Changeset eff536 for src

Timestamp:

Nov 15, 2012, 5:31:07 PM (12 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:

d0cd6d

Parents:

09eaac

git-author:

Michael Ankele <ankele@…> (09/07/12 13:55:53)

git-committer:

Frederik Heber <heber@…> (11/15/12 17:31:07)

Message:

AllAtomsInsideCuboid/SphereAction > AllAtomsInsideVolumeAction (using ShapeFactory)

Location:

src/Actions

Files:

• GlobalListOfActions.hpp (modified) (2 diffs)
• Makefile.am (modified) (6 diffs)
• SelectionAction/Atoms/AllAtomsInsideCuboidAction.cpp (deleted)
• SelectionAction/Atoms/AllAtomsInsideCuboidAction.def (deleted)
• SelectionAction/Atoms/AllAtomsInsideCuboidAction.hpp (deleted)
• SelectionAction/Atoms/AllAtomsInsideSphereAction.def (deleted)
• SelectionAction/Atoms/AllAtomsInsideSphereAction.hpp (deleted)
• SelectionAction/Atoms/AllAtomsInsideVolumeAction.cpp (moved) (moved from src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.cpp ) (4 diffs)
• SelectionAction/Atoms/AllAtomsInsideVolumeAction.def (added)
• SelectionAction/Atoms/AllAtomsInsideVolumeAction.hpp (added)
• SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.cpp (deleted)
• SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.def (deleted)
• SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.hpp (deleted)
• SelectionAction/Atoms/NotAllAtomsInsideSphereAction.def (deleted)
• SelectionAction/Atoms/NotAllAtomsInsideSphereAction.hpp (deleted)
• SelectionAction/Atoms/NotAllAtomsInsideVolumeAction.cpp (moved) (moved from src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.cpp ) (4 diffs)
• SelectionAction/Atoms/NotAllAtomsInsideVolumeAction.def (added)
• SelectionAction/Atoms/NotAllAtomsInsideVolumeAction.hpp (added)

src/Actions/GlobalListOfActions.hpp

@@ -101 +101 @@
   (SelectionNotAtomById) \
   (SelectionNotAtomByOrder) \
-  (SelectionAllAtomsInsideCuboid) \
   (SelectionAllAtoms) \
   (SelectionClearAllAtoms) \
@@ -107 +106 @@
   (SelectionNotAllAtoms) \
   (SelectionNotAtomByElement) \
-  (SelectionAllAtomsInsideSphere) \
+  (SelectionAllAtomsInsideVolume) \
   (SelectionAllAtomsOfMolecule) \
-  (SelectionNotAllAtomsInsideSphere) \
+  (SelectionNotAllAtomsInsideVolume) \
   (SelectionAtomByElement) \
   (SelectionNotAllAtomsOfMolecule) \
-  (SelectionNotAllAtomsInsideCuboid) \
   (SelectionAtomById) \
   (SelectionAtomByOrder) \

src/Actions/Makefile.am

@@ -306 +306 @@
 SELECTIONATOMACTIONSOURCE = \
   Actions/SelectionAction/Atoms/AllAtomsAction.cpp \
-  Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.cpp \
-  Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.cpp \
+  Actions/SelectionAction/Atoms/AllAtomsInsideVolumeAction.cpp \
   Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.cpp \
   Actions/SelectionAction/Atoms/AtomByElementAction.cpp \
@@ -315 +314 @@
   Actions/SelectionAction/Atoms/InvertAtomsAction.cpp \
   Actions/SelectionAction/Atoms/NotAllAtomsAction.cpp \
-  Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.cpp \
-  Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.cpp \
+  Actions/SelectionAction/Atoms/NotAllAtomsInsideVolumeAction.cpp \
   Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.cpp \
   Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp \
@@ -323 +321 @@
 SELECTIONATOMACTIONHEADER = \
   Actions/SelectionAction/Atoms/AllAtomsAction.hpp \
-  Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.hpp \
-  Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.hpp \
+  Actions/SelectionAction/Atoms/AllAtomsInsideVolumeAction.hpp \
   Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.hpp \
   Actions/SelectionAction/Atoms/AtomByElementAction.hpp \
@@ -332 +329 @@
   Actions/SelectionAction/Atoms/InvertAtomsAction.hpp \
   Actions/SelectionAction/Atoms/NotAllAtomsAction.hpp \
-  Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.hpp \
-  Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.hpp \
+  Actions/SelectionAction/Atoms/NotAllAtomsInsideVolumeAction.hpp \
   Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.hpp \
   Actions/SelectionAction/Atoms/NotAtomByElementAction.hpp \
@@ -340 +336 @@
 SELECTIONATOMACTIONDEFS = \
   Actions/SelectionAction/Atoms/AllAtomsAction.def \
-  Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.def \
-  Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.def \
+  Actions/SelectionAction/Atoms/AllAtomsInsideVolumeAction.def \
   Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.def \
   Actions/SelectionAction/Atoms/AtomByElementAction.def \
@@ -349 +344 @@
   Actions/SelectionAction/Atoms/InvertAtomsAction.def \
   Actions/SelectionAction/Atoms/NotAllAtomsAction.def \
-  Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.def \
-  Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.def \
+  Actions/SelectionAction/Atoms/NotAllAtomsInsideVolumeAction.def \
   Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.def \
   Actions/SelectionAction/Atoms/NotAtomByElementAction.def \

