--- trunk/src/applications/staticProps/SpatialStatistics.cpp	2013/11/07 16:42:46	1945
+++ trunk/src/applications/staticProps/SpatialStatistics.cpp	2014/10/22 12:23:59	2026
@@ -187,7 +187,7 @@ namespace OpenMD {
       }
         
       outStream << "#######################################################\n";
-      outStream << "# Standard Deviations in those quantities follow:\n";
+      outStream << "# 95% confidence intervals in those quantities follow:\n";
       outStream << "#######################################################\n";
       
       for (int j = 0; j < nBins_; j++) {
@@ -200,7 +200,7 @@ namespace OpenMD {
             
             int n = outputData->accumulator[j]->count();
             if (n != 0) {
-              writeStdDev( outStream, outputData, j );
+              writeErrorBars( outStream, outputData, j );
             }
           }
           outStream << std::endl;
@@ -257,7 +257,7 @@ namespace OpenMD {
     }
   }
 
-  void SpatialStatistics::writeStdDev(ostream& os, OutputData* dat, 
+  void SpatialStatistics::writeErrorBars(ostream& os, OutputData* dat, 
                                     unsigned int bin) {
     assert(int(bin) < nBins_);
     int n = dat->accumulator[bin]->count();
@@ -265,7 +265,7 @@ namespace OpenMD {
 
     if( dat->dataType == odtReal ) {
       RealType r;
-      dynamic_cast<Accumulator*>(dat->accumulator[bin])->getStdDev(r);      
+      dynamic_cast<Accumulator*>(dat->accumulator[bin])->get95percentConfidenceInterval(r);      
       if (isinf(r) || isnan(r) ) {      
         sprintf( painCave.errMsg,
                  "SpatialStatistics detected a numerical error writing:\n"
@@ -279,7 +279,7 @@ namespace OpenMD {
 
     } else if ( dat->dataType == odtVector3 ) {
       Vector3d v;
-      dynamic_cast<VectorAccumulator*>(dat->accumulator[bin])->getStdDev(v);
+      dynamic_cast<VectorAccumulator*>(dat->accumulator[bin])->get95percentConfidenceInterval(v);
       if (isinf(v[0]) || isnan(v[0]) || 
           isinf(v[1]) || isnan(v[1]) || 
           isinf(v[2]) || isnan(v[2]) ) {      
@@ -360,7 +360,18 @@ namespace OpenMD {
     bool hasCoordinateOrigin = rnemdParams->haveCoordinateOrigin();
     
     if (hasCoordinateOrigin) {
-      coordinateOrigin_ = rnemdParams->getCoordinateOrigin();
+        std::vector<RealType> co = rnemdParams->getCoordinateOrigin();
+        if (co.size() != 3) {
+          sprintf(painCave.errMsg,
+                  "RNEMD: Incorrect number of parameters specified for coordinateOrigin.\n"
+                  "\tthere should be 3 parameters, but %lu were specified.\n", 
+                  co.size());
+          painCave.isFatal = 1;
+          simError();      
+        }
+        coordinateOrigin_.x() = co[0];
+        coordinateOrigin_.y() = co[1];
+        coordinateOrigin_.z() = co[2];
     } else {
       coordinateOrigin_ = V3Zero;
     }