Changeset dddbfe for src/Parser/XyzParser.cpp

Timestamp:

Aug 6, 2010, 4:07:24 PM (14 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:

1bab08, e0ba10

Parents:

e97a44

git-author:

Frederik Heber <heber@…> (08/06/10 15:50:00)

git-committer:

Frederik Heber <heber@…> (08/06/10 16:07:24)

Message:

FIX: XyzParser::Load() did not create a molecule wherein all atoms were placed.

• BUGFIX: atom::setMolecule() invokes mol->AddAtom which again invokes setMolecule ... infinite loop, instead use insert()
• ChangeElementAction needs to remove and re-add the atom such that molecule is notified of element change.
• this makes later use of the molecule only possible via subgraph dissection.
• hence, we create a molecule, set it active and put it into World's deprecated MoleculeListClass.

File:

• src/Parser/XyzParser.cpp (modified) (3 diffs)

src/Parser/XyzParser.cpp

@@ -13 +13 @@
 #include "World.hpp"
 #include "atom.hpp"
+#include "molecule.hpp"
 #include "element.hpp"
 #include "periodentafel.hpp"
@@ -37 +38 @@
  */
 void XyzParser::load(istream* file) {
-  atom* newAtom;
+  atom* newAtom = NULL;
+  molecule* newmol = NULL;
   int numberOfAtoms;
   char commentBuffer[512], type[3];
@@ -46 +48 @@
   comment = commentBuffer;
 
+  newmol = World::getInstance().createMolecule();
+  newmol->ActiveFlag = true;
+  World::getInstance().getMolecules()->insert(newmol);
   for (int i = 0; i < numberOfAtoms; i++) {
     newAtom = World::getInstance().createAtom();
     *file >> type >> ws >> newAtom->x[0] >> ws >> newAtom->x[1] >> ws >> newAtom->x[2];
     newAtom->setType(World::getInstance().getPeriode()->FindElement(type));
+    newmol->AddAtom(newAtom);
   }
 }