Changeset b97a60 for src

Timestamp:

Feb 17, 2012, 3:24:18 PM (13 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, 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:

7d46e3

Parents:

3867a7

git-author:

Frederik Heber <heber@…> (01/06/12 14:37:36)

git-committer:

Frederik Heber <heber@…> (02/17/12 15:24:18)

Message:

Modified IdPool implementation to give either unique or continuous ids.

• added two class uniqueId and continuousId that get the id type via a template and contain a getNextId_impl(). Also, contains typedef is is_IdPool_trait:
  • uniqueId always return a greater id.
  • continuousId implements the old way.
• IdPool is now based on two templates, the second is the template that is inherited and its contained function used in getNextId().
• for atoms the id is the sole identifier for which we can guarantee uniqueness. For molecules uniqueness does not make sense.
• updated World's documentation on its id pools.

• TESTFIX: Filling/FillVoidWithMolecule - both changed because the order of the ids has changed. In one case the bonding id flipped, in the other one atom changed places in .xyz file. (Actually, it's surprising that this is the only glitch occuring due to the changing of the id policy).

Location:

src

Files:

• IdPool.hpp (modified) (3 diffs)
• IdPool_impl.hpp (modified) (5 diffs)
• IdPool_policy.hpp (added)
• World.cpp (modified) (1 diff)
• World.hpp (modified) (3 diffs)
• documentation/constructs/world.dox (modified) (1 diff)

src/IdPool.hpp

@@ -26 +26 @@
  * that stores the id).
  *
+ * Note that the external class \a idpolicy decides upon how the next id is
+ * produced, \sa IdPool_policy.hpp.
  */
-template <class T>
-class IdPool {
+template <class T, class idpolicy>
+class IdPool : public idpolicy {
+  // when trait is not of correct type this will produce an error
+  typedef typename idpolicy::is_IdPool_policy check_for_IdPool_trait;
 public:
   /** Constructor for class IdPool.
@@ -43 +47 @@
   ~IdPool();
 
-  /** Returns the next available id.
-   *
-   * @return free id that is reserved
-   */
-  T getNextId();
-
   /** Reserves a specific \a id.
    *
@@ -61 +59 @@
    */
   void releaseId(T id);
+
+  /** Returns the next available id.
+   *
+   * @return free id that is reserved
+   */
+  T getNextId();
 
 private:

src/IdPool_impl.hpp

@@ -18 +18 @@
 #include "CodePatterns/Log.hpp"
 
-template <class T>
-IdPool<T>::IdPool(const T _currId, const unsigned int _max_skips, const unsigned int _max_size) :
+template <class T, class idpolicy>
+IdPool<T,idpolicy>::IdPool(const T _currId, const unsigned int _max_skips, const unsigned int _max_size) :
   lastAction(NoAction),
   currId(_currId),
@@ -28 +28 @@
 {}
 
-template <class T>
-IdPool<T>::~IdPool()
+template <class T, class idpolicy>
+IdPool<T,idpolicy>::~IdPool()
 {}
 
-template <class T>
-T IdPool<T>::getNextId()
+template <class T, class idpolicy>
+T IdPool<T,idpolicy>::getNextId()
 {
   setLastAction(reserve);
-  // try to find an Id in the pool;
-  if(!pool.empty()) {
-    typename IdPool_t::iterator iter=pool.begin();
-    T id = iter->first;
-    range<T> newRange = makeRange(id+1,iter->last);
-    // we wont use this iterator anymore, so we don't care about invalidating
-    pool.erase(iter);
-    if(newRange.first<newRange.last)
-      pool.insert(newRange);
-    return id;
-  }
-  // Nothing in the pool... we are out of luck
-  return currId++;
+  return idpolicy::getNextId_impl(pool, currId);
 }
 
-template <class T>
-void IdPool<T>::releaseId(T id)
+template <class T, class idpolicy>
+void IdPool<T,idpolicy>::releaseId(T id)
 {
   setLastAction(release);
@@ -59 +47 @@
 }
 
-template <class T>
-bool IdPool<T>::reserveId(T id)
+template <class T, class idpolicy>
+bool IdPool<T,idpolicy>::reserveId(T id)
 {
   setLastAction(reserve);
@@ -100 +88 @@
 }
 
