Changeset 1ca488 for src


Ignore:
Timestamp:
Jan 26, 2010, 12:45:41 PM (15 years ago)
Author:
Tillmann Crueger <crueger@…>
Branches:
Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable
Children:
04b6f9
Parents:
8927ae (diff), 1cf5df (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.
Message:

Merge commit 'heber/Analysis_PairCorrelation' into MenuRefactoring

Conflicts:

Makefile.am
molecuilder/src/Makefile.am
molecuilder/src/builder.cpp
molecuilder/src/unittests/Makefile.am

Location:
src
Files:
4 added
20 edited

Legend:

Unmodified
Added
Removed

  • src/Makefile.am

    r8927ae r1ca488  
    1717UIHEADER = ${ACTIONSHEADER} ${VIEWHEADER} ${MENUHEADER} UIElements/UIFactory.hpp UIElements/TextUIFactory.hpp UIElements/MainWindow.hpp UIElements/TextWindow.hpp UIElements/Dialog.hpp UIElements/TextDialog.hpp
    1818
    19 SOURCE = ${ANALYSISSOURCE} ${ATOMSOURCE} ${UISOURCE} bond.cpp bondgraph.cpp boundary.cpp config.cpp element.cpp ellipsoid.cpp errorlogger.cpp graph.cpp helpers.cpp leastsquaremin.cpp linkedcell.cpp log.cpp logger.cpp memoryusageobserver.cpp moleculelist.cpp molecule.cpp molecule_dynamics.cpp molecule_fragmentation.cpp molecule_geometry.cpp molecule_graph.cpp molecule_pointcloud.cpp parser.cpp periodentafel.cpp tesselation.cpp tesselationhelpers.cpp vector.cpp verbose.cpp menu.cpp
    20 HEADER = ${ANALYSISHEADER} ${ATOMHEADER} ${UIHEADER} bond.hpp bondgraph.hpp boundary.hpp config.hpp defs.hpp element.hpp ellipsoid.hpp errorlogger.hpp graph.hpp helpers.hpp leastsquaremin.hpp linkedcell.hpp lists.hpp log.hpp logger.hpp memoryallocator.hpp memoryusageobserver.hpp molecule.hpp molecule_template.hpp parser.hpp periodentafel.hpp stackclass.hpp tesselation.hpp tesselationhelpers.hpp vector.hpp verbose.hpp menu.hpp
     19SOURCE = ${ANALYSISSOURCE} ${ATOMSOURCE} ${UISOURCE} bond.cpp bondgraph.cpp boundary.cpp config.cpp element.cpp ellipsoid.cpp errorlogger.cpp graph.cpp helpers.cpp info.cpp leastsquaremin.cpp linkedcell.cpp log.cpp logger.cpp memoryusageobserver.cpp moleculelist.cpp molecule.cpp molecule_dynamics.cpp molecule_fragmentation.cpp molecule_geometry.cpp molecule_graph.cpp molecule_pointcloud.cpp parser.cpp periodentafel.cpp tesselation.cpp tesselationhelpers.cpp vector.cpp verbose.cpp menu.cpp
     20HEADER = ${ANALYSISHEADER} ${ATOMHEADER} ${UIHEADER} bond.hpp bondgraph.hpp boundary.hpp config.hpp defs.hpp element.hpp ellipsoid.hpp errorlogger.hpp graph.hpp helpers.hpp info.hpp leastsquaremin.hpp linkedcell.hpp lists.hpp log.hpp logger.hpp memoryallocator.hpp memoryusageobserver.hpp molecule.hpp molecule_template.hpp parser.hpp periodentafel.hpp stackclass.hpp tesselation.hpp tesselationhelpers.hpp vector.hpp verbose.hpp menu.hpp
    2121
    2222BOOST_LIB = $(BOOST_LDFLAGS) $(BOOST_MPL_LIB)
    … …  
    3838#EXTRA_DIST = ${molecuilder_DATA}
    3939
     40FORCE:
     41$(srcdir)/.git-version: FORCE
     42        @if (test -d $(top_srcdir)/../.git && cd $(srcdir) && git describe HEAD) > .git-version-t 2>/dev/null \
     43          && ! diff .git-version-t $(srcdir)/.git-version >/dev/null 2>&1; then \
     44          mv -f .git-version-t $(srcdir)/.git-version; \
     45        else \
     46          rm -f .git-version-t; \
     47        fi
     48
     49EXTRA_DIST = $(srcdir)/.git-version
     50
     51$(srcdir)/version.c: $(srcdir)/.git-version
     52        echo "const char *ESPACKVersion = \"$(PACKAGE_NAME) -- git version: "`cat $(srcdir)/.git-version`"\";" > $@
     53
     54molecuilder_SOURCES += $(srcdir)/version.c

  • src/atom_bondedparticle.cpp

    r8927ae r1ca488  
    121121  bond *CandidateBond = NULL;
    122122
     123  NoBonds = CountBonds();
    123124  //Log() << Verbose(3) << "Walker " << *this << ": " << (int)this->type->NoValenceOrbitals << " > " << NoBonds << "?" << endl;
    124   NoBonds = CountBonds();
    125125  if ((int)(type->NoValenceOrbitals) > NoBonds) { // we have a mismatch, check all bonding partners for mismatch
    126126    for (BondList::const_iterator Runner = ListOfBonds.begin(); Runner != ListOfBonds.end(); (++Runner)) {
    127127      OtherWalker = (*Runner)->GetOtherAtom(this);
    128128      OtherNoBonds = OtherWalker->CountBonds();
    129       //Log() << Verbose(3) << "OtherWalker " << *OtherWalker << ": " << (int)OtherWalker->type->NoValenceOrbitals << " > " << NoBonds << "?" << endl;
    130       if ((int)(OtherWalker->type->NoValenceOrbitals) > NoBonds) { // check if possible candidate
     129      //Log() << Verbose(3) << "OtherWalker " << *OtherWalker << ": " << (int)OtherWalker->type->NoValenceOrbitals << " > " << OtherNoBonds << "?" << endl;
     130      if ((int)(OtherWalker->type->NoValenceOrbitals) > OtherNoBonds) { // check if possible candidate
    131131        if ((CandidateBond == NULL) || (ListOfBonds.size() > OtherWalker->ListOfBonds.size())) { // pick the one with fewer number of bonds first
    132132          CandidateBond = (*Runner);
    … …  
    137137    if ((CandidateBond != NULL)) {
    138138      CandidateBond->BondDegree++;
    139       Log() << Verbose(2) << "Increased bond degree for bond " << *CandidateBond << "." << endl;
     139      //Log() << Verbose(2) << "Increased bond degree for bond " << *CandidateBond << "." << endl;
    140140    } else {
    141       //Log() << Verbose(2) << "Could not find correct degree for atom " << *this << "." << endl;
     141      eLog() << Verbose(2) << "Could not find correct degree for atom " << *this << "." << endl;
    142142      FalseBondDegree++;
    143143    }

  • src/bondgraph.cpp

    r8927ae r1ca488  
    3535/** Parses the bond lengths in a given file and puts them int a matrix form.
    3636 * Allocates \a MatrixContainer for BondGraph::BondLengthMatrix, using MatrixContainer::ParseMatrix(),
    37  * but only if parsing is successfull. Otherwise variable is left as NULL.
     37 * but only if parsing is successful. Otherwise variable is left as NULL.
    3838 * \param *out output stream for debugging
    3939 * \param filename file with bond lengths to parse

  • src/boundary.cpp

    r8927ae r1ca488  
    1010#include "element.hpp"
    1111#include "helpers.hpp"
     12#include "info.hpp"
    1213#include "linkedcell.hpp"
    1314#include "log.hpp"
    … …  
    3334double *GetDiametersOfCluster(const Boundaries *BoundaryPtr, const molecule *mol, Tesselation *&TesselStruct, const bool IsAngstroem)
    3435{
     36        Info FunctionInfo(__func__);
    3537  // get points on boundary of NULL was given as parameter
    3638  bool BoundaryFreeFlag = false;
    … …  
    5355  } else {
    5456    BoundaryPoints = BoundaryPtr;
    55     Log() << Verbose(1) << "Using given boundary points set." << endl;
     57    Log() << Verbose(0) << "Using given boundary points set." << endl;
    5658  }
    5759  // determine biggest "diameter" of cluster for each axis
    … …  
    6769          //Log() << Verbose(1) << "Current component is " << component << ", Othercomponent is " << Othercomponent << "." << endl;
    6870          for (Boundaries::const_iterator runner = BoundaryPoints[axis].begin(); runner != BoundaryPoints[axis].end(); runner++) {
    69               //Log() << Verbose(2) << "Current runner is " << *(runner->second.second) << "." << endl;
     71              //Log() << Verbose(1) << "Current runner is " << *(runner->second.second) << "." << endl;
    7072              // seek for the neighbours pair where the Othercomponent sign flips
    7173              Neighbour = runner;
    … …  
    8284                  DistanceVector.CopyVector(&runner->second.second->x);
    8385                  DistanceVector.SubtractVector(&Neighbour->second.second->x);
    84                   //Log() << Verbose(3) << "OldComponent is " << OldComponent << ", new one is " << DistanceVector.x[Othercomponent] << "." << endl;
     86                  //Log() << Verbose(2) << "OldComponent is " << OldComponent << ", new one is " << DistanceVector.x[Othercomponent] << "." << endl;
    8587                } while ((runner != Neighbour) && (fabs(OldComponent / fabs(
    8688                  OldComponent) - DistanceVector.x[Othercomponent] / fabs(
    … …  
    9193                    OtherNeighbour = BoundaryPoints[axis].end();
    9294                  OtherNeighbour--;
    93                   //Log() << Verbose(2) << "The pair, where the sign of OtherComponent flips, is: " << *(Neighbour->second.second) << " and " << *(OtherNeighbour->second.second) << "." << endl;
     95                  //Log() << Verbose(1) << "The pair, where the sign of OtherComponent flips, is: " << *(Neighbour->second.second) << " and " << *(OtherNeighbour->second.second) << "." << endl;
    9496                  // now we have found the pair: Neighbour and OtherNeighbour
    9597                  OtherVector.CopyVector(&runner->second.second->x);
    9698                  OtherVector.SubtractVector(&OtherNeighbour->second.second->x);
    97                   //Log() << Verbose(2) << "Distances to Neighbour and OtherNeighbour are " << DistanceVector.x[component] << " and " << OtherVector.x[component] << "." << endl;
    98                   //Log() << Verbose(2) << "OtherComponents to Neighbour and OtherNeighbour are " << DistanceVector.x[Othercomponent] << " and " << OtherVector.x[Othercomponent] << "." << endl;
     99                  //Log() << Verbose(1) << "Distances to Neighbour and OtherNeighbour are " << DistanceVector.x[component] << " and " << OtherVector.x[component] << "." << endl;
     100                  //Log() << Verbose(1) << "OtherComponents to Neighbour and OtherNeighbour are " << DistanceVector.x[Othercomponent] << " and " << OtherVector.x[Othercomponent] << "." << endl;
    99101                  // do linear interpolation between points (is exact) to extract exact intersection between Neighbour and OtherNeighbour
    100102                  w1 = fabs(OtherVector.x[Othercomponent]);
    … …  
    103105                      * OtherVector.x[component]) / (w1 + w2));
    104106                  // mark if it has greater diameter
    105                   //Log() << Verbose(2) << "Comparing current greatest " << GreatestDiameter[component] << " to new " << tmp << "." << endl;
     107                  //Log() << Verbose(1) << "Comparing current greatest " << GreatestDiameter[component] << " to new " << tmp << "." << endl;
    106108                  GreatestDiameter[component] = (GreatestDiameter[component]
    107109                      > tmp) ? GreatestDiameter[component] : tmp;
    108110                } //else
    109               //Log() << Verbose(2) << "Saw no sign flip, probably top or bottom node." << endl;
     111              //Log() << Verbose(1) << "Saw no sign flip, probably top or bottom node." << endl;
    110112            }
    111113        }
    … …  
    135137Boundaries *GetBoundaryPoints(const molecule *mol, Tesselation *&TesselStruct)
    136138{
     139        Info FunctionInfo(__func__);
    137140  atom *Walker = NULL;
    138141  PointMap PointsOnBoundary;
    … …  
    149152  double angle = 0.;
    150153
    151   Log() << Verbose(1) << "Finding all boundary points." << endl;
    152154  // 3a. Go through every axis
    153155  for (int axis = 0; axis < NDIM; axis++) {
    … …  
    176178        angle = 0.; // otherwise it's a vector in Axis Direction and unimportant for boundary issues
    177179
    178       //Log() << Verbose(2) << "Checking sign in quadrant : " << ProjectedVector.Projection(&AngleReferenceNormalVector) << "." << endl;
     180      //Log() << Verbose(1) << "Checking sign in quadrant : " << ProjectedVector.Projection(&AngleReferenceNormalVector) << "." << endl;
    179181      if (ProjectedVector.ScalarProduct(&AngleReferenceNormalVector) > 0) {
    180182        angle = 2. * M_PI - angle;
    181183      }
    182       Log() << Verbose(2) << "Inserting " << *Walker << ": (r, alpha) = (" << radius << "," << angle << "): " << ProjectedVector << endl;
     184      Log() << Verbose(1) << "Inserting " << *Walker << ": (r, alpha) = (" << radius << "," << angle << "): " << ProjectedVector << endl;
    183185      BoundaryTestPair = BoundaryPoints[axis].insert(BoundariesPair(angle, DistancePair (radius, Walker)));
    184186      if (!BoundaryTestPair.second) { // same point exists, check first r, then distance of original vectors to center of gravity
    … …  
    210212    // printing all inserted for debugging
    211213    //    {
    212     //      Log() << Verbose(2) << "Printing list of candidates for axis " << axis << " which we have inserted so far." << endl;
     214    //      Log() << Verbose(1) << "Printing list of candidates for axis " << axis << " which we have inserted so far." << endl;
    213215    //      int i=0;
    214216    //      for(Boundaries::iterator runner = BoundaryPoints[axis].begin(); runner != BoundaryPoints[axis].end(); runner++) {
    215217    //        if (runner != BoundaryPoints[axis].begin())
    216     //          Log() << Verbose(2) << ", " << i << ": " << *runner->second.second;
     218    //          Log() << Verbose(0) << ", " << i << ": " << *runner->second.second;
    217219    //        else
    218     //          Log() << Verbose(2) << i << ": " << *runner->second.second;
     220    //          Log() << Verbose(0) << i << ": " << *runner->second.second;
    219221    //        i++;
    220222    //      }
    221     //      Log() << Verbose(2) << endl;
     223    //      Log() << Verbose(0) << endl;
    222224    //    }
    223225    // 3c. throw out points whose distance is less than the mean of left and right neighbours
    … …  
    249251          SideA.SubtractVector(MolCenter);
    250252          SideA.ProjectOntoPlane(&AxisVector);
    251           //          Log() << Verbose(0) << "SideA: " << SideA << endl;
     253          //          Log() << Verbose(1) << "SideA: " << SideA << endl;
    252254
    253255          SideB.CopyVector(&right->second.second->x);
    254256          SideB.SubtractVector(MolCenter);
    255257          SideB.ProjectOntoPlane(&AxisVector);
    256           //          Log() << Verbose(0) << "SideB: " << SideB << endl;
     258          //          Log() << Verbose(1) << "SideB: " << SideB << endl;
    257259
    258260          SideC.CopyVector(&left->second.second->x);
    259261          SideC.SubtractVector(&right->second.second->x);
    260262          SideC.ProjectOntoPlane(&AxisVector);
    261           //          Log() << Verbose(0) << "SideC: " << SideC << endl;
     263          //          Log() << Verbose(1) << "SideC: " << SideC << endl;
    262264
    263265          SideH.CopyVector(&runner->second.second->x);
    264266          SideH.SubtractVector(MolCenter);
    265267          SideH.ProjectOntoPlane(&AxisVector);
    266           //          Log() << Verbose(0) << "SideH: " << SideH << endl;
     268          //          Log() << Verbose(1) << "SideH: " << SideH << endl;
    267269
    268270          // calculate each length
    … …  
    277279          const double delta = SideC.Angle(&SideH);
    278280          const double MinDistance = a * sin(beta) / (sin(delta)) * (((alpha < M_PI / 2.) || (gamma < M_PI / 2.)) ? 1. : -1.);
    279           //Log() << Verbose(2) << " I calculated: a = " << a << ", h = " << h << ", beta(" << left->second.second->Name << "," << left->second.second->Name << "-" << right->second.second->Name << ") = " << beta << ", delta(" << left->second.second->Name << "," << runner->second.second->Name << ") = " << delta << ", Min = " << MinDistance << "." << endl;
     281          //Log() << Verbose(1) << " I calculated: a = " << a << ", h = " << h << ", beta(" << left->second.second->Name << "," << left->second.second->Name << "-" << right->second.second->Name << ") = " << beta << ", delta(" << left->second.second->Name << "," << runner->second.second->Name << ") = " << delta << ", Min = " << MinDistance << "." << endl;
    280282          Log() << Verbose(1) << "Checking CoG distance of runner " << *runner->second.second << " " << h << " against triangle's side length spanned by (" << *left->second.second << "," << *right->second.second << ") of " << MinDistance << "." << endl;
    281283          if ((fabs(h / fabs(h) - MinDistance / fabs(MinDistance)) < MYEPSILON) && ((h - MinDistance)) < -MYEPSILON) {
    … …  
    303305void FindConvexBorder(const molecule* mol, Tesselation *&TesselStruct, const LinkedCell *LCList, const char *filename)
    304306{
     307        Info FunctionInfo(__func__);
    305308  bool BoundaryFreeFlag = false;
    306309  Boundaries *BoundaryPoints = NULL;
    307 
    308   Log() << Verbose(1) << "Begin of FindConvexBorder" << endl;
    309310
    310311  if (TesselStruct != NULL) // free if allocated
    … …  
    317318      BoundaryPoints = GetBoundaryPoints(mol, TesselStruct);
    318319  } else {
    319       Log() << Verbose(1) << "Using given boundary points set." << endl;
     320      Log() << Verbose(0) << "Using given boundary points set." << endl;
    320321  }
    321322
    … …  
    323324  for (int axis=0; axis < NDIM; axis++)
    324325    {
    325       Log() << Verbose(2) << "Printing list of candidates for axis " << axis << " which we have inserted so far." << endl;
     326      Log() << Verbose(1) << "Printing list of candidates for axis " << axis << " which we have inserted so far." << endl;
    326327      int i=0;
    327328      for(Boundaries::iterator runner = BoundaryPoints[axis].begin(); runner != BoundaryPoints[axis].end(); runner++) {
    328329        if (runner != BoundaryPoints[axis].begin())
    329           Log() << Verbose(2) << ", " << i << ": " << *runner->second.second;
     330          Log() << Verbose(0) << ", " << i << ": " << *runner->second.second;
    330331        else
    331           Log() << Verbose(2) << i << ": " << *runner->second.second;
     332          Log() << Verbose(0) << i << ": " << *runner->second.second;
    332333        i++;
    333334      }
    334       Log() << Verbose(2) << endl;
     335      Log() << Verbose(0) << endl;
    335336    }
    336337
    … …  
    341342          eLog() << Verbose(2) << "Point " << *(runner->second.second) << " is already present!" << endl;
    342343
    343   Log() << Verbose(2) << "I found " << TesselStruct->PointsOnBoundaryCount << " points on the convex boundary." << endl;
     344  Log() << Verbose(0) << "I found " << TesselStruct->PointsOnBoundaryCount << " points on the convex boundary." << endl;
    344345  // now we have the whole set of edge points in the BoundaryList
    345346
    … …  
    347348  //  Log() << Verbose(1) << "Listing PointsOnBoundary:";
    348349  //  for(PointMap::iterator runner = PointsOnBoundary.begin(); runner != PointsOnBoundary.end(); runner++) {
    349   //    Log() << Verbose(1) << " " << *runner->second;
     350  //    Log() << Verbose(0) << " " << *runner->second;
    350351  //  }
    351   //  Log() << Verbose(1) << endl;
     352  //  Log() << Verbose(0) << endl;
    352353
    353354  // 3a. guess starting triangle
    … …  
    359360  // 3c. check whether all atoms lay inside the boundary, if not, add to boundary points, segment triangle into three with the new point
    360361  if (!TesselStruct->InsertStraddlingPoints(mol, LCList))
    361     Log() << Verbose(1) << "Insertion of straddling points failed!" << endl;
    362 
    363   Log() << Verbose(2) << "I created " << TesselStruct->TrianglesOnBoundary.size() << " intermediate triangles with " << TesselStruct->LinesOnBoundary.size() << " lines and " << TesselStruct->PointsOnBoundary.size() << " points." << endl;
     362    eLog() << Verbose(1) << "Insertion of straddling points failed!" << endl;
     363
     364  Log() << Verbose(0) << "I created " << TesselStruct->TrianglesOnBoundary.size() << " intermediate triangles with " << TesselStruct->LinesOnBoundary.size() << " lines and " << TesselStruct->PointsOnBoundary.size() << " points." << endl;
    364365
    365366  // 4. Store triangles in tecplot file
    … …  
    411412//    Log() << Verbose(1) << "Correction of concave tesselpoints failed!" << endl;
    412413
    413   Log() << Verbose(2) << "I created " << TesselStruct->TrianglesOnBoundary.size() << " triangles with " << TesselStruct->LinesOnBoundary.size() << " lines and " << TesselStruct->PointsOnBoundary.size() << " points." << endl;
     414  Log() << Verbose(0) << "I created " << TesselStruct->TrianglesOnBoundary.size() << " triangles with " << TesselStruct->LinesOnBoundary.size() << " lines and " << TesselStruct->PointsOnBoundary.size() << " points." << endl;
    414415
    415416  // 4. Store triangles in tecplot file
    … …  
    437438  if (BoundaryFreeFlag)
    438439    delete[] (BoundaryPoints);
    439 
    440   Log() << Verbose(1) << "End of FindConvexBorder" << endl;
    441440};
    442441
    … …  
    450449bool RemoveAllBoundaryPoints(class Tesselation *&TesselStruct, const molecule * const mol, const char * const filename)
    451450{
     451        Info FunctionInfo(__func__);
    452452  int i=0;
    453453  char number[MAXSTRINGSIZE];
    … …  
    460460  PointMap::iterator PointRunner;
    461461  while (!TesselStruct->PointsOnBoundary.empty()) {
    462     Log() << Verbose(2) << "Remaining points are: ";
     462    Log() << Verbose(1) << "Remaining points are: ";
    463463    for (PointMap::iterator PointSprinter = TesselStruct->PointsOnBoundary.begin(); PointSprinter != TesselStruct->PointsOnBoundary.end(); PointSprinter++)
    464       Log() << Verbose(2) << *(PointSprinter->second) << "\t";
    465     Log() << Verbose(2) << endl;
     464      Log() << Verbose(0) << *(PointSprinter->second) << "\t";
     465    Log() << Verbose(0) << endl;
    466466
    467467    PointRunner = TesselStruct->PointsOnBoundary.begin();
    … …  
    503503double ConvexizeNonconvexEnvelope(class Tesselation *&TesselStruct, const molecule * const mol, const char * const filename)
    504504{
     505        Info FunctionInfo(__func__);
    505506  double volume = 0;
    506507  class BoundaryPointSet *point = NULL;
    … …  
    516517  int run = 0;
    517518
    518   Log() << Verbose(0) << "Begin of ConvexizeNonconvexEnvelope" << endl;
    519 
    520519  // check whether there is something to work on
    521520  if (TesselStruct == NULL) {
    … …  
    539538      for (LineMap::iterator LineRunner = point->lines.begin(); LineRunner != point->lines.end(); LineRunner++) {
    540539        line = LineRunner->second;
    541         Log() << Verbose(2) << "INFO: Current line of point " << *point << " is " << *line << "." << endl;
     540        Log() << Verbose(1) << "INFO: Current line of point " << *point << " is " << *line << "." << endl;
    542541        if (!line->CheckConvexityCriterion()) {
    543542          // remove the point if needed
    … …  
    604603
    605604  // end
    606   Log() << Verbose(1) << "Volume is " << volume << "." << endl;
    607   Log() << Verbose(0) << "End of ConvexizeNonconvexEnvelope" << endl;
     605  Log() << Verbose(0) << "Volume is " << volume << "." << endl;
    608606  return volume;
    609607};
    … …  
    619617double VolumeOfConvexEnvelope(class Tesselation *TesselStruct, class config *configuration)
    620618{
     619        Info FunctionInfo(__func__);
    621620  bool IsAngstroem = configuration->GetIsAngstroem();
    622621  double volume = 0.;
    … …  
    625624
    626625  // 6a. Every triangle forms a pyramid with the center of gravity as its peak, sum up the volumes
    627   Log() << Verbose(1)
    628       << "Calculating the volume of the pyramids formed out of triangles and center of gravity."
    629       << endl;
    630626  for (TriangleMap::iterator runner = TesselStruct->TrianglesOnBoundary.begin(); runner != TesselStruct->TrianglesOnBoundary.end(); runner++)
    631627    { // go through every triangle, calculate volume of its pyramid with CoG as peak
    … …  
    642638      const double h = x.Norm(); // distance of CoG to triangle
    643639      const double PyramidVolume = (1. / 3.) * G * h; // this formula holds for _all_ pyramids (independent of n-edge base or (not) centered peak)
    644       Log() << Verbose(2) << "Area of triangle is " << setprecision(10) << G << " "
     640      Log() << Verbose(1) << "Area of triangle is " << setprecision(10) << G << " "
    645641          << (IsAngstroem ? "angstrom" : "atomiclength") << "^2, height is "
    646642          << h << " and the volume is " << PyramidVolume << " "
    … …  
    664660void StoreTrianglesinFile(const molecule * const mol, const Tesselation *&TesselStruct, const char *filename, const char *extraSuffix)
    665661{
     662        Info FunctionInfo(__func__);
    666663  // 4. Store triangles in tecplot file
    667664  if (filename != NULL) {
    … …  
    671668      OutputName.append(TecplotSuffix);
    672669      ofstream *tecplot = new ofstream(OutputName.c_str());
    673       WriteTecplotFile(tecplot, TesselStruct, mol, 0);
     670      WriteTecplotFile(tecplot, TesselStruct, mol, -1);
    674671      tecplot->close();
    675672      delete(tecplot);
    … …  
    698695void PrepareClustersinWater(config *configuration, molecule *mol, double ClusterVolume, double celldensity)
    699696{
     697        Info FunctionInfo(__func__);
    700698  bool IsAngstroem = true;
    701699  double *GreatestDiameter = NULL;
    … …  
    798796molecule * FillBoxWithMolecule(MoleculeListClass *List, molecule *filler, config &configuration, double distance[NDIM], double RandomAtomDisplacement, double RandomMolDisplacement, bool DoRandomRotation)
    799797{
     798        Info FunctionInfo(__func__);
    800799  molecule *Filling = new molecule(filler->elemente);
    801800  Vector CurrentPosition;
    … …  
    814813  double phi[NDIM];
    815814  class Tesselation *TesselStruct[List->ListOfMolecules.size()];
    816 
    817   Log() << Verbose(0) << "Begin of FillBoxWithMolecule" << endl;
    818815
    819816  i=0;
    … …  
    877874          for (int i=0;i<NDIM;i++)
    878875            FillerTranslations.x[i] = RandomMolDisplacement*(rand()/(RAND_MAX/2.) - 1.);
    879           Log() << Verbose(3) << "INFO: Translating this filler by " << FillerTranslations << "." << endl;
     876          Log() << Verbose(2) << "INFO: Translating this filler by " << FillerTranslations << "." << endl;
    880877
    881878          // go through all atoms
    … …  
    938935        delete(TesselStruct[i]);
    939936  }
    940   Log() << Verbose(0) << "End of FillBoxWithMolecule" << endl;
    941 
    942937  return Filling;
    943938};
    … …  
    951946 * \param RADIUS radius of the virtual sphere
    952947 * \param *filename filename prefix for output of vertex data
    953  */
    954 void FindNonConvexBorder(const molecule* const mol, Tesselation *&TesselStruct, const LinkedCell *&LCList, const double RADIUS, const char *filename = NULL)
     948 * \return true - tesselation successful, false - tesselation failed
     949 */
     950bool FindNonConvexBorder(const molecule* const mol, Tesselation *&TesselStruct, const LinkedCell *&LCList, const double RADIUS, const char *filename = NULL)
    955951{
     952        Info FunctionInfo(__func__);
    956953  bool freeLC = false;
    957   LineMap::iterator baseline;
     954  bool status = false;
     955  CandidateForTesselation *baseline;
    958956  LineMap::iterator testline;
    959   bool OneLoopWithoutSuccessFlag = false;  // marks whether we went once through all baselines without finding any without two triangles
     957  bool OneLoopWithoutSuccessFlag = true;  // marks whether we went once through all baselines without finding any without two triangles
    960958  bool TesselationFailFlag = false;
    961 
    962   Log() << Verbose(1) << "Entering search for non convex hull. " << endl;
     959  BoundaryTriangleSet *T = NULL;
     960
    963961  if (TesselStruct == NULL) {
    964962    Log() << Verbose(1) << "Allocating Tesselation struct ..." << endl;
    … …  
    970968  }
    971969
    972   Log() << Verbose(0) << "Begin of FindNonConvexBorder\n";
    973 
    974970  // initialise Linked Cell
    975971  if (LCList == NULL) {
    … …  
    982978
    983979  // 2. expand from there
    984   baseline = TesselStruct->LinesOnBoundary.begin();
    985   baseline++; // skip first line
    986   while ((baseline != TesselStruct->LinesOnBoundary.end()) || (OneLoopWithoutSuccessFlag)) {
    987     if (baseline->second->triangles.size() == 1) {
    988       CheckListOfBaselines(TesselStruct);
    989       // 3. find next triangle
    990       TesselationFailFlag = TesselStruct->FindNextSuitableTriangle(*(baseline->second), *(((baseline->second->triangles.begin()))->second), RADIUS, LCList); //the line is there, so there is a triangle, but only one.
    991       OneLoopWithoutSuccessFlag = OneLoopWithoutSuccessFlag || TesselationFailFlag;
    992       if (!TesselationFailFlag)
    993         eLog() << Verbose(2) << "FindNextSuitableTriangle failed." << endl;
    994 
    995       // write temporary envelope
    996       if (filename != NULL) {
    997         if ((DoSingleStepOutput && ((TesselStruct->TrianglesOnBoundary.size() % SingleStepWidth == 0)))) { // if we have a new triangle and want to output each new triangle configuration
    998           TesselStruct->Output(filename, mol);
    999         }
     980  while ((!TesselStruct->OpenLines.empty()) && (OneLoopWithoutSuccessFlag)) {
     981    // 2a. fill all new OpenLines
     982    Log() << Verbose(1) << "There are " << TesselStruct->OpenLines.size() << " open lines to scan for candidates:" << endl;
     983    for (CandidateMap::iterator Runner = TesselStruct->OpenLines.begin(); Runner != TesselStruct->OpenLines.end(); Runner++)
     984      Log() << Verbose(2) << *(Runner->second) << endl;
     985
     986    for (CandidateMap::iterator Runner = TesselStruct->OpenLines.begin(); Runner != TesselStruct->OpenLines.end(); Runner++) {
     987      baseline = Runner->second;
     988      if (baseline->pointlist.empty()) {
     989        T = (((baseline->BaseLine->triangles.begin()))->second);
     990        Log() << Verbose(1) << "Finding best candidate for open line " << *baseline->BaseLine << " of triangle " << *T << endl;
     991        TesselationFailFlag = TesselStruct->FindNextSuitableTriangle(*baseline, *T, RADIUS, LCList); //the line is there, so there is a triangle, but only one.
    1000992      }
    1001       if (TesselationFailFlag) {
    1002         baseline = TesselStruct->LinesOnBoundary.begin();
    1003         OneLoopWithoutSuccessFlag = false;
    1004         Log() << Verbose(2) << "Baseline set to begin." << endl;
     993    }
     994
     995    // 2b. search for smallest ShortestAngle among all candidates
     996    double ShortestAngle = 4.*M_PI;
     997    Log() << Verbose(1) << "There are " << TesselStruct->OpenLines.size() << " open lines to scan for the best candidates:" << endl;
     998    for (CandidateMap::iterator Runner = TesselStruct->OpenLines.begin(); Runner != TesselStruct->OpenLines.end(); Runner++)
     999      Log() << Verbose(2) << *(Runner->second) << endl;
     1000
     1001    for (CandidateMap::iterator Runner = TesselStruct->OpenLines.begin(); Runner != TesselStruct->OpenLines.end(); Runner++) {
     1002      if (Runner->second->ShortestAngle < ShortestAngle) {
     1003        baseline = Runner->second;
     1004        ShortestAngle = baseline->ShortestAngle;
     1005        //Log() << Verbose(1) << "New best candidate is " << *baseline->BaseLine << " with point " << *baseline->point << " and angle " << baseline->ShortestAngle << endl;
    10051006      }
    1006     } else {
    1007       //Log() << Verbose(1) << "Line " << *baseline->second << " has " << baseline->second->triangles.size() << " triangles adjacent" << endl;
    1008       if (baseline->second->triangles.size() != 2) {
    1009         eLog() << Verbose(0) << "TESSELATION FINISHED WITH INVALID TRIANGLE COUNT!" << endl;
    1010         performCriticalExit();
     1007    }
     1008    if ((ShortestAngle == 4.*M_PI) || (baseline->pointlist.empty()))
     1009      OneLoopWithoutSuccessFlag = false;
     1010    else {
     1011      TesselStruct->AddCandidateTriangle(*baseline);
     1012    }
     1013
     1014    // write temporary envelope
     1015    if (filename != NULL) {
     1016      if ((DoSingleStepOutput && ((TesselStruct->TrianglesOnBoundary.size() % SingleStepWidth == 0)))) { // if we have a new triangle and want to output each new triangle configuration
     1017        TesselStruct->Output(filename, mol);
    10111018      }
    10121019    }
    1013 
    1014     if ((baseline == TesselStruct->LinesOnBoundary.end()) && (OneLoopWithoutSuccessFlag)) {
    1015       baseline = TesselStruct->LinesOnBoundary.begin();   // restart if we reach end due to newly inserted lines
    1016       OneLoopWithoutSuccessFlag = false;
    1017     }
    1018     baseline++;
    1019   }
    1020   // check envelope for consistency
    1021   CheckListOfBaselines(TesselStruct);
    1022 
    1023   // look whether all points are inside of the convex envelope, otherwise add them via degenerated triangles
    1024   //->InsertStraddlingPoints(mol, LCList);
     1020  }
     1021//  // check envelope for consistency
     1022//  status = CheckListOfBaselines(TesselStruct);
     1023//
     1024//  // look whether all points are inside of the convex envelope, otherwise add them via degenerated triangles
     1025//  //->InsertStraddlingPoints(mol, LCList);
    10251026//  mol->GoToFirst();
    10261027//  class TesselPoint *Runner = NULL;
    … …  
    10371038//  }
    10381039
    1039   // Purges surplus triangles.
    1040   TesselStruct->RemoveDegeneratedTriangles();
     1040//  // Purges surplus triangles.
     1041//  TesselStruct->RemoveDegeneratedTriangles();
    10411042
    10421043  // check envelope for consistency
    1043   CheckListOfBaselines(TesselStruct);
     1044  status = CheckListOfBaselines(TesselStruct);
     1045
     1046  // store before correction
     1047  StoreTrianglesinFile(mol, (const Tesselation *&)TesselStruct, filename, "");
     1048
     1049  // correct degenerated polygons
     1050  TesselStruct->CorrectAllDegeneratedPolygons();
     1051
     1052  // check envelope for consistency
     1053  status = CheckListOfBaselines(TesselStruct);
    10441054
    10451055  // write final envelope
    … …  
    10491059  if (freeLC)
    10501060    delete(LCList);
    1051   Log() << Verbose(0) << "End of FindNonConvexBorder\n";
     1061
     1062  return status;
    10521063};
    10531064
    … …  
    10611072Vector* FindEmbeddingHole(MoleculeListClass *mols, molecule *srcmol)
    10621073{
     1074        Info FunctionInfo(__func__);
    10631075  Vector *Center = new Vector;
    10641076  Center->Zero();

  • src/boundary.hpp

    r8927ae r1ca488  
    3535
    3636#define DEBUG 1
    37 #define DoSingleStepOutput 1
    38 #define SingleStepWidth 1
     37#define DoSingleStepOutput 0
     38#define SingleStepWidth 10
    3939
    4040#define DistancePair pair < double, atom* >
    … …  
    5353Vector* FindEmbeddingHole(MoleculeListClass *mols, molecule *srcmol);
    5454void FindNextSuitablePoint(class BoundaryTriangleSet *BaseTriangle, class BoundaryLineSet *BaseLine, atom*& OptCandidate, Vector *OptCandidateCenter, double *ShortestAngle, const double RADIUS, LinkedCell *LC);
    55 void FindNonConvexBorder(const molecule* const mol, Tesselation *&TesselStruct, const LinkedCell *&LC, const double RADIUS, const char *tempbasename);
     55bool FindNonConvexBorder(const molecule* const mol, Tesselation *&TesselStruct, const LinkedCell *&LC, const double RADIUS, const char *tempbasename);
    5656Boundaries *GetBoundaryPoints(const molecule *mol, Tesselation *&TesselStruct);
    5757double * GetDiametersOfCluster(const Boundaries *BoundaryPtr, const molecule *mol, Tesselation *&TesselStruct, const bool IsAngstroem);

