--- trunk/src/selection/SelectionEvaluator.cpp	2010/05/10 17:28:26	1442
+++ trunk/src/selection/SelectionEvaluator.cpp	2012/10/01 18:21:15	1801
@@ -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).
  */
 
 #include <stack>
@@ -45,7 +46,7 @@
 #include "primitives/DirectionalAtom.hpp"
 #include "primitives/RigidBody.hpp"
 #include "primitives/Molecule.hpp"
-#include "io/basic_ifstrstream.hpp"
+#include "io/ifstrstream.hpp"
 
 namespace OpenMD {
 
@@ -149,7 +150,7 @@ namespace OpenMD {
     OpenMDBitSet bs;
     std::stack<OpenMDBitSet> stack; 
    
-    for (int pc = pcStart; pc < code.size(); ++pc) {
+    for (unsigned int pc = pcStart; pc < code.size(); ++pc) {
       Token instruction = code[pc];
 
       switch (instruction.tok) {
@@ -158,8 +159,7 @@ namespace OpenMD {
       case Token::expressionEnd:
         break;
       case Token::all:
-        bs = OpenMDBitSet(nStuntDouble);
-        bs.setAll();
+        bs = allInstruction();
         stack.push(bs);            
         break;
       case Token::none:
@@ -221,7 +221,6 @@ namespace OpenMD {
     int comparator = instruction.tok;
     int property = instruction.intValue;
     float comparisonValue = boost::any_cast<float>(instruction.value);
-    float propertyValue;
     OpenMDBitSet bs(nStuntDouble);
     bs.clearAll();
     
@@ -278,6 +277,9 @@ namespace OpenMD {
     case Token::z:
       propertyValue = sd->getPos().z();
       break;
+    case Token::r:
+      propertyValue = sd->getPos().length();
+      break;
     default:
       unrecognizedAtomProperty(property);
     }
@@ -444,7 +446,34 @@ namespace OpenMD {
     return bs;
   }
 
+  OpenMDBitSet SelectionEvaluator::allInstruction() {
+    OpenMDBitSet bs(nStuntDouble);
 
+    SimInfo::MoleculeIterator mi;
+    Molecule* mol;
+    Molecule::AtomIterator ai;
+    Atom* atom;
+    Molecule::RigidBodyIterator rbIter;
+    RigidBody* rb;
+
+    // Doing the loop insures that we're actually on this processor.
+
+    for (mol = info->beginMolecule(mi); mol != NULL; 
+         mol = info->nextMolecule(mi)) {
+
+      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
+        bs.setBitOn(atom->getGlobalIndex());
+      }
+     
+      for (rb = mol->beginRigidBody(rbIter); rb != NULL; 
+           rb = mol->nextRigidBody(rbIter)) {
+        bs.setBitOn(rb->getGlobalIndex());
+      }
+    }
+
+    return bs;
+  }
+
   OpenMDBitSet SelectionEvaluator::hull() {
     OpenMDBitSet bs(nStuntDouble);
     
@@ -453,8 +482,6 @@ namespace OpenMD {
     return bs;
   }
 
-
-
   RealType SelectionEvaluator::getCharge(Atom* atom) {
     RealType charge =0.0;
     AtomType* atomType = atom->getAtomType();