gmx::Constraints *constr,
gmx_enerdata_t *enerd,
t_fcdata *fcd,
- t_state *state,
+ int natoms,
+ gmx::ArrayRefWithPadding<gmx::RVec> x,
+ gmx::ArrayRefWithPadding<gmx::RVec> v,
+ matrix box,
+ gmx::ArrayRef<real> lambda,
+ history_t *hist,
gmx::ArrayRefWithPadding<gmx::RVec> f,
tensor force_vir,
const t_mdatoms *md,
const gmx_vsite_t *vsite,
const DDBalanceRegionHandler &ddBalanceRegionHandler)
{
+ auto xRvec = as_rvec_array(x.paddedArrayRef().data());
+ auto vRvec = as_rvec_array(v.paddedArrayRef().data());
+
int nshell;
t_shell *shell;
const t_idef *idef;
}
else
{
- nat = state->natoms;
+ nat = natoms;
}
for (i = 0; (i < 2); i++)
* before do_force is called, which normally puts all
* charge groups in the box.
*/
- auto xRef = state->x.arrayRefWithPadding().paddedArrayRef();
- put_atoms_in_box_omp(fr->ePBC, state->box, xRef.subArray(0, md->homenr), gmx_omp_nthreads_get(emntDefault));
+ auto xRef = x.paddedArrayRef();
+ put_atoms_in_box_omp(fr->ePBC, box, xRef.subArray(0, md->homenr), gmx_omp_nthreads_get(emntDefault));
if (graph)
{
- mk_mshift(fplog, graph, fr->ePBC, state->box, state->x.rvec_array());
+ mk_mshift(fplog, graph, fr->ePBC, box, xRvec);
}
}
/* After this all coordinate arrays will contain whole charge groups */
if (graph)
{
- shift_self(graph, state->box, state->x.rvec_array());
+ shift_self(graph, box, xRvec);
}
if (nflexcon)
}
acc_dir = shfc->acc_dir;
x_old = shfc->x_old;
- auto x = makeArrayRef(state->x);
- auto v = makeArrayRef(state->v);
+ auto xArrayRef = x.paddedArrayRef();
+ auto vArrayRef = v.paddedArrayRef();
for (i = 0; i < homenr; i++)
{
for (d = 0; d < DIM; d++)
{
shfc->x_old[i][d] =
- x[i][d] - v[i][d]*inputrec->delta_t;
+ xArrayRef[i][d] - vArrayRef[i][d]*inputrec->delta_t;
}
}
}
*/
if (shfc->bPredict && !bCont && (EI_STATE_VELOCITY(inputrec->eI) || bInit))
{
- predict_shells(fplog, state->x.rvec_array(), state->v.rvec_array(), inputrec->delta_t, nshell, shell,
+ predict_shells(fplog, xRvec, vRvec, inputrec->delta_t, nshell, shell,
md->massT, nullptr, bInit);
}
/* do_force expected the charge groups to be in the box */
if (graph)
{
- unshift_self(graph, state->box, state->x.rvec_array());
+ unshift_self(graph, box, xRvec);
}
/* Calculate the forces first time around */
if (gmx_debug_at)
{
- pr_rvecs(debug, 0, "x b4 do_force", state->x.rvec_array(), homenr);
+ pr_rvecs(debug, 0, "x b4 do_force", xRvec, homenr);
}
int shellfc_flags = force_flags | (bVerbose ? GMX_FORCE_ENERGY : 0);
do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, imdSession,
pull_work,
mdstep, nrnb, wcycle, top,
- state->box, state->x.arrayRefWithPadding(), &state->hist,
+ box, x, hist,
forceWithPadding[Min], force_vir, md, enerd, fcd,
- state->lambda, graph,
+ lambda, graph,
fr, ppForceWorkload, vsite, mu_tot, t, nullptr,
(bDoNS ? GMX_FORCE_NS : 0) | shellfc_flags,
ddBalanceRegionHandler);
{
init_adir(shfc,
constr, inputrec, cr, dd_ac1, mdstep, md, end,
- shfc->x_old, state->x.rvec_array(), state->x.rvec_array(), as_rvec_array(force[Min].data()),
+ shfc->x_old, xRvec, xRvec, as_rvec_array(force[Min].data()),
shfc->acc_dir,
- state->box, state->lambda, &dum);
+ box, lambda, &dum);
for (i = 0; i < end; i++)
{
* shell positions are updated, therefore the other particles must
* be set here, in advance.
*/
- std::copy(state->x.begin(),
- state->x.end(),
+ std::copy(x.paddedArrayRef().begin(),
+ x.paddedArrayRef().end(),
posWithPadding[Min].paddedArrayRef().begin());
- std::copy(state->x.begin(),
- state->x.end(),
+ std::copy(x.paddedArrayRef().begin(),
+ x.paddedArrayRef().end(),
posWithPadding[Try].paddedArrayRef().begin());
}
if (vsite)
{
construct_vsites(vsite, as_rvec_array(pos[Min].data()),
- inputrec->delta_t, state->v.rvec_array(),
+ inputrec->delta_t, vRvec,
idef->iparams, idef->il,
- fr->ePBC, fr->bMolPBC, cr, state->box);
+ fr->ePBC, fr->bMolPBC, cr, box);
}
if (nflexcon)
{
init_adir(shfc,
constr, inputrec, cr, dd_ac1, mdstep, md, end,
- x_old, state->x.rvec_array(),
+ x_old, xRvec,
as_rvec_array(pos[Min].data()),
as_rvec_array(force[Min].data()), acc_dir,
- state->box, state->lambda, &dum);
+ box, lambda, &dum);
directional_sd(pos[Min], pos[Try], acc_dir, end, fr->fc_stepsize);
}
/* do_force expected the charge groups to be in the box */
if (graph)
{
- unshift_self(graph, state->box, as_rvec_array(pos[Try].data()));
+ unshift_self(graph, box, as_rvec_array(pos[Try].data()));
}
if (gmx_debug_at)
do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, imdSession,
pull_work,
1, nrnb, wcycle,
- top, state->box, posWithPadding[Try], &state->hist,
+ top, box, posWithPadding[Try], hist,
forceWithPadding[Try], force_vir,
- md, enerd, fcd, state->lambda, graph,
+ md, enerd, fcd, lambda, graph,
fr, ppForceWorkload, vsite, mu_tot, t, nullptr,
shellfc_flags,
ddBalanceRegionHandler);
{
init_adir(shfc,
constr, inputrec, cr, dd_ac1, mdstep, md, end,
- x_old, state->x.rvec_array(),
+ x_old, xRvec,
as_rvec_array(pos[Try].data()),
as_rvec_array(force[Try].data()),
- acc_dir, state->box, state->lambda, &dum);
+ acc_dir, box, lambda, &dum);
for (i = 0; i < end; i++)
{
{
/* Correct the velocities for the flexible constraints */
invdt = 1/inputrec->delta_t;
- auto v = makeArrayRef(state->v);
+ auto vArrayRef = v.paddedArrayRef();
for (i = 0; i < end; i++)
{
for (d = 0; d < DIM; d++)
{
- v[i][d] += (pos[Try][i][d] - pos[Min][i][d])*invdt;
+ vArrayRef[i][d] += (pos[Try][i][d] - pos[Min][i][d])*invdt;
}
}
}
}
/* Copy back the coordinates and the forces */
- std::copy(pos[Min].begin(), pos[Min].end(), makeArrayRef(state->x).data());
+ std::copy(pos[Min].begin(), pos[Min].end(), x.paddedArrayRef().data());
std::copy(force[Min].begin(), force[Min].end(), f.unpaddedArrayRef().begin());
}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff