174 |
|
bend_set* theBends; |
175 |
|
torsion_set* theTorsions; |
176 |
|
|
177 |
– |
|
177 |
|
//init the forceField paramters |
178 |
|
|
179 |
|
the_ff->readParams(); |
181 |
|
|
182 |
|
// init the atoms |
183 |
|
|
184 |
+ |
double phi, theta, psi; |
185 |
+ |
double sux, suy, suz; |
186 |
+ |
double Axx, Axy, Axz, Ayx, Ayy, Ayz, Azx, Azy, Azz; |
187 |
|
double ux, uy, uz, u, uSqr; |
188 |
|
|
189 |
|
for (k = 0; k < nInfo; k++){ |
220 |
|
info[k].n_oriented++; |
221 |
|
molInfo.myAtoms[j] = dAtom; |
222 |
|
|
223 |
< |
ux = currentAtom->getOrntX(); |
224 |
< |
uy = currentAtom->getOrntY(); |
225 |
< |
uz = currentAtom->getOrntZ(); |
223 |
> |
// Directional Atoms have standard unit vectors which are oriented |
224 |
> |
// in space using the three Euler angles. We assume the standard |
225 |
> |
// unit vector was originally along the z axis below. |
226 |
> |
|
227 |
> |
phi = currentAtom->getEulerPhi(); |
228 |
> |
theta = currentAtom->getEulerTheta(); |
229 |
> |
psi = currentAtom->getEulerPsi(); |
230 |
> |
|
231 |
> |
Axx = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
232 |
> |
Axy = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
233 |
> |
Axz = sin(theta) * sin(psi); |
234 |
> |
|
235 |
> |
Ayx = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
236 |
> |
Ayy = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
237 |
> |
Ayz = sin(theta) * cos(psi); |
238 |
> |
|
239 |
> |
Azx = sin(phi) * sin(theta); |
240 |
> |
Azy = -cos(phi) * sin(theta); |
241 |
> |
Azz = cos(theta); |
242 |
> |
|
243 |
> |
sux = 0.0; |
244 |
> |
suy = 0.0; |
245 |
> |
suz = 1.0; |
246 |
|
|
247 |
+ |
ux = (Axx * sux) + (Ayx * suy) + (Azx * suz); |
248 |
+ |
uy = (Axy * sux) + (Ayy * suy) + (Azy * suz); |
249 |
+ |
uz = (Axz * sux) + (Ayz * suy) + (Azz * suz); |
250 |
+ |
|
251 |
|
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
252 |
|
|
253 |
|
u = sqrt(uSqr); |