  • src/builder.cpp

    r8927ae r1ca488  
    7373#include "Actions/ActionRegistry.hpp"
    7474#include "Actions/MethodAction.hpp"
    75 
     75#include "version.h"
     76
     77/********************************************* Subsubmenu routine ************************************/
     78#if 0
     79/** Submenu for adding atoms to the molecule.
     80 * \param *periode periodentafel
     81 * \param *molecule molecules with atoms
     82 */
     83static void AddAtoms(periodentafel *periode, molecule *mol)
     84{
     85  atom *first, *second, *third, *fourth;
     86  Vector **atoms;
     87  Vector x,y,z,n;  // coordinates for absolute point in cell volume
     88  double a,b,c;
     89  char choice;  // menu choice char
     90  bool valid;
     91
     92  Log() << Verbose(0) << "===========ADD ATOM============================" << endl;
     93  Log() << Verbose(0) << " a - state absolute coordinates of atom" << endl;
     94  Log() << Verbose(0) << " b - state relative coordinates of atom wrt to reference point" << endl;
     95  Log() << Verbose(0) << " c - state relative coordinates of atom wrt to already placed atom" << endl;
     96  Log() << Verbose(0) << " d - state two atoms, two angles and a distance" << endl;
     97  Log() << Verbose(0) << " e - least square distance position to a set of atoms" << endl;
     98  Log() << Verbose(0) << "all else - go back" << endl;
     99  Log() << Verbose(0) << "===============================================" << endl;
     100  Log() << Verbose(0) << "Note: Specifiy angles in degrees not multiples of Pi!" << endl;
     101  Log() << Verbose(0) << "INPUT: ";
     102  cin >> choice;
     103
     104  switch (choice) {
     105    default:
     106      eLog() << Verbose(2) << "Not a valid choice." << endl;
     107      break;
     108      case 'a': // absolute coordinates of atom
     109        Log() << Verbose(0) << "Enter absolute coordinates." << endl;
     110        first = new atom;
     111        first->x.AskPosition(mol->cell_size, false);
     112        first->type = periode->AskElement();  // give type
     113        mol->AddAtom(first);  // add to molecule
     114        break;
     115
     116      case 'b': // relative coordinates of atom wrt to reference point
     117        first = new atom;
     118        valid = true;
     119        do {
     120          if (!valid) eLog() << Verbose(2) << "Resulting position out of cell." << endl;
     121          Log() << Verbose(0) << "Enter reference coordinates." << endl;
     122          x.AskPosition(mol->cell_size, true);
     123          Log() << Verbose(0) << "Enter relative coordinates." << endl;
     124          first->x.AskPosition(mol->cell_size, false);
     125          first->x.AddVector((const Vector *)&x);
     126          Log() << Verbose(0) << "\n";
     127        } while (!(valid = mol->CheckBounds((const Vector *)&first->x)));
     128        first->type = periode->AskElement();  // give type
     129        mol->AddAtom(first);  // add to molecule
     130        break;
     131
     132      case 'c': // relative coordinates of atom wrt to already placed atom
     133        first = new atom;
     134        valid = true;
     135        do {
     136          if (!valid) eLog() << Verbose(2) << "Resulting position out of cell." << endl;
     137          second = mol->AskAtom("Enter atom number: ");
     138          Log() << Verbose(0) << "Enter relative coordinates." << endl;
     139          first->x.AskPosition(mol->cell_size, false);
     140          for (int i=NDIM;i--;) {
     141            first->x.x[i] += second->x.x[i];
     142          }
     143        } while (!(valid = mol->CheckBounds((const Vector *)&first->x)));
     144        first->type = periode->AskElement();  // give type
     145        mol->AddAtom(first);  // add to molecule
     146        break;
     147
     148    case 'd': // two atoms, two angles and a distance
     149        first = new atom;
     150        valid = true;
     151        do {
     152          if (!valid) {
     153            eLog() << Verbose(2) << "Resulting coordinates out of cell - " << first->x << endl;
     154          }
     155          Log() << Verbose(0) << "First, we need two atoms, the first atom is the central, while the second is the outer one." << endl;
     156          second = mol->AskAtom("Enter central atom: ");
     157          third = mol->AskAtom("Enter second atom (specifying the axis for first angle): ");
     158          fourth = mol->AskAtom("Enter third atom (specifying a plane for second angle): ");
     159          a = ask_value("Enter distance between central (first) and new atom: ");
     160          b = ask_value("Enter angle between new, first and second atom (degrees): ");
     161          b *= M_PI/180.;
     162          bound(&b, 0., 2.*M_PI);
     163          c = ask_value("Enter second angle between new and normal vector of plane defined by first, second and third atom (degrees): ");
     164          c *= M_PI/180.;
     165          bound(&c, -M_PI, M_PI);
     166          Log() << Verbose(0) << "radius: " << a << "\t phi: " << b*180./M_PI << "\t theta: " << c*180./M_PI << endl;
     167/*
     168          second->Output(1,1,(ofstream *)&cout);
     169          third->Output(1,2,(ofstream *)&cout);
     170          fourth->Output(1,3,(ofstream *)&cout);
     171          n.MakeNormalvector((const vector *)&second->x, (const vector *)&third->x, (const vector *)&fourth->x);
     172          x.Copyvector(&second->x);
     173          x.SubtractVector(&third->x);
     174          x.Copyvector(&fourth->x);
     175          x.SubtractVector(&third->x);
     176
     177          if (!z.SolveSystem(&x,&y,&n, b, c, a)) {
     178            Log() << Verbose(0) << "Failure solving self-dependent linear system!" << endl;
     179            continue;
     180          }
     181          Log() << Verbose(0) << "resulting relative coordinates: ";
     182          z.Output();
     183          Log() << Verbose(0) << endl;
     184          */
     185          // calc axis vector
     186          x.CopyVector(&second->x);
     187          x.SubtractVector(&third->x);
     188          x.Normalize();
     189          Log() << Verbose(0) << "x: ",
     190          x.Output();
     191          Log() << Verbose(0) << endl;
     192          z.MakeNormalVector(&second->x,&third->x,&fourth->x);
     193          Log() << Verbose(0) << "z: ",
     194          z.Output();
     195          Log() << Verbose(0) << endl;
     196          y.MakeNormalVector(&x,&z);
     197          Log() << Verbose(0) << "y: ",
     198          y.Output();
     199          Log() << Verbose(0) << endl;
     200
     201          // rotate vector around first angle
     202          first->x.CopyVector(&x);
     203          first->x.RotateVector(&z,b - M_PI);
     204          Log() << Verbose(0) << "Rotated vector: ",
     205          first->x.Output();
     206          Log() << Verbose(0) << endl;
     207          // remove the projection onto the rotation plane of the second angle
     208          n.CopyVector(&y);
     209          n.Scale(first->x.ScalarProduct(&y));
     210          Log() << Verbose(0) << "N1: ",
     211          n.Output();
     212          Log() << Verbose(0) << endl;
     213          first->x.SubtractVector(&n);
     214          Log() << Verbose(0) << "Subtracted vector: ",
     215          first->x.Output();
     216          Log() << Verbose(0) << endl;
     217          n.CopyVector(&z);
     218          n.Scale(first->x.ScalarProduct(&z));
     219          Log() << Verbose(0) << "N2: ",
     220          n.Output();
     221          Log() << Verbose(0) << endl;
     222          first->x.SubtractVector(&n);
     223          Log() << Verbose(0) << "2nd subtracted vector: ",
     224          first->x.Output();
     225          Log() << Verbose(0) << endl;
     226
     227          // rotate another vector around second angle
     228          n.CopyVector(&y);
     229          n.RotateVector(&x,c - M_PI);
     230          Log() << Verbose(0) << "2nd Rotated vector: ",
     231          n.Output();
     232          Log() << Verbose(0) << endl;
     233
     234          // add the two linear independent vectors
     235          first->x.AddVector(&n);
     236          first->x.Normalize();
     237          first->x.Scale(a);
     238          first->x.AddVector(&second->x);
     239
     240          Log() << Verbose(0) << "resulting coordinates: ";
     241          first->x.Output();
     242          Log() << Verbose(0) << endl;
     243        } while (!(valid = mol->CheckBounds((const Vector *)&first->x)));
     244        first->type = periode->AskElement();  // give type
     245        mol->AddAtom(first);  // add to molecule
     246        break;
     247
     248      case 'e': // least square distance position to a set of atoms
     249        first = new atom;
     250        atoms = new (Vector*[128]);
     251        valid = true;
     252        for(int i=128;i--;)
     253          atoms[i] = NULL;
     254        int i=0, j=0;
     255        Log() << Verbose(0) << "Now we need at least three molecules.\n";
     256        do {
     257          Log() << Verbose(0) << "Enter " << i+1 << "th atom: ";
     258          cin >> j;
     259          if (j != -1) {
     260            second = mol->FindAtom(j);
     261            atoms[i++] = &(second->x);
     262          }
     263        } while ((j != -1) && (i<128));
     264        if (i >= 2) {
     265          first->x.LSQdistance((const Vector **)atoms, i);
     266
     267          first->x.Output();
     268          first->type = periode->AskElement();  // give type
     269          mol->AddAtom(first);  // add to molecule
     270        } else {
     271          delete first;
     272          Log() << Verbose(0) << "Please enter at least two vectors!\n";
     273        }
     274        break;
     275  };
     276};
     277
     278/** Submenu for centering the atoms in the molecule.
     279 * \param *mol molecule with all the atoms
     280 */
     281static void CenterAtoms(molecule *mol)
     282{
     283  Vector x, y, helper;
     284  char choice;  // menu choice char
     285
     286  Log() << Verbose(0) << "===========CENTER ATOMS=========================" << endl;
     287  Log() << Verbose(0) << " a - on origin" << endl;
     288  Log() << Verbose(0) << " b - on center of gravity" << endl;
     289  Log() << Verbose(0) << " c - within box with additional boundary" << endl;
     290  Log() << Verbose(0) << " d - within given simulation box" << endl;
     291  Log() << Verbose(0) << "all else - go back" << endl;
     292  Log() << Verbose(0) << "===============================================" << endl;
     293  Log() << Verbose(0) << "INPUT: ";
     294  cin >> choice;
     295
     296  switch (choice) {
     297    default:
     298      Log() << Verbose(0) << "Not a valid choice." << endl;
     299      break;
     300    case 'a':
     301      Log() << Verbose(0) << "Centering atoms in config file on origin." << endl;
     302      mol->CenterOrigin();
     303      break;
     304    case 'b':
     305      Log() << Verbose(0) << "Centering atoms in config file on center of gravity." << endl;
     306      mol->CenterPeriodic();
     307      break;
     308    case 'c':
     309      Log() << Verbose(0) << "Centering atoms in config file within given additional boundary." << endl;
     310      for (int i=0;i<NDIM;i++) {
     311        Log() << Verbose(0) << "Enter axis " << i << " boundary: ";
     312        cin >> y.x[i];
     313      }
     314      mol->CenterEdge(&x);  // make every coordinate positive
     315      mol->Center.AddVector(&y); // translate by boundary
     316      helper.CopyVector(&y);
     317      helper.Scale(2.);
     318      helper.AddVector(&x);
     319      mol->SetBoxDimension(&helper);  // update Box of atoms by boundary
     320      break;
     321    case 'd':
     322      Log() << Verbose(1) << "Centering atoms in config file within given simulation box." << endl;
     323      for (int i=0;i<NDIM;i++) {
     324        Log() << Verbose(0) << "Enter axis " << i << " boundary: ";
     325        cin >> x.x[i];
     326      }
     327      // update Box of atoms by boundary
     328      mol->SetBoxDimension(&x);
     329      // center
     330      mol->CenterInBox();
     331      break;
     332  }
     333};
     334
     335/** Submenu for aligning the atoms in the molecule.
     336 * \param *periode periodentafel
     337 * \param *mol molecule with all the atoms
     338 */
     339static void AlignAtoms(periodentafel *periode, molecule *mol)
     340{
     341  atom *first, *second, *third;
     342  Vector x,n;
     343  char choice;  // menu choice char
     344
     345  Log() << Verbose(0) << "===========ALIGN ATOMS=========================" << endl;
     346  Log() << Verbose(0) << " a - state three atoms defining align plane" << endl;
     347  Log() << Verbose(0) << " b - state alignment vector" << endl;
     348  Log() << Verbose(0) << " c - state two atoms in alignment direction" << endl;
     349  Log() << Verbose(0) << " d - align automatically by least square fit" << endl;
     350  Log() << Verbose(0) << "all else - go back" << endl;
     351  Log() << Verbose(0) << "===============================================" << endl;
     352  Log() << Verbose(0) << "INPUT: ";
     353  cin >> choice;
     354
     355  switch (choice) {
     356    default:
     357    case 'a': // three atoms defining mirror plane
     358      first = mol->AskAtom("Enter first atom: ");
     359      second = mol->AskAtom("Enter second atom: ");
     360      third = mol->AskAtom("Enter third atom: ");
     361
     362      n.MakeNormalVector((const Vector *)&first->x,(const Vector *)&second->x,(const Vector *)&third->x);
     363      break;
     364    case 'b': // normal vector of mirror plane
     365      Log() << Verbose(0) << "Enter normal vector of mirror plane." << endl;
     366      n.AskPosition(mol->cell_size,0);
     367      n.Normalize();
     368      break;
     369    case 'c': // three atoms defining mirror plane
     370      first = mol->AskAtom("Enter first atom: ");
     371      second = mol->AskAtom("Enter second atom: ");
     372
     373      n.CopyVector((const Vector *)&first->x);
     374      n.SubtractVector((const Vector *)&second->x);
     375      n.Normalize();
     376      break;
     377    case 'd':
     378      char shorthand[4];
     379      Vector a;
     380      struct lsq_params param;
     381      do {
     382        fprintf(stdout, "Enter the element of atoms to be chosen: ");
     383        fscanf(stdin, "%3s", shorthand);
     384      } while ((param.type = periode->FindElement(shorthand)) == NULL);
     385      Log() << Verbose(0) << "Element is " << param.type->name << endl;
     386      mol->GetAlignvector(&param);
     387      for (int i=NDIM;i--;) {
     388        x.x[i] = gsl_vector_get(param.x,i);
     389        n.x[i] = gsl_vector_get(param.x,i+NDIM);
     390      }
     391      gsl_vector_free(param.x);
     392      Log() << Verbose(0) << "Offset vector: ";
     393      x.Output();
     394      Log() << Verbose(0) << endl;
     395      n.Normalize();
     396      break;
     397  };
     398  Log() << Verbose(0) << "Alignment vector: ";
     399  n.Output();
     400  Log() << Verbose(0) << endl;
     401  mol->Align(&n);
     402};
     403
     404/** Submenu for mirroring the atoms in the molecule.
     405 * \param *mol molecule with all the atoms
     406 */
     407static void MirrorAtoms(molecule *mol)
     408{
     409  atom *first, *second, *third;
     410  Vector n;
     411  char choice;  // menu choice char
     412
     413  Log() << Verbose(0) << "===========MIRROR ATOMS=========================" << endl;
     414  Log() << Verbose(0) << " a - state three atoms defining mirror plane" << endl;
     415  Log() << Verbose(0) << " b - state normal vector of mirror plane" << endl;
     416  Log() << Verbose(0) << " c - state two atoms in normal direction" << endl;
     417  Log() << Verbose(0) << "all else - go back" << endl;
     418  Log() << Verbose(0) << "===============================================" << endl;
     419  Log() << Verbose(0) << "INPUT: ";
     420  cin >> choice;
     421
     422  switch (choice) {
     423    default:
     424    case 'a': // three atoms defining mirror plane
     425      first = mol->AskAtom("Enter first atom: ");
     426      second = mol->AskAtom("Enter second atom: ");
     427      third = mol->AskAtom("Enter third atom: ");
     428
     429      n.MakeNormalVector((const Vector *)&first->x,(const Vector *)&second->x,(const Vector *)&third->x);
     430      break;
     431    case 'b': // normal vector of mirror plane
     432      Log() << Verbose(0) << "Enter normal vector of mirror plane." << endl;
     433      n.AskPosition(mol->cell_size,0);
     434      n.Normalize();
     435      break;
     436    case 'c': // three atoms defining mirror plane
     437      first = mol->AskAtom("Enter first atom: ");
     438      second = mol->AskAtom("Enter second atom: ");
     439
     440      n.CopyVector((const Vector *)&first->x);
     441      n.SubtractVector((const Vector *)&second->x);
     442      n.Normalize();
     443      break;
     444  };
     445  Log() << Verbose(0) << "Normal vector: ";
     446  n.Output();
     447  Log() << Verbose(0) << endl;
     448  mol->Mirror((const Vector *)&n);
     449};
     450
     451/** Submenu for removing the atoms from the molecule.
     452 * \param *mol molecule with all the atoms
     453 */
     454static void RemoveAtoms(molecule *mol)
     455{
     456  atom *first, *second;
     457  int axis;
     458  double tmp1, tmp2;
     459  char choice;  // menu choice char
     460
     461  Log() << Verbose(0) << "===========REMOVE ATOMS=========================" << endl;
     462  Log() << Verbose(0) << " a - state atom for removal by number" << endl;
     463  Log() << Verbose(0) << " b - keep only in radius around atom" << endl;
     464  Log() << Verbose(0) << " c - remove this with one axis greater value" << endl;
     465  Log() << Verbose(0) << "all else - go back" << endl;
     466  Log() << Verbose(0) << "===============================================" << endl;
     467  Log() << Verbose(0) << "INPUT: ";
     468  cin >> choice;
     469
     470  switch (choice) {
     471    default:
     472    case 'a':
     473      if (mol->RemoveAtom(mol->AskAtom("Enter number of atom within molecule: ")))
     474        Log() << Verbose(1) << "Atom removed." << endl;
     475      else
     476        Log() << Verbose(1) << "Atom not found." << endl;
     477      break;
     478    case 'b':
     479      second = mol->AskAtom("Enter number of atom as reference point: ");
     480      Log() << Verbose(0) << "Enter radius: ";
     481      cin >> tmp1;
     482      first = mol->start;
     483      second = first->next;
     484      while(second != mol->end) {
     485        first = second;
     486        second = first->next;
     487        if (first->x.DistanceSquared((const Vector *)&second->x) > tmp1*tmp1) // distance to first above radius ...
     488          mol->RemoveAtom(first);
     489      }
     490      break;
     491    case 'c':
     492      Log() << Verbose(0) << "Which axis is it: ";
     493      cin >> axis;
     494      Log() << Verbose(0) << "Lower boundary: ";
     495      cin >> tmp1;
     496      Log() << Verbose(0) << "Upper boundary: ";
     497      cin >> tmp2;
     498      first = mol->start;
     499      second = first->next;
     500      while(second != mol->end) {
     501        first = second;
     502        second = first->next;
     503        if ((first->x.x[axis] < tmp1) || (first->x.x[axis] > tmp2)) {// out of boundary ...
     504          //Log() << Verbose(0) << "Atom " << *first << " with " << first->x.x[axis] << " on axis " << axis << " is out of bounds [" << tmp1 << "," << tmp2 << "]." << endl;
     505          mol->RemoveAtom(first);
     506        }
     507      }
     508      break;
     509  };
     510  //mol->Output();
     511  choice = 'r';
     512};
     513
     514/** Submenu for measuring out the atoms in the molecule.
     515 * \param *periode periodentafel
     516 * \param *mol molecule with all the atoms
     517 */
     518static void MeasureAtoms(periodentafel *periode, molecule *mol, config *configuration)
     519{
     520  atom *first, *second, *third;
     521  Vector x,y;
     522  double min[256], tmp1, tmp2, tmp3;
     523  int Z;
     524  char choice;  // menu choice char
     525
     526  Log() << Verbose(0) << "===========MEASURE ATOMS=========================" << endl;
     527  Log() << Verbose(0) << " a - calculate bond length between one atom and all others" << endl;
     528  Log() << Verbose(0) << " b - calculate bond length between two atoms" << endl;
     529  Log() << Verbose(0) << " c - calculate bond angle" << endl;
     530  Log() << Verbose(0) << " d - calculate principal axis of the system" << endl;
     531  Log() << Verbose(0) << " e - calculate volume of the convex envelope" << endl;
     532  Log() << Verbose(0) << " f - calculate temperature from current velocity" << endl;
     533  Log() << Verbose(0) << " g - output all temperatures per step from velocities" << endl;
     534  Log() << Verbose(0) << "all else - go back" << endl;
     535  Log() << Verbose(0) << "===============================================" << endl;
     536  Log() << Verbose(0) << "INPUT: ";
     537  cin >> choice;
     538
     539  switch(choice) {
     540    default:
     541      Log() << Verbose(1) << "Not a valid choice." << endl;
     542      break;
     543    case 'a':
     544      first = mol->AskAtom("Enter first atom: ");
     545      for (int i=MAX_ELEMENTS;i--;)
     546        min[i] = 0.;
     547
     548      second = mol->start;
     549      while ((second->next != mol->end)) {
     550        second = second->next; // advance
     551        Z = second->type->Z;
     552        tmp1 = 0.;
     553        if (first != second) {
     554          x.CopyVector((const Vector *)&first->x);
     555          x.SubtractVector((const Vector *)&second->x);
     556          tmp1 = x.Norm();
     557        }
     558        if ((tmp1 != 0.) && ((min[Z] == 0.) || (tmp1 < min[Z]))) min[Z] = tmp1;
     559        //Log() << Verbose(0) << "Bond length between Atom " << first->nr << " and " << second->nr << ": " << tmp1 << " a.u." << endl;
     560      }
     561      for (int i=MAX_ELEMENTS;i--;)
     562        if (min[i] != 0.) Log() << Verbose(0) << "Minimum Bond length between " << first->type->name << " Atom " << first->nr << " and next Ion of type " << (periode->FindElement(i))->name << ": " << min[i] << " a.u." << endl;
     563      break;
     564
     565    case 'b':
     566      first = mol->AskAtom("Enter first atom: ");
     567      second = mol->AskAtom("Enter second atom: ");
     568      for (int i=NDIM;i--;)
     569        min[i] = 0.;
     570      x.CopyVector((const Vector *)&first->x);
     571      x.SubtractVector((const Vector *)&second->x);
     572      tmp1 = x.Norm();
     573      Log() << Verbose(1) << "Distance vector is ";
     574      x.Output();
     575      Log() << Verbose(0) << "." << endl << "Norm of distance is " << tmp1 << "." << endl;
     576      break;
     577
     578    case 'c':
     579      Log() << Verbose(0) << "Evaluating bond angle between three - first, central, last - atoms." << endl;
     580      first = mol->AskAtom("Enter first atom: ");
     581      second = mol->AskAtom("Enter central atom: ");
     582      third  = mol->AskAtom("Enter last atom: ");
     583      tmp1 = tmp2 = tmp3 = 0.;
     584      x.CopyVector((const Vector *)&first->x);
     585      x.SubtractVector((const Vector *)&second->x);
     586      y.CopyVector((const Vector *)&third->x);
     587      y.SubtractVector((const Vector *)&second->x);
     588      Log() << Verbose(0) << "Bond angle between first atom Nr." << first->nr << ", central atom Nr." << second->nr << " and last atom Nr." << third->nr << ": ";
     589      Log() << Verbose(0) << (acos(x.ScalarProduct((const Vector *)&y)/(y.Norm()*x.Norm()))/M_PI*180.) << " degrees" << endl;
     590      break;
     591    case 'd':
     592      Log() << Verbose(0) << "Evaluating prinicipal axis." << endl;
     593      Log() << Verbose(0) << "Shall we rotate? [0/1]: ";
     594      cin >> Z;
     595      if ((Z >=0) && (Z <=1))
     596        mol->PrincipalAxisSystem((bool)Z);
     597      else
     598        mol->PrincipalAxisSystem(false);
     599      break;
     600    case 'e':
     601      {
     602        Log() << Verbose(0) << "Evaluating volume of the convex envelope.";
     603        class Tesselation *TesselStruct = NULL;
     604        const LinkedCell *LCList = NULL;
     605        LCList = new LinkedCell(mol, 10.);
     606        FindConvexBorder(mol, TesselStruct, LCList, NULL);
     607        double clustervolume = VolumeOfConvexEnvelope(TesselStruct, configuration);
     608        Log() << Verbose(0) << "The tesselated surface area is " << clustervolume << "." << endl;\
     609        delete(LCList);
     610        delete(TesselStruct);
     611      }
     612      break;
     613    case 'f':
     614      mol->OutputTemperatureFromTrajectories((ofstream *)&cout, mol->MDSteps-1, mol->MDSteps);
     615      break;
     616    case 'g':
     617      {
     618        char filename[255];
     619        Log() << Verbose(0) << "Please enter filename: " << endl;
     620        cin >> filename;
     621        Log() << Verbose(1) << "Storing temperatures in " << filename << "." << endl;
     622        ofstream *output = new ofstream(filename, ios::trunc);
     623        if (!mol->OutputTemperatureFromTrajectories(output, 0, mol->MDSteps))
     624          Log() << Verbose(2) << "File could not be written." << endl;
     625        else
     626          Log() << Verbose(2) << "File stored." << endl;
     627        output->close();
     628        delete(output);
     629      }
     630      break;
     631  }
     632};
     633
     634/** Submenu for measuring out the atoms in the molecule.
     635 * \param *mol molecule with all the atoms
     636 * \param *configuration configuration structure for the to be written config files of all fragments
     637 */
     638static void FragmentAtoms(molecule *mol, config *configuration)
     639{
     640  int Order1;
     641  clock_t start, end;
     642
     643  Log() << Verbose(0) << "Fragmenting molecule with current connection matrix ..." << endl;
     644  Log() << Verbose(0) << "What's the desired bond order: ";
     645  cin >> Order1;
     646  if (mol->first->next != mol->last) {  // there are bonds
     647    start = clock();
     648    mol->FragmentMolecule(Order1, configuration);
     649    end = clock();
     650    Log() << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl;
     651  } else
     652    Log() << Verbose(0) << "Connection matrix has not yet been generated!" << endl;
     653};
     654
     655/********************************************** Submenu routine **************************************/
     656
     657/** Submenu for manipulating atoms.
     658 * \param *periode periodentafel
     659 * \param *molecules list of molecules whose atoms are to be manipulated
     660 */
     661static void ManipulateAtoms(periodentafel *periode, MoleculeListClass *molecules, config *configuration)
     662{
     663  atom *first, *second;
     664  molecule *mol = NULL;
     665  Vector x,y,z,n; // coordinates for absolute point in cell volume
     666  double *factor; // unit factor if desired
     667  double bond, minBond;
     668  char choice;  // menu choice char
     669  bool valid;
     670
     671  Log() << Verbose(0) << "=========MANIPULATE ATOMS======================" << endl;
     672  Log() << Verbose(0) << "a - add an atom" << endl;
     673  Log() << Verbose(0) << "r - remove an atom" << endl;
     674  Log() << Verbose(0) << "b - scale a bond between atoms" << endl;
     675  Log() << Verbose(0) << "u - change an atoms element" << endl;
     676  Log() << Verbose(0) << "l - measure lengths, angles, ... for an atom" << endl;
     677  Log() << Verbose(0) << "all else - go back" << endl;
     678  Log() << Verbose(0) << "===============================================" << endl;
     679  if (molecules->NumberOfActiveMolecules() > 1)
     680    eLog() << Verbose(2) << "There is more than one molecule active! Atoms will be added to each." << endl;
     681  Log() << Verbose(0) << "INPUT: ";
     682  cin >> choice;
     683
     684  switch (choice) {
     685    default:
     686      Log() << Verbose(0) << "Not a valid choice." << endl;
     687      break;
     688
     689    case 'a': // add atom
     690      for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
     691        if ((*ListRunner)->ActiveFlag) {
     692        mol = *ListRunner;
     693        Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
     694        AddAtoms(periode, mol);
     695      }
     696      break;
     697
     698    case 'b': // scale a bond
     699      for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
     700        if ((*ListRunner)->ActiveFlag) {
     701        mol = *ListRunner;
     702        Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
     703        Log() << Verbose(0) << "Scaling bond length between two atoms." << endl;
     704        first = mol->AskAtom("Enter first (fixed) atom: ");
     705        second = mol->AskAtom("Enter second (shifting) atom: ");
     706        minBond = 0.;
     707        for (int i=NDIM;i--;)
     708          minBond += (first->x.x[i]-second->x.x[i])*(first->x.x[i] - second->x.x[i]);
     709        minBond = sqrt(minBond);
     710        Log() << Verbose(0) << "Current Bond length between " << first->type->name << " Atom " << first->nr << " and " << second->type->name << " Atom " << second->nr << ": " << minBond << " a.u." << endl;
     711        Log() << Verbose(0) << "Enter new bond length [a.u.]: ";
     712        cin >> bond;
     713        for (int i=NDIM;i--;) {
     714          second->x.x[i] -= (second->x.x[i]-first->x.x[i])/minBond*(minBond-bond);
     715        }
     716        //Log() << Verbose(0) << "New coordinates of Atom " << second->nr << " are: ";
     717        //second->Output(second->type->No, 1);
     718      }
     719      break;
     720
     721    case 'c': // unit scaling of the metric
     722      for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
     723        if ((*ListRunner)->ActiveFlag) {
     724        mol = *ListRunner;
     725        Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
     726       Log() << Verbose(0) << "Angstroem -> Bohrradius: 1.8897261\t\tBohrradius -> Angstroem: 0.52917721" << endl;
     727       Log() << Verbose(0) << "Enter three factors: ";
     728       factor = new double[NDIM];
     729       cin >> factor[0];
     730       cin >> factor[1];
     731       cin >> factor[2];
     732       valid = true;
     733       mol->Scale((const double ** const)&factor);
     734       delete[](factor);
     735      }
     736     break;
     737
     738    case 'l': // measure distances or angles
     739      for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
     740        if ((*ListRunner)->ActiveFlag) {
     741        mol = *ListRunner;
     742        Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
     743        MeasureAtoms(periode, mol, configuration);
     744      }
     745      break;
     746
     747    case 'r': // remove atom
     748      for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
     749        if ((*ListRunner)->ActiveFlag) {
     750        mol = *ListRunner;
     751        Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
     752        RemoveAtoms(mol);
     753      }
     754      break;
     755
     756    case 'u': // change an atom's element
     757      for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
     758        if ((*ListRunner)->ActiveFlag) {
     759        int Z;
     760        mol = *ListRunner;
     761        Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
     762        first = NULL;
     763        do {
     764          Log() << Verbose(0) << "Change the element of which atom: ";
     765          cin >> Z;
     766        } while ((first = mol->FindAtom(Z)) == NULL);
     767        Log() << Verbose(0) << "New element by atomic number Z: ";
     768        cin >> Z;
     769        first->type = periode->FindElement(Z);
     770        Log() << Verbose(0) << "Atom " << first->nr << "'s element is " << first->type->name << "." << endl;
     771      }
     772      break;
     773  }
     774};
     775
     776/** Submenu for manipulating molecules.
     777 * \param *periode periodentafel
     778 * \param *molecules list of molecule to manipulate
     779 */
     780static void ManipulateMolecules(periodentafel *periode, MoleculeListClass *molecules, config *configuration)
     781{
     782  atom *first = NULL;
     783  Vector x,y,z,n; // coordinates for absolute point in cell volume
     784  int j, axis, count, faktor;
     785  char choice;  // menu choice char
     786  molecule *mol = NULL;
     787  element **Elements;
     788  Vector **vectors;
     789  MoleculeLeafClass *Subgraphs = NULL;
     790
     791  Log() << Verbose(0) << "=========MANIPULATE GLOBALLY===================" << endl;
     792  Log() << Verbose(0) << "c - scale by unit transformation" << endl;
     793  Log() << Verbose(0) << "d - duplicate molecule/periodic cell" << endl;
     794  Log() << Verbose(0) << "f - fragment molecule many-body bond order style" << endl;
     795  Log() << Verbose(0) << "g - center atoms in box" << endl;
     796  Log() << Verbose(0) << "i - realign molecule" << endl;
     797  Log() << Verbose(0) << "m - mirror all molecules" << endl;
     798  Log() << Verbose(0) << "o - create connection matrix" << endl;
     799  Log() << Verbose(0) << "t - translate molecule by vector" << endl;
     800  Log() << Verbose(0) << "all else - go back" << endl;
     801  Log() << Verbose(0) << "===============================================" << endl;
     802  if (molecules->NumberOfActiveMolecules() > 1)
     803    eLog() << Verbose(2) << "There is more than one molecule active! Atoms will be added to each." << endl;
     804  Log() << Verbose(0) << "INPUT: ";
     805  cin >> choice;
     806
     807  switch (choice) {
     808    default:
     809      Log() << Verbose(0) << "Not a valid choice." << endl;
     810      break;
     811
     812    case 'd': // duplicate the periodic cell along a given axis, given times
     813      for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
     814        if ((*ListRunner)->ActiveFlag) {
     815        mol = *ListRunner;
     816        Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
     817        Log() << Verbose(0) << "State the axis [(+-)123]: ";
     818        cin >> axis;
     819        Log() << Verbose(0) << "State the factor: ";
     820        cin >> faktor;
     821
     822        mol->CountAtoms(); // recount atoms
     823        if (mol->AtomCount != 0) {  // if there is more than none
     824          count = mol->AtomCount;  // is changed becausing of adding, thus has to be stored away beforehand
     825          Elements = new element *[count];
     826          vectors = new Vector *[count];
     827          j = 0;
     828          first = mol->start;
     829          while (first->next != mol->end) { // make a list of all atoms with coordinates and element
     830            first = first->next;
     831            Elements[j] = first->type;
     832            vectors[j] = &first->x;
     833            j++;
     834          }
     835          if (count != j)
     836            eLog() << Verbose(1) << "AtomCount " << count << " is not equal to number of atoms in molecule " << j << "!" << endl;
     837          x.Zero();
     838          y.Zero();
     839          y.x[abs(axis)-1] = mol->cell_size[(abs(axis) == 2) ? 2 : ((abs(axis) == 3) ? 5 : 0)] * abs(axis)/axis; // last term is for sign, first is for magnitude
     840          for (int i=1;i<faktor;i++) {  // then add this list with respective translation factor times
     841            x.AddVector(&y); // per factor one cell width further
     842            for (int k=count;k--;) { // go through every atom of the original cell
     843              first = new atom(); // create a new body
     844              first->x.CopyVector(vectors[k]);  // use coordinate of original atom
     845              first->x.AddVector(&x);     // translate the coordinates
     846              first->type = Elements[k];  // insert original element
     847              mol->AddAtom(first);        // and add to the molecule (which increments ElementsInMolecule, AtomCount, ...)
     848            }
     849          }
     850          if (mol->first->next != mol->last) // if connect matrix is present already, redo it
     851            mol->CreateAdjacencyList(mol->BondDistance, configuration->GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, NULL);
     852          // free memory
     853          delete[](Elements);
     854          delete[](vectors);
     855          // correct cell size
     856          if (axis < 0) { // if sign was negative, we have to translate everything
     857            x.Zero();
     858            x.AddVector(&y);
     859            x.Scale(-(faktor-1));
     860            mol->Translate(&x);
     861          }
     862          mol->cell_size[(abs(axis) == 2) ? 2 : ((abs(axis) == 3) ? 5 : 0)] *= faktor;
     863        }
     864      }
     865      break;
     866
     867    case 'f':
     868      FragmentAtoms(mol, configuration);
     869      break;
     870
     871    case 'g': // center the atoms
     872      for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
     873        if ((*ListRunner)->ActiveFlag) {
     874        mol = *ListRunner;
     875        Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
     876        CenterAtoms(mol);
     877      }
     878      break;
     879
     880    case 'i': // align all atoms
     881      for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
     882        if ((*ListRunner)->ActiveFlag) {
     883        mol = *ListRunner;
     884        Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
     885        AlignAtoms(periode, mol);
     886      }
     887      break;
     888
     889    case 'm': // mirror atoms along a given axis
     890      for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
     891        if ((*ListRunner)->ActiveFlag) {
     892        mol = *ListRunner;
     893        Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
     894        MirrorAtoms(mol);
     895      }
     896      break;
     897
     898    case 'o': // create the connection matrix
     899      for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
     900        if ((*ListRunner)->ActiveFlag) {
     901          mol = *ListRunner;
     902          double bonddistance;
     903          clock_t start,end;
     904          Log() << Verbose(0) << "What's the maximum bond distance: ";
     905          cin >> bonddistance;
     906          start = clock();
     907          mol->CreateAdjacencyList(bonddistance, configuration->GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, NULL);
     908          end = clock();
     909          Log() << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl;
     910        }
     911      break;
     912
     913    case 't': // translate all atoms
     914      for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
     915        if ((*ListRunner)->ActiveFlag) {
     916        mol = *ListRunner;
     917        Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
     918        Log() << Verbose(0) << "Enter translation vector." << endl;
     919        x.AskPosition(mol->cell_size,0);
     920        mol->Center.AddVector((const Vector *)&x);
     921     }
     922     break;
     923  }
     924  // Free all
     925  if (Subgraphs != NULL) {  // free disconnected subgraph list of DFS analysis was performed
     926    while (Subgraphs->next != NULL) {
     927      Subgraphs = Subgraphs->next;
     928      delete(Subgraphs->previous);
     929    }
     930    delete(Subgraphs);
     931  }
     932};
     933
     934
     935/** Submenu for creating new molecules.
     936 * \param *periode periodentafel
     937 * \param *molecules list of molecules to add to
     938 */
     939static void EditMolecules(periodentafel *periode, MoleculeListClass *molecules)
     940{
     941  char choice;  // menu choice char
     942  Vector center;
     943  int nr, count;
     944  molecule *mol = NULL;
     945
     946  Log() << Verbose(0) << "==========EDIT MOLECULES=====================" << endl;
     947  Log() << Verbose(0) << "c - create new molecule" << endl;
     948  Log() << Verbose(0) << "l - load molecule from xyz file" << endl;
     949  Log() << Verbose(0) << "n - change molecule's name" << endl;
     950  Log() << Verbose(0) << "N - give molecules filename" << endl;
     951  Log() << Verbose(0) << "p - parse atoms in xyz file into molecule" << endl;
     952  Log() << Verbose(0) << "r - remove a molecule" << endl;
     953  Log() << Verbose(0) << "all else - go back" << endl;
     954  Log() << Verbose(0) << "===============================================" << endl;
     955  Log() << Verbose(0) << "INPUT: ";
     956  cin >> choice;
     957
     958  switch (choice) {
     959    default:
     960      Log() << Verbose(0) << "Not a valid choice." << endl;
     961      break;
     962    case 'c':
     963      mol = new molecule(periode);
     964      molecules->insert(mol);
     965      break;
     966
     967    case 'l': // load from XYZ file
     968      {
     969        char filename[MAXSTRINGSIZE];
     970        Log() << Verbose(0) << "Format should be XYZ with: ShorthandOfElement\tX\tY\tZ" << endl;
     971        mol = new molecule(periode);
     972        do {
     973          Log() << Verbose(0) << "Enter file name: ";
     974          cin >> filename;
     975        } while (!mol->AddXYZFile(filename));
     976        mol->SetNameFromFilename(filename);
     977        // center at set box dimensions
     978        mol->CenterEdge(&center);
     979        mol->cell_size[0] = center.x[0];
     980        mol->cell_size[1] = 0;
     981        mol->cell_size[2] = center.x[1];
     982        mol->cell_size[3] = 0;
     983        mol->cell_size[4] = 0;
     984        mol->cell_size[5] = center.x[2];
     985        molecules->insert(mol);
     986      }
     987      break;
     988
     989    case 'n':
     990      {
     991        char filename[MAXSTRINGSIZE];
     992        do {
     993          Log() << Verbose(0) << "Enter index of molecule: ";
     994          cin >> nr;
     995          mol = molecules->ReturnIndex(nr);
     996        } while (mol == NULL);
     997        Log() << Verbose(0) << "Enter name: ";
     998        cin >> filename;
     999        strcpy(mol->name, filename);
     1000      }
     1001      break;
     1002
     1003    case 'N':
     1004      {
     1005        char filename[MAXSTRINGSIZE];
     1006        do {
     1007          Log() << Verbose(0) << "Enter index of molecule: ";
     1008          cin >> nr;
     1009          mol = molecules->ReturnIndex(nr);
     1010        } while (mol == NULL);
     1011        Log() << Verbose(0) << "Enter name: ";
     1012        cin >> filename;
     1013        mol->SetNameFromFilename(filename);
     1014      }
     1015      break;
     1016
     1017    case 'p': // parse XYZ file
     1018      {
     1019        char filename[MAXSTRINGSIZE];
     1020        mol = NULL;
     1021        do {
     1022          Log() << Verbose(0) << "Enter index of molecule: ";
     1023          cin >> nr;
     1024          mol = molecules->ReturnIndex(nr);
     1025        } while (mol == NULL);
     1026        Log() << Verbose(0) << "Format should be XYZ with: ShorthandOfElement\tX\tY\tZ" << endl;
     1027        do {
     1028          Log() << Verbose(0) << "Enter file name: ";
     1029          cin >> filename;
     1030        } while (!mol->AddXYZFile(filename));
     1031        mol->SetNameFromFilename(filename);
     1032      }
     1033      break;
     1034
     1035    case 'r':
     1036      Log() << Verbose(0) << "Enter index of molecule: ";
     1037      cin >> nr;
     1038      count = 1;
     1039      for(MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
     1040        if (nr == (*ListRunner)->IndexNr) {
     1041          mol = *ListRunner;
     1042          molecules->ListOfMolecules.erase(ListRunner);
     1043          delete(mol);
     1044          break;
     1045        }
     1046      break;
     1047  }
     1048};
     1049
     1050
     1051/** Submenu for merging molecules.
     1052 * \param *periode periodentafel
     1053 * \param *molecules list of molecules to add to
     1054 */
     1055static void MergeMolecules(periodentafel *periode, MoleculeListClass *molecules)
     1056{
     1057  char choice;  // menu choice char
     1058
     1059  Log() << Verbose(0) << "===========MERGE MOLECULES=====================" << endl;
     1060  Log() << Verbose(0) << "a - simple add of one molecule to another" << endl;
     1061  Log() << Verbose(0) << "e - embedding merge of two molecules" << endl;
     1062  Log() << Verbose(0) << "m - multi-merge of all molecules" << endl;
     1063  Log() << Verbose(0) << "s - scatter merge of two molecules" << endl;
     1064  Log() << Verbose(0) << "t - simple merge of two molecules" << endl;
     1065  Log() << Verbose(0) << "all else - go back" << endl;
     1066  Log() << Verbose(0) << "===============================================" << endl;
     1067  Log() << Verbose(0) << "INPUT: ";
     1068  cin >> choice;
     1069
     1070  switch (choice) {
     1071    default:
     1072      Log() << Verbose(0) << "Not a valid choice." << endl;
     1073      break;
     1074
     1075    case 'a':
     1076      {
     1077        int src, dest;
     1078        molecule *srcmol = NULL, *destmol = NULL;
     1079        {
     1080          do {
     1081            Log() << Verbose(0) << "Enter index of destination molecule: ";
     1082            cin >> dest;
     1083            destmol = molecules->ReturnIndex(dest);
     1084          } while ((destmol == NULL) && (dest != -1));
     1085          do {
     1086            Log() << Verbose(0) << "Enter index of source molecule to add from: ";
     1087            cin >> src;
     1088            srcmol = molecules->ReturnIndex(src);
     1089          } while ((srcmol == NULL) && (src != -1));
     1090          if ((src != -1) && (dest != -1))
     1091            molecules->SimpleAdd(srcmol, destmol);
     1092        }
     1093      }
     1094      break;
     1095
     1096    case 'e':
     1097      {
     1098        int src, dest;
     1099        molecule *srcmol = NULL, *destmol = NULL;
     1100        do {
     1101          Log() << Verbose(0) << "Enter index of matrix molecule (the variable one): ";
     1102          cin >> src;
     1103          srcmol = molecules->ReturnIndex(src);
     1104        } while ((srcmol == NULL) && (src != -1));
     1105        do {
     1106          Log() << Verbose(0) << "Enter index of molecule to merge into (the fixed one): ";
     1107          cin >> dest;
     1108          destmol = molecules->ReturnIndex(dest);
     1109        } while ((destmol == NULL) && (dest != -1));
     1110        if ((src != -1) && (dest != -1))
     1111          molecules->EmbedMerge(destmol, srcmol);
     1112      }
     1113      break;
     1114
     1115    case 'm':
     1116      {
     1117        int nr;
     1118        molecule *mol = NULL;
     1119        do {
     1120          Log() << Verbose(0) << "Enter index of molecule to merge into: ";
     1121          cin >> nr;
     1122          mol = molecules->ReturnIndex(nr);
     1123        } while ((mol == NULL) && (nr != -1));
     1124        if (nr != -1) {
     1125          int N = molecules->ListOfMolecules.size()-1;
     1126          int *src = new int(N);
     1127          for(MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
     1128            if ((*ListRunner)->IndexNr != nr)
     1129              src[N++] = (*ListRunner)->IndexNr;       
     1130          molecules->SimpleMultiMerge(mol, src, N);
     1131          delete[](src);
     1132        }
     1133      }
     1134      break;
     1135
     1136    case 's':
     1137      Log() << Verbose(0) << "Not implemented yet." << endl;
     1138      break;
     1139
     1140    case 't':
     1141      {
     1142        int src, dest;
     1143        molecule *srcmol = NULL, *destmol = NULL;
     1144        {
     1145          do {
     1146            Log() << Verbose(0) << "Enter index of destination molecule: ";
     1147            cin >> dest;
     1148            destmol = molecules->ReturnIndex(dest);
     1149          } while ((destmol == NULL) && (dest != -1));
     1150          do {
     1151            Log() << Verbose(0) << "Enter index of source molecule to merge into: ";
     1152            cin >> src;
     1153            srcmol = molecules->ReturnIndex(src);
     1154          } while ((srcmol == NULL) && (src != -1));
     1155          if ((src != -1) && (dest != -1))
     1156            molecules->SimpleMerge(srcmol, destmol);
     1157        }
     1158      }
     1159      break;
     1160  }
     1161};
     1162
     1163/********************************************** Test routine **************************************/
     1164
     1165/** Is called always as option 'T' in the menu.
     1166 * \param *molecules list of molecules
     1167 */
     1168static void testroutine(MoleculeListClass *molecules)
     1169{
     1170  // the current test routine checks the functionality of the KeySet&Graph concept:
     1171  // We want to have a multiindex (the KeySet) describing a unique subgraph
     1172  int i, comp, counter=0;
     1173
     1174  // create a clone
     1175  molecule *mol = NULL;
     1176  if (molecules->ListOfMolecules.size() != 0) // clone
     1177    mol = (molecules->ListOfMolecules.front())->CopyMolecule();
     1178  else {
     1179    eLog() << Verbose(0) << "I don't have anything to test on ... ";
     1180    performCriticalExit();
     1181    return;
     1182  }
     1183  atom *Walker = mol->start;
     1184
     1185  // generate some KeySets
     1186  Log() << Verbose(0) << "Generating KeySets." << endl;
     1187  KeySet TestSets[mol->AtomCount+1];
     1188  i=1;
     1189  while (Walker->next != mol->end) {
     1190    Walker = Walker->next;
     1191    for (int j=0;j<i;j++) {
     1192      TestSets[j].insert(Walker->nr);
     1193    }
     1194    i++;
     1195  }
     1196  Log() << Verbose(0) << "Testing insertion of already present item in KeySets." << endl;
     1197  KeySetTestPair test;
     1198  test = TestSets[mol->AtomCount-1].insert(Walker->nr);
     1199  if (test.second) {
     1200    Log() << Verbose(1) << "Insertion worked?!" << endl;
     1201  } else {
     1202    Log() << Verbose(1) << "Insertion rejected: Present object is " << (*test.first) << "." << endl;
     1203  }
     1204  TestSets[mol->AtomCount].insert(mol->end->previous->nr);
     1205  TestSets[mol->AtomCount].insert(mol->end->previous->previous->previous->nr);
     1206
     1207  // constructing Graph structure
     1208  Log() << Verbose(0) << "Generating Subgraph class." << endl;
     1209  Graph Subgraphs;
     1210
     1211  // insert KeySets into Subgraphs
     1212  Log() << Verbose(0) << "Inserting KeySets into Subgraph class." << endl;
     1213  for (int j=0;j<mol->AtomCount;j++) {
     1214    Subgraphs.insert(GraphPair (TestSets[j],pair<int, double>(counter++, 1.)));
     1215  }
     1216  Log() << Verbose(0) << "Testing insertion of already present item in Subgraph." << endl;
     1217  GraphTestPair test2;
     1218  test2 = Subgraphs.insert(GraphPair (TestSets[mol->AtomCount],pair<int, double>(counter++, 1.)));
     1219  if (test2.second) {
     1220    Log() << Verbose(1) << "Insertion worked?!" << endl;
     1221  } else {
     1222    Log() << Verbose(1) << "Insertion rejected: Present object is " << (*(test2.first)).second.first << "." << endl;
     1223  }
     1224
     1225  // show graphs
     1226  Log() << Verbose(0) << "Showing Subgraph's contents, checking that it's sorted." << endl;
     1227  Graph::iterator A = Subgraphs.begin();
     1228  while (A !=  Subgraphs.end()) {
     1229    Log() << Verbose(0) << (*A).second.first << ": ";
     1230    KeySet::iterator key = (*A).first.begin();
     1231    comp = -1;
     1232    while (key != (*A).first.end()) {
     1233      if ((*key) > comp)
     1234        Log() << Verbose(0) << (*key) << " ";
     1235      else
     1236        Log() << Verbose(0) << (*key) << "! ";
     1237      comp = (*key);
     1238      key++;
     1239    }
     1240    Log() << Verbose(0) << endl;
     1241    A++;
     1242  }
     1243  delete(mol);
     1244};
     1245
     1246#endif
    761247
    771248/** Parses the command line options.
    … …  
    1021273  int argptr;
    1031274  molecule *mol = NULL;
    104   string BondGraphFileName("");
     1275  string BondGraphFileName("\n");
    1051276  int verbosity = 0;
    1061277  strncpy(configuration.databasepath, LocalPath, MAXSTRINGSIZE-1);
    … …  
    2561427       mol = new molecule(periode);
    2571428       mol->ActiveFlag = true;
     1429       if (ConfigFileName != NULL)
     1430         mol->SetNameFromFilename(ConfigFileName);
    2581431       molecules->insert(mol);
     1432     }
     1433     if (configuration.BG == NULL) {
     1434       configuration.BG = new BondGraph(configuration.GetIsAngstroem());
     1435       if ((BondGraphFileName.empty()) && (configuration.BG->LoadBondLengthTable(BondGraphFileName))) {
     1436         Log() << Verbose(0) << "Bond length table loaded successfully." << endl;
     1437       } else {
     1438         eLog() << Verbose(1) << "Bond length table loading failed." << endl;
     1439       }
    2591440     }
    2601441
    … …  
    2801461                else {
    2811462                  Log() << Verbose(2) << "File found and parsed." << endl;
     1463                  // @TODO rather do the dissection afterwards
     1464//                  mol->SetNameFromFilename(argv[argptr]);
     1465//                  molecules->ListOfMolecules.remove(mol);
     1466//                  molecules->DissectMoleculeIntoConnectedSubgraphs(mol,&configuration);
     1467//                  delete(mol);
     1468//                  if (molecules->ListOfMolecules.size() != 0) {
     1469//                    for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
     1470//                      if ((*ListRunner)->ActiveFlag) {
     1471//                        mol = *ListRunner;
     1472//                        break;
     1473//                      }
     1474//                  }
    2821475                  configPresent = present;
    2831476                }
    … …  
    4981691                start = clock();
    4991692                LCList = new LinkedCell(Boundary, atof(argv[argptr])*2.);
    500                 FindNonConvexBorder(Boundary, T, LCList, atof(argv[argptr]), argv[argptr+1]);
     1693                if (!FindNonConvexBorder(Boundary, T, LCList, atof(argv[argptr]), argv[argptr+1]))
     1694                  ExitFlag = 255;
    5011695                //FindDistributionOfEllipsoids(T, &LCList, N, number, filename.c_str());
    5021696                end = clock();
    5031697                Log() << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl;
    5041698                delete(LCList);
     1699                delete(T);
    5051700                argptr+=2;
    5061701              }
    … …  
    7981993                if (volume != -1)
    7991994                  ExitFlag = 255;
    800                   eLog() << Verbose(0) << "Not enough arguments given for suspension: -u <density>" << endl;
     1995                  eLog() << Verbose(0) << "Not enough or invalid arguments given for suspension: -u <density>" << endl;
    8011996                  performCriticalExit();
    8021997              } else {
    … …  
    9702165
    9712166    {
     2167      cout << ESPACKVersion << endl;
     2168
     2169      setVerbosity(0);
     2170
    9722171      menuPopulaters populaters;
    9732172      populaters.MakeEditMoleculesMenu = populateEditMoleculesMenu;

  • src/config.cpp

    r8927ae r1ca488  
    140140void ConfigFileBuffer::MapIonTypesInBuffer(const int NoAtoms)
    141141{
    142   map<const char *, int, IonTypeCompare> LineList;
     142  map<const char *, int, IonTypeCompare> IonTypeLineMap;
    143143  if (LineMapping == NULL) {
    144144    eLog() << Verbose(0) << "map pointer is NULL: " << LineMapping << endl;
    … …  
    149149  // put all into hashed map
    150150  for (int i=0; i<NoAtoms; ++i) {
    151     LineList.insert(pair<const char *, int> (buffer[CurrentLine+i], CurrentLine+i));
     151    IonTypeLineMap.insert(pair<const char *, int> (buffer[CurrentLine+i], CurrentLine+i));
    152152  }
    153153
    154154  // fill map
    155155  int nr=0;
    156   for (map<const char *, int, IonTypeCompare>::iterator runner = LineList.begin(); runner != LineList.end(); ++runner) {
     156  for (map<const char *, int, IonTypeCompare>::iterator runner = IonTypeLineMap.begin(); runner != IonTypeLineMap.end(); ++runner) {
    157157    if (CurrentLine+nr < NoLines)
    158158      LineMapping[CurrentLine+(nr++)] = runner->second;
    … …  
    10561056
    10571057  // 2. parse the bond graph file if given
    1058   BG = new BondGraph(IsAngstroem);
    1059   if (BG->LoadBondLengthTable(BondGraphFileName)) {
    1060     Log() << Verbose(0) << "Bond length table loaded successfully." << endl;
    1061   } else {
    1062     eLog() << Verbose(1) << "Bond length table loading failed." << endl;
     1058  if (BG == NULL) {
     1059    BG = new BondGraph(IsAngstroem);
     1060    if (BG->LoadBondLengthTable(BondGraphFileName)) {
     1061      Log() << Verbose(0) << "Bond length table loaded successfully." << endl;
     1062    } else {
     1063      eLog() << Verbose(1) << "Bond length table loading failed." << endl;
     1064    }
    10631065  }
    10641066
    10651067  // 3. parse the molecule in
    10661068  LoadMolecule(mol, FileBuffer, periode, FastParsing);
     1069  mol->SetNameFromFilename(filename);
    10671070  mol->ActiveFlag = true;
     1071  MolList->insert(mol);
    10681072
    10691073  // 4. dissect the molecule into connected subgraphs
    1070   MolList->DissectMoleculeIntoConnectedSubgraphs(mol,this);
    1071 
    1072   delete(mol);
     1074  // don't do this here ...
     1075  //MolList->DissectMoleculeIntoConnectedSubgraphs(mol,this);
     1076  //delete(mol);
     1077
    10731078  delete(FileBuffer);
    10741079};
    … …  
    17821787  ofstream output;
    17831788  molecule *mol = new molecule(periode);
    1784 
    1785   if (!strcmp(configpath, GetDefaultPath())) {
     1789  mol->SetNameFromFilename(ConfigFileName);
     1790
     1791  if (!strcmp(configuration->configpath, configuration->GetDefaultPath())) {
    17861792    eLog() << Verbose(2) << "config is found under different path then stated in config file::defaultpath!" << endl;
    17871793  }
    … …  
    17911797  if (ConfigFileName != NULL)
    17921798    strcpy(filename, ConfigFileName);
    1793   else
     1799  if (output == NULL)
    17941800    strcpy(filename,"main_pcp_linux");
    17951801  Log() << Verbose(0) << "Saving as pdb input ";
    1796   if (SavePDB(filename, molecules))
     1802  if (configuration->SavePDB(filename, molecules))
    17971803    Log() << Verbose(0) << "done." << endl;
    17981804  else
    … …  
    18021808  if (ConfigFileName != NULL)
    18031809    strcpy(filename, ConfigFileName);
    1804   else
     1810  if (output == NULL)
    18051811    strcpy(filename,"main_pcp_linux");
    18061812  Log() << Verbose(0) << "Saving as tremolo data input ";
    1807   if (SaveTREMOLO(filename, molecules))
     1813  if (configuration->SaveTREMOLO(filename, molecules))
    18081814    Log() << Verbose(0) << "done." << endl;
    18091815  else
    … …  
    18301836  Log() << Verbose(0) << "Storing configuration ... " << endl;
    18311837  // get correct valence orbitals
    1832   mol->CalculateOrbitals(*this);
    1833   InitMaxMinStopStep = MaxMinStopStep = MaxPsiDouble;
     1838  mol->CalculateOrbitals(*configuration);
     1839  configuration->InitMaxMinStopStep = configuration->MaxMinStopStep = configuration->MaxPsiDouble;
    18341840  if (ConfigFileName != NULL) { // test the file name
    18351841    strcpy(filename, ConfigFileName);
    18361842    output.open(filename, ios::trunc);
    1837   } else if (strlen(configname) != 0) {
    1838     strcpy(filename, configname);
    1839     output.open(configname, ios::trunc);
     1843  } else if (strlen(configuration->configname) != 0) {
     1844    strcpy(filename, configuration->configname);
     1845    output.open(configuration->configname, ios::trunc);
    18401846    } else {
    18411847      strcpy(filename, DEFAULTCONFIG);
    … …  
    18451851  output.clear();
    18461852  Log() << Verbose(0) << "Saving of config file ";
    1847   if (Save(filename, periode, mol))
     1853  if (configuration->Save(filename, periode, mol))
    18481854    Log() << Verbose(0) << "successful." << endl;
    18491855  else
    … …  
    18561862    output.open(filename, ios::trunc);
    18571863  }
    1858   else {
     1864  if (output == NULL) {
    18591865    strcpy(filename,"main_pcp_linux");
    18601866    strcat(filename, ".xyz");
    … …  
    18791885  if (ConfigFileName != NULL)
    18801886    strcpy(filename, ConfigFileName);
    1881   else
     1887  if (output == NULL)
    18821888    strcpy(filename,"main_pcp_linux");
    18831889  Log() << Verbose(0) << "Saving as mpqc input ";
    1884   if (SaveMPQC(filename, mol))
     1890  if (configuration->SaveMPQC(filename, mol))
    18851891    Log() << Verbose(0) << "done." << endl;
    18861892  else
    18871893    Log() << Verbose(0) << "failed." << endl;
    18881894
    1889   if (!strcmp(configpath, GetDefaultPath())) {
     1895  if (!strcmp(configuration->configpath, configuration->GetDefaultPath())) {
    18901896    eLog() << Verbose(2) << "config is found under different path then stated in config file::defaultpath!" << endl;
    18911897  }

  • src/molecule.hpp

    r8927ae r1ca488  
    106106
    107107  // re-definition of virtual functions from PointCloud
     108  const char * const GetName() const;
    108109  Vector *GetCenter() const ;
    109110  TesselPoint *GetPoint() const ;

  • src/molecule_graph.cpp

    r8927ae r1ca488  
    11171117  bool status = true;
    11181118  if (ReferenceStack->IsEmpty()) {
    1119     eLog() << Verbose(0) << "ReferenceStack is empty!" << endl;
    1120     performCriticalExit();
     1119    Log() << Verbose(1) << "ReferenceStack is empty!" << endl;
    11211120    return false;
    11221121  }

  • src/molecule_pointcloud.cpp

    r8927ae r1ca488  
    1313/************************************* Functions for class molecule *********************************/
    1414
     15/** Returns a name for this point cloud, here the molecule's name.
     16 * \return name of point cloud
     17 */
     18const char * const molecule::GetName() const
     19{
     20  return name;
     21};
    1522
    1623/** Determine center of all atoms.

  • src/moleculelist.cpp

    r8927ae r1ca488  
    402402  input.open(line.c_str());
    403403  if (input == NULL) {
    404     eLog() << Verbose(0) << endl << "Unable to open " << line << ", is the directory correct?" << endl;
    405     performCriticalExit();
     404    Log() << Verbose(1) << endl << "Unable to open " << line << ", is the directory correct?" << endl;
    406405    return false;
    407406  }
    … …  
    760759  // 4a. create array of molecules to fill
    761760  const int MolCount = Subgraphs->next->Count();
     761  char number[MAXSTRINGSIZE];
    762762  molecule **molecules = Malloc<molecule *>(MolCount, "config::Load() - **molecules");
    763763  for (int i=0;i<MolCount;i++) {
    764764    molecules[i] = (molecule*) new molecule(mol->elemente);
    765765    molecules[i]->ActiveFlag = true;
     766    strncpy(molecules[i]->name, mol->name, MAXSTRINGSIZE);
     767    if (MolCount > 1) {
     768      sprintf(number, "-%d", i+1);
     769      strncat(molecules[i]->name, number, MAXSTRINGSIZE - strlen(mol->name) - 1);
     770    }
     771    cout << "MolName is " << molecules[i]->name << endl;
    766772    insert(molecules[i]);
    767773  }
    … …  
    800806    }
    801807  }
    802   // 4d. we don't need to redo bonds, as they are connected subgraphs and still maintained their ListOfBonds, but we have to remove them from first..last list
     808  // 4d. we don't need to redo bonds, as they are connected subgraphs and still maintain their ListOfBonds, but we have to remove them from first..last list
    803809  bond *Binder = mol->first;
    804810  while (mol->first->next != mol->last) {

  • src/parser.cpp

    r8927ae r1ca488  
    158158  //Log() << Verbose(0) << "Opening " << name << " ... "  << input << endl;
    159159  if (input == NULL) {
    160     eLog() << Verbose(0) << endl << "Unable to open " << name << ", is the directory correct?" << endl;
    161     performCriticalExit();
     160    eLog() << Verbose(1) << endl << "Unable to open " << name << ", is the directory correct?" << endl;
     161    //performCriticalExit();
    162162    return false;
    163163  }

