/* changing it so it rotates around the three principal axises - Adam Hogan */
void molecule_rotate_quaternion(molecule_t *molecule, double alpha, double beta, double gamma, int reverse_flag) {
atom_t *atom_ptr;
double com[3];
int i, ii, n;
double *new_coord_array;
/* count the number of atoms in a molecule, and allocate new coords array */
for(atom_ptr = molecule->atoms, n = 0; atom_ptr; atom_ptr = atom_ptr->next)
++n;
new_coord_array = calloc(n*3, sizeof(double));
memnullcheck(new_coord_array,n*3*sizeof(double),__LINE__-1, __FILE__);
/* save the com coordinate */
com[0] = molecule->com[0];
com[1] = molecule->com[1];
com[2] = molecule->com[2];
/* translate the molecule to the origin */
for(atom_ptr = molecule->atoms; atom_ptr; atom_ptr = atom_ptr->next) {
atom_ptr->pos[0] -= com[0];
atom_ptr->pos[1] -= com[1];
atom_ptr->pos[2] -= com[2];
}
/* construct the rotation quaternions */
struct quaternion first, second, third, total, total_conjugate, position, answer;
//total = quaternion with no rotation
quaternion_construct_xyzw(&total,0.,0.,0.,1.);
//first = rotation around z axis
quaternion_construct_axis_angle_degree(&first,0.,0.,1.,alpha);
//second = rotation around y axis
quaternion_construct_axis_angle_degree(&second,0.,1.,0.,beta);
//third = rotation around z axis
quaternion_construct_axis_angle_degree(&third,1.,0.,0.,gamma);
//combine all rotations into total
quaternion_multiplication(&first,&total,&total);
quaternion_multiplication(&second,&total,&total);
quaternion_multiplication(&third,&total,&total);
//if we are undoing a rotation we need to conjugate total
if (reverse_flag) quaternion_conjugate(&total,&total);
quaternion_conjugate(&total,&total_conjugate);
for(atom_ptr = molecule->atoms, i = 0; atom_ptr; atom_ptr = atom_ptr->next, i++) {
ii = i*3;
//position = position vector
quaternion_construct_xyzw(&position,atom_ptr->pos[0],atom_ptr->pos[1],atom_ptr->pos[2],0.);
//answer = total*(position*total_conjugate)
quaternion_multiplication(&position,&total_conjugate,&answer);
quaternion_multiplication(&total,&answer,&answer);
//set the new coords
new_coord_array[ii+0] = answer.x;
new_coord_array[ii+1] = answer.y;
new_coord_array[ii+2] = answer.z;
}
/* set the new coordinates and then translate back from the origin */
for(atom_ptr = molecule->atoms, i = 0; atom_ptr; atom_ptr = atom_ptr->next, i++) {
ii = i*3;
atom_ptr->pos[0] = new_coord_array[ii+0];
atom_ptr->pos[1] = new_coord_array[ii+1];
atom_ptr->pos[2] = new_coord_array[ii+2];
atom_ptr->pos[0] += com[0];
atom_ptr->pos[1] += com[1];
atom_ptr->pos[2] += com[2];
}
/* free our temporary array */
free(new_coord_array);
}
/* now with quaternions AH */
void rotate(system_t *system, molecule_t *molecule, pbc_t *pbc, double scale) {
atom_t *atom_ptr;
double u1, u2, u3;
double com[3];
int i, ii, n;
double *new_coord_array;
struct quaternion position_vector, rnd_rotation, rnd_rotation_conjugate, answer;
// create a random rotation
// http://planning.cs.uiuc.edu/node198.html
u1 = get_rand(system);
u2 = get_rand(system);
u3 = get_rand(system);
// simple linear interpolation for adjusting the scale
quaternion_construct_xyzw(&rnd_rotation, scale*sqrt(1-u1)*sin(2*M_PI*u2), scale*sqrt(1-u1)*cos(2*M_PI*u2), scale*sqrt(u1)*sin(2*M_PI*u3), 1-scale+scale*sqrt(u1)*cos(2*M_PI*u3)); /* make a random quaternion */
quaternion_normalize(&rnd_rotation);
quaternion_conjugate(&rnd_rotation, &rnd_rotation_conjugate); /* needed to transform coordinates */
/* count the number of atoms in a molecule, and allocate new coords array */
for (atom_ptr = molecule->atoms, n = 0; atom_ptr; atom_ptr = atom_ptr->next)
++n;
new_coord_array = calloc(n * 3, sizeof(double));
memnullcheck(new_coord_array, n * 3 * sizeof(double), __LINE__ - 1, __FILE__);
/* save the com coordinate */
com[0] = molecule->com[0];
com[1] = molecule->com[1];
com[2] = molecule->com[2];
/* translate the molecule to the origin */
for (atom_ptr = molecule->atoms; atom_ptr; atom_ptr = atom_ptr->next) {
atom_ptr->pos[0] -= com[0];
atom_ptr->pos[1] -= com[1];
atom_ptr->pos[2] -= com[2];
}
/* quaternion multiply */
for (atom_ptr = molecule->atoms, i = 0; atom_ptr; atom_ptr = atom_ptr->next, i++) {
ii = i * 3;
//position_vector = position
quaternion_construct_xyzw(&position_vector, atom_ptr->pos[0], atom_ptr->pos[1], atom_ptr->pos[2], 0.);
//answer = rnd_rotation*(position*rnd_rotation_conjugate)
quaternion_multiplication(&position_vector, &rnd_rotation_conjugate, &answer);
quaternion_multiplication(&rnd_rotation, &answer, &answer);
//set the new coords
new_coord_array[ii + 0] = answer.x;
new_coord_array[ii + 1] = answer.y;
new_coord_array[ii + 2] = answer.z;
}
/* set the new coordinates and then translate back from the origin */
for (atom_ptr = molecule->atoms, i = 0; atom_ptr; atom_ptr = atom_ptr->next, i++) {
ii = i * 3;
atom_ptr->pos[0] = new_coord_array[ii + 0];
atom_ptr->pos[1] = new_coord_array[ii + 1];
atom_ptr->pos[2] = new_coord_array[ii + 2];
atom_ptr->pos[0] += com[0];
atom_ptr->pos[1] += com[1];
atom_ptr->pos[2] += com[2];
}
/* free our temporary array */
free(new_coord_array);
}