src/Actions/SelectionAction/Atoms/AllAtomsInsideVolumeAction.cpp

@@ -22 +22 @@
 
 /*
- * AllAtomsInsideSphereAction.cpp
+ * AllAtomsInsideVolumeAction.cpp
  *
  *  Created on: Aug 9, 2010
- *      Author: heber
+ *      Author: heber, ankele
  */
 
@@ -41 +41 @@
 #include "CodePatterns/Verbose.hpp"
 #include "LinearAlgebra/Vector.hpp"
-#include "Shapes/BaseShapes.hpp"
-#include "Shapes/Shape.hpp"
-#include "Shapes/ShapeOps.hpp"
+#include "Shapes/ShapeFactory.hpp"
 #include "World.hpp"
 
@@ -50 +48 @@
 #include <string>
 
-#include "AllAtomsInsideSphereAction.hpp"
+#include "AllAtomsInsideVolumeAction.hpp"
 
 using namespace MoleCuilder;
 
 // and construct the stuff
-#include "AllAtomsInsideSphereAction.def"
+#include "AllAtomsInsideVolumeAction.def"
 #include "Action_impl_pre.hpp"
 /** =========== define the function ====================== */
-Action::state_ptr SelectionAllAtomsInsideSphereAction::performCall() {
-  LOG(1, "Selecting all atoms inside a sphere at " << params.position.get() << " with radius " << params.radius.get() << ".");
-  Shape s = translate(resize(Sphere(),params.radius.get()),params.position.get());
+Action::state_ptr SelectionAllAtomsInsideVolumeAction::performCall() {
+  LOG(1, "Selecting all atoms inside a volume.");
+  Shape s = ShapeFactory::getInstance().produce();
   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));
+  return Action::state_ptr(new SelectionAllAtomsInsideVolumeState(selectedAtoms, params));
 }
 
-Action::state_ptr SelectionAllAtomsInsideSphereAction::performUndo(Action::state_ptr _state) {
-  SelectionAllAtomsInsideSphereState *state = assert_cast<SelectionAllAtomsInsideSphereState*>(_state.get());
+Action::state_ptr SelectionAllAtomsInsideVolumeAction::performUndo(Action::state_ptr _state) {
+  SelectionAllAtomsInsideVolumeState *state = assert_cast<SelectionAllAtomsInsideVolumeState*>(_state.get());
 
-  World::getInstance().unselectAllAtoms(AtomsByShape(state->s));
+  Shape s = ShapeFactory::getInstance().produce();
+  World::getInstance().unselectAllAtoms(AtomsByShape(s));
   BOOST_FOREACH(atom *_atom, state->selectedAtoms)
     World::getInstance().selectAtom(_atom);
@@ -77 +76 @@
 }
 
-Action::state_ptr SelectionAllAtomsInsideSphereAction::performRedo(Action::state_ptr _state){
-  SelectionAllAtomsInsideSphereState *state = assert_cast<SelectionAllAtomsInsideSphereState*>(_state.get());
+Action::state_ptr SelectionAllAtomsInsideVolumeAction::performRedo(Action::state_ptr _state){
+  //SelectionAllAtomsInsideVolumeState *state = assert_cast<SelectionAllAtomsInsideVolumeState*>(_state.get());
 
