/* filter out epsilon margin separated points */
static int separate (int n, double **q, double epsilon)
{
if (epsilon <= 0.0) return n;
double epshalf = .5 * epsilon,
epsq = epsilon * epsilon,
d [3], r;
BOX *b, *g, **pb;
SET *item;
int i, m;
ERRMEM (b = malloc (n * sizeof (BOX)));
ERRMEM (pb = malloc (n * sizeof (BOX*)));
for (i = 0, g = b; i < n; i ++, g ++)
{
double *e = g->extents,
*p = q [i];
e [0] = p [0] - epshalf;
e [1] = p [1] - epshalf;
e [2] = p [2] - epshalf;
e [3] = p [0] + epshalf;
e [4] = p [1] + epshalf;
e [5] = p [2] + epshalf;
g->sgp = (void*) p;
g->body = NULL;
g->mark = NULL;
pb [i] = g;
}
hybrid (pb, n, NULL, overlap);
for (i = m = 0, g = b; i < n; i ++, g ++)
{
if (!g->mark)
{
double *a = (double*) g->sgp;
q [m ++] = a;
for (item = SET_First ((SET*)g->body); item; item = SET_Next (item))
{
BOX *adj = item->data;
double *b = (double*) adj->sgp;
SUB (a, b, d);
r = DOT (d, d);
if (r < epsq) adj->mark = (void*) 1; /* epsilon separation */
}
}
SET_Free (NULL, (SET**) &g->body);
}
free (pb);
free (b);
return m;
}
/* export data for fracture analysis in MoFEM (return number of exported analysis instances) */
int Fracture_Export_MoFEM (BODY *bod, double volume, double quality, FILE *output)
{
double extents [6], *q, *u, (*p) [3];
SOLFEC *sol = bod->dom->solfec;
int n, elno, fano;
FS *list, *it, *jt;
ELEMENT *ele;
FACE *fac;
MESH *msh;
KDT *kd;
if (!(bod->flags & BODY_CHECK_FRACTURE) || sol->mode == SOLFEC_WRITE) return 0;
list = fracture_state_read (bod);
if (list)
{
MESH *copy = MESH_Copy (bod->shape->data);
MESH_Update (copy, NULL, NULL, NULL); /* reference configuration */
msh = tetrahedralize1 (copy, volume, quality, -INT_MAX, -INT_MAX, NULL); /* generate tet mesh in reference configuration */
MESH_Destroy (copy);
/* allocate displacements on the tet mesh */
ERRMEM (q = malloc (6 * msh->nodes_count * sizeof (double)));
u = q + 3 * msh->nodes_count;
/* map faces to a kd-tree for quick point queries */
kd = KDT_Create (msh->nodes_count, (double*)msh->ref_nodes, 0.0);
for (ele = msh->surfeles; ele; ele = ele->next)
{
ELEMENT_Ref_Extents (msh, ele, extents);
for (fac = ele->faces; fac; fac = fac->next) KDT_Drop (kd, extents, fac);
}
//______________________________________________________
// output file start
for (fano = 0, fac = msh->faces; fac; fano ++, fac = fac->n) fac->index = fano; /* count and index faces */
ERRMEM (p = malloc (fano * sizeof (double [3]))); /* allocate face pressures */
elno = msh->surfeles_count + msh->bulkeles_count;
fprintf (output, "mOFF %d %d %d\n", msh->nodes_count, fano, elno); // file header
/* map displacements from the hex to the tet mesh */
FEM_Map_State (bod->shape->data, bod->conf, bod->velo, msh, q, u); /* only bod->disp to q mapping is used */
for (n = 0; n < msh->nodes_count; n ++)
{
fprintf (output, "%f %f %f %f %f %f\n", msh->ref_nodes [n][0], msh->ref_nodes [n][1], msh->ref_nodes [n][2], q[3*n], q[3*n+1], q[3*n+2]);
}
//______________________________________________________
/* rewind the list to the end to find the last element,
which corresponds to the earliest in time fracture instance */
