Changeset 354859

Timestamp:

Feb 16, 2010, 5:26:59 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:

7dad10, b1d8092

Parents:

7a1ce5

Message:

Moved control of molecules and periode to World.

Location:

src

Files:

• World.cpp (modified) (8 diffs)
• World.hpp (modified) (5 diffs)
• builder.cpp (modified) (6 diffs)

src/World.cpp

@@ -9 +9 @@
 
 #include "atom.hpp"
+#include "molecule.hpp"
+#include "periodentafel.hpp"
 #include "Descriptors/AtomDescriptor.hpp"
 
@@ -14 +16 @@
 
 /******************************* getter and setter ************************/
-periodentafel* World::getPeriode(){
+periodentafel *&World::getPeriode(){
   return periode;
 }
@@ -26 +28 @@
 }
 
+int World::numAtoms(){
+  return atoms.size();
+}
+
+int World::numMolecules(){
+  return molecules_deprecated->ListOfMolecules.size();
+}
+
+molecule* World::createMolecule(){
+  OBSERVE;
+  molecule *mol = NULL;
+  mol = new molecule(periode);
+  molecules_deprecated->insert(mol);
+  molecules.insert(mol);
+  mol->signOn(this);
+  return mol;
+}
+
+
 /******************************* Singleton Stuff **************************/
 
@@ -35 +56 @@
 
 World::World() :
-    dummyId(0)
+    dummyId(0),
+    periode(new periodentafel),
+    molecules_deprecated(new MoleculeListClass)
 {}
 
 World::~World()
-{}
+{
+  delete periode;
+}
 
 World* World::get(){
@@ -51 +76 @@
 
 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);
@@ -58 +87 @@
 
 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;
   {
@@ -81 +114 @@
 /******************************* deprecated Legacy Stuff ***********************/
 
-MoleculeListClass *World::getMolecules() {
-  return molecules;
+MoleculeListClass *&World::getMolecules() {
+  return molecules_deprecated;
 }
 
@@ -91 +124 @@
 }
 
+void World::destroyLegacy(){
+  //delete molecules_deprecated;
+}
+
 void World::unregisterAtom(atom *theAtom){
   OBSERVE;

src/World.hpp

@@ -12 +12 @@
 #include <map>
 #include <vector>
+#include <set>
 
 #include "Patterns/Observer.hpp"
@@ -20 +21 @@
 class MoleculeListClass;
 class atom;
+class molecule;
 class AtomDescriptor;
 class AtomDescriptor_impl;
@@ -29 +31 @@
 
   /***** getter and setter *****/
-  periodentafel* getPeriode();
+  // reference to pointer is used for legacy reason... reference will be removed latter to keep encapsulation of World object
+  periodentafel *&getPeriode();
   atom* getAtom(AtomDescriptor descriptor);
   std::vector<atom*> getAllAtoms(AtomDescriptor descriptor);
+  int numAtoms();
+  int numMolecules();
+
+  /***** Methods to work with the World *****/
+  molecule *createMolecule();
 private:
   periodentafel *periode;
   std::map<int,atom*> atoms;
+  std::set<molecule*> molecules;
 
 
@@ -57 +66 @@
    *****/
 public:
-  MoleculeListClass *getMolecules();
+  MoleculeListClass *&getMolecules();
 
   // functions used for the WorldContent template mechanism
@@ -63 +72 @@
   void unregisterAtom(atom *theAtom);
 private:
-  MoleculeListClass *molecules;
+  // this function cleans up anything that cannot be cleaned while the lock is active
+  // at a later point all these cleanups have to be moved to the World Class so the deadlock and
+  // race condition can both be avoided.
+  void destroyLegacy();
+
+  MoleculeListClass *molecules_deprecated;
 
   // this is needed to assign unique IDs to atoms... so far

src/builder.cpp

@@ -76 +76 @@
 #include "Actions/MethodAction.hpp"
 #include "Actions/small_actions.hpp"
+#include "World.hpp"
 #include "version.h"
 
