Changeset 82034f1 for src/Actions

Timestamp:

Sep 14, 2016, 6:43:46 PM (8 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_StructOpt_integration_tests, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, 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_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, GeometryObjects, Gui_displays_atomic_force_velocity, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, RotateToPrincipalAxisSystem_UndoRedo, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, Ubuntu_1604_changes, stable

Children:

291ad9

Parents:

964c63

git-author:

Frederik Heber <heber@…> (08/18/16 08:55:21)

git-committer:

Frederik Heber <heber@…> (09/14/16 18:43:46)

Message:

Added currently inactive alternative NN contribution calculation from direct summation.

• direct summation is exact and should alleviate problems with how to choose nfc. The both_sampled_potential is still required for fitting partial charges, hence we cannot remove it. Also, we need the multigrid summation for the full_sample grids (all charges).
• it is difficult to remove, as sampling requires touching all grid points per nuclei (!) due to with 1/r slow decay. Also, we need it for periodic boundary conditions.
• the direct calculation is implemented to check against the fragment results obtained via multigrid calculation (if correct e and not e_long is used). But is commented out.

File:

• src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) (2 diffs)

src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

@@ -152 +152 @@
   return result;
 }
+
+
+#ifdef HAVE_JOBMARKET
+/** This performs a direct sum calculation for the nuclei-nuclei interaction energy
+ * and forces for each fragment contained in \a shortrangedata.
+ *
+ * Results are (re)placed in \a _longrangedata.
+ *
+ * \warning This is only valid for fully open boundary conditions.
+ *
+ * \param _shortrangedata containing information on position and charges per fragment
+ * \param _longrangedata containing energy and forces on return
+ */
+static void calculateNucleiNucleiLongRangeContribution(
+    const std::map<JobId_t, MPQCData> &_shortrangedata,
+    std::map<JobId_t, VMGData>& _longrangedata
+    )
+{
+  ASSERT( _shortrangedata.size() == _longrangedata.size(),
+      "calculateNucleiNucleiLongRangeContribution() - shortrange and longrange data have inequal size.");
+  std::map<JobId_t, VMGData>::iterator longrangeiter = _longrangedata.begin();
+  std::map<JobId_t, MPQCData>::const_iterator iter = _shortrangedata.begin();
+  for (;iter != _shortrangedata.end(); ++iter, ++longrangeiter) {
+    const MPQCData &data = iter->second;
+    VMGData &longrange_data = longrangeiter->second;
+    // set long-range contributions to zero
+    longrange_data.nuclei_long = 0.;
+    longrange_data.forces.clear();
+    longrange_data.forces.resize(data.positions.size(), FragmentForces::force_t(3,0.));
+    longrange_data.hasForces = true;
+    // go through positions and evaluate sum naively
+    ASSERT( data.positions.size() == data.charges.size(),
+        "calculateNucleiNucleiLongRangeContribution() - positions and charges differ in size.");
+    std::vector< std::vector<double> >::const_iterator positer = data.positions.begin();
+    std::vector< double >::const_iterator chargeiter = data.charges.begin();
+    FragmentForces::iterator forceiter = longrange_data.forces.begin();
+    for (; (positer != data.positions.end()) && (chargeiter != data.charges.end());
+        ++positer, ++chargeiter, ++forceiter) {
+      ASSERT( positer->size() == NDIM,
+          "calculateNucleiNucleiLongRangeContribution() - position "
+          +toString(std::distance(data.positions.begin(), positer))+" has not 3 components.");
+      const Vector position((*positer)[0], (*positer)[1], (*positer)[2]);
+
+      std::vector< std::vector<double> >::const_iterator otherpositer = data.positions.begin();
+      std::vector< double >::const_iterator otherchargeiter = data.charges.begin();
+      for (; (otherpositer != data.positions.end()) && (otherchargeiter != data.charges.end());
+          ++otherpositer, ++otherchargeiter) {
+        if ((positer == otherpositer) || (chargeiter == otherchargeiter))
+          continue;
+        ASSERT( otherpositer->size() == NDIM,
+            "calculateNucleiNucleiLongRangeContribution() - other position "
+          +toString(std::distance(data.positions.begin(), otherpositer))+" has not 3 components.");
+        const Vector otherposition((*otherpositer)[0], (*otherpositer)[1], (*otherpositer)[2]);
+        const Vector distance = position - otherposition;
+        const double invsqrdist = 1./distance.Norm();
+        const double factor = (*otherchargeiter)*invsqrdist*invsqrdist*invsqrdist;
+        (*forceiter)[0] = factor*distance[0];
+        (*forceiter)[1] = factor*distance[1];
+        (*forceiter)[2] = factor*distance[2];
+        longrange_data.nuclei_long += 0.5*(*chargeiter)*(*otherchargeiter)*invsqrdist;
+      }
+    }
+  }
+}
+#endif
 
 ActionState::ptr FragmentationFragmentationAutomationAction::performCall() {
@@ -387 +452 @@
       Exitflag += vmgcontroller.getExitflag();
 
+      // now replace nuclei-nuclei contribution with values from direct summation (is exact for
+      // open boundary conditions
+      //
+      // NOTE: We need to calculate both_sampled_potential for fitting partial charges,
+      // nowhere else is this quantity needed.
+      //if (OpenBoundaryConditions)
+      //  calculateNucleiNucleiLongRangeContribution(shortrangedata, longrangedata_both);
+
       // go through either data and replace nuclei_long with contribution from both
       ASSERT( longrangedata.size() == longrangedata_both.size(),