#define OPENDIR '[' /* starting sign for directive */
#define CLOSEDIR ']' /* ending sign for directive */
-static void gen_pairs(const InteractionTypeParameters &nbs, InteractionTypeParameters *pairs, real fudge, int comb)
+static void gen_pairs(const InteractionsOfType &nbs, InteractionsOfType *pairs, real fudge, int comb)
{
real scaling;
int ntp = nbs.size();
forceParam[j] = scaling*existingParam[j];
forceParam[nrfp+j] = scaling*existingParam[j];
}
- pairs->interactionTypes.emplace_back(InteractionType(atomNumbers, forceParam));
+ pairs->interactionTypes.emplace_back(InteractionOfType(atomNumbers, forceParam));
i++;
}
}
PreprocessingAtomTypes *atypes,
std::vector<MoleculeInformation> *molinfo,
std::unique_ptr<MoleculeInformation> *intermolecular_interactions,
- gmx::ArrayRef<InteractionTypeParameters> plist,
+ gmx::ArrayRef<InteractionsOfType> interactions,
int *combination_rule,
double *reppow,
t_gromppopts *opts,
*reppow = 12.0; /* Default value for repulsion power */
/* Init the number of CMAP torsion angles and grid spacing */
- plist[F_CMAP].cmakeGridSpacing = 0;
- plist[F_CMAP].cmapAngles = 0;
+ interactions[F_CMAP].cmakeGridSpacing = 0;
+ interactions[F_CMAP].cmapAngles = 0;
bWarn_copy_A_B = bFEP;
break;
case Directive::d_bondtypes:
- push_bt(d, plist, 2, nullptr, &bondAtomType, pline, wi);
+ push_bt(d, interactions, 2, nullptr, &bondAtomType, pline, wi);
break;
case Directive::d_constrainttypes:
- push_bt(d, plist, 2, nullptr, &bondAtomType, pline, wi);
+ push_bt(d, interactions, 2, nullptr, &bondAtomType, pline, wi);
break;
case Directive::d_pairtypes:
if (bGenPairs)
}
else
{
- push_bt(d, plist, 2, atypes, nullptr, pline, wi);
+ push_bt(d, interactions, 2, atypes, nullptr, pline, wi);
}
break;
case Directive::d_angletypes:
- push_bt(d, plist, 3, nullptr, &bondAtomType, pline, wi);
+ push_bt(d, interactions, 3, nullptr, &bondAtomType, pline, wi);
break;
case Directive::d_dihedraltypes:
/* Special routine that can read both 2 and 4 atom dihedral definitions. */
- push_dihedraltype(d, plist, &bondAtomType, pline, wi);
+ push_dihedraltype(d, interactions, &bondAtomType, pline, wi);
break;
case Directive::d_nonbond_params:
break;
case Directive::d_cmaptypes:
- push_cmaptype(d, plist, 5, atypes, &bondAtomType, pline, wi);
+ push_cmaptype(d, interactions, 5, atypes, &bondAtomType, pline, wi);
break;
case Directive::d_moleculetype:
}
ntype = atypes->size();
ncombs = (ntype*(ntype+1))/2;
- generate_nbparams(*combination_rule, nb_funct, &(plist[nb_funct]), atypes, wi);
- ncopy = copy_nbparams(nbparam, nb_funct, &(plist[nb_funct]),
+ generate_nbparams(*combination_rule, nb_funct, &(interactions[nb_funct]), atypes, wi);
+ ncopy = copy_nbparams(nbparam, nb_funct, &(interactions[nb_funct]),
ntype);
fprintf(stderr, "Generated %d of the %d non-bonded parameter combinations\n", ncombs-ncopy, ncombs);
free_nbparam(nbparam, ntype);
if (bGenPairs)
{
- gen_pairs((plist[nb_funct]), &(plist[F_LJ14]), fudgeLJ, *combination_rule);
- ncopy = copy_nbparams(pair, nb_funct, &(plist[F_LJ14]),
