Changeset 55240c4 for src/atom.cpp

Timestamp:

Jun 21, 2010, 7:56:00 AM (16 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, Candidate_v1.7.0, 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:

2f40c0e

Parents:

1b2d30 (diff), da3024e (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'stable' into PcpAndMpqcParser

Conflicts:

molecuilder/src/Makefile.am

• a single space after a "\"

File:

• src/atom.cpp (modified) (9 diffs)

src/atom.cpp

@@ -4 +4 @@
  *
  */
+
+#include "Helpers/MemDebug.hpp"
 
 #include "atom.hpp"
@@ -14 +16 @@
 #include "vector.hpp"
 #include "World.hpp"
+#include "molecule.hpp"
 
 /************************************* Functions for class atom *************************************/
@@ -21 +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
@@ -29 +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
@@ -37 +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;
@@ -50 +51 @@
   res->FixedIon = FixedIon;
   res->node = &x;
+  res->mol = 0;
   World::getInstance().registerAtom(res);
   return res;
@@ -59 +61 @@
 atom::~atom()
 {
+  removeFromMolecule();
+  for(BondList::iterator iter=ListOfBonds.begin(); iter!=ListOfBonds.end();){
+    // deleting the bond will invalidate the iterator !!!
+    bond *bond =*(iter++);
+    delete(bond);
+  }
 };
 
@@ -67 +75 @@
 atom *atom::GetTrueFather()
 {
-  atom *walker = this;
-  do {
-    if (walker == walker->father) // top most father is the one that points on itself
-      break;
-    walker = walker->father;
-  } while (walker != NULL);
-  return walker;
+  if(father == this){ // top most father is the one that points on itself
+    return this;
+  }
+  else if(!father) {
+    return 0;
+  }
+  else {
+    return father->GetTrueFather();
+  }
 };
 
@@ -305 +315 @@
 }
 
-atomId_t atom::getId() {
+atomId_t atom::getId() const {
   return id;
 }
+
+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){