for (it = list; it->next; it = it->next) continue;
/* for (it = list; it; it = it->next) */
/* FIXME -- FIXME -- FIXME -- FIXME */
{
for (n = 0; n < fano; n ++)
{
SET (p [n], 0.0); /* zero face pressures */
}
for (jt = it; jt; jt = jt->inext) /* for each point force in this instance */
{
double (*ref) [3] = msh->ref_nodes;
double a [3], b [3], c [3], area;
SET *set = NULL, *item;
double *qa, *qb, *qc;
extents [0] = jt->point[0] - jt->radius - GEOMETRIC_EPSILON; /* set up search extents */
extents [1] = jt->point[1] - jt->radius - GEOMETRIC_EPSILON;
extents [2] = jt->point[2] - jt->radius - GEOMETRIC_EPSILON;
extents [3] = jt->point[0] + jt->radius + GEOMETRIC_EPSILON;
extents [4] = jt->point[1] + jt->radius + GEOMETRIC_EPSILON;
extents [5] = jt->point[2] + jt->radius + GEOMETRIC_EPSILON;
KDT_Pick_Extents (kd, extents, &set); /* pick kd-tree leaves within the extents */
for (item = SET_First (set); item; item = SET_Next (item))
{
KDT *leaf = item->data;
for (n = 0; n < leaf->n; n ++)
{
fac = leaf->data [n]; /* face dropped into this leaf */
qa = &q[3*fac->nodes[0]];
qb = &q[3*fac->nodes[1]];
qc = &q[3*fac->nodes[2]];
ADD (ref[fac->nodes[0]], qa, a); /* current face nodes */
ADD (ref[fac->nodes[1]], qb, b);
ADD (ref[fac->nodes[2]], qc, c);
TRIANGLE_AREA (a, b, c, area); /* current face area */
if (area > 0.0) /* XXX */
{
p [fac->index][0] += jt->force [0] / area; /* add up pressure */
p [fac->index][1] += jt->force [1] / area; /* FIXME: seems to be adding up to much pressure -> divided by area */
p [fac->index][2] += jt->force [2] / area;
}
}
}
SET_Free (NULL, &set);
}
for (fac = msh->faces, n=0; fac; fac = fac->n, n ++)
{
fprintf (output, "3 %d %d %d %g %g %g\n", fac->nodes[0], fac->nodes[1], fac->nodes[2], p[n][0], p[n][1], p[n][2]);
}
}
//______________________________________________________
for (ele = msh->surfeles; ele; ele = ele->next)
{
fprintf (output, "4 %d %d %d %d\n", ele->nodes[0], ele->nodes[1], ele->nodes[2], ele->nodes[3]);
}
for (ele = msh->bulkeles; ele; ele = ele->next)
{
fprintf (output, "4 %d %d %d %d\n", ele->nodes[0], ele->nodes[1], ele->nodes[2], ele->nodes[3]);
}
// output file complete
//______________________________________________________
fracture_state_free (list);
free (q);
free (p);
MESH_Destroy (msh);
}
return 0;
}
/* write fracture state */
static void fracture_state_write (DOM *dom)
{
char path [1024];
double R[3], r, (*disp) [3];
int i, n, dofs;
MESH *msh;
SET *item;
BODY *bod;
CON *con;
#if HDF5
int numbod;
PBF *f;
snprintf (path, 1024, "%s/fracture", dom->solfec->outpath);
ASSERT (f = PBF_Write (path, PBF_ON, PBF_ON), ERR_FILE_OPEN);
PBF_Time (f, &dom->time);
for (numbod = 0, bod = dom->bod; bod; bod = bod->next)
{
if (bod->fracture)
{
msh = bod->shape->data;
dofs = 3 * msh->nodes_count;
ERRMEM (disp = malloc (msh->nodes_count * sizeof (double [3])));
for (i = 0; i < msh->nodes_count; i ++)
{
SUB (msh->cur_nodes [i], msh->ref_nodes [i], disp [i]);
}
PBF_Uint (f, &bod->id, 1);
PBF_Int (f, &dofs, 1);
PBF_Double (f, (double*)disp, dofs);
n = SET_Size (bod->con);
PBF_Int (f, &n, 1);
for (item = SET_First (bod->con); item; item = SET_Next (item))
