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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 |
< |
* |
| 18 |
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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 |
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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 |
| 13 |
|
* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
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* distribution. |
| 28 |
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* arising out of the use of or inability to use software, even if the |
| 29 |
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* University of Notre Dame has been advised of the possibility of |
| 30 |
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* such damages. |
| 31 |
+ |
* |
| 32 |
+ |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
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* 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 |
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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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#ifndef PRIMITIVES_BOND_HPP |
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#define PRIMITIVES_BOND_HPP |
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|
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+ |
#include "primitives/ShortRangeInteraction.hpp" |
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#include "primitives/Atom.hpp" |
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#include "types/BondType.hpp" |
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|
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namespace oopse { |
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|
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class Bond { |
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> |
namespace OpenMD { |
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> |
|
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> |
class Bond : public ShortRangeInteraction { |
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public: |
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Bond(Atom* atom1, Atom* atom2, BondType* bt) : atom1_(atom1), atom2_(atom2), bondType_(bt) {} |
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> |
Bond(Atom* atom1, Atom* atom2, BondType* bt) : ShortRangeInteraction(), |
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> |
bondType_(bt) { |
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> |
atoms_.resize(2); |
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> |
atoms_[0] = atom1; |
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> |
atoms_[1] = atom2; |
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} |
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virtual ~Bond() {} |
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void calcForce() { |
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> |
void calcForce(bool doParticlePot) { |
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RealType len; |
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RealType dvdr; |
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Vector3d r12; |
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Vector3d force; |
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< |
|
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r12 = atom2_->getPos() - atom1_->getPos(); |
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> |
|
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> |
r12 = atoms_[1]->getPos() - atoms_[0]->getPos(); |
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|
len = r12.length(); |
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bondType_->calcForce(len, potential_, dvdr); |
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|
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> |
|
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force = r12 * (-dvdr / len); |
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|
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atom1_->addFrc(-force); |
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atom2_->addFrc(force); |
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> |
|
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> |
atoms_[0]->addFrc(-force); |
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> |
atoms_[1]->addFrc(force); |
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> |
if (doParticlePot) { |
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> |
atoms_[0]->addParticlePot(potential_); |
| 85 |
> |
atoms_[1]->addParticlePot(potential_); |
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> |
} |
| 87 |
|
} |
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< |
|
| 88 |
> |
|
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> |
RealType getValue(int snap) { |
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> |
Vector3d r12 = atoms_[1]->getPos(snap) - atoms_[0]->getPos(snap); |
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> |
return r12.length(); |
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> |
} |
| 93 |
> |
|
| 94 |
|
RealType getPotential() { |
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|
return potential_; |
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} |
| 97 |
< |
|
| 97 |
> |
|
| 98 |
|
Atom* getAtomA() { |
| 99 |
< |
return atom1_; |
| 99 |
> |
return atoms_[0]; |
| 100 |
|
} |
| 101 |
< |
|
| 101 |
> |
|
| 102 |
|
Atom* getAtomB() { |
| 103 |
< |
return atom2_; |
| 103 |
> |
return atoms_[1]; |
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|
} |
| 105 |
< |
|
| 105 |
> |
|
| 106 |
|
BondType* getBondType() { |
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|
return bondType_; |
| 108 |
|
} |
| 109 |
< |
|
| 109 |
> |
|
| 110 |
> |
virtual std::string getName() { return name_;} |
| 111 |
> |
/** Sets the name of this bond for selections */ |
| 112 |
> |
virtual void setName(const std::string& name) { name_ = name; } |
| 113 |
> |
|
| 114 |
> |
void accept(BaseVisitor* v) { |
| 115 |
> |
v->visit(this); |
| 116 |
> |
} |
| 117 |
> |
|
| 118 |
|
private: |
| 119 |
|
RealType potential_; |
| 96 |
– |
Atom* atom1_; |
| 97 |
– |
Atom* atom2_; |
| 120 |
|
BondType* bondType_; /**< bond type */ |
| 121 |
+ |
std::string name_; |
| 122 |
|
|
| 123 |
|
}; |
| 124 |
< |
|
| 102 |
< |
|
| 103 |
< |
|
| 104 |
< |
} //end namespace oopse |
| 124 |
> |
} //end namespace OpenMD |
| 125 |
|
#endif //PRIMITIVES_BOND_HPP |
