Changeset 164a33

Timestamp:

Feb 8, 2010, 3:29:35 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:

775d133

Parents:

1f1b23

git-author:

Frederik Heber <heber@…> (02/08/10 15:26:30)

git-committer:

Frederik Heber <heber@…> (02/08/10 15:29:35)

Message:

changed case 'C' of ParseCommandLineOptions to allow selecting between the three different pair correlation analysis functions.

• case 'C' now expects additional first parameter: A type which is E, S or P for element, surface or pair. Via a switch it selects either of the three functions.

Signed-off-by: Frederik Heber <heber@…>

File:

• src/builder.cpp (modified) (2 diffs)

src/builder.cpp

@@ -1412 +1412 @@
             Log() << Verbose(0) << "\t-B xx xy xz yy yz zz\tBound atoms by domain with given symmetric matrix of (xx,xy,xz,yy,yz,zz)." << endl;
             Log() << Verbose(0) << "\t-c x1 x2 x3\tCenter atoms in domain with a minimum distance to boundary of (x1,x2,x3)." << endl;
-            Log() << Verbose(0) << "\t-C <Z> <output> <bin output>\tPair Correlation analysis." << endl;
+            Log() << Verbose(0) << "\t-C <type> [parms] <output> <bin output>\tPair Correlation analysis." << endl;
             Log() << Verbose(0) << "\t-d x1 x2 x3\tDuplicate cell along each axis by given factor." << endl;
             Log() << Verbose(0) << "\t-D <bond distance>\tDepth-First-Search Analysis of the molecule, giving cycles and tree/back edges." << endl;
@@ -1678 +1678 @@
             case 'C':
               if (ExitFlag == 0) ExitFlag = 1;
-              if ((argptr+2 >= argc) || (!IsValidNumber(argv[argptr])) || (argv[argptr][0] == '-') || (argv[argptr+1][0] == '-') || (argv[argptr+2][0] == '-')) {
+              if ((argptr >= argc)) {
                 ExitFlag = 255;
-                eLog() << Verbose(0) << "Not enough or invalid arguments given for pair correlation analysis: -C <Z> <output> <bin output>" << endl;
+                eLog() << Verbose(0) << "Not enough or invalid arguments given for pair correlation analysis: -C <type: E/P/S> [more params] <output> <bin output>" << endl;
                 performCriticalExit();
               } else {
-                ofstream output(argv[argptr+1]);
-                ofstream binoutput(argv[argptr+2]);
-                const double radius = 5.;
-
-                // get the boundary
-                class molecule *Boundary = NULL;
-                class Tesselation *TesselStruct = NULL;
-                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++;
+                switch(argv[argptr][0]) {
+                  case 'E':
+                    {
+                      if ((argptr+4 >= argc) || (!IsValidNumber(argv[argptr+1])) ||  (!IsValidNumber(argv[argptr+2])) || (argv[argptr+1][0] == '-') || (argv[argptr+2][0] == '-') || (argv[argptr+3][0] == '-') || (argv[argptr+4][0] == '-')) {
+                        ExitFlag = 255;
+                        eLog() << Verbose(0) << "Not enough or invalid arguments given for pair correlation analysis: -C E <Z1> <Z2> <output> <bin output>" << endl;
+                        performCriticalExit();
+                      } else {
+                        ofstream output(argv[argptr+3]);
+                        ofstream binoutput(argv[argptr+4]);
+
+                        element *elemental = periode->FindElement((const int) atoi(argv[argptr]));
+                        element *elemental2 = periode->FindElement((const int) atoi(argv[argptr+1]));
+                        PairCorrelationMap *correlationmap = PairCorrelation(molecules, elemental, elemental2);
+                        //OutputCorrelationToSurface(&output, correlationmap);
+                        BinPairMap *binmap = BinData( correlationmap, 0.5, 0., 0. );
+                        OutputCorrelation ( &binoutput, binmap );
+                        output.close();
+                        binoutput.close();
+                        delete(binmap);
+                        delete(correlationmap);
+                        argptr+=5;
+                      }
+                    }
+                    break;
+
+                  case 'P':
+                    {
+                      if ((argptr+6 >= argc) || (!IsValidNumber(argv[argptr+1])) ||  (!IsValidNumber(argv[argptr+2])) || (!IsValidNumber(argv[argptr+3])) || (!IsValidNumber(argv[argptr+4])) || (argv[argptr+1][0] == '-') || (argv[argptr+2][0] == '-') || (argv[argptr+3][0] == '-') || (argv[argptr+4][0] == '-') || (argv[argptr+5][0] == '-') || (argv[argptr+6][0] == '-')) {
+                        ExitFlag = 255;
+                        eLog() << Verbose(0) << "Not enough or invalid arguments given for pair correlation analysis: -C P <Z1> <x> <y> <z> <output> <bin output>" << endl;
+                        performCriticalExit();
+                      } else {
+                        ofstream output(argv[argptr+5]);
+                        ofstream binoutput(argv[argptr+6]);
+
+                        element *elemental = periode->FindElement((const int) atoi(argv[argptr]));
+                        Vector *Point = new Vector((const double) atof(argv[argptr+1]),(const double) atof(argv[argptr+2]),(const double) atof(argv[argptr+3]));
+                        CorrelationToPointMap *correlationmap = CorrelationToPoint(molecules, elemental, Point);
+                        //OutputCorrelationToSurface(&output, correlationmap);
+                        BinPairMap *binmap = BinData( correlationmap, 0.5, 0., 0. );
+                        OutputCorrelation ( &binoutput, binmap );
+                        output.close();
+                        binoutput.close();
+                        delete(Point);
+                        delete(binmap);
+                        delete(correlationmap);
+                        argptr+=7;
+                      }
+                    }
+                    break;
+
+                  case 'S':
+                    {
+                      if ((argptr+3 >= argc) || (!IsValidNumber(argv[argptr+1])) || (argv[argptr+1][0] == '-') || (argv[argptr+2][0] == '-') || (argv[argptr+3][0] == '-')) {
+                        ExitFlag = 255;
+                        eLog() << Verbose(0) << "Not enough or invalid arguments given for pair correlation analysis: -C S <Z> <output> <bin output>" << endl;
+                        performCriticalExit();
+                      } else {
+                        ofstream output(argv[argptr+2]);
+                        ofstream binoutput(argv[argptr+3]);
+                        const double radius = 5.;
+
+
+                        // get the boundary
+                        class molecule *Boundary = NULL;
+                        class Tesselation *TesselStruct = NULL;
+                        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(Boundary, TesselStruct, LCList, radius, NULL);
+                        int ranges[NDIM] = {1,1,1};
+                        CorrelationToSurfaceMap *surfacemap = PeriodicCorrelationToSurface( molecules, elemental, TesselStruct, LCList, ranges );
+                        //OutputCorrelationToSurface(&output, surfacemap);
+                        BinPairMap *binmap = BinData( 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);
+                        delete(binmap);
+                        delete(surfacemap);
+                        argptr+=4;
+                      }
+                    }
+                    break;
+
+                  default:
+                    ExitFlag = 255;
+                    eLog() << Verbose(0) << "Invalid type given for pair correlation analysis: -C <type: E/P/S> [more params] <output> <bin output>" << endl;
+                    performCriticalExit();
+                    break;
                 }
-                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(Boundary, TesselStruct, LCList, radius, NULL);
-                int ranges[NDIM] = {1,1,1};
-                CorrelationToSurfaceMap *surfacemap = PeriodicCorrelationToSurface( molecules, elemental, TesselStruct, LCList, ranges );
-                OutputCorrelationToSurface(&output, surfacemap);
-                BinPairMap *binmap = BinData( surfacemap, 0.5, 0., 20. );
-                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);
-                argptr+=3;
               }
               break;