--- trunk/src/io/StatWriter.cpp	2005/01/12 22:41:40	246
+++ trunk/src/io/StatWriter.cpp	2010/04/20 19:59:45	1436
@@ -1,24 +1,15 @@
- /*
- * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
+/*
+ * Copyright (c) 2005, 2010 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.
@@ -37,6 +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).                        
  */
  
 #define _LARGEFILE_SOURCE64
@@ -45,90 +45,121 @@
 #include "io/StatWriter.hpp"
 #include "utils/simError.h"
 
-namespace oopse {
-StatWriter::StatWriter( const std::string& filename, const StatsBitSet& mask) : mask_(mask){
+namespace OpenMD {
+  StatsBitSet parseStatFileFormat(const std::string& format) {
+    StringTokenizer tokenizer(format, " ,;|\t\n\r");
+    StatsBitSet mask;
+    while(tokenizer.hasMoreTokens()) {
+        std::string token(tokenizer.nextToken());
+        toUpper(token);
+        Stats::StatsMapType::iterator i = Stats::statsMap.find(token);
+        if (i != Stats::statsMap.end()) {
+            mask.set(i->second);
+        } else {
+          sprintf( painCave.errMsg,
+	               "%s is not a valid statFileFormat keyword.\n", token.c_str() );
+          painCave.isFatal = 0;
+          painCave.severity = OPENMD_ERROR;
+          simError();            
+        }
+    }
+    
+    return mask;
+  }
+  
+  StatWriter::StatWriter( const std::string& filename, const StatsBitSet& mask) : mask_(mask){
 
 #ifdef IS_MPI
-  if(worldRank == 0 ){
+    if(worldRank == 0 ){
 #endif // is_mpi
 
-    statfile_.open(filename.c_str(), std::ios::out | std::ios::trunc );
+      statfile_.open(filename.c_str(), std::ios::out | std::ios::trunc );
     
-    if( !statfile_ ){
+      if( !statfile_ ){
       
-      sprintf( painCave.errMsg,
-           "Could not open \"%s\" for stat output.\n",
-           filename.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();
+      writeTitle();
     
 #ifdef IS_MPI
-  }
+    }
 
-  sprintf( checkPointMsg,
-               "Sucessfully opened output file for stating.\n");
-  MPIcheckPoint();
+    sprintf( checkPointMsg,
+	     "Sucessfully opened output file for stating.\n");
+    errorCheckPoint();
 #endif // is_mpi
 
-}
+  }
 
-StatWriter::~StatWriter( ){
+  StatWriter::~StatWriter( ){
 
 #ifdef IS_MPI
-  if(worldRank == 0 ){
+    if(worldRank == 0 ){
 #endif // is_mpi
 
-    statfile_.close();
+      statfile_.close();
 
 #ifdef IS_MPI
-  }
+    }
 #endif // is_mpi
-}
+  }
 
-void StatWriter::writeTitle() {
+  void StatWriter::writeTitle() {
 
 
 #ifdef IS_MPI
     if(worldRank == 0 ){
 #endif // is_mpi
 
-        //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;
+      //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    
-}
+  }
 
-void StatWriter::writeStat(const Stats& s){
+  void StatWriter::writeStat(const Stats& s){
 
 #ifdef IS_MPI
     if(worldRank == 0 ){
 #endif // is_mpi
 
-        statfile_.precision(8);
+      statfile_.precision(8);
+      for (int i =0; i < mask_.size(); ++i) {
+	if (mask_[i]) {
+          if (! std::isinf(s[i]) && ! std::isnan(s[i])){
+              statfile_ << "\t" << s[i];
+          }
+          else{
+            sprintf( painCave.errMsg,
+                     "Statwriter detected a numerical error writing: %s ",
+                     Stats::getTitle(i).c_str());
+            painCave.isFatal = 1;
+            simError();
+          }
+          
+	}
+      }
+      statfile_ << std::endl;
 
-        for (int i =0; i < mask_.size(); ++i) {
-            if (mask_[i]) {
-                statfile_ << "\t" << s[i];
-            }
-        }
-        statfile_ << std::endl;
+      statfile_.flush();
 
-        statfile_.flush();
-
 #ifdef IS_MPI
     }
+    errorCheckPoint();
 #endif // is_mpi
-}
+  }
 
 }