Clean up PME domain count passing

[gromacs.git] / src / gromacs / ewald / pme.cpp

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * Copyright (c) 2001-2004, The GROMACS development team.
 * Copyright (c) 2013,2014,2015,2016,2017,2018, 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 This file contains function definitions necessary for
 * computing energies and forces for the PME long-ranged part (Coulomb
 * and LJ).
 *
 * \author Erik Lindahl <erik@kth.se>
 * \author Berk Hess <hess@kth.se>
 * \ingroup module_ewald
 */
/* IMPORTANT FOR DEVELOPERS:
 *
 * Triclinic pme stuff isn't entirely trivial, and we've experienced
 * some bugs during development (many of them due to me). To avoid
 * this in the future, please check the following things if you make
 * changes in this file:
 *
 * 1. You should obtain identical (at least to the PME precision)
 *    energies, forces, and virial for
 *    a rectangular box and a triclinic one where the z (or y) axis is
 *    tilted a whole box side. For instance you could use these boxes:
 *
 *    rectangular       triclinic
 *     2  0  0           2  0  0
 *     0  2  0           0  2  0
 *     0  0  6           2  2  6
 *
 * 2. You should check the energy conservation in a triclinic box.
 *
 * It might seem an overkill, but better safe than sorry.
 * /Erik 001109
 */

#include "gmxpre.h"

#include "pme.h"

#include "config.h"

#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>

#include <cmath>

#include <algorithm>
#include <list>

#include "gromacs/domdec/domdec.h"
#include "gromacs/ewald/ewald-utils.h"
#include "gromacs/fft/parallel_3dfft.h"
#include "gromacs/fileio/pdbio.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/math/gmxcomplex.h"
#include "gromacs/math/invertmatrix.h"
#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/timing/cyclecounter.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/timing/walltime_accounting.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxmpi.h"
#include "gromacs/utility/gmxomp.h"
#include "gromacs/utility/logger.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
#include "gromacs/utility/unique_cptr.h"

#include "calculate-spline-moduli.h"
#include "pme-gather.h"
#include "pme-gpu-internal.h"
#include "pme-grid.h"
#include "pme-internal.h"
#include "pme-redistribute.h"
#include "pme-solve.h"
#include "pme-spline-work.h"
#include "pme-spread.h"

bool pme_gpu_supports_input(const t_inputrec *ir, std::string *error)
{
    std::list<std::string> errorReasons;
    if (!EEL_PME(ir->coulombtype))
    {
        errorReasons.push_back("systems that do not use PME for electrostatics");
    }
    if (ir->pme_order != 4)
    {
        errorReasons.push_back("interpolation orders other than 4");
    }
    if (ir->efep != efepNO)
    {
        errorReasons.push_back("free energy calculations (multiple grids)");
    }
    if (EVDW_PME(ir->vdwtype))
    {
        errorReasons.push_back("Lennard-Jones PME");
    }
#if GMX_DOUBLE
    {
        errorReasons.push_back("double precision");
    }
#endif
#if GMX_GPU != GMX_GPU_CUDA
    {
        errorReasons.push_back("non-CUDA build of GROMACS");
    }
#endif
    if (ir->cutoff_scheme == ecutsGROUP)
    {
        errorReasons.push_back("group cutoff scheme");
    }
    if (EI_TPI(ir->eI))
    {
        errorReasons.push_back("test particle insertion");
    }

    bool inputSupported = errorReasons.empty();
    if (!inputSupported && error)
    {
        std::string regressionTestMarker = "PME GPU does not support";
        // this prefix is tested for in the regression tests script gmxtest.pl
        *error = regressionTestMarker + ": " + gmx::joinStrings(errorReasons, "; ") + ".";
    }
    return inputSupported;
}

/*! \brief \libinternal
 * Finds out if PME with given inputs is possible to run on GPU.
 * This function is an internal final check, validating the whole PME structure on creation,
 * but it still duplicates the preliminary checks from the above (externally exposed) pme_gpu_supports_input() - just in case.
 *
 * \param[in]  pme          The PME structure.
 * \param[out] error        The error message if the input is not supported on GPU.
 * \returns                 True if this PME input is possible to run on GPU, false otherwise.
 */
static bool pme_gpu_check_restrictions(const gmx_pme_t *pme, std::string *error)
{
    std::list<std::string> errorReasons;
    if (pme->nnodes != 1)
    {
        errorReasons.push_back("PME decomposition");
    }
    if (pme->pme_order != 4)
    {
        errorReasons.push_back("interpolation orders other than 4");
    }
    if (pme->bFEP)
    {
        errorReasons.push_back("free energy calculations (multiple grids)");
    }
    if (pme->doLJ)
    {
        errorReasons.push_back("Lennard-Jones PME");
    }
#if GMX_DOUBLE
    {
        errorReasons.push_back("double precision");
    }
#endif
#if GMX_GPU != GMX_GPU_CUDA
    {
        errorReasons.push_back("non-CUDA build of GROMACS");
    }
#endif

    bool inputSupported = errorReasons.empty();
    if (!inputSupported && error)
    {
        std::string regressionTestMarker = "PME GPU does not support";
        // this prefix is tested for in the regression tests script gmxtest.pl
        *error = regressionTestMarker + ": " + gmx::joinStrings(errorReasons, "; ") + ".";
    }
    return inputSupported;
}

PmeRunMode pme_run_mode(const gmx_pme_t *pme)
{
    GMX_ASSERT(pme != nullptr, "Expecting valid PME data pointer");
    return pme->runMode;
}

/*! \brief Number of bytes in a cache line.
 *
 * Must also be a multiple of the SIMD and SIMD4 register size, to
 * preserve alignment.
 */
const int gmxCacheLineSize = 64;

//! Set up coordinate communication
static void setup_coordinate_communication(pme_atomcomm_t *atc)
{
    int nslab, n, i;
    int fw, bw;

    nslab = atc->nslab;

    n = 0;
    for (i = 1; i <= nslab/2; i++)
    {
        fw = (atc->nodeid + i) % nslab;
        bw = (atc->nodeid - i + nslab) % nslab;
        if (n < nslab - 1)
        {
            atc->node_dest[n] = fw;
            atc->node_src[n]  = bw;
            n++;
        }
        if (n < nslab - 1)
        {
            atc->node_dest[n] = bw;
            atc->node_src[n]  = fw;
            n++;
        }
    }
}

/*! \brief Round \p n up to the next multiple of \p f */
static int mult_up(int n, int f)
{
    return ((n + f - 1)/f)*f;
}

/*! \brief Return estimate of the load imbalance from the PME grid not being a good match for the number of PME ranks */
static double estimate_pme_load_imbalance(struct gmx_pme_t *pme)
{
    int    nma, nmi;
    double n1, n2, n3;

    nma = pme->nnodes_major;
    nmi = pme->nnodes_minor;

    n1 = mult_up(pme->nkx, nma)*mult_up(pme->nky, nmi)*pme->nkz;
    n2 = mult_up(pme->nkx, nma)*mult_up(pme->nkz, nmi)*pme->nky;
    n3 = mult_up(pme->nky, nma)*mult_up(pme->nkz, nmi)*pme->nkx;

