Changeset 9a0dc8

Timestamp:

Nov 10, 2009, 8:58:31 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:

f1ef60a

Parents:

36eb4e

Message:

Only biggest molecule is tesselated for now in ParseCommandLineOptions() - case 'N'
Signed-off-by: Frederik Heber <heber@…>

File:

• src/builder.cpp (modified) (1 diff)

src/builder.cpp

@@ -1747 +1747 @@
                 class Tesselation *T = NULL;
                 const LinkedCell *LCList = NULL;
-                string filename(argv[argptr+1]);
-                filename.append(".csv");
-                Log() << Verbose(0) << "Evaluating non-convex envelope.";
+                molecule * Boundary = NULL;
+                //string filename(argv[argptr+1]);
+                //filename.append(".csv");
+                Log() << Verbose(0) << "Evaluating non-convex envelope of biggest molecule.";
                 Log() << Verbose(1) << "Using rolling ball of radius " << atof(argv[argptr]) << " and storing tecplot data in " << argv[argptr+1] << "." << endl;
+                // find biggest molecule
+                int counter  = 0;
+                for (MoleculeList::iterator BigFinder = molecules->ListOfMolecules.begin(); BigFinder != molecules->ListOfMolecules.end(); BigFinder++) {
+                  (*BigFinder)->CountAtoms();
+                  if ((Boundary == NULL) || (Boundary->AtomCount < (*BigFinder)->AtomCount)) {
+                    Boundary = *BigFinder;
+                  }
+                  counter++;
+                }
+                Log() << Verbose(1) << "Biggest molecule has " << Boundary->AtomCount << " atoms." << endl;
                 start = clock();
-                LCList = new LinkedCell(mol, atof(argv[argptr])*2.);
-                FindNonConvexBorder(mol, T, LCList, atof(argv[argptr]), argv[argptr+1]);
+                LCList = new LinkedCell(Boundary, atof(argv[argptr])*2.);
+                FindNonConvexBorder(Boundary, T, LCList, atof(argv[argptr]), argv[argptr+1]);
                 //FindDistributionOfEllipsoids(T, &LCList, N, number, filename.c_str());
                 end = clock();