Changes in src/Actions/MapOfActions.cpp [112b09:980dd6]

File:

• src/Actions/MapOfActions.cpp (modified) (18 diffs)

src/Actions/MapOfActions.cpp

@@ -6 +6 @@
  */
 
-#include "Helpers/MemDebug.hpp"
-
 using namespace std;
 
@@ -14 +12 @@
 #include "Helpers/Assert.hpp"
 
+#include <boost/lexical_cast.hpp>
+#include <boost/optional.hpp>
+#include <boost/program_options.hpp>
+
 #include "CommandLineParser.hpp"
 #include "log.hpp"
 #include "verbose.hpp"
+
+#include "Actions/Values.hpp"
+
+void validate(boost::any& v, const std::vector<std::string>& values, VectorValue *, int)
+{
+  VectorValue VV;
+  if (values.size() != 3) {
+    cerr <<  "Specified vector does not have three components but " << values.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));
+  v = boost::any(VectorValue(VV));
+}
+
+void validate(boost::any& v, const std::vector<std::string>& values, BoxValue *, int)
+{
+  BoxValue BV;
+  if (values.size() != 6) {
+    cerr <<  "Specified vector does not have three components but " << values.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));
+  v = boost::any(BoxValue(BV));
+}
 
 /** Constructor of class MapOfActions.
@@ -51 +84 @@
   DescriptionMap["nonconvex-envelope"] = "create the non-convex envelope for a molecule";
   DescriptionMap["molecular-volume"] = "calculate the volume of a given molecule";
-  DescriptionMap["pair-correlation"] = "pair correlation analysis between two elements";
-  DescriptionMap["pair-correlation-point"] = "pair correlation analysis between atoms of a element to a given point";
-  DescriptionMap["pair-correlation-surface"] = "pair correlation analysis between atoms of a given element and a surface";
+  DescriptionMap["pair-correlation"] = "pair correlation analysis between two elements, element and point or element and surface";
   DescriptionMap["parse-xyz"] = "parse xyz file into World";
   DescriptionMap["principal-axis-system"] = "calculate the principal axis system of the specified molecule";
@@ -65 +96 @@
   DescriptionMap["save-temperature"] = "name of the temperature file to write to";
   DescriptionMap["scale-box"] = "scale box and atomic positions inside";
-  DescriptionMap["subspace-dissect"] = "dissect the molecular system into molecules representing disconnected subgraphs";
+  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";
   DescriptionMap["translate-mol"] = "translate molecule by given vector";
@@ -72 +103 @@
   DescriptionMap["version"] = "show version";
   // keys for values
+  DescriptionMap["atom-by-id"] = "index of an atom";
   DescriptionMap["bin-output-file"] = "name of the bin output file";
   DescriptionMap["bin-end"] = "start of the last bin";
   DescriptionMap["bin-start"] = "start of the first bin";
   DescriptionMap["bin-width"] = "width of the bins";
+  DescriptionMap["convex-file"] = "filename of the non-convex envelope";
   DescriptionMap["distance"] = "distance in space";
   DescriptionMap["distances"] = "list of three of distances in space, one for each axis direction";
-  DescriptionMap["element"] = "set of elements";
-  DescriptionMap["end-mol"] = "last or end step";
+  DescriptionMap["DoRotate"] = "whether to rotate or just report angles";
+  DescriptionMap["element"] = "single element";
+  DescriptionMap["elements"] = "set of elements";
+  DescriptionMap["end-step"] = "last or end step";
+  DescriptionMap["id-mapping"] = "whether the identity shall be used in mapping atoms onto atoms or some closest distance measure shall be used";
   DescriptionMap["input"] = "name of input file";
   DescriptionMap["length"] = "length in space";
@@ -85 +121 @@
   DescriptionMap["MaxDistance"] = "maximum distance in space";
   DescriptionMap["molecule-by-id"] = "index of a molecule";
+  DescriptionMap["molecule-by-name"] = "name of a molecule";
+  DescriptionMap["nonconvex-file"] = "filename of the non-convex envelope";
+  DescriptionMap["order"] = "order of a discretization, dissection, ...";
   DescriptionMap["output-file"] = "name of the output file";
   DescriptionMap["periodic"] = "system is constraint to periodic boundary conditions (y/n)";
   DescriptionMap["position"] = "position in R^3 space";
-  DescriptionMap["start-mol"] = "first or start step";
+  DescriptionMap["sphere-radius"] = "radius of tesselation sphere";
+  DescriptionMap["start-step"] = "first or start step";
 
   // short forms for the actions
@@ -110 +150 @@
   ShortFormMap["linear-interpolate"] = "L";
   ShortFormMap["nonconvex-envelope"] = "N";
-  ShortFormMap["pair-correlation"] = "CE";
-  ShortFormMap["pair-correlation-point"] = "CP";
-  ShortFormMap["pair-correlation-surface"] = "CS";
+  ShortFormMap["pair-correlation"] = "C";
   ShortFormMap["parse-xyz"] = "p";
   ShortFormMap["remove-atom"] = "r";
@@ -123 +161 @@
   ShortFormMap["scale-box"] = "s";
   ShortFormMap["set-basis"] = "M";
-  ShortFormMap["subspace-dissect"] = "I";
-  ShortFormMap["suspend-in-water"] = "U";
+  ShortFormMap["subgraph-dissect"] = "I";
+  ShortFormMap["suspend-in-water"] = "u";
   ShortFormMap["translate-mol"] = "t";
   ShortFormMap["verbose"] = "v";
@@ -131 +169 @@
 
