Changeset accebe

Timestamp:

Jun 2, 2010, 2:30:31 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:

116f37

Parents:

7fd416

git-author:

Frederik Heber <heber@…> (06/02/10 14:25:12)

git-committer:

Frederik Heber <heber@…> (06/02/10 14:30:31)

Message:

Fix of PrepareClustersInWater (at least it does not stumble over memory issues).

• note: this was just done to make check test Filling/2 work again (which only runs and does not check the output)
• GetBoundaryPoints() - using now left and right to have a good runner even if it is discarded/deleted, flag check when loop is through
• PrepareClustersinWater() - LCList is now a pointer and removed after FindConvexBorder()
• DOCUFIX: Tesselation::RemoveTesselationTriangle() - triangles attached to lines are printed starting on next line, not current
• BUGFIX: Tesselation::FlipBaseline() - as we remove the two connected triangles, the baseline who they are attached to will be deleted and removed, hence the loop over the line's triangles does not work. Now, we first put all into a list, then delete the triangles.

This was the last test to fail. All unit tests (33), all testsuite cases (45) and all tesselation tests (15) work.

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

Location:

src

Files:

• boundary.cpp (modified) (6 diffs)
• tesselation.cpp (modified) (2 diffs)

src/boundary.cpp

@@ -224 +224 @@
     do { // do as long as we still throw one out per round
       flag = false;
-      Boundaries::iterator left = BoundaryPoints[axis].end();
-      Boundaries::iterator right = BoundaryPoints[axis].end();
-      for (Boundaries::iterator runner = BoundaryPoints[axis].begin(); runner != BoundaryPoints[axis].end(); runner++) {
+      Boundaries::iterator left = BoundaryPoints[axis].begin();
+      Boundaries::iterator right = BoundaryPoints[axis].begin();
+      Boundaries::iterator runner = BoundaryPoints[axis].begin();
+      bool LoopOnceDone = false;
+      while (!LoopOnceDone) {
+        runner = right;
+        right++;
         // set neighbours correctly
         if (runner == BoundaryPoints[axis].begin()) {
@@ -234 +238 @@
         }
         left--;
-        right = runner;
-        right++;
         if (right == BoundaryPoints[axis].end()) {
           right = BoundaryPoints[axis].begin();
+          LoopOnceDone = true;
         }
         // check distance
@@ -277 +280 @@
             DoLog(1) && (Log() << Verbose(1) << "Throwing out " << *runner->second.second << "." << endl);
             BoundaryPoints[axis].erase(runner);
+            runner = right;
             flag = true;
           }
@@ -376 +380 @@
           TesselStruct->FlipBaseline(line);
           DoLog(1) && (Log() << Verbose(1) << "INFO: Correction of concave baselines worked." << endl);
+          LineRunner = TesselStruct->LinesOnBoundary.begin(); // LineRunner may have been erase if line was deleted from LinesOnBoundary
         }
       }
@@ -639 +644 @@
 /** Creates multiples of the by \a *mol given cluster and suspends them in water with a given final density.
  * We get cluster volume by VolumeOfConvexEnvelope() and its diameters by GetDiametersOfCluster()
+ * TODO: Here, we need a VolumeOfGeneralEnvelope (i.e. non-convex one)
  * \param *out output stream for debugging
  * \param *configuration needed for path to store convex envelope file
@@ -666 +672 @@
   GreatestDiameter = GetDiametersOfCluster(BoundaryPoints, mol, TesselStruct, IsAngstroem);
   BoundaryPoints = GetBoundaryPoints(mol, TesselStruct);
-  LinkedCell LCList(mol, 10.);
-  FindConvexBorder(mol, TesselStruct, &LCList, NULL);
+  LinkedCell *LCList = new LinkedCell(mol, 10.);
+  FindConvexBorder(mol, TesselStruct, (const LinkedCell *&)LCList, NULL);
+  delete (LCList);
+
 
   // some preparations beforehand

src/tesselation.cpp

@@ -1922 +1922 @@
         RemoveTesselationLine(triangle->lines[i]);
       } else {
-        DoLog(0) && (Log() << Verbose(0) << *triangle->lines[i] << " is still attached to another triangle: ");
+        DoLog(0) && (Log() << Verbose(0) << *triangle->lines[i] << " is still attached to another triangle: " << endl);
         OpenLines.insert(pair<BoundaryLineSet *, CandidateForTesselation *> (triangle->lines[i], NULL));
         for (TriangleMap::iterator TriangleRunner = triangle->lines[i]->triangles.begin(); TriangleRunner != triangle->lines[i]->triangles.end(); TriangleRunner++)
-          DoLog(0) && (Log() << Verbose(0) << "[" << (TriangleRunner->second)->Nr << "|" << *((TriangleRunner->second)->endpoints[0]) << ", " << *((TriangleRunner->second)->endpoints[1]) << ", " << *((TriangleRunner->second)->endpoints[2]) << "] \t");
+          DoLog(0) && (Log() << Verbose(0) << "\t[" << (TriangleRunner->second)->Nr << "|" << *((TriangleRunner->second)->endpoints[0]) << ", " << *((TriangleRunner->second)->endpoints[1]) << ", " << *((TriangleRunner->second)->endpoints[2]) << "] \t");
         DoLog(0) && (Log() << Verbose(0) << endl);
         //        for (int j=0;j<2;j++) {
@@ -2979 +2979 @@
   OldBaseLineNr = Base->Nr;
   m = 0;
-  for (TriangleMap::iterator runner = Base->triangles.begin(); runner != Base->triangles.end(); runner++) {
-    DoLog(0) && (Log() << Verbose(0) << "INFO: Deleting triangle " << *(runner->second) << "." << endl);
-    OldTriangleNrs[m++] = runner->second->Nr;
-    RemoveTesselationTriangle(runner->second);
+  // first obtain all triangle to delete ... (otherwise we pull the carpet (Base) from under the for-loop's feet)
+  list <BoundaryTriangleSet *> TrianglesOfBase;
+  for (TriangleMap::iterator runner = Base->triangles.begin(); runner != Base->triangles.end(); ++runner)
+    TrianglesOfBase.push_back(runner->second);
+  // .. then delete each triangle (which deletes the line as well)
+  for (list <BoundaryTriangleSet *>::iterator runner = TrianglesOfBase.begin(); !TrianglesOfBase.empty(); runner = TrianglesOfBase.begin()) {
+    DoLog(0) && (Log() << Verbose(0) << "INFO: Deleting triangle " << *(*runner) << "." << endl);
+    OldTriangleNrs[m++] = (*runner)->Nr;
+    RemoveTesselationTriangle((*runner));
+    TrianglesOfBase.erase(runner);
   }