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38 * \brief This file defines functions used in making the
41 * \author Berk Hess <hess@kth.se>
42 * \ingroup module_domdec
47 #include "gromacs/domdec/reversetopology.h"
54 #include "gromacs/math/vec.h"
55 #include "gromacs/domdec/domdec_constraints.h"
56 #include "gromacs/domdec/domdec_internal.h"
57 #include "gromacs/domdec/domdec_vsite.h"
58 #include "gromacs/domdec/options.h"
59 #include "gromacs/mdlib/gmx_omp_nthreads.h"
60 #include "gromacs/mdlib/vsite.h"
61 #include "gromacs/mdtypes/inputrec.h"
62 #include "gromacs/topology/atoms.h"
63 #include "gromacs/topology/mtop_util.h"
64 #include "gromacs/topology/topsort.h"
65 #include "gromacs/utility/arrayref.h"
66 #include "gromacs/utility/fatalerror.h"
69 using gmx::DDBondedChecking;
70 using gmx::ListOfLists;
73 /*! \brief Struct for the reverse topology: links bonded interactions to atoms */
74 struct gmx_reverse_top_t::Impl
76 //! Constructs a reverse topology from \p mtop
77 Impl(const gmx_mtop_t& mtop, bool useFreeEnergy, const ReverseTopOptions& reverseTopOptions);
79 //! @cond Doxygen_Suppress
80 //! Options for the setup of this reverse topology
81 const ReverseTopOptions options;
82 //! Are there interaction of type F_POSRES and/or F_FBPOSRES
83 bool hasPositionRestraints;
84 //! \brief Are there bondeds/exclusions between atoms?
85 bool bInterAtomicInteractions = false;
86 //! \brief Reverse ilist for all moltypes
87 std::vector<reverse_ilist_t> ril_mt;
88 //! \brief The size of ril_mt[?].index summed over all entries
89 int ril_mt_tot_size = 0;
90 //! \brief The sorting state of bondeds for free energy
91 int ilsort = ilsortUNKNOWN;
92 //! \brief molblock to global atom index for quick lookup of molblocks on atom index
93 std::vector<MolblockIndices> mbi;
95 //! \brief Do we have intermolecular interactions?
96 bool bIntermolecularInteractions = false;
97 //! \brief Intermolecular reverse ilist
98 reverse_ilist_t ril_intermol;
100 //! The number of bonded interactions computed from the full topology
101 int expectedNumGlobalBondedInteractions = 0;
103 /* Work data structures for multi-threading */
104 //! \brief Thread work array for local topology generation
105 std::vector<thread_work_t> th_work;
110 int nral_rt(int ftype)
112 int nral = NRAL(ftype);
113 if (interaction_function[ftype].flags & IF_VSITE)
115 /* With vsites the reverse topology contains an extra entry
116 * for storing if constructing atoms are vsites.
