Changeset 5b15ab

Timestamp:

Apr 29, 2008, 6:30:38 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:

2910e0

Parents:

555063

Message:

config::Load..() now get filename instead of pointer to file, bugfix for switch structure in command line parsin
g.

Load..() functions RetrieveConfigPath() - the path that is given for the config file on the command line - and p
ut it into config::configpath. This is necessary to allow later for a sensible storage path under fragmentation, as the old with defaultpath from the file was stupid, if the given path was wrong (whereas the config path always exists).
Switch structure in parsing the command line options needed to make better use of the already present flag in or
der to know when to just save and stop and when to continue to the interactive menu.

Location:

src

Files:

• builder.cpp (modified) (12 diffs)
• config.cpp (modified) (8 diffs)
• molecules.hpp (modified) (2 diffs)

src/builder.cpp

@@ -748 +748 @@
   char *ConfigFileName = NULL;
   char *ElementsFileName = NULL;
-  int flag = 1;
+  int flag = 0;
   int Z;
   int j, axis, count, faktor;
@@ -773 +773 @@
           case 'H':
           case '?':
+            flag=2;
             cout << "MoleCuilder suite" << endl << "==================" << endl << endl;
             cout << "Usage: " << argv[0] << "[-{acepsthH?vfrp}] [further arguments] [config file]" << endl; 
@@ -785 +786 @@
             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;
+            cout << "Note: config files must not begin with '-' !" << endl;
             break;
           case 'v':
           case 'V':
+            flag=2;
             cout << argv[0] << " " << VERSIONSTRING << endl;
             cout << "Build your own molecule position set." << endl;
-            return 0;
             break;
           case 'e':
@@ -827 +828 @@
         }
       } else {
+        test.close();
         ConfigFileName = argv[argc-1];
         cout << Verbose(1) << "Specified config file found, parsing ...";
-        switch (configuration.TestSyntax(&test, periode, mol)) {
+        switch (configuration.TestSyntax(ConfigFileName, periode, mol)) {
           case 1:
             cout << "new syntax." << endl;
-            configuration.Load(&test, periode, mol);
+            configuration.Load(ConfigFileName, periode, mol);
             config_present = present;
             break;
           case 0:
             cout << "old syntax." << endl;
-            configuration.LoadOld(&test, periode, mol);
+            configuration.LoadOld(ConfigFileName, periode, mol);
             config_present = present;
             break;
@@ -844 +846 @@
             config_present = empty;
        }
-        test.close();
       }
     } else
@@ -856 +857 @@
           switch(argv[argptr-1][1]) {
             case 'p':
+              flag = 1;
               cout << Verbose(1) << "Parsing xyz file for new atoms." << endl;
               if (!mol->AddXYZFile(argv[argptr++]))
@@ -871 +873 @@
             switch(argv[argptr-1][1]) {
               case 't':
+                flag = 1;
                 cout << Verbose(1) << "Translating all ions to new origin." << endl;
                 for (int i=0;i<3;i++)
@@ -878 +881 @@
                 break;
               case 'a':
+                flag = 1;
                 cout << Verbose(1) << "Adding new atom." << endl;
                 first = new atom;
@@ -894 +898 @@
                 break;
               case 's':
+                flag = 1;
                 j = -1;
                 cout << Verbose(1) << "Scaling all ion positions by factor." << endl;
@@ -914 +919 @@
                 break;
               case 'c':
+                flag = 1;
                 j = -1;
                 cout << Verbose(1) << "Centering atoms in config file within given additional boundary." << endl;
@@ -930 +936 @@
                 break;
               case 'r':
+                flag = 1;
                 cout << Verbose(1) << "Converting config file from supposed old to new syntax." << endl;
                 break;
               case 'f':
                 int i,j;
-                flag = 0;
+                flag = 1;
                 if (argc > argptr+3) {
                   cout << Verbose(0) << "Creating connection matrix..." << endl;
@@ -998 +1005 @@
           } else argptr++;
         } while (argptr < (argc-1));
-    if (flag)
+    if (flag == 1)  // 1 means save and exit
       SaveConfig(ConfigFileName, &configuration, periode, mol);
-    delete(mol);
-    delete(periode);
-    return (0);
+    if (flag > 1) { // 2 means just exit
+      delete(mol);
+      delete(periode);
+      return (0);
+    }
   }
 

src/config.cpp

@@ -16 +16 @@
   defaultpath = (char *) MallocString(sizeof(char)*255,"config constructor: mainname");
   pseudopotpath = (char *) MallocString(sizeof(char)*255,"config constructor: mainname");
+  configpath = (char *) MallocString(sizeof(char)*255,"config constructor: mainname");
   strcpy(mainname,"pcp");
-  strcpy(defaultpath,"not specified                                                                                                                                                                                                                                               ");
-  strcpy(pseudopotpath,"not specified                                                                                                                                                                                                                                               ");
+  strcpy(defaultpath,"not specified");
+  strcpy(pseudopotpath,"not specified");
   
