Actual source code: dmmbutil.cxx

petsc-3.6.1 2015-08-06
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  1: #include <petsc/private/dmmbimpl.h> /*I  "petscdmmoab.h"   I*/
  2: #include <petsc/private/vecimpl.h>

  4: #include <petscdmmoab.h>
  5: #include <MBTagConventions.hpp>
  6: #include <moab/ReadUtilIface.hpp>
  7: #include <moab/ScdInterface.hpp>
  8: #include <moab/CN.hpp>


 13: static PetscErrorCode DMMoabComputeDomainBounds_Private(moab::ParallelComm* pcomm, PetscInt dim, PetscInt neleglob, PetscInt *ise)
 14: {
 15:   PetscInt size,rank;
 16:   PetscInt fraction,remainder;
 17:   PetscInt starts[3],sizes[3];

 20:   if(dim<1 && dim>3) SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"The problem dimension is invalid: %D",dim);
 21: 
 22:   size=pcomm->size();
 23:   rank=pcomm->rank();
 24:   fraction=neleglob/size;    /* partition only by the largest dimension */
 25:   remainder=neleglob%size;   /* remainder after partition which gets evenly distributed by round-robin */

 27:   if(fraction==0) SETERRQ2(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"The leading dimension size should be greater than number of processors: %D < %D",neleglob,size);

 29:   starts[0]=starts[1]=starts[2]=0;       /* default dimensional element = 1 */
 30:   sizes[0]=sizes[1]=sizes[2]=neleglob;   /* default dimensional element = 1 */

 32:   if(rank < remainder) { /* This process gets "fraction+1" elements */
 33:     sizes[dim-1] = (fraction + 1);
 34:     starts[dim-1] = rank * (fraction+1);
 35:   } else { /* This process gets "fraction" elements */
 36:     sizes[dim-1] = fraction;
 37:     starts[dim-1] = (remainder*(fraction+1) + fraction*(rank-remainder));
 38:   }

 40:   for(int i=dim-1; i>=0; --i) {
 41:     ise[2*i]=starts[i];ise[2*i+1]=starts[i]+sizes[i];
 42:   }
 43:   return(0);
 44: }

 48: static void DMMoab_SetStructuredCoords_Private(PetscInt i, PetscInt j, PetscInt k, PetscReal hx, PetscReal hy, PetscReal hz, PetscInt vcount, std::vector<double*>& vcoords)
 49: {
 50:   vcoords[0][vcount] = i*hx;
 51:   vcoords[1][vcount] = j*hy;
 52:   vcoords[2][vcount] = k*hz;
 53: }

 57: static void DMMoab_SetTensorElementConnectivity_Private(PetscInt dim, moab::EntityType etype, PetscInt offset, PetscInt nele, PetscInt i, PetscInt j, PetscInt k, PetscInt vfirst, moab::EntityHandle *connectivity)
 58: {
 59:   std::vector<int>    subent_conn(pow(2,dim));  /* only linear edge, quad, hex supported now */

 61:   moab::CN::SubEntityVertexIndices(etype, dim, 0, subent_conn.data());

 63:   switch(dim) {
 64:     case 1:
 65:       connectivity[offset+subent_conn[0]] = vfirst+i;
 66:       connectivity[offset+subent_conn[1]] = vfirst+(i+1);
 67:       break;
 68:     case 2:
 69:       connectivity[offset+subent_conn[0]] = vfirst+i+j*(nele+1);
 70:       connectivity[offset+subent_conn[1]] = vfirst+(i+1)+j*(nele+1);
 71:       connectivity[offset+subent_conn[2]] = vfirst+(i+1)+(j+1)*(nele+1);
 72:       connectivity[offset+subent_conn[3]] = vfirst+i+(j+1)*(nele+1);
 73:       break;
 74:     case 3:
 75:     default:
 76:       connectivity[offset+subent_conn[0]] = vfirst+i+(nele+1)*(j+(nele+1)*k);
 77:       connectivity[offset+subent_conn[1]] = vfirst+(i+1)+(nele+1)*(j+(nele+1)*k);
 78:       connectivity[offset+subent_conn[2]] = vfirst+(i+1)+(nele+1)*((j+1)+(nele+1)*k);
 79:       connectivity[offset+subent_conn[3]] = vfirst+i+(nele+1)*((j+1)+(nele+1)*k);
 80:       connectivity[offset+subent_conn[4]] = vfirst+i+(nele+1)*(j+(nele+1)*(k+1));
 81:       connectivity[offset+subent_conn[5]] = vfirst+(i+1)+(nele+1)*(j+(nele+1)*(k+1));
 82:       connectivity[offset+subent_conn[6]] = vfirst+(i+1)+(nele+1)*((j+1)+(nele+1)*(k+1));
 83:       connectivity[offset+subent_conn[7]] = vfirst+i+(nele+1)*((j+1)+(nele+1)*(k+1));
 84:       break;
 85:   }
 86: }

 90: static void DMMoab_SetSimplexElementConnectivity_Private(PetscInt dim, PetscInt subelem, moab::EntityType etype, PetscInt offset, PetscInt nele, PetscInt i, PetscInt j, PetscInt k, PetscInt vfirst, moab::EntityHandle *connectivity)
 91: {
 92:   std::vector<int>    subent_conn(pow(2,dim));  /* only linear edge, quad, hex supported now */

 94:   moab::CN::SubEntityVertexIndices(etype, dim, 0, subent_conn.data());

 96:   switch(dim) {
 97:     case 1:
 98:       connectivity[offset+subent_conn[0]] = vfirst+i;
 99:       connectivity[offset+subent_conn[1]] = vfirst+(i+1);
100:       break;
101:     case 2:
102:       if (subelem) { /* 1 2 3 of a QUAD */
103:         connectivity[offset+subent_conn[0]] = vfirst+i+j*(nele+1);
104:         connectivity[offset+subent_conn[1]] = vfirst+(i+1)+j*(nele+1);
105:         connectivity[offset+subent_conn[2]] = vfirst+(i+1)+(j+1)*(nele+1);
106:       }
107:       else {        /* 3 4 1 of a QUAD */
108:         connectivity[offset+subent_conn[0]] = vfirst+(i+1)+(j+1)*(nele+1);
109:         connectivity[offset+subent_conn[1]] = vfirst+i+(j+1)*(nele+1);
110:         connectivity[offset+subent_conn[2]] = vfirst+i+j*(nele+1);
111:       }
112:       break;
113:     case 3:
114:     default:
115:       switch(subelem) {
116:         case 0: /* 0 1 2 5 of a HEX */
117:           connectivity[offset+subent_conn[0]] = vfirst+i+(nele+1)*(j+(nele+1)*k);
118:           connectivity[offset+subent_conn[1]] = vfirst+(i+1)+(nele+1)*(j+(nele+1)*k);
119:           connectivity[offset+subent_conn[2]] = vfirst+(i+1)+(nele+1)*((j+1)+(nele+1)*k);
120:           connectivity[offset+subent_conn[3]] = vfirst+(i+1)+(nele+1)*(j+(nele+1)*(k+1));
121:           break;
122:         case 1: /* 0 2 7 5 of a HEX */
123:           connectivity[offset+subent_conn[0]] = vfirst+i+(nele+1)*(j+(nele+1)*k);
124:           connectivity[offset+subent_conn[1]] = vfirst+(i+1)+(nele+1)*((j+1)+(nele+1)*k);
125:           connectivity[offset+subent_conn[2]] = vfirst+i+(nele+1)*((j+1)+(nele+1)*(k+1));
126:           connectivity[offset+subent_conn[3]] = vfirst+(i+1)+(nele+1)*(j+(nele+1)*(k+1));
127:           break;
128:         case 2: /* 0 2 3 7 of a HEX */
129:           connectivity[offset+subent_conn[0]] = vfirst+i+(nele+1)*(j+(nele+1)*k);
130:           connectivity[offset+subent_conn[1]] = vfirst+(i+1)+(nele+1)*((j+1)+(nele+1)*k);
131:           connectivity[offset+subent_conn[2]] = vfirst+i+(nele+1)*((j+1)+(nele+1)*k);
132:           connectivity[offset+subent_conn[3]] = vfirst+i+(nele+1)*((j+1)+(nele+1)*(k+1));
133:           break;
134:         case 3: /* 0 5 7 4 of a HEX */
135:           connectivity[offset+subent_conn[0]] = vfirst+i+(nele+1)*(j+(nele+1)*k);
136:           connectivity[offset+subent_conn[1]] = vfirst+(i+1)+(nele+1)*(j+(nele+1)*(k+1));
137:           connectivity[offset+subent_conn[2]] = vfirst+i+(nele+1)*((j+1)+(nele+1)*(k+1));
138:           connectivity[offset+subent_conn[3]] = vfirst+i+(nele+1)*(j+(nele+1)*(k+1));
139:           break;
140:         case 4: /* 2 7 5 6 of a HEX */
141:           connectivity[offset+subent_conn[0]] = vfirst+(i+1)+(nele+1)*((j+1)+(nele+1)*k);
142:           connectivity[offset+subent_conn[1]] = vfirst+i+(nele+1)*((j+1)+(nele+1)*(k+1));
143:           connectivity[offset+subent_conn[2]] = vfirst+(i+1)+(nele+1)*(j+(nele+1)*(k+1));
144:           connectivity[offset+subent_conn[3]] = vfirst+(i+1)+(nele+1)*((j+1)+(nele+1)*(k+1));
145:           break;
146:       }
147:       break;
148:   }
149: }