124 bool dd_check_ftype(const int ftype, const ReverseTopOptions& rtOptions)
126 return ((((interaction_function[ftype].flags & IF_BOND) != 0U)
127 && ((interaction_function[ftype].flags & IF_VSITE) == 0U)
128 && ((rtOptions.ddBondedChecking == DDBondedChecking::All)
129 || ((interaction_function[ftype].flags & IF_LIMZERO) == 0U)))
130 || (rtOptions.includeConstraints && (ftype == F_CONSTR || ftype == F_CONSTRNC))
131 || (rtOptions.includeSettles && ftype == F_SETTLE));
134 void global_atomnr_to_moltype_ind(ArrayRef<const MolblockIndices> molblockIndices,
141 const MolblockIndices* mbi = molblockIndices.data();
143 int end = molblockIndices.size(); /* exclusive */
146 /* binary search for molblock_ind */
149 mid = (start + end) / 2;
150 if (i_gl >= mbi[mid].a_end)
154 else if (i_gl < mbi[mid].a_start)
168 *mol = (i_gl - mbi->a_start) / mbi->natoms_mol;
169 *i_mol = (i_gl - mbi->a_start) - (*mol) * mbi->natoms_mol;
172 /*! \brief Returns the maximum number of exclusions per atom */
173 static int getMaxNumExclusionsPerAtom(const ListOfLists<int>& excls)
176 for (gmx::index at = 0; at < excls.ssize(); at++)
178 const auto list = excls[at];
179 const int numExcls = list.ssize();
181 GMX_RELEASE_ASSERT(numExcls != 1 || list[0] == at,
182 "With 1 exclusion we expect a self-exclusion");
184 maxNumExcls = std::max(maxNumExcls, numExcls);
190 /*! \brief Run the reverse ilist generation and store it in r_il when \p bAssign = TRUE */
191 static int low_make_reverse_ilist(const InteractionLists& il_mt,
194 const ReverseTopOptions& rtOptions,
195 gmx::ArrayRef<const int> r_index,
196 gmx::ArrayRef<int> r_il,
197 const AtomLinkRule atomLinkRule,
198 const bool assignReverseIlist)
200 const bool includeConstraints = rtOptions.includeConstraints;
201 const bool includeSettles = rtOptions.includeSettles;
202 const DDBondedChecking ddBondedChecking = rtOptions.ddBondedChecking;
206 for (int ftype = 0; ftype < F_NRE; ftype++)
208 if ((interaction_function[ftype].flags & (IF_BOND | IF_VSITE))
209 || (includeConstraints && (ftype == F_CONSTR || ftype == F_CONSTRNC))
210 || (includeSettles && ftype == F_SETTLE))
212 const bool isVSite = ((interaction_function[ftype].flags & IF_VSITE) != 0U);
213 const int nral = NRAL(ftype);
214 const auto& il = il_mt[ftype];
215 for (int i = 0; i < il.size(); i += 1 + nral)
217 const int* ia = il.iatoms.data() + i;
218 // Virtual sites should not be linked for bonded interactions
219 const int nlink = (atomLinkRule == AtomLinkRule::FirstAtom) ? 1 : (isVSite ? 0 : nral);
220 for (int link = 0; link < nlink; link++)
222 const int a = ia[1 + link];
223 if (assignReverseIlist)
225 GMX_ASSERT(!r_il.empty(), "with bAssign not allowed to be empty");
226 GMX_ASSERT(!r_index.empty(), "with bAssign not allowed to be empty");
227 r_il[r_index[a] + count[a]] = (ftype == F_CONSTRNC ? F_CONSTR : ftype);
228 r_il[r_index[a] + count[a] + 1] = ia[0];
229 for (int j = 1; j < 1 + nral; j++)
231 /* Store the molecular atom number */
232 r_il[r_index[a] + count[a] + 1 + j] = ia[j];
235 if (interaction_function[ftype].flags & IF_VSITE)
237 if (assignReverseIlist)
239 /* Add an entry to iatoms for storing
240 * which of the constructing atoms are
243 r_il[r_index[a] + count[a] + 2 + nral] = 0;
244 for (int j = 2; j < 1 + nral; j++)
246 if (atom[ia[j]].ptype == ParticleType::VSite)
248 r_il[r_index[a] + count[a] + 2 + nral] |= (2 << j);
255 /* We do not count vsites since they are always
256 * uniquely assigned and can be assigned
257 * to multiple nodes with recursive vsites.
