Changeset 237f93 for src/Actions/FragmentationAction

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.

File:

• src/Actions/FragmentationAction/MolecularDynamicsAction.cpp (modified) (2 diffs)

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());