Changeset b74f7d

Timestamp:

Mar 1, 2010, 8:41:21 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:

30d9e7

Parents:

821907

Message:

FIX: ParseCommandLineOptions - case 'C' used wrong LC width, case 'F' nows parses filler from file.

ParseCommandLineOptions:

• case 'C': Linked Cell width was set to fixed double of radius and was hence uncorrelated to the BinWidth. This is bad for subsequent DistanceToSurface() searches which use LC.
• case 'F': Filler molecules was encoded by hand so far, is now parsed from xyz file and the bond structure created by BondGraph.

File:

• src/builder.cpp (modified) (5 diffs)

src/builder.cpp

@@ -1419 +1419 @@
             Log() << Verbose(0) << "\t-E <id> <Z>\tChange atom <id>'s element to <Z>, <id> begins at 0." << endl;
             Log() << Verbose(0) << "\t-f <dist> <order>\tFragments the molecule in BOSSANOVA manner (with/out rings compressed) and stores config files in same dir as config (return code 0 - fragmented, 2 - no fragmentation necessary)." << endl;
-            Log() << Verbose(0) << "\t-F <dist_x> <dist_y> <dist_z> <epsilon> <randatom> <randmol> <DoRotate>\tFilling Box with water molecules." << endl;
-            Log() << Verbose(0) << "\t-FF <MaxDistance> <dist_x> <dist_y> <dist_z> <epsilon> <randatom> <randmol> <DoRotate>\tFilling Box with water molecules." << endl;
+            Log() << Verbose(0) << "\t-F <xyz of filler> <dist_x> <dist_y> <dist_z> <epsilon> <randatom> <randmol> <DoRotate>\tFilling Box with water molecules." << endl;
+            Log() << Verbose(0) << "\t-FF <MaxDistance> <xyz of filler> <dist_x> <dist_y> <dist_z> <epsilon> <randatom> <randmol> <DoRotate>\tFilling Box with water molecules." << endl;
             Log() << Verbose(0) << "\t-g <file>\tParses a bond length table from the given file." << endl;
             Log() << Verbose(0) << "\t-h/-H/-?\tGive this help screen." << endl;
@@ -1750 +1750 @@
                         ofstream output(argv[argptr+2]);
                         ofstream binoutput(argv[argptr+3]);
-                        const double radius = 5.;
+                        const double radius = 4.;
                         const double BinStart = atof(argv[argptr+4]);
                         const double BinEnd = atof(argv[argptr+5]);
+                        double LCWidth = 20.;
+                        if (BinEnd > 0) {
+                          if (BinEnd > 2.*radius)
+                              LCWidth = BinEnd;
+                          else
+                            LCWidth = 2.*radius;
+                        }
 
                         // get the boundary
@@ -1772 +1779 @@
                           (*BigFinder)->ActiveFlag = (*BigFinder == Boundary) ? false : true;
                         }
-                        LCList = new LinkedCell(Boundary, 2.*radius);
+                        LCList = new LinkedCell(Boundary, LCWidth);
                         element *elemental = periode->FindElement((const int) atoi(argv[argptr+1]));
                         FindNonConvexBorder(Boundary, TesselStruct, LCList, radius, NULL);
-                        int ranges[NDIM] = {1,1,1};
-                        CorrelationToSurfaceMap *surfacemap = PeriodicCorrelationToSurface( molecules, elemental, TesselStruct, LCList, ranges );
+                        //int ranges[NDIM] = {1,1,1};
+                        CorrelationToSurfaceMap *surfacemap = CorrelationToSurface( molecules, elemental, TesselStruct, LCList); // for Periodic..(): ..., ranges );
                         OutputCorrelationToSurface(&output, surfacemap);
+                        // check whether radius was appropriate
+                        {
+                        double start; double end;
+                        GetMinMax( surfacemap, start, end);
+                        if (LCWidth < end)
+                          eLog() << Verbose(1) << "Linked Cell width is smaller than the found range of values! Bins can only be correct up to: " << radius << "." << endl;
+                        }
                         BinPairMap *binmap = BinData( surfacemap, 0.5, BinStart, BinEnd );
                         OutputCorrelation ( &binoutput, binmap );
@@ -1824 +1838 @@
                 Log() << Verbose(0) << "Filling with maximum layer distance of " << MaxDistance << "." << endl;
               }
-              if (argptr+6 >=argc) {
+              if ((argptr+7 >=argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) || (!IsValidNumber(argv[argptr+3])) || (!IsValidNumber(argv[argptr+4])) || (!IsValidNumber(argv[argptr+5])) || (!IsValidNumber(argv[argptr+6])) || (!IsValidNumber(argv[argptr+7]))) {
                 ExitFlag = 255;
-                eLog() << Verbose(0) << "Not enough or invalid arguments given for filling box with water: -F <dist_x> <dist_y> <dist_z> <boundary> <randatom> <randmol> <DoRotate>" << endl;
+                eLog() << Verbose(0) << "Not enough or invalid arguments given for filling box with water: -F <xyz of filler> <dist_x> <dist_y> <dist_z> <boundary> <randatom> <randmol> <DoRotate>" << endl;
                 performCriticalExit();
               } else {
@@ -1833 +1847 @@
                 // construct water molecule
                 molecule *filler = new molecule(periode);
+                if (!filler->AddXYZFile(argv[argptr])) {
+                  eLog() << Verbose(0) << "Could not parse filler molecule from " << argv[argptr] << "." << endl;
+                }
+                filler->SetNameFromFilename(argv[argptr]);
+                configuration.BG->ConstructBondGraph(filler);
                 molecule *Filling = NULL;
-                atom *second = NULL, *third = NULL;
-//                first = new atom();
-//                first->type = periode->FindElement(5);
-//                first->x.Zero();
-//                filler->AddAtom(first);
-                first = new atom();
-                first->type = periode->FindElement(1);
-                first->x.Init(0.441, -0.143, 0.);
-                filler->AddAtom(first);
-                second = new atom();
-                second->type = periode->FindElement(1);
-                second->x.Init(-0.464, 1.137, 0.0);
-                filler->AddAtom(second);
-                third = new atom();
-                third->type = periode->FindElement(8);
-                third->x.Init(-0.464, 0.177, 0.);
-                filler->AddAtom(third);
-                filler->AddBond(first, third, 1);
-                filler->AddBond(second, third, 1);
                 // call routine
                 double distance[NDIM];
                 for (int i=0;i<NDIM;i++)
-                  distance[i] = atof(argv[argptr+i]);
-                Filling = FillBoxWithMolecule(molecules, filler, configuration, MaxDistance, distance, atof(argv[argptr+3]), atof(argv[argptr+4]), atof(argv[argptr+5]), atoi(argv[argptr+6]));
+                  distance[i] = atof(argv[argptr+i+1]);
+                Filling = FillBoxWithMolecule(molecules, filler, configuration, MaxDistance, distance, atof(argv[argptr+4]), atof(argv[argptr+5]), atof(argv[argptr+6]), atoi(argv[argptr+7]));
                 if (Filling != NULL) {
                   Filling->ActiveFlag = false;