Commit in lcdd on MAIN
include/lcdd/bfield/BoxDipole.hh+2-11.3 -> 1.4
                   /Cartesian3DMagneticFieldMap.hh+2-21.4 -> 1.5
                   /Dipole.hh+14-71.2 -> 1.3
                   /FieldManager.hh+10-101.3 -> 1.4
                   /MagneticFieldOverlay.hh+2-21.4 -> 1.5
                   /RZBData.hh+24-21.3 -> 1.4
                   /RZFieldMap.hh+39-131.2 -> 1.3
                   /Solenoid.hh+96-621.1 -> 1.2
include/lcdd/core/GeometryManager.hh+31-141.2 -> 1.3
                 /LCDDDetectorConstruction.hh+24-31.2 -> 1.3
                 /LCDDMessenger.hh+26-61.3 -> 1.4
                 /LCDDObjectStoreInspector.hh+9-21.3 -> 1.4
                 /LCDDParser.hh+86-231.3 -> 1.4
                 /LCDDProcessor.hh+188-111.3 -> 1.4
include/lcdd/detectors/CellReadout.hh+14-61.3 -> 1.4
src/lcdd/bfield/Dipole.cc+18-181.1 -> 1.2
               /FieldManager.cc+9-91.1 -> 1.2
               /MagneticFieldOverlay.cc+3-31.1 -> 1.2
               /RZFieldMap.cc+48-471.1 -> 1.2
               /Solenoid.cc+61-11.1 -> 1.2
src/lcdd/core/GeometryManager.cc+1-61.3 -> 1.4
             /LCDDLibLoad.cc+91.1 -> 1.2
             /LCDDMessenger.cc+131-1421.1 -> 1.2
             /LCDDParser.cc+1-61.2 -> 1.3
+848-396
24 modified files
add doxygen comments to headers in bfield and core packages

lcdd/include/lcdd/bfield
BoxDipole.hh 1.3 -> 1.4
diff -u -r1.3 -r1.4
--- BoxDipole.hh	2 Jul 2013 01:46:54 -0000	1.3
+++ BoxDipole.hh	2 Jul 2013 21:19:43 -0000	1.4
@@ -5,7 +5,8 @@
 #include "G4MagneticField.hh"
 
 /**
- * This is a G4MagneticField implementation that assigns fixed B-field components to a box-like region in world coordinates.
+ * This is a G4MagneticField implementation that assigns fixed B-field components to a box-like
+ * region with a possible offset in world coordinates.
  */
 class BoxDipole: public G4MagneticField
 {

lcdd/include/lcdd/bfield
Cartesian3DMagneticFieldMap.hh 1.4 -> 1.5
diff -u -r1.4 -r1.5
--- Cartesian3DMagneticFieldMap.hh	2 Jul 2013 01:46:54 -0000	1.4
+++ Cartesian3DMagneticFieldMap.hh	2 Jul 2013 21:19:43 -0000	1.5
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/include/lcdd/bfield/Cartesian3DMagneticFieldMap.hh,v 1.4 2013/07/02 01:46:54 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/include/lcdd/bfield/Cartesian3DMagneticFieldMap.hh,v 1.5 2013/07/02 21:19:43 jeremy Exp $
 
 #ifndef LCDD_BFIELD_CARTESIAN3DMAGNETICFIELDMAP_HH
 #define LCDD_BFIELD_CARTESIAN3DMAGNETICFIELDMAP_HH 1
@@ -51,7 +51,7 @@
     Cartesian3DMagneticFieldMap(const char* filename, double xOffset, double yOffset, double zOffset);
 
     /**
-     * Implementation of primary virtual method from G4MagneticField intercace.
+     * Implementation of primary virtual method from G4MagneticField interface.
      * @param[in]  Point  The point in 3D space.
      * @param[out] Bfield The output B-field data at the point.
      */

lcdd/include/lcdd/bfield
Dipole.hh 1.2 -> 1.3
diff -u -r1.2 -r1.3
--- Dipole.hh	2 Jul 2013 01:46:54 -0000	1.2
+++ Dipole.hh	2 Jul 2013 21:19:43 -0000	1.3
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/include/lcdd/bfield/Dipole.hh,v 1.2 2013/07/02 01:46:54 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/include/lcdd/bfield/Dipole.hh,v 1.3 2013/07/02 21:19:43 jeremy Exp $
 
 #ifndef LCDD_BFIELD_DIPOLE_HH
 #define LCDD_BFIELD_DIPOLE_HH 1
@@ -32,33 +32,40 @@
     }
 
 public:
+
     void GetFieldValue(const double Point[3], double *Bfield) const;
 
     void setZMax(double zmax);
+
     double getZMax();
 
     void setRMax(double rmax);
+
     double getRMax();
 
     void setZMin(double zmin);
+
     double getZMin();
 
     void addCoeff(double coeff);
+
     const std::vector<double>& getCoeffs();
 
     void setFieldUnit(double unit);
+
     double getFieldUnit();
 
     void setLengthUnit(double unit);
+
     double getLengthUnit();
 
 private:
-    double m_zmin;
-    double m_zmax;
-    double m_rmax;
-    double m_lunit;
-    double m_funit;
-    std::vector<double> m_coeffs;
+    double _zmin;
+    double _zmax;
+    double _rmax;
+    double _lunit;
+    double _funit;
+    std::vector<double> _coeffs;
 };
 
 #endif

lcdd/include/lcdd/bfield
FieldManager.hh 1.3 -> 1.4
diff -u -r1.3 -r1.4
--- FieldManager.hh	2 Jul 2013 01:46:54 -0000	1.3
+++ FieldManager.hh	2 Jul 2013 21:19:43 -0000	1.4
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/include/lcdd/bfield/FieldManager.hh,v 1.3 2013/07/02 01:46:54 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/include/lcdd/bfield/FieldManager.hh,v 1.4 2013/07/02 21:19:43 jeremy Exp $
 #ifndef LCDD_BFIELD_FIELDMANAGER_HH
 #define LCDD_BFIELD_FIELDMANAGER_HH 1
 
@@ -34,6 +34,12 @@
      */
     void setup();
 
+    /**
+     * Add a global magnetic field.
+     * @param[in] f The magnetic field.
+     */
+    void addGlobalField(G4MagneticField* f);
+
 private:
 
     /**
@@ -57,12 +63,6 @@
     void initialize(G4MagneticField* field);
 
     /**
-     * Add a global magnetic field.
-     * @param[in] f The magnetic field.
-     */
-    void addGlobalField(G4MagneticField* f);
-
-    /**
      * Add a magnetic field.
      * @param[in] f The magnetic field.
      */
@@ -74,10 +74,10 @@
 
 private:
 
-    std::vector<G4MagneticField*> m_globalfields;
-    std::vector<G4MagneticField*> m_allfields;
+    std::vector<G4MagneticField*> _globalfields;
+    std::vector<G4MagneticField*> _allfields;
 
-    static FieldManager* m_instance;
+    static FieldManager* _instance;
 };
 
 #endif

lcdd/include/lcdd/bfield
MagneticFieldOverlay.hh 1.4 -> 1.5
diff -u -r1.4 -r1.5
--- MagneticFieldOverlay.hh	2 Jul 2013 01:46:54 -0000	1.4
+++ MagneticFieldOverlay.hh	2 Jul 2013 21:19:43 -0000	1.5
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/include/lcdd/bfield/MagneticFieldOverlay.hh,v 1.4 2013/07/02 01:46:54 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/include/lcdd/bfield/MagneticFieldOverlay.hh,v 1.5 2013/07/02 21:19:43 jeremy Exp $
 #ifndef LCDD_BFIELD_MAGNETICFIELDOVERLAY_HH
 #define LCDD_BFIELD_MAGNETICFIELDOVERLAY_HH 1
 
@@ -34,7 +34,7 @@
     void GetFieldValue(const double Point[3], double *Bfield) const;
 
 private:
-    std::vector<G4MagneticField*> m_fields;
+    std::vector<G4MagneticField*> _fields;
 };
 
 #endif

lcdd/include/lcdd/bfield
RZBData.hh 1.3 -> 1.4
diff -u -r1.3 -r1.4
--- RZBData.hh	1 Jul 2013 22:10:34 -0000	1.3
+++ RZBData.hh	2 Jul 2013 21:19:43 -0000	1.4
@@ -1,17 +1,20 @@
-// $Header: /cvs/lcd/lcdd/include/lcdd/bfield/RZBData.hh,v 1.3 2013/07/01 22:10:34 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/include/lcdd/bfield/RZBData.hh,v 1.4 2013/07/02 21:19:43 jeremy Exp $
 
 #ifndef LCDD_BFIELD_RZBDATA_HH
 #define LCDD_BFIELD_RZBDATA_HH 1
 
 /**
- * @brief Represents a single row of a magnetic field defined by radius, z dimension, radial B-field strength, and z dimension B-field strength.
+ * This class represents a single data row of a B-field defined by
+ * radius, z dimension, radial B-field component, and z dimension B-field component.
  * @note Double values are multiplied by the field unit from the rz_field_map before they are inserted using this class.
+ * @todo Move code to source file.
  */
 class RZBData
 {
 public:
 
     /**
+     * Class constructor.
      * @param r  Radius
      * @param z  Z dimension
      * @param Br Radial field strength
@@ -22,27 +25,46 @@
     {
     }
 
+    /**
+     * Class destructor.
+     */
     virtual ~RZBData()
     {
     }
 
 public:
 
+    /**
+     * Get the radial coordinate.
+     * @return The radial coordinate.
+     */
     double r() const
     {
         return _r;
     }
 
