*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
//! Recursing function to help find all adjacent constraints.
-static void constr_recur(const t_blocka *at2con,
- const InteractionLists &ilist,
+static void constr_recur(const t_blocka* at2con,
+ const InteractionLists& ilist,
gmx::ArrayRef<const t_iparams> iparams,
- gmx_bool bTopB,
- int at, int depth, int nc, int *path,
- real r0, real r1, real *r2max,
- int *count)
+ gmx_bool bTopB,
+ int at,
+ int depth,
+ int nc,
+ int* path,
+ real r0,
+ real r1,
+ real* r2max,
+ int* count)
{
int c, con, a1;
gmx_bool bUse;
gmx::ArrayRef<const int> ia2 = ilist[F_CONSTRNC].iatoms;
/* Loop over all constraints connected to this atom */
- for (c = at2con->index[at]; c < at2con->index[at+1]; c++)
+ for (c = at2con->index[at]; c < at2con->index[at + 1]; c++)
{
con = at2con->a[c];
/* Do not walk over already used constraints */
}
if (bUse)
{
- const int *ia = constr_iatomptr(ia1, ia2, con);
+ const int* ia = constr_iatomptr(ia1, ia2, con);
/* Flexible constraints currently have length 0, which is incorrect */
if (!bTopB)
{
rn1 = r1 + len;
}
/* Assume angles of 120 degrees between all bonds */
- if (rn0*rn0 + rn1*rn1 + rn0*rn1 > *r2max)
+ if (rn0 * rn0 + rn1 * rn1 + rn0 * rn1 > *r2max)
{
- *r2max = rn0*rn0 + rn1*rn1 + r0*rn1;
+ *r2max = rn0 * rn0 + rn1 * rn1 + r0 * rn1;
if (debug)
{
- fprintf(debug, "Found longer constraint distance: r0 %5.3f r1 %5.3f rmax %5.3f\n", rn0, rn1, sqrt(*r2max));
+ fprintf(debug,
+ "Found longer constraint distance: r0 %5.3f r1 %5.3f rmax %5.3f\n", rn0,
+ rn1, sqrt(*r2max));
for (a1 = 0; a1 < depth; a1++)
{
- fprintf(debug, " %d %5.3f",
- path[a1],
+ fprintf(debug, " %d %5.3f", path[a1],
iparams[constr_iatomptr(ia1, ia2, con)[0]].constr.dA);
}
fprintf(debug, " %d %5.3f\n", con, len);
* so a call does not take more than a second,
* even for highly connected systems.
*/
- if (depth + 1 < nc && *count < 1000*nc)
+ if (depth + 1 < nc && *count < 1000 * nc)
{
if (ia[1] == at)
{
}
/* Recursion */
path[depth] = con;
- constr_recur(at2con, ilist, iparams,
- bTopB, a1, depth+1, nc, path, rn0, rn1, r2max, count);
+ constr_recur(at2con, ilist, iparams, bTopB, a1, depth + 1, nc, path, rn0, rn1, r2max, count);
path[depth] = -1;
}
}
}
//! Find the interaction radius needed for constraints for this molecule type.
-static real constr_r_max_moltype(const gmx_moltype_t *molt,
- gmx::ArrayRef<const t_iparams> iparams,
- const t_inputrec *ir)
+static real constr_r_max_moltype(const gmx_moltype_t* molt,
+ gmx::ArrayRef<const t_iparams> iparams,
+ const t_inputrec* ir)
{
- int natoms, *path, at, count;
+ int natoms, *path, at, count;
t_blocka at2con;
real r0, r1, r2maxA, r2maxB, rmax, lam0, lam1;
- if (molt->ilist[F_CONSTR].size() == 0 &&
- molt->ilist[F_CONSTRNC].size() == 0)
+ if (molt->ilist[F_CONSTR].size() == 0 && molt->ilist[F_CONSTRNC].size() == 0)
{
return 0;
}
natoms = molt->atoms.nr;
- at2con = make_at2con(*molt, iparams,
- flexibleConstraintTreatment(EI_DYNAMICS(ir->eI)));
- snew(path, 1+ir->nProjOrder);
- for (at = 0; at < 1+ir->nProjOrder; at++)
+ at2con = make_at2con(*molt, iparams, flexibleConstraintTreatment(EI_DYNAMICS(ir->eI)));
+ snew(path, 1 + ir->nProjOrder);
+ for (at = 0; at < 1 + ir->nProjOrder; at++)
{
path[at] = -1;
}
r1 = 0;
count = 0;
- constr_recur(&at2con, molt->ilist, iparams,
- FALSE, at, 0, 1+ir->nProjOrder, path, r0, r1, &r2maxA, &count);
+ constr_recur(&at2con, molt->ilist, iparams, FALSE, at, 0, 1 + ir->nProjOrder, path, r0, r1,
+ &r2maxA, &count);
}
if (ir->efep == efepNO)
{
r0 = 0;
r1 = 0;
count = 0;
- constr_recur(&at2con, molt->ilist, iparams,
- TRUE, at, 0, 1+ir->nProjOrder, path, r0, r1, &r2maxB, &count);
+ constr_recur(&at2con, molt->ilist, iparams, TRUE, at, 0, 1 + ir->nProjOrder, path, r0,
+ r1, &r2maxB, &count);
}
lam0 = ir->fepvals->init_lambda;
if (EI_DYNAMICS(ir->eI))
{
- lam0 += ir->init_step*ir->fepvals->delta_lambda;
+ lam0 += ir->init_step * ir->fepvals->delta_lambda;
}
- rmax = (1 - lam0)*sqrt(r2maxA) + lam0*sqrt(r2maxB);
+ rmax = (1 - lam0) * sqrt(r2maxA) + lam0 * sqrt(r2maxB);
if (EI_DYNAMICS(ir->eI))
{
- lam1 = ir->fepvals->init_lambda + (ir->init_step + ir->nsteps)*ir->fepvals->delta_lambda;
- rmax = std::max(rmax, (1 - lam1)*std::sqrt(r2maxA) + lam1*std::sqrt(r2maxB));
+ lam1 = ir->fepvals->init_lambda + (ir->init_step + ir->nsteps) * ir->fepvals->delta_lambda;
+ rmax = std::max(rmax, (1 - lam1) * std::sqrt(r2maxA) + lam1 * std::sqrt(r2maxB));
}
}
return rmax;
}
-real constr_r_max(const MDLogger &mdlog, const gmx_mtop_t *mtop, const t_inputrec *ir)
+real constr_r_max(const MDLogger& mdlog, const gmx_mtop_t* mtop, const t_inputrec* ir)
{
real rmax = 0;
- for (const gmx_moltype_t &molt : mtop->moltype)
+ for (const gmx_moltype_t& molt : mtop->moltype)
{
- rmax = std::max(rmax,
- constr_r_max_moltype(&molt,
- mtop->ffparams.iparams, ir));
+ rmax = std::max(rmax, constr_r_max_moltype(&molt, mtop->ffparams.iparams, ir));
}
- GMX_LOG(mdlog.info).appendTextFormatted(
- "Maximum distance for %d constraints, at 120 deg. angles, all-trans: %.3f nm",
- 1+ir->nProjOrder, rmax);
+ GMX_LOG(mdlog.info)
+ .appendTextFormatted(
+ "Maximum distance for %d constraints, at 120 deg. angles, all-trans: %.3f nm",
+ 1 + ir->nProjOrder, rmax);
return rmax;
}
-} // namespace gmx
+} // namespace gmx
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff