| 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 |
|
/** |
| 50 |
|
#ifndef PRIMITIVES_TORSION_HPP |
| 51 |
|
#define PRIMITIVES_TORSION_HPP |
| 52 |
|
|
| 53 |
+ |
#include "primitives/ShortRangeInteraction.hpp" |
| 54 |
|
#include "primitives/Atom.hpp" |
| 53 |
– |
|
| 55 |
|
#include "types/TorsionType.hpp" |
| 56 |
+ |
#include <limits> |
| 57 |
|
|
| 58 |
|
namespace OpenMD { |
| 59 |
|
struct TorsionData { |
| 71 |
|
/** |
| 72 |
|
* @class Torsion Torsion.hpp "types/Torsion.hpp" |
| 73 |
|
*/ |
| 74 |
< |
class Torsion { |
| 74 |
> |
class Torsion : public ShortRangeInteraction { |
| 75 |
|
public: |
| 76 |
+ |
using ShortRangeInteraction::getValue; |
| 77 |
+ |
using ShortRangeInteraction::getPrevValue; |
| 78 |
+ |
|
| 79 |
|
Torsion(Atom* atom1, Atom* atom2, Atom* atom3, Atom* atom4, TorsionType* tt); |
| 80 |
|
virtual ~Torsion() {} |
| 81 |
< |
virtual void calcForce(RealType& angle); |
| 82 |
< |
|
| 81 |
> |
virtual void calcForce(RealType& angle, bool doParticlePot); |
| 82 |
> |
|
| 83 |
> |
RealType getValue(int snapshotNo) { |
| 84 |
> |
Vector3d pos1 = atoms_[0]->getPos(snapshotNo); |
| 85 |
> |
Vector3d pos2 = atoms_[1]->getPos(snapshotNo); |
| 86 |
> |
Vector3d pos3 = atoms_[2]->getPos(snapshotNo); |
| 87 |
> |
Vector3d pos4 = atoms_[3]->getPos(snapshotNo); |
| 88 |
> |
|
| 89 |
> |
Vector3d r21 = pos1 - pos2; |
| 90 |
> |
Vector3d r32 = pos2 - pos3; |
| 91 |
> |
Vector3d r43 = pos3 - pos4; |
| 92 |
> |
|
| 93 |
> |
// Calculate the cross products and distances |
| 94 |
> |
Vector3d A = cross(r21, r32); |
| 95 |
> |
RealType rA = A.length(); |
| 96 |
> |
Vector3d B = cross(r32, r43); |
| 97 |
> |
RealType rB = B.length(); |
| 98 |
> |
|
| 99 |
> |
/* |
| 100 |
> |
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(); |
| 108 |
> |
B.normalize(); |
| 109 |
> |
|
| 110 |
> |
// Calculate the sin and cos |
| 111 |
> |
RealType cos_phi = dot(A, B) ; |
| 112 |
> |
if (cos_phi > 1.0) cos_phi = 1.0; |
| 113 |
> |
if (cos_phi < -1.0) cos_phi = -1.0; |
| 114 |
> |
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 |
|
}; |