    /* pme_solve is roughly double the cost of an fft */

    return (n1 + n2 + 3*n3)/(double)(6*pme->nkx*pme->nky*pme->nkz);
}

/*! \brief Initialize atom communication data structure */
static void init_atomcomm(struct gmx_pme_t *pme, pme_atomcomm_t *atc,
                          int dimind, gmx_bool bSpread)
{
    int thread;

    atc->dimind    = dimind;
    atc->nslab     = 1;
    atc->nodeid    = 0;
    atc->pd_nalloc = 0;
#if GMX_MPI
    if (pme->nnodes > 1)
    {
        atc->mpi_comm = pme->mpi_comm_d[dimind];
        MPI_Comm_size(atc->mpi_comm, &atc->nslab);
        MPI_Comm_rank(atc->mpi_comm, &atc->nodeid);
    }
    if (debug)
    {
        fprintf(debug, "For PME atom communication in dimind %d: nslab %d rank %d\n", atc->dimind, atc->nslab, atc->nodeid);
    }
#endif

    atc->bSpread   = bSpread;
    atc->pme_order = pme->pme_order;

    if (atc->nslab > 1)
    {
        snew(atc->node_dest, atc->nslab);
        snew(atc->node_src, atc->nslab);
        setup_coordinate_communication(atc);

        snew(atc->count_thread, pme->nthread);
        for (thread = 0; thread < pme->nthread; thread++)
        {
            snew(atc->count_thread[thread], atc->nslab);
        }
        atc->count = atc->count_thread[0];
        snew(atc->rcount, atc->nslab);
        snew(atc->buf_index, atc->nslab);
    }

    atc->nthread = pme->nthread;
    if (atc->nthread > 1)
    {
        snew(atc->thread_plist, atc->nthread);
    }
    snew(atc->spline, atc->nthread);
    for (thread = 0; thread < atc->nthread; thread++)
    {
        if (atc->nthread > 1)
        {
            snew(atc->thread_plist[thread].n, atc->nthread+2*gmxCacheLineSize);
            atc->thread_plist[thread].n += gmxCacheLineSize;
        }
    }
}

/*! \brief Destroy an atom communication data structure and its child structs */
static void destroy_atomcomm(pme_atomcomm_t *atc)
{
    sfree(atc->pd);
    if (atc->nslab > 1)
    {
        sfree(atc->node_dest);
        sfree(atc->node_src);
        for (int i = 0; i < atc->nthread; i++)
        {
            sfree(atc->count_thread[i]);
        }
        sfree(atc->count_thread);
        sfree(atc->rcount);
        sfree(atc->buf_index);

        sfree(atc->x);
        sfree(atc->coefficient);
        sfree(atc->f);
    }
    sfree(atc->idx);
    sfree(atc->fractx);

    sfree(atc->thread_idx);
    for (int i = 0; i < atc->nthread; i++)
    {
        if (atc->nthread > 1)
        {
            int *n_ptr = atc->thread_plist[i].n - gmxCacheLineSize;
            sfree(n_ptr);
            sfree(atc->thread_plist[i].i);
        }
        sfree(atc->spline[i].ind);
        for (int d = 0; d < ZZ; d++)
        {
            sfree(atc->spline[i].theta[d]);
            sfree(atc->spline[i].dtheta[d]);
        }
        sfree_aligned(atc->spline[i].ptr_dtheta_z);
        sfree_aligned(atc->spline[i].ptr_theta_z);
    }
    if (atc->nthread > 1)
    {
        sfree(atc->thread_plist);
    }
    sfree(atc->spline);
}

/*! \brief Initialize data structure for communication */
static void
init_overlap_comm(pme_overlap_t *  ol,
                  int              norder,
#if GMX_MPI
                  MPI_Comm         comm,
#endif
                  int              nnodes,
                  int              nodeid,
                  int              ndata,
                  int              commplainsize)
{
    gmx_bool         bCont;
#if GMX_MPI
    MPI_Status       stat;

    ol->mpi_comm = comm;
#endif

    ol->nnodes = nnodes;
    ol->nodeid = nodeid;

    /* Linear translation of the PME grid won't affect reciprocal space
     * calculations, so to optimize we only interpolate "upwards",
     * which also means we only have to consider overlap in one direction.
     * I.e., particles on this node might also be spread to grid indices
     * that belong to higher nodes (modulo nnodes)
     */

    ol->s2g0.resize(ol->nnodes + 1);
    ol->s2g1.resize(ol->nnodes);
    if (debug)
    {
        fprintf(debug, "PME slab boundaries:");
    }
    for (int i = 0; i < nnodes; i++)
    {
        /* s2g0 the local interpolation grid start.
         * s2g1 the local interpolation grid end.
         * Since in calc_pidx we divide particles, and not grid lines,
         * spatially uniform along dimension x or y, we need to round
         * s2g0 down and s2g1 up.
         */
        ol->s2g0[i] = (i * ndata + 0) / nnodes;
        ol->s2g1[i] = ((i + 1) * ndata + nnodes - 1) / nnodes + norder - 1;

        if (debug)
        {
            fprintf(debug, "  %3d %3d", ol->s2g0[i], ol->s2g1[i]);
        }
    }
    ol->s2g0[nnodes] = ndata;
    if (debug)
    {
        fprintf(debug, "\n");
    }

    /* Determine with how many nodes we need to communicate the grid overlap */
    int testRankCount = 0;
    do
    {
        testRankCount++;
        bCont = FALSE;
        for (int i = 0; i < nnodes; i++)
        {
            if ((i + testRankCount <  nnodes && ol->s2g1[i] > ol->s2g0[i + testRankCount]) ||
                (i + testRankCount >= nnodes && ol->s2g1[i] > ol->s2g0[i + testRankCount - nnodes] + ndata))
            {
                bCont = TRUE;
            }
        }
    }
    while (bCont && testRankCount < nnodes);

    ol->comm_data.resize(testRankCount - 1);
    ol->send_size = 0;

    for (size_t b = 0; b < ol->comm_data.size(); b++)
    {
        pme_grid_comm_t *pgc = &ol->comm_data[b];

        /* Send */
        pgc->send_id = (ol->nodeid + (b + 1)) % ol->nnodes;
        int fft_start = ol->s2g0[pgc->send_id];
        int fft_end   = ol->s2g0[pgc->send_id + 1];
        if (pgc->send_id < nodeid)
        {
            fft_start += ndata;
            fft_end   += ndata;
        }
        int send_index1  = ol->s2g1[nodeid];
        send_index1      = std::min(send_index1, fft_end);
        pgc->send_index0 = fft_start;
        pgc->send_nindex = std::max(0, send_index1 - pgc->send_index0);
        ol->send_size   += pgc->send_nindex;

        /* We always start receiving to the first index of our slab */
        pgc->recv_id     = (ol->nodeid - (b + 1) + ol->nnodes) % ol->nnodes;
        fft_start        = ol->s2g0[ol->nodeid];
        fft_end          = ol->s2g0[ol->nodeid + 1];
        int recv_index1  = ol->s2g1[pgc->recv_id];
        if (pgc->recv_id > nodeid)
        {
            recv_index1 -= ndata;
        }
        recv_index1      = std::min(recv_index1, fft_end);
        pgc->recv_index0 = fft_start;
        pgc->recv_nindex = std::max(0, recv_index1 - pgc->recv_index0);
    }

#if GMX_MPI
    /* Communicate the buffer sizes to receive */
    for (size_t b = 0; b < ol->comm_data.size(); b++)
    {
        MPI_Sendrecv(&ol->send_size, 1, MPI_INT, ol->comm_data[b].send_id, b,
                     &ol->comm_data[b].recv_size, 1, MPI_INT, ol->comm_data[b].recv_id, b,
                     ol->mpi_comm, &stat);
    }
#endif

    /* For non-divisible grid we need pme_order iso pme_order-1 */
    ol->sendbuf.resize(norder * commplainsize);
    ol->recvbuf.resize(norder * commplainsize);
}

int minimalPmeGridSize(int pmeOrder)
{
    /* The actual grid size limitations are:
     *   serial:        >= pme_order
     *   DD, no OpenMP: >= 2*(pme_order - 1)
     *   DD, OpenMP:    >= pme_order + 1
     * But we use the maximum for simplicity since in practice there is not
     * much performance difference between pme_order and 2*(pme_order -1).
     */
    int minimalSize = 2*(pmeOrder - 1);

