Changeset 54b953 for src

Timestamp:

Jun 11, 2010, 12:20:08 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:

77de81

Parents:

f0a3ec

git-author:

Frederik Heber <heber@…> (06/11/10 10:39:39)

git-committer:

Frederik Heber <heber@…> (06/11/10 12:20:08)

Message:

Case 'E' is now handled by CommandLineUI.

• TESTFIX: --element is required now.

Location:

src

Files:

• Actions/AtomAction/ChangeElementAction.cpp (modified) (1 diff)
• Actions/MapOfActions.cpp (modified) (6 diffs)
• builder.cpp (modified) (1 diff)

src/Actions/AtomAction/ChangeElementAction.cpp

@@ -36 +36 @@
   std::vector<element *> elements;
 
-  dialog->queryElement(NAME, &elements, MapOfActions::getInstance().getDescription(NAME));
-  dialog->queryAtom("atom-by-id", &first, MapOfActions::getInstance().getDescription("atom-by-id"));
+  dialog->queryAtom(NAME, &first, MapOfActions::getInstance().getDescription(NAME));
+  dialog->queryElement("element", &elements, MapOfActions::getInstance().getDescription("element"));
 
   if(dialog->display()) {
     delete dialog;
     ASSERT(elements.size() == 1, "Unequal to one element specified when changing an atom's element");
+    ASSERT(first != NULL, "No valid atom specified");
     DoLog(1) && (Log() << Verbose(1) << "Changing atom " << *first << " to element " << elements.at(0) << "." << endl);
     if (elements.at(0) != NULL) {

src/Actions/MapOfActions.cpp

@@ -103 +103 @@
   DescriptionMap["version"] = "show version";
   // keys for values
+  DescriptionMap["atom-by-id"] = "index of an atom";
   DescriptionMap["bin-output-file"] = "name of the bin output file";
   DescriptionMap["bin-end"] = "start of the last bin";
@@ -170 +171 @@
   TypeMap["center-in-box"] = Box;
   TypeMap["change-box"] = Box;
-  TypeMap["change-element"] = Element;
+  TypeMap["change-element"] = Atom;
   TypeMap["change-molname"] = String;
   TypeMap["convex-envelope"] = Molecule;
@@ -203 +204 @@
 
   // value types for the values
+  TypeMap["atom-by-id"] = Atom;
   TypeMap["bin-output-file"] = String;
   TypeMap["bin-end"] = Double;
@@ -225 +227 @@
   DefaultValue["bin-width"] = "0.5";
   DefaultValue["fastparsing"] = "0";
+  DefaultValue["atom-by-id"] = "-1";
   DefaultValue["molecule-by-id"] = "-1";
   DefaultValue["periodic"] = "0";
@@ -239 +242 @@
         generic.insert("change-box");
 //  generic.insert("change-molname");
-//      generic.insert("change-element");
+        generic.insert("change-element");
 //  generic.insert("convex-envelope");
         generic.insert("default-molname");
@@ -282 +285 @@
 
     // hidden arguments
+  generic.insert("atom-by-id");
   generic.insert("bin-end");
   generic.insert("bin-output-file");

src/builder.cpp

@@ -1804 +1804 @@
             case 'E':
               if (ExitFlag == 0) ExitFlag = 1;
-              if ((argptr+1 >= argc) || (!IsValidNumber(argv[argptr])) || (argv[argptr+1][0] == '-')) {
+              if ((argptr+2 >= argc) || (!IsValidNumber(argv[argptr]))) {
                 ExitFlag = 255;
-                DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for changing element: -E <atom nr.> <element>" << endl);
+                DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for changing element: -E <atom nr.> --element <Z>" << endl);
                 performCriticalExit();
               } else {
-                mol->getAtomCount();
-                SaveFlag = true;
-                DoLog(1) && (Log() << Verbose(1) << "Changing atom " << argv[argptr] << " to element " << argv[argptr+1] << "." << endl);
-                first = mol->FindAtom(atoi(argv[argptr]));
-                first->type = periode->FindElement(atoi(argv[argptr+1]));
-                argptr+=2;
+                ArgcList.insert(argptr-1);
+                ArgcList.insert(argptr);
+                ArgcList.insert(argptr+1);
+                ArgcList.insert(argptr+2);
+                argptr+=3;
               }
               break;