Changeset f01769 for src/Actions

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).

Location:

src/Actions

Files:

• AtomAction/ChangeElementAction.cpp (modified) (4 diffs)
• FillAction/FillRegularGridAction.cpp (modified) (1 diff)
• FillAction/FillSurfaceAction.cpp (modified) (2 diffs)
• FillAction/SuspendInMoleculeAction.cpp (modified) (2 diffs)
• MoleculeAction/RemoveAction.cpp (modified) (1 diff)
• SelectionAction/Atoms/AtomByIdAction.cpp (modified) (3 diffs)
• SelectionAction/Atoms/AtomByOrderAction.cpp (modified) (3 diffs)
• SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) (3 diffs)
• SelectionAction/Atoms/NotAtomByOrderAction.cpp (modified) (3 diffs)
• TesselationAction/ConvexEnvelopeAction.cpp (modified) (1 diff)
• WorldAction/RepeatBoxAction.cpp (modified) (5 diffs)
• WorldAction/RepeatBoxAction.def (modified) (1 diff)

src/Actions/AtomAction/ChangeElementAction.cpp

@@ -57 +57 @@
 /** =========== define the function ====================== */
 ActionState::ptr AtomChangeElementAction::performCall() {
-  atom *first = NULL;
-  molecule *mol = NULL;
-
   // create undo state
   ElementMap Elements;
@@ -68 +65 @@
 
   for (World::AtomSelectionIterator iter = World::getInstance().beginAtomSelection(); iter != World::getInstance().endAtomSelection(); ++iter) {
-    first = iter->second;
+    atom *first = iter->second;
     LOG(1, "Changing atom " << *first << " to element " << *params.elemental.get() << ".");
     first->setType(params.elemental.get());
@@ -77 +74 @@
 ActionState::ptr AtomChangeElementAction::performUndo(ActionState::ptr _state) {
   AtomChangeElementState *state = assert_cast<AtomChangeElementState*>(_state.get());
-  atom *first = NULL;
-  molecule *mol = NULL;
-
   for(ElementMap::const_iterator iter = state->Elements.begin(); iter != state->Elements.end(); ++iter) {
-    first = World::getInstance().getAtom(AtomById(iter->first));
+    atom *first = World::getInstance().getAtom(AtomById(iter->first));
     first->setType(iter->second);
   }
@@ -90 +84 @@
 ActionState::ptr AtomChangeElementAction::performRedo(ActionState::ptr _state){
   AtomChangeElementState *state = assert_cast<AtomChangeElementState*>(_state.get());
-  atom *first = NULL;
-  molecule *mol = NULL;
 
   for(ElementMap::const_iterator iter = state->Elements.begin(); iter != state->Elements.end(); ++iter) {
-    first = World::getInstance().getAtom(AtomById(iter->first));
+    atom *first = World::getInstance().getAtom(AtomById(iter->first));
     first->setType(state->params.elemental.get());
   }

src/Actions/FillAction/FillRegularGridAction.cpp

@@ -75 +75 @@
   }
   molecule *filler = *(molecules.begin());
-  for(molecule::const_iterator iter = filler->begin(); iter != filler->end(); ++iter)
+  for(molecule::const_iterator iter = const_cast<const molecule *>(filler)->begin();
+      iter != const_cast<const molecule *>(filler)->end(); ++iter)
     movedatoms.push_back( AtomicInfo(*(*iter)) );
   LOG(1, "INFO: Chosen molecule has " << filler->size() << " atoms.");

src/Actions/FillAction/FillSurfaceAction.cpp

@@ -78 +78 @@
   }
   molecule *filler = *(molecules.begin());
-  for(molecule::const_iterator iter = filler->begin(); iter != filler->end(); ++iter)
+  for(molecule::const_iterator iter = const_cast<const molecule *>(filler)->begin();
+      iter != const_cast<const molecule *>(filler)->end(); ++iter)
     movedatoms.push_back( AtomicInfo(*(*iter)) );
   LOG(1, "INFO: Chosen molecule has " << filler->size() << " atoms.");
@@ -87 +88 @@
   // determine center with respect to alignment axis
   Vector sum = zeroVec;
-  for (molecule::iterator it2=filler->begin();it2 !=filler->end();++it2) {
+  for (molecule::const_iterator it2=const_cast<const molecule *>(filler)->begin();
+      it2 !=const_cast<const molecule *>(filler)->end();++it2) {
     const Vector helper = (**it2).getPosition().partition(params.AlignedAxis.get()).second;
     sum += helper;

