/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright 2006- The GROMACS Authors
 * and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
 * Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
 *
 * 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
 * of the License, or (at your option) any later version.
 *
 * GROMACS is distributed in the hope that it will be useful,
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 *
 * You should have received a copy of the GNU Lesser General Public
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 */

/*! \internal \file
 *
 * \brief This file implements functions for domdec to use
 * while managing inter-atomic constraints.
 *
 * \author Berk Hess <hess@kth.se>
 * \ingroup module_domdec
 */

#include "gmxpre.h"

#include "domdec_constraints.h"

#include <cassert>

#include <algorithm>
#include <memory>

#include "gromacs/domdec/dlbtiming.h"
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/domdec/ga2la.h"
#include "gromacs/domdec/hashedmap.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/constr.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
#include "gromacs/mdtypes/atominfo.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/topology/mtop_lookup.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/listoflists.h"

#include "domdec_internal.h"
#include "domdec_specatomcomm.h"

using gmx::ListOfLists;

void dd_move_x_constraints(gmx_domdec_t*            dd,
                           const matrix             box,
                           gmx::ArrayRef<gmx::RVec> x0,
                           gmx::ArrayRef<gmx::RVec> x1,
                           bool                     bX1IsCoord)
{
    if (dd->constraint_comm)
    {
        dd_move_x_specat(dd, dd->constraint_comm.get(), box, x0.data(), x1.data(), bX1IsCoord);

        ddReopenBalanceRegionCpu(dd);
    }
}

gmx::ArrayRef<const int> dd_constraints_nlocalatoms(const gmx_domdec_t* dd)
{
    if (dd && dd->constraints)
    {
        return dd->constraints->con_nlocat;
    }
    else
    {
        return {};
    }
}

void dd_clear_local_constraint_indices(gmx_domdec_t* dd)
{
    gmx_domdec_constraints_t* dc = dd->constraints.get();

    std::fill(dc->gc_req.begin(), dc->gc_req.end(), false);

    if (dd->constraint_comm)
    {
        dc->ga2la->clearAndResizeHashTable();
    }
}

/*! \brief Walks over the constraints out from the local atoms into the non-local atoms and adds them to a list */
static void walk_out(int                       con,
                     int                       con_offset,
                     int                       a,
                     int                       offset,
                     int                       nrec,
                     gmx::ArrayRef<const int>  ia1,
                     gmx::ArrayRef<const int>  ia2,
                     const ListOfLists<int>&   at2con,
                     const gmx_ga2la_t&        ga2la,
                     gmx_bool                  bHomeConnect,
                     gmx_domdec_constraints_t* dc,
                     gmx_domdec_specat_comm_t* dcc,
                     InteractionList*          il_local,
                     std::vector<int>*         ireq)
{
    if (!dc->gc_req[con_offset + con])
    {
        /* Add this non-home constraint to the list */
        dc->con_gl.push_back(con_offset + con);
        dc->con_nlocat.push_back(bHomeConnect ? 1 : 0);
        dc->gc_req[con_offset + con]     = true;
        const int*         iap           = constr_iatomptr(ia1, ia2, con);
        const int          parameterType = iap[0];
        const int          a1_gl         = offset + iap[1];
        const int          a2_gl         = offset + iap[2];
        std::array<int, 2> atoms;
        /* The following indexing code can probably be optizimed */
        if (const int* a_loc = ga2la.findHome(a1_gl))
        {
            atoms[0] = *a_loc;
        }
        else
        {
            /* We set this index later */
            atoms[0] = -a1_gl - 1;
        }
        if (const int* a_loc = ga2la.findHome(a2_gl))
        {
            atoms[1] = *a_loc;
        }
        else
        {
            /* We set this index later */
            atoms[1] = -a2_gl - 1;
        }
        il_local->push_back(parameterType, atoms);
        dc->ncon++;
    }
    /* Check to not ask for the same atom more than once */
    if (!dc->ga2la->find(offset + a))
    {
        assert(dcc);
        /* Add this non-home atom to the list */
        ireq->push_back(offset + a);
        /* Temporarily mark with -2, we get the index later */
        dc->ga2la->insert(offset + a, -2);
    }

    if (nrec > 0)
    {
        /* Loop over the constraint connected to atom a */
        for (const int coni : at2con[a])
        {
            if (coni != con)
            {
                /* Walk further */
                const int* iap = constr_iatomptr(ia1, ia2, coni);
                const int  b   = (a == iap[1]) ? iap[2] : iap[1];
                if (!ga2la.findHome(offset + b))
                {
                    walk_out(coni, con_offset, b, offset, nrec - 1, ia1, ia2, at2con, ga2la, FALSE, dc, dcc, il_local, ireq);
                }
            }
        }
    }
}

