| 6 |
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* redistribute this software in source and binary code form, provided |
| 7 |
|
* that the following conditions are met: |
| 8 |
|
* |
| 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 |
< |
* |
| 18 |
< |
* 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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
/** |
| 59 |
|
#include "primitives/Bond.hpp" |
| 60 |
|
#include "primitives/Bend.hpp" |
| 61 |
|
#include "primitives/Torsion.hpp" |
| 62 |
+ |
#include "primitives/Inversion.hpp" |
| 63 |
|
#include "primitives/CutoffGroup.hpp" |
| 64 |
+ |
#include "utils/PropertyMap.hpp" |
| 65 |
|
|
| 66 |
< |
namespace oopse{ |
| 66 |
> |
namespace OpenMD{ |
| 67 |
|
|
| 68 |
|
class Constraint; |
| 69 |
|
|
| 78 |
|
typedef std::vector<Bond*>::iterator BondIterator; |
| 79 |
|
typedef std::vector<Bend*>::iterator BendIterator; |
| 80 |
|
typedef std::vector<Torsion*>::iterator TorsionIterator; |
| 81 |
+ |
typedef std::vector<Inversion*>::iterator InversionIterator; |
| 82 |
|
typedef std::vector<RigidBody*>::iterator RigidBodyIterator; |
| 83 |
|
typedef std::vector<CutoffGroup*>::iterator CutoffGroupIterator; |
| 84 |
|
typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator; |
| 88 |
|
|
| 89 |
|
Molecule(int stampId, int globalIndex, const std::string& molName); |
| 90 |
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virtual ~Molecule(); |
| 91 |
< |
|
| 91 |
> |
|
| 92 |
|
/** |
| 93 |
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* Returns the global index of this molecule. |
| 94 |
|
* @return the global index of this molecule |
| 133 |
|
|
| 134 |
|
/** add a torsion into this molecule*/ |
| 135 |
|
void addTorsion(Torsion* torsion); |
| 136 |
+ |
|
| 137 |
+ |
/** add an improper torsion into this molecule*/ |
| 138 |
+ |
void addInversion(Inversion* inversion); |
| 139 |
|
|
| 140 |
|
/** add a rigidbody into this molecule */ |
| 141 |
|
void addRigidBody(RigidBody *rb); |
| 169 |
|
unsigned int getNTorsions() { |
| 170 |
|
return torsions_.size(); |
| 171 |
|
} |
| 172 |
+ |
|
| 173 |
+ |
/** Returns the total number of improper torsions in this molecule */ |
| 174 |
+ |
unsigned int getNInversions() { |
| 175 |
+ |
return inversions_.size(); |
| 176 |
+ |
} |
| 177 |
|
|
| 178 |
|
/** Returns the total number of rigid bodies in this molecule */ |
| 179 |
|
unsigned int getNRigidBodies() { |
| 245 |
|
++i; |
| 246 |
|
return (i == torsions_.end()) ? NULL : *i; |
| 247 |
|
} |
| 248 |
+ |
|
| 249 |
+ |
Inversion* beginInversion(std::vector<Inversion*>::iterator& i) { |
| 250 |
+ |
i = inversions_.begin(); |
| 251 |
+ |
return (i == inversions_.end()) ? NULL : *i; |
| 252 |
+ |
} |
| 253 |
|
|
| 254 |
+ |
Inversion* nextInversion(std::vector<Inversion*>::iterator& i) { |
| 255 |
+ |
++i; |
| 256 |
+ |
return (i == inversions_.end()) ? NULL : *i; |
| 257 |
+ |
} |
| 258 |
+ |
|
| 259 |
|
RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i) { |
| 260 |
|
i = rigidBodies_.begin(); |
| 261 |
|
return (i == rigidBodies_.end()) ? NULL : *i; |
| 305 |
|
++i; |
| 306 |
|
return (i == constraintElems_.end()) ? NULL : *i; |
| 307 |
|
} |
| 308 |
< |
|
| 308 |
> |
|
| 309 |
|
/** |
| 310 |
|
* Returns the total potential energy of short range interaction |
| 311 |
|
* of this molecule |
| 329 |
|
} |
| 330 |
|
|
| 331 |
|
friend std::ostream& operator <<(std::ostream& o, Molecule& mol); |
| 332 |
+ |
|
| 333 |
+ |
//below functions are just forward functions |
| 334 |
+ |
/** |
| 335 |
+ |
* Adds property into property map |
| 336 |
+ |
* @param genData GenericData to be added into PropertyMap |
| 337 |
+ |
*/ |
| 338 |
+ |
void addProperty(GenericData* genData); |
| 339 |
+ |
|
| 340 |
+ |
/** |
| 341 |
+ |
* Removes property from PropertyMap by name |
| 342 |
+ |
* @param propName the name of property to be removed |
| 343 |
+ |
*/ |
| 344 |
+ |
void removeProperty(const std::string& propName); |
| 345 |
+ |
|
| 346 |
+ |
/** |
| 347 |
+ |
* clear all of the properties |
| 348 |
+ |
*/ |
| 349 |
+ |
void clearProperties(); |
| 350 |
+ |
|
| 351 |
+ |
/** |
| 352 |
+ |
* Returns all names of properties |
| 353 |
+ |
* @return all names of properties |
| 354 |
+ |
*/ |
| 355 |
+ |
std::vector<std::string> getPropertyNames(); |
| 356 |
+ |
|
| 357 |
+ |
/** |
| 358 |
+ |
* Returns all of the properties in PropertyMap |
| 359 |
+ |
* @return all of the properties in PropertyMap |
| 360 |
+ |
*/ |
| 361 |
+ |
std::vector<GenericData*> getProperties(); |
| 362 |
+ |
|
| 363 |
+ |
/** |
| 364 |
+ |
* Returns property |
| 365 |
+ |
* @param propName name of property |
| 366 |
+ |
* @return a pointer point to property with propName. If no property named propName |
| 367 |
+ |
* exists, return NULL |
| 368 |
+ |
*/ |
| 369 |
+ |
GenericData* getPropertyByName(const std::string& propName); |
| 370 |
|
|
| 371 |
|
private: |
| 372 |
|
|
| 376 |
|
std::vector<Bond*> bonds_; |
| 377 |
|
std::vector<Bend*> bends_; |
| 378 |
|
std::vector<Torsion*> torsions_; |
| 379 |
+ |
std::vector<Inversion*> inversions_; |
| 380 |
|
std::vector<RigidBody*> rigidBodies_; |
| 381 |
|
std::vector<StuntDouble*> integrableObjects_; |
| 382 |
|
std::vector<CutoffGroup*> cutoffGroups_; |
| 384 |
|
std::vector<ConstraintElem*> constraintElems_; |
| 385 |
|
int stampId_; |
| 386 |
|
std::string moleculeName_; |
| 387 |
+ |
PropertyMap properties_; |
| 388 |
+ |
|
| 389 |
|
}; |
| 390 |
|
|
| 391 |
< |
} //namespace oopse |
| 391 |
> |
} //namespace OpenMD |
| 392 |
|
#endif // |
