Changeset 3690e4 for src/Fragmentation/Interfragmenter.hpp

Timestamp:

Feb 2, 2016, 5:50:29 PM (9 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, 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_BoundInBox_CenterInBox_MoleculeActions, 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, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, 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:

9ae11c

Parents:

d1831e (diff), 62d092 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'Enhancing_Interdistance' into Candidate_v1.5.1

File:

• src/Fragmentation/Interfragmenter.hpp (modified) (3 diffs)

src/Fragmentation/Interfragmenter.hpp

@@ -14 +14 @@
 #endif
 
+#include <list>
+#include <map>
 #include <vector>
 
+#include "AtomIdSet.hpp"
 #include "Fragmentation/HydrogenSaturation_enum.hpp"
 
@@ -50 +53 @@
    */
   void operator()(
-      size_t MaxOrder,
-      double Rcut,
+      const size_t MaxOrder,
+      const double Rcut,
       const enum HydrogenTreatment treatment);
+
+  /** This finds the largest cut off distance (\a Rcut) such that when running
+   * operator() no additional inter-fragments would be produced.
+   *
+   * \param MaxOrder maximum order for fragments to interrelate
+   * \param _upperbound upper bound on \a Rcut above which we do not look
+   * \param treatment whether hydrogens are treated specially or not
+   * \return largest cutoff distance to cause no additional inter-fragments
+   */
+  double findLargestCutoff(
+      const size_t _MaxOrder,
+      const double _upperbound,
+      const enum HydrogenTreatment _treatment) const;
 
 private:
@@ -62 +78 @@
   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 std::vector<const atom *> candidates_t;
+
+  /** Helper function to get all atoms around a specific keyset not contained in
+   * the same molecule.
+   *
+   * \param _atoms all atoms of a fragment
+   * \param _Rcut desired distance cutoff
+   * \param _treatment whether hydrogens are treated special or not
+   */
+  candidates_t getNeighborsOutsideMolecule(
+      const AtomIdSet &_atoms,
+      const double _Rcut,
+      const enum HydrogenTreatment _treatment) const;
+
+  /** Helper function to return a fragment/KeySet map specific to all candidates.
+   *
+   * \param _candidates all neighboring atoms around keyset
+   * \param _atomkeyset map with all atoms and the KeySets they are contained in
+   * \return specific fragment map
+   */
+  atomkeyset_t getCandidatesSpecificKeySetMap(
+      const candidates_t &_candidates,
+      const atomkeyset_t &_atomkeyset) const;
+
+  /** For a given set of candidates atoms in \a _candidates and a \a _keyset
+   * we combine each fragment from either atom and place it into internal
+   * Graph.
+   *
+   * \param _MaxOrder maximum order
+   * \param _candidates all atoms neighboring the current out outside of its molecule
+   * \param _fragmentmap all keysets related to this atom
+   * \param _keyset current keyset (used as base for creating inter-fragments)
+   * \param _InterFragments container for all created inter-fragments
+   * \param _counter counts added fragments
+   */
+  void combineFragments(
+      const size_t _MaxOrder,
+      const candidates_t &_candidates,
+      atomkeyset_t &_fragmentmap,
+      const KeySet &_keyset,
+      Graph &_InterFragments,
+      int &_counter);
 
 private: