void cells_re_init(int new_cs)
{
CellPList tmp_local;
Cell *tmp_cells;
int tmp_n_cells,i;
CELL_TRACE(fprintf(stderr, "%d: cells_re_init: convert type (%d->%d)\n", this_node, cell_structure.type, new_cs));
invalidate_ghosts();
/*
CELL_TRACE({
int p;
for (p = 0; p < n_total_particles; p++)
if (local_particles[p])
fprintf(stderr, "%d: cells_re_init: got particle %d\n", this_node, p);
}
);
*/
topology_release(cell_structure.type);
/* MOVE old local_cell list to temporary buffer */
memcpy(&tmp_local,&local_cells,sizeof(CellPList));
init_cellplist(&local_cells);
/* MOVE old cells to temporary buffer */
tmp_cells = cells;
tmp_n_cells = n_cells;
cells = NULL;
n_cells = 0;
topology_init(new_cs, &tmp_local);
particle_invalidate_part_node();
/* finally deallocate the old cells */
realloc_cellplist(&tmp_local,0);
for(i=0;i<tmp_n_cells;i++)
realloc_particlelist(&tmp_cells[i],0);
free(tmp_cells);
CELL_TRACE(fprintf(stderr, "%d: old cells deallocated\n",this_node));
/*
CELL_TRACE({
int p;
for (p = 0; p < n_total_particles; p++)
if (local_particles[p])
fprintf(stderr, "%d: cells_re_init: now got particle %d\n", this_node, p);
}
);
*/
/* to enforce initialization of the ghost cells */
resort_particles = 1;
#ifdef ADDITIONAL_CHECKS
check_cells_consistency();
#endif
}
void local_sort_particles()
{
CELL_TRACE(fprintf(stderr, "%d: entering local_sort_particles\n", this_node));
/* first distribute strictly on nodes */
cells_resort_particles(CELL_GLOBAL_EXCHANGE);
CELL_TRACE(fprintf(stderr, "%d: sorting local cells\n", this_node));
/* now sort the local cells */
for (int c = 0; c < local_cells.n; c++) {
Cell *cell = local_cells.cell[c];
Particle *p = cell->part;
int np = cell->n;
#ifdef CELL_DEBUG
for (int id = 0; id < np; ++id) {
Cell *tgt_cell = cell_structure.position_to_cell(p[id].r.p);
if (tgt_cell != cell) {
fprintf(stderr, "%d: particle %d at position %lf %lf %lf is not in its expected cell. Have %ld, expected %ld\n", this_node, p[id].p.identity, p[id].r.p[0], p[id].r.p[1], p[id].r.p[2], (cell - cells)/sizeof(Cell*), (tgt_cell - cells) /sizeof(Cell*));
}
}
#endif
qsort(p, np, sizeof(Particle), compare_particles);
update_local_particles(cell);
}
CELL_TRACE(dump_particle_ordering());
CELL_TRACE(fprintf(stderr, "%d: leaving local_sort_particles\n", this_node));
}
void cells_on_geometry_change(int flags)
{
if (max_cut > 0.0) {
max_range = max_cut + skin;
}
else
/* if no interactions yet, we also don't need a skin */
max_range = 0.0;
CELL_TRACE(fprintf(stderr,"%d: on_geometry_change with max range %f\n", this_node, max_range));
switch (cell_structure.type) {
case CELL_STRUCTURE_DOMDEC:
dd_on_geometry_change(flags);
break;
case CELL_STRUCTURE_LAYERED:
/* there is no fast version, always redo everything. */
cells_re_init(CELL_STRUCTURE_LAYERED);
break;
case CELL_STRUCTURE_NSQUARE:
/* this cell system doesn't need to react, just tell
the others */
on_boxl_change();
break;
}
}
/** Revert the order of a communicator: After calling this the
communicator is working in reverted order with exchanged
communication types GHOST_SEND <-> GHOST_RECV. */
void dd_revert_comm_order(GhostCommunicator *comm)
{
int i,j,nlist2;
GhostCommunication tmp;
ParticleList *tmplist;
CELL_TRACE(fprintf(stderr,"%d: dd_revert_comm_order: anz comm: %d\n",this_node,comm->num));
/* revert order */
for(i=0; i<(comm->num/2); i++) {
tmp = comm->comm[i];
comm->comm[i] = comm->comm[comm->num-i-1];
comm->comm[comm->num-i-1] = tmp;
}
/* exchange SEND/RECV */
for(i=0; i<comm->num; i++) {
if(comm->comm[i].type == GHOST_SEND) comm->comm[i].type = GHOST_RECV;
else if(comm->comm[i].type == GHOST_RECV) comm->comm[i].type = GHOST_SEND;
else if(comm->comm[i].type == GHOST_LOCL) {
nlist2=comm->comm[i].n_part_lists/2;
for(j=0;j<nlist2;j++) {
tmplist = comm->comm[i].part_lists[j];
comm->comm[i].part_lists[j] = comm->comm[i].part_lists[j+nlist2];
comm->comm[i].part_lists[j+nlist2] = tmplist;
}
}
}
}
void nsq_topology_release()
{
CELL_TRACE(fprintf(stderr,"%d: nsq_topology_release:\n",this_node));
/* free ghost cell pointer list */
realloc_cellplist(&me_do_ghosts, 0);
free_comm(&cell_structure.ghost_cells_comm);
free_comm(&cell_structure.exchange_ghosts_comm);
free_comm(&cell_structure.update_ghost_pos_comm);
free_comm(&cell_structure.collect_ghost_force_comm);
}
void cells_pre_init()
{
CellPList tmp_local;
CELL_TRACE(fprintf(stderr, "%d: cells_pre_init\n",this_node));
/* her local_cells has to be a NULL pointer */
if(local_cells.cell != NULL) {
fprintf(stderr,"INTERNAL ERROR: wrong usage of cells_pre_init!\n");
errexit();
}
memcpy(&tmp_local,&local_cells,sizeof(CellPList));
dd_topology_init(&tmp_local);
}
void cells_resort_particles(int global_flag)
{
CELL_TRACE(fprintf(stderr, "%d: entering cells_resort_particles %d\n", this_node, global_flag));
invalidate_ghosts();
particle_invalidate_part_node();
n_verlet_updates++;
switch (cell_structure.type) {
case CELL_STRUCTURE_LAYERED:
layered_exchange_and_sort_particles(global_flag);
break;
case CELL_STRUCTURE_NSQUARE:
