Changeset e2925fd for src/Fragmentation/Automation

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.

Location:

src/Fragmentation/Automation

Files:

• VMGFragmentController.cpp (modified) (4 diffs)
• VMGFragmentController.hpp (modified) (3 diffs)

src/Fragmentation/Automation/VMGFragmentController.cpp

@@ -71 +71 @@
     const size_t near_field_cells,
     const size_t interpolation_degree,
+    const SampleParticles_t _SampleParticles,
+    const TreatGrid_t _TreatGrid,
     const MPQCData::DoValenceOnly_t _DoValenceOnly,
     const bool _DoPrintDebug)
@@ -86 +88 @@
         new VMGJob(
             next_id,
-            data.sampled_grid,
+            _TreatGrid == DoTreatGrid ?
+                data.sampled_grid :
+                SamplingGrid(data.sampled_grid.begin, data.sampled_grid.end, data.sampled_grid.level),
             data.positions,
             data.charges,
             near_field_cells,
             interpolation_degree,
+            _SampleParticles == DoSampleParticles,
             _DoPrintDebug) );
     jobs.push_back(testJob);
@@ -122 +127 @@
       iter != full_sampled_grid.end();
       ++iter) {
+    const SamplingGrid &grid = *iter;
     const JobId_t next_id = getAvailableId();
     LOG(1, "INFO: Creating full VMGJob with " << *iter
@@ -128 +134 @@
         new VMGJob(
             next_id,
-            *iter,
+            _TreatGrid == DoTreatGrid ?
+                grid :
+                SamplingGrid(grid.begin, grid.end, grid.level),
             positions,
             charges,
             near_field_cells,
             interpolation_degree,
+            _SampleParticles == DoSampleParticles,
             _DoPrintDebug) );
     jobs.push_back(testJob);

src/Fragmentation/Automation/VMGFragmentController.hpp

@@ -39 +39 @@
   {}
 
+  //>! Enumerization of possible treatment of nuclei point charges.
+  enum SampleParticles_t {
+    DontSampleParticles=0,
+    DoSampleParticles=1
+  };
+
+  //>! Enumerization of possible treatment of electronic charge distribution on grid.
+  enum TreatGrid_t {
+    DontTreatGrid=0,
+    DoTreatGrid=1
+  };
+
   /** Creates the long range jobs from finished short-range jobs.
    *
@@ -45 +57 @@
    * \param near_field_cells radius of b-splines for interpolation charges onto grid
    * \param interpolation_degree interpolation degree for newton interpolation from grid
+   * \param _SampleParticles whether to add nuclei charges to vmg calculation.
+   * \param _TreatGrid whether to add electron charge distribution to vmg calculation.
    * \param _DoValenceOnly whether to neglect core electron and nuclei charges
    * \param _DoPrintDebug whether we do print grid for debug visualization or not
@@ -53 +67 @@
       const size_t near_field_cells,
       const size_t interpolation_degree,
+      const SampleParticles_t _SampleParticles,
+      const TreatGrid_t _TreatGrid,
       const MPQCData::DoValenceOnly_t _DoValenceOnly,
       const bool _DoPrintDebug);