    GMX_RELEASE_ASSERT(pmeOrder >= 3, "pmeOrder has to be >= 3");
    GMX_RELEASE_ASSERT(minimalSize >= pmeOrder + 1, "The grid size should be >= pmeOrder + 1");

    return minimalSize;
}

bool gmx_pme_check_restrictions(int pme_order,
                                int nkx, int nky, int nkz,
                                int numPmeDomainsAlongX,
                                bool useThreads,
                                bool errorsAreFatal)
{
    if (pme_order > PME_ORDER_MAX)
    {
        if (!errorsAreFatal)
        {
            return false;
        }

        std::string message = gmx::formatString(
                    "pme_order (%d) is larger than the maximum allowed value (%d). Modify and recompile the code if you really need such a high order.",
                    pme_order, PME_ORDER_MAX);
        GMX_THROW(InconsistentInputError(message));
    }

    const int minGridSize = minimalPmeGridSize(pme_order);
    if (nkx < minGridSize ||
        nky < minGridSize ||
        nkz < minGridSize)
    {
        if (!errorsAreFatal)
        {
            return false;
        }
        std::string message = gmx::formatString(
                    "The PME grid sizes need to be >= 2*(pme_order-1) (%d)",
                    minGridSize);
        GMX_THROW(InconsistentInputError(message));
    }

    /* Check for a limitation of the (current) sum_fftgrid_dd code.
     * We only allow multiple communication pulses in dim 1, not in dim 0.
     */
    if (useThreads && (nkx < numPmeDomainsAlongX*pme_order &&
                       nkx != numPmeDomainsAlongX*(pme_order - 1)))
    {
        if (!errorsAreFatal)
        {
            return false;
        }
        gmx_fatal(FARGS, "The number of PME grid lines per rank along x is %g. But when using OpenMP threads, the number of grid lines per rank along x should be >= pme_order (%d) or = pmeorder-1. To resolve this issue, use fewer ranks along x (and possibly more along y and/or z) by specifying -dd manually.",
                  nkx/static_cast<double>(numPmeDomainsAlongX), pme_order);
    }

    return true;
}

/*! \brief Round \p enumerator */
static int div_round_up(int enumerator, int denominator)
{
    return (enumerator + denominator - 1)/denominator;
}

gmx_pme_t *gmx_pme_init(const t_commrec     *cr,
                        const NumPmeDomains &numPmeDomains,
                        const t_inputrec    *ir,
                        int                  homenr,
                        gmx_bool             bFreeEnergy_q,
                        gmx_bool             bFreeEnergy_lj,
                        gmx_bool             bReproducible,
                        real                 ewaldcoeff_q,
                        real                 ewaldcoeff_lj,
                        int                  nthread,
                        PmeRunMode           runMode,
                        PmeGpu              *pmeGpu,
                        gmx_device_info_t   *gpuInfo,
                        const gmx::MDLogger  & /*mdlog*/)
{
    int               use_threads, sum_use_threads, i;
    ivec              ndata;

    if (debug)
    {
        fprintf(debug, "Creating PME data structures.\n");
    }

    unique_cptr<gmx_pme_t, gmx_pme_destroy> pme(new gmx_pme_t());

    pme->sum_qgrid_tmp       = nullptr;
    pme->sum_qgrid_dd_tmp    = nullptr;

    pme->buf_nalloc          = 0;

    pme->nnodes              = 1;
    pme->bPPnode             = TRUE;

    pme->nnodes_major        = numPmeDomains.x;
    pme->nnodes_minor        = numPmeDomains.y;

#if GMX_MPI
    if (numPmeDomains.x*numPmeDomains.y > 1)
    {
        pme->mpi_comm = cr->mpi_comm_mygroup;

        MPI_Comm_rank(pme->mpi_comm, &pme->nodeid);
        MPI_Comm_size(pme->mpi_comm, &pme->nnodes);
        if (pme->nnodes != numPmeDomains.x*numPmeDomains.y)
        {
            gmx_incons("PME rank count mismatch");
        }
    }
    else
    {
        pme->mpi_comm = MPI_COMM_NULL;
    }
#endif

    if (pme->nnodes == 1)
    {
#if GMX_MPI
        pme->mpi_comm_d[0] = MPI_COMM_NULL;
        pme->mpi_comm_d[1] = MPI_COMM_NULL;
#endif
        pme->ndecompdim   = 0;
        pme->nodeid_major = 0;
        pme->nodeid_minor = 0;
#if GMX_MPI
        pme->mpi_comm_d[0] = pme->mpi_comm_d[1] = MPI_COMM_NULL;
#endif
    }
    else
    {
        if (numPmeDomains.y == 1)
        {
#if GMX_MPI
            pme->mpi_comm_d[0] = pme->mpi_comm;
            pme->mpi_comm_d[1] = MPI_COMM_NULL;
#endif
            pme->ndecompdim   = 1;
            pme->nodeid_major = pme->nodeid;
            pme->nodeid_minor = 0;

        }
        else if (numPmeDomains.x == 1)
        {
#if GMX_MPI
            pme->mpi_comm_d[0] = MPI_COMM_NULL;
            pme->mpi_comm_d[1] = pme->mpi_comm;
#endif
            pme->ndecompdim   = 1;
            pme->nodeid_major = 0;
            pme->nodeid_minor = pme->nodeid;
        }
        else
        {
            if (pme->nnodes % numPmeDomains.x != 0)
            {
                gmx_incons("For 2D PME decomposition, #PME ranks must be divisible by the number of domains along x");
            }
            pme->ndecompdim = 2;

#if GMX_MPI
            MPI_Comm_split(pme->mpi_comm, pme->nodeid % numPmeDomains.y,
                           pme->nodeid, &pme->mpi_comm_d[0]);  /* My communicator along major dimension */
            MPI_Comm_split(pme->mpi_comm, pme->nodeid/numPmeDomains.y,
                           pme->nodeid, &pme->mpi_comm_d[1]);  /* My communicator along minor dimension */

            MPI_Comm_rank(pme->mpi_comm_d[0], &pme->nodeid_major);
            MPI_Comm_size(pme->mpi_comm_d[0], &pme->nnodes_major);
            MPI_Comm_rank(pme->mpi_comm_d[1], &pme->nodeid_minor);
            MPI_Comm_size(pme->mpi_comm_d[1], &pme->nnodes_minor);
#endif
        }
        pme->bPPnode = thisRankHasDuty(cr, DUTY_PP);
    }

    pme->nthread = nthread;

    /* Check if any of the PME MPI ranks uses threads */
    use_threads = (pme->nthread > 1 ? 1 : 0);
#if GMX_MPI
    if (pme->nnodes > 1)
    {
        MPI_Allreduce(&use_threads, &sum_use_threads, 1, MPI_INT,
                      MPI_SUM, pme->mpi_comm);
    }
    else
#endif
    {
        sum_use_threads = use_threads;
    }
    pme->bUseThreads = (sum_use_threads > 0);

    if (ir->ePBC == epbcSCREW)
    {
        gmx_fatal(FARGS, "pme does not (yet) work with pbc = screw");
    }

    /* NOTE:
     * It is likely that the current gmx_pme_do() routine supports calculating
     * only Coulomb or LJ while gmx_pme_init() configures for both,
     * but that has never been tested.
     * It is likely that the current gmx_pme_do() routine supports calculating,
     * not calculating free-energy for Coulomb and/or LJ while gmx_pme_init()
     * configures with free-energy, but that has never been tested.
     */
    pme->doCoulomb     = EEL_PME(ir->coulombtype);
    pme->doLJ          = EVDW_PME(ir->vdwtype);
    pme->bFEP_q        = ((ir->efep != efepNO) && bFreeEnergy_q);
    pme->bFEP_lj       = ((ir->efep != efepNO) && bFreeEnergy_lj);
    pme->bFEP          = (pme->bFEP_q || pme->bFEP_lj);
    pme->nkx           = ir->nkx;
    pme->nky           = ir->nky;
    pme->nkz           = ir->nkz;
    pme->bP3M          = (ir->coulombtype == eelP3M_AD || getenv("GMX_PME_P3M") != nullptr);
    pme->pme_order     = ir->pme_order;
    pme->ewaldcoeff_q  = ewaldcoeff_q;
    pme->ewaldcoeff_lj = ewaldcoeff_lj;

