Changeset 09048c

Timestamp:

Oct 17, 2009, 4:54:46 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:

44a59b

Parents:

ad8b0d

Message:

Added case 'C' to ParseCommandLineOptions with CorrelationToSurface().

• new case 'C' with CorrelationToSurface()
• lots of changes in ParseCommandLineOptions() as all of the tests for ...[0] != '-' were wrong for numbers (e.g. -t -1. 0. 0. in translation case)
• small fix to BinData() as 0. was given instead of 0 for second argument of outmap (but should be integer)

Location:

src

Files:

• analysis_correlation.hpp (modified) (1 diff)
• builder.cpp (modified) (7 diffs)

src/analysis_correlation.hpp

@@ -114 +114 @@
     end = BinEnd;
     for (double runner = start; runner <= end; runner += BinWidth)
-      outmap->insert( pair<double, int> (runner, 0.) );
+      outmap->insert( pair<double, int> (runner, 0) );
   }
 

src/builder.cpp

@@ -1507 +1507 @@
             case 'a':
               if (ExitFlag == 0) ExitFlag = 1;
-              if ((argptr >= argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr+1]))) {
+              if ((argptr >= argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) || (!IsValidNumber(argv[argptr+3]))) {
                 ExitFlag = 255;
                 cerr << "Not enough or invalid arguments for adding atom: -a <element> <x> <y> <z>" << endl;
@@ -1579 +1579 @@
             case 'C':
               if (ExitFlag == 0) ExitFlag = 1;
-              if ((argptr+1 >= argc) || (argv[argptr+1][0] == '-') || (argv[argptr+2][0] == '-')) {
+              if ((argptr+2 >= argc) || (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 <output> <bin output>" << endl;
+                cerr << "Not enough or invalid arguments given for pair correlation analysis: -C <boundary conf> <output> <bin output>" << endl;
               } else {
                 SaveFlag = false;
-                ofstream output(argv[argptr]);
-                ofstream binoutput(argv[argptr+1]);
-                class Tesselation T;
+                ofstream output(argv[argptr+1]);
+                ofstream binoutput(argv[argptr+2]);
                 const double radius = 5.;
-                LinkedCell LCList(mol, 2.*radius);
+
+                // get the boundary
+                class molecule *Boundary = new molecule(periode);
+                struct ConfigFileBuffer *FileBuffer = NULL;
+                PrepareFileBuffer(argv[argptr], FileBuffer);
+                LoadMolecule(Boundary, FileBuffer, periode, false);
+                LinkedCell LCList(Boundary, 2.*radius);
                 element *oxygen = periode->FindElement(8);
-                FindNonConvexBorder((ofstream *)&cout, mol, &LCList, radius, NULL);
-                CorrelationToSurfaceMap *surfacemap = CorrelationToSurface( (ofstream *)&cout, mol, oxygen, mol->TesselStruct, &LCList );
+                FindNonConvexBorder((ofstream *)&cout, Boundary, &LCList, radius, NULL);
+
+                CorrelationToSurfaceMap *surfacemap = CorrelationToSurface( (ofstream *)&cout, mol, oxygen, Boundary->TesselStruct, &LCList );
                 BinPairMap *binmap = BinData( (ofstream *)&cout, surfacemap, 0.5, 0., 0. );
                 OutputCorrelation ( &binoutput, binmap );
                 output.close();
                 binoutput.close();
-                argptr+=2;
+                delete(FileBuffer);
+                delete(Boundary);
+                argptr+=3;
               }
               break;
@@ -1759 +1767 @@
             case 't':
               if (ExitFlag == 0) ExitFlag = 1;
-              if ((argptr+2 >= argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) ) {
+              if ((argptr+2 >= argc) || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) ) {
                 ExitFlag = 255;
                 cerr << "Not enough or invalid arguments given for translation: -t <x> <y> <z>" << endl;
@@ -1774 +1782 @@
             case 'T':
               if (ExitFlag == 0) ExitFlag = 1;
-              if ((argptr+2 >= argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) ) {
+              if ((argptr+2 >= argc) || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) ) {
                 ExitFlag = 255;
                 cerr << "Not enough or invalid arguments given for periodic translation: -T <x> <y> <z>" << endl;
@@ -1789 +1797 @@
             case 's':
               if (ExitFlag == 0) ExitFlag = 1;
-              if ((argptr >= argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr])) ) {
+              if ((argptr >= argc) || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) ) {
                 ExitFlag = 255;
-                cerr << "Not enough or invalid arguments given for scaling: -s <factor/[factor_x]> [factor_y] [factor_z]" << endl;
+                cerr << "Not enough or invalid arguments given for scaling: -s <factor_x> [factor_y] [factor_z]" << endl;
               } else {
                 SaveFlag = true;
@@ -1798 +1806 @@
                 factor = new double[NDIM];
                 factor[0] = atof(argv[argptr]);
-                if ((argptr < argc) && (IsValidNumber(argv[argptr])))
-                  argptr++;
-                factor[1] = atof(argv[argptr]);
-                if ((argptr < argc) && (IsValidNumber(argv[argptr])))
-                  argptr++;
-                factor[2] = atof(argv[argptr]);
+                factor[1] = atof(argv[argptr+1]);
+                factor[2] = atof(argv[argptr+2]);
                 mol->Scale(&factor);
                 for (int i=0;i<NDIM;i++) {
@@ -1811 +1815 @@
                 }
                 delete[](factor);
-                argptr+=1;
+                argptr+=3;
               }
               break;