Changeset bdc91e for src/linkedcell.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/linkedcell.cpp (modified) (4 diffs)

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;
   }