Changeset f01769 for src/Actions/WorldAction/RepeatBoxAction.cpp

Timestamp:

Jul 24, 2015, 4:44:34 PM (10 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:

a58c16

Parents:

1259df

git-author:

Frederik Heber <heber@…> (06/01/15 16:57:36)

git-committer:

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

Message:

Replaced World::getAtom() wherever possible by const version.

• some AtomSet member functions now have const atom ptr instead of atom ptr.
• molecule can return const and non-const AtomSet.
• added FromIdToConstAtom to allow iterate through atoms in molecule (which are stored by id, not by ptr) in const fashion.
• in molecule::isInMolecule() is now const, ::CopyMolecule..() is non-const (because copying involves father atom who is stored non-const).

File:

• src/Actions/WorldAction/RepeatBoxAction.cpp (modified) (5 diffs)

src/Actions/WorldAction/RepeatBoxAction.cpp

@@ -63 +63 @@
 void repeatMoleculesinDomain(
     std::vector< unsigned int > Repeater,
-    const std::vector<const molecule *> &AllMolecules)
+    const std::vector<molecule *> &AllMolecules)
 {
   LOG(0, "STATUS: Repeating box " << Repeater << " times for (x,y,z) axis.");
@@ -95 +95 @@
         if ((n[0] == 0) && (n[1] == 0) && (n[2] == 0))
           continue;
-        for (vector<const molecule *>::const_iterator MolRunner = AllMolecules.begin(); MolRunner != AllMolecules.end(); ++MolRunner) {
-          const molecule * const mol = *MolRunner;
+        for (vector<molecule *>::const_iterator MolRunner = AllMolecules.begin(); MolRunner != AllMolecules.end(); ++MolRunner) {
+          molecule * const mol = *MolRunner;
           LOG(2, "DEBUG: Current mol is " << mol->name << "." << endl);
           molecule * const newmol = mol->CopyMolecule();
@@ -114 +114 @@
 ActionState::ptr WorldRepeatBoxAction::performCall() {
   DoLog(0) && (Log() << Verbose(0) << "Using all molecules." << endl);
-  std::vector<const molecule *> AllMolecules =
-      const_cast<const World &>(World::getInstance()).getAllMolecules();
+  std::vector<molecule *> AllMolecules = World::getInstance().getAllMolecules();
 
   // prepare undo state
   RealSpaceMatrix olddomain = World::getInstance().getDomain().getM();
-  std::set<const molecule *> oldmolecules;
-  for(std::vector<const molecule *>::const_iterator iter = AllMolecules.begin();
+  std::set<molecule *> oldmolecules;
+  for(std::vector<molecule *>::const_iterator iter = AllMolecules.begin();
       iter != AllMolecules.end();
       ++iter)
@@ -136 +135 @@
 ActionState::ptr WorldRepeatBoxAction::performUndo(ActionState::ptr _state) {
   WorldRepeatBoxState *state = assert_cast<WorldRepeatBoxState*>(_state.get());
-  MoleculeListClass *molecules = World::getInstance().getMolecules();
 
   // set old domain
@@ -159 +157 @@
   WorldRepeatBoxState *state = assert_cast<WorldRepeatBoxState*>(_state.get());
 
-  std::vector<const molecule *> originalmolecules;
-  for(std::set<const molecule *>::const_iterator iter = state->oldmolecules.begin();
+  std::vector<molecule *> originalmolecules;
+  for(std::set<molecule *>::const_iterator iter = state->oldmolecules.begin();
       iter != state->oldmolecules.end();
       ++iter)