Changeset 7e51e1 for src/Atom

Timestamp:

Aug 20, 2014, 12:58:29 PM (11 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:

1e45f1f

Parents:

442495

git-author:

Frederik Heber <heber@…> (08/02/14 08:00:14)

git-committer:

Frederik Heber <heber@…> (08/20/14 12:58:29)

Message:

Extended UndoRedoHelpers.

• added removeLastStep(), addNewStep().
• FIX: some UndoRedoHelper functions did not have const arguments as they should.
• FIX: AtomicInfo did not set/store force vector of atom.
• added AtomInfo::removeTrajectoryStep() and BondedParticleInfo::...() to allow for removal of a time step in the course of undoing. Enhanced AtomInfo, atom, and TesselPoint by removeSteps(), similar to UpdateSteps().

Location:

src/Atom

Files:

• AtomicInfo.cpp (modified) (3 diffs)
• AtomicInfo.hpp (modified) (1 diff)
• TesselPoint.cpp (modified) (1 diff)
• TesselPoint.hpp (modified) (1 diff)
• atom.cpp (modified) (1 diff)
• atom.hpp (modified) (1 diff)
• atom_atominfo.cpp (modified) (1 diff)
• atom_atominfo.hpp (modified) (3 diffs)
• atom_bondedparticleinfo.cpp (modified) (1 diff)
• atom_bondedparticleinfo.hpp (modified) (1 diff)

src/Atom/AtomicInfo.cpp

@@ -61 +61 @@
     charge(_atom.getCharge()),
     Velocity(_atom.getAtomicVelocity()),
+    Force(_atom.getAtomicForce()),
     FatherId(_atom.father->getId()),
     MolId(0),
@@ -82 +83 @@
   _atom.setCharge(charge);
   _atom.setAtomicVelocity(Velocity);
+  _atom.setAtomicForce(Force);
 
   // set old id
@@ -117 +119 @@
   MolId = AI.MolId;
   Velocity = AI.Velocity;
+  Force = AI.Force;
   Id = AI.Id;
   Nr = AI.Nr;

src/Atom/AtomicInfo.hpp

@@ -40 +40 @@
   double charge;
   Vector Velocity;
+  Vector Force;
   atomId_t FatherId;
   moleculeId_t MolId;

src/Atom/TesselPoint.cpp

@@ -58 +58 @@
 };
 
+void TesselPoint::removeSteps()
+{
+  ASSERT(0, "TesselPoint::removeSteps() should never be called, TesselPoints don't have trajectories.");
+  AtomInfo::removeTrajectoryStep();
+};
+
 TesselPoint * TesselPoint::getTesselPoint()
 {

src/Atom/TesselPoint.hpp

@@ -39 +39 @@
   virtual void UpdateSteps();
 
+  /** Pops the last step in all trajectory vectors.
+   *
+   * This allows to decrease all trajectories contained in different classes
+   * by one consistently. This is implemented by the topmost class which calls
+   * the real functions, \sa removeTrajectoryStep(), by all necessary subclasses.
+   */
+  virtual void removeSteps();
+
   /** Getter for this.
    *

src/Atom/atom.cpp

@@ -100 +100 @@
   // append to ListOfBonds vector
   BondedParticleInfo::AppendTrajectoryStep();
+}
+
+void atom::removeSteps()
+{
+  LOG(4,"atom::removeSteps() called.");
+  // append to position, velocity and force vector
+  AtomInfo::removeTrajectoryStep();
+  // append to ListOfBonds vector
+  BondedParticleInfo::removeTrajectoryStep();
 }
 

src/Atom/atom.hpp

@@ -66 +66 @@
    */
   virtual void UpdateSteps();
+
+  /** Pops the last step in all trajectory vectors.
+   *
+   * This allows to decrease all trajectories contained in different classes
+   * by one consistently. This is implemented by the topmost class which calls
+   * the real functions, \sa removeTrajectoryStep(), by all necessary subclasses.
+   */
+  virtual void removeSteps();
 
   /** Output of a single atom with given numbering.

src/Atom/atom_atominfo.cpp

@@ -105 +105 @@
   AtomicForce.push_back(zeroVec);
   LOG(5,"AtomInfo::AppendTrajectoryStep() called, size is ("
+      << AtomicPosition.size() << ","
+      << AtomicVelocity.size() << ","
+      << AtomicForce.size() << ")");
+}
+
+void AtomInfo::removeTrajectoryStep()
+{
+  NOTIFY(TrajectoryChanged);
+  AtomicPosition.pop_back();
+  AtomicVelocity.pop_back();
+  AtomicForce.pop_back();
+  LOG(5,"AtomInfo::removeTrajectoryStep() called, size is ("
       << AtomicPosition.size() << ","
       << AtomicVelocity.size() << ","

src/Atom/atom_atominfo.hpp

@@ -36 +36 @@
 class RealSpaceMatrix;
 
+namespace MoleCuilder {
+  void removeLastStep(const std::vector<atomId_t> &atoms);
+};
+
 /********************************************** declarations *******************************/
 
@@ -53 +57 @@
    */
   virtual void UpdateSteps()=0;
+
+  /** Pops the last step in all trajectory vectors.
+   *
+   * This allows to decrease all trajectories contained in different classes
+   * by one consistently. This is implemented by the topmost class which calls
+   * the real functions, \sa removeTrajectoryStep(), by all necessary subclasses.
+   */
+  virtual void removeSteps()=0;
 
   /** DEPRECATED: Getter for element indicated by AtomicElement.
@@ -287 +299 @@
   void AppendTrajectoryStep();
 
+  /** Function used by this and inheriting classes to decrease the trajectory
+   * vectors by one.
+   */
+  void removeTrajectoryStep();
+
   // make these protected only such that deriving atom class still has full
   // access needed for clone and alike

src/Atom/atom_bondedparticleinfo.cpp

@@ -63 +63 @@
 }
 
+void BondedParticleInfo::removeTrajectoryStep()
+{
+  ListOfBonds.pop_back();
+  LOG(5,"BondedParticleInfo::removeTrajectoryStep() called, size is " << ListOfBonds.size());
+}
+
 const BondList& BondedParticleInfo::getListOfBonds() const
 {

src/Atom/atom_bondedparticleinfo.hpp

@@ -89 +89 @@
   void AppendTrajectoryStep();
 
+  /** Function used by this and inheriting classes to reduce the ListOfBonds
+   * vector by one.
+   */
+  void removeTrajectoryStep();
+
   std::vector<BondList> ListOfBonds; //!< list of all bonds
   static BondList emptyList;  //!< empty list to return when step is not present