Changeset 666e9e for src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp

Timestamp:

May 7, 2016, 7:05:19 AM (10 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_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_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:

a9099d

Parents:

0ba27c9

git-author:

Frederik Heber <heber@…> (02/17/16 18:24:55)

git-committer:

Frederik Heber <heber@…> (05/07/16 07:05:19)

Message:

VMGFragmentController and FragmentationAutomationAction accept UseImplicitCharge.

• this causes nuclei charges for the full solution to be taken from the ParticleRegistry that contains partial charges table and not the elementary charges.

File:

• src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) (5 diffs)

src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp

@@ -62 +62 @@
 
 #include "Descriptors/AtomIdDescriptor.hpp"
+#include "Atom/atom.hpp"
+#include "Element/element.hpp"
 #include "Fragmentation/Summation/Containers/FragmentationChargeDensity.hpp"
 #include "Fragmentation/Summation/Containers/FragmentationResultContainer.hpp"
@@ -86 +88 @@
 #endif
 #include "Helpers/defs.hpp"
+#include "Potentials/Particles/ParticleRegistry.hpp"
 #include "World.hpp"
 
@@ -672 +675 @@
 
     // Final phase: sum up and print result
+    IndexedVectors::indices_t implicit_indices;
+    if (params.UseImplicitCharges.get()) {
+      // place all in implicit charges that are not selected but contained in ParticleRegistry
+      const World &world = const_cast<const World &>(World::getInstance());
+      const ParticleRegistry &registry = const_cast<const ParticleRegistry &>(ParticleRegistry::getInstance());
+      const World::ConstAtomComposite &atoms = world.getAllAtoms();
+      for (World::ConstAtomComposite::const_iterator iter = atoms.begin();
+          iter != atoms.end(); ++iter) {
+        const atomId_t atomid = (*iter)->getId();
+        if (!world.isAtomSelected(atomid)) {
+          const std::string &symbol = (*iter)->getElement().getSymbol();
+          if (registry.isPresentByName(symbol))
+            implicit_indices.push_back(atomid);
+        }
+      }
+      LOG(2, "INFO: We added " << implicit_indices.size() << " indices due to implicit charges.");
+    }
+
     FragmentationLongRangeResults longrangeresults(
         shortrangedata,longrangeData,keysets, forcekeysets);
@@ -678 +699 @@
         longrangeData,
         fullsolutionData,
-        full_sample);
+        full_sample,
+        implicit_indices);
     printReceivedFullResults(longrangeresults);
 
@@ -698 +720 @@
     std::map<JobId_t, VMGData> longrangeData;
     FragmentationLongRangeResults longrangeresults(
-        shortrangedata,longrangeData,keysets, forcekeysets);
+        shortrangedata, longrangeData, keysets, forcekeysets);
     appendToHomologies(shortrangeresults, longrangeresults, false);
   }