Changeset 4885953

Timestamp:

Apr 29, 2008, 7:45:23 AM (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:

1fa5b7

Parents:

04980c

Message:

changed config file to first argument again and standard config name incorporated.

./molecuilder -e elements.db is hard to scan whether elements.db is the config file or a further argument, hence switch-back to old method of having it in the first place. (this also matches all the scripts written so far again).

Location:

src

Files:

• builder.cpp (modified) (10 diffs)
• defs.hpp (modified) (1 diff)

src/builder.cpp

@@ -700 +700 @@
   if (ConfigFileName != NULL) {
     output.open(ConfigFileName, ios::trunc);
-  } else {
+  } else if (strlen(configuration->configname) != 0) {
     output.open(configuration->configname, ios::trunc);
-  }
+    } else {
+      output.open(DEFAULTCONFIG, ios::trunc);
+    }
   if (configuration->Save(&output, periode, mol))
     cout << Verbose(0) << "Saving of config file successful." << endl;
@@ -779 +781 @@
           case '?':
             cout << "MoleCuilder suite" << endl << "==================" << endl << endl;
-            cout << "Usage: " << argv[0] << "[-{acepsthH?vfrp}] [further arguments] [config file]" << endl; 
+            cout << "Usage: " << argv[0] << "[config file] [-{acepsthH?vfrp}] [further arguments]" << 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;
@@ -814 +816 @@
           } else
             argptr++;
-    } while (argptr < (argc-1));
+    } while (argptr < argc);
+        
         // 2. Parse the element database
     if (periode->LoadPeriodentafel(ElementsFileName))
@@ -820 +823 @@
     else
       cout << Verbose(0) << "Element list loading failed." << endl;
+    
         // 3. Find config file name and parse if possible
-    if (argv[argc-1][0] != '-') {
+    if (argv[1][0] != '-') {
       cout << Verbose(0) << "Config file given." << endl;
-      test.open(argv[argc-1], ios::in);
+      test.open(argv[1], ios::in);
       if (test == NULL) {
         //return (1);
-        output.open(argv[argc-1], ios::out);
+        output.open(argv[1], ios::out);
         if (output == NULL) {
-          cout << Verbose(1) << "Specified config file " << argv[argc-1] << " not found." << endl;
+          cout << Verbose(1) << "Specified config file " << argv[1] << " not found." << endl;
           config_present = absent;
         } else {
           cout << "Empty configuration file." << endl;
-          ConfigFileName = argv[argc-1];
+          ConfigFileName = argv[1];
           config_present = empty;
           output.close();
@@ -838 +842 @@
       } else {
         test.close();
-        ConfigFileName = argv[argc-1];
+        ConfigFileName = argv[1];
         cout << Verbose(1) << "Specified config file found, parsing ...";
         switch (configuration.TestSyntax(ConfigFileName, periode, mol)) {
@@ -858 +862 @@
     } else
       config_present = absent;
+    
     // 4. parse again through options, now for those depending on elements db and config presence
     argptr = 1;
@@ -951 +956 @@
                 int i,j;
                 flag = 1;
-                if (argc > argptr+3) {
+                cout << "Fragmenting molecule with bond distance " << argv[argptr] << " angstroem, order of " << argv[argptr+1] << " and type " << argv[argptr+2] << "." << endl;
+                if (argc >= argptr+3) {
                   cout << Verbose(0) << "Creating connection matrix..." << endl;
                   start = clock();
@@ -1001 +1007 @@
                   cout << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl;
                   argptr+=2;
+                } else {
+                  cerr << "Not enough arguments for fragmentation: -f <max. bond distance> <bond order> <type>" << endl;
                 }
                 break;
@@ -1007 +1015 @@
                 break;
             }
-          } else {
-            cout << "Cannot apply command line parameter as no valid config file was found." << endl;
-            return 1;
           }
         }
           } else argptr++;
-        } while (argptr < (argc-1));
+        } while (argptr < argc);
     if (flag == 1) { // 1 means save and exit
       SaveConfig(ConfigFileName, &configuration, periode, mol);
@@ -1025 +1030 @@
     else
       cout << Verbose(0) << "Element list loading failed." << endl;
-    config_present = absent;
     configuration.RetrieveConfigPathAndName("main_pcp_linux");
   }

src/defs.hpp

@@ -38 +38 @@
 
 // various standard filenames
+#define DEFAULTCONFIG "main_pcp_linux"
 #define KEYSETFILE "KeySets.dat"
 #define ADJACENCYFILE "Adjacency.dat"