Changeset 06865e for src/Actions

Timestamp:

Nov 21, 2012, 12:46:32 PM (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:

c5feef

Parents:

358ddb

git-author:

Frederik Heber <heber@…> (08/10/12 16:37:46)

git-committer:

Frederik Heber <heber@…> (11/21/12 12:46:32)

Message:

FragmentationAutomationAction now also treats the case correctly with sets including superset.

• we don't need any extra... stuff, we just need to treate the last result extra.

File:

• src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) (8 diffs)

src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

@@ -49 +49 @@
 #include "Atom/atom.hpp"
 #include "Box.hpp"
+#include "Element/element.hpp"
 #include "Fragmentation/EnergyMatrix.hpp"
 #include "Fragmentation/ForceMatrix.hpp"
@@ -725 +726 @@
   size_t FragmentCounter = 0;
   createMatrixNrLookup(fragmentresults, MatrixNrLookup, FragmentCounter);
-  std::map< JobId_t, size_t > extraMatrixNrLookup;
-  size_t extraFragmentCounter = 0;
-  createMatrixNrLookup(longrangeresults, extraMatrixNrLookup, extraFragmentCounter);
 
   // initialise keysets
@@ -756 +754 @@
   std::vector<JobId_t> jobids(fragmentresults.size(), JobId::IllegalJob);
   std::transform(fragmentresults.begin(), fragmentresults.end(), jobids.begin(),
-      boost::bind(&FragmentResult::getId,
-          boost::bind(&FragmentResult::ptr::operator->, _1)));
-  // create a vector of all job ids from long-range
-  std::vector<JobId_t> extrajobids(longrangeresults.size(), JobId::IllegalJob);
-  std::transform(longrangeresults.begin(), longrangeresults.end(), extrajobids.begin(),
       boost::bind(&FragmentResult::getId,
           boost::bind(&FragmentResult::ptr::operator->, _1)));
@@ -776 +769 @@
       SumUpPerLevel<MPQCDataTimeMap_t, MPQCDataTimeVector_t>(
           fragmentData, jobids, MatrixNrLookup, container, subsetmap));
+    std::vector<MPQCDataFragmentMap_t> Result_Fragment_fused(
+      OrthogonalSumUpPerLevel<MPQCDataFragmentMap_t, MPQCDataFragmentVector_t>(
+          fragmentData, jobids, MatrixNrLookup, container, subsetmap));
 
     // force has extra converter
@@ -790 +786 @@
     boost::mpl::for_each<MPQCDataForceVector_t>(boost::ref(forceSummer));
 
+    // full solution has to treated extra and not used in summation
+    std::vector<VMGData> temp_longrangeData(longrangeData.begin(), --longrangeData.end());
+
     // obtain full grid
     std::vector<VMGDataMap_t> VMGData_Potential_fused;
-    convertDataTo<VMGData, VMGDataMap_t>(longrangeData, VMGData_Potential_fused);
+    convertDataTo<VMGData, VMGDataMap_t>(temp_longrangeData, VMGData_Potential_fused);
     OrthogonalFullSummator<VMGDataMap_t, VMGDataFused::sampled_potential> potentialSummer(
                 subsetmap,
                 VMGData_Potential_fused,
-                extrajobids,
+                jobids,
                 container->getContainer(),
-                extraMatrixNrLookup);
+                MatrixNrLookup);
     potentialSummer(subsetmap->getMaximumSubsetLevel());
-    full_sample = potentialSummer.getFullContribution();
+    SamplingGrid full_sample = longrangeData.back().sampled_potential;
+    full_sample -= potentialSummer.getFullContribution();
     LOG(0, "Remaining long-range energy from potential integral is " << full_sample.integral() << ".");
 
@@ -806 +806 @@
                 subsetmap,
                 VMGData_Potential_fused,
-                extrajobids,
+                jobids,
                 container->getContainer(),
-                extraMatrixNrLookup);
+                MatrixNrLookup);
     elongSummer(subsetmap->getMaximumSubsetLevel());
-    const double e_long = elongSummer.getFullContribution();
+    double e_long = longrangeData.back().e_long;
+    e_long -= elongSummer.getFullContribution();
     LOG(0, "Remaining long-range energy is " << e_long << ".");
 
@@ -903 +904 @@
 
   {
-//    const int level = LEVEL;
-//    const int GRID = pow(2, level);
-//    double begin[NDIM] = { 0., 0., 0. };
-//    const RealSpaceMatrix& M = World::getInstance().getDomain().getM();
-//    const double size = M.at(0,0);
-//    ASSERT( M.determinant() == size*size*size,
-//        "createLongRangeJobs() - current domain matrix "+toString(M)+" is not cubic.");
-    const std::vector< std::vector<double> > positions(full_fragment.getPositions());
-    const std::vector<double> charges(full_fragment.getCharges());
+    const World::AtomComposite &atoms = World::getInstance().getAllAtoms();
+    std::vector< std::vector<double> > positions;
+    positions.reserve(atoms.size());
+    std::vector<double> charges;
+    charges.reserve(atoms.size());
+    std::vector<double> position(3, 0.);
+    for (World::AtomComposite::const_iterator iter = atoms.begin();
+        iter != atoms.end(); ++iter) {
+      const Vector &pos = (*iter)->getPosition();
+      for (size_t i=0;i<3;++i) position[i] = pos[i];
+      positions.push_back(position);
+      charges.push_back((double)((*iter)->getElement().getAtomicNumber()));
+    }
     const JobId_t next_id = controller.getAvailableId();
     LOG(1, "INFO: Creating full VMGJob with " << full_sampled_grid.sampled_grid.size()
@@ -977 +982 @@
 #ifdef HAVE_VMG
   if (params.DoLongrange.get()) {
+  ASSERT( World::getInstance().getAllAtoms().size() != 0,
+      "FragmentationFragmentationAutomationAction::performCall() - please load the full molecule into the World before.");
+
   // obtain combined charge density
   LOG(1, "INFO: Parsing fragment files from " << params.path.get() << ".");