Changeset 3aa8a5 for src/Atom

Timestamp:

Dec 3, 2012, 9:50:01 AM (12 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:

4694df

Parents:

5197e5

git-author:

Frederik Heber <heber@…> (09/21/12 16:22:50)

git-committer:

Frederik Heber <heber@…> (12/03/12 09:50:01)

Message:

REFACTOR: AdjacencyList now just contains a single internal map.

• map may either be created from world for a given vector of atomids or parsed from file.
• Moved molecule::StoreAdjacencyFromFile() over to StoreToFile().
• removed atom_bondedparticle::OutputAdjacency().
• changed comparison functions into operator<,>,==,!=().
• adapted FragmentationAction and SaveAdjacencyAction due to new calls, the former also needs to check the adjacency file for existence.
• SaveAdjacencyAction does not split given filename into path and name anymore.
• TESTFIX: Fragmentation-MaxOrder is working again, removed XFAIL_IF.
• TESTFIX: Rewrite of AdjacencyListUnitTest due to heavily changed interface of AdjacencyList. Also wrongadjacencyfile3 was buggy.
• TESTFIX: regression test SaveAdjacency replaced tab by space and removed tab after last entry in test.adj.

Location:

src/Atom

Files:

• atom_bondedparticle.cpp (modified) (1 diff)
• atom_bondedparticle.hpp (modified) (1 diff)

src/Atom/atom_bondedparticle.cpp

@@ -79 +79 @@
   }
   ost << " -- TotalDegree: " << TotalDegree;
-};
-
-/** Output of atom::Nr along with all bond partners.
- * \param *AdjacencyFile output stream
- */
-void BondedParticle::OutputAdjacency(ofstream * const AdjacencyFile) const
-{
-  const BondList& ListOfBonds = getListOfBonds();
-  *AdjacencyFile << getNr() << "\t";
-  for (BondList::const_iterator Runner = ListOfBonds.begin(); Runner != ListOfBonds.end(); (++Runner))
-    *AdjacencyFile << (*Runner)->GetOtherAtom(this)->getNr() << "\t";
-  *AdjacencyFile << endl;
 };
 

src/Atom/atom_bondedparticle.hpp

@@ -47 +47 @@
   void resetBondDegree();
   void OutputBondOfAtom(std::ostream &ost) const;
-  void OutputAdjacency(ofstream * const AdjacencyFile) const;
   void OutputBonds(ofstream * const BondFile) const;
   void OutputOrder(ofstream *file) const;