| 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. Redistributions of source code must retain the above copyright |
| 10 |
* notice, this list of conditions and the following disclaimer. |
| 11 |
* |
| 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. |
| 16 |
* |
| 17 |
* This software is provided "AS IS," without a warranty of any |
| 18 |
* kind. All express or implied conditions, representations and |
| 19 |
* warranties, including any implied warranty of merchantability, |
| 20 |
* fitness for a particular purpose or non-infringement, are hereby |
| 21 |
* excluded. The University of Notre Dame and its licensors shall not |
| 22 |
* be liable for any damages suffered by licensee as a result of |
| 23 |
* using, modifying or distributing the software or its |
| 24 |
* derivatives. In no event will the University of Notre Dame or its |
| 25 |
* licensors be liable for any lost revenue, profit or data, or for |
| 26 |
* direct, indirect, special, consequential, incidental or punitive |
| 27 |
* damages, however caused and regardless of the theory of liability, |
| 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 |
| 44 |
#define _FILE_OFFSET_BITS 64 |
| 45 |
|
| 46 |
#include "io/StatWriter.hpp" |
| 47 |
#include "brains/Stats.hpp" |
| 48 |
#include "utils/simError.h" |
| 49 |
|
| 50 |
using namespace std; |
| 51 |
|
| 52 |
namespace OpenMD { |
| 53 |
|
| 54 |
StatWriter::StatWriter( const std::string& filename, Stats* stats) : stats_(stats){ |
| 55 |
|
| 56 |
#ifdef IS_MPI |
| 57 |
if(worldRank == 0 ){ |
| 58 |
#endif // is_mpi |
| 59 |
|
| 60 |
statfile_.open(filename.c_str(), std::ios::out | std::ios::trunc ); |
| 61 |
|
| 62 |
if( !statfile_ ){ |
| 63 |
|
| 64 |
sprintf( painCave.errMsg, |
| 65 |
"Could not open \"%s\" for stat output.\n", |
| 66 |
filename.c_str()); |
| 67 |
painCave.isFatal = 1; |
| 68 |
simError(); |
| 69 |
} |
| 70 |
|
| 71 |
writeTitle(); |
| 72 |
|
| 73 |
#ifdef IS_MPI |
| 74 |
} |
| 75 |
|
| 76 |
sprintf( checkPointMsg, |
| 77 |
"Sucessfully opened output file for stating.\n"); |
| 78 |
errorCheckPoint(); |
| 79 |
#endif // is_mpi |
| 80 |
|
| 81 |
} |
| 82 |
|
| 83 |
StatWriter::~StatWriter( ){ |
| 84 |
|
| 85 |
#ifdef IS_MPI |
| 86 |
if(worldRank == 0 ){ |
| 87 |
#endif // is_mpi |
| 88 |
|
| 89 |
statfile_.close(); |
| 90 |
|
| 91 |
#ifdef IS_MPI |
| 92 |
} |
| 93 |
#endif // is_mpi |
| 94 |
} |
| 95 |
|
| 96 |
|
| 97 |
void StatWriter::writeTitle() { |
| 98 |
|
| 99 |
Stats::StatsBitSet mask = stats_->getStatsMask(); |
| 100 |
|
| 101 |
#ifdef IS_MPI |
| 102 |
if(worldRank == 0 ){ |
| 103 |
#endif // is_mpi |
| 104 |
|
| 105 |
//write title |
| 106 |
statfile_ << "#"; |
| 107 |
for (int i = 0; i <mask.size(); ++i) { |
| 108 |
if (mask[i]) { |
| 109 |
statfile_ << "\t" << stats_->getTitle(i) << |
