Changeset a2295a for src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

Timestamp:

Dec 10, 2012, 10:10:57 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:

447481

Parents:

238868

git-author:

Frederik Heber <heber@…> (08/31/12 12:31:11)

git-committer:

Frederik Heber <heber@…> (12/10/12 10:10:57)

Message:

We now create one full potential VMGJob of each summed up grid per level.

• i.e. we now have a vector of full_sample and full_sample_solution.
• new fusion map VMGLongRangeMap_t and VMGLongRangeVector to print the summed up grids via writeTable<>.

File:

• src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) (11 diffs)

src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

@@ -247 +247 @@
     const std::map<JobId_t,MPQCData> &fragmentData,
     const std::string &KeySetFilename,
-    SamplingGrid &full_sample,
+    std::vector<SamplingGrid> &full_sample,
     Fragment &full_fragment)
 {
@@ -286 +286 @@
         fragmentData, MatrixNrLookup, container, subsetmap));
   // obtain full grid
-  full_sample = boost::fusion::at_key<MPQCDataFused::sampled_grid>(Result_Grid_fused.back());
+  full_sample.clear();
+  full_sample.reserve(Result_Grid_fused.size());
+  for (std::vector<MPQCDataGridMap_t>::const_iterator iter = ++Result_Grid_fused.begin();
+      iter !=Result_Grid_fused.end();
+      ++iter)
+    full_sample.push_back(boost::fusion::at_key<MPQCDataFused::sampled_grid>((*iter)));
   full_fragment = boost::fusion::at_key<MPQCDataFused::fragment>(Result_Fragment_fused.back());
 
@@ -459 +464 @@
  * @param fragmentData MPQCData resulting from the jobs
  * @param longrangeData VMGData resulting from long-range jobs
- * @param fullsolutionData VMGData resulting from long-range of full problem
+ * @param fullsolutionData VMGData resulting from long-range of full problem from level 2 onward
  * @param KeySetFilename filename with keysets to associate forces correctly
  * @param NoAtoms total number of atoms
@@ -467 +472 @@
     const std::map<JobId_t,MPQCData> &fragmentData,
     const std::map<JobId_t,VMGData> &longrangeData,
-    const VMGData &fullsolutionData,
+    const std::vector<VMGData> &fullsolutionData,
     const std::string &KeySetFilename,
     size_t NoAtoms,
-    SamplingGrid &full_sample)
+    std::vector<SamplingGrid> &full_sample)
 {
   // create lookup from job nr to fragment number
@@ -550 +555 @@
                 VMGMatrixNrLookup);
     epotentialSummer(subsetmap->getMaximumSubsetLevel());
-    SamplingGrid full_sample_solution = fullsolutionData.sampled_potential;
-//    LOG(0, "Remaining long-range energy from energy_potential is " << full_sample_solution.integral()-epotentialSummer.getFullContribution() << ".");
-    full_sample_solution -= potentialSummer.getFullContribution();
-    // multiply element-wise with charge distribution
-    LOG(0, "Remaining long-range potential integral is " << full_sample_solution.integral() << ".");
-    full_sample_solution *= full_sample;
-    LOG(0, "Remaining long-range energy from potential integral is " << full_sample_solution.integral() << ".");
+
+    std::vector<VMGDataLongRangeMap_t> Result_LongRange_fused;
+    Result_LongRange_fused.reserve(subsetmap->getMaximumSubsetLevel());
+    for (size_t level = 1; level <= subsetmap->getMaximumSubsetLevel(); ++level) {
+      // weight times correct charge density of the same level
+      // NOTE: potential for level 1 is not calculated as saturation hydrogen
+      // are not removed on this level yet
+      const size_t potentiallevel = level < 2 ? 0 : (level-2);
+      SamplingGrid charge_weight = boost::fusion::at_key<MPQCDataFused::sampled_grid>(Result_Grid_fused[level-1]);
+      SamplingGrid full_sample_solution = fullsolutionData[potentiallevel].sampled_potential;
+      SamplingGrid short_range_correction = potentialSummer(level);
+  //    LOG(0, "Remaining long-range energy from energy_potential is " << full_sample_solution.integral()-epotentialSummer.getFullContribution() << ".");
+      full_sample_solution -= short_range_correction;
+      // multiply element-wise with charge distribution
+      VMGDataLongRangeMap_t instance;
+      boost::fusion::at_key<VMGDataFused::potential_longrange>(instance) = full_sample_solution.integral();
+      LOG(0, "Remaining long-range potential integral of level " << level << " is "
+          << full_sample_solution.integral() << ".");
+      boost::fusion::at_key<VMGDataFused::potential_shortrange>(instance) = short_range_correction.integral();
+      LOG(0, "Short-range correction potential integral of level " << level << " is "
+          << short_range_correction.integral() << ".");
+      boost::fusion::at_key<VMGDataFused::energy_longrange>(instance) = full_sample_solution.integral(charge_weight);
+      LOG(0, "Remaining long-range energy from potential integral of level " << level << " is "
+          << full_sample_solution.integral(charge_weight) << ".");
+      boost::fusion::at_key<VMGDataFused::energy_shortrange>(instance) = short_range_correction.integral(charge_weight);
+      LOG(0, "Short-range correction energy from potential integral of level " << level << " is "
+          << short_range_correction.integral(charge_weight) << ".");
+      Result_LongRange_fused.push_back(instance);
+    }
+    {
+      //    LOG(0, "Remaining long-range energy from energy_potential is " << full_sample_solution.integral()-epotentialSummer.getFullContribution() << ".");
+      SamplingGrid full_sample_solution = fullsolutionData.back().sampled_potential;
+      SamplingGrid short_range_correction = potentialSummer.getFullContribution();
+      full_sample_solution -= short_range_correction;
+      // multiply element-wise with charge distribution
+      LOG(0, "Remaining long-range potential integral is " << full_sample_solution.integral() << ".");
+      LOG(0, "Short-range correction potential integral of level is " << short_range_correction.integral() << ".");
+      LOG(0, "Remaining long-range energy from potential integral is "
+          << full_sample_solution.integral(full_sample.back()) << ".");
+      LOG(0, "Short-range correction energy from potential integral is "
+          << short_range_correction.integral(full_sample.back()) << ".");
+    }
 
