Import Geant4 10.0.0 source tree

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+#----------------------------------------------------------------------------
+# Setup the project
+cmake_minimum_required(VERSION 2.6 FATAL_ERROR)
+project(dnageometry)
+
+#----------------------------------------------------------------------------
+# 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(dnageometry dnageometry.cc ${sources} ${headers})
+target_link_libraries(dnageometry ${Geant4_LIBRARIES} )
+
+#----------------------------------------------------------------------------
+# Copy all scripts to the build directory, i.e. the directory in which we
+# build microdosimetry. This is so that we can run the executable directly because it
+# relies on these scripts being in the current working directory.
+#
+set(dnageometry_SCRIPTS
+    dnageometry.mac vis.mac 
+    chromo1.dat 
+    chromo2.dat 
+    chromo3.dat 
+    chromo4.dat 
+    chromo5.dat 
+    chromo6.dat 
+    chromo7.dat 
+    chromo8.dat 
+    chromo9.dat 
+    chromo10.dat 
+    chromo11.dat 
+    chromo12.dat 
+    chromo13.dat 
+    chromo14.dat 
+    chromo15.dat 
+    chromo16.dat 
+    chromo17.dat 
+    chromo18.dat 
+    chromo19.dat 
+    chromo20.dat 
+    chromo21.dat 
+    chromo22.dat 
+    chromoX.dat 
+    chromoY.dat 
+  )
+
+foreach(_script ${dnageometry_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 dnageometry DESTINATION bin)
+
@@ -0,0 +1,13 @@
+     =========================================================
+ 		      Geant4 - dnageometry example
+     =========================================================
+
+                       Package History file
+                       --------------------
+
+26 Nov 2013 - L. Pandola, C. Villagrasa - tag dnageometry-V09-06-01
+- Updated README
+
+17 Sep 2013 - C. Villagrasa, S.Incerti - tag dnageometry-V09-06-00
+- Created example
+
@@ -0,0 +1,91 @@
+     =========================================================
+ 		  Geant4 - dnageometry example
+     =========================================================
+
+                                README file
+                          ----------------------
+
+                           CORRESPONDING AUTHOR 
+
+For any question, please contact:
+C. Villagrasa
+email: carmen.villagrasa@irsn.fr
+
+This example is provided by the Geant4-DNA collaboration
+Any report or published results obtained using the Geant4-DNA software 
+and the DNA geometry given in the Geom_DNA example 
+shall cite the following Geant4-DNA collaboration publications:
+[1] NIM B 298 (2013) 47-54
+[2] Med. Phys. 37 (2010) 4692-4708
+
+
+---->0. INTRODUCTION.                                                    
+                                                                       
+The dnageometry example offers the basic tools to simulate the track structure of different charge particles within a
+simplified geometrical model of the DNA molecule contained in a cell nucleus. 
+In this example, the DetectorConstruction file contains the placement of the 6 Gbp (base-pairs) of a human cell respecting five compaction levels in the structure of the DNA molecule: double helix, nucleosome, chromatin fiber, simple chromatin fiber loop and complex chromatin fiber loops.
+These complex chromatin fiber loops are then used to fill the chromosome territories using a constant density (~30-31 kbp/µm3.
+Even though this geometry defines different volumes for the DNA base, the back-bone region or the histone proteins, the material filling all these volumes in the simulation is liquid water (“G4_WATER”)
+
+In order to simulate all the energy transfer points of the track at nanometric level, the Geant4-DNA physics processes and models are used. 
+These processes and models are further described at:
+http://geant4-dna.org
+
+---->1. GEOMETRY SET-UP.
+ 
+As indicated in the introduction, the whole DNA molecule contained in a human cell with 5 different compaction levels is described in this geometry. In order to place the complex chromatin loops in each of the 43 chromosome territories, the files called “chromo-number.dat” are needed. 
+These 43 chromosome territories are then placed in an ellipsoid that has the typical dimensions of a human fibroblast cell nucleus.
+All the volumes in the geometry are made of liquid water (G4_WATER
+material) despite of what they geometrically represent.
+Particles are shot from a random (x,y)position covering the main central part of the cell nucleus and at z=2.99 µm from the center of the nucleus. This value allows the primary particle to be either inside the cell nucleus, either not far from the entrance surface so its energy loss before the cell nucleus entrance is negligible. 
+
+---->2. SET-UP 
+                                                                        
+Make sure G4LEDATA points to the low energy electromagnetic data files.
+
+The variable G4ANALYSIS_USE must be set to 1.
+
+The code can be compiled with gmake.
+
+---->3. HOW TO RUN THE EXAMPLE                                         
+
+In interactive mode, run:
+
+> $G4WORDIR/bin/$G4SYSTEM/dnageometry
+
+The macro dnageometry.mac is executed by default. A proton of 0.1 MeV is shot. This energy has been chosen because only a few minutes are needed for the proton to lose all its energy and thus the event to finish. Nevertheless, one should keep in mind that for this energy, protons do not traverse the whole cell nucleus width. 
+
+Visualization (DAWN) is not activated by default in dnageometry.mac. To get visualization, make sure to uncomment the #/control/execute vis.mac.
+We would like to warn the users that the time to visualize the whole DNA structure is extremely long.
+
+---->4. PHYSICS
+
+This example uses the Geant4-DNA processes, using the G4EmDNAPhysics constructor as in the dnaphysics example.
+
+---->5. SIMULATION OUTPUT AND RESULT ANALYZIS                                    
+
+The output results consist in a dnageometry.root file, containing only the information about the energy transfers located in the backbone region of the DNA double helix. Both strands are distinguished with different flags (1 or 2):
+- the type of particle for the current step
+- the type of process for the current step
+- the flag of the strand (1 or 2)
+- the track position of the current energy transfer (in nanometers) 
+- the energy deposit corresponding to the energy transfer (in eV)
+- the total energy loss along the current step (in eV)
+- the step length (in nm)
+
+
+This file can be easily analyzed using for example the provided ROOT macro 
+file plot.C; to do so :
+* be sure to have ROOT installed on your machine
+* be sure to be in the directory containing the ROOT files created by dnageometry
+* copy plot.C into this directory
+* from there, launch ROOT by typing root
+* under your ROOT session, type in : .X plot.C to execute the macro file
+* alternatively you can type directly under your session : root plot.C
+
+The naming scheme on the displayed ROOT plots can be seen in the SteppingAction.cc file.
+
+-------------------------------------------------------------------------
+
+
+
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+-277	277	-107.9	80.5085
+523	277	-107.9	-75.127
+-277	-523	-107.9	12.1997
+523	-523	-107.9	11.6449
+-523	523	-35.8	59.4937
+277	523	-35.8	17.6911
+-523	-277	-35.8	5.27645
+277	-277	-35.8	-34.4691
+-277	277	36.3	22.9216
+523	277	36.3	-86.5146
+-277	-523	36.3	82.7877
+523	-523	36.3	-34.4475
+-523	523	108.4	-8.50219
+277	523	108.4	-80.0714
+-523	-277	108.4	23.8609
+277	-277	108.4	-84.9823
+-277	277	180.5	22.7545
+523	277	180.5	-63.7451
+-277	-523	180.5	-42.2277
+523	-523	180.5	75.1419
+277	523	252.6	-0.527827
+-523	-277	252.6	-51.9576
+277	-277	252.6	0.873703
+-277	277	324.7	-51.7061
+523	277	324.7	-47.4331
+-277	-523	324.7	-61.6371
+523	-523	324.7	-48.8787
+-523	523	396.8	38.9275
+277	523	396.8	27.6496
+-523	-277	396.8	63.0528
+277	-277	396.8	83.5597
+-277	277	468.9	18.158
+523	277	468.9	77.9259
+-277	-523	468.9	5.75934
+523	-523	468.9	-60.1971
+-523	523	541	47.4196
+277	523	541	-66.5496
+-523	-277	541	35.0794
+277	-277	541	-77.0496
+-277	277	613.1	46.372
+523	277	613.1	38.5648
+-277	-523	613.1	-84.2619
+523	-523	613.1	-78.0755
+-523	523	685.2	-59.9374
+277	523	685.2	-74.3333
+-523	-277	685.2	35.7854
+277	-277	685.2	-54.9197
+-277	277	757.3	38.4212
+523	277	757.3	62.0403
+-277	-523	757.3	-7.14744
+523	-523	757.3	23.5631
+-523	523	829.4	-28.4875
+277	523	829.4	30.8949
+-523	-277	829.4	-65.5632
+277	-277	829.4	9.80635
+-277	277	901.5	73.4618
+523	277	901.5	-37.2002
+-277	-523	901.5	50.9277
+523	-523	901.5	22.3893
@@ -0,0 +1,122 @@
+//
+// ********************************************************************
+// * 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.          *
+// ********************************************************************
+//
+// This example is provided by the Geant4-DNA collaboration
+// Any report or published results obtained using the Geant4-DNA software 
+// and the DNA geometry given in the Geom_DNA example 
+// shall cite the following Geant4-DNA collaboration publications:
+// [1] NIM B 298 (2013) 47-54
+// [2] Med. Phys. 37 (2010) 4692-4708
+// The Geant4-DNA web site is available at http://geant4-dna.org
+//
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+
+#include "G4RunManager.hh"
+
+#include "G4UImanager.hh"
+#include "G4UIterminal.hh"
+#include "G4UItcsh.hh"
+
+#ifdef G4VIS_USE
+  #include "G4VisExecutive.hh"
+#endif
+
+#include "DetectorConstruction.hh"
+#include "PhysicsList.hh"
+#include "PrimaryGeneratorAction.hh"
+#include "RunAction.hh"
+#include "SteppingAction.hh"
+#include "HistoManager.hh"
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+
+int main(int argc,char** argv) 
+{
+  // Choose the Random engine
+  
+  G4Random::setTheEngine(new CLHEP::RanecuEngine);
+
+  // Construct the default run manager
+  G4RunManager * runManager = new G4RunManager;
+
+  // Set mandatory user initialization classes
+  DetectorConstruction* detector = new DetectorConstruction;
+  runManager->SetUserInitialization(detector);
+  
+  runManager->SetUserInitialization(new PhysicsList);
+
+  // Set mandatory user action classes
+  runManager->SetUserAction(new PrimaryGeneratorAction(detector));
+  PrimaryGeneratorAction* primary = new PrimaryGeneratorAction(detector);
+
+  HistoManager*  histo = new HistoManager();
+
+  // Set optional user action classes
+  RunAction* RunAct = new RunAction(detector,histo);
+  runManager->SetUserAction(RunAct);
+
+  runManager->SetUserAction(new SteppingAction(RunAct,detector,primary,histo));
+  
+#ifdef G4VIS_USE
+  G4VisManager* visManager = new G4VisExecutive;
+  visManager->Initialize();
+#endif
+   
+  // Initialize G4 kernel
+  runManager->Initialize();
+    
+  remove ("geom_dna.root");  
+    
+  // Get the pointer to the User Interface manager 
+  G4UImanager* UImanager = G4UImanager::GetUIpointer();  
+
+  if (argc==1)   // Define UI session for interactive mode.