+    /**
+     * Get the Z coordinate.
+     * @return The Z coordinate.
+     */
     double z() const
     {
         return _z;
     }
 
+    /**
+     * Get the BR field component.
+     * @return The BR field component.
+     */
     double Br() const
     {
         return _Br;
     }
 
+    /**
+     * Get BZ field component.
+     * @return The BZ field component.
+     */
     double Bz() const
     {
         return _Bz;

lcdd/include/lcdd/bfield
RZFieldMap.hh 1.2 -> 1.3
diff -u -r1.2 -r1.3
--- RZFieldMap.hh	1 Jul 2013 22:10:34 -0000	1.2
+++ RZFieldMap.hh	2 Jul 2013 21:19:43 -0000	1.3
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/include/lcdd/bfield/RZFieldMap.hh,v 1.2 2013/07/01 22:10:34 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/include/lcdd/bfield/RZFieldMap.hh,v 1.3 2013/07/02 21:19:43 jeremy Exp $
 
 #ifndef LCDD_BFIELD_RZFIELDMAP_HH
 #define LCDD_BFIELD_RZFIELDMAP_HH 1
@@ -21,35 +21,61 @@
 
 public:
 
+	/**
+	 * Class constructor.
+	 * @param[in] numBinsR  The number of bins in R.
+	 * @param[in] numBinsZ  The number of bins in Z.
+	 * @param[in] gridSizeR The size of a cell in R.
+	 * @param[in] gridSizeZ The size of a cell in Z.
+	 * @param[in] fieldData A list of RZBData forming the B-field grid.
+	 */
     RZFieldMap(int numBinsR, int numBinsZ, double gridSizeR, double gridSizeZ, std::vector<RZBData> fieldData);
 
+    /**
+     * Class destructor.
+     */
     virtual ~RZFieldMap();
 
 public:
+
+    /**
+     * Implementation of G4MagneticField::Initialize.
+     * @param[in]  Point  A point in global coordinates.
+     * @param[out] Bfield The B-field values at the point.
+    */
     void GetFieldValue(const double Point[3], double *Bfield) const;
 
 private:
+
+    /**
+     * Initialize the data arrays.
+     */
     void initializeArrays();
-    void fillArrays(std::vector<RZBData> fieldData);
-    void deleteArrays();
 
-private:
+    /**
+     * Fill the internal data arrays from the list of RZBData objects.
+     * @param[in] fieldData The list of RZBData points.
+     */
+    void fillArrays(std::vector<RZBData> fieldData);
 
-    void computeNumBins();
+    /**
+     * Delete the arrays containg the field data.
+     */
+    void deleteArrays();
 
 private:
 
-    int m_numBinsR;
-    int m_numBinsZ;
+    int _numBinsR;
+    int _numBinsZ;
 
-    double m_gridSizeR;
-    double m_gridSizeZ;
+    double _gridSizeR;
+    double _gridSizeZ;
 
-    double m_maxR;
-    double m_maxZ;
+    double _maxR;
+    double _maxZ;
 
-    double** m_BrArray;
-    double** m_BzArray;
+    double** _BrArray;
+    double** _BzArray;
 };
 
 #endif

lcdd/include/lcdd/bfield
Solenoid.hh 1.1 -> 1.2
diff -u -r1.1 -r1.2
--- Solenoid.hh	1 Jul 2013 21:00:40 -0000	1.1
+++ Solenoid.hh	2 Jul 2013 21:19:43 -0000	1.2
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/include/lcdd/bfield/Solenoid.hh,v 1.1 2013/07/01 21:00:40 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/include/lcdd/bfield/Solenoid.hh,v 1.2 2013/07/02 21:19:43 jeremy Exp $
 
 #ifndef LCDD_BFIELD_SOLENOID_HH
 #define LCDD_BFIELD_SOLENOID_HH 1
@@ -10,79 +10,113 @@
 #include <iostream>
 
 /**
- * @brief Simulation class for a simple magnetic solenoid.
+ * Geant4 implementation of a simple solenoidal field.
+ * @todo Move code to source file.
+ * @todo This class needs better documentation on the function of the inner/outer R and Z values.
  */
 class Solenoid: public G4MagneticField
 {
 
 public:
+
+	/**
+	 * Class constructor.
+	 * @todo Add fully qualified constructor.
+	 */
     Solenoid();
+
+    /**
+     * Class destructor.
+     */
     virtual ~Solenoid();
 
 public:
 
+    /**
+     * Implementation of G4MagneticField::Initialize to get B-field values from point.
+     * @param[in]  Point  A 3D point in global coordinates.
+     * @param[out] Bfield The B-field values at the point.
+     * @todo Use the inner and outer Z values.  They are currently ignored!
+     */
     void GetFieldValue(const double Point[3], double *Bfield) const;
 
-    void setInnerField(double d)
-    {
-        _innerField = d;
-    }
-
-    void setOuterField(double d)
-    {
-        _outerField = d;
-    }
-
-    void setInnerR(double d)
-    {
-        _innerR = d;
-    }
-
-    void setOuterR(double d)
-    {
-        _outerR = d;
-    }
-
-    void setInnerZ(double d)
-    {
-        _innerZ = d;
-    }
-
-    void setOuterZ(double d)
-    {
-        _outerZ = d;
-    }
-
-    double getInnerField() const
-    {
-        return _innerField;
-    }
-
-    double getOuterField() const
-    {
-        return _outerField;
-    }
-
-    double getInnerR() const
-    {
-        return _innerR;
-    }
-
-    double getOuterR() const
-    {
-        return _outerR;
-    }
-
-    double getInnerZ() const
-    {
-        return _innerZ;
-    }
-
-    double getOuterZ() const
-    {
-        return _outerZ;
-    }
-
+    /**
+     * Set the inner field value.
+     * @param[in] d The inner field value.
+     */
+    void setInnerField(double d);
+
+    /**
+     * Set the outer field value.
+     * @param[in] d The outer field value.
+     */
+    void setOuterField(double d);
+
+    /**
+     * Set the inner radius.
+     * @param[in] d The inner radius.
+     */
+    void setInnerR(double d);
+
+    /**
+     * Set the outer radius.
+     * @param[in] d The outer radius.
+     */
+    void setOuterR(double d);
+
+    /**
+     * Set the inner Z value.
+     * @param[in] d The inner Z value.
+     */
+    void setInnerZ(double d);
+
+    /**
+     * Set the outer Z value.
+     * @param[in] The outer Z value.
+     */
+    void setOuterZ(double d);
+
+    /**
+     * Get the B-field Z component within the inner radius.
+     * @return The field value within the inner radius.
+     */
+    double getInnerField() const;
+
+    /**
+     * Get the B-field Z component between the inner and outer radii.
+     * @return The field value outside the inner radius.
+     */
+    double getOuterField() const;
+
+    /**
+     * Get the inner radius.
+     * @return The inner radius.
+     */
+    double getInnerR() const;
+
+    /**
+     * Get the outer radius.
+     * @return The outer radius.
+     */
+    double getOuterR() const;
+
+    /**
+     * Get the inner Z value.
+     * @return The inner Z value.
+     *
+     */
+    double getInnerZ() const;
+
+    /**
+     * Get the outer Z value.
+     * @return The outer Z value.
+     */
+    double getOuterZ() const;
+
+    /**
+     * Print the magnetic field's information to an output stream.
+     * @param[in] os The output stream.
+     */
     void printOut(std::ostream &os);
 
 private:

lcdd/include/lcdd/core
GeometryManager.hh 1.2 -> 1.3
diff -u -r1.2 -r1.3
--- GeometryManager.hh	27 Jun 2013 23:42:24 -0000	1.2
+++ GeometryManager.hh	2 Jul 2013 21:19:43 -0000	1.3
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/include/lcdd/core/GeometryManager.hh,v 1.2 2013/06/27 23:42:24 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/include/lcdd/core/GeometryManager.hh,v 1.3 2013/07/02 21:19:43 jeremy Exp $
 
 #ifndef LCDD_GEOMETRYMANAGER_HH
 #define LCDD_GEOMETRYMANAGER_HH 1
@@ -9,45 +9,59 @@
 class G4String;
 
 /**
- * @class GeometryManager
- * @brief Singleton manager class with miscellaneous geometry utility functions.
+ * Singleton manager class with miscellaneous geometry utility and management functions.
  */
 class GeometryManager
 {
 public:
+
+	/**
+	 * Class destructor.
+	 */
     virtual ~GeometryManager();
+
+    /**
+     * Get the static instance of this class.
+     * @return This class's singleton instance.
+     */
     static GeometryManager* instance();
 
 protected:
+
+    /**
+     * Class constructor which is protected.
+     * @note Access an object of this class through its instance method.
+     */
     GeometryManager();
 
 public:
 
     /**
-     * Retrieve the world's logical volume from Geant4.
+     * Get the world's logical volume from Geant4.
+     * @return The current world's logical volume.
      */
     G4LogicalVolume* getWorldLogicalVolume() const;
 
     /**
-     * Retrieve the world's physical volume from Geant4.
+     * Get the world's physical volume from Geant4.
+     * @return The current world's physical volume.
      */
     G4VPhysicalVolume* getWorldPhysicalVolume() const;
 
     /**
-     * Hook for beginning the run.
+     * Begin of run hook for geometry setup.
+     * @param[in] run The G4Run that is starting.
      */
-    void beginRun(const G4Run*);
+    void beginRun(const G4Run* run);
 
