Changeset f4e1f5 for src

Timestamp:

Nov 4, 2009, 12:57:24 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:

eecd33

Parents:

3c349b

Message:

Closing ticket #47, case 'C' uses biggest molecule as surface for pair correlation.

File:

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

src/builder.cpp

@@ -1602 +1602 @@
             case 'C':
               if (ExitFlag == 0) ExitFlag = 1;
-              if ((argptr+2 >= argc) || (argv[argptr][0] == '-') || (argv[argptr+1][0] == '-') || (argv[argptr+2][0] == '-')) {
+              if ((argptr+2 >= argc) || (!IsValidNumber(argv[argptr])) || (argv[argptr][0] == '-') || (argv[argptr+1][0] == '-') || (argv[argptr+2][0] == '-')) {
                 ExitFlag = 255;
-                cerr << "Not enough or invalid arguments given for pair correlation analysis: -C <boundary conf> <output> <bin output>" << endl;
+                cerr << "Not enough or invalid arguments given for pair correlation analysis: -C <Z> <output> <bin output>" << endl;
               } else {
                 SaveFlag = false;
@@ -1612 +1612 @@
 
                 // get the boundary
-                class molecule *Boundary = new molecule(periode);
+                class molecule *Boundary = NULL;
                 class Tesselation *TesselStruct = NULL;
-                struct ConfigFileBuffer *FileBuffer = NULL;
-                PrepareFileBuffer(argv[argptr], FileBuffer);
-                LoadMolecule(Boundary, FileBuffer, periode, false);
                 const LinkedCell *LCList = NULL;
+                // find biggest molecule
+                for (MoleculeList::iterator BigFinder = molecules->ListOfMolecules.begin(); BigFinder != molecules->ListOfMolecules.end(); BigFinder++) {
+                  if ((Boundary == NULL) || (Boundary->AtomCount < (*BigFinder)->AtomCount)) {
+                    Boundary = *BigFinder;
+                  }
+                }
                 LCList = new LinkedCell(Boundary, 2.*radius);
-                element *oxygen = periode->FindElement(8);
+                element *elemental = periode->FindElement((const int) atoi(argv[argptr]));
                 FindNonConvexBorder((ofstream *)&cout, Boundary, TesselStruct, LCList, radius, NULL);
-                CorrelationToSurfaceMap *surfacemap = CorrelationToSurface( (ofstream *)&cout, mol, oxygen, TesselStruct, LCList );
+                CorrelationToSurfaceMap *surfacemap = CorrelationToSurface( (ofstream *)&cout, mol, elemental, TesselStruct, LCList );
                 BinPairMap *binmap = BinData( (ofstream *)&cout, surfacemap, 0.5, 0., 0. );
                 OutputCorrelation ( &binoutput, binmap );
@@ -1627 +1630 @@
                 binoutput.close();
                 delete(LCList);
-                delete(FileBuffer);
                 delete(TesselStruct);
-                delete(Boundary);
                 argptr+=3;
               }