{
con = item->data;
r = sqrt (con->area/ALG_PI);
PBF_Double (f, &r, 1);
if (bod == con->master)
{
PBF_Double (f, con->mpnt, 3);
}
else
{
PBF_Double (f, con->spnt, 3);
}
NVMUL (con->base, con->R, R);
PBF_Double (f, R, 3);
}
bod->fracture = 0;
free (disp);
numbod ++;
}
PBF_Int2 (f, "numbod", &numbod, 1);
}
PBF_Close (f);
#else
FILE *f;
XDR x;
#if MPI
snprintf (path, 1024, "%s/fracture%d.dat", dom->solfec->outpath, dom->rank);
#else
snprintf (path, 1024, "%s/fracture.dat", dom->solfec->outpath);
#endif
ASSERT (f = fopen (path, "a"), ERR_FILE_OPEN);
xdrstdio_create (&x, f, XDR_ENCODE);
for (bod = dom->bod; bod; bod = bod->next)
{
if (bod->fracture)
{
msh = bod->shape->data;
dofs = 3 * msh->nodes_count;
ERRMEM (disp = malloc (msh->nodes_count * sizeof (double [3])));
for (i = 0; i < msh->nodes_count; i ++)
{
SUB (msh->cur_nodes [i], msh->ref_nodes [i], disp [i]);
}
ASSERT (xdr_u_int (&x, &bod->id), ERR_FILE_WRITE);
ASSERT (xdr_int (&x, &dofs), ERR_FILE_WRITE);
ASSERT (xdr_vector (&x, (char*)disp, dofs, sizeof (double), (xdrproc_t)xdr_double), ERR_FILE_WRITE);
n = SET_Size (bod->con);
ASSERT (xdr_int (&x, &n), ERR_FILE_WRITE);
for (item = SET_First (bod->con); item; item = SET_Next (item))
{
con = item->data;
r = sqrt (con->area/ALG_PI);
ASSERT (xdr_double (&x, &r), ERR_FILE_WRITE);
if (bod == con->master)
{
ASSERT (xdr_vector (&x, (char*)con->mpnt, 3, sizeof (double), (xdrproc_t)xdr_double), ERR_FILE_WRITE);
}
else
{
ASSERT (xdr_vector (&x, (char*)con->spnt, 3, sizeof (double), (xdrproc_t)xdr_double), ERR_FILE_WRITE);
}
NVMUL (con->base, con->R, R);
ASSERT (xdr_vector (&x, (char*)R, 3, sizeof (double), (xdrproc_t)xdr_double), ERR_FILE_WRITE);
}
bod->fracture = 0;
free (disp);
}
}
xdr_destroy (&x);
fclose (f);
#endif
}
/* export data for fracture analysis in Yaffems (return number of exported analysis instances) */
int Fracture_Export_Yaffems (BODY *bod, double volume, double quality, FILE *output)
{
double extents [6], *q, *u, (*p) [3];
SOLFEC *sol = bod->dom->solfec;
int n, m, elno, fano;
FS *list, *it, *jt;
ELEMENT *ele;
FACE *fac;
MESH *msh;
KDT *kd;
if (!(bod->flags & BODY_CHECK_FRACTURE) || sol->mode == SOLFEC_WRITE) return 0;
list = fracture_state_read (bod);
if (list)
{
MESH *copy = MESH_Copy (bod->shape->data);
MESH_Update (copy, NULL, NULL, NULL); /* reference configuration */
msh = tetrahedralize1 (copy, volume, quality, -INT_MAX, -INT_MAX, NULL); /* generate tet mesh in reference configuration */
MESH_Destroy (copy);
/* allocate displacements on the tet mesh */
ERRMEM (q = malloc (6 * msh->nodes_count * sizeof (double)));
u = q + 3 * msh->nodes_count;
/* map faces to a kd-tree for quick point queries */
kd = KDT_Create (msh->nodes_count, (double*)msh->ref_nodes, 0.0);
for (ele = msh->surfeles; ele; ele = ele->next)
{
ELEMENT_Ref_Extents (msh, ele, extents);
for (fac = ele->faces; fac; fac = fac->next) KDT_Drop (kd, extents, fac);
}
fprintf (output, "%s\n", "# vtk DataFile Version 2.0");
fprintf (output, "%s\n", "Test Title");
fprintf (output, "ASCII\n");
fprintf (output, "\n");
fprintf (output, "DATASET UNSTRUCTURED_GRID\n");
