Changeset caa06ef for src

Timestamp:

Mar 1, 2011, 10:16:38 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:

5702cdb

Parents:

34c43a

git-author:

Frederik Heber <heber@…> (02/21/11 23:49:30)

git-committer:

Frederik Heber <heber@…> (03/01/11 10:16:38)

Message:

Added name to PointCloudAdaptor, set by constructor.

• name is used in Tesselation to store in file and difficult to obtain via the PointCloud (e.g. std::list have not name, need to be wrapped again, ...)
• removed expected-to-fail again from Tesselation/Convex, Tesselation/NonConvex, and Tesselation/BigNonConvex tests.

Location:

src

Files:

• Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) (1 diff)
• Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) (1 diff)
• Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified) (1 diff)
• Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) (1 diff)
• Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) (1 diff)
• IPointCloud.hpp (modified) (1 diff)
• PointCloudAdaptor.hpp (modified) (3 diffs)
• boundary.cpp (modified) (6 diffs)
• molecule_graph.cpp (modified) (1 diff)
• tesselation.cpp (modified) (1 diff)
• unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) (1 diff)
• unittests/LinkedCellUnitTest.cpp (modified) (1 diff)
• unittests/TesselationUnitTest.cpp (modified) (1 diff)
• unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) (1 diff)

src/Actions/AnalysisAction/MolecularVolumeAction.cpp

@@ -52 +52 @@
     const LinkedCell *LCList = NULL;
     DoLog(0) && (Log() << Verbose(0) << "Evaluating volume of the convex envelope.");
-    PointCloudAdaptor< molecule > cloud(mol);
+    PointCloudAdaptor< molecule > cloud(mol, mol->name);
     LCList = new LinkedCell(cloud, 10.);
     config * const configuration = World::getInstance().getConfig();

src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp

@@ -76 +76 @@
   std::vector<molecule*> molecules = World::getInstance().getSelectedMolecules();
   std::cout << "There are " << molecules.size() << " selected molecules." << std::endl;
-  PointCloudAdaptor<molecule> cloud(surfacemol);
+  PointCloudAdaptor<molecule> cloud(surfacemol, surfacemol->name);
   LCList = new LinkedCell(cloud, LCWidth);
   FindNonConvexBorder(surfacemol, TesselStruct, LCList, radius, NULL);

src/Actions/FragmentationAction/ConstructBondGraphAction.cpp

@@ -94 +94 @@
       list.push_back(AtomRunner->second);
     }
-    PointCloudAdaptor< TesselPointSTLList > cloud(&list);
+    PointCloudAdaptor< TesselPointSTLList > cloud(&list, "AtomSelection");
     LC = new LinkedCell(cloud, BondDistance);
 

src/Actions/TesselationAction/ConvexEnvelopeAction.cpp

@@ -56 +56 @@
     DoLog(1) && (Log() << Verbose(1) << "Storing tecplot convex data in " << params.filenameConvex << "." << endl);
     DoLog(1) && (Log() << Verbose(1) << "Storing tecplot non-convex data in " << params.filenameNonConvex << "." << endl);
-    PointCloudAdaptor<molecule> cloud(mol);
+    PointCloudAdaptor<molecule> cloud(mol, mol->name);
     LCList = new LinkedCell(cloud, 100.);
     //Boundaries *BoundaryPoints = NULL;

src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp

@@ -56 +56 @@
     DoLog(1) && (Log() << Verbose(1) << "Specified molecule has " << Boundary->getAtomCount() << " atoms." << endl);
     start = clock();
-    PointCloudAdaptor< molecule > cloud(Boundary);
+    PointCloudAdaptor< molecule > cloud(Boundary, Boundary->name);
     LCList = new LinkedCell(cloud, params.SphereRadius*2.);
     Success = FindNonConvexBorder(Boundary, T, LCList, params.SphereRadius, params.filename.string().c_str());

src/IPointCloud.hpp

@@ -24 +24 @@
 class IPointCloud {
 public:
-  virtual const char * const GetName() const=0;
+  virtual const std::string& GetName() const=0;
   virtual Vector *GetCenter() const=0;
   virtual TesselPoint *GetPoint()=0;

src/PointCloudAdaptor.hpp

@@ -26 +26 @@
 {
 public:
-  PointCloudAdaptor(container_type *_list) :
-    list(_list)
+  PointCloudAdaptor(container_type *_list, const std::string _name) :
+    list(_list),
+    name(_name)
   {}
   virtual ~PointCloudAdaptor()
@@ -34 +35 @@
   }
 
-  const char * const GetName() const
+  const std::string& GetName() const
   {
-    return "Unknown.";
+    return name;
   }
   Vector *GetCenter() const
@@ -90 +91 @@
   container_type *list;
   iterator_type InternalIterator;
+  const std::string name;
 };
 

src/boundary.cpp

@@ -377 +377 @@
 
   // 3b. go through all lines, that are not yet part of two triangles (only of one so far)
-  PointCloudAdaptor< molecule > cloud(const_cast<molecule *>(mol));
+  PointCloudAdaptor< molecule > cloud(const_cast<molecule *>(mol), mol->name);
   TesselStruct->TesselateOnBoundary(cloud);
 
