Changeset 3e4fb6

Timestamp:

Dec 28, 2011, 3:27:49 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:

53c7fc

Parents:

401f90

git-author:

Frederik Heber <heber@…> (12/23/11 14:48:37)

git-committer:

Frederik Heber <heber@…> (12/28/11 15:27:49)

Message:

Added template class IdPool used by World to manage defragmentable id pool.

• this is stuff from World factored into own class (was doubly present in World anyway).
• added short documentation to constructs/world.

Location:

src

Files:

• IdPool.hpp (added)
• IdPool_impl.hpp (added)
• Makefile.am (modified) (1 diff)
• World.cpp (modified) (10 diffs)
• World.hpp (modified) (6 diffs)
• documentation/constructs/world.dox (modified) (1 diff)

src/Makefile.am

@@ -196 +196 @@
   config.hpp \
   Formula.hpp \
+  IdPool.hpp \
+  IdPool_impl.hpp \
   linkedcell.hpp \
   MoleculeLeafClass.hpp \

src/World.cpp

@@ -45 +45 @@
 #include "WorldTime.hpp"
 
+#include "IdPool_impl.hpp"
+
 #include "CodePatterns/Singleton_impl.hpp"
 #include "CodePatterns/ObservedContainer_impl.hpp"
 
 using namespace MoleCuilder;
-
-const unsigned int MAX_POOL_FRAGMENTATION=20;
-const unsigned int MAX_FRAGMENTATION_SKIPS=100;
 
 /******************************* Notifications ************************/
@@ -188 +187 @@
   molecule *mol = NULL;
   mol = NewMolecule();
-  moleculeId_t id = getNextMoleculeId();
+  moleculeId_t id = moleculeIdPool.getNextId();
   ASSERT(!molecules.count(id),"proposed id did not specify an unused ID");
   mol->setId(id);
@@ -218 +217 @@
     selectedMolecules.erase(id);
   molecules.erase(id);
-  releaseMoleculeId(id);
+  moleculeIdPool.releaseId(id);
 }
 
 atom *World::createAtom(){
   OBSERVE;
-  atomId_t id = getNextAtomId();
+  atomId_t id = atomIdPool.getNextId();
   ASSERT(!atoms.count(id),"proposed id did not specify an unused ID");
   atom *res = NewAtom(id);
@@ -237 +236 @@
 int World::registerAtom(atom *atom){
   OBSERVE;
-  atomId_t id = getNextAtomId();
+  atomId_t id = atomIdPool.getNextId();
   atom->setId(id);
   atom->setWorld(this);
@@ -262 +261 @@
     selectedAtoms.erase(id);
   atoms.erase(id);
-  releaseAtomId(id);
+  atomIdPool.releaseId(id);
 }
 