153: static void DMMoab_SetElementConnectivity_Private(PetscBool useSimplex, PetscInt dim, moab::EntityType etype, PetscInt *ecount, PetscInt vpere, PetscInt nele, PetscInt i, PetscInt j, PetscInt k, PetscInt vfirst, moab::EntityHandle *connectivity)
154: {
155:   PetscInt m,subelem;
156:   if (useSimplex) {
157:     subelem=(dim==1 ? 1 : (dim==2 ? 2 : 5));
158:     for (m=0; m<subelem; m++)
159:       DMMoab_SetSimplexElementConnectivity_Private(dim, m, etype, (*ecount+m)*vpere, nele, i, j, k, vfirst, connectivity);

161:   }
162:   else {
163:     subelem=1;
164:     DMMoab_SetTensorElementConnectivity_Private(dim, etype, (*ecount)*vpere, nele, i, j, k, vfirst, connectivity);
165:   }
166:   *ecount+=subelem;
167: }


172: /*@
173:   DMMoabCreateBoxMesh - Creates a mesh on the tensor product (box) of intervals with user specified bounds.

175:   Collective on MPI_Comm

177:   Input Parameters:
178: + comm - The communicator for the DM object
179: . dim - The spatial dimension
180: . bounds - The bounds of the box specified with [x-left, x-right, y-bottom, y-top, z-bottom, z-top] depending on the spatial dimension
181: . nele - The number of discrete elements in each direction
182: . user_nghost - The number of ghosted layers needed in the partitioned mesh

184:   Output Parameter:
185: . dm  - The DM object

187:   Level: beginner

189: .keywords: DM, create
190: .seealso: DMSetType(), DMCreate(), DMMoabLoadFromFile()
191: @*/
192: PetscErrorCode DMMoabCreateBoxMesh(MPI_Comm comm, PetscInt dim, PetscBool useSimplex, const PetscReal* bounds, PetscInt nele, PetscInt user_nghost, DM *dm)
193: {
194:   PetscErrorCode  ierr;
195:   moab::ErrorCode merr;
196:   PetscInt        i,j,k,n,nprocs;
197:   DM_Moab        *dmmoab;
198:   moab::Interface *mbiface;
199:   moab::ParallelComm *pcomm;
200:   moab::ReadUtilIface* readMeshIface;

202:   moab::Tag  id_tag=PETSC_NULL;
203:   moab::Range         ownedvtx,ownedelms;
204:   moab::EntityHandle  vfirst,efirst,regionset,faceset,edgeset,vtxset;
205:   std::vector<double*> vcoords;
206:   moab::EntityHandle  *connectivity = 0;
207:   moab::EntityType etype=moab::MBHEX;
208:   PetscInt    ise[6];
209:   PetscReal   xse[6],defbounds[6];
210:   /* TODO: Fix nghost > 0 - now relying on exchange_ghost_cells */
211:   const PetscInt nghost=0;

213:   moab::Tag geom_tag;

215:   moab::Range adj,dim3,dim2;
216:   bool build_adjacencies=false;

218:   const PetscInt npts=nele+1;        /* Number of points in every dimension */
219:   PetscInt vpere=0,locnele=0,locnpts=0,ghnele,ghnpts;    /* Number of verts/element, vertices, elements owned by this process */

222:   if(dim < 1 || dim > 3) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"Invalid dimension argument for mesh: dim=[1,3].\n");

224:   MPI_Comm_size(comm, &nprocs);
225:   /* total number of vertices in all dimensions */
226:   n=pow(npts,dim);

228:   /* do some error checking */
229:   if(n < 2) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"Number of points must be >= 2.\n");
230:   if(nprocs > n) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"Number of processors must be less than or equal to number of elements.\n");
231:   if(nghost < 0) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"Number of ghost layers cannot be negative.\n");

233:   /* Create the basic DMMoab object and keep the default parameters created by DM impls */
234:   DMMoabCreateMoab(comm, PETSC_NULL, PETSC_NULL, PETSC_NULL, PETSC_NULL, dm);

