Changeset f63e41 for src/Atom

Timestamp:

Dec 14, 2012, 2:30:23 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:

8b886f

Parents:

cb2465

git-author:

Frederik Heber <heber@…> (11/14/12 10:37:48)

git-committer:

Frederik Heber <heber@…> (12/14/12 14:30:23)

Message:

Added Actions to add and remove a bond in between two atoms.

• added new menu "bond".
• added new CommandLineParser options "bond".
• added new regression test folder "bond".
• also added regression tests with undo/redo for the new actions.

Location:

src/Atom

Files:

• atom_bondedparticle.cpp (modified) (2 diffs)
• atom_bondedparticle.hpp (modified) (1 diff)
• atom_bondedparticleinfo.hpp (modified) (1 diff)

src/Atom/atom_bondedparticle.cpp

@@ -34 +34 @@
 
 #include "CodePatterns/MemDebug.hpp"
+
+#include <algorithm>
+#include <boost/bind.hpp>
 
 #include "atom.hpp"
@@ -116 +119 @@
 
   return newBond;
+}
+
+/** Removes a bond of this atom to a given \a Partner.
+ *
+ * @param _step time step
+ * @param Partner bond partner
+ */
+void BondedParticle::removeBond(const unsigned int _step, BondedParticle * const Partner)
+{
+  const BondList& ListOfBonds = getListOfBondsAtStep(_step);
+  BondList::const_iterator iter = std::find_if(ListOfBonds.begin(), ListOfBonds.end(),
+      boost::bind(
+          static_cast<bool (bond::*)(const ParticleInfo * const) const>(&bond::Contains),
+          _1,
+          boost::cref(Partner)));
+  if (iter != ListOfBonds.end()) {
+    delete *iter; //dstor takes care of unregistering and all
+  } else
+    ELOG(1, "BondedParticle::removeBond() - I cannot find the bond in between "
+        +toString(getName())+" and "+toString(Partner->getName())+".");
 }
 

src/Atom/atom_bondedparticle.hpp

@@ -38 +38 @@
 
   bond * const addBond(const unsigned int _step, BondedParticle* Partner);
+  void removeBond(const unsigned int _step, BondedParticle* Partner);
   void removeBond(bond *binder);
   void removeAllBonds();

src/Atom/atom_bondedparticleinfo.hpp

@@ -28 +28 @@
 class BondedParticle;
 
-#define BondList list<bond *>
+#define BondList std::list<bond *>
 
 /********************************************** declarations *******************************/