Add replacements for pbc enumerations

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

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 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
 * of the License, or (at your option) any later version.
 *
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/* \internal \file
 *
 * \brief Implements atom distribution functions.
 *
 * \author Berk Hess <hess@kth.se>
 * \ingroup module_domdec
 */

#include "gmxpre.h"

#include "distribute.h"

#include "config.h"

#include <vector>

#include "gromacs/domdec/domdec_network.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/df_history.h"
#include "gromacs/mdtypes/state.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/logger.h"

#include "atomdistribution.h"
#include "cellsizes.h"
#include "domdec_internal.h"
#include "utility.h"

static void distributeVecSendrecv(gmx_domdec_t                   *dd,
                                  gmx::ArrayRef<const gmx::RVec>  globalVec,
                                  gmx::ArrayRef<gmx::RVec>        localVec)
{
    if (DDMASTER(dd))
    {
        const t_block         &atomGroups = dd->comm->cgs_gl;

        std::vector<gmx::RVec> buffer;

        for (int rank = 0; rank < dd->nnodes; rank++)
        {
            if (rank != dd->rank)
            {
                const auto &domainGroups = dd->ma->domainGroups[rank];

                buffer.resize(domainGroups.numAtoms);

                int   localAtom = 0;
                for (const int &g : domainGroups.atomGroups)
                {
                    for (int globalAtom = atomGroups.index[g]; globalAtom < atomGroups.index[g + 1]; globalAtom++)
                    {
                        buffer[localAtom++] = globalVec[globalAtom];
                    }
                }
                GMX_RELEASE_ASSERT(localAtom == domainGroups.numAtoms, "The index count and number of indices should match");

#if GMX_MPI
                MPI_Send(buffer.data(), domainGroups.numAtoms*sizeof(gmx::RVec), MPI_BYTE,
                         rank, rank, dd->mpi_comm_all);
#endif
            }
        }

        const auto &domainGroups = dd->ma->domainGroups[dd->masterrank];
        int         localAtom    = 0;
        for (const int &g : domainGroups.atomGroups)
        {
            for (int globalAtom = atomGroups.index[g]; globalAtom < atomGroups.index[g + 1]; globalAtom++)
            {
                localVec[localAtom++] = globalVec[globalAtom];
            }
        }
    }
    else
    {
#if GMX_MPI
        int numHomeAtoms = dd->comm->atomRanges.numHomeAtoms();
        MPI_Recv(localVec.data(), numHomeAtoms*sizeof(gmx::RVec), MPI_BYTE, dd->masterrank,
                 MPI_ANY_TAG, dd->mpi_comm_all, MPI_STATUS_IGNORE);
#endif
    }
}

static void distributeVecScatterv(gmx_domdec_t                   *dd,
                                  gmx::ArrayRef<const gmx::RVec>  globalVec,
                                  gmx::ArrayRef<gmx::RVec>        localVec)
{
    int *sendCounts    = nullptr;
    int *displacements = nullptr;

    if (DDMASTER(dd))
    {
        AtomDistribution &ma = *dd->ma;

        get_commbuffer_counts(&ma, &sendCounts, &displacements);

        const t_block           &atomGroups = dd->comm->cgs_gl;

        gmx::ArrayRef<gmx::RVec> buffer = ma.rvecBuffer;
        int localAtom                   = 0;
        for (int rank = 0; rank < dd->nnodes; rank++)
        {
            const auto &domainGroups = ma.domainGroups[rank];
            for (const int &g : domainGroups.atomGroups)
            {
                for (int globalAtom = atomGroups.index[g]; globalAtom < atomGroups.index[g + 1]; globalAtom++)
                {
                    buffer[localAtom++] = globalVec[globalAtom];
                }
            }
        }
    }

    int numHomeAtoms = dd->comm->atomRanges.numHomeAtoms();
    dd_scatterv(dd, sendCounts, displacements,
                DDMASTER(dd) ? dd->ma->rvecBuffer.data() : nullptr,
                numHomeAtoms*sizeof(gmx::RVec), localVec.data());
}

