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root/OpenMD/trunk/src/applications/staticProps/SpatialStatistics.cpp
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Comparing trunk/src/applications/staticProps/SpatialStatistics.cpp (file contents):
Revision 1945 by gezelter, Thu Nov 7 16:42:46 2013 UTC vs.
Revision 2026 by gezelter, Wed Oct 22 12:23:59 2014 UTC

# Line 187 | 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 200 | 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 257 | 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();
# Line 265 | Line 265 | namespace OpenMD {
265  
266      if( dat->dataType == odtReal ) {
267        RealType r;
268 <      dynamic_cast<Accumulator*>(dat->accumulator[bin])->getStdDev(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"
# Line 279 | Line 279 | namespace OpenMD {
279  
280      } else if ( dat->dataType == odtVector3 ) {
281        Vector3d v;
282 <      dynamic_cast<VectorAccumulator*>(dat->accumulator[bin])->getStdDev(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]) ) {      
# Line 360 | Line 360 | namespace OpenMD {
360      bool hasCoordinateOrigin = rnemdParams->haveCoordinateOrigin();
361      
362      if (hasCoordinateOrigin) {
363 <      coordinateOrigin_ = rnemdParams->getCoordinateOrigin();
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      }

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