Changeset 98dbee

Timestamp:

Aug 9, 2013, 2:20:35 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:

1e1098

Parents:

bcc24f

git-author:

Frederik Heber <heber@…> (06/24/13 08:51:05)

git-committer:

Frederik Heber <heber@…> (08/09/13 14:20:35)

Message:

World now maintains HomologyContainer instance.

Location:

src

Files:

• Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) (4 diffs)
• World.cpp (modified) (3 diffs)
• World.hpp (modified) (3 diffs)

src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp

@@ -220 +220 @@
 }
 
-bool appendToHomologyFile(
-    const boost::filesystem::path &homology_file,
-    const FragmentationShortRangeResults &shortrangeresults,
-    const FragmentationLongRangeResults &longrangeresults
+void parseHomologiesFromFile(
+    const boost::filesystem::path &homology_file
     )
 {
-  /// read homology container (if present)
-  HomologyContainer homology_container;
+  HomologyContainer &homology_container = World::getInstance().getHomologies();
   if (boost::filesystem::exists(homology_file)) {
     std::ifstream returnstream(homology_file.string().c_str());
@@ -241 +238 @@
         << ", creating empty container.");
   }
+}
+
+void appendToHomologies(
+    const FragmentationShortRangeResults &shortrangeresults,
+    const FragmentationLongRangeResults &longrangeresults
+    )
+{
+  /// read homology container (if present)
+  HomologyContainer &homology_container = World::getInstance().getHomologies();
 
   /// append all fragments to a HomologyContainer
@@ -300 +306 @@
     }
   }
-
+}
+
+bool writeHomologiesToFile(
+    const boost::filesystem::path &homology_file
+    )
+{
   /// store homology container again
+  HomologyContainer &homology_container = World::getInstance().getHomologies();
   std::ofstream outputstream(homology_file.string().c_str());
   if (outputstream.good()) { // check if opened
@@ -414 +426 @@
 
     // append all keysets to homology file
+    appendToHomologies(shortrangeresults, longrangeresults);
     if (!params.homology_file.get().empty()) {
       const boost::filesystem::path &homology_file = params.homology_file.get();
       if (homology_file.string() != "") {
+        LOG(1, "INFO: Parsing HomologyGraphs from file " << homology_file.string() << ".");
+        parseHomologiesFromFile(homology_file);
         LOG(1, "INFO: Appending HomologyGraphs to file " << homology_file.string() << ".");
-        if (!appendToHomologyFile(homology_file, shortrangeresults, longrangeresults))
+        if (!writeHomologiesToFile(homology_file))
           return Action::failure;
       }

src/World.cpp

@@ -55 +55 @@
 #include "Descriptors/SelectiveIterator_impl.hpp"
 #include "Element/periodentafel.hpp"
+#include "Fragmentation/Homology/HomologyContainer.hpp"
 #include "Graph/BondGraph.hpp"
 #include "Graph/DepthFirstSearchAnalysis.hpp"
@@ -90 +91 @@
 {
   return BG;
+}
+
+HomologyContainer &World::getHomologies()
+{
+  return *homologies;
+}
+
+void World::resetHomologies(HomologyContainer *&_homologies)
+{
+  HomologyContainer *oldhomologies = homologies;
+
+  // install new instance, resetting given pointer
+  homologies = _homologies;
+  _homologies = NULL;
+
+  // delete old instance which also informs all observers
+  delete oldhomologies;
 }
 
@@ -769 +787 @@
     periode(new periodentafel(true)),
     configuration(new config),
+    homologies(new HomologyContainer()),
     Thermostats(new ThermoStatContainer),
     ExitFlag(0),

src/World.hpp

@@ -46 +46 @@
 class Box;
 class config;
+class HomologyContainer;
 class RealSpaceMatrix;
 class molecule;
@@ -142 +143 @@
    */
   void setBondGraph(BondGraph *_BG);
+
+  /** Getter for homology container.
+   *
+   * \return const reference to homology container.
+   */
+  HomologyContainer &getHomologies();
+
+  /** Setter for homology container.
+   *
+   * \param homologies reference to homologies, set to NULL
+   */
+  void resetHomologies(HomologyContainer *&homologies);
+
   /**
    * returns the configuration for the world.
@@ -455 +469 @@
   periodentafel *periode;
   config *configuration;
+  HomologyContainer *homologies;
   Box *cell_size;
   LinkedCell::LinkedCell_Controller *LCcontroller;