236:   /* get all the necessary handles from the private DM object */
237:   dmmoab = (DM_Moab*)(*dm)->data;
238:   mbiface = dmmoab->mbiface;
239:   pcomm = dmmoab->pcomm;
240:   id_tag = dmmoab->ltog_tag;
241:   nprocs = pcomm->size();
242:   dmmoab->dim = dim;

244:   /* create a file set to associate all entities in current mesh */
245:   merr = dmmoab->mbiface->create_meshset(moab::MESHSET_SET, dmmoab->fileset);MBERR("Creating file set failed", merr);

247:   /* No errors yet; proceed with building the mesh */
248:   merr = mbiface->query_interface(readMeshIface);MBERRNM(merr);

250:   PetscMemzero(ise,sizeof(PetscInt)*6);

252:   /* call the collective routine that computes the domain bounds for a structured mesh using MOAB */
253:   DMMoabComputeDomainBounds_Private(pcomm, dim, nele, ise);

255:   /* set some variables based on dimension */
256:   switch(dim) {
257:    case 1:
258:     vpere = 2;
259:     locnele = (ise[1]-ise[0]);
260:     locnpts = (ise[1]-ise[0]+1);
261:     ghnele = (nghost > 0 ? (ise[0] > nghost ? 1 : 0) + (ise[1] < nele - nghost ? 1 : 0) : 0 );
262:     ghnpts = (nghost > 0 ? (ise[0] > 0 ? 1 : 0) + (ise[1] < nele ? 1 : 0) : 0);
263:     etype = moab::MBEDGE;
264:     break;
265:    case 2:
266:     locnpts = (ise[1]-ise[0]+1)*(ise[3]-ise[2]+1);
267:     ghnpts = (nghost > 0 ? (ise[2] > 0 ? npts : 0) + (ise[3] < nele ? npts : 0) : 0);
268:     if (useSimplex) {
269:       vpere = 3;
270:       locnele = 2*(ise[1]-ise[0])*(ise[3]-ise[2]);
271:       ghnele = 2*(nghost > 0 ? (ise[2] > 0 ? nele : 0) + (ise[3] < nele ? nele : 0) : 0);
272:       etype = moab::MBTRI;
273:     }
274:     else {
275:       vpere = 4;
276:       locnele = (ise[1]-ise[0])*(ise[3]-ise[2]);
277:       ghnele = (nghost > 0 ? (ise[2] > 0 ? nele : 0) + (ise[3] < nele ? nele : 0) : 0);
278:       etype = moab::MBQUAD;
279:     }
280:     break;
281:    case 3:
282:    default:
283:     locnpts = (ise[1]-ise[0]+1)*(ise[3]-ise[2]+1)*(ise[5]-ise[4]+1);
284:     ghnpts = (nghost > 0 ? (ise[4] > 0 ? npts*npts : 0) + (ise[5] < nele ? npts*npts : 0) : 0);
285:     if (useSimplex) {
286:       vpere = 4;
287:       locnele = 5*(ise[1]-ise[0])*(ise[3]-ise[2])*(ise[5]-ise[4]);
288:       ghnele = 5*(nghost > 0 ? (ise[4] > 0 ? nele*nele : 0) + (ise[5] < nele ? nele*nele : 0) : 0);
289:       etype = moab::MBTET;
290:     }
291:     else {
292:       vpere = 8;
293:       locnele = (ise[1]-ise[0])*(ise[3]-ise[2])*(ise[5]-ise[4]);
294:       ghnele = (nghost > 0 ? (ise[4] > 0 ? nele*nele : 0) + (ise[5] < nele ? nele*nele : 0) : 0);
295:       etype = moab::MBHEX;
296:     }
297:     break;
298:   }

300:   /* we have a domain of size [1,1,1] - now compute local co-ordinate box */
301:   PetscMemzero(xse,sizeof(PetscReal)*6);
302:   for(i=0; i<6; ++i) {
303:     xse[i]=(PetscReal)ise[i]/nele;
304:   }

306:   /* Create vertexes and set the coodinate of each vertex */
307:   merr = readMeshIface->get_node_coords(3,locnpts+ghnpts,0,vfirst,vcoords,n);MBERRNM(merr);

309:   /* Compute the co-ordinates of vertices and global IDs */
310:   std::vector<int>    vgid(locnpts+ghnpts);
311:   int vcount=0;