src/Actions/FillAction/SuspendInMoleculeAction.cpp

@@ -122 +122 @@
     filler = *(molecules.begin());
   }
-  for(molecule::const_iterator iter = filler->begin(); iter != filler->end(); ++iter)
+  for(molecule::const_iterator iter = const_cast<const molecule *>(filler)->begin();
+      iter != const_cast<const molecule *>(filler)->end(); ++iter)
     movedatoms.push_back( AtomicInfo(*(*iter)) );
   LOG(1, "INFO: Chosen molecule has " << filler->size() << " atoms.");
@@ -174 +175 @@
       << fillermass << " atomicmassunit, and it's volume is "
       << fillervolume << (IsAngstroem ? " angstrom" : " atomiclength") << "^3.");
-  const double solventdensity = fillermass / fillervolume;
+//  const double solventdensity = fillermass / fillervolume;
 
   /// solve cubic polynomial

src/Actions/MoleculeAction/RemoveAction.cpp

@@ -68 +68 @@
       iter != molecules.end(); ++iter) {
     std::vector<AtomicInfo> Walkers;
-    for (molecule::const_iterator atomiter = (*iter)->begin();
-        atomiter != (*iter)->end(); ++atomiter) {
+    for (molecule::const_iterator atomiter = const_cast<const molecule *>(*iter)->begin();
+        atomiter != const_cast<const molecule *>(*iter)->end(); ++atomiter) {
       Walkers.push_back(AtomicInfo(**atomiter));
     }

src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp

@@ -65 +65 @@
   undoatomids.reserve(atomids.size());
   for (atomids_t::const_iterator iter = atomids.begin(); iter != atomids.end(); ++iter) {
-    const atom *Walker = World::getInstance().getAtom(AtomById(*iter));
+    const atom *Walker = const_cast<const World &>(World::getInstance()).
+        getAtom(AtomById(*iter));
     if (Walker != NULL) {
       if (!World::getInstance().isSelected(Walker)) {
@@ -104 +105 @@
 
   for (atomids_t::const_iterator iter = state->undoatomids.begin();
-      iter != state->undoatomids.end(); ++iter) {
-    const atom *Walker = World::getInstance().getAtom(AtomById(*iter));
-    World::getInstance().unselectAtom(Walker);
-  }
+      iter != state->undoatomids.end(); ++iter)
+    World::getInstance().unselectAllAtoms(AtomById(*iter));
 
   return ActionState::ptr(_state);
@@ -116 +115 @@
 
   for (atomids_t::const_iterator iter = state->undoatomids.begin();
-      iter != state->undoatomids.end(); ++iter) {
-    const atom *Walker = World::getInstance().getAtom(AtomById(*iter));
-    World::getInstance().selectAtom(Walker);
-  }
+      iter != state->undoatomids.end(); ++iter)
+    World::getInstance().selectAllAtoms(AtomById(*iter));
 
   return ActionState::ptr(_state);

src/Actions/SelectionAction/Atoms/AtomByOrderAction.cpp

@@ -54 +54 @@
 /** =========== define the function ====================== */
 ActionState::ptr SelectionAtomByOrderAction::performCall() {
-  const atom *Walker = World::getInstance().getAtom(AtomByOrder(params.order.get()));
+  const atom *Walker = const_cast<const World &>(World::getInstance()).
+      getAtom(AtomByOrder(params.order.get()));
   if (Walker != NULL) {
     if (!World::getInstance().isSelected(Walker)) {
@@ -73 +74 @@
   SelectionAtomByOrderState *state = assert_cast<SelectionAtomByOrderState*>(_state.get());
 
-  const atom *Walker = World::getInstance().getAtom(AtomById(state->WalkerId));
-  World::getInstance().unselectAtom(Walker);
+  World::getInstance().unselectAllAtoms(AtomById(state->WalkerId));
 
   return ActionState::ptr(_state);
@@ -82 +82 @@
   SelectionAtomByOrderState *state = assert_cast<SelectionAtomByOrderState*>(_state.get());
 
