44 |
|
double ox[3] = {0.0, 0.0, -0.0654}; |
45 |
|
double u[3] = {0, 0, 1}; |
46 |
|
double rotMatrix[3][3]; |
47 |
+ |
double rotTrans[3][3]; |
48 |
|
AtomInfo* atomInfo; |
49 |
|
double pos[3]; |
50 |
|
double vel[3]; |
79 |
|
datom->getPos(pos); |
80 |
|
datom->getQ(q); |
81 |
|
datom->getA(rotMatrix); |
82 |
+ |
|
83 |
+ |
// We need A^T to convert from body-fixed to space-fixed: |
84 |
+ |
transposeMat3(rotMatrix, rotTrans); |
85 |
|
|
86 |
|
//center of mass of the water molecule |
87 |
< |
matVecMul3(rotMatrix, u, newVec); |
87 |
> |
matVecMul3(rotTrans, u, newVec); |
88 |
|
atomInfo = new AtomInfo; |
89 |
|
atomInfo->AtomType = "X"; |
90 |
|
atomInfo->pos[0] = pos[0]; |
97 |
|
atomData->addAtomInfo(atomInfo); |
98 |
|
|
99 |
|
//oxygen |
100 |
< |
matVecMul3(rotMatrix, ox, newVec); |
100 |
> |
matVecMul3(rotTrans, ox, newVec); |
101 |
|
atomInfo = new AtomInfo; |
102 |
|
atomInfo->AtomType = "O"; |
103 |
|
atomInfo->pos[0] = pos[0] + newVec[0]; |
110 |
|
|
111 |
|
|
112 |
|
//hydrogen1 |
113 |
< |
matVecMul3(rotMatrix, h1, newVec); |
113 |
> |
matVecMul3(rotTrans, h1, newVec); |
114 |
|
atomInfo = new AtomInfo; |
115 |
|
atomInfo->AtomType = "H"; |
116 |
|
atomInfo->pos[0] = pos[0] + newVec[0]; |
122 |
|
atomData->addAtomInfo(atomInfo); |
123 |
|
|
124 |
|
//hydrogen2 |
125 |
< |
matVecMul3(rotMatrix, h2, newVec); |
125 |
> |
matVecMul3(rotTrans, h2, newVec); |
126 |
|
atomInfo = new AtomInfo; |
127 |
|
atomInfo->AtomType = "H"; |
128 |
|
atomInfo->pos[0] = pos[0] + newVec[0]; |