@@ -275 +274 @@
   }
   else{
-    if(reserveAtomId(newId)){
+    if(atomIdPool.reserveId(newId)){
       atoms.erase(oldId);
       atoms.insert(pair<atomId_t,atom*>(newId,target));
@@ -296 +295 @@
   }
   else{
-    if(reserveMoleculeId(newId)){
+    if(moleculeIdPool.reserveId(newId)){
       molecules.erase(oldId);
       molecules.insert(pair<moleculeId_t,molecule*>(newId,target));
@@ -326 +325 @@
   proc->signOff(this);
 }
-/******************************* IDManagement *****************************/
-
-// Atoms
-
-atomId_t World::getNextAtomId(){
-  // try to find an Id in the pool;
-  if(!atomIdPool.empty()){
-    atomIdPool_t::iterator iter=atomIdPool.begin();
-    atomId_t id = iter->first;
-    range<atomId_t> newRange = makeRange(id+1,iter->last);
-    // we wont use this iterator anymore, so we don't care about invalidating
-    atomIdPool.erase(iter);
-    if(newRange.first<newRange.last){
-      atomIdPool.insert(newRange);
-    }
-    return id;
-  }
-  // Nothing in the pool... we are out of luck
-  return currAtomId++;
-}
-
-void World::releaseAtomId(atomId_t id){
-  atomIdPool.insert(makeRange(id,id+1));
-  defragAtomIdPool();
-}
-
-bool World::reserveAtomId(atomId_t id){
-  if(id>=currAtomId ){
-    range<atomId_t> newRange = makeRange(currAtomId,id);
-    if(newRange.first<newRange.last){
-      atomIdPool.insert(newRange);
-    }
-    currAtomId=id+1;
-    defragAtomIdPool();
-    return true;
-  }
-  // look for a range that matches the request
-  for(atomIdPool_t::iterator iter=atomIdPool.begin();iter!=atomIdPool.end();++iter){
-    if(iter->isBefore(id)){
-      // we have covered all available ranges... nothing to be found here
-      break;
-    }
-    // no need to check first, since it has to be <=id, since otherwise we would have broken out
-    if(!iter->isBeyond(id)){
-      // we found a matching range... get the id from this range
-
-      // split up this range at the point of id
-      range<atomId_t> bottomRange = makeRange(iter->first,id);
-      range<atomId_t> topRange = makeRange(id+1,iter->last);
-      // remove this range
-      atomIdPool.erase(iter);
-      if(bottomRange.first<bottomRange.last){
-        atomIdPool.insert(bottomRange);
-      }
-      if(topRange.first<topRange.last){
-        atomIdPool.insert(topRange);
-      }
-      defragAtomIdPool();
-      return true;
-    }
-  }
-  // this ID could not be reserved
-  return false;
-}
-
-void World::defragAtomIdPool(){
-  // check if the situation is bad enough to make defragging neccessary
-  if((numAtomDefragSkips<MAX_FRAGMENTATION_SKIPS) &&
-     (atomIdPool.size()<lastAtomPoolSize+MAX_POOL_FRAGMENTATION)){
-    ++numAtomDefragSkips;
-    return;
-  }
-  for(atomIdPool_t::iterator iter = atomIdPool.begin();iter!=atomIdPool.end();){
-    // see if this range is adjacent to the next one
-    atomIdPool_t::iterator next = iter;
-    next++;
-    if(next!=atomIdPool.end() && (next->first==iter->last)){
-      // merge the two ranges
-      range<atomId_t> newRange = makeRange(iter->first,next->last);
-      atomIdPool.erase(iter);
-      atomIdPool.erase(next);
-      pair<atomIdPool_t::iterator,bool> res = atomIdPool.insert(newRange);
-      ASSERT(res.second,"Id-Pool was confused");
-      iter=res.first;
-      continue;
-    }
-    ++iter;
-  }
-  if(!atomIdPool.empty()){
-    // check if the last range is at the border
-    atomIdPool_t::iterator iter = atomIdPool.end();
-    iter--;
-    if(iter->last==currAtomId){
-      currAtomId=iter->first;
-      atomIdPool.erase(iter);
-    }
-  }
-  lastAtomPoolSize=atomIdPool.size();
-  numAtomDefragSkips=0;
-}
-
-// Molecules
-
-moleculeId_t World::getNextMoleculeId(){
-  // try to find an Id in the pool;
-  if(!moleculeIdPool.empty()){
-    moleculeIdPool_t::iterator iter=moleculeIdPool.begin();
-    moleculeId_t id = iter->first;
-    range<moleculeId_t> newRange = makeRange(id+1,iter->last);
-    // we wont use this iterator anymore, so we don't care about invalidating
-    moleculeIdPool.erase(iter);
-    if(newRange.first<newRange.last){
-      moleculeIdPool.insert(newRange);
-    }
-    return id;
-  }
-  // Nothing in the pool... we are out of luck
-  return currMoleculeId++;
-}
-
-void World::releaseMoleculeId(moleculeId_t id){
-  moleculeIdPool.insert(makeRange(id,id+1));
-  defragMoleculeIdPool();
-}
-
-bool World::reserveMoleculeId(moleculeId_t id){
-  if(id>=currMoleculeId ){
-    range<moleculeId_t> newRange = makeRange(currMoleculeId,id);
-    if(newRange.first<newRange.last){
-      moleculeIdPool.insert(newRange);
-    }
-    currMoleculeId=id+1;
-    defragMoleculeIdPool();
-    return true;
-  }
-  // look for a range that matches the request
-  for(moleculeIdPool_t::iterator iter=moleculeIdPool.begin();iter!=moleculeIdPool.end();++iter){
-    if(iter->isBefore(id)){
-      // we have coverd all available ranges... nothing to be found here
-      break;
-    }
-    // no need to check first, since it has to be <=id, since otherwise we would have broken out
-    if(!iter->isBeyond(id)){
-      // we found a matching range... get the id from this range
-
-      // split up this range at the point of id
-      range<moleculeId_t> bottomRange = makeRange(iter->first,id);
-      range<moleculeId_t> topRange = makeRange(id+1,iter->last);
-      // remove this range
-      moleculeIdPool.erase(iter);
-      if(bottomRange.first<bottomRange.last){
-        moleculeIdPool.insert(bottomRange);
-      }
-      if(topRange.first<topRange.last){
-        moleculeIdPool.insert(topRange);
-      }
-      defragMoleculeIdPool();
-      return true;
-    }
-  }
-  // this ID could not be reserved
-  return false;
-}
-
-void World::defragMoleculeIdPool(){
-  // check if the situation is bad enough to make defragging neccessary
-  if((numMoleculeDefragSkips<MAX_FRAGMENTATION_SKIPS) &&
-     (moleculeIdPool.size()<lastMoleculePoolSize+MAX_POOL_FRAGMENTATION)){
-    ++numMoleculeDefragSkips;
-    return;
-  }
-  for(moleculeIdPool_t::iterator iter = moleculeIdPool.begin();iter!=moleculeIdPool.end();){
-    // see if this range is adjacent to the next one
-    moleculeIdPool_t::iterator next = iter;
-    next++;
-    if(next!=moleculeIdPool.end() && (next->first==iter->last)){
-      // merge the two ranges
-      range<moleculeId_t> newRange = makeRange(iter->first,next->last);
-      moleculeIdPool.erase(iter);
-      moleculeIdPool.erase(next);
-      pair<moleculeIdPool_t::iterator,bool> res = moleculeIdPool.insert(newRange);
-      ASSERT(res.second,"Id-Pool was confused");
-      iter=res.first;
-      continue;
-    }
-    ++iter;
-  }
-  if(!moleculeIdPool.empty()){
-    // check if the last range is at the border
-    moleculeIdPool_t::iterator iter = moleculeIdPool.end();
-    iter--;
-    if(iter->last==currMoleculeId){
-      currMoleculeId=iter->first;
-      moleculeIdPool.erase(iter);
-    }
-  }
-  lastMoleculePoolSize=moleculeIdPool.size();
-  numMoleculeDefragSkips=0;
-}
-
 /******************************* Iterators ********************************/
 
