Changeset e2925fd for src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

Timestamp:

May 3, 2013, 9:46:45 AM (12 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:

a86666

Parents:

5281ff

git-author:

Frederik Heber <heber@…> (04/05/13 15:09:16)

git-committer:

Frederik Heber <heber@…> (05/03/13 09:46:45)

Message:

Split long-range calculations into two parts to overcome E-N-potential problems.

The general problem is that smeared-out nuclei charges cannot interact with
electron charge densities as they always overlap, hence we always make a large
error. The idea then is - as the potential energy is symmetric both
densities - to flip from N-E to E-N, i.\,e. to take the electron potential and
evaluate at nuclei positions instead of smeared-out nuclei charges with
eletronic charge distribution. However, then we need to make two calculations
for the four contributions: E-E, E-N and N-N, N-E (=E-N).

• new enums SampleParticles_t eventually tells InterfaceVMGJob whether to sample the nuclei charges onto the grid or not.
• TreatGrid_t tells InterfaceVMGJob whether to actually add the electronic charge onto the grid (this was added but is actually not required anymore).
• FragmentationAutomationAction::performCall() now creates twice as many long-range jobs. This requires two variables in VMGData for storing integrated long-range energy: electron_long, nuclei_long, as both calculations are combined into a single VMGData instance per fragment.
• Summation of long-range contributions is split into three instead of formerly two parts: electron (E-E), nuclei (N-N), and mixed (E-N). This allows to easierly check their cancellation. This needs new member in fusion map and name in printKeyNames.
• naturally, the enums have to be passed a long way: VMGFragmentController, VMGJob, VMGData.
• VMGData now has serialization version 1 due to new entry.
• we enhanced documentation in FragmentationLongRangeResults::operator()() of how and what is summed per level.
• FIX: InterfaceVMGJob::ImportRightHandSide() subtracted grid instead of adding it. Now, we set correct sign of electron charge distribution in MPQC.
• TESTFIX: Regression test AnalyseFragmentResults now has short- and long-range part. Long-range part is only diff'ed when the compiled code has the capabilities.

File:

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

src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

@@ -153 +153 @@
     vmgcontroller.setPort(params.port.get());
     const size_t NoJobs = shortrangedata.size()+full_sample.size();
-    vmgcontroller.requestIds(NoJobs);
-
-    // Phase Five: create VMGJobs
+    vmgcontroller.requestIds(2*NoJobs);
+
+    // Phase Five a: create VMGJobs for electronic charge distribution
     const size_t near_field_cells = params.near_field_cells.get();
     const size_t interpolation_degree = params.interpolation_degree.get();
@@ -163 +163 @@
         near_field_cells,
         interpolation_degree,
+        VMGFragmentController::DontSampleParticles,
+        VMGFragmentController::DoTreatGrid,
         params.DoValenceOnly.get() ? MPQCData::DoSampleValenceOnly : MPQCData::DontSampleValenceOnly,
         params.DoPrintDebug.get()))
-      // can't use the summed up fragment due to saturation hydrogens
-//      summedChargeDensity.getFragment(),
       return Action::failure;
 
-    // Phase Six: calculate result
+    // Phase Six a: calculate result
     vmgcontroller.waitforResults(NoJobs);
     vmgcontroller.getResults(longrangedata);
@@ -175 +175 @@
         "FragmentationFragmentationAutomationAction::performCall() - number of MPQCresults+"
         +toString(full_sample.size())+"="+toString(NoJobs)
-        +" and VMGresults "+toString(longrangedata.size())+" don't match.");
+        +" and first VMGresults "+toString(longrangedata.size())+" don't match.");
     Exitflag += vmgcontroller.getExitflag();
+
+    {
+      std::map<JobId_t, VMGData> longrangedata_both;
+      // Phase Five b: create VMGJobs for nuclei charge distributions
+      const size_t near_field_cells = params.near_field_cells.get();
+      const size_t interpolation_degree = params.interpolation_degree.get();
+      if (!vmgcontroller.createLongRangeJobs(
+          shortrangedata,
+          full_sample,
+          near_field_cells,
+          interpolation_degree,
+          VMGFragmentController::DoSampleParticles,
+          VMGFragmentController::DoTreatGrid,
+          params.DoValenceOnly.get() ? MPQCData::DoSampleValenceOnly : MPQCData::DontSampleValenceOnly,
+          params.DoPrintDebug.get()))
+        return Action::failure;
+
+      // Phase Six b: calculate result
+      vmgcontroller.waitforResults(NoJobs);
+      vmgcontroller.getResults(longrangedata_both);
+      ASSERT( NoJobs == longrangedata_both.size(),
+          "FragmentationFragmentationAutomationAction::performCall() - number of MPQCresults+"
+          +toString(full_sample.size())+"="+toString(NoJobs)
+          +" and second VMGresults "+toString(longrangedata_both.size())+" don't match.");
+      Exitflag += vmgcontroller.getExitflag();
+
+      // go through either data and replace nuclei_long with contribution from both
+      ASSERT( longrangedata.size() == longrangedata_both.size(),
+          "FragmentationFragmentationAutomationAction::performCall() - longrange results have different sizes.");
+      std::map<JobId_t, VMGData>::iterator destiter = longrangedata.begin();
+      std::map<JobId_t, VMGData>::iterator srciter = longrangedata_both.begin();
+      for (;destiter != longrangedata.end(); ++srciter, ++destiter)
+        destiter->second.nuclei_long = srciter->second.nuclei_long;
+    }
   }