    /* Always constant electrostatics coefficients */
    pme->epsilon_r     = ir->epsilon_r;

    /* Always constant LJ coefficients */
    pme->ljpme_combination_rule = ir->ljpme_combination_rule;

    // The box requires scaling with nwalls = 2, we store that condition as well
    // as the scaling factor
    delete pme->boxScaler;
    pme->boxScaler = new EwaldBoxZScaler(*ir);

    /* If we violate restrictions, generate a fatal error here */
    gmx_pme_check_restrictions(pme->pme_order,
                               pme->nkx, pme->nky, pme->nkz,
                               pme->nnodes_major,
                               pme->bUseThreads,
                               true);

    if (pme->nnodes > 1)
    {
        double imbal;

#if GMX_MPI
        MPI_Type_contiguous(DIM, GMX_MPI_REAL, &(pme->rvec_mpi));
        MPI_Type_commit(&(pme->rvec_mpi));
#endif

        /* Note that the coefficient spreading and force gathering, which usually
         * takes about the same amount of time as FFT+solve_pme,
         * is always fully load balanced
         * (unless the coefficient distribution is inhomogeneous).
         */

        imbal = estimate_pme_load_imbalance(pme.get());
        if (imbal >= 1.2 && pme->nodeid_major == 0 && pme->nodeid_minor == 0)
        {
            fprintf(stderr,
                    "\n"
                    "NOTE: The load imbalance in PME FFT and solve is %d%%.\n"
                    "      For optimal PME load balancing\n"
                    "      PME grid_x (%d) and grid_y (%d) should be divisible by #PME_ranks_x (%d)\n"
                    "      and PME grid_y (%d) and grid_z (%d) should be divisible by #PME_ranks_y (%d)\n"
                    "\n",
                    (int)((imbal-1)*100 + 0.5),
                    pme->nkx, pme->nky, pme->nnodes_major,
                    pme->nky, pme->nkz, pme->nnodes_minor);
        }
    }

    /* For non-divisible grid we need pme_order iso pme_order-1 */
    /* In sum_qgrid_dd x overlap is copied in place: take padding into account.
     * y is always copied through a buffer: we don't need padding in z,
     * but we do need the overlap in x because of the communication order.
     */
    init_overlap_comm(&pme->overlap[0], pme->pme_order,
#if GMX_MPI
                      pme->mpi_comm_d[0],
#endif
                      pme->nnodes_major, pme->nodeid_major,
                      pme->nkx,
                      (div_round_up(pme->nky, pme->nnodes_minor)+pme->pme_order)*(pme->nkz+pme->pme_order-1));

    /* Along overlap dim 1 we can send in multiple pulses in sum_fftgrid_dd.
     * We do this with an offset buffer of equal size, so we need to allocate
     * extra for the offset. That's what the (+1)*pme->nkz is for.
     */
    init_overlap_comm(&pme->overlap[1], pme->pme_order,
#if GMX_MPI
                      pme->mpi_comm_d[1],
#endif
                      pme->nnodes_minor, pme->nodeid_minor,
                      pme->nky,
                      (div_round_up(pme->nkx, pme->nnodes_major)+pme->pme_order+1)*pme->nkz);

    /* Double-check for a limitation of the (current) sum_fftgrid_dd code.
     * Note that gmx_pme_check_restrictions checked for this already.
     */
    if (pme->bUseThreads && (pme->overlap[0].comm_data.size() > 1))
    {
        gmx_incons("More than one communication pulse required for grid overlap communication along the major dimension while using threads");
    }

    snew(pme->bsp_mod[XX], pme->nkx);
    snew(pme->bsp_mod[YY], pme->nky);
    snew(pme->bsp_mod[ZZ], pme->nkz);

    pme->gpu     = pmeGpu; /* Carrying over the single GPU structure */
    pme->runMode = runMode;

    /* The required size of the interpolation grid, including overlap.
     * The allocated size (pmegrid_n?) might be slightly larger.
     */
    pme->pmegrid_nx = pme->overlap[0].s2g1[pme->nodeid_major] -
        pme->overlap[0].s2g0[pme->nodeid_major];
    pme->pmegrid_ny = pme->overlap[1].s2g1[pme->nodeid_minor] -
        pme->overlap[1].s2g0[pme->nodeid_minor];
    pme->pmegrid_nz_base = pme->nkz;
    pme->pmegrid_nz      = pme->pmegrid_nz_base + pme->pme_order - 1;
    set_grid_alignment(&pme->pmegrid_nz, pme->pme_order);
    pme->pmegrid_start_ix = pme->overlap[0].s2g0[pme->nodeid_major];
    pme->pmegrid_start_iy = pme->overlap[1].s2g0[pme->nodeid_minor];
    pme->pmegrid_start_iz = 0;

    make_gridindex_to_localindex(pme->nkx,
                                 pme->pmegrid_start_ix,
                                 pme->pmegrid_nx - (pme->pme_order-1),
                                 &pme->nnx, &pme->fshx);
    make_gridindex_to_localindex(pme->nky,
                                 pme->pmegrid_start_iy,
                                 pme->pmegrid_ny - (pme->pme_order-1),
                                 &pme->nny, &pme->fshy);
    make_gridindex_to_localindex(pme->nkz,
                                 pme->pmegrid_start_iz,
                                 pme->pmegrid_nz_base,
                                 &pme->nnz, &pme->fshz);

    pme->spline_work = make_pme_spline_work(pme->pme_order);

    ndata[0]    = pme->nkx;
    ndata[1]    = pme->nky;
    ndata[2]    = pme->nkz;
    /* It doesn't matter if we allocate too many grids here,
     * we only allocate and use the ones we need.
     */
    if (pme->doLJ)
    {
        pme->ngrids = ((ir->ljpme_combination_rule == eljpmeLB) ? DO_Q_AND_LJ_LB : DO_Q_AND_LJ);
    }
    else
    {
        pme->ngrids = DO_Q;
    }
    snew(pme->fftgrid, pme->ngrids);
    snew(pme->cfftgrid, pme->ngrids);
    snew(pme->pfft_setup, pme->ngrids);

    for (i = 0; i < pme->ngrids; ++i)
    {
        if ((i <  DO_Q && pme->doCoulomb && (i == 0 ||
                                             bFreeEnergy_q)) ||
            (i >= DO_Q && pme->doLJ && (i == 2 ||
                                        bFreeEnergy_lj ||
                                        ir->ljpme_combination_rule == eljpmeLB)))
        {
            pmegrids_init(&pme->pmegrid[i],
                          pme->pmegrid_nx, pme->pmegrid_ny, pme->pmegrid_nz,
                          pme->pmegrid_nz_base,
                          pme->pme_order,
                          pme->bUseThreads,
                          pme->nthread,
                          pme->overlap[0].s2g1[pme->nodeid_major]-pme->overlap[0].s2g0[pme->nodeid_major+1],
                          pme->overlap[1].s2g1[pme->nodeid_minor]-pme->overlap[1].s2g0[pme->nodeid_minor+1]);
            /* This routine will allocate the grid data to fit the FFTs */
            const auto allocateRealGridForGpu = (pme->runMode == PmeRunMode::Mixed) ? gmx::PinningPolicy::CanBePinned : gmx::PinningPolicy::CannotBePinned;
            gmx_parallel_3dfft_init(&pme->pfft_setup[i], ndata,
                                    &pme->fftgrid[i], &pme->cfftgrid[i],
                                    pme->mpi_comm_d,
                                    bReproducible, pme->nthread, allocateRealGridForGpu);

        }
    }

    if (!pme->bP3M)
    {
        /* Use plain SPME B-spline interpolation */
        make_bspline_moduli(pme->bsp_mod, pme->nkx, pme->nky, pme->nkz, pme->pme_order);
    }
    else
    {
        /* Use the P3M grid-optimized influence function */
        make_p3m_bspline_moduli(pme->bsp_mod, pme->nkx, pme->nky, pme->nkz, pme->pme_order);
    }

