Changeset e2925fd for src/Jobs

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/Jobs

Files:

• InterfaceVMGJob.cpp (modified) (5 diffs)
• InterfaceVMGJob.hpp (modified) (3 diffs)
• VMGJob.cpp (modified) (4 diffs)
• VMGJob.hpp (modified) (4 diffs)

src/Jobs/InterfaceVMGJob.cpp

@@ -71 +71 @@
     vmg_float _box_end,
     const int& near_field_cells,
+    const ImportParticles_t _ImportParticles,
     const bool _DoPrintDebug,
     int coarseningSteps,
@@ -80 +81 @@
   returndata(_returndata),
   level(levelMax),
+  ImportParticles(_ImportParticles),
   DoPrintDebug(_DoPrintDebug)
 {
@@ -134 +136 @@
       VMG::MG::GetFactory().GetObjectStorageVal<int>("PARTICLE_NEAR_FIELD_CELLS")));
 
-  // create smeared-out particle charges on particle_grid via splines
-  LOG(1, "INFO: Creating particle grid for " << particles.size() << " particles.");
-  for (std::list<Particle::Particle>::iterator iter = particles.begin();
-      iter != particles.end(); ++iter) {
-    LOG(2, "DEBUG: Current particle is at " << (*iter).Pos()
-        << " with charge " << (*iter).Charge() << ".");
-    spl.SetSpline(particle_grid, *iter);
+  if (ImportParticles == DoImportParticles) {
+    // create smeared-out particle charges on particle_grid via splines
+    LOG(1, "INFO: Creating particle grid for " << particles.size() << " particles.");
+    for (std::list<Particle::Particle>::iterator iter = particles.begin();
+        iter != particles.end(); ++iter) {
+      LOG(2, "DEBUG: Current particle is at " << (*iter).Pos()
+          << " with charge " << (*iter).Charge() << ".");
+      spl.SetSpline(particle_grid, *iter);
+    }
   }
 
@@ -155 +159 @@
       grid,
       sampled_input,
-      -1.);
+      1.);
 
   if (DoPrintDebug) {
@@ -360 +364 @@
   comm.PrintStringOnce("E_total*:       %e", e_long + e_short_peak + e_short_spline - e_self);
 
-  returndata.e_long = e;
+  returndata.nuclei_long = e_long;
+  returndata.electron_long = e_long;
 }

src/Jobs/InterfaceVMGJob.hpp

@@ -36 +36 @@
 {
 public:
+  enum ImportParticles_t {
+    DontImportParticles=0,
+    DoImportParticles=1,
+  };
+
   InterfaceVMGJob(const SamplingGrid &_sampled_input,
       VMGData &returndata,
@@ -46 +51 @@
       vmg_float _box_end,
       const int& near_field_cells,
+      const ImportParticles_t _ImportParticles=DoImportParticles,
       const bool _DoPrintDebug=false,
       int coarseningSteps=0,
@@ -74 +80 @@
   double box_end[3];
 
+  //!> whether we import particles (true) or evaluate only
+  const ImportParticles_t ImportParticles;
+
   //!> whether we do print grid for debug visualization or not
   const bool DoPrintDebug;

src/Jobs/VMGJob.cpp

@@ -83 +83 @@
     const size_t _near_field_cells,
     const size_t _interpolation_degree,
+    const bool _DoImportParticles,
     const bool _DoPrintDebug) :
   FragmentJob(_JobId),
@@ -90 +91 @@
   near_field_cells(_near_field_cells),
   interpolation_degree(_interpolation_degree),
+  DoImportParticles(_DoImportParticles),
+  DoPrintDebug(_DoPrintDebug),
   returndata(static_cast<const SamplingGridProperties &>(_density_grid)),
-  particles(),
-  DoPrintDebug(_DoPrintDebug)
+  particles()
 {}
 
@@ -99 +101 @@
   near_field_cells(3),
   interpolation_degree(3),
-  particles(),
-  DoPrintDebug(false)
+  DoImportParticles(true),
+  DoPrintDebug(false),
+  particles()
 {}
 
@@ -220 +223 @@
       density_grid.end[0]-density_grid.begin[0],
       near_field_cells,
+      DoImportParticles ?
+          VMGInterfaces::InterfaceVMGJob::DoImportParticles
+          : VMGInterfaces::InterfaceVMGJob::DontImportParticles,
       DoPrintDebug);
   new LevelOperatorCS(Stencils::RestrictionFullWeight, Stencils::InterpolationTrilinear);

src/Jobs/VMGJob.hpp

@@ -42 +42 @@
    * @param _interpolation_degree degree of interpolation polynomial for getting nuclei
    *        potential from grid
+   * @param _DoImportParticles whether we import particles (true) or evaluate only
    * @param _DoPrintDebug whether we do print grid for debug visualization or not
    */
@@ -50 +51 @@
       const size_t _near_field_cells,
       const size_t _interpolation_degree,
+      const bool _DoImportParticles=true,
       const bool _DoPrintDebug=false
       );
@@ -72 +74 @@
   //!> interpolation degree used in sampling the potential of the nuclei
   const size_t interpolation_degree;
+  //!> whether we import particles (true) or evaluate only
+  const bool DoImportParticles;
   //!> whether we do print grid for debug visualization or not
   const bool DoPrintDebug;
@@ -124 +128 @@
     ar & const_cast< size_t &>(near_field_cells);
     ar & const_cast< size_t &>(interpolation_degree);
+    ar & const_cast< bool &>(DoImportParticles);
     ar & const_cast< bool &>(DoPrintDebug);
     ar & returndata;