| 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). |
| 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 |
|
/** |
| 51 |
|
#ifndef PRIMITIVES_BOND_HPP |
| 52 |
|
#define PRIMITIVES_BOND_HPP |
| 53 |
|
|
| 54 |
+ |
#include "primitives/ShortRangeInteraction.hpp" |
| 55 |
|
#include "primitives/Atom.hpp" |
| 56 |
|
#include "types/BondType.hpp" |
| 57 |
|
|
| 58 |
|
namespace OpenMD { |
| 59 |
|
|
| 60 |
< |
class Bond { |
| 60 |
> |
class Bond : public ShortRangeInteraction { |
| 61 |
|
public: |
| 62 |
< |
Bond(Atom* atom1, Atom* atom2, BondType* bt) : atom1_(atom1), |
| 63 |
< |
atom2_(atom2), |
| 64 |
< |
bondType_(bt) {} |
| 62 |
> |
using ShortRangeInteraction::getValue; |
| 63 |
> |
using ShortRangeInteraction::getPrevValue; |
| 64 |
> |
Bond(Atom* atom1, Atom* atom2, BondType* bt) : ShortRangeInteraction(), |
| 65 |
> |
bondType_(bt) { |
| 66 |
> |
atoms_.resize(2); |
| 67 |
> |
atoms_[0] = atom1; |
| 68 |
> |
atoms_[1] = atom2; |
| 69 |
> |
} |
| 70 |
|
virtual ~Bond() {} |
| 71 |
< |
void calcForce() { |
| 71 |
> |
void calcForce(bool doParticlePot) { |
| 72 |
|
RealType len; |
| 73 |
|
RealType dvdr; |
| 74 |
|
Vector3d r12; |
| 75 |
|
Vector3d force; |
| 76 |
|
|
| 77 |
< |
r12 = atom2_->getPos() - atom1_->getPos(); |
| 77 |
> |
r12 = atoms_[1]->getPos() - atoms_[0]->getPos(); |
| 78 |
|
len = r12.length(); |
| 79 |
|
bondType_->calcForce(len, potential_, dvdr); |
| 80 |
|
|
| 81 |
|
force = r12 * (-dvdr / len); |
| 82 |
|
|
| 83 |
< |
atom1_->addFrc(-force); |
| 84 |
< |
atom2_->addFrc(force); |
| 85 |
< |
|
| 86 |
< |
atom1_->addParticlePot(potential_); |
| 87 |
< |
atom2_->addParticlePot(potential_); |
| 83 |
> |
atoms_[0]->addFrc(-force); |
| 84 |
> |
atoms_[1]->addFrc(force); |
| 85 |
> |
if (doParticlePot) { |
| 86 |
> |
atoms_[0]->addParticlePot(potential_); |
| 87 |
> |
atoms_[1]->addParticlePot(potential_); |
| 88 |
> |
} |
| 89 |
|
} |
| 90 |
|
|
| 91 |
+ |
RealType getValue(int snap) { |
| 92 |
+ |
Vector3d r12 = atoms_[1]->getPos(snap) - atoms_[0]->getPos(snap); |
| 93 |
+ |
return r12.length(); |
| 94 |
+ |
} |
| 95 |
+ |
|
| 96 |
|
RealType getPotential() { |
| 97 |
|
return potential_; |
| 98 |
|
} |
| 99 |
|
|
| 100 |
|
Atom* getAtomA() { |
| 101 |
< |
return atom1_; |
| 101 |
> |
return atoms_[0]; |
| 102 |
|
} |
| 103 |
|
|
| 104 |
|
Atom* getAtomB() { |
| 105 |
< |
return atom2_; |
| 105 |
> |
return atoms_[1]; |
| 106 |
|
} |
| 107 |
|
|
| 108 |
|
BondType* getBondType() { |
| 109 |
|
return bondType_; |
| 110 |
|
} |
| 111 |
+ |
|
| 112 |
+ |
virtual std::string getName() { return name_;} |
| 113 |
+ |
/** Sets the name of this bond for selections */ |
| 114 |
+ |
virtual void setName(const std::string& name) { name_ = name; } |
| 115 |
+ |
|
| 116 |
+ |
void accept(BaseVisitor* v) { |
| 117 |
+ |
v->visit(this); |
| 118 |
+ |
} |
| 119 |
|
|
| 120 |
|
private: |
| 121 |
|
RealType potential_; |
| 101 |
– |
Atom* atom1_; |
| 102 |
– |
Atom* atom2_; |
| 122 |
|
BondType* bondType_; /**< bond type */ |
| 123 |
< |
|
| 123 |
> |
std::string name_; |
| 124 |
> |
|
| 125 |
|
}; |
| 126 |
|
} //end namespace OpenMD |
| 127 |
|
#endif //PRIMITIVES_BOND_HPP |
