Actual source code: network.c

petsc-master 2020-10-23
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  1: #include <petsc/private/dmnetworkimpl.h>

  3: /*@
  4:   DMNetworkGetPlex - Gets the Plex DM associated with this network DM

  6:   Not collective

  8:   Input Parameters:
  9: + netdm - the dm object
 10: - plexmdm - the plex dm object

 12:   Level: Advanced

 14: .seealso: DMNetworkCreate()
 15: @*/
 16: PetscErrorCode DMNetworkGetPlex(DM netdm, DM *plexdm)
 17: {
 18:   DM_Network *network = (DM_Network*) netdm->data;

 21:   *plexdm = network->plex;
 22:   return(0);
 23: }

 25: /*@
 26:   DMNetworkGetSizes - Gets the the number of subnetworks and coupling subnetworks

 28:   Collective on dm

 30:   Input Parameters:
 31: + dm - the dm object
 32: . Nsubnet - global number of subnetworks
 33: - NsubnetCouple - global number of coupling subnetworks

 35:   Level: beginner

 37: .seealso: DMNetworkCreate()
 38: @*/
 39: PetscErrorCode DMNetworkGetSizes(DM netdm, PetscInt *Nsubnet, PetscInt *Ncsubnet)
 40: {
 41:   DM_Network *network = (DM_Network*) netdm->data;

 44:   *Nsubnet = network->nsubnet;
 45:   *Ncsubnet = network->ncsubnet;
 46:   return(0);
 47: }

 49: /*@
 50:   DMNetworkSetSizes - Sets the number of subnetworks, local and global vertices and edges for each subnetwork.

 52:   Collective on dm

 54:   Input Parameters:
 55: + dm - the dm object
 56: . Nsubnet - global number of subnetworks
 57: . nV - number of local vertices for each subnetwork
 58: . nE - number of local edges for each subnetwork
 59: . NsubnetCouple - global number of coupling subnetworks
 60: - nec - number of local edges for each coupling subnetwork

 62:    You cannot change the sizes once they have been set. nV, nE are arrays of length Nsubnet, and nec is array of length NsubnetCouple.

 64:    Level: beginner

 66: .seealso: DMNetworkCreate()
 67: @*/
 68: PetscErrorCode DMNetworkSetSizes(DM dm,PetscInt Nsubnet,PetscInt nV[], PetscInt nE[],PetscInt NsubnetCouple,PetscInt nec[])
 69: {
 71:   DM_Network     *network = (DM_Network*) dm->data;
 72:   PetscInt       a[2],b[2],i;

 76:   if (Nsubnet <= 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Number of subnetworks %D cannot be less than 1",Nsubnet);
 77:   if (NsubnetCouple < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Number of coupling subnetworks %D cannot be less than 0",NsubnetCouple);

 81:   if (network->nsubnet != 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Network sizes alread set, cannot resize the network");

 83:   if (!nV || !nE) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_NULL,"Local vertex size or edge size must be provided");

 85:   network->nsubnet  = Nsubnet + NsubnetCouple;
 86:   network->ncsubnet = NsubnetCouple;
 87:   PetscCalloc1(Nsubnet+NsubnetCouple,&network->subnet);

 89:   /* ----------------------------------------------------------
 90:    p=v or e; P=V or E
 91:    subnet[0].pStart   = 0
 92:    subnet[i+1].pStart = subnet[i].pEnd = subnet[i].pStart + (nE[i] or NV[i])
 93:    ----------------------------------------------------------------------- */
 94:   for (i=0; i < Nsubnet; i++) {
 95:     /* Get global number of vertices and edges for subnet[i] */
 96:     a[0] = nV[i]; a[1] = nE[i]; /* local number of vertices (excluding ghost) and edges */
 97:     MPIU_Allreduce(a,b,2,MPIU_INT,MPI_SUM,PetscObjectComm((PetscObject)dm));
 98:     network->subnet[i].Nvtx = b[0];
 99:     network->subnet[i].Nedge = b[1];

101:     network->subnet[i].nvtx   = nV[i]; /* local nvtx, without ghost */

103:     /* global subnet[].vStart and vEnd, used by DMNetworkLayoutSetUp() */
104:     network->subnet[i].vStart = network->NVertices;
105:     network->subnet[i].vEnd   = network->subnet[i].vStart + network->subnet[i].Nvtx;

107:     network->nVertices += nV[i];
108:     network->NVertices += network->subnet[i].Nvtx;

110:     network->subnet[i].nedge  = nE[i];
111:     network->subnet[i].eStart = network->nEdges;
112:     network->subnet[i].eEnd   = network->subnet[i].eStart + nE[i];
113:     network->nEdges += nE[i];
114:     network->NEdges += network->subnet[i].Nedge;
115:   }

117:   /* coupling subnetwork */
118:   for (; i < Nsubnet+NsubnetCouple; i++) {
119:     /* Get global number of coupling edges for subnet[i] */
120:     MPIU_Allreduce(nec+(i-Nsubnet),&network->subnet[i].Nedge,1,MPIU_INT,MPI_SUM,PetscObjectComm((PetscObject)dm));

122:     network->subnet[i].nvtx   = 0; /* We design coupling subnetwork such that it does not have its own vertices */
123:     network->subnet[i].vStart = network->nVertices;
124:     network->subnet[i].vEnd   = network->subnet[i].vStart;

126:     network->subnet[i].nedge  = nec[i-Nsubnet];
127:     network->subnet[i].eStart = network->nEdges;
128:     network->subnet[i].eEnd = network->subnet[i].eStart + nec[i-Nsubnet];
129:     network->nEdges += nec[i-Nsubnet];
130:     network->NEdges += network->subnet[i].Nedge;
131:   }
132:   return(0);
133: }

135: /*@
136:   DMNetworkSetEdgeList - Sets the list of local edges (vertex connectivity) for the network

138:   Logically collective on dm

140:   Input Parameters:
141: + dm - the dm object
142: . edgelist - list of edges for each subnetwork
143: - edgelistCouple - list of edges for each coupling subnetwork

145:   Notes:
146:   There is no copy involved in this operation, only the pointer is referenced. The edgelist should
147:   not be destroyed before the call to DMNetworkLayoutSetUp

149:   Level: beginner

151:   Example usage:
152:   Consider the following 2 separate networks and a coupling network:

154: .vb
155:  network 0: v0 -> v1 -> v2 -> v3
156:  network 1: v1 -> v2 -> v0
157:  coupling network: network 1: v2 -> network 0: v0
158: .ve

160:  The resulting input
161:    edgelist[0] = [0 1 | 1 2 | 2 3];
162:    edgelist[1] = [1 2 | 2 0]
163:    edgelistCouple[0] = [(network)1 (v)2 (network)0 (v)0].

165: .seealso: DMNetworkCreate, DMNetworkSetSizes
166: @*/
167: PetscErrorCode DMNetworkSetEdgeList(DM dm,PetscInt *edgelist[],PetscInt *edgelistCouple[])
168: {
169:   DM_Network *network = (DM_Network*) dm->data;
170:   PetscInt   i;

173:   for (i=0; i < (network->nsubnet-network->ncsubnet); i++) network->subnet[i].edgelist = edgelist[i];
174:   if (network->ncsubnet) {
175:     PetscInt j = 0;
176:     if (!edgelistCouple) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_NULL,"Must provide edgelist_couple");
177:     while (i < network->nsubnet) network->subnet[i++].edgelist = edgelistCouple[j++];
178:   }
179:   return(0);
180: }

182: /*@
183:   DMNetworkLayoutSetUp - Sets up the bare layout (graph) for the network

185:   Collective on dm

187:   Input Parameters:
188: . DM - the dmnetwork object

190:   Notes:
191:   This routine should be called after the network sizes and edgelists have been provided. It creates
192:   the bare layout of the network and sets up the network to begin insertion of components.

194:   All the components should be registered before calling this routine.

196:   Level: beginner

198: .seealso: DMNetworkSetSizes, DMNetworkSetEdgeList
199: @*/
200: PetscErrorCode DMNetworkLayoutSetUp(DM dm)
201: {
203:   DM_Network     *network = (DM_Network*)dm->data;
204:   PetscInt       numCorners=2,dim = 1; /* One dimensional network */
205:   PetscInt       i,j,ctr,nsubnet,*eowners,np,*edges,*subnetvtx,vStart;
206:   PetscInt       k,netid,vid, *vidxlTog,*edgelist_couple=NULL;
207:   const PetscInt *cone;
208:   MPI_Comm       comm;
209:   PetscMPIInt    size,rank;

212:   PetscObjectGetComm((PetscObject)dm,&comm);
213:   MPI_Comm_rank(comm,&rank);
214:   MPI_Comm_size(comm,&size);

216:   /* Create the local edgelist for the network by concatenating local input edgelists of the subnetworks */
217:   PetscCalloc1(2*network->nEdges,&edges);
218:   nsubnet = network->nsubnet - network->ncsubnet;
219:   ctr = 0;
220:   for (i=0; i < nsubnet; i++) {
221:     for (j = 0; j < network->subnet[i].nedge; j++) {
222:       edges[2*ctr]   = network->subnet[i].vStart + network->subnet[i].edgelist[2*j];
223:       edges[2*ctr+1] = network->subnet[i].vStart + network->subnet[i].edgelist[2*j+1];
224:       ctr++;
225:     }
226:   }

228:   /* Append local coupling edgelists of the subnetworks */
229:   i       = nsubnet; /* netid of coupling subnet */
230:   nsubnet = network->nsubnet;
231:   while (i < nsubnet) {
232:     edgelist_couple = network->subnet[i].edgelist;

234:     k = 0;
235:     for (j = 0; j < network->subnet[i].nedge; j++) {
236:       netid = edgelist_couple[k]; vid = edgelist_couple[k+1];
237:       edges[2*ctr] = network->subnet[netid].vStart + vid; k += 2;

239:       netid = edgelist_couple[k]; vid = edgelist_couple[k+1];
240:       edges[2*ctr+1] = network->subnet[netid].vStart + vid; k+=2;
241:       ctr++;
242:     }
243:     i++;
244:   }
245:   /*
246:   if (rank == 0) {
247:     PetscPrintf(PETSC_COMM_SELF,"[%d] edgelist:\n",rank);
248:     for (i=0; i < network->nEdges; i++) {
249:       PetscPrintf(PETSC_COMM_SELF,"[%D %D]",edges[2*i],edges[2*i+1]);
250:       printf("\n");
251:     }
252:   }
253:    */

255:   /* Create network->plex */
256:   DMCreate(comm,&network->plex);
257:   DMSetType(network->plex,DMPLEX);
258:   DMSetDimension(network->plex,dim);
259:   if (size == 1) {
260:     DMPlexBuildFromCellList(network->plex,network->nEdges,network->nVertices,numCorners,edges);
261:   } else {
262:     DMPlexBuildFromCellListParallel(network->plex,network->nEdges,network->nVertices,network->NVertices,numCorners,edges,NULL);
263:   }

