Changeset 158c594

Timestamp:

May 30, 2010, 11:40:04 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:

5ddb8a

Parents:

2a92ff

Message:

Case '-b' now handled by CommandLineUI and fixes.

• ParseCommandLineOptions() - rather use the old code still to check whether appropriate number of arguments present
• bound-in-box is just ensuring all atoms are within current box, i.e. no new box is specified (there is no pendant to that in ParseCommandLineOptions)
• WorldCenterInBox action however has to parse a box, corrected.

Location:

src

Files:

• Actions/MapOfActions.cpp (modified) (3 diffs)
• Actions/WorldAction/CenterInBoxAction.cpp (modified) (1 diff)
• builder.cpp (modified) (3 diffs)

src/Actions/MapOfActions.cpp

@@ -93 +93 @@
   ShortFormMap["bond-file"] = "A";
   ShortFormMap["boundary"] = "c";
-  ShortFormMap["bound-in-box"] = "B";
   ShortFormMap["change-box"] = "B";
   ShortFormMap["center-edge"] = "O";
@@ -134 +133 @@
   TypeMap["bond-table"] = String;
   TypeMap["boundary"] = Vector;
-  TypeMap["bound-in-box"] = ListOfDoubles;
   TypeMap["center-in-box"] = ListOfDoubles;
   TypeMap["change-box"] = ListOfDoubles;
@@ -190 +188 @@
 //  generic.insert("bound-in-box");
 //  generic.insert("center-edge");
-//  generic.insert("center-in-box");
+  generic.insert("center-in-box");
         generic.insert("change-box");
 //  generic.insert("change-molname");

src/Actions/WorldAction/CenterInBoxAction.cpp

@@ -33 +33 @@
   Dialog *dialog = UIFactory::getInstance().makeDialog();
 
-  dialog->queryEmpty(NAME, MapOfActions::getInstance().getDescription(NAME));
+  double * cell_size = World::getInstance().getDomain();
+  dialog->queryBox(NAME, &cell_size, MapOfActions::getInstance().getDescription(NAME));
 
   if(dialog->display()) {

src/builder.cpp

@@ -2171 +2171 @@
               break;
             case 's':
-              ArgcList.insert(argptr-1);
-              ArgcList.insert(argptr);
-              ArgcList.insert(argptr+1);
-              ArgcList.insert(argptr+2);
-              argptr+=3;
-              if (ExitFlag == 0) ExitFlag = 1;
+              if (ExitFlag == 0) ExitFlag = 1;
+              if ((argptr+2 >= argc) || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) ) {
+                ExitFlag = 255;
+                DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for scaling: -s <factor_x> [factor_y] [factor_z]" << endl);
+                performCriticalExit();
+              } else {
+                ArgcList.insert(argptr-1);
+                ArgcList.insert(argptr);
+                ArgcList.insert(argptr+1);
+                ArgcList.insert(argptr+2);
+                argptr+=3;
+              }
               break;
             case 'b':
@@ -2185 +2191 @@
                 performCriticalExit();
               } else {
-                SaveFlag = true;
-                j = -1;
-                DoLog(1) && (Log() << Verbose(1) << "Centering atoms in config file within given simulation box." << endl);
-                double * const cell_size = World::getInstance().getDomain();
-                for (int i=0;i<6;i++) {
-                  cell_size[i] = atof(argv[argptr+i]);
-                }
-                // center
-                mol->CenterInBox();
+                ArgcList.insert(argptr-1);
+                ArgcList.insert(argptr);
+                ArgcList.insert(argptr+1);
+                ArgcList.insert(argptr+2);
+                ArgcList.insert(argptr+3);
+                ArgcList.insert(argptr+4);
+                ArgcList.insert(argptr+5);
                 argptr+=6;
               }
@@ -2204 +2208 @@
                 performCriticalExit();
               } else {
-                SaveFlag = true;
-                j = -1;
-                DoLog(1) && (Log() << Verbose(1) << "Centering atoms in config file within given simulation box." << endl);
-                double * const cell_size = World::getInstance().getDomain();
-                for (int i=0;i<6;i++) {
-                  cell_size[i] = atof(argv[argptr+i]);
-                }
-                // center
-                mol->BoundInBox();
+                ArgcList.insert(argptr-1);
+                ArgcList.insert(argptr);
+                ArgcList.insert(argptr+1);
+                ArgcList.insert(argptr+2);
+                ArgcList.insert(argptr+3);
+                ArgcList.insert(argptr+4);
+                ArgcList.insert(argptr+5);
                 argptr+=6;
               }