Changeset 237f93 for src/Actions

Timestamp:

Apr 29, 2014, 12:42:43 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:

f47e00b

Parents:

ec7511

git-author:

Frederik Heber <heber@…> (02/04/14 20:32:08)

git-committer:

Frederik Heber <heber@…> (04/29/14 12:42:43)

Message:

FIX: MolecularDynamicsAction now prepares normally not inside performCall().

• added protected ActionSequence::removeAction() and pass-thru in MakroAction.
• added MakroAction::fillOwnDialog(): We did not cleanly implement the MakroAction's dialogs before. We need to populate queries from the sequeence of Actions and from the MakroAction itself (e.g. for loop count). For the latter, we need another new function for this.
• MolecularDynamicsAction removes output action from sequence if not desired.
• removed (another) fillAllDialog from MakroAction::performCall(). This has been the source of doubly occuring dialogs (and dialog becoming ever larger on multiple calls).
• MolecularDynamicsAction::prepare() also just uses ActionRegistry whose ref is passed as parameter and does not (directly) access ActionQueue.

Location:

src/Actions

Files:

• ActionSequence.cpp (modified) (1 diff)
• ActionSequence.hpp (modified) (1 diff)
• FragmentationAction/MolecularDynamicsAction.cpp (modified) (2 diffs)
• MakroAction.cpp (modified) (1 diff)
• MakroAction.hpp (modified) (2 diffs)
• MakroAction_impl_header.hpp (modified) (1 diff)
• MakroAction_impl_pre.hpp (modified) (1 diff)

src/Actions/ActionSequence.cpp

@@ -55 +55 @@
 void ActionSequence::addAction(Action* _action){
   actions.push_back(_action);
+}
+
+bool ActionSequence::removeAction(const std::string &name){
+  actionSet::iterator it=actions.begin();
+  for(; it!=actions.end(); it++){
+    if ((*it)->getName() == name) {
+      actions.erase(it);
+      break;
+    }
+  }
+  return it!=actions.end();
 }
 

src/Actions/ActionSequence.hpp

@@ -48 +48 @@
 
 protected:
+  /** removes the first occurence of an action name \a name from sequence.
+   *
+   * \param name name of action
+   * \return true - action removed, false - action not found
+   */
+  bool removeAction(const std::string &name);
+
   stateSet callAll(bool); // Dummy parameter to allow overloading
   Dialog* fillAllDialogs(Dialog *dialog);

src/Actions/FragmentationAction/MolecularDynamicsAction.cpp

@@ -59 +59 @@
 void FragmentationMolecularDynamicsAction::prepare(ActionRegistry &AR)
 {
-  isPrepared = false;
+  // perform a verlet-integration first, if there are already forces or velocities
+  // present. If not, we still copy the position cleanly into a new step where then
+  // forces are set according to summed fragmentary contributions. This is much cleaner.
+  actions.addAction(AR.getActionByName(std::string("verlet-integration")));
+  actions.addAction(AR.getActionByName(std::string("output")));
+  actions.addAction(AR.getActionByName(std::string("fragment-molecule")));
+  actions.addAction(AR.getActionByName(std::string("fragment-automation")));
+  actions.addAction(AR.getActionByName(std::string("analyse-fragment-results")));
+  isPrepared = true;
 }
 
@@ -70 +78 @@
 
 ActionState::ptr FragmentationMolecularDynamicsAction::performCall(){
-  // now we can truely prepare
-  ActionQueue &AQ = ActionQueue::getInstance();
-  // perform a verlet-integration first, if there are already forces or velocities
-  // present. If not, we still copy the position cleanly into a new step where then
-  // forces are set according to summed fragmentary contributions. This is much cleaner.
-  actions.addAction(AQ.getActionByName(std::string("verlet-integration")));
-  if (params.DoOutput.get())
-    actions.addAction(AQ.getActionByName(std::string("output")));
-  actions.addAction(AQ.getActionByName(std::string("fragment-molecule")));
-  actions.addAction(AQ.getActionByName(std::string("fragment-automation")));
-  actions.addAction(AQ.getActionByName(std::string("analyse-fragment-results")));
+
+  // set number of steps
   setLoop(params.steps.get());
-  isPrepared = true;
-
+  // remove output from sequence if not desired.
+  if (!params.DoOutput.get()) {
+#ifndef NDEBUG
+    bool status =
+#endif
+        removeAction(std::string("output"));
+    ASSERT( status,
+        "FragmentationMolecularDynamicsAction::performCall() - output not found in ActionSequence.");
+  }
+  // and call
   ActionState::ptr state(MakroAction::performCall());
 

src/Actions/MakroAction.cpp

@@ -87 +87 @@
 }
 
+bool MakroAction::removeAction(const std::string &name)
+{
+  actions.removeAction(name);
+}
+
+Dialog* MakroAction::fillOwnDialog(Dialog *dialog) {
+  return dialog;
+}
+
 Dialog* MakroAction::fillDialog(Dialog *dialog) {
+  dialog = fillOwnDialog(dialog);
   return actions.fillAllDialogs(dialog);
 }
 
 ActionState::ptr MakroAction::performCall(){
-  {
-    // create and run our dialog and also of all members of the sequence
-    Dialog* dialog = actions.fillAllDialogs(createDialog());
-    if (dialog->hasQueries()) {
-      if (!dialog->display())
-        // dialog error or aborted -> throw exception
-        throw ActionFailureException() << ActionNameString(getName());
-    }
-    delete(dialog);
-  }
+//  {
+//    // create and run our dialog and also of all members of the sequence
+//    Dialog* dialog = actions.fillAllDialogs(createDialog());
+//    if (dialog->hasQueries()) {
+//      if (!dialog->display())
+//        // dialog error or aborted -> throw exception
+//        throw ActionFailureException() << ActionNameString(getName());
+//    }
+//    delete(dialog);
+//  }
   ActionSequence::stateSet states = actions.callAll(true);
   return ActionState::ptr(new MakroActionState(states));

src/Actions/MakroAction.hpp

@@ -46 +46 @@
 
 protected:
-  virtual Dialog *fillDialog(Dialog *dialog);
+  /**
+   * MakroAction requires an own dialog for global options such as number of loop
+   * iterations, ... besides the dialog from each action in the sequence.
+   *
+   * However, fillDialog() calls ActionSequence::fillAllDialog(). Hence, the dialog
+   * for specific global options must be requested in an distinct function.
+   */
+  virtual Dialog * fillOwnDialog(Dialog*);
+
+  /** Pass-thru for removeAction to allow all derived MakroActions to manipulate action sequence.
+   *
+   * \param name name of action to remove
+   * \return true - action removed, false - action not found
+   * \sa ActionSequence::removeAction()
+   */
+  bool removeAction(const std::string &name);
 
   virtual ActionState::ptr performCall();
@@ -55 +70 @@
 
 private:
+  /** fillDialog is used to spawn sequence queries, hence must not be modified by
+   * derived MakroActions.
+   */
+  Dialog *fillDialog(Dialog *dialog);
+
   ActionSequence &actions;
 };

src/Actions/MakroAction_impl_header.hpp

@@ -234 +234 @@
 
 protected:
-  virtual Dialog * fillDialog(Dialog*);
+  virtual Dialog * fillOwnDialog(Dialog*);
 
   void startTimer() const;

src/Actions/MakroAction_impl_pre.hpp

@@ -292 +292 @@
 
 // =========== fill a dialog ===========
-Dialog* ACTION::fillDialog(Dialog *dialog) {
+Dialog* ACTION::fillOwnDialog(Dialog *dialog) {
         ASSERT(dialog,"No Dialog given when filling actionname's dialog");
 #if BOOST_PP_EQUAL(MAXPARAMTYPES,0)