Opal maps

This MR will implement Map tracking for:

• Quadrupole
• Dipole
• Drifts
• Bends

TODO list:

• Code implementation (@ganz_p): ThickTracker, Hamiltonian, MapAnalyser
• Doxygen documentation (@ganz_p)
• Documentation (@ganz_p)
• Code cleaning (@frey_m)
• Regression tests (@snuverink_j)
• Examples (@ganz_p)
• Jupyter notebook (@ganz_p)
• Use beam line order

Remaining issues:

• Output dumps in local coordinates only
• Dipole until 1st order
• Tune calculation not stable
• Space charge calculations needs to be verified
• Fringe fields for Bends

src/Algorithms/ThickTracker.cpp

@@ -279,15 +279,6 @@ void ThickTracker::execute() {
     msg<<"gamma: " << itsBunch_m->getInitialGamma()<< endl;
     msg<<"E0:  " << itsBunch_m->getM() <<endl;
 
-    std::ofstream tmap;
-    tmap.open ("TransferMap.txt");
-    tmap << std::setprecision(16);
-
-
-    std::ofstream tplot; // stat
-    tplot.open ("tunePlot.txt");
-    tmap << std::setprecision(16);
-
     std::ofstream disp; // stat
     disp.open("dispersion.txt");
     disp << std::setprecision(10);
@@ -300,10 +291,6 @@ void ThickTracker::execute() {
     //dispInitialVal[0][1]= -0.1681363086;
 
 
-    tplot.close();
-    tplot.open("tunePlot.txt", std::ios::app);
-
-
     setTime();
     
     double t = itsBunch_m->getT();
@@ -373,11 +360,7 @@ void ThickTracker::fillGaps_m() {
 void ThickTracker::track_m()
 {
     IpplTimings::startTimer(mapTracking_m);
-#ifdef PHIL_WRITE
-    std::ofstream tplot;
-    tplot.open("tunePlot.txt", std::ios::app);
-#endif
-
+    
     fMatrix_t tFMatrix;
     for (int i=0; i<6; i++){
         tFMatrix[i][i]=1.;
@@ -587,10 +570,9 @@ void ThickTracker::dump_m() {
     
     const std::size_t step = itsBunch_m->getGlobalTrackStep();
     
-    bool psDump   = (step + 1) % Options::psDumpFreq;
-    bool statDump = (step + 1) % Options::statDumpFreq;
+    bool psDump   = ((step + 1) % Options::psDumpFreq == 0);
+    bool statDump = ((step + 1) % Options::statDumpFreq == 0);
     
-
     // Sample fields at (xmin, ymin, zmin), (xmax, ymax, zmax) and the centroid location. We
     // are sampling the electric and magnetic fields at the back, front and
     // center of the beam.
@@ -635,6 +617,7 @@ void ThickTracker::update_m(const double& spos,
     itsBunch_m->calcBeamParameters();
     itsBunch_m->calcEMean();
     
+    //FIXME update time
 //     itsBunch_m->setT();