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root/OpenMD/branches/development/src/rnemd/RNEMD.cpp
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Comparing branches/development/src/rnemd/RNEMD.cpp (file contents):
Revision 1854 by gezelter, Thu Mar 28 20:54:06 2013 UTC vs.
Revision 1856 by gezelter, Tue Apr 2 21:30:34 2013 UTC

# Line 419 | Line 419 | namespace OpenMD {
419          velocity.accumulator.push_back( new VectorAccumulator() );
420        data_[VELOCITY] = velocity;
421        outputMap_["VELOCITY"] = VELOCITY;
422 +
423 +      OutputData angularVelocity;
424 +      angularVelocity.units = "angstroms^2/fs";
425 +      angularVelocity.title =  "AngularVelocity";  
426 +      angularVelocity.dataType = "Vector3d";
427 +      angularVelocity.accumulator.reserve(nBins_);
428 +      for (int i = 0; i < nBins_; i++)
429 +        angularVelocity.accumulator.push_back( new VectorAccumulator() );
430 +      data_[ANGULARVELOCITY] = angularVelocity;
431 +      outputMap_["ANGULARVELOCITY"] = ANGULARVELOCITY;
432  
433        OutputData density;
434        density.units =  "g cm^-3";
# Line 1610 | Line 1620 | namespace OpenMD {
1620                      //vel = (*sdi)->getVel();
1621                      rPos = (*sdi)->getPos() - coordinateOrigin_;
1622                      vel = ((*sdi)->getVel() - vh - cross(omegah, rPos)) * h
1623 <                      + ah + cross(bh, rPos);                  
1623 >                      + ah + cross(bh, rPos);    
1624                      (*sdi)->setVel(vel);
1625                      if (rnemdFluxType_ == rnemdFullKE) {
1626                        if ((*sdi)->isDirectional()) {
# Line 1751 | Line 1761 | namespace OpenMD {
1761    void RNEMD::collectData() {
1762      if (!doRNEMD_) return;
1763      Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1764 <
1764 >    
1765      // collectData can be called more frequently than the doRNEMD, so use the
1766      // computed area from the last exchange time:
1767 <
1768 <    areaAccumulator_->add(getDividingArea());
1767 >    RealType area = getDividingArea();
1768 >    areaAccumulator_->add(area);
1769      Mat3x3d hmat = currentSnap_->getHmat();
1770      seleMan_.setSelectionSet(evaluator_.evaluate());
1771  
# Line 1814 | Line 1824 | namespace OpenMD {
1824        Vector3d rPos = sd->getPos() - coordinateOrigin_;
1825        Vector3d aVel = cross(rPos, vel);
1826        
1827 <      if (binNo < nBins_)  {
1827 >      if (binNo >= 0 && binNo < nBins_)  {
1828          binCount[binNo]++;
1829          binMass[binNo] += mass;
1830          binPx[binNo] += mass*vel.x();
# Line 1914 | Line 1924 | namespace OpenMD {
1924              case VELOCITY:
1925                dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1926                break;
1927 <            case ANGULARVELOCITY:
1927 >            case ANGULARVELOCITY:  
1928                dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(aVel);
1929                break;
1930              case DENSITY:
# Line 2069 | Line 2079 | namespace OpenMD {
2079            if (outputMask_[i]) {
2080              if (data_[i].dataType == "RealType")
2081                writeReal(i,j);
2082 <            else if (data_[i].dataType == "Vector3d")
2082 >            else if (data_[i].dataType == "Vector3d")
2083                writeVector(i,j);
2084              else {
2085                sprintf( painCave.errMsg,
# Line 2126 | Line 2136 | namespace OpenMD {
2136      RealType s;
2137      int count;
2138      
2139 <    count = dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->count();
2139 >    count = data_[index].accumulator[bin]->count();
2140      if (count == 0) return;
2141      
2142      dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s);
# Line 2149 | Line 2159 | namespace OpenMD {
2159      Vector3d s;
2160      int count;
2161      
2162 <    count = dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->count();
2162 >    count = data_[index].accumulator[bin]->count();
2163 >
2164      if (count == 0) return;
2165  
2166      dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
# Line 2173 | Line 2184 | namespace OpenMD {
2184      RealType s;
2185      int count;
2186      
2187 <    count = dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->count();
2187 >    count = data_[index].accumulator[bin]->count();
2188      if (count == 0) return;
2189      
2190      dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getStdDev(s);
# Line 2196 | Line 2207 | namespace OpenMD {
2207      Vector3d s;
2208      int count;
2209      
2210 <    count = dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->count();
2210 >    count = data_[index].accumulator[bin]->count();
2211      if (count == 0) return;
2212  
2213      dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);

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