+  { 
+#ifdef _WIN32
+    G4UIsession * session = new G4UIterminal();
+#else
+    G4UIsession * session = new G4UIterminal(new G4UItcsh);
+#endif
+    UImanager->ApplyCommand("/control/execute dnageometry.mac");    
+    session->SessionStart();
+    delete session;
+  }
+  else           // Batch mode
+  { 
+    G4String command = "/control/execute ";
+    G4String fileName = argv[1];
+    UImanager->ApplyCommand(command+fileName);
+  }
+
+#ifdef G4VIS_USE
+  delete visManager;
+#endif
+
+  delete runManager;
+
+  return 0;
+}
+
@@ -0,0 +1,6 @@
+#/control/execute vis.mac
+/tracking/verbose 0 
+/gun/particle proton
+/gun/energy 0.1 MeV
+/run/initialize
+/run/beamOn 1
@@ -0,0 +1,90 @@
+//
+// ********************************************************************
+// * 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.          *
+// ********************************************************************
+//
+// This example is provided by the Geant4-DNA collaboration
+// Any report or published results obtained using the Geant4-DNA software 
+// and the DNA geometry given in the Geom_DNA example 
+// shall cite the following Geant4-DNA collaboration publications:
+// [1] NIM B 298 (2013) 47-54
+// [2] Med. Phys. 37 (2010) 4692-4708
+// The Geant4-DNA web site is available at http://geant4-dna.org
+//
+
+
+#ifndef ChromosomeParameterisation_H
+#define ChromosomeParameterisation_H 1
+
+#include "G4VPVParameterisation.hh"
+#include "G4ThreeVector.hh"
+#include "G4RotationMatrix.hh"
+#include <vector>
+
+class G4VPhysicalVolume;
+class G4Box;
+class G4Trd;
+class G4Trap;
+class G4Cons;
+class G4Orb;
+class G4Sphere;
+class G4Torus;
+class G4Para;
+class G4Hype;
+class G4Tubs;
+class G4Polycone;
+class G4Polyhedra;
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
+
+class ChromosomeParameterisation : public G4VPVParameterisation
+{ 
+public:
+  ChromosomeParameterisation(const char* filename);
+
+  virtual ~ChromosomeParameterisation();
+  inline int getNumRosettes() { return fPositions.size(); }
+   
+  void ComputeTransformation(const G4int copyNo,
+			     G4VPhysicalVolume* physVol) const;
+    
+  void ComputeDimensions (G4Tubs& rosette, const G4int copyNo, const G4VPhysicalVolume* physVol) const;
+
+private:  // Dummy declarations to get rid of warnings ...
+  void ComputeDimensions (G4Box&, const G4int, const G4VPhysicalVolume*) const {}
+  void ComputeDimensions (G4Trd&,const G4int,const G4VPhysicalVolume*) const {}
+  void ComputeDimensions (G4Trap&,const G4int,const G4VPhysicalVolume*) const {}
+  void ComputeDimensions (G4Cons&,const G4int,const G4VPhysicalVolume*) const {}
+  void ComputeDimensions (G4Sphere&,const G4int,const G4VPhysicalVolume*) const {}
+  void ComputeDimensions (G4Orb&,const G4int,const G4VPhysicalVolume*) const {}
+  void ComputeDimensions (G4Torus&,const G4int,const G4VPhysicalVolume*) const {}
+  void ComputeDimensions (G4Para&,const G4int,const G4VPhysicalVolume*) const {}
+  void ComputeDimensions (G4Hype&,const G4int,const G4VPhysicalVolume*) const {}
+  void ComputeDimensions (G4Polycone&,const G4int,const G4VPhysicalVolume*) const {}
+  void ComputeDimensions (G4Polyhedra&,const G4int,const G4VPhysicalVolume*) const {}
+
+  std::vector<G4ThreeVector*> fPositions;
+  std::vector<G4RotationMatrix*> fRotations;
+};
+
+#endif
@@ -0,0 +1,126 @@
+//
+// ********************************************************************
+// * 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.          *
+// ********************************************************************
+//
+// This example is provided by the Geant4-DNA collaboration
+// Any report or published results obtained using the Geant4-DNA software 
+// and the DNA geometry given in the Geom_DNA example 
+// shall cite the following Geant4-DNA collaboration publications:
+// [1] NIM B 298 (2013) 47-54
+// [2] Med. Phys. 37 (2010) 4692-4708
+// The Geant4-DNA web site is available at http://geant4-dna.org
+//
+//
+#ifndef DetectorConstruction_h
+#define DetectorConstruction_h 1
+
+#include "G4VUserDetectorConstruction.hh"
+#include "G4VPhysicalVolume.hh"
+#include "G4LogicalVolume.hh"
+#include "G4Box.hh"
+#include "G4Tubs.hh"
+#include "G4Ellipsoid.hh"
+#include "G4Orb.hh"
+#include "G4Trd.hh"
+#include "G4Trap.hh"
+#include "G4Torus.hh"
+#include "G4UnionSolid.hh"
+#include "G4Material.hh"
+#include "G4NistManager.hh"
+#include "G4PVPlacement.hh"
+#include "G4UserLimits.hh"
+#include "G4VisAttributes.hh"
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+
+
+class DetectorConstruction : public G4VUserDetectorConstruction
+{
+public:
+
+  DetectorConstruction();
+
+  ~DetectorConstruction();
+
+  G4VPhysicalVolume* Construct();
+                         
+private:
+   
+  G4VPhysicalVolume* physiWorld;
+  G4LogicalVolume*   logicWorld;
+  G4Box*             solidWorld;
+
+  G4VPhysicalVolume* physiTin;
+  G4LogicalVolume*   logicTin;
+  G4Box*             solidTin;
+
+  G4VPhysicalVolume* physiNucleus;
+  G4LogicalVolume*   logicNucleus;
+  G4Ellipsoid*       solidNucleus;
+
+  G4Tubs*            solidBoxros;
+  G4VPhysicalVolume* physiBox[48];
+  G4VPhysicalVolume* physiBoxros[48];
+  G4LogicalVolume*   logicBoxros;
+
+  G4RotationMatrix*  rotTrap;
+  G4ThreeVector      posTrap;
+
+  G4VPhysicalVolume* physiEnv;
+  G4LogicalVolume*   logicEnv;
+
+  G4LogicalVolume*   logicHistone;
+  G4Tubs*            solidHistone;
+
+  G4VPhysicalVolume* physiBp1[200];
+  G4LogicalVolume*   logicBp1;
+  G4Orb*             solidBp1;
+
+  G4VPhysicalVolume* physiBp2[200];
+  G4LogicalVolume*   logicBp2;
+  G4Orb*             solidBp2;
+
+  G4Orb*             solidSugar1;
+  G4Orb*             solidSugar2;
+  G4Orb*             solidSugar3;
+  G4Orb*             solidSugar4;
+
+  G4LogicalVolume*   logicSphere3;
+  G4Orb*             solidSphere3;
+
+  G4LogicalVolume*   logicSphere4;
+  G4Orb*             solidSphere4;
+
+  G4UnionSolid* uniDNA;
+  G4UnionSolid* uniDNA2;
+
+
+  G4Material*        waterMaterial;
+
+
+  void DefineMaterials();
+  G4VPhysicalVolume* ConstructDetector();     
+  void LoadChromosome(const char* filename, G4VPhysicalVolume* physiBox);
+};
+#endif
@@ -0,0 +1,107 @@
+//
+// ********************************************************************
+// * 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.          *
+// ********************************************************************
+//
+//---------------------------------------------------------------------------
+//
+// ClassName:   G4ElectronCapture
+//
+// Description: The process to kill e- to save CPU
+//
+// Author:      V.Ivanchenko 31 August 2010
+//
+//----------------------------------------------------------------------------
+//
+// Class description:
+//
+// G4ElectronCapture allows to remove unwanted e- from simulation in 
+// order to improve CPU performance. There are two parameters:
+//                 
+// 1) low energy threshold for e- kinetic energy (default 0)
+// 2) the name of G4Region where process is active
+// 
+//
+// If an electron track is killed then energy deposition is added to the step 
+//
+// This example is provided by the Geant4-DNA collaboration
+// Any report or published results obtained using the Geant4-DNA software 
+// and the DNA geometry given in the Geom_DNA example 
+// shall cite the following Geant4-DNA collaboration publications:
+// [1] NIM B 298 (2013) 47-54
+// [2] Med. Phys. 37 (2010) 4692-4708
+// The Geant4-DNA web site is available at http://geant4-dna.org
+//
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
+
+#ifndef ElectronCapture_h
+#define ElectronCapture_h 1
+
+#include "G4VDiscreteProcess.hh"
+#include "globals.hh"
+#include "G4ParticleChangeForGamma.hh"
+
+class G4Region;
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
+
+class G4ElectronCapture : public G4VDiscreteProcess
+{
+public:
+
+  G4ElectronCapture(const G4String& regName, G4double ekinlimit);
+
