Changeset 77b2d7 for src

Timestamp:

Jun 11, 2010, 3:21:51 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:

aacce8

Parents:

e2b47c

Message:

Cases 't' and 'T' are now handled by CommandLineUI.

• TESTFIX: both cases have "--molecule-by-id 0 --periodic 0/1" added.
• ParseCommandLineOptions()- case 'T' removed as is handled by --periodic switch.
• added missing Action instantiation to CommandLineWindow::populateMoleculeActions().

Location:

src

Files:

• Actions/MapOfActions.cpp (modified) (1 diff)
• Actions/MoleculeAction/TranslateAction.cpp (modified) (1 diff)
• UIElements/CommandLineUI/CommandLineWindow.cpp (modified) (2 diffs)
• builder.cpp (modified) (1 diff)

src/Actions/MapOfActions.cpp

@@ -268 +268 @@
 //      generic.insert("subspace-dissect");
   generic.insert("suspend-in-water");
-//  generic.insert("translate-mol");
+  generic.insert("translate-mol");
         generic.insert("verbose");
 //  generic.insert("verlet-integrate");

src/Actions/MoleculeAction/TranslateAction.cpp

@@ -56 +56 @@
   dialog->queryMolecule("molecule-by-id", &mol, MapOfActions::getInstance().getDescription("molecule-by-id"));
   dialog->queryBoolean("periodic", &periodic, MapOfActions::getInstance().getDescription("periodic"));
+  cout << "pre-dialog" << endl;
 
   if(dialog->display()) {
+    cout << "post-dialog" << endl;
     DoLog(1) && (Log() << Verbose(1) << "Translating all ions by given vector." << endl);
     if (periodic)

src/UIElements/CommandLineUI/CommandLineWindow.cpp

@@ -34 +34 @@
 #include "Actions/MoleculeAction/SaveBondsAction.hpp"
 #include "Actions/MoleculeAction/SaveTemperatureAction.hpp"
+#include "Actions/MoleculeAction/TranslateAction.hpp"
 #include "Actions/MoleculeAction/VerletIntegrationAction.hpp"
 #include "Actions/ParserAction/LoadXyzAction.hpp"
@@ -126 +127 @@
   new MoleculeSaveBondsAction();
   new MoleculeSaveTemperatureAction();
+  new MoleculeTranslateAction();
   new MoleculeVerletIntegrationAction();
 }

src/builder.cpp

@@ -2016 +2016 @@
             case 't':
               if (ExitFlag == 0) ExitFlag = 1;
-              if ((argptr+2 >= argc) || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) ) {
+              if ((argptr+4 >= 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 translation: -t <x> <y> <z>" << endl);
+                DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for translation: -t <x> <y> <z> --molecule-by-id <molecule_id> --periodic <0/1>" << endl);
                 performCriticalExit();
               } else {
-                if (ExitFlag == 0) ExitFlag = 1;
-                SaveFlag = true;
-                DoLog(1) && (Log() << Verbose(1) << "Translating all ions by given vector." << endl);
-                for (int i=NDIM;i--;)
-                  x[i] = atof(argv[argptr+i]);
-                mol->Translate((const Vector *)&x);
-                argptr+=3;
-              }
-              break;
-            case 'T':
-              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 periodic translation: -T <x> <y> <z>" << endl);
-                performCriticalExit();
-              } else {
-                if (ExitFlag == 0) ExitFlag = 1;
-                SaveFlag = true;
-                DoLog(1) && (Log() << Verbose(1) << "Translating all ions periodically by given vector." << endl);
-                for (int i=NDIM;i--;)
-                  x[i] = atof(argv[argptr+i]);
-                mol->TranslatePeriodically((const Vector *)&x);
-                argptr+=3;
+                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);
+                ArgcList.insert(argptr+6);
+                argptr+=7;
               }
               break;