@@ -823 +622 @@
     atoms(this),
     selectedAtoms(this),
-    currAtomId(0),
-    lastAtomPoolSize(0),
-    numAtomDefragSkips(0),
+    atomIdPool(0, 20, 100),
     molecules(this),
     selectedMolecules(this),
-    currMoleculeId(0),
-    lastMoleculePoolSize(0),
-    numMoleculeDefragSkips(0),
+    moleculeIdPool(0, 20,100),
     molecules_deprecated(new MoleculeListClass(this))
 {
@@ -873 +668 @@
 // Explicit instantiation of the singleton mechanism at this point
 
+// moleculeId_t und atomId_t sind gleicher Basistyp, deswegen nur einen von beiden konstruieren
+CONSTRUCT_IDPOOL(moleculeId_t)
+
 CONSTRUCT_SINGLETON(World)
 

src/World.hpp

@@ -9 +9 @@
 #define WORLD_HPP_
 
+// include config.h
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 /*********************************************** includes ***********************************/
 
@@ -18 +23 @@
 #include <boost/shared_ptr.hpp>
 
-#include "types.hpp"
 #include "Actions/ActionTrait.hpp"
+#include "AtomSet.hpp"
 #include "Descriptors/SelectiveIterator.hpp"
 #include "CodePatterns/Observer.hpp"
@@ -26 +31 @@
 #include "CodePatterns/ObservedContainer.hpp"
 #include "CodePatterns/Range.hpp"
-#include "AtomSet.hpp"
-
-// include config.h
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "IdPool.hpp"
+#include "types.hpp"
 
 // forward declarations
@@ -443 +444 @@
   AtomSet atoms;
   AtomSet selectedAtoms;
-  typedef std::set<range<atomId_t> > atomIdPool_t;
   /**
    * stores the pool for all available AtomIds below currAtomId
@@ -449 +449 @@
    * The pool contains ranges of free ids in the form [bottom,top).
    */
-  atomIdPool_t atomIdPool;
-  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;
+  IdPool<atomId_t> atomIdPool;
 
   MoleculeSet molecules;
   MoleculeSet selectedMolecules;
-  typedef std::set<range<atomId_t> > moleculeIdPool_t;
   /**
    * stores the pool for all available AtomIds below currAtomId
@@ -462 +458 @@
    * 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;
+  IdPool<moleculeId_t> moleculeIdPool;
+
 private:
   /**

src/documentation/constructs/world.dox

@@ -108 +108 @@
  * respectively.
  *
+ * \subsection world-internals-notes Notes on internals of the World
+ *
+ * \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
+ *
+ * For the latter 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