/*! \brief The number of integer item in the local state, used for broadcasting of the state */
#define NITEM_DD_INIT_LOCAL_STATE 5
-/*! \brief Struct for the reverse topology: links bonded interactions to atoms */
-struct gmx_reverse_top_t::Impl
-{
- //! Constructs a reverse topology from \p mtop
- Impl(const gmx_mtop_t& mtop, bool useFreeEnergy, const ReverseTopOptions& reverseTopOptions);
-
- //! @cond Doxygen_Suppress
- //! Options for the setup of this reverse topology
- const ReverseTopOptions options;
- //! Are there interaction of type F_POSRES and/or F_FBPOSRES
- bool hasPositionRestraints;
- //! \brief Are there bondeds/exclusions between atoms?
- bool bInterAtomicInteractions = false;
- //! \brief Reverse ilist for all moltypes
- std::vector<reverse_ilist_t> ril_mt;
- //! \brief The size of ril_mt[?].index summed over all entries
- int ril_mt_tot_size = 0;
- //! \brief The sorting state of bondeds for free energy
- int ilsort = ilsortUNKNOWN;
- //! \brief molblock to global atom index for quick lookup of molblocks on atom index
- std::vector<MolblockIndices> mbi;
-
- //! \brief Do we have intermolecular interactions?
- bool bIntermolecularInteractions = false;
- //! \brief Intermolecular reverse ilist
- reverse_ilist_t ril_intermol;
-
- /*! \brief Data to help check reverse topology construction
- *
- * Partitioning could incorrectly miss a bonded interaction.
- * However, checking for that requires a global communication
- * stage, which does not otherwise happen during partitioning. So,
- * for performance, we do that alongside the first global energy
- * reduction after a new DD is made. These variables handle
- * whether the check happens, its input for this domain, output
- * across all domains, and the expected value it should match. */
- /*! \{ */
- /*! \brief Number of bonded interactions found in the reverse
- * topology for this domain. */
- int numBondedInteractions = 0;
- /*! \brief Whether to check at the next global communication
- * stage the total number of bonded interactions found.
- *
- * Cleared after that number is found. */
- bool shouldCheckNumberOfBondedInteractions = false;
- /*! \brief The total number of bonded interactions found in
- * the reverse topology across all domains.
- *
- * Only has a value after reduction across all ranks, which is
- * removed when it is again time to check after a new
- * partition. */
- std::optional<int> numBondedInteractionsOverAllDomains;
- //! The number of bonded interactions computed from the full topology
- int expectedNumGlobalBondedInteractions = 0;
- /*! \} */
-
- /* Work data structures for multi-threading */
- //! \brief Thread work array for local topology generation
- std::vector<thread_work_t> th_work;
- //! @endcond
-};
-
-
-int nral_rt(int ftype)
-{
- int nral = NRAL(ftype);
- if (interaction_function[ftype].flags & IF_VSITE)
- {
- /* With vsites the reverse topology contains an extra entry
- * for storing if constructing atoms are vsites.
- */
- nral += 1;
- }
-
- return nral;
-}
-
-bool dd_check_ftype(const int ftype, const ReverseTopOptions& rtOptions)
-{
- return ((((interaction_function[ftype].flags & IF_BOND) != 0U)
- && ((interaction_function[ftype].flags & IF_VSITE) == 0U)
- && ((rtOptions.ddBondedChecking == DDBondedChecking::All)
- || ((interaction_function[ftype].flags & IF_LIMZERO) == 0U)))
- || (rtOptions.includeConstraints && (ftype == F_CONSTR || ftype == F_CONSTRNC))
- || (rtOptions.includeSettles && ftype == F_SETTLE));
-}
-
