Changeset 3aa8a5 for src/Graph/unittests

Timestamp:

Dec 3, 2012, 9:50:01 AM (12 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:

4694df

Parents:

5197e5

git-author:

Frederik Heber <heber@…> (09/21/12 16:22:50)

git-committer:

Frederik Heber <heber@…> (12/03/12 09:50:01)

Message:

REFACTOR: AdjacencyList now just contains a single internal map.

• map may either be created from world for a given vector of atomids or parsed from file.
• Moved molecule::StoreAdjacencyFromFile() over to StoreToFile().
• removed atom_bondedparticle::OutputAdjacency().
• changed comparison functions into operator<,>,==,!=().
• adapted FragmentationAction and SaveAdjacencyAction due to new calls, the former also needs to check the adjacency file for existence.
• SaveAdjacencyAction does not split given filename into path and name anymore.
• TESTFIX: Fragmentation-MaxOrder is working again, removed XFAIL_IF.
• TESTFIX: Rewrite of AdjacencyListUnitTest due to heavily changed interface of AdjacencyList. Also wrongadjacencyfile3 was buggy.
• TESTFIX: regression test SaveAdjacency replaced tab by space and removed tab after last entry in test.adj.

Location:

src/Graph/unittests

Files:

• AdjacencyListUnitTest.cpp (modified) (9 diffs)
• AdjacencyListUnitTest.hpp (modified) (2 diffs)

src/Graph/unittests/AdjacencyListUnitTest.cpp

@@ -65 +65 @@
 CPPUNIT_TEST_SUITE_REGISTRATION( AdjacencyListTest );
 
-static std::string adjacencyfile ="\
+const std::string adjacencyfile ="\
 1 2\n\
 2 1 3\n\
@@ -77 +77 @@
 10 9\n";
 
-static std::string wrongadjacencyfile1 ="\
+const std::string wrongadjacencyfile1 ="\
 1 2\n\
 2 1\n\
@@ -88 +88 @@
 10 9\n";
 
-static std::string wrongadjacencyfile2 ="\
+const std::string wrongadjacencyfile2 ="\
 1 2\n\
 2 1 3\n\
@@ -99 +99 @@
 9 8 10\n\
 10 9 11\n\
-11 10";
-
-static std::string wrongadjacencyfile3 ="\
+11 10\n";
+
+const std::string wrongadjacencyfile3 ="\
 1 2\n\
 2 1 3\n\
@@ -111 +111 @@
 8 7 9\n\
 9 8 10\n\
-10 9 11\n\
-11 10";
+10 9\n";
 
 // set up and tear down
@@ -167 +166 @@
 {
   std::stringstream input;
-  AdjacencyList fileChecker(input);
-  fileChecker.CreateMap(atomIds, fileChecker.ExternalAtomBondMap);
+  AdjacencyList FileAdjacency(input);
+  AdjacencyList WorldAdjacency(atomIds);
 
   // check size (it's 8*2 + 2*1 = 18 keys)
-  CPPUNIT_ASSERT_EQUAL( (size_t)18, fileChecker.ExternalAtomBondMap.size() );
-  CPPUNIT_ASSERT_EQUAL( (size_t)0, fileChecker.InternalAtomBondMap.size() );
+  CPPUNIT_ASSERT_EQUAL( (size_t)18, WorldAdjacency.atombondmap.size() );
+  CPPUNIT_ASSERT_EQUAL( (size_t)0, FileAdjacency.atombondmap.size() );
 
   // check equality
-  CPPUNIT_ASSERT( comparisonMap.size() == fileChecker.ExternalAtomBondMap.size() );
+  CPPUNIT_ASSERT( comparisonMap.size() == WorldAdjacency.atombondmap.size() );
 //  std::cout << "comparisonMap: " << comparisonMap << std::endl;
-//  std::cout << "fileChecker.InternalAtomBondMap: " << fileChecker.InternalAtomBondMap << std::endl;
-  CPPUNIT_ASSERT( comparisonMap == fileChecker.ExternalAtomBondMap );
+//  std::cout << "WorldAdjacency.atombondmap: " << WorldAdjacency.atombondmap << std::endl;
+  CPPUNIT_ASSERT( comparisonMap == WorldAdjacency.atombondmap );
 
   // check non-equality: more
   comparisonMap.insert( std::make_pair( (atomId_t)10, (atomId_t)8) );
-  CPPUNIT_ASSERT( comparisonMap != fileChecker.ExternalAtomBondMap );
+  CPPUNIT_ASSERT( comparisonMap != WorldAdjacency.atombondmap );
   comparisonMap.erase((atomId_t)10);
 
   // check non-equality: less
   comparisonMap.erase((atomId_t)9);
-  CPPUNIT_ASSERT( comparisonMap != fileChecker.ExternalAtomBondMap );
+  CPPUNIT_ASSERT( comparisonMap != WorldAdjacency.atombondmap );
 }
 
@@ -196 +195 @@
 {
   std::stringstream input(adjacencyfile);
-  AdjacencyList fileChecker(input);
-  std::vector<atomId_t> noids;
-  fileChecker.CreateMap(noids, fileChecker.ExternalAtomBondMap);
+  AdjacencyList FileAdjacency(input);
+  AdjacencyList WorldAdjacency;
 
