Changeset 6ca1f7

Timestamp:

May 30, 2010, 11:03:49 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:

2a92ff

Parents:

26f75a

git-author:

Frederik Heber <heber@…> (05/30/10 22:52:33)

git-committer:

Frederik Heber <heber@…> (05/30/10 23:03:49)

Message:

case '-B' now handled by CommandLineUI.

Location:

src

Files:

• Actions/MapOfActions.cpp (modified) (2 diffs)
• builder.cpp (modified) (10 diffs)

src/Actions/MapOfActions.cpp

@@ -93 +93 @@
   ShortFormMap["boundary"] = "c";
   ShortFormMap["bound-in-box"] = "B";
+  ShortFormMap["change-box"] = "B";
   ShortFormMap["center-edge"] = "O";
   ShortFormMap["center-in-box"] = "b";
@@ -189 +190 @@
 //  generic.insert("center-edge");
 //  generic.insert("center-in-box");
-//      generic.insert("change-box");
+        generic.insert("change-box");
 //  generic.insert("change-molname");
 //      generic.insert("change-element");

src/builder.cpp

@@ -1495 +1495 @@
  */
 static int ParseCommandLineOptions(int argc, char **argv, MoleculeListClass *&molecules, periodentafel *&periode,
-                                   config& configuration, char *&ConfigFileName, set<int> &ArgcList)
+                                   config& configuration, char **ConfigFileName, set<int> &ArgcList)
 {
   Vector x,y,z,n;  // coordinates for absolute point in cell volume
@@ -1540 +1540 @@
             break;
           case 'B':
+            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;
             if (ExitFlag == 0) ExitFlag = 1;
-            if ((argptr+5 >= argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) || (!IsValidNumber(argv[argptr+3])) || (!IsValidNumber(argv[argptr+4])) || (!IsValidNumber(argv[argptr+5])) ) {
-              ExitFlag = 255;
-              DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for bounding in box: -B <xx> <xy> <xz> <yy> <yz> <zz>" << endl);
-              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]);
-              }
-              argptr+=6;
-            }
             break;
           case 'e':
@@ -1626 +1620 @@
         } else {
           DoLog(0) && (Log() << Verbose(0) << "Empty configuration file." << endl);
-          ConfigFileName = argv[1];
+          strcpy(*ConfigFileName, argv[1]);
           configPresent = empty;
           output.close();
@@ -1632 +1626 @@
       } else {
         test.close();
-        ConfigFileName = argv[1];
+        strcpy(*ConfigFileName, argv[1]);
         DoLog(1) && (Log() << Verbose(1) << "Specified config file found, parsing ... ");
-        switch (configuration.TestSyntax(ConfigFileName, periode)) {
+        switch (configuration.TestSyntax(*ConfigFileName, periode)) {
           case 1:
             DoLog(0) && (Log() << Verbose(0) << "new syntax." << endl);
-            configuration.Load(ConfigFileName, BondGraphFileName, periode, molecules);
+            configuration.Load(*ConfigFileName, BondGraphFileName, periode, molecules);
             configPresent = present;
             break;
           case 0:
             DoLog(0) && (Log() << Verbose(0) << "old syntax." << endl);
-            configuration.LoadOld(ConfigFileName, BondGraphFileName, periode, molecules);
+            configuration.LoadOld(*ConfigFileName, BondGraphFileName, periode, molecules);
             configPresent = present;
             break;
@@ -1663 +1657 @@
        mol = World::getInstance().createMolecule();
        mol->ActiveFlag = true;
-       if (ConfigFileName != NULL)
-         mol->SetNameFromFilename(ConfigFileName);
+       if (*ConfigFileName != NULL)
+         mol->SetNameFromFilename(*ConfigFileName);
        molecules->insert(mol);
      }
@@ -2449 +2443 @@
     } while (argptr < argc);
     if (SaveFlag)
-      configuration.SaveAll(ConfigFileName, periode, molecules);
+      configuration.SaveAll(*ConfigFileName, periode, molecules);
   } else {  // no arguments, hence scan the elements db
     if (periode->LoadPeriodentafel(configuration.databasepath))
@@ -2490 +2484 @@
     int ExitFlag = 0;
     bool ArgumentsCopied = false;
+    char *ConfigFileName = new char[MAXSTRINGSIZE];
 
     // print version check whether arguments are present at all
@@ -2514 +2509 @@
       ArgcList.insert(0); // push back program!
       ArgcList.insert(1); // push back config file name
-      char ConfigFileName[MAXSTRINGSIZE];
       // handle arguments by ParseCommandLineOptions()
-      ExitFlag = ParseCommandLineOptions(argc,argv,World::getInstance().getMolecules(),World::getInstance().getPeriode(),*World::getInstance().getConfig(), (char *&)ConfigFileName, ArgcList);
+      ExitFlag = ParseCommandLineOptions(argc,argv,World::getInstance().getMolecules(),World::getInstance().getPeriode(),*World::getInstance().getConfig(), &ConfigFileName, ArgcList);
       // copy all remaining arguments to a new argv
       Arguments = Malloc<char *>(ArgcList.size(), "main - **Arguments");
@@ -2546 +2540 @@
     }
 
+    Log() << Verbose(0) << "Saving to " << ConfigFileName << "." << endl;
+    World::getInstance().getConfig()->SaveAll(ConfigFileName, World::getInstance().getPeriode(), World::getInstance().getMolecules());
     if(World::getInstance().getPeriode()->StorePeriodentafel(configuration->databasepath))
         Log() << Verbose(0) << "Saving of elements.db successful." << endl;
@@ -2558 +2554 @@
     Free(&Arguments);
   }
+  delete[](ConfigFileName);
 
   return (ExitFlag == 1 ? 0 : ExitFlag);