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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 |
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< |
* 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 |
|
* |
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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 |
|
* University of Notre Dame has been advised of the possibility of |
| 30 |
|
* such damages. |
| 31 |
+ |
* |
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+ |
* 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). |
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*/ |
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|
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/** |
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|
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#ifndef PRIMITIVES_BEND_HPP |
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#define PRIMITIVES_BEND_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/BendType.hpp" |
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– |
namespace oopse { |
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|
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< |
class Bend { |
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> |
namespace OpenMD { |
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> |
struct BendData { |
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> |
RealType angle; |
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> |
RealType potential; |
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> |
}; |
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> |
|
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> |
struct BendDataSet { |
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> |
RealType deltaV; |
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> |
BendData prev; |
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> |
BendData curr; |
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> |
}; |
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> |
|
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> |
class Bend : public ShortRangeInteraction { |
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public: |
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+ |
using ShortRangeInteraction::getValue; |
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+ |
using ShortRangeInteraction::getPrevValue; |
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Bend(Atom* atom1, Atom* atom2, Atom* atom3, BendType* bt) |
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: atom1_(atom1), atom2_(atom2), atom3_(atom3), bendType_(bt) {} |
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< |
|
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> |
: ShortRangeInteraction(), bendType_(bt) { |
| 76 |
> |
atoms_.resize(3); |
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> |
atoms_[0] = atom1; |
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> |
atoms_[1] = atom2; |
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> |
atoms_[2] = atom3; |
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> |
} |
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> |
|
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|
virtual ~Bend() {} |
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< |
virtual void calcForce(); |
| 84 |
< |
|
| 85 |
< |
double getPotential() { |
| 86 |
< |
return potential_; |
| 83 |
> |
virtual void calcForce(RealType& angle, bool doParticlePot); |
| 84 |
> |
|
| 85 |
> |
RealType getValue(int snapshotNo) { |
| 86 |
> |
Vector3d pos1 = atoms_[0]->getPos(snapshotNo); |
| 87 |
> |
Vector3d pos2 = atoms_[1]->getPos(snapshotNo); |
| 88 |
> |
Vector3d pos3 = atoms_[2]->getPos(snapshotNo); |
| 89 |
> |
|
| 90 |
> |
Vector3d r21 = pos1 - pos2; |
| 91 |
> |
RealType d21 = r21.length(); |
| 92 |
> |
|
| 93 |
> |
Vector3d r23 = pos3 - pos2; |
| 94 |
> |
RealType d23 = r23.length(); |
| 95 |
> |
|
| 96 |
> |
RealType cosTheta = dot(r21, r23) / (d21 * d23); |
| 97 |
> |
|
| 98 |
> |
//check roundoff |
| 99 |
> |
if (cosTheta > 1.0) { |
| 100 |
> |
cosTheta = 1.0; |
| 101 |
> |
} else if (cosTheta < -1.0) { |
| 102 |
> |
cosTheta = -1.0; |
| 103 |
> |
} |
| 104 |
> |
|
| 105 |
> |
return acos(cosTheta); |
| 106 |
|
} |
| 107 |
|
|
| 108 |
+ |
|
| 109 |
+ |
RealType getPotential() { |
| 110 |
+ |
return potential_; |
| 111 |
+ |
} |
| 112 |
+ |
|
| 113 |
|
Atom* getAtomA() { |
| 114 |
< |
return atom1_; |
| 114 |
> |
return atoms_[0]; |
| 115 |
|
} |
| 116 |
< |
|
| 116 |
> |
|
| 117 |
|
Atom* getAtomB() { |
| 118 |
< |
return atom2_; |
| 118 |
> |
return atoms_[1]; |
| 119 |
|
} |
| 120 |
< |
|
| 120 |
> |
|
| 121 |
|
Atom* getAtomC() { |
| 122 |
< |
return atom3_; |
| 122 |
> |
return atoms_[2]; |
| 123 |
|
} |
| 124 |
< |
|
| 124 |
> |
|
| 125 |
|
BendType * getBendType() { |
| 126 |
|
return bendType_; |
| 127 |
|
} |
| 128 |
+ |
|
| 129 |
+ |
virtual std::string getName() { return name_;} |
| 130 |
+ |
/** Sets the name of this bend for selections */ |
| 131 |
+ |
virtual void setName(const std::string& name) { name_ = name;} |
| 132 |
|
|
| 133 |
+ |
void accept(BaseVisitor* v) { |
| 134 |
+ |
v->visit(this); |
| 135 |
+ |
} |
| 136 |
+ |
|
| 137 |
|
protected: |
| 138 |
< |
|
| 139 |
< |
double potential_; |
| 87 |
< |
Atom* atom1_; |
| 88 |
< |
Atom* atom2_; |
| 89 |
< |
Atom* atom3_; |
| 138 |
> |
|
| 139 |
> |
RealType potential_; |
| 140 |
|
BendType* bendType_; /**< bend type */ |
| 141 |
+ |
std::string name_; |
| 142 |
|
|
| 143 |
|
}; |
| 144 |
< |
|
| 94 |
< |
|
| 95 |
< |
|
| 96 |
< |
} //end namespace oopse |
| 144 |
> |
} //end namespace OpenMD |
| 145 |
|
#endif //PRIMITIVES_BEND_HPP |
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|
|