    /* Use atc[0] for spreading */
    init_atomcomm(pme.get(), &pme->atc[0], numPmeDomains.x > 1 ? 0 : 1, TRUE);
    if (pme->ndecompdim >= 2)
    {
        init_atomcomm(pme.get(), &pme->atc[1], 1, FALSE);
    }

    if (pme->nnodes == 1)
    {
        pme->atc[0].n = homenr;
        pme_realloc_atomcomm_things(&pme->atc[0]);
    }

    pme->lb_buf1       = nullptr;
    pme->lb_buf2       = nullptr;
    pme->lb_buf_nalloc = 0;

    if (pme_gpu_active(pme.get()))
    {
        if (!pme->gpu)
        {
            // Initial check of validity of the data
            std::string errorString;
            bool        canRunOnGpu = pme_gpu_check_restrictions(pme.get(), &errorString);
            if (!canRunOnGpu)
            {
                GMX_THROW(gmx::NotImplementedError(errorString));
            }
        }

        pme_gpu_reinit(pme.get(), gpuInfo);
    }

    pme_init_all_work(&pme->solve_work, pme->nthread, pme->nkx);

    // no exception was thrown during the init, so we hand over the PME structure handle
    return pme.release();
}

void gmx_pme_reinit(struct gmx_pme_t **pmedata,
                    const t_commrec   *cr,
                    struct gmx_pme_t * pme_src,
                    const t_inputrec * ir,
                    const ivec         grid_size,
                    real               ewaldcoeff_q,
                    real               ewaldcoeff_lj)
{
    int        homenr;

    // Create a copy of t_inputrec fields that are used in gmx_pme_init().
    // TODO: This would be better as just copying a sub-structure that contains
    // all the PME parameters and nothing else.
    t_inputrec irc;
    irc.ePBC                   = ir->ePBC;
    irc.coulombtype            = ir->coulombtype;
    irc.vdwtype                = ir->vdwtype;
    irc.efep                   = ir->efep;
    irc.pme_order              = ir->pme_order;
    irc.epsilon_r              = ir->epsilon_r;
    irc.ljpme_combination_rule = ir->ljpme_combination_rule;
    irc.nkx                    = grid_size[XX];
    irc.nky                    = grid_size[YY];
    irc.nkz                    = grid_size[ZZ];

    if (pme_src->nnodes == 1)
    {
        homenr = pme_src->atc[0].n;
    }
    else
    {
        homenr = -1;
    }

    try
    {
        const gmx::MDLogger dummyLogger;
        // This is reinit which is currently only changing grid size/coefficients,
        // so we don't expect the actual logging.
        // TODO: when PME is an object, it should take reference to mdlog on construction and save it.
        GMX_ASSERT(pmedata, "Invalid PME pointer");
        NumPmeDomains numPmeDomains = { pme_src->nnodes_major, pme_src->nnodes_minor };
        *pmedata = gmx_pme_init(cr, numPmeDomains,
                                &irc, homenr, pme_src->bFEP_q, pme_src->bFEP_lj, FALSE, ewaldcoeff_q, ewaldcoeff_lj,
                                pme_src->nthread, pme_src->runMode, pme_src->gpu, nullptr, dummyLogger);
        //TODO this is mostly passing around current values
    }
    GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;

    /* We can easily reuse the allocated pme grids in pme_src */
    reuse_pmegrids(&pme_src->pmegrid[PME_GRID_QA], &(*pmedata)->pmegrid[PME_GRID_QA]);
    /* We would like to reuse the fft grids, but that's harder */
}

void gmx_pme_calc_energy(struct gmx_pme_t *pme, int n, rvec *x, real *q, real *V)
{
    pme_atomcomm_t *atc;
    pmegrids_t     *grid;

    if (pme->nnodes > 1)
    {
        gmx_incons("gmx_pme_calc_energy called in parallel");
    }
    if (pme->bFEP_q > 1)
    {
        gmx_incons("gmx_pme_calc_energy with free energy");
    }

    atc            = &pme->atc_energy;
    atc->nthread   = 1;
    if (atc->spline == nullptr)
    {
        snew(atc->spline, atc->nthread);
    }
    atc->nslab     = 1;
    atc->bSpread   = TRUE;
    atc->pme_order = pme->pme_order;
    atc->n         = n;
    pme_realloc_atomcomm_things(atc);
    atc->x           = x;
    atc->coefficient = q;

    /* We only use the A-charges grid */
    grid = &pme->pmegrid[PME_GRID_QA];

    /* Only calculate the spline coefficients, don't actually spread */
    spread_on_grid(pme, atc, nullptr, TRUE, FALSE, pme->fftgrid[PME_GRID_QA], FALSE, PME_GRID_QA);

    *V = gather_energy_bsplines(pme, grid->grid.grid, atc);
}

/*! \brief Calculate initial Lorentz-Berthelot coefficients for LJ-PME */
static void
calc_initial_lb_coeffs(struct gmx_pme_t *pme, real *local_c6, real *local_sigma)
{
    int  i;
    for (i = 0; i < pme->atc[0].n; ++i)
    {
        real sigma4;
        sigma4                     = local_sigma[i];
        sigma4                     = sigma4*sigma4;
        sigma4                     = sigma4*sigma4;
        pme->atc[0].coefficient[i] = local_c6[i] / sigma4;
    }
}

/*! \brief Calculate next Lorentz-Berthelot coefficients for LJ-PME */
static void
calc_next_lb_coeffs(struct gmx_pme_t *pme, real *local_sigma)
{
    int  i;

    for (i = 0; i < pme->atc[0].n; ++i)
    {
        pme->atc[0].coefficient[i] *= local_sigma[i];
    }
}

int gmx_pme_do(struct gmx_pme_t *pme,
               int start,       int homenr,
               rvec x[],        rvec f[],
               real chargeA[],  real chargeB[],
               real c6A[],      real c6B[],
               real sigmaA[],   real sigmaB[],
               matrix box,      const t_commrec *cr,
               int  maxshift_x, int maxshift_y,
               t_nrnb *nrnb,    gmx_wallcycle *wcycle,
               matrix vir_q,    matrix vir_lj,
               real *energy_q,  real *energy_lj,
               real lambda_q,   real lambda_lj,
               real *dvdlambda_q, real *dvdlambda_lj,
               int flags)
{
    GMX_ASSERT(pme->runMode == PmeRunMode::CPU, "gmx_pme_do should not be called on the GPU PME run.");

    int                  d, i, j, npme, grid_index, max_grid_index;
    int                  n_d;
    pme_atomcomm_t      *atc        = nullptr;
    pmegrids_t          *pmegrid    = nullptr;
    real                *grid       = nullptr;
    rvec                *f_d;
    real                *coefficient = nullptr;
    real                 energy_AB[4];
    matrix               vir_AB[4];
    real                 scale, lambda;
    gmx_bool             bClearF;
    gmx_parallel_3dfft_t pfft_setup;
    real              *  fftgrid;
    t_complex          * cfftgrid;
    int                  thread;
    gmx_bool             bFirst, bDoSplines;
    int                  fep_state;
    int                  fep_states_lj           = pme->bFEP_lj ? 2 : 1;
    const gmx_bool       bCalcEnerVir            = flags & GMX_PME_CALC_ENER_VIR;
    const gmx_bool       bBackFFT                = flags & (GMX_PME_CALC_F | GMX_PME_CALC_POT);
    const gmx_bool       bCalcF                  = flags & GMX_PME_CALC_F;

    assert(pme->nnodes > 0);
    assert(pme->nnodes == 1 || pme->ndecompdim > 0);

    if (pme->nnodes > 1)
    {
        atc      = &pme->atc[0];
        atc->npd = homenr;
        if (atc->npd > atc->pd_nalloc)
        {
            atc->pd_nalloc = over_alloc_dd(atc->npd);
            srenew(atc->pd, atc->pd_nalloc);
        }
        for (d = pme->ndecompdim-1; d >= 0; d--)
        {
            atc           = &pme->atc[d];
            atc->maxshift = (atc->dimind == 0 ? maxshift_x : maxshift_y);
        }
    }
    else
    {
        atc = &pme->atc[0];
        /* This could be necessary for TPI */
        pme->atc[0].n = homenr;
        if (DOMAINDECOMP(cr))
        {
            pme_realloc_atomcomm_things(atc);
        }
        atc->x = x;
        atc->f = f;
    }

    matrix scaledBox;
    pme->boxScaler->scaleBox(box, scaledBox);

    gmx::invertBoxMatrix(scaledBox, pme->recipbox);
    bFirst = TRUE;

    /* For simplicity, we construct the splines for all particles if
     * more than one PME calculations is needed. Some optimization
     * could be done by keeping track of which atoms have splines
     * constructed, and construct new splines on each pass for atoms
     * that don't yet have them.
     */

    bDoSplines = pme->bFEP || (pme->doCoulomb && pme->doLJ);

    /* We need a maximum of four separate PME calculations:
     * grid_index=0: Coulomb PME with charges from state A
     * grid_index=1: Coulomb PME with charges from state B
     * grid_index=2: LJ PME with C6 from state A
     * grid_index=3: LJ PME with C6 from state B
     * For Lorentz-Berthelot combination rules, a separate loop is used to
     * calculate all the terms
     */

    /* If we are doing LJ-PME with LB, we only do Q here */
    max_grid_index = (pme->ljpme_combination_rule == eljpmeLB) ? DO_Q : DO_Q_AND_LJ;

    for (grid_index = 0; grid_index < max_grid_index; ++grid_index)
    {
        /* Check if we should do calculations at this grid_index
         * If grid_index is odd we should be doing FEP
         * If grid_index < 2 we should be doing electrostatic PME
         * If grid_index >= 2 we should be doing LJ-PME
         */
        if ((grid_index <  DO_Q && (!pme->doCoulomb ||
                                    (grid_index == 1 && !pme->bFEP_q))) ||
            (grid_index >= DO_Q && (!pme->doLJ ||
                                    (grid_index == 3 && !pme->bFEP_lj))))
        {
            continue;
        }
        /* Unpack structure */
        pmegrid    = &pme->pmegrid[grid_index];
        fftgrid    = pme->fftgrid[grid_index];
        cfftgrid   = pme->cfftgrid[grid_index];
        pfft_setup = pme->pfft_setup[grid_index];
        switch (grid_index)
        {
            case 0: coefficient = chargeA + start; break;
            case 1: coefficient = chargeB + start; break;
            case 2: coefficient = c6A + start; break;
            case 3: coefficient = c6B + start; break;
        }

        grid = pmegrid->grid.grid;

        if (debug)
        {
            fprintf(debug, "PME: number of ranks = %d, rank = %d\n",
                    cr->nnodes, cr->nodeid);
            fprintf(debug, "Grid = %p\n", (void*)grid);
            if (grid == nullptr)
            {
                gmx_fatal(FARGS, "No grid!");
            }
        }

        if (pme->nnodes == 1)
        {
            atc->coefficient = coefficient;
        }
        else
        {
            wallcycle_start(wcycle, ewcPME_REDISTXF);
            do_redist_pos_coeffs(pme, cr, start, homenr, bFirst, x, coefficient);

            wallcycle_stop(wcycle, ewcPME_REDISTXF);
        }

        if (debug)
        {
            fprintf(debug, "Rank= %6d, pme local particles=%6d\n",
                    cr->nodeid, atc->n);
        }

        if (flags & GMX_PME_SPREAD)
        {
            wallcycle_start(wcycle, ewcPME_SPREAD);

            /* Spread the coefficients on a grid */
            spread_on_grid(pme, &pme->atc[0], pmegrid, bFirst, TRUE, fftgrid, bDoSplines, grid_index);

            if (bFirst)
            {
                inc_nrnb(nrnb, eNR_WEIGHTS, DIM*atc->n);
            }
            inc_nrnb(nrnb, eNR_SPREADBSP,
                     pme->pme_order*pme->pme_order*pme->pme_order*atc->n);

            if (!pme->bUseThreads)
            {
                wrap_periodic_pmegrid(pme, grid);

                /* sum contributions to local grid from other nodes */
#if GMX_MPI
                if (pme->nnodes > 1)
                {
                    gmx_sum_qgrid_dd(pme, grid, GMX_SUM_GRID_FORWARD);
                }
#endif

                copy_pmegrid_to_fftgrid(pme, grid, fftgrid, grid_index);
            }

            wallcycle_stop(wcycle, ewcPME_SPREAD);

            /* TODO If the OpenMP and single-threaded implementations
               converge, then spread_on_grid() and
               copy_pmegrid_to_fftgrid() will perhaps live in the same
               source file.
             */
        }

        /* Here we start a large thread parallel region */
#pragma omp parallel num_threads(pme->nthread) private(thread)
        {
            try
            {
                thread = gmx_omp_get_thread_num();
                if (flags & GMX_PME_SOLVE)
                {
                    int loop_count;

                    /* do 3d-fft */
                    if (thread == 0)
                    {
                        wallcycle_start(wcycle, ewcPME_FFT);
                    }
                    gmx_parallel_3dfft_execute(pfft_setup, GMX_FFT_REAL_TO_COMPLEX,
                                               thread, wcycle);
                    if (thread == 0)
                    {
                        wallcycle_stop(wcycle, ewcPME_FFT);
                    }

                    /* solve in k-space for our local cells */
                    if (thread == 0)
                    {
                        wallcycle_start(wcycle, (grid_index < DO_Q ? ewcPME_SOLVE : ewcLJPME));
                    }
                    if (grid_index < DO_Q)
                    {
                        loop_count =
                            solve_pme_yzx(pme, cfftgrid,
                                          scaledBox[XX][XX]*scaledBox[YY][YY]*scaledBox[ZZ][ZZ],
                                          bCalcEnerVir,
                                          pme->nthread, thread);
                    }
                    else
                    {
                        loop_count =
                            solve_pme_lj_yzx(pme, &cfftgrid, FALSE,
                                             scaledBox[XX][XX]*scaledBox[YY][YY]*scaledBox[ZZ][ZZ],
                                             bCalcEnerVir,
                                             pme->nthread, thread);
                    }

                    if (thread == 0)
                    {
                        wallcycle_stop(wcycle, (grid_index < DO_Q ? ewcPME_SOLVE : ewcLJPME));
                        inc_nrnb(nrnb, eNR_SOLVEPME, loop_count);
                    }
                }

                if (bBackFFT)
                {
                    /* do 3d-invfft */
                    if (thread == 0)
                    {
                        wallcycle_start(wcycle, ewcPME_FFT);
                    }
                    gmx_parallel_3dfft_execute(pfft_setup, GMX_FFT_COMPLEX_TO_REAL,
                                               thread, wcycle);
                    if (thread == 0)
                    {
                        wallcycle_stop(wcycle, ewcPME_FFT);


                        if (pme->nodeid == 0)
                        {
                            real ntot = pme->nkx*pme->nky*pme->nkz;
                            npme  = static_cast<int>(ntot*std::log(ntot)/std::log(2.0));
                            inc_nrnb(nrnb, eNR_FFT, 2*npme);
                        }

