Changeset d55743e for src

Timestamp:

Jun 11, 2010, 2:37:51 PM (15 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:

f4bd01

Parents:

77de81

Message:

Case 'r' is now handled by CommandLineUI.

Location:

src

Files:

• Actions/AtomAction/RemoveAction.cpp (modified) (2 diffs)
• Actions/MapOfActions.cpp (modified) (1 diff)
• builder.cpp (modified) (1 diff)

src/Actions/AtomAction/RemoveAction.cpp

@@ -10 +10 @@
 #include "Descriptors/AtomDescriptor.hpp"
 #include "log.hpp"
+#include "molecule.hpp"
 #include "verbose.hpp"
 #include "World.hpp"
@@ -40 +41 @@
     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;

src/Actions/MapOfActions.cpp

@@ -257 +257 @@
 //      generic.insert("parse-xyz");
 //  generic.insert("principal-axis-system");
-//  generic.insert("remove-atom");
+  generic.insert("remove-atom");
 //  generic.insert("remove-sphere");
   generic.insert("repeat-box");

src/builder.cpp

@@ -2097 +2097 @@
                 performCriticalExit();
               } else {
-                mol->getAtomCount();
-                SaveFlag = true;
-                DoLog(1) && (Log() << Verbose(1) << "Removing atom " << argv[argptr] << "." << endl);
-                atom *first = mol->FindAtom(atoi(argv[argptr]));
-                mol->RemoveAtom(first);
+                ArgcList.insert(argptr-1);
+                ArgcList.insert(argptr);
                 argptr+=1;
               }