259 if (ddBondedChecking == DDBondedChecking::All
260 || !(interaction_function[ftype].flags & IF_LIMZERO))
265 count[a] += 2 + nral_rt(ftype);
274 int make_reverse_ilist(const InteractionLists& ilist,
275 const t_atoms* atoms,
276 const ReverseTopOptions& rtOptions,
277 const AtomLinkRule atomLinkRule,
278 reverse_ilist_t* ril_mt)
280 /* Count the interactions */
281 const int nat_mt = atoms->nr;
282 std::vector<int> count(nat_mt);
283 low_make_reverse_ilist(ilist, atoms->atom, count.data(), rtOptions, {}, {}, atomLinkRule, FALSE);
285 ril_mt->index.push_back(0);
286 for (int i = 0; i < nat_mt; i++)
288 ril_mt->index.push_back(ril_mt->index[i] + count[i]);
291 ril_mt->il.resize(ril_mt->index[nat_mt]);
293 /* Store the interactions */
294 int nint_mt = low_make_reverse_ilist(
295 ilist, atoms->atom, count.data(), rtOptions, ril_mt->index, ril_mt->il, atomLinkRule, TRUE);
297 ril_mt->numAtomsInMolecule = atoms->nr;
302 gmx_reverse_top_t::gmx_reverse_top_t(const gmx_mtop_t& mtop,
304 const ReverseTopOptions& reverseTopOptions) :
305 impl_(std::make_unique<Impl>(mtop, useFreeEnergy, reverseTopOptions))
309 gmx_reverse_top_t::~gmx_reverse_top_t() {}
311 const ReverseTopOptions& gmx_reverse_top_t::options() const
313 return impl_->options;
316 const reverse_ilist_t& gmx_reverse_top_t::interactionListForMoleculeType(int moleculeType) const
318 return impl_->ril_mt[moleculeType];
321 int gmx_reverse_top_t::expectedNumGlobalBondedInteractions() const
323 return impl_->expectedNumGlobalBondedInteractions;
326 ArrayRef<const MolblockIndices> gmx_reverse_top_t::molblockIndices() const
331 bool gmx_reverse_top_t::hasIntermolecularInteractions() const
333 return impl_->bIntermolecularInteractions;
336 const reverse_ilist_t& gmx_reverse_top_t::interactionListForIntermolecularInteractions() const
338 return impl_->ril_intermol;
341 bool gmx_reverse_top_t::hasInterAtomicInteractions() const
343 return impl_->bInterAtomicInteractions;
346 bool gmx_reverse_top_t::hasPositionRestraints() const
348 return impl_->hasPositionRestraints;
351 ArrayRef<thread_work_t> gmx_reverse_top_t::threadWorkObjects() const
353 return impl_->th_work;
356 bool gmx_reverse_top_t::doSorting() const
358 return impl_->ilsort != ilsortNO_FE;
361 /*! \brief Generate the reverse topology */
362 gmx_reverse_top_t::Impl::Impl(const gmx_mtop_t& mtop,
363 const bool useFreeEnergy,
364 const ReverseTopOptions& reverseTopOptions) :
365 options(reverseTopOptions),
366 hasPositionRestraints(gmx_mtop_ftype_count(mtop, F_POSRES) + gmx_mtop_ftype_count(mtop, F_FBPOSRES) > 0),
367 bInterAtomicInteractions(mtop.bIntermolecularInteractions)
369 bInterAtomicInteractions = mtop.bIntermolecularInteractions;
370 ril_mt.resize(mtop.moltype.size());
372 std::vector<int> nint_mt;
373 for (size_t mt = 0; mt < mtop.moltype.size(); mt++)
375 const gmx_moltype_t& molt = mtop.moltype[mt];
376 if (molt.atoms.nr > 1)
378 bInterAtomicInteractions = true;
381 /* Make the atom to interaction list for this molecule type */
382 int numberOfInteractions = make_reverse_ilist(
383 molt.ilist, &molt.atoms, options, AtomLinkRule::FirstAtom, &ril_mt[mt]);
384 nint_mt.push_back(numberOfInteractions);
386 ril_mt_tot_size += ril_mt[mt].index[molt.atoms.nr];
390 fprintf(debug, "The total size of the atom to interaction index is %d integers\n", ril_mt_tot_size);
