Changeset 29f7c1 for src/molecule.hpp

Timestamp:

Feb 11, 2016, 8:07:50 AM (9 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:

951aa6

Parents:

c0f2fc

git-author:

Frederik Heber <heber@…> (12/29/15 19:49:43)

git-committer:

Frederik Heber <heber@…> (02/11/16 08:07:50)

Message:

Molecule now has maps with old values for bond counts and element number per atom.

• this allows to update the total bond count and the formula in an O(N log N) fashion.

File:

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

src/molecule.hpp

@@ -94 +94 @@
 private:
   Formula formula;
-  Cacheable<size_t> NoNonHydrogen; //!< number of non-hydrogen atoms in molecule
-  Cacheable<int> BondCount; //!< number of atoms, brought up-to-date by doCountBonds()
+  size_t NoNonHydrogen; //!< number of non-hydrogen atoms in molecule
+  int BondCount; //!< number of atoms, brought up-to-date by doCountBonds()
   moleculeId_t id;
   AtomIdSet atomIds; //<!set of atomic ids to check uniqueness of atoms
@@ -136 +136 @@
   int getAtomCount() const;
   size_t doCountNoNonHydrogen() const;
-  size_t getNoNonHydrogen() const;
-  int getBondCount() const;
   int doCountBonds() const;
+  size_t getNoNonHydrogen() const{
+    return NoNonHydrogen;
+  }
+
+  int getBondCount() const{
+    return BondCount;
+  }
   moleculeId_t getId() const;
   void setId(moleculeId_t);
@@ -357 +362 @@
       > AtomDistanceMap_t;
   std::vector<AtomDistanceMap_t> BoundingBoxSweepingAxis;
+
+  //!> typedef for a map with current bond counts per atom
+  typedef std::map<atomId_t, size_t> BondCountsPerAtom_t;
+
+  //!> current bond counts per atom to update the BondCount
+  BondCountsPerAtom_t BondCountsPerAtom;
+
+  //!> typedef for a map with current element per atom
+  typedef std::map<atomId_t, atomicNumber_t> ElementPerAtom_t;
+
+  //!> current element per atom to update the BondCount
+  ElementPerAtom_t ElementPerAtom;
 
   //!> make setMolecule friend to access associateAtomWithMolecule()