-template <class T>
-void IdPool<T>::defragIdPool()
+template <class T, class idpolicy>
+void IdPool<T,idpolicy>::defragIdPool()
 {
   // check if the situation is bad enough to make defragging neccessary
@@ -142 +130 @@
  * at a chosen place.
  */
-#define CONSTRUCT_IDPOOL(name) \
-    template name IdPool< name >::getNextId(); \
-    template bool IdPool< name >::reserveId( name ); \
-    template void IdPool< name >::releaseId( name ); \
-    template void IdPool< name >::setLastAction(const enum Actions _action); \
-    template void IdPool< name >::defragIdPool() ;
+#define CONSTRUCT_IDPOOL(name, idpolicy) \
+    template name IdPool< name, idpolicy >::getNextId(); \
+    template bool IdPool< name, idpolicy >::reserveId( name ); \
+    template void IdPool< name, idpolicy >::releaseId( name ); \
+    template void IdPool< name, idpolicy >::setLastAction(const enum Actions _action); \
+    template void IdPool< name, idpolicy >::defragIdPool() ;
 
 #endif /* IDPOOL_IMPL_HPP_ */

src/World.cpp

@@ -693 +693 @@
 
 // moleculeId_t und atomId_t sind gleicher Basistyp, deswegen nur einen von beiden konstruieren
-CONSTRUCT_IDPOOL(moleculeId_t)
+CONSTRUCT_IDPOOL(atomId_t, uniqueId)
+CONSTRUCT_IDPOOL(moleculeId_t, continuousId)
 
 CONSTRUCT_SINGLETON(World)

src/World.hpp

@@ -32 +32 @@
 #include "CodePatterns/Observer/ObservedContainer.hpp"
 #include "CodePatterns/Range.hpp"
+#include "IdPool_policy.hpp"
 #include "IdPool.hpp"
 #include "LinkedCell/LinkedCell_View.hpp"
@@ -465 +466 @@
    * The pool contains ranges of free ids in the form [bottom,top).
    */
-  IdPool<atomId_t> atomIdPool;
+  IdPool<atomId_t, uniqueId> atomIdPool;
 
   MoleculeSet molecules;
@@ -474 +475 @@
    * The pool contains ranges of free ids in the form [bottom,top).
    */
-  IdPool<moleculeId_t> moleculeIdPool;
+  IdPool<moleculeId_t, continuousId> moleculeIdPool;
 
 private:

src/documentation/constructs/world.dox

@@ -112 +112 @@
  * \paragraph world-internals-notes-idpool
  *
- * The World has an idpool to manage the ids of atoms and molecules, i.e. such
- * that they are:
- * -# unique
- * -# not loosely spread over the whole range of possible, but tightly packed
+ * The World has an idpool to manage the ids of atoms and molecules. The IdPool
+ * inherits policies, such that ids are given in a unique (uniqueId) or
+ * continuous (continousId) fashion.
+ * The id of an atom is the sole identifier for which we can guarantee
+ * uniqueness. Due to undo and redo actions the memory address is not a good
+ * identifier. This is however required for FormatParser's that need
+ * to store their additionalAtomData at program exit and have to safely identify
+ * the data with its atoms. This can only be accomplished via the id. Hence,
+ * we use the unique policy there.
+ * The id of a molecule however is more of a convenience, to distinguish it from
+ * the currently present others. A molecule may change very often and it is also
+ * a compound structure that may change slightly (when a new bond to another atom
+ * occurs). Thus, the concept of the id as a unique identifier does not make
+ * sense. Hence, we use the continuous policy here.
  *
- * For the latter to work we have a class IdPool that manages the ids and
+ * Note that IdPool::reserveId() has to ascertain that we may sweep through ids
+ * available to (undone) AtomRemoveAction or (redone) AtomAddAction in sublinear
+ * time. For this to work we have a class IdPool that manages the ids and
  * defragments the pool from time to time by combining ranges of released ids.
  *
- * \date 2011-10-31
+ * \date 2012-01-06
  *
  */