ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/branches/development/src/io/StatWriter.cpp
(Generate patch)

Comparing branches/development/src/io/StatWriter.cpp (file contents):
Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC vs.
Revision 1767 by gezelter, Fri Jul 6 22:01:58 2012 UTC

# Line 36 | Line 36
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).                        
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 + #ifdef _MSC_VER
46 + #define isnan(x) _isnan((x))
47 + #define isinf(x) (!_finite(x) && !_isnan(x))
48 + #endif
49  
50   #include "io/StatWriter.hpp"
51 + #include "brains/Stats.hpp"
52   #include "utils/simError.h"
53  
54   using namespace std;
55  
56   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 –  }
57    
58 <  StatWriter::StatWriter( const std::string& filename, const StatsBitSet& mask) : mask_(mask){
59 <
58 >  StatWriter::StatWriter( const std::string& filename, Stats* stats) : stats_(stats){
59 >    
60   #ifdef IS_MPI
61      if(worldRank == 0 ){
62   #endif // is_mpi
63 <
63 >      
64        statfile_.open(filename.c_str(), std::ios::out | std::ios::trunc );
65      
66        if( !statfile_ ){
# Line 111 | Line 97 | namespace OpenMD {
97   #endif // is_mpi
98    }
99  
100 +
101    void StatWriter::writeTitle() {
102  
103 +    Stats::StatsBitSet mask = stats_->getStatsMask();    
104  
105   #ifdef IS_MPI
106      if(worldRank == 0 ){
# Line 120 | Line 108 | namespace OpenMD {
108  
109        //write title
110        statfile_ << "#";
111 <      for (int i =0; i < mask_.size(); ++i) {
112 <        if (mask_[i]) {
113 <          statfile_ << "\t" << Stats::getTitle(i) << "(" << Stats::getUnits(i) << ")";
111 >      for (unsigned int i = 0; i <mask.size(); ++i) {
112 >        if (mask[i]) {
113 >          statfile_ << "\t" << stats_->getTitle(i) <<
114 >            "(" << stats_->getUnits(i) << ")";
115          }
116        }
117        statfile_ << std::endl;
# Line 132 | Line 121 | namespace OpenMD {
121   #endif // is_mpi    
122    }
123  
124 <  void StatWriter::writeStat(const Stats& s){
125 <
124 >  void StatWriter::writeStat() {
125 >    
126   #ifdef IS_MPI
127      if(worldRank == 0 ){
128   #endif // is_mpi
129  
130 +      Stats::StatsBitSet mask = stats_->getStatsMask();
131        statfile_.precision(8);
132 <      for (int i =0; i < mask_.size(); ++i) {
133 <        if (mask_[i]) {
134 <          if (! isinf(s[i]) && ! isnan(s[i])){
135 <            statfile_ << "\t" << s[i];
136 <          }
137 <          else{
132 >      for (unsigned int i = 0; i < mask.size(); ++i) {
133 >        if (mask[i]) {
134 >          if (stats_->getDataType(i) == "RealType")
135 >            writeReal(i);
136 >          else if (stats_->getDataType(i) == "Vector3d")
137 >            writeVector(i);
138 >          else if (stats_->getDataType(i) == "Mat3x3d")
139 >            writeMatrix(i);
140 >          else {
141              sprintf( painCave.errMsg,
142 <                     "StatWriter detected a numerical error writing: %s ",
143 <                     Stats::getTitle(i).c_str());
142 >                     "StatWriter found an unknown data type for: %s ",
143 >                     stats_->getTitle(i).c_str());
144              painCave.isFatal = 1;
145              simError();
146 <          }          
147 <        }
146 >          }
147 >        }
148        }
149 +            
150        statfile_ << std::endl;
157 –
151        statfile_.flush();
152  
153   #ifdef IS_MPI
# Line 163 | Line 156 | namespace OpenMD {
156   #endif // is_mpi
157    }
158  
159 +  void StatWriter::writeReal(int i) {
160 +
161 +    RealType s = stats_->getRealData(i);
162 +
163 +    if (! isinf(s) && ! isnan(s)) {
164 +      statfile_ << "\t" << s;
165 +    } else{
166 +      sprintf( painCave.errMsg,
167 +               "StatWriter detected a numerical error writing: %s ",
168 +               stats_->getTitle(i).c_str());
169 +      painCave.isFatal = 1;
170 +      simError();
171 +    }    
172 +  }
173 +
174 +  void StatWriter::writeVector(int i) {
175 +
176 +    Vector3d s = stats_->getVectorData(i);
177 +    if (isinf(s[0]) || isnan(s[0]) ||
178 +        isinf(s[1]) || isnan(s[1]) ||
179 +        isinf(s[2]) || isnan(s[2]) ) {      
180 +      sprintf( painCave.errMsg,
181 +               "StatWriter detected a numerical error writing: %s",
182 +               stats_->getTitle(i).c_str());
183 +      painCave.isFatal = 1;
184 +      simError();
185 +    } else {
186 +      statfile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
187 +    }
188 +  }
189 +
190 +  void StatWriter::writeMatrix(int i) {
191 +
192 +    Mat3x3d s = stats_->getMatrixData(i);
193 +
194 +    for (unsigned int i = 0; i < 3; i++) {
195 +      for (unsigned int j = 0; j < 3; j++) {
196 +        if (isinf(s(i,j)) || isnan(s(i,j))) {      
197 +          sprintf( painCave.errMsg,
198 +                   "StatWriter detected a numerical error writing: %s",
199 +                   stats_->getTitle(i).c_str());
200 +          painCave.isFatal = 1;
201 +          simError();
202 +        } else {
203 +          statfile_ << "\t" << s(i,j);
204 +        }
205 +      }
206 +    }
207 +  }    
208   }

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines