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root/OpenMD/trunk/src/applications/staticProps/SpatialStatistics.cpp
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Comparing:
branches/development/src/applications/staticProps/SpatialStatistics.cpp (file contents), Revision 1874 by gezelter, Wed May 15 15:09:35 2013 UTC vs.
trunk/src/applications/staticProps/SpatialStatistics.cpp (file contents), Revision 2026 by gezelter, Wed Oct 22 12:23:59 2014 UTC

# Line 43 | Line 43
43   #include "applications/staticProps/SpatialStatistics.hpp"
44   #include "io/DumpReader.hpp"
45   #include "primitives/Molecule.hpp"
46 + #ifdef _MSC_VER
47 + #define isnan(x) _isnan((x))
48 + #define isinf(x) (!_finite(x) && !_isnan(x))
49 + #endif
50  
51   namespace OpenMD {
52    
# Line 137 | Line 141 | namespace OpenMD {
141        processStuntDouble( sd, bin );
142  
143        dynamic_cast<Accumulator *>(counts_->accumulator[bin])->add(1);
144 <    }      
144 >    }
145    }
146    
147  
# Line 183 | Line 187 | namespace OpenMD {
187        }
188          
189        outStream << "#######################################################\n";
190 <      outStream << "# Standard Deviations in those quantities follow:\n";
190 >      outStream << "# 95% confidence intervals in those quantities follow:\n";
191        outStream << "#######################################################\n";
192        
193        for (int j = 0; j < nBins_; j++) {
# Line 196 | Line 200 | namespace OpenMD {
200              
201              int n = outputData->accumulator[j]->count();
202              if (n != 0) {
203 <              writeStdDev( outStream, outputData, j );
203 >              writeErrorBars( outStream, outputData, j );
204              }
205            }
206            outStream << std::endl;
# Line 221 | Line 225 | namespace OpenMD {
225      int n = dat->accumulator[bin]->count();
226      if (n == 0) return;
227  
224 –    RealType r;
225 –    Vector3d v;
226 –
228      if( dat->dataType == odtReal ) {
229 +      RealType r;
230        dynamic_cast<Accumulator*>(dat->accumulator[bin])->getAverage(r);      
231        if (isinf(r) || isnan(r) ) {      
232          sprintf( painCave.errMsg,
233                   "SpatialStatistics detected a numerical error writing:\n"
234 <                 "\t%s for bin %d",
234 >                 "\t%s for bin %u",
235                   dat->title.c_str(), bin);
236          painCave.isFatal = 1;
237          simError();
# Line 238 | Line 240 | namespace OpenMD {
240        os << "\t" << r;      
241  
242      } else if ( dat->dataType == odtVector3 ) {
243 +      Vector3d v;
244        dynamic_cast<VectorAccumulator*>(dat->accumulator[bin])->getAverage(v);
245        if (isinf(v[0]) || isnan(v[0]) ||
246            isinf(v[1]) || isnan(v[1]) ||
247            isinf(v[2]) || isnan(v[2]) ) {      
248          sprintf( painCave.errMsg,
249                   "SpatialStatistics detected a numerical error writing:\n"
250 <                 "\t%s for bin %d",
250 >                 "\t%s for bin %u",
251                   dat->title.c_str(), bin);
252          painCave.isFatal = 1;
253          simError();
# Line 254 | Line 257 | namespace OpenMD {
257      }
258    }
259  
260 <  void SpatialStatistics::writeStdDev(ostream& os, OutputData* dat,
260 >  void SpatialStatistics::writeErrorBars(ostream& os, OutputData* dat,
261                                      unsigned int bin) {
262      assert(int(bin) < nBins_);
263      int n = dat->accumulator[bin]->count();
264      if (n == 0) return;
265  
263 –    RealType r;
264 –    Vector3d v;
265 –
266      if( dat->dataType == odtReal ) {
