Changeset 266237 for src/atom.hpp

Timestamp:

Oct 18, 2009, 2:51:38 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, 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:

174e0e

Parents:

b8b75d

git-author:

Frederik Heber <heber@…> (10/18/09 14:15:37)

git-committer:

Frederik Heber <heber@…> (10/18/09 14:51:38)

Message:

Huge refactoring: molecule::ListOfBondsPerAtom and molecule::NumberOfBondsPerAtom removed, atom::ListOfBonds introduced. Unit Test for ListOfBonds manipulation introduced.

• changes to class atom:
  • ~atom(): removes all bonds it is part of and unlink()s
  • new functions: CountBonds() - counts bonds times BondDegree, OutputGraphInfo() - graph data is output, OutputComponentNumber() - output of component numbers, OutputAdjacency() - indices of this and its neighbours, CorrectBondDegree() - corrects bond degree incrementally (by at most one) -- all since ListOfBonds is now local info
  • OutputBondOfAtom() - does not need ListOfBondsPerAtom, ... as ListOfBonds is now local info
  • new functions for ListOfBonds access: RegisterBond(), UnregisterBond(), UnregisterAllBonds() (the latter only remove from the list, do not delete, as molecule still has a global list of all bonds and does deletion.)

• changes to class bond:
  • ~bond() uses unlink(), uses UnregisterBond() on leftatom and rightatom
  • removed unused bond::GetFirstBond() and bond::GetLastBond()
  • GetOtherAtom() has now const parameter

• changes to builder.cpp: removed CreateListOfBondsPerAtom() calls, as the creation of the global arrays is not necessary anymore

• changes to LinkedCell: LinkedCell::CheckBounds(int[NDIM]) does not admonish out of bonds as this is not desired for the local offset which may become out of bounds.

• changes to lists.hpp templates: BUGFIX: unlink() now sets ->next and ->previous to NULL, cleanup() uses removedwithoutcheck()

• new templates for molecule.hpp: SumPerAtom() allows for summation of the return value of atom:...() member fiunctions. This is needed e.g. for atom::CorrectBondDegree()

• changes to MoleculeListClass:
  • changes due to ListOfBondsPerAtom -> atom::ListOfBonds: AddHydrogenCorrection(), FillBondStructureFromReference()

• changes to class molecule:
  • changes due to ListOfBondsPerAtom -> atom::ListOfBonds: GuesstimateFragmentCount(), FragmentMolecule(), FillSPListandLabelVertices(), ScanForPeriodicCorrection(), DeterminePeriodicCenter(), CyclicStructureAnalysis(), InitComponentNumbers(), FindNextUnused(), CheckAdjacencyFileAgainstMolecule(), PickLocalBackEdges(), BreadthFirstSearchAdd(), BuildInducedSubgraph(), CheckForConnectedSubgraph(), molecule(), ~molecule(), AddHydrogenReplacementAtom(), RemoveBonds(), OutputListOfBonds(), removed CreateListOfBondsPerAtom()
  • due to removal of CreateListOfBonds(): FragmentMolecule(), CreateAdjacencyListFromDbondFile(), CreateAdjacencyList(), SetNextComponentNumber()
  • ActOnAllAtoms() used: CreateAdjacencyList() - uses atom::OutputBondOfAtom(), StoreAdjacencyToFile() - uses atom::OutputAdjacency(),
  • SumPerAtom() used: CorrectBondDegree() - uses atom::CorrectBondDegree(),
  • function removed: molecule::CountAtomsBonds() - shifted to atom::CountBonds(), OutputComponentNumber() - shifted to atom::OutputComponentNumber()
  • CountCyclicBonds() - manipulates molecule::NoCyclicBonds directly.
  • rewritten DepthFirstSearchAnalysis() - refactored to CyclicBondAnalysis(), OutputGraphInfoPerAtom(), OutputGraphInfoPerBond()
  • rewritten RemoveAtom() - uses RemoveBonds()
  • FIX: rewritten CleanupMolecule() - cleanup was wrong order, now is first bonds, then atoms
  • rewritten BreadthFirstSearchAdd() - uses molecule::CopyBond() (equal code was present multiple(!) times before)
  • new functions CyclicBondAnalysis(), OutputGraphInfoPerAtom(), OutputGraphInfoPerBond(), CopyBond()

• New UnitTest for ListOfBonds:
  • tests AddBond(), RemoveAtom(), RemoveBond(), RemoveBonds() and simple deletion of atoms or bonds, where afterwards chain lists of bonds should remain intact.

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

File:

• src/atom.hpp (modified) (5 diffs)

src/atom.hpp

@@ -19 +19 @@
 
 #include <iostream>
+#include <list>
 #include <vector>
 
@@ -32 +33 @@
 class ForceMatrix;
 class Vector;
+
+#define BondList list<bond *>
 
 /********************************************** declarations *******************************/
@@ -50 +53 @@
     Vector v;       //!< velocity vector of atom, giving last velocity within cell
     Vector F;       //!< Force vector of atom, giving last force within cell
+    BondList ListOfBonds; //!< list of all bonds
     element *type;  //!< pointing to element
     atom *previous; //!< previous atom in molecule list
@@ -76 +80 @@
   bool OutputTrajectory(ofstream *out, int *ElementNo, int *AtomNo, int step) const;
   bool OutputTrajectoryXYZ(ofstream *out, int step) const;
-  bool OutputBondOfAtom(ofstream *out, int *NumberOfBondsPerAtom, bond ***ListOfBondsPerAtom) const;
+  bool OutputBondOfAtom(ofstream *out) const;
+  void OutputAdjacency(ofstream *AdjacencyFile) const;
+
 
   void EqualsFather ( atom *ptr, atom **res );
@@ -96 +102 @@
   // bond order stuff
   void OutputOrder(ofstream *file);
+  void OutputGraphInfo(ofstream *out) const;
+  void OutputComponentNumber(ofstream *out) const;
+  int CountBonds() const;
+  int CorrectBondDegree(ofstream *out);
+
+  bool RegisterBond(bond *Binder);
+  bool UnregisterBond(bond *Binder);
+  void UnregisterAllBond();
 
   // constraint potential and dynamics stuff