Changeset bdc91e for src/boundary.cpp

Timestamp:

Jul 1, 2010, 2:33:13 PM (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:

edb454

Parents:

8e0c63

git-author:

Frederik Heber <heber@…> (07/01/10 14:26:41)

git-committer:

Frederik Heber <heber@…> (07/01/10 14:33:13)

Message:

MEMFIXES: Tesselation routines were leaking memory.

• FindConvexBorder() - new parameter *BoundartyPts and checks whether it has to GetBoundaryPoints() or not.
• PrepareClustersInWater()
  • MEMFIX: TesselStruct not removed.
  • MEMFIX: GreatestDiameter not removed.
  • MEMFIX: LCList not removed.
  • MEMFIX: BoundaryPoints not removed.
  • GetDiametersOfCluster() uses calculated BoundaryPoints.
• Tesselation::InsertStraddlingPoints()
  • MEMFIX: triangles not removed.
  • MEMFIX: Use Flag to avoid memory leak in case of early return.
• BUGFIX: LinkedCell::GetNeighbourBounds() - returns wrong bounds if current cell is out of bounds and made unnecessary calculations.
• FIX: made type conversion in divison explicit: molecule::CenterOrigin(), molecule::DetermineCenterOfAll(), molecule::DetermineCenterOfGravity()
• Tesselation::FindStartingTriangle() - introduced map for wrapped coordinates axis
• MEMFIX: TriangleIntersectionList::GatherIntersectionsWithTriangles() - used scoped_ptr to avoid memory loss of points

Signed-off-by: Frederik Heber <heber@…>

File:

• src/boundary.cpp (modified) (8 diffs)

src/boundary.cpp

@@ -296 +296 @@
  * \param *out output stream for debugging
  * \param *mol molecule structure with Atom's and Bond's.
+ * \param *BoundaryPts set of boundary points to use or NULL
  * \param *TesselStruct Tesselation filled with points, lines and triangles on boundary on return
  * \param *LCList atoms in LinkedCell list
@@ -301 +302 @@
  * \return *TesselStruct is filled with convex boundary and tesselation is stored under \a *filename.
  */
-void FindConvexBorder(const molecule* mol, Tesselation *&TesselStruct, const LinkedCell *LCList, const char *filename)
+void FindConvexBorder(const molecule* mol, Boundaries *BoundaryPts, Tesselation *&TesselStruct, const LinkedCell *LCList, const char *filename)
 {
         Info FunctionInfo(__func__);
@@ -312 +313 @@
 
   // 1. Find all points on the boundary
-  if (BoundaryPoints == NULL) {
-      BoundaryFreeFlag = true;
-      BoundaryPoints = GetBoundaryPoints(mol, TesselStruct);
+  if (BoundaryPts == NULL) {
+    BoundaryFreeFlag = true;
+    BoundaryPoints = GetBoundaryPoints(mol, TesselStruct);
   } else {
-      DoLog(0) && (Log() << Verbose(0) << "Using given boundary points set." << endl);
+    BoundaryPoints = BoundaryPts;
+    DoLog(0) && (Log() << Verbose(0) << "Using given boundary points set." << endl);
   }
 
 // printing all inserted for debugging
-  for (int axis=0; axis < NDIM; axis++)
-    {
-      DoLog(1) && (Log() << Verbose(1) << "Printing list of candidates for axis " << axis << " which we have inserted so far." << endl);
-      int i=0;
-      for(Boundaries::iterator runner = BoundaryPoints[axis].begin(); runner != BoundaryPoints[axis].end(); runner++) {
-        if (runner != BoundaryPoints[axis].begin())
-          DoLog(0) && (Log() << Verbose(0) << ", " << i << ": " << *runner->second.second);
-        else
-          DoLog(0) && (Log() << Verbose(0) << i << ": " << *runner->second.second);
-        i++;
-      }
-      DoLog(0) && (Log() << Verbose(0) << endl);
-    }
+  for (int axis=0; axis < NDIM; axis++) {
+    DoLog(1) && (Log() << Verbose(1) << "Printing list of candidates for axis " << axis << " which we have inserted so far." << endl);
+    int i=0;
+    for(Boundaries::iterator runner = BoundaryPoints[axis].begin(); runner != BoundaryPoints[axis].end(); runner++) {
+      if (runner != BoundaryPoints[axis].begin())
+        DoLog(0) && (Log() << Verbose(0) << ", " << i << ": " << *runner->second.second);
+      else
+        DoLog(0) && (Log() << Verbose(0) << i << ": " << *runner->second.second);
+      i++;
+    }
+    DoLog(0) && (Log() << Verbose(0) << endl);
+  }
 
   // 2. fill the boundary point list
@@ -338 +339 @@
     for (Boundaries::iterator runner = BoundaryPoints[axis].begin(); runner != BoundaryPoints[axis].end(); runner++)
         if (!TesselStruct->AddBoundaryPoint(runner->second.second, 0))
-          DoeLog(2) && (eLog()<< Verbose(2) << "Point " << *(runner->second.second) << " is already present!" << endl);
+          DoLog(2) && (Log()<< Verbose(2) << "Point " << *(runner->second.second) << " is already present." << endl);
 
   DoLog(0) && (Log() << Verbose(0) << "I found " << TesselStruct->PointsOnBoundaryCount << " points on the convex boundary." << endl);
@@ -672 +673 @@
 
   IsAngstroem = configuration->GetIsAngstroem();
+  BoundaryPoints = GetBoundaryPoints(mol, TesselStruct);
   GreatestDiameter = GetDiametersOfCluster(BoundaryPoints, mol, TesselStruct, IsAngstroem);
-  BoundaryPoints = GetBoundaryPoints(mol, TesselStruct);
   LinkedCell *LCList = new LinkedCell(mol, 10.);
-  FindConvexBorder(mol, TesselStruct, (const LinkedCell *&)LCList, NULL);
+  FindConvexBorder(mol, BoundaryPoints, TesselStruct, (const LinkedCell *&)LCList, NULL);
   delete (LCList);
+  delete[] BoundaryPoints;
 
 
@@ -684 +686 @@
   else
     clustervolume = ClusterVolume;
+
+  delete TesselStruct;
 
   for (int i = 0; i < NDIM; i++)
@@ -736 +740 @@
     mol->CenterInBox();
   }
+  delete GreatestDiameter;
   // update Box of atoms by boundary
   mol->SetBoxDimension(&BoxLengths);
@@ -892 +897 @@
             }
       }
+  for (MoleculeList::iterator ListRunner = List->ListOfMolecules.begin(); ListRunner != List->ListOfMolecules.end(); ListRunner++) {
+    delete LCList[*ListRunner];
+    delete TesselStruct[(*ListRunner)];
+  }
   delete[](M);
   delete[](MInverse);