Changeset 1024cb for src/unittests/LinkedCellUnitTest.cpp

Timestamp:

May 31, 2010, 5:32:27 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:

e08c46

Parents:

42af9e (diff), a7b761b (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.

git-author:

Frederik Heber <heber@…> (05/31/10 17:29:30)

git-committer:

Frederik Heber <heber@…> (05/31/10 17:32:27)

Message:

Merge commit 'jupiter/MoleculeStartEndSwitch' into CommandLineActionMapping

Conflicts:

molecuilder/src/Makefile.am
molecuilder/src/builder.cpp
molecuilder/src/config.cpp
molecuilder/src/helpers.hpp
molecuilder/src/molecule.cpp
molecuilder/src/molecule_dynamics.cpp
molecuilder/src/molecule_fragmentation.cpp
molecuilder/src/molecule_geometry.cpp
molecuilder/src/molecule_graph.cpp
molecuilder/src/moleculelist.cpp
molecuilder/src/unittests/AnalysisCorrelationToPointUnitTest.cpp
molecuilder/src/unittests/listofbondsunittest.cpp

Integration of MoleculeStartEndSwitch had the following consequences:

• no more AtomCount -> getAtomCount()
• no more start/end -> begin(), end() and iterator
• no more decent ordering in atomic ids (hence, Simple_configuration/8 and Domain/5, Domain/6 now check by comparing sorted xyz, not confs)

There is still a huge problem with bonds. One test runs into an endless loop.

Signed-off-by: Frederik Heber <heber@…>

File:

• src/unittests/LinkedCellUnitTest.cpp (modified) (6 diffs)

src/unittests/LinkedCellUnitTest.cpp

@@ -60 +60 @@
 
   // check that TestMolecule was correctly constructed
-  CPPUNIT_ASSERT_EQUAL( TestMolecule->AtomCount, 3*3*3 );
-  Walker = TestMolecule->start->next;
-  CPPUNIT_ASSERT( TestMolecule->end != Walker );
+  CPPUNIT_ASSERT_EQUAL( TestMolecule->getAtomCount(), 3*3*3 );
 };
 
@@ -187 +185 @@
 {
   // check all atoms
-  atom *Walker = TestMolecule->start;
-  while (Walker->next != TestMolecule->end) {
-    Walker = Walker->next;
-    CPPUNIT_ASSERT_EQUAL( true, LC->SetIndexToNode(Walker) );
+  for(molecule::iterator iter = TestMolecule->begin(); iter != TestMolecule->end();++iter){
+    CPPUNIT_ASSERT_EQUAL( true, LC->SetIndexToNode(*iter) );
   }
 
   // check internal vectors, returns false, because this atom is not in LC-list!
-  Walker = World::getInstance().createAtom();
-  Walker->setName("test");
-  Walker->x= Vector(1,1,1);
-  CPPUNIT_ASSERT_EQUAL( false, LC->SetIndexToNode(Walker) );
-  World::getInstance().destroyAtom(Walker);
+  atom *newAtom = World::getInstance().createAtom();
+  newAtom->setName("test");
+  newAtom->x= Vector(1,1,1);
+  CPPUNIT_ASSERT_EQUAL( false, LC->SetIndexToNode(newAtom) );
+  World::getInstance().destroyAtom(newAtom);
 
   // check out of bounds vectors
-  Walker = World::getInstance().createAtom();
-  Walker->setName("test");
-  Walker->x = Vector(0,-1,0);
-  CPPUNIT_ASSERT_EQUAL( false, LC->SetIndexToNode(Walker) );
-  World::getInstance().destroyAtom(Walker);
+  newAtom = World::getInstance().createAtom();
+  newAtom->setName("test");
+  newAtom->x = Vector(0,-1,0);
+  CPPUNIT_ASSERT_EQUAL( false, LC->SetIndexToNode(newAtom) );
+  World::getInstance().destroyAtom(newAtom);
 };
 
@@ -277 +273 @@
   size = ListOfPoints->size();
   CPPUNIT_ASSERT_EQUAL( (size_t)27, size );
-  Walker = TestMolecule->start;
-  Walker = TestMolecule->start;
-  while (Walker->next != TestMolecule->end) {
-    Walker = Walker->next;
-    ListOfPoints->remove(Walker);
+
+  for(molecule::iterator iter = TestMolecule->begin(); iter != TestMolecule->end(); ++iter){
+    ListOfPoints->remove((*iter));
     size--;
     CPPUNIT_ASSERT_EQUAL( size, ListOfPoints->size() );
@@ -296 +290 @@
   size=ListOfPoints->size();
   CPPUNIT_ASSERT_EQUAL( (size_t)8, size );
-  Walker = TestMolecule->start;
-  while (Walker->next != TestMolecule->end) {
-    Walker = Walker->next;
-    if ((Walker->x[0] <2) && (Walker->x[1] <2) && (Walker->x[2] <2)) {
-      ListOfPoints->remove(Walker);
+  for(molecule::iterator iter = TestMolecule->begin(); iter != TestMolecule->end(); ++iter){
+    if (((*iter)->x[0] <2) && ((*iter)->x[1] <2) && ((*iter)->x[2] <2)) {
+      ListOfPoints->remove(*iter);
       size--;
       CPPUNIT_ASSERT_EQUAL( size, ListOfPoints->size() );
@@ -316 +308 @@
   size=ListOfPoints->size();
   CPPUNIT_ASSERT_EQUAL( (size_t)27, size );
-  Walker = TestMolecule->start;
-  while (Walker->next != TestMolecule->end) {
-    Walker = Walker->next;
-    ListOfPoints->remove(Walker);
+  for(molecule::iterator iter = TestMolecule->begin(); iter!=TestMolecule->end();++iter){
+    ListOfPoints->remove(*iter);
     size--;
     CPPUNIT_ASSERT_EQUAL( size, ListOfPoints->size() );
@@ -345 +335 @@
   size = ListOfPoints->size();
   CPPUNIT_ASSERT_EQUAL( (size_t)7, size );
-  Walker = TestMolecule->start;
-  while (Walker->next != TestMolecule->end) {
-    Walker = Walker->next;
-    if ((Walker->x.DistanceSquared(tester) - 1.) < MYEPSILON ) {
-      ListOfPoints->remove(Walker);
+  for(molecule::iterator iter = TestMolecule->begin(); iter!=TestMolecule->end();++iter){
+    if (((*iter)->x.DistanceSquared(tester) - 1.) < MYEPSILON ) {
+      ListOfPoints->remove(*iter);
       size--;
       CPPUNIT_ASSERT_EQUAL( size, ListOfPoints->size() );