Changeset 88c8ec for src/Atom

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/Atom

Files:

• CopyAtoms/CopyAtoms_withBonds.cpp (modified) (2 diffs)
• atom_bondedparticle.cpp (modified) (6 diffs)
• atom_bondedparticle.hpp (modified) (2 diffs)
• atom_bondedparticleinfo.hpp (modified) (2 diffs)
• unittests/CopyAtomsInterfaceUnitTest.cpp (modified) (2 diffs)

src/Atom/CopyAtoms/CopyAtoms_withBonds.cpp

@@ -63 +63 @@
     for(BondList::const_iterator iter = ListOfBonds.begin(); iter != ListOfBonds.end(); ++iter) {
       // check both bond partners have been copied
-      const bond * const Binder = *iter;
+      const bond::ptr Binder = *iter;
       if (*original_iter == Binder->leftatom) {
         LookupMap_t::const_iterator leftiter = LookupMap.find(Binder->leftatom);
@@ -71 +71 @@
           atom * const LeftAtom = leftiter->second;
           atom * const RightAtom = rightiter->second;
-          bond * const NewBond = LeftAtom->addBond(WorldTime::getTime(), RightAtom);
+          bond::ptr const NewBond = LeftAtom->addBond(WorldTime::getTime(), RightAtom);
           LOG(3, "DEBUG: Creating copy bond between original " << Binder->leftatom->getId()
               << " and " << Binder->rightatom->getId() << ": " << *NewBond << ".");

src/Atom/atom_bondedparticle.cpp

@@ -104 +104 @@
  * @return const pointer to created bond or to already present bonds
  */
-bond * const BondedParticle::addBond(const unsigned int _step, BondedParticle* Partner)
+bond::ptr const BondedParticle::addBond(const unsigned int _step, BondedParticle* Partner)
 {
   const BondList &bondlist = getListOfBondsAtStep(_step);
@@ -145 +145 @@
  * @param Binder bond to remove
  */
-void BondedParticle::removeBond(bond * binder)
+void BondedParticle::removeBond(bond::ptr binder)
 {
   UnregisterBond(binder);
@@ -177 +177 @@
  * \param *Binder bond to insert
  */
-bool BondedParticle::RegisterBond(const unsigned int _step, bond * const Binder)
+bool BondedParticle::RegisterBond(const unsigned int _step, bond::ptr const Binder)
 {
   OBSERVE;
@@ -203 +203 @@
  * \param *Binder bond to remove
  */
-bool BondedParticle::UnregisterBond(bond * const Binder)
+bool BondedParticle::UnregisterBond(bond::ptr const Binder)
 {
   OBSERVE;
@@ -253 +253 @@
  * @return >=0 - first time step where bond appears, -1 - bond not present in lists
  */
-int BondedParticle::ContainsBondAtStep(bond *Binder) const
+int BondedParticle::ContainsBondAtStep(bond::ptr Binder) const
 {
   int step = -1;
@@ -286 +286 @@
   int FalseBondDegree = 0;
   atom *OtherWalker = NULL;
-  bond *CandidateBond = NULL;
+  bond::ptr CandidateBond = NULL;
 
   NoBonds = CountBonds();

src/Atom/atom_bondedparticle.hpp

@@ -37 +37 @@
   virtual ~BondedParticle();
 
-  bond * const addBond(const unsigned int _step, BondedParticle* Partner);
+  bond::ptr const addBond(const unsigned int _step, BondedParticle* Partner);
   void removeBond(const unsigned int _step, BondedParticle* Partner);
-  void removeBond(bond *binder);
+  void removeBond(bond::ptr binder);
   void removeAllBonds();
   void removeAllBonds(const unsigned int _step);
@@ -54 +54 @@
 
 protected:
-  bool RegisterBond(const unsigned int _step, bond * const Binder);
-  bool UnregisterBond(bond * const Binder);
+  bool RegisterBond(const unsigned int _step, bond::ptr const Binder);
+  bool UnregisterBond(bond::ptr const Binder);
   void UnregisterAllBond(const unsigned int _step);
 
-  int ContainsBondAtStep(bond *Binder) const;
+  int ContainsBondAtStep(bond::ptr Binder) const;
 
 };

src/Atom/atom_bondedparticleinfo.hpp

@@ -20 +20 @@
 
 #include "atom_observable.hpp"
+#include "Bond/bond.hpp"
 
 #include <list>
@@ -25 +26 @@
 /****************************************** forward declarations *****************************/
 
-class bond;
 class BondedParticle;
 
-#define BondList std::list<bond *>
+#define BondList list<bond::ptr >
 
 /********************************************** declarations *******************************/

src/Atom/unittests/CopyAtomsInterfaceUnitTest.cpp

@@ -129 +129 @@
     const BondList & ListOfBonds = atoms[0]->getListOfBonds();
     CPPUNIT_ASSERT( !ListOfBonds.empty() );
-    const bond * const _bond = *ListOfBonds.begin();
+    bond::ptr const _bond = *ListOfBonds.begin();
     CPPUNIT_ASSERT( _bond->GetOtherAtom(atoms[0]) == atoms[1] );
   }
@@ -144 +144 @@
     const BondList & ListOfBonds = copyMethod.CopiedAtoms[0]->getListOfBonds();
     CPPUNIT_ASSERT( !ListOfBonds.empty() );
-    const bond * const _bond = *ListOfBonds.begin();
+    bond::ptr const _bond = *ListOfBonds.begin();
     CPPUNIT_ASSERT( _bond->GetOtherAtom(copyMethod.CopiedAtoms[0]) == copyMethod.CopiedAtoms[1] );
   }