| 6 |
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* redistribute this software in source and binary code form, provided |
| 7 |
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* that the following conditions are met: |
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|
* |
| 9 |
< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
| 11 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
| 13 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
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< |
* 2. Redistributions of source code must retain the above copyright |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
|
* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
|
* distribution. |
| 28 |
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* arising out of the use of or inability to use software, even if the |
| 29 |
|
* University of Notre Dame has been advised of the possibility of |
| 30 |
|
* such damages. |
| 31 |
+ |
* |
| 32 |
+ |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
+ |
* research, please cite the appropriate papers when you publish your |
| 34 |
+ |
* work. Good starting points are: |
| 35 |
+ |
* |
| 36 |
+ |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
+ |
* [4] Vardeman & Gezelter, in progress (2009). |
| 40 |
|
*/ |
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|
|
| 42 |
|
/** |
| 53 |
|
#include "utils/MemoryUtils.hpp" |
| 54 |
|
#include "utils/simError.h" |
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|
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< |
namespace oopse { |
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> |
namespace OpenMD { |
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Molecule::Molecule(int stampId, int globalIndex, const std::string& molName) |
| 58 |
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: stampId_(stampId), globalIndex_(globalIndex), moleculeName_(molName) { |
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} |
| 64 |
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MemoryUtils::deletePointers(bonds_); |
| 65 |
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MemoryUtils::deletePointers(bends_); |
| 66 |
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MemoryUtils::deletePointers(torsions_); |
| 67 |
+ |
MemoryUtils::deletePointers(inversions_); |
| 68 |
|
MemoryUtils::deletePointers(rigidBodies_); |
| 69 |
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MemoryUtils::deletePointers(cutoffGroups_); |
| 70 |
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MemoryUtils::deletePointers(constraintPairs_); |
| 98 |
|
torsions_.push_back(torsion); |
| 99 |
|
} |
| 100 |
|
} |
| 101 |
+ |
|
| 102 |
+ |
void Molecule::addInversion(Inversion* inversion) { |
| 103 |
+ |
if (std::find(inversions_.begin(), inversions_.end(), inversion) == |
| 104 |
+ |
inversions_.end()) { |
| 105 |
+ |
inversions_.push_back(inversion); |
| 106 |
+ |
} |
| 107 |
+ |
} |
| 108 |
|
|
| 109 |
|
void Molecule::addRigidBody(RigidBody *rb) { |
| 110 |
|
if (std::find(rigidBodies_.begin(), rigidBodies_.end(), rb) == |
| 245 |
|
Bond* bond; |
| 246 |
|
Bend* bend; |
| 247 |
|
Torsion* torsion; |
| 248 |
+ |
Inversion* inversion; |
| 249 |
|
Molecule::BondIterator bondIter;; |
| 250 |
|
Molecule::BendIterator bendIter; |
| 251 |
|
Molecule::TorsionIterator torsionIter; |
| 252 |
+ |
Molecule::InversionIterator inversionIter; |
| 253 |
|
|
| 254 |
|
RealType potential = 0.0; |
| 255 |
|
|
| 266 |
|
potential += torsion->getPotential(); |
| 267 |
|
} |
| 268 |
|
|
| 269 |
+ |
for (inversion = beginInversion(inversionIter); torsion != NULL; |
| 270 |
+ |
inversion = nextInversion(inversionIter)) { |
| 271 |
+ |
potential += inversion->getPotential(); |
| 272 |
+ |
} |
| 273 |
+ |
|
| 274 |
|
return potential; |
| 275 |
|
|
| 276 |
|
} |
| 277 |
|
|
| 278 |
+ |
void Molecule::addProperty(GenericData* genData) { |
| 279 |
+ |
properties_.addProperty(genData); |
| 280 |
+ |
} |
| 281 |
+ |
|
| 282 |
+ |
void Molecule::removeProperty(const std::string& propName) { |
| 283 |
+ |
properties_.removeProperty(propName); |
| 284 |
+ |
} |
| 285 |
+ |
|
| 286 |
+ |
void Molecule::clearProperties() { |
| 287 |
+ |
properties_.clearProperties(); |
| 288 |
+ |
} |
| 289 |
+ |
|
| 290 |
+ |
std::vector<std::string> Molecule::getPropertyNames() { |
| 291 |
+ |
return properties_.getPropertyNames(); |
| 292 |
+ |
} |
| 293 |
+ |
|
| 294 |
+ |
std::vector<GenericData*> Molecule::getProperties() { |
| 295 |
+ |
return properties_.getProperties(); |
| 296 |
+ |
} |
| 297 |
+ |
|
| 298 |
+ |
GenericData* Molecule::getPropertyByName(const std::string& propName) { |
| 299 |
+ |
return properties_.getPropertyByName(propName); |
| 300 |
+ |
} |
| 301 |
+ |
|
| 302 |
+ |
|
| 303 |
+ |
|
| 304 |
+ |
|
| 305 |
|
std::ostream& operator <<(std::ostream& o, Molecule& mol) { |
| 306 |
|
o << std::endl; |
| 307 |
|
o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl; |
| 309 |
|
o << mol.getNBonds() << " bonds" << std::endl; |
| 310 |
|
o << mol.getNBends() << " bends" << std::endl; |
| 311 |
|
o << mol.getNTorsions() << " torsions" << std::endl; |
| 312 |
+ |
o << mol.getNInversions() << " inversions" << std::endl; |
| 313 |
|
o << mol.getNRigidBodies() << " rigid bodies" << std::endl; |
| 314 |
|
o << mol.getNIntegrableObjects() << "integrable objects" << std::endl; |
| 315 |
|
o << mol.getNCutoffGroups() << "cutoff groups" << std::endl; |
| 317 |
|
return o; |
| 318 |
|
} |
| 319 |
|
|
| 320 |
< |
}//end namespace oopse |
| 320 |
> |
}//end namespace OpenMD |
