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37 * \brief Implements atom distribution functions.
39 * \author Berk Hess <hess@kth.se>
40 * \ingroup module_domdec
45 #include "distribute.h"
51 #include "gromacs/domdec/domdec_network.h"
52 #include "gromacs/math/vec.h"
53 #include "gromacs/mdtypes/commrec.h"
54 #include "gromacs/mdtypes/df_history.h"
55 #include "gromacs/mdtypes/state.h"
56 #include "gromacs/topology/topology.h"
57 #include "gromacs/utility/enumerationhelpers.h"
58 #include "gromacs/utility/fatalerror.h"
59 #include "gromacs/utility/logger.h"
61 #include "atomdistribution.h"
62 #include "cellsizes.h"
63 #include "domdec_internal.h"
66 static void distributeVecSendrecv(gmx_domdec_t* dd,
67 gmx::ArrayRef<const gmx::RVec> globalVec,
68 gmx::ArrayRef<gmx::RVec> localVec)
72 std::vector<gmx::RVec> buffer;
74 for (int rank = 0; rank < dd->nnodes; rank++)
78 const auto& domainGroups = dd->ma->domainGroups[rank];
80 buffer.resize(domainGroups.numAtoms);
83 for (const int& globalAtom : domainGroups.atomGroups)
85 buffer[localAtom++] = globalVec[globalAtom];
87 GMX_RELEASE_ASSERT(localAtom == domainGroups.numAtoms,
88 "The index count and number of indices should match");
91 MPI_Send(buffer.data(), domainGroups.numAtoms * sizeof(gmx::RVec), MPI_BYTE, rank, rank, dd->mpi_comm_all);
96 const auto& domainGroups = dd->ma->domainGroups[dd->masterrank];
98 for (const int& globalAtom : domainGroups.atomGroups)
100 localVec[localAtom++] = globalVec[globalAtom];
106 int numHomeAtoms = dd->comm->atomRanges.numHomeAtoms();
107 MPI_Recv(localVec.data(),
108 numHomeAtoms * sizeof(gmx::RVec),
118 static void distributeVecScatterv(gmx_domdec_t* dd,
119 gmx::ArrayRef<const gmx::RVec> globalVec,
120 gmx::ArrayRef<gmx::RVec> localVec)
122 int* sendCounts = nullptr;
123 int* displacements = nullptr;
127 AtomDistribution& ma = *dd->ma;
129 get_commbuffer_counts(&ma, &sendCounts, &displacements);
131 gmx::ArrayRef<gmx::RVec> buffer = ma.rvecBuffer;
133 for (int rank = 0; rank < dd->nnodes; rank++)
135 const auto& domainGroups = ma.domainGroups[rank];
136 for (const int& globalAtom : domainGroups.atomGroups)
138 buffer[localAtom++] = globalVec[globalAtom];
143 int numHomeAtoms = dd->comm->atomRanges.numHomeAtoms();
147 DDMASTER(dd) ? dd->ma->rvecBuffer.data() : nullptr,
148 numHomeAtoms * sizeof(gmx::RVec),
152 static void distributeVec(gmx_domdec_t* dd,
153 gmx::ArrayRef<const gmx::RVec> globalVec,
154 gmx::ArrayRef<gmx::RVec> localVec)
156 if (dd->nnodes <= c_maxNumRanksUseSendRecvForScatterAndGather)
158 distributeVecSendrecv(dd, globalVec, localVec);
162 distributeVecScatterv(dd, globalVec, localVec);
166 static void dd_distribute_dfhist(gmx_domdec_t* dd, df_history_t* dfhist)
168 if (dfhist == nullptr)
173 dd_bcast(dd, sizeof(int), &dfhist->bEquil);
174 dd_bcast(dd, sizeof(int), &dfhist->nlambda);
175 dd_bcast(dd, sizeof(real), &dfhist->wl_delta);
177 if (dfhist->nlambda > 0)
179 int nlam = dfhist->nlambda;
180 dd_bcast(dd, sizeof(int) * nlam, dfhist->n_at_lam);
181 dd_bcast(dd, sizeof(real) * nlam, dfhist->wl_histo);
182 dd_bcast(dd, sizeof(real) * nlam, dfhist->sum_weights);
183 dd_bcast(dd, sizeof(real) * nlam, dfhist->sum_dg);
184 dd_bcast(dd, sizeof(real) * nlam, dfhist->sum_minvar);
185 dd_bcast(dd, sizeof(real) * nlam, dfhist->sum_variance);
187 for (int i = 0; i < nlam; i++)
189 dd_bcast(dd, sizeof(real) * nlam, dfhist->accum_p[i]);
190 dd_bcast(dd, sizeof(real) * nlam, dfhist->accum_m[i]);
191 dd_bcast(dd, sizeof(real) * nlam, dfhist->accum_p2[i]);
