--- trunk/src/UseTheForce/ForceField.hpp	2008/07/04 20:54:29	1275
+++ branches/development/src/UseTheForce/ForceField.hpp	2011/09/13 22:05:04	1627
@@ -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).                        
  */
  
 /**
@@ -55,7 +55,7 @@
 #include <utility>
 #include <vector>
 
-#include "io/basic_ifstrstream.hpp"
+#include "io/ifstrstream.hpp"
 #include "io/ForceFieldOptions.hpp"
 #include "utils/TypeContainer.hpp"
 #include "utils/Tuple.hpp"
@@ -65,8 +65,7 @@
 #include "types/TorsionType.hpp"
 #include "types/InversionType.hpp"
 #include "types/NonBondedInteractionType.hpp"
-#include "UseTheForce/fForceOptions.h"
-namespace oopse {
+namespace OpenMD {
 
   /**
    * @class ForceField ForceField.hpp ''UseTheForce/ForceField.hpp"
@@ -83,9 +82,9 @@ namespace oopse {
     typedef TypeContainer<InversionType, 4> InversionTypeContainer;
     typedef TypeContainer<NonBondedInteractionType, 2> NonBondedInteractionTypeContainer;
     
-    ForceField(); 
+    ForceField();
     
-    virtual ~ForceField();
+    virtual ~ForceField() {};
 
     std::string getForceFieldFileName() {
       return forceFieldFileName_;
@@ -98,6 +97,7 @@ namespace oopse {
     virtual void parse(const std::string& filename) = 0;  
 
     AtomType* getAtomType(const std::string &at);
+    AtomType* getAtomType(int ident);
     BondType* getBondType(const std::string &at1, const std::string &at2);
     BendType* getBendType(const std::string &at1, const std::string &at2,
                           const std::string &at3);
@@ -138,9 +138,19 @@ namespace oopse {
     unsigned int getNAtomType() {
       return atomTypeCont_.size();
     }
+
+    AtomTypeContainer* getAtomTypes() {
+      return &atomTypeCont_;
+    }
+    
+    NonBondedInteractionTypeContainer* getNonBondedInteractionTypes() {
+      return &nonBondedInteractionTypeCont_;
+    }
         
     bool addAtomType(const std::string &at, AtomType* atomType);
 
+    bool replaceAtomType(const std::string &at, AtomType* atomType);
+
     bool addBondType(const std::string &at1, const std::string &at2, 
                      BondType* bondType);
 
@@ -163,9 +173,6 @@ namespace oopse {
     
     ForceFieldOptions& getForceFieldOptions() {return forceFieldOptions_;}
 
-    void setFortranForceOptions(void);
-
- 
   protected:
 
     AtomTypeContainer atomTypeCont_;    
@@ -175,15 +182,14 @@ namespace oopse {
     InversionTypeContainer inversionTypeCont_;
     NonBondedInteractionTypeContainer nonBondedInteractionTypeCont_;
     ForceFieldOptions forceFieldOptions_;
+    std::map<int, std::string> atypeIdentToName;
     
   private:  
-    std::string ffPath_;
-    
-    std::string wildCardAtomTypeName_;
-    
+    std::string ffPath_;    
+    std::string wildCardAtomTypeName_;    
     std::string forceFieldFileName_;    
     
   };
-}//end namespace oopse
+}//end namespace OpenMD
 #endif