265:   DMPlexGetChart(network->plex,&network->pStart,&network->pEnd);
266:   DMPlexGetHeightStratum(network->plex,0,&network->eStart,&network->eEnd);
267:   DMPlexGetHeightStratum(network->plex,1,&network->vStart,&network->vEnd);
268:   vStart = network->vStart;

270:   PetscSectionCreate(comm,&network->DataSection);
271:   PetscSectionCreate(comm,&network->DofSection);
272:   PetscSectionSetChart(network->DataSection,network->pStart,network->pEnd);
273:   PetscSectionSetChart(network->DofSection,network->pStart,network->pEnd);

275:   network->dataheadersize = sizeof(struct _p_DMNetworkComponentHeader)/sizeof(DMNetworkComponentGenericDataType);
276:   np = network->pEnd - network->pStart;
277:   PetscCalloc2(np,&network->header,np,&network->cvalue);

279:   /* Create vidxlTog: maps local vertex index to global index */
280:   np = network->vEnd - vStart;
281:   PetscMalloc2(np,&vidxlTog,size+1,&eowners);
282:   ctr = 0;
283:   for (i=network->eStart; i<network->eEnd; i++) {
284:     DMNetworkGetConnectedVertices(dm,i,&cone);
285:     vidxlTog[cone[0] - vStart] = edges[2*ctr];
286:     vidxlTog[cone[1] - vStart] = edges[2*ctr+1];
287:     ctr++;
288:   }
289:   PetscFree(edges);

291:   /* Create vertices and edges array for the subnetworks */
292:   for (j=0; j < network->nsubnet; j++) {
293:     PetscCalloc1(network->subnet[j].nedge,&network->subnet[j].edges);

295:     /* Temporarily setting nvtx and nedge to 0 so we can use them as counters in the below for loop.
296:        These get updated when the vertices and edges are added. */
297:     network->subnet[j].nvtx  = 0;
298:     network->subnet[j].nedge = 0;
299:   }
300:   PetscCalloc1(np,&network->subnetvtx);


303:   /* Get edge ownership */
304:   np = network->eEnd - network->eStart;
305:   MPI_Allgather(&np,1,MPIU_INT,eowners+1,1,MPIU_INT,comm);
306:   eowners[0] = 0;
307:   for (i=2; i<=size; i++) eowners[i] += eowners[i-1];

309:   i = 0; j = 0;
310:   while (i < np) { /* local edges, including coupling edges */
311:     network->header[i].index = i + eowners[rank];   /* Global edge index */

313:     if (j < network->nsubnet && i < network->subnet[j].eEnd) {
314:       network->header[i].subnetid = j; /* Subnetwork id */
315:       network->subnet[j].edges[network->subnet[j].nedge++] = i;

317:       network->header[i].ndata = 0;
318:       PetscSectionAddDof(network->DataSection,i,network->dataheadersize);
319:       network->header[i].offset[0] = 0;
320:       network->header[i].offsetvarrel[0] = 0;
321:       i++;
322:     }
323:     if (i >= network->subnet[j].eEnd) j++;
324:   }

326:   /* Count network->subnet[*].nvtx */
327:   for (i=vStart; i<network->vEnd; i++) { /* local vertices, including ghosts */
328:     k = vidxlTog[i-vStart];
329:     for (j=0; j < network->nsubnet; j++) {
330:       if (network->subnet[j].vStart <= k && k < network->subnet[j].vEnd) {
331:         network->subnet[j].nvtx++;
332:         break;
333:       }
334:     }
335:   }

337:   /* Set network->subnet[*].vertices on array network->subnetvtx */
338:   subnetvtx = network->subnetvtx;
339:   for (j=0; j<network->nsubnet; j++) {
340:     network->subnet[j].vertices = subnetvtx;
341:     subnetvtx                  += network->subnet[j].nvtx;
342:     network->subnet[j].nvtx = 0;
343:   }

345:   /* Set vertex array for the subnetworks */
346:   for (i=vStart; i<network->vEnd; i++) { /* local vertices, including ghosts */
347:     network->header[i].index = vidxlTog[i-vStart]; /*  Global vertex index */

349:     k = vidxlTog[i-vStart];
350:     for (j=0; j < network->nsubnet; j++) {
351:       if (network->subnet[j].vStart <= k && k < network->subnet[j].vEnd) {
352:         network->header[i].subnetid = j;
353:         network->subnet[j].vertices[network->subnet[j].nvtx++] = i;
354:         break;
355:       }
356:     }

358:     network->header[i].ndata = 0;
359:     PetscSectionAddDof(network->DataSection,i,network->dataheadersize);
360:     network->header[i].offset[0] = 0;
361:     network->header[i].offsetvarrel[0] = 0;
362:   }

364:   PetscFree2(vidxlTog,eowners);
365:   return(0);
366: }

368: /*@C
369:   DMNetworkGetSubnetworkInfo - Returns the info for the subnetwork

371:   Input Parameters:
372: + dm - the DM object
373: - id   - the ID (integer) of the subnetwork

375:   Output Parameters:
376: + nv    - number of vertices (local)
377: . ne    - number of edges (local)
378: . vtx   - local vertices for this subnetwork
379: - edge  - local edges for this subnetwork

381:   Notes:
382:   Cannot call this routine before DMNetworkLayoutSetup()

384:   Level: intermediate

386: .seealso: DMNetworkLayoutSetUp, DMNetworkCreate
387: @*/
388: PetscErrorCode DMNetworkGetSubnetworkInfo(DM dm,PetscInt id,PetscInt *nv, PetscInt *ne,const PetscInt **vtx, const PetscInt **edge)
389: {
390:   DM_Network *network = (DM_Network*)dm->data;

393:   if (id >= network->nsubnet) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Subnet ID %D exceeds the num of subnets %D",id,network->nsubnet);
394:   *nv   = network->subnet[id].nvtx;
395:   *ne   = network->subnet[id].nedge;
396:   *vtx  = network->subnet[id].vertices;
397:   *edge = network->subnet[id].edges;
398:   return(0);
399: }

401: /*@C
402:   DMNetworkGetSubnetworkCoupleInfo - Returns the info for the coupling subnetwork

404:   Input Parameters:
405: + dm - the DM object
406: - id   - the ID (integer) of the coupling subnetwork

408:   Output Parameters:
409: + ne - number of edges (local)
410: - edge  - local edges for this coupling subnetwork

412:   Notes:
413:   Cannot call this routine before DMNetworkLayoutSetup()

415:   Level: intermediate

417: .seealso: DMNetworkGetSubnetworkInfo, DMNetworkLayoutSetUp, DMNetworkCreate
418: @*/
419: PetscErrorCode DMNetworkGetSubnetworkCoupleInfo(DM dm,PetscInt id,PetscInt *ne,const PetscInt **edge)
420: {
421:   DM_Network *net = (DM_Network*)dm->data;
422:   PetscInt   id1;

425:   if (net->ncsubnet) {
426:     if (id >= net->ncsubnet) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Subnet ID %D exceeds the num of coupling subnets %D",id,net->ncsubnet);

428:     id1   = id + net->nsubnet - net->ncsubnet;
429:     *ne   = net->subnet[id1].nedge;
430:     *edge = net->subnet[id1].edges;
431:   } else {
432:     *ne   = 0;
433:     *edge = NULL;
434:   }
435:   return(0);
436: }

438: /*@C
439:   DMNetworkRegisterComponent - Registers the network component

441:   Logically collective on dm

443:   Input Parameters:
444: + dm   - the network object
445: . name - the component name
446: - size - the storage size in bytes for this component data

448:    Output Parameters:
449: .   key - an integer key that defines the component

451:    Notes
452:    This routine should be called by all processors before calling DMNetworkLayoutSetup().

454:    Level: beginner

456: .seealso: DMNetworkLayoutSetUp, DMNetworkCreate
457: @*/
458: PetscErrorCode DMNetworkRegisterComponent(DM dm,const char *name,size_t size,PetscInt *key)
459: {
460:   PetscErrorCode        ierr;
461:   DM_Network            *network = (DM_Network*) dm->data;
462:   DMNetworkComponent    *component=&network->component[network->ncomponent];
463:   PetscBool             flg=PETSC_FALSE;
464:   PetscInt              i;

467:   for (i=0; i < network->ncomponent; i++) {
468:     PetscStrcmp(component->name,name,&flg);
469:     if (flg) {
470:       *key = i;
471:       return(0);
472:     }
473:   }
474:   if (network->ncomponent == MAX_COMPONENTS) {
475:     SETERRQ1(PetscObjectComm((PetscObject)dm),PETSC_ERR_ARG_OUTOFRANGE,"Number of components registered exceeds the max %D",MAX_COMPONENTS);
476:   }

478:   PetscStrcpy(component->name,name);
479:   component->size = size/sizeof(DMNetworkComponentGenericDataType);
480:   *key = network->ncomponent;
481:   network->ncomponent++;
482:   return(0);
483: }

485: /*@
486:   DMNetworkGetVertexRange - Get the bounds [start, end) for the vertices.

488:   Not Collective

490:   Input Parameters:
491: . dm - The DMNetwork object

493:   Output Parameters:
494: + vStart - The first vertex point
495: - vEnd   - One beyond the last vertex point

497:   Level: beginner

499: .seealso: DMNetworkGetEdgeRange
500: @*/
501: PetscErrorCode DMNetworkGetVertexRange(DM dm,PetscInt *vStart,PetscInt *vEnd)
502: {
503:   DM_Network     *network = (DM_Network*)dm->data;

506:   if (vStart) *vStart = network->vStart;
507:   if (vEnd) *vEnd = network->vEnd;
508:   return(0);
509: }

511: /*@
512:   DMNetworkGetEdgeRange - Get the bounds [start, end) for the edges.

514:   Not Collective

516:   Input Parameters:
517: . dm - The DMNetwork object

519:   Output Parameters:
520: + eStart - The first edge point
521: - eEnd   - One beyond the last edge point

523:   Level: beginner

525: .seealso: DMNetworkGetVertexRange
526: @*/
527: PetscErrorCode DMNetworkGetEdgeRange(DM dm,PetscInt *eStart,PetscInt *eEnd)
528: {
529:   DM_Network     *network = (DM_Network*)dm->data;

532:   if (eStart) *eStart = network->eStart;
533:   if (eEnd) *eEnd = network->eEnd;
534:   return(0);
535: }

537: /*@
538:   DMNetworkGetGlobalEdgeIndex - Get the user global numbering for the edge.