192 dd_bcast(dd, sizeof(real) * nlam, dfhist->accum_m2[i]);
193 dd_bcast(dd, sizeof(real) * nlam, dfhist->Tij[i]);
194 dd_bcast(dd, sizeof(real) * nlam, dfhist->Tij_empirical[i]);
199 static void dd_distribute_state(gmx_domdec_t* dd, const t_state* state, t_state* state_local)
201 int nh = state_local->nhchainlength;
205 GMX_RELEASE_ASSERT(state->nhchainlength == nh,
206 "The global and local Nose-Hoover chain lengths should match");
208 for (auto i : gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, real>::keys())
210 state_local->lambda[i] = state->lambda[i];
212 state_local->fep_state = state->fep_state;
213 state_local->veta = state->veta;
214 state_local->vol0 = state->vol0;
215 copy_mat(state->box, state_local->box);
216 copy_mat(state->box_rel, state_local->box_rel);
217 copy_mat(state->boxv, state_local->boxv);
218 copy_mat(state->svir_prev, state_local->svir_prev);
219 copy_mat(state->fvir_prev, state_local->fvir_prev);
220 if (state->dfhist != nullptr)
222 copy_df_history(state_local->dfhist, state->dfhist);
224 for (int i = 0; i < state_local->ngtc; i++)
226 for (int j = 0; j < nh; j++)
228 state_local->nosehoover_xi[i * nh + j] = state->nosehoover_xi[i * nh + j];
229 state_local->nosehoover_vxi[i * nh + j] = state->nosehoover_vxi[i * nh + j];
231 state_local->therm_integral[i] = state->therm_integral[i];
233 for (int i = 0; i < state_local->nnhpres; i++)
235 for (int j = 0; j < nh; j++)
237 state_local->nhpres_xi[i * nh + j] = state->nhpres_xi[i * nh + j];
238 state_local->nhpres_vxi[i * nh + j] = state->nhpres_vxi[i * nh + j];
241 state_local->baros_integral = state->baros_integral;
244 (static_cast<int>(FreeEnergyPerturbationCouplingType::Count) * sizeof(real)),
245 state_local->lambda.data());
246 dd_bcast(dd, sizeof(int), &state_local->fep_state);
247 dd_bcast(dd, sizeof(real), &state_local->veta);
248 dd_bcast(dd, sizeof(real), &state_local->vol0);
249 dd_bcast(dd, sizeof(state_local->box), state_local->box);
250 dd_bcast(dd, sizeof(state_local->box_rel), state_local->box_rel);
251 dd_bcast(dd, sizeof(state_local->boxv), state_local->boxv);
252 dd_bcast(dd, sizeof(state_local->svir_prev), state_local->svir_prev);
253 dd_bcast(dd, sizeof(state_local->fvir_prev), state_local->fvir_prev);
254 dd_bcast(dd, ((state_local->ngtc * nh) * sizeof(double)), state_local->nosehoover_xi.data());
255 dd_bcast(dd, ((state_local->ngtc * nh) * sizeof(double)), state_local->nosehoover_vxi.data());
256 dd_bcast(dd, state_local->ngtc * sizeof(double), state_local->therm_integral.data());
257 dd_bcast(dd, ((state_local->nnhpres * nh) * sizeof(double)), state_local->nhpres_xi.data());
258 dd_bcast(dd, ((state_local->nnhpres * nh) * sizeof(double)), state_local->nhpres_vxi.data());
260 /* communicate df_history -- required for restarting from checkpoint */
261 dd_distribute_dfhist(dd, state_local->dfhist);
263 state_change_natoms(state_local, dd->comm->atomRanges.numHomeAtoms());
265 if (state_local->flags & enumValueToBitMask(StateEntry::X))
267 distributeVec(dd, DDMASTER(dd) ? state->x : gmx::ArrayRef<const gmx::RVec>(), state_local->x);
269 if (state_local->flags & enumValueToBitMask(StateEntry::V))
271 distributeVec(dd, DDMASTER(dd) ? state->v : gmx::ArrayRef<const gmx::RVec>(), state_local->v);
273 if (state_local->flags & enumValueToBitMask(StateEntry::Cgp))
275 distributeVec(dd, DDMASTER(dd) ? state->cg_p : gmx::ArrayRef<const gmx::RVec>(), state_local->cg_p);
279 /* Computes and returns the domain index for the given atom group.
