8 |
|
Vector3d pos2 = atom2_->getPos(); |
9 |
|
Vector3d pos3 = atom3_->getPos(); |
10 |
|
|
11 |
< |
Vector3d r12 = pos1 - pos2; |
12 |
< |
double d12 = r12.length(); |
11 |
> |
Vector3d r21 = pos1 - pos2; |
12 |
> |
double d21 = r21.length(); |
13 |
|
|
14 |
< |
double d12inv = 1.0 / d12; |
14 |
> |
double d21inv = 1.0 / d21; |
15 |
|
|
16 |
< |
Vector3d r32 = pos3 - pos2; |
17 |
< |
double d32 = r32.length(); |
16 |
> |
Vector3d r23 = pos3 - pos2; |
17 |
> |
double d23 = r23.length(); |
18 |
|
|
19 |
< |
double d32inv = 1.0 / d32; |
19 |
> |
double d23inv = 1.0 / d23; |
20 |
|
|
21 |
< |
double cosTheta = dot(r12, r32) / (d12 * d32); |
21 |
> |
double cosTheta = dot(r21, r23) / (d21 * d23); |
22 |
|
|
23 |
|
//check roundoff |
24 |
|
if (cosTheta > 1.0) { |
29 |
|
|
30 |
|
double theta = acos(cosTheta); |
31 |
|
|
32 |
< |
double firstDerivative; |
32 |
> |
double dVdTheta; |
33 |
|
|
34 |
< |
bendType_->calcForce(theta, firstDerivative, potential_); |
34 |
> |
bendType_->calcForce(theta, potential_, dVdTheta); |
35 |
|
|
36 |
|
double sinTheta = sqrt(1.0 - cosTheta * cosTheta); |
37 |
|
|
38 |
< |
if (fabs(sinTheta) < 1.0E-12) { |
39 |
< |
sinTheta = 1.0E-12; |
38 |
> |
if (fabs(sinTheta) < 1.0E-6) { |
39 |
> |
sinTheta = 1.0E-6; |
40 |
|
} |
41 |
|
|
42 |
< |
double commonFactor1 = -firstDerivative / sinTheta * d12inv; |
43 |
< |
double commonFactor2 = -firstDerivative / sinTheta * d32inv; |
42 |
> |
double commonFactor1 = dVdTheta / sinTheta * d21inv; |
43 |
> |
double commonFactor2 = dVdTheta / sinTheta * d23inv; |
44 |
|
|
45 |
< |
Vector3d force1 = commonFactor1*(r12*(d12inv*cosTheta) - r32*d32inv); |
45 |
> |
Vector3d force1 = commonFactor1 * (r23 * d23inv - r21*d21inv*cosTheta); |
46 |
> |
Vector3d force3 = commonFactor2 * (r21 * d21inv - r23*d23inv*cosTheta); |
47 |
|
|
47 |
– |
Vector3d force3 = commonFactor2*(r32*(d32inv*cosTheta) - r12*d12inv); |
48 |
– |
|
48 |
|
//total force in current bend is zero |
49 |
|
Vector3d force2 = force1 + force3; |
50 |
|
force2 *= -1.0; |