Changeset db7e6d for src

Timestamp:

Oct 6, 2011, 4:06:10 PM (13 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:

37b2575

Parents:

7188b1

git-author:

Frederik Heber <heber@…> (09/01/11 16:25:34)

git-committer:

Frederik Heber <heber@…> (10/06/11 16:06:10)

Message:

BondedParticle:: register and unregister are private.

• adding and removing bonds is possible via addBond(), removeBond().
• this wat we encapsulate the register and unregister and make sure that never a lone bond remains at one side.
• adapted:
  • BondGraph::CreateAdjacency()
• Register and UnregisterBond are OBSERVEd.
• bond::Contains() is const member function now

Location:

src

Files:

• Actions/GraphAction/CreateAdjacencyAction.cpp (modified) (1 diff)
• Bond/bond.cpp (modified) (3 diffs)
• Bond/bond.hpp (modified) (1 diff)
• Graph/BondGraph.cpp (modified) (1 diff)
• Graph/BondGraph.hpp (modified) (1 diff)
• atom_bondedparticle.cpp (modified) (8 diffs)
• atom_bondedparticle.hpp (modified) (2 diffs)

src/Actions/GraphAction/CreateAdjacencyAction.cpp

@@ -141 +141 @@
                             if (status) { // create bond if distance is smaller
 //                              Log() << Verbose(1) << "Adding Bond between " << *Walker << " and " << *OtherWalker << " in distance " << sqrt(distance) << "." << endl;
-                              bond * const Binder = new bond(Walker->father, OtherWalker->father, 1);
+                              //const bond * Binder =
+                                  Walker->father->addBond(WorldTime::getTime(), OtherWalker->father);
                               BondCount++;
-                              Walker->father->RegisterBond(WorldTime::getTime(),Binder);
-                              OtherWalker->father->RegisterBond(WorldTime::getTime(),Binder);
                             } else {
 //                              Log() << Verbose(1) << "Not Adding: distance too great." << endl;

src/Bond/bond.cpp

@@ -63 +63 @@
   // remove this node from the list structure
   if (leftatom != NULL)
-    leftatom->UnregisterBond(this);
+    leftatom->removeBond(this);
   // there might be self-bonds
   if ((leftatom != rightatom) && (rightatom != NULL))
-    rightatom->UnregisterBond(this);
+    rightatom->removeBond(this);
 };
 
@@ -94 +94 @@
  * \return true if it is either bond::leftatom or bond::rightatom, false otherwise
  */
-bool bond::Contains(const ParticleInfo * const ptr)
+bool bond::Contains(const ParticleInfo * const ptr) const
 {
   return ((leftatom == ptr) || (rightatom == ptr));
@@ -103 +103 @@
  * \return true if it is either bond::leftatom or bond::rightatom, false otherwise
  */
-bool bond::Contains(const int number)
+bool bond::Contains(const int number) const
 {
   return ((leftatom->getNr() == number) || (rightatom->getNr() == number));

src/Bond/bond.hpp

@@ -44 +44 @@
   atom * GetOtherAtom(const ParticleInfo * const Atom) const;
 
-  bool Contains(const ParticleInfo * const ptr);
-  bool Contains(const int nr);
+  bool Contains(const ParticleInfo * const ptr) const;
+  bool Contains(const int nr) const;
   double GetDistance() const;
   double GetDistanceSquared() const;

src/Graph/BondGraph.cpp

@@ -199 +199 @@
                           if (status) { // create bond if distance is smaller
                             LOG(1, "ACCEPT: Adding Bond between " << *Walker << " and " << *OtherWalker << " in distance " << sqrt(distance) << ".");
-                            bond * Binder = new bond(Walker->father, OtherWalker->father, 1);
-                            Walker->father->RegisterBond(WorldTime::getTime(), Binder);
-                            OtherWalker->father->RegisterBond(WorldTime::getTime(), Binder);
+                            //const bond * Binder =
+                              Walker->father->addBond(WorldTime::getTime(), OtherWalker->father);
                             BondCount++;
                           } else {

src/Graph/BondGraph.hpp

@@ -230 +230 @@
 
       LOG(3, "INFO: Creating bond between atoms " << atom1 << " and " << atom2 << ".");
-      bond * const Binder = new bond(Walker, OtherWalker, 1);
-      Walker->RegisterBond(WorldTime::getTime(), Binder);
-      OtherWalker->RegisterBond(WorldTime::getTime(), Binder);
+      //const bond * Binder =
+          Walker->addBond(WorldTime::getTime(), OtherWalker);
       bondcounter++;
     }

src/atom_bondedparticle.cpp

@@ -27 +27 @@
 #include "CodePatterns/Verbose.hpp"
 #include "element.hpp"
+#include "WorldTime.hpp"
 
