Changeset e65de8 for src/unittests

Timestamp:

Jul 25, 2010, 9:43:56 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:

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/unittests

Files:

• AnalysisCorrelationToPointUnitTest.cpp (modified) (4 diffs)
• AnalysisCorrelationToPointUnitTest.hpp (modified) (1 diff)
• AnalysisCorrelationToSurfaceUnitTest.cpp (modified) (10 diffs)
• AnalysisCorrelationToSurfaceUnitTest.hpp (modified) (1 diff)
• AnalysisPairCorrelationUnitTest.cpp (modified) (3 diffs)
• AnalysisPairCorrelationUnitTest.hpp (modified) (1 diff)

src/unittests/AnalysisCorrelationToPointUnitTest.cpp

@@ -16 +16 @@
 #include "analysis_correlation.hpp"
 #include "AnalysisCorrelationToPointUnitTest.hpp"
+
+#include "Descriptors/MoleculeDescriptor.hpp"
 
 #include "atom.hpp"
@@ -38 +40 @@
 
   // init private all pointers to zero
-  TestList = NULL;
   TestMolecule = NULL;
   pointmap = NULL;
@@ -71 +72 @@
   CPPUNIT_ASSERT_EQUAL( TestMolecule->getAtomCount(), 4 );
 
-  TestList = World::getInstance().getMolecules();
-  TestList->insert(TestMolecule);
   TestMolecule->ActiveFlag = true;
 
@@ -79 +78 @@
 
   // init maps
-  pointmap = CorrelationToPoint( (MoleculeListClass * const)TestList, elements, (const Vector *)point );
+  World::getInstance().selectAllMolecules(AllMolecules());
+  allMolecules = World::getInstance().getSelectedMolecules();
+  CPPUNIT_ASSERT_EQUAL( (size_t) 1, allMolecules.size());
+  pointmap = CorrelationToPoint( allMolecules, elements, (const Vector *)point );
   binmap = NULL;
 

src/unittests/AnalysisCorrelationToPointUnitTest.hpp

@@ -35 +35 @@
 private:
 
-      MoleculeListClass *TestList;
+      std::vector<molecule *> allMolecules;
       molecule *TestMolecule;
       element *hydrogen;

src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp

@@ -16 +16 @@
 #include "analysis_correlation.hpp"
 #include "AnalysisCorrelationToSurfaceUnitTest.hpp"
+
+#include "Descriptors/MoleculeDescriptor.hpp"
 
 #include "atom.hpp"
@@ -45 +47 @@
 
   // init private all pointers to zero
-  TestList = NULL;
   TestSurfaceMolecule = NULL;
   surfacemap = NULL;
@@ -83 +84 @@
   CPPUNIT_ASSERT_EQUAL( TestSurfaceMolecule->getAtomCount(), 4 );
 
-  TestList = World::getInstance().getMolecules();
   TestSurfaceMolecule->ActiveFlag = true;
-  TestList->insert(TestSurfaceMolecule);
 
   // init tesselation and linked cell
@@ -116 +115 @@
   TestSurfaceMolecule->AddAtom(Walker);
 
-  TestSurfaceMolecule->ActiveFlag = true;
-  TestList->insert(TestSurfaceMolecule);
+  World::getInstance().selectAllMolecules(AllMolecules());
+  allMolecules = World::getInstance().getSelectedMolecules();
+  CPPUNIT_ASSERT_EQUAL( (size_t) 2, allMolecules.size());
 
   // init maps
@@ -146 +146 @@
 {
   CPPUNIT_ASSERT_EQUAL( 4, TestSurfaceMolecule->getAtomCount() );
-  CPPUNIT_ASSERT_EQUAL( (size_t)2, TestList->ListOfMolecules.size() );
+  CPPUNIT_ASSERT_EQUAL( (size_t)2, allMolecules.size() );
   CPPUNIT_ASSERT_EQUAL( (size_t)4, Surface->PointsOnBoundary.size() );
   CPPUNIT_ASSERT_EQUAL( (size_t)6, Surface->LinesOnBoundary.size() );
@@ -156 +156 @@
   // do the pair correlation
   elements.push_back(hydrogen);
-  surfacemap = CorrelationToSurface( TestList, elements, Surface, LC );
+  surfacemap = CorrelationToSurface( allMolecules, elements, Surface, LC );
 //  OutputCorrelationToSurface ( (ofstream *)&cout, surfacemap );
   CPPUNIT_ASSERT( surfacemap != NULL );
@@ -166 +166 @@
   BinPairMap::iterator tester;
   elements.push_back(hydrogen);
-  surfacemap = CorrelationToSurface( TestList, elements, Surface, LC );
+  surfacemap = CorrelationToSurface( allMolecules, elements, Surface, LC );
   // put pair correlation into bins and check with no range
 //  OutputCorrelationToSurface ( (ofstream *)&cout, surfacemap );
@@ -182 +182 @@
   BinPairMap::iterator tester;
   elements.push_back(hydrogen);
-  surfacemap = CorrelationToSurface( TestList, elements, Surface, LC );
+  surfacemap = CorrelationToSurface( allMolecules, elements, Surface, LC );
 //  OutputCorrelationToSurface ( (ofstream *)&cout, surfacemap );
   // ... and check with [0., 2.] range
@@ -201 +201 @@
   BinPairMap::iterator tester;
   elements.push_back(carbon);
-  surfacemap = CorrelationToSurface( TestList, elements, Surface, LC );
+  surfacemap = CorrelationToSurface( allMolecules, elements, Surface, LC );
 //  OutputCorrelationToSurface ( (ofstream *)&cout, surfacemap );
   // put pair correlation into bins and check with no range
@@ -221 +221 @@
   BinPairMap::iterator tester;
   elements.push_back(carbon);
-  surfacemap = CorrelationToSurface( TestList, elements, Surface, LC );
+  surfacemap = CorrelationToSurface( allMolecules, elements, Surface, LC );
 //  OutputCorrelationToSurface ( (ofstream *)&cout, surfacemap );
   // ... and check with [0., 2.] range

src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp

@@ -43 +43 @@
 private:
 
-      MoleculeListClass *TestList;
+      std::vector<molecule *> allMolecules;
       molecule *TestSurfaceMolecule;
       element *hydrogen;

src/unittests/AnalysisPairCorrelationUnitTest.cpp

@@ -16 +16 @@
 #include "analysis_correlation.hpp"
 #include "AnalysisPairCorrelationUnitTest.hpp"
+
+#include "Descriptors/MoleculeDescriptor.hpp"
 
 #include "World.hpp"
@@ -42 +44 @@
 
   // init private all pointers to zero
-  TestList = NULL;
   TestMolecule = NULL;
   correlationmap = NULL;
@@ -76 +77 @@
   CPPUNIT_ASSERT_EQUAL( TestMolecule->getAtomCount(), 4 );
 
-  TestList = World::getInstance().getMolecules();
-  TestMolecule->ActiveFlag = true;
-  TestList->insert(TestMolecule);
-
   // init maps
-  correlationmap = PairCorrelation( TestList, elements);
+  World::getInstance().selectAllMolecules(AllMolecules());
+  allMolecules = World::getInstance().getSelectedMolecules();
+  CPPUNIT_ASSERT_EQUAL( (size_t) 1, allMolecules.size());
+  correlationmap = PairCorrelation( allMolecules, elements);
   binmap = NULL;
 

src/unittests/AnalysisPairCorrelationUnitTest.hpp

@@ -35 +35 @@
 private:
 
-      MoleculeListClass *TestList;
+      std::vector<molecule *> allMolecules;
       molecule *TestMolecule;
       element *hydrogen;