+  virtual ~G4ElectronCapture();
+
+  void SetKinEnergyLimit(G4double);
+
+  virtual void BuildPhysicsTable(const G4ParticleDefinition&);
+
+  virtual G4bool IsApplicable(const G4ParticleDefinition&);
+
+  virtual G4double PostStepGetPhysicalInteractionLength( const G4Track& track,
+							 G4double previousStepSize,
+							 G4ForceCondition* condition);
+
+  virtual G4VParticleChange* PostStepDoIt(const G4Track&, const G4Step&);
+
+protected:
+
+  virtual G4double GetMeanFreePath(const G4Track&, G4double,G4ForceCondition*);
+
+private:
+
+  // hide assignment operator as private
+  G4ElectronCapture(const G4ElectronCapture&);
+  G4ElectronCapture& operator = (const G4ElectronCapture &right);
+
+  G4double kinEnergyThreshold;
+  G4String regionName;
+  G4Region* region;
+  G4ParticleChangeForGamma fParticleChange;
+};
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
+
+#endif
+
@@ -0,0 +1,68 @@
+//
+// ********************************************************************
+// * 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.          *
+// ********************************************************************
+//
+// This example is provided by the Geant4-DNA collaboration
+// Any report or published results obtained using the Geant4-DNA software 
+// and the DNA geometry given in the Geom_DNA example 
+// shall cite the following Geant4-DNA collaboration publications:
+// [1] NIM B 298 (2013) 47-54
+// [2] Med. Phys. 37 (2010) 4692-4708
+// The Geant4-DNA web site is available at http://geant4-dna.org
+//
+
+#ifndef HistoManager_h
+#define HistoManager_h 1
+
+#include "globals.hh"
+#include "g4root.hh"
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
+
+class HistoManager
+{
+  public:
+
+    HistoManager();
+   ~HistoManager();
+
+    void SetFileName   (const G4String& name) { fileName[0] = name;};
+    void book();
+    void save();
+    void FillNtuple(G4int id, G4int col, G4double e, G4double weight = 1.0);
+    void FillNtupleIColumn(G4int icol, G4int ival);
+    void FillNtupleFColumn(G4int icol, G4float ival);
+    void FillNtupleDColumn(G4int icol, G4double ival);
+    void AddNtupleRow();
+    
+  private:
+
+    G4String         fileName[2];
+    G4bool           factoryOn;       
+};
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
+
+#endif
+
@@ -0,0 +1,72 @@
+//
+// ********************************************************************
+// * 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.          *
+// ********************************************************************
+//
+// This example is provided by the Geant4-DNA collaboration
+// Any report or published results obtained using the Geant4-DNA software 
+// and the DNA geometry given in the Geom_DNA example 
+// shall cite the following Geant4-DNA collaboration publications:
+// [1] NIM B 298 (2013) 47-54
+// [2] Med. Phys. 37 (2010) 4692-4708
+// The Geant4-DNA web site is available at http://geant4-dna.org
+//
+
+#ifndef PhysicsList_h
+#define PhysicsList_h 1
+
+#include "G4VModularPhysicsList.hh"
+#include "globals.hh"
+
+class G4VPhysicsConstructor;
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
+
+class PhysicsList: public G4VModularPhysicsList
+{
+  public:
+    PhysicsList();
+   ~PhysicsList();
+
+    void ConstructParticle();
+    void ConstructProcess();
+
+    void SetCuts();
+    void SetCutForGamma(G4double);
+    void SetCutForElectron(G4double);
+    void SetCutForPositron(G4double);
+      
+  private:
+    G4double cutForGamma;
+    G4double cutForElectron;
+    G4double cutForPositron;
+    G4double currentDefaultCut;
+    
+    G4VPhysicsConstructor*  emPhysicsList;
+    
+};
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
+
+#endif
+
@@ -0,0 +1,61 @@
+//
+// ********************************************************************
+// * 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.          *
+// ********************************************************************
+//
+// This example is provided by the Geant4-DNA collaboration
+// Any report or published results obtained using the Geant4-DNA software 
+// and the DNA geometry given in the Geom_DNA example 
+// shall cite the following Geant4-DNA collaboration publications:
+// [1] NIM B 298 (2013) 47-54
+// [2] Med. Phys. 37 (2010) 4692-4708
+// The Geant4-DNA web site is available at http://geant4-dna.org
+//
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+
+#ifndef PrimaryGeneratorAction_h
+#define PrimaryGeneratorAction_h 1
+
+#include "G4VUserPrimaryGeneratorAction.hh"
+#include "G4ParticleGun.hh"
+#include "DetectorConstruction.hh"
+#include "G4Event.hh"
+#include "G4ParticleTable.hh"
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+
+class PrimaryGeneratorAction : public G4VUserPrimaryGeneratorAction
+{
+public:
+
+  PrimaryGeneratorAction(DetectorConstruction*);    
+  ~PrimaryGeneratorAction();
+  
+  void GeneratePrimaries(G4Event*);
+
+private:
+
+  G4ParticleGun*           particleGun;
+  DetectorConstruction*    Detector;
+};
+#endif
@@ -0,0 +1,65 @@
+//
+// ********************************************************************
+// * 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.          *
+// ********************************************************************
+//
+// This example is provided by the Geant4-DNA collaboration
+// Any report or published results obtained using the Geant4-DNA software 
+// and the DNA geometry given in the Geom_DNA example 
+// shall cite the following Geant4-DNA collaboration publications:
+// [1] NIM B 298 (2013) 47-54
+// [2] Med. Phys. 37 (2010) 4692-4708
+// The Geant4-DNA web site is available at http://geant4-dna.org
+//
+
+#ifndef RunAction_h
+#define RunAction_h 1
+
+#include "DetectorConstruction.hh"
+#include "HistoManager.hh"
+
+#include "G4UserRunAction.hh"
+#include "globals.hh"
+#include <iostream>
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+
+class G4Run;
+
+class RunAction : public G4UserRunAction
+{
+public:
+  
+  RunAction(DetectorConstruction*, HistoManager *);
+  ~RunAction();
+
+  void BeginOfRunAction(const G4Run*);
+  void EndOfRunAction(const G4Run*);
+
+private:
+
+  DetectorConstruction* Detector;    
+  HistoManager* Histo;
+  
+};
+#endif
@@ -0,0 +1,65 @@
+//
+// ********************************************************************
+// * 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.          *
+// ********************************************************************
+//
+// This example is provided by the Geant4-DNA collaboration
+// Any report or published results obtained using the Geant4-DNA software 
+// and the DNA geometry given in the Geom_DNA example 
+// shall cite the following Geant4-DNA collaboration publications:
+// [1] NIM B 298 (2013) 47-54
+// [2] Med. Phys. 37 (2010) 4692-4708
+// The Geant4-DNA web site is available at http://geant4-dna.org
+//
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+
+#ifndef SteppingAction_h
+#define SteppingAction_h 1
+
+#include "G4UserSteppingAction.hh"
+
+class RunAction;
+class DetectorConstruction;
+class PrimaryGeneratorAction;
+class HistoManager;
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+
+class SteppingAction : public G4UserSteppingAction
+{
+public:
+
+  SteppingAction(RunAction*, DetectorConstruction*, PrimaryGeneratorAction*, HistoManager *);
+  ~SteppingAction();
+  
+  void UserSteppingAction(const G4Step*);
+  
+private:
+
+  RunAction*              Run;
+  DetectorConstruction*   Detector; 
+  PrimaryGeneratorAction* Primary;
+  HistoManager* 	  Histo;
+      
+};
+#endif
@@ -0,0 +1,32 @@
+// *********************************************************************
+// To execute this macro under ROOT, 
+//   1 - launch ROOT (usually type 'root' at your machine's prompt)
+//   2 - type '.X plot.C' at the ROOT session prompt
+// This macro needs the output ROOT file
+// *********************************************************************
+{