nsq_balance_particles(global_flag);
break;
case CELL_STRUCTURE_DOMDEC:
dd_exchange_and_sort_particles(global_flag);
break;
}
#ifdef ADDITIONAL_CHECKS
/* at the end of the day, everything should be consistent again */
check_particle_consistency();
#endif
ghost_communicator(&cell_structure.ghost_cells_comm);
ghost_communicator(&cell_structure.exchange_ghosts_comm);
resort_particles = 0;
rebuild_verletlist = 1;
on_resort_particles();
CELL_TRACE(dump_particle_ordering());
CELL_TRACE(fprintf(stderr, "%d: leaving cells_resort_particles\n", this_node));
}
/** Create communicators for cell structure domain decomposition. (see \ref GhostCommunicator) */
void le_dd_prepare_comm(le_dd_comms_manager *mgr, GhostCommunicator *comm, int data_parts)
{
static int le_cells_state_physical = 1;
int dir,lr,i,cnt, num, n_comm_cells[3], send_rec, thisCommCount;
int lc[3],hc[3], neighbor_index;
#ifdef LE_DEBUG
if( comms_log != NULL ){ fclose(comms_log);comms_log=NULL;}
char vLogName[64];
sprintf(vLogName, "%i_comms_%i.dat", comms_count++,this_node);
comms_log = fopen(vLogName, "w");
#endif
CELL_TRACE(fprintf(stderr,"%d: neighbours:", this_node));
CELL_TRACE(for(i = 0; i < my_neighbor_count; i++)fprintf(stderr," %d",node_neighbors[i]);)
void realloc_cells(int size)
{
int i;
CELL_TRACE(fprintf(stderr, "%d: realloc_cells %d\n", this_node, size));
/* free all memory associated with cells to be deleted. */
for(i=size; i<n_cells; i++) {
realloc_particlelist(&cells[i],0);
}
/* resize the cell list */
if(size != n_cells) {
cells = (Cell *) realloc(cells, sizeof(Cell)*size);
}
/* initialize new cells */
for(i=n_cells; i<size; i++) {
init_particlelist(&cells[i]);
}
n_cells = size;
}
/** Fill a communication cell pointer list. Fill the cell pointers of
all cells which are inside a rectangular subgrid of the 3D cell
grid (\ref DomainDecomposition::ghost_cell_grid) starting from the
lower left corner lc up to the high top corner hc. The cell
pointer list part_lists must already be large enough.
\param part_lists List of cell pointers to store the result.
\param lc lower left corner of the subgrid.
\param hc high up corner of the subgrid.
*/
int dd_fill_comm_cell_lists(Cell **part_lists, int lc[3], int hc[3])
{
int i,m,n,o,c=0;
/* sanity check */
for(i=0; i<3; i++) {
if(lc[i]<0 || lc[i] >= dd.ghost_cell_grid[i]) return 0;
if(hc[i]<0 || hc[i] >= dd.ghost_cell_grid[i]) return 0;
if(lc[i] > hc[i]) return 0;
}
for(o=lc[0]; o<=hc[0]; o++)
for(n=lc[1]; n<=hc[1]; n++)
for(m=lc[2]; m<=hc[2]; m++) {
i = get_linear_index(o,n,m,dd.ghost_cell_grid);
CELL_TRACE(fprintf(stderr,"%d: dd_fill_comm_cell_list: add cell %d\n",this_node,i));
part_lists[c] = &cells[i];
c++;
}
return c;
}
/** Calculate cell grid dimensions, cell sizes and number of cells.
* Calculates the cell grid, based on \ref local_box_l and \ref
* max_range. If the number of cells is larger than \ref
* max_num_cells, it increases max_range until the number of cells is
* smaller or equal \ref max_num_cells. It sets: \ref
* DomainDecomposition::cell_grid, \ref
* DomainDecomposition::ghost_cell_grid, \ref
* DomainDecomposition::cell_size, \ref
* DomainDecomposition::inv_cell_size, and \ref n_cells.
*/
void dd_create_cell_grid()
{
int i,n_local_cells,new_cells,min_ind;
double cell_range[3], min_size, scale, volume;
CELL_TRACE(fprintf(stderr, "%d: dd_create_cell_grid: max_range %f\n",this_node,max_range));
CELL_TRACE(fprintf(stderr, "%d: dd_create_cell_grid: local_box %f-%f, %f-%f, %f-%f,\n",this_node,my_left[0],my_right[0],my_left[1],my_right[1],my_left[2],my_right[2]));
/* initialize */
cell_range[0]=cell_range[1]=cell_range[2] = max_range;
if (max_range < ROUND_ERROR_PREC*box_l[0]) {
/* this is the initialization case */
#ifdef LEES_EDWARDS
dd.cell_grid[0] = 2;
dd.cell_grid[1] = 1;
dd.cell_grid[2] = 1;
n_local_cells = 2;
#else
n_local_cells = dd.cell_grid[0] = dd.cell_grid[1] = dd.cell_grid[2]=1;
#endif
}
else {
/* Calculate initial cell grid */
volume = local_box_l[0];
for(i=1;i<3;i++) volume *= local_box_l[i];
scale = pow(max_num_cells/volume, 1./3.);
for(i=0;i<3;i++) {
/* this is at least 1 */
dd.cell_grid[i] = (int)ceil(local_box_l[i]*scale);
cell_range[i] = local_box_l[i]/dd.cell_grid[i];
if ( cell_range[i] < max_range ) {
/* ok, too many cells for this direction, set to minimum */
dd.cell_grid[i] = (int)floor(local_box_l[i]/max_range);
if ( dd.cell_grid[i] < 1 ) {
ostringstream msg;
msg << "interaction range " << max_range << " in direction "
<< i << " is larger than the local box size " << local_box_l[i];
runtimeError(msg);
dd.cell_grid[i] = 1;
}
#ifdef LEES_EDWARDS
if ( (i == 0) && (dd.cell_grid[0] < 2) ) {
ostringstream msg;
msg << "interaction range " << max_range << " in direction "
<< i << " is larger than half the local box size " << local_box_l[i] << "/2";
runtimeError(msg);
dd.cell_grid[0] = 2;
}
#endif
cell_range[i] = local_box_l[i]/dd.cell_grid[i];
}
}
/* It may be necessary to asymmetrically assign the scaling to the coordinates, which the above approach will not do.
