Changeset 70aeed for src/Fragmentation

Timestamp:

May 18, 2016, 10:02:07 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, 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:

d9dbef

Parents:

d410e25

git-author:

Frederik Heber <heber@…> (03/07/16 18:58:56)

git-committer:

Frederik Heber <heber@…> (05/18/16 22:02:07)

Message:

Added additional "force" keysets to AtomFragmentsMap.

Location:

src/Fragmentation/Homology

Files:

• AtomFragmentsMap.cpp (modified) (2 diffs)
• AtomFragmentsMap.hpp (modified) (6 diffs)

src/Fragmentation/Homology/AtomFragmentsMap.cpp

@@ -69 +69 @@
       }
     }
+    // add empty entry to fullkeysets, too (if already present, we ignore that)
+    fullkeysets.insert( std::make_pair(keyset, indices_t()) );
   }
   LOG(2, "DEBUG: There are now " << atommap.size() << " entries in lookup.");
@@ -109 +111 @@
 }
 
+bool AtomFragmentsMap::addFullKeyset(const KeySet &_keyset, const indices_t &_fullkeyset)
+{
+  FragmentFullKeysetMap_t::iterator iter = fullkeysets.find(_keyset);
+  if ((iter == fullkeysets.end()) || (!iter->second.empty()))
+    return false;
+  else {
+    iter->second = _fullkeyset;
+  }
+  return true;
+}
+
+const AtomFragmentsMap::indices_t &
+AtomFragmentsMap::getFullKeyset(const KeySet &_keyset) const
+{
+  static indices_t emptyset;
+  FragmentFullKeysetMap_t::const_iterator iter = fullkeysets.find(_keyset);
+  if (iter == fullkeysets.end())
+    return emptyset;
+  else
+    return iter->second;
+}
+
+bool AtomFragmentsMap::checkCompleteness() const
+{
+  bool status = true;
+  for (FragmentFullKeysetMap_t::const_iterator iter = fullkeysets.begin();
+      iter != fullkeysets.end(); ++iter)
+    status &= (iter->second.size() != 0);
+
+  return status;
+}
+
 CONSTRUCT_SINGLETON(AtomFragmentsMap)
 

src/Fragmentation/Homology/AtomFragmentsMap.hpp

@@ -19 +19 @@
 #include <list>
 #include <map>
+#include <vector>
 
 #include <boost/serialization/export.hpp>
-#include <boost/serialization/set.hpp>
 #include <boost/serialization/list.hpp>
 #include <boost/serialization/map.hpp>
+#include <boost/serialization/set.hpp>
+#include <boost/serialization/vector.hpp>
 #include <boost/serialization/version.hpp>
 
@@ -52 +54 @@
   { atommap.clear(); }
 
+  typedef std::vector<atomId_t> indices_t;
   typedef std::list<KeySet> keysets_t;
   //!> typedef for the internal map
   typedef std::map<atomId_t, keysets_t> AtomFragmentsMap_t;
+  typedef std::map<KeySet, indices_t > FragmentFullKeysetMap_t;
 
   /** Getter for full stored map.
@@ -62 +66 @@
   const AtomFragmentsMap_t& getMap() const
   { return atommap; }
+
+  /** Allows to add the full keyset, with excluded hydrogens, to add
+   * to a given \a _keyset
+   *
+   * \param _keyset keyset to a fragment without hydrogens
+   * \param _fullkeyset full keyset with excluded hydrogens to associate with \a _keyset
+   * \return true - insertion ok, else - index set already present
+   */
+  bool addFullKeyset(const KeySet &_keyset, const indices_t &_fullkeyset);
+
+  /** Getter for the full key set, i.e. including excluded hydrogens, for a
+   * given \a _keyset without them.
+   *
+   * \param _keyset keyset to a fragment without hydrogens
+   * \return full index set containing all keys from \a _keyset and all excluded
+   *         hydrogens
+   */
+  const indices_t &getFullKeyset(const KeySet &_keyset) const;
 
   /** Getter to map cut down to given selection of atoms.
@@ -72 +94 @@
       const std::vector<atomId_t> &_candidates,
       size_t _MaxOrder) const;
+
+  /** Checks whether we have a full keyset for every keyset contained.
+   *
+   * \return true - is complete, false - else
+   */
+  bool checkCompleteness() const;
+
 private:
   //!> grant singleton pattern access to private cstor/dstor
@@ -87 +116 @@
 
 private:
-  //!> internal map filled on instantiation
+  //!> internal map associating atoms and fragments
   AtomFragmentsMap_t atommap;
+
+  //!> internal map to get from keyset (without hydrogens) to full keyset, i.e. forcekeyset
+  FragmentFullKeysetMap_t fullkeysets;
 
 private:
@@ -97 +129 @@
   {
     ar & atommap;
+    ar & fullkeysets;
   }
 };