   // value types for the actions
-  TypeMap["add-atom"] = Atom;
+  TypeMap["add-atom"] = Element;
   TypeMap["bond-file"] = String;
   TypeMap["bond-table"] = String;
   TypeMap["boundary"] = Vector;
-  TypeMap["center-in-box"] = ListOfDoubles;
-  TypeMap["change-box"] = ListOfDoubles;
-  TypeMap["change-element"] = Element;
+  TypeMap["center-in-box"] = Box;
+  TypeMap["change-box"] = Box;
+  TypeMap["change-element"] = Atom;
   TypeMap["change-molname"] = String;
   TypeMap["convex-envelope"] = Molecule;
@@ -143 +181 @@
   TypeMap["depth-first-search"] = Double;
   TypeMap["element-db"] = String;
-  TypeMap["end-mol"] = Molecule;
   TypeMap["fastparsing"] = Boolean;
   TypeMap["fill-molecule"] = String;
@@ -152 +189 @@
   TypeMap["nonconvex-envelope"] = Molecule;
   TypeMap["parse-xyz"] = String;
-  TypeMap["principal-axis-system"] = Axis;
+  TypeMap["pair-correlation"] = String;
+  TypeMap["principal-axis-system"] = Molecule;
   TypeMap["remove-atom"] = Atom;
-  TypeMap["remove-sphere"] = Atom;
+  TypeMap["remove-sphere"] = Double;
   TypeMap["repeat-box"] = Vector;
   TypeMap["rotate-to-pas"] = Molecule;
@@ -162 +200 @@
   TypeMap["scale-box"] = Vector;
   TypeMap["set-basis"] = String;
-  TypeMap["start-mol"] = Molecule;
-  TypeMap["suspend-in-water"] = Molecule;
+  TypeMap["subgraph-dissect"] = None;
+  TypeMap["suspend-in-water"] = Double;
   TypeMap["translate-mol"] = Vector;
   TypeMap["verlet-integrate"] = String;
@@ -169 +207 @@
 
   // value types for the values
+  TypeMap["atom-by-id"] = Atom;
   TypeMap["bin-output-file"] = String;
   TypeMap["bin-end"] = Double;
   TypeMap["bin-start"] = Double;
+  TypeMap["bin-width"] = Double;
+  TypeMap["convex-file"] = String;
   TypeMap["distance"] = Double;
-  TypeMap["distances"] = ListOfDoubles;
-  TypeMap["elements"] = Element;
+  TypeMap["distances"] = Vector;
+  TypeMap["DoRotate"] = Boolean;
+  TypeMap["element"] = Element;
   TypeMap["elements"] = ListOfElements;
+  TypeMap["end-step"] = Integer;
+  TypeMap["id-mapping"] = Boolean;
   TypeMap["length"] = Double;
-  TypeMap["lengths"] = ListOfDoubles;
+  TypeMap["lengths"] = Vector;
   TypeMap["MaxDistance"] = Double;
   TypeMap["molecule-by-id"] = Molecule;
+  TypeMap["molecule-by-name"] = Molecule;
+  TypeMap["nonconvex-file"] = String;
+  TypeMap["order"] = Integer;
   TypeMap["output-file"] = String;
   TypeMap["periodic"] = Boolean;
   TypeMap["position"] = Vector;
+  TypeMap["sphere-radius"] = Double;
+  TypeMap["start-step"] = Integer;
 
   // default values for any action that needs one (always string!)
+  DefaultValue["bin-width"] = "0.5";
+  DefaultValue["fastparsing"] = "0";
+  DefaultValue["atom-by-id"] = "-1";
   DefaultValue["molecule-by-id"] = "-1";
+  DefaultValue["periodic"] = "0";
 
