Changeset 73f80e for src

Timestamp:

Apr 27, 2008, 12:59:18 PM (17 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:

206887

Parents:

cf959d

Message:

new elementsdb-switch and command line options parsing parts moved around to accomodate.

New switch (just sets a variable) made some moving around necessary. Elements db cannot be parsed right at the start anymore, neither the config file before the command line switches. Hence, the following is now in operation:

1. first parse through all options for stuff just setting variables, giving help et al
2. parse elements db
3. parse config file if present
4. parse again through options for those that actually operate on a given configuration or add atoms (parsing xyz) ...

This was necessary, as 'make check' could not be made workable otherwise and its "bad behaviour" if the code assumes the elements.db to be in the same dir as the exe.

File:

• src/builder.cpp (modified) (8 diffs)

src/builder.cpp

@@ -694 +694 @@
   ofstream output;
 
+  cout << Verbose(0) << "Storing configuration ... " << endl;
   // get correct valence orbitals
   mol->CalculateOrbitals(*configuration);
@@ -746 +747 @@
   char filename[255];
   char *ConfigFileName = NULL;
+  char *ElementsFileName = NULL;
   int flag = 1;
   int Z;
@@ -757 +759 @@
   element **Elements;
   vector **Vectors;
-
-  // load element list
-  periode->LoadPeriodentafel();
-  cout << Verbose(1) << "Element list loaded." << endl;  
-  
-  // parse config file if given
+  int argptr;
+
+  // =========================== PARSE COMMAND LINE OPTIONS ====================================
   if (argc >= 1) { // config file specified as option
-        if (argv[argc-1][0] != '-') {
+    // 1. : Parse options that just set variables or print help
+        argptr = 1;
+        do {
+          if (argv[argptr][0] == '-') {
+        cout << Verbose(0) << "Recognized command line argument: " << argv[argptr][1] << ".\n";
+        argptr++;
+        switch(argv[argptr-1][1]) {
+          case 'h':
+          case 'H':
+          case '?':
+            cout << "MoleCuilder suite" << endl << "==================" << endl << endl;
+            cout << "Usage: " << argv[0] << "[-{acepsthH?vfrp}] [further arguments] [config file]" << endl; 
+            cout << "or simply " << argv[0] << " without arguments for interactive session." << endl;
+            cout << "\t-a Z x1 x2 x3\tAdd new atom of element Z at coordinates (x1,x2,x3)." << endl;
+            cout << "\t-c x1 x2 x3\tCenter atoms in domain with a minimum distance to boundary of (x1,x2,x3)." << endl;
+            cout << "\t-e <file>\tSets the element database to be parsed from this file (default: elements.db in same dir as " << argv[0] << ")." << endl;
+            cout << "\t-h/-H/-?\tGive this help screen." << endl;
+            cout << "\t-p <file>\tParse given xyz file and create raw config file from it." << endl;
+            cout << "\t-r\t\tConvert file from an old pcp syntax." << endl;
+            cout << "\t-t x1 x2 x3\tTranslate all atoms by this vector (x1,x2,x3)." << endl;
+            cout << "\t-s x1 x2 x3\tScale all atom coordinates by this vector (x1,x2,x3)." << endl;
+            cout << "\t-v/-V\t\tGives version information." << endl;
+            return 0;
+            break;
+          case 'v':
+          case 'V':
+            cout << argv[0] << " " << VERSIONSTRING << endl;
+            cout << "Build your own molecule position set." << endl;
+            return 0;
+            break;
+          case 'e':
+            cout << "Using " << argv[argptr] << " as elements database." << endl;
+            ElementsFileName = argv[argptr];
+            argptr+=1;
+            break;
+          default:   // no match? Step on
+            argptr++;
+            break;
+        }
+          } else
+            argptr++;
+    } while (argptr < (argc-1));
+        // 2. Parse the element database
+    if (periode->LoadPeriodentafel(ElementsFileName))
+      cout << Verbose(0) << "Element list loaded successfully." << endl;
+    else
+      cout << Verbose(0) << "Element list loading failed." << endl;
+        // 3. Find config file name and parse if possible
+    if (argv[argc-1][0] != '-') {
       cout << Verbose(0) << "Config file given." << endl;
       test.open(argv[argc-1], ios::in);
@@ -799 +846 @@
         test.close();
       }
-        } else
-          config_present = absent;
-        int argptr = 1;
-        do {
-          if (argv[argptr][0] == '-') {
-        cout << Verbose(0) << "Recognized command line argument: " << argv[argptr][1] << ".\n";
+    } else
+      config_present = absent;
+    // 4. parse again through options, now for those depending on elements db and config presence
+    argptr = 1;
+    do {
+      if (argv[argptr][0] == '-') {
         argptr++;
-        switch(argv[argptr-1][1]) {
-          case 'h':
-          case 'H':
-          case '?':
-            cout << "MoleCuilder suite" << endl << "==================" << endl << endl;
-            cout << "Usage: " << argv[0] << "[-{acsthH?vfrp}] [further arguments] [config file]" << endl; 
-            cout << "or simply " << argv[0] << " without arguments for interactive session." << endl;
-            cout << "\t-a Z x1 x2 x3\tAdd new atom of element Z at coordinates (x1,x2,x3)." << endl;
-            cout << "\t-c x1 x2 x3\tCenter atoms in domain with a minimum distance to boundary of (x1,x2,x3)." << endl;
-            cout << "\t-h/-H/-?\tGive this help screen." << endl;
-            cout << "\t-p <file>\tParse given xyz file and create raw config file from it." << endl;
-            cout << "\t-r\t\tConvert file from an old pcp syntax." << endl;
-            cout << "\t-t x1 x2 x3\tTranslate all atoms by this vector (x1,x2,x3)." << endl;
-            cout << "\t-s x1 x2 x3\tScale all atom coordinates by this vector (x1,x2,x3)." << endl;
-            cout << "\t-v/-V\t\tGives version information." << endl;
-            return 0;
-            break;
-          case 'v':
-          case 'V':
-            cout << argv[0] << " " << VERSIONSTRING << endl;
-            cout << "Build your own molecule position set." << endl;
-            return 0;
-            break;
-          default:    
-            break;
-        }
         if ((config_present == present) || (config_present == empty)) {
           switch(argv[argptr-1][1]) {
@@ -840 +861 @@
               else
                 cout << Verbose(2) << "File found and parsed." << endl;
+                config_present = present;
               break;
-            default:
+            default:   // no match? Don't step on (this is done in next switch's default)
               break;
           }
@@ -965 +987 @@
                 }
                 break;
-              default:
+              default:   // no match? Step on
+                argptr++;
                 break;
             }
@@ -991 +1014 @@
     }
   }
+
+  // =========================== START INTERACTIVE SESSION ====================================
 
   // now the main construction loop
@@ -1197 +1222 @@
   
   // save element data base
-  if (periode->StorePeriodentafel())
+  if (periode->StorePeriodentafel()) //ElementsFileName
     cout << Verbose(0) << "Saving of elements.db successful." << endl;
   else