# | 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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