static void distributeVec(gmx_domdec_t                   *dd,
                          gmx::ArrayRef<const gmx::RVec>  globalVec,
                          gmx::ArrayRef<gmx::RVec>        localVec)
{
    if (dd->nnodes <= c_maxNumRanksUseSendRecvForScatterAndGather)
    {
        distributeVecSendrecv(dd, globalVec, localVec);
    }
    else
    {
        distributeVecScatterv(dd, globalVec, localVec);
    }
}

static void dd_distribute_dfhist(gmx_domdec_t *dd, df_history_t *dfhist)
{
    if (dfhist == nullptr)
    {
        return;
    }

    dd_bcast(dd, sizeof(int), &dfhist->bEquil);
    dd_bcast(dd, sizeof(int), &dfhist->nlambda);
    dd_bcast(dd, sizeof(real), &dfhist->wl_delta);

    if (dfhist->nlambda > 0)
    {
        int nlam = dfhist->nlambda;
        dd_bcast(dd, sizeof(int)*nlam, dfhist->n_at_lam);
        dd_bcast(dd, sizeof(real)*nlam, dfhist->wl_histo);
        dd_bcast(dd, sizeof(real)*nlam, dfhist->sum_weights);
        dd_bcast(dd, sizeof(real)*nlam, dfhist->sum_dg);
        dd_bcast(dd, sizeof(real)*nlam, dfhist->sum_minvar);
        dd_bcast(dd, sizeof(real)*nlam, dfhist->sum_variance);

        for (int i = 0; i < nlam; i++)
        {
            dd_bcast(dd, sizeof(real)*nlam, dfhist->accum_p[i]);
            dd_bcast(dd, sizeof(real)*nlam, dfhist->accum_m[i]);
            dd_bcast(dd, sizeof(real)*nlam, dfhist->accum_p2[i]);
            dd_bcast(dd, sizeof(real)*nlam, dfhist->accum_m2[i]);
            dd_bcast(dd, sizeof(real)*nlam, dfhist->Tij[i]);
            dd_bcast(dd, sizeof(real)*nlam, dfhist->Tij_empirical[i]);
        }
    }
}

static void dd_distribute_state(gmx_domdec_t *dd,
                                const t_state *state, t_state *state_local,
                                PaddedVector<gmx::RVec> *f)
{
    int nh = state_local->nhchainlength;

    if (DDMASTER(dd))
    {
        GMX_RELEASE_ASSERT(state->nhchainlength == nh, "The global and local Nose-Hoover chain lengths should match");

        for (int i = 0; i < efptNR; i++)
        {
            state_local->lambda[i] = state->lambda[i];
        }
        state_local->fep_state = state->fep_state;
        state_local->veta      = state->veta;
        state_local->vol0      = state->vol0;
        copy_mat(state->box, state_local->box);
        copy_mat(state->box_rel, state_local->box_rel);
        copy_mat(state->boxv, state_local->boxv);
        copy_mat(state->svir_prev, state_local->svir_prev);
        copy_mat(state->fvir_prev, state_local->fvir_prev);
        if (state->dfhist != nullptr)
        {
            copy_df_history(state_local->dfhist, state->dfhist);
        }
        for (int i = 0; i < state_local->ngtc; i++)
        {
            for (int j = 0; j < nh; j++)
            {
                state_local->nosehoover_xi[i*nh+j]        = state->nosehoover_xi[i*nh+j];
                state_local->nosehoover_vxi[i*nh+j]       = state->nosehoover_vxi[i*nh+j];
            }
            state_local->therm_integral[i] = state->therm_integral[i];
        }
        for (int i = 0; i < state_local->nnhpres; i++)
        {
            for (int j = 0; j < nh; j++)
            {
                state_local->nhpres_xi[i*nh+j]        = state->nhpres_xi[i*nh+j];
                state_local->nhpres_vxi[i*nh+j]       = state->nhpres_vxi[i*nh+j];
            }
        }
        state_local->baros_integral = state->baros_integral;
    }
    dd_bcast(dd, ((efptNR)*sizeof(real)), state_local->lambda.data());
    dd_bcast(dd, sizeof(int), &state_local->fep_state);
    dd_bcast(dd, sizeof(real), &state_local->veta);
    dd_bcast(dd, sizeof(real), &state_local->vol0);
    dd_bcast(dd, sizeof(state_local->box), state_local->box);
    dd_bcast(dd, sizeof(state_local->box_rel), state_local->box_rel);
    dd_bcast(dd, sizeof(state_local->boxv), state_local->boxv);
    dd_bcast(dd, sizeof(state_local->svir_prev), state_local->svir_prev);
    dd_bcast(dd, sizeof(state_local->fvir_prev), state_local->fvir_prev);
    dd_bcast(dd, ((state_local->ngtc*nh)*sizeof(double)), state_local->nosehoover_xi.data());
    dd_bcast(dd, ((state_local->ngtc*nh)*sizeof(double)), state_local->nosehoover_vxi.data());
    dd_bcast(dd, state_local->ngtc*sizeof(double), state_local->therm_integral.data());
    dd_bcast(dd, ((state_local->nnhpres*nh)*sizeof(double)), state_local->nhpres_xi.data());
    dd_bcast(dd, ((state_local->nnhpres*nh)*sizeof(double)), state_local->nhpres_vxi.data());

