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root/OpenMD/trunk/src/rnemd/RNEMD.cpp
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Comparing trunk/src/rnemd/RNEMD.cpp (file contents):
Revision 1971 by gezelter, Fri Feb 28 13:25:13 2014 UTC vs.
Revision 1980 by gezelter, Sat Apr 5 21:17:12 2014 UTC

# Line 857 | Line 857 | namespace OpenMD {
857            
858            Vector3d min_vel;
859            Vector3d max_vel = max_sd->getVel();
860 <          MPI_Status* status;
860 >          MPI_Status status;
861  
862            // point-to-point swap of the velocity vector
863            MPI_Sendrecv(max_vel.getArrayPointer(), 3, MPI_REALTYPE,
864                         min_vals.rank, 0,
865                         min_vel.getArrayPointer(), 3, MPI_REALTYPE,
866 <                       min_vals.rank, 0, MPI_COMM_WORLD, status);
866 >                       min_vals.rank, 0, MPI_COMM_WORLD, &status);
867            
868            switch(rnemdFluxType_) {
869            case rnemdKE :
# Line 878 | Line 878 | namespace OpenMD {
878                             MPI_REALTYPE, min_vals.rank, 1,
879                             min_angMom.getArrayPointer(), 3,
880                             MPI_REALTYPE, min_vals.rank, 1,
881 <                           MPI_COMM_WORLD, status);
881 >                           MPI_COMM_WORLD, &status);
882                
883                max_sd->setJ(min_angMom);
884              }
# Line 903 | Line 903 | namespace OpenMD {
903            
904            Vector3d max_vel;
905            Vector3d min_vel = min_sd->getVel();
906 <          MPI_Status* status;
906 >          MPI_Status status;
907            
908            // point-to-point swap of the velocity vector
909            MPI_Sendrecv(min_vel.getArrayPointer(), 3, MPI_REALTYPE,
910                         max_vals.rank, 0,
911                         max_vel.getArrayPointer(), 3, MPI_REALTYPE,
912 <                       max_vals.rank, 0, MPI_COMM_WORLD, status);
912 >                       max_vals.rank, 0, MPI_COMM_WORLD, &status);
913            
914            switch(rnemdFluxType_) {
915            case rnemdKE :
# Line 924 | Line 924 | namespace OpenMD {
924                             MPI_REALTYPE, max_vals.rank, 1,
925                             max_angMom.getArrayPointer(), 3,
926                             MPI_REALTYPE, max_vals.rank, 1,
927 <                           MPI_COMM_WORLD, status);
927 >                           MPI_COMM_WORLD, &status);
928                
929                min_sd->setJ(max_angMom);
930              }
# Line 2239 | Line 2239 | namespace OpenMD {
2239        }        
2240  
2241        rnemdFile_ << "#######################################################\n";
2242 <      rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
2242 >      rnemdFile_ << "# 95% confidence intervals in those quantities follow:\n";
2243        rnemdFile_ << "#######################################################\n";
2244  
2245  
# Line 2248 | Line 2248 | namespace OpenMD {
2248          for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2249            if (outputMask_[i]) {
2250              if (data_[i].dataType == "RealType")
2251 <              writeRealStdDev(i,j);
2251 >              writeRealErrorBars(i,j);
2252              else if (data_[i].dataType == "Vector3d")
2253 <              writeVectorStdDev(i,j);
2253 >              writeVectorErrorBars(i,j);
2254              else {
2255                sprintf( painCave.errMsg,
2256                         "RNEMD found an unknown data type for: %s ",
# Line 2321 | Line 2321 | namespace OpenMD {
2321      }
2322    }  
2323  
2324 <  void RNEMD::writeRealStdDev(int index, unsigned int bin) {
2324 >  void RNEMD::writeRealErrorBars(int index, unsigned int bin) {
2325      if (!doRNEMD_) return;
2326      assert(index >=0 && index < ENDINDEX);
2327      assert(int(bin) < nBins_);
# Line 2331 | Line 2331 | namespace OpenMD {
2331      count = data_[index].accumulator[bin]->count();
2332      if (count == 0) return;
2333      
2334 <    dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getStdDev(s);
2334 >    dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->get95percentConfidenceInterval(s);
2335      
2336      if (! isinf(s) && ! isnan(s)) {
2337        rnemdFile_ << "\t" << s;
# Line 2344 | Line 2344 | namespace OpenMD {
2344      }    
2345    }
2346    
2347 <  void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
2347 >  void RNEMD::writeVectorErrorBars(int index, unsigned int bin) {
2348      if (!doRNEMD_) return;
2349      assert(index >=0 && index < ENDINDEX);
2350      assert(int(bin) < nBins_);
# Line 2354 | Line 2354 | namespace OpenMD {
2354      count = data_[index].accumulator[bin]->count();
2355      if (count == 0) return;
2356  
2357 <    dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
2357 >    dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->get95percentConfidenceInterval(s);
2358      if (isinf(s[0]) || isnan(s[0]) ||
2359          isinf(s[1]) || isnan(s[1]) ||
2360          isinf(s[2]) || isnan(s[2]) ) {      

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