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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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