Changeset 372c912 for src

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:

766767

Parents:

b8f0b25

git-author:

Frederik Heber <heber@…> (09/27/12 16:24:25)

git-committer:

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

Message:

Extended HomologyGraph to also be constructable from IndexSet reference.

• we templated logic in getNodesFromSet() and getEdgesFromSet() and have a version for either KeySet (int) or IndexSet (size_t) that instantiates the template accordingly.
• also extended the stub by two more dummy functions such that we avoid still the clutter of World, atom, ...

Location:

src/Fragmentation/Homology

Files:

• HomologyGraph.cpp (modified) (1 diff)
• HomologyGraph.hpp (modified) (3 diffs)
• HomologyGraph_getFromKeyset.cpp (modified) (2 diffs)
• unittests/stubs/HomologyGraph_getFromKeysetStub.cpp (modified) (2 diffs)

src/Fragmentation/Homology/HomologyGraph.cpp

@@ -49 +49 @@
   nodes(detail::getNodesFromKeySet(keyset)),
   edges(detail::getEdgesFromKeySet(keyset))
+{}
+
+HomologyGraph::HomologyGraph(const IndexSet &index) :
+  nodes(detail::getNodesFromIndexSet(index)),
+  edges(detail::getEdgesFromIndexSet(index))
 {}
 

src/Fragmentation/Homology/HomologyGraph.hpp

@@ -24 +24 @@
 #include "Fragmentation/Homology/FragmentNode.hpp"
 
+class IndexSet;
 class KeySet;
 
@@ -72 +73 @@
   HomologyGraph(const KeySet &keyset);
 
+  /** Constructor for class HomologyGraph from a IndexSet (i.e. from atoms in the World).
+   *
+   * @param index global ids of atoms to pick
+   */
+  HomologyGraph(const IndexSet &index);
+
   /** Destructor for class HomologyGraph.
    *
@@ -119 +126 @@
   const HomologyGraph::nodes_t getNodesFromKeySet(const KeySet &keyset);
   const HomologyGraph::edges_t getEdgesFromKeySet(const KeySet &keyset);
+  const HomologyGraph::nodes_t getNodesFromIndexSet(const IndexSet &keyset);
+  const HomologyGraph::edges_t getEdgesFromIndexSet(const IndexSet &keyset);
 };
 

src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp

@@ -45 +45 @@
 #include "Descriptors/AtomIdDescriptor.hpp"
 #include "Fragmentation/KeySet.hpp"
+#include "Fragmentation/Summation/IndexSet.hpp"
 #include "World.hpp"
 
@@ -51 +52 @@
 // in all the cludder of World, atom, molecule, and so on ...
 