/*! \brief Looks up SETTLE constraints for a range of charge-groups */
static void atoms_to_settles(gmx_domdec_t*                         dd,
                             const gmx_mtop_t&                     mtop,
                             gmx::ArrayRef<const int64_t>          atomInfo,
                             gmx::ArrayRef<const std::vector<int>> at2settle_mt,
                             int                                   cg_start,
                             int                                   cg_end,
                             InteractionList*                      ils_local,
                             std::vector<int>*                     ireq)
{
    const gmx_ga2la_t& ga2la = *dd->ga2la;
    int                nral  = NRAL(F_SETTLE);

    int mb = 0;
    for (int a = cg_start; a < cg_end; a++)
    {
        if (atomInfo[a] & gmx::sc_atomInfo_Settle)
        {
            int a_gl  = dd->globalAtomIndices[a];
            int a_mol = 0;
            mtopGetMolblockIndex(mtop, a_gl, &mb, nullptr, &a_mol);

            const gmx_molblock_t* molb   = &mtop.molblock[mb];
            int                   settle = at2settle_mt[molb->type][a_mol];

            if (settle >= 0)
            {
                int offset = a_gl - a_mol;

                const int* ia1 = mtop.moltype[molb->type].ilist[F_SETTLE].iatoms.data();

                int      a_gls[3];
                gmx_bool bAssign = FALSE;
                int      nlocal  = 0;
                for (int sa = 0; sa < nral; sa++)
                {
                    int a_glsa = offset + ia1[settle * (1 + nral) + 1 + sa];
                    a_gls[sa]  = a_glsa;
                    if (ga2la.findHome(a_glsa))
                    {
                        if (nlocal == 0 && a_gl == a_glsa)
                        {
                            bAssign = TRUE;
                        }
                        nlocal++;
                    }
                }

                if (bAssign)
                {
                    const int          parameterType = ia1[settle * 4];
                    std::array<int, 3> atoms;
                    for (int sa = 0; sa < nral; sa++)
                    {
                        if (const int* a_loc = ga2la.findHome(a_gls[sa]))
                        {
                            atoms[sa] = *a_loc;
                        }
                        else
                        {
                            atoms[sa] = -a_gls[sa] - 1;
                            /* Add this non-home atom to the list */
                            ireq->push_back(a_gls[sa]);
                            /* A check on double atom requests is
                             * not required for settle.
                             */
                        }
                    }
                    ils_local->push_back(parameterType, atoms);
                }
            }
        }
    }
}

/*! \brief Looks up constraint for the local atoms */
static void atoms_to_constraints(gmx_domdec_t*                         dd,
                                 const gmx_mtop_t&                     mtop,
                                 gmx::ArrayRef<const int64_t>          atomInfo,
                                 gmx::ArrayRef<const ListOfLists<int>> at2con_mt,
                                 int                                   nrec,
                                 InteractionList*                      ilc_local,
                                 std::vector<int>*                     ireq)
{
    gmx_domdec_constraints_t* dc  = dd->constraints.get();
    gmx_domdec_specat_comm_t* dcc = dd->constraint_comm.get();

    const gmx_ga2la_t& ga2la = *dd->ga2la;

    dc->con_gl.clear();
    dc->con_nlocat.clear();

    int mb    = 0;
    int nhome = 0;
    for (int a = 0; a < dd->numHomeAtoms; a++)
    {
        if (atomInfo[a] & gmx::sc_atomInfo_Constraint)
        {
            int a_gl  = dd->globalAtomIndices[a];
            int molnr = 0;
            int a_mol = 0;
            mtopGetMolblockIndex(mtop, a_gl, &mb, &molnr, &a_mol);

            const gmx_molblock_t& molb = mtop.molblock[mb];

            gmx::ArrayRef<const int> ia1 = mtop.moltype[molb.type].ilist[F_CONSTR].iatoms;
            gmx::ArrayRef<const int> ia2 = mtop.moltype[molb.type].ilist[F_CONSTRNC].iatoms;

            /* Calculate the global constraint number offset for the molecule.
             * This is only required for the global index to make sure
             * that we use each constraint only once.
             */
            const int con_offset = dc->molb_con_offset[mb] + molnr * dc->molb_ncon_mol[mb];

