| 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: |
| 8 |
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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 |
< |
* |
| 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, 234107 (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 |
|
/** |
| 63 |
|
#include "primitives/CutoffGroup.hpp" |
| 64 |
|
#include "utils/PropertyMap.hpp" |
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|
|
| 66 |
< |
namespace oopse{ |
| 66 |
> |
namespace OpenMD{ |
| 67 |
|
|
| 68 |
|
class Constraint; |
| 69 |
|
|
| 84 |
|
typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator; |
| 85 |
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typedef std::vector<ConstraintPair*>::iterator ConstraintPairIterator; |
| 86 |
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typedef std::vector<ConstraintElem*>::iterator ConstraintElemIterator; |
| 87 |
+ |
typedef std::vector<Atom*>::iterator FluctuatingChargeIterator; |
| 88 |
|
|
| 89 |
< |
|
| 88 |
< |
Molecule(int stampId, int globalIndex, const std::string& molName); |
| 89 |
> |
Molecule(int stampId, int globalIndex, const std::string& molName, int region); |
| 90 |
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virtual ~Molecule(); |
| 91 |
< |
|
| 91 |
> |
|
| 92 |
|
/** |
| 93 |
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* Returns the global index of this molecule. |
| 94 |
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* @return the global index of this molecule |
| 106 |
|
*/ |
| 107 |
|
int getStampId() { |
| 108 |
|
return stampId_; |
| 109 |
+ |
} |
| 110 |
+ |
int getRegion() { |
| 111 |
+ |
return region_; |
| 112 |
|
} |
| 113 |
|
|
| 114 |
|
/** Returns the name of the molecule */ |
| 118 |
|
|
| 119 |
|
/** |
| 120 |
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* Sets the global index of this molecule. |
| 121 |
< |
* @param new global index to be set |
| 121 |
> |
* @param index new global index to be set |
| 122 |
|
*/ |
| 123 |
|
void setGlobalIndex(int index) { |
| 124 |
|
globalIndex_ = index; |
| 125 |
|
} |
| 126 |
+ |
|
| 127 |
+ |
void setConstrainTotalCharge(bool ctc) { |
| 128 |
+ |
constrainTotalCharge_ = ctc; |
| 129 |
+ |
} |
| 130 |
|
|
| 131 |
< |
|
| 131 |
> |
bool constrainTotalCharge() { |
| 132 |
> |
return constrainTotalCharge_; |
| 133 |
> |
} |
| 134 |
> |
|
| 135 |
|
/** add an atom into this molecule */ |
| 136 |
|
void addAtom(Atom* atom); |
| 137 |
|
|
| 204 |
|
unsigned int getNConstraintPairs() { |
| 205 |
|
return constraintPairs_.size(); |
| 206 |
|
} |
| 207 |
< |
|
| 207 |
> |
|
| 208 |
> |
/** Returns the total number of fluctuating charges in this molecule */ |
| 209 |
> |
unsigned int getNFluctuatingCharges() { |
| 210 |
> |
return fluctuatingCharges_.size(); |
| 211 |
> |
} |
| 212 |
> |
|
| 213 |
|
Atom* getAtomAt(unsigned int i) { |
| 214 |
|
assert(i < atoms_.size()); |
| 215 |
|
return atoms_[i]; |
| 320 |
|
++i; |
| 321 |
|
return (i == constraintElems_.end()) ? NULL : *i; |
| 322 |
|
} |
| 323 |
+ |
|
| 324 |
+ |
Atom* beginFluctuatingCharge(std::vector<Atom*>::iterator& i) { |
| 325 |
+ |
i = fluctuatingCharges_.begin(); |
| 326 |
+ |
return (i == fluctuatingCharges_.end()) ? NULL : *i; |
| 327 |
+ |
} |
| 328 |
+ |
|
| 329 |
+ |
Atom* nextFluctuatingCharge(std::vector<Atom*>::iterator& i) { |
| 330 |
+ |
++i; |
| 331 |
+ |
return (i == fluctuatingCharges_.end()) ? NULL : *i; |
| 332 |
+ |
} |
| 333 |
+ |
|
| 334 |
|
|
| 335 |
|
/** |
| 336 |
|
* Returns the total potential energy of short range interaction |
| 408 |
|
std::vector<CutoffGroup*> cutoffGroups_; |
| 409 |
|
std::vector<ConstraintPair*> constraintPairs_; |
| 410 |
|
std::vector<ConstraintElem*> constraintElems_; |
| 411 |
+ |
std::vector<Atom*> fluctuatingCharges_; |
| 412 |
|
int stampId_; |
| 413 |
+ |
int region_; |
| 414 |
|
std::string moleculeName_; |
| 415 |
|
PropertyMap properties_; |
| 416 |
+ |
bool constrainTotalCharge_; |
| 417 |
|
|
| 418 |
|
}; |
| 419 |
|
|
| 420 |
< |
} //namespace oopse |
| 420 |
> |
} //namespace OpenMD |
| 421 |
|
#endif // |