  • src/tesselation.cpp

    r8927ae r1ca488  
    99
    1010#include "helpers.hpp"
     11#include "info.hpp"
    1112#include "linkedcell.hpp"
    1213#include "log.hpp"
    … …  
    2223/** Constructor of BoundaryPointSet.
    2324 */
    24 BoundaryPointSet::BoundaryPointSet()
    25 {
    26   LinesCount = 0;
    27   Nr = -1;
    28   value = 0.;
     25BoundaryPointSet::BoundaryPointSet() :
     26    LinesCount(0),
     27    value(0.),
     28    Nr(-1)
     29{
     30        Info FunctionInfo(__func__);
     31        Log() << Verbose(1) << "Adding noname." << endl;
    2932};
    3033
    … …  
    3235 * \param *Walker TesselPoint this boundary point represents
    3336 */
    34 BoundaryPointSet::BoundaryPointSet(TesselPoint * Walker)
    35 {
    36   node = Walker;
    37   LinesCount = 0;
    38   Nr = Walker->nr;
    39   value = 0.;
     37BoundaryPointSet::BoundaryPointSet(TesselPoint * Walker) :
     38  LinesCount(0),
     39  node(Walker),
     40  value(0.),
     41  Nr(Walker->nr)
     42{
     43        Info FunctionInfo(__func__);
     44  Log() << Verbose(1) << "Adding Node " << *Walker << endl;
    4045};
    4146
    … …  
    4651BoundaryPointSet::~BoundaryPointSet()
    4752{
    48   //Log() << Verbose(5) << "Erasing point nr. " << Nr << "." << endl;
     53        Info FunctionInfo(__func__);
     54  //Log() << Verbose(0) << "Erasing point nr. " << Nr << "." << endl;
    4955  if (!lines.empty())
    5056    eLog() << Verbose(2) << "Memory Leak! I " << *this << " am still connected to some lines." << endl;
    … …  
    5763void BoundaryPointSet::AddLine(class BoundaryLineSet *line)
    5864{
    59   Log() << Verbose(6) << "Adding " << *this << " to line " << *line << "."
     65        Info FunctionInfo(__func__);
     66  Log() << Verbose(1) << "Adding " << *this << " to line " << *line << "."
    6067      << endl;
    6168  if (line->endpoints[0] == this)
    … …  
    8592/** Constructor of BoundaryLineSet.
    8693 */
    87 BoundaryLineSet::BoundaryLineSet()
    88 {
     94BoundaryLineSet::BoundaryLineSet() :
     95    Nr(-1)
     96{
     97        Info FunctionInfo(__func__);
    8998  for (int i = 0; i < 2; i++)
    9099    endpoints[i] = NULL;
    91   Nr = -1;
    92100};
    93101
    … …  
    99107BoundaryLineSet::BoundaryLineSet(class BoundaryPointSet *Point[2], const int number)
    100108{
     109        Info FunctionInfo(__func__);
    101110  // set number
    102111  Nr = number;
    … …  
    106115  Point[0]->AddLine(this); //Taken out, to check whether we can avoid unwanted double adding.
    107116  Point[1]->AddLine(this); //
     117  // set skipped to false
     118  skipped = false;
    108119  // clear triangles list
    109   Log() << Verbose(5) << "New Line with endpoints " << *this << "." << endl;
     120  Log() << Verbose(0) << "New Line with endpoints " << *this << "." << endl;
    110121};
    111122
    … …  
    116127BoundaryLineSet::~BoundaryLineSet()
    117128{
     129        Info FunctionInfo(__func__);
    118130  int Numbers[2];
    119131
    … …  
    134146        for (LineMap::iterator Runner = erasor.first; Runner != erasor.second; Runner++)
    135147          if ((*Runner).second == this) {
    136             //Log() << Verbose(5) << "Removing Line Nr. " << Nr << " in boundary point " << *endpoints[i] << "." << endl;
     148            //Log() << Verbose(0) << "Removing Line Nr. " << Nr << " in boundary point " << *endpoints[i] << "." << endl;
    137149            endpoints[i]->lines.erase(Runner);
    138150            break;
    … …  
    140152      } else { // there's just a single line left
    141153        if (endpoints[i]->lines.erase(Nr)) {
    142           //Log() << Verbose(5) << "Removing Line Nr. " << Nr << " in boundary point " << *endpoints[i] << "." << endl;
     154          //Log() << Verbose(0) << "Removing Line Nr. " << Nr << " in boundary point " << *endpoints[i] << "." << endl;
    143155        }
    144156      }
    145157      if (endpoints[i]->lines.empty()) {
    146         //Log() << Verbose(5) << *endpoints[i] << " has no more lines it's attached to, erasing." << endl;
     158        //Log() << Verbose(0) << *endpoints[i] << " has no more lines it's attached to, erasing." << endl;
    147159        if (endpoints[i] != NULL) {
    148160          delete(endpoints[i]);
    … …  
    161173void BoundaryLineSet::AddTriangle(class BoundaryTriangleSet *triangle)
    162174{
    163   Log() << Verbose(6) << "Add " << triangle->Nr << " to line " << *this << "." << endl;
     175        Info FunctionInfo(__func__);
     176  Log() << Verbose(0) << "Add " << triangle->Nr << " to line " << *this << "." << endl;
    164177  triangles.insert(TrianglePair(triangle->Nr, triangle));
    165178};
    … …  
    171184bool BoundaryLineSet::IsConnectedTo(class BoundaryLineSet *line)
    172185{
     186        Info FunctionInfo(__func__);
    173187  if ((endpoints[0] == line->endpoints[0]) || (endpoints[1] == line->endpoints[0]) || (endpoints[0] == line->endpoints[1]) || (endpoints[1] == line->endpoints[1]))
    174188    return true;
    … …  
    185199bool BoundaryLineSet::CheckConvexityCriterion()
    186200{
     201        Info FunctionInfo(__func__);
    187202  Vector BaseLineCenter, BaseLineNormal, BaseLine, helper[2], NormalCheck;
    188203  // get the two triangles
    189204  if (triangles.size() != 2) {
    190     eLog() << Verbose(1) << "Baseline " << *this << " is connected to less than two triangles, Tesselation incomplete!" << endl;
     205    eLog() << Verbose(0) << "Baseline " << *this << " is connected to less than two triangles, Tesselation incomplete!" << endl;
    191206    return true;
    192207  }
    193208  // check normal vectors
    194209  // have a normal vector on the base line pointing outwards
    195   //Log() << Verbose(3) << "INFO: " << *this << " has vectors at " << *(endpoints[0]->node->node) << " and at " << *(endpoints[1]->node->node) << "." << endl;
     210  //Log() << Verbose(0) << "INFO: " << *this << " has vectors at " << *(endpoints[0]->node->node) << " and at " << *(endpoints[1]->node->node) << "." << endl;
    196211  BaseLineCenter.CopyVector(endpoints[0]->node->node);
    197212  BaseLineCenter.AddVector(endpoints[1]->node->node);
    … …  
    199214  BaseLine.CopyVector(endpoints[0]->node->node);
    200215  BaseLine.SubtractVector(endpoints[1]->node->node);
    201   //Log() << Verbose(3) << "INFO: Baseline is " << BaseLine << " and its center is at " << BaseLineCenter << "." << endl;
     216  //Log() << Verbose(0) << "INFO: Baseline is " << BaseLine << " and its center is at " << BaseLineCenter << "." << endl;
    202217
    203218  BaseLineNormal.Zero();
    … …  
    207222  class BoundaryPointSet *node = NULL;
    208223  for(TriangleMap::iterator runner = triangles.begin(); runner != triangles.end(); runner++) {
    209     //Log() << Verbose(3) << "INFO: NormalVector of " << *(runner->second) << " is " << runner->second->NormalVector << "." << endl;
     224    //Log() << Verbose(0) << "INFO: NormalVector of " << *(runner->second) << " is " << runner->second->NormalVector << "." << endl;
    210225    NormalCheck.AddVector(&runner->second->NormalVector);
    211226    NormalCheck.Scale(sign);
    … …  
    214229      BaseLineNormal.CopyVector(&runner->second->NormalVector);   // yes, copy second on top of first
    215230    else {
    216       Log() << Verbose(1) << "CRITICAL: Triangle " << *runner->second << " has zero normal vector!" << endl;
    217       exit(255);
     231      eLog() << Verbose(0) << "Triangle " << *runner->second << " has zero normal vector!" << endl;
    218232    }
    219233    node = runner->second->GetThirdEndpoint(this);
    220234    if (node != NULL) {
    221       //Log() << Verbose(3) << "INFO: Third node for triangle " << *(runner->second) << " is " << *node << " at " << *(node->node->node) << "." << endl;
     235      //Log() << Verbose(0) << "INFO: Third node for triangle " << *(runner->second) << " is " << *node << " at " << *(node->node->node) << "." << endl;
    222236      helper[i].CopyVector(node->node->node);
    223237      helper[i].SubtractVector(&BaseLineCenter);
    224238      helper[i].MakeNormalVector(&BaseLine);  // we want to compare the triangle's heights' angles!
    225       //Log() << Verbose(4) << "INFO: Height vector with respect to baseline is " << helper[i] << "." << endl;
     239      //Log() << Verbose(0) << "INFO: Height vector with respect to baseline is " << helper[i] << "." << endl;
    226240      i++;
    227241    } else {
    228       //eLog() << Verbose(1) << "I cannot find third node in triangle, something's wrong." << endl;
     242      eLog() << Verbose(1) << "I cannot find third node in triangle, something's wrong." << endl;
    229243      return true;
    230244    }
    231245  }
    232   //Log() << Verbose(3) << "INFO: BaselineNormal is " << BaseLineNormal << "." << endl;
     246  //Log() << Verbose(0) << "INFO: BaselineNormal is " << BaseLineNormal << "." << endl;
    233247  if (NormalCheck.NormSquared() < MYEPSILON) {
    234     Log() << Verbose(3) << "ACCEPT: Normalvectors of both triangles are the same: convex." << endl;
     248    Log() << Verbose(0) << "ACCEPT: Normalvectors of both triangles are the same: convex." << endl;
    235249    return true;
    236250  }
    … …  
    238252  double angle = GetAngle(helper[0], helper[1], BaseLineNormal);
    239253  if ((angle - M_PI) > -MYEPSILON) {
    240     Log() << Verbose(3) << "ACCEPT: Angle is greater than pi: convex." << endl;
     254    Log() << Verbose(0) << "ACCEPT: Angle is greater than pi: convex." << endl;
    241255    return true;
    242256  } else {
    243     Log() << Verbose(3) << "REJECT: Angle is less than pi: concave." << endl;
     257    Log() << Verbose(0) << "REJECT: Angle is less than pi: concave." << endl;
    244258    return false;
    245259  }
    … …  
    252266bool BoundaryLineSet::ContainsBoundaryPoint(class BoundaryPointSet *point)
    253267{
     268        Info FunctionInfo(__func__);
    254269  for(int i=0;i<2;i++)
    255270    if (point == endpoints[i])
    … …  
    264279class BoundaryPointSet *BoundaryLineSet::GetOtherEndpoint(class BoundaryPointSet *point)
    265280{
     281        Info FunctionInfo(__func__);
    266282  if (endpoints[0] == point)
    267283    return endpoints[1];
    … …  
    286302/** Constructor for BoundaryTriangleSet.
    287303 */
    288 BoundaryTriangleSet::BoundaryTriangleSet()
    289 {
     304BoundaryTriangleSet::BoundaryTriangleSet() :
     305  Nr(-1)
     306{
     307        Info FunctionInfo(__func__);
    290308  for (int i = 0; i < 3; i++)
    291309    {
    … …  
    293311      lines[i] = NULL;
    294312    }
    295   Nr = -1;
    296313};
    297314
    … …  
    300317 * \param number number of triangle
    301318 */
    302 BoundaryTriangleSet::BoundaryTriangleSet(class BoundaryLineSet *line[3], int number)
    303 {
     319BoundaryTriangleSet::BoundaryTriangleSet(class BoundaryLineSet *line[3], int number) :
     320  Nr(number)
     321{
     322        Info FunctionInfo(__func__);
    304323  // set number
    305   Nr = number;
    306324  // set lines
    307   Log() << Verbose(5) << "New triangle " << Nr << ":" << endl;
    308   for (int i = 0; i < 3; i++)
    309     {
    310       lines[i] = line[i];
    311       lines[i]->AddTriangle(this);
    312     }
     325  for (int i = 0; i < 3; i++) {
     326    lines[i] = line[i];
     327    lines[i]->AddTriangle(this);
     328  }
    313329  // get ascending order of endpoints
    314   map<int, class BoundaryPointSet *> OrderMap;
     330  PointMap OrderMap;
    315331  for (int i = 0; i < 3; i++)
    316332    // for all three lines
    317     for (int j = 0; j < 2; j++)
    318       { // for both endpoints
    319         OrderMap.insert(pair<int, class BoundaryPointSet *> (
    320             line[i]->endpoints[j]->Nr, line[i]->endpoints[j]));
    321         // and we don't care whether insertion fails
    322       }
     333    for (int j = 0; j < 2; j++) { // for both endpoints
     334      OrderMap.insert(pair<int, class BoundaryPointSet *> (
     335          line[i]->endpoints[j]->Nr, line[i]->endpoints[j]));
     336      // and we don't care whether insertion fails
     337    }
    323338  // set endpoints
    324339  int Counter = 0;
    325   Log() << Verbose(6) << " with end points ";
    326   for (map<int, class BoundaryPointSet *>::iterator runner = OrderMap.begin(); runner
    327       != OrderMap.end(); runner++)
    328     {
    329       endpoints[Counter] = runner->second;
    330       Log() << Verbose(0) << " " << *endpoints[Counter];
    331       Counter++;
    332     }
    333   if (Counter < 3)
    334     {
    335       eLog() << Verbose(0) << "ERROR! We have a triangle with only two distinct endpoints!" << endl;
    336       performCriticalExit();
    337     }
    338   Log() << Verbose(0) << "." << endl;
     340  Log() << Verbose(0) << "New triangle " << Nr << " with end points: " << endl;
     341  for (PointMap::iterator runner = OrderMap.begin(); runner != OrderMap.end(); runner++) {
     342    endpoints[Counter] = runner->second;
     343    Log() << Verbose(0) << " " << *endpoints[Counter] << endl;
     344    Counter++;
     345  }
     346  if (Counter < 3) {
     347    eLog() << Verbose(0) << "We have a triangle with only two distinct endpoints!" << endl;
     348    performCriticalExit();
     349  }
    339350};
    340351
    … …  
    345356BoundaryTriangleSet::~BoundaryTriangleSet()
    346357{
     358        Info FunctionInfo(__func__);
    347359  for (int i = 0; i < 3; i++) {
    348360    if (lines[i] != NULL) {
    349361      if (lines[i]->triangles.erase(Nr)) {
    350         //Log() << Verbose(5) << "Triangle Nr." << Nr << " erased in line " << *lines[i] << "." << endl;
     362        //Log() << Verbose(0) << "Triangle Nr." << Nr << " erased in line " << *lines[i] << "." << endl;
    351363      }
    352364      if (lines[i]->triangles.empty()) {
    353           //Log() << Verbose(5) << *lines[i] << " is no more attached to any triangle, erasing." << endl;
     365          //Log() << Verbose(0) << *lines[i] << " is no more attached to any triangle, erasing." << endl;
    354366          delete (lines[i]);
    355367          lines[i] = NULL;
    … …  
    357369    }
    358370  }
    359   //Log() << Verbose(5) << "Erasing triangle Nr." << Nr << " itself." << endl;
     371  //Log() << Verbose(0) << "Erasing triangle Nr." << Nr << " itself." << endl;
    360372};
    361373
    … …  
    366378void BoundaryTriangleSet::GetNormalVector(Vector &OtherVector)
    367379{
     380        Info FunctionInfo(__func__);
    368381  // get normal vector
    369382  NormalVector.MakeNormalVector(endpoints[0]->node->node, endpoints[1]->node->node, endpoints[2]->node->node);
    … …  
    372385  if (NormalVector.ScalarProduct(&OtherVector) > 0.)
    373386    NormalVector.Scale(-1.);
     387  Log() << Verbose(1) << "Normal Vector is " << NormalVector << "." << endl;
    374388};
    375389
    … …  
    388402bool BoundaryTriangleSet::GetIntersectionInsideTriangle(Vector *MolCenter, Vector *x, Vector *Intersection)
    389403{
     404        Info FunctionInfo(__func__);
    390405  Vector CrossPoint;
    391406  Vector helper;
    392407
    393408  if (!Intersection->GetIntersectionWithPlane(&NormalVector, endpoints[0]->node->node, MolCenter, x)) {
    394     Log() << Verbose(1) << "Alas! Intersection with plane failed - at least numerically - the intersection is not on the plane!" << endl;
     409    eLog() << Verbose(1) << "Alas! Intersection with plane failed - at least numerically - the intersection is not on the plane!" << endl;
    395410    return false;
    396411  }
    … …  
    408423  } while (CrossPoint.NormSquared() < MYEPSILON);
    409424  if (i==3) {
    410     eLog() << Verbose(1) << "Could not find any cross points, something's utterly wrong here!" << endl;
    411     exit(255);
     425    eLog() << Verbose(0) << "Could not find any cross points, something's utterly wrong here!" << endl;
    412426  }
    413427  CrossPoint.SubtractVector(endpoints[i%3]->node->node);  // cross point was returned as absolute vector
    … …  
    428442bool BoundaryTriangleSet::ContainsBoundaryLine(class BoundaryLineSet *line)
    429443{
     444        Info FunctionInfo(__func__);
    430445  for(int i=0;i<3;i++)
    431446    if (line == lines[i])
    … …  
    440455bool BoundaryTriangleSet::ContainsBoundaryPoint(class BoundaryPointSet *point)
    441456{
     457        Info FunctionInfo(__func__);
    442458  for(int i=0;i<3;i++)
    443459    if (point == endpoints[i])
    … …  
    452468bool BoundaryTriangleSet::ContainsBoundaryPoint(class TesselPoint *point)
    453469{
     470        Info FunctionInfo(__func__);
    454471  for(int i=0;i<3;i++)
    455472    if (point == endpoints[i]->node)
    … …  
    464481bool BoundaryTriangleSet::IsPresentTupel(class BoundaryPointSet *Points[3])
    465482{
     483        Info FunctionInfo(__func__);
    466484  return (((endpoints[0] == Points[0])
    467485            || (endpoints[0] == Points[1])
    … …  
    485503bool BoundaryTriangleSet::IsPresentTupel(class BoundaryTriangleSet *T)
    486504{
     505        Info FunctionInfo(__func__);
    487506  return (((endpoints[0] == T->endpoints[0])
    488507            || (endpoints[0] == T->endpoints[1])
    … …  
    506525class BoundaryPointSet *BoundaryTriangleSet::GetThirdEndpoint(class BoundaryLineSet *line)
    507526{
     527        Info FunctionInfo(__func__);
    508528  // sanity check
    509529  if (!ContainsBoundaryLine(line))
    … …  
    522542void BoundaryTriangleSet::GetCenter(Vector *center)
    523543{
     544        Info FunctionInfo(__func__);
    524545  center->Zero();
    525546  for(int i=0;i<3;i++)
    … …  
    534555ostream &operator <<(ostream &ost, const BoundaryTriangleSet &a)
    535556{
    536   ost << "[" << a.Nr << "|" << a.endpoints[0]->node->Name << " at " << *a.endpoints[0]->node->node << ","
    537       << a.endpoints[1]->node->Name << " at " << *a.endpoints[1]->node->node << "," << a.endpoints[2]->node->Name << " at " << *a.endpoints[2]->node->node << "]";
     557  ost << "[" << a.Nr << "|" << a.endpoints[0]->node->Name << "," << a.endpoints[1]->node->Name << "," << a.endpoints[2]->node->Name << "]";
     558//  ost << "[" << a.Nr << "|" << a.endpoints[0]->node->Name << " at " << *a.endpoints[0]->node->node << ","
     559//      << a.endpoints[1]->node->Name << " at " << *a.endpoints[1]->node->node << "," << a.endpoints[2]->node->Name << " at " << *a.endpoints[2]->node->node << "]";
    538560  return ost;
    539561};
    540562
     563// ======================================== Polygons on Boundary =================================
     564
     565/** Constructor for BoundaryPolygonSet.
     566 */
     567BoundaryPolygonSet::BoundaryPolygonSet() :
     568  Nr(-1)
     569{
     570  Info FunctionInfo(__func__);
     571};
     572
     573/** Destructor of BoundaryPolygonSet.
     574 * Just clears endpoints.
     575 * \note When removing triangles from a class Tesselation, use RemoveTesselationTriangle()
     576 */
     577BoundaryPolygonSet::~BoundaryPolygonSet()
     578{
     579  Info FunctionInfo(__func__);
     580  endpoints.clear();
     581  Log() << Verbose(1) << "Erasing polygon Nr." << Nr << " itself." << endl;
     582};
     583
     584/** Calculates the normal vector for this triangle.
     585 * Is made unique by comparison with \a OtherVector to point in the other direction.
     586 * \param &OtherVector direction vector to make normal vector unique.
     587 * \return allocated vector in normal direction
     588 */
     589Vector * BoundaryPolygonSet::GetNormalVector(const Vector &OtherVector) const
     590{
     591  Info FunctionInfo(__func__);
     592  // get normal vector
     593  Vector TemporaryNormal;
     594  Vector *TotalNormal = new Vector;
     595  PointSet::const_iterator Runner[3];
     596  for (int i=0;i<3; i++) {
     597    Runner[i] = endpoints.begin();
     598    for (int j = 0; j<i; j++) { // go as much further
     599      Runner[i]++;
     600      if (Runner[i] == endpoints.end()) {
     601        eLog() << Verbose(0) << "There are less than three endpoints in the polygon!" << endl;
     602        performCriticalExit();
     603      }
     604    }
     605  }
     606  TotalNormal->Zero();
     607  int counter=0;
     608  for (; Runner[2] != endpoints.end(); ) {
     609    TemporaryNormal.MakeNormalVector((*Runner[0])->node->node, (*Runner[1])->node->node, (*Runner[2])->node->node);
     610    for (int i=0;i<3;i++) // increase each of them
     611      Runner[i]++;
     612    TotalNormal->AddVector(&TemporaryNormal);
     613  }
     614  TotalNormal->Scale(1./(double)counter);
     615
     616  // make it always point inward (any offset vector onto plane projected onto normal vector suffices)
     617  if (TotalNormal->ScalarProduct(&OtherVector) > 0.)
     618    TotalNormal->Scale(-1.);
     619  Log() << Verbose(1) << "Normal Vector is " << *TotalNormal << "." << endl;
     620
     621  return TotalNormal;
     622};
     623
     624/** Calculates the center point of the triangle.
     625 * Is third of the sum of all endpoints.
     626 * \param *center central point on return.
     627 */
     628void BoundaryPolygonSet::GetCenter(Vector * const center) const
     629{
     630  Info FunctionInfo(__func__);
     631  center->Zero();
     632  int counter = 0;
     633  for(PointSet::const_iterator Runner = endpoints.begin(); Runner != endpoints.end(); Runner++) {
     634    center->AddVector((*Runner)->node->node);
     635    counter++;
     636  }
     637  center->Scale(1./(double)counter);
     638  Log() << Verbose(1) << "Center is at " << *center << "." << endl;
     639}
     640
     641/** Checks whether the polygons contains all three endpoints of the triangle.
     642 * \param *triangle triangle to test
     643 * \return true - triangle is contained polygon, false - is not
     644 */
     645bool BoundaryPolygonSet::ContainsBoundaryTriangle(const BoundaryTriangleSet * const triangle) const
     646{
     647  Info FunctionInfo(__func__);
     648  return ContainsPresentTupel(triangle->endpoints, 3);
     649};
     650
     651/** Checks whether the polygons contains both endpoints of the line.
     652 * \param *line line to test
     653 * \return true - line is of the triangle, false - is not
     654 */
     655bool BoundaryPolygonSet::ContainsBoundaryLine(const BoundaryLineSet * const line) const
     656{
     657  Info FunctionInfo(__func__);
     658  return ContainsPresentTupel(line->endpoints, 2);
     659};
     660
     661/** Checks whether point is any of the three endpoints this triangle contains.
     662 * \param *point point to test
     663 * \return true - point is of the triangle, false - is not
     664 */
     665bool BoundaryPolygonSet::ContainsBoundaryPoint(const BoundaryPointSet * const point) const
     666{
     667  Info FunctionInfo(__func__);
     668  for(PointSet::const_iterator Runner = endpoints.begin(); Runner != endpoints.end(); Runner++) {
     669    Log() << Verbose(0) << "Checking against " << **Runner << endl;
     670    if (point == (*Runner)) {
     671      Log() << Verbose(0) << " Contained." << endl;
     672      return true;
     673    }
     674  }
     675  Log() << Verbose(0) << " Not contained." << endl;
     676  return false;
     677};
     678
     679/** Checks whether point is any of the three endpoints this triangle contains.
     680 * \param *point TesselPoint to test
     681 * \return true - point is of the triangle, false - is not
     682 */
     683bool BoundaryPolygonSet::ContainsBoundaryPoint(const TesselPoint * const point) const
     684{
     685  Info FunctionInfo(__func__);
     686  for(PointSet::const_iterator Runner = endpoints.begin(); Runner != endpoints.end(); Runner++)
     687    if (point == (*Runner)->node) {
     688      Log() << Verbose(0) << " Contained." << endl;
     689      return true;
     690    }
     691  Log() << Verbose(0) << " Not contained." << endl;
     692  return false;
     693};
     694
     695/** Checks whether given array of \a *Points coincide with polygons's endpoints.
     696 * \param **Points pointer to an array of BoundaryPointSet
     697 * \param dim dimension of array
     698 * \return true - set of points is contained in polygon, false - is not
     699 */
     700bool BoundaryPolygonSet::ContainsPresentTupel(const BoundaryPointSet * const * Points, const int dim) const
     701{
     702  Info FunctionInfo(__func__);
     703  int counter = 0;
     704  Log() << Verbose(1) << "Polygon is " << *this << endl;
     705  for(int i=0;i<dim;i++) {
     706    Log() << Verbose(1) << " Testing endpoint " << *Points[i] << endl;
     707    if (ContainsBoundaryPoint(Points[i])) {
     708      counter++;
     709    }
     710  }
     711
     712  if (counter == dim)
     713    return true;
     714  else
     715    return false;
     716};
     717
     718/** Checks whether given PointList coincide with polygons's endpoints.
     719 * \param &endpoints PointList
     720 * \return true - set of points is contained in polygon, false - is not
     721 */
     722bool BoundaryPolygonSet::ContainsPresentTupel(const PointSet &endpoints) const
     723{
     724  Info FunctionInfo(__func__);
     725  size_t counter = 0;
     726  Log() << Verbose(1) << "Polygon is " << *this << endl;
     727  for(PointSet::const_iterator Runner = endpoints.begin(); Runner != endpoints.end(); Runner++) {
     728    Log() << Verbose(1) << " Testing endpoint " << **Runner << endl;
     729    if (ContainsBoundaryPoint(*Runner))
     730      counter++;
     731  }
     732
     733  if (counter == endpoints.size())
     734    return true;
     735  else
     736    return false;
     737};
     738
     739/** Checks whether given set of \a *Points coincide with polygons's endpoints.
     740 * \param *P pointer to BoundaryPolygonSet
     741 * \return true - is the very triangle, false - is not
     742 */
     743bool BoundaryPolygonSet::ContainsPresentTupel(const BoundaryPolygonSet * const P) const
     744{
     745  return ContainsPresentTupel((const PointSet)P->endpoints);
     746};
     747
     748/** Gathers all the endpoints' triangles in a unique set.
     749 * \return set of all triangles
     750 */
     751TriangleSet * BoundaryPolygonSet::GetAllContainedTrianglesFromEndpoints() const
     752{
     753  Info FunctionInfo(__func__);
     754  pair <TriangleSet::iterator, bool> Tester;
     755  TriangleSet *triangles = new TriangleSet;
     756
     757  for(PointSet::const_iterator Runner = endpoints.begin(); Runner != endpoints.end(); Runner++)
     758    for(LineMap::const_iterator Walker = (*Runner)->lines.begin(); Walker != (*Runner)->lines.end(); Walker++)
     759      for(TriangleMap::const_iterator Sprinter = (Walker->second)->triangles.begin(); Sprinter != (Walker->second)->triangles.end(); Sprinter++) {
     760        //Log() << Verbose(0) << " Testing triangle " << *(Sprinter->second) << endl;
     761        if (ContainsBoundaryTriangle(Sprinter->second)) {
     762          Tester = triangles->insert(Sprinter->second);
     763          if (Tester.second)
     764            Log() << Verbose(0) << "Adding triangle " << *(Sprinter->second) << endl;
     765        }
     766      }
     767
     768  Log() << Verbose(1) << "The Polygon of " << endpoints.size() << " endpoints has " << triangles->size() << " unique triangles in total." << endl;
     769  return triangles;
     770};
     771
     772/** Fills the endpoints of this polygon from the triangles attached to \a *line.
     773 * \param *line lines with triangles attached
     774 * \return true - polygon contains endpoints, false - line was NULL
     775 */
     776bool BoundaryPolygonSet::FillPolygonFromTrianglesOfLine(const BoundaryLineSet * const line)
     777{
     778  Info FunctionInfo(__func__);
     779  pair <PointSet::iterator, bool> Tester;
     780  if (line == NULL)
     781    return false;
     782  Log() << Verbose(1) << "Filling polygon from line " << *line << endl;
     783  for(TriangleMap::const_iterator Runner = line->triangles.begin(); Runner != line->triangles.end(); Runner++) {
     784    for (int i=0;i<3;i++) {
     785      Tester = endpoints.insert((Runner->second)->endpoints[i]);
     786      if (Tester.second)
     787        Log() << Verbose(1) << "  Inserting endpoint " << *((Runner->second)->endpoints[i]) << endl;
     788    }
     789  }
     790
     791  return true;
     792};
     793
     794/** output operator for BoundaryPolygonSet.
     795 * \param &ost output stream
     796 * \param &a boundary polygon
     797 */
     798ostream &operator <<(ostream &ost, const BoundaryPolygonSet &a)
     799{
     800  ost << "[" << a.Nr << "|";
     801  for(PointSet::const_iterator Runner = a.endpoints.begin(); Runner != a.endpoints.end();) {
     802   ost << (*Runner)->node->Name;
     803   Runner++;
     804   if (Runner != a.endpoints.end())
     805     ost << ",";
     806  }
     807  ost<< "]";
     808  return ost;
     809};
     810
    541811// =========================================================== class TESSELPOINT ===========================================
    542812
    … …  
    545815TesselPoint::TesselPoint()
    546816{
     817  Info FunctionInfo(__func__);
    547818  node = NULL;
    548819  nr = -1;
    … …  
    554825TesselPoint::~TesselPoint()
    555826{
     827  Info FunctionInfo(__func__);
    556828};
    557829
    … …  
    568840ostream & TesselPoint::operator << (ostream &ost)
    569841{
    570   ost << "[" << (Name) << "|" << this << "]";
     842        Info FunctionInfo(__func__);
     843  ost << "[" << (nr) << "|" << this << "]";
    571844  return ost;
    572845};
    … …  
    579852PointCloud::PointCloud()
    580853{
    581 
     854        Info FunctionInfo(__func__);
    582855};
    583856
    … …  
    586859PointCloud::~PointCloud()
    587860{
    588 
     861        Info FunctionInfo(__func__);
    589862};
    590863
    … …  
    593866/** Constructor of class CandidateForTesselation.
    594867 */
    595 CandidateForTesselation::CandidateForTesselation(TesselPoint *candidate, BoundaryLineSet* line, Vector OptCandidateCenter, Vector OtherOptCandidateCenter) {
    596   point = candidate;
    597   BaseLine = line;
     868CandidateForTesselation::CandidateForTesselation (BoundaryLineSet* line) :
     869  BaseLine(line),
     870  ShortestAngle(2.*M_PI),
     871  OtherShortestAngle(2.*M_PI)
     872{
     873        Info FunctionInfo(__func__);
     874};
     875
     876
     877/** Constructor of class CandidateForTesselation.
     878 */
     879CandidateForTesselation::CandidateForTesselation (TesselPoint *candidate, BoundaryLineSet* line, Vector OptCandidateCenter, Vector OtherOptCandidateCenter) :
     880    BaseLine(line),
     881    ShortestAngle(2.*M_PI),
     882    OtherShortestAngle(2.*M_PI)
     883{
     884        Info FunctionInfo(__func__);
    598885  OptCenter.CopyVector(&OptCandidateCenter);
    599886  OtherOptCenter.CopyVector(&OtherOptCandidateCenter);
    … …  
    603890 */
    604891CandidateForTesselation::~CandidateForTesselation() {
    605   point = NULL;
    606892  BaseLine = NULL;
    607893};
    608894
     895/** output operator for CandidateForTesselation.
     896 * \param &ost output stream
     897 * \param &a boundary line
     898 */
     899ostream & operator <<(ostream &ost, const  CandidateForTesselation &a)
     900{
     901  ost << "[" << a.BaseLine->Nr << "|" << a.BaseLine->endpoints[0]->node->Name << "," << a.BaseLine->endpoints[1]->node->Name << "] with ";
     902  if (a.pointlist.empty())
     903    ost << "no candidate.";
     904  else {
     905    ost << "candidate";
     906    if (a.pointlist.size() != 1)
     907      ost << "s ";
     908    else
     909      ost << " ";
     910    for (TesselPointList::const_iterator Runner = a.pointlist.begin(); Runner != a.pointlist.end(); Runner++)
     911      ost << *(*Runner) << " ";
     912    ost << " at angle " << (a.ShortestAngle)<< ".";
     913  }
     914
     915  return ost;
     916};
     917
     918
    609919// =========================================================== class TESSELATION ===========================================
    610920
    611921/** Constructor of class Tesselation.
    612922 */
    613 Tesselation::Tesselation()
    614 {
    615   PointsOnBoundaryCount = 0;
    616   LinesOnBoundaryCount = 0;
    617   TrianglesOnBoundaryCount = 0;
    618   InternalPointer = PointsOnBoundary.begin();
    619   LastTriangle = NULL;
    620   TriangleFilesWritten = 0;
     923Tesselation::Tesselation() :
     924  PointsOnBoundaryCount(0),
     925  LinesOnBoundaryCount(0),
     926  TrianglesOnBoundaryCount(0),
     927  LastTriangle(NULL),
     928  TriangleFilesWritten(0),
     929  InternalPointer(PointsOnBoundary.begin())
     930{
     931        Info FunctionInfo(__func__);
    621932}
    622933;
    … …  
    627938Tesselation::~Tesselation()
    628939{
    629   Log() << Verbose(1) << "Free'ing TesselStruct ... " << endl;
     940        Info FunctionInfo(__func__);
     941  Log() << Verbose(0) << "Free'ing TesselStruct ... " << endl;
    630942  for (TriangleMap::iterator runner = TrianglesOnBoundary.begin(); runner != TrianglesOnBoundary.end(); runner++) {
    631943    if (runner->second != NULL) {
    … …  
    635947      eLog() << Verbose(1) << "The triangle " << runner->first << " has already been free'd." << endl;
    636948  }
    637   Log() << Verbose(1) << "This envelope was written to file " << TriangleFilesWritten << " times(s)." << endl;
     949  Log() << Verbose(0) << "This envelope was written to file " << TriangleFilesWritten << " times(s)." << endl;
    638950}
    639951;
    … …  
    644956Vector * Tesselation::GetCenter(ofstream *out) const
    645957{
     958        Info FunctionInfo(__func__);
    646959  Vector *Center = new Vector(0.,0.,0.);
    647960  int num=0;
    … …  
    659972TesselPoint * Tesselation::GetPoint() const
    660973{
     974        Info FunctionInfo(__func__);
    661975  return (InternalPointer->second->node);
    662976};
    … …  
    667981TesselPoint * Tesselation::GetTerminalPoint() const
    668982{
     983        Info FunctionInfo(__func__);
    669984  PointMap::const_iterator Runner = PointsOnBoundary.end();
    670985  Runner--;
    … …  
    677992void Tesselation::GoToNext() const
    678993{
     994        Info FunctionInfo(__func__);
    679995  if (InternalPointer != PointsOnBoundary.end())
    680996    InternalPointer++;
    … …  
    6861002void Tesselation::GoToPrevious() const
    6871003{
     1004        Info FunctionInfo(__func__);
    6881005  if (InternalPointer != PointsOnBoundary.begin())
    6891006    InternalPointer--;
    … …  
    6951012void Tesselation::GoToFirst() const
    6961013{
     1014        Info FunctionInfo(__func__);
    6971015  InternalPointer = PointsOnBoundary.begin();
    6981016};
    … …  
    7031021void Tesselation::GoToLast() const
    7041022{
     1023        Info FunctionInfo(__func__);
    7051024  InternalPointer = PointsOnBoundary.end();
    7061025  InternalPointer--;
    … …  
    7121031bool Tesselation::IsEmpty() const
    7131032{
     1033        Info FunctionInfo(__func__);
    7141034  return (PointsOnBoundary.empty());
    7151035};
    … …  
    7201040bool Tesselation::IsEnd() const
    7211041{
     1042        Info FunctionInfo(__func__);
    7221043  return (InternalPointer == PointsOnBoundary.end());
    7231044};
    … …  
    7321053Tesselation::GuessStartingTriangle()
    7331054{
     1055        Info FunctionInfo(__func__);
    7341056  // 4b. create a starting triangle
    7351057  // 4b1. create all distances
    … …  
    7781100          baseline->second.first->second->node->node,
    7791101          baseline->second.second->second->node->node);
    780       Log() << Verbose(2) << "Plane vector of candidate triangle is ";
    781       PlaneVector.Output();
    782       Log() << Verbose(0) << endl;
     1102      Log() << Verbose(2) << "Plane vector of candidate triangle is " << PlaneVector << endl;
    7831103      // 4. loop over all points
    7841104      double sign = 0.;
    … …  
    7961116          if (fabs(distance) < 1e-4) // we need to have a small epsilon around 0 which is still ok
    7971117            continue;
    798           Log() << Verbose(3) << "Projection of " << checker->second->node->Name
    799               << " yields distance of " << distance << "." << endl;
     1118          Log() << Verbose(2) << "Projection of " << checker->second->node->Name << " yields distance of " << distance << "." << endl;
    8001119          tmp = distance / fabs(distance);
    8011120          // 4b. Any have different sign to than before? (i.e. would lie outside convex hull with this starting triangle)
    … …  
    8501169      if (checker == PointsOnBoundary.end())
    8511170        {
    852           Log() << Verbose(0) << "Looks like we have a candidate!" << endl;
     1171          Log() << Verbose(2) << "Looks like we have a candidate!" << endl;
    8531172          break;
    8541173        }
    … …  
    8801199  else
    8811200    {
    882       Log() << Verbose(1) << "No starting triangle found." << endl;
    883       exit(255);
     1201      eLog() << Verbose(0) << "No starting triangle found." << endl;
    8841202    }
    8851203}
    … …  
    9011219void Tesselation::TesselateOnBoundary(const PointCloud * const cloud)
    9021220{
     1221        Info FunctionInfo(__func__);
    9031222  bool flag;
    9041223  PointMap::iterator winner;
    … …  
    9191238        // get peak point with respect to this base line's only triangle
    9201239        BTS = baseline->second->triangles.begin()->second; // there is only one triangle so far
    921         Log() << Verbose(2) << "Current baseline is between " << *(baseline->second) << "." << endl;
     1240        Log() << Verbose(0) << "Current baseline is between " << *(baseline->second) << "." << endl;
    9221241        for (int i = 0; i < 3; i++)
    9231242          if ((BTS->endpoints[i] != baseline->second->endpoints[0]) && (BTS->endpoints[i] != baseline->second->endpoints[1]))
    9241243            peak = BTS->endpoints[i];
    925         Log() << Verbose(3) << " and has peak " << *peak << "." << endl;
     1244        Log() << Verbose(1) << " and has peak " << *peak << "." << endl;
    9261245
    9271246        // prepare some auxiliary vectors
    … …  
    9381257          CenterVector.AddVector(BTS->endpoints[i]->node->node);
    9391258        CenterVector.Scale(1. / 3.);
    940         Log() << Verbose(4) << "CenterVector of base triangle is " << CenterVector << endl;
     1259        Log() << Verbose(2) << "CenterVector of base triangle is " << CenterVector << endl;
    9411260
    9421261        // normal vector of triangle
    … …  
    9451264        BTS->GetNormalVector(NormalVector);
    9461265        NormalVector.CopyVector(&BTS->NormalVector);
    947         Log() << Verbose(4) << "NormalVector of base triangle is " << NormalVector << endl;
     1266        Log() << Verbose(2) << "NormalVector of base triangle is " << NormalVector << endl;
    9481267
    9491268        // vector in propagation direction (out of triangle)
    … …  
    9521271        TempVector.CopyVector(&CenterVector);
    9531272        TempVector.SubtractVector(baseline->second->endpoints[0]->node->node); // TempVector is vector on triangle plane pointing from one baseline egde towards center!
    954         //Log() << Verbose(2) << "Projection of propagation onto temp: " << PropagationVector.Projection(&TempVector) << "." << endl;
     1273        //Log() << Verbose(0) << "Projection of propagation onto temp: " << PropagationVector.Projection(&TempVector) << "." << endl;
    9551274        if (PropagationVector.ScalarProduct(&TempVector) > 0) // make sure normal propagation vector points outward from baseline
    9561275          PropagationVector.Scale(-1.);
    957         Log() << Verbose(4) << "PropagationVector of base triangle is " << PropagationVector << endl;
     1276        Log() << Verbose(2) << "PropagationVector of base triangle is " << PropagationVector << endl;
    9581277        winner = PointsOnBoundary.end();
    9591278
    … …  
    9611280        for (PointMap::iterator target = PointsOnBoundary.begin(); target != PointsOnBoundary.end(); target++) {
    9621281          if ((target->second != baseline->second->endpoints[0]) && (target->second != baseline->second->endpoints[1])) { // don't take the same endpoints
    963             Log() << Verbose(3) << "Target point is " << *(target->second) << ":" << endl;
     1282            Log() << Verbose(1) << "Target point is " << *(target->second) << ":" << endl;
    9641283
    9651284            // first check direction, so that triangles don't intersect
    … …  
    9681287            VirtualNormalVector.ProjectOntoPlane(&NormalVector);
    9691288            TempAngle = VirtualNormalVector.Angle(&PropagationVector);
    970             Log() << Verbose(4) << "VirtualNormalVector is " << VirtualNormalVector << " and PropagationVector is " << PropagationVector << "." << endl;
     1289            Log() << Verbose(2) << "VirtualNormalVector is " << VirtualNormalVector << " and PropagationVector is " << PropagationVector << "." << endl;
    9711290            if (TempAngle > (M_PI/2.)) { // no bends bigger than Pi/2 (90 degrees)
    972               Log() << Verbose(4) << "Angle on triangle plane between propagation direction and base line to " << *(target->second) << " is " << TempAngle << ", bad direction!" << endl;
     1291              Log() << Verbose(2) << "Angle on triangle plane between propagation direction and base line to " << *(target->second) << " is " << TempAngle << ", bad direction!" << endl;
    9731292              continue;
    9741293            } else
    975               Log() << Verbose(4) << "Angle on triangle plane between propagation direction and base line to " << *(target->second) << " is " << TempAngle << ", good direction!" << endl;
     1294              Log() << Verbose(2) << "Angle on triangle plane between propagation direction and base line to " << *(target->second) << " is " << TempAngle << ", good direction!" << endl;
    9761295
    9771296            // check first and second endpoint (if any connecting line goes to target has at least not more than 1 triangle)
    … …  
    9791298            LineChecker[1] = baseline->second->endpoints[1]->lines.find(target->first);
    9801299            if (((LineChecker[0] != baseline->second->endpoints[0]->lines.end()) && (LineChecker[0]->second->triangles.size() == 2))) {
    981               Log() << Verbose(4) << *(baseline->second->endpoints[0]) << " has line " << *(LineChecker[0]->second) << " to " << *(target->second) << " as endpoint with " << LineChecker[0]->second->triangles.size() << " triangles." << endl;
     1300              Log() << Verbose(2) << *(baseline->second->endpoints[0]) << " has line " << *(LineChecker[0]->second) << " to " << *(target->second) << " as endpoint with " << LineChecker[0]->second->triangles.size() << " triangles." << endl;
    9821301              continue;
    9831302            }
    9841303            if (((LineChecker[1] != baseline->second->endpoints[1]->lines.end()) && (LineChecker[1]->second->triangles.size() == 2))) {
    985               Log() << Verbose(4) << *(baseline->second->endpoints[1]) << " has line " << *(LineChecker[1]->second) << " to " << *(target->second) << " as endpoint with " << LineChecker[1]->second->triangles.size() << " triangles." << endl;
     1304              Log() << Verbose(2) << *(baseline->second->endpoints[1]) << " has line " << *(LineChecker[1]->second) << " to " << *(target->second) << " as endpoint with " << LineChecker[1]->second->triangles.size() << " triangles." << endl;
    9861305              continue;
    9871306            }
    … …  
    10001319            helper.ProjectOntoPlane(&TempVector);
    10011320            if (fabs(helper.NormSquared()) < MYEPSILON) {
    1002               Log() << Verbose(4) << "Chosen set of vectors is linear dependent." << endl;
     1321              Log() << Verbose(2) << "Chosen set of vectors is linear dependent." << endl;
    10031322              continue;
    10041323            }
    … …  
    10171336            // calculate angle
    10181337            TempAngle = NormalVector.Angle(&VirtualNormalVector);
    1019             Log() << Verbose(4) << "NormalVector is " << VirtualNormalVector << " and the angle is " << TempAngle << "." << endl;
     1338            Log() << Verbose(2) << "NormalVector is " << VirtualNormalVector << " and the angle is " << TempAngle << "." << endl;
    10201339            if ((SmallestAngle - TempAngle) > MYEPSILON) { // set to new possible winner
    10211340              SmallestAngle = TempAngle;
    10221341              winner = target;
    1023               Log() << Verbose(4) << "New winner " << *winner->second->node << " due to smaller angle between normal vectors." << endl;
     1342              Log() << Verbose(2) << "New winner " << *winner->second->node << " due to smaller angle between normal vectors." << endl;
    10241343            } else if (fabs(SmallestAngle - TempAngle) < MYEPSILON) { // check the angle to propagation, both possible targets are in one plane! (their normals have same angle)
    10251344              // hence, check the angles to some normal direction from our base line but in this common plane of both targets...
    … …  
    10391358                SmallestAngle = TempAngle;
    10401359                winner = target;
    1041                 Log() << Verbose(4) << "New winner " << *winner->second->node << " due to smaller angle " << TempAngle << " to propagation direction." << endl;
     1360                Log() << Verbose(2) << "New winner " << *winner->second->node << " due to smaller angle " << TempAngle << " to propagation direction." << endl;
    10421361              } else
    1043                 Log() << Verbose(4) << "Keeping old winner " << *winner->second->node << " due to smaller angle to propagation direction." << endl;
     1362                Log() << Verbose(2) << "Keeping old winner " << *winner->second->node << " due to smaller angle to propagation direction." << endl;
    10441363            } else
    1045               Log() << Verbose(4) << "Keeping old winner " << *winner->second->node << " due to smaller angle between normal vectors." << endl;
     1364              Log() << Verbose(2) << "Keeping old winner " << *winner->second->node << " due to smaller angle between normal vectors." << endl;
    10461365          }
    10471366        } // end of loop over all boundary points
    … …  
    10491368        // 5b. The point of the above whose triangle has the greatest angle with the triangle the current line belongs to (it only belongs to one, remember!): New triangle
    10501369        if (winner != PointsOnBoundary.end()) {
    1051           Log() << Verbose(2) << "Winning target point is " << *(winner->second) << " with angle " << SmallestAngle << "." << endl;
     1370          Log() << Verbose(0) << "Winning target point is " << *(winner->second) << " with angle " << SmallestAngle << "." << endl;
    10521371          // create the lins of not yet present
    10531372          BLS[0] = baseline->second;
    … …  
    10791398          TrianglesOnBoundaryCount++;
    10801399        } else {
    1081           Log() << Verbose(1) << "I could not determine a winner for this baseline " << *(baseline->second) << "." << endl;
     1400          eLog() << Verbose(2) << "I could not determine a winner for this baseline " << *(baseline->second) << "." << endl;
    10821401        }
    10831402
    10841403        // 5d. If the set of lines is not yet empty, go to 5. and continue
    10851404      } else
    1086         Log() << Verbose(2) << "Baseline candidate " << *(baseline->second) << " has a triangle count of " << baseline->second->triangles.size() << "." << endl;
     1405        Log() << Verbose(0) << "Baseline candidate " << *(baseline->second) << " has a triangle count of " << baseline->second->triangles.size() << "." << endl;
    10871406  } while (flag);
    10881407
    … …  
    10991418bool Tesselation::InsertStraddlingPoints(const PointCloud *cloud, const LinkedCell *LC)
    11001419{
     1420        Info FunctionInfo(__func__);
    11011421  Vector Intersection, Normal;
    11021422  TesselPoint *Walker = NULL;
    … …  
    11051425  bool AddFlag = false;
    11061426  LinkedCell *BoundaryPoints = NULL;
    1107 
    1108   Log() << Verbose(1) << "Begin of InsertStraddlingPoints" << endl;
    11091427
    11101428  cloud->GoToFirst();
    … …  
    11171435    }
    11181436    Walker = cloud->GetPoint();
    1119     Log() << Verbose(2) << "Current point is " << *Walker << "." << endl;
     1437    Log() << Verbose(0) << "Current point is " << *Walker << "." << endl;
    11201438    // get the next triangle
    11211439    triangles = FindClosestTrianglesToPoint(Walker->node, BoundaryPoints);
    11221440    BTS = triangles->front();
    11231441    if ((triangles == NULL) || (BTS->ContainsBoundaryPoint(Walker))) {
    1124       Log() << Verbose(2) << "No triangles found, probably a tesselation point itself." << endl;
     1442      Log() << Verbose(0) << "No triangles found, probably a tesselation point itself." << endl;
    11251443      cloud->GoToNext();
    11261444      continue;
    11271445    } else {
    11281446    }
    1129     Log() << Verbose(2) << "Closest triangle is " << *BTS << "." << endl;
     1447    Log() << Verbose(0) << "Closest triangle is " << *BTS << "." << endl;
    11301448    // get the intersection point
    11311449    if (BTS->GetIntersectionInsideTriangle(Center, Walker->node, &Intersection)) {
    1132       Log() << Verbose(2) << "We have an intersection at " << Intersection << "." << endl;
     1450      Log() << Verbose(0) << "We have an intersection at " << Intersection << "." << endl;
    11331451      // we have the intersection, check whether in- or outside of boundary
    11341452      if ((Center->DistanceSquared(Walker->node) - Center->DistanceSquared(&Intersection)) < -MYEPSILON) {
    11351453        // inside, next!
    1136         Log() << Verbose(2) << *Walker << " is inside wrt triangle " << *BTS << "." << endl;
     1454        Log() << Verbose(0) << *Walker << " is inside wrt triangle " << *BTS << "." << endl;
