Changeset 583081

Timestamp:

Feb 24, 2011, 7:33:17 PM (14 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:

af897f

Parents:

38c44b

git-author:

Frederik Heber <heber@…> (02/24/11 15:13:07)

git-committer:

Frederik Heber <heber@…> (02/24/11 19:33:17)

Message:

New function BondedParticle::ClearBondsAtStep(), used by MoleculeLeafClass::FillBondStructureFromReference().

Location:

src

Files:

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

src/atom_bondedparticle.cpp

@@ -165 +165 @@
   ListOfBonds.clear();
 };
+
+/** Removes all bonds of given \a _step with freeing memory.
+ *
+ * @param _step time step whose bonds to free
+ */
+void BondedParticle::ClearBondsAtStep(const unsigned int _step)
+{
+  //LOG(3,"INFO: Clearing all bonds of " << *this << ": " << ListOfBonds[_step]);
+  for (BondList::iterator iter = (ListOfBonds[_step]).begin();
+      !(ListOfBonds[_step]).empty();
+      iter = (ListOfBonds[_step]).begin()) {
+    //LOG(3,"INFO: Clearing bond (" << *iter << ") " << *(*iter) << " of list " << &ListOfBonds);
+    delete((*iter)); // will also unregister with us and remove from list
+  }
+}
 
 /** Searches for the time step where the given bond \a *Binder is a bond of this particle.

src/atom_bondedparticle.hpp

@@ -42 +42 @@
   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;
   int CorrectBondDegree();

src/moleculelist.cpp

@@ -24 +24 @@
 #include <gsl/gsl_heapsort.h>
 
-#include "World.hpp"
 #include "atom.hpp"
 #include "bond.hpp"
 #include "bondgraph.hpp"
 #include "boundary.hpp"
+#include "Box.hpp"
+#include "CodePatterns/Assert.hpp"
+#include "CodePatterns/Log.hpp"
+#include "CodePatterns/Verbose.hpp"
 #include "config.hpp"
 #include "element.hpp"
+#include "Helpers/fast_functions.hpp"
 #include "Helpers/helpers.hpp"
+#include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "linkedcell.hpp"
 #include "lists.hpp"
-#include "CodePatterns/Verbose.hpp"
-#include "CodePatterns/Log.hpp"
 #include "molecule.hpp"
 #include "periodentafel.hpp"
 #include "tesselation.hpp"
-#include "CodePatterns/Assert.hpp"
-#include "LinearAlgebra/RealSpaceMatrix.hpp"
-#include "Box.hpp"
-
-#include "Helpers/fast_functions.hpp"
-
-#include "CodePatterns/Assert.hpp"
+#include "World.hpp"
+#include "WorldTime.hpp"
 
 /*********************************** Functions for class MoleculeListClass *************************/
@@ -786 +784 @@
  * \param **&ListOfLocalAtoms Lookup table for this subgraph and index of each atom in \a *reference, may be NULL on start, then it is filled
  * \param FreeList true - ***ListOfLocalAtoms is free'd before return, false - it is not
- * \return true - success, false - faoilure
+ * \return true - success, false - failure
  */
 bool MoleculeLeafClass::FillBondStructureFromReference(const molecule * const reference, atom **&ListOfLocalAtoms, bool FreeList)
@@ -805 +803 @@
     DoLog(1) && (Log() << Verbose(1) << "Creating adjacency list for subgraph " << Leaf << "." << endl);
     // remove every bond from the list
-    for(molecule::iterator AtomRunner = Leaf->begin(); AtomRunner != Leaf->end(); ++AtomRunner) {
-      BondList& ListOfBonds = (*AtomRunner)->getListOfBonds();
-      for(BondList::iterator BondRunner = ListOfBonds.begin();
-          !ListOfBonds.empty();
-          BondRunner = ListOfBonds.begin())
-        if ((*BondRunner)->leftatom == *AtomRunner)
-          delete((*BondRunner));
-    }
+    for_each(Leaf->begin(), Leaf->end(),
+        boost::bind(&BondedParticle::ClearBondsAtStep,_1,WorldTime::getTime()));