     // TODO: Extract long-range corrections to forces
@@ -567 +607 @@
                 VMGMatrixNrLookup);
     elongSummer(subsetmap->getMaximumSubsetLevel());
-    double e_long = fullsolutionData.e_long;
+    double e_long = fullsolutionData.back().e_long;
     e_long -= elongSummer.getFullContribution();
     LOG(0, "Remaining long-range energy is " << e_long << ".");
@@ -577 +617 @@
             Result_Energy_fused, MaxLevel);
     LOG(0, "Energy table is \n" << energyresult);
+
+    const std::string gridresult =
+        writeTable<VMGDataLongRangeMap_t, VMGDataLongRangeVector_t >()(
+            Result_LongRange_fused, MaxLevel);
+    LOG(0, "LongRange table is \n" << gridresult);
+
     const std::string eigenvalueresult;
-
     LOG(0, "Eigenvalue table is \n" << eigenvalueresult);
+
     const std::string forceresult =
         writeTable<MPQCDataForceMap_t, MPQCDataForceVector_t>()(
@@ -635 +681 @@
   // obtain combined charge density
   LOG(1, "INFO: Parsing fragment files from " << params.path.get() << ".");
-  SamplingGrid full_sample;
+  std::vector<SamplingGrid> full_sample; // have charges from level 2 onward summed up
   Fragment full_fragment;
   sumUpChargeDensity(
@@ -644 +690 @@
 
   // Phase Four: obtain more ids
-  vmgcontroller.requestIds(fragmentData.size()+1);
+  vmgcontroller.requestIds(fragmentData.size()+full_sample.size());
 
   // Phase Five: create VMGJobs
@@ -652 +698 @@
 
   // Phase Six: calculate result
-  vmgcontroller.waitforResults(fragmentData.size()+1);
+  vmgcontroller.waitforResults(fragmentData.size()+full_sample.size());
   std::map<JobId_t, VMGData> longrangeData;
   vmgcontroller.getResults(longrangeData);
-  ASSERT( fragmentData.size()+1 == longrangeData.size(),
-      "FragmentationFragmentationAutomationAction::performCall() - number of MPQCresults+1 "
-      +toString(fragmentData.size()+1)+" and VMGresults "+toString(longrangeData.size())+" don't match.");
-
-  // remove full solution from map (must be highest id), has to be treated extra
-  VMGData fullsolutionData = (--longrangeData.end())->second;
-  longrangeData.erase(--longrangeData.end());
+  ASSERT( fragmentData.size()+full_sample.size() == longrangeData.size(),
+      "FragmentationFragmentationAutomationAction::performCall() - number of MPQCresults+"
+      +toString(full_sample.size())+" "+toString(fragmentData.size()+full_sample.size())
+      +" and VMGresults "+toString(longrangeData.size())+" don't match.");
+
+  // remove full solution corresponding to full_sample from map (must be highest ids), has to be treated extra
+  std::map<JobId_t, VMGData>::iterator iter = longrangeData.end();
+  for (size_t i=0;i<full_sample.size();++i)
+    --iter;
+  std::map<JobId_t, VMGData>::iterator remove_iter = iter;
+  std::vector<VMGData> fullsolutionData;
+  for (; iter != longrangeData.end(); ++iter)
+    fullsolutionData.push_back(iter->second);
+  longrangeData.erase(remove_iter, longrangeData.end());
 
   // Final phase: print result
@@ -674 +727 @@
         full_sample);
 
-    // create debug jobs to print the summed-up potential to vtk files
-    debugcontroller.requestIds(1);
-    if (!debugcontroller.createDebugJobs(std::vector<SamplingGrid>(1,full_sample)))
-      return Action::failure;
-    debugcontroller.waitforResults(1);
-    std::map<JobId_t, std::string> debugData;
-    debugcontroller.getResults(debugData);
+    if (!full_sample.empty()) {
+      // create debug jobs to print the summed-up potential to vtk files
+      debugcontroller.requestIds(full_sample.size());
+      if (!debugcontroller.createDebugJobs(full_sample))
+        return Action::failure;
+      debugcontroller.waitforResults(full_sample.size());
+      std::map<JobId_t, std::string> debugData;
+      debugcontroller.getResults(debugData);
+    }
   }
   }