Changeset 270bdf for src/Actions/FragmentationAction

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:

97445f

Parents:

9b3262b

git-author:

Frederik Heber <heber@…> (06/01/15 07:22:29)

git-committer:

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

Message:

atom::getMolecule() now returns ptr to const molecule.

• changed some places where getMolecule() was used. Most of them required only const access anyway. World is allowed to const'cast the constness away as it commands over molecules anyway.

File:

• src/Actions/FragmentationAction/FragmentationAction.cpp (modified) (5 diffs)

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -40 +40 @@
 #include "CodePatterns/Log.hpp"
 #include "Descriptors/AtomSelectionDescriptor.hpp"
+#include "Descriptors/MoleculeIdDescriptor.hpp"
 #include "Fragmentation/Exporters/ExportGraph_ToFiles.hpp"
 #include "Fragmentation/Exporters/ExportGraph_ToJobs.hpp"
@@ -95 +96 @@
 
   // go through all atoms, note down their molecules and group them
-  typedef std::multimap<molecule *, atom *> clusters_t;
+  typedef std::multimap<const molecule *, atom *> clusters_t;
   typedef std::vector<atomId_t> atomids_t;
   atomids_t atomids;
@@ -105 +106 @@
   }
   {
-    std::vector<molecule *> molecules;
+    std::vector<const molecule *> molecules;
     molecules.insert( molecules.end(), MapKeyIterator<clusters_t::const_iterator>(clusters.begin()),
         MapKeyIterator<clusters_t::const_iterator>(clusters.end()) );
@@ -149 +150 @@
       iter = advanceiter) {
     // get iterator to past last atom in this molecule
-    molecule * mol = iter->first;
+    const molecule * mol = iter->first;
     advanceiter = clusters.upper_bound(mol);
 
@@ -161 +162 @@
         << " atoms, out of " << mol->getAtomCount() << ".");
     const enum HydrogenTreatment treatment =  params.HowtoTreatHydrogen.get() ? ExcludeHydrogen : IncludeHydrogen;
-    Fragmentation Fragmenter(mol, *FileChecker, treatment);
+    molecule * non_const_mol = World::getInstance().getMolecule(MoleculeById(mol->getId()));
+    Fragmentation Fragmenter(non_const_mol, *FileChecker, treatment);
 
     // perform fragmentation