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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
| 14 |
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* documentation and/or other materials provided with the |
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* distribution. |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
| 30 |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
| 34 |
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* work. Good starting points are: |
| 35 |
+ |
* |
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+ |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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|
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/** |
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#include "utils/MemoryUtils.hpp" |
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#include "utils/simError.h" |
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|
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namespace oopse { |
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Molecule::Molecule(int stampId, int globalIndex, const std::string& molName) |
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: stampId_(stampId), globalIndex_(globalIndex), moleculeName_(molName) { |
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> |
namespace OpenMD { |
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> |
Molecule::Molecule(int stampId, int globalIndex, const std::string& molName, |
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> |
int region) : stampId_(stampId), |
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> |
globalIndex_(globalIndex), |
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> |
moleculeName_(molName), |
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> |
region_(region), |
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> |
constrainTotalCharge_(false) { |
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} |
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|
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Molecule::~Molecule() { |
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MemoryUtils::deletePointers(cutoffGroups_); |
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MemoryUtils::deletePointers(constraintPairs_); |
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MemoryUtils::deletePointers(constraintElems_); |
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+ |
|
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// integrableObjects_ don't own the objects |
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integrableObjects_.clear(); |
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+ |
fluctuatingCharges_.clear(); |
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|
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} |
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|
| 144 |
|
void Molecule::complete() { |
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|
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std::set<Atom*> rigidAtoms; |
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+ |
Atom* atom; |
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AtomIterator ai; |
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RigidBody* rb; |
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std::vector<RigidBody*>::iterator rbIter; |
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> |
RigidBodyIterator rbIter; |
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|
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< |
|
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> |
// Get list of all the atoms that are part of rigid bodies |
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> |
|
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|
for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) { |
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|
rigidAtoms.insert(rb->getBeginAtomIter(), rb->getEndAtomIter()); |
| 156 |
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} |
| 157 |
|
|
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< |
Atom* atom; |
| 159 |
< |
AtomIterator ai; |
| 158 |
> |
// add any atom that wasn't part of a rigid body to the list of integrableObjects |
| 159 |
> |
|
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|
for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) { |
| 161 |
|
|
| 162 |
< |
if (rigidAtoms.find(*ai) == rigidAtoms.end()) { |
| 162 |
> |
if (rigidAtoms.find(atom) == rigidAtoms.end()) { |
| 163 |
|
|
| 164 |
|
// If an atom does not belong to a rigid body, it is an |
| 165 |
|
// integrable object |
| 166 |
|
|
| 167 |
< |
integrableObjects_.push_back(*ai); |
| 167 |
> |
integrableObjects_.push_back(atom); |
| 168 |
|
} |
| 169 |
|
} |
| 170 |
|
|
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< |
//find all free atoms (which do not belong to rigid bodies) |
| 162 |
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// performs the "difference" operation from set theory, the output |
| 163 |
< |
// range contains a copy of every element that is contained in |
| 164 |
< |
// [allAtoms.begin(), allAtoms.end()) and not contained in |
| 165 |
< |
// [rigidAtoms.begin(), rigidAtoms.end()). |
| 166 |
< |
//std::set_difference(allAtoms.begin(), allAtoms.end(), rigidAtoms.begin(), rigidAtoms.end(), |
| 167 |
< |
// std::back_inserter(integrableObjects_)); |
| 171 |
> |
// then add the rigid bodies themselves to the integrableObjects |
| 172 |
|
|
| 169 |
– |
//if (integrableObjects_.size() != allAtoms.size() - rigidAtoms.size()) { |
| 170 |
– |
// //Some atoms in rigidAtoms are not in allAtoms, something must be wrong |
| 171 |
– |
// sprintf(painCave.errMsg, "Atoms in rigidbody are not in the atom list of the same molecule"); |
| 172 |
– |
// |
| 173 |
– |
// painCave.isFatal = 1; |
| 174 |
– |
// simError(); |
| 175 |
– |
//} |
| 173 |
|
for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) { |
| 174 |
|
integrableObjects_.push_back(rb); |
| 175 |
|
} |
| 176 |
< |
//integrableObjects_.insert(integrableObjects_.end(), rigidBodies_.begin(), rigidBodies_.end()); |
| 176 |
> |
|
| 177 |
> |
// find the atoms that are fluctuating charges and add them to the |
| 178 |
> |
// fluctuatingCharges_ vector |
| 179 |
> |
|
| 180 |
> |
for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) { |
| 181 |
> |
if ( atom->isFluctuatingCharge() ) |
| 182 |
> |
fluctuatingCharges_.push_back( atom ); |
| 183 |
> |
} |
| 184 |
> |
|
| 185 |
|
} |
| 186 |
|
|
| 187 |
|
RealType Molecule::getMass() { |
| 304 |
|
return properties_.getPropertyByName(propName); |
| 305 |
|
} |
| 306 |
|
|
| 302 |
– |
|
| 303 |
– |
|
| 304 |
– |
|
| 307 |
|
std::ostream& operator <<(std::ostream& o, Molecule& mol) { |
| 308 |
|
o << std::endl; |
| 309 |
|
o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl; |
| 313 |
|
o << mol.getNTorsions() << " torsions" << std::endl; |
| 314 |
|
o << mol.getNInversions() << " inversions" << std::endl; |
| 315 |
|
o << mol.getNRigidBodies() << " rigid bodies" << std::endl; |
| 316 |
< |
o << mol.getNIntegrableObjects() << "integrable objects" << std::endl; |
| 317 |
< |
o << mol.getNCutoffGroups() << "cutoff groups" << std::endl; |
| 318 |
< |
o << mol.getNConstraintPairs() << "constraint pairs" << std::endl; |
| 316 |
> |
o << mol.getNIntegrableObjects() << " integrable objects" << std::endl; |
| 317 |
> |
o << mol.getNCutoffGroups() << " cutoff groups" << std::endl; |
| 318 |
> |
o << mol.getNConstraintPairs() << " constraint pairs" << std::endl; |
| 319 |
> |
o << mol.getNFluctuatingCharges() << " fluctuating charges" << std::endl; |
| 320 |
|
return o; |
| 321 |
|
} |
| 322 |
|
|
| 323 |
< |
}//end namespace oopse |
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> |
}//end namespace OpenMD |
