Changeset e6317b for src/Actions/AtomAction

Timestamp:

Jun 16, 2010, 12:24:21 PM (15 years ago)

Author:

Tillmann Crueger <crueger@…>

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:

492279

Parents:

f8e486 (diff), 980dd6 (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:

Broken: Merge commit 'Gitosis/stable' into stable

Conflicts:

molecuilder/src/Actions/AnalysisAction/PairCorrelationToPointAction.cpp
molecuilder/src/Actions/AnalysisAction/PairCorrelationToSurfaceAction.cpp
molecuilder/src/Makefile.am

Location:

src/Actions/AtomAction

Files:

• AddAction.cpp (modified) (2 diffs)
• ChangeElementAction.cpp (modified) (2 diffs)
• RemoveAction.cpp (modified) (2 diffs)

src/Actions/AtomAction/AddAction.cpp

@@ -9 +9 @@
 
 #include "Actions/AtomAction/AddAction.hpp"
-#include "CommandLineParser.hpp"
 #include "atom.hpp"
 #include "element.hpp"
 #include "log.hpp"
-#include "periodentafel.hpp"
+#include "molecule.hpp"
 #include "vector.hpp"
 #include "verbose.hpp"
@@ -38 +37 @@
 Action::state_ptr AtomAddAction::performCall() {
   Dialog *dialog = UIFactory::getInstance().makeDialog();
-  int Z = -1;
+  std::vector<element *> elements;
   Vector position;
 
-  dialog->queryInt(NAME, &Z, MapOfActions::getInstance().getDescription(NAME));
+  dialog->queryElement(NAME, &elements, MapOfActions::getInstance().getDescription(NAME));
   dialog->queryVector("position", &position, World::getInstance().getDomain(), true, MapOfActions::getInstance().getDescription("position"));
+  cout << "pre-dialog" << endl;
 
   if(dialog->display()) {
+    cout << "post-dialog" << endl;
     delete dialog;
-    atom * first = World::getInstance().createAtom();
-    first->type = World::getInstance().getPeriode()->FindElement(Z);
-    first->x = position;
-    if (first->type != NULL) {
+    if (elements.size() == 1) {
+      atom * first = World::getInstance().createAtom();
+      first->type = *(elements.begin());
+      first->x = position;
       DoLog(1) && (Log() << Verbose(1) << "Adding new atom with element " << first->type->name << " at " << (first->x) << "." << endl);
+      // 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 Action::success;
     } else {
       DoeLog(1) && (eLog()<< Verbose(1) << "Could not find the specified element." << endl);
-      World::getInstance().destroyAtom(first);
       return Action::failure;
     }

src/Actions/AtomAction/ChangeElementAction.cpp

@@ -9 +9 @@
 
 #include "Actions/AtomAction/ChangeElementAction.hpp"
-#include "CommandLineParser.hpp"
 #include "atom.hpp"
 #include "log.hpp"
@@ -36 +35 @@
 Action::state_ptr AtomChangeElementAction::performCall() {
   Dialog *dialog = UIFactory::getInstance().makeDialog();
-  int Z = -1;
   atom *first = NULL;
-  element *elemental = NULL;
+  std::vector<element *> elements;
 
-  dialog->queryElement(NAME, (const element **) &elemental, MapOfActions::getInstance().getDescription(NAME));
-  dialog->queryAtom("atom-by-id", &first, MapOfActions::getInstance().getDescription("atom-by-id"));
+  dialog->queryAtom(NAME, &first, MapOfActions::getInstance().getDescription(NAME));
+  dialog->queryElement("element", &elements, MapOfActions::getInstance().getDescription("element"));
 
   if(dialog->display()) {
     delete dialog;
-    DoLog(1) && (Log() << Verbose(1) << "Changing atom " << *first << " to element " << elemental << "." << endl);
-    if (elemental != NULL) {
-      first->type = elemental;
+    ASSERT(elements.size() == 1, "Unequal to one element specified when changing an atom's element");
+    ASSERT(first != NULL, "No valid atom specified");
+    DoLog(1) && (Log() << Verbose(1) << "Changing atom " << *first << " to element " << elements.at(0) << "." << endl);
+    if (elements.at(0) != NULL) {
+      first->type = elements.at(0);
       return Action::success;
     } else

src/Actions/AtomAction/RemoveAction.cpp

@@ -9 +9 @@
 
 #include "Actions/AtomAction/RemoveAction.hpp"
-#include "CommandLineParser.hpp"
 #include "atom.hpp"
 #include "Descriptors/AtomDescriptor.hpp"
 #include "log.hpp"
+#include "molecule.hpp"
 #include "verbose.hpp"
 #include "World.hpp"
@@ -43 +43 @@
     delete dialog;
     DoLog(1) && (Log() << Verbose(1) << "Removing atom " << first->getId() << "." << endl);
+    // TODO: this is not necessary when atoms and their storing to file are handled by the World
+    // simply try to erase in every molecule found
+    std::vector<molecule *> molecules = World::getInstance().getAllMolecules();
+    for (std::vector<molecule *>::iterator iter = molecules.begin();iter != molecules.end(); ++iter) {
+      (*iter)->erase(first);
+    }
     World::getInstance().destroyAtom(first);
     return Action::success;