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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 1437 by gezelter, Wed Apr 21 14:59:18 2010 UTC

# Line 1 | Line 1
1 < /*
2 < * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
1 > /*
2 > * Copyright (c) 2005, 2010 The University of Notre Dame. All Rights Reserved.
3   *
4   * The University of Notre Dame grants you ("Licensee") a
5   * non-exclusive, royalty free, license to use, modify and
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 > using namespace std;
49  
50 + namespace OpenMD {
51 +  StatsBitSet parseStatFileFormat(const std::string& format) {
52 +    StringTokenizer tokenizer(format, " ,;|\t\n\r");
53 +    StatsBitSet mask;
54 +    while(tokenizer.hasMoreTokens()) {
55 +        std::string token(tokenizer.nextToken());
56 +        toUpper(token);
57 +        Stats::StatsMapType::iterator i = Stats::statsMap.find(token);
58 +        if (i != Stats::statsMap.end()) {
59 +            mask.set(i->second);
60 +        } else {
61 +          sprintf( painCave.errMsg,
62 +                       "%s is not a valid statFileFormat keyword.\n", token.c_str() );
63 +          painCave.isFatal = 0;
64 +          painCave.severity = OPENMD_ERROR;
65 +          simError();            
66 +        }
67 +    }
68 +    
69 +    return mask;
70 +  }
71 +  
72 +  StatWriter::StatWriter( const std::string& filename, const StatsBitSet& mask) : mask_(mask){
73 +
74   #ifdef IS_MPI
75 <  if(worldRank == 0 ){
75 >    if(worldRank == 0 ){
76   #endif // is_mpi
77  
78 <    statfile_.open(filename.c_str(), std::ios::out | std::ios::trunc );
78 >      statfile_.open(filename.c_str(), std::ios::out | std::ios::trunc );
79      
80 <    if( !statfile_ ){
80 >      if( !statfile_ ){
81        
82 <      sprintf( painCave.errMsg,
83 <           "Could not open \"%s\" for stat output.\n",
84 <           filename.c_str());
85 <      painCave.isFatal = 1;
86 <      simError();
87 <    }
82 >        sprintf( painCave.errMsg,
83 >                 "Could not open \"%s\" for stat output.\n",
84 >                 filename.c_str());
85 >        painCave.isFatal = 1;
86 >        simError();
87 >      }
88  
89 <    writeTitle();
89 >      writeTitle();
90      
91   #ifdef IS_MPI
92 <  }
92 >    }
93  
94 <  sprintf( checkPointMsg,
95 <               "Sucessfully opened output file for stating.\n");
96 <  MPIcheckPoint();
94 >    sprintf( checkPointMsg,
95 >             "Sucessfully opened output file for stating.\n");
96 >    errorCheckPoint();
97   #endif // is_mpi
98  
99 < }
99 >  }
100  
101 < StatWriter::~StatWriter( ){
101 >  StatWriter::~StatWriter( ){
102  
103   #ifdef IS_MPI
104 <  if(worldRank == 0 ){
104 >    if(worldRank == 0 ){
105   #endif // is_mpi
106  
107 <    statfile_.close();
107 >      statfile_.close();
108  
109   #ifdef IS_MPI
110 <  }
110 >    }
111   #endif // is_mpi
112 < }
112 >  }
113  
114 < void StatWriter::writeTitle() {
114 >  void StatWriter::writeTitle() {
115  
116  
117   #ifdef IS_MPI
118      if(worldRank == 0 ){
119   #endif // is_mpi
120  
121 <        //write title
122 <        statfile_ << "#";
123 <        for (int i =0; i < mask_.size(); ++i) {
124 <            if (mask_[i]) {
125 <            statfile_ << "\t" << Stats::getTitle(i) << "(" << Stats::getUnits(i) << ")";
126 <            }
127 <        }
128 <        statfile_ << std::endl;
121 >      //write title
122 >      statfile_ << "#";
123 >      for (int i =0; i < mask_.size(); ++i) {
124 >        if (mask_[i]) {
125 >          statfile_ << "\t" << Stats::getTitle(i) << "(" << Stats::getUnits(i) << ")";
126 >        }
127 >      }
128 >      statfile_ << std::endl;
129  
130   #ifdef IS_MPI
131 <  }
131 >    }
132   #endif // is_mpi    
133 < }
133 >  }
134  
135 < void StatWriter::writeStat(const Stats& s){
135 >  void StatWriter::writeStat(const Stats& s){
136  
137   #ifdef IS_MPI
138      if(worldRank == 0 ){
139   #endif // is_mpi
140  
141 <        statfile_.precision(8);
141 >      statfile_.precision(8);
142 >      for (int i =0; i < mask_.size(); ++i) {
143 >        if (mask_[i]) {
144 >          if (! isinf(s[i]) && ! isnan(s[i])){
145 >            statfile_ << "\t" << s[i];
146 >          }
147 >          else{
148 >            sprintf( painCave.errMsg,
149 >                     "StatWriter detected a numerical error writing: %s ",
150 >                     Stats::getTitle(i).c_str());
151 >            painCave.isFatal = 1;
152 >            simError();
153 >          }          
154 >        }
155 >      }
156 >      statfile_ << std::endl;
157  
158 <        for (int i =0; i < mask_.size(); ++i) {
121 <            if (mask_[i]) {
122 <                statfile_ << "\t" << s[i];
123 <            }
124 <        }
125 <        statfile_ << std::endl;
158 >      statfile_.flush();
159  
127 –        statfile_.flush();
128 –
160   #ifdef IS_MPI
161      }
162 +    errorCheckPoint();
163   #endif // is_mpi
164 < }
164 >  }
165  
166   }

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