Changeset d45ed9

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:

bd6e5c

Parents:

b0bc13

git-author:

Frederik Heber <heber@…> (03/07/16 13:03:23)

git-committer:

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

Message:

Abstracted atom -> fragment association out of Interfragmenter.

Location:

src/Fragmentation

Files:

• AtomFragmentsMap.cpp (added)
• AtomFragmentsMap.hpp (added)
• Interfragmenter.cpp (modified) (3 diffs)
• Interfragmenter.hpp (modified) (2 diffs)
• Makefile.am (modified) (2 diffs)

src/Fragmentation/Interfragmenter.cpp

@@ -49 +49 @@
 #include "LinkedCell/types.hpp"
 #include "World.hpp"
-
-
-Interfragmenter::atomkeyset_t Interfragmenter::getAtomKeySetMap(
-    size_t _MaxOrder
-    ) const
-{
-  /// create a map of atom to keyset (below equal MaxOrder)
-  atomkeyset_t atomkeyset;
-  LOG(1, "INFO: Placing all atoms and their keysets into a map.");
-  for (Graph::const_iterator keysetiter = TotalGraph.begin();
-      keysetiter != TotalGraph.end(); ++keysetiter) {
-    const KeySet &keyset = keysetiter->first;
-    LOG(2, "DEBUG: Current keyset is " << keyset);
-    const AtomIdSet atoms(keyset);
-    const size_t atoms_size = atoms.getAtomIds().size();
-    if ((atoms_size > _MaxOrder) || (atoms_size == 0))
-      continue;
-    for (AtomIdSet::const_iterator atomiter = atoms.begin();
-        atomiter != atoms.end(); ++atomiter) {
-      // either create new list ...
-      std::pair<atomkeyset_t::iterator, bool> inserter =
-          atomkeyset.insert( std::make_pair(*atomiter, keysets_t(1, &keyset) ));
-      // ... or push to end
-      if (inserter.second) {
-        LOG(3, "DEBUG: Created new entry in map.");
-      } else {
-        LOG(3, "DEBUG: Added keyset to present entry.");
-        inserter.first->second.push_back(&keyset);
-      }
-    }
-  }
-  LOG(2, "DEBUG: There are " << atomkeyset.size() << " entries in lookup.");
-
-  return atomkeyset;
-}
 
 static Vector getAtomIdSetCenter(
@@ -204 +169 @@
     const enum HydrogenTreatment treatment)
 {
-  atomkeyset_t atomkeyset = getAtomKeySetMap(MaxOrder);
+  AtomFragmentsMap AtomFragments(TotalGraph, MaxOrder);
+  const atomkeyset_t &atomkeyset = AtomFragments.getMap();
 
   Graph InterFragments;
@@ -245 +211 @@
   // place all atoms into LC grid with some upper bound
   const LinkedCell::LinkedCell_View view = World::getInstance().getLinkedCell(_upperbound);
-
-  atomkeyset_t atomkeyset = getAtomKeySetMap(_MaxOrder);
 
   // go through each atom and find closest atom not in the same keyset

src/Fragmentation/Interfragmenter.hpp

@@ -19 +19 @@
 
 #include "AtomIdSet.hpp"
+#include "Fragmentation/AtomFragmentsMap.hpp"
 #include "Fragmentation/HydrogenSaturation_enum.hpp"
 
@@ -71 +72 @@
 
 private:
-  /** Helper to translate a keyset into a set of atoms.
-   *
-   * \param keyset
-   * \return vector of atom refs
-   */
-  std::vector<atom *> getAtomsFromKeySet(const KeySet &keyset) const;
 
-  typedef std::list<const KeySet *> keysets_t;
-  typedef std::map<const atom *, keysets_t > atomkeyset_t;
-
-  /** Helper function to create a map of atoms and their fragments/keysets.
-   *
-   * \param _MaxOrder maximum order
-   * \return map with atoms as a keys and fragments as values
-   */
-  atomkeyset_t getAtomKeySetMap(size_t _MaxOrder) const;
+  typedef AtomFragmentsMap::keysets_t keysets_t;
+  typedef AtomFragmentsMap::AtomFragmentsMap_t atomkeyset_t;
 
   typedef std::vector<const atom *> candidates_t;

src/Fragmentation/Makefile.am

@@ -17 +17 @@
         Fragmentation/Homology/HomologyGraph.cpp \
         Fragmentation/AdaptivityMap.cpp \
+        Fragmentation/AtomFragmentsMap.cpp \
         Fragmentation/BondsPerShortestPath.cpp \
         Fragmentation/EnergyMatrix.cpp \
@@ -46 +47 @@
         Fragmentation/Homology/HomologyGraph.hpp \
         Fragmentation/AdaptivityMap.hpp \
+        Fragmentation/AtomFragmentsMap.hpp \
         Fragmentation/AtomMask.hpp \
         Fragmentation/BondsPerShortestPath.hpp \