313:   if (!bounds) { /* default box mesh is defined on a unit-cube */
314:     defbounds[0]=0.0; defbounds[1]=1.0;
315:     defbounds[2]=0.0; defbounds[3]=1.0;
316:     defbounds[4]=0.0; defbounds[5]=1.0;
317:     bounds=defbounds;
318:   }
319:   else {
320:     /* validate the bounds data */
321:     if(bounds[0] >= bounds[1]) SETERRQ2(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"X-dim: Left boundary cannot be greater than right. [%G >= %G]\n",bounds[0],bounds[1]);
322:     if(dim > 1 && (bounds[2] >= bounds[3])) SETERRQ2(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"Y-dim: Left boundary cannot be greater than right. [%G >= %G]\n",bounds[2],bounds[3]);
323:     if(dim > 2 && (bounds[4] >= bounds[5])) SETERRQ2(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"Z-dim: Left boundary cannot be greater than right. [%G >= %G]\n",bounds[4],bounds[5]);
324:   }

326:   const double hx=(bounds[1]-bounds[0])/nele;
327:   const double hy=(dim > 1 ? (bounds[3]-bounds[2])/nele : 0.0);
328:   const double hz=(dim > 2 ? (bounds[5]-bounds[4])/nele : 0.0);

330:   /* create all the owned vertices */
331:   for (k = ise[4]; k <= ise[5]; k++) {
332:     for (j = ise[2]; j <= ise[3]; j++) {
333:       for (i = ise[0]; i <= ise[1]; i++, vcount++) {
334:         DMMoab_SetStructuredCoords_Private(i,j,k,hx,hy,hz,vcount,vcoords);
335:         vgid[vcount] = (k*npts+j)*npts+i+1;
336:       }
337:     }
338:   }

340:   /* create ghosted vertices requested by user - below the current plane */
341:   if (ise[2*dim-2] > 0) {
342:     for (k = (dim==3?ise[4]-nghost:ise[4]); k <= (dim==3?ise[4]-1:ise[5]); k++) {
343:       for (j = (dim==2?ise[2]-nghost:ise[2]); j <= (dim==2?ise[2]-1:ise[3]); j++) {
344:         for (i = (dim>1?ise[0]:ise[0]-nghost); i <= (dim>1?ise[1]:ise[0]-1); i++, vcount++) {
345:           DMMoab_SetStructuredCoords_Private(i,j,k,hx,hy,hz,vcount,vcoords);
346:           vgid[vcount] = (k*npts+j)*npts+i+1;
347:         }
348:       }
349:     }
350:   }

352:   /* create ghosted vertices requested by user - above the current plane */
353:   if (ise[2*dim-1] < nele) {
354:     for (k = (dim==3?ise[5]+1:ise[4]); k <= (dim==3?ise[5]+nghost:ise[5]); k++) {
355:       for (j = (dim==2?ise[3]+1:ise[2]); j <= (dim==2?ise[3]+nghost:ise[3]); j++) {
356:         for (i = (dim>1?ise[0]:ise[1]+1); i <= (dim>1?ise[1]:ise[1]+nghost); i++, vcount++) {
357:           DMMoab_SetStructuredCoords_Private(i,j,k,hx,hy,hz,vcount,vcoords);
358:           vgid[vcount] = (k*npts+j)*npts+i+1;
359:         }
360:       }
361:     }
362:   }

364:   if (locnpts+ghnpts != vcount) SETERRQ2(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"Created the wrong number of vertices! (%D!=%D)",locnpts+ghnpts,vcount);

366:   merr = mbiface->get_entities_by_type(0,moab::MBVERTEX,ownedvtx,true);MBERRNM(merr);

368:   /* The global ID tag is applied to each owned
369:      vertex. It acts as an global identifier which MOAB uses to
370:      assemble the individual pieces of the mesh:
371:      Set the global ID indices */
372:   merr = mbiface->tag_set_data(id_tag,ownedvtx,vgid.data());MBERRNM(merr);
373: 
374:   /* Create elements between mesh points using the ReadUtilInterface 
375:      get the reference to element connectivities for all local elements from the ReadUtilInterface */
376:   merr = readMeshIface->get_element_connect (locnele+ghnele,vpere,etype,1,efirst,connectivity);MBERRNM(merr);

378:   /* offset appropriately so that only local ID and not global ID numbers are set for connectivity array */
379:   vfirst-=vgid[0]-1;

381:    /* 3. Loop over elements in 3 nested loops over i, j, k; for each (i,j,k):
382:          and then set the connectivity for each element appropriately */
383:   int ecount=0;