     /**
-     * Attach the RegionInformation to the world's region.
+     * Attach the RegionInformation to the world's.
      */
     void setupWorldRegionInformation();
 
-//#ifdef HAVE_G4PVPLACEMENT_CHECKOVERLAPS
-
     /**
-     * Check overlaps starting with the world volume
-     * and recursing to daughters.
+     * Check overlaps starting with the world volume and recursing to daughters.
+     * @note Overlaps are printed to cout by Geant4.
      */
     void checkOverlaps() const;
 
@@ -55,20 +69,23 @@
      * Check for overlaps by calling CheckOverlaps on all daughters
      * of a given logical volume, with possible recursion to
      * daughters.
+     * @note Overlaps are printed to cout by Geant4.
      */
     void checkOverlaps(G4LogicalVolume*, bool recurse=true) const;
 
     /**
      * Check for overlaps of a named logical volume by looking it
      * up in the volume store, with possible recursion to daughters.
+     * @note Overlaps are print to cout by Geant4.
      */
     void checkOverlaps(const G4String&, bool recurse=true) const;
 
-//#endif
-
 private:
 
+    /** The static instance of this class. */
     static GeometryManager* m_instance;
+
+    /** Indicates whether world region information was added or not. */
     bool m_worldRegionIsSetup;
 };
 

lcdd/include/lcdd/core
LCDDDetectorConstruction.hh 1.2 -> 1.3
diff -u -r1.2 -r1.3
--- LCDDDetectorConstruction.hh	1 Jul 2013 21:00:41 -0000	1.2
+++ LCDDDetectorConstruction.hh	2 Jul 2013 21:19:43 -0000	1.3
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/include/lcdd/core/LCDDDetectorConstruction.hh,v 1.2 2013/07/01 21:00:41 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/include/lcdd/core/LCDDDetectorConstruction.hh,v 1.3 2013/07/02 21:19:43 jeremy Exp $
 #ifndef LCDD_CORE_LCDDDETECTORCONSTRUCTION_HH
 #define LCDD_CORE_LCDDDETECTORCONSTRUCTION_HH 1
 
@@ -13,21 +13,42 @@
 class LCDDObjectStoreInspector;
 
 /**
- * @brief Implementation of G4VUserDetectorConstruction for LCDD.
- * @note  Minimal functionality; mostly just hands control to other classes.
+ * Implementation of G4VUserDetectorConstruction for all LCDD geometries.
+ * @note This class has minimal functionality; it mostly hands control to other LCDD classes.
  */
 class LCDDDetectorConstruction: public G4VUserDetectorConstruction
 {
 
 public:
+
+	/**
+	 * Class constructor.
+	 */
     LCDDDetectorConstruction();
+
+    /**
+     * Class destructor.
+     */
     ~LCDDDetectorConstruction();
 
 public:
 
+    /**
+     * Construct the geometry.
+     * @return The world physical volume.
+     */
     virtual G4VPhysicalVolume* Construct();
 
+    /**
+     * Set the world volume of the built geometry.
+     * @param[in] pv The world's physical volume.
+     */
     void setWorldVolume(G4VPhysicalVolume *pv);
+
+    /**
+     * Get the world volume of this construction.
+     * @return The world volume.
+     */
     G4VPhysicalVolume* getWorldVolume();
 
 private:

lcdd/include/lcdd/core
LCDDMessenger.hh 1.3 -> 1.4
diff -u -r1.3 -r1.4
--- LCDDMessenger.hh	1 Jul 2013 22:10:34 -0000	1.3
+++ LCDDMessenger.hh	2 Jul 2013 21:19:43 -0000	1.4
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/include/lcdd/core/LCDDMessenger.hh,v 1.3 2013/07/01 22:10:34 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/include/lcdd/core/LCDDMessenger.hh,v 1.4 2013/07/02 21:19:43 jeremy Exp $
 
 #ifndef LCDD_CORE_LCDDMESSENGER_HH
 #define LCDD_CORE_LCDDMESSENGER_HH 1
@@ -11,22 +11,44 @@
 class LCDDDetectorConstruction;
 
 /**
- * @brief G4UImessenger for LCDD commands.
+ * G4UImessenger implementation for various LCDD commands.
+ * @todo This class should create the "stores" directory also.
  */
 class LCDDMessenger: public G4UImessenger
 {
 
 public:
+
+	/**
+	 * Class constructor.
+	 */
     LCDDMessenger();
+
+    /**
+     * Class destructor.
+     */
     virtual ~LCDDMessenger();
 
 public:
 
-    virtual void SetNewValue(G4UIcommand *cmd, G4String newVals);
-    virtual G4String GetCurrentValue(G4UIcommand *cmd);
+    /**
+     * Execute a command on this messner.
+     * @param[in] cmd     The command to execute.
+     * @param[in] newVals The command's argument values.
+     */
+    void SetNewValue(G4UIcommand *cmd, G4String newVals);
+
+    /**
+     * Get the current value of the messenger.
+     * @warning This is not actually implemented and just returns a dummy value.
+     */
+    G4String GetCurrentValue(G4UIcommand *cmd);
 
 private:
 
+    /**
+     * Define the directory and commands for this messenger.
+     */
     void defineCommands();
 
 private:
@@ -37,10 +59,8 @@
     G4UIcommand* m_setSetupNameCmd;
     G4UIcommand* m_setVersionCmd;
     G4UIcommand* m_dumpCmd;
-#ifdef HAVE_G4PVPLACEMENT_CHECKOVERLAPS
     G4UIcommand* m_checkOverlapsCmd;
     G4UIcommand* m_checkOverlapsRecurseCmd;
-#endif
 };
 // class
 #endif

lcdd/include/lcdd/core
LCDDObjectStoreInspector.hh 1.3 -> 1.4
diff -u -r1.3 -r1.4
--- LCDDObjectStoreInspector.hh	1 Jul 2013 21:00:41 -0000	1.3
+++ LCDDObjectStoreInspector.hh	2 Jul 2013 21:19:43 -0000	1.4
@@ -1,4 +1,4 @@
-// $Id: LCDDObjectStoreInspector.hh,v 1.3 2013/07/01 21:00:41 jeremy Exp $
+// $Id: LCDDObjectStoreInspector.hh,v 1.4 2013/07/02 21:19:43 jeremy Exp $
 #ifndef LCDD_CORE_LCDDOBJECTSTOREINSPECTOR_HH
 #define LCDD_CORE_LCDDOBJECTSTOREINSPECTOR_HH 1
 
@@ -8,13 +8,17 @@
 #include "lcdd/core/LCDDProcessor.hh"
 
 /**
- * @brief Creates the inspector instances for looking at Geant4 LCDD object stores.
+ * Creates specific instances of the StoreInspector for looking at information in Geant4 and LCDD object stores.
  */
 class LCDDObjectStoreInspector
 {
 
 public:
 
+	/**
+	 * Class constructor.
+	 * @brief Constructor that defines instances of StoreInspector for specific types.
+	 */
     LCDDObjectStoreInspector()
     {
         m_materialInspector = new G4MaterialStoreInspector("G4Material", G4Material::GetMaterialTable());
@@ -29,6 +33,9 @@
         m_visInspector = new G4VisAttributeInspector("G4VisAttributes", LCDDProcessor::instance()->getVisAttributesStore());
     }
 
+    /**
+     * Class destructor.
+     */
     virtual ~LCDDObjectStoreInspector()
     {
         delete m_materialInspector;

lcdd/include/lcdd/core
LCDDParser.hh 1.3 -> 1.4
diff -u -r1.3 -r1.4
--- LCDDParser.hh	1 Jul 2013 22:10:34 -0000	1.3
+++ LCDDParser.hh	2 Jul 2013 21:19:43 -0000	1.4
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/include/lcdd/core/LCDDParser.hh,v 1.3 2013/07/01 22:10:34 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/include/lcdd/core/LCDDParser.hh,v 1.4 2013/07/02 21:19:43 jeremy Exp $
 
 #ifndef LCDD_CORE_LCDDPARSER_HH
 #define LCDD_CORE_LCDDPARSER_HH 1
@@ -10,57 +10,120 @@
 class G4VPhysicalVolume;
 
 /**
- * @brief Parser for LCDD format.
+ * Parser for reading in the LCDD XML format to Geant4 runtime.
+ * @todo See https://jira.slac.stanford.edu/browse/LCDD-11
+ *       Make version and setup name supported parameters.
  */
 class LCDDParser
 {
+
+private:
+
+	/**
+	 * Class constructor, which is private because this class
+	 * is accessed as a singleton.
+	 */
+    LCDDParser();
+
 public:
 
+    /**
+     * Class destructor.
+     */
     virtual ~LCDDParser();
 
+    /**
+     * Get the static instance of this class.
+     */
     static LCDDParser* instance();
 
-protected:
-
-    LCDDParser();
-
 public:
 
-    // initialize required XML machinery
-    void initialize();
-    void initializeParser();
-
-    // call in G4 DetectorConstruction
+    /**
+     * Initialize the parser and build the geometry.
+     * @return The geometry's world volume.
+     */
     G4VPhysicalVolume* construct();
 
-    // cleanup
+    /**
+     * End of build hook.  Calls Finalize method of the SAX processor.
+     */
     void finalize();
 
-    // set all parms
-    void setupParserConfig(const std::string& URI, const std::string& setupName, const std::string& version);
-
-    // set from instance vars
-    void setupParserConfig();
-
-    // set parms
+    /**
+     * Set the URI of the LCDD or GDML file to build.
+     * @param[in] URI The URI of the LCDD file.
+     */
     void setURI(std::string URI);
+
+    /**
+     * Set the name of the GDML setup to load.
+     * @param[in] setupName The name of the setup.
+     * @warning Currently ignored by the parser.
+     */
     void setSetupName(std::string setupName);
+
+    /**
+     * Set the version.
+     * @param[in[ version The version.
+     * @warning Not sure what this does!
+     */
     void setVersion(std::string version);
 
