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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/timing/wallcycle.h"
52 #include "pairlistsets.h"
53 #include "pairsearch.h"
57 void nbnxn_put_on_grid(nonbonded_verlet_t *nb_verlet,
60 const rvec lowerCorner,
61 const rvec upperCorner,
62 const gmx::UpdateGroupsCog *updateGroupsCog,
63 gmx::Range<int> atomRange,
65 gmx::ArrayRef<const int> atomInfo,
66 gmx::ArrayRef<const gmx::RVec> x,
70 nb_verlet->pairSearch_->putOnGrid(box, gridIndex, lowerCorner, upperCorner,
71 updateGroupsCog, atomRange, atomDensity,
72 atomInfo, 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,
79 gmx::ArrayRef<const int> atomInfo,
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], zones->cg_range[zone+1] },
102 bool nonbonded_verlet_t::isDynamicPruningStepCpu(int64_t step) const
104 return pairlistSets_->isDynamicPruningStepCpu(step);
107 bool nonbonded_verlet_t::isDynamicPruningStepGpu(int64_t step) const
109 return pairlistSets_->isDynamicPruningStepGpu(step);
112 gmx::ArrayRef<const int> nonbonded_verlet_t::getLocalAtomOrder() const
114 /* Return the atom order for the home cell (index 0) */
115 const Nbnxm::Grid &grid = pairSearch_->gridSet().grids()[0];
117 const int numIndices = grid.atomIndexEnd() - grid.firstAtomInColumn(0);
119 return gmx::constArrayRefFromArray(pairSearch_->gridSet().atomIndices().data(), numIndices);
122 void nonbonded_verlet_t::setLocalAtomOrder()
124 pairSearch_->setLocalAtomOrder();
127 void nonbonded_verlet_t::setAtomProperties(const t_mdatoms &mdatoms,
128 gmx::ArrayRef<const int> atomInfo)
130 nbnxn_atomdata_set(nbat.get(), pairSearch_->gridSet(), &mdatoms, atomInfo.data());
133 void nonbonded_verlet_t::convertCoordinates(const gmx::AtomLocality locality,
134 const bool fillLocal,
135 gmx::ArrayRef<const gmx::RVec> coordinates)
137 wallcycle_start(wcycle_, ewcNB_XF_BUF_OPS);
138 wallcycle_sub_start(wcycle_, ewcsNB_X_BUF_OPS);
140 nbnxn_atomdata_copy_x_to_nbat_x(pairSearch_->gridSet(), locality, fillLocal,
141 as_rvec_array(coordinates.data()),
144 wallcycle_sub_stop(wcycle_, ewcsNB_X_BUF_OPS);
145 wallcycle_stop(wcycle_, ewcNB_XF_BUF_OPS);
148 void nonbonded_verlet_t::convertCoordinatesGpu(const gmx::AtomLocality locality,
149 const bool fillLocal,
150 DeviceBuffer<float> d_x,
151 GpuEventSynchronizer *xReadyOnDevice)
153 wallcycle_start(wcycle_, ewcNB_XF_BUF_OPS);
154 wallcycle_sub_start(wcycle_, ewcsNB_X_BUF_OPS);
156 nbnxn_atomdata_x_to_nbat_x_gpu(pairSearch_->gridSet(), locality, fillLocal,
161 wallcycle_sub_stop(wcycle_, ewcsNB_X_BUF_OPS);
162 wallcycle_stop(wcycle_, ewcNB_XF_BUF_OPS);
165 gmx::ArrayRef<const int> nonbonded_verlet_t::getGridIndices() const
167 return pairSearch_->gridSet().cells();
171 nonbonded_verlet_t::atomdata_add_nbat_f_to_f(const gmx::AtomLocality locality,
172 gmx::ArrayRef<gmx::RVec> force)
175 /* Skip the reduction if there was no short-range GPU work to do
176 * (either NB or both NB and bonded work). */
177 if (!pairlistIsSimple() && !haveGpuShortRangeWork(locality))
182 wallcycle_start(wcycle_, ewcNB_XF_BUF_OPS);
183 wallcycle_sub_start(wcycle_, ewcsNB_F_BUF_OPS);
185 reduceForces(nbat.get(), locality, pairSearch_->gridSet(), as_rvec_array(force.data()));
187 wallcycle_sub_stop(wcycle_, ewcsNB_F_BUF_OPS);
188 wallcycle_stop(wcycle_, ewcNB_XF_BUF_OPS);
192 nonbonded_verlet_t::atomdata_add_nbat_f_to_f_gpu(const gmx::AtomLocality locality,
193 DeviceBuffer<float> totalForcesDevice,
194 void *forcesPmeDevice,
195 gmx::ArrayRef<GpuEventSynchronizer* const> dependencyList,
196 bool useGpuFPmeReduction,
197 bool accumulateForce)
200 GMX_ASSERT((useGpuFPmeReduction == (forcesPmeDevice != nullptr)),
201 "GPU PME force reduction is only valid when a non-null GPU PME force pointer is available");
203 /* Skip the reduction if there was no short-range GPU work to do
204 * (either NB or both NB and bonded work). */
205 if (!pairlistIsSimple() && !haveGpuShortRangeWork(locality))
210 wallcycle_start(wcycle_, ewcNB_XF_BUF_OPS);
211 wallcycle_sub_start(wcycle_, ewcsNB_F_BUF_OPS);
213 reduceForcesGpu(locality, totalForcesDevice, pairSearch_->gridSet(), forcesPmeDevice, dependencyList, gpu_nbv, useGpuFPmeReduction, accumulateForce);
215 wallcycle_sub_stop(wcycle_, ewcsNB_F_BUF_OPS);
216 wallcycle_stop(wcycle_, ewcNB_XF_BUF_OPS);
220 nonbonded_verlet_t::atomdata_init_add_nbat_f_to_f_gpu(GpuEventSynchronizer* const localReductionDone)
223 wallcycle_start(wcycle_, ewcNB_XF_BUF_OPS);
224 wallcycle_sub_start(wcycle_, ewcsNB_F_BUF_OPS);
226 const Nbnxm::GridSet &gridSet = pairSearch_->gridSet();
228 Nbnxm::nbnxn_gpu_init_add_nbat_f_to_f(gridSet.cells().data(),
230 gridSet.numRealAtomsTotal(),
233 wallcycle_sub_stop(wcycle_, ewcsNB_F_BUF_OPS);
234 wallcycle_stop(wcycle_, ewcNB_XF_BUF_OPS);
237 real nonbonded_verlet_t::pairlistInnerRadius() const
239 return pairlistSets_->params().rlistInner;
242 real nonbonded_verlet_t::pairlistOuterRadius() const
244 return pairlistSets_->params().rlistOuter;
247 void nonbonded_verlet_t::changePairlistRadii(real rlistOuter,
250 pairlistSets_->changePairlistRadii(rlistOuter, rlistInner);
254 nonbonded_verlet_t::atomdata_init_copy_x_to_nbat_x_gpu()
256 Nbnxm::nbnxn_gpu_init_x_to_nbat_x(pairSearch_->gridSet(), gpu_nbv);
259 void nonbonded_verlet_t::insertNonlocalGpuDependency(const gmx::InteractionLocality interactionLocality)
261 Nbnxm::nbnxnInsertNonlocalGpuDependency(gpu_nbv, interactionLocality);
264 void nonbonded_verlet_t::wait_nonlocal_x_copy_D2H_done()
266 Nbnxm::nbnxn_wait_nonlocal_x_copy_D2H_done(gpu_nbv);
269 void nonbonded_verlet_t::stream_local_wait_for_nonlocal()
271 Nbnxm::nbnxn_stream_local_wait_for_nonlocal(gpu_nbv);