = "INFO" ":" "compiler[" COMPILER_ID "]";
+#ifdef SIMULATE_ID
+char const* info_simulate = "INFO" ":" "simulate[" SIMULATE_ID "]";
+#endif
+
+#ifdef __QNXNTO__
+char const* qnxnto = "INFO" ":" "qnxnto[]";
+#endif
+
+#define STRINGIFY_HELPER(X) #X
+#define STRINGIFY(X) STRINGIFY_HELPER(X)
+
+/* Identify known platforms by name.  */
+#if defined(__linux) || defined(__linux__) || defined(linux)
+# define PLATFORM_ID "Linux"
+
+#elif defined(__CYGWIN__)
+# define PLATFORM_ID "Cygwin"
+
+#elif defined(__MINGW32__)
+# define PLATFORM_ID "MinGW"
+
+#elif defined(__APPLE__)
+# define PLATFORM_ID "Darwin"
+
+#elif defined(_WIN32) || defined(__WIN32__) || defined(WIN32)
+# define PLATFORM_ID "Windows"
+
+#elif defined(__FreeBSD__) || defined(__FreeBSD)
+# define PLATFORM_ID "FreeBSD"
+
+#elif defined(__NetBSD__) || defined(__NetBSD)
+# define PLATFORM_ID "NetBSD"
+
+#elif defined(__OpenBSD__) || defined(__OPENBSD)
+# define PLATFORM_ID "OpenBSD"
+
+#elif defined(__sun) || defined(sun)
+# define PLATFORM_ID "SunOS"
+
+#elif defined(_AIX) || defined(__AIX) || defined(__AIX__) || defined(__aix) || defined(__aix__)
+# define PLATFORM_ID "AIX"
+
+#elif defined(__sgi) || defined(__sgi__) || defined(_SGI)
+# define PLATFORM_ID "IRIX"
+
+#elif defined(__hpux) || defined(__hpux__)
+# define PLATFORM_ID "HP-UX"
+
+#elif defined(__HAIKU__)
+# define PLATFORM_ID "Haiku"
+
+#elif defined(__BeOS) || defined(__BEOS__) || defined(_BEOS)
+# define PLATFORM_ID "BeOS"
+
+#elif defined(__QNX__) || defined(__QNXNTO__)
+# define PLATFORM_ID "QNX"
+
+#elif defined(__tru64) || defined(_tru64) || defined(__TRU64__)
+# define PLATFORM_ID "Tru64"
+
+#elif defined(__riscos) || defined(__riscos__)
+# define PLATFORM_ID "RISCos"
+
+#elif defined(__sinix) || defined(__sinix__) || defined(__SINIX__)
+# define PLATFORM_ID "SINIX"
+
+#elif defined(__UNIX_SV__)
+# define PLATFORM_ID "UNIX_SV"
+
+#elif defined(__bsdos__)
+# define PLATFORM_ID "BSDOS"
+
+#elif defined(_MPRAS) || defined(MPRAS)
+# define PLATFORM_ID "MP-RAS"
+
+#elif defined(__osf) || defined(__osf__)
+# define PLATFORM_ID "OSF1"
+
+#elif defined(_SCO_SV) || defined(SCO_SV) || defined(sco_sv)
+# define PLATFORM_ID "SCO_SV"
+
+#elif defined(__ultrix) || defined(__ultrix__) || defined(_ULTRIX)
+# define PLATFORM_ID "ULTRIX"
+
+#elif defined(__XENIX__) || defined(_XENIX) || defined(XENIX)
+# define PLATFORM_ID "Xenix"
+
+#elif defined(__WATCOMC__)
+# if defined(__LINUX__)
+#  define PLATFORM_ID "Linux"
+
+# elif defined(__DOS__)
+#  define PLATFORM_ID "DOS"
+
+# elif defined(__OS2__)
+#  define PLATFORM_ID "OS2"
+
+# elif defined(__WINDOWS__)
+#  define PLATFORM_ID "Windows3x"
+
+# else /* unknown platform */
+#  define PLATFORM_ID ""
+# endif
+
+#else /* unknown platform */
+# define PLATFORM_ID ""
+
+#endif
+
+/* For windows compilers MSVC and Intel we can determine
+   the architecture of the compiler being used.  This is because
+   the compilers do not have flags that can change the architecture,
+   but rather depend on which compiler is being used
+*/
+#if defined(_WIN32) && defined(_MSC_VER)
+# if defined(_M_IA64)
+#  define ARCHITECTURE_ID "IA64"
+
+# elif defined(_M_X64) || defined(_M_AMD64)
+#  define ARCHITECTURE_ID "x64"
+
+# elif defined(_M_IX86)
+#  define ARCHITECTURE_ID "X86"
+
+# elif defined(_M_ARM)
+#  if _M_ARM == 4
+#   define ARCHITECTURE_ID "ARMV4I"
+#  elif _M_ARM == 5
+#   define ARCHITECTURE_ID "ARMV5I"
+#  else
+#   define ARCHITECTURE_ID "ARMV" STRINGIFY(_M_ARM)
+#  endif
+
+# elif defined(_M_MIPS)
+#  define ARCHITECTURE_ID "MIPS"
+
+# elif defined(_M_SH)
+#  define ARCHITECTURE_ID "SHx"
+
+# else /* unknown architecture */
+#  define ARCHITECTURE_ID ""
+# endif
+
+#elif defined(__WATCOMC__)
+# if defined(_M_I86)
+#  define ARCHITECTURE_ID "I86"
+
+# elif defined(_M_IX86)
+#  define ARCHITECTURE_ID "X86"
+
+# else /* unknown architecture */
+#  define ARCHITECTURE_ID ""
+# endif
+
+#else
+#  define ARCHITECTURE_ID ""
+#endif
+
+/* Convert integer to decimal digit literals.  */
+#define DEC(n)                   \
+  ('0' + (((n) / 10000000)%10)), \
+  ('0' + (((n) / 1000000)%10)),  \
+  ('0' + (((n) / 100000)%10)),   \
+  ('0' + (((n) / 10000)%10)),    \
+  ('0' + (((n) / 1000)%10)),     \
+  ('0' + (((n) / 100)%10)),      \
+  ('0' + (((n) / 10)%10)),       \
+  ('0' +  ((n) % 10))
+
+/* Convert integer to hex digit literals.  */
+#define HEX(n)             \
+  ('0' + ((n)>>28 & 0xF)), \
+  ('0' + ((n)>>24 & 0xF)), \
+  ('0' + ((n)>>20 & 0xF)), \
+  ('0' + ((n)>>16 & 0xF)), \
+  ('0' + ((n)>>12 & 0xF)), \
+  ('0' + ((n)>>8  & 0xF)), \
+  ('0' + ((n)>>4  & 0xF)), \
+  ('0' + ((n)     & 0xF))
+
+/* Construct a string literal encoding the version number components. */
+#ifdef COMPILER_VERSION_MAJOR
+char const info_version[] = {
+  'I', 'N', 'F', 'O', ':',
+  'c','o','m','p','i','l','e','r','_','v','e','r','s','i','o','n','[',
+  COMPILER_VERSION_MAJOR,
+# ifdef COMPILER_VERSION_MINOR
+  '.', COMPILER_VERSION_MINOR,
+#  ifdef COMPILER_VERSION_PATCH
+   '.', COMPILER_VERSION_PATCH,
+#   ifdef COMPILER_VERSION_TWEAK
+    '.', COMPILER_VERSION_TWEAK,
+#   endif
+#  endif
+# endif
+  ']','\0'};
+#endif
+
+/* Construct a string literal encoding the version number components. */
+#ifdef SIMULATE_VERSION_MAJOR
+char const info_simulate_version[] = {
+  'I', 'N', 'F', 'O', ':',
+  's','i','m','u','l','a','t','e','_','v','e','r','s','i','o','n','[',
+  SIMULATE_VERSION_MAJOR,
+# ifdef SIMULATE_VERSION_MINOR
+  '.', SIMULATE_VERSION_MINOR,
+#  ifdef SIMULATE_VERSION_PATCH
+   '.', SIMULATE_VERSION_PATCH,
+#   ifdef SIMULATE_VERSION_TWEAK
+    '.', SIMULATE_VERSION_TWEAK,
+#   endif
+#  endif
+# endif
+  ']','\0'};
+#endif
+
+/* Construct the string literal in pieces to prevent the source from
+   getting matched.  Store it in a pointer rather than an array
+   because some compilers will just produce instructions to fill the
+   array rather than assigning a pointer to a static array.  */
+char const* info_platform = "INFO" ":" "platform[" PLATFORM_ID "]";
+char const* info_arch = "INFO" ":" "arch[" ARCHITECTURE_ID "]";
+
+
+
+
+/*--------------------------------------------------------------------------*/
+
+int main(int argc, char* argv[])
+{
+  int require = 0;
+  require += info_compiler[argc];
+  require += info_platform[argc];
+#ifdef COMPILER_VERSION_MAJOR
+  require += info_version[argc];
+#endif
+#ifdef SIMULATE_ID
+  require += info_simulate[argc];
+#endif
+#ifdef SIMULATE_VERSION_MAJOR
+  require += info_simulate_version[argc];
+#endif
+  (void)argv;
+  return require;
+}

SciFiSim/CMakeFiles/CMakeOutput.log

@@ -0,0 +1,777 @@
+The system is: Linux - 3.2.0-40-generic - x86_64
+Compiling the C compiler identification source file "CMakeCCompilerId.c" succeeded.
+Compiler: /usr/bin/cc 
+Build flags: 
+Id flags: 
+
+The output was:
+0
+
+
+Compilation of the C compiler identification source "CMakeCCompilerId.c" produced "a.out"
+
+The C compiler identification is GNU, found in "/work/leverington/SciFiMatG4/SciFiSim/CMakeFiles/2.8.12.2/CompilerIdC/a.out"
+
+Compiling the CXX compiler identification source file "CMakeCXXCompilerId.cpp" succeeded.
+Compiler: /usr/bin/c++ 
+Build flags: 
+Id flags: 
+
+The output was:
+0
+
+
+Compilation of the CXX compiler identification source "CMakeCXXCompilerId.cpp" produced "a.out"
+
+The CXX compiler identification is GNU, found in "/work/leverington/SciFiMatG4/SciFiSim/CMakeFiles/2.8.12.2/CompilerIdCXX/a.out"
+
+Determining if the C compiler works passed with the following output:
+Change Dir: /work/leverington/SciFiMatG4/SciFiSim/CMakeFiles/CMakeTmp
+
+Run Build Command:/usr/bin/gmake "cmTryCompileExec3512762732/fast"
+/usr/bin/gmake -f CMakeFiles/cmTryCompileExec3512762732.dir/build.make CMakeFiles/cmTryCompileExec3512762732.dir/build
+gmake[1]: Entering directory `/auto/sigma0/leverington/SciFiMatG4/SciFiSim/CMakeFiles/CMakeTmp'
+/usr/bin/cmake -E cmake_progress_report /work/leverington/SciFiMatG4/SciFiSim/CMakeFiles/CMakeTmp/CMakeFiles 1
+Building C object CMakeFiles/cmTryCompileExec3512762732.dir/testCCompiler.c.o
+/usr/bin/cc    -o CMakeFiles/cmTryCompileExec3512762732.dir/testCCompiler.c.o   -c /work/leverington/SciFiMatG4/SciFiSim/CMakeFiles/CMakeTmp/testCCompiler.c
+Linking C executable cmTryCompileExec3512762732
+/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec3512762732.dir/link.txt --verbose=1
+/usr/bin/cc       CMakeFiles/cmTryCompileExec3512762732.dir/testCCompiler.c.o  -o cmTryCompileExec3512762732 -rdynamic 
+gmake[1]: Leaving directory `/auto/sigma0/leverington/SciFiMatG4/SciFiSim/CMakeFiles/CMakeTmp'
+
+
+Detecting C compiler ABI info compiled with the following output:
+Change Dir: /work/leverington/SciFiMatG4/SciFiSim/CMakeFiles/CMakeTmp
+
+Run Build Command:/usr/bin/gmake "cmTryCompileExec2437466663/fast"
+/usr/bin/gmake -f CMakeFiles/cmTryCompileExec2437466663.dir/build.make CMakeFiles/cmTryCompileExec2437466663.dir/build
+gmake[1]: Entering directory `/auto/sigma0/leverington/SciFiMatG4/SciFiSim/CMakeFiles/CMakeTmp'
+/usr/bin/cmake -E cmake_progress_report /work/leverington/SciFiMatG4/SciFiSim/CMakeFiles/CMakeTmp/CMakeFiles 1
+Building C object CMakeFiles/cmTryCompileExec2437466663.dir/CMakeCCompilerABI.c.o
+/usr/bin/cc    -o CMakeFiles/cmTryCompileExec2437466663.dir/CMakeCCompilerABI.c.o   -c /usr/share/cmake/Modules/CMakeCCompilerABI.c
+Linking C executable cmTryCompileExec2437466663
+/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec2437466663.dir/link.txt --verbose=1
+/usr/bin/cc     -v CMakeFiles/cmTryCompileExec2437466663.dir/CMakeCCompilerABI.c.o  -o cmTryCompileExec2437466663 -rdynamic  
+Using built-in specs.
+Target: x86_64-redhat-linux
+Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
+Thread model: posix
+gcc version 4.4.7 20120313 (Red Hat 4.4.7-11) (GCC) 
+COMPILER_PATH=/local/lcg/releases/LCGCMT/LCGCMT_76root6/LCG_Settings/../../../LCG_76root6/gcc/4.8.1/x86_64-slc6/lib/gcc/x86_64-unknown-linux-gnu/4.8.1/:/usr/libexec/gcc/x86_64-redhat-linux/4.4.7/:/usr/libexec/gcc/x86_64-redhat-linux/4.4.7/:/usr/libexec/gcc/x86_64-redhat-linux/:/usr/lib/gcc/x86_64-redhat-linux/4.4.7/:/usr/lib/gcc/x86_64-redhat-linux/:/usr/libexec/gcc/x86_64-redhat-linux/4.4.7/:/usr/libexec/gcc/x86_64-redhat-linux/:/usr/lib/gcc/x86_64-redhat-linux/4.4.7/:/usr/lib/gcc/x86_64-redhat-linux/
+LIBRARY_PATH=/usr/lib/gcc/x86_64-redhat-linux/4.4.7/:/usr/lib/gcc/x86_64-redhat-linux/4.4.7/:/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/:/lib/../lib64/:/usr/lib/../lib64/:/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../:/lib/:/usr/lib/
+COLLECT_GCC_OPTIONS='-v' '-o' 'cmTryCompileExec2437466663' '-rdynamic' '-mtune=generic'
+ /usr/libexec/gcc/x86_64-redhat-linux/4.4.7/collect2 --eh-frame-hdr --build-id -m elf_x86_64 --hash-style=gnu -export-dynamic -dynamic-linker /lib64/ld-linux-x86-64.so.2 -o cmTryCompileExec2437466663 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtbegin.o -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.. CMakeFiles/cmTryCompileExec2437466663.dir/CMakeCCompilerABI.c.o -lgcc --as-needed -lgcc_s --no-as-needed -lc -lgcc --as-needed -lgcc_s --no-as-needed /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtend.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crtn.o
+gmake[1]: Leaving directory `/auto/sigma0/leverington/SciFiMatG4/SciFiSim/CMakeFiles/CMakeTmp'
+
+
+Parsed C implicit link information from above output:
+  link line regex: [^( *|.*[/\])(ld|([^/\]+-)?ld|collect2)[^/\]*( |$)]
+  ignore line: [Change Dir: /work/leverington/SciFiMatG4/SciFiSim/CMakeFiles/CMakeTmp]
+  ignore line: []
+  ignore line: [Run Build Command:/usr/bin/gmake "cmTryCompileExec2437466663/fast"]
+  ignore line: [/usr/bin/gmake -f CMakeFiles/cmTryCompileExec2437466663.dir/build.make CMakeFiles/cmTryCompileExec2437466663.dir/build]
+  ignore line: [gmake[1]: Entering directory `/auto/sigma0/leverington/SciFiMatG4/SciFiSim/CMakeFiles/CMakeTmp']
+  ignore line: [/usr/bin/cmake -E cmake_progress_report /work/leverington/SciFiMatG4/SciFiSim/CMakeFiles/CMakeTmp/CMakeFiles 1]
+  ignore line: [Building C object CMakeFiles/cmTryCompileExec2437466663.dir/CMakeCCompilerABI.c.o]
+  ignore line: [/usr/bin/cc    -o CMakeFiles/cmTryCompileExec2437466663.dir/CMakeCCompilerABI.c.o   -c /usr/share/cmake/Modules/CMakeCCompilerABI.c]
+  ignore line: [Linking C executable cmTryCompileExec2437466663]
+  ignore line: [/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec2437466663.dir/link.txt --verbose=1]
+  ignore line: [/usr/bin/cc     -v CMakeFiles/cmTryCompileExec2437466663.dir/CMakeCCompilerABI.c.o  -o cmTryCompileExec2437466663 -rdynamic  ]
+  ignore line: [Using built-in specs.]
+  ignore line: [Target: x86_64-redhat-linux]
+  ignore line: [Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux]
+  ignore line: [Thread model: posix]
+  ignore line: [gcc version 4.4.7 20120313 (Red Hat 4.4.7-11) (GCC) ]
+  ignore line: [COMPILER_PATH=/local/lcg/releases/LCGCMT/LCGCMT_76root6/LCG_Settings/../../../LCG_76root6/gcc/4.8.1/x86_64-slc6/lib/gcc/x86_64-unknown-linux-gnu/4.8.1/:/usr/libexec/gcc/x86_64-redhat-linux/4.4.7/:/usr/libexec/gcc/x86_64-redhat-linux/4.4.7/:/usr/libexec/gcc/x86_64-redhat-linux/:/usr/lib/gcc/x86_64-redhat-linux/4.4.7/:/usr/lib/gcc/x86_64-redhat-linux/:/usr/libexec/gcc/x86_64-redhat-linux/4.4.7/:/usr/libexec/gcc/x86_64-redhat-linux/:/usr/lib/gcc/x86_64-redhat-linux/4.4.7/:/usr/lib/gcc/x86_64-redhat-linux/]
+  ignore line: [LIBRARY_PATH=/usr/lib/gcc/x86_64-redhat-linux/4.4.7/:/usr/lib/gcc/x86_64-redhat-linux/4.4.7/:/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/:/lib/../lib64/:/usr/lib/../lib64/:/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../:/lib/:/usr/lib/]
+  ignore line: [COLLECT_GCC_OPTIONS='-v' '-o' 'cmTryCompileExec2437466663' '-rdynamic' '-mtune=generic']
+  link line: [ /usr/libexec/gcc/x86_64-redhat-linux/4.4.7/collect2 --eh-frame-hdr --build-id -m elf_x86_64 --hash-style=gnu -export-dynamic -dynamic-linker /lib64/ld-linux-x86-64.so.2 -o cmTryCompileExec2437466663 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtbegin.o -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.. CMakeFiles/cmTryCompileExec2437466663.dir/CMakeCCompilerABI.c.o -lgcc --as-needed -lgcc_s --no-as-needed -lc -lgcc --as-needed -lgcc_s --no-as-needed /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtend.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crtn.o]
+    arg [/usr/libexec/gcc/x86_64-redhat-linux/4.4.7/collect2] ==> ignore
+    arg [--eh-frame-hdr] ==> ignore
+    arg [--build-id] ==> ignore
+    arg [-m] ==> ignore
+    arg [elf_x86_64] ==> ignore
+    arg [--hash-style=gnu] ==> ignore
+    arg [-export-dynamic] ==> ignore
+    arg [-dynamic-linker] ==> ignore
+    arg [/lib64/ld-linux-x86-64.so.2] ==> ignore
+    arg [-o] ==> ignore
+    arg [cmTryCompileExec2437466663] ==> ignore
+    arg [/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o] ==> ignore
+    arg [/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crti.o] ==> ignore
+    arg [/usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtbegin.o] ==> ignore
+    arg [-L/usr/lib/gcc/x86_64-redhat-linux/4.4.7] ==> dir [/usr/lib/gcc/x86_64-redhat-linux/4.4.7]
+    arg [-L/usr/lib/gcc/x86_64-redhat-linux/4.4.7] ==> dir [/usr/lib/gcc/x86_64-redhat-linux/4.4.7]
+    arg [-L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64] ==> dir [/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64]
+    arg [-L/lib/../lib64] ==> dir [/lib/../lib64]
+    arg [-L/usr/lib/../lib64] ==> dir [/usr/lib/../lib64]
+    arg [-L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../..] ==> dir [/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../..]
+    arg [CMakeFiles/cmTryCompileExec2437466663.dir/CMakeCCompilerABI.c.o] ==> ignore
+    arg [-lgcc] ==> lib [gcc]
+    arg [--as-needed] ==> ignore
+    arg [-lgcc_s] ==> lib [gcc_s]
+    arg [--no-as-needed] ==> ignore
+    arg [-lc] ==> lib [c]
+    arg [-lgcc] ==> lib [gcc]
+    arg [--as-needed] ==> ignore
+    arg [-lgcc_s] ==> lib [gcc_s]
+    arg [--no-as-needed] ==> ignore
+    arg [/usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtend.o] ==> ignore
+    arg [/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crtn.o] ==> ignore
+  remove lib [gcc]
+  remove lib [gcc_s]
+  remove lib [gcc]
+  remove lib [gcc_s]
+  collapse library dir [/usr/lib/gcc/x86_64-redhat-linux/4.4.7] ==> [/usr/lib/gcc/x86_64-redhat-linux/4.4.7]
+  collapse library dir [/usr/lib/gcc/x86_64-redhat-linux/4.4.7] ==> [/usr/lib/gcc/x86_64-redhat-linux/4.4.7]
+  collapse library dir [/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64] ==> [/usr/lib64]
+  collapse library dir [/lib/../lib64] ==> [/lib64]
+  collapse library dir [/usr/lib/../lib64] ==> [/usr/lib64]
+  collapse library dir [/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../..] ==> [/usr/lib]
+  implicit libs: [c]
+  implicit dirs: [/usr/lib/gcc/x86_64-redhat-linux/4.4.7;/usr/lib64;/lib64;/usr/lib]
+  implicit fwks: []
+
+
+Determining if the CXX compiler works passed with the following output:
+Change Dir: /work/leverington/SciFiMatG4/SciFiSim/CMakeFiles/CMakeTmp
+
+Run Build Command:/usr/bin/gmake "cmTryCompileExec1842514690/fast"
+/usr/bin/gmake -f CMakeFiles/cmTryCompileExec1842514690.dir/build.make CMakeFiles/cmTryCompileExec1842514690.dir/build
+gmake[1]: Entering directory `/auto/sigma0/leverington/SciFiMatG4/SciFiSim/CMakeFiles/CMakeTmp'
+/usr/bin/cmake -E cmake_progress_report /work/leverington/SciFiMatG4/SciFiSim/CMakeFiles/CMakeTmp/CMakeFiles 1
+Building CXX object CMakeFiles/cmTryCompileExec1842514690.dir/testCXXCompiler.cxx.o
+/usr/bin/c++     -o CMakeFiles/cmTryCompileExec1842514690.dir/testCXXCompiler.cxx.o -c /work/leverington/SciFiMatG4/SciFiSim/CMakeFiles/CMakeTmp/testCXXCompiler.cxx
+Linking CXX executable cmTryCompileExec1842514690
+/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec1842514690.dir/link.txt --verbose=1
+/usr/bin/c++        CMakeFiles/cmTryCompileExec1842514690.dir/testCXXCompiler.cxx.o  -o cmTryCompileExec1842514690 -rdynamic 
+gmake[1]: Leaving directory `/auto/sigma0/leverington/SciFiMatG4/SciFiSim/CMakeFiles/CMakeTmp'
+
+
+Detecting CXX compiler ABI info compiled with the following output:
+Change Dir: /work/leverington/SciFiMatG4/SciFiSim/CMakeFiles/CMakeTmp
+
+Run Build Command:/usr/bin/gmake "cmTryCompileExec1517364131/fast"
+/usr/bin/gmake -f CMakeFiles/cmTryCompileExec1517364131.dir/build.make CMakeFiles/cmTryCompileExec1517364131.dir/build
+gmake[1]: Entering directory `/auto/sigma0/leverington/SciFiMatG4/SciFiSim/CMakeFiles/CMakeTmp'
+/usr/bin/cmake -E cmake_progress_report /work/leverington/SciFiMatG4/SciFiSim/CMakeFiles/CMakeTmp/CMakeFiles 1
+Building CXX object CMakeFiles/cmTryCompileExec1517364131.dir/CMakeCXXCompilerABI.cpp.o
+/usr/bin/c++     -o CMakeFiles/cmTryCompileExec1517364131.dir/CMakeCXXCompilerABI.cpp.o -c /usr/share/cmake/Modules/CMakeCXXCompilerABI.cpp
+Linking CXX executable cmTryCompileExec1517364131
+/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec1517364131.dir/link.txt --verbose=1
+/usr/bin/c++      -v CMakeFiles/cmTryCompileExec1517364131.dir/CMakeCXXCompilerABI.cpp.o  -o cmTryCompileExec1517364131 -rdynamic  
+Using built-in specs.
+Target: x86_64-redhat-linux
+Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
+Thread model: posix
+gcc version 4.4.7 20120313 (Red Hat 4.4.7-11) (GCC) 
+COMPILER_PATH=/local/lcg/releases/LCGCMT/LCGCMT_76root6/LCG_Settings/../../../LCG_76root6/gcc/4.8.1/x86_64-slc6/lib/gcc/x86_64-unknown-linux-gnu/4.8.1/:/usr/libexec/gcc/x86_64-redhat-linux/4.4.7/:/usr/libexec/gcc/x86_64-redhat-linux/4.4.7/:/usr/libexec/gcc/x86_64-redhat-linux/:/usr/lib/gcc/x86_64-redhat-linux/4.4.7/:/usr/lib/gcc/x86_64-redhat-linux/:/usr/libexec/gcc/x86_64-redhat-linux/4.4.7/:/usr/libexec/gcc/x86_64-redhat-linux/:/usr/lib/gcc/x86_64-redhat-linux/4.4.7/:/usr/lib/gcc/x86_64-redhat-linux/
+LIBRARY_PATH=/usr/lib/gcc/x86_64-redhat-linux/4.4.7/:/usr/lib/gcc/x86_64-redhat-linux/4.4.7/:/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/:/lib/../lib64/:/usr/lib/../lib64/:/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../:/lib/:/usr/lib/
+COLLECT_GCC_OPTIONS='-v' '-o' 'cmTryCompileExec1517364131' '-rdynamic' '-shared-libgcc' '-mtune=generic'
+ /usr/libexec/gcc/x86_64-redhat-linux/4.4.7/collect2 --eh-frame-hdr --build-id -m elf_x86_64 --hash-style=gnu -export-dynamic -dynamic-linker /lib64/ld-linux-x86-64.so.2 -o cmTryCompileExec1517364131 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtbegin.o -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.. CMakeFiles/cmTryCompileExec1517364131.dir/CMakeCXXCompilerABI.cpp.o -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtend.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crtn.o
+gmake[1]: Leaving directory `/auto/sigma0/leverington/SciFiMatG4/SciFiSim/CMakeFiles/CMakeTmp'
+
+
+Parsed CXX implicit link information from above output:
+  link line regex: [^( *|.*[/\])(ld|([^/\]+-)?ld|collect2)[^/\]*( |$)]
+  ignore line: [Change Dir: /work/leverington/SciFiMatG4/SciFiSim/CMakeFiles/CMakeTmp]
+  ignore line: []
+  ignore line: [Run Build Command:/usr/bin/gmake "cmTryCompileExec1517364131/fast"]
+  ignore line: [/usr/bin/gmake -f CMakeFiles/cmTryCompileExec1517364131.dir/build.make CMakeFiles/cmTryCompileExec1517364131.dir/build]
+  ignore line: [gmake[1]: Entering directory `/auto/sigma0/leverington/SciFiMatG4/SciFiSim/CMakeFiles/CMakeTmp']
+  ignore line: [/usr/bin/cmake -E cmake_progress_report /work/leverington/SciFiMatG4/SciFiSim/CMakeFiles/CMakeTmp/CMakeFiles 1]
+  ignore line: [Building CXX object CMakeFiles/cmTryCompileExec1517364131.dir/CMakeCXXCompilerABI.cpp.o]
+  ignore line: [/usr/bin/c++     -o CMakeFiles/cmTryCompileExec1517364131.dir/CMakeCXXCompilerABI.cpp.o -c /usr/share/cmake/Modules/CMakeCXXCompilerABI.cpp]
+  ignore line: [Linking CXX executable cmTryCompileExec1517364131]
+  ignore line: [/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec1517364131.dir/link.txt --verbose=1]
+  ignore line: [/usr/bin/c++      -v CMakeFiles/cmTryCompileExec1517364131.dir/CMakeCXXCompilerABI.cpp.o  -o cmTryCompileExec1517364131 -rdynamic  ]
+  ignore line: [Using built-in specs.]
+  ignore line: [Target: x86_64-redhat-linux]
+  ignore line: [Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux]
+  ignore line: [Thread model: posix]
+  ignore line: [gcc version 4.4.7 20120313 (Red Hat 4.4.7-11) (GCC) ]
+  ignore line: [COMPILER_PATH=/local/lcg/releases/LCGCMT/LCGCMT_76root6/LCG_Settings/../../../LCG_76root6/gcc/4.8.1/x86_64-slc6/lib/gcc/x86_64-unknown-linux-gnu/4.8.1/:/usr/libexec/gcc/x86_64-redhat-linux/4.4.7/:/usr/libexec/gcc/x86_64-redhat-linux/4.4.7/:/usr/libexec/gcc/x86_64-redhat-linux/:/usr/lib/gcc/x86_64-redhat-linux/4.4.7/:/usr/lib/gcc/x86_64-redhat-linux/:/usr/libexec/gcc/x86_64-redhat-linux/4.4.7/:/usr/libexec/gcc/x86_64-redhat-linux/:/usr/lib/gcc/x86_64-redhat-linux/4.4.7/:/usr/lib/gcc/x86_64-redhat-linux/]
+  ignore line: [LIBRARY_PATH=/usr/lib/gcc/x86_64-redhat-linux/4.4.7/:/usr/lib/gcc/x86_64-redhat-linux/4.4.7/:/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/:/lib/../lib64/:/usr/lib/../lib64/:/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../:/lib/:/usr/lib/]
+  ignore line: [COLLECT_GCC_OPTIONS='-v' '-o' 'cmTryCompileExec1517364131' '-rdynamic' '-shared-libgcc' '-mtune=generic']
+  link line: [ /usr/libexec/gcc/x86_64-redhat-linux/4.4.7/collect2 --eh-frame-hdr --build-id -m elf_x86_64 --hash-style=gnu -export-dynamic -dynamic-linker /lib64/ld-linux-x86-64.so.2 -o cmTryCompileExec1517364131 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtbegin.o -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.. CMakeFiles/cmTryCompileExec1517364131.dir/CMakeCXXCompilerABI.cpp.o -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtend.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crtn.o]
+    arg [/usr/libexec/gcc/x86_64-redhat-linux/4.4.7/collect2] ==> ignore
+    arg [--eh-frame-hdr] ==> ignore
+    arg [--build-id] ==> ignore
+    arg [-m] ==> ignore
+    arg [elf_x86_64] ==> ignore
+    arg [--hash-style=gnu] ==> ignore
+    arg [-export-dynamic] ==> ignore
+    arg [-dynamic-linker] ==> ignore
+    arg [/lib64/ld-linux-x86-64.so.2] ==> ignore
+    arg [-o] ==> ignore
+    arg [cmTryCompileExec1517364131] ==> ignore
+    arg [/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o] ==> ignore
+    arg [/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crti.o] ==> ignore
+    arg [/usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtbegin.o] ==> ignore
+    arg [-L/usr/lib/gcc/x86_64-redhat-linux/4.4.7] ==> dir [/usr/lib/gcc/x86_64-redhat-linux/4.4.7]
+    arg [-L/usr/lib/gcc/x86_64-redhat-linux/4.4.7] ==> dir [/usr/lib/gcc/x86_64-redhat-linux/4.4.7]
+    arg [-L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64] ==> dir [/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64]
+    arg [-L/lib/../lib64] ==> dir [/lib/../lib64]
+    arg [-L/usr/lib/../lib64] ==> dir [/usr/lib/../lib64]
+    arg [-L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../..] ==> dir [/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../..]
+    arg [CMakeFiles/cmTryCompileExec1517364131.dir/CMakeCXXCompilerABI.cpp.o] ==> ignore
+    arg [-lstdc++] ==> lib [stdc++]
+    arg [-lm] ==> lib [m]
+    arg [-lgcc_s] ==> lib [gcc_s]
+    arg [-lgcc] ==> lib [gcc]
+    arg [-lc] ==> lib [c]
+    arg [-lgcc_s] ==> lib [gcc_s]
+    arg [-lgcc] ==> lib [gcc]
+    arg [/usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtend.o] ==> ignore
+    arg [/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crtn.o] ==> ignore
+  remove lib [gcc_s]
+  remove lib [gcc]
+  remove lib [gcc_s]
+  remove lib [gcc]
+  collapse library dir [/usr/lib/gcc/x86_64-redhat-linux/4.4.7] ==> [/usr/lib/gcc/x86_64-redhat-linux/4.4.7]
+  collapse library dir [/usr/lib/gcc/x86_64-redhat-linux/4.4.7] ==> [/usr/lib/gcc/x86_64-redhat-linux/4.4.7]
+  collapse library dir [/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64] ==> [/usr/lib64]
+  collapse library dir [/lib/../lib64] ==> [/lib64]
+  collapse library dir [/usr/lib/../lib64] ==> [/usr/lib64]
+  collapse library dir [/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../..] ==> [/usr/lib]
+  implicit libs: [stdc++;m;c]
+  implicit dirs: [/usr/lib/gcc/x86_64-redhat-linux/4.4.7;/usr/lib64;/lib64;/usr/lib]
+  implicit fwks: []
+
+
+The system is: Linux - 3.2.0-96-generic - x86_64
+Compiling the C compiler identification source file "CMakeCCompilerId.c" succeeded.
+Compiler: /usr/bin/cc 
+Build flags: 
+Id flags: 
+
+The output was:
+0
+
+
+Compilation of the C compiler identification source "CMakeCCompilerId.c" produced "a.out"
+
+The C compiler identification is GNU, found in "/work/SciFiMatG4_v2/SciFiSim/CMakeFiles/3.3.2/CompilerIdC/a.out"
+
+Compiling the CXX compiler identification source file "CMakeCXXCompilerId.cpp" succeeded.
+Compiler: /usr/bin/c++ 
+Build flags: 
+Id flags: 
+
+The output was:
+0
+
+
+Compilation of the CXX compiler identification source "CMakeCXXCompilerId.cpp" produced "a.out"
+
+The CXX compiler identification is GNU, found in "/work/SciFiMatG4_v2/SciFiSim/CMakeFiles/3.3.2/CompilerIdCXX/a.out"
+
+Determining if the C compiler works passed with the following output:
+Change Dir: /work/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp
+
+Run Build Command:"/usr/bin/make" "cmTC_e6fd2/fast"
+/usr/bin/make -f CMakeFiles/cmTC_e6fd2.dir/build.make CMakeFiles/cmTC_e6fd2.dir/build
+make[1]: Entering directory `/media/work/work2/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp'
+Building C object CMakeFiles/cmTC_e6fd2.dir/testCCompiler.c.o
+/usr/bin/cc    -o CMakeFiles/cmTC_e6fd2.dir/testCCompiler.c.o   -c /work/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp/testCCompiler.c
+Linking C executable cmTC_e6fd2
+/home/leverington/Programs/cmake-3.3.2-Linux-x86_64/bin/cmake -E cmake_link_script CMakeFiles/cmTC_e6fd2.dir/link.txt --verbose=1
+/usr/bin/cc       CMakeFiles/cmTC_e6fd2.dir/testCCompiler.c.o  -o cmTC_e6fd2 -rdynamic 
+make[1]: Leaving directory `/media/work/work2/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp'
+
+
+Detecting C compiler ABI info compiled with the following output:
+Change Dir: /work/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp
+
+Run Build Command:"/usr/bin/make" "cmTC_47e25/fast"
+/usr/bin/make -f CMakeFiles/cmTC_47e25.dir/build.make CMakeFiles/cmTC_47e25.dir/build
+make[1]: Entering directory `/media/work/work2/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp'
+Building C object CMakeFiles/cmTC_47e25.dir/CMakeCCompilerABI.c.o
+/usr/bin/cc    -o CMakeFiles/cmTC_47e25.dir/CMakeCCompilerABI.c.o   -c /home/leverington/Programs/cmake-3.3.2-Linux-x86_64/share/cmake-3.3/Modules/CMakeCCompilerABI.c
+Linking C executable cmTC_47e25
+/home/leverington/Programs/cmake-3.3.2-Linux-x86_64/bin/cmake -E cmake_link_script CMakeFiles/cmTC_47e25.dir/link.txt --verbose=1
+/usr/bin/cc      -v CMakeFiles/cmTC_47e25.dir/CMakeCCompilerABI.c.o  -o cmTC_47e25 -rdynamic  
+Using built-in specs.
+COLLECT_GCC=/usr/bin/cc
+COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.8/lto-wrapper
+Target: x86_64-linux-gnu
+Configured with: ../src/configure -v --with-pkgversion='Ubuntu 4.8.1-2ubuntu1~12.04' --with-bugurl=file:///usr/share/doc/gcc-4.8/README.Bugs --enable-languages=c,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.8 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.8 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-gnu-unique-object --enable-plugin --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-4.8-amd64/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-4.8-amd64 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-4.8-amd64 --with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
+Thread model: posix
+gcc version 4.8.1 (Ubuntu 4.8.1-2ubuntu1~12.04) 
+COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/4.8/:/usr/lib/gcc/x86_64-linux-gnu/4.8/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/4.8/:/usr/lib/gcc/x86_64-linux-gnu/
+LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/4.8/:/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../:/lib/:/usr/lib/
+COLLECT_GCC_OPTIONS='-v' '-o' 'cmTC_47e25' '-rdynamic' '-mtune=generic' '-march=x86-64'
+ /usr/lib/gcc/x86_64-linux-gnu/4.8/collect2 --sysroot=/ --build-id --eh-frame-hdr -m elf_x86_64 --hash-style=gnu --as-needed -export-dynamic -dynamic-linker /lib64/ld-linux-x86-64.so.2 -z relro -o cmTC_47e25 /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/crt1.o /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/4.8/crtbegin.o -L/usr/lib/gcc/x86_64-linux-gnu/4.8 -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../.. CMakeFiles/cmTC_47e25.dir/CMakeCCompilerABI.c.o -lgcc --as-needed -lgcc_s --no-as-needed -lc -lgcc --as-needed -lgcc_s --no-as-needed /usr/lib/gcc/x86_64-linux-gnu/4.8/crtend.o /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/crtn.o
+make[1]: Leaving directory `/media/work/work2/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp'
+
+
+Parsed C implicit link information from above output:
+  link line regex: [^( *|.*[/\])(ld|([^/\]+-)?ld|collect2)[^/\]*( |$)]
+  ignore line: [Change Dir: /work/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp]
+  ignore line: []
+  ignore line: [Run Build Command:"/usr/bin/make" "cmTC_47e25/fast"]
+  ignore line: [/usr/bin/make -f CMakeFiles/cmTC_47e25.dir/build.make CMakeFiles/cmTC_47e25.dir/build]
+  ignore line: [make[1]: Entering directory `/media/work/work2/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp']
+  ignore line: [Building C object CMakeFiles/cmTC_47e25.dir/CMakeCCompilerABI.c.o]
+  ignore line: [/usr/bin/cc    -o CMakeFiles/cmTC_47e25.dir/CMakeCCompilerABI.c.o   -c /home/leverington/Programs/cmake-3.3.2-Linux-x86_64/share/cmake-3.3/Modules/CMakeCCompilerABI.c]
+  ignore line: [Linking C executable cmTC_47e25]
+  ignore line: [/home/leverington/Programs/cmake-3.3.2-Linux-x86_64/bin/cmake -E cmake_link_script CMakeFiles/cmTC_47e25.dir/link.txt --verbose=1]
+  ignore line: [/usr/bin/cc      -v CMakeFiles/cmTC_47e25.dir/CMakeCCompilerABI.c.o  -o cmTC_47e25 -rdynamic  ]
+  ignore line: [Using built-in specs.]
+  ignore line: [COLLECT_GCC=/usr/bin/cc]
+  ignore line: [COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.8/lto-wrapper]
+  ignore line: [Target: x86_64-linux-gnu]
+  ignore line: [Configured with: ../src/configure -v --with-pkgversion='Ubuntu 4.8.1-2ubuntu1~12.04' --with-bugurl=file:///usr/share/doc/gcc-4.8/README.Bugs --enable-languages=c,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.8 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.8 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-gnu-unique-object --enable-plugin --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-4.8-amd64/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-4.8-amd64 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-4.8-amd64 --with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu]
+  ignore line: [Thread model: posix]
+  ignore line: [gcc version 4.8.1 (Ubuntu 4.8.1-2ubuntu1~12.04) ]
+  ignore line: [COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/4.8/:/usr/lib/gcc/x86_64-linux-gnu/4.8/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/4.8/:/usr/lib/gcc/x86_64-linux-gnu/]
+  ignore line: [LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/4.8/:/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../:/lib/:/usr/lib/]
+  ignore line: [COLLECT_GCC_OPTIONS='-v' '-o' 'cmTC_47e25' '-rdynamic' '-mtune=generic' '-march=x86-64']
+  link line: [ /usr/lib/gcc/x86_64-linux-gnu/4.8/collect2 --sysroot=/ --build-id --eh-frame-hdr -m elf_x86_64 --hash-style=gnu --as-needed -export-dynamic -dynamic-linker /lib64/ld-linux-x86-64.so.2 -z relro -o cmTC_47e25 /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/crt1.o /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/4.8/crtbegin.o -L/usr/lib/gcc/x86_64-linux-gnu/4.8 -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../.. CMakeFiles/cmTC_47e25.dir/CMakeCCompilerABI.c.o -lgcc --as-needed -lgcc_s --no-as-needed -lc -lgcc --as-needed -lgcc_s --no-as-needed /usr/lib/gcc/x86_64-linux-gnu/4.8/crtend.o /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/crtn.o]
+    arg [/usr/lib/gcc/x86_64-linux-gnu/4.8/collect2] ==> ignore
+    arg [--sysroot=/] ==> ignore
+    arg [--build-id] ==> ignore
+    arg [--eh-frame-hdr] ==> ignore
+    arg [-m] ==> ignore
+    arg [elf_x86_64] ==> ignore
+    arg [--hash-style=gnu] ==> ignore
+    arg [--as-needed] ==> ignore
+    arg [-export-dynamic] ==> ignore
+    arg [-dynamic-linker] ==> ignore
+    arg [/lib64/ld-linux-x86-64.so.2] ==> ignore
+    arg [-zrelro] ==> ignore
+    arg [-o] ==> ignore
+    arg [cmTC_47e25] ==> ignore
+    arg [/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/crt1.o] ==> ignore
+    arg [/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/crti.o] ==> ignore
+    arg [/usr/lib/gcc/x86_64-linux-gnu/4.8/crtbegin.o] ==> ignore
+    arg [-L/usr/lib/gcc/x86_64-linux-gnu/4.8] ==> dir [/usr/lib/gcc/x86_64-linux-gnu/4.8]
+    arg [-L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu] ==> dir [/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu]
+    arg [-L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib] ==> dir [/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib]
+    arg [-L/lib/x86_64-linux-gnu] ==> dir [/lib/x86_64-linux-gnu]
+    arg [-L/lib/../lib] ==> dir [/lib/../lib]
+    arg [-L/usr/lib/x86_64-linux-gnu] ==> dir [/usr/lib/x86_64-linux-gnu]
+    arg [-L/usr/lib/../lib] ==> dir [/usr/lib/../lib]
+    arg [-L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../..] ==> dir [/usr/lib/gcc/x86_64-linux-gnu/4.8/../../..]
+    arg [CMakeFiles/cmTC_47e25.dir/CMakeCCompilerABI.c.o] ==> ignore
+    arg [-lgcc] ==> lib [gcc]
+    arg [--as-needed] ==> ignore
+    arg [-lgcc_s] ==> lib [gcc_s]
+    arg [--no-as-needed] ==> ignore
+    arg [-lc] ==> lib [c]
+    arg [-lgcc] ==> lib [gcc]
+    arg [--as-needed] ==> ignore
+    arg [-lgcc_s] ==> lib [gcc_s]
+    arg [--no-as-needed] ==> ignore
+    arg [/usr/lib/gcc/x86_64-linux-gnu/4.8/crtend.o] ==> ignore
+    arg [/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/crtn.o] ==> ignore
+  remove lib [gcc]
+  remove lib [gcc_s]
+  remove lib [gcc]
+  remove lib [gcc_s]
+  collapse library dir [/usr/lib/gcc/x86_64-linux-gnu/4.8] ==> [/usr/lib/gcc/x86_64-linux-gnu/4.8]
+  collapse library dir [/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu] ==> [/usr/lib/x86_64-linux-gnu]
+  collapse library dir [/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib] ==> [/usr/lib]
+  collapse library dir [/lib/x86_64-linux-gnu] ==> [/lib/x86_64-linux-gnu]
+  collapse library dir [/lib/../lib] ==> [/lib]
+  collapse library dir [/usr/lib/x86_64-linux-gnu] ==> [/usr/lib/x86_64-linux-gnu]
+  collapse library dir [/usr/lib/../lib] ==> [/usr/lib]
+  collapse library dir [/usr/lib/gcc/x86_64-linux-gnu/4.8/../../..] ==> [/usr/lib]
+  implicit libs: [c]
+  implicit dirs: [/usr/lib/gcc/x86_64-linux-gnu/4.8;/usr/lib/x86_64-linux-gnu;/usr/lib;/lib/x86_64-linux-gnu;/lib]
+  implicit fwks: []
+
+
+
+
+Detecting C [-std=c11] compiler features compiled with the following output:
+Change Dir: /work/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp
+
+Run Build Command:"/usr/bin/make" "cmTC_6ac00/fast"
+/usr/bin/make -f CMakeFiles/cmTC_6ac00.dir/build.make CMakeFiles/cmTC_6ac00.dir/build
+make[1]: Entering directory `/media/work/work2/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp'
+Building C object CMakeFiles/cmTC_6ac00.dir/feature_tests.c.o
+/usr/bin/cc   -std=c11 -o CMakeFiles/cmTC_6ac00.dir/feature_tests.c.o   -c /work/SciFiMatG4_v2/SciFiSim/CMakeFiles/feature_tests.c
+Linking C executable cmTC_6ac00
+/home/leverington/Programs/cmake-3.3.2-Linux-x86_64/bin/cmake -E cmake_link_script CMakeFiles/cmTC_6ac00.dir/link.txt --verbose=1
+/usr/bin/cc       CMakeFiles/cmTC_6ac00.dir/feature_tests.c.o  -o cmTC_6ac00 -rdynamic 
+make[1]: Leaving directory `/media/work/work2/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp'
+
+
+    Feature record: C_FEATURE:1c_function_prototypes
+    Feature record: C_FEATURE:1c_restrict
+    Feature record: C_FEATURE:1c_static_assert
+    Feature record: C_FEATURE:1c_variadic_macros
+
+
+Detecting C [-std=c99] compiler features compiled with the following output:
+Change Dir: /work/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp
+
+Run Build Command:"/usr/bin/make" "cmTC_bb9a9/fast"
+/usr/bin/make -f CMakeFiles/cmTC_bb9a9.dir/build.make CMakeFiles/cmTC_bb9a9.dir/build
+make[1]: Entering directory `/media/work/work2/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp'
+Building C object CMakeFiles/cmTC_bb9a9.dir/feature_tests.c.o
+/usr/bin/cc   -std=c99 -o CMakeFiles/cmTC_bb9a9.dir/feature_tests.c.o   -c /work/SciFiMatG4_v2/SciFiSim/CMakeFiles/feature_tests.c
+Linking C executable cmTC_bb9a9
+/home/leverington/Programs/cmake-3.3.2-Linux-x86_64/bin/cmake -E cmake_link_script CMakeFiles/cmTC_bb9a9.dir/link.txt --verbose=1
+/usr/bin/cc       CMakeFiles/cmTC_bb9a9.dir/feature_tests.c.o  -o cmTC_bb9a9 -rdynamic 
+make[1]: Leaving directory `/media/work/work2/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp'
+
+
+    Feature record: C_FEATURE:1c_function_prototypes
+    Feature record: C_FEATURE:1c_restrict
+    Feature record: C_FEATURE:0c_static_assert
+    Feature record: C_FEATURE:1c_variadic_macros
+
+
+Detecting C [-std=c90] compiler features compiled with the following output:
+Change Dir: /work/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp
+
+Run Build Command:"/usr/bin/make" "cmTC_dd63f/fast"
+/usr/bin/make -f CMakeFiles/cmTC_dd63f.dir/build.make CMakeFiles/cmTC_dd63f.dir/build
+make[1]: Entering directory `/media/work/work2/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp'
+Building C object CMakeFiles/cmTC_dd63f.dir/feature_tests.c.o
+/usr/bin/cc   -std=c90 -o CMakeFiles/cmTC_dd63f.dir/feature_tests.c.o   -c /work/SciFiMatG4_v2/SciFiSim/CMakeFiles/feature_tests.c
+Linking C executable cmTC_dd63f
+/home/leverington/Programs/cmake-3.3.2-Linux-x86_64/bin/cmake -E cmake_link_script CMakeFiles/cmTC_dd63f.dir/link.txt --verbose=1
+/usr/bin/cc       CMakeFiles/cmTC_dd63f.dir/feature_tests.c.o  -o cmTC_dd63f -rdynamic 
+make[1]: Leaving directory `/media/work/work2/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp'
+
+
+    Feature record: C_FEATURE:1c_function_prototypes
+    Feature record: C_FEATURE:0c_restrict
+    Feature record: C_FEATURE:0c_static_assert
+    Feature record: C_FEATURE:0c_variadic_macros
+Determining if the CXX compiler works passed with the following output:
+Change Dir: /work/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp
+
+Run Build Command:"/usr/bin/make" "cmTC_5d2b2/fast"
+/usr/bin/make -f CMakeFiles/cmTC_5d2b2.dir/build.make CMakeFiles/cmTC_5d2b2.dir/build
+make[1]: Entering directory `/media/work/work2/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp'
+Building CXX object CMakeFiles/cmTC_5d2b2.dir/testCXXCompiler.cxx.o
+/usr/bin/c++     -o CMakeFiles/cmTC_5d2b2.dir/testCXXCompiler.cxx.o -c /work/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp/testCXXCompiler.cxx
+Linking CXX executable cmTC_5d2b2
+/home/leverington/Programs/cmake-3.3.2-Linux-x86_64/bin/cmake -E cmake_link_script CMakeFiles/cmTC_5d2b2.dir/link.txt --verbose=1
+/usr/bin/c++        CMakeFiles/cmTC_5d2b2.dir/testCXXCompiler.cxx.o  -o cmTC_5d2b2 -rdynamic 
+make[1]: Leaving directory `/media/work/work2/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp'
+
+
+Detecting CXX compiler ABI info compiled with the following output:
+Change Dir: /work/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp
+
+Run Build Command:"/usr/bin/make" "cmTC_98d78/fast"
+/usr/bin/make -f CMakeFiles/cmTC_98d78.dir/build.make CMakeFiles/cmTC_98d78.dir/build
+make[1]: Entering directory `/media/work/work2/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp'
+Building CXX object CMakeFiles/cmTC_98d78.dir/CMakeCXXCompilerABI.cpp.o
+/usr/bin/c++     -o CMakeFiles/cmTC_98d78.dir/CMakeCXXCompilerABI.cpp.o -c /home/leverington/Programs/cmake-3.3.2-Linux-x86_64/share/cmake-3.3/Modules/CMakeCXXCompilerABI.cpp
+Linking CXX executable cmTC_98d78
+/home/leverington/Programs/cmake-3.3.2-Linux-x86_64/bin/cmake -E cmake_link_script CMakeFiles/cmTC_98d78.dir/link.txt --verbose=1
+/usr/bin/c++       -v CMakeFiles/cmTC_98d78.dir/CMakeCXXCompilerABI.cpp.o  -o cmTC_98d78 -rdynamic  
+Using built-in specs.
+COLLECT_GCC=/usr/bin/c++
+COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.8/lto-wrapper
+Target: x86_64-linux-gnu
+Configured with: ../src/configure -v --with-pkgversion='Ubuntu 4.8.1-2ubuntu1~12.04' --with-bugurl=file:///usr/share/doc/gcc-4.8/README.Bugs --enable-languages=c,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.8 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.8 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-gnu-unique-object --enable-plugin --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-4.8-amd64/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-4.8-amd64 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-4.8-amd64 --with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
+Thread model: posix
+gcc version 4.8.1 (Ubuntu 4.8.1-2ubuntu1~12.04) 
+COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/4.8/:/usr/lib/gcc/x86_64-linux-gnu/4.8/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/4.8/:/usr/lib/gcc/x86_64-linux-gnu/
+LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/4.8/:/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../:/lib/:/usr/lib/
+COLLECT_GCC_OPTIONS='-v' '-o' 'cmTC_98d78' '-rdynamic' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
+ /usr/lib/gcc/x86_64-linux-gnu/4.8/collect2 --sysroot=/ --build-id --eh-frame-hdr -m elf_x86_64 --hash-style=gnu --as-needed -export-dynamic -dynamic-linker /lib64/ld-linux-x86-64.so.2 -z relro -o cmTC_98d78 /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/crt1.o /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/4.8/crtbegin.o -L/usr/lib/gcc/x86_64-linux-gnu/4.8 -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../.. CMakeFiles/cmTC_98d78.dir/CMakeCXXCompilerABI.cpp.o -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/x86_64-linux-gnu/4.8/crtend.o /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/crtn.o
+make[1]: Leaving directory `/media/work/work2/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp'
+
+
+Parsed CXX implicit link information from above output:
+  link line regex: [^( *|.*[/\])(ld|([^/\]+-)?ld|collect2)[^/\]*( |$)]
+  ignore line: [Change Dir: /work/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp]
+  ignore line: []
+  ignore line: [Run Build Command:"/usr/bin/make" "cmTC_98d78/fast"]
+  ignore line: [/usr/bin/make -f CMakeFiles/cmTC_98d78.dir/build.make CMakeFiles/cmTC_98d78.dir/build]
+  ignore line: [make[1]: Entering directory `/media/work/work2/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp']
+  ignore line: [Building CXX object CMakeFiles/cmTC_98d78.dir/CMakeCXXCompilerABI.cpp.o]
+  ignore line: [/usr/bin/c++     -o CMakeFiles/cmTC_98d78.dir/CMakeCXXCompilerABI.cpp.o -c /home/leverington/Programs/cmake-3.3.2-Linux-x86_64/share/cmake-3.3/Modules/CMakeCXXCompilerABI.cpp]
+  ignore line: [Linking CXX executable cmTC_98d78]
+  ignore line: [/home/leverington/Programs/cmake-3.3.2-Linux-x86_64/bin/cmake -E cmake_link_script CMakeFiles/cmTC_98d78.dir/link.txt --verbose=1]
+  ignore line: [/usr/bin/c++       -v CMakeFiles/cmTC_98d78.dir/CMakeCXXCompilerABI.cpp.o  -o cmTC_98d78 -rdynamic  ]
+  ignore line: [Using built-in specs.]
+  ignore line: [COLLECT_GCC=/usr/bin/c++]
+  ignore line: [COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.8/lto-wrapper]
+  ignore line: [Target: x86_64-linux-gnu]
+  ignore line: [Configured with: ../src/configure -v --with-pkgversion='Ubuntu 4.8.1-2ubuntu1~12.04' --with-bugurl=file:///usr/share/doc/gcc-4.8/README.Bugs --enable-languages=c,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.8 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.8 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-gnu-unique-object --enable-plugin --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-4.8-amd64/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-4.8-amd64 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-4.8-amd64 --with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu]
+  ignore line: [Thread model: posix]
+  ignore line: [gcc version 4.8.1 (Ubuntu 4.8.1-2ubuntu1~12.04) ]
+  ignore line: [COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/4.8/:/usr/lib/gcc/x86_64-linux-gnu/4.8/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/4.8/:/usr/lib/gcc/x86_64-linux-gnu/]
+  ignore line: [LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/4.8/:/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../:/lib/:/usr/lib/]
+  ignore line: [COLLECT_GCC_OPTIONS='-v' '-o' 'cmTC_98d78' '-rdynamic' '-shared-libgcc' '-mtune=generic' '-march=x86-64']
+  link line: [ /usr/lib/gcc/x86_64-linux-gnu/4.8/collect2 --sysroot=/ --build-id --eh-frame-hdr -m elf_x86_64 --hash-style=gnu --as-needed -export-dynamic -dynamic-linker /lib64/ld-linux-x86-64.so.2 -z relro -o cmTC_98d78 /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/crt1.o /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/4.8/crtbegin.o -L/usr/lib/gcc/x86_64-linux-gnu/4.8 -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../.. CMakeFiles/cmTC_98d78.dir/CMakeCXXCompilerABI.cpp.o -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/x86_64-linux-gnu/4.8/crtend.o /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/crtn.o]
+    arg [/usr/lib/gcc/x86_64-linux-gnu/4.8/collect2] ==> ignore
+    arg [--sysroot=/] ==> ignore
+    arg [--build-id] ==> ignore
+    arg [--eh-frame-hdr] ==> ignore
+    arg [-m] ==> ignore
+    arg [elf_x86_64] ==> ignore
+    arg [--hash-style=gnu] ==> ignore
+    arg [--as-needed] ==> ignore
+    arg [-export-dynamic] ==> ignore
+    arg [-dynamic-linker] ==> ignore
+    arg [/lib64/ld-linux-x86-64.so.2] ==> ignore
+    arg [-zrelro] ==> ignore
+    arg [-o] ==> ignore
+    arg [cmTC_98d78] ==> ignore
+    arg [/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/crt1.o] ==> ignore
+    arg [/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/crti.o] ==> ignore
+    arg [/usr/lib/gcc/x86_64-linux-gnu/4.8/crtbegin.o] ==> ignore
+    arg [-L/usr/lib/gcc/x86_64-linux-gnu/4.8] ==> dir [/usr/lib/gcc/x86_64-linux-gnu/4.8]
+    arg [-L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu] ==> dir [/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu]
+    arg [-L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib] ==> dir [/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib]
+    arg [-L/lib/x86_64-linux-gnu] ==> dir [/lib/x86_64-linux-gnu]
+    arg [-L/lib/../lib] ==> dir [/lib/../lib]
+    arg [-L/usr/lib/x86_64-linux-gnu] ==> dir [/usr/lib/x86_64-linux-gnu]
+    arg [-L/usr/lib/../lib] ==> dir [/usr/lib/../lib]
+    arg [-L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../..] ==> dir [/usr/lib/gcc/x86_64-linux-gnu/4.8/../../..]
+    arg [CMakeFiles/cmTC_98d78.dir/CMakeCXXCompilerABI.cpp.o] ==> ignore
+    arg [-lstdc++] ==> lib [stdc++]
+    arg [-lm] ==> lib [m]
+    arg [-lgcc_s] ==> lib [gcc_s]
+    arg [-lgcc] ==> lib [gcc]
+    arg [-lc] ==> lib [c]
+    arg [-lgcc_s] ==> lib [gcc_s]
+    arg [-lgcc] ==> lib [gcc]
+    arg [/usr/lib/gcc/x86_64-linux-gnu/4.8/crtend.o] ==> ignore
+    arg [/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/crtn.o] ==> ignore
+  remove lib [gcc_s]
+  remove lib [gcc]
+  remove lib [gcc_s]
+  remove lib [gcc]
+  collapse library dir [/usr/lib/gcc/x86_64-linux-gnu/4.8] ==> [/usr/lib/gcc/x86_64-linux-gnu/4.8]
+  collapse library dir [/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu] ==> [/usr/lib/x86_64-linux-gnu]
+  collapse library dir [/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib] ==> [/usr/lib]
+  collapse library dir [/lib/x86_64-linux-gnu] ==> [/lib/x86_64-linux-gnu]
+  collapse library dir [/lib/../lib] ==> [/lib]
+  collapse library dir [/usr/lib/x86_64-linux-gnu] ==> [/usr/lib/x86_64-linux-gnu]
+  collapse library dir [/usr/lib/../lib] ==> [/usr/lib]
+  collapse library dir [/usr/lib/gcc/x86_64-linux-gnu/4.8/../../..] ==> [/usr/lib]
+  implicit libs: [stdc++;m;c]
+  implicit dirs: [/usr/lib/gcc/x86_64-linux-gnu/4.8;/usr/lib/x86_64-linux-gnu;/usr/lib;/lib/x86_64-linux-gnu;/lib]
+  implicit fwks: []
+
+
+
+
+Detecting CXX [-std=c++1y] compiler features compiled with the following output:
+Change Dir: /work/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp
+
+Run Build Command:"/usr/bin/make" "cmTC_dd430/fast"
+/usr/bin/make -f CMakeFiles/cmTC_dd430.dir/build.make CMakeFiles/cmTC_dd430.dir/build
+make[1]: Entering directory `/media/work/work2/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp'
+Building CXX object CMakeFiles/cmTC_dd430.dir/feature_tests.cxx.o
+/usr/bin/c++    -std=c++1y -o CMakeFiles/cmTC_dd430.dir/feature_tests.cxx.o -c /work/SciFiMatG4_v2/SciFiSim/CMakeFiles/feature_tests.cxx
+Linking CXX executable cmTC_dd430
+/home/leverington/Programs/cmake-3.3.2-Linux-x86_64/bin/cmake -E cmake_link_script CMakeFiles/cmTC_dd430.dir/link.txt --verbose=1
+/usr/bin/c++        CMakeFiles/cmTC_dd430.dir/feature_tests.cxx.o  -o cmTC_dd430 -rdynamic 
+make[1]: Leaving directory `/media/work/work2/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp'
+
+
+    Feature record: CXX_FEATURE:0cxx_aggregate_default_initializers
+    Feature record: CXX_FEATURE:1cxx_alias_templates
+    Feature record: CXX_FEATURE:1cxx_alignas
+    Feature record: CXX_FEATURE:1cxx_alignof
+    Feature record: CXX_FEATURE:1cxx_attributes
+    Feature record: CXX_FEATURE:0cxx_attribute_deprecated
+    Feature record: CXX_FEATURE:1cxx_auto_type
+    Feature record: CXX_FEATURE:0cxx_binary_literals
+    Feature record: CXX_FEATURE:1cxx_constexpr
+    Feature record: CXX_FEATURE:0cxx_contextual_conversions
+    Feature record: CXX_FEATURE:1cxx_decltype
+    Feature record: CXX_FEATURE:0cxx_decltype_auto
+    Feature record: CXX_FEATURE:1cxx_decltype_incomplete_return_types
+    Feature record: CXX_FEATURE:1cxx_default_function_template_args
+    Feature record: CXX_FEATURE:1cxx_defaulted_functions
+    Feature record: CXX_FEATURE:1cxx_defaulted_move_initializers
+    Feature record: CXX_FEATURE:1cxx_delegating_constructors
+    Feature record: CXX_FEATURE:1cxx_deleted_functions
+    Feature record: CXX_FEATURE:0cxx_digit_separators
+    Feature record: CXX_FEATURE:1cxx_enum_forward_declarations
+    Feature record: CXX_FEATURE:1cxx_explicit_conversions
+    Feature record: CXX_FEATURE:1cxx_extended_friend_declarations
+    Feature record: CXX_FEATURE:1cxx_extern_templates
+    Feature record: CXX_FEATURE:1cxx_final
+    Feature record: CXX_FEATURE:1cxx_func_identifier
+    Feature record: CXX_FEATURE:1cxx_generalized_initializers
+    Feature record: CXX_FEATURE:0cxx_generic_lambdas
+    Feature record: CXX_FEATURE:1cxx_inheriting_constructors
+    Feature record: CXX_FEATURE:1cxx_inline_namespaces
+    Feature record: CXX_FEATURE:1cxx_lambdas
+    Feature record: CXX_FEATURE:0cxx_lambda_init_captures
+    Feature record: CXX_FEATURE:1cxx_local_type_template_args
+    Feature record: CXX_FEATURE:1cxx_long_long_type
+    Feature record: CXX_FEATURE:1cxx_noexcept
+    Feature record: CXX_FEATURE:1cxx_nonstatic_member_init
+    Feature record: CXX_FEATURE:1cxx_nullptr
+    Feature record: CXX_FEATURE:1cxx_override
+    Feature record: CXX_FEATURE:1cxx_range_for
+    Feature record: CXX_FEATURE:1cxx_raw_string_literals
+    Feature record: CXX_FEATURE:1cxx_reference_qualified_functions
+    Feature record: CXX_FEATURE:0cxx_relaxed_constexpr
+    Feature record: CXX_FEATURE:0cxx_return_type_deduction
+    Feature record: CXX_FEATURE:1cxx_right_angle_brackets
+    Feature record: CXX_FEATURE:1cxx_rvalue_references
+    Feature record: CXX_FEATURE:1cxx_sizeof_member
+    Feature record: CXX_FEATURE:1cxx_static_assert
+    Feature record: CXX_FEATURE:1cxx_strong_enums
+    Feature record: CXX_FEATURE:1cxx_template_template_parameters
+    Feature record: CXX_FEATURE:1cxx_thread_local
+    Feature record: CXX_FEATURE:1cxx_trailing_return_types
+    Feature record: CXX_FEATURE:1cxx_unicode_literals
+    Feature record: CXX_FEATURE:1cxx_uniform_initialization
+    Feature record: CXX_FEATURE:1cxx_unrestricted_unions
+    Feature record: CXX_FEATURE:1cxx_user_literals
+    Feature record: CXX_FEATURE:0cxx_variable_templates
+    Feature record: CXX_FEATURE:1cxx_variadic_macros
+    Feature record: CXX_FEATURE:1cxx_variadic_templates
+
+
+Detecting CXX [-std=c++11] compiler features compiled with the following output:
+Change Dir: /work/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp
+
+Run Build Command:"/usr/bin/make" "cmTC_a5620/fast"
+/usr/bin/make -f CMakeFiles/cmTC_a5620.dir/build.make CMakeFiles/cmTC_a5620.dir/build
+make[1]: Entering directory `/media/work/work2/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp'
+Building CXX object CMakeFiles/cmTC_a5620.dir/feature_tests.cxx.o
+/usr/bin/c++    -std=c++11 -o CMakeFiles/cmTC_a5620.dir/feature_tests.cxx.o -c /work/SciFiMatG4_v2/SciFiSim/CMakeFiles/feature_tests.cxx
+Linking CXX executable cmTC_a5620
+/home/leverington/Programs/cmake-3.3.2-Linux-x86_64/bin/cmake -E cmake_link_script CMakeFiles/cmTC_a5620.dir/link.txt --verbose=1
+/usr/bin/c++        CMakeFiles/cmTC_a5620.dir/feature_tests.cxx.o  -o cmTC_a5620 -rdynamic 
+make[1]: Leaving directory `/media/work/work2/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp'
+
+
+    Feature record: CXX_FEATURE:0cxx_aggregate_default_initializers
+    Feature record: CXX_FEATURE:1cxx_alias_templates
+    Feature record: CXX_FEATURE:1cxx_alignas
+    Feature record: CXX_FEATURE:1cxx_alignof
+    Feature record: CXX_FEATURE:1cxx_attributes
+    Feature record: CXX_FEATURE:0cxx_attribute_deprecated
+    Feature record: CXX_FEATURE:1cxx_auto_type
+    Feature record: CXX_FEATURE:0cxx_binary_literals
+    Feature record: CXX_FEATURE:1cxx_constexpr
+    Feature record: CXX_FEATURE:0cxx_contextual_conversions
+    Feature record: CXX_FEATURE:1cxx_decltype
+    Feature record: CXX_FEATURE:0cxx_decltype_auto
+    Feature record: CXX_FEATURE:1cxx_decltype_incomplete_return_types
+    Feature record: CXX_FEATURE:1cxx_default_function_template_args
+    Feature record: CXX_FEATURE:1cxx_defaulted_functions
+    Feature record: CXX_FEATURE:1cxx_defaulted_move_initializers
+    Feature record: CXX_FEATURE:1cxx_delegating_constructors
+    Feature record: CXX_FEATURE:1cxx_deleted_functions
+    Feature record: CXX_FEATURE:0cxx_digit_separators
+    Feature record: CXX_FEATURE:1cxx_enum_forward_declarations
+    Feature record: CXX_FEATURE:1cxx_explicit_conversions
+    Feature record: CXX_FEATURE:1cxx_extended_friend_declarations
+    Feature record: CXX_FEATURE:1cxx_extern_templates
+    Feature record: CXX_FEATURE:1cxx_final
+    Feature record: CXX_FEATURE:1cxx_func_identifier
+    Feature record: CXX_FEATURE:1cxx_generalized_initializers
+    Feature record: CXX_FEATURE:0cxx_generic_lambdas
+    Feature record: CXX_FEATURE:1cxx_inheriting_constructors
+    Feature record: CXX_FEATURE:1cxx_inline_namespaces
+    Feature record: CXX_FEATURE:1cxx_lambdas
+    Feature record: CXX_FEATURE:0cxx_lambda_init_captures
+    Feature record: CXX_FEATURE:1cxx_local_type_template_args
+    Feature record: CXX_FEATURE:1cxx_long_long_type
+    Feature record: CXX_FEATURE:1cxx_noexcept
+    Feature record: CXX_FEATURE:1cxx_nonstatic_member_init
+    Feature record: CXX_FEATURE:1cxx_nullptr
+    Feature record: CXX_FEATURE:1cxx_override
+    Feature record: CXX_FEATURE:1cxx_range_for
+    Feature record: CXX_FEATURE:1cxx_raw_string_literals
+    Feature record: CXX_FEATURE:1cxx_reference_qualified_functions
+    Feature record: CXX_FEATURE:0cxx_relaxed_constexpr
+    Feature record: CXX_FEATURE:0cxx_return_type_deduction
+    Feature record: CXX_FEATURE:1cxx_right_angle_brackets
+    Feature record: CXX_FEATURE:1cxx_rvalue_references
+    Feature record: CXX_FEATURE:1cxx_sizeof_member
+    Feature record: CXX_FEATURE:1cxx_static_assert
+    Feature record: CXX_FEATURE:1cxx_strong_enums
+    Feature record: CXX_FEATURE:1cxx_template_template_parameters
+    Feature record: CXX_FEATURE:1cxx_thread_local
+    Feature record: CXX_FEATURE:1cxx_trailing_return_types
+    Feature record: CXX_FEATURE:1cxx_unicode_literals
+    Feature record: CXX_FEATURE:1cxx_uniform_initialization
+    Feature record: CXX_FEATURE:1cxx_unrestricted_unions
+    Feature record: CXX_FEATURE:1cxx_user_literals
+    Feature record: CXX_FEATURE:0cxx_variable_templates
+    Feature record: CXX_FEATURE:1cxx_variadic_macros
+    Feature record: CXX_FEATURE:1cxx_variadic_templates
+
+
+Detecting CXX [-std=c++98] compiler features compiled with the following output:
+Change Dir: /work/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp
+
+Run Build Command:"/usr/bin/make" "cmTC_0f614/fast"
+/usr/bin/make -f CMakeFiles/cmTC_0f614.dir/build.make CMakeFiles/cmTC_0f614.dir/build
+make[1]: Entering directory `/media/work/work2/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp'
+Building CXX object CMakeFiles/cmTC_0f614.dir/feature_tests.cxx.o
+/usr/bin/c++    -std=c++98 -o CMakeFiles/cmTC_0f614.dir/feature_tests.cxx.o -c /work/SciFiMatG4_v2/SciFiSim/CMakeFiles/feature_tests.cxx
+Linking CXX executable cmTC_0f614
+/home/leverington/Programs/cmake-3.3.2-Linux-x86_64/bin/cmake -E cmake_link_script CMakeFiles/cmTC_0f614.dir/link.txt --verbose=1
+/usr/bin/c++        CMakeFiles/cmTC_0f614.dir/feature_tests.cxx.o  -o cmTC_0f614 -rdynamic 
+make[1]: Leaving directory `/media/work/work2/SciFiMatG4_v2/SciFiSim/CMakeFiles/CMakeTmp'
+
+
+    Feature record: CXX_FEATURE:0cxx_aggregate_default_initializers
+    Feature record: CXX_FEATURE:0cxx_alias_templates
+    Feature record: CXX_FEATURE:0cxx_alignas
+    Feature record: CXX_FEATURE:0cxx_alignof
+    Feature record: CXX_FEATURE:0cxx_attributes
+    Feature record: CXX_FEATURE:0cxx_attribute_deprecated
+    Feature record: CXX_FEATURE:0cxx_auto_type
+    Feature record: CXX_FEATURE:0cxx_binary_literals
+    Feature record: CXX_FEATURE:0cxx_constexpr
+    Feature record: CXX_FEATURE:0cxx_contextual_conversions
+    Feature record: CXX_FEATURE:0cxx_decltype
+    Feature record: CXX_FEATURE:0cxx_decltype_auto
+    Feature record: CXX_FEATURE:0cxx_decltype_incomplete_return_types
+    Feature record: CXX_FEATURE:0cxx_default_function_template_args
+    Feature record: CXX_FEATURE:0cxx_defaulted_functions
+    Feature record: CXX_FEATURE:0cxx_defaulted_move_initializers
+    Feature record: CXX_FEATURE:0cxx_delegating_constructors
+    Feature record: CXX_FEATURE:0cxx_deleted_functions
+    Feature record: CXX_FEATURE:0cxx_digit_separators
+    Feature record: CXX_FEATURE:0cxx_enum_forward_declarations
+    Feature record: CXX_FEATURE:0cxx_explicit_conversions
+    Feature record: CXX_FEATURE:0cxx_extended_friend_declarations
+    Feature record: CXX_FEATURE:0cxx_extern_templates
+    Feature record: CXX_FEATURE:0cxx_final
+    Feature record: CXX_FEATURE:0cxx_func_identifier
+    Feature record: CXX_FEATURE:0cxx_generalized_initializers
+    Feature record: CXX_FEATURE:0cxx_generic_lambdas
+    Feature record: CXX_FEATURE:0cxx_inheriting_constructors
+    Feature record: CXX_FEATURE:0cxx_inline_namespaces
+    Feature record: CXX_FEATURE:0cxx_lambdas
+    Feature record: CXX_FEATURE:0cxx_lambda_init_captures
+    Feature record: CXX_FEATURE:0cxx_local_type_template_args
+    Feature record: CXX_FEATURE:0cxx_long_long_type
+    Feature record: CXX_FEATURE:0cxx_noexcept
+    Feature record: CXX_FEATURE:0cxx_nonstatic_member_init
+    Feature record: CXX_FEATURE:0cxx_nullptr
+    Feature record: CXX_FEATURE:0cxx_override
+    Feature record: CXX_FEATURE:0cxx_range_for
+    Feature record: CXX_FEATURE:0cxx_raw_string_literals
+    Feature record: CXX_FEATURE:0cxx_reference_qualified_functions
+    Feature record: CXX_FEATURE:0cxx_relaxed_constexpr
+    Feature record: CXX_FEATURE:0cxx_return_type_deduction
+    Feature record: CXX_FEATURE:0cxx_right_angle_brackets
+    Feature record: CXX_FEATURE:0cxx_rvalue_references
+    Feature record: CXX_FEATURE:0cxx_sizeof_member
+    Feature record: CXX_FEATURE:0cxx_static_assert
+    Feature record: CXX_FEATURE:0cxx_strong_enums
+    Feature record: CXX_FEATURE:1cxx_template_template_parameters
+    Feature record: CXX_FEATURE:0cxx_thread_local
+    Feature record: CXX_FEATURE:0cxx_trailing_return_types
+    Feature record: CXX_FEATURE:0cxx_unicode_literals
+    Feature record: CXX_FEATURE:0cxx_uniform_initialization
+    Feature record: CXX_FEATURE:0cxx_unrestricted_unions
+    Feature record: CXX_FEATURE:0cxx_user_literals
+    Feature record: CXX_FEATURE:0cxx_variable_templates
+    Feature record: CXX_FEATURE:0cxx_variadic_macros
+    Feature record: CXX_FEATURE:0cxx_variadic_templates

