"If you know what you are doing you can %s"
"set the environment variable GMX_MAXCONSTRWARN to -1,\n"
"but normally it is better to fix the problem",
- (eConstrAlg == econtLINCS) ? "LINCS" : "SETTLE", warncount,
+ (eConstrAlg == econtLINCS) ? "LINCS" : "SETTLE",
+ warncount,
(eConstrAlg == econtLINCS) ? "adjust the lincs warning threshold in your mdp file\nor " : "\n");
}
ii = i;
}
mtopGetAtomAndResidueName(mtop, ii, &molb, &anm, &resnr, &resnm, nullptr);
- gmx_fprintf_pdb_atomline(out, epdbATOM, ii + 1, anm, ' ', resnm, ' ', resnr, ' ',
- 10 * x[i][XX], 10 * x[i][YY], 10 * x[i][ZZ], 1.0, 0.0, "");
+ gmx_fprintf_pdb_atomline(out,
+ epdbATOM,
+ ii + 1,
+ anm,
+ ' ',
+ resnm,
+ ' ',
+ resnr,
+ ' ',
+ 10 * x[i][XX],
+ 10 * x[i][YY],
+ 10 * x[i][ZZ],
+ 1.0,
+ 0.0,
+ "");
}
fprintf(out, "TER\n");
tensor constraintsVirial,
ConstraintVariable econq)
{
- return impl_->apply(bLog, bEner, step, delta_step, step_scaling, std::move(x),
- std::move(xprime), min_proj, box, lambda, dvdlambda, std::move(v),
- computeVirial, constraintsVirial, econq);
+ return impl_->apply(bLog,
+ bEner,
+ step,
+ delta_step,
+ step_scaling,
+ std::move(x),
+ std::move(xprime),
+ min_proj,
+ box,
+ lambda,
+ dvdlambda,
+ std::move(v),
+ computeVirial,
+ constraintsVirial,
+ econq);
}
bool Constraints::Impl::apply(bool bLog,
*/
if (cr->dd)
{
- dd_move_x_constraints(cr->dd, box, x.unpaddedArrayRef(), xprime.unpaddedArrayRef(),
+ dd_move_x_constraints(cr->dd,
+ box,
+ x.unpaddedArrayRef(),
+ xprime.unpaddedArrayRef(),
econq == ConstraintVariable::Positions);
if (!v.empty())
if (lincsd != nullptr)
{
- bOK = constrain_lincs(bLog || bEner, ir, step, lincsd, inverseMasses_, cr, ms, x, xprime,
- min_proj, box, pbc_null, hasMassPerturbedAtoms_, lambda, dvdlambda,
- invdt, v.unpaddedArrayRef(), computeVirial, constraintsVirial, econq,
- nrnb, maxwarn, &warncount_lincs);
+ bOK = constrain_lincs(bLog || bEner,
+ ir,
+ step,
+ lincsd,
+ inverseMasses_,
+ cr,
+ ms,
+ x,
+ xprime,
+ min_proj,
+ box,
+ pbc_null,
+ hasMassPerturbedAtoms_,
+ lambda,
+ dvdlambda,
+ invdt,
+ v.unpaddedArrayRef(),
+ computeVirial,
+ constraintsVirial,
+ econq,
+ nrnb,
+ maxwarn,
+ &warncount_lincs);
if (!bOK && maxwarn < INT_MAX)
{
if (log != nullptr)
{
- fprintf(log, "Constraint error in algorithm %s at step %s\n",
- econstr_names[econtLINCS], gmx_step_str(step, buf));
+ fprintf(log,
+ "Constraint error in algorithm %s at step %s\n",
+ econstr_names[econtLINCS],
+ gmx_step_str(step, buf));
}
bDump = TRUE;
}
if (shaked != nullptr)
{
- bOK = constrain_shake(log, shaked.get(), inverseMasses_, *idef, ir, x.unpaddedArrayRef(),
- xprime.unpaddedArrayRef(), min_proj, pbc_null, nrnb, lambda,
- dvdlambda, invdt, v.unpaddedArrayRef(), computeVirial,
- constraintsVirial, maxwarn < INT_MAX, econq);
+ bOK = constrain_shake(log,
+ shaked.get(),
+ inverseMasses_,
+ *idef,
+ ir,
+ x.unpaddedArrayRef(),
+ xprime.unpaddedArrayRef(),
+ min_proj,
+ pbc_null,
+ nrnb,
+ lambda,
+ dvdlambda,
+ invdt,
+ v.unpaddedArrayRef(),
+ computeVirial,
+ constraintsVirial,
+ maxwarn < INT_MAX,
+ econq);
if (!bOK && maxwarn < INT_MAX)
{
if (log != nullptr)
{
- fprintf(log, "Constraint error in algorithm %s at step %s\n",
- econstr_names[econtSHAKE], gmx_step_str(step, buf));
+ fprintf(log,
+ "Constraint error in algorithm %s at step %s\n",
+ econstr_names[econtSHAKE],
+ gmx_step_str(step, buf));
}
bDump = TRUE;
}
clear_mat(threadConstraintsVirial[th]);
}
- csettle(*settled, nth, th, pbc_null, x, xprime, invdt, v, computeVirial,
+ csettle(*settled,
+ nth,
+ th,
+ pbc_null,
+ x,
+ xprime,
+ invdt,
+ v,
+ computeVirial,
th == 0 ? constraintsVirial : threadConstraintsVirial[th],
th == 0 ? &bSettleErrorHasOccurred0 : &bSettleErrorHasOccurred[th]);
}
if (start_th >= 0 && end_th - start_th > 0)
{
- settle_proj(*settled, econq, end_th - start_th,
+ settle_proj(*settled,
+ econq,
+ end_th - start_th,
settle.iatoms.data() + start_th * (1 + NRAL(F_SETTLE)),
- pbc_null, x.unpaddedArrayRef(), xprime.unpaddedArrayRef(),
- min_proj, calcvir_atom_end,
+ pbc_null,
+ x.unpaddedArrayRef(),
+ xprime.unpaddedArrayRef(),
+ min_proj,
+ calcvir_atom_end,
th == 0 ? constraintsVirial : threadConstraintsVirial[th]);
}
}
if (bDump)
{
- dump_confs(log, step, mtop, start, numHomeAtoms_, cr, x.unpaddedArrayRef(),
- xprime.unpaddedArrayRef(), box);
+ dump_confs(log, step, mtop, start, numHomeAtoms_, cr, x.unpaddedArrayRef(), xprime.unpaddedArrayRef(), box);
}
if (econq == ConstraintVariable::Positions)
t = ir.init_t;
}
set_pbc(&pbc, ir.pbcType, box);
- pull_constraint(pull_work, masses_, &pbc, cr, ir.delta_t, t,
+ pull_constraint(pull_work,
+ masses_,
+ &pbc,
+ cr,
+ ir.delta_t,
+ t,
as_rvec_array(x.unpaddedArrayRef().data()),
as_rvec_array(xprime.unpaddedArrayRef().data()),
- as_rvec_array(v.unpaddedArrayRef().data()), constraintsVirial);
+ as_rvec_array(v.unpaddedArrayRef().data()),
+ constraintsVirial);
}
if (ed && delta_step > 0)
{
/* apply the essential dynamics constraints here */
- do_edsam(&ir, step, cr, as_rvec_array(xprime.unpaddedArrayRef().data()),
- as_rvec_array(v.unpaddedArrayRef().data()), box, ed);
+ do_edsam(&ir,
+ step,
+ cr,
+ as_rvec_array(xprime.unpaddedArrayRef().data()),
+ as_rvec_array(v.unpaddedArrayRef().data()),
+ box,
+ ed);
}
}
wallcycle_stop(wcycle, ewcCONSTR);
gmx::ArrayRef<const t_iparams> iparams,
FlexibleConstraintTreatment flexibleConstraintTreatment)
{
- return makeAtomsToConstraintsList(moltype.atoms.nr, makeConstArrayRef(moltype.ilist), iparams,
- flexibleConstraintTreatment);
+ return makeAtomsToConstraintsList(
+ moltype.atoms.nr, makeConstArrayRef(moltype.ilist), iparams, flexibleConstraintTreatment);
}
//! Return the number of flexible constraints in the \c ilist and \c iparams.