    /* communicate df_history -- required for restarting from checkpoint */
    dd_distribute_dfhist(dd, state_local->dfhist);

    dd_resize_state(state_local, f, dd->comm->atomRanges.numHomeAtoms());

    if (state_local->flags & (1 << estX))
    {
        distributeVec(dd, DDMASTER(dd) ? state->x : gmx::ArrayRef<const gmx::RVec>(), state_local->x);
    }
    if (state_local->flags & (1 << estV))
    {
        distributeVec(dd, DDMASTER(dd) ? state->v : gmx::ArrayRef<const gmx::RVec>(), state_local->v);
    }
    if (state_local->flags & (1 << estCGP))
    {
        distributeVec(dd, DDMASTER(dd) ? state->cg_p : gmx::ArrayRef<const gmx::RVec>(), state_local->cg_p);
    }
}

/* Computes and returns the domain index for the given atom group.
 *
 * Also updates the coordinates in pos for PBC, when necessary.
 */
static inline int
computeAtomGroupDomainIndex(const gmx_domdec_t                         &dd,
                            const gmx_ddbox_t                          &ddbox,
                            const matrix                               &triclinicCorrectionMatrix,
                            gmx::ArrayRef < const std::vector < real>>  cellBoundaries,
                            int                                         atomBegin,
                            int                                         atomEnd,
                            const matrix                                box,
                            rvec                                       *pos)
{
    /* Set the reference location cg_cm for assigning the group */
    rvec cog;
    int  numAtoms = atomEnd - atomBegin;
    if (numAtoms == 1)
    {
        copy_rvec(pos[atomBegin], cog);
    }
    else
    {
        real invNumAtoms = 1/static_cast<real>(numAtoms);

        clear_rvec(cog);
        for (int a = atomBegin; a < atomEnd; a++)
        {
            rvec_inc(cog, pos[a]);
        }
        for (int d = 0; d < DIM; d++)
        {
            cog[d] *= invNumAtoms;
        }
    }
    /* Put the charge group in the box and determine the cell index ind */
    ivec ind;
    for (int d = DIM - 1; d >= 0; d--)
    {
        real pos_d = cog[d];
        if (d < dd.npbcdim)
        {
            bool bScrew = (dd.bScrewPBC && d == XX);
            if (ddbox.tric_dir[d] && dd.nc[d] > 1)
            {
                /* Use triclinic coordinates for this dimension */
                for (int j = d + 1; j < DIM; j++)
                {
                    pos_d += cog[j]*triclinicCorrectionMatrix[j][d];
                }
            }
            while (pos_d >= box[d][d])
            {
                pos_d -= box[d][d];
                rvec_dec(cog, box[d]);
                if (bScrew)
                {
                    cog[YY] = box[YY][YY] - cog[YY];
                    cog[ZZ] = box[ZZ][ZZ] - cog[ZZ];
                }
                for (int a = atomBegin; a < atomEnd; a++)
                {
                    rvec_dec(pos[a], box[d]);
                    if (bScrew)
                    {
                        pos[a][YY] = box[YY][YY] - pos[a][YY];
                        pos[a][ZZ] = box[ZZ][ZZ] - pos[a][ZZ];
                    }
                }
            }
            while (pos_d < 0)
            {
                pos_d += box[d][d];
                rvec_inc(cog, box[d]);
                if (bScrew)
                {
                    cog[YY] = box[YY][YY] - cog[YY];
                    cog[ZZ] = box[ZZ][ZZ] - cog[ZZ];
                }
                for (int a = atomBegin; a < atomEnd; a++)
                {
                    rvec_inc(pos[a], box[d]);
                    if (bScrew)
                    {
                        pos[a][YY] = box[YY][YY] - pos[a][YY];
                        pos[a][ZZ] = box[ZZ][ZZ] - pos[a][ZZ];
                    }
                }
            }
        }
        /* This could be done more efficiently */
        ind[d] = 0;
        while (ind[d] + 1 < dd.nc[d] && pos_d >= cellBoundaries[d][ind[d] + 1])
        {
            ind[d]++;
        }
    }

