Changeset d927ab

Timestamp:

Mar 28, 2012, 3:17:39 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:

5e6534

Parents:

3e1b7b

git-author:

Frederik Heber <heber@…> (03/22/12 17:39:02)

git-committer:

Frederik Heber <heber@…> (03/28/12 15:17:39)

Message:

Renamed AtomByShape -> AtomsByShape and speedup due to LinkedCell usage.

• since each Shape implements Shape::getRadius() and ::getCenter(), we may use the LinkedCell construct to obtain a smaller neighborhood faster.

Location:

src

Files:

• Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.cpp (modified) (3 diffs)
• Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.cpp (modified) (3 diffs)
• Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.cpp (modified) (3 diffs)
• Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.cpp (modified) (3 diffs)
• Descriptors/AtomShapeDescriptor.cpp (modified) (1 diff)
• Descriptors/AtomShapeDescriptor.hpp (modified) (1 diff)
• Descriptors/AtomShapeDescriptor_impl.hpp (modified) (1 diff)

src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.cpp

@@ -54 +54 @@
   LOG(1, "Selecting all atoms inside a rotated " << RotationMatrix << " cuboid at " << params.position << " and extension of " << params.extension << ".");
   Shape s = translate(transform(stretch(Cuboid(),params.extension),RotationMatrix),params.position);
-  std::vector<atom *> selectedAtoms = World::getInstance().getAllAtoms(AtomsBySelection() && AtomByShape(s));
-  World::getInstance().selectAllAtoms(AtomByShape(s));
+  std::vector<atom *> selectedAtoms = World::getInstance().getAllAtoms(AtomsBySelection() && AtomsByShape(s));
+  World::getInstance().selectAllAtoms(AtomsByShape(s));
   LOG(0, World::getInstance().countSelectedAtoms() << " atoms selected.");
   return Action::state_ptr(new SelectionAllAtomsInsideCuboidState(selectedAtoms, s, params));
@@ -63 +63 @@
   SelectionAllAtomsInsideCuboidState *state = assert_cast<SelectionAllAtomsInsideCuboidState*>(_state.get());
 
-  World::getInstance().unselectAllAtoms(AtomByShape(state->s));
+  World::getInstance().unselectAllAtoms(AtomsByShape(state->s));
   BOOST_FOREACH(atom *_atom, state->selectedAtoms)
     World::getInstance().selectAtom(_atom);
@@ -74 +74 @@
   RealSpaceMatrix RotationMatrix;
 
-  World::getInstance().selectAllAtoms(AtomByShape(state->s));
+  World::getInstance().selectAllAtoms(AtomsByShape(state->s));
 
   return Action::state_ptr(_state);

src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.cpp

@@ -49 +49 @@
   LOG(1, "Selecting all atoms inside a sphere at " << params.position << " with radius " << params.radius << ".");
   Shape s = translate(resize(Sphere(),params.radius),params.position);
-  std::vector<atom *> selectedAtoms = World::getInstance().getAllAtoms(AtomsBySelection() && AtomByShape(s));
-  World::getInstance().selectAllAtoms(AtomByShape(s));
+  std::vector<atom *> selectedAtoms = World::getInstance().getAllAtoms(AtomsBySelection() && AtomsByShape(s));
+  World::getInstance().selectAllAtoms(AtomsByShape(s));
   LOG(0, World::getInstance().countSelectedAtoms() << " atoms selected.");
   return Action::state_ptr(new SelectionAllAtomsInsideSphereState(selectedAtoms, s, params));
@@ -58 +58 @@
   SelectionAllAtomsInsideSphereState *state = assert_cast<SelectionAllAtomsInsideSphereState*>(_state.get());
 
-  World::getInstance().unselectAllAtoms(AtomByShape(state->s));
+  World::getInstance().unselectAllAtoms(AtomsByShape(state->s));
   BOOST_FOREACH(atom *_atom, state->selectedAtoms)
     World::getInstance().selectAtom(_atom);
@@ -68 +68 @@
   SelectionAllAtomsInsideSphereState *state = assert_cast<SelectionAllAtomsInsideSphereState*>(_state.get());
 
-  World::getInstance().selectAllAtoms(AtomByShape(state->s));
+  World::getInstance().selectAllAtoms(AtomsByShape(state->s));
 
   return Action::state_ptr(_state);

src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.cpp

@@ -53 +53 @@
   LOG(1, "Unselecting all atoms inside a rotated " << RotationMatrix << " cuboid at " << params.position << " and extension of " << params.extension << ".");
   Shape s = translate(transform(stretch(Cuboid(),params.extension),RotationMatrix),params.position);
-  std::vector<atom *> unselectedAtoms = World::getInstance().getAllAtoms((!AtomsBySelection()) && AtomByShape(s));
-  World::getInstance().unselectAllAtoms(AtomByShape(s));
+  std::vector<atom *> unselectedAtoms = World::getInstance().getAllAtoms((!AtomsBySelection()) && AtomsByShape(s));
+  World::getInstance().unselectAllAtoms(AtomsByShape(s));
   LOG(0, World::getInstance().countSelectedAtoms() << " atoms remain selected.");
   return Action::state_ptr(new SelectionNotAllAtomsInsideCuboidState(unselectedAtoms, s, params));
@@ -62 +62 @@
   SelectionNotAllAtomsInsideCuboidState *state = assert_cast<SelectionNotAllAtomsInsideCuboidState*>(_state.get());
 