385:   /* create ghosted elements requested by user - below the current plane */
386:   if (ise[2*dim-2] >= nghost) {
387:     for (k = (dim==3?ise[4]-nghost:ise[4]); k < (dim==3?ise[4]:std::max(ise[5],1)); k++) {
388:       for (j = (dim==2?ise[2]-nghost:ise[2]); j < (dim==2?ise[2]:std::max(ise[3],1)); j++) {
389:         for (i = (dim>1?ise[0]:ise[0]-nghost); i < (dim>1?std::max(ise[1],1):ise[0]); i++) {
390:           DMMoab_SetElementConnectivity_Private(useSimplex, dim, etype, &ecount, vpere, nele, i, j, k, vfirst, connectivity);
391:         }
392:       }
393:     }
394:   }

396:   /* create owned elements requested by user */
397:   for (k = ise[4]; k < std::max(ise[5],1); k++) {
398:     for (j = ise[2]; j < std::max(ise[3],1); j++) {
399:       for (i = ise[0]; i < std::max(ise[1],1); i++) {
400:         DMMoab_SetElementConnectivity_Private(useSimplex, dim, etype, &ecount, vpere, nele, i, j, k, vfirst, connectivity);
401:       }
402:     }
403:   }

405:   /* create ghosted elements requested by user - above the current plane */
406:   if (ise[2*dim-1] <= nele-nghost) {
407:     for (k = (dim==3?ise[5]:ise[4]); k < (dim==3?ise[5]+nghost:std::max(ise[5],1)); k++) {
408:       for (j = (dim==2?ise[3]:ise[2]); j < (dim==2?ise[3]+nghost:std::max(ise[3],1)); j++) {
409:         for (i = (dim>1?ise[0]:ise[1]); i < (dim>1?std::max(ise[1],1):ise[1]+nghost); i++) {
410:           DMMoab_SetElementConnectivity_Private(useSimplex, dim, etype, &ecount, vpere, nele, i, j, k, vfirst, connectivity);
411:         }
412:       }
413:     }
414:   }

416:   merr = readMeshIface->update_adjacencies(efirst,locnele+ghnele,vpere,connectivity);MBERRNM(merr);
417: 
418:   /* 2. Get the vertices and hexes from moab and check their numbers against I*J*K and (I-1)*(J-1)*(K-1), resp.
419:         first '0' specifies "root set", or entire MOAB instance, second the entity dimension being requested */
420:   merr = mbiface->get_entities_by_dimension(0, dim, ownedelms);MBERRNM(merr);

422:   if (locnele+ghnele != (int) ownedelms.size())
423:     SETERRQ2(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"Created the wrong number of elements! (%D!=%D)",locnele+ghnele,ownedelms.size());
424:   else if(locnpts+ghnpts != (int) ownedvtx.size())
425:     SETERRQ2(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"Created the wrong number of vertices! (%D!=%D)",locnpts+ghnpts,ownedvtx.size());
426:   else
427:     PetscInfo2(NULL, "Created %D elements and %D vertices.\n", ownedelms.size(), ownedvtx.size());

429:   /* lets create some sets */
430:   merr = mbiface->tag_get_handle(GEOM_DIMENSION_TAG_NAME, 1, moab::MB_TYPE_INTEGER, geom_tag, moab::MB_TAG_SPARSE|moab::MB_TAG_CREAT);MBERRNM(merr);

432:   merr = mbiface->create_meshset(moab::MESHSET_SET, regionset);MBERRNM(merr);
433:   merr = mbiface->add_entities(regionset, ownedelms);MBERRNM(merr);
434:   merr = mbiface->tag_set_data(geom_tag, &regionset, 1, &dmmoab->dim);MBERRNM(merr);
435:   merr = mbiface->add_parent_child(dmmoab->fileset,regionset);MBERRNM(merr);
436:   merr = mbiface->unite_meshset(dmmoab->fileset, regionset);MBERRNM(merr);

438:   merr = mbiface->create_meshset(moab::MESHSET_SET, vtxset);MBERRNM(merr);
439:   merr = mbiface->add_entities(vtxset, ownedvtx);MBERRNM(merr);
440:   merr = mbiface->add_parent_child(dmmoab->fileset,vtxset);MBERRNM(merr);
441:   merr = mbiface->unite_meshset(dmmoab->fileset, vtxset);MBERRNM(merr);

443:   if (build_adjacencies) {
444:     // generate all lower dimensional adjacencies
445:     merr = mbiface->get_adjacencies( ownedelms, dim-1, true, adj, moab::Interface::UNION );MBERRNM(merr);
446:     merr = dmmoab->pcomm->get_part_entities(dim2, dim-1);MBERRNM(merr);
447:     adj.merge(dim2);