    return dd_index(dd.nc, ind);
}


static std::vector < std::vector < int>>
getAtomGroupDistribution(const gmx::MDLogger &mdlog,
                         const gmx_mtop_t &mtop,
                         const matrix box, const gmx_ddbox_t &ddbox,
                         rvec pos[],
                         gmx_domdec_t *dd)
{
    AtomDistribution &ma = *dd->ma;

    /* Clear the count */
    for (int rank = 0; rank < dd->nnodes; rank++)
    {
        ma.domainGroups[rank].numAtoms = 0;
    }

    matrix triclinicCorrectionMatrix;
    make_tric_corr_matrix(dd->npbcdim, box, triclinicCorrectionMatrix);

    ivec       npulse;
    const auto cellBoundaries =
        set_dd_cell_sizes_slb(dd, &ddbox, setcellsizeslbMASTER, npulse);

    const t_block *cgs     = &dd->comm->cgs_gl;
    const int     *cgindex = cgs->index;

    std::vector < std::vector < int>> indices(dd->nnodes);

    if (dd->comm->useUpdateGroups)
    {
        int atomOffset = 0;
        for (const gmx_molblock_t &molblock : mtop.molblock)
        {
            const auto &updateGrouping = dd->comm->updateGroupingPerMoleculetype[molblock.type];

            for (int mol = 0; mol < molblock.nmol; mol++)
            {
                for (int g = 0; g < updateGrouping.numBlocks(); g++)
                {
                    const auto &block       = updateGrouping.block(g);
                    const int   atomBegin   = atomOffset + block.begin();
                    const int   atomEnd     = atomOffset + block.end();
                    const int   domainIndex =
                        computeAtomGroupDomainIndex(*dd, ddbox, triclinicCorrectionMatrix,
                                                    cellBoundaries,
                                                    atomBegin, atomEnd, box,
                                                    pos);

                    for (int atomIndex : block)
                    {
                        indices[domainIndex].push_back(atomOffset + atomIndex);
                    }
                    ma.domainGroups[domainIndex].numAtoms += block.size();
                }

                atomOffset += updateGrouping.fullRange().end();
            }
        }

        GMX_RELEASE_ASSERT(atomOffset == mtop.natoms, "Should distribute all atoms");
    }
    else
    {
        /* Compute the center of geometry for all atoms or charge groups */
        for (int icg = 0; icg < cgs->nr; icg++)
        {
            int domainIndex =
                computeAtomGroupDomainIndex(*dd, ddbox, triclinicCorrectionMatrix,
                                            cellBoundaries,
                                            cgindex[icg], cgindex[icg + 1], box,
                                            pos);

            indices[domainIndex].push_back(icg);
            ma.domainGroups[domainIndex].numAtoms += cgindex[icg + 1] - cgindex[icg];
        }
    }

    {
        // Use double for the sums to avoid natoms^2 overflowing
        // (65537^2 > 2^32)
        int    nat_sum, nat_min, nat_max;
        double nat2_sum;

        nat_sum  = 0;
        nat2_sum = 0;
        nat_min  = ma.domainGroups[0].numAtoms;
        nat_max  = ma.domainGroups[0].numAtoms;
        for (int rank = 0; rank < dd->nnodes; rank++)
        {
            int numAtoms  = ma.domainGroups[rank].numAtoms;
            nat_sum      += numAtoms;
            // convert to double to avoid integer overflows when squaring
            nat2_sum     += gmx::square(double(numAtoms));
            nat_min       = std::min(nat_min, numAtoms);
            nat_max       = std::max(nat_max, numAtoms);
        }
        nat_sum  /= dd->nnodes;
        nat2_sum /= dd->nnodes;

