Changeset 3867a7 for src/Atom

Timestamp:

Feb 17, 2012, 3:24:18 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:

b97a60

Parents:

9f8b01

git-author:

Frederik Heber <heber@…> (01/06/12 15:38:26)

git-committer:

Frederik Heber <heber@…> (02/17/12 15:24:18)

Message:

AtomicInfo now stores Father by id not ref.

• this migh have caused a crash before with Remove- and UndoActins by:
  • additionalAtomData pointing nowhere because the id might have changed.
  • father is stored as ref and not as id. If it's its own father, the ref is wrong.
  • molecule is given as ref and not as id.
• atom::setMolecule() - NULL ref is allowed.
• AtomicInfo: stores ids and not refs, first calls changeId then assigns father and mol (who both need updated id).

Location:

src/Atom

Files:

• AtomicInfo.cpp (modified) (5 diffs)
• AtomicInfo.hpp (modified) (1 diff)
• atom.cpp (modified) (1 diff)

src/Atom/AtomicInfo.cpp

@@ -22 +22 @@
 #include "atom.hpp"
 #include "AtomicInfo.hpp"
+#include "Descriptors/AtomIdDescriptor.hpp"
+#include "Descriptors/MoleculeIdDescriptor.hpp"
 #include "Element/element.hpp"
 #include "LinearAlgebra/Vector.hpp"
+#include "molecule.hpp"
+#include "World.hpp"
 
 /********************************** Functions for class AtomicInfo **********************************/
@@ -29 +33 @@
 AtomicInfo::AtomicInfo() :
     Type(NULL),
-    Father(NULL),
-    Id(-1)
+    FatherId(0),
+    MolId(0),
+    Id(0)
 {}
 AtomicInfo::AtomicInfo(const atom &_atom) :
@@ -36 +41 @@
     Type(_atom.getType()),
     Velocity(_atom.getAtomicVelocity()),
-    Father(_atom.father),
-    Mol(_atom.getMolecule()),
+    FatherId(_atom.father->getId()),
+    MolId(_atom.getMolecule()->getId()),
     Id(_atom.getId())
 {}
@@ -49 +54 @@
   _atom.setPosition(Position);
   _atom.setType(Type);
-  _atom.father = const_cast<atom *>(Father); // TODO: Actually, atom::father should be const atom *!
-  _atom.setMolecule(const_cast<molecule *>(Mol)); // this is ok, mol is const within AtomicInfo, but not outside (atoms need to register)
   _atom.setAtomicVelocity(Velocity);
-  if (_atom.getId() == Id)
-    return true;
+
+  // set old id
+  bool status = true;
+  if (_atom.getId() != Id)
+    status = _atom.changeId(Id);
+
+  // set its father
+  atom * const _father = World::getInstance().getAtom(AtomById(FatherId));
+  if (_father == NULL)
+    _atom.father = &_atom;
   else
-    return (_atom.changeId(Id));
+    _atom.father = _father;
+
+  // setting molecule
+  molecule * const _mol = World::getInstance().getMolecule(MoleculeById(MolId));
+  if (_mol != NULL)
+    _atom.setMolecule(_mol); // this is ok, mol is const within AtomicInfo, but not outside (atoms need to register)
+
+  return status;
 }
 
@@ -68 +86 @@
   Position = AI.Position;
   Type = AI.Type;
-  Father = AI.Father;
-  Mol = AI.Mol;
+  FatherId = AI.FatherId;
+  MolId = AI.MolId;
   Velocity = AI.Velocity;
   Id = AI.Id;

src/Atom/AtomicInfo.hpp

@@ -38 +38 @@
   const element * Type;
   Vector Velocity;
-  const atom * Father;
-  const molecule * Mol;
+  atomId_t FatherId;
+  moleculeId_t MolId;
   atomId_t Id;
 };

src/Atom/atom.cpp

@@ -297 +297 @@
   removeFromMolecule();
   mol = _mol;
-  if(!mol->containsAtom(this)){
+  if ((mol) && (!mol->containsAtom(this)))
     mol->insert(this);
-  }
 }