--- branches/development/src/primitives/RigidBody.cpp 2013/01/29 19:10:04 1842 +++ branches/development/src/primitives/RigidBody.cpp 2013/02/20 15:39:39 1850 @@ -35,7 +35,7 @@ * * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). - * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). + * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). */ @@ -229,11 +229,15 @@ namespace OpenMD { Vector3d trq(0.0); Vector3d ef(0.0); Vector3d pos = this->getPos(); - + AtomType* atype; + int eCount = 0; + int sl = ((snapshotMan_->getCurrentSnapshot())->*storage_).getStorageLayout(); - + for (unsigned int i = 0; i < atoms_.size(); i++) { + atype = atoms_[i]->getAtomType(); + afrc = atoms_[i]->getFrc(); apos = atoms_[i]->getPos(); rpos = apos - pos; @@ -252,15 +256,16 @@ namespace OpenMD { trq += atrq; } - if (sl & DataStorage::dslElectricField) { + if ((sl & DataStorage::dslElectricField) && (atype->isElectrostatic())) { ef += atoms_[i]->getElectricField(); + eCount++; } } addFrc(frc); addTrq(trq); - if (sl & DataStorage::dslElectricField) { - ef /= atoms_.size(); + if (sl & DataStorage::dslElectricField) { + ef /= eCount; setElectricField(ef); } @@ -275,7 +280,9 @@ namespace OpenMD { Vector3d frc(0.0); Vector3d trq(0.0); Vector3d ef(0.0); - + AtomType* atype; + int eCount = 0; + Vector3d pos = this->getPos(); Mat3x3d tau_(0.0); @@ -283,6 +290,8 @@ namespace OpenMD { for (unsigned int i = 0; i < atoms_.size(); i++) { + atype = atoms_[i]->getAtomType(); + afrc = atoms_[i]->getFrc(); apos = atoms_[i]->getPos(); rpos = apos - pos; @@ -300,8 +309,10 @@ namespace OpenMD { atrq = atoms_[i]->getTrq(); trq += atrq; } - if (sl & DataStorage::dslElectricField) { + + if ((sl & DataStorage::dslElectricField) && (atype->isElectrostatic())) { ef += atoms_[i]->getElectricField(); + eCount++; } tau_(0,0) -= rpos[0]*afrc[0]; @@ -319,7 +330,7 @@ namespace OpenMD { addTrq(trq); if (sl & DataStorage::dslElectricField) { - ef /= atoms_.size(); + ef /= eCount; setElectricField(ef); }