--- branches/development/src/UseTheForce/ForceField.hpp	2010/07/09 23:08:25	1465
+++ branches/development/src/brains/ForceField.hpp	2012/05/26 18:13:43	1725
@@ -36,7 +36,8 @@
  * [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).                        
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
  
 /**
@@ -55,8 +56,9 @@
 #include <utility>
 #include <vector>
 
-#include "io/basic_ifstrstream.hpp"
+#include "io/ifstrstream.hpp"
 #include "io/ForceFieldOptions.hpp"
+#include "io/SectionParserManager.hpp"
 #include "utils/TypeContainer.hpp"
 #include "utils/Tuple.hpp"
 #include "types/AtomType.hpp"
@@ -65,17 +67,12 @@
 #include "types/TorsionType.hpp"
 #include "types/InversionType.hpp"
 #include "types/NonBondedInteractionType.hpp"
-#include "UseTheForce/fForceOptions.h"
+
 namespace OpenMD {
 
-  /**
-   * @class ForceField ForceField.hpp ''UseTheForce/ForceField.hpp"
-   * @brief
-   */
   class ForceField{
 
   public:
-
     typedef TypeContainer<AtomType, 1> AtomTypeContainer;
     typedef TypeContainer<BondType, 2> BondTypeContainer;
     typedef TypeContainer<BendType, 3> BendTypeContainer;
@@ -83,9 +80,9 @@ namespace OpenMD {
     typedef TypeContainer<InversionType, 4> InversionTypeContainer;
     typedef TypeContainer<NonBondedInteractionType, 2> NonBondedInteractionTypeContainer;
     
-    ForceField(); 
+    ForceField(std::string ffName);
     
-    virtual ~ForceField();
+    virtual ~ForceField() {};
 
     std::string getForceFieldFileName() {
       return forceFieldFileName_;
@@ -95,9 +92,10 @@ namespace OpenMD {
       forceFieldFileName_ = filename;
     }
         
-    virtual void parse(const std::string& filename) = 0;  
+    virtual void parse(const std::string& filename);  
 
     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);
@@ -138,6 +136,14 @@ namespace OpenMD {
     unsigned int getNAtomType() {
       return atomTypeCont_.size();
     }
+
+    AtomTypeContainer* getAtomTypes() {
+      return &atomTypeCont_;
+    }
+    
+    NonBondedInteractionTypeContainer* getNonBondedInteractionTypes() {
+      return &nonBondedInteractionTypeCont_;
+    }
         
     bool addAtomType(const std::string &at, AtomType* atomType);
 
@@ -165,9 +171,6 @@ namespace OpenMD {
     
     ForceFieldOptions& getForceFieldOptions() {return forceFieldOptions_;}
 
-    void setFortranForceOptions(void);
-
- 
   protected:
 
     AtomTypeContainer atomTypeCont_;    
@@ -177,12 +180,13 @@ namespace OpenMD {
     InversionTypeContainer inversionTypeCont_;
     NonBondedInteractionTypeContainer nonBondedInteractionTypeCont_;
     ForceFieldOptions forceFieldOptions_;
+    std::map<int, std::string> atypeIdentToName;
+    SectionParserManager spMan_;
+
     
   private:  
-    std::string ffPath_;
-    
-    std::string wildCardAtomTypeName_;
-    
+    std::string ffPath_;    
+    std::string wildCardAtomTypeName_;    
     std::string forceFieldFileName_;    
     
   };