+template <typename T>
+const HomologyGraph::nodes_t getNodesFromSet(const std::set<T> &keyset)
+{
+  HomologyGraph::nodes_t nodes;
+  for (typename std::set<T>::const_iterator iter = keyset.begin();
+      iter != keyset.end(); ++iter) {
+    const atom *Walker = World::getInstance().getAtom(AtomById(*iter));
+    if (Walker != NULL) {
+      const BondList& ListOfBonds = Walker->getListOfBonds();
+#ifndef NDEBUG
+    std::pair<HomologyGraph::nodes_t::iterator,bool> inserter =
+#endif
+        nodes.insert( FragmentNode(Walker->getElementNo(), ListOfBonds.size()) );
+    } else {
+      ELOG(0, "Id " << *iter << " is not associated with any atom.");
+    }
+  }
+  return nodes;
+}
+
+template <typename T>
+const HomologyGraph::edges_t getEdgesFromSet(const std::set<T> &keyset)
+{
+  HomologyGraph::edges_t edges;
+  for (typename std::set<T>::const_iterator iter = keyset.begin();
+      iter != keyset.end(); ++iter) {
+    const atom *Walker = World::getInstance().getAtom(AtomById(*iter));
+    if (Walker != NULL) {
+      const BondList& ListOfBonds = Walker->getListOfBonds();
+      for (BondList::const_iterator bonditer = ListOfBonds.begin();
+          bonditer != ListOfBonds.end(); ++bonditer) {
+        const atom *OtherWalker = (*bonditer)->GetOtherAtom(Walker);
+        if (Walker->getId() < OtherWalker->getId())
+          edges.insert( FragmentEdge( Walker->getElementNo(), OtherWalker->getElementNo()) );
+      }
+    } else {
+      ELOG(0, "Id " << *iter << " is not associated with any atom.");
+    }
+  }
+  return edges;
+}
+
 namespace detail {
-  const HomologyGraph::nodes_t getNodesFromKeySet(const KeySet &keyset)
-  {
-    HomologyGraph::nodes_t nodes;
-    for (KeySet::const_iterator iter = keyset.begin();
-        iter != keyset.end(); ++iter) {
-      const atom *Walker = World::getInstance().getAtom(AtomById(*iter));
-      if (Walker != NULL) {
-        const BondList& ListOfBonds = Walker->getListOfBonds();
-  #ifndef NDEBUG
-      std::pair<HomologyGraph::nodes_t::iterator,bool> inserter =
-  #endif
-          nodes.insert( FragmentNode(Walker->getElementNo(), ListOfBonds.size()) );
-      } else {
-        ELOG(0, "Id " << *iter << " is not associated with any atom.");
-      }
-    }
-    return nodes;
+  const HomologyGraph::nodes_t getNodesFromKeySet(const KeySet &keyset) {
+    return getNodesFromSet<int>(keyset);
   }
-
-  const HomologyGraph::edges_t getEdgesFromKeySet(const KeySet &keyset)
-  {
-    HomologyGraph::edges_t edges;
-    for (KeySet::const_iterator iter = keyset.begin();
-        iter != keyset.end(); ++iter) {
-      const atom *Walker = World::getInstance().getAtom(AtomById(*iter));
-      if (Walker != NULL) {
-        const BondList& ListOfBonds = Walker->getListOfBonds();
-        for (BondList::const_iterator bonditer = ListOfBonds.begin();
-            bonditer != ListOfBonds.begin(); ++iter) {
-          const atom *OtherWalker = (*bonditer)->GetOtherAtom(Walker);
-          if (Walker->getId() < OtherWalker->getId())
-            edges.insert( FragmentEdge( Walker->getElementNo(), OtherWalker->getElementNo()) );
-        }
-      } else {
-        ELOG(0, "Id " << *iter << " is not associated with any atom.");
-      }
-    }
-    return edges;
+  const HomologyGraph::nodes_t getNodesFromIndexSet(const IndexSet &keyset) {
+    return getNodesFromSet<size_t>(keyset);
+  }
+  const HomologyGraph::edges_t getEdgesFromKeySet(const KeySet &keyset) {
+    return getEdgesFromSet<int>(keyset);
+  }
+  const HomologyGraph::edges_t getEdgesFromIndexSet(const IndexSet &keyset) {
+    return getEdgesFromSet<size_t>(keyset);
   }
 };  /* namespace detail */

src/Fragmentation/Homology/unittests/stubs/HomologyGraph_getFromKeysetStub.cpp

@@ -39 +39 @@
 #include "Fragmentation/Homology/HomologyGraph.hpp"
 #include "Fragmentation/KeySet.hpp"
+#include "Fragmentation/Summation/IndexSet.hpp"
 
 namespace detail {
@@ -52 +53 @@
   }
 
+  const HomologyGraph::nodes_t getNodesFromIndexSet(const IndexSet &keyset)
+  {
+    return HomologyGraph::nodes_t();
+  }
+
+  const HomologyGraph::edges_t getEdgesFromIndexSet(const IndexSet &keyset)
+  {
+    return HomologyGraph::edges_t();
+  }
+
 };  /* namespace detail */