For a symmetric box, it gives a symmetric result. Here we correct that. */
for (;;) {
n_local_cells = dd.cell_grid[0] * dd.cell_grid[1] * dd.cell_grid[2];
/* done */
if (n_local_cells <= max_num_cells)
break;
/* find coordinate with the smallest cell range */
min_ind = 0;
min_size = cell_range[0];
#ifdef LEES_EDWARDS
for (i = 2; i >= 1; i--) {/*preferably have thin slices in z or y... this is more efficient for Lees Edwards*/
#else
for (i = 1; i < 3; i++) {
#endif
if (dd.cell_grid[i] > 1 && cell_range[i] < min_size) {
min_ind = i;
min_size = cell_range[i];
}
}
CELL_TRACE(fprintf(stderr, "%d: minimal coordinate %d, size %f, grid %d\n", this_node,min_ind, min_size, dd.cell_grid[min_ind]));
dd.cell_grid[min_ind]--;
cell_range[min_ind] = local_box_l[min_ind]/dd.cell_grid[min_ind];
}
CELL_TRACE(fprintf(stderr, "%d: final %d %d %d\n", this_node, dd.cell_grid[0], dd.cell_grid[1], dd.cell_grid[2]));
/* sanity check */
if (n_local_cells < min_num_cells) {
ostringstream msg;
msg << "number of cells "<< n_local_cells << " is smaller than minimum " << min_num_cells <<
" (interaction range too large or min_num_cells too large)";
runtimeError(msg);
}
}
/* quit program if unsuccesful */
if(n_local_cells > max_num_cells) {
ostringstream msg;
msg << "no suitable cell grid found ";
runtimeError(msg);
}
/* now set all dependent variables */
new_cells=1;
for(i=0;i<3;i++) {
dd.ghost_cell_grid[i] = dd.cell_grid[i]+2;
#ifdef LEES_EDWARDS
//Hack alert: only the boundary y-layers actually need the extra-thick ghost cell grid,
//so some memory (and copies) are wasted in the name of simpler code.
if( i == 0 ){dd.ghost_cell_grid[i]++;}
#endif
new_cells *= dd.ghost_cell_grid[i];
dd.cell_size[i] = local_box_l[i]/(double)dd.cell_grid[i];
dd.inv_cell_size[i] = 1.0 / dd.cell_size[i];
}
max_skin = dmin(dmin(dd.cell_size[0],dd.cell_size[1]),dd.cell_size[2]) - max_cut;
/* allocate cell array and cell pointer arrays */
realloc_cells(new_cells);
realloc_cellplist(&local_cells, local_cells.n = n_local_cells);
realloc_cellplist(&ghost_cells, ghost_cells.n = new_cells-n_local_cells);
CELL_TRACE(fprintf(stderr, "%d: dd_create_cell_grid, n_cells=%d, local_cells.n=%d, ghost_cells.n=%d, dd.ghost_cell_grid=(%d,%d,%d)\n", this_node, n_cells,local_cells.n,ghost_cells.n,dd.ghost_cell_grid[0],dd.ghost_cell_grid[1],dd.ghost_cell_grid[2]));
}
/** Fill local_cells list and ghost_cells list for use with domain
decomposition. \ref cells::cells is assumed to be a 3d grid with size
\ref DomainDecomposition::ghost_cell_grid . */
void dd_mark_cells()
{
int m,n,o,cnt_c=0,cnt_l=0,cnt_g=0;
DD_CELLS_LOOP(m,n,o) {
#ifdef LEES_EDWARDS
/* convenient for LE if a cell knows where it is*/
cells[cnt_c].myIndex[0] = m;
cells[cnt_c].myIndex[1] = n;
cells[cnt_c].myIndex[2] = o;
#endif
if(DD_IS_LOCAL_CELL(m,n,o)) local_cells.cell[cnt_l++] = &cells[cnt_c++];
else ghost_cells.cell[cnt_g++] = &cells[cnt_c++];
}
void check_particle_consistency()
{
Particle *part;
Cell *cell;
int n, np, dir, c, p;
int cell_part_cnt=0, ghost_part_cnt=0, local_part_cnt=0;
int cell_err_cnt=0;
/* checks: part_id, part_pos, local_particles id */
for (c = 0; c < local_cells.n; c++) {
cell = local_cells.cell[c];
cell_part_cnt += cell->n;
part = cell->part;
np = cell->n;
for(n=0; n<cell->n ; n++) {
if(part[n].p.identity < 0 || part[n].p.identity > max_seen_particle) {
fprintf(stderr,"%d: check_particle_consistency: ERROR: Cell %d Part %d has corrupted id=%d\n",
this_node,c,n,cell->part[n].p.identity);
errexit();
}
for(dir=0;dir<3;dir++) {
if(PERIODIC(dir) && (part[n].r.p[dir] < -ROUND_ERROR_PREC || part[n].r.p[dir] - box_l[dir] > ROUND_ERROR_PREC)) {
fprintf(stderr,"%d: check_particle_consistency: ERROR: illegal pos[%d]=%f of part %d id=%d in cell %d\n",
this_node,dir,part[n].r.p[dir],n,part[n].p.identity,c);
errexit();
}
}
if(local_particles[part[n].p.identity] != &part[n]) {
fprintf(stderr,"%d: check_particle_consistency: ERROR: address mismatch for part id %d: local: %p cell: %p in cell %d\n",
this_node,part[n].p.identity,local_particles[part[n].p.identity],
&part[n],c);
errexit();
}
}
}
for (c = 0; c < ghost_cells.n; c++) {
cell = ghost_cells.cell[c];
if(cell->n>0) {
ghost_part_cnt += cell->n;
fprintf(stderr,"%d: check_particle_consistency: WARNING: ghost_cell %d contains %d particles!\n",
this_node,c,cell->n);
}
}
CELL_TRACE(fprintf(stderr,"%d: check_particle_consistency: %d particles in cells, %d particles in ghost_cells.\n",
this_node,cell_part_cnt, ghost_part_cnt));
/* checks: local particle id */
for(n=0; n< max_seen_particle+1; n++) {
if(local_particles[n] != NULL) {
local_part_cnt ++;
if(local_particles[n]->p.identity != n) {
fprintf(stderr,"%d: check_particle_consistency: ERROR: local_particles part %d has corrupted id %d\n",
this_node,n,local_particles[n]->p.identity);
errexit();
}
}
}
CELL_TRACE(fprintf(stderr,"%d: check_particle_consistency: %d particles in local_particles.\n",
this_node,local_part_cnt));
/* EXIT on severe errors */
if(cell_err_cnt>0) {
fprintf(stderr,"%d: check_particle_consistency: %d ERRORS detected in cell structure!\n",this_node,cell_err_cnt);
errexit();
}
if(local_part_cnt != cell_part_cnt) {
fprintf(stderr,"%d: check_particle_consistency: ERROR: %d parts in cells but %d parts in local_particles\n",
this_node,cell_part_cnt,local_part_cnt);
for (c = 0; c < local_cells.n; c++) {
for(p = 0; p < local_cells.cell[c]->n; p++)
fprintf(stderr, "%d: got particle %d in cell %d\n", this_node, local_cells.cell[c]->part[p].p.identity, c);
}
for(p = 0; p < n_total_particles; p++)
if (local_particles[p])
fprintf(stderr, "%d: got particle %d in local_particles\n", this_node, p);
if(ghost_part_cnt==0) errexit();
}
if(ghost_part_cnt>0) {
fprintf(stderr,"%d: check_particle_consistency: ERROR: Found %d illegal ghost particles!\n",
this_node,ghost_part_cnt);
errexit();
}
}
void nsq_balance_particles()
{
int i, n, surplus, s_node, tmp, lack, l_node, transfer;
int pp = cells_get_n_particles();
int *ppnode = malloc(n_nodes*sizeof(int));
/* minimal difference between node shares */
int minshare = n_total_particles/n_nodes;
int maxshare = minshare + 1;
CELL_TRACE(fprintf(stderr, "%d: nsq_balance_particles: load %d-%d\n", this_node, minshare, maxshare));
MPI_Allgather(&pp, 1, MPI_INT, ppnode, 1, MPI_INT, MPI_COMM_WORLD);
for (;;) {
/* find node with most excessive particles */
surplus = -1;
s_node = -1;
for (n = 0; n < n_nodes; n++) {
tmp = ppnode[n] - minshare;
CELL_TRACE(fprintf(stderr, "%d: nsq_balance_particles: node %d has %d\n", this_node, n, ppnode[n]));
if (tmp > surplus) {
surplus = tmp;
s_node = n;
}
}
CELL_TRACE(fprintf(stderr, "%d: nsq_balance_particles: excess %d on node %d\n", this_node, surplus, s_node));
/* find node with most lacking particles */
lack = -1;
l_node = -1;
for (n = 0; n < n_nodes; n++) {
tmp = maxshare - ppnode[n];
if (tmp > lack) {
lack = tmp;
l_node = n;
}
}
CELL_TRACE(fprintf(stderr, "%d: nsq_balance_particles: lack %d on node %d\n", this_node, lack, l_node));
/* should not happen: minshare or maxshare wrong or more likely,
the algorithm */
if (s_node == -1 || l_node == -1) {
fprintf(stderr, "%d: Particle load balancing failed\n", this_node);
break;
}
/* exit if all nodes load is withing min and max share */
if (lack <= 1 && surplus <= 1)
break;
transfer = lack < surplus ? lack : surplus;
if (s_node == this_node) {
ParticleList send_buf;
init_particlelist(&send_buf);
realloc_particlelist(&send_buf, send_buf.n = transfer);
for (i = 0; i < transfer; i++) {
memcpy(&send_buf.part[i], &local->part[--local->n], sizeof(Particle));
}
realloc_particlelist(local, local->n);
update_local_particles(local);
send_particles(&send_buf, l_node);
#ifdef ADDITIONAL_CHECKS
check_particle_consistency();
#endif
}
else if (l_node == this_node) {
recv_particles(local, s_node);
#ifdef ADDITIONAL_CHECKS
check_particle_consistency();
#endif
}
ppnode[s_node] -= transfer;
ppnode[l_node] += transfer;
}
CELL_TRACE(fprintf(stderr, "%d: nsq_balance_particles: done\n", this_node));
free(ppnode);
}
void nsq_topology_init(CellPList *old)
{
Particle *part;
int n, c, p, np, ntodo, diff;
CELL_TRACE(fprintf(stderr, "%d: nsq_topology_init, %d\n", this_node, old->n));
cell_structure.type = CELL_STRUCTURE_NSQUARE;
cell_structure.position_to_node = map_position_node_array;
cell_structure.position_to_cell = nsq_position_to_cell;
realloc_cells(n_nodes);
/* mark cells */
local = &cells[this_node];
realloc_cellplist(&local_cells, local_cells.n = 1);
local_cells.cell[0] = local;
realloc_cellplist(&ghost_cells, ghost_cells.n = n_nodes - 1);
c = 0;
for (n = 0; n < n_nodes; n++)
if (n != this_node)
ghost_cells.cell[c++] = &cells[n];
/* distribute force calculation work */
ntodo = (n_nodes + 3)/2;
init_cellplist(&me_do_ghosts);
realloc_cellplist(&me_do_ghosts, ntodo);
for (n = 0; n < n_nodes; n++) {
diff = n - this_node;
/* simple load balancing formula. Basically diff % n, where n >= n_nodes, n odd.