-    // get parms
+    /**
+     * Get the URI parameter value.
+     * @return The current URI.
+     */
     const std::string& URI();
+
+    /**
+     * Get the current setup name.
+     * @return The current setup name.
+     */
     const std::string& setupName();
-    const std::string& version();
 
-    // set world volume ptr
-    void setWorld(G4VPhysicalVolume *world);
+    /**
+     * Get the current version.
+     * @return The current version.
+     */
+    const std::string& version();
 
+    /**
+     * Check if the current setup is valid.
+     * @return True if valid; false if not.
+     */
     bool isValidSetup();
 
 private:
 
+    /**
+     * Initialize the XML parser.  This is just a wrapped for initializeParser.
+     */
+    void initialize();
+
+    /**
+     * Initialize the parser.
+     */
+    void initializeParser();
+
+    /**
+     * Add the subscriber for handling LCDD extension elements on the volume tags.
+     */
     void addVolumeExtendedSubscriber();
 
+    /**
+     * Set all parser parameters.
+     * @param[in] URI       The location of the geometry file.
+     * @param[in] setupName The setup name.
+     * @param[in] version   The version.
+     */
+    void setupParserConfig(const std::string& URI, const std::string& setupName, const std::string& version);
+
+    /**
+     * This sets up the parser configuration from the current instance variables.
+     */
+    void setupParserConfig();
+
 private:
 
     SAXProcessor m_sxp;

lcdd/include/lcdd/core
LCDDProcessor.hh 1.3 -> 1.4
diff -u -r1.3 -r1.4
--- LCDDProcessor.hh	1 Jul 2013 22:10:34 -0000	1.3
+++ LCDDProcessor.hh	2 Jul 2013 21:19:43 -0000	1.4
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/include/lcdd/core/LCDDProcessor.hh,v 1.3 2013/07/01 22:10:34 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/include/lcdd/core/LCDDProcessor.hh,v 1.4 2013/07/02 21:19:43 jeremy Exp $
 
 #ifndef LCDD_CORE_LCDDPROCESSOR_HH
 #define LCDD_CORE_LCDDPROCESSOR_HH 1
@@ -19,84 +19,261 @@
 class G4Run;
 
 /**
- * @brief Register and find LCDD elements, except idspecs which have own manager.
+ * This class is used to register LCDD objects created by subscribers when parsing the input XML.
  * @note  This is the LCDD equivalent of the GDMLProcessor class.
  */
 class LCDDProcessor
 {
 
-public:
+private:
 
+	/**
+	 * Class constructor, which is private because class is accessed via singleton.
+	 */
     LCDDProcessor();
+
+public:
+
+    /**
+     * Class destructor.
+     */
     virtual ~LCDDProcessor();
 
+    /**
+     * Get the static instance of this class.
+     * @return The singleton instance of this class.
+     */
     static LCDDProcessor* instance();
 
 public:
+
+    /** Name to SensitiveDetector map. */
     typedef std::map<std::string, SensitiveDetector*> SensitiveDetectors;
+
+    /** Name to magnetic field map. */
     typedef std::map<std::string, G4MagneticField*> MagneticFields;
+
+    /** Name to regions map. */
     typedef std::map<std::string, G4Region*> Regions;
+
+    /** Name to vis attributes map. */
     typedef std::map<std::string, G4VisAttributes*> VisAttributes;
+
+    /** Name to physics limit map. */
     typedef std::map<std::string, PhysicsLimitSet*> LimitSets;
 
 public:
 
-    // header
+    /**
+     * Get the header record.
+     * @return The LCDD header record.
+     */
     const LCDDHeaderRecord* getHeader() const;
+
+    /**
+     * Set the header record.
+     * @param[in] h The header record.
+     */
     void setHeader(LCDDHeaderRecord* h);
 
-    // detector name
+    /**
+     * Get the name of the detector.
+     */
     std::string getDetectorName() const;
 
-    // Sensitive Detectors
+    /**
+     * Add a named SensitiveDetector.
+     * @param[in] name The name of the detector.
+     * @param[in] sd   The sensitive detector.
+     */
     void addSensitiveDetector(std::string& name, SensitiveDetector* sd);
 
+    /**
+     * Get a SensitiveDetector by name.
+     * @param[in] The name of the detector.
+     */
     SensitiveDetector* getSensitiveDetector(const std::string& name);
+
+    /**
+     * Get a SensitiveDetector by name.
+     * @param[in] The name of the detector.
+     */
     SensitiveDetector* getSensitiveDetector(const char* name);
 
+    /**
+     * Get an iterator pointing at the beginning of the SD map.
+     * @return An iterator pointing at the first SD in the map.
+     */
     LCDDProcessor::SensitiveDetectors::const_iterator getSensitiveDetectorsBegin();
+
+    /**
+     * Get an iterator pointing at the end of the SD map.
+     * @return An iterator pointing to the end of the SD map.
+     */
     LCDDProcessor::SensitiveDetectors::const_iterator getSensitiveDetectorsEnd();
 
-    // Mag Field
+    /**
+     * Add a magnetic field by name.
+     * @param[in] name The name of the magnetic field.
+     * @param[in] mag  The magnetic field object.
+     */
     void addMagneticField(std::string& name, G4MagneticField* mag);
+
+    /**
+     * Get a magnetic field by name.
+     * @param[in] name The name of the magnetic field.
+     */
     G4MagneticField* getMagneticField(const std::string& name);
+
+    /**
+     * Get a magnetic field by name.
+     * @param[in] name The name of the magnetic field.
+     */
     G4MagneticField* getMagneticField(const char* name);
 
+    /**
+     * Get an iterator pointing at the first magnetic field in the map.
+     * @return An iterator pointing at the first magnetic field in the map.
+     */
     LCDDProcessor::MagneticFields::const_iterator getMagneticFieldsBegin();
+
+    /**
+     * Get an iterator pointing at the end of the magnetic field map.
+     * @return An iterator pointing at the end of the magnetic field map.
+     */
     LCDDProcessor::MagneticFields::const_iterator getMagneticFieldsEnd();
 
-    // Passes mag through to LCDDFieldManager.
+    /**
+     * Add a global magnetic field.
+     * @param[in] mag The magnetic field to add.
+     */
     void addGlobalField(G4MagneticField* mag);
 
-    // Regions
+    /**
+     * Add a region by name.
+     * @param[in] name The name of the region.
+     * @param[in] reg  The region to add.
+     */
     void addRegion(std::string& name, G4Region* reg);
 
+    /**
+     * Get a region by name.
+     * @param[in] name The name of the region.
+     * @return The region.
+     */
     G4Region* getRegion(const std::string& name);
+
+    /**
+     * Get a region by name.
+     * @param[in] name The name of the region.
+     * @return The region.
+     */
     G4Region* getRegion(const char* name);
 
+    /**
+     * Get an iterator pointing to the first region in the map.
+     * @return An iterator pointing to the first region in the map.
+     */
     LCDDProcessor::Regions::const_iterator getRegionsBegin();
+
+    /**
+     * Get an iterator pointing to the end of the region map.
+     * @return An iterator pointing to the end of the region map.
+     */
     LCDDProcessor::Regions::const_iterator getRegionsEnd();
 
-    // user limit set
+    /**
+     * Add a PhysicsLimitSet by name.
+     * @param[in] name The name of the physics limit set.
+     * @param[in] lim  The PhysicsLimitSet object to register.
+     */
     void addLimitSet(std::string& name, PhysicsLimitSet* lim);
+
+    /**
+     * Get a PhysicsLimitSet by name.
+     * @param[in] name The name of the PhysicsLimitSet object.
+     * @return The matching PhysicsLimitSet object.
+     */
     PhysicsLimitSet* getLimitSet(const std::string& name);
+
+    /**
+     * Get a PhysicsLimitSet by name.
+     * @param[in] name The name of the PhysicsLimitSet object.
+     * @return The matching PhysicsLimitSet object.
+     */
     PhysicsLimitSet* getLimitSet(const char* name);
+
+    /**
+     * Get an iterator pointing to the first PhysicsLimitSet in the map.
+     * @return An iterator pointing to the first PhysicsLimitSet in the map.
+     */
     LCDDProcessor::LimitSets::const_iterator getLimitSetsBegin();
+
+    /**
+     * Get an iterator pointing to the end of the PhysicsLimitSet map.
+     * @return An iterator pointing to the end of the PhysicsLimitSet.
+     */
     LCDDProcessor::LimitSets::const_iterator getLimitSetsEnd();
 
-    // Vis Attributes
+    /**
+     * Add VisAttributes by name.
+     * @param[in] name The name of the VisAttributes to add.
+     * @param[in] vis  The VisAttributes object to add.
+     */
     void addVisAttributes(std::string& name, G4VisAttributes* vis);
 
+    /**
+     * Get VisAttributes by name.
+     * @param[in] The name of the VisAttributes.
+     */
     G4VisAttributes* getVisAttributes(const std::string& name);
+
+    /**
+     * Get VisAttributes by name.
+     * @param[in] The name of the VisAttributes.
+     */
     G4VisAttributes* getVisAttributes(const char* name);
 
