Changeset 9a8a6b

Timestamp:

Jan 31, 2016, 12:46:56 PM (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:

6a922b

Parents:

08d9df7 (diff), ceaab1 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'AtomAlwaysHasMolecule' into Candidate_v1.5.1

Files:

• src/Actions/AtomAction/AddAction.cpp (modified) (3 diffs)
• src/Actions/AtomAction/AddAction.def (modified) (1 diff)
• src/Atom/atom.cpp (modified) (1 diff)
• src/molecule.cpp (modified) (1 diff)
• src/molecule.hpp (modified) (1 diff)
• tests/regression/Atoms/Add/post/test.pdb (modified) (1 diff)

src/Actions/AtomAction/AddAction.cpp

@@ -55 +55 @@
 #include "Action_impl_pre.hpp"
 /** =========== define the function ====================== */
+
+atom * getNewAtom(const AtomAddAction::AtomAddParameters &_params)
+{
+  atom * first = World::getInstance().createAtom();
+  first->setType(_params.elemental.get());
+  first->setPosition(_params.position.get());
+
+  return first;
+}
+
+std::vector<atomId_t> createAtoms(
+    const AtomAddAction::AtomAddParameters &_params,
+    std::vector<molecule *> &_molecules)
+{
+  std::vector<atomId_t> ids;
+  if (!_molecules.empty()) {
+    if (_molecules.size() == 1) {
+        atom *first = getNewAtom(_params);
+        molecule *mol = *_molecules.begin();
+        LOG(1, "Adding new atom with element " << first->getType()->getName()
+            << " at " << (first->getPosition()) << " to selected molecule "
+            << mol->getName()+".");
+        mol->AddAtom(first);
+      ids.push_back(first->getId());
+    }
+  } else {
+    atom *first = getNewAtom(_params);
+    molecule *mol = World::getInstance().createMolecule();
+    mol->setName("none");
+    mol->AddAtom(first);
+    LOG(1, "Adding new atom with element " << first->getType()->getName()
+        << " at " << (first->getPosition()) << " to new molecule.");
+    ids.push_back(first->getId());
+  }
+
+  return ids;
+}
+
 ActionState::ptr AtomAddAction::performCall() {
   // execute action
-  atom * first = World::getInstance().createAtom();
-  first->setType(params.elemental.get());
-  first->setPosition(params.position.get());
-  LOG(1, "Adding new atom with element " << first->getType()->getName() << " at " << (first->getPosition()) << ".");
-  // TODO: remove when all of World's atoms are stored.
-  std::vector<molecule *> molecules = World::getInstance().getAllMolecules();
-  if (!molecules.empty()) {
-    std::vector<molecule *>::iterator iter = molecules.begin();
-    (*iter)->AddAtom(first);
-  }
-  return ActionState::ptr(new AtomAddState(first->getId(), params));
+  std::vector<molecule *> molecules = World::getInstance().getSelectedMolecules();
+  std::vector<atomId_t> ids = createAtoms(params, molecules);
+
+  if (molecules.size() > 1)
+     return Action::failure;
+  else
+    return ActionState::ptr(new AtomAddState(ids, params));
 }
 
@@ -73 +107 @@
   AtomAddState *state = assert_cast<AtomAddState*>(_state.get());
 
-  LOG(1, "Removing atom with id " << state->id << ".");
-  World::getInstance().destroyAtom(state->id);
+  for (std::vector<atomId_t>::const_iterator iter = state->ids.begin();
+      iter != state->ids.end(); ++iter) {
+    LOG(1, "Removing atom with id " << *iter << ".");
+    World::getInstance().destroyAtom(*iter);
+  }
 
   return ActionState::ptr(_state);
@@ -82 +119 @@
   AtomAddState *state = assert_cast<AtomAddState*>(_state.get());
 
-  atom * first = World::getInstance().createAtom();
-  first->setType(state->params.elemental.get());
-  first->setPosition(state->params.position.get());
-  LOG(1, "Re-adding new atom with element " << state->params.elemental.get()->getName() << " at " << state->params.position.get() << ".");
-  // TODO: remove when all of World's atoms are stored.
-  std::vector<molecule *> molecules = World::getInstance().getAllMolecules();
-  if (!molecules.empty()) {
-    std::vector<molecule *>::iterator iter = molecules.begin();
-    (*iter)->AddAtom(first);
+  std::vector<molecule *> molecules = World::getInstance().getSelectedMolecules();
+  std::vector<atomId_t> newids = createAtoms(params, molecules);
+
+  if (newids.size() != state->ids.size()) {
+    STATUS("Could not recreate all atoms after undo.");
+    for (std::vector<atomId_t>::const_iterator iter = newids.begin(); iter != newids.end();++iter)
+      World::getInstance().destroyAtom(*iter);
+    return Action::failure;
   }
-  if (first->getId() != state->id)
-    if (!first->changeId(state->id)) {
-      STATUS("Could not change atom id "+toString(first->getId())+"->"+toString(state->id)+".");
-      return Action::failure;
-    }
 
-  return ActionState::ptr(_state);
+  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);
 }
 

src/Actions/AtomAction/AddAction.def

@@ -27 +27 @@
 (BoxVectorValidator())
 
-#define statetypes (const atomId_t)
-#define statereferences (id)
+#define statetypes (std::vector<atomId_t>)
+#define statereferences (ids)
 
 // some defines for all the names, you may use ACTION, STATE and PARAMS

src/Atom/atom.cpp

@@ -264 +264 @@
   // first we move ourselves in the world
   // the world lets us know if that succeeded
+  atomId_t oldid = id;
   if(world->changeAtomId(id,newId,this)){
     OBSERVE;
     id = newId;
+    if (mol != NULL)
+      mol->changeAtomId(oldid, newId);
     NOTIFY(IndexChanged);
     return true;

src/molecule.cpp

@@ -168 +168 @@
     return false;
   }
+}
+
+bool molecule::changeAtomId(int oldId, int newId)
+{
+  OBSERVE;
+  if ((!atomIds.contains( oldId )) || (atomIds.contains( newId )))
+    return false;
+  atomIds.erase( oldId );
+  atomIds.insert( newId );
+  return true;
 }
 

src/molecule.hpp

@@ -237 +237 @@
    */
   bool changeAtomNr(int oldNr, int newNr, atom* target=0);
+
+  friend bool atom::changeId(atomId_t newId);
+  /**
+   * used when changing an ParticleInfo::Id.
+   * Note that this number is global (and the molecule uses it to know which atoms belong to it)
+   *
+   * @param oldId old Id
+   * @param newId new Id to set
+   * @return indicates wether the change could be done or not.
+   */
+  bool changeAtomId(int oldId, int newId);
 
   /** Updates the internal lookup fro local to global indices.

tests/regression/Atoms/Add/post/test.pdb

@@ -1 +1 @@
 REMARK created by molecuilder on Wed Feb  2 18:06:07 2011
-ATOM      1 H01 0-   00         10.000  10.000  10.000  0.00  0.00           H 0
+ATOM      1 H01 0non 01         10.000  10.000  10.000  0.00  0.00           H 0
 END