Changeset 270bdf

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.

Location:

src

Files:

• Actions/AtomAction/ChangeElementAction.cpp (modified) (3 diffs)
• Actions/AtomAction/SaturateAction.cpp (modified) (1 diff)
• Actions/FragmentationAction/FragmentationAction.cpp (modified) (5 diffs)
• Atom/CopyAtoms/CopyAtoms_withBonds.cpp (modified) (2 diffs)
• Atom/atom.cpp (modified) (1 diff)
• Atom/atom.hpp (modified) (1 diff)
• Descriptors/MoleculeOfAtomSelectionDescriptor.cpp (modified) (3 diffs)
• Fragmentation/Interfragmenter.cpp (modified) (1 diff)
• World.cpp (modified) (3 diffs)

src/Actions/AtomAction/ChangeElementAction.cpp

@@ -70 +70 @@
     first = iter->second;
     LOG(1, "Changing atom " << *first << " to element " << *params.elemental.get() << ".");
-    mol = first->getMolecule();
-    first->removeFromMolecule(); // remove atom
     first->setType(params.elemental.get());
-    mol->AddAtom(first);  // add atom to ensure correctness of formula
   }
   return ActionState::ptr(UndoState);
@@ -85 +82 @@
   for(ElementMap::const_iterator iter = state->Elements.begin(); iter != state->Elements.end(); ++iter) {
     first = World::getInstance().getAtom(AtomById(iter->first));
-    mol = first->getMolecule();
-    first->removeFromMolecule(); // remove atom
     first->setType(iter->second);
-    mol->AddAtom(first);  // add atom to ensure correctness of formula
   }
 
@@ -101 +95 @@
   for(ElementMap::const_iterator iter = state->Elements.begin(); iter != state->Elements.end(); ++iter) {
     first = World::getInstance().getAtom(AtomById(iter->first));
-    mol = first->getMolecule();
-    first->removeFromMolecule(); // remove atom
     first->setType(state->params.elemental.get());
-    mol->AddAtom(first);  // add atom to ensure correctness of formula
   }
 

src/Actions/AtomAction/SaturateAction.cpp

@@ -67 +67 @@
 
     // if atom is attached to molecule, add hydrogens there, too
-    molecule * mol = _atom->getMolecule();
-    if (mol == NULL) {
+    molecule * mol = NULL;
+    if (_atom->getMolecule() == NULL) {
       mol = World::getInstance().createMolecule();
       mol->AddAtom(_atom);
+    } else {
+      mol = World::getInstance().getMolecule(MoleculeById(_atom->getMolecule()->getId()));
     }
+    ASSERT( mol != NULL,
+        "ChangeElementAction::performCall() - mol is still NULL." );
 
     // add the hydrogens

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

src/Atom/CopyAtoms/CopyAtoms_withBonds.cpp

@@ -42 +42 @@
 #include "CodePatterns/Assert.hpp"
 #include "CodePatterns/Log.hpp"
+#include "Descriptors/MoleculeIdDescriptor.hpp"
 #include "molecule.hpp"
 #include "WorldTime.hpp"
@@ -93 +94 @@
       original_iter != _atoms.end(); ++original_iter) {
     const atom * const _atom = *original_iter;
-    molecule * const mol = _atom->getMolecule();
+    const 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]);
+      molecule * non_const_mol = World::getInstance().getMolecule(MoleculeById(mol->getId()));
+      non_const_mol->AddAtom(LookupMap[_atom]);
     }
   }

src/Atom/atom.cpp

@@ -304 +304 @@
 }
 
-molecule* atom::getMolecule() const {
+const molecule* atom::getMolecule() const {
   return mol;
 }

src/Atom/atom.hpp

@@ -193 +193 @@
     * \return containing molecule
     */
-   molecule* getMolecule() const;
+   const molecule* getMolecule() const;
 
    /** Erases the atom in atom::mol's list of atoms and sets it to zero.

src/Descriptors/MoleculeOfAtomSelectionDescriptor.cpp

@@ -35 +35 @@
 #include "CodePatterns/MemDebug.hpp"
 
+#include "Descriptors/MoleculeIdDescriptor.hpp"
 #include "Descriptors/MoleculeOfAtomSelectionDescriptor.hpp"
 #include "Descriptors/MoleculeOfAtomSelectionDescriptor_impl.hpp"
@@ -62 +63 @@
       iter != set.end_internal();
       ++iter) {
-    if (iter->second->getMolecule())
-      return iter->second->getMolecule();
+    if (iter->second->getMolecule()) {
+      return World::getInstance().getMolecule(MoleculeById(iter->second->getMolecule()->getId()));
+    }
   }
   return 0;
@@ -77 +79 @@
       ++iter) {
     if (iter->second->getMolecule()) {
-      inserter = temp.insert( iter->second->getMolecule() );
+      molecule * const _mol =
+          World::getInstance().getMolecule(
+              MoleculeById(iter->second->getMolecule()->getId()));
+      inserter = temp.insert( _mol );
       if (inserter.second)
-        res.push_back(iter->second->getMolecule());
+        res.push_back(_mol);
     }
   }

src/Fragmentation/Interfragmenter.cpp

@@ -103 +103 @@
     /// go through linked cell and get all neighboring atoms up to Rcut
     Vector center;
-    molecule *_mol = (*atoms.begin())->getMolecule();
+    const molecule *_mol = (*atoms.begin())->getMolecule();
     for (AtomIdSet::const_iterator iter = atoms.begin();
         iter != atoms.end(); ++iter) {

src/World.cpp

@@ -360 +360 @@
   }
   // check if it's the last atom
-  molecule *_mol = atom->getMolecule();
+  molecule *_mol = const_cast<molecule *>(atom->getMolecule());
   if ((_mol == NULL) || (_mol->getAtomCount() > 1))
     _mol = NULL;
@@ -764 +764 @@
   NOTIFY(SelectionChanged);
   ASSERT(_atom,"Invalid atom pointer in selection of MoleculeOfAtom");
-  molecule *mol=_atom->getMolecule();
+  const molecule *mol=_atom->getMolecule();
   // the atom might not be part of a molecule
   if(mol){
@@ -805 +805 @@
   NOTIFY(SelectionChanged);
   ASSERT(_atom,"Invalid atom pointer in selection of MoleculeOfAtom");
-  molecule *mol=_atom->getMolecule();
+  const molecule *mol=_atom->getMolecule();
   // the atom might not be part of a molecule
   if(mol){