static void prepare_ghost_cell(Cell *cell, int size)
{
#ifdef GHOSTS_HAVE_BONDS
// free all allocated information, will be resent
{
int np = cell->n;
Particle *part = cell->part;
for (int p = 0; p < np; p++) {
free_particle(part + p);
}
}
#endif
realloc_particlelist(cell, cell->n = size);
// invalidate pointers etc
{
int np = cell->n;
Particle *part = cell->part;
for (int p = 0; p < np; p++) {
Particle *pt = &part[p];
// no bonds or exclusions
pt->bl.e = 0;
pt->bl.n = 0;
pt->bl.max = 0;
#ifdef EXCLUSIONS
pt->el.e = 0;
pt->el.n = 0;
pt->el.max = 0;
#endif
#ifdef GHOST_FLAG
//init ghost variable
pt->l.ghost=1;
#endif
}
}
}
void send_particles(ParticleList *particles, int node)
{
int pc;
/* Dynamic data, bonds and exclusions */
IntList local_dyn;
PART_TRACE(fprintf(stderr, "%d: send_particles %d to %d\n", this_node, particles->n, node));
MPI_Send(&particles->n, 1, MPI_INT, node, REQ_SNDRCV_PART, comm_cart);
MPI_Send(particles->part, particles->n*sizeof(Particle),
MPI_BYTE, node, REQ_SNDRCV_PART, comm_cart);
init_intlist(&local_dyn);
for (pc = 0; pc < particles->n; pc++) {
Particle *p = &particles->part[pc];
int size = local_dyn.n + p->bl.n;
#ifdef EXCLUSIONS
size += p->el.n;
#endif
realloc_intlist(&local_dyn, size);
memcpy(local_dyn.e + local_dyn.n, p->bl.e, p->bl.n*sizeof(int));
local_dyn.n += p->bl.n;
#ifdef EXCLUSIONS
memcpy(local_dyn.e + local_dyn.n, p->el.e, p->el.n*sizeof(int));
local_dyn.n += p->el.n;
#endif
}
PART_TRACE(fprintf(stderr, "%d: send_particles sending %d bond ints\n", this_node, local_dyn.n));
if (local_dyn.n > 0) {
MPI_Send(local_dyn.e, local_dyn.n*sizeof(int),
MPI_BYTE, node, REQ_SNDRCV_PART, comm_cart);
realloc_intlist(&local_dyn, 0);
}
/* remove particles from this nodes local list and free data */
for (pc = 0; pc < particles->n; pc++) {
local_particles[particles->part[pc].p.identity] = NULL;
free_particle(&particles->part[pc]);
}
realloc_particlelist(particles, particles->n = 0);
}
void local_remove_particle(int part)
{
int ind, c;
Particle *p = local_particles[part];
ParticleList *pl = NULL, *tmp;
/* the tricky - say ugly - part: determine
the cell the particle is located in by checking
wether the particle address is inside the array */
for (c = 0; c < local_cells.n; c++) {
tmp = local_cells.cell[c];
ind = p - tmp->part;
if (ind >= 0 && ind < tmp->n) {
pl = tmp;
break;
}
}
if (!pl) {
fprintf(stderr, "%d: INTERNAL ERROR: could not find cell of particle %d, exiting\n",
this_node, part);
errexit();
}
free_particle(p);
/* remove local_particles entry */
local_particles[p->p.identity] = NULL;
if (&pl->part[pl->n - 1] != p) {
/* move last particle to free position */
memcpy(p, &pl->part[pl->n - 1], sizeof(Particle));
/* update the local_particles array for the moved particle */
local_particles[p->p.identity] = p;
}
pl->n--;
}
int tclcommand_writemd(ClientData data, Tcl_Interp *interp,
int argc, char **argv)
{
static int end_num = -1;
char *row;
int p, i;
struct MDHeader header;
int tcl_file_mode;
Tcl_Channel channel;
if (argc < 3) {
#if defined(ELECTROSTATICS) && defined(DIPOLES)
Tcl_AppendResult(interp, "wrong # args: should be \"",
argv[0], " <file> ?posx|posy|posz|q|mx|my|mz|vx|vy|vz|fx|fy|fz|type?* ...\"",
(char *) NULL);
#else
#ifdef ELECTROSTATICS
Tcl_AppendResult(interp, "wrong # args: should be \"",
argv[0], " <file> ?posx|posy|posz|q|vx|vy|vz|fx|fy|fz|type?* ...\"",
(char *) NULL);
#endif
#ifdef DIPOLES
Tcl_AppendResult(interp, "wrong # args: should be \"",
argv[0], " <file> ?posx|posy|posz|mx|my|mz|vx|vy|vz|fx|fy|fz|type?* ...\"",
