void
SelectionData::restoreOriginalPositions(const t_topology *top)
{
if (isDynamic())
{
gmx_ana_pos_t &p = rawPositions_;
gmx_ana_indexmap_update(&p.m, rootElement().v.u.g,
hasFlag(gmx::efSelection_DynamicMask));
refreshMassesAndCharges(top);
}
}
/*!
* \param[in] pc Position calculation data.
* \param[in,out] p Output positions, initialized previously with
* gmx_ana_poscalc_init_pos() using \p pc.
* \param[in] g Index group to use for the update.
* \param[in] x Current positions of the atoms.
* \param[in] pbc PBC data, or NULL if no PBC should be used.
*
* gmx_ana_poscalc_init_frame() should be called for each frame before calling
* this function.
*/
void
gmx_ana_poscalc_update(gmx_ana_poscalc_t *pc, gmx_ana_pos_t *p,
gmx_ana_index_t *g, rvec x[], t_pbc *pbc)
{
int i, j, bi, bj;
if (pc->bEval == TRUE && !(pc->flags & POS_MASKONLY))
{
return;
}
if (pc->sbase)
{
gmx_ana_poscalc_update(pc->sbase, NULL, NULL, x, pbc);
}
if (!p)
{
p = pc->p;
}
if (!g)
{
g = &pc->gmax;
}
p->g = g;
/* Update the index map */
if (pc->flags & POS_DYNAMIC)
{
gmx_ana_indexmap_update(&p->m, g, FALSE);
p->nr = p->m.nr;
}
else if (pc->flags & POS_MASKONLY)
{
gmx_ana_indexmap_update(&p->m, g, TRUE);
if (pc->bEval)
return;
}
if (!(pc->flags & POS_DYNAMIC))
{
pc->bEval = TRUE;
}
/* Evaluate the positions */
if (pc->sbase)
{
/* TODO: It might be faster to evaluate the positions within this
* loop instead of in the beginning. */
if (pc->flags & POS_DYNAMIC)
{
for (bi = 0; bi < p->nr; ++bi)
{
bj = pc->baseid[p->m.refid[bi]];
copy_rvec(pc->sbase->p->x[bj], p->x[bi]);
}
}
else
{
for (bi = 0; bi < p->nr; ++bi)
{
bj = pc->baseid[bi];
copy_rvec(pc->sbase->p->x[bj], p->x[bi]);
}
}
}
else /* pc->sbase is NULL */
{
if (pc->flags & POS_DYNAMIC)
{
pc->b.nr = p->m.mapb.nr;
pc->b.index = p->m.mapb.index;
pc->b.nra = g->isize;
pc->b.a = g->index;
}
/* Here, we assume that the topology has been properly initialized,
* and do not check the return values of gmx_calc_comg*(). */
switch (pc->type)
{
case POS_ATOM:
for (i = 0; i < pc->b.nra; ++i)
{
copy_rvec(x[pc->b.a[i]], p->x[i]);
}
break;
case POS_ALL:
gmx_calc_comg(pc->coll->top, x, pc->b.nra, pc->b.a, pc->flags & POS_MASS, p->x[0]);
break;
case POS_ALL_PBC:
gmx_calc_comg_pbc(pc->coll->top, x, pbc, pc->b.nra, pc->b.a, pc->flags & POS_MASS, p->x[0]);
break;
default:
gmx_calc_comg_blocka(pc->coll->top, x, &pc->b, pc->flags & POS_MASS, p->x);
break;
}
}
}
static int
print_data(t_topology *top, t_trxframe *fr, t_pbc *pbc,
int nr, gmx_ana_selection_t *sel[], void *data)
{
t_dsdata *d = (t_dsdata *)data;
int g, i, b, mask;
real normfac;
/* Write the sizes of the groups, possibly normalized */
if (d->sfp)
{
fprintf(d->sfp, "%11.3f", fr->time);
for (g = 0; g < nr; ++g)
{
normfac = d->bFracNorm ? 1.0 / sel[g]->cfrac : 1.0;
fprintf(d->sfp, " %8.3f", sel[g]->p.nr * normfac / d->size[g]);
}
fprintf(d->sfp, "\n");
}
/* Write the covered fraction */
if (d->cfp)
{
fprintf(d->cfp, "%11.3f", fr->time);
for (g = 0; g < nr; ++g)
{
fprintf(d->cfp, " %6.4f", sel[g]->cfrac);
}
fprintf(d->cfp, "\n");
}
/* Write the actual indices */
if (d->ifp)
{
if (!d->bDump)
{
fprintf(d->ifp, "%11.3f", fr->time);
}
for (g = 0; g < nr; ++g)
{
if (!d->bDump)
{
fprintf(d->ifp, " %d", sel[g]->p.nr);
}
for (i = 0; i < sel[g]->p.nr; ++i)
{
fprintf(d->ifp, " %d", sel[g]->p.m.mapid[i]+1);
}
}
fprintf(d->ifp, "\n");
}
/* Write masks */
if (d->mfp)
{
gmx_ana_indexmap_update(d->mmap, sel[0]->g, TRUE);
if (!d->bDump)
{
fprintf(d->mfp, "%11.3f", fr->time);
}
for (b = 0; b < d->mmap->nr; ++b)
{
mask = (d->mmap->refid[b] == -1 ? 0 : 1);
fprintf(d->mfp, d->bDump ? "%d\n" : " %d", mask);
}
if (!d->bDump)
{
fprintf(d->mfp, "\n");
}
}
return 0;
}
/*!
* \param[in] pc Position calculation data.
* \param[in,out] p Output positions, initialized previously with
* gmx_ana_poscalc_init_pos() using \p pc.
* \param[in] g Index group to use for the update.
* \param[in] fr Current frame.
* \param[in] pbc PBC data, or NULL if no PBC should be used.
*
* gmx_ana_poscalc_init_frame() should be called for each frame before calling
* this function.
*/
void
gmx_ana_poscalc_update(gmx_ana_poscalc_t *pc, gmx_ana_pos_t *p,
gmx_ana_index_t *g, t_trxframe *fr, t_pbc *pbc)
{
int i, bi, bj;
if (pc->bEval == true && !(pc->flags & POS_MASKONLY))
{
return;
}
if (pc->sbase)
{
gmx_ana_poscalc_update(pc->sbase, NULL, NULL, fr, pbc);
}
if (!p)
{
p = pc->p;
}
if (!g)
{
g = &pc->gmax;
}
gmx_ana_pos_set_evalgrp(p, g);
/* Update the index map */
if (pc->flags & POS_DYNAMIC)
{
gmx_ana_indexmap_update(&p->m, g, false);
p->nr = p->m.nr;
}
else if (pc->flags & POS_MASKONLY)
{
gmx_ana_indexmap_update(&p->m, g, true);
if (pc->bEval)
{
return;
}
}
if (!(pc->flags & POS_DYNAMIC))
{
pc->bEval = true;
}
/* Evaluate the positions */
if (pc->sbase)
{
/* TODO: It might be faster to evaluate the positions within this
* loop instead of in the beginning. */
if (pc->flags & POS_DYNAMIC)
{
for (bi = 0; bi < p->nr; ++bi)
{
bj = pc->baseid[p->m.refid[bi]];
copy_rvec(pc->sbase->p->x[bj], p->x[bi]);
}
if (p->v)
{
for (bi = 0; bi < p->nr; ++bi)
{
bj = pc->baseid[p->m.refid[bi]];
copy_rvec(pc->sbase->p->v[bj], p->v[bi]);
}
}
if (p->f)
{
for (bi = 0; bi < p->nr; ++bi)
{
bj = pc->baseid[p->m.refid[bi]];
copy_rvec(pc->sbase->p->f[bj], p->f[bi]);
}
}
}
else
{
for (bi = 0; bi < p->nr; ++bi)
{
bj = pc->baseid[bi];
copy_rvec(pc->sbase->p->x[bj], p->x[bi]);
}
if (p->v)
{
for (bi = 0; bi < p->nr; ++bi)
{
bj = pc->baseid[bi];
copy_rvec(pc->sbase->p->v[bj], p->v[bi]);
}
}
if (p->f)
{
for (bi = 0; bi < p->nr; ++bi)
{
bj = pc->baseid[bi];
copy_rvec(pc->sbase->p->f[bj], p->f[bi]);
}
}
}
}
else /* pc->sbase is NULL */
{
if (pc->flags & POS_DYNAMIC)
{
pc->b.nr = p->m.mapb.nr;
pc->b.index = p->m.mapb.index;
pc->b.nra = g->isize;
pc->b.a = g->index;
}
if (p->v && !fr->bV)
{
for (i = 0; i < pc->b.nra; ++i)
{
clear_rvec(p->v[i]);
}
}
if (p->f && !fr->bF)
{
for (i = 0; i < pc->b.nra; ++i)
{
clear_rvec(p->f[i]);
}
}
/* Here, we assume that the topology has been properly initialized,
* and do not check the return values of gmx_calc_comg*(). */
t_topology *top = pc->coll->top_;
bool bMass = pc->flags & POS_MASS;
switch (pc->type)
{
case POS_ATOM:
for (i = 0; i < pc->b.nra; ++i)
{
copy_rvec(fr->x[pc->b.a[i]], p->x[i]);
}
if (p->v && fr->bV)
{
for (i = 0; i < pc->b.nra; ++i)
{
copy_rvec(fr->v[pc->b.a[i]], p->v[i]);
}
}
if (p->f && fr->bF)
{
for (i = 0; i < pc->b.nra; ++i)
