Changeset ea7a50 for src

Timestamp:

Feb 22, 2012, 11:26:49 AM (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:

3dfd9c

Parents:

52ed5b

git-author:

Frederik Heber <heber@…> (01/06/12 17:53:45)

git-committer:

Frederik Heber <heber@…> (02/22/12 11:26:49)

Message:

Rewrote some of the descriptors such that they access World's AtomSet and MoleculeSet directly.

• this is the way they are intended. They are friends of the World and may use the sets directly without causing update()s although they return non- const references. This is because here we need not be careful as no atoms are destroyed or added.
• In most cases we had implemented both predicate() and new find() and findAll() that were not necessary (default find..() would do the job better).
• This concerned: AtomOfMoleculeSelectionDescriptor, MoleculeNameDescriptor, MoleculeOfAtomSelectionDescriptor, MoleculeOrderDescriptor, and MoleculePtrDescriptor.
• We left the specific implementation for AtomIdDescriptor and MoleculeIdDescriptor as they directly access World's Atom- and MoleculeSet and may thus find ids significantly faster.
• NOTE: so far some tests are broken and this needs to be fixed yet.

Location:

src

Files:

• Descriptors/AtomOfMoleculeSelectionDescriptor.cpp (modified) (3 diffs)
• Descriptors/AtomOfMoleculeSelectionDescriptor_impl.hpp (modified) (1 diff)
• Descriptors/MoleculeNameDescriptor.cpp (modified) (1 diff)
• Descriptors/MoleculeNameDescriptor_impl.hpp (modified) (1 diff)
• Descriptors/MoleculeOfAtomSelectionDescriptor.cpp (modified) (3 diffs)
• Descriptors/MoleculeOfAtomSelectionDescriptor_impl.hpp (modified) (1 diff)
• Descriptors/MoleculeOrderDescriptor.cpp (modified) (3 diffs)
• Descriptors/MoleculeOrderDescriptor_impl.hpp (modified) (1 diff)
• Descriptors/MoleculePtrDescriptor.cpp (modified) (1 diff)
• Descriptors/MoleculePtrDescriptor_impl.hpp (modified) (1 diff)
• World.hpp (modified) (1 diff)
• documentation/constructs/descriptors.dox (modified) (1 diff)

src/Descriptors/AtomOfMoleculeSelectionDescriptor.cpp

@@ -37 +37 @@
 
 atom* AtomOfMoleculeSelectionDescriptor_impl::find(){
-  World &instance = World::getInstance();
-  for (World::MoleculeSelectionIterator iter = instance.beginMoleculeSelection();
-      iter != instance.endMoleculeSelection();
+  World::MoleculeSet &set = getSelectedMolecules();
+  for (World::MoleculeSet::internal_iterator iter = set.begin_internal();
+      iter != set.end_internal();
       ++iter) {
     if (iter->second->begin() != iter->second->end())
@@ -49 +49 @@
 std::vector<atom*> AtomOfMoleculeSelectionDescriptor_impl::findAll(){
   std::vector<atom*> res;
-  World &instance = World::getInstance();
-  for (World::MoleculeSelectionIterator iter = instance.beginMoleculeSelection();
-      iter != instance.endMoleculeSelection();
+  World::MoleculeSet &set = getSelectedMolecules();
+  for (World::MoleculeSet::internal_iterator iter = set.begin_internal();
+      iter != set.end_internal();
       ++iter) {
     std::copy(iter->second->begin(), iter->second->end(), res.begin());
@@ -58 +58 @@
 }
 
