Changeset 4e10f5 for src/Actions/AnalysisAction

Timestamp:

Jul 7, 2010, 4:08:32 PM (15 years ago)

Author:

Tillmann Crueger <crueger@…>

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:

77a570

Parents:

5630bd (diff), 192f6e (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'stable' into StructureRefactoring

Conflicts:

src/Actions/WorldAction/CenterOnEdgeAction.cpp
src/Actions/WorldAction/ChangeBoxAction.cpp
src/Actions/WorldAction/RepeatBoxAction.cpp
src/Actions/WorldAction/ScaleBoxAction.cpp
src/World.cpp
src/boundary.cpp

Location:

src/Actions/AnalysisAction

Files:

• MolecularVolumeAction.cpp (modified) (1 diff)
• PairCorrelationAction.cpp (modified) (6 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/AnalysisAction/PairCorrelationAction.cpp

@@ -82 +82 @@
     output.open(outputname.c_str());
     binoutput.open(binoutputname.c_str());
-    PairCorrelationMap *correlationmap = NULL;
     if (type == "E") {
       PairCorrelationMap *correlationmap = NULL;
@@ -89 +88 @@
       else
         correlationmap = PairCorrelation(World::getInstance().getMolecules(), elements);
-      //OutputCorrelationToSurface(&output, correlationmap);
+      OutputPairCorrelation(&output, correlationmap);
       binmap = BinData( correlationmap, BinWidth, BinStart, BinEnd );
+      OutputCorrelation ( &binoutput, binmap );
+      delete(binmap);
+      delete(correlationmap);
     } else if (type == "P")  {
       cout << "Point to correlate to is  " << Point << endl;
@@ -98 +100 @@
       else
         correlationmap = CorrelationToPoint(molecules, elements, &Point);
-      //OutputCorrelationToSurface(&output, correlationmap);
+      OutputCorrelationToPoint(&output, correlationmap);
       binmap = BinData( correlationmap, BinWidth, BinStart, BinEnd );
+      OutputCorrelation ( &binoutput, binmap );
+      delete(binmap);
+      delete(correlationmap);
     } else if (type == "S") {
       ASSERT(Boundary != NULL, "No molecule specified for SurfaceCorrelation.");
@@ -106 +111 @@
       if (BinEnd > 0) {
         if (BinEnd > 2.*radius)
-            LCWidth = BinEnd;
+          LCWidth = BinEnd;
         else
           LCWidth = 2.*radius;
@@ -129 +134 @@
       else
         surfacemap = CorrelationToSurface( molecules, elements, TesselStruct, LCList);
+      delete LCList;
       OutputCorrelationToSurface(&output, surfacemap);
+      // re-set ActiveFlag
+      counter = 0;
+      for (MoleculeList::iterator BigFinder = molecules->ListOfMolecules.begin(); BigFinder != molecules->ListOfMolecules.end(); BigFinder++) {
+        (*BigFinder)->ActiveFlag = Actives[counter++];
+      }
+      delete[] Actives;
       // check whether radius was appropriate
       {
@@ -138 +150 @@
       }
       binmap = BinData( surfacemap, BinWidth, BinStart, BinEnd );
-    } else
+      OutputCorrelation ( &binoutput, binmap );
+      delete TesselStruct;  // surfacemap contains refs to triangles! delete here, not earlier!
+      delete(binmap);
+      delete(surfacemap);
+    } else {
       return Action::failure;
-    OutputCorrelation ( &binoutput, binmap );
+    }
     output.close();
     binoutput.close();
-    delete(binmap);
-    delete(correlationmap);
     delete dialog;
     return Action::success;