* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, 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.
if (r - i > 0.01 || r - i < -0.01)
{
- gmx_fatal(FARGS, "A non-integer value (%f) was supplied for '%s' in %s", r, name,
+ gmx_fatal(FARGS,
+ "A non-integer value (%f) was supplied for '%s' in %s",
+ r,
+ name,
interaction_function[ftype].longname);
}
if (i < limit)
{
- gmx_fatal(FARGS, "Value of '%s' in %s is %d, which is smaller than the minimum of %d", name,
- interaction_function[ftype].longname, i, limit);
+ gmx_fatal(FARGS,
+ "Value of '%s' in %s is %d, which is smaller than the minimum of %d",
+ name,
+ interaction_function[ftype].longname,
+ i,
+ limit);
}
return i;
}
-static void set_ljparams(int comb, double reppow, double v, double w, real* c6, real* c12)
+static void set_ljparams(CombinationRule comb, double reppow, double v, double w, real* c6, real* c12)
{
- if (comb == eCOMB_ARITHMETIC || comb == eCOMB_GEOM_SIG_EPS)
+ if (comb == CombinationRule::Arithmetic || comb == CombinationRule::GeomSigEps)
{
if (v >= 0)
{
/* A return value of 0 means parameters were assigned successfully,
* returning -1 means this is an all-zero interaction that should not be added.
*/
-static int assign_param(t_functype ftype, t_iparams* newparam, gmx::ArrayRef<const real> old, int comb, double reppow)
+static int assign_param(t_functype ftype,
+ t_iparams* newparam,
+ gmx::ArrayRef<const real> old,
+ CombinationRule comb,
+ double reppow)
{
bool all_param_zero = true;
{
case F_G96ANGLES:
/* Post processing of input data: store cosine iso angle itself */
- newparam->harmonic.rA = cos(old[0] * DEG2RAD);
+ newparam->harmonic.rA = cos(old[0] * gmx::c_deg2Rad);
newparam->harmonic.krA = old[1];
- newparam->harmonic.rB = cos(old[2] * DEG2RAD);
+ newparam->harmonic.rB = cos(old[2] * gmx::c_deg2Rad);
newparam->harmonic.krB = old[3];
break;
case F_G96BONDS:
newparam->thole.a = old[0];
newparam->thole.alpha1 = old[1];
newparam->thole.alpha2 = old[2];
- if ((old[1] > 0) && (old[2] > 0))
- {
- newparam->thole.rfac = old[0] * gmx::invsixthroot(old[1] * old[2]);
- }
- else
- {
- newparam->thole.rfac = 1;
- }
break;
case F_BHAM:
newparam->bham.a = old[0];
gmx_fatal(FARGS,
"Invalid geometry for flat-bottomed position restraint.\n"
"Expected number between 1 and %d. Found %d\n",
- efbposresNR - 1, newparam->fbposres.geom);
+ efbposresNR - 1,
+ newparam->fbposres.geom);
}
newparam->fbposres.r = old[1];
newparam->fbposres.k = old[2];
newparam->settle.doh = old[0];
newparam->settle.dhh = old[1];
break;
+ case F_VSITE1:
case F_VSITE2:
case F_VSITE2FD:
case F_VSITE3:
newparam->vsite.f = old[5];
break;
case F_VSITE3FAD:
- newparam->vsite.a = old[1] * cos(DEG2RAD * old[0]);
- newparam->vsite.b = old[1] * sin(DEG2RAD * old[0]);
+ newparam->vsite.a = old[1] * cos(gmx::c_deg2Rad * old[0]);
+ newparam->vsite.b = old[1] * sin(gmx::c_deg2Rad * old[0]);
newparam->vsite.c = old[2];
newparam->vsite.d = old[3];
newparam->vsite.e = old[4];
static int enter_params(gmx_ffparams_t* ffparams,
t_functype ftype,
gmx::ArrayRef<const real> forceparams,
- int comb,
+ CombinationRule comb,
real reppow,
int start,
bool bAppend)
{
t_iparams newparam;
- int type;
int rc;
if ((rc = assign_param(ftype, &newparam, forceparams, comb, reppow)) < 0)
if (!bAppend)
{
- for (type = start; (type < ffparams->numTypes()); type++)
+ if (ftype != F_DISRES)
{
- if (ffparams->functype[type] == ftype)
+ for (int type = start; type < ffparams->numTypes(); type++)
{
- if (memcmp(&newparam, &ffparams->iparams[type], static_cast<size_t>(sizeof(newparam))) == 0)
+ // Note that the first condition is always met by starting the loop at start
+ if (ffparams->functype[type] == ftype
+ && memcmp(&newparam, &ffparams->iparams[type], static_cast<size_t>(sizeof(newparam))) == 0)
{
return type;
}
}
}
+ else
+ {
+ // Distance restraints should have unique labels and pairs with the same label
+ // should be consecutive, so we here we only need to check the last type in the list.
