Changeset 1e45f1f for src/Actions/MoleculeAction

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:

d5f7b8

Parents:

7e51e1

git-author:

Frederik Heber <heber@…> (08/02/14 09:43:22)

git-committer:

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

Message:

Extended VerletIntegrationAction wirth Undo/Redo.

• using new UndoRedoHelpers for this.
• VerletForceIntegration::operator() does not return bool anymore, check for empty atom set is done in Action.
• TESTFIX: Removed XFAIl from regression tests verlet-integration.

Location:

src/Actions/MoleculeAction

Files:

• VerletIntegrationAction.cpp (modified) (5 diffs)
• VerletIntegrationAction.def (modified) (2 diffs)

src/Actions/MoleculeAction/VerletIntegrationAction.cpp

@@ -3 +3 @@
  * Description: creates and alters molecular systems
  * Copyright (C)  2010-2012 University of Bonn. All rights reserved.
+ * Copyright (C)  2013-2014 Frederik Heber. All rights reserved.
  * 
  *
@@ -35 +36 @@
 #include "CodePatterns/MemDebug.hpp"
 
+#include "Actions/UndoRedoHelpers.hpp"
 #include "Atom/atom.hpp"
+#include "Atom/AtomicInfo.hpp"
 #include "Atom/AtomSet.hpp"
 #include "CodePatterns/Log.hpp"
@@ -53 +56 @@
 using namespace MoleCuilder;
 
+enum {
+  PositionIndex=0,
+  VelocityIndex=1,
+  ForceIndex=2,
+  MAXINDEX
+} VectorIndexType;
+
 // and construct the stuff
 #include "VerletIntegrationAction.def"
@@ -64 +74 @@
   }
   // we always operate relative to current time step
-  size_t CurrentStep = WorldTime::getInstance().getTime();
+  const size_t CurrentStep = WorldTime::getInstance().getTime();
   VerletForceIntegration<std::vector<atom *> > Verlet(set, params.Deltat.get(), true);
   // parse forces into next step
@@ -74 +84 @@
       LOG(2, "File " << params.forcesfile.get() << " found and parsed.");
   }
+
+  // create undo state for all selected atoms (undo info)
+  std::vector<AtomicInfo> UndoInfo;
+  UndoInfo.reserve(set.size());
+  {
+    for (World::AtomSelectionConstIterator iter = World::getInstance().beginAtomSelection();
+        iter != World::getInstance().endAtomSelection();
+        ++iter)
+      UndoInfo.push_back(AtomicInfo(*(iter->second)));
+  }
+
   // perform velocity verlet update
-  bool status = Verlet(CurrentStep+1, 1, 0, params.FixedCenterOfMass.get());
-  if (!status) {
-    ELOG(1, "Velocity verlet failed.");
-    return Action::failure;
-  } else {
-    LOG(2, "DEBUG: Successfully performed updates on velocity and position.");
-    // increment to next time step
-    World::getInstance().setTime(CurrentStep+1);
+  Verlet(CurrentStep+1, 1, 0, params.FixedCenterOfMass.get());
+  LOG(0, "STATUS: Successfully performed updates on velocity and position.");
+  // increment to next time step
+  World::getInstance().setTime(CurrentStep+1);
+
+  // create undo state for all selected atoms (redo info):
+  // we need:
+  // -# forces from last step (possible parsing forces file, already in UndoInfo)
+  // -# velocities from last step (..UpdateU(), already in UndoInfo)
+  // -# current position (..UpdateX())
+  std::vector<Vectors_t> UpdatedStep(MAXINDEX);
+  UpdatedStep[PositionIndex].reserve(set.size());
+  UpdatedStep[VelocityIndex].reserve(set.size());
+  UpdatedStep[ForceIndex].reserve(set.size());
+  {
+    for (World::AtomSelectionConstIterator iter = World::getInstance().beginAtomSelection();
+        iter != World::getInstance().endAtomSelection();
+        ++iter) {
+      UpdatedStep[PositionIndex].push_back(iter->second->getPositionAtStep(CurrentStep+1));
+      UpdatedStep[VelocityIndex].push_back(iter->second->getAtomicVelocityAtStep(CurrentStep));
+      UpdatedStep[ForceIndex].push_back(iter->second->getAtomicForceAtStep(CurrentStep));
+    }
   }
-  return Action::success;
+  MoleculeVerletIntegrationState *UndoState =
+      new MoleculeVerletIntegrationState(UndoInfo, UpdatedStep, params);
+
+  return ActionState::ptr(UndoState);
 }
 
 ActionState::ptr MoleculeVerletIntegrationAction::performUndo(ActionState::ptr _state) {
-//  MoleculeVerletIntegrationState *state = assert_cast<MoleculeVerletIntegrationState*>(_state.get());
+  MoleculeVerletIntegrationState *state =
+      assert_cast<MoleculeVerletIntegrationState*>(_state.get());
 
-//  string newName = state->mol->getName();
-//  state->mol->setName(state->lastName);
+  // go back one step
+  const size_t CurrentStep = WorldTime::getInstance().getTime();
+  World::getInstance().setTime(CurrentStep-1);
 
-  STATUS("Undo of MoleculeVerletIntegrationAction not implemented.");
-  return Action::failure;
+  // remove current step for all modified atoms
+  removeLastStep(getIdsFromAtomicInfo(state->UndoInfo));
+
+  // and set back the old step (forces have been changed)
+  SetAtomsFromAtomicInfo(state->UndoInfo);
+
+  return ActionState::ptr(_state);
 }
 
 ActionState::ptr MoleculeVerletIntegrationAction::performRedo(ActionState::ptr _state){
-  STATUS("Rddo of MoleculeVerletIntegrationAction not implemented.");
-  return Action::failure;
+  MoleculeVerletIntegrationState *state =
+      assert_cast<MoleculeVerletIntegrationState*>(_state.get());
+
+  // set forces and velocities
+  ResetAtomVelocity(state->UndoInfo, state->UpdatedStep[VelocityIndex]);
+  ResetAtomForce(state->UndoInfo, state->UpdatedStep[ForceIndex]);
+
+  // set stored new state
+  addNewStep(state->UndoInfo);
+
+  // add a new time step
+  size_t CurrentStep = WorldTime::getInstance().getTime();
+  World::getInstance().setTime(CurrentStep+1);
+
+  // and set positions of the new step
+  ResetAtomPosition(state->UndoInfo, state->UpdatedStep[PositionIndex]);
+
+  return ActionState::ptr(_state);
 }
 

src/Actions/MoleculeAction/VerletIntegrationAction.def

@@ -7 +7 @@
 
 // all includes and forward declarations necessary for non-integral types below
-class MoleculeListClass;
+#include "LinearAlgebra/Vector.hpp"
+#include <vector>
+typedef std::vector<Vector> Vectors_t;
 
 #include "Parameters/Validators/DummyValidator.hpp"
@@ -27 +29 @@
 (DummyValidator< bool >())
 
-#undef statetypes
-#undef statereferences
+#define statetypes (std::vector<AtomicInfo>)(std::vector<Vectors_t>)
+#define statereferences (UndoInfo)(UpdatedStep)
 
 // some defines for all the names, you may use ACTION, STATE and PARAMS