--- trunk/src/UseTheForce/ForceField.cpp	2008/09/10 19:40:06	1289
+++ branches/development/src/UseTheForce/ForceField.cpp	2010/12/29 19:59:21	1532
@@ -6,19 +6,10 @@
  * redistribute this software in source and binary code form, provided
  * that the following conditions are met:
  *
- * 1. Acknowledgement of the program authors must be made in any
- *    publication of scientific results based in part on use of the
- *    program.  An acceptable form of acknowledgement is citation of
- *    the article in which the program was described (Matthew
- *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
- *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
- *    Parallel Simulation Engine for Molecular Dynamics,"
- *    J. Comput. Chem. 26, pp. 252-271 (2005))
- *
- * 2. Redistributions of source code must retain the above copyright
+ * 1. Redistributions of source code must retain the above copyright
  *    notice, this list of conditions and the following disclaimer.
  *
- * 3. Redistributions in binary form must reproduce the above copyright
+ * 2. Redistributions in binary form must reproduce the above copyright
  *    notice, this list of conditions and the following disclaimer in the
  *    documentation and/or other materials provided with the
  *    distribution.
@@ -37,6 +28,15 @@
  * arising out of the use of or inability to use software, even if the
  * University of Notre Dame has been advised of the possibility of
  * such damages.
+ *
+ * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
+ * research, please cite the appropriate papers when you publish your
+ * work.  Good starting points are:
+ *                                                                      
+ * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
+ * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
+ * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
+ * [4]  Vardeman & Gezelter, in progress (2009).                        
  */
  
 /**
@@ -51,27 +51,19 @@
 #include "UseTheForce/ForceField.hpp"
 #include "utils/simError.h"
 #include "utils/Tuple.hpp"
-#include "UseTheForce/DarkSide/atype_interface.h"
-#include "UseTheForce/DarkSide/fForceOptions_interface.h"
-#include "UseTheForce/DarkSide/switcheroo_interface.h"
-namespace oopse {
+namespace OpenMD {
 
   ForceField::ForceField() { 
+
     char* tempPath; 
     tempPath = getenv("FORCE_PARAM_PATH");
-
+    
     if (tempPath == NULL) {
       //convert a macro from compiler to a string in c++
       STR_DEFINE(ffPath_, FRC_PATH );
     } else {
       ffPath_ = tempPath;
     }
-  }
-
-
-  ForceField::~ForceField() {
-    deleteAtypes();
-    deleteSwitch();
   }
 
   AtomType* ForceField::getAtomType(const std::string &at) {
@@ -348,7 +340,7 @@ namespace oopse {
     keys.push_back(at4);    
 
     //try exact match first
-    InversionType* inversionType = inversionTypeCont_.find(keys);
+    InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys);
     if (inversionType) {
       return inversionType;
     } else {
@@ -410,7 +402,7 @@ namespace oopse {
 	      myKeys.push_back((*k)->getName());
 	      myKeys.push_back((*l)->getName());
 	      
-	      InversionType* inversionType = inversionTypeCont_.find(myKeys);
+	      InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys);
 	      if (inversionType) { 
 		foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) );
 	      }
@@ -429,7 +421,7 @@ namespace oopse {
         int jklscore = foundInversions[0].second;
         std::vector<std::string> theKeys = foundInversions[0].third;
         
-        InversionType* bestType = inversionTypeCont_.find(theKeys);
+        InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys);
         return bestType;
       } else {
 	//if no exact match found, try wild card match
@@ -586,13 +578,13 @@ namespace oopse {
 	} else {
 	  sprintf( painCave.errMsg,
 		   "Can not cast GenericData to LJParam\n");
-	  painCave.severity = OOPSE_ERROR;
+	  painCave.severity = OPENMD_ERROR;
 	  painCave.isFatal = 1;
 	  simError();          
 	}            
       } else {
 	sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
-	painCave.severity = OOPSE_ERROR;
+	painCave.severity = OPENMD_ERROR;
 	painCave.isFatal = 1;
 	simError();          
       }
@@ -622,7 +614,7 @@ namespace oopse {
 		 "\tHave you tried setting the FORCE_PARAM_PATH environment "
 		 "variable?\n",
 		 forceFieldFilename.c_str() );
-	painCave.severity = OOPSE_ERROR;
+	painCave.severity = OPENMD_ERROR;
 	painCave.isFatal = 1;
 	simError();
       }
@@ -630,9 +622,4 @@ namespace oopse {
     return ffStream;
   }
 
-  void ForceField::setFortranForceOptions(){
-    ForceOptions theseFortranOptions;
-    forceFieldOptions_.makeFortranOptions(theseFortranOptions);
-    setfForceOptions(&theseFortranOptions);
-  }
-} //end namespace oopse
+} //end namespace OpenMD