Changeset e6317b for src/Actions/WorldAction

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/WorldAction

Files:

• AddEmptyBoundaryAction.cpp (modified) (1 diff)
• BoundInBoxAction.cpp (modified) (1 diff)
• CenterInBoxAction.cpp (modified) (1 diff)
• CenterOnEdgeAction.cpp (modified) (1 diff)
• ChangeBoxAction.cpp (modified) (1 diff)
• RemoveSphereOfAtomsAction.cpp (modified) (2 diffs)
• RepeatBoxAction.cpp (modified) (1 diff)
• ScaleBoxAction.cpp (modified) (1 diff)
• SetDefaultNameAction.cpp (modified) (2 diffs)
• SetGaussianBasisAction.cpp (modified) (2 diffs)

src/Actions/WorldAction/AddEmptyBoundaryAction.cpp

@@ -9 +9 @@
 
 #include "Actions/WorldAction/AddEmptyBoundaryAction.hpp"
-#include "CommandLineParser.hpp"
 #include "atom.hpp"
 #include "log.hpp"

src/Actions/WorldAction/BoundInBoxAction.cpp

@@ -9 +9 @@
 
 #include "Actions/WorldAction/BoundInBoxAction.hpp"
-#include "CommandLineParser.hpp"
 #include "log.hpp"
 #include "molecule.hpp"

src/Actions/WorldAction/CenterInBoxAction.cpp

@@ -9 +9 @@
 
 #include "Actions/WorldAction/CenterInBoxAction.hpp"
-#include "CommandLineParser.hpp"
 #include "log.hpp"
 #include "molecule.hpp"

src/Actions/WorldAction/CenterOnEdgeAction.cpp

@@ -9 +9 @@
 
 #include "Actions/WorldAction/CenterOnEdgeAction.hpp"
-#include "CommandLineParser.hpp"
 #include "atom.hpp"
 #include "log.hpp"

src/Actions/WorldAction/ChangeBoxAction.cpp

@@ -9 +9 @@
 
 #include "Actions/WorldAction/ChangeBoxAction.hpp"
-#include "CommandLineParser.hpp"
 #include "log.hpp"
 #include "verbose.hpp"

src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp

@@ -9 +9 @@
 
 #include "Actions/WorldAction/RemoveSphereOfAtomsAction.hpp"
-#include "CommandLineParser.hpp"
 #include "atom.hpp"
 #include "Descriptors/AtomDescriptor.hpp"
 #include "log.hpp"
+#include "molecule.hpp"
 #include "vector.hpp"
 #include "verbose.hpp"
@@ -38 +38 @@
   Dialog *dialog = UIFactory::getInstance().makeDialog();
   double radius = 0.;
-  atom *first = NULL;
+  Vector point;
 
   dialog->queryDouble(NAME, &radius, MapOfActions::getInstance().getDescription(NAME));
-  dialog->queryAtom("atom-by-id", &first, MapOfActions::getInstance().getDescription("atom-by-id"));
+  dialog->queryVector("position", &point, World::getInstance().getDomain(), false, MapOfActions::getInstance().getDescription("position"));
 
   if(dialog->display()) {
     delete dialog;
-    DoLog(1) && (Log() << Verbose(1) << "Removing atoms around " << first->nr << " with radius " << radius << "." << endl);
+    DoLog(1) && (Log() << Verbose(1) << "Removing atoms around " << point << " with radius " << radius << "." << endl);
     vector<atom*> AllAtoms = World::getInstance().getAllAtoms();
-    vector<atom*>::iterator AtomAdvancer = AllAtoms.begin();
-    for (vector<atom*>::iterator AtomRunner = AtomAdvancer; AtomRunner != AllAtoms.end(); ) {
-      ++AtomAdvancer;
-      if (first != *AtomRunner) // dont't destroy reference ...
-        if (first->x.DistanceSquared((*AtomRunner)->x) > radius*radius) // distance to first above radius ...
-          World::getInstance().destroyAtom(*AtomRunner);
+    vector<molecule *> molecules = World::getInstance().getAllMolecules();
+    for (vector<atom*>::iterator AtomRunner = AllAtoms.begin(); AtomRunner != AllAtoms.end(); ++AtomRunner) {
+      if (point.DistanceSquared((*AtomRunner)->x) > radius*radius) { // distance to first above radius ...
+        // TODO: This is not necessary anymore when atoms are completely handled by World (create/destroy and load/save)
+        for (vector<molecule *>::iterator iter = molecules.begin();iter != molecules.end();++iter)
+          (*iter)->erase(*AtomRunner);
+        World::getInstance().destroyAtom(*AtomRunner);
+      }
     }
-    World::getInstance().destroyAtom(first);
     return Action::success;
   } else {

src/Actions/WorldAction/RepeatBoxAction.cpp

@@ -9 +9 @@
 
 #include "Actions/WorldAction/RepeatBoxAction.hpp"
-#include "CommandLineParser.hpp"
 #include "atom.hpp"
 #include "log.hpp"

src/Actions/WorldAction/ScaleBoxAction.cpp

@@ -9 +9 @@
 
 #include "Actions/WorldAction/ScaleBoxAction.hpp"
-#include "CommandLineParser.hpp"
 #include "atom.hpp"
 #include "log.hpp"

src/Actions/WorldAction/SetDefaultNameAction.cpp

@@ -9 +9 @@
 
 #include "Actions/WorldAction/SetDefaultNameAction.hpp"
-#include "CommandLineParser.hpp"
 #include "log.hpp"
+#include "verbose.hpp"
 #include "World.hpp"
 
@@ -39 +39 @@
 
   if(dialog->display()) {
-    char outputname[MAXSTRINGSIZE];
-    strcpy(outputname, defaultname.c_str());
-    World::getInstance().setDefaultName(outputname);
+    World::getInstance().setDefaultName(defaultname);
+    DoLog(0) && (Log() << Verbose(0) << "Default name of new molecules set to " << World::getInstance().getDefaultName() << "." << endl);
     delete dialog;
     return Action::success;

src/Actions/WorldAction/SetGaussianBasisAction.cpp

@@ -9 +9 @@
 
 #include "Actions/WorldAction/SetGaussianBasisAction.hpp"
-#include "CommandLineParser.hpp"
 #include "config.hpp"
+#include "log.hpp"
+#include "verbose.hpp"
 #include "World.hpp"
 
@@ -33 +34 @@
 Action::state_ptr WorldSetGaussianBasisAction::performCall() {
   Dialog *dialog = UIFactory::getInstance().makeDialog();
-
-  dialog->queryString(NAME, &World::getInstance().getConfig()->basis, MapOfActions::getInstance().getDescription(NAME));
+  config *configuration = World::getInstance().getConfig();
+  dialog->queryString(NAME, &(configuration->basis), MapOfActions::getInstance().getDescription(NAME));
 
   if(dialog->display()) {
+    DoLog(1) && (Log() << Verbose(1) << "Setting MPQC basis to " << configuration->basis << "." << endl);
     delete dialog;
     return Action::success;