Changeset caf5d6 for src

Timestamp:

Dec 11, 2008, 3:23:01 PM (16 years ago)

Author:

Christian Neuen <neuen@…>

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:

e4ea46

Parents:

f714979

Message:

Atom indices are now correctly processed.

Location:

src

Files:

• boundary.cpp (modified) (12 diffs)
• boundary.hpp (modified) (2 diffs)
• molecules.cpp (modified) (3 diffs)

src/boundary.cpp

@@ -1018 +1018 @@
 };
 
-
-
-
-
-
-//====================================================================================================================
-//
-// ab hier habe ich das verzapft.
-//
-//====================================================================================================================
+void Tesselation::AddTrianglePoint(atom* Candidate, int n)
+{
+          PointTestPair InsertUnique;
+          TPS[n] = new class BoundaryPointSet(Candidate);
+          InsertUnique = PointsOnBoundary.insert( PointPair(Candidate->nr, TPS[n]) );
+          if (InsertUnique.second)  // if new point was not present before, increase counter
+          {
+                  PointsOnBoundaryCount++;
+          }
+          else
+          {
+                  delete TPS[n];
+                  cout << Verbose(2) << "Atom " << *((InsertUnique.first)->second->node) << " gibt's schon in der PointMap." << endl;
+                  TPS[n] = (InsertUnique.first)->second;
+          }
+};
+
+/*
+ * Function tries to add line from current Points in BPS to BoundaryLineSet.
+ * If succesfull it raises the line count and iserts the new line into the BLS, 
+ * if unsuccesfull, it writes the line which had been present into the BLS, deleting the new constructed one.  
+ */
+
+void Tesselation::AddTriangleLine(int n)
+{
+          LineMap::iterator LineWalker;
+          BLS[n] = new class BoundaryLineSet(BPS, BPS[1]->node->nr);
+          if ((BPS[0]->lines.find(BPS[1]->node->nr))->second->endpoints[0] == BLS[n]->endpoints[0]
+              and (BPS[0]->lines.find(BPS[1]->node->nr))->second->endpoints[1] == BLS[n]->endpoints[1]) 
+                  //If a line is there, how do I recognize that beyond a shadow of a doubt? 
+          {
+                  delete BLS[n];
+                  cout << Verbose(2) << "Tried to add an existing line, handled it." << endl;
+                  LineWalker = LinesOnBoundary.end();
+                  
+                  while(LineWalker->second->endpoints[0] != BLS[n]->endpoints[0] or LineWalker->second->endpoints[1] != BLS[n]->endpoints[1])
+                  {
+                          cout << Verbose(1) << "Looking for line which already exists"<< endl; 
+                          LineWalker--;
+                  }
+                  BLS[n]=LineWalker->second;
+          }
+          else
+          {
+                  cout << Verbose(2) << "Adding line which has not been used before." << endl;
+                  BPS[1]->lines.insert( LinePair(BPS[0]->node->nr, BLS[n]) );
+                  BPS[2]->lines.insert( LinePair(BPS[1]->node->nr, BLS[n]) );
+                  
+                  LinesOnBoundary.insert( LinePair(LinesOnBoundaryCount, BLS[n]));
+                  LinesOnBoundaryCount++;
+                  
+          }
+};
+
+/*
+ * Function tries to add Triangle just created to Triangle and remarks if already existent (Failure of algorithm). 
+ * Furthermore it adds the triangle to all of its lines, in order to recognize those which are saturated later.
+ */
+
+void Tesselation::AddTriangleToLines()
+{
+        cout <<Verbose(1) << "Adding triangle to its lines" <<endl;
+        int i=0;
+        TrianglesOnBoundary.insert(TrianglePair(TrianglesOnBoundaryCount, BTS));
+        TrianglesOnBoundaryCount++;
+        for (i=0; i<3; i++)
+        {
+                BLS[i]->AddTriangle(BTS);
+        }
+};
+
+
 
