Changeset 34e0592 for src/boundary.cpp

Timestamp:

Aug 20, 2009, 7:48:07 AM (16 years ago)

Author:

Frederik Heber <heber@…>

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, Candidate_v1.7.0, 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:

78b73c, 9ba9ee

Parents:

1d9b7aa (diff), 7c14ec (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.

git-author:

Frederik Heber <heber@…> (08/19/09 14:40:33)

git-committer:

Frederik Heber <heber@…> (08/20/09 07:48:07)

Message:

Merge branch 'ConcaveHull' of ​ssh://stud64d-02/home/metzler/workspace/espack into Ticket14

Conflicts:

molecuilder/src/boundary.cpp
molecuilder/src/tesselation.cpp

• in boundary.cpp: FindConvexBorder() - overlay due to PickFarthestofTwoBaselines()
• in tesselation.cpp: CheckConvexityCriterion() - overlay due to verbosity change on return, getAngle() -> GetAngle()

File:

• src/boundary.cpp (modified) (23 diffs)

src/boundary.cpp

@@ -118 +118 @@
  * \param *mol molecule structure with atom positions
  */
-void write_vrml_file(ofstream *out, ofstream *vrmlfile, class Tesselation *Tess, class molecule *mol)
+void WriteVrmlFile(ofstream *out, ofstream *vrmlfile, class Tesselation *Tess, class molecule *mol)
 {
   atom *Walker = mol->start;
@@ -172 +172 @@
  * \param *mol molecule structure with atom positions
  */
-void write_raster3d_file(ofstream *out, ofstream *rasterfile, class Tesselation *Tess, class molecule *mol)
+void WriteRaster3dFile(ofstream *out, ofstream *rasterfile, class Tesselation *Tess, class molecule *mol)
 {
   atom *Walker = mol->start;
@@ -227 +227 @@
  * \param N arbitrary number to differentiate various zones in the tecplot format
  */
-void write_tecplot_file(ofstream *out, ofstream *tecplot, class Tesselation *TesselStruct, class molecule *mol, int N)
+void WriteTecplotFile(ofstream *out, ofstream *tecplot, class Tesselation *TesselStruct, class molecule *mol, int N)
 {
   if ((tecplot != NULL) && (TesselStruct != NULL)) {
@@ -440 +440 @@
  * \return *TesselStruct is filled with convex boundary and tesselation is stored under \a *filename.
  */
-void Find_convex_border(ofstream *out, molecule* mol, class LinkedCell *LCList, const char *filename)
+void FindConvexBorder(ofstream *out, molecule* mol, class LinkedCell *LCList, const char *filename)
 {
   bool BoundaryFreeFlag = false;
   Boundaries *BoundaryPoints = NULL;
 
-  cout << Verbose(1) << "Begin of find_convex_border" << endl;
+  cout << Verbose(1) << "Begin of FindConvexBorder" << endl;
 
   if (mol->TesselStruct != NULL) // free if allocated
@@ -509 +509 @@
       OutputName.append(TecplotSuffix);
       ofstream *tecplot = new ofstream(OutputName.c_str());
-      write_tecplot_file(out, tecplot, mol->TesselStruct, mol, 0);
+      WriteTecplotFile(out, tecplot, mol->TesselStruct, mol, 0);
       tecplot->close();
       delete(tecplot);
@@ -518 +518 @@
       OutputName.append(Raster3DSuffix);
       ofstream *rasterplot = new ofstream(OutputName.c_str());
-      write_raster3d_file(out, rasterplot, mol->TesselStruct, mol);
+      WriteRaster3dFile(out, rasterplot, mol->TesselStruct, mol);
       rasterplot->close();
       delete(rasterplot);
@@ -556 +556 @@
       OutputName.append(TecplotSuffix);
       ofstream *tecplot = new ofstream(OutputName.c_str());
-      write_tecplot_file(out, tecplot, mol->TesselStruct, mol, 0);
+      WriteTecplotFile(out, tecplot, mol->TesselStruct, mol, 0);
       tecplot->close();
       delete(tecplot);
@@ -564 +564 @@
       OutputName.append(Raster3DSuffix);
       ofstream *rasterplot = new ofstream(OutputName.c_str());
-      write_raster3d_file(out, rasterplot, mol->TesselStruct, mol);
+      WriteRaster3dFile(out, rasterplot, mol->TesselStruct, mol);
       rasterplot->close();
       delete(rasterplot);
@@ -575 +575 @@
     delete[] (BoundaryPoints);
 
-  cout << Verbose(1) << "End of find_convex_border" << endl;
+  cout << Verbose(1) << "End of FindConvexBorder" << endl;
 };
 
@@ -732 +732 @@
       OutputName.append(TecplotSuffix);
       ofstream *tecplot = new ofstream(OutputName.c_str());
-      write_tecplot_file(out, tecplot, mol->TesselStruct, mol, 0);
+      WriteTecplotFile(out, tecplot, mol->TesselStruct, mol, 0);
       tecplot->close();
       delete(tecplot);
@@ -741 +741 @@
       OutputName.append(Raster3DSuffix);
       ofstream *rasterplot = new ofstream(OutputName.c_str());
-      write_raster3d_file(out, rasterplot, mol->TesselStruct, mol);
+      WriteRaster3dFile(out, rasterplot, mol->TesselStruct, mol);
       rasterplot->close();
       delete(rasterplot);
@@ -816 +816 @@
   class Tesselation *TesselStruct = NULL;
   LinkedCell LCList(mol, 10.);
-  Find_convex_border(out, mol, &LCList, NULL);
+  FindConvexBorder(out, mol, &LCList, NULL);
   double clustervolume;
   if (ClusterVolume == 0)
@@ -957 +957 @@
     if ((*ListRunner)->TesselStruct == NULL) {
       *out << Verbose(1) << "Pre-creating tesselation for molecule " << *ListRunner << "." << endl;
-      Find_non_convex_border((ofstream *)&cout, (*ListRunner), LCList[i], NULL, 5.);
+      FindNonConvexBorder((ofstream *)&cout, (*ListRunner), LCList[i], NULL, 5.);
     }
     i++;
@@ -1082 +1082 @@
  * \para RADIUS radius of the virtual sphere
  */
-void Find_non_convex_border(ofstream *out, molecule* mol, class LinkedCell *LCList, const char *filename, const double RADIUS)
+void FindNonConvexBorder(ofstream *out, molecule* mol, class LinkedCell *LCList, const char *filename, const double RADIUS)
 {
   int N = 0;
@@ -1101 +1101 @@
   LineMap::iterator baseline;
   LineMap::iterator testline;
-  *out << Verbose(0) << "Begin of Find_non_convex_border\n";
+  *out << Verbose(0) << "Begin of FindNonConvexBorder\n";
   bool flag = false;  // marks whether we went once through all baselines without finding any without two triangles
   bool failflag = false;
@@ -1110 +1110 @@
   }
 
-  mol->TesselStruct->Find_starting_triangle(out, RADIUS, LCList);
+  mol->TesselStruct->FindStartingTriangle(out, RADIUS, LCList);
 
   baseline = mol->TesselStruct->LinesOnBoundary.begin();
@@ -1119 +1119 @@
   while ((baseline != mol->TesselStruct->LinesOnBoundary.end()) || (flag)) {
     if (baseline->second->triangles.size() == 1) {
-      failflag = mol->TesselStruct->Find_next_suitable_triangle(out, *(baseline->second), *(((baseline->second->triangles.begin()))->second), RADIUS, N, LCList); //the line is there, so there is a triangle, but only one.
+      failflag = mol->TesselStruct->FindNextSuitableTriangle(out, *(baseline->second), *(((baseline->second->triangles.begin()))->second), RADIUS, N, LCList); //the line is there, so there is a triangle, but only one.
       flag = flag || failflag;
       if (!failflag)
-        cerr << "WARNING: Find_next_suitable_triangle failed." << endl;
+        cerr << "WARNING: FindNextSuitableTriangle failed." << endl;
       // write temporary envelope
       if ((DoSingleStepOutput && (mol->TesselStruct->TrianglesOnBoundaryCount % SingleStepWidth == 0))) { // if we have a new triangle and want to output each new triangle configuration
@@ -1138 +1138 @@
             *out << Verbose(1) << "Writing temporary non convex hull to file " << NameofTempFile << ".\n";
             tempstream = new ofstream(NameofTempFile.c_str(), ios::trunc);
-            write_tecplot_file(out, tempstream, mol->TesselStruct, mol, TriangleFilesWritten);
+            WriteTecplotFile(out, tempstream, mol->TesselStruct, mol, TriangleFilesWritten);
             tempstream->close();
             tempstream->flush();
@@ -1152 +1152 @@
             *out << Verbose(1) << "Writing temporary non convex hull to file " << NameofTempFile << ".\n";
             tempstream = new ofstream(NameofTempFile.c_str(), ios::trunc);
-            write_raster3d_file(out, tempstream, mol->TesselStruct, mol);
+            WriteRaster3dFile(out, tempstream, mol->TesselStruct, mol);
     //        // include the current position of the virtual sphere in the temporary raster3d file
     //        // make the circumsphere's center absolute again
@@ -1191 +1191 @@
   }
 
+  // Purges surplus triangles.
+  mol->TesselStruct->RemoveDegeneratedTriangles();
+
   // write final envelope
   if (filename != 0) {
@@ -1198 +1201 @@
       OutputName.append(TecplotSuffix);
       ofstream *tecplot = new ofstream(OutputName.c_str());
-      write_tecplot_file(out, tecplot, mol->TesselStruct, mol, -1);
+      WriteTecplotFile(out, tecplot, mol->TesselStruct, mol, -1);
       tecplot->close();
       delete(tecplot);
@@ -1206 +1209 @@
       OutputName.append(Raster3DSuffix);
       ofstream *raster = new ofstream(OutputName.c_str());
-      write_raster3d_file(out, raster, mol->TesselStruct, mol);
+      WriteRaster3dFile(out, raster, mol->TesselStruct, mol);
       raster->close();
       delete(raster);
@@ -1257 +1260 @@
 //    << "for atom " << a << " (inside)." << endl;
 
-
   if (freeLC)
     delete(LCList);
-  *out << Verbose(0) << "End of Find_non_convex_border\n";
+  *out << Verbose(0) << "End of FindNonConvexBorder\n";
 };