540:   Not Collective

542:   Input Parameters:
543: + dm - DMNetwork object
544: - p  - edge point

546:   Output Parameters:
547: . index - user global numbering for the edge

549:   Level: intermediate

551: .seealso: DMNetworkGetGlobalVertexIndex
552: @*/
553: PetscErrorCode DMNetworkGetGlobalEdgeIndex(DM dm,PetscInt p,PetscInt *index)
554: {
555:   PetscErrorCode    ierr;
556:   DM_Network        *network = (DM_Network*)dm->data;
557:   PetscInt          offsetp;
558:   DMNetworkComponentHeader header;

561:   if (!dm->setupcalled) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONGSTATE,"Must call DMSetUp() first");
562:   PetscSectionGetOffset(network->DataSection,p,&offsetp);
563:   header = (DMNetworkComponentHeader)(network->componentdataarray+offsetp);
564:   *index = header->index;
565:   return(0);
566: }

568: /*@
569:   DMNetworkGetGlobalVertexIndex - Get the user global numbering for the vertex.

571:   Not Collective

573:   Input Parameters:
574: + dm - DMNetwork object
575: - p  - vertex point

577:   Output Parameters:
578: . index - user global numbering for the vertex

580:   Level: intermediate

582: .seealso: DMNetworkGetGlobalEdgeIndex
583: @*/
584: PetscErrorCode DMNetworkGetGlobalVertexIndex(DM dm,PetscInt p,PetscInt *index)
585: {
586:   PetscErrorCode    ierr;
587:   DM_Network        *network = (DM_Network*)dm->data;
588:   PetscInt          offsetp;
589:   DMNetworkComponentHeader header;

592:   if (!dm->setupcalled) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONGSTATE,"Must call DMSetUp() first");
593:   PetscSectionGetOffset(network->DataSection,p,&offsetp);
594:   header = (DMNetworkComponentHeader)(network->componentdataarray+offsetp);
595:   *index = header->index;
596:   return(0);
597: }

599: /*
600:   DMNetworkGetComponentKeyOffset - Gets the type along with the offset for indexing the
601:                                     component value from the component data array

603:   Not Collective

605:   Input Parameters:
606: + dm      - The DMNetwork object
607: . p       - vertex/edge point
608: - compnum - component number

610:   Output Parameters:
611: + compkey - the key obtained when registering the component
612: - offset  - offset into the component data array associated with the vertex/edge point

614:   Notes:
615:   Typical usage:

617:   DMNetworkGetComponentDataArray(dm, &arr);
618:   DMNetworkGetVertex/EdgeRange(dm,&Start,&End);
619:   Loop over vertices or edges
620:     DMNetworkGetNumComponents(dm,v,&numcomps);
621:     Loop over numcomps
622:       DMNetworkGetComponentKeyOffset(dm,v,compnum,&key,&offset);
623:       compdata = (UserCompDataType)(arr+offset);

625:   Level: intermediate

627: .seealso: DMNetworkGetNumComponents, DMNetworkGetComponentDataArray,
628: */
629: PetscErrorCode DMNetworkGetComponentKeyOffset(DM dm,PetscInt p, PetscInt compnum, PetscInt *compkey, PetscInt *offset)
630: {
631:   PetscErrorCode           ierr;
632:   PetscInt                 offsetp;
633:   DMNetworkComponentHeader header;
634:   DM_Network               *network = (DM_Network*)dm->data;

637:   PetscSectionGetOffset(network->DataSection,p,&offsetp);
638:   header = (DMNetworkComponentHeader)(network->componentdataarray+offsetp);
639:   if (compkey) *compkey = header->key[compnum];
640:   if (offset) *offset  = offsetp+network->dataheadersize+header->offset[compnum];
641:   return(0);
642: }

644: /*@
645:   DMNetworkGetComponent - Returns the network component and its key

647:   Not Collective

649:   Input Parameters:
650: + dm - DMNetwork object
651: . p  - edge or vertex point
652: - compnum - component number

654:   Output Parameters:
655: + compkey - the key set for this computing during registration
656: - component - the component data

658:   Notes:
659:   Typical usage:

661:   DMNetworkGetVertex/EdgeRange(dm,&Start,&End);
662:   Loop over vertices or edges
663:     DMNetworkGetNumComponents(dm,v,&numcomps);
664:     Loop over numcomps
665:       DMNetworkGetComponent(dm,v,compnum,&key,&component);

667:   Level: beginner

669: .seealso: DMNetworkGetNumComponents, DMNetworkGetVariableOffset
670: @*/
671: PetscErrorCode DMNetworkGetComponent(DM dm, PetscInt p, PetscInt compnum, PetscInt *key, void **component)
672: {
674:   DM_Network     *network = (DM_Network*)dm->data;
675:   PetscInt       offsetd = 0;

678:   DMNetworkGetComponentKeyOffset(dm,p,compnum,key,&offsetd);
679:   *component = network->componentdataarray+offsetd;
680:   return(0);
681: }

683: /*@
684:   DMNetworkAddComponent - Adds a network component at the given point (vertex/edge)

686:   Not Collective

688:   Input Parameters:
689: + dm           - The DMNetwork object
690: . p            - vertex/edge point
691: . componentkey - component key returned while registering the component
692: - compvalue    - pointer to the data structure for the component

694:   Level: beginner

696: .seealso: DMNetworkGetVertexRange, DMNetworkGetEdgeRange, DMNetworkRegisterComponent
697: @*/
698: PetscErrorCode DMNetworkAddComponent(DM dm, PetscInt p,PetscInt componentkey,void* compvalue)
699: {
700:   DM_Network               *network = (DM_Network*)dm->data;
701:   DMNetworkComponent       *component = &network->component[componentkey];
702:   DMNetworkComponentHeader header = &network->header[p];
703:   DMNetworkComponentValue  cvalue = &network->cvalue[p];
704:   PetscErrorCode           ierr;

707:   if (header->ndata == MAX_DATA_AT_POINT) SETERRQ1(PetscObjectComm((PetscObject)dm),PETSC_ERR_ARG_OUTOFRANGE,"Number of components at a point exceeds the max %D",MAX_DATA_AT_POINT);

709:   header->size[header->ndata] = component->size;
710:   PetscSectionAddDof(network->DataSection,p,component->size);
711:   header->key[header->ndata] = componentkey;
712:   if (header->ndata != 0) header->offset[header->ndata] = header->offset[header->ndata-1] + header->size[header->ndata-1];
713:   header->nvar[header->ndata] = 0;

715:   cvalue->data[header->ndata] = (void*)compvalue;
716:   header->ndata++;
717:   return(0);
718: }

720: /*@
721:   DMNetworkSetComponentNumVariables - Sets the number of variables for a component

723:   Not Collective

725:   Input Parameters:
726: + dm           - The DMNetwork object
727: . p            - vertex/edge point
728: . compnum      - component number (First component added = 0, second = 1, ...)
729: - nvar         - number of variables for the component

731:   Level: beginner

733: .seealso: DMNetworkAddComponent(), DMNetworkGetNumComponents(),DMNetworkRegisterComponent()
734: @*/
735: PetscErrorCode DMNetworkSetComponentNumVariables(DM dm, PetscInt p,PetscInt compnum,PetscInt nvar)
736: {
737:   DM_Network               *network = (DM_Network*)dm->data;
738:   DMNetworkComponentHeader header = &network->header[p];
739:   PetscErrorCode           ierr;

742:   DMNetworkAddNumVariables(dm,p,nvar);
743:   header->nvar[compnum] = nvar;
744:   if (compnum != 0) header->offsetvarrel[compnum] = header->offsetvarrel[compnum-1] + header->nvar[compnum-1];
745:   return(0);
746: }

748: /*@
749:   DMNetworkGetNumComponents - Get the number of components at a vertex/edge

751:   Not Collective

753:   Input Parameters:
754: + dm - The DMNetwork object
755: - p  - vertex/edge point

757:   Output Parameters:
758: . numcomponents - Number of components at the vertex/edge

760:   Level: beginner

762: .seealso: DMNetworkRegisterComponent, DMNetworkAddComponent
763: @*/
764: PetscErrorCode DMNetworkGetNumComponents(DM dm,PetscInt p,PetscInt *numcomponents)
765: {
767:   PetscInt       offset;
768:   DM_Network     *network = (DM_Network*)dm->data;

771:   PetscSectionGetOffset(network->DataSection,p,&offset);
772:   *numcomponents = ((DMNetworkComponentHeader)(network->componentdataarray+offset))->ndata;
773:   return(0);
774: }

776: /*@
777:   DMNetworkGetVariableOffset - Get the offset for accessing the variable associated with the given vertex/edge from the local vector.

779:   Not Collective

781:   Input Parameters:
782: + dm     - The DMNetwork object
783: - p      - the edge/vertex point

785:   Output Parameters:
786: . offset - the offset

788:   Level: beginner

790: .seealso: DMNetworkGetVariableGlobalOffset, DMGetLocalVector
791: @*/
792: PetscErrorCode DMNetworkGetVariableOffset(DM dm,PetscInt p,PetscInt *offset)
793: {
795:   DM_Network     *network = (DM_Network*)dm->data;

798:   PetscSectionGetOffset(network->plex->localSection,p,offset);
799:   return(0);
800: }

802: /*@
803:   DMNetworkGetVariableGlobalOffset - Get the global offset for the variable associated with the given vertex/edge from the global vector.

805:   Not Collective

807:   Input Parameters:
808: + dm      - The DMNetwork object
809: - p       - the edge/vertex point

811:   Output Parameters:
812: . offsetg - the offset

814:   Level: beginner

816: .seealso: DMNetworkGetVariableOffset, DMGetLocalVector
817: @*/
818: PetscErrorCode DMNetworkGetVariableGlobalOffset(DM dm,PetscInt p,PetscInt *offsetg)
819: {
821:   DM_Network     *network = (DM_Network*)dm->data;

824:   PetscSectionGetOffset(network->plex->globalSection,p,offsetg);
825:   if (*offsetg < 0) *offsetg = -(*offsetg + 1); /* Convert to actual global offset for ghost vertex */
826:   return(0);
827: }

829: /*@
830:   DMNetworkGetComponentVariableOffset - Get the offset for accessing the variable associated with a component for the given vertex/edge from the local vector.

832:   Not Collective

834:   Input Parameters:
835: + dm     - The DMNetwork object
836: . p      - the edge/vertex point
837: - compnum - component number

839:   Output Parameters:
840: . offset - the offset

842:   Level: intermediate

844: .seealso: DMNetworkGetVariableGlobalOffset(), DMGetLocalVector(), DMNetworkSetComponentNumVariables()
845: @*/
846: PetscErrorCode DMNetworkGetComponentVariableOffset(DM dm,PetscInt p,PetscInt compnum,PetscInt *offset)
847: {
849:   DM_Network     *network = (DM_Network*)dm->data;
850:   PetscInt       offsetp,offsetd;
851:   DMNetworkComponentHeader header;

854:   DMNetworkGetVariableOffset(dm,p,&offsetp);
855:   PetscSectionGetOffset(network->DataSection,p,&offsetd);
856:   header = (DMNetworkComponentHeader)(network->componentdataarray+offsetd);
857:   *offset = offsetp + header->offsetvarrel[compnum];
858:   return(0);
859: }

861: /*@
862:   DMNetworkGetComponentVariableGlobalOffset - Get the global offset for accessing the variable associated with a component for the given vertex/edge from the local vector.

