--- trunk/src/io/SectionParser.cpp	2005/04/15 22:04:00	507
+++ branches/development/src/io/SectionParser.cpp	2011/11/22 20:38:56	1665
@@ -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.
@@ -37,11 +28,21 @@
  * 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, 24107 (2008).          
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
  
 #include "io/SectionParser.hpp"
 #include "utils/Trim.hpp"
-namespace oopse {
+namespace OpenMD {
 
   void SectionParser::parse(std::istream& input, ForceField& ff, int lineNo) {
     const int bufferSize = 65535;
@@ -51,37 +52,41 @@ namespace oopse {
       ++lineNo;
       line = trimLeftCopy(buffer);
       //a line begins with "//" is comment
+      // let's also call lines starting with # and ! as comments
       if (isEndSection(line)) {
-	break;
-      } else if ( line.empty() || (line.size() >= 2 && line[0] == '/' && line[1] == '/')) {
-	continue;
+        break;
+      } else if ( line.empty() || 
+                  (line.size() >= 2 && line[0] == '/' && line[1] == '/') ||
+                  (line.size() >= 1 && line[0] == '#') || 
+                  (line.size() >= 1 && line[0] == '!') ) {
+        continue;
       } else {
-	parseLine(ff, line, lineNo);
+        parseLine(ff, line, lineNo);
       }
     }
   }
-
+  
   bool SectionParser::isEndSection(const std::string& line) {
     StringTokenizer tokenizer(line);
-
+    
     if (tokenizer.countTokens() >= 2) {
       std::string keyword = tokenizer.nextToken();
-
+      
       if (keyword != "end"){
-	return false;
+        return false;
       } 
-
+      
       std::string section = tokenizer.nextToken();
       if (section == sectionName_) {
-	return true;
+        return true;
       }else {
-	return false;
+        return false;
       }
-        
+      
     }else {
       return false;
     }
-        
+    
   }
 
-}//namespace oopse
+}//namespace OpenMD