--- trunk/src/utils/LocalIndexManager.hpp	2009/11/25 20:02:06	1390
+++ trunk/src/utils/LocalIndexManager.hpp	2013/12/05 18:19:26	1953
@@ -35,8 +35,9 @@
  *                                                                      
  * [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).                        
+ * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
  
 /**
@@ -64,34 +65,31 @@ namespace OpenMD {
   class IndexListContainer{
   public:
     static const int MAX_INTEGER = 2147483647;
-    typedef std::list<std::pair<int, int> >::iterator  IndexListContainerIterator;
+    typedef std::list<std::pair<int, int> >::iterator IndexListContainerIterator;
 
-        
     IndexListContainer(int minIndex = 0, int maxIndex = MAX_INTEGER) 
       :minIndex_(minIndex), maxIndex_(maxIndex) {
-            
-	indexContainer_.push_back(std::make_pair(minIndex, maxIndex));
-      }
+      indexContainer_.push_back(std::make_pair(minIndex, maxIndex));
+    }
         
-    int pop() {
-            
+    int pop() {            
       if (indexContainer_.empty()) {
 	std::cerr << "" << std::endl;
       }
 
-      IndexListContainerIterator i = indexContainer_.begin();
       int result;
             
       result = indexContainer_.front().first;
             
       if (indexContainer_.front().first  == indexContainer_.front().second) {
 	indexContainer_.pop_front();
-      } else if (indexContainer_.front().first < indexContainer_.front().second) {
+      } else if (indexContainer_.front().first < 
+                 indexContainer_.front().second) {
 	++indexContainer_.front().first;
       } else {
 	std::cerr << "" << std::endl;
       }
-
+      
       return result;
     }
 
@@ -100,7 +98,7 @@ namespace OpenMD {
      *
      */
     void insert(int index) {
-      IndexListContainerIterator insertPos = internalInsert(index, index);            
+      IndexListContainerIterator insertPos = internalInsert(index, index);
       merge(insertPos);
     }
 
@@ -110,7 +108,8 @@ namespace OpenMD {
      * @param endIndex
      */
     void insert(int beginIndex, int endIndex) {
-      IndexListContainerIterator insertPos = internalInsert(beginIndex, endIndex); 
+      IndexListContainerIterator insertPos = internalInsert(beginIndex, 
+                                                            endIndex); 
       merge(insertPos);            
     }
 
@@ -128,7 +127,6 @@ namespace OpenMD {
       std::unique(indices.begin(), indices.end());
 
       std::vector<int>::iterator i;
-      IndexListContainerIterator insertPos;
       int beginIndex;
 
       beginIndex = indices[0];
@@ -139,8 +137,6 @@ namespace OpenMD {
 	  beginIndex = *i;
 	}
       }
-            
-            
     }
         
     std::vector<int> getIndicesBefore(int index) {
@@ -164,20 +160,15 @@ namespace OpenMD {
 	  indexContainer_.erase(indexContainer_.begin(), i);
 	  break;
 	} else {
-
 	  for (int j = (*i).first; j < index; ++j) {
 	    result.push_back(j);
-	  }
-                        
+	  }                        
 	  (*i).first =  index;                   
 	  indexContainer_.erase(indexContainer_.begin(), i);
 	  break;
 	}
-                
       }
-
       return result;
-
     }
         
     int getMaxIndex() {
@@ -196,10 +187,7 @@ namespace OpenMD {
       if (endIndex > maxIndex_) {
 	std::cerr << "" << std::endl;
       }
-
-                      
-      IndexListContainerIterator j;
-
+      
       IndexListContainerIterator i = indexContainer_.begin();  
       for (; i != indexContainer_.end(); ++i) {
 	if ((*i).first > endIndex) {
@@ -294,11 +282,116 @@ namespace OpenMD {
     void releaseRigidBodyIndex(std::vector<int> indices) {
       rigidBodyIndexContainer_.insert(indices);
     }
- 
+
+    int getNextCutoffGroupIndex() {
+      return cutoffGroupIndexContainer_.pop();
+    }
+
+    std::vector<int> getCutoffGroupIndicesBefore(int index) {
+      return cutoffGroupIndexContainer_.getIndicesBefore(index);
+    }
+        
+    void releaseCutoffGroupIndex(int index) {
+      cutoffGroupIndexContainer_.insert(index);
+    }
+
+    void releaseCutoffGroupIndex(int beginIndex, int endIndex) {
+      cutoffGroupIndexContainer_.insert(beginIndex, endIndex);
+    }
+
+    void releaseCutoffGroupIndex(std::vector<int> indices) {
+      cutoffGroupIndexContainer_.insert(indices);
+    }
+    
+    int getNextBondIndex() {
+      return bondIndexContainer_.pop();
+    }
+
+    std::vector<int> getBondIndicesBefore(int index) {
+      return bondIndexContainer_.getIndicesBefore(index);
+    }
+        
+    void releaseBondIndex(int index) {
+      bondIndexContainer_.insert(index);
+    }
+
+    void releaseBondIndex(int beginIndex, int endIndex) {
+      bondIndexContainer_.insert(beginIndex, endIndex);
+    }
+
+    void releaseBondIndex(std::vector<int> indices) {
+      bondIndexContainer_.insert(indices);
+    }
+
+    int getNextBendIndex() {
+      return bendIndexContainer_.pop();
+    }
+
+    std::vector<int> getBendIndicesBefore(int index) {
+      return bendIndexContainer_.getIndicesBefore(index);
+    }
+        
+    void releaseBendIndex(int index) {
+      bendIndexContainer_.insert(index);
+    }
+
+    void releaseBendIndex(int beginIndex, int endIndex) {
+      bendIndexContainer_.insert(beginIndex, endIndex);
+    }
+
+    void releaseBendIndex(std::vector<int> indices) {
+      bendIndexContainer_.insert(indices);
+    }
+
+    int getNextTorsionIndex() {
+      return torsionIndexContainer_.pop();
+    }
+
+    std::vector<int> getTorsionIndicesBefore(int index) {
+      return torsionIndexContainer_.getIndicesBefore(index);
+    }
+        
+    void releaseTorsionIndex(int index) {
+      torsionIndexContainer_.insert(index);
+    }
+
+    void releaseTorsionIndex(int beginIndex, int endIndex) {
+      torsionIndexContainer_.insert(beginIndex, endIndex);
+    }
+
+    void releaseTorsionIndex(std::vector<int> indices) {
+      torsionIndexContainer_.insert(indices);
+    }
+
+    int getNextInversionIndex() {
+      return inversionIndexContainer_.pop();
+    }
+
+    std::vector<int> getInversionIndicesBefore(int index) {
+      return inversionIndexContainer_.getIndicesBefore(index);
+    }
+        
+    void releaseInversionIndex(int index) {
+      inversionIndexContainer_.insert(index);
+    }
+
+    void releaseInversionIndex(int beginIndex, int endIndex) {
+      inversionIndexContainer_.insert(beginIndex, endIndex);
+    }
+
+    void releaseInversionIndex(std::vector<int> indices) {
+      inversionIndexContainer_.insert(indices);
+    }
+
   private:
 
     IndexListContainer atomIndexContainer_;
     IndexListContainer rigidBodyIndexContainer_;
+    IndexListContainer cutoffGroupIndexContainer_;
+    IndexListContainer bondIndexContainer_;
+    IndexListContainer bendIndexContainer_;
+    IndexListContainer torsionIndexContainer_;
+    IndexListContainer inversionIndexContainer_;
   };
 
 } //end namespace OpenMD