Changeset 88c8ec for src/Bond

Timestamp:

Jan 17, 2013, 10:59:15 PM (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:

c8302f3

Parents:

d6b6ce

git-author:

Frederik Heber <heber@…> (10/29/12 00:28:46)

git-committer:

Frederik Heber <heber@…> (01/17/13 22:59:15)

Message:

REFACTOR: Replaced all "bond *" appearances by bond::ptr.

• this is preparatory for making bond::ptr a boost::shared_ptr of bond.
• NOTE: We had to remove a const prefix at four or five places and forward declarations had to be replaced by the true inclusion of bond.hpp at tne or so files. Apart from that, the replacement has been very smooth.

Location:

src/Bond

Files:

• BondInfo.cpp (modified) (3 diffs)
• BondInfo.hpp (modified) (2 diffs)
• bond.cpp (modified) (1 diff)
• bond.hpp (modified) (1 diff)

src/Bond/BondInfo.cpp ¶

@@ -49 +49 @@
 #include "WorldTime.hpp"
 
-BondInfo::BondInfo(const bond * _bond) :
+BondInfo::BondInfo(const bond::ptr _bond) :
   leftid(_bond->leftatom->getId()),
   rightid(_bond->rightatom->getId()),
@@ -65 +65 @@
   }
   const BondList &leftbonds = leftatom->getListOfBonds();
-  boost::function< bool (const bond *)> predicate =
+  boost::function< bool (const bond::ptr )> predicate =
       boost::bind(static_cast<bool (bond::*)(const int) const>(&bond::Contains), _1, rightid);
   if (std::find_if(leftbonds.begin(), leftbonds.end(), predicate) != leftbonds.end())
@@ -76 +76 @@
   // create bond
   LOG(3, "DEBUG: Re-creating bond " << leftid << "<->" << rightid << ".");
-  bond * const _bond = leftatom->addBond(WorldTime::getTime(), rightatom);
+  bond::ptr const _bond = leftatom->addBond(WorldTime::getTime(), rightatom);
   _bond->BondDegree = degree;
   return true;

src/Bond/BondInfo.hpp ¶

@@ -16 +16 @@
 
 #include "types.hpp"
+#include "Bond/bond.hpp"
 
-class bond;
 
 /** Structure for containing bond state information.
@@ -29 +29 @@
    * @param _bond bond whose state to store
    */
-  BondInfo(const bond * _bond);
+  BondInfo(const bond::ptr _bond);
 
   /** Recreates the bond whose state is contained in this BondInfo.

src/Bond/bond.cpp ¶

@@ -41 +41 @@
 
 
-/***************************************** Functions for class bond ********************************/
+/***************************************** Functions for class bond::ptr *******************************/
 
 /** Empty Constructor for class bond.

src/Bond/bond.hpp ¶

@@ -37 +37 @@
 class bond : public GraphEdge, public BondObservable
 {
-  public:
+public:
+  //!> typedef for a bond ptr
+  typedef bond* ptr;
+
   atom *leftatom;    //!< first bond partner
   atom *rightatom;  //!< second bond partner