    11371455      } else {
    11381456        // outside!
    1139         Log() << Verbose(2) << *Walker << " is outside wrt triangle " << *BTS << "." << endl;
     1457        Log() << Verbose(0) << *Walker << " is outside wrt triangle " << *BTS << "." << endl;
    11401458        class BoundaryLineSet *OldLines[3], *NewLines[3];
    11411459        class BoundaryPointSet *OldPoints[3], *NewPoint;
    … …  
    11471465        Normal.CopyVector(&BTS->NormalVector);
    11481466        // add Walker to boundary points
    1149         Log() << Verbose(2) << "Adding " << *Walker << " to BoundaryPoints." << endl;
     1467        Log() << Verbose(0) << "Adding " << *Walker << " to BoundaryPoints." << endl;
    11501468        AddFlag = true;
    11511469        if (AddBoundaryPoint(Walker,0))
    … …  
    11541472          continue;
    11551473        // remove triangle
    1156         Log() << Verbose(2) << "Erasing triangle " << *BTS << "." << endl;
     1474        Log() << Verbose(0) << "Erasing triangle " << *BTS << "." << endl;
    11571475        TrianglesOnBoundary.erase(BTS->Nr);
    11581476        delete(BTS);
    … …  
    11621480          BPS[1] = OldPoints[i];
    11631481          NewLines[i] = new class BoundaryLineSet(BPS, LinesOnBoundaryCount);
    1164           Log() << Verbose(3) << "Creating new line " << *NewLines[i] << "." << endl;
     1482          Log() << Verbose(1) << "Creating new line " << *NewLines[i] << "." << endl;
    11651483          LinesOnBoundary.insert(LinePair(LinesOnBoundaryCount, NewLines[i])); // no need for check for unique insertion as BPS[0] is definitely a new one
    11661484          LinesOnBoundaryCount++;
    … …  
    11731491            if (NewLines[j]->IsConnectedTo(BLS[0])) {
    11741492              if (n>2) {
    1175                 Log() << Verbose(1) << BLS[0] << " connects to all of the new lines?!" << endl;
     1493                eLog() << Verbose(2) << BLS[0] << " connects to all of the new lines?!" << endl;
    11761494                return false;
    11771495              } else
    … …  
    11841502          BTS->GetNormalVector(Normal);
    11851503          Normal.Scale(-1.);
    1186           Log() << Verbose(2) << "Created new triangle " << *BTS << "." << endl;
     1504          Log() << Verbose(0) << "Created new triangle " << *BTS << "." << endl;
    11871505          TrianglesOnBoundary.insert(TrianglePair(TrianglesOnBoundaryCount, BTS));
    11881506          TrianglesOnBoundaryCount++;
    … …  
    11981516  // exit
    11991517  delete(Center);
    1200   Log() << Verbose(1) << "End of InsertStraddlingPoints" << endl;
    12011518  return true;
    12021519};
    … …  
    12091526bool Tesselation::AddBoundaryPoint(TesselPoint * Walker, const int n)
    12101527{
     1528        Info FunctionInfo(__func__);
    12111529  PointTestPair InsertUnique;
    12121530  BPS[n] = new class BoundaryPointSet(Walker);
    … …  
    12301548void Tesselation::AddTesselationPoint(TesselPoint* Candidate, const int n)
    12311549{
     1550        Info FunctionInfo(__func__);
    12321551  PointTestPair InsertUnique;
    12331552  TPS[n] = new class BoundaryPointSet(Candidate);
    … …  
    12371556  } else {
    12381557    delete TPS[n];
    1239     Log() << Verbose(4) << "Node " << *((InsertUnique.first)->second->node) << " is already present in PointsOnBoundary." << endl;
     1558    Log() << Verbose(0) << "Node " << *((InsertUnique.first)->second->node) << " is already present in PointsOnBoundary." << endl;
    12401559    TPS[n] = (InsertUnique.first)->second;
    12411560  }
    … …  
    12501569void Tesselation::SetTesselationPoint(TesselPoint* Candidate, const int n) const
    12511570{
     1571        Info FunctionInfo(__func__);
    12521572  PointMap::const_iterator FindPoint = PointsOnBoundary.find(Candidate->nr);
    12531573  if (FindPoint != PointsOnBoundary.end())
    … …  
    12671587  bool insertNewLine = true;
    12681588
    1269   if (a->lines.find(b->node->nr) != a->lines.end()) {
    1270     LineMap::iterator FindLine = a->lines.find(b->node->nr);
     1589  LineMap::iterator FindLine = a->lines.find(b->node->nr);
     1590  if (FindLine != a->lines.end()) {
     1591    Log() << Verbose(1) << "INFO: There is at least one line between " << *a << " and " << *b << ": " << *(FindLine->second) << "." << endl;
     1592
    12711593    pair<LineMap::iterator,LineMap::iterator> FindPair;
    12721594    FindPair = a->lines.equal_range(b->node->nr);
    1273     Log() << Verbose(5) << "INFO: There is at least one line between " << *a << " and " << *b << ": " << *(FindLine->second) << "." << endl;
    12741595
    12751596    for (FindLine = FindPair.first; FindLine != FindPair.second; FindLine++) {
    … …  
    12771598      if (FindLine->second->triangles.size() < 2) {
    12781599        insertNewLine = false;
    1279         Log() << Verbose(4) << "Using existing line " << *FindLine->second << endl;
     1600        Log() << Verbose(0) << "Using existing line " << *FindLine->second << endl;
    12801601
    12811602        BPS[0] = FindLine->second->endpoints[0];
    12821603        BPS[1] = FindLine->second->endpoints[1];
    12831604        BLS[n] = FindLine->second;
     1605
     1606        // remove existing line from OpenLines
     1607        CandidateMap::iterator CandidateLine = OpenLines.find(BLS[n]);
     1608        if (CandidateLine != OpenLines.end()) {
     1609          Log() << Verbose(1) << " Removing line from OpenLines." << endl;
     1610          delete(CandidateLine->second);
     1611          OpenLines.erase(CandidateLine);
     1612        } else {
     1613          eLog() << Verbose(1) << "Line exists and is attached to less than two triangles, but not in OpenLines!" << endl;
     1614        }
    12841615
    12851616        break;
    … …  
    13041635void Tesselation::AlwaysAddTesselationTriangleLine(class BoundaryPointSet *a, class BoundaryPointSet *b, const int n)
    13051636{
    1306   Log() << Verbose(4) << "Adding line [" << LinesOnBoundaryCount << "|" << *(a->node) << " and " << *(b->node) << "." << endl;
     1637        Info FunctionInfo(__func__);
     1638  Log() << Verbose(0) << "Adding open line [" << LinesOnBoundaryCount << "|" << *(a->node) << " and " << *(b->node) << "." << endl;
    13071639  BPS[0] = a;
    13081640  BPS[1] = b;
    … …  
    13121644  // increase counter
    13131645  LinesOnBoundaryCount++;
     1646  // also add to open lines
     1647  CandidateForTesselation *CFT = new CandidateForTesselation(BLS[n]);
     1648  OpenLines.insert(pair< BoundaryLineSet *, CandidateForTesselation *> (BLS[n], CFT));
    13141649};
    13151650
    … …  
    13191654void Tesselation::AddTesselationTriangle()
    13201655{
     1656        Info FunctionInfo(__func__);
    13211657  Log() << Verbose(1) << "Adding triangle to global TrianglesOnBoundary map." << endl;
    13221658
    … …  
    13371673void Tesselation::AddTesselationTriangle(const int nr)
    13381674{
    1339   Log() << Verbose(1) << "Adding triangle to global TrianglesOnBoundary map." << endl;
     1675        Info FunctionInfo(__func__);
     1676  Log() << Verbose(0) << "Adding triangle to global TrianglesOnBoundary map." << endl;
    13401677
    13411678  // add triangle to global map
    … …  
    13551692void Tesselation::RemoveTesselationTriangle(class BoundaryTriangleSet *triangle)
    13561693{
     1694        Info FunctionInfo(__func__);
    13571695  if (triangle == NULL)
    13581696    return;
    13591697  for (int i = 0; i < 3; i++) {
    13601698    if (triangle->lines[i] != NULL) {
    1361       Log() << Verbose(5) << "Removing triangle Nr." << triangle->Nr << " in line " << *triangle->lines[i] << "." << endl;
     1699      Log() << Verbose(0) << "Removing triangle Nr." << triangle->Nr << " in line " << *triangle->lines[i] << "." << endl;
    13621700      triangle->lines[i]->triangles.erase(triangle->Nr);
    13631701      if (triangle->lines[i]->triangles.empty()) {
    1364           Log() << Verbose(5) << *triangle->lines[i] << " is no more attached to any triangle, erasing." << endl;
     1702          Log() << Verbose(0) << *triangle->lines[i] << " is no more attached to any triangle, erasing." << endl;
    13651703          RemoveTesselationLine(triangle->lines[i]);
    13661704      } else {
    1367         Log() << Verbose(5) << *triangle->lines[i] << " is still attached to another triangle: ";
     1705        Log() << Verbose(0) << *triangle->lines[i] << " is still attached to another triangle: ";
     1706        OpenLines.insert(pair< BoundaryLineSet *, CandidateForTesselation *> (triangle->lines[i], NULL));
    13681707        for(TriangleMap::iterator TriangleRunner = triangle->lines[i]->triangles.begin(); TriangleRunner != triangle->lines[i]->triangles.end(); TriangleRunner++)
    13691708          Log() << Verbose(0) << "[" << (TriangleRunner->second)->Nr << "|" << *((TriangleRunner->second)->endpoints[0]) << ", " << *((TriangleRunner->second)->endpoints[1]) << ", " << *((TriangleRunner->second)->endpoints[2]) << "] \t";
    13701709        Log() << Verbose(0) << endl;
    13711710//        for (int j=0;j<2;j++) {
    1372 //          Log() << Verbose(5) << "Lines of endpoint " << *(triangle->lines[i]->endpoints[j]) << ": ";
     1711//          Log() << Verbose(0) << "Lines of endpoint " << *(triangle->lines[i]->endpoints[j]) << ": ";
    13731712//          for(LineMap::iterator LineRunner = triangle->lines[i]->endpoints[j]->lines.begin(); LineRunner != triangle->lines[i]->endpoints[j]->lines.end(); LineRunner++)
    13741713//            Log() << Verbose(0) << "[" << *(LineRunner->second) << "] \t";
    … …  
    13821721
    13831722  if (TrianglesOnBoundary.erase(triangle->Nr))
    1384     Log() << Verbose(5) << "Removing triangle Nr. " << triangle->Nr << "." << endl;
     1723    Log() << Verbose(0) << "Removing triangle Nr. " << triangle->Nr << "." << endl;
    13851724  delete(triangle);
    13861725};
    … …  
    13921731void Tesselation::RemoveTesselationLine(class BoundaryLineSet *line)
    13931732{
     1733        Info FunctionInfo(__func__);
    13941734  int Numbers[2];
    13951735
    … …  
    14121752        for (LineMap::iterator Runner = erasor.first; Runner != erasor.second; Runner++)
    14131753          if ((*Runner).second == line) {
    1414             Log() << Verbose(5) << "Removing Line Nr. " << line->Nr << " in boundary point " << *line->endpoints[i] << "." << endl;
     1754            Log() << Verbose(0) << "Removing Line Nr. " << line->Nr << " in boundary point " << *line->endpoints[i] << "." << endl;
    14151755            line->endpoints[i]->lines.erase(Runner);
    14161756            break;
    … …  
    14181758      } else { // there's just a single line left
    14191759        if (line->endpoints[i]->lines.erase(line->Nr))
    1420           Log() << Verbose(5) << "Removing Line Nr. " << line->Nr << " in boundary point " << *line->endpoints[i] << "." << endl;
     1760          Log() << Verbose(0) << "Removing Line Nr. " << line->Nr << " in boundary point " << *line->endpoints[i] << "." << endl;
    14211761      }
    14221762      if (line->endpoints[i]->lines.empty()) {
    1423         Log() << Verbose(5) << *line->endpoints[i] << " has no more lines it's attached to, erasing." << endl;
     1763        Log() << Verbose(0) << *line->endpoints[i] << " has no more lines it's attached to, erasing." << endl;
    14241764        RemoveTesselationPoint(line->endpoints[i]);
    14251765      } else {
    1426         Log() << Verbose(5) << *line->endpoints[i] << " has still lines it's attached to: ";
     1766        Log() << Verbose(0) << *line->endpoints[i] << " has still lines it's attached to: ";
    14271767        for(LineMap::iterator LineRunner = line->endpoints[i]->lines.begin(); LineRunner != line->endpoints[i]->lines.end(); LineRunner++)
    14281768          Log() << Verbose(0) << "[" << *(LineRunner->second) << "] \t";
    … …  
    14371777
    14381778  if (LinesOnBoundary.erase(line->Nr))
    1439     Log() << Verbose(5) << "Removing line Nr. " << line->Nr << "." << endl;
     1779    Log() << Verbose(0) << "Removing line Nr. " << line->Nr << "." << endl;
    14401780  delete(line);
    14411781};
    … …  
    14481788void Tesselation::RemoveTesselationPoint(class BoundaryPointSet *point)
    14491789{
     1790        Info FunctionInfo(__func__);
    14501791  if (point == NULL)
    14511792    return;
    14521793  if (PointsOnBoundary.erase(point->Nr))
    1453     Log() << Verbose(5) << "Removing point Nr. " << point->Nr << "." << endl;
     1794    Log() << Verbose(0) << "Removing point Nr. " << point->Nr << "." << endl;
    14541795  delete(point);
    14551796};
    … …  
    14661807int Tesselation::CheckPresenceOfTriangle(TesselPoint *Candidates[3]) const
    14671808{
     1809        Info FunctionInfo(__func__);
    14681810  int adjacentTriangleCount = 0;
    14691811  class BoundaryPointSet *Points[3];
    14701812
    1471   Log() << Verbose(2) << "Begin of CheckPresenceOfTriangle" << endl;
    14721813  // builds a triangle point set (Points) of the end points
    14731814  for (int i = 0; i < 3; i++) {
    … …  
    14881829          for (; (FindLine != Points[i]->lines.end()) && (FindLine->first == Points[j]->node->nr); FindLine++) {
    14891830            TriangleMap *triangles = &FindLine->second->triangles;
    1490             Log() << Verbose(3) << "Current line is " << FindLine->first << ": " << *(FindLine->second) << " with triangles " << triangles << "." << endl;
     1831            Log() << Verbose(1) << "Current line is " << FindLine->first << ": " << *(FindLine->second) << " with triangles " << triangles << "." << endl;
    14911832            for (TriangleMap::const_iterator FindTriangle = triangles->begin(); FindTriangle != triangles->end(); FindTriangle++) {
    14921833              if (FindTriangle->second->IsPresentTupel(Points)) {
    … …  
    14941835              }
    14951836            }
    1496             Log() << Verbose(3) << "end." << endl;
     1837            Log() << Verbose(1) << "end." << endl;
    14971838          }
    14981839          // Only one of the triangle lines must be considered for the triangle count.
    1499           //Log() << Verbose(2) << "Found " << adjacentTriangleCount << " adjacent triangles for the point set." << endl;
     1840          //Log() << Verbose(0) << "Found " << adjacentTriangleCount << " adjacent triangles for the point set." << endl;
    15001841          //return adjacentTriangleCount;
    15011842        }
    … …  
    15041845  }
    15051846
    1506   Log() << Verbose(2) << "Found " << adjacentTriangleCount << " adjacent triangles for the point set." << endl;
    1507   Log() << Verbose(2) << "End of CheckPresenceOfTriangle" << endl;
     1847  Log() << Verbose(0) << "Found " << adjacentTriangleCount << " adjacent triangles for the point set." << endl;
    15081848  return adjacentTriangleCount;
    15091849};
    … …  
    15191859class BoundaryTriangleSet * Tesselation::GetPresentTriangle(TesselPoint *Candidates[3])
    15201860{
     1861        Info FunctionInfo(__func__);
    15211862  class BoundaryTriangleSet *triangle = NULL;
    15221863  class BoundaryPointSet *Points[3];
    … …  
    15481889          }
    15491890          // Only one of the triangle lines must be considered for the triangle count.
    1550           //Log() << Verbose(2) << "Found " << adjacentTriangleCount << " adjacent triangles for the point set." << endl;
     1891          //Log() << Verbose(0) << "Found " << adjacentTriangleCount << " adjacent triangles for the point set." << endl;
    15511892          //return adjacentTriangleCount;
    15521893        }
    … …  
    15691910void Tesselation::FindStartingTriangle(const double RADIUS, const LinkedCell *LC)
    15701911{
    1571   Log() << Verbose(1) << "Begin of FindStartingTriangle\n";
     1912        Info FunctionInfo(__func__);
    15721913  int i = 0;
    1573   TesselPoint* FirstPoint = NULL;
    1574   TesselPoint* SecondPoint = NULL;
    15751914  TesselPoint* MaxPoint[NDIM];
     1915  TesselPoint* Temporary;
    15761916  double maxCoordinate[NDIM];
    1577   Vector Oben;
     1917  BoundaryLineSet BaseLine;
    15781918  Vector helper;
    15791919  Vector Chord;
    15801920  Vector SearchDirection;
    1581 
    1582   Oben.Zero();
     1921  Vector CircleCenter;  // center of the circle, i.e. of the band of sphere's centers
     1922  Vector CirclePlaneNormal; // normal vector defining the plane this circle lives in
     1923  Vector SphereCenter;
     1924  Vector NormalVector;
     1925
     1926  NormalVector.Zero();
    15831927
    15841928  for (i = 0; i < 3; i++) {
    … …  
    15931937      for (LC->n[(i+2)%NDIM]=0;LC->n[(i+2)%NDIM]<LC->N[(i+2)%NDIM];LC->n[(i+2)%NDIM]++) {
    15941938        const LinkedNodes *List = LC->GetCurrentCell();
    1595         //Log() << Verbose(2) << "Current cell is " << LC->n[0] << ", " << LC->n[1] << ", " << LC->n[2] << " with No. " << LC->index << "." << endl;
     1939        //Log() << Verbose(1) << "Current cell is " << LC->n[0] << ", " << LC->n[1] << ", " << LC->n[2] << " with No. " << LC->index << "." << endl;
    15961940        if (List != NULL) {
    15971941          for (LinkedNodes::const_iterator Runner = List->begin();Runner != List->end();Runner++) {
    15981942            if ((*Runner)->node->x[i] > maxCoordinate[i]) {
    1599               Log() << Verbose(2) << "New maximal for axis " << i << " node is " << *(*Runner) << " at " << *(*Runner)->node << "." << endl;
     1943              Log() << Verbose(1) << "New maximal for axis " << i << " node is " << *(*Runner) << " at " << *(*Runner)->node << "." << endl;
    16001944              maxCoordinate[i] = (*Runner)->node->x[i];
    16011945              MaxPoint[i] = (*Runner);
    … …  
    16081952  }
    16091953
    1610   Log() << Verbose(2) << "Found maximum coordinates: ";
     1954  Log() << Verbose(1) << "Found maximum coordinates: ";
    16111955  for (int i=0;i<NDIM;i++)
    16121956    Log() << Verbose(0) << i << ": " << *MaxPoint[i] << "\t";
    … …  
    16141958
    16151959  BTS = NULL;
    1616   CandidateList *OptCandidates = new CandidateList();
    16171960  for (int k=0;k<NDIM;k++) {
    1618     Oben.Zero();
    1619     Oben.x[k] = 1.;
    1620     FirstPoint = MaxPoint[k];
    1621     Log() << Verbose(1) << "Coordinates of start node at " << *FirstPoint->node << "." << endl;
     1961    NormalVector.Zero();
     1962    NormalVector.x[k] = 1.;
     1963    BaseLine.endpoints[0] = new BoundaryPointSet(MaxPoint[k]);
     1964    Log() << Verbose(0) << "Coordinates of start node at " << *BaseLine.endpoints[0]->node << "." << endl;
    16221965
    16231966    double ShortestAngle;
    1624     TesselPoint* OptCandidate = NULL;
    16251967    ShortestAngle = 999999.; // This will contain the angle, which will be always positive (when looking for second point), when looking for third point this will be the quadrant.
    16261968
    1627     FindSecondPointForTesselation(FirstPoint, Oben, OptCandidate, &ShortestAngle, RADIUS, LC); // we give same point as next candidate as its bonds are looked into in find_second_...
    1628     SecondPoint = OptCandidate;
    1629     if (SecondPoint == NULL)  // have we found a second point?
     1969    FindSecondPointForTesselation(BaseLine.endpoints[0]->node, NormalVector, Temporary, &ShortestAngle, RADIUS, LC); // we give same point as next candidate as its bonds are looked into in find_second_...
     1970    if (Temporary == NULL)  // have we found a second point?
    16301971      continue;
    1631 
    1632     helper.CopyVector(FirstPoint->node);
    1633     helper.SubtractVector(SecondPoint->node);
    1634     helper.Normalize();
    1635     Oben.ProjectOntoPlane(&helper);
    1636     Oben.Normalize();
    1637     helper.VectorProduct(&Oben);
     1972    BaseLine.endpoints[1] = new BoundaryPointSet(Temporary);
     1973
     1974    // construct center of circle
     1975    CircleCenter.CopyVector(BaseLine.endpoints[0]->node->node);
     1976    CircleCenter.AddVector(BaseLine.endpoints[1]->node->node);
     1977    CircleCenter.Scale(0.5);
     1978
     1979    // construct normal vector of circle
     1980    CirclePlaneNormal.CopyVector(BaseLine.endpoints[0]->node->node);
     1981    CirclePlaneNormal.SubtractVector(BaseLine.endpoints[1]->node->node);
     1982
     1983    double radius = CirclePlaneNormal.NormSquared();
     1984    double CircleRadius = sqrt(RADIUS*RADIUS - radius/4.);
     1985
     1986    NormalVector.ProjectOntoPlane(&CirclePlaneNormal);
     1987    NormalVector.Normalize();
    16381988    ShortestAngle = 2.*M_PI; // This will indicate the quadrant.
    16391989
    1640     Chord.CopyVector(FirstPoint->node); // bring into calling function
    1641     Chord.SubtractVector(SecondPoint->node);
    1642     double radius = Chord.ScalarProduct(&Chord);
    1643     double CircleRadius = sqrt(RADIUS*RADIUS - radius/4.);
    1644     helper.CopyVector(&Oben);
    1645     helper.Scale(CircleRadius);
    1646     // Now, oben and helper are two orthonormalized vectors in the plane defined by Chord (not normalized)
     1990    SphereCenter.CopyVector(&NormalVector);
     1991    SphereCenter.Scale(CircleRadius);
     1992    SphereCenter.AddVector(&CircleCenter);
     1993    // Now, NormalVector and SphereCenter are two orthonormalized vectors in the plane defined by CirclePlaneNormal (not normalized)
    16471994
    16481995    // look in one direction of baseline for initial candidate
    1649     SearchDirection.MakeNormalVector(&Chord, &Oben);  // whether we look "left" first or "right" first is not important ...
     1996    SearchDirection.MakeNormalVector(&CirclePlaneNormal, &NormalVector);  // whether we look "left" first or "right" first is not important ...
    16501997
    16511998    // adding point 1 and point 2 and add the line between them
    1652     Log() << Verbose(1) << "Coordinates of start node at " << *FirstPoint->node << "." << endl;
    1653     AddTesselationPoint(FirstPoint, 0);
    1654     Log() << Verbose(1) << "Found second point is at " << *SecondPoint->node << ".\n";
    1655     AddTesselationPoint(SecondPoint, 1);
    1656     AddTesselationLine(TPS[0], TPS[1], 0);
    1657 
    1658     //Log() << Verbose(2) << "INFO: OldSphereCenter is at " << helper << ".\n";
    1659     FindThirdPointForTesselation(Oben, SearchDirection, helper, BLS[0], NULL, *&OptCandidates, &ShortestAngle, RADIUS, LC);
    1660     Log() << Verbose(1) << "List of third Points is ";
    1661     for (CandidateList::iterator it = OptCandidates->begin(); it != OptCandidates->end(); ++it) {
    1662         Log() << Verbose(0) << " " << *(*it)->point;
    1663     }
    1664     Log() << Verbose(0) << endl;
    1665 
    1666     for (CandidateList::iterator it = OptCandidates->begin(); it != OptCandidates->end(); ++it) {
    1667       // add third triangle point
    1668       AddTesselationPoint((*it)->point, 2);
    1669       // add the second and third line
    1670       AddTesselationLine(TPS[1], TPS[2], 1);
    1671       AddTesselationLine(TPS[0], TPS[2], 2);
    1672       // ... and triangles to the Maps of the Tesselation class
    1673       BTS = new class BoundaryTriangleSet(BLS, TrianglesOnBoundaryCount);
    1674       AddTesselationTriangle();
    1675       // ... and calculate its normal vector (with correct orientation)
    1676       (*it)->OptCenter.Scale(-1.);
    1677       Log() << Verbose(2) << "Anti-Oben is currently " << (*it)->OptCenter << "." << endl;
    1678       BTS->GetNormalVector((*it)->OptCenter);  // vector to compare with should point inwards
    1679       Log() << Verbose(0) << "==> Found starting triangle consists of " << *FirstPoint << ", " << *SecondPoint << " and "
    1680       << *(*it)->point << " with normal vector " << BTS->NormalVector << ".\n";
    1681 
    1682       // if we do not reach the end with the next step of iteration, we need to setup a new first line
    1683       if (it != OptCandidates->end()--) {
    1684         FirstPoint = (*it)->BaseLine->endpoints[0]->node;
    1685         SecondPoint = (*it)->point;
    1686         // adding point 1 and point 2 and the line between them
    1687         AddTesselationPoint(FirstPoint, 0);
    1688         AddTesselationPoint(SecondPoint, 1);
    1689         AddTesselationLine(TPS[0], TPS[1], 0);
    1690       }
    1691       Log() << Verbose(2) << "Projection is " << BTS->NormalVector.ScalarProduct(&Oben) << "." << endl;
    1692     }
     1999    Log() << Verbose(0) << "Coordinates of start node at " << *BaseLine.endpoints[0]->node << "." << endl;
     2000    Log() << Verbose(0) << "Found second point is at " << *BaseLine.endpoints[1]->node << ".\n";
     2001
     2002    //Log() << Verbose(1) << "INFO: OldSphereCenter is at " << helper << ".\n";
     2003    CandidateForTesselation OptCandidates(&BaseLine);
     2004    FindThirdPointForTesselation(NormalVector, SearchDirection, SphereCenter, OptCandidates, NULL, RADIUS, LC);
     2005    Log() << Verbose(0) << "List of third Points is:" << endl;
     2006    for (TesselPointList::iterator it = OptCandidates.pointlist.begin(); it != OptCandidates.pointlist.end(); it++) {
     2007        Log() << Verbose(0) << " " << *(*it) << endl;
     2008    }
     2009
     2010    BTS = NULL;
     2011    AddCandidateTriangle(OptCandidates);
     2012//    delete(BaseLine.endpoints[0]);
     2013//    delete(BaseLine.endpoints[1]);
     2014
    16932015    if (BTS != NULL) // we have created one starting triangle
    16942016      break;
    16952017    else {
    16962018      // remove all candidates from the list and then the list itself
    1697       class CandidateForTesselation *remover = NULL;
    1698       for (CandidateList::iterator it = OptCandidates->begin(); it != OptCandidates->end(); ++it) {
    1699         remover = *it;
    1700         delete(remover);
    1701       }
    1702       OptCandidates->clear();
    1703     }
    1704   }
    1705 
    1706   // remove all candidates from the list and then the list itself
    1707   class CandidateForTesselation *remover = NULL;
    1708   for (CandidateList::iterator it = OptCandidates->begin(); it != OptCandidates->end(); ++it) {
    1709     remover = *it;
    1710     delete(remover);
    1711   }
    1712   delete(OptCandidates);
    1713   Log() << Verbose(1) << "End of FindStartingTriangle\n";
     2019      OptCandidates.pointlist.clear();
     2020    }
     2021  }
    17142022};
    17152023
    17162024/** Checks for a given baseline and a third point candidate whether baselines of the found triangle don't have even better candidates.
    17172025 * This is supposed to prevent early closing of the tesselation.
    1718  * \param *BaseRay baseline, i.e. not \a *OptCandidate
     2026 * \param CandidateLine CandidateForTesselation with baseline and shortestangle , i.e. not \a *OptCandidate
    17192027 * \param *ThirdNode third point in triangle, not in BoundaryLineSet::endpoints
    1720  * \param ShortestAngle path length on this circle band for the current \a *ThirdNode
    17212028 * \param RADIUS radius of sphere
    17222029 * \param *LC LinkedCell structure
    17232030 * \return true - there is a better candidate (smaller angle than \a ShortestAngle), false - no better TesselPoint candidate found
    17242031 */
    1725 bool Tesselation::HasOtherBaselineBetterCandidate(const BoundaryLineSet * const BaseRay, const TesselPoint * const ThirdNode, double ShortestAngle, double RADIUS, const LinkedCell * const LC) const
    1726 {
    1727   bool result = false;
    1728   Vector CircleCenter;
    1729   Vector CirclePlaneNormal;
    1730   Vector OldSphereCenter;
    1731   Vector SearchDirection;
    1732   Vector helper;
    1733   TesselPoint *OtherOptCandidate = NULL;
    1734   double OtherShortestAngle = 2.*M_PI; // This will indicate the quadrant.
    1735   double radius, CircleRadius;
    1736   BoundaryLineSet *Line = NULL;
    1737   BoundaryTriangleSet *T = NULL;
    1738 
    1739   Log() << Verbose(1) << "Begin of HasOtherBaselineBetterCandidate" << endl;
    1740 
    1741   // check both other lines
    1742   PointMap::const_iterator FindPoint = PointsOnBoundary.find(ThirdNode->nr);
    1743   if (FindPoint != PointsOnBoundary.end()) {
    1744     for (int i=0;i<2;i++) {
    1745       LineMap::const_iterator FindLine = (FindPoint->second)->lines.find(BaseRay->endpoints[0]->node->nr);
    1746       if (FindLine != (FindPoint->second)->lines.end()) {
    1747         Line = FindLine->second;
    1748         Log() << Verbose(1) << "Found line " << *Line << "." << endl;
    1749         if (Line->triangles.size() == 1) {
    1750           T = Line->triangles.begin()->second;
    1751           // construct center of circle
    1752           CircleCenter.CopyVector(Line->endpoints[0]->node->node);
    1753           CircleCenter.AddVector(Line->endpoints[1]->node->node);
    1754           CircleCenter.Scale(0.5);
    1755 
    1756           // construct normal vector of circle
    1757           CirclePlaneNormal.CopyVector(Line->endpoints[0]->node->node);
    1758           CirclePlaneNormal.SubtractVector(Line->endpoints[1]->node->node);
    1759 
    1760           // calculate squared radius of circle
    1761           radius = CirclePlaneNormal.ScalarProduct(&CirclePlaneNormal);
    1762           if (radius/4. < RADIUS*RADIUS) {
    1763             CircleRadius = RADIUS*RADIUS - radius/4.;
    1764             CirclePlaneNormal.Normalize();
    1765             //Log() << Verbose(2) << "INFO: CircleCenter is at " << CircleCenter << ", CirclePlaneNormal is " << CirclePlaneNormal << " with circle radius " << sqrt(CircleRadius) << "." << endl;
    1766 
    1767             // construct old center
    1768             GetCenterofCircumcircle(&OldSphereCenter, *T->endpoints[0]->node->node, *T->endpoints[1]->node->node, *T->endpoints[2]->node->node);
    1769             helper.CopyVector(&T->NormalVector);  // normal vector ensures that this is correct center of the two possible ones
    1770             radius = Line->endpoints[0]->node->node->DistanceSquared(&OldSphereCenter);
    1771             helper.Scale(sqrt(RADIUS*RADIUS - radius));
    1772             OldSphereCenter.AddVector(&helper);
    1773             OldSphereCenter.SubtractVector(&CircleCenter);
    1774             //Log() << Verbose(2) << "INFO: OldSphereCenter is at " << OldSphereCenter << "." << endl;
    1775 
    1776             // construct SearchDirection
    1777             SearchDirection.MakeNormalVector(&T->NormalVector, &CirclePlaneNormal);
    1778             helper.CopyVector(Line->endpoints[0]->node->node);
    1779             helper.SubtractVector(ThirdNode->node);
    1780             if (helper.ScalarProduct(&SearchDirection) < -HULLEPSILON)// ohoh, SearchDirection points inwards!
    1781               SearchDirection.Scale(-1.);
    1782             SearchDirection.ProjectOntoPlane(&OldSphereCenter);
    1783             SearchDirection.Normalize();
    1784             Log() << Verbose(2) << "INFO: SearchDirection is " << SearchDirection << "." << endl;
    1785             if (fabs(OldSphereCenter.ScalarProduct(&SearchDirection)) > HULLEPSILON) {
    1786               // rotated the wrong way!
    1787               eLog() << Verbose(1) << "SearchDirection and RelativeOldSphereCenter are still not orthogonal!" << endl;
    1788             }
    1789 
    1790             // add third point
    1791             CandidateList *OptCandidates = new CandidateList();
    1792             FindThirdPointForTesselation(T->NormalVector, SearchDirection, OldSphereCenter, Line, ThirdNode, OptCandidates, &OtherShortestAngle, RADIUS, LC);
    1793             for (CandidateList::iterator it = OptCandidates->begin(); it != OptCandidates->end(); ++it) {
    1794               if (((*it)->point == BaseRay->endpoints[0]->node) || ((*it)->point == BaseRay->endpoints[1]->node)) // skip if it's the same triangle than suggested
    1795                 continue;
    1796               Log() << Verbose(1) << " Third point candidate is " << *(*it)->point
    1797               << " with circumsphere's center at " << (*it)->OptCenter << "." << endl;
    1798               Log() << Verbose(1) << " Baseline is " << *BaseRay << endl;
    1799 
    1800               // check whether all edges of the new triangle still have space for one more triangle (i.e. TriangleCount <2)
    1801               TesselPoint *PointCandidates[3];
    1802               PointCandidates[0] = (*it)->point;
    1803               PointCandidates[1] = BaseRay->endpoints[0]->node;
    1804               PointCandidates[2] = BaseRay->endpoints[1]->node;
    1805               bool check=false;
    1806               int existentTrianglesCount = CheckPresenceOfTriangle(PointCandidates);
    1807               // If there is no triangle, add it regularly.
    1808               if (existentTrianglesCount == 0) {
    1809                 SetTesselationPoint((*it)->point, 0);
    1810                 SetTesselationPoint(BaseRay->endpoints[0]->node, 1);
    1811                 SetTesselationPoint(BaseRay->endpoints[1]->node, 2);
    1812 
    1813                 if (CheckLineCriteriaForDegeneratedTriangle((const BoundaryPointSet ** const )TPS)) {
    1814                   OtherOptCandidate = (*it)->point;
    1815                   check = true;
    1816                 }
    1817               } else if ((existentTrianglesCount >= 1) && (existentTrianglesCount <= 3)) { // If there is a planar region within the structure, we need this triangle a second time.
    1818                 SetTesselationPoint((*it)->point, 0);
    1819                 SetTesselationPoint(BaseRay->endpoints[0]->node, 1);
    1820                 SetTesselationPoint(BaseRay->endpoints[1]->node, 2);
    1821 
    1822                 // We demand that at most one new degenerate line is created and that this line also already exists (which has to be the case due to existentTrianglesCount == 1)
    1823                 // i.e. at least one of the three lines must be present with TriangleCount <= 1
    1824                 if (CheckLineCriteriaForDegeneratedTriangle((const BoundaryPointSet ** const)TPS)) {
    1825                   OtherOptCandidate = (*it)->point;
    1826                   check = true;
    1827                 }
    1828               }
    1829 
    1830               if (check) {
    1831                 if (ShortestAngle > OtherShortestAngle) {
    1832                   Log() << Verbose(1) << "There is a better candidate than " << *ThirdNode << " with " << ShortestAngle << " from baseline " << *Line << ": " << *OtherOptCandidate << " with " << OtherShortestAngle << "." << endl;
    1833                   result = true;
    1834                   break;
    1835                 }
    1836               }
    1837             }
    1838             delete(OptCandidates);
    1839             if (result)
    1840               break;
    1841           } else {
    1842             Log() << Verbose(1) << "Circumcircle for base line " << *Line << " and base triangle " << T << " is too big!" << endl;
    1843           }
    1844         } else {
    1845           eLog() << Verbose(2) << "Baseline is connected to two triangles already?" << endl;
    1846         }
    1847       } else {
    1848         Log() << Verbose(2) << "No present baseline between " << BaseRay->endpoints[0] << " and candidate " << *ThirdNode << "." << endl;
    1849       }
    1850     }
    1851   } else {
    1852     eLog() << Verbose(1) << "Could not find the TesselPoint " << *ThirdNode << "." << endl;
    1853   }
    1854 
    1855   Log() << Verbose(1) << "End of HasOtherBaselineBetterCandidate" << endl;
    1856 
    1857   return result;
    1858 };
     2032//bool Tesselation::HasOtherBaselineBetterCandidate(CandidateForTesselation &CandidateLine, const TesselPoint * const ThirdNode, double RADIUS, const LinkedCell * const LC) const
     2033//{
     2034//      Info FunctionInfo(__func__);
     2035//  bool result = false;
     2036//  Vector CircleCenter;
     2037//  Vector CirclePlaneNormal;
     2038//  Vector OldSphereCenter;
     2039//  Vector SearchDirection;
     2040//  Vector helper;
     2041//  TesselPoint *OtherOptCandidate = NULL;
     2042//  double OtherShortestAngle = 2.*M_PI; // This will indicate the quadrant.
     2043//  double radius, CircleRadius;
     2044//  BoundaryLineSet *Line = NULL;
     2045//  BoundaryTriangleSet *T = NULL;
     2046//
     2047//  // check both other lines
     2048//  PointMap::const_iterator FindPoint = PointsOnBoundary.find(ThirdNode->nr);
     2049//  if (FindPoint != PointsOnBoundary.end()) {
     2050//    for (int i=0;i<2;i++) {
     2051//      LineMap::const_iterator FindLine = (FindPoint->second)->lines.find(BaseRay->endpoints[0]->node->nr);
     2052//      if (FindLine != (FindPoint->second)->lines.end()) {
     2053//        Line = FindLine->second;
     2054//        Log() << Verbose(0) << "Found line " << *Line << "." << endl;
     2055//        if (Line->triangles.size() == 1) {
     2056//          T = Line->triangles.begin()->second;
     2057//          // construct center of circle
     2058//          CircleCenter.CopyVector(Line->endpoints[0]->node->node);
     2059//          CircleCenter.AddVector(Line->endpoints[1]->node->node);
     2060//          CircleCenter.Scale(0.5);
     2061//
     2062//          // construct normal vector of circle
     2063//          CirclePlaneNormal.CopyVector(Line->endpoints[0]->node->node);
     2064//          CirclePlaneNormal.SubtractVector(Line->endpoints[1]->node->node);
     2065//
     2066//          // calculate squared radius of circle
     2067//          radius = CirclePlaneNormal.ScalarProduct(&CirclePlaneNormal);
     2068//          if (radius/4. < RADIUS*RADIUS) {
     2069//            CircleRadius = RADIUS*RADIUS - radius/4.;
     2070//            CirclePlaneNormal.Normalize();
     2071//            //Log() << Verbose(1) << "INFO: CircleCenter is at " << CircleCenter << ", CirclePlaneNormal is " << CirclePlaneNormal << " with circle radius " << sqrt(CircleRadius) << "." << endl;
     2072//
     2073//            // construct old center
     2074//            GetCenterofCircumcircle(&OldSphereCenter, *T->endpoints[0]->node->node, *T->endpoints[1]->node->node, *T->endpoints[2]->node->node);
     2075//            helper.CopyVector(&T->NormalVector);  // normal vector ensures that this is correct center of the two possible ones
     2076//            radius = Line->endpoints[0]->node->node->DistanceSquared(&OldSphereCenter);
     2077//            helper.Scale(sqrt(RADIUS*RADIUS - radius));
     2078//            OldSphereCenter.AddVector(&helper);
     2079//            OldSphereCenter.SubtractVector(&CircleCenter);
     2080//            //Log() << Verbose(1) << "INFO: OldSphereCenter is at " << OldSphereCenter << "." << endl;
     2081//
     2082//            // construct SearchDirection
     2083//            SearchDirection.MakeNormalVector(&T->NormalVector, &CirclePlaneNormal);
     2084//            helper.CopyVector(Line->endpoints[0]->node->node);
     2085//            helper.SubtractVector(ThirdNode->node);
     2086//            if (helper.ScalarProduct(&SearchDirection) < -HULLEPSILON)// ohoh, SearchDirection points inwards!
     2087//              SearchDirection.Scale(-1.);
     2088//            SearchDirection.ProjectOntoPlane(&OldSphereCenter);
     2089//            SearchDirection.Normalize();
     2090//            Log() << Verbose(1) << "INFO: SearchDirection is " << SearchDirection << "." << endl;
     2091//            if (fabs(OldSphereCenter.ScalarProduct(&SearchDirection)) > HULLEPSILON) {
     2092//              // rotated the wrong way!
     2093//              eLog() << Verbose(1) << "SearchDirection and RelativeOldSphereCenter are still not orthogonal!" << endl;
     2094//            }
     2095//
     2096//            // add third point
     2097//            FindThirdPointForTesselation(T->NormalVector, SearchDirection, OldSphereCenter, OptCandidates, ThirdNode, RADIUS, LC);
     2098//            for (TesselPointList::iterator it = OptCandidates.pointlist.begin(); it != OptCandidates.pointlist.end(); ++it) {
     2099//              if (((*it) == BaseRay->endpoints[0]->node) || ((*it) == BaseRay->endpoints[1]->node)) // skip if it's the same triangle than suggested
     2100//                continue;
     2101//              Log() << Verbose(0) << " Third point candidate is " << (*it)
     2102//              << " with circumsphere's center at " << (*it)->OptCenter << "." << endl;
     2103//              Log() << Verbose(0) << " Baseline is " << *BaseRay << endl;
     2104//
     2105//              // check whether all edges of the new triangle still have space for one more triangle (i.e. TriangleCount <2)
     2106//              TesselPoint *PointCandidates[3];
     2107//              PointCandidates[0] = (*it);
     2108//              PointCandidates[1] = BaseRay->endpoints[0]->node;
     2109//              PointCandidates[2] = BaseRay->endpoints[1]->node;
     2110//              bool check=false;
     2111//              int existentTrianglesCount = CheckPresenceOfTriangle(PointCandidates);
     2112//              // If there is no triangle, add it regularly.
     2113//              if (existentTrianglesCount == 0) {
     2114//                SetTesselationPoint((*it), 0);
     2115//                SetTesselationPoint(BaseRay->endpoints[0]->node, 1);
     2116//                SetTesselationPoint(BaseRay->endpoints[1]->node, 2);
     2117//
     2118//                if (CheckLineCriteriaForDegeneratedTriangle((const BoundaryPointSet ** const )TPS)) {
     2119//                  OtherOptCandidate = (*it);
     2120//                  check = true;
     2121//                }
     2122//              } else if ((existentTrianglesCount >= 1) && (existentTrianglesCount <= 3)) { // If there is a planar region within the structure, we need this triangle a second time.
     2123//                SetTesselationPoint((*it), 0);
     2124//                SetTesselationPoint(BaseRay->endpoints[0]->node, 1);
     2125//                SetTesselationPoint(BaseRay->endpoints[1]->node, 2);
     2126//
     2127//                // We demand that at most one new degenerate line is created and that this line also already exists (which has to be the case due to existentTrianglesCount == 1)
     2128//                // i.e. at least one of the three lines must be present with TriangleCount <= 1
     2129//                if (CheckLineCriteriaForDegeneratedTriangle((const BoundaryPointSet ** const)TPS)) {
     2130//                  OtherOptCandidate = (*it);
     2131//                  check = true;
     2132//                }
     2133//              }
     2134//
     2135//              if (check) {
     2136//                if (ShortestAngle > OtherShortestAngle) {
     2137//                  Log() << Verbose(0) << "There is a better candidate than " << *ThirdNode << " with " << ShortestAngle << " from baseline " << *Line << ": " << *OtherOptCandidate << " with " << OtherShortestAngle << "." << endl;
     2138//                  result = true;
     2139//                  break;
     2140//                }
     2141//              }
     2142//            }
     2143//            delete(OptCandidates);
     2144//            if (result)
     2145//              break;
     2146//          } else {
     2147//            Log() << Verbose(0) << "Circumcircle for base line " << *Line << " and base triangle " << T << " is too big!" << endl;
     2148//          }
     2149//        } else {
     2150//          eLog() << Verbose(2) << "Baseline is connected to two triangles already?" << endl;
     2151//        }
     2152//      } else {
     2153//        Log() << Verbose(1) << "No present baseline between " << BaseRay->endpoints[0] << " and candidate " << *ThirdNode << "." << endl;
     2154//      }
     2155//    }
     2156//  } else {
     2157//    eLog() << Verbose(1) << "Could not find the TesselPoint " << *ThirdNode << "." << endl;
     2158//  }
     2159//
     2160//  return result;
     2161//};
    18592162
    18602163/** This function finds a triangle to a line, adjacent to an existing one.
    18612164 * @param out output stream for debugging
    1862  * @param Line current baseline to search from
     2165 * @param CandidateLine current cadndiate baseline to search from
    18632166 * @param T current triangle which \a Line is edge of
    18642167 * @param RADIUS radius of the rolling ball
    … …  
    18662169 * @param *LC LinkedCell structure with neighbouring points
    18672170 */
    1868 bool Tesselation::FindNextSuitableTriangle(BoundaryLineSet &Line, BoundaryTriangleSet &T, const double& RADIUS, const LinkedCell *LC)
    1869 {
    1870   Log() << Verbose(0) << "Begin of FindNextSuitableTriangle\n";
     2171bool Tesselation::FindNextSuitableTriangle(CandidateForTesselation &CandidateLine, BoundaryTriangleSet &T, const double& RADIUS, const LinkedCell *LC)
     2172{
     2173        Info FunctionInfo(__func__);
    18712174  bool result = true;
    1872   CandidateList *OptCandidates = new CandidateList();
    18732175
    18742176  Vector CircleCenter;
    18752177  Vector CirclePlaneNormal;
    1876   Vector OldSphereCenter;
     2178  Vector RelativeSphereCenter;
    18772179  Vector SearchDirection;
    18782180  Vector helper;
    18792181  TesselPoint *ThirdNode = NULL;
    18802182  LineMap::iterator testline;
    1881   double ShortestAngle = 2.*M_PI; // This will indicate the quadrant.
    18822183  double radius, CircleRadius;
    18832184
    1884   Log() << Verbose(1) << "Current baseline is " << Line << " of triangle " << T << "." << endl;
    18852185  for (int i=0;i<3;i++)
    1886     if ((T.endpoints[i]->node != Line.endpoints[0]->node) && (T.endpoints[i]->node != Line.endpoints[1]->node))
     2186    if ((T.endpoints[i]->node != CandidateLine.BaseLine->endpoints[0]->node) && (T.endpoints[i]->node != CandidateLine.BaseLine->endpoints[1]->node)) {
    18872187      ThirdNode = T.endpoints[i]->node;
     2188      break;
     2189    }
     2190  Log() << Verbose(0) << "Current baseline is " << *CandidateLine.BaseLine << " with ThirdNode " << *ThirdNode << " of triangle " << T << "." << endl;
    18882191
    18892192  // construct center of circle
    1890   CircleCenter.CopyVector(Line.endpoints[0]->node->node);
    1891   CircleCenter.AddVector(Line.endpoints[1]->node->node);
     2193  CircleCenter.CopyVector(CandidateLine.BaseLine->endpoints[0]->node->node);
     2194  CircleCenter.AddVector(CandidateLine.BaseLine->endpoints[1]->node->node);
    18922195  CircleCenter.Scale(0.5);
    18932196
    18942197  // construct normal vector of circle
    1895   CirclePlaneNormal.CopyVector(Line.endpoints[0]->node->node);
    1896   CirclePlaneNormal.SubtractVector(Line.endpoints[1]->node->node);
     2198  CirclePlaneNormal.CopyVector(CandidateLine.BaseLine->endpoints[0]->node->node);
     2199  CirclePlaneNormal.SubtractVector(CandidateLine.BaseLine->endpoints[1]->node->node);
    18972200
    18982201  // calculate squared radius of circle
    18992202  radius = CirclePlaneNormal.ScalarProduct(&CirclePlaneNormal);
    19002203  if (radius/4. < RADIUS*RADIUS) {
     2204    // construct relative sphere center with now known CircleCenter
     2205    RelativeSphereCenter.CopyVector(&T.SphereCenter);
     2206    RelativeSphereCenter.SubtractVector(&CircleCenter);
     2207
    19012208    CircleRadius = RADIUS*RADIUS - radius/4.;
    19022209    CirclePlaneNormal.Normalize();
    1903     //Log() << Verbose(2) << "INFO: CircleCenter is at " << CircleCenter << ", CirclePlaneNormal is " << CirclePlaneNormal << " with circle radius " << sqrt(CircleRadius) << "." << endl;
    1904 
    1905     // construct old center
    1906     GetCenterofCircumcircle(&OldSphereCenter, *T.endpoints[0]->node->node, *T.endpoints[1]->node->node, *T.endpoints[2]->node->node);
    1907     helper.CopyVector(&T.NormalVector);  // normal vector ensures that this is correct center of the two possible ones
    1908     radius = Line.endpoints[0]->node->node->DistanceSquared(&OldSphereCenter);
    1909     helper.Scale(sqrt(RADIUS*RADIUS - radius));
    1910     OldSphereCenter.AddVector(&helper);
    1911     OldSphereCenter.SubtractVector(&CircleCenter);
    1912     //Log() << Verbose(2) << "INFO: OldSphereCenter is at " << OldSphereCenter << "." << endl;
    1913 
    1914     // construct SearchDirection
    1915     SearchDirection.MakeNormalVector(&T.NormalVector, &CirclePlaneNormal);
    1916     helper.CopyVector(Line.endpoints[0]->node->node);
     2210    Log() << Verbose(1) << "INFO: CircleCenter is at " << CircleCenter << ", CirclePlaneNormal is " << CirclePlaneNormal << " with circle radius " << sqrt(CircleRadius) << "." << endl;
     2211
     2212    Log() << Verbose(1) << "INFO: OldSphereCenter is at " << T.SphereCenter << "." << endl;
     2213
     2214    // construct SearchDirection and an "outward pointer"
     2215    SearchDirection.MakeNormalVector(&RelativeSphereCenter, &CirclePlaneNormal);
     2216    helper.CopyVector(&CircleCenter);
    19172217    helper.SubtractVector(ThirdNode->node);
    19182218    if (helper.ScalarProduct(&SearchDirection) < -HULLEPSILON)// ohoh, SearchDirection points inwards!
    19192219      SearchDirection.Scale(-1.);
    1920     SearchDirection.ProjectOntoPlane(&OldSphereCenter);
    1921     SearchDirection.Normalize();
    1922     Log() << Verbose(2) << "INFO: SearchDirection is " << SearchDirection << "." << endl;
    1923     if (fabs(OldSphereCenter.ScalarProduct(&SearchDirection)) > HULLEPSILON) {
     2220    Log() << Verbose(1) << "INFO: SearchDirection is " << SearchDirection << "." << endl;
     2221    if (fabs(RelativeSphereCenter.ScalarProduct(&SearchDirection)) > HULLEPSILON) {
    19242222      // rotated the wrong way!
    19252223      eLog() << Verbose(1) << "SearchDirection and RelativeOldSphereCenter are still not orthogonal!" << endl;
    … …  
    19272225
    19282226    // add third point
    1929     FindThirdPointForTesselation(T.NormalVector, SearchDirection, OldSphereCenter, &Line, ThirdNode, OptCandidates, &ShortestAngle, RADIUS, LC);
     2227    FindThirdPointForTesselation(T.NormalVector, SearchDirection, T.SphereCenter, CandidateLine, ThirdNode, RADIUS, LC);
    19302228
    19312229  } else {
    1932     Log() << Verbose(1) << "Circumcircle for base line " << Line << " and base triangle " << T << " is too big!" << endl;
    1933   }
