Changes in src/World.hpp [cf0ca1:43dad6]

File:

• src/World.hpp (modified) (12 diffs)

src/World.hpp

@@ -23 +23 @@
 #include "Patterns/Cacheable.hpp"
 #include "Patterns/Singleton.hpp"
-#include "Patterns/ObservedContainer.hpp"
 
 // include config.h
@@ -35 +34 @@
 class AtomDescriptor_impl;
 template<typename T> class AtomsCalculation;
-class Box;
 class config;
 class ManipulateAtomsProcess;
-class Matrix;
 class molecule;
 class MoleculeDescriptor;
@@ -46 +43 @@
 class ThermoStatContainer;
 
-
 /****************************************** forward declarations *****************************/
 
@@ -62 +58 @@
 friend class MoleculeDescriptor_impl;
 friend class MoleculeDescriptor;
-// coupling with descriptors over selection
-friend class AtomSelectionDescriptor_impl;
-friend class MoleculeSelectionDescriptor_impl;
 
 // Actions, calculations etc associated with the World
@@ -72 +65 @@
 
   // Types for Atom and Molecule structures
-  typedef ObservedContainer<std::map<atomId_t,atom*> > AtomSet;
-  typedef ObservedContainer<std::map<moleculeId_t,molecule*> > MoleculeSet;
+  typedef std::map<atomId_t,atom*> AtomSet;
+  typedef std::map<moleculeId_t,molecule*> MoleculeSet;
 
   /***** getter and setter *****/
@@ -132 +125 @@
    * get the domain size as a symmetric matrix (6 components)
    */
-  Box& getDomain();
-
-  /**
-   * Set the domain size from a matrix object
-   *
-   * Matrix needs to be symmetric
-   */
-  void setDomain(const Matrix &mat);
+  double * getDomain();
 
   /**
@@ -221 +207 @@
   ManipulateAtomsProcess* manipulateAtoms(boost::function<void(atom*)>,std::string);
 
-  /****
-   * Iterators to use internal data structures
-   * All these iterators are observed to track changes.
-   * There is a corresponding protected section with unobserved iterators,
-   * which can be used internally when the extra speed is needed
-   */
-
-  typedef SelectiveIterator<atom*,AtomSet,AtomDescriptor>       AtomIterator;
-
-  /**
-   * returns an iterator over all Atoms matching a given descriptor.
-   * This iterator is observed, so don't keep it around unnecessary to
-   * avoid unintended blocking.
-   */
-  AtomIterator getAtomIter(AtomDescriptor descr);
-  AtomIterator getAtomIter();
-
-  AtomIterator atomEnd();
-
-  typedef SelectiveIterator<molecule*,MoleculeSet,MoleculeDescriptor>   MoleculeIterator;
-
-  /**
-   * returns an iterator over all Molecules matching a given descriptor.
-   * This iterator is observed, so don't keep it around unnecessary to
-   * avoid unintended blocking.
-   */
-  MoleculeIterator getMoleculeIter(MoleculeDescriptor descr);
-  MoleculeIterator getMoleculeIter();
-
-  MoleculeIterator moleculeEnd();
-
-  /******** Selections of molecules and Atoms *************/
-  void clearAtomSelection();
-  void selectAtom(atom*);
-  void selectAtom(atomId_t);
-  void selectAllAtoms(AtomDescriptor);
-  void selectAtomsOfMolecule(molecule*);
-  void selectAtomsOfMolecule(moleculeId_t);
-  void unselectAtom(atom*);
-  void unselectAtom(atomId_t);
-  void unselectAllAtoms(AtomDescriptor);
-  void unselectAtomsOfMolecule(molecule*);
-  void unselectAtomsOfMolecule(moleculeId_t);
-
-  void clearMoleculeSelection();
-  void selectMolecule(molecule*);
-  void selectMolecule(moleculeId_t);
-  void selectAllMoleculess(MoleculeDescriptor);
-  void selectMoleculeOfAtom(atom*);
-  void selectMoleculeOfAtom(atomId_t);
-  void unselectMolecule(molecule*);
-  void unselectMolecule(moleculeId_t);
-  void unselectAllMoleculess(MoleculeDescriptor);
-  void unselectMoleculeOfAtom(atom*);
-  void unselectMoleculeOfAtom(atomId_t);
-
-  /******************** Iterators to selections *****************/
-  typedef AtomSet::iterator AtomSelectionIterator;
-  AtomSelectionIterator beginAtomSelection();
-  AtomSelectionIterator endAtomSelection();
-
-  typedef MoleculeSet::iterator MoleculeSelectionIterator;
-  MoleculeSelectionIterator beginMoleculeSelection();
-  MoleculeSelectionIterator endMoleculeSelection();
-
 protected:
-  /****
-   * Iterators to use internal data structures
-   * All these iterators are unobserved for speed reasons.
-   * There is a corresponding public section to these methods,
-   * which produce observed iterators.*/
+  /**** Iterators to use internal data structures */
 
