Simplify vsite PBC handling

[gromacs.git] / src / gromacs / domdec / domdec_topology.cpp

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 2006 - 2014, The GROMACS development team.
 * Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by
 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 * and including many others, as listed in the AUTHORS file in the
 * top-level source directory and at http://www.gromacs.org.
 *
 * GROMACS is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
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/*! \internal \file
 *
 * \brief This file defines functions used by the domdec module
 * while managing the construction, use and error checking for
 * topologies local to a DD rank.
 *
 * \author Berk Hess <hess@kth.se>
 * \ingroup module_domdec
 */

#include "gmxpre.h"

#include <cassert>
#include <cstdlib>
#include <cstring>

#include <algorithm>
#include <memory>
#include <string>

#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_network.h"
#include "gromacs/domdec/ga2la.h"
#include "gromacs/gmxlib/chargegroup.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/forcerec.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/mdatom.h"
#include "gromacs/mdtypes/state.h"
#include "gromacs/pbcutil/mshift.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topsort.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/logger.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/strconvert.h"
#include "gromacs/utility/stringstream.h"
#include "gromacs/utility/stringutil.h"
#include "gromacs/utility/textwriter.h"

#include "domdec_constraints.h"
#include "domdec_internal.h"
#include "domdec_vsite.h"
#include "dump.h"

/*! \brief The number of integer item in the local state, used for broadcasting of the state */
#define NITEM_DD_INIT_LOCAL_STATE 5

struct reverse_ilist_t
{
    std::vector<int> index;              /* Index for each atom into il          */
    std::vector<int> il;                 /* ftype|type|a0|...|an|ftype|...       */
    int              numAtomsInMolecule; /* The number of atoms in this molecule */
};

struct MolblockIndices
{
    int  a_start;
    int  a_end;
    int  natoms_mol;
    int  type;
};

/*! \brief Struct for thread local work data for local topology generation */
struct thread_work_t
{
    t_idef                    idef;       /**< Partial local topology */
    std::unique_ptr<VsitePbc> vsitePbc;   /**< vsite PBC structure */
    int                       nbonded;    /**< The number of bondeds in this struct */
    t_blocka                  excl;       /**< List of exclusions */
    int                       excl_count; /**< The total exclusion count for \p excl */
};

/*! \brief Struct for the reverse topology: links bonded interactions to atomsx */
struct gmx_reverse_top_t
{
    //! @cond Doxygen_Suppress
    //! \brief Do we require all exclusions to be assigned?
    bool                         bExclRequired = false;
    //! \brief The maximum number of exclusions one atom can have
    int                          n_excl_at_max = 0;
    //! \brief Are there constraints in this revserse top?
    bool                         bConstr = false;
    //! \brief Are there settles in this revserse top?
    bool                         bSettle = false;
    //! \brief All bonded interactions have to be assigned?
    bool                         bBCheck = false;
    //! \brief Are there bondeds/exclusions between charge-groups?
    bool                         bInterCGInteractions = 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;

    /* Work data structures for multi-threading */
    //! \brief Thread work array for local topology generation
    std::vector<thread_work_t> th_work;
    //! @endcond
};

/*! \brief Returns the number of atom entries for il in gmx_reverse_top_t */
static int nral_rt(int ftype)
{
    int nral;

    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;
}

/*! \brief Return whether interactions of type \p ftype need to be assigned exactly once */
static gmx_bool dd_check_ftype(int ftype, gmx_bool bBCheck,
                               gmx_bool bConstr, gmx_bool bSettle)
{
    return ((((interaction_function[ftype].flags & IF_BOND) != 0u) &&
             ((interaction_function[ftype].flags & IF_VSITE) == 0u) &&
             (bBCheck || ((interaction_function[ftype].flags & IF_LIMZERO) == 0u))) ||
            (bConstr && (ftype == F_CONSTR || ftype == F_CONSTRNC)) ||
            (bSettle && ftype == F_SETTLE));
}

/*! \brief Help print error output when interactions are missing */
static std::string
print_missing_interactions_mb(t_commrec *cr,
                              const gmx_reverse_top_t *rt,
                              const char *moltypename,
                              const reverse_ilist_t *ril,
                              int a_start, int a_end,
                              int nat_mol, int nmol,
                              const t_idef *idef)
{
    int                     *assigned;
    int                      nril_mol = ril->index[nat_mol];
    snew(assigned, nmol*nril_mol);
    gmx::StringOutputStream  stream;
    gmx::TextWriter          log(&stream);

    gmx::ArrayRef<const int> gatindex = cr->dd->globalAtomIndices;
    for (int ftype = 0; ftype < F_NRE; ftype++)
    {
        if (dd_check_ftype(ftype, rt->bBCheck, rt->bConstr, rt->bSettle))
        {
            int            nral = NRAL(ftype);
            const t_ilist *il   = &idef->il[ftype];
            const t_iatom *ia   = il->iatoms;
            for (int i = 0; i < il->nr; i += 1+nral)
            {
                int a0 = gatindex[ia[1]];
                /* Check if this interaction is in
                 * the currently checked molblock.
                 */
                if (a0 >= a_start && a0 < a_end)
                {
                    int  mol    = (a0 - a_start)/nat_mol;
                    int  a0_mol = (a0 - a_start) - mol*nat_mol;
                    int  j_mol  = ril->index[a0_mol];
                    bool found  = false;
                    while (j_mol < ril->index[a0_mol+1] && !found)
                    {
                        int j       = mol*nril_mol + j_mol;
                        int ftype_j = ril->il[j_mol];
                        /* Here we need to check if this interaction has
                         * not already been assigned, since we could have
                         * multiply defined interactions.
                         */
                        if (ftype == ftype_j && ia[0] == ril->il[j_mol+1] &&
                            assigned[j] == 0)
                        {
                            /* Check the atoms */
                            found = true;
                            for (int a = 0; a < nral; a++)
                            {
                                if (gatindex[ia[1+a]] !=
                                    a_start + mol*nat_mol + ril->il[j_mol+2+a])
                                {
                                    found = false;
                                }
                            }
                            if (found)
                            {
                                assigned[j] = 1;
                            }
                        }
                        j_mol += 2 + nral_rt(ftype_j);
                    }
                    if (!found)
                    {
                        gmx_incons("Some interactions seem to be assigned multiple times");
                    }
                }
                ia += 1 + nral;
            }
        }
    }

    gmx_sumi(nmol*nril_mol, assigned, cr);

    int nprint = 10;
    int i      = 0;
    for (int mol = 0; mol < nmol; mol++)
    {
        int j_mol = 0;
        while (j_mol < nril_mol)
        {
            int ftype = ril->il[j_mol];
            int nral  = NRAL(ftype);
            int j     = mol*nril_mol + j_mol;
            if (assigned[j] == 0 &&
                !(interaction_function[ftype].flags & IF_VSITE))
            {
                if (DDMASTER(cr->dd))
                {
                    if (i == 0)
                    {
                        log.writeLineFormatted("Molecule type '%s'", moltypename);
                        log.writeLineFormatted(
                                "the first %d missing interactions, except for exclusions:", nprint);
                    }
                    log.writeStringFormatted("%20s atoms",
                                             interaction_function[ftype].longname);
                    int a;
                    for (a = 0; a < nral; a++)
                    {
                        log.writeStringFormatted("%5d", ril->il[j_mol+2+a]+1);
                    }
                    while (a < 4)
                    {
                        log.writeString("     ");
                        a++;
                    }
                    log.writeString(" global");
                    for (a = 0; a < nral; a++)
                    {
                        log.writeStringFormatted("%6d",
                                                 a_start+mol*nat_mol+ril->il[j_mol+2+a]+1);
                    }
                    log.ensureLineBreak();
                }
                i++;
                if (i >= nprint)
                {
                    break;
                }
            }
            j_mol += 2 + nral_rt(ftype);
        }
    }

    sfree(assigned);
    return stream.toString();
}

/*! \brief Help print error output when interactions are missing */
static void print_missing_interactions_atoms(const gmx::MDLogger &mdlog,
                                             t_commrec           *cr,
                                             const gmx_mtop_t    *mtop,
                                             const t_idef        *idef)
{
    const gmx_reverse_top_t *rt = cr->dd->reverse_top;

    /* Print the atoms in the missing interactions per molblock */
    int a_end = 0;
    for (const gmx_molblock_t &molb :  mtop->molblock)
    {
        const gmx_moltype_t &moltype  = mtop->moltype[molb.type];
        int                  a_start  = a_end;
        a_end                        = a_start + molb.nmol*moltype.atoms.nr;

        GMX_LOG(mdlog.warning).appendText(
                print_missing_interactions_mb(cr, rt,
                                              *(moltype.name),
                                              &rt->ril_mt[molb.type],
                                              a_start, a_end, moltype.atoms.nr,
                                              molb.nmol,
                                              idef));
    }
}

void dd_print_missing_interactions(const gmx::MDLogger  &mdlog,
                                   t_commrec            *cr,
                                   int                   local_count,
                                   const gmx_mtop_t     *top_global,
                                   const gmx_localtop_t *top_local,
                                   const t_state        *state_local)
{
    int             ndiff_tot, cl[F_NRE], n, ndiff, rest_global, rest_local;
    int             ftype, nral;
    gmx_domdec_t   *dd;

    dd = cr->dd;

    GMX_LOG(mdlog.warning).appendText(
            "Not all bonded interactions have been properly assigned to the domain decomposition cells");

    ndiff_tot = local_count - dd->nbonded_global;

    for (ftype = 0; ftype < F_NRE; ftype++)
    {
        nral      = NRAL(ftype);
        cl[ftype] = top_local->idef.il[ftype].nr/(1+nral);
    }

    gmx_sumi(F_NRE, cl, cr);

    if (DDMASTER(dd))
    {
        GMX_LOG(mdlog.warning).appendText("A list of missing interactions:");
        rest_global = dd->nbonded_global;
        rest_local  = local_count;
        for (ftype = 0; ftype < F_NRE; ftype++)
        {
            /* In the reverse and local top all constraints are merged
             * into F_CONSTR. So in the if statement we skip F_CONSTRNC
             * and add these constraints when doing F_CONSTR.
             */
            if (((interaction_function[ftype].flags & IF_BOND) &&
                 (dd->reverse_top->bBCheck
                  || !(interaction_function[ftype].flags & IF_LIMZERO)))
                || (dd->reverse_top->bConstr && ftype == F_CONSTR)
                || (dd->reverse_top->bSettle && ftype == F_SETTLE))
            {
                n    = gmx_mtop_ftype_count(top_global, ftype);
                if (ftype == F_CONSTR)
                {
                    n += gmx_mtop_ftype_count(top_global, F_CONSTRNC);
                }
                ndiff = cl[ftype] - n;
                if (ndiff != 0)
                {
                    GMX_LOG(mdlog.warning).appendTextFormatted(
                            "%20s of %6d missing %6d",
                            interaction_function[ftype].longname, n, -ndiff);
                }
                rest_global -= n;
                rest_local  -= cl[ftype];
            }
        }

        ndiff = rest_local - rest_global;
        if (ndiff != 0)
        {
            GMX_LOG(mdlog.warning).appendTextFormatted(
                    "%20s of %6d missing %6d", "exclusions",
                    rest_global, -ndiff);
        }
    }

    print_missing_interactions_atoms(mdlog, cr, top_global, &top_local->idef);
    write_dd_pdb("dd_dump_err", 0, "dump", top_global, cr,
                 -1, state_local->x.rvec_array(), state_local->box);

    std::string errorMessage;

    if (ndiff_tot > 0)
    {
        errorMessage = "One or more interactions were assigned to multiple domains of the domain decompostion. Please report this bug.";
    }
    else
    {
        errorMessage = gmx::formatString("%d of the %d bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (%g nm) or the two-body cut-off distance (%g nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck", -ndiff_tot, cr->dd->nbonded_global, dd_cutoff_multibody(dd), dd_cutoff_twobody(dd));
    }
    gmx_fatal_collective(FARGS, cr->mpi_comm_mygroup, MASTER(cr), "%s", errorMessage.c_str());
}

/*! \brief Return global topology molecule information for global atom index \p i_gl */
static void global_atomnr_to_moltype_ind(const gmx_reverse_top_t *rt,
                                         int i_gl,
                                         int *mb, int *mt, int *mol, int *i_mol)
{
    const MolblockIndices *mbi   = rt->mbi.data();
    int                    start = 0;
    int                    end   = rt->mbi.size(); /* exclusive */
    int                    mid;

    /* 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 Count the exclusions for all atoms in \p cgs */
static void count_excls(const t_block *cgs, const t_blocka *excls,
                        int *n_excl, int *n_intercg_excl, int *n_excl_at_max)
{
    int cg, at0, at1, at, excl, atj;

    *n_excl         = 0;
    *n_intercg_excl = 0;
    *n_excl_at_max  = 0;
    for (cg = 0; cg < cgs->nr; cg++)
    {
        at0 = cgs->index[cg];
        at1 = cgs->index[cg+1];
        for (at = at0; at < at1; at++)
        {
            for (excl = excls->index[at]; excl < excls->index[at+1]; excl++)
            {
                atj = excls->a[excl];
                if (atj > at)
                {
                    (*n_excl)++;
                    if (atj < at0 || atj >= at1)
                    {
                        (*n_intercg_excl)++;
                    }
                }
            }

            *n_excl_at_max = std::max(*n_excl_at_max,
                                      excls->index[at+1] - excls->index[at]);
        }
    }
}

/*! \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,
                                  gmx_bool bConstr, gmx_bool bSettle,
                                  gmx_bool bBCheck,
                                  gmx::ArrayRef<const int> r_index,
                                  gmx::ArrayRef<int>       r_il,
                                  gmx_bool bLinkToAllAtoms,
                                  gmx_bool bAssign)
{
    int            ftype, j, nlink, link;
    int            a;
    int            nint;

    nint = 0;
    for (ftype = 0; ftype < F_NRE; ftype++)
    {
        if ((interaction_function[ftype].flags & (IF_BOND | IF_VSITE)) ||
            (bConstr && (ftype == F_CONSTR || ftype == F_CONSTRNC)) ||
            (bSettle && ftype == F_SETTLE))
        {
            const bool  bVSite = ((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;
                if (bLinkToAllAtoms)
                {
                    if (bVSite)
                    {
                        /* We don't need the virtual sites for the cg-links */
                        nlink = 0;
                    }
                    else
                    {
                        nlink = nral;
                    }
                }
                else
                {
                    /* Couple to the first atom in the interaction */
                    nlink = 1;
                }
                for (link = 0; link < nlink; link++)
                {
                    a = ia[1+link];
                    if (bAssign)
                    {
                        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 (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 (bAssign)
                        {
                            /* 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 (j = 2; j < 1+nral; j++)
                            {
                                if (atom[ia[j]].ptype == eptVSite)
                                {
                                    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 (bBCheck ||
                            !(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,
                              gmx_bool bConstr, gmx_bool bSettle,
                              gmx_bool bBCheck,
                              gmx_bool bLinkToAllAtoms,
                              reverse_ilist_t *ril_mt)
{
    int nat_mt, *count, i, nint_mt;

    /* Count the interactions */
    nat_mt = atoms->nr;
    snew(count, nat_mt);
    low_make_reverse_ilist(ilist, atoms->atom,
                           count,
                           bConstr, bSettle, bBCheck,
                           {}, {},
                           bLinkToAllAtoms, FALSE);

    ril_mt->index.push_back(0);
    for (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 */
    nint_mt =
        low_make_reverse_ilist(ilist, atoms->atom,
                               count,
                               bConstr, bSettle, bBCheck,
                               ril_mt->index, ril_mt->il,
                               bLinkToAllAtoms, TRUE);

    sfree(count);

    ril_mt->numAtomsInMolecule = atoms->nr;

    return nint_mt;
}

/*! \brief Generate the reverse topology */
static gmx_reverse_top_t make_reverse_top(const gmx_mtop_t *mtop, gmx_bool bFE,
                                          gmx_bool bConstr, gmx_bool bSettle,
                                          gmx_bool bBCheck, int *nint)
{
    gmx_reverse_top_t  rt;

    /* Should we include constraints (for SHAKE) in rt? */
    rt.bConstr = bConstr;
    rt.bSettle = bSettle;
    rt.bBCheck = bBCheck;

    rt.bInterCGInteractions = mtop->bIntermolecularInteractions;
    rt.ril_mt.resize(mtop->moltype.size());
    rt.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.cgs.nr > 1)
        {
            rt.bInterCGInteractions = true;
        }

        /* Make the atom to interaction list for this molecule type */
        int numberOfInteractions =
            make_reverse_ilist(molt.ilist, &molt.atoms,
                               rt.bConstr, rt.bSettle, rt.bBCheck, FALSE,
                               &rt.ril_mt[mt]);
        nint_mt.push_back(numberOfInteractions);

        rt.ril_mt_tot_size += rt.ril_mt[mt].index[molt.atoms.nr];
    }
    if (debug)
    {
        fprintf(debug, "The total size of the atom to interaction index is %d integers\n", rt.ril_mt_tot_size);
    }

    *nint = 0;
    for (const gmx_molblock_t &molblock : mtop->molblock)
    {
        *nint += molblock.nmol*nint_mt[molblock.type];
    }

    /* Make an intermolecular reverse top, if necessary */
    rt.bIntermolecularInteractions = mtop->bIntermolecularInteractions;
    if (rt.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");

        *nint +=
            make_reverse_ilist(*mtop->intermolecular_ilist,
                               &atoms_global,
                               rt.bConstr, rt.bSettle, rt.bBCheck, FALSE,
                               &rt.ril_intermol);
    }

    if (bFE && gmx_mtop_bondeds_free_energy(mtop))
    {
        rt.ilsort = ilsortFE_UNSORTED;
    }
    else
    {
        rt.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       mbi;
        mbi.a_start                          = i;
        i                                   += molb.nmol*numAtomsPerMol;
        mbi.a_end                            = i;
        mbi.natoms_mol                       = numAtomsPerMol;
        mbi.type                             = molb.type;
        rt.mbi.push_back(mbi);
    }

    rt.th_work.resize(gmx_omp_nthreads_get(emntDomdec));

    return rt;
}

void dd_make_reverse_top(FILE *fplog,
                         gmx_domdec_t *dd, const gmx_mtop_t *mtop,
                         const gmx_vsite_t *vsite,
                         const t_inputrec *ir, gmx_bool bBCheck)
{
    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).
     */

    dd->reverse_top  = new gmx_reverse_top_t;
    *dd->reverse_top =
        make_reverse_top(mtop, ir->efep != efepNO,
                         !dd->splitConstraints, !dd->splitSettles,
                         bBCheck, &dd->nbonded_global);

    gmx_reverse_top_t *rt = dd->reverse_top;