281 * Also updates the coordinates in pos for PBC, when necessary.
283 static inline int computeAtomGroupDomainIndex(const gmx_domdec_t& dd,
284 const gmx_ddbox_t& ddbox,
285 const matrix& triclinicCorrectionMatrix,
286 gmx::ArrayRef<const std::vector<real>> cellBoundaries,
292 /* Set the reference location cg_cm for assigning the group */
294 int numAtoms = atomEnd - atomBegin;
297 copy_rvec(pos[atomBegin], cog);
301 real invNumAtoms = 1 / static_cast<real>(numAtoms);
304 for (int a = atomBegin; a < atomEnd; a++)
306 rvec_inc(cog, pos[a]);
308 for (int d = 0; d < DIM; d++)
310 cog[d] *= invNumAtoms;
313 /* Put the charge group in the box and determine the cell index ind */
315 for (int d = DIM - 1; d >= 0; d--)
318 if (d < dd.unitCellInfo.npbcdim)
320 bool bScrew = (dd.unitCellInfo.haveScrewPBC && d == XX);
321 if (ddbox.tric_dir[d] && dd.numCells[d] > 1)
323 /* Use triclinic coordinates for this dimension */
324 for (int j = d + 1; j < DIM; j++)
326 pos_d += cog[j] * triclinicCorrectionMatrix[j][d];
329 while (pos_d >= box[d][d])
332 rvec_dec(cog, box[d]);
335 cog[YY] = box[YY][YY] - cog[YY];
336 cog[ZZ] = box[ZZ][ZZ] - cog[ZZ];
338 for (int a = atomBegin; a < atomEnd; a++)
340 rvec_dec(pos[a], box[d]);
343 pos[a][YY] = box[YY][YY] - pos[a][YY];
344 pos[a][ZZ] = box[ZZ][ZZ] - pos[a][ZZ];
351 rvec_inc(cog, box[d]);
354 cog[YY] = box[YY][YY] - cog[YY];
355 cog[ZZ] = box[ZZ][ZZ] - cog[ZZ];
357 for (int a = atomBegin; a < atomEnd; a++)
359 rvec_inc(pos[a], box[d]);
362 pos[a][YY] = box[YY][YY] - pos[a][YY];
363 pos[a][ZZ] = box[ZZ][ZZ] - pos[a][ZZ];
368 /* This could be done more efficiently */
370 while (ind[d] + 1 < dd.numCells[d] && pos_d >= cellBoundaries[d][ind[d] + 1])
376 return dd_index(dd.numCells, ind);
380 static std::vector<std::vector<int>> getAtomGroupDistribution(const gmx::MDLogger& mdlog,
381 const gmx_mtop_t& mtop,
383 const gmx_ddbox_t& ddbox,
387 AtomDistribution& ma = *dd->ma;
389 /* Clear the count */
390 for (int rank = 0; rank < dd->nnodes; rank++)
392 ma.domainGroups[rank].numAtoms = 0;
395 matrix triclinicCorrectionMatrix;
396 make_tric_corr_matrix(dd->unitCellInfo.npbcdim, box, triclinicCorrectionMatrix);
399 const auto cellBoundaries = set_dd_cell_sizes_slb(dd, &ddbox, setcellsizeslbMASTER, npulse);
401 std::vector<std::vector<int>> indices(dd->nnodes);
403 if (dd->comm->systemInfo.useUpdateGroups)
406 for (const gmx_molblock_t& molblock : mtop.molblock)
408 const auto& updateGrouping =
409 dd->comm->systemInfo.updateGroupingsPerMoleculeType[molblock.type];
411 for (int mol = 0; mol < molblock.nmol; mol++)
413 for (int g = 0; g < updateGrouping.numBlocks(); g++)
415 const auto& block = updateGrouping.block(g);
416 const int atomBegin = atomOffset + block.begin();
417 const int atomEnd = atomOffset + block.end();
418 const int domainIndex = computeAtomGroupDomainIndex(
419 *dd, ddbox, triclinicCorrectionMatrix, cellBoundaries, atomBegin, atomEnd, box, pos);
421 for (int atomIndex : block)
423 indices[domainIndex].push_back(atomOffset + atomIndex);
425 ma.domainGroups[domainIndex].numAtoms += block.size();
428 atomOffset += updateGrouping.fullRange().end();
432 GMX_RELEASE_ASSERT(atomOffset == mtop.natoms, "Should distribute all atoms");
436 /* Compute the center of geometry for all atoms */