+ gen_pairs((interactions[nb_funct]), &(interactions[F_LJ14]), fudgeLJ, *combination_rule);
+ ncopy = copy_nbparams(pair, nb_funct, &(interactions[F_LJ14]),
ntype);
fprintf(stderr, "Generated %d of the %d 1-4 parameter combinations\n", ncombs-ncopy, ncombs);
free_nbparam(pair, ntype);
case Directive::d_pairs:
GMX_RELEASE_ASSERT(mi0, "Need to have a valid MoleculeInformation object to work on");
- push_bond(d, plist, mi0->plist, &(mi0->atoms), atypes, pline, FALSE,
+ push_bond(d, interactions, mi0->interactions, &(mi0->atoms), atypes, pline, FALSE,
bGenPairs, *fudgeQQ, bZero, &bWarn_copy_A_B, wi);
break;
case Directive::d_pairs_nb:
GMX_RELEASE_ASSERT(mi0, "Need to have a valid MoleculeInformation object to work on");
- push_bond(d, plist, mi0->plist, &(mi0->atoms), atypes, pline, FALSE,
+ push_bond(d, interactions, mi0->interactions, &(mi0->atoms), atypes, pline, FALSE,
FALSE, 1.0, bZero, &bWarn_copy_A_B, wi);
break;
case Directive::d_water_polarization:
case Directive::d_thole_polarization:
GMX_RELEASE_ASSERT(mi0, "Need to have a valid MoleculeInformation object to work on");
- push_bond(d, plist, mi0->plist, &(mi0->atoms), atypes, pline, TRUE,
+ push_bond(d, interactions, mi0->interactions, &(mi0->atoms), atypes, pline, TRUE,
bGenPairs, *fudgeQQ, bZero, &bWarn_copy_A_B, wi);
break;
case Directive::d_cmap:
GMX_RELEASE_ASSERT(mi0, "Need to have a valid MoleculeInformation object to work on");
- push_cmap(d, plist, mi0->plist, &(mi0->atoms), atypes, pline, wi);
+ push_cmap(d, interactions, mi0->interactions, &(mi0->atoms), atypes, pline, wi);
break;
case Directive::d_vsitesn:
GMX_RELEASE_ASSERT(mi0, "Need to have a valid MoleculeInformation object to work on");
- push_vsitesn(d, mi0->plist, &(mi0->atoms), pline, wi);
+ push_vsitesn(d, mi0->interactions, &(mi0->atoms), pline, wi);
break;
case Directive::d_exclusions:
GMX_ASSERT(!exclusionBlocks.empty(), "exclusionBlocks must always be allocated so exclusions can be processed");
t_nextnb nnb;
generate_excl(mi0->nrexcl,
mi0->atoms.nr,
- mi0->plist,
+ mi0->interactions,
&nnb,
&(mi0->excls));
gmx::mergeExclusions(&(mi0->excls), exclusionBlocks[whichmol]);
- make_shake(mi0->plist, &mi0->atoms, opts->nshake);
+ make_shake(mi0->interactions, &mi0->atoms, opts->nshake);
done_nnb(&nnb);
convert_moltype_couple(mi0, dcatt, *fudgeQQ,
opts->couple_lam0, opts->couple_lam1,
opts->bCoupleIntra,
- nb_funct, &(plist[nb_funct]), wi);
+ nb_funct, &(interactions[nb_funct]), wi);
}
stupid_fill_block(&mi0->mols, mi0->atoms.nr, TRUE);
mi0->bProcessed = TRUE;
t_gromppopts *opts,
bool bZero,
t_symtab *symtab,
- gmx::ArrayRef<InteractionTypeParameters> plist,
+ gmx::ArrayRef<InteractionsOfType> interactions,
int *combination_rule,
double *repulsion_power,
real *fudgeQQ,
title = read_topol(topfile, tmpfile, opts->define, opts->include,
symtab, atypes,
molinfo, intermolecular_interactions,
- plist, combination_rule, repulsion_power,
+ interactions, combination_rule, repulsion_power,
opts, fudgeQQ, molblock,
ffParametrizedWithHBondConstraints,
ir->efep != efepNO, bZero,
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff