if (((m <= 0.0) || (mB <= 0.0)) && ((pt == eptAtom) || (pt == eptNucleus)))
{
ri = atoms->atom[i].resind;
- sprintf(buf, "atom %s (Res %s-%d) has mass %g (state A) / %g (state B)\n",
- *(atoms->atomname[i]), *(atoms->resinfo[ri].name), atoms->resinfo[ri].nr, m, mB);
+ sprintf(buf,
+ "atom %s (Res %s-%d) has mass %g (state A) / %g (state B)\n",
+ *(atoms->atomname[i]),
+ *(atoms->resinfo[ri].name),
+ atoms->resinfo[ri].nr,
+ m,
+ mB);
warning_error(wi, buf);
}
else if (((m != 0) || (mB != 0)) && (pt == eptVSite))
"virtual site %s (Res %s-%d) has non-zero mass %g (state A) / %g (state "
"B)\n"
" Check your topology.\n",
- *(atoms->atomname[i]), *(atoms->resinfo[ri].name), atoms->resinfo[ri].nr, m, mB);
+ *(atoms->atomname[i]),
+ *(atoms->resinfo[ri].name),
+ atoms->resinfo[ri].nr,
+ m,
+ mB);
warning_error(wi, buf);
/* The following statements make LINCS break! */
/* atoms->atom[i].m=0; */
{
/* we should print here which directives should have
been present, and which actually are */
- gmx_fatal(FARGS, "%s\nInvalid order for directive %s",
- cpp_error(&handle, eCPP_SYNTAX), dir2str(newd));
+ gmx_fatal(FARGS,
+ "%s\nInvalid order for directive %s",
+ cpp_error(&handle, eCPP_SYNTAX),
+ dir2str(newd));
/* d = Directive::d_invalid; */
}
case Directive::d_defaults:
if (bReadDefaults)
{
- gmx_fatal(FARGS, "%s\nFound a second defaults directive.\n",
+ gmx_fatal(FARGS,
+ "%s\nFound a second defaults directive.\n",
cpp_error(&handle, eCPP_SYNTAX));
}
bReadDefaults = TRUE;
- nscan = sscanf(pline, "%s%s%s%lf%lf%lf", nb_str, comb_str, genpairs,
- &fLJ, &fQQ, &fPOW);
+ nscan = sscanf(
+ pline, "%s%s%s%lf%lf%lf", nb_str, comb_str, genpairs, &fLJ, &fQQ, &fPOW);
if (nscan < 2)
{
too_few(wi);
break;
case Directive::d_atomtypes:
- push_at(symtab, atypes, &bondAtomType, pline, nb_funct, &nbparam,
- bGenPairs ? &pair : nullptr, wi);
+ push_at(symtab,
+ atypes,
+ &bondAtomType,
+ pline,
+ nb_funct,
+ &nbparam,
+ bGenPairs ? &pair : nullptr,
+ wi);
break;
case Directive::d_bondtypes: // Intended to fall through
|| opts->couple_lam1 == ecouplamNONE
|| opts->couple_lam1 == ecouplamQ))
{
- dcatt = add_atomtype_decoupled(symtab, atypes, &nbparam,
- bGenPairs ? &pair : nullptr);
+ dcatt = add_atomtype_decoupled(
+ symtab, atypes, &nbparam, bGenPairs ? &pair : nullptr);
}
ntype = atypes->size();
ncombs = (ntype * (ntype + 1)) / 2;
- generate_nbparams(*combination_rule, nb_funct,
- &(interactions[nb_funct]), atypes, wi);
+ generate_nbparams(
+ *combination_rule, nb_funct, &(interactions[nb_funct]), atypes, wi);
ncopy = copy_nbparams(nbparam, nb_funct, &(interactions[nb_funct]), ntype);
GMX_LOG(logger.info)
.asParagraph()
.appendTextFormatted(
"Generated %d of the %d non-bonded parameter "
"combinations",
- ncombs - ncopy, ncombs);
+ ncombs - ncopy,
+ ncombs);
free_nbparam(nbparam, ntype);
if (bGenPairs)
{
- gen_pairs((interactions[nb_funct]), &(interactions[F_LJ14]),
- fudgeLJ, *combination_rule);
+ gen_pairs((interactions[nb_funct]),
+ &(interactions[F_LJ14]),
+ fudgeLJ,
+ *combination_rule);
ncopy = copy_nbparams(pair, nb_funct, &(interactions[F_LJ14]), ntype);
GMX_LOG(logger.info)
.asParagraph()
.appendTextFormatted(
"Generated %d of the %d 1-4 parameter "
