Changeset 4e6a60 for src

Timestamp:

Oct 5, 2013, 9:33:18 AM (11 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:

94453f1

Parents:

291eca

git-author:

Frederik Heber <heber@…> (09/03/13 09:55:47)

git-committer:

Frederik Heber <heber@…> (10/05/13 09:33:18)

Message:

Added CoordinatorFactory that returns the correct Coordinator for a given graph.

• extended HomologyGraph interface by getter for nodes and edges.
• CoordinatorFactory::create() decides by number of nodes and connected_edges which coordinator to return.

Location:

src

Files:

• Fragmentation/Homology/HomologyGraph.hpp (modified) (1 diff)
• Potentials/InternalCoordinates/Coordinator.hpp (modified) (2 diffs)
• Potentials/InternalCoordinates/CoordinatorFactory.cpp (modified) (3 diffs)
• Potentials/InternalCoordinates/CoordinatorFactory.hpp (added)
• Potentials/Makefile.am (modified) (2 diffs)

src/Fragmentation/Homology/HomologyGraph.hpp

@@ -158 +158 @@
   void printEdges(std::ostream& ost) const;
 
+  /** Getter for the nodes contained in this graph.
+   *
+   * \return const ref to vector of FragmentNode
+   */
+  const nodes_t &getNodes() const
+  { return nodes; }
+
+  /** Getter for the edges contained in this graph.
+   *
+   * \return const ref to vector of FragmentEdge
+   */
+  const edges_t &getEdges() const
+  { return edges; }
+
 private:
   //!> information on the nodes of the graph

src/Potentials/InternalCoordinates/Coordinator.hpp

@@ -16 +16 @@
 #include "FunctionApproximation/FunctionModel.hpp"
 
+#include <boost/shared_ptr.hpp>
+
 /** This class is the interface for all functors converting
  * a list of distances (arguments_t) into internal coordinates.
@@ -22 +24 @@
 struct Coordinator
 {
+  typedef boost::shared_ptr<Coordinator> ptr;
+
   virtual double operator()(const FunctionModel::arguments_t &arguments) const=0;
 };

src/Potentials/InternalCoordinates/CoordinatorFactory.cpp

@@ -38 +38 @@
 #include "CoordinatorFactory.hpp"
 #include "Fragmentation/Homology/HomologyGraph.hpp"
-//#include "Fragmentation/Homology/FragmentEdge.hpp"
 #include "Fragmentation/Homology/FragmentNode.hpp"
+
+#include "CodePatterns/Assert.hpp"
 
 #include "TwoBody_Length.hpp"
@@ -75 +76 @@
         nodeiter != nodes.end();
         ++nodeiter) {
-      if (nodeiter->connected_edges == 3)
+      if (nodeiter->first.getConnectedEdges() == 3)
         tripleEdge = true;
     }
@@ -86 +87 @@
   default:
     ASSERT( 0, "CoordinatorFactory::create() - I don't have a coordinator for "+
-        toString(fragment)+".");
+        toString(graph)+".");
     break;
   }

src/Potentials/Makefile.am

@@ -13 +13 @@
   Potentials/PotentialSerializer.cpp \
   Potentials/SerializablePotential.cpp \
+  Potentials/InternalCoordinates/CoordinatorFactory.cpp \
   Potentials/InternalCoordinates/FourBody_ImproperAngle.cpp \
   Potentials/InternalCoordinates/FourBody_TorsionAngle.cpp \
@@ -34 +35 @@
   Potentials/helpers.hpp \
   Potentials/InternalCoordinates/Coordinator.hpp \
+  Potentials/InternalCoordinates/CoordinatorFactory.hpp \
   Potentials/InternalCoordinates/FourBody_ImproperAngle.hpp \
   Potentials/InternalCoordinates/FourBody_TorsionAngle.hpp \