@@ -2164 +2165 @@
 /********************************************** Main routine **************************************/
 
+void cleanUp(config *configuration){
+  World::destroy();
+  delete(configuration);
+  Log() << Verbose(0) <<  "Maximum of allocated memory: "
+    << MemoryUsageObserver::getInstance()->getMaximumUsedMemory() << endl;
+  Log() << Verbose(0) <<  "Remaining non-freed memory: "
+    << MemoryUsageObserver::getInstance()->getUsedMemorySize() << endl;
+  MemoryUsageObserver::purgeInstance();
+  logger::purgeInstance();
+  errorLogger::purgeInstance();
+  UIFactory::purgeInstance();
+  ActionRegistry::purgeRegistry();
+}
+
 int main(int argc, char **argv)
 {
-  periodentafel *periode = new periodentafel;
-    MoleculeListClass *molecules = new MoleculeListClass;
     molecule *mol = NULL;
     config *configuration = new config;
@@ -2178 +2191 @@
     setVerbosity(0);
     /* structure of ParseCommandLineOptions will be refactored later */
-    j = ParseCommandLineOptions(argc, argv, molecules, periode, *configuration, ConfigFileName);
+    j = ParseCommandLineOptions(argc, argv,  World::get()->getMolecules(), World::get()->getPeriode(), *configuration, ConfigFileName);
     switch (j){
         case 255:
         case 2:
         case 1:
-            delete (molecules);
-            delete (periode);
-            delete (configuration);
-            Log() << Verbose(0) << "Maximum of allocated memory: " << MemoryUsageObserver::getInstance()->getMaximumUsedMemory() << endl;
-            Log() << Verbose(0) << "Remaining non-freed memory: " << MemoryUsageObserver::getInstance()->getUsedMemorySize() << endl;
-            MemoryUsageObserver::getInstance()->purgeInstance();
-            logger::purgeInstance();
-            errorLogger::purgeInstance();
+            cleanUp(configuration);
             return (j == 1 ? 0 : j);
         default:
             break;
     }
-    if(molecules->ListOfMolecules.size() == 0){
-        mol = new molecule(periode);
+    if(World::get()->numMolecules() == 0){
+        mol = World::get()->createMolecule();
         if(mol->cell_size[0] == 0.){
             Log() << Verbose(0) << "enter lower tridiagonal form of basis matrix" << endl << endl;
@@ -2204 +2210 @@
             }
         }
-
         mol->ActiveFlag = true;
-        molecules->insert(mol);
     }
 
@@ -2218 +2222 @@
 
       UIFactory::makeUserInterface(UIFactory::Text);
-      MainWindow *mainWindow = UIFactory::get()->makeMainWindow(populaters,molecules, configuration, periode, ConfigFileName);
+      MainWindow *mainWindow = UIFactory::get()->makeMainWindow(populaters,World::get()->getMolecules(), configuration, World::get()->getPeriode(), ConfigFileName);
       mainWindow->display();
       delete mainWindow;
     }
 
-    if(periode->StorePeriodentafel(configuration->databasepath))
+    if(World::get()->getPeriode()->StorePeriodentafel(configuration->databasepath))
         Log() << Verbose(0) << "Saving of elements.db successful." << endl;
 
@@ -2229 +2233 @@
         Log() << Verbose(0) << "Saving of elements.db failed." << endl;
 
-    delete (molecules);
-    delete(periode);
-  delete(configuration);
-
-
-
-  Log() << Verbose(0) <<  "Maximum of allocated memory: "
-    << MemoryUsageObserver::getInstance()->getMaximumUsedMemory() << endl;
-  Log() << Verbose(0) <<  "Remaining non-freed memory: "
-    << MemoryUsageObserver::getInstance()->getUsedMemorySize() << endl;
-  MemoryUsageObserver::purgeInstance();
-  logger::purgeInstance();
-  errorLogger::purgeInstance();
-  UIFactory::purgeInstance();
-  ActionRegistry::purgeRegistry();
+  cleanUp(configuration);
   return (0);
 }