Changeset 116f37 for src

Timestamp:

Jun 2, 2010, 2:38:07 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:

584a2a

Parents:

accebe

Message:

Case '-c' is now handled by CommandLineUI.

• BUGFIX: WorldAddEmptyBoundaryAction() - forgot to add boundary on atom translation.

Location:

src

Files:

• Actions/MapOfActions.cpp (modified) (1 diff)
• Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) (1 diff)
• builder.cpp (modified) (1 diff)

src/Actions/MapOfActions.cpp

@@ -185 +185 @@
 //  generic.insert("bond-file");
 //      generic.insert("bond-table");
-//  generic.insert("boundary");
+  generic.insert("boundary");
 //  generic.insert("bound-in-box");
 //  generic.insert("center-edge");

src/Actions/WorldAction/AddEmptyBoundaryAction.cpp

@@ -69 +69 @@
     AtomRunner = AllAtoms.begin();
     for (; AtomRunner != AllAtoms.end(); ++AtomRunner)
-      (*AtomRunner)->x -= Min;
+      (*AtomRunner)->x -= Min - boundary;
     delete dialog;
     return Action::success;

src/builder.cpp

@@ -2226 +2226 @@
                 performCriticalExit();
               } else {
-                SaveFlag = true;
-                j = -1;
-                DoLog(1) && (Log() << Verbose(1) << "Centering atoms in config file within given additional boundary." << endl);
-                // make every coordinate positive
-                mol->CenterEdge(&x);
-                // update Box of atoms by boundary
-                mol->SetBoxDimension(&x);
-                // translate each coordinate by boundary
-                double * const cell_size = World::getInstance().getDomain();
-                j=-1;
-                for (int i=0;i<NDIM;i++) {
-                  j += i+1;
-                  x[i] = atof(argv[argptr+i]);
-                  cell_size[j] += x[i]*2.;
-                }
-                mol->Translate((const Vector *)&x);
+                ArgcList.insert(argptr-1);
+                ArgcList.insert(argptr);
+                ArgcList.insert(argptr+1);
+                ArgcList.insert(argptr+2);
                 argptr+=3;
               }