Changeset 0ba27c9 for src/Fragmentation/Summation/Containers

Timestamp:

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

666e9e

Parents:

276e2f

git-author:

Frederik Heber <heber@…> (02/29/16 12:10:11)

git-committer:

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

Message:

FragmentationLongRangeResults now takes additional implicit charge indices.

• this is required as we obtain more force vectors from the long-range calculations as we have indices for. This is because implicit charges are not associated to any fragment, hence their indices are unknown. However, we nonetheless submit them as extra particles/nuclei to the long-range solver and hence obtain long-range forces for each of them.

Location:

src/Fragmentation/Summation/Containers

Files:

• FragmentationLongRangeResults.cpp (modified) (2 diffs)
• FragmentationLongRangeResults.hpp (modified) (3 diffs)

src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp

@@ -103 +103 @@
     std::map<JobId_t,VMGData> &longrangeData,
     const std::vector<VMGData> &fullsolutionData,
-    const std::vector<SamplingGrid> &full_sample)
+    const std::vector<SamplingGrid> &full_sample,
+    const IndexedVectors::indices_t &_implicit_charges_indices)
 {
   MaxLevel = subsetmap->getMaximumSetLevel();
@@ -148 +149 @@
         sorted_indices.insert(arrayiter->begin(), arrayiter->end());
       }
+      // add additionally those from implicit charges which are not associated to
+      // any fragment and hence are unknown so far.
+      sorted_indices.insert(_implicit_charges_indices.begin(), _implicit_charges_indices.end());
       sorted_indices.erase(-1);
       fullindices.insert(fullindices.begin(), sorted_indices.begin(), sorted_indices.end());

src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.hpp

@@ -34 +34 @@
 #include "Fragmentation/Summation/Containers/VMGDataMap.hpp"
 #include "Fragmentation/Summation/SetValues/SamplingGrid.hpp"
+#include "Fragmentation/Summation/SetValues/IndexedVectors.hpp"
 
 /** FragmentationLongRangeResults contains the summed up results per level resulting
@@ -64 +65 @@
    * @param fullsolutionData long-range solution
    * @param full_sample sampled density
+   * @param _implicit_charges_indices indices of implicit charges that do not
+   *        belong to other fragments (we obtain forces for those from the
+   *        long-range calculation but we lack the indices)
    */
   void operator()(
@@ -69 +73 @@
       std::map<JobId_t,VMGData> &longrangeData,
       const std::vector<VMGData> &fullsolutionData,
-      const std::vector<SamplingGrid> &full_sample);
+      const std::vector<SamplingGrid> &full_sample,
+      const IndexedVectors::indices_t &_implicit_charges_indices = IndexedVectors::indices_t());
 
   size_t getMaxLevel() const {