864:   Not Collective

866:   Input Parameters:
867: + dm     - The DMNetwork object
868: . p      - the edge/vertex point
869: - compnum - component number

871:   Output Parameters:
872: . offsetg - the global offset

874:   Level: intermediate

876: .seealso: DMNetworkGetVariableGlobalOffset(), DMNetworkGetComponentVariableOffset(), DMGetLocalVector(), DMNetworkSetComponentNumVariables()
877: @*/
878: PetscErrorCode DMNetworkGetComponentVariableGlobalOffset(DM dm,PetscInt p,PetscInt compnum,PetscInt *offsetg)
879: {
881:   DM_Network     *network = (DM_Network*)dm->data;
882:   PetscInt       offsetp,offsetd;
883:   DMNetworkComponentHeader header;

886:   DMNetworkGetVariableGlobalOffset(dm,p,&offsetp);
887:   PetscSectionGetOffset(network->DataSection,p,&offsetd);
888:   header = (DMNetworkComponentHeader)(network->componentdataarray+offsetd);
889:   *offsetg = offsetp + header->offsetvarrel[compnum];
890:   return(0);
891: }

893: /*@
894:   DMNetworkGetEdgeOffset - Get the offset for accessing the variable associated with the given edge from the local subvector.

896:   Not Collective

898:   Input Parameters:
899: + dm     - The DMNetwork object
900: - p      - the edge point

902:   Output Parameters:
903: . offset - the offset

905:   Level: intermediate

907: .seealso: DMNetworkGetVariableGlobalOffset, DMGetLocalVector
908: @*/
909: PetscErrorCode DMNetworkGetEdgeOffset(DM dm,PetscInt p,PetscInt *offset)
910: {
912:   DM_Network     *network = (DM_Network*)dm->data;


916:   PetscSectionGetOffset(network->edge.DofSection,p,offset);
917:   return(0);
918: }

920: /*@
921:   DMNetworkGetVertexOffset - Get the offset for accessing the variable associated with the given vertex from the local subvector.

923:   Not Collective

925:   Input Parameters:
926: + dm     - The DMNetwork object
927: - p      - the vertex point

929:   Output Parameters:
930: . offset - the offset

932:   Level: intermediate

934: .seealso: DMNetworkGetVariableGlobalOffset, DMGetLocalVector
935: @*/
936: PetscErrorCode DMNetworkGetVertexOffset(DM dm,PetscInt p,PetscInt *offset)
937: {
939:   DM_Network     *network = (DM_Network*)dm->data;


943:   p -= network->vStart;

945:   PetscSectionGetOffset(network->vertex.DofSection,p,offset);
946:   return(0);
947: }
948: /*@
949:   DMNetworkAddNumVariables - Add number of variables associated with a given point.

951:   Not Collective

953:   Input Parameters:
954: + dm   - The DMNetworkObject
955: . p    - the vertex/edge point
956: - nvar - number of additional variables

958:   Level: beginner

960: .seealso: DMNetworkSetNumVariables
961: @*/
962: PetscErrorCode DMNetworkAddNumVariables(DM dm,PetscInt p,PetscInt nvar)
963: {
965:   DM_Network     *network = (DM_Network*)dm->data;

968:   PetscSectionAddDof(network->DofSection,p,nvar);
969:   return(0);
970: }

972: /*@
973:   DMNetworkGetNumVariables - Gets number of variables for a vertex/edge point.

975:   Not Collective

977:   Input Parameters:
978: + dm   - The DMNetworkObject
979: - p    - the vertex/edge point

981:   Output Parameters:
982: . nvar - number of variables

984:   Level: beginner

986: .seealso: DMNetworkAddNumVariables, DMNetworkSddNumVariables
987: @*/
988: PetscErrorCode DMNetworkGetNumVariables(DM dm,PetscInt p,PetscInt *nvar)
989: {
991:   DM_Network     *network = (DM_Network*)dm->data;

994:   PetscSectionGetDof(network->DofSection,p,nvar);
995:   return(0);
996: }

998: /*@
999:   DMNetworkSetNumVariables - Sets number of variables for a vertex/edge point.

1001:   Not Collective

1003:   Input Parameters:
1004: + dm   - The DMNetworkObject
1005: . p    - the vertex/edge point
1006: - nvar - number of variables

1008:   Level: beginner

1010: .seealso: DMNetworkAddNumVariables
1011: @*/
1012: PetscErrorCode DMNetworkSetNumVariables(DM dm,PetscInt p,PetscInt nvar)
1013: {
1015:   DM_Network     *network = (DM_Network*)dm->data;

1018:   PetscSectionSetDof(network->DofSection,p,nvar);
1019:   return(0);
1020: }

1022: /* Sets up the array that holds the data for all components and its associated section. This
1023:    function is called during DMSetUp() */
1024: PetscErrorCode DMNetworkComponentSetUp(DM dm)
1025: {
1026:   PetscErrorCode           ierr;
1027:   DM_Network               *network = (DM_Network*)dm->data;
1028:   PetscInt                 arr_size,p,offset,offsetp,ncomp,i;
1029:   DMNetworkComponentHeader header;
1030:   DMNetworkComponentValue  cvalue;
1031:   DMNetworkComponentGenericDataType *componentdataarray;

1034:   PetscSectionSetUp(network->DataSection);
1035:   PetscSectionGetStorageSize(network->DataSection,&arr_size);
1036:   PetscMalloc1(arr_size,&network->componentdataarray);
1037:   componentdataarray = network->componentdataarray;
1038:   for (p = network->pStart; p < network->pEnd; p++) {
1039:     PetscSectionGetOffset(network->DataSection,p,&offsetp);
1040:     /* Copy header */
1041:     header = &network->header[p];
1042:     PetscMemcpy(componentdataarray+offsetp,header,network->dataheadersize*sizeof(DMNetworkComponentGenericDataType));
1043:     /* Copy data */
1044:     cvalue = &network->cvalue[p];
1045:     ncomp = header->ndata;
1046:     for (i = 0; i < ncomp; i++) {
1047:       offset = offsetp + network->dataheadersize + header->offset[i];
1048:       PetscMemcpy(componentdataarray+offset,cvalue->data[i],header->size[i]*sizeof(DMNetworkComponentGenericDataType));
1049:     }
1050:   }
1051:   return(0);
1052: }

1054: /* Sets up the section for dofs. This routine is called during DMSetUp() */
1055: PetscErrorCode DMNetworkVariablesSetUp(DM dm)
1056: {
1058:   DM_Network     *network = (DM_Network*)dm->data;

1061:   PetscSectionSetUp(network->DofSection);
1062:   return(0);
1063: }

1065: /*
1066:   DMNetworkGetComponentDataArray - Returns the component data array

1068:   Not Collective

1070:   Input Parameters:
1071: . dm - The DMNetwork Object

1073:   Output Parameters:
1074: . componentdataarray - array that holds data for all components

1076:   Level: intermediate

1078: .seealso: DMNetworkGetComponentKeyOffset, DMNetworkGetNumComponents
1079: */
1080: PetscErrorCode DMNetworkGetComponentDataArray(DM dm,DMNetworkComponentGenericDataType **componentdataarray)
1081: {
1082:   DM_Network     *network = (DM_Network*)dm->data;

1085:   *componentdataarray = network->componentdataarray;
1086:   return(0);
1087: }

1089: /* Get a subsection from a range of points */
1090: PetscErrorCode DMNetworkGetSubSection_private(PetscSection master, PetscInt pstart, PetscInt pend,PetscSection *subsection)
1091: {
1093:   PetscInt       i, nvar;

1096:   PetscSectionCreate(PetscObjectComm((PetscObject)master), subsection);
1097:   PetscSectionSetChart(*subsection, 0, pend - pstart);
1098:   for (i = pstart; i < pend; i++) {
1099:     PetscSectionGetDof(master,i,&nvar);
1100:     PetscSectionSetDof(*subsection, i - pstart, nvar);
1101:   }

1103:   PetscSectionSetUp(*subsection);
1104:   return(0);
1105: }

1107: /* Create a submap of points with a GlobalToLocal structure */
1108: PetscErrorCode DMNetworkSetSubMap_private(PetscInt pstart, PetscInt pend, ISLocalToGlobalMapping *map)
1109: {
1111:   PetscInt       i, *subpoints;

1114:   /* Create index sets to map from "points" to "subpoints" */
1115:   PetscMalloc1(pend - pstart, &subpoints);
1116:   for (i = pstart; i < pend; i++) {
1117:     subpoints[i - pstart] = i;
1118:   }
1119:   ISLocalToGlobalMappingCreate(PETSC_COMM_WORLD,1,pend-pstart,subpoints,PETSC_COPY_VALUES,map);
1120:   PetscFree(subpoints);
1121:   return(0);
1122: }

1124: /*@
1125:   DMNetworkAssembleGraphStructures - Assembles vertex and edge data structures. Must be called after DMNetworkDistribute.

1127:   Collective

1129:   Input Parameters:
1130: . dm   - The DMNetworkObject

1132:   Note: the routine will create alternative orderings for the vertices and edges. Assume global network points are:

1134:   points = [0 1 2 3 4 5 6]

1136:   where edges = [0,1,2,3] and vertices = [4,5,6]. The new orderings will be specific to the subset (i.e vertices = [0,1,2] <- [4,5,6]).

1138:   With this new ordering a local PetscSection, global PetscSection and PetscSF will be created specific to the subset.