    1934 
    1935   if (OptCandidates->begin() == OptCandidates->end()) {
     2230    Log() << Verbose(0) << "Circumcircle for base line " << *CandidateLine.BaseLine << " and base triangle " << T << " is too big!" << endl;
     2231  }
     2232
     2233  if (CandidateLine.pointlist.empty()) {
    19362234    eLog() << Verbose(2) << "Could not find a suitable candidate." << endl;
    19372235    return false;
    19382236  }
    1939   Log() << Verbose(1) << "Third Points are ";
    1940   for (CandidateList::iterator it = OptCandidates->begin(); it != OptCandidates->end(); ++it) {
    1941     Log() << Verbose(1) << " " << *(*it)->point << endl;
    1942   }
    1943 
    1944   BoundaryLineSet *BaseRay = &Line;
    1945   for (CandidateList::iterator it = OptCandidates->begin(); it != OptCandidates->end(); ++it) {
    1946     Log() << Verbose(1) << " Third point candidate is " << *(*it)->point
    1947     << " with circumsphere's center at " << (*it)->OptCenter << "." << endl;
    1948     Log() << Verbose(1) << " Baseline is " << *BaseRay << endl;
    1949 
    1950     // check whether all edges of the new triangle still have space for one more triangle (i.e. TriangleCount <2)
    1951     TesselPoint *PointCandidates[3];
    1952     PointCandidates[0] = (*it)->point;
    1953     PointCandidates[1] = BaseRay->endpoints[0]->node;
    1954     PointCandidates[2] = BaseRay->endpoints[1]->node;
    1955     int existentTrianglesCount = CheckPresenceOfTriangle(PointCandidates);
    1956 
    1957     BTS = NULL;
    1958     // check for present edges and whether we reach better candidates from them
    1959     if (HasOtherBaselineBetterCandidate(BaseRay, (*it)->point, ShortestAngle, RADIUS, LC) ) {
    1960       result = false;
    1961       break;
    1962     } else {
    1963       // If there is no triangle, add it regularly.
    1964       if (existentTrianglesCount == 0) {
    1965         AddTesselationPoint((*it)->point, 0);
    1966         AddTesselationPoint(BaseRay->endpoints[0]->node, 1);
    1967         AddTesselationPoint(BaseRay->endpoints[1]->node, 2);
    1968 
    1969         if (CheckLineCriteriaForDegeneratedTriangle((const BoundaryPointSet ** const )TPS)) {
    1970           AddTesselationLine(TPS[0], TPS[1], 0);
    1971           AddTesselationLine(TPS[0], TPS[2], 1);
    1972           AddTesselationLine(TPS[1], TPS[2], 2);
    1973 
    1974           BTS = new class BoundaryTriangleSet(BLS, TrianglesOnBoundaryCount);
    1975           AddTesselationTriangle();
    1976           (*it)->OptCenter.Scale(-1.);
    1977           BTS->GetNormalVector((*it)->OptCenter);
    1978           (*it)->OptCenter.Scale(-1.);
    1979 
    1980           Log() << Verbose(0) << "--> New triangle with " << *BTS << " and normal vector " << BTS->NormalVector
    1981             << " for this triangle ... " << endl;
    1982         //Log() << Verbose(1) << "We have "<< TrianglesOnBoundaryCount << " for line " << *BaseRay << "." << endl;
    1983         } else {
    1984           eLog() << Verbose(2) << "This triangle consisting of ";
    1985           Log() << Verbose(0) << *(*it)->point << ", ";
    1986           Log() << Verbose(0) << *BaseRay->endpoints[0]->node << " and ";
    1987           Log() << Verbose(0) << *BaseRay->endpoints[1]->node << " ";
    1988           Log() << Verbose(0) << "exists and is not added, as it does not seem helpful!" << endl;
    1989           result = false;
    1990         }
    1991       } else if ((existentTrianglesCount >= 1) && (existentTrianglesCount <= 3)) { // If there is a planar region within the structure, we need this triangle a second time.
    1992           AddTesselationPoint((*it)->point, 0);
    1993           AddTesselationPoint(BaseRay->endpoints[0]->node, 1);
    1994           AddTesselationPoint(BaseRay->endpoints[1]->node, 2);
    1995 
    1996           // We demand that at most one new degenerate line is created and that this line also already exists (which has to be the case due to existentTrianglesCount == 1)
    1997           // i.e. at least one of the three lines must be present with TriangleCount <= 1
    1998           if (CheckLineCriteriaForDegeneratedTriangle((const BoundaryPointSet ** const)TPS)) {
    1999             AddTesselationLine(TPS[0], TPS[1], 0);
    2000             AddTesselationLine(TPS[0], TPS[2], 1);
    2001             AddTesselationLine(TPS[1], TPS[2], 2);
    2002 
    2003             BTS = new class BoundaryTriangleSet(BLS, TrianglesOnBoundaryCount);
    2004             AddTesselationTriangle();  // add to global map
    2005 
    2006             (*it)->OtherOptCenter.Scale(-1.);
    2007             BTS->GetNormalVector((*it)->OtherOptCenter);
    2008             (*it)->OtherOptCenter.Scale(-1.);
    2009 
    2010             eLog() << Verbose(2) << "--> WARNING: Special new triangle with " << *BTS << " and normal vector " << BTS->NormalVector << " for this triangle ... " << endl;
    2011             Log() << Verbose(1) << "We have "<< BaseRay->triangles.size() << " for line " << BaseRay << "." << endl;
    2012           } else {
    2013             eLog() << Verbose(2) << "This triangle consisting of " << *(*it)->point << ", " << *BaseRay->endpoints[0]->node << " and " << *BaseRay->endpoints[1]->node << " " << "exists and is not added, as it does not seem helpful!" << endl;
    2014             result = false;
    2015           }
    2016       } else {
    2017         Log() << Verbose(1) << "This triangle consisting of ";
    2018         Log() << Verbose(0) << *(*it)->point << ", ";
    2019         Log() << Verbose(0) << *BaseRay->endpoints[0]->node << " and ";
    2020         Log() << Verbose(0) << *BaseRay->endpoints[1]->node << " ";
    2021         Log() << Verbose(0) << "is invalid!" << endl;
    2022         result = false;
    2023       }
    2024     }
    2025 
    2026     // set baseline to new ray from ref point (here endpoints[0]->node) to current candidate (here (*it)->point))
    2027     BaseRay = BLS[0];
    2028     if ((BTS != NULL) && (BTS->NormalVector.NormSquared() < MYEPSILON)) {
    2029       eLog() << Verbose(1) << "Triangle " << *BTS << " has zero normal vector!" << endl;
    2030       exit(255);
    2031     }
    2032 
    2033   }
    2034 
    2035   // remove all candidates from the list and then the list itself
    2036   class CandidateForTesselation *remover = NULL;
    2037   for (CandidateList::iterator it = OptCandidates->begin(); it != OptCandidates->end(); ++it) {
    2038     remover = *it;
    2039     delete(remover);
    2040   }
    2041   delete(OptCandidates);
    2042   Log() << Verbose(0) << "End of FindNextSuitableTriangle\n";
     2237  Log() << Verbose(0) << "Third Points are: " << endl;
     2238  for (TesselPointList::iterator it = CandidateLine.pointlist.begin(); it != CandidateLine.pointlist.end(); ++it) {
     2239    Log() << Verbose(0) << " " << *(*it) << endl;
     2240  }
     2241
     2242  return true;
     2243
     2244//  BoundaryLineSet *BaseRay = CandidateLine.BaseLine;
     2245//  for (CandidateList::iterator it = OptCandidates->begin(); it != OptCandidates->end(); ++it) {
     2246//    Log() << Verbose(0) << "Third point candidate is " << *(*it)->point
     2247//    << " with circumsphere's center at " << (*it)->OptCenter << "." << endl;
     2248//    Log() << Verbose(0) << "Baseline is " << *BaseRay << endl;
     2249//
     2250//    // check whether all edges of the new triangle still have space for one more triangle (i.e. TriangleCount <2)
     2251//    TesselPoint *PointCandidates[3];
     2252//    PointCandidates[0] = (*it)->point;
     2253//    PointCandidates[1] = BaseRay->endpoints[0]->node;
     2254//    PointCandidates[2] = BaseRay->endpoints[1]->node;
     2255//    int existentTrianglesCount = CheckPresenceOfTriangle(PointCandidates);
     2256//
     2257//    BTS = NULL;
     2258//    // check for present edges and whether we reach better candidates from them
     2259//    //if (HasOtherBaselineBetterCandidate(BaseRay, (*it)->point, ShortestAngle, RADIUS, LC) ) {
     2260//    if (0) {
     2261//      result = false;
     2262//      break;
     2263//    } else {
     2264//      // If there is no triangle, add it regularly.
     2265//      if (existentTrianglesCount == 0) {
     2266//        AddTesselationPoint((*it)->point, 0);
     2267//        AddTesselationPoint(BaseRay->endpoints[0]->node, 1);
     2268//        AddTesselationPoint(BaseRay->endpoints[1]->node, 2);
     2269//
     2270//        if (CheckLineCriteriaForDegeneratedTriangle((const BoundaryPointSet ** const )TPS)) {
     2271//          CandidateLine.point = (*it)->point;
     2272//          CandidateLine.OptCenter.CopyVector(&((*it)->OptCenter));
     2273//          CandidateLine.OtherOptCenter.CopyVector(&((*it)->OtherOptCenter));
     2274//          CandidateLine.ShortestAngle = ShortestAngle;
     2275//        } else {
     2276////          eLog() << Verbose(1) << "This triangle consisting of ";
     2277////          Log() << Verbose(0) << *(*it)->point << ", ";
     2278////          Log() << Verbose(0) << *BaseRay->endpoints[0]->node << " and ";
     2279////          Log() << Verbose(0) << *BaseRay->endpoints[1]->node << " ";
     2280////          Log() << Verbose(0) << "exists and is not added, as it 0x80000000006fc150(does not seem helpful!" << endl;
     2281//          result = false;
     2282//        }
     2283//      } else if ((existentTrianglesCount >= 1) && (existentTrianglesCount <= 3)) { // If there is a planar region within the structure, we need this triangle a second time.
     2284//          AddTesselationPoint((*it)->point, 0);
     2285//          AddTesselationPoint(BaseRay->endpoints[0]->node, 1);
     2286//          AddTesselationPoint(BaseRay->endpoints[1]->node, 2);
     2287//
     2288//          // We demand that at most one new degenerate line is created and that this line also already exists (which has to be the case due to existentTrianglesCount == 1)
     2289//          // i.e. at least one of the three lines must be present with TriangleCount <= 1
     2290//          if (CheckLineCriteriaForDegeneratedTriangle((const BoundaryPointSet ** const)TPS) || CandidateLine.BaseLine->skipped) {
     2291//            CandidateLine.point = (*it)->point;
     2292//            CandidateLine.OptCenter.CopyVector(&(*it)->OptCenter);
     2293//            CandidateLine.OtherOptCenter.CopyVector(&(*it)->OtherOptCenter);
     2294//            CandidateLine.ShortestAngle = ShortestAngle+2.*M_PI;
     2295//
     2296//          } else {
     2297////            eLog() << Verbose(1) << "This triangle consisting of " << *(*it)->point << ", " << *BaseRay->endpoints[0]->node << " and " << *BaseRay->endpoints[1]->node << " " << "exists and is not added, as it does not seem helpful!" << endl;
     2298//            result = false;
     2299//          }
     2300//      } else {
     2301////        Log() << Verbose(1) << "This triangle consisting of ";
     2302////        Log() << Verbose(0) << *(*it)->point << ", ";
     2303////        Log() << Verbose(0) << *BaseRay->endpoints[0]->node << " and ";
     2304////        Log() << Verbose(0) << *BaseRay->endpoints[1]->node << " ";
     2305////        Log() << Verbose(0) << "is invalid!" << endl;
     2306//        result = false;
     2307//      }
     2308//    }
     2309//
     2310//    // set baseline to new ray from ref point (here endpoints[0]->node) to current candidate (here (*it)->point))
     2311//    BaseRay = BLS[0];
     2312//    if ((BTS != NULL) && (BTS->NormalVector.NormSquared() < MYEPSILON)) {
     2313//      eLog() << Verbose(1) << "Triangle " << *BTS << " has zero normal vector!" << endl;
     2314//      exit(255);
     2315//    }
     2316//
     2317//  }
     2318//
     2319//  // remove all candidates from the list and then the list itself
     2320//  class CandidateForTesselation *remover = NULL;
     2321//  for (CandidateList::iterator it = OptCandidates->begin(); it != OptCandidates->end(); ++it) {
     2322//    remover = *it;
     2323//    delete(remover);
     2324//  }
     2325//  delete(OptCandidates);
    20432326  return result;
     2327};
     2328
     2329/** Adds the present line and candidate point from \a &CandidateLine to the Tesselation.
     2330 * \param CandidateLine triangle to add
     2331 * \NOTE we need the copy operator here as the original CandidateForTesselation is removed in AddTesselationLine()
     2332 */
     2333void Tesselation::AddCandidateTriangle(CandidateForTesselation CandidateLine)
     2334{
     2335        Info FunctionInfo(__func__);
     2336  Vector Center;
     2337  TesselPoint * const TurningPoint = CandidateLine.BaseLine->endpoints[0]->node;
     2338
     2339  // fill the set of neighbours
     2340  Center.CopyVector(CandidateLine.BaseLine->endpoints[1]->node->node);
     2341  Center.SubtractVector(TurningPoint->node);
     2342  set<TesselPoint*> SetOfNeighbours;
     2343  SetOfNeighbours.insert(CandidateLine.BaseLine->endpoints[1]->node);
     2344  for (TesselPointList::iterator Runner = CandidateLine.pointlist.begin(); Runner != CandidateLine.pointlist.end(); Runner++)
     2345    SetOfNeighbours.insert(*Runner);
     2346  TesselPointList *connectedClosestPoints = GetCircleOfSetOfPoints(&SetOfNeighbours, TurningPoint, &Center);
     2347
     2348  // go through all angle-sorted candidates (in degenerate n-nodes case we may have to add multiple triangles)
     2349  TesselPointList::iterator Runner = connectedClosestPoints->begin();
     2350  TesselPointList::iterator Sprinter = Runner;
     2351  Sprinter++;
     2352  while(Sprinter != connectedClosestPoints->end()) {
     2353    // add the points
     2354    AddTesselationPoint(TurningPoint, 0);
     2355    AddTesselationPoint((*Runner), 1);
     2356    AddTesselationPoint((*Sprinter), 2);
     2357
     2358
     2359    // add the lines
     2360    AddTesselationLine(TPS[0], TPS[1], 0);
     2361    AddTesselationLine(TPS[0], TPS[2], 1);
     2362    AddTesselationLine(TPS[1], TPS[2], 2);
     2363
     2364    // add the triangles
     2365    BTS = new class BoundaryTriangleSet(BLS, TrianglesOnBoundaryCount);
     2366    AddTesselationTriangle();
     2367    BTS->GetCenter(&Center);
     2368    Center.SubtractVector(&CandidateLine.OptCenter);
     2369    BTS->SphereCenter.CopyVector(&CandidateLine.OptCenter);
     2370    BTS->GetNormalVector(Center);
     2371
     2372    Log() << Verbose(0) << "--> New triangle with " << *BTS << " and normal vector " << BTS->NormalVector << "." << endl;
     2373    Runner = Sprinter;
     2374    Sprinter++;
     2375  }
     2376  delete(connectedClosestPoints);
    20442377};
    20452378
    … …  
    20532386class BoundaryPointSet *Tesselation::IsConvexRectangle(class BoundaryLineSet *Base)
    20542387{
     2388        Info FunctionInfo(__func__);
    20552389  class BoundaryPointSet *Spot = NULL;
    20562390  class BoundaryLineSet *OtherBase;
    … …  
    20642398  OtherBase = new class BoundaryLineSet(BPS,-1);
    20652399
    2066   Log() << Verbose(3) << "INFO: Current base line is " << *Base << "." << endl;
    2067   Log() << Verbose(3) << "INFO: Other base line is " << *OtherBase << "." << endl;
     2400  Log() << Verbose(1) << "INFO: Current base line is " << *Base << "." << endl;
     2401  Log() << Verbose(1) << "INFO: Other base line is " << *OtherBase << "." << endl;
    20682402
    20692403  // get the closest point on each line to the other line
    … …  
    20852419  delete(ClosestPoint);
    20862420  if ((distance[0] * distance[1]) > 0)  { // have same sign?
    2087     Log() << Verbose(3) << "REJECT: Both SKPs have same sign: " << distance[0] << " and " << distance[1]  << ". " << *Base << "' rectangle is concave." << endl;
     2421    Log() << Verbose(1) << "REJECT: Both SKPs have same sign: " << distance[0] << " and " << distance[1]  << ". " << *Base << "' rectangle is concave." << endl;
    20882422    if (distance[0] < distance[1]) {
    20892423      Spot = Base->endpoints[0];
    … …  
    20932427    return Spot;
    20942428  } else {  // different sign, i.e. we are in between
    2095     Log() << Verbose(3) << "ACCEPT: Rectangle of triangles of base line " << *Base << " is convex." << endl;
     2429    Log() << Verbose(0) << "ACCEPT: Rectangle of triangles of base line " << *Base << " is convex." << endl;
    20962430    return NULL;
    20972431  }
    … …  
    21012435void Tesselation::PrintAllBoundaryPoints(ofstream *out) const
    21022436{
     2437        Info FunctionInfo(__func__);
    21032438  // print all lines
    2104   Log() << Verbose(1) << "Printing all boundary points for debugging:" << endl;
     2439  Log() << Verbose(0) << "Printing all boundary points for debugging:" << endl;
    21052440  for (PointMap::const_iterator PointRunner = PointsOnBoundary.begin();PointRunner != PointsOnBoundary.end(); PointRunner++)
    2106     Log() << Verbose(2) << *(PointRunner->second) << endl;
     2441    Log() << Verbose(0) << *(PointRunner->second) << endl;
    21072442};
    21082443
    21092444void Tesselation::PrintAllBoundaryLines(ofstream *out) const
    21102445{
     2446        Info FunctionInfo(__func__);
    21112447  // print all lines
    2112   Log() << Verbose(1) << "Printing all boundary lines for debugging:" << endl;
     2448  Log() << Verbose(0) << "Printing all boundary lines for debugging:" << endl;
    21132449  for (LineMap::const_iterator LineRunner = LinesOnBoundary.begin(); LineRunner != LinesOnBoundary.end(); LineRunner++)
    2114     Log() << Verbose(2) << *(LineRunner->second) << endl;
     2450    Log() << Verbose(0) << *(LineRunner->second) << endl;
    21152451};
    21162452
    21172453void Tesselation::PrintAllBoundaryTriangles(ofstream *out) const
    21182454{
     2455        Info FunctionInfo(__func__);
    21192456  // print all triangles
    2120   Log() << Verbose(1) << "Printing all boundary triangles for debugging:" << endl;
     2457  Log() << Verbose(0) << "Printing all boundary triangles for debugging:" << endl;
    21212458  for (TriangleMap::const_iterator TriangleRunner = TrianglesOnBoundary.begin(); TriangleRunner != TrianglesOnBoundary.end(); TriangleRunner++)
    2122     Log() << Verbose(2) << *(TriangleRunner->second) << endl;
     2459    Log() << Verbose(0) << *(TriangleRunner->second) << endl;
    21232460};
    21242461
    … …  
    21302467double Tesselation::PickFarthestofTwoBaselines(class BoundaryLineSet *Base)
    21312468{
     2469        Info FunctionInfo(__func__);
    21322470  class BoundaryLineSet *OtherBase;
    21332471  Vector *ClosestPoint[2];
    … …  
    21412479  OtherBase = new class BoundaryLineSet(BPS,-1);
    21422480
    2143   Log() << Verbose(3) << "INFO: Current base line is " << *Base << "." << endl;
    2144   Log() << Verbose(3) << "INFO: Other base line is " << *OtherBase << "." << endl;
     2481  Log() << Verbose(0) << "INFO: Current base line is " << *Base << "." << endl;
     2482  Log() << Verbose(0) << "INFO: Other base line is " << *OtherBase << "." << endl;
    21452483
    21462484  // get the closest point on each line to the other line
    … …  
    21622500
    21632501  if (Distance.NormSquared() < MYEPSILON) { // check for intersection
    2164     Log() << Verbose(3) << "REJECT: Both lines have an intersection: Nothing to do." << endl;
     2502    Log() << Verbose(0) << "REJECT: Both lines have an intersection: Nothing to do." << endl;
    21652503    return false;
    21662504  } else { // check for sign against BaseLineNormal
    … …  
    21722510    }
    21732511    for (TriangleMap::iterator runner = Base->triangles.begin(); runner != Base->triangles.end(); runner++) {
    2174       Log() << Verbose(4) << "INFO: Adding NormalVector " << runner->second->NormalVector << " of triangle " << *(runner->second) << "." << endl;
     2512      Log() << Verbose(1) << "INFO: Adding NormalVector " << runner->second->NormalVector << " of triangle " << *(runner->second) << "." << endl;
    21752513      BaseLineNormal.AddVector(&(runner->second->NormalVector));
    21762514    }
    … …  
    21782516
    21792517    if (Distance.ScalarProduct(&BaseLineNormal) > MYEPSILON) { // Distance points outwards, hence OtherBase higher than Base -> flip
    2180       Log() << Verbose(2) << "ACCEPT: Other base line would be higher: Flipping baseline." << endl;
     2518      Log() << Verbose(0) << "ACCEPT: Other base line would be higher: Flipping baseline." << endl;
    21812519      // calculate volume summand as a general tetraeder
    21822520      return volume;
    21832521    } else {  // Base higher than OtherBase -> do nothing
    2184       Log() << Verbose(2) << "REJECT: Base line is higher: Nothing to do." << endl;
     2522      Log() << Verbose(0) << "REJECT: Base line is higher: Nothing to do." << endl;
    21852523      return 0.;
    21862524    }
    … …  
    21972535class BoundaryLineSet * Tesselation::FlipBaseline(class BoundaryLineSet *Base)
    21982536{
     2537        Info FunctionInfo(__func__);
    21992538  class BoundaryLineSet *OldLines[4], *NewLine;
    22002539  class BoundaryPointSet *OldPoints[2];
    … …  
    22032542  int i,m;
    22042543
    2205   Log() << Verbose(1) << "Begin of FlipBaseline" << endl;
    2206 
    22072544  // calculate NormalVector for later use
    22082545  BaseLineNormal.Zero();
    … …  
    22122549  }
    22132550  for (TriangleMap::iterator runner = Base->triangles.begin(); runner != Base->triangles.end(); runner++) {
    2214     Log() << Verbose(4) << "INFO: Adding NormalVector " << runner->second->NormalVector << " of triangle " << *(runner->second) << "." << endl;
     2551    Log() << Verbose(1) << "INFO: Adding NormalVector " << runner->second->NormalVector << " of triangle " << *(runner->second) << "." << endl;
    22152552    BaseLineNormal.AddVector(&(runner->second->NormalVector));
    22162553  }
    … …  
    22252562  i=0;
    22262563  m=0;
    2227   Log() << Verbose(3) << "The four old lines are: ";
     2564  Log() << Verbose(0) << "The four old lines are: ";
    22282565  for(TriangleMap::iterator runner = Base->triangles.begin(); runner != Base->triangles.end(); runner++)
    22292566    for (int j=0;j<3;j++) // all of their endpoints and baselines
    … …  
    22332570      }
    22342571  Log() << Verbose(0) << endl;
    2235   Log() << Verbose(3) << "The two old points are: ";
     2572  Log() << Verbose(0) << "The two old points are: ";
    22362573  for(TriangleMap::iterator runner = Base->triangles.begin(); runner != Base->triangles.end(); runner++)
    22372574    for (int j=0;j<3;j++) // all of their endpoints and baselines
    … …  
    22592596
    22602597  // remove triangles and baseline removes itself
    2261   Log() << Verbose(3) << "INFO: Deleting baseline " << *Base << " from global list." << endl;
     2598  Log() << Verbose(0) << "INFO: Deleting baseline " << *Base << " from global list." << endl;
    22622599  OldBaseLineNr = Base->Nr;
    22632600  m=0;
    22642601  for(TriangleMap::iterator runner = Base->triangles.begin(); runner != Base->triangles.end(); runner++) {
    2265     Log() << Verbose(3) << "INFO: Deleting triangle " << *(runner->second) << "." << endl;
     2602    Log() << Verbose(0) << "INFO: Deleting triangle " << *(runner->second) << "." << endl;
    22662603    OldTriangleNrs[m++] = runner->second->Nr;
    22672604    RemoveTesselationTriangle(runner->second);
    … …  
    22732610  NewLine = new class BoundaryLineSet(BPS, OldBaseLineNr);
    22742611  LinesOnBoundary.insert(LinePair(OldBaseLineNr, NewLine)); // no need for check for unique insertion as NewLine is definitely a new one
    2275   Log() << Verbose(3) << "INFO: Created new baseline " << *NewLine << "." << endl;
     2612  Log() << Verbose(0) << "INFO: Created new baseline " << *NewLine << "." << endl;
    22762613
    22772614  // construct new triangles with flipped baseline
    … …  
    22882625    BTS->GetNormalVector(BaseLineNormal);
    22892626    AddTesselationTriangle(OldTriangleNrs[0]);
    2290     Log() << Verbose(3) << "INFO: Created new triangle " << *BTS << "." << endl;
     2627    Log() << Verbose(0) << "INFO: Created new triangle " << *BTS << "." << endl;
    22912628
    22922629    BLS[0] = (i==2 ? OldLines[3] : OldLines[2]);
    … …  
    22962633    BTS->GetNormalVector(BaseLineNormal);
    22972634    AddTesselationTriangle(OldTriangleNrs[1]);
    2298     Log() << Verbose(3) << "INFO: Created new triangle " << *BTS << "." << endl;
     2635    Log() << Verbose(0) << "INFO: Created new triangle " << *BTS << "." << endl;
    22992636  } else {
    2300     Log() << Verbose(1) << "The four old lines do not connect, something's utterly wrong here!" << endl;
     2637    eLog() << Verbose(0) << "The four old lines do not connect, something's utterly wrong here!" << endl;
    23012638    return NULL;
    23022639  }
    23032640
    2304   Log() << Verbose(1) << "End of FlipBaseline" << endl;
    23052641  return NewLine;
    23062642};
    … …  
    23172653void Tesselation::FindSecondPointForTesselation(TesselPoint* a, Vector Oben, TesselPoint*& OptCandidate, double Storage[3], double RADIUS, const LinkedCell *LC)
    23182654{
    2319   Log() << Verbose(2) << "Begin of FindSecondPointForTesselation" << endl;
     2655        Info FunctionInfo(__func__);
    23202656  Vector AngleCheck;
    23212657  class TesselPoint* Candidate = NULL;
    … …  
    23382674    Nupper[i] = ((N[i]+1) < LC->N[i]) ? N[i]+1 : LC->N[i]-1;
    23392675  }
    2340   Log() << Verbose(3) << "LC Intervals from [" << N[0] << "<->" << LC->N[0] << ", " << N[1] << "<->" << LC->N[1] << ", " << N[2] << "<->" << LC->N[2] << "] :"
     2676  Log() << Verbose(0) << "LC Intervals from [" << N[0] << "<->" << LC->N[0] << ", " << N[1] << "<->" << LC->N[1] << ", " << N[2] << "<->" << LC->N[2] << "] :"
    23412677    << " [" << Nlower[0] << "," << Nupper[0] << "], " << " [" << Nlower[1] << "," << Nupper[1] << "], " << " [" << Nlower[2] << "," << Nupper[2] << "], " << endl;
    23422678
    … …  
    23452681      for (LC->n[2] = Nlower[2]; LC->n[2] <= Nupper[2]; LC->n[2]++) {
    23462682        const LinkedNodes *List = LC->GetCurrentCell();
    2347         //Log() << Verbose(2) << "Current cell is " << LC->n[0] << ", " << LC->n[1] << ", " << LC->n[2] << " with No. " << LC->index << "." << endl;
     2683        //Log() << Verbose(1) << "Current cell is " << LC->n[0] << ", " << LC->n[1] << ", " << LC->n[2] << " with No. " << LC->index << "." << endl;
    23482684        if (List != NULL) {
    23492685          for (LinkedNodes::const_iterator Runner = List->begin(); Runner != List->end(); Runner++) {
    … …  
    23762712                angle = AngleCheck.Angle(&Oben);
    23772713                if (angle < Storage[0]) {
    2378                   //Log() << Verbose(3) << "Old values of Storage: %lf %lf \n", Storage[0], Storage[1]);
    2379                   Log() << Verbose(3) << "Current candidate is " << *Candidate << ": Is a better candidate with distance " << norm << " and angle " << angle << " to oben " << Oben << ".\n";
     2714                  //Log() << Verbose(1) << "Old values of Storage: %lf %lf \n", Storage[0], Storage[1]);
     2715                  Log() << Verbose(1) << "Current candidate is " << *Candidate << ": Is a better candidate with distance " << norm << " and angle " << angle << " to oben " << Oben << ".\n";
    23802716                  OptCandidate = Candidate;
    23812717                  Storage[0] = angle;
    2382                   //Log() << Verbose(3) << "Changing something in Storage: %lf %lf. \n", Storage[0], Storage[2]);
     2718                  //Log() << Verbose(1) << "Changing something in Storage: %lf %lf. \n", Storage[0], Storage[2]);
    23832719                } else {
    2384                   //Log() << Verbose(3) << "Current candidate is " << *Candidate << ": Looses with angle " << angle << " to a better candidate " << *OptCandidate << endl;
     2720                  //Log() << Verbose(1) << "Current candidate is " << *Candidate << ": Looses with angle " << angle << " to a better candidate " << *OptCandidate << endl;
    23852721                }
    23862722              } else {
    2387                 //Log() << Verbose(3) << "Current candidate is " << *Candidate << ": Refused due to Radius " << norm << endl;
     2723                //Log() << Verbose(1) << "Current candidate is " << *Candidate << ": Refused due to Radius " << norm << endl;
    23882724              }
    23892725            } else {
    2390               //Log() << Verbose(3) << "Current candidate is " << *Candidate << ": Candidate is equal to first endpoint." << *a << "." << endl;
     2726              //Log() << Verbose(1) << "Current candidate is " << *Candidate << ": Candidate is equal to first endpoint." << *a << "." << endl;
    23912727            }
    23922728          }
    23932729        } else {
    2394           Log() << Verbose(3) << "Linked cell list is empty." << endl;
     2730          Log() << Verbose(0) << "Linked cell list is empty." << endl;
    23952731        }
    23962732      }
    2397   Log() << Verbose(2) << "End of FindSecondPointForTesselation" << endl;
    23982733};
    23992734
    … …  
    24242759 * @param SearchDirection general direction where to search for the next point, relative to center of BaseLine
    24252760 * @param OldSphereCenter center of sphere for base triangle, relative to center of BaseLine, giving null angle for the parameter circle
    2426  * @param BaseLine BoundaryLineSet with the current base line
     2761 * @param CandidateLine CandidateForTesselation with the current base line and list of candidates and ShortestAngle
    24272762 * @param ThirdNode third point to avoid in search
    2428  * @param candidates list of equally good candidates to return
    2429  * @param ShortestAngle the current path length on this circle band for the current OptCandidate
    24302763 * @param RADIUS radius of sphere
    24312764 * @param *LC LinkedCell structure with neighbouring points
    24322765 */
    2433 void Tesselation::FindThirdPointForTesselation(Vector &NormalVector, Vector &SearchDirection, Vector &OldSphereCenter, class BoundaryLineSet *BaseLine, const class TesselPoint  * const ThirdNode, CandidateList* &candidates, double *ShortestAngle, const double RADIUS, const LinkedCell *LC) const
    2434 {
     2766void Tesselation::FindThirdPointForTesselation(Vector &NormalVector, Vector &SearchDirection, Vector &OldSphereCenter, CandidateForTesselation &CandidateLine, const class TesselPoint  * const ThirdNode, const double RADIUS, const LinkedCell *LC) const
     2767{
     2768        Info FunctionInfo(__func__);
    24352769  Vector CircleCenter;  // center of the circle, i.e. of the band of sphere's centers
    24362770  Vector CirclePlaneNormal; // normal vector defining the plane this circle lives in
    … …  
    24402774  Vector NewNormalVector;   // normal vector of the Candidate's triangle
    24412775  Vector helper, OptCandidateCenter, OtherOptCandidateCenter;
     2776  Vector RelativeOldSphereCenter;
     2777  Vector NewPlaneCenter;
    24422778  double CircleRadius; // radius of this circle
    24432779  double radius;
     2780  double otherradius;
    24442781  double alpha, Otheralpha; // angles (i.e. parameter for the circle).
    24452782  int N[NDIM], Nlower[NDIM], Nupper[NDIM];
    24462783  TesselPoint *Candidate = NULL;
    2447   CandidateForTesselation *optCandidate = NULL;
    2448 
    2449   Log() << Verbose(1) << "Begin of FindThirdPointForTesselation" << endl;
    2450 
    2451   Log() << Verbose(2) << "INFO: NormalVector of BaseTriangle is " << NormalVector << "." << endl;
     2784
     2785  Log() << Verbose(1) << "INFO: NormalVector of BaseTriangle is " << NormalVector << "." << endl;
    24522786
    24532787  // construct center of circle
    2454   CircleCenter.CopyVector(BaseLine->endpoints[0]->node->node);
    2455   CircleCenter.AddVector(BaseLine->endpoints[1]->node->node);
     2788  CircleCenter.CopyVector(CandidateLine.BaseLine->endpoints[0]->node->node);
     2789  CircleCenter.AddVector(CandidateLine.BaseLine->endpoints[1]->node->node);
    24562790  CircleCenter.Scale(0.5);
    24572791
    24582792  // construct normal vector of circle
    2459   CirclePlaneNormal.CopyVector(BaseLine->endpoints[0]->node->node);
    2460   CirclePlaneNormal.SubtractVector(BaseLine->endpoints[1]->node->node);
     2793  CirclePlaneNormal.CopyVector(CandidateLine.BaseLine->endpoints[0]->node->node);
     2794  CirclePlaneNormal.SubtractVector(CandidateLine.BaseLine->endpoints[1]->node->node);
     2795
     2796  RelativeOldSphereCenter.CopyVector(&OldSphereCenter);
     2797  RelativeOldSphereCenter.SubtractVector(&CircleCenter);
    24612798
    24622799  // calculate squared radius TesselPoint *ThirdNode,f circle
    2463   radius = CirclePlaneNormal.ScalarProduct(&CirclePlaneNormal);
    2464   if (radius/4. < RADIUS*RADIUS) {
    2465     CircleRadius = RADIUS*RADIUS - radius/4.;
     2800  radius = CirclePlaneNormal.NormSquared()/4.;
     2801  if (radius < RADIUS*RADIUS) {
     2802    CircleRadius = RADIUS*RADIUS - radius;
    24662803    CirclePlaneNormal.Normalize();
    2467     //Log() << Verbose(2) << "INFO: CircleCenter is at " << CircleCenter << ", CirclePlaneNormal is " << CirclePlaneNormal << " with circle radius " << sqrt(CircleRadius) << "." << endl;
     2804    Log() << Verbose(1) << "INFO: CircleCenter is at " << CircleCenter << ", CirclePlaneNormal is " << CirclePlaneNormal << " with circle radius " << sqrt(CircleRadius) << "." << endl;
    24682805
    24692806    // test whether old center is on the band's plane
    2470     if (fabs(OldSphereCenter.ScalarProduct(&CirclePlaneNormal)) > HULLEPSILON) {
    2471       eLog() << Verbose(1) << "Something's very wrong here: OldSphereCenter is not on the band's plane as desired by " << fabs(OldSphereCenter.ScalarProduct(&CirclePlaneNormal)) << "!" << endl;
    2472       OldSphereCenter.ProjectOntoPlane(&CirclePlaneNormal);
    2473     }
    2474     radius = OldSphereCenter.ScalarProduct(&OldSphereCenter);
     2807    if (fabs(RelativeOldSphereCenter.ScalarProduct(&CirclePlaneNormal)) > HULLEPSILON) {
     2808      eLog() << Verbose(1) << "Something's very wrong here: RelativeOldSphereCenter is not on the band's plane as desired by " << fabs(RelativeOldSphereCenter.ScalarProduct(&CirclePlaneNormal)) << "!" << endl;
     2809      RelativeOldSphereCenter.ProjectOntoPlane(&CirclePlaneNormal);
     2810    }
     2811    radius = RelativeOldSphereCenter.NormSquared();
    24752812    if (fabs(radius - CircleRadius) < HULLEPSILON) {
    2476       //Log() << Verbose(2) << "INFO: OldSphereCenter is at " << OldSphereCenter << "." << endl;
     2813      Log() << Verbose(1) << "INFO: RelativeOldSphereCenter is at " << RelativeOldSphereCenter << "." << endl;
    24772814
    24782815      // check SearchDirection
    2479       //Log() << Verbose(2) << "INFO: SearchDirection is " << SearchDirection << "." << endl;
    2480       if (fabs(OldSphereCenter.ScalarProduct(&SearchDirection)) > HULLEPSILON) {  // rotated the wrong way!
     2816      Log() << Verbose(1) << "INFO: SearchDirection is " << SearchDirection << "." << endl;
     2817      if (fabs(RelativeOldSphereCenter.ScalarProduct(&SearchDirection)) > HULLEPSILON) {  // rotated the wrong way!
    24812818        eLog() << Verbose(1) << "SearchDirection and RelativeOldSphereCenter are not orthogonal!" << endl;
    24822819      }
    … …  
    24862823        for(int i=0;i<NDIM;i++) // store indices of this cell
    24872824        N[i] = LC->n[i];
    2488         //Log() << Verbose(2) << "INFO: Center cell is " << N[0] << ", " << N[1] << ", " << N[2] << " with No. " << LC->index << "." << endl;
     2825        //Log() << Verbose(1) << "INFO: Center cell is " << N[0] << ", " << N[1] << ", " << N[2] << " with No. " << LC->index << "." << endl;
    24892826      } else {
    24902827        eLog() << Verbose(1) << "Vector " << CircleCenter << " is outside of LinkedCell's bounding box." << endl;
    … …  
    24922829      }
    24932830      // then go through the current and all neighbouring cells and check the contained points for possible candidates
    2494       //Log() << Verbose(2) << "LC Intervals:";
     2831      //Log() << Verbose(1) << "LC Intervals:";
    24952832      for (int i=0;i<NDIM;i++) {
    24962833        Nlower[i] = ((N[i]-1) >= 0) ? N[i]-1 : 0;
    … …  
    25032840          for (LC->n[2] = Nlower[2]; LC->n[2] <= Nupper[2]; LC->n[2]++) {
    25042841            const LinkedNodes *List = LC->GetCurrentCell();
    2505             //Log() << Verbose(2) << "Current cell is " << LC->n[0] << ", " << LC->n[1] << ", " << LC->n[2] << " with No. " << LC->index << "." << endl;
     2842            //Log() << Verbose(1) << "Current cell is " << LC->n[0] << ", " << LC->n[1] << ", " << LC->n[2] << " with No. " << LC->index << "." << endl;
    25062843            if (List != NULL) {
    25072844              for (LinkedNodes::const_iterator Runner = List->begin(); Runner != List->end(); Runner++) {
    … …  
    25092846
    25102847                // check for three unique points
    2511                 //Log() << Verbose(2) << "INFO: Current Candidate is " << *Candidate << " at " << Candidate->node << "." << endl;
    2512                 if ((Candidate != BaseLine->endpoints[0]->node) && (Candidate != BaseLine->endpoints[1]->node) ){
    2513 
    2514                   // construct both new centers
    2515                   GetCenterofCircumcircle(&NewSphereCenter, *BaseLine->endpoints[0]->node->node, *BaseLine->endpoints[1]->node->node, *Candidate->node);
    2516                   OtherNewSphereCenter.CopyVector(&NewSphereCenter);
    2517 
    2518                   if ((NewNormalVector.MakeNormalVector(BaseLine->endpoints[0]->node->node, BaseLine->endpoints[1]->node->node, Candidate->node))
    2519                   && (fabs(NewNormalVector.ScalarProduct(&NewNormalVector)) > HULLEPSILON)
     2848                Log() << Verbose(2) << "INFO: Current Candidate is " << *Candidate << " for BaseLine " << *CandidateLine.BaseLine << " with OldSphereCenter " << OldSphereCenter << "." << endl;
     2849                if ((Candidate != CandidateLine.BaseLine->endpoints[0]->node) && (Candidate != CandidateLine.BaseLine->endpoints[1]->node) ){
     2850
     2851                  // find center on the plane
     2852                  GetCenterofCircumcircle(&NewPlaneCenter, *CandidateLine.BaseLine->endpoints[0]->node->node, *CandidateLine.BaseLine->endpoints[1]->node->node, *Candidate->node);
     2853                  Log() << Verbose(1) << "INFO: NewPlaneCenter is " << NewPlaneCenter << "." << endl;
     2854
     2855                  if (NewNormalVector.MakeNormalVector(CandidateLine.BaseLine->endpoints[0]->node->node, CandidateLine.BaseLine->endpoints[1]->node->node, Candidate->node)
     2856                  && (fabs(NewNormalVector.NormSquared()) > HULLEPSILON)
    25202857                  ) {
    2521                     helper.CopyVector(&NewNormalVector);
    2522                     //Log() << Verbose(2) << "INFO: NewNormalVector is " << NewNormalVector << "." << endl;
    2523                     radius = BaseLine->endpoints[0]->node->node->DistanceSquared(&NewSphereCenter);
     2858                    Log() << Verbose(1) << "INFO: NewNormalVector is " << NewNormalVector << "." << endl;
     2859                    radius = CandidateLine.BaseLine->endpoints[0]->node->node->DistanceSquared(&NewPlaneCenter);
     2860                    Log() << Verbose(1) << "INFO: CircleCenter is at " << CircleCenter << ", CirclePlaneNormal is " << CirclePlaneNormal << " with circle radius " << sqrt(CircleRadius) << "." << endl;
     2861                    Log() << Verbose(1) << "INFO: SearchDirection is " << SearchDirection << "." << endl;
     2862                    Log() << Verbose(1) << "INFO: Radius of CircumCenterCircle is " << radius << "." << endl;
    25242863                    if (radius < RADIUS*RADIUS) {
     2864                      otherradius = CandidateLine.BaseLine->endpoints[1]->node->node->DistanceSquared(&NewPlaneCenter);
     2865                      if (fabs(radius - otherradius) > HULLEPSILON) {
     2866                        eLog() << Verbose(1) << "Distance to center of circumcircle is not the same from each corner of the triangle: " << fabs(radius-otherradius) << endl;
     2867                      }
     2868                      // construct both new centers
     2869                      NewSphereCenter.CopyVector(&NewPlaneCenter);
     2870                      OtherNewSphereCenter.CopyVector(&NewPlaneCenter);
     2871                      helper.CopyVector(&NewNormalVector);
    25252872                      helper.Scale(sqrt(RADIUS*RADIUS - radius));
    2526                       //Log() << Verbose(2) << "INFO: Distance of NewCircleCenter to NewSphereCenter is " << helper.Norm() << " with sphere radius " << RADIUS << "." << endl;
     2873                      Log() << Verbose(2) << "INFO: Distance of NewPlaneCenter " << NewPlaneCenter << " to either NewSphereCenter is " << helper.Norm() << " of vector " << helper << " with sphere radius " << RADIUS << "." << endl;
    25272874                      NewSphereCenter.AddVector(&helper);
    2528                       NewSphereCenter.SubtractVector(&CircleCenter);
    2529                       //Log() << Verbose(2) << "INFO: NewSphereCenter is at " << NewSphereCenter << "." << endl;
    2530 
     2875                      Log() << Verbose(2) << "INFO: NewSphereCenter is at " << NewSphereCenter << "." << endl;
    25312876                      // OtherNewSphereCenter is created by the same vector just in the other direction
    25322877                      helper.Scale(-1.);
    25332878                      OtherNewSphereCenter.AddVector(&helper);
    2534                       OtherNewSphereCenter.SubtractVector(&CircleCenter);
    2535                       //Log() << Verbose(2) << "INFO: OtherNewSphereCenter is at " << OtherNewSphereCenter << "." << endl;
     2879                      Log() << Verbose(2) << "INFO: OtherNewSphereCenter is at " << OtherNewSphereCenter << "." << endl;
    25362880
    25372881                      alpha = GetPathLengthonCircumCircle(CircleCenter, CirclePlaneNormal, CircleRadius, NewSphereCenter, OldSphereCenter, NormalVector, SearchDirection);
    25382882                      Otheralpha = GetPathLengthonCircumCircle(CircleCenter, CirclePlaneNormal, CircleRadius, OtherNewSphereCenter, OldSphereCenter, NormalVector, SearchDirection);
    25392883                      alpha = min(alpha, Otheralpha);
     2884
    25402885                      // if there is a better candidate, drop the current list and add the new candidate
    25412886                      // otherwise ignore the new candidate and keep the list
    2542                       if (*ShortestAngle > (alpha - HULLEPSILON)) {
    2543                         optCandidate = new CandidateForTesselation(Candidate, BaseLine, OptCandidateCenter, OtherOptCandidateCenter);
     2887                      if (CandidateLine.ShortestAngle > (alpha - HULLEPSILON)) {
    25442888                        if (fabs(alpha - Otheralpha) > MYEPSILON) {
    2545                           optCandidate->OptCenter.CopyVector(&NewSphereCenter);
    2546                           optCandidate->OtherOptCenter.CopyVector(&OtherNewSphereCenter);
     2889                          CandidateLine.OptCenter.CopyVector(&NewSphereCenter);
     2890                          CandidateLine.OtherOptCenter.CopyVector(&OtherNewSphereCenter);
    25472891                        } else {
    2548                           optCandidate->OptCenter.CopyVector(&OtherNewSphereCenter);
    2549                           optCandidate->OtherOptCenter.CopyVector(&NewSphereCenter);
     2892                          CandidateLine.OptCenter.CopyVector(&OtherNewSphereCenter);
     2893                          CandidateLine.OtherOptCenter.CopyVector(&NewSphereCenter);
    25502894                        }
    25512895                        // if there is an equal candidate, add it to the list without clearing the list
    2552                         if ((*ShortestAngle - HULLEPSILON) < alpha) {
    2553                           candidates->push_back(optCandidate);
    2554                           Log() << Verbose(2) << "ACCEPT: We have found an equally good candidate: " << *(optCandidate->point) << " with "
    2555                             << alpha << " and circumsphere's center at " << optCandidate->OptCenter << "." << endl;
     2896                        if ((CandidateLine.ShortestAngle - HULLEPSILON) < alpha) {
     2897                          CandidateLine.pointlist.push_back(Candidate);
     2898                          Log() << Verbose(0) << "ACCEPT: We have found an equally good candidate: " << *(Candidate) << " with "
     2899                            << alpha << " and circumsphere's center at " << CandidateLine.OptCenter << "." << endl;
    25562900                        } else {
    25572901                          // remove all candidates from the list and then the list itself
    2558                           class CandidateForTesselation *remover = NULL;
    2559                           for (CandidateList::iterator it = candidates->begin(); it != candidates->end(); ++it) {
    2560                             remover = *it;
    2561                             delete(remover);
    2562                           }
    2563                           candidates->clear();
    2564                           candidates->push_back(optCandidate);
    2565                           Log() << Verbose(2) << "ACCEPT: We have found a better candidate: " << *(optCandidate->point) << " with "
    2566                             << alpha << " and circumsphere's center at " << optCandidate->OptCenter << "." << endl;
     2902                          CandidateLine.pointlist.clear();
     2903                          CandidateLine.pointlist.push_back(Candidate);
     2904                          Log() << Verbose(0) << "ACCEPT: We have found a better candidate: " << *(Candidate) << " with "
     2905                            << alpha << " and circumsphere's center at " << CandidateLine.OptCenter << "." << endl;
    25672906                        }
    2568                         *ShortestAngle = alpha;
    2569                         //Log() << Verbose(2) << "INFO: There are " << candidates->size() << " candidates in the list now." << endl;
     2907                        CandidateLine.ShortestAngle = alpha;
     2908                        Log() << Verbose(0) << "INFO: There are " << CandidateLine.pointlist.size() << " candidates in the list now." << endl;
    25702909                      } else {
    2571                         if ((optCandidate != NULL) && (optCandidate->point != NULL)) {
    2572                           //Log() << Verbose(2) << "REJECT: Old candidate " << *(optCandidate->point) << " with " << *ShortestAngle << " is better than new one " << *Candidate << " with " << alpha << " ." << endl;
     2910                        if ((Candidate != NULL) && (CandidateLine.pointlist.begin() != CandidateLine.pointlist.end())) {
     2911                          Log() << Verbose(1) << "REJECT: Old candidate " << *(Candidate) << " with " << CandidateLine.ShortestAngle << " is better than new one " << *Candidate << " with " << alpha << " ." << endl;
    25732912                        } else {
    2574                           //Log() << Verbose(2) << "REJECT: Candidate " << *Candidate << " with " << alpha << " was rejected." << endl;
     2913                          Log() << Verbose(1) << "REJECT: Candidate " << *Candidate << " with " << alpha << " was rejected." << endl;
    25752914                        }
    25762915                      }
    2577 
    25782916                    } else {
    2579                       //Log() << Verbose(2) << "REJECT: NewSphereCenter " << NewSphereCenter << " for " << *Candidate << " is too far away: " << radius << "." << endl;
     2917                      Log() << Verbose(1) << "REJECT: NewSphereCenter " << NewSphereCenter << " for " << *Candidate << " is too far away: " << radius << "." << endl;
    25802918                    }
    25812919                  } else {
    2582                     //Log() << Verbose(2) << "REJECT: Three points from " << *BaseLine << " and Candidate " << *Candidate << " are linear-dependent." << endl;
     2920                    Log() << Verbose(1) << "REJECT: Three points from " << *CandidateLine.BaseLine << " and Candidate " << *Candidate << " are linear-dependent." << endl;
    25832921                  }
    25842922                } else {
    25852923                  if (ThirdNode != NULL) {
    2586                     //Log() << Verbose(2) << "REJECT: Base triangle " << *BaseLine << " and " << *ThirdNode << " contains Candidate " << *Candidate << "." << endl;
     2924                    Log() << Verbose(1) << "REJECT: Base triangle " << *CandidateLine.BaseLine << " and " << *ThirdNode << " contains Candidate " << *Candidate << "." << endl;
    25872925                  } else {
    2588                     //Log() << Verbose(2) << "REJECT: Base triangle " << *BaseLine << " contains Candidate " << *Candidate << "." << endl;
     2926                    Log() << Verbose(1) << "REJECT: Base triangle " << *CandidateLine.BaseLine << " contains Candidate " << *Candidate << "." << endl;
    25892927                  }
    25902928                }
    … …  
    25972935  } else {
    25982936    if (ThirdNode != NULL)
    2599       Log() << Verbose(2) << "Circumcircle for base line " << *BaseLine << " and third node " << *ThirdNode << " is too big!" << endl;
     2937      Log() << Verbose(1) << "Circumcircle for base line " << *CandidateLine.BaseLine << " and third node " << *ThirdNode << " is too big!" << endl;
    26002938    else
    2601       Log() << Verbose(2) << "Circumcircle for base line " << *BaseLine << " is too big!" << endl;
    2602   }
    2603 
    2604   //Log() << Verbose(2) << "INFO: Sorting candidate list ..." << endl;
    2605   if (candidates->size() > 1) {
    2606     candidates->unique();
    2607     candidates->sort(SortCandidates);
    2608   }
    2609 
    2610   Log() << Verbose(1) << "End of FindThirdPointForTesselation" << endl;
     2939      Log() << Verbose(1) << "Circumcircle for base line " << *CandidateLine.BaseLine << " is too big!" << endl;
     2940  }
     2941
     2942  Log() << Verbose(1) << "INFO: Sorting candidate list ..." << endl;
     2943  if (CandidateLine.pointlist.size() > 1) {
     2944    CandidateLine.pointlist.unique();
     2945    CandidateLine.pointlist.sort(); //SortCandidates);
     2946  }
    26112947};
    26122948
    … …  
    26182954class BoundaryPointSet *Tesselation::GetCommonEndpoint(const BoundaryLineSet * line1, const BoundaryLineSet * line2) const
    26192955{
     2956        Info FunctionInfo(__func__);
    26202957  const BoundaryLineSet * lines[2] = { line1, line2 };
    26212958  class BoundaryPointSet *node = NULL;
    … …  
    26312968          { // if insertion fails, we have common endpoint
    26322969            node = OrderTest.first->second;
    2633             Log() << Verbose(5) << "Common endpoint of lines " << *line1
     2970            Log() << Verbose(1) << "Common endpoint of lines " << *line1
    26342971                << " and " << *line2 << " is: " << *node << "." << endl;
    26352972            j = 2;
    … …  
    26482985list<BoundaryTriangleSet*> * Tesselation::FindClosestTrianglesToPoint(const Vector *x, const LinkedCell* LC) const
    26492986{
     2987        Info FunctionInfo(__func__);
    26502988  TesselPoint *trianglePoints[3];
    26512989  TesselPoint *SecondPoint = NULL;
    … …  
    26532991
    26542992  if (LinesOnBoundary.empty()) {
    2655     Log() << Verbose(0) << "Error: There is no tesselation structure to compare the point with, please create one first.";
     2993    eLog() << Verbose(1) << "Error: There is no tesselation structure to compare the point with, please create one first.";
    26562994    return NULL;
    26572995  }
    … …  
    26612999  // check whether closest point is "too close" :), then it's inside
    26623000  if (trianglePoints[0] == NULL) {
    2663     Log() << Verbose(2) << "Is the only point, no one else is closeby." << endl;
     3001    Log() << Verbose(0) << "Is the only point, no one else is closeby." << endl;
    26643002    return NULL;
    26653003  }
    26663004  if (trianglePoints[0]->node->DistanceSquared(x) < MYEPSILON) {
    2667     Log() << Verbose(3) << "Point is right on a tesselation point, no nearest triangle." << endl;
     3005    Log() << Verbose(1) << "Point is right on a tesselation point, no nearest triangle." << endl;
    26683006    PointMap::const_iterator PointRunner = PointsOnBoundary.find(trianglePoints[0]->nr);
    26693007    triangles = new list<BoundaryTriangleSet*>;
    … …  
    26893027    }
    26903028  } else {
    2691     list<TesselPoint*> *connectedClosestPoints = GetCircleOfConnectedPoints(trianglePoints[0], x);
     3029    set<TesselPoint*> *connectedPoints = GetAllConnectedPoints(trianglePoints[0]);
     3030    TesselPointList *connectedClosestPoints = GetCircleOfSetOfPoints(connectedPoints, trianglePoints[0], x);
     3031    delete(connectedPoints);
    26923032    if (connectedClosestPoints != NULL) {
    26933033      trianglePoints[1] = connectedClosestPoints->front();
    … …  
    26973037          eLog() << Verbose(1) << "IsInnerPoint encounters serious error, point " << i << " not found." << endl;
    26983038        }
    2699         //Log() << Verbose(2) << "List of triangle points:" << endl;
    2700         //Log() << Verbose(3) << *trianglePoints[i] << endl;
     3039        //Log() << Verbose(1) << "List of triangle points:" << endl;
     3040        //Log() << Verbose(2) << *trianglePoints[i] << endl;
    27013041      }
    27023042
    27033043      triangles = FindTriangles(trianglePoints);
    2704       Log() << Verbose(2) << "List of possible triangles:" << endl;
     3044      Log() << Verbose(1) << "List of possible triangles:" << endl;
    27053045      for(list<BoundaryTriangleSet*>::iterator Runner = triangles->begin(); Runner != triangles->end(); Runner++)
    2706         Log() << Verbose(3) << **Runner << endl;
     3046        Log() << Verbose(2) << **Runner << endl;
    27073047
    27083048      delete(connectedClosestPoints);
    27093049    } else {
    27103050      triangles = NULL;
    2711       Log() << Verbose(1) << "There is no circle of connected points!" << endl;
     3051      eLog() << Verbose(2) << "There is no circle of connected points!" << endl;
    27123052    }
    27133053  }
    … …  
    27293069class BoundaryTriangleSet * Tesselation::FindClosestTriangleToPoint(const Vector *x, const LinkedCell* LC) const
    27303070{
     3071        Info FunctionInfo(__func__);
    27313072  class BoundaryTriangleSet *result = NULL;
    27323073  list<BoundaryTriangleSet*> *triangles = FindClosestTrianglesToPoint(x, LC);
    … …  
    27383079  if (triangles->size() == 1) { // there is no degenerate case
    27393080    result = triangles->front();
    2740     Log() << Verbose(2) << "Normal Vector of this triangle is " << result->NormalVector << "." << endl;
     3081    Log() << Verbose(1) << "Normal Vector of this triangle is " << result->NormalVector << "." << endl;
    27413082  } else {
    27423083    result = triangles->front();
    27433084    result->GetCenter(&Center);
    27443085    Center.SubtractVector(x);
    2745     Log() << Verbose(2) << "Normal Vector of this front side is " << result->NormalVector << "." << endl;
     3086    Log() << Verbose(1) << "Normal Vector of this front side is " << result->NormalVector << "." << endl;
    27463087    if (Center.ScalarProduct(&result->NormalVector) < 0) {
    27473088      result = triangles->back();
    2748       Log() << Verbose(2) << "Normal Vector of this back side is " << result->NormalVector << "." << endl;
     3089      Log() << Verbose(1) << "Normal Vector of this back side is " << result->NormalVector << "." << endl;
    27493090      if (Center.ScalarProduct(&result->NormalVector) < 0) {
    27503091        eLog() << Verbose(1) << "Front and back side yield NormalVector in wrong direction!" << endl;
    … …  
    27653106bool Tesselation::IsInnerPoint(const Vector &Point, const LinkedCell* const LC) const
    27663107{
     3108        Info FunctionInfo(__func__);
    27673109  class BoundaryTriangleSet *result = FindClosestTriangleToPoint(&Point, LC);
    27683110  Vector Center;
    … …  
    27743116
    27753117  result->GetCenter(&Center);
    2776   Log() << Verbose(3) << "INFO: Central point of the triangle is " << Center << "." << endl;
     3118  Log() << Verbose(2) << "INFO: Central point of the triangle is " << Center << "." << endl;
    27773119  Center.SubtractVector(&Point);
    2778   Log() << Verbose(3) << "INFO: Vector from center to point to test is " << Center << "." << endl;
     3120  Log() << Verbose(2) << "INFO: Vector from center to point to test is " << Center << "." << endl;
    27793121  if (Center.ScalarProduct(&result->NormalVector) > -MYEPSILON) {
    27803122    Log() << Verbose(1) << Point << " is an inner point." << endl;
    … …  
    27953137bool Tesselation::IsInnerPoint(const TesselPoint * const Point, const LinkedCell* const LC) const
    27963138{
     3139        Info FunctionInfo(__func__);
    27973140  return IsInnerPoint(*(Point->node), LC);
    27983141}
    … …  
    28063149set<TesselPoint*> * Tesselation::GetAllConnectedPoints(const TesselPoint* const Point) const
    28073150{
     3151        Info FunctionInfo(__func__);
    28083152  set<TesselPoint*> *connectedPoints = new set<TesselPoint*>;
    28093153  class BoundaryPointSet *ReferencePoint = NULL;
    28103154  TesselPoint* current;
    28113155  bool takePoint = false;
    2812 
    2813   Log() << Verbose(3) << "Begin of GetAllConnectedPoints" << endl;
    28143156
    28153157  // find the respective boundary point
    … …  
    28183160    ReferencePoint = PointRunner->second;
    28193161  } else {
    2820     Log() << Verbose(2) << "GetAllConnectedPoints() could not find the BoundaryPoint belonging to " << *Point << "." << endl;
     3162    eLog() << Verbose(2) << "GetAllConnectedPoints() could not find the BoundaryPoint belonging to " << *Point << "." << endl;
    28213163    ReferencePoint = NULL;
    28223164  }
    … …  
    28423184
    28433185   if (takePoint) {
    2844      Log() << Verbose(5) << "INFO: Endpoint " << *current << " of line " << *(findLines->second) << " is enlisted." << endl;
     3186     Log() << Verbose(1) << "INFO: Endpoint " << *current << " of line " << *(findLines->second) << " is enlisted." << endl;
    28453187     connectedPoints->insert(current);
    28463188   }
    … …  
    28543196  }
    28553197
    2856   Log() << Verbose(3) << "End of GetAllConnectedPoints" << endl;
    28573198  return connectedPoints;
    28583199};
    … …  
    28663207 *
    28673208 * @param *out output stream for debugging
     3209 * @param *SetOfNeighbours all points for which the angle should be calculated
    28683210 * @param *Point of which get all connected points
    28693211 * @param *Reference Reference vector for zero angle or NULL for no preference
    28703212 * @return list of the all points linked to the provided one
    28713213 */
    2872 list<TesselPoint*> * Tesselation::GetCircleOfConnectedPoints(const TesselPoint* const Point, const Vector * const Reference) const
    2873 {
     3214list<TesselPoint*> * Tesselation::GetCircleOfSetOfPoints(set<TesselPoint*> *SetOfNeighbours, const TesselPoint* const Point, const Vector * const Reference) const
     3215{
     3216        Info FunctionInfo(__func__);
    28743217  map<double, TesselPoint*> anglesOfPoints;
    2875   set<TesselPoint*> *connectedPoints = GetAllConnectedPoints(Point);
    28763218  list<TesselPoint*> *connectedCircle = new list<TesselPoint*>;
    28773219  Vector center;
    … …  
    28813223  Vector helper;
    28823224
    2883   if (connectedPoints == NULL) {
    2884     Log() << Verbose(2) << "Could not find any connected points!" << endl;
     3225  if (SetOfNeighbours == NULL) {
     3226    eLog() << Verbose(2) << "Could not find any connected points!" << endl;
    28853227    delete(connectedCircle);
    28863228    return NULL;
    28873229  }
    2888   Log() << Verbose(2) << "Begin of GetCircleOfConnectedPoints" << endl;
    28893230
    28903231  // calculate central point
    2891   for (set<TesselPoint*>::const_iterator TesselRunner = connectedPoints->begin(); TesselRunner != connectedPoints->end(); TesselRunner++)
     3232  for (set<TesselPoint*>::const_iterator TesselRunner = SetOfNeighbours->begin(); TesselRunner != SetOfNeighbours->end(); TesselRunner++)
    28923233    center.AddVector((*TesselRunner)->node);
    28933234  //Log() << Verbose(0) << "Summed vectors " << center << "; number of points " << connectedPoints.size()
    28943235  //  << "; scale factor " << 1.0/connectedPoints.size();
    2895   center.Scale(1.0/connectedPoints->size());
    2896   Log() << Verbose(4) << "INFO: Calculated center of all circle points is " << center << "." << endl;
     3236  center.Scale(1.0/SetOfNeighbours->size());
     3237  Log() << Verbose(1) << "INFO: Calculated center of all circle points is " << center << "." << endl;
    28973238
    28983239  // projection plane of the circle is at the closes Point and normal is pointing away from center of all circle points
    … …  
    29003241  PlaneNormal.SubtractVector(&center);
    29013242  PlaneNormal.Normalize();
    2902   Log() << Verbose(4) << "INFO: Calculated plane normal of circle is " << PlaneNormal << "." << endl;
     3243  Log() << Verbose(1) << "INFO: Calculated plane normal of circle is " << PlaneNormal << "." << endl;
    29033244
    29043245  // construct one orthogonal vector
    … …  
    29093250  }
    29103251  if ((Reference == NULL) || (AngleZero.NormSquared() < MYEPSILON )) {
    2911     Log() << Verbose(4) << "Using alternatively " << *(*connectedPoints->begin())->node << " as angle 0 referencer." << endl;
    2912     AngleZero.CopyVector((*connectedPoints->begin())->node);
     3252    Log() << Verbose(1) << "Using alternatively " << *(*SetOfNeighbours->begin())->node << " as angle 0 referencer." << endl;
     3253    AngleZero.CopyVector((*SetOfNeighbours->begin())->node);
    29133254    AngleZero.SubtractVector(Point->node);
    29143255    AngleZero.ProjectOntoPlane(&PlaneNormal);
    … …  
    29183259    }
    29193260  }
    2920   Log() << Verbose(4) << "INFO: Reference vector on this plane representing angle 0 is " << AngleZero << "." << endl;
     3261  Log() << Verbose(1) << "INFO: Reference vector on this plane representing angle 0 is " << AngleZero << "." << endl;
    29213262  if (AngleZero.NormSquared() > MYEPSILON)
    29223263    OrthogonalVector.MakeNormalVector(&PlaneNormal, &AngleZero);
    29233264  else
    29243265    OrthogonalVector.MakeNormalVector(&PlaneNormal);
    2925   Log() << Verbose(4) << "INFO: OrthogonalVector on plane is " << OrthogonalVector << "." << endl;
     3266  Log() << Verbose(1) << "INFO: OrthogonalVector on plane is " << OrthogonalVector << "." << endl;
    29263267
    29273268  // go through all connected points and calculate angle
    2928   for (set<TesselPoint*>::iterator listRunner = connectedPoints->begin(); listRunner != connectedPoints->end(); listRunner++) {
     3269  for (set<TesselPoint*>::iterator listRunner = SetOfNeighbours->begin(); listRunner != SetOfNeighbours->end(); listRunner++) {
    29293270    helper.CopyVector((*listRunner)->node);
    29303271    helper.SubtractVector(Point->node);
    29313272    helper.ProjectOntoPlane(&PlaneNormal);
    29323273    double angle = GetAngle(helper, AngleZero, OrthogonalVector);
    2933     Log() << Verbose(3) << "INFO: Calculated angle is " << angle << " for point " << **listRunner << "." << endl;
     3274    Log() << Verbose(0) << "INFO: Calculated angle is " << angle << " for point " << **listRunner << "." << endl;
    29343275    anglesOfPoints.insert(pair<double, TesselPoint*>(angle, (*listRunner)));
    29353276  }
    … …  
    29383279    connectedCircle->push_back(AngleRunner->second);
    29393280  }
    2940 
    2941   delete(connectedPoints);
    2942 
    2943   Log() << Verbose(2) << "End of GetCircleOfConnectedPoints" << endl;
    29443281
    29453282  return connectedCircle;
    … …  
    29543291list<list<TesselPoint*> *> * Tesselation::GetPathsOfConnectedPoints(const TesselPoint* const Point) const
    29553292{
     3293        Info FunctionInfo(__func__);
    29563294  map<double, TesselPoint*> anglesOfPoints;
    29573295  list<list<TesselPoint*> *> *ListOfPaths = new list<list<TesselPoint*> *>;
    … …  
    29983336        StartLine = CurrentLine;
    29993337        CurrentPoint = CurrentLine->GetOtherEndpoint(ReferencePoint);
    3000         Log() << Verbose(3)<< "INFO: Beginning path retrieval at " << *CurrentPoint << " of line " << *CurrentLine << "." << endl;
     3338        Log() << Verbose(1)<< "INFO: Beginning path retrieval at " << *CurrentPoint << " of line " << *CurrentLine << "." << endl;
    30013339        do {
    30023340          // push current one
    3003           Log() << Verbose(3) << "INFO: Putting " << *CurrentPoint << " at end of path." << endl;
     3341          Log() << Verbose(1) << "INFO: Putting " << *CurrentPoint << " at end of path." << endl;
    30043342          connectedPath->push_back(CurrentPoint->node);
    30053343
    30063344          // find next triangle
    30073345          for (TriangleMap::iterator Runner = CurrentLine->triangles.begin(); Runner != CurrentLine->triangles.end(); Runner++) {
    3008             Log() << Verbose(3) << "INFO: Inspecting triangle " << *Runner->second << "." << endl;
     3346            Log() << Verbose(1) << "INFO: Inspecting triangle " << *Runner->second << "." << endl;
    30093347            if ((Runner->second != triangle)) { // look for first triangle not equal to old one
    30103348              triangle = Runner->second;
    … …  
    30133351                if (!TriangleRunner->second) {
    30143352                  TriangleRunner->second = true;
    3015                   Log() << Verbose(3) << "INFO: Connecting triangle is " << *triangle << "." << endl;
     3353                  Log() << Verbose(1) << "INFO: Connecting triangle is " << *triangle << "." << endl;
    30163354                  break;
    30173355                } else {
    3018                   Log() << Verbose(3) << "INFO: Skipping " << *triangle << ", as we have already visited it." << endl;
     3356                  Log() << Verbose(1) << "INFO: Skipping " << *triangle << ", as we have already visited it." << endl;
    30193357                  triangle = NULL;
    30203358                }
    … …  
    30313369            if ((triangle->lines[i] != CurrentLine) && (triangle->lines[i]->ContainsBoundaryPoint(ReferencePoint))) { // not the current line and still containing Point
    30323370              CurrentLine = triangle->lines[i];
    3033               Log() << Verbose(3) << "INFO: Connecting line is " << *CurrentLine << "." << endl;
     3371              Log() << Verbose(1) << "INFO: Connecting line is " << *CurrentLine << "." << endl;
    30343372              break;
    30353373            }
    … …  
    30453383        } while (CurrentLine != StartLine);
    30463384        // last point is missing, as it's on start line
    3047         Log() << Verbose(3) << "INFO: Putting " << *CurrentPoint << " at end of path." << endl;
     3385        Log() << Verbose(1) << "INFO: Putting " << *CurrentPoint << " at end of path." << endl;
    30483386        if (StartLine->GetOtherEndpoint(ReferencePoint)->node != connectedPath->back())
    30493387          connectedPath->push_back(StartLine->GetOtherEndpoint(ReferencePoint)->node);
    … …  
    30513389        ListOfPaths->push_back(connectedPath);
    30523390      } else {
    3053         Log() << Verbose(3) << "INFO: Skipping " << *runner->second << ", as we have already visited it." << endl;
     3391        Log() << Verbose(1) << "INFO: Skipping " << *runner->second << ", as we have already visited it." << endl;
    30543392      }
    30553393    }
    … …  
    30693407list<list<TesselPoint*> *> * Tesselation::GetClosedPathsOfConnectedPoints(const TesselPoint* const Point) const
    30703408{
     3409        Info FunctionInfo(__func__);
    30713410  list<list<TesselPoint*> *> *ListofPaths = GetPathsOfConnectedPoints(Point);
    30723411  list<list<TesselPoint*> *> *ListofClosedPaths = new list<list<TesselPoint*> *>;
    … …  
    30823421    connectedPath = *ListRunner;
    30833422
    3084     Log() << Verbose(2) << "INFO: Current path is " << connectedPath << "." << endl;
     3423    Log() << Verbose(1) << "INFO: Current path is " << connectedPath << "." << endl;
    30853424
    30863425    // go through list, look for reappearance of starting Point and count
    … …  
    30923431      if ((*CircleRunner == *CircleStart) && (CircleRunner != CircleStart)) { // is not the very first point
    30933432        // we have a closed circle from Marker to new Marker
    3094         Log() << Verbose(3) << count+1 << ". closed path consists of: ";
     3433        Log() << Verbose(1) << count+1 << ". closed path consists of: ";
    30953434        newPath = new list<TesselPoint*>;
    30963435        list<TesselPoint*>::iterator CircleSprinter = Marker;
    … …  
    31083447    }
    31093448  }
    3110   Log() << Verbose(3) << "INFO: " << count << " closed additional path(s) have been created." << endl;
     3449  Log() << Verbose(1) << "INFO: " << count << " closed additional path(s) have been created." << endl;
    31113450
    31123451  // delete list of paths
    … …  
    31303469set<BoundaryTriangleSet*> *Tesselation::GetAllTriangles(const BoundaryPointSet * const Point) const
    31313470{
     3471        Info FunctionInfo(__func__);
    31323472  set<BoundaryTriangleSet*> *connectedTriangles = new set<BoundaryTriangleSet*>;
    31333473
    … …  
    31683508    return 0.;
    31693509  } else
    3170     Log() << Verbose(2) << "Removing point " << *point << " from tesselated boundary ..." << endl;
     3510    Log() << Verbose(0) << "Removing point " << *point << " from tesselated boundary ..." << endl;
    31713511
    31723512  // copy old location for the volume
    … …  
    31983538  NormalVector.Zero();
    31993539  for (map<class BoundaryTriangleSet *, int>::iterator Runner = Candidates.begin(); Runner != Candidates.end(); Runner++) {
    3200     Log() << Verbose(3) << "INFO: Removing triangle " << *(Runner->first) << "." << endl;
     3540    Log() << Verbose(1) << "INFO: Removing triangle " << *(Runner->first) << "." << endl;
    32013541    NormalVector.SubtractVector(&Runner->first->NormalVector); // has to point inward
    32023542    RemoveTesselationTriangle(Runner->first);
    … …  
    32283568        smallestangle = 0.;
    32293569        for (MiddleNode = connectedPath->begin(); MiddleNode != connectedPath->end(); MiddleNode++) {
    3230           Log() << Verbose(3) << "INFO: MiddleNode is " << **MiddleNode << "." << endl;
     3570          Log() << Verbose(1) << "INFO: MiddleNode is " << **MiddleNode << "." << endl;
    32313571          // construct vectors to next and previous neighbour
    32323572          StartNode = MiddleNode;
    … …  
    32563596        MiddleNode = EndNode;
    32573597        if (MiddleNode == connectedPath->end()) {
    3258           Log() << Verbose(1) << "CRITICAL: Could not find a smallest angle!" << endl;
    3259           exit(255);
     3598          eLog() << Verbose(0) << "CRITICAL: Could not find a smallest angle!" << endl;
     3599          performCriticalExit();
    32603600        }
    32613601        StartNode = MiddleNode;
    … …  
    32663606        if (EndNode == connectedPath->end())
    32673607          EndNode = connectedPath->begin();
    3268         Log() << Verbose(4) << "INFO: StartNode is " << **StartNode << "." << endl;
    3269         Log() << Verbose(4) << "INFO: MiddleNode is " << **MiddleNode << "." << endl;
    3270         Log() << Verbose(4) << "INFO: EndNode is " << **EndNode << "." << endl;
    3271         Log() << Verbose(3) << "INFO: Attempting to create triangle " << (*StartNode)->Name << ", " << (*MiddleNode)->Name << " and " << (*EndNode)->Name << "." << endl;
     3608        Log() << Verbose(2) << "INFO: StartNode is " << **StartNode << "." << endl;
     3609        Log() << Verbose(2) << "INFO: MiddleNode is " << **MiddleNode << "." << endl;
     3610        Log() << Verbose(2) << "INFO: EndNode is " << **EndNode << "." << endl;
     3611        Log() << Verbose(1) << "INFO: Attempting to create triangle " << (*StartNode)->Name << ", " << (*MiddleNode)->Name << " and " << (*EndNode)->Name << "." << endl;
    32723612        TriangleCandidates[0] = *StartNode;
    32733613        TriangleCandidates[1] = *MiddleNode;
    … …  
    32753615        triangle = GetPresentTriangle(TriangleCandidates);
    32763616        if (triangle != NULL) {
    3277           eLog() << Verbose(2) << "New triangle already present, skipping!" << endl;
     3617          eLog() << Verbose(0) << "New triangle already present, skipping!" << endl;
    32783618          StartNode++;
    32793619          MiddleNode++;
    … …  
    32873627          continue;
    32883628        }
    3289         Log() << Verbose(5) << "Adding new triangle points."<< endl;
     3629        Log() << Verbose(3) << "Adding new triangle points."<< endl;
    32903630        AddTesselationPoint(*StartNode, 0);
    32913631        AddTesselationPoint(*MiddleNode, 1);
    32923632        AddTesselationPoint(*EndNode, 2);
    3293         Log() << Verbose(5) << "Adding new triangle lines."<< endl;
     3633        Log() << Verbose(3) << "Adding new triangle lines."<< endl;
    32943634        AddTesselationLine(TPS[0], TPS[1], 0);
    32953635        AddTesselationLine(TPS[0], TPS[2], 1);
    … …  
    33063646        // prepare nodes for next triangle
    33073647        StartNode = EndNode;
    3308         Log() << Verbose(4) << "Removing " << **MiddleNode << " from closed path, remaining points: " << connectedPath->size() << "." << endl;
     3648        Log() << Verbose(2) << "Removing " << **MiddleNode << " from closed path, remaining points: " << connectedPath->size() << "." << endl;
    33093649        connectedPath->remove(*MiddleNode); // remove the middle node (it is surrounded by triangles)
    33103650        if (connectedPath->size() == 2) { // we are done
    … …  
    33133653          break;
    33143654        } else if (connectedPath->size() < 2) { // something's gone wrong!
    3315           Log() << Verbose(1) << "CRITICAL: There are only two endpoints left!" << endl;
    3316           exit(255);
     3655          eLog() << Verbose(0) << "CRITICAL: There are only two endpoints left!" << endl;
     3656          performCriticalExit();
    33173657        } else {
    33183658          MiddleNode = StartNode;
    … …  
    33423682          if (maxgain != 0) {
    33433683            volume += maxgain;
    3344             Log() << Verbose(3) << "Flipping baseline with highest volume" << **Candidate << "." << endl;
     3684            Log() << Verbose(1) << "Flipping baseline with highest volume" << **Candidate << "." << endl;
    33453685            OtherBase = FlipBaseline(*Candidate);
    33463686            NewLines.erase(Candidate);
    … …  
    33533693      delete(connectedPath);
    33543694    }
    3355     Log() << Verbose(1) << count << " triangles were created." << endl;
     3695    Log() << Verbose(0) << count << " triangles were created." << endl;
    33563696  } else {
    33573697    while (!ListOfClosedPaths->empty()) {
    … …  
    33613701      delete(connectedPath);
    33623702    }
    3363     Log() << Verbose(1) << "No need to create any triangles." << endl;
     3703    Log() << Verbose(0) << "No need to create any triangles." << endl;
    33643704  }
    33653705  delete(ListOfClosedPaths);
    33663706
    3367   Log() << Verbose(1) << "Removed volume is " << volume << "." << endl;
     3707  Log() << Verbose(0) << "Removed volume is " << volume << "." << endl;
    33683708
    33693709  return volume;
    … …  
    33823722list<BoundaryTriangleSet*> *Tesselation::FindTriangles(const TesselPoint* const Points[3]) const
    33833723{
     3724        Info FunctionInfo(__func__);
    33843725  list<BoundaryTriangleSet*> *result = new list<BoundaryTriangleSet*>;
    33853726  LineMap::const_iterator FindLine;
    … …  
    34223763}
    34233764
     3765struct BoundaryLineSetCompare {
     3766  bool operator() (const BoundaryLineSet * const a, const BoundaryLineSet * const b) {
     3767    int lowerNra = -1;
     3768    int lowerNrb = -1;
     3769
     3770    if (a->endpoints[0] < a->endpoints[1])
     3771      lowerNra = 0;
     3772    else
     3773      lowerNra = 1;
     3774
     3775    if (b->endpoints[0] < b->endpoints[1])
     3776      lowerNrb = 0;
     3777    else
     3778      lowerNrb = 1;
     3779
     3780    if (a->endpoints[lowerNra] < b->endpoints[lowerNrb])
     3781      return true;
     3782    else if (a->endpoints[lowerNra] > b->endpoints[lowerNrb])
     3783      return false;
     3784    else {  // both lower-numbered endpoints are the same ...
     3785     if (a->endpoints[(lowerNra+1)%2] < b->endpoints[(lowerNrb+1)%2])
     3786       return true;
     3787     else if (a->endpoints[(lowerNra+1)%2] > b->endpoints[(lowerNrb+1)%2])
     3788       return false;
     3789    }
     3790    return false;
     3791  };
     3792};
     3793
     3794#define UniqueLines set < class BoundaryLineSet *, BoundaryLineSetCompare>
     3795
    34243796/**
    34253797 * Finds all degenerated lines within the tesselation structure.
    … …  
    34303802map<int, int> * Tesselation::FindAllDegeneratedLines()
    34313803{
    3432   map<int, class BoundaryLineSet *> AllLines;
     3804        Info FunctionInfo(__func__);
     3805        UniqueLines AllLines;
    34333806  map<int, int> * DegeneratedLines = new map<int, int>;
    34343807
    34353808  // sanity check
    34363809  if (LinesOnBoundary.empty()) {
    3437     Log() << Verbose(1) << "Warning: FindAllDegeneratedTriangles() was called without any tesselation structure.";
     3810    eLog() << Verbose(2) << "FindAllDegeneratedTriangles() was called without any tesselation structure.";
    34383811    return DegeneratedLines;
    34393812  }
    34403813
    34413814  LineMap::iterator LineRunner1;
    3442   pair<LineMap::iterator, bool> tester;
     3815  pair< UniqueLines::iterator, bool> tester;
    34433816  for (LineRunner1 = LinesOnBoundary.begin(); LineRunner1 != LinesOnBoundary.end(); ++LineRunner1) {
    3444     tester = AllLines.insert( pair<int,BoundaryLineSet *> (LineRunner1->second->endpoints[0]->Nr, LineRunner1->second) );
    3445     if ((!tester.second) && (tester.first->second->endpoints[1]->Nr == LineRunner1->second->endpoints[1]->Nr)) { // found degenerated line
    3446       DegeneratedLines->insert ( pair<int, int> (LineRunner1->second->Nr, tester.first->second->Nr) );
    3447       DegeneratedLines->insert ( pair<int, int> (tester.first->second->Nr, LineRunner1->second->Nr) );
     3817    tester = AllLines.insert( LineRunner1->second );
     3818    if (!tester.second) { // found degenerated line
     3819      DegeneratedLines->insert ( pair<int, int> (LineRunner1->second->Nr, (*tester.first)->Nr) );
     3820      DegeneratedLines->insert ( pair<int, int> ((*tester.first)->Nr, LineRunner1->second->Nr) );
    34483821    }
    34493822  }
    … …  
    34513824  AllLines.clear();
    34523825
    3453   Log() << Verbose(1) << "FindAllDegeneratedLines() found " << DegeneratedLines->size() << " lines." << endl;
     3826  Log() << Verbose(0) << "FindAllDegeneratedLines() found " << DegeneratedLines->size() << " lines." << endl;
    34543827  map<int,int>::iterator it;
    3455   for (it = DegeneratedLines->begin(); it != DegeneratedLines->end(); it++)
    3456       Log() << Verbose(2) << (*it).first << " => " << (*it).second << endl;
     3828  for (it = DegeneratedLines->begin(); it != DegeneratedLines->end(); it++) {
     3829    const LineMap::const_iterator Line1 = LinesOnBoundary.find((*it).first);
     3830    const LineMap::const_iterator Line2 = LinesOnBoundary.find((*it).second);
     3831    if (Line1 != LinesOnBoundary.end() && Line2 != LinesOnBoundary.end())
     3832      Log() << Verbose(0) << *Line1->second << " => " << *Line2->second << endl;
     3833    else
     3834      eLog() << Verbose(1) << "Either " << (*it).first << " or " << (*it).second << " are not in LinesOnBoundary!" << endl;
     3835  }
    34573836
    34583837  return DegeneratedLines;
    … …  
    34673846map<int, int> * Tesselation::FindAllDegeneratedTriangles()
    34683847{
     3848        Info FunctionInfo(__func__);
    34693849  map<int, int> * DegeneratedLines = FindAllDegeneratedLines();
    34703850  map<int, int> * DegeneratedTriangles = new map<int, int>;
    … …  
    34943874  delete(DegeneratedLines);
    34953875
    3496   Log() << Verbose(1) << "FindAllDegeneratedTriangles() found " << DegeneratedTriangles->size() << " triangles:" << endl;
     3876  Log() << Verbose(0) << "FindAllDegeneratedTriangles() found " << DegeneratedTriangles->size() << " triangles:" << endl;
    34973877  map<int,int>::iterator it;
    34983878  for (it = DegeneratedTriangles->begin(); it != DegeneratedTriangles->end(); it++)
    3499       Log() << Verbose(2) << (*it).first << " => " << (*it).second << endl;
     3879      Log() << Verbose(0) << (*it).first << " => " << (*it).second << endl;
    35003880
    35013881  return DegeneratedTriangles;
    … …  
    35083888void Tesselation::RemoveDegeneratedTriangles()
    35093889{
     3890        Info FunctionInfo(__func__);
    35103891  map<int, int> * DegeneratedTriangles = FindAllDegeneratedTriangles();
    35113892  TriangleMap::iterator finder;
    35123893  BoundaryTriangleSet *triangle = NULL, *partnerTriangle = NULL;
    35133894  int count  = 0;
    3514 
    3515   Log() << Verbose(1) << "Begin of RemoveDegeneratedTriangles" << endl;
    35163895
    35173896  for (map<int, int>::iterator TriangleKeyRunner = DegeneratedTriangles->begin();
    … …  
    35723951      // erase the pair
    35733952      count += (int) DegeneratedTriangles->erase(triangle->Nr);
    3574       Log() << Verbose(1) << "RemoveDegeneratedTriangles() removes triangle " << *triangle << "." << endl;
     3953      Log() << Verbose(0) << "RemoveDegeneratedTriangles() removes triangle " << *triangle << "." << endl;
    35753954      RemoveTesselationTriangle(triangle);
    35763955      count += (int) DegeneratedTriangles->erase(partnerTriangle->Nr);
    3577       Log() << Verbose(1) << "RemoveDegeneratedTriangles() removes triangle " << *partnerTriangle << "." << endl;
     3956      Log() << Verbose(0) << "RemoveDegeneratedTriangles() removes triangle " << *partnerTriangle << "." << endl;
    35783957      RemoveTesselationTriangle(partnerTriangle);
    35793958    } else {
    3580       Log() << Verbose(1) << "RemoveDegeneratedTriangles() does not remove triangle " << *triangle
     3959      Log() << Verbose(0) << "RemoveDegeneratedTriangles() does not remove triangle " << *triangle
    35813960        << " and its partner " << *partnerTriangle << " because it is essential for at"
    35823961        << " least one of the endpoints to be kept in the tesselation structure." << endl;
    … …  
    35843963  }
    35853964  delete(DegeneratedTriangles);
    3586 
    3587   Log() << Verbose(1) << "RemoveDegeneratedTriangles() removed " << count << " triangles:" << endl;
    3588   Log() << Verbose(1) << "End of RemoveDegeneratedTriangles" << endl;
     3965  if (count > 0)
     3966    LastTriangle = NULL;
     3967
     3968  Log() << Verbose(0) << "RemoveDegeneratedTriangles() removed " << count << " triangles:" << endl;
    35893969}
    35903970
    … …  
    35993979void Tesselation::AddBoundaryPointByDegeneratedTriangle(class TesselPoint *point, LinkedCell *LC)
    36003980{
    3601   Log() << Verbose(2) << "Begin of AddBoundaryPointByDegeneratedTriangle" << endl;
    3602 
     3981        Info FunctionInfo(__func__);
    36033982  // find nearest boundary point
    36043983  class TesselPoint *BackupPoint = NULL;
    … …  
    36163995    return;
    36173996  }
    3618   Log() << Verbose(2) << "Nearest point on boundary is " << NearestPoint->Name << "." << endl;
     3997  Log() << Verbose(0) << "Nearest point on boundary is " << NearestPoint->Name << "." << endl;
    36193998
    36203999  // go through its lines and find the best one to split
    … …  
    36494028
    36504029  // create new triangle to connect point (connects automatically with the missing spot of the chosen line)
    3651   Log() << Verbose(5) << "Adding new triangle points."<< endl;
     4030  Log() << Verbose(2) << "Adding new triangle points."<< endl;
    36524031  AddTesselationPoint((BestLine->endpoints[0]->node), 0);
    36534032  AddTesselationPoint((BestLine->endpoints[1]->node), 1);
    36544033  AddTesselationPoint(point, 2);
    3655   Log() << Verbose(5) << "Adding new triangle lines."<< endl;
     4034  Log() << Verbose(2) << "Adding new triangle lines."<< endl;
    36564035  AddTesselationLine(TPS[0], TPS[1], 0);
    36574036  AddTesselationLine(TPS[0], TPS[2], 1);
    … …  
    36604039  BTS->GetNormalVector(TempTriangle->NormalVector);
    36614040  BTS->NormalVector.Scale(-1.);
    3662   Log() << Verbose(3) << "INFO: NormalVector of new triangle is " << BTS->NormalVector << "." << endl;
     4041  Log() << Verbose(1) << "INFO: NormalVector of new triangle is " << BTS->NormalVector << "." << endl;
    36634042  AddTesselationTriangle();
    36644043
    36654044  // create other side of this triangle and close both new sides of the first created triangle
    3666   Log() << Verbose(5) << "Adding new triangle points."<< endl;
     4045  Log() << Verbose(2) << "Adding new triangle points."<< endl;
    36674046  AddTesselationPoint((BestLine->endpoints[0]->node), 0);
    36684047  AddTesselationPoint((BestLine->endpoints[1]->node), 1);
    36694048  AddTesselationPoint(point, 2);
    3670   Log() << Verbose(5) << "Adding new triangle lines."<< endl;
     4049  Log() << Verbose(2) << "Adding new triangle lines."<< endl;
    36714050  AddTesselationLine(TPS[0], TPS[1], 0);
    36724051  AddTesselationLine(TPS[0], TPS[2], 1);
    … …  
    36744053  BTS = new class BoundaryTriangleSet(BLS, TrianglesOnBoundaryCount);
    36754054  BTS->GetNormalVector(TempTriangle->NormalVector);
    3676   Log() << Verbose(3) << "INFO: NormalVector of other new triangle is " << BTS->NormalVector << "." << endl;
     4055  Log() << Verbose(1) << "INFO: NormalVector of other new triangle is " << BTS->NormalVector << "." << endl;
    36774056  AddTesselationTriangle();
    36784057
    … …  
    36814060    if ((BTS->lines[i]->ContainsBoundaryPoint(BestLine->endpoints[0])) && (BTS->lines[i]->ContainsBoundaryPoint(BestLine->endpoints[1]))) {
    36824061      if (BestLine == BTS->lines[i]){
    3683         Log() << Verbose(1) << "CRITICAL: BestLine is same as found line, something's wrong here!" << endl;
    3684         exit(255);
     4062        eLog() << Verbose(0) << "BestLine is same as found line, something's wrong here!" << endl;
     4063        performCriticalExit();
    36854064      }
    36864065      BTS->lines[i]->triangles.insert( pair<int, class BoundaryTriangleSet *> (TempTriangle->Nr, TempTriangle) );
    … …  
    36894068    }
    36904069  }
    3691 
    3692   // exit
    3693   Log() << Verbose(2) << "End of AddBoundaryPointByDegeneratedTriangle" << endl;
    36944070};
    36954071
    … …  
    37014077void Tesselation::Output(const char *filename, const PointCloud * const cloud)
    37024078{
     4079        Info FunctionInfo(__func__);
    37034080  ofstream *tempstream = NULL;
    37044081  string NameofTempFile;
    … …  
    37134090      NameofTempFile.erase(npos, 1);
    37144091      NameofTempFile.append(TecplotSuffix);
    3715       Log() << Verbose(1) << "Writing temporary non convex hull to file " << NameofTempFile << ".\n";
     4092      Log() << Verbose(0) << "Writing temporary non convex hull to file " << NameofTempFile << ".\n";
    37164093      tempstream = new ofstream(NameofTempFile.c_str(), ios::trunc);
    37174094      WriteTecplotFile(tempstream, this, cloud, TriangleFilesWritten);
    … …  
    37274104      NameofTempFile.erase(npos, 1);
    37284105      NameofTempFile.append(Raster3DSuffix);
    3729       Log() << Verbose(1) << "Writing temporary non convex hull to file " << NameofTempFile << ".\n";
     4106      Log() << Verbose(0) << "Writing temporary non convex hull to file " << NameofTempFile << ".\n";
    37304107      tempstream = new ofstream(NameofTempFile.c_str(), ios::trunc);
    37314108      WriteRaster3dFile(tempstream, this, cloud);
    … …  
    37394116    TriangleFilesWritten++;
    37404117};
     4118
     4119struct BoundaryPolygonSetCompare {
     4120  bool operator()(const BoundaryPolygonSet * s1, const BoundaryPolygonSet * s2) const {
     4121    if (s1->endpoints.size() < s2->endpoints.size())
     4122      return true;
     4123    else if (s1->endpoints.size() > s2->endpoints.size())
     4124      return false;
     4125    else { // equality of number of endpoints
     4126      PointSet::const_iterator Walker1 = s1->endpoints.begin();
     4127      PointSet::const_iterator Walker2 = s2->endpoints.begin();
     4128      while ((Walker1 != s1->endpoints.end()) || (Walker2 != s2->endpoints.end())) {
     4129        if ((*Walker1)->Nr < (*Walker2)->Nr)
     4130          return true;
     4131        else if ((*Walker1)->Nr > (*Walker2)->Nr)
     4132          return false;
     4133        Walker1++;
     4134        Walker2++;
     4135      }
     4136      return false;
     4137    }
     4138  }
     4139};
     4140
     4141#define UniquePolygonSet set < BoundaryPolygonSet *, BoundaryPolygonSetCompare>
     4142
     4143/** Finds all degenerated polygons and calls ReTesselateDegeneratedPolygon()/
     4144 * \return number of polygons found
     4145 */
     4146int Tesselation::CorrectAllDegeneratedPolygons()
     4147{
     4148  Info FunctionInfo(__func__);
     4149
     4150  /// 2. Go through all BoundaryPointSet's, check their triangles' NormalVector
     4151  map <int, int> *DegeneratedTriangles = FindAllDegeneratedTriangles();
     4152  set < BoundaryPointSet *> EndpointCandidateList;
     4153  pair < set < BoundaryPointSet *>::iterator, bool > InsertionTester;
     4154  pair < map < int, Vector *>::iterator, bool > TriangleInsertionTester;
     4155  for (PointMap::const_iterator Runner = PointsOnBoundary.begin(); Runner != PointsOnBoundary.end(); Runner++) {
     4156    Log() << Verbose(0) << "Current point is " << *Runner->second << "." << endl;
     4157    map < int, Vector *> TriangleVectors;
     4158    // gather all NormalVectors
     4159    Log() << Verbose(1) << "Gathering triangles ..." << endl;
     4160    for (LineMap::const_iterator LineRunner = (Runner->second)->lines.begin(); LineRunner != (Runner->second)->lines.end(); LineRunner++)
     4161      for (TriangleMap::const_iterator TriangleRunner = (LineRunner->second)->triangles.begin(); TriangleRunner != (LineRunner->second)->triangles.end(); TriangleRunner++) {
     4162        if (DegeneratedTriangles->find(TriangleRunner->second->Nr) == DegeneratedTriangles->end()) {
     4163          TriangleInsertionTester = TriangleVectors.insert( pair< int, Vector *> ((TriangleRunner->second)->Nr, &((TriangleRunner->second)->NormalVector)) );
     4164          if (TriangleInsertionTester.second)
     4165            Log() << Verbose(1) << " Adding triangle " << *(TriangleRunner->second) << " to triangles to check-list." << endl;
     4166        } else {
     4167          Log() << Verbose(1) << " NOT adding triangle " << *(TriangleRunner->second) << " as it's a simply degenerated one." << endl;
     4168        }
     4169      }
     4170    // check whether there are two that are parallel
     4171    Log() << Verbose(1) << "Finding two parallel triangles ..." << endl;
     4172    for (map < int, Vector *>::iterator VectorWalker = TriangleVectors.begin(); VectorWalker != TriangleVectors.end(); VectorWalker++)
     4173      for (map < int, Vector *>::iterator VectorRunner = VectorWalker; VectorRunner != TriangleVectors.end(); VectorRunner++)
     4174        if (VectorWalker != VectorRunner) { // skip equals
     4175          const double SCP = VectorWalker->second->ScalarProduct(VectorRunner->second);  // ScalarProduct should result in -1. for degenerated triangles
     4176          Log() << Verbose(1) << "Checking " << *VectorWalker->second<< " against " << *VectorRunner->second << ": " << SCP << endl;
     4177          if (fabs(SCP + 1.) < ParallelEpsilon) {
     4178            InsertionTester = EndpointCandidateList.insert((Runner->second));
     4179            if (InsertionTester.second)
     4180              Log() << Verbose(0) << " Adding " << *Runner->second << " to endpoint candidate list." << endl;
     4181            // and break out of both loops
     4182            VectorWalker = TriangleVectors.end();
     4183            VectorRunner = TriangleVectors.end();
     4184            break;
     4185          }
     4186        }
     4187  }
     4188
     4189  /// 3. Find connected endpoint candidates and put them into a polygon
     4190  UniquePolygonSet ListofDegeneratedPolygons;
     4191  BoundaryPointSet *Walker = NULL;
     4192  BoundaryPointSet *OtherWalker = NULL;
     4193  BoundaryPolygonSet *Current = NULL;
     4194  stack <BoundaryPointSet*> ToCheckConnecteds;
     4195  while (!EndpointCandidateList.empty()) {
     4196    Walker = *(EndpointCandidateList.begin());
     4197    if (Current == NULL) {  // create a new polygon with current candidate
     4198      Log() << Verbose(0) << "Starting new polygon set at point " << *Walker << endl;
     4199      Current = new BoundaryPolygonSet;
     4200      Current->endpoints.insert(Walker);
     4201      EndpointCandidateList.erase(Walker);
     4202      ToCheckConnecteds.push(Walker);
     4203    }
     4204
     4205    // go through to-check stack
     4206    while (!ToCheckConnecteds.empty()) {
     4207      Walker = ToCheckConnecteds.top(); // fetch ...
     4208      ToCheckConnecteds.pop(); // ... and remove
     4209      for (LineMap::const_iterator LineWalker = Walker->lines.begin(); LineWalker != Walker->lines.end(); LineWalker++) {
     4210        OtherWalker = (LineWalker->second)->GetOtherEndpoint(Walker);
     4211        Log() << Verbose(1) << "Checking " << *OtherWalker << endl;
     4212        set < BoundaryPointSet *>::iterator Finder = EndpointCandidateList.find(OtherWalker);
     4213        if (Finder != EndpointCandidateList.end()) {  // found a connected partner
     4214          Log() << Verbose(1) << " Adding to polygon." << endl;
     4215          Current->endpoints.insert(OtherWalker);
     4216          EndpointCandidateList.erase(Finder);  // remove from candidates
     4217          ToCheckConnecteds.push(OtherWalker);  // but check its partners too
     4218        } else {
     4219          Log() << Verbose(1) << " is not connected to " << *Walker << endl;
     4220        }
     4221      }
     4222    }
     4223
     4224    Log() << Verbose(0) << "Final polygon is " << *Current << endl;
     4225    ListofDegeneratedPolygons.insert(Current);
     4226    Current = NULL;
     4227  }
     4228
     4229  const int counter = ListofDegeneratedPolygons.size();
     4230
     4231  Log() << Verbose(0) << "The following " << counter << " degenerated polygons have been found: " << endl;
     4232  for (UniquePolygonSet::iterator PolygonRunner = ListofDegeneratedPolygons.begin(); PolygonRunner != ListofDegeneratedPolygons.end(); PolygonRunner++)
     4233    Log() << Verbose(0) << " " << **PolygonRunner << endl;
     4234
     4235  /// 4. Go through all these degenerated polygons
     4236  for (UniquePolygonSet::iterator PolygonRunner = ListofDegeneratedPolygons.begin(); PolygonRunner != ListofDegeneratedPolygons.end(); PolygonRunner++) {
     4237    stack <int> TriangleNrs;
     4238    Vector NormalVector;
     4239    /// 4a. Gather all triangles of this polygon
     4240    TriangleSet *T = (*PolygonRunner)->GetAllContainedTrianglesFromEndpoints();
     4241
     4242    // check whether number is bigger than 2, otherwise it's just a simply degenerated one and nothing to do.
     4243    if (T->size() == 2) {
     4244      Log() << Verbose(1) << " Skipping degenerated polygon, is just a (already simply degenerated) triangle." << endl;
     4245      delete(T);
     4246      continue;
     4247    }
     4248
     4249    // check whether number is even
     4250    // If this case occurs, we have to think about it!
     4251    // The Problem is probably due to two degenerated polygons being connected by a bridging, non-degenerated polygon, as somehow one node has
     4252    // connections to either polygon ...
     4253    if (T->size() % 2 != 0) {
     4254      eLog() << Verbose(0) << " degenerated polygon contains an odd number of triangles, probably contains bridging non-degenerated ones, too!" << endl;
     4255      performCriticalExit();
     4256    }
     4257
     4258    TriangleSet::iterator TriangleWalker = T->begin();  // is the inner iterator
     4259    /// 4a. Get NormalVector for one side (this is "front")
     4260    NormalVector.CopyVector(&(*TriangleWalker)->NormalVector);
     4261    Log() << Verbose(1) << "\"front\" defining triangle is " << **TriangleWalker << " and Normal vector of \"front\" side is " << NormalVector << endl;
     4262    TriangleWalker++;
     4263    TriangleSet::iterator TriangleSprinter = TriangleWalker; // is the inner advanced iterator
     4264    /// 4b. Remove all triangles whose NormalVector is in opposite direction (i.e. "back")
     4265    BoundaryTriangleSet *triangle = NULL;
     4266    while (TriangleSprinter != T->end()) {
     4267      TriangleWalker = TriangleSprinter;
     4268      triangle = *TriangleWalker;
     4269      TriangleSprinter++;
     4270      Log() << Verbose(1) << "Current triangle to test for removal: " << *triangle << endl;
     4271      if (triangle->NormalVector.ScalarProduct(&NormalVector) < 0) { // if from other side, then delete and remove from list
     4272        Log() << Verbose(1) << " Removing ... " << endl;
     4273        TriangleNrs.push(triangle->Nr);
     4274        T->erase(TriangleWalker);
     4275        RemoveTesselationTriangle(triangle);
     4276      } else
     4277        Log() << Verbose(1) << " Keeping ... " << endl;
     4278    }
     4279    /// 4c. Copy all "front" triangles but with inverse NormalVector
     4280    TriangleWalker = T->begin();
     4281    while (TriangleWalker != T->end()) {  // go through all front triangles
     4282      Log() << Verbose(1) << " Re-creating triangle " << **TriangleWalker << " with NormalVector " << (*TriangleWalker)->NormalVector << endl;
     4283      for (int i = 0; i < 3; i++)
     4284        AddTesselationPoint((*TriangleWalker)->endpoints[i]->node, i);
     4285      AddTesselationLine(TPS[0], TPS[1], 0);
     4286      AddTesselationLine(TPS[0], TPS[2], 1);
     4287      AddTesselationLine(TPS[1], TPS[2], 2);
     4288      if (TriangleNrs.empty())
     4289        eLog() << Verbose(0) << "No more free triangle numbers!" << endl;
     4290      BTS = new BoundaryTriangleSet(BLS, TriangleNrs.top()); // copy triangle ...
     4291      AddTesselationTriangle(); // ... and add
     4292      TriangleNrs.pop();
     4293      BTS->NormalVector.CopyVector(&(*TriangleWalker)->NormalVector);
     4294      BTS->NormalVector.Scale(-1.);
     4295      TriangleWalker++;
     4296    }
     4297    if (!TriangleNrs.empty()) {
     4298      eLog() << Verbose(0) << "There have been less triangles created than removed!" << endl;
     4299    }
     4300    delete(T);  // remove the triangleset
     4301  }
     4302
     4303  map<int, int> * SimplyDegeneratedTriangles = FindAllDegeneratedTriangles();
     4304  Log() << Verbose(0) << "Final list of simply degenerated triangles found, containing " << SimplyDegeneratedTriangles->size() << " triangles:" << endl;
     4305  map<int,int>::iterator it;
     4306  for (it = SimplyDegeneratedTriangles->begin(); it != SimplyDegeneratedTriangles->end(); it++)
     4307      Log() << Verbose(0) << (*it).first << " => " << (*it).second << endl;
     4308  delete(SimplyDegeneratedTriangles);
     4309
     4310  /// 5. exit
     4311  UniquePolygonSet::iterator PolygonRunner;
     4312  while (!ListofDegeneratedPolygons.empty()) {
     4313    PolygonRunner = ListofDegeneratedPolygons.begin();
     4314    delete(*PolygonRunner);
     4315    ListofDegeneratedPolygons.erase(PolygonRunner);
     4316  }
     4317
     4318  return counter;
     4319};

