Changeset d29b31 for src/Fragmentation/Summation/Containers

Timestamp:

Oct 17, 2013, 7:24:42 AM (11 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:

92f978

Parents:

6531a7

git-author:

Frederik Heber <heber@…> (10/05/13 13:31:14)

git-committer:

Frederik Heber <heber@…> (10/17/13 07:24:42)

Message:

Longrange energy is now also calculated for level 1.

• level 1 sum is incorrect within a molecule but correct between molecules.
• TESTFIX: both analysing long range results required new ..LongRangeResults.dat as level 1 full_potential is missing for new summation.
• TESTFIX: note that only change in O/PBC's .._LongRangeEnergy.dat is additional line for level 1. All other values are exactly the same as must be expected. (and .._Times.dat required replacement, too)

Location:

src/Fragmentation/Summation/Containers

Files:

• FragmentationChargeDensity.cpp (modified) (1 diff)
• FragmentationLongRangeResults.cpp (modified) (4 diffs)

src/Fragmentation/Summation/Containers/FragmentationChargeDensity.cpp

@@ -93 +93 @@
 {
   std::vector<SamplingGrid> full_sample;
-  full_sample.reserve(Result_Grid_fused.size()-1);
-  // skip level 1, as the saturation hydrogen do not yet cancel each other
-  for (std::vector<MPQCDataGridMap_t>::const_iterator iter = ++Result_Grid_fused.begin();
+  full_sample.reserve(Result_Grid_fused.size());
+  for (std::vector<MPQCDataGridMap_t>::const_iterator iter = Result_Grid_fused.begin();
       iter !=Result_Grid_fused.end();
       ++iter)

src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp

@@ -130 +130 @@
 
     Result_LongRangeIntegrated_fused.reserve(MaxLevel);
-    {
-      // NOTE: potential for level 1 is not calculated as saturation hydrogen
-      // are not removed on this level yet
-      VMGDataLongRangeMap_t instance;
-      boost::fusion::at_key<VMGDataFused::electron_longrange>(instance) = 0.;
-      boost::fusion::at_key<VMGDataFused::electron_shortrange>(instance) = 0.;
-      boost::fusion::at_key<VMGDataFused::mixed_longrange>(instance) = 0.;
-      boost::fusion::at_key<VMGDataFused::mixed_shortrange>(instance) = 0.;
-      boost::fusion::at_key<VMGDataFused::nuclei_longrange>(instance) = 0.;
-      boost::fusion::at_key<VMGDataFused::nuclei_shortrange>(instance) = 0.;
-      boost::fusion::at_key<VMGDataFused::total_longrange>(instance) = 0.;
-      boost::fusion::at_key<VMGDataFused::total_shortrange>(instance) = 0.;
-      Result_LongRangeIntegrated_fused.push_back(instance);
-    }
-    for (size_t level = 2; level <= MaxLevel; ++level) {
+    // NOTE: potential for level 1 is wrongly calculated within a molecule
+    // as saturation hydrogen are not removed on this level yet
+    for (size_t level = 1; level <= MaxLevel; ++level) {
       // We have calculated three different contributions: e-e, e-n+n-n, and n-n.
       // And we want to have e-e+e-n, n-n+n-e (where e-n = n-e).
@@ -152 +140 @@
       // first we obtain the full e-e energy as potential times charge on the
       // respective level.
-      // \note that sampled_potential starts at level 2 because we do not calculate
-      // for level 1 as there saturated hydrogens are still present, leaving the
-      // result to be nonsense.
       const SamplingGrid &charge_weight =
           boost::fusion::at_key<MPQCDataFused::sampled_grid>(Result_Grid_fused[level-1]);
-      SamplingGrid full_sample_solution = fullsolutionData[level-2].sampled_potential;
+      SamplingGrid full_sample_solution = fullsolutionData[level-1].sampled_potential;
       full_sample_solution *= charge_weight;
       double electron_solution_energy = full_sample_solution.integral();
@@ -172 +157 @@
 
       // then, we obtain the e-n+n-n full solution in the same way
-      double nuclei_solution_energy = fullsolutionData[level-2].nuclei_long;
+      double nuclei_solution_energy = fullsolutionData[level-1].nuclei_long;
       double nuclei_short_range_energy =
           boost::fusion::at_key<VMGDataFused::nuclei_long>(Result_LongRange_fused[level-1]);
@@ -178 +163 @@
 
       // and also the e-n full solution
-      double both_solution_energy = fullsolutionData[level-2].electron_long;
+      double both_solution_energy = fullsolutionData[level-1].electron_long;
       double both_short_range_energy =
           boost::fusion::at_key<VMGDataFused::electron_long>(Result_LongRange_fused[level-1]);