Changeset ec87e4 for src/Graph/CheckAgainstAdjacencyFile.hpp

Timestamp:

Oct 25, 2011, 12:08:02 PM (13 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:

708798

Parents:

5fd0f4

git-author:

Frederik Heber <heber@…> (10/17/11 15:23:42)

git-committer:

Frederik Heber <heber@…> (10/25/11 12:08:02)

Message:

Rewrite of CheckAgainstAdjacencyFile.

• we now construct two multimaps -- one from file, the other from World's selected atoms -- and compare these two.
• added unit test on the class.

File:

• src/Graph/CheckAgainstAdjacencyFile.hpp (modified) (2 diffs)

src/Graph/CheckAgainstAdjacencyFile.hpp

@@ -16 +16 @@
 #include <iosfwd>
 #include <map>
+#include <set>
+
+#include "types.hpp"
+#include "World.hpp"
 
 class atom;
@@ -21 +25 @@
 class CheckAgainstAdjacencyFile
 {
+  //!> Unit test is granted access to internal data
+  friend class CheckAgainstAdjacencyFileTest;
 public:
-  CheckAgainstAdjacencyFile();
+  CheckAgainstAdjacencyFile(World::AtomSet::const_iterator AtomMapBegin, World::AtomSet::const_iterator AtomMapEnd);
   ~CheckAgainstAdjacencyFile();
 
-  bool operator()(std::ifstream &File, std::map<int, atom*> ListOfAtoms);
+  bool operator()(std::istream &File);
 
 private:
-  enum {MAXBONDS=8};
-
-  int *CurrentBonds;
+  typedef std::set<atomId_t> KeysSet;
+  typedef std::set<atomId_t> ValuesSet;
+  typedef std::pair<atomId_t, atomId_t> AtomBondPair;
+  typedef std::multimap< atomId_t, atomId_t > AtomBondMap;
+  typedef std::pair<AtomBondMap::const_iterator, AtomBondMap::const_iterator> AtomBondRange;
+  AtomBondMap InternalAtomBondMap;
+  AtomBondMap ExternalAtomBondMap;
   bool status;
   int NonMatchNumber;
 
-  void CompareBonds(const atom *&Walker, size_t &CurrentBondsOfAtom, int AtomNr, std::map<int, atom*> &ListOfAtoms);
+  void CreateInternalMap(World::AtomSet::const_iterator &AtomMapBegin, World::AtomSet::const_iterator &AtomMapEnd);
+  bool ParseInExternalMap(std::istream &File);
+  bool CompareInternalExternalMap();
 };