/*!
* \param[in,out] dest Destination positions.
* \param[in] src Source positions.
* \param[in] bFirst If true, memory is allocated for \p dest and a full
* copy is made; otherwise, only variable parts are copied, and no memory
* is allocated.
*
* \p dest should have been initialized somehow (calloc() is enough).
*/
void
gmx_ana_pos_copy(gmx_ana_pos_t *dest, gmx_ana_pos_t *src, bool bFirst)
{
if (bFirst)
{
gmx_ana_pos_reserve(dest, src->count(), 0);
if (src->v)
{
gmx_ana_pos_reserve_velocities(dest);
}
if (src->f)
{
gmx_ana_pos_reserve_forces(dest);
}
}
memcpy(dest->x, src->x, src->count()*sizeof(*dest->x));
if (dest->v)
{
GMX_ASSERT(src->v, "src velocities should be non-null if dest velocities are allocated");
memcpy(dest->v, src->v, src->count()*sizeof(*dest->v));
}
if (dest->f)
{
GMX_ASSERT(src->f, "src forces should be non-null if dest forces are allocated");
memcpy(dest->f, src->f, src->count()*sizeof(*dest->f));
}
gmx_ana_indexmap_copy(&dest->m, &src->m, bFirst);
}
/*!
* \param[in,out] dest Destination positions.
* \param[in] src Source positions.
* \param[in] bFirst If true, memory is allocated for \p dest and a full
* copy is made; otherwise, only variable parts are copied, and no memory
* is allocated.
*
* \p dest should have been initialized somehow (calloc() is enough).
*/
void
gmx_ana_pos_copy(gmx_ana_pos_t *dest, gmx_ana_pos_t *src, bool bFirst)
{
if (bFirst)
{
gmx_ana_pos_reserve(dest, src->nr, 0);
if (src->v)
{
gmx_ana_pos_reserve_velocities(dest);
}
if (src->f)
{
gmx_ana_pos_reserve_forces(dest);
}
}
dest->nr = src->nr;
memcpy(dest->x, src->x, dest->nr*sizeof(*dest->x));
if (dest->v)
{
memcpy(dest->v, src->v, dest->nr*sizeof(*dest->v));
}
if (dest->f)
{
memcpy(dest->f, src->f, dest->nr*sizeof(*dest->f));
}
gmx_ana_indexmap_copy(&dest->m, &src->m, bFirst);
dest->g = src->g;
}
/*!
* \param[in,out] pos Position data structure.
* \param[in] n Maximum number of positions.
* \param[in] isize Maximum number of atoms.
* \param[in] bVelocities Whether to reserve space for velocities.
* \param[in] bForces Whether to reserve space for forces.
*
* Ensures that enough memory is allocated in \p pos to calculate \p n
* positions from \p isize atoms.
*
* This method needs to be called instead of gmx_ana_pos_reserve() if the
* intent is to use gmx_ana_pos_append_init()/gmx_ana_pos_append().
*/
void
gmx_ana_pos_reserve_for_append(gmx_ana_pos_t *pos, int n, int isize,
bool bVelocities, bool bForces)
{
gmx_ana_pos_reserve(pos, n, isize);
snew(pos->m.mapb.a, isize);
pos->m.mapb.nalloc_a = isize;
if (bVelocities)
{
gmx_ana_pos_reserve_velocities(pos);
}
if (bForces)
{
gmx_ana_pos_reserve_forces(pos);
}
}
/*!
* \param[in] pc Position calculation data structure.
* \param[out] p Output positions.
*
* Calls to gmx_ana_poscalc_update() using \p pc should use only positions
* initialized with this function.
* The \c p->g pointer is initialized to point to an internal group that
* contains the maximum index group set with gmx_ana_poscalc_set_maxindex().
*/
void
gmx_ana_poscalc_init_pos(gmx_ana_poscalc_t *pc, gmx_ana_pos_t *p)
{
gmx_ana_indexmap_init(&p->m, &pc->gmax, pc->coll->top_, pc->itype);
/* Only do the static optimization when there is no completion */
if (!(pc->flags & POS_DYNAMIC) && pc->b.nra == pc->gmax.isize)
{
gmx_ana_indexmap_set_static(&p->m, &pc->b);
}
gmx_ana_pos_reserve(p, p->m.mapb.nr, 0);
if (pc->flags & POS_VELOCITIES)
{
gmx_ana_pos_reserve_velocities(p);
}
if (pc->flags & POS_FORCES)
{
gmx_ana_pos_reserve_forces(p);
}
}
