double CMSF (int type,int nh,double lambda, double sin_theta)
/*
* return Cromer-Mann fit for the atomic scattering factor:
* sin_theta is the sine of half the angle between incoming and scattered
* vectors. See g_sq.h for a short description of CM fit.
*/
{
int i;
double tmp = 0.0, k2;
/*
* united atoms case
* CH2 / CH3 groups
*/
if (nh > 0) {
tmp = (CMSF (return_atom_type ("C"),0,lambda, sin_theta) +
nh*CMSF (return_atom_type ("H"),0,lambda, sin_theta));
}
/* all atom case */
else {
k2 = (sqr (sin_theta) / sqr (10.0 * lambda));
tmp = CM_t[type].c;
for (i = 0; (i < 4); i++)
tmp += CM_t[type].a[i] * exp (-CM_t[type].b[i] * k2);
}
return tmp;
}
extern double CMSF (gmx_structurefactors_t *gsf, int type, int nh, double lambda, double sin_theta)
/*
* return Cromer-Mann fit for the atomic scattering factor:
* sin_theta is the sine of half the angle between incoming and scattered
* vectors. See g_sq.h for a short description of CM fit.
*/
{
int i, success;
double tmp = 0.0, k2;
real *a, *b;
real c;
snew(a, 4);
snew(b, 4);
/*
*
* f0[k] = c + [SUM a_i*EXP(-b_i*(k^2)) ]
* i=1,4
*/
/*
* united atoms case
* CH2 / CH3 groups
*/
if (nh > 0)
{
tmp = (CMSF (gsf, return_atom_type ("C", gsf), 0, lambda, sin_theta) +
nh*CMSF (gsf, return_atom_type ("H", gsf), 0, lambda, sin_theta));
}
/* all atom case */
else
{
k2 = (sqr (sin_theta) / sqr (10.0 * lambda));
success = gmx_structurefactors_get_sf(gsf, type, a, b, &c);
tmp = c;
for (i = 0; (i < 4); i++)
{
tmp += a[i] * exp (-b[i] * k2);
}
}
return tmp;
}
void rearrange_atoms (reduced_atom * positions, t_trxframe *fr, atom_id * index,
int isize, t_topology * top, bool flag)
/* given the group's index, return the (continuous) array of atoms */
{
int i;
if (flag)
for (i = 0; i < isize; i++)
positions[i].t =
return_atom_type (*(top->atoms.atomname[index[i]]));
for (i = 0; i < isize; i++)
copy_rvec (fr->x[index[i]], positions[i].x);
}
extern void rearrange_atoms (reduced_atom_t * positions, t_trxframe *fr, atom_id * index,
int isize, t_topology * top, gmx_bool flag, gmx_structurefactors_t *gsf)
/* given the group's index, return the (continuous) array of atoms */
{
int i;
reduced_atom *pos = (reduced_atom *)positions;
if (flag)
{
for (i = 0; i < isize; i++)
{
pos[i].t =
return_atom_type (*(top->atoms.atomname[index[i]]), gsf);
}
}
for (i = 0; i < isize; i++)
{
copy_rvec (fr->x[index[i]], pos[i].x);
}
}
