| 27 |
|
int atomIndex, SimState* myConfig ){ |
| 28 |
|
|
| 29 |
|
int i,j,k; |
| 30 |
< |
double r[3]; |
| 30 |
> |
double r[3], ji[3]; |
| 31 |
|
double phi, theta, psi; |
| 32 |
|
double sux, suy, suz; |
| 33 |
|
double Axx, Axy, Axz, Ayx, Ayy, Ayz, Azx, Azy, Azz; |
| 50 |
|
atomArray[j]->setCoords(); |
| 51 |
|
|
| 52 |
|
// Directional Atoms have standard unit vectors which are oriented |
| 53 |
< |
// in space using the three Euler angles. We assume the standard |
| 54 |
< |
// unit vector was originally along the z axis below. |
| 53 |
> |
// in space using the three Euler angles. |
| 54 |
|
|
| 55 |
|
phi = currAtom->getEulerPhi() * M_PI / 180.0; |
| 56 |
|
theta = currAtom->getEulerTheta() * M_PI / 180.0; |
| 57 |
|
psi = currAtom->getEulerPsi()* M_PI / 180.0; |
| 58 |
< |
|
| 59 |
< |
Axx = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
| 61 |
< |
Axy = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
| 62 |
< |
Axz = sin(theta) * sin(psi); |
| 63 |
< |
|
| 64 |
< |
Ayx = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
| 65 |
< |
Ayy = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
| 66 |
< |
Ayz = sin(theta) * cos(psi); |
| 67 |
< |
|
| 68 |
< |
Azx = sin(phi) * sin(theta); |
| 69 |
< |
Azy = -cos(phi) * sin(theta); |
| 70 |
< |
Azz = cos(theta); |
| 71 |
< |
|
| 72 |
< |
sux = 0.0; |
| 73 |
< |
suy = 0.0; |
| 74 |
< |
suz = 1.0; |
| 75 |
< |
|
| 76 |
< |
ux = (Axx * sux) + (Ayx * suy) + (Azx * suz); |
| 77 |
< |
uy = (Axy * sux) + (Ayy * suy) + (Azy * suz); |
| 78 |
< |
uz = (Axz * sux) + (Ayz * suy) + (Azz * suz); |
| 79 |
< |
|
| 80 |
< |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
| 81 |
< |
|
| 82 |
< |
u = sqrt( uSqr ); |
| 83 |
< |
ux = ux / u; |
| 84 |
< |
uy = uy / u; |
| 85 |
< |
uz = uz / u; |
| 86 |
< |
|
| 87 |
< |
dAtom->setSUx( ux ); |
| 88 |
< |
dAtom->setSUy( uy ); |
| 89 |
< |
dAtom->setSUz( uz ); |
| 90 |
< |
|
| 58 |
> |
|
| 59 |
> |
dAtom->setUnitFrameFromEuler(phi, theta, psi); |
| 60 |
|
dAtom->setA( A ); |
| 61 |
+ |
|
| 62 |
+ |
ji[0] = 0.0; |
| 63 |
+ |
ji[1] = 0.0; |
| 64 |
+ |
ji[2] = 0.0; |
| 65 |
+ |
dAtom->setJ( ji ); |
| 66 |
|
|
| 93 |
– |
dAtom->setJx( 0.0 ); |
| 94 |
– |
dAtom->setJy( 0.0 ); |
| 95 |
– |
dAtom->setJz( 0.0 ); |
| 96 |
– |
|
| 67 |
|
} |
| 68 |
|
else{ |
| 69 |
< |
atomArray[j] = new GeneralAtom( j, myConfig); |
| 69 |
> |
atomArray[j] = new Atom( j, myConfig); |
| 70 |
|
atomArray[j]->setCoords(); |
| 71 |
|
} |
| 72 |
|
|
