--- trunk/src/selection/SelectionCompiler.cpp	2010/05/10 17:28:26	1442
+++ trunk/src/selection/SelectionCompiler.cpp	2015/03/05 16:30:23	2069
@@ -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).
  */
 
 #include "selection/SelectionCompiler.hpp"
@@ -51,12 +52,12 @@ namespace OpenMD {
     lineNumbers.clear();
     lineIndices.clear();
     aatokenCompiled.clear();
-        
+
     if (internalCompile()) {
       return true;
     }
-    
-    int icharEnd;
+      
+    std::size_t icharEnd;
     if ((icharEnd = script.find('\r', ichCurrentCommand)) == std::string::npos &&
         (icharEnd = script.find('\n', ichCurrentCommand)) == std::string::npos) {
       icharEnd = script.size();
@@ -118,12 +119,14 @@ namespace OpenMD {
 	//    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)));
@@ -176,7 +179,7 @@ namespace OpenMD {
 	continue;
       }
 
-      if (ltoken.size() == 0) {
+      if (ltoken.empty()) {
 	return commandExpected();
       }
         
@@ -371,7 +374,7 @@ namespace OpenMD {
       return false;
     }
     cchToken = ichT - ichToken;
-    return true;
+    return isInteger(script.substr(ichToken, cchToken).c_str());
   }
 
   bool SelectionCompiler::lookingAtLookupToken() {
@@ -440,7 +443,7 @@ namespace OpenMD {
 
   bool SelectionCompiler::compileExpression() {
     /** todo */
-    int i = 1;
+    unsigned int i = 1;
     int tokCommand = atokenCommand[0].tok;
     if (tokCommand == Token::define) {
       i = 2;
@@ -572,6 +575,7 @@ namespace OpenMD {
       // 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();
@@ -664,7 +668,7 @@ namespace OpenMD {
   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 '[' :
@@ -688,7 +692,6 @@ namespace OpenMD {
     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();