Changeset d1ba0d for src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

Timestamp:

Dec 14, 2012, 5:39:41 PM (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:

bfbd4a

Parents:

e71325

git-author:

Frederik Heber <heber@…> (09/28/12 08:57:14)

git-committer:

Frederik Heber <heber@…> (12/14/12 17:39:41)

Message:

FIX: Forces-Factors are now written with global ids, HomologyContainer relies on it.

• in FragmentationAutomationAction::performCall() we now use the ForceKeySets to create the HomologyGraph (which has global ids with hydrogens).

File:

• src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) (1 diff)

src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

@@ -408 +408 @@
 
   // convert KeySetContainer to IndexSetContainer
-  IndexSetContainer::ptr container(new IndexSetContainer(ForceKeySet));
-  for (IndexSetContainer::Container_t::const_iterator iter = container->getContainer().begin();
-      iter != container->getContainer().end(); ++iter) // go through each IndexSet
-  {
+  IndexSetContainer::ptr Container(new IndexSetContainer(KeySet));
+  IndexSetContainer::ptr ForceContainer(new IndexSetContainer(ForceKeySet));
+  const IndexSetContainer::Container_t Indices = Container->getContainer();
+  const IndexSetContainer::Container_t ForceIndices = ForceContainer->getContainer();
+  IndexSetContainer::Container_t::const_iterator iter = Indices.begin();
+  IndexSetContainer::Container_t::const_iterator forceiter = ForceIndices.begin();
+  for (;iter != Indices.end(); ++iter, ++forceiter) // go through each IndexSet
+  {
+    // create graph from the force indices (i.e. with hydrogens)
+    HomologyGraph graph(**forceiter);
+    // obtain information for value of HomologyContainer entry with normal indices
     const IndexSet::ptr &index = *iter;
-    HomologyGraph graph(*index);
     HomologyContainer::value_t value;
     std::map<IndexSet::ptr, MPQCDataFragmentMap_t>::const_iterator fragmentiter