fprintf (output, "POINTS %d float\n", msh->nodes_count);
for (n = 0; n < msh->nodes_count; n ++)
{
fprintf (output, "%f %f %f\n", msh->ref_nodes [n][0], msh->ref_nodes [n][1], msh->ref_nodes [n][2]);
}
for (fano = 0, fac = msh->faces; fac; fano ++, fac = fac->n) fac->index = fano; /* count and index faces */
ERRMEM (p = malloc (fano * sizeof (double [3]))); /* allocate face pressures */
elno = msh->surfeles_count + msh->bulkeles_count;
fprintf (output, "\n");
fprintf (output, "CELLS %d %d\n", elno + fano, elno*5 + fano*4);
for (ele = msh->surfeles; ele; ele = ele->next)
{
fprintf (output, "4 %d %d %d %d\n", ele->nodes[0], ele->nodes[1], ele->nodes[2], ele->nodes[3]);
}
for (ele = msh->bulkeles; ele; ele = ele->next)
{
fprintf (output, "4 %d %d %d %d\n", ele->nodes[0], ele->nodes[1], ele->nodes[2], ele->nodes[3]);
}
for (fac = msh->faces; fac; fac = fac->n)
{
fprintf (output, "3 %d %d %d\n", fac->nodes[0], fac->nodes[1], fac->nodes[2]);
}
fprintf (output, "\n");
fprintf (output, "CELL_TYPES %d\n", elno + fano);
for (n = 0; n < elno; n++)
{
fprintf (output, "10\n");
}
for (n = 0; n < fano; n++)
{
fprintf (output, "5\n");
}
fprintf (output, "\n");
fprintf (output, "POINT_DATA %d\n", msh->nodes_count);
for (it = list, m = 0; it; it = it->next, m ++)
{
/* map displacements from the hex to the tet mesh */
FEM_Map_State (bod->shape->data, it->disp, bod->velo, msh, q, u); /* only it->disp to q mapping is used */
fprintf (output, "\n");
fprintf (output, "VECTORS disp%d float\n", m+1);
for (n = 0; n < msh->nodes_count; n ++)
{
fprintf (output, "%f %f %f\n", q[3*n], q[3*n+1], q[3*n+2]);
}
}
fprintf (output, "\n");
fprintf (output, "CELL_DATA %d\n", elno + fano);
for (it = list, m = 0; it; it = it->next, m ++)
{
fprintf (output, "\n");
fprintf (output, "VECTORS pres%d float\n", m);
for (n = 0; n < elno; n ++) /* skip elements */
{
fprintf (output, "0 0 0\n");
}
for (n = 0; n < fano; n ++)
{
SET (p [n], 0.0); /* zero face pressures */
}
for (jt = it; jt; jt = jt->inext) /* for each point force in this instance */
{
double (*ref) [3] = msh->ref_nodes;
double a [3], b [3], c [3], area;
SET *set = NULL, *item;
double *qa, *qb, *qc;
extents [0] = jt->point[0] - jt->radius - GEOMETRIC_EPSILON; /* set up search extents */
extents [1] = jt->point[1] - jt->radius - GEOMETRIC_EPSILON;
extents [2] = jt->point[2] - jt->radius - GEOMETRIC_EPSILON;
extents [3] = jt->point[0] + jt->radius + GEOMETRIC_EPSILON;
extents [4] = jt->point[1] + jt->radius + GEOMETRIC_EPSILON;
extents [5] = jt->point[2] + jt->radius + GEOMETRIC_EPSILON;
KDT_Pick_Extents (kd, extents, &set); /* pick kd-tree leaves within the extents */
for (item = SET_First (set); item; item = SET_Next (item))
{
KDT *leaf = item->data;
for (n = 0; n < leaf->n; n ++)
{
fac = leaf->data [n]; /* face dropped into this leaf */
qa = &q[3*fac->nodes[0]];
qb = &q[3*fac->nodes[1]];
qc = &q[3*fac->nodes[2]];
ADD (ref[fac->nodes[0]], qa, a); /* current face nodes */
ADD (ref[fac->nodes[1]], qb, b);
ADD (ref[fac->nodes[2]], qc, c);
TRIANGLE_AREA (a, b, c, area); /* current face area */
if (area > 0.0) /* XXX */
{
