Changeset e2925fd for src/Fragmentation/Summation/Containers

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/Summation/Containers

Files:

• FragmentationLongRangeResults.cpp (modified) (2 diffs)
• VMGData.cpp (modified) (2 diffs)
• VMGData.hpp (modified) (2 diffs)
• VMGDataFused.hpp (modified) (2 diffs)
• VMGDataMap.hpp (modified) (4 diffs)
• VMGData_printKeyNames.hpp (modified) (1 diff)

src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp

@@ -129 +129 @@
       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.;
@@ -136 +138 @@
     }
     for (size_t level = 2; level <= MaxLevel; ++level) {
-      // we have to fill in the remainder values in the LongRangeMap by hand
-      // weight times correct charge density of the same 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).
+      // For each of these three contributions we have a full solution and summed
+      // up short range solutions.
+
+      // 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;
       full_sample_solution *= charge_weight;
+      double electron_solution_energy = full_sample_solution.integral();
+
+      // then we subtract the summed-up short-range e-e interaction energy from
+      // the full solution.
       const SamplingGrid &short_range_correction =
           boost::fusion::at_key<VMGDataFused::sampled_potential>(Result_LongRange_fused[level-1]);
+      double electron_short_range_energy = short_range_correction.integral();
       full_sample_solution -= short_range_correction;
-      double full_solution_energy = fullsolutionData[level-2].e_long;
-      const double short_range_energy =
-          boost::fusion::at_key<VMGDataFused::energy_long>(Result_LongRange_fused[level-1]);
-      full_solution_energy -= short_range_energy;
-
-      // multiply element-wise with charge distribution
+      electron_solution_energy -= electron_short_range_energy;
+      ASSERT( fabs(electron_solution_energy - full_sample_solution.integral()) < 1e-7,
+          "FragmentationLongRangeResults::operator() - integral and energy are not exchangeable.");
+
+      // 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_short_range_energy =
+          boost::fusion::at_key<VMGDataFused::nuclei_long>(Result_LongRange_fused[level-1]);
+      nuclei_solution_energy -= nuclei_short_range_energy;
+
+      // and also the e-n full solution
+      double both_solution_energy = fullsolutionData[level-2].electron_long;
+      double both_short_range_energy =
+          boost::fusion::at_key<VMGDataFused::electron_long>(Result_LongRange_fused[level-1]);
+      both_solution_energy -= both_short_range_energy;
+
+      // energies from interpolation at nuclei position has factor of 1/2 already
+      electron_solution_energy *= .5;
+      electron_short_range_energy *= .5;
+
+      // At last, we subtract e-n from n-n+e-n for full solution and short-range
+      // correction.
+      nuclei_solution_energy -= both_solution_energy;
+      nuclei_short_range_energy -= both_short_range_energy;
+
       VMGDataLongRangeMap_t instance;
-      boost::fusion::at_key<VMGDataFused::electron_longrange>(instance) = .5*full_sample_solution.integral();
+      boost::fusion::at_key<VMGDataFused::electron_longrange>(instance) = electron_solution_energy;
 //      LOG(0, "Remaining long-range potential integral of level " << level << " is "
 //          << full_sample_solution.integral() << ".");
-      boost::fusion::at_key<VMGDataFused::electron_shortrange>(instance) = .5*short_range_correction.integral();
+      boost::fusion::at_key<VMGDataFused::electron_shortrange>(instance) = electron_short_range_energy;
 //      LOG(0, "Short-range correction potential integral of level " << level << " is "
 //          << short_range_correction.integral() << ".");
-      boost::fusion::at_key<VMGDataFused::nuclei_longrange>(instance) = full_solution_energy;
+      boost::fusion::at_key<VMGDataFused::mixed_longrange>(instance) = both_solution_energy;
 //      LOG(0, "Remaining long-range energy from potential integral of level " << level << " is "
 //          << full_solution_energy << ".");
-      boost::fusion::at_key<VMGDataFused::nuclei_shortrange>(instance) = short_range_energy;
+      boost::fusion::at_key<VMGDataFused::mixed_shortrange>(instance) = both_short_range_energy;
+//      LOG(0, "Short-range correction energy from potential integral of level " << level << " is "
+//          << short_range_energy << ".");
+      boost::fusion::at_key<VMGDataFused::nuclei_longrange>(instance) = nuclei_solution_energy;
+//      LOG(0, "Remaining long-range energy from potential integral of level " << level << " is "
+//          << full_solution_energy << ".");
+      boost::fusion::at_key<VMGDataFused::nuclei_shortrange>(instance) = nuclei_short_range_energy;
 //      LOG(0, "Short-range correction energy from potential integral of level " << level << " is "
 //          << short_range_energy << ".");
       boost::fusion::at_key<VMGDataFused::total_longrange>(instance) =
-          boost::fusion::at_key<VMGDataFused::electron_longrange>(instance) - full_solution_energy;
+          boost::fusion::at_key<VMGDataFused::electron_longrange>(instance)
+          + 2.*boost::fusion::at_key<VMGDataFused::mixed_longrange>(instance)
+          + boost::fusion::at_key<VMGDataFused::nuclei_longrange>(instance);
       boost::fusion::at_key<VMGDataFused::total_shortrange>(instance) =
-          boost::fusion::at_key<VMGDataFused::electron_shortrange>(instance) - short_range_energy;
+          boost::fusion::at_key<VMGDataFused::electron_shortrange>(instance)
+          + 2.*boost::fusion::at_key<VMGDataFused::mixed_shortrange>(instance)
+          + boost::fusion::at_key<VMGDataFused::nuclei_shortrange>(instance);
       Result_LongRangeIntegrated_fused.push_back(instance);
     }

