--- trunk/src/selection/IndexFinder.cpp	2005/12/02 15:38:03	770
+++ trunk/src/selection/IndexFinder.cpp	2015/01/09 19:06:35	2052
@@ -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.
@@ -37,59 +28,96 @@
  * 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, 234107 (2008).          
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
 #include "selection/IndexFinder.hpp"
 #include "primitives/Molecule.hpp"
-namespace oopse {
+namespace OpenMD {
 
-
-
   IndexFinder::IndexFinder(SimInfo* info) : info_(info){
-    nStuntDoubles_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
-    bitSets_.resize(info_->getNGlobalMolecules());
+    nObjects_.push_back(info_->getNGlobalAtoms()+info_->getNGlobalRigidBodies());
+    nObjects_.push_back(info_->getNGlobalBonds());
+    nObjects_.push_back(info_->getNGlobalBends());
+    nObjects_.push_back(info_->getNGlobalTorsions());
+    nObjects_.push_back(info_->getNGlobalInversions());
+    nObjects_.push_back(info_->getNGlobalMolecules());
+
+    selectionSets_.resize(info_->getNGlobalMolecules());
     init();
   }
 
-
   void IndexFinder::init() {
 
     SimInfo::MoleculeIterator mi;
-    Molecule* mol;
     Molecule::AtomIterator ai;
-    Atom* atom;
     Molecule::RigidBodyIterator rbIter;
+    Molecule::BondIterator bondIter;
+    Molecule::BendIterator bendIter;
+    Molecule::TorsionIterator torsionIter;
+    Molecule::InversionIterator inversionIter;
+
+    Molecule* mol;
+    Atom* atom;
     RigidBody* rb;
+    Bond* bond;
+    Bend* bend;
+    Torsion* torsion;
+    Inversion* inversion;    
     
-    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
+    for (mol = info_->beginMolecule(mi); mol != NULL; 
+         mol = info_->nextMolecule(mi)) {
            
-      OOPSEBitSet bs(nStuntDoubles_);
+      SelectionSet ss(nObjects_);
+      ss.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
+
       for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
-	bs.setBitOn(atom->getGlobalIndex());
+	ss.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
       }
-
-      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
-	bs.setBitOn(rb->getGlobalIndex());
+      for (rb = mol->beginRigidBody(rbIter); rb != NULL; 
+           rb = mol->nextRigidBody(rbIter)) {
+        ss.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
       }
+      for (bond = mol->beginBond(bondIter); bond != NULL; 
+           bond = mol->nextBond(bondIter)) {
+        ss.bitsets_[BOND].setBitOn(bond->getGlobalIndex());
+      }   
+      for (bend = mol->beginBend(bendIter); bend != NULL; 
+           bend = mol->nextBend(bendIter)) {
+        ss.bitsets_[BEND].setBitOn(bend->getGlobalIndex());
+      }   
+      for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; 
+           torsion = mol->nextTorsion(torsionIter)) {
+        ss.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex());
+      }   
+      for (inversion = mol->beginInversion(inversionIter); inversion != NULL; 
+           inversion = mol->nextInversion(inversionIter)) {
+        ss.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex());
+      }   
 
-      bitSets_[mol->getGlobalIndex()] = bs;
-    }    
-
+      selectionSets_[mol->getGlobalIndex()] = ss;
+    }
   }
 
-  OOPSEBitSet IndexFinder::find(int molIndex){
-    return bitSets_[molIndex];
+  SelectionSet IndexFinder::find(int molIndex){
+    return selectionSets_[molIndex];
   }
 
-  OOPSEBitSet IndexFinder::find(int begMolIndex, int endMolIndex){
-    OOPSEBitSet bs(nStuntDoubles_);
+  SelectionSet IndexFinder::find(int begMolIndex, int endMolIndex){
+    SelectionSet ss(nObjects_);
         
     for (int i = begMolIndex; i < endMolIndex; ++i) {
-      bs |= bitSets_[i];
-    }
-    
-    return bs;
+      ss |= selectionSets_[i];
+    }    
+    return ss;
   }
-
-
 }