Changeset cc2ee5 for src/builder.cpp

Timestamp:

Dec 29, 2008, 9:46:58 PM (16 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:

a98603

Parents:

02bfde

git-author:

Frederik Heber <heber@…> (12/29/08 21:26:43)

git-committer:

Frederik Heber <heber@…> (12/29/08 21:46:58)

Message:

Just a temporary commit

File:

• src/builder.cpp (modified) (3 diffs, 1 prop)

src/builder.cpp

@@ -259 +259 @@
 static void CenterAtoms(molecule *mol)
 {
-  Vector x, y;
+  Vector x, y, helper;
   char choice;  // menu choice char
 
@@ -292 +292 @@
       mol->CenterEdge((ofstream *)&cout, &x);  // make every coordinate positive
       mol->Translate(&y); // translate by boundary
-      mol->SetBoxDimension(&(x+y*2));  // update Box of atoms by boundary
+      helper.CopyVector(&y);
+      helper.Scale(2.);
+      helper.AddVector(&x);
+      mol->SetBoxDimension(&helper);  // update Box of atoms by boundary
       break;
     case 'd':
@@ -1004 +1007 @@
               }
               break;
-            case 'A':
-                ExitFlag = 1;
-                if ((argptr >= argc) || (argv[argptr][0] == '-')){
-                        ExitFlag =255;
-                        cerr << "Missing source file for bonds in molecule: -A <bond sourcefile>" << endl;
-                }
-                else{
-                        cout << "Parsing bonds from " << argv[argptr] << "." << endl;
-                    ifstream *input = new ifstream(argv[argptr]);
-                        mol->CreateAdjacencyList2((ofstream *)&cout, input);
-                        input->close();
-                }
-                break;
-            case 'N':
-                ExitFlag = 1;
-                if ((argptr >= argc) || (argv[argptr][0] == '-')){
-                        ExitFlag = 255;
-                        cerr << "Not enough or invalid arguments given for non-convex envelope: -o <tecplot output file>" << endl;
-                        }
-                else {
-                        cout << Verbose(0) << "Evaluating npn-convex envelope.";
-                        ofstream *output = new ofstream(argv[argptr], ios::trunc);
-                        cout << Verbose(1) << "Storing tecplot data in " << argv[argptr] << "." << endl;
-                        Find_non_convex_border((ofstream *)&cout, output, mol);
-                        output->close();
-                        delete(output);
-                        argptr+=1;
-                        }
-                break;
+                                                case 'A':
+                                                        ExitFlag = 1;
+                                                        if ((argptr >= argc) || (!IsValidNumber(argv[argptr])) || (argv[argptr][0] == '-')) {
+                                                                ExitFlag =255;
+                                                                cerr << "Missing source file for bonds in molecule: -A <bond sourcefile>" << endl;
+                                                        } else {
+                                                                cout << "Parsing bonds from " << argv[argptr] << "." << endl;
+                                                                ifstream *input = new ifstream(argv[argptr]);
+                                                                mol->CreateAdjacencyList2((ofstream *)&cout, input);
+                                                                input->close();
+                                                        }
+                                                        break;
+                                                case 'N':
+                                                        ExitFlag = 1;
+                                                        if ((argptr+1 >= argc) || (argv[argptr+1][0] == '-')){
+                                                                ExitFlag = 255;
+                                                                cerr << "Not enough or invalid arguments given for non-convex envelope: -o <radius> <tecplot output file>" << endl;
+                                                        } else {
+                                                                cout << Verbose(0) << "Evaluating npn-convex envelope.";
+                                                                string TempName(argv[argptr+1]);
+                                                                TempName.append(".r3d");
+                                                                ofstream *output = new ofstream(TempName.c_str(), ios::trunc);
+                                                                cout << Verbose(1) << "Using rolling ball of radius " << atof(argv[argptr]) << " and storing tecplot data in " << argv[argptr+1] << "." << endl;
+                                                                Find_non_convex_border((ofstream *)&cout, output, mol, argv[argptr+1], atof(argv[argptr]));
+                                                                output->close();
+                                                                delete(output);
+                                                                argptr+=2;
+                                                        }
+                                                        break;
             case 'T':
               ExitFlag = 1;