| 1621 | 
  | 
                    rPos = (*sdi)->getPos() - coordinateOrigin_; | 
| 1622 | 
  | 
                    vel = ((*sdi)->getVel() - vh - cross(omegah, rPos)) * h  | 
| 1623 | 
  | 
                      + ah + cross(bh, rPos);      | 
| 1624 | 
– | 
                    cerr << "setting vel to " << vel << "\n"; | 
| 1624 | 
  | 
                    (*sdi)->setVel(vel); | 
| 1625 | 
  | 
                    if (rnemdFluxType_ == rnemdFullKE) { | 
| 1626 | 
  | 
                      if ((*sdi)->isDirectional()) { | 
| 1717 | 
  | 
    if (!doRNEMD_) return; | 
| 1718 | 
  | 
    trialCount_++; | 
| 1719 | 
  | 
 | 
| 1721 | 
– | 
    cerr << "trialCount = " << trialCount_ << "\n"; | 
| 1720 | 
  | 
    // object evaluator: | 
| 1721 | 
  | 
    evaluator_.loadScriptString(rnemdObjectSelection_); | 
| 1722 | 
  | 
    seleMan_.setSelectionSet(evaluator_.evaluate()); | 
| 1762 | 
  | 
    if (!doRNEMD_) return; | 
| 1763 | 
  | 
    Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); | 
| 1764 | 
  | 
     | 
| 1767 | 
– | 
    cerr << "collecting data\n"; | 
| 1765 | 
  | 
    // collectData can be called more frequently than the doRNEMD, so use the  | 
| 1766 | 
  | 
    // computed area from the last exchange time: | 
| 1767 | 
  | 
    RealType area = getDividingArea(); |