Changes in src/boundary.cpp [6e5084:d74077]

File:

• src/boundary.cpp (modified) (12 diffs)

src/boundary.cpp

@@ -6 +6 @@
 #include "Helpers/MemDebug.hpp"
 
-#include "Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp"
+#include "BoundaryPointSet.hpp"
+#include "BoundaryLineSet.hpp"
+#include "BoundaryTriangleSet.hpp"
+#include "CandidateForTesselation.hpp"
+#include "BoundaryPolygonSet.hpp"
+#include "TesselPoint.hpp"
 #include "World.hpp"
 #include "atom.hpp"
@@ -13 +18 @@
 #include "config.hpp"
 #include "element.hpp"
-#include "Helpers/helpers.hpp"
-#include "Helpers/Info.hpp"
+#include "helpers.hpp"
+#include "info.hpp"
 #include "linkedcell.hpp"
-#include "Helpers/Verbose.hpp"
-#include "Helpers/Log.hpp"
+#include "verbose.hpp"
+#include "log.hpp"
 #include "molecule.hpp"
 #include "tesselation.hpp"
 #include "tesselationhelpers.hpp"
 #include "World.hpp"
-#include "LinearAlgebra/Plane.hpp"
-#include "LinearAlgebra/Matrix.hpp"
+#include "Plane.hpp"
+#include "Matrix.hpp"
 #include "Box.hpp"
 
@@ -87 +92 @@
               if (Neighbour == BoundaryPoints[axis].end()) // make it wrap around
                 Neighbour = BoundaryPoints[axis].begin();
-              DistanceVector = runner->second.second->x - Neighbour->second.second->x;
+              DistanceVector = (runner->second.second->getPosition()) - (Neighbour->second.second->getPosition());
               do { // seek for neighbour pair where it flips
                   OldComponent = DistanceVector[Othercomponent];
@@ -93 +98 @@
                   if (Neighbour == BoundaryPoints[axis].end()) // make it wrap around
                     Neighbour = BoundaryPoints[axis].begin();
-                  DistanceVector = runner->second.second->x - Neighbour->second.second->x;
+                  DistanceVector = (runner->second.second->getPosition()) - (Neighbour->second.second->getPosition());
                   //Log() << Verbose(2) << "OldComponent is " << OldComponent << ", new one is " << DistanceVector.x[Othercomponent] << "." << endl;
                 } while ((runner != Neighbour) && (fabs(OldComponent / fabs(
@@ -105 +110 @@
                   //Log() << Verbose(1) << "The pair, where the sign of OtherComponent flips, is: " << *(Neighbour->second.second) << " and " << *(OtherNeighbour->second.second) << "." << endl;
                   // now we have found the pair: Neighbour and OtherNeighbour
-                  OtherVector = runner->second.second->x - OtherNeighbour->second.second->x;
+                  OtherVector = (runner->second.second->getPosition()) - (OtherNeighbour->second.second->getPosition());
                   //Log() << Verbose(1) << "Distances to Neighbour and OtherNeighbour are " << DistanceVector.x[component] << " and " << OtherVector.x[component] << "." << endl;
                   //Log() << Verbose(1) << "OtherComponents to Neighbour and OtherNeighbour are " << DistanceVector.x[Othercomponent] << " and " << OtherVector.x[Othercomponent] << "." << endl;
@@ -173 +178 @@
     // 3b. construct set of all points, transformed into cylindrical system and with left and right neighbours
     for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
-      ProjectedVector = (*iter)->x - (*MolCenter);
+      ProjectedVector = (*iter)->getPosition() - (*MolCenter);
       ProjectedVector.ProjectOntoPlane(AxisVector);
 
@@ -199 +204 @@
           DoLog(2) && (Log() << Verbose(2) << "Keeping new vector due to larger projected distance " << ProjectedVectorNorm << "." << endl);
         } else if (fabs(ProjectedVectorNorm - BoundaryTestPair.first->second.first) < MYEPSILON) {
-          helper = (*iter)->x;
-          helper -= *MolCenter;
+          helper = (*iter)->getPosition() - (*MolCenter);
           const double oldhelperNorm = helper.NormSquared();
-          helper = BoundaryTestPair.first->second.second->x - (*MolCenter);
+          helper = BoundaryTestPair.first->second.second->getPosition() - (*MolCenter);
           if (helper.NormSquared() < oldhelperNorm) {
             BoundaryTestPair.first->second.second = (*iter);
@@ -255 +259 @@
         {
           Vector SideA, SideB, SideC, SideH;
-          SideA = left->second.second->x - (*MolCenter);
+          SideA = left->second.second->getPosition() - (*MolCenter);
           SideA.ProjectOntoPlane(AxisVector);
           //          Log() << Verbose(1) << "SideA: " << SideA << endl;
 
-          SideB = right->second.second->x -(*MolCenter);
+          SideB = right->second.second->getPosition() -(*MolCenter);
           SideB.ProjectOntoPlane(AxisVector);
           //          Log() << Verbose(1) << "SideB: " << SideB << endl;
 
-          SideC = left->second.second->x - right->second.second->x;
+          SideC = left->second.second->getPosition() - right->second.second->getPosition();
           SideC.ProjectOntoPlane(AxisVector);
           //          Log() << Verbose(1) << "SideC: " << SideC << endl;
 
-          SideH = runner->second.second->x -(*MolCenter);
+          SideH = runner->second.second->getPosition() -(*MolCenter);
           SideH.ProjectOntoPlane(AxisVector);
           //          Log() << Verbose(1) << "SideH: " << SideH << endl;
@@ -675 +679 @@
   double cellvolume = 0.;
 
-  // transform to PAS by Action
-  Vector MainAxis(0.,0.,1.);
-  MoleculeRotateToPrincipalAxisSystem(MainAxis);
+  // transform to PAS
+  mol->PrincipalAxisSystem(true);
 
   IsAngstroem = configuration->GetIsAngstroem();
@@ -701 +704 @@
   // sum up the atomic masses
   for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
-      totalmass += (*iter)->type->mass;
+      totalmass += (*iter)->getType()->mass;
   }
   DoLog(0) && (Log() << Verbose(0) << "RESULT: The summed mass is " << setprecision(10) << totalmass << " atomicmassunit." << endl);
@@ -857 +860 @@
 
           // ... and put at new position
-          Inserter = (*iter)->x;
+          Inserter = (*iter)->getPosition();
           if (DoRandomRotation)
             Inserter *= Rotations;
@@ -882 +885 @@
             // copy atom ...
             CopyAtoms[(*iter)->nr] = (*iter)->clone();
-            CopyAtoms[(*iter)->nr]->x = Inserter;
+            (*CopyAtoms[(*iter)->nr]).setPosition(Inserter);
             Filling->AddAtom(CopyAtoms[(*iter)->nr]);
-            DoLog(4) && (Log() << Verbose(4) << "Filling atom " << **iter << ", translated to " << AtomTranslations << ", at final position is " << (CopyAtoms[(*iter)->nr]->x) << "." << endl);
+            DoLog(1) && (Log() << Verbose(1) << "Filling atom " << **iter << ", translated to " << AtomTranslations << ", at final position is " << (CopyAtoms[(*iter)->nr]->getPosition()) << "." << endl);
           } else {
             DoLog(1) && (Log() << Verbose(1) << "INFO: Position at " << Inserter << " is inner point, within boundary or outside of MaxDistance." << endl);