"combinations",
- ncombs - ncopy, ncombs);
+ ncombs - ncopy,
+ ncombs);
free_nbparam(pair, ntype);
}
/* Copy GBSA parameters to atomtype array? */
GMX_RELEASE_ASSERT(
mi0,
"Need to have a valid MoleculeInformation object to work on");
- push_bond(d, interactions, mi0->interactions, &(mi0->atoms), atypes,
- pline, FALSE, bGenPairs, *fudgeQQ, bZero, &bWarn_copy_A_B, wi);
+ 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, interactions, mi0->interactions, &(mi0->atoms), atypes,
- pline, FALSE, FALSE, 1.0, bZero, &bWarn_copy_A_B, wi);
+ push_bond(d,
+ interactions,
+ mi0->interactions,
+ &(mi0->atoms),
+ atypes,
+ pline,
+ FALSE,
+ FALSE,
+ 1.0,
+ bZero,
+ &bWarn_copy_A_B,
+ wi);
break;
case Directive::d_vsites2:
GMX_RELEASE_ASSERT(
mi0,
"Need to have a valid MoleculeInformation object to work on");
- push_bond(d, interactions, mi0->interactions, &(mi0->atoms), atypes,
- pline, TRUE, bGenPairs, *fudgeQQ, bZero, &bWarn_copy_A_B, wi);
+ 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(
.asParagraph()
.appendTextFormatted(
"Excluding %d bonded neighbours molecule type '%s'",
- mi0->nrexcl, *mi0->name);
+ mi0->nrexcl,
+ *mi0->name);
sum_q(&mi0->atoms, nrcopies, &qt, &qBt);
if (!mi0->bProcessed)
{
if (bCouple)
{
- convert_moltype_couple(mi0, dcatt, *fudgeQQ, opts->couple_lam0,
- opts->couple_lam1, opts->bCoupleIntra,
- nb_funct, &(interactions[nb_funct]), wi);
+ convert_moltype_couple(mi0,
+ dcatt,
+ *fudgeQQ,
+ opts->couple_lam0,
+ opts->couple_lam1,
+ opts->bCoupleIntra,
+ nb_funct,
+ &(interactions[nb_funct]),
+ wi);
}
stupid_fill_block(&mi0->mols, mi0->atoms.nr, TRUE);
mi0->bProcessed = TRUE;
}
GMX_LOG(logger.info)
.asParagraph()
- .appendTextFormatted("Coupling %d copies of molecule type '%s'", nmol_couple,
- opts->couple_moltype);
+ .appendTextFormatted(
+ "Coupling %d copies of molecule type '%s'", nmol_couple, opts->couple_moltype);
}
/* this is not very clean, but fixes core dump on empty system name */
}
if (fabs(qBt) > 1e-4 && !gmx_within_tol(qBt, qt, 1e-6))
{
- sprintf(warn_buf, "State B has non-zero total charge: %.6f\n%s\n", qBt,
- floating_point_arithmetic_tip);
+ sprintf(warn_buf, "State B has non-zero total charge: %.6f\n%s\n", qBt, floating_point_arithmetic_tip);
warning_note(wi, warn_buf);
}
if (usingFullRangeElectrostatics && (fabs(qt) > 1e-4 || fabs(qBt) > 1e-4))
{
GMX_LOG(logger.info).asParagraph().appendTextFormatted("processing topology...");
}
- title = read_topol(topfile, tmpfile, opts->define, opts->include, symtab, atypes, molinfo,
- intermolecular_interactions, interactions, combination_rule, repulsion_power,
- opts, fudgeQQ, molblock, ffParametrizedWithHBondConstraints,
- ir->efep != efepNO, bZero, EEL_FULL(ir->coulombtype), wi, logger);
+ title = read_topol(topfile,
+ tmpfile,
+ opts->define,
+ opts->include,
+ symtab,
+ atypes,
+ molinfo,
+ intermolecular_interactions,
+ interactions,
+ combination_rule,
+ repulsion_power,
+ opts,
+ fudgeQQ,
+ molblock,
+ ffParametrizedWithHBondConstraints,
+ ir->efep != efepNO,
+ bZero,
+ EEL_FULL(ir->coulombtype),
+ wi,
+ logger);
if ((*combination_rule != eCOMB_GEOMETRIC) && (ir->vdwtype == evdwUSER))
{
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff