Merge branch 'develop' into svn: speedup compilation further

.gitattributes

@@ -141,6 +141,7 @@ classic/5.0/src/Algorithms/TrackIntegrator.cpp -text
 classic/5.0/src/Algorithms/TrackIntegrator.h -text
 classic/5.0/src/Algorithms/Tracker.cpp -text
 classic/5.0/src/Algorithms/Tracker.h -text
+classic/5.0/src/Algorithms/Vektor.h -text
 classic/5.0/src/Algorithms/rbendmap.h -text
 classic/5.0/src/BeamlineCore/BeamBeamRep.cpp -text
 classic/5.0/src/BeamlineCore/BeamBeamRep.h -text

classic/5.0/src/AbsBeamline/AttributeSet.cpp

@@ -20,6 +20,7 @@
 // ------------------------------------------------------------------------
 
 #include "AbsBeamline/AttributeSet.h"
+#include "Channels/Channel.h"
 #include "AbsBeamline/ElementBase.h"
 #include "Channels/DirectChannel.h"
 

classic/5.0/src/AbsBeamline/AttributeSet.h

@@ -22,13 +22,14 @@
 //
 // ------------------------------------------------------------------------
 
-#include "Channels/Channel.h"
+//#include "Channels/Channel.h"
 #include <functional>
 #include <string>
 #include <map>
 
 class ElementBase;
-
+class Channel;
+class ConstChannel;
 
 // Class AttributeSet
 // ------------------------------------------------------------------------

classic/5.0/src/AbsBeamline/Collimator.cpp

@@ -24,6 +24,7 @@
 #include "AbsBeamline/BeamlineVisitor.h"
 #include "Fields/Fieldmap.hh"
 #include "Structure/LossDataSink.h"
+#include "H5hut.h"
 #include <memory>
 
 extern Inform *gmsg;

classic/5.0/src/AbsBeamline/Collimator.h

@@ -25,13 +25,11 @@
 #include "AbsBeamline/Component.h"
 #include "AbsBeamline/BeamlineVisitor.h"
 #include "BeamlineGeometry/StraightGeometry.h"
-#include "Algorithms/PBunchDefs.h"
 
-#include <hdf5.h>
-#include "H5hut.h"
+//#include "H5hut.h"
 #include <vector>
 
-
+typedef struct h5_file h5_file_t;
 class LossDataSink;
 
 // Class Collimator

classic/5.0/src/AbsBeamline/Component.h

@@ -25,7 +25,7 @@
 
 #include "AbsBeamline/ElementBase.h"
 #include "Fields/EMField.h"
-#include "Algorithms/PBunchDefs.h"
+#include "Algorithms/Vektor.h"
 
 #define EPS_MISALIGNMENT 1e-8
 

classic/5.0/src/AbsBeamline/CyclotronValley.cpp

@@ -23,8 +23,6 @@
 #include "Algorithms/PartBunch.h"
 #include "Fields/Fieldmap.hh"
 #include "Physics/Physics.h"
-#include "ValueDefinitions/RealVariable.h"
-#include "Structure/BoundaryGeometry.h"
 
 #include <iostream>
 #include <fstream>

classic/5.0/src/AbsBeamline/ElementBase.cpp

@@ -27,8 +27,6 @@
 #include "Channels/Channel.h"
 #include <string>
 
-//#include "BeamlineGeometry/Euclid3D.h"
-//#include "BeamlineGeometry/Geometry.h"
 #include "Structure/BoundaryGeometry.h"
 #include "Solvers/WakeFunction.hh"
 #include "Solvers/SurfacePhysicsHandler.hh"

classic/5.0/src/AbsBeamline/Monitor.cpp

@@ -23,6 +23,9 @@
 #include "Algorithms/PartBunch.h"
 #include "Fields/Fieldmap.hh"
 #include "AbsBeamline/BeamlineVisitor.h"
+
+#include "H5hut.h"
+
 #include <fstream>
 #include <memory>
 

classic/5.0/src/AbsBeamline/Monitor.h

@@ -26,10 +26,10 @@
 #include "BeamlineGeometry/StraightGeometry.h"
 //#include "Algorithms/PBunchDefs.h"
 
-#include <hdf5.h>
-#include "H5hut.h"
-#include <list>
+//#include "H5hut.h"
 
+#include <list>
+typedef struct h5_file h5_file_t;
 class PartBunch;
 
 // Class Monitor

classic/5.0/src/AbsBeamline/ParallelPlate.cpp

@@ -24,8 +24,6 @@
 #include "Algorithms/PartBunch.h"
 #include "Fields/Fieldmap.hh"
 #include "Physics/Physics.h"
-#include "ValueDefinitions/RealVariable.h"
-#include "Structure/BoundaryGeometry.h"
 
 #include <iostream>
 #include <fstream>

classic/5.0/src/AbsBeamline/RBend.cpp

@@ -19,6 +19,7 @@
 // ------------------------------------------------------------------------
 
 #include "AbsBeamline/RBend.h"
+#include "Algorithms/PartBunch.h"
 #include "AbsBeamline/BeamlineVisitor.h"
 #include "Fields/Fieldmap.hh"
 #include <iostream>

classic/5.0/src/AbsBeamline/RFCavity.cpp

@@ -22,8 +22,6 @@
 #include "AbsBeamline/BeamlineVisitor.h"
 #include "Algorithms/PartBunch.h"
 #include "Fields/Fieldmap.hh"
-#include "ValueDefinitions/RealVariable.h"
-#include "Structure/BoundaryGeometry.h"
 
 #include "gsl/gsl_interp.h"
 #include "gsl/gsl_spline.h"
@@ -513,16 +511,6 @@ void RFCavity::initialise(PartBunch *bunch, const double &scaleFactor) {
 
     RefPartBunch_m = bunch;
 
-    //    The variable doPhase is not used; If it should be used in the future the following
-    //    lines have to be implemented on the OPAL side
-    //    (THIS IS THE CLASSICS SIDE AND OPAL OBJECTS ARE INAPPROPRIATE HERE)
-    //     bool doPhase  = true;
-    //     RealVariable *ar = dynamic_cast<RealVariable *>(OpalData::getInstance()->find("OMITPHASE"));
-    //     if (ar) {
-    //         doPhase = false;
-    //         msg << "Phase of particle is not considered "<< endl;
-    //     }
-
     INFOMSG("q= " << RefPartBunch_m->getQ() << " m= " << RefPartBunch_m->getM() / 1.0E9 << endl);
 
 

classic/5.0/src/AbsBeamline/SBend.cpp

@@ -20,6 +20,7 @@
 
 #include "Algorithms/PartPusher.h"
 #include "AbsBeamline/SBend.h"
+#include "Algorithms/PartBunch.h"
 #include "AbsBeamline/BeamlineVisitor.h"
 #include "Fields/Fieldmap.hh"
 #include <iostream>

classic/5.0/src/Algorithms/PBunchDefs.h

-//#include "Ippl.h"
 #ifndef PBUNCHDEFS_H
 #define PBUNCHDEFS_H
 
+#include "Algorithms/Vektor.h"
 #include "Particle/IntCIC.h"
 #include "Particle/IntNGP.h"
 #include "Particle/IntSUDS.h"
@@ -26,7 +26,7 @@ typedef InterpolatorTraits<double, 3, IntrplCIC_t>::Cache_t Pcache_t;
 
 typedef UniformCartesian<3, double> Mesh_t;
 
-typedef ParticleSpatialLayout<double, 3>::SingleParticlePos_t Vector_t;
+//typedef ParticleSpatialLayout<double, 3>::SingleParticlePos_t Vector_t;
 
 typedef ParticleSpatialLayout< double, 3, Mesh_t  > Layout_t;
 

classic/5.0/src/Algorithms/PartBins.cpp

 #include <cfloat>
 #include <vector>
 #include "Algorithms/PartBins.h"
+#include "Algorithms/PBunchDefs.h"
 #include "Physics/Physics.h"
 extern Inform *gmsg;
 

classic/5.0/src/Algorithms/PartBins.h

@@ -17,7 +17,7 @@
 #define OPAL_Bins_HH
 
 #ifndef PartBinTest
-#include "Ippl.h"
+#include "Algorithms/PBunchDefs.h"
 #else
 #include "ranlib.h"
 #define Inform ostream
@@ -124,7 +124,7 @@ public:
     void resetPartInBin_cyc(size_t newPartNum[], int binID);
     /** update particles number in bin after particle deletion */
     void updatePartInBin(size_t countLost[]);
-    /** update local particles number in bin after particle deletion */    
+    /** update local particles number in bin after particle deletion */
     void updatePartInBin_cyc(size_t countLost[]);
 
     void updateDeletedPartsInBin(size_t countLost[]) ;
@@ -253,10 +253,6 @@ public:
     size_t getTotalNumPerBin(int b);
 
