--- trunk/src/io/SectionParser.cpp	2005/01/12 22:41:40	246
+++ branches/development/src/io/SectionParser.cpp	2010/07/09 23:08:25	1465
@@ -1,4 +1,4 @@
- /*
+/*
  * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
  *
  * The University of Notre Dame grants you ("Licensee") a
@@ -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.
@@ -37,51 +28,64 @@
  * 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]  Vardeman & Gezelter, in progress (2009).                        
  */
  
 #include "io/SectionParser.hpp"
 #include "utils/Trim.hpp"
-namespace oopse {
+namespace OpenMD {
 
-void SectionParser::parse(std::istream& input, ForceField& ff, int lineNo) {
+  void SectionParser::parse(std::istream& input, ForceField& ff, int lineNo) {
     const int bufferSize = 65535;
     char buffer[bufferSize];
     std::string line;
     while(input.getline(buffer, bufferSize)) {
-        /**@todo */
-        line = trimLeftCopy(buffer);
-        //a line begins with "//" is comment
-        if (isEndSection(line)) {
-            break;
-        } else if ( line.empty() || (line.size() >= 2 && line[0] == '/' && line[1] == '/')) {
-            continue;
-        } else {
-            parseLine(ff, line, lineNo);
-        }
+      ++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] == '/') ||
+                  (line.size() >= 1 && line[0] == '#') || 
+                  (line.size() >= 1 && line[0] == '!') ) {
+        continue;
+      } else {
+        parseLine(ff, line, lineNo);
+      }
     }
-}
-
-bool SectionParser::isEndSection(const std::string& line) {
+  }
+  
+  bool SectionParser::isEndSection(const std::string& line) {
     StringTokenizer tokenizer(line);
-
+    
     if (tokenizer.countTokens() >= 2) {
-        std::string keyword = tokenizer.nextToken();
-
-        if (keyword != "end"){
-            return false;
-        } 
-
-        std::string section = tokenizer.nextToken();
-        if (section == sectionName_) {
-            return true;
-        }else {
-            return false;
-        }
-        
-    }else {
+      std::string keyword = tokenizer.nextToken();
+      
+      if (keyword != "end"){
         return false;
+      } 
+      
+      std::string section = tokenizer.nextToken();
+      if (section == sectionName_) {
+        return true;
+      }else {
+        return false;
+      }
+      
+    }else {
+      return false;
     }
-        
-}
+    
+  }
 
-}//namespace oopse
+}//namespace OpenMD