src/Fragmentation/Summation/Containers/VMGData.cpp

@@ -42 +42 @@
 VMGData::VMGData(const SamplingGridProperties &_props) :
   sampled_potential(_props),
-  e_long(0.)
+  nuclei_long(0.),
+  electron_long(0.)
 {}
 
@@ -50 +51 @@
 std::ostream & operator<<(std::ostream &ost, const VMGData &data)
 {
-  ost << "Long-Range energy: " << data.e_long << std::endl;
+  ost << "Nuclei long-Range energy: " << data.nuclei_long << std::endl;
+  ost << "Electron long-Range energy: " << data.electron_long << std::endl;
   return ost;
 }

src/Fragmentation/Summation/Containers/VMGData.hpp

@@ -42 +42 @@
   //!> sampled potential on the grid as output
   SamplingGrid sampled_potential;
-  //!> long-range contribution to energy
-  double e_long;
+  //!> nuclei long-range contribution to energy
+  double nuclei_long;
+  //!> electron long-range contribution to energy
+  double electron_long;
 
 private:
@@ -52 +54 @@
   {
     ar & sampled_potential;
-    ar & e_long;
+    if (version > 0)
+      ar & nuclei_long;
+    ar & electron_long;
   }
 };
+
+BOOST_CLASS_VERSION(VMGData, 1)
 
 std::ostream & operator<<(std::ostream &ost, const VMGData &data);

src/Fragmentation/Summation/Containers/VMGDataFused.hpp

@@ -27 +27 @@
   struct sampled_potential {};
   struct energy_potential {};
-  struct energy_long {};
+  struct nuclei_long {};
+  struct electron_long {};
 
   // keys for longrange
@@ -35 +36 @@
   struct nuclei_longrange {};
   struct nuclei_shortrange {};
+  struct mixed_longrange {};
+  struct mixed_shortrange {};
   struct total_longrange {};
   struct total_shortrange {};

src/Fragmentation/Summation/Containers/VMGDataMap.hpp

@@ -32 +32 @@
     boost::fusion::pair<VMGDataFused::sampled_potential, SamplingGrid >,
     boost::fusion::pair<VMGDataFused::energy_potential, double >,
-    boost::fusion::pair<VMGDataFused::energy_long, double >
+    boost::fusion::pair<VMGDataFused::nuclei_long, double >,
+    boost::fusion::pair<VMGDataFused::electron_long, double >
 > VMGDataMap_t;
 
@@ -38 +39 @@
     VMGDataFused::sampled_potential,
     VMGDataFused::energy_potential,
-    VMGDataFused::energy_long
+    VMGDataFused::nuclei_long,
+    VMGDataFused::electron_long
 > VMGDataVector_t;
 
@@ -51 +53 @@
     boost::fusion::pair<VMGDataFused::electron_longrange, double >,
     boost::fusion::pair<VMGDataFused::electron_shortrange, double >,
+    boost::fusion::pair<VMGDataFused::mixed_longrange, double >,
+    boost::fusion::pair<VMGDataFused::mixed_shortrange, double >,
     boost::fusion::pair<VMGDataFused::nuclei_longrange, double >,
     boost::fusion::pair<VMGDataFused::nuclei_shortrange, double >,
@@ -60 +64 @@
     VMGDataFused::electron_longrange,
     VMGDataFused::electron_shortrange,
+    VMGDataFused::mixed_longrange,
+    VMGDataFused::mixed_shortrange,
     VMGDataFused::nuclei_longrange,
     VMGDataFused::nuclei_shortrange,

src/Fragmentation/Summation/Containers/VMGData_printKeyNames.hpp

@@ -36 +36 @@
         (sampled_potential) \
   (energy_potential) \
-  (energy_long) \
+  (nuclei_long) \
+  (electron_long) \
   (electron_longrange) \
   (electron_shortrange) \
+  (mixed_longrange) \
+  (mixed_shortrange) \
   (nuclei_longrange) \
   (nuclei_shortrange) \