const real lambda,
unsigned short* cFREEZE)
{
- impl_->setConstraints(top, numAtoms, numHomeAtoms, masses, inverseMasses, hasMassPerturbedAtoms,
- lambda, cFREEZE);
+ impl_->setConstraints(
+ top, numAtoms, numHomeAtoms, masses, inverseMasses, hasMassPerturbedAtoms, lambda, cFREEZE);
}
/*! \brief Makes a per-moleculetype container of mappings from atom
if (ir.eConstrAlg == econtLINCS)
{
- lincsd = init_lincs(log, mtop, nflexcon, at2con_mt,
- DOMAINDECOMP(cr) && ddHaveSplitConstraints(*cr->dd), ir.nLincsIter,
+ lincsd = init_lincs(log,
+ mtop,
+ nflexcon,
+ at2con_mt,
+ DOMAINDECOMP(cr) && ddHaveSplitConstraints(*cr->dd),
+ ir.nLincsIter,
ir.nProjOrder);
}
bool computeEnergy = false;
bool computeVirial = false;
/* constrain the current position */
- constr->apply(needsLogging, computeEnergy, step, 0, 1.0, x, x, {}, box, lambda, &dvdl_dum, {},
- computeVirial, nullptr, gmx::ConstraintVariable::Positions);
+ constr->apply(needsLogging,
+ computeEnergy,
+ step,
+ 0,
+ 1.0,
+ x,
+ x,
+ {},
+ box,
+ lambda,
+ &dvdl_dum,
+ {},
+ computeVirial,
+ nullptr,
+ gmx::ConstraintVariable::Positions);
if (EI_VV(ir->eI))
{
/* constrain the inital velocity, and save it */
/* also may be useful if we need the ekin from the halfstep for velocity verlet */
- constr->apply(needsLogging, computeEnergy, step, 0, 1.0, x, v, v.unpaddedArrayRef(), box, lambda,
- &dvdl_dum, {}, computeVirial, nullptr, gmx::ConstraintVariable::Velocities);
+ constr->apply(needsLogging,
+ computeEnergy,
+ step,
+ 0,
+ 1.0,
+ x,
+ v,
+ v.unpaddedArrayRef(),
+ box,
+ lambda,
+ &dvdl_dum,
+ {},
+ computeVirial,
+ nullptr,
+ gmx::ConstraintVariable::Velocities);
}
/* constrain the inital velocities at t-dt/2 */
if (EI_STATE_VELOCITY(ir->eI) && ir->eI != eiVV)
fprintf(fplog, "\nConstraining the coordinates at t0-dt (step %s)\n", gmx_step_str(step, buf));
}
dvdl_dum = 0;
- constr->apply(needsLogging, computeEnergy, step, -1, 1.0, x, savex.arrayRefWithPadding(),
- {}, box, lambda, &dvdl_dum, v, computeVirial, nullptr,
+ constr->apply(needsLogging,
+ computeEnergy,
+ step,
+ -1,
+ 1.0,
+ x,
+ savex.arrayRefWithPadding(),
+ {},
+ box,
+ lambda,
+ &dvdl_dum,
+ v,
+ computeVirial,
+ nullptr,
gmx::ConstraintVariable::Positions);
for (i = start; i < end; i++)
{
if (constr != nullptr)
{
- constr->apply(do_log, do_ene, step, 1, 1.0, state->x.arrayRefWithPadding(),
- state->v.arrayRefWithPadding(), state->v.arrayRefWithPadding().unpaddedArrayRef(),
- state->box, state->lambda[efptBONDED], dvdlambda, ArrayRefWithPadding<RVec>(),
- computeVirial, constraintsVirial, ConstraintVariable::Velocities);
+ constr->apply(do_log,
+ do_ene,
+ step,
+ 1,
+ 1.0,
+ state->x.arrayRefWithPadding(),
+ state->v.arrayRefWithPadding(),
+ state->v.arrayRefWithPadding().unpaddedArrayRef(),
+ state->box,
+ state->lambda[efptBONDED],
+ dvdlambda,
+ ArrayRefWithPadding<RVec>(),
+ computeVirial,
+ constraintsVirial,
+ ConstraintVariable::Velocities);
}
}
{
if (constr != nullptr)
{
- constr->apply(do_log, do_ene, step, 1, 1.0, state->x.arrayRefWithPadding(), std::move(xp),
- ArrayRef<RVec>(), state->box, state->lambda[efptBONDED], dvdlambda,
- state->v.arrayRefWithPadding(), computeVirial, constraintsVirial,
+ constr->apply(do_log,
+ do_ene,
+ step,
+ 1,
+ 1.0,
+ state->x.arrayRefWithPadding(),
+ std::move(xp),
+ ArrayRef<RVec>(),
+ state->box,
+ state->lambda[efptBONDED],
+ dvdlambda,
+ state->v.arrayRefWithPadding(),
+ computeVirial,
+ constraintsVirial,
ConstraintVariable::Positions);
}
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff