--- trunk/src/mdParser/SimplePreprocessor.hpp	2006/03/29 22:24:59	924
+++ trunk/src/mdParser/SimplePreprocessor.hpp	2009/11/25 20:02:06	1390
@@ -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.
@@ -37,6 +28,15 @@
  * 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).                        
  */
 
 #ifndef MDPARSER_SIMPLEPREPROCESSOR_HPP
@@ -47,46 +47,48 @@
 #include <sstream>
 #include "utils/StringTokenizer.hpp"
 #include "utils/Trim.hpp"
-#include "utils/OOPSEException.hpp"
+#include "utils/OpenMDException.hpp"
 #include "utils/simError.h"
 
 
 /**
  * @class SimplePreprocessor
  * @brief A simple preprocessor.
- * @note only support #include #ifdef, #ifndef, #endif, #define and #undef, c-like multiple line
- *  comment is not support, macro substitude is not support.
+ * @note only supports #include #ifdef, #ifndef, #endif, #define and #undef, c-like multiple line
+ *  comment is not supported, macro substitute is not supported.
  */
-namespace oopse { 
+namespace OpenMD { 
 class SimplePreprocessor {
     public:
-        bool preprocess(const std::string& filename, ostream& os) {
+        bool preprocess(std::istream& myStream, const std::string& filename, int startingLine, ostream& os) {
             std::set<std::string> defineSet;
             std::stack<bool> ifStates;
 
             ifStates.push(true);
-            return doPreprocess(filename, os, defineSet, ifStates);
+            return doPreprocess(myStream, filename, startingLine, os, defineSet, ifStates);
         }
         
     private:
-        bool doPreprocess(const std::string& filename, ostream& os, std::set<std::string>& defineSet, std::stack<bool>& ifStates) {
-            std::ifstream input(filename.c_str());
-            if (!input.is_open()) {
-                std::stringstream ss;
-                ss << "Can not open " << filename << " for preprocessing\n";
-                
-                sprintf(painCave.errMsg,
-                        "Can not open (%s) for processing. \n"
-                        "\tPlease check md file name syntax.\n", filename.c_str());
-                
-                painCave.isFatal = 1;
-                simError();
-                
-                throw OOPSEException(ss.str());                
-            }
-            int lineNo =1;
+        bool doPreprocess(std::istream& myStream, const std::string& filename, int startingLine, ostream& os, std::set<std::string>& defineSet, std::stack<bool>& ifStates) {
+            //std::ifstream input(filename.c_str());
+            //if (!input.is_open()) {
+            //    std::stringstream ss;
+            //    ss << "Can not open " << filename << " for preprocessing\n";
+            //    
+            //    sprintf(painCave.errMsg,
+            //            "Can not open (%s) for processing. \n"
+            //            "\tPlease check md file name syntax.\n", filename.c_str());
+            //    
+            //    painCave.isFatal = 1;
+            //    simError();
+            //    
+            //    throw OpenMDException(ss.str());                
+            //}
+            int lineNo = startingLine;
             os << "#line " << lineNo << " \"" << filename << "\"\n";
-            while(input.getline(buffer, bufferSize)) {
+            const int bufferSize = 1024;
+            char buffer[bufferSize];
+            while(myStream.getline(buffer, bufferSize)) {
               ++lineNo;
               std::string line = trimLeftCopy(buffer);
               if (!line.empty() && line[0] == '#') {
@@ -108,7 +110,14 @@ class SimplePreprocessor {
                             SimplePreprocessor subPreprocessor;
                             std::string includeFilename = tokens[1];
                             includeFilename = includeFilename.substr(1, includeFilename.length() -2);
-                            bool ret = subPreprocessor.doPreprocess(includeFilename, os, defineSet, ifStates);
+                            std::ifstream includeStream(includeFilename.c_str());
+                            if (!includeStream.is_open()) {
+                                std::stringstream ss;
+                                ss << "Can not open " << includeFilename << " for preprocessing\n";
+                                throw OpenMDException(ss.str()); 
+                            }
+                            
+                            bool ret = subPreprocessor.doPreprocess(includeStream, includeFilename, 1, os, defineSet, ifStates);
                             if (!ret) {
                                 std::cout << "Error in preprocessing\n";
                                 return false;
@@ -135,7 +144,7 @@ class SimplePreprocessor {
                            }
                            os << std::endl;
                         } else {
-                            std::cout << tokens[0] << " is not support" << std::endl;
+                            std::cout << tokens[0] << " is not supported (yet)." << std::endl;
                             return false;
                         }
                     }else {
@@ -152,8 +161,6 @@ class SimplePreprocessor {
         }
     private:
         
-        const static int bufferSize = 1024;
-        char buffer[bufferSize];
 };
 
 }