Changeset 8ad68b for src/Actions/AtomAction/AddAction.cpp

Timestamp:

Feb 7, 2016, 5:57:03 AM (9 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:

918a6c

Parents:

5cf341

git-author:

Frederik Heber <heber@…> (10/28/15 12:09:43)

git-committer:

Frederik Heber <heber@…> (02/07/16 05:57:03)

Message:

AddAction and UndoRedoHelpers' AddAtomsFromAtomicInfo use recreate..().

File:

• src/Actions/AtomAction/AddAction.cpp (modified) (4 diffs)

src/Actions/AtomAction/AddAction.cpp

@@ -65 +65 @@
 }
 
+atom * regetNewAtom(const AtomAddAction::AtomAddParameters &_params, const atomId_t _id)
+{
+  atom * first = World::getInstance().recreateAtom(_id);
+  first->setType(_params.elemental.get());
+  first->setPosition(_params.position.get());
+
+  return first;
+}
+
 std::vector<atomId_t> createAtoms(
     const AtomAddAction::AtomAddParameters &_params,
@@ -91 +100 @@
 
   return ids;
+}
+
+std::vector<atomId_t> recreateAtoms(
+    const AtomAddAction::AtomAddParameters &_params,
+    const std::vector<atomId_t> &_ids,
+    std::vector<molecule *> &_molecules)
+{
+  molecule *mol = NULL;
+  if (!_molecules.empty()) {
+    ASSERT (_molecules.size() == 1,
+        "recreateAtoms() - more than one molecules given.");
+    mol = *_molecules.begin();
+  } else {
+    mol = World::getInstance().createMolecule();
+    mol->setName("none");
+  }
+  std::vector<atomId_t> newids;
+  for (std::vector<atomId_t>::const_iterator iter = _ids.begin();
+      iter != _ids.end(); ++iter) {
+    atom *first = regetNewAtom(_params, *iter);
+    if (first != NULL) {
+      newids.push_back(first->getId());
+      mol->AddAtom(first);
+      LOG(1, "Adding new atom with element " << first->getType()->getName()
+          << " at " << (first->getPosition()) << " to new molecule.");
+    } else {
+      ELOG(1, "Could not recreate atom with id " << *iter);
+      break;
+    }
+  }
+
+  return newids;
 }
 
@@ -120 +161 @@
 
   std::vector<molecule *> molecules = World::getInstance().getSelectedMolecules();
-  std::vector<atomId_t> newids = createAtoms(params, molecules);
-
+  std::vector<atomId_t> newids = recreateAtoms(state->params, state->ids, molecules);
   if (newids.size() != state->ids.size()) {
     STATUS("Could not recreate all atoms after undo.");
@@ -128 +168 @@
     return Action::failure;
   }
-
-  std::vector<atomId_t>::const_iterator newiter = newids.begin();
-  std::vector<atomId_t>::const_iterator olditer = state->ids.begin();
-  bool status=true;
-  for (; newiter != newids.end(); ++newiter, ++olditer) {
-    atom * first = World::getInstance().getAtom(AtomById(*newiter));
-    ASSERT( first != NULL,
-        "AtomAddAction::performRedo() - re-created atom not present?");
-    if (first->getId() != *olditer)
-      if (!first->changeId(*olditer)) {
-        STATUS("Could not change atom id "+toString(first->getId())+"->"+toString(*olditer)+".");
-        // remove all created atoms
-        for (std::vector<atomId_t>::const_iterator iter = state->ids.begin(); iter != olditer;++iter)
-          World::getInstance().destroyAtom(*iter);
-        olditer = state->ids.end();
-        for (std::vector<atomId_t>::const_iterator iter = newiter; iter != newids.end();++iter)
-          World::getInstance().destroyAtom(*iter);
-        status = false;
-        break;
-      }
-  }
-  ASSERT( olditer == state->ids.end(),
-      "AtomAddAction::performRedo() - after all unequal amount of ids in new and old?");
-
-  if (!status) {
-    return Action::failure;
-  } else
-    return ActionState::ptr(_state);
+  return ActionState::ptr(_state);
 }