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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 1855 by gezelter, Tue Apr 2 18:31:51 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 >                    cerr << "setting vel to " << vel << "\n";
1625                      (*sdi)->setVel(vel);
1626                      if (rnemdFluxType_ == rnemdFullKE) {
1627                        if ((*sdi)->isDirectional()) {
# Line 1707 | Line 1718 | namespace OpenMD {
1718      if (!doRNEMD_) return;
1719      trialCount_++;
1720  
1721 +    cerr << "trialCount = " << trialCount_ << "\n";
1722      // object evaluator:
1723      evaluator_.loadScriptString(rnemdObjectSelection_);
1724      seleMan_.setSelectionSet(evaluator_.evaluate());
# Line 1751 | Line 1763 | namespace OpenMD {
1763    void RNEMD::collectData() {
1764      if (!doRNEMD_) return;
1765      Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1766 <
1766 >    
1767 >    cerr << "collecting data\n";
1768      // collectData can be called more frequently than the doRNEMD, so use the
1769      // computed area from the last exchange time:
1770 <
1771 <    areaAccumulator_->add(getDividingArea());
1770 >    RealType area = getDividingArea();
1771 >    areaAccumulator_->add(area);
1772      Mat3x3d hmat = currentSnap_->getHmat();
1773      seleMan_.setSelectionSet(evaluator_.evaluate());
1774  
# Line 1814 | Line 1827 | namespace OpenMD {
1827        Vector3d rPos = sd->getPos() - coordinateOrigin_;
1828        Vector3d aVel = cross(rPos, vel);
1829        
1830 <      if (binNo < nBins_)  {
1830 >      if (binNo >= 0 && binNo < nBins_)  {
1831          binCount[binNo]++;
1832          binMass[binNo] += mass;
1833          binPx[binNo] += mass*vel.x();
# Line 1914 | Line 1927 | namespace OpenMD {
1927              case VELOCITY:
1928                dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1929                break;
1930 <            case ANGULARVELOCITY:
1930 >            case ANGULARVELOCITY:  
1931                dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(aVel);
1932                break;
1933              case DENSITY:
# Line 2069 | Line 2082 | namespace OpenMD {
2082            if (outputMask_[i]) {
2083              if (data_[i].dataType == "RealType")
2084                writeReal(i,j);
2085 <            else if (data_[i].dataType == "Vector3d")
2085 >            else if (data_[i].dataType == "Vector3d")
2086                writeVector(i,j);
2087              else {
2088                sprintf( painCave.errMsg,
# Line 2126 | Line 2139 | namespace OpenMD {
2139      RealType s;
2140      int count;
2141      
2142 <    count = dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->count();
2142 >    count = data_[index].accumulator[bin]->count();
2143      if (count == 0) return;
2144      
2145      dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s);
# Line 2149 | Line 2162 | namespace OpenMD {
2162      Vector3d s;
2163      int count;
2164      
2165 <    count = dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->count();
2165 >    count = data_[index].accumulator[bin]->count();
2166 >
2167      if (count == 0) return;
2168  
2169      dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
# Line 2173 | Line 2187 | namespace OpenMD {
2187      RealType s;
2188      int count;
2189      
2190 <    count = dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->count();
2190 >    count = data_[index].accumulator[bin]->count();
2191      if (count == 0) return;
2192      
2193      dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getStdDev(s);
# Line 2196 | Line 2210 | namespace OpenMD {
2210      Vector3d s;
2211      int count;
2212      
2213 <    count = dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->count();
2213 >    count = data_[index].accumulator[bin]->count();
2214      if (count == 0) return;
2215  
2216      dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);

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