Changeset 77de81

Timestamp:

Jun 11, 2010, 2:20:11 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:

d55743e

Parents:

54b953

git-author:

Frederik Heber <heber@…> (06/11/10 14:18:22)

git-committer:

Frederik Heber <heber@…> (06/11/10 14:20:11)

Message:

Cases 'J' and 'j' are now handled by CommandLineUI.

• TESTFIX: "--molecule-by-id 0" added to calls.

Files:

• src/Actions/MapOfActions.cpp (modified) (1 diff)
• src/builder.cpp (modified) (1 diff)
• tests/regression/testsuite-molecules.at (modified) (1 diff)

src/Actions/MapOfActions.cpp

@@ -261 +261 @@
   generic.insert("repeat-box");
   generic.insert("rotate-to-pas");
-//      generic.insert("save-adjacency");
-//  generic.insert("save-bonds");
+        generic.insert("save-adjacency");
+  generic.insert("save-bonds");
 //  generic.insert("save-temperature");
   generic.insert("scale-box");

src/builder.cpp

@@ -1851 +1851 @@
             case 'J':
               if (ExitFlag == 0) ExitFlag = 1;
+              if ((argptr+2 >= argc) || (argv[argptr][0] == '-')) {
+                ExitFlag =255;
+                DoeLog(0) && (eLog()<< Verbose(0) << "Missing path of adjacency file: -J <path> --molecule-by-id <molecule_id>" << endl);
+                performCriticalExit();
+              } else {
+                ArgcList.insert(argptr-1);
+                ArgcList.insert(argptr);
+                ArgcList.insert(argptr+1);
+                ArgcList.insert(argptr+2);
+                argptr+=3;
+              }
+              break;
+
+            case 'j':
+              if (ExitFlag == 0) ExitFlag = 1;
               if ((argptr >= argc) || (argv[argptr][0] == '-')) {
                 ExitFlag =255;
-                DoeLog(0) && (eLog()<< Verbose(0) << "Missing path of adjacency file: -j <path>" << endl);
+                DoeLog(0) && (eLog()<< Verbose(0) << "Missing path of bonds file: -j <path> --molecule-by-id <molecule_id>" << endl);
                 performCriticalExit();
               } else {
-                DoLog(0) && (Log() << Verbose(0) << "Storing adjacency to path " << argv[argptr] << "." << endl);
-                configuration.BG->ConstructBondGraph(mol);
-                mol->StoreAdjacencyToFile(NULL, argv[argptr]);
-                argptr+=1;
-              }
-              break;
-
-            case 'j':
-              if (ExitFlag == 0) ExitFlag = 1;
-              if ((argptr >= argc) || (argv[argptr][0] == '-')) {
-                ExitFlag =255;
-                DoeLog(0) && (eLog()<< Verbose(0) << "Missing path of bonds file: -j <path>" << endl);
-                performCriticalExit();
-              } else {
-                DoLog(0) && (Log() << Verbose(0) << "Storing bonds to path " << argv[argptr] << "." << endl);
-                configuration.BG->ConstructBondGraph(mol);
-                mol->StoreBondsToFile(NULL, argv[argptr]);
-                argptr+=1;
+                ArgcList.insert(argptr-1);
+                ArgcList.insert(argptr);
+                ArgcList.insert(argptr+1);
+                ArgcList.insert(argptr+2);
+                argptr+=3;
               }
               break;

tests/regression/testsuite-molecules.at

@@ -12 +12 @@
 AT_KEYWORDS([Molecules])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/2/pre/test.conf .], 0)
-AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 1 -j test.dbond], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 1 -j test.dbond --molecule-by-id 0], 0, [stdout], [stderr])
 AT_CHECK([file=test.dbond; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/2/post/$file], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 1 -J test.adj], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 1 -J test.adj --molecule-by-id 0], 0, [stdout], [stderr])
 AT_CHECK([file=test.adj; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/2/post/$file], 0, [ignore], [ignore])
 AT_CLEANUP