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root/OpenMD/trunk/src/io/StatWriter.cpp
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Comparing trunk/src/io/StatWriter.cpp (file contents):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# 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 {
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
# Line 70 | Line 91 | namespace oopse {
91  
92      sprintf( checkPointMsg,
93               "Sucessfully opened output file for stating.\n");
94 <    MPIcheckPoint();
94 >    errorCheckPoint();
95   #endif // is_mpi
96  
97    }
# Line 116 | Line 137 | namespace oopse {
137   #endif // is_mpi
138  
139        statfile_.precision(8);
119 –
140        for (int i =0; i < mask_.size(); ++i) {
141          if (mask_[i]) {
142            statfile_ << "\t" << s[i];

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