| 6 |
|
* 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 |
|
* 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; |
| 84 |
> |
typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator; |
| 85 |
|
typedef std::vector<ConstraintPair*>::iterator ConstraintPairIterator; |
| 86 |
|
typedef std::vector<ConstraintElem*>::iterator ConstraintElemIterator; |
| 87 |
< |
|
| 88 |
< |
|
| 87 |
> |
|
| 88 |
> |
|
| 89 |
|
Molecule(int stampId, int globalIndex, const std::string& molName); |
| 90 |
|
virtual ~Molecule(); |
| 91 |
|
|
| 96 |
|
int getGlobalIndex() { |
| 97 |
|
return globalIndex_; |
| 98 |
|
} |
| 99 |
< |
|
| 99 |
> |
|
| 100 |
|
/** |
| 101 |
|
* Returns the stamp id of this molecule |
| 102 |
< |
* @note Ideally, every molecule should keep a pointer of its molecule stamp instead of its |
| 103 |
< |
* stamp id. However, the pointer will become invalid, if the molecule migrate to other processor. |
| 102 |
> |
* @note Ideally, every molecule should keep a pointer of its |
| 103 |
> |
* molecule stamp instead of its stamp id. However, the pointer |
| 104 |
> |
* will become invalid, if the molecule migrate to other |
| 105 |
> |
* processor. |
| 106 |
|
*/ |
| 107 |
|
int getStampId() { |
| 108 |
|
return stampId_; |
| 109 |
|
} |
| 110 |
< |
|
| 110 |
> |
|
| 111 |
|
/** Returns the name of the molecule */ |
| 112 |
|
std::string getType() { |
| 113 |
|
return moleculeName_; |
| 114 |
|
} |
| 115 |
< |
|
| 115 |
> |
|
| 116 |
|
/** |
| 117 |
|
* Sets the global index of this molecule. |
| 118 |
|
* @param new global index to be set |
| 120 |
|
void setGlobalIndex(int index) { |
| 121 |
|
globalIndex_ = index; |
| 122 |
|
} |
| 123 |
< |
|
| 124 |
< |
|
| 123 |
> |
|
| 124 |
> |
|
| 125 |
|
/** add an atom into this molecule */ |
| 126 |
|
void addAtom(Atom* atom); |
| 127 |
< |
|
| 127 |
> |
|
| 128 |
|
/** add a bond into this molecule */ |
| 129 |
|
void addBond(Bond* bond); |
| 130 |
< |
|
| 130 |
> |
|
| 131 |
|
/** add a bend into this molecule */ |
| 132 |
|
void addBend(Bend* bend); |
| 133 |
< |
|
| 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); |
| 142 |
< |
|
| 142 |
> |
|
| 143 |
|
/** add a cutoff group into this molecule */ |
| 144 |
|
void addCutoffGroup(CutoffGroup* cp); |
| 145 |
< |
|
| 145 |
> |
|
| 146 |
|
void addConstraintPair(ConstraintPair* consPair); |
| 147 |
< |
|
| 147 |
> |
|
| 148 |
|
void addConstraintElem(ConstraintElem* consElem); |
| 149 |
< |
|
| 149 |
> |
|
| 150 |
|
/** */ |
| 151 |
|
void complete(); |
| 152 |
< |
|
| 152 |
> |
|
| 153 |
|
/** Returns the total number of atoms in this molecule */ |
| 154 |
|
unsigned int getNAtoms() { |
| 155 |
|
return atoms_.size(); |
| 156 |
|
} |
| 157 |
< |
|
| 157 |
> |
|
| 158 |
|
/** Returns the total number of bonds in this molecule */ |
| 159 |
|
unsigned int getNBonds(){ |
| 160 |
|
return bonds_.size(); |
| 161 |
|
} |
| 162 |
< |
|
| 162 |
> |
|
| 163 |
|
/** Returns the total number of bends in this molecule */ |