 
-
-
-
-
 private:
 
     /** Defines energy threshold for rebining */

classic/5.0/src/Algorithms/PartBinsCyc.h

@@ -17,7 +17,6 @@
 #define OPAL_BinsCyc_HH
 
 #ifndef PartBinTest
-#include "Ippl.h"
 #else
 #include "ranlib.h"
 #define Inform ostream

classic/5.0/src/Algorithms/PartBunch.h

@@ -20,11 +20,12 @@
 //
 // ------------------------------------------------------------------------
 
-//#include "Ippl.h"
+#include "Ippl.h"
 #include "PBunchDefs.h"
 #include "Algorithms/Particle.h"
 #include "FixedAlgebra/FMatrix.h"
 #include "FixedAlgebra/FVector.h"
+#include "Algorithms/PartBins.h"
 #include "Algorithms/PartBinsCyc.h"
 #include "Algorithms/PartData.h"
 #include "Utilities/SwitcherError.h"
@@ -34,12 +35,9 @@
 #include <vector>
 
 
-//class PartBunch;
 class Distribution;
 class LossDataSink;
 class FieldSolver;
-//#include "Structure/FieldSolver.h"
-
 class ListElem;
 
 template <class T, int, int> class FMatrix;

classic/5.0/src/Algorithms/PartPusher.h

 #ifndef CLASSIC_PartPusher_H
 #define CLASSIC_PartPusher_H
 
-#include "Algorithms/PartBunch.h"
+#include "Algorithms/Vektor.h"
 #include "Algorithms/PartData.h"
 #include "Physics/Physics.h"
-#include "Ippl.h"
 
 class BorisPusher {
 public:
@@ -37,17 +36,17 @@ inline void BorisPusher::kick(const Vector_t &R, Vector_t &P, const Vector_t &Ef
 
 
 inline void BorisPusher::kick(const Vector_t &R, Vector_t &P, const Vector_t &Ef, const Vector_t &Bf, const double &dt, const double &mass, const double &charge) const {
-	
-	// Implementation follows chapter 4-4, p. 61 - 63 from 
+
+	// Implementation follows chapter 4-4, p. 61 - 63 from
 	// Birdsall, C. K. and Langdon, A. B. (1985). Plasma physics via computer simulation.
 	//
 	// Up to finite precision effects, the new implementation is equivalent to the old one, but uses less floating point operations.
 	//
-	// Relativistic variant implemented below is described in chapter 15-4, p. 356 - 357. However, since other units are used here, small 
-	// modifications are required. The relativistic variant can be derived from the nonrelativistic one by replacing 
-	//     mass 
-	// by 
-	//     gamma * rest mass 
+	// Relativistic variant implemented below is described in chapter 15-4, p. 356 - 357. However, since other units are used here, small
+	// modifications are required. The relativistic variant can be derived from the nonrelativistic one by replacing
+	//     mass
+	// by
+	//     gamma * rest mass
 	// and transforming the units.
 	//
 	// Parameters:
@@ -63,17 +62,17 @@ inline void BorisPusher::kick(const Vector_t &R, Vector_t &P, const Vector_t &Ef
 
 	// Half step E
 	P += 0.5 * dt * charge * c / mass * Ef;
-	
+
 	// Full step B
 	double const gamma = sqrt(1.0 + dot(P, P));
 	Vector_t const t = 0.5 * dt * charge * c * c / (gamma * mass) * Bf;
 	Vector_t const w = P + cross(P, t);
 	Vector_t const s = 2.0 / (1.0 + dot(t, t)) * t;
 	P += cross(w, s);
-	
+
 	// Half step E
 	P += 0.5 * dt * charge * c / mass * Ef;
-	
+
 }