The node itself is also left out, as it is treated differently */
if (((diff > 0 && (diff % 2) == 0) ||
(diff < 0 && ((-diff) % 2) == 1))) {
CELL_TRACE(fprintf(stderr, "%d: doing interactions with %d\n", this_node, n));
me_do_ghosts.cell[me_do_ghosts.n++] = &cells[n];
}
}
/* create communicators */
nsq_prepare_comm(&cell_structure.ghost_cells_comm, GHOSTTRANS_PARTNUM);
nsq_prepare_comm(&cell_structure.exchange_ghosts_comm, GHOSTTRANS_PROPRTS | GHOSTTRANS_POSITION);
nsq_prepare_comm(&cell_structure.update_ghost_pos_comm, GHOSTTRANS_POSITION);
nsq_prepare_comm(&cell_structure.collect_ghost_force_comm, GHOSTTRANS_FORCE);
/* here we just decide what to transfer where */
if (n_nodes > 1) {
for (n = 0; n < n_nodes; n++) {
/* use the prefetched send buffers. Node 0 transmits first and never prefetches. */
if (this_node == 0 || this_node != n) {
cell_structure.ghost_cells_comm.comm[n].type = GHOST_BCST;
cell_structure.exchange_ghosts_comm.comm[n].type = GHOST_BCST;
cell_structure.update_ghost_pos_comm.comm[n].type = GHOST_BCST;
}
else {
cell_structure.ghost_cells_comm.comm[n].type = GHOST_BCST | GHOST_PREFETCH;
cell_structure.exchange_ghosts_comm.comm[n].type = GHOST_BCST | GHOST_PREFETCH;
cell_structure.update_ghost_pos_comm.comm[n].type = GHOST_BCST | GHOST_PREFETCH;
}
cell_structure.collect_ghost_force_comm.comm[n].type = GHOST_RDCE;
}
/* first round: all nodes except the first one prefetch their send data */
if (this_node != 0) {
cell_structure.ghost_cells_comm.comm[0].type |= GHOST_PREFETCH;
cell_structure.exchange_ghosts_comm.comm[0].type |= GHOST_PREFETCH;
cell_structure.update_ghost_pos_comm.comm[0].type |= GHOST_PREFETCH;
}
}
/* copy particles */
for (c = 0; c < old->n; c++) {
part = old->cell[c]->part;
np = old->cell[c]->n;
for (p = 0; p < np; p++)
append_unindexed_particle(local, &part[p]);
}
update_local_particles(local);
}
void check_particles()
{
Particle *part;
int *is_here;
Cell *cell;
int n, np, dir, c, p;
int cell_part_cnt=0, local_part_cnt=0;
int cell_err_cnt=0;
double skin2 = (skin != -1) ? skin/2 : 0;
CELL_TRACE(fprintf(stderr, "%d: entering check_particles\n", this_node));
/* check the consistency of particle_nodes */
/* to this aim the array is broadcasted temporarily */
if (this_node != 0)
particle_node = malloc((max_seen_particle + 1)*sizeof(int));
is_here = malloc((max_seen_particle + 1)*sizeof(int));
memset(is_here, 0, (max_seen_particle + 1)*sizeof(int));
MPI_Bcast(particle_node, max_seen_particle + 1, MPI_INT, 0, MPI_COMM_WORLD);
/* checks: part_id, part_pos, local_particles id */
for (c = 0; c < local_cells.n; c++) {
cell = local_cells.cell[c];
cell_part_cnt += cell->n;
part = cell->part;
np = cell->n;
for(n=0; n<cell->n ; n++) {
if(part[n].p.identity < 0 || part[n].p.identity > max_seen_particle) {
fprintf(stderr,"%d: check_particles: ERROR: Cell %d Part %d has corrupted id=%d\n",
this_node,c,n,cell->part[n].p.identity);
errexit();
}
is_here[part[n].p.identity] = 1;
for(dir=0;dir<3;dir++) {
if(PERIODIC(dir) && (part[n].r.p[dir] < -skin2 || part[n].r.p[dir] > box_l[dir] + skin2)) {
fprintf(stderr,"%d: check_particles: ERROR: illegal pos[%d]=%f of part %d id=%d in cell %d\n",
this_node,dir,part[n].r.p[dir],n,part[n].p.identity,c);
errexit();
}
}
if(local_particles[part[n].p.identity] != &part[n]) {
fprintf(stderr,"%d: check_particles: ERROR: address mismatch for part id %d: local: %p cell: %p in cell %d\n",
this_node,part[n].p.identity,local_particles[part[n].p.identity],
&part[n],c);
errexit();
}
if (particle_node[part[n].p.identity] != this_node) {
fprintf(stderr,"%d: check_particles: ERROR: node for particle %d wrong\n",
this_node,part[n].p.identity);
errexit();
}
}
}
CELL_TRACE(fprintf(stderr,"%d: check_particles: %d particles in local cells.\n",
this_node,cell_part_cnt));
/* checks: local particle id */
for(n = 0; n <= max_seen_particle; n++) {
if(local_particles[n] != NULL) {
local_part_cnt ++;
if(local_particles[n]->p.identity != n) {
fprintf(stderr,"%d: check_particles: ERROR: local_particles part %d has corrupted id %d\n",
this_node,n,local_particles[n]->p.identity);
errexit();
}
}
}
CELL_TRACE(fprintf(stderr,"%d: check_particles: %d particles in local_particles.\n",
this_node,local_part_cnt));
/* EXIT on severe errors */
if(cell_err_cnt>0) {
fprintf(stderr,"%d: check_particles: %d ERRORS detected in cell structure!\n",this_node,cell_err_cnt);
errexit();
}
/* check whether the particles on my node are actually here */
for (p = 0; p <= max_seen_particle; p++) {
if (particle_node[p] == this_node) {
if (!is_here[p]) {
fprintf(stderr,"%d: check_particles: ERROR: particle %d on this node, but not in local cell\n", this_node, p);
}
}
}
free(is_here);
if (this_node != 0) {
free(particle_node);
particle_node = NULL;
}
else {
/* check whether the total count of particles is ok */
c = 0;
for (p = 0; p <= max_seen_particle; p++)
if (particle_node[p] != -1) c++;
if (c != n_total_particles) {
fprintf(stderr,"%d: check_particles: #particles in particle_node inconsistent\n", this_node);
errexit();
}
CELL_TRACE(fprintf(stderr,"%d: check_particles: %d particles in particle_node.\n",
this_node,c));
}
CELL_TRACE(fprintf(stderr, "%d: leaving check_particles\n", this_node));
}
/** Calculate cell grid dimensions, cell sizes and number of cells.
* Calculates the cell grid, based on \ref local_box_l and \ref
* max_range. If the number of cells is larger than \ref
* max_num_cells, it increases max_range until the number of cells is
* smaller or equal \ref max_num_cells. It sets: \ref
* DomainDecomposition::cell_grid, \ref
* DomainDecomposition::ghost_cell_grid, \ref
* DomainDecomposition::cell_size, \ref
* DomainDecomposition::inv_cell_size, and \ref n_cells.
*/
void dd_create_cell_grid()
{
int i,n_local_cells,new_cells,min_ind;
double cell_range[3], min_size, scale, volume;
CELL_TRACE(fprintf(stderr, "%d: dd_create_cell_grid: max_range %f\n",this_node,max_range));
CELL_TRACE(fprintf(stderr, "%d: dd_create_cell_grid: local_box %f-%f, %f-%f, %f-%f,\n",this_node,my_left[0],my_right[0],my_left[1],my_right[1],my_left[2],my_right[2]));
/* initialize */
cell_range[0]=cell_range[1]=cell_range[2] = max_range;
if (max_range < ROUND_ERROR_PREC*box_l[0]) {
/* this is the initialization case */
n_local_cells = dd.cell_grid[0] = dd.cell_grid[1] = dd.cell_grid[2]=1;
}
else {
/* Calculate initial cell grid */
volume = local_box_l[0];
for(i=1;i<3;i++) volume *= local_box_l[i];
scale = pow(max_num_cells/volume, 1./3.);
for(i=0;i<3;i++) {
/* this is at least 1 */
dd.cell_grid[i] = (int)ceil(local_box_l[i]*scale);
cell_range[i] = local_box_l[i]/dd.cell_grid[i];
if ( cell_range[i] < max_range ) {
/* ok, too many cells for this direction, set to minimum */
dd.cell_grid[i] = (int)floor(local_box_l[i]/max_range);
if ( dd.cell_grid[i] < 1 ) {
char *error_msg = runtime_error(ES_INTEGER_SPACE + 2*ES_DOUBLE_SPACE + 128);
ERROR_SPRINTF(error_msg, "{002 interaction range %g in direction %d is larger than the local box size %g} ",
max_range, i, local_box_l[i]);
dd.cell_grid[i] = 1;
}
cell_range[i] = local_box_l[i]/dd.cell_grid[i];
}
}
/* It may be necessary to asymmetrically assign the scaling to the coordinates, which the above approach will not do.