            /* The global atom number offset for this molecule */
            const int offset = a_gl - a_mol;
            /* Loop over the constraints connected to atom a_mol in the molecule */
            const auto& at2con = at2con_mt[molb.type];
            for (const int con : at2con[a_mol])
            {
                const int* iap   = constr_iatomptr(ia1, ia2, con);
                int        b_mol = 0;
                if (a_mol == iap[1])
                {
                    b_mol = iap[2];
                }
                else
                {
                    b_mol = iap[1];
                }
                if (const int* a_loc = ga2la.findHome(offset + b_mol))
                {
                    /* Add this fully home constraint at the first atom */
                    if (a_mol < b_mol)
                    {
                        dc->con_gl.push_back(con_offset + con);
                        dc->con_nlocat.push_back(2);
                        const int          b_lo          = *a_loc;
                        const int          parameterType = iap[0];
                        std::array<int, 2> atoms;
                        atoms[0] = (a_gl == iap[1] ? a : b_lo);
                        atoms[1] = (a_gl == iap[1] ? b_lo : a);
                        ilc_local->push_back(parameterType, atoms);
                        dc->ncon++;
                        nhome++;
                    }
                }
                else
                {
                    /* We need the nrec constraints coupled to this constraint,
                     * so we need to walk out of the home cell by nrec+1 atoms,
                     * since already atom bg is not locally present.
                     * Therefore we call walk_out with nrec recursions to go
                     * after this first call.
                     */
                    walk_out(con, con_offset, b_mol, offset, nrec, ia1, ia2, at2con, ga2la, TRUE, dc, dcc, ilc_local, ireq);
                }
            }
        }
    }

    GMX_ASSERT(dc->con_gl.size() == static_cast<size_t>(dc->ncon),
               "con_gl size should match the number of constraints");
    GMX_ASSERT(dc->con_nlocat.size() == static_cast<size_t>(dc->ncon),
               "con_nlocat size should match the number of constraints");

    if (debug)
    {
        fprintf(debug,
                "Constraints: home %3d border %3d atoms: %3zu\n",
                nhome,
                dc->ncon - nhome,
                dd->constraint_comm ? ireq->size() : 0);
    }
}

int dd_make_local_constraints(gmx_domdec_t*                  dd,
                              int                            at_start,
                              const struct gmx_mtop_t&       mtop,
                              gmx::ArrayRef<const int64_t>   atomInfo,
                              gmx::Constraints*              constr,
                              int                            nrec,
                              gmx::ArrayRef<InteractionList> il_local)
{
    // This code should not be called unless this condition is true,
    // because that's the only time init_domdec_constraints is
    // called...
    GMX_RELEASE_ASSERT(dd->comm->systemInfo.mayHaveSplitConstraints || dd->comm->systemInfo.mayHaveSplitSettles,
                       "dd_make_local_constraints called when there are no local constraints");
    // ... and init_domdec_constraints always sets
    // dd->constraint_comm...
    GMX_RELEASE_ASSERT(
            dd->constraint_comm,
            "Invalid use of dd_make_local_constraints before construction of constraint_comm");
    // ... which static analysis needs to be reassured about, because
    // otherwise, when dd->splitSettles is
    // true. dd->constraint_comm is unilaterally dereferenced before
    // the call to atoms_to_settles.

    gmx_domdec_constraints_t* dc = dd->constraints.get();

    InteractionList* ilc_local = &il_local[F_CONSTR];
    InteractionList* ils_local = &il_local[F_SETTLE];

    dc->ncon = 0;
    gmx::ArrayRef<const ListOfLists<int>> at2con_mt;
    std::vector<int>*                     ireq = nullptr;
    ilc_local->clear();
    if (dd->constraint_comm)
    {
        // TODO Perhaps gmx_domdec_constraints_t should keep a valid constr?
        GMX_RELEASE_ASSERT(constr != nullptr, "Must have valid constraints object");
        at2con_mt = constr->atom2constraints_moltype();
        ireq      = &dc->requestedGlobalAtomIndices[0];
        ireq->clear();
    }

    gmx::ArrayRef<const std::vector<int>> at2settle_mt;
    /* When settle works inside charge groups, we assigned them already */
    if (dd->comm->systemInfo.mayHaveSplitSettles)
    {
        // TODO Perhaps gmx_domdec_constraints_t should keep a valid constr?
        GMX_RELEASE_ASSERT(constr != nullptr, "Must have valid constraints object");
        at2settle_mt = constr->atom2settle_moltype();
        ils_local->clear();
    }

    if (at2settle_mt.empty())
    {
        atoms_to_constraints(dd, mtop, atomInfo, at2con_mt, nrec, ilc_local, ireq);
    }
    else
    {
        /* Do the constraints, if present, on the first thread.
         * Do the settles on all other threads.
         */
        const int t0_set = ((!at2con_mt.empty() && dc->nthread > 1) ? 1 : 0);

