Changeset bdc91e

Timestamp:

Jul 1, 2010, 2:33:13 PM (14 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@…>

Location:

src

Files:

• Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) (1 diff)
• Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) (1 diff)
• Actions/WorldAction/RepeatBoxAction.cpp (modified) (1 diff)
• Legacy/oldmenu.cpp (modified) (1 diff)
• boundary.cpp (modified) (8 diffs)
• boundary.hpp (modified) (1 diff)
• linkedcell.cpp (modified) (4 diffs)
• molecule_geometry.cpp (modified) (3 diffs)
• tesselation.cpp (modified) (5 diffs)
• tesselationhelpers.cpp (modified) (2 diffs)
• triangleintersectionlist.cpp (modified) (2 diffs)

src/Actions/AnalysisAction/MolecularVolumeAction.cpp

@@ -47 +47 @@
     LCList = new LinkedCell(mol, 10.);
     config * const configuration = World::getInstance().getConfig();
-    //FindConvexBorder(mol, LCList, argv[argptr]);
+    Boundaries *BoundaryPoints = NULL;
+    //FindConvexBorder(mol, BoundaryPoints, TesselStruct, LCList, argv[argptr]);
     FindNonConvexBorder(mol, TesselStruct, LCList, 5., NULL);
     //RemoveAllBoundaryPoints(TesselStruct, mol, argv[argptr]);

src/Actions/TesselationAction/ConvexEnvelopeAction.cpp

@@ -70 +70 @@
     DoLog(1) && (Log() << Verbose(1) << "Storing tecplot non-convex data in " << filenameNonConvex << "." << endl);
     LCList = new LinkedCell(mol, 100.);
-    //FindConvexBorder(mol, LCList, argv[argptr]);
+    Boundaries *BoundaryPoints = NULL;
+    //FindConvexBorder(mol, BoundaryPoints, TesselStruct, LCList, argv[argptr]);
     // TODO: Beide Funktionen sollten streams anstelle des Filenamen benutzen, besser fuer unit tests
     FindNonConvexBorder(mol, TesselStruct, LCList, 50., filenameNonConvex.c_str());

src/Actions/WorldAction/RepeatBoxAction.cpp

@@ -69 +69 @@
         Repeater[axis] = 1;
       }
-      cell_size[(abs(axis+1) == 2) ? 2 : ((abs(axis+2) == 3) ? 5 : 0)] *= Repeater[axis];
+      cell_size[ ((axis == 1) ? 2 : (axis == 2) ? 5 : 0) ] *= Repeater[axis];
     }
 

src/Legacy/oldmenu.cpp

@@ -576 +576 @@
         const LinkedCell *LCList = NULL;
         LCList = new LinkedCell(mol, 10.);
-        FindConvexBorder(mol, TesselStruct, LCList, NULL);
+        Boundaries *BoundaryPoints = NULL;
+        FindConvexBorder(mol, BoundaryPoints TesselStruct, LCList, NULL);
         double clustervolume = VolumeOfConvexEnvelope(TesselStruct, configuration);
         Log() << Verbose(0) << "The tesselated surface area is " << clustervolume << "." << endl;\

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);

src/boundary.hpp

@@ -50 +50 @@
 double ConvexizeNonconvexEnvelope(class Tesselation *&TesselStruct, const molecule * const mol, const char * const filename);
 molecule * FillBoxWithMolecule(MoleculeListClass *List, molecule *filler, config &configuration, const double MaxDistance, const double distance[NDIM], const double boundary, const double RandomAtomDisplacement, const double RandomMolDisplacement, const bool DoRandomRotation);
-void FindConvexBorder(const molecule* const mol, Tesselation *&TesselStruct, const LinkedCell *LCList, const char *filename);
+void FindConvexBorder(const molecule* const mol, Boundaries *BoundaryPts, Tesselation *&TesselStruct, const LinkedCell *LCList, const char *filename);
 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);

src/linkedcell.cpp

@@ -187 +187 @@
     N[i] = 0;
   index = -1;
-  max.Zero();
-  min.Zero();
 };
 
@@ -199 +197 @@
   for(int i=0;i<NDIM;i++)
     status = status && ((n[i] >=0) && (n[i] < N[i]));
-  if (!status)
-  DoeLog(1) && (eLog()<< Verbose(1) << "indices are out of bounds!" << endl);
+//  if (!status)
+//    DoeLog(1) && (eLog()<< Verbose(1) << "indices are out of bounds!" << endl);
   return status;
 };
@@ -279 +277 @@
 
 /** Calculates the interval bounds of the linked cell grid.
- * \param *lower lower bounds
- * \param *upper upper bounds
+ * \param lower lower bounds
+ * \param upper upper bounds
  * \param step how deep to check the neighbouring cells (i.e. number of layers to check)
  */
@@ -286 +284 @@
 {
   for (int i=0;i<NDIM;i++) {
-    lower[i] = n[i];
-    for (int s=step; s>0;--s)
-      if ((n[i]-s) >= 0) {
-        lower[i] = n[i]-s;
-        break;
-      }
-    upper[i] = n[i];
-    for (int s=step; s>0;--s)
-      if ((n[i]+s) < N[i]) {
-        upper[i] = n[i]+s;
-        break;
-      }
+    lower[i] = n[i]-step;
+    if (lower[i] < 0)
+      lower[i] = 0;
+    if (lower[i] >= N[i])
+      lower[i] = N[i]-1;
+    upper[i] = n[i]+step;
+    if (upper[i] >= N[i])
+      upper[i] = N[i]-1;
+    if (upper[i] < 0)
+      upper[i] = 0;
     //Log() << Verbose(0) << "axis " << i << " has bounds [" << lower[i] << "," << upper[i] << "]" << endl;
   }

src/molecule_geometry.cpp

@@ -120 +120 @@
       Center += (*iter)->x;
     }
-    Center.Scale(-1./Num); // divide through total number (and sign for direction)
+    Center.Scale(-1./(double)Num); // divide through total number (and sign for direction)
     Translate(&Center);
     Center.Zero();
@@ -142 +142 @@
       (*a) += (*iter)->x;
     }
-    a->Scale(1./Num); // divide through total mass (and sign for direction)
+    a->Scale(1./(double)Num); // divide through total mass (and sign for direction)
   }
   return a;
@@ -181 +181 @@
       (*a) += tmp;
     }
-    a->Scale(1./Num); // divide through total mass (and sign for direction)
+    a->Scale(1./Num); // divide through total mass
   }
 //  Log() << Verbose(1) << "Resulting center of gravity: ";

src/tesselation.cpp

@@ -1648 +1648 @@
   bool AddFlag = false;
   LinkedCell *BoundaryPoints = NULL;
+  bool SuccessFlag = true;
 
