Changeset b3d687 for src/Atom/CopyAtoms/CopyAtoms_withBonds.cpp

Timestamp:

Apr 5, 2012, 3:57:16 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:

5cdd83

Parents:

259887

git-author:

Frederik Heber <heber@…> (04/05/12 08:14:13)

git-committer:

Frederik Heber <heber@…> (04/05/12 15:57:16)

Message:

FIX: Filler::operator() did not create a molecule for each cloned cluster.

• so far we assume (in AtomicInfo) that each atoms always belongs to a molecule. However, the CopyAtomsInterface copies without creating new molecules or associating copied ones with the old molecules.
• AtomicInfo asserts that atom is associated to a molecule.
• CopyAtoms_withBonds now associates cloned atoms with molecule of original atom.
• Filler::operator() creates a molecule for each cloned cluster and associates all atoms in the cluster with it.
• This [closes #180].

File:

• src/Atom/CopyAtoms/CopyAtoms_withBonds.cpp (modified) (2 diffs)

src/Atom/CopyAtoms/CopyAtoms_withBonds.cpp

@@ -26 +26 @@
 #include "CodePatterns/Assert.hpp"
 #include "CodePatterns/Log.hpp"
+#include "molecule.hpp"
 #include "WorldTime.hpp"
 
@@ -72 +73 @@
   }
 
+  // associate cloned atoms with molecule from original atom
+  for (AtomVector::const_iterator original_iter = _atoms.begin();
+      original_iter != _atoms.end(); ++original_iter) {
+    const atom * const _atom = *original_iter;
+    molecule * const mol = _atom->getMolecule();
+    if (mol != NULL) {
+      ASSERT( LookupMap.count(_atom),
+          "CopyAtoms_withBonds::operator() - atom "+toString(_atom)+" not found in LookupMap.");
+      mol->AddAtom(LookupMap[_atom]);
+    }
+  }
+
   // print copied atoms
   if (DoLog(3))