+gROOT->Reset();
+gStyle->SetPalette(1);
+gROOT->SetStyle("Plain");
+Double_t scale;
+	
+c1 = new TCanvas ("c1","",20,20,1000,500);
+
+TFile f("dnageometry.root"); 
+
+TNtuple* ntuple;
+ntuple = (TNtuple*)f->Get("ntuple"); 
+     
+c1.cd(1);
+gStyle->SetOptStat(000000);
+  
+ntuple->SetMarkerColor(2);
+ntuple->SetMarkerStyle(20);
+ntuple->SetMarkerSize(1);
+ntuple->Draw("x/1000:y/1000:z/1000","flagVolume==1","");
+
+ntuple->SetMarkerColor(4);
+ntuple->SetMarkerStyle(24);
+ntuple->Draw("x/1000:y/1000:z/1000","flagVolume==2","same");
+  
+}
@@ -0,0 +1,92 @@
+//
+// ********************************************************************
+// * 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.          *
+// ********************************************************************
+//
+// This example is provided by the Geant4-DNA collaboration
+// Any report or published results obtained using the Geant4-DNA software 
+// and the DNA geometry given in the Geom_DNA example 
+// shall cite the following Geant4-DNA collaboration publications:
+// [1] NIM B 298 (2013) 47-54
+// [2] Med. Phys. 37 (2010) 4692-4708
+// The Geant4-DNA web site is available at http://geant4-dna.org
+//
+
+#include "G4VPhysicalVolume.hh"
+#include "G4ThreeVector.hh"
+#include "G4Box.hh"
+#include "ChromosomeParameterisation.hh"
+#include <fstream>
+#include "G4SystemOfUnits.hh"
+
+using namespace std;
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+
+ChromosomeParameterisation::ChromosomeParameterisation(const char* filename)
+{
+  ifstream f(filename, ios::in);
+  if (!f)
+    return;
+
+  fPositions.reserve(100);
+  fRotations.reserve(100);
+
+  while (!f.eof())
+  {
+    double x, y, z, rot;
+    f >> x >> y >> z >> rot;
+    fPositions.push_back(new G4ThreeVector(x * nanometer, y * nanometer, z * nanometer));
+    fRotations.push_back(new G4RotationMatrix(0, 0, rot * degree));
+  }
+}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+
+ChromosomeParameterisation::~ChromosomeParameterisation()
+{
+  unsigned int i;
+  for (i = 0; i < fPositions.size(); i++)
+    delete fPositions[i];
+  for (i = 0; i < fRotations.size(); i++)
+    delete fRotations[i];
+}
+   
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+
+void ChromosomeParameterisation::ComputeDimensions(
+    G4Tubs& /*rosette*/, const G4int /*copyNo*/, const G4VPhysicalVolume* /*physVol*/) const
+{
+  
+}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+
+void ChromosomeParameterisation::ComputeTransformation(
+    const G4int copyNo, G4VPhysicalVolume* physVol) const
+{
+  // see passive vs active method to specify
+  // this transformation
+  physVol->SetTranslation(*fPositions[copyNo]);
+  physVol->SetRotation(fRotations[copyNo]);
+}
@@ -0,0 +1,412 @@
+//
+// ********************************************************************
+// * 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.          *
+// ********************************************************************
+//
+// This example is provided by the Geant4-DNA collaboration
+// Any report or published results obtained using the Geant4-DNA software 
+// and the DNA geometry given in the Geom_DNA example 
+// shall cite the following Geant4-DNA collaboration publications:
+// [1] NIM B 298 (2013) 47-54
+// [2] Med. Phys. 37 (2010) 4692-4708
+// The Geant4-DNA web site is available at http://geant4-dna.org
+//
+#include "ChromosomeParameterisation.hh"
+#include "DetectorConstruction.hh"
+#include "Randomize.hh"
+#include "time.h"
+#include "G4Region.hh"
+#include "G4ProductionCuts.hh"
+#include "CLHEP/Random/Randomize.h"
+#include "G4PVParameterised.hh"
+#include <fstream>
+#include <vector>
+#include "G4SystemOfUnits.hh"
+
+#define countof(x) (sizeof(x) / sizeof(x[0]))
+
+using namespace std;
+
+static G4VisAttributes visInvBlue(false, G4Colour(0.0, 0.0, 1.0));
+static G4VisAttributes visInvWhite(false, G4Colour(1.0, 1.0, 1.0));
+static G4VisAttributes visInvPink(false, G4Colour(1.0, 0.0, 1.0));
+static G4VisAttributes visInvCyan(false, G4Colour(0.0, 1.0, 1.0));
+static G4VisAttributes visInvRed(false, G4Colour(1.0, 0.0, 0.0));
+static G4VisAttributes visInvGreen(false, G4Colour(0.0, 1.0, 0.0));
+static G4VisAttributes visBlue(true, G4Colour(0.0, 0.0, 1.0));
+static G4VisAttributes visWhite(true, G4Colour(1.0, 1.0, 1.0));
+static G4VisAttributes visPink(true, G4Colour(1.0, 0.0, 1.0));
+static G4VisAttributes visCyan(true, G4Colour(0.0, 1.0, 1.0));
+static G4VisAttributes visRed(true, G4Colour(1.0, 0.0, 0.0));
+static G4VisAttributes visGreen(true, G4Colour(0.0, 1.0, 0.0));
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+
+DetectorConstruction::DetectorConstruction()
+:physiWorld(NULL), logicWorld(NULL), solidWorld(NULL)
+{}  
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+
+DetectorConstruction::~DetectorConstruction()
+{}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+
+G4VPhysicalVolume* DetectorConstruction::Construct()
+{
+  DefineMaterials();
+  return ConstructDetector();
+}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+
+void DetectorConstruction::DefineMaterials()
+{ 
+  // Water is defined from NIST material database
+  G4NistManager *man = G4NistManager::Instance();
+  waterMaterial = man->FindOrBuildMaterial("G4_WATER");
+}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+
+void DetectorConstruction::LoadChromosome(const char* filename, G4VPhysicalVolume* chromBox)
+{
+  ChromosomeParameterisation* cp = new ChromosomeParameterisation(filename);
+  new G4PVParameterised("box ros", logicBoxros, chromBox, kUndefined, cp->getNumRosettes(), cp);
+
+  G4cout << filename << " done" << G4endl;
+}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+
+G4VPhysicalVolume* DetectorConstruction::ConstructDetector()
+{
+  char name[256];
+
+  /**************************************************************************************************************/
+  //                                            World
+  /*************************************************************************************************************/  
+
+  solidWorld = new G4Box("world", 10.0*mm, 10.0*mm, 10.0*mm);
+  logicWorld = new G4LogicalVolume(solidWorld, waterMaterial, "world"); 
+  physiWorld = new G4PVPlacement(0, G4ThreeVector(), "world", logicWorld, NULL, false, 0);
+  logicWorld->SetVisAttributes(&visInvWhite);
+
+  /**************************************************************************************************************/
+  //                                            Box nucleus
+  /*************************************************************************************************************/ 
+
+  solidTin = new G4Box("tin", 13*micrometer, 10*micrometer, 5*micrometer);
+  logicTin = new G4LogicalVolume(solidTin, waterMaterial, "tin");    
+  physiTin = new G4PVPlacement(0, G4ThreeVector(), "tin", logicTin, physiWorld, false, 0);
+  logicTin->SetVisAttributes(&visInvWhite);
+
+  /*************************************************************************************************************/
+  //                                            Cell nucleus
+  /*************************************************************************************************************/ 
+
+  solidNucleus = new G4Ellipsoid("nucleus", 11.82*micrometer, 8.52*micrometer, 3*micrometer, 0, 0); 
+  logicNucleus = new G4LogicalVolume(solidNucleus, waterMaterial, "logic nucleus");
+  physiNucleus = new G4PVPlacement(0,G4ThreeVector(), "physi nucleus", logicNucleus, physiTin, false, 0);
+  logicNucleus->SetVisAttributes(&visPink);
+
+  /*************************************************************************************************************/
+  //                                    Chromosomes territories
+  /*************************************************************************************************************/
+  // NOTE: The only supported values for the rotation are 0 and 90 degrees on the Y axis.
+  float chromosomePositionSizeRotation[][7] = {
+    {4.467, 2.835, 0, 1.557, 1.557, 1.557, 90},
+    {-4.467, 2.835, 0, 1.557, 1.557, 1.557, 0},
+    {4.423, -2.831, 0, 1.553, 1.553, 1.553, 90},
+    {-4.423, -2.831, 0, 1.553, 1.553, 1.553, 0},
+    {1.455, 5.63, 0, 1.455, 1.455, 1.455, 0},
+    {-1.455, 5.63, 0, 1.455, 1.455, 1.455, 90},
+    {1.435, 0, 1.392, 1.435, 1.435, 1.435, 0},
+    {-1.435, 0, 1.392, 1.435, 1.435, 1.435, 90},
+    {1.407, 0, -1.450, 1.407, 1.407, 1.407, 90}, // 5 right
+    {-1.407, 0, -1.450, 1.407, 1.407, 1.407, 0}, // 5 left
+    {1.380, -5.437, 0, 1.380, 1.380, 1.380, 0},
+    {-1.380, -5.437, 0, 1.380, 1.380, 1.380, 90},
+    {1.347, 2.782, -1.150, 1.347, 1.347, 1.347, 90},
+    {-1.347, 2.782, -1.150, 1.347, 1.347, 1.347, 0},
+    {1.311, -2.746, -1.220, 1.311, 1.311, 1.311, 90},
+    {-1.311, -2.746, -1.220, 1.311, 1.311, 1.311, 0},
+    {7.251, -2.541, 0, 1.275, 1.275, 1.275, 0},
+    {-6.701, 0, -0.85, 1.275, 1.275, 1.275, 90},
+    {4.148, 0, 1.278, 1.278, 1.278, 1.278, 90}, // 10 right
+    {-4.148, 0, 1.278, 1.278, 1.278, 1.278, 0}, // 10 left
+    {4.147, 0, -1.277, 1.277, 1.277, 1.277, 0},
+    {-4.147, 0, -1.277, 1.277, 1.277, 1.277, 90},
+    {8.930, 0.006, 0, 1.272, 1.272, 1.272, 90},
+    {-7.296, 2.547, 0, 1.272, 1.272, 1.272, 90},
+    {1.207, -2.642, 1.298, 1.207, 1.207, 1.207, 0},
+    {-1.207, -2.642, 1.298, 1.207, 1.207, 1.207, 90},
+    {1.176, 2.611, 1.368, 1.176, 1.176, 1.176, 0},
+    {-1.176, 2.611, 1.368, 1.176, 1.176, 1.176, 90},
+    {4.065, 5.547, 0, 1.155, 1.155, 1.155, 90}, // 15 right
+    {-4.065, 5.547, 0, 1.155, 1.155, 1.155, 0}, // 15 left
+    {6.542, 0.159, 1.116, 1.116, 1.116, 1.116, 0},
+    {-9.092, 0, 0, 1.116, 1.116, 1.116, 0},
+    {6.507, 0.159, -1.081, 1.081, 1.081, 1.081, 90},
+    {-7.057, -2.356, 0, 1.081, 1.081, 1.081, 90},
+    {3.824, -5.448, 0, 1.064, 1.064, 1.064, 90},
+    {-3.824, -5.448, 0, 1.064, 1.064, 1.064, 0},
+    {5.883, -5.379, 0, 0.995, 0.995, 0.995, 0},
+    {-9.133, -2.111, 0, 0.995, 0.995, 0.995, 0},
+    {6.215, 5.387, 0, 0.995, 0.995, 0.995, 0}, // 20 right
+    {-6.971, -4.432, 0, 0.995, 0.995, 0.995, 90}, // 20 left
+    {9.583, 2.177, 0, 0.899, 0.899, 0.899, 90},
+    {-9.467, 2.03, 0, 0.899, 0.899, 0.899, 0},
+    {9.440, -2.180, 0, 0.914, 0.914, 0.914, 90},
+    {-6.34, 0, 1.339, 0.914, 0.914, 0.914, 0},
+    {-6.947, 4.742, 0, 0.923, 0.923, 0.923, 90}, // Y
+    {7.354, 2.605, 0, 1.330, 1.330, 1.330, 0} // X
+  };
+  G4RotationMatrix* rotch = new G4RotationMatrix;
+  rotch->rotateY(90 * degree);
+
+  for (unsigned int i = 0; i < countof(chromosomePositionSizeRotation); i++)
+  {
+    float* p = &chromosomePositionSizeRotation[i][0];
+    float* size = &chromosomePositionSizeRotation[i][3];
+    float rotation = chromosomePositionSizeRotation[i][6];
+    G4ThreeVector pos(p[0] * micrometer, p[1] * micrometer, p[2] * micrometer);
+    G4RotationMatrix* rot = rotation == 0 ? 0 : rotch;
+
+    snprintf(name, countof(name), "box%d%c", (i / 2) + 1, i % 2 ? 'l' : 'r');
+    G4Box* solidBox = new G4Box(name, size[0] * micrometer, size[1] * micrometer, size[2] * micrometer);
+    G4LogicalVolume* logicBox = new G4LogicalVolume(solidBox, waterMaterial, name);
+    physiBox[i] = new G4PVPlacement(rot, pos, "chromo", logicBox, physiNucleus, false, 0);
+    logicBox->SetVisAttributes(&visBlue);
+  }
+
+  /***************************************************************************************************/
+
+// chromatin fiber envelope
+  G4Tubs* solidEnv = new G4Tubs("chromatin fiber", 0, 15.4 * nanometer, 80.5 * nanometer, 0 * degree, 360 * degree);
+  logicEnv = new G4LogicalVolume(solidEnv, waterMaterial, "LV chromatin fiber");
+  logicEnv->SetVisAttributes(&visInvPink);
+
+
+// Histones
+  solidHistone = new G4Tubs("solid histone", 0, 3.25 * nanometer, 2.85 * nanometer, 0*degree,360*degree); 
+  logicHistone = new G4LogicalVolume(solidHistone,waterMaterial,"logic histone");
+
+
+//Base pair
+	solidBp1 = new G4Orb("blue sphere",0.17*nanometer); 
+	logicBp1 = new G4LogicalVolume(solidBp1,waterMaterial,"logic blue sphere");
+	solidBp2 = new G4Orb("pink sphere",0.17*nanometer); 
+	logicBp2 = new G4LogicalVolume(solidBp2,waterMaterial,"logic pink sphere");	
+
+
+//Phosphodiester group
+ 	solidSugar1 = new G4Orb("sugar 1", 0.48*nanometer); 
+  	solidSugar2 = new G4Orb("sugar 2", 0.48*nanometer); 
+  		G4ThreeVector posi(0.180248* nanometer,0.32422* nanometer,0.00784 * nanometer);
+  	uniDNA = new G4UnionSolid("move", solidSugar1, solidSugar2, 0, posi);
+
+ 	solidSugar3 = new G4Orb("sugar 3", 0.48*nanometer); 
+  	solidSugar4 = new G4Orb("sugar 4", 0.48*nanometer); 
+ 		 G4ThreeVector posi2(-0.128248* nanometer,0.41227* nanometer,0.03584 * nanometer);
+  	uniDNA2 = new G4UnionSolid("move2", solidSugar3, solidSugar4, 0, posi2);
+
+
+
+/**********************************************************************************************************************
+					     Phosphodiester group Position
+**********************************************************************************************************************/
+	for(G4int n=2;n<200;n++)
+		{
+		G4float SP1[2][3]={{(-0.6*nanometer)*cos(n*0.26),0,(0.6*nanometer)*sin(n*0.26)},{(0.6*nanometer)*cos(n*0.26),0,(-0.6*nanometer)*sin(0.26*n)}};
+		G4float matriceSP1[3][3]={{cos(n*0.076),-sin(n*0.076),0},{sin(n*0.076),cos(n*0.076),0},{0,0,1}};
+		G4float matriceSP2[2][3];
+
+			for(G4int i=0;i<3;i++)
+			{
+			G4float sumSP1=0;
+			G4float sumSP2=0;
+				for(G4int j=0;j<3;j++)
+				{
+				sumSP1+=matriceSP1[i][j]*SP1[0][j];
+				sumSP2+=matriceSP1[i][j]*SP1[1][j];
+				}
+			matriceSP2[0][i] = sumSP1;
+			matriceSP2[1][i] = sumSP2;
+			}
+		G4float heliceSP[3]={(4.85*nanometer)*cos(n*0.076),(4.85*nanometer)*sin(n*0.076),(n*0.026*nanometer)};
+			for(G4int i=0;i<3;i++)
+			{
+			matriceSP2[0][i]+=heliceSP[i];
+			matriceSP2[1][i]+=heliceSP[i];
+			}
+			G4ThreeVector posSugar1(matriceSP2[0][2],matriceSP2[0][1],(matriceSP2[0][0])-(4.25*nanometer));
+			G4ThreeVector posSugar2(matriceSP2[1][2],matriceSP2[1][1],(matriceSP2[1][0])-(5.45*nanometer));
+
+    snprintf(name, countof(name), "sugar %d", n);
+    solidSphere3 = new G4Orb(name, 0.48*nanometer);
+    uniDNA = new G4UnionSolid("move", uniDNA, solidSphere3, 0, posSugar1);
+
+    snprintf(name, countof(name), "sugar %d", n);
+    solidSphere4 = new G4Orb(name, 0.48*nanometer);
+    uniDNA2 = new G4UnionSolid("move2", uniDNA2, solidSphere4, 0, posSugar2);
+}
+	logicSphere3 = new G4LogicalVolume(uniDNA,waterMaterial,"logic sugar 2");
+	logicSphere4 = new G4LogicalVolume(uniDNA2,waterMaterial,"logic sugar 4");
+
+/**********************************************************************************************************************
+					      Base pair Position
+**********************************************************************************************************************/
+	for(G4int n=0;n<200;n++)
+		{
+		G4float bp1[2][3]={{(-0.34*nanometer)*cos(n*0.26),0,(0.34*nanometer)*sin(n*0.26)},{(0.34*nanometer)*cos(n*0.26),0,(-0.34*nanometer)*sin(0.26*n)}};
+		G4float matriceBP1[3][3]={{cos(n*0.076),-sin(n*0.076),0},{sin(n*0.076),cos(n*0.076),0},{0,0,1}};
+		G4float matriceBP2[2][3];
+
+			for(G4int i=0;i<3;i++)
+			{
+			G4float sumBP1=0;
+			G4float sumBP2=0;
+				for(G4int j=0;j<3;j++)
+				{
+				sumBP1+=matriceBP1[i][j]*bp1[0][j];
+				sumBP2+=matriceBP1[i][j]*bp1[1][j];
+				}
+			matriceBP2[0][i] = sumBP1;
+			matriceBP2[1][i] = sumBP2;
+			}
+		G4float heliceBP[3]={(4.8*nanometer)*cos(n*0.076),(4.8*nanometer)*sin(n*0.076),n*0.026*nanometer};
+
+			for(G4int i=0;i<3;i++)
+			{
+			matriceBP2[0][i]+=heliceBP[i];
+			matriceBP2[1][i]+=heliceBP[i];
+			}
+			G4ThreeVector position1(matriceBP2[0][2],matriceBP2[0][1],matriceBP2[0][0]-(4.25*nanometer));
+			G4ThreeVector position2(matriceBP2[1][2],matriceBP2[1][1],matriceBP2[1][0]-(5.45*nanometer));
+
+		 physiBp1[n] = new G4PVPlacement(0,position1,logicBp1,"physi blue sphere",logicSphere3,false,0);
+		 physiBp2[n] = new G4PVPlacement(0,position2,logicBp2,"physi pink sphere",logicSphere4,false,0);
+}
+
+
+  /**************************************************************************************************************/
+  //                                    Box continaing the chromatin flowers
+  /*************************************************************************************************************/  
+
+  solidBoxros = new G4Tubs("solid box ros", 0*nanometer, 399*nanometer, 20*nanometer, 0*degree, 360*degree);  
+  logicBoxros = new G4LogicalVolume(solidBoxros, waterMaterial, "box ros");
+  logicBoxros->SetVisAttributes(&visInvBlue);
+
+  /**************************************************************************************************************/
+  //                    		Initial position of different elements
+  /*************************************************************************************************************/  
+
+  // Chromatin fiber position
+  for (G4int i = 0; i < 7; i++) {
+    G4RotationMatrix* rotFiber = new G4RotationMatrix;
+    rotFiber->rotateX(90*degree);
+    rotFiber->rotateY(i *25.72*degree);
+    G4ThreeVector posFiber = G4ThreeVector(0, 152*nanometer, 0);
+    posFiber.rotateZ(i*25.72*degree);
+    new G4PVPlacement(rotFiber, posFiber, logicEnv, "physi env", logicBoxros, false, 0);
+
+    rotFiber = new G4RotationMatrix;
+    rotFiber->rotateX(90 * degree);
+    rotFiber->rotateY((7 + i) * 25.72 *degree);
+    posFiber = G4ThreeVector(0, 152 *nanometer, 0);
+    posFiber.rotateZ((7 + i) * 25.72*degree);
+    new G4PVPlacement(rotFiber, posFiber, logicEnv, "physi env", logicBoxros, false, 0);
+
+    rotFiber = new G4RotationMatrix;
+    rotFiber->rotateX(90 * degree);
+    rotFiber->rotateY((25.72 + (i - 14) * 51.43) * degree);
+    posFiber = G4ThreeVector(-36.5 * nanometer, 312 * nanometer, 0);
+    posFiber.rotateZ((i - 14) * 51.43 * degree);
+    new G4PVPlacement(rotFiber, posFiber, logicEnv, "physi env", logicBoxros, false, 0);
+
+    rotFiber = new G4RotationMatrix;
+    rotFiber->rotateX(90 * degree);
+    rotFiber->rotateY(180 * degree);
+    rotFiber->rotateY((i - 21) * 51.43 * degree);
+    posFiber = G4ThreeVector(-103 * nanometer, 297 * nanometer, 0);
+    posFiber.rotateZ((i - 21) * 51.43 * degree);
+    new G4PVPlacement(rotFiber, posFiber, logicEnv, "physi env", logicBoxros, false, 0);
+
+
+  }
+
+  
+// DNA and histone positions
+  for (int j = 0; j < 90; j++) {
+  // DNA (bp-SP) 
+   		G4RotationMatrix* rotStrand1 = new G4RotationMatrix;
+    			rotStrand1->rotateZ(j*-51.43*degree);
+		G4ThreeVector posStrand1(-2.7*nanometer,9.35*nanometer,(-69.9*nanometer)+(j*1.67*nanometer));
+    			posStrand1.rotateZ(j*51.43*degree);
+		new G4PVPlacement(rotStrand1,posStrand1,logicSphere3,"physi sugar 2",logicEnv,false,0);
+
+		G4RotationMatrix* rotStrand2 = new G4RotationMatrix;
+    			rotStrand2->rotateZ(j* -51.43*degree);
+		G4ThreeVector posStrand2(-2.7*nanometer,9.35*nanometer,(-68.7*nanometer)+(j*1.67*nanometer));
+    			posStrand2.rotateZ(j*51.43*degree);
+		new G4PVPlacement(rotStrand2,posStrand2,logicSphere4,"physi sugar 4",logicEnv,false,0);
+	
+    // histones
+    		G4RotationMatrix* rotHistone = new G4RotationMatrix;
+    		rotHistone->rotateY(90*degree);
+    		rotHistone->rotateX(j*(-51.43*degree));
+    		G4ThreeVector posHistone(0.0,9.35 *nanometer,(-74.15+ j*1.67)*nanometer);
+   		 posHistone.rotateZ(j*51.43*degree);
+    		new G4PVPlacement(rotHistone, posHistone, logicHistone, "PV histone", logicEnv, false, 0);
+				}
+
+//Loading flower box position for each chromosome territory
+
+  for (int k = 0; k < 22; k++)
+  {
+    snprintf(name, countof(name), "chromo%d.dat", k + 1);
+    LoadChromosome(name, physiBox[k * 2]);
+    LoadChromosome(name, physiBox[k * 2 + 1]);
+  }
+
+  LoadChromosome("chromoY.dat", physiBox[44]);
+  LoadChromosome("chromoX.dat", physiBox[45]);
+
+  /**************************************************************************************************************/
+  //                    		Visualisation colors
+  /*************************************************************************************************************/
+ 		
+		logicBp1->SetVisAttributes(&visInvCyan);
+  		logicBp2->SetVisAttributes(&visInvPink);
+
+ 		logicSphere3->SetVisAttributes(&visInvWhite);
+  		logicSphere4->SetVisAttributes(&visInvRed);
+
+  		logicHistone->SetVisAttributes(&visInvBlue);
+
+
+  G4cout << "Geometry has been loaded" << G4endl;
+  return physiWorld;
+}
@@ -0,0 +1,139 @@
+//
+// ********************************************************************
+// * 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.          *
+// ********************************************************************
+//
+//---------------------------------------------------------------------------
+//
+// ClassName:   G4ElectronCapture
+//
+// Description: The process to kill particles to save CPU
+//
+// Author:      V.Ivanchenko 31 August 2010
+//
+//----------------------------------------------------------------------------
+//
+// This example is provided by the Geant4-DNA collaboration
+// Any report or published results obtained using the Geant4-DNA software 
+// and the DNA geometry given in the Geom_DNA example 
+// shall cite the following Geant4-DNA collaboration publications:
+// [1] NIM B 298 (2013) 47-54
+// [2] Med. Phys. 37 (2010) 4692-4708
+// The Geant4-DNA web site is available at http://geant4-dna.org
+//
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
+
+#include "G4ElectronCapture.hh"
+#include "G4SystemOfUnits.hh"
+#include "G4ParticleDefinition.hh"
+#include "G4Step.hh"
+#include "G4Track.hh"
+#include "G4Region.hh"
+#include "G4RegionStore.hh"
+#include "G4Electron.hh"
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
+
+G4ElectronCapture::G4ElectronCapture(const G4String& regName, G4double ekinlim)
+  : G4VDiscreteProcess("eCapture", fElectromagnetic), kinEnergyThreshold(ekinlim),
+    regionName(regName), region(0)
+{
+  if(regName == "" || regName == "world") { 
+    regionName = "DefaultRegionForTheWorld";
+  }
+  pParticleChange = &fParticleChange;
+}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
+
+G4ElectronCapture::~G4ElectronCapture() 
+{}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
+
+void G4ElectronCapture::SetKinEnergyLimit(G4double val)
+{
+  kinEnergyThreshold = val;
+  if(verboseLevel > 0) {
+    G4cout << "### G4ElectronCapture: Tracking cut E(MeV) = " 
+	   << kinEnergyThreshold/MeV << G4endl;
+  }
+}
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
+
+void G4ElectronCapture::BuildPhysicsTable(const G4ParticleDefinition&)
+{
+  region = (G4RegionStore::GetInstance())->GetRegion(regionName);
+  if(region && verboseLevel > 0) {
+    G4cout << "### G4ElectronCapture: Tracking cut E(MeV) = " 
+	   << kinEnergyThreshold/MeV << " is assigned to " << regionName 
+	   << G4endl;
+  }
+}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
+
+G4bool G4ElectronCapture::IsApplicable(const G4ParticleDefinition&)
+{
+  return true;
+}
+
+G4double 
+G4ElectronCapture::PostStepGetPhysicalInteractionLength(const G4Track& aTrack,
+							G4double, 
+							G4ForceCondition* condition)
+{
+  // condition is set to "Not Forced"
+  *condition = NotForced;
+  
+  G4double limit = DBL_MAX; 
+  if(region) {
+    if(aTrack.GetVolume()->GetLogicalVolume()->GetRegion() == region && 
+	 aTrack.GetKineticEnergy() < kinEnergyThreshold) { limit = 0.0; }
+  }
+  return limit;
+}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
+
+G4VParticleChange* G4ElectronCapture::PostStepDoIt(const G4Track& aTrack, 
+						   const G4Step&)
+{
+  pParticleChange->Initialize(aTrack);
+  pParticleChange->ProposeTrackStatus(fStopAndKill);
+  pParticleChange->ProposeLocalEnergyDeposit(aTrack.GetKineticEnergy());
+  fParticleChange.SetProposedKineticEnergy(0.0);
+  return pParticleChange;
+}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
+
+G4double G4ElectronCapture::GetMeanFreePath(const G4Track&,G4double,
+					    G4ForceCondition*)
+{
+  return DBL_MAX;
+}    
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
+
+
@@ -0,0 +1,136 @@
+//
+// ********************************************************************
+// * 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.          *
+// ********************************************************************
+//
+// This example is provided by the Geant4-DNA collaboration
+// Any report or published results obtained using the Geant4-DNA software 
