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40 * \brief This file implements functions for domdec to use
41 * while managing inter-atomic constraints.
43 * \author Berk Hess <hess@kth.se>
44 * \ingroup module_domdec
49 #include "domdec_constraints.h"
56 #include "gromacs/domdec/dlbtiming.h"
57 #include "gromacs/domdec/domdec.h"
58 #include "gromacs/domdec/domdec_struct.h"
59 #include "gromacs/domdec/ga2la.h"
60 #include "gromacs/domdec/hashedmap.h"
61 #include "gromacs/math/vec.h"
62 #include "gromacs/mdlib/constr.h"
63 #include "gromacs/mdlib/gmx_omp_nthreads.h"
64 #include "gromacs/mdtypes/commrec.h"
65 #include "gromacs/mdtypes/forcerec.h" // only for GET_CGINFO_*
66 #include "gromacs/pbcutil/ishift.h"
67 #include "gromacs/topology/ifunc.h"
68 #include "gromacs/topology/mtop_lookup.h"
69 #include "gromacs/utility/exceptions.h"
70 #include "gromacs/utility/fatalerror.h"
71 #include "gromacs/utility/gmxassert.h"
72 #include "gromacs/utility/listoflists.h"
74 #include "domdec_internal.h"
75 #include "domdec_specatomcomm.h"
77 using gmx::ListOfLists;
79 /*! \brief Struct used during constraint setup with domain decomposition */
80 struct gmx_domdec_constraints_t
82 //! @cond Doxygen_Suppress
83 std::vector<int> molb_con_offset; /**< Offset in the constraint array for each molblock */
84 std::vector<int> molb_ncon_mol; /**< The number of constraints per molecule for each molblock */
86 int ncon; /**< The fully local and conneced constraints */
87 /* The global constraint number, only required for clearing gc_req */
88 std::vector<int> con_gl; /**< Global constraint indices for local constraints */
89 std::vector<int> con_nlocat; /**< Number of local atoms (2/1/0) for each constraint */
91 std::vector<bool> gc_req; /**< Boolean that tells if a global constraint index has been requested; note: size global #constraints */
93 /* Hash table for keeping track of requests */
94 std::unique_ptr<gmx::HashedMap<int>> ga2la; /**< Global to local communicated constraint atom only index */
96 /* Multi-threading stuff */
97 int nthread; /**< Number of threads used for DD constraint setup */
98 std::vector<InteractionList> ils; /**< Constraint ilist working arrays, size \p nthread */
100 /* Buffers for requesting atoms */
101 std::vector<std::vector<int>> requestedGlobalAtomIndices; /**< Buffers for requesting global atom indices, one per thread */
106 void dd_move_x_constraints(gmx_domdec_t* dd,
108 gmx::ArrayRef<gmx::RVec> x0,
109 gmx::ArrayRef<gmx::RVec> x1,
112 if (dd->constraint_comm)
115 dd, dd->constraint_comm, box, as_rvec_array(x0.data()), as_rvec_array(x1.data()), bX1IsCoord);
117 ddReopenBalanceRegionCpu(dd);
121 gmx::ArrayRef<const int> dd_constraints_nlocalatoms(const gmx_domdec_t* dd)
123 if (dd && dd->constraints)
125 return dd->constraints->con_nlocat;
133 void dd_clear_local_constraint_indices(gmx_domdec_t* dd)
135 gmx_domdec_constraints_t* dc = dd->constraints;
137 std::fill(dc->gc_req.begin(), dc->gc_req.end(), false);
139 if (dd->constraint_comm)
145 /*! \brief Walks over the constraints out from the local atoms into the non-local atoms and adds them to a list */
146 static void walk_out(int con,
151 gmx::ArrayRef<const int> ia1,
152 gmx::ArrayRef<const int> ia2,
153 const ListOfLists<int>& at2con,
154 const gmx_ga2la_t& ga2la,
155 gmx_bool bHomeConnect,
156 gmx_domdec_constraints_t* dc,
157 gmx_domdec_specat_comm_t* dcc,
158 InteractionList* il_local,
159 std::vector<int>* ireq)
161 if (!dc->gc_req[con_offset + con])
163 /* Add this non-home constraint to the list */