{
copy_rvec(fr->f[pc->b.a[i]], p->f[i]);
}
}
break;
case POS_ALL:
gmx_calc_comg(top, fr->x, pc->b.nra, pc->b.a, bMass, p->x[0]);
if (p->v && fr->bV)
{
gmx_calc_comg(top, fr->v, pc->b.nra, pc->b.a, bMass, p->v[0]);
}
if (p->f && fr->bF)
{
gmx_calc_comg_f(top, fr->f, pc->b.nra, pc->b.a, bMass, p->f[0]);
}
break;
case POS_ALL_PBC:
gmx_calc_comg_pbc(top, fr->x, pbc, pc->b.nra, pc->b.a, bMass, p->x[0]);
if (p->v && fr->bV)
{
gmx_calc_comg(top, fr->v, pc->b.nra, pc->b.a, bMass, p->v[0]);
}
if (p->f && fr->bF)
{
gmx_calc_comg_f(top, fr->f, pc->b.nra, pc->b.a, bMass, p->f[0]);
}
break;
default:
gmx_calc_comg_blocka(top, fr->x, &pc->b, bMass, p->x);
if (p->v && fr->bV)
{
gmx_calc_comg_blocka(top, fr->v, &pc->b, bMass, p->v);
}
if (p->f && fr->bF)
{
gmx_calc_comg_blocka(top, fr->f, &pc->b, bMass, p->f);
}
break;
}
}
}
static int
print_data(t_topology *top, t_trxframe *fr, t_pbc *pbc,
int nr, gmx_ana_selection_t *sel[], void *data)
{
t_dsdata *d = (t_dsdata *)data;
int g, i, b, mask;
real normfac;
char buf2[100],*buf,*nl;
static int bFirstFrame=1;
/* Write the sizes of the groups, possibly normalized */
if (d->sfp)
{
fprintf(d->sfp, "%11.3f", fr->time);
for (g = 0; g < nr; ++g)
{
normfac = d->bFracNorm ? 1.0 / sel[g]->cfrac : 1.0;
fprintf(d->sfp, " %8.3f", sel[g]->p.nr * normfac / d->size[g]);
}
fprintf(d->sfp, "\n");
}
/* Write the covered fraction */
if (d->cfp)
{
fprintf(d->cfp, "%11.3f", fr->time);
for (g = 0; g < nr; ++g)
{
fprintf(d->cfp, " %6.4f", sel[g]->cfrac);
}
fprintf(d->cfp, "\n");
}
/* Write the actual indices */
if (d->ifp)
{
if (!d->bDump)
{
fprintf(d->ifp, "%11.3f", fr->time);
}
for (g = 0; g < nr; ++g)
{
if (!d->bDump)
{
fprintf(d->ifp, " %d", sel[g]->p.nr);
}
for (i = 0; i < sel[g]->p.nr; ++i)
{
if (sel[g]->p.m.type == INDEX_RES && d->routt[0] == 'n')
{
fprintf(d->ifp, " %d", top->atoms.resinfo[sel[g]->p.m.mapid[i]].nr);
}
else
{
fprintf(d->ifp, " %d", sel[g]->p.m.mapid[i]+1);
}
}
}
fprintf(d->ifp, "\n");
}
if (d->block)
{
for (g = 0; g < nr; ++g)
{
if (sel[g]->bDynamic || bFirstFrame)
{
buf = strdup(sel[g]->name);
while ((nl = strchr(buf, ' ')) != NULL)
{
*nl = '_';
}
if (sel[g]->bDynamic)
{
sprintf(buf2, "_%.3f", fr->time);
srenew(buf, strlen(buf) + strlen(buf2) + 1);
strcat(buf, buf2);
}
add_grp(d->block, &d->gnames, sel[g]->p.nr, sel[g]->p.m.mapid, buf);
sfree(buf);
}
}
}
/* Write masks */
if (d->mfp)
{
gmx_ana_indexmap_update(d->mmap, sel[0]->g, TRUE);
if (!d->bDump)
{
fprintf(d->mfp, "%11.3f", fr->time);
}
for (b = 0; b < d->mmap->nr; ++b)
{
mask = (d->mmap->refid[b] == -1 ? 0 : 1);
fprintf(d->mfp, d->bDump ? "%d\n" : " %d", mask);
}
if (!d->bDump)
{
fprintf(d->mfp, "\n");
}
}
bFirstFrame = 0;
return 0;
}
