--- trunk/src/utils/MoLocator.cpp 2005/12/02 15:38:03 770 +++ trunk/src/utils/MoLocator.cpp 2009/11/25 20:02:06 1390 @@ -6,19 +6,10 @@ * redistribute this software in source and binary code form, provided * that the following conditions are met: * - * 1. Acknowledgement of the program authors must be made in any - * publication of scientific results based in part on use of the - * program. An acceptable form of acknowledgement is citation of - * the article in which the program was described (Matthew - * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher - * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented - * Parallel Simulation Engine for Molecular Dynamics," - * J. Comput. Chem. 26, pp. 252-271 (2005)) - * - * 2. Redistributions of source code must retain the above copyright + * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * - * 3. Redistributions in binary form must reproduce the above copyright + * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the * distribution. @@ -37,6 +28,15 @@ * arising out of the use of or inability to use software, even if the * University of Notre Dame has been advised of the possibility of * such damages. + * + * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your + * research, please cite the appropriate papers when you publish your + * work. Good starting points are: + * + * [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). */ #include @@ -48,7 +48,7 @@ #include "utils/MoLocator.hpp" #include "types/AtomType.hpp" -namespace oopse { +namespace OpenMD { MoLocator::MoLocator( MoleculeStamp* theStamp, ForceField* theFF){ myStamp = theStamp; @@ -58,6 +58,7 @@ namespace oopse { } void MoLocator::placeMol( const Vector3d& offset, const Vector3d& ort, Molecule* mol){ + Vector3d newCoor; Vector3d curRefCoor; RotMat3x3d rotMat = latVec2RotMat(ort); @@ -78,8 +79,8 @@ namespace oopse { newCoor = rotMat * refCoords[i]; newCoor += offset; - - integrableObject->setPos( newCoor); + + integrableObject->setPos(newCoor); integrableObject->setVel(V3Zero); if(integrableObject->isDirectional()){ @@ -94,13 +95,13 @@ namespace oopse { RigidBodyStamp* rbStamp; int nAtoms; int nRigidBodies; - std::vector mass; + std::vector mass; Vector3d coor; Vector3d refMolCom; int nAtomsInRb; - double totMassInRb; - double currAtomMass; - double molMass; + RealType totMassInRb; + RealType currAtomMass; + RealType molMass; nAtoms= myStamp->getNAtoms(); nRigidBodies = myStamp->getNRigidBodies(); @@ -182,8 +183,8 @@ namespace oopse { refCoords[i] -= refMolCom; } - double getAtomMass(const std::string& at, ForceField* myFF) { - double mass; + RealType getAtomMass(const std::string& at, ForceField* myFF) { + RealType mass; AtomType* atomType= myFF->getAtomType(at); if (atomType != NULL) { mass = atomType->getMass(); @@ -194,9 +195,9 @@ namespace oopse { return mass; } - double getMolMass(MoleculeStamp *molStamp, ForceField *myFF) { + RealType getMolMass(MoleculeStamp *molStamp, ForceField *myFF) { int nAtoms; - double totMass = 0; + RealType totMass = 0; nAtoms = molStamp->getNAtoms(); for(size_t i = 0; i < nAtoms; i++) { @@ -207,9 +208,9 @@ namespace oopse { } RotMat3x3d latVec2RotMat(const Vector3d& lv){ - double theta =acos(lv[2]); - double phi = atan2(lv[1], lv[0]); - double psi = 0; + RealType theta =acos(lv[2]); + RealType phi = atan2(lv[1], lv[0]); + RealType psi = 0; return RotMat3x3d(phi, theta, psi);