   // Atoms
-  typedef SelectiveIterator<atom*,AtomSet::set_t,AtomDescriptor>        internal_AtomIterator;
+  typedef SelectiveIterator<atom*,AtomSet,AtomDescriptor> AtomIterator;
 
   /**
@@ -300 +217 @@
    * used for internal purposes, like AtomProcesses and AtomCalculations.
    */
-  internal_AtomIterator getAtomIter_internal(AtomDescriptor descr);
+  AtomIterator getAtomIter(AtomDescriptor descr);
 
   /**
@@ -308 +225 @@
    * used for internal purposes, like AtomProcesses and AtomCalculations.
    */
-  internal_AtomIterator atomEnd_internal();
+  AtomIterator atomEnd();
 
   // Molecules
-  typedef SelectiveIterator<molecule*,MoleculeSet::set_t,MoleculeDescriptor>   internal_MoleculeIterator;
-
+
+  typedef SelectiveIterator<molecule*,MoleculeSet,MoleculeDescriptor> MoleculeIterator;
 
   /**
@@ -318 +235 @@
    * used for internal purposes, like MoleculeProcesses and MoleculeCalculations.
    */
-  internal_MoleculeIterator getMoleculeIter_internal(MoleculeDescriptor descr);
+  MoleculeIterator getMoleculeIter(MoleculeDescriptor descr);
 
   /**
@@ -326 +243 @@
    * used for internal purposes, like MoleculeProcesses and MoleculeCalculations.
    */
-  internal_MoleculeIterator moleculeEnd_internal();
+  MoleculeIterator moleculeEnd();
 
 
@@ -337 +254 @@
   void releaseAtomId(atomId_t);
   bool reserveAtomId(atomId_t);
-  void defragAtomIdPool();
-
-  moleculeId_t getNextMoleculeId();
-  void releaseMoleculeId(moleculeId_t);
-  bool reserveMoleculeId(moleculeId_t);
-  void defragMoleculeIdPool();
 
   periodentafel *periode;
   config *configuration;
-  Box *cell_size;
+  static double *cell_size;
   std::string defaultName;
   class ThermoStatContainer *Thermostats;
   int ExitFlag;
-private:
-
+public:
   AtomSet atoms;
-  AtomSet selectedAtoms;
-  typedef std::set<std::pair<atomId_t, atomId_t> > atomIdPool_t;
-  /**
-   * stores the pool for all available AtomIds below currAtomId
-   *
-   * The pool contains ranges of free ids in the form [bottom,top).
-   */
-  atomIdPool_t atomIdPool;
+private:
+  std::set<atomId_t> atomIdPool; //<!stores the pool for all available AtomIds below currAtomId
   atomId_t currAtomId; //!< stores the next available Id for atoms
-  size_t lastAtomPoolSize; //!< size of the pool after last defrag, to skip some defrags
-  unsigned int numAtomDefragSkips;
-
   MoleculeSet molecules;
-  MoleculeSet selectedMolecules;
-  typedef std::set<std::pair<moleculeId_t, moleculeId_t> > moleculeIdPool_t;
-  /**
-   * stores the pool for all available AtomIds below currAtomId
-   *
-   * The pool contains ranges of free ids in the form [bottom,top).
-   */
-  moleculeIdPool_t moleculeIdPool;
   moleculeId_t currMoleculeId;
-  size_t lastMoleculePoolSize; //!< size of the pool after last defrag, to skip some defrags
-  unsigned int numMoleculeDefragSkips;
 private:
   /**