+    /**
+     * Get an iterator pointing to the first VisAttributes in the map.
+     * @return An iterator pointing to the first VisAttributes in the map.
+     */
     LCDDProcessor::VisAttributes::const_iterator getVisAttributesBegin();
+
+    /**
+     * Get an iterator pointing to the end of the VisAttributes map.
+     * @return An iterator pointing to the end of the VisAttributes map.
+     */
     LCDDProcessor::VisAttributes::const_iterator getVisAttributesEnd();
 
+    /**
+     * Get the map of VisAttributes.
+     * @return The map of VisAttributes.
+     */
     const LCDDProcessor::VisAttributes* getVisAttributesStore() const;
+
+    /**
+     * Get the map of SDs.
+     * @return The map of SDs.
+     */
     const LCDDProcessor::SensitiveDetectors* getSensitiveDetectorStore() const;
+
+    /**
+     * Get the map of magnetic fields.
+     * @return The map of magnetic fields.
+     */
     const LCDDProcessor::MagneticFields* getMagneticFieldStore() const;
+
+    /**
+     * Get the map of regions.
+     * @return The map of regions.
+     */
     const LCDDProcessor::Regions* getRegionStore() const;
+
+    /**
+     * Get the map of PhysicsLimitSets.
+     * @return The map of PhysicsLimitSets.
+     */
     const LCDDProcessor::LimitSets* getLimitSetStore() const;
 
 private:

lcdd/include/lcdd/detectors
CellReadout.hh 1.3 -> 1.4
diff -u -r1.3 -r1.4
--- CellReadout.hh	1 Jul 2013 22:10:34 -0000	1.3
+++ CellReadout.hh	2 Jul 2013 21:19:44 -0000	1.4
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/include/lcdd/detectors/CellReadout.hh,v 1.3 2013/07/01 22:10:34 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/include/lcdd/detectors/CellReadout.hh,v 1.4 2013/07/02 21:19:44 jeremy Exp $
 
 #ifndef LCDD_DETECTORS_CELLREADOUT_HH
 #define LCDD_DETECTORS_CELLREADOUT_HH 1
@@ -9,8 +9,7 @@
 #include <string>
 
 /**
- * @brief This is a pure virtual base class for cell readouts to implement.
- * @note Not currently usable by the SD classes.
+ * This is a pure virtual base class for calorimeter cell readouts to implement.
  * @fixme Move to DDSegmentation package.
  */
 class CellReadout
@@ -44,25 +43,34 @@
 
     /**
      * Compute cell ID from local position.
+     * @param[in] pos A 2D position.
+     * @return A CellId from the position.
      */
-    virtual CellId cellId(Position2D) = 0;
+    virtual CellId cellId(Position2D pos) = 0;
 
     /**
      * Compute local position of a cell ID.
+     * @param[in] id The cell id.
+     * @return The position from the CellId.
      */
-    virtual Position2D position(CellId) = 0;
+    virtual Position2D position(CellId id) = 0;
 
     /**
      * Create a list of neighbor cells from a cell ID.
+     * @param[in] id The cell id.
+     * @return The list of Neighbors for the given CellId.
      */
-    virtual Neighbors neighbors(CellId) = 0;
+    virtual Neighbors neighbors(CellId id) = 0;
 
     /**
      * Get the list of field names.
+     * @return The list of field names defined by the readout.
      */
     const FieldNames& fieldNames();
 
 protected:
+
+    /** The list of field names. */
     FieldNames m_fieldNames;
 };
 

lcdd/src/lcdd/bfield
Dipole.cc 1.1 -> 1.2
diff -u -r1.1 -r1.2
--- Dipole.cc	1 Jul 2013 21:00:44 -0000	1.1
+++ Dipole.cc	2 Jul 2013 21:19:44 -0000	1.2
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/src/lcdd/bfield/Dipole.cc,v 1.1 2013/07/01 21:00:44 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/src/lcdd/bfield/Dipole.cc,v 1.2 2013/07/02 21:19:44 jeremy Exp $
 
 // LCDD
 #include "lcdd/bfield/Dipole.hh"
@@ -23,20 +23,20 @@
     double r = sqrt(Point[0] * Point[0] + Point[1] * Point[1]);
 
     // Check if z coordinate is within dipole z bounds.
-    if (z > m_zmin && z < m_zmax && r < m_rmax) {
+    if (z > _zmin && z < _zmax && r < _rmax) {
 
         // Convert to absolute value z and apply specified length unit.
-        double zc = fabs(z) / m_lunit;
+        double zc = fabs(z) / _lunit;
 
         //std::cout << "zc = " << zc << std::endl;
 
         // Apply all coefficients to this z coordinate.
-        for (size_t i = 0; i < m_coeffs.size(); ++i) {
-            bx += m_coeffs[i] * pow(zc, i);
+        for (size_t i = 0; i < _coeffs.size(); ++i) {
+            bx += _coeffs[i] * pow(zc, i);
         }
 
         // Convert to specified field unit.
-        bx *= m_funit;
+        bx *= _funit;
 
         // Flip sign for negative z.
         if (z < 0) {
@@ -55,60 +55,60 @@
 
 void Dipole::setZMax(double zmax)
 {
-    m_zmax = zmax;
+    _zmax = zmax;
 }
 
 double Dipole::getZMax()
 {
-    return m_zmax;
+    return _zmax;
 }
 
 void Dipole::setZMin(double zmin)
 {
-    m_zmin = zmin;
+    _zmin = zmin;
 }
 
 double Dipole::getZMin()
 {
-    return m_zmin;
+    return _zmin;
 }
 
 void Dipole::setRMax(double rmax)
 {
-    m_rmax = rmax;
+    _rmax = rmax;
 }
 
 double Dipole::getRMax()
 {
-    return m_rmax;
+    return _rmax;
 }
 
 void Dipole::addCoeff(double coeff)
 {
-    m_coeffs.push_back(coeff);
+    _coeffs.push_back(coeff);
 }
 
 const std::vector<double>& Dipole::getCoeffs()
 {
-    return m_coeffs;
+    return _coeffs;
 }
 
 void Dipole::setFieldUnit(double unit)
 {
-    m_funit = unit;
+    _funit = unit;
 }
 
 double Dipole::getFieldUnit()
 {
-    return m_funit;
+    return _funit;
 }
 
 void Dipole::setLengthUnit(double unit)
 {
-    m_lunit = unit;
+    _lunit = unit;
 }
 
 double Dipole::getLengthUnit()
 {
-    return m_lunit;
+    return _lunit;
 }

lcdd/src/lcdd/bfield
FieldManager.cc 1.1 -> 1.2
diff -u -r1.1 -r1.2
--- FieldManager.cc	1 Jul 2013 21:00:44 -0000	1.1
+++ FieldManager.cc	2 Jul 2013 21:19:44 -0000	1.2
@@ -1,10 +1,10 @@
-// $Header: /cvs/lcd/lcdd/src/lcdd/bfield/FieldManager.cc,v 1.1 2013/07/01 21:00:44 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/src/lcdd/bfield/FieldManager.cc,v 1.2 2013/07/02 21:19:44 jeremy Exp $
 
 // LCDD
 #include "lcdd/bfield/FieldManager.hh"
 #include "lcdd/core/LCDDProcessor.hh"
 
-FieldManager* FieldManager::m_instance = 0;
+FieldManager* FieldManager::_instance = 0;
 
 FieldManager::~FieldManager()
 {
@@ -12,10 +12,10 @@
 
 FieldManager* FieldManager::instance()
 {
-    if (m_instance == 0) {
-        m_instance = new FieldManager();
+    if (_instance == 0) {
+        _instance = new FieldManager();
     }
-    return m_instance;
+    return _instance;
 }
 
 MagneticFieldOverlay* FieldManager::makeOverlay(std::vector<G4MagneticField*> fields)
@@ -33,9 +33,9 @@
     G4MagneticField* field = 0;
 
     // Setup only the global fields specified in global_field.
-    if (m_globalfields.size() != 0) {
+    if (_globalfields.size() != 0) {
         // Use specific list of global fields registered with LCDDFieldManager.
-        field = setup(m_globalfields);
+        field = setup(_globalfields);
     }
     // No global fields, so treat all fields registered with LCDDProcessor
     // as global.
@@ -82,12 +82,12 @@
 
 void FieldManager::addGlobalField(G4MagneticField* f)
 {
-    m_globalfields.push_back(f);
+    _globalfields.push_back(f);
 }
 
 void FieldManager::addField(G4MagneticField* f)
 {
-    m_allfields.push_back(f);
+    _allfields.push_back(f);
 }
 
 FieldManager::FieldManager()

lcdd/src/lcdd/bfield
MagneticFieldOverlay.cc 1.1 -> 1.2
diff -u -r1.1 -r1.2
--- MagneticFieldOverlay.cc	26 Jun 2013 23:50:59 -0000	1.1
+++ MagneticFieldOverlay.cc	2 Jul 2013 21:19:44 -0000	1.2
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/src/lcdd/bfield/MagneticFieldOverlay.cc,v 1.1 2013/06/26 23:50:59 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/src/lcdd/bfield/MagneticFieldOverlay.cc,v 1.2 2013/07/02 21:19:44 jeremy Exp $
 
 // LCDD
 #include "lcdd/bfield/MagneticFieldOverlay.hh"
@@ -17,7 +17,7 @@
 void MagneticFieldOverlay::addMagneticField(G4MagneticField* field)
 {
     if (field != 0) {
-        m_fields.push_back(field);
+        _fields.push_back(field);
     }
 }
 
@@ -29,7 +29,7 @@
     //std::cout << "MagneticFieldOverlay::GetFieldValue" << std::endl;
 
