First commit

.gitignore

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+/build/
+CMakeLists.txt.user
+GNUmakefile

CMakeLists.txt

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+
+#----------------------------------------------------------------------------
+# Setup the project
+cmake_minimum_required(VERSION 2.6 FATAL_ERROR)
+project(SDDproject)
+
+#----------------------------------------------------------------------------
+# 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)
+
+#----------------------------------------------------------------------------
+# 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(SDD SDD.cc ${sources} ${headers})
+target_link_libraries(SDD ${Geant4_LIBRARIES})
+
+#----------------------------------------------------------------------------
+# Copy all scripts to the build directory, i.e. the directory in which we
+# build SDD. This is so that we can run the executable directly because it
+# relies on these scripts being in the current working directory.
+#
+set(SDD_SCRIPTS
+  SDD.in
+  init_vis.mac
+  vis.mac
+  )
+
+foreach(_script ${SDD_SCRIPTS})
+  configure_file(
+    ${PROJECT_SOURCE_DIR}/${_script}
+    ${PROJECT_BINARY_DIR}/${_script}
+    COPYONLY
+    )
+endforeach()
+
+set(ENV{MYG4VERBOSE} "false")
+
+#----------------------------------------------------------------------------
+# For internal Geant4 use - but has no effect if you build this
+# example standalone
+#
+add_custom_target(SDDproject DEPENDS SDD)
+
+#----------------------------------------------------------------------------
+# Install the executable to 'bin' directory under CMAKE_INSTALL_PREFIX
+#
+install(TARGETS SDD DESTINATION bin)
+
+

History

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+-------------------------------------------------------------------
+
+     =========================================================
+         Silicon drift detector (SDD) simulation on Geant4
+     =========================================================
+
+Author: Kunal Kumar (kunal.kumar@ovgu.de)
+
+Citation: Kumar K, Fachet M, Hoeschen C. High-Spatial-Resolution Benchtop X-ray Fluorescence Imaging 
+through Bragg-Diffraction-Based Focusing with Bent Mosaic Graphite Crystals: A Simulation Study. 
+Int J Mol Sci. 2024 Apr 26;25(9):4733. doi: 10.3390/ijms25094733. PMID: 38731956; PMCID: PMC11083219.
+
+DOI: 10.3390/ijms25094733; PMID: 38731956; PMCID: PMC11083219
+
+
+                       ----------------
+                       SDD History file
+                       ----------------
+
+     ----------------------------------------------------------
+         * Reverse chronological order (last date on top) *
+     ----------------------------------------------------------
+
+15/11/23 K. Kumar
+- Created.