    /* With the Verlet scheme, exclusions are handled in the non-bonded
     * kernels and only exclusions inside the cut-off lead to exclusion
     * forces. Since each atom pair is treated at most once in the non-bonded
     * kernels, it doesn't matter if the exclusions for the same atom pair
     * appear multiple times in the exclusion list. In contrast, the, old,
     * group cut-off scheme loops over a list of exclusions, so there each
     * excluded pair should appear exactly once.
     */
    rt->bExclRequired = (ir->cutoff_scheme == ecutsGROUP &&
                         inputrecExclForces(ir));

    int nexcl          = 0;
    dd->n_intercg_excl = 0;
    rt->n_excl_at_max  = 0;
    for (const gmx_molblock_t &molb : mtop->molblock)
    {
        int                  n_excl_mol, n_excl_icg, n_excl_at_max;

        const gmx_moltype_t &molt = mtop->moltype[molb.type];
        count_excls(&molt.cgs, &molt.excls,
                    &n_excl_mol, &n_excl_icg, &n_excl_at_max);
        nexcl              += molb.nmol*n_excl_mol;
        dd->n_intercg_excl += molb.nmol*n_excl_icg;
        rt->n_excl_at_max   = std::max(rt->n_excl_at_max, n_excl_at_max);
    }
    if (rt->bExclRequired)
    {
        dd->nbonded_global += nexcl;
        if (EEL_FULL(ir->coulombtype) && dd->n_intercg_excl > 0 && fplog)
        {
            fprintf(fplog, "There are %d inter charge-group exclusions,\n"
                    "will use an extra communication step for exclusion forces for %s\n",
                    dd->n_intercg_excl, eel_names[ir->coulombtype]);
        }
    }

    if (vsite && vsite->numInterUpdategroupVsites > 0)
    {
        if (fplog)
        {
            fprintf(fplog, "There are %d inter update-group virtual sites,\n"
                    "will an extra communication step for selected coordinates and forces\n",
                    vsite->numInterUpdategroupVsites);
        }
        init_domdec_vsites(dd, vsite->numInterUpdategroupVsites);
    }

    if (dd->splitConstraints || dd->splitSettles)
    {
        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
 * have more work to do than other kinds of interactions, and the
 * complex way nral (and thus vector contents) depends on ftype
 * confuses static analysis tools unless we fuse the vsite
 * atom-indexing organization code with the ifunc-adding code, so that
 * they can see that nral is the same value. */
static inline void
add_ifunc_for_vsites(t_iatom *tiatoms, const gmx_ga2la_t &ga2la,
                     int nral, gmx_bool bHomeA,
                     int a, int a_gl, int a_mol,
                     const t_iatom *iatoms,
                     t_ilist *il)
{
    t_iatom *liatoms;

    if (il->nr+1+nral > il->nalloc)
    {
        il->nalloc = over_alloc_large(il->nr+1+nral);
        srenew(il->iatoms, il->nalloc);
    }
    liatoms = il->iatoms + il->nr;
    il->nr += 1 + nral;

    /* Copy the type */
    tiatoms[0] = iatoms[0];

    if (bHomeA)
    {
        /* We know the local index of the first atom */
        tiatoms[1] = a;
    }
    else
    {
        /* Convert later in make_local_vsites */
        tiatoms[1] = -a_gl - 1;
    }

    for (int k = 2; k < 1+nral; k++)
    {
        int ak_gl = a_gl + iatoms[k] - a_mol;
        if (const int *homeIndex = ga2la.findHome(ak_gl))
        {
            tiatoms[k] = *homeIndex;
        }
        else
        {
            /* Copy the global index, convert later in make_local_vsites */
            tiatoms[k] = -(ak_gl + 1);
        }
        // Note that ga2la_get_home always sets the third parameter if
        // it returns TRUE
    }
    for (int k = 0; k < 1+nral; k++)
    {
        liatoms[k] = tiatoms[k];
    }
}

/*! \brief Store a bonded interaction at the end of \p il */
static inline void add_ifunc(int nral, const t_iatom *tiatoms, t_ilist *il)
{
    t_iatom *liatoms;
    int      k;

    if (il->nr+1+nral > il->nalloc)
    {
        il->nalloc = over_alloc_large(il->nr+1+nral);
        srenew(il->iatoms, il->nalloc);
    }
    liatoms = il->iatoms + il->nr;
    for (k = 0; k <= nral; k++)
    {
        liatoms[k] = tiatoms[k];
    }
    il->nr += 1 + nral;
}

/*! \brief Store a position restraint in idef and iatoms, complex because the parameters are different for each entry */
static void add_posres(int mol, int a_mol, int numAtomsInMolecule,
                       const gmx_molblock_t *molb,
                       t_iatom *iatoms, const t_iparams *ip_in,
                       t_idef *idef)
{
    int        n, a_molb;
    t_iparams *ip;

    /* This position restraint has not been added yet,
     * so it's index is the current number of position restraints.
     */
    n = idef->il[F_POSRES].nr/2;
    if (n+1 > idef->iparams_posres_nalloc)
    {
        idef->iparams_posres_nalloc = over_alloc_dd(n+1);
        srenew(idef->iparams_posres, idef->iparams_posres_nalloc);
    }
    ip = &idef->iparams_posres[n];
    /* Copy the force constants */
    *ip = ip_in[iatoms[0]];

    /* Get the position restraint coordinates from the molblock */
    a_molb = mol*numAtomsInMolecule + a_mol;
    GMX_ASSERT(a_molb < ssize(molb->posres_xA), "We need a sufficient number of position restraint coordinates");
    ip->posres.pos0A[XX] = molb->posres_xA[a_molb][XX];
    ip->posres.pos0A[YY] = molb->posres_xA[a_molb][YY];
    ip->posres.pos0A[ZZ] = molb->posres_xA[a_molb][ZZ];
    if (!molb->posres_xB.empty())
    {
        ip->posres.pos0B[XX] = molb->posres_xB[a_molb][XX];
        ip->posres.pos0B[YY] = molb->posres_xB[a_molb][YY];
        ip->posres.pos0B[ZZ] = molb->posres_xB[a_molb][ZZ];
    }
    else
    {
        ip->posres.pos0B[XX] = ip->posres.pos0A[XX];
        ip->posres.pos0B[YY] = ip->posres.pos0A[YY];
        ip->posres.pos0B[ZZ] = ip->posres.pos0A[ZZ];
    }
    /* Set the parameter index for idef->iparams_posre */
    iatoms[0] = n;
}

/*! \brief Store a flat-bottomed position restraint in idef and iatoms, complex because the parameters are different for each entry */
static void add_fbposres(int mol, int a_mol, int numAtomsInMolecule,
                         const gmx_molblock_t *molb,
                         t_iatom *iatoms, const t_iparams *ip_in,
                         t_idef *idef)
{
    int        n, a_molb;
    t_iparams *ip;

    /* This flat-bottom position restraint has not been added yet,
     * so it's index is the current number of position restraints.
     */
    n = idef->il[F_FBPOSRES].nr/2;
    if (n+1 > idef->iparams_fbposres_nalloc)
    {
        idef->iparams_fbposres_nalloc = over_alloc_dd(n+1);
        srenew(idef->iparams_fbposres, idef->iparams_fbposres_nalloc);
    }
    ip = &idef->iparams_fbposres[n];
    /* Copy the force constants */
    *ip = ip_in[iatoms[0]];

    /* Get the position restraint coordinats from the molblock */
    a_molb = mol*numAtomsInMolecule + a_mol;
    GMX_ASSERT(a_molb < ssize(molb->posres_xA), "We need a sufficient number of position restraint coordinates");
    /* Take reference positions from A position of normal posres */
    ip->fbposres.pos0[XX] = molb->posres_xA[a_molb][XX];
    ip->fbposres.pos0[YY] = molb->posres_xA[a_molb][YY];
    ip->fbposres.pos0[ZZ] = molb->posres_xA[a_molb][ZZ];

    /* Note: no B-type for flat-bottom posres */

    /* Set the parameter index for idef->iparams_posre */
    iatoms[0] = n;
}

/*! \brief Store a virtual site interaction, complex because of PBC and recursion */
static void add_vsite(const gmx_ga2la_t &ga2la,
                      gmx::ArrayRef<const int> index,
                      gmx::ArrayRef<const int> rtil,
                      int ftype, int nral,
                      gmx_bool bHomeA, int a, int a_gl, int a_mol,
                      const t_iatom *iatoms,
                      t_idef *idef)
{
    int     k;
    t_iatom tiatoms[1+MAXATOMLIST];
    int     j, ftype_r, nral_r;

    /* Add this interaction to the local topology */
    add_ifunc_for_vsites(tiatoms, ga2la, nral, bHomeA, a, a_gl, a_mol, iatoms, &idef->il[ftype]);

    if (iatoms[1+nral])
    {
        /* Check for recursion */
        for (k = 2; k < 1+nral; k++)
        {
            if ((iatoms[1+nral] & (2<<k)) && (tiatoms[k] < 0))
            {
                /* This construction atoms is a vsite and not a home atom */
                if (gmx_debug_at)
                {
                    fprintf(debug, "Constructing atom %d of vsite atom %d is a vsite and non-home\n", iatoms[k]+1, a_mol+1);
                }
                /* Find the vsite construction */

                /* Check all interactions assigned to this atom */
                j = index[iatoms[k]];
                while (j < index[iatoms[k]+1])
                {
                    ftype_r = rtil[j++];
                    nral_r  = NRAL(ftype_r);
                    if (interaction_function[ftype_r].flags & IF_VSITE)
                    {
                        /* Add this vsite (recursion) */
                        add_vsite(ga2la, index, rtil, ftype_r, nral_r,
                                  FALSE, -1, a_gl+iatoms[k]-iatoms[1], iatoms[k],
                                  rtil.data() + j,
                                  idef);
                    }
                    j += 1 + nral_rt(ftype_r);
                }
            }
        }
    }
}

/*! \brief Build the index that maps each local atom to its local atom group */
static void makeLocalAtomGroupsFromAtoms(gmx_domdec_t *dd)
{
    const gmx::RangePartitioning &atomGrouping = dd->atomGrouping();

    dd->localAtomGroupFromAtom.clear();

    for (size_t g = 0; g < dd->globalAtomGroupIndices.size(); g++)
    {
        for (int gmx_unused a : atomGrouping.block(g))
        {
            dd->localAtomGroupFromAtom.push_back(g);
        }
    }
}

/*! \brief Returns the squared distance between charge groups \p i and \p j */
static real dd_dist2(t_pbc *pbc_null, rvec *cg_cm, const int *la2lc, int i, int j)
{
    rvec dx;

    if (pbc_null)
    {
        pbc_dx_aiuc(pbc_null, cg_cm[la2lc[i]], cg_cm[la2lc[j]], dx);
    }
    else
    {
        rvec_sub(cg_cm[la2lc[i]], cg_cm[la2lc[j]], dx);
    }

    return norm2(dx);
}

/*! \brief Append t_blocka block structures 1 to nsrc in src to *dest */
static void combine_blocka(t_blocka                           *dest,
                           gmx::ArrayRef<const thread_work_t>  src)
{
    int ni = src.back().excl.nr;
    int na = 0;
    for (const thread_work_t &th_work : src)
    {
        na += th_work.excl.nra;
    }
    if (ni + 1 > dest->nalloc_index)
    {
        dest->nalloc_index = over_alloc_large(ni+1);
        srenew(dest->index, dest->nalloc_index);
    }
    if (dest->nra + na > dest->nalloc_a)
    {
        dest->nalloc_a = over_alloc_large(dest->nra+na);
        srenew(dest->a, dest->nalloc_a);
    }
    for (gmx::index s = 1; s < src.ssize(); s++)
    {
        for (int i = dest->nr + 1; i < src[s].excl.nr + 1; i++)
        {
            dest->index[i] = dest->nra + src[s].excl.index[i];
        }
        for (int i = 0; i < src[s].excl.nra; i++)
        {
            dest->a[dest->nra+i] = src[s].excl.a[i];
        }
        dest->nr   = src[s].excl.nr;
        dest->nra += src[s].excl.nra;
    }
}

/*! \brief Append t_idef structures 1 to nsrc in src to *dest */
static void combine_idef(t_idef                             *dest,
                         gmx::ArrayRef<const thread_work_t>  src)
{
    int ftype;

    for (ftype = 0; ftype < F_NRE; ftype++)
    {
        int n = 0;
        for (gmx::index s = 1; s < src.ssize(); s++)
        {
            n += src[s].idef.il[ftype].nr;
        }
        if (n > 0)
        {
            t_ilist *ild;

            ild = &dest->il[ftype];

            if (ild->nr + n > ild->nalloc)
            {
                ild->nalloc = over_alloc_large(ild->nr+n);
                srenew(ild->iatoms, ild->nalloc);
            }

            for (gmx::index s = 1; s < src.ssize(); s++)
            {
                const t_ilist &ils = src[s].idef.il[ftype];

                for (int i = 0; i < ils.nr; i++)
                {
                    ild->iatoms[ild->nr + i] = ils.iatoms[i];
                }

                ild->nr += ils.nr;
            }

            /* Position restraints need an additional treatment */
            if (ftype == F_POSRES || ftype == F_FBPOSRES)
            {
                int          nposres       = dest->il[ftype].nr/2;
                // TODO: Simplify this code using std::vector
                t_iparams * &iparams_dest  = (ftype == F_POSRES ? dest->iparams_posres : dest->iparams_fbposres);
                int         &posres_nalloc = (ftype == F_POSRES ? dest->iparams_posres_nalloc : dest->iparams_fbposres_nalloc);
                if (nposres > posres_nalloc)
                {
                    posres_nalloc = over_alloc_large(nposres);
                    srenew(iparams_dest, posres_nalloc);
                }

                /* Set nposres to the number of original position restraints in dest */
                for (gmx::index s = 1; s < src.ssize(); s++)
                {
                    nposres -= src[s].idef.il[ftype].nr/2;
                }

                for (gmx::index s = 1; s < src.ssize(); s++)
                {
                    const t_iparams *iparams_src = (ftype == F_POSRES ? src[s].idef.iparams_posres : src[s].idef.iparams_fbposres);

                    for (int i = 0; i < src[s].idef.il[ftype].nr/2; i++)
                    {
                        /* Correct the index into iparams_posres */
                        dest->il[ftype].iatoms[nposres*2] = nposres;
                        /* Copy the position restraint force parameters */
                        iparams_dest[nposres]             = iparams_src[i];
                        nposres++;
                    }
                }
            }
        }
    }
}

/*! \brief Check and when available assign bonded interactions for local atom i
 */
static inline void
check_assign_interactions_atom(int i, int i_gl,
                               int mol, int i_mol,
                               int numAtomsInMolecule,
                               gmx::ArrayRef<const int> index,
                               gmx::ArrayRef<const int> rtil,
                               gmx_bool bInterMolInteractions,
                               int ind_start, int ind_end,
                               const gmx_domdec_t *dd,
                               const gmx_domdec_zones_t *zones,
                               const gmx_molblock_t *molb,
                               gmx_bool bRCheckMB, const ivec rcheck, gmx_bool bRCheck2B,
                               real rc2,
                               int *la2lc,
                               t_pbc *pbc_null,
                               rvec *cg_cm,
                               const t_iparams *ip_in,
                               t_idef *idef,
                               int iz,
                               gmx_bool bBCheck,
                               int *nbonded_local)
{
    int j;

    j = ind_start;
    while (j < ind_end)
    {
        t_iatom   tiatoms[1 + MAXATOMLIST];

        const int ftype  = rtil[j++];
        auto      iatoms = gmx::constArrayRefFromArray(rtil.data() + j, rtil.size() - j);
        const int nral   = NRAL(ftype);
        if (interaction_function[ftype].flags & IF_VSITE)
        {
            assert(!bInterMolInteractions);
            /* The vsite construction goes where the vsite itself is */
            if (iz == 0)
            {
                add_vsite(*dd->ga2la, index, rtil, ftype, nral,
                          TRUE, i, i_gl, i_mol,
                          iatoms.data(), idef);
            }
            j += 1 + nral + 2;
        }
        else
        {
            gmx_bool bUse;

            /* Copy the type */
            tiatoms[0] = iatoms[0];

            if (nral == 1)
            {
                assert(!bInterMolInteractions);
                /* Assign single-body interactions to the home zone */
                if (iz == 0)
                {
                    bUse       = TRUE;
                    tiatoms[1] = i;
                    if (ftype == F_POSRES)
                    {
                        add_posres(mol, i_mol, numAtomsInMolecule,
                                   molb, tiatoms, ip_in, idef);
                    }
                    else if (ftype == F_FBPOSRES)
                    {
                        add_fbposres(mol, i_mol, numAtomsInMolecule,
                                     molb, tiatoms, ip_in, idef);
                    }
                }
                else
                {
                    bUse = FALSE;
                }
            }
            else if (nral == 2)
            {
                /* This is a two-body interaction, we can assign
                 * analogous to the non-bonded assignments.
                 */
                int k_gl;

                if (!bInterMolInteractions)
                {
                    /* Get the global index using the offset in the molecule */
                    k_gl = i_gl + iatoms[2] - i_mol;
                }
                else
                {
                    k_gl = iatoms[2];
                }
                if (const auto *entry = dd->ga2la->find(k_gl))
                {
                    int kz = entry->cell;
                    if (kz >= zones->n)
                    {
                        kz -= zones->n;
                    }
                    /* Check zone interaction assignments */
                    bUse = ((iz < zones->nizone &&
                             iz <= kz &&
                             kz >= zones->izone[iz].j0 &&
                             kz <  zones->izone[iz].j1) ||
                            (kz < zones->nizone &&
                                  iz > kz &&
                             iz >= zones->izone[kz].j0 &&
                             iz <  zones->izone[kz].j1));
                    if (bUse)
                    {
                        GMX_ASSERT(ftype != F_CONSTR || (iz == 0 && kz == 0),
                                   "Constraint assigned here should only involve home atoms");

                        tiatoms[1] = i;
                        tiatoms[2] = entry->la;
                        /* If necessary check the cgcm distance */
                        if (bRCheck2B &&
                            dd_dist2(pbc_null, cg_cm, la2lc,
                                     tiatoms[1], tiatoms[2]) >= rc2)
                        {
                            bUse = FALSE;
                        }
                    }
                }
                else
                {
                    bUse = false;
                }
            }
            else
            {
                /* Assign this multi-body bonded interaction to
                 * the local node if we have all the atoms involved
                 * (local or communicated) and the minimum zone shift
                 * in each dimension is zero, for dimensions
                 * with 2 DD cells an extra check may be necessary.
                 */
                ivec k_zero, k_plus;
                int  k;

                bUse = TRUE;
                clear_ivec(k_zero);
                clear_ivec(k_plus);
                for (k = 1; k <= nral && bUse; k++)
                {
                    int k_gl;
                    if (!bInterMolInteractions)
                    {
                        /* Get the global index using the offset in the molecule */
                        k_gl = i_gl + iatoms[k] - i_mol;
                    }
                    else
                    {
                        k_gl = iatoms[k];
                    }
                    const auto *entry = dd->ga2la->find(k_gl);
                    if (entry == nullptr || entry->cell >= zones->n)
                    {
                        /* We do not have this atom of this interaction
                         * locally, or it comes from more than one cell
                         * away.
                         */
                        bUse = FALSE;
                    }
                    else
                    {
                        int d;

                        tiatoms[k] = entry->la;
                        for (d = 0; d < DIM; d++)
                        {
                            if (zones->shift[entry->cell][d] == 0)
                            {
                                k_zero[d] = k;
                            }
                            else
                            {
                                k_plus[d] = k;
                            }
                        }
                    }
                }
                bUse = (bUse &&
                        (k_zero[XX] != 0) && (k_zero[YY] != 0) && (k_zero[ZZ] != 0));
                if (bRCheckMB)
                {
                    int d;

                    for (d = 0; (d < DIM && bUse); d++)
                    {
                        /* Check if the cg_cm distance falls within
                         * the cut-off to avoid possible multiple
                         * assignments of bonded interactions.
                         */
                        if (rcheck[d] &&
                            k_plus[d] &&
                            dd_dist2(pbc_null, cg_cm, la2lc,
                                     tiatoms[k_zero[d]], tiatoms[k_plus[d]]) >= rc2)
                        {
                            bUse = FALSE;
                        }
                    }
                }
            }
            if (bUse)
            {
                /* Add this interaction to the local topology */
                add_ifunc(nral, tiatoms, &idef->il[ftype]);
                /* Sum so we can check in global_stat
                 * if we have everything.
                 */
                if (bBCheck ||
                    !(interaction_function[ftype].flags & IF_LIMZERO))
                {
                    (*nbonded_local)++;
                }
            }
            j += 1 + nral;
        }
    }
}

