add cmake file

CMakeLists.txt

+#----------------------------------------------------------------------------
+# Setup the project
+cmake_minimum_required(VERSION 2.6 FATAL_ERROR)
+project(Ge2SOS)
+
+#----------------------------------------------------------------------------
+# 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
+#
+include(${Geant4_USE_FILE})
+
+#----------------------------------------------------------------------------
+# Locate sources and headers for this project
+#
+include_directories(${PROJECT_SOURCE_DIR}/include 
+                    ${Geant4_INCLUDE_DIR})
+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(Ge2SOS Ge2SOS.cc ${sources} ${headers})
+target_link_libraries(Ge2SOS ${Geant4_LIBRARIES} )
+
+#----------------------------------------------------------------------------
+# Copy all scripts to the build directory, i.e. the directory in which we
+# build OpNovice. This is so that we can run the executable directly because it
+# relies on these scripts being in the current working directory.
+#
+set(Ge2SOS_SCRIPTS
+    vis.mac
+    gui.mac
+    )
+
+foreach(_script ${Ge2SOS_SCRIPTS})
+  configure_file(
+    ${PROJECT_SOURCE_DIR}/${_script}
+    ${PROJECT_BINARY_DIR}/${_script}
+    COPYONLY
+    )
+endforeach()
+
+#----------------------------------------------------------------------------
+# Install the executable to 'bin' directory under CMAKE_INSTALL_PREFIX
+#
+install(TARGETS Ge2SOS DESTINATION bin)
+

scan_att.sh

+#!/bin/sh
+for thick in {1..1..1}
+do
+        echo $thick
+	for job in {1..5..1}
+	do
+		for energy in {1..10..1} 
+		do
+			 FILE="run_E_${energy}_collimator_thickness_${thick}mm_job_${job}.mac"
+
+			 /bin/cat <<EOM >$FILE
+/process/em/fluo true
+/process/em/auger true
+/process/em/augerCascade true
+/process/em/pixe true
+
+/Ge2SOS/det/setOutputDirectory /nfs/tegile/work/experiences/detecteurs/manzanillas/LEAPS_INNOV/Geant4_output/
+#select detector type: options are 0: detector without collimator and direct beam, 1 detector with collimator and direct beam, 2 and 3 same as 0 and 1 but with sample and beam on sample
+/Ge2SOS/det/setDetectorType 0
+/Ge2SOS/det/setSetupName run_${job}
+#select output format, options are: csv root hdf5
+/Ge2SOS/det/setDataType csv
+/Ge2SOS/det/setNTargetSamples 1
+/Ge2SOS/det/setGeDetectorThickness 4. mm
+/Ge2SOS/det/setCollimatorThickness ${thick}. mm
+#select material of the collimator, recomended options: titanium_grade1, titanium_grade2, tungsten_alloy, G4_BRASS, G4_Pb
+/Ge2SOS/det/setCollimatorMat G4_Pb
+/Ge2SOS/det/setBeWindowRadius 16.0 mm
+#Set the position of the collimator, a values between -37 and 37 mm (size of samples)
+#Choise of source type: 0 gamma,1 Fe-55,2 Cs-137; 1 Bi-207; 2 Sr-90; 3 e-
+/run/initialize
+/Ge2SOS/gun/sourceType 0
+/Ge2SOS/gun/sourceDiameter 16.0 mm
+/Ge2SOS/gun/sourceEnergy ${energy}.0  keV
+
+/run/beamOn 500000
+EOM
+		FILEJOB="job_E_${energy}_${thick}mm_job_${job}.sh"
+
+                /bin/cat <<EOM >$FILEJOB
+#!/bin/bash
+#SBATCH -n 1
+#SBATCH --qos=parallel
+#SBATCH --partition=sumo
+#SBATCH --time=2:00:00
+#SBATCH --cpus-per-task=2
+#
+source ~/environment_GeSOS.sh
+./Ge2SOS -m run_E_${energy}_collimator_thickness_${thick}mm_job_${job}.mac 
+exit 0
+EOM
+sbatch $FILEJOB
+		done
+
+	done
+done
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