+World::MoleculeSet& AtomOfMoleculeSelectionDescriptor_impl::getSelectedMolecules(){
+  return World::getInstance().selectedMolecules;
+}
+
 AtomDescriptor AtomsByMoleculeSelection(){
   return AtomDescriptor(AtomDescriptor::impl_ptr(new AtomOfMoleculeSelectionDescriptor_impl()));

src/Descriptors/AtomOfMoleculeSelectionDescriptor_impl.hpp

@@ -26 +26 @@
   virtual atom* find();
   virtual std::vector<atom*> findAll();
+
+  World::MoleculeSet& getSelectedMolecules();
 };
 

src/Descriptors/MoleculeNameDescriptor.cpp

@@ -42 +42 @@
   return MoleculeDescriptor(MoleculeDescriptor::impl_ptr(new MoleculeNameDescriptor_impl(name)));
 }
-
-molecule *MoleculeNameDescriptor_impl::find(){
-  World::MoleculeSet &molecules = getMolecules();
-  World::MoleculeSet::iterator res = molecules.begin();
-  for (; res != molecules.end(); res++)
-    if (res->second->name == name)
-      break;
-  return (res!=molecules.end())?((*res).second):0;
-}
-
-vector<molecule*> MoleculeNameDescriptor_impl::findAll(){
-  vector<molecule *> foundMolecules;
-  World::MoleculeSet &molecules = getMolecules();
-  World::MoleculeSet::iterator res = molecules.begin();
-  for (; res != molecules.end(); res++)
-    if (res->second->name == name)
-      foundMolecules.push_back(res->second);
-  return foundMolecules;
-}

src/Descriptors/MoleculeNameDescriptor_impl.hpp

@@ -18 +18 @@
   bool predicate(std::pair<moleculeId_t,molecule*> molecule);
 
-protected:
-  virtual molecule *find();
-  virtual std::vector<molecule*> findAll();
 private:
   std::string name;

src/Descriptors/MoleculeOfAtomSelectionDescriptor.cpp

@@ -43 +43 @@
 
 molecule* MoleculeOfAtomSelectionDescriptor_impl::find(){
-  World &instance = World::getInstance();
-  for (World::AtomSelectionIterator iter = instance.beginAtomSelection();
-      iter != instance.endAtomSelection();
+  World::AtomSet &set = getSelectedAtoms();
+  for (World::AtomSet::internal_iterator iter = set.begin_internal();
+      iter != set.end_internal();
       ++iter) {
-    if (iter->second->getMolecule() != NULL)
+    if (iter->second->getMolecule())
       return iter->second->getMolecule();
   }
@@ -57 +57 @@
   std::set<molecule*> temp;
   std::pair< std::set<molecule*>::iterator, bool> inserter;
-  World &instance = World::getInstance();
-  for (World::AtomSelectionIterator iter = instance.beginAtomSelection();
-      iter != instance.endAtomSelection();
+  World::AtomSet &set = getSelectedAtoms();
+  for (World::AtomSet::internal_iterator iter = set.begin_internal();
+      iter != set.end_internal();
       ++iter) {
-    if (iter->second->getMolecule() != NULL) {
+    if (iter->second->getMolecule()) {
       inserter = temp.insert( iter->second->getMolecule() );
       if (inserter.second)
@@ -70 +70 @@
 }
 
+World::AtomSet& MoleculeOfAtomSelectionDescriptor_impl::getSelectedAtoms(){
+  return World::getInstance().selectedAtoms;
+}
+
 MoleculeDescriptor MoleculesByAtomSelection(){
   return MoleculeDescriptor(MoleculeDescriptor::impl_ptr(new MoleculeOfAtomSelectionDescriptor_impl()));

src/Descriptors/MoleculeOfAtomSelectionDescriptor_impl.hpp

@@ -26 +26 @@
   virtual molecule* find();
   virtual std::vector<molecule*> findAll();
+
+  World::AtomSet& getSelectedAtoms();
 };
 

src/Descriptors/MoleculeOrderDescriptor.cpp

@@ -45 +45 @@
 }
 
-molecule *MoleculeOrderDescriptor_impl::find(){
+World::MoleculeSet& MoleculeOrderDescriptor_impl::getMolecules()
+{
+  return World::getInstance().molecules;
+}
+
+molecule* MoleculeOrderDescriptor_impl::find() {
   World::MoleculeSet &molecules = getMolecules();
 