1140:   Level: intermediate

1142: @*/
1143: PetscErrorCode DMNetworkAssembleGraphStructures(DM dm)
1144: {
1146:   MPI_Comm       comm;
1147:   PetscMPIInt    rank, size;
1148:   DM_Network     *network = (DM_Network*)dm->data;

1151:   PetscObjectGetComm((PetscObject)dm,&comm);
1152:   MPI_Comm_rank(comm, &rank);
1153:   MPI_Comm_size(comm, &size);

1155:   /* Create maps for vertices and edges */
1156:   DMNetworkSetSubMap_private(network->vStart,network->vEnd,&network->vertex.mapping);
1157:   DMNetworkSetSubMap_private(network->eStart,network->eEnd,&network->edge.mapping);

1159:   /* Create local sub-sections */
1160:   DMNetworkGetSubSection_private(network->DofSection,network->vStart,network->vEnd,&network->vertex.DofSection);
1161:   DMNetworkGetSubSection_private(network->DofSection,network->eStart,network->eEnd,&network->edge.DofSection);

1163:   if (size > 1) {
1164:     PetscSFGetSubSF(network->plex->sf, network->vertex.mapping, &network->vertex.sf);

1166:     PetscSectionCreateGlobalSection(network->vertex.DofSection, network->vertex.sf, PETSC_FALSE, PETSC_FALSE, &network->vertex.GlobalDofSection);
1167:     PetscSFGetSubSF(network->plex->sf, network->edge.mapping, &network->edge.sf);
1168:     PetscSectionCreateGlobalSection(network->edge.DofSection, network->edge.sf, PETSC_FALSE, PETSC_FALSE, &network->edge.GlobalDofSection);
1169:   } else {
1170:     /* create structures for vertex */
1171:     PetscSectionClone(network->vertex.DofSection,&network->vertex.GlobalDofSection);
1172:     /* create structures for edge */
1173:     PetscSectionClone(network->edge.DofSection,&network->edge.GlobalDofSection);
1174:   }

1176:   /* Add viewers */
1177:   PetscObjectSetName((PetscObject)network->edge.GlobalDofSection,"Global edge dof section");
1178:   PetscObjectSetName((PetscObject)network->vertex.GlobalDofSection,"Global vertex dof section");
1179:   PetscSectionViewFromOptions(network->edge.GlobalDofSection, NULL, "-edge_global_section_view");
1180:   PetscSectionViewFromOptions(network->vertex.GlobalDofSection, NULL, "-vertex_global_section_view");
1181:   return(0);
1182: }

1184: /*@
1185:   DMNetworkDistribute - Distributes the network and moves associated component data.

1187:   Collective

1189:   Input Parameter:
1190: + DM - the DMNetwork object
1191: - overlap - The overlap of partitions, 0 is the default

1193:   Notes:
1194:   Distributes the network with <overlap>-overlapping partitioning of the edges.

1196:   Level: intermediate

1198: .seealso: DMNetworkCreate
1199: @*/
1200: PetscErrorCode DMNetworkDistribute(DM *dm,PetscInt overlap)
1201: {
1202:   MPI_Comm       comm;
1204:   PetscMPIInt    size;
1205:   DM_Network     *oldDMnetwork = (DM_Network*)((*dm)->data);
1206:   DM_Network     *newDMnetwork;
1207:   PetscSF        pointsf=NULL;
1208:   DM             newDM;
1209:   PetscInt       j,e,v,offset,*subnetvtx;
1210:   PetscPartitioner         part;
1211:   DMNetworkComponentHeader header;

1214:   PetscObjectGetComm((PetscObject)*dm,&comm);
1215:   MPI_Comm_size(comm, &size);
1216:   if (size == 1) return(0);

1218:   DMNetworkCreate(PetscObjectComm((PetscObject)*dm),&newDM);
1219:   newDMnetwork = (DM_Network*)newDM->data;
1220:   newDMnetwork->dataheadersize = sizeof(struct _p_DMNetworkComponentHeader)/sizeof(DMNetworkComponentGenericDataType);

1222:   /* Enable runtime options for petscpartitioner */
1223:   DMPlexGetPartitioner(oldDMnetwork->plex,&part);
1224:   PetscPartitionerSetFromOptions(part);

1226:   /* Distribute plex dm and dof section */
1227:   DMPlexDistribute(oldDMnetwork->plex,overlap,&pointsf,&newDMnetwork->plex);

1229:   /* Distribute dof section */
1230:   PetscSectionCreate(PetscObjectComm((PetscObject)*dm),&newDMnetwork->DofSection);
1231:   PetscSFDistributeSection(pointsf,oldDMnetwork->DofSection,NULL,newDMnetwork->DofSection);
1232:   PetscSectionCreate(PetscObjectComm((PetscObject)*dm),&newDMnetwork->DataSection);

1234:   /* Distribute data and associated section */
1235:   DMPlexDistributeData(newDMnetwork->plex,pointsf,oldDMnetwork->DataSection,MPIU_INT,(void*)oldDMnetwork->componentdataarray,newDMnetwork->DataSection,(void**)&newDMnetwork->componentdataarray);

1237:   PetscSectionGetChart(newDMnetwork->DataSection,&newDMnetwork->pStart,&newDMnetwork->pEnd);
1238:   DMPlexGetHeightStratum(newDMnetwork->plex,0, &newDMnetwork->eStart,&newDMnetwork->eEnd);
1239:   DMPlexGetHeightStratum(newDMnetwork->plex,1,&newDMnetwork->vStart,&newDMnetwork->vEnd);
1240:   newDMnetwork->nEdges    = newDMnetwork->eEnd - newDMnetwork->eStart;
1241:   newDMnetwork->nVertices = newDMnetwork->vEnd - newDMnetwork->vStart;
1242:   newDMnetwork->NVertices = oldDMnetwork->NVertices;
1243:   newDMnetwork->NEdges    = oldDMnetwork->NEdges;

1245:   /* Set Dof section as the section for dm */
1246:   DMSetLocalSection(newDMnetwork->plex,newDMnetwork->DofSection);
1247:   DMGetGlobalSection(newDMnetwork->plex,&newDMnetwork->GlobalDofSection);

1249:   /* Set up subnetwork info in the newDM */
1250:   newDMnetwork->nsubnet  = oldDMnetwork->nsubnet;
1251:   newDMnetwork->ncsubnet = oldDMnetwork->ncsubnet;
1252:   PetscCalloc1(newDMnetwork->nsubnet,&newDMnetwork->subnet);
1253:   /* Copy over the global number of vertices and edges in each subnetwork. Note that these are already
1254:      calculated in DMNetworkLayoutSetUp()
1255:   */
1256:   for (j=0; j < newDMnetwork->nsubnet; j++) {
1257:     newDMnetwork->subnet[j].Nvtx  = oldDMnetwork->subnet[j].Nvtx;
1258:     newDMnetwork->subnet[j].Nedge = oldDMnetwork->subnet[j].Nedge;
1259:   }

1261:   for (e = newDMnetwork->eStart; e < newDMnetwork->eEnd; e++) {
1262:     PetscSectionGetOffset(newDMnetwork->DataSection,e,&offset);
1263:     header = (DMNetworkComponentHeader)(newDMnetwork->componentdataarray+offset);
1264:     newDMnetwork->subnet[header->subnetid].nedge++;
1265:   }

1267:   for (v = newDMnetwork->vStart; v < newDMnetwork->vEnd; v++) {
1268:     PetscSectionGetOffset(newDMnetwork->DataSection,v,&offset);
1269:     header = (DMNetworkComponentHeader)(newDMnetwork->componentdataarray+offset);
1270:     newDMnetwork->subnet[header->subnetid].nvtx++;
1271:   }

1273:   /* Now create the vertices and edge arrays for the subnetworks */
1274:   PetscCalloc1(newDMnetwork->vEnd-newDMnetwork->vStart,&newDMnetwork->subnetvtx);
1275:   subnetvtx = newDMnetwork->subnetvtx;

1277:   for (j=0; j<newDMnetwork->nsubnet; j++) {
1278:     PetscCalloc1(newDMnetwork->subnet[j].nedge,&newDMnetwork->subnet[j].edges);
1279:     newDMnetwork->subnet[j].vertices = subnetvtx;
1280:     subnetvtx                       += newDMnetwork->subnet[j].nvtx;

1282:     /* Temporarily setting nvtx and nedge to 0 so we can use them as counters in the below for loop.
1283:        These get updated when the vertices and edges are added. */
1284:     newDMnetwork->subnet[j].nvtx = newDMnetwork->subnet[j].nedge = 0;
1285:   }

1287:   /* Set the vertices and edges in each subnetwork */
1288:   for (e = newDMnetwork->eStart; e < newDMnetwork->eEnd; e++) {
1289:     PetscSectionGetOffset(newDMnetwork->DataSection,e,&offset);
1290:     header = (DMNetworkComponentHeader)(newDMnetwork->componentdataarray+offset);
1291:     newDMnetwork->subnet[header->subnetid].edges[newDMnetwork->subnet[header->subnetid].nedge++] = e;
1292:   }

1294:   for (v = newDMnetwork->vStart; v < newDMnetwork->vEnd; v++) {
1295:     PetscSectionGetOffset(newDMnetwork->DataSection,v,&offset);
1296:     header = (DMNetworkComponentHeader)(newDMnetwork->componentdataarray+offset);
1297:     newDMnetwork->subnet[header->subnetid].vertices[newDMnetwork->subnet[header->subnetid].nvtx++] = v;
1298:   }

1300:   newDM->setupcalled = (*dm)->setupcalled;
1301:   newDMnetwork->distributecalled = PETSC_TRUE;

1303:   /* Destroy point SF */
1304:   PetscSFDestroy(&pointsf);

1306:   DMDestroy(dm);
1307:   *dm  = newDM;
1308:   return(0);
1309: }

1311: /*@C
1312:   PetscSFGetSubSF - Returns an SF for a specific subset of points. Leaves are re-numbered to reflect the new ordering.

1314:   Input Parameters:
1315: + masterSF - the original SF structure
1316: - map      - a ISLocalToGlobal mapping that contains the subset of points

1318:   Output Parameters:
1319: . subSF    - a subset of the masterSF for the desired subset.