p [fac->index][0] += jt->force [0] / area; /* add up pressure */
p [fac->index][1] += jt->force [1] / area;
p [fac->index][2] += jt->force [2] / area;
}
}
}
SET_Free (NULL, &set);
}
for (n = 0; n < fano; n ++)
{
fprintf (output, "%g %g %g\n", p[n][0], p[n][1], p[n][2]);
}
}
fracture_state_free (list);
free (q);
free (p);
return m;
}
return 0;
}
/* map rigid onto FEM state */
int dom_rigid_to_fem (DOM *dom, PBF *bf, SET *subset)
{
for (; bf; bf = bf->next)
{
if (PBF_Label (bf, "DOM"))
{
/* read iover */
int iover = 2;
if (PBF_Label (bf, "IOVER"))
{
PBF_Int (bf, &iover, 1);
}
ASSERT_TEXT (iover >= 3, "Output files are too old for RIGID_TO_FEM to work");
/* read body states */
if (subset)
{
#if POSIX
for (SET *item = SET_First (subset); item; item = SET_Next (item))
{
regex_t xp;
char *pattern = item->data;
int error = regcomp (&xp, pattern, 0);
if (error != 0)
{
char *message = get_regerror (error, &xp);
fprintf (stderr, "-->\n");
fprintf (stderr, "Regular expression ERROR --> %s\n", message);
fprintf (stderr, "<--\n");
regfree (&xp);
free (message);
return 0;
}
for (BODY *bod = dom->bod; bod; bod = bod->next)
{
if (bod->label && regexec (&xp, bod->label, 0, NULL, 0) == 0)
{
if (PBF_Label (bf, bod->label))
{
double conf [12],
velo [6],
energy [4];
int rkind;
int rconf;
int rdofs;
PBF_Int (bf, &rkind, 1);
PBF_Int (bf, &rconf, 1);
PBF_Int (bf, &rdofs, 1);
if (bod->kind == FEM && rkind == RIG)
{
PBF_Double (bf, conf, 12);
PBF_Double (bf, velo, 6);
PBF_Double (bf, energy, 4);
BODY_From_Rigid (bod, conf, conf+9, velo, velo+3);
}
else
{
ASSERT_TEXT (((bod->kind == RIG || bod->kind == OBS) &&
(rkind == RIG || rkind == OBS)) || bod->kind == (unsigned)rkind, "Body kind mismatch when reading state");
ASSERT_TEXT (BODY_Conf_Size (bod) == rconf, "Body configuration size mismatch when reading state");
ASSERT_TEXT (bod->dofs == rdofs, "Body dofs size mismatch when reading state");
BODY_Read_State (bod, bf, 0); /* use 0 state to skip reading of rkind, rnconf, rdofs */
}
}
}
}
regfree (&xp);
}
#else
ASSERT_TEXT (0, "Regular expressions require POSIX support --> recompile Solfec with POSIX=yes");
return 0;
#endif
}
else
{
ASSERT (PBF_Label (bf, "BODS"), ERR_FILE_FORMAT);
int nbod;
PBF_Int (bf, &nbod, 1);
for (int n = 0; n < nbod; n ++)
{
double conf [12], velo [6], energy [4];
unsigned int id;
BODY *bod;
int rank;
PBF_Uint (bf, &id, 1);
bod = MAP_Find (dom->idb, (void*) (long) id, NULL);
if (bod) /* update state of existing bodies only */
{
int rkind;
int rconf;
int rdofs;
PBF_Int (bf, &rkind, 1);
PBF_Int (bf, &rconf, 1);
PBF_Int (bf, &rdofs, 1);
if (bod->kind == FEM && rkind == RIG)
{
PBF_Double (bf, conf, 12);
PBF_Double (bf, velo, 6);
PBF_Double (bf, energy, 4);
if (bf->parallel == PBF_ON)
{
PBF_Int (bf, &rank, 1);
}
BODY_From_Rigid (bod, conf, conf+9, velo, velo+3);
}
else
{
ASSERT_TEXT (((bod->kind == RIG || bod->kind == OBS) &&
(rkind == RIG || rkind == OBS)) || bod->kind == (unsigned)rkind, "Body kind mismatch when reading state");
ASSERT_TEXT (BODY_Conf_Size (bod) == rconf, "Body configuration size mismatch when reading state");
ASSERT_TEXT (bod->dofs == rdofs, "Body dofs size mismatch when reading state");
BODY_Read_State (bod, bf, 0); /* use 0 state to skip reading of rkind, rnconf, rdofs */
}
}
else /* mock read */
{
int rkind;
int rconf;
int rdofs;
PBF_Int (bf, &rkind, 1);
PBF_Int (bf, &rconf, 1);
PBF_Int (bf, &rdofs, 1);
double *conf;
double *velo;
double energy[10];
int rank;
ERRMEM (conf = malloc (sizeof(double) * rconf));
ERRMEM (velo = malloc (sizeof(double) * rdofs));
PBF_Double (bf, conf, rconf);
PBF_Double (bf, velo, rdofs);
PBF_Double (bf, energy, BODY_ENERGY_SIZE(rkind));
if (bf->parallel == PBF_ON)
{
PBF_Int (bf, &rank, 1);
}
free (conf);
free (velo);
}
}
}
}
}
return 1;
}
/* initialize domain state */
int dom_init_state (DOM *dom, PBF *bf, SET *subset)
{
for (; bf; bf = bf->next)
{
if (PBF_Label (bf, "DOM"))
{
/* read iover */
int iover = 2;
if (PBF_Label (bf, "IOVER"))
{
PBF_Int (bf, &iover, 1);
}
ASSERT_TEXT (iover >= 3, "Output files are too old for INITIALISE_STATE to work");
/* read body states */
if (subset)
{
#if POSIX
for (SET *item = SET_First (subset); item; item = SET_Next (item))
{
regex_t xp;
char *pattern = item->data;
int error = regcomp (&xp, pattern, 0);
if (error != 0)
{
char *message = get_regerror (error, &xp);
fprintf (stderr, "-->\n");
fprintf (stderr, "Regular expression ERROR --> %s\n", message);
fprintf (stderr, "<--\n");
regfree (&xp);
free (message);
return 0;
}
for (BODY *bod = dom->bod; bod; bod = bod->next)
{
if (bod->label && regexec (&xp, bod->label, 0, NULL, 0) == 0)
{
if (PBF_Label (bf, bod->label))
{
BODY_Read_State (bod, bf, iover);
}
}
}
regfree (&xp);
}
#else
ASSERT_TEXT (0, "Regular expressions require POSIX support --> recompile Solfec with POSIX=yes");
return 0;
#endif
}
else
{
ASSERT (PBF_Label (bf, "BODS"), ERR_FILE_FORMAT);
int nbod;
PBF_Int (bf, &nbod, 1);
for (int n = 0; n < nbod; n ++)
{
unsigned int id;
BODY *bod;
PBF_Uint (bf, &id, 1);
bod = MAP_Find (dom->idb, (void*) (long) id, NULL);
if (bod) /* update state of existing bodies only */
{
BODY_Read_State (bod, bf, iover);
}
else /* mock read */
{
int rkind;
int rconf;
int rdofs;
PBF_Int (bf, &rkind, 1);
PBF_Int (bf, &rconf, 1);
PBF_Int (bf, &rdofs, 1);
double *conf;
double *velo;
double energy[10];
int rank;
ERRMEM (conf = malloc (sizeof(double) * rconf));
ERRMEM (velo = malloc (sizeof(double) * rdofs));
PBF_Double (bf, conf, rconf);
PBF_Double (bf, velo, rdofs);
PBF_Double (bf, energy, BODY_ENERGY_SIZE(rkind));
if (bf->parallel == PBF_ON)
{
PBF_Int (bf, &rank, 1);
}
free (conf);
free (velo);
}
}
}
}
}
return 1;
}
/* write new bodies data */
static void write_new_bodies (DOM *dom)
{
if (dom->newb == NULL) return; /* nothing to write */
#if HDF5
PBF *bf = dom->solfec->bf;
int isize = 0, ints = 0, *i = NULL;
int dsize = 0, doubles = 0;
double *d = NULL;
SET *item;
int n;
PBF_Push (bf, "NEWBOD");
n = SET_Size (dom->newb);
PBF_Int2 (bf, "count", &n, 1);
for (item = SET_First (dom->newb); item; item = SET_Next (item))
{
BODY_Pack (item->data, &dsize, &d, &doubles, &isize, &i, &ints);
}
PBF_Int2 (bf, "ints", &ints, 1);
PBF_Int2 (bf, "i", i, ints);
PBF_Int2 (bf, "doubles", &doubles, 1);
PBF_Double2 (bf, "d", d, doubles);
free (d);
free (i);
PBF_Pop (bf);
#else
char *path, *ext;
FILE *file;
XDR xdr;
path = SOLFEC_Alloc_File_Name (dom->solfec, 16);
ext = path + strlen (path);
#if MPI
sprintf (ext, ".bod.%d", dom->rank);
#else
sprintf (ext, ".bod");
#endif
ASSERT (file = fopen (path, "a"), ERR_FILE_OPEN);
xdrstdio_create (&xdr, file, XDR_ENCODE);
int isize = 0, ints, *i = NULL;
int dsize = 0, doubles;
double *d = NULL;
SET *item;
for (item = SET_First (dom->newb); item; item = SET_Next (item))
{
doubles = ints = 0;
BODY_Pack (item->data, &dsize, &d, &doubles, &isize, &i, &ints);
ASSERT (xdr_int (&xdr, &doubles), ERR_PBF_WRITE);
ASSERT (xdr_vector (&xdr, (char*)d, doubles, sizeof (double), (xdrproc_t)xdr_double), ERR_PBF_WRITE);
ASSERT (xdr_int (&xdr, &ints), ERR_PBF_WRITE);
ASSERT (xdr_vector (&xdr, (char*)i, ints, sizeof (int), (xdrproc_t)xdr_int), ERR_PBF_WRITE);
}
free (d);
free (i);
xdr_destroy (&xdr);
fclose (file);
free (path);
#endif
}
/* create rank coloring using adjacency graph between processors derived from the W graph */
static int* processor_coloring (GAUSS_SEIDEL *gs, LOCDYN *ldy)
{
int i, n, m, ncpu, rank, *color, *size, *disp, *adj;
SET *adjcpu, *item;
MEM setmem;
DIAB *dia;
OFFB *blk;
CON *con;
adjcpu = NULL;
rank = ldy->dom->rank;
ncpu = ldy->dom->ncpu;
MEM_Init (&setmem, sizeof (SET), 128);
ERRMEM (color = MEM_CALLOC (ncpu * sizeof (int)));
ERRMEM (disp = malloc (sizeof (int [ncpu + 1])));
ERRMEM (size = malloc (sizeof (int [ncpu])));
/* collaps W adjacency into processor adjacency */
for (dia = ldy->dia; dia; dia = dia->n)
{
for (blk = dia->adjext; blk; blk = blk->n)
{
con = (CON*) blk->dia;
SET_Insert (&setmem, &adjcpu, (void*) (long) con->rank, NULL);
}
}
n = SET_Size (adjcpu);
MPI_Allgather (&n, 1, MPI_INT, size, 1, MPI_INT, MPI_COMM_WORLD);
for (i = disp [0] = 0; i < ncpu - 1; i ++) disp [i+1] = disp [i] + size [i];
for (i = 0, item = SET_First (adjcpu); item; i ++, item = SET_Next (item)) color [i] = (int) (long) item->data;
m = disp [ncpu] = (disp [ncpu-1] + size [ncpu-1]);
ERRMEM (adj = malloc (sizeof (int [m])));
MPI_Allgatherv (color, n, MPI_INT, adj, size, disp, MPI_INT, MPI_COMM_WORLD); /* gather graph adjacency */
for (i = 0; i < ncpu; i ++) color [i] = 0; /* zero colors */
for (i = 0; i < ncpu; i ++) /* simple BFS coloring */
{
int *j, *k;
do
{
color [i] ++; /* start from first color */
for (j = &adj[disp[i]], k = &adj[disp[i+1]]; j < k; j ++) /* for each adjacent vertex */
{
if (color [*j] == color [i]) break; /* see whether the trial color exists in the adjacency */
}
}
while (j < k); /* if so try next color */
}
for (m = i = 0; i < ncpu; i ++) m = MAX (m, color [i]); /* compute number of colors */
gs->colors = m; /* record number of colors */
if (rank == 0 && ldy->dom->verbose && gs->verbose)
{
#if DEBUG
for (i = 0; i < ncpu; i ++)
{
int *j, *k;
printf ("GAUSS_SEIDEL: RANK %d [%d] ADJCPU:", i, color [i]);
for (j = &adj[disp[i]], k = &adj[disp[i+1]]; j < k; j ++) printf (" %d [%d]", *j, color [*j]);
printf ("\n");
}
#endif
printf ("GAUSS_SEIDEL: PROCESSOR COLORS = %d\n", m);
}
MEM_Release (&setmem);
free (size);
free (disp);
free (adj);
return color;
}
