#include "pull.h"
#include "gmx_ga2la.h"
-static void pull_set_pbcatom(t_commrec *cr, t_pullgrp *pg,
+static void pull_set_pbcatom(t_commrec *cr, t_pull_group *pgrp,
t_mdatoms *md, rvec *x,
rvec x_pbc)
{
{
if (DOMAINDECOMP(cr))
{
- if (!ga2la_get_home(cr->dd->ga2la, pg->pbcatom, &a))
+ if (!ga2la_get_home(cr->dd->ga2la, pgrp->pbcatom, &a))
{
a = -1;
}
}
else
{
- a = pg->pbcatom;
+ a = pgrp->pbcatom;
}
if (a >= md->start && a < md->start+md->homenr)
}
else
{
- copy_rvec(x[pg->pbcatom], x_pbc);
+ copy_rvec(x[pgrp->pbcatom], x_pbc);
}
}
int g, n, m;
n = 0;
- for (g = 0; g < 1+pull->ngrp; g++)
+ for (g = 0; g < pull->ngroup; g++)
{
- if ((g == 0 && PULL_CYL(pull)) || pull->grp[g].pbcatom == -1)
+ if ((g == 0 && PULL_CYL(pull)) || pull->group[g].pbcatom == -1)
{
clear_rvec(x_pbc[g]);
}
else
{
- pull_set_pbcatom(cr, &pull->grp[g], md, x, x_pbc[g]);
+ pull_set_pbcatom(cr, &pull->group[g], md, x, x_pbc[g]);
for (m = 0; m < DIM; m++)
{
if (pull->dim[m] == 0)
if (cr && PAR(cr) && n > 0)
{
/* Sum over the nodes to get x_pbc from the home node of pbcatom */
- gmx_sum((1+pull->ngrp)*DIM, x_pbc[0], cr);
+ gmx_sum(pull->ngroup*DIM, x_pbc[0], cr);
}
}
static void make_cyl_refgrps(t_commrec *cr, t_pull *pull, t_mdatoms *md,
t_pbc *pbc, double t, rvec *x, rvec *xp)
{
- int g, i, ii, m, start, end;
- rvec g_x, dx, dir;
- double r0_2, sum_a, sum_ap, dr2, mass, weight, wmass, wwmass, inp;
- t_pullgrp *pref, *pgrp, *pdyna;
- gmx_ga2la_t ga2la = NULL;
+ int c, i, ii, m, start, end;
+ rvec g_x, dx, dir;
+ double r0_2, sum_a, sum_ap, dr2, mass, weight, wmass, wwmass, inp;
+ t_pull_coord *pcrd;
+ t_pull_group *pref, *pgrp, *pdyna;
+ gmx_ga2la_t ga2la = NULL;
if (pull->dbuf_cyl == NULL)
{
- snew(pull->dbuf_cyl, pull->ngrp*4);
+ snew(pull->dbuf_cyl, pull->ncoord*4);
}
if (cr && DOMAINDECOMP(cr))
r0_2 = dsqr(pull->cyl_r0);
/* loop over all groups to make a reference group for each*/
- pref = &pull->grp[0];
- for (g = 1; g < 1+pull->ngrp; g++)
+ for (c = 0; c < pull->ncoord; c++)
{
- pgrp = &pull->grp[g];
- pdyna = &pull->dyna[g];
- copy_rvec(pgrp->vec, dir);
+ pcrd = &pull->coord[c];
+
+ /* pref will be the same group for all pull coordinates */
+ pref = &pull->group[pcrd->group[0]];
+ pgrp = &pull->group[pcrd->group[1]];
+ pdyna = &pull->dyna[c];
+ copy_rvec(pcrd->vec, dir);
sum_a = 0;
sum_ap = 0;
wmass = 0;
for (m = 0; m < DIM; m++)
{
- g_x[m] = pgrp->x[m] - pgrp->vec[m]*(pgrp->init[0] + pgrp->rate*t);
+ g_x[m] = pgrp->x[m] - pcrd->vec[m]*(pcrd->init + pcrd->rate*t);
}
/* loop over all atoms in the main ref group */
for (i = 0; i < pref->nat; i++)
{
- ii = pull->grp[0].ind[i];
+ ii = pref->ind[i];
if (ga2la)
{
if (!ga2la_get_home(ga2la, pref->ind[i], &ii))
}
}
}
- pull->dbuf_cyl[(g-1)*4+0] = wmass;
- pull->dbuf_cyl[(g-1)*4+1] = wwmass;
- pull->dbuf_cyl[(g-1)*4+2] = sum_a;
- pull->dbuf_cyl[(g-1)*4+3] = sum_ap;
+ pull->dbuf_cyl[c*4+0] = wmass;
+ pull->dbuf_cyl[c*4+1] = wwmass;
+ pull->dbuf_cyl[c*4+2] = sum_a;
+ pull->dbuf_cyl[c*4+3] = sum_ap;
}
if (cr && PAR(cr))
{
/* Sum the contributions over the nodes */
- gmx_sumd(pull->ngrp*4, pull->dbuf_cyl, cr);
+ gmx_sumd(pull->ncoord*4, pull->dbuf_cyl, cr);
}
- for (g = 1; g < 1+pull->ngrp; g++)
+ for (c = 0; c < pull->ncoord; c++)
{
- pgrp = &pull->grp[g];
- pdyna = &pull->dyna[g];
+ pcrd = &pull->coord[c];
+
+ pdyna = &pull->dyna[c];
+ pgrp = &pull->group[pcrd->group[1]];
- wmass = pull->dbuf_cyl[(g-1)*4+0];
- wwmass = pull->dbuf_cyl[(g-1)*4+1];
+ wmass = pull->dbuf_cyl[c*4+0];
+ wwmass = pull->dbuf_cyl[c*4+1];
pdyna->wscale = wmass/wwmass;
pdyna->invtm = 1.0/(pdyna->wscale*wmass);
for (m = 0; m < DIM; m++)
{
- g_x[m] = pgrp->x[m] - pgrp->vec[m]*(pgrp->init[0] + pgrp->rate*t);
- pdyna->x[m] = g_x[m] + pgrp->vec[m]*pull->dbuf_cyl[(g-1)*4+2]/wmass;
+ g_x[m] = pgrp->x[m] - pcrd->vec[m]*(pcrd->init + pcrd->rate*t);
+ pdyna->x[m] = g_x[m] + pcrd->vec[m]*pull->dbuf_cyl[c*4+2]/wmass;
if (xp)
{
- pdyna->xp[m] = g_x[m] + pgrp->vec[m]*pull->dbuf_cyl[(g-1)*4+3]/wmass;
+ pdyna->xp[m] = g_x[m] + pcrd->vec[m]*pull->dbuf_cyl[c*4+3]/wmass;
}
}
if (debug)
{
fprintf(debug, "Pull cylinder group %d:%8.3f%8.3f%8.3f m:%8.3f\n",
- g, pdyna->x[0], pdyna->x[1],
+ c, pdyna->x[0], pdyna->x[1],
pdyna->x[2], 1.0/pdyna->invtm);
}
}
t_pull *pull, t_mdatoms *md, t_pbc *pbc, double t,
rvec x[], rvec *xp)
{
- int g, i, ii, m;
- real mass, w, wm, twopi_box = 0;
- double wmass, wwmass, invwmass;
- dvec com, comp;
- double cm, sm, cmp, smp, ccm, csm, ssm, csw, snw;
- rvec *xx[2], x_pbc = {0, 0, 0}, dx;
- t_pullgrp *pgrp;
+ int g, i, ii, m;
+ real mass, w, wm, twopi_box = 0;
+ double wmass, wwmass, invwmass;
+ dvec com, comp;
+ double cm, sm, cmp, smp, ccm, csm, ssm, csw, snw;
+ rvec *xx[2], x_pbc = {0, 0, 0}, dx;
+ t_pull_group *pgrp;
if (pull->rbuf == NULL)
{
- snew(pull->rbuf, 1+pull->ngrp);
+ snew(pull->rbuf, pull->ngroup);
}
if (pull->dbuf == NULL)
{
- snew(pull->dbuf, 3*(1+pull->ngrp));
+ snew(pull->dbuf, 3*pull->ngroup);
}
if (pull->bRefAt)
twopi_box = 2.0*M_PI/pbc->box[pull->cosdim][pull->cosdim];
}
- for (g = 0; g < 1+pull->ngrp; g++)
+ for (g = 0; g < pull->ngroup; g++)
{
- pgrp = &pull->grp[g];
+ pgrp = &pull->group[g];
clear_dvec(com);
clear_dvec(comp);
wmass = 0;
if (cr && PAR(cr))
{
/* Sum the contributions over the nodes */
- gmx_sumd((1+pull->ngrp)*3*DIM, pull->dbuf[0], cr);
+ gmx_sumd(pull->ngroup*3*DIM, pull->dbuf[0], cr);
}
- for (g = 0; g < 1+pull->ngrp; g++)
+ for (g = 0; g < pull->ngroup; g++)
{
- pgrp = &pull->grp[g];
+ pgrp = &pull->group[g];
if (pgrp->nat > 0 && !(g == 0 && PULL_CYL(pull)))
{
if (pgrp->epgrppbc != epgrppbcCOS)
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff