/*!
* \param[in,out] dest Destination data structure.
* \param[in] src Source mapping.
* \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_indexmap_copy(gmx_ana_indexmap_t *dest, gmx_ana_indexmap_t *src, bool bFirst)
{
if (bFirst)
{
gmx_ana_indexmap_reserve(dest, src->b.nr, src->b.nra);
dest->type = src->type;
dest->b.nr = src->b.nr;
dest->b.nra = src->b.nra;
std::memcpy(dest->orgid, src->orgid, dest->b.nr*sizeof(*dest->orgid));
std::memcpy(dest->b.index, src->b.index, (dest->b.nr+1)*sizeof(*dest->b.index));
std::memcpy(dest->b.a, src->b.a, dest->b.nra*sizeof(*dest->b.a));
}
dest->mapb.nr = src->mapb.nr;
dest->mapb.nra = src->mapb.nra;
if (src->mapb.nalloc_a > 0)
{
if (bFirst)
{
snew(dest->mapb.a, src->mapb.nalloc_a);
dest->mapb.nalloc_a = src->mapb.nalloc_a;
}
std::memcpy(dest->mapb.a, src->mapb.a, dest->mapb.nra*sizeof(*dest->mapb.a));
}
else
{
dest->mapb.a = src->mapb.a;
}
std::memcpy(dest->refid, src->refid, dest->mapb.nr*sizeof(*dest->refid));
std::memcpy(dest->mapid, src->mapid, dest->mapb.nr*sizeof(*dest->mapid));
std::memcpy(dest->mapb.index, src->mapb.index, (dest->mapb.nr+1)*sizeof(*dest->mapb.index));
dest->bStatic = src->bStatic;
}
/*!
* \param[in,out] pos Position data structure.
* \param[in] n Maximum number of positions.
* \param[in] isize Maximum number of atoms.
*
* Ensures that enough memory is allocated in \p pos to calculate \p n
* positions from \p isize atoms.
*/
void
gmx_ana_pos_reserve(gmx_ana_pos_t *pos, int n, int isize)
{
GMX_RELEASE_ASSERT(n >= 0, "Invalid position allocation count");
// Always reserve at least one entry to make NULL checks against pos->x
// and gmx_ana_pos_reserve_velocities/forces() work as expected in the case
// that there are actually no positions.
if (n == 0)
{
n = 1;
}
if (pos->nalloc_x < n)
{
pos->nalloc_x = n;
srenew(pos->x, n);
if (pos->v)
{
srenew(pos->v, n);
}
if (pos->f)
{
srenew(pos->f, n);
}
}
if (isize > 0)
{
gmx_ana_indexmap_reserve(&pos->m, n, isize);
}
}
/*!
* \param[in,out] m Mapping structure to initialize.
* \param[in] g Index group to map
* (can be NULL if \p type is \ref INDEX_UNKNOWN).
* \param[in] top Topology structure
* (can be NULL if \p type is not \ref INDEX_RES or \ref INDEX_MOL).
* \param[in] type Type of mapping to construct.
*
* Initializes a new index group mapping.
* The index group provided to gmx_ana_indexmap_update() should always be a
* subset of the \p g given here.
*
* \p m should have been initialized somehow (calloc() is enough).
*/
void
gmx_ana_indexmap_init(gmx_ana_indexmap_t *m, gmx_ana_index_t *g,
t_topology *top, e_index_t type)
{
int i, ii, mi;
m->type = type;
gmx_ana_index_make_block(&m->b, top, g, type, false);
gmx_ana_indexmap_reserve(m, m->b.nr, m->b.nra);
for (i = mi = 0; i < m->b.nr; ++i)
{
ii = (type == INDEX_UNKNOWN ? 0 : m->b.a[m->b.index[i]]);
switch (type)
{
case INDEX_ATOM:
m->orgid[i] = ii;
break;
case INDEX_RES:
m->orgid[i] = top->atoms.atom[ii].resind;
break;
case INDEX_MOL:
while (top->mols.index[mi+1] <= ii)
{
++mi;
}
m->orgid[i] = mi;
break;
case INDEX_ALL:
case INDEX_UNKNOWN:
m->orgid[i] = 0;
break;
}
}
for (i = 0; i < m->b.nr; ++i)
{
m->refid[i] = i;
m->mapid[i] = m->orgid[i];
}
m->mapb.nr = m->b.nr;
m->mapb.nra = m->b.nra;
m->mapb.a = m->b.a;
std::memcpy(m->mapb.index, m->b.index, (m->b.nr+1)*sizeof(*(m->mapb.index)));
m->bStatic = true;
}
/*!
* \param[in,out] dest Destination data structure.
* \param[in] src Source mapping.
* \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_indexmap_copy(gmx_ana_indexmap_t *dest, gmx_ana_indexmap_t *src, bool bFirst)
{
if (bFirst)
{
gmx_ana_indexmap_reserve(dest, src->b.nr, src->b.nra);
dest->type = src->type;
dest->b.nr = src->b.nr;
dest->b.nra = src->b.nra;
dest->bStatic = src->bStatic;
dest->bMapStatic = src->bMapStatic;
memcpy(dest->orgid, src->orgid, dest->b.nr*sizeof(*dest->orgid));
memcpy(dest->b.index, src->b.index, (dest->b.nr+1)*sizeof(*dest->b.index));
memcpy(dest->b.a, src->b.a, dest->b.nra*sizeof(*dest->b.a));
}
dest->nr = src->nr;
dest->mapb.nr = src->mapb.nr;
memcpy(dest->refid, src->refid, dest->nr*sizeof(*dest->refid));
memcpy(dest->mapid, src->mapid, dest->nr*sizeof(*dest->mapid));
memcpy(dest->mapb.index, src->mapb.index,(dest->mapb.nr+1)*sizeof(*dest->mapb.index));
}
/*!
* \param[in,out] pos Position data structure.
* \param[in] n Maximum number of positions.
* \param[in] isize Maximum number of atoms.
*
* Ensures that enough memory is allocated in \p pos to calculate \p n
* positions from \p isize atoms.
*/
void
gmx_ana_pos_reserve(gmx_ana_pos_t *pos, int n, int isize)
{
if (pos->nalloc_x < n)
{
pos->nalloc_x = n;
srenew(pos->x, n);
if (pos->v)
{
srenew(pos->v, n);
}
if (pos->f)
{
srenew(pos->f, n);
}
}
if (isize > 0)
{
gmx_ana_indexmap_reserve(&pos->m, n, isize);
}
}
/*!
* \param[in,out] m Mapping structure to initialize.
* \param[in] g Index group to map
* (can be NULL if \p type is \ref INDEX_UNKNOWN).
* \param[in] top Topology structure
* (can be NULL if \p type is not \ref INDEX_RES or \ref INDEX_MOL).
* \param[in] type Type of mapping to construct.
*
* Initializes a new index group mapping.
* The index group provided to gmx_ana_indexmap_update() should always be a
* subset of the \p g given here.
*
* \p m should have been initialized somehow (calloc() is enough).
*/
void
gmx_ana_indexmap_init(gmx_ana_indexmap_t *m, gmx_ana_index_t *g,
t_topology *top, e_index_t type)
{
m->type = type;
gmx_ana_index_make_block(&m->b, top, g, type, false);
gmx_ana_indexmap_reserve(m, m->b.nr, m->b.nra);
int id = -1;
for (int i = 0; i < m->b.nr; ++i)
{
const int ii = (type == INDEX_UNKNOWN ? 0 : m->b.a[m->b.index[i]]);
next_group_index(ii, top, type, &id);
m->refid[i] = i;
m->mapid[i] = id;
m->orgid[i] = id;
}
m->mapb.nr = m->b.nr;
m->mapb.nra = m->b.nra;
m->mapb.a = m->b.a;
std::memcpy(m->mapb.index, m->b.index, (m->b.nr+1)*sizeof(*(m->mapb.index)));
m->bStatic = true;
}