Changeset d24ef58 for src/Actions

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:

bccbe9

Parents:

3b74fa

git-author:

Frederik Heber <frederik.heber@…> (05/17/17 11:34:16)

git-committer:

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

Message:

Extracted conversion to boost::graph into distinct struct.

• BoostGraphCreator allows to convert sets of atoms into a boost::graph while using an additional predicate.

File:

• src/Actions/MoleculeAction/StretchBondAction.cpp (modified) (6 diffs)

src/Actions/MoleculeAction/StretchBondAction.cpp

@@ -35 +35 @@
 #include <boost/graph/adjacency_list.hpp>
 #include <boost/graph/breadth_first_search.hpp>
-#include <boost/graph/subgraph.hpp>
 
 //#include "CodePatterns/MemDebug.hpp"
@@ -41 +40 @@
 #include "Actions/MoleculeAction/StretchBondAction.hpp"
 
+#include <boost/bind.hpp>
+
+#include "CodePatterns/Assert.hpp"
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"
@@ -49 +51 @@
 #include "Bond/bond.hpp"
 #include "Descriptors/AtomIdDescriptor.hpp"
+#include "Graph/BoostGraphCreator.hpp"
 #include "molecule.hpp"
 #include "World.hpp"
@@ -85 +88 @@
 {
   return distance_recorder<DistanceMap>(d);
+}
+
+static bool addEdgePredicate(
+    const bond &_bond,
+    const std::vector<atomId_t> &_atomids)
+{
+  ASSERT(_atomids.size() == (size_t)2,
+      "addEdgePredicate() - atomids must contain exactly two ids.");
+  // do not add selected edge
+  return ((_bond.leftatom->getId() != _atomids[0])
+      || (_bond.rightatom->getId() != _atomids[1]));
 }
 
@@ -118 +132 @@
   // shift either set as desired. If not, then we simply shift each atom,
   // leaving the other positions untouched.
-  typedef boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS,
-      boost::no_property, boost::no_property > UndirectedGraph;
 
   // convert BondGraph into boost::graph
-  UndirectedGraph molgraph(mol->getAtomCount());
-  size_t no_edges = 0;
-  for(molecule::const_iterator iter = const_cast<const molecule * const>(mol)->begin();
-      iter != const_cast<const molecule * const>(mol)->end(); ++iter) {
-    LOG(2, "DEBUG: Looking at node " << (*iter)->getId());
-    const BondList& ListOfBonds = (*iter)->getListOfBonds();
-    for(BondList::const_iterator bonditer = ListOfBonds.begin();
-        bonditer != ListOfBonds.end(); ++bonditer) {
-      const unsigned int &leftid = (*bonditer)->leftatom->getId();
-      const unsigned int &rightid = (*bonditer)->rightatom->getId();
-      // only add each edge once and do not add selected edge
-      if ((leftid == (*iter)->getId())
-          && ((leftid != atomids[0]) || (rightid != atomids[1]))) {
-        LOG(1, "DEBUG: ADDING edge " << leftid << " <-> " << rightid);
-        boost::add_edge(leftid, rightid, molgraph);
-        ++no_edges;
-      } else {
-        LOG(1, "DEBUG: Discarding edge " << leftid << " <-> " << rightid);
-      }
-    }
-  }
-  typedef boost::property_map < boost::adjacency_list <>, boost::vertex_index_t >::type index_map_t;
-  index_map_t index_map = boost::get(boost::vertex_index, molgraph);
-  const size_t num_vertices = boost::num_vertices(molgraph);
-  LOG(2, "DEBUG: We have " << num_vertices << " nodes and " << no_edges
-      << " edges in the molecule graph.");
-
+  BoostGraphCreator BGcreator;
+  BGcreator.createFromMolecule(*mol,
+      boost::bind(addEdgePredicate, _1, boost::ref(atomids)));
+  const BoostGraphCreator::UndirectedGraph &molgraph = BGcreator.get();
+
+  const size_t num_vertices = BGcreator.getNumVertices();
   std::vector< std::vector<size_t> > distances;
   for (size_t i=0;i<2;++i) {
@@ -184 +175 @@
   // go through the molecule and stretch each atom in either set of nodes
   if (bondside_sets[0].empty()) {
+    const BoostGraphCreator::index_map_t index_map = BGcreator.getIndexMap();
     for (molecule::iterator iter = mol->begin(); iter != mol->end(); ++iter) {
       const Vector &position = (*iter)->getPosition();