Changes in src/Actions/MapOfActions.cpp [39af9f:8540f0]

File:

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

src/Actions/MapOfActions.cpp

@@ -50 +50 @@
   v = boost::any(BoxValue(BV));
 }
+
 
 /** Constructor of class MapOfActions.
@@ -84 +85 @@
   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, element and point or element and surface";
+  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["parse-xyz"] = "parse xyz file into World";
   DescriptionMap["principal-axis-system"] = "calculate the principal axis system of the specified molecule";
@@ -110 +113 @@
   DescriptionMap["distances"] = "list of three of distances in space, one for each axis direction";
   DescriptionMap["DoRotate"] = "whether to rotate or just report angles";
-  DescriptionMap["element"] = "single element";
-  DescriptionMap["elements"] = "set of elements";
+  DescriptionMap["element"] = "set of elements";
   DescriptionMap["end-mol"] = "last or end step";
   DescriptionMap["input"] = "name of input file";
@@ -118 +120 @@
   DescriptionMap["MaxDistance"] = "maximum distance in space";
   DescriptionMap["molecule-by-id"] = "index of a molecule";
-  DescriptionMap["molecule-by-name"] = "name of a molecule";
   DescriptionMap["order"] = "order of a discretization, dissection, ...";
   DescriptionMap["output-file"] = "name of the output file";
@@ -145 +146 @@
   ShortFormMap["linear-interpolate"] = "L";
   ShortFormMap["nonconvex-envelope"] = "N";
-  ShortFormMap["pair-correlation"] = "C";
+  ShortFormMap["pair-correlation"] = "CE";
+  ShortFormMap["pair-correlation-point"] = "CP";
+  ShortFormMap["pair-correlation-surface"] = "CS";
   ShortFormMap["parse-xyz"] = "p";
   ShortFormMap["remove-atom"] = "r";
@@ -185 +188 @@
   TypeMap["nonconvex-envelope"] = Molecule;
   TypeMap["parse-xyz"] = String;
-  TypeMap["pair-correlation"] = String;
-  TypeMap["principal-axis-system"] = Molecule;
+  TypeMap["principal-axis-system"] = Axis;
   TypeMap["remove-atom"] = Atom;
   TypeMap["remove-sphere"] = Atom;
@@ -206 +208 @@
   TypeMap["bin-end"] = Double;
   TypeMap["bin-start"] = Double;
-  TypeMap["bin-width"] = Double;
   TypeMap["distance"] = Double;
   TypeMap["distances"] = Vector;
@@ -216 +217 @@
   TypeMap["MaxDistance"] = Double;
   TypeMap["molecule-by-id"] = Molecule;
-  TypeMap["molecule-by-name"] = Molecule;
   TypeMap["order"] = Integer;
   TypeMap["output-file"] = String;
@@ -224 +224 @@
   // default values for any action that needs one (always string!)
   DefaultValue["molecule-by-id"] = "-1";
-  DefaultValue["bin-width"] = "0.5";
-  DefaultValue["periodic"] = "0";
 
 
@@ -231 +229 @@
 //      generic.insert("add-atom");
 //  generic.insert("bond-file");
-        generic.insert("bond-table");
+//      generic.insert("bond-table");
   generic.insert("boundary");
 //  generic.insert("bound-in-box");
@@ -242 +240 @@
 //      generic.insert("default-molname");
         generic.insert("depth-first-search");
-        generic.insert("element-db");
+//      generic.insert("element-db");
 //      generic.insert("fastparsing");
   generic.insert("fill-molecule");
@@ -250 +248 @@
 //  generic.insert("molecular-volume");
 //  generic.insert("nonconvex-envelope");
-        generic.insert("pair-correlation");
+//      generic.insert("pair-correlation");
+//      generic.insert("pair-correlation-point");
+//      generic.insert("pair-correlation-surface");
 //      generic.insert("parse-xyz");
 //  generic.insert("principal-axis-system");
@@ -256 +256 @@
 //  generic.insert("remove-sphere");
   generic.insert("repeat-box");
-  generic.insert("rotate-to-pas");
+//  generic.insert("rotate-to-pas");
 //      generic.insert("save-adjacency");
 //  generic.insert("save-bonds");
@@ -269 +269 @@
         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");
@@ -275 +278 @@
     generic.insert("input");
 //  generic.insert("length");
+//  generic.insert("output-file");
+//  generic.insert("periodic");
+//  generic.insert("position");
 //  generic.insert("start-mol");
 
@@ -281 +287 @@
 
     // hidden arguments
-  generic.insert("bin-end");
-  generic.insert("bin-output-file");
-  generic.insert("bin-start");
-  generic.insert("bin-width");
   generic.insert("distance");
   generic.insert("DoRotate");
   generic.insert("distances");
-  generic.insert("element");
-  generic.insert("elements");
   generic.insert("lengths");
   generic.insert("MaxDistance");
   generic.insert("molecule-by-id");
-  generic.insert("molecule-by-name");
   generic.insert("order");
-  generic.insert("output-file");
-  generic.insert("periodic");
-  generic.insert("position");
 }
 
@@ -545 +541 @@
 }
 
-/** 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;
-}