added os-specific defines from cmake required by memtestG80

[gromacs/qmmm-gamess-us.git] / src / mdlib / domdec.c

/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
 *
 * 
 * This file is part of Gromacs        Copyright (c) 1991-2008
 * David van der Spoel, Erik Lindahl, Berk Hess, University of Groningen.
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 * To help us fund GROMACS development, we humbly ask that you cite
 * the research papers on the package. Check out http://www.gromacs.org
 * 
 * And Hey:
 * Gnomes, ROck Monsters And Chili Sauce
 */

#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <stdio.h>
#include <time.h>
#include <math.h>
#include <string.h>
#include <stdlib.h>
#include "typedefs.h"
#include "smalloc.h"
#include "vec.h"
#include "domdec.h"
#include "domdec_network.h"
#include "nrnb.h"
#include "pbc.h"
#include "chargegroup.h"
#include "constr.h"
#include "mdatoms.h"
#include "names.h"
#include "pdbio.h"
#include "futil.h"
#include "force.h"
#include "pme.h"
#include "pull.h"
#include "gmx_wallcycle.h"
#include "mdrun.h"
#include "nsgrid.h"
#include "shellfc.h"
#include "mtop_util.h"
#include "gmxfio.h"
#include "gmx_ga2la.h"

#ifdef GMX_LIB_MPI
#include <mpi.h>
#endif
#ifdef GMX_THREADS
#include "tmpi.h"
#endif

#define DDRANK(dd,rank)    (rank)
#define DDMASTERRANK(dd)   (dd->masterrank)

typedef struct gmx_domdec_master
{
    /* The cell boundaries */
    real **cell_x;
    /* The global charge group division */
    int  *ncg;     /* Number of home charge groups for each node */
    int  *index;   /* Index of nnodes+1 into cg */
    int  *cg;      /* Global charge group index */
    int  *nat;     /* Number of home atoms for each node. */
    int  *ibuf;    /* Buffer for communication */
    rvec *vbuf;    /* Buffer for state scattering and gathering */
} gmx_domdec_master_t;

typedef struct
{
    /* The numbers of charge groups to send and receive for each cell
     * that requires communication, the last entry contains the total
     * number of atoms that needs to be communicated.
     */
    int nsend[DD_MAXIZONE+2];
    int nrecv[DD_MAXIZONE+2];
    /* The charge groups to send */
    int *index;
    int nalloc;
    /* The atom range for non-in-place communication */
    int cell2at0[DD_MAXIZONE];
    int cell2at1[DD_MAXIZONE];
} gmx_domdec_ind_t;

typedef struct
{
    int  np;                   /* Number of grid pulses in this dimension */
    int  np_dlb;               /* For dlb, for use with edlbAUTO          */
    gmx_domdec_ind_t *ind;     /* The indices to communicate, size np     */
    int  np_nalloc;
    bool bInPlace;             /* Can we communicate in place?            */
} gmx_domdec_comm_dim_t;

typedef struct
{
    bool *bCellMin;    /* Temp. var.: is this cell size at the limit     */
    real *cell_f;      /* State var.: cell boundaries, box relative      */
    real *old_cell_f;  /* Temp. var.: old cell size                      */
    real *cell_f_max0; /* State var.: max lower boundary, incl neighbors */
    real *cell_f_min1; /* State var.: min upper boundary, incl neighbors */
    real *bound_min;   /* Temp. var.: lower limit for cell boundary      */
    real *bound_max;   /* Temp. var.: upper limit for cell boundary      */
    bool bLimited;     /* State var.: is DLB limited in this dim and row */
    real *buf_ncd;     /* Temp. var.                                     */
} gmx_domdec_root_t;

#define DD_NLOAD_MAX 9

/* Here floats are accurate enough, since these variables
 * only influence the load balancing, not the actual MD results.
 */
typedef struct
{
    int  nload;
    float *load;
    float sum;
    float max;
    float sum_m;
    float cvol_min;
    float mdf;
    float pme;
    int   flags;
} gmx_domdec_load_t;

typedef struct
{
    int  nsc;
    int  ind_gl;
    int  ind;
} gmx_cgsort_t;

typedef struct
{
    gmx_cgsort_t *sort1,*sort2;
    int  sort_nalloc;
    gmx_cgsort_t *sort_new;
    int  sort_new_nalloc;
    int  *ibuf;
    int  ibuf_nalloc;
} gmx_domdec_sort_t;

typedef struct
{
    rvec *v;
    int  nalloc;
} vec_rvec_t;

/* This enum determines the order of the coordinates.
 * ddnatHOME and ddnatZONE should be first and second,
 * the others can be ordered as wanted.
 */
enum { ddnatHOME, ddnatZONE, ddnatVSITE, ddnatCON, ddnatNR };

enum { edlbAUTO, edlbNO, edlbYES, edlbNR };
const char *edlb_names[edlbNR] = { "auto", "no", "yes" };

typedef struct
{
    int  dimind;   /* The dimension index                                    */
    int  nslab;    /* The number of PME slabs in this dimension              */
    real *slb_dim_f; /* Cell sizes for determining the PME comm. with SLB    */
    int  *pp_min;  /* The minimum pp node location, size nslab               */
    int  *pp_max;  /* The maximum pp node location,size nslab                */
    int  maxshift; /* The maximum shift for coordinate redistribution in PME */
} gmx_ddpme_t;

typedef struct
{
    real min0;    /* The minimum bottom of this zone                        */
    real max1;    /* The maximum top of this zone                           */
    real mch0;    /* The maximum bottom communicaton height for this zone   */
    real mch1;    /* The maximum top communicaton height for this zone      */
    real p1_0;    /* The bottom value of the first cell in this zone        */
    real p1_1;    /* The top value of the first cell in this zone           */
} gmx_ddzone_t;

typedef struct gmx_domdec_comm
{
    /* All arrays are indexed with 0 to dd->ndim (not Cartesian indexing),
     * unless stated otherwise.
     */

    /* The number of decomposition dimensions for PME, 0: no PME */
    int  npmedecompdim;
    /* The number of nodes doing PME (PP/PME or only PME) */
    int  npmenodes;
    int  npmenodes_major;
    int  npmenodes_minor;
    /* The communication setup including the PME only nodes */
    bool bCartesianPP_PME;
    ivec ntot;
    int  cartpmedim;
    int  *pmenodes;          /* size npmenodes                         */
    int  *ddindex2simnodeid; /* size npmenodes, only with bCartesianPP
                              * but with bCartesianPP_PME              */
    gmx_ddpme_t ddpme[2];
    
    /* The DD particle-particle nodes only */
    bool bCartesianPP;
    int  *ddindex2ddnodeid; /* size npmenode, only with bCartesianPP_PME */
    
    /* The global charge groups */
    t_block cgs_gl;

    /* Should we sort the cgs */
    int  nstSortCG;
    gmx_domdec_sort_t *sort;
    
    /* Are there bonded and multi-body interactions between charge groups? */
    bool bInterCGBondeds;
    bool bInterCGMultiBody;

    /* Data for the optional bonded interaction atom communication range */
    bool bBondComm;
    t_blocka *cglink;
    char *bLocalCG;

    /* The DLB option */
    int  eDLB;
    /* Are we actually using DLB? */
    bool bDynLoadBal;

    /* Cell sizes for static load balancing, first index cartesian */
    real **slb_frac;
    
    /* The width of the communicated boundaries */
    real cutoff_mbody;
    real cutoff;
    /* The minimum cell size (including triclinic correction) */
    rvec cellsize_min;
    /* For dlb, for use with edlbAUTO */
    rvec cellsize_min_dlb;
    /* The lower limit for the DD cell size with DLB */
    real cellsize_limit;
    /* Effectively no NB cut-off limit with DLB for systems without PBC? */
    bool bVacDLBNoLimit;

    /* tric_dir is only stored here because dd_get_ns_ranges needs it */
    ivec tric_dir;
    /* box0 and box_size are required with dim's without pbc and -gcom */
    rvec box0;
    rvec box_size;
    
    /* The cell boundaries */
    rvec cell_x0;
    rvec cell_x1;

    /* The old location of the cell boundaries, to check cg displacements */
    rvec old_cell_x0;
    rvec old_cell_x1;

    /* The communication setup and charge group boundaries for the zones */
    gmx_domdec_zones_t zones;
    
    /* The zone limits for DD dimensions 1 and 2 (not 0), determined from
     * cell boundaries of neighboring cells for dynamic load balancing.
     */
    gmx_ddzone_t zone_d1[2];
    gmx_ddzone_t zone_d2[2][2];
    
    /* The coordinate/force communication setup and indices */
    gmx_domdec_comm_dim_t cd[DIM];
    /* The maximum number of cells to communicate with in one dimension */
    int  maxpulse;
    
    /* Which cg distribution is stored on the master node */
    int master_cg_ddp_count;
    
    /* The number of cg's received from the direct neighbors */
    int  zone_ncg1[DD_MAXZONE];
    
    /* The atom counts, the range for each type t is nat[t-1] <= at < nat[t] */
    int  nat[ddnatNR];
    
    /* Communication buffer for general use */
    int  *buf_int;
    int  nalloc_int;

     /* Communication buffer for general use */
    vec_rvec_t vbuf;
    
    /* Communication buffers only used with multiple grid pulses */
    int  *buf_int2;
    int  nalloc_int2;
    vec_rvec_t vbuf2;
    
    /* Communication buffers for local redistribution */
    int  **cggl_flag;
    int  cggl_flag_nalloc[DIM*2];
    rvec **cgcm_state;
    int  cgcm_state_nalloc[DIM*2];
    
    /* Cell sizes for dynamic load balancing */
    gmx_domdec_root_t **root;
    real *cell_f_row;
    real cell_f0[DIM];
    real cell_f1[DIM];
    real cell_f_max0[DIM];
    real cell_f_min1[DIM];
    
    /* Stuff for load communication */
    bool bRecordLoad;
    gmx_domdec_load_t *load;
#ifdef GMX_MPI
    MPI_Comm *mpi_comm_load;
#endif
    /* Cycle counters */
    float cycl[ddCyclNr];
    int   cycl_n[ddCyclNr];
    float cycl_max[ddCyclNr];
    /* Flop counter (0=no,1=yes,2=with (eFlop-1)*5% noise */
    int eFlop;
    double flop;
    int    flop_n;
    /* Have often have did we have load measurements */
    int    n_load_have;
    /* Have often have we collected the load measurements */
    int    n_load_collect;
    
    /* Statistics */
    double sum_nat[ddnatNR-ddnatZONE];
    int    ndecomp;
    int    nload;
    double load_step;
    double load_sum;
    double load_max;
    ivec   load_lim;
    double load_mdf;
    double load_pme;

    /* The last partition step */
    gmx_large_int_t partition_step;

    /* Debugging */
    int  nstDDDump;
    int  nstDDDumpGrid;
    int  DD_debug;
} gmx_domdec_comm_t;

/* The size per charge group of the cggl_flag buffer in gmx_domdec_comm_t */
#define DD_CGIBS 2

/* The flags for the cggl_flag buffer in gmx_domdec_comm_t */
#define DD_FLAG_NRCG  65535
#define DD_FLAG_FW(d) (1<<(16+(d)*2))
#define DD_FLAG_BW(d) (1<<(16+(d)*2+1))

/* Zone permutation required to obtain consecutive charge groups
 * for neighbor searching.
 */
static const int zone_perm[3][4] = { {0,0,0,0},{1,0,0,0},{3,0,1,2} };

/* dd_zo and dd_zp3/dd_zp2 are set up such that i zones with non-zero
 * components see only j zones with that component 0.
 */

/* The DD zone order */
static const ivec dd_zo[DD_MAXZONE] =
  {{0,0,0},{1,0,0},{1,1,0},{0,1,0},{0,1,1},{0,0,1},{1,0,1},{1,1,1}};

/* The 3D setup */
#define dd_z3n  8
#define dd_zp3n 4
static const ivec dd_zp3[dd_zp3n] = {{0,0,8},{1,3,6},{2,5,6},{3,5,7}};

/* The 2D setup */
#define dd_z2n  4
#define dd_zp2n 2
static const ivec dd_zp2[dd_zp2n] = {{0,0,4},{1,3,4}};

/* The 1D setup */
#define dd_z1n  2
#define dd_zp1n 1
static const ivec dd_zp1[dd_zp1n] = {{0,0,2}};

/* Factors used to avoid problems due to rounding issues */
#define DD_CELL_MARGIN       1.0001
#define DD_CELL_MARGIN2      1.00005
/* Factor to account for pressure scaling during nstlist steps */
#define DD_PRES_SCALE_MARGIN 1.02

/* Allowed performance loss before we DLB or warn */
#define DD_PERF_LOSS 0.05

#define DD_CELL_F_SIZE(dd,di) ((dd)->nc[(dd)->dim[(di)]]+1+(di)*2+1+(di))

/* Use separate MPI send and receive commands
 * when nnodes <= GMX_DD_NNODES_SENDRECV.
 * This saves memory (and some copying for small nnodes).
 * For high parallelization scatter and gather calls are used.
 */
#define GMX_DD_NNODES_SENDRECV 4


/*
#define dd_index(n,i) ((((i)[ZZ]*(n)[YY] + (i)[YY])*(n)[XX]) + (i)[XX])

static void index2xyz(ivec nc,int ind,ivec xyz)
{
  xyz[XX] = ind % nc[XX];
  xyz[YY] = (ind / nc[XX]) % nc[YY];
  xyz[ZZ] = ind / (nc[YY]*nc[XX]);
}
*/

/* This order is required to minimize the coordinate communication in PME
 * which uses decomposition in the x direction.
 */
#define dd_index(n,i) ((((i)[XX]*(n)[YY] + (i)[YY])*(n)[ZZ]) + (i)[ZZ])

static void ddindex2xyz(ivec nc,int ind,ivec xyz)
{
    xyz[XX] = ind / (nc[YY]*nc[ZZ]);
    xyz[YY] = (ind / nc[ZZ]) % nc[YY];
    xyz[ZZ] = ind % nc[ZZ];
}

static int ddcoord2ddnodeid(gmx_domdec_t *dd,ivec c)
{
    int ddindex;
    int ddnodeid=-1;
    
    ddindex = dd_index(dd->nc,c);
    if (dd->comm->bCartesianPP_PME)
    {
        ddnodeid = dd->comm->ddindex2ddnodeid[ddindex];
    }
    else if (dd->comm->bCartesianPP)
    {
#ifdef GMX_MPI
        MPI_Cart_rank(dd->mpi_comm_all,c,&ddnodeid);
#endif
    }
    else
    {
        ddnodeid = ddindex;
    }
    
    return ddnodeid;
}

static bool dynamic_dd_box(gmx_ddbox_t *ddbox,t_inputrec *ir)
{
    return (ddbox->nboundeddim < DIM || DYNAMIC_BOX(*ir));
}

int ddglatnr(gmx_domdec_t *dd,int i)
{
    int atnr;
    
    if (dd == NULL)
    {
        atnr = i + 1;
    }
    else
    {
        if (i >= dd->comm->nat[ddnatNR-1])
        {
            gmx_fatal(FARGS,"glatnr called with %d, which is larger than the local number of atoms (%d)",i,dd->comm->nat[ddnatNR-1]);
        }
        atnr = dd->gatindex[i] + 1;
    }
    
    return atnr;
}

t_block *dd_charge_groups_global(gmx_domdec_t *dd)
{
    return &dd->comm->cgs_gl;
}

static void vec_rvec_init(vec_rvec_t *v)
{
    v->nalloc = 0;
    v->v      = NULL;
}

static void vec_rvec_check_alloc(vec_rvec_t *v,int n)
{
    if (n > v->nalloc)
    {
        v->nalloc = over_alloc_dd(n);
        srenew(v->v,v->nalloc);
    }
}

void dd_store_state(gmx_domdec_t *dd,t_state *state)
{
    int i;
    
    if (state->ddp_count != dd->ddp_count)
    {
        gmx_incons("The state does not the domain decomposition state");
    }
    
    state->ncg_gl = dd->ncg_home;
    if (state->ncg_gl > state->cg_gl_nalloc)
    {
        state->cg_gl_nalloc = over_alloc_dd(state->ncg_gl);
        srenew(state->cg_gl,state->cg_gl_nalloc);
    }
    for(i=0; i<state->ncg_gl; i++)
    {
        state->cg_gl[i] = dd->index_gl[i];
    }
    
    state->ddp_count_cg_gl = dd->ddp_count;
}

gmx_domdec_zones_t *domdec_zones(gmx_domdec_t *dd)
{
    return &dd->comm->zones;
}

void dd_get_ns_ranges(gmx_domdec_t *dd,int icg,
                      int *jcg0,int *jcg1,ivec shift0,ivec shift1)
{
    gmx_domdec_zones_t *zones;
    int izone,d,dim;

    zones = &dd->comm->zones;

    izone = 0;
    while (icg >= zones->izone[izone].cg1)
    {
        izone++;
    }
    
    if (izone == 0)
    {
        *jcg0 = icg;
    }
    else if (izone < zones->nizone)
    {
        *jcg0 = zones->izone[izone].jcg0;
    }
    else
    {
        gmx_fatal(FARGS,"DD icg %d out of range: izone (%d) >= nizone (%d)",
                  icg,izone,zones->nizone);
    }
        
    *jcg1 = zones->izone[izone].jcg1;
    
    for(d=0; d<dd->ndim; d++)
    {
        dim = dd->dim[d];
        shift0[dim] = zones->izone[izone].shift0[dim];
        shift1[dim] = zones->izone[izone].shift1[dim];
        if (dd->comm->tric_dir[dim] || (dd->bGridJump && d > 0))
        {
            /* A conservative approach, this can be optimized */
            shift0[dim] -= 1;
            shift1[dim] += 1;
        }
    }
}

int dd_natoms_vsite(gmx_domdec_t *dd)
{
    return dd->comm->nat[ddnatVSITE];
}

void dd_get_constraint_range(gmx_domdec_t *dd,int *at_start,int *at_end)
{
    *at_start = dd->comm->nat[ddnatCON-1];
    *at_end   = dd->comm->nat[ddnatCON];
}

void dd_move_x(gmx_domdec_t *dd,matrix box,rvec x[])
{
    int  nzone,nat_tot,n,d,p,i,j,at0,at1,zone;
    int  *index,*cgindex;
    gmx_domdec_comm_t *comm;
    gmx_domdec_comm_dim_t *cd;
    gmx_domdec_ind_t *ind;
    rvec shift={0,0,0},*buf,*rbuf;
    bool bPBC,bScrew;
    
    comm = dd->comm;
    
    cgindex = dd->cgindex;
    
    buf = comm->vbuf.v;

    nzone = 1;
    nat_tot = dd->nat_home;
    for(d=0; d<dd->ndim; d++)
    {
        bPBC   = (dd->ci[dd->dim[d]] == 0);
        bScrew = (bPBC && dd->bScrewPBC && dd->dim[d] == XX);
        if (bPBC)
        {
            copy_rvec(box[dd->dim[d]],shift);
        }
        cd = &comm->cd[d];
        for(p=0; p<cd->np; p++)
        {
            ind = &cd->ind[p];
            index = ind->index;
            n = 0;
            if (!bPBC)
            {
                for(i=0; i<ind->nsend[nzone]; i++)
                {
                    at0 = cgindex[index[i]];
                    at1 = cgindex[index[i]+1];
                    for(j=at0; j<at1; j++)
                    {
                        copy_rvec(x[j],buf[n]);
                        n++;
                    }
                }
            }
            else if (!bScrew)
            {
                for(i=0; i<ind->nsend[nzone]; i++)
                {
                    at0 = cgindex[index[i]];
                    at1 = cgindex[index[i]+1];
                    for(j=at0; j<at1; j++)
                    {
                        /* We need to shift the coordinates */
                        rvec_add(x[j],shift,buf[n]);
                        n++;
                    }
                }
            }
            else
            {
                for(i=0; i<ind->nsend[nzone]; i++)
                {
                    at0 = cgindex[index[i]];
                    at1 = cgindex[index[i]+1];
                    for(j=at0; j<at1; j++)
                    {
                        /* Shift x */
                        buf[n][XX] = x[j][XX] + shift[XX];
                        /* Rotate y and z.
                         * This operation requires a special shift force
                         * treatment, which is performed in calc_vir.
                         */
                        buf[n][YY] = box[YY][YY] - x[j][YY];
                        buf[n][ZZ] = box[ZZ][ZZ] - x[j][ZZ];
                        n++;
                    }
                }
            }
            
            if (cd->bInPlace)
            {
                rbuf = x + nat_tot;
            }
            else
            {
                rbuf = comm->vbuf2.v;
            }
            /* Send and receive the coordinates */
            dd_sendrecv_rvec(dd, d, dddirBackward,
                             buf,  ind->nsend[nzone+1],
                             rbuf, ind->nrecv[nzone+1]);
            if (!cd->bInPlace)
            {
                j = 0;
                for(zone=0; zone<nzone; zone++)
                {
                    for(i=ind->cell2at0[zone]; i<ind->cell2at1[zone]; i++)
                    {
                        copy_rvec(rbuf[j],x[i]);
                        j++;
                    }
                }
            }
            nat_tot += ind->nrecv[nzone+1];
        }
        nzone += nzone;
    }
}

void dd_move_f(gmx_domdec_t *dd,rvec f[],rvec *fshift)
{
    int  nzone,nat_tot,n,d,p,i,j,at0,at1,zone;
    int  *index,*cgindex;
    gmx_domdec_comm_t *comm;
    gmx_domdec_comm_dim_t *cd;
    gmx_domdec_ind_t *ind;
    rvec *buf,*sbuf;
    ivec vis;
    int  is;
    bool bPBC,bScrew;
    
    comm = dd->comm;
    
    cgindex = dd->cgindex;

    buf = comm->vbuf.v;

    n = 0;
    nzone = comm->zones.n/2;
    nat_tot = dd->nat_tot;
    for(d=dd->ndim-1; d>=0; d--)
    {
        bPBC   = (dd->ci[dd->dim[d]] == 0);
        bScrew = (bPBC && dd->bScrewPBC && dd->dim[d] == XX);
        if (fshift == NULL && !bScrew)
        {
            bPBC = FALSE;
        }
        /* Determine which shift vector we need */
        clear_ivec(vis);
        vis[dd->dim[d]] = 1;
        is = IVEC2IS(vis);
        
        cd = &comm->cd[d];
        for(p=cd->np-1; p>=0; p--) {
            ind = &cd->ind[p];
            nat_tot -= ind->nrecv[nzone+1];
            if (cd->bInPlace)
            {
                sbuf = f + nat_tot;
            }
            else
            {
                sbuf = comm->vbuf2.v;
                j = 0;
                for(zone=0; zone<nzone; zone++)
                {
                    for(i=ind->cell2at0[zone]; i<ind->cell2at1[zone]; i++)
                    {
                        copy_rvec(f[i],sbuf[j]);
                        j++;
                    }
                }
            }
            /* Communicate the forces */
            dd_sendrecv_rvec(dd, d, dddirForward,
                             sbuf, ind->nrecv[nzone+1],
                             buf,  ind->nsend[nzone+1]);
            index = ind->index;
            /* Add the received forces */
            n = 0;
            if (!bPBC)
            {
                for(i=0; i<ind->nsend[nzone]; i++)
                {
                    at0 = cgindex[index[i]];
                    at1 = cgindex[index[i]+1];
                    for(j=at0; j<at1; j++)
                    {
                        rvec_inc(f[j],buf[n]);
                        n++;
                    }
                } 
            }
            else if (!bScrew)
            {
                for(i=0; i<ind->nsend[nzone]; i++)
                {
                    at0 = cgindex[index[i]];
                    at1 = cgindex[index[i]+1];
                    for(j=at0; j<at1; j++)
                    {
                        rvec_inc(f[j],buf[n]);
                        /* Add this force to the shift force */
                        rvec_inc(fshift[is],buf[n]);
                        n++;
                    }
                }
            }
            else
            {
                for(i=0; i<ind->nsend[nzone]; i++)
                {
                    at0 = cgindex[index[i]];
                    at1 = cgindex[index[i]+1];
                    for(j=at0; j<at1; j++)
                    {
                        /* Rotate the force */
                        f[j][XX] += buf[n][XX];
                        f[j][YY] -= buf[n][YY];
                        f[j][ZZ] -= buf[n][ZZ];
                        if (fshift)
                        {
                            /* Add this force to the shift force */
                            rvec_inc(fshift[is],buf[n]);
                        }
                        n++;
                    }
                }
            }
        }
        nzone /= 2;
    }
}

void dd_atom_spread_real(gmx_domdec_t *dd,real v[])
{
    int  nzone,nat_tot,n,d,p,i,j,at0,at1,zone;
    int  *index,*cgindex;
    gmx_domdec_comm_t *comm;
    gmx_domdec_comm_dim_t *cd;
    gmx_domdec_ind_t *ind;
    real *buf,*rbuf;
    
    comm = dd->comm;
    
    cgindex = dd->cgindex;
    
    buf = &comm->vbuf.v[0][0];

    nzone = 1;
    nat_tot = dd->nat_home;
    for(d=0; d<dd->ndim; d++)
    {
        cd = &comm->cd[d];
        for(p=0; p<cd->np; p++)
        {
            ind = &cd->ind[p];
            index = ind->index;
            n = 0;
            for(i=0; i<ind->nsend[nzone]; i++)
            {
                at0 = cgindex[index[i]];
                at1 = cgindex[index[i]+1];
                for(j=at0; j<at1; j++)
                {
                    buf[n] = v[j];
                    n++;
                }
            }
            
            if (cd->bInPlace)
            {
                rbuf = v + nat_tot;
            }
            else
            {
                rbuf = &comm->vbuf2.v[0][0];
            }
            /* Send and receive the coordinates */
            dd_sendrecv_real(dd, d, dddirBackward,
                             buf,  ind->nsend[nzone+1],
                             rbuf, ind->nrecv[nzone+1]);
            if (!cd->bInPlace)
            {
                j = 0;
                for(zone=0; zone<nzone; zone++)
                {
                    for(i=ind->cell2at0[zone]; i<ind->cell2at1[zone]; i++)
                    {
                        v[i] = rbuf[j];
                        j++;
                    }
                }
            }
            nat_tot += ind->nrecv[nzone+1];
        }
        nzone += nzone;
    }
}

void dd_atom_sum_real(gmx_domdec_t *dd,real v[])
{
    int  nzone,nat_tot,n,d,p,i,j,at0,at1,zone;
    int  *index,*cgindex;
    gmx_domdec_comm_t *comm;
    gmx_domdec_comm_dim_t *cd;
    gmx_domdec_ind_t *ind;
    real *buf,*sbuf;
    
    comm = dd->comm;
    
    cgindex = dd->cgindex;

    buf = &comm->vbuf.v[0][0];

    n = 0;
    nzone = comm->zones.n/2;
    nat_tot = dd->nat_tot;
    for(d=dd->ndim-1; d>=0; d--)
    {
        cd = &comm->cd[d];
        for(p=cd->np-1; p>=0; p--) {
            ind = &cd->ind[p];
            nat_tot -= ind->nrecv[nzone+1];
            if (cd->bInPlace)
            {
                sbuf = v + nat_tot;
            }
            else
            {
                sbuf = &comm->vbuf2.v[0][0];
                j = 0;
                for(zone=0; zone<nzone; zone++)
                {
                    for(i=ind->cell2at0[zone]; i<ind->cell2at1[zone]; i++)
                    {
                        sbuf[j] = v[i];
                        j++;
                    }
                }
            }
            /* Communicate the forces */
            dd_sendrecv_real(dd, d, dddirForward,
                             sbuf, ind->nrecv[nzone+1],
                             buf,  ind->nsend[nzone+1]);
            index = ind->index;
            /* Add the received forces */
            n = 0;
            for(i=0; i<ind->nsend[nzone]; i++)
            {
                at0 = cgindex[index[i]];
                at1 = cgindex[index[i]+1];
                for(j=at0; j<at1; j++)
                {
                    v[j] += buf[n];
                    n++;
                }
            } 
        }
        nzone /= 2;
    }
}

static void print_ddzone(FILE *fp,int d,int i,int j,gmx_ddzone_t *zone)
{
    fprintf(fp,"zone d0 %d d1 %d d2 %d  min0 %6.3f max1 %6.3f mch0 %6.3f mch1 %6.3f p1_0 %6.3f p1_1 %6.3f\n",
            d,i,j,
            zone->min0,zone->max1,
            zone->mch0,zone->mch0,
            zone->p1_0,zone->p1_1);
}

static void dd_sendrecv_ddzone(const gmx_domdec_t *dd,
                               int ddimind,int direction,
                               gmx_ddzone_t *buf_s,int n_s,
                               gmx_ddzone_t *buf_r,int n_r)
{
    rvec vbuf_s[5*2],vbuf_r[5*2];
    int i;

    for(i=0; i<n_s; i++)
    {
        vbuf_s[i*2  ][0] = buf_s[i].min0;
        vbuf_s[i*2  ][1] = buf_s[i].max1;
        vbuf_s[i*2  ][2] = buf_s[i].mch0;
        vbuf_s[i*2+1][0] = buf_s[i].mch1;
        vbuf_s[i*2+1][1] = buf_s[i].p1_0;
        vbuf_s[i*2+1][2] = buf_s[i].p1_1;
    }

    dd_sendrecv_rvec(dd, ddimind, direction,
                     vbuf_s, n_s*2,
                     vbuf_r, n_r*2);

    for(i=0; i<n_r; i++)
    {
        buf_r[i].min0 = vbuf_r[i*2  ][0];
        buf_r[i].max1 = vbuf_r[i*2  ][1];
        buf_r[i].mch0 = vbuf_r[i*2  ][2];
        buf_r[i].mch1 = vbuf_r[i*2+1][0];
        buf_r[i].p1_0 = vbuf_r[i*2+1][1];
        buf_r[i].p1_1 = vbuf_r[i*2+1][2];
    }
}

static void dd_move_cellx(gmx_domdec_t *dd,gmx_ddbox_t *ddbox,
                          rvec cell_ns_x0,rvec cell_ns_x1)
{
    int  d,d1,dim,dim1,pos,buf_size,i,j,k,p,npulse,npulse_min;
    gmx_ddzone_t *zp,buf_s[5],buf_r[5],buf_e[5];
    rvec extr_s[2],extr_r[2];
    rvec dh;
    real dist_d,c=0,det;
    gmx_domdec_comm_t *comm;
    bool bPBC,bUse;

    comm = dd->comm;

    for(d=1; d<dd->ndim; d++)
    {
        dim = dd->dim[d];
        zp = (d == 1) ? &comm->zone_d1[0] : &comm->zone_d2[0][0];
        zp->min0 = cell_ns_x0[dim];
        zp->max1 = cell_ns_x1[dim];
        zp->mch0 = cell_ns_x0[dim];
        zp->mch1 = cell_ns_x1[dim];
        zp->p1_0 = cell_ns_x0[dim];
        zp->p1_1 = cell_ns_x1[dim];
    }
    
    for(d=dd->ndim-2; d>=0; d--)
    {
        dim  = dd->dim[d];
        bPBC = (dim < ddbox->npbcdim);

        /* Use an rvec to store two reals */
        extr_s[d][0] = comm->cell_f0[d+1];
        extr_s[d][1] = comm->cell_f1[d+1];
        extr_s[d][2] = 0;

        pos = 0;
        /* Store the extremes in the backward sending buffer,
         * so the get updated separately from the forward communication.
         */
        for(d1=d; d1<dd->ndim-1; d1++)
        {
            /* We invert the order to be able to use the same loop for buf_e */
            buf_s[pos].min0 = extr_s[d1][1];
            buf_s[pos].max1 = extr_s[d1][0];
            buf_s[pos].mch0 = 0;
            buf_s[pos].mch1 = 0;
            /* Store the cell corner of the dimension we communicate along */
            buf_s[pos].p1_0 = comm->cell_x0[dim];
            buf_s[pos].p1_1 = 0;
            pos++;
        }

        buf_s[pos] = (dd->ndim == 2) ? comm->zone_d1[0] : comm->zone_d2[0][0];
        pos++;

        if (dd->ndim == 3 && d == 0)
        {
            buf_s[pos] = comm->zone_d2[0][1];
            pos++;
            buf_s[pos] = comm->zone_d1[0];
            pos++;
        }

        /* We only need to communicate the extremes
         * in the forward direction
         */
        npulse = comm->cd[d].np;
        if (bPBC)
        {
            /* Take the minimum to avoid double communication */
            npulse_min = min(npulse,dd->nc[dim]-1-npulse);
        }
        else
        {
            /* Without PBC we should really not communicate over
             * the boundaries, but implementing that complicates
             * the communication setup and therefore we simply
             * do all communication, but ignore some data.
             */
            npulse_min = npulse;
        }
        for(p=0; p<npulse_min; p++)
        {
            /* Communicate the extremes forward */
            bUse = (bPBC || dd->ci[dim] > 0);

            dd_sendrecv_rvec(dd, d, dddirForward,
                             extr_s+d, dd->ndim-d-1,
                             extr_r+d, dd->ndim-d-1);

            if (bUse)
            {
                for(d1=d; d1<dd->ndim-1; d1++)
                {
                    extr_s[d1][0] = max(extr_s[d1][0],extr_r[d1][0]);
                    extr_s[d1][1] = min(extr_s[d1][1],extr_r[d1][1]);
                }
            }
        }

        buf_size = pos;
        for(p=0; p<npulse; p++)
        {
            /* Communicate all the zone information backward */
            bUse = (bPBC || dd->ci[dim] < dd->nc[dim] - 1);

            dd_sendrecv_ddzone(dd, d, dddirBackward,
                               buf_s, buf_size,
                               buf_r, buf_size);

            clear_rvec(dh);
            if (p > 0)
            {
                for(d1=d+1; d1<dd->ndim; d1++)
                {
                    /* Determine the decrease of maximum required
                     * communication height along d1 due to the distance along d,
                     * this avoids a lot of useless atom communication.
                     */
                    dist_d = comm->cell_x1[dim] - buf_r[0].p1_0;

                    if (ddbox->tric_dir[dim])
                    {
                        /* c is the off-diagonal coupling between the cell planes
                         * along directions d and d1.
                         */
                        c = ddbox->v[dim][dd->dim[d1]][dim];
                    }
                    else
                    {
                        c = 0;
                    }
                    det = (1 + c*c)*comm->cutoff*comm->cutoff - dist_d*dist_d;
                    if (det > 0)
                    {
                        dh[d1] = comm->cutoff - (c*dist_d + sqrt(det))/(1 + c*c);
                    }
                    else
                    {
                        /* A negative value signals out of range */
                        dh[d1] = -1;
                    }
                }
            }

