Changeset d93d2c for src

Timestamp:

Feb 11, 2016, 8:03:36 AM (9 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:

cbd409

Parents:

45b45d

git-author:

Frederik Heber <heber@…> (02/08/16 15:47:17)

git-committer:

Frederik Heber <heber@…> (02/11/16 08:03:36)

Message:

FIX: Long-range forces were not added onto atom's forces.

• this was with highest level forces obtained from fragmentation for the short-range interactions but not for the long-range interactions.
• TESTS: added additional tests to Fragmentation AnalyseFragmentationResults to compare long-range forces written to tremolo file in the same way as is already done with short-range.
• TESTFIX: Needed to re-calculate all Fragment result files, did for short-range and both long-range versions. Energies slightly changed and thus also derived values.

File:

• src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) (3 diffs)

src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp

@@ -533 +533 @@
 }
 
+static void AddForces(
+    const IndexedVectors::indexedvectors_t &_forces,
+    const bool _IsAngstroem)
+{
+  for(IndexedVectors::indexedvectors_t::const_iterator iter = _forces.begin();
+      iter != _forces.end(); ++iter) {
+    const IndexedVectors::index_t &index = iter->first;
+    const IndexedVectors::vector_t &forcevector = iter->second;
+    ASSERT( forcevector.size() == NDIM,
+        "printReceivedShortResults() - obtained force vector has incorrect dimension.");
+    // note that mpqc calculates a gradient, hence force pointing into opposite direction
+    // we have to mind different units here: MPQC has a_o, while we may have angstroem
+    Vector ForceVector(-forcevector[0], -forcevector[1], -forcevector[2]);
+    if (_IsAngstroem)
+      for (size_t i=0;i<NDIM;++i)
+        ForceVector[i] *= AtomicLengthToAngstroem;
+    atom *_atom = World::getInstance().getAtom(AtomById(index));
+    if(_atom != NULL)
+      _atom->setAtomicForce(_atom->getAtomicForce() + ForceVector);
+    else
+      ELOG(2, "Could not find atom to id " << index << ".");
+  }
+}
+
 ActionState::ptr FragmentationAnalyseFragmentationResultsAction::performCall() {
 
@@ -617 +641 @@
   // adding obtained forces
   if ( const_cast<const World &>(World::getInstance()).getAllAtoms().size() != 0) {
-    const IndexedVectors::indexedvectors_t forces =
+    const IndexedVectors::indexedvectors_t shortrange_forces =
         boost::fusion::at_key<MPQCDataFused::forces>(
             shortrangeresults.Result_Force_fused.back()
             ).getVectors();
-        ;
-    for(IndexedVectors::indexedvectors_t::const_iterator iter = forces.begin();
-        iter != forces.end(); ++iter) {
-      const IndexedVectors::index_t &index = iter->first;
-      const IndexedVectors::vector_t &forcevector = iter->second;
-      ASSERT( forcevector.size() == NDIM,
-          "printReceivedShortResults() - obtained force vector has incorrect dimension.");
-      // note that mpqc calculates a gradient, hence force pointing into opposite direction
-      // we have to mind different units here: MPQC has a_o, while we may have angstroem
-      Vector ForceVector(-forcevector[0], -forcevector[1], -forcevector[2]);
-      if (IsAngstroem)
-        for (size_t i=0;i<NDIM;++i)
-          ForceVector[i] *= AtomicLengthToAngstroem;
-      atom *_atom = World::getInstance().getAtom(AtomById(index));
-      if(_atom != NULL)
-        _atom->setAtomicForce(_atom->getAtomicForce() + ForceVector);
-      else
-        ELOG(2, "Could not find atom to id " << index << ".");
-    }
+    AddForces(shortrange_forces,IsAngstroem);
   } else {
     LOG(1, "INFO: Full molecule not loaded, hence will not add forces to atoms.");
@@ -675 +681 @@
     printReceivedFullResults(longrangeresults);
 
+    // add long-range forces
+    if ( const_cast<const World &>(World::getInstance()).getAllAtoms().size() != 0) {
+      const IndexedVectors::indexedvectors_t longrange_forces =
+          boost::fusion::at_key<VMGDataFused::forces_longrange>(
+              longrangeresults.Result_ForcesLongRangeIntegrated_fused.back()
+              ).getVectors();
+      AddForces(longrange_forces,IsAngstroem);
+    } else {
+      LOG(1, "INFO: Full molecule not loaded, hence will not add forces to atoms.");
+    }
+
     // append all keysets to homology file
     appendToHomologies(shortrangeresults, longrangeresults, params.DoStoreGrids.get());