Changeset 957c42 for src/World.cpp

Timestamp:

Feb 25, 2010, 11:15:22 AM (16 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, 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:

5a7243

Parents:

0188ea (diff), 244d26 (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 'StructureRefactoring' into MenuRefactoring

File:

• src/World.cpp (modified) (9 diffs)

src/World.cpp

@@ -12 +12 @@
 #include "periodentafel.hpp"
 #include "Descriptors/AtomDescriptor.hpp"
+#include "Descriptors/AtomDescriptor_impl.hpp"
+#include "Actions/ManipulateAtomsProcess.hpp"
 
 using namespace std;
@@ -28 +30 @@
 }
 
+vector<atom*> World::getAllAtoms(){
+  return getAllAtoms(AllAtoms());
+}
+
 int World::numAtoms(){
   return atoms.size();
@@ -36 +42 @@
 }
 
+/******************** Methods to change World state *********************/
+
 molecule* World::createMolecule(){
   OBSERVE;
@@ -41 +49 @@
   mol = new molecule(periode);
   molecules_deprecated->insert(mol);
-  molecules.insert(mol);
+  assert(!molecules.count(currMoleculeId));
+  // store the molecule by ID
+  molecules[currMoleculeId++] = mol;
   mol->signOn(this);
   return mol;
 }
 
+
+atom *World::createAtom(){
+  OBSERVE;
+  atom *res = NewAtom();
+  assert(!atoms.count(currAtomId));
+  res->setId(currAtomId++);
+  res->setWorld(this);
+  // store the atom by ID
+  atoms[res->getId()] = res;
+  return res;
+}
+
+int World::registerAtom(atom *atom){
+  OBSERVE;
+  assert(!atoms.count(currAtomId));
+  atom->setId(currAtomId++);
+  atom->setWorld(this);
+  atoms[atom->getId()] = atom;
+  return atom->getId();
+}
+
+void World::destroyAtom(atom* atom){
+  OBSERVE;
+  int id = atom->getId();
+  destroyAtom(id);
+}
+
+void World::destroyAtom(int id) {
+  OBSERVE;
+  atom *atom = atoms[id];
+  assert(atom);
+  DeleteAtom(atom);
+  atoms.erase(id);
+}
+
+ManipulateAtomsProcess* World::manipulateAtoms(boost::function<void(atom*)> op,std::string name,AtomDescriptor descr){
+  return new ManipulateAtomsProcess(op, descr,name,true);
+}
+
+ManipulateAtomsProcess* World::manipulateAtoms(boost::function<void(atom*)> op,std::string name){
+  return manipulateAtoms(op,name,AllAtoms());
+}
+
+/********************* Internal Change methods for double Callback and Observer mechanism ********/
+
+void World::doManipulate(ManipulateAtomsProcess *proc){
+  proc->signOn(this);
+  {
+    OBSERVE;
+    proc->doManipulate(this);
+  }
+  proc->signOff(this);
+}
+
+/******************************* Iterators ********************************/
+
+/*
+ * Actual Implementation of the iterators can be found in WorldIterators.cpp
+ */
+
+World::AtomIterator World::getAtomIter(AtomDescriptor descr){
+  return AtomIterator(descr,this);
+}
+
+World::AtomSet::iterator World::atomEnd(){
+  return atoms.end();
+}
 
 /******************************* Singleton Stuff **************************/
@@ -53 +130 @@
 boost::mutex World::worldLock;
 
-
-
 World::World() :
-    dummyId(0),
+    currAtomId(0),
+    currMoleculeId(0),
     periode(new periodentafel),
-    molecules_deprecated(new MoleculeListClass)
+    molecules_deprecated(new MoleculeListClass),
+    atoms(),
+    molecules()
 {
   molecules_deprecated->signOn(this);
@@ -65 +143 @@
 World::~World()
 {
+  delete molecules_deprecated;
   delete periode;
+  AtomSet::iterator iter;
+  for(iter=atoms.begin();iter!=atoms.end();++iter){
+    DeleteAtom((*iter).second);
+  }
+  atoms.clear();
 }
 
@@ -78 +162 @@
 
 void World::destroy(){
-  // For legacy reasons all atoms have to be destroyed first, since unregistering would cause deadlocks otherwise
-  theWorld->destroyLegacy();
-  //WARNING: at this point we have a small race condition, when sombody now tries to access the world.
-
   // boost supports RAII-Style locking, so we don't need to unlock
   boost::mutex::scoped_lock guard(worldLock);
@@ -89 +169 @@
 
 World* World::reset(){
-  // For legacy reasons all atoms have to be destroyed first, since unregistering would cause deadlocks otherwise
-  theWorld->destroyLegacy();
-  //WARNING: at this point we have a small race condition, when sombody now tries to access the world.
-
   World* oldWorld = 0;
   {
@@ -119 +195 @@
   return molecules_deprecated;
 }
-
-// some legacy stuff to let the World know about items created outside
-void World::registerAtom(atom *theAtom){
-  OBSERVE;
-  atoms[dummyId++] = theAtom;
-}
-
-void World::destroyLegacy(){
-  //delete molecules_deprecated;
-}
-
-void World::unregisterAtom(atom *theAtom){
-  OBSERVE;
-  atoms.erase(theAtom->getId());
-}