            /* Accumulate the extremes over all pulses */
            for(i=0; i<buf_size; i++)
            {
                if (p == 0)
                {
                    buf_e[i] = buf_r[i];
                }
                else
                {
                    if (bUse)
                    {
                        buf_e[i].min0 = min(buf_e[i].min0,buf_r[i].min0);
                        buf_e[i].max1 = max(buf_e[i].max1,buf_r[i].max1);
                    }

                    if (dd->ndim == 3 && d == 0 && i == buf_size - 1)
                    {
                        d1 = 1;
                    }
                    else
                    {
                        d1 = d + 1;
                    }
                    if (bUse && dh[d1] >= 0)
                    {
                        buf_e[i].mch0 = max(buf_e[i].mch0,buf_r[i].mch0-dh[d1]);
                        buf_e[i].mch1 = max(buf_e[i].mch1,buf_r[i].mch1-dh[d1]);
                    }
                }
                /* Copy the received buffer to the send buffer,
                 * to pass the data through with the next pulse.
                 */
                buf_s[i] = buf_r[i];
            }
            if (((bPBC || dd->ci[dim]+npulse < dd->nc[dim]) && p == npulse-1) ||
                (!bPBC && dd->ci[dim]+1+p == dd->nc[dim]-1))
            {
                /* Store the extremes */ 
                pos = 0;

                for(d1=d; d1<dd->ndim-1; d1++)
                {
                    extr_s[d1][1] = min(extr_s[d1][1],buf_e[pos].min0);
                    extr_s[d1][0] = max(extr_s[d1][0],buf_e[pos].max1);
                    pos++;
                }

                if (d == 1 || (d == 0 && dd->ndim == 3))
                {
                    for(i=d; i<2; i++)
                    {
                        comm->zone_d2[1-d][i] = buf_e[pos];
                        pos++;
                    }
                }
                if (d == 0)
                {
                    comm->zone_d1[1] = buf_e[pos];
                    pos++;
                }
            }
        }
    }
    
    if (dd->ndim >= 2)
    {
        dim = dd->dim[1];
        for(i=0; i<2; i++)
        {
            if (debug)
            {
                print_ddzone(debug,1,i,0,&comm->zone_d1[i]);
            }
            cell_ns_x0[dim] = min(cell_ns_x0[dim],comm->zone_d1[i].min0);
            cell_ns_x1[dim] = max(cell_ns_x1[dim],comm->zone_d1[i].max1);
        }
    }
    if (dd->ndim >= 3)
    {
        dim = dd->dim[2];
        for(i=0; i<2; i++)
        {
            for(j=0; j<2; j++)
            {
                if (debug)
                {
                    print_ddzone(debug,2,i,j,&comm->zone_d2[i][j]);
                }
                cell_ns_x0[dim] = min(cell_ns_x0[dim],comm->zone_d2[i][j].min0);
                cell_ns_x1[dim] = max(cell_ns_x1[dim],comm->zone_d2[i][j].max1);
            }
        }
    }
    for(d=1; d<dd->ndim; d++)
    {
        comm->cell_f_max0[d] = extr_s[d-1][0];
        comm->cell_f_min1[d] = extr_s[d-1][1];
        if (debug)
        {
            fprintf(debug,"Cell fraction d %d, max0 %f, min1 %f\n",
                    d,comm->cell_f_max0[d],comm->cell_f_min1[d]);
        }
    }
}

static void dd_collect_cg(gmx_domdec_t *dd,
                          t_state *state_local)
{
    gmx_domdec_master_t *ma=NULL;
    int buf2[2],*ibuf,i,ncg_home=0,*cg=NULL,nat_home=0;
    t_block *cgs_gl;

    if (state_local->ddp_count == dd->comm->master_cg_ddp_count)
    {
        /* The master has the correct distribution */
        return;
    }
    
    if (state_local->ddp_count == dd->ddp_count)
    {
        ncg_home = dd->ncg_home;
        cg       = dd->index_gl;
        nat_home = dd->nat_home;
    } 
    else if (state_local->ddp_count_cg_gl == state_local->ddp_count)
    {
        cgs_gl = &dd->comm->cgs_gl;

        ncg_home = state_local->ncg_gl;
        cg       = state_local->cg_gl;
        nat_home = 0;
        for(i=0; i<ncg_home; i++)
        {
            nat_home += cgs_gl->index[cg[i]+1] - cgs_gl->index[cg[i]];
        }
    }
    else
    {
        gmx_incons("Attempted to collect a vector for a state for which the charge group distribution is unknown");
    }
    
    buf2[0] = dd->ncg_home;
    buf2[1] = dd->nat_home;
    if (DDMASTER(dd))
    {
        ma = dd->ma;
        ibuf = ma->ibuf;
    }
    else
    {
        ibuf = NULL;
    }
    /* Collect the charge group and atom counts on the master */
    dd_gather(dd,2*sizeof(int),buf2,ibuf);
    
    if (DDMASTER(dd))
    {
        ma->index[0] = 0;
        for(i=0; i<dd->nnodes; i++)
        {
            ma->ncg[i] = ma->ibuf[2*i];
            ma->nat[i] = ma->ibuf[2*i+1];
            ma->index[i+1] = ma->index[i] + ma->ncg[i];
            
        }
        /* Make byte counts and indices */
        for(i=0; i<dd->nnodes; i++)
        {
            ma->ibuf[i] = ma->ncg[i]*sizeof(int);
            ma->ibuf[dd->nnodes+i] = ma->index[i]*sizeof(int);
        }
        if (debug)
        {
            fprintf(debug,"Initial charge group distribution: ");
            for(i=0; i<dd->nnodes; i++)
                fprintf(debug," %d",ma->ncg[i]);
            fprintf(debug,"\n");
        }
    }
    
    /* Collect the charge group indices on the master */
    dd_gatherv(dd,
               dd->ncg_home*sizeof(int),dd->index_gl,
               DDMASTER(dd) ? ma->ibuf : NULL,
               DDMASTER(dd) ? ma->ibuf+dd->nnodes : NULL,
               DDMASTER(dd) ? ma->cg : NULL);
    
    dd->comm->master_cg_ddp_count = state_local->ddp_count;
}

static void dd_collect_vec_sendrecv(gmx_domdec_t *dd,
                                    rvec *lv,rvec *v)
{
    gmx_domdec_master_t *ma;
    int  n,i,c,a,nalloc=0;
    rvec *buf=NULL;
    t_block *cgs_gl;

    ma = dd->ma;
    
    if (!DDMASTER(dd))
    {
#ifdef GMX_MPI
        MPI_Send(lv,dd->nat_home*sizeof(rvec),MPI_BYTE,DDMASTERRANK(dd),
                 dd->rank,dd->mpi_comm_all);
#endif
    } else {
        /* Copy the master coordinates to the global array */
        cgs_gl = &dd->comm->cgs_gl;

        n = DDMASTERRANK(dd);
        a = 0;
        for(i=ma->index[n]; i<ma->index[n+1]; i++)
        {
            for(c=cgs_gl->index[ma->cg[i]]; c<cgs_gl->index[ma->cg[i]+1]; c++)
            {
                copy_rvec(lv[a++],v[c]);
            }
        }
        
        for(n=0; n<dd->nnodes; n++)
        {
            if (n != dd->rank)
            {
                if (ma->nat[n] > nalloc)
                {
                    nalloc = over_alloc_dd(ma->nat[n]);
                    srenew(buf,nalloc);
                }
#ifdef GMX_MPI
                MPI_Recv(buf,ma->nat[n]*sizeof(rvec),MPI_BYTE,DDRANK(dd,n),
                         n,dd->mpi_comm_all,MPI_STATUS_IGNORE);
#endif
                a = 0;
                for(i=ma->index[n]; i<ma->index[n+1]; i++)
                {
                    for(c=cgs_gl->index[ma->cg[i]]; c<cgs_gl->index[ma->cg[i]+1]; c++)
                    {
                        copy_rvec(buf[a++],v[c]);
                    }
                }
            }
        }
        sfree(buf);
    }
}

static void get_commbuffer_counts(gmx_domdec_t *dd,
                                  int **counts,int **disps)
{
    gmx_domdec_master_t *ma;
    int n;

    ma = dd->ma;
    
    /* Make the rvec count and displacment arrays */
    *counts  = ma->ibuf;
    *disps   = ma->ibuf + dd->nnodes;
    for(n=0; n<dd->nnodes; n++)
    {
        (*counts)[n] = ma->nat[n]*sizeof(rvec);
        (*disps)[n]  = (n == 0 ? 0 : (*disps)[n-1] + (*counts)[n-1]);
    }
}

static void dd_collect_vec_gatherv(gmx_domdec_t *dd,
                                   rvec *lv,rvec *v)
{
    gmx_domdec_master_t *ma;
    int  *rcounts=NULL,*disps=NULL;
    int  n,i,c,a;
    rvec *buf=NULL;
    t_block *cgs_gl;
    
    ma = dd->ma;
    
    if (DDMASTER(dd))
    {
        get_commbuffer_counts(dd,&rcounts,&disps);

        buf = ma->vbuf;
    }
    
    dd_gatherv(dd,dd->nat_home*sizeof(rvec),lv,rcounts,disps,buf);

    if (DDMASTER(dd))
    {
        cgs_gl = &dd->comm->cgs_gl;

        a = 0;
        for(n=0; n<dd->nnodes; n++)
        {
            for(i=ma->index[n]; i<ma->index[n+1]; i++)
            {
                for(c=cgs_gl->index[ma->cg[i]]; c<cgs_gl->index[ma->cg[i]+1]; c++)
                {
                    copy_rvec(buf[a++],v[c]);
                }
            }
        }
    }
}

void dd_collect_vec(gmx_domdec_t *dd,
                    t_state *state_local,rvec *lv,rvec *v)
{
    gmx_domdec_master_t *ma;
    int  n,i,c,a,nalloc=0;
    rvec *buf=NULL;
    
    dd_collect_cg(dd,state_local);

    if (dd->nnodes <= GMX_DD_NNODES_SENDRECV)
    {
        dd_collect_vec_sendrecv(dd,lv,v);
    }
    else
    {
        dd_collect_vec_gatherv(dd,lv,v);
    }
}


void dd_collect_state(gmx_domdec_t *dd,
                      t_state *state_local,t_state *state)
{
    int est,i,j,nh;

    nh = state->nhchainlength;

    if (DDMASTER(dd))
    {
        state->lambda = state_local->lambda;
        state->veta = state_local->veta;
        state->vol0 = state_local->vol0;
        copy_mat(state_local->box,state->box);
        copy_mat(state_local->boxv,state->boxv);
        copy_mat(state_local->svir_prev,state->svir_prev);
        copy_mat(state_local->fvir_prev,state->fvir_prev);
        copy_mat(state_local->pres_prev,state->pres_prev);


        for(i=0; i<state_local->ngtc; i++)
        {
            for(j=0; j<nh; j++) {
                state->nosehoover_xi[i*nh+j]        = state_local->nosehoover_xi[i*nh+j];
                state->nosehoover_vxi[i*nh+j]       = state_local->nosehoover_vxi[i*nh+j];
            }
            state->therm_integral[i] = state_local->therm_integral[i];            
        }
        for(i=0; i<state_local->nnhpres; i++) 
        {
            for(j=0; j<nh; j++) {
                state->nhpres_xi[i*nh+j]        = state_local->nhpres_xi[i*nh+j];
                state->nhpres_vxi[i*nh+j]       = state_local->nhpres_vxi[i*nh+j];
            }
        }
    }
    for(est=0; est<estNR; est++)
    {
        if (EST_DISTR(est) && state_local->flags & (1<<est))
        {
            switch (est) {
            case estX:
                dd_collect_vec(dd,state_local,state_local->x,state->x);
                break;
            case estV:
                dd_collect_vec(dd,state_local,state_local->v,state->v);
                break;
            case estSDX:
                dd_collect_vec(dd,state_local,state_local->sd_X,state->sd_X);
                break;
            case estCGP:
                dd_collect_vec(dd,state_local,state_local->cg_p,state->cg_p);
                break;
            case estLD_RNG:
                if (state->nrngi == 1)
                {
                    if (DDMASTER(dd))
                    {
                        for(i=0; i<state_local->nrng; i++)
                        {
                            state->ld_rng[i] = state_local->ld_rng[i];
                        }
                    }
                }
                else
                {
                    dd_gather(dd,state_local->nrng*sizeof(state->ld_rng[0]),
                              state_local->ld_rng,state->ld_rng);
                }
                break;
            case estLD_RNGI:
                if (state->nrngi == 1)
                {
                   if (DDMASTER(dd))
                    {
                        state->ld_rngi[0] = state_local->ld_rngi[0];
                    } 
                }
                else
                {
                    dd_gather(dd,sizeof(state->ld_rngi[0]),
                              state_local->ld_rngi,state->ld_rngi);
                }
                break;
            case estDISRE_INITF:
            case estDISRE_RM3TAV:
            case estORIRE_INITF:
            case estORIRE_DTAV:
                break;
            default:
                gmx_incons("Unknown state entry encountered in dd_collect_state");
            }
        }
    }
}

static void dd_realloc_fr_cg(t_forcerec *fr,int nalloc)
{
    if (debug)
    {
        fprintf(debug,"Reallocating forcerec: currently %d, required %d, allocating %d\n",fr->cg_nalloc,nalloc,over_alloc_dd(nalloc));
    }
    fr->cg_nalloc = over_alloc_dd(nalloc);
    srenew(fr->cg_cm,fr->cg_nalloc);
    srenew(fr->cginfo,fr->cg_nalloc);
}

static void dd_realloc_state(t_state *state,rvec **f,int nalloc)
{
    int est;

    if (debug)
    {
        fprintf(debug,"Reallocating state: currently %d, required %d, allocating %d\n",state->nalloc,nalloc,over_alloc_dd(nalloc));
    }

    state->nalloc = over_alloc_dd(nalloc);
    
    for(est=0; est<estNR; est++)
    {
        if (EST_DISTR(est) && state->flags & (1<<est))
        {
            switch(est) {
            case estX:
                srenew(state->x,state->nalloc);
                break;
            case estV:
                srenew(state->v,state->nalloc);
                break;
            case estSDX:
                srenew(state->sd_X,state->nalloc);
                break;
            case estCGP:
                srenew(state->cg_p,state->nalloc);
                break;
            case estLD_RNG:
            case estLD_RNGI:
            case estDISRE_INITF:
            case estDISRE_RM3TAV:
            case estORIRE_INITF:
            case estORIRE_DTAV:
                /* No reallocation required */
                break;
            default:
                gmx_incons("Unknown state entry encountered in dd_realloc_state");            
            }
        }
    }
    
    if (f != NULL)
    {
        srenew(*f,state->nalloc);
    }
}

static void dd_distribute_vec_sendrecv(gmx_domdec_t *dd,t_block *cgs,
                                       rvec *v,rvec *lv)
{
    gmx_domdec_master_t *ma;
    int  n,i,c,a,nalloc=0;
    rvec *buf=NULL;
    
    if (DDMASTER(dd))
    {
        ma  = dd->ma;
        
        for(n=0; n<dd->nnodes; n++)
        {
            if (n != dd->rank)
            {
                if (ma->nat[n] > nalloc)
                {
                    nalloc = over_alloc_dd(ma->nat[n]);
                    srenew(buf,nalloc);
                }
                /* Use lv as a temporary buffer */
                a = 0;
                for(i=ma->index[n]; i<ma->index[n+1]; i++)
                {
                    for(c=cgs->index[ma->cg[i]]; c<cgs->index[ma->cg[i]+1]; c++)
                    {
                        copy_rvec(v[c],buf[a++]);
                    }
                }
                if (a != ma->nat[n])
                {
                    gmx_fatal(FARGS,"Internal error a (%d) != nat (%d)",
                              a,ma->nat[n]);
                }
                
#ifdef GMX_MPI
                MPI_Send(buf,ma->nat[n]*sizeof(rvec),MPI_BYTE,
                         DDRANK(dd,n),n,dd->mpi_comm_all);
#endif
            }
        }
        sfree(buf);
        n = DDMASTERRANK(dd);
        a = 0;
        for(i=ma->index[n]; i<ma->index[n+1]; i++)
        {
            for(c=cgs->index[ma->cg[i]]; c<cgs->index[ma->cg[i]+1]; c++)
            {
                copy_rvec(v[c],lv[a++]);
            }
        }
    }
    else
    {
#ifdef GMX_MPI
        MPI_Recv(lv,dd->nat_home*sizeof(rvec),MPI_BYTE,DDMASTERRANK(dd),
                 MPI_ANY_TAG,dd->mpi_comm_all,MPI_STATUS_IGNORE);
#endif
    }
}

static void dd_distribute_vec_scatterv(gmx_domdec_t *dd,t_block *cgs,
                                       rvec *v,rvec *lv)
{
    gmx_domdec_master_t *ma;
    int  *scounts=NULL,*disps=NULL;
    int  n,i,c,a,nalloc=0;
    rvec *buf=NULL;
    
    if (DDMASTER(dd))
    {
        ma  = dd->ma;
     
        get_commbuffer_counts(dd,&scounts,&disps);

        buf = ma->vbuf;
        a = 0;
        for(n=0; n<dd->nnodes; n++)
        {
            for(i=ma->index[n]; i<ma->index[n+1]; i++)
            {
                for(c=cgs->index[ma->cg[i]]; c<cgs->index[ma->cg[i]+1]; c++)
                {
                    copy_rvec(v[c],buf[a++]);
                }
            }
        }
    }

    dd_scatterv(dd,scounts,disps,buf,dd->nat_home*sizeof(rvec),lv);
}

static void dd_distribute_vec(gmx_domdec_t *dd,t_block *cgs,rvec *v,rvec *lv)
{
    if (dd->nnodes <= GMX_DD_NNODES_SENDRECV)
    {
        dd_distribute_vec_sendrecv(dd,cgs,v,lv);
    }
    else
    {
        dd_distribute_vec_scatterv(dd,cgs,v,lv);
    }
}

static void dd_distribute_state(gmx_domdec_t *dd,t_block *cgs,
                                t_state *state,t_state *state_local,
                                rvec **f)
{
    int  i,j,ngtch,ngtcp,nh;

    nh = state->nhchainlength;

    if (DDMASTER(dd))
    {
        state_local->lambda = state->lambda;
        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);
        for(i=0; i<state_local->ngtc; i++)
        {
            for(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(i=0; i<state_local->nnhpres; i++)
        {
            for(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];
            }
        }
    }
    dd_bcast(dd,sizeof(real),&state_local->lambda);
    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);
    dd_bcast(dd,((state_local->ngtc*nh)*sizeof(double)),state_local->nosehoover_vxi);
    dd_bcast(dd,state_local->ngtc*sizeof(double),state_local->therm_integral);
    dd_bcast(dd,((state_local->nnhpres*nh)*sizeof(double)),state_local->nhpres_xi);
    dd_bcast(dd,((state_local->nnhpres*nh)*sizeof(double)),state_local->nhpres_vxi);

    if (dd->nat_home > state_local->nalloc)
    {
        dd_realloc_state(state_local,f,dd->nat_home);
    }
    for(i=0; i<estNR; i++)
    {
        if (EST_DISTR(i) && state_local->flags & (1<<i))
        {
            switch (i) {
            case estX:
                dd_distribute_vec(dd,cgs,state->x,state_local->x);
                break;
            case estV:
                dd_distribute_vec(dd,cgs,state->v,state_local->v);
                break;
            case estSDX:
                dd_distribute_vec(dd,cgs,state->sd_X,state_local->sd_X);
                break;
            case estCGP:
                dd_distribute_vec(dd,cgs,state->cg_p,state_local->cg_p);
                break;
            case estLD_RNG:
                if (state->nrngi == 1)
                {
                    dd_bcastc(dd,
                              state_local->nrng*sizeof(state_local->ld_rng[0]),
                              state->ld_rng,state_local->ld_rng);
                }
                else
                {
                    dd_scatter(dd,
                               state_local->nrng*sizeof(state_local->ld_rng[0]),
                               state->ld_rng,state_local->ld_rng);
                }
                break;
            case estLD_RNGI:
                if (state->nrngi == 1)
                {
                    dd_bcastc(dd,sizeof(state_local->ld_rngi[0]),
                              state->ld_rngi,state_local->ld_rngi);
                }
                else
                {
                     dd_scatter(dd,sizeof(state_local->ld_rngi[0]),
                               state->ld_rngi,state_local->ld_rngi);
                }   
                break;
            case estDISRE_INITF:
            case estDISRE_RM3TAV:
            case estORIRE_INITF:
            case estORIRE_DTAV:
                /* Not implemented yet */
                break;
            default:
                gmx_incons("Unknown state entry encountered in dd_distribute_state");
            }
        }
    }
}

static char dim2char(int dim)
{
    char c='?';
    
    switch (dim)
    {
    case XX: c = 'X'; break;
    case YY: c = 'Y'; break;
    case ZZ: c = 'Z'; break;
    default: gmx_fatal(FARGS,"Unknown dim %d",dim);
    }
    
    return c;
}

static void write_dd_grid_pdb(const char *fn,gmx_large_int_t step,
                              gmx_domdec_t *dd,matrix box,gmx_ddbox_t *ddbox)
{
    rvec grid_s[2],*grid_r=NULL,cx,r;
    char fname[STRLEN],format[STRLEN],buf[22];
    FILE *out;
    int  a,i,d,z,y,x;
    matrix tric;
    real vol;

    copy_rvec(dd->comm->cell_x0,grid_s[0]);
    copy_rvec(dd->comm->cell_x1,grid_s[1]);
    
    if (DDMASTER(dd))
    {
        snew(grid_r,2*dd->nnodes);
    }
    
    dd_gather(dd,2*sizeof(rvec),grid_s[0],DDMASTER(dd) ? grid_r[0] : NULL);
    
    if (DDMASTER(dd))
    {
        for(d=0; d<DIM; d++)
        {
            for(i=0; i<DIM; i++)
            {
                if (d == i)
                {
                    tric[d][i] = 1;
                }
                else
                {
                    if (dd->nc[d] > 1 && d < ddbox->npbcdim)
                    {
                        tric[d][i] = box[i][d]/box[i][i];
                    }
                    else
                    {
                        tric[d][i] = 0;
                    }
                }
            }
        }
        sprintf(fname,"%s_%s.pdb",fn,gmx_step_str(step,buf));
        sprintf(format,"%s%s\n",pdbformat,"%6.2f%6.2f");
        out = gmx_fio_fopen(fname,"w");
        gmx_write_pdb_box(out,dd->bScrewPBC ? epbcSCREW : epbcXYZ,box);
        a = 1;
        for(i=0; i<dd->nnodes; i++)
        {
            vol = dd->nnodes/(box[XX][XX]*box[YY][YY]*box[ZZ][ZZ]);
            for(d=0; d<DIM; d++)
            {
                vol *= grid_r[i*2+1][d] - grid_r[i*2][d];
            }
            for(z=0; z<2; z++)
            {
                for(y=0; y<2; y++)
                {
                    for(x=0; x<2; x++)
                    {
                        cx[XX] = grid_r[i*2+x][XX];
                        cx[YY] = grid_r[i*2+y][YY];
                        cx[ZZ] = grid_r[i*2+z][ZZ];
                        mvmul(tric,cx,r);
                        fprintf(out,format,"ATOM",a++,"CA","GLY",' ',1+i,
                                10*r[XX],10*r[YY],10*r[ZZ],1.0,vol);
                    }
                }
            }
            for(d=0; d<DIM; d++)
            {
                for(x=0; x<4; x++)
                {
                    switch(d)
                    {
                    case 0: y = 1 + i*8 + 2*x; break;
                    case 1: y = 1 + i*8 + 2*x - (x % 2); break;
                    case 2: y = 1 + i*8 + x; break;
                    }
                    fprintf(out,"%6s%5d%5d\n","CONECT",y,y+(1<<d));
                }
            }
        }
        gmx_fio_fclose(out);
        sfree(grid_r);
    }
}

void write_dd_pdb(const char *fn,gmx_large_int_t step,const char *title,
                  gmx_mtop_t *mtop,t_commrec *cr,
                  int natoms,rvec x[],matrix box)
{
    char fname[STRLEN],format[STRLEN],format4[STRLEN],buf[22];
    FILE *out;
    int  i,ii,resnr,c;
    char *atomname,*resname;
    real b;
    gmx_domdec_t *dd;
    
    dd = cr->dd;
    if (natoms == -1)
    {
        natoms = dd->comm->nat[ddnatVSITE];
    }
    
    sprintf(fname,"%s_%s_n%d.pdb",fn,gmx_step_str(step,buf),cr->sim_nodeid);
    
    sprintf(format,"%s%s\n",pdbformat,"%6.2f%6.2f");
    sprintf(format4,"%s%s\n",pdbformat4,"%6.2f%6.2f");
    
    out = gmx_fio_fopen(fname,"w");
    
    fprintf(out,"TITLE     %s\n",title);
    gmx_write_pdb_box(out,dd->bScrewPBC ? epbcSCREW : epbcXYZ,box);
    for(i=0; i<natoms; i++)
    {
        ii = dd->gatindex[i];
        gmx_mtop_atominfo_global(mtop,ii,&atomname,&resnr,&resname);
        if (i < dd->comm->nat[ddnatZONE])
        {
            c = 0;
            while (i >= dd->cgindex[dd->comm->zones.cg_range[c+1]])
            {
                c++;
            }
            b = c;
        }
        else if (i < dd->comm->nat[ddnatVSITE])
        {
            b = dd->comm->zones.n;
        }
        else
        {
            b = dd->comm->zones.n + 1;
        }
        fprintf(out,strlen(atomname)<4 ? format : format4,
                "ATOM",(ii+1)%100000,
                atomname,resname,' ',(resnr+1)%10000,' ',
                10*x[i][XX],10*x[i][YY],10*x[i][ZZ],1.0,b);
    }
    fprintf(out,"TER\n");
    
    gmx_fio_fclose(out);
}

real dd_cutoff_mbody(gmx_domdec_t *dd)
{
    gmx_domdec_comm_t *comm;
    int  di;
    real r;

    comm = dd->comm;

    r = -1;
    if (comm->bInterCGBondeds)
    {
        if (comm->cutoff_mbody > 0)
        {
            r = comm->cutoff_mbody;
        }
        else
        {
            /* cutoff_mbody=0 means we do not have DLB */
            r = comm->cellsize_min[dd->dim[0]];
            for(di=1; di<dd->ndim; di++)
            {
                r = min(r,comm->cellsize_min[dd->dim[di]]);
            }
            if (comm->bBondComm)
            {
                r = max(r,comm->cutoff_mbody);
            }
            else
            {
                r = min(r,comm->cutoff);
            }
        }
    }

    return r;
}

real dd_cutoff_twobody(gmx_domdec_t *dd)
{
    real r_mb;

    r_mb = dd_cutoff_mbody(dd);

    return max(dd->comm->cutoff,r_mb);
}


static void dd_cart_coord2pmecoord(gmx_domdec_t *dd,ivec coord,ivec coord_pme)
{
    int nc,ntot;
    
    nc   = dd->nc[dd->comm->cartpmedim];
    ntot = dd->comm->ntot[dd->comm->cartpmedim];
    copy_ivec(coord,coord_pme);
    coord_pme[dd->comm->cartpmedim] =
        nc + (coord[dd->comm->cartpmedim]*(ntot - nc) + (ntot - nc)/2)/nc;
}

static int low_ddindex2pmeindex(int ndd,int npme,int ddindex)
{
    /* Here we assign a PME node to communicate with this DD node
     * by assuming that the major index of both is x.
     * We add cr->npmenodes/2 to obtain an even distribution.
     */
    return (ddindex*npme + npme/2)/ndd;
}

static int ddindex2pmeindex(const gmx_domdec_t *dd,int ddindex)
{
    return low_ddindex2pmeindex(dd->nnodes,dd->comm->npmenodes,ddindex);
}

static int cr_ddindex2pmeindex(const t_commrec *cr,int ddindex)
{
    return low_ddindex2pmeindex(cr->dd->nnodes,cr->npmenodes,ddindex);
}

static int *dd_pmenodes(t_commrec *cr)
{
    int *pmenodes;
    int n,i,p0,p1;
    
    snew(pmenodes,cr->npmenodes);
    n = 0;
    for(i=0; i<cr->dd->nnodes; i++) {
        p0 = cr_ddindex2pmeindex(cr,i);
        p1 = cr_ddindex2pmeindex(cr,i+1);
        if (i+1 == cr->dd->nnodes || p1 > p0) {
            if (debug)
                fprintf(debug,"pmenode[%d] = %d\n",n,i+1+n);
            pmenodes[n] = i + 1 + n;
            n++;
        }
    }

    return pmenodes;
}

static int gmx_ddcoord2pmeindex(t_commrec *cr,int x,int y,int z)
{
    gmx_domdec_t *dd;
    ivec coords,coords_pme,nc;
    int  slab;
    
    dd = cr->dd;
    /*
      if (dd->comm->bCartesian) {
      gmx_ddindex2xyz(dd->nc,ddindex,coords);
      dd_coords2pmecoords(dd,coords,coords_pme);
      copy_ivec(dd->ntot,nc);
      nc[dd->cartpmedim]         -= dd->nc[dd->cartpmedim];
      coords_pme[dd->cartpmedim] -= dd->nc[dd->cartpmedim];
      
      slab = (coords_pme[XX]*nc[YY] + coords_pme[YY])*nc[ZZ] + coords_pme[ZZ];
      } else {
      slab = (ddindex*cr->npmenodes + cr->npmenodes/2)/dd->nnodes;
      }
    */
    coords[XX] = x;
    coords[YY] = y;
    coords[ZZ] = z;
    slab = ddindex2pmeindex(dd,dd_index(dd->nc,coords));
    
    return slab;
}

static int ddcoord2simnodeid(t_commrec *cr,int x,int y,int z)
{
    gmx_domdec_comm_t *comm;
    ivec coords;
    int  ddindex,nodeid=-1;
    
    comm = cr->dd->comm;
    
    coords[XX] = x;
    coords[YY] = y;
    coords[ZZ] = z;
    if (comm->bCartesianPP_PME)
    {
#ifdef GMX_MPI
        MPI_Cart_rank(cr->mpi_comm_mysim,coords,&nodeid);
#endif
    }
    else
    {
        ddindex = dd_index(cr->dd->nc,coords);
        if (comm->bCartesianPP)
        {
            nodeid = comm->ddindex2simnodeid[ddindex];
        }
        else
        {
            if (comm->pmenodes)
            {
                nodeid = ddindex + gmx_ddcoord2pmeindex(cr,x,y,z);
            }
            else
            {
                nodeid = ddindex;
            }
        }
    }
  
    return nodeid;
}

static int dd_simnode2pmenode(t_commrec *cr,int sim_nodeid)
{
    gmx_domdec_t *dd;
    gmx_domdec_comm_t *comm;
    ivec coord,coord_pme;
    int  i;
    int  pmenode=-1;
    
    dd = cr->dd;
    comm = dd->comm;
    
    /* This assumes a uniform x domain decomposition grid cell size */
    if (comm->bCartesianPP_PME)
    {
#ifdef GMX_MPI
        MPI_Cart_coords(cr->mpi_comm_mysim,sim_nodeid,DIM,coord);
        if (coord[comm->cartpmedim] < dd->nc[comm->cartpmedim])
        {
            /* This is a PP node */
            dd_cart_coord2pmecoord(dd,coord,coord_pme);
            MPI_Cart_rank(cr->mpi_comm_mysim,coord_pme,&pmenode);
        }
#endif
    }
    else if (comm->bCartesianPP)
    {
        if (sim_nodeid < dd->nnodes)
        {
            pmenode = dd->nnodes + ddindex2pmeindex(dd,sim_nodeid);
        }
    }
    else
    {
        /* This assumes DD cells with identical x coordinates
         * are numbered sequentially.
         */
        if (dd->comm->pmenodes == NULL)
        {
            if (sim_nodeid < dd->nnodes)
            {
                /* The DD index equals the nodeid */
                pmenode = dd->nnodes + ddindex2pmeindex(dd,sim_nodeid);
            }
        }
        else
        {
            i = 0;
            while (sim_nodeid > dd->comm->pmenodes[i])
            {
                i++;
            }
            if (sim_nodeid < dd->comm->pmenodes[i])
            {
                pmenode = dd->comm->pmenodes[i];
            }
        }
    }
    
    return pmenode;
}

bool gmx_pmeonlynode(t_commrec *cr,int sim_nodeid)
{
    bool bPMEOnlyNode;
    
    if (DOMAINDECOMP(cr))
    {
        bPMEOnlyNode = (dd_simnode2pmenode(cr,sim_nodeid) == -1);
    }
    else
    {
        bPMEOnlyNode = FALSE;
    }
    
    return bPMEOnlyNode;
}

void get_pme_ddnodes(t_commrec *cr,int pmenodeid,
                     int *nmy_ddnodes,int **my_ddnodes,int *node_peer)
{
    gmx_domdec_t *dd;
    int x,y,z;
    ivec coord,coord_pme;
    
    dd = cr->dd;
    
    snew(*my_ddnodes,(dd->nnodes+cr->npmenodes-1)/cr->npmenodes);
    
    *nmy_ddnodes = 0;
    for(x=0; x<dd->nc[XX]; x++)
    {
        for(y=0; y<dd->nc[YY]; y++)
        {
            for(z=0; z<dd->nc[ZZ]; z++)
            {
                if (dd->comm->bCartesianPP_PME)
                {
                    coord[XX] = x;
                    coord[YY] = y;
                    coord[ZZ] = z;
                    dd_cart_coord2pmecoord(dd,coord,coord_pme);
                    if (dd->ci[XX] == coord_pme[XX] &&
                        dd->ci[YY] == coord_pme[YY] &&
                        dd->ci[ZZ] == coord_pme[ZZ])
                        (*my_ddnodes)[(*nmy_ddnodes)++] = ddcoord2simnodeid(cr,x,y,z);
                }
                else
                {
                    /* The slab corresponds to the nodeid in the PME group */
                    if (gmx_ddcoord2pmeindex(cr,x,y,z) == pmenodeid)
                    {
                        (*my_ddnodes)[(*nmy_ddnodes)++] = ddcoord2simnodeid(cr,x,y,z);
                    }
                }
            }
        }
    }
    
