Changeset 59fff1 for src/Analysis

Timestamp:

Dec 28, 2011, 3:25:49 PM (13 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:

afa9d8

Parents:

30c753

git-author:

Frederik Heber <heber@…> (12/23/11 10:09:37)

git-committer:

Frederik Heber <heber@…> (12/28/11 15:25:49)

Message:

Replaced the molecule::const_iterator by a true const version of the transform_iterator.

• lots of places used const_iterator where it made no sense, atom some others one could have sensibly done so but details prevented it, e.g.
  • FormatParserStorage::save() requires vector<atom*> not const atom *,
  • Boundaries (and most of Tesselation for that) requires atom *, not const atom *.
• Added new function molecule::isInMolecule() to check whether atomic id is in molecule::atomIds.
• Added const version of atom::GetTrueFather().

Location:

src/Analysis

Files:

• analysis_correlation.cpp (modified) (7 diffs)
• analysis_correlation.hpp (modified) (1 diff)

src/Analysis/analysis_correlation.cpp ¶

@@ -212 +212 @@
     LOG(1,"INFO: Resulting relative angle for molecule " << _mol->getName()
         << " is " << angle << ".");
-    outmap->insert ( make_pair (angle, *iter ) );
+    outmap->insert ( std::make_pair (angle, *iter ) );
     ++i;
   }
@@ -322 +322 @@
                 distance = domain.periodicDistance((*iter)->getPosition(),(*runner)->getPosition());
                 //LOG(1, "Inserting " << *(*iter) << " and " << *(*runner));
-                outmap->insert ( pair<double, pair <atom *, atom*> > (distance, pair<atom *, atom*> ((*iter), (*runner)) ) );
+                outmap->insert (
+                    std::pair<double, std::pair <const atom *, const atom*> > (
+                        distance,
+                        std::pair<const atom *, const atom*> ((*iter), (*runner))
+                        )
+                    );
               }
           }
@@ -403 +408 @@
                               distance = checkX.distance(checkOtherX);
                               //LOG(1, "Inserting " << *(*iter) << " and " << *(*runner));
-                              outmap->insert ( pair<double, pair <atom *, atom*> > (distance, pair<atom *, atom*> ((*iter), (*runner)) ) );
+                              outmap->insert (
+                                  std::pair<double, std::pair <const atom *, const atom*> > (
+                                      distance,
+                                      std::pair<const atom *, const atom*> (
+                                          (*iter),
+                                          (*runner))
+                                      )
+                                  );
                             }
                       }
@@ -444 +456 @@
           distance = domain.periodicDistance((*iter)->getPosition(),*point);
           LOG(4, "Current distance is " << distance << ".");
-          outmap->insert ( pair<double, pair<atom *, const Vector*> >(distance, pair<atom *, const Vector*> ((*iter), point) ) );
+          outmap->insert (
+              std::pair<double, std::pair<const atom *, const Vector*> >(
+                  distance,
+                  std::pair<const atom *, const Vector*> (
+                      (*iter),
+                      point)
+                  )
+              );
         }
     }
@@ -491 +510 @@
                 distance = checkX.distance(*point);
                 LOG(4, "Current distance is " << distance << ".");
-                outmap->insert ( pair<double, pair<atom *, const Vector*> >(distance, pair<atom *, const Vector*> (*iter, point) ) );
+                outmap->insert (
+                    std::pair<double,
+                    std::pair<const atom *, const Vector*> >(
+                        distance,
+                        std::pair<const atom *, const Vector*> (
+                            *iter,
+                            point)
+                        )
+                    );
               }
         }
@@ -533 +560 @@
           distance = Intersections.GetSmallestDistance();
           triangle = Intersections.GetClosestTriangle();
-          outmap->insert ( pair<double, pair<atom *, BoundaryTriangleSet*> >(distance, pair<atom *, BoundaryTriangleSet*> ((*iter), triangle) ) );
+          outmap->insert (
+              std::pair<double,
+              std::pair<const atom *, BoundaryTriangleSet*> >(
+                  distance,
+                  std::pair<const atom *, BoundaryTriangleSet*> (
+                      (*iter),
+                      triangle)
+                  )
+              );
         }
     }
@@ -597 +632 @@
               }
           // insert
-          outmap->insert ( pair<double, pair<atom *, BoundaryTriangleSet*> >(ShortestDistance, pair<atom *, BoundaryTriangleSet*> (*iter, ShortestTriangle) ) );
+          outmap->insert (
+              std::pair<double,
+              std::pair<const atom *, BoundaryTriangleSet*> >(
+                  ShortestDistance,
+                  std::pair<const atom *, BoundaryTriangleSet*> (
+                      *iter,
+                      ShortestTriangle)
+                  )
+              );
           //LOG(1, "INFO: Inserting " << Walker << " with distance " << ShortestDistance << " to " << *ShortestTriangle << ".");
         }

src/Analysis/analysis_correlation.hpp ¶

@@ -46 +46 @@
 /********************************************** definitions *********************************/
 
-typedef multimap<double, pair<atom *, atom *> > PairCorrelationMap;
-typedef multimap<double, atom * > DipoleAngularCorrelationMap;
-typedef multimap<double, pair<molecule *, molecule *> > DipoleCorrelationMap;
-typedef multimap<double, pair<atom *, const Vector *> > CorrelationToPointMap;
-typedef multimap<double, pair<atom *, BoundaryTriangleSet *> > CorrelationToSurfaceMap;
+typedef multimap<double, pair<const atom *, const atom *> > PairCorrelationMap;
+typedef multimap<double, const atom * > DipoleAngularCorrelationMap;
+typedef multimap<double, pair<const molecule *, const molecule *> > DipoleCorrelationMap;
+typedef multimap<double, pair<const atom *, const Vector *> > CorrelationToPointMap;
+typedef multimap<double, pair<const atom *, BoundaryTriangleSet *> > CorrelationToSurfaceMap;
 typedef map<double, int> BinPairMap;