| 1 |
|
/* |
| 2 |
< |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 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. |
| 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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
#define _LARGEFILE_SOURCE64 |
| 46 |
|
#include "io/StatWriter.hpp" |
| 47 |
|
#include "utils/simError.h" |
| 48 |
|
|
| 49 |
< |
namespace oopse { |
| 49 |
> |
using namespace std; |
| 50 |
> |
|
| 51 |
> |
namespace OpenMD { |
| 52 |
|
StatsBitSet parseStatFileFormat(const std::string& format) { |
| 53 |
|
StringTokenizer tokenizer(format, " ,;|\t\n\r"); |
| 54 |
|
StatsBitSet mask; |
| 62 |
|
sprintf( painCave.errMsg, |
| 63 |
|
"%s is not a valid statFileFormat keyword.\n", token.c_str() ); |
| 64 |
|
painCave.isFatal = 0; |
| 65 |
< |
painCave.severity = OOPSE_ERROR; |
| 65 |
> |
painCave.severity = OPENMD_ERROR; |
| 66 |
|
simError(); |
| 67 |
|
} |
| 68 |
|
} |
| 140 |
|
#endif // is_mpi |
| 141 |
|
|
| 142 |
|
statfile_.precision(8); |
| 140 |
– |
|
| 143 |
|
for (int i =0; i < mask_.size(); ++i) { |
| 144 |
|
if (mask_[i]) { |
| 145 |
< |
statfile_ << "\t" << s[i]; |
| 145 |
> |
if (! isinf(s[i]) && ! isnan(s[i])){ |
| 146 |
> |
statfile_ << "\t" << s[i]; |
| 147 |
> |
} |
| 148 |
> |
else{ |
| 149 |
> |
sprintf( painCave.errMsg, |
| 150 |
> |
"StatWriter detected a numerical error writing: %s ", |
| 151 |
> |
Stats::getTitle(i).c_str()); |
| 152 |
> |
painCave.isFatal = 1; |
| 153 |
> |
simError(); |
| 154 |
> |
} |
| 155 |
|
} |
| 156 |
|
} |
| 157 |
|
statfile_ << std::endl; |
| 160 |
|
|
| 161 |
|
#ifdef IS_MPI |
| 162 |
|
} |
| 163 |
+ |
errorCheckPoint(); |
| 164 |
|
#endif // is_mpi |
| 165 |
|
} |
| 166 |
|
|
