Changeset b6d8a9 for src


Ignore:
Timestamp:
Jul 27, 2009, 2:08:27 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:
3c4f04
Parents:
a20e6a
Message:

BUGFIX: ManipulateAtoms() had mol = NULL

File:
1 edited

Legend:

Unmodified
Added
Removed
  • src/builder.cpp

    ra20e6a rb6d8a9  
    878878      for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
    879879        if ((*ListRunner)->ActiveFlag) {
    880         double bonddistance;
    881         clock_t start,end;
    882         cout << Verbose(0) << "What's the maximum bond distance: ";
    883         cin >> bonddistance;
    884         start = clock();
    885         mol->CreateAdjacencyList((ofstream *)&cout, bonddistance, configuration->GetIsAngstroem());
    886         mol->CreateListOfBondsPerAtom((ofstream *)&cout);
    887         end = clock();
    888         cout << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl;
    889       }
     880          mol = *ListRunner;
     881          double bonddistance;
     882          clock_t start,end;
     883          cout << Verbose(0) << "What's the maximum bond distance: ";
     884          cin >> bonddistance;
     885          start = clock();
     886          mol->CreateAdjacencyList((ofstream *)&cout, bonddistance, configuration->GetIsAngstroem());
     887          mol->CreateListOfBondsPerAtom((ofstream *)&cout);
     888          end = clock();
     889          cout << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl;
     890        }
    890891      break;
    891892
     
    13261327  clock_t start,end;
    13271328  int argptr;
     1329  molecule *mol = NULL;
    13281330  strncpy(configuration.databasepath, LocalPath, MAXSTRINGSIZE-1);
    1329 
    1330   // simply create a new molecule, wherein the config file is loaded and the manipulation takes place
    1331   molecule *mol = new molecule(periode);
    1332   mol->ActiveFlag = true;
    1333   molecules->insert(mol);
    13341331
    13351332  if (argc > 1) { // config file specified as option
     
    13751372            cout << "\t-v/-V\t\tGives version information." << endl;
    13761373            cout << "Note: config files must not begin with '-' !" << endl;
    1377             delete(mol);
    1378             delete(periode);
    13791374            return (1);
    13801375            break;
     
    13831378            cout << argv[0] << " " << VERSIONSTRING << endl;
    13841379            cout << "Build your own molecule position set." << endl;
    1385             delete(mol);
    1386             delete(periode);
    13871380            return (1);
    13881381            break;
     
    14181411    // 3. Find config file name and parse if possible
    14191412    if (argv[1][0] != '-') {
     1413      // simply create a new molecule, wherein the config file is loaded and the manipulation takes place
     1414      mol = new molecule(periode);
     1415      mol->ActiveFlag = true;
     1416      molecules->insert(mol);
     1417
    14201418      cout << Verbose(0) << "Config file given." << endl;
    14211419      test.open(argv[1], ios::in);
     
    19531951  j = ParseCommandLineOptions(argc, argv, molecules, periode, configuration, ConfigFileName);
    19541952  switch(j) {
    1955     case 0:  // something went wrong
     1953    case 255:  // something went wrong
    19561954      delete(molecules); // also free's all molecules contained
    19571955      delete(periode);
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