--- trunk/src/UseTheForce/ForceField.cpp	2005/04/15 22:04:00	507
+++ trunk/src/UseTheForce/ForceField.cpp	2007/12/06 20:04:02	1195
@@ -50,6 +50,8 @@
 #include "UseTheForce/ForceField.hpp"
 #include "utils/simError.h"
 #include "UseTheForce/DarkSide/atype_interface.h"
+#include "UseTheForce/DarkSide/fForceOptions_interface.h"
+#include "UseTheForce/DarkSide/switcheroo_interface.h"
 namespace oopse {
 
   ForceField::ForceField() { 
@@ -67,6 +69,7 @@ namespace oopse {
 
   ForceField::~ForceField() {
     deleteAtypes();
+    deleteSwitch();
   }
 
   AtomType* ForceField::getAtomType(const std::string &at) {
@@ -75,7 +78,8 @@ namespace oopse {
     return atomTypeCont_.find(keys);
   }
 
-  BondType* ForceField::getBondType(const std::string &at1, const std::string &at2) {
+  BondType* ForceField::getBondType(const std::string &at1, 
+				    const std::string &at2) {
     std::vector<std::string> keys;
     keys.push_back(at1);
     keys.push_back(at2);    
@@ -88,10 +92,10 @@ namespace oopse {
       //if no exact match found, try wild card match
       return bondTypeCont_.find(keys, wildCardAtomTypeName_);
     }
-
   }
 
-  BendType* ForceField::getBendType(const std::string &at1, const std::string &at2,
+  BendType* ForceField::getBendType(const std::string &at1, 
+				    const std::string &at2,
 				    const std::string &at3) {
     std::vector<std::string> keys;
     keys.push_back(at1);
@@ -108,8 +112,10 @@ namespace oopse {
     }
   }
 
-  TorsionType* ForceField::getTorsionType(const std::string &at1, const std::string &at2,
-					  const std::string &at3, const std::string &at4) {
+  TorsionType* ForceField::getTorsionType(const std::string &at1, 
+					  const std::string &at2,
+					  const std::string &at3, 
+					  const std::string &at4) {
     std::vector<std::string> keys;
     keys.push_back(at1);
     keys.push_back(at2);    
@@ -125,17 +131,33 @@ namespace oopse {
     }
     
     return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
-
   }
 
-  BondType* ForceField::getExactBondType(const std::string &at1, const std::string &at2){ 
+  NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) {
     std::vector<std::string> keys;
     keys.push_back(at1);
     keys.push_back(at2);    
+    
+    //try exact match first
+    NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(keys);
+    if (nbiType) {
+      return nbiType;
+    } else {
+      //if no exact match found, try wild card match
+      return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_);
+    }    
+  }
+  
+  BondType* ForceField::getExactBondType(const std::string &at1, 
+					 const std::string &at2){ 
+    std::vector<std::string> keys;
+    keys.push_back(at1);
+    keys.push_back(at2);    
     return bondTypeCont_.find(keys);
   }
-
-  BendType* ForceField::getExactBendType(const std::string &at1, const std::string &at2,
+  
+  BendType* ForceField::getExactBendType(const std::string &at1, 
+					 const std::string &at2,
 					 const std::string &at3){ 
     std::vector<std::string> keys;
     keys.push_back(at1);
@@ -143,9 +165,11 @@ namespace oopse {
     keys.push_back(at3);    
     return bendTypeCont_.find(keys);
   }
-
-  TorsionType* ForceField::getExactTorsionType(const std::string &at1, const std::string &at2,
-					       const std::string &at3, const std::string &at4){ 
+  
+  TorsionType* ForceField::getExactTorsionType(const std::string &at1, 
+					       const std::string &at2,
+					       const std::string &at3, 
+					       const std::string &at4){ 
     std::vector<std::string> keys;
     keys.push_back(at1);
     keys.push_back(at2);    
@@ -153,20 +177,29 @@ namespace oopse {
     keys.push_back(at4);   
     return torsionTypeCont_.find(keys);
   }
+
+  NonBondedInteractionType* ForceField::getExactNonBondedInteractionType(const std::string &at1, const std::string &at2){ 
+    std::vector<std::string> keys;
+    keys.push_back(at1);
+    keys.push_back(at2);    
+    return nonBondedInteractionTypeCont_.find(keys);
+  }
+
+
   bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
     std::vector<std::string> keys;
     keys.push_back(at);
     return atomTypeCont_.add(keys, atomType);
   }
 
-  bool ForceField::addBondType(const std::string &at1, const std::string &at2, BondType* bondType) {
+  bool ForceField::addBondType(const std::string &at1, const std::string &at2,
+			       BondType* bondType) {
     std::vector<std::string> keys;
     keys.push_back(at1);
     keys.push_back(at2);    
-    return bondTypeCont_.add(keys, bondType);
-
+    return bondTypeCont_.add(keys, bondType);    
   }
-
+  
   bool ForceField::addBendType(const std::string &at1, const std::string &at2,
 			       const std::string &at3, BendType* bendType) {
     std::vector<std::string> keys;
@@ -175,9 +208,12 @@ namespace oopse {
     keys.push_back(at3);    
     return bendTypeCont_.add(keys, bendType);
   }
-
-  bool ForceField::addTorsionType(const std::string &at1, const std::string &at2,
-				  const std::string &at3, const std::string &at4, TorsionType* torsionType) {
+  
+  bool ForceField::addTorsionType(const std::string &at1, 
+				  const std::string &at2,
+				  const std::string &at3, 
+				  const std::string &at4, 
+				  TorsionType* torsionType) {
     std::vector<std::string> keys;
     keys.push_back(at1);
     keys.push_back(at2);    
@@ -186,22 +222,31 @@ namespace oopse {
     return torsionTypeCont_.add(keys, torsionType);
   }
 
-  double ForceField::getRcutFromAtomType(AtomType* at) {
+  bool ForceField::addNonBondedInteractionType(const std::string &at1, 
+					       const std::string &at2, 
+					       NonBondedInteractionType* nbiType) {
+    std::vector<std::string> keys;
+    keys.push_back(at1);
+    keys.push_back(at2);    
+    return nonBondedInteractionTypeCont_.add(keys, nbiType);
+  }
+  
+  RealType ForceField::getRcutFromAtomType(AtomType* at) {
     /**@todo */
     GenericData* data;
-    double rcut = 0.0;
-
+    RealType rcut = 0.0;
+    
     if (at->isLennardJones()) {
       data = at->getPropertyByName("LennardJones");
       if (data != NULL) {
 	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
-
+	
 	if (ljData != NULL) {
 	  LJParam ljParam = ljData->getData();
-
+	  
 	  //by default use 2.5*sigma as cutoff radius
 	  rcut = 2.5 * ljParam.sigma;
-                
+          
 	} else {
 	  sprintf( painCave.errMsg,
 		   "Can not cast GenericData to LJParam\n");
@@ -216,11 +261,10 @@ namespace oopse {
 	simError();          
       }
     }
-
     return rcut;    
   }
+  
 
-
   ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
     std::string forceFieldFilename(filename);
     ifstrstream* ffStream = new ifstrstream();
@@ -247,9 +291,12 @@ namespace oopse {
 	simError();
       }
     }  
-
     return ffStream;
-
   }
 
+  void ForceField::setFortranForceOptions(){
+    ForceOptions theseFortranOptions;
+    forceFieldOptions_.makeFortranOptions(theseFortranOptions);
+    setfForceOptions(&theseFortranOptions);
+  }
 } //end namespace oopse