449:     /* create face sets */
450:     merr = mbiface->create_meshset(moab::MESHSET_SET, faceset);MBERRNM(merr);
451:     merr = mbiface->add_entities(faceset, adj);MBERRNM(merr);
452:     merr = mbiface->add_parent_child(dmmoab->fileset,faceset);MBERRNM(merr);
453:     i=dim-1;
454:     merr = mbiface->tag_set_data(geom_tag, &faceset, 1, &i);MBERRNM(merr);
455:     merr = mbiface->unite_meshset(dmmoab->fileset, faceset);MBERRNM(merr);
456:     PetscInfo2(NULL, "Found %d %d-Dim quantities.\n", adj.size(), dim-1);

458:     if (dim > 2) {
459:       dim2.clear();
460:       /* create edge sets, if appropriate i.e., if dim=3 */
461:       merr = mbiface->create_meshset(moab::MESHSET_SET, edgeset);MBERRNM(merr);
462:       merr = mbiface->get_adjacencies(adj, dim-1, true, dim2, moab::Interface::UNION );MBERRNM(merr);
463:       merr = mbiface->add_entities(edgeset, dim2);MBERRNM(merr);
464:       merr = mbiface->add_parent_child(dmmoab->fileset,edgeset);MBERRNM(merr);
465:       i=dim-2;
466:       merr = mbiface->tag_set_data(geom_tag, &edgeset, 1, &i);MBERRNM(merr);
467:       merr = mbiface->unite_meshset(dmmoab->fileset, edgeset);MBERRNM(merr);
468:       PetscInfo2(NULL, "Found %d %d-Dim quantities.\n", adj.size(), dim-2);
469:     }
470:   }

472:   /* check the handles */
473:   merr = pcomm->check_all_shared_handles();MBERRV(mbiface,merr);

475:   /* resolve the shared entities by exchanging information to adjacent processors */
476:   merr = mbiface->get_entities_by_type(dmmoab->fileset,etype,ownedelms,true);MBERRNM(merr);
477:   merr = pcomm->resolve_shared_ents(dmmoab->fileset,ownedelms,dim,dim-1,NULL,&id_tag);MBERRV(mbiface,merr);

479:   merr = pcomm->exchange_ghost_cells(dim,0,user_nghost,dim,true,false,&dmmoab->fileset);MBERRV(mbiface,merr);

481:   /* Reassign global IDs on all entities. */
482:   merr = pcomm->assign_global_ids(dmmoab->fileset,dim,1,false,true,false);MBERRNM(merr);

484:   /* Everything is set up, now just do a tag exchange to update tags
485:      on all of the ghost vertexes */
486:   merr = mbiface->get_entities_by_type(dmmoab->fileset,moab::MBVERTEX,ownedvtx,true);MBERRNM(merr);
487:   merr = mbiface->get_entities_by_dimension(dmmoab->fileset, dim, ownedelms);MBERRNM(merr);
488: 
489:   merr = pcomm->exchange_tags(id_tag,ownedvtx);MBERRV(mbiface,merr);
490:   merr = pcomm->exchange_tags(id_tag,ownedelms);MBERRV(mbiface,merr);
491:   return(0);
492: }


497: PetscErrorCode DMMoab_GetReadOptions_Private(PetscBool by_rank, PetscInt numproc, PetscInt dim, MoabReadMode mode, PetscInt dbglevel, const char* dm_opts, const char* extra_opts, const char** read_opts)
498: {
499:   char           *ropts;
500:   char           ropts_par[PETSC_MAX_PATH_LEN];
501:   char           ropts_dbg[PETSC_MAX_PATH_LEN];

505:   PetscMalloc(PETSC_MAX_PATH_LEN,&ropts);
506:   PetscMemzero(&ropts_par,PETSC_MAX_PATH_LEN);
507:   PetscMemzero(&ropts_dbg,PETSC_MAX_PATH_LEN);

509:   /* do parallel read unless using only one processor */
510:   if (numproc > 1) {
511:     PetscSNPrintf(ropts_par, PETSC_MAX_PATH_LEN, "PARALLEL=%s;PARTITION=PARALLEL_PARTITION;PARTITION_DISTRIBUTE;PARALLEL_RESOLVE_SHARED_ENTS;PARALLEL_GHOSTS=%d.0.1%s;",MoabReadModes[mode],dim,(by_rank ? ";PARTITION_BY_RANK":""));
512:   }