                        /* Note: this wallcycle region is closed below
                           outside an OpenMP region, so take care if
                           refactoring code here. */
                        wallcycle_start(wcycle, ewcPME_GATHER);
                    }

                    copy_fftgrid_to_pmegrid(pme, fftgrid, grid, grid_index, pme->nthread, thread);
                }
            } GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
        }
        /* End of thread parallel section.
         * With MPI we have to synchronize here before gmx_sum_qgrid_dd.
         */

        if (bBackFFT)
        {
            /* distribute local grid to all nodes */
#if GMX_MPI
            if (pme->nnodes > 1)
            {
                gmx_sum_qgrid_dd(pme, grid, GMX_SUM_GRID_BACKWARD);
            }
#endif

            unwrap_periodic_pmegrid(pme, grid);
        }

        if (bCalcF)
        {
            /* interpolate forces for our local atoms */


            /* If we are running without parallelization,
             * atc->f is the actual force array, not a buffer,
             * therefore we should not clear it.
             */
            lambda  = grid_index < DO_Q ? lambda_q : lambda_lj;
            bClearF = (bFirst && PAR(cr));
#pragma omp parallel for num_threads(pme->nthread) schedule(static)
            for (thread = 0; thread < pme->nthread; thread++)
            {
                try
                {
                    gather_f_bsplines(pme, grid, bClearF, atc,
                                      &atc->spline[thread],
                                      pme->bFEP ? (grid_index % 2 == 0 ? 1.0-lambda : lambda) : 1.0);
                }
                GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
            }


            inc_nrnb(nrnb, eNR_GATHERFBSP,
                     pme->pme_order*pme->pme_order*pme->pme_order*pme->atc[0].n);
            /* Note: this wallcycle region is opened above inside an OpenMP
               region, so take care if refactoring code here. */
            wallcycle_stop(wcycle, ewcPME_GATHER);
        }

        if (bCalcEnerVir)
        {
            /* This should only be called on the master thread
             * and after the threads have synchronized.
             */
            if (grid_index < 2)
            {
                get_pme_ener_vir_q(pme->solve_work, pme->nthread, &energy_AB[grid_index], vir_AB[grid_index]);
            }
            else
            {
                get_pme_ener_vir_lj(pme->solve_work, pme->nthread, &energy_AB[grid_index], vir_AB[grid_index]);
            }
        }
        bFirst = FALSE;
    } /* of grid_index-loop */

    /* For Lorentz-Berthelot combination rules in LJ-PME, we need to calculate
     * seven terms. */

    if (pme->doLJ && pme->ljpme_combination_rule == eljpmeLB)
    {
        /* Loop over A- and B-state if we are doing FEP */
        for (fep_state = 0; fep_state < fep_states_lj; ++fep_state)
        {
            real *local_c6 = nullptr, *local_sigma = nullptr, *RedistC6 = nullptr, *RedistSigma = nullptr;
            if (pme->nnodes == 1)
            {
                if (pme->lb_buf1 == nullptr)
                {
                    pme->lb_buf_nalloc = pme->atc[0].n;
                    snew(pme->lb_buf1, pme->lb_buf_nalloc);
                }
                pme->atc[0].coefficient = pme->lb_buf1;
                switch (fep_state)
                {
                    case 0:
                        local_c6      = c6A;
                        local_sigma   = sigmaA;
                        break;
                    case 1:
                        local_c6      = c6B;
                        local_sigma   = sigmaB;
                        break;
                    default:
                        gmx_incons("Trying to access wrong FEP-state in LJ-PME routine");
                }
            }
            else
            {
                atc = &pme->atc[0];
                switch (fep_state)
                {
                    case 0:
                        RedistC6      = c6A;
                        RedistSigma   = sigmaA;
                        break;
                    case 1:
                        RedistC6      = c6B;
                        RedistSigma   = sigmaB;
                        break;
                    default:
                        gmx_incons("Trying to access wrong FEP-state in LJ-PME routine");
                }
                wallcycle_start(wcycle, ewcPME_REDISTXF);

                do_redist_pos_coeffs(pme, cr, start, homenr, bFirst, x, RedistC6);
                if (pme->lb_buf_nalloc < atc->n)
                {
                    pme->lb_buf_nalloc = atc->nalloc;
                    srenew(pme->lb_buf1, pme->lb_buf_nalloc);
                    srenew(pme->lb_buf2, pme->lb_buf_nalloc);
                }
                local_c6 = pme->lb_buf1;
                for (i = 0; i < atc->n; ++i)
                {
                    local_c6[i] = atc->coefficient[i];
                }

                do_redist_pos_coeffs(pme, cr, start, homenr, FALSE, x, RedistSigma);
                local_sigma = pme->lb_buf2;
                for (i = 0; i < atc->n; ++i)
                {
                    local_sigma[i] = atc->coefficient[i];
                }

                wallcycle_stop(wcycle, ewcPME_REDISTXF);
            }
            calc_initial_lb_coeffs(pme, local_c6, local_sigma);

            /*Seven terms in LJ-PME with LB, grid_index < 2 reserved for electrostatics*/
            for (grid_index = 2; grid_index < 9; ++grid_index)
            {
                /* Unpack structure */
                pmegrid    = &pme->pmegrid[grid_index];
                fftgrid    = pme->fftgrid[grid_index];
                pfft_setup = pme->pfft_setup[grid_index];
                calc_next_lb_coeffs(pme, local_sigma);
                grid = pmegrid->grid.grid;

                if (flags & GMX_PME_SPREAD)
                {
                    wallcycle_start(wcycle, ewcPME_SPREAD);
                    /* Spread the c6 on a grid */
                    spread_on_grid(pme, &pme->atc[0], pmegrid, bFirst, TRUE, fftgrid, bDoSplines, grid_index);

                    if (bFirst)
                    {
                        inc_nrnb(nrnb, eNR_WEIGHTS, DIM*atc->n);
                    }

                    inc_nrnb(nrnb, eNR_SPREADBSP,
                             pme->pme_order*pme->pme_order*pme->pme_order*atc->n);
                    if (pme->nthread == 1)
                    {
                        wrap_periodic_pmegrid(pme, grid);
                        /* sum contributions to local grid from other nodes */
#if GMX_MPI
                        if (pme->nnodes > 1)
                        {
                            gmx_sum_qgrid_dd(pme, grid, GMX_SUM_GRID_FORWARD);
                        }
#endif
                        copy_pmegrid_to_fftgrid(pme, grid, fftgrid, grid_index);
                    }
                    wallcycle_stop(wcycle, ewcPME_SPREAD);
                }
                /*Here we start a large thread parallel region*/
#pragma omp parallel num_threads(pme->nthread) private(thread)
                {
                    try
                    {
                        thread = gmx_omp_get_thread_num();
                        if (flags & GMX_PME_SOLVE)
                        {
                            /* do 3d-fft */
                            if (thread == 0)
                            {
                                wallcycle_start(wcycle, ewcPME_FFT);
                            }

                            gmx_parallel_3dfft_execute(pfft_setup, GMX_FFT_REAL_TO_COMPLEX,
                                                       thread, wcycle);
                            if (thread == 0)
                            {
                                wallcycle_stop(wcycle, ewcPME_FFT);
                            }
                        }
                    }
                    GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
                }
                bFirst = FALSE;
            }
            if (flags & GMX_PME_SOLVE)
            {
                /* solve in k-space for our local cells */
#pragma omp parallel num_threads(pme->nthread) private(thread)
                {
                    try
                    {
                        int loop_count;
                        thread = gmx_omp_get_thread_num();
                        if (thread == 0)
                        {
                            wallcycle_start(wcycle, ewcLJPME);
                        }

