Changeset e65de8 for src/Actions/AnalysisAction

Timestamp:

Jul 25, 2010, 9:43:56 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:

a8a010

Parents:

521bbf

Message:

Fixed all correlations for new selected sets of molecules.

• MapOfActions: added missing action names point-correlation and surface-correlation.
• BUGFIX: AnalysisPairCorrelationAction::createDialog() - needs to query for multiple element_s_.
• BUGFIX: MapOfActions::queryCurrentValue() - added values twice, due to ..ID or Z was not set to -1 after push_back.
• TESTFIX: Analysis/* all needed --select-all-molecules in front.
• TESTFIX: Analysis/4 need additional --unselect-molecule-by-id 207 to avoid correlating againts itself.
• TESTFIX: changed all correlation unit tests, i.e. replaced TestList by allMolecules from getSelectedMolecules().
• analysis_correlation.[ch]pp:
  • Replaced MoleculeListClass by const std::vector<molecule *>
  • ActiveFlag check is removed, we hand over getSelectedMolecules() from World (or any other vector of molecules) instead.

Location:

src/Actions/AnalysisAction

Files:

• PairCorrelationAction.cpp (modified) (3 diffs)
• PointCorrelationAction.cpp (modified) (3 diffs)
• SurfaceCorrelationAction.cpp (modified) (4 diffs)

src/Actions/AnalysisAction/PairCorrelationAction.cpp

@@ -41 +41 @@
   Dialog *dialog = UIFactory::getInstance().makeDialog();
 
-  dialog->queryElement("elements", ValueStorage::getInstance().getDescription("elements"));
+  dialog->queryElements("elements", ValueStorage::getInstance().getDescription("elements"));
   dialog->queryDouble("bin-start", ValueStorage::getInstance().getDescription("bin-start"));
   dialog->queryDouble("bin-width", ValueStorage::getInstance().getDescription("bin-width"));
@@ -67 +67 @@
   Vector Point;
   BinPairMap *binmap = NULL;
-  MoleculeListClass *molecules = World::getInstance().getMolecules();
 
   // obtain information
@@ -82 +81 @@
   binoutput.open(binoutputname.c_str());
   PairCorrelationMap *correlationmap = NULL;
+  std::vector<molecule*> molecules = World::getInstance().getSelectedMolecules();
   if (periodic)
-    correlationmap = PeriodicPairCorrelation(World::getInstance().getMolecules(), elements, ranges);
+    correlationmap = PeriodicPairCorrelation(molecules, elements, ranges);
   else
-    correlationmap = PairCorrelation(World::getInstance().getMolecules(), elements);
+    correlationmap = PairCorrelation(molecules, elements);
   OutputPairCorrelation(&output, correlationmap);
   binmap = BinData( correlationmap, BinWidth, BinStart, BinEnd );

src/Actions/AnalysisAction/PointCorrelationAction.cpp

@@ -42 +42 @@
 
   dialog->queryVector("position", false, ValueStorage::getInstance().getDescription("position"));
-  dialog->queryElement("elements", ValueStorage::getInstance().getDescription("elements"));
+  dialog->queryElements("elements", ValueStorage::getInstance().getDescription("elements"));
   dialog->queryDouble("bin-start", ValueStorage::getInstance().getDescription("bin-start"));
   dialog->queryDouble("bin-width", ValueStorage::getInstance().getDescription("bin-width"));
@@ -68 +68 @@
   Vector Point;
   BinPairMap *binmap = NULL;
-  MoleculeListClass *molecules = World::getInstance().getMolecules();
 
   // obtain information
@@ -85 +84 @@
   cout << "Point to correlate to is  " << Point << endl;
   CorrelationToPointMap *correlationmap = NULL;
+  for(std::vector< element *>::iterator iter = elements.begin(); iter != elements.end(); ++iter)
+    cout << "element is " << (*iter)->symbol << endl;
+  std::vector<molecule*> molecules = World::getInstance().getSelectedMolecules();
   if (periodic)
     correlationmap  = PeriodicCorrelationToPoint(molecules, elements, &Point, ranges);

src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp

@@ -42 +42 @@
 
   dialog->queryMolecule("molecule-by-id", ValueStorage::getInstance().getDescription("molecule-by-id"));
-  dialog->queryElement("elements", ValueStorage::getInstance().getDescription("elements"));
+  dialog->queryElements("elements", ValueStorage::getInstance().getDescription("elements"));
   dialog->queryDouble("bin-start", ValueStorage::getInstance().getDescription("bin-start"));
   dialog->queryDouble("bin-width", ValueStorage::getInstance().getDescription("bin-width"));
@@ -68 +68 @@
   Vector Point;
   BinPairMap *binmap = NULL;
-  MoleculeListClass *molecules = World::getInstance().getMolecules();
 
   // obtain information
@@ -97 +96 @@
   const LinkedCell *LCList = NULL;
   // find biggest molecule
-  int counter  = molecules->ListOfMolecules.size();
-  bool *Actives = new bool[counter];
-  counter = 0;
-  for (MoleculeList::iterator BigFinder = molecules->ListOfMolecules.begin(); BigFinder != molecules->ListOfMolecules.end(); BigFinder++) {
-    Actives[counter++] = (*BigFinder)->ActiveFlag;
-    (*BigFinder)->ActiveFlag = (*BigFinder == Boundary) ? false : true;
-  }
+  std::vector<molecule*> molecules = World::getInstance().getSelectedMolecules();
+  int counter  = molecules.size();
   LCList = new LinkedCell(Boundary, LCWidth);
   FindNonConvexBorder(Boundary, TesselStruct, LCList, radius, NULL);
@@ -113 +107 @@
   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
   {