    /* The last PP-only node is the peer node */
    *node_peer = (*my_ddnodes)[*nmy_ddnodes-1];
    
    if (debug)
    {
        fprintf(debug,"Receive coordinates from PP nodes:");
        for(x=0; x<*nmy_ddnodes; x++)
        {
            fprintf(debug," %d",(*my_ddnodes)[x]);
        }
        fprintf(debug,"\n");
    }
}

static bool receive_vir_ener(t_commrec *cr)
{
    gmx_domdec_comm_t *comm;
    int  pmenode,coords[DIM],rank;
    bool bReceive;
    
    bReceive = TRUE;
    if (cr->npmenodes < cr->dd->nnodes)
    {
        comm = cr->dd->comm;
        if (comm->bCartesianPP_PME)
        {
            pmenode = dd_simnode2pmenode(cr,cr->sim_nodeid);
#ifdef GMX_MPI
            MPI_Cart_coords(cr->mpi_comm_mysim,cr->sim_nodeid,DIM,coords);
            coords[comm->cartpmedim]++;
            if (coords[comm->cartpmedim] < cr->dd->nc[comm->cartpmedim])
            {
                MPI_Cart_rank(cr->mpi_comm_mysim,coords,&rank);
                if (dd_simnode2pmenode(cr,rank) == pmenode)
                {
                    /* This is not the last PP node for pmenode */
                    bReceive = FALSE;
                }
            }
#endif  
        }
        else
        {
            pmenode = dd_simnode2pmenode(cr,cr->sim_nodeid);
            if (cr->sim_nodeid+1 < cr->nnodes &&
                dd_simnode2pmenode(cr,cr->sim_nodeid+1) == pmenode)
            {
                /* This is not the last PP node for pmenode */
                bReceive = FALSE;
            }
        }
    }
    
    return bReceive;
}

static void set_zones_ncg_home(gmx_domdec_t *dd)
{
    gmx_domdec_zones_t *zones;
    int i;

    zones = &dd->comm->zones;

    zones->cg_range[0] = 0;
    for(i=1; i<zones->n+1; i++)
    {
        zones->cg_range[i] = dd->ncg_home;
    }
}

static void rebuild_cgindex(gmx_domdec_t *dd,int *gcgs_index,t_state *state)
{
    int nat,i,*ind,*dd_cg_gl,*cgindex,cg_gl;
    
    ind = state->cg_gl;
    dd_cg_gl = dd->index_gl;
    cgindex  = dd->cgindex;
    nat = 0;
    cgindex[0] = nat;
    for(i=0; i<state->ncg_gl; i++)
    {
        cgindex[i] = nat;
        cg_gl = ind[i];
        dd_cg_gl[i] = cg_gl;
        nat += gcgs_index[cg_gl+1] - gcgs_index[cg_gl];
    }
    cgindex[i] = nat;
    
    dd->ncg_home = state->ncg_gl;
    dd->nat_home = nat;

    set_zones_ncg_home(dd);
}

static int ddcginfo(const cginfo_mb_t *cginfo_mb,int cg)
{
    while (cg >= cginfo_mb->cg_end)
    {
        cginfo_mb++;
    }

    return cginfo_mb->cginfo[(cg - cginfo_mb->cg_start) % cginfo_mb->cg_mod];
}

static void dd_set_cginfo(int *index_gl,int cg0,int cg1,
                          t_forcerec *fr,char *bLocalCG)
{
    cginfo_mb_t *cginfo_mb;
    int *cginfo;
    int cg;

    if (fr != NULL)
    {
        cginfo_mb = fr->cginfo_mb;
        cginfo    = fr->cginfo;

        for(cg=cg0; cg<cg1; cg++)
        {
            cginfo[cg] = ddcginfo(cginfo_mb,index_gl[cg]);
        }
    }

    if (bLocalCG != NULL)
    {
        for(cg=cg0; cg<cg1; cg++)
        {
            bLocalCG[index_gl[cg]] = TRUE;
        }
    }
}

static void make_dd_indices(gmx_domdec_t *dd,int *gcgs_index,int cg_start)
{
    int nzone,zone,zone1,cg0,cg,cg_gl,a,a_gl;
    int *zone2cg,*zone_ncg1,*index_gl,*gatindex;
    gmx_ga2la_t *ga2la;
    char *bLocalCG;

    bLocalCG = dd->comm->bLocalCG;

    if (dd->nat_tot > dd->gatindex_nalloc)
    {
        dd->gatindex_nalloc = over_alloc_dd(dd->nat_tot);
        srenew(dd->gatindex,dd->gatindex_nalloc);
    }

    nzone      = dd->comm->zones.n;
    zone2cg    = dd->comm->zones.cg_range;
    zone_ncg1  = dd->comm->zone_ncg1;
    index_gl   = dd->index_gl;
    gatindex   = dd->gatindex;

    if (zone2cg[1] != dd->ncg_home)
    {
        gmx_incons("dd->ncg_zone is not up to date");
    }
    
    /* Make the local to global and global to local atom index */
    a = dd->cgindex[cg_start];
    for(zone=0; zone<nzone; zone++)
    {
        if (zone == 0)
        {
            cg0 = cg_start;
        }
        else
        {
            cg0 = zone2cg[zone];
        }
        for(cg=cg0; cg<zone2cg[zone+1]; cg++)
        {
            zone1 = zone;
            if (cg - cg0 >= zone_ncg1[zone])
            {
                /* Signal that this cg is from more than one zone away */
                zone1 += nzone;
            }
            cg_gl = index_gl[cg];
            for(a_gl=gcgs_index[cg_gl]; a_gl<gcgs_index[cg_gl+1]; a_gl++)
            {
                gatindex[a] = a_gl;
                ga2la_set(dd->ga2la,a_gl,a,zone1);
                a++;
            }
        }
    }
}

static int check_bLocalCG(gmx_domdec_t *dd,int ncg_sys,const char *bLocalCG,
                          const char *where)
{
    int ncg,i,ngl,nerr;

    nerr = 0;
    if (bLocalCG == NULL)
    {
        return nerr;
    }
    for(i=0; i<dd->ncg_tot; i++)
    {
        if (!bLocalCG[dd->index_gl[i]])
        {
            fprintf(stderr,
                    "DD node %d, %s: cg %d, global cg %d is not marked in bLocalCG (ncg_home %d)\n",dd->rank,where,i+1,dd->index_gl[i]+1,dd->ncg_home);
            nerr++;
        }
    }
    ngl = 0;
    for(i=0; i<ncg_sys; i++)
    {
        if (bLocalCG[i])
        {
            ngl++;
        }
    }
    if (ngl != dd->ncg_tot)
    {
        fprintf(stderr,"DD node %d, %s: In bLocalCG %d cgs are marked as local, whereas there are %d\n",dd->rank,where,ngl,dd->ncg_tot);
        nerr++;
    }

    return nerr;
}

static void check_index_consistency(gmx_domdec_t *dd,
                                    int natoms_sys,int ncg_sys,
                                    const char *where)
{
    int  nerr,ngl,i,a,cell;
    int  *have;

    nerr = 0;

    if (dd->comm->DD_debug > 1)
    {
        snew(have,natoms_sys);
        for(a=0; a<dd->nat_tot; a++)
        {
            if (have[dd->gatindex[a]] > 0)
            {
                fprintf(stderr,"DD node %d: global atom %d occurs twice: index %d and %d\n",dd->rank,dd->gatindex[a]+1,have[dd->gatindex[a]],a+1);
            }
            else
            {
                have[dd->gatindex[a]] = a + 1;
            }
        }
        sfree(have);
    }

    snew(have,dd->nat_tot);

    ngl  = 0;
    for(i=0; i<natoms_sys; i++)
    {
        if (ga2la_get(dd->ga2la,i,&a,&cell))
        {
            if (a >= dd->nat_tot)
            {
                fprintf(stderr,"DD node %d: global atom %d marked as local atom %d, which is larger than nat_tot (%d)\n",dd->rank,i+1,a+1,dd->nat_tot);
                nerr++;
            }
            else
            {
                have[a] = 1;
                if (dd->gatindex[a] != i)
                {
                    fprintf(stderr,"DD node %d: global atom %d marked as local atom %d, which has global atom index %d\n",dd->rank,i+1,a+1,dd->gatindex[a]+1);
                    nerr++;
                }
            }
            ngl++;
        }
    }
    if (ngl != dd->nat_tot)
    {
        fprintf(stderr,
                "DD node %d, %s: %d global atom indices, %d local atoms\n",
                dd->rank,where,ngl,dd->nat_tot);
    }
    for(a=0; a<dd->nat_tot; a++)
    {
        if (have[a] == 0)
        {
            fprintf(stderr,
                    "DD node %d, %s: local atom %d, global %d has no global index\n",
                    dd->rank,where,a+1,dd->gatindex[a]+1);
        }
    }
    sfree(have);

    nerr += check_bLocalCG(dd,ncg_sys,dd->comm->bLocalCG,where);

    if (nerr > 0) {
        gmx_fatal(FARGS,"DD node %d, %s: %d atom/cg index inconsistencies",
                  dd->rank,where,nerr);
    }
}

static void clear_dd_indices(gmx_domdec_t *dd,int cg_start,int a_start)
{
    int  i;
    char *bLocalCG;

    if (a_start == 0)
    {
        /* Clear the whole list without searching */
        ga2la_clear(dd->ga2la);
    }
    else
    {
        for(i=a_start; i<dd->nat_tot; i++)
        {
            ga2la_del(dd->ga2la,dd->gatindex[i]);
        }
    }

    bLocalCG = dd->comm->bLocalCG;
    if (bLocalCG)
    {
        for(i=cg_start; i<dd->ncg_tot; i++)
        {
            bLocalCG[dd->index_gl[i]] = FALSE;
        }
    }

    dd_clear_local_vsite_indices(dd);
    
    if (dd->constraints)
    {
        dd_clear_local_constraint_indices(dd);
    }
}

static real grid_jump_limit(gmx_domdec_comm_t *comm,int dim_ind)
{
    real grid_jump_limit;

    /* The distance between the boundaries of cells at distance
     * x+-1,y+-1 or y+-1,z+-1 is limited by the cut-off restrictions
     * and by the fact that cells should not be shifted by more than
     * half their size, such that cg's only shift by one cell
     * at redecomposition.
     */
    grid_jump_limit = comm->cellsize_limit;
    if (!comm->bVacDLBNoLimit)
    {
        grid_jump_limit = max(grid_jump_limit,
                              comm->cutoff/comm->cd[dim_ind].np);
    }

    return grid_jump_limit;
}

static void check_grid_jump(gmx_large_int_t step,gmx_domdec_t *dd,gmx_ddbox_t *ddbox)
{
    gmx_domdec_comm_t *comm;
    int  d,dim;
    real limit,bfac;
    
    comm = dd->comm;
    
    for(d=1; d<dd->ndim; d++)
    {
        dim = dd->dim[d];
        limit = grid_jump_limit(comm,d);
        bfac = ddbox->box_size[dim];
        if (ddbox->tric_dir[dim])
        {
            bfac *= ddbox->skew_fac[dim];
        }
        if ((comm->cell_f1[d] - comm->cell_f_max0[d])*bfac <  limit ||
            (comm->cell_f0[d] - comm->cell_f_min1[d])*bfac > -limit)
        {
            char buf[22];
            gmx_fatal(FARGS,"Step %s: The domain decomposition grid has shifted too much in the %c-direction around cell %d %d %d\n",
                      gmx_step_str(step,buf),
                      dim2char(dim),dd->ci[XX],dd->ci[YY],dd->ci[ZZ]);
        }
    }
}

static int dd_load_count(gmx_domdec_comm_t *comm)
{
    return (comm->eFlop ? comm->flop_n : comm->cycl_n[ddCyclF]);
}

static float dd_force_load(gmx_domdec_comm_t *comm)
{
    float load;
    
    if (comm->eFlop)
    {
        load = comm->flop;
        if (comm->eFlop > 1)
        {
            load *= 1.0 + (comm->eFlop - 1)*(0.1*rand()/RAND_MAX - 0.05);
        }
    } 
    else
    {
        load = comm->cycl[ddCyclF];
        if (comm->cycl_n[ddCyclF] > 1)
        {
            /* Subtract the maximum of the last n cycle counts
             * to get rid of possible high counts due to other soures,
             * for instance system activity, that would otherwise
             * affect the dynamic load balancing.
             */
            load -= comm->cycl_max[ddCyclF];
        }
    }
    
    return load;
}

static void set_slb_pme_dim_f(gmx_domdec_t *dd,int dimind,real **dim_f)
{
    gmx_domdec_comm_t *comm;
    int i;
    
    comm = dd->comm;
    
    if (dd->dim[dimind] != dimind)
    {
        *dim_f = NULL;
        return;
    }
    
    snew(*dim_f,dd->nc[dimind]+1);
    (*dim_f)[0] = 0;
    for(i=1; i<dd->nc[dimind]; i++)
    {
        if (comm->slb_frac[dimind])
        {
            (*dim_f)[i] = (*dim_f)[i-1] + comm->slb_frac[dimind][i-1];
        }
        else
        {
            (*dim_f)[i] = (real)i/(real)dd->nc[dimind];
        }
    }
    (*dim_f)[dd->nc[dimind]] = 1;
}

static void init_ddpme(gmx_domdec_t *dd,gmx_ddpme_t *ddpme,
                       int dimind,int nslab)
{
    int  pmeindex,slab,nso,i;
    ivec xyz;
    
    ddpme->dimind = dimind;
    ddpme->nslab  = nslab;

    if (nslab <= 1)
    {
        return;
    }

    nso = dd->comm->npmenodes/nslab;
    /* Determine for each PME slab the PP location range for dimension dim */
    snew(ddpme->pp_min,nslab);
    snew(ddpme->pp_max,nslab);
    for(slab=0; slab<nslab; slab++) {
        ddpme->pp_min[slab] = dd->nc[dd->dim[dimind]] - 1;
        ddpme->pp_max[slab] = 0;
    }
    for(i=0; i<dd->nnodes; i++) {
        ddindex2xyz(dd->nc,i,xyz);
        /* For y only use our y/z slab.
         * This assumes that the PME x grid size matches the DD grid size.
         */
        if (dimind == 0 || xyz[XX] == dd->ci[XX]) {
            pmeindex = ddindex2pmeindex(dd,i);
            if (dimind == 0) {
                slab = pmeindex/nso;
            } else {
                slab = pmeindex % nslab;
            }
            ddpme->pp_min[slab] = min(ddpme->pp_min[slab],xyz[dimind]);
            ddpme->pp_max[slab] = max(ddpme->pp_max[slab],xyz[dimind]);
        }
    }

    set_slb_pme_dim_f(dd,ddpme->dimind,&ddpme->slb_dim_f);
}

int dd_pme_maxshift0(gmx_domdec_t *dd)
{
    return dd->comm->ddpme[0].maxshift;
}

int dd_pme_maxshift1(gmx_domdec_t *dd)
{
    return dd->comm->ddpme[1].maxshift;
}

static void set_pme_maxshift(gmx_domdec_t *dd,gmx_ddpme_t *ddpme,
                             bool bUniform,gmx_ddbox_t *ddbox,real *cell_f)
{
    gmx_domdec_comm_t *comm;
    int  dim,nc,ns,s;
    int  *xmin,*xmax;
    real range,pme_boundary;
    int  sh;
    
    comm = dd->comm;
    dim = ddpme->dimind;
    nc  = dd->nc[dim];
    ns  = ddpme->nslab;
    
    if (dd->dim[dim] != dim)
    {
        /* PP decomposition is not along dim: the worst situation */
        sh = ns/2;
    }
    else if (ns <= 3 || (bUniform && ns == nc))
    {
        /* The optimal situation */
        sh = 1;
    }
    else
    {
        /* We need to check for all pme nodes which nodes they
         * could possibly need to communicate with.
         */
        xmin = ddpme->pp_min;
        xmax = ddpme->pp_max;
        /* Allow for atoms to be maximally 2/3 times the cut-off
         * out of their DD cell. This is a reasonable balance between
         * between performance and support for most charge-group/cut-off
         * combinations.
         */
        range  = 2.0/3.0*comm->cutoff/ddbox->box_size[dim];
        /* Avoid extra communication when we are exactly at a boundary */
        range *= 0.999;
        
        sh = 1;
        for(s=0; s<ns; s++)
        {
            /* PME slab s spreads atoms between box frac. s/ns and (s+1)/ns */
            pme_boundary = (real)s/ns;
            while (sh+1 < ns &&
                   ((s-(sh+1) >= 0 &&
                     cell_f[xmax[s-(sh+1)   ]+1]     + range > pme_boundary) ||
                    (s-(sh+1) <  0 &&
                     cell_f[xmax[s-(sh+1)+ns]+1] - 1 + range > pme_boundary)))
            {
                sh++;
            }
            pme_boundary = (real)(s+1)/ns;
            while (sh+1 < ns &&
                   ((s+(sh+1) <  ns &&
                     cell_f[xmin[s+(sh+1)   ]  ]     - range < pme_boundary) ||
                    (s+(sh+1) >= ns &&
                     cell_f[xmin[s+(sh+1)-ns]  ] + 1 - range < pme_boundary)))
            {
                sh++;
            }
        }
    }
    
    ddpme->maxshift = sh;
    
    if (debug)
    {
        fprintf(debug,"PME slab communication range for dimind %d is %d\n",
                ddpme->dimind,ddpme->maxshift);
    }
}

static void check_box_size(gmx_domdec_t *dd,gmx_ddbox_t *ddbox)
{
    int d,dim;
    
    for(d=0; d<dd->ndim; d++)
    {
        dim = dd->dim[d];
        if (dim < ddbox->nboundeddim &&
            ddbox->box_size[dim]*ddbox->skew_fac[dim] <
            dd->nc[dim]*dd->comm->cellsize_limit*DD_CELL_MARGIN)
        {
            gmx_fatal(FARGS,"The %c-size of the box (%f) times the triclinic skew factor (%f) is smaller than the number of DD cells (%d) times the smallest allowed cell size (%f)\n",
                      dim2char(dim),ddbox->box_size[dim],ddbox->skew_fac[dim],
                      dd->nc[dim],dd->comm->cellsize_limit);
        }
    }
}

static void set_dd_cell_sizes_slb(gmx_domdec_t *dd,gmx_ddbox_t *ddbox,
                                  bool bMaster,ivec npulse)
{
    gmx_domdec_comm_t *comm;
    int  d,j;
    rvec cellsize_min;
    real *cell_x,cell_dx,cellsize;
    
    comm = dd->comm;
    
    for(d=0; d<DIM; d++)
    {
        cellsize_min[d] = ddbox->box_size[d]*ddbox->skew_fac[d];
        npulse[d] = 1;
        if (dd->nc[d] == 1 || comm->slb_frac[d] == NULL)
        {
            /* Uniform grid */
            cell_dx = ddbox->box_size[d]/dd->nc[d];
            if (bMaster)
            {
                for(j=0; j<dd->nc[d]+1; j++)
                {
                    dd->ma->cell_x[d][j] = ddbox->box0[d] + j*cell_dx;
                }
            }
            else
            {
                comm->cell_x0[d] = ddbox->box0[d] + (dd->ci[d]  )*cell_dx;
                comm->cell_x1[d] = ddbox->box0[d] + (dd->ci[d]+1)*cell_dx;
            }
            cellsize = cell_dx*ddbox->skew_fac[d];
            while (cellsize*npulse[d] < comm->cutoff && npulse[d] < dd->nc[d]-1)
            {
                npulse[d]++;
            }
            cellsize_min[d] = cellsize;
        }
        else
        {
            /* Statically load balanced grid */
            /* Also when we are not doing a master distribution we determine
             * all cell borders in a loop to obtain identical values
             * to the master distribution case and to determine npulse.
             */
            if (bMaster)
            {
                cell_x = dd->ma->cell_x[d];
            }
            else
            {
                snew(cell_x,dd->nc[d]+1);
            }
            cell_x[0] = ddbox->box0[d];
            for(j=0; j<dd->nc[d]; j++)
            {
                cell_dx = ddbox->box_size[d]*comm->slb_frac[d][j];
                cell_x[j+1] = cell_x[j] + cell_dx;
                cellsize = cell_dx*ddbox->skew_fac[d];
                while (cellsize*npulse[d] < comm->cutoff &&
                       npulse[d] < dd->nc[d]-1)
                {
                    npulse[d]++;
                }
                cellsize_min[d] = min(cellsize_min[d],cellsize);
            }
            if (!bMaster)
            {
                comm->cell_x0[d] = cell_x[dd->ci[d]];
                comm->cell_x1[d] = cell_x[dd->ci[d]+1];
                sfree(cell_x);
            }
        }
        /* The following limitation is to avoid that a cell would receive
         * some of its own home charge groups back over the periodic boundary.
         * Double charge groups cause trouble with the global indices.
         */
        if (d < ddbox->npbcdim &&
            dd->nc[d] > 1 && npulse[d] >= dd->nc[d])
        {
            gmx_fatal_collective(FARGS,DDMASTER(dd),
                                 "The box size in direction %c (%f) times the triclinic skew factor (%f) is too small for a cut-off of %f with %d domain decomposition cells, use 1 or more than %d %s or increase the box size in this direction",
                                 dim2char(d),ddbox->box_size[d],ddbox->skew_fac[d],
                                 comm->cutoff,
                                 dd->nc[d],dd->nc[d],
                                 dd->nnodes > dd->nc[d] ? "cells" : "processors");
        }
    }
    
    if (!comm->bDynLoadBal)
    {
        copy_rvec(cellsize_min,comm->cellsize_min);
    }
   
    for(d=0; d<comm->npmedecompdim; d++)
    {
        set_pme_maxshift(dd,&comm->ddpme[d],
                         comm->slb_frac[dd->dim[d]]==NULL,ddbox,
                         comm->ddpme[d].slb_dim_f);
    }
}


static void dd_cell_sizes_dlb_root_enforce_limits(gmx_domdec_t *dd,
                                       int d,int dim,gmx_domdec_root_t *root,
                                       gmx_ddbox_t *ddbox,
                                       bool bUniform,gmx_large_int_t step, real cellsize_limit_f, int range[])
{
    gmx_domdec_comm_t *comm;
    int  ncd,i,j,nmin,nmin_old;
    bool bLimLo,bLimHi;
    real *cell_size;
    real fac,halfway,cellsize_limit_f_i,region_size;
    bool bPBC,bLastHi=FALSE;
    int nrange[]={range[0],range[1]};

    region_size= root->cell_f[range[1]]-root->cell_f[range[0]];  

    comm = dd->comm;

    ncd = dd->nc[dim];

    bPBC = (dim < ddbox->npbcdim);

    cell_size = root->buf_ncd;

    if (debug) 
    {
        fprintf(debug,"enforce_limits: %d %d\n",range[0],range[1]);
    }

    /* First we need to check if the scaling does not make cells
     * smaller than the smallest allowed size.
     * We need to do this iteratively, since if a cell is too small,
     * it needs to be enlarged, which makes all the other cells smaller,
     * which could in turn make another cell smaller than allowed.
     */
    for(i=range[0]; i<range[1]; i++)
    {
        root->bCellMin[i] = FALSE;
    }
    nmin = 0;
    do
    {
        nmin_old = nmin;
        /* We need the total for normalization */
        fac = 0;
        for(i=range[0]; i<range[1]; i++)
        {
            if (root->bCellMin[i] == FALSE)
            {
                fac += cell_size[i];
            }
        }
        fac = ( region_size - nmin*cellsize_limit_f)/fac; /* substracting cells already set to cellsize_limit_f */
        /* Determine the cell boundaries */
        for(i=range[0]; i<range[1]; i++)
        {
            if (root->bCellMin[i] == FALSE)
            {
                cell_size[i] *= fac;
                if (!bPBC && (i == 0 || i == dd->nc[dim] -1))
                {
                    cellsize_limit_f_i = 0;
                }
                else
                {
                    cellsize_limit_f_i = cellsize_limit_f;
                }
                if (cell_size[i] < cellsize_limit_f_i)
                {
                    root->bCellMin[i] = TRUE;
                    cell_size[i] = cellsize_limit_f_i;
                    nmin++;
                }
            }
            root->cell_f[i+1] = root->cell_f[i] + cell_size[i];
        }
    }
    while (nmin > nmin_old);
    
    i=range[1]-1;
    cell_size[i] = root->cell_f[i+1] - root->cell_f[i];
    /* For this check we should not use DD_CELL_MARGIN,
     * but a slightly smaller factor,
     * since rounding could get use below the limit.
     */
    if (bPBC && cell_size[i] < cellsize_limit_f*DD_CELL_MARGIN2/DD_CELL_MARGIN)
    {
        char buf[22];
        gmx_fatal(FARGS,"Step %s: the dynamic load balancing could not balance dimension %c: box size %f, triclinic skew factor %f, #cells %d, minimum cell size %f\n",
                  gmx_step_str(step,buf),
                  dim2char(dim),ddbox->box_size[dim],ddbox->skew_fac[dim],
                  ncd,comm->cellsize_min[dim]);
    }
    
    root->bLimited = (nmin > 0) || (range[0]>0) || (range[1]<ncd);
    
    if (!bUniform)
    {
        /* Check if the boundary did not displace more than halfway
         * each of the cells it bounds, as this could cause problems,
         * especially when the differences between cell sizes are large.
         * If changes are applied, they will not make cells smaller
         * than the cut-off, as we check all the boundaries which
         * might be affected by a change and if the old state was ok,
         * the cells will at most be shrunk back to their old size.
         */
        for(i=range[0]+1; i<range[1]; i++)
        {
            halfway = 0.5*(root->old_cell_f[i] + root->old_cell_f[i-1]);
            if (root->cell_f[i] < halfway)
            {
                root->cell_f[i] = halfway;
                /* Check if the change also causes shifts of the next boundaries */
                for(j=i+1; j<range[1]; j++)
                {
                    if (root->cell_f[j] < root->cell_f[j-1] + cellsize_limit_f)
                        root->cell_f[j] =  root->cell_f[j-1] + cellsize_limit_f;
                }
            }
            halfway = 0.5*(root->old_cell_f[i] + root->old_cell_f[i+1]);
            if (root->cell_f[i] > halfway)
            {
                root->cell_f[i] = halfway;
                /* Check if the change also causes shifts of the next boundaries */
                for(j=i-1; j>=range[0]+1; j--)
                {
                    if (root->cell_f[j] > root->cell_f[j+1] - cellsize_limit_f)
                        root->cell_f[j] = root->cell_f[j+1] - cellsize_limit_f;
                }
            }
        }
    }
    
    /* nrange is defined as [lower, upper) range for new call to enforce_limits */
    /* find highest violation of LimLo (a) and the following violation of LimHi (thus the lowest following) (b)
     * then call enforce_limits for (oldb,a), (a,b). In the next step: (b,nexta). oldb and nexta can be the boundaries.
     * for a and b nrange is used */
    if (d > 0)
    {
        /* Take care of the staggering of the cell boundaries */
        if (bUniform)
        {
            for(i=range[0]; i<range[1]; i++)
            {
                root->cell_f_max0[i] = root->cell_f[i];
                root->cell_f_min1[i] = root->cell_f[i+1];
            }
        }
        else
        {
            for(i=range[0]+1; i<range[1]; i++)
            {
                bLimLo = (root->cell_f[i] < root->bound_min[i]);
                bLimHi = (root->cell_f[i] > root->bound_max[i]);
                if (bLimLo && bLimHi)
                {
                    /* Both limits violated, try the best we can */
                    /* For this case we split the original range (range) in two parts and care about the other limitiations in the next iteration. */
                    root->cell_f[i] = 0.5*(root->bound_min[i] + root->bound_max[i]);
                    nrange[0]=range[0];
                    nrange[1]=i;
                    dd_cell_sizes_dlb_root_enforce_limits(dd, d, dim, root, ddbox, bUniform, step, cellsize_limit_f, nrange);

                    nrange[0]=i;
                    nrange[1]=range[1];
                    dd_cell_sizes_dlb_root_enforce_limits(dd, d, dim, root, ddbox, bUniform, step, cellsize_limit_f, nrange);

                    return;
                }
                else if (bLimLo)
                {
                    /* root->cell_f[i] = root->bound_min[i]; */
                    nrange[1]=i;  /* only store violation location. There could be a LimLo violation following with an higher index */
                    bLastHi=FALSE;
                }
                else if (bLimHi && !bLastHi)
                {
                    bLastHi=TRUE;
                    if (nrange[1] < range[1])   /* found a LimLo before */
                    {
                        root->cell_f[nrange[1]] = root->bound_min[nrange[1]];
                        dd_cell_sizes_dlb_root_enforce_limits(dd, d, dim, root, ddbox, bUniform, step, cellsize_limit_f, nrange);
                        nrange[0]=nrange[1];
                    }
                    root->cell_f[i] = root->bound_max[i];
                    nrange[1]=i; 
                    dd_cell_sizes_dlb_root_enforce_limits(dd, d, dim, root, ddbox, bUniform, step, cellsize_limit_f, nrange);
                    nrange[0]=i;
                    nrange[1]=range[1];
                }
            }
            if (nrange[1] < range[1])   /* found last a LimLo */
            {
                root->cell_f[nrange[1]] = root->bound_min[nrange[1]];
                dd_cell_sizes_dlb_root_enforce_limits(dd, d, dim, root, ddbox, bUniform, step, cellsize_limit_f, nrange);
                nrange[0]=nrange[1];
                nrange[1]=range[1];
                dd_cell_sizes_dlb_root_enforce_limits(dd, d, dim, root, ddbox, bUniform, step, cellsize_limit_f, nrange);
            } 
            else if (nrange[0] > range[0]) /* found at least one LimHi */
            {
                dd_cell_sizes_dlb_root_enforce_limits(dd, d, dim, root, ddbox, bUniform, step, cellsize_limit_f, nrange);
            }
        }
    }
}


static void set_dd_cell_sizes_dlb_root(gmx_domdec_t *dd,
                                       int d,int dim,gmx_domdec_root_t *root,
                                       gmx_ddbox_t *ddbox,bool bDynamicBox,
                                       bool bUniform,gmx_large_int_t step)
{
    gmx_domdec_comm_t *comm;
    int  ncd,d1,i,j,pos;
    real *cell_size;
    real load_aver,load_i,imbalance,change,change_max,sc;
    real cellsize_limit_f,dist_min_f,dist_min_f_hard,space;
    real change_limit = 0.1;
    real relax = 0.5;
    bool bPBC;
    int range[] = { 0, 0 };

    comm = dd->comm;

    ncd = dd->nc[dim];

    bPBC = (dim < ddbox->npbcdim);

    cell_size = root->buf_ncd;

    /* Store the original boundaries */
    for(i=0; i<ncd+1; i++)
    {
        root->old_cell_f[i] = root->cell_f[i];
    }
    if (bUniform) {
        for(i=0; i<ncd; i++)
        {
            cell_size[i] = 1.0/ncd;
        }
    }
    else if (dd_load_count(comm))
    {
        load_aver = comm->load[d].sum_m/ncd;
        change_max = 0;
        for(i=0; i<ncd; i++)
        {
            /* Determine the relative imbalance of cell i */
            load_i = comm->load[d].load[i*comm->load[d].nload+2];
            imbalance = (load_i - load_aver)/(load_aver>0 ? load_aver : 1);
            /* Determine the change of the cell size using underrelaxation */
            change = -relax*imbalance;
            change_max = max(change_max,max(change,-change));
        }
        /* Limit the amount of scaling.
         * We need to use the same rescaling for all cells in one row,
         * otherwise the load balancing might not converge.
         */
        sc = relax;
        if (change_max > change_limit)
        {
            sc *= change_limit/change_max;
        }
        for(i=0; i<ncd; i++)
        {
            /* Determine the relative imbalance of cell i */
            load_i = comm->load[d].load[i*comm->load[d].nload+2];
            imbalance = (load_i - load_aver)/(load_aver>0 ? load_aver : 1);
            /* Determine the change of the cell size using underrelaxation */
            change = -sc*imbalance;
            cell_size[i] = (root->cell_f[i+1]-root->cell_f[i])*(1 + change);
        }
    }
    
    cellsize_limit_f  = comm->cellsize_min[dim]/ddbox->box_size[dim];
    cellsize_limit_f *= DD_CELL_MARGIN;
    dist_min_f_hard        = grid_jump_limit(comm,d)/ddbox->box_size[dim];
    dist_min_f       = dist_min_f_hard * DD_CELL_MARGIN;
    if (ddbox->tric_dir[dim])
    {
        cellsize_limit_f /= ddbox->skew_fac[dim];
        dist_min_f       /= ddbox->skew_fac[dim];
    }
    if (bDynamicBox && d > 0)
    {
        dist_min_f *= DD_PRES_SCALE_MARGIN;
    }
    if (d > 0 && !bUniform)
    {
        /* Make sure that the grid is not shifted too much */
        for(i=1; i<ncd; i++) {
            if (root->cell_f_min1[i] - root->cell_f_max0[i-1] < 2 * dist_min_f_hard) 
            {
                gmx_incons("Inconsistent DD boundary staggering limits!");
            }
            root->bound_min[i] = root->cell_f_max0[i-1] + dist_min_f;
            space = root->cell_f[i] - (root->cell_f_max0[i-1] + dist_min_f);
            if (space > 0) {
                root->bound_min[i] += 0.5*space;
            }
            root->bound_max[i] = root->cell_f_min1[i] - dist_min_f;
            space = root->cell_f[i] - (root->cell_f_min1[i] - dist_min_f);
            if (space < 0) {
                root->bound_max[i] += 0.5*space;
            }
            if (debug)
            {
                fprintf(debug,
                        "dim %d boundary %d %.3f < %.3f < %.3f < %.3f < %.3f\n",
                        d,i,
                        root->cell_f_max0[i-1] + dist_min_f,
                        root->bound_min[i],root->cell_f[i],root->bound_max[i],
                        root->cell_f_min1[i] - dist_min_f);
            }
        }
    }
    range[1]=ncd;
    root->cell_f[0] = 0;
    root->cell_f[ncd] = 1;
    dd_cell_sizes_dlb_root_enforce_limits(dd, d, dim, root, ddbox, bUniform, step, cellsize_limit_f, range);