     Bfield[0] = Bfield[1] = Bfield[2] = 0.;
-    for (std::vector<G4MagneticField*>::const_iterator iter = m_fields.begin(); iter != m_fields.end(); iter++) {
+    for (std::vector<G4MagneticField*>::const_iterator iter = _fields.begin(); iter != _fields.end(); iter++) {
         (*iter)->GetFieldValue(Point, Bfield);
     }
 

lcdd/src/lcdd/bfield
RZFieldMap.cc 1.1 -> 1.2
diff -u -r1.1 -r1.2
--- RZFieldMap.cc	1 Jul 2013 21:00:44 -0000	1.1
+++ RZFieldMap.cc	2 Jul 2013 21:19:44 -0000	1.2
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/src/lcdd/bfield/RZFieldMap.cc,v 1.1 2013/07/01 21:00:44 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/src/lcdd/bfield/RZFieldMap.cc,v 1.2 2013/07/02 21:19:44 jeremy Exp $
 
 // LCDD
 #include "lcdd/bfield/RZFieldMap.hh"
@@ -19,7 +19,7 @@
 #endif
 
 RZFieldMap::RZFieldMap(int numBinsR, int numBinsZ, double gridSizeR, double gridSizeZ, std::vector<RZBData> fieldData) :
-        m_numBinsR(numBinsR), m_numBinsZ(numBinsZ), m_gridSizeR(gridSizeR), m_gridSizeZ(gridSizeZ), m_BrArray(0), m_BzArray(0)
+        _numBinsR(numBinsR), _numBinsZ(numBinsZ), _gridSizeR(gridSizeR), _gridSizeZ(gridSizeZ), _BrArray(0), _BzArray(0)
 {
 
 #ifdef FIELD_MAP_DEBUG
@@ -45,29 +45,30 @@
         G4Exception("", "", FatalException, "gridSizeZ must be >= 0");
     }
 
-    m_maxR = (numBinsR - 1) * m_gridSizeR;
-    m_maxZ = (numBinsZ - 1) * m_gridSizeZ;
+    _maxR = (numBinsR - 1) * _gridSizeR;
+    _maxZ = (numBinsZ - 1) * _gridSizeZ;
 
     initializeArrays();
+
     fillArrays(fieldData);
 }
 
 void RZFieldMap::initializeArrays()
 {
     // Make two 2D arrays of numBinsZ x numBinsR 
-    m_BrArray = new double*[m_numBinsZ];
-    m_BzArray = new double*[m_numBinsZ];
+    _BrArray = new double*[_numBinsZ];
+    _BzArray = new double*[_numBinsZ];
 
-    for (int i = 0; i < m_numBinsZ; i++) {
-        m_BrArray[i] = new double[m_numBinsR];
-        m_BzArray[i] = new double[m_numBinsR];
+    for (int i = 0; i < _numBinsZ; i++) {
+        _BrArray[i] = new double[_numBinsR];
+        _BzArray[i] = new double[_numBinsR];
     }
 
     // Initialize arrays to all 0's.
-    for (int i = 0; i < m_numBinsZ; i++) {
-        for (int j = 0; j < m_numBinsR; j++) {
-            m_BrArray[i][j] = 0;
-            m_BzArray[i][j] = 0;
+    for (int i = 0; i < _numBinsZ; i++) {
+        for (int j = 0; j < _numBinsR; j++) {
+            _BrArray[i][j] = 0;
+            _BzArray[i][j] = 0;
         }
     }
 }
@@ -77,15 +78,15 @@
     for (std::vector<RZBData>::iterator iter = fieldData.begin(); iter != fieldData.end(); iter++) {
         RZBData rzb = *iter;
 
-        int iz = (int) ((rzb.z() + 0.0001) / m_gridSizeZ);
-        int ir = (int) ((rzb.r() + 0.0001) / m_gridSizeR);
+        int iz = (int) ((rzb.z() + 0.0001) / _gridSizeZ);
+        int ir = (int) ((rzb.r() + 0.0001) / _gridSizeR);
 
-        m_BzArray[iz][ir] = rzb.Bz();
-        m_BrArray[iz][ir] = rzb.Br();
+        _BzArray[iz][ir] = rzb.Bz();
+        _BrArray[iz][ir] = rzb.Br();
 
 #ifdef FIELD_MAP_DEBUG
         cout << "ir iz = " << ir << " " << iz << endl;
-        cout << "Br Bz = " << m_BrArray[iz][ir] << " " << m_BzArray[iz][ir] << endl;
+        cout << "Br Bz = " << _BrArray[iz][ir] << " " << _BzArray[iz][ir] << endl;
         cout << endl;
 #endif
     }
@@ -98,18 +99,18 @@
 
 void RZFieldMap::deleteArrays()
 {
-    for (int i = 0; i < m_numBinsZ; i++) {
-        delete[] m_BrArray[i];
-        delete[] m_BzArray[i];
+    for (int i = 0; i < _numBinsZ; i++) {
+        delete[] _BrArray[i];
+        delete[] _BzArray[i];
     }
-    delete[] m_BrArray;
-    delete[] m_BzArray;
+    delete[] _BrArray;
+    delete[] _BzArray;
 }
 
 /**
- * Compute B field at given point using the arrays of Br and Bz field strengths.
+ * Compute B-field at given point using the arrays of Br and Bz field components.
  *
- * This function is based on Takashi's FORTRAN code at
+ * This function is based on Takashi's FORTRAN code:
  *
  * /afs/slac/www/accel/nlc/local/systems/beamdelivery/geant/SDNEW/solenoid.f
  *
@@ -129,19 +130,19 @@
     double hr = 0;
 
     // Check for z or r out of range.
-    if (fabs(z) >= m_maxZ || r >= m_maxR) {
+    if (fabs(z) >= _maxZ || r >= _maxR) {
 #ifdef FIELD_MAP_DEBUG
         cout << "OUT OF RANGE: z r = " << fabs(z) << " " << r << endl;
-        cout << "MAX: maxZ maxR " << m_maxZ << " " << m_maxR << endl;
+        cout << "MAX: maxZ maxR " << _maxZ << " " << _maxR << endl;
 #endif
         return;
     }
 
     // Compute z bin.
-    int iz = (int) ((fabs(z) + 0.001) / m_gridSizeZ);
+    int iz = (int) ((fabs(z) + 0.001) / _gridSizeZ);
 
     // Compute r bin.
-    int ir = (int) ((r + 0.001) / m_gridSizeR);
+    int ir = (int) ((r + 0.001) / _gridSizeR);
 
     // Adjust for iz out of range.
 //   int izfar = 0;
@@ -160,7 +161,7 @@
     }
 
 // Check for Z overflow on iz+1.
-    if (iz + 1 >= m_numBinsZ) {
+    if (iz + 1 >= _numBinsZ) {
 #ifdef FIELD_MAP_DEBUG
         cout << "ERROR: iz overflow" << endl;
         cout << "iz=" << iz << endl;
@@ -170,7 +171,7 @@
     }
 
     // Check for R overflow on ir+1.
-    if (ir + 1 >= m_numBinsR) {
+    if (ir + 1 >= _numBinsR) {
 #ifdef FIELD_MAP_DEBUG
         cout << "ERROR: ir overflow" << endl;
         cout << "ir=" << ir << endl;
@@ -180,13 +181,13 @@
     }
 
 #ifdef FIELD_MAP_DEBUG
-    cout << "dz " << m_gridSizeZ << " dr " << m_gridSizeR << endl;
+    cout << "dz " << _gridSizeZ << " dr " << _gridSizeR << endl;
     cout << "z " << z << " r " << r << endl;
     cout << "iz " << iz << " ir " << ir << endl;
 #endif
 
-    double bz0 = m_BzArray[iz][ir];
-    double br0 = m_BrArray[iz][ir];
+    double bz0 = _BzArray[iz][ir];
+    double br0 = _BrArray[iz][ir];
 
 #ifdef FIELD_MAP_DEBUG
     cout << "bz0 " << bz0 << " br0 " << br0 << endl;
@@ -199,14 +200,14 @@
     double brdr = 0.;
 
     if (r > 0.0) {
-        delr = r - float(ir) * m_gridSizeR;
+        delr = r - float(ir) * _gridSizeR;
 
 #ifdef FIELD_MAP_DEBUG
-        if ( iz+1 == m_gridSizeZ-1 ) {
+        if ( iz+1 == _gridSizeZ-1 ) {
             cout << "WARNING: iz+1 == gridSizeZ-1" << endl;
         }
 
-        if ( ir+1 == m_gridSizeR-1 ) {
+        if ( ir+1 == _gridSizeR-1 ) {
             cout << "WARNING: ir+1 == gridSizeR-1" << endl;
         }
 #endif
@@ -215,35 +216,35 @@
         cout << "checking brarray access ..." << endl;
         cout << "iz+1=" << iz+1 << endl;
         cout << "ir=" << ir << endl;
-        cout << m_BrArray[iz+1][ir] << endl;
+        cout << _BrArray[iz+1][ir] << endl;
         cout << "m_BrArray[iz+1][ir] is ok" << endl;
         cout << "iz=" << iz << endl;
         cout << "ir+1=" << ir+1 << endl;
-        cout << m_BrArray[iz][ir+1] << endl;
+        cout << _BrArray[iz][ir+1] << endl;
         cout << "m_BrArray[iz][ir+1] is ok" << endl;
         cout << "done" << endl;
 #endif
 
