Changeset 766767

Timestamp:

Dec 14, 2012, 5:39:41 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:

17c03f

Parents:

372c912

git-author:

Frederik Heber <heber@…> (09/27/12 16:26:02)

git-committer:

Frederik Heber <heber@…> (12/14/12 17:39:41)

Message:

appendToHomologyFile() now constructs the HomologyGraph and its values.

• i.e. now we truely append our calculated fragments to the HomologyContainer.

File:

• src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) (4 diffs)

src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

@@ -64 +64 @@
 #include "Fragmentation/ForceMatrix.hpp"
 #include "Fragmentation/Fragmentation.hpp"
+#include "Fragmentation/HydrogenSaturation_enum.hpp"
 #include "Fragmentation/Homology/HomologyContainer.hpp"
 #include "Fragmentation/Homology/HomologyGraph.hpp"
+#include "Fragmentation/KeySet.hpp"
+#include "Fragmentation/KeySetsContainer.hpp"
 #include "Fragmentation/SetValues/Fragment.hpp"
 #include "Fragmentation/SetValues/Histogram.hpp"
 #include "Fragmentation/SetValues/IndexedVectors.hpp"
-#include "Fragmentation/HydrogenSaturation_enum.hpp"
-#include "Fragmentation/KeySet.hpp"
-#include "Fragmentation/KeySetsContainer.hpp"
+#include "Fragmentation/Summation/IndexSetContainer.hpp"
 #include "Fragmentation/Summation/writeTable.hpp"
 #include "Graph/DepthFirstSearchAnalysis.hpp"
@@ -388 +389 @@
 }
 
-bool appendToHomologyFile(const boost::filesystem::path &homology_file)
+bool appendToHomologyFile(
+    const boost::filesystem::path &homology_file,
+    const FragmentationResults &results,
+    const std::string &KeySetFilename)
 {
   // read homology container (if present)
@@ -408 +412 @@
   // append all fragments to a HomologyContainer
   HomologyContainer::container_t values;
-  // TODO: prepare HomologyGraphs ...
+  KeySetsContainer ForceKeySet;
+  {
+    // forces need keysets including hydrogens
+    std::stringstream filename;
+    filename << FRAGMENTPREFIX << FORCESFILE;
+#ifndef NDEBUG
+    bool status =
+#endif
+        ForceKeySet.ParseKeySets(KeySetFilename, filename.str(), results.Result_perIndexSet_Energy.size());
+    ASSERT( status,
+        "FragmentationResults::FragmentationResults() - ParseKeySets() of "
+        +toString(FORCESFILE)+" failed.");
+  }
+  // convert KeySetContainer to IndexSetContainer
+  IndexSetContainer::ptr container(new IndexSetContainer(ForceKeySet));
+  for (IndexSetContainer::Container_t::const_iterator iter = container->getContainer().begin();
+      iter != container->getContainer().end(); ++iter) // go through each IndexSet
+  {
+    const IndexSet::ptr &index = *iter;
+    HomologyGraph graph(*index);
+    HomologyContainer::value_t value;
+    std::map<IndexSet::ptr, MPQCDataFragmentMap_t>::const_iterator fragmentiter
+        = results.Result_perIndexSet_Fragment.find(index);
+    ASSERT( fragmentiter != results.Result_perIndexSet_Fragment.end(),
+        "appendToHomologyFile() - cannot find index "+toString(*index)
+        +" in FragmentResults.");
+    value.first = boost::fusion::at_key<MPQCDataFused::fragment>(fragmentiter->second);
+    std::map<IndexSet::ptr, MPQCDataEnergyMap_t>::const_iterator energyiter
+        = results.Result_perIndexSet_Energy.find(index);
+    ASSERT( energyiter != results.Result_perIndexSet_Energy.end(),
+        "appendToHomologyFile() - cannot find index "+toString(*index)
+        +" in FragmentResults.");
+    value.second = boost::fusion::at_key<MPQCDataFused::energy_total>(energyiter->second);
+    values.insert( std::make_pair( graph, value) );
+  }
   homology_container.insert(values);
 
@@ -531 +569 @@
     if (homology_file.string() != "") {
       LOG(1, "INFO: Appending HomologyGraphs to file " << homology_file.string() << ".");
-      if (!appendToHomologyFile(homology_file))
+      if (!appendToHomologyFile(homology_file, results, params.path.get()))
         Exitflag = 1;
     }