Changeset bccbe9 for src/Graph

Timestamp:

Jul 12, 2017, 7:10:31 PM (7 years ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

Action_Thermostats, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_StructOpt_integration_tests, AutomationFragmentation_failures, Candidate_v1.6.1, ChemicalSpaceEvaluator, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Exclude_Hydrogens_annealWithBondGraph, Fix_Verbose_Codepatterns, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, Gui_displays_atomic_force_velocity, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, PythonUI_with_named_parameters, Recreated_GuiChecks, StoppableMakroAction, TremoloParser_IncreasedPrecision

Children:

6e5b8d

Parents:

d24ef58

git-author:

Frederik Heber <frederik.heber@…> (05/18/17 17:45:47)

git-committer:

Frederik Heber <frederik.heber@…> (07/12/17 19:10:31)

Message:

Extracted extraction (subset of) nodes from BoostGraph into BreadthFirstSearchGatherer.

• also added helper namespace BoostGraphHelpers.
• we now treat the vertex indices and vertex names properly. Before that they had to coincide. Now, the name is the atomic id associated with the node and the index is the boost::graph internal index.

Location:

src/Graph

Files:

• BoostGraphCreator.cpp (modified) (3 diffs)
• BoostGraphCreator.hpp (modified) (4 diffs)
• BoostGraphHelpers.hpp (added)
• BreadthFirstSearchGatherer.cpp (added)
• BreadthFirstSearchGatherer.hpp (added)
• Makefile.am (modified) (2 diffs)

src/Graph/BoostGraphCreator.cpp

@@ -85 +85 @@
       std::back_inserter(atomids), getAtomId);
   ASSERT( _atoms.size() == atomids.size(),
-      "BoostGraphCreator::createFromAtom() - atomids and atoms differ in size?");
+      "BoostGraphCreator::createFromAtom() - atomids "
+      +toString(atomids.size())+" and atoms "+toString(_atoms.size())
+      +" differ in size?");
   std::sort(atomids.begin(), atomids.end());
   const predicate_t predicate = boost::bind(inSetPredicate, boost::ref(atomids), _1);
@@ -95 +97 @@
 }
 
+BoostGraphCreator::nodeId_t BoostGraphCreator::getNodeId(
+    const atomId_t &_atomid) const
+{
+  atomids_nodeids_t::const_iterator iter =
+      atomids_nodeids.find(_atomid);
+  return (iter == atomids_nodeids.end()) ? (nodeId_t)-1 : iter->second;
+}
+
 template <typename iterator>
 void BoostGraphCreator::createFromRange(
@@ -101 +111 @@
     const size_t &_no_nodes,
     const predicate_t &_pred
-    ) {
-  // convert BondGraph into boost::graph
-  UndirectedGraph molgraph(_no_nodes);
+    )
+{
+  graph = UndirectedGraph();
+
+  // add vertices
   for(iterator iter = _begin; iter != _end; ++iter) {
-    LOG(2, "DEBUG: Looking at node " << (*iter)->getId());
+    const atomId_t atomid = (*iter)->getId();
+    Vertex v = boost::add_vertex(atomid, graph);
+    const atomId_t vertexname = boost::get(boost::get(boost::vertex_name, graph), v);
+    const nodeId_t vertexindex = boost::get(boost::get(boost::vertex_index, graph), v);
+    LOG(2, "DEBUG: Adding node " << vertexindex << " associated to atom #" << vertexname);
+    ASSERT( vertexname == atomid,
+        "BoostGraphCreator::createFromRange() - atomid "+toString(atomid)
+        +" is not name of vertex "+toString(vertexname)+".");
+    atomids_nodeids.insert( std::make_pair(vertexname, vertexindex) );
+  }
+
+  // add edges
+  for(iterator iter = _begin; iter != _end; ++iter) {
+    LOG(2, "DEBUG: Looking at atom " << (*iter)->getId());
     const BondList& ListOfBonds = (*iter)->getListOfBonds();
     for(BondList::const_iterator bonditer = ListOfBonds.begin();
         bonditer != ListOfBonds.end(); ++bonditer) {
+      LOG(2, "DEBUG: Looking at bond " << *(*bonditer));
       const atomId_t leftid = (*bonditer)->leftatom->getId();
+      const nodeId_t leftnodeid = getNodeId(leftid);
       const atomId_t rightid = (*bonditer)->rightatom->getId();
+      const nodeId_t rightnodeid = getNodeId(rightid);
       // only pick each bond once and evaluate predicate
       if ((leftid == (*iter)->getId())
           && (_pred(**bonditer))) {
-        LOG(3, "DEBUG: ADDING edge " << leftid << " <-> " << rightid);
-        boost::add_edge(leftid, rightid, graph);
+        LOG(3, "DEBUG: ADDING edge " << leftnodeid << " <-> " << rightnodeid);
+        boost::add_edge(leftnodeid, rightnodeid, graph);
       } else {
-        LOG(3, "DEBUG: Discarding edge " << leftid << " <-> " << rightid);
+        LOG(3, "DEBUG: Discarding edge " << leftnodeid << " <-> " << rightnodeid);
       }
     }

src/Graph/BoostGraphCreator.hpp

@@ -15 +15 @@
 #endif
 
+#include <map>
 #include <vector>
 
 #include <boost/function.hpp>
 #include <boost/graph/adjacency_list.hpp>
+
+#include "types.hpp"
 
 class atom;
@@ -32 +35 @@
   //!> typedef for an undirected graph using boost::graph
   typedef boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS,
-      boost::no_property, boost::no_property > UndirectedGraph;
+      boost::property<boost::vertex_name_t, atomId_t>, boost::no_property > UndirectedGraph;
   //!> typedef for a map of graph node indices
-  typedef boost::property_map < boost::adjacency_list <>, boost::vertex_index_t >::type index_map_t;
+  typedef boost::property_map < UndirectedGraph, boost::vertex_index_t >::type index_map_t;
+  typedef boost::property_map < UndirectedGraph, boost::vertex_index_t >::const_type const_index_map_t;
+  //!> typedef for a map of graph node indices
+  typedef boost::property_map < UndirectedGraph, boost::vertex_name_t >::type name_map_t;
+  typedef boost::property_map < UndirectedGraph, boost::vertex_name_t >::const_type const_name_map_t;
   //!> typedef for the  predicate to evaluate for adding the current edge or not
   typedef boost::function<bool (const bond &)> predicate_t;
+  //!> typedef for a Vertex
+  typedef boost::graph_traits<UndirectedGraph>::vertex_descriptor Vertex;
+  //!> typedef for vertex iterator
+  typedef boost::graph_traits<UndirectedGraph>::vertex_iterator vertex_iter;
 
+  //!> typedef for a node id
+  typedef size_t nodeId_t;
+  //!> typedef for map converting between node id in graph and the associated atomic id
+  typedef std::map<atomId_t, nodeId_t> atomids_nodeids_t;
 
   /** Creates the boost::graph using all atoms and bonds in the given \a _mol.
@@ -89 +104 @@
   }
 
+  /** Returns the node id to a given atom id \a _atomid.
+   *
+   * \param _atomid atom id
+   * \return node id
+   */
+  nodeId_t getNodeId(const atomId_t &_atomid) const;
+
 private:
   /** General purpose function that contains the internal logic of walking the
@@ -114 +136 @@
   //!> internal graph that is created by creator functions
   UndirectedGraph graph;
+  //!> external property map for all the atomic ids of each graph node
+  atomids_nodeids_t atomids_nodeids;
 };
 

src/Graph/Makefile.am

@@ -3 +3 @@
 
 GRAPHSOURCE = \
+        Graph/AdjacencyList.cpp \
         Graph/BondGraph.cpp \
         Graph/BoostGraphCreator.cpp \
+        Graph/BreadthFirstSearchGatherer.cpp \
         Graph/BuildInducedSubgraph.cpp \
-        Graph/AdjacencyList.cpp \
         Graph/ConnectedSubgraph.cpp \
         Graph/CyclicStructureAnalysis.cpp \
@@ -12 +13 @@
                                   
 GRAPHHEADER = \
+        Graph/AdjacencyList.hpp \
         Graph/BondGraph.hpp \
         Graph/BoostGraphCreator.hpp \
+        Graph/BoostGraphHelpers.hpp \
+        Graph/BreadthFirstSearchGatherer.hpp \
         Graph/BuildInducedSubgraph.hpp \
-        Graph/AdjacencyList.hpp \
         Graph/ConnectedSubgraph.hpp \
         Graph/CyclicStructureAnalysis.hpp \