--- trunk/src/primitives/Molecule.cpp 2008/01/23 16:38:22 1211 +++ branches/development/src/primitives/Molecule.cpp 2012/05/24 01:29:59 1718 @@ -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). */ /** @@ -53,9 +54,10 @@ #include "utils/MemoryUtils.hpp" #include "utils/simError.h" -namespace oopse { +namespace OpenMD { Molecule::Molecule(int stampId, int globalIndex, const std::string& molName) - : stampId_(stampId), globalIndex_(globalIndex), moleculeName_(molName) { + : stampId_(stampId), globalIndex_(globalIndex), moleculeName_(molName), + constrainTotalCharge_(false) { } Molecule::~Molecule() { @@ -64,12 +66,15 @@ namespace oopse { MemoryUtils::deletePointers(bonds_); MemoryUtils::deletePointers(bends_); MemoryUtils::deletePointers(torsions_); + MemoryUtils::deletePointers(inversions_); MemoryUtils::deletePointers(rigidBodies_); MemoryUtils::deletePointers(cutoffGroups_); MemoryUtils::deletePointers(constraintPairs_); MemoryUtils::deletePointers(constraintElems_); + // integrableObjects_ don't own the objects integrableObjects_.clear(); + fluctuatingCharges_.clear(); } @@ -97,6 +102,13 @@ namespace oopse { torsions_.push_back(torsion); } } + + void Molecule::addInversion(Inversion* inversion) { + if (std::find(inversions_.begin(), inversions_.end(), inversion) == + inversions_.end()) { + inversions_.push_back(inversion); + } + } void Molecule::addRigidBody(RigidBody *rb) { if (std::find(rigidBodies_.begin(), rigidBodies_.end(), rb) == @@ -129,46 +141,44 @@ namespace oopse { void Molecule::complete() { std::set rigidAtoms; + Atom* atom; + AtomIterator ai; RigidBody* rb; - std::vector::iterator rbIter; + RigidBodyIterator rbIter; - + // Get list of all the atoms that are part of rigid bodies + for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) { rigidAtoms.insert(rb->getBeginAtomIter(), rb->getEndAtomIter()); } - Atom* atom; - AtomIterator ai; + // add any atom that wasn't part of a rigid body to the list of integrableObjects + for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) { - if (rigidAtoms.find(*ai) == rigidAtoms.end()) { + if (rigidAtoms.find(atom) == rigidAtoms.end()) { // If an atom does not belong to a rigid body, it is an // integrable object - integrableObjects_.push_back(*ai); + integrableObjects_.push_back(atom); } } - //find all free atoms (which do not belong to rigid bodies) - // performs the "difference" operation from set theory, the output - // range contains a copy of every element that is contained in - // [allAtoms.begin(), allAtoms.end()) and not contained in - // [rigidAtoms.begin(), rigidAtoms.end()). - //std::set_difference(allAtoms.begin(), allAtoms.end(), rigidAtoms.begin(), rigidAtoms.end(), - // std::back_inserter(integrableObjects_)); + // then add the rigid bodies themselves to the integrableObjects - //if (integrableObjects_.size() != allAtoms.size() - rigidAtoms.size()) { - // //Some atoms in rigidAtoms are not in allAtoms, something must be wrong - // sprintf(painCave.errMsg, "Atoms in rigidbody are not in the atom list of the same molecule"); - // - // painCave.isFatal = 1; - // simError(); - //} for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) { integrableObjects_.push_back(rb); } - //integrableObjects_.insert(integrableObjects_.end(), rigidBodies_.begin(), rigidBodies_.end()); + + // find the atoms that are fluctuating charges and add them to the + // fluctuatingCharges_ vector + + for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) { + if ( atom->isFluctuatingCharge() ) + fluctuatingCharges_.push_back( atom ); + } + } RealType Molecule::getMass() { @@ -237,9 +247,11 @@ namespace oopse { Bond* bond; Bend* bend; Torsion* torsion; + Inversion* inversion; Molecule::BondIterator bondIter;; Molecule::BendIterator bendIter; Molecule::TorsionIterator torsionIter; + Molecule::InversionIterator inversionIter; RealType potential = 0.0; @@ -256,10 +268,39 @@ namespace oopse { potential += torsion->getPotential(); } + for (inversion = beginInversion(inversionIter); torsion != NULL; + inversion = nextInversion(inversionIter)) { + potential += inversion->getPotential(); + } + return potential; } + void Molecule::addProperty(GenericData* genData) { + properties_.addProperty(genData); + } + + void Molecule::removeProperty(const std::string& propName) { + properties_.removeProperty(propName); + } + + void Molecule::clearProperties() { + properties_.clearProperties(); + } + + std::vector Molecule::getPropertyNames() { + return properties_.getPropertyNames(); + } + + std::vector Molecule::getProperties() { + return properties_.getProperties(); + } + + GenericData* Molecule::getPropertyByName(const std::string& propName) { + return properties_.getPropertyByName(propName); + } + std::ostream& operator <<(std::ostream& o, Molecule& mol) { o << std::endl; o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl; @@ -267,11 +308,13 @@ namespace oopse { o << mol.getNBonds() << " bonds" << std::endl; o << mol.getNBends() << " bends" << std::endl; o << mol.getNTorsions() << " torsions" << std::endl; + o << mol.getNInversions() << " inversions" << std::endl; o << mol.getNRigidBodies() << " rigid bodies" << std::endl; - o << mol.getNIntegrableObjects() << "integrable objects" << std::endl; - o << mol.getNCutoffGroups() << "cutoff groups" << std::endl; - o << mol.getNConstraintPairs() << "constraint pairs" << std::endl; + o << mol.getNIntegrableObjects() << " integrable objects" << std::endl; + o << mol.getNCutoffGroups() << " cutoff groups" << std::endl; + o << mol.getNConstraintPairs() << " constraint pairs" << std::endl; + o << mol.getNFluctuatingCharges() << " fluctuating charges" << std::endl; return o; } -}//end namespace oopse +}//end namespace OpenMD