Changeset e6a9c1 for src/World.cpp

Timestamp:

Mar 4, 2010, 10:40:52 AM (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:

63b56a7

Parents:

6a661c (diff), 66e95e (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 'MenuRefactoring' into QT4Refactoring

Conflicts:

molecuilder/src/Makefile.am

File:

• src/World.cpp (modified) (8 diffs)

src/World.cpp

@@ -13 +13 @@
 #include "Descriptors/AtomDescriptor.hpp"
 #include "Descriptors/AtomDescriptor_impl.hpp"
+#include "Descriptors/MoleculeDescriptor.hpp"
+#include "Descriptors/MoleculeDescriptor_impl.hpp"
 #include "Actions/ManipulateAtomsProcess.hpp"
 
@@ -22 +24 @@
 }
 
+// Atoms
+
 atom* World::getAtom(AtomDescriptor descriptor){
   return descriptor.find();
@@ -36 +40 @@
 int World::numAtoms(){
   return atoms.size();
+}
+
+// Molecules
+
+molecule *World::getMolecule(MoleculeDescriptor descriptor){
+  return descriptor.find();
+}
+
+std::vector<molecule*> World::getAllMolecules(MoleculeDescriptor descriptor){
+  return descriptor.findAll();
 }
 
@@ -72 +86 @@
 atom *World::createAtom(){
   OBSERVE;
-  atom *res = NewAtom();
-  assert(!atoms.count(currAtomId));
-  res->setId(currAtomId++);
+  atomId_t id = getNextAtomId();
+  atom *res = NewAtom(id);
   res->setWorld(this);
   // store the atom by ID
@@ -83 +96 @@
 int World::registerAtom(atom *atom){
   OBSERVE;
-  assert(!atoms.count(currAtomId));
-  atom->setId(currAtomId++);
+  atomId_t id = getNextAtomId();
+  atom->setId(id);
   atom->setWorld(this);
   atoms[atom->getId()] = atom;
@@ -102 +115 @@
   DeleteAtom(atom);
   atoms.erase(id);
+  releaseAtomId(id);
+}
+
+bool World::changeAtomId(atomId_t oldId, atomId_t newId, atom* target){
+  OBSERVE;
+  // in case this call did not originate from inside the atom, we redirect it,
+  // to also let it know that it has changed
+  if(!target){
+    target = atoms[oldId];
+    assert(target && "Atom with that ID not found");
+    return target->changeId(newId);
+  }
+  else{
+    if(reserveAtomId(newId)){
+      atoms.erase(oldId);
+      atoms.insert(pair<atomId_t,atom*>(newId,target));
+      return true;
+    }
+    else{
+      return false;
+    }
+  }
 }
 
@@ -122 +157 @@
   proc->signOff(this);
 }
+/******************************* IDManagement *****************************/
+
+// Atoms
+
+atomId_t World::getNextAtomId(){
+  // see if we can reuse some Id
+  if(atomIdPool.empty()){
+    return currAtomId++;
+  }
+  else{
+    // we give out the first ID from the pool
+    atomId_t id = *(atomIdPool.begin());
+    atomIdPool.erase(id);
+  }
+}
+
+void World::releaseAtomId(atomId_t id){
+  atomIdPool.insert(id);
+  // defragmentation of the pool
+  set<atomId_t>::reverse_iterator iter;
+  // go through all Ids in the pool that lie immediately below the border
+  while(!atomIdPool.empty() && *(atomIdPool.rbegin())==(currAtomId-1)){
+    atomIdPool.erase(--currAtomId);
+  }
+}
+
+bool World::reserveAtomId(atomId_t id){
+  if(id>=currAtomId ){
+    // add all ids between the new one and current border as available
+    for(atomId_t pos=currAtomId; pos<id; ++pos){
+      atomIdPool.insert(pos);
+    }
+    currAtomId=id+1;
+    return true;
+  }
+  else if(atomIdPool.count(id)){
+    atomIdPool.erase(id);
+    return true;
+  }
+  else{
+    // this ID could not be reserved
+    return false;
+  }
+}
+
+// Molecules
 
 /******************************* Iterators ********************************/
@@ -135 +216 @@
 World::AtomSet::iterator World::atomEnd(){
   return atoms.end();
+}
+
+World::MoleculeIterator World::getMoleculeIter(MoleculeDescriptor descr){
+  return MoleculeIterator(descr,this);
+}
+
+World::MoleculeSet::iterator World::moleculeEnd(){
+  return molecules.end();
 }