1321:   Level: intermediate
1322: @*/
1323: PetscErrorCode PetscSFGetSubSF(PetscSF mastersf, ISLocalToGlobalMapping map, PetscSF *subSF) {

1325:   PetscErrorCode        ierr;
1326:   PetscInt              nroots, nleaves, *ilocal_sub;
1327:   PetscInt              i, *ilocal_map, nroots_sub, nleaves_sub = 0;
1328:   PetscInt              *local_points, *remote_points;
1329:   PetscSFNode           *iremote_sub;
1330:   const PetscInt        *ilocal;
1331:   const PetscSFNode     *iremote;

1334:   PetscSFGetGraph(mastersf,&nroots,&nleaves,&ilocal,&iremote);

1336:   /* Look for leaves that pertain to the subset of points. Get the local ordering */
1337:   PetscMalloc1(nleaves,&ilocal_map);
1338:   ISGlobalToLocalMappingApply(map,IS_GTOLM_MASK,nleaves,ilocal,NULL,ilocal_map);
1339:   for (i = 0; i < nleaves; i++) {
1340:     if (ilocal_map[i] != -1) nleaves_sub += 1;
1341:   }
1342:   /* Re-number ilocal with subset numbering. Need information from roots */
1343:   PetscMalloc2(nroots,&local_points,nroots,&remote_points);
1344:   for (i = 0; i < nroots; i++) local_points[i] = i;
1345:   ISGlobalToLocalMappingApply(map,IS_GTOLM_MASK,nroots,local_points,NULL,local_points);
1346:   PetscSFBcastBegin(mastersf, MPIU_INT, local_points, remote_points);
1347:   PetscSFBcastEnd(mastersf, MPIU_INT, local_points, remote_points);
1348:   /* Fill up graph using local (that is, local to the subset) numbering. */
1349:   PetscMalloc1(nleaves_sub,&ilocal_sub);
1350:   PetscMalloc1(nleaves_sub,&iremote_sub);
1351:   nleaves_sub = 0;
1352:   for (i = 0; i < nleaves; i++) {
1353:     if (ilocal_map[i] != -1) {
1354:       ilocal_sub[nleaves_sub] = ilocal_map[i];
1355:       iremote_sub[nleaves_sub].rank = iremote[i].rank;
1356:       iremote_sub[nleaves_sub].index = remote_points[ilocal[i]];
1357:       nleaves_sub += 1;
1358:     }
1359:   }
1360:   PetscFree2(local_points,remote_points);
1361:   ISLocalToGlobalMappingGetSize(map,&nroots_sub);

1363:   /* Create new subSF */
1364:   PetscSFCreate(PETSC_COMM_WORLD,subSF);
1365:   PetscSFSetFromOptions(*subSF);
1366:   PetscSFSetGraph(*subSF,nroots_sub,nleaves_sub,ilocal_sub,PETSC_OWN_POINTER,iremote_sub,PETSC_COPY_VALUES);
1367:   PetscFree(ilocal_map);
1368:   PetscFree(iremote_sub);
1369:   return(0);
1370: }

1372: /*@C
1373:   DMNetworkGetSupportingEdges - Return the supporting edges for this vertex point

1375:   Not Collective

1377:   Input Parameters:
1378: + dm - The DMNetwork object
1379: - p  - the vertex point

1381:   Output Parameters:
1382: + nedges - number of edges connected to this vertex point
1383: - edges  - List of edge points

1385:   Level: beginner

1387:   Fortran Notes:
1388:   Since it returns an array, this routine is only available in Fortran 90, and you must
1389:   include petsc.h90 in your code.

1391: .seealso: DMNetworkCreate, DMNetworkGetConnectedVertices
1392: @*/
1393: PetscErrorCode DMNetworkGetSupportingEdges(DM dm,PetscInt vertex,PetscInt *nedges,const PetscInt *edges[])
1394: {
1396:   DM_Network     *network = (DM_Network*)dm->data;

1399:   DMPlexGetSupportSize(network->plex,vertex,nedges);
1400:   DMPlexGetSupport(network->plex,vertex,edges);
1401:   return(0);
1402: }

1404: /*@C
1405:   DMNetworkGetConnectedVertices - Return the connected vertices for this edge point

1407:   Not Collective

1409:   Input Parameters:
1410: + dm - The DMNetwork object
1411: - p  - the edge point

1413:   Output Parameters:
1414: . vertices  - vertices connected to this edge

1416:   Level: beginner

1418:   Fortran Notes:
1419:   Since it returns an array, this routine is only available in Fortran 90, and you must
1420:   include petsc.h90 in your code.

1422: .seealso: DMNetworkCreate, DMNetworkGetSupportingEdges
1423: @*/
1424: PetscErrorCode DMNetworkGetConnectedVertices(DM dm,PetscInt edge,const PetscInt *vertices[])
1425: {
1427:   DM_Network     *network = (DM_Network*)dm->data;

1430:   DMPlexGetCone(network->plex,edge,vertices);
1431:   return(0);
1432: }

1434: /*@
1435:   DMNetworkIsGhostVertex - Returns TRUE if the vertex is a ghost vertex

1437:   Not Collective

1439:   Input Parameters:
1440: + dm - The DMNetwork object
1441: - p  - the vertex point

1443:   Output Parameter:
1444: . isghost - TRUE if the vertex is a ghost point

1446:   Level: beginner

1448: .seealso: DMNetworkCreate, DMNetworkGetConnectedVertices, DMNetworkGetVertexRange
1449: @*/
1450: PetscErrorCode DMNetworkIsGhostVertex(DM dm,PetscInt p,PetscBool *isghost)
1451: {
1453:   DM_Network     *network = (DM_Network*)dm->data;
1454:   PetscInt       offsetg;
1455:   PetscSection   sectiong;

1458:   if (!dm->setupcalled) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONGSTATE,"Must call DMSetUp() first");
1459:   *isghost = PETSC_FALSE;
1460:   DMGetGlobalSection(network->plex,&sectiong);
1461:   PetscSectionGetOffset(sectiong,p,&offsetg);
1462:   if (offsetg < 0) *isghost = PETSC_TRUE;
1463:   return(0);
1464: }

1466: PetscErrorCode DMSetUp_Network(DM dm)
1467: {
1469:   DM_Network     *network=(DM_Network*)dm->data;

1472:   DMNetworkComponentSetUp(dm);
1473:   DMNetworkVariablesSetUp(dm);

1475:   DMSetLocalSection(network->plex,network->DofSection);
1476:   DMGetGlobalSection(network->plex,&network->GlobalDofSection);

1478:   dm->setupcalled = PETSC_TRUE;
1479:   DMViewFromOptions(dm,NULL,"-dm_view");
1480:   return(0);
1481: }

1483: /*@
1484:     DMNetworkHasJacobian - Sets global flag for using user's sub Jacobian matrices
1485:                             -- replaced by DMNetworkSetOption(network,userjacobian,PETSC_TURE)?

1487:     Collective

1489:     Input Parameters:
1490: +   dm - The DMNetwork object
1491: .   eflg - turn the option on (PETSC_TRUE) or off (PETSC_FALSE) if user provides Jacobian for edges
1492: -   vflg - turn the option on (PETSC_TRUE) or off (PETSC_FALSE) if user provides Jacobian for vertices

1494:     Level: intermediate

1496: @*/
1497: PetscErrorCode DMNetworkHasJacobian(DM dm,PetscBool eflg,PetscBool vflg)
1498: {
1499:   DM_Network     *network=(DM_Network*)dm->data;
1501:   PetscInt       nVertices = network->nVertices;

1504:   network->userEdgeJacobian   = eflg;
1505:   network->userVertexJacobian = vflg;

1507:   if (eflg && !network->Je) {
1508:     PetscCalloc1(3*network->nEdges,&network->Je);
1509:   }

1511:   if (vflg && !network->Jv && nVertices) {
1512:     PetscInt       i,*vptr,nedges,vStart=network->vStart;
1513:     PetscInt       nedges_total;
1514:     const PetscInt *edges;

1516:     /* count nvertex_total */
1517:     nedges_total = 0;
1518:     PetscMalloc1(nVertices+1,&vptr);

1520:     vptr[0] = 0;
1521:     for (i=0; i<nVertices; i++) {
1522:       DMNetworkGetSupportingEdges(dm,i+vStart,&nedges,&edges);
1523:       nedges_total += nedges;
1524:       vptr[i+1] = vptr[i] + 2*nedges + 1;
1525:     }

1527:     PetscCalloc1(2*nedges_total+nVertices,&network->Jv);
1528:     network->Jvptr = vptr;
1529:   }
1530:   return(0);
1531: }

1533: /*@
1534:     DMNetworkEdgeSetMatrix - Sets user-provided Jacobian matrices for this edge to the network

1536:     Not Collective

1538:     Input Parameters:
1539: +   dm - The DMNetwork object
1540: .   p  - the edge point
1541: -   J - array (size = 3) of Jacobian submatrices for this edge point:
1542:         J[0]: this edge
1543:         J[1] and J[2]: connected vertices, obtained by calling DMNetworkGetConnectedVertices()

1545:     Level: advanced

1547: .seealso: DMNetworkVertexSetMatrix
1548: @*/
1549: PetscErrorCode DMNetworkEdgeSetMatrix(DM dm,PetscInt p,Mat J[])
1550: {
1551:   DM_Network     *network=(DM_Network*)dm->data;

1554:   if (!network->Je) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_ORDER,"Must call DMNetworkHasJacobian() collectively before calling DMNetworkEdgeSetMatrix");

1556:   if (J) {
1557:     network->Je[3*p]   = J[0];
1558:     network->Je[3*p+1] = J[1];
1559:     network->Je[3*p+2] = J[2];
1560:   }
1561:   return(0);
1562: }

1564: /*@
1565:     DMNetworkVertexSetMatrix - Sets user-provided Jacobian matrix for this vertex to the network

1567:     Not Collective

1569:     Input Parameters:
1570: +   dm - The DMNetwork object
1571: .   p  - the vertex point
1572: -   J - array of Jacobian (size = 2*(num of supporting edges) + 1) submatrices for this vertex point:
1573:         J[0]:       this vertex
1574:         J[1+2*i]:   i-th supporting edge
1575:         J[1+2*i+1]: i-th connected vertex

1577:     Level: advanced

1579: .seealso: DMNetworkEdgeSetMatrix
1580: @*/
1581: PetscErrorCode DMNetworkVertexSetMatrix(DM dm,PetscInt p,Mat J[])
1582: {
1584:   DM_Network     *network=(DM_Network*)dm->data;
1585:   PetscInt       i,*vptr,nedges,vStart=network->vStart;
1586:   const PetscInt *edges;

1589:   if (!network->Jv) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_ORDER,"Must call DMNetworkHasJacobian() collectively before calling DMNetworkVertexSetMatrix");

1591:   if (J) {
1592:     vptr = network->Jvptr;
1593:     network->Jv[vptr[p-vStart]] = J[0]; /* Set Jacobian for this vertex */

1595:     /* Set Jacobian for each supporting edge and connected vertex */
1596:     DMNetworkGetSupportingEdges(dm,p,&nedges,&edges);
1597:     for (i=1; i<=2*nedges; i++) network->Jv[vptr[p-vStart]+i] = J[i];
1598:   }
1599:   return(0);
1600: }

1602: PETSC_STATIC_INLINE PetscErrorCode MatSetPreallocationDenseblock_private(PetscInt nrows,PetscInt *rows,PetscInt ncols,PetscBool ghost,Vec vdnz,Vec vonz)
1603: {
1605:   PetscInt       j;
1606:   PetscScalar    val=(PetscScalar)ncols;

1609:   if (!ghost) {
1610:     for (j=0; j<nrows; j++) {
1611:       VecSetValues(vdnz,1,&rows[j],&val,ADD_VALUES);
1612:     }
1613:   } else {
1614:     for (j=0; j<nrows; j++) {
1615:       VecSetValues(vonz,1,&rows[j],&val,ADD_VALUES);
1616:     }
1617:   }
1618:   return(0);
1619: }

1621: PETSC_STATIC_INLINE PetscErrorCode MatSetPreallocationUserblock_private(Mat Ju,PetscInt nrows,PetscInt *rows,PetscInt ncols,PetscBool ghost,Vec vdnz,Vec vonz)
1622: {
1624:   PetscInt       j,ncols_u;
1625:   PetscScalar    val;

1628:   if (!ghost) {
1629:     for (j=0; j<nrows; j++) {
1630:       MatGetRow(Ju,j,&ncols_u,NULL,NULL);
1631:       val = (PetscScalar)ncols_u;
1632:       VecSetValues(vdnz,1,&rows[j],&val,ADD_VALUES);
1633:       MatRestoreRow(Ju,j,&ncols_u,NULL,NULL);
1634:     }
1635:   } else {
1636:     for (j=0; j<nrows; j++) {
1637:       MatGetRow(Ju,j,&ncols_u,NULL,NULL);
1638:       val = (PetscScalar)ncols_u;
1639:       VecSetValues(vonz,1,&rows[j],&val,ADD_VALUES);
1640:       MatRestoreRow(Ju,j,&ncols_u,NULL,NULL);
1641:     }
1642:   }
1643:   return(0);
1644: }

1646: PETSC_STATIC_INLINE PetscErrorCode MatSetPreallocationblock_private(Mat Ju,PetscInt nrows,PetscInt *rows,PetscInt ncols,PetscBool ghost,Vec vdnz,Vec vonz)
1647: {

1651:   if (Ju) {
1652:     MatSetPreallocationUserblock_private(Ju,nrows,rows,ncols,ghost,vdnz,vonz);
1653:   } else {
1654:     MatSetPreallocationDenseblock_private(nrows,rows,ncols,ghost,vdnz,vonz);
1655:   }
1656:   return(0);
1657: }

1659: PETSC_STATIC_INLINE PetscErrorCode MatSetDenseblock_private(PetscInt nrows,PetscInt *rows,PetscInt ncols,PetscInt cstart,Mat *J)
1660: {
1662:   PetscInt       j,*cols;
1663:   PetscScalar    *zeros;

1666:   PetscCalloc2(ncols,&cols,nrows*ncols,&zeros);
1667:   for (j=0; j<ncols; j++) cols[j] = j+ cstart;
1668:   MatSetValues(*J,nrows,rows,ncols,cols,zeros,INSERT_VALUES);
1669:   PetscFree2(cols,zeros);
1670:   return(0);
1671: }

1673: PETSC_STATIC_INLINE PetscErrorCode MatSetUserblock_private(Mat Ju,PetscInt nrows,PetscInt *rows,PetscInt ncols,PetscInt cstart,Mat *J)
1674: {
1676:   PetscInt       j,M,N,row,col,ncols_u;
1677:   const PetscInt *cols;
1678:   PetscScalar    zero=0.0;

1681:   MatGetSize(Ju,&M,&N);
1682:   if (nrows != M || ncols != N) SETERRQ4(PetscObjectComm((PetscObject)Ju),PETSC_ERR_USER,"%D by %D must equal %D by %D",nrows,ncols,M,N);

1684:   for (row=0; row<nrows; row++) {
1685:     MatGetRow(Ju,row,&ncols_u,&cols,NULL);
1686:     for (j=0; j<ncols_u; j++) {
1687:       col = cols[j] + cstart;
1688:       MatSetValues(*J,1,&rows[row],1,&col,&zero,INSERT_VALUES);
1689:     }
1690:     MatRestoreRow(Ju,row,&ncols_u,&cols,NULL);
1691:   }
1692:   return(0);
1693: }

1695: PETSC_STATIC_INLINE PetscErrorCode MatSetblock_private(Mat Ju,PetscInt nrows,PetscInt *rows,PetscInt ncols,PetscInt cstart,Mat *J)
1696: {

1700:   if (Ju) {
1701:     MatSetUserblock_private(Ju,nrows,rows,ncols,cstart,J);
1702:   } else {
1703:     MatSetDenseblock_private(nrows,rows,ncols,cstart,J);
1704:   }
1705:   return(0);
1706: }

1708: /* Creates a GlobalToLocal mapping with a Local and Global section. This is akin to the routine DMGetLocalToGlobalMapping but without the need of providing a dm.
1709: */
1710: PetscErrorCode CreateSubGlobalToLocalMapping_private(PetscSection globalsec, PetscSection localsec, ISLocalToGlobalMapping *ltog)
1711: {
1713:   PetscInt       i,size,dof;
1714:   PetscInt       *glob2loc;

1717:   PetscSectionGetStorageSize(localsec,&size);
1718:   PetscMalloc1(size,&glob2loc);

1720:   for (i = 0; i < size; i++) {
1721:     PetscSectionGetOffset(globalsec,i,&dof);
1722:     dof = (dof >= 0) ? dof : -(dof + 1);
1723:     glob2loc[i] = dof;
1724:   }

1726:   ISLocalToGlobalMappingCreate(PETSC_COMM_WORLD,1,size,glob2loc,PETSC_OWN_POINTER,ltog);
1727: #if 0
1728:   PetscIntView(size,glob2loc,PETSC_VIEWER_STDOUT_WORLD);
1729: #endif
1730:   return(0);
1731: }

1733: #include <petsc/private/matimpl.h>

1735: PetscErrorCode DMCreateMatrix_Network_Nest(DM dm,Mat *J)
1736: {
1738:   DM_Network     *network = (DM_Network*)dm->data;
1739:   PetscMPIInt    rank, size;
1740:   PetscInt       eDof,vDof;
1741:   Mat            j11,j12,j21,j22,bA[2][2];
1742:   MPI_Comm       comm;
1743:   ISLocalToGlobalMapping eISMap,vISMap;

1746:   PetscObjectGetComm((PetscObject)dm,&comm);
1747:   MPI_Comm_rank(comm,&rank);
1748:   MPI_Comm_size(comm,&size);

1750:   PetscSectionGetConstrainedStorageSize(network->edge.GlobalDofSection,&eDof);
1751:   PetscSectionGetConstrainedStorageSize(network->vertex.GlobalDofSection,&vDof);

1753:   MatCreate(comm, &j11);
1754:   MatSetSizes(j11, eDof, eDof, PETSC_DETERMINE, PETSC_DETERMINE);
1755:   MatSetType(j11, MATMPIAIJ);

1757:   MatCreate(comm, &j12);
1758:   MatSetSizes(j12, eDof, vDof, PETSC_DETERMINE ,PETSC_DETERMINE);
1759:   MatSetType(j12, MATMPIAIJ);

1761:   MatCreate(comm, &j21);
1762:   MatSetSizes(j21, vDof, eDof, PETSC_DETERMINE, PETSC_DETERMINE);
1763:   MatSetType(j21, MATMPIAIJ);

1765:   MatCreate(comm, &j22);
1766:   MatSetSizes(j22, vDof, vDof, PETSC_DETERMINE, PETSC_DETERMINE);
1767:   MatSetType(j22, MATMPIAIJ);

1769:   bA[0][0] = j11;
1770:   bA[0][1] = j12;
1771:   bA[1][0] = j21;
1772:   bA[1][1] = j22;

1774:   CreateSubGlobalToLocalMapping_private(network->edge.GlobalDofSection,network->edge.DofSection,&eISMap);
1775:   CreateSubGlobalToLocalMapping_private(network->vertex.GlobalDofSection,network->vertex.DofSection,&vISMap);

1777:   MatSetLocalToGlobalMapping(j11,eISMap,eISMap);
1778:   MatSetLocalToGlobalMapping(j12,eISMap,vISMap);
1779:   MatSetLocalToGlobalMapping(j21,vISMap,eISMap);
1780:   MatSetLocalToGlobalMapping(j22,vISMap,vISMap);

1782:   MatSetUp(j11);
1783:   MatSetUp(j12);
1784:   MatSetUp(j21);
1785:   MatSetUp(j22);

1787:   MatCreateNest(comm,2,NULL,2,NULL,&bA[0][0],J);
1788:   MatSetUp(*J);
1789:   MatNestSetVecType(*J,VECNEST);
1790:   MatDestroy(&j11);
1791:   MatDestroy(&j12);
1792:   MatDestroy(&j21);
1793:   MatDestroy(&j22);

1795:   MatAssemblyBegin(*J,MAT_FINAL_ASSEMBLY);
1796:   MatAssemblyEnd(*J,MAT_FINAL_ASSEMBLY);
1797:   MatSetOption(*J,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);

1799:   /* Free structures */
1800:   ISLocalToGlobalMappingDestroy(&eISMap);
1801:   ISLocalToGlobalMappingDestroy(&vISMap);
1802:   return(0);
1803: }

1805: PetscErrorCode DMCreateMatrix_Network(DM dm,Mat *J)
1806: {
1808:   DM_Network     *network = (DM_Network*)dm->data;
1809:   PetscInt       eStart,eEnd,vStart,vEnd,rstart,nrows,*rows,localSize;
1810:   PetscInt       cstart,ncols,j,e,v;
1811:   PetscBool      ghost,ghost_vc,ghost2,isNest;
1812:   Mat            Juser;
1813:   PetscSection   sectionGlobal;
1814:   PetscInt       nedges,*vptr=NULL,vc,*rows_v; /* suppress maybe-uninitialized warning */
1815:   const PetscInt *edges,*cone;
1816:   MPI_Comm       comm;
1817:   MatType        mtype;
1818:   Vec            vd_nz,vo_nz;
1819:   PetscInt       *dnnz,*onnz;
1820:   PetscScalar    *vdnz,*vonz;

1823:   mtype = dm->mattype;
1824:   PetscStrcmp(mtype,MATNEST,&isNest);
1825:   if (isNest) {
1826:     DMCreateMatrix_Network_Nest(dm,J);
1827:     MatSetDM(*J,dm);
1828:     return(0);
1829:   }

1831:   if (!network->userEdgeJacobian && !network->userVertexJacobian) {
1832:     /* user does not provide Jacobian blocks */
1833:     DMCreateMatrix_Plex(network->plex,J);
1834:     MatSetDM(*J,dm);
1835:     return(0);
1836:   }

1838:   MatCreate(PetscObjectComm((PetscObject)dm),J);
1839:   DMGetGlobalSection(network->plex,&sectionGlobal);
1840:   PetscSectionGetConstrainedStorageSize(sectionGlobal,&localSize);
1841:   MatSetSizes(*J,localSize,localSize,PETSC_DETERMINE,PETSC_DETERMINE);

1843:   MatSetType(*J,MATAIJ);
1844:   MatSetFromOptions(*J);

1846:   /* (1) Set matrix preallocation */
1847:   /*------------------------------*/
1848:   PetscObjectGetComm((PetscObject)dm,&comm);
1849:   VecCreate(comm,&vd_nz);
1850:   VecSetSizes(vd_nz,localSize,PETSC_DECIDE);
1851:   VecSetFromOptions(vd_nz);
1852:   VecSet(vd_nz,0.0);
1853:   VecDuplicate(vd_nz,&vo_nz);

