Changeset e791dc for src/molecule.hpp

Timestamp:

Apr 3, 2012, 8:00:19 AM (14 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:

2a3124

Parents:

108968

git-author:

Frederik Heber <heber@…> (03/13/12 17:52:00)

git-committer:

Frederik Heber <heber@…> (04/03/12 08:00:19)

Message:

Removed molecule::doCountAtom() and added molecule::doCountNoNonHydrogen().

• since the conversion of molecule to being a container for a set of atomicId_t counting atoms is just an unnecessary O(N^{2), since we count through all of them. With atomIds.size() however the number of atoms is always known.}
• Hence, moleucle::AtomCount is no longer a Cacheable, but NoNoHydrogen is now such a one. LazyEvaluation is only sensible when the evaluations are few. Due to updates from the GUI however, atomcount is constantly requested.
• FIX: removed doCountAtom() calls in some functions in analysis_correlation.

File:

• src/molecule.hpp (modified) (3 diffs)

src/molecule.hpp

@@ -74 +74 @@
 
   int MDSteps; //!< The number of MD steps in Trajectories
-  mutable int NoNonHydrogen; //!< number of non-hydrogen atoms in molecule
   mutable int NoNonBonds; //!< number of non-hydrogen bonds in molecule
   mutable int NoCyclicBonds; //!< number of cyclic bonds in molecule, by DepthFirstSearchAnalysis()
@@ -83 +82 @@
 private:
   Formula formula;
-  Cacheable<int> AtomCount; //!< number of atoms, brought up-to-date by doCountAtoms()
+  Cacheable<size_t> NoNonHydrogen; //!< number of non-hydrogen atoms in molecule
   Cacheable<int> BondCount; //!< number of atoms, brought up-to-date by doCountBonds()
   moleculeId_t id;
@@ -98 +97 @@
   const std::string getName() const;
   int getAtomCount() const;
-  int doCountAtoms();
+  size_t doCountNoNonHydrogen() const;
+  size_t getNoNonHydrogen() const;
   int getBondCount() const;
   int doCountBonds() const;