For a symmetric box, it gives a symmetric result. Here we correct that. */
for (;;) {
n_local_cells = dd.cell_grid[0];
for (i = 1; i < 3; i++)
n_local_cells *= dd.cell_grid[i];
/* done */
if (n_local_cells <= max_num_cells)
break;
/* find coordinate with the smallest cell range */
min_ind = 0;
min_size = cell_range[0];
for (i = 1; i < 3; i++)
if (dd.cell_grid[i] > 1 && cell_range[i] < min_size) {
min_ind = i;
min_size = cell_range[i];
}
CELL_TRACE(fprintf(stderr, "%d: minimal coordinate %d, size %f, grid %d\n", this_node,min_ind, min_size, dd.cell_grid[min_ind]));
dd.cell_grid[min_ind]--;
cell_range[min_ind] = local_box_l[min_ind]/dd.cell_grid[min_ind];
}
CELL_TRACE(fprintf(stderr, "%d: final %d %d %d\n", this_node, dd.cell_grid[0], dd.cell_grid[1], dd.cell_grid[2]));
/* sanity check */
if (n_local_cells < min_num_cells) {
char *error_msg = runtime_error(ES_INTEGER_SPACE + 2*ES_DOUBLE_SPACE + 128);
ERROR_SPRINTF(error_msg, "{001 number of cells %d is smaller than minimum %d (interaction range too large or min_num_cells too large)} ",
n_local_cells, min_num_cells);
}
}
/* quit program if unsuccesful */
if(n_local_cells > max_num_cells) {
char *error_msg = runtime_error(128);
ERROR_SPRINTF(error_msg, "{003 no suitable cell grid found} ");
}
/* now set all dependent variables */
new_cells=1;
for(i=0;i<3;i++) {
dd.ghost_cell_grid[i] = dd.cell_grid[i]+2;
new_cells *= dd.ghost_cell_grid[i];
dd.cell_size[i] = local_box_l[i]/(double)dd.cell_grid[i];
dd.inv_cell_size[i] = 1.0 / dd.cell_size[i];
}
max_skin = dmin(dmin(dd.cell_size[0],dd.cell_size[1]),dd.cell_size[2]) - max_cut;
/* allocate cell array and cell pointer arrays */
realloc_cells(new_cells);
realloc_cellplist(&local_cells, local_cells.n = n_local_cells);
realloc_cellplist(&ghost_cells, ghost_cells.n = new_cells-n_local_cells);
CELL_TRACE(fprintf(stderr, "%d: dd_create_cell_grid, n_cells=%d, local_cells.n=%d, ghost_cells.n=%d, dd.ghost_cell_grid=(%d,%d,%d)\n", this_node, n_cells,local_cells.n,ghost_cells.n,dd.ghost_cell_grid[0],dd.ghost_cell_grid[1],dd.ghost_cell_grid[2]));
}
static void recalc_maximal_cutoff_nonbonded()
{
int i, j;
CELL_TRACE(fprintf(stderr, "%d: recalc_maximal_cutoff_nonbonded\n", this_node));
recalc_global_maximal_nonbonded_cutoff();
CELL_TRACE(fprintf(stderr, "%d: recalc_maximal_cutoff_nonbonded: max_cut_global = %f\n", this_node, max_cut_global));
max_cut_nonbonded = max_cut_global;
for (i = 0; i < n_particle_types; i++)
for (j = i; j < n_particle_types; j++) {
double max_cut_current = 0;
IA_parameters *data = get_ia_param(i, j);
#ifdef LENNARD_JONES
if(max_cut_current < (data->LJ_cut+data->LJ_offset))
max_cut_current = (data->LJ_cut+data->LJ_offset);
#endif
#ifdef INTER_DPD
{
double max_cut_tmp = (data->dpd_r_cut > data->dpd_tr_cut) ?
data->dpd_r_cut : data->dpd_tr_cut;
if (max_cut_current < max_cut_tmp)
max_cut_current = max_cut_tmp;
}
#endif
#ifdef LENNARD_JONES_GENERIC
if (max_cut_current < (data->LJGEN_cut+data->LJGEN_offset))
max_cut_current = (data->LJGEN_cut+data->LJGEN_offset);
#endif
#ifdef LJ_ANGLE
if (max_cut_current < (data->LJANGLE_cut))
max_cut_current = (data->LJANGLE_cut);
#endif
#ifdef SMOOTH_STEP
if (max_cut_current < data->SmSt_cut)
max_cut_current = data->SmSt_cut;
#endif
#ifdef HERTZIAN
if (max_cut_current < data->Hertzian_sig)
max_cut_current = data->Hertzian_sig;
#endif
#ifdef GAUSSIAN
if (max_cut_current < data->Gaussian_cut)
max_cut_current = data->Gaussian_cut;
#endif
#ifdef BMHTF_NACL
if (max_cut_current < data->BMHTF_cut)
max_cut_current = data->BMHTF_cut;
#endif
#ifdef MORSE
if (max_cut_current < data->MORSE_cut)
max_cut_current = data->MORSE_cut;
#endif
#ifdef BUCKINGHAM
if (max_cut_current < data->BUCK_cut)
max_cut_current = data->BUCK_cut;
#endif
#ifdef SOFT_SPHERE
if (max_cut_current < data->soft_cut)
max_cut_current = data->soft_cut;
#endif
#ifdef HAT
if (max_cut_current < data->HAT_r)
max_cut_current = data->HAT_r;
#endif
#ifdef LJCOS
{
double max_cut_tmp = data->LJCOS_cut + data->LJCOS_offset;
if (max_cut_current < max_cut_tmp)
max_cut_current = max_cut_tmp;
}
#endif
#ifdef LJCOS2
{
double max_cut_tmp = data->LJCOS2_cut + data->LJCOS2_offset;
if (max_cut_current < max_cut_tmp)
max_cut_current = max_cut_tmp;
}
#endif
#ifdef GAY_BERNE
if (max_cut_current < data->GB_cut)
max_cut_current = data->GB_cut;
#endif
#ifdef TABULATED
if (max_cut_current < data->TAB_maxval)
max_cut_current = data->TAB_maxval;
#endif
#ifdef TUNABLE_SLIP
