Changeset 1024cb for src/molecule.hpp

Timestamp:

May 31, 2010, 5:32:27 PM (16 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, Candidate_v1.7.0, Candidate_v1.7.1, 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:

e08c46

Parents:

42af9e (diff), a7b761b (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.

git-author:

Frederik Heber <heber@…> (05/31/10 17:29:30)

git-committer:

Frederik Heber <heber@…> (05/31/10 17:32:27)

Message:

Merge commit 'jupiter/MoleculeStartEndSwitch' into CommandLineActionMapping

Conflicts:

molecuilder/src/Makefile.am
molecuilder/src/builder.cpp
molecuilder/src/config.cpp
molecuilder/src/helpers.hpp
molecuilder/src/molecule.cpp
molecuilder/src/molecule_dynamics.cpp
molecuilder/src/molecule_fragmentation.cpp
molecuilder/src/molecule_geometry.cpp
molecuilder/src/molecule_graph.cpp
molecuilder/src/moleculelist.cpp
molecuilder/src/unittests/AnalysisCorrelationToPointUnitTest.cpp
molecuilder/src/unittests/listofbondsunittest.cpp

Integration of MoleculeStartEndSwitch had the following consequences:

• no more AtomCount -> getAtomCount()
• no more start/end -> begin(), end() and iterator
• no more decent ordering in atomic ids (hence, Simple_configuration/8 and Domain/5, Domain/6 now check by comparing sorted xyz, not confs)

There is still a huge problem with bonds. One test runs into an endless loop.

Signed-off-by: Frederik Heber <heber@…>

File:

• src/molecule.hpp (modified) (9 diffs)

src/molecule.hpp

@@ -34 +34 @@
 #include "tesselation.hpp"
 #include "Patterns/Observer.hpp"
+#include "Patterns/ObservedIterator.hpp"
 #include "Patterns/Cacheable.hpp"
 
@@ -90 +91 @@
   friend molecule *NewMolecule();
   friend void DeleteMolecule(molecule *);
+
   public:
+    typedef std::set<atom*> atomSet;
+    typedef ObservedIterator<atomSet> iterator;
+    typedef atomSet::const_iterator const_iterator;
+
     const periodentafel * const elemente; //!< periodic table with each element
-    atom *start;        //!< start of atom list
-    atom *end;          //!< end of atom list
+    // old deprecated atom handling
+    //atom *start;        //!< start of atom list
+    //atom *end;          //!< end of atom list
     bond *first;        //!< start of bond list
     bond *last;         //!< end of bond list
     int MDSteps;        //!< The number of MD steps in Trajectories
-    int AtomCount;          //!< number of atoms, brought up-to-date by CountAtoms()
+    //int AtomCount;          //!< number of atoms, brought up-to-date by CountAtoms()
     int BondCount;          //!< number of atoms, brought up-to-date by CountBonds()
     int ElementCount;       //!< how many unique elements are therein
@@ -112 +119 @@
   private:
     Cacheable<string> formula;
+    Cacheable<int>    AtomCount;
     moleculeId_t id;
+    atomSet atoms; //<!set of atoms
   protected:
+    //void CountAtoms();
+    /**
+     * this iterator type should be used for internal variables, \
+     * since it will not lock
+     */
+    typedef atomSet::iterator internal_iterator;
+
+
     molecule(const periodentafel * const teil);
     virtual ~molecule();
@@ -121 +138 @@
   //getter and setter
   const std::string getName();
+  int getAtomCount() const;
+  int doCountAtoms();
   moleculeId_t getId();
   void setId(moleculeId_t);
@@ -127 +146 @@
   std::string calcFormula();
 
+  iterator begin();
+  const_iterator begin() const;
+  iterator end();
+  const_iterator end() const;
+  bool empty() const;
+  size_t size() const;
+  const_iterator erase( const_iterator loc );
+  const_iterator erase( atom *& key );
+  const_iterator find (  atom *& key ) const;
+  pair<iterator,bool> insert ( atom * const key );
+
 
   // re-definition of virtual functions from PointCloud
@@ -132 +162 @@
   Vector *GetCenter() const ;
   TesselPoint *GetPoint() const ;
-  TesselPoint *GetTerminalPoint() const ;
   int GetMaxId() const;
   void GoToNext() const ;
-  void GoToPrevious() const ;
   void GoToFirst() const ;
-  void GoToLast() const ;
   bool IsEmpty() const ;
   bool IsEnd() const ;
@@ -232 +259 @@
 
   /// Count and change present atoms' coordination.
-  void CountAtoms();
   void CountElements();
   void CalculateOrbitals(class config &configuration);
@@ -302 +328 @@
   bool StoreForcesFile(MoleculeListClass *BondFragments, char *path, int *SortIndex);
   bool CreateMappingLabelsToConfigSequence(int *&SortIndex);
+  bool CreateFatherLookupTable(atom **&LookupTable, int count = 0);
   void BreadthFirstSearchAdd(molecule *Mol, atom **&AddedAtomList, bond **&AddedBondList, atom *Root, bond *Bond, int BondOrder, bool IsAngstroem);
   /// -# BOSSANOVA
@@ -330 +357 @@
   private:
   int last_atom;      //!< number given to last atom
-  mutable atom *InternalPointer;  //!< internal pointer for PointCloud
+  mutable internal_iterator InternalPointer;  //!< internal pointer for PointCloud
 };