Changeset d713ce for src

Timestamp:

May 18, 2016, 10:02:06 PM (9 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, 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_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, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, 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:

16d67a

Parents:

bd6e5c

git-author:

Frederik Heber <heber@…> (03/07/16 14:01:17)

git-committer:

Frederik Heber <heber@…> (05/18/16 22:02:06)

Message:

AtomFragmentsMap is now a Singleton and part of Homology code.

Location:

src/Fragmentation

Files:

• Homology/AtomFragmentsMap.cpp (moved) (moved from src/Fragmentation/AtomFragmentsMap.cpp ) (3 diffs)
• Homology/AtomFragmentsMap.hpp (moved) (moved from src/Fragmentation/AtomFragmentsMap.hpp ) (3 diffs)
• Interfragmenter.cpp (modified) (1 diff)
• Interfragmenter.hpp (modified) (1 diff)
• Makefile.am (modified) (4 diffs)

src/Fragmentation/Homology/AtomFragmentsMap.cpp

@@ -37 +37 @@
 
 #include "CodePatterns/Log.hpp"
+#include "CodePatterns/Singleton_impl.hpp"
 
 #include "AtomFragmentsMap.hpp"
@@ -44 +45 @@
 #include "Fragmentation/KeySet.hpp"
 
-AtomFragmentsMap::AtomFragmentsMap(
+void AtomFragmentsMap::insert(
     const Graph &_graph,
     size_t _MaxOrder)
 {
   /// create a map of atom to keyset (below equal MaxOrder)
-  LOG(1, "INFO: Placing all atoms and their keysets into a map.");
+  LOG(1, "INFO: Placing all atoms and their keysets into internal map.");
   for (Graph::const_iterator keysetiter = _graph.begin();
       keysetiter != _graph.end(); ++keysetiter) {
@@ -70 +71 @@
     }
   }
-  LOG(2, "DEBUG: There are " << atommap.size() << " entries in lookup.");
+  LOG(2, "DEBUG: There are now " << atommap.size() << " entries in lookup.");
 }
+
+CONSTRUCT_SINGLETON(AtomFragmentsMap)

src/Fragmentation/Homology/AtomFragmentsMap.hpp

@@ -15 +15 @@
 #endif
 
+#include "CodePatterns/Singleton.hpp"
+
 #include <list>
 #include <map>
@@ -26 +28 @@
  * the (known) fragments it takes part in.
  *
+ * In the HomologyGraph and its -Container we do not have this information
+ * any longer. However, we need this in order to make statements about atomic
+ * properties from calculated fragment properties.
+ *
  */
-class AtomFragmentsMap
+class AtomFragmentsMap : public Singleton<AtomFragmentsMap>
 {
 public:
-  AtomFragmentsMap(
+  //** Function to insert new fragments into storage container.
+  void insert(
       const Graph &_graph,
       size_t _MaxOrder);
+
+  /** Function to clear the container.
+   *
+   */
+  void clear()
+  { atommap.clear(); }
 
   typedef std::list<KeySet> keysets_t;
@@ -42 +55 @@
 
 private:
+  //!> grant singleton pattern access to private cstor/dstor
+  friend class Singleton<AtomFragmentsMap>;
+
+  /** Private default cstor.
+   *
+   */
+  AtomFragmentsMap() {}
+
+  /** Private default dstor.
+   *
+   */
+  ~AtomFragmentsMap() {}
+
+private:
   //!> internal map filled on instantiation
   AtomFragmentsMap_t atommap;

src/Fragmentation/Interfragmenter.cpp

@@ -170 +170 @@
     const enum HydrogenTreatment treatment)
 {
-  AtomFragmentsMap AtomFragments(TotalGraph, MaxOrder);
-  const atomkeyset_t &atomkeyset = AtomFragments.getMap();
+  AtomFragmentsMap& atomfragments_container = AtomFragmentsMap::getInstance();
+  atomfragments_container.insert(TotalGraph, MaxOrder);
+  const atomkeyset_t &atomkeyset = atomfragments_container.getMap();
 
   Graph InterFragments;

src/Fragmentation/Interfragmenter.hpp

@@ -19 +19 @@
 
 #include "AtomIdSet.hpp"
-#include "Fragmentation/AtomFragmentsMap.hpp"
+#include "Fragmentation/Homology/AtomFragmentsMap.hpp"
 #include "Fragmentation/HydrogenSaturation_enum.hpp"
 

src/Fragmentation/Makefile.am

@@ -12 +12 @@
         Fragmentation/Exporters/SphericalPointDistribution.cpp \
         Fragmentation/Exporters/SphericalPointDistribution_getPoints.cpp \
+        Fragmentation/Homology/AtomFragmentsMap.cpp \
         Fragmentation/Homology/FragmentEdge.cpp \
         Fragmentation/Homology/FragmentNode.cpp \
@@ -17 +18 @@
         Fragmentation/Homology/HomologyGraph.cpp \
         Fragmentation/AdaptivityMap.cpp \
-        Fragmentation/AtomFragmentsMap.cpp \
         Fragmentation/BondsPerShortestPath.cpp \
         Fragmentation/EnergyMatrix.cpp \
@@ -42 +42 @@
         Fragmentation/Exporters/SaturationDistanceMaximizer.hpp \
         Fragmentation/Exporters/SphericalPointDistribution.hpp \
+        Fragmentation/Homology/AtomFragmentsMap.hpp \
         Fragmentation/Homology/FragmentEdge.hpp \
         Fragmentation/Homology/FragmentNode.hpp \
@@ -47 +48 @@
         Fragmentation/Homology/HomologyGraph.hpp \
         Fragmentation/AdaptivityMap.hpp \
-        Fragmentation/AtomFragmentsMap.hpp \
         Fragmentation/AtomMask.hpp \
         Fragmentation/BondsPerShortestPath.hpp \