Changeset fa0b18

Timestamp:

Jul 8, 2010, 12:51:15 PM (14 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:

40f928

Parents:

61ea5b

Message:

Added Observed and Selectiv iterators over internal Structures of the World.

Location:

src

Files:

• Actions/AtomsCalculation_impl.hpp (modified) (1 diff)
• Actions/ManipulateAtomsProcess.cpp (modified) (1 diff)
• Descriptors/AtomIdDescriptor.cpp (modified) (1 diff)
• World.cpp (modified) (3 diffs)
• World.hpp (modified) (6 diffs)

src/Actions/AtomsCalculation_impl.hpp

@@ -33 +33 @@
   Process::setMaxSteps(steps);
   Process::start();
-  for(World::AtomIterator iter=world->getAtomIter(descr);iter!=world->atomEnd();++iter){
+  for(World::internal_AtomIterator
+      iter=world->getAtomIter_internal(descr);
+      iter!=world->atomEnd_internal();
+      ++iter){
+
     Process::setCurrStep(iter.getCount());
     res->push_back(op(*iter));

src/Actions/ManipulateAtomsProcess.cpp

@@ -53 +53 @@
   setMaxSteps(world->numAtoms());
   start();
-  for(World::AtomIterator iter=world->getAtomIter(descr);iter!=world->atomEnd();++iter){
+  for(World::internal_AtomIterator
+      iter=world->getAtomIter_internal(descr);
+      iter!=world->atomEnd_internal();
+      ++iter){
+
     setCurrStep(iter.getCount());
     operation(*iter);

src/Descriptors/AtomIdDescriptor.cpp

@@ -12 +12 @@
 
 #include "atom.hpp"
+#include "AtomSet_impl.hpp"
 
 using namespace std;

src/World.cpp

@@ -9 +9 @@
 
 #include "World.hpp"
+#include "AtomSet_impl.hpp"
 
 #include "atom.hpp"
@@ -265 +266 @@
 /******************************* Iterators ********************************/
 
+// external parts with observers
+
+CONSTRUCT_SELECTIVE_ITERATOR(atom*,World::AtomSet,AtomDescriptor);
+
+World::AtomIterator
+World::getAtomIter(AtomDescriptor descr){
+    return AtomIterator(descr,atoms);
+}
+
+World::AtomIterator
+World::getAtomIter(){
+    return AtomIterator(AllAtoms(),atoms);
+}
+
+World::AtomIterator
+World::atomEnd(){
+  return AtomIterator(AllAtoms(),atoms,atoms.end());
+}
+
+// Internal parts, without observers
+
 // Build the AtomIterator from template
-CONSTRUCT_SELECTIVE_ITERATOR(atom*,World::AtomSet,AtomDescriptor);
-
-
-World::AtomIterator World::getAtomIter(AtomDescriptor descr){
-  return AtomIterator(descr,atoms);
-}
-
-World::AtomIterator World::atomEnd(){
-  return AtomIterator(AllAtoms(),atoms,atoms.end());
+CONSTRUCT_SELECTIVE_ITERATOR(atom*,World::AtomSet::set_t,AtomDescriptor);
+
+
+World::internal_AtomIterator
+World::getAtomIter_internal(AtomDescriptor descr){
+  return internal_AtomIterator(descr,atoms.getContent());
+}
+
+World::internal_AtomIterator
+World::atomEnd_internal(){
+  return internal_AtomIterator(AllAtoms(),atoms.getContent(),atoms.end_internal());
 }
 
@@ -296 +320 @@
     Thermostats(new ThermoStatContainer),
     ExitFlag(0),
-    atoms(),
+    atoms(this),
     currAtomId(0),
     molecules(),

src/World.hpp

@@ -23 +23 @@
 #include "Patterns/Cacheable.hpp"
 #include "Patterns/Singleton.hpp"
+#include "AtomSet.hpp"
 
 // include config.h
@@ -45 +46 @@
 class ThermoStatContainer;
 
+
 /****************************************** forward declarations *****************************/
 
@@ -67 +69 @@
 
   // Types for Atom and Molecule structures
-  typedef std::map<atomId_t,atom*> AtomSet;
+  typedef _AtomSet AtomSet;
   typedef std::map<moleculeId_t,molecule*> MoleculeSet;
 
@@ -216 +218 @@
   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 ca 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();
+
 protected:
-  /**** Iterators to use internal data structures */
+  /****
+   * 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.*/
 
   // Atoms
-  typedef SelectiveIterator<atom*,AtomSet,AtomDescriptor> AtomIterator;
+  typedef AtomSet::selective_internal_iterator internal_AtomIterator;
 
   /**
@@ -226 +251 @@
    * used for internal purposes, like AtomProcesses and AtomCalculations.
    */
-  AtomIterator getAtomIter(AtomDescriptor descr);
+  internal_AtomIterator getAtomIter_internal(AtomDescriptor descr);
 
   /**
@@ -234 +259 @@
    * used for internal purposes, like AtomProcesses and AtomCalculations.
    */
-  AtomIterator atomEnd();
+  internal_AtomIterator atomEnd_internal();
 
   // Molecules