/*! \brief This function looks up and assigns bonded interactions for zone iz.
 *
 * With thread parallelizing each thread acts on a different atom range:
 * at_start to at_end.
 */
static int make_bondeds_zone(gmx_domdec_t *dd,
                             const gmx_domdec_zones_t *zones,
                             const std::vector<gmx_molblock_t> &molb,
                             gmx_bool bRCheckMB, ivec rcheck, gmx_bool bRCheck2B,
                             real rc2,
                             int *la2lc, t_pbc *pbc_null, rvec *cg_cm,
                             const t_iparams *ip_in,
                             t_idef *idef,
                             int izone,
                             gmx::RangePartitioning::Block atomRange)
{
    int                mb, mt, mol, i_mol;
    gmx_bool           bBCheck;
    gmx_reverse_top_t *rt;
    int                nbonded_local;

    rt = dd->reverse_top;

    bBCheck = rt->bBCheck;

    nbonded_local = 0;

    for (int i : atomRange)
    {
        /* Get the global atom number */
        const int i_gl = dd->globalAtomIndices[i];
        global_atomnr_to_moltype_ind(rt, i_gl, &mb, &mt, &mol, &i_mol);
        /* Check all intramolecular interactions assigned to this atom */
        gmx::ArrayRef<const int>       index = rt->ril_mt[mt].index;
        gmx::ArrayRef<const t_iatom>   rtil  = rt->ril_mt[mt].il;

        check_assign_interactions_atom(i, i_gl, mol, i_mol,
                                       rt->ril_mt[mt].numAtomsInMolecule,
                                       index, rtil, FALSE,
                                       index[i_mol], index[i_mol+1],
                                       dd, zones,
                                       &molb[mb],
                                       bRCheckMB, rcheck, bRCheck2B, rc2,
                                       la2lc,
                                       pbc_null,
                                       cg_cm,
                                       ip_in,
                                       idef,
                                       izone,
                                       bBCheck,
                                       &nbonded_local);


        if (rt->bIntermolecularInteractions)
        {
            /* Check all intermolecular interactions assigned to this atom */
            index = rt->ril_intermol.index;
            rtil  = rt->ril_intermol.il;

            check_assign_interactions_atom(i, i_gl, mol, i_mol,
                                           rt->ril_mt[mt].numAtomsInMolecule,
                                           index, rtil, TRUE,
                                           index[i_gl], index[i_gl + 1],
                                           dd, zones,
                                           &molb[mb],
                                           bRCheckMB, rcheck, bRCheck2B, rc2,
                                           la2lc,
                                           pbc_null,
                                           cg_cm,
                                           ip_in,
                                           idef,
                                           izone,
                                           bBCheck,
                                           &nbonded_local);
        }
    }

    return nbonded_local;
}

/*! \brief Set the exclusion data for i-zone \p iz for the case of no exclusions */
static void set_no_exclusions_zone(const gmx_domdec_t       *dd,
                                   const gmx_domdec_zones_t *zones,
                                   int                       iz,
                                   t_blocka                 *lexcls)
{
    const auto zone = dd->atomGrouping().subRange(zones->cg_range[iz],
                                                  zones->cg_range[iz + 1]);

    for (int a : zone)
    {
        lexcls->index[a + 1] = lexcls->nra;
    }
}

/*! \brief Set the exclusion data for i-zone \p iz
 *
 * This is a legacy version for the group scheme of the same routine below.
 * Here charge groups and distance checks to ensure unique exclusions
 * are supported.
 */
static int make_exclusions_zone_cg(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
                                   const std::vector<gmx_moltype_t> &moltype,
                                   gmx_bool bRCheck, real rc2,
                                   int *la2lc, t_pbc *pbc_null, rvec *cg_cm,
                                   const int *cginfo,
                                   t_blocka *lexcls,
                                   int iz,
                                   int cg_start, int cg_end)
{
    int                n_excl_at_max;
    int                mb, mt, mol;
    const t_blocka    *excls;

    const gmx_ga2la_t &ga2la  = *dd->ga2la;

    const auto         jRange =
        dd->atomGrouping().subRange(zones->izone[iz].jcg0,
                                    zones->izone[iz].jcg1);

    n_excl_at_max = dd->reverse_top->n_excl_at_max;

    /* We set the end index, but note that we might not start at zero here */
    lexcls->nr = dd->atomGrouping().subRange(0, cg_end).size();

    int n     = lexcls->nra;
    int count = 0;
    for (int cg = cg_start; cg < cg_end; cg++)
    {
        if (n + (cg_end - cg_start)*n_excl_at_max > lexcls->nalloc_a)
        {
            lexcls->nalloc_a = over_alloc_large(n + (cg_end - cg_start)*n_excl_at_max);
            srenew(lexcls->a, lexcls->nalloc_a);
        }
        const auto atomGroup = dd->atomGrouping().block(cg);
        if (GET_CGINFO_EXCL_INTER(cginfo[cg]) ||
            !GET_CGINFO_EXCL_INTRA(cginfo[cg]))
        {
            /* Copy the exclusions from the global top */
            for (int la : atomGroup)
            {
                lexcls->index[la] = n;
                int a_gl          = dd->globalAtomIndices[la];
                int a_mol;
                global_atomnr_to_moltype_ind(dd->reverse_top, a_gl, &mb, &mt, &mol, &a_mol);
                excls = &moltype[mt].excls;
                for (int j = excls->index[a_mol]; j < excls->index[a_mol+1]; j++)
                {
                    int aj_mol = excls->a[j];
                    /* This computation of jla is only correct intra-cg */
                    int jla = la + aj_mol - a_mol;
                    if (atomGroup.inRange(jla))
                    {
                        /* This is an intra-cg exclusion. We can skip
                         *  the global indexing and distance checking.
                         */
                        /* Intra-cg exclusions are only required
                         * for the home zone.
                         */
                        if (iz == 0)
                        {
                            lexcls->a[n++] = jla;
                            /* Check to avoid double counts */
                            if (jla > la)
                            {
                                count++;
                            }
                        }
                    }
                    else
                    {
                        /* This is a inter-cg exclusion */
                        /* Since exclusions are pair interactions,
                         * just like non-bonded interactions,
                         * they can be assigned properly up
                         * to the DD cutoff (not cutoff_min as
                         * for the other bonded interactions).
                         */
                        if (const auto *jEntry = ga2la.find(a_gl + aj_mol - a_mol))
                        {
                            if (iz == 0 && jEntry->cell == 0)
                            {
                                lexcls->a[n++] = jEntry->la;
                                /* Check to avoid double counts */
                                if (jEntry->la > la)
                                {
                                    count++;
                                }
                            }
                            else if (jRange.inRange(jEntry->la) &&
                                     (!bRCheck ||
                                      dd_dist2(pbc_null, cg_cm, la2lc, la, jEntry->la) < rc2))
                            {
                                /* jla > la, since jRange.begin() > la */
                                lexcls->a[n++] = jEntry->la;
                                count++;
                            }
                        }
                    }
                }
            }
        }
        else
        {
            /* There are no inter-cg excls and this cg is self-excluded.
             * These exclusions are only required for zone 0,
             * since other zones do not see themselves.
             */
            if (iz == 0)
            {
                for (int la : atomGroup)
                {
                    lexcls->index[la] = n;
                    for (int j : atomGroup)
                    {
                        lexcls->a[n++] = j;
                    }
                }
                count += (atomGroup.size()*(atomGroup.size() - 1))/2;
            }
            else
            {
                /* We don't need exclusions for this cg */
                for (int la : atomGroup)
                {
                    lexcls->index[la] = n;
                }
            }
        }
    }

    lexcls->index[lexcls->nr] = n;
    lexcls->nra               = n;

    return count;
}

/*! \brief Set the exclusion data for i-zone \p iz */
static void make_exclusions_zone(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
                                 const std::vector<gmx_moltype_t> &moltype,
                                 const int *cginfo, t_blocka *lexcls, int iz,
                                 int at_start, int at_end,
                                 const gmx::ArrayRef<const int> intermolecularExclusionGroup)
{
    int                n_excl_at_max, n, at;

    const gmx_ga2la_t &ga2la  = *dd->ga2la;

    const auto         jRange =
        dd->atomGrouping().subRange(zones->izone[iz].jcg0,
                                    zones->izone[iz].jcg1);

    n_excl_at_max = dd->reverse_top->n_excl_at_max;

    /* We set the end index, but note that we might not start at zero here */
    lexcls->nr = at_end;

    n = lexcls->nra;
    for (at = at_start; at < at_end; at++)
    {
        if (n + 1000 > lexcls->nalloc_a)
        {
            lexcls->nalloc_a = over_alloc_large(n + 1000);
            srenew(lexcls->a, lexcls->nalloc_a);
        }

        if (GET_CGINFO_EXCL_INTER(cginfo[at]))
        {
            int             a_gl, mb, mt, mol, a_mol, j;
            const t_blocka *excls;

            if (n + n_excl_at_max > lexcls->nalloc_a)
            {
                lexcls->nalloc_a = over_alloc_large(n + n_excl_at_max);
                srenew(lexcls->a, lexcls->nalloc_a);
            }

            /* Copy the exclusions from the global top */
            lexcls->index[at] = n;
            a_gl              = dd->globalAtomIndices[at];
            global_atomnr_to_moltype_ind(dd->reverse_top, a_gl,
                                         &mb, &mt, &mol, &a_mol);
            excls = &moltype[mt].excls;
            for (j = excls->index[a_mol]; j < excls->index[a_mol + 1]; j++)
            {
                const int aj_mol = excls->a[j];

                if (const auto *jEntry = ga2la.find(a_gl + aj_mol - a_mol))
                {
                    /* This check is not necessary, but it can reduce
                     * the number of exclusions in the list, which in turn
                     * can speed up the pair list construction a bit.
                     */
                    if (jRange.inRange(jEntry->la))
                    {
                        lexcls->a[n++] = jEntry->la;
                    }
                }
            }
        }
        else
        {
            /* We don't need exclusions for this atom */
            lexcls->index[at] = n;
        }

        bool isExcludedAtom = !intermolecularExclusionGroup.empty() &&
            std::find(intermolecularExclusionGroup.begin(),
                      intermolecularExclusionGroup.end(),
                      dd->globalAtomIndices[at]) !=
            intermolecularExclusionGroup.end();

        if (isExcludedAtom)
        {
            if (n + intermolecularExclusionGroup.ssize() > lexcls->nalloc_a)
            {
                lexcls->nalloc_a =
                    over_alloc_large(n + intermolecularExclusionGroup.size());
                srenew(lexcls->a, lexcls->nalloc_a);
            }
            for (int qmAtomGlobalIndex : intermolecularExclusionGroup)
            {
                if (const auto *entry = dd->ga2la->find(qmAtomGlobalIndex))
                {
                    lexcls->a[n++] = entry->la;
                }
            }
        }
    }

    lexcls->index[lexcls->nr] = n;
    lexcls->nra               = n;
}


/*! \brief Ensure we have enough space in \p ba for \p nindex_max indices */
static void check_alloc_index(t_blocka *ba, int nindex_max)
{
    if (nindex_max+1 > ba->nalloc_index)
    {
        ba->nalloc_index = over_alloc_dd(nindex_max+1);
        srenew(ba->index, ba->nalloc_index);
    }
}

/*! \brief Ensure that we have enough space for exclusion storate in \p lexcls */
static void check_exclusions_alloc(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
                                   t_blocka *lexcls)
{
    int nr = dd->atomGrouping().subRange(0, zones->izone[zones->nizone - 1].cg1).size();

    check_alloc_index(lexcls, nr);

    for (size_t thread = 1; thread < dd->reverse_top->th_work.size(); thread++)
    {
        check_alloc_index(&dd->reverse_top->th_work[thread].excl, nr);
    }
}

/*! \brief Set the total count indexes for the local exclusions, needed by several functions */
static void finish_local_exclusions(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
                                    t_blocka *lexcls)
{
    const auto nonhomeIzonesAtomRange =
        dd->atomGrouping().subRange(zones->izone[0].cg1,
                                    zones->izone[zones->nizone - 1].cg1);

    if (dd->n_intercg_excl == 0)
    {
        /* There are no exclusions involving non-home charge groups,
         * but we need to set the indices for neighborsearching.
         */
        for (int la : nonhomeIzonesAtomRange)
        {
            lexcls->index[la] = lexcls->nra;
        }

        /* nr is only used to loop over the exclusions for Ewald and RF,
         * so we can set it to the number of home atoms for efficiency.
         */
        lexcls->nr = nonhomeIzonesAtomRange.begin();
    }
    else
    {
        lexcls->nr = nonhomeIzonesAtomRange.end();
    }
}

/*! \brief Clear a t_idef struct */
static void clear_idef(t_idef *idef)
{
    int  ftype;

    /* Clear the counts */
    for (ftype = 0; ftype < F_NRE; ftype++)
    {
        idef->il[ftype].nr = 0;
    }
}

/*! \brief Generate and store all required local bonded interactions in \p idef and local exclusions in \p lexcls */
static int make_local_bondeds_excls(gmx_domdec_t *dd,
                                    gmx_domdec_zones_t *zones,
                                    const gmx_mtop_t *mtop,
                                    const int *cginfo,
                                    gmx_bool bRCheckMB, ivec rcheck, gmx_bool bRCheck2B,
                                    real rc,
                                    int *la2lc, t_pbc *pbc_null, rvec *cg_cm,
                                    t_idef *idef,
                                    t_blocka *lexcls, int *excl_count)
{
    int                nzone_bondeds, nzone_excl;
    int                izone, cg0, cg1;
    real               rc2;
    int                nbonded_local;
    int                thread;
    gmx_reverse_top_t *rt;

    if (dd->reverse_top->bInterCGInteractions)
    {
        nzone_bondeds = zones->n;
    }
    else
    {
        /* Only single charge group (or atom) molecules, so interactions don't
         * cross zone boundaries and we only need to assign in the home zone.
         */
        nzone_bondeds = 1;
    }

    if (dd->n_intercg_excl > 0)
    {
        /* We only use exclusions from i-zones to i- and j-zones */
        nzone_excl = zones->nizone;
    }
    else
    {
        /* There are no inter-cg exclusions and only zone 0 sees itself */
        nzone_excl = 1;
    }

    check_exclusions_alloc(dd, zones, lexcls);

    rt = dd->reverse_top;

    rc2 = rc*rc;

    /* Clear the counts */
    clear_idef(idef);
    nbonded_local = 0;

    lexcls->nr    = 0;
    lexcls->nra   = 0;
    *excl_count   = 0;

    for (izone = 0; izone < nzone_bondeds; izone++)
    {
        cg0 = zones->cg_range[izone];
        cg1 = zones->cg_range[izone + 1];

        const int numThreads = rt->th_work.size();
#pragma omp parallel for num_threads(numThreads) schedule(static)
        for (thread = 0; thread < numThreads; thread++)
        {
            try
            {
                int       cg0t, cg1t;
                t_idef   *idef_t;
                t_blocka *excl_t;

                cg0t = cg0 + ((cg1 - cg0)* thread   )/numThreads;
                cg1t = cg0 + ((cg1 - cg0)*(thread+1))/numThreads;

                if (thread == 0)
                {
                    idef_t = idef;
                }
                else
                {
                    idef_t = &rt->th_work[thread].idef;
                    clear_idef(idef_t);
                }

                rt->th_work[thread].nbonded =
                    make_bondeds_zone(dd, zones,
                                      mtop->molblock,
                                      bRCheckMB, rcheck, bRCheck2B, rc2,
                                      la2lc, pbc_null, cg_cm, idef->iparams,
                                      idef_t,
                                      izone,
                                      dd->atomGrouping().subRange(cg0t, cg1t));

                if (izone < nzone_excl)
                {
                    if (thread == 0)
                    {
                        excl_t = lexcls;
                    }
                    else
                    {
                        excl_t      = &rt->th_work[thread].excl;
                        excl_t->nr  = 0;
                        excl_t->nra = 0;
                    }

                    if (dd->atomGrouping().allBlocksHaveSizeOne() &&
                        !rt->bExclRequired)
                    {
                        /* No charge groups and no distance check required */
                        make_exclusions_zone(dd, zones, mtop->moltype, cginfo,
                                             excl_t, izone, cg0t,
                                             cg1t,
                                             mtop->intermolecularExclusionGroup);
                    }
                    else
                    {
                        rt->th_work[thread].excl_count =
                            make_exclusions_zone_cg(dd, zones,
                                                    mtop->moltype, bRCheck2B, rc2,
                                                    la2lc, pbc_null, cg_cm, cginfo,
                                                    excl_t,
                                                    izone,
                                                    cg0t, cg1t);
                    }
                }
            }
            GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
        }

        if (rt->th_work.size() > 1)
        {
            combine_idef(idef, rt->th_work);
        }

        for (const thread_work_t &th_work : rt->th_work)
        {
            nbonded_local += th_work.nbonded;
        }

        if (izone < nzone_excl)
        {
            if (rt->th_work.size() > 1)
            {
                combine_blocka(lexcls, rt->th_work);
            }

            for (const thread_work_t &th_work : rt->th_work)
            {
                *excl_count += th_work.excl_count;
            }
        }
    }

    /* Some zones might not have exclusions, but some code still needs to
     * loop over the index, so we set the indices here.
     */
    for (izone = nzone_excl; izone < zones->nizone; izone++)
    {
        set_no_exclusions_zone(dd, zones, izone, lexcls);
    }

    finish_local_exclusions(dd, zones, lexcls);
    if (debug)
    {
        fprintf(debug, "We have %d exclusions, check count %d\n",
                lexcls->nra, *excl_count);
    }

    return nbonded_local;
}

void dd_make_local_cgs(gmx_domdec_t *dd, t_block *lcgs)
{
    lcgs->nr    = dd->globalAtomGroupIndices.size();
    lcgs->index = dd->atomGrouping_.rawIndex().data();
}

void dd_make_local_top(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
                       int npbcdim, matrix box,
                       rvec cellsize_min, const ivec npulse,
                       t_forcerec *fr,
                       rvec *cgcm_or_x,
                       const gmx_mtop_t &mtop, gmx_localtop_t *ltop)
{
    gmx_bool bRCheckMB, bRCheck2B;
    real     rc = -1;
    ivec     rcheck;
    int      d, nexcl;
    t_pbc    pbc, *pbc_null = nullptr;

    if (debug)
    {
        fprintf(debug, "Making local topology\n");
    }

    dd_make_local_cgs(dd, &ltop->cgs);

    bRCheckMB   = FALSE;
    bRCheck2B   = FALSE;

    if (dd->reverse_top->bInterCGInteractions)
    {
        /* We need to check to which cell bondeds should be assigned */
        rc = dd_cutoff_twobody(dd);
        if (debug)
        {
            fprintf(debug, "Two-body bonded cut-off distance is %g\n", rc);
        }

        /* Should we check cg_cm distances when assigning bonded interactions? */
        for (d = 0; d < DIM; d++)
        {
            rcheck[d] = FALSE;
            /* Only need to check for dimensions where the part of the box
             * that is not communicated is smaller than the cut-off.
             */
            if (d < npbcdim && dd->nc[d] > 1 &&
                (dd->nc[d] - npulse[d])*cellsize_min[d] < 2*rc)
            {
                if (dd->nc[d] == 2)
                {
                    rcheck[d] = TRUE;
                    bRCheckMB = TRUE;
                }
                /* Check for interactions between two atoms,
                 * where we can allow interactions up to the cut-off,
                 * instead of up to the smallest cell dimension.
                 */
                bRCheck2B = TRUE;
            }
            if (debug)
            {
                fprintf(debug,
                        "dim %d cellmin %f bonded rcheck[%d] = %d, bRCheck2B = %s\n",
                        d, cellsize_min[d], d, rcheck[d], gmx::boolToString(bRCheck2B));
            }
        }
        if (bRCheckMB || bRCheck2B)
        {
            makeLocalAtomGroupsFromAtoms(dd);
            if (fr->bMolPBC)
            {
                pbc_null = set_pbc_dd(&pbc, fr->ePBC, dd->nc, TRUE, box);
            }
            else
            {
                pbc_null = nullptr;
            }
        }
    }

    dd->nbonded_local =
        make_local_bondeds_excls(dd, zones, &mtop, fr->cginfo,
                                 bRCheckMB, rcheck, bRCheck2B, rc,
                                 dd->localAtomGroupFromAtom.data(),
                                 pbc_null, cgcm_or_x,
                                 &ltop->idef,
                                 &ltop->excls, &nexcl);

