Changeset 4fc93f

Timestamp:

Nov 26, 2009, 11:40:01 AM (15 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, 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:

491876, 5ae39c

Parents:

27bd2f

Message:

removing automatic dissection on loading, Tesselations test now checks for return value only not for precise order of the triangles.

• FindNonConvexBorder() returns bool depending on the result of CheckListOfBaselines()
• BUG: ParseCommandLineOptions(): case 'p' (parsing) does not dissect the molecule, as we have to wait for e.g. '-A' before we may use the bond structure. Same for config::Load()

Files:

• src/boundary.cpp (modified) (4 diffs)
• src/boundary.hpp (modified) (1 diff)
• src/builder.cpp (modified) (2 diffs)
• src/config.cpp (modified) (1 diff)
• tests/Tesselations/defs.in (added)

src/boundary.cpp

@@ -946 +946 @@
  * \param RADIUS radius of the virtual sphere
  * \param *filename filename prefix for output of vertex data
- */
-void FindNonConvexBorder(const molecule* const mol, Tesselation *&TesselStruct, const LinkedCell *&LCList, const double RADIUS, const char *filename = NULL)
+ * \return true - tesselation successful, false - tesselation failed
+ */
+bool FindNonConvexBorder(const molecule* const mol, Tesselation *&TesselStruct, const LinkedCell *&LCList, const double RADIUS, const char *filename = NULL)
 {
         Info FunctionInfo(__func__);
   bool freeLC = false;
+  bool status = false;
   CandidateForTesselation *baseline;
   LineMap::iterator testline;
@@ -1017 +1019 @@
     }
   }
-  // check envelope for consistency
-  CheckListOfBaselines(TesselStruct);
-
-  // look whether all points are inside of the convex envelope, otherwise add them via degenerated triangles
-  //->InsertStraddlingPoints(mol, LCList);
+//  // check envelope for consistency
+//  status = CheckListOfBaselines(TesselStruct);
+//
+//  // look whether all points are inside of the convex envelope, otherwise add them via degenerated triangles
+//  //->InsertStraddlingPoints(mol, LCList);
 //  mol->GoToFirst();
 //  class TesselPoint *Runner = NULL;
@@ -1038 +1040 @@
 //  // Purges surplus triangles.
 //  TesselStruct->RemoveDegeneratedTriangles();
-//
-//  // check envelope for consistency
-//  CheckListOfBaselines(TesselStruct);
+
+  // check envelope for consistency
+  status = CheckListOfBaselines(TesselStruct);
 
   // write final envelope
@@ -1048 +1050 @@
   if (freeLC)
     delete(LCList);
+
+  return status;
 };
 

src/boundary.hpp

@@ -53 +53 @@
 Vector* FindEmbeddingHole(MoleculeListClass *mols, molecule *srcmol);
 void FindNextSuitablePoint(class BoundaryTriangleSet *BaseTriangle, class BoundaryLineSet *BaseLine, atom*& OptCandidate, Vector *OptCandidateCenter, double *ShortestAngle, const double RADIUS, LinkedCell *LC);
-void FindNonConvexBorder(const molecule* const mol, Tesselation *&TesselStruct, const LinkedCell *&LC, const double RADIUS, const char *tempbasename);
+bool FindNonConvexBorder(const molecule* const mol, Tesselation *&TesselStruct, const LinkedCell *&LC, const double RADIUS, const char *tempbasename);
 Boundaries *GetBoundaryPoints(const molecule *mol, Tesselation *&TesselStruct);
 double * GetDiametersOfCluster(const Boundaries *BoundaryPtr, const molecule *mol, Tesselation *&TesselStruct, const bool IsAngstroem);

src/builder.cpp

@@ -1574 +1574 @@
                 else {
                   Log() << Verbose(2) << "File found and parsed." << endl;
-                  mol->SetNameFromFilename(argv[argptr]);
-                  molecules->ListOfMolecules.remove(mol);
-                  molecules->DissectMoleculeIntoConnectedSubgraphs(mol,&configuration);
-                  delete(mol);
-                  if (molecules->ListOfMolecules.size() != 0) {
-                    for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
-                      if ((*ListRunner)->ActiveFlag) {
-                        mol = *ListRunner;
-                        break;
-                      }
-                  }
+                  // @TODO rather do the dissection afterwards
+//                  mol->SetNameFromFilename(argv[argptr]);
+//                  molecules->ListOfMolecules.remove(mol);
+//                  molecules->DissectMoleculeIntoConnectedSubgraphs(mol,&configuration);
+//                  delete(mol);
+//                  if (molecules->ListOfMolecules.size() != 0) {
+//                    for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
+//                      if ((*ListRunner)->ActiveFlag) {
+//                        mol = *ListRunner;
+//                        break;
+//                      }
+//                  }
                   configPresent = present;
                 }
@@ -1803 +1804 @@
                 start = clock();
                 LCList = new LinkedCell(Boundary, atof(argv[argptr])*2.);
-                FindNonConvexBorder(Boundary, T, LCList, atof(argv[argptr]), argv[argptr+1]);
+                if (!FindNonConvexBorder(Boundary, T, LCList, atof(argv[argptr]), argv[argptr+1]))
+                  ExitFlag = 255;
                 //FindDistributionOfEllipsoids(T, &LCList, N, number, filename.c_str());
                 end = clock();

src/config.cpp

@@ -1069 +1069 @@
   mol->SetNameFromFilename(filename);
   mol->ActiveFlag = true;
+  MolList->insert(mol);
 
   // 4. dissect the molecule into connected subgraphs
-  MolList->DissectMoleculeIntoConnectedSubgraphs(mol,this);
+  // don't do this here ...
+  //MolList->DissectMoleculeIntoConnectedSubgraphs(mol,this);
 
   delete(mol);