164 dc->con_gl.push_back(con_offset + con);
165 dc->con_nlocat.push_back(bHomeConnect ? 1 : 0);
166 dc->gc_req[con_offset + con] = true;
167 const int* iap = constr_iatomptr(ia1, ia2, con);
168 const int parameterType = iap[0];
169 const int a1_gl = offset + iap[1];
170 const int a2_gl = offset + iap[2];
171 std::array<int, 2> atoms;
172 /* The following indexing code can probably be optizimed */
173 if (const int* a_loc = ga2la.findHome(a1_gl))
179 /* We set this index later */
180 atoms[0] = -a1_gl - 1;
182 if (const int* a_loc = ga2la.findHome(a2_gl))
188 /* We set this index later */
189 atoms[1] = -a2_gl - 1;
191 il_local->push_back(parameterType, atoms);
194 /* Check to not ask for the same atom more than once */
195 if (!dc->ga2la->find(offset + a))
198 /* Add this non-home atom to the list */
199 ireq->push_back(offset + a);
200 /* Temporarily mark with -2, we get the index later */
201 dc->ga2la->insert(offset + a, -2);
206 /* Loop over the constraint connected to atom a */
207 for (const int coni : at2con[a])
212 const int* iap = constr_iatomptr(ia1, ia2, coni);
213 const int b = (a == iap[1]) ? iap[2] : iap[1];
214 if (!ga2la.findHome(offset + b))
216 walk_out(coni, con_offset, b, offset, nrec - 1, ia1, ia2, at2con, ga2la, FALSE, dc, dcc, il_local, ireq);
223 /*! \brief Looks up SETTLE constraints for a range of charge-groups */
224 static void atoms_to_settles(gmx_domdec_t* dd,
225 const gmx_mtop_t& mtop,
227 gmx::ArrayRef<const std::vector<int>> at2settle_mt,
230 InteractionList* ils_local,
231 std::vector<int>* ireq)
233 const gmx_ga2la_t& ga2la = *dd->ga2la;
234 int nral = NRAL(F_SETTLE);
237 for (int a = cg_start; a < cg_end; a++)
239 if (GET_CGINFO_SETTLE(cginfo[a]))
241 int a_gl = dd->globalAtomIndices[a];
243 mtopGetMolblockIndex(mtop, a_gl, &mb, nullptr, &a_mol);
245 const gmx_molblock_t* molb = &mtop.molblock[mb];
246 int settle = at2settle_mt[molb->type][a_mol];
250 int offset = a_gl - a_mol;
252 const int* ia1 = mtop.moltype[molb->type].ilist[F_SETTLE].iatoms.data();
255 gmx_bool bAssign = FALSE;
257 for (int sa = 0; sa < nral; sa++)
259 int a_glsa = offset + ia1[settle * (1 + nral) + 1 + sa];
261 if (ga2la.findHome(a_glsa))
263 if (nlocal == 0 && a_gl == a_glsa)
273 const int parameterType = ia1[settle * 4];
274 std::array<int, 3> atoms;
275 for (int sa = 0; sa < nral; sa++)
277 if (const int* a_loc = ga2la.findHome(a_gls[sa]))
283 atoms[sa] = -a_gls[sa] - 1;
284 /* Add this non-home atom to the list */
285 ireq->push_back(a_gls[sa]);
286 /* A check on double atom requests is
287 * not required for settle.
291 ils_local->push_back(parameterType, atoms);
298 /*! \brief Looks up constraint for the local atoms */
299 static void atoms_to_constraints(gmx_domdec_t* dd,
300 const gmx_mtop_t& mtop,
302 gmx::ArrayRef<const ListOfLists<int>> at2con_mt,
304 InteractionList* ilc_local,
305 std::vector<int>* ireq)
307 gmx_domdec_constraints_t* dc = dd->constraints;
308 gmx_domdec_specat_comm_t* dcc = dd->constraint_comm;
310 const gmx_ga2la_t& ga2la = *dd->ga2la;
313 dc->con_nlocat.clear();
317 for (int a = 0; a < dd->ncg_home; a++)
319 if (GET_CGINFO_CONSTR(cginfo[a]))
321 int a_gl = dd->globalAtomIndices[a];
324 mtopGetMolblockIndex(mtop, a_gl, &mb, &molnr, &a_mol);
326 const gmx_molblock_t& molb = mtop.molblock[mb];
328 gmx::ArrayRef<const int> ia1 = mtop.moltype[molb.type].ilist[F_CONSTR].iatoms;
329 gmx::ArrayRef<const int> ia2 = mtop.moltype[molb.type].ilist[F_CONSTRNC].iatoms;
331 /* Calculate the global constraint number offset for the molecule.