@@ -645 +645 @@
 {
         Info FunctionInfo(__func__);
-  PointCloudAdaptor< molecule > cloud(const_cast<molecule *>(mol));
+  PointCloudAdaptor< molecule > cloud(const_cast<molecule *>(mol), mol->name);
   // 4. Store triangles in tecplot file
   if (filename != NULL) {
@@ -700 +700 @@
   BoundaryPoints = GetBoundaryPoints(mol, TesselStruct);
   GreatestDiameter = GetDiametersOfCluster(BoundaryPoints, mol, TesselStruct, IsAngstroem);
-  PointCloudAdaptor< molecule > cloud(mol);
+  PointCloudAdaptor< molecule > cloud(mol, mol->name);
   LinkedCell *LCList = new LinkedCell(cloud, 10.);
   FindConvexBorder(mol, BoundaryPoints, TesselStruct, (const LinkedCell *&)LCList, NULL);
@@ -810 +810 @@
     if ((*ListRunner)->getAtomCount() > 0) {
       DoLog(1) && (Log() << Verbose(1) << "Pre-creating linked cell lists for molecule " << *ListRunner << "." << endl);
-      PointCloudAdaptor< molecule > cloud(*ListRunner);
+      PointCloudAdaptor< molecule > cloud(*ListRunner, (*ListRunner)->name);
       LCList[(*ListRunner)] = new LinkedCell(cloud, 10.); // get linked cell list
       DoLog(1) && (Log() << Verbose(1) << "Pre-creating tesselation for molecule " << *ListRunner << "." << endl);
@@ -1087 +1087 @@
     if ((*ListRunner)->getAtomCount() > 0) {
       DoLog(1) && (Log() << Verbose(1) << "Pre-creating linked cell lists for molecule " << *ListRunner << "." << endl);
-      PointCloudAdaptor< molecule > cloud(*ListRunner);
+      PointCloudAdaptor< molecule > cloud(*ListRunner, (*ListRunner)->name);
       LCList[(*ListRunner)] = new LinkedCell(cloud, 10.); // get linked cell list
     }
@@ -1240 +1240 @@
 
   // initialise Linked Cell
-  PointCloudAdaptor< molecule > cloud(mol);
+  PointCloudAdaptor< molecule > cloud(mol, mol->name);
   if (LCList == NULL) {
     LCList = new LinkedCell(cloud, 2.*RADIUS);

src/molecule_graph.cpp

@@ -162 +162 @@
   if ((getAtomCount() > 1) && (bonddistance > 0.1)) {
     DoLog(2) && (Log() << Verbose(2) << "Creating Linked Cell structure ... " << endl);
-    PointCloudAdaptor<molecule> cloud(this);
+    PointCloudAdaptor<molecule> cloud(this, name);
     LC = new LinkedCell(cloud, bonddistance);
 

src/tesselation.cpp

@@ -426 +426 @@
 
   cloud.GoToFirst();
-  PointCloudAdaptor< Tesselation, MapValueIterator<Tesselation::iterator> > newcloud(this);
+  PointCloudAdaptor< Tesselation, MapValueIterator<Tesselation::iterator> > newcloud(this, cloud.GetName());
   BoundaryPoints = new LinkedCell(newcloud, 5.);
   while (!cloud.IsEnd()) { // we only have to go once through all points, as boundary can become only bigger

src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp

@@ -100 +100 @@
   // init tesselation and linked cell
   Surface = new Tesselation;
-  PointCloudAdaptor<molecule> cloud(TestSurfaceMolecule);
+  PointCloudAdaptor<molecule> cloud(TestSurfaceMolecule, TestSurfaceMolecule->name);
   LC = new LinkedCell(cloud, 5.);
   FindNonConvexBorder(TestSurfaceMolecule, Surface, (const LinkedCell *&)LC, 2.5, NULL);

src/unittests/LinkedCellUnitTest.cpp

@@ -71 +71 @@
 
   // construct linked cell
-  PointCloudAdaptor<molecule> cloud(TestMolecule);
+  PointCloudAdaptor<molecule> cloud(TestMolecule, TestMolecule->name);
   LC = new LinkedCell (cloud, 1.);
   CPPUNIT_ASSERT(LC != NULL && "could not create LinkedCell");

src/unittests/TesselationUnitTest.cpp

@@ -73 +73 @@
 
   // create linkedcell
-  PointCloudAdaptor<TesselPointSTLList> cloud(&Corners);
+  PointCloudAdaptor<TesselPointSTLList> cloud(&Corners, "TesselPointSTLList");
   LinkedList = new LinkedCell(cloud, 2.*SPHERERADIUS);
 

src/unittests/Tesselation_InsideOutsideUnitTest.cpp

@@ -96 +96 @@
 
   // create linkedcell
-  PointCloudAdaptor< TesselPointSTLList > cloud(&Corners);
+  PointCloudAdaptor< TesselPointSTLList > cloud(&Corners, "TesselPointSTLList");
   LinkedList = new LinkedCell(cloud, 2.*SPHERERADIUS);