 /*!
@@ -1039 +1101 @@
  *  with all neighbours of the candidate.
  */
-void Find_next_suitable_point(atom* a, atom* b, atom* Candidate, int n, Vector *Chord, Vector *d1, Vector *OldNormal, atom*& Opt_Candidate, double *Storage, const double RADIUS, molecule* mol, bool problem)
+void Find_next_suitable_point(atom* a, atom* b, atom* Candidate, atom* Parent, int n, Vector *Chord, Vector *d1, Vector *OldNormal, atom*& Opt_Candidate, double *Storage, const double RADIUS, molecule* mol, bool problem)
 {
   /* OldNormal is normal vector on the old triangle
@@ -1108 +1170 @@
       {
                   Walker = mol->ListOfBondsPerAtom[Candidate->nr][i]->GetOtherAtom(Candidate);
-
-                  Find_next_suitable_point(a, b, Walker, n+1, Chord, d1, OldNormal, Opt_Candidate, Storage, RADIUS, mol, problem);  //call function again
+                  if (Walker->nr == Parent->nr){
+                          continue;
+                  }
+                  else{
+                          Find_next_suitable_point(a, b, Walker, Candidate, n+1, Chord, d1, OldNormal, Opt_Candidate, Storage, RADIUS, mol, problem);  //call function again
+                  }
       }
   }
@@ -1123 +1189 @@
   Vector helper;
   Vector Chord;
-  atom* Walker;
+  //atom* Walker;
 
   double Storage[2];
@@ -1156 +1222 @@
 
   cout << Verbose(1) << "Looking for third point candidates for triangle ... " << endl;
-  Find_next_suitable_point(Line.endpoints[0]->node, Line.endpoints[1]->node, Line.endpoints[0]->node, 0, &Chord, &direction1, &(T.NormalVector), Opt_Candidate, Storage, RADIUS, mol,0);
-
-  if (N>-1)
+  Find_next_suitable_point(Line.endpoints[0]->node, Line.endpoints[1]->node, Line.endpoints[0]->node, Line.endpoints[1]->node, 0, &Chord, &direction1, &(T.NormalVector), Opt_Candidate, Storage, RADIUS, mol,0);
+  Find_next_suitable_point(Line.endpoints[0]->node, Line.endpoints[1]->node, Line.endpoints[1]->node, Line.endpoints[0]->node, 0, &Chord, &direction1, &(T.NormalVector), Opt_Candidate, Storage, RADIUS, mol,0);
+
+  if (N>7)
   {
           cout << Verbose(1) << "No new Atom found, triangle construction will crash" << endl;
           write_tecplot_file(out, tecplot, this, mol);
           tecplot->flush();
-          Find_next_suitable_point(Line.endpoints[0]->node, Line.endpoints[1]->node, Line.endpoints[0]->node, 0, &Chord, &direction1, &(T.NormalVector), Opt_Candidate, Storage, RADIUS, mol, 1);
-
+          Find_next_suitable_point(Line.endpoints[0]->node, Line.endpoints[1]->node, Line.endpoints[0]->node, Line.endpoints[1]->node, 0, &Chord, &direction1, &(T.NormalVector), Opt_Candidate, Storage, RADIUS, mol, 1);
+          Find_next_suitable_point(Line.endpoints[0]->node, Line.endpoints[1]->node, Line.endpoints[1]->node, Line.endpoints[0]->node, 0, &Chord, &direction1, &(T.NormalVector), Opt_Candidate, Storage, RADIUS, mol, 1);
   }
   // Konstruiere nun neues Dreieck am Ende der Liste der Dreiecke
@@ -1170 +1237 @@
   cout << Verbose(1) << "Adding exactly one Walker for reasons completely unknown to me ... " << endl;
   cout << " Optimal candidate is " << *Opt_Candidate << endl;
-  AddPoint(Opt_Candidate);
-  cout << " Optimal candidate is " << *Opt_Candidate << endl;
-
-  BPS[0] = new class BoundaryPointSet(Opt_Candidate);
-  cout << " Optimal candidate is " << *Opt_Candidate << endl;
-  BPS[1] = new class BoundaryPointSet(Line.endpoints[0]->node);
-  cout << " Optimal candidate is " << *Opt_Candidate << endl;
-  BLS[0] = new class BoundaryLineSet(BPS , LinesOnBoundaryCount);
-  cout << " Optimal candidate is " << *Opt_Candidate << endl;
-  BPS[0] = new class BoundaryPointSet(Opt_Candidate);
-
-  BPS[1] = new class BoundaryPointSet(Line.endpoints[1]->node);
-  BLS[1] = new class BoundaryLineSet(BPS , LinesOnBoundaryCount);
-  BLS[2] = new class BoundaryLineSet(Line);
+
+  AddTrianglePoint(Opt_Candidate, 0);
+  AddTrianglePoint(Line.endpoints[0]->node, 1);
+  AddTrianglePoint(Line.endpoints[1]->node, 2);
+  
+  BPS[0] = TPS[0];
+  BPS[1] = TPS[1];
+  AddTriangleLine(0);
+  BPS[0] = TPS[0];
+  BPS[1] = TPS[2];
+  AddTriangleLine(1);
+  BPS[0] = TPS[1];
+  BPS[1] = TPS[2];
+  AddTriangleLine(2);
 
