Changeset a5551b for src/builder.cpp

Timestamp:

Nov 4, 2009, 2:54:31 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:

c9bce3e

Parents:

eecd33

Message:

Closed ticket #48 (AnalysisCorrelation...() take MoleculeListClass instead of molecule).

• ParseCommandLineOptions() - case C: ActiveFlag ist set for all but the boundary molecule (i.e. the biggest).
• changed parameters of PairCorrelation(), CorrelationToPoint(), CorrelationToSurface()
• adapted unit tests: AnalysisPairCorrelationUnitTest, AnalysisPairCorrelationUnitTest, AnalysisCorrelationToPointUnitTest

• MISSING: AnalysisCorrelationToSurfaceUnitTest yet only deals with a single molecule instead of multiple ones ...

File:

• src/builder.cpp (modified) (1 diff)

src/builder.cpp

@@ -1616 +1616 @@
                 const LinkedCell *LCList = NULL;
                 // find biggest molecule
+                int counter  = 0;
                 for (MoleculeList::iterator BigFinder = molecules->ListOfMolecules.begin(); BigFinder != molecules->ListOfMolecules.end(); BigFinder++) {
                   if ((Boundary == NULL) || (Boundary->AtomCount < (*BigFinder)->AtomCount)) {
                     Boundary = *BigFinder;
                   }
+                  counter++;
+                }
+                bool *Actives = Malloc<bool>(counter, "ParseCommandLineOptions() - case C -- *Actives");
+                counter = 0;
+                for (MoleculeList::iterator BigFinder = molecules->ListOfMolecules.begin(); BigFinder != molecules->ListOfMolecules.end(); BigFinder++) {
+                  Actives[counter] = (*BigFinder)->ActiveFlag;
+                  (*BigFinder)->ActiveFlag = (*BigFinder == Boundary) ? false : true;
                 }
                 LCList = new LinkedCell(Boundary, 2.*radius);
                 element *elemental = periode->FindElement((const int) atoi(argv[argptr]));
                 FindNonConvexBorder((ofstream *)&cout, Boundary, TesselStruct, LCList, radius, NULL);
-                CorrelationToSurfaceMap *surfacemap = CorrelationToSurface( (ofstream *)&cout, mol, elemental, TesselStruct, LCList );
+                CorrelationToSurfaceMap *surfacemap = CorrelationToSurface( (ofstream *)&cout, molecules, elemental, TesselStruct, LCList );
                 BinPairMap *binmap = BinData( (ofstream *)&cout, surfacemap, 0.5, 0., 0. );
                 OutputCorrelation ( &binoutput, binmap );
                 output.close();
                 binoutput.close();
+                for (MoleculeList::iterator BigFinder = molecules->ListOfMolecules.begin(); BigFinder != molecules->ListOfMolecules.end(); BigFinder++)
+                  (*BigFinder)->ActiveFlag = Actives[counter];
+                Free(&Actives);
                 delete(LCList);
                 delete(TesselStruct);