5 |
|
|
6 |
|
#include "simError.h" |
7 |
|
#include "MoLocator.hpp" |
8 |
+ |
#include "MatVec3.h" |
9 |
|
|
10 |
|
MoLocator::MoLocator( MoleculeStamp* theStamp, ForceFields* theFF){ |
11 |
|
|
21 |
|
Vector3d angMomentum(0.0, 0.0, 0.0); |
22 |
|
double quaternion[4]; |
23 |
|
vector<StuntDouble*> myIntegrableObjects; |
24 |
< |
|
24 |
> |
double rotMat[3][3]; |
25 |
> |
|
26 |
|
quaternion[0] = 1.0; |
27 |
|
quaternion[1] = 0.0; |
28 |
|
quaternion[2] = 0.0; |
29 |
|
quaternion[3] = 0.0; |
30 |
|
|
31 |
+ |
latVec2RotMat(ort, rotMat); |
32 |
+ |
|
33 |
|
myIntegrableObjects = mol->getIntegrableObjects(); |
34 |
|
|
35 |
|
if(myIntegrableObjects.size() != nIntegrableObjects){ |
43 |
|
|
44 |
|
for(int i=0; i<nIntegrableObjects; i++) { |
45 |
|
|
46 |
< |
newCoor = refCoords[i] + offset; |
47 |
< |
myIntegrableObjects[i]->setPos( newCoor.vec); |
48 |
< |
myIntegrableObjects[i]->setVel(velocity.vec); |
46 |
> |
//calculate the reference coordinate for integrable objects after rotation |
47 |
> |
matVecMul3(rotMat, refCoords[i].vec, newCoor.vec); |
48 |
> |
newCoor += offset; |
49 |
|
|
50 |
< |
if(myIntegrableObjects[i]->isDirectional()){ |
51 |
< |
myIntegrableObjects[i]->setQ(quaternion); |
52 |
< |
myIntegrableObjects[i]->setJ(angMomentum.vec); |
53 |
< |
} |
50 |
> |
myIntegrableObjects[i]->setPos( newCoor.vec); |
51 |
> |
myIntegrableObjects[i]->setVel(velocity.vec); |
52 |
> |
|
53 |
> |
if(myIntegrableObjects[i]->isDirectional()){ |
54 |
> |
myIntegrableObjects[i]->setA(rotMat); |
55 |
> |
myIntegrableObjects[i]->setJ(angMomentum.vec); |
56 |
> |
} |
57 |
|
} |
58 |
|
|
59 |
|
} |
70 |
|
double currAtomMass; |
71 |
|
double molMass; |
72 |
|
|
66 |
– |
mass.resize(nIntegrableObjects); |
67 |
– |
|
73 |
|
nAtoms= myStamp->getNAtoms(); |
74 |
|
nRigidBodies = myStamp->getNRigidBodies(); |
75 |
|
|
145 |
|
refCoords[i] -= refMolCom; |
146 |
|
} |
147 |
|
|
148 |
+ |
|
149 |
+ |
void latVec2RotMat(const Vector3d& lv, double rotMat[3][3]){ |
150 |
+ |
|
151 |
+ |
double theta, phi, psi; |
152 |
+ |
|
153 |
+ |
theta =acos(lv.z); |
154 |
+ |
phi = atan2(lv.y, lv.x); |
155 |
+ |
psi = 0; |
156 |
+ |
|
157 |
+ |
rotMat[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
158 |
+ |
rotMat[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
159 |
+ |
rotMat[0][2] = sin(theta) * sin(psi); |
160 |
+ |
|
161 |
+ |
rotMat[1][0] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
162 |
+ |
rotMat[1][1] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
163 |
+ |
rotMat[1][2] = sin(theta) * cos(psi); |
164 |
+ |
|
165 |
+ |
rotMat[2][0] = sin(phi) * sin(theta); |
166 |
+ |
rotMat[2][1] = -cos(phi) * sin(theta); |
167 |
+ |
rotMat[2][2] = cos(theta); |
168 |
+ |
} |
169 |
+ |
|