-        brdz = (m_BrArray[iz + 1][ir] - br0) / m_gridSizeZ;
-        brdr = (m_BrArray[iz][ir + 1] - br0) / m_gridSizeR;
+        brdz = (_BrArray[iz + 1][ir] - br0) / _gridSizeZ;
+        brdr = (_BrArray[iz][ir + 1] - br0) / _gridSizeR;
 #ifdef FIELD_MAP_DEBUG
-        cout << "br= " << m_BrArray[iz+1][ir] << " " << m_BrArray[iz][ir+1] << endl;
+        cout << "br= " << _BrArray[iz+1][ir] << " " << _BrArray[iz][ir+1] << endl;
 #endif
     }
 
-    delz = fabs(z) - float(iz) * m_gridSizeZ;
+    delz = fabs(z) - float(iz) * _gridSizeZ;
 
 #ifdef FIELD_MAP_DEBUG
     cout << " z " << z << " abs(z) " << fabs(z) << " iz " << iz << endl;
-    cout << " float(iz-1) " << float(iz-1) << " dz " << m_gridSizeZ << endl;
+    cout << " float(iz-1) " << float(iz-1) << " dz " << _gridSizeZ << endl;
     cout << " delz " << delz << endl;
 #endif
 
-    double bzdz = (m_BzArray[iz + 1][ir] - bz0) / m_gridSizeZ;
-    double bzdr = (m_BzArray[iz][ir + 1] - bz0) / m_gridSizeR;
+    double bzdz = (_BzArray[iz + 1][ir] - bz0) / _gridSizeZ;
+    double bzdr = (_BzArray[iz][ir + 1] - bz0) / _gridSizeR;
 
 #ifdef FIELD_MAP_DEBUG
-    cout << "bz= " << m_BzArray[iz+1][ir] << " " << m_BzArray[iz][ir+1] << endl;
+    cout << "bz= " << _BzArray[iz+1][ir] << " " << _BzArray[iz][ir+1] << endl;
 #endif
 
 //   if(izfar==1) {

lcdd/src/lcdd/bfield
Solenoid.cc 1.1 -> 1.2
diff -u -r1.1 -r1.2
--- Solenoid.cc	1 Jul 2013 21:00:44 -0000	1.1
+++ Solenoid.cc	2 Jul 2013 21:19:44 -0000	1.2
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/src/lcdd/bfield/Solenoid.cc,v 1.1 2013/07/01 21:00:44 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/src/lcdd/bfield/Solenoid.cc,v 1.2 2013/07/02 21:19:44 jeremy Exp $
 
 // LCDD
 #include "lcdd/bfield/Solenoid.hh"
@@ -47,3 +47,63 @@
     os << "outerZ <" << _outerZ << ">" << std::endl;
     os << std::endl;
 }
+
+void Solenoid::setInnerField(double d)
+{
+    _innerField = d;
+}
+
+void Solenoid::setOuterField(double d)
+{
+    _outerField = d;
+}
+
+void Solenoid::setInnerR(double d)
+{
+    _innerR = d;
+}
+
+void Solenoid::setOuterR(double d)
+{
+    _outerR = d;
+}
+
+void Solenoid::setInnerZ(double d)
+{
+    _innerZ = d;
+}
+
+void Solenoid::setOuterZ(double d)
+{
+    _outerZ = d;
+}
+
+double Solenoid::getInnerField() const
+{
+    return _innerField;
+}
+
+double Solenoid::getOuterField() const
+{
+    return _outerField;
+}
+
+double Solenoid::getInnerR() const
+{
+    return _innerR;
+}
+
+double Solenoid::getOuterR() const
+{
+    return _outerR;
+}
+
+double Solenoid::getInnerZ() const
+{
+    return _innerZ;
+}
+
+double Solenoid::getOuterZ() const
+{
+    return _outerZ;
+}

lcdd/src/lcdd/core
GeometryManager.cc 1.3 -> 1.4
diff -u -r1.3 -r1.4
--- GeometryManager.cc	1 Jul 2013 22:10:34 -0000	1.3
+++ GeometryManager.cc	2 Jul 2013 21:19:44 -0000	1.4
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/src/lcdd/core/GeometryManager.cc,v 1.3 2013/07/01 22:10:34 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/src/lcdd/core/GeometryManager.cc,v 1.4 2013/07/02 21:19:44 jeremy Exp $
 
 // LCDD
 #include "lcdd/core/GeometryManager.hh"
@@ -72,8 +72,6 @@
     m_worldRegionIsSetup = true;
 }
 
-#ifdef HAVE_G4PVPLACEMENT_CHECKOVERLAPS
-
 void GeometryManager::checkOverlaps() const
 {
     checkOverlaps(getWorldLogicalVolume(), true);
@@ -117,6 +115,3 @@
         G4cerr << "WARNING: The logical volume named <" << name << "> was not found in the G4LogicalVolumeStore!" << std::endl;
     }
 }
-
-#endif
-

lcdd/src/lcdd/core
LCDDLibLoad.cc 1.1 -> 1.2
diff -u -r1.1 -r1.2
--- LCDDLibLoad.cc	26 Jun 2013 23:50:59 -0000	1.1
+++ LCDDLibLoad.cc	2 Jul 2013 21:19:44 -0000	1.2
@@ -5,6 +5,9 @@
 extern "C"
 {
 
+/**
+ * Function for loading LCDD SAX processes.
+ */
 void LCDDLoadProcesses()
 {
 
@@ -66,6 +69,9 @@
     LOAD_COMPONENT(limitProcess);
 }
 
+/**
+ * Function for loading LCDD subscribers.
+ */
 void LCDDLoadSubscribers()
 {
     // subscribers
@@ -102,6 +108,9 @@
     LOAD_COMPONENT(limitsetSubscriber);
 }
 
+/**
+ * Function for loading LCDD processes and subscribers.
+ */
 void LCDDLibLoad()
 {
     LCDDLoadProcesses();

lcdd/src/lcdd/core
LCDDMessenger.cc 1.1 -> 1.2
diff -u -r1.1 -r1.2
--- LCDDMessenger.cc	26 Jun 2013 23:50:59 -0000	1.1
+++ LCDDMessenger.cc	2 Jul 2013 21:19:44 -0000	1.2
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/src/lcdd/core/LCDDMessenger.cc,v 1.1 2013/06/26 23:50:59 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/src/lcdd/core/LCDDMessenger.cc,v 1.2 2013/07/02 21:19:44 jeremy Exp $
 
 // LCDD
 #include "lcdd/core/LCDDMessenger.hh"
@@ -15,153 +15,142 @@
 // STL
 #include <cassert>
 
-LCDDMessenger::LCDDMessenger()
-{
-    // define UI commands
-    defineCommands();
+LCDDMessenger::LCDDMessenger() {
+	// define UI commands
+	defineCommands();
 }
 
-LCDDMessenger::~LCDDMessenger()
-{
-    delete m_setupCmd;
-    delete m_setURICmd;
-    delete m_setSetupNameCmd;
-    delete m_setVersionCmd;
-    delete m_lcddDir;
+LCDDMessenger::~LCDDMessenger() {
+	delete m_setupCmd;
+	delete m_setURICmd;
+	delete m_setSetupNameCmd;
+	delete m_setVersionCmd;
+	delete m_lcddDir;
 }
 
-void LCDDMessenger::SetNewValue(G4UIcommand *cmd, G4String newVals)
-{
-    LCDDParser* parser = LCDDParser::instance();
-
-    G4String singleArg = newVals;
-    std::istringstream is((const char*) newVals);
-
-    if (cmd == m_setURICmd) {
-        parser->setURI(singleArg);
-    } else if (cmd == m_setSetupNameCmd) {
-        parser->setSetupName(singleArg);
-    } else if (cmd == m_setVersionCmd) {
-        parser->setVersion(singleArg);
-    } else if (cmd == m_setupCmd) {
-        G4String uri, setup, version;
-
-        is >> uri >> setup >> version;
-
-        parser->setURI(uri);
-        parser->setSetupName(setup);
-        parser->setVersion(version);
-    } else if (cmd == m_dumpCmd) {
-        //std::cout<<"arg: "<<singleArg<<std::endl;
-        NistElementsDump::writeXml(singleArg);
-    }
-#ifdef HAVE_G4PVPLACEMENT_CHECKOVERLAPS
-    else if (cmd==m_checkOverlapsCmd || cmd==m_checkOverlapsRecurseCmd)
-    {
-
-        bool recurse=false;
-
-        if (cmd == m_checkOverlapsRecurseCmd)
-        {
-            recurse=true;
-        }
-
-        G4String vol("");
-        is >> vol;
-
-        G4cout << "vol=" << vol << G4endl;
-        G4cout << "recurse=" << recurse << G4endl;
-
-        if (newVals != "")
-        {
-            // Check the named volume with optional recursion.
-            GeometryManager::instance()->checkOverlaps(vol, recurse);
-        }
-        else
-        {
-            // No volume.  Check the world, which is always done recursively!
-            GeometryManager::instance()->checkOverlaps();
-        }
-    }
-#endif
-    else {
-        G4cerr << "WARNING: Unknown cmd to LCDDMessenger - " << cmd << G4endl;
-    }
+void LCDDMessenger::SetNewValue(G4UIcommand *cmd, G4String newVals) {
+	LCDDParser* parser = LCDDParser::instance();
+
+	G4String singleArg = newVals;
+	std::istringstream is((const char*) newVals);
+
+	if (cmd == m_setURICmd) {
+		parser->setURI(singleArg);
+	} else if (cmd == m_setSetupNameCmd) {
+		parser->setSetupName(singleArg);
+	} else if (cmd == m_setVersionCmd) {
+		parser->setVersion(singleArg);
+	} else if (cmd == m_setupCmd) {
+		G4String uri, setup, version;
+
+		is >> uri >> setup >> version;
+
+		parser->setURI(uri);
+		parser->setSetupName(setup);
+		parser->setVersion(version);
+	} else if (cmd == m_dumpCmd) {
+		//std::cout<<"arg: "<<singleArg<<std::endl;
+		NistElementsDump::writeXml(singleArg);
+	} else if (cmd == m_checkOverlapsCmd || cmd == m_checkOverlapsRecurseCmd) {
+
+		bool recurse = false;
+
+		if (cmd == m_checkOverlapsRecurseCmd) {
+			recurse = true;
+		}
+
+		G4String vol("");
+		is >> vol;
+
+		G4cout << "vol=" << vol << G4endl;
+		G4cout << "recurse=" << recurse << G4endl;
+
+		if (newVals != "") {
+			// Check the named volume with optional recursion.
+			GeometryManager::instance()->checkOverlaps(vol, recurse);
+		} else {
+			// No volume.  Check the world, which is always done recursively!
+			GeometryManager::instance()->checkOverlaps();
+		}
+	} else {
+		G4cerr << "WARNING: Unknown cmd to LCDDMessenger - " << cmd << G4endl;
+	}
 }
 