-  World::getInstance().selectAllAtoms(AtomByShape(state->s));
+  World::getInstance().selectAllAtoms(AtomsByShape(state->s));
   BOOST_FOREACH(atom *_atom, state->unselectedAtoms)
     World::getInstance().unselectAtom(_atom);
@@ -73 +73 @@
   RealSpaceMatrix RotationMatrix;
 
-  World::getInstance().unselectAllAtoms(AtomByShape(state->s));
+  World::getInstance().unselectAllAtoms(AtomsByShape(state->s));
 
   return Action::state_ptr(_state);

src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.cpp

@@ -49 +49 @@
   LOG(1, "Unselecting all atoms inside a sphere at " << params.position << " with radius " << params.radius << ".");
   Shape s = translate(resize(Sphere(),params.radius),params.position);
-  std::vector<atom *> unselectedAtoms = World::getInstance().getAllAtoms((!AtomsBySelection()) && AtomByShape(s));
-  World::getInstance().unselectAllAtoms(AtomByShape(s));
+  std::vector<atom *> unselectedAtoms = World::getInstance().getAllAtoms((!AtomsBySelection()) && AtomsByShape(s));
+  World::getInstance().unselectAllAtoms(AtomsByShape(s));
   LOG(0, World::getInstance().countSelectedAtoms() << " atoms remain selected.");
   return Action::state_ptr(new SelectionNotAllAtomsInsideSphereState(unselectedAtoms, s, params));
@@ -58 +58 @@
   SelectionNotAllAtomsInsideSphereState *state = assert_cast<SelectionNotAllAtomsInsideSphereState*>(_state.get());
 
-  World::getInstance().selectAllAtoms(AtomByShape(state->s));
+  World::getInstance().selectAllAtoms(AtomsByShape(state->s));
   BOOST_FOREACH(atom *_atom, state->unselectedAtoms)
     World::getInstance().unselectAtom(_atom);
@@ -68 +68 @@
   SelectionNotAllAtomsInsideSphereState *state = assert_cast<SelectionNotAllAtomsInsideSphereState*>(_state.get());
 
-  World::getInstance().unselectAllAtoms(AtomByShape(state->s));
+  World::getInstance().unselectAllAtoms(AtomsByShape(state->s));
 
   return Action::state_ptr(_state);

src/Descriptors/AtomShapeDescriptor.cpp

@@ -35 +35 @@
 }
 
+atom* AtomShapeDescriptor_impl::find(){
+  LinkedCell::LinkedCell_View view = World::getInstance().getLinkedCell(shape.getRadius());
+  LinkedCell::LinkedList list = view.getPointsInsideSphere(shape.getRadius(), shape.getCenter());
+  for (LinkedCell::LinkedList::iterator iter = list.begin(); iter != list.end(); ++iter) {
+    atom * const _atom = static_cast<atom *>(const_cast<TesselPoint *>(*iter));
+    if (shape.isInside(_atom->getPosition()))
+      return _atom;
+  }
+  return NULL;
+}
 
-AtomDescriptor AtomByShape(const Shape &shape){
+std::vector<atom*> AtomShapeDescriptor_impl::findAll(){
+  LinkedCell::LinkedCell_View view = World::getInstance().getLinkedCell(shape.getRadius());
+  LinkedCell::LinkedList list = view.getPointsInsideSphere(shape.getRadius(), shape.getCenter());
+  std::vector<atom*> res;
+  for (LinkedCell::LinkedList::iterator iter = list.begin(); iter != list.end(); ++iter) {
+    atom * const _atom = static_cast<atom *>(const_cast<TesselPoint *>(*iter));
+    if (shape.isInside(_atom->getPosition()))
+      res.push_back(_atom);
+  }
+  return res;
+}
+
+
+AtomDescriptor AtomsByShape(const Shape &shape){
   return AtomDescriptor(AtomDescriptor::impl_ptr(new AtomShapeDescriptor_impl(shape)));
 }

src/Descriptors/AtomShapeDescriptor.hpp

@@ -20 +20 @@
 class Shape;
 
-AtomDescriptor AtomByShape(const Shape &shape);
+AtomDescriptor AtomsByShape(const Shape &shape);
 
 #endif /* ATOMSHAPEDESCRIPTOR_HPP_ */

src/Descriptors/AtomShapeDescriptor_impl.hpp

@@ -27 +27 @@
   bool predicate(std::pair<atomId_t,atom*> atom);
 private:
+  virtual atom* find();
+  virtual std::vector<atom*> findAll();
+
   Shape shape;
 };