        GMX_LOG(mdlog.info).appendTextFormatted(
                "Atom distribution over %d domains: av %d stddev %d min %d max %d",
                dd->nnodes,
                nat_sum,
                gmx::roundToInt(std::sqrt(nat2_sum - gmx::square(static_cast<double>(nat_sum)))),
                nat_min, nat_max);
    }

    return indices;
}

static void distributeAtomGroups(const gmx::MDLogger &mdlog,
                                 gmx_domdec_t *dd,
                                 const gmx_mtop_t &mtop,
                                 const matrix box, const gmx_ddbox_t *ddbox,
                                 rvec pos[])
{
    AtomDistribution *ma = dd->ma.get();
    int              *ibuf, buf2[2] = { 0, 0 };
    gmx_bool          bMaster = DDMASTER(dd);

    std::vector < std::vector < int>> groupIndices;

    if (bMaster)
    {
        GMX_ASSERT(box && pos, "box or pos not set on master");

        if (dd->bScrewPBC)
        {
            check_screw_box(box);
        }

        groupIndices = getAtomGroupDistribution(mdlog, mtop, box, *ddbox, pos, dd);

        for (int rank = 0; rank < dd->nnodes; rank++)
        {
            ma->intBuffer[rank*2]     = groupIndices[rank].size();
            ma->intBuffer[rank*2 + 1] = ma->domainGroups[rank].numAtoms;
        }
        ibuf = ma->intBuffer.data();
    }
    else
    {
        ibuf = nullptr;
    }
    dd_scatter(dd, 2*sizeof(int), ibuf, buf2);

    dd->ncg_home = buf2[0];
    dd->comm->atomRanges.setEnd(DDAtomRanges::Type::Home, buf2[1]);
    dd->globalAtomGroupIndices.resize(dd->ncg_home);
    dd->globalAtomIndices.resize(dd->comm->atomRanges.numHomeAtoms());

    if (bMaster)
    {
        ma->atomGroups.clear();

        int groupOffset = 0;
        for (int rank = 0; rank < dd->nnodes; rank++)
        {
            ma->intBuffer[rank]                = groupIndices[rank].size()*sizeof(int);
            ma->intBuffer[dd->nnodes + rank]   = groupOffset*sizeof(int);

            ma->atomGroups.insert(ma->atomGroups.end(),
                                  groupIndices[rank].begin(), groupIndices[rank].end());

            ma->domainGroups[rank].atomGroups  = gmx::constArrayRefFromArray(ma->atomGroups.data() + groupOffset, groupIndices[rank].size());

            groupOffset                            += groupIndices[rank].size();
        }
    }

    dd_scatterv(dd,
                bMaster ? ma->intBuffer.data() : nullptr,
                bMaster ? ma->intBuffer.data() + dd->nnodes : nullptr,
                bMaster ? ma->atomGroups.data() : nullptr,
                dd->ncg_home*sizeof(int), dd->globalAtomGroupIndices.data());

    if (debug)
    {
        fprintf(debug, "Home charge groups:\n");
        for (int i = 0; i < dd->ncg_home; i++)
        {
            fprintf(debug, " %d", dd->globalAtomGroupIndices[i]);
            if (i % 10 == 9)
            {
                fprintf(debug, "\n");
            }
        }
        fprintf(debug, "\n");
    }
}

void distributeState(const gmx::MDLogger     &mdlog,
                     gmx_domdec_t            *dd,
                     const gmx_mtop_t        &mtop,
                     t_state                 *state_global,
                     const gmx_ddbox_t       &ddbox,
                     t_state                 *state_local,
                     PaddedVector<gmx::RVec> *f)
{
    rvec *xGlobal = (DDMASTER(dd) ? state_global->x.rvec_array() : nullptr);

    distributeAtomGroups(mdlog, dd, mtop,
                         DDMASTER(dd) ? state_global->box : nullptr,
                         &ddbox, xGlobal);

    dd_distribute_state(dd, state_global, state_local, f);
}