Changeset 2fd88d1 for src/Fragmentation

Timestamp:

May 18, 2016, 10:02:06 PM (9 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, 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_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, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, 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:

3004d2

Parents:

78202b

git-author:

Frederik Heber <heber@…> (03/11/16 00:38:44)

git-committer:

Frederik Heber <heber@…> (05/18/16 22:02:06)

Message:

AtomFragmentsMap now may return partial map on a vector of atoms with limited order.

Location:

src/Fragmentation

Files:

• Homology/AtomFragmentsMap.cpp (modified) (3 diffs)
• Homology/AtomFragmentsMap.hpp (modified) (2 diffs)
• Interfragmenter.cpp (modified) (1 diff)

src/Fragmentation/Homology/AtomFragmentsMap.cpp

@@ -46 +46 @@
 
 void AtomFragmentsMap::insert(
-    const Graph &_graph,
-    size_t _MaxOrder)
+    const Graph &_graph)
 {
   /// create a map of atom to keyset (below equal MaxOrder)
@@ -55 +54 @@
     const KeySet &keyset = keysetiter->first;
     LOG(2, "DEBUG: Current keyset is " << keyset);
-    if ((keyset.size() > _MaxOrder) || (keyset.empty()))
+    if (keyset.empty())
       continue;
     for (KeySet::const_iterator keyiter = keyset.begin();
@@ -74 +73 @@
 }
 
+AtomFragmentsMap::AtomFragmentsMap_t AtomFragmentsMap::getMap(
+    const std::vector<atomId_t> &_candidates,
+    size_t _MaxOrder) const
+{
+  typedef std::vector<atomId_t> candidates_t;
+  AtomFragmentsMap_t fragmentmap;
+  for (candidates_t::const_iterator candidateiter = _candidates.begin();
+      candidateiter != _candidates.end(); ++candidateiter) {
+    const atomId_t atomid = *candidateiter;
+    const AtomFragmentsMap_t::const_iterator iter = atommap.find(atomid);
+    ASSERT( iter != atommap.end(),
+        "AtomFragmentsMap::getMap() - could not find atom "
+        +toString(atomid)+" in lookup.");
+    // due to MaxOrder we need to copy selectively and hence look at each KeySet in turn
+    const keysets_t &keysets = iter->second;
+    for (keysets_t::const_iterator keyiter = keysets.begin();
+        keyiter != keysets.end(); ++keyiter) {
+      const KeySet &keyset = *keyiter;
+      if ((keyset.size() > _MaxOrder) || (keyset.empty()))
+        continue;
+      std::pair<AtomFragmentsMap_t::iterator, bool> inserter =
+          fragmentmap.insert( std::make_pair(atomid, keysets_t(1, keyset) ));
+      // ... or push to end
+      if (inserter.second) {
+        LOG(3, "DEBUG: Created new entry in lookup map.");
+      } else {
+        LOG(3, "DEBUG: Added keyset to present entry in lookup map.");
+        inserter.first->second.push_back(keyset);
+      }
+    }
+  }
+  LOG(4, "DEBUG: Copied part of lookup map contains " << fragmentmap.size() << " keys.");
+
+  return fragmentmap;
+}
+
 CONSTRUCT_SINGLETON(AtomFragmentsMap)
 

src/Fragmentation/Homology/AtomFragmentsMap.hpp

@@ -44 +44 @@
   //** Function to insert new fragments into storage container.
   void insert(
-      const Graph &_graph,
-      size_t _MaxOrder);
+      const Graph &_graph);
 
   /** Function to clear the container.
@@ -57 +56 @@
   typedef std::map<atomId_t, keysets_t> AtomFragmentsMap_t;
 
+  /** Getter for full stored map.
+   *
+   * \return const ref to internal map
+   */
   const AtomFragmentsMap_t& getMap() const
   { return atommap; }
 
+  /** Getter to map cut down to given selection of atoms.
+   *
+   * \param _candidates subset of atoms
+   * \param _MaxOrder constrain returned fragment list to contain at most this size
+   * \return map with fragments for each of the candidates
+   */
+  AtomFragmentsMap_t getMap(
+      const std::vector<atomId_t> &_candidates,
+      size_t _MaxOrder) const;
 private:
   //!> grant singleton pattern access to private cstor/dstor

src/Fragmentation/Interfragmenter.cpp

@@ -171 +171 @@
 {
   AtomFragmentsMap& atomfragments_container = AtomFragmentsMap::getInstance();
-  atomfragments_container.insert(TotalGraph, MaxOrder);
+  atomfragments_container.insert(TotalGraph);
   const atomkeyset_t &atomkeyset = atomfragments_container.getMap();