+// and the DNA geometry given in the Geom_DNA example 
+// shall cite the following Geant4-DNA collaboration publications:
+// [1] NIM B 298 (2013) 47-54
+// [2] Med. Phys. 37 (2010) 4692-4708
+// The Geant4-DNA web site is available at http://geant4-dna.org
+//
+
+#include "HistoManager.hh"
+#include "G4UnitsTable.hh"
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
+
+HistoManager::HistoManager()
+{
+  fileName[0]  = "dnageometry";
+  factoryOn = false;
+}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
+
+HistoManager::~HistoManager()
+{
+}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
+
+void HistoManager::book()
+{
+  G4AnalysisManager* analysisManager = G4AnalysisManager::Instance();
+  analysisManager->SetVerboseLevel(1);
+  
+  G4String extension = analysisManager->GetFileType();
+  fileName[1] = fileName[0] + "." + extension;
+  
+  // open output file
+  
+  G4bool fileOpen = analysisManager->OpenFile(fileName[0]);
+  if (!fileOpen) {
+    G4cout << "\n---> HistoManager::book(): cannot open " << fileName[1] 
+           << G4endl;
+    return;
+  }  
+
+  // create ntuple
+  
+  analysisManager->SetFirstHistoId(1);
+  
+  analysisManager->CreateNtuple("ntuple","geom_dna");
+  
+  analysisManager->CreateNtupleDColumn("flagParticle");
+  analysisManager->CreateNtupleDColumn("flagProcess");
+  analysisManager->CreateNtupleDColumn("flagVolume");
+  analysisManager->CreateNtupleDColumn("x");
+  analysisManager->CreateNtupleDColumn("y");
+  analysisManager->CreateNtupleDColumn("z");
+  analysisManager->CreateNtupleDColumn("edep");
+  analysisManager->CreateNtupleDColumn("stepLength");
+  
+  factoryOn = true;
+  
+  G4cout << "\n----> Histogram file is opened in " << fileName[1] << G4endl;
+}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
+
+void HistoManager::save()
+{
+  if (factoryOn) {
+    G4AnalysisManager* analysisManager = G4AnalysisManager::Instance();    
+    analysisManager->Write();
+    analysisManager->CloseFile();
+    G4cout << "\n----> Histograms are saved in " << fileName[1] << G4endl;
+      
+    delete G4AnalysisManager::Instance();
+    factoryOn = false;
+  }         
+}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
+
+void HistoManager::FillNtupleIColumn(G4int icol, G4int ival)
+{
+  G4AnalysisManager* analysisManager = G4AnalysisManager::Instance();
+  analysisManager->FillNtupleIColumn(icol,ival);
+}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
+
+void HistoManager::FillNtupleFColumn(G4int icol, G4float fval)
+{
+  G4AnalysisManager* analysisManager = G4AnalysisManager::Instance();
+  analysisManager->FillNtupleFColumn(icol,fval);
+}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
+
+void HistoManager::FillNtupleDColumn(G4int icol, G4double dval)
+{
+  G4AnalysisManager* analysisManager = G4AnalysisManager::Instance();
+  analysisManager->FillNtupleDColumn(icol,dval);
+}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
+
+void HistoManager::AddNtupleRow()
+{
+  G4AnalysisManager* analysisManager = G4AnalysisManager::Instance();
+  analysisManager->AddNtupleRow();
+}
@@ -0,0 +1,96 @@
+//
+// ********************************************************************
+// * 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.          *
+// ********************************************************************
+//
+// This example is provided by the Geant4-DNA collaboration
+// Any report or published results obtained using the Geant4-DNA software 
+// and the DNA geometry given in the Geom_DNA example 
+// shall cite the following Geant4-DNA collaboration publications:
+// [1] NIM B 298 (2013) 47-54
+// [2] Med. Phys. 37 (2010) 4692-4708
+// The Geant4-DNA web site is available at http://geant4-dna.org
+//
+#include "PhysicsList.hh"
+#include "G4SystemOfUnits.hh"
+#include "G4EmDNAPhysics.hh"
+ 
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
+
+PhysicsList::PhysicsList() 
+: G4VModularPhysicsList()
+{
+  currentDefaultCut   = 1.0*micrometer;
+  cutForGamma         = currentDefaultCut;
+  cutForElectron      = currentDefaultCut;
+  cutForPositron      = currentDefaultCut;
+
+  SetVerboseLevel(1);
+
+  // EM physics
+  emPhysicsList = new G4EmDNAPhysics();
+}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
+
+PhysicsList::~PhysicsList()
+{
+}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
+
+void PhysicsList::ConstructParticle()
+{
+  emPhysicsList->ConstructParticle();
+}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
+
+void PhysicsList::ConstructProcess()
+{
+  // Transportation
+  //
+  AddTransportation();
+
+  // Electromagnetic physics list
+  //
+  emPhysicsList->ConstructProcess(); 
+}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
+
+#include "G4Gamma.hh"
+#include "G4Electron.hh"
+#include "G4Positron.hh"
+
+void PhysicsList::SetCuts()
+{
+ // fixe lower limit for cut
+ G4ProductionCutsTable::GetProductionCutsTable()->SetEnergyRange(100*eV, 1*GeV);
+  
+ // set cut values for gamma at first and for e- second and next for e+,
+ // because some processes for e+/e- need cut values for gamma
+ SetCutValue(cutForGamma, "gamma");
+ SetCutValue(cutForElectron, "e-");
+ SetCutValue(cutForPositron, "e+");
+}
@@ -0,0 +1,72 @@
+//
+// ********************************************************************
+// * 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.          *
+// ********************************************************************
+//
+// This example is provided by the Geant4-DNA collaboration
+// Any report or published results obtained using the Geant4-DNA software 
+// and the DNA geometry given in the Geom_DNA example 
+// shall cite the following Geant4-DNA collaboration publications:
+// [1] NIM B 298 (2013) 47-54
+// [2] Med. Phys. 37 (2010) 4692-4708
+// The Geant4-DNA web site is available at http://geant4-dna.org
+//
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+  
+#include "PrimaryGeneratorAction.hh"
+#include "G4SystemOfUnits.hh"
+#include "Randomize.hh"
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+
+PrimaryGeneratorAction::PrimaryGeneratorAction(DetectorConstruction* DC)
+:Detector(DC)
+{
+  G4int n_particle = 1;
+  particleGun  = new G4ParticleGun(n_particle);
+
+  // default gun parameters
+  particleGun->SetParticleEnergy(1.*MeV);
+  particleGun->SetParticleMomentumDirection(G4ThreeVector(0.,0.,1.));
+  
+}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+
+PrimaryGeneratorAction::~PrimaryGeneratorAction()
+{
+  delete particleGun;
+}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+
+void PrimaryGeneratorAction::GeneratePrimaries(G4Event* anEvent)
+{
+G4double x0,y0,z0;
+
+x0=((16.0*G4UniformRand())-8.0)*micrometer;
+y0=((8.0*G4UniformRand())-4.0)*micrometer;
+z0=-2.99*micrometer;
+  particleGun->SetParticlePosition(G4ThreeVector(x0,y0,z0));
+  particleGun->GeneratePrimaryVertex(anEvent);
+}
@@ -0,0 +1,63 @@
+//
+// ********************************************************************
+// * 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.          *
+// ********************************************************************
+//
+// This example is provided by the Geant4-DNA collaboration
+// Any report or published results obtained using the Geant4-DNA software 
+// and the DNA geometry given in the Geom_DNA example 
+// shall cite the following Geant4-DNA collaboration publications:
+// [1] NIM B 298 (2013) 47-54
+// [2] Med. Phys. 37 (2010) 4692-4708
+// The Geant4-DNA web site is available at http://geant4-dna.org
+//
+#include "RunAction.hh"
+#include "G4Run.hh"
+#include "G4ParticleDefinition.hh"
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+
+RunAction::RunAction(DetectorConstruction* det, HistoManager* his)
+    :Detector(det),Histo(his)
+{}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+
+RunAction::~RunAction()
+{}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+
+void RunAction::BeginOfRunAction(const G4Run*)
+{  
+  // Histograms
+  Histo->book();
+}
+ 
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+
+void RunAction::EndOfRunAction(const G4Run*)
+{
+  //save histograms      
+  Histo->save();
+}
@@ -0,0 +1,137 @@
+//
+// ********************************************************************
+// * 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.          *
