Changeset e2b47c for src

Timestamp:

Jun 11, 2010, 3:07:11 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:

77b2d7

Parents:

9d2a92

Message:

Case 'R' is now handled by CommandLineUI.

• again, for each atom to remove all molecules are gone through and it is tried to be erased (due to storing done molecule- not atom-wise)
• TESTFIX: "--position" introduced

Location:

src

Files:

• Actions/MapOfActions.cpp (modified) (2 diffs)
• Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified) (2 diffs)
• builder.cpp (modified) (1 diff)

src/Actions/MapOfActions.cpp

@@ -189 +189 @@
   TypeMap["principal-axis-system"] = Molecule;
   TypeMap["remove-atom"] = Atom;
-  TypeMap["remove-sphere"] = Atom;
+  TypeMap["remove-sphere"] = Double;
   TypeMap["repeat-box"] = Vector;
   TypeMap["rotate-to-pas"] = Molecule;
@@ -258 +258 @@
 //  generic.insert("principal-axis-system");
   generic.insert("remove-atom");
-//  generic.insert("remove-sphere");
+  generic.insert("remove-sphere");
   generic.insert("repeat-box");
   generic.insert("rotate-to-pas");

src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp

@@ -10 +10 @@
 #include "Descriptors/AtomDescriptor.hpp"
 #include "log.hpp"
+#include "molecule.hpp"
 #include "vector.hpp"
 #include "verbose.hpp"
@@ -35 +36 @@
   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/builder.cpp

@@ -2000 +2000 @@
             case 'R':
               if (ExitFlag == 0) ExitFlag = 1;
-              if ((argptr+3 >= argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) || (!IsValidNumber(argv[argptr+3])))  {
+              if ((argptr+4 >= argc) || (argv[argptr][0] == '-'))  {
                 ExitFlag = 255;
-                DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for removing atoms: -R <x> <y> <z> <distance>" << endl);
+                DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for removing atoms: -R <distance> --position <x> <y> <z>" << endl);
                 performCriticalExit();
               } else {
-                SaveFlag = true;
-                const double radius = atof(argv[argptr+3]);
-                Vector point(atof(argv[argptr]),atof(argv[argptr+1]),atof(argv[argptr+2]));
-                DoLog(1) && (Log() << Verbose(1) << "Removing atoms around " << point << " with radius " << radius << "." << endl);
-                atom *Walker = NULL;
-                molecule::iterator advancer = mol->begin();
-                for(molecule::iterator iter = advancer; advancer != mol->end();) {
-                  iter = advancer++;
-                  if ((*iter)->x.DistanceSquared(point) > radius*radius){ // distance to first above radius ...
-                    Walker = (*iter);
-                    DoLog(1) && (Log() << Verbose(1) << "Removing atom " << *Walker << "." << endl);
-                    mol->RemoveAtom(*(iter));
-                    World::getInstance().destroyAtom(Walker);
-                  }
-                }
-                argptr+=4;
+                ArgcList.insert(argptr-1);
+                ArgcList.insert(argptr);
+                ArgcList.insert(argptr+1);
+                ArgcList.insert(argptr+2);
+                ArgcList.insert(argptr+3);
+                ArgcList.insert(argptr+4);
+                argptr+=5;
               }
               break;