393 expectedNumGlobalBondedInteractions = 0;
394 for (const gmx_molblock_t& molblock : mtop.molblock)
396 expectedNumGlobalBondedInteractions += molblock.nmol * nint_mt[molblock.type];
399 /* Make an intermolecular reverse top, if necessary */
400 bIntermolecularInteractions = mtop.bIntermolecularInteractions;
401 if (bIntermolecularInteractions)
403 t_atoms atoms_global;
405 atoms_global.nr = mtop.natoms;
406 atoms_global.atom = nullptr; /* Only used with virtual sites */
408 GMX_RELEASE_ASSERT(mtop.intermolecular_ilist,
409 "We should have an ilist when intermolecular interactions are on");
411 expectedNumGlobalBondedInteractions += make_reverse_ilist(
412 *mtop.intermolecular_ilist, &atoms_global, options, AtomLinkRule::FirstAtom, &ril_intermol);
415 if (useFreeEnergy && gmx_mtop_bondeds_free_energy(&mtop))
417 ilsort = ilsortFE_UNSORTED;
421 ilsort = ilsortNO_FE;
424 /* Make a molblock index for fast searching */
426 for (size_t mb = 0; mb < mtop.molblock.size(); mb++)
428 const gmx_molblock_t& molb = mtop.molblock[mb];
429 const int numAtomsPerMol = mtop.moltype[molb.type].atoms.nr;
430 MolblockIndices mbiMolblock;
431 mbiMolblock.a_start = i;
432 i += molb.nmol * numAtomsPerMol;
433 mbiMolblock.a_end = i;
434 mbiMolblock.natoms_mol = numAtomsPerMol;
435 mbiMolblock.type = molb.type;
436 mbi.push_back(mbiMolblock);
439 for (int th = 0; th < gmx_omp_nthreads_get(ModuleMultiThread::Domdec); th++)
441 th_work.emplace_back(mtop.ffparams);
445 void dd_make_reverse_top(FILE* fplog,
447 const gmx_mtop_t& mtop,
448 const gmx::VirtualSitesHandler* vsite,
449 const t_inputrec& inputrec,
450 const DDBondedChecking ddBondedChecking)
454 fprintf(fplog, "\nLinking all bonded interactions to atoms\n");
457 /* If normal and/or settle constraints act only within charge groups,
458 * we can store them in the reverse top and simply assign them to domains.
459 * Otherwise we need to assign them to multiple domains and set up
460 * the parallel version constraint algorithm(s).
462 GMX_RELEASE_ASSERT(ddBondedChecking == DDBondedChecking::ExcludeZeroLimit
463 || ddBondedChecking == DDBondedChecking::All,
464 "Invalid enum value for mdrun -ddcheck");
465 const ReverseTopOptions rtOptions(ddBondedChecking,
466 !dd->comm->systemInfo.mayHaveSplitConstraints,
467 !dd->comm->systemInfo.mayHaveSplitSettles);
469 dd->reverse_top = std::make_unique<gmx_reverse_top_t>(
470 mtop, inputrec.efep != FreeEnergyPerturbationType::No, rtOptions);
472 dd->haveExclusions = false;
473 for (const gmx_molblock_t& molb : mtop.molblock)
475 const int maxNumExclusionsPerAtom = getMaxNumExclusionsPerAtom(mtop.moltype[molb.type].excls);
476 // We checked above that max 1 exclusion means only self exclusions
477 if (maxNumExclusionsPerAtom > 1)
479 dd->haveExclusions = true;
483 const int numInterUpdategroupVirtualSites =
484 (vsite == nullptr ? 0 : vsite->numInterUpdategroupVirtualSites());
485 if (numInterUpdategroupVirtualSites > 0)
490 "There are %d inter update-group virtual sites,\n"
491 "will perform an extra communication step for selected coordinates and "
493 numInterUpdategroupVirtualSites);
495 init_domdec_vsites(dd, numInterUpdategroupVirtualSites);
498 if (dd->comm->systemInfo.mayHaveSplitConstraints || dd->comm->systemInfo.mayHaveSplitSettles)
500 init_domdec_constraints(dd, mtop);
504 fprintf(fplog, "\n");