Changes in src/Actions/MapOfActions.cpp [986ed3:b540f3]

File:

• src/Actions/MapOfActions.cpp (modified) (17 diffs)

src/Actions/MapOfActions.cpp

@@ -17 +17 @@
 #include <boost/optional.hpp>
 #include <boost/program_options.hpp>
-
-#include <iostream>
 
 #include "CommandLineParser.hpp"
@@ -67 +65 @@
 #include "Actions/WorldAction/SetDefaultNameAction.hpp"
 #include "Actions/WorldAction/SetGaussianBasisAction.hpp"
+#include "Actions/WorldAction/SetOutputFormatsAction.hpp"
 #include "Actions/Values.hpp"
 
@@ -72 +71 @@
 {
   VectorValue VV;
-  if (values.size() != 3) {
-    cerr <<  "Specified vector does not have three components but " << values.size() << endl;
+  std::vector<std::string> components;
+
+  // split comma-separated values
+  if (values.size() != 1) {
+    cerr <<  "Not one vector but " << components.size() << " given " << endl;
+    throw boost::program_options::validation_error("Unequal to one vector given");
+  }
+  std::string argument(values.at(0));
+  std::string::iterator Aiter = argument.begin();
+  std::string::iterator Biter = argument.begin();
+  for (; Aiter != argument.end(); ++Aiter) {
+    if (*Aiter == ',') {
+      components.push_back(string(Biter,Aiter));
+      do {
+        Aiter++;
+      } while (*Aiter == ' ' || *Aiter == '\t');
+      Biter = Aiter;
+    }
+  }
+  components.push_back(string(Biter,argument.end()));
+
+  if (components.size() != 3) {
+    cerr <<  "Specified vector does not have three components but " << components.size() << endl;
     throw boost::program_options::validation_error("Specified vector does not have three components");
   }
-  VV.x = boost::lexical_cast<double>(values.at(0));
-  VV.y = boost::lexical_cast<double>(values.at(1));
-  VV.z = boost::lexical_cast<double>(values.at(2));
+  VV.x = boost::lexical_cast<double>(components.at(0));
+  VV.y = boost::lexical_cast<double>(components.at(1));
+  VV.z = boost::lexical_cast<double>(components.at(2));
   v = boost::any(VectorValue(VV));
 }
@@ -85 +105 @@
 {
   BoxValue BV;
-  if (values.size() != 6) {
-    cerr <<  "Specified vector does not have three components but " << values.size() << endl;
+  std::vector<std::string> components;
+
+  // split comma-separated values
+  if (values.size() != 1) {
+    cerr <<  "Not one vector but " << components.size() << " given " << endl;
+    throw boost::program_options::validation_error("Unequal to one vector given");
+  }
+  std::string argument(values.at(0));
+  std::string::iterator Aiter = argument.begin();
+  std::string::iterator Biter = argument.begin();
+  for (; Aiter != argument.end(); ++Aiter) {
+    if (*Aiter == ',') {
+      components.push_back(string(Biter,Aiter));
+      do {
+        Aiter++;
+      } while (*Aiter == ' ' || *Aiter == '\t');
+      Biter = Aiter;
+    }
+  }
+  components.push_back(string(Biter,argument.end()));
+
+  if (components.size() != 6) {
+    cerr <<  "Specified vector does not have three components but " << components.size() << endl;
     throw boost::program_options::validation_error("Specified symmetric box matrix does not have six components");
   }
-  BV.xx = boost::lexical_cast<double>(values.at(0));
-  BV.xy = boost::lexical_cast<double>(values.at(1));
-  BV.xz = boost::lexical_cast<double>(values.at(2));
-  BV.yy = boost::lexical_cast<double>(values.at(3));
-  BV.yz = boost::lexical_cast<double>(values.at(4));
-  BV.zz = boost::lexical_cast<double>(values.at(5));
+  BV.xx = boost::lexical_cast<double>(components.at(0));
+  BV.xy = boost::lexical_cast<double>(components.at(1));
+  BV.xz = boost::lexical_cast<double>(components.at(2));
+  BV.yy = boost::lexical_cast<double>(components.at(3));
+  BV.yz = boost::lexical_cast<double>(components.at(4));
+  BV.zz = boost::lexical_cast<double>(components.at(5));
   v = boost::any(BoxValue(BV));
 }
@@ -130 +171 @@
   DescriptionMap["input"] = "specify input files";
   DescriptionMap["linear-interpolate"] = "linear interpolation in discrete steps between start and end position of a molecule";
+  DescriptionMap["molecular-volume"] = "calculate the volume of a given molecule";
   DescriptionMap["nonconvex-envelope"] = "create the non-convex envelope for a molecule";
-  DescriptionMap["molecular-volume"] = "calculate the volume of a given molecule";
-  DescriptionMap["output"] = "specify output formats";
+  DescriptionMap["output"] = "write output files";
+  DescriptionMap["set-output"] = "specify output formats";
   DescriptionMap["pair-correlation"] = "pair correlation analysis between two elements, element and point or element and surface";
   DescriptionMap["parse-xyz"] = "parse xyz file into World";
@@ -140 +182 @@
   DescriptionMap["repeat-box"] = "create periodic copies of the simulation box per axis";
   DescriptionMap["rotate-to-pas"] = "calculate the principal axis system of the specified molecule and rotate specified axis to align with main axis";
-  DescriptionMap["set-basis"] = "set the name of the gaussian basis set for MPQC";
   DescriptionMap["save-adjacency"] = "name of the adjacency file to write to";
   DescriptionMap["save-bonds"] = "name of the bonds file to write to";
@@ -146 +187 @@
   DescriptionMap["SaveXyz"] = "save world as xyz file";
   DescriptionMap["scale-box"] = "scale box and atomic positions inside";
+  DescriptionMap["set-basis"] = "set the name of the gaussian basis set for MPQC";
+  DescriptionMap["set-output"] = "specify output formats";
   DescriptionMap["subgraph-dissect"] = "dissect the molecular system into molecules representing disconnected subgraphs";
   DescriptionMap["suspend-in-water"] = "suspend the given molecule in water such that in the domain the mean density is as specified";
@@ -189 +232 @@
   ShortFormMap["center-in-box"] = "b";
   ShortFormMap["change-element"] = "E";
-  ShortFormMap["convex-envelope"] = "o";
+//  ShortFormMap["convex-envelope"] = "x";
   ShortFormMap["default-molname"] = "X";
   ShortFormMap["depth-first-search"] = "D";
@@ -200 +243 @@
   ShortFormMap["linear-interpolate"] = "L";
   ShortFormMap["nonconvex-envelope"] = "N";
+//  ShortFormMap["output"] = "o";
   ShortFormMap["pair-correlation"] = "C";
   ShortFormMap["parse-xyz"] = "p";
@@ -211 +255 @@
   ShortFormMap["scale-box"] = "s";
   ShortFormMap["set-basis"] = "M";
+  ShortFormMap["set-output"] = "o";
   ShortFormMap["subgraph-dissect"] = "I";
   ShortFormMap["suspend-in-water"] = "u";
@@ -238 +283 @@
   TypeMap["molecular-volume"] = Molecule;
   TypeMap["nonconvex-envelope"] = Molecule;
-  TypeMap["output"] = String;
+  TypeMap["output"] = None;
   TypeMap["parse-xyz"] = String;
   TypeMap["pair-correlation"] = String;
@@ -251 +296 @@
   TypeMap["scale-box"] = Vector;
   TypeMap["set-basis"] = String;
+  TypeMap["set-output"] = ListOfString;
   TypeMap["subgraph-dissect"] = None;
   TypeMap["suspend-in-water"] = Double;
@@ -349 +395 @@
   MenuContainsActionMap.insert( pair<std::string, std::string> ("world", "default-molname") );
   MenuContainsActionMap.insert( pair<std::string, std::string> ("world", "set-basis") );
+  MenuContainsActionMap.insert( pair<std::string, std::string> ("world", "set-output") );
 
   // put actions into command line category
@@ -386 +433 @@
   generic.insert("scale-box");
   generic.insert("set-basis");
+  generic.insert("set-output");
         generic.insert("subgraph-dissect");
   generic.insert("suspend-in-water");
@@ -484 +532 @@
   new WorldSetDefaultNameAction();
   new WorldSetGaussianBasisAction();
+  new WorldSetOutputFormatsAction();
 }
 
@@ -561 +610 @@
               ;
             break;
+          case ListOfString:
+            ListRunner->second->add_options()
+              (getKeyAndShortForm(*OptionRunner).c_str(),
+                  po::value< vector<std::string> >()->multitoken(),
+                  getDescription(*OptionRunner).c_str())
+              ;
+            break;
           case Axis:
             ListRunner->second->add_options()
@@ -573 +629 @@
             ListRunner->second->add_options()
               (getKeyAndShortForm(*OptionRunner).c_str(),
-                  po::value<VectorValue>()->multitoken(),
+                  po::value<VectorValue>(),
                   getDescription(*OptionRunner).c_str())
               ;