-/*! \brief Return global topology molecule information for global atom index \p i_gl */
-static void global_atomnr_to_moltype_ind(ArrayRef<const MolblockIndices> molblockIndices,
- int i_gl,
- int* mb,
- int* mt,
- int* mol,
- int* i_mol)
-{
- const MolblockIndices* mbi = molblockIndices.data();
- int start = 0;
- int end = molblockIndices.size(); /* exclusive */
- int mid = 0;
-
- /* binary search for molblock_ind */
- while (TRUE)
- {
- mid = (start + end) / 2;
- if (i_gl >= mbi[mid].a_end)
- {
- start = mid + 1;
- }
- else if (i_gl < mbi[mid].a_start)
- {
- end = mid;
- }
- else
- {
- break;
- }
- }
-
- *mb = mid;
- mbi += mid;
-
- *mt = mbi->type;
- *mol = (i_gl - mbi->a_start) / mbi->natoms_mol;
- *i_mol = (i_gl - mbi->a_start) - (*mol) * mbi->natoms_mol;
-}
-
-/*! \brief Returns the maximum number of exclusions per atom */
-static int getMaxNumExclusionsPerAtom(const ListOfLists<int>& excls)
-{
- int maxNumExcls = 0;
- for (gmx::index at = 0; at < excls.ssize(); at++)
- {
- const auto list = excls[at];
- const int numExcls = list.ssize();
-
- GMX_RELEASE_ASSERT(numExcls != 1 || list[0] == at,
- "With 1 exclusion we expect a self-exclusion");
-
- maxNumExcls = std::max(maxNumExcls, numExcls);
- }
-
- return maxNumExcls;
-}
-
-/*! \brief Run the reverse ilist generation and store it in r_il when \p bAssign = TRUE */
-static int low_make_reverse_ilist(const InteractionLists& il_mt,
- const t_atom* atom,
- int* count,
- const ReverseTopOptions& rtOptions,
- gmx::ArrayRef<const int> r_index,
- gmx::ArrayRef<int> r_il,
- const AtomLinkRule atomLinkRule,
- const bool assignReverseIlist)
-{
- const bool includeConstraints = rtOptions.includeConstraints;
- const bool includeSettles = rtOptions.includeSettles;
- const DDBondedChecking ddBondedChecking = rtOptions.ddBondedChecking;
-
- int nint = 0;
-
- for (int ftype = 0; ftype < F_NRE; ftype++)
- {
- if ((interaction_function[ftype].flags & (IF_BOND | IF_VSITE))
- || (includeConstraints && (ftype == F_CONSTR || ftype == F_CONSTRNC))
- || (includeSettles && ftype == F_SETTLE))
- {
- const bool isVSite = ((interaction_function[ftype].flags & IF_VSITE) != 0U);
- const int nral = NRAL(ftype);
- const auto& il = il_mt[ftype];
- for (int i = 0; i < il.size(); i += 1 + nral)
- {
- const int* ia = il.iatoms.data() + i;
- // Virtual sites should not be linked for bonded interactions
- const int nlink = (atomLinkRule == AtomLinkRule::FirstAtom) ? 1 : (isVSite ? 0 : nral);
- for (int link = 0; link < nlink; link++)
- {
- const int a = ia[1 + link];
- if (assignReverseIlist)
- {
- GMX_ASSERT(!r_il.empty(), "with bAssign not allowed to be empty");
- GMX_ASSERT(!r_index.empty(), "with bAssign not allowed to be empty");
- r_il[r_index[a] + count[a]] = (ftype == F_CONSTRNC ? F_CONSTR : ftype);
- r_il[r_index[a] + count[a] + 1] = ia[0];
- for (int j = 1; j < 1 + nral; j++)
- {
- /* Store the molecular atom number */
- r_il[r_index[a] + count[a] + 1 + j] = ia[j];
- }
- }
- if (interaction_function[ftype].flags & IF_VSITE)
- {
- if (assignReverseIlist)
- {
- /* Add an entry to iatoms for storing
- * which of the constructing atoms are
- * vsites again.
- */
- r_il[r_index[a] + count[a] + 2 + nral] = 0;
- for (int j = 2; j < 1 + nral; j++)
- {
- if (atom[ia[j]].ptype == ParticleType::VSite)
- {
- r_il[r_index[a] + count[a] + 2 + nral] |= (2 << j);
- }
- }
- }
- }
- else
- {
- /* We do not count vsites since they are always
- * uniquely assigned and can be assigned
- * to multiple nodes with recursive vsites.
- */
- if (ddBondedChecking == DDBondedChecking::All
- || !(interaction_function[ftype].flags & IF_LIMZERO))
- {
- nint++;
- }
- }
- count[a] += 2 + nral_rt(ftype);
- }
- }
- }
- }
-
- return nint;
-}
-
-/*! \brief Make the reverse ilist: a list of bonded interactions linked to atoms */
-static int make_reverse_ilist(const InteractionLists& ilist,
- const t_atoms* atoms,
- const ReverseTopOptions& rtOptions,
- const AtomLinkRule atomLinkRule,
- reverse_ilist_t* ril_mt)
-{
- /* Count the interactions */
- const int nat_mt = atoms->nr;
- std::vector<int> count(nat_mt);
- low_make_reverse_ilist(ilist, atoms->atom, count.data(), rtOptions, {}, {}, atomLinkRule, FALSE);
-
- ril_mt->index.push_back(0);
- for (int i = 0; i < nat_mt; i++)
- {
- ril_mt->index.push_back(ril_mt->index[i] + count[i]);
- count[i] = 0;
- }
- ril_mt->il.resize(ril_mt->index[nat_mt]);
-
- /* Store the interactions */
- int nint_mt = low_make_reverse_ilist(
- ilist, atoms->atom, count.data(), rtOptions, ril_mt->index, ril_mt->il, atomLinkRule, TRUE);
-
- ril_mt->numAtomsInMolecule = atoms->nr;
-
- return nint_mt;
-}
-
-gmx_reverse_top_t::gmx_reverse_top_t(const gmx_mtop_t& mtop,
- bool useFreeEnergy,
- const ReverseTopOptions& reverseTopOptions) :
- impl_(std::make_unique<Impl>(mtop, useFreeEnergy, reverseTopOptions))
-{
-}
-
-gmx_reverse_top_t::~gmx_reverse_top_t() {}
-
-const ReverseTopOptions& gmx_reverse_top_t::options() const
-{
- return impl_->options;
-}
-
-const reverse_ilist_t& gmx_reverse_top_t::interactionListForMoleculeType(int moleculeType) const
-{
- return impl_->ril_mt[moleculeType];
-}
-
-int gmx_reverse_top_t::expectedNumGlobalBondedInteractions() const
-{
- return impl_->expectedNumGlobalBondedInteractions;
-}
-
-ArrayRef<const MolblockIndices> gmx_reverse_top_t::molblockIndices() const
-{
- return impl_->mbi;
-}
-
-bool gmx_reverse_top_t::hasIntermolecularInteractions() const
-{
- return impl_->bIntermolecularInteractions;
-}
-
-const reverse_ilist_t& gmx_reverse_top_t::interactionListForIntermolecularInteractions() const
-{
- return impl_->ril_intermol;
-}
-
-bool gmx_reverse_top_t::hasInterAtomicInteractions() const
-{
- return impl_->bInterAtomicInteractions;
-}
-
-bool gmx_reverse_top_t::hasPositionRestraints() const
-{
- return impl_->hasPositionRestraints;
-}
-
-ArrayRef<thread_work_t> gmx_reverse_top_t::threadWorkObjects() const
-{
- return impl_->th_work;
-}
-
-bool gmx_reverse_top_t::doSorting() const
-{
- return impl_->ilsort != ilsortNO_FE;
-}
-
-/*! \brief Generate the reverse topology */
-gmx_reverse_top_t::Impl::Impl(const gmx_mtop_t& mtop,
- const bool useFreeEnergy,
- const ReverseTopOptions& reverseTopOptions) :
- options(reverseTopOptions),
- hasPositionRestraints(gmx_mtop_ftype_count(mtop, F_POSRES) + gmx_mtop_ftype_count(mtop, F_FBPOSRES) > 0),
- bInterAtomicInteractions(mtop.bIntermolecularInteractions)
-{
- bInterAtomicInteractions = mtop.bIntermolecularInteractions;
- ril_mt.resize(mtop.moltype.size());
- ril_mt_tot_size = 0;
- std::vector<int> nint_mt;
- for (size_t mt = 0; mt < mtop.moltype.size(); mt++)
- {
- const gmx_moltype_t& molt = mtop.moltype[mt];
- if (molt.atoms.nr > 1)
- {
- bInterAtomicInteractions = true;
- }
-
- /* Make the atom to interaction list for this molecule type */
- int numberOfInteractions = make_reverse_ilist(
- molt.ilist, &molt.atoms, options, AtomLinkRule::FirstAtom, &ril_mt[mt]);
- nint_mt.push_back(numberOfInteractions);
-
- ril_mt_tot_size += ril_mt[mt].index[molt.atoms.nr];
- }
- if (debug)
- {
- fprintf(debug, "The total size of the atom to interaction index is %d integers\n", ril_mt_tot_size);
- }
-
- expectedNumGlobalBondedInteractions = 0;
- for (const gmx_molblock_t& molblock : mtop.molblock)
- {
- expectedNumGlobalBondedInteractions += molblock.nmol * nint_mt[molblock.type];
- }
-
- /* Make an intermolecular reverse top, if necessary */
- bIntermolecularInteractions = mtop.bIntermolecularInteractions;
- if (bIntermolecularInteractions)
- {
- t_atoms atoms_global;
-
- atoms_global.nr = mtop.natoms;
- atoms_global.atom = nullptr; /* Only used with virtual sites */
-
- GMX_RELEASE_ASSERT(mtop.intermolecular_ilist,
- "We should have an ilist when intermolecular interactions are on");
-
- expectedNumGlobalBondedInteractions += make_reverse_ilist(
- *mtop.intermolecular_ilist, &atoms_global, options, AtomLinkRule::FirstAtom, &ril_intermol);
- }
-
- if (useFreeEnergy && gmx_mtop_bondeds_free_energy(&mtop))
- {
- ilsort = ilsortFE_UNSORTED;
- }
- else
- {
- ilsort = ilsortNO_FE;
- }
-
- /* Make a molblock index for fast searching */
- int i = 0;
- for (size_t mb = 0; mb < mtop.molblock.size(); mb++)
- {
- const gmx_molblock_t& molb = mtop.molblock[mb];
- const int numAtomsPerMol = mtop.moltype[molb.type].atoms.nr;
- MolblockIndices mbiMolblock;
- mbiMolblock.a_start = i;
- i += molb.nmol * numAtomsPerMol;
- mbiMolblock.a_end = i;
- mbiMolblock.natoms_mol = numAtomsPerMol;
- mbiMolblock.type = molb.type;
- mbi.push_back(mbiMolblock);
- }
-
- for (int th = 0; th < gmx_omp_nthreads_get(ModuleMultiThread::Domdec); th++)
- {
- th_work.emplace_back(mtop.ffparams);
- }
-}
-
-void dd_make_reverse_top(FILE* fplog,
- gmx_domdec_t* dd,
- const gmx_mtop_t& mtop,
- const gmx::VirtualSitesHandler* vsite,
- const t_inputrec& inputrec,
- const DDBondedChecking ddBondedChecking)
-{
- if (fplog)
- {
- fprintf(fplog, "\nLinking all bonded interactions to atoms\n");
- }
-
- /* If normal and/or settle constraints act only within charge groups,
- * we can store them in the reverse top and simply assign them to domains.
- * Otherwise we need to assign them to multiple domains and set up
- * the parallel version constraint algorithm(s).
- */
- GMX_RELEASE_ASSERT(ddBondedChecking == DDBondedChecking::ExcludeZeroLimit
- || ddBondedChecking == DDBondedChecking::All,
- "Invalid enum value for mdrun -ddcheck");
- const ReverseTopOptions rtOptions(ddBondedChecking,
- !dd->comm->systemInfo.mayHaveSplitConstraints,
- !dd->comm->systemInfo.mayHaveSplitSettles);
-
- dd->reverse_top = std::make_unique<gmx_reverse_top_t>(
- mtop, inputrec.efep != FreeEnergyPerturbationType::No, rtOptions);
-
- dd->haveExclusions = false;
- for (const gmx_molblock_t& molb : mtop.molblock)
- {
- const int maxNumExclusionsPerAtom = getMaxNumExclusionsPerAtom(mtop.moltype[molb.type].excls);
- // We checked above that max 1 exclusion means only self exclusions
- if (maxNumExclusionsPerAtom > 1)
- {
- dd->haveExclusions = true;
- }
- }
-
- const int numInterUpdategroupVirtualSites =
- (vsite == nullptr ? 0 : vsite->numInterUpdategroupVirtualSites());
- if (numInterUpdategroupVirtualSites > 0)
- {
- if (fplog)
- {
- fprintf(fplog,
- "There are %d inter update-group virtual sites,\n"
- "will perform an extra communication step for selected coordinates and "
- "forces\n",
- numInterUpdategroupVirtualSites);
- }
- init_domdec_vsites(dd, numInterUpdategroupVirtualSites);
- }
-
- if (dd->comm->systemInfo.mayHaveSplitConstraints || dd->comm->systemInfo.mayHaveSplitSettles)
- {
- init_domdec_constraints(dd, mtop);
- }
- if (fplog)
- {
- fprintf(fplog, "\n");
- }
-}
-
/*! \brief Store a vsite interaction at the end of \p il
*
* This routine is very similar to add_ifunc, but vsites interactions
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff