- Timestamp:
- Jul 27, 2009, 2:08:27 PM (15 years ago)
- 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
- File:
-
- 1 edited
Legend:
- Unmodified
- Added
- Removed
-
src/builder.cpp
ra20e6a rb6d8a9 878 878 for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++) 879 879 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 } 890 891 break; 891 892 … … 1326 1327 clock_t start,end; 1327 1328 int argptr; 1329 molecule *mol = NULL; 1328 1330 strncpy(configuration.databasepath, LocalPath, MAXSTRINGSIZE-1); 1329 1330 // simply create a new molecule, wherein the config file is loaded and the manipulation takes place1331 molecule *mol = new molecule(periode);1332 mol->ActiveFlag = true;1333 molecules->insert(mol);1334 1331 1335 1332 if (argc > 1) { // config file specified as option … … 1375 1372 cout << "\t-v/-V\t\tGives version information." << endl; 1376 1373 cout << "Note: config files must not begin with '-' !" << endl; 1377 delete(mol);1378 delete(periode);1379 1374 return (1); 1380 1375 break; … … 1383 1378 cout << argv[0] << " " << VERSIONSTRING << endl; 1384 1379 cout << "Build your own molecule position set." << endl; 1385 delete(mol);1386 delete(periode);1387 1380 return (1); 1388 1381 break; … … 1418 1411 // 3. Find config file name and parse if possible 1419 1412 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 1420 1418 cout << Verbose(0) << "Config file given." << endl; 1421 1419 test.open(argv[1], ios::in); … … 1953 1951 j = ParseCommandLineOptions(argc, argv, molecules, periode, configuration, ConfigFileName); 1954 1952 switch(j) { 1955 case 0: // something went wrong1953 case 255: // something went wrong 1956 1954 delete(molecules); // also free's all molecules contained 1957 1955 delete(periode);
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