+ // This changes the complexity from quadratic to linear in the number of restraints.
+ const int type = ffparams->numTypes() - 1;
+ if (type >= 0 && ffparams->functype[type] == ftype
+ && memcmp(&newparam, &ffparams->iparams[type], static_cast<size_t>(sizeof(newparam))) == 0)
+ {
+ return type;
+ }
+ }
}
- else
- {
- type = ffparams->numTypes();
- }
+
+ const int type = ffparams->numTypes();
ffparams->iparams.push_back(newparam);
ffparams->functype.push_back(ftype);
static void enter_function(const InteractionsOfType* p,
t_functype ftype,
- int comb,
+ CombinationRule comb,
real reppow,
gmx_ffparams_t* ffparams,
InteractionList* il,
{
int start = ffparams->numTypes();
- for (auto& parm : p->interactionTypes)
+ for (const auto& parm : p->interactionTypes)
{
int type = enter_params(ffparams, ftype, parm.forceParam(), comb, reppow, start, bAppend);
/* Type==-1 is used as a signal that this interaction is all-zero and should not be added. */
gmx::ArrayRef<const InteractionsOfType> nbtypes,
gmx::ArrayRef<const MoleculeInformation> mi,
const MoleculeInformation* intermolecular_interactions,
- int comb,
+ CombinationRule comb,
double reppow,
real fudgeQQ,
gmx_mtop_t* mtop)
ffp->reppow = reppow;
enter_function(&(nbtypes[F_LJ]), static_cast<t_functype>(F_LJ), comb, reppow, ffp, nullptr, TRUE, TRUE);
- enter_function(&(nbtypes[F_BHAM]), static_cast<t_functype>(F_BHAM), comb, reppow, ffp, nullptr,
- TRUE, TRUE);
+ enter_function(
+ &(nbtypes[F_BHAM]), static_cast<t_functype>(F_BHAM), comb, reppow, ffp, nullptr, TRUE, TRUE);
for (size_t mt = 0; mt < mtop->moltype.size(); mt++)
{
if ((i != F_LJ) && (i != F_BHAM)
&& ((flags & IF_BOND) || (flags & IF_VSITE) || (flags & IF_CONSTRAINT)))
{
- enter_function(&(interactions[i]), static_cast<t_functype>(i), comb, reppow, ffp,
- &molt->ilist[i], FALSE, (i == F_POSRES || i == F_FBPOSRES));
+ enter_function(&(interactions[i]),
+ static_cast<t_functype>(i),
+ comb,
+ reppow,
+ ffp,
+ &molt->ilist[i],
+ FALSE,
+ (i == F_POSRES || i == F_FBPOSRES));
}
}
}
}
else
{
- enter_function(&(interactions[i]), static_cast<t_functype>(i), comb, reppow,
- ffp, &(*mtop->intermolecular_ilist)[i], FALSE, FALSE);
+ enter_function(&(interactions[i]),
+ static_cast<t_functype>(i),
+ comb,
+ reppow,
+ ffp,
+ &(*mtop->intermolecular_ilist)[i],
+ FALSE,
+ FALSE);
mtop->bIntermolecularInteractions = TRUE;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff