Changeset adb5cda for src/molecule.hpp

Timestamp:

Dec 28, 2011, 3:25:49 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:

401f90

Parents:

afa9d8

git-author:

Frederik Heber <heber@…> (12/23/11 15:17:07)

git-committer:

Frederik Heber <heber@…> (12/28/11 15:25:49)

Message:

Removed typedef molecule::atomSet and some commented-out, deprecated sections.

• required changes to LinearInterpolationBetweenSteps, MinimiseConstrainedPotential, MinimiseConstrainedPotential, and VerletForceIntegration.
• replaced molecule::atomset by World::AtomComposite.

File:

• src/molecule.hpp (modified) (4 diffs)

src/molecule.hpp

@@ -78 +78 @@
 
 public:
-  typedef ATOMSET(std::set) atomSet;
   typedef std::set<atomId_t> atomIdSet;
   typedef boost::transform_iterator<FromIdToAtom, atomIdSet::iterator, atom *, atomId_t> iterator;
@@ -84 +83 @@
 
   const periodentafel * const elemente; //!< periodic table with each element
-  // 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
   mutable int NoNonHydrogen; //!< number of non-hydrogen atoms in molecule
@@ -94 +88 @@
   mutable int NoCyclicBonds; //!< number of cyclic bonds in molecule, by DepthFirstSearchAnalysis()
   bool ActiveFlag; //!< in a MoleculeListClass used to discern active from inactive molecules
-  //Vector Center;      //!< Center of molecule in a global box
   int IndexNr; //!< index of molecule in a MoleculeListClass
   char name[MAXSTRINGSIZE]; //!< arbitrary name
@@ -105 +98 @@
   atomIdSet atomIds; //<!set of atomic ids to check uniqueness 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);