                        loop_count =
                            solve_pme_lj_yzx(pme, &pme->cfftgrid[2], TRUE,
                                             scaledBox[XX][XX]*scaledBox[YY][YY]*scaledBox[ZZ][ZZ],
                                             bCalcEnerVir,
                                             pme->nthread, thread);
                        if (thread == 0)
                        {
                            wallcycle_stop(wcycle, ewcLJPME);
                            inc_nrnb(nrnb, eNR_SOLVEPME, loop_count);
                        }
                    }
                    GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
                }
            }

            if (bCalcEnerVir)
            {
                /* This should only be called on the master thread and
                 * after the threads have synchronized.
                 */
                get_pme_ener_vir_lj(pme->solve_work, pme->nthread, &energy_AB[2+fep_state], vir_AB[2+fep_state]);
            }

            if (bBackFFT)
            {
                bFirst = !pme->doCoulomb;
                calc_initial_lb_coeffs(pme, local_c6, local_sigma);
                for (grid_index = 8; grid_index >= 2; --grid_index)
                {
                    /* Unpack structure */
                    pmegrid    = &pme->pmegrid[grid_index];
                    fftgrid    = pme->fftgrid[grid_index];
                    pfft_setup = pme->pfft_setup[grid_index];
                    grid       = pmegrid->grid.grid;
                    calc_next_lb_coeffs(pme, local_sigma);
#pragma omp parallel num_threads(pme->nthread) private(thread)
                    {
                        try
                        {
                            thread = gmx_omp_get_thread_num();
                            /* do 3d-invfft */
                            if (thread == 0)
                            {
                                wallcycle_start(wcycle, ewcPME_FFT);
                            }

                            gmx_parallel_3dfft_execute(pfft_setup, GMX_FFT_COMPLEX_TO_REAL,
                                                       thread, wcycle);
                            if (thread == 0)
                            {
                                wallcycle_stop(wcycle, ewcPME_FFT);


                                if (pme->nodeid == 0)
                                {
                                    real ntot = pme->nkx*pme->nky*pme->nkz;
                                    npme  = static_cast<int>(ntot*std::log(ntot)/std::log(2.0));
                                    inc_nrnb(nrnb, eNR_FFT, 2*npme);
                                }
                                wallcycle_start(wcycle, ewcPME_GATHER);
                            }

                            copy_fftgrid_to_pmegrid(pme, fftgrid, grid, grid_index, pme->nthread, thread);
                        }
                        GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
                    } /*#pragma omp parallel*/

                    /* distribute local grid to all nodes */
#if GMX_MPI
                    if (pme->nnodes > 1)
                    {
                        gmx_sum_qgrid_dd(pme, grid, GMX_SUM_GRID_BACKWARD);
                    }
#endif

                    unwrap_periodic_pmegrid(pme, grid);

                    if (bCalcF)
                    {
                        /* interpolate forces for our local atoms */
                        bClearF = (bFirst && PAR(cr));
                        scale   = pme->bFEP ? (fep_state < 1 ? 1.0-lambda_lj : lambda_lj) : 1.0;
                        scale  *= lb_scale_factor[grid_index-2];

#pragma omp parallel for num_threads(pme->nthread) schedule(static)
                        for (thread = 0; thread < pme->nthread; thread++)
                        {
                            try
                            {
                                gather_f_bsplines(pme, grid, bClearF, &pme->atc[0],
                                                  &pme->atc[0].spline[thread],
                                                  scale);
                            }
                            GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
                        }


                        inc_nrnb(nrnb, eNR_GATHERFBSP,
                                 pme->pme_order*pme->pme_order*pme->pme_order*pme->atc[0].n);
                    }
                    wallcycle_stop(wcycle, ewcPME_GATHER);

                    bFirst = FALSE;
                } /* for (grid_index = 8; grid_index >= 2; --grid_index) */
            }     /* if (bCalcF) */
        }         /* for (fep_state = 0; fep_state < fep_states_lj; ++fep_state) */
    }             /* if ((flags & GMX_PME_DO_LJ) && pme->ljpme_combination_rule == eljpmeLB) */

    if (bCalcF && pme->nnodes > 1)
    {
        wallcycle_start(wcycle, ewcPME_REDISTXF);
        for (d = 0; d < pme->ndecompdim; d++)
        {
            atc = &pme->atc[d];
            if (d == pme->ndecompdim - 1)
            {
                n_d = homenr;
                f_d = f + start;
            }
            else
            {
                n_d = pme->atc[d+1].n;
                f_d = pme->atc[d+1].f;
            }
            if (DOMAINDECOMP(cr))
            {
                dd_pmeredist_f(pme, atc, n_d, f_d,
                               d == pme->ndecompdim-1 && pme->bPPnode);
            }
        }

        wallcycle_stop(wcycle, ewcPME_REDISTXF);
    }

    if (bCalcEnerVir)
    {
        if (pme->doCoulomb)
        {
            if (!pme->bFEP_q)
            {
                *energy_q = energy_AB[0];
                m_add(vir_q, vir_AB[0], vir_q);
            }
            else
            {
                *energy_q       = (1.0-lambda_q)*energy_AB[0] + lambda_q*energy_AB[1];
                *dvdlambda_q   += energy_AB[1] - energy_AB[0];
                for (i = 0; i < DIM; i++)
                {
                    for (j = 0; j < DIM; j++)
                    {
                        vir_q[i][j] += (1.0-lambda_q)*vir_AB[0][i][j] +
                            lambda_q*vir_AB[1][i][j];
                    }
                }
            }
            if (debug)
            {
                fprintf(debug, "Electrostatic PME mesh energy: %g\n", *energy_q);
            }
        }
        else
        {
            *energy_q = 0;
        }

        if (pme->doLJ)
        {
            if (!pme->bFEP_lj)
            {
                *energy_lj = energy_AB[2];
                m_add(vir_lj, vir_AB[2], vir_lj);
            }
            else
            {
                *energy_lj     = (1.0-lambda_lj)*energy_AB[2] + lambda_lj*energy_AB[3];
                *dvdlambda_lj += energy_AB[3] - energy_AB[2];
                for (i = 0; i < DIM; i++)
                {
                    for (j = 0; j < DIM; j++)
                    {
                        vir_lj[i][j] += (1.0-lambda_lj)*vir_AB[2][i][j] + lambda_lj*vir_AB[3][i][j];
                    }
                }
            }
            if (debug)
            {
                fprintf(debug, "Lennard-Jones PME mesh energy: %g\n", *energy_lj);
            }
        }
        else
        {
            *energy_lj = 0;
        }
    }
    return 0;
}

void gmx_pme_destroy(gmx_pme_t *pme)
{
    if (!pme)
    {
        return;
    }

    delete pme->boxScaler;

    sfree(pme->nnx);
    sfree(pme->nny);
    sfree(pme->nnz);
    sfree(pme->fshx);
    sfree(pme->fshy);
    sfree(pme->fshz);

    for (int i = 0; i < pme->ngrids; ++i)
    {
        pmegrids_destroy(&pme->pmegrid[i]);
    }
    if (pme->pfft_setup)
    {
        for (int i = 0; i < pme->ngrids; ++i)
        {
            gmx_parallel_3dfft_destroy(pme->pfft_setup[i]);
        }
    }
    sfree(pme->fftgrid);
    sfree(pme->cfftgrid);
    sfree(pme->pfft_setup);

    for (int i = 0; i < std::max(1, pme->ndecompdim); i++) //pme->atc[0] is always allocated
    {
        destroy_atomcomm(&pme->atc[i]);
    }

    for (int i = 0; i < DIM; i++)
    {
        sfree(pme->bsp_mod[i]);
    }

    sfree(pme->lb_buf1);
    sfree(pme->lb_buf2);

    sfree(pme->bufv);
    sfree(pme->bufr);

    if (pme->solve_work)
    {
        pme_free_all_work(&pme->solve_work, pme->nthread);
    }

    sfree(pme->sum_qgrid_tmp);
    sfree(pme->sum_qgrid_dd_tmp);

    destroy_pme_spline_work(pme->spline_work);

    if (pme_gpu_active(pme) && pme->gpu)
    {
        pme_gpu_destroy(pme->gpu);
    }

    delete pme;
}

void gmx_pme_reinit_atoms(const gmx_pme_t *pme, const int nAtoms, const real *charges)
{
    if (pme_gpu_active(pme))
    {
        pme_gpu_reinit_atoms(pme->gpu, nAtoms, charges);
    }
    // TODO: handle the CPU case here; handle the whole t_mdatoms
}