@@ -53 +58 @@
     return NULL;
   } else if (id > 0) {
-    World::MoleculeSet::const_iterator res = molecules.begin();
-    for (; res != molecules.end(); ++res) { // when iterator is normal, ++ goes forward!
+    World::MoleculeSet::internal_iterator res = molecules.begin_internal();
+    for (; res != molecules.end_internal(); ++res) { // when iterator is normal, ++ goes forward!
       ++i;
       if (id == i)
@@ -61 +66 @@
     mol = res->second;
   } else {
-    World::MoleculeSet::const_reverse_iterator res = molecules.rbegin();
-    for (; res != molecules.rend(); --res) {  // when iterator is reverse, ++ goes backward!
+    World::MoleculeSet::reverse_internal_iterator res = molecules.rbegin_internal();
+    for (; res != molecules.rend_internal(); --res) {  // when iterator is reverse, ++ goes backward!
       --i;
       if (id == i)

src/Descriptors/MoleculeOrderDescriptor_impl.hpp

@@ -21 +21 @@
   virtual molecule *find();
   virtual std::vector<molecule*> findAll();
+
+  World::MoleculeSet& getMolecules();
+
 private:
   int id;

src/Descriptors/MoleculePtrDescriptor.cpp

@@ -44 +44 @@
   return MoleculeDescriptor(MoleculeDescriptor::impl_ptr(new MoleculePtrDescriptor_impl(ptr)));
 }
-
-molecule *MoleculePtrDescriptor_impl::find(){
-  World::MoleculeSet &molecules = getMolecules();
-  World::MoleculeSet::iterator res = molecules.find(ptr->getId());
-  return (res!=molecules.end())?((*res).second):0;
-}
-
-vector<molecule*> MoleculePtrDescriptor_impl::findAll(){
-  molecule *res = find();
-  return (res)?(vector<molecule*>(1,res)):(vector<molecule*>());
-}

src/Descriptors/MoleculePtrDescriptor_impl.hpp

@@ -20 +20 @@
   bool predicate(std::pair<moleculeId_t,molecule*> molecule);
 
-protected:
-  virtual molecule *find();
-  virtual std::vector<molecule*> findAll();
 private:
   molecule * ptr;

src/World.hpp

@@ -87 +87 @@
 // coupling with descriptors over selection
 friend class AtomSelectionDescriptor_impl;
+friend class AtomOfMoleculeSelectionDescriptor_impl;
+friend class MoleculeOfAtomSelectionDescriptor_impl;
+friend class MoleculeOrderDescriptor_impl;
 friend class MoleculeSelectionDescriptor_impl;
 

src/documentation/constructs/descriptors.dox

@@ -73 +73 @@
  *  - currently selected molecules: MoleculesBySelection()
  *
+ * \subsection descriptors-world Descriptors and the World
  *
- * \date 2011-10-31
+ *  In the World we make heavy use of descriptors. However, the World is also
+ *  responsibly of informing connected Observers about removal or insertion of
+ *  atoms or molecules.
+ *  That's why its containers are protectedly constructed as ObservedContainers.
+ *  Whenever you walk through them with a normal iterator, afterwards an update()
+ *  is initiated. Only if you use a const_interator, this is prevented. But this
+ *  at the natural disadvantage that the reference may only be used in constant
+ *  environment.
+ *  Descriptors however may return non-const reference. And we rely heavily on
+ *  these to cheaply give us the correct reference for a given id, element type,
+ *  and so on. So how do we do this?
+ *
+ *  Some of the descriptors are friends of the World and may use its internal
+ *  containers directly, see AtomSelectionDescriptor_impl. Thus it can quickly
+ *  walk through the atoms and find the correct one without causing huge delays
+ *  by unnecessarily calling forth an update().
+ *
+ *
+ * \date 2012-01-06
  *
  */