Changeset f01769 for src/Actions/FillAction

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:

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/FillAction

Files:

• FillRegularGridAction.cpp (modified) (1 diff)
• FillSurfaceAction.cpp (modified) (2 diffs)
• SuspendInMoleculeAction.cpp (modified) (2 diffs)

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