#pragma omp parallel for num_threads(dc->nthread) schedule(static)
        for (int thread = 0; thread < dc->nthread; thread++)
        {
            try
            {
                if (!at2con_mt.empty() && thread == 0)
                {
                    atoms_to_constraints(dd, mtop, atomInfo, at2con_mt, nrec, ilc_local, ireq);
                }

                if (thread >= t0_set)
                {
                    /* Distribute the settle check+assignments over
                     * dc->nthread or dc->nthread-1 threads.
                     */
                    const int cg0 = (dd->numHomeAtoms * (thread - t0_set)) / (dc->nthread - t0_set);
                    const int cg1 = (dd->numHomeAtoms * (thread - t0_set + 1)) / (dc->nthread - t0_set);

                    InteractionList* ilst = (thread == t0_set) ? ils_local : &dc->ils[thread];
                    ilst->clear();

                    std::vector<int>& ireqt = dc->requestedGlobalAtomIndices[thread];
                    if (thread > 0)
                    {
                        ireqt.clear();
                    }

                    atoms_to_settles(dd, mtop, atomInfo, at2settle_mt, cg0, cg1, ilst, &ireqt);
                }
            }
            GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
        }

        /* Combine the generate settles and requested indices */
        for (int thread = 1; thread < dc->nthread; thread++)
        {
            if (thread > t0_set)
            {
                ils_local->append(dc->ils[thread]);
            }

            const std::vector<int>& ireqt = dc->requestedGlobalAtomIndices[thread];
            ireq->insert(ireq->end(), ireqt.begin(), ireqt.end());
        }

        if (debug)
        {
            fprintf(debug, "Settles: total %3d\n", ils_local->size() / 4);
        }
    }

    int at_end = 0;
    if (dd->constraint_comm)
    {
        at_end = setup_specat_communication(dd,
                                            ireq,
                                            dd->constraint_comm.get(),
                                            dd->constraints->ga2la.get(),
                                            at_start,
                                            2,
                                            "constraint",
                                            " or lincs-order");

        /* Fill in the missing indices */
        gmx::HashedMap<int>* ga2la_specat = dd->constraints->ga2la.get();

        int nral1 = 1 + NRAL(F_CONSTR);
        for (int i = 0; i < ilc_local->size(); i += nral1)
        {
            int* iap = ilc_local->iatoms.data() + i;
            for (int j = 1; j < nral1; j++)
            {
                if (iap[j] < 0)
                {
                    const int* a = ga2la_specat->find(-iap[j] - 1);
                    GMX_ASSERT(a, "We have checked before that this atom index has been set");
                    iap[j] = *a;
                }
            }
        }

        nral1 = 1 + NRAL(F_SETTLE);
        for (int i = 0; i < ils_local->size(); i += nral1)
        {
            int* iap = ils_local->iatoms.data() + i;
            for (int j = 1; j < nral1; j++)
            {
                if (iap[j] < 0)
                {
                    const int* a = ga2la_specat->find(-iap[j] - 1);
                    GMX_ASSERT(a, "We have checked before that this atom index has been set");
                    iap[j] = *a;
                }
            }
        }
    }
    else
    {
        // Currently unreachable
        at_end = at_start;
    }

    return at_end;
}

void init_domdec_constraints(gmx_domdec_t* dd, const gmx_mtop_t& mtop)
{
    if (debug)
    {
        fprintf(debug, "Begin init_domdec_constraints\n");
    }

    dd->constraints              = std::make_unique<gmx_domdec_constraints_t>();
    gmx_domdec_constraints_t* dc = dd->constraints.get();

    dc->molb_con_offset.resize(mtop.molblock.size());
    dc->molb_ncon_mol.resize(mtop.molblock.size());

    int ncon = 0;
    for (size_t mb = 0; mb < mtop.molblock.size(); mb++)
    {
        const gmx_molblock_t* molb = &mtop.molblock[mb];
        dc->molb_con_offset[mb]    = ncon;
        dc->molb_ncon_mol[mb]      = mtop.moltype[molb->type].ilist[F_CONSTR].size() / 3
                                + mtop.moltype[molb->type].ilist[F_CONSTRNC].size() / 3;
        ncon += molb->nmol * dc->molb_ncon_mol[mb];
    }

    if (ncon > 0)
    {
        dc->gc_req.resize(ncon);
    }

    /* Use a hash table for the global to local index.
     * The number of keys is a rough estimate, it will be optimized later.
     */
    int numKeysEstimate = std::min(mtop.natoms / 20, mtop.natoms / (2 * dd->nnodes));
    dc->ga2la           = std::make_unique<gmx::HashedMap<int>>(numKeysEstimate);

    dc->nthread = gmx_omp_nthreads_get(ModuleMultiThread::Domdec);
    dc->ils.resize(dc->nthread);

    dd->constraint_comm = std::make_unique<gmx_domdec_specat_comm_t>();

    dc->requestedGlobalAtomIndices.resize(dc->nthread);
}
