Changeset 28e203

Timestamp:

Dec 14, 2012, 5:39:42 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:

91a565

Parents:

d058e6

git-author:

Frederik Heber <heber@…> (09/28/12 16:22:03)

git-committer:

Frederik Heber <heber@…> (12/14/12 17:39:42)

Message:

FIX: nodes_t and edges_t in HomologyGraph must be a map.

• there may be multiples of the same node or edge. Hence, now we store the count in a map.
• changed operator<<() accordingly.

Location:

src/Fragmentation/Homology

Files:

• HomologyGraph.cpp (modified) (1 diff)
• HomologyGraph.hpp (modified) (3 diffs)
• HomologyGraph_getFromKeyset.cpp (modified) (3 diffs)
• unittests/HomologyContainerUnitTest.cpp (modified) (1 diff)
• unittests/HomologyGraphUnitTest.cpp (modified) (1 diff)

src/Fragmentation/Homology/HomologyGraph.cpp

@@ -108 +108 @@
       nodeiter != graph.nodes.end();
       ++nodeiter)
-    ost << *nodeiter << " ";
+    ost << nodeiter->second << "x " << nodeiter->first << ", ";
   for (HomologyGraph::edges_t::const_iterator edgeiter = graph.edges.begin();
       edgeiter != graph.edges.end();
       ++edgeiter)
-    ost << *edgeiter << " ";
+    ost << edgeiter->second << "x " << edgeiter->first << ", ";
   return ost;
 }

src/Fragmentation/Homology/HomologyGraph.hpp

@@ -16 +16 @@
 
 #include <boost/serialization/export.hpp>
-#include <boost/serialization/set.hpp>
+#include <boost/serialization/map.hpp>
 
-#include <set>
+#include <map>
 #include <iosfwd>
 
@@ -46 +46 @@
 public:
   //!> typedef for a set of nodes representing node information
-  typedef std::set<FragmentNode> nodes_t;
+  typedef std::map<FragmentNode, size_t> nodes_t;
   //!> typedef for a set of nodes representing edge information
-  typedef std::set<FragmentEdge> edges_t;
+  typedef std::map<FragmentEdge, size_t> edges_t;
 public:
   /** Default constructor for class HomologyGraph.
@@ -92 +92 @@
   }
 
+  /** Checks whether this graph contains a specific \a node.
+   *
+   * @param node node to look for
+   * @param count how often this node must occur
+   * @return true - graph contains this node at least once, false - else
+   */
+  bool hasNode(const FragmentNode &node, const size_t count = 1) const {
+    nodes_t::const_iterator iter = nodes.find(node);
+    if (iter == nodes.end())
+      return count == 0;
+    else
+      return (iter->second == count);
+  }
+
+  /** Checks whether this graph contains a specific \a edge.
+   *
+   * @param edge edge to look for
+   * @param count how often this edge must occur
+   * @return true - graph contains this edge at least once, false - else
+   */
+  bool hasEdge(const FragmentEdge &edge, const size_t count = 1) const {
+    edges_t::const_iterator iter = edges.find(edge);
+    if (iter == edges.end())
+      return count == 0;
+    else
+      return (iter->second == count);
+  }
+
   /** Assignment operator for class HomologyGraph.
    *

