Changeset d1fc7f

Timestamp:

Sep 6, 2008, 3:06:51 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:

a6b7fb

Parents:

a8aadf6

Message:

BUGFIX: Moved case 'a' in ParseCommandLineOptions() to the config_present == empty option switch.

If atoms were added to an newly-created and empty configuration file, this would not work, as the config file was still empty and hence config_present != present, so far needed for case 'a'. Now, it is moved in the vicinity of case 'P', where it belongs to and if the first atom is added, config_present is set to present.

File:

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

src/builder.cpp

@@ -901 +901 @@
               }
               break;
+            case 'a':
+              ExitFlag = 1;
+              SaveFlag = true;
+              cout << Verbose(1) << "Adding new atom with element " << argv[argptr] << " at (" << argv[argptr+1] << "," << argv[argptr+2] << "," << argv[argptr+3] << "), ";
+              first = new atom;
+              first->type = periode->FindElement(atoi(argv[argptr]));
+              if (first->type != NULL)
+                cout << Verbose(2) << "found element " << first->type->name << endl;
+              for (int i=NDIM;i--;)
+                first->x.x[i] = atof(argv[argptr+1+i]);
+              if (first->type != NULL) {
+                mol->AddAtom(first);  // add to molecule
+                if ((config_present == empty) && (mol->AtomCount != 0))
+                  config_present = present;
+              } else
+                cerr << Verbose(1) << "Could not find the specified element." << endl; 
+              argptr+=4;
+              break;
             default:   // no match? Don't step on (this is done in next switch's default)
               break;
@@ -945 +963 @@
               mol->Translate((const Vector *)&x);
               argptr+=3;
-              break;
-            case 'a':
-              ExitFlag = 1;
-              SaveFlag = true;
-              cout << Verbose(1) << "Adding new atom with element " << argv[argptr] << " at (" << argv[argptr+1] << "," << argv[argptr+2] << "," << argv[argptr+3] << "), ";
-              first = new atom;
-              first->type = periode->FindElement(atoi(argv[argptr]));
-              if (first->type != NULL)
-                cout << Verbose(2) << "found element " << first->type->name << endl;
-              for (int i=NDIM;i--;)
-                first->x.x[i] = atof(argv[argptr+1+i]);
-              if (first->type != NULL)
-                mol->AddAtom(first);  // add to molecule
-              else
-                cerr << Verbose(1) << "Could not find the specified element." << endl; 
-              argptr+=4;
               break;
             case 's':