#endif // GMX_SIMD_HAVE_REAL
/*! \brief LINCS projection, works on derivatives of the coordinates. */
-static void do_lincsp(const rvec* x,
- rvec* f,
- rvec* fp,
- t_pbc* pbc,
- Lincs* lincsd,
- int th,
- real* invmass,
- ConstraintVariable econq,
- bool bCalcDHDL,
- bool bCalcVir,
- tensor rmdf)
+static void do_lincsp(ArrayRefWithPadding<const RVec> xPadded,
+ ArrayRefWithPadding<RVec> fPadded,
+ ArrayRef<RVec> fp,
+ t_pbc* pbc,
+ Lincs* lincsd,
+ int th,
+ real* invmass,
+ ConstraintVariable econq,
+ bool bCalcDHDL,
+ bool bCalcVir,
+ tensor rmdf)
{
const int b0 = lincsd->task[th].b0;
const int b1 = lincsd->task[th].b1;
gmx::ArrayRef<real> rhs2 = lincsd->tmp2;
gmx::ArrayRef<real> sol = lincsd->tmp3;
+ const rvec* x = as_rvec_array(xPadded.paddedArrayRef().data());
+ rvec* f = as_rvec_array(fPadded.paddedArrayRef().data());
+
#if GMX_SIMD_HAVE_REAL
/* This SIMD code does the same as the plain-C code after the #else.
* The only difference is that we always call pbc code, as with SIMD
/* 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, fp);
+ lincs_update_atoms(lincsd, th, 1.0, sol, r, (econq != ConstraintVariable::Force) ? invmass : nullptr,
+ as_rvec_array(fp.data()));
if (bCalcDHDL)
{
#endif // GMX_SIMD_HAVE_REAL
//! Implements LINCS constraining.
-static void do_lincs(const rvec* x,
- rvec* xp,
- const matrix box,
- t_pbc* pbc,
- Lincs* lincsd,
- int th,
- const real* invmass,
- const t_commrec* cr,
- bool bCalcDHDL,
- real wangle,
- bool* bWarn,
- real invdt,
- rvec* gmx_restrict v,
- bool bCalcVir,
- tensor vir_r_m_dr)
+static void do_lincs(ArrayRefWithPadding<const RVec> xPadded,
+ ArrayRefWithPadding<RVec> xpPadded,
+ const matrix box,
+ t_pbc* pbc,
+ Lincs* lincsd,
+ int th,
+ const real* invmass,
+ const t_commrec* cr,
+ bool bCalcDHDL,
+ real wangle,
+ bool* bWarn,
+ real invdt,
+ ArrayRef<RVec> vRef,
+ bool bCalcVir,
+ tensor vir_r_m_dr)
{
+ const rvec* x = as_rvec_array(xPadded.paddedArrayRef().data());
+ rvec* xp = as_rvec_array(xpPadded.paddedArrayRef().data());
+ rvec* gmx_restrict v = as_rvec_array(vRef.data());
+
const int b0 = lincsd->task[th].b0;
const int b1 = lincsd->task[th].b1;
/* Communicate the corrected non-local coordinates */
if (DOMAINDECOMP(cr))
{
- dd_move_x_constraints(cr->dd, box, xp, nullptr, FALSE);
+ dd_move_x_constraints(cr->dd, box, xpPadded.unpaddedArrayRef(), ArrayRef<RVec>(), FALSE);
}
}
#pragma omp barrier
//! Issues a warning when LINCS constraints cannot be satisfied.
static void lincs_warning(gmx_domdec_t* dd,
- const rvec* x,
- rvec* xprime,
+ ArrayRef<const RVec> x,
+ ArrayRef<const RVec> xprime,
t_pbc* pbc,
int ncons,
gmx::ArrayRef<const AtomPair> atoms,
};
//! Determine how well the constraints have been satisfied.
-static LincsDeviations makeLincsDeviations(const Lincs& lincsd, const rvec* x, const t_pbc* pbc)
+static LincsDeviations makeLincsDeviations(const Lincs& lincsd, ArrayRef<const RVec> x, const t_pbc* pbc)
{
LincsDeviations result;
const ArrayRef<const AtomPair> atoms = lincsd.atoms;
return result;
}
-bool constrain_lincs(bool computeRmsd,
- const t_inputrec& ir,
- int64_t step,
- Lincs* lincsd,
- const t_mdatoms& md,
- const t_commrec* cr,
- const gmx_multisim_t* ms,
- const rvec* x,
- rvec* xprime,
- rvec* min_proj,
- const matrix box,
- t_pbc* pbc,
- real lambda,
- real* dvdlambda,
- real invdt,
- rvec* v,
- bool bCalcVir,
- tensor vir_r_m_dr,
- ConstraintVariable econq,
- t_nrnb* nrnb,
- int maxwarn,
- int* warncount)
+bool constrain_lincs(bool computeRmsd,
+ const t_inputrec& ir,
+ int64_t step,
+ Lincs* lincsd,
+ const t_mdatoms& md,
+ const t_commrec* cr,
+ const gmx_multisim_t* ms,
+ ArrayRefWithPadding<const RVec> xPadded,
+ ArrayRefWithPadding<RVec> xprimePadded,
+ ArrayRef<RVec> min_proj,
+ const matrix box,
+ t_pbc* pbc,
+ real lambda,
+ real* dvdlambda,
+ real invdt,
+ ArrayRef<RVec> v,
+ bool bCalcVir,
+ tensor vir_r_m_dr,
+ ConstraintVariable econq,
+ t_nrnb* nrnb,
+ int maxwarn,
+ int* warncount)
{
bool bOK = TRUE;
return bOK;
}
+ ArrayRef<const RVec> x = xPadded.unpaddedArrayRef();
+ ArrayRef<RVec> xprime = xprimePadded.unpaddedArrayRef();
+
if (econq == ConstraintVariable::Positions)
{
/* We can't use bCalcDHDL here, since NULL can be passed for dvdlambda
clear_mat(lincsd->task[th].vir_r_m_dr);
- do_lincs(x, xprime, box, pbc, lincsd, th, md.invmass, cr, bCalcDHDL, ir.LincsWarnAngle,
- &bWarn, invdt, v, bCalcVir, th == 0 ? vir_r_m_dr : lincsd->task[th].vir_r_m_dr);
+ do_lincs(xPadded, xprimePadded, box, pbc, lincsd, th, md.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
}
{
int th = gmx_omp_get_thread_num();
- do_lincsp(x, xprime, min_proj, pbc, lincsd, th, md.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, md.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
}
{
inc_nrnb(nrnb, eNR_LINCSMAT, lincsd->nOrder * lincsd->ncc_triangle);
}
- if (v)
+ if (!v.empty())
{
inc_nrnb(nrnb, eNR_CONSTR_V, lincsd->nc_real * 2);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff