use fastIsInside and count the number of intersections

src/Algorithms/ParallelCyclotronTracker.cpp

@@ -1718,6 +1718,7 @@ void ParallelCyclotronTracker::Tracker_RK4() {
     // main integration loop
     *gmsg << "* ---------------------------- Start tracking ----------------------------" << endl;
     for(; step_m < maxSteps_m; step_m++) {
+	*gmsg << "step_m=" << step_m << endl;
         bool dumpEachTurn = false;
         if(initialTotalNum_m > 2) {
             // single particle dumping

src/Solvers/MGPoissonSolver.cpp

@@ -204,9 +204,9 @@ void MGPoissonSolver::computePotential(Field_t &rho, Vector_t hr) {
     IpplTimings::startTimer(FunctionTimer3_m);
     int id = 0;
 
-    for (int idx = localId[0].first(); idx <= localId[0].last(); idx++) {
+    for (int idz = localId[2].first(); idz <= localId[2].last(); idz++) {
         for (int idy = localId[1].first(); idy <= localId[1].last(); idy++) {
-    	     for (int idz = localId[2].first(); idz <= localId[2].last(); idz++) {
+    	    for (int idx = localId[0].first(); idx <= localId[0].last(); idx++) {
                  if (bp->isInside(idx, idy, idz)) 
                     RHS->Values()[id++] = rho[idx][idy][idz].get();
             }
@@ -299,9 +299,9 @@ void MGPoissonSolver::computePotential(Field_t &rho, Vector_t hr) {
     id = 0;
     rho = 0.0;
 
-    for (int idx = localId[0].first(); idx <= localId[0].last(); idx++) {
+    for (int idz = localId[2].first(); idz <= localId[2].last(); idz++) {
         for (int idy = localId[1].first(); idy <= localId[1].last(); idy++) {
-    	     for (int idz = localId[2].first(); idz <= localId[2].last(); idz++) {
+    	    for (int idx = localId[0].first(); idx <= localId[0].last(); idx++) {
                   NDIndex<3> l(Index(idx, idx), Index(idy, idy), Index(idz, idz));
                   if (bp->isInside(idx, idy, idz))
                      rho.localElement(l) = LHS->Values()[id++];
@@ -316,9 +316,9 @@ void MGPoissonSolver::redistributeWithRCB(NDIndex<3> localId) {
 
     int numMyGridPoints = 0;
 
-    for (int idx = localId[0].first(); idx <= localId[0].last(); idx++) {
+    for (int idz = localId[2].first(); idz <= localId[2].last(); idz++) {
         for (int idy = localId[1].first(); idy <= localId[1].last(); idy++) {
-    	     for (int idz = localId[2].first(); idz <= localId[2].last(); idz++) {
+    	    for (int idx = localId[0].first(); idx <= localId[0].last(); idx++) {
                  if (bp->isInside(idx, idy, idz))
                     numMyGridPoints++;
              }
@@ -334,9 +334,9 @@ void MGPoissonSolver::redistributeWithRCB(NDIndex<3> localId) {
     coords->ExtractView(&v, &stride);
     stride2 = 2 * stride;
 
-    for (int idx = localId[0].first(); idx <= localId[0].last(); idx++) {
+    for (int idz = localId[2].first(); idz <= localId[2].last(); idz++) {
         for (int idy = localId[1].first(); idy <= localId[1].last(); idy++) {
-    	     for (int idz = localId[2].first(); idz <= localId[2].last(); idz++) {
+    	    for (int idx = localId[0].first(); idx <= localId[0].last(); idx++) {
                  if (bp->isInside(idx, idy, idz)) {
                     v[0] = (double)idx;
                     v[stride] = (double)idy;
@@ -375,9 +375,9 @@ void MGPoissonSolver::IPPLToMap3D(NDIndex<3> localId) {
     int NumMyElements = 0;
     vector<int> MyGlobalElements;
 
-    for (int idx = localId[0].first(); idx <= localId[0].last(); idx++) {
+    for (int idz = localId[2].first(); idz <= localId[2].last(); idz++) {
         for (int idy = localId[1].first(); idy <= localId[1].last(); idy++) {
-    	     for (int idz = localId[2].first(); idz <= localId[2].last(); idz++) {
+            for (int idx = localId[0].first(); idx <= localId[0].last(); idx++) {
                  if (bp->isInside(idx, idy, idz)) {
                     MyGlobalElements.push_back(bp->getIdx(idx, idy, idz));
                     NumMyElements++;
@@ -385,7 +385,6 @@ void MGPoissonSolver::IPPLToMap3D(NDIndex<3> localId) {
             }
 	}
     }
-
     Map = new Epetra_Map(-1, NumMyElements, &MyGlobalElements[0], 0, Comm);
 }
 

src/Structure/BoundaryGeometry.cpp

@@ -1848,13 +1848,13 @@ BoundaryGeometry::intersectLineSegmentBoundary4PartInside (
                 assert (intersect_result != -1);
                 exit (42);              // terminate even if NDEBUG is set
             case 0:                     // no intersection
+            case 2:                     // both points are outside
             case 4:                     // both points are inside
                 intersect_result = 0;
                 break;              
             case 1:                     // line and triangle are in same plane
-            case 2:                     // both points are outside
             case 3:                     // unique intersection in segment
-                *gmsg << "* Intersection test returned: " << intersect_result << endl;
+                //*gmsg << "* Intersection test returned: " << intersect_result << endl;
                 triangle_id = (*it);
                 goto done;
             };

src/Structure/FieldSolver.cpp

@@ -246,7 +246,7 @@ void FieldSolver::initSolver(PartBunch &b) {
         std::vector<BoundaryGeometry *> geometries;
         for(unsigned int i = 0; i <= geoms.length(); i++) {
             if(geoms[i] == ',' || i == geoms.length()) {
-                BoundaryGeometry *geom = BoundaryGeometry::find(tmp)->clone(getOpalName() + string("_geometry"));
+                BoundaryGeometry *geom = BoundaryGeometry::find(Attributes::getString(itsAttr[GEOMETRY]))->clone(getOpalName() + string("_geometry"));
                 if(geom != 0) {
                     geometries.push_back(geom);
                 }