-  World::getInstance().selectAllAtoms(AtomsByShape(state->s));
+  Shape s = ShapeFactory::getInstance().produce();
+  World::getInstance().selectAllAtoms(AtomsByShape(s));
 
   return Action::state_ptr(_state);
 }
 
-bool SelectionAllAtomsInsideSphereAction::canUndo() {
+bool SelectionAllAtomsInsideVolumeAction::canUndo() {
   return true;
 }
 
-bool SelectionAllAtomsInsideSphereAction::shouldUndo() {
+bool SelectionAllAtomsInsideVolumeAction::shouldUndo() {
   return true;
 }

src/Actions/SelectionAction/Atoms/NotAllAtomsInsideVolumeAction.cpp

@@ -22 +22 @@
 
 /*
- * NotAllAtomsInsideSphereAction.cpp
+ * NotAllAtomsInsideVolumeAction.cpp
  *
  *  Created on: Aug 9, 2010
@@ -41 +41 @@
 #include "CodePatterns/Verbose.hpp"
 #include "LinearAlgebra/Vector.hpp"
-#include "Shapes/BaseShapes.hpp"
-#include "Shapes/Shape.hpp"
-#include "Shapes/ShapeOps.hpp"
+#include "Shapes/ShapeFactory.hpp"
 #include "World.hpp"
 
@@ -50 +48 @@
 #include <string>
 
-#include "NotAllAtomsInsideSphereAction.hpp"
+#include "NotAllAtomsInsideVolumeAction.hpp"
 
 using namespace MoleCuilder;
 
 // and construct the stuff
-#include "NotAllAtomsInsideSphereAction.def"
+#include "NotAllAtomsInsideVolumeAction.def"
 #include "Action_impl_pre.hpp"
 /** =========== define the function ====================== */
-Action::state_ptr SelectionNotAllAtomsInsideSphereAction::performCall() {
-  LOG(1, "Unselecting all atoms inside a sphere at " << params.position.get() << " with radius " << params.radius.get() << ".");
-  Shape s = translate(resize(Sphere(),params.radius.get()),params.position.get());
+Action::state_ptr SelectionNotAllAtomsInsideVolumeAction::performCall() {
+  LOG(1, "Unselecting all atoms inside a volume.");
+  Shape s = ShapeFactory::getInstance().produce();
   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));
+  return Action::state_ptr(new SelectionNotAllAtomsInsideVolumeState(unselectedAtoms, params));
 }
 
-Action::state_ptr SelectionNotAllAtomsInsideSphereAction::performUndo(Action::state_ptr _state) {
-  SelectionNotAllAtomsInsideSphereState *state = assert_cast<SelectionNotAllAtomsInsideSphereState*>(_state.get());
+Action::state_ptr SelectionNotAllAtomsInsideVolumeAction::performUndo(Action::state_ptr _state) {
+  SelectionNotAllAtomsInsideVolumeState *state = assert_cast<SelectionNotAllAtomsInsideVolumeState*>(_state.get());
 
-  World::getInstance().selectAllAtoms(AtomsByShape(state->s));
+  Shape s = ShapeFactory::getInstance().produce();
+  World::getInstance().selectAllAtoms(AtomsByShape(s));
   BOOST_FOREACH(atom *_atom, state->unselectedAtoms)
     World::getInstance().unselectAtom(_atom);
@@ -77 +76 @@
 }
 
-Action::state_ptr SelectionNotAllAtomsInsideSphereAction::performRedo(Action::state_ptr _state){
-  SelectionNotAllAtomsInsideSphereState *state = assert_cast<SelectionNotAllAtomsInsideSphereState*>(_state.get());
+Action::state_ptr SelectionNotAllAtomsInsideVolumeAction::performRedo(Action::state_ptr _state){
+  //SelectionNotAllAtomsInsideVolumeState *state = assert_cast<SelectionNotAllAtomsInsideVolumeState*>(_state.get());
 
-  World::getInstance().unselectAllAtoms(AtomsByShape(state->s));
+  Shape s = ShapeFactory::getInstance().produce();
+  World::getInstance().unselectAllAtoms(AtomsByShape(s));
 
   return Action::state_ptr(_state);
 }
 
-bool SelectionNotAllAtomsInsideSphereAction::canUndo() {
+bool SelectionNotAllAtomsInsideVolumeAction::canUndo() {
   return true;
 }
 
-bool SelectionNotAllAtomsInsideSphereAction::shouldUndo() {
+bool SelectionNotAllAtomsInsideVolumeAction::shouldUndo() {
   return true;
 }