Changeset 42af9e for src/molecule_fragmentation.cpp

Timestamp:

May 31, 2010, 2:33:11 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:

1024cb

Parents:

920c70

git-author:

Frederik Heber <heber@…> (05/31/10 14:27:12)

git-committer:

Frederik Heber <heber@…> (05/31/10 14:33:11)

Message:

MEMFIXES: no more default saving/loading of element's db, config::SaveTREMOLO(), molecule::CreateMappingLabelsToConfigSequence()

• ParseCommandLineOptions() - loading element's db only when path was given
• main() - default storing at end removed, should be handled by config::~config()
• config::SaveTREMOLO() - LocalNotoGlobalNoMap is now an STL map, id must not be continuous, so old way is very error-prone
• molecule::CreateMappingLabelsToConfigSequence() - don't delete SortIndex (is done in FragmentMolecule)
• molecule::FragmentMolecule() - dont' delete FragmentList in the block
• testsuite-simple_configuration.at - removing atoms around sphere is not broken anymore, changed testsuite accordingly.

Signed-off-by: Frederik Heber <heber@…>

File:

• src/molecule_fragmentation.cpp (modified) (4 diffs)

src/molecule_fragmentation.cpp

@@ -516 +516 @@
   int AtomNo = 0;
   SetIndexedArrayForEachAtomTo( SortIndex, &atom::nr, &IncrementalAbsoluteValue, AtomNo );
-  delete[](SortIndex);
 
   return true;
@@ -542 +541 @@
 {
   MoleculeListClass *BondFragments = NULL;
-  int *SortIndex = NULL;
   int *MinimumRingSize = new int[AtomCount];
   int FragmentCounter;
@@ -685 +683 @@
   if (BondFragments->ListOfMolecules.size() != 0) {
     // create the SortIndex from BFS labels to order in the config file
+    int *SortIndex = NULL;
     CreateMappingLabelsToConfigSequence(SortIndex);
 
@@ -718 +717 @@
     // free memory for bond part
     DoLog(1) && (Log() << Verbose(1) << "Freeing bond memory" << endl);
-    delete[](FragmentList); // remove bond molecule from memory
     delete[](SortIndex);
   } else {