SciFiSim/CMakeFiles/CMakeRuleHashes.txt

@@ -0,0 +1,2 @@
+# Hashes of file build rules.
+887067886e476ebf1513a83a71192e3e CMakeFiles/DEPENDS

SciFiSim/CMakeFiles/DEPENDS.dir/DependInfo.cmake

@@ -0,0 +1,8 @@
+# The set of languages for which implicit dependencies are needed:
+set(CMAKE_DEPENDS_LANGUAGES
+  )
+# The set of files for implicit dependencies of each language:
+
+# Targets to which this target links.
+set(CMAKE_TARGET_LINKED_INFO_FILES
+  )

SciFiSim/CMakeFiles/DEPENDS.dir/build.make

@@ -0,0 +1,72 @@
+# CMAKE generated file: DO NOT EDIT!
+# Generated by "Unix Makefiles" Generator, CMake Version 3.3
+
+# Delete rule output on recipe failure.
+.DELETE_ON_ERROR:
+
+
+#=============================================================================
+# Special targets provided by cmake.
+
+# Disable implicit rules so canonical targets will work.
+.SUFFIXES:
+
+
+# Remove some rules from gmake that .SUFFIXES does not remove.
+SUFFIXES =
+
+.SUFFIXES: .hpux_make_needs_suffix_list
+
+
+# Suppress display of executed commands.
+$(VERBOSE).SILENT:
+
+
+# A target that is always out of date.
+cmake_force:
+
+.PHONY : cmake_force
+
+#=============================================================================
+# Set environment variables for the build.
+
+# The shell in which to execute make rules.
+SHELL = /bin/sh
+
+# The CMake executable.
+CMAKE_COMMAND = /home/leverington/Programs/cmake-3.3.2-Linux-x86_64/bin/cmake
+
+# The command to remove a file.
+RM = /home/leverington/Programs/cmake-3.3.2-Linux-x86_64/bin/cmake -E remove -f
+
+# Escaping for special characters.
+EQUALS = =
+
+# The top-level source directory on which CMake was run.
+CMAKE_SOURCE_DIR = /work/SciFiMatG4_v2/SciFiSim
+
+# The top-level build directory on which CMake was run.
+CMAKE_BINARY_DIR = /work/SciFiMatG4_v2/SciFiSim
+
+# Utility rule file for DEPENDS.
+
+# Include the progress variables for this target.
+include CMakeFiles/DEPENDS.dir/progress.make
+
+DEPENDS: CMakeFiles/DEPENDS.dir/build.make
+
+.PHONY : DEPENDS
+
+# Rule to build all files generated by this target.
+CMakeFiles/DEPENDS.dir/build: DEPENDS
+
+.PHONY : CMakeFiles/DEPENDS.dir/build
+
+CMakeFiles/DEPENDS.dir/clean:
+	$(CMAKE_COMMAND) -P CMakeFiles/DEPENDS.dir/cmake_clean.cmake
+.PHONY : CMakeFiles/DEPENDS.dir/clean
+
+CMakeFiles/DEPENDS.dir/depend:
+	cd /work/SciFiMatG4_v2/SciFiSim && $(CMAKE_COMMAND) -E cmake_depends "Unix Makefiles" /work/SciFiMatG4_v2/SciFiSim /work/SciFiMatG4_v2/SciFiSim /work/SciFiMatG4_v2/SciFiSim /work/SciFiMatG4_v2/SciFiSim /work/SciFiMatG4_v2/SciFiSim/CMakeFiles/DEPENDS.dir/DependInfo.cmake --color=$(COLOR)
+.PHONY : CMakeFiles/DEPENDS.dir/depend
+

SciFiSim/CMakeFiles/DEPENDS.dir/cmake_clean.cmake

@@ -0,0 +1,5 @@
+
+# Per-language clean rules from dependency scanning.
+foreach(lang )
+  include(CMakeFiles/DEPENDS.dir/cmake_clean_${lang}.cmake OPTIONAL)
+endforeach()

SciFiSim/CMakeFiles/DEPENDS.dir/progress.make

@@ -0,0 +1 @@
+

SciFiSim/CMakeFiles/Makefile2

@@ -0,0 +1,140 @@
+# CMAKE generated file: DO NOT EDIT!
+# Generated by "Unix Makefiles" Generator, CMake Version 3.3
+
+# Default target executed when no arguments are given to make.
+default_target: all
+
+.PHONY : default_target
+
+# The main recursive all target
+all:
+
+.PHONY : all
+
+# The main recursive preinstall target
+preinstall:
+
+.PHONY : preinstall
+
+#=============================================================================
+# Special targets provided by cmake.
+
+# Disable implicit rules so canonical targets will work.
+.SUFFIXES:
+
+
+# Remove some rules from gmake that .SUFFIXES does not remove.
+SUFFIXES =
+
+.SUFFIXES: .hpux_make_needs_suffix_list
+
+
+# Suppress display of executed commands.
+$(VERBOSE).SILENT:
+
+
+# A target that is always out of date.
+cmake_force:
+
+.PHONY : cmake_force
+
+#=============================================================================
+# Set environment variables for the build.
+
+# The shell in which to execute make rules.
+SHELL = /bin/sh
+
+# The CMake executable.
+CMAKE_COMMAND = /home/leverington/Programs/cmake-3.3.2-Linux-x86_64/bin/cmake
+
+# The command to remove a file.
+RM = /home/leverington/Programs/cmake-3.3.2-Linux-x86_64/bin/cmake -E remove -f
+
+# Escaping for special characters.
+EQUALS = =
+
+# The top-level source directory on which CMake was run.
+CMAKE_SOURCE_DIR = /work/SciFiMatG4_v2/SciFiSim
+
+# The top-level build directory on which CMake was run.
+CMAKE_BINARY_DIR = /work/SciFiMatG4_v2/SciFiSim
+
+#=============================================================================
+# Target rules for target CMakeFiles/DEPENDS.dir
+
+# All Build rule for target.
+CMakeFiles/DEPENDS.dir/all:
+	$(MAKE) -f CMakeFiles/DEPENDS.dir/build.make CMakeFiles/DEPENDS.dir/depend
+	$(MAKE) -f CMakeFiles/DEPENDS.dir/build.make CMakeFiles/DEPENDS.dir/build
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --progress-dir=/work/SciFiMatG4_v2/SciFiSim/CMakeFiles --progress-num= "Built target DEPENDS"
+.PHONY : CMakeFiles/DEPENDS.dir/all
+
+# Build rule for subdir invocation for target.
+CMakeFiles/DEPENDS.dir/rule: cmake_check_build_system
+	$(CMAKE_COMMAND) -E cmake_progress_start /work/SciFiMatG4_v2/SciFiSim/CMakeFiles 0
+	$(MAKE) -f CMakeFiles/Makefile2 CMakeFiles/DEPENDS.dir/all
+	$(CMAKE_COMMAND) -E cmake_progress_start /work/SciFiMatG4_v2/SciFiSim/CMakeFiles 0
+.PHONY : CMakeFiles/DEPENDS.dir/rule
+
+# Convenience name for target.
+DEPENDS: CMakeFiles/DEPENDS.dir/rule
+
+.PHONY : DEPENDS
+
+# clean rule for target.
+CMakeFiles/DEPENDS.dir/clean:
+	$(MAKE) -f CMakeFiles/DEPENDS.dir/build.make CMakeFiles/DEPENDS.dir/clean
+.PHONY : CMakeFiles/DEPENDS.dir/clean
+
+# clean rule for target.
+clean: CMakeFiles/DEPENDS.dir/clean
+
+.PHONY : clean
+
+#=============================================================================
+# Target rules for target CMakeFiles/scifiSim.dir
+
+# All Build rule for target.
+CMakeFiles/scifiSim.dir/all:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/depend
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/build
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --progress-dir=/work/SciFiMatG4_v2/SciFiSim/CMakeFiles --progress-num=1,2,3,4,5,6,7,8,9,10,11,12,13 "Built target scifiSim"
+.PHONY : CMakeFiles/scifiSim.dir/all
+
+# Include target in all.
+all: CMakeFiles/scifiSim.dir/all
+
+.PHONY : all
+
+# Build rule for subdir invocation for target.
+CMakeFiles/scifiSim.dir/rule: cmake_check_build_system
+	$(CMAKE_COMMAND) -E cmake_progress_start /work/SciFiMatG4_v2/SciFiSim/CMakeFiles 13
+	$(MAKE) -f CMakeFiles/Makefile2 CMakeFiles/scifiSim.dir/all
+	$(CMAKE_COMMAND) -E cmake_progress_start /work/SciFiMatG4_v2/SciFiSim/CMakeFiles 0
+.PHONY : CMakeFiles/scifiSim.dir/rule
+
+# Convenience name for target.
+scifiSim: CMakeFiles/scifiSim.dir/rule
+
+.PHONY : scifiSim
+
+# clean rule for target.
+CMakeFiles/scifiSim.dir/clean:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/clean
+.PHONY : CMakeFiles/scifiSim.dir/clean
+
+# clean rule for target.
+clean: CMakeFiles/scifiSim.dir/clean
+
+.PHONY : clean
+
+#=============================================================================
+# Special targets to cleanup operation of make.
+
+# Special rule to run CMake to check the build system integrity.
+# No rule that depends on this can have commands that come from listfiles
+# because they might be regenerated.
+cmake_check_build_system:
+	$(CMAKE_COMMAND) -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR) --check-build-system CMakeFiles/Makefile.cmake 0
+.PHONY : cmake_check_build_system
+

SciFiSim/CMakeFiles/TargetDirectories.txt

@@ -0,0 +1,2 @@
+/work/SciFiMatG4_v2/SciFiSim/CMakeFiles/DEPENDS.dir
+/work/SciFiMatG4_v2/SciFiSim/CMakeFiles/scifiSim.dir

SciFiSim/CMakeFiles/cmake.check_cache

@@ -0,0 +1 @@
+# This file is generated by cmake for dependency checking of the CMakeCache.txt file

SciFiSim/CMakeFiles/feature_tests.c

@@ -0,0 +1,34 @@
+
+  const char features[] = {""
+"C_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 404
+"1"
+#else
+"0"
+#endif
+"c_function_prototypes\n"
+"C_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 404 && defined(__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
+"1"
+#else
+"0"
+#endif
+"c_restrict\n"
+"C_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 406 && defined(__STDC_VERSION__) && __STDC_VERSION__ >= 201000L
+"1"
+#else
+"0"
+#endif
+"c_static_assert\n"
+"C_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 404 && defined(__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
+"1"
+#else
+"0"
+#endif
+"c_variadic_macros\n"
+
+};
+
+int main(int argc, char** argv) { (void)argv; return features[argc]; }

SciFiSim/CMakeFiles/feature_tests.cxx

@@ -0,0 +1,405 @@
+
+  const char features[] = {""
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 500 && __cplusplus >= 201402L
+"1"
+#else
+"0"
+#endif
+"cxx_aggregate_default_initializers\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 407 && __cplusplus >= 201103L
+"1"
+#else
+"0"
+#endif
+"cxx_alias_templates\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 408 && __cplusplus >= 201103L
+"1"
+#else
+"0"
+#endif
+"cxx_alignas\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 408 && __cplusplus >= 201103L
+"1"
+#else
+"0"
+#endif
+"cxx_alignof\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 408 && __cplusplus >= 201103L
+"1"
+#else
+"0"
+#endif
+"cxx_attributes\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 409 && __cplusplus > 201103L
+"1"
+#else
+"0"
+#endif
+"cxx_attribute_deprecated\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 404 && (__cplusplus >= 201103L || (defined(__GXX_EXPERIMENTAL_CXX0X__) && __GXX_EXPERIMENTAL_CXX0X__))
+"1"
+#else
+"0"
+#endif
+"cxx_auto_type\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 409 && __cplusplus > 201103L
+"1"
+#else
+"0"
+#endif
+"cxx_binary_literals\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 406 && (__cplusplus >= 201103L || (defined(__GXX_EXPERIMENTAL_CXX0X__) && __GXX_EXPERIMENTAL_CXX0X__))
+"1"
+#else
+"0"
+#endif
+"cxx_constexpr\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 409 && __cplusplus > 201103L
+"1"
+#else
+"0"
+#endif
+"cxx_contextual_conversions\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 404 && (__cplusplus >= 201103L || (defined(__GXX_EXPERIMENTAL_CXX0X__) && __GXX_EXPERIMENTAL_CXX0X__))
+"1"
+#else
+"0"
+#endif
+"cxx_decltype\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 409 && __cplusplus > 201103L
+"1"
+#else
+"0"
+#endif
+"cxx_decltype_auto\n"
+"CXX_FEATURE:"
+#if ((__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__) >= 40801) && __cplusplus >= 201103L
+"1"
+#else
+"0"
+#endif
+"cxx_decltype_incomplete_return_types\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 404 && (__cplusplus >= 201103L || (defined(__GXX_EXPERIMENTAL_CXX0X__) && __GXX_EXPERIMENTAL_CXX0X__))
+"1"
+#else
+"0"
+#endif
+"cxx_default_function_template_args\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 404 && (__cplusplus >= 201103L || (defined(__GXX_EXPERIMENTAL_CXX0X__) && __GXX_EXPERIMENTAL_CXX0X__))
+"1"
+#else
+"0"
+#endif
+"cxx_defaulted_functions\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 406 && (__cplusplus >= 201103L || (defined(__GXX_EXPERIMENTAL_CXX0X__) && __GXX_EXPERIMENTAL_CXX0X__))
+"1"
+#else
+"0"
+#endif
+"cxx_defaulted_move_initializers\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 407 && __cplusplus >= 201103L
+"1"
+#else
+"0"
+#endif
+"cxx_delegating_constructors\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 404 && (__cplusplus >= 201103L || (defined(__GXX_EXPERIMENTAL_CXX0X__) && __GXX_EXPERIMENTAL_CXX0X__))
+"1"
+#else
+"0"
+#endif
+"cxx_deleted_functions\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 409 && __cplusplus > 201103L
+"1"
+#else
+"0"
+#endif
+"cxx_digit_separators\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 406 && (__cplusplus >= 201103L || (defined(__GXX_EXPERIMENTAL_CXX0X__) && __GXX_EXPERIMENTAL_CXX0X__))
+"1"
+#else
+"0"
+#endif
+"cxx_enum_forward_declarations\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 405 && (__cplusplus >= 201103L || (defined(__GXX_EXPERIMENTAL_CXX0X__) && __GXX_EXPERIMENTAL_CXX0X__))
+"1"
+#else
+"0"
+#endif
+"cxx_explicit_conversions\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 407 && __cplusplus >= 201103L
+"1"
+#else
+"0"
+#endif
+"cxx_extended_friend_declarations\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 404 && (__cplusplus >= 201103L || (defined(__GXX_EXPERIMENTAL_CXX0X__) && __GXX_EXPERIMENTAL_CXX0X__))
+"1"
+#else
+"0"
+#endif
+"cxx_extern_templates\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 407 && __cplusplus >= 201103L
+"1"
+#else
+"0"
+#endif
+"cxx_final\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 404 && (__cplusplus >= 201103L || (defined(__GXX_EXPERIMENTAL_CXX0X__) && __GXX_EXPERIMENTAL_CXX0X__))
+"1"
+#else
+"0"
+#endif
+"cxx_func_identifier\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 404 && (__cplusplus >= 201103L || (defined(__GXX_EXPERIMENTAL_CXX0X__) && __GXX_EXPERIMENTAL_CXX0X__))
+"1"
+#else
+"0"
+#endif
+"cxx_generalized_initializers\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 409 && __cplusplus > 201103L
+"1"
+#else
+"0"
+#endif
+"cxx_generic_lambdas\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 408 && __cplusplus >= 201103L
+"1"
+#else
+"0"
+#endif
+"cxx_inheriting_constructors\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 404 && (__cplusplus >= 201103L || (defined(__GXX_EXPERIMENTAL_CXX0X__) && __GXX_EXPERIMENTAL_CXX0X__))
+"1"
+#else
+"0"
+#endif
+"cxx_inline_namespaces\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 405 && (__cplusplus >= 201103L || (defined(__GXX_EXPERIMENTAL_CXX0X__) && __GXX_EXPERIMENTAL_CXX0X__))
+"1"
+#else
+"0"
+#endif
+"cxx_lambdas\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 409 && __cplusplus > 201103L
+"1"
+#else
+"0"
+#endif
+"cxx_lambda_init_captures\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 405 && (__cplusplus >= 201103L || (defined(__GXX_EXPERIMENTAL_CXX0X__) && __GXX_EXPERIMENTAL_CXX0X__))
+"1"
+#else
+"0"
+#endif
+"cxx_local_type_template_args\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 404 && (__cplusplus >= 201103L || (defined(__GXX_EXPERIMENTAL_CXX0X__) && __GXX_EXPERIMENTAL_CXX0X__))
+"1"
+#else
+"0"
+#endif
+"cxx_long_long_type\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 406 && (__cplusplus >= 201103L || (defined(__GXX_EXPERIMENTAL_CXX0X__) && __GXX_EXPERIMENTAL_CXX0X__))
+"1"
+#else
+"0"
+#endif
+"cxx_noexcept\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 407 && __cplusplus >= 201103L
+"1"
+#else
+"0"
+#endif
+"cxx_nonstatic_member_init\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 406 && (__cplusplus >= 201103L || (defined(__GXX_EXPERIMENTAL_CXX0X__) && __GXX_EXPERIMENTAL_CXX0X__))
+"1"
+#else
+"0"
+#endif
+"cxx_nullptr\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 407 && __cplusplus >= 201103L
+"1"
+#else
+"0"
+#endif
+"cxx_override\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 406 && (__cplusplus >= 201103L || (defined(__GXX_EXPERIMENTAL_CXX0X__) && __GXX_EXPERIMENTAL_CXX0X__))
+"1"
+#else
+"0"
+#endif
+"cxx_range_for\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 405 && (__cplusplus >= 201103L || (defined(__GXX_EXPERIMENTAL_CXX0X__) && __GXX_EXPERIMENTAL_CXX0X__))
+"1"
+#else
+"0"
+#endif
+"cxx_raw_string_literals\n"
+"CXX_FEATURE:"
+#if ((__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__) >= 40801) && __cplusplus >= 201103L
+"1"
+#else
+"0"
+#endif
+"cxx_reference_qualified_functions\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 500 && __cplusplus >= 201402L
+"1"
+#else
+"0"
+#endif
+"cxx_relaxed_constexpr\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 409 && __cplusplus > 201103L
+"1"
+#else
+"0"
+#endif
+"cxx_return_type_deduction\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 404 && (__cplusplus >= 201103L || (defined(__GXX_EXPERIMENTAL_CXX0X__) && __GXX_EXPERIMENTAL_CXX0X__))
+"1"
+#else
+"0"
+#endif
+"cxx_right_angle_brackets\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 404 && (__cplusplus >= 201103L || (defined(__GXX_EXPERIMENTAL_CXX0X__) && __GXX_EXPERIMENTAL_CXX0X__))
+"1"
+#else
+"0"
+#endif
+"cxx_rvalue_references\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 404 && (__cplusplus >= 201103L || (defined(__GXX_EXPERIMENTAL_CXX0X__) && __GXX_EXPERIMENTAL_CXX0X__))
+"1"
+#else
+"0"
+#endif
+"cxx_sizeof_member\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 404 && (__cplusplus >= 201103L || (defined(__GXX_EXPERIMENTAL_CXX0X__) && __GXX_EXPERIMENTAL_CXX0X__))
+"1"
+#else
+"0"
+#endif
+"cxx_static_assert\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 404 && (__cplusplus >= 201103L || (defined(__GXX_EXPERIMENTAL_CXX0X__) && __GXX_EXPERIMENTAL_CXX0X__))
+"1"
+#else
+"0"
+#endif
+"cxx_strong_enums\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 404 && __cplusplus
+"1"
+#else
+"0"
+#endif
+"cxx_template_template_parameters\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 408 && __cplusplus >= 201103L
+"1"
+#else
+"0"
+#endif
+"cxx_thread_local\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 404 && (__cplusplus >= 201103L || (defined(__GXX_EXPERIMENTAL_CXX0X__) && __GXX_EXPERIMENTAL_CXX0X__))
+"1"
+#else
+"0"
+#endif
+"cxx_trailing_return_types\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 404 && (__cplusplus >= 201103L || (defined(__GXX_EXPERIMENTAL_CXX0X__) && __GXX_EXPERIMENTAL_CXX0X__))
+"1"
+#else
+"0"
+#endif
+"cxx_unicode_literals\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 404 && (__cplusplus >= 201103L || (defined(__GXX_EXPERIMENTAL_CXX0X__) && __GXX_EXPERIMENTAL_CXX0X__))
+"1"
+#else
+"0"
+#endif
+"cxx_uniform_initialization\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 406 && (__cplusplus >= 201103L || (defined(__GXX_EXPERIMENTAL_CXX0X__) && __GXX_EXPERIMENTAL_CXX0X__))
+"1"
+#else
+"0"
+#endif
+"cxx_unrestricted_unions\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 407 && __cplusplus >= 201103L
+"1"
+#else
+"0"
+#endif
+"cxx_user_literals\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 500 && __cplusplus >= 201402L
+"1"
+#else
+"0"
+#endif
+"cxx_variable_templates\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 404 && (__cplusplus >= 201103L || (defined(__GXX_EXPERIMENTAL_CXX0X__) && __GXX_EXPERIMENTAL_CXX0X__))
+"1"
+#else
+"0"
+#endif
+"cxx_variadic_macros\n"
+"CXX_FEATURE:"
+#if (__GNUC__ * 100 + __GNUC_MINOR__) >= 404 && (__cplusplus >= 201103L || (defined(__GXX_EXPERIMENTAL_CXX0X__) && __GXX_EXPERIMENTAL_CXX0X__))
+"1"
+#else
+"0"
+#endif
+"cxx_variadic_templates\n"
+
+};
+
+int main(int argc, char** argv) { (void)argv; return features[argc]; }

SciFiSim/CMakeFiles/progress.marks

@@ -0,0 +1 @@
+13

SciFiSim/CMakeFiles/scifiSim.dir/DependInfo.cmake

@@ -0,0 +1,50 @@
+# The set of languages for which implicit dependencies are needed:
+set(CMAKE_DEPENDS_LANGUAGES
+  "CXX"
+  )
+# The set of files for implicit dependencies of each language:
+set(CMAKE_DEPENDS_CHECK_CXX
+  "/work/SciFiMatG4_v2/SciFiSim/scifiSim.cc" "/work/SciFiMatG4_v2/SciFiSim/CMakeFiles/scifiSim.dir/scifiSim.cc.o"
+  "/work/SciFiMatG4_v2/SciFiSim/src/ActionInitialization.cc" "/work/SciFiMatG4_v2/SciFiSim/CMakeFiles/scifiSim.dir/src/ActionInitialization.cc.o"
+  "/work/SciFiMatG4_v2/SciFiSim/src/Analysis.cc" "/work/SciFiMatG4_v2/SciFiSim/CMakeFiles/scifiSim.dir/src/Analysis.cc.o"
+  "/work/SciFiMatG4_v2/SciFiSim/src/DetectorConstruction.cc" "/work/SciFiMatG4_v2/SciFiSim/CMakeFiles/scifiSim.dir/src/DetectorConstruction.cc.o"
+  "/work/SciFiMatG4_v2/SciFiSim/src/EventAction.cc" "/work/SciFiMatG4_v2/SciFiSim/CMakeFiles/scifiSim.dir/src/EventAction.cc.o"
+  "/work/SciFiMatG4_v2/SciFiSim/src/Parameters.cc" "/work/SciFiMatG4_v2/SciFiSim/CMakeFiles/scifiSim.dir/src/Parameters.cc.o"
+  "/work/SciFiMatG4_v2/SciFiSim/src/PhysicsList.cc" "/work/SciFiMatG4_v2/SciFiSim/CMakeFiles/scifiSim.dir/src/PhysicsList.cc.o"
+  "/work/SciFiMatG4_v2/SciFiSim/src/PrimaryGeneratorAction.cc" "/work/SciFiMatG4_v2/SciFiSim/CMakeFiles/scifiSim.dir/src/PrimaryGeneratorAction.cc.o"
+  "/work/SciFiMatG4_v2/SciFiSim/src/RunAction.cc" "/work/SciFiMatG4_v2/SciFiSim/CMakeFiles/scifiSim.dir/src/RunAction.cc.o"
+  "/work/SciFiMatG4_v2/SciFiSim/src/SensitiveDetector.cc" "/work/SciFiMatG4_v2/SciFiSim/CMakeFiles/scifiSim.dir/src/SensitiveDetector.cc.o"
+  "/work/SciFiMatG4_v2/SciFiSim/src/StackingAction.cc" "/work/SciFiMatG4_v2/SciFiSim/CMakeFiles/scifiSim.dir/src/StackingAction.cc.o"
+  "/work/SciFiMatG4_v2/SciFiSim/src/SteppingAction.cc" "/work/SciFiMatG4_v2/SciFiSim/CMakeFiles/scifiSim.dir/src/SteppingAction.cc.o"
+  )
+set(CMAKE_CXX_COMPILER_ID "GNU")
+
+# Preprocessor definitions for this target.
+set(CMAKE_TARGET_DEFINITIONS_CXX
+  "G4INTY_USE_QT"
+  "G4INTY_USE_XT"
+  "G4UI_USE"
+  "G4UI_USE_QT"
+  "G4UI_USE_TCSH"
+  "G4VERBOSE"
+  "G4VIS_USE"
+  "G4VIS_USE_OPENGL"
+  "G4VIS_USE_OPENGLQT"
+  "G4VIS_USE_OPENGLX"
+  "G4_STORE_TRAJECTORY"
+  )
+
+# The include file search paths:
+set(CMAKE_CXX_TARGET_INCLUDE_PATH
+  "/work/geant4.10.02.p01-install/include/Geant4"
+  "/usr/include/qt4"
+  "/usr/include/qt4/QtCore"
+  "/usr/include/qt4/QtGui"
+  "/usr/include/qt4/QtOpenGL"
+  "include"
+  "/usr/local/include"
+  )
+
+# Targets to which this target links.
+set(CMAKE_TARGET_LINKED_INFO_FILES
+  )

SciFiSim/CMakeFiles/scifiSim.dir/build.make

@@ -0,0 +1,452 @@
+# CMAKE generated file: DO NOT EDIT!
+# Generated by "Unix Makefiles" Generator, CMake Version 3.3
+
+# Delete rule output on recipe failure.
+.DELETE_ON_ERROR:
+
+
+#=============================================================================
+# Special targets provided by cmake.
+
+# Disable implicit rules so canonical targets will work.
+.SUFFIXES:
+
+
+# Remove some rules from gmake that .SUFFIXES does not remove.
+SUFFIXES =
+
+.SUFFIXES: .hpux_make_needs_suffix_list
+
+
+# Suppress display of executed commands.
+$(VERBOSE).SILENT:
+
+
+# A target that is always out of date.
+cmake_force:
+
+.PHONY : cmake_force
+
+#=============================================================================
+# Set environment variables for the build.
+
+# The shell in which to execute make rules.
+SHELL = /bin/sh
+
+# The CMake executable.
+CMAKE_COMMAND = /home/leverington/Programs/cmake-3.3.2-Linux-x86_64/bin/cmake
+
+# The command to remove a file.
+RM = /home/leverington/Programs/cmake-3.3.2-Linux-x86_64/bin/cmake -E remove -f
+
+# Escaping for special characters.
+EQUALS = =
+
+# The top-level source directory on which CMake was run.
+CMAKE_SOURCE_DIR = /work/SciFiMatG4_v2/SciFiSim
+
+# The top-level build directory on which CMake was run.
+CMAKE_BINARY_DIR = /work/SciFiMatG4_v2/SciFiSim
+
+# Include any dependencies generated for this target.
+include CMakeFiles/scifiSim.dir/depend.make
+
+# Include the progress variables for this target.
+include CMakeFiles/scifiSim.dir/progress.make
+
+# Include the compile flags for this target's objects.
+include CMakeFiles/scifiSim.dir/flags.make
+
+CMakeFiles/scifiSim.dir/scifiSim.cc.o: CMakeFiles/scifiSim.dir/flags.make
+CMakeFiles/scifiSim.dir/scifiSim.cc.o: scifiSim.cc
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green --progress-dir=/work/SciFiMatG4_v2/SciFiSim/CMakeFiles --progress-num=$(CMAKE_PROGRESS_1) "Building CXX object CMakeFiles/scifiSim.dir/scifiSim.cc.o"
+	/usr/bin/c++   $(CXX_DEFINES) $(CXX_FLAGS) -o CMakeFiles/scifiSim.dir/scifiSim.cc.o -c /work/SciFiMatG4_v2/SciFiSim/scifiSim.cc
+
+CMakeFiles/scifiSim.dir/scifiSim.cc.i: cmake_force
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green "Preprocessing CXX source to CMakeFiles/scifiSim.dir/scifiSim.cc.i"
+	/usr/bin/c++  $(CXX_DEFINES) $(CXX_FLAGS) -E /work/SciFiMatG4_v2/SciFiSim/scifiSim.cc > CMakeFiles/scifiSim.dir/scifiSim.cc.i
+
+CMakeFiles/scifiSim.dir/scifiSim.cc.s: cmake_force
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green "Compiling CXX source to assembly CMakeFiles/scifiSim.dir/scifiSim.cc.s"
+	/usr/bin/c++  $(CXX_DEFINES) $(CXX_FLAGS) -S /work/SciFiMatG4_v2/SciFiSim/scifiSim.cc -o CMakeFiles/scifiSim.dir/scifiSim.cc.s
+
+CMakeFiles/scifiSim.dir/scifiSim.cc.o.requires:
+
+.PHONY : CMakeFiles/scifiSim.dir/scifiSim.cc.o.requires
+
+CMakeFiles/scifiSim.dir/scifiSim.cc.o.provides: CMakeFiles/scifiSim.dir/scifiSim.cc.o.requires
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/scifiSim.cc.o.provides.build
+.PHONY : CMakeFiles/scifiSim.dir/scifiSim.cc.o.provides
+
+CMakeFiles/scifiSim.dir/scifiSim.cc.o.provides.build: CMakeFiles/scifiSim.dir/scifiSim.cc.o
+
+
+CMakeFiles/scifiSim.dir/src/RunAction.cc.o: CMakeFiles/scifiSim.dir/flags.make
+CMakeFiles/scifiSim.dir/src/RunAction.cc.o: src/RunAction.cc
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green --progress-dir=/work/SciFiMatG4_v2/SciFiSim/CMakeFiles --progress-num=$(CMAKE_PROGRESS_2) "Building CXX object CMakeFiles/scifiSim.dir/src/RunAction.cc.o"
+	/usr/bin/c++   $(CXX_DEFINES) $(CXX_FLAGS) -o CMakeFiles/scifiSim.dir/src/RunAction.cc.o -c /work/SciFiMatG4_v2/SciFiSim/src/RunAction.cc
+
+CMakeFiles/scifiSim.dir/src/RunAction.cc.i: cmake_force
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green "Preprocessing CXX source to CMakeFiles/scifiSim.dir/src/RunAction.cc.i"
+	/usr/bin/c++  $(CXX_DEFINES) $(CXX_FLAGS) -E /work/SciFiMatG4_v2/SciFiSim/src/RunAction.cc > CMakeFiles/scifiSim.dir/src/RunAction.cc.i
+
+CMakeFiles/scifiSim.dir/src/RunAction.cc.s: cmake_force
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green "Compiling CXX source to assembly CMakeFiles/scifiSim.dir/src/RunAction.cc.s"
+	/usr/bin/c++  $(CXX_DEFINES) $(CXX_FLAGS) -S /work/SciFiMatG4_v2/SciFiSim/src/RunAction.cc -o CMakeFiles/scifiSim.dir/src/RunAction.cc.s
+
+CMakeFiles/scifiSim.dir/src/RunAction.cc.o.requires:
+
+.PHONY : CMakeFiles/scifiSim.dir/src/RunAction.cc.o.requires
+
+CMakeFiles/scifiSim.dir/src/RunAction.cc.o.provides: CMakeFiles/scifiSim.dir/src/RunAction.cc.o.requires
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/RunAction.cc.o.provides.build
+.PHONY : CMakeFiles/scifiSim.dir/src/RunAction.cc.o.provides
+
+CMakeFiles/scifiSim.dir/src/RunAction.cc.o.provides.build: CMakeFiles/scifiSim.dir/src/RunAction.cc.o
+
+
+CMakeFiles/scifiSim.dir/src/PhysicsList.cc.o: CMakeFiles/scifiSim.dir/flags.make
+CMakeFiles/scifiSim.dir/src/PhysicsList.cc.o: src/PhysicsList.cc
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green --progress-dir=/work/SciFiMatG4_v2/SciFiSim/CMakeFiles --progress-num=$(CMAKE_PROGRESS_3) "Building CXX object CMakeFiles/scifiSim.dir/src/PhysicsList.cc.o"
+	/usr/bin/c++   $(CXX_DEFINES) $(CXX_FLAGS) -o CMakeFiles/scifiSim.dir/src/PhysicsList.cc.o -c /work/SciFiMatG4_v2/SciFiSim/src/PhysicsList.cc
+
+CMakeFiles/scifiSim.dir/src/PhysicsList.cc.i: cmake_force
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green "Preprocessing CXX source to CMakeFiles/scifiSim.dir/src/PhysicsList.cc.i"
+	/usr/bin/c++  $(CXX_DEFINES) $(CXX_FLAGS) -E /work/SciFiMatG4_v2/SciFiSim/src/PhysicsList.cc > CMakeFiles/scifiSim.dir/src/PhysicsList.cc.i
+
+CMakeFiles/scifiSim.dir/src/PhysicsList.cc.s: cmake_force
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green "Compiling CXX source to assembly CMakeFiles/scifiSim.dir/src/PhysicsList.cc.s"
+	/usr/bin/c++  $(CXX_DEFINES) $(CXX_FLAGS) -S /work/SciFiMatG4_v2/SciFiSim/src/PhysicsList.cc -o CMakeFiles/scifiSim.dir/src/PhysicsList.cc.s
+
+CMakeFiles/scifiSim.dir/src/PhysicsList.cc.o.requires:
+
+.PHONY : CMakeFiles/scifiSim.dir/src/PhysicsList.cc.o.requires
+
+CMakeFiles/scifiSim.dir/src/PhysicsList.cc.o.provides: CMakeFiles/scifiSim.dir/src/PhysicsList.cc.o.requires
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/PhysicsList.cc.o.provides.build
+.PHONY : CMakeFiles/scifiSim.dir/src/PhysicsList.cc.o.provides
+
+CMakeFiles/scifiSim.dir/src/PhysicsList.cc.o.provides.build: CMakeFiles/scifiSim.dir/src/PhysicsList.cc.o
+
+
+CMakeFiles/scifiSim.dir/src/ActionInitialization.cc.o: CMakeFiles/scifiSim.dir/flags.make
+CMakeFiles/scifiSim.dir/src/ActionInitialization.cc.o: src/ActionInitialization.cc
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green --progress-dir=/work/SciFiMatG4_v2/SciFiSim/CMakeFiles --progress-num=$(CMAKE_PROGRESS_4) "Building CXX object CMakeFiles/scifiSim.dir/src/ActionInitialization.cc.o"
+	/usr/bin/c++   $(CXX_DEFINES) $(CXX_FLAGS) -o CMakeFiles/scifiSim.dir/src/ActionInitialization.cc.o -c /work/SciFiMatG4_v2/SciFiSim/src/ActionInitialization.cc
+
+CMakeFiles/scifiSim.dir/src/ActionInitialization.cc.i: cmake_force
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green "Preprocessing CXX source to CMakeFiles/scifiSim.dir/src/ActionInitialization.cc.i"
+	/usr/bin/c++  $(CXX_DEFINES) $(CXX_FLAGS) -E /work/SciFiMatG4_v2/SciFiSim/src/ActionInitialization.cc > CMakeFiles/scifiSim.dir/src/ActionInitialization.cc.i
+
+CMakeFiles/scifiSim.dir/src/ActionInitialization.cc.s: cmake_force
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green "Compiling CXX source to assembly CMakeFiles/scifiSim.dir/src/ActionInitialization.cc.s"
+	/usr/bin/c++  $(CXX_DEFINES) $(CXX_FLAGS) -S /work/SciFiMatG4_v2/SciFiSim/src/ActionInitialization.cc -o CMakeFiles/scifiSim.dir/src/ActionInitialization.cc.s
+
+CMakeFiles/scifiSim.dir/src/ActionInitialization.cc.o.requires:
+
+.PHONY : CMakeFiles/scifiSim.dir/src/ActionInitialization.cc.o.requires
+
+CMakeFiles/scifiSim.dir/src/ActionInitialization.cc.o.provides: CMakeFiles/scifiSim.dir/src/ActionInitialization.cc.o.requires
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/ActionInitialization.cc.o.provides.build
+.PHONY : CMakeFiles/scifiSim.dir/src/ActionInitialization.cc.o.provides
+
+CMakeFiles/scifiSim.dir/src/ActionInitialization.cc.o.provides.build: CMakeFiles/scifiSim.dir/src/ActionInitialization.cc.o
+
+
+CMakeFiles/scifiSim.dir/src/Analysis.cc.o: CMakeFiles/scifiSim.dir/flags.make
+CMakeFiles/scifiSim.dir/src/Analysis.cc.o: src/Analysis.cc
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green --progress-dir=/work/SciFiMatG4_v2/SciFiSim/CMakeFiles --progress-num=$(CMAKE_PROGRESS_5) "Building CXX object CMakeFiles/scifiSim.dir/src/Analysis.cc.o"
+	/usr/bin/c++   $(CXX_DEFINES) $(CXX_FLAGS) -o CMakeFiles/scifiSim.dir/src/Analysis.cc.o -c /work/SciFiMatG4_v2/SciFiSim/src/Analysis.cc
+
+CMakeFiles/scifiSim.dir/src/Analysis.cc.i: cmake_force
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green "Preprocessing CXX source to CMakeFiles/scifiSim.dir/src/Analysis.cc.i"
+	/usr/bin/c++  $(CXX_DEFINES) $(CXX_FLAGS) -E /work/SciFiMatG4_v2/SciFiSim/src/Analysis.cc > CMakeFiles/scifiSim.dir/src/Analysis.cc.i
+
+CMakeFiles/scifiSim.dir/src/Analysis.cc.s: cmake_force
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green "Compiling CXX source to assembly CMakeFiles/scifiSim.dir/src/Analysis.cc.s"
+	/usr/bin/c++  $(CXX_DEFINES) $(CXX_FLAGS) -S /work/SciFiMatG4_v2/SciFiSim/src/Analysis.cc -o CMakeFiles/scifiSim.dir/src/Analysis.cc.s
+
+CMakeFiles/scifiSim.dir/src/Analysis.cc.o.requires:
+
+.PHONY : CMakeFiles/scifiSim.dir/src/Analysis.cc.o.requires
+
+CMakeFiles/scifiSim.dir/src/Analysis.cc.o.provides: CMakeFiles/scifiSim.dir/src/Analysis.cc.o.requires
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/Analysis.cc.o.provides.build
+.PHONY : CMakeFiles/scifiSim.dir/src/Analysis.cc.o.provides
+
+CMakeFiles/scifiSim.dir/src/Analysis.cc.o.provides.build: CMakeFiles/scifiSim.dir/src/Analysis.cc.o
+
+
+CMakeFiles/scifiSim.dir/src/Parameters.cc.o: CMakeFiles/scifiSim.dir/flags.make
+CMakeFiles/scifiSim.dir/src/Parameters.cc.o: src/Parameters.cc
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green --progress-dir=/work/SciFiMatG4_v2/SciFiSim/CMakeFiles --progress-num=$(CMAKE_PROGRESS_6) "Building CXX object CMakeFiles/scifiSim.dir/src/Parameters.cc.o"
+	/usr/bin/c++   $(CXX_DEFINES) $(CXX_FLAGS) -o CMakeFiles/scifiSim.dir/src/Parameters.cc.o -c /work/SciFiMatG4_v2/SciFiSim/src/Parameters.cc
+
+CMakeFiles/scifiSim.dir/src/Parameters.cc.i: cmake_force
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green "Preprocessing CXX source to CMakeFiles/scifiSim.dir/src/Parameters.cc.i"
+	/usr/bin/c++  $(CXX_DEFINES) $(CXX_FLAGS) -E /work/SciFiMatG4_v2/SciFiSim/src/Parameters.cc > CMakeFiles/scifiSim.dir/src/Parameters.cc.i
+
+CMakeFiles/scifiSim.dir/src/Parameters.cc.s: cmake_force
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green "Compiling CXX source to assembly CMakeFiles/scifiSim.dir/src/Parameters.cc.s"
+	/usr/bin/c++  $(CXX_DEFINES) $(CXX_FLAGS) -S /work/SciFiMatG4_v2/SciFiSim/src/Parameters.cc -o CMakeFiles/scifiSim.dir/src/Parameters.cc.s
+
+CMakeFiles/scifiSim.dir/src/Parameters.cc.o.requires:
+
+.PHONY : CMakeFiles/scifiSim.dir/src/Parameters.cc.o.requires
+
+CMakeFiles/scifiSim.dir/src/Parameters.cc.o.provides: CMakeFiles/scifiSim.dir/src/Parameters.cc.o.requires
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/Parameters.cc.o.provides.build
+.PHONY : CMakeFiles/scifiSim.dir/src/Parameters.cc.o.provides
+
+CMakeFiles/scifiSim.dir/src/Parameters.cc.o.provides.build: CMakeFiles/scifiSim.dir/src/Parameters.cc.o
+
+
+CMakeFiles/scifiSim.dir/src/EventAction.cc.o: CMakeFiles/scifiSim.dir/flags.make
+CMakeFiles/scifiSim.dir/src/EventAction.cc.o: src/EventAction.cc
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green --progress-dir=/work/SciFiMatG4_v2/SciFiSim/CMakeFiles --progress-num=$(CMAKE_PROGRESS_7) "Building CXX object CMakeFiles/scifiSim.dir/src/EventAction.cc.o"
+	/usr/bin/c++   $(CXX_DEFINES) $(CXX_FLAGS) -o CMakeFiles/scifiSim.dir/src/EventAction.cc.o -c /work/SciFiMatG4_v2/SciFiSim/src/EventAction.cc
+
+CMakeFiles/scifiSim.dir/src/EventAction.cc.i: cmake_force
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green "Preprocessing CXX source to CMakeFiles/scifiSim.dir/src/EventAction.cc.i"
+	/usr/bin/c++  $(CXX_DEFINES) $(CXX_FLAGS) -E /work/SciFiMatG4_v2/SciFiSim/src/EventAction.cc > CMakeFiles/scifiSim.dir/src/EventAction.cc.i
+
+CMakeFiles/scifiSim.dir/src/EventAction.cc.s: cmake_force
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green "Compiling CXX source to assembly CMakeFiles/scifiSim.dir/src/EventAction.cc.s"
+	/usr/bin/c++  $(CXX_DEFINES) $(CXX_FLAGS) -S /work/SciFiMatG4_v2/SciFiSim/src/EventAction.cc -o CMakeFiles/scifiSim.dir/src/EventAction.cc.s
+
+CMakeFiles/scifiSim.dir/src/EventAction.cc.o.requires:
+
+.PHONY : CMakeFiles/scifiSim.dir/src/EventAction.cc.o.requires
+
+CMakeFiles/scifiSim.dir/src/EventAction.cc.o.provides: CMakeFiles/scifiSim.dir/src/EventAction.cc.o.requires
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/EventAction.cc.o.provides.build
+.PHONY : CMakeFiles/scifiSim.dir/src/EventAction.cc.o.provides
+
+CMakeFiles/scifiSim.dir/src/EventAction.cc.o.provides.build: CMakeFiles/scifiSim.dir/src/EventAction.cc.o
+
+
+CMakeFiles/scifiSim.dir/src/SensitiveDetector.cc.o: CMakeFiles/scifiSim.dir/flags.make
+CMakeFiles/scifiSim.dir/src/SensitiveDetector.cc.o: src/SensitiveDetector.cc
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green --progress-dir=/work/SciFiMatG4_v2/SciFiSim/CMakeFiles --progress-num=$(CMAKE_PROGRESS_8) "Building CXX object CMakeFiles/scifiSim.dir/src/SensitiveDetector.cc.o"
+	/usr/bin/c++   $(CXX_DEFINES) $(CXX_FLAGS) -o CMakeFiles/scifiSim.dir/src/SensitiveDetector.cc.o -c /work/SciFiMatG4_v2/SciFiSim/src/SensitiveDetector.cc
+
+CMakeFiles/scifiSim.dir/src/SensitiveDetector.cc.i: cmake_force
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green "Preprocessing CXX source to CMakeFiles/scifiSim.dir/src/SensitiveDetector.cc.i"
+	/usr/bin/c++  $(CXX_DEFINES) $(CXX_FLAGS) -E /work/SciFiMatG4_v2/SciFiSim/src/SensitiveDetector.cc > CMakeFiles/scifiSim.dir/src/SensitiveDetector.cc.i
+
+CMakeFiles/scifiSim.dir/src/SensitiveDetector.cc.s: cmake_force
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green "Compiling CXX source to assembly CMakeFiles/scifiSim.dir/src/SensitiveDetector.cc.s"
+	/usr/bin/c++  $(CXX_DEFINES) $(CXX_FLAGS) -S /work/SciFiMatG4_v2/SciFiSim/src/SensitiveDetector.cc -o CMakeFiles/scifiSim.dir/src/SensitiveDetector.cc.s
+
+CMakeFiles/scifiSim.dir/src/SensitiveDetector.cc.o.requires:
+
+.PHONY : CMakeFiles/scifiSim.dir/src/SensitiveDetector.cc.o.requires
+
+CMakeFiles/scifiSim.dir/src/SensitiveDetector.cc.o.provides: CMakeFiles/scifiSim.dir/src/SensitiveDetector.cc.o.requires
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/SensitiveDetector.cc.o.provides.build
+.PHONY : CMakeFiles/scifiSim.dir/src/SensitiveDetector.cc.o.provides
+
+CMakeFiles/scifiSim.dir/src/SensitiveDetector.cc.o.provides.build: CMakeFiles/scifiSim.dir/src/SensitiveDetector.cc.o
+
+
+CMakeFiles/scifiSim.dir/src/PrimaryGeneratorAction.cc.o: CMakeFiles/scifiSim.dir/flags.make
+CMakeFiles/scifiSim.dir/src/PrimaryGeneratorAction.cc.o: src/PrimaryGeneratorAction.cc
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green --progress-dir=/work/SciFiMatG4_v2/SciFiSim/CMakeFiles --progress-num=$(CMAKE_PROGRESS_9) "Building CXX object CMakeFiles/scifiSim.dir/src/PrimaryGeneratorAction.cc.o"
+	/usr/bin/c++   $(CXX_DEFINES) $(CXX_FLAGS) -o CMakeFiles/scifiSim.dir/src/PrimaryGeneratorAction.cc.o -c /work/SciFiMatG4_v2/SciFiSim/src/PrimaryGeneratorAction.cc
+
+CMakeFiles/scifiSim.dir/src/PrimaryGeneratorAction.cc.i: cmake_force
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green "Preprocessing CXX source to CMakeFiles/scifiSim.dir/src/PrimaryGeneratorAction.cc.i"
+	/usr/bin/c++  $(CXX_DEFINES) $(CXX_FLAGS) -E /work/SciFiMatG4_v2/SciFiSim/src/PrimaryGeneratorAction.cc > CMakeFiles/scifiSim.dir/src/PrimaryGeneratorAction.cc.i
+
+CMakeFiles/scifiSim.dir/src/PrimaryGeneratorAction.cc.s: cmake_force
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green "Compiling CXX source to assembly CMakeFiles/scifiSim.dir/src/PrimaryGeneratorAction.cc.s"
+	/usr/bin/c++  $(CXX_DEFINES) $(CXX_FLAGS) -S /work/SciFiMatG4_v2/SciFiSim/src/PrimaryGeneratorAction.cc -o CMakeFiles/scifiSim.dir/src/PrimaryGeneratorAction.cc.s
+
+CMakeFiles/scifiSim.dir/src/PrimaryGeneratorAction.cc.o.requires:
+
+.PHONY : CMakeFiles/scifiSim.dir/src/PrimaryGeneratorAction.cc.o.requires
+
+CMakeFiles/scifiSim.dir/src/PrimaryGeneratorAction.cc.o.provides: CMakeFiles/scifiSim.dir/src/PrimaryGeneratorAction.cc.o.requires
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/PrimaryGeneratorAction.cc.o.provides.build
+.PHONY : CMakeFiles/scifiSim.dir/src/PrimaryGeneratorAction.cc.o.provides
+
+CMakeFiles/scifiSim.dir/src/PrimaryGeneratorAction.cc.o.provides.build: CMakeFiles/scifiSim.dir/src/PrimaryGeneratorAction.cc.o
+
+
+CMakeFiles/scifiSim.dir/src/SteppingAction.cc.o: CMakeFiles/scifiSim.dir/flags.make
+CMakeFiles/scifiSim.dir/src/SteppingAction.cc.o: src/SteppingAction.cc
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green --progress-dir=/work/SciFiMatG4_v2/SciFiSim/CMakeFiles --progress-num=$(CMAKE_PROGRESS_10) "Building CXX object CMakeFiles/scifiSim.dir/src/SteppingAction.cc.o"
+	/usr/bin/c++   $(CXX_DEFINES) $(CXX_FLAGS) -o CMakeFiles/scifiSim.dir/src/SteppingAction.cc.o -c /work/SciFiMatG4_v2/SciFiSim/src/SteppingAction.cc
+
+CMakeFiles/scifiSim.dir/src/SteppingAction.cc.i: cmake_force
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green "Preprocessing CXX source to CMakeFiles/scifiSim.dir/src/SteppingAction.cc.i"
+	/usr/bin/c++  $(CXX_DEFINES) $(CXX_FLAGS) -E /work/SciFiMatG4_v2/SciFiSim/src/SteppingAction.cc > CMakeFiles/scifiSim.dir/src/SteppingAction.cc.i
+
+CMakeFiles/scifiSim.dir/src/SteppingAction.cc.s: cmake_force
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green "Compiling CXX source to assembly CMakeFiles/scifiSim.dir/src/SteppingAction.cc.s"
+	/usr/bin/c++  $(CXX_DEFINES) $(CXX_FLAGS) -S /work/SciFiMatG4_v2/SciFiSim/src/SteppingAction.cc -o CMakeFiles/scifiSim.dir/src/SteppingAction.cc.s
+
+CMakeFiles/scifiSim.dir/src/SteppingAction.cc.o.requires:
+
+.PHONY : CMakeFiles/scifiSim.dir/src/SteppingAction.cc.o.requires
+
+CMakeFiles/scifiSim.dir/src/SteppingAction.cc.o.provides: CMakeFiles/scifiSim.dir/src/SteppingAction.cc.o.requires
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/SteppingAction.cc.o.provides.build
+.PHONY : CMakeFiles/scifiSim.dir/src/SteppingAction.cc.o.provides
+
+CMakeFiles/scifiSim.dir/src/SteppingAction.cc.o.provides.build: CMakeFiles/scifiSim.dir/src/SteppingAction.cc.o
+
+
+CMakeFiles/scifiSim.dir/src/StackingAction.cc.o: CMakeFiles/scifiSim.dir/flags.make
+CMakeFiles/scifiSim.dir/src/StackingAction.cc.o: src/StackingAction.cc
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green --progress-dir=/work/SciFiMatG4_v2/SciFiSim/CMakeFiles --progress-num=$(CMAKE_PROGRESS_11) "Building CXX object CMakeFiles/scifiSim.dir/src/StackingAction.cc.o"
+	/usr/bin/c++   $(CXX_DEFINES) $(CXX_FLAGS) -o CMakeFiles/scifiSim.dir/src/StackingAction.cc.o -c /work/SciFiMatG4_v2/SciFiSim/src/StackingAction.cc
+
+CMakeFiles/scifiSim.dir/src/StackingAction.cc.i: cmake_force
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green "Preprocessing CXX source to CMakeFiles/scifiSim.dir/src/StackingAction.cc.i"
+	/usr/bin/c++  $(CXX_DEFINES) $(CXX_FLAGS) -E /work/SciFiMatG4_v2/SciFiSim/src/StackingAction.cc > CMakeFiles/scifiSim.dir/src/StackingAction.cc.i
+
+CMakeFiles/scifiSim.dir/src/StackingAction.cc.s: cmake_force
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green "Compiling CXX source to assembly CMakeFiles/scifiSim.dir/src/StackingAction.cc.s"
+	/usr/bin/c++  $(CXX_DEFINES) $(CXX_FLAGS) -S /work/SciFiMatG4_v2/SciFiSim/src/StackingAction.cc -o CMakeFiles/scifiSim.dir/src/StackingAction.cc.s
+
+CMakeFiles/scifiSim.dir/src/StackingAction.cc.o.requires:
+
+.PHONY : CMakeFiles/scifiSim.dir/src/StackingAction.cc.o.requires
+
+CMakeFiles/scifiSim.dir/src/StackingAction.cc.o.provides: CMakeFiles/scifiSim.dir/src/StackingAction.cc.o.requires
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/StackingAction.cc.o.provides.build
+.PHONY : CMakeFiles/scifiSim.dir/src/StackingAction.cc.o.provides
+
+CMakeFiles/scifiSim.dir/src/StackingAction.cc.o.provides.build: CMakeFiles/scifiSim.dir/src/StackingAction.cc.o
+
+
+CMakeFiles/scifiSim.dir/src/DetectorConstruction.cc.o: CMakeFiles/scifiSim.dir/flags.make
+CMakeFiles/scifiSim.dir/src/DetectorConstruction.cc.o: src/DetectorConstruction.cc
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green --progress-dir=/work/SciFiMatG4_v2/SciFiSim/CMakeFiles --progress-num=$(CMAKE_PROGRESS_12) "Building CXX object CMakeFiles/scifiSim.dir/src/DetectorConstruction.cc.o"
+	/usr/bin/c++   $(CXX_DEFINES) $(CXX_FLAGS) -o CMakeFiles/scifiSim.dir/src/DetectorConstruction.cc.o -c /work/SciFiMatG4_v2/SciFiSim/src/DetectorConstruction.cc
+
+CMakeFiles/scifiSim.dir/src/DetectorConstruction.cc.i: cmake_force
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green "Preprocessing CXX source to CMakeFiles/scifiSim.dir/src/DetectorConstruction.cc.i"
+	/usr/bin/c++  $(CXX_DEFINES) $(CXX_FLAGS) -E /work/SciFiMatG4_v2/SciFiSim/src/DetectorConstruction.cc > CMakeFiles/scifiSim.dir/src/DetectorConstruction.cc.i
+
+CMakeFiles/scifiSim.dir/src/DetectorConstruction.cc.s: cmake_force
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green "Compiling CXX source to assembly CMakeFiles/scifiSim.dir/src/DetectorConstruction.cc.s"
+	/usr/bin/c++  $(CXX_DEFINES) $(CXX_FLAGS) -S /work/SciFiMatG4_v2/SciFiSim/src/DetectorConstruction.cc -o CMakeFiles/scifiSim.dir/src/DetectorConstruction.cc.s
+
+CMakeFiles/scifiSim.dir/src/DetectorConstruction.cc.o.requires:
+
+.PHONY : CMakeFiles/scifiSim.dir/src/DetectorConstruction.cc.o.requires
+
+CMakeFiles/scifiSim.dir/src/DetectorConstruction.cc.o.provides: CMakeFiles/scifiSim.dir/src/DetectorConstruction.cc.o.requires
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/DetectorConstruction.cc.o.provides.build
+.PHONY : CMakeFiles/scifiSim.dir/src/DetectorConstruction.cc.o.provides
+
+CMakeFiles/scifiSim.dir/src/DetectorConstruction.cc.o.provides.build: CMakeFiles/scifiSim.dir/src/DetectorConstruction.cc.o
+
+
+# Object files for target scifiSim
+scifiSim_OBJECTS = \
+"CMakeFiles/scifiSim.dir/scifiSim.cc.o" \
+"CMakeFiles/scifiSim.dir/src/RunAction.cc.o" \
+"CMakeFiles/scifiSim.dir/src/PhysicsList.cc.o" \
+"CMakeFiles/scifiSim.dir/src/ActionInitialization.cc.o" \
+"CMakeFiles/scifiSim.dir/src/Analysis.cc.o" \
+"CMakeFiles/scifiSim.dir/src/Parameters.cc.o" \
+"CMakeFiles/scifiSim.dir/src/EventAction.cc.o" \
+"CMakeFiles/scifiSim.dir/src/SensitiveDetector.cc.o" \
+"CMakeFiles/scifiSim.dir/src/PrimaryGeneratorAction.cc.o" \
+"CMakeFiles/scifiSim.dir/src/SteppingAction.cc.o" \
+"CMakeFiles/scifiSim.dir/src/StackingAction.cc.o" \
+"CMakeFiles/scifiSim.dir/src/DetectorConstruction.cc.o"
+
+# External object files for target scifiSim
+scifiSim_EXTERNAL_OBJECTS =
+
+scifiSim: CMakeFiles/scifiSim.dir/scifiSim.cc.o
+scifiSim: CMakeFiles/scifiSim.dir/src/RunAction.cc.o
+scifiSim: CMakeFiles/scifiSim.dir/src/PhysicsList.cc.o
+scifiSim: CMakeFiles/scifiSim.dir/src/ActionInitialization.cc.o
+scifiSim: CMakeFiles/scifiSim.dir/src/Analysis.cc.o
+scifiSim: CMakeFiles/scifiSim.dir/src/Parameters.cc.o
+scifiSim: CMakeFiles/scifiSim.dir/src/EventAction.cc.o
+scifiSim: CMakeFiles/scifiSim.dir/src/SensitiveDetector.cc.o
+scifiSim: CMakeFiles/scifiSim.dir/src/PrimaryGeneratorAction.cc.o
+scifiSim: CMakeFiles/scifiSim.dir/src/SteppingAction.cc.o
+scifiSim: CMakeFiles/scifiSim.dir/src/StackingAction.cc.o
+scifiSim: CMakeFiles/scifiSim.dir/src/DetectorConstruction.cc.o
+scifiSim: CMakeFiles/scifiSim.dir/build.make
+scifiSim: /work/geant4.10.02.p01-install/lib/libG4Tree.so
+scifiSim: /work/geant4.10.02.p01-install/lib/libG4GMocren.so
+scifiSim: /work/geant4.10.02.p01-install/lib/libG4visHepRep.so
+scifiSim: /work/geant4.10.02.p01-install/lib/libG4RayTracer.so
+scifiSim: /work/geant4.10.02.p01-install/lib/libG4VRML.so
+scifiSim: /work/geant4.10.02.p01-install/lib/libG4OpenGL.so
+scifiSim: /work/geant4.10.02.p01-install/lib/libG4gl2ps.so
+scifiSim: /work/geant4.10.02.p01-install/lib/libG4interfaces.so
+scifiSim: /work/geant4.10.02.p01-install/lib/libG4persistency.so
+scifiSim: /work/geant4.10.02.p01-install/lib/libG4analysis.so
+scifiSim: /work/geant4.10.02.p01-install/lib/libG4error_propagation.so
+scifiSim: /work/geant4.10.02.p01-install/lib/libG4readout.so
+scifiSim: /work/geant4.10.02.p01-install/lib/libG4physicslists.so
+scifiSim: /work/geant4.10.02.p01-install/lib/libG4parmodels.so
+scifiSim: /work/geant4.10.02.p01-install/lib/libG4FR.so
+scifiSim: /work/geant4.10.02.p01-install/lib/libG4vis_management.so
+scifiSim: /work/geant4.10.02.p01-install/lib/libG4modeling.so
+scifiSim: /usr/lib/x86_64-linux-gnu/libGLU.so
+scifiSim: /usr/lib/x86_64-linux-gnu/libGL.so
+scifiSim: /usr/lib/x86_64-linux-gnu/libSM.so
+scifiSim: /usr/lib/x86_64-linux-gnu/libICE.so
+scifiSim: /usr/lib/x86_64-linux-gnu/libX11.so
+scifiSim: /usr/lib/x86_64-linux-gnu/libXext.so
+scifiSim: /usr/lib/x86_64-linux-gnu/libXmu.so
+scifiSim: /usr/lib/x86_64-linux-gnu/libQtOpenGL.so
+scifiSim: /usr/lib/x86_64-linux-gnu/libQtGui.so
+scifiSim: /usr/lib/x86_64-linux-gnu/libQtCore.so
+scifiSim: /work/geant4.10.02.p01-install/lib/libG4run.so
+scifiSim: /work/geant4.10.02.p01-install/lib/libG4event.so
+scifiSim: /work/geant4.10.02.p01-install/lib/libG4tracking.so
+scifiSim: /work/geant4.10.02.p01-install/lib/libG4processes.so
+scifiSim: /work/geant4.10.02.p01-install/lib/libG4zlib.so
+scifiSim: /usr/lib/x86_64-linux-gnu/libexpat.so
+scifiSim: /work/geant4.10.02.p01-install/lib/libG4digits_hits.so
+scifiSim: /work/geant4.10.02.p01-install/lib/libG4track.so
+scifiSim: /work/geant4.10.02.p01-install/lib/libG4particles.so
+scifiSim: /work/geant4.10.02.p01-install/lib/libG4geometry.so
+scifiSim: /work/geant4.10.02.p01-install/lib/libG4materials.so
+scifiSim: /work/geant4.10.02.p01-install/lib/libG4graphics_reps.so
+scifiSim: /work/geant4.10.02.p01-install/lib/libG4intercoms.so
+scifiSim: /work/geant4.10.02.p01-install/lib/libG4global.so
+scifiSim: /work/geant4.10.02.p01-install/lib/libG4clhep.so
+scifiSim: CMakeFiles/scifiSim.dir/link.txt
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --green --bold --progress-dir=/work/SciFiMatG4_v2/SciFiSim/CMakeFiles --progress-num=$(CMAKE_PROGRESS_13) "Linking CXX executable scifiSim"
+	$(CMAKE_COMMAND) -E cmake_link_script CMakeFiles/scifiSim.dir/link.txt --verbose=$(VERBOSE)
+
+# Rule to build all files generated by this target.
+CMakeFiles/scifiSim.dir/build: scifiSim
+
+.PHONY : CMakeFiles/scifiSim.dir/build
+
+CMakeFiles/scifiSim.dir/requires: CMakeFiles/scifiSim.dir/scifiSim.cc.o.requires
+CMakeFiles/scifiSim.dir/requires: CMakeFiles/scifiSim.dir/src/RunAction.cc.o.requires
+CMakeFiles/scifiSim.dir/requires: CMakeFiles/scifiSim.dir/src/PhysicsList.cc.o.requires
+CMakeFiles/scifiSim.dir/requires: CMakeFiles/scifiSim.dir/src/ActionInitialization.cc.o.requires
+CMakeFiles/scifiSim.dir/requires: CMakeFiles/scifiSim.dir/src/Analysis.cc.o.requires
+CMakeFiles/scifiSim.dir/requires: CMakeFiles/scifiSim.dir/src/Parameters.cc.o.requires
+CMakeFiles/scifiSim.dir/requires: CMakeFiles/scifiSim.dir/src/EventAction.cc.o.requires
+CMakeFiles/scifiSim.dir/requires: CMakeFiles/scifiSim.dir/src/SensitiveDetector.cc.o.requires
+CMakeFiles/scifiSim.dir/requires: CMakeFiles/scifiSim.dir/src/PrimaryGeneratorAction.cc.o.requires
+CMakeFiles/scifiSim.dir/requires: CMakeFiles/scifiSim.dir/src/SteppingAction.cc.o.requires
+CMakeFiles/scifiSim.dir/requires: CMakeFiles/scifiSim.dir/src/StackingAction.cc.o.requires
+CMakeFiles/scifiSim.dir/requires: CMakeFiles/scifiSim.dir/src/DetectorConstruction.cc.o.requires
+
+.PHONY : CMakeFiles/scifiSim.dir/requires
+
+CMakeFiles/scifiSim.dir/clean:
+	$(CMAKE_COMMAND) -P CMakeFiles/scifiSim.dir/cmake_clean.cmake
+.PHONY : CMakeFiles/scifiSim.dir/clean
+
+CMakeFiles/scifiSim.dir/depend:
+	cd /work/SciFiMatG4_v2/SciFiSim && $(CMAKE_COMMAND) -E cmake_depends "Unix Makefiles" /work/SciFiMatG4_v2/SciFiSim /work/SciFiMatG4_v2/SciFiSim /work/SciFiMatG4_v2/SciFiSim /work/SciFiMatG4_v2/SciFiSim /work/SciFiMatG4_v2/SciFiSim/CMakeFiles/scifiSim.dir/DependInfo.cmake --color=$(COLOR)
+.PHONY : CMakeFiles/scifiSim.dir/depend
+