(char *) NULL);
#endif
#endif
return (TCL_ERROR);
}
if ((channel = Tcl_GetChannel(interp, argv[1], &tcl_file_mode)) == NULL)
return (TCL_ERROR);
if (!(tcl_file_mode & TCL_WRITABLE)) {
Tcl_AppendResult(interp, "\"", argv[1], "\" not writeable", (char *) NULL);
return (TCL_ERROR);
}
/* tune channel to binary translation, e.g. none */
Tcl_SetChannelOption(interp, channel, "-translation", "binary");
/* assemble rows */
argc -= 2;
argv += 2;
row = (char*)malloc(sizeof(char)*argc);
for (i = 0; i < argc; i++) {
if (!strncmp(*argv, "posx", strlen(*argv))) {
row[i] = POSX;
}
else if (!strncmp(*argv, "posy", strlen(*argv))) {
row[i] = POSY;
}
else if (!strncmp(*argv, "posz", strlen(*argv))) {
row[i] = POSZ;
}
#ifdef MASS
else if (!strncmp(*argv, "mass", strlen(*argv))) {
row[i] = MASSES;
}
#endif
else if (!strncmp(*argv, "q", strlen(*argv))) {
row[i] = Q;
}
#ifdef DIPOLES
else if (!strncmp(*argv, "mx", strlen(*argv))) {
row[i] = MX;
}
else if (!strncmp(*argv, "my", strlen(*argv))) {
row[i] = MY;
}
else if (!strncmp(*argv, "mz", strlen(*argv))) {
row[i] = MZ;
}
#endif
else if (!strncmp(*argv, "vx", strlen(*argv))) {
row[i] = VX;
}
else if (!strncmp(*argv, "vy", strlen(*argv))) {
row[i] = VY;
}
else if (!strncmp(*argv, "vz", strlen(*argv))) {
row[i] = VZ;
}
else if (!strncmp(*argv, "fx", strlen(*argv))) {
row[i] = FX;
}
else if (!strncmp(*argv, "fy", strlen(*argv))) {
row[i] = FY;
}
else if (!strncmp(*argv, "fz", strlen(*argv))) {
row[i] = FZ;
}
else if (!strncmp(*argv, "type", strlen(*argv))) {
row[i] = TYPE;
}
else {
Tcl_AppendResult(interp, "no particle data field \"", *argv, "\"?",
(char *) NULL);
free(row);
return (TCL_ERROR);
}
argv++;
}
if (!particle_node)
build_particle_node();
/* write header and row data */
memmove(header.magic, MDMAGIC, 4*sizeof(char));
header.n_rows = argc;
Tcl_Write(channel, (char *)&header, sizeof(header));
Tcl_Write(channel, row, header.n_rows*sizeof(char));
for (p = 0; p <= max_seen_particle; p++) {
Particle data;
if (get_particle_data(p, &data) == ES_OK) {
unfold_position(data.r.p, data.m.v, data.l.i);
/* write particle index */
Tcl_Write(channel, (char *)&p, sizeof(int));
for (i = 0; i < header.n_rows; i++) {
switch (row[i]) {
case POSX: Tcl_Write(channel, (char *)&data.r.p[0], sizeof(double)); break;
case POSY: Tcl_Write(channel, (char *)&data.r.p[1], sizeof(double)); break;
case POSZ: Tcl_Write(channel, (char *)&data.r.p[2], sizeof(double)); break;
case VX: Tcl_Write(channel, (char *)&data.m.v[0], sizeof(double)); break;
case VY: Tcl_Write(channel, (char *)&data.m.v[1], sizeof(double)); break;
case VZ: Tcl_Write(channel, (char *)&data.m.v[2], sizeof(double)); break;
case FX: Tcl_Write(channel, (char *)&data.f.f[0], sizeof(double)); break;
case FY: Tcl_Write(channel, (char *)&data.f.f[1], sizeof(double)); break;
case FZ: Tcl_Write(channel, (char *)&data.f.f[2], sizeof(double)); break;
#ifdef MASS
case MASSES: Tcl_Write(channel, (char *)&data.p.mass, sizeof(double)); break;
#endif
#ifdef ELECTROSTATICS
case Q: Tcl_Write(channel, (char *)&data.p.q, sizeof(double)); break;
#endif
#ifdef DIPOLES
case MX: Tcl_Write(channel, (char *)&data.r.dip[0], sizeof(double)); break;
case MY: Tcl_Write(channel, (char *)&data.r.dip[1], sizeof(double)); break;
case MZ: Tcl_Write(channel, (char *)&data.r.dip[2], sizeof(double)); break;
#endif
case TYPE: Tcl_Write(channel, (char *)&data.p.type, sizeof(int)); break;
}
}
free_particle(&data);
}
}
/* end marker */
Tcl_Write(channel, (char *)&end_num, sizeof(int));
free(row);
return TCL_OK;
}
