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Comparing trunk/src/io/StatWriter.cpp (file contents):
Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 1 | Line 1
1 < /*
1 > /*
2   * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3   *
4   * The University of Notre Dame grants you ("Licensee") a
# Line 6 | Line 6
6   * redistribute this software in source and binary code form, provided
7   * that the following conditions are met:
8   *
9 < * 1. Acknowledgement of the program authors must be made in any
10 < *    publication of scientific results based in part on use of the
11 < *    program.  An acceptable form of acknowledgement is citation of
12 < *    the article in which the program was described (Matthew
13 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 < *    Parallel Simulation Engine for Molecular Dynamics,"
16 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 < *
18 < * 2. Redistributions of source code must retain the above copyright
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
28   * arising out of the use of or inability to use software, even if the
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31 + *
32 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 + * research, please cite the appropriate papers when you publish your
34 + * work.  Good starting points are:
35 + *                                                                      
36 + * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37 + * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 + * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 + * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41  
42   #define _LARGEFILE_SOURCE64
# Line 45 | Line 45
45   #include "io/StatWriter.hpp"
46   #include "utils/simError.h"
47  
48 < namespace oopse {
49 < StatWriter::StatWriter( const std::string& filename, const StatsBitSet& mask) : mask_(mask){
48 > namespace OpenMD {
49 >  StatsBitSet parseStatFileFormat(const std::string& format) {
50 >    StringTokenizer tokenizer(format, " ,;|\t\n\r");
51 >    StatsBitSet mask;
52 >    while(tokenizer.hasMoreTokens()) {
53 >        std::string token(tokenizer.nextToken());
54 >        toUpper(token);
55 >        Stats::StatsMapType::iterator i = Stats::statsMap.find(token);
56 >        if (i != Stats::statsMap.end()) {
57 >            mask.set(i->second);
58 >        } else {
59 >          sprintf( painCave.errMsg,
60 >                       "%s is not a valid statFileFormat keyword.\n", token.c_str() );
61 >          painCave.isFatal = 0;
62 >          painCave.severity = OPENMD_ERROR;
63 >          simError();            
64 >        }
65 >    }
66 >    
67 >    return mask;
68 >  }
69 >  
70 >  StatWriter::StatWriter( const std::string& filename, const StatsBitSet& mask) : mask_(mask){
71  
72   #ifdef IS_MPI
73 <  if(worldRank == 0 ){
73 >    if(worldRank == 0 ){
74   #endif // is_mpi
75  
76 <    statfile_.open(filename.c_str(), std::ios::out | std::ios::trunc );
76 >      statfile_.open(filename.c_str(), std::ios::out | std::ios::trunc );
77      
78 <    if( !statfile_ ){
78 >      if( !statfile_ ){
79        
80 <      sprintf( painCave.errMsg,
81 <           "Could not open \"%s\" for stat output.\n",
82 <           filename.c_str());
83 <      painCave.isFatal = 1;
84 <      simError();
85 <    }
80 >        sprintf( painCave.errMsg,
81 >                 "Could not open \"%s\" for stat output.\n",
82 >                 filename.c_str());
83 >        painCave.isFatal = 1;
84 >        simError();
85 >      }
86  
87 <    writeTitle();
87 >      writeTitle();
88      
89   #ifdef IS_MPI
90 <  }
90 >    }
91  
92 <  sprintf( checkPointMsg,
93 <               "Sucessfully opened output file for stating.\n");
94 <  MPIcheckPoint();
92 >    sprintf( checkPointMsg,
93 >             "Sucessfully opened output file for stating.\n");
94 >    errorCheckPoint();
95   #endif // is_mpi
96  
97 < }
97 >  }
98  
99 < StatWriter::~StatWriter( ){
99 >  StatWriter::~StatWriter( ){
100  
101   #ifdef IS_MPI
102 <  if(worldRank == 0 ){
102 >    if(worldRank == 0 ){
103   #endif // is_mpi
104  
105 <    statfile_.close();
105 >      statfile_.close();
106  
107   #ifdef IS_MPI
108 <  }
108 >    }
109   #endif // is_mpi
110 < }
110 >  }
111  
112 < void StatWriter::writeTitle() {
112 >  void StatWriter::writeTitle() {
113  
114  
115   #ifdef IS_MPI
116      if(worldRank == 0 ){
117   #endif // is_mpi
118  
119 <        //write title
120 <        statfile_ << "#";
121 <        for (int i =0; i < mask_.size(); ++i) {
122 <            if (mask_[i]) {
123 <            statfile_ << "\t" << Stats::getTitle(i) << "(" << Stats::getUnits(i) << ")";
124 <            }
125 <        }
126 <        statfile_ << std::endl;
119 >      //write title
120 >      statfile_ << "#";
121 >      for (int i =0; i < mask_.size(); ++i) {
122 >        if (mask_[i]) {
123 >          statfile_ << "\t" << Stats::getTitle(i) << "(" << Stats::getUnits(i) << ")";
124 >        }
125 >      }
126 >      statfile_ << std::endl;
127  
128   #ifdef IS_MPI
129 <  }
129 >    }
130   #endif // is_mpi    
131 < }
131 >  }
132  
133 < void StatWriter::writeStat(const Stats& s){
133 >  void StatWriter::writeStat(const Stats& s){
134  
135   #ifdef IS_MPI
136      if(worldRank == 0 ){
137   #endif // is_mpi
138  
139 <        statfile_.precision(8);
139 >      statfile_.precision(8);
140 >      for (int i =0; i < mask_.size(); ++i) {
141 >        if (mask_[i]) {
142 >          statfile_ << "\t" << s[i];
143 >        }
144 >      }
145 >      statfile_ << std::endl;
146  
147 <        for (int i =0; i < mask_.size(); ++i) {
121 <            if (mask_[i]) {
122 <                statfile_ << "\t" << s[i];
123 <            }
124 <        }
125 <        statfile_ << std::endl;
147 >      statfile_.flush();
148  
127 –        statfile_.flush();
128 –
149   #ifdef IS_MPI
150      }
151   #endif // is_mpi
152 < }
152 >  }
153  
154   }

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