Changeset d948b4 for src/Atom

Timestamp:

Mar 22, 2013, 12:04:17 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:

ddeed2

Parents:

31021ab

git-author:

Frederik Heber <heber@…> (03/01/13 19:28:42)

git-committer:

Frederik Heber <heber@…> (03/22/13 00:04:17)

Message:

atom_bondedparticle::addBond() returns no longer const bond::ptr.

• this comes in the way when we want to set the bond degree right away.
• also added convenience functions for addBond() and removedBond() that act on the current time step.

Location:

src/Atom

Files:

• atom_bondedparticle.cpp (modified) (3 diffs)
• atom_bondedparticle.hpp (modified) (1 diff)

src/Atom/atom_bondedparticle.cpp

@@ -102 +102 @@
  * @param _step time step to access
  * @param bonding partner
- * @return const pointer to created bond or to already present bonds
- */
-bond::ptr const BondedParticle::addBond(const unsigned int _step, BondedParticle* Partner)
+ * @return pointer to created bond or to already present bonds
+ */
+bond::ptr BondedParticle::addBond(const unsigned int _step, BondedParticle* Partner)
 {
   const BondList &bondlist = getListOfBondsAtStep(_step);
@@ -119 +119 @@
 
   return newBond;
+}
+
+/**
+ * Adds a bond between this bonded particle and another. Returns present instance if this
+ * bond already exists.
+ *
+ * @param bonding partner
+ * @return pointer to created bond or to already present bonds
+ */
+bond::ptr BondedParticle::addBond(BondedParticle* Partner)
+{
+  addBond(WorldTime::getTime(), Partner);
 }
 
@@ -175 +187 @@
     ELOG(1, "BondedParticle::removeBond() - I cannot find the bond in between "
         +toString(getName())+" and "+toString(Partner->getName())+".");
+}
+
+/** Removes a bond of this atom to a given \a Partner.
+ *
+ * @param Partner bond partner
+ */
+void BondedParticle::removeBond(BondedParticle * const Partner)
+{
+  removeBond(WorldTime::getTime(), Partner);
 }
 

src/Atom/atom_bondedparticle.hpp

@@ -44 +44 @@
   virtual ~BondedParticle();
 
-  bond::ptr const addBond(const unsigned int _step, BondedParticle* Partner);
+  bond::ptr addBond(const unsigned int _step, BondedParticle* Partner);
+  bond::ptr addBond(BondedParticle* Partner);
   void removeBond(const unsigned int _step, BondedParticle* Partner);
+  void removeBond(BondedParticle* Partner);
   void removeBond(bond::ptr &binder);
   void removeAllBonds();