   // check size (it's 8*2 + 2*1 = 18 keys)
-  CPPUNIT_ASSERT_EQUAL( (size_t)0, fileChecker.ExternalAtomBondMap.size() );
-  CPPUNIT_ASSERT_EQUAL( (size_t)18, fileChecker.InternalAtomBondMap.size() );
+  CPPUNIT_ASSERT_EQUAL( (size_t)0, WorldAdjacency.atombondmap.size() );
+  CPPUNIT_ASSERT_EQUAL( (size_t)18, FileAdjacency.atombondmap.size() );
 
   // check equality
-  CPPUNIT_ASSERT( comparisonMap.size() == fileChecker.InternalAtomBondMap.size() );
-  CPPUNIT_ASSERT( comparisonMap == fileChecker.InternalAtomBondMap );
+  CPPUNIT_ASSERT( comparisonMap.size() == FileAdjacency.atombondmap.size() );
+  CPPUNIT_ASSERT( comparisonMap == FileAdjacency.atombondmap );
 
   // check non-equality: more
   comparisonMap.insert( std::make_pair( (atomId_t)10, (atomId_t)8) );
-  CPPUNIT_ASSERT( comparisonMap != fileChecker.InternalAtomBondMap );
+  CPPUNIT_ASSERT( comparisonMap != FileAdjacency.atombondmap );
   comparisonMap.erase((atomId_t)10);
 
   // check non-equality: less
   comparisonMap.erase((atomId_t)9);
-  CPPUNIT_ASSERT( comparisonMap != fileChecker.InternalAtomBondMap );
-}
-
-/** Unit tests for AdjacencyList::CompareInternalExternalMap().
- *
- */
-void AdjacencyListTest::CompareInternalExternalMapTest()
+  CPPUNIT_ASSERT( comparisonMap != FileAdjacency.atombondmap );
+}
+
+/** Unit tests for AdjacencyList::StoreToFile().
+ *
+ */
+void AdjacencyListTest::StoreToFileTest()
 {
   std::stringstream input(adjacencyfile);
-  AdjacencyList fileChecker(input);
+  AdjacencyList FileAdjacency(input);
+
+  // check size (it's 8*2 + 2*1 = 18 keys)
+  CPPUNIT_ASSERT_EQUAL( (size_t)18, FileAdjacency.atombondmap.size() );
+
+  // store to file
+  std::stringstream output;
+  FileAdjacency.StoreToFile(output);
+  CPPUNIT_ASSERT_EQUAL( input.str(), output.str() );
+}
+
+/** Unit tests for AdjacencyList::operator<().
+ *
+ */
+void AdjacencyListTest::operatorGreaterLessTest()
+{
+  std::stringstream input(adjacencyfile);
+  AdjacencyList FileAdjacency(input);
+  AdjacencyList WorldAdjacency;
+
+  // assert empty set is subset of some filled set (empty sets should always return true)
+  CPPUNIT_ASSERT( FileAdjacency.atombondmap.size() != WorldAdjacency.atombondmap.size() );
+  CPPUNIT_ASSERT( FileAdjacency.atombondmap != WorldAdjacency.atombondmap );
+  CPPUNIT_ASSERT( WorldAdjacency < FileAdjacency );
+  CPPUNIT_ASSERT( !(WorldAdjacency > FileAdjacency) );
+
+  // parse in external map
+  WorldAdjacency.CreateMap(atomIds);
+
+  // assert equality after parsing
+  CPPUNIT_ASSERT_EQUAL( FileAdjacency.atombondmap.size(), WorldAdjacency.atombondmap.size() );
+  CPPUNIT_ASSERT_EQUAL( FileAdjacency.atombondmap, WorldAdjacency.atombondmap );
+  CPPUNIT_ASSERT( WorldAdjacency < FileAdjacency );
+  CPPUNIT_ASSERT( WorldAdjacency > FileAdjacency );
+
+  // remove one entry from the world
+  WorldAdjacency.atombondmap.erase((atomId_t)9);
+  CPPUNIT_ASSERT( WorldAdjacency < FileAdjacency );
+  CPPUNIT_ASSERT( !(WorldAdjacency > FileAdjacency) );
+}
+
+/** Unit tests for AdjacencyList::operator==().
+ *
+ */
+void AdjacencyListTest::operatorEqualTest()
+{
+  std::stringstream input(adjacencyfile);
+  AdjacencyList FileAdjacency(input);
+  AdjacencyList WorldAdjacency;
 
   // assert equality before parsing (empty sets should always return true)
-  CPPUNIT_ASSERT( fileChecker.ExternalAtomBondMap.size() != fileChecker.InternalAtomBondMap.size() );
-  CPPUNIT_ASSERT( fileChecker.ExternalAtomBondMap != fileChecker.InternalAtomBondMap );
-  CPPUNIT_ASSERT( fileChecker.CompareInternalExternalMap() );
+  CPPUNIT_ASSERT( FileAdjacency.atombondmap.size() != WorldAdjacency.atombondmap.size() );
+  CPPUNIT_ASSERT( FileAdjacency.atombondmap != WorldAdjacency.atombondmap );
+  CPPUNIT_ASSERT( WorldAdjacency != FileAdjacency );
 
   // parse in external map
-  fileChecker.CreateMap(atomIds, fileChecker.ExternalAtomBondMap);
+  WorldAdjacency.CreateMap(atomIds);
 
   // assert equality after parsing
-  CPPUNIT_ASSERT_EQUAL( fileChecker.ExternalAtomBondMap.size(), fileChecker.InternalAtomBondMap.size() );
-  CPPUNIT_ASSERT_EQUAL( fileChecker.ExternalAtomBondMap, fileChecker.InternalAtomBondMap );
-  CPPUNIT_ASSERT( fileChecker.CompareInternalExternalMap() );
+  CPPUNIT_ASSERT_EQUAL( FileAdjacency.atombondmap.size(), WorldAdjacency.atombondmap.size() );
+  CPPUNIT_ASSERT_EQUAL( FileAdjacency.atombondmap, WorldAdjacency.atombondmap );
+  CPPUNIT_ASSERT( WorldAdjacency == FileAdjacency );
 }
 
@@ -245 +291 @@
 void AdjacencyListTest::CheckAgainstSubsetTest()
 {
+  AdjacencyList WorldAdjacency(atomIds);
   {
     // parse right
     std::stringstream input(adjacencyfile);
-    AdjacencyList fileChecker(input);
-    CPPUNIT_ASSERT( fileChecker.CheckAgainstSubset(atomIds) );
+    AdjacencyList FileAdjacency(input);
+    CPPUNIT_ASSERT( (WorldAdjacency > FileAdjacency) && (WorldAdjacency < FileAdjacency) );
   }
   {
     // parse wrong1 (more atoms in the world than in file, hence wrong)
     std::stringstream input(wrongadjacencyfile1);
-    AdjacencyList fileChecker(input);
-    CPPUNIT_ASSERT( !fileChecker.CheckAgainstSubset(atomIds) );
+    AdjacencyList FileAdjacency(input);
+    CPPUNIT_ASSERT( !(WorldAdjacency < FileAdjacency) && (WorldAdjacency > FileAdjacency) );
   }
   {
@@ -262 +309 @@
     std::remove_copy_if(atomIds.begin(), atomIds.end(), std::back_inserter(validids), boost::lambda::_1 == (atomId_t)2);
     CPPUNIT_ASSERT_EQUAL( (size_t)ATOM_COUNT-1, validids.size() );
+    AdjacencyList RestrictedWorldAdjacency(validids);
     // parse wrong1 (more atoms in the world than in file, hence wrong)
     std::stringstream input(wrongadjacencyfile1);
-    AdjacencyList fileChecker(input);
-    CPPUNIT_ASSERT( fileChecker.CheckAgainstSubset(validids) );
+    AdjacencyList FileAdjacency(input);
+    CPPUNIT_ASSERT( RestrictedWorldAdjacency == FileAdjacency );
   }
   {
     // parse wrong2 (there is no atom 10, but present in file. hence true)
     std::stringstream input(wrongadjacencyfile2);
-    AdjacencyList fileChecker(input);
-    CPPUNIT_ASSERT( !fileChecker.CheckAgainstSubset(atomIds) );
-  }
-  {
-    // parse wrong3 (6 is not connected)
+    AdjacencyList FileAdjacency(input);
+    CPPUNIT_ASSERT( !(WorldAdjacency > FileAdjacency) && (WorldAdjacency < FileAdjacency) );
+  }
+  {
+    // parse wrong3 (6 is skipped in connection, hence neither is subset)
     std::stringstream input(wrongadjacencyfile3);
-    AdjacencyList fileChecker(input);
-    CPPUNIT_ASSERT( !fileChecker.CheckAgainstSubset(atomIds) );
-  }
-}
+    AdjacencyList FileAdjacency(input);
+//    WorldAdjacency.StoreToFile((std::ostream &)std::cout);
+//    FileAdjacency.StoreToFile((std::ostream &)std::cout);
+    CPPUNIT_ASSERT( WorldAdjacency != FileAdjacency );
+  }
+}

src/Graph/unittests/AdjacencyListUnitTest.hpp

@@ -32 +32 @@
   CPPUNIT_TEST ( CreateMapTest );
   CPPUNIT_TEST ( ParseIntoMapTest );
-  CPPUNIT_TEST ( CompareInternalExternalMapTest );
+  CPPUNIT_TEST ( StoreToFileTest );
+  CPPUNIT_TEST ( operatorGreaterLessTest );
+  CPPUNIT_TEST ( operatorEqualTest );
   CPPUNIT_TEST ( CheckAgainstSubsetTest );
   CPPUNIT_TEST_SUITE_END();
@@ -42 +44 @@
   void CreateMapTest();
   void ParseIntoMapTest();
-  void CompareInternalExternalMapTest();
+  void StoreToFileTest();
+  void operatorGreaterLessTest();
+  void operatorEqualTest();
   void CheckAgainstSubsetTest();