--- trunk/src/selection/SelectionCompiler.cpp	2005/04/15 22:04:00	507
+++ trunk/src/selection/SelectionCompiler.cpp	2014/07/16 14:42:50	2010
@@ -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.
@@ -37,24 +28,35 @@
  * 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/SelectionCompiler.hpp"
 #include "utils/StringUtils.hpp"
-namespace oopse {
+namespace OpenMD {
 
-  bool SelectionCompiler::compile(const std::string& filename, const std::string& script) {
+  bool SelectionCompiler::compile(const std::string& filename, 
+                                  const std::string& script) {
 
     this->filename = filename;
     this->script = script;
     lineNumbers.clear();
     lineIndices.clear();
     aatokenCompiled.clear();
-        
+
     if (internalCompile()) {
       return true;
     }
-    
+      
     int icharEnd;
     if ((icharEnd = script.find('\r', ichCurrentCommand)) == std::string::npos &&
         (icharEnd = script.find('\n', ichCurrentCommand)) == std::string::npos) {
@@ -117,12 +119,14 @@ namespace oopse {
 	//    ltoken.push_back(Token(Token::string, str));
 	//    continue;
 	//}
-	if (lookingAtDecimal((tokCommand & Token::negnums) != 0)) {
+	//if (lookingAtDecimal((tokCommand & Token::negnums) != 0)) {
+        if (lookingAtDecimal((tokCommand) != 0)) {
 	  float value = lexi_cast<float>(script.substr(ichToken, cchToken));        
 	  ltoken.push_back(Token(Token::decimal, boost::any(value)));
 	  continue;
 	}
-	if (lookingAtInteger((tokCommand & Token::negnums) != 0)) {
+	//if (lookingAtInteger((tokCommand & Token::negnums) != 0)) {
+        if (lookingAtInteger((tokCommand) != 0)) {
 
 	  int val = lexi_cast<int>(script.substr(ichToken, cchToken));
 	  ltoken.push_back(Token(Token::integer,   boost::any(val)));
@@ -175,7 +179,7 @@ namespace oopse {
 	continue;
       }
 
-      if (ltoken.size() == 0) {
+      if (ltoken.empty()) {
 	return commandExpected();
       }
         
@@ -370,7 +374,7 @@ namespace oopse {
       return false;
     }
     cchToken = ichT - ichToken;
-    return true;
+    return isInteger(script.substr(ichToken, cchToken).c_str());
   }
 
   bool SelectionCompiler::lookingAtLookupToken() {
@@ -439,7 +443,7 @@ namespace oopse {
 
   bool SelectionCompiler::compileExpression() {
     /** todo */
-    int i = 1;
+    unsigned int i = 1;
     int tokCommand = atokenCommand[0].tok;
     if (tokCommand == Token::define) {
       i = 2;
@@ -571,6 +575,7 @@ namespace oopse {
       // fall into the code and below and just add the token
     case Token::all:
     case Token::none:
+    case Token::hull:
       return addTokenToPostfix(tokenNext());
     case Token::leftparen:
       tokenNext();
@@ -663,7 +668,7 @@ namespace oopse {
   bool SelectionCompiler::isNameValid(const std::string& name) {
     int nbracket = 0;
     int ndot = 0;
-    for (int i =0 ; i < name.size(); ++i) {
+    for (unsigned int i = 0 ; i < name.size(); ++i) {
       switch(name[i]) {
 
       case '[' :
@@ -687,7 +692,6 @@ namespace oopse {
     if (token.tok == Token::integer) {
       int index = boost::any_cast<int>(token.value);
       int tok = tokPeek();
-      std::cout << "Token::to is " << Token::to << ", tok = " << tok << std::endl;
       if (tok == Token::to) {
 	tokenNext();
 	tok = tokPeek();