   ProcPEGamma=8;
@@ -86 +87 @@
   Free((void **)&defaultpath, "config::~config: *defaultpath");
   Free((void **)&pseudopotpath, "config::~config: *pseudopotpath");
+  Free((void **)&configpath, "config::~config: *configpath");
 };
 
@@ -352 +354 @@
 
 /** Tests whether a given configuration file adhears to old or new syntax.
- * \param *file input file stream being the opened config file
+ * \param *filename filename of config file to be tested
  * \param *periode pointer to a periodentafel class with all elements
  * \param *mol pointer to molecule containing all atoms of the molecule
  * \return 0 - old syntax, 1 - new syntax, -1 - unknown syntax 
  */
-int config::TestSyntax(ifstream *file, periodentafel *periode, molecule *mol)
+int config::TestSyntax(char *filename, periodentafel *periode, molecule *mol)
 {
   int test;
+  ifstream file(filename);
+  
   // search file for keyword: ProcPEGamma (new syntax)
-  if (ParseForParameter(1,file,"ProcPEGamma", 0, 1, 1, int_type, &test, 1, optional))
+  if (ParseForParameter(1,&file,"ProcPEGamma", 0, 1, 1, int_type, &test, 1, optional)) {
+    file.close();
     return 1;
+  }
   // search file for keyword: ProcsGammaPsi (old syntax)
-  if (ParseForParameter(1,file,"ProcsGammaPsi", 0, 1, 1, int_type, &test, 1, optional))
+  if (ParseForParameter(1,&file,"ProcsGammaPsi", 0, 1, 1, int_type, &test, 1, optional)) {
+    file.close();
     return 0;
+  }
+  file.close();
   return -1;
 }
@@ -394 +403 @@
 };
 
+/** Retrieves the path in the given config file name.
+ * \param *filename config file string
+ */
+void config::RetrieveConfigPath(char *filename)
+{
+  int last = -1;
+  for(int i=0;i<255;i++) {
+    if (filename[i] == '/')
+      last = i;
+    if (filename[i] == '\0')
+      break;
+  }
+  if (last == -1) { // no path in front, set to local directory.
+    strcpy(configpath, "./");
+  } else {
+    strncpy(configpath, filename, last+1);
+    if (last < 254)
+      configpath[last+1]='\0';
+  }
+  cout << "Found configpath: " << configpath << ", dir slash was found at " << last << "." << endl;
+};
+
+
 /** Initializes config file structure by loading elements from a give file.
  * \param *file input file stream being the opened config file
@@ -399 +431 @@
  * \param *mol pointer to molecule containing all atoms of the molecule 
  */
-void config::Load(ifstream *file, periodentafel *periode, molecule *mol)
+void config::Load(char *filename, periodentafel *periode, molecule *mol)
 {
+  ifstream *file = new ifstream(filename);
+  if (file == NULL) {
+    cerr << "ERROR: config file " << filename << " missing!" << endl;
+    return;
+  }
+  RetrieveConfigPath(filename);
   // ParseParameters
   
@@ -615 +653 @@
     }
   }
+  file->close();
+  delete(file);
 };
 
@@ -622 +662 @@
  * \param *mol pointer to molecule containing all atoms of the molecule 
  */
-void config::LoadOld(ifstream *file, periodentafel *periode, molecule *mol)
+void config::LoadOld(char *filename, periodentafel *periode, molecule *mol)
 {
+  ifstream *file = new ifstream(filename);
+  if (file == NULL) {
+    cerr << "ERROR: config file " << filename << " missing!" << endl;
+    return;
+  }
+  RetrieveConfigPath(filename);
   // ParseParameters
   
@@ -810 +856 @@
     }
   }   
+  file->close();
+  delete(file);
 };
 

src/molecules.hpp

@@ -612 +612 @@
     int ProcPEGamma;
     int ProcPEPsi;
+    char *configpath;
     
     private:
@@ -674 +675 @@
   ~config();
 
-  int TestSyntax(ifstream *file, periodentafel *periode, molecule *mol);
-  void Load(ifstream *file, periodentafel *periode, molecule *mol);
-  void LoadOld(ifstream *file, periodentafel *periode, molecule *mol);
+  int TestSyntax(char *filename, periodentafel *periode, molecule *mol);
+  void Load(char *filename, periodentafel *periode, molecule *mol);
+  void LoadOld(char *filename, periodentafel *periode, molecule *mol);
+  void RetrieveConfigPath(char *filename);
   bool Save(ofstream *file, periodentafel *periode, molecule *mol) const;
   void Edit(molecule *mol);