README

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+-------------------------------------------------------------------
+
+     =========================================================
+        Silicon drift detector (SDD) simulation on Geant4
+     =========================================================
+
+                                SDD
+                            -----------
+==========================================================================================================
+
+ This simulation code implements a silicon drift detector (SDD) for x-ray fluorescence and
+ spectrometry applications. The detector parameters are based on Amptek XR100 FastSDD X-ray
+ detector (Amptek Inc., Bedford, MA, USA). 
+
+ Author: Kunal Kumar (kunal.kumar@ovgu.de)
+
+ Citation: Kumar K, Fachet M, Hoeschen C. High-Spatial-Resolution Benchtop X-ray Fluorescence Imaging
+ through Bragg-Diffraction-Based Focusing with Bent Mosaic Graphite Crystals: A Simulation Study.
+ Int J Mol Sci. 2024 Apr 26;25(9):4733. doi: 10.3390/ijms25094733. PMID: 38731956; PMCID: PMC11083219.
+
+ DOI: 10.3390/ijms25094733; PMID: 38731956; PMCID: PMC11083219
+
+ =========================================================================================================
+
+ 1- GEOMETRY DEFINITION
+
+   The geometry is constructed in the SDDDetectorConstruction class. The parameters for geometry are taken
+   from the user manual (Amptek Silicon Drift Detector XR-100FastSDD). Available online: https://www.amptek.com/-/media/ametekamptek/documents/resources/products/user-manuals/xr100-1mm-fastsdd-user-manual-b4.pdf?la=en&revision=24e8eb09-6164-48ba-8336-e572f84bf5c1
+
+ 2- PHYSICS LIST
+
+   The physics list is based on the Geant4 TestEm5 example (electromagnetic/TestEm5/src/PhysicsList.cc).
+   Low-energy EM physics is implemented using the Penelope model.
+
+ 3- PRIMARY GENERATOR
+
+   The primary generator is defined in the SDDPrimaryGeneratorAction class.
+   The default kinematics is a 45 keV monoenergetic gamma pencil beam. See
+   SDD.in.
+
+ 4- SDD DETECTOR MODEL
+
+   The detector model is based on analytical equations implementing Fano noise and electronic noise. The parameters
+   are obtained from the Amptek user manual and application Notes (Amptek Silicon Drift Detector XR-100FastSDD). Available online: https://www.amptek.com/-/media/ametekamptek/documents/resources/application-notes/high-sensitivity-detectors-for-xrf.pdf?la=en&revision=9d04dd37-c2ea-4f89-ad58-55579a8574b1
+
+ 5- HOW TO RUN
+
+    - Execute SDD in the 'interactive mode' with visualization:
+        % ./SDD
+      and type in the commands from SDD.in line by line:  
+        Idle> /control/verbose 2
+        Idle> /tracking/verbose 1
+        Idle> /run/beamOn 10 
+        Idle> ...
+        Idle> exit
+      or
+        Idle> /control/execute SDD.in
+        ....
+        Idle> exit
+
+    - Execute SDD in the 'batch' mode from macro files 
+      (without visualization)
+        % ./SDD SDD.in
+        % ./SDD SDD.in > SDD.out
+
+