if (max_cut_current < data->TUNABLE_SLIP_r_cut)
max_cut_current = data->TUNABLE_SLIP_r_cut;
#endif
#ifdef CATALYTIC_REACTIONS
if (max_cut_current < data->REACTION_range)
max_cut_current = data->REACTION_range;
#endif
#ifdef MOL_CUT
if (data->mol_cut_type != 0) {
if (max_cut_current < data->mol_cut_cutoff)
max_cut_current = data->mol_cut_cutoff;
max_cut_current += 2.0* max_cut_bonded;
}
#endif
IA_parameters *data_sym = get_ia_param(j, i);
/* no interaction ever touched it, at least no real
short-ranged one (that writes to the nonbonded energy) */
data_sym->particlesInteract =
data->particlesInteract = (max_cut_current > 0.0);
/* take into account any electrostatics */
if (max_cut_global > max_cut_current)
max_cut_current = max_cut_global;
data_sym->max_cut =
data->max_cut = max_cut_current;
if (max_cut_current > max_cut_nonbonded)
max_cut_nonbonded = max_cut_current;
CELL_TRACE(fprintf(stderr, "%d: pair %d,%d max_cut total %f\n",
this_node, i, j, data->max_cut));
}
}
static void recalc_maximal_cutoff_nonbonded()
{
int i, j;
CELL_TRACE(fprintf(stderr, "%d: recalc_maximal_cutoff_nonbonded\n", this_node));
recalc_global_maximal_nonbonded_and_long_range_cutoff();
CELL_TRACE(fprintf(stderr, "%d: recalc_maximal_cutoff_nonbonded: max_cut_global = %f\n", this_node, max_cut_global));
max_cut_nonbonded = max_cut_global;
for (i = 0; i < n_particle_types; i++)
for (j = i; j < n_particle_types; j++) {
double max_cut_current = 0;
IA_parameters *data = get_ia_param(i, j);
#ifdef LENNARD_JONES
if(max_cut_current < (data->LJ_cut+data->LJ_offset))
max_cut_current = (data->LJ_cut+data->LJ_offset);
#endif
#ifdef INTER_DPD
{
double max_cut_tmp = (data->dpd_r_cut > data->dpd_tr_cut) ?
data->dpd_r_cut : data->dpd_tr_cut;
if (max_cut_current < max_cut_tmp)
max_cut_current = max_cut_tmp;
}
#endif
#ifdef LENNARD_JONES_GENERIC
if (max_cut_current < (data->LJGEN_cut+data->LJGEN_offset))
max_cut_current = (data->LJGEN_cut+data->LJGEN_offset);
#endif
#ifdef LJ_ANGLE
if (max_cut_current < (data->LJANGLE_cut))
max_cut_current = (data->LJANGLE_cut);
#endif
#ifdef SMOOTH_STEP
if (max_cut_current < data->SmSt_cut)
max_cut_current = data->SmSt_cut;
#endif
#ifdef HERTZIAN
if (max_cut_current < data->Hertzian_sig)
max_cut_current = data->Hertzian_sig;
#endif
#ifdef GAUSSIAN
if (max_cut_current < data->Gaussian_cut)
max_cut_current = data->Gaussian_cut;
#endif
#ifdef BMHTF_NACL
if (max_cut_current < data->BMHTF_cut)
max_cut_current = data->BMHTF_cut;
#endif
#ifdef MORSE
if (max_cut_current < data->MORSE_cut)
max_cut_current = data->MORSE_cut;
#endif
#ifdef BUCKINGHAM
if (max_cut_current < data->BUCK_cut)
max_cut_current = data->BUCK_cut;
#endif
#ifdef SOFT_SPHERE
if (max_cut_current < data->soft_cut)
max_cut_current = data->soft_cut;
#endif
#ifdef AFFINITY
if (max_cut_current < data->affinity_cut)
max_cut_current = data->affinity_cut;
#endif
#ifdef MEMBRANE_COLLISION
if (max_cut_current < data->membrane_cut)
max_cut_current = data->membrane_cut;
#endif
#ifdef HAT
if (max_cut_current < data->HAT_r)
max_cut_current = data->HAT_r;
#endif
#ifdef LJCOS
{
double max_cut_tmp = data->LJCOS_cut + data->LJCOS_offset;
if (max_cut_current < max_cut_tmp)
max_cut_current = max_cut_tmp;
}
#endif
#ifdef LJCOS2
{
double max_cut_tmp = data->LJCOS2_cut + data->LJCOS2_offset;
if (max_cut_current < max_cut_tmp)
max_cut_current = max_cut_tmp;
}
#endif
#ifdef COS2
{
double max_cut_tmp = data->COS2_cut + data->COS2_offset;
if (max_cut_current < max_cut_tmp)
max_cut_current = max_cut_tmp;
}
#endif
#ifdef GAY_BERNE
if (max_cut_current < data->GB_cut)
max_cut_current = data->GB_cut;
#endif
#ifdef TABULATED
if (max_cut_current < data->TAB_maxval)
max_cut_current = data->TAB_maxval;
#endif
#ifdef TUNABLE_SLIP
if (max_cut_current < data->TUNABLE_SLIP_r_cut)
max_cut_current = data->TUNABLE_SLIP_r_cut;
#endif
#ifdef CATALYTIC_REACTIONS
if (max_cut_current < data->REACTION_range)
max_cut_current = data->REACTION_range;
#endif
#ifdef MOL_CUT
if (data->mol_cut_type != 0) {
if (max_cut_current < data->mol_cut_cutoff)
max_cut_current = data->mol_cut_cutoff;
max_cut_current += 2.0* max_cut_bonded;
}
#endif
IA_parameters *data_sym = get_ia_param(j, i);
/* no interaction ever touched it, at least no real
short-ranged one (that writes to the nonbonded energy) */
data_sym->particlesInteract =
data->particlesInteract = (max_cut_current > 0.0);
/* Bigger cutoffs are chosen due to dpd and the like.
Coulomb and dipolar interactions are handled in the Verlet lists
separately. */
max_cut_current =std::max(max_cut_current,max_cut_global_without_coulomb_and_dipolar);
data_sym->max_cut =
data->max_cut = max_cut_current;
if (max_cut_current > max_cut_nonbonded)
max_cut_nonbonded = max_cut_current;
CELL_TRACE(fprintf(stderr, "%d: pair %d,%d max_cut total %f\n",
this_node, i, j, data->max_cut));
}
}
/** Create communicators for cell structure domain decomposition. (see \ref GhostCommunicator) */
void dd_prepare_comm(GhostCommunicator *comm, int data_parts)
{
int dir,lr,i,cnt, num, n_comm_cells[3];
int lc[3],hc[3],done[3]={0,0,0};
/* calculate number of communications */
num = 0;
for(dir=0; dir<3; dir++) {
for(lr=0; lr<2; lr++) {
#ifdef PARTIAL_PERIODIC
/* No communication for border of non periodic direction */
if( PERIODIC(dir) || (boundary[2*dir+lr] == 0) )
#endif
{
if(node_grid[dir] == 1 ) num++;
else num += 2;
}
}
}
/* prepare communicator */
CELL_TRACE(fprintf(stderr,"%d Create Communicator: prep_comm data_parts %d num %d\n",this_node,data_parts,num));
prepare_comm(comm, data_parts, num);
/* number of cells to communicate in a direction */
n_comm_cells[0] = dd.cell_grid[1] * dd.cell_grid[2];
n_comm_cells[1] = dd.cell_grid[2] * dd.ghost_cell_grid[0];
n_comm_cells[2] = dd.ghost_cell_grid[0] * dd.ghost_cell_grid[1];
cnt=0;
/* direction loop: x, y, z */
for(dir=0; dir<3; dir++) {
lc[(dir+1)%3] = 1-done[(dir+1)%3];
lc[(dir+2)%3] = 1-done[(dir+2)%3];
hc[(dir+1)%3] = dd.cell_grid[(dir+1)%3]+done[(dir+1)%3];
hc[(dir+2)%3] = dd.cell_grid[(dir+2)%3]+done[(dir+2)%3];
/* lr loop: left right */
/* here we could in principle build in a one sided ghost
communication, simply by taking the lr loop only over one
value */
for(lr=0; lr<2; lr++) {
if(node_grid[dir] == 1) {
/* just copy cells on a single node */
#ifdef PARTIAL_PERIODIC
if( PERIODIC(dir ) || (boundary[2*dir+lr] == 0) )
#endif
{
comm->comm[cnt].type = GHOST_LOCL;
comm->comm[cnt].node = this_node;
/* Buffer has to contain Send and Recv cells -> factor 2 */
comm->comm[cnt].part_lists = malloc(2*n_comm_cells[dir]*sizeof(ParticleList *));
comm->comm[cnt].n_part_lists = 2*n_comm_cells[dir];
/* prepare folding of ghost positions */
if((data_parts & GHOSTTRANS_POSSHFTD) && boundary[2*dir+lr] != 0)
comm->comm[cnt].shift[dir] = boundary[2*dir+lr]*box_l[dir];
/* fill send comm cells */
lc[(dir+0)%3] = hc[(dir+0)%3] = 1+lr*(dd.cell_grid[(dir+0)%3]-1);
dd_fill_comm_cell_lists(comm->comm[cnt].part_lists,lc,hc);
CELL_TRACE(fprintf(stderr,"%d: prep_comm %d copy to grid (%d,%d,%d)-(%d,%d,%d)\n",this_node,cnt,
lc[0],lc[1],lc[2],hc[0],hc[1],hc[2]));
/* fill recv comm cells */
lc[(dir+0)%3] = hc[(dir+0)%3] = 0+(1-lr)*(dd.cell_grid[(dir+0)%3]+1);
/* place recieve cells after send cells */
dd_fill_comm_cell_lists(&comm->comm[cnt].part_lists[n_comm_cells[dir]],lc,hc);
CELL_TRACE(fprintf(stderr,"%d: prep_comm %d copy from grid (%d,%d,%d)-(%d,%d,%d)\n",this_node,cnt,lc[0],lc[1],lc[2],hc[0],hc[1],hc[2]));
cnt++;
}
}
else {
/* i: send/recv loop */
for(i=0; i<2; i++) {
#ifdef PARTIAL_PERIODIC
if( PERIODIC(dir) || (boundary[2*dir+lr] == 0) )
#endif
if((node_pos[dir]+i)%2==0) {
comm->comm[cnt].type = GHOST_SEND;
comm->comm[cnt].node = node_neighbors[2*dir+lr];
comm->comm[cnt].part_lists = malloc(n_comm_cells[dir]*sizeof(ParticleList *));
comm->comm[cnt].n_part_lists = n_comm_cells[dir];
/* prepare folding of ghost positions */
if((data_parts & GHOSTTRANS_POSSHFTD) && boundary[2*dir+lr] != 0)
comm->comm[cnt].shift[dir] = boundary[2*dir+lr]*box_l[dir];
lc[(dir+0)%3] = hc[(dir+0)%3] = 1+lr*(dd.cell_grid[(dir+0)%3]-1);
dd_fill_comm_cell_lists(comm->comm[cnt].part_lists,lc,hc);
CELL_TRACE(fprintf(stderr,"%d: prep_comm %d send to node %d grid (%d,%d,%d)-(%d,%d,%d)\n",this_node,cnt,
comm->comm[cnt].node,lc[0],lc[1],lc[2],hc[0],hc[1],hc[2]));
cnt++;
}
#ifdef PARTIAL_PERIODIC
if( PERIODIC(dir) || (boundary[2*dir+(1-lr)] == 0) )
#endif
if((node_pos[dir]+(1-i))%2==0) {
comm->comm[cnt].type = GHOST_RECV;
comm->comm[cnt].node = node_neighbors[2*dir+(1-lr)];
comm->comm[cnt].part_lists = malloc(n_comm_cells[dir]*sizeof(ParticleList *));
comm->comm[cnt].n_part_lists = n_comm_cells[dir];
lc[(dir+0)%3] = hc[(dir+0)%3] = 0+(1-lr)*(dd.cell_grid[(dir+0)%3]+1);
dd_fill_comm_cell_lists(comm->comm[cnt].part_lists,lc,hc);
CELL_TRACE(fprintf(stderr,"%d: prep_comm %d recv from node %d grid (%d,%d,%d)-(%d,%d,%d)\n",this_node,cnt,
comm->comm[cnt].node,lc[0],lc[1],lc[2],hc[0],hc[1],hc[2]));
cnt++;
}
}
}
done[dir]=1;
}
}
}