--- trunk/src/UseTheForce/ForceField.cpp	2008/07/14 12:35:58	1277
+++ trunk/src/UseTheForce/ForceField.cpp	2009/11/25 20:02:06	1390
@@ -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).                        
  */
  
 /**
@@ -54,7 +54,7 @@
 #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; 
@@ -124,7 +124,6 @@ namespace oopse {
 	  myKeys.push_back((*i)->getName());
 	  myKeys.push_back((*j)->getName());
 
-          std::cerr << "looking for " << myKeys[0] << " " << myKeys[1] << "\n";
 	  BondType* bondType = bondTypeCont_.find(myKeys);
 	  if (bondType) {
 	    foundBonds.push_back(std::make_pair(bondTypeScore, myKeys));
@@ -142,7 +141,6 @@ namespace oopse {
         int bestScore = foundBonds[0].first;
         std::vector<std::string> theKeys = foundBonds[0].second;
         
-        std::cout << "best matching bond = " << theKeys[0] << "\t" << theKeys[1]  << "\t(score = "<< bestScore << ")\n";      
         BondType* bestType = bondTypeCont_.find(theKeys);
         
         return bestType;
@@ -226,10 +224,8 @@ namespace oopse {
         std::sort(foundBends.begin(), foundBends.end());
         int jscore = foundBends[0].first;
         int ikscore = foundBends[0].second;
-        std::vector<std::string> theKeys = foundBends[0].third;
+        std::vector<std::string> theKeys = foundBends[0].third;       
         
-        std::cout << "best matching bend = " << theKeys[0] << "\t" <<theKeys[1]  << "\t" << theKeys[2] << "\t(scores = "<< jscore << "\t" << ikscore << ")\n";      
-        
         BendType* bestType = bendTypeCont_.find(theKeys);  
         return bestType;
       } else {        
@@ -332,8 +328,6 @@ namespace oopse {
         int ilscore = foundTorsions[0].second;
         std::vector<std::string> theKeys = foundTorsions[0].third;
         
-        std::cout << "best matching torsion = " << theKeys[0] << "\t" <<theKeys[1]  << "\t" << theKeys[2] << "\t" << theKeys[3] << "\t(scores = "<< jkscore << "\t" << ilscore << ")\n";
-                
         TorsionType* bestType = torsionTypeCont_.find(theKeys);
         return bestType;
       } else {
@@ -354,7 +348,7 @@ 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 {
@@ -416,7 +410,7 @@ 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) );
 	      }
@@ -435,9 +429,7 @@ namespace oopse {
         int jklscore = foundInversions[0].second;
         std::vector<std::string> theKeys = foundInversions[0].third;
         
-        std::cout << "best matching inversion = " << theKeys[0] << "\t" <<theKeys[1]  << "\t" << theKeys[2] << "\t" << theKeys[3] << "\t(scores = "<< iscore << "\t" << jklscore << ")\n";
-                
-        InversionType* bestType = inversionTypeCont_.find(theKeys);
+        InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys);
         return bestType;
       } else {
 	//if no exact match found, try wild card match
@@ -515,6 +507,12 @@ namespace oopse {
     std::vector<std::string> keys;
     keys.push_back(at);
     return atomTypeCont_.add(keys, atomType);
+  }
+
+  bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) {
+    std::vector<std::string> keys;
+    keys.push_back(at);
+    return atomTypeCont_.replace(keys, atomType);
   }
 
   bool ForceField::addBondType(const std::string &at1, const std::string &at2,
@@ -588,13 +586,13 @@ 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();          
       }
@@ -624,7 +622,7 @@ 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();
       }
@@ -637,4 +635,4 @@ namespace oopse {
     forceFieldOptions_.makeFortranOptions(theseFortranOptions);
     setfForceOptions(&theseFortranOptions);
   }
-} //end namespace oopse
+} //end namespace OpenMD