src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp

@@ -58 +58 @@
   for (typename std::set<T>::const_iterator iter = keyset.begin();
       iter != keyset.end(); ++iter) {
+//    LOG(2, "DEBUG: Current global id is " << *iter << ".");
     const atom *Walker = World::getInstance().getAtom(AtomById(*iter));
     if (Walker != NULL) {
+      size_t NoBonds = 0;
       const BondList& ListOfBonds = Walker->getListOfBonds();
-#ifndef NDEBUG
+      for (BondList::const_iterator bonditer = ListOfBonds.begin();
+          bonditer != ListOfBonds.end(); ++bonditer) {
+        const atom *OtherWalker = (*bonditer)->GetOtherAtom(Walker);
+        if (keyset.count(OtherWalker->getId()))
+          ++NoBonds;
+      }
+//      LOG(2, "DEBUG: Adding node " << Walker->getId() << " with element "
+//          << Walker->getElementNo() << " and " << NoBonds << " bonds.");
     std::pair<HomologyGraph::nodes_t::iterator,bool> inserter =
-#endif
-        nodes.insert( FragmentNode(Walker->getElementNo(), ListOfBonds.size()) );
+        nodes.insert( std::make_pair(FragmentNode(Walker->getElementNo(), NoBonds), (size_t)1) );
+    if (!inserter.second)
+      inserter.first->second += (size_t)1;
     } else {
-      ELOG(0, "Id " << *iter << " is not associated with any atom.");
+      ELOG(3, "Skipping id " << *iter << ", is not associated with any atom.");
     }
   }
@@ -78 +88 @@
   for (typename std::set<T>::const_iterator iter = keyset.begin();
       iter != keyset.end(); ++iter) {
+//    LOG(2, "DEBUG: Current global id is " << *iter << ".");
     const atom *Walker = World::getInstance().getAtom(AtomById(*iter));
     if (Walker != NULL) {
@@ -84 +95 @@
           bonditer != ListOfBonds.end(); ++bonditer) {
         const atom *OtherWalker = (*bonditer)->GetOtherAtom(Walker);
-        if (Walker->getId() < OtherWalker->getId())
-          edges.insert( FragmentEdge( Walker->getElementNo(), OtherWalker->getElementNo()) );
+//        LOG(2, "DEBUG: Neighbor is " << OtherWalker->getId() << ".");
+        if ((keyset.count(OtherWalker->getId())) && (Walker->getId() < OtherWalker->getId())) {
+//          LOG(1, "DEBUG: Adding edge " << Walker->getId() << " and " << OtherWalker->getId() << ".");
+          std::pair<HomologyGraph::edges_t::iterator,bool> inserter =
+              edges.insert( std::make_pair(FragmentEdge( Walker->getElementNo(), OtherWalker->getElementNo()), (size_t)1) );
+          if (!inserter.second)
+            inserter.first->second += (size_t)1;
+        }
       }
     } else {
-      ELOG(0, "Id " << *iter << " is not associated with any atom.");
+      ELOG(3, "Skipping id " << *iter << ", is not associated with any atom.");
     }
   }

src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.cpp

@@ -68 +68 @@
   // add nodes
   nodes +=
-      FragmentNode(1,1),
-      FragmentNode(1,4),
-      FragmentNode(2,2),
-      FragmentNode(2,4);
+      std::make_pair(FragmentNode(1,1),1),
+      std::make_pair(FragmentNode(1,4),1),
+      std::make_pair(FragmentNode(2,2),1),
+      std::make_pair(FragmentNode(2,4),1);
   othernodes +=
-      FragmentNode(1,1),
-      FragmentNode(1,4);
+      std::make_pair(FragmentNode(1,1),1),
+      std::make_pair(FragmentNode(1,4),1);
 
   // add edges
   edges +=
-      FragmentEdge(1,1),
-      FragmentEdge(1,4),
-      FragmentEdge(2,2),
-      FragmentEdge(2,4);
+      std::make_pair(FragmentEdge(1,1),1),
+      std::make_pair(FragmentEdge(1,4),1),
+      std::make_pair(FragmentEdge(2,2),1),
+      std::make_pair(FragmentEdge(2,4),1);
   otheredges +=
-      FragmentEdge(1,4),
-      FragmentEdge(2,2);
+      std::make_pair(FragmentEdge(1,4),1),
+      std::make_pair(FragmentEdge(2,2),1);
 
   // construct graphs

src/Fragmentation/Homology/unittests/HomologyGraphUnitTest.cpp

@@ -71 +71 @@
 
   // add nodes
-  nodes += FragmentNode(1,1),FragmentNode(1,4), FragmentNode(2,2), FragmentNode(2,4);
-  othernodes += FragmentNode(1,1),FragmentNode(1,4);
+  nodes +=
+      std::make_pair(FragmentNode(1,1),1),
+      std::make_pair(FragmentNode(1,4),1),
+      std::make_pair(FragmentNode(2,2),1),
+      std::make_pair(FragmentNode(2,4),1);
+  othernodes +=
+      std::make_pair(FragmentNode(1,1),1),
+      std::make_pair(FragmentNode(1,4),1);
 
   // add edges
-  edges += FragmentEdge(1,1),FragmentEdge(1,4), FragmentEdge(2,2), FragmentEdge(2,4);
-  otheredges += FragmentEdge(1,4),FragmentEdge(2,2);
+  edges +=
+      std::make_pair(FragmentEdge(1,1),1),
+      std::make_pair(FragmentEdge(1,4),1),
+      std::make_pair(FragmentEdge(2,2),1),
+      std::make_pair(FragmentEdge(2,4),1);
+  otheredges +=
+      std::make_pair(FragmentEdge(1,4),1),
+      std::make_pair(FragmentEdge(2,2),1);
 
   // construct graph