| 1 |
< |
/* |
| 1 |
> |
/* |
| 2 |
|
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
|
* |
| 4 |
|
* The University of Notre Dame grants you ("Licensee") a |
| 43 |
|
|
| 44 |
|
namespace oopse { |
| 45 |
|
|
| 46 |
< |
Torsion::Torsion(Atom *atom1, Atom *atom2, Atom *atom3, Atom *atom4, |
| 47 |
< |
TorsionType *tt) : |
| 46 |
> |
Torsion::Torsion(Atom *atom1, Atom *atom2, Atom *atom3, Atom *atom4, |
| 47 |
> |
TorsionType *tt) : |
| 48 |
|
atom1_(atom1), atom2_(atom2), atom3_(atom3), atom4_(atom4), torsionType_(tt) { } |
| 49 |
|
|
| 50 |
< |
void Torsion::calcForce() { |
| 50 |
> |
void Torsion::calcForce(RealType& angle) { |
| 51 |
> |
|
| 52 |
|
Vector3d pos1 = atom1_->getPos(); |
| 53 |
|
Vector3d pos2 = atom2_->getPos(); |
| 54 |
|
Vector3d pos3 = atom3_->getPos(); |
| 60 |
|
|
| 61 |
|
// Calculate the cross products and distances |
| 62 |
|
Vector3d A = cross(r21, r32); |
| 63 |
< |
double rA = A.length(); |
| 63 |
> |
RealType rA = A.length(); |
| 64 |
|
Vector3d B = cross(r32, r43); |
| 65 |
< |
double rB = B.length(); |
| 65 |
> |
RealType rB = B.length(); |
| 66 |
|
Vector3d C = cross(r32, A); |
| 67 |
< |
double rC = C.length(); |
| 67 |
> |
RealType rC = C.length(); |
| 68 |
|
|
| 69 |
|
A.normalize(); |
| 70 |
|
B.normalize(); |
| 71 |
|
C.normalize(); |
| 72 |
|
|
| 73 |
|
// Calculate the sin and cos |
| 74 |
< |
double cos_phi = dot(A, B) ; |
| 75 |
< |
double sin_phi = dot(C, B); |
| 74 |
> |
RealType cos_phi = dot(A, B) ; |
| 75 |
> |
if (cos_phi > 1.0) cos_phi = 1.0; |
| 76 |
> |
if (cos_phi < -1.0) cos_phi = -1.0; |
| 77 |
|
|
| 78 |
< |
double dVdPhi; |
| 79 |
< |
torsionType_->calcForce(cos_phi, sin_phi, potential_, dVdPhi); |
| 78 |
< |
|
| 78 |
> |
RealType dVdcosPhi; |
| 79 |
> |
torsionType_->calcForce(cos_phi, potential_, dVdcosPhi); |
| 80 |
|
Vector3d f1; |
| 81 |
|
Vector3d f2; |
| 82 |
|
Vector3d f3; |
| 83 |
|
|
| 84 |
< |
// Next, we want to calculate the forces. In order |
| 85 |
< |
// to do that, we first need to figure out whether the |
| 85 |
< |
// sin or cos form will be more stable. For this, |
| 86 |
< |
// just look at the value of phi |
| 87 |
< |
//if (fabs(sin_phi) > 0.1) { |
| 88 |
< |
// use the sin version to avoid 1/cos terms |
| 84 |
> |
Vector3d dcosdA = (cos_phi * A - B) /rA; |
| 85 |
> |
Vector3d dcosdB = (cos_phi * B - A) /rB; |
| 86 |
|
|
| 87 |
< |
Vector3d dcosdA = (cos_phi * A - B) /rA; |
| 88 |
< |
Vector3d dcosdB = (cos_phi * B - A) /rB; |
| 89 |
< |
|
| 90 |
< |
double dVdcosPhi = -dVdPhi / sin_phi; |
| 94 |
< |
|
| 95 |
< |
f1 = dVdcosPhi * cross(r32, dcosdA); |
| 96 |
< |
f2 = dVdcosPhi * ( cross(r43, dcosdB) - cross(r21, dcosdA)); |
| 97 |
< |
f3 = dVdcosPhi * cross(dcosdB, r32); |
| 98 |
< |
|
| 99 |
< |
/** @todo fix below block, must be something wrong with the sign somewhere */ |
| 100 |
< |
//} else { |
| 101 |
< |
// This angle is closer to 0 or 180 than it is to |
| 102 |
< |
// 90, so use the cos version to avoid 1/sin terms |
| 103 |
< |
|
| 104 |
< |
//double dVdsinPhi = dVdPhi /cos_phi; |
| 105 |
< |
//Vector3d dsindB = (sin_phi * B - C) /rB; |
| 106 |
< |
//Vector3d dsindC = (sin_phi * C - B) /rC; |
| 107 |
< |
|
| 108 |
< |
//f1.x() = dVdsinPhi*((r32.y()*r32.y() + r32.z()*r32.z())*dsindC.x() - r32.x()*r32.y()*dsindC.y() - r32.x()*r32.z()*dsindC.z()); |
| 109 |
< |
|
| 110 |
< |
//f1.y() = dVdsinPhi*((r32.z()*r32.z() + r32.x()*r32.x())*dsindC.y() - r32.y()*r32.z()*dsindC.z() - r32.y()*r32.x()*dsindC.x()); |
| 111 |
< |
|
| 112 |
< |
//f1.z() = dVdsinPhi*((r32.x()*r32.x() + r32.y()*r32.y())*dsindC.z() - r32.z()*r32.x()*dsindC.x() - r32.z()*r32.y()*dsindC.y()); |
| 113 |
< |
|
| 114 |
< |
//f2.x() = dVdsinPhi*(-(r32.y()*r21.y() + r32.z()*r21.z())*dsindC.x() + (2.0*r32.x()*r21.y() - r21.x()*r32.y())*dsindC.y() |
| 115 |
< |
//+ (2.0*r32.x()*r21.z() - r21.x()*r32.z())*dsindC.z() + dsindB.z()*r43.y() - dsindB.y()*r43.z()); |
| 116 |
< |
|
| 117 |
< |
//f2.y() = dVdsinPhi*(-(r32.z()*r21.z() + r32.x()*r21.x())*dsindC.y() + (2.0*r32.y()*r21.z() - r21.y()*r32.z())*dsindC.z() |
| 118 |
< |
//+ (2.0*r32.y()*r21.x() - r21.y()*r32.x())*dsindC.x() + dsindB.x()*r43.z() - dsindB.z()*r43.x()); |
| 119 |
< |
|
| 120 |
< |
//f2.z() = dVdsinPhi*(-(r32.x()*r21.x() + r32.y()*r21.y())*dsindC.z() + (2.0*r32.z()*r21.x() - r21.z()*r32.x())*dsindC.x() |
| 121 |
< |
//+(2.0*r32.z()*r21.y() - r21.z()*r32.y())*dsindC.y() + dsindB.y()*r43.x() - dsindB.x()*r43.y()); |
| 122 |
< |
|
| 123 |
< |
//f3 = dVdsinPhi * cross(r32, dsindB); |
| 124 |
< |
|
| 125 |
< |
//} |
| 126 |
< |
|
| 87 |
> |
f1 = dVdcosPhi * cross(r32, dcosdA); |
| 88 |
> |
f2 = dVdcosPhi * ( cross(r43, dcosdB) - cross(r21, dcosdA)); |
| 89 |
> |
f3 = dVdcosPhi * cross(dcosdB, r32); |
| 90 |
> |
|
| 91 |
|
atom1_->addFrc(f1); |
| 92 |
|
atom2_->addFrc(f2 - f1); |
| 93 |
|
atom3_->addFrc(f3 - f2); |
| 94 |
|
atom4_->addFrc(-f3); |
| 95 |
< |
} |
| 95 |
> |
angle = acos(cos_phi) /M_PI * 180.0; |
| 96 |
> |
} |
| 97 |
|
|
| 98 |
|
} |
