Changeset 9445081 for src/Fragmentation

Timestamp:

Nov 4, 2016, 9:37:51 AM (8 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_StructOpt_integration_tests, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, 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_ChronosMutex, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, GeometryObjects, Gui_displays_atomic_force_velocity, IndependentFragmentGrids_IntegrationTest, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, RotateToPrincipalAxisSystem_UndoRedo, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, ThirdParty_MPQC_rebuilt_buildsystem, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, Ubuntu_1604_changes, stable

Children:

ea63cb

Parents:

041a79

git-author:

Frederik Heber <heber@…> (10/04/16 08:06:18)

git-committer:

Frederik Heber <heber@…> (11/04/16 09:37:51)

Message:

FragmentJobQueue additionally stores the bond graph as an edge set per fragment/job.

• added SaturatedFragment::getEdges() that returns the set of edges, indices rewritten (starting at 0), and hydrogens included, i.e. matching with the lines in the output config.
• ExportGraph_ToJobs::operator() additionally queries for the edge set and places it in the JobQueue.

Location:

src/Fragmentation

Files:

• Automation/FragmentJobQueue.cpp (modified) (3 diffs)
• Automation/FragmentJobQueue.hpp (modified) (6 diffs)
• Exporters/ExportGraph_ToJobs.cpp (modified) (4 diffs)
• Exporters/SaturatedFragment.cpp (modified) (1 diff)
• Exporters/SaturatedFragment.hpp (modified) (2 diffs)

src/Fragmentation/Automation/FragmentJobQueue.cpp

@@ -51 +51 @@
 #include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "World.hpp"
-
 
 void FragmentJobQueue::parsejob(const std::string &filename, const unsigned int level)
@@ -132 +131 @@
 }
 
+bool FragmentJobQueue::addEdgesPerFragmentFromFiles(
+    const boost::filesystem::path &path
+    )
+{
+  ASSERT(0,
+      "FragmentJobQueue::addFullKeySetsFromFiles() - is not implemented, yet.");
+  return false;
+}
+
 void FragmentJobQueue::clear()
 {
@@ -137 +145 @@
   KeySets.clear();
   FullKeySets.clear();
+  edges_per_fragment.clear();
 }
 

src/Fragmentation/Automation/FragmentJobQueue.hpp

@@ -20 +20 @@
 #include "CodePatterns/Singleton.hpp"
 
+#include "Fragmentation/EdgesPerFragment.hpp"
 #include "Fragmentation/KeySetsContainer.hpp"
 #include "Fragmentation/parseKeySetFile.hpp"
 #include "Jobs/MPQCJob.hpp"
+#include "types.hpp"
 
 /** FragmentJobQueue is a static instance to contain all present fragment
@@ -45 +47 @@
 
 public:
+  typedef FragmentationEdges::edges_per_fragment_t edges_per_fragment_t;
 
   /** Pushes a vector of jobs into the queue.
    *
    * \param _jobs new jobs to push
-   * \param KeySet KeySet of all (non-hydrogen) atoms
-   * \param FullKeySet KeySet of all atoms except saturation hydrogens
+   * \param _KeySet KeySet of all (non-hydrogen) atoms
+   * \param _FullKeySet KeySet of all atoms except saturation hydrogens
+   * \param _edges_per_fragment edges of bond graph of all fragments
    */
   void addJobs(
       std::vector<FragmentJob::ptr> &_jobs,
       const KeySetsContainer &_KeySets,
-      const KeySetsContainer &_FullKeySets);
+      const KeySetsContainer &_FullKeySets,
+      const edges_per_fragment_t &_edges_per_fragment);
 
   /** Returns ref to jobs.
@@ -96 +101 @@
       );
 
+  /** Adds edges after fragments have been added by file.
+   *
+   */
+  bool addEdgesPerFragmentFromFiles(
+      const boost::filesystem::path &path
+      );
+
   /** Getter for the container of all KeySets to the jobs.
    *
@@ -107 +119 @@
    */
   const KeySetsContainer& getFullKeySets() const { return FullKeySets; }
+
+  /** Getter for the container of all edges of the bond graph over all jobs.
+   *
+   * \return const ref to container
+   */
+  const edges_per_fragment_t& getEdgesPerFragment() const { return edges_per_fragment; }
 
   /* Empties contained jobs and all KeySets.
@@ -130 +148 @@
   //!> container for all KeySet's with all except saturation hydrogen to the jobs
   KeySetsContainer FullKeySets;
+  //!> container for all edges of the bond graph of each fragments
+  edges_per_fragment_t edges_per_fragment;
 };
 
@@ -136 +156 @@
     std::vector<FragmentJob::ptr> &_jobs,
     const KeySetsContainer &_KeySets,
-    const KeySetsContainer &_FullKeySets)
+    const KeySetsContainer &_FullKeySets,
+    const edges_per_fragment_t &_edges_per_fragment)
 {
   jobs.insert(jobs.end(), _jobs.begin(), _jobs.end());
   KeySets.insert(_KeySets);
   FullKeySets.insert(_FullKeySets);
+  edges_per_fragment.reserve(edges_per_fragment.size()+_edges_per_fragment.size());
+  edges_per_fragment.insert(
+      edges_per_fragment.end(),
+      _edges_per_fragment.begin(), _edges_per_fragment.end());
 }
 

src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp

@@ -227 +227 @@
   KeySetsContainer KeySets;
   KeySetsContainer FullKeySets;
+  FragmentJobQueue::edges_per_fragment_t edges_per_fragment;
   jobs.reserve(TotalGraph.size());
   LOG(1, "INFO: Creating " << TotalGraph.size() << " possible bond fragmentation jobs.");
@@ -255 +256 @@
     const KeySet &set = CurrentFragment->getKeySet();
     LOG(2, "INFO: Creating bond fragment job for set " << set << ".");
+
+    // gather all edges
+    FragmentationEdges::edges_t edges = CurrentFragment->getEdges();
 
     SamplingGridProperties fragment_window(grid);
@@ -315 +319 @@
       KeySets.insert(indices, order);
       FullKeySets.insert(forceindices, order);
+      edges_per_fragment.push_back(edges);
     }
     // store force index reference file
@@ -326 +331 @@
 
   // push final jobs
-  FragmentJobQueue::getInstance().addJobs(jobs, KeySets, FullKeySets);
+  FragmentJobQueue::getInstance().addJobs(jobs, KeySets, FullKeySets, edges_per_fragment);
 
   return true;

src/Fragmentation/Exporters/SaturatedFragment.cpp

@@ -667 +667 @@
   return std::make_pair(minimum, maximum);
 }
+
+static FragmentationEdges::edges_t createEdgesFromAtoms(
+    const std::vector<atom *> &_atoms,
+    const KeySet &_FullMolecule)
+{
+  FragmentationEdges::edges_t edges;
+  for (std::vector<atom *>::const_iterator iter = _atoms.begin();
+      iter != _atoms.end(); ++iter) {
+    const atom * const walker = *iter;
+    const atomId_t &walkerid = walker->getId();
+    const BondList &ListOfBonds = walker->getListOfBonds();
+    for (BondList::const_iterator bonditer = ListOfBonds.begin();
+        bonditer != ListOfBonds.end(); ++bonditer) {
+      const atom * const OtherWalker = (*bonditer)->GetOtherAtom(walker);
+      const atomId_t &otherwalkerid = OtherWalker->getId();
+      if (walkerid < otherwalkerid) {
+        // check if it's in fullkeysets (also contains excluded and saturation hydrogens)
+        if (_FullMolecule.count(otherwalkerid))
+          edges.push_back( FragmentationEdges::edge_t(walkerid, otherwalkerid) );
+      }
+    }
+  }
+  return edges;
+}
+
+typedef std::map<atomId_t, atomId_t> idtable_t;
+
+static idtable_t createIdTable(
+    const std::vector<atom *> &_atoms)
+{
+  idtable_t idtable;
+  atomId_t newid = 0;
+  for (std::vector<atom *>::const_iterator iter = _atoms.begin();
+      iter != _atoms.end(); ++iter) {
+    const atom * const walker = *iter;
+    const atomId_t &walkerid = walker->getId();
+    idtable.insert( std::make_pair(walkerid, newid++) );
+  }
+  return idtable;
+}
+
+static atomId_t getTranslatedId(
+    const idtable_t &_idtable,
+    const atomId_t &_id
+    )
+{
+  idtable_t::const_iterator iter = _idtable.find(_id);
+  if (iter != _idtable.end())
+    return iter->second;
+  else {
+    ASSERT( 0,
+        "getTranslatedId() - idtable does not contain id in FullMolecule?");
+    return (atomId_t)-1;
+  }
+}
+
+static void rewriteEdgeIndices(
+    FragmentationEdges::edges_t &_edges,
+    const idtable_t &_idtable)
+{
+  for (FragmentationEdges::edges_t::iterator edgeiter = _edges.begin();
+      edgeiter != _edges.end(); ++edgeiter) {
+    FragmentationEdges::edge_t &edge = *edgeiter;
+    edge.first = getTranslatedId(_idtable, edge.first);
+    edge.second = getTranslatedId(_idtable, edge.second);
+  }
+}
+
+FragmentationEdges::edges_t SaturatedFragment::getEdges() const
+{
+  // gather all edges
+  const std::vector<atom *> atoms = gatherAllAtoms(FullMolecule);
+  FragmentationEdges::edges_t edges = createEdgesFromAtoms(atoms, FullMolecule);
+
+  // translate each edge
+  std::map<atomId_t, atomId_t> idtable = createIdTable(atoms);
+
+  // rewrite indices of edges in correct order
+  rewriteEdgeIndices(edges, idtable);
+
+  // for debugging output edges
+  LOG(2, "DEBUG: FullMolecule is : " << FullMolecule << " with edges " << edges);
+
+  return edges;
+}

src/Fragmentation/Exporters/SaturatedFragment.hpp

@@ -20 +20 @@
 #include "Atom/atom_bondedparticleinfo.hpp"
 #include "Bond/bond.hpp"
+#include "Fragmentation/EdgesPerFragment.hpp"
 #include "Fragmentation/KeySet.hpp"
 #include "Fragmentation/HydrogenSaturation_enum.hpp"
@@ -106 +107 @@
    */
   std::pair<Vector, Vector> getRoughBoundingBox() const;
+
+  /** Returns the edges of the bond graph of this fragment.
+   *
+   * \return set of edges
+   */
+  FragmentationEdges::edges_t getEdges() const;
 
   /** Prints the config of the fragment of \a _type to \a out.