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

@@ -9,7 +9,7 @@
 //
 // ------------------------------------------------------------------------
 //
-// $Author: ganz $
+// $Author: ganz_p $
 //
 // ------------------------------------------------------------------------
 
@@ -23,7 +23,7 @@
 #include "Beamlines/Beamline.h"
 #include "Beamlines/FlaggedBeamline.h"
 
-#include "Classic/Algorithms/PartData.h"  //for the beam reference
+#include "Classic/Algorithms/PartData.h"
 
 #include "Utilities/Options.h"
 #include "Utilities/Util.h"
@@ -42,6 +42,7 @@ ThickTracker::ThickTracker(const Beamline &beamline,
     , hamiltonian_m(1)
     , RefPartR_m(0.0)
     , RefPartP_m(0.0)
+    , itsDataSink_m(nullptr)
     , itsOpalBeamline_m(beamline.getOrigin3D(), beamline.getCoordTransformationTo())
     , zstart_m(0.0)
     , zstop_m(0.0)
@@ -182,6 +183,7 @@ void ThickTracker::insertFringeField(SBend* pSBend, lstruct_t& mBL,
 
 /**
  * @brief Algorithm for Thick Map-Tracking
+ *
  */
 void ThickTracker::execute() {
     
@@ -230,7 +232,8 @@ void ThickTracker::execute() {
 
 
 void ThickTracker::checkElementOrder_m() {
-    // check order of beamline
+
+    // check order of beam line
     FieldList elements = itsOpalBeamline_m.getElementByType(ElementBase::ANY);
     beamline_t::const_iterator el = elements_m.cbegin();
     
@@ -510,7 +513,7 @@ void ThickTracker::advanceDispersion_m(fMatrix_t tempMatrix,
         FMatrix<double, 2, 1> dxi, dyi, dx, dy;
     
         for (int i=0; i<2; i++){
-            dxi[i][0]= initialVal[0][i];
+            dxi[i][0]= initialVal[0][i]; //
             dyi[i][0]= initialVal[0][i+2];
     
             subdx[i][0]=tempMatrix[i][5]*itsBunch_m->getInitialBeta();