Changeset 34e0013 for src/builder.cpp

Timestamp:

Oct 30, 2009, 4:09:29 PM (16 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:

fa649a

Parents:

b21a64

Message:

BondGraph is initialized within config::Load(), as it has to happen after parsing options and before loading molecule. And various fixes.

• FIX: BondGraph::LoadBondLengthTable() - scans into TempContainer, which is later given over to BondLengthMatrix or NULL'd if parsing failed.
• BondGraph::ConstructBondGraph() adapted to above, uses both bonds functions depending on present BondLengthMatrix.
• FIX: BondGraph::GetBondLength() - checks whether BondLengthMatrix is NULL.
• config::Load() and ..LoadOld() get additionally the BondLengthFilename and allocates and parses BondGraph.
• builder.cpp ParseCommandLineOptions() has been adapted to above changes.
• FIX: molecule::CreateAdjacencyList() checks whether bonddistance is > 1. (otherwise quite useless and yielding too many cells).

File:

• src/builder.cpp (modified) (3 diffs)

src/builder.cpp

@@ -1451 +1451 @@
       return 1;
     }
-    // 3b. Find config file name and parse if possible
+    // 3b. Find config file name and parse if possible, also BondGraphFileName
     if (argv[1][0] != '-') {
       // simply create a new molecule, wherein the config file is loaded and the manipulation takes place
@@ -1479 +1479 @@
           case 1:
             cout << "new syntax." << endl;
-            configuration.Load(ConfigFileName, periode, mol);
+            configuration.Load(ConfigFileName, BondGraphFileName, periode, mol);
             configPresent = present;
             break;
           case 0:
             cout << "old syntax." << endl;
-            configuration.LoadOld(ConfigFileName, periode, mol);
+            configuration.LoadOld(ConfigFileName, BondGraphFileName, periode, mol);
             configPresent = present;
             break;
@@ -1494 +1494 @@
     } else
       configPresent = absent;
-    // 3c. parse the bond graph file if given
-    configuration.BG = new BondGraph(configuration.GetIsAngstroem());
-    if (configuration.BG->LoadBondLengthTable((ofstream *)&cout, BondGraphFileName)) {
-      cout << Verbose(0) << "Bond length table loaded successfully." << endl;
-    } else {
-      cout << Verbose(0) << "Bond length table loading failed." << endl;
-      return 1;
-    }
     // 4. parse again through options, now for those depending on elements db and config presence
     argptr = 1;