514:   if (dbglevel) {
515:     if (numproc>1) {
516:       PetscSNPrintf(ropts_dbg, PETSC_MAX_PATH_LEN, "%sCPUTIME;DEBUG_IO=%d;DEBUG_PIO=%d;",dbglevel,dbglevel);
517:     }
518:     else {
519:       PetscSNPrintf(ropts_dbg, PETSC_MAX_PATH_LEN, "%sCPUTIME;DEBUG_IO=%d;",dbglevel);
520:     }
521:   }

523:   PetscSNPrintf(ropts, PETSC_MAX_PATH_LEN, "%s%s%s%s",ropts_par,ropts_dbg,(extra_opts?extra_opts:""),(dm_opts?dm_opts:""));
524:   *read_opts = ropts;
525:   return(0);
526: }


531: /*@
532:   DMMoabLoadFromFile - Creates a DM object by loading the mesh from a user specified file.

534:   Collective on MPI_Comm

536:   Input Parameters:
537: + comm - The communicator for the DM object
538: . dim - The spatial dimension
539: . filename - The name of the mesh file to be loaded
540: . usrreadopts - The options string to read a MOAB mesh. 
541:   Reference (Parallel Mesh Initialization: http://www.mcs.anl.gov/~fathom/moab-docs/html/contents.html#fivetwo)

543:   Output Parameter:
544: . dm  - The DM object

546:   Level: beginner

548: .keywords: DM, create

550: .seealso: DMSetType(), DMCreate(), DMMoabCreateBoxMesh()
551: @*/
552: PetscErrorCode DMMoabLoadFromFile(MPI_Comm comm,PetscInt dim,const char* filename, const char* usrreadopts, DM *dm)
553: {
554:   moab::ErrorCode merr;
555:   PetscInt        nprocs;
556:   DM_Moab        *dmmoab;
557:   moab::Interface *mbiface;
558:   moab::ParallelComm *pcomm;
559:   moab::Range verts,elems;
560:   const char *readopts;


566:   /* Create the basic DMMoab object and keep the default parameters created by DM impls */
567:   DMMoabCreateMoab(comm, PETSC_NULL, PETSC_NULL, PETSC_NULL, PETSC_NULL, dm);

569:   /* get all the necessary handles from the private DM object */
570:   dmmoab = (DM_Moab*)(*dm)->data;
571:   mbiface = dmmoab->mbiface;
572:   pcomm = dmmoab->pcomm;
573:   nprocs = pcomm->size();
574:   /* TODO: Decipher dimension based on the loaded mesh instead of getting from user */
575:   dmmoab->dim = dim;

577:   /* create a file set to associate all entities in current mesh */
578:   merr = dmmoab->mbiface->create_meshset(moab::MESHSET_SET, dmmoab->fileset);MBERR("Creating file set failed", merr);

580:   /* add mesh loading options specific to the DM */
581:   DMMoab_GetReadOptions_Private(dmmoab->partition_by_rank, nprocs, dim, dmmoab->read_mode,
582:                                         dmmoab->rw_dbglevel, dmmoab->extra_read_options, usrreadopts, &readopts);

584:   PetscInfo2(*dm, "Reading file %s with options: %s\n",filename,readopts);

586:   /* Load the mesh from a file. */
587:   merr = mbiface->load_file(filename, &dmmoab->fileset, readopts);MBERRVM(mbiface,"Reading MOAB file failed.", merr);

589:   /* Reassign global IDs on all entities. */
590:   merr = pcomm->assign_global_ids(dmmoab->fileset,dim,1,true,true,true);MBERRNM(merr);

592:   /* load the local vertices */
593:   merr = mbiface->get_entities_by_type(dmmoab->fileset, moab::MBVERTEX, verts, true);MBERRNM(merr);
594:   /* load the local elements */
595:   merr = mbiface->get_entities_by_dimension(dmmoab->fileset, dim, elems, true);MBERRNM(merr);

597:   /* Everything is set up, now just do a tag exchange to update tags
598:      on all of the ghost vertexes */
599:   merr = pcomm->exchange_tags(dmmoab->ltog_tag,verts);MBERRV(mbiface,merr);
600:   merr = pcomm->exchange_tags(dmmoab->ltog_tag,elems);MBERRV(mbiface,merr);

602:   merr = pcomm->exchange_ghost_cells(dim,0,1,0,true,true,&dmmoab->fileset);MBERRV(mbiface,merr);

604:   merr = pcomm->collective_sync_partition();MBERR("Collective sync failed", merr);

606:   PetscInfo3(*dm, "MOAB file '%s' was successfully loaded. Found %D vertices and %D elements.\n", filename, verts.size(), elems.size());
607:   PetscFree(readopts);
608:   return(0);
609: }