Changeset 4eb4fe for src/unittests/LinkedCellUnitTest.cpp

Timestamp:

May 18, 2010, 3:20:52 PM (16 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, Candidate_v1.7.0, 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:

673c7f, b0e9c9

Parents:

5079a0

Message:

"-e <db path>" not necessary anymore.

Removed necessity of specifying path to databases (this was one check of molecuilder/test/testsuite.at which cannot be fulfilled anymore with boost::program_options)
For this to work a great number of small changes have been necessary:

class periodentafel:

• all .db files merged into const char * arrays in elements_db.cpp
• periodentafel rewritten:
  • each database has its own function and uses a istream: LoadElementsDatabase(), LoadValenceDatabase(), LoadOrbitalsDatabase(), LoadHBondAngleDatabase(), LoadHBondLengthsDatabase()
  • constructor periodentafel::LoadPeriodentafel() calls each function on the above const char * arrays
  • it is still possible to call LoadPeriodentafel with an external path.
• FindElement(), AskElement() and EnterElement return element * const instead of const element * (i.e. the contents of the pointer is const (the element) not the pointer itself which is very vexatious (i.e. FindElement() yields const element * which can subsequently not be used for RemoveElement(), ...)
• parsedElems is not needed anymore. Instead we operate on map elements directly
• new unittest periodentafelTest which is made friend of periodentafel to be able to access private loading functions directly

A number of unit tests had to be changed (all that create elements during setUp() which is now unnecessary)

• element creation removed: AnalysisCorrelationToPointUnitTest, AnalysisCorrelationToSurfaceUnitTest, AnalysisPairCorrelationUnitTest, CountBondsTest, LinkedCellTest, ParserUnitTest, AnalysisBondsTest, BondGraphTest, ListOfBondsTest
• adapted parsed bond table (carbon is no Z=6 not 2): AnalysisBondsTest, BondGraphTest

Some of the analysis_bonds function's signatures were changed in the process:

• have const element * instead of element *: MinMeanMaxBondDistanceBetweenElements(), CountHydrogenBridgeBonds()

Finally, the respective tests are removed from molecuilder/tests/testsuite.at.

File:

• src/unittests/LinkedCellUnitTest.cpp (modified) (2 diffs)

src/unittests/LinkedCellUnitTest.cpp

@@ -38 +38 @@
   atom *Walker = NULL;
 
-  // init private all pointers to zero
-  TestMolecule = NULL;
-  hydrogen = NULL;
-  tafel = NULL;
-
   // construct element
-  hydrogen = new element;
-  hydrogen->Z = 1;
-  hydrogen->CovalentRadius = 0.23;
-  strcpy(hydrogen->name, "hydrogen");
-  strcpy(hydrogen->symbol, "H");
-
-  // construct periodentafel
-  tafel = World::getInstance().getPeriode();
-  tafel->AddElement(hydrogen);
+  hydrogen = World::getInstance().getPeriode()->FindElement(1);
+  CPPUNIT_ASSERT(hydrogen != NULL && "could not find element hydrogen");
 
   // construct molecule (water molecule)
   TestMolecule = World::getInstance().createMolecule();
+  CPPUNIT_ASSERT(TestMolecule != NULL && "could not create molecule");
   for (double x=0.5;x<3;x+=1.)
     for (double y=0.5;y<3;y+=1.)
       for (double z=0.5;z<3;z+=1.) {
         Walker = World::getInstance().createAtom();
+        CPPUNIT_ASSERT(Walker != NULL && "could not create atom");
         Walker->type = hydrogen;
         *Walker->node = Vector(x, y, z );
@@ -67 +57 @@
   // construct linked cell
   LC = new LinkedCell (TestMolecule, 1.);
+  CPPUNIT_ASSERT(LC != NULL && "could not create LinkedCell");
 
   // check that TestMolecule was correctly constructed