nice to account to its own subtimer, but first
wallcycle needs to be extended to support calling from
multiple threads. */
- v = cmap_dihs(nbn, iatoms.data() + nb0, iparams.data(), &idef.cmap_grid, x, f, fshift,
- pbc, lambda[efptFTYPE], &(dvdl[efptFTYPE]), md, fcd, global_atom_index);
+ v = cmap_dihs(nbn,
+ iatoms.data() + nb0,
+ iparams.data(),
+ &idef.cmap_grid,
+ x,
+ f,
+ fshift,
+ pbc,
+ lambda[efptFTYPE],
+ &(dvdl[efptFTYPE]),
+ md,
+ fcd,
+ global_atom_index);
}
else
{
- v = calculateSimpleBond(ftype, nbn, iatoms.data() + nb0, iparams.data(), x, f, fshift,
- pbc, lambda[efptFTYPE], &(dvdl[efptFTYPE]), md, fcd,
- global_atom_index, flavor);
+ v = calculateSimpleBond(ftype,
+ nbn,
+ iatoms.data() + nb0,
+ iparams.data(),
+ x,
+ f,
+ fshift,
+ pbc,
+ lambda[efptFTYPE],
+ &(dvdl[efptFTYPE]),
+ md,
+ fcd,
+ global_atom_index,
+ flavor);
}
}
else
/* TODO The execution time for pairs might be nice to account
to its own subtimer, but first wallcycle needs to be
extended to support calling from multiple threads. */
- do_pairs(ftype, nbn, iatoms.data() + nb0, iparams.data(), x, f, fshift, pbc, lambda, dvdl,
- md, fr, havePerturbedInteractions, stepWork, grpp, global_atom_index);
+ do_pairs(ftype,
+ nbn,
+ iatoms.data() + nb0,
+ iparams.data(),
+ x,
+ f,
+ fshift,
+ pbc,
+ lambda,
+ dvdl,
+ md,
+ fr,
+ havePerturbedInteractions,
+ stepWork,
+ grpp,
+ global_atom_index);
}
if (thread == 0)
if (!ilist.empty() && ftype_is_bonded_potential(ftype))
{
ArrayRef<const int> iatoms = gmx::makeConstArrayRef(ilist.iatoms);
- v = calc_one_bond(thread, ftype, idef, iatoms, idef.numNonperturbedInteractions[ftype],
- bt->workDivision, x, ft, fshift, fr, pbc_null, grpp, nrnb,
- lambda, dvdlt, md, fcd, stepWork, global_atom_index);
+ v = calc_one_bond(thread,
+ ftype,
+ idef,
+ iatoms,
+ idef.numNonperturbedInteractions[ftype],
+ bt->workDivision,
+ x,
+ ft,
+ fshift,
+ fr,
+ pbc_null,
+ grpp,
+ nrnb,
+ lambda,
+ dvdlt,
+ md,
+ fcd,
+ stepWork,
+ global_atom_index);
epot[ftype] += v;
}
}
/* The dummy array is to have a place to store the dhdl at other values
of lambda, which will be thrown away in the end */
real dvdl[efptNR] = { 0 };
- calcBondedForces(idef, bt, x, fr, fr->bMolPBC ? pbc : nullptr,
- as_rvec_array(forceWithShiftForces.shiftForces().data()), enerd, nrnb,
- lambda, dvdl, md, fcd, stepWork, global_atom_index);
+ calcBondedForces(idef,
+ bt,
+ x,
+ fr,
+ fr->bMolPBC ? pbc : nullptr,
+ as_rvec_array(forceWithShiftForces.shiftForces().data()),
+ enerd,
+ nrnb,
+ lambda,
+ dvdl,
+ md,
+ fcd,
+ stepWork,
+ global_atom_index);
wallcycle_sub_stop(wcycle, ewcsLISTED);
wallcycle_sub_start(wcycle, ewcsLISTED_BUF_OPS);
/* We already have the forces, so we use temp buffers here */
std::fill(forceBufferLambda.begin(), forceBufferLambda.end(), 0.0_real);
- std::fill(shiftForceBufferLambda.begin(), shiftForceBufferLambda.end(),
+ std::fill(shiftForceBufferLambda.begin(),
+ shiftForceBufferLambda.end(),
gmx::RVec{ 0.0_real, 0.0_real, 0.0_real });
rvec4* f = reinterpret_cast<rvec4*>(forceBufferLambda.data());
rvec* fshift = as_rvec_array(shiftForceBufferLambda.data());
gmx::StepWorkload tempFlags;
tempFlags.computeEnergy = true;
- real v = calc_one_bond(0, ftype, idef, iatomsPerturbed, iatomsPerturbed.ssize(),
- workDivision, x, f, fshift, fr, pbc_null, grpp, nrnb, lambda,
- dvdl.data(), md, fcd, tempFlags, global_atom_index);
+ real v = calc_one_bond(0,
+ ftype,
+ idef,
+ iatomsPerturbed,
+ iatomsPerturbed.ssize(),
+ workDivision,
+ x,
+ f,
+ fshift,
+ fr,
+ pbc_null,
+ grpp,
+ nrnb,
+ lambda,
+ dvdl.data(),
+ md,
+ fcd,
+ tempFlags,
+ global_atom_index);
epot[ftype] += v;
}
}
if (fcdata->orires->nr > 0)
{
GMX_ASSERT(!xWholeMolecules.empty(), "Need whole molecules for orienation restraints");
- enerd->term[F_ORIRESDEV] = calc_orires_dev(
- ms, idef.il[F_ORIRES].size(), idef.il[F_ORIRES].iatoms.data(), idef.iparams.data(),
- md, xWholeMolecules, x, fr->bMolPBC ? pbc : nullptr, fcdata->orires, hist);
+ enerd->term[F_ORIRESDEV] = calc_orires_dev(ms,
+ idef.il[F_ORIRES].size(),
+ idef.il[F_ORIRES].iatoms.data(),
+ idef.iparams.data(),
+ md,
+ xWholeMolecules,
+ x,
+ fr->bMolPBC ? pbc : nullptr,
+ fcdata->orires,
+ hist);
}
if (fcdata->disres->nres > 0)
{
- calc_disres_R_6(cr, ms, idef.il[F_DISRES].size(), idef.il[F_DISRES].iatoms.data(), x,
- fr->bMolPBC ? pbc : nullptr, fcdata->disres, hist);
+ calc_disres_R_6(cr,
+ ms,
+ idef.il[F_DISRES].size(),
+ idef.il[F_DISRES].iatoms.data(),
+ x,
+ fr->bMolPBC ? pbc : nullptr,
+ fcdata->disres,
+ hist);
}
wallcycle_sub_stop(wcycle, ewcsRESTRAINTS);
}
- calc_listed(wcycle, idef, threading_.get(), x, forceOutputs, fr, pbc, enerd, nrnb, lambda, md,
- fcdata, global_atom_index, stepWork);
+ calc_listed(wcycle, idef, threading_.get(), x, forceOutputs, fr, pbc, enerd, nrnb, lambda, md, fcdata, global_atom_index, stepWork);
/* Check if we have to determine energy differences
* at foreign lambda's.
{
lam_i[j] = (i == 0 ? lambda[j] : fepvals->all_lambda[j][i - 1]);
}
- calc_listed_lambda(idef, threading_.get(), x, fr, pbc, forceBufferLambda_,
- shiftForceBufferLambda_, &(enerd->foreign_grpp), enerd->foreign_term,
- dvdl, nrnb, lam_i, md, fcdata, global_atom_index);
+ calc_listed_lambda(idef,
+ threading_.get(),
+ x,
+ fr,
+ pbc,
+ forceBufferLambda_,
+ shiftForceBufferLambda_,
+ &(enerd->foreign_grpp),
+ enerd->foreign_term,
+ dvdl,
+ nrnb,
+ lam_i,
+ md,
+ fcdata,
+ global_atom_index);
sum_epot(enerd->foreign_grpp, enerd->foreign_term);
const double dvdlSum = std::accumulate(std::begin(dvdl), std::end(dvdl), 0.);
std::fill(std::begin(dvdl), std::end(dvdl), 0.0);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff