--- trunk/src/utils/MoLocator.cpp 2005/04/14 21:20:36 501 +++ trunk/src/utils/MoLocator.cpp 2012/08/22 02:28:28 1782 @@ -1,4 +1,4 @@ - /* +/* * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. * * The University of Notre Dame grants you ("Licensee") a @@ -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, 24107 (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; @@ -58,6 +59,7 @@ namespace oopse { } void MoLocator::placeMol( const Vector3d& offset, const Vector3d& ort, Molecule* mol){ + Vector3d newCoor; Vector3d curRefCoor; RotMat3x3d rotMat = latVec2RotMat(ort); @@ -71,20 +73,20 @@ namespace oopse { } 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); } } } @@ -92,30 +94,30 @@ namespace oopse { void MoLocator::calcRef( void ){ AtomStamp* currAtomStamp; RigidBodyStamp* rbStamp; - int nAtoms; + unsigned 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(); - for(size_t i=0; igetAtom(i); + currAtomStamp = myStamp->getAtomStamp(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", - myStamp->getID(), - currAtomStamp->getType() ); + myStamp->getName().c_str(), + currAtomStamp->getType().c_str()); painCave.isFatal = 1; simError(); @@ -138,7 +140,7 @@ namespace oopse { for(int i = 0; i < nRigidBodies; i++){ - rbStamp = myStamp->getRigidBody(i); + rbStamp = myStamp->getRigidBodyStamp(i); nAtomsInRb = rbStamp->getNMembers(); coor.x() = 0.0; @@ -148,7 +150,7 @@ namespace oopse { for(int j = 0; j < nAtomsInRb; j++){ - currAtomStamp = myStamp->getAtom(rbStamp->getMember(j)); + currAtomStamp = myStamp->getAtomStamp(rbStamp->getMemberAt(j)); currAtomMass = getAtomMass(currAtomStamp->getType(), myFF); totMassInRb += currAtomMass; @@ -178,12 +180,12 @@ namespace oopse { //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++) - refCoords[i] -= refMolCom; + for(int i = 0; i < nIntegrableObjects; i++) + 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(); @@ -194,22 +196,22 @@ namespace oopse { return mass; } - double getMolMass(MoleculeStamp *molStamp, ForceField *myFF) { - int nAtoms; - double totMass = 0; + RealType getMolMass(MoleculeStamp *molStamp, ForceField *myFF) { + unsigned int nAtoms; + RealType totMass = 0; nAtoms = molStamp->getNAtoms(); - for(size_t i = 0; i < nAtoms; i++) { - AtomStamp *currAtomStamp = molStamp->getAtom(i); + for(unsigned int i = 0; i < nAtoms; i++) { + AtomStamp *currAtomStamp = molStamp->getAtomStamp(i); totMass += getAtomMass(currAtomStamp->getType(), myFF); } return totMass; } 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);