   cloud->GoToFirst();
@@ -1661 +1662 @@
     // get the next triangle
     triangles = FindClosestTrianglesToVector(Walker->node, BoundaryPoints);
-    BTS = triangles->front();
-    if ((triangles == NULL) || (BTS->ContainsBoundaryPoint(Walker))) {
+    if (triangles != NULL)
+      BTS = triangles->front();
+    else
+      BTS = NULL;
+    delete triangles;
+    if ((BTS == NULL) || (BTS->ContainsBoundaryPoint(Walker))) {
       DoLog(0) && (Log() << Verbose(0) << "No triangles found, probably a tesselation point itself." << endl);
       cloud->GoToNext();
@@ -1732 +1737 @@
     } else { // something is wrong with FindClosestTriangleToPoint!
       DoeLog(1) && (eLog() << Verbose(1) << "The closest triangle did not produce an intersection!" << endl);
-      return false;
+      SuccessFlag = false;
+      break;
     }
     cloud->GoToNext();
@@ -1739 +1745 @@
   // exit
   delete (Center);
-  return true;
+  delete (BoundaryPoints);
+  return SuccessFlag;
 }
 ;
@@ -2242 +2249 @@
   for (int i = 0; i < NDIM; i++) { // each axis
     LC->n[i] = LC->N[i] - 1; // current axis is topmost cell
-    for (LC->n[(i + 1) % NDIM] = 0; LC->n[(i + 1) % NDIM] < LC->N[(i + 1) % NDIM]; LC->n[(i + 1) % NDIM]++)
-      for (LC->n[(i + 2) % NDIM] = 0; LC->n[(i + 2) % NDIM] < LC->N[(i + 2) % NDIM]; LC->n[(i + 2) % NDIM]++) {
+    const int map[NDIM] = {i, (i + 1) % NDIM, (i + 2) % NDIM};
+    for (LC->n[map[1]] = 0; LC->n[map[1]] < LC->N[map[1]]; LC->n[map[1]]++)
+      for (LC->n[map[2]] = 0; LC->n[map[2]] < LC->N[map[2]]; LC->n[map[2]]++) {
         const LinkedCell::LinkedNodes *List = LC->GetCurrentCell();
         //Log() << Verbose(1) << "Current cell is " << LC->n[0] << ", " << LC->n[1] << ", " << LC->n[2] << " with No. " << LC->index << "." << endl;
         if (List != NULL) {
           for (LinkedCell::LinkedNodes::const_iterator Runner = List->begin(); Runner != List->end(); Runner++) {
-            if ((*Runner)->node->at(i) > maxCoordinate[i]) {
-              DoLog(1) && (Log() << Verbose(1) << "New maximal for axis " << i << " node is " << *(*Runner) << " at " << *(*Runner)->node << "." << endl);
-              maxCoordinate[i] = (*Runner)->node->at(i);
-              MaxPoint[i] = (*Runner);
+            if ((*Runner)->node->at(map[0]) > maxCoordinate[map[0]]) {
+              DoLog(1) && (Log() << Verbose(1) << "New maximal for axis " << map[0] << " node is " << *(*Runner) << " at " << *(*Runner)->node << "." << endl);
+              maxCoordinate[map[0]] = (*Runner)->node->at(map[0]);
+              MaxPoint[map[0]] = (*Runner);
             }
           }

src/tesselationhelpers.cpp

@@ -589 +589 @@
           }
         } else {
-          eLog() << Verbose(1) << "The current cell " << LC->n[0] << "," << LC->n[1] << ","
-            << LC->n[2] << " is invalid!" << endl;
+          DoeLog(1) && (eLog() << Verbose(1) << "The current cell " << LC->n[0] << "," << LC->n[1] << "," << LC->n[2] << " is invalid!" << endl);
         }
       }
@@ -645 +644 @@
           }
         } else {
-          eLog() << Verbose(1) << "The current cell " << LC->n[0] << "," << LC->n[1] << ","
-            << LC->n[2] << " is invalid!" << endl;
+          DoeLog(1) && (eLog() << Verbose(1) << "The current cell " << LC->n[0] << "," << LC->n[1] << "," << LC->n[2] << " is invalid!" << endl);
         }
       }

src/triangleintersectionlist.cpp

@@ -10 +10 @@
 
 #include "Helpers/MemDebug.hpp"
+
+#include <boost/scoped_ptr.hpp>
 
 #include "triangleintersectionlist.hpp"
@@ -118 +120 @@
 
   // get closest points
-  DistanceToPointMap * points = Tess->FindClosestBoundaryPointsToVector(Point,Vicinity);
+  boost::scoped_ptr< DistanceToPointMap > points(Tess->FindClosestBoundaryPointsToVector(Point,Vicinity));
   if (points == NULL) {
     DoeLog(1) && (eLog()<< Verbose(1) << "There is no nearest point: too far away from the surface." << endl);