Changeset a251a3 for src/builder.cpp

Timestamp:

May 26, 2008, 10:52:00 AM (18 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, Candidate_v1.7.0, 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:

9a1b84

Parents:

040f93

Message:

molecule::CreateAdjacencyList() now needs IsAngstroem as parameter

This is necessary, as the database values (covalent radii et al) are in Angstroem, hence don't match if we use Bohrradii as length unit instead. CreateAdjacencyList() converts units and now finds correct bond structure and fragments properly.

File:

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

src/builder.cpp

@@ -931 +931 @@
                 cout << Verbose(0) << "Creating connection matrix..." << endl;
                 start = clock();
-                mol->CreateAdjacencyList((ofstream *)&cout, atof(argv[argptr++]));
+                mol->CreateAdjacencyList((ofstream *)&cout, atof(argv[argptr++]), configuration.GetIsAngstroem());
                 cout << Verbose(0) << "Fragmenting molecule with current connection matrix ..." << endl;
                 if (mol->first->next != mol->last) {
@@ -1116 +1116 @@
           }
           if (mol->first->next != mol->last) // if connect matrix is present already, redo it
-            mol->CreateAdjacencyList((ofstream *)&cout, mol->BondDistance);
+            mol->CreateAdjacencyList((ofstream *)&cout, mol->BondDistance, configuration.GetIsAngstroem());
           // free memory
           delete[](Elements);
@@ -1159 +1159 @@
         cin >> tmp1;
         start = clock();
-        mol->CreateAdjacencyList((ofstream *)&cout, tmp1);
+        mol->CreateAdjacencyList((ofstream *)&cout, tmp1, configuration.GetIsAngstroem());
         //mol->CreateListOfBondsPerAtom((ofstream *)&cout);
         Subgraphs = mol->DepthFirstSearchAnalysis((ofstream *)&cout, false, MinimumRingSize);