 
   // list of generic actions
-//      generic.insert("add-atom");
-//  generic.insert("bond-file");
-//      generic.insert("bond-table");
+        generic.insert("add-atom");
+  generic.insert("bond-file");
+        generic.insert("bond-table");
   generic.insert("boundary");
 //  generic.insert("bound-in-box");
@@ -198 +251 @@
         generic.insert("change-box");
 //  generic.insert("change-molname");
-//      generic.insert("change-element");
-//  generic.insert("convex-envelope");
-//      generic.insert("default-molname");
-//      generic.insert("depth-first-search");
-//      generic.insert("element-db");
-//      generic.insert("fastparsing");
-//  generic.insert("fill-molecule");
-//  generic.insert("fragment-mol");
+        generic.insert("change-element");
+  generic.insert("convex-envelope");
+        generic.insert("default-molname");
+        generic.insert("depth-first-search");
+        generic.insert("element-db");
+        generic.insert("fastparsing");
+  generic.insert("fill-molecule");
+  generic.insert("fragment-mol");
   generic.insert("help");
-//      generic.insert("linear-interpolate");
+        generic.insert("linear-interpolate");
 //  generic.insert("molecular-volume");
-//  generic.insert("nonconvex-envelope");
-//      generic.insert("pair-correlation");
-//      generic.insert("pair-correlation-point");
-//      generic.insert("pair-correlation-surface");
+  generic.insert("nonconvex-envelope");
+        generic.insert("pair-correlation");
 //      generic.insert("parse-xyz");
 //  generic.insert("principal-axis-system");
-//  generic.insert("remove-atom");
-//  generic.insert("remove-sphere");
-    generic.insert("repeat-box");
-//  generic.insert("rotate-to-pas");
-//      generic.insert("save-adjacency");
-//  generic.insert("save-bonds");
-//  generic.insert("save-temperature");
+  generic.insert("remove-atom");
+  generic.insert("remove-sphere");
+  generic.insert("repeat-box");
+  generic.insert("rotate-to-pas");
+        generic.insert("save-adjacency");
+  generic.insert("save-bonds");
+  generic.insert("save-temperature");
   generic.insert("scale-box");
-//  generic.insert("set-basis");
-//      generic.insert("subspace-dissect");
-//  generic.insert("suspend-in-water");
-//  generic.insert("translate-mol");
+  generic.insert("set-basis");
+        generic.insert("subgraph-dissect");
+  generic.insert("suspend-in-water");
+  generic.insert("translate-mol");
         generic.insert("verbose");
-//  generic.insert("verlet-integrate");
+  generic.insert("verlet-integrate");
         generic.insert("version");
-//      // list of generic values
-//      generic.insert("bin-output-file");
-//  generic.insert("bin-end");
-//  generic.insert("bin-start");
-//  generic.insert("distance");
-//  generic.insert("distances");
-//  generic.insert("element");
-//  generic.insert("end-mol");
-    generic.insert("input");
-//  generic.insert("length");
-//  generic.insert("lengths");
-//  generic.insert("MaxDistance");
-//  generic.insert("molecule-by-id");
-//  generic.insert("output-file");
-//  generic.insert("periodic");
-//  generic.insert("position");
-//  generic.insert("start-mol");
 
     // positional arguments
-    inputfile.insert("input");
+  generic.insert("input");
+  inputfile.insert("input");
+
+    // hidden arguments
+  generic.insert("atom-by-id");
+  generic.insert("bin-end");
+  generic.insert("bin-output-file");
+  generic.insert("bin-start");
+  generic.insert("bin-width");
+  generic.insert("convex-file");
+  generic.insert("distance");
+  generic.insert("DoRotate");
+  generic.insert("distances");
+  generic.insert("element");
+  generic.insert("elements");
+  generic.insert("end-step");
+  generic.insert("id-mapping");
+  generic.insert("lengths");
+  generic.insert("MaxDistance");
+  generic.insert("molecule-by-id");
+  generic.insert("molecule-by-name");
+  generic.insert("nonconvex-file");
+  generic.insert("order");
+  generic.insert("output-file");
+  generic.insert("periodic");
+  generic.insert("position");
+  generic.insert("sphere-radius");
+  generic.insert("start-step");
 }
 
@@ -286 +347 @@
               ;
             break;
+          case Box:
+            ListRunner->second->add_options()
+              (getKeyAndShortForm(*OptionRunner).c_str(),
+                  po::value<BoxValue>()->multitoken(),
+                  getDescription(*OptionRunner).c_str())
+              ;
+            break;
           case Integer:
             ListRunner->second->add_options()
@@ -339 +407 @@
             ListRunner->second->add_options()
               (getKeyAndShortForm(*OptionRunner).c_str(),
-                  po::value< vector<double> >()->multitoken(),
-                  getDescription(*OptionRunner).c_str())
-              ;
-            break;
-          case Box:
-            ListRunner->second->add_options()
-              (getKeyAndShortForm(*OptionRunner).c_str(),
-                  po::value< vector<double> >(),
+                  po::value<VectorValue>()->multitoken(),
                   getDescription(*OptionRunner).c_str())
               ;
@@ -385 +446 @@
             ListRunner->second->add_options()
               (getKeyAndShortForm(*OptionRunner).c_str(),
-                  DefaultValue.find(*OptionRunner) != DefaultValue.end() ?
-                        po::value< int >()->default_value(atoi(DefaultValue[*OptionRunner].c_str())) :
-                        po::value< int >(),
+                  po::value< vector<int> >(),
                   getDescription(*OptionRunner).c_str())
               ;
@@ -497 +556 @@
 }
 
+/** Returns the inverse to MapOfActions::ShortFormMap, i.e. lookup actionname for its short form.
+ * \return map from short form of action to name of action
+ */
+map <std::string, std::string> MapOfActions::getShortFormToActionMap()
+{
+  map <std::string, std::string> result;
+
+  for (map<std::string, std::string>::iterator iter = ShortFormMap.begin(); iter != ShortFormMap.end();  ++iter)
+    result[iter->second] = iter->first;
+
+  return result;
+}