Changeset bb4408 for src/Actions/ParserAction/LoadXyzAction.cpp

Timestamp:

Aug 13, 2010, 4:36:03 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:

a19d73e

Parents:

0adac1

git-author:

Frederik Heber <heber@…> (08/13/10 16:18:01)

git-committer:

Frederik Heber <heber@…> (08/13/10 16:36:03)

Message:

BUGFIX: Removed adding of parsed atoms in LoadXyzAction.

• a molecule is created and added already in XyzParser::load().
• this caused the id of a newly parsed in xyz file to be 2 instead of 1 and the creation of an empty molecule.

File:

• src/Actions/ParserAction/LoadXyzAction.cpp (modified) (1 diff)

src/Actions/ParserAction/LoadXyzAction.cpp

@@ -79 +79 @@
   input.open(filename.c_str());
   if (!input.fail()) {
-    // TODO: Remove the insertion into molecule when saving does not depend on them anymore. Also, remove molecule.hpp include
-    set <atom*> UniqueList;
-    {
-      vector<atom *> ListBefore = World::getInstance().getAllAtoms();
-      for (vector<atom *>::iterator runner = ListBefore.begin();runner != ListBefore.end(); ++runner)
-        UniqueList.insert(*runner);
-    }
     XyzParser parser; // briefly instantiate a parser which is removed at end of focus
     parser.load(&input);
-    {
-      vector<atom *> ListAfter = World::getInstance().getAllAtoms();
-      pair< set<atom *>::iterator, bool > Inserter;
-      if (UniqueList.size() != ListAfter.size()) { // only create if new atoms have been parsed
-        MoleculeListClass *molecules = World::getInstance().getMolecules();
-        molecule *mol = World::getInstance().createMolecule();
-        molecules->insert(mol);
-        for (vector<atom *>::iterator runner = ListAfter.begin(); runner != ListAfter.end(); ++runner) {
-          Inserter = UniqueList.insert(*runner);
-          if (Inserter.second) { // if not present, then new (just parsed) atom, add ...
-            cout << "Adding new atom " << **runner << " to new mol." << endl;
-            mol->AddAtom(*runner);
-          }
-        }
-        mol->doCountAtoms();
-      } else {
-        cout << "No atoms parsed?" << endl;
-      }
-    }
   } else {
     DoeLog(1) && (eLog() << Verbose(1) << "Could not open file " << filename << "." << endl);