267 <      dynamic_cast<Accumulator*>(dat->accumulator[bin])->getStdDev(r);      
267 >      RealType r;
268 >      dynamic_cast<Accumulator*>(dat->accumulator[bin])->get95percentConfidenceInterval(r);      
269        if (isinf(r) || isnan(r) ) {      
270          sprintf( painCave.errMsg,
271                   "SpatialStatistics detected a numerical error writing:\n"
272 <                 "\tstandard deviation of %s for bin %d",
272 >                 "\tstandard deviation of %s for bin %u",
273                   dat->title.c_str(), bin);
274          painCave.isFatal = 1;
275          simError();
# Line 277 | Line 278 | namespace OpenMD {
278        os << "\t" << r;      
279  
280      } else if ( dat->dataType == odtVector3 ) {
281 <      dynamic_cast<VectorAccumulator*>(dat->accumulator[bin])->getStdDev(v);
281 >      Vector3d v;
282 >      dynamic_cast<VectorAccumulator*>(dat->accumulator[bin])->get95percentConfidenceInterval(v);
283        if (isinf(v[0]) || isnan(v[0]) ||
284            isinf(v[1]) || isnan(v[1]) ||
285            isinf(v[2]) || isnan(v[2]) ) {      
286          sprintf( painCave.errMsg,
287                   "SpatialStatistics detected a numerical error writing:\n"
288 <                 "\tstandard deviation of %s for bin %d",
288 >                 "\tstandard deviation of %s for bin %u",
289                   dat->title.c_str(), bin);
290          painCave.isFatal = 1;
291          simError();
# Line 321 | Line 323 | namespace OpenMD {
323    }
324  
325    SlabStatistics::~SlabStatistics() {
324 –    delete z_;
326    }
327  
328  
329    void SlabStatistics::processFrame(int istep) {
330      RealType z;
331 +
332      hmat_ = currentSnapshot_->getHmat();
333      for (int i = 0; i < nBins_; i++) {
334        z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat_(2,2);
# Line 349 | Line 351 | namespace OpenMD {
351  
352    ShellStatistics::ShellStatistics(SimInfo* info, const string& filename,
353                                     const string& sele, int nbins) :
354 <    SpatialStatistics(info, filename, sele, nbins){
354 >    SpatialStatistics(info, filename, sele, nbins), coordinateOrigin_(V3Zero) {
355      
354 –    coordinateOrigin_ = V3Zero;
356      binWidth_ = 1.0;
357  
358 +    Globals* simParams = info->getSimParams();
359 +    RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
360 +    bool hasCoordinateOrigin = rnemdParams->haveCoordinateOrigin();
361 +    
362 +    if (hasCoordinateOrigin) {
363 +        std::vector<RealType> co = rnemdParams->getCoordinateOrigin();
364 +        if (co.size() != 3) {
365 +          sprintf(painCave.errMsg,
366 +                  "RNEMD: Incorrect number of parameters specified for coordinateOrigin.\n"
367 +                  "\tthere should be 3 parameters, but %lu were specified.\n",
368 +                  co.size());
369 +          painCave.isFatal = 1;
370 +          simError();      
371 +        }
372 +        coordinateOrigin_.x() = co[0];
373 +        coordinateOrigin_.y() = co[1];
374 +        coordinateOrigin_.z() = co[2];
375 +    } else {
376 +      coordinateOrigin_ = V3Zero;
377 +    }
378 +    
379      r_ = new OutputData;
380      r_->units =  "Angstroms";
381      r_->title =  "R";
# Line 371 | Line 393 | namespace OpenMD {
393    }
394  
395    ShellStatistics::~ShellStatistics() {
374 –    delete r_;
396    }
397  
398 <  int ShellStatistics::getBin(Vector3d pos) {    
398 >  int ShellStatistics::getBin(Vector3d pos) {
399      Vector3d rPos = pos - coordinateOrigin_;
400      return int(rPos.length() / binWidth_);
401    }

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