  • src/tesselation.hpp

    r8927ae r1ca488  
    2323#include <list>
    2424#include <set>
     25#include <stack>
    2526
    2627#include "atom_particleinfo.hpp"
    … …  
    4748#define VRMLSUffix ".wrl"
    4849
     50#define ParallelEpsilon 1e-3
     51
    4952// ======================================================= some template functions =========================================
    5053
    5154#define PointMap map < int, class BoundaryPointSet * >
     55#define PointSet set < class BoundaryPointSet * >
     56#define PointList list < class BoundaryPointSet * >
    5257#define PointPair pair < int, class BoundaryPointSet * >
    5358#define PointTestPair pair < PointMap::iterator, bool >
     59
    5460#define CandidateList list <class CandidateForTesselation *>
     61#define CandidateMap map <class BoundaryLineSet *, class CandidateForTesselation *>
    5562
    5663#define LineMap multimap < int, class BoundaryLineSet * >
     64#define LineSet set < class BoundaryLineSet * >
     65#define LineList list < class BoundaryLineSet * >
    5766#define LinePair pair < int, class BoundaryLineSet * >
    5867#define LineTestPair pair < LineMap::iterator, bool >
    5968
    6069#define TriangleMap map < int, class BoundaryTriangleSet * >
     70#define TriangleSet set < class BoundaryTriangleSet * >
     71#define TriangleList list < class BoundaryTriangleSet * >
    6172#define TrianglePair pair < int, class BoundaryTriangleSet * >
    6273#define TriangleTestPair pair < TrianglePair::iterator, bool >
    6374
     75#define PolygonMap map < int, class BoundaryPolygonSet * >
     76#define PolygonSet set < class BoundaryPolygonSet * >
     77#define PolygonList list < class BoundaryPolygonSet * >
     78
    6479#define DistanceMultiMap multimap <double, pair < PointMap::iterator, PointMap::iterator> >
    6580#define DistanceMultiMapPair pair <double, pair < PointMap::iterator, PointMap::iterator> >
     81
     82#define TesselPointList list <TesselPoint *>
     83#define TesselPointSet set <TesselPoint *>
    6684
    6785/********************************************** declarations *******************************/
    … …  
    114132    TriangleMap triangles;
    115133    int Nr;
     134    bool skipped;
    116135};
    117136
    … …  
    139158    class BoundaryLineSet *lines[3];
    140159    Vector NormalVector;
     160    Vector SphereCenter;
    141161    int Nr;
    142162};
    143163
    144164ostream & operator << (ostream &ost, const BoundaryTriangleSet &a);
     165
     166
     167// ======================================================== class BoundaryTriangleSet =======================================
     168
     169/** Set of BoundaryPointSet.
     170 * This is just meant as a container for a group of endpoints, extending the node, line, triangle concept. However, this has
     171 * only marginally something to do with the tesselation. Hence, there is no incorporation into the bookkeeping of the Tesselation
     172 * class (i.e. no allocation, no deletion).
     173 * \note we assume that the set of endpoints reside (more or less) on a plane.
     174 */
     175class BoundaryPolygonSet {
     176  public:
     177    BoundaryPolygonSet();
     178    ~BoundaryPolygonSet();
     179
     180    Vector * GetNormalVector(const Vector &NormalVector) const;
     181    void GetCenter(Vector *center) const;
     182    bool ContainsBoundaryLine(const BoundaryLineSet * const line) const;
     183    bool ContainsBoundaryPoint(const BoundaryPointSet * const point) const;
     184    bool ContainsBoundaryPoint(const TesselPoint * const point) const;
     185    bool ContainsBoundaryTriangle(const BoundaryTriangleSet * const point) const;
     186    bool ContainsPresentTupel(const BoundaryPointSet * const * Points, const int dim) const;
     187    bool ContainsPresentTupel(const BoundaryPolygonSet * const P) const;
     188    bool ContainsPresentTupel(const PointSet &endpoints) const;
     189    TriangleSet * GetAllContainedTrianglesFromEndpoints() const;
     190    bool FillPolygonFromTrianglesOfLine(const BoundaryLineSet * const line);
     191
     192    PointSet endpoints;
     193    int Nr;
     194};
     195
     196ostream & operator << (ostream &ost, const BoundaryPolygonSet &a);
    145197
    146198// =========================================================== class TESSELPOINT ===========================================
    … …  
    170222  virtual ~PointCloud();
    171223
     224  virtual const char * const GetName() const { return "unknown"; };
    172225  virtual Vector *GetCenter() const { return NULL; };
    173226  virtual TesselPoint *GetPoint() const { return NULL; };
    … …  
    177230  virtual void GoToFirst() const {};
    178231  virtual void GoToLast() const {};
    179   virtual bool IsEmpty() const { return false; };
    180   virtual bool IsEnd() const { return false; };
     232  virtual bool IsEmpty() const { return true; };
     233  virtual bool IsEnd() const { return true; };
    181234};
    182235
    … …  
    185238class CandidateForTesselation {
    186239  public :
     240  CandidateForTesselation(BoundaryLineSet* currentBaseLine);
    187241  CandidateForTesselation(TesselPoint* candidate, BoundaryLineSet* currentBaseLine, Vector OptCandidateCenter, Vector OtherOptCandidateCenter);
    188242  ~CandidateForTesselation();
    189243
    190   TesselPoint *point;
     244  TesselPointList pointlist;
    191245  BoundaryLineSet *BaseLine;
    192246  Vector OptCenter;
    193247  Vector OtherOptCenter;
    194 };
     248  double ShortestAngle;
     249  double OtherShortestAngle;
     250};
     251
     252ostream & operator <<(ostream &ost, const  CandidateForTesselation &a);
    195253
    196254// =========================================================== class TESSELATION ===========================================
    … …  
    210268    void AddTesselationTriangle();
    211269    void AddTesselationTriangle(const int nr);
     270    void AddCandidateTriangle(CandidateForTesselation CandidateLine);
    212271    void RemoveTesselationTriangle(class BoundaryTriangleSet *triangle);
    213272    void RemoveTesselationLine(class BoundaryLineSet *line);
    … …  
    218277    void FindStartingTriangle(const double RADIUS, const LinkedCell *LC);
    219278    void FindSecondPointForTesselation(class TesselPoint* a, Vector Oben, class TesselPoint*& OptCandidate, double Storage[3], double RADIUS, const LinkedCell *LC);
    220     void FindThirdPointForTesselation(Vector &NormalVector, Vector &SearchDirection, Vector &OldSphereCenter, class BoundaryLineSet *BaseLine, const class TesselPoint * const ThirdNode, CandidateList* &candidates, double *ShortestAngle, const double RADIUS, const LinkedCell *LC) const;
    221     bool FindNextSuitableTriangle(BoundaryLineSet &Line, BoundaryTriangleSet &T, const double& RADIUS, const LinkedCell *LC);
     279    void FindThirdPointForTesselation(Vector &NormalVector, Vector &SearchDirection, Vector &OldSphereCenter, CandidateForTesselation &CandidateLine, const class TesselPoint  * const ThirdNode, const double RADIUS, const LinkedCell *LC) const;
     280    bool FindNextSuitableTriangle(CandidateForTesselation &CandidateLine, BoundaryTriangleSet &T, const double& RADIUS, const LinkedCell *LC);
    222281    int CheckPresenceOfTriangle(class TesselPoint *Candidates[3]) const;
    223282    class BoundaryTriangleSet * GetPresentTriangle(TesselPoint *Candidates[3]);
    … …  
    235294    void RemoveDegeneratedTriangles();
    236295    void AddBoundaryPointByDegeneratedTriangle(class TesselPoint *point, LinkedCell *LC);
     296    int CorrectAllDegeneratedPolygons();
    237297
    238298    set<TesselPoint*> * GetAllConnectedPoints(const TesselPoint* const Point) const;
    … …  
    240300    list<list<TesselPoint*> *> * GetPathsOfConnectedPoints(const TesselPoint* const Point) const;
    241301    list<list<TesselPoint*> *> * GetClosedPathsOfConnectedPoints(const TesselPoint* const Point) const;
    242     list<TesselPoint*> * GetCircleOfConnectedPoints(const TesselPoint* const Point, const Vector * const Reference = NULL) const;
     302    list<TesselPoint*> * GetCircleOfSetOfPoints(set<TesselPoint*> *SetOfNeighbours, const TesselPoint* const Point, const Vector * const Reference = NULL) const;
    243303    class BoundaryPointSet *GetCommonEndpoint(const BoundaryLineSet * line1, const BoundaryLineSet * line2) const;
    244304    list<BoundaryTriangleSet*> *FindTriangles(const TesselPoint* const Points[3]) const;
    … …  
    259319    PointMap PointsOnBoundary;
    260320    LineMap LinesOnBoundary;
     321    CandidateMap OpenLines;
    261322    TriangleMap TrianglesOnBoundary;
    262323    int PointsOnBoundaryCount;
    … …  
    286347    mutable PointMap::const_iterator InternalPointer;
    287348
    288     bool HasOtherBaselineBetterCandidate(const BoundaryLineSet * const BaseRay, const TesselPoint * const OptCandidate, double ShortestAngle, double RADIUS, const LinkedCell * const LC) const;
     349    //bool HasOtherBaselineBetterCandidate(const BoundaryLineSet * const BaseRay, const TesselPoint * const OptCandidate, double ShortestAngle, double RADIUS, const LinkedCell * const LC) const;
    289350};
    290351

  • src/tesselationhelpers.cpp

    r8927ae r1ca488  
    88#include <fstream>
    99
     10#include "info.hpp"
    1011#include "linkedcell.hpp"
    1112#include "log.hpp"
    … …  
    1516#include "verbose.hpp"
    1617
    17 double DetGet(gsl_matrix * const A, const int inPlace) {
     18double DetGet(gsl_matrix * const A, const int inPlace)
     19{
     20        Info FunctionInfo(__func__);
    1821  /*
    1922  inPlace = 1 => A is replaced with the LU decomposed copy.
    … …  
    4548void GetSphere(Vector * const center, const Vector &a, const Vector &b, const Vector &c, const double RADIUS)
    4649{
     50        Info FunctionInfo(__func__);
    4751  gsl_matrix *A = gsl_matrix_calloc(3,3);
    4852  double m11, m12, m13, m14;
    … …  
    111115    const double HalfplaneIndicator, const double AlternativeIndicator, const double alpha, const double beta, const double gamma, const double RADIUS, const double Umkreisradius)
    112116{
     117        Info FunctionInfo(__func__);
    113118  Vector TempNormal, helper;
    114119  double Restradius;
    115120  Vector OtherCenter;
    116   Log() << Verbose(3) << "Begin of GetCenterOfSphere.\n";
    117121  Center->Zero();
    118122  helper.CopyVector(&a);
    … …  
    128132  Center->Scale(1./(sin(2.*alpha) + sin(2.*beta) + sin(2.*gamma)));
    129133  NewUmkreismittelpunkt->CopyVector(Center);
    130   Log() << Verbose(4) << "Center of new circumference is " << *NewUmkreismittelpunkt << ".\n";
     134  Log() << Verbose(1) << "Center of new circumference is " << *NewUmkreismittelpunkt << ".\n";
    131135  // Here we calculated center of circumscribing circle, using barycentric coordinates
    132   Log() << Verbose(4) << "Center of circumference is " << *Center << " in direction " << *Direction << ".\n";
     136  Log() << Verbose(1) << "Center of circumference is " << *Center << " in direction " << *Direction << ".\n";
    133137
    134138  TempNormal.CopyVector(&a);
    … …  
    154158  TempNormal.Normalize();
    155159  Restradius = sqrt(RADIUS*RADIUS - Umkreisradius*Umkreisradius);
    156   Log() << Verbose(4) << "Height of center of circumference to center of sphere is " << Restradius << ".\n";
     160  Log() << Verbose(1) << "Height of center of circumference to center of sphere is " << Restradius << ".\n";
    157161  TempNormal.Scale(Restradius);
    158   Log() << Verbose(4) << "Shift vector to sphere of circumference is " << TempNormal << ".\n";
     162  Log() << Verbose(1) << "Shift vector to sphere of circumference is " << TempNormal << ".\n";
    159163
    160164  Center->AddVector(&TempNormal);
    161   Log() << Verbose(0) << "Center of sphere of circumference is " << *Center << ".\n";
     165  Log() << Verbose(1) << "Center of sphere of circumference is " << *Center << ".\n";
    162166  GetSphere(&OtherCenter, a, b, c, RADIUS);
    163   Log() << Verbose(0) << "OtherCenter of sphere of circumference is " << OtherCenter << ".\n";
    164   Log() << Verbose(3) << "End of GetCenterOfSphere.\n";
     167  Log() << Verbose(1) << "OtherCenter of sphere of circumference is " << OtherCenter << ".\n";
    165168};
    166169
    … …  
    174177void GetCenterofCircumcircle(Vector * const Center, const Vector &a, const Vector &b, const Vector &c)
    175178{
     179        Info FunctionInfo(__func__);
    176180  Vector helper;
    177181  double alpha, beta, gamma;
    … …  
    186190  beta = M_PI - SideC.Angle(&SideA);
    187191  gamma = M_PI - SideA.Angle(&SideB);
    188   //Log() << Verbose(3) << "INFO: alpha = " << alpha/M_PI*180. << ", beta = " << beta/M_PI*180. << ", gamma = " << gamma/M_PI*180. << "." << endl;
     192  //Log() << Verbose(1) << "INFO: alpha = " << alpha/M_PI*180. << ", beta = " << beta/M_PI*180. << ", gamma = " << gamma/M_PI*180. << "." << endl;
    189193  if (fabs(M_PI - alpha - beta - gamma) > HULLEPSILON) {
    190194    eLog() << Verbose(1) << "GetCenterofCircumcircle: Sum of angles " << (alpha+beta+gamma)/M_PI*180. << " > 180 degrees by " << fabs(M_PI - alpha - beta - gamma)/M_PI*180. << "!" << endl;
    … …  
    219223double GetPathLengthonCircumCircle(const Vector &CircleCenter, const Vector &CirclePlaneNormal, const double CircleRadius, const Vector &NewSphereCenter, const Vector &OldSphereCenter, const Vector &NormalVector, const Vector &SearchDirection)
    220224{
     225        Info FunctionInfo(__func__);
    221226  Vector helper;
    222227  double radius, alpha;
    223 
    224   helper.CopyVector(&NewSphereCenter);
     228  Vector RelativeOldSphereCenter;
     229  Vector RelativeNewSphereCenter;
     230
     231  RelativeOldSphereCenter.CopyVector(&OldSphereCenter);
     232  RelativeOldSphereCenter.SubtractVector(&CircleCenter);
     233  RelativeNewSphereCenter.CopyVector(&NewSphereCenter);
     234  RelativeNewSphereCenter.SubtractVector(&CircleCenter);
     235  helper.CopyVector(&RelativeNewSphereCenter);
    225236  // test whether new center is on the parameter circle's plane
    226237  if (fabs(helper.ScalarProduct(&CirclePlaneNormal)) > HULLEPSILON) {
    … …  
    228239    helper.ProjectOntoPlane(&CirclePlaneNormal);
    229240  }
    230   radius = helper.ScalarProduct(&helper);
     241  radius = helper.NormSquared();
    231242  // test whether the new center vector has length of CircleRadius
    232243  if (fabs(radius - CircleRadius) > HULLEPSILON)
    233244    eLog() << Verbose(1) << "The projected center of the new sphere has radius " << radius << " instead of " << CircleRadius << "." << endl;
    234   alpha = helper.Angle(&OldSphereCenter);
     245  alpha = helper.Angle(&RelativeOldSphereCenter);
    235246  // make the angle unique by checking the halfplanes/search direction
    236247  if (helper.ScalarProduct(&SearchDirection) < -HULLEPSILON)  // acos is not unique on [0, 2.*M_PI), hence extra check to decide between two half intervals
    237248    alpha = 2.*M_PI - alpha;
    238   //Log() << Verbose(2) << "INFO: RelativeNewSphereCenter is " << helper << ", RelativeOldSphereCenter is " << OldSphereCenter << " and resulting angle is " << alpha << "." << endl;
    239   radius = helper.Distance(&OldSphereCenter);
     249  Log() << Verbose(1) << "INFO: RelativeNewSphereCenter is " << helper << ", RelativeOldSphereCenter is " << RelativeOldSphereCenter << " and resulting angle is " << alpha << "." << endl;
     250  radius = helper.Distance(&RelativeOldSphereCenter);
    240251  helper.ProjectOntoPlane(&NormalVector);
    241252  // check whether new center is somewhat away or at least right over the current baseline to prevent intersecting triangles
    242253  if ((radius > HULLEPSILON) || (helper.Norm() < HULLEPSILON)) {
    243     //Log() << Verbose(2) << "INFO: Distance between old and new center is " << radius << " and between new center and baseline center is " << helper.Norm() << "." << endl;
     254    Log() << Verbose(1) << "INFO: Distance between old and new center is " << radius << " and between new center and baseline center is " << helper.Norm() << "." << endl;
    244255    return alpha;
    245256  } else {
    246     //Log() << Verbose(1) << "INFO: NewSphereCenter " << helper << " is too close to OldSphereCenter" << OldSphereCenter << "." << endl;
     257    Log() << Verbose(1) << "INFO: NewSphereCenter " << RelativeNewSphereCenter << " is too close to RelativeOldSphereCenter" << RelativeOldSphereCenter << "." << endl;
    247258    return 2.*M_PI;
    248259  }
    … …  
    264275double MinIntersectDistance(const gsl_vector * x, void *params)
    265276{
     277        Info FunctionInfo(__func__);
    266278  double retval = 0;
    267279  struct Intersection *I = (struct Intersection *)params;
    … …  
    284296
    285297  retval = HeightA.ScalarProduct(&HeightA) + HeightB.ScalarProduct(&HeightB);
    286   //Log() << Verbose(2) << "MinIntersectDistance called, result: " << retval << endl;
     298  //Log() << Verbose(1) << "MinIntersectDistance called, result: " << retval << endl;
    287299
    288300  return retval;
    … …  
    304316bool existsIntersection(const Vector &point1, const Vector &point2, const Vector &point3, const Vector &point4)
    305317{
     318        Info FunctionInfo(__func__);
    306319  bool result;
    307320
    … …  
    351364
    352365        if (status == GSL_SUCCESS) {
    353           Log() << Verbose(2) << "converged to minimum" <<  endl;
     366          Log() << Verbose(1) << "converged to minimum" <<  endl;
    354367        }
    355368    } while (status == GSL_CONTINUE && iter < 100);
    … …  
    376389  t2 = HeightB.ScalarProduct(&SideB)/SideB.ScalarProduct(&SideB);
    377390
    378   Log() << Verbose(2) << "Intersection " << intersection << " is at "
     391  Log() << Verbose(1) << "Intersection " << intersection << " is at "
    379392    << t1 << " for (" << point1 << "," << point2 << ") and at "
    380393    << t2 << " for (" << point3 << "," << point4 << "): ";
    381394
    382395  if (((t1 >= 0) && (t1 <= 1)) && ((t2 >= 0) && (t2 <= 1))) {
    383     Log() << Verbose(0) << "true intersection." << endl;
     396    Log() << Verbose(1) << "true intersection." << endl;
    384397    result = true;
    385398  } else {
    386     Log() << Verbose(0) << "intersection out of region of interest." << endl;
     399    Log() << Verbose(1) << "intersection out of region of interest." << endl;
    387400    result = false;
    388401  }
    … …  
    407420double GetAngle(const Vector &point, const Vector &reference, const Vector &OrthogonalVector)
    408421{
     422        Info FunctionInfo(__func__);
    409423  if (reference.IsZero())
    410424    return M_PI;
    … …  
    418432  }
    419433
    420   Log() << Verbose(4) << "INFO: " << point << " has angle " << phi << " with respect to reference " << reference << "." << endl;
     434  Log() << Verbose(1) << "INFO: " << point << " has angle " << phi << " with respect to reference " << reference << "." << endl;
    421435
    422436  return phi;
    … …  
    433447double CalculateVolumeofGeneralTetraeder(const Vector &a, const Vector &b, const Vector &c, const Vector &d)
    434448{
     449        Info FunctionInfo(__func__);
    435450  Vector Point, TetraederVector[3];
    436451  double volume;
    … …  
    456471bool CheckLineCriteriaForDegeneratedTriangle(const BoundaryPointSet * const nodes[3])
    457472{
     473        Info FunctionInfo(__func__);
    458474  bool result = false;
    459475  int counter = 0;
    … …  
    482498    }
    483499  if ((!result) && (counter > 1)) {
    484     Log() << Verbose(2) << "INFO: Degenerate triangle is ok, at least two, here " << counter << ", existing lines are used." << endl;
     500    Log() << Verbose(1) << "INFO: Degenerate triangle is ok, at least two, here " << counter << ", existing lines are used." << endl;
    485501    result = true;
    486502  }
    … …  
    489505
    490506
    491 /** Sort function for the candidate list.
    492  */
    493 bool SortCandidates(const CandidateForTesselation* candidate1, const CandidateForTesselation* candidate2)
    494 {
    495   Vector BaseLineVector, OrthogonalVector, helper;
    496   if (candidate1->BaseLine != candidate2->BaseLine) {  // sanity check
    497     eLog() << Verbose(1) << "sortCandidates was called for two different baselines: " << candidate1->BaseLine << " and " << candidate2->BaseLine << "." << endl;
    498     //return false;
    499     exit(1);
    500   }
    501   // create baseline vector
    502   BaseLineVector.CopyVector(candidate1->BaseLine->endpoints[1]->node->node);
    503   BaseLineVector.SubtractVector(candidate1->BaseLine->endpoints[0]->node->node);
    504   BaseLineVector.Normalize();
    505 
    506   // create normal in-plane vector to cope with acos() non-uniqueness on [0,2pi] (note that is pointing in the "right" direction already, hence ">0" test!)
    507   helper.CopyVector(candidate1->BaseLine->endpoints[0]->node->node);
    508   helper.SubtractVector(candidate1->point->node);
    509   OrthogonalVector.CopyVector(&helper);
    510   helper.VectorProduct(&BaseLineVector);
    511   OrthogonalVector.SubtractVector(&helper);
    512   OrthogonalVector.Normalize();
    513 
    514   // calculate both angles and correct with in-plane vector
    515   helper.CopyVector(candidate1->point->node);
    516   helper.SubtractVector(candidate1->BaseLine->endpoints[0]->node->node);
    517   double phi = BaseLineVector.Angle(&helper);
    518   if (OrthogonalVector.ScalarProduct(&helper) > 0) {
    519     phi = 2.*M_PI - phi;
    520   }
    521   helper.CopyVector(candidate2->point->node);
    522   helper.SubtractVector(candidate1->BaseLine->endpoints[0]->node->node);
    523   double psi = BaseLineVector.Angle(&helper);
    524   if (OrthogonalVector.ScalarProduct(&helper) > 0) {
    525     psi = 2.*M_PI - psi;
    526   }
    527 
    528   Log() << Verbose(2) << *candidate1->point << " has angle " << phi << endl;
    529   Log() << Verbose(2) << *candidate2->point << " has angle " << psi << endl;
    530 
    531   // return comparison
    532   return phi < psi;
    533 };
     507///** Sort function for the candidate list.
     508// */
     509//bool SortCandidates(const CandidateForTesselation* candidate1, const CandidateForTesselation* candidate2)
     510//{
     511//      Info FunctionInfo(__func__);
     512//  Vector BaseLineVector, OrthogonalVector, helper;
     513//  if (candidate1->BaseLine != candidate2->BaseLine) {  // sanity check
     514//    eLog() << Verbose(1) << "sortCandidates was called for two different baselines: " << candidate1->BaseLine << " and " << candidate2->BaseLine << "." << endl;
     515//    //return false;
     516//    exit(1);
     517//  }
     518//  // create baseline vector
     519//  BaseLineVector.CopyVector(candidate1->BaseLine->endpoints[1]->node->node);
     520//  BaseLineVector.SubtractVector(candidate1->BaseLine->endpoints[0]->node->node);
     521//  BaseLineVector.Normalize();
     522//
     523//  // create normal in-plane vector to cope with acos() non-uniqueness on [0,2pi] (note that is pointing in the "right" direction already, hence ">0" test!)
     524//  helper.CopyVector(candidate1->BaseLine->endpoints[0]->node->node);
     525//  helper.SubtractVector(candidate1->point->node);
     526//  OrthogonalVector.CopyVector(&helper);
     527//  helper.VectorProduct(&BaseLineVector);
     528//  OrthogonalVector.SubtractVector(&helper);
     529//  OrthogonalVector.Normalize();
     530//
     531//  // calculate both angles and correct with in-plane vector
     532//  helper.CopyVector(candidate1->point->node);
     533//  helper.SubtractVector(candidate1->BaseLine->endpoints[0]->node->node);
     534//  double phi = BaseLineVector.Angle(&helper);
     535//  if (OrthogonalVector.ScalarProduct(&helper) > 0) {
     536//    phi = 2.*M_PI - phi;
     537//  }
     538//  helper.CopyVector(candidate2->point->node);
     539//  helper.SubtractVector(candidate1->BaseLine->endpoints[0]->node->node);
     540//  double psi = BaseLineVector.Angle(&helper);
     541//  if (OrthogonalVector.ScalarProduct(&helper) > 0) {
     542//    psi = 2.*M_PI - psi;
     543//  }
     544//
     545//  Log() << Verbose(1) << *candidate1->point << " has angle " << phi << endl;
     546//  Log() << Verbose(1) << *candidate2->point << " has angle " << psi << endl;
     547//
     548//  // return comparison
     549//  return phi < psi;
     550//};
    534551
    535552/**
    … …  
    543560TesselPoint* FindSecondClosestPoint(const Vector* Point, const LinkedCell* const LC)
    544561{
     562        Info FunctionInfo(__func__);
    545563  TesselPoint* closestPoint = NULL;
    546564  TesselPoint* secondClosestPoint = NULL;
    … …  
    553571  for(int i=0;i<NDIM;i++) // store indices of this cell
    554572    N[i] = LC->n[i];
    555   Log() << Verbose(2) << "INFO: Center cell is " << N[0] << ", " << N[1] << ", " << N[2] << " with No. " << LC->index << "." << endl;
     573  Log() << Verbose(1) << "INFO: Center cell is " << N[0] << ", " << N[1] << ", " << N[2] << " with No. " << LC->index << "." << endl;
    556574
    557575  LC->GetNeighbourBounds(Nlower, Nupper);
    558   //Log() << Verbose(0) << endl;
     576  //Log() << Verbose(1) << endl;
    559577  for (LC->n[0] = Nlower[0]; LC->n[0] <= Nupper[0]; LC->n[0]++)
    560578    for (LC->n[1] = Nlower[1]; LC->n[1] <= Nupper[1]; LC->n[1]++)
    561579      for (LC->n[2] = Nlower[2]; LC->n[2] <= Nupper[2]; LC->n[2]++) {
    562580        const LinkedNodes *List = LC->GetCurrentCell();
    563         //Log() << Verbose(3) << "The current cell " << LC->n[0] << "," << LC->n[1] << "," << LC->n[2] << endl;
     581        //Log() << Verbose(1) << "The current cell " << LC->n[0] << "," << LC->n[1] << "," << LC->n[2] << endl;
    564582        if (List != NULL) {
    565583          for (LinkedNodes::const_iterator Runner = List->begin(); Runner != List->end(); Runner++) {
    … …  
    597615TesselPoint* FindClosestPoint(const Vector* Point, TesselPoint *&SecondPoint, const LinkedCell* const LC)
    598616{
     617        Info FunctionInfo(__func__);
    599618  TesselPoint* closestPoint = NULL;
    600619  SecondPoint = NULL;
    … …  
    607626  for(int i=0;i<NDIM;i++) // store indices of this cell
    608627    N[i] = LC->n[i];
    609   Log() << Verbose(3) << "INFO: Center cell is " << N[0] << ", " << N[1] << ", " << N[2] << " with No. " << LC->index << "." << endl;
     628  Log() << Verbose(1) << "INFO: Center cell is " << N[0] << ", " << N[1] << ", " << N[2] << " with No. " << LC->index << "." << endl;
    610629
    611630  LC->GetNeighbourBounds(Nlower, Nupper);
    612   //Log() << Verbose(0) << endl;
     631  //Log() << Verbose(1) << endl;
    613632  for (LC->n[0] = Nlower[0]; LC->n[0] <= Nupper[0]; LC->n[0]++)
    614633    for (LC->n[1] = Nlower[1]; LC->n[1] <= Nupper[1]; LC->n[1]++)
    615634      for (LC->n[2] = Nlower[2]; LC->n[2] <= Nupper[2]; LC->n[2]++) {
    616635        const LinkedNodes *List = LC->GetCurrentCell();
    617         //Log() << Verbose(3) << "The current cell " << LC->n[0] << "," << LC->n[1] << "," << LC->n[2] << endl;
     636        //Log() << Verbose(1) << "The current cell " << LC->n[0] << "," << LC->n[1] << "," << LC->n[2] << endl;
    618637        if (List != NULL) {
    619638          for (LinkedNodes::const_iterator Runner = List->begin(); Runner != List->end(); Runner++) {
    … …  
    626645              distance = currentNorm;
    627646              closestPoint = (*Runner);
    628               //Log() << Verbose(2) << "INFO: New Nearest Neighbour is " << *closestPoint << "." << endl;
     647              //Log() << Verbose(1) << "INFO: New Nearest Neighbour is " << *closestPoint << "." << endl;
    629648            } else if (currentNorm < secondDistance) {
    630649              secondDistance = currentNorm;
    631650              SecondPoint = (*Runner);
    632               //Log() << Verbose(2) << "INFO: New Second Nearest Neighbour is " << *SecondPoint << "." << endl;
     651              //Log() << Verbose(1) << "INFO: New Second Nearest Neighbour is " << *SecondPoint << "." << endl;
    633652            }
    634653          }
    … …  
    640659  // output
    641660  if (closestPoint != NULL) {
    642     Log() << Verbose(2) << "Closest point is " << *closestPoint;
     661    Log() << Verbose(1) << "Closest point is " << *closestPoint;
    643662    if (SecondPoint != NULL)
    644663      Log() << Verbose(0) << " and second closest is " << *SecondPoint;
    … …  
    656675Vector * GetClosestPointBetweenLine(const BoundaryLineSet * const Base, const BoundaryLineSet * const OtherBase)
    657676{
     677        Info FunctionInfo(__func__);
    658678  // construct the plane of the two baselines (i.e. take both their directional vectors)
    659679  Vector Normal;
    … …  
    666686  Normal.VectorProduct(&OtherBaseline);
    667687  Normal.Normalize();
    668   Log() << Verbose(4) << "First direction is " << Baseline << ", second direction is " << OtherBaseline << ", normal of intersection plane is " << Normal << "." << endl;
     688  Log() << Verbose(1) << "First direction is " << Baseline << ", second direction is " << OtherBaseline << ", normal of intersection plane is " << Normal << "." << endl;
    669689
    670690  // project one offset point of OtherBase onto this plane (and add plane offset vector)
    … …  
    683703  Normal.CopyVector(Intersection);
    684704  Normal.SubtractVector(Base->endpoints[0]->node->node);
    685   Log() << Verbose(3) << "Found closest point on " << *Base << " at " << *Intersection << ", factor in line is " << fabs(Normal.ScalarProduct(&Baseline)/Baseline.NormSquared()) << "." << endl;
     705  Log() << Verbose(1) << "Found closest point on " << *Base << " at " << *Intersection << ", factor in line is " << fabs(Normal.ScalarProduct(&Baseline)/Baseline.NormSquared()) << "." << endl;
    686706
    687707  return Intersection;
    … …  
    696716double DistanceToTrianglePlane(const Vector *x, const BoundaryTriangleSet * const triangle)
    697717{
     718        Info FunctionInfo(__func__);
    698719  double distance = 0.;
    699720  if (x == NULL) {
    … …  
    712733void WriteVrmlFile(ofstream * const vrmlfile, const Tesselation * const Tess, const PointCloud * const cloud)
    713734{
     735        Info FunctionInfo(__func__);
    714736  TesselPoint *Walker = NULL;
    715737  int i;
    … …  
    755777void IncludeSphereinRaster3D(ofstream * const rasterfile, const Tesselation * const Tess, const PointCloud * const cloud)
    756778{
     779        Info FunctionInfo(__func__);
    757780  Vector helper;
    758   // include the current position of the virtual sphere in the temporary raster3d file
    759   Vector *center = cloud->GetCenter();
    760   // make the circumsphere's center absolute again
    761   helper.CopyVector(Tess->LastTriangle->endpoints[0]->node->node);
    762   helper.AddVector(Tess->LastTriangle->endpoints[1]->node->node);
    763   helper.AddVector(Tess->LastTriangle->endpoints[2]->node->node);
    764   helper.Scale(1./3.);
    765   helper.SubtractVector(center);
    766   // and add to file plus translucency object
    767   *rasterfile << "# current virtual sphere\n";
    768   *rasterfile << "8\n  25.0    0.6     -1.0 -1.0 -1.0     0.2        0 0 0 0\n";
    769   *rasterfile << "2\n  " << helper.x[0] << " " << helper.x[1] << " " << helper.x[2] << "\t" << 5. << "\t1 0 0\n";
    770   *rasterfile << "9\n  terminating special property\n";
    771   delete(center);
     781
     782  if (Tess->LastTriangle != NULL) {
     783    // include the current position of the virtual sphere in the temporary raster3d file
     784    Vector *center = cloud->GetCenter();
     785    // make the circumsphere's center absolute again
     786    helper.CopyVector(Tess->LastTriangle->endpoints[0]->node->node);
     787    helper.AddVector(Tess->LastTriangle->endpoints[1]->node->node);
     788    helper.AddVector(Tess->LastTriangle->endpoints[2]->node->node);
     789    helper.Scale(1./3.);
     790    helper.SubtractVector(center);
     791    // and add to file plus translucency object
     792    *rasterfile << "# current virtual sphere\n";
     793    *rasterfile << "8\n  25.0    0.6     -1.0 -1.0 -1.0     0.2        0 0 0 0\n";
     794    *rasterfile << "2\n  " << helper.x[0] << " " << helper.x[1] << " " << helper.x[2] << "\t" << 5. << "\t1 0 0\n";
     795    *rasterfile << "9\n  terminating special property\n";
     796    delete(center);
     797  }
    772798};
    773799
    … …  
    780806void WriteRaster3dFile(ofstream * const rasterfile, const Tesselation * const Tess, const PointCloud * const cloud)
    781807{
     808        Info FunctionInfo(__func__);
    782809  TesselPoint *Walker = NULL;
    783810  int i;
    … …  
    825852void WriteTecplotFile(ofstream * const tecplot, const Tesselation * const TesselStruct, const PointCloud * const cloud, const int N)
    826853{
     854        Info FunctionInfo(__func__);
    827855  if ((tecplot != NULL) && (TesselStruct != NULL)) {
    828856    // write header
    829857    *tecplot << "TITLE = \"3D CONVEX SHELL\"" << endl;
    830858    *tecplot << "VARIABLES = \"X\" \"Y\" \"Z\" \"U\"" << endl;
    831     *tecplot << "ZONE T=\"" << N << "-";
    832     for (int i=0;i<3;i++)
    833       *tecplot << (i==0 ? "" : "_") << TesselStruct->LastTriangle->endpoints[i]->node->Name;
     859    *tecplot << "ZONE T=\"";
     860    if (N < 0) {
     861      *tecplot << cloud->GetName();
     862    } else {
     863      *tecplot << N << "-";
     864      for (int i=0;i<3;i++)
     865        *tecplot << (i==0 ? "" : "_") << TesselStruct->LastTriangle->endpoints[i]->node->Name;
     866    }
    834867    *tecplot << "\", N=" << TesselStruct->PointsOnBoundary.size() << ", E=" << TesselStruct->TrianglesOnBoundary.size() << ", DATAPACKING=POINT, ZONETYPE=FETRIANGLE" << endl;
    835868    int i=0;
    … …  
    840873
    841874    // print atom coordinates
    842     Log() << Verbose(2) << "The following triangles were created:";
    843875    int Counter = 1;
    844876    TesselPoint *Walker = NULL;
    … …  
    850882    *tecplot << endl;
    851883    // print connectivity
     884    Log() << Verbose(1) << "The following triangles were created:" << endl;
    852885    for (TriangleMap::const_iterator runner = TesselStruct->TrianglesOnBoundary.begin(); runner != TesselStruct->TrianglesOnBoundary.end(); runner++) {
    853       Log() << Verbose(0) << " " << runner->second->endpoints[0]->node->Name << "<->" << runner->second->endpoints[1]->node->Name << "<->" << runner->second->endpoints[2]->node->Name;
     886      Log() << Verbose(1) << " " << runner->second->endpoints[0]->node->Name << "<->" << runner->second->endpoints[1]->node->Name << "<->" << runner->second->endpoints[2]->node->Name << endl;
    854887      *tecplot << LookupList[runner->second->endpoints[0]->node->nr] << " " << LookupList[runner->second->endpoints[1]->node->nr] << " " << LookupList[runner->second->endpoints[2]->node->nr] << endl;
    855888    }
    856889    delete[] (LookupList);
    857     Log() << Verbose(0) << endl;
    858890  }
    859891};
    … …  
    866898void CalculateConcavityPerBoundaryPoint(const Tesselation * const TesselStruct)
    867899{
     900        Info FunctionInfo(__func__);
    868901  class BoundaryPointSet *point = NULL;
    869902  class BoundaryLineSet *line = NULL;
    870903
    871   //Log() << Verbose(2) << "Begin of CalculateConcavityPerBoundaryPoint" << endl;
    872904  // calculate remaining concavity
    873905  for (PointMap::const_iterator PointRunner = TesselStruct->PointsOnBoundary.begin(); PointRunner != TesselStruct->PointsOnBoundary.end(); PointRunner++) {
    … …  
    877909    for (LineMap::iterator LineRunner = point->lines.begin(); LineRunner != point->lines.end(); LineRunner++) {
    878910      line = LineRunner->second;
    879       //Log() << Verbose(2) << "INFO: Current line of point " << *point << " is " << *line << "." << endl;
     911      //Log() << Verbose(1) << "INFO: Current line of point " << *point << " is " << *line << "." << endl;
    880912      if (!line->CheckConvexityCriterion())
    881913        point->value += 1;
    882914    }
    883915  }
    884   //Log() << Verbose(2) << "End of CalculateConcavityPerBoundaryPoint" << endl;
    885916};
    886917
    … …  
    893924bool CheckListOfBaselines(const Tesselation * const TesselStruct)
    894925{
     926        Info FunctionInfo(__func__);
    895927  LineMap::const_iterator testline;
    896928  bool result = false;
    … …  
    900932  for (testline = TesselStruct->LinesOnBoundary.begin(); testline != TesselStruct->LinesOnBoundary.end(); testline++) {
    901933    if (testline->second->triangles.size() != 2) {
    902       Log() << Verbose(1) << *testline->second << "\t" << testline->second->triangles.size() << endl;
     934      Log() << Verbose(2) << *testline->second << "\t" << testline->second->triangles.size() << endl;
    903935      counter++;
    904936    }
    … …  
    911943}
    912944
     945/** Counts the number of triangle pairs that contain the given polygon.
     946 * \param *P polygon with endpoints to look for
     947 * \param *T set of triangles to create pairs from containing \a *P
     948 */
     949int CountTrianglePairContainingPolygon(const BoundaryPolygonSet * const P, const TriangleSet * const T)
     950{
     951  Info FunctionInfo(__func__);
     952  // check number of endpoints in *P
     953  if (P->endpoints.size() != 4) {
     954    eLog() << Verbose(1) << "CountTrianglePairContainingPolygon works only on polygons with 4 nodes!" << endl;
     955    return 0;
     956  }
     957
     958  // check number of triangles in *T
     959  if (T->size() < 2) {
     960    eLog() << Verbose(1) << "Not enough triangles to have pairs!" << endl;
     961    return 0;
     962  }
     963
     964  Log() << Verbose(0) << "Polygon is " << *P << endl;
     965  // create each pair, get the endpoints and check whether *P is contained.
     966  int counter = 0;
     967  PointSet Trianglenodes;
     968  class BoundaryPolygonSet PairTrianglenodes;
     969  for(TriangleSet::iterator Walker = T->begin(); Walker != T->end(); Walker++) {
     970    for (int i=0;i<3;i++)
     971      Trianglenodes.insert((*Walker)->endpoints[i]);
     972
     973    for(TriangleSet::iterator PairWalker = Walker; PairWalker != T->end(); PairWalker++) {
     974      if (Walker != PairWalker) { // skip first
     975        PairTrianglenodes.endpoints = Trianglenodes;
     976        for (int i=0;i<3;i++)
     977          PairTrianglenodes.endpoints.insert((*PairWalker)->endpoints[i]);
     978        const int size = PairTrianglenodes.endpoints.size();
     979        if (size == 4) {
     980          Log() << Verbose(0) << " Current pair of triangles: " << **Walker << "," << **PairWalker << " with " << size << " distinct endpoints:" << PairTrianglenodes << endl;
     981          // now check
     982          if (PairTrianglenodes.ContainsPresentTupel(P)) {
     983            counter++;
     984            Log() << Verbose(0) << "  ACCEPT: Matches with " << *P << endl;
     985          } else {
     986            Log() << Verbose(0) << "  REJECT: No match with " << *P << endl;
     987          }
     988        } else {
     989          Log() << Verbose(0) << "  REJECT: Less than four endpoints." << endl;
     990        }
     991      }
     992    }
     993    Trianglenodes.clear();
     994  }
     995  return counter;
     996};
     997
     998/** Checks whether two give polygons have two or more points in common.
     999 * \param *P1 first polygon
     1000 * \param *P2 second polygon
     1001 * \return true - are connected, false = are note
     1002 */
     1003bool ArePolygonsEdgeConnected(const BoundaryPolygonSet * const P1, const BoundaryPolygonSet * const P2)
     1004{
     1005  Info FunctionInfo(__func__);
     1006  int counter = 0;
     1007  for(PointSet::const_iterator Runner = P1->endpoints.begin(); Runner != P1->endpoints.end(); Runner++) {
     1008    if (P2->ContainsBoundaryPoint((*Runner))) {
     1009      counter++;
     1010      Log() << Verbose(1) << *(*Runner) << " of second polygon is found in the first one." << endl;
     1011      return true;
     1012    }
     1013  }
     1014  return false;
     1015};
     1016
     1017/** Combines second into the first and deletes the second.
     1018 * \param *P1 first polygon, contains all nodes on return
     1019 * \param *&P2 second polygon, is deleted.
     1020 */
     1021void CombinePolygons(BoundaryPolygonSet * const P1, BoundaryPolygonSet * &P2)
     1022{
     1023  Info FunctionInfo(__func__);
     1024  pair <PointSet::iterator, bool> Tester;
     1025  for(PointSet::iterator Runner = P2->endpoints.begin(); Runner != P2->endpoints.end(); Runner++) {
     1026    Tester = P1->endpoints.insert((*Runner));
     1027    if (Tester.second)
     1028      Log() << Verbose(0) << "Inserting endpoint " << *(*Runner) << " into first polygon." << endl;
     1029  }
     1030  P2->endpoints.clear();
     1031  delete(P2);
     1032};
     1033

  • src/tesselationhelpers.hpp

    r8927ae r1ca488  
    7272bool CheckListOfBaselines(const Tesselation * const TesselStruct);
    7373
     74int CountTrianglePairContainingPolygon(const BoundaryPolygonSet * const P, const TriangleSet * const T);
     75bool ArePolygonsEdgeConnected(const BoundaryPolygonSet * const P1, const BoundaryPolygonSet * const P2);
     76void CombinePolygons(BoundaryPolygonSet * const P1, BoundaryPolygonSet * &P2);
     77
    7478
    7579#endif /* TESSELATIONHELPERS_HPP_ */

  • src/unittests/Makefile.am

    r8927ae r1ca488  
    66MENUTESTS = ActionSequenceTest
    77
    8 TESTS = ActOnAllUnitTest AnalysisBondsUnitTests AnalysisCorrelationToPointUnitTest AnalysisCorrelationToSurfaceUnitTest AnalysisPairCorrelationUnitTest BondGraphUnitTest ListOfBondsUnitTest LogUnitTest MemoryUsageObserverUnitTest MemoryAllocatorUnitTest StackClassUnitTest VectorUnitTest ${MENUTESTS}
     8TESTS = ActOnAllUnitTest AnalysisBondsUnitTests AnalysisCorrelationToPointUnitTest AnalysisCorrelationToSurfaceUnitTest AnalysisPairCorrelationUnitTest BondGraphUnitTest InfoUnitTest ListOfBondsUnitTest LogUnitTest MemoryUsageObserverUnitTest MemoryAllocatorUnitTest StackClassUnitTest VectorUnitTest ${MENUTESTS}
     9
    910check_PROGRAMS = $(TESTS)
    1011noinst_PROGRAMS = $(TESTS)
    … …  
    2728BondGraphUnitTest_SOURCES = bondgraphunittest.cpp bondgraphunittest.hpp
    2829BondGraphUnitTest_LDADD = ../libmolecuilder.a
     30
     31InfoUnitTest_SOURCES = infounittest.cpp infounittest.hpp
     32InfoUnitTest_LDADD = ../libmolecuilder.a
    2933
    3034ListOfBondsUnitTest_SOURCES = listofbondsunittest.cpp listofbondsunittest.hpp

  • src/vector.cpp

    r8927ae r1ca488  
    480480  else
    481481    return false;
     482};
     483
     484/** Checks whether vector is normal to \a *normal.
     485 * @return true - vector is normalized, false - vector is not
     486 */
     487bool Vector::IsEqualTo(const Vector * const a) const
     488{
     489  bool status = true;
     490  for (int i=0;i<NDIM;i++) {
     491    if (fabs(x[i] - a->x[i]) > MYEPSILON)
     492      status = false;
     493  }
     494  return status;
    482495};
    483496

  • src/vector.hpp

    r8927ae r1ca488  
    4242  bool IsOne() const;
    4343  bool IsNormalTo(const Vector * const normal) const;
     44  bool IsEqualTo(const Vector * const a) const;
    4445
    4546  void AddVector(const Vector * const y);

  • src/verbose.cpp

    r8927ae r1ca488  
    11using namespace std;
    22
     3#include "info.hpp"
    34#include "verbose.hpp"
    45
    … …  
    910ostream& Verbose::print (ostream &ost) const
    1011{
    11   for (int i=Verbosity;i--;)
     12  for (int i=Verbosity+Info::verbosity;i--;)
    1213    ost.put('\t');
    1314  //Log() << Verbose(0) << "Verbose(.) called." << endl;
    … …  
    2223bool Verbose::DoOutput(int verbosityLevel) const
    2324{
    24   return (verbosityLevel >= Verbosity);
     25  return (verbosityLevel >= Verbosity+Info::verbosity);
    2526};
    2627
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