-G4String LCDDMessenger::GetCurrentValue(G4UIcommand *)
-{
-    return G4String("");
+G4String LCDDMessenger::GetCurrentValue(G4UIcommand *) {
+	return G4String("");
 }
 
-void LCDDMessenger::defineCommands()
-{
-    G4UIparameter *p;
-
-    // LCDD directory
-    m_lcddDir = new G4UIdirectory("/lcdd/");
-    m_lcddDir->SetGuidance("XML detector description and geometry commands. [LCDD]");
-
-    // set URL for input geometry file
-    m_setURICmd = new G4UIcommand("/lcdd/url", this);
-    m_setURICmd->SetGuidance("Set the Uniform Resource Locator (URL) for the input geometry file.");
-    m_setURICmd->AvailableForStates(G4State_PreInit);
-
-    p = new G4UIparameter("URI", 's', false);
-    m_setURICmd->SetParameter(p);
-
-    // set name of GDML setup
-    m_setSetupNameCmd = new G4UIcommand("/lcdd/setupName", this);
-    m_setSetupNameCmd->SetGuidance("Set GDML setup name.");
-    m_setSetupNameCmd->AvailableForStates(G4State_PreInit);
-
-    p = new G4UIparameter("SetupName", 's', false);
-    m_setSetupNameCmd->SetParameter(p);
-
-    // set version of GDML setup
-    m_setVersionCmd = new G4UIcommand("/lcdd/version", this);
-    m_setVersionCmd->SetGuidance("Set GDML version tag.");
-    m_setVersionCmd->AvailableForStates(G4State_PreInit);
-
-    p = new G4UIparameter("Version", 's', false);
-    m_setVersionCmd->SetParameter(p);
-
-    // setup URI, Setup and Version in one command
-    m_setupCmd = new G4UIcommand("/lcdd/setup", this);
-    m_setupCmd->SetGuidance("Set URI, SetupName and Version with a single command.");
-    m_setupCmd->AvailableForStates(G4State_PreInit);
-
-    p = new G4UIparameter("URI", 's', false);
-    p->SetGuidance("URI is a URL to the input file.  It MUST NOT contain unescaped spaces.");
-    m_setupCmd->SetParameter(p);
-
-    p = new G4UIparameter("SetupName", 's', true);
-    m_setupCmd->SetParameter(p);
-
-    p = new G4UIparameter("Version", 's', true);
-    m_setupCmd->SetParameter(p);
-
-    m_dumpCmd = new G4UIcommand("/lcdd/dumpNistElements", this);
-    m_dumpCmd->SetGuidance("Dump NIST elements to file as GDML fragment, including lambda and X0.");
-    p = new G4UIparameter("Filename", 's', true);
-    p->SetDefaultValue("NistElements.xml");
-    m_dumpCmd->SetParameter(p);
-
-#ifdef HAVE_G4PVPLACEMENT_CHECKOVERLAPS
-    // Check overlaps.
-    m_checkOverlapsCmd = new G4UIcommand("/lcdd/checkOverlaps",this);
-    m_checkOverlapsCmd->SetGuidance("Call CheckOverlaps on a given volume or the world volume (no arguments).");
-
-    p = new G4UIparameter("Volume",'s',true);
-    p->SetDefaultValue("");
-    m_checkOverlapsCmd->SetParameter(p);
-
-    // Check overlaps with recursion to daughters.
-    m_checkOverlapsRecurseCmd = new G4UIcommand("/lcdd/checkOverlapsRecurse",this);
-    m_checkOverlapsRecurseCmd->SetGuidance("Call CheckOverlaps on a given volume and recursively check daughters.");
-
-    p = new G4UIparameter("Volume",'s',true);
-    p->SetDefaultValue("");
-    m_checkOverlapsRecurseCmd->SetParameter(p);
-#endif
+void LCDDMessenger::defineCommands() {
+	G4UIparameter *p;
+
+	// LCDD directory
+	m_lcddDir = new G4UIdirectory("/lcdd/");
+	m_lcddDir->SetGuidance(
+			"XML detector description and geometry commands. [LCDD]");
+
+	// set URL for input geometry file
+	m_setURICmd = new G4UIcommand("/lcdd/url", this);
+	m_setURICmd->SetGuidance(
+			"Set the Uniform Resource Locator (URL) for the input geometry file.");
+	m_setURICmd->AvailableForStates(G4State_PreInit);
+
+	p = new G4UIparameter("URI", 's', false);
+	m_setURICmd->SetParameter(p);
+
+	// set name of GDML setup
+	m_setSetupNameCmd = new G4UIcommand("/lcdd/setupName", this);
+	m_setSetupNameCmd->SetGuidance("Set GDML setup name.");
+	m_setSetupNameCmd->AvailableForStates(G4State_PreInit);
+
+	p = new G4UIparameter("SetupName", 's', false);
+	m_setSetupNameCmd->SetParameter(p);
+
+	// set version of GDML setup
+	m_setVersionCmd = new G4UIcommand("/lcdd/version", this);
+	m_setVersionCmd->SetGuidance("Set GDML version tag.");
+	m_setVersionCmd->AvailableForStates(G4State_PreInit);
+
+	p = new G4UIparameter("Version", 's', false);
+	m_setVersionCmd->SetParameter(p);
+
+	// setup URI, Setup and Version in one command
+	m_setupCmd = new G4UIcommand("/lcdd/setup", this);
+	m_setupCmd->SetGuidance(
+			"Set URI, SetupName and Version with a single command.");
+	m_setupCmd->AvailableForStates(G4State_PreInit);
+
+	p = new G4UIparameter("URI", 's', false);
+	p->SetGuidance(
+			"URI is a URL to the input file.  It MUST NOT contain unescaped spaces.");
+	m_setupCmd->SetParameter(p);
+
+	p = new G4UIparameter("SetupName", 's', true);
+	m_setupCmd->SetParameter(p);
+
+	p = new G4UIparameter("Version", 's', true);
+	m_setupCmd->SetParameter(p);
+
+	m_dumpCmd = new G4UIcommand("/lcdd/dumpNistElements", this);
+	m_dumpCmd->SetGuidance(
+			"Dump NIST elements to file as GDML fragment, including lambda and X0.");
+	p = new G4UIparameter("Filename", 's', true);
+	p->SetDefaultValue("NistElements.xml");
+	m_dumpCmd->SetParameter(p);
+
+	// Check overlaps.
+	m_checkOverlapsCmd = new G4UIcommand("/lcdd/checkOverlaps",this);
+	m_checkOverlapsCmd->SetGuidance("Call CheckOverlaps on a given volume or the world volume (no arguments).");
+
+	p = new G4UIparameter("Volume",'s',true);
+	p->SetDefaultValue("");
+	m_checkOverlapsCmd->SetParameter(p);
+
+	// Check overlaps with recursion to daughters.
+	m_checkOverlapsRecurseCmd = new G4UIcommand("/lcdd/checkOverlapsRecurse",this);
+	m_checkOverlapsRecurseCmd->SetGuidance("Call CheckOverlaps on a given volume and recursively check daughters.");
+
+	p = new G4UIparameter("Volume",'s',true);
+	p->SetDefaultValue("");
+	m_checkOverlapsRecurseCmd->SetParameter(p);
 }

lcdd/src/lcdd/core
LCDDParser.cc 1.2 -> 1.3
diff -u -r1.2 -r1.3
--- LCDDParser.cc	1 Jul 2013 21:00:44 -0000	1.2
+++ LCDDParser.cc	2 Jul 2013 21:19:44 -0000	1.3
@@ -1,4 +1,4 @@
-// $Header: /cvs/lcd/lcdd/src/lcdd/core/LCDDParser.cc,v 1.2 2013/07/01 21:00:44 jeremy Exp $
+// $Header: /cvs/lcd/lcdd/src/lcdd/core/LCDDParser.cc,v 1.3 2013/07/02 21:19:44 jeremy Exp $
 
 // LCDD
 #include "lcdd/core/LCDDParser.hh"
@@ -146,11 +146,6 @@
     return m_version;
 }
 
-void LCDDParser::setWorld(G4VPhysicalVolume *world)
-{
-    m_world = world;
-}
-
 bool LCDDParser::isValidSetup()
 {
     bool valid = true;
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