+// ********************************************************************
+//
+// This example is provided by the Geant4-DNA collaboration
+// Any report or published results obtained using the Geant4-DNA software 
+// and the DNA geometry given in the Geom_DNA example 
+// shall cite the following Geant4-DNA collaboration publications:
+// [1] NIM B 298 (2013) 47-54
+// [2] Med. Phys. 37 (2010) 4692-4708
+// The Geant4-DNA web site is available at http://geant4-dna.org
+//
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+
+#include "SteppingAction.hh"
+#include "RunAction.hh"
+#include "DetectorConstruction.hh"
+#include "PrimaryGeneratorAction.hh"
+#include "HistoManager.hh"
+
+#include "G4SystemOfUnits.hh"
+#include "G4SteppingManager.hh"
+#include "G4VTouchable.hh"
+#include "G4VPhysicalVolume.hh"
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+
+SteppingAction::SteppingAction(RunAction* run,DetectorConstruction* det,PrimaryGeneratorAction* pri, HistoManager* his)
+:Run(run),Detector(det),Primary(pri),Histo(his)
+{}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+
+SteppingAction::~SteppingAction()
+{}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
+
+void SteppingAction::UserSteppingAction(const G4Step* step)
+{ 
+ G4double flagParticle=0.;
+ G4double flagProcess=0.;
+ G4double flagVolume=0.;
+ G4double x,y,z,xp,yp,zp;
+ G4double dE;
+ 
+ dE=step->GetTotalEnergyDeposit()/eV;
+ 
+ if (step->GetTrack()->GetDynamicParticle()->GetDefinition() ->GetParticleName() == "e-")       flagParticle = 10;    
+ if (step->GetTrack()->GetDynamicParticle()->GetDefinition() ->GetParticleName() == "proton")   flagParticle = 20;
+ if (step->GetTrack()->GetDynamicParticle()->GetDefinition() ->GetParticleName() == "hydrogen") flagParticle = 30;
+ if (step->GetTrack()->GetDynamicParticle()->GetDefinition() ->GetParticleName() == "alpha")    flagParticle = 40;
+ if (step->GetTrack()->GetDynamicParticle()->GetDefinition() ->GetParticleName() == "alpha+")   flagParticle = 50;
+ if (step->GetTrack()->GetDynamicParticle()->GetDefinition() ->GetParticleName() == "helium")   flagParticle = 60;
+
+
+ if (step->GetPostStepPoint()->GetProcessDefinedStep()->GetProcessName()=="e-_G4DNAElastic")		flagProcess =11;
+ if (step->GetPostStepPoint()->GetProcessDefinedStep()->GetProcessName()=="e-_G4DNAExcitation")		flagProcess =12;
+ if (step->GetPostStepPoint()->GetProcessDefinedStep()->GetProcessName()=="e-_G4DNAIonisation")		flagProcess =13;
+ if (step->GetPostStepPoint()->GetProcessDefinedStep()->GetProcessName()=="e-_G4DNAAttachment")		flagProcess =14;
+ if (step->GetPostStepPoint()->GetProcessDefinedStep()->GetProcessName()=="e-_G4DNAVibExcitation")	flagProcess =15;
+ if (step->GetPostStepPoint()->GetProcessDefinedStep()->GetProcessName()=="eCapture")			flagProcess =16;
+//  if (step->GetPostStepPoint()->GetProcessDefinedStep()->GetProcessName()=="msc")				flagProcess =17;
+
+ if (step->GetPostStepPoint()->GetProcessDefinedStep()->GetProcessName()=="proton_G4DNAExcitation")	flagProcess =21;
+ if (step->GetPostStepPoint()->GetProcessDefinedStep()->GetProcessName()=="proton_G4DNAIonisation")	flagProcess =22;
+ if (step->GetPostStepPoint()->GetProcessDefinedStep()->GetProcessName()=="proton_G4DNAChargeDecrease")	flagProcess =23;
+
+ if (step->GetPostStepPoint()->GetProcessDefinedStep()->GetProcessName()=="hydrogen_G4DNAExcitation")	flagProcess =31;
+ if (step->GetPostStepPoint()->GetProcessDefinedStep()->GetProcessName()=="hydrogen_G4DNAIonisation")	flagProcess =32;
+ if (step->GetPostStepPoint()->GetProcessDefinedStep()->GetProcessName()=="hydrogen_G4DNAChargeIncrease")	flagProcess =33;
+
+ if (step->GetPostStepPoint()->GetProcessDefinedStep()->GetProcessName()=="alpha_G4DNAExcitation")		flagProcess =41;
+ if (step->GetPostStepPoint()->GetProcessDefinedStep()->GetProcessName()=="alpha_G4DNAIonisation")		flagProcess =42;
+ if (step->GetPostStepPoint()->GetProcessDefinedStep()->GetProcessName()=="alpha_G4DNAChargeDecrease")	flagProcess =43;
+
+ if (step->GetPostStepPoint()->GetProcessDefinedStep()->GetProcessName()=="alpha+_G4DNAExcitation")	flagProcess =51;
+ if (step->GetPostStepPoint()->GetProcessDefinedStep()->GetProcessName()=="alpha+_G4DNAIonisation")	flagProcess =52;
+ if (step->GetPostStepPoint()->GetProcessDefinedStep()->GetProcessName()=="alpha+_G4DNAChargeDecrease")	flagProcess =53;
+ if (step->GetPostStepPoint()->GetProcessDefinedStep()->GetProcessName()=="alpha+_G4DNAChargeIncrease")	flagProcess =54;
+
+ if (step->GetPostStepPoint()->GetProcessDefinedStep()->GetProcessName()=="helium_G4DNAExcitation")	flagProcess =61;
+ if (step->GetPostStepPoint()->GetProcessDefinedStep()->GetProcessName()=="helium_G4DNAIonisation")	flagProcess =62;
+ if (step->GetPostStepPoint()->GetProcessDefinedStep()->GetProcessName()=="helium_G4DNAChargeIncrease")	flagProcess =63;
+
+// if (step->GetPreStepPoint()->GetProcessDefinedStep()->GetProcessName()=="hIoni")				flagProcess =24;
+// if (step->GetPreStepPoint()->GetProcessDefinedStep()->GetProcessName()=="eIoni")				flagProcess =18;
+ 
+ if (step->GetPreStepPoint()->GetPhysicalVolume()->GetName()=="physi sugar 2") flagVolume=1;
+  
+ if (step->GetPreStepPoint()->GetPhysicalVolume()->GetName()=="physi sugar 4") flagVolume=2;
+ 
+ if (flagVolume !=0 && dE!=0 )
+ {
+ 
+   x=step->GetPreStepPoint()->GetPosition().x()/nanometer;
+   y=step->GetPreStepPoint()->GetPosition().y()/nanometer;
+   z=step->GetPreStepPoint()->GetPosition().z()/nanometer;
+   xp=step->GetPostStepPoint()->GetPosition().x()/nanometer;
+   yp=step->GetPostStepPoint()->GetPosition().y()/nanometer;
+   zp=step->GetPostStepPoint()->GetPosition().z()/nanometer;
+   
+   Histo->FillNtupleDColumn(0, flagParticle);
+   Histo->FillNtupleDColumn(1, flagProcess);
+   Histo->FillNtupleDColumn(2, flagVolume);
+   Histo->FillNtupleDColumn(3, xp);
+   Histo->FillNtupleDColumn(4, yp);
+   Histo->FillNtupleDColumn(5, zp);
+   Histo->FillNtupleDColumn(6, dE );
+   Histo->FillNtupleDColumn(7, std::sqrt((x-xp)*(x-xp)+(y-yp)*(y-yp)+(z-zp)*(z-zp)));
+   
+   Histo->AddNtupleRow();   
+ }
+ 
+ 
+}    
@@ -0,0 +1,68 @@
+# Use this open statement to create an OpenGL view:
+#/vis/open OGL 600x400-0+0
+#
+# Use this open statement to create a .prim file suitable for
+# viewing in DAWN:
+/vis/open DAWNFILE
+#
+# Use this open statement to create a .heprep file suitable for
+# viewing in HepRApp:
+#/vis/open HepRepFile
+#
+# Use this open statement to create a .wrl file suitable for
+# viewing in a VRML viewer:
+#/vis/open VRML2FILE
+#
+# Disable auto refresh and quieten vis messages whilst scene and
+# trajectories are established:
+/vis/viewer/set/autoRefresh false
+/vis/verbose errors
+#
+# Draw geometry:
+/vis/drawVolume
+#
+# Specify view angle:
+/vis/viewer/set/viewpointThetaPhi -90. 0.
+#
+# Specify zoom value:
+#/vis/viewer/zoom 2.
+#
+# Specify style (surface or wireframe):
+#/vis/viewer/set/style wireframe
+#
+# Draw coordinate axes:
+#/vis/scene/add/axes 0 0 0 1 m
+#
+# Draw smooth trajectories at end of event, showing trajectory points
+# as markers 2 pixels wide:
+/vis/scene/add/trajectories smooth
+/vis/modeling/trajectories/create/drawByCharge
+/vis/modeling/trajectories/drawByCharge-0/default/setDrawStepPts true
+/vis/modeling/trajectories/drawByCharge-0/default/setStepPtsSize 2
+# (if too many tracks cause core dump => /tracking/storeTrajectory 0)
+#
+# Draw hits at end of event:
+#/vis/scene/add/hits
+#
+# To draw only gammas:
+#/vis/filtering/trajectories/create/particleFilter
+#/vis/filtering/trajectories/particleFilter-0/add gamma
+#
+# To invert the above, drawing all particles except gammas,
+# keep the above two lines but also add:
+#/vis/filtering/trajectories/particleFilter-0/invert true
+#
+# Many other options are available with /vis/modeling and /vis/filtering.
+# For example, to select colour by particle ID:
+#/vis/modeling/trajectories/create/drawByParticleID
+#/vis/modeling/trajectories/drawByParticleID-0/set e- blue
+#
+# To superimpose all of the events from a given run:
+/vis/scene/endOfEventAction accumulate
+#
+# Re-establish auto refreshing and verbosity:
+/vis/viewer/set/autoRefresh true
+/vis/verbose warnings
+#
+# For file-based drivers, use this to create an empty detector view:
+#/vis/viewer/flush