-  const atom *Walker = World::getInstance().getAtom(AtomById(state->WalkerId));
-  World::getInstance().selectAtom(Walker);
+  World::getInstance().selectAllAtoms(AtomById(state->WalkerId));
 
   return ActionState::ptr(_state);

src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp

@@ -65 +65 @@
   undoatomids.reserve(atomids.size());
   for (atomids_t::const_iterator iter = atomids.begin(); iter != atomids.end(); ++iter) {
-    const atom *Walker = World::getInstance().getAtom(AtomById(*iter));
+    const atom *Walker = const_cast<const World &>(World::getInstance()).
+        getAtom(AtomById(*iter));
     if (Walker != NULL) {
       if (World::getInstance().isSelected(Walker)) {
@@ -104 +105 @@
 
   for (atomids_t::const_iterator iter = state->undoatomids.begin();
-      iter != state->undoatomids.end(); ++iter) {
-    const atom *Walker = World::getInstance().getAtom(AtomById(*iter));
-    World::getInstance().selectAtom(Walker);
-  }
+      iter != state->undoatomids.end(); ++iter)
+    World::getInstance().selectAllAtoms(AtomById(*iter));
 
   return ActionState::ptr(_state);
@@ -116 +115 @@
 
   for (atomids_t::const_iterator iter = state->undoatomids.begin();
-      iter != state->undoatomids.end(); ++iter) {
-    const atom *Walker = World::getInstance().getAtom(AtomById(*iter));
-    World::getInstance().unselectAtom(Walker);
-  }
+      iter != state->undoatomids.end(); ++iter)
+    World::getInstance().unselectAllAtoms(AtomById(*iter));
 
   return ActionState::ptr(_state);

src/Actions/SelectionAction/Atoms/NotAtomByOrderAction.cpp

@@ -54 +54 @@
 /** =========== define the function ====================== */
 ActionState::ptr SelectionNotAtomByOrderAction::performCall() {
-  const atom * Walker = World::getInstance().getAtom(AtomByOrder(params.order.get()));
+  const atom * Walker = const_cast<const World &>(World::getInstance()).
+      getAtom(AtomByOrder(params.order.get()));
   if (Walker != NULL) {
     if (World::getInstance().isSelected(Walker)) {
@@ -73 +74 @@
   SelectionNotAtomByOrderState *state = assert_cast<SelectionNotAtomByOrderState*>(_state.get());
 
-  const atom * Walker = World::getInstance().getAtom(AtomById(state->WalkerId));
-  World::getInstance().selectAtom(Walker);
+  World::getInstance().selectAllAtoms(AtomById(state->WalkerId));
 
   return ActionState::ptr(_state);
@@ -82 +82 @@
   SelectionNotAtomByOrderState *state = assert_cast<SelectionNotAtomByOrderState*>(_state.get());
 
-  const atom * Walker = World::getInstance().getAtom(AtomById(state->WalkerId));
-  World::getInstance().unselectAtom(Walker);
+  World::getInstance().unselectAllAtoms(AtomById(state->WalkerId));
 
   return ActionState::ptr(_state);

src/Actions/TesselationAction/ConvexEnvelopeAction.cpp

@@ -86 +86 @@
     // we check whether all molecule's atoms are still inside
     std::vector<std::string> outside_atoms;
-    for(molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter)
+    for(molecule::const_iterator iter = const_cast<const molecule *>(mol)->begin();
+        iter != const_cast<const molecule *>(mol)->end(); ++iter)
       if (!TesselStruct->IsInnerPoint((*iter)->getPosition(), LCList))
         outside_atoms.push_back((*iter)->getName());

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)

src/Actions/WorldAction/RepeatBoxAction.def

@@ -28 +28 @@
 (STLVectorValidator< std::vector< unsigned int > >(NDIM, NDIM))
 
-#define statetypes (RealSpaceMatrix)(std::set< const molecule *>)
+#define statetypes (RealSpaceMatrix)(std::set< molecule *>)
 #define statereferences (olddomain)(oldmolecules)