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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 |
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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 |
+ |
* |
| 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 |
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*/ |
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|
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|
/** |
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|
#ifndef PRIMITIVES_TORSION_HPP |
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#define PRIMITIVES_TORSION_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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– |
|
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#include "types/TorsionType.hpp" |
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+ |
#include <limits> |
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|
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< |
namespace oopse { |
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> |
namespace OpenMD { |
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struct TorsionData { |
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RealType angle; |
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RealType potential; |
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/** |
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* @class Torsion Torsion.hpp "types/Torsion.hpp" |
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*/ |
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< |
class Torsion { |
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> |
class Torsion : 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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|
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Torsion(Atom* atom1, Atom* atom2, Atom* atom3, Atom* atom4, TorsionType* tt); |
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virtual ~Torsion() {} |
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< |
virtual void calcForce(RealType& angle); |
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< |
|
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> |
virtual void calcForce(RealType& angle, bool doParticlePot); |
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> |
|
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> |
RealType getValue(int snapshotNo) { |
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> |
Vector3d pos1 = atoms_[0]->getPos(snapshotNo); |
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> |
Vector3d pos2 = atoms_[1]->getPos(snapshotNo); |
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> |
Vector3d pos3 = atoms_[2]->getPos(snapshotNo); |
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> |
Vector3d pos4 = atoms_[3]->getPos(snapshotNo); |
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> |
|
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> |
Vector3d r21 = pos1 - pos2; |
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> |
Vector3d r32 = pos2 - pos3; |
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> |
Vector3d r43 = pos3 - pos4; |
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> |
|
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> |
// Calculate the cross products and distances |
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> |
Vector3d A = cross(r21, r32); |
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> |
RealType rA = A.length(); |
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> |
Vector3d B = cross(r32, r43); |
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> |
RealType rB = B.length(); |
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> |
|
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> |
/* |
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> |
If either of the two cross product vectors is tiny, that means |
| 101 |
> |
the three atoms involved are colinear, and the torsion angle is |
| 102 |
> |
going to be undefined. The easiest check for this problem is |
| 103 |
> |
to use the product of the two lengths. |
| 104 |
> |
*/ |
| 105 |
> |
if (rA * rB < OpenMD::epsilon) return numeric_limits<double>::quiet_NaN(); |
| 106 |
> |
|
| 107 |
> |
A.normalize(); |
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> |
B.normalize(); |
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> |
|
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> |
// Calculate the sin and cos |
| 111 |
> |
RealType cos_phi = dot(A, B) ; |
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> |
if (cos_phi > 1.0) cos_phi = 1.0; |
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> |
if (cos_phi < -1.0) cos_phi = -1.0; |
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> |
return acos(cos_phi); |
| 115 |
> |
} |
| 116 |
> |
|
| 117 |
> |
|
| 118 |
|
RealType getPotential() { |
| 119 |
|
return potential_; |
| 120 |
|
} |
| 121 |
|
|
| 122 |
|
Atom* getAtomA() { |
| 123 |
< |
return atom1_; |
| 123 |
> |
return atoms_[0]; |
| 124 |
|
} |
| 125 |
|
|
| 126 |
|
Atom* getAtomB() { |
| 127 |
< |
return atom2_; |
| 127 |
> |
return atoms_[1]; |
| 128 |
|
} |
| 129 |
|
|
| 130 |
|
Atom* getAtomC() { |
| 131 |
< |
return atom3_; |
| 131 |
> |
return atoms_[2]; |
| 132 |
|
} |
| 133 |
|
|
| 134 |
|
Atom* getAtomD() { |
| 135 |
< |
return atom4_; |
| 135 |
> |
return atoms_[3]; |
| 136 |
|
} |
| 137 |
|
|
| 138 |
|
TorsionType * getTorsionType() { |
| 139 |
|
return torsionType_; |
| 140 |
|
} |
| 141 |
|
|
| 142 |
< |
protected: |
| 142 |
> |
virtual std::string getName() { return name_;} |
| 143 |
> |
/** Sets the name of this torsion for selections */ |
| 144 |
> |
virtual void setName(const std::string& name) { name_ = name;} |
| 145 |
|
|
| 146 |
< |
Atom* atom1_; |
| 147 |
< |
Atom* atom2_; |
| 148 |
< |
Atom* atom3_; |
| 107 |
< |
Atom* atom4_; |
| 146 |
> |
void accept(BaseVisitor* v) { |
| 147 |
> |
v->visit(this); |
| 148 |
> |
} |
| 149 |
|
|
| 150 |
+ |
protected: |
| 151 |
+ |
|
| 152 |
|
TorsionType* torsionType_; |
| 153 |
+ |
std::string name_; |
| 154 |
|
|
| 155 |
|
RealType potential_; |
| 156 |
|
}; |
