--- trunk/src/io/StatWriter.cpp	2004/09/24 04:16:43	2
+++ trunk/src/io/StatWriter.cpp	2005/04/15 22:04:00	507
@@ -1,114 +1,134 @@
+/*
+ * 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
+ *    notice, this list of conditions and the following disclaimer.
+ *
+ * 3. 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.
+ *
+ * This software is provided "AS IS," without a warranty of any
+ * kind. All express or implied conditions, representations and
+ * warranties, including any implied warranty of merchantability,
+ * fitness for a particular purpose or non-infringement, are hereby
+ * excluded.  The University of Notre Dame and its licensors shall not
+ * be liable for any damages suffered by licensee as a result of
+ * using, modifying or distributing the software or its
+ * derivatives. In no event will the University of Notre Dame or its
+ * licensors be liable for any lost revenue, profit or data, or for
+ * direct, indirect, special, consequential, incidental or punitive
+ * damages, however caused and regardless of the theory of liability,
+ * 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.
+ */
+ 
 #define _LARGEFILE_SOURCE64
 #define _FILE_OFFSET_BITS 64
 
-#include <string.h>
-#include <iostream>
-#include <fstream>
+#include "io/StatWriter.hpp"
+#include "utils/simError.h"
 
-#include "ReadWrite.hpp"
-#include "simError.h"
+namespace oopse {
+  StatWriter::StatWriter( const std::string& filename, const StatsBitSet& mask) : mask_(mask){
 
-
-StatWriter::StatWriter( SimInfo* the_entry_plug ){
-
-  entry_plug = the_entry_plug;
-
 #ifdef IS_MPI
-  if(worldRank == 0 ){
+    if(worldRank == 0 ){
 #endif // is_mpi
 
-    outName =  entry_plug->statusName;
-
-    //std::cerr << "Opening " << outName << " for stat\n";
-
-    outFile.open(outName.c_str(), ios::out | ios::trunc );
+      statfile_.open(filename.c_str(), std::ios::out | std::ios::trunc );
     
-    if( !outFile ){
+      if( !statfile_ ){
       
-      sprintf( painCave.errMsg,
-	       "Could not open \"%s\" for stat output.\n",
-	       outName.c_str());
-      painCave.isFatal = 1;
-      simError();
+	sprintf( painCave.errMsg,
+		 "Could not open \"%s\" for stat output.\n",
+		 filename.c_str());
+	painCave.isFatal = 1;
+	simError();
+      }
+
+      writeTitle();
+    
+#ifdef IS_MPI
     }
 
-    //outFile.setf( ios::scientific );
-    outFile << "#time(fs)\tE_tot\tV\tKE\tT(K)\tP(atm)\tVol(A^3)\tH_conserved";
+    sprintf( checkPointMsg,
+	     "Sucessfully opened output file for stating.\n");
+    MPIcheckPoint();
+#endif // is_mpi
 
-    if (entry_plug->useSolidThermInt || entry_plug->useLiquidThermInt)
-      outFile << "\tV_raw";
-    
-    if (entry_plug->useSolidThermInt) 
-      outFile << "\tV_harm";
+  }
 
-    outFile << "\n";
+  StatWriter::~StatWriter( ){
 
-    
 #ifdef IS_MPI
-  }
+    if(worldRank == 0 ){
+#endif // is_mpi
 
-  sprintf( checkPointMsg,
-	   "Sucessfully opened output file for stating.\n");
-  MPIcheckPoint();
+      statfile_.close();
+
+#ifdef IS_MPI
+    }
 #endif // is_mpi
+  }
 
-  tStats = new Thermo( entry_plug );
-}
+  void StatWriter::writeTitle() {
 
-StatWriter::~StatWriter( ){
 
 #ifdef IS_MPI
-  if(worldRank == 0 ){
+    if(worldRank == 0 ){
 #endif // is_mpi
 
-    outFile.close();
-    delete tStats;
+      //write title
+      statfile_ << "#";
+      for (int i =0; i < mask_.size(); ++i) {
+	if (mask_[i]) {
+	  statfile_ << "\t" << Stats::getTitle(i) << "(" << Stats::getUnits(i) << ")";
+	}
+      }
+      statfile_ << std::endl;
 
 #ifdef IS_MPI
+    }
+#endif // is_mpi    
   }
-#endif // is_mpi
-}
 
-void StatWriter::writeStat( double currentTime ){
+  void StatWriter::writeStat(const Stats& s){
 
-  double totE, potE, kinE, temp, press, vol;
-  double conservedQuantity;
-
-  totE = tStats->getTotalE();
-  potE = tStats->getPotential();
-  kinE = tStats->getKinetic();
-  temp = tStats->getTemperature();
-  press = tStats->getPressure();
-  vol = tStats->getVolume();
-  conservedQuantity = entry_plug->the_integrator->getConservedQuantity();
-
 #ifdef IS_MPI
-  if(worldRank == 0 ){
+    if(worldRank == 0 ){
 #endif // is_mpi
 
-    outFile.precision(8);
-    outFile
-      << currentTime << "\t"
-      << totE << "\t"
-      << potE << "\t"
-      << kinE << "\t"
-      << temp << "\t"
-      << press << "\t"
-      << vol << "\t"
-      << conservedQuantity;
+      statfile_.precision(8);
 
-    if (entry_plug->useSolidThermInt || entry_plug->useLiquidThermInt)
-      outFile << "\t" << entry_plug->vRaw;
-    
-    if (entry_plug->useSolidThermInt) 
-      outFile << "\t" << entry_plug->vHarm;
+      for (int i =0; i < mask_.size(); ++i) {
+	if (mask_[i]) {
+	  statfile_ << "\t" << s[i];
+	}
+      }
+      statfile_ << std::endl;
 
-    outFile << "\n";
+      statfile_.flush();
 
-    outFile.flush();
-
 #ifdef IS_MPI
-  }
+    }
 #endif // is_mpi
-}
+  }
 
+}