SDD.cc

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+//
+// ********************************************************************
+// * License and Disclaimer                                           *
+// *                                                                  *
+// * The  Geant4 software  is  copyright of the Copyright Holders  of *
+// * the Geant4 Collaboration.  It is provided  under  the terms  and *
+// * conditions of the Geant4 Software License,  included in the file *
+// * LICENSE and available at  http://cern.ch/geant4/license .  These *
+// * include a list of copyright holders.                             *
+// *                                                                  *
+// * Neither the authors of this software system, nor their employing *
+// * institutes,nor the agencies providing financial support for this *
+// * work  make  any representation or  warranty, express or implied, *
+// * regarding  this  software system or assume any liability for its *
+// * use.  Please see the license in the file  LICENSE  and URL above *
+// * for the full disclaimer and the limitation of liability.         *
+// *                                                                  *
+// * This  code  implementation is the result of  the  scientific and *
+// * technical work of the GEANT4 collaboration.                      *
+// * By using,  copying,  modifying or  distributing the software (or *
+// * any work based  on the software)  you  agree  to acknowledge its *
+// * use  in  resulting  scientific  publications,  and indicate your *
+// * acceptance of all terms of the Geant4 Software license.          *
+// ********************************************************************
+//
+// GEANT4 tag $Name: SDD-01-00
+//
+// Author: Kunal Kumar (kunal.kumar@ovgu.de)
+//
+// Citation: Kumar K, Fachet M, Hoeschen C. High-Spatial-Resolution Benchtop X-ray Fluorescence Imaging through Bragg-Diffraction-Based Focusing with Bent Mosaic Graphite Crystals: A Simulation Study. Int J Mol Sci. 2024 Apr 26;25(9):4733. doi: 10.3390/ijms25094733. PMID: 38731956; PMCID: PMC11083219.
+//
+// DOI: 10.3390/ijms25094733; PMID: 38731956; PMCID: PMC11083219
+//
+// History:
+// -----------
+// 15 Nov 2023 - Kunal Kumar:     Created. Built using B1 base example
+// -------------------------------------------------------------------
+//
+/// \file SDD.cc
+/// \brief Main program of SDD
+//
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
+
+#include "SDDDetectorConstruction.hh"
+#include "SDDActionInitialization.hh"
+#include "SDDPhysicsList.hh"
+
+#ifdef G4MULTITHREADED
+#include "G4MTRunManager.hh"
+#else
+#include "G4RunManager.hh"
+#endif
+
+#include "G4UImanager.hh"
+#include "G4VisExecutive.hh"
+#include "G4UIExecutive.hh"
+#include "Randomize.hh"
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
+
+int main(int argc,char** argv)
+{
+    // Detect interactive mode (if no arguments) and define UI session
+    //
+    G4UIExecutive* ui = 0;
+    if ( argc == 1 ) {
+        ui = new G4UIExecutive(argc, argv);
+    }
+
+    // Choose the Random engine
+    G4Random::setTheEngine(new CLHEP::RanecuEngine);
+
+    // Construct the default run manager
+    //
+#ifdef G4MULTITHREADED
+    G4MTRunManager* runManager = new G4MTRunManager;
+    runManager->SetNumberOfThreads(8);
+#else
+    G4RunManager* runManager = new G4RunManager;
+#endif
+
+    //
+    // Set mandatory initialization classes
+    //
+
+    G4bool visualize = false;
+    if (ui)
+        visualize = true;
+
+
+    // Detector construction
+    runManager->SetUserInitialization(new SDDDetectorConstruction(visualize));
+
+    // Physics list
+    G4VModularPhysicsList* physicsList = new SDDPhysicsList();
+    runManager->SetUserInitialization(physicsList);
+
+    // User action initialization
+    runManager->SetUserInitialization(new SDDActionInitialization());
+
+    G4VisManager* visManager = NULL;
+    if (ui)
+    {
+        visManager = new G4VisExecutive;
+        visManager->Initialize();
+    }
+
+    // Pointer to UI manager
+    G4UImanager* UImanager = G4UImanager::GetUIpointer();
+
+    // Macro or UI session
+    //
+    if ( ! ui )
+    {
+        // batch mode
+        G4String command = "/control/execute ";
+        G4String fileName = argv[1];
+        UImanager->ApplyCommand(command+fileName);
+    }
+    else
+    {
+        // interactive mode
+        UImanager->ApplyCommand("/control/execute init_vis.mac");
+        ui->SessionStart();
+        delete ui;
+    }
+
+    if (ui)
+    {
+        delete visManager;
+    }
+    delete runManager;
+}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....

SDD.in

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+# Macro file for SDD
+
+/control/verbose 0
+/tracking/verbose 0
+/run/verbose 0
+
+#
+/run/initialize
+
+#
+# Energy loss setup and maximum post-step interaction length
+/process/eLoss/fluct false
+/process/eLoss/StepFunction 1 1 mm
+/process/em/fluo true
+/process/em/auger true
+/process/em/pixe true
+
+### Spatial (beam) properties ##############
+
+/gps/pos/type Beam
+/gps/pos/shape Circle
+/gps/pos/centre 0. 0. 200. mm
+/gps/pos/rot1 1 0 0
+/gps/pos/rot2 0 1 0
+/gps/pos/halfx 0.16 mm
+/gps/pos/halfy 0.16 mm
+/gps/pos/sigma_x 0.13588 mm
+/gps/pos/sigma_y 0.13588  mm
+
+### Energy (beam) properties ##############
+
+## Monochromatic incident photon energies
+/gps/ene/type Gauss
+/gps/ene/mono 45.0 keV
+/gps/ene/sigma 0.2 keV
+
+## Polychromatic incident photon energy distribution (needs a text file)
+#/gps/ene/type Arb
+#/gps/hist/type arb
+#/control/execute myFile.hist
+#/gps/hist/inter Lin
+
+### Angular (beam) properties ##############
+
+/gps/ang/type iso
+/gps/ang/rot1 1 0 0
+/gps/ang/rot2 0 1 0
+/gps/ang/mintheta 0 deg
+/gps/ang/maxtheta 0.01 deg
+/gps/ang/minphi 0 deg
+/gps/ang/maxphi 360 deg
+
+##########################################
+
+/run/printProgress 1000000
+
+#/run/beamOn  50000000