Changeset 945797

Timestamp:

Sep 6, 2016, 2:36:46 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_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, 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:

ce70d25

Parents:

29ce5f

git-author:

Frederik Heber <heber@…> (09/01/16 14:45:46)

git-committer:

Frederik Heber <heber@…> (09/06/16 14:36:46)

Message:

FIX: PotentialTrainer::getFirstGraphwithSpecifiedElements() did not match graph exactly.

• we just checked for the set of elements to be contained but the given set of elements needs to be matched exactly, e.g. CNH4 contains CH4 but is not what we want.

Location:

src/Potentials

Files:

• PotentialTrainer.cpp (modified) (2 diffs)
• PotentialTrainer.hpp (modified) (1 diff)

src/Potentials/PotentialTrainer.cpp

@@ -192 +192 @@
   ASSERT( !counts_per_charge.empty(),
       "getFirstGraphwithSpecifiedElements() - charge counts are empty?");
-  LOG(2, "DEBUG: counts_per_charge is " << counts_per_charge << ".");
+  LOG(1, "DEBUG: counts_per_charge is " << counts_per_charge << ".");
   // we want to check each (unique) key only once
   HomologyContainer::const_key_iterator olditer = homologies.key_end();
@@ -203 +203 @@
     else
       olditer = iter;
-    // if it's a new key, check if every element has the right number of counts
-    Extractors::elementcounts_t::const_iterator countiter = counts_per_charge.begin();
-    for (; countiter != counts_per_charge.end(); ++countiter)
-      if (!(*iter).hasTimesAtomicNumber(
-          static_cast<size_t>(countiter->first),
-          static_cast<size_t>(countiter->second))
-          )
-        break;
-    if( countiter == counts_per_charge.end())
+    // check whether we have the same set of atomic numbers
+    const HomologyGraph::nodes_t &nodes = (*iter).getNodes();
+    Extractors::elementcounts_t nodes_counts_per_charge;
+    for (HomologyGraph::nodes_t::const_iterator nodeiter = nodes.begin();
+        nodeiter != nodes.end(); ++nodeiter) {
+      const Extractors::element_t elem = nodeiter->first.getAtomicNumber();
+      const std::pair<Extractors::elementcounts_t::iterator, bool> inserter =
+          nodes_counts_per_charge.insert( std::make_pair(elem, (Extractors::count_t)nodeiter->second ) );
+      if (!inserter.second)
+        inserter.first->second += (Extractors::count_t)nodeiter->second;
+    }
+    LOG(1, "DEBUG: Node (" << *iter << ")'s counts_per_charge is " << nodes_counts_per_charge << ".");
+    if (counts_per_charge == nodes_counts_per_charge)
       return *iter;
   }

src/Potentials/PotentialTrainer.hpp

@@ -40 +40 @@
         const unsigned int _best_of_howmany) const;
 
+  /** Get the first matching homologous graph based only on the number of nodes.
+   *
+   * We could directly access the equal_range in the HomologyContainer we if were
+   * specified the full HomologyGraph. However, if we have only get "CH4", then
+   * we lack the bonding structure, hence one half of the graph is missing.
+   *
+   * Therefore, we step through all graphs and get the first to match exactly
+   * with the number of specified element.s
+   *
+   * \param homologies container sorted by homologous fragments/graphs
+   * \param types fragment specification, e.g. "CH4"
+   * \return the first matching HomologyGraph
+   */
   static
   HomologyGraph getFirstGraphwithSpecifiedElements(