| 164 |
|
unsigned int getNBends() { |
| 165 |
|
return bends_.size(); |
| 166 |
|
} |
| 167 |
< |
|
| 167 |
> |
|
| 168 |
|
/** Returns the total number of torsions in this molecule */ |
| 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() { |
| 180 |
|
return rigidBodies_.size(); |
| 181 |
|
} |
| 182 |
< |
|
| 182 |
> |
|
| 183 |
|
/** Returns the total number of integrable objects in this molecule */ |
| 184 |
|
unsigned int getNIntegrableObjects() { |
| 185 |
|
return integrableObjects_.size(); |
| 186 |
|
} |
| 187 |
< |
|
| 187 |
> |
|
| 188 |
|
/** Returns the total number of cutoff groups in this molecule */ |
| 189 |
|
unsigned int getNCutoffGroups() { |
| 190 |
|
return cutoffGroups_.size(); |
| 191 |
|
} |
| 192 |
< |
|
| 192 |
> |
|
| 193 |
|
/** Returns the total number of constraints in this molecule */ |
| 194 |
|
unsigned int getNConstraintPairs() { |
| 195 |
|
return constraintPairs_.size(); |
| 196 |
|
} |
| 197 |
< |
|
| 197 |
> |
|
| 198 |
|
Atom* getAtomAt(unsigned int i) { |
| 199 |
|
assert(i < atoms_.size()); |
| 200 |
|
return atoms_[i]; |
| 201 |
|
} |
| 202 |
< |
|
| 202 |
> |
|
| 203 |
|
RigidBody* getRigidBodyAt(unsigned int i) { |
| 204 |
|
assert(i < rigidBodies_.size()); |
| 205 |
|
return rigidBodies_[i]; |
| 206 |
|
} |
| 207 |
< |
|
| 207 |
> |
|
| 208 |
|
Atom* beginAtom(std::vector<Atom*>::iterator& i) { |
| 209 |
|
i = atoms_.begin(); |
| 210 |
|
return (i == atoms_.end()) ? NULL : *i; |
| 211 |
|
} |
| 212 |
< |
|
| 212 |
> |
|
| 213 |
|
Atom* nextAtom(std::vector<Atom*>::iterator& i) { |
| 214 |
|
++i; |
| 215 |
|
return (i == atoms_.end()) ? NULL : *i; |
| 216 |
|
} |
| 217 |
< |
|
| 217 |
> |
|
| 218 |
|
Bond* beginBond(std::vector<Bond*>::iterator& i) { |
| 219 |
|
i = bonds_.begin(); |
| 220 |
|
return (i == bonds_.end()) ? NULL : *i; |
| 221 |
|
} |
| 222 |
< |
|
| 222 |
> |
|
| 223 |
|
Bond* nextBond(std::vector<Bond*>::iterator& i) { |
| 224 |
|
++i; |
| 225 |
|
return (i == bonds_.end()) ? NULL : *i; |
| 226 |
< |
|
| 226 |
> |
|
| 227 |
|
} |
| 228 |
< |
|
| 228 |
> |
|
| 229 |
|
Bend* beginBend(std::vector<Bend*>::iterator& i) { |
| 230 |
|
i = bends_.begin(); |
| 231 |
|
return (i == bends_.end()) ? NULL : *i; |
| 232 |
|
} |
| 233 |
< |
|
| 233 |
> |
|
| 234 |
|
Bend* nextBend(std::vector<Bend*>::iterator& i) { |
| 235 |
|
++i; |
| 236 |
|
return (i == bends_.end()) ? NULL : *i; |
| 237 |
|
} |
| 238 |
< |
|
| 238 |
> |
|
| 239 |
|
Torsion* beginTorsion(std::vector<Torsion*>::iterator& i) { |
| 240 |
|
i = torsions_.begin(); |
| 241 |
|
return (i == torsions_.end()) ? NULL : *i; |
| 242 |
|
} |
| 243 |
< |
|
| 243 |
> |
|
| 244 |
|
Torsion* nextTorsion(std::vector<Torsion*>::iterator& i) { |
| 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; |
| 262 |
|
} |
| 263 |
< |
|
| 263 |
> |
|
| 264 |
|
RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i) { |
| 265 |
|
++i; |
| 266 |
|
return (i == rigidBodies_.end()) ? NULL : *i; |
| 267 |
|
} |
| 268 |
< |
|
| 268 |
> |
|
| 269 |
|
StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i) { |
| 270 |
|
i = integrableObjects_.begin(); |
| 271 |
|
return (i == integrableObjects_.end()) ? NULL : *i; |
| 272 |
|
} |
| 273 |
< |
|
| 273 |
> |
|
| 274 |
|
StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i) { |
| 275 |
|
++i; |
| 276 |
|
return (i == integrableObjects_.end()) ? NULL : *i; |
| 277 |
|
} |
| 278 |
< |
|
| 278 |
> |
|
| 279 |
|
CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i) { |
| 280 |
|
i = cutoffGroups_.begin(); |
| 281 |
|
return (i == cutoffGroups_.end()) ? NULL : *i; |
| 282 |
|
} |
| 283 |
|
|
| 284 |
< |
CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) { |
| 284 |
> |
CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) { |
| 285 |
|
++i; |
| 286 |
|
return (i == cutoffGroups_.end()) ? NULL : *i; |
| 287 |
|
} |
| 288 |
< |
|
| 288 |
> |
|
| 289 |
|
ConstraintPair* beginConstraintPair(std::vector<ConstraintPair*>::iterator& i) { |
| 290 |
|
i = constraintPairs_.begin(); |
| 291 |
|
return (i == constraintPairs_.end()) ? NULL : *i; |
| 292 |
|
} |
| 293 |
< |
|
| 293 |
> |
|
| 294 |
|
ConstraintPair* nextConstraintPair(std::vector<ConstraintPair*>::iterator& i) { |
| 295 |
|
++i; |
| 296 |
|
return (i == constraintPairs_.end()) ? NULL : *i; |
| 297 |
|
} |
| 298 |
< |
|
| 298 |
> |
|
| 299 |
|
ConstraintElem* beginConstraintElem(std::vector<ConstraintElem*>::iterator& i) { |
| 300 |
|
i = constraintElems_.begin(); |
| 301 |
|
return (i == constraintElems_.end()) ? NULL : *i; |
| 302 |
|
} |
| 303 |
< |
|
| 303 |
> |
|
| 304 |
|
ConstraintElem* nextConstraintElem(std::vector<ConstraintElem*>::iterator& i) { |
| 305 |
|
++i; |
| 306 |
|
return (i == constraintElems_.end()) ? NULL : *i; |
| 307 |
|
} |
| 308 |
|
|
| 309 |
< |
/** return the total potential energy of short range interaction of this molecule */ |
| 309 |
> |
/** |
| 310 |
> |
* Returns the total potential energy of short range interaction |
| 311 |
> |
* of this molecule |
| 312 |
> |
*/ |
| 313 |
|
RealType getPotential(); |
| 314 |
< |
|
| 314 |
> |
|
| 315 |
|
/** get total mass of this molecule */ |
| 316 |
|
RealType getMass(); |
| 317 |
< |
|
| 317 |
> |
|
| 318 |
|
/** return the center of mass of this molecule */ |
| 319 |
|
Vector3d getCom(); |
| 320 |
< |
|
| 320 |
> |
|
| 321 |
|
/** Moves the center of this molecule */ |
| 322 |
|
void moveCom(const Vector3d& delta); |
| 323 |
< |
|
| 323 |
> |
|
| 324 |
|
/** Returns the velocity of center of mass of this molecule */ |
| 325 |
|
Vector3d getComVel(); |
| 326 |
|
|
| 329 |
|
} |
| 330 |
|
|
| 331 |
|
friend std::ostream& operator <<(std::ostream& o, Molecule& mol); |
| 332 |
< |
|
| 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 |
< |
|
| 372 |
> |
|
| 373 |
|
int globalIndex_; |
| 374 |
< |
|
| 374 |
> |
|
| 375 |
|
std::vector<Atom*> atoms_; |
| 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 // |
