Changeset 6ca578 for src/Actions

Timestamp:

Nov 8, 2012, 1:13:19 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:

40698b

Parents:

188639

git-author:

Frederik Heber <heber@…> (07/26/12 11:29:18)

git-committer:

Frederik Heber <heber@…> (11/08/12 13:13:19)

Message:

Simple use of OrthogonalSummation in FragmentationAutomationAction.

• so far, we just make use of the already parsed in keysets, translate it to IndexSets and sum up the energy.total found in MPQCData.
• note that internal MPQCJob just creates empty MPQCData regardless of the actual job.
• TESTFIX: regression tests tests/JobMarket/molecuilderrun does not check for the resulting energy and forces as we only get empty results.
• libMolecuilderUI now requires libMolecuilderFragmentationSummation.

File:

• src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) (5 diffs)

src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

@@ -39 +39 @@
 #include "CodePatterns/MemDebug.hpp"
 
+#include <boost/assign.hpp>
+
+#include "CodePatterns/Assert.hpp"
 #include "CodePatterns/Info.hpp"
 #include "CodePatterns/Log.hpp"
@@ -49 +52 @@
 #include "Fragmentation/Fragmentation.hpp"
 #include "Fragmentation/HydrogenSaturation_enum.hpp"
+#include "Fragmentation/KeySet.hpp"
 #include "Fragmentation/KeySetsContainer.hpp"
+#include "Fragmentation/Summation/OrthogonalSummation.hpp"
+#include "Fragmentation/Summation/SetValue.hpp"
 #include "Graph/DepthFirstSearchAnalysis.hpp"
 #include "Jobs/MPQCJob.hpp"
@@ -63 +69 @@
 
 using namespace MoleCuilder;
+
+using namespace boost::assign;
 
 // and construct the stuff
@@ -146 +154 @@
   ForceMatrix Force;
   ForceMatrix ForceFragments;
-  KeySetsContainer KeySet;
 
   // align fragments
@@ -235 +242 @@
     return false;
 
+  // initialise indices
+  KeySetsContainer KeySet;
+  if (!Energy.InitialiseIndices()) return false;
+
+  if (!Force.ParseIndices(KeySetFilename.c_str())) return false;
+
+  if (!KeySet.ParseKeySets(KeySetFilename.c_str(), Force.RowCounter, Force.MatrixCounter)) return false;
+
+  /// prepare for OrthogonalSummation
+
+  // gather all present indices in AllIndices
+  IndexSet::ptr AllIndices(new IndexSet);
+  for (KeySetsContainer::ArrayOfIntVectors::const_iterator iter = KeySet.KeySets.begin();
+      iter != KeySet.KeySets.end(); ++iter)
+    for(KeySetsContainer::IntVector::const_iterator keyiter = (*iter).begin();
+        keyiter != (*iter).end(); ++keyiter) {
+      if (*keyiter != -1)
+        (*AllIndices) += *keyiter;
+    }
+  LOG(1, "INFO: AllIndices is " << AllIndices << ".");
+  // create container with all keysets
+  IndexSetContainer::ptr container(new IndexSetContainer(AllIndices));
+  for (KeySetsContainer::ArrayOfIntVectors::const_iterator iter = KeySet.KeySets.begin();
+      iter != KeySet.KeySets.end(); ++iter) {
+    IndexSet tempset;
+    for(KeySetsContainer::IntVector::const_iterator keyiter = (*iter).begin();
+        keyiter != (*iter).end(); ++keyiter)
+      if (*keyiter != -1)
+        tempset += *keyiter;
+    container->insert(tempset);
+  }
+  // create the map of all keysets
+  SubsetMap::ptr subsetmap(new SubsetMap(*container));
+
+  // associate each index set with its value
+  {
+    const IndexSetContainer::Container_t &_container = container->getContainer();
+    OrthogonalSummation<double>::InputSets_t indices(_container.begin(), _container.end());
+    OrthogonalSummation<double>::InputValues_t values(_container.size(), 0.);
+    std::vector<MPQCData>::const_iterator dataiter = fragmentData.begin();
+    std::vector<FragmentResult::ptr>::const_iterator resultiter = results.begin();
+    for (; dataiter != fragmentData.end(); ++dataiter, ++resultiter) {
+      const MPQCData &extractedData = *dataiter;
+      values[ MatrixNrLookup[(*resultiter)->getId()] ] = extractedData.energies.total;
+    }
+
+    // create the summation functor and evaluate
+    OrthogonalSummation<double> OS(indices, values, subsetmap);
+    const double energyresult = OS();
+    LOG(0, "STATUS: Resulting energy is " << energyresult << ".");
+  }
 
   // combine all found data
-  if (!Energy.InitialiseIndices()) return false;
-
-  if (!Force.ParseIndices(KeySetFilename.c_str())) return false;
-
-  if (!KeySet.ParseKeySets(KeySetFilename.c_str(), Force.RowCounter, Force.MatrixCounter)) return false;
-
   if (!KeySet.ParseManyBodyTerms()) return false;