--- trunk/src/io/RestReader.hpp	2005/04/15 22:04:00	507
+++ branches/development/src/io/RestReader.hpp	2010/07/09 23:08:25	1465
@@ -1,24 +1,15 @@
-/*
- * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
+/* 
+ * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. 
  *
  * The University of Notre Dame grants you ("Licensee") a
  * non-exclusive, royalty free, license to use, modify and
  * 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.
@@ -37,56 +28,106 @@
  * 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.
- */
-#ifndef IO_RESTREADER_HPP
-#define IO_RESTREADER_HPP
-
-#define _LARGEFILE_SOURCE64
-#ifndef _FILE_OFFSET_BITS
-#define _FILE_OFFSET_BITS 64
-#endif
-#include <iostream>
-#include <fstream>
+ *
+ * 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).                        
+ */ 
+  
+/** 
+ * @file RestReader.hpp 
+ */ 
+ 
+#ifndef IO_RESTREADER_HPP 
+#define IO_RESTREADER_HPP 
+ 
+#include <cstdio>
 #include <string>
-#include <stdio.h>
-#include <stdlib.h>
-#include <unistd.h>
-#include <sys/types.h>
-#include <sys/stat.h>
-
 #include "brains/SimInfo.hpp"
 #include "primitives/StuntDouble.hpp"
 
-namespace oopse {
-    
+namespace OpenMD { 
+ 
+  /** 
+   * @class RestReader RestReader.hpp "io/RestReader.hpp" 
+   */ 
+  class RestReader { 
+  public: 
+    RestReader(SimInfo* info, const std::string &filename, 
+                           std::vector<int> stuntDoubleIndex) 
+      : info_(info), filename_(filename){
+      stuntDoubleIndex_ = stuntDoubleIndex;
+#ifdef IS_MPI 
+      
+      if (worldRank == 0) { 
+#endif 
+        
+        inFile_ = new std::ifstream(filename_.c_str()); 
+        
+        if (inFile_->fail()) { 
+          sprintf(painCave.errMsg, 
+                  "RestReader: Cannot open file: %s\n", 
+                  filename_.c_str()); 
+          painCave.isFatal = 1; 
+          simError(); 
+        } 
+        
+#ifdef IS_MPI 
+        
+      } 
+      
+      strcpy(checkPointMsg, "Reference file opened for reading successfully."); 
+      errorCheckPoint(); 
+      
+#endif 
+      
+      return;
+    }
 
-  /**
-   * @class RestReader RestReader.hpp "io/RestReader.hpp"
-   * @for extra file reading when using thermodynamic integration
-   */
-  class RestReader {
-    
-  public:
-    RestReader( SimInfo* theInfo );
-    ~RestReader();
-    
-    void readIdealCrystal();
-    void readZangle();
-    void zeroZangle();
-    
-  private:
-    char* parseIdealLine(char* readLine, StuntDouble* sd);
-    char *idealName;
-    FILE *inAngFile;
-    FILE *inIdealFile;
-    std::string inAngFileName;
-    std::string inIdealFileName;
-    bool isScanned;
-    
-    double angleTransfer;
-    std::vector<fpos_t*> framePos;
-    SimInfo *info_;
-  };
+    void readReferenceStructure(void);
 
-} //end namespace oopse
+    ~RestReader(){
+#ifdef IS_MPI
+      if (worldRank == 0){
+#endif 
+        
+        delete inFile_;
+        
+#ifdef IS_MPI       
+      } 
+      
+      strcpy(checkPointMsg, "Reference file closed successfully."); 
+      errorCheckPoint();
 #endif
+    }
+    
+  protected: 
+    void parseDumpLine(const std::string& line);
+    void readStuntDoubles(std::istream& inpuStream);
+    void readFrameProperties(std::istream& inputStream);
+    void scanFile(void);
+    void readSet(void);
+  private: 
+
+    SimInfo* info_;
+
+    std::vector<Vector3d> all_pos_;
+    std::vector<int> stuntDoubleIndex_;
+
+    std::istream* inFile_;
+    std::string filename_;
+
+    std::streampos framePos_;
+
+    const static int bufferSize = 4096;
+    char buffer[bufferSize];
+  };
+ 
+}      //end namespace OpenMD 
+ 
+#endif //IO_RESTREADER_HPP