Changes in src/builder.cpp [97ebf8:50dfda]

File:

• src/builder.cpp (modified) (10 diffs)

src/builder.cpp ¶

@@ -77 +77 @@
 #include "Actions/ActionRegistry.hpp"
 #include "Actions/ActionHistory.hpp"
-#include "Actions/MapOfActions.hpp"
 #include "Actions/MethodAction.hpp"
 #include "Actions/MoleculeAction/ChangeNameAction.hpp"
@@ -1481 +1480 @@
 
 /** Parses the command line options.
- * Note that this function is from now on transitional. All commands that are not passed
- * here are handled by CommandLineParser and the actions of CommandLineUIFactory.
  * \param argc argument count
  * \param **argv arguments array
@@ -1490 +1487 @@
  * \param *ConfigFileName pointer to config file name in **argv
  * \param *PathToDatabases pointer to db's path in **argv
- * \param &ArgcList list of arguments that we do not parse here
  * \return exit code (0 - successful, all else - something's wrong)
  */
-static int ParseCommandLineOptions(int argc, char **argv, MoleculeListClass *&molecules, periodentafel *&periode,
-                                   config& configuration, char *&ConfigFileName, list<int> &ArgcList)
+static int ParseCommandLineOptions(int argc, char **argv, MoleculeListClass *&molecules, periodentafel *&periode,\
+                                   config& configuration, char *&ConfigFileName)
 {
   Vector x,y,z,n;  // coordinates for absolute point in cell volume
@@ -1512 +1508 @@
   molecule *mol = NULL;
   string BondGraphFileName("\n");
+  int verbosity = 0;
   strncpy(configuration.databasepath, LocalPath, MAXSTRINGSIZE-1);
 
@@ -1525 +1522 @@
           case 'H':
           case '?':
-            ArgcList.push_back(argptr-1);
-            return(1);
+            DoLog(0) && (Log() << Verbose(0) << "MoleCuilder suite" << endl << "==================" << endl << endl);
+            DoLog(0) && (Log() << Verbose(0) << "Usage: " << argv[0] << "[config file] [-{acefpsthH?vfrp}] [further arguments]" << endl);
+            DoLog(0) && (Log() << Verbose(0) << "or simply " << argv[0] << " without arguments for interactive session." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-a Z x1 x2 x3\tAdd new atom of element Z at coordinates (x1,x2,x3)." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-A <source>\tCreate adjacency list from bonds parsed from 'dbond'-style file." <<endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-b xx xy xz yy yz zz\tCenter atoms in domain with given symmetric matrix of (xx,xy,xz,yy,yz,zz)." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-B xx xy xz yy yz zz\tBound atoms by domain with given symmetric matrix of (xx,xy,xz,yy,yz,zz)." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-c x1 x2 x3\tCenter atoms in domain with a minimum distance to boundary of (x1,x2,x3)." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-C <type> [params] <output> <bin output> <BinWidth> <BinStart> <BinEnd>\tPair Correlation analysis." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-d x1 x2 x3\tDuplicate cell along each axis by given factor." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-D <bond distance>\tDepth-First-Search Analysis of the molecule, giving cycles and tree/back edges." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-e <file>\tSets the databases path to be parsed (default: ./)." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-E <id> <Z>\tChange atom <id>'s element to <Z>, <id> begins at 0." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-f <dist> <order>\tFragments the molecule in BOSSANOVA manner (with/out rings compressed) and stores config files in same dir as config (return code 0 - fragmented, 2 - no fragmentation necessary)." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-F <xyz of filler> <dist_x> <dist_y> <dist_z> <epsilon> <randatom> <randmol> <DoRotate>\tFilling Box with water molecules." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-FF <MaxDistance> <xyz of filler> <dist_x> <dist_y> <dist_z> <epsilon> <randatom> <randmol> <DoRotate>\tFilling Box with water molecules." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-g <file>\tParses a bond length table from the given file." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-h/-H/-?\tGive this help screen." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-I\t Dissect current system of molecules into a set of disconnected (subgraphs of) molecules." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-j\t<path> Store all bonds to file." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-J\t<path> Store adjacency per atom to file." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-L <step0> <step1> <prefix>\tStore a linear interpolation between two configurations <step0> and <step1> into single config files with prefix <prefix> and as Trajectories into the current config file." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-m <0/1>\tCalculate (0)/ Align in(1) PAS with greatest EV along z axis." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-M <basis>\tSetting basis to store to MPQC config files." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-n\tFast parsing (i.e. no trajectories are looked for)." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-N <radius> <file>\tGet non-convex-envelope." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-o <out>\tGet volume of the convex envelope (and store to tecplot file)." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-O\tCenter atoms in origin." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-p <file>\tParse given xyz file and create raw config file from it." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-P <file>\tParse given forces file and append as an MD step to config file via Verlet." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-r <id>\t\tRemove an atom with given id." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-R <id> <radius>\t\tRemove all atoms out of sphere around a given one." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-s x1 x2 x3\tScale all atom coordinates by this vector (x1,x2,x3)." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-S <file> Store temperatures from the config file in <file>." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-t x1 x2 x3\tTranslate all atoms by this vector (x1,x2,x3)." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-T x1 x2 x3\tTranslate periodically all atoms by this vector (x1,x2,x3)." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-u rho\tsuspend in water solution and output necessary cell lengths, average density rho and repetition." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-v\t\tsets verbosity (more is more)." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-V\t\tGives version information." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-X\t\tset default name of a molecule." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "Note: config files must not begin with '-' !" << endl);
+            return (1);
             break;
           case 'v':
-            ArgcList.push_back(argptr-1);
-            return(1);
+            while (argv[argptr-1][verbosity+1] == 'v') {
+              verbosity++;
+            }
+            setVerbosity(verbosity);
+            DoLog(0) && (Log() << Verbose(0) << "Setting verbosity to " << verbosity << "." << endl);
             break;
           case 'V':
-            ArgcList.push_back(argptr-1);
-            ArgcList.push_back(argptr);
-            argptr++;
+            DoLog(0) && (Log() << Verbose(0) << argv[0] << " " << VERSIONSTRING << endl);
+            DoLog(0) && (Log() << Verbose(0) << "Build your own molecule position set." << endl);
+            return (1);
             break;
           case 'B':
@@ -2475 +2515 @@
 
