Changeset 63fb7a for src/Actions/MoleculeAction

Timestamp:

Jul 24, 2015, 4:44:34 PM (9 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:

1259df

Parents:

795c0f

git-author:

Frederik Heber <heber@…> (06/01/15 08:48:35)

git-committer:

Frederik Heber <heber@…> (07/24/15 16:44:34)

Message:

Replaced getMolecule() by const access version where possible.

• so far this is done done via const_casting the World.

File:

• src/Actions/MoleculeAction/StretchBondAction.cpp (modified) (3 diffs)

src/Actions/MoleculeAction/StretchBondAction.cpp

@@ -61 +61 @@
     return Action::failure;
   }
-  const molecule *mol = atoms[0]->getMolecule();
+  molecule *mol = World::getInstance().
+      getMolecule(MoleculeById(atoms[0]->getMolecule()->getId()));
   if (mol != atoms[1]->getMolecule()) {
     STATUS("The two selected atoms must belong to the same molecule.");
@@ -101 +102 @@
   const Vector NegativeShift = -state->shift * state->bondplane.getNormal();
   Box &domain = World::getInstance().getDomain();
-  for (molecule::iterator iter = state->mol->begin();
-      iter != state->mol->end(); ++iter) {
+  molecule *mol = World::getInstance().
+      getMolecule(MoleculeById(state->mol->getId()));
+  for (molecule::iterator iter = mol->begin();
+      iter != mol->end(); ++iter) {
     const Vector &position = (*iter)->getPosition();
     // for each atom determine on which side of plane it is and shift accordingly
@@ -122 +125 @@
   const Vector NegativeShift = -state->shift * state->bondplane.getNormal();
   Box &domain = World::getInstance().getDomain();
-  for (molecule::iterator iter = state->mol->begin();
-      iter != state->mol->end(); ++iter) {
+  molecule *mol = World::getInstance().
+      getMolecule(MoleculeById(state->mol->getId()));
+  for (molecule::iterator iter = mol->begin();
+      iter != mol->end(); ++iter) {
     const Vector &position = (*iter)->getPosition();
     // for each atom determine on which side of plane it is and shift accordingly