Changeset 6cfa36

Timestamp:

Jun 11, 2010, 3:41:41 PM (15 years ago)

Author:

Tillmann Crueger <crueger@…>

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:

a80241

Parents:

6d6b54

Message:

Made atoms remove themselves from molecules upon destruction

Location:

src

Files:

• atom.cpp (modified) (7 diffs)
• atom.hpp (modified) (4 diffs)
• molecule.cpp (modified) (3 diffs)
• molecule.hpp (modified) (1 diff)
• unittests/listofbondsunittest.cpp (modified) (1 diff)

src/atom.cpp

@@ -16 +16 @@
 #include "vector.hpp"
 #include "World.hpp"
+#include "molecule.hpp"
 
 /************************************* Functions for class atom *************************************/
@@ -23 +24 @@
  */
 atom::atom() :
-  previous(NULL), next(NULL), father(this), sort(&nr)
+  father(this), sort(&nr), mol(0)
 {
   node = &x;  // TesselPoint::x can only be referenced from here
@@ -31 +32 @@
  */
 atom::atom(atom *pointer) :
-    ParticleInfo(pointer),
-    previous(NULL), next(NULL), father(pointer), sort(&nr)
+    ParticleInfo(pointer),father(pointer), sort(&nr)
 {
   type = pointer->type;  // copy element of atom
@@ -39 +39 @@
   FixedIon = pointer->FixedIon;
   node = &x;
+  mol = 0;
 };
 
 atom *atom::clone(){
   atom *res = new atom(this);
-  res->previous=0;
-  res->next=0;
   res->father = this;
   res->sort = &res->nr;
@@ -52 +51 @@
   res->FixedIon = FixedIon;
   res->node = &x;
+  res->mol = 0;
   World::getInstance().registerAtom(res);
   return res;
@@ -61 +61 @@
 atom::~atom()
 {
+  removeFromMolecule();
 };
 
@@ -313 +314 @@
 }
 
+void atom::setMolecule(molecule *_mol){
+  // take this atom from the old molecule
+  removeFromMolecule();
+  mol = _mol;
+  if(!mol->containsAtom(this)){
+    mol->AddAtom(this);
+  }
+}
+
+void atom::removeFromMolecule(){
+  if(mol){
+    if(mol->containsAtom(this)){
+      mol->erase(this);
+    }
+    mol=0;
+  }
+}
+
+
 atom* NewAtom(atomId_t _id){
   atom * res =new atom();

src/atom.hpp

@@ -34 +34 @@
 class Vector;
 class World;
+class molecule;
 
 /********************************************** declarations *******************************/
@@ -44 +45 @@
   friend void  DeleteAtom(atom*);
   public:
-    atom *previous; //!< previous atom in molecule list
-    atom *next;     //!< next atom in molecule list
     atom *father;   //!< In many-body bond order fragmentations points to originating atom
     int *sort;      //!< sort criteria
@@ -89 +88 @@
    virtual void setId(atomId_t);
 
+   void setMolecule(molecule*);
+   void removeFromMolecule();
+
   protected:
+
     /**
      * Protected constructor to ensure construction of atoms through the world.
@@ -108 +111 @@
     virtual ~atom();
   private:
+    molecule *mol; // !< the molecule this atom belongs to
     World* world;
     atomId_t id;

src/molecule.cpp

@@ -145 +145 @@
   molecule::const_iterator iter = loc;
   iter--;
+  atom* atom = *loc;
   atoms.erase( loc );
+  atom->removeFromMolecule();
   return iter;
 }
 
-molecule::const_iterator molecule::erase( atom *& key )
+molecule::const_iterator molecule::erase( atom * key )
 {
   cout << "trying to erase atom" << endl;
   molecule::const_iterator iter = find(key);
   if (iter != end()){
-    // remove this position and step forward (post-increment)
     atoms.erase( iter++ );
+    key->removeFromMolecule();
   }
   return iter;
 }
 
-molecule::const_iterator molecule::find ( atom *& key ) const
+molecule::const_iterator molecule::find ( atom * key ) const
 {
   return atoms.find( key );
@@ -169 +171 @@
   pair<atomSet::iterator,bool> res = atoms.insert(key);
   return pair<iterator,bool>(iterator(res.first,this),res.second);
+}
+
+bool molecule::containsAtom(atom* key){
+  return atoms.count(key);
 }
 
@@ -194 +200 @@
     }
     insert(pointer);
+    pointer->setMolecule(this);
   }
   return true;

src/molecule.hpp

@@ -153 +153 @@
   size_t size() const;
   const_iterator erase( const_iterator loc );
-  const_iterator erase( atom *& key );
-  const_iterator find (  atom *& key ) const;
+  const_iterator erase( atom * key );
+  const_iterator find (  atom * key ) const;
   pair<iterator,bool> insert ( atom * const key );
+  bool containsAtom(atom* key);
 
 

src/unittests/listofbondsunittest.cpp

@@ -261 +261 @@
   CPPUNIT_ASSERT( Binder != NULL );
 
+  CPPUNIT_ASSERT_EQUAL( (size_t) 1, atom1->ListOfBonds.size() );
+  CPPUNIT_ASSERT_EQUAL( (size_t) 1, atom2->ListOfBonds.size() );
+
   // remove atom2
   World::getInstance().destroyAtom(atom2);