 void cleanUp(){
+  UIFactory::purgeInstance();
   World::purgeInstance();
   Log() << Verbose(0) <<  "Maximum of allocated memory: "
@@ -2483 +2524 @@
   logger::purgeInstance();
   errorLogger::purgeInstance();
-  UIFactory::purgeInstance();
-  MapOfActions::purgeInstance();
   CommandLineParser::purgeInstance();
   ActionRegistry::purgeInstance();
@@ -2497 +2536 @@
     ofstream output;
     string line;
-    char **Arguments = NULL;
-    int ArgcSize = 0;
-    bool ArgumentsCopied = false;
 
     cout << ESPACKVersion << endl;
@@ -2507 +2543 @@
     ActionHistory::init();
 
-    // Parse command line options and if present create respective UI
     {
-      list<int> ArgcList;
-      ArgcList.push_back(0); // push back program!
-      ArgcList.push_back(1); // push back config file name
-      char ConfigFileName[MAXSTRINGSIZE];
-      // handle arguments by ParseCommandLineOptions()
-      ParseCommandLineOptions(argc,argv,World::getInstance().getMolecules(),World::getInstance().getPeriode(),*World::getInstance().getConfig(), (char *&)ConfigFileName, ArgcList);
-      // copy all remaining arguments to a new argv
-      Arguments = Malloc<char *>(ArgcList.size(), "main - **Arguments");
-      cout << "The following arguments are handled by CommandLineParser: ";
-      for (list<int>::iterator ArgcRunner = ArgcList.begin(); ArgcRunner != ArgcList.end(); ++ArgcRunner) {
-        Arguments[ArgcSize] = Malloc<char>(strlen(argv[*ArgcRunner])+2, "main - *Arguments[]");
-        strcpy(Arguments[ArgcSize], argv[*ArgcRunner]);
-        cout << " " << argv[*ArgcRunner];
-        ArgcSize++;
-      }
-      cout << endl;
-      ArgumentsCopied = true;
-      // handle remaining arguments by CommandLineParser
-      MapOfActions::getInstance().AddOptionsToParser();
-      CommandLineParser::getInstance().Run(ArgcSize,Arguments);
-      if (!CommandLineParser::getInstance().isEmpty()) {
-        DoLog(0) && (Log() << Verbose(0) << "Setting UI to CommandLine." << endl);
+      // Parse command line options and if present create respective UI
+      CommandLineParser::getInstance().generic.add_options()
+          ("help,h", "produce help message")
+          ("version,v", "show version")
+          ("parse-xyz,p", po::value< vector<string> >(), "parse xyz file into World")
+          ;
+      CommandLineParser::getInstance().Run(argc,argv);
+      if (!CommandLineParser::getInstance().isEmpty())
         UIFactory::makeUserInterface(UIFactory::CommandLine);
-      } else {
-        DoLog(0) && (Log() << Verbose(0) << "Setting UI to Text." << endl);
+      else
         UIFactory::makeUserInterface(UIFactory::Text);
-      }
     }
 
@@ -2550 +2569 @@
         Log() << Verbose(0) << "Saving of elements.db failed." << endl;
 
-  // free the new argv
-  if (ArgumentsCopied) {
-    for (int i=0; i<ArgcSize;i++)
-      Free(&Arguments[i]);
-    Free(&Arguments);
-  }
-
   cleanUp();
+
   Memory::getState();
   return (0);