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38 * Implements the Nbnxm class
40 * \author Berk Hess <hess@kth.se>
41 * \ingroup module_nbnxm
48 #include "gromacs/domdec/domdec_struct.h"
49 #include "gromacs/nbnxm/atomdata.h"
50 #include "gromacs/timing/wallcycle.h"
52 #include "pairsearch.h"
56 void nbnxn_put_on_grid(nonbonded_verlet_t *nb_verlet,
59 const rvec lowerCorner,
60 const rvec upperCorner,
61 const gmx::UpdateGroupsCog *updateGroupsCog,
66 gmx::ArrayRef<const gmx::RVec> x,
70 nb_verlet->pairSearch_->putOnGrid(box, ddZone, lowerCorner, upperCorner,
71 updateGroupsCog, atomStart, atomEnd, atomDensity,
72 atinfo, x, numAtomsMoved, move,
73 nb_verlet->nbat.get());
76 /* Calls nbnxn_put_on_grid for all non-local domains */
77 void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t *nbv,
78 const struct gmx_domdec_zones_t *zones,
80 gmx::ArrayRef<const gmx::RVec> x)
82 for (int zone = 1; zone < zones->n; zone++)
85 for (int d = 0; d < DIM; d++)
87 c0[d] = zones->size[zone].bb_x0[d];
88 c1[d] = zones->size[zone].bb_x1[d];
91 nbnxn_put_on_grid(nbv, nullptr,
94 zones->cg_range[zone],
95 zones->cg_range[zone+1],
103 gmx::ArrayRef<const int> nonbonded_verlet_t::getLocalAtomOrder() const
105 /* Return the atom order for the home cell (index 0) */
106 const Nbnxm::Grid &grid = pairSearch_->gridSet().grids()[0];
108 const int numIndices = grid.atomIndexEnd() - grid.firstAtomInColumn(0);
110 return gmx::constArrayRefFromArray(pairSearch_->gridSet().atomIndices().data(), numIndices);
113 void nonbonded_verlet_t::setLocalAtomOrder()
115 pairSearch_->setLocalAtomOrder();
118 void nonbonded_verlet_t::setAtomProperties(const t_mdatoms &mdatoms,
121 nbnxn_atomdata_set(nbat.get(), pairSearch_->gridSet(), &mdatoms, &atinfo);
124 void nonbonded_verlet_t::setCoordinates(const Nbnxm::AtomLocality locality,
125 const bool fillLocal,
126 gmx::ArrayRef<const gmx::RVec> x,
127 gmx_wallcycle *wcycle)
129 wallcycle_start(wcycle, ewcNB_XF_BUF_OPS);
130 wallcycle_sub_start(wcycle, ewcsNB_X_BUF_OPS);
132 nbnxn_atomdata_copy_x_to_nbat_x(pairSearch_->gridSet(), locality, fillLocal,
133 as_rvec_array(x.data()),
136 wallcycle_sub_stop(wcycle, ewcsNB_X_BUF_OPS);
137 wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
140 void nonbonded_verlet_t::getLocalNumCells(int *numCellsX,
141 int *numCellsY) const
143 pairSearch_->gridSet().getLocalNumCells(numCellsX, numCellsY);
146 gmx::ArrayRef<const int> nonbonded_verlet_t::getGridIndices() const
148 return pairSearch_->gridSet().cells();
152 nonbonded_verlet_t::atomdata_add_nbat_f_to_f(const Nbnxm::AtomLocality locality,
154 gmx_wallcycle *wcycle)
156 /* Skip the non-local reduction if there was no non-local work to do */
157 if (!pairlistIsSimple() &&
158 locality == Nbnxm::AtomLocality::NonLocal &&
159 pairlistSets().pairlistSet(Nbnxm::InteractionLocality::NonLocal).gpuList()->sci.empty())
164 wallcycle_start(wcycle, ewcNB_XF_BUF_OPS);
165 wallcycle_sub_start(wcycle, ewcsNB_F_BUF_OPS);
167 reduceForces(nbat.get(), locality, pairSearch_->gridSet(), f);
169 wallcycle_sub_stop(wcycle, ewcsNB_F_BUF_OPS);
170 wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);