437 for (int atom = 0; atom < mtop.natoms; atom++)
439 int domainIndex = computeAtomGroupDomainIndex(
440 *dd, ddbox, triclinicCorrectionMatrix, cellBoundaries, atom, atom + 1, box, pos);
442 indices[domainIndex].push_back(atom);
443 ma.domainGroups[domainIndex].numAtoms += 1;
448 // Use double for the sums to avoid natoms^2 overflowing
452 int nat_min = ma.domainGroups[0].numAtoms;
453 int nat_max = ma.domainGroups[0].numAtoms;
454 for (int rank = 0; rank < dd->nnodes; rank++)
456 int numAtoms = ma.domainGroups[rank].numAtoms;
458 // convert to double to avoid integer overflows when squaring
459 nat2_sum += gmx::square(double(numAtoms));
460 nat_min = std::min(nat_min, numAtoms);
461 nat_max = std::max(nat_max, numAtoms);
463 nat_sum /= dd->nnodes;
464 nat2_sum /= dd->nnodes;
467 .appendTextFormatted(
468 "Atom distribution over %d domains: av %d stddev %d min %d max %d",
471 gmx::roundToInt(std::sqrt(nat2_sum - gmx::square(static_cast<double>(nat_sum)))),
479 static void distributeAtomGroups(const gmx::MDLogger& mdlog,
481 const gmx_mtop_t& mtop,
483 const gmx_ddbox_t* ddbox,
486 AtomDistribution* ma = dd->ma.get();
487 int * ibuf = nullptr, buf2[2] = { 0, 0 };
488 gmx_bool bMaster = DDMASTER(dd);
490 std::vector<std::vector<int>> groupIndices;
494 GMX_ASSERT(box && pos, "box or pos not set on master");
496 if (dd->unitCellInfo.haveScrewPBC)
498 check_screw_box(box);
501 groupIndices = getAtomGroupDistribution(mdlog, mtop, box, *ddbox, pos, dd);
503 for (int rank = 0; rank < dd->nnodes; rank++)
505 ma->intBuffer[rank * 2] = groupIndices[rank].size();
506 ma->intBuffer[rank * 2 + 1] = ma->domainGroups[rank].numAtoms;
508 ibuf = ma->intBuffer.data();
514 dd_scatter(dd, 2 * sizeof(int), ibuf, buf2);
516 dd->ncg_home = buf2[0];
517 dd->comm->atomRanges.setEnd(DDAtomRanges::Type::Home, buf2[1]);
518 dd->globalAtomGroupIndices.resize(dd->ncg_home);
519 dd->globalAtomIndices.resize(dd->comm->atomRanges.numHomeAtoms());
523 ma->atomGroups.clear();
526 for (int rank = 0; rank < dd->nnodes; rank++)
528 ma->intBuffer[rank] = groupIndices[rank].size() * sizeof(int);
529 ma->intBuffer[dd->nnodes + rank] = groupOffset * sizeof(int);
531 ma->atomGroups.insert(
532 ma->atomGroups.end(), groupIndices[rank].begin(), groupIndices[rank].end());
534 ma->domainGroups[rank].atomGroups = gmx::constArrayRefFromArray(
535 ma->atomGroups.data() + groupOffset, groupIndices[rank].size());
537 groupOffset += groupIndices[rank].size();
542 bMaster ? ma->intBuffer.data() : nullptr,
543 bMaster ? ma->intBuffer.data() + dd->nnodes : nullptr,
544 bMaster ? ma->atomGroups.data() : nullptr,
545 dd->ncg_home * sizeof(int),
546 dd->globalAtomGroupIndices.data());
550 fprintf(debug, "Home charge groups:\n");
551 for (int i = 0; i < dd->ncg_home; i++)
553 fprintf(debug, " %d", dd->globalAtomGroupIndices[i]);
556 fprintf(debug, "\n");
559 fprintf(debug, "\n");
563 void distributeState(const gmx::MDLogger& mdlog,
565 const gmx_mtop_t& mtop,
566 t_state* state_global,
567 const gmx_ddbox_t& ddbox,
568 t_state* state_local)
570 rvec* xGlobal = (DDMASTER(dd) ? state_global->x.rvec_array() : nullptr);
572 distributeAtomGroups(mdlog, dd, mtop, DDMASTER(dd) ? state_global->box : nullptr, &ddbox, xGlobal);
574 dd_distribute_state(dd, state_global, state_local);