Changeset e598f5

Timestamp:

Sep 9, 2016, 5:04:06 PM (9 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_StructOpt_integration_tests, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, 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_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, GeometryObjects, Gui_displays_atomic_force_velocity, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, Ubuntu_1604_changes, stable

Children:

ce0f63

Parents:

4fa333

git-author:

Frederik Heber <heber@…> (09/01/16 21:18:19)

git-committer:

Frederik Heber <heber@…> (09/09/16 17:04:06)

Message:

FIX: appendToHomologies() sorted force keysets which brough them out of sequence with keysets.

• we converted them from KeySetsContainer to IndexSetContainer but the conversion does not take place in the same manner as for the normal keysets as there is a different amount of (valid) keysets depending on the number of saturation hydrogen.
• now we use the original containers which are in the same order (we checked that thoroughly via debugging) and convert to IndexSet when needed.
• TEST: Removed all XFAIL from AnalyseFragmentationResults regression tests.

Files:

• src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) (1 diff)
• tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) (6 diffs)

src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp

@@ -303 +303 @@
 
   // convert KeySetContainer to IndexSetContainer
-  IndexSetContainer::ptr ForceContainer(new IndexSetContainer(shortrangeresults.getForceKeySet()));
-  const IndexSetContainer::Container_t &Indices = shortrangeresults.getContainer();
-  const IndexSetContainer::Container_t &ForceIndices = ForceContainer->getContainer();
-  ASSERT( Indices.size() == ForceIndices.size(),
-      "appendToHomologies() - Indices ("+toString(Indices.size())
-      +") and ForceIndices ("+toString(ForceIndices.size())+") sizes differ.");
-  IndexSetContainer::Container_t::const_iterator iter = Indices.begin();
-  IndexSetContainer::Container_t::const_iterator forceiter = ForceIndices.begin();
+  // BUG: Conversion changes order w.r.t to Indices(!)
+  const IndexSetContainer::Container_t &container = shortrangeresults.getContainer();
+  const KeySetsContainer &Indices = shortrangeresults.getKeySet();
+  const KeySetsContainer &ForceIndices = shortrangeresults.getForceKeySet();
+  if (Indices.KeySets.size() != ForceIndices.KeySets.size()) {
+    ELOG(1, "appendToHomologies() - Indices (" << Indices.KeySets.size()
+        << ") and ForceIndices (" << ForceIndices.KeySets.size() << ") sizes differ.");
+    return false;
+  }
+  KeySetsContainer::ArrayOfIntVectors::const_iterator iter = Indices.KeySets.begin();
+  KeySetsContainer::ArrayOfIntVectors::const_iterator forceiter = ForceIndices.KeySets.begin();
 
   /// go through all fragments
-  for (;iter != Indices.end(); ++iter, ++forceiter) // go through each IndexSet
+  for (;iter != Indices.KeySets.end(); ++iter, ++forceiter) // go through each IndexSet
   {
     /// create new graph entry in HomologyContainer which is (key,value) type
-    LOG(1, "INFO: Creating new graph with " << **forceiter << ".");
-    HomologyGraph graph(**forceiter);
-    const IndexSet::ptr &index = *iter;
-    if (!(**forceiter).contains(**iter)) {
+    LOG(1, "INFO: Creating new graph with " << *forceiter << ".");
+    IndexSet forceindexset;
+    forceindexset.insert(forceiter->begin(), forceiter->end());
+    const HomologyGraph graph(forceindexset);
+    // get index set entity from container for lookup to fragment result
+    IndexSet::ptr indexset(new IndexSet);
+    indexset->insert(iter->begin(), iter->end());
+    if (!forceindexset.contains(*indexset)) {
       // this caught an error with faulty KeySetsContainer::insert().
       // indexset and forceindexset need to be in same order and differ
       // only in forceindexset contains extra indices for saturation hydrogens
-      ELOG(1, "appendToHomologies() - force index set " << (**forceiter)
-          << " does not contain index set " << (**iter) << ".");
+      ELOG(1, "appendToHomologies() - force index set " << forceindexset
+          << " does not contain index set " << (*indexset) << ".");
       return false;
     }
+    const IndexSetContainer::Container_t::const_iterator indexiter =
+        std::lower_bound(container.begin(), container.end(), indexset);
+    const IndexSet::ptr &index = *indexiter;
+    ASSERT( *index == *indexset,
+        "appendToHomologies() - could not find index set "+toString(*indexset)
+        +" in the sorted IndexSetContainer.");
+ 
 
     /// we fill the value structure

tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at

@@ -24 +24 @@
 AT_SETUP([Fragmentation - Analyse short-range fragmentation results])
 AT_KEYWORDS([fragmentation analyse-fragment-results])
-AT_XFAIL_IF([/bin/true])
 
 file=BondFragmentShortRangeResults.dat
@@ -41 +40 @@
 AT_SETUP([Fragmentation - Analyse short-range fragmentation results with forces])
 AT_KEYWORDS([fragmentation analyse-fragment-results forces])
-AT_XFAIL_IF([/bin/true])
 
 file=BondFragmentShortRangeResults.dat
@@ -57 +55 @@
 AT_SETUP([Fragmentation - Analyse long-range fragmentation results with OBC])
 AT_KEYWORDS([fragmentation analyse-fragment-results])
-AT_XFAIL_IF([/bin/true])
 
 file=BondFragmentLongRangeResults_OBC.dat
@@ -78 +75 @@
 AT_SETUP([Fragmentation - Analyse long-range fragmentation results with OBC and forces])
 AT_KEYWORDS([fragmentation analyse-fragment-results forces longrange])
-AT_XFAIL_IF([/bin/true])
 
 file=BondFragmentLongRangeResults_OBC.dat
@@ -96 +92 @@
 AT_SETUP([Fragmentation - Analyse long-range fragmentation results with PBC])
 AT_KEYWORDS([fragmentation analyse-fragment-results])
-AT_XFAIL_IF([/bin/true])
 
 file=BondFragmentLongRangeResults_PBC.dat
@@ -117 +112 @@
 AT_SETUP([Fragmentation - Analyse long-range fragmentation results with PBC and forces])
 AT_KEYWORDS([fragmentation analyse-fragment-results forces longrange])
-AT_XFAIL_IF([/bin/true])
 
 file=BondFragmentLongRangeResults_PBC.dat