--- trunk/src/utils/MoLocator.cpp 2006/05/17 21:51:42 963 +++ trunk/src/utils/MoLocator.cpp 2015/03/07 21:41:51 2071 @@ -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 +28,16 @@ * 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, 234107 (2008). + * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). */ #include @@ -48,7 +49,7 @@ #include "utils/MoLocator.hpp" #include "types/AtomType.hpp" -namespace oopse { +namespace OpenMD { MoLocator::MoLocator( MoleculeStamp* theStamp, ForceField* theFF){ myStamp = theStamp; @@ -57,34 +58,37 @@ namespace oopse { calcRef(); } - void MoLocator::placeMol( const Vector3d& offset, const Vector3d& ort, Molecule* mol){ + void MoLocator::placeMol( const Vector3d& offset, const Vector3d& ort, + Molecule* mol) { + Vector3d newCoor; Vector3d curRefCoor; RotMat3x3d rotMat = latVec2RotMat(ort); if(mol->getNIntegrableObjects() != nIntegrableObjects){ sprintf( painCave.errMsg, - "MoLocator error.\n" - " The number of integrable objects of MoleculeStamp is not the same as that of Molecule\n"); + "MoLocator::placeMol error.\n" + "\tThe number of integrable objects of MoleculeStamp is not\n" + "\tthe same as that of Molecule\n"); painCave.isFatal = 1; simError(); } Molecule::IntegrableObjectIterator ii; - StuntDouble* integrableObject; + StuntDouble* sd; int i; - for (integrableObject = mol->beginIntegrableObject(ii), i = 0; integrableObject != NULL; - integrableObject = mol->nextIntegrableObject(ii), ++i) { + for (sd = mol->beginIntegrableObject(ii), i = 0; sd != NULL; + sd = mol->nextIntegrableObject(ii), ++i) { newCoor = rotMat * refCoords[i]; newCoor += offset; + + sd->setPos(newCoor); + sd->setVel(V3Zero); - integrableObject->setPos( newCoor); - integrableObject->setVel(V3Zero); - - if(integrableObject->isDirectional()){ - integrableObject->setA(rotMat * integrableObject->getA()); - integrableObject->setJ(V3Zero); + if(sd->isDirectional()){ + sd->setA(rotMat * sd->getA()); + sd->setJ(V3Zero); } } } @@ -92,28 +96,25 @@ namespace oopse { void MoLocator::calcRef( void ){ AtomStamp* currAtomStamp; RigidBodyStamp* rbStamp; - int nAtoms; - int nRigidBodies; std::vector mass; Vector3d coor; Vector3d refMolCom; - int nAtomsInRb; RealType totMassInRb; RealType currAtomMass; RealType molMass; - nAtoms= myStamp->getNAtoms(); - nRigidBodies = myStamp->getNRigidBodies(); + std::size_t nAtoms= myStamp->getNAtoms(); + std::size_t nRigidBodies = myStamp->getNRigidBodies(); - for(size_t i=0; igetAtomStamp(i); if( !currAtomStamp->havePosition() ){ sprintf( painCave.errMsg, - "MoLocator error.\n" - " Component %s, atom %s does not have a position specified.\n" - " This means MoLocator cannot initalize it's position.\n", + "MoLocator::calcRef error.\n" + "\tComponent %s, atom %s does not have a position specified.\n" + "\tThis means MoLocator cannot initalize it's position.\n", myStamp->getName().c_str(), currAtomStamp->getType().c_str()); @@ -136,17 +137,17 @@ namespace oopse { } } - for(int i = 0; i < nRigidBodies; i++){ + for(std::size_t i = 0; i < nRigidBodies; i++){ rbStamp = myStamp->getRigidBodyStamp(i); - nAtomsInRb = rbStamp->getNMembers(); + std::size_t nAtomsInRb = rbStamp->getNMembers(); coor.x() = 0.0; coor.y() = 0.0; coor.z() = 0.0; totMassInRb = 0.0; - for(int j = 0; j < nAtomsInRb; j++){ + for(std::size_t j = 0; j < nAtomsInRb; j++){ currAtomStamp = myStamp->getAtomStamp(rbStamp->getMemberAt(j)); currAtomMass = getAtomMass(currAtomStamp->getType(), myFF); @@ -169,24 +170,24 @@ namespace oopse { refMolCom.y() = 0; refMolCom.z() = 0; - for(int i = 0; i < nIntegrableObjects; i++){ + for(std::size_t i = 0; i < nIntegrableObjects; i++){ refMolCom += refCoords[i] * mass[i]; molMass += mass[i]; } refMolCom /= molMass; - //move the reference center of mass to (0,0,0) and adjust the reference coordinate - //of the integrabel objects - for(int i = 0; i < nIntegrableObjects; i++) + //move the reference center of mass to (0,0,0) and adjust the + //reference coordinate of the integrabel objects + for(std::size_t i = 0; i < nIntegrableObjects; i++) refCoords[i] -= refMolCom; } - RealType getAtomMass(const std::string& at, ForceField* myFF) { + RealType MoLocator::getAtomMass(const std::string& at, ForceField* myFF) { RealType mass; AtomType* atomType= myFF->getAtomType(at); if (atomType != NULL) { - mass = atomType->getMass(); + mass = atomType->getMass(); } else { mass = 0.0; std::cerr << "Can not find AtomType: " << at << std::endl; @@ -194,25 +195,25 @@ namespace oopse { return mass; } - RealType getMolMass(MoleculeStamp *molStamp, ForceField *myFF) { - int nAtoms; + RealType MoLocator::getMolMass(MoleculeStamp *molStamp, ForceField *myFF) { + unsigned int nAtoms; RealType totMass = 0; nAtoms = molStamp->getNAtoms(); - for(size_t i = 0; i < nAtoms; i++) { + for(std::size_t i = 0; i < nAtoms; i++) { AtomStamp *currAtomStamp = molStamp->getAtomStamp(i); totMass += getAtomMass(currAtomStamp->getType(), myFF); } return totMass; } - RotMat3x3d latVec2RotMat(const Vector3d& lv){ + + RotMat3x3d MoLocator::latVec2RotMat(const Vector3d& lv){ RealType theta =acos(lv[2]); RealType phi = atan2(lv[1], lv[0]); RealType psi = 0; - return RotMat3x3d(phi, theta, psi); - + return RotMat3x3d(phi, theta, psi); } }