    /* After the checks above, the cells should obey the cut-off
     * restrictions, but it does not hurt to check.
     */
    for(i=0; i<ncd; i++)
    {
        if (debug)
        {
            fprintf(debug,"Relative bounds dim %d  cell %d: %f %f\n",
                    dim,i,root->cell_f[i],root->cell_f[i+1]);
        }

        if ((bPBC || (i != 0 && i != dd->nc[dim]-1)) &&
            root->cell_f[i+1] - root->cell_f[i] <
            cellsize_limit_f/DD_CELL_MARGIN)
        {
            char buf[22];
            fprintf(stderr,
                    "\nWARNING step %s: direction %c, cell %d too small: %f\n",
                    gmx_step_str(step,buf),dim2char(dim),i,
                    (root->cell_f[i+1] - root->cell_f[i])
                    *ddbox->box_size[dim]*ddbox->skew_fac[dim]);
        }
    }
    
    pos = ncd + 1;
    /* Store the cell boundaries of the lower dimensions at the end */
    for(d1=0; d1<d; d1++)
    {
        root->cell_f[pos++] = comm->cell_f0[d1];
        root->cell_f[pos++] = comm->cell_f1[d1];
    }
    
    if (d < comm->npmedecompdim)
    {
        /* The master determines the maximum shift for
         * the coordinate communication between separate PME nodes.
         */
        set_pme_maxshift(dd,&comm->ddpme[d],bUniform,ddbox,root->cell_f);
    }
    root->cell_f[pos++] = comm->ddpme[0].maxshift;
    if (d >= 1)
    {
        root->cell_f[pos++] = comm->ddpme[1].maxshift;
    }
}    

static void relative_to_absolute_cell_bounds(gmx_domdec_t *dd,
                                             gmx_ddbox_t *ddbox,int dimind)
{
    gmx_domdec_comm_t *comm;
    int dim;

    comm = dd->comm;

    /* Set the cell dimensions */
    dim = dd->dim[dimind];
    comm->cell_x0[dim] = comm->cell_f0[dimind]*ddbox->box_size[dim];
    comm->cell_x1[dim] = comm->cell_f1[dimind]*ddbox->box_size[dim];
    if (dim >= ddbox->nboundeddim)
    {
        comm->cell_x0[dim] += ddbox->box0[dim];
        comm->cell_x1[dim] += ddbox->box0[dim];
    }
}

static void distribute_dd_cell_sizes_dlb(gmx_domdec_t *dd,
                                         int d,int dim,real *cell_f_row,
                                         gmx_ddbox_t *ddbox)
{
    gmx_domdec_comm_t *comm;
    int d1,dim1,pos;

    comm = dd->comm;

#ifdef GMX_MPI
    /* Each node would only need to know two fractions,
     * but it is probably cheaper to broadcast the whole array.
     */
    MPI_Bcast(cell_f_row,DD_CELL_F_SIZE(dd,d)*sizeof(real),MPI_BYTE,
              0,comm->mpi_comm_load[d]);
#endif
    /* Copy the fractions for this dimension from the buffer */
    comm->cell_f0[d] = cell_f_row[dd->ci[dim]  ];
    comm->cell_f1[d] = cell_f_row[dd->ci[dim]+1];
    /* The whole array was communicated, so set the buffer position */
    pos = dd->nc[dim] + 1;
    for(d1=0; d1<=d; d1++)
    {
        if (d1 < d)
        {
            /* Copy the cell fractions of the lower dimensions */
            comm->cell_f0[d1] = cell_f_row[pos++];
            comm->cell_f1[d1] = cell_f_row[pos++];
        }
        relative_to_absolute_cell_bounds(dd,ddbox,d1);
    }
    /* Convert the communicated shift from float to int */
    comm->ddpme[0].maxshift = (int)(cell_f_row[pos++] + 0.5);
    if (d >= 1)
    {
        comm->ddpme[1].maxshift = (int)(cell_f_row[pos++] + 0.5);
    }
}

static void set_dd_cell_sizes_dlb_change(gmx_domdec_t *dd,
                                         gmx_ddbox_t *ddbox,bool bDynamicBox,
                                         bool bUniform,gmx_large_int_t step)
{
    gmx_domdec_comm_t *comm;
    int d,dim,d1;
    bool bRowMember,bRowRoot;
    real *cell_f_row;
    
    comm = dd->comm;

    for(d=0; d<dd->ndim; d++)
    {
        dim = dd->dim[d];
        bRowMember = TRUE;
        bRowRoot = TRUE;
        for(d1=d; d1<dd->ndim; d1++)
        {
            if (dd->ci[dd->dim[d1]] > 0)
            {
                if (d1 > d)
                {
                    bRowMember = FALSE;
                }
                bRowRoot = FALSE;
            }
        }
        if (bRowMember)
        {
            if (bRowRoot)
            {
                set_dd_cell_sizes_dlb_root(dd,d,dim,comm->root[d],
                                           ddbox,bDynamicBox,bUniform,step);
                cell_f_row = comm->root[d]->cell_f;
            }
            else
            {
                cell_f_row = comm->cell_f_row;
            }
            distribute_dd_cell_sizes_dlb(dd,d,dim,cell_f_row,ddbox);
        }
    }
}    

static void set_dd_cell_sizes_dlb_nochange(gmx_domdec_t *dd,gmx_ddbox_t *ddbox)
{
    int d;

    /* This function assumes the box is static and should therefore
     * not be called when the box has changed since the last
     * call to dd_partition_system.
     */
    for(d=0; d<dd->ndim; d++)
    {
        relative_to_absolute_cell_bounds(dd,ddbox,d); 
    }
}



static void set_dd_cell_sizes_dlb(gmx_domdec_t *dd,
                                  gmx_ddbox_t *ddbox,bool bDynamicBox,
                                  bool bUniform,bool bDoDLB,gmx_large_int_t step,
                                  gmx_wallcycle_t wcycle)
{
    gmx_domdec_comm_t *comm;
    int dim;

    comm = dd->comm;
    
    if (bDoDLB)
    {
        wallcycle_start(wcycle,ewcDDCOMMBOUND);
        set_dd_cell_sizes_dlb_change(dd,ddbox,bDynamicBox,bUniform,step);
        wallcycle_stop(wcycle,ewcDDCOMMBOUND);
    }
    else if (bDynamicBox)
    {
        set_dd_cell_sizes_dlb_nochange(dd,ddbox);
    }
    
    /* Set the dimensions for which no DD is used */
    for(dim=0; dim<DIM; dim++) {
        if (dd->nc[dim] == 1) {
            comm->cell_x0[dim] = 0;
            comm->cell_x1[dim] = ddbox->box_size[dim];
            if (dim >= ddbox->nboundeddim)
            {
                comm->cell_x0[dim] += ddbox->box0[dim];
                comm->cell_x1[dim] += ddbox->box0[dim];
            }
        }
    }
}

static void realloc_comm_ind(gmx_domdec_t *dd,ivec npulse)
{
    int d,np,i;
    gmx_domdec_comm_dim_t *cd;
    
    for(d=0; d<dd->ndim; d++)
    {
        cd = &dd->comm->cd[d];
        np = npulse[dd->dim[d]];
        if (np > cd->np_nalloc)
        {
            if (debug)
            {
                fprintf(debug,"(Re)allocing cd for %c to %d pulses\n",
                        dim2char(dd->dim[d]),np);
            }
            if (DDMASTER(dd) && cd->np_nalloc > 0)
            {
                fprintf(stderr,"\nIncreasing the number of cell to communicate in dimension %c to %d for the first time\n",dim2char(dd->dim[d]),np);
            }
            srenew(cd->ind,np);
            for(i=cd->np_nalloc; i<np; i++)
            {
                cd->ind[i].index  = NULL;
                cd->ind[i].nalloc = 0;
            }
            cd->np_nalloc = np;
        }
        cd->np = np;
    }
}


static void set_dd_cell_sizes(gmx_domdec_t *dd,
                              gmx_ddbox_t *ddbox,bool bDynamicBox,
                              bool bUniform,bool bDoDLB,gmx_large_int_t step,
                              gmx_wallcycle_t wcycle)
{
    gmx_domdec_comm_t *comm;
    int  d;
    ivec npulse;
    
    comm = dd->comm;

    /* Copy the old cell boundaries for the cg displacement check */
    copy_rvec(comm->cell_x0,comm->old_cell_x0);
    copy_rvec(comm->cell_x1,comm->old_cell_x1);
    
    if (comm->bDynLoadBal)
    {
        if (DDMASTER(dd))
        {
            check_box_size(dd,ddbox);
        }
        set_dd_cell_sizes_dlb(dd,ddbox,bDynamicBox,bUniform,bDoDLB,step,wcycle);
    }
    else
    {
        set_dd_cell_sizes_slb(dd,ddbox,FALSE,npulse);
        realloc_comm_ind(dd,npulse);
    }
    
    if (debug)
    {
        for(d=0; d<DIM; d++)
        {
            fprintf(debug,"cell_x[%d] %f - %f skew_fac %f\n",
                    d,comm->cell_x0[d],comm->cell_x1[d],ddbox->skew_fac[d]);
        }
    }
}

static void comm_dd_ns_cell_sizes(gmx_domdec_t *dd,
                                  gmx_ddbox_t *ddbox,
                                  rvec cell_ns_x0,rvec cell_ns_x1,
                                  gmx_large_int_t step)
{
    gmx_domdec_comm_t *comm;
    int dim_ind,dim;
    
    comm = dd->comm;

    for(dim_ind=0; dim_ind<dd->ndim; dim_ind++)
    {
        dim = dd->dim[dim_ind];
        
        /* Without PBC we don't have restrictions on the outer cells */
        if (!(dim >= ddbox->npbcdim && 
              (dd->ci[dim] == 0 || dd->ci[dim] == dd->nc[dim] - 1)) &&
            comm->bDynLoadBal &&
            (comm->cell_x1[dim] - comm->cell_x0[dim])*ddbox->skew_fac[dim] <
            comm->cellsize_min[dim])
        {
            char buf[22];
            gmx_fatal(FARGS,"Step %s: The %c-size (%f) times the triclinic skew factor (%f) is smaller than the smallest allowed cell size (%f) for domain decomposition grid cell %d %d %d",
                      gmx_step_str(step,buf),dim2char(dim),
                      comm->cell_x1[dim] - comm->cell_x0[dim],
                      ddbox->skew_fac[dim],
                      dd->comm->cellsize_min[dim],
                      dd->ci[XX],dd->ci[YY],dd->ci[ZZ]);
        }
    }
    
    if ((dd->bGridJump && dd->ndim > 1) || ddbox->nboundeddim < DIM)
    {
        /* Communicate the boundaries and update cell_ns_x0/1 */
        dd_move_cellx(dd,ddbox,cell_ns_x0,cell_ns_x1);
        if (dd->bGridJump && dd->ndim > 1)
        {
            check_grid_jump(step,dd,ddbox);
        }
    }
}

static void make_tric_corr_matrix(int npbcdim,matrix box,matrix tcm)
{
    if (YY < npbcdim)
    {
        tcm[YY][XX] = -box[YY][XX]/box[YY][YY];
    }
    else
    {
        tcm[YY][XX] = 0;
    }
    if (ZZ < npbcdim)
    {
        tcm[ZZ][XX] = -(box[ZZ][YY]*tcm[YY][XX] + box[ZZ][XX])/box[ZZ][ZZ];
        tcm[ZZ][YY] = -box[ZZ][YY]/box[ZZ][ZZ];
    }
    else
    {
        tcm[ZZ][XX] = 0;
        tcm[ZZ][YY] = 0;
    }
}

static void check_screw_box(matrix box)
{
    /* Mathematical limitation */
    if (box[YY][XX] != 0 || box[ZZ][XX] != 0)
    {
        gmx_fatal(FARGS,"With screw pbc the unit cell can not have non-zero off-diagonal x-components");
    }
    
    /* Limitation due to the asymmetry of the eighth shell method */
    if (box[ZZ][YY] != 0)
    {
        gmx_fatal(FARGS,"pbc=screw with non-zero box_zy is not supported");
    }
}

static void distribute_cg(FILE *fplog,gmx_large_int_t step,
                          matrix box,ivec tric_dir,t_block *cgs,rvec pos[],
                          gmx_domdec_t *dd)
{
    gmx_domdec_master_t *ma;
    int **tmp_ind=NULL,*tmp_nalloc=NULL;
    int  i,icg,j,k,k0,k1,d,npbcdim;
    matrix tcm;
    rvec box_size,cg_cm;
    ivec ind;
    real nrcg,inv_ncg,pos_d;
    atom_id *cgindex;
    bool bUnbounded,bScrew;

    ma = dd->ma;
    
    if (tmp_ind == NULL)
    {
        snew(tmp_nalloc,dd->nnodes);
        snew(tmp_ind,dd->nnodes);
        for(i=0; i<dd->nnodes; i++)
        {
            tmp_nalloc[i] = over_alloc_large(cgs->nr/dd->nnodes+1);
            snew(tmp_ind[i],tmp_nalloc[i]);
        }
    }
    
    /* Clear the count */
    for(i=0; i<dd->nnodes; i++)
    {
        ma->ncg[i] = 0;
        ma->nat[i] = 0;
    }
    
    make_tric_corr_matrix(dd->npbcdim,box,tcm);
    
    cgindex = cgs->index;
    
    /* Compute the center of geometry for all charge groups */
    for(icg=0; icg<cgs->nr; icg++)
    {
        k0      = cgindex[icg];
        k1      = cgindex[icg+1];
        nrcg    = k1 - k0;
        if (nrcg == 1)
        {
            copy_rvec(pos[k0],cg_cm);
        }
        else
        {
            inv_ncg = 1.0/nrcg;
            
            clear_rvec(cg_cm);
            for(k=k0; (k<k1); k++)
            {
                rvec_inc(cg_cm,pos[k]);
            }
            for(d=0; (d<DIM); d++)
            {
                cg_cm[d] *= inv_ncg;
            }
        }
        /* Put the charge group in the box and determine the cell index */
        for(d=DIM-1; d>=0; d--) {
            pos_d = cg_cm[d];
            if (d < dd->npbcdim)
            {
                bScrew = (dd->bScrewPBC && d == XX);
                if (tric_dir[d] && dd->nc[d] > 1)
                {
                    /* Use triclinic coordintates for this dimension */
                    for(j=d+1; j<DIM; j++)
                    {
                        pos_d += cg_cm[j]*tcm[j][d];
                    }
                }
                while(pos_d >= box[d][d])
                {
                    pos_d -= box[d][d];
                    rvec_dec(cg_cm,box[d]);
                    if (bScrew)
                    {
                        cg_cm[YY] = box[YY][YY] - cg_cm[YY];
                        cg_cm[ZZ] = box[ZZ][ZZ] - cg_cm[ZZ];
                    }
                    for(k=k0; (k<k1); k++)
                    {
                        rvec_dec(pos[k],box[d]);
                        if (bScrew)
                        {
                            pos[k][YY] = box[YY][YY] - pos[k][YY];
                            pos[k][ZZ] = box[ZZ][ZZ] - pos[k][ZZ];
                        }
                    }
                }
                while(pos_d < 0)
                {
                    pos_d += box[d][d];
                    rvec_inc(cg_cm,box[d]);
                    if (bScrew)
                    {
                        cg_cm[YY] = box[YY][YY] - cg_cm[YY];
                        cg_cm[ZZ] = box[ZZ][ZZ] - cg_cm[ZZ];
                    }
                    for(k=k0; (k<k1); k++)
                    {
                        rvec_inc(pos[k],box[d]);
                        if (bScrew) {
                            pos[k][YY] = box[YY][YY] - pos[k][YY];
                            pos[k][ZZ] = box[ZZ][ZZ] - pos[k][ZZ];
                        }
                    }
                }
            }
            /* This could be done more efficiently */
            ind[d] = 0;
            while(ind[d]+1 < dd->nc[d] && pos_d >= ma->cell_x[d][ind[d]+1])
            {
                ind[d]++;
            }
        }
        i = dd_index(dd->nc,ind);
        if (ma->ncg[i] == tmp_nalloc[i])
        {
            tmp_nalloc[i] = over_alloc_large(ma->ncg[i]+1);
            srenew(tmp_ind[i],tmp_nalloc[i]);
        }
        tmp_ind[i][ma->ncg[i]] = icg;
        ma->ncg[i]++;
        ma->nat[i] += cgindex[icg+1] - cgindex[icg];
    }
    
    k1 = 0;
    for(i=0; i<dd->nnodes; i++)
    {
        ma->index[i] = k1;
        for(k=0; k<ma->ncg[i]; k++)
        {
            ma->cg[k1++] = tmp_ind[i][k];
        }
    }
    ma->index[dd->nnodes] = k1;
    
    for(i=0; i<dd->nnodes; i++)
    {
        sfree(tmp_ind[i]);
    }
    sfree(tmp_ind);
    sfree(tmp_nalloc);
    
    if (fplog)
    {
        char buf[22];
        fprintf(fplog,"Charge group distribution at step %s:",
                gmx_step_str(step,buf));
        for(i=0; i<dd->nnodes; i++)
        {
            fprintf(fplog," %d",ma->ncg[i]);
        }
        fprintf(fplog,"\n");
    }
}

static void get_cg_distribution(FILE *fplog,gmx_large_int_t step,gmx_domdec_t *dd,
                                t_block *cgs,matrix box,gmx_ddbox_t *ddbox,
                                rvec pos[])
{
    gmx_domdec_master_t *ma=NULL;
    ivec npulse;
    int  i,cg_gl;
    int  *ibuf,buf2[2] = { 0, 0 };
    
    if (DDMASTER(dd))
    {
        ma = dd->ma;
        
        if (dd->bScrewPBC)
        {
            check_screw_box(box);
        }
    
        set_dd_cell_sizes_slb(dd,ddbox,TRUE,npulse);
    
        distribute_cg(fplog,step,box,ddbox->tric_dir,cgs,pos,dd);
        for(i=0; i<dd->nnodes; i++)
        {
            ma->ibuf[2*i]   = ma->ncg[i];
            ma->ibuf[2*i+1] = ma->nat[i];
        }
        ibuf = ma->ibuf;
    }
    else
    {
        ibuf = NULL;
    }
    dd_scatter(dd,2*sizeof(int),ibuf,buf2);
    
    dd->ncg_home = buf2[0];
    dd->nat_home = buf2[1];
    dd->ncg_tot  = dd->ncg_home;
    dd->nat_tot  = dd->nat_home;
    if (dd->ncg_home > dd->cg_nalloc || dd->cg_nalloc == 0)
    {
        dd->cg_nalloc = over_alloc_dd(dd->ncg_home);
        srenew(dd->index_gl,dd->cg_nalloc);
        srenew(dd->cgindex,dd->cg_nalloc+1);
    }
    if (DDMASTER(dd))
    {
        for(i=0; i<dd->nnodes; i++)
        {
            ma->ibuf[i] = ma->ncg[i]*sizeof(int);
            ma->ibuf[dd->nnodes+i] = ma->index[i]*sizeof(int);
        }
    }
    
    dd_scatterv(dd,
                DDMASTER(dd) ? ma->ibuf : NULL,
                DDMASTER(dd) ? ma->ibuf+dd->nnodes : NULL,
                DDMASTER(dd) ? ma->cg : NULL,
                dd->ncg_home*sizeof(int),dd->index_gl);
    
    /* Determine the home charge group sizes */
    dd->cgindex[0] = 0;
    for(i=0; i<dd->ncg_home; i++)
    {
        cg_gl = dd->index_gl[i];
        dd->cgindex[i+1] =
            dd->cgindex[i] + cgs->index[cg_gl+1] - cgs->index[cg_gl];
    }
    
    if (debug)
    {
        fprintf(debug,"Home charge groups:\n");
        for(i=0; i<dd->ncg_home; i++)
        {
            fprintf(debug," %d",dd->index_gl[i]);
            if (i % 10 == 9) 
                fprintf(debug,"\n");
        }
        fprintf(debug,"\n");
    }
}

static int compact_and_copy_vec_at(int ncg,int *move,
                                   int *cgindex,
                                   int nvec,int vec,
                                   rvec *src,gmx_domdec_comm_t *comm,
                                   bool bCompact)
{
    int m,icg,i,i0,i1,nrcg;
    int home_pos;
    int pos_vec[DIM*2];
    
    home_pos = 0;

    for(m=0; m<DIM*2; m++)
    {
        pos_vec[m] = 0;
    }
    
    i0 = 0;
    for(icg=0; icg<ncg; icg++)
    {
        i1 = cgindex[icg+1];
        m = move[icg];
        if (m == -1)
        {
            if (bCompact)
            {
                /* Compact the home array in place */
                for(i=i0; i<i1; i++)
                {
                    copy_rvec(src[i],src[home_pos++]);
                }
            }
        }
        else
        {
            /* Copy to the communication buffer */
            nrcg = i1 - i0;
            pos_vec[m] += 1 + vec*nrcg;
            for(i=i0; i<i1; i++)
            {
                copy_rvec(src[i],comm->cgcm_state[m][pos_vec[m]++]);
            }
            pos_vec[m] += (nvec - vec - 1)*nrcg;
        }
        if (!bCompact)
        {
            home_pos += i1 - i0;
        }
        i0 = i1;
    }
    
    return home_pos;
}

static int compact_and_copy_vec_cg(int ncg,int *move,
                                   int *cgindex,
                                   int nvec,rvec *src,gmx_domdec_comm_t *comm,
                                   bool bCompact)
{
    int m,icg,i0,i1,nrcg;
    int home_pos;
    int pos_vec[DIM*2];
    
    home_pos = 0;
    
    for(m=0; m<DIM*2; m++)
    {
        pos_vec[m] = 0;
    }
    
    i0 = 0;
    for(icg=0; icg<ncg; icg++)
    {
        i1 = cgindex[icg+1];
        m = move[icg];
        if (m == -1)
        {
            if (bCompact)
            {
                /* Compact the home array in place */
                copy_rvec(src[icg],src[home_pos++]);
            }
        }
        else
        {
            nrcg = i1 - i0;
            /* Copy to the communication buffer */
            copy_rvec(src[icg],comm->cgcm_state[m][pos_vec[m]]);
            pos_vec[m] += 1 + nrcg*nvec;
        }
        i0 = i1;
    }
    if (!bCompact)
    {
        home_pos = ncg;
    }
    
    return home_pos;
}

static int compact_ind(int ncg,int *move,
                       int *index_gl,int *cgindex,
                       int *gatindex,
                       gmx_ga2la_t ga2la,char *bLocalCG,
                       int *cginfo)
{
    int cg,nat,a0,a1,a,a_gl;
    int home_pos;

    home_pos = 0;
    nat = 0;
    for(cg=0; cg<ncg; cg++)
    {
        a0 = cgindex[cg];
        a1 = cgindex[cg+1];
        if (move[cg] == -1)
        {
            /* Compact the home arrays in place.
             * Anything that can be done here avoids access to global arrays.
             */
            cgindex[home_pos] = nat;
            for(a=a0; a<a1; a++)
            {
                a_gl = gatindex[a];
                gatindex[nat] = a_gl;
                /* The cell number stays 0, so we don't need to set it */
                ga2la_change_la(ga2la,a_gl,nat);
                nat++;
            }
            index_gl[home_pos] = index_gl[cg];
            cginfo[home_pos]   = cginfo[cg];
            /* The charge group remains local, so bLocalCG does not change */
            home_pos++;
        }
        else
        {
            /* Clear the global indices */
            for(a=a0; a<a1; a++)
            {
                ga2la_del(ga2la,gatindex[a]);
            }
            if (bLocalCG)
            {
                bLocalCG[index_gl[cg]] = FALSE;
            }
        }
    }
    cgindex[home_pos] = nat;
    
    return home_pos;
}

static void clear_and_mark_ind(int ncg,int *move,
                               int *index_gl,int *cgindex,int *gatindex,
                               gmx_ga2la_t ga2la,char *bLocalCG,
                               int *cell_index)
{
    int cg,a0,a1,a;
    
    for(cg=0; cg<ncg; cg++)
    {
        if (move[cg] >= 0)
        {
            a0 = cgindex[cg];
            a1 = cgindex[cg+1];
            /* Clear the global indices */
            for(a=a0; a<a1; a++)
            {
                ga2la_del(ga2la,gatindex[a]);
            }
            if (bLocalCG)
            {
                bLocalCG[index_gl[cg]] = FALSE;
            }
            /* Signal that this cg has moved using the ns cell index.
             * Here we set it to -1.
             * fill_grid will change it from -1 to 4*grid->ncells.
             */
            cell_index[cg] = -1;
        }
    }
}

static void print_cg_move(FILE *fplog,
                          gmx_domdec_t *dd,
                          gmx_large_int_t step,int cg,int dim,int dir,
                          real limitd,
                          rvec cm_old,rvec cm_new,real pos_d)
{
    gmx_domdec_comm_t *comm;
    char buf[22];

    comm = dd->comm;

    fprintf(fplog,"\nStep %s:\n",gmx_step_str(step,buf));
    fprintf(fplog,"The charge group starting at atom %d moved than the distance allowed by the domain decomposition (%f) in direction %c\n",
            ddglatnr(dd,dd->cgindex[cg]),limitd,dim2char(dim));
    fprintf(fplog,"distance out of cell %f\n",
            dir==1 ? pos_d - comm->cell_x1[dim] : pos_d - comm->cell_x0[dim]);
    fprintf(fplog,"Old coordinates: %8.3f %8.3f %8.3f\n",
            cm_old[XX],cm_old[YY],cm_old[ZZ]);
    fprintf(fplog,"New coordinates: %8.3f %8.3f %8.3f\n",
            cm_new[XX],cm_new[YY],cm_new[ZZ]);
    fprintf(fplog,"Old cell boundaries in direction %c: %8.3f %8.3f\n",
            dim2char(dim),
            comm->old_cell_x0[dim],comm->old_cell_x1[dim]);
    fprintf(fplog,"New cell boundaries in direction %c: %8.3f %8.3f\n",
            dim2char(dim),
            comm->cell_x0[dim],comm->cell_x1[dim]);
}

static void cg_move_error(FILE *fplog,
                          gmx_domdec_t *dd,
                          gmx_large_int_t step,int cg,int dim,int dir,
                          real limitd,
                          rvec cm_old,rvec cm_new,real pos_d)
{
    if (fplog)
    {
        print_cg_move(fplog, dd,step,cg,dim,dir,limitd,cm_old,cm_new,pos_d);
    }
    print_cg_move(stderr,dd,step,cg,dim,dir,limitd,cm_old,cm_new,pos_d);
    gmx_fatal(FARGS,
              "A charge group moved too far between two domain decomposition steps\n"
              "This usually means that your system is not well equilibrated");
}

static void rotate_state_atom(t_state *state,int a)
{
    int est;

    for(est=0; est<estNR; est++)
    {
        if (EST_DISTR(est) && state->flags & (1<<est)) {
            switch (est) {
            case estX:
                /* Rotate the complete state; for a rectangular box only */
                state->x[a][YY] = state->box[YY][YY] - state->x[a][YY];
                state->x[a][ZZ] = state->box[ZZ][ZZ] - state->x[a][ZZ];
                break;
            case estV:
                state->v[a][YY] = -state->v[a][YY];
                state->v[a][ZZ] = -state->v[a][ZZ];
                break;
            case estSDX:
                state->sd_X[a][YY] = -state->sd_X[a][YY];
                state->sd_X[a][ZZ] = -state->sd_X[a][ZZ];
                break;
            case estCGP:
                state->cg_p[a][YY] = -state->cg_p[a][YY];
                state->cg_p[a][ZZ] = -state->cg_p[a][ZZ];
                break;
            case estDISRE_INITF:
            case estDISRE_RM3TAV:
            case estORIRE_INITF:
            case estORIRE_DTAV:
                /* These are distances, so not affected by rotation */
                break;
            default:
                gmx_incons("Unknown state entry encountered in rotate_state_atom");            
            }
        }
    }
}

static int dd_redistribute_cg(FILE *fplog,gmx_large_int_t step,
                              gmx_domdec_t *dd,ivec tric_dir,
                              t_state *state,rvec **f,
                              t_forcerec *fr,t_mdatoms *md,
                              bool bCompact,
                              t_nrnb *nrnb)
{
    int  *move;
    int  npbcdim;
    int  ncg[DIM*2],nat[DIM*2];
    int  c,i,cg,k,k0,k1,d,dim,dim2,dir,d2,d3,d4,cell_d;
    int  mc,cdd,nrcg,ncg_recv,nat_recv,nvs,nvr,nvec,vec;
    int  sbuf[2],rbuf[2];
    int  home_pos_cg,home_pos_at,ncg_stay_home,buf_pos;
    int  flag;
    bool bV=FALSE,bSDX=FALSE,bCGP=FALSE;
    bool bScrew;
    ivec dev;
    real inv_ncg,pos_d;
    matrix tcm;
    rvec *cg_cm,cell_x0,cell_x1,limitd,limit0,limit1,cm_new;
    atom_id *cgindex;
    cginfo_mb_t *cginfo_mb;
    gmx_domdec_comm_t *comm;
    
    if (dd->bScrewPBC)
    {
        check_screw_box(state->box);
    }
    
    comm  = dd->comm;
    cg_cm = fr->cg_cm;
    
    for(i=0; i<estNR; i++)
    {
        if (EST_DISTR(i))
        {
            switch (i)
            {
            case estX:   /* Always present */            break;
            case estV:   bV   = (state->flags & (1<<i)); break;
            case estSDX: bSDX = (state->flags & (1<<i)); break;
            case estCGP: bCGP = (state->flags & (1<<i)); break;
            case estLD_RNG:
            case estLD_RNGI:
            case estDISRE_INITF:
            case estDISRE_RM3TAV:
            case estORIRE_INITF:
            case estORIRE_DTAV:
                /* No processing required */
                break;
            default:
            gmx_incons("Unknown state entry encountered in dd_redistribute_cg");
            }
        }
    }
    
    if (dd->ncg_tot > comm->nalloc_int)
    {
        comm->nalloc_int = over_alloc_dd(dd->ncg_tot);
        srenew(comm->buf_int,comm->nalloc_int);
    }
    move = comm->buf_int;
    
    /* Clear the count */
    for(c=0; c<dd->ndim*2; c++)
    {
        ncg[c] = 0;
        nat[c] = 0;
    }

    npbcdim = dd->npbcdim;

    for(d=0; (d<DIM); d++)
    {
        limitd[d] = dd->comm->cellsize_min[d];
        if (d >= npbcdim && dd->ci[d] == 0)
        {
            cell_x0[d] = -GMX_FLOAT_MAX;
        }
        else
        {
            cell_x0[d] = comm->cell_x0[d];
        }
        if (d >= npbcdim && dd->ci[d] == dd->nc[d] - 1)
        {
            cell_x1[d] = GMX_FLOAT_MAX;
        }
        else
        {
            cell_x1[d] = comm->cell_x1[d];
        }
        limit0[d] = comm->old_cell_x0[d] - limitd[d];
        limit1[d] = comm->old_cell_x1[d] + limitd[d];
    }
    
    make_tric_corr_matrix(npbcdim,state->box,tcm);
    
    cgindex = dd->cgindex;
    
    /* Compute the center of geometry for all home charge groups
     * and put them in the box and determine where they should go.
     */
    for(cg=0; cg<dd->ncg_home; cg++)
    {
        k0   = cgindex[cg];
        k1   = cgindex[cg+1];
        nrcg = k1 - k0;
        if (nrcg == 1)
        {
            copy_rvec(state->x[k0],cm_new);
        }
        else
        {
            inv_ncg = 1.0/nrcg;
            
            clear_rvec(cm_new);
            for(k=k0; (k<k1); k++)
            {
                rvec_inc(cm_new,state->x[k]);
            }
            for(d=0; (d<DIM); d++)
            {
                cm_new[d] = inv_ncg*cm_new[d];
            }
        }
        
        clear_ivec(dev);
        /* Do pbc and check DD cell boundary crossings */
        for(d=DIM-1; d>=0; d--)
        {
            if (dd->nc[d] > 1)
            {
                bScrew = (dd->bScrewPBC && d == XX);
                /* Determine the location of this cg in lattice coordinates */
                pos_d = cm_new[d];
                if (tric_dir[d])
                {
                    for(d2=d+1; d2<DIM; d2++)
                    {
                        pos_d += cm_new[d2]*tcm[d2][d];
                    }
                }
                /* Put the charge group in the triclinic unit-cell */
                if (pos_d >= cell_x1[d])
                {
                    if (pos_d >= limit1[d])
                    {
                        cg_move_error(fplog,dd,step,cg,d,1,limitd[d],
                                      cg_cm[cg],cm_new,pos_d);
                    }
                    dev[d] = 1;
                    if (dd->ci[d] == dd->nc[d] - 1)
                    {
                        rvec_dec(cm_new,state->box[d]);
                        if (bScrew)
                        {
                            cm_new[YY] = state->box[YY][YY] - cm_new[YY];
                            cm_new[ZZ] = state->box[ZZ][ZZ] - cm_new[ZZ];
                        }
                        for(k=k0; (k<k1); k++)
                        {
                            rvec_dec(state->x[k],state->box[d]);
                            if (bScrew)
                            {
                                rotate_state_atom(state,k);
                            }
                        }
                    }
                }
                else if (pos_d < cell_x0[d])
                {
                    if (pos_d < limit0[d])
                    {
                        cg_move_error(fplog,dd,step,cg,d,-1,limitd[d],
                                      cg_cm[cg],cm_new,pos_d);
                    }
                    dev[d] = -1;
                    if (dd->ci[d] == 0)
                    {
                        rvec_inc(cm_new,state->box[d]);
                        if (bScrew)
                        {
                            cm_new[YY] = state->box[YY][YY] - cm_new[YY];
                            cm_new[ZZ] = state->box[ZZ][ZZ] - cm_new[ZZ];
                        }
                        for(k=k0; (k<k1); k++)
                        {
                            rvec_inc(state->x[k],state->box[d]);
                            if (bScrew)
                            {
                                rotate_state_atom(state,k);
                            }
                        }
                    }
                }
            }
            else if (d < npbcdim)
            {
                /* Put the charge group in the rectangular unit-cell */
                while (cm_new[d] >= state->box[d][d])
                {
                    rvec_dec(cm_new,state->box[d]);
                    for(k=k0; (k<k1); k++)
                    {
                        rvec_dec(state->x[k],state->box[d]);
                    }
                }
                while (cm_new[d] < 0)
                {
                    rvec_inc(cm_new,state->box[d]);
                    for(k=k0; (k<k1); k++)
                    {
                        rvec_inc(state->x[k],state->box[d]);
                    }
                }
            }
        }
    
        copy_rvec(cm_new,cg_cm[cg]);
        
        /* Determine where this cg should go */
        flag = 0;
        mc = -1;
        for(d=0; d<dd->ndim; d++)
        {
            dim = dd->dim[d];
            if (dev[dim] == 1)
            {
                flag |= DD_FLAG_FW(d);
                if (mc == -1)
                {
                    mc = d*2;
                }
            }
            else if (dev[dim] == -1)
            {
                flag |= DD_FLAG_BW(d);
                if (mc == -1) {
                    if (dd->nc[dim] > 2)
                    {
                        mc = d*2 + 1;
                    }
                    else
                    {
                        mc = d*2;
                    }
                }
            }
        }
        move[cg] = mc;
        if (mc >= 0)
        {
            if (ncg[mc]+1 > comm->cggl_flag_nalloc[mc])
            {
                comm->cggl_flag_nalloc[mc] = over_alloc_dd(ncg[mc]+1);
                srenew(comm->cggl_flag[mc],comm->cggl_flag_nalloc[mc]*DD_CGIBS);
            }
            comm->cggl_flag[mc][ncg[mc]*DD_CGIBS  ] = dd->index_gl[cg];
            /* We store the cg size in the lower 16 bits
             * and the place where the charge group should go
             * in the next 6 bits. This saves some communication volume.
             */
            comm->cggl_flag[mc][ncg[mc]*DD_CGIBS+1] = nrcg | flag;
            ncg[mc] += 1;
            nat[mc] += nrcg;
        }
    }
    
    inc_nrnb(nrnb,eNR_CGCM,dd->nat_home);
    inc_nrnb(nrnb,eNR_RESETX,dd->ncg_home);
    
    nvec = 1;
    if (bV)
    {
        nvec++;
    }
    if (bSDX)
    {
        nvec++;
    }
    if (bCGP)
    {
        nvec++;
    }
    
    /* Make sure the communication buffers are large enough */
    for(mc=0; mc<dd->ndim*2; mc++)
    {
        nvr = ncg[mc] + nat[mc]*nvec;
        if (nvr > comm->cgcm_state_nalloc[mc])
        {
            comm->cgcm_state_nalloc[mc] = over_alloc_dd(nvr);
            srenew(comm->cgcm_state[mc],comm->cgcm_state_nalloc[mc]);
        }
    }
    
    /* Recalculating cg_cm might be cheaper than communicating,
     * but that could give rise to rounding issues.
     */
    home_pos_cg =
        compact_and_copy_vec_cg(dd->ncg_home,move,cgindex,
                                nvec,cg_cm,comm,bCompact);
    
    vec = 0;
    home_pos_at =
        compact_and_copy_vec_at(dd->ncg_home,move,cgindex,
                                nvec,vec++,state->x,comm,bCompact);
    if (bV)
    {
        compact_and_copy_vec_at(dd->ncg_home,move,cgindex,
                                nvec,vec++,state->v,comm,bCompact);
    }
    if (bSDX)
    {
        compact_and_copy_vec_at(dd->ncg_home,move,cgindex,
                                nvec,vec++,state->sd_X,comm,bCompact);
    }
    if (bCGP)
    {
        compact_and_copy_vec_at(dd->ncg_home,move,cgindex,
                                nvec,vec++,state->cg_p,comm,bCompact);
    }
    
    if (bCompact)
    {
        compact_ind(dd->ncg_home,move,
                    dd->index_gl,dd->cgindex,dd->gatindex,
                    dd->ga2la,comm->bLocalCG,
                    fr->cginfo);
    }
    else
    {
        clear_and_mark_ind(dd->ncg_home,move,
                           dd->index_gl,dd->cgindex,dd->gatindex,
                           dd->ga2la,comm->bLocalCG,
                           fr->ns.grid->cell_index);
    }
    
    cginfo_mb = fr->cginfo_mb;

    ncg_stay_home = home_pos_cg;
    for(d=0; d<dd->ndim; d++)
    {
        dim = dd->dim[d];
        ncg_recv = 0;
        nat_recv = 0;
        nvr      = 0;
        for(dir=0; dir<(dd->nc[dim]==2 ? 1 : 2); dir++)
        {
            cdd = d*2 + dir;
            /* Communicate the cg and atom counts */
            sbuf[0] = ncg[cdd];
            sbuf[1] = nat[cdd];
            if (debug)
            {
                fprintf(debug,"Sending ddim %d dir %d: ncg %d nat %d\n",
                        d,dir,sbuf[0],sbuf[1]);
            }
            dd_sendrecv_int(dd, d, dir, sbuf, 2, rbuf, 2);
            
            if ((ncg_recv+rbuf[0])*DD_CGIBS > comm->nalloc_int)
            {
                comm->nalloc_int = over_alloc_dd((ncg_recv+rbuf[0])*DD_CGIBS);
                srenew(comm->buf_int,comm->nalloc_int);
            }
            
            /* Communicate the charge group indices, sizes and flags */
            dd_sendrecv_int(dd, d, dir,
                            comm->cggl_flag[cdd], sbuf[0]*DD_CGIBS,
                            comm->buf_int+ncg_recv*DD_CGIBS, rbuf[0]*DD_CGIBS);
            
            nvs = ncg[cdd] + nat[cdd]*nvec;
            i   = rbuf[0]  + rbuf[1] *nvec;
            vec_rvec_check_alloc(&comm->vbuf,nvr+i);
            
            /* Communicate cgcm and state */
            dd_sendrecv_rvec(dd, d, dir,
                             comm->cgcm_state[cdd], nvs,
                             comm->vbuf.v+nvr, i);
            ncg_recv += rbuf[0];
            nat_recv += rbuf[1];
            nvr      += i;
        }
        
        /* Process the received charge groups */
        buf_pos = 0;
        for(cg=0; cg<ncg_recv; cg++)
        {
            flag = comm->buf_int[cg*DD_CGIBS+1];
            mc = -1;
            if (d < dd->ndim-1)
            {
                /* Check which direction this cg should go */
                for(d2=d+1; (d2<dd->ndim && mc==-1); d2++)
                {
                    if (dd->bGridJump)
                    {
                        /* The cell boundaries for dimension d2 are not equal
                         * for each cell row of the lower dimension(s),
                         * therefore we might need to redetermine where
                         * this cg should go.
                         */
                        dim2 = dd->dim[d2];
                        /* If this cg crosses the box boundary in dimension d2
                         * we can use the communicated flag, so we do not
                         * have to worry about pbc.
                         */
                        if (!((dd->ci[dim2] == dd->nc[dim2]-1 &&
                               (flag & DD_FLAG_FW(d2))) ||
                              (dd->ci[dim2] == 0 &&
                               (flag & DD_FLAG_BW(d2)))))
                        {
                            /* Clear the two flags for this dimension */
                            flag &= ~(DD_FLAG_FW(d2) | DD_FLAG_BW(d2));
                            /* Determine the location of this cg
                             * in lattice coordinates
                             */
                            pos_d = comm->vbuf.v[buf_pos][dim2];
                            if (tric_dir[dim2])
                            {
                                for(d3=dim2+1; d3<DIM; d3++)
                                {
                                    pos_d +=
                                        comm->vbuf.v[buf_pos][d3]*tcm[d3][dim2];
                                }
                            }
                            /* Check of we are not at the box edge.
                             * pbc is only handled in the first step above,
                             * but this check could move over pbc while
                             * the first step did not due to different rounding.
                             */
                            if (pos_d >= cell_x1[dim2] &&
                                dd->ci[dim2] != dd->nc[dim2]-1)
                            {
                                flag |= DD_FLAG_FW(d2);
                            }
                            else if (pos_d < cell_x0[dim2] &&
                                     dd->ci[dim2] != 0)
                            {
                                flag |= DD_FLAG_BW(d2);
                            }
                            comm->buf_int[cg*DD_CGIBS+1] = flag;
                        }
                    }
                    /* Set to which neighboring cell this cg should go */
                    if (flag & DD_FLAG_FW(d2))
                    {
                        mc = d2*2;
                    }
                    else if (flag & DD_FLAG_BW(d2))
                    {
                        if (dd->nc[dd->dim[d2]] > 2)
                        {
                            mc = d2*2+1;
                        }
                        else
                        {
                            mc = d2*2;
                        }
                    }
                }
            }
            
            nrcg = flag & DD_FLAG_NRCG;
            if (mc == -1)
            {
                if (home_pos_cg+1 > dd->cg_nalloc)
                {
                    dd->cg_nalloc = over_alloc_dd(home_pos_cg+1);
                    srenew(dd->index_gl,dd->cg_nalloc);
                    srenew(dd->cgindex,dd->cg_nalloc+1);
                }
                /* Set the global charge group index and size */
                dd->index_gl[home_pos_cg] = comm->buf_int[cg*DD_CGIBS];
                dd->cgindex[home_pos_cg+1] = dd->cgindex[home_pos_cg] + nrcg;
                /* Copy the state from the buffer */
                if (home_pos_cg >= fr->cg_nalloc)
                {
                    dd_realloc_fr_cg(fr,home_pos_cg+1);
                    cg_cm = fr->cg_cm;
                }
                copy_rvec(comm->vbuf.v[buf_pos++],cg_cm[home_pos_cg]);
                /* Set the cginfo */
                fr->cginfo[home_pos_cg] = ddcginfo(cginfo_mb,
                                                   dd->index_gl[home_pos_cg]);
                if (comm->bLocalCG)
                {
                    comm->bLocalCG[dd->index_gl[home_pos_cg]] = TRUE;
                }

                if (home_pos_at+nrcg > state->nalloc)
                {
                    dd_realloc_state(state,f,home_pos_at+nrcg);
                }
                for(i=0; i<nrcg; i++)
                {
                    copy_rvec(comm->vbuf.v[buf_pos++],
                              state->x[home_pos_at+i]);
                }
                if (bV)
                {
                    for(i=0; i<nrcg; i++)
                    {
                        copy_rvec(comm->vbuf.v[buf_pos++],
                                  state->v[home_pos_at+i]);
                    }
                }
                if (bSDX)
                {
                    for(i=0; i<nrcg; i++)
                    {
                        copy_rvec(comm->vbuf.v[buf_pos++],
                                  state->sd_X[home_pos_at+i]);
                    }
                }
                if (bCGP)
                {
                    for(i=0; i<nrcg; i++)
                    {
                        copy_rvec(comm->vbuf.v[buf_pos++],
                                  state->cg_p[home_pos_at+i]);
                    }
                }
                home_pos_cg += 1;
                home_pos_at += nrcg;
            }
            else
            {
                /* Reallocate the buffers if necessary  */
                if (ncg[mc]+1 > comm->cggl_flag_nalloc[mc])
                {
                    comm->cggl_flag_nalloc[mc] = over_alloc_dd(ncg[mc]+1);
                    srenew(comm->cggl_flag[mc],comm->cggl_flag_nalloc[mc]*DD_CGIBS);
                }
                nvr = ncg[mc] + nat[mc]*nvec;
                if (nvr + 1 + nrcg*nvec > comm->cgcm_state_nalloc[mc])
                {
                    comm->cgcm_state_nalloc[mc] = over_alloc_dd(nvr + 1 + nrcg*nvec);
                    srenew(comm->cgcm_state[mc],comm->cgcm_state_nalloc[mc]);
                }
                /* Copy from the receive to the send buffers */
                memcpy(comm->cggl_flag[mc] + ncg[mc]*DD_CGIBS,
                       comm->buf_int + cg*DD_CGIBS,
                       DD_CGIBS*sizeof(int));
                memcpy(comm->cgcm_state[mc][nvr],
                       comm->vbuf.v[buf_pos],
                       (1+nrcg*nvec)*sizeof(rvec));
                buf_pos += 1 + nrcg*nvec;
                ncg[mc] += 1;
                nat[mc] += nrcg;
            }
        }
    }
    
    /* With sorting (!bCompact) the indices are now only partially up to date
     * and ncg_home and nat_home are not the real count, since there are
     * "holes" in the arrays for the charge groups that moved to neighbors.
     */
    dd->ncg_home = home_pos_cg;
    dd->nat_home = home_pos_at;

    if (debug)
    {
        fprintf(debug,"Finished repartitioning\n");
    }

    return ncg_stay_home;
}

void dd_cycles_add(gmx_domdec_t *dd,float cycles,int ddCycl)
{
    dd->comm->cycl[ddCycl] += cycles;
    dd->comm->cycl_n[ddCycl]++;
    if (cycles > dd->comm->cycl_max[ddCycl])
    {
        dd->comm->cycl_max[ddCycl] = cycles;
    }
}

static double force_flop_count(t_nrnb *nrnb)
{
    int i;
    double sum;
    const char *name;

    sum = 0;
    for(i=eNR_NBKERNEL010; i<eNR_NBKERNEL_FREE_ENERGY; i++)
    {
        /* To get closer to the real timings, we half the count
         * for the normal loops and again half it for water loops.
         */
        name = nrnb_str(i);
        if (strstr(name,"W3") != NULL || strstr(name,"W4") != NULL)
        {
            sum += nrnb->n[i]*0.25*cost_nrnb(i);
        }
        else
        {
            sum += nrnb->n[i]*0.50*cost_nrnb(i);
        }
    }
    for(i=eNR_NBKERNEL_FREE_ENERGY; i<=eNR_NB14; i++)
    {
        name = nrnb_str(i);
        if (strstr(name,"W3") != NULL || strstr(name,"W4") != NULL)
        sum += nrnb->n[i]*cost_nrnb(i);
    }
    for(i=eNR_BONDS; i<=eNR_WALLS; i++)
    {
        sum += nrnb->n[i]*cost_nrnb(i);
    }

    return sum;
}

void dd_force_flop_start(gmx_domdec_t *dd,t_nrnb *nrnb)
{
    if (dd->comm->eFlop)
    {
        dd->comm->flop -= force_flop_count(nrnb);
    }
}
void dd_force_flop_stop(gmx_domdec_t *dd,t_nrnb *nrnb)
{
    if (dd->comm->eFlop)
    {
        dd->comm->flop += force_flop_count(nrnb);
        dd->comm->flop_n++;
    }
}  

static void clear_dd_cycle_counts(gmx_domdec_t *dd)
{
    int i;
    
    for(i=0; i<ddCyclNr; i++)
    {
        dd->comm->cycl[i] = 0;
        dd->comm->cycl_n[i] = 0;
        dd->comm->cycl_max[i] = 0;
    }
    dd->comm->flop = 0;
    dd->comm->flop_n = 0;
}

static void get_load_distribution(gmx_domdec_t *dd,gmx_wallcycle_t wcycle)
{
    gmx_domdec_comm_t *comm;
    gmx_domdec_load_t *load;
    gmx_domdec_root_t *root=NULL;
    int  d,dim,cid,i,pos;
    float cell_frac=0,sbuf[DD_NLOAD_MAX];
    bool bSepPME;
    
    if (debug)
    {
        fprintf(debug,"get_load_distribution start\n");
    }

    wallcycle_start(wcycle,ewcDDCOMMLOAD);
    
    comm = dd->comm;
    
    bSepPME = (dd->pme_nodeid >= 0);
    
    for(d=dd->ndim-1; d>=0; d--)
    {
        dim = dd->dim[d];
        /* Check if we participate in the communication in this dimension */
        if (d == dd->ndim-1 || 
            (dd->ci[dd->dim[d+1]]==0 && dd->ci[dd->dim[dd->ndim-1]]==0))
        {
            load = &comm->load[d];
            if (dd->bGridJump)
            {
                cell_frac = comm->cell_f1[d] - comm->cell_f0[d];
            }
            pos = 0;
            if (d == dd->ndim-1)
            {
                sbuf[pos++] = dd_force_load(comm);
                sbuf[pos++] = sbuf[0];
                if (dd->bGridJump)
                {
                    sbuf[pos++] = sbuf[0];
                    sbuf[pos++] = cell_frac;
                    if (d > 0)
                    {
                        sbuf[pos++] = comm->cell_f_max0[d];
                        sbuf[pos++] = comm->cell_f_min1[d];
                    }
                }
                if (bSepPME)
                {
                    sbuf[pos++] = comm->cycl[ddCyclPPduringPME];
                    sbuf[pos++] = comm->cycl[ddCyclPME];
                }
            }
            else
            {
                sbuf[pos++] = comm->load[d+1].sum;
                sbuf[pos++] = comm->load[d+1].max;
                if (dd->bGridJump)
                {
                    sbuf[pos++] = comm->load[d+1].sum_m;
                    sbuf[pos++] = comm->load[d+1].cvol_min*cell_frac;
                    sbuf[pos++] = comm->load[d+1].flags;
                    if (d > 0)
                    {
                        sbuf[pos++] = comm->cell_f_max0[d];
                        sbuf[pos++] = comm->cell_f_min1[d];
                    }
                }
                if (bSepPME)
                {
                    sbuf[pos++] = comm->load[d+1].mdf;
                    sbuf[pos++] = comm->load[d+1].pme;
                }
            }
            load->nload = pos;
            /* Communicate a row in DD direction d.
             * The communicators are setup such that the root always has rank 0.
             */
#ifdef GMX_MPI
            MPI_Gather(sbuf      ,load->nload*sizeof(float),MPI_BYTE,
                       load->load,load->nload*sizeof(float),MPI_BYTE,
                       0,comm->mpi_comm_load[d]);
#endif
            if (dd->ci[dim] == dd->master_ci[dim])
            {
                /* We are the root, process this row */
                if (comm->bDynLoadBal)
                {
                    root = comm->root[d];
                }
                load->sum = 0;
                load->max = 0;
                load->sum_m = 0;
                load->cvol_min = 1;
                load->flags = 0;
                load->mdf = 0;
                load->pme = 0;
                pos = 0;
                for(i=0; i<dd->nc[dim]; i++)
                {
                    load->sum += load->load[pos++];
                    load->max = max(load->max,load->load[pos]);
                    pos++;
                    if (dd->bGridJump)
                    {
                        if (root->bLimited)
                        {
                            /* This direction could not be load balanced properly,
                             * therefore we need to use the maximum iso the average load.
                             */
                            load->sum_m = max(load->sum_m,load->load[pos]);
                        }
                        else
                        {
                            load->sum_m += load->load[pos];
                        }
                        pos++;
                        load->cvol_min = min(load->cvol_min,load->load[pos]);
                        pos++;
                        if (d < dd->ndim-1)
                        {
                            load->flags = (int)(load->load[pos++] + 0.5);
                        }
                        if (d > 0)
                        {
                            root->cell_f_max0[i] = load->load[pos++];
                            root->cell_f_min1[i] = load->load[pos++];
                        }
                    }
                    if (bSepPME)
                    {
                        load->mdf = max(load->mdf,load->load[pos]);
                        pos++;
                        load->pme = max(load->pme,load->load[pos]);
                        pos++;
                    }
                }
                if (comm->bDynLoadBal && root->bLimited)
                {
                    load->sum_m *= dd->nc[dim];
                    load->flags |= (1<<d);
                }
            }
        }
    }

    if (DDMASTER(dd))
    {
        comm->nload      += dd_load_count(comm);
        comm->load_step  += comm->cycl[ddCyclStep];
        comm->load_sum   += comm->load[0].sum;
        comm->load_max   += comm->load[0].max;
        if (comm->bDynLoadBal)
        {
            for(d=0; d<dd->ndim; d++)
            {
                if (comm->load[0].flags & (1<<d))
                {
                    comm->load_lim[d]++;
                }
            }
        }
        if (bSepPME)
        {
            comm->load_mdf += comm->load[0].mdf;
            comm->load_pme += comm->load[0].pme;
        }
    }

    wallcycle_stop(wcycle,ewcDDCOMMLOAD);
    
    if (debug)
    {
        fprintf(debug,"get_load_distribution finished\n");
    }
}

static float dd_force_imb_perf_loss(gmx_domdec_t *dd)
{
    /* Return the relative performance loss on the total run time
     * due to the force calculation load imbalance.
     */
    if (dd->comm->nload > 0)
    {
        return
            (dd->comm->load_max*dd->nnodes - dd->comm->load_sum)/
            (dd->comm->load_step*dd->nnodes);
    }
    else
    {
        return 0;
    }
}

static void print_dd_load_av(FILE *fplog,gmx_domdec_t *dd)
{
    char  buf[STRLEN];
    int   npp,npme,nnodes,d,limp;
    float imbal,pme_f_ratio,lossf,lossp=0;
    bool  bLim;
    gmx_domdec_comm_t *comm;

    comm = dd->comm;
    if (DDMASTER(dd) && comm->nload > 0)
    {
        npp    = dd->nnodes;
        npme   = (dd->pme_nodeid >= 0) ? comm->npmenodes : 0;
        nnodes = npp + npme;
        imbal = comm->load_max*npp/comm->load_sum - 1;
        lossf = dd_force_imb_perf_loss(dd);
        sprintf(buf," Average load imbalance: %.1f %%\n",imbal*100);
        fprintf(fplog,"%s",buf);
        fprintf(stderr,"\n");
        fprintf(stderr,"%s",buf);
        sprintf(buf," Part of the total run time spent waiting due to load imbalance: %.1f %%\n",lossf*100);
        fprintf(fplog,"%s",buf);
        fprintf(stderr,"%s",buf);
        bLim = FALSE;
        if (comm->bDynLoadBal)
        {
            sprintf(buf," Steps where the load balancing was limited by -rdd, -rcon and/or -dds:");
            for(d=0; d<dd->ndim; d++)
            {
                limp = (200*comm->load_lim[d]+1)/(2*comm->nload);
                sprintf(buf+strlen(buf)," %c %d %%",dim2char(dd->dim[d]),limp);
                if (limp >= 50)
                {
                    bLim = TRUE;
                }
            }
            sprintf(buf+strlen(buf),"\n");
            fprintf(fplog,"%s",buf);
            fprintf(stderr,"%s",buf);
        }
        if (npme > 0)
        {
            pme_f_ratio = comm->load_pme/comm->load_mdf;
            lossp = (comm->load_pme -comm->load_mdf)/comm->load_step;
            if (lossp <= 0)
            {
                lossp *= (float)npme/(float)nnodes;
            }
            else
            {
                lossp *= (float)npp/(float)nnodes;
            }
            sprintf(buf," Average PME mesh/force load: %5.3f\n",pme_f_ratio);
            fprintf(fplog,"%s",buf);
            fprintf(stderr,"%s",buf);
            sprintf(buf," Part of the total run time spent waiting due to PP/PME imbalance: %.1f %%\n",fabs(lossp)*100);
            fprintf(fplog,"%s",buf);
            fprintf(stderr,"%s",buf);
        }
        fprintf(fplog,"\n");
        fprintf(stderr,"\n");
        
        if (lossf >= DD_PERF_LOSS)
        {
            sprintf(buf,
                    "NOTE: %.1f %% performance was lost due to load imbalance\n"
                    "      in the domain decomposition.\n",lossf*100);
            if (!comm->bDynLoadBal)
            {
                sprintf(buf+strlen(buf),"      You might want to use dynamic load balancing (option -dlb.)\n");
            }
            else if (bLim)
            {
                sprintf(buf+strlen(buf),"      You might want to decrease the cell size limit (options -rdd, -rcon and/or -dds).\n");
            }
            fprintf(fplog,"%s\n",buf);
            fprintf(stderr,"%s\n",buf);
        }
        if (npme > 0 && fabs(lossp) >= DD_PERF_LOSS)
        {
            sprintf(buf,
                    "NOTE: %.1f %% performance was lost because the PME nodes\n"
                    "      had %s work to do than the PP nodes.\n"
                    "      You might want to %s the number of PME nodes\n"
                    "      or %s the cut-off and the grid spacing.\n",
                    fabs(lossp*100),
                    (lossp < 0) ? "less"     : "more",
                    (lossp < 0) ? "decrease" : "increase",
                    (lossp < 0) ? "decrease" : "increase");
            fprintf(fplog,"%s\n",buf);
            fprintf(stderr,"%s\n",buf);
        }
    }
}

static float dd_vol_min(gmx_domdec_t *dd)
{
    return dd->comm->load[0].cvol_min*dd->nnodes;
}

static bool dd_load_flags(gmx_domdec_t *dd)
{
    return dd->comm->load[0].flags;
}

static float dd_f_imbal(gmx_domdec_t *dd)
{
    return dd->comm->load[0].max*dd->nnodes/dd->comm->load[0].sum - 1;
}

static float dd_pme_f_ratio(gmx_domdec_t *dd)
{
    return dd->comm->load[0].pme/dd->comm->load[0].mdf;
}

static void dd_print_load(FILE *fplog,gmx_domdec_t *dd,gmx_large_int_t step)
{
    int flags,d;
    char buf[22];
    
    flags = dd_load_flags(dd);
    if (flags)
    {
        fprintf(fplog,
                "DD  load balancing is limited by minimum cell size in dimension");
        for(d=0; d<dd->ndim; d++)
        {
            if (flags & (1<<d))
            {
                fprintf(fplog," %c",dim2char(dd->dim[d]));
            }
        }
        fprintf(fplog,"\n");
    }
    fprintf(fplog,"DD  step %s",gmx_step_str(step,buf));
    if (dd->comm->bDynLoadBal)
    {
        fprintf(fplog,"  vol min/aver %5.3f%c",
                dd_vol_min(dd),flags ? '!' : ' ');
    }
    fprintf(fplog," load imb.: force %4.1f%%",dd_f_imbal(dd)*100);
    if (dd->comm->cycl_n[ddCyclPME])
    {
        fprintf(fplog,"  pme mesh/force %5.3f",dd_pme_f_ratio(dd));
    }
    fprintf(fplog,"\n\n");
}

static void dd_print_load_verbose(gmx_domdec_t *dd)
{
    if (dd->comm->bDynLoadBal)
    {
        fprintf(stderr,"vol %4.2f%c ",
                dd_vol_min(dd),dd_load_flags(dd) ? '!' : ' ');
    }
    fprintf(stderr,"imb F %2d%% ",(int)(dd_f_imbal(dd)*100+0.5));
    if (dd->comm->cycl_n[ddCyclPME])
    {
        fprintf(stderr,"pme/F %4.2f ",dd_pme_f_ratio(dd));
    }
}

#ifdef GMX_MPI
static void make_load_communicator(gmx_domdec_t *dd,MPI_Group g_all,
                                   int dim_ind,ivec loc)
{
    MPI_Group g_row;
    MPI_Comm  c_row;
    int  dim,i,*rank;
    ivec loc_c;
    gmx_domdec_root_t *root;
    
    dim = dd->dim[dim_ind];
    copy_ivec(loc,loc_c);
    snew(rank,dd->nc[dim]);
    for(i=0; i<dd->nc[dim]; i++)
    {
        loc_c[dim] = i;
        rank[i] = dd_index(dd->nc,loc_c);
    }
    /* Here we create a new group, that does not necessarily
     * include our process. But MPI_Comm_create needs to be
     * called by all the processes in the original communicator.
     * Calling MPI_Group_free afterwards gives errors, so I assume
     * also the group is needed by all processes. (B. Hess)
     */
    MPI_Group_incl(g_all,dd->nc[dim],rank,&g_row);
    MPI_Comm_create(dd->mpi_comm_all,g_row,&c_row);
    if (c_row != MPI_COMM_NULL)
    {
        /* This process is part of the group */
        dd->comm->mpi_comm_load[dim_ind] = c_row;
        if (dd->comm->eDLB != edlbNO)
        {
            if (dd->ci[dim] == dd->master_ci[dim])
            {
                /* This is the root process of this row */
                snew(dd->comm->root[dim_ind],1);
                root = dd->comm->root[dim_ind];
                snew(root->cell_f,DD_CELL_F_SIZE(dd,dim_ind));
                snew(root->old_cell_f,dd->nc[dim]+1);
                snew(root->bCellMin,dd->nc[dim]);
                if (dim_ind > 0)
                {
                    snew(root->cell_f_max0,dd->nc[dim]);
                    snew(root->cell_f_min1,dd->nc[dim]);
                    snew(root->bound_min,dd->nc[dim]);
                    snew(root->bound_max,dd->nc[dim]);
                }
                snew(root->buf_ncd,dd->nc[dim]);
            }
            else
            {
                /* This is not a root process, we only need to receive cell_f */
                snew(dd->comm->cell_f_row,DD_CELL_F_SIZE(dd,dim_ind));
            }
        }
        if (dd->ci[dim] == dd->master_ci[dim])
        {
            snew(dd->comm->load[dim_ind].load,dd->nc[dim]*DD_NLOAD_MAX);
        }
    }
    sfree(rank);
}
#endif

static void make_load_communicators(gmx_domdec_t *dd)
{
#ifdef GMX_MPI
  MPI_Group g_all;
  int  dim0,dim1,i,j;
  ivec loc;

  if (debug)
    fprintf(debug,"Making load communicators\n");

  MPI_Comm_group(dd->mpi_comm_all,&g_all);
  
  snew(dd->comm->load,dd->ndim);
  snew(dd->comm->mpi_comm_load,dd->ndim);
  
  clear_ivec(loc);
  make_load_communicator(dd,g_all,0,loc);
  if (dd->ndim > 1) {
    dim0 = dd->dim[0];
    for(i=0; i<dd->nc[dim0]; i++) {
      loc[dim0] = i;
      make_load_communicator(dd,g_all,1,loc);
    }
  }
  if (dd->ndim > 2) {
    dim0 = dd->dim[0];
    for(i=0; i<dd->nc[dim0]; i++) {
      loc[dim0] = i;
      dim1 = dd->dim[1];
      for(j=0; j<dd->nc[dim1]; j++) {
          loc[dim1] = j;
          make_load_communicator(dd,g_all,2,loc);
      }
    }
  }

  MPI_Group_free(&g_all);

  if (debug)
    fprintf(debug,"Finished making load communicators\n");
#endif
}

void setup_dd_grid(FILE *fplog,gmx_domdec_t *dd)
{
    bool bZYX;
    int  d,dim,i,j,m;
    ivec tmp,s;
    int  nzone,nzonep;
    ivec dd_zp[DD_MAXIZONE];
    gmx_domdec_zones_t *zones;
    gmx_domdec_ns_ranges_t *izone;
    
    for(d=0; d<dd->ndim; d++)
    {
        dim = dd->dim[d];
        copy_ivec(dd->ci,tmp);
        tmp[dim] = (tmp[dim] + 1) % dd->nc[dim];
        dd->neighbor[d][0] = ddcoord2ddnodeid(dd,tmp);
        copy_ivec(dd->ci,tmp);
        tmp[dim] = (tmp[dim] - 1 + dd->nc[dim]) % dd->nc[dim];
        dd->neighbor[d][1] = ddcoord2ddnodeid(dd,tmp);
        if (debug)
        {
            fprintf(debug,"DD rank %d neighbor ranks in dir %d are + %d - %d\n",
                    dd->rank,dim,
                    dd->neighbor[d][0],
                    dd->neighbor[d][1]);
        }
    }
    
    if (DDMASTER(dd))
    {
        fprintf(stderr,"Making %dD domain decomposition %d x %d x %d\n",
            dd->ndim,dd->nc[XX],dd->nc[YY],dd->nc[ZZ]);
    }
    if (fplog)
    {
        fprintf(fplog,"\nMaking %dD domain decomposition grid %d x %d x %d, home cell index %d %d %d\n\n",
                dd->ndim,
                dd->nc[XX],dd->nc[YY],dd->nc[ZZ],
                dd->ci[XX],dd->ci[YY],dd->ci[ZZ]);
    }
    switch (dd->ndim)
    {
    case 3:
        nzone  = dd_z3n;
        nzonep = dd_zp3n;
        for(i=0; i<nzonep; i++)
        {
            copy_ivec(dd_zp3[i],dd_zp[i]);
        }
        break;
    case 2:
        nzone  = dd_z2n;
        nzonep = dd_zp2n;
        for(i=0; i<nzonep; i++)
        {
            copy_ivec(dd_zp2[i],dd_zp[i]);
        }
        break;
    case 1:
        nzone  = dd_z1n;
        nzonep = dd_zp1n;
        for(i=0; i<nzonep; i++)
        {
            copy_ivec(dd_zp1[i],dd_zp[i]);
        }
        break;
    default:
        gmx_fatal(FARGS,"Can only do 1, 2 or 3D domain decomposition");
        nzone = 0;
        nzonep = 0;
    }

    zones = &dd->comm->zones;

    for(i=0; i<nzone; i++)
    {
        m = 0;
        clear_ivec(zones->shift[i]);
        for(d=0; d<dd->ndim; d++)
        {
            zones->shift[i][dd->dim[d]] = dd_zo[i][m++];
        }
    }
    
    zones->n = nzone;
    for(i=0; i<nzone; i++)
    {
        for(d=0; d<DIM; d++)
        {
            s[d] = dd->ci[d] - zones->shift[i][d];
            if (s[d] < 0)
            {
                s[d] += dd->nc[d];
            }
            else if (s[d] >= dd->nc[d])
            {
                s[d] -= dd->nc[d];
            }
        }
    }
    zones->nizone = nzonep;
    for(i=0; i<zones->nizone; i++)
    {
        if (dd_zp[i][0] != i)
        {
            gmx_fatal(FARGS,"Internal inconsistency in the dd grid setup");
        }
        izone = &zones->izone[i];
        izone->j0 = dd_zp[i][1];
        izone->j1 = dd_zp[i][2];
        for(dim=0; dim<DIM; dim++)
        {
            if (dd->nc[dim] == 1)
            {
                /* All shifts should be allowed */
                izone->shift0[dim] = -1;
                izone->shift1[dim] = 1;
            }
            else
            {
                /*
                  izone->shift0[d] = 0;
                  izone->shift1[d] = 0;
                  for(j=izone->j0; j<izone->j1; j++) {
                  if (dd->shift[j][d] > dd->shift[i][d])
                  izone->shift0[d] = -1;
                  if (dd->shift[j][d] < dd->shift[i][d])
                  izone->shift1[d] = 1;
                  }
                */
                
                int shift_diff;
                
