/* Compute normalized x i-j vectors, store in r.
* Compute the inner product of r and xp i-j and store in rhs1.
*/
- calc_dr_x_f_simd(b0, b1, atoms, x, f, blc.data(), pbc_simd, as_rvec_array(r.data()),
- rhs1.data(), sol.data());
+ calc_dr_x_f_simd(
+ b0, b1, atoms, x, f, blc.data(), pbc_simd, as_rvec_array(r.data()), rhs1.data(), sol.data());
#else // GMX_SIMD_HAVE_REAL
/* When constraining forces, we should not use mass weighting,
* so we pass invmass=NULL, which results in the use of 1 for all atoms.
*/
- lincs_update_atoms(lincsd, th, 1.0, sol, r, (econq != ConstraintVariable::Force) ? invmass : nullptr,
+ lincs_update_atoms(lincsd,
+ th,
+ 1.0,
+ sol,
+ r,
+ (econq != ConstraintVariable::Force) ? invmass : nullptr,
as_rvec_array(fp.data()));
if (bCalcDHDL)
/* Compute normalized x i-j vectors, store in r.
* Compute the inner product of r and xp i-j and store in rhs1.
*/
- calc_dr_x_xp_simd(b0, b1, atoms, x, xp, bllen.data(), blc.data(), pbc_simd,
- as_rvec_array(r.data()), rhs1.data(), sol.data());
+ calc_dr_x_xp_simd(
+ b0, b1, atoms, x, xp, bllen.data(), blc.data(), pbc_simd, as_rvec_array(r.data()), rhs1.data(), sol.data());
#else // GMX_SIMD_HAVE_REAL
}
#if GMX_SIMD_HAVE_REAL
- calc_dist_iter_simd(b0, b1, atoms, xp, bllen.data(), blc.data(), pbc_simd, wfac,
- rhs1.data(), sol.data(), bWarn);
+ calc_dist_iter_simd(
+ b0, b1, atoms, xp, bllen.data(), blc.data(), pbc_simd, wfac, rhs1.data(), sol.data(), bWarn);
#else
- calc_dist_iter(b0, b1, atoms, xp, bllen.data(), blc.data(), pbc, wfac, rhs1.data(),
- sol.data(), bWarn);
+ calc_dist_iter(b0, b1, atoms, xp, bllen.data(), blc.data(), pbc, wfac, rhs1.data(), sol.data(), bWarn);
/* 20*ncons flops */
#endif // GMX_SIMD_HAVE_REAL
if (debug)
{
fprintf(debug, "The %d constraints participate in %d triangles\n", li->nc, li->ntriangle);
- fprintf(debug, "There are %d constraint couplings, of which %d in triangles\n", li->ncc,
- li->ncc_triangle);
+ fprintf(debug, "There are %d constraint couplings, of which %d in triangles\n", li->ncc, li->ncc_triangle);
if (li->ntriangle > 0 && li->ntask > 1)
{
fprintf(debug,
li->bTaskDep = (li->ntask > 1 && bMoreThanTwoSeq);
if (debug)
{
- fprintf(debug, "LINCS: using %d threads, tasks are %sdependent\n", li->ntask,
- li->bTaskDep ? "" : "in");
+ fprintf(debug, "LINCS: using %d threads, tasks are %sdependent\n", li->ntask, li->bTaskDep ? "" : "in");
}
if (li->ntask == 1)
{
"%d constraints are involved in constraint triangles,\n"
"will apply an additional matrix expansion of order %d for couplings\n"
"between constraints inside triangles\n",
- li->ncg_triangle, li->nOrder);
+ li->ncg_triangle,
+ li->nOrder);
}
}
if (debug)
{
- fprintf(debug, "Number of constraints is %d, padded %d, couplings %d\n", li->nc_real,
- li->nc, li->ncc);
+ fprintf(debug, "Number of constraints is %d, padded %d, couplings %d\n", li->nc_real, li->nc, li->ncc);
}
if (li->ntask > 1)
real cosine = ::iprod(v0, v1) / (d0 * d1);
if (cosine < wfac)
{
- fprintf(stderr, " %6d %6d %5.1f %8.4f %8.4f %8.4f\n", ddglatnr(dd, i),
- ddglatnr(dd, j), RAD2DEG * std::acos(cosine), d0, d1, bllen[b]);
+ fprintf(stderr,
+ " %6d %6d %5.1f %8.4f %8.4f %8.4f\n",
+ ddglatnr(dd, i),
+ ddglatnr(dd, j),
+ RAD2DEG * std::acos(cosine),
+ d0,
+ d1,
+ bllen[b]);
if (!std::isfinite(d1))
{
gmx_fatal(FARGS, "Bond length not finite.");
{
LincsDeviations deviations = makeLincsDeviations(*lincsd, xprime, pbc);
fprintf(debug, " Rel. Constraint Deviation: RMS MAX between atoms\n");
- fprintf(debug, " Before LINCS %.6f %.6f %6d %6d\n",
+ fprintf(debug,
+ " Before LINCS %.6f %.6f %6d %6d\n",
std::sqrt(deviations.sumSquaredDeviation / deviations.numConstraints),
deviations.maxDeviation,
ddglatnr(cr->dd, lincsd->atoms[deviations.indexOfMaxDeviation].index1),
clear_mat(lincsd->task[th].vir_r_m_dr);
- do_lincs(xPadded, xprimePadded, box, pbc, lincsd, th, invmass, cr, bCalcDHDL,
- ir.LincsWarnAngle, &bWarn, invdt, v, bCalcVir,
+ do_lincs(xPadded,
+ xprimePadded,
+ box,
+ pbc,
+ lincsd,
+ th,
+ invmass,
+ cr,
+ bCalcDHDL,
+ ir.LincsWarnAngle,
+ &bWarn,
+ invdt,
+ v,
+ bCalcVir,
th == 0 ? vir_r_m_dr : lincsd->task[th].vir_r_m_dr);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
if (printDebugOutput)
{
- fprintf(debug, " After LINCS %.6f %.6f %6d %6d\n\n",
+ fprintf(debug,
+ " After LINCS %.6f %.6f %6d %6d\n\n",
std::sqrt(deviations.sumSquaredDeviation / deviations.numConstraints),
deviations.maxDeviation,
ddglatnr(cr->dd, lincsd->atoms[deviations.indexOfMaxDeviation].index1),
", time %g (ps) LINCS WARNING%s\n"
"relative constraint deviation after LINCS:\n"
"rms %.6f, max %.6f (between atoms %d and %d)\n",
- step, ir.init_t + step * ir.delta_t, simMesg.c_str(),
+ step,
+ ir.init_t + step * ir.delta_t,
+ simMesg.c_str(),
std::sqrt(deviations.sumSquaredDeviation / deviations.numConstraints),
deviations.maxDeviation,
ddglatnr(cr->dd, lincsd->atoms[deviations.indexOfMaxDeviation].index1),
ddglatnr(cr->dd, lincsd->atoms[deviations.indexOfMaxDeviation].index2));
- lincs_warning(cr->dd, x, xprime, pbc, lincsd->nc, lincsd->atoms, lincsd->bllen,
- ir.LincsWarnAngle, maxwarn, warncount);
+ lincs_warning(
+ cr->dd, x, xprime, pbc, lincsd->nc, lincsd->atoms, lincsd->bllen, ir.LincsWarnAngle, maxwarn, warncount);
}
bOK = (deviations.maxDeviation < 0.5);
}
{
int th = gmx_omp_get_thread_num();
- do_lincsp(xPadded, xprimePadded, min_proj, pbc, lincsd, th, invmass, econq,
- bCalcDHDL, bCalcVir, th == 0 ? vir_r_m_dr : lincsd->task[th].vir_r_m_dr);
+ do_lincsp(xPadded,
+ xprimePadded,
+ min_proj,
+ pbc,
+ lincsd,
+ th,
+ invmass,
+ econq,
+ bCalcDHDL,
+ bCalcVir,
+ th == 0 ? vir_r_m_dr : lincsd->task[th].vir_r_m_dr);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff