| 60 |
|
Vector3d pos3 = atom1_->getPos(); |
| 61 |
|
Vector3d pos4 = atom4_->getPos(); |
| 62 |
|
|
| 63 |
< |
Vector3d r21 = pos1 - pos2; |
| 64 |
< |
Vector3d r32 = pos2 - pos3; |
| 63 |
> |
/*std::ofstream myfile; |
| 64 |
> |
myfile.open("Inversion", std::ios::app); |
| 65 |
> |
myfile << atom1_->getType() << " - atom1; " |
| 66 |
> |
<< atom2_->getType() << " - atom2; " |
| 67 |
> |
<< atom3_->getType() << " - atom3; " |
| 68 |
> |
<< atom4_->getType() << " - atom4; " |
| 69 |
> |
<< std::endl; |
| 70 |
> |
*/ |
| 71 |
> |
Vector3d r31 = pos1 - pos3; |
| 72 |
> |
Vector3d r23 = pos3 - pos2; |
| 73 |
|
Vector3d r43 = pos3 - pos4; |
| 74 |
|
|
| 75 |
|
// Calculate the cross products and distances |
| 76 |
< |
Vector3d A = cross(r21, r32); |
| 76 |
> |
Vector3d A = cross(r31, r43); |
| 77 |
|
RealType rA = A.length(); |
| 78 |
< |
Vector3d B = cross(r32, r43); |
| 78 |
> |
Vector3d B = cross(r43, r23); |
| 79 |
|
RealType rB = B.length(); |
| 80 |
< |
Vector3d C = cross(r32, A); |
| 81 |
< |
RealType rC = C.length(); |
| 80 |
> |
//Vector3d C = cross(r23, A); |
| 81 |
> |
//RealType rC = C.length(); |
| 82 |
|
|
| 83 |
|
A.normalize(); |
| 84 |
|
B.normalize(); |
| 85 |
< |
C.normalize(); |
| 85 |
> |
//C.normalize(); |
| 86 |
|
|
| 87 |
|
// Calculate the sin and cos |
| 88 |
|
RealType cos_phi = dot(A, B) ; |
| 89 |
< |
if (cos_phi > 1.0) cos_phi = 1.0; |
| 90 |
< |
if (cos_phi < -1.0) cos_phi = -1.0; |
| 89 |
> |
if (cos_phi > 1.0) {cos_phi = 1.0; std::cout << "!!!! cos_phi is bigger than 1.0" |
| 90 |
> |
<< std::endl;} |
| 91 |
> |
if (cos_phi < -1.0) {cos_phi = -1.0; std::cout << "!!!! cos_phi is less than -1.0" |
| 92 |
> |
<< std::endl;} |
| 93 |
> |
//std::cout << "We actually use this inversion!!!!" << std::endl; |
| 94 |
|
|
| 84 |
– |
|
| 95 |
|
RealType dVdcosPhi; |
| 96 |
+ |
//cos_phi = 2.0*cos_phi*cos_phi - 1.0; |
| 97 |
|
inversionType_->calcForce(cos_phi, potential_, dVdcosPhi); |
| 98 |
< |
Vector3d f1; |
| 99 |
< |
Vector3d f2; |
| 100 |
< |
Vector3d f3; |
| 98 |
> |
Vector3d f1 ; |
| 99 |
> |
Vector3d f2 ; |
| 100 |
> |
Vector3d f3 ; |
| 101 |
|
|
| 102 |
|
Vector3d dcosdA = (cos_phi * A - B) /rA; |
| 103 |
|
Vector3d dcosdB = (cos_phi * B - A) /rB; |
| 104 |
|
|
| 105 |
< |
f1 = dVdcosPhi * cross(r32, dcosdA); |
| 106 |
< |
f2 = dVdcosPhi * ( cross(r43, dcosdB) - cross(r21, dcosdA)); |
| 107 |
< |
f3 = dVdcosPhi * cross(dcosdB, r32); |
| 105 |
> |
f1 = dVdcosPhi * cross(r43, dcosdA); |
| 106 |
> |
f2 = dVdcosPhi * ( cross(r23, dcosdB) - cross(r31, dcosdA)); |
| 107 |
> |
f3 = dVdcosPhi * cross(dcosdB, r43); |
| 108 |
|
|
| 109 |
|
// In OOPSE's version of an improper torsion, the central atom |
| 110 |
|
// comes first. However, to get the planarity in a typical cosine |
| 116 |
|
|
| 117 |
|
// Confusing enough? Good. |
| 118 |
|
|
| 119 |
< |
atom3_->addFrc(f1); |
| 120 |
< |
atom1_->addFrc(f2 - f1); |
| 121 |
< |
atom2_->addFrc(f3 - f2); |
| 122 |
< |
atom4_->addFrc(-f3); |
| 119 |
> |
atom2_->addFrc(f1); |
| 120 |
> |
atom1_->addFrc(f2 - f1 + f3); |
| 121 |
> |
atom4_->addFrc(-f2); |
| 122 |
> |
atom3_->addFrc(-f3); |
| 123 |
> |
|
| 124 |
|
angle = acos(cos_phi) /M_PI * 180.0; |
| 125 |
|
} |
| 126 |
|
|