 /** Constructor of class BondedParticle.
@@ -93 +94 @@
 
 /**
- * Adds a bond between this bonded particle and another. Does nothing if this
+ * Adds a bond between this bonded particle and another. Returns present instance if this
  * bond already exists.
  *
  * @param _step time step to access
- * \param bonding partner
- */
-void BondedParticle::addBond(const unsigned int _step, BondedParticle* Partner) {
-  if (IsBondedTo(_step, Partner)) {
-    return;
+ * @param bonding partner
+ * @return const reference to created bond or to already present bonds
+ */
+const bond * BondedParticle::addBond(const unsigned int _step, BondedParticle* Partner)
+{
+  const BondList &bondlist = getListOfBondsAtStep(_step);
+  for (BondList::const_iterator runner = bondlist.begin();
+      runner != bondlist.end();
+      runner++) {
+    if ((*runner)->Contains(Partner))
+      return *runner;
   }
 
@@ -107 +114 @@
   RegisterBond(_step, newBond);
   Partner->RegisterBond(_step, newBond);
+
+  return newBond;
+}
+
+/** Removes a bond for this atom.
+ *
+ * @param Binder bond to remove
+ */
+void BondedParticle::removeBond(bond * binder)
+{
+  UnregisterBond(binder);
 }
 
@@ -115 +133 @@
 bool BondedParticle::RegisterBond(const unsigned int _step, bond *Binder)
 {
+  OBSERVE;
   bool status = false;
   if (Binder != NULL) {
     if (Binder->Contains(this)) {
+      if (WorldTime::getTime() == _step)
+        NOTIFY(AtomObservable::BondsChanged);
       //LOG(3,"INFO: Registering bond "<< *Binder << " with atom " << *this << " at step " << _step);
       BondList& ListOfBonds = getListOfBondsAtStep(_step);
@@ -137 +158 @@
 bool BondedParticle::UnregisterBond(bond *Binder)
 {
+  OBSERVE;
   bool status = false;
   ASSERT(Binder != NULL, "BondedParticle::UnregisterBond() - Binder is NULL.");
   const int step = ContainsBondAtStep(Binder);
   if (step != -1) {
+    NOTIFY(AtomObservable::BondsChanged);
     //LOG(3,"INFO: Unregistering bond "<< *Binder << " from list " << &ListOfBonds << " of atom " << *this << " at step " << step);
     ListOfBonds[step].remove(Binder);
@@ -164 +187 @@
 void BondedParticle::ClearBondsAtStep(const unsigned int _step)
 {
+  OBSERVE;
+  if (WorldTime::getTime() == _step)
+    NOTIFY(AtomObservable::BondsChanged);
   //LOG(3,"INFO: Clearing all bonds of " << *this << ": " << ListOfBonds[_step]);
   for (BondList::iterator iter = (ListOfBonds[_step]).begin();
@@ -178 +204 @@
  * @return >=0 - first time step where bond appears, -1 - bond not present in lists
  */
-int BondedParticle::ContainsBondAtStep(bond *Binder)
+int BondedParticle::ContainsBondAtStep(bond *Binder) const
 {
   int step = -1;
@@ -205 +231 @@
 int BondedParticle::CorrectBondDegree()
 {
+  OBSERVE;
+  NOTIFY(AtomObservable::BondsChanged);
   int NoBonds = 0;
   int OtherNoBonds = 0;

src/atom_bondedparticle.hpp

@@ -37 +37 @@
   virtual ~BondedParticle();
 
-  void addBond(const unsigned int _step, BondedParticle* Partner);
-  bool RegisterBond(const unsigned int _step, bond *Binder);
-  bool UnregisterBond(bond *Binder);
+  const bond * addBond(const unsigned int _step, BondedParticle* Partner);
+  void removeBond(bond *binder);
   bool IsBondedTo(const unsigned int _step, BondedParticle * const BondPartner) const;
-  void UnregisterAllBond(const unsigned int _step);
   void ClearBondsAtStep(const unsigned int _step);
   int CountBonds() const;
@@ -52 +50 @@
   std::ostream & operator << (std::ostream &ost) const;
 
-private:
-  int ContainsBondAtStep(bond *Binder);
+protected:
+  bool RegisterBond(const unsigned int _step, bond *Binder);
+  bool UnregisterBond(bond *Binder);
+  void UnregisterAllBond(const unsigned int _step);
+
+  int ContainsBondAtStep(bond *Binder) const;
 
 };