    /* The ilist is not sorted yet,
     * we can only do this when we have the charge arrays.
     */
    ltop->idef.ilsort = ilsortUNKNOWN;

    if (dd->reverse_top->bExclRequired)
    {
        dd->nbonded_local += nexcl;
    }

    ltop->atomtypes  = mtop.atomtypes;
}

void dd_sort_local_top(gmx_domdec_t *dd, const t_mdatoms *mdatoms,
                       gmx_localtop_t *ltop)
{
    if (dd->reverse_top->ilsort == ilsortNO_FE)
    {
        ltop->idef.ilsort = ilsortNO_FE;
    }
    else
    {
        gmx_sort_ilist_fe(&ltop->idef, mdatoms->chargeA, mdatoms->chargeB);
    }
}

void dd_init_local_top(const gmx_mtop_t &top_global,
                       gmx_localtop_t   *top)
{
    /* TODO: Get rid of the const casts below, e.g. by using a reference */
    top->idef.ntypes     = top_global.ffparams.numTypes();
    top->idef.atnr       = top_global.ffparams.atnr;
    top->idef.functype   = const_cast<t_functype *>(top_global.ffparams.functype.data());
    top->idef.iparams    = const_cast<t_iparams *>(top_global.ffparams.iparams.data());
    top->idef.fudgeQQ    = top_global.ffparams.fudgeQQ;
    top->idef.cmap_grid  = new gmx_cmap_t;
    *top->idef.cmap_grid = top_global.ffparams.cmap_grid;

    top->idef.ilsort        = ilsortUNKNOWN;
    top->useInDomainDecomp_ = true;
}

void dd_init_local_state(gmx_domdec_t *dd,
                         const t_state *state_global, t_state *state_local)
{
    int buf[NITEM_DD_INIT_LOCAL_STATE];

    if (DDMASTER(dd))
    {
        buf[0] = state_global->flags;
        buf[1] = state_global->ngtc;
        buf[2] = state_global->nnhpres;
        buf[3] = state_global->nhchainlength;
        buf[4] = state_global->dfhist ? state_global->dfhist->nlambda : 0;
    }
    dd_bcast(dd, NITEM_DD_INIT_LOCAL_STATE*sizeof(int), buf);

    init_gtc_state(state_local, buf[1], buf[2], buf[3]);
    init_dfhist_state(state_local, buf[4]);
    state_local->flags = buf[0];
}

/*! \brief Check if a link is stored in \p link between charge groups \p cg_gl and \p cg_gl_j and if not so, store a link */
static void check_link(t_blocka *link, int cg_gl, int cg_gl_j)
{
    int      k;
    gmx_bool bFound;

    bFound = FALSE;
    for (k = link->index[cg_gl]; k < link->index[cg_gl+1]; k++)
    {
        GMX_RELEASE_ASSERT(link->a, "Inconsistent NULL pointer while making charge-group links");
        if (link->a[k] == cg_gl_j)
        {
            bFound = TRUE;
        }
    }
    if (!bFound)
    {
        GMX_RELEASE_ASSERT(link->a || link->index[cg_gl+1]+1 > link->nalloc_a,
                           "Inconsistent allocation of link");
        /* Add this charge group link */
        if (link->index[cg_gl+1]+1 > link->nalloc_a)
        {
            link->nalloc_a = over_alloc_large(link->index[cg_gl+1]+1);
            srenew(link->a, link->nalloc_a);
        }
        link->a[link->index[cg_gl+1]] = cg_gl_j;
        link->index[cg_gl+1]++;
    }
}

/*! \brief Return a vector of the charge group index for all atoms */
static std::vector<int> make_at2cg(const t_block &cgs)
{
    std::vector<int> at2cg(cgs.index[cgs.nr]);
    for (int cg = 0; cg < cgs.nr; cg++)
    {
        for (int a = cgs.index[cg]; a < cgs.index[cg + 1]; a++)
        {
            at2cg[a] = cg;
        }
    }

    return at2cg;
}

t_blocka *make_charge_group_links(const gmx_mtop_t *mtop, gmx_domdec_t *dd,
                                  cginfo_mb_t *cginfo_mb)
{
    gmx_bool            bExclRequired;
    t_blocka           *link;
    cginfo_mb_t        *cgi_mb;

    /* For each charge group make a list of other charge groups
     * in the system that a linked to it via bonded interactions
     * which are also stored in reverse_top.
     */

    bExclRequired = dd->reverse_top->bExclRequired;

    reverse_ilist_t ril_intermol;
    if (mtop->bIntermolecularInteractions)
    {
        if (ncg_mtop(mtop) < mtop->natoms)
        {
            gmx_fatal(FARGS, "The combination of intermolecular interactions, charge groups and domain decomposition is not supported. Use cutoff-scheme=Verlet (which removes the charge groups) or run without domain decomposition.");
        }

        t_atoms atoms;

        atoms.nr   = mtop->natoms;
        atoms.atom = nullptr;

        GMX_RELEASE_ASSERT(mtop->intermolecular_ilist, "We should have an ilist when intermolecular interactions are on");

        make_reverse_ilist(*mtop->intermolecular_ilist,
                           &atoms,
                           FALSE, FALSE, FALSE, TRUE, &ril_intermol);
    }

    snew(link, 1);
    snew(link->index, ncg_mtop(mtop)+1);
    link->nalloc_a = 0;
    link->a        = nullptr;

    link->index[0] = 0;
    int cg_offset  = 0;
    int ncgi       = 0;
    for (size_t mb = 0; mb < mtop->molblock.size(); mb++)
    {
        const gmx_molblock_t &molb = mtop->molblock[mb];
        if (molb.nmol == 0)
        {
            continue;
        }
        const gmx_moltype_t &molt  = mtop->moltype[molb.type];
        const t_block       &cgs   = molt.cgs;
        const t_blocka      &excls = molt.excls;
        std::vector<int>     a2c   = make_at2cg(cgs);
        /* Make a reverse ilist in which the interactions are linked
         * to all atoms, not only the first atom as in gmx_reverse_top.
         * The constraints are discarded here.
         */
        reverse_ilist_t ril;
        make_reverse_ilist(molt.ilist, &molt.atoms,
                           FALSE, FALSE, FALSE, TRUE, &ril);

        cgi_mb = &cginfo_mb[mb];

        int mol;
        for (mol = 0; mol < (mtop->bIntermolecularInteractions ? molb.nmol : 1); mol++)
        {
            for (int cg = 0; cg < cgs.nr; cg++)
            {
                int cg_gl            = cg_offset + cg;
                link->index[cg_gl+1] = link->index[cg_gl];
                for (int a = cgs.index[cg]; a < cgs.index[cg + 1]; a++)
                {
                    int i = ril.index[a];
                    while (i < ril.index[a+1])
                    {
                        int ftype = ril.il[i++];
                        int nral  = NRAL(ftype);
                        /* Skip the ifunc index */
                        i++;
                        for (int j = 0; j < nral; j++)
                        {
                            int aj = ril.il[i + j];
                            if (a2c[aj] != cg)
                            {
                                check_link(link, cg_gl, cg_offset+a2c[aj]);
                            }
                        }
                        i += nral_rt(ftype);
                    }
                    if (bExclRequired)
                    {
                        /* Exclusions always go both ways */
                        for (int j = excls.index[a]; j < excls.index[a + 1]; j++)
                        {
                            int aj = excls.a[j];
                            if (a2c[aj] != cg)
                            {
                                check_link(link, cg_gl, cg_offset+a2c[aj]);
                            }
                        }
                    }

                    if (mtop->bIntermolecularInteractions)
                    {
                        int i = ril_intermol.index[a];
                        while (i < ril_intermol.index[a+1])
                        {
                            int ftype = ril_intermol.il[i++];
                            int nral  = NRAL(ftype);
                            /* Skip the ifunc index */
                            i++;
                            for (int j = 0; j < nral; j++)
                            {
                                /* Here we assume we have no charge groups;
                                 * this has been checked above.
                                 */
                                int aj = ril_intermol.il[i + j];
                                check_link(link, cg_gl, aj);
                            }
                            i += nral_rt(ftype);
                        }
                    }
                }
                if (link->index[cg_gl+1] - link->index[cg_gl] > 0)
                {
                    SET_CGINFO_BOND_INTER(cgi_mb->cginfo[cg]);
                    ncgi++;
                }
            }

            cg_offset += cgs.nr;
        }
        int nlink_mol = link->index[cg_offset] - link->index[cg_offset - cgs.nr];

        if (debug)
        {
            fprintf(debug, "molecule type '%s' %d cgs has %d cg links through bonded interac.\n", *molt.name, cgs.nr, nlink_mol);
        }

        if (molb.nmol > mol)
        {
            /* Copy the data for the rest of the molecules in this block */
            link->nalloc_a += (molb.nmol - mol)*nlink_mol;
            srenew(link->a, link->nalloc_a);
            for (; mol < molb.nmol; mol++)
            {
                for (int cg = 0; cg < cgs.nr; cg++)
                {
                    int cg_gl              = cg_offset + cg;
                    link->index[cg_gl + 1] =
                        link->index[cg_gl + 1 - cgs.nr] + nlink_mol;
                    for (int j = link->index[cg_gl]; j < link->index[cg_gl+1]; j++)
                    {
                        link->a[j] = link->a[j - nlink_mol] + cgs.nr;
                    }
                    if (link->index[cg_gl+1] - link->index[cg_gl] > 0 &&
                        cg_gl - cgi_mb->cg_start < cgi_mb->cg_mod)
                    {
                        SET_CGINFO_BOND_INTER(cgi_mb->cginfo[cg_gl - cgi_mb->cg_start]);
                        ncgi++;
                    }
                }
                cg_offset += cgs.nr;
            }
        }
    }

    if (debug)
    {
        fprintf(debug, "Of the %d charge groups %d are linked via bonded interactions\n", ncg_mtop(mtop), ncgi);
    }

    return link;
}

typedef struct {
    real r2;
    int  ftype;
    int  a1;
    int  a2;
} bonded_distance_t;

/*! \brief Compare distance^2 \p r2 against the distance in \p bd and if larger store it along with \p ftype and atom indices \p a1 and \p a2 */
static void update_max_bonded_distance(real r2, int ftype, int a1, int a2,
                                       bonded_distance_t *bd)
{
    if (r2 > bd->r2)
    {
        bd->r2    = r2;
        bd->ftype = ftype;
        bd->a1    = a1;
        bd->a2    = a2;
    }
}

/*! \brief Set the distance, function type and atom indices for the longest distance between charge-groups of molecule type \p molt for two-body and multi-body bonded interactions */
static void bonded_cg_distance_mol(const gmx_moltype_t *molt,
                                   const std::vector<int> &at2cg,
                                   gmx_bool bBCheck, gmx_bool bExcl, rvec *cg_cm,
                                   bonded_distance_t *bd_2b,
                                   bonded_distance_t *bd_mb)
{
    for (int ftype = 0; ftype < F_NRE; ftype++)
    {
        if (dd_check_ftype(ftype, bBCheck, FALSE, FALSE))
        {
            const auto    &il   = molt->ilist[ftype];
            int            nral = NRAL(ftype);
            if (nral > 1)
            {
                for (int i = 0; i < il.size(); i += 1+nral)
                {
                    for (int ai = 0; ai < nral; ai++)
                    {
                        int cgi = at2cg[il.iatoms[i+1+ai]];
                        for (int aj = ai + 1; aj < nral; aj++)
                        {
                            int cgj = at2cg[il.iatoms[i+1+aj]];
                            if (cgi != cgj)
                            {
                                real rij2 = distance2(cg_cm[cgi], cg_cm[cgj]);

                                update_max_bonded_distance(rij2, ftype,
                                                           il.iatoms[i+1+ai],
                                                           il.iatoms[i+1+aj],
                                                           (nral == 2) ? bd_2b : bd_mb);
                            }
                        }
                    }
                }
            }
        }
    }
    if (bExcl)
    {
        const t_blocka *excls = &molt->excls;
        for (int ai = 0; ai < excls->nr; ai++)
        {
            int cgi = at2cg[ai];
            for (int j = excls->index[ai]; j < excls->index[ai+1]; j++)
            {
                int cgj = at2cg[excls->a[j]];
                if (cgi != cgj)
                {
                    real rij2 = distance2(cg_cm[cgi], cg_cm[cgj]);

                    /* There is no function type for exclusions, use -1 */
                    update_max_bonded_distance(rij2, -1, ai, excls->a[j], bd_2b);
                }
            }
        }
    }
}

/*! \brief Set the distance, function type and atom indices for the longest atom distance involved in intermolecular interactions for two-body and multi-body bonded interactions */
static void bonded_distance_intermol(const InteractionLists &ilists_intermol,
                                     gmx_bool bBCheck,
                                     const rvec *x, int ePBC, const matrix box,
                                     bonded_distance_t *bd_2b,
                                     bonded_distance_t *bd_mb)
{
    t_pbc pbc;

    set_pbc(&pbc, ePBC, box);

    for (int ftype = 0; ftype < F_NRE; ftype++)
    {
        if (dd_check_ftype(ftype, bBCheck, FALSE, FALSE))
        {
            const auto    &il   = ilists_intermol[ftype];
            int            nral = NRAL(ftype);

            /* No nral>1 check here, since intermol interactions always
             * have nral>=2 (and the code is also correct for nral=1).
             */
            for (int i = 0; i < il.size(); i += 1+nral)
            {
                for (int ai = 0; ai < nral; ai++)
                {
                    int atom_i = il.iatoms[i + 1 + ai];

                    for (int aj = ai + 1; aj < nral; aj++)
                    {
                        rvec dx;
                        real rij2;

                        int  atom_j = il.iatoms[i + 1 + aj];

                        pbc_dx(&pbc, x[atom_i], x[atom_j], dx);

                        rij2 = norm2(dx);

                        update_max_bonded_distance(rij2, ftype,
                                                   atom_i, atom_j,
                                                   (nral == 2) ? bd_2b : bd_mb);
                    }
                }
            }
        }
    }
}

//! Returns whether \p molt has at least one virtual site
static bool moltypeHasVsite(const gmx_moltype_t &molt)
{
    bool hasVsite = false;
    for (int i = 0; i < F_NRE; i++)
    {
        if ((interaction_function[i].flags & IF_VSITE) &&
            molt.ilist[i].size() > 0)
        {
            hasVsite = true;
        }
    }

    return hasVsite;
}

//! Compute charge group centers of mass for molecule \p molt
static void get_cgcm_mol(const gmx_moltype_t *molt,
                         const gmx_ffparams_t *ffparams,
                         int ePBC, t_graph *graph, const matrix box,
                         const rvec *x, rvec *xs, rvec *cg_cm)
{
    int n, i;

    if (ePBC != epbcNONE)
    {
        mk_mshift(nullptr, graph, ePBC, box, x);

        shift_x(graph, box, x, xs);
        /* By doing an extra mk_mshift the molecules that are broken
         * because they were e.g. imported from another software
         * will be made whole again. Such are the healing powers
         * of GROMACS.
         */
        mk_mshift(nullptr, graph, ePBC, box, xs);
    }
    else
    {
        /* We copy the coordinates so the original coordinates remain
         * unchanged, just to be 100% sure that we do not affect
         * binary reproducibility of simulations.
         */
        n = molt->cgs.index[molt->cgs.nr];
        for (i = 0; i < n; i++)
        {
            copy_rvec(x[i], xs[i]);
        }
    }

    if (moltypeHasVsite(*molt))
    {
        /* Convert to old, deprecated format */
        t_ilist ilist[F_NRE];
        for (int ftype = 0; ftype < F_NRE; ftype++)
        {
            if (interaction_function[ftype].flags & IF_VSITE)
            {
                ilist[ftype].nr     = molt->ilist[ftype].size();
                ilist[ftype].iatoms = const_cast<int *>(molt->ilist[ftype].iatoms.data());
            }
        }

        construct_vsites(nullptr, xs, 0.0, nullptr,
                         ffparams->iparams.data(), ilist,
                         epbcNONE, TRUE, nullptr, nullptr);
    }

    calc_cgcm(nullptr, 0, molt->cgs.nr, &molt->cgs, xs, cg_cm);
}

void dd_bonded_cg_distance(const gmx::MDLogger &mdlog,
                           const gmx_mtop_t *mtop,
                           const t_inputrec *ir,
                           const rvec *x, const matrix box,
                           gmx_bool bBCheck,
                           real *r_2b, real *r_mb)
{
    gmx_bool           bExclRequired;
    int                at_offset;
    t_graph            graph;
    rvec              *xs, *cg_cm;
    bonded_distance_t  bd_2b = { 0, -1, -1, -1 };
    bonded_distance_t  bd_mb = { 0, -1, -1, -1 };

    bExclRequired = inputrecExclForces(ir);

    *r_2b     = 0;
    *r_mb     = 0;
    at_offset = 0;
    for (const gmx_molblock_t &molb : mtop->molblock)
    {
        const gmx_moltype_t &molt = mtop->moltype[molb.type];
        if (molt.cgs.nr == 1 || molb.nmol == 0)
        {
            at_offset += molb.nmol*molt.atoms.nr;
        }
        else
        {
            if (ir->ePBC != epbcNONE)
            {
                mk_graph_moltype(molt, &graph);
            }

            std::vector<int> at2cg = make_at2cg(molt.cgs);
            snew(xs, molt.atoms.nr);
            snew(cg_cm, molt.cgs.nr);
            for (int mol = 0; mol < molb.nmol; mol++)
            {
                get_cgcm_mol(&molt, &mtop->ffparams, ir->ePBC, &graph, box,
                             x+at_offset, xs, cg_cm);

                bonded_distance_t bd_mol_2b = { 0, -1, -1, -1 };
                bonded_distance_t bd_mol_mb = { 0, -1, -1, -1 };

                bonded_cg_distance_mol(&molt, at2cg, bBCheck, bExclRequired, cg_cm,
                                       &bd_mol_2b, &bd_mol_mb);

                /* Process the mol data adding the atom index offset */
                update_max_bonded_distance(bd_mol_2b.r2, bd_mol_2b.ftype,
                                           at_offset + bd_mol_2b.a1,
                                           at_offset + bd_mol_2b.a2,
                                           &bd_2b);
                update_max_bonded_distance(bd_mol_mb.r2, bd_mol_mb.ftype,
                                           at_offset + bd_mol_mb.a1,
                                           at_offset + bd_mol_mb.a2,
                                           &bd_mb);

                at_offset += molt.atoms.nr;
            }
            sfree(cg_cm);
            sfree(xs);
            if (ir->ePBC != epbcNONE)
            {
                done_graph(&graph);
            }
        }
    }

    if (mtop->bIntermolecularInteractions)
    {
        if (ncg_mtop(mtop) < mtop->natoms)
        {
            gmx_fatal(FARGS, "The combination of intermolecular interactions, charge groups and domain decomposition is not supported. Use cutoff-scheme=Verlet (which removes the charge groups) or run without domain decomposition.");
        }

        GMX_RELEASE_ASSERT(mtop->intermolecular_ilist, "We should have an ilist when intermolecular interactions are on");

        bonded_distance_intermol(*mtop->intermolecular_ilist,
                                 bBCheck,
                                 x, ir->ePBC, box,
                                 &bd_2b, &bd_mb);
    }

    *r_2b = sqrt(bd_2b.r2);
    *r_mb = sqrt(bd_mb.r2);

    if (*r_2b > 0 || *r_mb > 0)
    {
        GMX_LOG(mdlog.info).appendText("Initial maximum distances in bonded interactions:");
        if (*r_2b > 0)
        {
            GMX_LOG(mdlog.info).appendTextFormatted(
                    "    two-body bonded interactions: %5.3f nm, %s, atoms %d %d",
                    *r_2b, (bd_2b.ftype >= 0) ? interaction_function[bd_2b.ftype].longname : "Exclusion",
                    bd_2b.a1 + 1, bd_2b.a2 + 1);
        }
        if (*r_mb > 0)
        {
            GMX_LOG(mdlog.info).appendTextFormatted(
                    "  multi-body bonded interactions: %5.3f nm, %s, atoms %d %d",
                    *r_mb, interaction_function[bd_mb.ftype].longname,
                    bd_mb.a1 + 1, bd_mb.a2 + 1);
        }
    }
}