                /* Assume the shift are not more than 1 cell */
                izone->shift0[dim] = 1;
                izone->shift1[dim] = -1;
                for(j=izone->j0; j<izone->j1; j++)
                {
                    shift_diff = zones->shift[j][dim] - zones->shift[i][dim];
                    if (shift_diff < izone->shift0[dim])
                    {
                        izone->shift0[dim] = shift_diff;
                    }
                    if (shift_diff > izone->shift1[dim])
                    {
                        izone->shift1[dim] = shift_diff;
                    }
                }
            }
        }
    }
    
    if (dd->comm->eDLB != edlbNO)
    {
        snew(dd->comm->root,dd->ndim);
    }
    
    if (dd->comm->bRecordLoad)
    {
        make_load_communicators(dd);
    }
}

static void make_pp_communicator(FILE *fplog,t_commrec *cr,int reorder)
{
    gmx_domdec_t *dd;
    gmx_domdec_comm_t *comm;
    int  i,rank,*buf;
    ivec periods;
#ifdef GMX_MPI
    MPI_Comm comm_cart;
#endif
    
    dd = cr->dd;
    comm = dd->comm;
    
#ifdef GMX_MPI
    if (comm->bCartesianPP)
    {
        /* Set up cartesian communication for the particle-particle part */
        if (fplog)
        {
            fprintf(fplog,"Will use a Cartesian communicator: %d x %d x %d\n",
                    dd->nc[XX],dd->nc[YY],dd->nc[ZZ]);
        }
        
        for(i=0; i<DIM; i++)
        {
            periods[i] = TRUE;
        }
        MPI_Cart_create(cr->mpi_comm_mygroup,DIM,dd->nc,periods,reorder,
                        &comm_cart);
        /* We overwrite the old communicator with the new cartesian one */
        cr->mpi_comm_mygroup = comm_cart;
    }
    
    dd->mpi_comm_all = cr->mpi_comm_mygroup;
    MPI_Comm_rank(dd->mpi_comm_all,&dd->rank);
    
    if (comm->bCartesianPP_PME)
    {
        /* Since we want to use the original cartesian setup for sim,
         * and not the one after split, we need to make an index.
         */
        snew(comm->ddindex2ddnodeid,dd->nnodes);
        comm->ddindex2ddnodeid[dd_index(dd->nc,dd->ci)] = dd->rank;
        gmx_sumi(dd->nnodes,comm->ddindex2ddnodeid,cr);
        /* Get the rank of the DD master,
         * above we made sure that the master node is a PP node.
         */
        if (MASTER(cr))
        {
            rank = dd->rank;
        }
        else
        {
            rank = 0;
        }
        MPI_Allreduce(&rank,&dd->masterrank,1,MPI_INT,MPI_SUM,dd->mpi_comm_all);
    }
    else if (comm->bCartesianPP)
    {
        if (cr->npmenodes == 0)
        {
            /* The PP communicator is also
             * the communicator for this simulation
             */
            cr->mpi_comm_mysim = cr->mpi_comm_mygroup;
        }
        cr->nodeid = dd->rank;
        
        MPI_Cart_coords(dd->mpi_comm_all,dd->rank,DIM,dd->ci);
        
        /* We need to make an index to go from the coordinates
         * to the nodeid of this simulation.
         */
        snew(comm->ddindex2simnodeid,dd->nnodes);
        snew(buf,dd->nnodes);
        if (cr->duty & DUTY_PP)
        {
            buf[dd_index(dd->nc,dd->ci)] = cr->sim_nodeid;
        }
        /* Communicate the ddindex to simulation nodeid index */
        MPI_Allreduce(buf,comm->ddindex2simnodeid,dd->nnodes,MPI_INT,MPI_SUM,
                      cr->mpi_comm_mysim);
        sfree(buf);
        
        /* Determine the master coordinates and rank.
         * The DD master should be the same node as the master of this sim.
         */
        for(i=0; i<dd->nnodes; i++)
        {
            if (comm->ddindex2simnodeid[i] == 0)
            {
                ddindex2xyz(dd->nc,i,dd->master_ci);
                MPI_Cart_rank(dd->mpi_comm_all,dd->master_ci,&dd->masterrank);
            }
        }
        if (debug)
        {
            fprintf(debug,"The master rank is %d\n",dd->masterrank);
        }
    }
    else
    {
        /* No Cartesian communicators */
        /* We use the rank in dd->comm->all as DD index */
        ddindex2xyz(dd->nc,dd->rank,dd->ci);
        /* The simulation master nodeid is 0, so the DD master rank is also 0 */
        dd->masterrank = 0;
        clear_ivec(dd->master_ci);
    }
#endif
  
    if (fplog)
    {
        fprintf(fplog,
                "Domain decomposition nodeid %d, coordinates %d %d %d\n\n",
                dd->rank,dd->ci[XX],dd->ci[YY],dd->ci[ZZ]);
    }
    if (debug)
    {
        fprintf(debug,
                "Domain decomposition nodeid %d, coordinates %d %d %d\n\n",
                dd->rank,dd->ci[XX],dd->ci[YY],dd->ci[ZZ]);
    }
}

static void receive_ddindex2simnodeid(t_commrec *cr)
{
    gmx_domdec_t *dd;
    
    gmx_domdec_comm_t *comm;
    int  *buf;
    
    dd = cr->dd;
    comm = dd->comm;
    
#ifdef GMX_MPI
    if (!comm->bCartesianPP_PME && comm->bCartesianPP)
    {
        snew(comm->ddindex2simnodeid,dd->nnodes);
        snew(buf,dd->nnodes);
        if (cr->duty & DUTY_PP)
        {
            buf[dd_index(dd->nc,dd->ci)] = cr->sim_nodeid;
        }
#ifdef GMX_MPI
        /* Communicate the ddindex to simulation nodeid index */
        MPI_Allreduce(buf,comm->ddindex2simnodeid,dd->nnodes,MPI_INT,MPI_SUM,
                      cr->mpi_comm_mysim);
#endif
        sfree(buf);
    }
#endif
}

static gmx_domdec_master_t *init_gmx_domdec_master_t(gmx_domdec_t *dd,
                                                     int ncg,int natoms)
{
    gmx_domdec_master_t *ma;
    int i;

    snew(ma,1);
    
    snew(ma->ncg,dd->nnodes);
    snew(ma->index,dd->nnodes+1);
    snew(ma->cg,ncg);
    snew(ma->nat,dd->nnodes);
    snew(ma->ibuf,dd->nnodes*2);
    snew(ma->cell_x,DIM);
    for(i=0; i<DIM; i++)
    {
        snew(ma->cell_x[i],dd->nc[i]+1);
    }

    if (dd->nnodes <= GMX_DD_NNODES_SENDRECV)
    {
        ma->vbuf = NULL;
    }
    else
    {
        snew(ma->vbuf,natoms);
    }

    return ma;
}

static void split_communicator(FILE *fplog,t_commrec *cr,int dd_node_order,
                               int reorder)
{
    gmx_domdec_t *dd;
    gmx_domdec_comm_t *comm;
    int  i,rank;
    bool bDiv[DIM];
    ivec periods;
#ifdef GMX_MPI
    MPI_Comm comm_cart;
#endif
    
    dd = cr->dd;
    comm = dd->comm;
    
    if (comm->bCartesianPP)
    {
        for(i=1; i<DIM; i++)
        {
            bDiv[i] = ((cr->npmenodes*dd->nc[i]) % (dd->nnodes) == 0);
        }
        if (bDiv[YY] || bDiv[ZZ])
        {
            comm->bCartesianPP_PME = TRUE;
            /* If we have 2D PME decomposition, which is always in x+y,
             * we stack the PME only nodes in z.
             * Otherwise we choose the direction that provides the thinnest slab
             * of PME only nodes as this will have the least effect
             * on the PP communication.
             * But for the PME communication the opposite might be better.
             */
            if (bDiv[ZZ] && (comm->npmenodes_minor > 1 ||
                             !bDiv[YY] ||
                             dd->nc[YY] > dd->nc[ZZ]))
            {
                comm->cartpmedim = ZZ;
            }
            else
            {
                comm->cartpmedim = YY;
            }
            comm->ntot[comm->cartpmedim]
                += (cr->npmenodes*dd->nc[comm->cartpmedim])/dd->nnodes;
        }
        else if (fplog)
        {
            fprintf(fplog,"#pmenodes (%d) is not a multiple of nx*ny (%d*%d) or nx*nz (%d*%d)\n",cr->npmenodes,dd->nc[XX],dd->nc[YY],dd->nc[XX],dd->nc[ZZ]);
            fprintf(fplog,
                    "Will not use a Cartesian communicator for PP <-> PME\n\n");
        }
    }
    
#ifdef GMX_MPI
    if (comm->bCartesianPP_PME)
    {
        if (fplog)
        {
            fprintf(fplog,"Will use a Cartesian communicator for PP <-> PME: %d x %d x %d\n",comm->ntot[XX],comm->ntot[YY],comm->ntot[ZZ]);
        }
        
        for(i=0; i<DIM; i++)
        {
            periods[i] = TRUE;
        }
        MPI_Cart_create(cr->mpi_comm_mysim,DIM,comm->ntot,periods,reorder,
                        &comm_cart);
        
        MPI_Comm_rank(comm_cart,&rank);
        if (MASTERNODE(cr) && rank != 0)
        {
            gmx_fatal(FARGS,"MPI rank 0 was renumbered by MPI_Cart_create, we do not allow this");
        }
        
        /* With this assigment we loose the link to the original communicator
         * which will usually be MPI_COMM_WORLD, unless have multisim.
         */
        cr->mpi_comm_mysim = comm_cart;
        cr->sim_nodeid = rank;
        
        MPI_Cart_coords(cr->mpi_comm_mysim,cr->sim_nodeid,DIM,dd->ci);
        
        if (fplog)
        {
            fprintf(fplog,"Cartesian nodeid %d, coordinates %d %d %d\n\n",
                    cr->sim_nodeid,dd->ci[XX],dd->ci[YY],dd->ci[ZZ]);
        }
        
        if (dd->ci[comm->cartpmedim] < dd->nc[comm->cartpmedim])
        {
            cr->duty = DUTY_PP;
        }
        if (cr->npmenodes == 0 ||
            dd->ci[comm->cartpmedim] >= dd->nc[comm->cartpmedim])
        {
            cr->duty = DUTY_PME;
        }
        
        /* Split the sim communicator into PP and PME only nodes */
        MPI_Comm_split(cr->mpi_comm_mysim,
                       cr->duty,
                       dd_index(comm->ntot,dd->ci),
                       &cr->mpi_comm_mygroup);
    }
    else
    {
        switch (dd_node_order)
        {
        case ddnoPP_PME:
            if (fplog)
            {
                fprintf(fplog,"Order of the nodes: PP first, PME last\n");
            }
            break;
        case ddnoINTERLEAVE:
            /* Interleave the PP-only and PME-only nodes,
             * as on clusters with dual-core machines this will double
             * the communication bandwidth of the PME processes
             * and thus speed up the PP <-> PME and inter PME communication.
             */
            if (fplog)
            {
                fprintf(fplog,"Interleaving PP and PME nodes\n");
            }
            comm->pmenodes = dd_pmenodes(cr);
            break;
        case ddnoCARTESIAN:
            break;
        default:
            gmx_fatal(FARGS,"Unknown dd_node_order=%d",dd_node_order);
        }
    
        if (dd_simnode2pmenode(cr,cr->sim_nodeid) == -1)
        {
            cr->duty = DUTY_PME;
        }
        else
        {
            cr->duty = DUTY_PP;
        }
        
        /* Split the sim communicator into PP and PME only nodes */
        MPI_Comm_split(cr->mpi_comm_mysim,
                       cr->duty,
                       cr->nodeid,
                       &cr->mpi_comm_mygroup);
        MPI_Comm_rank(cr->mpi_comm_mygroup,&cr->nodeid);
    }
#endif

    if (fplog)
    {
        fprintf(fplog,"This is a %s only node\n\n",
                (cr->duty & DUTY_PP) ? "particle-particle" : "PME-mesh");
    }
}

void make_dd_communicators(FILE *fplog,t_commrec *cr,int dd_node_order)
{
    gmx_domdec_t *dd;
    gmx_domdec_comm_t *comm;
    int CartReorder;
    
    dd = cr->dd;
    comm = dd->comm;
    
    copy_ivec(dd->nc,comm->ntot);
    
    comm->bCartesianPP = (dd_node_order == ddnoCARTESIAN);
    comm->bCartesianPP_PME = FALSE;
    
    /* Reorder the nodes by default. This might change the MPI ranks.
     * Real reordering is only supported on very few architectures,
     * Blue Gene is one of them.
     */
    CartReorder = (getenv("GMX_NO_CART_REORDER") == NULL);
    
    if (cr->npmenodes > 0)
    {
        /* Split the communicator into a PP and PME part */
        split_communicator(fplog,cr,dd_node_order,CartReorder);
        if (comm->bCartesianPP_PME)
        {
            /* We (possibly) reordered the nodes in split_communicator,
             * so it is no longer required in make_pp_communicator.
             */
            CartReorder = FALSE;
        }
    }
    else
    {
        /* All nodes do PP and PME */
#ifdef GMX_MPI    
        /* We do not require separate communicators */
        cr->mpi_comm_mygroup = cr->mpi_comm_mysim;
#endif
    }
    
    if (cr->duty & DUTY_PP)
    {
        /* Copy or make a new PP communicator */
        make_pp_communicator(fplog,cr,CartReorder);
    }
    else
    {
        receive_ddindex2simnodeid(cr);
    }
    
    if (!(cr->duty & DUTY_PME))
    {
        /* Set up the commnuication to our PME node */
        dd->pme_nodeid = dd_simnode2pmenode(cr,cr->sim_nodeid);
        dd->pme_receive_vir_ener = receive_vir_ener(cr);
        if (debug)
        {
            fprintf(debug,"My pme_nodeid %d receive ener %d\n",
                    dd->pme_nodeid,dd->pme_receive_vir_ener);
        }
    }
    else
    {
        dd->pme_nodeid = -1;
    }

    if (DDMASTER(dd))
    {
        dd->ma = init_gmx_domdec_master_t(dd,
                                          comm->cgs_gl.nr,
                                          comm->cgs_gl.index[comm->cgs_gl.nr]);
    }
}

static real *get_slb_frac(FILE *fplog,const char *dir,int nc,const char *size_string)
{
    real *slb_frac,tot;
    int  i,n;
    double dbl;
    
    slb_frac = NULL;
    if (nc > 1 && size_string != NULL)
    {
        if (fplog)
        {
            fprintf(fplog,"Using static load balancing for the %s direction\n",
                    dir);
        }
        snew(slb_frac,nc);
        tot = 0;
        for (i=0; i<nc; i++)
        {
            dbl = 0;
            sscanf(size_string,"%lf%n",&dbl,&n);
            if (dbl == 0)
            {
                gmx_fatal(FARGS,"Incorrect or not enough DD cell size entries for direction %s: '%s'",dir,size_string);
            }
            slb_frac[i] = dbl;
            size_string += n;
            tot += slb_frac[i];
        }
        /* Normalize */
        if (fplog)
        {
            fprintf(fplog,"Relative cell sizes:");
        }
        for (i=0; i<nc; i++)
        {
            slb_frac[i] /= tot;
            if (fplog)
            {
                fprintf(fplog," %5.3f",slb_frac[i]);
            }
        }
        if (fplog)
        {
            fprintf(fplog,"\n");
        }
    }
    
    return slb_frac;
}

static int multi_body_bondeds_count(gmx_mtop_t *mtop)
{
    int n,nmol,ftype;
    gmx_mtop_ilistloop_t iloop;
    t_ilist *il;
    
    n = 0;
    iloop = gmx_mtop_ilistloop_init(mtop);
    while (gmx_mtop_ilistloop_next(iloop,&il,&nmol))
    {
        for(ftype=0; ftype<F_NRE; ftype++)
        {
            if ((interaction_function[ftype].flags & IF_BOND) &&
                NRAL(ftype) >  2)
            {
                n += nmol*il[ftype].nr/(1 + NRAL(ftype));
            }
        }
  }

  return n;
}

static int dd_nst_env(FILE *fplog,const char *env_var,int def)
{
    char *val;
    int  nst;
    
    nst = def;
    val = getenv(env_var);
    if (val)
    {
        if (sscanf(val,"%d",&nst) <= 0)
        {
            nst = 1;
        }
        if (fplog)
        {
            fprintf(fplog,"Found env.var. %s = %s, using value %d\n",
                    env_var,val,nst);
        }
    }
    
    return nst;
}

static void dd_warning(t_commrec *cr,FILE *fplog,const char *warn_string)
{
    if (MASTER(cr))
    {
        fprintf(stderr,"\n%s\n",warn_string);
    }
    if (fplog)
    {
        fprintf(fplog,"\n%s\n",warn_string);
    }
}

static void check_dd_restrictions(t_commrec *cr,gmx_domdec_t *dd,
                                  t_inputrec *ir,FILE *fplog)
{
    if (ir->ePBC == epbcSCREW &&
        (dd->nc[XX] == 1 || dd->nc[YY] > 1 || dd->nc[ZZ] > 1))
    {
        gmx_fatal(FARGS,"With pbc=%s can only do domain decomposition in the x-direction",epbc_names[ir->ePBC]);
    }

    if (ir->ns_type == ensSIMPLE)
    {
        gmx_fatal(FARGS,"Domain decomposition does not support simple neighbor searching, use grid searching or use particle decomposition");
    }

    if (ir->nstlist == 0)
    {
        gmx_fatal(FARGS,"Domain decomposition does not work with nstlist=0");
    }

    if (ir->comm_mode == ecmANGULAR && ir->ePBC != epbcNONE)
    {
        dd_warning(cr,fplog,"comm-mode angular will give incorrect results when the comm group partially crosses a periodic boundary");
    }
}

static real average_cellsize_min(gmx_domdec_t *dd,gmx_ddbox_t *ddbox)
{
    int  di,d;
    real r;

    r = ddbox->box_size[XX];
    for(di=0; di<dd->ndim; di++)
    {
        d = dd->dim[di];
        /* Check using the initial average cell size */
        r = min(r,ddbox->box_size[d]*ddbox->skew_fac[d]/dd->nc[d]);
    }

    return r;
}

static int check_dlb_support(FILE *fplog,t_commrec *cr,
                             const char *dlb_opt,bool bRecordLoad,
                             unsigned long Flags,t_inputrec *ir)
{
    gmx_domdec_t *dd;
    int  eDLB=-1;
    char buf[STRLEN];

    switch (dlb_opt[0])
    {
    case 'a': eDLB = edlbAUTO; break;
    case 'n': eDLB = edlbNO;   break;
    case 'y': eDLB = edlbYES;  break;
    default: gmx_incons("Unknown dlb_opt");
    }

    if (Flags & MD_RERUN)
    {
        return edlbNO;
    }

    if (!EI_DYNAMICS(ir->eI))
    {
        if (eDLB == edlbYES)
        {
            sprintf(buf,"NOTE: dynamic load balancing is only supported with dynamics, not with integrator '%s'\n",EI(ir->eI));
            dd_warning(cr,fplog,buf);
        }
            
        return edlbNO;
    }

    if (!bRecordLoad)
    {
        dd_warning(cr,fplog,"NOTE: Cycle counting is not supported on this architecture, will not use dynamic load balancing\n");

        return edlbNO;
    }

    if (Flags & MD_REPRODUCIBLE)
    {
        switch (eDLB)
        {
                        case edlbNO: 
                                break;
                        case edlbAUTO:
                                dd_warning(cr,fplog,"NOTE: reproducability requested, will not use dynamic load balancing\n");
                                eDLB = edlbNO;
                                break;
                        case edlbYES:
                                dd_warning(cr,fplog,"WARNING: reproducability requested with dynamic load balancing, the simulation will NOT be binary reproducable\n");
                                break;
                        default:
                                gmx_fatal(FARGS,"Death horror: undefined case (%d) for load balancing choice",eDLB);
                                break;
        }
    }

    return eDLB;
}

static void set_dd_dim(FILE *fplog,gmx_domdec_t *dd)
{
    int dim;

    dd->ndim = 0;
    if (getenv("GMX_DD_ORDER_ZYX"))
    {
        /* Decomposition order z,y,x */
        if (fplog)
        {
            fprintf(fplog,"Using domain decomposition order z, y, x\n");
        }
        for(dim=DIM-1; dim>=0; dim--)
        {
            if (dd->nc[dim] > 1)
            {
                dd->dim[dd->ndim++] = dim;
            }
        }
    }
    else
    {
        /* Decomposition order x,y,z */
        for(dim=0; dim<DIM; dim++)
        {
            if (dd->nc[dim] > 1)
            {
                dd->dim[dd->ndim++] = dim;
            }
        }
    }
}

static gmx_domdec_comm_t *init_dd_comm()
{
    gmx_domdec_comm_t *comm;
    int  i;

    snew(comm,1);
    snew(comm->cggl_flag,DIM*2);
    snew(comm->cgcm_state,DIM*2);
    for(i=0; i<DIM*2; i++)
    {
        comm->cggl_flag_nalloc[i]  = 0;
        comm->cgcm_state_nalloc[i] = 0;
    }
    
    comm->nalloc_int = 0;
    comm->buf_int    = NULL;

    vec_rvec_init(&comm->vbuf);

    comm->n_load_have    = 0;
    comm->n_load_collect = 0;

    for(i=0; i<ddnatNR-ddnatZONE; i++)
    {
        comm->sum_nat[i] = 0;
    }
    comm->ndecomp = 0;
    comm->nload   = 0;
    comm->load_step = 0;
    comm->load_sum  = 0;
    comm->load_max  = 0;
    clear_ivec(comm->load_lim);
    comm->load_mdf  = 0;
    comm->load_pme  = 0;

    return comm;
}

gmx_domdec_t *init_domain_decomposition(FILE *fplog,t_commrec *cr,
                                        unsigned long Flags,
                                        ivec nc,
                                        real comm_distance_min,real rconstr,
                                        const char *dlb_opt,real dlb_scale,
                                        const char *sizex,const char *sizey,const char *sizez,
                                        gmx_mtop_t *mtop,t_inputrec *ir,
                                        matrix box,rvec *x,
                                        gmx_ddbox_t *ddbox,
                                        int *npme_major,int *npme_minor)
{
    gmx_domdec_t *dd;
    gmx_domdec_comm_t *comm;
    int  recload;
    int  d,i,j;
    real r_2b,r_mb,r_bonded=-1,r_bonded_limit=-1,limit,acs;
    bool bC;
    char buf[STRLEN];
    
    if (fplog)
    {
        fprintf(fplog,
                "\nInitializing Domain Decomposition on %d nodes\n",cr->nnodes);
    }
    
    snew(dd,1);
    dd->comm = init_dd_comm();
    comm = dd->comm;
    snew(comm->cggl_flag,DIM*2);
    snew(comm->cgcm_state,DIM*2);

    dd->npbcdim   = ePBC2npbcdim(ir->ePBC);
    dd->bScrewPBC = (ir->ePBC == epbcSCREW);
    
    dd->bSendRecv2      = dd_nst_env(fplog,"GMX_DD_SENDRECV2",0);
    comm->eFlop         = dd_nst_env(fplog,"GMX_DLB_FLOP",0);
    recload             = dd_nst_env(fplog,"GMX_DD_LOAD",1);
    comm->nstSortCG     = dd_nst_env(fplog,"GMX_DD_SORT",1);
    comm->nstDDDump     = dd_nst_env(fplog,"GMX_DD_DUMP",0);
    comm->nstDDDumpGrid = dd_nst_env(fplog,"GMX_DD_DUMP_GRID",0);
    comm->DD_debug      = dd_nst_env(fplog,"GMX_DD_DEBUG",0);

    dd->pme_recv_f_alloc = 0;
    dd->pme_recv_f_buf = NULL;

    if (dd->bSendRecv2 && fplog)
    {
        fprintf(fplog,"Will use two sequential MPI_Sendrecv calls instead of two simultaneous non-blocking MPI_Irecv and MPI_Isend pairs for constraint and vsite communication\n");
    }
    if (comm->eFlop)
    {
        if (fplog)
        {
            fprintf(fplog,"Will load balance based on FLOP count\n");
        }
        if (comm->eFlop > 1)
        {
            srand(1+cr->nodeid);
        }
        comm->bRecordLoad = TRUE;
    }
    else
    {
        comm->bRecordLoad = (wallcycle_have_counter() && recload > 0);
                             
    }
    
    comm->eDLB = check_dlb_support(fplog,cr,dlb_opt,comm->bRecordLoad,Flags,ir);
    
    comm->bDynLoadBal = (comm->eDLB == edlbYES);
    if (fplog)
    {
        fprintf(fplog,"Dynamic load balancing: %s\n",edlb_names[comm->eDLB]);
    }
    dd->bGridJump = comm->bDynLoadBal;
    
    if (comm->nstSortCG)
    {
        if (fplog)
        {
            if (comm->nstSortCG == 1)
            {
                fprintf(fplog,"Will sort the charge groups at every domain (re)decomposition\n");
            }
            else
            {
                fprintf(fplog,"Will sort the charge groups every %d steps\n",
                        comm->nstSortCG);
            }
        }
        snew(comm->sort,1);
    }
    else
    {
        if (fplog)
        {
            fprintf(fplog,"Will not sort the charge groups\n");
        }
    }
    
    comm->bInterCGBondeds = (ncg_mtop(mtop) > mtop->mols.nr);
    if (comm->bInterCGBondeds)
    {
        comm->bInterCGMultiBody = (multi_body_bondeds_count(mtop) > 0);
    }
    else
    {
        comm->bInterCGMultiBody = FALSE;
    }
    
    dd->bInterCGcons = inter_charge_group_constraints(mtop);

    if (ir->rlistlong == 0)
    {
        /* Set the cut-off to some very large value,
         * so we don't need if statements everywhere in the code.
         * We use sqrt, since the cut-off is squared in some places.
         */
        comm->cutoff   = GMX_CUTOFF_INF;
    }
    else
    {
        comm->cutoff   = ir->rlistlong;
    }
    comm->cutoff_mbody = 0;
    
    comm->cellsize_limit = 0;
    comm->bBondComm = FALSE;

    if (comm->bInterCGBondeds)
    {
        if (comm_distance_min > 0)
        {
            comm->cutoff_mbody = comm_distance_min;
            if (Flags & MD_DDBONDCOMM)
            {
                comm->bBondComm = (comm->cutoff_mbody > comm->cutoff);
            }
            else
            {
                comm->cutoff = max(comm->cutoff,comm->cutoff_mbody);
            }
            r_bonded_limit = comm->cutoff_mbody;
        }
        else if (ir->bPeriodicMols)
        {
            /* Can not easily determine the required cut-off */
            dd_warning(cr,fplog,"NOTE: Periodic molecules: can not easily determine the required minimum bonded cut-off, using half the non-bonded cut-off\n");
            comm->cutoff_mbody = comm->cutoff/2;
            r_bonded_limit = comm->cutoff_mbody;
        }
        else
        {
            if (MASTER(cr))
            {
                dd_bonded_cg_distance(fplog,dd,mtop,ir,x,box,
                                      Flags & MD_DDBONDCHECK,&r_2b,&r_mb);
            }
            gmx_bcast(sizeof(r_2b),&r_2b,cr);
            gmx_bcast(sizeof(r_mb),&r_mb,cr);

            /* We use an initial margin of 10% for the minimum cell size,
             * except when we are just below the non-bonded cut-off.
             */
            if (Flags & MD_DDBONDCOMM)
            {
                if (max(r_2b,r_mb) > comm->cutoff)
                {
                    r_bonded       = max(r_2b,r_mb);
                    r_bonded_limit = 1.1*r_bonded;
                    comm->bBondComm = TRUE;
                }
                else
                {
                    r_bonded       = r_mb;
                    r_bonded_limit = min(1.1*r_bonded,comm->cutoff);
                }
                /* We determine cutoff_mbody later */
            }
            else
            {
                /* No special bonded communication,
                 * simply increase the DD cut-off.
                 */
                r_bonded_limit     = 1.1*max(r_2b,r_mb);
                comm->cutoff_mbody = r_bonded_limit;
                comm->cutoff       = max(comm->cutoff,comm->cutoff_mbody);
            }
        }
        comm->cellsize_limit = max(comm->cellsize_limit,r_bonded_limit);
        if (fplog)
        {
            fprintf(fplog,
                    "Minimum cell size due to bonded interactions: %.3f nm\n",
                    comm->cellsize_limit);
        }
    }

    if (dd->bInterCGcons && rconstr <= 0)
    {
        /* There is a cell size limit due to the constraints (P-LINCS) */
        rconstr = constr_r_max(fplog,mtop,ir);
        if (fplog)
        {
            fprintf(fplog,
                    "Estimated maximum distance required for P-LINCS: %.3f nm\n",
                    rconstr);
            if (rconstr > comm->cellsize_limit)
            {
                fprintf(fplog,"This distance will limit the DD cell size, you can override this with -rcon\n");
            }
        }
    }
    else if (rconstr > 0 && fplog)
    {
        /* Here we do not check for dd->bInterCGcons,
         * because one can also set a cell size limit for virtual sites only
         * and at this point we don't know yet if there are intercg v-sites.
         */
        fprintf(fplog,
                "User supplied maximum distance required for P-LINCS: %.3f nm\n",
                rconstr);
    }
    comm->cellsize_limit = max(comm->cellsize_limit,rconstr);

    comm->cgs_gl = gmx_mtop_global_cgs(mtop);

    if (nc[XX] > 0)
    {
        copy_ivec(nc,dd->nc);
        set_dd_dim(fplog,dd);
        set_ddbox_cr(cr,&dd->nc,ir,box,&comm->cgs_gl,x,ddbox);

        if (cr->npmenodes == -1)
        {
            cr->npmenodes = 0;
        }
        acs = average_cellsize_min(dd,ddbox);
        if (acs < comm->cellsize_limit)
        {
            if (fplog)
            {
                fprintf(fplog,"ERROR: The initial cell size (%f) is smaller than the cell size limit (%f)\n",acs,comm->cellsize_limit);
            }
            gmx_fatal_collective(FARGS,MASTER(cr),
                                 "The initial cell size (%f) is smaller than the cell size limit (%f), change options -dd, -rdd or -rcon, see the log file for details",
                                 acs,comm->cellsize_limit);
        }
    }
    else
    {
        set_ddbox_cr(cr,NULL,ir,box,&comm->cgs_gl,x,ddbox);

        /* We need to choose the optimal DD grid and possibly PME nodes */
        limit = dd_choose_grid(fplog,cr,dd,ir,mtop,box,ddbox,
                               comm->eDLB!=edlbNO,dlb_scale,
                               comm->cellsize_limit,comm->cutoff,
                               comm->bInterCGBondeds,comm->bInterCGMultiBody);
        
        if (dd->nc[XX] == 0)
        {
            bC = (dd->bInterCGcons && rconstr > r_bonded_limit);
            sprintf(buf,"Change the number of nodes or mdrun option %s%s%s",
                    !bC ? "-rdd" : "-rcon",
                    comm->eDLB!=edlbNO ? " or -dds" : "",
                    bC ? " or your LINCS settings" : "");

            gmx_fatal_collective(FARGS,MASTER(cr),
                                 "There is no domain decomposition for %d nodes that is compatible with the given box and a minimum cell size of %g nm\n"
                                 "%s\n"
                                 "Look in the log file for details on the domain decomposition",
                                 cr->nnodes-cr->npmenodes,limit,buf);
        }
        set_dd_dim(fplog,dd);
    }

    if (fplog)
    {
        fprintf(fplog,
                "Domain decomposition grid %d x %d x %d, separate PME nodes %d\n",
                dd->nc[XX],dd->nc[YY],dd->nc[ZZ],cr->npmenodes);
    }
    
    dd->nnodes = dd->nc[XX]*dd->nc[YY]*dd->nc[ZZ];
    if (cr->nnodes - dd->nnodes != cr->npmenodes)
    {
        gmx_fatal(FARGS,"The size of the domain decomposition grid (%d) does not match the number of nodes (%d). The total number of nodes is %d",
                  dd->nnodes,cr->nnodes - cr->npmenodes,cr->nnodes);
    }
    if (cr->npmenodes > dd->nnodes)
    {
        gmx_fatal(FARGS,"The number of separate PME node (%d) is larger than the number of PP nodes (%d), this is not supported.",cr->npmenodes,dd->nnodes);
    }
    if (cr->npmenodes > 0)
    {
        comm->npmenodes = cr->npmenodes;
    }
    else
    {
        comm->npmenodes = dd->nnodes;
    }

    if (EEL_PME(ir->coulombtype))
    {
        if (comm->npmenodes > dd->nc[XX] && comm->npmenodes % dd->nc[XX] == 0 &&
            getenv("GMX_PMEONEDD") == NULL)
        {
            comm->npmedecompdim   = 2;
            comm->npmenodes_major = dd->nc[XX];
            comm->npmenodes_minor = comm->npmenodes/comm->npmenodes_major;
        }
        else
        {
            comm->npmedecompdim   = 1;
            comm->npmenodes_major = comm->npmenodes;
            comm->npmenodes_minor = comm->npmenodes/comm->npmenodes_major;
        }
        if (fplog)
        {
            fprintf(fplog,"PME domain decomposition: %d x %d x %d\n",
                    comm->npmenodes_major,comm->npmenodes_minor,1);
        }
    }
    else
    {
        comm->npmedecompdim   = 0;
        comm->npmenodes_major = 0;
        comm->npmenodes_minor = 0;
    }
    
    /* Technically we don't need both of these, but it simplifies code not having to recalculate it */
    *npme_major = comm->npmenodes_major;
    *npme_minor = comm->npmenodes_minor;
        
    snew(comm->slb_frac,DIM);
    if (comm->eDLB == edlbNO)
    {
        comm->slb_frac[XX] = get_slb_frac(fplog,"x",dd->nc[XX],sizex);
        comm->slb_frac[YY] = get_slb_frac(fplog,"y",dd->nc[YY],sizey);
        comm->slb_frac[ZZ] = get_slb_frac(fplog,"z",dd->nc[ZZ],sizez);
    }

    if (comm->bInterCGBondeds && comm->cutoff_mbody == 0)
    {
        if (comm->bBondComm || comm->eDLB != edlbNO)
        {
            /* Set the bonded communication distance to halfway
             * the minimum and the maximum,
             * since the extra communication cost is nearly zero.
             */
            acs = average_cellsize_min(dd,ddbox);
            comm->cutoff_mbody = 0.5*(r_bonded + acs);
            if (comm->eDLB != edlbNO)
            {
                /* Check if this does not limit the scaling */
                comm->cutoff_mbody = min(comm->cutoff_mbody,dlb_scale*acs);
            }
            if (!comm->bBondComm)
            {
                /* Without bBondComm do not go beyond the n.b. cut-off */
                comm->cutoff_mbody = min(comm->cutoff_mbody,comm->cutoff);
                if (comm->cellsize_limit >= comm->cutoff)
                {
                    /* We don't loose a lot of efficieny
                     * when increasing it to the n.b. cut-off.
                     * It can even be slightly faster, because we need
                     * less checks for the communication setup.
                     */
                    comm->cutoff_mbody = comm->cutoff;
                }
            }
            /* Check if we did not end up below our original limit */
            comm->cutoff_mbody = max(comm->cutoff_mbody,r_bonded_limit);

            if (comm->cutoff_mbody > comm->cellsize_limit)
            {
                comm->cellsize_limit = comm->cutoff_mbody;
            }
        }
        /* Without DLB and cutoff_mbody<cutoff, cutoff_mbody is dynamic */
    }

    if (debug)
    {
        fprintf(debug,"Bonded atom communication beyond the cut-off: %d\n"
                "cellsize limit %f\n",
                comm->bBondComm,comm->cellsize_limit);
    }
    
    if (MASTER(cr))
    {
        check_dd_restrictions(cr,dd,ir,fplog);
    }

    comm->partition_step = INT_MIN;
    dd->ddp_count = 0;

    clear_dd_cycle_counts(dd);

    return dd;
}

static void set_dlb_limits(gmx_domdec_t *dd)

{
    int d;

    for(d=0; d<dd->ndim; d++)
    {
        dd->comm->cd[d].np = dd->comm->cd[d].np_dlb;
        dd->comm->cellsize_min[dd->dim[d]] =
            dd->comm->cellsize_min_dlb[dd->dim[d]];
    }
}


static void turn_on_dlb(FILE *fplog,t_commrec *cr,gmx_large_int_t step)
{
    gmx_domdec_t *dd;
    gmx_domdec_comm_t *comm;
    real cellsize_min;
    int  d,nc,i;
    char buf[STRLEN];
    
    dd = cr->dd;
    comm = dd->comm;
    
    if (fplog)
    {
        fprintf(fplog,"At step %s the performance loss due to force load imbalance is %.1f %%\n",gmx_step_str(step,buf),dd_force_imb_perf_loss(dd)*100);
    }

    cellsize_min = comm->cellsize_min[dd->dim[0]];
    for(d=1; d<dd->ndim; d++)
    {
        cellsize_min = min(cellsize_min,comm->cellsize_min[dd->dim[d]]);
    }

    if (cellsize_min < comm->cellsize_limit*1.05)
    {
        dd_warning(cr,fplog,"NOTE: the minimum cell size is smaller than 1.05 times the cell size limit, will not turn on dynamic load balancing\n");

        /* Change DLB from "auto" to "no". */
        comm->eDLB = edlbNO;

        return;
    }

    dd_warning(cr,fplog,"NOTE: Turning on dynamic load balancing\n");
    comm->bDynLoadBal = TRUE;
    dd->bGridJump = TRUE;
    
    set_dlb_limits(dd);

    /* We can set the required cell size info here,
     * so we do not need to communicate this.
     * The grid is completely uniform.
     */
    for(d=0; d<dd->ndim; d++)
    {
        if (comm->root[d])
        {
            comm->load[d].sum_m = comm->load[d].sum;

            nc = dd->nc[dd->dim[d]];
            for(i=0; i<nc; i++)
            {
                comm->root[d]->cell_f[i]    = i/(real)nc;
                if (d > 0)
                {
                    comm->root[d]->cell_f_max0[i] =  i   /(real)nc;
                    comm->root[d]->cell_f_min1[i] = (i+1)/(real)nc;
                }
            }
            comm->root[d]->cell_f[nc] = 1.0;
        }
    }
}

static char *init_bLocalCG(gmx_mtop_t *mtop)
{
    int  ncg,cg;
    char *bLocalCG;
    
    ncg = ncg_mtop(mtop);
    snew(bLocalCG,ncg);
    for(cg=0; cg<ncg; cg++)
    {
        bLocalCG[cg] = FALSE;
    }

    return bLocalCG;
}

void dd_init_bondeds(FILE *fplog,
                     gmx_domdec_t *dd,gmx_mtop_t *mtop,
                     gmx_vsite_t *vsite,gmx_constr_t constr,
                     t_inputrec *ir,bool bBCheck,cginfo_mb_t *cginfo_mb)
{
    gmx_domdec_comm_t *comm;
    bool bBondComm;
    int  d;

    dd_make_reverse_top(fplog,dd,mtop,vsite,constr,ir,bBCheck);

    comm = dd->comm;

    if (comm->bBondComm)
    {
        /* Communicate atoms beyond the cut-off for bonded interactions */
        comm = dd->comm;

        comm->cglink = make_charge_group_links(mtop,dd,cginfo_mb);

        comm->bLocalCG = init_bLocalCG(mtop);
    }
    else
    {
        /* Only communicate atoms based on cut-off */
        comm->cglink   = NULL;
        comm->bLocalCG = NULL;
    }
}

static void print_dd_settings(FILE *fplog,gmx_domdec_t *dd,
                              t_inputrec *ir,
                              bool bDynLoadBal,real dlb_scale,
                              gmx_ddbox_t *ddbox)
{
    gmx_domdec_comm_t *comm;
    int  d;
    ivec np;
    real limit,shrink;
    char buf[64];

    if (fplog == NULL)
    {
        return;
    }

    comm = dd->comm;

    if (bDynLoadBal)
    {
        fprintf(fplog,"The maximum number of communication pulses is:");
        for(d=0; d<dd->ndim; d++)
        {
            fprintf(fplog," %c %d",dim2char(dd->dim[d]),comm->cd[d].np_dlb);
        }
        fprintf(fplog,"\n");
        fprintf(fplog,"The minimum size for domain decomposition cells is %.3f nm\n",comm->cellsize_limit);
        fprintf(fplog,"The requested allowed shrink of DD cells (option -dds) is: %.2f\n",dlb_scale);
        fprintf(fplog,"The allowed shrink of domain decomposition cells is:");
        for(d=0; d<DIM; d++)
        {
            if (dd->nc[d] > 1)
            {
                if (d >= ddbox->npbcdim && dd->nc[d] == 2)
                {
                    shrink = 0;
                }
                else
                {
                    shrink =
                        comm->cellsize_min_dlb[d]/
                        (ddbox->box_size[d]*ddbox->skew_fac[d]/dd->nc[d]);
                }
                fprintf(fplog," %c %.2f",dim2char(d),shrink);
            }
        }
        fprintf(fplog,"\n");
    }
    else
    {
        set_dd_cell_sizes_slb(dd,ddbox,FALSE,np);
        fprintf(fplog,"The initial number of communication pulses is:");
        for(d=0; d<dd->ndim; d++)
        {
            fprintf(fplog," %c %d",dim2char(dd->dim[d]),np[dd->dim[d]]);
        }
        fprintf(fplog,"\n");
        fprintf(fplog,"The initial domain decomposition cell size is:");
        for(d=0; d<DIM; d++) {
            if (dd->nc[d] > 1)
            {
                fprintf(fplog," %c %.2f nm",
                        dim2char(d),dd->comm->cellsize_min[d]);
            }
        }
        fprintf(fplog,"\n\n");
    }
    
    if (comm->bInterCGBondeds || dd->vsite_comm || dd->constraint_comm)
    {
        fprintf(fplog,"The maximum allowed distance for charge groups involved in interactions is:\n");
        fprintf(fplog,"%40s  %-7s %6.3f nm\n",
                "non-bonded interactions","",comm->cutoff);

        if (bDynLoadBal)
        {
            limit = dd->comm->cellsize_limit;
        }
        else
        {
            if (dynamic_dd_box(ddbox,ir))
            {
                fprintf(fplog,"(the following are initial values, they could change due to box deformation)\n");
            }
            limit = dd->comm->cellsize_min[XX];
            for(d=1; d<DIM; d++)
            {
                limit = min(limit,dd->comm->cellsize_min[d]);
            }
        }

        if (comm->bInterCGBondeds)
        {
            fprintf(fplog,"%40s  %-7s %6.3f nm\n",
                    "two-body bonded interactions","(-rdd)",
                    max(comm->cutoff,comm->cutoff_mbody));
            fprintf(fplog,"%40s  %-7s %6.3f nm\n",
                    "multi-body bonded interactions","(-rdd)",
                    (comm->bBondComm || dd->bGridJump) ? comm->cutoff_mbody : min(comm->cutoff,limit));
        }
        if (dd->vsite_comm)
        {
            fprintf(fplog,"%40s  %-7s %6.3f nm\n",
                    "virtual site constructions","(-rcon)",limit);
        }
        if (dd->constraint_comm)
        {
            sprintf(buf,"atoms separated by up to %d constraints",
                    1+ir->nProjOrder);
            fprintf(fplog,"%40s  %-7s %6.3f nm\n",
                    buf,"(-rcon)",limit);
        }
        fprintf(fplog,"\n");
    }
    
    fflush(fplog);
}

void set_dd_parameters(FILE *fplog,gmx_domdec_t *dd,real dlb_scale,
                       t_inputrec *ir,t_forcerec *fr,
                       gmx_ddbox_t *ddbox)
{
    gmx_domdec_comm_t *comm;
    int  d,dim,npulse,npulse_d_max,npulse_d;
    bool bNoCutOff;
    int  natoms_tot;
    real vol_frac;

    comm = dd->comm;

    bNoCutOff = (ir->rvdw == 0 || ir->rcoulomb == 0);

    if (EEL_PME(ir->coulombtype))
    {
        init_ddpme(dd,&comm->ddpme[0],0,comm->npmenodes_major);
        if (comm->npmedecompdim >= 2)
        {
            init_ddpme(dd,&comm->ddpme[1],1,
                       comm->npmenodes/comm->npmenodes_major);
        }
    }
    else
    {
        comm->npmenodes = 0;
        if (dd->pme_nodeid >= 0)
        {
            gmx_fatal(FARGS,"Can not have separate PME nodes without PME electrostatics");
        }
    }
    
    /* If each molecule is a single charge group
     * or we use domain decomposition for each periodic dimension,
     * we do not need to take pbc into account for the bonded interactions.
     */
    if (fr->ePBC == epbcNONE || !comm->bInterCGBondeds ||
        (dd->nc[XX]>1 && dd->nc[YY]>1 && (dd->nc[ZZ]>1 || fr->ePBC==epbcXY)))
    {
        fr->bMolPBC = FALSE;
    }
    else
    {
        fr->bMolPBC = TRUE;
    }
        
    if (debug)
    {
        fprintf(debug,"The DD cut-off is %f\n",comm->cutoff);
    }
    if (comm->eDLB != edlbNO)
    {
        /* Determine the maximum number of comm. pulses in one dimension */
        
        comm->cellsize_limit = max(comm->cellsize_limit,comm->cutoff_mbody);
        
        /* Determine the maximum required number of grid pulses */
        if (comm->cellsize_limit >= comm->cutoff)
        {
            /* Only a single pulse is required */
            npulse = 1;
        }
        else if (!bNoCutOff && comm->cellsize_limit > 0)
        {
            /* We round down slightly here to avoid overhead due to the latency
             * of extra communication calls when the cut-off
             * would be only slightly longer than the cell size.
             * Later cellsize_limit is redetermined,
             * so we can not miss interactions due to this rounding.
             */
            npulse = (int)(0.96 + comm->cutoff/comm->cellsize_limit);
        }
        else
        {
            /* There is no cell size limit */
            npulse = max(dd->nc[XX]-1,max(dd->nc[YY]-1,dd->nc[ZZ]-1));
        }

        if (!bNoCutOff && npulse > 1)
        {
            /* See if we can do with less pulses, based on dlb_scale */
            npulse_d_max = 0;
            for(d=0; d<dd->ndim; d++)
            {
                dim = dd->dim[d];
                npulse_d = (int)(1 + dd->nc[dim]*comm->cutoff
                                 /(ddbox->box_size[dim]*ddbox->skew_fac[dim]*dlb_scale));
                npulse_d_max = max(npulse_d_max,npulse_d);
            }
            npulse = min(npulse,npulse_d_max);
        }
        
        /* This env var can override npulse */
        d = dd_nst_env(fplog,"GMX_DD_NPULSE",0);
        if (d > 0)
        {
            npulse = d;
        }

        comm->maxpulse = 1;
        comm->bVacDLBNoLimit = (ir->ePBC == epbcNONE);
        for(d=0; d<dd->ndim; d++)
        {
            comm->cd[d].np_dlb = min(npulse,dd->nc[dd->dim[d]]-1);
            comm->cd[d].np_nalloc = comm->cd[d].np_dlb;
            snew(comm->cd[d].ind,comm->cd[d].np_nalloc);
            comm->maxpulse = max(comm->maxpulse,comm->cd[d].np_dlb);
            if (comm->cd[d].np_dlb < dd->nc[dd->dim[d]]-1)
            {
                comm->bVacDLBNoLimit = FALSE;
            }
        }
        
        /* cellsize_limit is set for LINCS in init_domain_decomposition */
        if (!comm->bVacDLBNoLimit)
        {
            comm->cellsize_limit = max(comm->cellsize_limit,
                                       comm->cutoff/comm->maxpulse);
        }
        comm->cellsize_limit = max(comm->cellsize_limit,comm->cutoff_mbody);
        /* Set the minimum cell size for each DD dimension */
        for(d=0; d<dd->ndim; d++)
        {
            if (comm->bVacDLBNoLimit ||
                comm->cd[d].np_dlb*comm->cellsize_limit >= comm->cutoff)
            {
                comm->cellsize_min_dlb[dd->dim[d]] = comm->cellsize_limit;
            }
            else
            {
                comm->cellsize_min_dlb[dd->dim[d]] =
                    comm->cutoff/comm->cd[d].np_dlb;
            }
        }
        if (comm->cutoff_mbody <= 0)
        {
            comm->cutoff_mbody = min(comm->cutoff,comm->cellsize_limit);
        }
        if (comm->bDynLoadBal)
        {
            set_dlb_limits(dd);
        }
    }
    
    print_dd_settings(fplog,dd,ir,comm->bDynLoadBal,dlb_scale,ddbox);
    if (comm->eDLB == edlbAUTO)
    {
        if (fplog)
        {
            fprintf(fplog,"When dynamic load balancing gets turned on, these settings will change to:\n");
        }
        print_dd_settings(fplog,dd,ir,TRUE,dlb_scale,ddbox);
    }

    vol_frac = 1/(real)dd->nnodes + comm_box_frac(dd->nc,comm->cutoff,ddbox);
    if (debug)
    {
        fprintf(debug,"Volume fraction for all DD zones: %f\n",vol_frac);
    }
    natoms_tot = comm->cgs_gl.index[comm->cgs_gl.nr];
   
    dd->ga2la = ga2la_init(natoms_tot,vol_frac*natoms_tot);
}

static void merge_cg_buffers(int ncell,
                             gmx_domdec_comm_dim_t *cd, int pulse,
                             int  *ncg_cell,
                             int  *index_gl, int  *recv_i,
                             rvec *cg_cm,    rvec *recv_vr,
                             int *cgindex,
                             cginfo_mb_t *cginfo_mb,int *cginfo)
{
    gmx_domdec_ind_t *ind,*ind_p;
    int p,cell,c,cg,cg0,cg1,cg_gl,nat;
    int shift,shift_at;
    
    ind = &cd->ind[pulse];
    
    /* First correct the already stored data */
    shift = ind->nrecv[ncell];
    for(cell=ncell-1; cell>=0; cell--)
    {
        shift -= ind->nrecv[cell];
        if (shift > 0)
        {
            /* Move the cg's present from previous grid pulses */
            cg0 = ncg_cell[ncell+cell];
            cg1 = ncg_cell[ncell+cell+1];
            cgindex[cg1+shift] = cgindex[cg1];
            for(cg=cg1-1; cg>=cg0; cg--)
            {
                index_gl[cg+shift] = index_gl[cg];
                copy_rvec(cg_cm[cg],cg_cm[cg+shift]);
                cgindex[cg+shift] = cgindex[cg];
                cginfo[cg+shift] = cginfo[cg];
            }
            /* Correct the already stored send indices for the shift */
            for(p=1; p<=pulse; p++)
            {
                ind_p = &cd->ind[p];
                cg0 = 0;
                for(c=0; c<cell; c++)
                {
                    cg0 += ind_p->nsend[c];
                }
                cg1 = cg0 + ind_p->nsend[cell];
                for(cg=cg0; cg<cg1; cg++)
                {
                    ind_p->index[cg] += shift;
                }
            }
        }
    }

    /* Merge in the communicated buffers */
    shift = 0;
    shift_at = 0;
    cg0 = 0;
    for(cell=0; cell<ncell; cell++)
    {
        cg1 = ncg_cell[ncell+cell+1] + shift;
        if (shift_at > 0)
        {
            /* Correct the old cg indices */
            for(cg=ncg_cell[ncell+cell]; cg<cg1; cg++)
            {
                cgindex[cg+1] += shift_at;
            }
        }
        for(cg=0; cg<ind->nrecv[cell]; cg++)
        {
            /* Copy this charge group from the buffer */
            index_gl[cg1] = recv_i[cg0];
            copy_rvec(recv_vr[cg0],cg_cm[cg1]);
            /* Add it to the cgindex */
            cg_gl = index_gl[cg1];
            cginfo[cg1] = ddcginfo(cginfo_mb,cg_gl);
            nat = GET_CGINFO_NATOMS(cginfo[cg1]);
            cgindex[cg1+1] = cgindex[cg1] + nat;
            cg0++;
            cg1++;
            shift_at += nat;
        }
        shift += ind->nrecv[cell];
        ncg_cell[ncell+cell+1] = cg1;
    }
}

static void make_cell2at_index(gmx_domdec_comm_dim_t *cd,
                               int nzone,int cg0,const int *cgindex)
{
    int cg,zone,p;
    
    /* Store the atom block boundaries for easy copying of communication buffers
     */
    cg = cg0;
    for(zone=0; zone<nzone; zone++)
    {
        for(p=0; p<cd->np; p++) {
            cd->ind[p].cell2at0[zone] = cgindex[cg];
            cg += cd->ind[p].nrecv[zone];
            cd->ind[p].cell2at1[zone] = cgindex[cg];
        }
    }
}

static bool missing_link(t_blocka *link,int cg_gl,char *bLocalCG)
{
    int  i;
    bool bMiss;

    bMiss = FALSE;
    for(i=link->index[cg_gl]; i<link->index[cg_gl+1]; i++)
    {
        if (!bLocalCG[link->a[i]])
        {
            bMiss = TRUE;
        }
    }

    return bMiss;
}

static void setup_dd_communication(gmx_domdec_t *dd,
                                   matrix box,gmx_ddbox_t *ddbox,t_forcerec *fr)
{
    int dim_ind,dim,dim0,dim1=-1,dim2=-1,dimd,p,nat_tot;
    int nzone,nzone_send,zone,zonei,cg0,cg1;
    int c,i,j,cg,cg_gl,nrcg;
    int *zone_cg_range,pos_cg,*index_gl,*cgindex,*recv_i;
    gmx_domdec_comm_t *comm;
    gmx_domdec_zones_t *zones;
    gmx_domdec_comm_dim_t *cd;
    gmx_domdec_ind_t *ind;
    cginfo_mb_t *cginfo_mb;
    bool bBondComm,bDist2B,bDistMB,bDistMB_pulse,bDistBonded,bScrew;
    real r_mb,r_comm2,r_scomm2,r_bcomm2,r,r_0,r_1,r2,rb2,r2inc,inv_ncg,tric_sh;
    rvec rb,rn;
    real corner[DIM][4],corner_round_0=0,corner_round_1[4];
    real bcorner[DIM],bcorner_round_1=0;
    ivec tric_dist;
    rvec *cg_cm,*normal,*v_d,*v_0=NULL,*v_1=NULL,*recv_vr;
    real skew_fac2_d,skew_fac_01;
    rvec sf2_round;
    int  nsend,nat;
    
    if (debug)
    {
        fprintf(debug,"Setting up DD communication\n");
    }
    
    comm  = dd->comm;
    cg_cm = fr->cg_cm;

    for(dim_ind=0; dim_ind<dd->ndim; dim_ind++)
    {
        dim = dd->dim[dim_ind];

        /* Check if we need to use triclinic distances */
        tric_dist[dim_ind] = 0;
        for(i=0; i<=dim_ind; i++)
        {
            if (ddbox->tric_dir[dd->dim[i]])
            {
                tric_dist[dim_ind] = 1;
            }
        }
    }

    bBondComm = comm->bBondComm;

    /* Do we need to determine extra distances for multi-body bondeds? */
    bDistMB = (comm->bInterCGMultiBody && dd->bGridJump && dd->ndim > 1);
    
    /* Do we need to determine extra distances for only two-body bondeds? */
    bDist2B = (bBondComm && !bDistMB);

    r_comm2  = sqr(comm->cutoff);
    r_bcomm2 = sqr(comm->cutoff_mbody);

    if (debug)
    {
        fprintf(debug,"bBondComm %d, r_bc %f\n",bBondComm,sqrt(r_bcomm2));
    }

    zones = &comm->zones;
    
    dim0 = dd->dim[0];
    /* The first dimension is equal for all cells */
    corner[0][0] = comm->cell_x0[dim0];
    if (bDistMB)
    {
        bcorner[0] = corner[0][0];
    }
    if (dd->ndim >= 2)
    {
        dim1 = dd->dim[1];
        /* This cell row is only seen from the first row */
        corner[1][0] = comm->cell_x0[dim1];
        /* All rows can see this row */
        corner[1][1] = comm->cell_x0[dim1];
        if (dd->bGridJump)
        {
            corner[1][1] = max(comm->cell_x0[dim1],comm->zone_d1[1].mch0);
            if (bDistMB)
            {
                /* For the multi-body distance we need the maximum */
                bcorner[1] = max(comm->cell_x0[dim1],comm->zone_d1[1].p1_0);
            }
        }
        /* Set the upper-right corner for rounding */
        corner_round_0 = comm->cell_x1[dim0];
        
        if (dd->ndim >= 3)
        {
            dim2 = dd->dim[2];
            for(j=0; j<4; j++)
            {
                corner[2][j] = comm->cell_x0[dim2];
            }
            if (dd->bGridJump)
            {
                /* Use the maximum of the i-cells that see a j-cell */
                for(i=0; i<zones->nizone; i++)
                {
                    for(j=zones->izone[i].j0; j<zones->izone[i].j1; j++)
                    {
                        if (j >= 4)
                        {
                            corner[2][j-4] =
                                max(corner[2][j-4],
                                    comm->zone_d2[zones->shift[i][dim0]][zones->shift[i][dim1]].mch0);
                        }
                    }
                }
                if (bDistMB)
                {
                    /* For the multi-body distance we need the maximum */
                    bcorner[2] = comm->cell_x0[dim2];
                    for(i=0; i<2; i++)
                    {
                        for(j=0; j<2; j++)
                        {
                            bcorner[2] = max(bcorner[2],
                                             comm->zone_d2[i][j].p1_0);
                        }
                    }
                }
            }
            
            /* Set the upper-right corner for rounding */
            /* Cell (0,0,0) and cell (1,0,0) can see cell 4 (0,1,1)
             * Only cell (0,0,0) can see cell 7 (1,1,1)
             */
            corner_round_1[0] = comm->cell_x1[dim1];
            corner_round_1[3] = comm->cell_x1[dim1];
            if (dd->bGridJump)
            {
                corner_round_1[0] = max(comm->cell_x1[dim1],
                                        comm->zone_d1[1].mch1);
                if (bDistMB)
                {
                    /* For the multi-body distance we need the maximum */
                    bcorner_round_1 = max(comm->cell_x1[dim1],
                                          comm->zone_d1[1].p1_1);
                }
            }
        }
    }
    
    /* Triclinic stuff */
    normal = ddbox->normal;
    skew_fac_01 = 0;
    if (dd->ndim >= 2)
    {
        v_0 = ddbox->v[dim0];
        if (ddbox->tric_dir[dim0] && ddbox->tric_dir[dim1])
        {
            /* Determine the coupling coefficient for the distances
             * to the cell planes along dim0 and dim1 through dim2.
             * This is required for correct rounding.
             */
            skew_fac_01 =
                ddbox->v[dim0][dim1+1][dim0]*ddbox->v[dim1][dim1+1][dim1];
            if (debug)
            {
                fprintf(debug,"\nskew_fac_01 %f\n",skew_fac_01);
            }
        }
    }
    if (dd->ndim >= 3)
    {
        v_1 = ddbox->v[dim1];
    }
    
    zone_cg_range = zones->cg_range;
    index_gl = dd->index_gl;
    cgindex  = dd->cgindex;
    cginfo_mb = fr->cginfo_mb;
    
    zone_cg_range[0]   = 0;
    zone_cg_range[1]   = dd->ncg_home;
    comm->zone_ncg1[0] = dd->ncg_home;
    pos_cg             = dd->ncg_home;
    
    nat_tot = dd->nat_home;
    nzone = 1;
    for(dim_ind=0; dim_ind<dd->ndim; dim_ind++)
    {
        dim = dd->dim[dim_ind];
        cd = &comm->cd[dim_ind];
        
        if (dim >= ddbox->npbcdim && dd->ci[dim] == 0)
        {
            /* No pbc in this dimension, the first node should not comm. */
            nzone_send = 0;
        }
        else
        {
            nzone_send = nzone;
        }

        bScrew = (dd->bScrewPBC && dim == XX);
        
        v_d = ddbox->v[dim];
        skew_fac2_d = sqr(ddbox->skew_fac[dim]);

        cd->bInPlace = TRUE;
        for(p=0; p<cd->np; p++)
        {
            /* Only atoms communicated in the first pulse are used
             * for multi-body bonded interactions or for bBondComm.
             */
            bDistBonded   = ((bDistMB || bDist2B) && p == 0);
            bDistMB_pulse = (bDistMB && bDistBonded);

            ind = &cd->ind[p];
            nsend = 0;
            nat = 0;
            for(zone=0; zone<nzone_send; zone++)
            {
                if (tric_dist[dim_ind] && dim_ind > 0)
                {
                    /* Determine slightly more optimized skew_fac's
                     * for rounding.
                     * This reduces the number of communicated atoms
                     * by about 10% for 3D DD of rhombic dodecahedra.
                     */
                    for(dimd=0; dimd<dim; dimd++)
                    {
                        sf2_round[dimd] = 1;
                        if (ddbox->tric_dir[dimd])
                        {
                            for(i=dd->dim[dimd]+1; i<DIM; i++)
                            {
                                /* If we are shifted in dimension i
                                 * and the cell plane is tilted forward
                                 * in dimension i, skip this coupling.
                                 */
                                if (!(zones->shift[nzone+zone][i] &&
                                      ddbox->v[dimd][i][dimd] >= 0))
                                {
                                    sf2_round[dimd] +=
                                        sqr(ddbox->v[dimd][i][dimd]);
                                }
                            }
                            sf2_round[dimd] = 1/sf2_round[dimd];
                        }
                    }
                }

                zonei = zone_perm[dim_ind][zone];
                if (p == 0)
                {
                    /* Here we permutate the zones to obtain a convenient order
                     * for neighbor searching
                     */
                    cg0 = zone_cg_range[zonei];
                    cg1 = zone_cg_range[zonei+1];
                }
                else
                {
                    /* Look only at the cg's received in the previous grid pulse
                     */
                    cg1 = zone_cg_range[nzone+zone+1];
                    cg0 = cg1 - cd->ind[p-1].nrecv[zone];
                }
                ind->nsend[zone] = 0;
                for(cg=cg0; cg<cg1; cg++)
                {
                    r2  = 0;
                    rb2 = 0;
                    if (tric_dist[dim_ind] == 0)
                    {
                        /* Rectangular direction, easy */
                        r = cg_cm[cg][dim] - corner[dim_ind][zone];
                        if (r > 0)
                        {
                            r2 += r*r;
                        }
                        if (bDistMB_pulse)
                        {
                            r = cg_cm[cg][dim] - bcorner[dim_ind];
                            if (r > 0)
                            {
                                rb2 += r*r;
                            }
                        }
                        /* Rounding gives at most a 16% reduction
                         * in communicated atoms
                         */
                        if (dim_ind >= 1 && (zonei == 1 || zonei == 2))
                        {
                            r = cg_cm[cg][dim0] - corner_round_0;
                            /* This is the first dimension, so always r >= 0 */
                            r2 += r*r;
                            if (bDistMB_pulse)
                            {
                                rb2 += r*r;
                            }
                        }
                        if (dim_ind == 2 && (zonei == 2 || zonei == 3))
                        {
                            r = cg_cm[cg][dim1] - corner_round_1[zone];
                            if (r > 0)
                            {
                                r2 += r*r;
                            }
                            if (bDistMB_pulse)
                            {
                                r = cg_cm[cg][dim1] - bcorner_round_1;
                                if (r > 0)
                                {
                                    rb2 += r*r;
                                }
                            }
                        }
                    }
                    else
                    {
                        /* Triclinic direction, more complicated */
                        clear_rvec(rn);
                        clear_rvec(rb);
                        /* Rounding, conservative as the skew_fac multiplication
                         * will slightly underestimate the distance.
                         */
                        if (dim_ind >= 1 && (zonei == 1 || zonei == 2))
                        {
                            rn[dim0] = cg_cm[cg][dim0] - corner_round_0;
                            for(i=dim0+1; i<DIM; i++)
                            {
                                rn[dim0] -= cg_cm[cg][i]*v_0[i][dim0];
                            }
                            r2 = rn[dim0]*rn[dim0]*sf2_round[dim0];
                            if (bDistMB_pulse)
                            {
                                rb[dim0] = rn[dim0];
                                rb2 = r2;
                            }
                            /* Take care that the cell planes along dim0 might not
                             * be orthogonal to those along dim1 and dim2.
                             */
                            for(i=1; i<=dim_ind; i++)
                            {
                                dimd = dd->dim[i];
                                if (normal[dim0][dimd] > 0)
                                {
                                    rn[dimd] -= rn[dim0]*normal[dim0][dimd];
                                    if (bDistMB_pulse)
                                    {
                                        rb[dimd] -= rb[dim0]*normal[dim0][dimd];
                                    }
                                }
                            }
                        }
                        if (dim_ind == 2 && (zonei == 2 || zonei == 3))
                        {
                            rn[dim1] += cg_cm[cg][dim1] - corner_round_1[zone];
                            tric_sh = 0;
                            for(i=dim1+1; i<DIM; i++)
                            {
                                tric_sh -= cg_cm[cg][i]*v_1[i][dim1];
                            }
                            rn[dim1] += tric_sh;
                            if (rn[dim1] > 0)
                            {
                                r2 += rn[dim1]*rn[dim1]*sf2_round[dim1];
                                /* Take care of coupling of the distances
                                 * to the planes along dim0 and dim1 through dim2.
                                 */
                                r2 -= rn[dim0]*rn[dim1]*skew_fac_01;
                                /* Take care that the cell planes along dim1
                                 * might not be orthogonal to that along dim2.
                                 */
                                if (normal[dim1][dim2] > 0)
                                {
                                    rn[dim2] -= rn[dim1]*normal[dim1][dim2];
                                }
                            }
                            if (bDistMB_pulse)
                            {
                                rb[dim1] +=
                                    cg_cm[cg][dim1] - bcorner_round_1 + tric_sh;
                                if (rb[dim1] > 0)
                                {
                                    rb2 += rb[dim1]*rb[dim1]*sf2_round[dim1];
                                    /* Take care of coupling of the distances
                                     * to the planes along dim0 and dim1 through dim2.
                                     */
                                    rb2 -= rb[dim0]*rb[dim1]*skew_fac_01;
                                    /* Take care that the cell planes along dim1
                                     * might not be orthogonal to that along dim2.
                                     */
                                    if (normal[dim1][dim2] > 0)
                                    {
                                        rb[dim2] -= rb[dim1]*normal[dim1][dim2];
                                    }
                                }
                            }
                        }
                        /* The distance along the communication direction */
                        rn[dim] += cg_cm[cg][dim] - corner[dim_ind][zone];
                        tric_sh = 0;
                        for(i=dim+1; i<DIM; i++)
                        {
                            tric_sh -= cg_cm[cg][i]*v_d[i][dim];
                        }
                        rn[dim] += tric_sh;
                        if (rn[dim] > 0)
                        {
                            r2 += rn[dim]*rn[dim]*skew_fac2_d;
                            /* Take care of coupling of the distances
                             * to the planes along dim0 and dim1 through dim2.
                             */
                            if (dim_ind == 1 && zonei == 1)
                            {
                                r2 -= rn[dim0]*rn[dim]*skew_fac_01;
                            }
                        }
                        if (bDistMB_pulse)
                        {
                            clear_rvec(rb);
                            rb[dim] += cg_cm[cg][dim] - bcorner[dim_ind] + tric_sh;
                            if (rb[dim] > 0)
                            {
                                rb2 += rb[dim]*rb[dim]*skew_fac2_d;
                                /* Take care of coupling of the distances
                                 * to the planes along dim0 and dim1 through dim2.
                                 */
                                if (dim_ind == 1 && zonei == 1)
                                {
                                    rb2 -= rb[dim0]*rb[dim]*skew_fac_01;
                                }
                            }
                        }
                    }
                    
                    if (r2 < r_comm2 ||
                        (bDistBonded &&
                         ((bDistMB && rb2 < r_bcomm2) ||
                          (bDist2B && r2  < r_bcomm2)) &&
                         (!bBondComm ||
                          (GET_CGINFO_BOND_INTER(fr->cginfo[cg]) &&
                           missing_link(comm->cglink,index_gl[cg],
                                        comm->bLocalCG)))))
                    {
                        /* Make an index to the local charge groups */
                        if (nsend+1 > ind->nalloc)
                        {
                            ind->nalloc = over_alloc_large(nsend+1);
                            srenew(ind->index,ind->nalloc);
                        }
                        if (nsend+1 > comm->nalloc_int)
                        {
                            comm->nalloc_int = over_alloc_large(nsend+1);
                            srenew(comm->buf_int,comm->nalloc_int);
                        }
                        ind->index[nsend] = cg;
                        comm->buf_int[nsend] = index_gl[cg];
                        ind->nsend[zone]++;
                        vec_rvec_check_alloc(&comm->vbuf,nsend+1);

                        if (dd->ci[dim] == 0)
                        {
                            /* Correct cg_cm for pbc */
                            rvec_add(cg_cm[cg],box[dim],comm->vbuf.v[nsend]);
                            if (bScrew)
                            {
                                comm->vbuf.v[nsend][YY] =
                                    box[YY][YY]-comm->vbuf.v[nsend][YY];
                                comm->vbuf.v[nsend][ZZ] =
                                    box[ZZ][ZZ]-comm->vbuf.v[nsend][ZZ];
                            }
                        }
                        else
                        {
                            copy_rvec(cg_cm[cg],comm->vbuf.v[nsend]);
                        }
                        nsend++;
                        nat += cgindex[cg+1] - cgindex[cg];
                    }
                }
            }
            /* Clear the counts in case we do not have pbc */
            for(zone=nzone_send; zone<nzone; zone++)
            {
                ind->nsend[zone] = 0;
            }
            ind->nsend[nzone]   = nsend;
            ind->nsend[nzone+1] = nat;
            /* Communicate the number of cg's and atoms to receive */
            dd_sendrecv_int(dd, dim_ind, dddirBackward,
                            ind->nsend, nzone+2,
                            ind->nrecv, nzone+2);
            
            /* The rvec buffer is also required for atom buffers of size nsend
             * in dd_move_x and dd_move_f.
             */
            vec_rvec_check_alloc(&comm->vbuf,ind->nsend[nzone+1]);

            if (p > 0)
            {
                /* We can receive in place if only the last zone is not empty */
                for(zone=0; zone<nzone-1; zone++)
                {
                    if (ind->nrecv[zone] > 0)
                    {
                        cd->bInPlace = FALSE;
                    }
                }
                if (!cd->bInPlace)
                {
                    /* The int buffer is only required here for the cg indices */
                    if (ind->nrecv[nzone] > comm->nalloc_int2)
                    {
                        comm->nalloc_int2 = over_alloc_dd(ind->nrecv[nzone]);
                        srenew(comm->buf_int2,comm->nalloc_int2);
                    }
                    /* The rvec buffer is also required for atom buffers
                     * of size nrecv in dd_move_x and dd_move_f.
                     */
                    i = max(cd->ind[0].nrecv[nzone+1],ind->nrecv[nzone+1]);
                    vec_rvec_check_alloc(&comm->vbuf2,i);
                }
            }
            
            /* Make space for the global cg indices */
            if (pos_cg + ind->nrecv[nzone] > dd->cg_nalloc
                || dd->cg_nalloc == 0)
            {
                dd->cg_nalloc = over_alloc_dd(pos_cg + ind->nrecv[nzone]);
                srenew(index_gl,dd->cg_nalloc);
                srenew(cgindex,dd->cg_nalloc+1);
            }
            /* Communicate the global cg indices */
            if (cd->bInPlace)
            {
                recv_i = index_gl + pos_cg;
            }
            else
            {
                recv_i = comm->buf_int2;
            }
            dd_sendrecv_int(dd, dim_ind, dddirBackward,
                            comm->buf_int, nsend,
                            recv_i,        ind->nrecv[nzone]);

            /* Make space for cg_cm */
            if (pos_cg + ind->nrecv[nzone] > fr->cg_nalloc)
            {
                dd_realloc_fr_cg(fr,pos_cg + ind->nrecv[nzone]);
                cg_cm = fr->cg_cm;
            }
            /* Communicate cg_cm */
            if (cd->bInPlace)
            {
                recv_vr = cg_cm + pos_cg;
            }
            else
            {
                recv_vr = comm->vbuf2.v;
            }
            dd_sendrecv_rvec(dd, dim_ind, dddirBackward,
                             comm->vbuf.v, nsend,
                             recv_vr,      ind->nrecv[nzone]);
            
            /* Make the charge group index */
            if (cd->bInPlace)
            {
                zone = (p == 0 ? 0 : nzone - 1);
                while (zone < nzone)
                {
                    for(cg=0; cg<ind->nrecv[zone]; cg++)
                    {
                        cg_gl = index_gl[pos_cg];
                        fr->cginfo[pos_cg] = ddcginfo(cginfo_mb,cg_gl);
                        nrcg = GET_CGINFO_NATOMS(fr->cginfo[pos_cg]);
                        cgindex[pos_cg+1] = cgindex[pos_cg] + nrcg;
                        if (bBondComm)
                        {
                            /* Update the charge group presence,
                             * so we can use it in the next pass of the loop.
                             */
                            comm->bLocalCG[cg_gl] = TRUE;
                        }
                        pos_cg++;
                    }
                    if (p == 0)
                    {
                        comm->zone_ncg1[nzone+zone] = ind->nrecv[zone];
                    }
                    zone++;
                    zone_cg_range[nzone+zone] = pos_cg;
                }
            }
            else
            {
                /* This part of the code is never executed with bBondComm. */
                merge_cg_buffers(nzone,cd,p,zone_cg_range,
                                 index_gl,recv_i,cg_cm,recv_vr,
                                 cgindex,fr->cginfo_mb,fr->cginfo);
                pos_cg += ind->nrecv[nzone];
            }
            nat_tot += ind->nrecv[nzone+1];
        }
        if (!cd->bInPlace)
        {
            /* Store the atom block for easy copying of communication buffers */
            make_cell2at_index(cd,nzone,zone_cg_range[nzone],cgindex);
        }
        nzone += nzone;
    }
    dd->index_gl = index_gl;
    dd->cgindex  = cgindex;
    
    dd->ncg_tot = zone_cg_range[zones->n];
    dd->nat_tot = nat_tot;
    comm->nat[ddnatHOME] = dd->nat_home;
    for(i=ddnatZONE; i<ddnatNR; i++)
    {
        comm->nat[i] = dd->nat_tot;
    }

    if (!bBondComm)
    {
        /* We don't need to update cginfo, since that was alrady done above.
         * So we pass NULL for the forcerec.
         */
        dd_set_cginfo(dd->index_gl,dd->ncg_home,dd->ncg_tot,
                      NULL,comm->bLocalCG);
    }

    if (debug)
    {
        fprintf(debug,"Finished setting up DD communication, zones:");
        for(c=0; c<zones->n; c++)
        {
            fprintf(debug," %d",zones->cg_range[c+1]-zones->cg_range[c]);
        }
        fprintf(debug,"\n");
    }
}

static void set_cg_boundaries(gmx_domdec_zones_t *zones)
{
    int c;
    
    for(c=0; c<zones->nizone; c++)
    {
        zones->izone[c].cg1  = zones->cg_range[c+1];
        zones->izone[c].jcg0 = zones->cg_range[zones->izone[c].j0];
        zones->izone[c].jcg1 = zones->cg_range[zones->izone[c].j1];
    }
}

static int comp_cgsort(const void *a,const void *b)
{
    int comp;
    
    gmx_cgsort_t *cga,*cgb;
    cga = (gmx_cgsort_t *)a;
    cgb = (gmx_cgsort_t *)b;
    
    comp = cga->nsc - cgb->nsc;
    if (comp == 0)
    {
        comp = cga->ind_gl - cgb->ind_gl;
    }
    
    return comp;
}

static void order_int_cg(int n,gmx_cgsort_t *sort,
                         int *a,int *buf)
{
    int i;
    
    /* Order the data */
    for(i=0; i<n; i++)
    {
        buf[i] = a[sort[i].ind];
    }
    
    /* Copy back to the original array */
    for(i=0; i<n; i++)
    {
        a[i] = buf[i];
    }
}

static void order_vec_cg(int n,gmx_cgsort_t *sort,
                         rvec *v,rvec *buf)
{
    int i;
    
    /* Order the data */
    for(i=0; i<n; i++)
    {
        copy_rvec(v[sort[i].ind],buf[i]);
    }
    
    /* Copy back to the original array */
    for(i=0; i<n; i++)
    {
        copy_rvec(buf[i],v[i]);
    }
}

static void order_vec_atom(int ncg,int *cgindex,gmx_cgsort_t *sort,
                           rvec *v,rvec *buf)
{
    int a,atot,cg,cg0,cg1,i;
    
    /* Order the data */
    a = 0;
    for(cg=0; cg<ncg; cg++)
    {
        cg0 = cgindex[sort[cg].ind];
        cg1 = cgindex[sort[cg].ind+1];
        for(i=cg0; i<cg1; i++)
        {
            copy_rvec(v[i],buf[a]);
            a++;
        }
    }
    atot = a;
    
    /* Copy back to the original array */
    for(a=0; a<atot; a++)
    {
        copy_rvec(buf[a],v[a]);
    }
}

static void ordered_sort(int nsort2,gmx_cgsort_t *sort2,
                         int nsort_new,gmx_cgsort_t *sort_new,
                         gmx_cgsort_t *sort1)
{
    int i1,i2,i_new;
    
    /* The new indices are not very ordered, so we qsort them */
    qsort(sort_new,nsort_new,sizeof(sort_new[0]),comp_cgsort);
    
    /* sort2 is already ordered, so now we can merge the two arrays */
    i1 = 0;
    i2 = 0;
    i_new = 0;
    while(i2 < nsort2 || i_new < nsort_new)
    {
        if (i2 == nsort2)
        {
            sort1[i1++] = sort_new[i_new++];
        }
        else if (i_new == nsort_new)
        {
            sort1[i1++] = sort2[i2++];
        }
        else if (sort2[i2].nsc < sort_new[i_new].nsc ||
                 (sort2[i2].nsc == sort_new[i_new].nsc &&
                  sort2[i2].ind_gl < sort_new[i_new].ind_gl))
        {
            sort1[i1++] = sort2[i2++];
        }
        else
        {
            sort1[i1++] = sort_new[i_new++];
        }
    }
}

static void dd_sort_state(gmx_domdec_t *dd,int ePBC,
                          rvec *cgcm,t_forcerec *fr,t_state *state,
                          int ncg_home_old)
{
    gmx_domdec_sort_t *sort;
    gmx_cgsort_t *cgsort,*sort_i;
    int  ncg_new,nsort2,nsort_new,i,cell_index,*ibuf,cgsize;
    rvec *vbuf;
    
    sort = dd->comm->sort;
    
    if (dd->ncg_home > sort->sort_nalloc)
    {
        sort->sort_nalloc = over_alloc_dd(dd->ncg_home);
        srenew(sort->sort1,sort->sort_nalloc);
        srenew(sort->sort2,sort->sort_nalloc);
    }
    
    if (ncg_home_old >= 0)
    {
        /* The charge groups that remained in the same ns grid cell
         * are completely ordered. So we can sort efficiently by sorting
         * the charge groups that did move into the stationary list.
         */
        ncg_new = 0;
        nsort2 = 0;
        nsort_new = 0;
        for(i=0; i<dd->ncg_home; i++)
        {
            /* Check if this cg did not move to another node */
            cell_index = fr->ns.grid->cell_index[i];
            if (cell_index !=  4*fr->ns.grid->ncells)
            {
                if (i >= ncg_home_old || cell_index != sort->sort1[i].nsc)
                {
                    /* This cg is new on this node or moved ns grid cell */
                    if (nsort_new >= sort->sort_new_nalloc)
                    {
                        sort->sort_new_nalloc = over_alloc_dd(nsort_new+1);
                        srenew(sort->sort_new,sort->sort_new_nalloc);
                    }
                    sort_i = &(sort->sort_new[nsort_new++]);
                }
                else
                {
                    /* This cg did not move */
                    sort_i = &(sort->sort2[nsort2++]);
                }
                /* Sort on the ns grid cell indices
                 * and the global topology index
                 */
                sort_i->nsc    = cell_index;
                sort_i->ind_gl = dd->index_gl[i];
                sort_i->ind    = i;
                ncg_new++;
            }
        }
        if (debug)
        {
            fprintf(debug,"ordered sort cgs: stationary %d moved %d\n",
                    nsort2,nsort_new);
        }
        /* Sort efficiently */
        ordered_sort(nsort2,sort->sort2,nsort_new,sort->sort_new,sort->sort1);
    }
    else
    {
        cgsort = sort->sort1;
        ncg_new = 0;
        for(i=0; i<dd->ncg_home; i++)
        {
            /* Sort on the ns grid cell indices
             * and the global topology index
             */
            cgsort[i].nsc    = fr->ns.grid->cell_index[i];
            cgsort[i].ind_gl = dd->index_gl[i];
            cgsort[i].ind    = i;
            if (cgsort[i].nsc != 4*fr->ns.grid->ncells)
            {
                ncg_new++;
            }
        }
        if (debug)
        {
            fprintf(debug,"qsort cgs: %d new home %d\n",dd->ncg_home,ncg_new);
        }
        /* Determine the order of the charge groups using qsort */
        qsort(cgsort,dd->ncg_home,sizeof(cgsort[0]),comp_cgsort);
    }
    cgsort = sort->sort1;
    
    /* We alloc with the old size, since cgindex is still old */
    vec_rvec_check_alloc(&dd->comm->vbuf,dd->cgindex[dd->ncg_home]);
    vbuf = dd->comm->vbuf.v;
    
    /* Remove the charge groups which are no longer at home here */
    dd->ncg_home = ncg_new;
    
    /* Reorder the state */
    for(i=0; i<estNR; i++)
    {
        if (EST_DISTR(i) && state->flags & (1<<i))
        {
            switch (i)
            {
            case estX:
                order_vec_atom(dd->ncg_home,dd->cgindex,cgsort,state->x,vbuf);
                break;
            case estV:
                order_vec_atom(dd->ncg_home,dd->cgindex,cgsort,state->v,vbuf);
                break;
            case estSDX:
                order_vec_atom(dd->ncg_home,dd->cgindex,cgsort,state->sd_X,vbuf);
                break;
            case estCGP:
                order_vec_atom(dd->ncg_home,dd->cgindex,cgsort,state->cg_p,vbuf);
                break;
            case estLD_RNG:
            case estLD_RNGI:
            case estDISRE_INITF:
            case estDISRE_RM3TAV:
            case estORIRE_INITF:
            case estORIRE_DTAV:
                /* No ordering required */
                break;
            default:
                gmx_incons("Unknown state entry encountered in dd_sort_state");
                break;
            }
        }
    }
    /* Reorder cgcm */
    order_vec_cg(dd->ncg_home,cgsort,cgcm,vbuf);
    
    if (dd->ncg_home+1 > sort->ibuf_nalloc)
    {
        sort->ibuf_nalloc = over_alloc_dd(dd->ncg_home+1);
        srenew(sort->ibuf,sort->ibuf_nalloc);
    }
    ibuf = sort->ibuf;
    /* Reorder the global cg index */
    order_int_cg(dd->ncg_home,cgsort,dd->index_gl,ibuf);
    /* Reorder the cginfo */
    order_int_cg(dd->ncg_home,cgsort,fr->cginfo,ibuf);
    /* Rebuild the local cg index */
    ibuf[0] = 0;
    for(i=0; i<dd->ncg_home; i++)
    {
        cgsize = dd->cgindex[cgsort[i].ind+1] - dd->cgindex[cgsort[i].ind];
        ibuf[i+1] = ibuf[i] + cgsize;
    }
    for(i=0; i<dd->ncg_home+1; i++)
    {
        dd->cgindex[i] = ibuf[i];
    }
    /* Set the home atom number */
    dd->nat_home = dd->cgindex[dd->ncg_home];
    
    /* Copy the sorted ns cell indices back to the ns grid struct */
    for(i=0; i<dd->ncg_home; i++)
    {
        fr->ns.grid->cell_index[i] = cgsort[i].nsc;
    }
    fr->ns.grid->nr = dd->ncg_home;
}

static void add_dd_statistics(gmx_domdec_t *dd)
{
    gmx_domdec_comm_t *comm;
    int ddnat;
    
    comm = dd->comm;
    
    for(ddnat=ddnatZONE; ddnat<ddnatNR; ddnat++)
    {
        comm->sum_nat[ddnat-ddnatZONE] +=
            comm->nat[ddnat] - comm->nat[ddnat-1];
    }
    comm->ndecomp++;
}

void reset_dd_statistics_counters(gmx_domdec_t *dd)
{
    gmx_domdec_comm_t *comm;
    int ddnat;
    
    comm = dd->comm;

    /* Reset all the statistics and counters for total run counting */
    for(ddnat=ddnatZONE; ddnat<ddnatNR; ddnat++)
    {
        comm->sum_nat[ddnat-ddnatZONE] = 0;
    }
    comm->ndecomp = 0;
    comm->nload = 0;
    comm->load_step = 0;
    comm->load_sum = 0;
    comm->load_max = 0;
    clear_ivec(comm->load_lim);
    comm->load_mdf = 0;
    comm->load_pme = 0;
}

void print_dd_statistics(t_commrec *cr,t_inputrec *ir,FILE *fplog)
{
    gmx_domdec_comm_t *comm;
    int ddnat;
    double av;
   
    comm = cr->dd->comm;
    
    gmx_sumd(ddnatNR-ddnatZONE,comm->sum_nat,cr);
    
    if (fplog == NULL)
    {
        return;
    }
    
    fprintf(fplog,"\n    D O M A I N   D E C O M P O S I T I O N   S T A T I S T I C S\n\n");
            
    for(ddnat=ddnatZONE; ddnat<ddnatNR; ddnat++)
    {
        av = comm->sum_nat[ddnat-ddnatZONE]/comm->ndecomp;
        switch(ddnat)
        {
        case ddnatZONE:
            fprintf(fplog,
                    " av. #atoms communicated per step for force:  %d x %.1f\n",
                    2,av);
            break;
        case ddnatVSITE:
            if (cr->dd->vsite_comm)
            {
                fprintf(fplog,
                        " av. #atoms communicated per step for vsites: %d x %.1f\n",
                        (EEL_PME(ir->coulombtype) || ir->coulombtype==eelEWALD) ? 3 : 2,
                        av);
            }
            break;
        case ddnatCON:
            if (cr->dd->constraint_comm)
            {
                fprintf(fplog,
                        " av. #atoms communicated per step for LINCS:  %d x %.1f\n",
                        1 + ir->nLincsIter,av);
            }
            break;
        default:
            gmx_incons(" Unknown type for DD statistics");
        }
    }
    fprintf(fplog,"\n");
    
    if (comm->bRecordLoad && EI_DYNAMICS(ir->eI))
    {
        print_dd_load_av(fplog,cr->dd);
    }
}

void dd_partition_system(FILE            *fplog,
                         gmx_large_int_t      step,
                         t_commrec       *cr,
                         bool            bMasterState,
                         int             nstglobalcomm,
                         t_state         *state_global,
                         gmx_mtop_t      *top_global,
                         t_inputrec      *ir,
                         t_state         *state_local,
                         rvec            **f,
                         t_mdatoms       *mdatoms,
                         gmx_localtop_t  *top_local,
                         t_forcerec      *fr,
                         gmx_vsite_t     *vsite,
                         gmx_shellfc_t   shellfc,
                         gmx_constr_t    constr,
                         t_nrnb          *nrnb,
                         gmx_wallcycle_t wcycle,
                         bool            bVerbose)
{
    gmx_domdec_t *dd;
    gmx_domdec_comm_t *comm;
    gmx_ddbox_t ddbox;
    t_block *cgs_gl;
    gmx_large_int_t step_pcoupl;
    rvec cell_ns_x0,cell_ns_x1;
    int  i,j,n,cg0=0,ncg_home_old=-1,nat_f_novirsum;
    bool bBoxChanged,bNStGlobalComm,bDoDLB,bCheckDLB,bTurnOnDLB,bLogLoad;
    bool bRedist,bSortCG,bResortAll;
    ivec ncells_old,np;
    real grid_density;
    char sbuf[22];
        
    dd = cr->dd;
    comm = dd->comm;

    bBoxChanged = (bMasterState || DEFORM(*ir));
    if (ir->epc != epcNO)
    {
        /* With nstcalcenery > 1 pressure coupling happens.
         * one step after calculating the energies.
         * Box scaling happens at the end of the MD step,
         * after the DD partitioning.
         * We therefore have to do DLB in the first partitioning
         * after an MD step where P-coupling occured.
         * We need to determine the last step in which p-coupling occurred.
         * MRS -- need to validate this for vv?
         */
        n = ir->nstcalcenergy;
        if (n == 1)
        {
            step_pcoupl = step - 1;
        }
        else
        {
            step_pcoupl = ((step - 1)/n)*n + 1;
        }
        if (step_pcoupl >= comm->partition_step)
        {
            bBoxChanged = TRUE;
        }
    }

    bNStGlobalComm = (step >= comm->partition_step + nstglobalcomm);

    if (!comm->bDynLoadBal)
    {
        bDoDLB = FALSE;
    }
    else
    {
        /* Should we do dynamic load balacing this step?
         * Since it requires (possibly expensive) global communication,
         * we might want to do DLB less frequently.
         */
        if (bBoxChanged || ir->epc != epcNO)
        {
            bDoDLB = bBoxChanged;
        }
        else
        {
            bDoDLB = bNStGlobalComm;
        }
    }

    /* Check if we have recorded loads on the nodes */
    if (comm->bRecordLoad && dd_load_count(comm))
    {
        if (comm->eDLB == edlbAUTO && !comm->bDynLoadBal)
        {
            /* Check if we should use DLB at the second partitioning
             * and every 100 partitionings,
             * so the extra communication cost is negligible.
             */
            n = max(100,nstglobalcomm);
            bCheckDLB = (comm->n_load_collect == 0 ||
                         comm->n_load_have % n == n-1);
        }
        else
        {
            bCheckDLB = FALSE;
        }
        
        /* Print load every nstlog, first and last step to the log file */
        bLogLoad = ((ir->nstlog > 0 && step % ir->nstlog == 0) ||
                    comm->n_load_collect == 0 ||
                    (step + ir->nstlist > ir->init_step + ir->nsteps));

        /* Avoid extra communication due to verbose screen output
         * when nstglobalcomm is set.
         */
        if (bDoDLB || bLogLoad || bCheckDLB ||
            (bVerbose && (ir->nstlist == 0 || nstglobalcomm <= ir->nstlist)))
        {
            get_load_distribution(dd,wcycle);
            if (DDMASTER(dd))
            {
                if (bLogLoad)
                {
                    dd_print_load(fplog,dd,step-1);
                }
                if (bVerbose)
                {
                    dd_print_load_verbose(dd);
                }
            }
            comm->n_load_collect++;

            if (bCheckDLB) {
                /* Since the timings are node dependent, the master decides */
                if (DDMASTER(dd))
                {
                    bTurnOnDLB =
                        (dd_force_imb_perf_loss(dd) >= DD_PERF_LOSS);
                    if (debug)
                    {
                        fprintf(debug,"step %s, imb loss %f\n",
                                gmx_step_str(step,sbuf),
                                dd_force_imb_perf_loss(dd));
                    }
                }
                dd_bcast(dd,sizeof(bTurnOnDLB),&bTurnOnDLB);
                if (bTurnOnDLB)
                {
                    turn_on_dlb(fplog,cr,step);
                    bDoDLB = TRUE;
                }
            }
        }
        comm->n_load_have++;
    }

    cgs_gl = &comm->cgs_gl;

    bRedist = FALSE;
    if (bMasterState)
    {
        /* Clear the old state */
        clear_dd_indices(dd,0,0);

        set_ddbox(dd,bMasterState,cr,ir,state_global->box,
                  TRUE,cgs_gl,state_global->x,&ddbox);
    
        get_cg_distribution(fplog,step,dd,cgs_gl,
                            state_global->box,&ddbox,state_global->x);
        
        dd_distribute_state(dd,cgs_gl,
                            state_global,state_local,f);
        
        dd_make_local_cgs(dd,&top_local->cgs);
        
        if (dd->ncg_home > fr->cg_nalloc)
        {
            dd_realloc_fr_cg(fr,dd->ncg_home);
        }
        calc_cgcm(fplog,0,dd->ncg_home,
                  &top_local->cgs,state_local->x,fr->cg_cm);
        
        inc_nrnb(nrnb,eNR_CGCM,dd->nat_home);
        
        dd_set_cginfo(dd->index_gl,0,dd->ncg_home,fr,comm->bLocalCG);

        cg0 = 0;
    }
    else if (state_local->ddp_count != dd->ddp_count)
    {
        if (state_local->ddp_count > dd->ddp_count)
        {
            gmx_fatal(FARGS,"Internal inconsistency state_local->ddp_count (%d) > dd->ddp_count (%d)",state_local->ddp_count,dd->ddp_count);
        }
        
        if (state_local->ddp_count_cg_gl != state_local->ddp_count)
        {
            gmx_fatal(FARGS,"Internal inconsistency state_local->ddp_count_cg_gl (%d) != state_local->ddp_count (%d)",state_local->ddp_count_cg_gl,state_local->ddp_count);
        }
        
        /* Clear the old state */
        clear_dd_indices(dd,0,0);
        
        /* Build the new indices */
        rebuild_cgindex(dd,cgs_gl->index,state_local);
        make_dd_indices(dd,cgs_gl->index,0);
        
        /* Redetermine the cg COMs */
        calc_cgcm(fplog,0,dd->ncg_home,
                  &top_local->cgs,state_local->x,fr->cg_cm);
        
        inc_nrnb(nrnb,eNR_CGCM,dd->nat_home);

        dd_set_cginfo(dd->index_gl,0,dd->ncg_home,fr,comm->bLocalCG);

        set_ddbox(dd,bMasterState,cr,ir,state_local->box,
                  TRUE,&top_local->cgs,state_local->x,&ddbox);

        bRedist = comm->bDynLoadBal;
    }
    else
    {
        /* We have the full state, only redistribute the cgs */

        /* Clear the non-home indices */
        clear_dd_indices(dd,dd->ncg_home,dd->nat_home);

        /* Avoid global communication for dim's without pbc and -gcom */
        if (!bNStGlobalComm)
        {
            copy_rvec(comm->box0    ,ddbox.box0    );
            copy_rvec(comm->box_size,ddbox.box_size);
        }
        set_ddbox(dd,bMasterState,cr,ir,state_local->box,
                  bNStGlobalComm,&top_local->cgs,state_local->x,&ddbox);

        bBoxChanged = TRUE;
        bRedist = TRUE;
    }
    /* For dim's without pbc and -gcom */
    copy_rvec(ddbox.box0    ,comm->box0    );
    copy_rvec(ddbox.box_size,comm->box_size);
    
    set_dd_cell_sizes(dd,&ddbox,dynamic_dd_box(&ddbox,ir),bMasterState,bDoDLB,
                      step,wcycle);
    
    if (comm->nstDDDumpGrid > 0 && step % comm->nstDDDumpGrid == 0)
    {
        write_dd_grid_pdb("dd_grid",step,dd,state_local->box,&ddbox);
    }
    
    /* Check if we should sort the charge groups */
    if (comm->nstSortCG > 0)
    {
        bSortCG = (bMasterState ||
                   (bRedist && (step % comm->nstSortCG == 0)));
    }
    else
    {
        bSortCG = FALSE;
    }

    ncg_home_old = dd->ncg_home;

    if (bRedist)
    {
        cg0 = dd_redistribute_cg(fplog,step,dd,ddbox.tric_dir,
                                 state_local,f,fr,mdatoms,
                                 !bSortCG,nrnb);
    }
    
    get_nsgrid_boundaries(fr->ns.grid,dd,
                          state_local->box,&ddbox,&comm->cell_x0,&comm->cell_x1,
                          dd->ncg_home,fr->cg_cm,
                          cell_ns_x0,cell_ns_x1,&grid_density);

    if (bBoxChanged)
    {
        comm_dd_ns_cell_sizes(dd,&ddbox,cell_ns_x0,cell_ns_x1,step);
    }

    copy_ivec(fr->ns.grid->n,ncells_old);
    grid_first(fplog,fr->ns.grid,dd,&ddbox,fr->ePBC,
               state_local->box,cell_ns_x0,cell_ns_x1,
               fr->rlistlong,grid_density);
    /* We need to store tric_dir for dd_get_ns_ranges called from ns.c */
    copy_ivec(ddbox.tric_dir,comm->tric_dir);

    if (bSortCG)
    {
        /* Sort the state on charge group position.
         * This enables exact restarts from this step.
         * It also improves performance by about 15% with larger numbers
         * of atoms per node.
         */
        
        /* Fill the ns grid with the home cell,
         * so we can sort with the indices.
         */
        set_zones_ncg_home(dd);
        fill_grid(fplog,&comm->zones,fr->ns.grid,dd->ncg_home,
                  0,dd->ncg_home,fr->cg_cm);
        
        /* Check if we can user the old order and ns grid cell indices
         * of the charge groups to sort the charge groups efficiently.
         */
        bResortAll = (bMasterState ||
                      fr->ns.grid->n[XX] != ncells_old[XX] ||
                      fr->ns.grid->n[YY] != ncells_old[YY] ||
                      fr->ns.grid->n[ZZ] != ncells_old[ZZ]);

        if (debug)
        {
            fprintf(debug,"Step %s, sorting the %d home charge groups\n",
                    gmx_step_str(step,sbuf),dd->ncg_home);
        }
        dd_sort_state(dd,ir->ePBC,fr->cg_cm,fr,state_local,
                      bResortAll ? -1 : ncg_home_old);
        /* Rebuild all the indices */
        cg0 = 0;
        ga2la_clear(dd->ga2la);
    }
    
    /* Setup up the communication and communicate the coordinates */
    setup_dd_communication(dd,state_local->box,&ddbox,fr);
    
    /* Set the indices */
    make_dd_indices(dd,cgs_gl->index,cg0);

    /* Set the charge group boundaries for neighbor searching */
    set_cg_boundaries(&comm->zones);
    
    /*
    write_dd_pdb("dd_home",step,"dump",top_global,cr,
                 -1,state_local->x,state_local->box);
    */
    
    /* Extract a local topology from the global topology */
    for(i=0; i<dd->ndim; i++)
    {
        np[dd->dim[i]] = comm->cd[i].np;
    }
    dd_make_local_top(fplog,dd,&comm->zones,dd->npbcdim,state_local->box,
                      comm->cellsize_min,np,
                      fr,vsite,top_global,top_local);
    
    /* Set up the special atom communication */
    n = comm->nat[ddnatZONE];
    for(i=ddnatZONE+1; i<ddnatNR; i++)
    {
        switch(i)
        {
        case ddnatVSITE:
            if (vsite && vsite->n_intercg_vsite)
            {
                n = dd_make_local_vsites(dd,n,top_local->idef.il);
            }
            break;
        case ddnatCON:
            if (dd->bInterCGcons)
            {
                /* Only for inter-cg constraints we need special code */
                n = dd_make_local_constraints(dd,n,top_global,
                                              constr,ir->nProjOrder,
                                              &top_local->idef.il[F_CONSTR]);
            }
            break;
        default:
            gmx_incons("Unknown special atom type setup");
        }
        comm->nat[i] = n;
    }
    
    /* Make space for the extra coordinates for virtual site
     * or constraint communication.
     */
    state_local->natoms = comm->nat[ddnatNR-1];
    if (state_local->natoms > state_local->nalloc)
    {
        dd_realloc_state(state_local,f,state_local->natoms);
    }

    if (fr->bF_NoVirSum)
    {
        if (vsite && vsite->n_intercg_vsite)
        {
            nat_f_novirsum = comm->nat[ddnatVSITE];
        }
        else
        {
            if (EEL_FULL(ir->coulombtype) && dd->n_intercg_excl > 0)
            {
                nat_f_novirsum = dd->nat_tot;
            }
            else
            {
                nat_f_novirsum = dd->nat_home;
            }
        }
    }
    else
    {
        nat_f_novirsum = 0;
    }

    /* Set the number of atoms required for the force calculation.
     * Forces need to be constrained when using a twin-range setup
     * or with energy minimization. For simple simulations we could
     * avoid some allocation, zeroing and copying, but this is
     * probably not worth the complications ande checking.
     */
    forcerec_set_ranges(fr,dd->ncg_home,dd->ncg_tot,
                        comm->nat[ddnatCON],nat_f_novirsum);

    /* We make the all mdatoms up to nat_tot_con.
     * We could save some work by only setting invmass
     * between nat_tot and nat_tot_con.
     */
    /* This call also sets the new number of home particles to dd->nat_home */
    atoms2md(top_global,ir,
             comm->nat[ddnatCON],dd->gatindex,0,dd->nat_home,mdatoms);

    /* Now we have the charges we can sort the FE interactions */
    dd_sort_local_top(dd,mdatoms,top_local);

    if (shellfc)
    {
        /* Make the local shell stuff, currently no communication is done */
        make_local_shells(cr,mdatoms,shellfc);
    }
    
        if (ir->implicit_solvent)
    {
        make_local_gb(cr,fr->born,ir->gb_algorithm);
    }
        
    if (!(cr->duty & DUTY_PME))
    {
        /* Send the charges to our PME only node */
        gmx_pme_send_q(cr,mdatoms->nChargePerturbed,
                       mdatoms->chargeA,mdatoms->chargeB,
                       comm->ddpme[0].maxshift,comm->ddpme[1].maxshift);
    }
    
    if (constr)
    {
        set_constraints(constr,top_local,ir,mdatoms,cr);
    }
    
    if (ir->ePull != epullNO)
    {
        /* Update the local pull groups */
        dd_make_local_pull_groups(dd,ir->pull,mdatoms);
    }

    add_dd_statistics(dd);
    
    /* Make sure we only count the cycles for this DD partitioning */
    clear_dd_cycle_counts(dd);
    
    /* Because the order of the atoms might have changed since
     * the last vsite construction, we need to communicate the constructing
     * atom coordinates again (for spreading the forces this MD step).
     */
    dd_move_x_vsites(dd,state_local->box,state_local->x);
    
    if (comm->nstDDDump > 0 && step % comm->nstDDDump == 0)
    {
        dd_move_x(dd,state_local->box,state_local->x);
        write_dd_pdb("dd_dump",step,"dump",top_global,cr,
                     -1,state_local->x,state_local->box);
    }

    /* Store the partitioning step */
    comm->partition_step = step;
    
    /* Increase the DD partitioning counter */
    dd->ddp_count++;
    /* The state currently matches this DD partitioning count, store it */
    state_local->ddp_count = dd->ddp_count;
    if (bMasterState)
    {
        /* The DD master node knows the complete cg distribution,
         * store the count so we can possibly skip the cg info communication.
         */
        comm->master_cg_ddp_count = (bSortCG ? 0 : dd->ddp_count);
    }

    if (comm->DD_debug > 0)
    {
        /* Set the env var GMX_DD_DEBUG if you suspect corrupted indices */
        check_index_consistency(dd,top_global->natoms,ncg_mtop(top_global),
                                "after partitioning");
    }
}