void make_local_shells(t_commrec *cr,t_mdatoms *md,
struct gmx_shellfc *shfc)
{
t_shell *shell;
int a0,a1,*ind,nshell,i;
gmx_domdec_t *dd=NULL;
if (PAR(cr)) {
if (DOMAINDECOMP(cr)) {
dd = cr->dd;
a0 = 0;
a1 = dd->nat_home;
} else {
pd_at_range(cr,&a0,&a1);
}
} else {
/* Single node: we need all shells, just copy the pointer */
shfc->nshell = shfc->nshell_gl;
shfc->shell = shfc->shell_gl;
return;
}
ind = shfc->shell_index_gl;
nshell = 0;
shell = shfc->shell;
for(i=a0; i<a1; i++) {
if (md->ptype[i] == eptShell) {
if (nshell+1 > shfc->shell_nalloc) {
shfc->shell_nalloc = over_alloc_dd(nshell+1);
srenew(shell,shfc->shell_nalloc);
}
if (dd) {
shell[nshell] = shfc->shell_gl[ind[dd->gatindex[i]]];
} else {
shell[nshell] = shfc->shell_gl[ind[i]];
}
/* With inter-cg shells we can no do shell prediction,
* so we do not need the nuclei numbers.
*/
if (!shfc->bInterCG) {
shell[nshell].nucl1 = i + shell[nshell].nucl1 - shell[nshell].shell;
if (shell[nshell].nnucl > 1)
shell[nshell].nucl2 = i + shell[nshell].nucl2 - shell[nshell].shell;
if (shell[nshell].nnucl > 2)
shell[nshell].nucl3 = i + shell[nshell].nucl3 - shell[nshell].shell;
}
shell[nshell].shell = i;
nshell++;
}
}
shfc->nshell = nshell;
shfc->shell = shell;
}
void init_pull(FILE *fplog, t_inputrec *ir, int nfile, const t_filenm fnm[],
gmx_mtop_t *mtop, t_commrec *cr, const output_env_t oenv, real lambda,
gmx_bool bOutFile, unsigned long Flags)
{
t_pull *pull;
t_pull_group *pgrp;
int c, g, start = 0, end = 0, m;
pull = ir->pull;
pull->ePBC = ir->ePBC;
switch (pull->ePBC)
{
case epbcNONE: pull->npbcdim = 0; break;
case epbcXY: pull->npbcdim = 2; break;
default: pull->npbcdim = 3; break;
}
if (fplog)
{
gmx_bool bAbs, bCos;
bAbs = FALSE;
for (c = 0; c < pull->ncoord; c++)
{
if (pull->group[pull->coord[c].group[0]].nat == 0 ||
pull->group[pull->coord[c].group[1]].nat == 0)
{
bAbs = TRUE;
}
}
fprintf(fplog, "\nWill apply %s COM pulling in geometry '%s'\n",
EPULLTYPE(ir->ePull), EPULLGEOM(pull->eGeom));
fprintf(fplog, "with %d pull coordinate%s and %d group%s\n",
pull->ncoord, pull->ncoord == 1 ? "" : "s",
pull->ngroup, pull->ngroup == 1 ? "" : "s");
if (bAbs)
{
fprintf(fplog, "with an absolute reference\n");
}
bCos = FALSE;
for (g = 0; g < pull->ngroup; g++)
{
if (pull->group[g].nat > 1 &&
pull->group[g].pbcatom < 0)
{
/* We are using cosine weighting */
fprintf(fplog, "Cosine weighting is used for group %d\n", g);
bCos = TRUE;
}
}
if (bCos)
{
please_cite(fplog, "Engin2010");
}
}
/* We always add the virial contribution,
* except for geometry = direction_periodic where this is impossible.
*/
pull->bVirial = (pull->eGeom != epullgDIRPBC);
if (getenv("GMX_NO_PULLVIR") != NULL)
{
if (fplog)
{
fprintf(fplog, "Found env. var., will not add the virial contribution of the COM pull forces\n");
}
pull->bVirial = FALSE;
}
if (cr && PARTDECOMP(cr))
{
pd_at_range(cr, &start, &end);
}
pull->rbuf = NULL;
pull->dbuf = NULL;
pull->dbuf_cyl = NULL;
pull->bRefAt = FALSE;
pull->cosdim = -1;
for (g = 0; g < pull->ngroup; g++)
{
pgrp = &pull->group[g];
pgrp->epgrppbc = epgrppbcNONE;
if (pgrp->nat > 0)
{
/* Determine if we need to take PBC into account for calculating
* the COM's of the pull groups.
*/
for (m = 0; m < pull->npbcdim; m++)
{
if (pull->dim[m] && pgrp->nat > 1)
{
if (pgrp->pbcatom >= 0)
{
pgrp->epgrppbc = epgrppbcREFAT;
pull->bRefAt = TRUE;
}
else
{
if (pgrp->weight)
{
gmx_fatal(FARGS, "Pull groups can not have relative weights and cosine weighting at same time");
}
pgrp->epgrppbc = epgrppbcCOS;
if (pull->cosdim >= 0 && pull->cosdim != m)
{
gmx_fatal(FARGS, "Can only use cosine weighting with pulling in one dimension (use mdp option pull_dim)");
}
pull->cosdim = m;
}
}
}
/* Set the indices */
init_pull_group_index(fplog, cr, start, end, g, pgrp, pull->dim, mtop, ir, lambda);
if (PULL_CYL(pull) && pgrp->invtm == 0)
{
gmx_fatal(FARGS, "Can not have frozen atoms in a cylinder pull group");
}
}
else
{
/* Absolute reference, set the inverse mass to zero */
pgrp->invtm = 0;
pgrp->wscale = 1;
}
}
/* if we use dynamic reference groups, do some initialising for them */
if (PULL_CYL(pull))
{
if (ir->ePull == epullCONSTRAINT && pull->ncoord > 1)
{
/* We can't easily update the single reference group with multiple
* constraints. This would require recalculating COMs.
*/
gmx_fatal(FARGS, "Constraint COM pulling supports only one coordinate with geometry=cylinder, you can use umbrella pulling with multiple coordinates");
}
for (c = 0; c < pull->ncoord; c++)
{
if (pull->group[pull->coord[c].group[0]].nat == 0)
{
gmx_fatal(FARGS, "Dynamic reference groups are not supported when using absolute reference!\n");
}
}
snew(pull->dyna, pull->ncoord);
}
/* Only do I/O when we are doing dynamics and if we are the MASTER */
pull->out_x = NULL;
pull->out_f = NULL;
if (bOutFile)
{
if (pull->nstxout > 0)
{
pull->out_x = open_pull_out(opt2fn("-px", nfile, fnm), pull, oenv, TRUE, Flags);
}
if (pull->nstfout > 0)
{
pull->out_f = open_pull_out(opt2fn("-pf", nfile, fnm), pull, oenv,
FALSE, Flags);
}
}
}
