Changeset 61fc12

Timestamp:

Sep 9, 2016, 1:51:43 PM (8 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:

4fa333

Parents:

34af97

git-author:

Frederik Heber <heber@…> (09/01/16 20:33:43)

git-committer:

Frederik Heber <heber@…> (09/09/16 13:51:43)

Message:

FIX: FragmentBOSSANOVA got full molecule as restricted keyset.

• although only selected atoms are used to construct the AtomMask, still the full molecule was used for bond partners from the (restricted) set of root nodes. This lead to globalsaturationpositions missing spots for those atoms outside the selected set.

File:

• src/Fragmentation/Fragmentation.cpp (modified) (2 diffs)

src/Fragmentation/Fragmentation.cpp

@@ -271 +271 @@
     NumMoleculesOfOrder[i] = 0;
 
-  // Construct the complete KeySet which we need for topmost level only (but for all Roots)
-  KeySet CompleteMolecule;
-  for (molecule::const_iterator iter = const_cast<const molecule *>(mol)->begin();
-      iter != const_cast<const molecule *>(mol)->end();
-      ++iter) {
-    CompleteMolecule.insert((*iter)->GetTrueFather()->getNr());
-  }
+  // Construct the restricted key set (contained in the root stack), i.e. which atoms take part
+  KeySet RestrictedKeyset;
+  for (KeyStack::const_iterator iter = RootStack.begin(); iter != RootStack.end(); ++iter)
+    RestrictedKeyset.insert(*iter);
 
   // this can easily be seen: if Order is 5, then the number of levels for each lower order is the total sum of the number of levels above, as
@@ -312 +309 @@
 
       // Create list of Graphs of current Bond Order (i.e. F_{ij})
-      NumMoleculesOfOrder[RootNr] = PSG(CompleteMolecule, treatment);
+      NumMoleculesOfOrder[RootNr] = PSG(RestrictedKeyset, treatment);
 
       // output resulting number