332 * This is only required for the global index to make sure
333 * that we use each constraint only once.
335 const int con_offset = dc->molb_con_offset[mb] + molnr * dc->molb_ncon_mol[mb];
337 /* The global atom number offset for this molecule */
338 const int offset = a_gl - a_mol;
339 /* Loop over the constraints connected to atom a_mol in the molecule */
340 const auto& at2con = at2con_mt[molb.type];
341 for (const int con : at2con[a_mol])
343 const int* iap = constr_iatomptr(ia1, ia2, con);
353 if (const int* a_loc = ga2la.findHome(offset + b_mol))
355 /* Add this fully home constraint at the first atom */
358 dc->con_gl.push_back(con_offset + con);
359 dc->con_nlocat.push_back(2);
360 const int b_lo = *a_loc;
361 const int parameterType = iap[0];
362 std::array<int, 2> atoms;
363 atoms[0] = (a_gl == iap[1] ? a : b_lo);
364 atoms[1] = (a_gl == iap[1] ? b_lo : a);
365 ilc_local->push_back(parameterType, atoms);
372 /* We need the nrec constraints coupled to this constraint,
373 * so we need to walk out of the home cell by nrec+1 atoms,
374 * since already atom bg is not locally present.
375 * Therefore we call walk_out with nrec recursions to go
376 * after this first call.
378 walk_out(con, con_offset, b_mol, offset, nrec, ia1, ia2, at2con, ga2la, TRUE, dc, dcc, ilc_local, ireq);
384 GMX_ASSERT(dc->con_gl.size() == static_cast<size_t>(dc->ncon),
385 "con_gl size should match the number of constraints");
386 GMX_ASSERT(dc->con_nlocat.size() == static_cast<size_t>(dc->ncon),
387 "con_nlocat size should match the number of constraints");
392 "Constraints: home %3d border %3d atoms: %3zu\n",
395 dd->constraint_comm ? ireq->size() : 0);
399 int dd_make_local_constraints(gmx_domdec_t* dd,
401 const struct gmx_mtop_t& mtop,
403 gmx::Constraints* constr,
405 gmx::ArrayRef<InteractionList> il_local)
407 // This code should not be called unless this condition is true,
408 // because that's the only time init_domdec_constraints is
410 GMX_RELEASE_ASSERT(dd->comm->systemInfo.haveSplitConstraints || dd->comm->systemInfo.haveSplitSettles,
411 "dd_make_local_constraints called when there are no local constraints");
412 // ... and init_domdec_constraints always sets
413 // dd->constraint_comm...
416 "Invalid use of dd_make_local_constraints before construction of constraint_comm");
417 // ... which static analysis needs to be reassured about, because
418 // otherwise, when dd->splitSettles is
419 // true. dd->constraint_comm is unilaterally dereferenced before
420 // the call to atoms_to_settles.
422 gmx_domdec_constraints_t* dc = dd->constraints;
424 InteractionList* ilc_local = &il_local[F_CONSTR];
425 InteractionList* ils_local = &il_local[F_SETTLE];
428 gmx::ArrayRef<const ListOfLists<int>> at2con_mt;
429 std::vector<int>* ireq = nullptr;
431 if (dd->constraint_comm)
433 // TODO Perhaps gmx_domdec_constraints_t should keep a valid constr?
434 GMX_RELEASE_ASSERT(constr != nullptr, "Must have valid constraints object");
435 at2con_mt = constr->atom2constraints_moltype();
436 ireq = &dc->requestedGlobalAtomIndices[0];
440 gmx::ArrayRef<const std::vector<int>> at2settle_mt;
441 /* When settle works inside charge groups, we assigned them already */
442 if (dd->comm->systemInfo.haveSplitSettles)
444 // TODO Perhaps gmx_domdec_constraints_t should keep a valid constr?
445 GMX_RELEASE_ASSERT(constr != nullptr, "Must have valid constraints object");
446 at2settle_mt = constr->atom2settle_moltype();
450 if (at2settle_mt.empty())
452 atoms_to_constraints(dd, mtop, cginfo, at2con_mt, nrec, ilc_local, ireq);
456 /* Do the constraints, if present, on the first thread.
457 * Do the settles on all other threads.
459 const int t0_set = ((!at2con_mt.empty() && dc->nthread > 1) ? 1 : 0);
461 #pragma omp parallel for num_threads(dc->nthread) schedule(static)
462 for (int thread = 0; thread < dc->nthread; thread++)
466 if (!at2con_mt.empty() && thread == 0)
468 atoms_to_constraints(dd, mtop, cginfo, at2con_mt, nrec, ilc_local, ireq);
471 if (thread >= t0_set)
473 /* Distribute the settle check+assignments over
474 * dc->nthread or dc->nthread-1 threads.
476 const int cg0 = (dd->ncg_home * (thread - t0_set)) / (dc->nthread - t0_set);
477 const int cg1 = (dd->ncg_home * (thread - t0_set + 1)) / (dc->nthread - t0_set);
479 InteractionList* ilst = (thread == t0_set) ? ils_local : &dc->ils[thread];
482 std::vector<int>& ireqt = dc->requestedGlobalAtomIndices[thread];
488 atoms_to_settles(dd, mtop, cginfo, at2settle_mt, cg0, cg1, ilst, &ireqt);
491 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
494 /* Combine the generate settles and requested indices */
495 for (int thread = 1; thread < dc->nthread; thread++)
499 ils_local->append(dc->ils[thread]);
502 const std::vector<int>& ireqt = dc->requestedGlobalAtomIndices[thread];
503 ireq->insert(ireq->end(), ireqt.begin(), ireqt.end());
508 fprintf(debug, "Settles: total %3d\n", ils_local->size() / 4);
513 if (dd->constraint_comm)
515 at_end = setup_specat_communication(dd,
518 dd->constraints->ga2la.get(),
524 /* Fill in the missing indices */
525 gmx::HashedMap<int>* ga2la_specat = dd->constraints->ga2la.get();
527 int nral1 = 1 + NRAL(F_CONSTR);
528 for (int i = 0; i < ilc_local->size(); i += nral1)
530 int* iap = ilc_local->iatoms.data() + i;
531 for (int j = 1; j < nral1; j++)
535 const int* a = ga2la_specat->find(-iap[j] - 1);
536 GMX_ASSERT(a, "We have checked before that this atom index has been set");
542 nral1 = 1 + NRAL(F_SETTLE);
543 for (int i = 0; i < ils_local->size(); i += nral1)
545 int* iap = ils_local->iatoms.data() + i;
546 for (int j = 1; j < nral1; j++)
550 const int* a = ga2la_specat->find(-iap[j] - 1);
551 GMX_ASSERT(a, "We have checked before that this atom index has been set");
559 // Currently unreachable
566 void init_domdec_constraints(gmx_domdec_t* dd, const gmx_mtop_t& mtop)
570 fprintf(debug, "Begin init_domdec_constraints\n");
573 dd->constraints = new gmx_domdec_constraints_t;
574 gmx_domdec_constraints_t* dc = dd->constraints;
576 dc->molb_con_offset.resize(mtop.molblock.size());
577 dc->molb_ncon_mol.resize(mtop.molblock.size());
580 for (size_t mb = 0; mb < mtop.molblock.size(); mb++)
582 const gmx_molblock_t* molb = &mtop.molblock[mb];
583 dc->molb_con_offset[mb] = ncon;
584 dc->molb_ncon_mol[mb] = mtop.moltype[molb->type].ilist[F_CONSTR].size() / 3
585 + mtop.moltype[molb->type].ilist[F_CONSTRNC].size() / 3;
586 ncon += molb->nmol * dc->molb_ncon_mol[mb];
591 dc->gc_req.resize(ncon);
594 /* Use a hash table for the global to local index.
595 * The number of keys is a rough estimate, it will be optimized later.
597 int numKeysEstimate = std::min(mtop.natoms / 20, mtop.natoms / (2 * dd->nnodes));
598 dc->ga2la = std::make_unique<gmx::HashedMap<int>>(numKeysEstimate);
600 dc->nthread = gmx_omp_nthreads_get(ModuleMultiThread::Domdec);
601 dc->ils.resize(dc->nthread);
603 dd->constraint_comm = new gmx_domdec_specat_comm_t;
605 dc->requestedGlobalAtomIndices.resize(dc->nthread);