SciFiSim/CMakeFiles/scifiSim.dir/cmake_clean.cmake

@@ -0,0 +1,21 @@
+file(REMOVE_RECURSE
+  "CMakeFiles/scifiSim.dir/scifiSim.cc.o"
+  "CMakeFiles/scifiSim.dir/src/RunAction.cc.o"
+  "CMakeFiles/scifiSim.dir/src/PhysicsList.cc.o"
+  "CMakeFiles/scifiSim.dir/src/ActionInitialization.cc.o"
+  "CMakeFiles/scifiSim.dir/src/Analysis.cc.o"
+  "CMakeFiles/scifiSim.dir/src/Parameters.cc.o"
+  "CMakeFiles/scifiSim.dir/src/EventAction.cc.o"
+  "CMakeFiles/scifiSim.dir/src/SensitiveDetector.cc.o"
+  "CMakeFiles/scifiSim.dir/src/PrimaryGeneratorAction.cc.o"
+  "CMakeFiles/scifiSim.dir/src/SteppingAction.cc.o"
+  "CMakeFiles/scifiSim.dir/src/StackingAction.cc.o"
+  "CMakeFiles/scifiSim.dir/src/DetectorConstruction.cc.o"
+  "scifiSim.pdb"
+  "scifiSim"
+)
+
+# Per-language clean rules from dependency scanning.
+foreach(lang CXX)
+  include(CMakeFiles/scifiSim.dir/cmake_clean_${lang}.cmake OPTIONAL)
+endforeach()

SciFiSim/CMakeFiles/scifiSim.dir/depend.make

@@ -0,0 +1,2 @@
+# Empty dependencies file for scifiSim.
+# This may be replaced when dependencies are built.

SciFiSim/CMakeFiles/scifiSim.dir/flags.make

@@ -0,0 +1,8 @@
+# CMAKE generated file: DO NOT EDIT!
+# Generated by "Unix Makefiles" Generator, CMake Version 3.3
+
+# compile CXX with /usr/bin/c++
+CXX_FLAGS =  -W -Wall -pedantic -Wno-non-virtual-dtor -Wno-long-long -Wwrite-strings -Wpointer-arith -Woverloaded-virtual -Wno-variadic-macros -Wshadow -pipe -DG4USE_STD11 -std=c++11  -isystem /work/geant4.10.02.p01-install/include/Geant4 -isystem /usr/include/qt4 -isystem /usr/include/qt4/QtCore -isystem /usr/include/qt4/QtGui -isystem /usr/include/qt4/QtOpenGL -I/work/SciFiMatG4_v2/SciFiSim/include -I/usr/local/include    -std=c++11
+
+CXX_DEFINES = -DG4INTY_USE_QT -DG4INTY_USE_XT -DG4UI_USE -DG4UI_USE_QT -DG4UI_USE_TCSH -DG4VERBOSE -DG4VIS_USE -DG4VIS_USE_OPENGL -DG4VIS_USE_OPENGLQT -DG4VIS_USE_OPENGLX -DG4_STORE_TRAJECTORY
+

SciFiSim/CMakeFiles/scifiSim.dir/link.txt

@@ -0,0 +1 @@
+/usr/bin/c++    -W -Wall -pedantic -Wno-non-virtual-dtor -Wno-long-long -Wwrite-strings -Wpointer-arith -Woverloaded-virtual -Wno-variadic-macros -Wshadow -pipe -DG4USE_STD11 -std=c++11     CMakeFiles/scifiSim.dir/scifiSim.cc.o CMakeFiles/scifiSim.dir/src/RunAction.cc.o CMakeFiles/scifiSim.dir/src/PhysicsList.cc.o CMakeFiles/scifiSim.dir/src/ActionInitialization.cc.o CMakeFiles/scifiSim.dir/src/Analysis.cc.o CMakeFiles/scifiSim.dir/src/Parameters.cc.o CMakeFiles/scifiSim.dir/src/EventAction.cc.o CMakeFiles/scifiSim.dir/src/SensitiveDetector.cc.o CMakeFiles/scifiSim.dir/src/PrimaryGeneratorAction.cc.o CMakeFiles/scifiSim.dir/src/SteppingAction.cc.o CMakeFiles/scifiSim.dir/src/StackingAction.cc.o CMakeFiles/scifiSim.dir/src/DetectorConstruction.cc.o  -o scifiSim -rdynamic /work/geant4.10.02.p01-install/lib/libG4Tree.so /work/geant4.10.02.p01-install/lib/libG4GMocren.so /work/geant4.10.02.p01-install/lib/libG4visHepRep.so /work/geant4.10.02.p01-install/lib/libG4RayTracer.so /work/geant4.10.02.p01-install/lib/libG4VRML.so /work/geant4.10.02.p01-install/lib/libG4OpenGL.so /work/geant4.10.02.p01-install/lib/libG4gl2ps.so /work/geant4.10.02.p01-install/lib/libG4interfaces.so /work/geant4.10.02.p01-install/lib/libG4persistency.so /work/geant4.10.02.p01-install/lib/libG4analysis.so /work/geant4.10.02.p01-install/lib/libG4error_propagation.so /work/geant4.10.02.p01-install/lib/libG4readout.so /work/geant4.10.02.p01-install/lib/libG4physicslists.so /work/geant4.10.02.p01-install/lib/libG4parmodels.so -L/usr/local/lib -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -pthread -lm -ldl -rdynamic /work/geant4.10.02.p01-install/lib/libG4FR.so /work/geant4.10.02.p01-install/lib/libG4vis_management.so /work/geant4.10.02.p01-install/lib/libG4modeling.so -lGLU -lGL -lSM -lICE -lX11 -lXext -lXmu -lQtOpenGL -lQtGui -lQtCore /work/geant4.10.02.p01-install/lib/libG4run.so /work/geant4.10.02.p01-install/lib/libG4event.so /work/geant4.10.02.p01-install/lib/libG4tracking.so /work/geant4.10.02.p01-install/lib/libG4processes.so /work/geant4.10.02.p01-install/lib/libG4zlib.so -lexpat /work/geant4.10.02.p01-install/lib/libG4digits_hits.so /work/geant4.10.02.p01-install/lib/libG4track.so /work/geant4.10.02.p01-install/lib/libG4particles.so /work/geant4.10.02.p01-install/lib/libG4geometry.so /work/geant4.10.02.p01-install/lib/libG4materials.so /work/geant4.10.02.p01-install/lib/libG4graphics_reps.so /work/geant4.10.02.p01-install/lib/libG4intercoms.so /work/geant4.10.02.p01-install/lib/libG4global.so /work/geant4.10.02.p01-install/lib/libG4clhep.so -Wl,-rpath,/work/geant4.10.02.p01-install/lib 

SciFiSim/CMakeFiles/scifiSim.dir/progress.make

@@ -0,0 +1,14 @@
+CMAKE_PROGRESS_1 = 1
+CMAKE_PROGRESS_2 = 2
+CMAKE_PROGRESS_3 = 3
+CMAKE_PROGRESS_4 = 4
+CMAKE_PROGRESS_5 = 5
+CMAKE_PROGRESS_6 = 6
+CMAKE_PROGRESS_7 = 7
+CMAKE_PROGRESS_8 = 8
+CMAKE_PROGRESS_9 = 9
+CMAKE_PROGRESS_10 = 10
+CMAKE_PROGRESS_11 = 11
+CMAKE_PROGRESS_12 = 12
+CMAKE_PROGRESS_13 = 13
+

SciFiSim/CMakeLists.txt

@@ -0,0 +1,81 @@
+# $Id: CMakeLists.txt 86065 2014-11-07 08:51:15Z gcosmo $
+
+#----------------------------------------------------------------------------
+# Setup the project
+cmake_minimum_required(VERSION 2.6 FATAL_ERROR)
+project(scifiSim)
+
+#----------------------------------------------------------------------------
+# Find Geant4 package, activating all available UI and Vis drivers by default
+# You can set WITH_GEANT4_UIVIS to OFF via the command line or ccmake/cmake-gui
+# to build a batch mode only executable
+#
+option(WITH_GEANT4_UIVIS "Build example with Geant4 UI and Vis drivers" ON)
+if(WITH_GEANT4_UIVIS)
+  find_package(Geant4 REQUIRED ui_all vis_all)
+else()
+  find_package(Geant4 REQUIRED)
+endif()
+
+#----------------------------------------------------------------------------
+# Setup Geant4 include directories and compile definitions
+# Setup include directory for this project
+#
+include(${Geant4_USE_FILE})
+include_directories(${PROJECT_SOURCE_DIR}/include)
+
+#include("FindROOT.cmake")
+set(CMAKE_MODULE_PATH$ENV{ROOTSYS}/etc/cmake)
+find_package(ROOT REQUIRED)
+list(APPEND libs $ENV{ROOTSYS}/lib)
+include_directories($ENV{ROOTSYS}/include)
+message(status $ENV{ROOTSYS}/include)
+
+
+#----------------------------------------------------------------------------
+# Locate sources and headers for this project
+# NB: headers are included so they will show up in IDEs
+#
+file(GLOB sources ${PROJECT_SOURCE_DIR}/src/*.cc)
+file(GLOB headers ${PROJECT_SOURCE_DIR}/include/*.hh)
+
+#----------------------------------------------------------------------------
+# Add the executable, and link it to the Geant4 libraries
+#
+add_executable(scifiSim scifiSim.cc ${sources} ${headers})
+target_link_libraries(scifiSim ${Geant4_LIBRARIES} ${ROOT_LIBRARIES})
+
+#----------------------------------------------------------------------------
+# Copy all scripts to the build directory, i.e. the directory in which we
+# build B1. This is so that we can run the executable directly because it
+# relies on these scripts being in the current working directory.
+#
+set(EXAMPLEB1_SCRIPTS
+#  exampleB1.in
+#  exampleB1.out
+#  init_vis.mac
+#  run1.mac
+#  run2.mac
+#  vis.mac
+  )
+
+foreach(_script ${EXAMPLEB1_SCRIPTS})
+  configure_file(
+    ${PROJECT_SOURCE_DIR}/${_script}
+    ${PROJECT_BINARY_DIR}/${_script}
+    COPYONLY
+    )
+endforeach()
+
+#----------------------------------------------------------------------------
+# For internal Geant4 use - but has no effect if you build this
+# example standalone
+#
+add_custom_target(DEPENDS)
+
+#----------------------------------------------------------------------------
+# Install the executable to 'bin' directory under CMAKE_INSTALL_PREFIX
+#
+install(TARGETS DESTINATION bin)
+
+

SciFiSim/FindROOT.cmake

@@ -0,0 +1,160 @@
+# - Finds ROOT instalation
+# This module sets up ROOT information 
+# It defines:
+# ROOT_FOUND          If the ROOT is found
+# ROOT_INCLUDE_DIR    PATH to the include directory
+# ROOT_LIBRARIES      Most common libraries
+# ROOT_LIBRARY_DIR    PATH to the library directory 
+
+
+find_program(ROOT_CONFIG_EXECUTABLE root-config
+  PATHS $ENV{ROOTSYS}/bin)
+
+if(NOT ROOT_CONFIG_EXECUTABLE)
+  set(ROOT_FOUND FALSE)
+else()    
+  set(ROOT_FOUND TRUE)
+
+  execute_process(
+    COMMAND ${ROOT_CONFIG_EXECUTABLE} --prefix 
+    OUTPUT_VARIABLE ROOTSYS 
+    OUTPUT_STRIP_TRAILING_WHITESPACE)
+
+  execute_process(
+    COMMAND ${ROOT_CONFIG_EXECUTABLE} --version 
+    OUTPUT_VARIABLE ROOT_VERSION
+    OUTPUT_STRIP_TRAILING_WHITESPACE)
+
+  execute_process(
+    COMMAND ${ROOT_CONFIG_EXECUTABLE} --incdir
+    OUTPUT_VARIABLE ROOT_INCLUDE_DIR
+    OUTPUT_STRIP_TRAILING_WHITESPACE)
+
+  execute_process(
+    COMMAND ${ROOT_CONFIG_EXECUTABLE} --libs
+    OUTPUT_VARIABLE ROOT_LIBRARIES
+    OUTPUT_STRIP_TRAILING_WHITESPACE)
+
+  #set(ROOT_LIBRARIES ${ROOT_LIBRARIES} -lThread -lMinuit -lHtml -lVMC -lEG -lGeom -lTreePlayer -lXMLIO -lProof)
+  #set(ROOT_LIBRARIES ${ROOT_LIBRARIES} -lProofPlayer -lMLP -lSpectrum -lEve -lRGL -lGed -lXMLParser -lPhysics)
+  set(ROOT_LIBRARY_DIR ${ROOTSYS}/lib)
+
+  # Make variables changeble to the advanced user
+  mark_as_advanced(ROOT_CONFIG_EXECUTABLE)
+
+  if(NOT ROOT_FIND_QUIETLY)
+    message(STATUS "Found ROOT ${ROOT_VERSION} in ${ROOTSYS}")
+  endif()
+endif()
+
+
+include(CMakeParseArguments)
+find_program(ROOTCINT_EXECUTABLE rootcint PATHS $ENV{ROOTSYS}/bin)
+find_program(GENREFLEX_EXECUTABLE genreflex PATHS $ENV{ROOTSYS}/bin)
+find_package(GCCXML)
+
+#----------------------------------------------------------------------------
+# function ROOT_GENERATE_DICTIONARY( dictionary   
+#                                    header1 header2 ... 
+#                                    LINKDEF linkdef1 ... 
+#                                    OPTIONS opt1...)
+function(ROOT_GENERATE_DICTIONARY dictionary)
+  CMAKE_PARSE_ARGUMENTS(ARG "" "" "LINKDEF;OPTIONS" "" ${ARGN})
+  #---Get the list of header files-------------------------
+  set(headerfiles)
+  foreach(fp ${ARG_UNPARSED_ARGUMENTS})
+    file(GLOB files ${fp})
+    if(files)
+      foreach(f ${files})
+        if(NOT f MATCHES LinkDef)
+          set(headerfiles ${headerfiles} ${f})
+        endif()
+      endforeach()
+    else()
+      set(headerfiles ${headerfiles} ${fp})
+    endif()
+  endforeach()
+  #---Get the list of include directories------------------
+  get_directory_property(incdirs INCLUDE_DIRECTORIES)
+  set(includedirs) 
+  foreach( d ${incdirs})    
+   set(includedirs ${includedirs} -I${d})
+  endforeach()
+  #---Get LinkDef.h file------------------------------------
+  set(linkdefs)
+  foreach( f ${ARG_LINKDEF})
+    if( IS_ABSOLUTE ${f})
+      set(linkdefs ${linkdefs} ${f})
+    else() 
+      if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/inc/${f})
+        set(linkdefs ${linkdefs} ${CMAKE_CURRENT_SOURCE_DIR}/inc/${f})
+      else()
+        set(linkdefs ${linkdefs} ${CMAKE_CURRENT_SOURCE_DIR}/${f})
+      endif()
+    endif()
+  endforeach()
+  #---call rootcint------------------------------------------
+  add_custom_command(OUTPUT ${dictionary}.cxx ${dictionary}.h
+                     COMMAND ${ROOTCINT_EXECUTABLE} -cint -f  ${dictionary}.cxx 
+                                          -c ${ARG_OPTIONS} ${includedirs} ${headerfiles} ${linkdefs} 
+                     DEPENDS ${headerfiles} ${linkdefs})
+endfunction()
+
+#----------------------------------------------------------------------------
+# function REFLEX_GENERATE_DICTIONARY(dictionary   
+#                                     header1 header2 ... 
+#                                     SELECTION selectionfile ... 
+#                                     OPTIONS opt1...)
+function(REFLEX_GENERATE_DICTIONARY dictionary)  
+  CMAKE_PARSE_ARGUMENTS(ARG "" "" "SELECTION;OPTIONS" "" ${ARGN})
+  #---Get the list of header files-------------------------
+  set(headerfiles)
+  foreach(fp ${ARG_UNPARSED_ARGUMENTS})
+    file(GLOB files ${fp})
+    if(files)
+      foreach(f ${files})
+        set(headerfiles ${headerfiles} ${f})
+      endforeach()
+    else()
+      set(headerfiles ${headerfiles} ${fp})
+    endif()
+  endforeach()
+  #---Get Selection file------------------------------------
+  if(IS_ABSOLUTE ${ARG_SELECTION})
+    set(selectionfile ${ARG_SELECTION})
+  else() 
+    set(selectionfile ${CMAKE_CURRENT_SOURCE_DIR}/${ARG_SELECTION})
+  endif()
+  #---Get the list of include directories------------------
+  get_directory_property(incdirs INCLUDE_DIRECTORIES)
+  set(includedirs) 
+  foreach( d ${incdirs})    
+    set(includedirs ${includedirs} -I${d})
+  endforeach()
+  #---Get preprocessor definitions--------------------------
+  get_directory_property(defs COMPILE_DEFINITIONS)
+  foreach( d ${defs})    
+   set(definitions ${definitions} -D${d})
+  endforeach()
+  #---Nanes and others---------------------------------------
+  set(gensrcdict ${dictionary}.cpp)
+  if(MSVC)
+    set(gccxmlopts "--gccxmlopt=\"--gccxml-compiler cl\"")
+  else()
+    #set(gccxmlopts "--gccxmlopt=\'--gccxml-cxxflags -m64 \'")
+    set(gccxmlopts)
+  endif()  
+  #set(rootmapname ${dictionary}Dict.rootmap)
+  #set(rootmapopts --rootmap=${rootmapname} --rootmap-lib=${libprefix}${dictionary}Dict)
+  #---Check GCCXML and get path-----------------------------
+  if(GCCXML)
+    get_filename_component(gccxmlpath ${GCCXML} PATH)
+  else()
+    message(WARNING "GCCXML not found. Install and setup your environment to find 'gccxml' executable")
+  endif()
+  #---Actual command----------------------------------------
+  add_custom_command(OUTPUT ${gensrcdict} ${rootmapname}     
+                     COMMAND ${GENREFLEX_EXECUTABLE} ${headerfiles} -o ${gensrcdict} ${gccxmlopts} ${rootmapopts} --select=${selectionfile}
+                             --gccxmlpath=${gccxmlpath} ${ARG_OPTIONS} ${includedirs} ${definitions}
+                     DEPENDS ${headerfiles} ${selectionfile})
+endfunction()

SciFiSim/GNUmakefile

@@ -0,0 +1,38 @@
+# $Id: GNUmakefile 42 2010-01-15 15:48:21Z vnivanch $
+# --------------------------------------------------------------
+# GNUmakefile for examples module.  Gabriele Cosmo, 06/04/98. 
+# Modified by Mirco Deckenhoff 11/09/13
+# --------------------------------------------------------------
+
+name := scifiSim
+G4TARGET := $(name)
+G4EXLIB := true
+
+.PHONY: all
+all: lib bin
+ifndef G4SYSTEM
+    G4SYSTEM = Linux-g++
+endif
+
+ifndef G4LIB
+    G4LIB = /work/geant4.10.1-install/lib64
+endif
+
+ifndef G4INSTALL
+    G4INSTALL = /work/geant4.10.1-install/share/Geant4-10.1.0/geant4make
+endif
+
+include $(G4INSTALL)/config/architecture.gmk
+
+#Add ROOT options for compilation
+
+CPPFLAGS += `root-config --cflags --ldflags`
+LDFLAGS  += `root-config --libs --glibs`
+
+CPPFLAGS += `geant4-config --cflags`
+LDFLAGS += `geant4-config --libs`
+
+CPPFLAGS += -std=c++11
+
+include $(G4INSTALL)/config/binmake.gmk
+

SciFiSim/GNUmakefile~

@@ -0,0 +1,38 @@
+# $Id: GNUmakefile 42 2010-01-15 15:48:21Z vnivanch $
+# --------------------------------------------------------------
+# GNUmakefile for examples module.  Gabriele Cosmo, 06/04/98. 
+# Modified by Mirco Deckenhoff 11/09/13
+# --------------------------------------------------------------
+
+name := scifiSim
+G4TARGET := $(name)
+G4EXLIB := true
+
+.PHONY: all
+all: lib bin
+ifndef G4SYSTEM
+    G4SYSTEM = Linux-g++
+endif
+
+ifndef G4LIB
+    G4LIB = /work/roessler/geant4.10.00.p02-install/lib64
+endif
+
+ifndef G4INSTALL
+    G4INSTALL = /work/roessler/geant4.10.00.p02-install/share/Geant4-10.0.2/geant4make
+endif
+
+include $(G4INSTALL)/config/architecture.gmk
+
+#Add ROOT options for compilation
+
+CPPFLAGS += `root-config --cflags`
+LDFLAGS  += `root-config --libs`
+
+CPPFLAGS += `geant4-config --cflags`
+LDFLAGS += `geant4-config --libs`
+
+CPPFLAGS += -std=c++11
+
+include $(G4INSTALL)/config/binmake.gmk
+

SciFiSim/Makefile

@@ -0,0 +1,558 @@
+# CMAKE generated file: DO NOT EDIT!
+# Generated by "Unix Makefiles" Generator, CMake Version 3.3
+
+# Default target executed when no arguments are given to make.
+default_target: all
+
+.PHONY : default_target
+
+# Allow only one "make -f Makefile2" at a time, but pass parallelism.
+.NOTPARALLEL:
+
+
+#=============================================================================
+# Special targets provided by cmake.
+
+# Disable implicit rules so canonical targets will work.
+.SUFFIXES:
+
+
+# Remove some rules from gmake that .SUFFIXES does not remove.
+SUFFIXES =
+
+.SUFFIXES: .hpux_make_needs_suffix_list
+
+
+# Suppress display of executed commands.
+$(VERBOSE).SILENT:
+
+
+# A target that is always out of date.
+cmake_force:
+
+.PHONY : cmake_force
+
+#=============================================================================
+# Set environment variables for the build.
+
+# The shell in which to execute make rules.
+SHELL = /bin/sh
+
+# The CMake executable.
+CMAKE_COMMAND = /home/leverington/Programs/cmake-3.3.2-Linux-x86_64/bin/cmake
+
+# The command to remove a file.
+RM = /home/leverington/Programs/cmake-3.3.2-Linux-x86_64/bin/cmake -E remove -f
+
+# Escaping for special characters.
+EQUALS = =
+
+# The top-level source directory on which CMake was run.
+CMAKE_SOURCE_DIR = /work/SciFiMatG4_v2/SciFiSim
+
+# The top-level build directory on which CMake was run.
+CMAKE_BINARY_DIR = /work/SciFiMatG4_v2/SciFiSim
+
+#=============================================================================
+# Targets provided globally by CMake.
+
+# Special rule for the target rebuild_cache
+rebuild_cache:
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Running CMake to regenerate build system..."
+	/home/leverington/Programs/cmake-3.3.2-Linux-x86_64/bin/cmake -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR)
+.PHONY : rebuild_cache
+
+# Special rule for the target rebuild_cache
+rebuild_cache/fast: rebuild_cache
+
+.PHONY : rebuild_cache/fast
+
+# Special rule for the target list_install_components
+list_install_components:
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Only default component available"
+.PHONY : list_install_components
+
+# Special rule for the target list_install_components
+list_install_components/fast: list_install_components
+
+.PHONY : list_install_components/fast
+
+# Special rule for the target install
+install: preinstall
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Install the project..."
+	/home/leverington/Programs/cmake-3.3.2-Linux-x86_64/bin/cmake -P cmake_install.cmake
+.PHONY : install
+
+# Special rule for the target install
+install/fast: preinstall/fast
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Install the project..."
+	/home/leverington/Programs/cmake-3.3.2-Linux-x86_64/bin/cmake -P cmake_install.cmake
+.PHONY : install/fast
+
+# Special rule for the target install/local
+install/local: preinstall
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Installing only the local directory..."
+	/home/leverington/Programs/cmake-3.3.2-Linux-x86_64/bin/cmake -DCMAKE_INSTALL_LOCAL_ONLY=1 -P cmake_install.cmake
+.PHONY : install/local
+
+# Special rule for the target install/local
+install/local/fast: install/local
+
+.PHONY : install/local/fast
+
+# Special rule for the target edit_cache
+edit_cache:
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Running CMake cache editor..."
+	/home/leverington/Programs/cmake-3.3.2-Linux-x86_64/bin/ccmake -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR)
+.PHONY : edit_cache
+
+# Special rule for the target edit_cache
+edit_cache/fast: edit_cache
+
+.PHONY : edit_cache/fast
+
+# The main all target
+all: cmake_check_build_system
+	$(CMAKE_COMMAND) -E cmake_progress_start /work/SciFiMatG4_v2/SciFiSim/CMakeFiles /work/SciFiMatG4_v2/SciFiSim/CMakeFiles/progress.marks
+	$(MAKE) -f CMakeFiles/Makefile2 all
+	$(CMAKE_COMMAND) -E cmake_progress_start /work/SciFiMatG4_v2/SciFiSim/CMakeFiles 0
+.PHONY : all
+
+# The main clean target
+clean:
+	$(MAKE) -f CMakeFiles/Makefile2 clean
+.PHONY : clean
+
+# The main clean target
+clean/fast: clean
+
+.PHONY : clean/fast
+
+# Prepare targets for installation.
+preinstall: all
+	$(MAKE) -f CMakeFiles/Makefile2 preinstall
+.PHONY : preinstall
+
+# Prepare targets for installation.
+preinstall/fast:
+	$(MAKE) -f CMakeFiles/Makefile2 preinstall
+.PHONY : preinstall/fast
+
+# clear depends
+depend:
+	$(CMAKE_COMMAND) -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR) --check-build-system CMakeFiles/Makefile.cmake 1
+.PHONY : depend
+
+#=============================================================================
+# Target rules for targets named DEPENDS
+
+# Build rule for target.
+DEPENDS: cmake_check_build_system
+	$(MAKE) -f CMakeFiles/Makefile2 DEPENDS
+.PHONY : DEPENDS
+
+# fast build rule for target.
+DEPENDS/fast:
+	$(MAKE) -f CMakeFiles/DEPENDS.dir/build.make CMakeFiles/DEPENDS.dir/build
+.PHONY : DEPENDS/fast
+
+#=============================================================================
+# Target rules for targets named scifiSim
+
+# Build rule for target.
+scifiSim: cmake_check_build_system
+	$(MAKE) -f CMakeFiles/Makefile2 scifiSim
+.PHONY : scifiSim
+
+# fast build rule for target.
+scifiSim/fast:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/build
+.PHONY : scifiSim/fast
+
+scifiSim.o: scifiSim.cc.o
+
+.PHONY : scifiSim.o
+
+# target to build an object file
+scifiSim.cc.o:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/scifiSim.cc.o
+.PHONY : scifiSim.cc.o
+
+scifiSim.i: scifiSim.cc.i
+
+.PHONY : scifiSim.i
+
+# target to preprocess a source file
+scifiSim.cc.i:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/scifiSim.cc.i
+.PHONY : scifiSim.cc.i
+
+scifiSim.s: scifiSim.cc.s
+
+.PHONY : scifiSim.s
+
+# target to generate assembly for a file
+scifiSim.cc.s:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/scifiSim.cc.s
+.PHONY : scifiSim.cc.s
+
+src/ActionInitialization.o: src/ActionInitialization.cc.o
+
+.PHONY : src/ActionInitialization.o
+
+# target to build an object file
+src/ActionInitialization.cc.o:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/ActionInitialization.cc.o
+.PHONY : src/ActionInitialization.cc.o
+
+src/ActionInitialization.i: src/ActionInitialization.cc.i
+
+.PHONY : src/ActionInitialization.i
+
+# target to preprocess a source file
+src/ActionInitialization.cc.i:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/ActionInitialization.cc.i
+.PHONY : src/ActionInitialization.cc.i
+
+src/ActionInitialization.s: src/ActionInitialization.cc.s
+
+.PHONY : src/ActionInitialization.s
+
+# target to generate assembly for a file
+src/ActionInitialization.cc.s:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/ActionInitialization.cc.s
+.PHONY : src/ActionInitialization.cc.s
+
+src/Analysis.o: src/Analysis.cc.o
+
+.PHONY : src/Analysis.o
+
+# target to build an object file
+src/Analysis.cc.o:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/Analysis.cc.o
+.PHONY : src/Analysis.cc.o
+
+src/Analysis.i: src/Analysis.cc.i
+
+.PHONY : src/Analysis.i
+
+# target to preprocess a source file
+src/Analysis.cc.i:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/Analysis.cc.i
+.PHONY : src/Analysis.cc.i
+
+src/Analysis.s: src/Analysis.cc.s
+
+.PHONY : src/Analysis.s
+
+# target to generate assembly for a file
+src/Analysis.cc.s:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/Analysis.cc.s
+.PHONY : src/Analysis.cc.s
+
+src/DetectorConstruction.o: src/DetectorConstruction.cc.o
+
+.PHONY : src/DetectorConstruction.o
+
+# target to build an object file
+src/DetectorConstruction.cc.o:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/DetectorConstruction.cc.o
+.PHONY : src/DetectorConstruction.cc.o
+
+src/DetectorConstruction.i: src/DetectorConstruction.cc.i
+
+.PHONY : src/DetectorConstruction.i
+
+# target to preprocess a source file
+src/DetectorConstruction.cc.i:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/DetectorConstruction.cc.i
+.PHONY : src/DetectorConstruction.cc.i
+
+src/DetectorConstruction.s: src/DetectorConstruction.cc.s
+
+.PHONY : src/DetectorConstruction.s
+
+# target to generate assembly for a file
+src/DetectorConstruction.cc.s:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/DetectorConstruction.cc.s
+.PHONY : src/DetectorConstruction.cc.s
+
+src/EventAction.o: src/EventAction.cc.o
+
+.PHONY : src/EventAction.o
+
+# target to build an object file
+src/EventAction.cc.o:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/EventAction.cc.o
+.PHONY : src/EventAction.cc.o
+
+src/EventAction.i: src/EventAction.cc.i
+
+.PHONY : src/EventAction.i
+
+# target to preprocess a source file
+src/EventAction.cc.i:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/EventAction.cc.i
+.PHONY : src/EventAction.cc.i
+
+src/EventAction.s: src/EventAction.cc.s
+
+.PHONY : src/EventAction.s
+
+# target to generate assembly for a file
+src/EventAction.cc.s:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/EventAction.cc.s
+.PHONY : src/EventAction.cc.s
+
+src/Parameters.o: src/Parameters.cc.o
+
+.PHONY : src/Parameters.o
+
+# target to build an object file
+src/Parameters.cc.o:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/Parameters.cc.o
+.PHONY : src/Parameters.cc.o
+
+src/Parameters.i: src/Parameters.cc.i
+
+.PHONY : src/Parameters.i
+
+# target to preprocess a source file
+src/Parameters.cc.i:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/Parameters.cc.i
+.PHONY : src/Parameters.cc.i
+
+src/Parameters.s: src/Parameters.cc.s
+
+.PHONY : src/Parameters.s
+
+# target to generate assembly for a file
+src/Parameters.cc.s:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/Parameters.cc.s
+.PHONY : src/Parameters.cc.s
+
+src/PhysicsList.o: src/PhysicsList.cc.o
+
+.PHONY : src/PhysicsList.o
+
+# target to build an object file
+src/PhysicsList.cc.o:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/PhysicsList.cc.o
+.PHONY : src/PhysicsList.cc.o
+
+src/PhysicsList.i: src/PhysicsList.cc.i
+
+.PHONY : src/PhysicsList.i
+
+# target to preprocess a source file
+src/PhysicsList.cc.i:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/PhysicsList.cc.i
+.PHONY : src/PhysicsList.cc.i
+
+src/PhysicsList.s: src/PhysicsList.cc.s
+
+.PHONY : src/PhysicsList.s
+
+# target to generate assembly for a file
+src/PhysicsList.cc.s:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/PhysicsList.cc.s
+.PHONY : src/PhysicsList.cc.s
+
+src/PrimaryGeneratorAction.o: src/PrimaryGeneratorAction.cc.o
+
+.PHONY : src/PrimaryGeneratorAction.o
+
+# target to build an object file
+src/PrimaryGeneratorAction.cc.o:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/PrimaryGeneratorAction.cc.o
+.PHONY : src/PrimaryGeneratorAction.cc.o
+
+src/PrimaryGeneratorAction.i: src/PrimaryGeneratorAction.cc.i
+
+.PHONY : src/PrimaryGeneratorAction.i
+
+# target to preprocess a source file
+src/PrimaryGeneratorAction.cc.i:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/PrimaryGeneratorAction.cc.i
+.PHONY : src/PrimaryGeneratorAction.cc.i
+
+src/PrimaryGeneratorAction.s: src/PrimaryGeneratorAction.cc.s
+
+.PHONY : src/PrimaryGeneratorAction.s
+
+# target to generate assembly for a file
+src/PrimaryGeneratorAction.cc.s:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/PrimaryGeneratorAction.cc.s
+.PHONY : src/PrimaryGeneratorAction.cc.s
+
+src/RunAction.o: src/RunAction.cc.o
+
+.PHONY : src/RunAction.o
+
+# target to build an object file
+src/RunAction.cc.o:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/RunAction.cc.o
+.PHONY : src/RunAction.cc.o
+
+src/RunAction.i: src/RunAction.cc.i
+
+.PHONY : src/RunAction.i
+
+# target to preprocess a source file
+src/RunAction.cc.i:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/RunAction.cc.i
+.PHONY : src/RunAction.cc.i
+
+src/RunAction.s: src/RunAction.cc.s
+
+.PHONY : src/RunAction.s
+
+# target to generate assembly for a file
+src/RunAction.cc.s:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/RunAction.cc.s
+.PHONY : src/RunAction.cc.s
+
+src/SensitiveDetector.o: src/SensitiveDetector.cc.o
+
+.PHONY : src/SensitiveDetector.o
+
+# target to build an object file
+src/SensitiveDetector.cc.o:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/SensitiveDetector.cc.o
+.PHONY : src/SensitiveDetector.cc.o
+
+src/SensitiveDetector.i: src/SensitiveDetector.cc.i
+
+.PHONY : src/SensitiveDetector.i
+
+# target to preprocess a source file
+src/SensitiveDetector.cc.i:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/SensitiveDetector.cc.i
+.PHONY : src/SensitiveDetector.cc.i
+
+src/SensitiveDetector.s: src/SensitiveDetector.cc.s
+
+.PHONY : src/SensitiveDetector.s
+
+# target to generate assembly for a file
+src/SensitiveDetector.cc.s:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/SensitiveDetector.cc.s
+.PHONY : src/SensitiveDetector.cc.s
+
+src/StackingAction.o: src/StackingAction.cc.o
+
+.PHONY : src/StackingAction.o
+
+# target to build an object file
+src/StackingAction.cc.o:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/StackingAction.cc.o
+.PHONY : src/StackingAction.cc.o
+
+src/StackingAction.i: src/StackingAction.cc.i
+
+.PHONY : src/StackingAction.i
+
+# target to preprocess a source file
+src/StackingAction.cc.i:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/StackingAction.cc.i
+.PHONY : src/StackingAction.cc.i
+
+src/StackingAction.s: src/StackingAction.cc.s
+
+.PHONY : src/StackingAction.s
+
+# target to generate assembly for a file
+src/StackingAction.cc.s:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/StackingAction.cc.s
+.PHONY : src/StackingAction.cc.s
+
+src/SteppingAction.o: src/SteppingAction.cc.o
+
+.PHONY : src/SteppingAction.o
+
+# target to build an object file
+src/SteppingAction.cc.o:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/SteppingAction.cc.o
+.PHONY : src/SteppingAction.cc.o
+
+src/SteppingAction.i: src/SteppingAction.cc.i
+
+.PHONY : src/SteppingAction.i
+
+# target to preprocess a source file
+src/SteppingAction.cc.i:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/SteppingAction.cc.i
+.PHONY : src/SteppingAction.cc.i
+
+src/SteppingAction.s: src/SteppingAction.cc.s
+
+.PHONY : src/SteppingAction.s
+
+# target to generate assembly for a file
+src/SteppingAction.cc.s:
+	$(MAKE) -f CMakeFiles/scifiSim.dir/build.make CMakeFiles/scifiSim.dir/src/SteppingAction.cc.s
+.PHONY : src/SteppingAction.cc.s
+
+# Help Target
+help:
+	@echo "The following are some of the valid targets for this Makefile:"
+	@echo "... all (the default if no target is provided)"
+	@echo "... clean"
+	@echo "... depend"
+	@echo "... rebuild_cache"
+	@echo "... list_install_components"
+	@echo "... install"
+	@echo "... install/local"
+	@echo "... DEPENDS"
+	@echo "... edit_cache"
+	@echo "... scifiSim"
+	@echo "... scifiSim.o"
+	@echo "... scifiSim.i"
+	@echo "... scifiSim.s"
+	@echo "... src/ActionInitialization.o"
+	@echo "... src/ActionInitialization.i"
+	@echo "... src/ActionInitialization.s"
+	@echo "... src/Analysis.o"
+	@echo "... src/Analysis.i"
+	@echo "... src/Analysis.s"
+	@echo "... src/DetectorConstruction.o"
+	@echo "... src/DetectorConstruction.i"
+	@echo "... src/DetectorConstruction.s"
+	@echo "... src/EventAction.o"
+	@echo "... src/EventAction.i"
+	@echo "... src/EventAction.s"
+	@echo "... src/Parameters.o"
+	@echo "... src/Parameters.i"
+	@echo "... src/Parameters.s"
+	@echo "... src/PhysicsList.o"
+	@echo "... src/PhysicsList.i"
+	@echo "... src/PhysicsList.s"
+	@echo "... src/PrimaryGeneratorAction.o"
+	@echo "... src/PrimaryGeneratorAction.i"
+	@echo "... src/PrimaryGeneratorAction.s"
+	@echo "... src/RunAction.o"
+	@echo "... src/RunAction.i"
+	@echo "... src/RunAction.s"
+	@echo "... src/SensitiveDetector.o"
+	@echo "... src/SensitiveDetector.i"
+	@echo "... src/SensitiveDetector.s"
+	@echo "... src/StackingAction.o"
+	@echo "... src/StackingAction.i"
+	@echo "... src/StackingAction.s"
+	@echo "... src/SteppingAction.o"
+	@echo "... src/SteppingAction.i"
+	@echo "... src/SteppingAction.s"
+.PHONY : help
+
+
+
+#=============================================================================
+# Special targets to cleanup operation of make.
+
+# Special rule to run CMake to check the build system integrity.
+# No rule that depends on this can have commands that come from listfiles
+# because they might be regenerated.
+cmake_check_build_system:
+	$(CMAKE_COMMAND) -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR) --check-build-system CMakeFiles/Makefile.cmake 0
+.PHONY : cmake_check_build_system
+

SciFiSim/ParameterExplanation.txt

@@ -0,0 +1,15 @@
+wrandomSeed; // random seed for random engine
+randomNumber; // random number for detector strip positioning
+threadNumb; // the thread number
+fibreLength; // length of fibre in meter
+semiAxisZ; // semi axis of fibre in z in millimeter
+semiAxisY; // semi axis of fibre in y in millimeter
+triggerX; // x-size of Trigger in mm
+triggerY; // y-size of Trigger in mm
+triggerZ; // z-size of Trigger in mm
+triggerXPos; // x-position of Trigger in millimeter
+triggerZPos; // z-position of Trigger in millimeter
+probabilityOfPhotonLossAtSurface; // probability that a photon is killed when reaching fibre surface
+placeMirror; // place a mirror at fibre end
+mirrorReflectivity; // reflectivity of mirror at fibre end
+detectorMaterial; // place a mirror at fibre end

SciFiSim/cmake_install.cmake

@@ -0,0 +1,44 @@
+# Install script for directory: /work/SciFiMatG4_v2/SciFiSim
+
+# Set the install prefix
+if(NOT DEFINED CMAKE_INSTALL_PREFIX)
+  set(CMAKE_INSTALL_PREFIX "/usr/local")
+endif()
+string(REGEX REPLACE "/$" "" CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}")
+
+# Set the install configuration name.
+if(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
+  if(BUILD_TYPE)
+    string(REGEX REPLACE "^[^A-Za-z0-9_]+" ""
+           CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}")
+  else()
+    set(CMAKE_INSTALL_CONFIG_NAME "")
+  endif()
+  message(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"")
+endif()
+
+# Set the component getting installed.
+if(NOT CMAKE_INSTALL_COMPONENT)
+  if(COMPONENT)
+    message(STATUS "Install component: \"${COMPONENT}\"")
+    set(CMAKE_INSTALL_COMPONENT "${COMPONENT}")
+  else()
+    set(CMAKE_INSTALL_COMPONENT)
+  endif()
+endif()
+
+# Install shared libraries without execute permission?
+if(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
+  set(CMAKE_INSTALL_SO_NO_EXE "1")
+endif()
+
+if(CMAKE_INSTALL_COMPONENT)
+  set(CMAKE_INSTALL_MANIFEST "install_manifest_${CMAKE_INSTALL_COMPONENT}.txt")
+else()
+  set(CMAKE_INSTALL_MANIFEST "install_manifest.txt")
+endif()
+
+string(REPLACE ";" "\n" CMAKE_INSTALL_MANIFEST_CONTENT
+       "${CMAKE_INSTALL_MANIFEST_FILES}")
+file(WRITE "/work/SciFiMatG4_v2/SciFiSim/${CMAKE_INSTALL_MANIFEST}"
+     "${CMAKE_INSTALL_MANIFEST_CONTENT}")

SciFiSim/cmake_uninstall.cmake

@@ -0,0 +1,25 @@
+# - uninstall target template
+#
+if (NOT EXISTS "/work/roessler/SciFiSim/install_manifest.txt")
+    message(FATAL_ERROR "Cannot find install manifest: \"/work/roessler/SciFiSim/install_manifest.txt\"")
+endif(NOT EXISTS "/work/roessler/SciFiSim/install_manifest.txt")
+
+file(READ "/work/roessler/SciFiSim/install_manifest.txt" files)
+string(REGEX REPLACE "\n" ";" files "${files}")
+
+foreach (file ${files})
+    message(STATUS "Uninstalling \"$ENV{DESTDIR}${file}\"")
+    if (EXISTS "$ENV{DESTDIR}${file}")
+        execute_process(
+            COMMAND /auto/lhcb/lib/contrib/CMake/2.8.9/Linux-i386/bin/cmake -E remove "$ENV{DESTDIR}${file}"
+            OUTPUT_VARIABLE rm_out
+            RESULT_VARIABLE rm_retval
+        )
+        if(NOT ${rm_retval} EQUAL 0)
+            message(FATAL_ERROR "Problem when removing \"$ENV{DESTDIR}${file}\"")
+        endif (NOT ${rm_retval} EQUAL 0)
+    else (EXISTS "$ENV{DESTDIR}${file}")
+        message(STATUS "File \"$ENV{DESTDIR}${file}\" does not exist.")
+    endif (EXISTS "$ENV{DESTDIR}${file}")
+endforeach(file)
+

SciFiSim/cmake_uninstall.cmake.in

@@ -0,0 +1,25 @@
+# - uninstall target template
+#
+if (NOT EXISTS "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt")
+    message(FATAL_ERROR "Cannot find install manifest: \"@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt\"")
+endif(NOT EXISTS "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt")
+
+file(READ "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt" files)
+string(REGEX REPLACE "\n" ";" files "${files}")
+
+foreach (file ${files})
+    message(STATUS "Uninstalling \"$ENV{DESTDIR}${file}\"")
+    if (EXISTS "$ENV{DESTDIR}${file}")
+        execute_process(
+            COMMAND @CMAKE_COMMAND@ -E remove "$ENV{DESTDIR}${file}"
+            OUTPUT_VARIABLE rm_out
+            RESULT_VARIABLE rm_retval
+        )
+        if(NOT ${rm_retval} EQUAL 0)
+            message(FATAL_ERROR "Problem when removing \"$ENV{DESTDIR}${file}\"")
+        endif (NOT ${rm_retval} EQUAL 0)
+    else (EXISTS "$ENV{DESTDIR}${file}")
+        message(STATUS "File \"$ENV{DESTDIR}${file}\" does not exist.")
+    endif (EXISTS "$ENV{DESTDIR}${file}")
+endforeach(file)
+

SciFiSim/geant4_validate_sources.cmake

@@ -0,0 +1,152 @@
+# - Validate sources listed in sources.cmake with those on disk
+# This file is configured by Geant4 to locate all sources.cmake files in 
+# the source tree used by the current build tree. 
+#
+# We have to parse the sources.cmake files for the headers and sources 
+# because these files use the include_directories command, which is non 
+# scriptable. A simple REGEX is used to find all the .cc, .hh and .icc 
+# files listed in eah sources.cmake file. These lists are compared with 
+# a GLOB of those in the include and src directories of the module 
+# corresponding to the sources.cmake file.
+#
+# Warnings are printed when a mismatch is detected.
+#
+# Note that certain modules have configurable source lists and so we 
+# expect these to show a mismatch. We allow for this by providing the 
+# variable:
+#
+#  GEANT4_FALSEPOSITIVE_SOURCES  List of all source files (.cc, .hh, .icc)
+#                                that may result in false positive mismatch.
+#
+# As this file is configured by Geant4's CMake system the generated
+# file "geant4_validate_sources.cmake" SHOULD NOT BE EDITED
+#
+
+#-----------------------------------------------------------------------
+# List all sources that we know cause false positives, e.g. obsolete,
+# but still on disk
+#
+set(GEANT4_FALSEPOSITIVE_SOURCES
+  # - Xaw is deprecated...
+  G4UIXaw.hh
+  G4UIXaw.cc
+  # - OpenGL Wt not yet supported....
+  G4OpenGLImmediateWt.hh
+  G4OpenGLImmediateWtViewer.hh
+  G4OpenGLWtViewer.hh
+  G4OpenGLImmediateWt.cc
+  G4OpenGLImmediateWtViewer.cc
+  G4OpenGLWtViewer.cc
+  # - VRML has icc files in the src/ directory. These are only used 
+  #   internally but validate_sources assumes icc files will be in 
+  #   include/
+  #   They are covered in sources.cmake though!
+  G4VRML1SceneHandlerFunc.icc
+  G4VRML2SceneHandlerFunc.icc
+  # - Documentation of processes/hadronic/models/cascade/cascade
+  # lists some sources in in comments. These do not correspond to
+  # real sources so we can safely filter them
+  # TODO : Improve regex to identify comments!!!!
+  T1xxChannel.cc
+  XXChannel.cc
+  )
+
+#-----------------------------------------------------------------------
+# First locate our current source tree
+#
+set(GEANT4_SOURCE_TREE "/work/leverington/geant4.10.1-build/source")
+message(STATUS "Scanning source tree ${GEANT4_SOURCE_TREE}")
+
+#-----------------------------------------------------------------------
+# Now find all of the sources.cmake files...
+#
+file(GLOB_RECURSE GEANT4_SOURCESCMAKE_FILES
+  ${GEANT4_SOURCE_TREE}/*/sources.cmake
+  )
+list(LENGTH GEANT4_SOURCESCMAKE_FILES GEANT4_SOURCESCMAKE_COUNT)
+message(STATUS "Located ${GEANT4_SOURCESCMAKE_COUNT} sources.cmake files")
+
+#-----------------------------------------------------------------------
+# Parse each modules and process...
+#
+foreach(_sourcesfile ${GEANT4_SOURCESCMAKE_FILES})
+  # - Where are we?
+  get_filename_component(_sourcesfile_location ${_sourcesfile} PATH)
+
+  # - Find on disk files...
+  file(GLOB 
+    _ondisk_hh
+    RELATIVE ${_sourcesfile_location}/include
+    ${_sourcesfile_location}/include/*.hh
+    ${_sourcesfile_location}/include/*.icc
+    )
+  file(GLOB 
+    _ondisk_cc
+    RELATIVE ${_sourcesfile_location}/src
+    ${_sourcesfile_location}/src/*.cc
+    )
+
+  # - Find files listed in sources.cmake
+  # Ouch, we have to use a READ, because we can't load the module directly
+  # due to it using the non scriptable command include_directories.
+  file(READ ${_sourcesfile} _sourcesfile_contents)
+  string(REGEX MATCHALL "[A-Z0-9a-z_]+\\.cc" _sources_cc "${_sourcesfile_contents}")
+  string(REGEX MATCHALL "[A-Z0-9a-z_]+\\.(hh|icc)" _sources_hh "${_sourcesfile_contents}")
+
+  # - If we take the difference of each list (in both directions), 
+  #   then there should be no mismatch if resulting lists are empty.
+  # - On disk, but not in sources
+  set(_cmp_ondisk ${_ondisk_hh} ${_ondisk_cc})
+  set(_cmp_sources ${_sources_hh} ${_sources_cc})
+  list(REMOVE_ITEM _cmp_ondisk ${_cmp_sources})
+  set(_missing_in_sources ${_cmp_ondisk})
+
+  # - In sources, but not on disk
+  set(_cmp_ondisk ${_ondisk_hh} ${_ondisk_cc})
+  set(_cmp_sources ${_sources_hh} ${_sources_cc})
+  list(REMOVE_ITEM _cmp_sources ${_cmp_ondisk})
+  set(_missing_on_disk ${_cmp_sources})
+
+  # - Remove known false positives - can probably move this to above
+  # difference calculation.
+  if(_missing_in_sources)
+    list(REMOVE_ITEM _missing_in_sources ${GEANT4_FALSEPOSITIVE_SOURCES})
+  endif()
+  if(_missing_on_disk)
+    list(REMOVE_ITEM _missing_on_disk ${GEANT4_FALSEPOSITIVE_SOURCES})
+  endif()
+
+  # - Report if either list is not empty
+  if(_missing_in_sources OR _missing_on_disk)
+    message(" ")
+    message("Problems detected in ${_sourcesfile_location}:")
+    set(GEANT4_BUILD_ISINCONSISTENT TRUE)
+
+    # - New/Obsolete File Error
+    if(_missing_in_sources)
+      message("Sources on disk but not listed in sources.cmake:")
+      foreach(_m ${_missing_in_sources})
+        message("  ${_m}")
+      endforeach()
+    endif()
+
+    # - Removed File Error - In general, should be picked up at standard
+    # CMake run time, but we double report here to be paranoid.
+    if(_missing_on_disk)
+      message("Sources listed in sources.cmake but not on disk:")
+      foreach(_m ${_missing_on_disk})
+        message("  ${_m}")
+      endforeach()
+    endif()
+  endif()
+endforeach()
+
+#-----------------------------------------------------------------------
+# Final fail?
+#
+if(GEANT4_BUILD_ISINCONSISTENT)
+  message(FATAL_ERROR "Inconsistent Geant4 build detected!")
+else()
+  message(STATUS "Geant4 build appears consistent")
+endif()
+

SciFiSim/geant4_validate_sources.cmake~

@@ -0,0 +1,152 @@
+# - Validate sources listed in sources.cmake with those on disk
+# This file is configured by Geant4 to locate all sources.cmake files in 
+# the source tree used by the current build tree. 
+#
+# We have to parse the sources.cmake files for the headers and sources 
+# because these files use the include_directories command, which is non 
+# scriptable. A simple REGEX is used to find all the .cc, .hh and .icc 
+# files listed in eah sources.cmake file. These lists are compared with 
+# a GLOB of those in the include and src directories of the module 
+# corresponding to the sources.cmake file.
+#
+# Warnings are printed when a mismatch is detected.
+#
+# Note that certain modules have configurable source lists and so we 
+# expect these to show a mismatch. We allow for this by providing the 
+# variable:
+#
+#  GEANT4_FALSEPOSITIVE_SOURCES  List of all source files (.cc, .hh, .icc)
+#                                that may result in false positive mismatch.
+#
+# As this file is configured by Geant4's CMake system the generated
+# file "geant4_validate_sources.cmake" SHOULD NOT BE EDITED
+#
+
+#-----------------------------------------------------------------------
+# List all sources that we know cause false positives, e.g. obsolete,
+# but still on disk
+#
+set(GEANT4_FALSEPOSITIVE_SOURCES
+  # - Xaw is deprecated...
+  G4UIXaw.hh
+  G4UIXaw.cc
+  # - OpenGL Wt not yet supported....
+  G4OpenGLImmediateWt.hh
+  G4OpenGLImmediateWtViewer.hh
+  G4OpenGLWtViewer.hh
+  G4OpenGLImmediateWt.cc
+  G4OpenGLImmediateWtViewer.cc
+  G4OpenGLWtViewer.cc
+  # - VRML has icc files in the src/ directory. These are only used 
+  #   internally but validate_sources assumes icc files will be in 
+  #   include/
+  #   They are covered in sources.cmake though!
+  G4VRML1SceneHandlerFunc.icc
+  G4VRML2SceneHandlerFunc.icc
+  # - Documentation of processes/hadronic/models/cascade/cascade
+  # lists some sources in in comments. These do not correspond to
+  # real sources so we can safely filter them
+  # TODO : Improve regex to identify comments!!!!
+  T1xxChannel.cc
+  XXChannel.cc
+  )
+
+#-----------------------------------------------------------------------
+# First locate our current source tree
+#
+set(GEANT4_SOURCE_TREE "/work/roessler/geant4.10.00.p02/source")
+message(STATUS "Scanning source tree ${GEANT4_SOURCE_TREE}")
+
+#-----------------------------------------------------------------------
+# Now find all of the sources.cmake files...
+#
+file(GLOB_RECURSE GEANT4_SOURCESCMAKE_FILES
+  ${GEANT4_SOURCE_TREE}/*/sources.cmake
+  )
+list(LENGTH GEANT4_SOURCESCMAKE_FILES GEANT4_SOURCESCMAKE_COUNT)
+message(STATUS "Located ${GEANT4_SOURCESCMAKE_COUNT} sources.cmake files")
+
+#-----------------------------------------------------------------------
+# Parse each modules and process...
+#
+foreach(_sourcesfile ${GEANT4_SOURCESCMAKE_FILES})
+  # - Where are we?
+  get_filename_component(_sourcesfile_location ${_sourcesfile} PATH)
+
+  # - Find on disk files...
+  file(GLOB 
+    _ondisk_hh
+    RELATIVE ${_sourcesfile_location}/include
+    ${_sourcesfile_location}/include/*.hh
+    ${_sourcesfile_location}/include/*.icc
+    )
+  file(GLOB 
+    _ondisk_cc
+    RELATIVE ${_sourcesfile_location}/src
+    ${_sourcesfile_location}/src/*.cc
+    )
+
+  # - Find files listed in sources.cmake
+  # Ouch, we have to use a READ, because we can't load the module directly
+  # due to it using the non scriptable command include_directories.
+  file(READ ${_sourcesfile} _sourcesfile_contents)
+  string(REGEX MATCHALL "[A-Z0-9a-z_]+\\.cc" _sources_cc "${_sourcesfile_contents}")
+  string(REGEX MATCHALL "[A-Z0-9a-z_]+\\.(hh|icc)" _sources_hh "${_sourcesfile_contents}")
+
+  # - If we take the difference of each list (in both directions), 
+  #   then there should be no mismatch if resulting lists are empty.
+  # - On disk, but not in sources
+  set(_cmp_ondisk ${_ondisk_hh} ${_ondisk_cc})
+  set(_cmp_sources ${_sources_hh} ${_sources_cc})
+  list(REMOVE_ITEM _cmp_ondisk ${_cmp_sources})
+  set(_missing_in_sources ${_cmp_ondisk})
+
+  # - In sources, but not on disk
+  set(_cmp_ondisk ${_ondisk_hh} ${_ondisk_cc})
+  set(_cmp_sources ${_sources_hh} ${_sources_cc})
+  list(REMOVE_ITEM _cmp_sources ${_cmp_ondisk})
+  set(_missing_on_disk ${_cmp_sources})
+
+  # - Remove known false positives - can probably move this to above
+  # difference calculation.
+  if(_missing_in_sources)
+    list(REMOVE_ITEM _missing_in_sources ${GEANT4_FALSEPOSITIVE_SOURCES})
+  endif()
+  if(_missing_on_disk)
+    list(REMOVE_ITEM _missing_on_disk ${GEANT4_FALSEPOSITIVE_SOURCES})
+  endif()
+
+  # - Report if either list is not empty
+  if(_missing_in_sources OR _missing_on_disk)
+    message(" ")
+    message("Problems detected in ${_sourcesfile_location}:")
+    set(GEANT4_BUILD_ISINCONSISTENT TRUE)
+
+    # - New/Obsolete File Error
+    if(_missing_in_sources)
+      message("Sources on disk but not listed in sources.cmake:")
+      foreach(_m ${_missing_in_sources})
+        message("  ${_m}")
+      endforeach()
+    endif()
+
+    # - Removed File Error - In general, should be picked up at standard
+    # CMake run time, but we double report here to be paranoid.
+    if(_missing_on_disk)
+      message("Sources listed in sources.cmake but not on disk:")
+      foreach(_m ${_missing_on_disk})
+        message("  ${_m}")
+      endforeach()
+    endif()
+  endif()
+endforeach()
+
+#-----------------------------------------------------------------------
+# Final fail?
+#
+if(GEANT4_BUILD_ISINCONSISTENT)
+  message(FATAL_ERROR "Inconsistent Geant4 build detected!")
+else()
+  message(STATUS "Geant4 build appears consistent")
+endif()
+

SciFiSim/include/#SteppingAction.hh#

@@ -0,0 +1,62 @@
+// Written by Peter Stromberger
+// based on work of Mirco Deckenhoff
+
+#ifndef SteppingAction_H
+#define SteppingAction_H 1
+
+ 
+#include "globals.hh"
+#include "G4UserSteppingAction.hh"
+#include "G4OpBoundaryProcess.hh"
+#include "EventAction.hh"
+#include "G4ParticleDefinition.hh"
+#include "PrimaryGeneratorAction.hh"
+#include "TFile.h"
+#include "TH2F.h"
+#include "TH1F.h"
+#include "TTree.h"
+#include "TObject.h"
+
+
+
+
+class SteppingAction : public G4UserSteppingAction
+{
+  
+
+
+public:
+    SteppingAction(EventAction* eventAction, PrimaryGeneratorAction* pGA);
+    virtual ~SteppingAction();
+    virtual void UserSteppingAction( const G4Step* );
+
+  TFile * doseFile;
+  TH2F * dosehist50invfb;
+  Float_t dose;
+  
+private:
+    const char* primParticle;
+  G4ParticleDefinition* primDefinition;
+  PrimaryGeneratorAction* pGA;
+  EventAction* fEventAction;
+  G4int creatorProcess;
+  G4OpBoundaryProcess* opBoundaryProcess;
+  
+  
+   TFile *f = (TFile*)gROOT->GetListOfFiles()->FindObject("dose.root");
+
+  
+  TH2F * dosehist50invfb = (TH2F*)doseFile->Get("dosehist50invfb");
+
+  if (dosehist50invfb){
+    dosehist50invfb->SetDirectory(0);
+  }
+  
+
+
+
+};
+
+
+
+#endif

SciFiSim/include/ActionInitialization.hh

@@ -0,0 +1,27 @@
+/*
+ *	Author	: Peter Stromberger
+ *	Email	: stromberger@physi.uni-heidelberg.de
+ *	Date	: 14.05.2014
+ *
+ *	Description: Definition of the ActionInitialization class
+ *
+ *	file: ActionInitialization.hh
+ */
+
+#ifndef ActionInitialization_h
+#define ActionInitialization_h 1
+
+#include "G4VUserActionInitialization.hh"
+
+
+class ActionInitialization : public G4VUserActionInitialization{
+
+public:
+    ActionInitialization();
+    virtual ~ActionInitialization();
+
+    virtual void BuildForMaster() const;
+    virtual void Build() const;
+};
+
+#endif

SciFiSim/include/Analysis.hh

@@ -0,0 +1,203 @@
+// Written by Peter Stromberger
+// based on work of Mirco Deckenhoff
+
+
+#ifndef ANALYSIS_HH_
+#define ANALYSIS_HH_ 1
+
+#include "G4Event.hh"
+#include "G4Run.hh"
+#include "G4ThreeVector.hh"
+#include "TFile.h"
+#include "TH2F.h"
+#include "TH1F.h"
+#include "TTree.h"
+#include "TObject.h"
+
+#include <vector>
+#include <iostream>
+
+
+class Analysis {
+
+public:
+  
+    static Analysis* GetInstance()
+    {
+        if ( Analysis::singleton == NULL ) Analysis::singleton = new Analysis();
+    
+        return Analysis::singleton;
+    }
+
+    virtual ~Analysis() {};
+    void PrepareNewEvent(const G4Event* anEvent);
+    void PrepareNewRun(const G4Run* anRun);
+    void EndOfRun();
+    void Close();
+
+
+    // Adds a new row to the tree : detectedPhotons
+    void FillDetectedPhotons(Double_t runID, Double_t eventID, Double_t detNumb, Double_t xPixel,
+                             Double_t yPixel, Double_t energy,
+                             Double_t time, Double_t length, Double_t absTime,
+                             Double_t x, Double_t y, Double_t z,
+                             Double_t px, Double_t py, Double_t pz,
+                             Double_t vertexX, Double_t vertexY, Double_t vertexZ,
+                             Double_t vertexPx, Double_t vertexPy, Double_t vertexPz,
+                             Int_t trackId,
+                             Int_t creatorProcess, Int_t parentId);
+	
+    // Adds a new to to the tree : trigger
+    void FillTrigger(Double_t runID, Double_t eventID, Double_t edep,
+                     Double_t xPos, Double_t yPos, Double_t zPos);
+
+    // Adds a new to to the tree : initialParticle
+    void FillInitialParticle(Double_t runID, Double_t eventID,
+                             Double_t energy, Double_t xMom, Double_t yMom, Double_t zMom);
+
+    // Adds a new to to the tree : primaryParticleTrack
+    void FillPrimaryParticleTrack(Double_t runID, Double_t eventID, Double_t xPos, Double_t yPos, Double_t zPos);
+
+    // Adds a new to to the tree : energyTrack
+    void FillEnergyTrack(Double_t runID, Double_t eventID, Double_t energy, Double_t trackL);
+
+    void SetGpsPosition(G4ThreeVector position);
+    void SetGpsDirection(G4ThreeVector directtion);
+
+
+  
+
+    char* FileName();
+
+
+    void IncreaseReflectionsAtMirror(Int_t trackId);
+    void IncreaseReflectionsAtFibreSurface(Int_t trackId);
+    void IncreaseTotalReflectionsAtCladCladInterface(Int_t trackId);
+    void IncreaseTotalReflectionsAtCoreCladInterface(Int_t trackId);
+    void IncreaseFresnelReflectionsAtCladCladInterface(Int_t trackId);
+    void IncreaseFresnelReflectionsAtCoreCladInterface(Int_t trackId);
+
+    void IncreaseRefractionsAtCladCladInterface(Int_t trackId);
+    void IncreaseRefractionsAtCoreCladInterface(Int_t trackId);
+
+    void IncreaseRayleighScatterings(Int_t trackId);
+
+    void IncreaseReflectionRefractionAndScatteringVectors(Int_t trackId);
+
+
+    void IncreaseLengthInCore(Int_t trackId, Float_t lengthValue);
+    void IncreaseLengthInInnerCladding(Int_t trackId, Float_t lengthValue);
+    void IncreaseLengthInOuterCladding(Int_t trackId, Float_t lengthValue);
+
+    void IncreaseLengthVectors(Int_t trackId);
+  
+
+private:
+
+    Analysis();
+    static Analysis* singleton;
+
+    TFile* dataFile;
+    
+    char fileName[40];
+  
+  TH1F * h_energy;
+  TH1F * h_trackL;
+
+    TTree* detectedPhotons;
+    TTree* trigger;
+    TTree* primaryParticleTrack;
+    TTree* initialParticle;
+    TTree* energyTrack;
+
+
+    Float_t runIDBuffer;
+    Float_t eventIDBuffer;
+    Float_t detNumbBuffer;
+    Float_t xPixelBuffer;
+    Float_t yPixelBuffer;
+    Float_t xPosBuffer;
+    Float_t yPosBuffer;
+    Float_t zPosBuffer;
+    Float_t energyBuffer;
+    Float_t wavelengthBuffer;
+    Float_t timeBuffer;
+    Float_t lengthBuffer;
+    Float_t xMomBuffer;
+    Float_t yMomBuffer;
+    Float_t zMomBuffer;
+    Float_t edepBuffer;
+
+    Float_t gpsPositionX;
+    Float_t gpsPositionY;
+    Float_t gpsPositionZ;
+
+    Float_t gpsDirectionX;
+    Float_t gpsDirectionY;
+    Float_t gpsDirectionZ;
+
+    Int_t runIdBuffer;
+    Int_t eventIdBuffer;
+    Int_t trackIdBuffer;
+
+    Int_t creatorProcessBuffer;
+    Int_t parentIdBuffer;
+
+    Float_t xBuffer;
+    Float_t yBuffer;
+    Float_t zBuffer;
+    Float_t absTimeBuffer;
+
+    Int_t materialBuffer;
+    Int_t sectionNoBuffer;
+    Float_t doseBuffer;
+    Float_t attLengthBuffer;
+
+    Float_t pxBuffer;
+    Float_t pyBuffer;
+    Float_t pzBuffer;
+
+
+    Float_t vertexXBuffer;
+    Float_t vertexYBuffer;
+    Float_t vertexZBuffer;
+
+    Float_t vertexPxBuffer;
+    Float_t vertexPyBuffer;
+    Float_t vertexPzBuffer;
+
+    std::vector<Int_t> reflectionsAtMirror;
+    std::vector<Int_t> reflectionsAtFibreSurface;
+    std::vector<Int_t> reflectionsTotalAtCladCladInterface;
+    std::vector<Int_t> reflectionsTotalAtCoreCladInterface;
+    std::vector<Int_t> reflectionsFresnelAtCladCladInterface;
+    std::vector<Int_t> reflectionsFresnelAtCoreCladInterface;
+
+    std::vector<Int_t> refractionsAtCladCladInterface;
+    std::vector<Int_t> refractionsAtCoreCladInterface;
+
+    std::vector<Int_t> rayleighScatterings;
+
+    Int_t reflMirrBuffer;
+    Int_t reflSurfBuffer;
+    Int_t reflTotalCladCladBuffer;
+    Int_t reflTotalCoreCladBuffer;
+    Int_t reflFresnelCladCladBuffer;
+    Int_t reflFresnelCoreCladBuffer;
+
+    Int_t refracCladCladBuffer;
+    Int_t refracCoreCladBuffer;
+
+    Int_t rayleighScatteringsBuffer;
+
+
+    std::vector<Float_t> lengthInCore;
+    std::vector<Float_t> lengthInInnerCladding;
+    std::vector<Float_t> lengthInOuterCladding;
+
+    Float_t lengthInCoreBuffer;
+    Float_t lengthInInnerCladdingBuffer;
+    Float_t lengthInOuterCladdingBuffer;
+};
+
+#endif

SciFiSim/include/Analysis.hh~

@@ -0,0 +1,199 @@
+// Written by Peter Stromberger
+// based on work of Mirco Deckenhoff
+
+
+#ifndef ANALYSIS_HH_
+#define ANALYSIS_HH_ 1
+
+#include "G4Event.hh"
+#include "G4Run.hh"
+#include "G4ThreeVector.hh"
+#include "TFile.h"
+#include "TH2F.h"
+#include "TH1F.h"
+#include "TTree.h"
+#include "TObject.h"
+
+#include <vector>
+#include <iostream>
+
+
+class Analysis {
+
+public:
+  
+    static Analysis* GetInstance()
+    {
+        if ( Analysis::singleton == NULL ) Analysis::singleton = new Analysis();
+    
+        return Analysis::singleton;
+    }
+
+    virtual ~Analysis() {};
+    void PrepareNewEvent(const G4Event* anEvent);
+    void PrepareNewRun(const G4Run* anRun);
+    void EndOfRun();
+    void Close();
+
+
+    // Adds a new row to the tree : detectedPhotons
+    void FillDetectedPhotons(Double_t runID, Double_t eventID, Double_t detNumb, Double_t xPixel,
+                             Double_t yPixel, Double_t energy,
+                             Double_t time, Double_t length, Double_t absTime,
+                             Double_t x, Double_t y, Double_t z,
+                             Double_t px, Double_t py, Double_t pz,
+                             Double_t vertexX, Double_t vertexY, Double_t vertexZ,
+                             Double_t vertexPx, Double_t vertexPy, Double_t vertexPz,
+                             Int_t trackId,
+                             Int_t creatorProcess, Int_t parentId);
+	
+    // Adds a new to to the tree : trigger
+    void FillTrigger(Double_t runID, Double_t eventID, Double_t edep,
+                     Double_t xPos, Double_t yPos, Double_t zPos);
+
+    // Adds a new to to the tree : initialParticle
+    void FillInitialParticle(Double_t runID, Double_t eventID,
+                             Double_t energy, Double_t xMom, Double_t yMom, Double_t zMom);
+
+    // Adds a new to to the tree : primaryParticleTrack
+    void FillPrimaryParticleTrack(Double_t runID, Double_t eventID, Double_t xPos, Double_t yPos, Double_t zPos);
+
+    // Adds a new to to the tree : energyTrack
+    void FillEnergyTrack(Double_t runID, Double_t eventID, Double_t energy, Double_t trackL);
+
+    void SetGpsPosition(G4ThreeVector position);
+    void SetGpsDirection(G4ThreeVector directtion);
+
+
+  
+
+    char* FileName();
+
+
+    void IncreaseReflectionsAtMirror(Int_t trackId);
+    void IncreaseReflectionsAtFibreSurface(Int_t trackId);
+    void IncreaseTotalReflectionsAtCladCladInterface(Int_t trackId);
+    void IncreaseTotalReflectionsAtCoreCladInterface(Int_t trackId);
+    void IncreaseFresnelReflectionsAtCladCladInterface(Int_t trackId);
+    void IncreaseFresnelReflectionsAtCoreCladInterface(Int_t trackId);
+
+    void IncreaseRefractionsAtCladCladInterface(Int_t trackId);
+    void IncreaseRefractionsAtCoreCladInterface(Int_t trackId);
+
+    void IncreaseRayleighScatterings(Int_t trackId);
+
+    void IncreaseReflectionRefractionAndScatteringVectors(Int_t trackId);
+
+
+    void IncreaseLengthInCore(Int_t trackId, Float_t lengthValue);
+    void IncreaseLengthInInnerCladding(Int_t trackId, Float_t lengthValue);
+    void IncreaseLengthInOuterCladding(Int_t trackId, Float_t lengthValue);
+
+    void IncreaseLengthVectors(Int_t trackId);
+  
+
+private:
+
+    Analysis();
+    static Analysis* singleton;
+
+    TFile* dataFile;
+    char fileName[40];
+
+    TTree* detectedPhotons;
+    TTree* trigger;
+    TTree* primaryParticleTrack;
+    TTree* initialParticle;
+    TTree* energyTrack;
+
+
+    Float_t runIDBuffer;
+    Float_t eventIDBuffer;
+    Float_t detNumbBuffer;
+    Float_t xPixelBuffer;
+    Float_t yPixelBuffer;
+    Float_t xPosBuffer;
+    Float_t yPosBuffer;
+    Float_t zPosBuffer;
+    Float_t energyBuffer;
+    Float_t wavelengthBuffer;
+    Float_t timeBuffer;
+    Float_t lengthBuffer;
+    Float_t xMomBuffer;
+    Float_t yMomBuffer;
+    Float_t zMomBuffer;
+    Float_t edepBuffer;
+
+    Float_t gpsPositionX;
+    Float_t gpsPositionY;
+    Float_t gpsPositionZ;
+
+    Float_t gpsDirectionX;
+    Float_t gpsDirectionY;
+    Float_t gpsDirectionZ;
+
+    Int_t runIdBuffer;
+    Int_t eventIdBuffer;
+    Int_t trackIdBuffer;
+
+    Int_t creatorProcessBuffer;
+    Int_t parentIdBuffer;
+
+    Float_t xBuffer;
+    Float_t yBuffer;
+    Float_t zBuffer;
+    Float_t absTimeBuffer;
+
+    Int_t materialBuffer;
+    Int_t sectionNoBuffer;
+    Float_t doseBuffer;
+    Float_t attLengthBuffer;
+
+    Float_t pxBuffer;
+    Float_t pyBuffer;
+    Float_t pzBuffer;
+
+
+    Float_t vertexXBuffer;
+    Float_t vertexYBuffer;
+    Float_t vertexZBuffer;
+
+    Float_t vertexPxBuffer;
+    Float_t vertexPyBuffer;
+    Float_t vertexPzBuffer;
+
+    std::vector<Int_t> reflectionsAtMirror;
+    std::vector<Int_t> reflectionsAtFibreSurface;
+    std::vector<Int_t> reflectionsTotalAtCladCladInterface;
+    std::vector<Int_t> reflectionsTotalAtCoreCladInterface;
+    std::vector<Int_t> reflectionsFresnelAtCladCladInterface;
+    std::vector<Int_t> reflectionsFresnelAtCoreCladInterface;
+
+    std::vector<Int_t> refractionsAtCladCladInterface;
+    std::vector<Int_t> refractionsAtCoreCladInterface;
+
+    std::vector<Int_t> rayleighScatterings;
+
+    Int_t reflMirrBuffer;
+    Int_t reflSurfBuffer;
+    Int_t reflTotalCladCladBuffer;
+    Int_t reflTotalCoreCladBuffer;
+    Int_t reflFresnelCladCladBuffer;
+    Int_t reflFresnelCoreCladBuffer;
+
+    Int_t refracCladCladBuffer;
+    Int_t refracCoreCladBuffer;
+
+    Int_t rayleighScatteringsBuffer;
+
+
+    std::vector<Float_t> lengthInCore;
+    std::vector<Float_t> lengthInInnerCladding;
+    std::vector<Float_t> lengthInOuterCladding;
+
+    Float_t lengthInCoreBuffer;
+    Float_t lengthInInnerCladdingBuffer;
+    Float_t lengthInOuterCladdingBuffer;
+};
+
+#endif

SciFiSim/include/Convert.hh

@@ -0,0 +1,57 @@
+// Written by Peter Stromberger
+
+#ifndef CONVERT_h
+#define CONVERT_h 1
+
+#include "G4UIcommand.hh"
+#include "globals.hh"
+
+class C
+{
+public:
+
+    static G4String c(G4int);
+    static G4String c1(G4int);
+    static G4String c2(G4int);
+    static G4String c3(G4int);
+};
+
+
+inline G4String C::c(G4int i)
+{
+    return G4UIcommand::ConvertToString(i);
+}
+
+
+inline G4String C::c1(G4int i)
+{
+    G4String r;
+    if(i <10)
+        r = "00";
+    if(i > 9 && i < 100)
+        r = "0";
+    if(i > 99)
+        r = "";
+
+    return r+G4UIcommand::ConvertToString(i);
+}
+
+inline G4String C::c2(G4int i)
+{
+    return G4UIcommand::ConvertToString(i);
+}
+
+inline G4String C::c3(G4int i)
+{
+    G4String r;
+
+    if( i< 10)
+        r = "0";
+    if(i > 9)
+        r = "";
+		
+    return r+G4UIcommand::ConvertToString(i);
+}
+
+#endif
+

SciFiSim/include/DetectorConstruction.hh

@@ -0,0 +1,100 @@
+// Written by Peter Stromberger
+// based on work of Mirco Deckenhoff
+
+#ifndef DetectorConstruction_h
+#define DetectorConstruction_h 1
+
+#include "globals.hh"
+#include "G4VUserDetectorConstruction.hh"
+#include "G4ThreeVector.hh"
+
+
+class G4Element;
+class G4Material;
+class G4LogicalVolume;
+class G4MaterialPropertiesTable;
+
+class DetectorConstruction : public G4VUserDetectorConstruction
+{
+public:
+    DetectorConstruction();
+    ~DetectorConstruction();
+   
+    G4VPhysicalVolume* Construct();
+
+  G4LogicalVolume* GetScoringVolume() const { return fScoringVolume; }
+
+
+ protected:
+    G4LogicalVolume*  fScoringVolume;
+
+private:
+
+    /* ++ methods ++ */
+    void DefineMaterials();
+    void DefineMaterialProperties();
+    void ConstructFiber(); // Constructs and places the fibres
+  void ConstructFiberSheet(); // Constructs and places the fibres
+    G4ThreeVector objectPos(G4int, G4int); // for positioning of multiple fibres
+    G4ThreeVector objectPos(G4int, G4int, G4double);// for positioning of detector
+    G4ThreeVector objectPos(G4int, G4int, G4int, G4int, G4double); // pixel positioning
+
+    /* ++ attributes ++ */
+
+    // geometry
+    G4double detector_x, detector_y, detector_z;
+    G4double scint_x, scint_y, scint_z;
+    G4int Nj, Nk;
+    G4double xDist, yDist;
+    G4double stripWidth, stripHeight;
+    G4double airGap, pixelDimX, pixelDimY, epoxy_strip_width;
+    int Nx, Ny;
+  G4bool fMirrorToggle;
+  G4double fMirrorPolish, fMirrorReflectivity, fMirrorZ, fMirrorRmax;
+  G4double fWorldSizeX, fWorldSizeY,fWorldSizeZ;
+    // materials
+    G4Material *Vacuum;
+    G4Material *Air;
+    G4Material *Pstyrene;
+    G4Material *PMMA;
+    G4Material *PMMA2;
+    G4Material *Epoxy;
+    G4Material *Glue;
+    G4Material *TiO2;
+    G4Material *Abs_plastic;
+    G4Material *alu;
+
+    // material properties
+    G4MaterialPropertiesTable* MPTPStyrene;
+
+    //world
+    G4LogicalVolume * fLogicWorld;
+    G4VPhysicalVolume * fPhysiWorld;
+
+    // detector assembly
+    G4LogicalVolume * airbox_log;
+    G4VPhysicalVolume * airbox_phys;
+    
+    // detector assembly
+    G4LogicalVolume * detector_log;
+    G4VPhysicalVolume * detector_phys;
+    
+  
+    // epoxybox
+    G4LogicalVolume* epoxyLog;
+    G4VPhysicalVolume* epoxyPhy;
+
+    // abs plastic
+    G4LogicalVolume* absLog;
+    G4VPhysicalVolume* absPhy;
+
+
+    // materials and properties for fibre sections
+    G4Material* scintCoreMaterial;
+    G4Material* innerCladdingMaterial;
+    G4Material* outerCladdingMaterial;
+
+
+};
+
+#endif

SciFiSim/include/DetectorConstruction.hh~

@@ -0,0 +1,96 @@
+// Written by Peter Stromberger
+// based on work of Mirco Deckenhoff
+
+#ifndef DetectorConstruction_h
+#define DetectorConstruction_h 1
+
+#include "globals.hh"
+#include "G4VUserDetectorConstruction.hh"
+#include "G4ThreeVector.hh"
+
+
+class G4Element;
+class G4Material;
+class G4LogicalVolume;
+class G4MaterialPropertiesTable;
+
+class DetectorConstruction : public G4VUserDetectorConstruction
+{
+public:
+    DetectorConstruction();
+    ~DetectorConstruction();
+   
+    G4VPhysicalVolume* Construct();
+
+  G4LogicalVolume* GetScoringVolume() const { return fScoringVolume; }
+
+
+ protected:
+    G4LogicalVolume*  fScoringVolume;
+
+private:
+
+    /* ++ methods ++ */
+    void DefineMaterials();
+    void DefineMaterialProperties();
+    void ConstructFiber(); // Constructs and places the fibres
+  void ConstructFiberSheet(); // Constructs and places the fibres
+    G4ThreeVector objectPos(G4int, G4int); // for positioning of multiple fibres
+    G4ThreeVector objectPos(G4int, G4int, G4double);// for positioning of detector
+    G4ThreeVector objectPos(G4int, G4int, G4int, G4int, G4double); // pixel positioning
+
+    /* ++ attributes ++ */
+
+    // geometry
+    G4double detector_x, detector_y, detector_z;
+    G4double scint_x, scint_y, scint_z;
+    G4int Nj, Nk;
+    G4double xDist, yDist;
+    G4double stripWidth, stripHeight;
+    G4double airGap, pixelDimX, pixelDimY, epoxy_strip_width;
+    int Nx, Ny;
+  G4bool fMirrorToggle;
+  G4double fMirrorPolish, fMirrorReflectivity, fMirrorZ, fMirrorRmax;
+  G4double fWorldSizeX, fWorldSizeY,fWorldSizeZ;
+    // materials
+    G4Material *Vacuum;
+    G4Material *Air;
+    G4Material *Pstyrene;
+    G4Material *PMMA;
+    G4Material *PMMA2;
+    G4Material *Epoxy;
+    G4Material *Glue;
+    G4Material *TiO2;
+    G4Material *Abs_plastic;
+    G4Material *alu;
+
+    // material properties
+    G4MaterialPropertiesTable* MPTPStyrene;
+
+    //world
+    G4LogicalVolume * fLogicWorld;
+    G4VPhysicalVolume * fPhysiWorld;
+
+    // detector assembly
+    G4LogicalVolume * detector_log;
+    G4VPhysicalVolume * detector_phys;
+    
+  
+    // epoxybox
+    G4LogicalVolume* epoxyLog;
+    G4VPhysicalVolume* epoxyPhy;
+
+    // abs plastic
+    G4LogicalVolume* absLog;
+    G4VPhysicalVolume* absPhy;
+
+
+    // materials and properties for fibre sections
+    G4Material* scintCoreMaterial;
+    G4Material* innerCladdingMaterial;
+    G4Material* outerCladdingMaterial;
+
+
+};
+
+#endif

SciFiSim/include/EventAction.hh

@@ -0,0 +1,40 @@
+// Written by Peter Stromberger
+// based on work of Mirco Deckenhoff
+ 
+#ifndef EventAction_h
+#define EventAction_h 1
+
+#include "G4UserEventAction.hh"
+#include "globals.hh"
+
+class G4Event;
+
+
+class EventAction : public G4UserEventAction
+{
+public:
+    EventAction();
+    ~EventAction();
+
+public:
+    void BeginOfEventAction(const G4Event* anEvent);
+    void EndOfEventAction(const G4Event*);
+
+    void AddCore(G4double de, G4double dl);
+
+private:
+    G4double fEnergy;
+    G4double fTrackL;
+
+};
+
+
+inline void EventAction::AddCore(G4double de, G4double dl)
+{
+    fEnergy += de;
+    fTrackL += dl;
+}
+
+#endif
+
+    

SciFiSim/include/Parameters.hh

@@ -0,0 +1,170 @@
+// Written by Peter Stromberger
+// based on work of Mirco Deckenhoff
+
+
+#ifndef PARAMETERS_HH_
+#define PARAMETERS_HH_ 1
+
+#include "G4Event.hh"
+#include "G4Run.hh"
+
+#include "TFile.h"
+#include "TH2F.h"
+#include "TH1F.h"
+#include "TTree.h"
+#include "TObject.h"
+
+
+
+
+class Parameters
+{
+
+public:
+  
+    static Parameters* GetInstance()
+    {
+        if ( Parameters::singleton == NULL ) Parameters::singleton = new Parameters();
+        return Parameters::singleton;
+    }
+
+    virtual ~Parameters();
+
+
+    char* ParameterOutputFileName();
+
+    G4double RandomSeed();
+    G4double RandomNumber();
+    G4double FibreLength();
+    G4double SemiAxisZ();
+    G4double SemiAxisY();
+    G4double ProbabilityOfPhotonLossAtSurface();
+    G4bool PlaceMirror();
+    G4double MirrorReflectivity();
+    G4bool DetectorMaterial();
+  
+    G4double TriggerX();
+    G4double TriggerY();
+    G4double TriggerZ();
+  
+    G4double TriggerXPos();
+    G4double TriggerZPos();
+
+    char* EmissionSpectrumFileName();
+    G4int NumberOfEnergies();
+    G4double* Energy;
+    G4double* Intensity;
+    G4int NumberOfInterpolatedPoints();
+
+    char* WlsAbsSpectrumFileName();
+    G4int NumberOfWlsAbsEnergies();
+    G4double* WlsAbsEnergy;
+    G4double* WlsAbsLength;
+
+    char* WlsEmissionSpectrumFileName();
+    G4int NumberOfWlsEmissionEnergies();
+    G4double* WlsEmissionEnergy;
+    G4double* WlsEmissionIntensity;
+
+    G4double ScintillationYield();
+    G4double ResolutionScale();
+    G4double DecayTimeFast();
+    G4double DecayTimeSlow();
+    G4double YieldRatio();
+    G4double BirksConstant();
+
+    G4double WlsDecayTime();
+
+    char* RefractiveIndexVacuum();
+    char* RefractiveIndexCore();
+    char* RefractiveIndexClad1();
+    char* RefractiveIndexClad2();
+
+    char* AbsorptionCore();
+    char* AbsorptionClad1();
+    char* AbsorptionClad2();
+ 
+    char* AbsorptionFromIrradiationCore();
+    char* AbsorptionFromIrradiationClad1();
+    char* AbsorptionFromIrradiationClad2();
+
+    char* SectionsFileName();
+    G4int NumberOfSections();
+
+    char* RayleighCore();
+    char* RayleighClad1();
+    char* RayleighClad2();
+
+    // Conversion factor between wavelength and energy
+    const static G4double hcPERe;
+
+
+private:
+
+    Parameters();
+    static Parameters* singleton;
+
+
+    char parameterOutputFileName[50];
+
+    G4double randomSeed;
+    G4double randomNumber;
+    G4double fibreLength;
+    G4double semiAxisZ;
+    G4double semiAxisY;
+    G4double probabilityOfPhotonLossAtSurface;
+    G4bool placeMirror;
+    G4double mirrorReflectivity;
+    G4bool detectorMaterial;
+  
+    G4double triggerX;
+    G4double triggerY;
+    G4double triggerZ;
+  
+    G4double triggerXPos;
+    G4double triggerZPos;
+
+    char emissionSpectrumFileName[256];
+    G4int numberOfEnergies;
+    //  G4double[] energy;
+    //  G4double[] intensity;
+    G4int numberOfInterpolatedPoints;
+
+    char wlsAbsSpectrumFileName[256];
+    G4int numberOfWlsAbsEnergies;
+
+    char wlsEmissionSpectrumFileName[256];
+    G4int numberOfWlsEmissionEnergies;
+
+    G4double scintillationYield;
+    G4double resolutionScale;
+    G4double decayTimeFast;
+    G4double decayTimeSlow;
+    G4double yieldRatio;
+    G4double birksConstant;
+
+    G4double wlsDecayTime;
+
+    char refractiveIndexVacuum[256];
+    char refractiveIndexCore[256];
+    char refractiveIndexClad1[256];
+    char refractiveIndexClad2[256];
+
+    char absorptionCore[512];
+    char absorptionClad1[512];
+    char absorptionClad2[512];
+ 
+    char absorptionFromIrradiationCore[512];
+    char absorptionFromIrradiationClad1[512];
+    char absorptionFromIrradiationClad2[512];
+
+    char sectionsFileName[80];
+    G4int numberOfSections;
+
+    char rayleighCore[512];
+    char rayleighClad1[512];
+    char rayleighClad2[512];
+
+};
+
+#endif

SciFiSim/include/PhysicsList.hh

@@ -0,0 +1,24 @@
+// $Id: PhysicsList.hh,v 1.7 2006/06/29 17:53:59 gunter Exp $
+//
+
+#ifndef PhysicsList_h
+#define PhysicsList_h 1
+
+#include "globals.hh"
+#include "G4VModularPhysicsList.hh"
+
+
+class PhysicsList : public G4VModularPhysicsList
+{
+public:
+    PhysicsList();
+
+public:
+    void ConstructParticle();
+    void SetCuts();
+
+};
+
+
+#endif /* PhysicsList_h */
+

SciFiSim/include/PrimaryGeneratorAction.hh

@@ -0,0 +1,29 @@
+// Written by Peter Stromberger
+// based on work of Mirco Deckenhoff
+
+#ifndef PrimaryGeneratorAction_h
+#define PrimaryGeneratorAction_h 1
+
+
+#include "globals.hh"
+#include "G4VUserPrimaryGeneratorAction.hh"
+#include "G4GeneralParticleSource.hh"
+
+class PrimaryGeneratorAction : public G4VUserPrimaryGeneratorAction
+{
+public:
+    PrimaryGeneratorAction();
+    ~PrimaryGeneratorAction();
+
+    void GeneratePrimaries(G4Event*);
+    void SetOptPhotonPolar();
+    void SetOptPhotonPolar(G4double);
+    G4GeneralParticleSource* GetGun();
+
+private:  
+    G4GeneralParticleSource * InitializeGPS();
+    G4GeneralParticleSource * gun;
+};
+
+
+#endif

SciFiSim/include/RunAction.hh

@@ -0,0 +1,30 @@
+//
+// $Id: RunAction.hh,v 1.9 2006/06/29 17:54:10 gunter Exp $
+// GEANT4 tag $Name: geant4-09-01-ref-02 $
+
+#ifndef RunAction_h
+#define RunAction_h 1
+
+#include "globals.hh"
+#include "G4UserRunAction.hh"
+
+
+class G4Timer;
+class G4Run;
+
+class RunAction : public G4UserRunAction
+{
+public:
+    RunAction();
+    ~RunAction();
+
+public:
+    void BeginOfRunAction(const G4Run* aRun);
+    void EndOfRunAction(const G4Run* aRun);
+
+private:
+    G4Timer* timer;
+};
+
+
+#endif /*RunAction_h*/

SciFiSim/include/SensitiveDetector.hh

@@ -0,0 +1,23 @@
+// Written by Peter Stromberger
+// based on work of Mirco Deckenhoff
+
+#ifndef SensitiveDetector_h
+#define SensitiveDetector_h 1
+
+#include "G4VSensitiveDetector.hh"
+
+class G4Step;
+class G4TouchableHistory;
+class G4HCofThisEvent;
+
+class SensitiveDetector : public G4VSensitiveDetector
+{
+public:
+    SensitiveDetector(G4String SDname);
+    ~SensitiveDetector();
+
+    G4bool ProcessHits(G4Step * step, G4TouchableHistory * ROhist);
+};
+
+#endif
+

SciFiSim/include/StackingAction.hh

@@ -0,0 +1,35 @@
+// Written by Peter Stromberger
+// based on work of Mirco Deckenhoff
+
+#ifndef StackingAction_H
+#define StackingAction_H 1
+
+#include "globals.hh"
+#include "G4UserStackingAction.hh"
+
+#include <map>
+
+class G4VProcess;
+
+class StackingAction : public G4UserStackingAction
+{
+public:
+    StackingAction();
+    ~StackingAction();
+
+public:
+    G4ClassificationOfNewTrack ClassifyNewTrack(const G4Track* aTrack);
+    void NewStage();
+    void PrepareNewEvent();
+
+private:
+    G4int gammaCounter;
+    typedef std::map<const G4VProcess*,G4int> ProcMap;
+    ProcMap procs;
+    void AddProcess(const G4VProcess*);
+    void Reset();
+};
+
+
+#endif
+

SciFiSim/include/SteppingAction.hh

@@ -0,0 +1,51 @@
+// Written by Peter Stromberger
+// based on work of Mirco Deckenhoff
+
+#ifndef SteppingAction_H
+#define SteppingAction_H 1
+
+ 
+#include "globals.hh"
+#include "G4UserSteppingAction.hh"
+#include "G4OpBoundaryProcess.hh"
+#include "EventAction.hh"
+#include "G4ParticleDefinition.hh"
+#include "PrimaryGeneratorAction.hh"
+#include "TFile.h"
+#include "TH2F.h"
+#include "TH1F.h"
+#include "TTree.h"
+#include "TObject.h"
+
+
+
+
+class SteppingAction : public G4UserSteppingAction
+{
+  
+
+
+public:
+    SteppingAction(EventAction* eventAction, PrimaryGeneratorAction* pGA);
+    virtual ~SteppingAction();
+    virtual void UserSteppingAction( const G4Step* );
+
+
+private:
+    const char* primParticle;
+    G4ParticleDefinition* primDefinition;
+    PrimaryGeneratorAction* pGA;
+    EventAction* fEventAction;
+    G4int creatorProcess;
+    G4OpBoundaryProcess* opBoundaryProcess;
+
+
+  
+ 
+
+
+};
+
+
+
+#endif

SciFiSim/include/SteppingAction.hh~

@@ -0,0 +1,58 @@
+// Written by Peter Stromberger
+// based on work of Mirco Deckenhoff
+
+#ifndef SteppingAction_H
+#define SteppingAction_H 1
+
+ 
+#include "globals.hh"
+#include "G4UserSteppingAction.hh"
+#include "G4OpBoundaryProcess.hh"
+#include "EventAction.hh"
+#include "G4ParticleDefinition.hh"
+#include "PrimaryGeneratorAction.hh"
+#include "TFile.h"
+#include "TH2F.h"
+#include "TH1F.h"
+#include "TTree.h"
+#include "TObject.h"
+
+
+
+
+class SteppingAction : public G4UserSteppingAction
+{
+  
+
+
+public:
+    SteppingAction(EventAction* eventAction, PrimaryGeneratorAction* pGA);
+    virtual ~SteppingAction();
+    virtual void UserSteppingAction( const G4Step* );
+
+
+private:
+    const char* primParticle;
+    G4ParticleDefinition* primDefinition;
+    PrimaryGeneratorAction* pGA;
+    EventAction* fEventAction;
+    G4int creatorProcess;
+    G4OpBoundaryProcess* opBoundaryProcess;
+
+  
+  TFile * doseFile = new TFile("dose.root","READ");
+  Float_t dose;
+  
+   TH2F * dosehist50invfb = (TH2F*)doseFile->Get("dosehist50invfb");
+  if (dosehist50invfb){
+    dosehist50invfb->SetDirectory(0);
+  }
+  //  dosehist50invfb->SetDirectory(0)
+
+
+
+};
+
+
+
+#endif

SciFiSim/old.md5

@@ -0,0 +1,2 @@
+431f92380100d8b8021a25843f9994c1  /home/lhcb/roessler/geant4_workdir/bin/Linux-g++/scifiSim
+6d78d4562e149bd687f3ecb9cec78279  /home/lhcb/roessler/geant4_workdir/bin/Linux-g++/scifiSim

SciFiSim/outFile_32584.root.parameters

@@ -0,0 +1,61 @@
+Length of fibre: 0 m 
+Semi axis of fibre in z: 0 mm 
+Semi axis of fibre in y: 0 mm 
+Probability to lose photons at fibre surface: 0
+Mirror placement at fibre end: 0
+Reflectivity of mirror at fibre end: 0
+Detector material vacuum/polystyrene (0/1): 0
+Used emission spectrum: ""
+Number of energies: 0
+Energy / eV 	 Intensity
+Number of interpolated points per emission spectrum interval: 0
+Used wls absorption spectrum: ""
+Number of wls absorption energies: 0
+Energy / eV 	 WLS Absorption Length / m
+Used wls emission spectrum: ""
+Number of wls emission energies: 0
+Energy / eV 	 WLS emission intensity
+Formulae to calculate refractive indices in
+ - vacuum: ""
+ - core: ""
+ - inner cladding: ""
+ - outer cladding: ""
+ with x in nm.
+Scintillation yield: 0/keV
+Resolution scale: 0
+Fast decay time: 0 ns
+Slow decay time: 0 ns
+Yield ratio: 0
+Birks constant: 0 mm/MeV
+WLS decay time: 0 ns
+Formulae to calculate absorption [1/m] in
+ - core: ""
+ - inner cladding: ""
+ - outer cladding: ""
+ with x in nm.
+Formulae to calculate absorption due to irradiation [1/m] in
+ - core: ""
+ - inner cladding: ""
+ - outer cladding: ""
+ with x in nm and y in kGy.
+Used sections file: ""
+Number of sections: 0
+Formulae to calculate Rayleigh scattering [1/m] in
+ - core: 
+ - inner cladding: 
+ - outer cladding: 
+
+Scintillation emission spectrum:
+Energy/eV	Wavelength/nm	Intensity
+
+WLS emission spectrum:
+Energy/eV	Wavelength/nm	Intensity
+
+WLS absorption length / m:
+Energy/eV	Wavelength/nm	Absorption length
+
+Refractive indices:
+Energy/eV	Wavelength/nm	Vacuum	Clad2	Clad1	Core
+
+Rayleigh scattering length / m:
+Energy/eV	Wavelength/nm	Clad2	Clad1	Core

SciFiSim/outFile_32703.root.parameters

@@ -0,0 +1,61 @@
+Length of fibre: 0 m 
+Semi axis of fibre in z: 0 mm 
+Semi axis of fibre in y: 0 mm 
+Probability to lose photons at fibre surface: 0
+Mirror placement at fibre end: 0
+Reflectivity of mirror at fibre end: 0
+Detector material vacuum/polystyrene (0/1): 0
+Used emission spectrum: ""
+Number of energies: 0
+Energy / eV 	 Intensity
+Number of interpolated points per emission spectrum interval: 0
+Used wls absorption spectrum: ""
+Number of wls absorption energies: 0
+Energy / eV 	 WLS Absorption Length / m
+Used wls emission spectrum: ""
+Number of wls emission energies: 0
+Energy / eV 	 WLS emission intensity
+Formulae to calculate refractive indices in
+ - vacuum: ""
+ - core: ""
+ - inner cladding: ""
+ - outer cladding: ""
+ with x in nm.
+Scintillation yield: 0/keV
+Resolution scale: 0
+Fast decay time: 0 ns
+Slow decay time: 0 ns
+Yield ratio: 0
+Birks constant: 0 mm/MeV
+WLS decay time: 0 ns
+Formulae to calculate absorption [1/m] in
+ - core: ""
+ - inner cladding: ""
+ - outer cladding: ""
+ with x in nm.
+Formulae to calculate absorption due to irradiation [1/m] in
+ - core: ""
+ - inner cladding: ""
+ - outer cladding: ""
+ with x in nm and y in kGy.
+Used sections file: ""
+Number of sections: 0
+Formulae to calculate Rayleigh scattering [1/m] in
+ - core: 
+ - inner cladding: 
+ - outer cladding: 
+
+Scintillation emission spectrum:
+Energy/eV	Wavelength/nm	Intensity
+
+WLS emission spectrum:
+Energy/eV	Wavelength/nm	Intensity
+
+WLS absorption length / m:
+Energy/eV	Wavelength/nm	Absorption length
+
+Refractive indices:
+Energy/eV	Wavelength/nm	Vacuum	Clad2	Clad1	Core
+
+Rayleigh scattering length / m:
+Energy/eV	Wavelength/nm	Clad2	Clad1	Core

SciFiSim/randomEngineSeed.txt

@@ -0,0 +1 @@
+0

SciFiSim/scifiSim.cc

@@ -0,0 +1,124 @@
+// Written by Peter Stromberger
+// based on work of Mirco Deckenhoff
+// modified by Bastian Rössler
+
+#include "G4RunManager.hh"
+//#include "G4MTRunManager.hh"
+#include "G4UImanager.hh"
+#include "G4Version.hh"
+
+#include "G4VisExecutive.hh"
+#if  G4VERSION_NUMBER>=930
+#include "G4UIExecutive.hh"
+#else
+#include "G4UIterminal.hh"
+#include "G4UItcsh.hh"
+#endif
+
+#include "DetectorConstruction.hh"
+#include "PrimaryGeneratorAction.hh"
+#include "StackingAction.hh"
+#include "SteppingAction.hh"
+
+#include "EventAction.hh"
+#include "RunAction.hh"
+
+#include "Analysis.hh"
+#include "Parameters.hh"
+
+#include "PhysicsList.hh"
+#include "ActionInitialization.hh"
+
+#include "Randomize.hh"
+
+// for file output
+#include <iostream>
+#include <fstream>
+
+int main(int argc,char** argv)
+{
+
+    // Set the seed for the random engine and save to file
+    G4int seed = Parameters::GetInstance()->RandomSeed();
+    G4Random::setTheEngine(new CLHEP::RanecuEngine);
+    G4Random::setTheSeed(seed);
+   
+    std::ofstream myfile;
+    myfile.open("randomEngineSeed.txt");
+    myfile << seed;
+    myfile.close();
+
+    G4RunManager * runManager = new G4RunManager();
+  
+
+    // mandatory Initialization classes
+    G4VUserDetectorConstruction* detector = new DetectorConstruction();
+    runManager->SetUserInitialization(detector);
+
+    G4VUserPhysicsList* physics = new PhysicsList();
+    runManager->SetUserInitialization(physics);
+
+    // mandatory User Action classes
+    runManager->SetUserInitialization(new ActionInitialization());
+
+    // Initialize G4 kernel
+    runManager->Initialize();
+      
+    //Initilize the visualization manager
+    G4VisManager* visManager = new G4VisExecutive();
+    visManager->Initialize();
+  
+     
+    // Get the pointer to the User Interface manager
+    //
+    G4UImanager * UImanager = G4UImanager::GetUIpointer();
+
+    if (argc!=1)
+    {  // batch mode
+        //command line contains name of the macro to execute
+        G4String command = "/control/execute ";
+        G4String fileName = argv[1];
+        UImanager->ApplyCommand(command+fileName);
+    }
+    else
+    {           // interactive mode : define UI session
+        
+#if  G4VERSION_NUMBER>=930
+        //New since G4 9.3: UI executive setups up
+        //correct UI depending on env variables
+        G4UIExecutive * ui = new G4UIExecutive(argc,argv);
+        //If UI has graphics execute special macro: opens OpenGL Qt driver
+        if (ui->IsGUI())
+            UImanager->ApplyCommand("/control/execute visQt.mac");
+        else
+            UImanager->ApplyCommand("/control/execute vis.mac");
+#else
+        //Older versions of G4: UI selected by user
+  #ifdef G4UI_USE_TCSH
+        G4UIsession * ui = new G4UIterminal(new G4UItcsh);
+  #else
+        G4UIsession * ui = new G4UIterminal();
+  #endif
+        UImanager->ApplyCommand("/control/execute vis.mac");
+#endif
+        ui->SessionStart();
+        delete ui;
+    }
+
+    // Free the store: user actions, physics_list and detector_description are
+    //                 owned and deleted by the run manager, so they should not
+    //                 be deleted in the main() program !
+
+    Analysis::GetInstance()->Close();
+
+
+    delete runManager;
+
+    if(Analysis::GetInstance()!=NULL)
+        delete Analysis::GetInstance();
+
+    if(Parameters::GetInstance()!=NULL)
+        delete Parameters::GetInstance();
+
+    return 0;
+}

SciFiSim/src/ActionInitialization.cc

@@ -0,0 +1,37 @@
+// Written by Peter Stromberger
+// based on work of Mirco Deckenhoff
+// modified by Bastian Rössler
+
+#include "ActionInitialization.hh"
+#include "PrimaryGeneratorAction.hh"
+#include "RunAction.hh"
+#include "EventAction.hh"
+
+#include "StackingAction.hh"
+#include "SteppingAction.hh"
+
+
+// constructor
+ActionInitialization::ActionInitialization() : G4VUserActionInitialization() {}
+
+// destructor
+ActionInitialization::~ActionInitialization() {}
+
+// methods
+
+void ActionInitialization::BuildForMaster() const
+{
+    SetUserAction( new RunAction);
+}
+
+void ActionInitialization::Build() const
+{
+	PrimaryGeneratorAction* pGA = new PrimaryGeneratorAction;
+	SetUserAction( pGA);
+	SetUserAction( new RunAction);
+	EventAction* eventAction = new EventAction;
+	SetUserAction( eventAction);
+	SetUserAction( new StackingAction);
+	SetUserAction( new SteppingAction(eventAction, pGA));
+}
+

SciFiSim/src/Analysis.cc

@@ -0,0 +1,444 @@
+// Written by Peter Stromberger
+// based on work of Mirco Deckenhoff
+// modified by Bastian Rössler
+
+#include "Analysis.hh"
+#include "Parameters.hh"
+#include <ctime>
+#include <fstream>
+
+
+Analysis* Analysis::singleton = 0;
+
+Analysis::Analysis()
+{
+    // Set file name for simulation output
+    G4int threadNumber;
+    std::ifstream inFile;
+    inFile.open("threadNumber.txt");
+    inFile >> threadNumber;
+    inFile.close();
+
+    sprintf(fileName,"outFile_%i.root", threadNumber);
+
+    detectedPhotons = new TTree("DetectedPhotons","Photons detected at the detector strip.");
+
+    detectedPhotons->Branch("runID", &runIDBuffer, "runID/F"); //modifed by me
+    detectedPhotons->Branch("eventID", &eventIDBuffer, "eventID/F"); //modifed by me
+    detectedPhotons->Branch("detNumb", &detNumbBuffer, "detNumb/F"); //modifed by me
+
+    detectedPhotons->Branch("xPixel", &xPixelBuffer, "xPixel/F"); //modifed by me
+    detectedPhotons->Branch("yPixel", &yPixelBuffer, "yPixel/F"); //modifed by me
+    detectedPhotons->Branch("energy",&energyBuffer,"energy/F");
+    detectedPhotons->Branch("wavelength",&wavelengthBuffer,"wavelength/F");
+    detectedPhotons->Branch("localtime",&timeBuffer,"localtime/F");
+    detectedPhotons->Branch("abstime",&absTimeBuffer,"abstime/F");
+    detectedPhotons->Branch("length",&lengthBuffer,"length/F");
+    detectedPhotons->Branch("x",&xBuffer,"x/F");
+    detectedPhotons->Branch("y",&yBuffer,"y/F");
+    detectedPhotons->Branch("z",&zBuffer,"z/F");
+    detectedPhotons->Branch("px",&pxBuffer,"px/F");
+    detectedPhotons->Branch("py",&pyBuffer,"py/F");
+    detectedPhotons->Branch("pz",&pzBuffer,"pz/F");
+    detectedPhotons->Branch("vertexX",&vertexXBuffer,"vertexX/F");
+    detectedPhotons->Branch("vertexY",&vertexYBuffer,"vertexY/F");
+    detectedPhotons->Branch("vertexZ",&vertexZBuffer,"vertexZ/F");
+    detectedPhotons->Branch("vertexPx",&vertexPxBuffer,"vertexPx/F");
+    detectedPhotons->Branch("vertexPy",&vertexPyBuffer,"vertexPy/F");
+    detectedPhotons->Branch("vertexPz",&vertexPzBuffer,"vertexPz/F");
+    detectedPhotons->Branch("gpsPosX",&gpsPositionX,"gpsPosX/F");
+    detectedPhotons->Branch("gpsPosY",&gpsPositionY,"gpsPosY/F");
+    detectedPhotons->Branch("gpsPosZ",&gpsPositionZ,"gpsPosZ/F");
+    detectedPhotons->Branch("gpsDirX",&gpsDirectionX,"gpsPosX/F");
+    detectedPhotons->Branch("gpsDirY",&gpsDirectionY,"gpsPosY/F");
+    detectedPhotons->Branch("gpsDirZ",&gpsDirectionZ,"gpsPosZ/F");
+    detectedPhotons->Branch("runId",&runIdBuffer,"runId/I");
+    detectedPhotons->Branch("eventId",&eventIdBuffer,"eventId/I");
+    detectedPhotons->Branch("trackId",&trackIdBuffer,"trackId/I");
+    detectedPhotons->Branch("creatorProcess",&creatorProcessBuffer,"creatorProcess/I");
+    detectedPhotons->Branch("parentId",&parentIdBuffer,"parentId/I");
+    detectedPhotons->Branch("reflMirr",&reflMirrBuffer,"reflMirr/I");
+    detectedPhotons->Branch("reflSurf",&reflSurfBuffer,"reflSurf/I");
+    detectedPhotons->Branch("reflTotalCladClad",&reflTotalCladCladBuffer,"reflTotalCladClad/I");
+    detectedPhotons->Branch("reflTotalCoreClad",&reflTotalCoreCladBuffer,"reflTotalCoreClad/I");
+    detectedPhotons->Branch("reflFresnelCladClad",&reflFresnelCladCladBuffer,"reflFresnelCladClad/I");
+    detectedPhotons->Branch("reflFresnelCoreClad",&reflFresnelCoreCladBuffer,"reflFresnelCoreClad/I");
+    detectedPhotons->Branch("refracCladClad",&refracCladCladBuffer,"refracCladClad/I");
+    detectedPhotons->Branch("refracCoreClad",&refracCoreCladBuffer,"refracCoreClad/I");
+    detectedPhotons->Branch("rayleighScatterings",&rayleighScatteringsBuffer,"rayleighScatterings/I");
+    detectedPhotons->Branch("lengthInCore",&lengthInCoreBuffer,"lengthInCore/F");
+    detectedPhotons->Branch("lengthInInnerCladding",&lengthInInnerCladdingBuffer,"lengthInInnerCladding/F");
+    detectedPhotons->Branch("lengthInOuterCladding",&lengthInOuterCladdingBuffer,"lengthInOuterCladding/F");
+
+    trigger = new TTree("Trigger","Hits in the trigger.");
+  
+    trigger->Branch("runID", &runIDBuffer, "runID/F");
+    trigger->Branch("eventID", &eventIDBuffer, "eventID/F");
+    trigger->Branch("edep", &edepBuffer, "edep/F");
+    trigger->Branch("xPos", &xPosBuffer, "xPos/F");
+    trigger->Branch("yPos", &yPosBuffer, "yPos/F");
+    trigger->Branch("zPos", &zPosBuffer, "zPos/F");
+	
+    energyTrack = new TTree("EnergyTrack", "Deposited energy and tracklength in core of fibre.");
+
+    energyTrack->Branch("runID", &runIDBuffer, "runID/F");
+    energyTrack->Branch("eventID", &eventIDBuffer, "eventID/F");
+    energyTrack->Branch("edep", &energyBuffer, "edep/F");
+    energyTrack->Branch("trackL", &lengthBuffer, "trackL/F");
+
+    h_energy = new TH1F("h_energy","h_energy",200,0.0,1.0);
+    h_trackL = new TH1F("h_trackL","h_trackL",400,0.0,2.0);
+
+    primaryParticleTrack = new TTree("PrimaryParticleTrack", "Track of the primary particles");
+
+    primaryParticleTrack->Branch("runID", &runIDBuffer, "runID/F");
+    primaryParticleTrack->Branch("eventID", &eventIDBuffer, "eventID/F");
+    primaryParticleTrack->Branch("xPos", &xPosBuffer, "xPos/F");
+    primaryParticleTrack->Branch("yPos", &yPosBuffer, "yPos/F");
+    primaryParticleTrack->Branch("zPos", &zPosBuffer, "zPos/F");
+
+    initialParticle = new TTree("InitialParticle", "Initial Particle");
+  
+    initialParticle->Branch("runID", &runIDBuffer, "runID/F");
+    initialParticle->Branch("eventID", &eventIDBuffer, "eventID/F");
+    initialParticle->Branch("energy", &energyBuffer, "energy/F");
+    initialParticle->Branch("xMom", &xMomBuffer, "xMom/F");
+    initialParticle->Branch("yMom", &yMomBuffer, "yMom/F");
+    initialParticle->Branch("zMom", &zMomBuffer, "zMom/F");
+ 
+
+
+}
+
+
+void Analysis::PrepareNewRun(const G4Run* aRun)
+{
+    runIdBuffer = aRun->GetRunID();
+}
+
+
+void Analysis::EndOfRun()
+{
+    dataFile = new TFile(fileName,"update");
+
+    detectedPhotons->Write("",TObject::kOverwrite);
+    trigger->Write("", TObject::kOverwrite);
+    primaryParticleTrack->Write("", TObject::kOverwrite);
+    initialParticle->Write("", TObject::kOverwrite);
+    energyTrack->Write("", TObject::kOverwrite);
+    h_energy->Write("", TObject::kOverwrite);
+    h_trackL->Write("", TObject::kOverwrite);
+    G4cout << "Data written to file " << fileName << G4endl;
+
+    dataFile->Close();
+
+    G4cout << "Data file closed: " << fileName << G4endl;
+
+    delete dataFile;
+}
+
+
+void Analysis::Close()
+{
+    delete detectedPhotons;
+    delete trigger;
+    delete initialParticle;
+    delete energyTrack;
+}
+
+
+void Analysis::PrepareNewEvent(const G4Event* anEvent)
+{
+    eventIdBuffer = anEvent->GetEventID();
+
+    reflectionsAtMirror.resize(0);
+    reflectionsAtFibreSurface.resize(0);
+    reflectionsTotalAtCladCladInterface.resize(0);
+    reflectionsTotalAtCoreCladInterface.resize(0);
+    reflectionsFresnelAtCladCladInterface.resize(0);
+    reflectionsFresnelAtCoreCladInterface.resize(0);
+
+    refractionsAtCladCladInterface.resize(0);
+    refractionsAtCoreCladInterface.resize(0);
+
+    rayleighScatterings.resize(0);
+
+    lengthInCore.resize(0);
+    lengthInInnerCladding.resize(0);
+    lengthInOuterCladding.resize(0);
+}
+
+void Analysis::FillInitialParticle(Double_t runID, Double_t eventID, Double_t energy, Double_t xMom, Double_t yMom, Double_t zMom)
+{
+    if(initialParticle != NULL)
+    {
+        runIDBuffer = runID;
+        eventIDBuffer = eventID;
+        energyBuffer = energy;
+        xMomBuffer = xMom;
+        yMomBuffer = yMom;
+        zMomBuffer = zMom;
+	initialParticle->Fill();
+    }
+    else
+        G4cout << "Nullpointer to initialParticle tree." << G4endl;
+}
+
+void Analysis::FillTrigger(Double_t runID, Double_t eventID, Double_t edep, Double_t xPos, Double_t yPos, Double_t zPos)
+{
+    if(trigger != NULL)
+    {
+        runIDBuffer = runID;
+        eventIDBuffer = eventID;
+        edepBuffer = edep;
+        xPosBuffer = xPos;
+        yPosBuffer = yPos;
+        zPosBuffer = zPos;
+
+	trigger->Fill();
+    }
+    else
+    {
+        G4cout << "Nullpointer to trigger tree." << G4endl;
+    }
+}
+
+void Analysis::FillEnergyTrack(Double_t runID, Double_t eventID, Double_t energy, Double_t trackL)
+{
+    if(energyTrack != NULL)
+    {
+        runIDBuffer = runID;
+        eventIDBuffer = eventID;
+        energyBuffer = energy;
+        lengthBuffer = trackL;
+	energyTrack->Fill();
+	h_energy->Fill(energy);
+	h_trackL->Fill(trackL);
+    }
+    else
+    {
+        G4cout << "Nullpointer to energyTrack tree" << G4endl;
+    }
+}
+
+void Analysis::FillPrimaryParticleTrack(Double_t runID, Double_t eventID,
+                                        Double_t xPos, Double_t yPos, Double_t zPos)
+{
+    if(primaryParticleTrack != NULL)
+    {
+        runIDBuffer = runID;
+        eventIDBuffer = eventID;
+        xPosBuffer = xPos;
+        yPosBuffer = yPos;
+        zPosBuffer = zPos;
+	primaryParticleTrack->Fill();
+    }
+    else
+    {
+        G4cout << "Nullpointer to primaryParticleTrack tree" << G4endl;
+    }
+}
+
+void Analysis::FillDetectedPhotons(Double_t runID, Double_t eventID, Double_t detNumb, Double_t xPixel,
+                                   Double_t yPixel, Double_t energy,
+                                   Double_t time, Double_t length, Double_t absTime,
+                                   Double_t x, Double_t y, Double_t z,
+                                   Double_t px, Double_t py, Double_t pz,
+                                   Double_t vertexX, Double_t vertexY, Double_t vertexZ,
+                                   Double_t vertexPx, Double_t vertexPy, Double_t vertexPz,
+                                   Int_t trackId,
+                                   Int_t creatorProcess, Int_t parentId)
+{
+    if(detectedPhotons!=NULL)
+    {
+        runIDBuffer   = runID;
+        eventIDBuffer = eventID;
+        detNumbBuffer = detNumb;
+        xPixelBuffer = xPixel;
+        yPixelBuffer = yPixel;
+
+        energyBuffer = energy;
+        timeBuffer = time;
+        lengthBuffer = length;
+
+        wavelengthBuffer = 1239.842/energy;
+
+        absTimeBuffer = absTime;
+        xBuffer = x;
+        yBuffer = y;
+        zBuffer = z;
+
+        pxBuffer = px;
+        pyBuffer = py;
+        pzBuffer = pz;
+
+        vertexXBuffer = vertexX;
+        vertexYBuffer = vertexY;
+        vertexZBuffer = vertexZ;
+
+        vertexPxBuffer = vertexPx;
+        vertexPyBuffer = vertexPy;
+        vertexPzBuffer = vertexPz;
+
+        trackIdBuffer = trackId;
+
+        creatorProcessBuffer = creatorProcess;
+        parentIdBuffer = parentId;
+
+        reflMirrBuffer = reflectionsAtMirror[trackId];
+        reflSurfBuffer = reflectionsAtFibreSurface[trackId];
+        reflTotalCladCladBuffer = reflectionsTotalAtCladCladInterface[trackId];
+        reflTotalCoreCladBuffer = reflectionsTotalAtCoreCladInterface[trackId];
+        reflFresnelCladCladBuffer = reflectionsFresnelAtCladCladInterface[trackId];
+        reflFresnelCoreCladBuffer = reflectionsFresnelAtCoreCladInterface[trackId];
+
+        refracCladCladBuffer = refractionsAtCladCladInterface[trackId];
+        refracCoreCladBuffer = refractionsAtCoreCladInterface[trackId];
+
+        rayleighScatteringsBuffer = rayleighScatterings[trackId];
+
+        lengthInCoreBuffer = lengthInCore[trackId];
+        lengthInInnerCladdingBuffer = lengthInInnerCladding[trackId];
+        lengthInOuterCladdingBuffer = lengthInOuterCladding[trackId];
+
+	detectedPhotons->Fill();
+    }
+    else
+    {
+        G4cout << G4endl << "Pointer to detectedPhotons tree is NULL!" << G4endl;
+    }
+}
+
+char* Analysis::FileName()
+{
+    return fileName;
+}
+
+void Analysis::SetGpsPosition(G4ThreeVector position)
+{
+    gpsPositionX = position[0];
+    gpsPositionY = position[1];
+    gpsPositionZ = position[2];
+}
+
+void Analysis::IncreaseReflectionsAtMirror(Int_t trackId)
+{
+    reflectionsAtMirror[trackId]++;
+}
+
+
+void Analysis::SetGpsDirection(G4ThreeVector direction)
+{
+    gpsDirectionX = direction[0];
+    gpsDirectionY = direction[1];
+    gpsDirectionZ = direction[2];
+}
+
+void Analysis::IncreaseReflectionsAtFibreSurface(Int_t trackId)
+{
+    reflectionsAtFibreSurface[trackId]++;
+}
+
+
+void Analysis::IncreaseTotalReflectionsAtCladCladInterface(Int_t trackId)
+{
+    reflectionsTotalAtCladCladInterface[trackId]++;
+}
+
+
+void Analysis::IncreaseTotalReflectionsAtCoreCladInterface(Int_t trackId)
+{
+    reflectionsTotalAtCoreCladInterface[trackId]++;
+}
+
+
+void Analysis::IncreaseFresnelReflectionsAtCladCladInterface(Int_t trackId)
+{
+    reflectionsFresnelAtCladCladInterface[trackId]++;
+}
+
+
+void Analysis::IncreaseFresnelReflectionsAtCoreCladInterface(Int_t trackId)
+{
+    reflectionsFresnelAtCoreCladInterface[trackId]++;
+}
+
+
+void Analysis::IncreaseRefractionsAtCladCladInterface(Int_t trackId)
+{
+    refractionsAtCladCladInterface[trackId]++;
+}
+
+
+void Analysis::IncreaseRefractionsAtCoreCladInterface(Int_t trackId)
+{
+    refractionsAtCoreCladInterface[trackId]++;
+}
+
+
+void Analysis::IncreaseRayleighScatterings(Int_t trackId)
+{
+    rayleighScatterings[trackId]++;
+}
+
+
+void Analysis::IncreaseReflectionRefractionAndScatteringVectors(Int_t trackId)
+{
+    for(int i=reflectionsAtMirror.size(); i<trackId+1; i++)
+        reflectionsAtMirror.push_back(0);
+
+    for(int i=reflectionsAtFibreSurface.size(); i<trackId+1; i++)
+        reflectionsAtFibreSurface.push_back(0);
+
+    for(int i=reflectionsTotalAtCladCladInterface.size(); i<trackId+1; i++)
+        reflectionsTotalAtCladCladInterface.push_back(0);
+
+    for(int i=reflectionsTotalAtCoreCladInterface.size(); i<trackId+1; i++)
+        reflectionsTotalAtCoreCladInterface.push_back(0);
+
+    for(int i=reflectionsFresnelAtCladCladInterface.size(); i<trackId+1; i++)
+        reflectionsFresnelAtCladCladInterface.push_back(0);
+
+    for(int i=reflectionsFresnelAtCoreCladInterface.size(); i<trackId+1; i++)
+        reflectionsFresnelAtCoreCladInterface.push_back(0);
+
+    for(int i=refractionsAtCladCladInterface.size(); i<trackId+1; i++)
+        refractionsAtCladCladInterface.push_back(0);
+
+    for(int i=refractionsAtCoreCladInterface.size(); i<trackId+1; i++)
+        refractionsAtCoreCladInterface.push_back(0);
+
+    for(int i=rayleighScatterings.size(); i<trackId+1; i++)
+        rayleighScatterings.push_back(0);
+}
+
+
+void Analysis::IncreaseLengthInCore(Int_t trackId, Float_t lengthValue)
+{
+    lengthInCore[trackId] += lengthValue;
+}
+
+
+void Analysis::IncreaseLengthInInnerCladding(Int_t trackId, Float_t lengthValue)
+{
+    lengthInInnerCladding[trackId] += lengthValue;
+}
+
+
+void Analysis::IncreaseLengthInOuterCladding(Int_t trackId, Float_t lengthValue)
+{
+    lengthInOuterCladding[trackId] += lengthValue;
+}
+
+
+void Analysis::IncreaseLengthVectors(Int_t trackId)
+{
+    for(int i=lengthInCore.size(); i<trackId+1; i++)
+        lengthInCore.push_back(0);
+
+    for(int i=lengthInInnerCladding.size(); i<trackId+1; i++)
+        lengthInInnerCladding.push_back(0);
+
+    for(int i=lengthInOuterCladding.size(); i<trackId+1; i++)
+        lengthInOuterCladding.push_back(0);
+}

SciFiSim/src/Analysis.cc~

@@ -0,0 +1,444 @@
+// Written by Peter Stromberger
+// based on work of Mirco Deckenhoff
+// modified by Bastian Rössler
+
+#include "Analysis.hh"
+#include "Parameters.hh"
+#include <ctime>
+#include <fstream>
+
+
+Analysis* Analysis::singleton = 0;
+
+Analysis::Analysis()
+{
+    // Set file name for simulation output
+    G4int threadNumber;
+    std::ifstream inFile;
+    inFile.open("threadNumber.txt");
+    inFile >> threadNumber;
+    inFile.close();
+
+    sprintf(fileName,"outFile_%i.root", threadNumber);
+
+    detectedPhotons = new TTree("DetectedPhotons","Photons detected at the detector strip.");
+
+    detectedPhotons->Branch("runID", &runIDBuffer, "runID/F"); //modifed by me
+    detectedPhotons->Branch("eventID", &eventIDBuffer, "eventID/F"); //modifed by me
+    detectedPhotons->Branch("detNumb", &detNumbBuffer, "detNumb/F"); //modifed by me
+
+    detectedPhotons->Branch("xPixel", &xPixelBuffer, "xPixel/F"); //modifed by me
+    detectedPhotons->Branch("yPixel", &yPixelBuffer, "yPixel/F"); //modifed by me
+    detectedPhotons->Branch("energy",&energyBuffer,"energy/F");
+    detectedPhotons->Branch("wavelength",&wavelengthBuffer,"wavelength/F");
+    detectedPhotons->Branch("localtime",&timeBuffer,"localtime/F");
+    detectedPhotons->Branch("abstime",&absTimeBuffer,"abstime/F");
+    detectedPhotons->Branch("length",&lengthBuffer,"length/F");
+    detectedPhotons->Branch("x",&xBuffer,"x/F");
+    detectedPhotons->Branch("y",&yBuffer,"y/F");
+    detectedPhotons->Branch("z",&zBuffer,"z/F");
+    detectedPhotons->Branch("px",&pxBuffer,"px/F");
+    detectedPhotons->Branch("py",&pyBuffer,"py/F");
+    detectedPhotons->Branch("pz",&pzBuffer,"pz/F");
+    detectedPhotons->Branch("vertexX",&vertexXBuffer,"vertexX/F");
+    detectedPhotons->Branch("vertexY",&vertexYBuffer,"vertexY/F");
+    detectedPhotons->Branch("vertexZ",&vertexZBuffer,"vertexZ/F");
+    detectedPhotons->Branch("vertexPx",&vertexPxBuffer,"vertexPx/F");
+    detectedPhotons->Branch("vertexPy",&vertexPyBuffer,"vertexPy/F");
+    detectedPhotons->Branch("vertexPz",&vertexPzBuffer,"vertexPz/F");
+    detectedPhotons->Branch("gpsPosX",&gpsPositionX,"gpsPosX/F");
+    detectedPhotons->Branch("gpsPosY",&gpsPositionY,"gpsPosY/F");
+    detectedPhotons->Branch("gpsPosZ",&gpsPositionZ,"gpsPosZ/F");
+    detectedPhotons->Branch("gpsDirX",&gpsDirectionX,"gpsPosX/F");
+    detectedPhotons->Branch("gpsDirY",&gpsDirectionY,"gpsPosY/F");
+    detectedPhotons->Branch("gpsDirZ",&gpsDirectionZ,"gpsPosZ/F");
+    detectedPhotons->Branch("runId",&runIdBuffer,"runId/I");
+    detectedPhotons->Branch("eventId",&eventIdBuffer,"eventId/I");
+    detectedPhotons->Branch("trackId",&trackIdBuffer,"trackId/I");
+    detectedPhotons->Branch("creatorProcess",&creatorProcessBuffer,"creatorProcess/I");
+    detectedPhotons->Branch("parentId",&parentIdBuffer,"parentId/I");
+    detectedPhotons->Branch("reflMirr",&reflMirrBuffer,"reflMirr/I");
+    detectedPhotons->Branch("reflSurf",&reflSurfBuffer,"reflSurf/I");
+    detectedPhotons->Branch("reflTotalCladClad",&reflTotalCladCladBuffer,"reflTotalCladClad/I");
+    detectedPhotons->Branch("reflTotalCoreClad",&reflTotalCoreCladBuffer,"reflTotalCoreClad/I");
+    detectedPhotons->Branch("reflFresnelCladClad",&reflFresnelCladCladBuffer,"reflFresnelCladClad/I");
+    detectedPhotons->Branch("reflFresnelCoreClad",&reflFresnelCoreCladBuffer,"reflFresnelCoreClad/I");
+    detectedPhotons->Branch("refracCladClad",&refracCladCladBuffer,"refracCladClad/I");
+    detectedPhotons->Branch("refracCoreClad",&refracCoreCladBuffer,"refracCoreClad/I");
+    detectedPhotons->Branch("rayleighScatterings",&rayleighScatteringsBuffer,"rayleighScatterings/I");
+    detectedPhotons->Branch("lengthInCore",&lengthInCoreBuffer,"lengthInCore/F");
+    detectedPhotons->Branch("lengthInInnerCladding",&lengthInInnerCladdingBuffer,"lengthInInnerCladding/F");
+    detectedPhotons->Branch("lengthInOuterCladding",&lengthInOuterCladdingBuffer,"lengthInOuterCladding/F");
+
+    trigger = new TTree("Trigger","Hits in the trigger.");
+  
+    trigger->Branch("runID", &runIDBuffer, "runID/F");
+    trigger->Branch("eventID", &eventIDBuffer, "eventID/F");
+    trigger->Branch("edep", &edepBuffer, "edep/F");
+    trigger->Branch("xPos", &xPosBuffer, "xPos/F");
+    trigger->Branch("yPos", &yPosBuffer, "yPos/F");
+    trigger->Branch("zPos", &zPosBuffer, "zPos/F");
+	
+    energyTrack = new TTree("EnergyTrack", "Deposited energy and tracklength in core of fibre.");
+
+    energyTrack->Branch("runID", &runIDBuffer, "runID/F");
+    energyTrack->Branch("eventID", &eventIDBuffer, "eventID/F");
+    energyTrack->Branch("edep", &energyBuffer, "edep/F");
+    energyTrack->Branch("trackL", &lengthBuffer, "trackL/F");
+
+    h_energy = new TH1F("h_energy","h_energy",200,0.0,1.0);
+    h_trackL = new TH1F("h_trackL","h_trackL",400,0.0,2.0);
+
+    primaryParticleTrack = new TTree("PrimaryParticleTrack", "Track of the primary particles");
+
+    primaryParticleTrack->Branch("runID", &runIDBuffer, "runID/F");
+    primaryParticleTrack->Branch("eventID", &eventIDBuffer, "eventID/F");
+    primaryParticleTrack->Branch("xPos", &xPosBuffer, "xPos/F");
+    primaryParticleTrack->Branch("yPos", &yPosBuffer, "yPos/F");
+    primaryParticleTrack->Branch("zPos", &zPosBuffer, "zPos/F");
+
+    initialParticle = new TTree("InitialParticle", "Initial Particle");
+  
+    initialParticle->Branch("runID", &runIDBuffer, "runID/F");
+    initialParticle->Branch("eventID", &eventIDBuffer, "eventID/F");
+    initialParticle->Branch("energy", &energyBuffer, "energy/F");
+    initialParticle->Branch("xMom", &xMomBuffer, "xMom/F");
+    initialParticle->Branch("yMom", &yMomBuffer, "yMom/F");
+    initialParticle->Branch("zMom", &zMomBuffer, "zMom/F");
+ 
+
+
+}
+
+
+void Analysis::PrepareNewRun(const G4Run* aRun)
+{
+    runIdBuffer = aRun->GetRunID();
+}
+
+
+void Analysis::EndOfRun()
+{
+    dataFile = new TFile(fileName,"update");
+
+    //detectedPhotons->Write("",TObject::kOverwrite);
+    //trigger->Write("", TObject::kOverwrite);
+    // primaryParticleTrack->Write("", TObject::kOverwrite);
+    //initialParticle->Write("", TObject::kOverwrite);
+    //   energyTrack->Write("", TObject::kOverwrite);
+    h_energy->Write("", TObject::kOverwrite);
+    h_trackL->Write("", TObject::kOverwrite);
+    G4cout << "Data written to file " << fileName << G4endl;
+
+    dataFile->Close();
+
+    G4cout << "Data file closed: " << fileName << G4endl;
+
+    delete dataFile;
+}
+
+
+void Analysis::Close()
+{
+    delete detectedPhotons;
+    delete trigger;
+    delete initialParticle;
+    delete energyTrack;
+}
+
+
+void Analysis::PrepareNewEvent(const G4Event* anEvent)
+{
+    eventIdBuffer = anEvent->GetEventID();
+
+    reflectionsAtMirror.resize(0);
+    reflectionsAtFibreSurface.resize(0);
+    reflectionsTotalAtCladCladInterface.resize(0);
+    reflectionsTotalAtCoreCladInterface.resize(0);
+    reflectionsFresnelAtCladCladInterface.resize(0);
+    reflectionsFresnelAtCoreCladInterface.resize(0);
+
+    refractionsAtCladCladInterface.resize(0);
+    refractionsAtCoreCladInterface.resize(0);
+
+    rayleighScatterings.resize(0);
+
+    lengthInCore.resize(0);
+    lengthInInnerCladding.resize(0);
+    lengthInOuterCladding.resize(0);
+}
+
+void Analysis::FillInitialParticle(Double_t runID, Double_t eventID, Double_t energy, Double_t xMom, Double_t yMom, Double_t zMom)
+{
+    if(initialParticle != NULL)
+    {
+        runIDBuffer = runID;
+        eventIDBuffer = eventID;
+        energyBuffer = energy;
+        xMomBuffer = xMom;
+        yMomBuffer = yMom;
+        zMomBuffer = zMom;
+	//  initialParticle->Fill();
+    }
+    else
+        G4cout << "Nullpointer to initialParticle tree." << G4endl;
+}
+
+void Analysis::FillTrigger(Double_t runID, Double_t eventID, Double_t edep, Double_t xPos, Double_t yPos, Double_t zPos)
+{
+    if(trigger != NULL)
+    {
+        runIDBuffer = runID;
+        eventIDBuffer = eventID;
+        edepBuffer = edep;
+        xPosBuffer = xPos;
+        yPosBuffer = yPos;
+        zPosBuffer = zPos;
+
+	//   trigger->Fill();
+    }
+    else
+    {
+        G4cout << "Nullpointer to trigger tree." << G4endl;
+    }
+}
+
+void Analysis::FillEnergyTrack(Double_t runID, Double_t eventID, Double_t energy, Double_t trackL)
+{
+    if(energyTrack != NULL)
+    {
+        runIDBuffer = runID;
+        eventIDBuffer = eventID;
+        energyBuffer = energy;
+        lengthBuffer = trackL;
+	//        energyTrack->Fill();
+	h_energy->Fill(energy);
+	h_trackL->Fill(trackL);
+    }
+    else
+    {
+        G4cout << "Nullpointer to energyTrack tree" << G4endl;
+    }
+}
+
+void Analysis::FillPrimaryParticleTrack(Double_t runID, Double_t eventID,
+                                        Double_t xPos, Double_t yPos, Double_t zPos)
+{
+    if(primaryParticleTrack != NULL)
+    {
+        runIDBuffer = runID;
+        eventIDBuffer = eventID;
+        xPosBuffer = xPos;
+        yPosBuffer = yPos;
+        zPosBuffer = zPos;
+	//  primaryParticleTrack->Fill();
+    }
+    else
+    {
+        G4cout << "Nullpointer to primaryParticleTrack tree" << G4endl;
+    }
+}
+
+void Analysis::FillDetectedPhotons(Double_t runID, Double_t eventID, Double_t detNumb, Double_t xPixel,
+                                   Double_t yPixel, Double_t energy,
+                                   Double_t time, Double_t length, Double_t absTime,
+                                   Double_t x, Double_t y, Double_t z,
+                                   Double_t px, Double_t py, Double_t pz,
+                                   Double_t vertexX, Double_t vertexY, Double_t vertexZ,
+                                   Double_t vertexPx, Double_t vertexPy, Double_t vertexPz,
+                                   Int_t trackId,
+                                   Int_t creatorProcess, Int_t parentId)
+{
+    if(detectedPhotons!=NULL)
+    {
+        runIDBuffer   = runID;
+        eventIDBuffer = eventID;
+        detNumbBuffer = detNumb;
+        xPixelBuffer = xPixel;
+        yPixelBuffer = yPixel;
+
+        energyBuffer = energy;
+        timeBuffer = time;
+        lengthBuffer = length;
+
+        wavelengthBuffer = 1239.842/energy;
+
+        absTimeBuffer = absTime;
+        xBuffer = x;
+        yBuffer = y;
+        zBuffer = z;
+
+        pxBuffer = px;
+        pyBuffer = py;
+        pzBuffer = pz;
+
+        vertexXBuffer = vertexX;
+        vertexYBuffer = vertexY;
+        vertexZBuffer = vertexZ;
+
+        vertexPxBuffer = vertexPx;
+        vertexPyBuffer = vertexPy;
+        vertexPzBuffer = vertexPz;
+
+        trackIdBuffer = trackId;
+
+        creatorProcessBuffer = creatorProcess;
+        parentIdBuffer = parentId;
+
+        reflMirrBuffer = reflectionsAtMirror[trackId];
+        reflSurfBuffer = reflectionsAtFibreSurface[trackId];
+        reflTotalCladCladBuffer = reflectionsTotalAtCladCladInterface[trackId];
+        reflTotalCoreCladBuffer = reflectionsTotalAtCoreCladInterface[trackId];
+        reflFresnelCladCladBuffer = reflectionsFresnelAtCladCladInterface[trackId];
+        reflFresnelCoreCladBuffer = reflectionsFresnelAtCoreCladInterface[trackId];
+
+        refracCladCladBuffer = refractionsAtCladCladInterface[trackId];
+        refracCoreCladBuffer = refractionsAtCoreCladInterface[trackId];
+
+        rayleighScatteringsBuffer = rayleighScatterings[trackId];
+
+        lengthInCoreBuffer = lengthInCore[trackId];
+        lengthInInnerCladdingBuffer = lengthInInnerCladding[trackId];
+        lengthInOuterCladdingBuffer = lengthInOuterCladding[trackId];
+
+	//   detectedPhotons->Fill();
+    }
+    else
+    {
+        G4cout << G4endl << "Pointer to detectedPhotons tree is NULL!" << G4endl;
+    }
+}
+
+char* Analysis::FileName()
+{
+    return fileName;
+}
+
+void Analysis::SetGpsPosition(G4ThreeVector position)
+{
+    gpsPositionX = position[0];
+    gpsPositionY = position[1];
+    gpsPositionZ = position[2];
+}
+
+void Analysis::IncreaseReflectionsAtMirror(Int_t trackId)
+{
+    reflectionsAtMirror[trackId]++;
+}
+
+
+void Analysis::SetGpsDirection(G4ThreeVector direction)
+{
+    gpsDirectionX = direction[0];
+    gpsDirectionY = direction[1];
+    gpsDirectionZ = direction[2];
+}
+
+void Analysis::IncreaseReflectionsAtFibreSurface(Int_t trackId)
+{
+    reflectionsAtFibreSurface[trackId]++;
+}
+
+
+void Analysis::IncreaseTotalReflectionsAtCladCladInterface(Int_t trackId)
+{
+    reflectionsTotalAtCladCladInterface[trackId]++;
+}
+
+
+void Analysis::IncreaseTotalReflectionsAtCoreCladInterface(Int_t trackId)
+{
+    reflectionsTotalAtCoreCladInterface[trackId]++;
+}
+
+
+void Analysis::IncreaseFresnelReflectionsAtCladCladInterface(Int_t trackId)
+{
+    reflectionsFresnelAtCladCladInterface[trackId]++;
+}
+
+
+void Analysis::IncreaseFresnelReflectionsAtCoreCladInterface(Int_t trackId)
+{
+    reflectionsFresnelAtCoreCladInterface[trackId]++;
+}
+
+
+void Analysis::IncreaseRefractionsAtCladCladInterface(Int_t trackId)
+{
+    refractionsAtCladCladInterface[trackId]++;
+}
+
+
+void Analysis::IncreaseRefractionsAtCoreCladInterface(Int_t trackId)
+{
+    refractionsAtCoreCladInterface[trackId]++;
+}
+
+
+void Analysis::IncreaseRayleighScatterings(Int_t trackId)
+{
+    rayleighScatterings[trackId]++;
+}
+
+
+void Analysis::IncreaseReflectionRefractionAndScatteringVectors(Int_t trackId)
+{
+    for(int i=reflectionsAtMirror.size(); i<trackId+1; i++)
+        reflectionsAtMirror.push_back(0);
+
+    for(int i=reflectionsAtFibreSurface.size(); i<trackId+1; i++)
+        reflectionsAtFibreSurface.push_back(0);
+
+    for(int i=reflectionsTotalAtCladCladInterface.size(); i<trackId+1; i++)
+        reflectionsTotalAtCladCladInterface.push_back(0);
+
+    for(int i=reflectionsTotalAtCoreCladInterface.size(); i<trackId+1; i++)
+        reflectionsTotalAtCoreCladInterface.push_back(0);
+
+    for(int i=reflectionsFresnelAtCladCladInterface.size(); i<trackId+1; i++)
+        reflectionsFresnelAtCladCladInterface.push_back(0);
+
+    for(int i=reflectionsFresnelAtCoreCladInterface.size(); i<trackId+1; i++)
+        reflectionsFresnelAtCoreCladInterface.push_back(0);
+
+    for(int i=refractionsAtCladCladInterface.size(); i<trackId+1; i++)
+        refractionsAtCladCladInterface.push_back(0);
+
+    for(int i=refractionsAtCoreCladInterface.size(); i<trackId+1; i++)
+        refractionsAtCoreCladInterface.push_back(0);
+
+    for(int i=rayleighScatterings.size(); i<trackId+1; i++)
+        rayleighScatterings.push_back(0);
+}
+
+
+void Analysis::IncreaseLengthInCore(Int_t trackId, Float_t lengthValue)
+{
+    lengthInCore[trackId] += lengthValue;
+}
+
+
+void Analysis::IncreaseLengthInInnerCladding(Int_t trackId, Float_t lengthValue)
+{
+    lengthInInnerCladding[trackId] += lengthValue;
+}
+
+
+void Analysis::IncreaseLengthInOuterCladding(Int_t trackId, Float_t lengthValue)
+{
+    lengthInOuterCladding[trackId] += lengthValue;
+}
+
+
+void Analysis::IncreaseLengthVectors(Int_t trackId)
+{
+    for(int i=lengthInCore.size(); i<trackId+1; i++)
+        lengthInCore.push_back(0);
+
+    for(int i=lengthInInnerCladding.size(); i<trackId+1; i++)
+        lengthInInnerCladding.push_back(0);
+
+    for(int i=lengthInOuterCladding.size(); i<trackId+1; i++)
+        lengthInOuterCladding.push_back(0);
+}

SciFiSim/src/DetectorConstruction.cc

@@ -0,0 +1,913 @@
+// Written by Peter Stromberger
+// based on work of Mirco Deckenhoff
+// modified by Bastian Rössler
+
+#include "G4Navigator.hh"
+#include "DetectorConstruction.hh"
+#include "G4Material.hh"
+#include "G4LogicalBorderSurface.hh"
+#include "G4LogicalSkinSurface.hh"
+#include "G4Box.hh"
+#include "G4Tubs.hh"
+#include "G4EllipticalTube.hh"
+#include "G4SubtractionSolid.hh"
+#include "G4LogicalVolume.hh"
+#include "G4RotationMatrix.hh"
+#include "G4PVPlacement.hh"
+#include "G4OpBoundaryProcess.hh"
+#include "G4MaterialPropertyVector.hh"
+#include "G4NistManager.hh"
+#include "G4VisAttributes.hh"
+#include "G4Colour.hh"
+#include "G4PVParameterised.hh"
+#include "SensitiveDetector.hh"
+#include "G4SDManager.hh"
+#include "Analysis.hh"
+#include "Parameters.hh"
+#include "TF1.h"
+#include "TF2.h"
+#include "Randomize.hh"
+#include <fstream>
+#include <sstream>
+#include "G4SystemOfUnits.hh"
+#include "G4VPVParameterisation.hh"
+#include "Convert.hh"
+#include <math.h>
+#include <stdlib.h> 
+#include <time.h>  
+#include <iostream>
+#include <fstream>
+
+DetectorConstruction::DetectorConstruction()
+: G4VUserDetectorConstruction(),
+  fScoringVolume(0)
+{
+    // Size of experimental hall and fibre length //
+    detector_x = 10*cm;
+    detector_y = 2*cm;
+    detector_z = (Parameters::GetInstance()->FibreLength()+0.5)/2.*m+1*cm;
+    scint_z = Parameters::GetInstance()->FibreLength()/2.*m;
+
+    // mat/detector dimensions
+    Nj = 1; //rows of fibre in Y
+    Nk = 10; // number of fibers in X
+  
+    xDist = 0.275 *4* mm; //horizontal pitch of fibres (each row staggered by xDist/2)
+    yDist = 0.210 *4* mm; //vertical pitch of rows 
+    stripWidth = 1.0 * mm; //SiPM channel width
+    stripHeight = 1.00 * mm; //SiPM channel height
+
+    airGap = 0.001 * mm; //airgap between epoxy and fibre
+    pixelDimX = 0.05 * mm; // pixel dimension X
+    pixelDimY = 0.05 * mm; //pixel dimension Y
+    epoxy_strip_width = 0.1*mm; //epoxy thickness over SiPM silicon
+	
+    Nx = 20; // number of SiPM pixels in X
+    Ny = 20; // number of SiPM pixels in Y
+
+    //Geant4 World
+    fWorldSizeX = 1000*cm;
+    fWorldSizeY = 1000*cm;
+    fWorldSizeZ = 1000*cm;
+    
+    fMirrorToggle = true; //mirror at the end of the fibre mat
+    fMirrorPolish = 1.;   //polish parameter
+    fMirrorReflectivity = 0.8; //reflectivity parameter
+
+   
+    fMirrorZ = 0.1*mm; //mirror thickness
+    fMirrorRmax = 0.250*mm; //TODO
+}
+
+DetectorConstruction::~DetectorConstruction(){}
+
+void DetectorConstruction::DefineMaterials() 
+{
+    // Get nist material manager
+    G4NistManager* man = G4NistManager::Instance();
+    // Option to switch on/off checking of volumes overlaps
+    //
+    G4bool checkOverlaps = true;
+    
+
+    // Elements to cunstruct inner cladding material (PMMA)
+    G4double densityPMMA = 1190*kg/m3;
+    std::vector<G4String> PMMA_elm;
+    std::vector<G4int> PMMA_nbAtoms;
+    PMMA_elm.push_back("H"); PMMA_nbAtoms.push_back(8);
+    PMMA_elm.push_back("C"); PMMA_nbAtoms.push_back(5);
+    PMMA_elm.push_back("O"); PMMA_nbAtoms.push_back(2);
+    PMMA = man->ConstructNewMaterial("PMMA", PMMA_elm, PMMA_nbAtoms, densityPMMA);
+    
+  	// Elements to cunstruct outer cladding material (PTFEMA)
+    G4double densityPMMA2 = 1430*kg/m3;
+    std::vector<G4String> PMMA2_elm;
+    std::vector<G4int> PMMA2_nbAtoms;
+    PMMA2_elm.push_back("H"); PMMA2_nbAtoms.push_back(7);
+    PMMA2_elm.push_back("C"); PMMA2_nbAtoms.push_back(6);
+    PMMA2_elm.push_back("O"); PMMA2_nbAtoms.push_back(2);
+    PMMA2_elm.push_back("F"); PMMA2_nbAtoms.push_back(3);
+    PMMA2 = man->ConstructNewMaterial("PMMA2", PMMA2_elm, PMMA2_nbAtoms, densityPMMA2=1430*kg/m3);
+  
+    // Glue (Epo-Tek 301)
+    G4double Glue_density = 1.15*g/cm3;
+    std::vector<G4String> Glue_elm;
+    std::vector<G4int>	Glue_nbAtoms;
+    Glue_elm.push_back("C"); Glue_nbAtoms.push_back(19);
+    Glue_elm.push_back("H"); Glue_nbAtoms.push_back(27);
+    Glue_elm.push_back("O"); Glue_nbAtoms.push_back(3);
+    Glue = man->ConstructNewMaterial("Glue",Glue_elm, Glue_nbAtoms, Glue_density);
+  
+    // TiO2
+    G4double TiO2_density = 4.26*g/cm3;
+    std::vector<G4String> TiO2_elm;
+    std::vector<G4int>	TiO2_nbAtoms;
+    TiO2_elm.push_back("Ti"); TiO2_nbAtoms.push_back(1);
+    TiO2_elm.push_back("Ti"); TiO2_nbAtoms.push_back(2);
+    TiO2 = man->ConstructNewMaterial("TiO2",TiO2_elm, TiO2_nbAtoms, TiO2_density);
+  
+    // Abs plastic
+    G4double Abs_density = 1.07*g/cm3;
+    std::vector<G4String> Abs_elm;
+    std::vector<G4int> Abs_nbAtoms;
+    Abs_elm.push_back("H"); Abs_nbAtoms.push_back(17);
+    Abs_elm.push_back("C"); Abs_nbAtoms.push_back(13);
+    Abs_elm.push_back("N"); Abs_nbAtoms.push_back(1);
+    Abs_plastic = man->ConstructNewMaterial("Abs_plastic", Abs_elm, Abs_nbAtoms, Abs_density);
+
+    // Epoxy
+    G4double Epoxy_density = 1.5*g/cm3;
+    Epoxy = new G4Material("Epoxy", Epoxy_density, 2);
+    Epoxy->AddMaterial(TiO2, 25*perCent);
+    Epoxy->AddMaterial(Glue, 75*perCent);
+
+    // Environment
+    Air     = man->FindOrBuildMaterial("G4_AIR");
+    Vacuum  = man->FindOrBuildMaterial("G4_Galactic");
+
+    // Polystyrene   G4_POLYSTYRENE
+    Pstyrene = man->FindOrBuildMaterial("G4_POLYSTYRENE");
+
+    // Aluminium
+    alu = man->FindOrBuildMaterial("G4_Al");
+
+    // Core sections
+    G4String materialNameCore = "ScintCoreMaterial";
+    scintCoreMaterial = new G4Material(materialNameCore,Pstyrene->GetDensity(),1);
+    scintCoreMaterial->AddMaterial(Pstyrene,1.);
+
+    // Inner cladding sections
+    G4String materialNameCladding1 = "InnerCladdingMaterial";
+    innerCladdingMaterial = new G4Material(materialNameCladding1,PMMA->GetDensity(),1);
+    innerCladdingMaterial->AddMaterial(PMMA,1.);
+
+    // Outer cladding sections
+    G4String materialNameCladding2 = "OuterCladdingMaterial";
+    outerCladdingMaterial = new G4Material(materialNameCladding2,PMMA2->GetDensity(),1);
+    outerCladdingMaterial->AddMaterial(PMMA2,1.);
+}
+
+
+
+
+void DetectorConstruction::DefineMaterialProperties() 
+{
+    // Initialise considered ENERGIES and EMISSION SPECTRA for scintillation and wls
+
+    const G4int numInterpolPoints = Parameters::GetInstance()->NumberOfInterpolatedPoints();
+
+    // Set scintillation emmision spectrum
+    G4int E_NUMENTRIES = Parameters::GetInstance()->NumberOfEnergies();
+    G4double* Energy = new G4double[E_NUMENTRIES];
+    for(int i=0; i<E_NUMENTRIES; i++)
+        Energy[i] = Parameters::GetInstance()->Energy[i]*eV;
+
+    G4double* ScintilEnergyDist = new G4double[E_NUMENTRIES];
+    for(int i=0; i<E_NUMENTRIES; i++)
+        ScintilEnergyDist[i] = Parameters::GetInstance()->Intensity[i];
+
+    G4MaterialPropertyVector* scintSpecVector = new G4MaterialPropertyVector(Energy, ScintilEnergyDist, E_NUMENTRIES);
+    scintSpecVector->SetSpline(true);
+
+    // Set the Birks Constant for the Polystyrene scintillator
+    Pstyrene->GetIonisation()->SetBirksConstant(Parameters::GetInstance()->BirksConstant()*mm/MeV);
+
+    // Set wls emmision spectrum
+    G4int WLS_E_NUMENTRIES = Parameters::GetInstance()->NumberOfWlsEmissionEnergies();
+    G4double* WlsEnergy = new G4double[WLS_E_NUMENTRIES];
+    for(int i=0; i<WLS_E_NUMENTRIES; i++)
+        WlsEnergy[i] = Parameters::GetInstance()->WlsEmissionEnergy[i]*eV;
+
+    G4double* WlsEnergyDist = new G4double[WLS_E_NUMENTRIES];
+    for(int i=0; i<WLS_E_NUMENTRIES; i++)
+        WlsEnergyDist[i] = Parameters::GetInstance()->WlsEmissionIntensity[i];
+
+    G4MaterialPropertyVector* wlsSpecVector = new G4MaterialPropertyVector(WlsEnergy, WlsEnergyDist, WLS_E_NUMENTRIES);
+  	wlsSpecVector->SetSpline(true);
+
+    if(numInterpolPoints>0)
+    {
+        // Interpolate scintillation spectrum
+
+        const G4int E_NUMENTRIES_New = (E_NUMENTRIES-1)*(numInterpolPoints+1)+1;
+        G4double* NewEnergy = new G4double[E_NUMENTRIES_New];
+        G4double* NewValue = new G4double[E_NUMENTRIES_New];
+        G4double* scintInterpolValue = new G4double[numInterpolPoints];
+    
+        for(int j=0; j<E_NUMENTRIES-1; j++)
+        {
+            G4double interpolDist = (Energy[j+1]-Energy[j])/(numInterpolPoints+1);
+            NewEnergy[j*(numInterpolPoints+1)] = Energy[j];
+            NewValue[j*(numInterpolPoints+1)] = scintSpecVector->Value(Energy[j]);
+
+            for(int k=0; k<numInterpolPoints; k++)
+            {
+                scintInterpolValue[k] = scintSpecVector->Value(Energy[j]+(k+1)*interpolDist);
+                NewEnergy[j*(numInterpolPoints+1)+(k+1)] = Energy[j]+(k+1)*interpolDist;
+
+                if(scintInterpolValue[k]>=0)
+                {
+                    NewValue[j*(numInterpolPoints+1)+(k+1)] = scintInterpolValue[k];
+                }
+                else
+                {
+                    NewValue[j*(numInterpolPoints+1)+(k+1)] = 0;
+                    G4cout << "Warning: Intensity of emission spectrum set to 0 for energy "
+                        << NewEnergy[j*(numInterpolPoints+1)+(k+1)]*1e6
+                        << " eV.\nSpline interpolation led to negative value!"  << G4endl;
+				}
+            }
+        }
+        
+        NewEnergy[E_NUMENTRIES_New-1] = Energy[E_NUMENTRIES-1];
+        NewValue[E_NUMENTRIES_New-1] = scintSpecVector->Value(Energy[E_NUMENTRIES-1]);
+    
+        delete[] Energy;
+        delete[] ScintilEnergyDist;
+        delete scintSpecVector;
+
+        E_NUMENTRIES = E_NUMENTRIES_New;
+        Energy = new G4double[E_NUMENTRIES];
+        ScintilEnergyDist = new G4double[E_NUMENTRIES];
+
+        for(int i=0; i<E_NUMENTRIES; i++)
+        {
+            Energy[i] = NewEnergy[i];
+            ScintilEnergyDist[i] = NewValue[i];
+    	}
+
+        scintSpecVector = new G4MaterialPropertyVector(Energy, ScintilEnergyDist, E_NUMENTRIES);
+        scintSpecVector->SetSpline(true);
+   
+        delete[] NewEnergy;
+        delete[] NewValue;
+        delete[] scintInterpolValue;
+
+
+        // Interpolate wls spectrum
+    
+        const G4int WLS_E_NUMENTRIES_New = (WLS_E_NUMENTRIES-1)*(numInterpolPoints+1)+1;
+        NewEnergy = new G4double[WLS_E_NUMENTRIES_New];
+        NewValue = new G4double[WLS_E_NUMENTRIES_New];
+
+        G4double* wlsInterpolValue = new G4double[numInterpolPoints];
+    
+        for(int j=0; j<WLS_E_NUMENTRIES-1; j++)
+        {
+            G4double interpolDist = (WlsEnergy[j+1]-WlsEnergy[j])/(numInterpolPoints+1);
+            NewEnergy[j*(numInterpolPoints+1)] = WlsEnergy[j];
+            NewValue[j*(numInterpolPoints+1)] = wlsSpecVector->Value(WlsEnergy[j]);
+
+            for(int k=0; k<numInterpolPoints; k++)
+            {
+                wlsInterpolValue[k] = wlsSpecVector->Value(WlsEnergy[j]+(k+1)*interpolDist);
+                NewEnergy[j*(numInterpolPoints+1)+(k+1)] = WlsEnergy[j]+(k+1)*interpolDist;
+                if(wlsInterpolValue[k]>=0)
+                {
+                    NewValue[j*(numInterpolPoints+1)+(k+1)] = wlsInterpolValue[k];
+                }
+                else
+                {
+                    NewValue[j*(numInterpolPoints+1)+(k+1)] = 0;
+                    G4cout << "Warning: Intensity of WLS emission spectrum set to 0 for energy "
+                           << NewEnergy[j*(numInterpolPoints+1)+(k+1)]*1e6
+                           << " eV.\nSpline interpolation led to negative value!" << G4endl;
+                }
+            }
+        }
+        
+        NewEnergy[WLS_E_NUMENTRIES_New-1] = WlsEnergy[WLS_E_NUMENTRIES-1];
+        NewValue[WLS_E_NUMENTRIES_New-1] = wlsSpecVector->Value(WlsEnergy[WLS_E_NUMENTRIES-1]);
+    
+        delete[] WlsEnergy;
+        delete[] WlsEnergyDist;
+        delete wlsSpecVector;
+
+        WLS_E_NUMENTRIES = WLS_E_NUMENTRIES_New;
+        WlsEnergy = new G4double[WLS_E_NUMENTRIES];
+        WlsEnergyDist = new G4double[WLS_E_NUMENTRIES];
+
+        for(int i=0; i<WLS_E_NUMENTRIES; i++)
+        {
+            WlsEnergy[i] = NewEnergy[i];
+            WlsEnergyDist[i] = NewValue[i];
+        }
+
+        wlsSpecVector = new G4MaterialPropertyVector(WlsEnergy, WlsEnergyDist, WLS_E_NUMENTRIES);
+        wlsSpecVector->SetSpline(true);
+
+        delete[] NewEnergy;
+        delete[] NewValue;
+        delete[] wlsInterpolValue;
+    }
+
+    // Save spectra to parameter file
+    std::ofstream parameterOutputFile;
+    parameterOutputFile.open(Parameters::GetInstance()->ParameterOutputFileName(), std::ios_base::app);
+    
+    parameterOutputFile << G4endl << "Scintillation emission spectrum:" << G4endl;
+    parameterOutputFile << "Energy/eV\tWavelength/nm\tIntensity" << "\n";
+    for(int i=0; i<E_NUMENTRIES; i++)
+    {
+        parameterOutputFile << Energy[i]*1e6 << "\t" << Parameters::hcPERe/Energy[i]*1e3
+                            << "\t" << ScintilEnergyDist[i]<< "\n";
+	}
+
+    parameterOutputFile << G4endl << "WLS emission spectrum:" << G4endl;
+    parameterOutputFile << "Energy/eV\tWavelength/nm\tIntensity" << "\n";
+    for(int i=0; i<WLS_E_NUMENTRIES; i++)
+    {
+        parameterOutputFile << WlsEnergy[i]*1e6 << "\t" << Parameters::hcPERe/WlsEnergy[i]*1e3
+                            << "\t" << WlsEnergyDist[i]<< "\n";
+	}
+    
+    parameterOutputFile.close();
+
+    // WLS ABSORPTION
+    const G4int WLS_ABS_ENTRIES = Parameters::GetInstance()->NumberOfWlsAbsEnergies();
+    G4double* WlsAbsEnergy = new G4double[WLS_ABS_ENTRIES];
+    G4double* WlsAbsLength = new G4double[WLS_ABS_ENTRIES];
+
+    for(int j=0; j<WLS_ABS_ENTRIES; j++)
+    {
+        WlsAbsEnergy[j] = Parameters::GetInstance()->WlsAbsEnergy[j]*eV;
+        WlsAbsLength[j] = Parameters::GetInstance()->WlsAbsLength[j]*m;
+    }
+
+    // Save WLS absorption lengths to parameter file
+    parameterOutputFile.open(Parameters::GetInstance()->ParameterOutputFileName(), std::ios_base::app);
+    parameterOutputFile << G4endl << "WLS absorption length / m:" << G4endl;
+    parameterOutputFile << "Energy/eV\tWavelength/nm\tAbsorption length" << "\n";
+    for(int i=0; i<WLS_ABS_ENTRIES; i++)
+    {
+        parameterOutputFile << WlsAbsEnergy[i]*1e6 << "\t" << Parameters::hcPERe/WlsAbsEnergy[i]*1e3
+                            << "\t" << WlsAbsLength[i]*1e-3 << "\n";
+	}
+    parameterOutputFile.close();
+
+    // REFRACTIVE INDICES
+
+    G4double* Vacuum_RIND = new G4double[E_NUMENTRIES];
+    G4double* Pstyrene_RIND = new G4double[E_NUMENTRIES];
+    G4double* PMMA_RIND = new G4double[E_NUMENTRIES];
+    G4double* PMMA2_RIND = new G4double[E_NUMENTRIES];
+    G4double* Epoxy_RIND = new G4double[E_NUMENTRIES];
+	
+    // Functions are saved in parameter-file
+    // todo: write this functions in c++ code
+    TF1 vacuumRind("vacuumRind",Parameters::GetInstance()->RefractiveIndexVacuum(),300,800);
+    TF1 coreRind("coreRind",Parameters::GetInstance()->RefractiveIndexCore(),300,800);
+    TF1 clad1Rind("clad1Rind",Parameters::GetInstance()->RefractiveIndexClad1(),300,800);
+    TF1 clad2Rind("clad2Rind",Parameters::GetInstance()->RefractiveIndexClad2(),300,800);
+
+    for(int i=0; i<E_NUMENTRIES; i++)
+    {
+        double wavelengthNanometer = Parameters::hcPERe/Energy[i]*1e3;
+        Vacuum_RIND[i] = vacuumRind.Eval(wavelengthNanometer);
+        Pstyrene_RIND[i] = coreRind.Eval(wavelengthNanometer);
+        PMMA_RIND[i] = clad1Rind.Eval(wavelengthNanometer);
+        PMMA2_RIND[i] = clad2Rind.Eval(wavelengthNanometer);
+        Epoxy_RIND[i] = 1.59;
+    }
+
+    // Save refractive indices to parameter file
+
+    parameterOutputFile.open(Parameters::GetInstance()->ParameterOutputFileName(), std::ios_base::app);
+    parameterOutputFile << G4endl << "Refractive indices:" << G4endl;
+    parameterOutputFile << "Energy/eV\tWavelength/nm\tVacuum\tClad2\tClad1\tCore" << "\n";
+    for(int i=0; i<E_NUMENTRIES; i++)
+    {
+        parameterOutputFile << Energy[i]*1e6 << "\t" << Parameters::hcPERe/Energy[i]*1e3
+                            << "\t" << Vacuum_RIND[i]<< "\t" << PMMA2_RIND[i] << "\t"
+                            << PMMA_RIND[i] << "\t" << Pstyrene_RIND[i] << "\n";
+    }
+    parameterOutputFile.close();
+
+
+    // Set material properties table of Vacuum
+
+    G4double* Vacuum_ABS = new G4double[E_NUMENTRIES];
+    G4double* Epoxy_ABS = new G4double[E_NUMENTRIES];
+    for(int i=0; i<E_NUMENTRIES; i++){
+        Vacuum_ABS[i] = 5e4*m; // absorption length in vacuum...
+        Epoxy_ABS[i] = 1*m;
+    }
+
+    G4MaterialPropertiesTable *Vacuum_mt = new G4MaterialPropertiesTable();
+    Vacuum_mt->AddProperty("RINDEX", Energy, Vacuum_RIND,E_NUMENTRIES);
+    Vacuum_mt->AddProperty("ABSLENGTH",Energy,Vacuum_ABS,E_NUMENTRIES);
+    Vacuum->SetMaterialPropertiesTable(Vacuum_mt);
+
+    G4MaterialPropertiesTable *Epoxy_mt = new G4MaterialPropertiesTable();
+    Epoxy_mt->AddProperty("RINDEX", Energy, Epoxy_RIND, E_NUMENTRIES);
+    Epoxy_mt->AddProperty("ABSLENGTH", Energy, Epoxy_ABS, E_NUMENTRIES);
+    Glue->SetMaterialPropertiesTable(Epoxy_mt);
+
+    // give air same material properties as vacuum
+    Air->SetMaterialPropertiesTable(Vacuum_mt);
+
+    // RAYLEIGH SCATTERING
+
+    G4double* Pstyrene_RAYLEIGH = new G4double[E_NUMENTRIES];
+    G4double* PMMA_RAYLEIGH = new G4double[E_NUMENTRIES];
+    G4double* PMMA2_RAYLEIGH = new G4double[E_NUMENTRIES];
+
+    TF1 coreRayleigh("coreRayleigh",Parameters::GetInstance()->RayleighCore(),300,800);
+    TF1 clad1Rayleigh("clad1Rayleigh",Parameters::GetInstance()->RayleighClad1(),300,800);
+    TF1 clad2Rayleigh("clad2Rayleigh",Parameters::GetInstance()->RayleighClad2(),300,800);
+  
+    // Calculate scattering lengths
+  
+    for(int j=0; j<E_NUMENTRIES; j++)
+    {
+        double wavelengthNanometer = Parameters::hcPERe/Energy[j]*1e3;
+        // todo : write this functions in c++
+        Pstyrene_RAYLEIGH[j] = 1./coreRayleigh.Eval(wavelengthNanometer)*m;
+        PMMA_RAYLEIGH[j] 		= 1./clad1Rayleigh.Eval(wavelengthNanometer)*m;
+        PMMA2_RAYLEIGH[j] 	= 1./clad2Rayleigh.Eval(wavelengthNanometer)*m;
+  	}
+
+    // Save Rayleigh scattering lengths to parameter file
+
+    parameterOutputFile.open(Parameters::GetInstance()->ParameterOutputFileName(), std::ios_base::app);
+    parameterOutputFile << G4endl << "Rayleigh scattering length / m:" << G4endl;
+    parameterOutputFile << "Energy/eV\tWavelength/nm\tClad2\tClad1\tCore" << "\n";
+    for(int i=0; i<E_NUMENTRIES; i++)
+    {
+    parameterOutputFile << Energy[i]*1e6 << "\t" << Parameters::hcPERe/Energy[i]*1e3
+                        << "\t" << PMMA2_RAYLEIGH[i]*1e-3 << "\t" << PMMA_RAYLEIGH[i]*1e-3
+                        << "\t" << Pstyrene_RAYLEIGH[i]*1e-3 << "\n";
+    }
+    parameterOutputFile.close();
+
+
+
+    // Material properties table
+
+    G4MaterialPropertiesTable* scintCoreMaterialProperties = new G4MaterialPropertiesTable();
+    G4MaterialPropertiesTable* innerCladMaterialProperties = new G4MaterialPropertiesTable();
+    G4MaterialPropertiesTable* outerCladMaterialProperties = new G4MaterialPropertiesTable();
+
+    // Set refractive indices
+
+    scintCoreMaterialProperties->AddProperty("RINDEX",Energy,Pstyrene_RIND,E_NUMENTRIES)->SetSpline(true);
+    innerCladMaterialProperties->AddProperty("RINDEX",Energy,PMMA_RIND,E_NUMENTRIES)->SetSpline(true);
+    outerCladMaterialProperties->AddProperty("RINDEX",Energy,PMMA2_RIND,E_NUMENTRIES)->SetSpline(true);
+
+    // Set absorption
+
+    // todo : write functions in c++ code
+    TF1 coreAbs("coreAbs",Parameters::GetInstance()->AbsorptionCore(),300,800);
+    TF1 clad1Abs("clad1Abs",Parameters::GetInstance()->AbsorptionClad1(),300,800);
+    TF1 clad2Abs("clad2Abs",Parameters::GetInstance()->AbsorptionClad2(),300,800);
+
+    G4double* Pstyrene_ABSLENGTH = new G4double[E_NUMENTRIES];
+    G4double* PMMA_ABSLENGTH = new G4double[E_NUMENTRIES];
+    G4double* PMMA2_ABSLENGTH = new G4double[E_NUMENTRIES];
+
+    // Calculate absorption lengths
+
+    for(int j=0; j<E_NUMENTRIES; j++)
+    {
+        double wavelengthNanometer = Parameters::hcPERe/Energy[j]*1e3;
+
+        Pstyrene_ABSLENGTH[j] = 1./coreAbs.Eval(wavelengthNanometer)*m;
+        PMMA_ABSLENGTH[j] 	 = 1./clad1Abs.Eval(wavelengthNanometer)*m;
+        PMMA2_ABSLENGTH[j] 	 = 1./clad2Abs.Eval(wavelengthNanometer)*m;
+    }
+    
+    scintCoreMaterialProperties->AddProperty("ABSLENGTH",Energy,Pstyrene_ABSLENGTH,E_NUMENTRIES)->SetSpline(true);
+    innerCladMaterialProperties->AddProperty("ABSLENGTH",Energy,PMMA_ABSLENGTH,E_NUMENTRIES)->SetSpline(true);
+    outerCladMaterialProperties->AddProperty("ABSLENGTH",Energy,PMMA2_ABSLENGTH,E_NUMENTRIES)->SetSpline(true);
+    
+    delete[] Pstyrene_ABSLENGTH;
+    delete[] PMMA_ABSLENGTH;
+    delete[] PMMA2_ABSLENGTH;
+
+    // Set Rayleigh scattering
+
+    scintCoreMaterialProperties->AddProperty("RAYLEIGH",Energy,Pstyrene_RAYLEIGH,E_NUMENTRIES)->SetSpline(true);
+    innerCladMaterialProperties->AddProperty("RAYLEIGH",Energy,PMMA_RAYLEIGH,E_NUMENTRIES)->SetSpline(true);
+    outerCladMaterialProperties->AddProperty("RAYLEIGH",Energy,PMMA2_RAYLEIGH,E_NUMENTRIES)->SetSpline(true);
+
+    // Set scintillation and WLS properties
+
+    scintCoreMaterialProperties->AddProperty("FASTCOMPONENT",scintSpecVector);
+    scintCoreMaterialProperties->AddProperty("SLOWCOMPONENT",scintSpecVector);
+    scintCoreMaterialProperties->AddProperty("WLSCOMPONENT",wlsSpecVector);
+
+
+    scintCoreMaterialProperties->AddConstProperty("SCINTILLATIONYIELD",
+                                                  Parameters::GetInstance()->ScintillationYield()/keV);
+    scintCoreMaterialProperties->AddConstProperty("RESOLUTIONSCALE",
+                                                  Parameters::GetInstance()->ResolutionScale());
+    scintCoreMaterialProperties->AddConstProperty("FASTTIMECONSTANT",
+                                                  Parameters::GetInstance()->DecayTimeFast()*ns);
+    scintCoreMaterialProperties->AddConstProperty("SLOWTIMECONSTANT",
+                                                  Parameters::GetInstance()->DecayTimeSlow()*ns);
+    scintCoreMaterialProperties->AddConstProperty("YIELDRATIO", Parameters::GetInstance()->YieldRatio());
+    // Is set in "PhysicsList.hh" as well due to inconsistency in Geant4 (G4OpticalPhsysics default value)
+
+    scintCoreMaterialProperties->AddProperty("WLSABSLENGTH",
+                                             WlsAbsEnergy,WlsAbsLength,WLS_ABS_ENTRIES)->SetSpline(true);
+	
+    scintCoreMaterialProperties->AddConstProperty("WLSTIMECONSTANT", Parameters::GetInstance()->WlsDecayTime()*ns);
+
+    // Assign material properties tables
+
+    scintCoreMaterial->SetMaterialPropertiesTable(scintCoreMaterialProperties);
+    innerCladdingMaterial->SetMaterialPropertiesTable(innerCladMaterialProperties);
+    outerCladdingMaterial->SetMaterialPropertiesTable(outerCladMaterialProperties);
+
+    // Set the Birks Constant for the Polystyrene scintillator
+    scintCoreMaterial->GetIonisation()->SetBirksConstant(Parameters::GetInstance()->BirksConstant()*mm/MeV);
+
+    delete[] Energy;
+    delete[] ScintilEnergyDist;
+
+    delete[] WlsEnergy;
+    delete[] WlsEnergyDist;
+
+    delete[] WlsAbsEnergy;
+    delete[] WlsAbsLength;
+
+    delete[] Vacuum_RIND;
+    delete[] Vacuum_ABS;
+
+    delete[] Pstyrene_RIND;
+    delete[] PMMA_RIND;
+    delete[] PMMA2_RIND;
+
+    delete[] Pstyrene_RAYLEIGH;
+    delete[] PMMA_RAYLEIGH;
+    delete[] PMMA2_RAYLEIGH;
+}
+
+
+
+G4VPhysicalVolume* DetectorConstruction::Construct()
+{
+    DefineMaterials();
+    DefineMaterialProperties();
+
+    // Placing the world (experimental hall)
+
+     //--------------------------------------------------
+     // World
+     //--------------------------------------------------
+   
+     G4Box * world_box =
+                       new G4Box("World", fWorldSizeX, fWorldSizeY, fWorldSizeZ);
+   
+     fLogicWorld = new G4LogicalVolume(world_box,
+                                      Air,
+                                      "World");
+   
+     fPhysiWorld = new G4PVPlacement(0,G4ThreeVector(0.,0.,0.), fLogicWorld,"World", 0, false, 0);
+
+  
+
+    G4Box* detector_box = new G4Box("Detector",detector_x,detector_y,detector_z);
+    detector_log = new G4LogicalVolume(detector_box,Air,"Detector");
+    detector_phys = new G4PVPlacement(0,G4ThreeVector(0. , 0., scint_z ),detector_log,"Detector",fLogicWorld,false,0);
+
+
+    // Epoxy (a sheet of epoxy that the fibres are embedded inside)
+    G4double xEpoxy = 0.5*(Nk*xDist+2*Parameters::GetInstance()->SemiAxisZ()*mm)+5*mm;
+    G4double yEpoxy = 0.5*(Nj*yDist+2*Parameters::GetInstance()->SemiAxisZ()*mm)+0.5*mm;
+    G4Box* epoxyBox = new G4Box("EpoxyBox",xEpoxy, yEpoxy, scint_z);
+    epoxyLog = new G4LogicalVolume(epoxyBox, Epoxy, "EpoxyBox", 0, 0, 0);
+    epoxyPhy = new G4PVPlacement(0, G4ThreeVector() , epoxyLog, "EpoxyBox", detector_log, false, 0);
+
+
+
+   //--------------------------------------------------
+    // Mirror for reflection at one of the end
+    //--------------------------------------------------
+  
+    // Place the mirror only if the user wants the mirror
+    if (fMirrorToggle) {  
+  
+       G4VSolid* solidMirror = new G4Box("Mirror",
+                                         xEpoxy,
+                                         yEpoxy,
+                                         fMirrorZ);
+   
+       G4LogicalVolume* logicMirror = new G4LogicalVolume(solidMirror,
+                                                          alu,
+                                                          "Mirror");
+ 
+     G4OpticalSurface* mirrorSurface = new G4OpticalSurface("MirrorSurface",
+                                                              glisur,
+                                                              ground,
+                                                              dielectric_metal,
+                                                              fMirrorPolish);
+  
+       G4MaterialPropertiesTable* mirrorSurfaceProperty =
+                                                new G4MaterialPropertiesTable();
+  
+       G4double p_mirror[] = {2.00*eV, 3.47*eV};
+       const G4int nbins = sizeof(p_mirror)/sizeof(G4double);
+       G4double refl_mirror[] = {fMirrorReflectivity,fMirrorReflectivity};
+       assert(sizeof(refl_mirror) == sizeof(p_mirror));
+       G4double effi_mirror[] = {0, 0};
+       assert(sizeof(effi_mirror) == sizeof(effi_mirror));
+  
+       mirrorSurfaceProperty->
+                         AddProperty("REFLECTIVITY",p_mirror,refl_mirror,nbins);
+       mirrorSurfaceProperty->
+                         AddProperty("EFFICIENCY",p_mirror,effi_mirror,nbins);
+  
+       mirrorSurface -> SetMaterialPropertiesTable(mirrorSurfaceProperty);
+  
+       new G4PVPlacement(0,
+                         G4ThreeVector(0.0,0.0,-scint_z-2*fMirrorZ),
+                         logicMirror,
+                         "Mirror",
+                         detector_log,
+                         false,
+                         0);
+  
+       new G4LogicalSkinSurface("MirrorSurface",logicMirror,mirrorSurface);
+    }
+
+
+
+    // ABS plastic (some dead material)
+    G4double xABS = xEpoxy;
+    G4double yABS = 2.5*mm;
+    G4double zABS = scint_z;
+    G4Box* absBox = new G4Box("AbsBox", xABS, yABS/2., zABS);
+    absLog = new G4LogicalVolume(absBox, Abs_plastic, "AbsBox", 0, 0,0);
+    //absPhy = new G4PVPlacement(0, G4ThreeVector(0., -(yEpoxy+yABS/2.), 0.), absLog, "AbsBox", detector_log, false, 0);
+
+    ConstructFiber(); //place the fibres
+    // ConstructFiberSheet();
+
+    /* ++ Construction and placement of the detector strips ++ */
+
+    // Epoxy layer infront of det strip
+    G4VSolid* epoxy_strip = new G4Box("EpoxyStrip",  stripWidth/2., stripHeight/2., epoxy_strip_width/2.);
+    G4LogicalVolume* epoxy_strip_log = new G4LogicalVolume(epoxy_strip, Glue, "EpoxyStrip", 0, 0, 0);
+    
+    //place the pixels at the end of the fibre mat
+    G4VSolid* pixelS = new G4Box("Pixel", pixelDimX/2., pixelDimY/2., stripWidth/2.);
+    G4LogicalVolume* pixelL = new G4LogicalVolume(pixelS, Glue, "Pixel", 0, 0, 0);
+
+    SensitiveDetector* sensitive = new SensitiveDetector("/Sensitive");
+    G4SDManager* sdman = G4SDManager::GetSDMpointer();
+    sdman->AddNewDetector(sensitive);
+    pixelL->SetSensitiveDetector(sensitive);
+
+    //    G4int Nk_s = ceil(((G4double)Nk)*(xDist/stripWidth)); // Determ. autom. nb. of detector strips.
+    G4int Nk_s = Nk;//set to the same number of SiPMs as the number of fibres
+
+    for(int k = 0; k < Nk_s; k++) //for every sipm
+    {
+        new G4PVPlacement(0, objectPos(Nj/2, k, scint_z+epoxy_strip_width/2.+airGap), epoxy_strip_log,
+                          "EpoxyStrip", detector_log, false, 0);
+
+        for(int i = 0; i < Nx; i++) //rows of pixels in each SiPM
+        {
+	  for(int j = 0; j < Ny; j++){ //columns of pixels in each SiPM
+	    //  new G4PVPlacement(0, objectPos(Nj/2, i, j, k, scint_z+stripWidth/2.+epoxy_strip_width+airGap), pixelL, "SensitiveDetector"+C::c1(k)+C::c2(i)+C::c3(j), detector_log, false, 0);
+		// C::c1(k)+C::c2(i)+C::c3(j) = "kkkijj" with 0-padding in front
+		// this currently breaks if i>9
+		/// need C::c1(k)+C::c3(i)+C::c3(j)
+	    new G4PVPlacement(0, objectPos(Nj/2, i, j, k, scint_z+stripWidth/2.+epoxy_strip_width+airGap), pixelL, "SensitiveDetector"+C::c1(k)+C::c3(i)+C::c3(j), detector_log, false, 0);
+            }
+        }
+    }
+	/* ++ End of Constr. and placem. of det. strips ++ */
+
+    /*  Construction and placement of trigger
+     *  Trigger should have the same x,y-dimensions as epoxyBox
+     */
+  
+    G4double xTrigger = xEpoxy;//Parameters::GetInstance()->TriggerX()*mm;
+    G4double yTrigger = Parameters::GetInstance()->TriggerY()*mm;
+    G4double zTrigger = scint_z*2.0;//;Parameters::GetInstance()->TriggerZ()*mm;
+  
+    G4double triggerXPos = 0.0; //Parameters::GetInstance()->TriggerXPos()*mm;
+    G4double triggerZPos = 0.0; //Parameters::GetInstance()->TriggerZPos()*mm;
+
+    G4VSolid* triggerS = new G4Box("Trigger", xTrigger/2., yTrigger/2., zTrigger/2.);
+    G4LogicalVolume* triggerL = new G4LogicalVolume(triggerS, Air, "Trigger", 0, 0, 0);
+    new G4PVPlacement(0 , G4ThreeVector(triggerXPos, -(yEpoxy+yTrigger/2.+yABS), triggerZPos),
+                      triggerL, "Trigger", detector_log, false, 0);
+	
+    return fPhysiWorld;
+}
+
+
+void DetectorConstruction::ConstructFiberSheet()
+{
+  //a generic sheet of scintillator
+  // dimensions
+  
+    G4double dim_z;
+    G4double sphi, ephi;
+    dim_z = scint_z;
+    sphi = 0.00*deg;
+    ephi = 360.*deg;
+  G4double xEpoxy = 0.5*(Nk*xDist+2*Parameters::GetInstance()->SemiAxisZ()*mm)+5*mm;
+            // Scintillating core
+    //   G4Tubs* coreSection_tube = new G4Tubs("CoreSection",core_rZmin,core_rZmax,dim_z, sphi,ephi);
+    //	    G4Box* coreSection_tube= new G4Box("CoreSection",  stripWidth/3., 0.85*mm, epoxy_strip_width/2.);
+	    G4Box* CoreBox = new G4Box("CoreBox",xEpoxy-1*mm, 0.8294/2.0*mm, scint_z);
+            G4LogicalVolume *coreSection_log = new G4LogicalVolume(CoreBox,
+                                                                   scintCoreMaterial, "CoreSection",0,0,0);
+            
+            new G4PVPlacement(0, G4ThreeVector(), coreSection_log, "Core", epoxyLog, true, 0);
+
+}
+void DetectorConstruction::ConstructFiber()
+{
+    // dimensions
+    G4double dim_z;
+    G4double sphi, ephi;
+    G4double core_rZmin,core_rZmax;
+    G4double core_rYmin,core_rYmax;
+    G4double clad1_rZmin,clad1_rZmax;
+    G4double clad1_rYmin,clad1_rYmax;
+    G4double clad2_rZmin,clad2_rZmax;
+    G4double clad2_rYmin,clad2_rYmax;
+
+    dim_z = scint_z;
+    sphi = 0.00*deg;
+    ephi = 360.*deg;
+
+    core_rZmin = 0.00*cm;
+    core_rYmin = 0.00*cm;
+
+    core_rZmax = Parameters::GetInstance()->SemiAxisZ()*(88./100.)*mm;
+    core_rYmax = Parameters::GetInstance()->SemiAxisY()*(88./100.)*mm;
+
+    clad1_rZmin = core_rZmax;
+    clad1_rYmin = core_rYmax;
+
+    clad1_rZmax = core_rZmax + 3./88.*core_rZmax*2.;
+    clad1_rYmax = core_rYmax + 3./88.*core_rYmax*2.;
+
+    clad2_rZmin = clad1_rZmax;
+    clad2_rYmin = clad1_rYmax;
+
+    clad2_rZmax = Parameters::GetInstance()->SemiAxisZ()*mm;
+    clad2_rYmax = Parameters::GetInstance()->SemiAxisY()*mm;
+
+    G4ThreeVector origin;
+    /* ++ Fibre Placement ++ */
+    for(int j = 0; j < Nj; j++)
+    {
+        for(int k = 0; k < Nk; k++)
+        {
+            origin = objectPos(j,k);
+      
+            // Outer cladding
+            G4Tubs* clad2Section_tube = new G4Tubs("Cladding2Section",clad2_rZmin,clad2_rZmax,dim_z, sphi,ephi);
+            G4LogicalVolume *clad2Section_log = new G4LogicalVolume(clad2Section_tube,
+                                                                    outerCladdingMaterial, "Cladding2Section",0,0,0);
+
+            new G4PVPlacement(0, origin, clad2Section_log, "Cladding2"+C::c(j)+C::c(k), epoxyLog, true, 0);
+
+
+            // Inner cladding
+            G4Tubs* clad1Section_tube = new G4Tubs("Cladding1Section",clad1_rZmin,clad1_rZmax,dim_z, sphi,ephi);
+            G4LogicalVolume *clad1Section_log = new G4LogicalVolume(clad1Section_tube,
+                                                                    innerCladdingMaterial, "Cladding1Section",0,0,0);
+      
+            new G4PVPlacement(0, origin, clad1Section_log, "Cladding1"+C::c(j)+C::c(k), epoxyLog, true, 0);
+
+            // Scintillating core
+            G4Tubs* coreSection_tube = new G4Tubs("CoreSection",core_rZmin,core_rZmax,dim_z, sphi,ephi);
+            G4LogicalVolume *coreSection_log = new G4LogicalVolume(coreSection_tube,
+                                                                   scintCoreMaterial, "CoreSection",0,0,0);
+            
+            new G4PVPlacement(0, origin, coreSection_log, "Core"+C::c(j)+C::c(k), epoxyLog, true, 0);
+        }
+    }
+	/* ++ End of Fibre Placement ++ */
+}
+
+
+// for fibre placement
+G4ThreeVector DetectorConstruction::objectPos(G4int j, G4int k)
+{	
+    G4double xOffset = xDist*(((G4double)Nk)/2.)-Parameters::GetInstance()->SemiAxisZ()*mm/2.;
+    G4double yOffset = yDist*(((G4double)Nj)/2.)-Parameters::GetInstance()->SemiAxisZ()*mm;
+	
+    G4double xDispl;
+    G4double xsigma = (-0.49*j*j + 7.0*j-1.8)/1000.;
+    G4double xvar = G4RandGauss::shoot(0.,xsigma);
+    while(fabs(xvar)>=0.020*mm) {
+      xvar = G4RandGauss::shoot(0.,xsigma);
+    }
+	
+    j % 2 == 0 ? xDispl = 0. : xDispl = xDist/2.;
+	
+    G4ThreeVector origin(xDist*k+xDispl-xOffset+xvar, -yDist*j+yOffset, 0.);
+    
+    // print detector positions into file
+    std::ofstream outFile;
+    outFile.open("fibrePos.txt",std::ios::app);
+    outFile << origin.x() << "\t" << origin.y() << std::endl;
+    outFile.close();
+    
+    //G4cout << "Placing Fibre[" << k << ":" << j << "]: " << origin << G4endl;
+    
+    //G4cout << origin.x() << "\t" << origin.y() << G4endl;
+    
+    return origin;
+}
+
+// for detector placement
+G4ThreeVector DetectorConstruction::objectPos(G4int j, G4int k, G4double zPos)
+{	
+    G4double randomN = Parameters::GetInstance()->RandomNumber();
+    G4double offset = (stripWidth/2.)*randomN;
+	
+    // Save random number
+    std::ofstream myfile;
+    myfile.open("randomN.txt");
+    myfile << randomN;
+    myfile.close();
+	
+    G4double xOffset = xDist*(((G4double)Nk)/2.)-Parameters::GetInstance()->SemiAxisZ()*mm/2.;
+    G4double yOffset = yDist*(((G4double)Nj)/2.)-Parameters::GetInstance()->SemiAxisZ()*mm;
+	
+    G4double xDispl;
+	
+    j % 2 == 0 ? xDispl = 0. : xDispl = xDist/2.;
+	
+    //    G4ThreeVector origin(stripWidth*k+xDispl-xOffset-offset, -yDist*j+yOffset, zPos);
+    G4ThreeVector origin(xDist*k+xDispl-xOffset-offset, -yDist*j+yOffset, zPos); //set at fibre position
+
+    // print detector positions into file
+    std::ofstream detFile;
+    detFile.open("detPos.txt",std::ios::app);
+    detFile << k << " " << stripWidth*k+xDispl-xOffset-offset << std::endl;
+    detFile.close();
+    
+    return origin;
+}
+
+// for detector placement
+G4ThreeVector DetectorConstruction::objectPos(G4int j, G4int i, G4int j2, G4int k, G4double zPos)
+{	
+    G4double randomN = Parameters::GetInstance()->RandomNumber();
+    G4double offset = (stripWidth/2.)*randomN;
+	
+    // Save random number
+    //std::ofstream myfile;
+    //myfile.open("randomN.txt");
+    //myfile << randomN;
+    //myfile.close();
+	
+    G4double xOffset = xDist*(((G4double)Nk)/2.)-Parameters::GetInstance()->SemiAxisZ()*mm/2.;
+    G4double yOffset = yDist*(((G4double)Nj)/2.)-Parameters::GetInstance()->SemiAxisZ()*mm + 3/2*pixelDimY;
+	
+    G4double xDispl;
+	
+    j % 2 == 0 ? xDispl = 0. : xDispl = xDist/2.;
+
+    // print detector positions into file
+    //std::ofstream detFile;
+    //detFile.open("detPos.txt",std::ios::app);
+    //detFile << k << " " << stripWidth*k+xDispl-xOffset-offset << std::endl;
+    //detFile.close();
+
+    G4double pixelX = pixelDimX + i*pixelDimX - stripWidth/2.;
+    G4double pixelY = -pixelDimY/2. + j2*pixelDimY - stripHeight/2.;
+
+    //  G4ThreeVector origin(stripWidth*k+xDispl-xOffset-offset + pixelX, -yDist*j+yOffset + pixelY, zPos);
+    G4ThreeVector origin(xDist*k+xDispl-xOffset-offset + pixelX, -yDist*j+yOffset + pixelY, zPos); //start at fibre postion
+
+    std::ofstream detFileY;
+    detFileY.open("detPosY.txt",std::ios::app);
+    detFileY << k << " " << -yDist*j+yOffset + pixelY << std::endl;
+    detFileY.close();
+	
+    return origin;
+}
+
+

SciFiSim/src/DetectorConstruction.cc~

@@ -0,0 +1,884 @@
+// Written by Peter Stromberger
+// based on work of Mirco Deckenhoff
+// modified by Bastian Rössler
+
+
+#include "DetectorConstruction.hh"
+#include "G4Material.hh"
+#include "G4LogicalBorderSurface.hh"
+#include "G4LogicalSkinSurface.hh"
+#include "G4Box.hh"
+#include "G4Tubs.hh"
+#include "G4EllipticalTube.hh"
+#include "G4SubtractionSolid.hh"
+#include "G4LogicalVolume.hh"
+#include "G4RotationMatrix.hh"
+#include "G4PVPlacement.hh"
+#include "G4OpBoundaryProcess.hh"
+#include "G4MaterialPropertyVector.hh"
+#include "G4NistManager.hh"
+#include "G4VisAttributes.hh"
+#include "G4Colour.hh"
+#include "G4PVParameterised.hh"
+#include "SensitiveDetector.hh"
+#include "G4SDManager.hh"
+#include "Analysis.hh"
+#include "Parameters.hh"
+#include "TF1.h"
+#include "TF2.h"
+#include "Randomize.hh"
+#include <fstream>
+#include <sstream>
+#include "G4SystemOfUnits.hh"
+#include "G4VPVParameterisation.hh"
+#include "Convert.hh"
+#include <math.h>
+#include <stdlib.h> 
+#include <time.h>  
+#include <iostream>
+#include <fstream>
+
+DetectorConstruction::DetectorConstruction()
+: G4VUserDetectorConstruction(),
+  fScoringVolume(0)
+{
+    // Size of experimental hall and fibre length //
+    expHall_x = 35*mm/2.+0.5*m;
+    expHall_y = 10*mm/2.+0.5*m;
+    expHall_z = (Parameters::GetInstance()->FibreLength()+0.5)/2.*m+0.5*m;
+    scint_z = Parameters::GetInstance()->FibreLength()/2.*m;
+
+    // mat/detector dimensions
+    Nj = 8;
+    Nk = 128;
+  
+    xDist = 0.350 * mm;
+    yDist = 0.185 * mm;
+    stripWidth = 0.25 * mm;
+    stripHeight = 1.62 * mm;
+
+    airGap = 0.001 * mm;
+    pixelDimX = 0.0625 * mm;
+    pixelDimY = 0.0675 * mm;
+    epoxy_strip_width = 0.1*mm;
+	
+    Nx = 4;
+    Ny = 24;
+
+    
+    fMirrorToggle = true;
+    fMirrorPolish = 1.;
+    fMirrorReflectivity = 0.8;
+
+   
+    fMirrorZ = 0.1*mm;
+    fMirrorRmax = 0.250*mm;
+}
+
+DetectorConstruction::~DetectorConstruction(){}
+
+void DetectorConstruction::DefineMaterials() 
+{
+    // Get nist material manager
+    G4NistManager* man = G4NistManager::Instance();
+    // Option to switch on/off checking of volumes overlaps
+    //
+    G4bool checkOverlaps = true;
+    
+
+    // Elements to cunstruct inner cladding material (PMMA)
+    G4double densityPMMA = 1190*kg/m3;
+    std::vector<G4String> PMMA_elm;
+    std::vector<G4int> PMMA_nbAtoms;
+    PMMA_elm.push_back("H"); PMMA_nbAtoms.push_back(8);
+    PMMA_elm.push_back("C"); PMMA_nbAtoms.push_back(5);
+    PMMA_elm.push_back("O"); PMMA_nbAtoms.push_back(2);
+    PMMA = man->ConstructNewMaterial("PMMA", PMMA_elm, PMMA_nbAtoms, densityPMMA);
+    
+  	// Elements to cunstruct outer cladding material (PTFEMA)
+    G4double densityPMMA2 = 1430*kg/m3;
+    std::vector<G4String> PMMA2_elm;
+    std::vector<G4int> PMMA2_nbAtoms;
+    PMMA2_elm.push_back("H"); PMMA2_nbAtoms.push_back(7);
+    PMMA2_elm.push_back("C"); PMMA2_nbAtoms.push_back(6);
+    PMMA2_elm.push_back("O"); PMMA2_nbAtoms.push_back(2);
+    PMMA2_elm.push_back("F"); PMMA2_nbAtoms.push_back(3);
+    PMMA2 = man->ConstructNewMaterial("PMMA2", PMMA2_elm, PMMA2_nbAtoms, densityPMMA2=1430*kg/m3);
+  
+    // Glue (Epo-Tek 301)
+    G4double Glue_density = 1.15*g/cm3;
+    std::vector<G4String> Glue_elm;
+    std::vector<G4int>	Glue_nbAtoms;
+    Glue_elm.push_back("C"); Glue_nbAtoms.push_back(19);
+    Glue_elm.push_back("H"); Glue_nbAtoms.push_back(27);
+    Glue_elm.push_back("O"); Glue_nbAtoms.push_back(3);
+    Glue = man->ConstructNewMaterial("Glue",Glue_elm, Glue_nbAtoms, Glue_density);
+  
+    // TiO2
+    G4double TiO2_density = 4.26*g/cm3;
+    std::vector<G4String> TiO2_elm;
+    std::vector<G4int>	TiO2_nbAtoms;
+    TiO2_elm.push_back("Ti"); TiO2_nbAtoms.push_back(1);
+    TiO2_elm.push_back("Ti"); TiO2_nbAtoms.push_back(2);
+    TiO2 = man->ConstructNewMaterial("TiO2",TiO2_elm, TiO2_nbAtoms, TiO2_density);
+  
+    // Abs plastic
+    G4double Abs_density = 1.07*g/cm3;
+    std::vector<G4String> Abs_elm;
+    std::vector<G4int> Abs_nbAtoms;
+    Abs_elm.push_back("H"); Abs_nbAtoms.push_back(17);
+    Abs_elm.push_back("C"); Abs_nbAtoms.push_back(13);
+    Abs_elm.push_back("N"); Abs_nbAtoms.push_back(1);
+    Abs_plastic = man->ConstructNewMaterial("Abs_plastic", Abs_elm, Abs_nbAtoms, Abs_density);
+
+    // Epoxy
+    G4double Epoxy_density = 1.5*g/cm3;
+    Epoxy = new G4Material("Epoxy", Epoxy_density, 2);
+    Epoxy->AddMaterial(TiO2, 25*perCent);
+    Epoxy->AddMaterial(Glue, 75*perCent);
+
+    // Environment
+    Air     = man->FindOrBuildMaterial("G4_AIR");
+    Vacuum  = man->FindOrBuildMaterial("G4_Galactic");
+
+    // Polystyrene   G4_POLYSTYRENE
+    Pstyrene = man->FindOrBuildMaterial("G4_POLYSTYRENE");
+
+    // Aluminium
+    alu = man->FindOrBuildMaterial("G4_Al");
+
+    // Core sections
+    G4String materialNameCore = "ScintCoreMaterial";
+    scintCoreMaterial = new G4Material(materialNameCore,Pstyrene->GetDensity(),1);
+    scintCoreMaterial->AddMaterial(Pstyrene,1.);
+
+    // Inner cladding sections
+    G4String materialNameCladding1 = "InnerCladdingMaterial";
+    innerCladdingMaterial = new G4Material(materialNameCladding1,PMMA->GetDensity(),1);
+    innerCladdingMaterial->AddMaterial(PMMA,1.);
+
+    // Outer cladding sections
+    G4String materialNameCladding2 = "OuterCladdingMaterial";
+    outerCladdingMaterial = new G4Material(materialNameCladding2,PMMA2->GetDensity(),1);
+    outerCladdingMaterial->AddMaterial(PMMA2,1.);
+}
+
+
+
+
+void DetectorConstruction::DefineMaterialProperties() 
+{
+    // Initialise considered ENERGIES and EMISSION SPECTRA for scintillation and wls
+
+    const G4int numInterpolPoints = Parameters::GetInstance()->NumberOfInterpolatedPoints();
+
+    // Set scintillation emmision spectrum
+    G4int E_NUMENTRIES = Parameters::GetInstance()->NumberOfEnergies();
+    G4double* Energy = new G4double[E_NUMENTRIES];
+    for(int i=0; i<E_NUMENTRIES; i++)
+        Energy[i] = Parameters::GetInstance()->Energy[i]*eV;
+
+    G4double* ScintilEnergyDist = new G4double[E_NUMENTRIES];
+    for(int i=0; i<E_NUMENTRIES; i++)
+        ScintilEnergyDist[i] = Parameters::GetInstance()->Intensity[i];
+
+    G4MaterialPropertyVector* scintSpecVector = new G4MaterialPropertyVector(Energy, ScintilEnergyDist, E_NUMENTRIES);
+    scintSpecVector->SetSpline(true);
+
+    // Set the Birks Constant for the Polystyrene scintillator
+    Pstyrene->GetIonisation()->SetBirksConstant(Parameters::GetInstance()->BirksConstant()*mm/MeV);
+
+    // Set wls emmision spectrum
+    G4int WLS_E_NUMENTRIES = Parameters::GetInstance()->NumberOfWlsEmissionEnergies();
+    G4double* WlsEnergy = new G4double[WLS_E_NUMENTRIES];
+    for(int i=0; i<WLS_E_NUMENTRIES; i++)
+        WlsEnergy[i] = Parameters::GetInstance()->WlsEmissionEnergy[i]*eV;
+
+    G4double* WlsEnergyDist = new G4double[WLS_E_NUMENTRIES];
+    for(int i=0; i<WLS_E_NUMENTRIES; i++)
+        WlsEnergyDist[i] = Parameters::GetInstance()->WlsEmissionIntensity[i];
+
+    G4MaterialPropertyVector* wlsSpecVector = new G4MaterialPropertyVector(WlsEnergy, WlsEnergyDist, WLS_E_NUMENTRIES);
+  	wlsSpecVector->SetSpline(true);
+
+    if(numInterpolPoints>0)
+    {
+        // Interpolate scintillation spectrum
+
+        const G4int E_NUMENTRIES_New = (E_NUMENTRIES-1)*(numInterpolPoints+1)+1;
+        G4double* NewEnergy = new G4double[E_NUMENTRIES_New];
+        G4double* NewValue = new G4double[E_NUMENTRIES_New];
+        G4double* scintInterpolValue = new G4double[numInterpolPoints];
+    
+        for(int j=0; j<E_NUMENTRIES-1; j++)
+        {
+            G4double interpolDist = (Energy[j+1]-Energy[j])/(numInterpolPoints+1);
+            NewEnergy[j*(numInterpolPoints+1)] = Energy[j];
+            NewValue[j*(numInterpolPoints+1)] = scintSpecVector->Value(Energy[j]);
+
+            for(int k=0; k<numInterpolPoints; k++)
+            {
+                scintInterpolValue[k] = scintSpecVector->Value(Energy[j]+(k+1)*interpolDist);
+                NewEnergy[j*(numInterpolPoints+1)+(k+1)] = Energy[j]+(k+1)*interpolDist;
+
+                if(scintInterpolValue[k]>=0)
+                {
+                    NewValue[j*(numInterpolPoints+1)+(k+1)] = scintInterpolValue[k];
+                }
+                else
+                {
+                    NewValue[j*(numInterpolPoints+1)+(k+1)] = 0;
+                    G4cout << "Warning: Intensity of emission spectrum set to 0 for energy "
+                        << NewEnergy[j*(numInterpolPoints+1)+(k+1)]*1e6
+                        << " eV.\nSpline interpolation led to negative value!"  << G4endl;
+				}
+            }
+        }
+        
+        NewEnergy[E_NUMENTRIES_New-1] = Energy[E_NUMENTRIES-1];
+        NewValue[E_NUMENTRIES_New-1] = scintSpecVector->Value(Energy[E_NUMENTRIES-1]);
+    
+        delete[] Energy;
+        delete[] ScintilEnergyDist;
+        delete scintSpecVector;
+
+        E_NUMENTRIES = E_NUMENTRIES_New;
+        Energy = new G4double[E_NUMENTRIES];
+        ScintilEnergyDist = new G4double[E_NUMENTRIES];
+
+        for(int i=0; i<E_NUMENTRIES; i++)
+        {
+            Energy[i] = NewEnergy[i];
+            ScintilEnergyDist[i] = NewValue[i];
+    	}
+
+        scintSpecVector = new G4MaterialPropertyVector(Energy, ScintilEnergyDist, E_NUMENTRIES);
+        scintSpecVector->SetSpline(true);
+   
+        delete[] NewEnergy;
+        delete[] NewValue;
+        delete[] scintInterpolValue;
+
+
+        // Interpolate wls spectrum
+    
+        const G4int WLS_E_NUMENTRIES_New = (WLS_E_NUMENTRIES-1)*(numInterpolPoints+1)+1;
+        NewEnergy = new G4double[WLS_E_NUMENTRIES_New];
+        NewValue = new G4double[WLS_E_NUMENTRIES_New];
+
+        G4double* wlsInterpolValue = new G4double[numInterpolPoints];
+    
+        for(int j=0; j<WLS_E_NUMENTRIES-1; j++)
+        {
+            G4double interpolDist = (WlsEnergy[j+1]-WlsEnergy[j])/(numInterpolPoints+1);
+            NewEnergy[j*(numInterpolPoints+1)] = WlsEnergy[j];
+            NewValue[j*(numInterpolPoints+1)] = wlsSpecVector->Value(WlsEnergy[j]);
+
+            for(int k=0; k<numInterpolPoints; k++)
+            {
+                wlsInterpolValue[k] = wlsSpecVector->Value(WlsEnergy[j]+(k+1)*interpolDist);
+                NewEnergy[j*(numInterpolPoints+1)+(k+1)] = WlsEnergy[j]+(k+1)*interpolDist;
+                if(wlsInterpolValue[k]>=0)
+                {
+                    NewValue[j*(numInterpolPoints+1)+(k+1)] = wlsInterpolValue[k];
+                }
+                else
+                {
+                    NewValue[j*(numInterpolPoints+1)+(k+1)] = 0;
+                    G4cout << "Warning: Intensity of WLS emission spectrum set to 0 for energy "
+                           << NewEnergy[j*(numInterpolPoints+1)+(k+1)]*1e6
+                           << " eV.\nSpline interpolation led to negative value!" << G4endl;
+                }
+            }
+        }
+        
+        NewEnergy[WLS_E_NUMENTRIES_New-1] = WlsEnergy[WLS_E_NUMENTRIES-1];
+        NewValue[WLS_E_NUMENTRIES_New-1] = wlsSpecVector->Value(WlsEnergy[WLS_E_NUMENTRIES-1]);
+    
+        delete[] WlsEnergy;
+        delete[] WlsEnergyDist;
+        delete wlsSpecVector;
+
+        WLS_E_NUMENTRIES = WLS_E_NUMENTRIES_New;
+        WlsEnergy = new G4double[WLS_E_NUMENTRIES];
+        WlsEnergyDist = new G4double[WLS_E_NUMENTRIES];
+
+        for(int i=0; i<WLS_E_NUMENTRIES; i++)
+        {
+            WlsEnergy[i] = NewEnergy[i];
+            WlsEnergyDist[i] = NewValue[i];
+        }
+
+        wlsSpecVector = new G4MaterialPropertyVector(WlsEnergy, WlsEnergyDist, WLS_E_NUMENTRIES);
+        wlsSpecVector->SetSpline(true);
+
+        delete[] NewEnergy;
+        delete[] NewValue;
+        delete[] wlsInterpolValue;
+    }
+
+    // Save spectra to parameter file
+    std::ofstream parameterOutputFile;
+    parameterOutputFile.open(Parameters::GetInstance()->ParameterOutputFileName(), std::ios_base::app);
+    
+    parameterOutputFile << G4endl << "Scintillation emission spectrum:" << G4endl;
+    parameterOutputFile << "Energy/eV\tWavelength/nm\tIntensity" << "\n";
+    for(int i=0; i<E_NUMENTRIES; i++)
+    {
+        parameterOutputFile << Energy[i]*1e6 << "\t" << Parameters::hcPERe/Energy[i]*1e3
+                            << "\t" << ScintilEnergyDist[i]<< "\n";
+	}
+
+    parameterOutputFile << G4endl << "WLS emission spectrum:" << G4endl;
+    parameterOutputFile << "Energy/eV\tWavelength/nm\tIntensity" << "\n";
+    for(int i=0; i<WLS_E_NUMENTRIES; i++)
+    {
+        parameterOutputFile << WlsEnergy[i]*1e6 << "\t" << Parameters::hcPERe/WlsEnergy[i]*1e3
+                            << "\t" << WlsEnergyDist[i]<< "\n";
+	}
+    
+    parameterOutputFile.close();
+
+    // WLS ABSORPTION
+    const G4int WLS_ABS_ENTRIES = Parameters::GetInstance()->NumberOfWlsAbsEnergies();
+    G4double* WlsAbsEnergy = new G4double[WLS_ABS_ENTRIES];
+    G4double* WlsAbsLength = new G4double[WLS_ABS_ENTRIES];
+
+    for(int j=0; j<WLS_ABS_ENTRIES; j++)
+    {
+        WlsAbsEnergy[j] = Parameters::GetInstance()->WlsAbsEnergy[j]*eV;
+        WlsAbsLength[j] = Parameters::GetInstance()->WlsAbsLength[j]*m;
+    }
+
+    // Save WLS absorption lengths to parameter file
+    parameterOutputFile.open(Parameters::GetInstance()->ParameterOutputFileName(), std::ios_base::app);
+    parameterOutputFile << G4endl << "WLS absorption length / m:" << G4endl;
+    parameterOutputFile << "Energy/eV\tWavelength/nm\tAbsorption length" << "\n";
+    for(int i=0; i<WLS_ABS_ENTRIES; i++)
+    {
+        parameterOutputFile << WlsAbsEnergy[i]*1e6 << "\t" << Parameters::hcPERe/WlsAbsEnergy[i]*1e3
+                            << "\t" << WlsAbsLength[i]*1e-3 << "\n";
+	}
+    parameterOutputFile.close();
+
+    // REFRACTIVE INDICES
+
+    G4double* Vacuum_RIND = new G4double[E_NUMENTRIES];
+    G4double* Pstyrene_RIND = new G4double[E_NUMENTRIES];
+    G4double* PMMA_RIND = new G4double[E_NUMENTRIES];
+    G4double* PMMA2_RIND = new G4double[E_NUMENTRIES];
+    G4double* Epoxy_RIND = new G4double[E_NUMENTRIES];
+	
+    // Functions are saved in parameter-file
+    // todo: write this functions in c++ code
+    TF1 vacuumRind("vacuumRind",Parameters::GetInstance()->RefractiveIndexVacuum(),300,800);
+    TF1 coreRind("coreRind",Parameters::GetInstance()->RefractiveIndexCore(),300,800);
+    TF1 clad1Rind("clad1Rind",Parameters::GetInstance()->RefractiveIndexClad1(),300,800);
+    TF1 clad2Rind("clad2Rind",Parameters::GetInstance()->RefractiveIndexClad2(),300,800);
+
+    for(int i=0; i<E_NUMENTRIES; i++)
+    {
+        double wavelengthNanometer = Parameters::hcPERe/Energy[i]*1e3;
+        Vacuum_RIND[i] = vacuumRind.Eval(wavelengthNanometer);
+        Pstyrene_RIND[i] = coreRind.Eval(wavelengthNanometer);
+        PMMA_RIND[i] = clad1Rind.Eval(wavelengthNanometer);
+        PMMA2_RIND[i] = clad2Rind.Eval(wavelengthNanometer);
+        Epoxy_RIND[i] = 1.59;
+    }
+
+    // Save refractive indices to parameter file
+
+    parameterOutputFile.open(Parameters::GetInstance()->ParameterOutputFileName(), std::ios_base::app);
+    parameterOutputFile << G4endl << "Refractive indices:" << G4endl;
+    parameterOutputFile << "Energy/eV\tWavelength/nm\tVacuum\tClad2\tClad1\tCore" << "\n";
+    for(int i=0; i<E_NUMENTRIES; i++)
+    {
+        parameterOutputFile << Energy[i]*1e6 << "\t" << Parameters::hcPERe/Energy[i]*1e3
+                            << "\t" << Vacuum_RIND[i]<< "\t" << PMMA2_RIND[i] << "\t"
+                            << PMMA_RIND[i] << "\t" << Pstyrene_RIND[i] << "\n";
+    }
+    parameterOutputFile.close();
+
+
+    // Set material properties table of Vacuum
+
+    G4double* Vacuum_ABS = new G4double[E_NUMENTRIES];
+    G4double* Epoxy_ABS = new G4double[E_NUMENTRIES];
+    for(int i=0; i<E_NUMENTRIES; i++){
+        Vacuum_ABS[i] = 5e4*m; // absorption length in vacuum...
+        Epoxy_ABS[i] = 1*m;
+    }
+
+    G4MaterialPropertiesTable *Vacuum_mt = new G4MaterialPropertiesTable();
+    Vacuum_mt->AddProperty("RINDEX", Energy, Vacuum_RIND,E_NUMENTRIES);
+    Vacuum_mt->AddProperty("ABSLENGTH",Energy,Vacuum_ABS,E_NUMENTRIES);
+    Vacuum->SetMaterialPropertiesTable(Vacuum_mt);
+
+    G4MaterialPropertiesTable *Epoxy_mt = new G4MaterialPropertiesTable();
+    Epoxy_mt->AddProperty("RINDEX", Energy, Epoxy_RIND, E_NUMENTRIES);
+    Epoxy_mt->AddProperty("ABSLENGTH", Energy, Epoxy_ABS, E_NUMENTRIES);
+    Glue->SetMaterialPropertiesTable(Epoxy_mt);
+
+    // give air same material properties as vacuum
+    Air->SetMaterialPropertiesTable(Vacuum_mt);
+
+    // RAYLEIGH SCATTERING
+
+    G4double* Pstyrene_RAYLEIGH = new G4double[E_NUMENTRIES];
+    G4double* PMMA_RAYLEIGH = new G4double[E_NUMENTRIES];
+    G4double* PMMA2_RAYLEIGH = new G4double[E_NUMENTRIES];
+
+    TF1 coreRayleigh("coreRayleigh",Parameters::GetInstance()->RayleighCore(),300,800);
+    TF1 clad1Rayleigh("clad1Rayleigh",Parameters::GetInstance()->RayleighClad1(),300,800);
+    TF1 clad2Rayleigh("clad2Rayleigh",Parameters::GetInstance()->RayleighClad2(),300,800);
+  
+    // Calculate scattering lengths
+  
+    for(int j=0; j<E_NUMENTRIES; j++)
+    {
+        double wavelengthNanometer = Parameters::hcPERe/Energy[j]*1e3;
+        // todo : write this functions in c++
+        Pstyrene_RAYLEIGH[j] = 1./coreRayleigh.Eval(wavelengthNanometer)*m;
+        PMMA_RAYLEIGH[j] 		= 1./clad1Rayleigh.Eval(wavelengthNanometer)*m;
+        PMMA2_RAYLEIGH[j] 	= 1./clad2Rayleigh.Eval(wavelengthNanometer)*m;
+  	}
+
+    // Save Rayleigh scattering lengths to parameter file
+
+    parameterOutputFile.open(Parameters::GetInstance()->ParameterOutputFileName(), std::ios_base::app);
+    parameterOutputFile << G4endl << "Rayleigh scattering length / m:" << G4endl;
+    parameterOutputFile << "Energy/eV\tWavelength/nm\tClad2\tClad1\tCore" << "\n";
+    for(int i=0; i<E_NUMENTRIES; i++)
+    {
+    parameterOutputFile << Energy[i]*1e6 << "\t" << Parameters::hcPERe/Energy[i]*1e3
+                        << "\t" << PMMA2_RAYLEIGH[i]*1e-3 << "\t" << PMMA_RAYLEIGH[i]*1e-3
+                        << "\t" << Pstyrene_RAYLEIGH[i]*1e-3 << "\n";
+    }
+    parameterOutputFile.close();
+
+
+
+    // Material properties table
+
+    G4MaterialPropertiesTable* scintCoreMaterialProperties = new G4MaterialPropertiesTable();
+    G4MaterialPropertiesTable* innerCladMaterialProperties = new G4MaterialPropertiesTable();
+    G4MaterialPropertiesTable* outerCladMaterialProperties = new G4MaterialPropertiesTable();
+
+    // Set refractive indices
+
+    scintCoreMaterialProperties->AddProperty("RINDEX",Energy,Pstyrene_RIND,E_NUMENTRIES)->SetSpline(true);
+    innerCladMaterialProperties->AddProperty("RINDEX",Energy,PMMA_RIND,E_NUMENTRIES)->SetSpline(true);
+    outerCladMaterialProperties->AddProperty("RINDEX",Energy,PMMA2_RIND,E_NUMENTRIES)->SetSpline(true);
+
+    // Set absorption
+
+    // todo : write functions in c++ code
+    TF1 coreAbs("coreAbs",Parameters::GetInstance()->AbsorptionCore(),300,800);
+    TF1 clad1Abs("clad1Abs",Parameters::GetInstance()->AbsorptionClad1(),300,800);
+    TF1 clad2Abs("clad2Abs",Parameters::GetInstance()->AbsorptionClad2(),300,800);
+
+    G4double* Pstyrene_ABSLENGTH = new G4double[E_NUMENTRIES];
+    G4double* PMMA_ABSLENGTH = new G4double[E_NUMENTRIES];
+    G4double* PMMA2_ABSLENGTH = new G4double[E_NUMENTRIES];
+
+    // Calculate absorption lengths
+
+    for(int j=0; j<E_NUMENTRIES; j++)
+    {
+        double wavelengthNanometer = Parameters::hcPERe/Energy[j]*1e3;
+
+        Pstyrene_ABSLENGTH[j] = 1./coreAbs.Eval(wavelengthNanometer)*m;
+        PMMA_ABSLENGTH[j] 	 = 1./clad1Abs.Eval(wavelengthNanometer)*m;
+        PMMA2_ABSLENGTH[j] 	 = 1./clad2Abs.Eval(wavelengthNanometer)*m;
+    }
+    
+    scintCoreMaterialProperties->AddProperty("ABSLENGTH",Energy,Pstyrene_ABSLENGTH,E_NUMENTRIES)->SetSpline(true);
+    innerCladMaterialProperties->AddProperty("ABSLENGTH",Energy,PMMA_ABSLENGTH,E_NUMENTRIES)->SetSpline(true);
+    outerCladMaterialProperties->AddProperty("ABSLENGTH",Energy,PMMA2_ABSLENGTH,E_NUMENTRIES)->SetSpline(true);
+    
+    delete[] Pstyrene_ABSLENGTH;
+    delete[] PMMA_ABSLENGTH;
+    delete[] PMMA2_ABSLENGTH;
+
+    // Set Rayleigh scattering
+
+    scintCoreMaterialProperties->AddProperty("RAYLEIGH",Energy,Pstyrene_RAYLEIGH,E_NUMENTRIES)->SetSpline(true);
+    innerCladMaterialProperties->AddProperty("RAYLEIGH",Energy,PMMA_RAYLEIGH,E_NUMENTRIES)->SetSpline(true);
+    outerCladMaterialProperties->AddProperty("RAYLEIGH",Energy,PMMA2_RAYLEIGH,E_NUMENTRIES)->SetSpline(true);
+
+    // Set scintillation and WLS properties
+
+    scintCoreMaterialProperties->AddProperty("FASTCOMPONENT",scintSpecVector);
+    scintCoreMaterialProperties->AddProperty("SLOWCOMPONENT",scintSpecVector);
+    scintCoreMaterialProperties->AddProperty("WLSCOMPONENT",wlsSpecVector);
+
+
+    scintCoreMaterialProperties->AddConstProperty("SCINTILLATIONYIELD",
+                                                  Parameters::GetInstance()->ScintillationYield()/keV);
+    scintCoreMaterialProperties->AddConstProperty("RESOLUTIONSCALE",
+                                                  Parameters::GetInstance()->ResolutionScale());
+    scintCoreMaterialProperties->AddConstProperty("FASTTIMECONSTANT",
+                                                  Parameters::GetInstance()->DecayTimeFast()*ns);
+    scintCoreMaterialProperties->AddConstProperty("SLOWTIMECONSTANT",
+                                                  Parameters::GetInstance()->DecayTimeSlow()*ns);
+    scintCoreMaterialProperties->AddConstProperty("YIELDRATIO", Parameters::GetInstance()->YieldRatio());
+    // Is set in "PhysicsList.hh" as well due to inconsistency in Geant4 (G4OpticalPhsysics default value)
+
+    scintCoreMaterialProperties->AddProperty("WLSABSLENGTH",
+                                             WlsAbsEnergy,WlsAbsLength,WLS_ABS_ENTRIES)->SetSpline(true);
+	
+    scintCoreMaterialProperties->AddConstProperty("WLSTIMECONSTANT", Parameters::GetInstance()->WlsDecayTime()*ns);
+
+    // Assign material properties tables
+
+    scintCoreMaterial->SetMaterialPropertiesTable(scintCoreMaterialProperties);
+    innerCladdingMaterial->SetMaterialPropertiesTable(innerCladMaterialProperties);
+    outerCladdingMaterial->SetMaterialPropertiesTable(outerCladMaterialProperties);
+
+    // Set the Birks Constant for the Polystyrene scintillator
+    scintCoreMaterial->GetIonisation()->SetBirksConstant(Parameters::GetInstance()->BirksConstant()*mm/MeV);
+
+    delete[] Energy;
+    delete[] ScintilEnergyDist;
+
+    delete[] WlsEnergy;
+    delete[] WlsEnergyDist;
+
+    delete[] WlsAbsEnergy;
+    delete[] WlsAbsLength;
+
+    delete[] Vacuum_RIND;
+    delete[] Vacuum_ABS;
+
+    delete[] Pstyrene_RIND;
+    delete[] PMMA_RIND;
+    delete[] PMMA2_RIND;
+
+    delete[] Pstyrene_RAYLEIGH;
+    delete[] PMMA_RAYLEIGH;
+    delete[] PMMA2_RAYLEIGH;
+}
+
+
+
+G4VPhysicalVolume* DetectorConstruction::Construct()
+{
+    DefineMaterials();
+    DefineMaterialProperties();
+
+    // Placing the world (experimental hall)
+    G4Box* expHall_box = new G4Box("World",expHall_x,expHall_y,expHall_z);
+    expHall_log = new G4LogicalVolume(expHall_box,Air,"World",0,0,0);
+    expHall_phys = new G4PVPlacement(0,G4ThreeVector(),expHall_log,"World",0,false,0);
+
+
+    // Epoxy
+    G4double xEpoxy = 0.5*(Nk*xDist+2*Parameters::GetInstance()->SemiAxisZ()*mm)+5*mm;
+    G4double yEpoxy = 0.5*(Nj*yDist+2*Parameters::GetInstance()->SemiAxisZ()*mm)+0.2*mm;
+    G4Box* epoxyBox = new G4Box("EpoxyBox",xEpoxy, yEpoxy, scint_z);
+    epoxyLog = new G4LogicalVolume(epoxyBox, Epoxy, "EpoxyBox", 0, 0, 0);
+    epoxyPhy = new G4PVPlacement(0, G4ThreeVector() , epoxyLog, "EpoxyBox", expHall_log, false, 0);
+
+
+
+   //--------------------------------------------------
+    // Mirror for reflection at one of the end
+    //--------------------------------------------------
+  
+    // Place the mirror only if the user wants the mirror
+    if (fMirrorToggle) {  
+  
+       G4VSolid* solidMirror = new G4Box("Mirror",
+                                         xEpoxy,
+                                         yEpoxy,
+                                         fMirrorZ);
+   
+       G4LogicalVolume* logicMirror = new G4LogicalVolume(solidMirror,
+                                                          alu,
+                                                          "Mirror");
+ 
+     G4OpticalSurface* mirrorSurface = new G4OpticalSurface("MirrorSurface",
+                                                              glisur,
+                                                              ground,
+                                                              dielectric_metal,
+                                                              fMirrorPolish);
+  
+       G4MaterialPropertiesTable* mirrorSurfaceProperty =
+                                                new G4MaterialPropertiesTable();
+  
+       G4double p_mirror[] = {2.00*eV, 3.47*eV};
+       const G4int nbins = sizeof(p_mirror)/sizeof(G4double);
+       G4double refl_mirror[] = {fMirrorReflectivity,fMirrorReflectivity};
+       assert(sizeof(refl_mirror) == sizeof(p_mirror));
+       G4double effi_mirror[] = {0, 0};
+       assert(sizeof(effi_mirror) == sizeof(effi_mirror));
+  
+       mirrorSurfaceProperty->
+                         AddProperty("REFLECTIVITY",p_mirror,refl_mirror,nbins);
+       mirrorSurfaceProperty->
+                         AddProperty("EFFICIENCY",p_mirror,effi_mirror,nbins);
+  
+       mirrorSurface -> SetMaterialPropertiesTable(mirrorSurfaceProperty);
+  
+       new G4PVPlacement(0,
+                         G4ThreeVector(0.0,0.0,-scint_z-2*fMirrorZ),
+                         logicMirror,
+                         "Mirror",
+                         expHall_log,
+                         false,
+                         0);
+  
+       new G4LogicalSkinSurface("MirrorSurface",logicMirror,mirrorSurface);
+    }
+
+
+
+    // ABS plastic
+    G4double xABS = xEpoxy;
+    G4double yABS = 2.5*mm;
+    G4double zABS = scint_z;
+    G4Box* absBox = new G4Box("AbsBox", xABS, yABS/2., zABS);
+    absLog = new G4LogicalVolume(absBox, Abs_plastic, "AbsBox", 0, 0,0);
+    absPhy = new G4PVPlacement(0, G4ThreeVector(0., -(yEpoxy+yABS/2.), 0.), absLog, "AbsBox", expHall_log, false, 0);
+
+     ConstructFiber();
+    // ConstructFiberSheet();
+
+    /* ++ Construction and placement of the detector strips ++ */
+
+    // Epoxy layer infront of det strip
+    G4VSolid* epoxy_strip = new G4Box("EpoxyStrip",  stripWidth/2., stripHeight/2., epoxy_strip_width/2.);
+    G4LogicalVolume* epoxy_strip_log = new G4LogicalVolume(epoxy_strip, Glue, "EpoxyStrip", 0, 0, 0);
+    
+    
+    G4VSolid* pixelS = new G4Box("Pixel", pixelDimX/2., pixelDimY/2., stripWidth/2.);
+    G4LogicalVolume* pixelL = new G4LogicalVolume(pixelS, Glue, "Pixel", 0, 0, 0);
+
+    SensitiveDetector* sensitive = new SensitiveDetector("/Sensitive");
+    G4SDManager* sdman = G4SDManager::GetSDMpointer();
+    sdman->AddNewDetector(sensitive);
+    pixelL->SetSensitiveDetector(sensitive);
+
+    G4int Nk_s = ceil(((G4double)Nk)*(xDist/stripWidth)); // Determ. autom. nb. of detector strips.
+    for(int k = 1; k < Nk_s-1; k++)
+    {
+        new G4PVPlacement(0, objectPos(Nj/2, k, scint_z+epoxy_strip_width/2.+airGap), epoxy_strip_log,
+                          "EpoxyStrip", expHall_log, false, 0);
+
+        for(int i = 0; i < Nx; i++)
+        {
+            for(int j = 0; j < Ny; j++){
+                new G4PVPlacement(0, objectPos(Nj/2, i, j, k, scint_z+stripWidth/2.+epoxy_strip_width+airGap),
+                                  pixelL, "SensitiveDetector"+C::c1(k)+C::c2(i)+C::c3(j), expHall_log, false, 0);
+            }
+        }
+    }
+	/* ++ End of Constr. and placem. of det. strips ++ */
+
+    /*  Construction and placement of trigger
+     *  Trigger should have the same x,y-dimensions as epoxyBox
+     */
+  
+    G4double xTrigger = xEpoxy;//Parameters::GetInstance()->TriggerX()*mm;
+    G4double yTrigger = Parameters::GetInstance()->TriggerY()*mm;
+    G4double zTrigger = scint_z*2.0;//;Parameters::GetInstance()->TriggerZ()*mm;
+  
+    G4double triggerXPos = 0.0; //Parameters::GetInstance()->TriggerXPos()*mm;
+    G4double triggerZPos = 0.0; //Parameters::GetInstance()->TriggerZPos()*mm;
+
+    G4VSolid* triggerS = new G4Box("Trigger", xTrigger/2., yTrigger/2., zTrigger/2.);
+    G4LogicalVolume* triggerL = new G4LogicalVolume(triggerS, Air, "Trigger", 0, 0, 0);
+    new G4PVPlacement(0 , G4ThreeVector(triggerXPos, -(yEpoxy+yTrigger/2.+yABS), triggerZPos),
+                      triggerL, "Trigger", expHall_log, false, 0);
+	
+    return expHall_phys;
+}
+
+
+void DetectorConstruction::ConstructFiberSheet()
+{
+    // dimensions
+    G4double dim_z;
+    G4double sphi, ephi;
+    dim_z = scint_z;
+    sphi = 0.00*deg;
+    ephi = 360.*deg;
+  G4double xEpoxy = 0.5*(Nk*xDist+2*Parameters::GetInstance()->SemiAxisZ()*mm)+5*mm;
+            // Scintillating core
+    //   G4Tubs* coreSection_tube = new G4Tubs("CoreSection",core_rZmin,core_rZmax,dim_z, sphi,ephi);
+    //	    G4Box* coreSection_tube= new G4Box("CoreSection",  stripWidth/3., 0.85*mm, epoxy_strip_width/2.);
+	    G4Box* CoreBox = new G4Box("CoreBox",xEpoxy-1*mm, 0.8294/2.0*mm, scint_z);
+            G4LogicalVolume *coreSection_log = new G4LogicalVolume(CoreBox,
+                                                                   scintCoreMaterial, "CoreSection",0,0,0);
+            
+            new G4PVPlacement(0, G4ThreeVector(), coreSection_log, "Core", epoxyLog, true, 0);
+
+}
+void DetectorConstruction::ConstructFiber()
+{
+    // dimensions
+    G4double dim_z;
+    G4double sphi, ephi;
+    G4double core_rZmin,core_rZmax;
+    G4double core_rYmin,core_rYmax;
+    G4double clad1_rZmin,clad1_rZmax;
+    G4double clad1_rYmin,clad1_rYmax;
+    G4double clad2_rZmin,clad2_rZmax;
+    G4double clad2_rYmin,clad2_rYmax;
+
+    dim_z = scint_z;
+    sphi = 0.00*deg;
+    ephi = 360.*deg;
+
+    core_rZmin = 0.00*cm;
+    core_rYmin = 0.00*cm;
+
+    core_rZmax = Parameters::GetInstance()->SemiAxisZ()*(88./100.)*mm;
+    core_rYmax = Parameters::GetInstance()->SemiAxisY()*(88./100.)*mm;
+
+    clad1_rZmin = core_rZmax;
+    clad1_rYmin = core_rYmax;
+
+    clad1_rZmax = core_rZmax + 3./88.*core_rZmax*2.;
+    clad1_rYmax = core_rYmax + 3./88.*core_rYmax*2.;
+
+    clad2_rZmin = clad1_rZmax;
+    clad2_rYmin = clad1_rYmax;
+
+    clad2_rZmax = Parameters::GetInstance()->SemiAxisZ()*mm;
+    clad2_rYmax = Parameters::GetInstance()->SemiAxisY()*mm;
+
+    G4ThreeVector origin;
+    /* ++ Fibre Placement ++ */
+    for(int j = 0; j < Nj; j++)
+    {
+        for(int k = 0; k < Nk; k++)
+        {
+            origin = objectPos(j,k);
+      
+            // Outer cladding
+            G4Tubs* clad2Section_tube = new G4Tubs("Cladding2Section",clad2_rZmin,clad2_rZmax,dim_z, sphi,ephi);
+            G4LogicalVolume *clad2Section_log = new G4LogicalVolume(clad2Section_tube,
+                                                                    outerCladdingMaterial, "Cladding2Section",0,0,0);
+
+            new G4PVPlacement(0, origin, clad2Section_log, "Cladding2"+C::c(j)+C::c(k), epoxyLog, true, 0);
+
+
+            // Inner cladding
+            G4Tubs* clad1Section_tube = new G4Tubs("Cladding1Section",clad1_rZmin,clad1_rZmax,dim_z, sphi,ephi);
+            G4LogicalVolume *clad1Section_log = new G4LogicalVolume(clad1Section_tube,
+                                                                    innerCladdingMaterial, "Cladding1Section",0,0,0);
+      
+            new G4PVPlacement(0, origin, clad1Section_log, "Cladding1"+C::c(j)+C::c(k), epoxyLog, true, 0);
+
+            // Scintillating core
+            G4Tubs* coreSection_tube = new G4Tubs("CoreSection",core_rZmin,core_rZmax,dim_z, sphi,ephi);
+            G4LogicalVolume *coreSection_log = new G4LogicalVolume(coreSection_tube,
+                                                                   scintCoreMaterial, "CoreSection",0,0,0);
+            
+            new G4PVPlacement(0, origin, coreSection_log, "Core"+C::c(j)+C::c(k), epoxyLog, true, 0);
+        }
+    }
+	/* ++ End of Fibre Placement ++ */
+}
+
+
+// for fibre placement
+G4ThreeVector DetectorConstruction::objectPos(G4int j, G4int k)
+{	
+    G4double xOffset = xDist*(((G4double)Nk)/2.)-Parameters::GetInstance()->SemiAxisZ()*mm/2.;
+    G4double yOffset = yDist*(((G4double)Nj)/2.)-Parameters::GetInstance()->SemiAxisZ()*mm;
+	
+    G4double xDispl;
+    G4double xsigma = (-0.49*j*j + 7.0*j-1.8)/1000.;
+    G4double xvar = G4RandGauss::shoot(0.,xsigma);
+    while(fabs(xvar)>=0.020*mm) {
+      xvar = G4RandGauss::shoot(0.,xsigma);
+    }
+	
+    j % 2 == 0 ? xDispl = 0. : xDispl = xDist/2.;
+	
+    G4ThreeVector origin(xDist*k+xDispl-xOffset+xvar, -yDist*j+yOffset, 0.);
+    
+    // print detector positions into file
+    std::ofstream outFile;
+    outFile.open("fibrePos.txt",std::ios::app);
+    outFile << origin.x() << "\t" << origin.y() << std::endl;
+    outFile.close();
+    
+    //G4cout << "Placing Fibre[" << k << ":" << j << "]: " << origin << G4endl;
+    
+    //G4cout << origin.x() << "\t" << origin.y() << G4endl;
+    
+    return origin;
+}
+
+// for detector placement
+G4ThreeVector DetectorConstruction::objectPos(G4int j, G4int k, G4double zPos)
+{	
+    G4double randomN = Parameters::GetInstance()->RandomNumber();
+    G4double offset = (stripWidth/2.)*randomN;
+	
+    // Save random number
+    std::ofstream myfile;
+    myfile.open("randomN.txt");
+    myfile << randomN;
+    myfile.close();
+	
+    G4double xOffset = xDist*(((G4double)Nk)/2.)-Parameters::GetInstance()->SemiAxisZ()*mm/2.;
+    G4double yOffset = yDist*(((G4double)Nj)/2.)-Parameters::GetInstance()->SemiAxisZ()*mm;
+	
+    G4double xDispl;
+	
+    j % 2 == 0 ? xDispl = 0. : xDispl = xDist/2.;
+	
+    G4ThreeVector origin(stripWidth*k+xDispl-xOffset-offset, -yDist*j+yOffset, zPos);
+
+    // print detector positions into file
+    std::ofstream detFile;
+    detFile.open("detPos.txt",std::ios::app);
+    detFile << k << " " << stripWidth*k+xDispl-xOffset-offset << std::endl;
+    detFile.close();
+    
+    return origin;
+}
+
+// for detector placement
+G4ThreeVector DetectorConstruction::objectPos(G4int j, G4int i, G4int j2, G4int k, G4double zPos)
+{	
+    G4double randomN = Parameters::GetInstance()->RandomNumber();
+    G4double offset = (stripWidth/2.)*randomN;
+	
+    // Save random number
+    //std::ofstream myfile;
+    //myfile.open("randomN.txt");
+    //myfile << randomN;
+    //myfile.close();
+	
+    G4double xOffset = xDist*(((G4double)Nk)/2.)-Parameters::GetInstance()->SemiAxisZ()*mm/2.;
+    G4double yOffset = yDist*(((G4double)Nj)/2.)-Parameters::GetInstance()->SemiAxisZ()*mm + 3/2*pixelDimY;
+	
+    G4double xDispl;
+	
+    j % 2 == 0 ? xDispl = 0. : xDispl = xDist/2.;
+
+    // print detector positions into file
+    //std::ofstream detFile;
+    //detFile.open("detPos.txt",std::ios::app);
+    //detFile << k << " " << stripWidth*k+xDispl-xOffset-offset << std::endl;
+    //detFile.close();
+
+    G4double pixelX = pixelDimX/2. + i*pixelDimX - stripWidth/2.;
+    G4double pixelY = pixelDimY/2. + j2*pixelDimY - stripHeight/2.;
+
+    G4ThreeVector origin(stripWidth*k+xDispl-xOffset-offset + pixelX, -yDist*j+yOffset + pixelY, zPos);
+
+    std::ofstream detFileY;
+    detFileY.open("detPosY.txt",std::ios::app);
+    detFileY << k << " " << -yDist*j+yOffset + pixelY << std::endl;
+    detFileY.close();
+	
+    return origin;
+}
+
+

SciFiSim/src/EventAction.cc

@@ -0,0 +1,40 @@
+// Written by Peter Stromberger
+// based on work of Mirco Deckenhoff
+// modified by Bastian Rössler
+
+
+#include "EventAction.hh"
+
+#include "G4Event.hh"
+#include "G4EventManager.hh"
+#include "G4TrajectoryContainer.hh"
+#include "G4Trajectory.hh"
+#include "G4VVisManager.hh"
+#include "G4ios.hh"
+
+#include "Analysis.hh"
+#include "G4RunManager.hh"
+ 
+EventAction::EventAction() : fEnergy(0.), fTrackL(0.)
+{}
+
+ 
+EventAction::~EventAction()
+{}
+
+ 
+void EventAction::BeginOfEventAction(const G4Event* anEvent)
+{
+    G4cout << "# Event " << anEvent->GetEventID() << " start." << G4endl;
+    Analysis::GetInstance()->PrepareNewEvent(anEvent);
+
+    fEnergy = 0.0;
+    fTrackL = 0.0;
+}
+
+ 
+void EventAction::EndOfEventAction(const G4Event* anEvent)
+{
+    G4double runID = (G4double) G4RunManager::GetRunManager()->GetCurrentRun()->GetRunID();
+    Analysis::GetInstance()->FillEnergyTrack(runID,	anEvent->GetEventID(), fEnergy, fTrackL);
+}

SciFiSim/src/Parameters.cc

@@ -0,0 +1,597 @@
+// Written by Peter Stromberger
+// based on work of Mirco Deckenhoff
+// modified by Bastian Rössler
+
+
+
+
+#include "Analysis.hh"
+#include "Parameters.hh"
+
+#include <fstream>
+#include <vector>
+
+
+
+Parameters* Parameters::singleton = 0;
+
+Parameters::Parameters()
+{
+
+    //// Read parameter values and set corresponding variables ////
+
+    G4cout << ">>> Constructor of Parameter class called <<<" << G4endl;
+
+    //char parameterFileName[40] = "parameterFiles/parameters.dat";
+    
+#if defined __APPLE__
+    char parameterFileName[200] = "/Users/basti/Programming/LHCb/SciFiSim-Xcode/SimulationData/parameterFiles/parameters.dat";
+    #pragma message("Compiling for MacOSX")
+#else
+    char parameterFileName[40] = "parameterFiles/parameters.dat";
+    #pragma message("Compiling for Linux")
+#endif
+    std::ifstream parameterFile;
+    parameterFile.open(parameterFileName);
+
+    if(parameterFile.good())
+    {
+        parameterFile >> randomSeed; // random seed for random engine
+        parameterFile >> randomNumber; // random number for detector strip positioning
+        randomNumber = randomNumber/32767.0; // max random number in bourne shell random number generator
+        parameterFile >> fibreLength; // length of fibre in meter
+        parameterFile >> semiAxisZ; // semi axis of fibre in z in millimeter
+        parameterFile >> semiAxisY; // semi axis of fibre in y in millimeter
+        parameterFile >> triggerX; // x-size of Trigger in mm
+        parameterFile >> triggerY; // y-size of Trigger in mm
+        parameterFile >> triggerZ; // z-size of Trigger in mm
+        parameterFile >> triggerXPos; // x-position of Trigger in millimeter
+        parameterFile >> triggerZPos; // z-position of Trigger in millimeter
+        parameterFile >> probabilityOfPhotonLossAtSurface; // probability that a photon is killed when reaching fibre surface
+      
+        if(probabilityOfPhotonLossAtSurface<0 || probabilityOfPhotonLossAtSurface>1)
+          probabilityOfPhotonLossAtSurface = 1;
+      
+        parameterFile >> placeMirror; // place a mirror at fibre end
+        parameterFile >> mirrorReflectivity; // reflectivity of mirror at fibre end
+        parameterFile >> detectorMaterial; // place a mirror at fibre end
+
+        parameterFile.ignore(256,'\n');
+        parameterFile.peek();
+        parameterFile.getline(emissionSpectrumFileName,256);
+        
+        G4cout << "Emission FIle: " << emissionSpectrumFileName << G4endl;
+        
+        std::ifstream emissionFile;
+        emissionFile.open(emissionSpectrumFileName);
+      
+        if(emissionFile.good())
+        {
+            std::vector<G4double> energyVector;
+            std::vector<G4double> intensityVector;
+            G4double readValue1;
+            G4double readValue2;
+            numberOfEnergies = 0;
+          
+            while(emissionFile >> readValue1)
+            {
+                if(emissionFile >> readValue2)
+                {
+                    energyVector.push_back(readValue1);
+                    intensityVector.push_back(readValue2);
+                    numberOfEnergies ++;
+                }
+            }
+      
+            Energy = new G4double[numberOfEnergies];
+            Intensity = new G4double[numberOfEnergies];
+          
+            for(int i=0; i<numberOfEnergies; i++)
+            {
+                Energy[i] = energyVector[i];
+                Intensity[i] = intensityVector[i];
+            }
+        }
+        else
+        {
+            G4cout << "Could not read emission spectrum file: " << emissionSpectrumFileName <<" !" << G4endl;
+        }
+      
+        emissionFile.close();
+        parameterFile >> numberOfInterpolatedPoints; // number of points to be interpolated within each emission spectrum interval
+
+        parameterFile.ignore(256,'\n');
+        parameterFile.peek();
+        parameterFile.getline(wlsAbsSpectrumFileName,256);
+        std::ifstream wlsAbsFile;
+        wlsAbsFile.open(wlsAbsSpectrumFileName);
+    
+        if(wlsAbsFile.good())
+        {
+            std::vector<G4double> wlsAbsEnergyVector;
+            std::vector<G4double> wlsAbsLengthVector;
+            G4double readValue1;
+            G4double readValue2;
+            numberOfWlsAbsEnergies = 0;
+          
+            while(wlsAbsFile >> readValue1)
+            {
+                if(wlsAbsFile >> readValue2)
+                {
+                    wlsAbsEnergyVector.push_back(readValue1);
+                    wlsAbsLengthVector.push_back(readValue2);
+                    numberOfWlsAbsEnergies ++;
+                }
+            }
+      
+            WlsAbsEnergy = new G4double[numberOfWlsAbsEnergies];
+            WlsAbsLength = new G4double[numberOfWlsAbsEnergies];
+          
+            for(int i=0; i<numberOfWlsAbsEnergies; i++)
+            {
+                WlsAbsEnergy[i] = wlsAbsEnergyVector[i];
+                WlsAbsLength[i] = wlsAbsLengthVector[i];
+            }
+        }
+        else
+        {
+            G4cout << "Could not read wls absorption spectrum file: " << wlsAbsSpectrumFileName <<" !" << G4endl;
+        }
+      
+        wlsAbsFile.close();
+
+        parameterFile.getline(wlsEmissionSpectrumFileName,256);
+        std::ifstream wlsEmissionFile;
+        wlsEmissionFile.open(wlsEmissionSpectrumFileName);
+    
+        if(wlsEmissionFile.good())
+        {
+            std::vector<G4double> wlsEmissionEnergyVector;
+            std::vector<G4double> wlsEmissionIntensityVector;
+            G4double readValue1;
+            G4double readValue2;
+            numberOfWlsEmissionEnergies = 0;
+            
+            while(wlsEmissionFile >> readValue1)
+            {
+                if(wlsEmissionFile >> readValue2)
+                {
+                    wlsEmissionEnergyVector.push_back(readValue1);
+                    wlsEmissionIntensityVector.push_back(readValue2);
+                    numberOfWlsEmissionEnergies ++;
+                }
+            }
+      
+            WlsEmissionEnergy = new G4double[numberOfWlsEmissionEnergies];
+            WlsEmissionIntensity = new G4double[numberOfWlsEmissionEnergies];
+      
+            for(int i=0; i<numberOfWlsEmissionEnergies; i++)
+            {
+                WlsEmissionEnergy[i] = wlsEmissionEnergyVector[i];
+                WlsEmissionIntensity[i] = wlsEmissionIntensityVector[i];
+            }
+        }
+        else
+        {
+            G4cout << "Could not read wls emission spectrum file: " << wlsEmissionSpectrumFileName <<" !" << G4endl;
+        }
+        
+        wlsEmissionFile.close();
+
+        parameterFile >> scintillationYield; //scintillation yield in photons per keV
+        parameterFile >> resolutionScale; // width of gaussian to generate photon number
+        parameterFile >> decayTimeFast; // fast decay time of excited states in ns
+        parameterFile >> decayTimeSlow; // slow decay time of excited states in ns
+        parameterFile >> yieldRatio; // ratio of fast component and total scintillation yield
+        parameterFile >> birksConstant; // Birk's constant in mm/MeV
+
+        parameterFile >> wlsDecayTime; // decay time of wls excited states in ns
+
+        parameterFile.ignore(256,'\n');
+        parameterFile.peek();
+        parameterFile.getline(refractiveIndexVacuum,256);
+        parameterFile.getline(refractiveIndexCore,256);
+        parameterFile.getline(refractiveIndexClad1,256);
+        parameterFile.getline(refractiveIndexClad2,256);
+
+        parameterFile.getline(absorptionCore,512);
+        parameterFile.getline(absorptionClad1,512);
+        parameterFile.getline(absorptionClad2,512);
+
+        parameterFile.getline(absorptionFromIrradiationCore,512);
+        parameterFile.getline(absorptionFromIrradiationClad1,512);
+        parameterFile.getline(absorptionFromIrradiationClad2,512);
+
+        parameterFile.getline(sectionsFileName,80);
+        std::ifstream sectionsFile;
+        sectionsFile.open(sectionsFileName);
+    
+        if(sectionsFile.good())
+            sectionsFile >> numberOfSections;
+        else
+            G4cout << "Could not read sections file: " << sectionsFileName <<" !" << G4endl;
+    
+        sectionsFile.close();
+
+        parameterFile.getline(rayleighCore,512);
+        parameterFile.getline(rayleighClad1,512);
+        parameterFile.getline(rayleighClad2,512);
+    }
+    else
+    {
+        G4cout << "Could not read parameter file: " << parameterFileName <<" !" << G4endl;
+    }
+
+    parameterFile.close();
+
+
+
+  //// Open file to store parameters ////
+
+    sprintf(parameterOutputFileName,"%s.parameters",Analysis::GetInstance()->FileName());
+
+    std::ofstream parameterOutputFile;
+    parameterOutputFile.open(parameterOutputFileName);
+
+    parameterOutputFile << "Length of fibre: ";
+    parameterOutputFile << fibreLength << " m \n";
+    parameterOutputFile << "Semi axis of fibre in z: ";
+    parameterOutputFile << semiAxisZ << " mm \n";
+    parameterOutputFile << "Semi axis of fibre in y: ";
+    parameterOutputFile << semiAxisY << " mm \n";
+    parameterOutputFile << "Probability to lose photons at fibre surface: ";
+    parameterOutputFile << probabilityOfPhotonLossAtSurface << "\n";
+    parameterOutputFile << "Mirror placement at fibre end: ";
+    parameterOutputFile << placeMirror << "\n";
+    parameterOutputFile << "Reflectivity of mirror at fibre end: ";
+    parameterOutputFile << mirrorReflectivity << "\n";
+    parameterOutputFile << "Detector material vacuum/polystyrene (0/1): ";
+    parameterOutputFile << detectorMaterial << "\n";
+    parameterOutputFile << "Used emission spectrum: \"";
+    parameterOutputFile << emissionSpectrumFileName << "\"\n";
+    parameterOutputFile << "Number of energies: ";
+    parameterOutputFile << numberOfEnergies << "\n";
+    parameterOutputFile << "Energy / eV \t Intensity\n";
+  
+    for(int i=0; i<numberOfEnergies; i++)
+        parameterOutputFile << Energy[i] << "\t" << Intensity[i] <<"\n";
+  
+    parameterOutputFile << "Number of interpolated points per emission spectrum interval: ";
+    parameterOutputFile << numberOfInterpolatedPoints << "\n";
+    parameterOutputFile << "Used wls absorption spectrum: \"";
+    parameterOutputFile << wlsAbsSpectrumFileName << "\"\n";
+    parameterOutputFile << "Number of wls absorption energies: ";
+    parameterOutputFile << numberOfWlsAbsEnergies << "\n";
+    parameterOutputFile << "Energy / eV \t WLS Absorption Length / m\n";
+  
+    for(int i=0; i<numberOfWlsAbsEnergies; i++)
+        parameterOutputFile << WlsAbsEnergy[i] << "\t" << WlsAbsLength[i] <<"\n";
+  
+    parameterOutputFile << "Used wls emission spectrum: \"";
+    parameterOutputFile << wlsEmissionSpectrumFileName << "\"\n";
+    parameterOutputFile << "Number of wls emission energies: ";
+    parameterOutputFile << numberOfWlsEmissionEnergies << "\n";
+    parameterOutputFile << "Energy / eV \t WLS emission intensity\n";
+    
+    for(int i=0; i<numberOfWlsEmissionEnergies; i++)
+        parameterOutputFile << WlsEmissionEnergy[i] << "\t" << WlsEmissionIntensity[i] <<"\n";
+  
+    parameterOutputFile << "Formulae to calculate refractive indices in\n";
+    parameterOutputFile << " - vacuum: \"" << refractiveIndexVacuum << "\"\n";
+    parameterOutputFile << " - core: \"" << refractiveIndexCore << "\"\n";
+    parameterOutputFile << " - inner cladding: \"" << refractiveIndexClad1 << "\"\n";
+    parameterOutputFile << " - outer cladding: \"" << refractiveIndexClad2 << "\"\n";
+    parameterOutputFile << " with x in nm.\n";
+    parameterOutputFile << "Scintillation yield: " << scintillationYield << "/keV\n";
+    parameterOutputFile << "Resolution scale: " << resolutionScale << "\n";
+    parameterOutputFile << "Fast decay time: " << decayTimeFast << " ns\n";
+    parameterOutputFile << "Slow decay time: " << decayTimeSlow << " ns\n";
+    parameterOutputFile << "Yield ratio: " << yieldRatio << "\n";
+    parameterOutputFile << "Birks constant: " << birksConstant << " mm/MeV\n";
+    parameterOutputFile << "WLS decay time: " << wlsDecayTime << " ns\n";
+    parameterOutputFile << "Formulae to calculate absorption [1/m] in\n";
+    parameterOutputFile << " - core: \"" << absorptionCore << "\"\n";
+    parameterOutputFile << " - inner cladding: \"" << absorptionClad1 << "\"\n";
+    parameterOutputFile << " - outer cladding: \"" << absorptionClad2 << "\"\n";
+    parameterOutputFile << " with x in nm.\n";
+    parameterOutputFile << "Formulae to calculate absorption due to irradiation [1/m] in\n";
+    parameterOutputFile << " - core: \"" << absorptionFromIrradiationCore << "\"\n";
+    parameterOutputFile << " - inner cladding: \"" << absorptionFromIrradiationClad1 << "\"\n";
+    parameterOutputFile << " - outer cladding: \"" << absorptionFromIrradiationClad2 << "\"\n";
+    parameterOutputFile << " with x in nm and y in kGy.\n";
+    parameterOutputFile << "Used sections file: \"";
+    parameterOutputFile << sectionsFileName << "\"\n";
+    parameterOutputFile << "Number of sections: ";
+    parameterOutputFile << numberOfSections << "\n";
+    parameterOutputFile << "Formulae to calculate Rayleigh scattering [1/m] in\n";
+    parameterOutputFile << " - core: " << rayleighCore << "\n";
+    parameterOutputFile << " - inner cladding: " << rayleighClad1 << "\n";
+    parameterOutputFile << " - outer cladding: " << rayleighClad2 << "\n";
+
+    parameterOutputFile.close();
+
+    G4cout << "Simulation parameters written to \"" << parameterOutputFileName << "\"" << G4endl;
+}
+
+
+
+
+Parameters::~Parameters() {
+    if(numberOfEnergies != 0)
+    {
+        delete[] Energy;
+        delete[] Intensity;
+    }
+    if(numberOfWlsAbsEnergies != 0)
+    {
+        delete[] WlsAbsEnergy;
+        delete[] WlsAbsLength;
+    }
+    if(numberOfWlsEmissionEnergies != 0)
+    {
+        delete[] WlsEmissionEnergy;
+        delete[] WlsEmissionIntensity;
+    }
+}
+
+
+
+
+
+char* Parameters::ParameterOutputFileName()
+{
+    return parameterOutputFileName;
+}
+
+G4double Parameters::RandomSeed()
+{
+    return randomSeed;
+}
+
+G4double Parameters::RandomNumber()
+{
+    return randomNumber;
+}
+
+G4double Parameters::FibreLength()
+{
+    return fibreLength;
+}
+
+
+G4double Parameters::SemiAxisZ()
+{
+    return semiAxisZ;
+}
+
+
+G4double Parameters::SemiAxisY()
+{
+    return semiAxisY;
+}
+
+
+G4double Parameters::TriggerX()
+{
+    return triggerX;
+}
+
+G4double Parameters::TriggerY()
+{
+	return triggerY;
+}
+
+G4double Parameters::TriggerZ()
+{
+	return triggerZ;
+}
+
+G4double Parameters::TriggerXPos()
+{
+	return triggerXPos;
+}
+
+G4double Parameters::TriggerZPos()
+{
+	return triggerZPos;
+}
+
+G4double Parameters::ProbabilityOfPhotonLossAtSurface()
+{
+    return probabilityOfPhotonLossAtSurface;
+}
+
+
+G4bool Parameters::PlaceMirror()
+{
+    return placeMirror;
+}
+
+
+G4double Parameters::MirrorReflectivity()
+{
+    return mirrorReflectivity;
+}
+
+
+G4bool Parameters::DetectorMaterial()
+{
+    return detectorMaterial;
+}
+
+
+char* Parameters::EmissionSpectrumFileName()
+{
+    return emissionSpectrumFileName;
+}
+
+
+G4int Parameters::NumberOfEnergies()
+{
+    return numberOfEnergies;
+}
+
+
+G4int Parameters::NumberOfInterpolatedPoints()
+{
+    return numberOfInterpolatedPoints;
+}
+
+
+char* Parameters::WlsAbsSpectrumFileName()
+{
+    return wlsAbsSpectrumFileName;
+}
+
+
+G4int Parameters::NumberOfWlsAbsEnergies()
+{
+    return numberOfWlsAbsEnergies;
+}
+
+
+char* Parameters::WlsEmissionSpectrumFileName()
+{
+    return wlsEmissionSpectrumFileName;
+}
+
+
+G4int Parameters::NumberOfWlsEmissionEnergies()
+{
+    return numberOfWlsEmissionEnergies;
+}
+
+
+G4double Parameters::ScintillationYield()
+{
+    return scintillationYield;
+}
+
+
+G4double Parameters::ResolutionScale()
+{
+    return resolutionScale;
+}
+ 
+
+G4double Parameters::DecayTimeFast()
+{
+  return decayTimeFast;
+}
+ 
+
+G4double Parameters::DecayTimeSlow()
+{
+    return decayTimeSlow;
+}
+ 
+
+G4double Parameters::YieldRatio()
+{
+    return yieldRatio;
+}
+ 
+
+G4double Parameters::BirksConstant()
+{
+    return birksConstant;
+}
+
+
+G4double Parameters::WlsDecayTime()
+{
+    return wlsDecayTime;
+}
+ 
+
+char* Parameters::RefractiveIndexVacuum()
+{
+  return refractiveIndexVacuum;
+}
+
+
+char* Parameters::RefractiveIndexCore()
+{
+    return refractiveIndexCore;
+}
+
+
+char* Parameters::RefractiveIndexClad1()
+{
+    return refractiveIndexClad1;
+}
+
+
+char* Parameters::RefractiveIndexClad2()
+{
+    return refractiveIndexClad2;
+}
+
+
+char* Parameters::AbsorptionCore()
+{
+    return absorptionCore;
+}
+
+
+char* Parameters::AbsorptionClad1()
+{
+    return absorptionClad1;
+}
+
+
+char* Parameters::AbsorptionClad2()
+{
+    return absorptionClad2;
+}
+
+ 
+char* Parameters::AbsorptionFromIrradiationCore()
+{
+    return absorptionFromIrradiationCore;
+}
+
+
+char* Parameters::AbsorptionFromIrradiationClad1()
+{
+    return absorptionFromIrradiationClad1;
+}
+
+
+char* Parameters::AbsorptionFromIrradiationClad2()
+{
+    return absorptionFromIrradiationClad1;
+}
+
+
+char* Parameters::SectionsFileName()
+{
+    return sectionsFileName;
+}
+
+
+G4int Parameters::NumberOfSections()
+{
+    return numberOfSections;
+}
+
+
+char* Parameters::RayleighCore()
+{
+    return rayleighCore;
+}
+
+
+char* Parameters::RayleighClad1()
+{
+    return rayleighClad1;
+}
+
+
+char* Parameters::RayleighClad2()
+{
+    return rayleighClad2;
+}
+
+
+const G4double  Parameters::hcPERe = 1.239842e-6;  // unit: V*m

SciFiSim/src/PhysicsList.cc

@@ -0,0 +1,68 @@
+// Written by Mirco DECKENHOFF based on
+//
+// $Id: PhysicsList.cc,v 1.17 2009/11/10 05:16:23 gum Exp $
+//
+//
+// modified by Peter Stromberger
+// modified by Bastian Rössler
+
+#include "PhysicsList.hh"
+
+#include "G4EmStandardPhysics.hh"
+#include "G4DecayPhysics.hh"
+#include "G4OpticalPhysics.hh"
+#include "G4ProcessManager.hh"
+#include "G4ParticleTypes.hh"
+#include "G4hIonisation.hh"
+
+#include "Parameters.hh"
+
+#include "G4SystemOfUnits.hh"
+
+PhysicsList::PhysicsList() :  G4VModularPhysicsList()
+{
+    // default cut value  (1.0mm)
+    defaultCutValue = 1.0*mm;
+
+    // * EM Physics
+    RegisterPhysics( new G4EmStandardPhysics() );
+
+    
+    // * Optical Physics
+    G4OpticalPhysics* opticalPhysics = new G4OpticalPhysics();
+    RegisterPhysics( opticalPhysics );
+
+    // adjust some parameters for the optical physics
+    opticalPhysics->SetWLSTimeProfile("exponential");
+
+    opticalPhysics->SetScintillationYieldFactor(1.0);
+    opticalPhysics->SetScintillationExcitationRatio(Parameters::GetInstance()->YieldRatio());
+
+    opticalPhysics->SetMaxNumPhotonsPerStep(100);
+    opticalPhysics->SetMaxBetaChangePerStep(10.0);
+    
+    // opticalPhysics->SetTrackSecondariesFirst(true);
+       
+}
+
+
+
+void PhysicsList::ConstructParticle()
+{
+    // Constructs all paricles
+    G4VModularPhysicsList::ConstructParticle();
+}
+
+
+
+void PhysicsList::SetCuts()
+{
+    //  " G4VUserPhysicsList::SetCutsWithDefault" method sets
+    //   the default cut value for all particle types
+    //
+    SetCutsWithDefault();
+  
+    if (verboseLevel>0)
+        DumpCutValuesTable();
+}
+

SciFiSim/src/PhysicsList.cc~

@@ -0,0 +1,68 @@
+// Written by Mirco DECKENHOFF based on
+//
+// $Id: PhysicsList.cc,v 1.17 2009/11/10 05:16:23 gum Exp $
+//
+//
+// modified by Peter Stromberger
+// modified by Bastian Rössler
+
+#include "PhysicsList.hh"
+
+#include "G4EmStandardPhysics.hh"
+#include "G4DecayPhysics.hh"
+#include "G4OpticalPhysics.hh"
+#include "G4ProcessManager.hh"
+#include "G4ParticleTypes.hh"
+#include "G4hIonisation.hh"
+
+#include "Parameters.hh"
+
+#include "G4SystemOfUnits.hh"
+
+PhysicsList::PhysicsList() :  G4VModularPhysicsList()
+{
+    // default cut value  (1.0mm)
+    defaultCutValue = 1.0*mm;
+
+    // * EM Physics
+    RegisterPhysics( new G4EmStandardPhysics() );
+
+    /*
+    // * Optical Physics
+    G4OpticalPhysics* opticalPhysics = new G4OpticalPhysics();
+    RegisterPhysics( opticalPhysics );
+
+    // adjust some parameters for the optical physics
+    opticalPhysics->SetWLSTimeProfile("exponential");
+
+    opticalPhysics->SetScintillationYieldFactor(1.0);
+    opticalPhysics->SetScintillationExcitationRatio(Parameters::GetInstance()->YieldRatio());
+
+    opticalPhysics->SetMaxNumPhotonsPerStep(100);
+    opticalPhysics->SetMaxBetaChangePerStep(10.0);
+    */
+    // opticalPhysics->SetTrackSecondariesFirst(true);
+       
+}
+
+
+
+void PhysicsList::ConstructParticle()
+{
+    // Constructs all paricles
+    G4VModularPhysicsList::ConstructParticle();
+}
+
+
+
+void PhysicsList::SetCuts()
+{
+    //  " G4VUserPhysicsList::SetCutsWithDefault" method sets
+    //   the default cut value for all particle types
+    //
+    SetCutsWithDefault();
+  
+    if (verboseLevel>0)
+        DumpCutValuesTable();
+}
+

SciFiSim/src/PrimaryGeneratorAction.cc

@@ -0,0 +1,88 @@
+// Written by Peter Stromberger
+// based on work of Mirco Deckenhoff
+// modified by Bastian Rössler
+
+#include "PrimaryGeneratorAction.hh"
+#include "G4Event.hh"
+#include "G4ParticleGun.hh"
+#include "G4GeneralParticleSource.hh"
+#include "G4ParticleTable.hh"
+#include "G4ParticleDefinition.hh"
+#include "Randomize.hh"
+#include "Analysis.hh"
+#include "G4SystemOfUnits.hh"
+
+#include "G4RunManager.hh"
+
+PrimaryGeneratorAction::PrimaryGeneratorAction()
+{
+  gun = InitializeGPS();
+}
+
+void PrimaryGeneratorAction::GeneratePrimaries(G4Event* anEvent)
+{ 
+    gun->GeneratePrimaryVertex(anEvent);
+    
+    G4double runID = (G4double) G4RunManager::GetRunManager()->GetCurrentRun()->GetRunID();
+    G4double eventID = (G4double) anEvent->GetEventID();
+    G4double energy = (G4double) gun->GetParticleEnergy();
+    G4double xMom = (G4double) gun->GetParticleMomentumDirection()[0];
+    G4double yMom = (G4double) gun->GetParticleMomentumDirection()[1];
+    G4double zMom = (G4double) gun->GetParticleMomentumDirection()[2];
+    
+    Analysis::GetInstance()->FillInitialParticle(runID, eventID, energy, xMom, yMom, zMom);
+
+    // Necessery?
+    Analysis::GetInstance()->SetGpsPosition(gun->GetParticlePosition());
+    Analysis::GetInstance()->SetGpsDirection(gun->GetParticleMomentumDirection());
+}
+
+PrimaryGeneratorAction::~PrimaryGeneratorAction()
+{
+    delete gun;
+}
+
+G4GeneralParticleSource* PrimaryGeneratorAction::GetGun()
+{
+    return gun;
+}
+
+G4GeneralParticleSource* PrimaryGeneratorAction::InitializeGPS()
+{
+    G4GeneralParticleSource * gps = new G4GeneralParticleSource();
+    return gps;
+}
+
+
+void PrimaryGeneratorAction::SetOptPhotonPolar()
+{
+    G4double angle = G4UniformRand() * 360.0*deg;
+    SetOptPhotonPolar(angle);
+}
+
+
+void PrimaryGeneratorAction::SetOptPhotonPolar(G4double angle)
+{
+    if (gun->GetParticleDefinition()->GetParticleName() != "opticalphoton")
+    {
+        G4cout << "--> warning from PrimaryGeneratorAction::SetOptPhotonPolar() :"
+        "the particleGun is not an opticalphoton" << G4endl;
+        return;
+    }
+     	       
+    G4ThreeVector normal (1., 0., 0.);
+    G4ThreeVector kphoton = gun->GetParticleMomentumDirection();
+    G4ThreeVector product = normal.cross(kphoton);
+    G4double modul2 = product*product;
+ 
+    G4ThreeVector e_perpend (0., 0., 1.);
+    
+    if (modul2 > 0.)
+        e_perpend = (1./std::sqrt(modul2))*product;
+    
+    G4ThreeVector e_paralle = e_perpend.cross(kphoton);
+ 
+    G4ThreeVector polar = std::cos(angle)*e_paralle + std::sin(angle)*e_perpend;
+    gun->SetParticlePolarization(polar);
+}
+

SciFiSim/src/RunAction.cc

@@ -0,0 +1,43 @@
+// Written by Mirco DECKENHOFF
+// based on
+// $Id: RunAction.cc,v 1.10 2006/06/29 17:54:31 gunter Exp $
+// GEANT4 tag $Name: geant4-09-01-ref-02 $
+//
+// modified by Bastian Rössler
+
+#include "G4Timer.hh"
+
+#include "RunAction.hh"
+
+#include "G4Run.hh"
+
+#include "Analysis.hh"
+
+
+RunAction::RunAction()
+{
+    timer = new G4Timer;
+}
+
+
+RunAction::~RunAction()
+{
+    delete timer;
+}
+
+
+void RunAction::BeginOfRunAction(const G4Run* aRun)
+{
+    G4cout << "### Run " << aRun->GetRunID() << " start." << G4endl;
+    timer->Start();
+    Analysis::GetInstance()->PrepareNewRun(aRun);
+    G4cout << "Analysis Instance Address: " << Analysis::GetInstance() << G4endl;
+}
+
+
+void RunAction::EndOfRunAction(const G4Run* aRun)
+{   
+    timer->Stop();
+    G4cout << "number of event = " << aRun->GetNumberOfEvent() << " \t" << *timer << G4endl;
+    Analysis::GetInstance()->EndOfRun(/*aRun*/);
+}

SciFiSim/src/SensitiveDetector.cc

@@ -0,0 +1,90 @@
+// Written by Peter Stromberger
+// based on work of Mirco Deckenhoff
+// modified by Bastian Rössler
+
+
+#include "SensitiveDetector.hh"
+#include "G4TouchableHistory.hh"
+#include "G4Step.hh"
+#include "G4HCofThisEvent.hh"
+#include "G4HCtable.hh"
+#include "G4UnitsTable.hh"
+#include "G4VProcess.hh"
+#include "G4ParticleTypes.hh"
+#include "Analysis.hh"
+#include "G4UIcommand.hh"
+#include "G4EventManager.hh"
+#include "G4RunManager.hh"
+
+
+
+SensitiveDetector::SensitiveDetector(G4String SDname): G4VSensitiveDetector(SDname){}
+
+SensitiveDetector::~SensitiveDetector(){}
+
+G4bool SensitiveDetector::ProcessHits(G4Step * step, G4TouchableHistory *)
+{
+    G4TouchableHandle touchable = step->GetPreStepPoint()->GetTouchableHandle();
+
+    /* ++ particle is at geometry boundary and an optical photon (for SiPM) ++ */
+    if(step->GetPreStepPoint()->GetStepStatus() == fGeomBoundary
+       && step->GetTrack()->GetDefinition() == G4OpticalPhoton::OpticalPhotonDefinition())
+    {
+        if(step->GetStepLength() != 0) // Avoid division by zero and counting reflected photons
+        {
+            G4int creatorProcessId = 0;
+
+            if(step->GetTrack()->GetCreatorProcess()->GetProcessName() == "Scintillation")
+                creatorProcessId = 1;
+
+            if (step->GetTrack()->GetCreatorProcess()->GetProcessName() == "Cerenkov")
+                creatorProcessId = 2;
+
+            if (step->GetTrack()->GetCreatorProcess()->GetProcessName() == "OpWLS")
+                creatorProcessId = 3;
+	
+            G4double myRunID = (G4double) G4RunManager::GetRunManager()->GetCurrentRun()->GetRunID();
+
+            G4double myEventID = (G4double) G4EventManager::GetEventManager()->GetConstCurrentEvent()->GetEventID();
+      				
+            G4double myDetectorID = G4UIcommand::ConvertToDouble((G4String)
+                                                                 (step->GetPreStepPoint()->GetPhysicalVolume()->GetName()).substr(17,3));
+			
+            G4double xPixel = G4UIcommand::ConvertToDouble((G4String)
+                                                           (step->GetPreStepPoint()->GetPhysicalVolume()->GetName()).substr(20,2));
+
+            G4double yPixel = G4UIcommand::ConvertToDouble((G4String)
+                                                           (step->GetPreStepPoint()->GetPhysicalVolume()->GetName()).substr(22,2));
+				
+            Analysis::GetInstance()->FillDetectedPhotons(myRunID,
+                                                         myEventID,
+                                                         myDetectorID,
+                                                         xPixel,
+                                                         yPixel,
+                                                         step->GetTrack()->GetTotalEnergy()*1e6,
+                                                         step->GetTrack()->GetLocalTime()-step->GetDeltaTime(),
+                                                         step->GetTrack()->GetTrackLength()-step->GetStepLength(),
+                                                         step->GetTrack()->GetGlobalTime()-step->GetDeltaTime(),
+                                                         step->GetTrack()->GetPosition()[0]-step->GetDeltaPosition()[0],
+                                                         step->GetTrack()->GetPosition()[1]-step->GetDeltaPosition()[1],
+                                                         step->GetTrack()->GetPosition()[2]-step->GetDeltaPosition()[2],
+                                                         step->GetDeltaPosition()[0]/step->GetStepLength(),
+                                                         step->GetDeltaPosition()[1]/step->GetStepLength(),
+                                                         step->GetDeltaPosition()[2]/step->GetStepLength(),
+                                                         step->GetTrack()->GetVertexPosition()[0],
+                                                         step->GetTrack()->GetVertexPosition()[1],
+                                                         step->GetTrack()->GetVertexPosition()[2],
+                                                         step->GetTrack()->GetVertexMomentumDirection()[0],
+                                                         step->GetTrack()->GetVertexMomentumDirection()[1],
+                                                         step->GetTrack()->GetVertexMomentumDirection()[2],
+                                                         step->GetTrack()->GetTrackID(),
+                                                         creatorProcessId,
+                                                         step->GetTrack()->GetParentID());
+        }
+		
+        // Also kill reflected photons to avoid many reflections without detection
+        step->GetTrack()->SetTrackStatus(fKillTrackAndSecondaries);
+    }
+  
+    return true;
+}

SciFiSim/src/StackingAction.cc

@@ -0,0 +1,91 @@
+// Written by Peter Stromberger
+// based on work of Mirco Deckenhoff
+// modified by Bastian Rössler
+
+
+#include "StackingAction.hh"
+
+#include "G4ParticleDefinition.hh"
+#include "G4ParticleTypes.hh"
+#include "G4Track.hh"
+#include "G4ios.hh"
+
+#include "G4VProcess.hh"
+
+#include "Analysis.hh"
+
+
+#include "G4EventManager.hh"
+#include "G4RunManager.hh"
+
+StackingAction::StackingAction(): gammaCounter(0){}
+
+
+StackingAction::~StackingAction(){}
+
+
+G4ClassificationOfNewTrack StackingAction::ClassifyNewTrack(const G4Track * aTrack)
+{
+    /* ++ StackingAction for optical photons ++ */
+    if(aTrack->GetDefinition() == G4OpticalPhoton::OpticalPhotonDefinition())
+    {
+        Analysis::GetInstance()->IncreaseReflectionRefractionAndScatteringVectors(aTrack->GetTrackID());
+        Analysis::GetInstance()->IncreaseLengthVectors(aTrack->GetTrackID());
+
+        if(aTrack->GetParentID()>0) // particle is secondary
+        {
+            gammaCounter++;
+            G4int creatorProcessId = 0;
+
+            if(aTrack->GetCreatorProcess()->GetProcessName() == "Scintillation")
+                creatorProcessId = 1;
+
+            if(aTrack->GetCreatorProcess()->GetProcessName() == "Cerenkov")
+                creatorProcessId = 2;
+
+            if(aTrack->GetCreatorProcess()->GetProcessName() == "OpWLS")
+                creatorProcessId = 3;
+
+            if (aTrack->GetCreatorProcess())
+                AddProcess(aTrack->GetCreatorProcess());// classify here
+        }
+    }
+    /* ++ End of StackingAction of optical photons ++ */
+
+    return fUrgent;
+}
+
+
+void StackingAction::NewStage()
+{
+    G4cout << "Number of optical photons produced in this event : " << gammaCounter << G4endl << G4endl;
+
+    for(ProcMap::iterator it=procs.begin() ; it!=procs.end() ; ++it)
+        G4cout << " Process " << it->first->GetProcessName() << " generated " << it->second << " photons" << G4endl;
+
+    G4cout<<G4endl;
+}
+
+
+void StackingAction::PrepareNewEvent()
+{ 
+    gammaCounter = 0;
+    Reset();
+}
+
+
+void StackingAction::AddProcess(const G4VProcess * p)
+{ 
+    ProcMap::iterator it = procs.find(p);
+
+    if (it!=procs.end())
+        it->second++;
+    else
+        procs[p]=1;
+}
+
+void StackingAction::Reset()
+{ 
+    for (ProcMap::iterator it = procs.begin() ; it!=procs.end() ; ++it)
+        it->second=0;
+}

SciFiSim/src/SteppingAction.cc

@@ -0,0 +1,211 @@
+// Written by Peter Stromberger
+// based on work of Mirco Deckenhoff
+// modified by Bastian Rössler
+
+
+#include "SteppingAction.hh"
+#include "G4Step.hh"
+#include "G4VTouchable.hh"
+#include "G4SteppingManager.hh"
+#include "G4UnitsTable.hh"
+#include "G4ParticleTypes.hh"
+#include "G4ProcessManager.hh"
+#include "G4VProcess.hh"
+#include "G4ProcessVector.hh"
+#include "EventAction.hh"
+#include <string>
+#include "Parameters.hh"
+#include "Analysis.hh"
+#include "G4RunManager.hh"
+#include "Randomize.hh"
+#include "G4SystemOfUnits.hh"
+
+
+SteppingAction::SteppingAction(EventAction* eventAction, PrimaryGeneratorAction* p)
+{
+    creatorProcess = -1;
+    fEventAction = eventAction;
+    pGA = p;
+}
+
+SteppingAction::~SteppingAction(){}
+
+void SteppingAction::UserSteppingAction( const G4Step * step )
+{
+
+    primDefinition = (pGA->GetGun())->GetParticleDefinition();
+    primParticle = (primDefinition->GetParticleName()).c_str();
+
+    /* ++ SteppingAction for optical photons ++ */
+    if(step->GetTrack()->GetDefinition() == G4OpticalPhoton::OpticalPhotonDefinition())
+    {
+        G4int trackId = step->GetTrack()->GetTrackID();
+        G4double stepLength = step->GetStepLength();
+    
+        G4String prePhysicalVolumeName = step->GetPreStepPoint()->GetPhysicalVolume()->GetName();
+        G4String postPhysicalVolumeName = "";
+
+        // PostStep does only exist if the particle is not exiting the EpoxyBox volume!
+        if(step->GetTrack()->GetTrackStatus() != fStopAndKill)
+            postPhysicalVolumeName = step->GetPostStepPoint()->GetPhysicalVolume()->GetName();
+
+    
+        // Kill photons at fibre surface
+        // Count the reflections and refractions
+    
+        if(step->GetPostStepPoint()->GetStepStatus()==fGeomBoundary)
+        {
+            if(postPhysicalVolumeName == "EpoxyBox" && prePhysicalVolumeName.substr(0,9) == "Cladding2")
+            {
+                if(Parameters::GetInstance()->ProbabilityOfPhotonLossAtSurface() == 1)
+                    step->GetTrack()->SetTrackStatus(fStopAndKill);
+
+                if(Parameters::GetInstance()->ProbabilityOfPhotonLossAtSurface() < 1
+                   && Parameters::GetInstance()->ProbabilityOfPhotonLossAtSurface() > 0)
+                {
+                    G4double randomNumber = CLHEP::RandFlat::shoot();
+
+                    if(Parameters::GetInstance()->ProbabilityOfPhotonLossAtSurface() < randomNumber)
+                    {
+                        if (step->GetStepLength() > 0)
+                            Analysis::GetInstance()->IncreaseReflectionsAtFibreSurface(trackId);
+                    }
+                    else
+                        step->GetTrack()->SetTrackStatus(fStopAndKill);
+                }
+
+                if (step->GetStepLength() > 0)
+                    Analysis::GetInstance()->IncreaseReflectionsAtFibreSurface(trackId);
+            }
+            if(postPhysicalVolumeName == "Mirror")
+                Analysis::GetInstance()->IncreaseReflectionsAtMirror(trackId);
+      
+       
+            // Retrieve status of the photon boundary process
+      
+      
+            G4OpBoundaryProcessStatus theBoundaryStatus = Undefined;
+      
+            G4ProcessManager* OpManager = G4OpticalPhoton::OpticalPhoton()->GetProcessManager();
+      
+            if(OpManager)
+            {
+                G4int MAXofPostStepLoops = OpManager->GetPostStepProcessVector()->entries();
+                G4ProcessVector* fPostStepDoItVector = OpManager->GetPostStepProcessVector(typeDoIt);
+	
+                for(G4int i = 0; i<MAXofPostStepLoops; i++)
+                {
+                    G4VProcess* fCurrentProcess = (*fPostStepDoItVector)[i];
+                    opBoundaryProcess = dynamic_cast<G4OpBoundaryProcess*>(fCurrentProcess);
+	  			
+                    if(opBoundaryProcess)
+                    {
+                        theBoundaryStatus = opBoundaryProcess->GetStatus();
+                        break;
+                    }
+                }
+            }
+      
+            if(theBoundaryStatus != Undefined)
+            {
+                if((prePhysicalVolumeName.substr(0,9) == "Cladding1" && postPhysicalVolumeName.substr(0,9) == "Cladding2")
+                   || (prePhysicalVolumeName.substr(0,9) == "Cladding2" && postPhysicalVolumeName.substr(0,9) == "Cladding1"))
+                {
+                    if(theBoundaryStatus == TotalInternalReflection)
+                        Analysis::GetInstance()->IncreaseTotalReflectionsAtCladCladInterface(trackId);
+
+                    if(theBoundaryStatus == FresnelReflection)
+                        Analysis::GetInstance()->IncreaseFresnelReflectionsAtCladCladInterface(trackId);
+
+                    if(theBoundaryStatus == FresnelRefraction)
+                        Analysis::GetInstance()->IncreaseRefractionsAtCladCladInterface(trackId);
+                }
+
+                if ((prePhysicalVolumeName.substr(0,4) == "Core" && postPhysicalVolumeName.substr(0,9) == "Cladding1")
+                    || (prePhysicalVolumeName.substr(0,9) == "Cladding1" && postPhysicalVolumeName.substr(0,9) == "Core"))
+                {
+                    if(theBoundaryStatus == TotalInternalReflection)
+                        Analysis::GetInstance()->IncreaseTotalReflectionsAtCoreCladInterface(trackId);
+
+                    if(theBoundaryStatus == FresnelReflection)
+                        Analysis::GetInstance()->IncreaseFresnelReflectionsAtCoreCladInterface(trackId);
+
+                    if(theBoundaryStatus == FresnelRefraction)
+                        Analysis::GetInstance()->IncreaseRefractionsAtCoreCladInterface(trackId);
+                }
+            }
+        }
+        else // Check for Rayleigh scattering
+            if (step->GetDeltaMomentum()[0] != 0 || step->GetDeltaMomentum()[1] != 0 || step->GetDeltaMomentum()[2] != 0)
+                Analysis::GetInstance()->IncreaseRayleighScatterings(trackId);
+
+      
+        // Store length per volume
+
+        if (prePhysicalVolumeName.substr(0,4) == "Core")
+            Analysis::GetInstance()->IncreaseLengthInCore(trackId,stepLength);
+
+        if (prePhysicalVolumeName.substr(0,9) == "Cladding1")
+            Analysis::GetInstance()->IncreaseLengthInInnerCladding(trackId,stepLength);
+
+        if (prePhysicalVolumeName.substr(0,9) == "Cladding2")
+            Analysis::GetInstance()->IncreaseLengthInOuterCladding(trackId,stepLength);
+
+
+
+        // Store photons killed by OpWLS process, if not primary particle
+
+        if(step->GetTrack()->GetParentID() > 0 && step->GetTrack()->GetTrackStatus() == fStopAndKill && step->GetSecondary()->size() == 1)
+        {
+            G4int creatorProcessId = 0;
+
+            if(step->GetTrack()->GetCreatorProcess()->GetProcessName() == "Scintillation")
+                creatorProcessId = 1;
+
+            if(step->GetTrack()->GetCreatorProcess()->GetProcessName() == "Cerenkov")
+                creatorProcessId = 2;
+
+            if(step->GetTrack()->GetCreatorProcess()->GetProcessName() == "OpWLS")
+                creatorProcessId = 3;
+        }
+
+
+
+    }
+    /* ++ End of SteppingAction of optical photons. ++ */
+
+
+    /* ++ SteppingAction for electrons and muon ++ */
+    if((step->GetTrack()->GetDefinition() == primDefinition))
+    {
+        G4double runID = (G4double) G4RunManager::GetRunManager()->GetCurrentRun()->GetRunID();
+        G4double eventID = (G4double) G4EventManager::GetEventManager()->GetConstCurrentEvent()->GetEventID();
+	
+        Analysis::GetInstance()->FillPrimaryParticleTrack(runID,
+                                                          eventID,
+                                                          step->GetTrack()->GetPosition()[0],
+                                                          step->GetTrack()->GetPosition()[1],
+                                                          step->GetTrack()->GetPosition()[2]);
+
+        G4String prePhysicalVolumeName = step->GetPreStepPoint()->GetPhysicalVolume()->GetName();
+        if (prePhysicalVolumeName.substr(0,4) == "Core")
+        {
+            G4double edep = step->GetTotalEnergyDeposit();
+            G4double stepLength = step->GetStepLength();
+
+            fEventAction->AddCore(edep, stepLength);
+        }
+		
+        if (prePhysicalVolumeName == "Trigger")
+        {
+            G4double edep = step->GetTotalEnergyDeposit();
+            Analysis::GetInstance()->FillTrigger(runID,
+                                                 eventID,
+                                                 edep,
+                                                 step->GetTrack()->GetPosition()[0],
+                                                 step->GetTrack()->GetPosition()[1],
+                                                 step->GetTrack()->GetPosition()[2]);
+        }
+    }
+    /* ++ End of SteppingAction for electrons and muon ++ */
+}

SciFiSim/src/SteppingAction.cc~

@@ -0,0 +1,221 @@
+// Written by Peter Stromberger
+// based on work of Mirco Deckenhoff
+// modified by Bastian Rössler
+
+
+#include "SteppingAction.hh"
+#include "G4Step.hh"
+#include "G4VTouchable.hh"
+#include "G4SteppingManager.hh"
+#include "G4UnitsTable.hh"
+#include "G4ParticleTypes.hh"
+#include "G4ProcessManager.hh"
+#include "G4VProcess.hh"
+#include "G4ProcessVector.hh"
+#include "EventAction.hh"
+#include <string>
+#include "Parameters.hh"
+#include "Analysis.hh"
+#include "G4RunManager.hh"
+#include "Randomize.hh"
+#include "G4SystemOfUnits.hh"
+
+
+SteppingAction::SteppingAction(EventAction* eventAction, PrimaryGeneratorAction* p)
+{
+    creatorProcess = -1;
+    fEventAction = eventAction;
+    pGA = p;
+}
+
+SteppingAction::~SteppingAction(){}
+
+void SteppingAction::UserSteppingAction( const G4Step * step )
+{
+
+    primDefinition = (pGA->GetGun())->GetParticleDefinition();
+    primParticle = (primDefinition->GetParticleName()).c_str();
+
+    /* ++ SteppingAction for optical photons ++ */
+    if(step->GetTrack()->GetDefinition() == G4OpticalPhoton::OpticalPhotonDefinition())
+    {
+        G4int trackId = step->GetTrack()->GetTrackID();
+        G4double stepLength = step->GetStepLength();
+    
+        G4String prePhysicalVolumeName = step->GetPreStepPoint()->GetPhysicalVolume()->GetName();
+        G4String postPhysicalVolumeName = "";
+
+        // PostStep does only exist if the particle is not exiting the EpoxyBox volume!
+        if(step->GetTrack()->GetTrackStatus() != fStopAndKill)
+            postPhysicalVolumeName = step->GetPostStepPoint()->GetPhysicalVolume()->GetName();
+
+    
+        // Kill photons at fibre surface
+        // Count the reflections and refractions
+    
+        if(step->GetPostStepPoint()->GetStepStatus()==fGeomBoundary)
+        {
+            if(postPhysicalVolumeName == "EpoxyBox" && prePhysicalVolumeName.substr(0,9) == "Cladding2")
+            {
+                if(Parameters::GetInstance()->ProbabilityOfPhotonLossAtSurface() == 1)
+                    step->GetTrack()->SetTrackStatus(fStopAndKill);
+
+                if(Parameters::GetInstance()->ProbabilityOfPhotonLossAtSurface() < 1
+                   && Parameters::GetInstance()->ProbabilityOfPhotonLossAtSurface() > 0)
+                {
+                    G4double randomNumber = CLHEP::RandFlat::shoot();
+
+                    if(Parameters::GetInstance()->ProbabilityOfPhotonLossAtSurface() < randomNumber)
+                    {
+                        if (step->GetStepLength() > 0)
+                            Analysis::GetInstance()->IncreaseReflectionsAtFibreSurface(trackId);
+                    }
+                    else
+                        step->GetTrack()->SetTrackStatus(fStopAndKill);
+                }
+
+                if (step->GetStepLength() > 0)
+                    Analysis::GetInstance()->IncreaseReflectionsAtFibreSurface(trackId);
+            }
+            if(postPhysicalVolumeName == "Mirror")
+                Analysis::GetInstance()->IncreaseReflectionsAtMirror(trackId);
+      
+       
+            // Retrieve status of the photon boundary process
+      
+      
+            G4OpBoundaryProcessStatus theBoundaryStatus = Undefined;
+      
+            G4ProcessManager* OpManager = G4OpticalPhoton::OpticalPhoton()->GetProcessManager();
+      
+            if(OpManager)
+            {
+                G4int MAXofPostStepLoops = OpManager->GetPostStepProcessVector()->entries();
+                G4ProcessVector* fPostStepDoItVector = OpManager->GetPostStepProcessVector(typeDoIt);
+	
+                for(G4int i = 0; i<MAXofPostStepLoops; i++)
+                {
+                    G4VProcess* fCurrentProcess = (*fPostStepDoItVector)[i];
+                    opBoundaryProcess = dynamic_cast<G4OpBoundaryProcess*>(fCurrentProcess);
+	  			
+                    if(opBoundaryProcess)
+                    {
+                        theBoundaryStatus = opBoundaryProcess->GetStatus();
+                        break;
+                    }
+                }
+            }
+      
+            if(theBoundaryStatus != Undefined)
+            {
+                if((prePhysicalVolumeName.substr(0,9) == "Cladding1" && postPhysicalVolumeName.substr(0,9) == "Cladding2")
+                   || (prePhysicalVolumeName.substr(0,9) == "Cladding2" && postPhysicalVolumeName.substr(0,9) == "Cladding1"))
+                {
+                    if(theBoundaryStatus == TotalInternalReflection)
+                        Analysis::GetInstance()->IncreaseTotalReflectionsAtCladCladInterface(trackId);
+
+                    if(theBoundaryStatus == FresnelReflection)
+                        Analysis::GetInstance()->IncreaseFresnelReflectionsAtCladCladInterface(trackId);
+
+                    if(theBoundaryStatus == FresnelRefraction)
+                        Analysis::GetInstance()->IncreaseRefractionsAtCladCladInterface(trackId);
+                }
+
+                if ((prePhysicalVolumeName.substr(0,4) == "Core" && postPhysicalVolumeName.substr(0,9) == "Cladding1")
+                    || (prePhysicalVolumeName.substr(0,9) == "Cladding1" && postPhysicalVolumeName.substr(0,9) == "Core"))
+                {
+                    if(theBoundaryStatus == TotalInternalReflection)
+                        Analysis::GetInstance()->IncreaseTotalReflectionsAtCoreCladInterface(trackId);
+
+                    if(theBoundaryStatus == FresnelReflection)
+                        Analysis::GetInstance()->IncreaseFresnelReflectionsAtCoreCladInterface(trackId);
+
+                    if(theBoundaryStatus == FresnelRefraction)
+                        Analysis::GetInstance()->IncreaseRefractionsAtCoreCladInterface(trackId);
+                }
+            }
+        }
+        else // Check for Rayleigh scattering
+            if (step->GetDeltaMomentum()[0] != 0 || step->GetDeltaMomentum()[1] != 0 || step->GetDeltaMomentum()[2] != 0)
+                Analysis::GetInstance()->IncreaseRayleighScatterings(trackId);
+
+      
+        // Store length per volume
+
+        if (prePhysicalVolumeName.substr(0,4) == "Core")
+            Analysis::GetInstance()->IncreaseLengthInCore(trackId,stepLength);
+
+        if (prePhysicalVolumeName.substr(0,9) == "Cladding1")
+            Analysis::GetInstance()->IncreaseLengthInInnerCladding(trackId,stepLength);
+
+        if (prePhysicalVolumeName.substr(0,9) == "Cladding2")
+            Analysis::GetInstance()->IncreaseLengthInOuterCladding(trackId,stepLength);
+
+
+
+        // Store photons killed by OpWLS process, if not primary particle
+
+        if(step->GetTrack()->GetParentID() > 0 && step->GetTrack()->GetTrackStatus() == fStopAndKill && step->GetSecondary()->size() == 1)
+        {
+            G4int creatorProcessId = 0;
+
+            if(step->GetTrack()->GetCreatorProcess()->GetProcessName() == "Scintillation")
+                creatorProcessId = 1;
+
+            if(step->GetTrack()->GetCreatorProcess()->GetProcessName() == "Cerenkov")
+                creatorProcessId = 2;
+
+            if(step->GetTrack()->GetCreatorProcess()->GetProcessName() == "OpWLS")
+                creatorProcessId = 3;
+        }
+
+
+	// Radiation damage
+	dose = h_dose->GetBinContent(1,1 );
+	dose = 0;
+	std::cout <<  step->GetTrack()->GetPosition().x() << " " <<  step->GetTrack()->GetPosition().y() << " " << step->GetTrack()->GetPosition().z() << " " << dose << "\n ";
+
+	G4float attlength = 100.*1./(dose * 1.5*exp(9.412 -0.0256721 * 1240./(step->GetTrack()->GetTotalEnergy()/eV)) ); 
+	double xf = G4UniformRand();
+	//std::cout << xf << " " << attlength<< " " <<  1240./(step->GetTrack()->GetTotalEnergy()/eV) << "\n";
+	 if(xf>(exp(-stepLength*cm/attlength)) ){  //randomly kill photon based on attenuation length
+	   step->GetTrack()->SetTrackStatus(fStopAndKill);}
+
+    }
+    /* ++ End of SteppingAction of optical photons. ++ */
+
+
+    /* ++ SteppingAction for electrons and muon ++ */
+    if((step->GetTrack()->GetDefinition() == primDefinition))
+    {
+        G4double runID = (G4double) G4RunManager::GetRunManager()->GetCurrentRun()->GetRunID();
+        G4double eventID = (G4double) G4EventManager::GetEventManager()->GetConstCurrentEvent()->GetEventID();
+
+        Analysis::GetInstance()->FillPrimaryParticleTrack(runID,
+                                                          eventID,
+                                                          step->GetTrack()->GetPosition()[0],
+                                                          step->GetTrack()->GetPosition()[1],
+                                                          step->GetTrack()->GetPosition()[2]);
+
+        G4String prePhysicalVolumeName = step->GetPreStepPoint()->GetPhysicalVolume()->GetName();
+        if (prePhysicalVolumeName.substr(0,4) == "Core")
+        {
+            G4double edep = step->GetTotalEnergyDeposit();
+            G4double stepLength = step->GetStepLength();
+
+            fEventAction->AddCore(edep, stepLength);
+        }
+		
+        if (prePhysicalVolumeName == "Trigger")
+        {
+            G4double edep = step->GetTotalEnergyDeposit();
+            Analysis::GetInstance()->FillTrigger(runID,
+                                                 eventID,
+                                                 edep,
+                                                 step->GetTrack()->GetPosition()[0],
+                                                 step->GetTrack()->GetPosition()[1],
+                                                 step->GetTrack()->GetPosition()[2]);
+        }
+    }
+    /* ++ End of SteppingAction for electrons and muon ++ */
+}

SciFiSim/src/dosehist.C

@@ -0,0 +1,72 @@
+
+{
+Double_t dosebig[25][30] = {
+   { 1.34E+01, 1.45E+01, 7.95E+00, 5.45E+00, 4.17E+00, 3.37E+00, 2.81E+00, 2.55E+00, 2.24E+00, 2.02E+00, 1.83E+00, 1.68E+00, 1.55E+00, 1.43E+00, 1.34E+00, 1.28E+00, 1.20E+00, 1.15E+00, 1.06E+00, 9.75E-01, 9.35E-01, 8.60E-01, 7.95E-01, 7.45E-01, 6.85E-01, 6.20E-01, 5.80E-01, 5.20E-01, 4.96E-01, 4.65E-01} , 
+   { 7.20E+00, 6.20E+00, 4.64E+00, 3.47E+00, 2.68E+00, 2.28E+00, 1.98E+00, 1.66E+00, 1.50E+00, 1.38E+00, 1.27E+00, 1.16E+00, 1.04E+00, 9.85E-01, 9.15E-01, 8.95E-01, 8.45E-01, 7.75E-01, 7.25E-01, 6.95E-01, 6.60E-01, 6.00E-01, 5.40E-01, 5.30E-01, 4.66E-01, 4.20E-01, 3.99E-01, 3.64E-01, 3.33E-01, 2.90E-01} , 
+   { 2.74E+00, 2.55E+00, 2.23E+00, 2.04E+00, 1.65E+00, 1.47E+00, 1.29E+00, 1.25E+00, 1.06E+00, 9.70E-01, 8.85E-01, 8.50E-01, 7.75E-01, 7.20E-01, 6.75E-01, 6.65E-01, 6.10E-01, 5.65E-01, 5.50E-01, 5.10E-01, 4.74E-01, 4.51E-01, 4.06E-01, 3.80E-01, 3.75E-01, 3.16E-01, 2.86E-01, 2.72E-01, 2.54E-01, 1.89E-01} , 
+   { 1.57E+00, 1.39E+00, 1.31E+00, 1.30E+00, 1.12E+00, 1.06E+00, 9.55E-01, 8.70E-01, 8.30E-01, 7.90E-01, 6.95E-01, 6.45E-01, 6.10E-01, 5.65E-01, 5.50E-01, 4.86E-01, 5.10E-01, 4.66E-01, 4.30E-01, 4.41E-01, 3.89E-01, 3.59E-01, 3.20E-01, 3.35E-01, 2.98E-01, 2.73E-01, 2.67E-01, 2.27E-01, 2.10E-01, 1.54E-01} , 
+   { 1.00E+00, 9.00E-01, 9.10E-01, 9.15E-01, 8.25E-01, 8.00E-01, 7.40E-01, 6.75E-01, 6.65E-01, 5.80E-01, 5.35E-01, 5.10E-01, 4.60E-01, 4.58E-01, 4.09E-01, 3.93E-01, 3.78E-01, 3.63E-01, 3.52E-01, 3.49E-01, 2.88E-01, 2.78E-01, 2.64E-01, 2.56E-01, 2.44E-01, 2.23E-01, 2.21E-01, 1.97E-01, 1.73E-01, 1.37E-01} , 
+   { 6.60E-01, 6.20E-01, 6.10E-01, 6.30E-01, 5.95E-01, 5.65E-01, 5.55E-01, 5.10E-01, 4.96E-01, 4.92E-01, 4.90E-01, 3.97E-01, 4.07E-01, 3.47E-01, 3.38E-01, 3.10E-01, 2.93E-01, 2.92E-01, 2.65E-01, 2.65E-01, 2.40E-01, 2.48E-01, 2.06E-01, 2.10E-01, 2.40E-01, 1.98E-01, 1.85E-01, 1.89E-01, 1.38E-01, 1.34E-01} , 
+   { 4.83E-01, 4.77E-01, 4.60E-01, 4.75E-01, 4.39E-01, 4.12E-01, 4.47E-01, 4.00E-01, 3.78E-01, 3.65E-01, 3.43E-01, 3.31E-01, 2.85E-01, 3.22E-01, 2.85E-01, 2.54E-01, 2.53E-01, 2.49E-01, 2.48E-01, 2.20E-01, 2.17E-01, 1.95E-01, 1.99E-01, 1.80E-01, 1.75E-01, 1.68E-01, 1.77E-01, 1.51E-01, 1.37E-01, 1.10E-01} , 
+   { 3.89E-01, 3.67E-01, 3.61E-01, 3.74E-01, 3.70E-01, 3.45E-01, 3.45E-01, 3.11E-01, 2.97E-01, 3.11E-01, 2.93E-01, 2.65E-01, 2.68E-01, 2.23E-01, 2.11E-01, 2.26E-01, 2.18E-01, 1.97E-01, 1.97E-01, 1.88E-01, 1.97E-01, 1.72E-01, 1.66E-01, 1.75E-01, 1.44E-01, 1.60E-01, 1.41E-01, 1.40E-01, 1.05E-01, 1.19E-01} , 
+   { 3.18E-01, 2.54E-01, 3.06E-01, 2.89E-01, 2.74E-01, 2.80E-01, 2.57E-01, 2.59E-01, 2.51E-01, 2.45E-01, 2.62E-01, 2.36E-01, 2.15E-01, 2.12E-01, 1.96E-01, 2.12E-01, 1.78E-01, 1.75E-01, 1.69E-01, 1.64E-01, 1.64E-01, 1.62E-01, 1.53E-01, 1.49E-01, 1.47E-01, 1.49E-01, 1.42E-01, 1.20E-01, 1.01E-01, 9.00E-02} , 
+   { 2.75E-01, 2.51E-01, 2.24E-01, 2.69E-01, 2.34E-01, 2.28E-01, 2.30E-01, 1.96E-01, 2.08E-01, 2.27E-01, 2.09E-01, 1.91E-01, 2.14E-01, 1.79E-01, 1.79E-01, 2.05E-01, 1.79E-01, 1.58E-01, 1.88E-01, 1.49E-01, 1.57E-01, 1.30E-01, 1.32E-01, 1.39E-01, 1.32E-01, 1.18E-01, 1.34E-01, 1.05E-01, 9.65E-02, 8.65E-02} , 
+   { 2.35E-01, 2.34E-01, 2.27E-01, 2.17E-01, 2.41E-01, 2.21E-01, 2.01E-01, 1.87E-01, 2.04E-01, 1.85E-01, 1.75E-01, 1.69E-01, 1.79E-01, 1.92E-01, 1.56E-01, 1.79E-01, 1.78E-01, 1.41E-01, 1.45E-01, 1.41E-01, 1.36E-01, 1.44E-01, 1.11E-01, 1.24E-01, 1.13E-01, 1.29E-01, 1.02E-01, 9.30E-02, 9.65E-02, 8.40E-02} , 
+   { 1.89E-01, 1.72E-01, 1.94E-01, 1.94E-01, 2.07E-01, 2.42E-01, 2.02E-01, 1.80E-01, 1.80E-01, 1.54E-01, 1.60E-01, 1.67E-01, 1.57E-01, 1.39E-01, 1.57E-01, 1.46E-01, 1.62E-01, 1.35E-01, 1.29E-01, 1.32E-01, 1.25E-01, 1.13E-01, 1.05E-01, 1.02E-01, 1.12E-01, 9.75E-02, 8.85E-02, 9.10E-02, 7.35E-02, 9.00E-02} , 
+   { 1.56E-01, 1.40E-01, 1.52E-01, 1.70E-01, 1.55E-01, 1.48E-01, 1.54E-01, 1.61E-01, 1.58E-01, 1.54E-01, 1.34E-01, 1.43E-01, 1.40E-01, 1.41E-01, 1.26E-01, 1.17E-01, 1.20E-01, 1.05E-01, 1.11E-01, 1.06E-01, 1.03E-01, 9.50E-02, 1.02E-01, 8.65E-02, 9.45E-02, 9.35E-02, 7.05E-02, 6.70E-02, 7.55E-02, 5.80E-02} , 
+   { 1.50E-01, 1.34E-01, 1.23E-01, 1.50E-01, 1.35E-01, 1.28E-01, 1.32E-01, 1.43E-01, 1.13E-01, 1.20E-01, 1.35E-01, 1.15E-01, 1.07E-01, 1.15E-01, 1.17E-01, 1.09E-01, 1.09E-01, 1.11E-01, 9.85E-02, 9.25E-02, 8.95E-02, 7.65E-02, 8.30E-02, 7.75E-02, 7.05E-02, 7.60E-02, 5.95E-02, 8.25E-02, 6.20E-02, 7.45E-02} , 
+   { 1.29E-01, 1.08E-01, 1.05E-01, 1.28E-01, 1.33E-01, 1.18E-01, 1.11E-01, 1.30E-01, 1.13E-01, 1.01E-01, 1.05E-01, 9.20E-02, 9.35E-02, 9.30E-02, 9.45E-02, 1.17E-01, 1.00E-01, 8.75E-02, 9.15E-02, 8.45E-02, 5.95E-02, 6.50E-02, 7.65E-02, 7.45E-02, 7.05E-02, 7.50E-02, 5.40E-02, 5.75E-02, 5.65E-02, 5.40E-02} , 
+   { 1.46E-01, 1.07E-01, 1.13E-01, 1.08E-01, 1.11E-01, 1.07E-01, 9.65E-02, 9.80E-02, 9.65E-02, 8.60E-02, 8.45E-02, 9.80E-02, 9.05E-02, 1.06E-01, 8.30E-02, 8.35E-02, 7.80E-02, 8.00E-02, 6.80E-02, 7.10E-02, 6.65E-02, 7.10E-02, 7.35E-02, 6.45E-02, 5.40E-02, 5.50E-02, 5.60E-02, 6.30E-02, 5.10E-02, 4.84E-02} , 
+   { 1.15E-01, 9.80E-02, 9.65E-02, 1.08E-01, 1.00E-01, 1.32E-01, 8.25E-02, 9.90E-02, 9.30E-02, 8.40E-02, 8.75E-02, 7.70E-02, 9.30E-02, 7.65E-02, 7.70E-02, 8.00E-02, 7.20E-02, 7.10E-02, 6.90E-02, 6.95E-02, 6.25E-02, 5.90E-02, 7.15E-02, 6.10E-02, 5.10E-02, 5.10E-02, 5.20E-02, 5.80E-02, 6.35E-02, 4.94E-02} , 
+   { 1.13E-01, 1.01E-01, 1.08E-01, 1.16E-01, 8.75E-02, 8.80E-02, 7.55E-02, 8.20E-02, 8.20E-02, 8.80E-02, 8.20E-02, 8.55E-02, 7.40E-02, 6.80E-02, 6.85E-02, 7.40E-02, 6.70E-02, 6.20E-02, 5.85E-02, 5.55E-02, 5.65E-02, 6.15E-02, 5.90E-02, 6.50E-02, 5.20E-02, 5.60E-02, 4.47E-02, 4.64E-02, 3.90E-02, 5.55E-02} , 
+   { 9.35E-02, 7.60E-02, 7.45E-02, 8.60E-02, 8.85E-02, 7.30E-02, 5.95E-02, 6.60E-02, 7.25E-02, 7.05E-02, 7.00E-02, 7.50E-02, 6.90E-02, 7.30E-02, 6.30E-02, 6.45E-02, 6.05E-02, 5.95E-02, 5.60E-02, 5.20E-02, 4.72E-02, 5.25E-02, 5.65E-02, 4.89E-02, 3.86E-02, 4.41E-02, 4.57E-02, 3.96E-02, 4.49E-02, 5.15E-02} , 
+   { 7.65E-02, 6.10E-02, 6.20E-02, 7.85E-02, 6.95E-02, 6.15E-02, 7.50E-02, 7.80E-02, 6.30E-02, 5.60E-02, 4.98E-02, 6.45E-02, 6.05E-02, 4.74E-02, 6.20E-02, 5.50E-02, 5.85E-02, 4.84E-02, 4.11E-02, 4.64E-02, 5.25E-02, 4.39E-02, 4.03E-02, 4.15E-02, 3.31E-02, 3.77E-02, 3.87E-02, 3.65E-02, 4.22E-02, 3.39E-02} , 
+   { 6.55E-02, 5.30E-02, 5.45E-02, 5.90E-02, 5.25E-02, 5.70E-02, 5.75E-02, 5.10E-02, 5.95E-02, 4.73E-02, 5.85E-02, 5.90E-02, 5.35E-02, 5.70E-02, 5.10E-02, 4.50E-02, 5.10E-02, 5.10E-02, 4.80E-02, 4.16E-02, 4.56E-02, 4.21E-02, 4.22E-02, 3.65E-02, 3.55E-02, 3.69E-02, 3.99E-02, 3.91E-02, 3.20E-02, 2.36E-02} , 
+   { 6.05E-02, 4.49E-02, 3.60E-02, 4.88E-02, 6.15E-02, 4.71E-02, 5.40E-02, 4.40E-02, 5.15E-02, 5.30E-02, 4.63E-02, 4.52E-02, 5.95E-02, 6.90E-02, 3.83E-02, 4.28E-02, 4.57E-02, 3.39E-02, 4.74E-02, 4.59E-02, 3.64E-02, 4.23E-02, 4.00E-02, 3.39E-02, 3.47E-02, 2.82E-02, 3.14E-02, 3.44E-02, 2.83E-02, 3.07E-02} , 
+   { 4.42E-02, 3.93E-02, 3.97E-02, 4.28E-02, 4.25E-02, 4.61E-02, 3.78E-02, 3.64E-02, 4.53E-02, 4.21E-02, 4.04E-02, 4.10E-02, 4.33E-02, 4.15E-02, 3.29E-02, 3.88E-02, 3.14E-02, 3.34E-02, 3.60E-02, 3.53E-02, 3.64E-02, 3.60E-02, 2.79E-02, 2.96E-02, 3.28E-02, 2.95E-02, 2.75E-02, 2.83E-02, 2.64E-02, 2.49E-02} , 
+   { 5.20E-02, 3.80E-02, 4.32E-02, 3.51E-02, 3.67E-02, 4.66E-02, 3.98E-02, 3.43E-02, 4.17E-02, 4.25E-02, 3.50E-02, 3.88E-02, 3.69E-02, 3.79E-02, 4.09E-02, 3.51E-02, 3.53E-02, 4.07E-02, 3.25E-02, 3.10E-02, 4.01E-02, 3.75E-02, 2.81E-02, 2.72E-02, 2.77E-02, 2.57E-02, 3.09E-02, 2.49E-02, 2.65E-02, 1.74E-02} , 
+   { 3.84E-02, 3.99E-02, 3.29E-02, 3.76E-02, 3.31E-02, 3.33E-02, 3.40E-02, 3.55E-02, 3.63E-02, 3.01E-02, 3.40E-02, 4.82E-02, 3.13E-02, 4.77E-02, 3.41E-02, 4.30E-02, 3.45E-02, 3.01E-02, 3.07E-02, 2.94E-02, 2.56E-02, 2.21E-02, 2.40E-02, 2.43E-02, 2.66E-02, 2.44E-02, 1.98E-02, 2.55E-02, 2.41E-02, 2.00E-02}
+   };
+
+Double_t dosesmall[20][20] = 
+  {{3.705,3.97,3.43,3.615,3.375,3.27,3.515,3.74,3.29,3.42,3.985,3.415,3.32,3.305,3.765,3.22,3.37,2.855,3.23,3.145},
+   {4.565,4,3.98,3.735,3.995,3.73,3.6,3.495,3.73,4.06,3.865,4.355,3.745,3.535,3.47,3.17,3.835,3.425,3.19,3.29},
+   {  4.65,4.37,4.09,4.29,4.65,4.62,4.04,3.845,4.375,4.09,4.05,4.885,4.35,4.705,3.905,4.06,3.82,3.665,3.61,3.67},
+   { 4.905,4.74,5.1,4.62,4.425,4.625,4.695,4.395,4.685,4.335,4.665,4.575,4.485,4.725,5,4.715,4.055,4.32,4.76,4.225},
+   { 5.55,6.35,5.3,5.15,5.25,5.35,5.05,5.25,5.6,5.4,5.25,4.68,4.645,4.98,4.555,4.935,4.725,4.485,4.51,4.135},
+   { 6,6.55,6.35,6.5,6,5.55,5.65,6.15,5.95,5.75,5.75,5.55,5.6,5.3,4.71,5.15,4.905,5.6,4.565,4.38},
+   { 7.35,7.6,6.9,7.1,6.9,7.05,6.3,6.7,6.45,7.75,5.8,5.7,6,5.6,5.85,5.4,5.9,5.55,5.55,4.835},
+   { 8.65,8.45,18.65,7.6,8,8.9,7.55,7.4,7.7,6.45,8.35,7.5,6.95,7.55,7.2,7.2,7.05,6.1,6.2,5.6},
+   { 11.45,11.5,11.4,11.1,15.25,10.5,9.5,9.15,8.25,8.15,8.35,8.65,8.25,8.7,7.8,7.5,7,6.8,6.7,5.85},
+   { 15.75,16.6,15.9,16.95,14.05,15.8,13.2,12.35,12.95,11.25,10.5,10,9.7,9.85,8.95,8.25,7.9,7.75,7.45,7.3},
+   { 20.8,5.4,20.8,19.05,19.1,17.05,16.55,17.25,13.5,12.65,11.9,12.05,11.15,11.5,10.25,9.65,9.6,8.3,8.95,8.2},
+   { 24.85,23.95,22.6,21.85,22.5,18.9,20.7,22.4,17.05,15.65,13.45,12.05,11.85,10.7,10.5,10.25,9.65,9.3,8.65,7.95},
+   { 3.575,6.7,12.65,22.2,20.35,28.85,18.7,17.55,17.85,16.5,13.95,12.65,12.45,11.7,10.45,9.85,9.15,8.85,8.2,8.8},
+   { 0,0,0,1.665,14.75,27.4,28.7,20,19.75,18.65,26.45,14.3,13.6,13.25,11.5,11.2,10.7,11.1,9,9.15},
+   { 0,0,0,0,0,12.2,26.5,22.45,20.9,20.45,22,17.2,14.75,13.15,13.1,11.3,11.35,9.75,10.85,8.65},
+   { 0,0,0,0,0,0,27.25,27.1,25.65,20.9,22.5,18.65,15.7,13.6,14,11.65,10.65,9.6,9.7,8.45},
+   { 0,0,0,0,0,0,11.8,30.05,26.45,37.8,23.45,22.5,17.3,15.05,13.7,11.65,11.85,10.7,9.95,8.9},
+   { 0,0,0,0,0,0,0,29.65,32.05,26.4,22.95,27.95,17.65,14.6,13.3,12.2,11.9,10.75,10.3,10.1},
+   { 0,0,0,0,0,0,0,13.1,38.05,30.2,35.8,21.65,19.4,15.45,14.05,12.95,12.6,11,10.55,9.5},
+   { 0,0,0,0,0,0,0,8.25,37.85,28.8,32,23.35,19.85,17.65,15.35,12.75,12.35,10.95,10.25,9.35}};
+
+ TFile f("dose.root","recreate");
+TH2F * dosehist50invfb = new TH2F("dosehist50invfb","dosehist50invfb",300,0,300,250,0,250);
+
+for (unsigned int i = 0;i<250;i++){
+  for (unsigned int j = 0;j<300;j++){
+    dosehist50invfb->SetBinContent(j+1,i+1,dosebig[floor(i/10)][floor(j/10)]);
+  }
+ }
+
+
+for (unsigned int i = 0;i<20;i++){
+  for (unsigned int j = 0;j<20;j++){
+    dosehist50invfb->SetBinContent(j+1,20-i,dosesmall[i][j]);
+  }
+ }
+
+dosehist50invfb->Draw("coloz");
+ dosehist50invfb->Write();
+ f.Close();
+}

SciFiSim/src/dosehist.C~

@@ -0,0 +1,71 @@
+
+{
+Double_t dosebig[25][30] = {
+   { 1.34E+01, 1.45E+01, 7.95E+00, 5.45E+00, 4.17E+00, 3.37E+00, 2.81E+00, 2.55E+00, 2.24E+00, 2.02E+00, 1.83E+00, 1.68E+00, 1.55E+00, 1.43E+00, 1.34E+00, 1.28E+00, 1.20E+00, 1.15E+00, 1.06E+00, 9.75E-01, 9.35E-01, 8.60E-01, 7.95E-01, 7.45E-01, 6.85E-01, 6.20E-01, 5.80E-01, 5.20E-01, 4.96E-01, 4.65E-01} , 
+   { 7.20E+00, 6.20E+00, 4.64E+00, 3.47E+00, 2.68E+00, 2.28E+00, 1.98E+00, 1.66E+00, 1.50E+00, 1.38E+00, 1.27E+00, 1.16E+00, 1.04E+00, 9.85E-01, 9.15E-01, 8.95E-01, 8.45E-01, 7.75E-01, 7.25E-01, 6.95E-01, 6.60E-01, 6.00E-01, 5.40E-01, 5.30E-01, 4.66E-01, 4.20E-01, 3.99E-01, 3.64E-01, 3.33E-01, 2.90E-01} , 
+   { 2.74E+00, 2.55E+00, 2.23E+00, 2.04E+00, 1.65E+00, 1.47E+00, 1.29E+00, 1.25E+00, 1.06E+00, 9.70E-01, 8.85E-01, 8.50E-01, 7.75E-01, 7.20E-01, 6.75E-01, 6.65E-01, 6.10E-01, 5.65E-01, 5.50E-01, 5.10E-01, 4.74E-01, 4.51E-01, 4.06E-01, 3.80E-01, 3.75E-01, 3.16E-01, 2.86E-01, 2.72E-01, 2.54E-01, 1.89E-01} , 
+   { 1.57E+00, 1.39E+00, 1.31E+00, 1.30E+00, 1.12E+00, 1.06E+00, 9.55E-01, 8.70E-01, 8.30E-01, 7.90E-01, 6.95E-01, 6.45E-01, 6.10E-01, 5.65E-01, 5.50E-01, 4.86E-01, 5.10E-01, 4.66E-01, 4.30E-01, 4.41E-01, 3.89E-01, 3.59E-01, 3.20E-01, 3.35E-01, 2.98E-01, 2.73E-01, 2.67E-01, 2.27E-01, 2.10E-01, 1.54E-01} , 
+   { 1.00E+00, 9.00E-01, 9.10E-01, 9.15E-01, 8.25E-01, 8.00E-01, 7.40E-01, 6.75E-01, 6.65E-01, 5.80E-01, 5.35E-01, 5.10E-01, 4.60E-01, 4.58E-01, 4.09E-01, 3.93E-01, 3.78E-01, 3.63E-01, 3.52E-01, 3.49E-01, 2.88E-01, 2.78E-01, 2.64E-01, 2.56E-01, 2.44E-01, 2.23E-01, 2.21E-01, 1.97E-01, 1.73E-01, 1.37E-01} , 
+   { 6.60E-01, 6.20E-01, 6.10E-01, 6.30E-01, 5.95E-01, 5.65E-01, 5.55E-01, 5.10E-01, 4.96E-01, 4.92E-01, 4.90E-01, 3.97E-01, 4.07E-01, 3.47E-01, 3.38E-01, 3.10E-01, 2.93E-01, 2.92E-01, 2.65E-01, 2.65E-01, 2.40E-01, 2.48E-01, 2.06E-01, 2.10E-01, 2.40E-01, 1.98E-01, 1.85E-01, 1.89E-01, 1.38E-01, 1.34E-01} , 
+   { 4.83E-01, 4.77E-01, 4.60E-01, 4.75E-01, 4.39E-01, 4.12E-01, 4.47E-01, 4.00E-01, 3.78E-01, 3.65E-01, 3.43E-01, 3.31E-01, 2.85E-01, 3.22E-01, 2.85E-01, 2.54E-01, 2.53E-01, 2.49E-01, 2.48E-01, 2.20E-01, 2.17E-01, 1.95E-01, 1.99E-01, 1.80E-01, 1.75E-01, 1.68E-01, 1.77E-01, 1.51E-01, 1.37E-01, 1.10E-01} , 
+   { 3.89E-01, 3.67E-01, 3.61E-01, 3.74E-01, 3.70E-01, 3.45E-01, 3.45E-01, 3.11E-01, 2.97E-01, 3.11E-01, 2.93E-01, 2.65E-01, 2.68E-01, 2.23E-01, 2.11E-01, 2.26E-01, 2.18E-01, 1.97E-01, 1.97E-01, 1.88E-01, 1.97E-01, 1.72E-01, 1.66E-01, 1.75E-01, 1.44E-01, 1.60E-01, 1.41E-01, 1.40E-01, 1.05E-01, 1.19E-01} , 
+   { 3.18E-01, 2.54E-01, 3.06E-01, 2.89E-01, 2.74E-01, 2.80E-01, 2.57E-01, 2.59E-01, 2.51E-01, 2.45E-01, 2.62E-01, 2.36E-01, 2.15E-01, 2.12E-01, 1.96E-01, 2.12E-01, 1.78E-01, 1.75E-01, 1.69E-01, 1.64E-01, 1.64E-01, 1.62E-01, 1.53E-01, 1.49E-01, 1.47E-01, 1.49E-01, 1.42E-01, 1.20E-01, 1.01E-01, 9.00E-02} , 
+   { 2.75E-01, 2.51E-01, 2.24E-01, 2.69E-01, 2.34E-01, 2.28E-01, 2.30E-01, 1.96E-01, 2.08E-01, 2.27E-01, 2.09E-01, 1.91E-01, 2.14E-01, 1.79E-01, 1.79E-01, 2.05E-01, 1.79E-01, 1.58E-01, 1.88E-01, 1.49E-01, 1.57E-01, 1.30E-01, 1.32E-01, 1.39E-01, 1.32E-01, 1.18E-01, 1.34E-01, 1.05E-01, 9.65E-02, 8.65E-02} , 
+   { 2.35E-01, 2.34E-01, 2.27E-01, 2.17E-01, 2.41E-01, 2.21E-01, 2.01E-01, 1.87E-01, 2.04E-01, 1.85E-01, 1.75E-01, 1.69E-01, 1.79E-01, 1.92E-01, 1.56E-01, 1.79E-01, 1.78E-01, 1.41E-01, 1.45E-01, 1.41E-01, 1.36E-01, 1.44E-01, 1.11E-01, 1.24E-01, 1.13E-01, 1.29E-01, 1.02E-01, 9.30E-02, 9.65E-02, 8.40E-02} , 
+   { 1.89E-01, 1.72E-01, 1.94E-01, 1.94E-01, 2.07E-01, 2.42E-01, 2.02E-01, 1.80E-01, 1.80E-01, 1.54E-01, 1.60E-01, 1.67E-01, 1.57E-01, 1.39E-01, 1.57E-01, 1.46E-01, 1.62E-01, 1.35E-01, 1.29E-01, 1.32E-01, 1.25E-01, 1.13E-01, 1.05E-01, 1.02E-01, 1.12E-01, 9.75E-02, 8.85E-02, 9.10E-02, 7.35E-02, 9.00E-02} , 
+   { 1.56E-01, 1.40E-01, 1.52E-01, 1.70E-01, 1.55E-01, 1.48E-01, 1.54E-01, 1.61E-01, 1.58E-01, 1.54E-01, 1.34E-01, 1.43E-01, 1.40E-01, 1.41E-01, 1.26E-01, 1.17E-01, 1.20E-01, 1.05E-01, 1.11E-01, 1.06E-01, 1.03E-01, 9.50E-02, 1.02E-01, 8.65E-02, 9.45E-02, 9.35E-02, 7.05E-02, 6.70E-02, 7.55E-02, 5.80E-02} , 
+   { 1.50E-01, 1.34E-01, 1.23E-01, 1.50E-01, 1.35E-01, 1.28E-01, 1.32E-01, 1.43E-01, 1.13E-01, 1.20E-01, 1.35E-01, 1.15E-01, 1.07E-01, 1.15E-01, 1.17E-01, 1.09E-01, 1.09E-01, 1.11E-01, 9.85E-02, 9.25E-02, 8.95E-02, 7.65E-02, 8.30E-02, 7.75E-02, 7.05E-02, 7.60E-02, 5.95E-02, 8.25E-02, 6.20E-02, 7.45E-02} , 
+   { 1.29E-01, 1.08E-01, 1.05E-01, 1.28E-01, 1.33E-01, 1.18E-01, 1.11E-01, 1.30E-01, 1.13E-01, 1.01E-01, 1.05E-01, 9.20E-02, 9.35E-02, 9.30E-02, 9.45E-02, 1.17E-01, 1.00E-01, 8.75E-02, 9.15E-02, 8.45E-02, 5.95E-02, 6.50E-02, 7.65E-02, 7.45E-02, 7.05E-02, 7.50E-02, 5.40E-02, 5.75E-02, 5.65E-02, 5.40E-02} , 
+   { 1.46E-01, 1.07E-01, 1.13E-01, 1.08E-01, 1.11E-01, 1.07E-01, 9.65E-02, 9.80E-02, 9.65E-02, 8.60E-02, 8.45E-02, 9.80E-02, 9.05E-02, 1.06E-01, 8.30E-02, 8.35E-02, 7.80E-02, 8.00E-02, 6.80E-02, 7.10E-02, 6.65E-02, 7.10E-02, 7.35E-02, 6.45E-02, 5.40E-02, 5.50E-02, 5.60E-02, 6.30E-02, 5.10E-02, 4.84E-02} , 
+   { 1.15E-01, 9.80E-02, 9.65E-02, 1.08E-01, 1.00E-01, 1.32E-01, 8.25E-02, 9.90E-02, 9.30E-02, 8.40E-02, 8.75E-02, 7.70E-02, 9.30E-02, 7.65E-02, 7.70E-02, 8.00E-02, 7.20E-02, 7.10E-02, 6.90E-02, 6.95E-02, 6.25E-02, 5.90E-02, 7.15E-02, 6.10E-02, 5.10E-02, 5.10E-02, 5.20E-02, 5.80E-02, 6.35E-02, 4.94E-02} , 
+   { 1.13E-01, 1.01E-01, 1.08E-01, 1.16E-01, 8.75E-02, 8.80E-02, 7.55E-02, 8.20E-02, 8.20E-02, 8.80E-02, 8.20E-02, 8.55E-02, 7.40E-02, 6.80E-02, 6.85E-02, 7.40E-02, 6.70E-02, 6.20E-02, 5.85E-02, 5.55E-02, 5.65E-02, 6.15E-02, 5.90E-02, 6.50E-02, 5.20E-02, 5.60E-02, 4.47E-02, 4.64E-02, 3.90E-02, 5.55E-02} , 
+   { 9.35E-02, 7.60E-02, 7.45E-02, 8.60E-02, 8.85E-02, 7.30E-02, 5.95E-02, 6.60E-02, 7.25E-02, 7.05E-02, 7.00E-02, 7.50E-02, 6.90E-02, 7.30E-02, 6.30E-02, 6.45E-02, 6.05E-02, 5.95E-02, 5.60E-02, 5.20E-02, 4.72E-02, 5.25E-02, 5.65E-02, 4.89E-02, 3.86E-02, 4.41E-02, 4.57E-02, 3.96E-02, 4.49E-02, 5.15E-02} , 
+   { 7.65E-02, 6.10E-02, 6.20E-02, 7.85E-02, 6.95E-02, 6.15E-02, 7.50E-02, 7.80E-02, 6.30E-02, 5.60E-02, 4.98E-02, 6.45E-02, 6.05E-02, 4.74E-02, 6.20E-02, 5.50E-02, 5.85E-02, 4.84E-02, 4.11E-02, 4.64E-02, 5.25E-02, 4.39E-02, 4.03E-02, 4.15E-02, 3.31E-02, 3.77E-02, 3.87E-02, 3.65E-02, 4.22E-02, 3.39E-02} , 
+   { 6.55E-02, 5.30E-02, 5.45E-02, 5.90E-02, 5.25E-02, 5.70E-02, 5.75E-02, 5.10E-02, 5.95E-02, 4.73E-02, 5.85E-02, 5.90E-02, 5.35E-02, 5.70E-02, 5.10E-02, 4.50E-02, 5.10E-02, 5.10E-02, 4.80E-02, 4.16E-02, 4.56E-02, 4.21E-02, 4.22E-02, 3.65E-02, 3.55E-02, 3.69E-02, 3.99E-02, 3.91E-02, 3.20E-02, 2.36E-02} , 
+   { 6.05E-02, 4.49E-02, 3.60E-02, 4.88E-02, 6.15E-02, 4.71E-02, 5.40E-02, 4.40E-02, 5.15E-02, 5.30E-02, 4.63E-02, 4.52E-02, 5.95E-02, 6.90E-02, 3.83E-02, 4.28E-02, 4.57E-02, 3.39E-02, 4.74E-02, 4.59E-02, 3.64E-02, 4.23E-02, 4.00E-02, 3.39E-02, 3.47E-02, 2.82E-02, 3.14E-02, 3.44E-02, 2.83E-02, 3.07E-02} , 
+   { 4.42E-02, 3.93E-02, 3.97E-02, 4.28E-02, 4.25E-02, 4.61E-02, 3.78E-02, 3.64E-02, 4.53E-02, 4.21E-02, 4.04E-02, 4.10E-02, 4.33E-02, 4.15E-02, 3.29E-02, 3.88E-02, 3.14E-02, 3.34E-02, 3.60E-02, 3.53E-02, 3.64E-02, 3.60E-02, 2.79E-02, 2.96E-02, 3.28E-02, 2.95E-02, 2.75E-02, 2.83E-02, 2.64E-02, 2.49E-02} , 
+   { 5.20E-02, 3.80E-02, 4.32E-02, 3.51E-02, 3.67E-02, 4.66E-02, 3.98E-02, 3.43E-02, 4.17E-02, 4.25E-02, 3.50E-02, 3.88E-02, 3.69E-02, 3.79E-02, 4.09E-02, 3.51E-02, 3.53E-02, 4.07E-02, 3.25E-02, 3.10E-02, 4.01E-02, 3.75E-02, 2.81E-02, 2.72E-02, 2.77E-02, 2.57E-02, 3.09E-02, 2.49E-02, 2.65E-02, 1.74E-02} , 
+   { 3.84E-02, 3.99E-02, 3.29E-02, 3.76E-02, 3.31E-02, 3.33E-02, 3.40E-02, 3.55E-02, 3.63E-02, 3.01E-02, 3.40E-02, 4.82E-02, 3.13E-02, 4.77E-02, 3.41E-02, 4.30E-02, 3.45E-02, 3.01E-02, 3.07E-02, 2.94E-02, 2.56E-02, 2.21E-02, 2.40E-02, 2.43E-02, 2.66E-02, 2.44E-02, 1.98E-02, 2.55E-02, 2.41E-02, 2.00E-02}
+   };
+
+Double_t dosesmall[20][20] = 
+  {{3.705,3.97,3.43,3.615,3.375,3.27,3.515,3.74,3.29,3.42,3.985,3.415,3.32,3.305,3.765,3.22,3.37,2.855,3.23,3.145},
+   {4.565,4,3.98,3.735,3.995,3.73,3.6,3.495,3.73,4.06,3.865,4.355,3.745,3.535,3.47,3.17,3.835,3.425,3.19,3.29},
+   {  4.65,4.37,4.09,4.29,4.65,4.62,4.04,3.845,4.375,4.09,4.05,4.885,4.35,4.705,3.905,4.06,3.82,3.665,3.61,3.67},
+   { 4.905,4.74,5.1,4.62,4.425,4.625,4.695,4.395,4.685,4.335,4.665,4.575,4.485,4.725,5,4.715,4.055,4.32,4.76,4.225},
+   { 5.55,6.35,5.3,5.15,5.25,5.35,5.05,5.25,5.6,5.4,5.25,4.68,4.645,4.98,4.555,4.935,4.725,4.485,4.51,4.135},
+   { 6,6.55,6.35,6.5,6,5.55,5.65,6.15,5.95,5.75,5.75,5.55,5.6,5.3,4.71,5.15,4.905,5.6,4.565,4.38},
+   { 7.35,7.6,6.9,7.1,6.9,7.05,6.3,6.7,6.45,7.75,5.8,5.7,6,5.6,5.85,5.4,5.9,5.55,5.55,4.835},
+   { 8.65,8.45,18.65,7.6,8,8.9,7.55,7.4,7.7,6.45,8.35,7.5,6.95,7.55,7.2,7.2,7.05,6.1,6.2,5.6},
+   { 11.45,11.5,11.4,11.1,15.25,10.5,9.5,9.15,8.25,8.15,8.35,8.65,8.25,8.7,7.8,7.5,7,6.8,6.7,5.85},
+   { 15.75,16.6,15.9,16.95,14.05,15.8,13.2,12.35,12.95,11.25,10.5,10,9.7,9.85,8.95,8.25,7.9,7.75,7.45,7.3},
+   { 20.8,5.4,20.8,19.05,19.1,17.05,16.55,17.25,13.5,12.65,11.9,12.05,11.15,11.5,10.25,9.65,9.6,8.3,8.95,8.2},
+   { 24.85,23.95,22.6,21.85,22.5,18.9,20.7,22.4,17.05,15.65,13.45,12.05,11.85,10.7,10.5,10.25,9.65,9.3,8.65,7.95},
+   { 3.575,6.7,12.65,22.2,20.35,28.85,18.7,17.55,17.85,16.5,13.95,12.65,12.45,11.7,10.45,9.85,9.15,8.85,8.2,8.8},
+   { 0,0,0,1.665,14.75,27.4,28.7,20,19.75,18.65,26.45,14.3,13.6,13.25,11.5,11.2,10.7,11.1,9,9.15},
+   { 0,0,0,0,0,12.2,26.5,22.45,20.9,20.45,22,17.2,14.75,13.15,13.1,11.3,11.35,9.75,10.85,8.65},
+   { 0,0,0,0,0,0,27.25,27.1,25.65,20.9,22.5,18.65,15.7,13.6,14,11.65,10.65,9.6,9.7,8.45},
+   { 0,0,0,0,0,0,11.8,30.05,26.45,37.8,23.45,22.5,17.3,15.05,13.7,11.65,11.85,10.7,9.95,8.9},
+   { 0,0,0,0,0,0,0,29.65,32.05,26.4,22.95,27.95,17.65,14.6,13.3,12.2,11.9,10.75,10.3,10.1},
+   { 0,0,0,0,0,0,0,13.1,38.05,30.2,35.8,21.65,19.4,15.45,14.05,12.95,12.6,11,10.55,9.5},
+   { 0,0,0,0,0,0,0,8.25,37.85,28.8,32,23.35,19.85,17.65,15.35,12.75,12.35,10.95,10.25,9.35}};
+
+
+TH2F * dosehist50invfb = new TH2F("dosehist50invfb","dosehist50invfb",300,0,300,250,0,250);
+
+for (unsigned int i = 0;i<250;i++){
+  for (unsigned int j = 0;j<300;j++){
+    dosehist50invfb->SetBinContent(j+1,i+1,dosebig[floor(i/10)][floor(j/10)]);
+  }
+ }
+
+
+for (unsigned int i = 0;i<20;i++){
+  for (unsigned int j = 0;j<20;j++){
+    dosehist50invfb->SetBinContent(j+1,20-i,dosesmall[i][j]);
+  }
+ }
+
+dosehist50invfb->Draw("coloz");
+
+}

SimulationData/G4History.macro

@@ -0,0 +1,93 @@
+/event/verbose 0
+/run/verbose 2
+/vis/open OGL 600x600-0+0
+/vis/sceneHandler/create OGL
+/vis/viewer/create ! ! 600x600-0+0
+/vis/viewer/refresh
+/vis/viewer/set/autoRefresh false
+/vis/verbose errors
+/vis/drawVolume
+/vis/scene/create
+/vis/scene/add/volume world -1 -1 none m 0 0 0 0 0 0
+/vis/sceneHandler/attach
+/vis/scene/add/trajectories smooth
+/tracking/storeTrajectory 2
+/vis/scene/notifyHandlers
+/tracking/storeTrajectory 2
+/vis/geometry/set/visibility World 0 false
+/vis/scene/notifyHandlers
+/vis/geometry/set/visibility Detector 0 true
+/vis/scene/notifyHandlers
+/vis/geometry/set/visibility EpoxyBox 0 false
+/vis/scene/notifyHandlers
+/vis/geometry/set/visibility AbsBox 0 false
+/vis/scene/notifyHandlers
+/vis/geometry/set/visibility EpoxyStrip 0 true
+/vis/scene/notifyHandlers
+/vis/geometry/set/visibility Pixel 0 true
+/vis/scene/notifyHandlers
+/vis/geometry/set/visibility Trigger 0 false
+/vis/scene/notifyHandlers
+/vis/geometry/set/colour all 0 0 0 0
+/vis/scene/notifyHandlers
+/vis/geometry/set/colour Cladding2Section 1 0. 0.5 0.5
+/vis/scene/notifyHandlers
+/vis/geometry/set/colour Cladding1Section 0 0.5 0.5 0.5
+/vis/scene/notifyHandlers
+/vis/geometry/set/colour CoreSection 0 0.5 0.0 0.5
+/vis/scene/notifyHandlers
+/vis/geometry/set/colour Pixel 0 0.0 0.5 0.0 1.0
+/vis/scene/notifyHandlers
+/vis/geometry/set/colour EpoxyStrip 0 .90 .90 1.0 .3
+/vis/scene/notifyHandlers
+/vis/geometry/set/colour EpoxyBox 0 0.9 0.9 0.9 1.
+/vis/scene/notifyHandlers
+/vis/geometry/set/colour Detector 0 0.0 0.1 0.1 .0
+/vis/scene/notifyHandlers
+/vis/viewer/set/viewpointVector -1 0 0
+/vis/viewer/set/lightsVector -1 0 0
+/vis/viewer/set/style surface
+/vis/viewer/set/lineSegmentsPerCircle 100
+/vis/viewer/set/targetPoint 0.0 0.0 .250 m
+/vis/viewer/set/viewpointThetaPhi 10 -20
+/vis/viewer/zoomTo 10
+/vis/viewer/set/background white
+/vis/scene/notifyHandlers
+/vis/modeling/trajectories/create/drawByCharge
+/vis/modeling/trajectories/create/drawByCharge
+/vis/modeling/trajectories/drawByCharge-0/default/setDrawStepPts true
+/vis/scene/notifyHandlers scene-0
+/vis/scene/notifyHandlers scene-0
+/vis/modeling/trajectories/drawByCharge-0/default/setStepPtsSize 2
+/vis/scene/notifyHandlers scene-0
+/vis/scene/notifyHandlers scene-0
+/vis/modeling/trajectories/drawByCharge-0/set 1 blue
+/vis/scene/notifyHandlers scene-0
+/vis/modeling/trajectories/drawByCharge-0/set -1 red
+/vis/scene/notifyHandlers scene-0
+/vis/scene/notifyHandlers scene-0
+/vis/modeling/trajectories/list
+/vis/modeling/trajectories/select drawByCharge-0
+/vis/scene/endOfEventAction accumulate
+/vis/viewer/set/autoRefresh true
+/vis/viewer/refresh
+/vis/viewer/refresh
+/vis/verbose warnings
+/gps/particle mu-
+/gps/ene/mono 4 GeV
+/gps/pos/type Plane
+/gps/pos/shape Square
+/gps/pos/halfx 5 mm
+/gps/pos/halfy 5 mm
+/gps/pos/halfz 5 mm
+/gps/pos/rot2 0 0 1
+/gps/pos/centre 0. 5.0 5. mm
+/gps/ang/type iso
+/gps/ang/mintheta 0.0 deg
+/gps/ang/maxtheta 1.0 deg
+/gps/ang/minphi 0.0 deg
+/gps/ang/maxphi 0.1 deg
+/run/beamOn 1
+/vis/scene/notifyHandlers scene-0
+/run/beamOn 1
+/run/beamOn 1

SimulationData/MyAnalysis/GNUmakefile

@@ -0,0 +1,33 @@
+PROGNAME = myanalysis
+SOURCEFILES = myanalysis.C
+OBJS    = $(patsubst %.C, %.o, $(SOURCEFILES))
+
+ROOTCFLAGS   := $(shell root-config --cflags)
+ROOTLIBS     := $(shell root-config --libs)
+ROOTGLIBS    := $(shell root-config --glibs)
+
+GSLCFLAGS   := $(shell gsl-config --cflags)
+GSLLIBS     := $(shell gsl-config --libs)
+GSLGLIBS    := $(shell gsl-config --glibs)
+
+
+
+LDFLAGS       = -O 
+LIBS         += $(ROOTLIBS) $(GSLLIBS)
+CFLAGS       += $(ROOTCFLAGS) $(GSLCFLAGS) 
+
+#  Not sure why Minuit isn't being included -- put in by hand
+#
+LIBS         += -lMinuit
+
+%.o: %.C
+	g++ ${CFLAGS} -std=c++17 -c  -g -o $@ $<
+
+$(PROGNAME):    $(OBJS)
+	g++ -o $@ $(OBJS) $(LDFLAGS) $(LIBS)
+
+test:
+	@echo $(ROOTCFLAGS)
+
+clean:	
+	-rm -f ${PROGNAME} ${OBJS}

SimulationData/MyAnalysis/GNUmakefile~

@@ -0,0 +1,33 @@
+PROGNAME = myanalysis
+SOURCEFILES = myanalysis.C
+OBJS    = $(patsubst %.C, %.o, $(SOURCEFILES))
+
+ROOTCFLAGS   := $(shell root-config --cflags)
+ROOTLIBS     := $(shell root-config --libs)
+ROOTGLIBS    := $(shell root-config --glibs)
+
+GSLCFLAGS   := $(shell gsl-config --cflags)
+GSLLIBS     := $(shell gsl-config --libs)
+GSLGLIBS    := $(shell gsl-config --glibs)
+
+
+
+LDFLAGS       = -O
+LIBS         += $(ROOTLIBS) $(GSLLIBS)
+CFLAGS       += $(ROOTCFLAGS) $(GSLCFLAGS) -std=c++17
+
+#  Not sure why Minuit isn't being included -- put in by hand
+#
+LIBS         += -lMinuit
+
+%.o: %.cc
+	g++ ${CFLAGS} -c  -g -o $@ $<
+
+$(PROGNAME):    $(OBJS)
+	g++ -o $@ $(OBJS) $(LDFLAGS) $(LIBS)
+
+test:
+	@echo $(ROOTCFLAGS)
+
+clean:	
+	-rm -f ${PROGNAME} ${OBJS}

SimulationData/MyAnalysis/myanalysis.C

@@ -0,0 +1,210 @@
+#define myanalysis_cxx
+#include "myanalysis.h"
+#include <TH2.h>
+#include <TStyle.h>
+#include <TCanvas.h>
+#include <TTree.h>
+#include <TFrame.h>
+#include <TH1F.h>
+#include <TBenchmark.h>
+#include <TRandom.h>
+#include <TSystem.h>
+#include <iostream>
+
+void myanalysis::Loop()
+{
+//   In a ROOT session, you can do:
+//      root> .L MyAnalysis/myanalysis.C
+//      root> myanalysis t
+//      root> t.Loop();       // Loop on all entries
+//
+
+//     This is the loop skeleton where:
+//    jentry is the global entry number in the chain
+//    ientry is the entry number in the current Tree
+//  Note that the argument to GetEntry must be:
+//    jentry for TChain::GetEntry
+//    ientry for TTree::GetEntry and TBranch::GetEntry
+//
+//       To read only selected branches, Insert statements like:
+// METHOD1:
+//    fChain->SetBranchStatus("*",0);  // disable all branches
+//    fChain->SetBranchStatus("branchname",1);  // activate branchname
+// METHOD2: replace line
+//    fChain->GetEntry(jentry);       //read all branches
+//by  b_branchname->GetEntry(ientry); //read only this branch
+   if (fChain == 0) return;
+
+   Long64_t nentries = fChain->GetEntriesFast();
+   int lasteventID = 0;
+   int nPhotoelectrons = 0;
+   bool sameEvent_bool = true;
+   int eventDiff = 0;
+   float countphotons = 0;
+   std::vector<int>   unique_detectorCopy_vec;
+   std::vector<int>   hits_detectorCopy_vec;
+
+
+   TFile * outfile = new TFile("myanalysis_out.root", "RECREATE");
+   if ( outfile->IsOpen() ) printf("OUTPUT file opened successfully\n");
+   TH1F * nphotons = new TH1F("nphotons","nphotons per event",500,0,1000);
+   // Create a TTree
+   TTree *t = new TTree("tvec","Tree with vectors");
+   t->Branch("runID_vec",&runID_vec);
+   t->Branch("eventID_vec",&eventID_vec);
+   t->Branch("detNumb_vec",&detNumb_vec);
+   t->Branch("xPixel_vec",&xPixel_vec);
+   t->Branch("yPixel_vec",&yPixel_vec);
+   t->Branch("energy_vec",&energy_vec);
+   t->Branch("wavelength_vec",&wavelength_vec);
+   t->Branch("localtime_vec",&localtime_vec);
+   t->Branch("abstime_vec",&abstime_vec);
+   t->Branch("length_vec",&length_vec);
+   t->Branch("x_vec",&x_vec);
+   t->Branch("y_vec",&y_vec);
+   t->Branch("z_vec",&z_vec);
+   t->Branch("px_vec",&px_vec);
+   t->Branch("py_vec",&py_vec);
+   t->Branch("pz_vec",&pz_vec);
+   t->Branch("vertexX_vec",&vertexX_vec);
+   t->Branch("vertexY_vec",&vertexY_vec);
+   t->Branch("vertexZ_vec",&vertexZ_vec);
+   t->Branch("vertexPx_vec",&vertexPx_vec);
+   t->Branch("vertexPy_vec",&vertexPy_vec);
+   t->Branch("vertexPz_vec",&vertexPz_vec);
+   t->Branch("gpsPosX_vec",&gpsPosX_vec);
+   t->Branch("gpsPosY_vec",&gpsPosY_vec);
+   t->Branch("gpsPosZ_vec",&gpsPosZ_vec);
+   t->Branch("runId_vec",&runId_vec);
+   t->Branch("eventId_vec",&eventId_vec);
+   t->Branch("trackId_vec",&trackId_vec);
+   t->Branch("creatorProcess_vec",&creatorProcess_vec);
+   t->Branch("parentId_vec",&parentId_vec);
+   t->Branch("lengthInCore_vec",&lengthInCore_vec);
+   t->Branch("lengthInInnerCladding_vec",&lengthInInnerCladding_vec);
+   t->Branch("lengthInOuterCladding_vec",&lengthInOuterCladding_vec);
+   //  t->Branch("detectorCopy_vec",&detectorCopy_vec);
+   // t->Branch("subdetectorCopy_vec",&subdetectorCopy_vec);
+   t->Branch("countphotons",&countphotons);
+
+   
+   Long64_t nbytes = 0, nb = 0;
+   for (Long64_t jentry=0; jentry<nentries;jentry++) {
+      Long64_t ientry = LoadTree(jentry);
+      if (ientry < 0) break;
+      nb = fChain->GetEntry(jentry);   nbytes += nb;
+      // if (Cut(ientry) < 0) continue;
+
+      
+
+      if (ientry==0) {lasteventID = eventID;}
+      
+      if(eventID == lasteventID) {sameEvent_bool = true;}
+      else {
+	eventDiff = eventID - lasteventID;
+	sameEvent_bool = false; 
+      }
+
+
+      if (sameEvent_bool == false ){
+
+	lasteventID = eventID;
+
+	for (int kk = 0; kk<eventDiff;kk++){
+	  std::cout << xPixel_vec.size() << std::endl;
+	  countphotons = xPixel_vec.size(); 
+	  nphotons->Fill( xPixel_vec.size() );
+	  t->Fill();
+	
+	  runID_vec.clear();		        
+	  eventID_vec.clear();		        
+	  detNumb_vec.clear();		        
+	  xPixel_vec.clear();		        
+	  yPixel_vec.clear();		        
+	  energy_vec.clear();		        
+	  wavelength_vec.clear();		        
+	  localtime_vec.clear();		        
+	  abstime_vec.clear();		        
+	  length_vec.clear();		        
+	  x_vec.clear();			        
+	  y_vec.clear();			        
+	  z_vec.clear();			        
+	  px_vec.clear();			        
+	  py_vec.clear();			        
+	  pz_vec.clear();			        
+	  vertexX_vec.clear();		        
+	  vertexY_vec.clear();		        
+	  vertexZ_vec.clear();		        
+	  vertexPx_vec.clear();		        
+	  vertexPy_vec.clear();		        
+	  vertexPz_vec.clear();		        
+	  gpsPosX_vec.clear();		        
+	  gpsPosY_vec.clear();		        
+	  gpsPosZ_vec.clear();		        
+	  gpsDirX_vec.clear();		        
+	  gpsDirY_vec.clear();		        
+	  gpsDirZ_vec.clear();		        
+	  runId_vec.clear();		        
+	  eventId_vec.clear();		        
+	  trackId_vec.clear();		        
+	  creatorProcess_vec.clear();	        
+	  parentId_vec.clear();		        
+	  lengthInCore_vec.clear();	        
+	  lengthInInnerCladding_vec.clear();       
+	  lengthInOuterCladding_vec.clear();       
+	  //   detectorCopy_vec.clear();	        
+	  //  subdetectorCopy_vec.clear();             
+	}
+	sameEvent_bool = true;
+      }
+
+      if (sameEvent_bool == true){
+	runID_vec.push_back(runID);
+	eventID_vec.push_back(eventID);
+	detNumb_vec.push_back(detNumb);
+	xPixel_vec.push_back(xPixel);
+	yPixel_vec.push_back(yPixel);
+	energy_vec.push_back(energy);
+	wavelength_vec.push_back(wavelength);
+	localtime_vec.push_back(localtime);
+	abstime_vec.push_back(abstime);
+	length_vec.push_back(length);
+	x_vec.push_back(x);
+	y_vec.push_back(y);
+	z_vec.push_back(z);
+	px_vec.push_back(px);
+	py_vec.push_back(py);
+	pz_vec.push_back(pz);
+	vertexX_vec.push_back(vertexX);
+	vertexY_vec.push_back(vertexY);
+	vertexZ_vec.push_back(vertexZ);
+	vertexPx_vec.push_back(vertexPx);
+	vertexPy_vec.push_back(vertexPy);
+	vertexPz_vec.push_back(vertexPz);
+	gpsPosX_vec.push_back(gpsPosX);
+	gpsPosY_vec.push_back(gpsPosY);
+	gpsPosZ_vec.push_back(gpsPosZ);
+	gpsDirX_vec.push_back(gpsDirX);
+	gpsDirY_vec.push_back(gpsDirY);
+	gpsDirZ_vec.push_back(gpsDirZ);
+	runId_vec.push_back(runId);
+	eventId_vec.push_back(eventId);
+	trackId_vec.push_back(trackId);
+	creatorProcess_vec.push_back(creatorProcess);
+	parentId_vec.push_back(parentId);
+	lengthInCore_vec.push_back(lengthInCore);
+	lengthInInnerCladding_vec.push_back(lengthInInnerCladding);
+	lengthInOuterCladding_vec.push_back(lengthInOuterCladding);
+	//	detectorCopy_vec.push_back(detectorCopy);
+	//   	subdetectorCopy_vec.push_back(subdetectorCopy);
+	
+      }
+      
+
+   
+      
+   }//end of loop
+   outfile->Write();
+
+   delete outfile;  
+}

SimulationData/MyAnalysis/myanalysis.C~

@@ -0,0 +1,205 @@
+#define myanalysis_cxx
+#include "myanalysis.h"
+#include <TH2.h>
+#include <TStyle.h>
+#include <TCanvas.h>
+#include <TTree.h>
+#include <TFrame.h>
+#include <TH1F.h>
+#include <TBenchmark.h>
+#include <TRandom.h>
+#include <TSystem.h>
+#include <iostream>
+
+void myanalysis::Loop()
+{
+//   In a ROOT session, you can do:
+//      root> .L myanalysis.C
+//      root> myanalysis t
+//      root> t.GetEntry(12); // Fill t data members with entry number 12
+//      root> t.Show();       // Show values of entry 12
+//      root> t.Show(16);     // Read and show values of entry 16
+//      root> t.Loop();       // Loop on all entries
+//
+
+//     This is the loop skeleton where:
+//    jentry is the global entry number in the chain
+//    ientry is the entry number in the current Tree
+//  Note that the argument to GetEntry must be:
+//    jentry for TChain::GetEntry
+//    ientry for TTree::GetEntry and TBranch::GetEntry
+//
+//       To read only selected branches, Insert statements like:
+// METHOD1:
+//    fChain->SetBranchStatus("*",0);  // disable all branches
+//    fChain->SetBranchStatus("branchname",1);  // activate branchname
+// METHOD2: replace line
+//    fChain->GetEntry(jentry);       //read all branches
+//by  b_branchname->GetEntry(ientry); //read only this branch
+   if (fChain == 0) return;
+
+   Long64_t nentries = fChain->GetEntriesFast();
+   int lasteventID = 0;
+   int nPhotoelectrons = 0;
+   bool sameEvent_bool = true;
+
+   std::vector<int>   unique_detectorCopy_vec;
+   std::vector<int>   hits_detectorCopy_vec;
+
+
+   TFile * outfile = new TFile("myanalysis_out.root", "RECREATE");
+   if ( outfile->IsOpen() ) printf("OUTPUT file opened successfully\n");
+   // Create a TTree
+   TTree *t = new TTree("tvec","Tree with vectors");
+   t->Branch("runID_vec",&runID_vec);
+   t->Branch("eventID_vec",&eventID_vec);
+   t->Branch("detNumb_vec",&detNumb_vec);
+   t->Branch("xPixel_vec",&xPixel_vec);
+   t->Branch("yPixel_vec",&yPixel_vec);
+   t->Branch("energy_vec",&energy_vec);
+   t->Branch("wavelength_vec",&wavelength_vec);
+   t->Branch("localtime_vec",&localtime_vec);
+   t->Branch("abstime_vec",&abstime_vec);
+   t->Branch("length_vec",&length_vec);
+   t->Branch("x_vec",&x_vec);
+   t->Branch("y_vec",&y_vec);
+   t->Branch("z_vec",&z_vec);
+   t->Branch("px_vec",&px_vec);
+   t->Branch("py_vec",&py_vec);
+   t->Branch("pz_vec",&pz_vec);
+   t->Branch("vertexX_vec",&vertexX_vec);
+   t->Branch("vertexY_vec",&vertexY_vec);
+   t->Branch("vertexZ_vec",&vertexZ_vec);
+   t->Branch("vertexPx_vec",&vertexPx_vec);
+   t->Branch("vertexPy_vec",&vertexPy_vec);
+   t->Branch("vertexPz_vec",&vertexPz_vec);
+   t->Branch("gpsPosX_vec",&gpsPosX_vec);
+   t->Branch("gpsPosY_vec",&gpsPosY_vec);
+   t->Branch("gpsPosZ_vec",&gpsPosZ_vec);
+   t->Branch("runId_vec",&runId_vec);
+   t->Branch("eventId_vec",&eventId_vec);
+   t->Branch("trackId_vec",&trackId_vec);
+   t->Branch("creatorProcess_vec",&creatorProcess_vec);
+   t->Branch("parentId_vec",&parentId_vec);
+   t->Branch("lengthInCore_vec",&lengthInCore_vec);
+   t->Branch("lengthInInnerCladding_vec",&lengthInInnerCladding_vec);
+   t->Branch("lengthInOuterCladding_vec",&lengthInOuterCladding_vec);
+   //  t->Branch("detectorCopy_vec",&detectorCopy_vec);
+   // t->Branch("subdetectorCopy_vec",&subdetectorCopy_vec);
+
+   
+   Long64_t nbytes = 0, nb = 0;
+   for (Long64_t jentry=0; jentry<nentries;jentry++) {
+      Long64_t ientry = LoadTree(jentry);
+      if (ientry < 0) break;
+      nb = fChain->GetEntry(jentry);   nbytes += nb;
+      // if (Cut(ientry) < 0) continue;
+
+      
+
+      if (ientry==0) {lasteventID = eventID;}
+      
+      if(eventID == lasteventID) {sameEvent_bool = true;}
+      else { sameEvent_bool = false; }
+
+
+      if (sameEvent_bool == false ){
+	lasteventID = eventID;
+
+	
+	std::cout << xPixel_vec.size() << " " << uniqCnt << ": ";
+	std::cout << std::endl;
+
+	t->Fill();
+	runID_vec.clear();		        
+	eventID_vec.clear();		        
+	detNumb_vec.clear();		        
+	xPixel_vec.clear();		        
+	yPixel_vec.clear();		        
+	energy_vec.clear();		        
+	wavelength_vec.clear();		        
+	localtime_vec.clear();		        
+	abstime_vec.clear();		        
+	length_vec.clear();		        
+	x_vec.clear();			        
+	y_vec.clear();			        
+	z_vec.clear();			        
+	px_vec.clear();			        
+	py_vec.clear();			        
+	pz_vec.clear();			        
+	vertexX_vec.clear();		        
+	vertexY_vec.clear();		        
+	vertexZ_vec.clear();		        
+	vertexPx_vec.clear();		        
+	vertexPy_vec.clear();		        
+	vertexPz_vec.clear();		        
+	gpsPosX_vec.clear();		        
+	gpsPosY_vec.clear();		        
+	gpsPosZ_vec.clear();		        
+	gpsDirX_vec.clear();		        
+	gpsDirY_vec.clear();		        
+	gpsDirZ_vec.clear();		        
+        runId_vec.clear();		        
+        eventId_vec.clear();		        
+        trackId_vec.clear();		        
+        creatorProcess_vec.clear();	        
+        parentId_vec.clear();		        
+	lengthInCore_vec.clear();	        
+	lengthInInnerCladding_vec.clear();       
+	lengthInOuterCladding_vec.clear();       
+	//   detectorCopy_vec.clear();	        
+	//  subdetectorCopy_vec.clear();             
+	
+	sameEvent_bool = true;
+      }
+
+      if (sameEvent_bool == true){
+	runID_vec.push_back(runID);
+	eventID_vec.push_back(eventID);
+	detNumb_vec.push_back(detNumb);
+	xPixel_vec.push_back(xPixel);
+	yPixel_vec.push_back(yPixel);
+	energy_vec.push_back(energy);
+	wavelength_vec.push_back(wavelength);
+	localtime_vec.push_back(localtime);
+	abstime_vec.push_back(abstime);
+	length_vec.push_back(length);
+	x_vec.push_back(x);
+	y_vec.push_back(y);
+	z_vec.push_back(z);
+	px_vec.push_back(px);
+	py_vec.push_back(py);
+	pz_vec.push_back(pz);
+	vertexX_vec.push_back(vertexX);
+	vertexY_vec.push_back(vertexY);
+	vertexZ_vec.push_back(vertexZ);
+	vertexPx_vec.push_back(vertexPx);
+	vertexPy_vec.push_back(vertexPy);
+	vertexPz_vec.push_back(vertexPz);
+	gpsPosX_vec.push_back(gpsPosX);
+	gpsPosY_vec.push_back(gpsPosY);
+	gpsPosZ_vec.push_back(gpsPosZ);
+	gpsDirX_vec.push_back(gpsDirX);
+	gpsDirY_vec.push_back(gpsDirY);
+	gpsDirZ_vec.push_back(gpsDirZ);
+	runId_vec.push_back(runId);
+	eventId_vec.push_back(eventId);
+	trackId_vec.push_back(trackId);
+	creatorProcess_vec.push_back(creatorProcess);
+	parentId_vec.push_back(parentId);
+	lengthInCore_vec.push_back(lengthInCore);
+	lengthInInnerCladding_vec.push_back(lengthInInnerCladding);
+	lengthInOuterCladding_vec.push_back(lengthInOuterCladding);
+	//	detectorCopy_vec.push_back(detectorCopy);
+	//   	subdetectorCopy_vec.push_back(subdetectorCopy);
+	
+      }
+      
+
+   
+      
+   }//end of loop
+   outfile->Write();
+
+   delete outfile;  
+}

SimulationData/MyAnalysis/myanalysis.h

@@ -0,0 +1,308 @@
+//////////////////////////////////////////////////////////
+// This class has been automatically generated on
+// Tue Apr 21 13:01:22 2020 by ROOT version 6.12/06
+// from TTree DetectedPhotons/Photons detected at the detector strip.
+// found on file: outFile_1.root
+//////////////////////////////////////////////////////////
+
+#ifndef myanalysis_h
+#define myanalysis_h
+
+#include <TROOT.h>
+#include <TChain.h>
+#include <TFile.h>
+#include <vector>
+
+//#ifdef __MAKECINT__
+//#pragma link C++ class vector<float>+;
+//#pragma link C++ class vector<int>+;
+//#endif
+
+// Header file for the classes stored in the TTree if any.
+
+class myanalysis {
+public :
+   TTree          *fChain;   //!pointer to the analyzed TTree or TChain
+   Int_t           fCurrent; //!current Tree number in a TChain
+
+// Fixed size dimensions of array or collections stored in the TTree if any.
+
+   // Declaration of leaf types
+   Float_t   runID;		        
+   Float_t   eventID;		        
+   Float_t   detNumb;		        
+   Float_t   xPixel;		        
+   Float_t   yPixel;		        
+   Float_t   energy;		        
+   Float_t   wavelength;		        
+   Float_t   localtime;		        
+   Float_t   abstime;		        
+   Float_t   length;		        
+   Float_t   x;			        
+   Float_t   y;			        
+   Float_t   z;			        
+   Float_t   px;			        
+   Float_t   py;			        
+   Float_t   pz;			        
+   Float_t   vertexX;		        
+   Float_t   vertexY;		        
+   Float_t   vertexZ;		        
+   Float_t   vertexPx;		        
+   Float_t   vertexPy;		        
+   Float_t   vertexPz;		        
+   Float_t   gpsPosX;		        
+   Float_t   gpsPosY;		        
+   Float_t   gpsPosZ;		        
+   Float_t   gpsDirX;		        
+   Float_t   gpsDirY;		        
+   Float_t   gpsDirZ;		        
+   Int_t     runId;		        
+   Int_t     eventId;		        
+   Int_t     trackId;		        
+   Int_t     creatorProcess;	        
+   Int_t     parentId;		        
+   Int_t     reflMirr;		        
+   Int_t     reflSurf;		        
+   Int_t     reflTotalCladClad;	        
+   Int_t     reflTotalCoreClad;	        
+   Int_t     reflFresnelCladClad;	        
+   Int_t     reflFresnelCoreClad;	        
+   Int_t     refracCladClad;	        
+   Int_t     refracCoreClad;	        
+   Int_t     rayleighScatterings;	        
+   Float_t   lengthInCore;	        
+   Float_t   lengthInInnerCladding;       
+   Float_t   lengthInOuterCladding;       
+   //  Int_t     detectorCopy;	        
+   //  Int_t     subdetectorCopy;             
+
+   // List of branches
+   TBranch        *b_runID;   //!
+   TBranch        *b_eventID;   //!
+   TBranch        *b_detNumb;   //!
+   TBranch        *b_xPixel;   //!
+   TBranch        *b_yPixel;   //!
+   TBranch        *b_energy;   //!
+   TBranch        *b_wavelength;   //!
+   TBranch        *b_localtime;   //!
+   TBranch        *b_abstime;   //!
+   TBranch        *b_length;   //!
+   TBranch        *b_x;   //!
+   TBranch        *b_y;   //!
+   TBranch        *b_z;   //!
+   TBranch        *b_px;   //!
+   TBranch        *b_py;   //!
+   TBranch        *b_pz;   //!
+   TBranch        *b_vertexX;   //!
+   TBranch        *b_vertexY;   //!
+   TBranch        *b_vertexZ;   //!
+   TBranch        *b_vertexPx;   //!
+   TBranch        *b_vertexPy;   //!
+   TBranch        *b_vertexPz;   //!
+   TBranch        *b_gpsPosX;   //!
+   TBranch        *b_gpsPosY;   //!
+   TBranch        *b_gpsPosZ;   //!
+   TBranch        *b_runId;   //!
+   TBranch        *b_eventId;   //!
+   TBranch        *b_trackId;   //!
+   TBranch        *b_creatorProcess;   //!
+   TBranch        *b_parentId;   //!
+   TBranch        *b_reflMirr;   //!
+   TBranch        *b_reflSurf;   //!
+   TBranch        *b_reflTotalCladClad;   //!
+   TBranch        *b_reflTotalCoreClad;   //!
+   TBranch        *b_reflFresnelCladClad;   //!
+   TBranch        *b_reflFresnelCoreClad;   //!
+   TBranch        *b_refracCladClad;   //!
+   TBranch        *b_refracCoreClad;   //!
+   TBranch        *b_rayleighScatterings;   //!
+   TBranch        *b_lengthInCore;   //!
+   TBranch        *b_lengthInInnerCladding;   //!
+   TBranch        *b_lengthInOuterCladding;   //!
+   //  TBranch        *b_detectorCopy;   //!
+   //TBranch        *b_subdetectorCopy;   //!
+
+   myanalysis(TTree *tree=0);
+   virtual ~myanalysis();
+   virtual Int_t    Cut(Long64_t entry);
+   virtual Int_t    GetEntry(Long64_t entry);
+   virtual Long64_t LoadTree(Long64_t entry);
+   virtual void     Init(TTree *tree);
+   virtual void     Loop();
+   virtual Bool_t   Notify();
+   virtual void     Show(Long64_t entry = -1);
+
+   
+   std::vector<float>         runID_vec;
+   std::vector<float>         eventID_vec;
+   std::vector<float>         detNumb_vec;
+   std::vector<float>         xPixel_vec;
+   std::vector<float>         yPixel_vec;
+   std::vector<float>         energy_vec;
+   std::vector<float>         wavelength_vec;
+   std::vector<float>         localtime_vec;
+   std::vector<float>         abstime_vec;
+   std::vector<float>         length_vec;
+   std::vector<float>         x_vec;
+   std::vector<float>         y_vec;
+   std::vector<float>         z_vec;
+   std::vector<float>         px_vec;
+   std::vector<float>         py_vec;
+   std::vector<float>         pz_vec;
+   std::vector<float>         vertexX_vec;
+   std::vector<float>         vertexY_vec;
+   std::vector<float>         vertexZ_vec;
+   std::vector<float>         vertexPx_vec;
+   std::vector<float>         vertexPy_vec;
+   std::vector<float>         vertexPz_vec;
+   std::vector<float>         gpsPosX_vec;
+   std::vector<float>         gpsPosY_vec;
+   std::vector<float>         gpsPosZ_vec;
+   std::vector<float>         gpsDirX_vec;
+   std::vector<float>         gpsDirY_vec;
+   std::vector<float>         gpsDirZ_vec;
+   std::vector<int>           runId_vec;
+   std::vector<int>           eventId_vec;
+   std::vector<int>           trackId_vec;
+   std::vector<int>           creatorProcess_vec;
+   std::vector<int>           parentId_vec;
+   std::vector<int>           reflMirr_vec;
+   std::vector<int>           reflSurf_vec;
+   std::vector<int>           reflTotalCladClad_vec;
+   std::vector<int>           reflTotalCoreClad_vec;
+   std::vector<int>           reflFresnelCladClad_vec;
+   std::vector<int>           reflFresnelCoreClad_vec;
+   std::vector<int>           refracCladClad_vec;
+   std::vector<int>           refracCoreClad_vec;
+   std::vector<int>           rayleighScatterings_vec;
+   std::vector<float>         lengthInCore_vec;
+   std::vector<float>         lengthInInnerCladding_vec;
+   std::vector<float>         lengthInOuterCladding_vec;
+   //  std::vector<int>           detectorCopy_vec;
+   //   std::vector<int>           subdetectorCopy_vec;
+ 
+};
+
+#endif
+
+#ifdef myanalysis_cxx
+myanalysis::myanalysis(TTree *tree) : fChain(0) 
+{
+// if parameter tree is not specified (or zero), connect the file
+// used to generate this class and read the Tree.
+   if (tree == 0) {
+      TFile *f = (TFile*)gROOT->GetListOfFiles()->FindObject("outFile_1.root");
+      if (!f || !f->IsOpen()) {
+         f = new TFile("outFile_1.root");
+      }
+      f->GetObject("DetectedPhotons",tree);
+
+   }
+   Init(tree);
+}
+
+myanalysis::~myanalysis()
+{
+   if (!fChain) return;
+   delete fChain->GetCurrentFile();
+}
+
+Int_t myanalysis::GetEntry(Long64_t entry)
+{
+// Read contents of entry.
+   if (!fChain) return 0;
+   return fChain->GetEntry(entry);
+}
+Long64_t myanalysis::LoadTree(Long64_t entry)
+{
+// Set the environment to read one entry
+   if (!fChain) return -5;
+   Long64_t centry = fChain->LoadTree(entry);
+   if (centry < 0) return centry;
+   if (fChain->GetTreeNumber() != fCurrent) {
+      fCurrent = fChain->GetTreeNumber();
+      Notify();
+   }
+   return centry;
+}
+
+void myanalysis::Init(TTree *tree)
+{
+   // The Init() function is called when the selector needs to initialize
+   // a new tree or chain. Typically here the branch addresses and branch
+   // pointers of the tree will be set.
+   // It is normally not necessary to make changes to the generated
+   // code, but the routine can be extended by the user if needed.
+   // Init() will be called many times when running on PROOF
+   // (once per file to be processed).
+
+   // Set branch addresses and branch pointers
+   if (!tree) return;
+   fChain = tree;
+   fCurrent = -1;
+   fChain->SetMakeClass(1);
+
+   fChain->SetBranchAddress("runID", &runID, &b_runID);
+   fChain->SetBranchAddress("eventID", &eventID, &b_eventID);
+   fChain->SetBranchAddress("detNumb", &detNumb, &b_detNumb);
+   fChain->SetBranchAddress("xPixel", &xPixel, &b_xPixel);
+   fChain->SetBranchAddress("yPixel", &yPixel, &b_yPixel);
+   fChain->SetBranchAddress("energy", &energy, &b_energy);
+   fChain->SetBranchAddress("wavelength", &wavelength, &b_wavelength);
+   fChain->SetBranchAddress("localtime", &localtime, &b_localtime);
+   fChain->SetBranchAddress("abstime", &abstime, &b_abstime);
+   fChain->SetBranchAddress("length", &length, &b_length);
+   fChain->SetBranchAddress("x", &x, &b_x);
+   fChain->SetBranchAddress("y", &y, &b_y);
+   fChain->SetBranchAddress("z", &z, &b_z);
+   fChain->SetBranchAddress("px", &px, &b_px);
+   fChain->SetBranchAddress("py", &py, &b_py);
+   fChain->SetBranchAddress("pz", &pz, &b_pz);
+   fChain->SetBranchAddress("vertexX", &vertexX, &b_vertexX);
+   fChain->SetBranchAddress("vertexY", &vertexY, &b_vertexY);
+   fChain->SetBranchAddress("vertexZ", &vertexZ, &b_vertexZ);
+   fChain->SetBranchAddress("vertexPx", &vertexPx, &b_vertexPx);
+   fChain->SetBranchAddress("vertexPy", &vertexPy, &b_vertexPy);
+   fChain->SetBranchAddress("vertexPz", &vertexPz, &b_vertexPz);
+   fChain->SetBranchAddress("gpsPosX", &gpsPosX, &b_gpsPosX);
+   fChain->SetBranchAddress("gpsPosY", &gpsPosY, &b_gpsPosY);
+   fChain->SetBranchAddress("gpsPosZ", &gpsPosZ, &b_gpsPosZ);
+   fChain->SetBranchAddress("runId", &runId, &b_runId);
+   fChain->SetBranchAddress("eventId", &eventId, &b_eventId);
+   fChain->SetBranchAddress("trackId", &trackId, &b_trackId);
+   fChain->SetBranchAddress("creatorProcess", &creatorProcess, &b_creatorProcess);
+   fChain->SetBranchAddress("parentId", &parentId, &b_parentId);
+   fChain->SetBranchAddress("lengthInCore", &lengthInCore, &b_lengthInCore);
+   fChain->SetBranchAddress("lengthInInnerCladding", &lengthInInnerCladding, &b_lengthInInnerCladding);
+   fChain->SetBranchAddress("lengthInOuterCladding", &lengthInOuterCladding, &b_lengthInOuterCladding);
+   //  fChain->SetBranchAddress("detectorCopy", &detectorCopy, &b_detectorCopy);
+   // fChain->SetBranchAddress("subdetectorCopy", &subdetectorCopy, &b_subdetectorCopy);
+   Notify();
+}
+
+Bool_t myanalysis::Notify()
+{
+   // The Notify() function is called when a new file is opened. This
+   // can be either for a new TTree in a TChain or when when a new TTree
+   // is started when using PROOF. It is normally not necessary to make changes
+   // to the generated code, but the routine can be extended by the
+   // user if needed. The return value is currently not used.
+
+   return kTRUE;
+}
+
+void myanalysis::Show(Long64_t entry)
+{
+// Print contents of entry.
+// If entry is not specified, print current entry
+   if (!fChain) return;
+   fChain->Show(entry);
+}
+Int_t myanalysis::Cut(Long64_t entry)
+{
+// This function may be called from Loop.
+// returns  1 if entry is accepted.
+// returns -1 otherwise.
+   return 1;
+}
+#endif // #ifdef myanalysis_cxx

SimulationData/MyAnalysis/myanalysis.h~

@@ -0,0 +1,308 @@
+//////////////////////////////////////////////////////////
+// This class has been automatically generated on
+// Tue Apr 21 13:01:22 2020 by ROOT version 6.12/06
+// from TTree DetectedPhotons/Photons detected at the detector strip.
+// found on file: outFile_1.root
+//////////////////////////////////////////////////////////
+
+#ifndef myanalysis_h
+#define myanalysis_h
+
+#include <TROOT.h>
+#include <TChain.h>
+#include <TFile.h>
+#include <vector>
+
+//#ifdef __MAKECINT__
+//#pragma link C++ class vector<float>+;
+//#pragma link C++ class vector<int>+;
+//#endif
+
+// Header file for the classes stored in the TTree if any.
+
+class myanalysis {
+public :
+   TTree          *fChain;   //!pointer to the analyzed TTree or TChain
+   Int_t           fCurrent; //!current Tree number in a TChain
+
+// Fixed size dimensions of array or collections stored in the TTree if any.
+
+   // Declaration of leaf types
+   Float_t   runID;		        
+   Float_t   eventID;		        
+   Float_t   detNumb;		        
+   Float_t   xPixel;		        
+   Float_t   yPixel;		        
+   Float_t   energy;		        
+   Float_t   wavelength;		        
+   Float_t   localtime;		        
+   Float_t   abstime;		        
+   Float_t   length;		        
+   Float_t   x;			        
+   Float_t   y;			        
+   Float_t   z;			        
+   Float_t   px;			        
+   Float_t   py;			        
+   Float_t   pz;			        
+   Float_t   vertexX;		        
+   Float_t   vertexY;		        
+   Float_t   vertexZ;		        
+   Float_t   vertexPx;		        
+   Float_t   vertexPy;		        
+   Float_t   vertexPz;		        
+   Float_t   gpsPosX;		        
+   Float_t   gpsPosY;		        
+   Float_t   gpsPosZ;		        
+   Float_t   gpsDirX;		        
+   Float_t   gpsDirY;		        
+   Float_t   gpsDirZ;		        
+   Int_t     runId;		        
+   Int_t     eventId;		        
+   Int_t     trackId;		        
+   Int_t     creatorProcess;	        
+   Int_t     parentId;		        
+   Int_t     reflMirr;		        
+   Int_t     reflSurf;		        
+   Int_t     reflTotalCladClad;	        
+   Int_t     reflTotalCoreClad;	        
+   Int_t     reflFresnelCladClad;	        
+   Int_t     reflFresnelCoreClad;	        
+   Int_t     refracCladClad;	        
+   Int_t     refracCoreClad;	        
+   Int_t     rayleighScatterings;	        
+   Float_t   lengthInCore;	        
+   Float_t   lengthInInnerCladding;       
+   Float_t   lengthInOuterCladding;       
+   Int_t     detectorCopy;	        
+   Int_t     subdetectorCopy;             
+
+   // List of branches
+   TBranch        *b_runID;   //!
+   TBranch        *b_eventID;   //!
+   TBranch        *b_detNumb;   //!
+   TBranch        *b_xPixel;   //!
+   TBranch        *b_yPixel;   //!
+   TBranch        *b_energy;   //!
+   TBranch        *b_wavelength;   //!
+   TBranch        *b_localtime;   //!
+   TBranch        *b_abstime;   //!
+   TBranch        *b_length;   //!
+   TBranch        *b_x;   //!
+   TBranch        *b_y;   //!
+   TBranch        *b_z;   //!
+   TBranch        *b_px;   //!
+   TBranch        *b_py;   //!
+   TBranch        *b_pz;   //!
+   TBranch        *b_vertexX;   //!
+   TBranch        *b_vertexY;   //!
+   TBranch        *b_vertexZ;   //!
+   TBranch        *b_vertexPx;   //!
+   TBranch        *b_vertexPy;   //!
+   TBranch        *b_vertexPz;   //!
+   TBranch        *b_gpsPosX;   //!
+   TBranch        *b_gpsPosY;   //!
+   TBranch        *b_gpsPosZ;   //!
+   TBranch        *b_runId;   //!
+   TBranch        *b_eventId;   //!
+   TBranch        *b_trackId;   //!
+   TBranch        *b_creatorProcess;   //!
+   TBranch        *b_parentId;   //!
+   TBranch        *b_reflMirr;   //!
+   TBranch        *b_reflSurf;   //!
+   TBranch        *b_reflTotalCladClad;   //!
+   TBranch        *b_reflTotalCoreClad;   //!
+   TBranch        *b_reflFresnelCladClad;   //!
+   TBranch        *b_reflFresnelCoreClad;   //!
+   TBranch        *b_refracCladClad;   //!
+   TBranch        *b_refracCoreClad;   //!
+   TBranch        *b_rayleighScatterings;   //!
+   TBranch        *b_lengthInCore;   //!
+   TBranch        *b_lengthInInnerCladding;   //!
+   TBranch        *b_lengthInOuterCladding;   //!
+   TBranch        *b_detectorCopy;   //!
+   TBranch        *b_subdetectorCopy;   //!
+
+   myanalysis(TTree *tree=0);
+   virtual ~myanalysis();
+   virtual Int_t    Cut(Long64_t entry);
+   virtual Int_t    GetEntry(Long64_t entry);
+   virtual Long64_t LoadTree(Long64_t entry);
+   virtual void     Init(TTree *tree);
+   virtual void     Loop();
+   virtual Bool_t   Notify();
+   virtual void     Show(Long64_t entry = -1);
+
+   
+   std::vector<float>         runID_vec;
+   std::vector<float>         eventID_vec;
+   std::vector<float>         detNumb_vec;
+   std::vector<float>         xPixel_vec;
+   std::vector<float>         yPixel_vec;
+   std::vector<float>         energy_vec;
+   std::vector<float>         wavelength_vec;
+   std::vector<float>         localtime_vec;
+   std::vector<float>         abstime_vec;
+   std::vector<float>         length_vec;
+   std::vector<float>         x_vec;
+   std::vector<float>         y_vec;
+   std::vector<float>         z_vec;
+   std::vector<float>         px_vec;
+   std::vector<float>         py_vec;
+   std::vector<float>         pz_vec;
+   std::vector<float>         vertexX_vec;
+   std::vector<float>         vertexY_vec;
+   std::vector<float>         vertexZ_vec;
+   std::vector<float>         vertexPx_vec;
+   std::vector<float>         vertexPy_vec;
+   std::vector<float>         vertexPz_vec;
+   std::vector<float>         gpsPosX_vec;
+   std::vector<float>         gpsPosY_vec;
+   std::vector<float>         gpsPosZ_vec;
+   std::vector<float>         gpsDirX_vec;
+   std::vector<float>         gpsDirY_vec;
+   std::vector<float>         gpsDirZ_vec;
+   std::vector<int>           runId_vec;
+   std::vector<int>           eventId_vec;
+   std::vector<int>           trackId_vec;
+   std::vector<int>           creatorProcess_vec;
+   std::vector<int>           parentId_vec;
+   std::vector<int>           reflMirr_vec;
+   std::vector<int>           reflSurf_vec;
+   std::vector<int>           reflTotalCladClad_vec;
+   std::vector<int>           reflTotalCoreClad_vec;
+   std::vector<int>           reflFresnelCladClad_vec;
+   std::vector<int>           reflFresnelCoreClad_vec;
+   std::vector<int>           refracCladClad_vec;
+   std::vector<int>           refracCoreClad_vec;
+   std::vector<int>           rayleighScatterings_vec;
+   std::vector<float>         lengthInCore_vec;
+   std::vector<float>         lengthInInnerCladding_vec;
+   std::vector<float>         lengthInOuterCladding_vec;
+   std::vector<int>           detectorCopy_vec;
+   std::vector<int>           subdetectorCopy_vec;
+   
+};
+
+#endif
+
+#ifdef myanalysis_cxx
+myanalysis::myanalysis(TTree *tree) : fChain(0) 
+{
+// if parameter tree is not specified (or zero), connect the file
+// used to generate this class and read the Tree.
+   if (tree == 0) {
+      TFile *f = (TFile*)gROOT->GetListOfFiles()->FindObject("outFile_1.root");
+      if (!f || !f->IsOpen()) {
+         f = new TFile("outFile_1.root");
+      }
+      f->GetObject("DetectedPhotons",tree);
+
+   }
+   Init(tree);
+}
+
+myanalysis::~myanalysis()
+{
+   if (!fChain) return;
+   delete fChain->GetCurrentFile();
+}
+
+Int_t myanalysis::GetEntry(Long64_t entry)
+{
+// Read contents of entry.
+   if (!fChain) return 0;
+   return fChain->GetEntry(entry);
+}
+Long64_t myanalysis::LoadTree(Long64_t entry)
+{
+// Set the environment to read one entry
+   if (!fChain) return -5;
+   Long64_t centry = fChain->LoadTree(entry);
+   if (centry < 0) return centry;
+   if (fChain->GetTreeNumber() != fCurrent) {
+      fCurrent = fChain->GetTreeNumber();
+      Notify();
+   }
+   return centry;
+}
+
+void myanalysis::Init(TTree *tree)
+{
+   // The Init() function is called when the selector needs to initialize
+   // a new tree or chain. Typically here the branch addresses and branch
+   // pointers of the tree will be set.
+   // It is normally not necessary to make changes to the generated
+   // code, but the routine can be extended by the user if needed.
+   // Init() will be called many times when running on PROOF
+   // (once per file to be processed).
+
+   // Set branch addresses and branch pointers
+   if (!tree) return;
+   fChain = tree;
+   fCurrent = -1;
+   fChain->SetMakeClass(1);
+
+   fChain->SetBranchAddress("runID", &runID, &b_runID);
+   fChain->SetBranchAddress("eventID", &eventID, &b_eventID);
+   fChain->SetBranchAddress("detNumb", &detNumb, &b_detNumb);
+   fChain->SetBranchAddress("xPixel", &xPixel, &b_xPixel);
+   fChain->SetBranchAddress("yPixel", &yPixel, &b_yPixel);
+   fChain->SetBranchAddress("energy", &energy, &b_energy);
+   fChain->SetBranchAddress("wavelength", &wavelength, &b_wavelength);
+   fChain->SetBranchAddress("localtime", &localtime, &b_localtime);
+   fChain->SetBranchAddress("abstime", &abstime, &b_abstime);
+   fChain->SetBranchAddress("length", &length, &b_length);
+   fChain->SetBranchAddress("x", &x, &b_x);
+   fChain->SetBranchAddress("y", &y, &b_y);
+   fChain->SetBranchAddress("z", &z, &b_z);
+   fChain->SetBranchAddress("px", &px, &b_px);
+   fChain->SetBranchAddress("py", &py, &b_py);
+   fChain->SetBranchAddress("pz", &pz, &b_pz);
+   fChain->SetBranchAddress("vertexX", &vertexX, &b_vertexX);
+   fChain->SetBranchAddress("vertexY", &vertexY, &b_vertexY);
+   fChain->SetBranchAddress("vertexZ", &vertexZ, &b_vertexZ);
+   fChain->SetBranchAddress("vertexPx", &vertexPx, &b_vertexPx);
+   fChain->SetBranchAddress("vertexPy", &vertexPy, &b_vertexPy);
+   fChain->SetBranchAddress("vertexPz", &vertexPz, &b_vertexPz);
+   fChain->SetBranchAddress("gpsPosX", &gpsPosX, &b_gpsPosX);
+   fChain->SetBranchAddress("gpsPosY", &gpsPosY, &b_gpsPosY);
+   fChain->SetBranchAddress("gpsPosZ", &gpsPosZ, &b_gpsPosZ);
+   fChain->SetBranchAddress("runId", &runId, &b_runId);
+   fChain->SetBranchAddress("eventId", &eventId, &b_eventId);
+   fChain->SetBranchAddress("trackId", &trackId, &b_trackId);
+   fChain->SetBranchAddress("creatorProcess", &creatorProcess, &b_creatorProcess);
+   fChain->SetBranchAddress("parentId", &parentId, &b_parentId);
+   fChain->SetBranchAddress("lengthInCore", &lengthInCore, &b_lengthInCore);
+   fChain->SetBranchAddress("lengthInInnerCladding", &lengthInInnerCladding, &b_lengthInInnerCladding);
+   fChain->SetBranchAddress("lengthInOuterCladding", &lengthInOuterCladding, &b_lengthInOuterCladding);
+   fChain->SetBranchAddress("detectorCopy", &detectorCopy, &b_detectorCopy);
+   fChain->SetBranchAddress("subdetectorCopy", &subdetectorCopy, &b_subdetectorCopy);
+   Notify();
+}
+
+Bool_t myanalysis::Notify()
+{
+   // The Notify() function is called when a new file is opened. This
+   // can be either for a new TTree in a TChain or when when a new TTree
+   // is started when using PROOF. It is normally not necessary to make changes
+   // to the generated code, but the routine can be extended by the
+   // user if needed. The return value is currently not used.
+
+   return kTRUE;
+}
+
+void myanalysis::Show(Long64_t entry)
+{
+// Print contents of entry.
+// If entry is not specified, print current entry
+   if (!fChain) return;
+   fChain->Show(entry);
+}
+Int_t myanalysis::Cut(Long64_t entry)
+{
+// This function may be called from Loop.
+// returns  1 if entry is accepted.
+// returns -1 otherwise.
+   return 1;
+}
+#endif // #ifdef myanalysis_cxx

SimulationData/edep.C

@@ -0,0 +1,96 @@
+
+{
+   gROOT->Reset();
+
+   gROOT->Reset();
+   gStyle.SetStripDecimals(0);
+   gStyle.SetPadLeftMargin(.15);
+   gStyle.SetPadRightMargin(.05);
+   gStyle.SetPadBottomMargin(.15);
+   gStyle->SetOptStat(1);
+   gStyle->SetOptFit(0);
+   gStyle->SetOptTitle(1); 
+   
+
+   TCanvas * c1 = new TCanvas("c1","multipads",800,800);
+   gStyle->SetPadBorderMode(0);
+   gStyle->SetFrameBorderMode(0);
+   Float_t small = 1e-5;
+   c1->Divide(1,3,small,small);
+   
+   TFile *_file0 = TFile::Open("Sept142015/outFile_5layer_0.275mm.root");
+   TH1F *h1 = new TH1F("h1","5 layer 0.275mm",200,0.0,0.7);
+   h1->GetYaxis()->SetRangeUser(0,6500);
+
+   TFile *_file1 = TFile::Open("Sept142015/outFile_6layer_0.275mm.root");
+   TH1F *h2 = new TH1F("h2","6 layer 0.275mm",200,0.0,0.7);
+   h2->GetYaxis()->SetRangeUser(0,6500);
+
+   TFile *_file2 = TFile::Open("Sept142015/outFile_7layer_0.300mm.root");
+   TH1F *h3 = new TH1F("h3","7 layer 0.300mm",200,0.0,0.7);
+   h3->GetYaxis()->SetRangeUser(0,6500);
+
+   TFile *_file3 = TFile::Open("Sept142015/outFile_7layer_0.325mm.root");
+   TH1F *h4 = new TH1F("h4","7 layer 0.325mm",200,0.0,0.7);
+   h4->GetYaxis()->SetRangeUser(0,6500);
+
+   TFile *_file4 = TFile::Open("Sept142015/outFile_8layer_0.350mm.root");
+   TH1F *h5 = new TH1F("h5","8 layer 0.350mm",200,0.0,0.7);
+   h5->GetYaxis()->SetRangeUser(0,6500);
+
+   TFile *_file5 = TFile::Open("Sept142015/outFile_8layer_0.375mm.root");
+   TH1F *h6 = new TH1F("h6","8 layer 0.375mm",200,0.0,0.7);
+   h6->GetYaxis()->SetRangeUser(0,6500);
+
+
+
+   _file0->cd();
+   EnergyTrack->Project("h1","edep");
+   _file1->cd();
+   EnergyTrack->Project("h2","edep");
+   _file2->cd();
+   EnergyTrack->Project("h3","edep");
+   _file3->cd();
+   EnergyTrack->Project("h4","edep");
+   _file4->cd();
+   EnergyTrack->Project("h5","edep");
+   _file5->cd();
+   EnergyTrack->Project("h6","edep");
+   
+   c1->cd(1);
+   gPad->SetBottomMargin(small);
+   _file0->cd();
+   h1->Draw();
+   
+   c1->cd(2);
+   gPad->SetTopMargin(small);
+   gPad->SetBottomMargin(small);
+    h2->Draw();
+
+   c1->cd(3);
+   gPad->SetTopMargin(small);
+    h3->Draw();
+
+    TCanvas * c2 = new TCanvas("c2","multipads",800,800);
+   gStyle->SetPadBorderMode(0);
+   gStyle->SetFrameBorderMode(0);
+   Float_t small = 1e-5;
+   c2->Divide(1,3,small,small);
+
+   c2->cd(1);
+   gPad->SetTopMargin(small);
+   gPad->SetBottomMargin(small);
+    h4->Draw();
+
+   c2->cd(2);
+   gPad->SetTopMargin(small);
+   gPad->SetBottomMargin(small);
+   h5->Draw();
+   
+   c2->cd(3);
+   gPad->SetTopMargin(small);
+   gPad->SetTickx();
+   h6->Draw();
+
+
+}      

SimulationData/muongun.mac

@@ -0,0 +1,25 @@
+/control/verbose 0
+/tracking/verbose 0
+/event/verbose 0
+/gps/verbose 0
+
+/gps/particle mu-
+/gps/ene/mono 4 GeV
+/gps/pos/type Plane
+/gps/pos/shape Square
+/gps/pos/halfx 2 mm
+/gps/pos/halfy 2 mm
+/gps/pos/halfz 2 mm
+/gps/pos/rot2 0 0 1 # sets the x-y plane of source in the global x-z plane.
+/gps/pos/centre 0. 5.0 5. mm
+/gps/ang/type iso
+/gps/ang/mintheta   0.0 deg
+/gps/ang/maxtheta   1.0 deg
+/gps/ang/minphi 0.0 deg
+/gps/ang/maxphi 0.1 deg
+
+
+/run/beamOn 200
+#/run/beamOn 10
+
+