--- trunk/src/io/RestReader.cpp 2010/01/22 21:31:12 1409 +++ branches/development/src/io/RestReader.cpp 2012/07/09 14:15:52 1769 @@ -36,7 +36,8 @@ * [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). - * [4] Vardeman & Gezelter, in progress (2009). + * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). */ @@ -279,9 +280,9 @@ namespace OpenMD { int index = tokenizer.nextTokenAsInt(); - StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index); + StuntDouble* sd = info_->getIOIndexToIntegrableObject(index); - if (integrableObject == NULL) { + if (sd == NULL) { return; } @@ -309,7 +310,7 @@ namespace OpenMD { } case 'q' : { - if (integrableObject->isDirectional()) { + if (sd->isDirectional()) { q[0] = tokenizer.nextTokenAsDouble(); q[1] = tokenizer.nextTokenAsDouble(); @@ -331,7 +332,7 @@ namespace OpenMD { } case 'j' : { Vector3d ji; - if (integrableObject->isDirectional()) { + if (sd->isDirectional()) { ji[0] = tokenizer.nextTokenAsDouble(); ji[1] = tokenizer.nextTokenAsDouble(); ji[2] = tokenizer.nextTokenAsDouble(); @@ -365,7 +366,7 @@ namespace OpenMD { all_pos_[index] = pos; // is this io restrained? - GenericData* data = integrableObject->getPropertyByName("Restraint"); + GenericData* data = sd->getPropertyByName("Restraint"); ObjectRestraint* oRest; if (data != NULL) { @@ -376,7 +377,7 @@ namespace OpenMD { // an ObjectRestraint: oRest = dynamic_cast(restData->getData()); if (oRest != NULL) { - if (integrableObject->isDirectional()) { + if (sd->isDirectional()) { oRest->setReferenceStructure(pos, q.toRotationMatrix3()); } else { oRest->setReferenceStructure(pos);