| 110 |
"(" << stats_->getUnits(i) << ")"; |
| 111 |
} |
| 112 |
} |
| 113 |
statfile_ << std::endl; |
| 114 |
|
| 115 |
#ifdef IS_MPI |
| 116 |
} |
| 117 |
#endif // is_mpi |
| 118 |
} |
| 119 |
|
| 120 |
void StatWriter::writeStat() { |
| 121 |
|
| 122 |
#ifdef IS_MPI |
| 123 |
if(worldRank == 0 ){ |
| 124 |
#endif // is_mpi |
| 125 |
|
| 126 |
Stats::StatsBitSet mask = stats_->getStatsMask(); |
| 127 |
statfile_.precision(8); |
| 128 |
for (int i = 0; i < mask.size(); ++i) { |
| 129 |
if (mask[i]) { |
| 130 |
if (stats_->getDataType(i) == "RealType") |
| 131 |
writeReal(i); |
| 132 |
else if (stats_->getDataType(i) == "Vector3d") |
| 133 |
writeVector(i); |
| 134 |
else if (stats_->getDataType(i) == "Mat3x3d") |
| 135 |
writeMatrix(i); |
| 136 |
else { |
| 137 |
sprintf( painCave.errMsg, |
| 138 |
"StatWriter found an unknown data type for: %s ", |
| 139 |
stats_->getTitle(i).c_str()); |
| 140 |
painCave.isFatal = 1; |
| 141 |
simError(); |
| 142 |
} |
| 143 |
} |
| 144 |
} |
| 145 |
|
| 146 |
statfile_ << std::endl; |
| 147 |
statfile_.flush(); |
| 148 |
|
| 149 |
#ifdef IS_MPI |
| 150 |
} |
| 151 |
errorCheckPoint(); |
| 152 |
#endif // is_mpi |
| 153 |
} |
| 154 |
|
| 155 |
void StatWriter::writeReal(int i) { |
| 156 |
|
| 157 |
RealType s = stats_->getRealData(i); |
| 158 |
|
| 159 |
if (! isinf(s) && ! isnan(s)) { |
| 160 |
statfile_ << "\t" << s; |
| 161 |
} else{ |
| 162 |
sprintf( painCave.errMsg, |
| 163 |
"StatWriter detected a numerical error writing: %s ", |
| 164 |
stats_->getTitle(i).c_str()); |
| 165 |
painCave.isFatal = 1; |
| 166 |
simError(); |
| 167 |
} |
| 168 |
} |
| 169 |
|
| 170 |
void StatWriter::writeVector(int i) { |
| 171 |
|
| 172 |
Vector3d s = stats_->getVectorData(i); |
| 173 |
if (isinf(s[0]) || isnan(s[0]) || |
| 174 |
isinf(s[1]) || isnan(s[1]) || |
| 175 |
isinf(s[2]) || isnan(s[2]) ) { |
| 176 |
sprintf( painCave.errMsg, |
| 177 |
"StatWriter detected a numerical error writing: %s", |
| 178 |
stats_->getTitle(i).c_str()); |
| 179 |
painCave.isFatal = 1; |
| 180 |
simError(); |
| 181 |
} else { |
| 182 |
statfile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2]; |
| 183 |
} |
| 184 |
} |
| 185 |
|
| 186 |
void StatWriter::writeMatrix(int i) { |
| 187 |
|
| 188 |
Mat3x3d s = stats_->getMatrixData(i); |
| 189 |
|
| 190 |
for (unsigned int i = 0; i < 3; i++) { |
| 191 |
for (unsigned int j = 0; j < 3; j++) { |
| 192 |
if (isinf(s(i,j)) || isnan(s(i,j))) { |
| 193 |
sprintf( painCave.errMsg, |
| 194 |
"StatWriter detected a numerical error writing: %s", |
| 195 |
stats_->getTitle(i).c_str()); |
| 196 |
painCave.isFatal = 1; |
| 197 |
simError(); |
| 198 |
} else { |
| 199 |
statfile_ << "\t" << s(i,j); |
| 200 |
} |
| 201 |
} |
| 202 |
} |
| 203 |
} |
| 204 |
} |