   BTS = new class BoundaryTriangleSet(BLS, TrianglesOnBoundaryCount);
-  TrianglesOnBoundary.insert( TrianglePair(TrianglesOnBoundaryCount, BTS) );
-  TrianglesOnBoundaryCount++;
-
-  cout << Verbose(1) << "Checking for already present lines ... " << endl;
-  for(int i=0; i<NDIM; i++) // sind Linien bereits vorhanden ???
-  {
-          if ( (LinesOnBoundary.insert( LinePair(LinesOnBoundaryCount, BTS->lines[i]))).second);
-          {
-                  LinesOnBoundaryCount++;
-          }
-  }
+  AddTriangleToLines();
+  
+  
   cout << Verbose(1) << "Constructing normal vector for this triangle ... " << endl;
 
@@ -1210 +1269 @@
 
 
-void Find_second_point_for_Tesselation(atom* a, atom* Candidate, int n, Vector Oben, atom*& Opt_Candidate, double Storage[2], molecule* mol, double RADIUS)
+void Find_second_point_for_Tesselation(atom* a, atom* Candidate, atom* Parent, int n, Vector Oben, atom*& Opt_Candidate, double Storage[2], molecule* mol, double RADIUS)
 {
         cout << Verbose(1) << "Looking for second point of starting triangle, recursive level "<< n <<endl;;
@@ -1234 +1293 @@
                         }
                         else{
-                                cout << Verbose(1) << "Supposedly looses to better candidate" << Opt_Candidate->nr << endl;
+                                cout << Verbose(1) << "Supposedly looses to a better candidate" << Opt_Candidate->nr << endl;
                         }
                 }
@@ -1244 +1303 @@
       {
           Walker = mol->ListOfBondsPerAtom[Candidate->nr][i]->GetOtherAtom(Candidate);
-          Find_second_point_for_Tesselation(a, Walker, n+1, Oben, Opt_Candidate, Storage, mol, RADIUS);
+          if (Walker->nr == Parent->nr)
+                  continue;
+          else
+                  Find_second_point_for_Tesselation(a, Walker, Candidate, n+1, Oben, Opt_Candidate, Storage, mol, RADIUS);
       };
     };
@@ -1306 +1368 @@
   cout << Verbose(1) << "Number of Bonds: " << mol->NumberOfBondsPerAtom[FirstPoint->nr] << endl;
 
-  Find_second_point_for_Tesselation(FirstPoint, mol->ListOfBondsPerAtom[FirstPoint->nr][0]->GetOtherAtom(FirstPoint), 0, Oben, Opt_Candidate, Storage, mol, RADIUS);
+  Find_second_point_for_Tesselation(FirstPoint, mol->ListOfBondsPerAtom[FirstPoint->nr][0]->GetOtherAtom(FirstPoint), FirstPoint, 0, Oben, Opt_Candidate, Storage, mol, RADIUS);
 
 
@@ -1322 +1384 @@
 
   cout << Verbose(1) << "Looking for third point candidates \n";
-  Find_next_suitable_point(FirstPoint, SecondPoint, mol->ListOfBondsPerAtom[FirstPoint->nr][0]->GetOtherAtom(FirstPoint), 0, &Chord, &helper, &Oben, Opt_Candidate, Storage, RADIUS, mol, 0);
+  Find_next_suitable_point(FirstPoint, SecondPoint, SecondPoint, FirstPoint, 0, &Chord, &helper, &Oben, Opt_Candidate, Storage, RADIUS, mol, 0);
 
 
   //Starting Triangle is Walker, SecondPoint, Opt_Candidate
 
-  AddPoint(FirstPoint);
-  AddPoint(SecondPoint);
-  AddPoint(Opt_Candidate);
-
-  cout << Verbose(1) << "The found starting triangle consists of " << *FirstPoint << ", " << *SecondPoint << " and " << *Opt_Candidate << "." << endl;
-
-  BPS[0] = new class BoundaryPointSet(FirstPoint);
-  BPS[1] = new class BoundaryPointSet(SecondPoint);
+    cout << Verbose(1) << "The found starting triangle consists of " << *FirstPoint << ", " << *SecondPoint << " and " << *Opt_Candidate << "." << endl;
+
+  AddTrianglePoint(FirstPoint, 0);
+  AddTrianglePoint(SecondPoint, 1);
+  AddTrianglePoint(Opt_Candidate, 2);
+  
+  BPS[0] = TPS[0];
+  BPS[1] = TPS[1];
   BLS[0] = new class BoundaryLineSet(BPS , LinesOnBoundaryCount);
-  BPS[0] = new class BoundaryPointSet(FirstPoint);
-  BPS[1] = new class BoundaryPointSet(Opt_Candidate);
+  BPS[0] = TPS[1];
+  BPS[1] = TPS[2];
   BLS[1] = new class BoundaryLineSet(BPS , LinesOnBoundaryCount);
-  BPS[0] = new class BoundaryPointSet(Opt_Candidate);
-  BPS[1] = new class BoundaryPointSet(SecondPoint);
+  BPS[0] = TPS[0];
+  BPS[1] = TPS[2];
   BLS[2] = new class BoundaryLineSet(BPS , LinesOnBoundaryCount);
 
@@ -1366 +1428 @@
         int N =0;
         struct Tesselation *Tess = new Tesselation;
-        cout << Verbose(1) << "Entering finding of non convex hull. " << endl;
+        cout << Verbose(1) << "Entering search for non convex hull. " << endl;
         cout << flush;
         const double RADIUS =6.;

src/boundary.hpp

@@ -82 +82 @@
     void GuessStartingTriangle(ofstream *out);
     void AddPoint(atom * Walker);
+    void AddTrianglePoint(atom* Candidate, int n);
+    void AddTriangleLine(int n);
+    void AddTriangleToLines();
     void Find_starting_triangle(molecule* mol, const double RADIUS);
     void Find_next_suitable_triangle(ofstream *out, ofstream *tecplot, molecule* mol, BoundaryLineSet &Line, BoundaryTriangleSet &T, const double& RADIUS, int N);
@@ -88 +91 @@
     LineMap LinesOnBoundary;
     TriangleMap TrianglesOnBoundary;
+    class BoundaryPointSet *TPS[3]; //this is a Storage for pointers to triangle points, this and BPS[2] needed due to AddLine restrictions 
     class BoundaryPointSet *BPS[2];
     class BoundaryLineSet *BLS[3];

src/molecules.cpp

@@ -1518 +1518 @@
 {
   atom *walker = NULL;
-  int No = 0;
+  int AtomNo = 0, ElementNo;
   time_t now;
+  element *runner = NULL;
 
   now = time((time_t *)NULL);   // Get the system time and put it into 'now' as 'calender time'
@@ -1525 +1526 @@
   while (walker->next != end) { // go through every atom and count
     walker = walker->next;
-    No++;
+    AtomNo++;
   }
   if (out != NULL) {
-    *out << No << "\n\tCreated by molecuilder on " << ctime(&now);
-    walker = start;
-    while (walker->next != end) { // go through every atom of this element
-      walker = walker->next;
-      walker->OutputXYZLine(out);
+    *out << AtomNo << "\n\tCreated by molecuilder on " << ctime(&now);
+    ElementNo = 0;
+    runner = elemente->start;
+    while (runner->next != elemente->end) { // go through every element
+                runner = runner->next;
+      if (ElementsInMolecule[runner->Z]) { // if this element got atoms
+        ElementNo++;
+        walker = start;
+        while (walker->next != end) { // go through every atom of this element
+          walker = walker->next;
+          if (walker->type == runner) { // if this atom fits to element
+            walker->OutputXYZLine(out);
+          }
+        }
+      }
     }
     return true;
@@ -1716 +1727 @@
                         };
                         AddBond(Walker, OtherWalker); //Add the bond between the two atoms with respective indices.
-                        BondCount++; //Increase bond count of molecule
+                        
                 }