1855:   /* Set preallocation for edges */
1856:   /*-----------------------------*/
1857:   DMNetworkGetEdgeRange(dm,&eStart,&eEnd);

1859:   PetscMalloc1(localSize,&rows);
1860:   for (e=eStart; e<eEnd; e++) {
1861:     /* Get row indices */
1862:     DMNetworkGetVariableGlobalOffset(dm,e,&rstart);
1863:     DMNetworkGetNumVariables(dm,e,&nrows);
1864:     if (nrows) {
1865:       for (j=0; j<nrows; j++) rows[j] = j + rstart;

1867:       /* Set preallocation for conntected vertices */
1868:       DMNetworkGetConnectedVertices(dm,e,&cone);
1869:       for (v=0; v<2; v++) {
1870:         DMNetworkGetNumVariables(dm,cone[v],&ncols);

1872:         if (network->Je) {
1873:           Juser = network->Je[3*e+1+v]; /* Jacobian(e,v) */
1874:         } else Juser = NULL;
1875:         DMNetworkIsGhostVertex(dm,cone[v],&ghost);
1876:         MatSetPreallocationblock_private(Juser,nrows,rows,ncols,ghost,vd_nz,vo_nz);
1877:       }

1879:       /* Set preallocation for edge self */
1880:       cstart = rstart;
1881:       if (network->Je) {
1882:         Juser = network->Je[3*e]; /* Jacobian(e,e) */
1883:       } else Juser = NULL;
1884:       MatSetPreallocationblock_private(Juser,nrows,rows,nrows,PETSC_FALSE,vd_nz,vo_nz);
1885:     }
1886:   }

1888:   /* Set preallocation for vertices */
1889:   /*--------------------------------*/
1890:   DMNetworkGetVertexRange(dm,&vStart,&vEnd);
1891:   if (vEnd - vStart) vptr = network->Jvptr;

1893:   for (v=vStart; v<vEnd; v++) {
1894:     /* Get row indices */
1895:     DMNetworkGetVariableGlobalOffset(dm,v,&rstart);
1896:     DMNetworkGetNumVariables(dm,v,&nrows);
1897:     if (!nrows) continue;

1899:     DMNetworkIsGhostVertex(dm,v,&ghost);
1900:     if (ghost) {
1901:       PetscMalloc1(nrows,&rows_v);
1902:     } else {
1903:       rows_v = rows;
1904:     }

1906:     for (j=0; j<nrows; j++) rows_v[j] = j + rstart;

1908:     /* Get supporting edges and connected vertices */
1909:     DMNetworkGetSupportingEdges(dm,v,&nedges,&edges);

1911:     for (e=0; e<nedges; e++) {
1912:       /* Supporting edges */
1913:       DMNetworkGetVariableGlobalOffset(dm,edges[e],&cstart);
1914:       DMNetworkGetNumVariables(dm,edges[e],&ncols);

1916:       if (network->Jv) {
1917:         Juser = network->Jv[vptr[v-vStart]+2*e+1]; /* Jacobian(v,e) */
1918:       } else Juser = NULL;
1919:       MatSetPreallocationblock_private(Juser,nrows,rows_v,ncols,ghost,vd_nz,vo_nz);

1921:       /* Connected vertices */
1922:       DMNetworkGetConnectedVertices(dm,edges[e],&cone);
1923:       vc = (v == cone[0]) ? cone[1]:cone[0];
1924:       DMNetworkIsGhostVertex(dm,vc,&ghost_vc);

1926:       DMNetworkGetNumVariables(dm,vc,&ncols);

1928:       if (network->Jv) {
1929:         Juser = network->Jv[vptr[v-vStart]+2*e+2]; /* Jacobian(v,vc) */
1930:       } else Juser = NULL;
1931:       if (ghost_vc||ghost) {
1932:         ghost2 = PETSC_TRUE;
1933:       } else {
1934:         ghost2 = PETSC_FALSE;
1935:       }
1936:       MatSetPreallocationblock_private(Juser,nrows,rows_v,ncols,ghost2,vd_nz,vo_nz);
1937:     }

1939:     /* Set preallocation for vertex self */
1940:     DMNetworkIsGhostVertex(dm,v,&ghost);
1941:     if (!ghost) {
1942:       DMNetworkGetVariableGlobalOffset(dm,v,&cstart);
1943:       if (network->Jv) {
1944:         Juser = network->Jv[vptr[v-vStart]]; /* Jacobian(v,v) */
1945:       } else Juser = NULL;
1946:       MatSetPreallocationblock_private(Juser,nrows,rows_v,nrows,PETSC_FALSE,vd_nz,vo_nz);
1947:     }
1948:     if (ghost) {
1949:       PetscFree(rows_v);
1950:     }
1951:   }

1953:   VecAssemblyBegin(vd_nz);
1954:   VecAssemblyBegin(vo_nz);

1956:   PetscMalloc2(localSize,&dnnz,localSize,&onnz);

1958:   VecAssemblyEnd(vd_nz);
1959:   VecAssemblyEnd(vo_nz);

1961:   VecGetArray(vd_nz,&vdnz);
1962:   VecGetArray(vo_nz,&vonz);
1963:   for (j=0; j<localSize; j++) {
1964:     dnnz[j] = (PetscInt)PetscRealPart(vdnz[j]);
1965:     onnz[j] = (PetscInt)PetscRealPart(vonz[j]);
1966:   }
1967:   VecRestoreArray(vd_nz,&vdnz);
1968:   VecRestoreArray(vo_nz,&vonz);
1969:   VecDestroy(&vd_nz);
1970:   VecDestroy(&vo_nz);

1972:   MatSeqAIJSetPreallocation(*J,0,dnnz);
1973:   MatMPIAIJSetPreallocation(*J,0,dnnz,0,onnz);
1974:   MatSetOption(*J,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);

1976:   PetscFree2(dnnz,onnz);

1978:   /* (2) Set matrix entries for edges */
1979:   /*----------------------------------*/
1980:   for (e=eStart; e<eEnd; e++) {
1981:     /* Get row indices */
1982:     DMNetworkGetVariableGlobalOffset(dm,e,&rstart);
1983:     DMNetworkGetNumVariables(dm,e,&nrows);
1984:     if (nrows) {
1985:       for (j=0; j<nrows; j++) rows[j] = j + rstart;

1987:       /* Set matrix entries for conntected vertices */
1988:       DMNetworkGetConnectedVertices(dm,e,&cone);
1989:       for (v=0; v<2; v++) {
1990:         DMNetworkGetVariableGlobalOffset(dm,cone[v],&cstart);
1991:         DMNetworkGetNumVariables(dm,cone[v],&ncols);

1993:         if (network->Je) {
1994:           Juser = network->Je[3*e+1+v]; /* Jacobian(e,v) */
1995:         } else Juser = NULL;
1996:         MatSetblock_private(Juser,nrows,rows,ncols,cstart,J);
1997:       }

1999:       /* Set matrix entries for edge self */
2000:       cstart = rstart;
2001:       if (network->Je) {
2002:         Juser = network->Je[3*e]; /* Jacobian(e,e) */
2003:       } else Juser = NULL;
2004:       MatSetblock_private(Juser,nrows,rows,nrows,cstart,J);
2005:     }
2006:   }

2008:   /* Set matrix entries for vertices */
2009:   /*---------------------------------*/
2010:   for (v=vStart; v<vEnd; v++) {
2011:     /* Get row indices */
2012:     DMNetworkGetVariableGlobalOffset(dm,v,&rstart);
2013:     DMNetworkGetNumVariables(dm,v,&nrows);
2014:     if (!nrows) continue;

2016:     DMNetworkIsGhostVertex(dm,v,&ghost);
2017:     if (ghost) {
2018:       PetscMalloc1(nrows,&rows_v);
2019:     } else {
2020:       rows_v = rows;
2021:     }
2022:     for (j=0; j<nrows; j++) rows_v[j] = j + rstart;

2024:     /* Get supporting edges and connected vertices */
2025:     DMNetworkGetSupportingEdges(dm,v,&nedges,&edges);

2027:     for (e=0; e<nedges; e++) {
2028:       /* Supporting edges */
2029:       DMNetworkGetVariableGlobalOffset(dm,edges[e],&cstart);
2030:       DMNetworkGetNumVariables(dm,edges[e],&ncols);

2032:       if (network->Jv) {
2033:         Juser = network->Jv[vptr[v-vStart]+2*e+1]; /* Jacobian(v,e) */
2034:       } else Juser = NULL;
2035:       MatSetblock_private(Juser,nrows,rows_v,ncols,cstart,J);

2037:       /* Connected vertices */
2038:       DMNetworkGetConnectedVertices(dm,edges[e],&cone);
2039:       vc = (v == cone[0]) ? cone[1]:cone[0];

2041:       DMNetworkGetVariableGlobalOffset(dm,vc,&cstart);
2042:       DMNetworkGetNumVariables(dm,vc,&ncols);

2044:       if (network->Jv) {
2045:         Juser = network->Jv[vptr[v-vStart]+2*e+2]; /* Jacobian(v,vc) */
2046:       } else Juser = NULL;
2047:       MatSetblock_private(Juser,nrows,rows_v,ncols,cstart,J);
2048:     }

2050:     /* Set matrix entries for vertex self */
2051:     if (!ghost) {
2052:       DMNetworkGetVariableGlobalOffset(dm,v,&cstart);
2053:       if (network->Jv) {
2054:         Juser = network->Jv[vptr[v-vStart]]; /* Jacobian(v,v) */
2055:       } else Juser = NULL;
2056:       MatSetblock_private(Juser,nrows,rows_v,nrows,cstart,J);
2057:     }
2058:     if (ghost) {
2059:       PetscFree(rows_v);
2060:     }
2061:   }
2062:   PetscFree(rows);

2064:   MatAssemblyBegin(*J,MAT_FINAL_ASSEMBLY);
2065:   MatAssemblyEnd(*J,MAT_FINAL_ASSEMBLY);

2067:   MatSetDM(*J,dm);
2068:   return(0);
2069: }

2071: PetscErrorCode DMDestroy_Network(DM dm)
2072: {
2074:   DM_Network     *network = (DM_Network*)dm->data;
2075:   PetscInt       j;

2078:   if (--network->refct > 0) return(0);
2079:   if (network->Je) {
2080:     PetscFree(network->Je);
2081:   }
2082:   if (network->Jv) {
2083:     PetscFree(network->Jvptr);
2084:     PetscFree(network->Jv);
2085:   }

2087:   ISLocalToGlobalMappingDestroy(&network->vertex.mapping);
2088:   PetscSectionDestroy(&network->vertex.DofSection);
2089:   PetscSectionDestroy(&network->vertex.GlobalDofSection);
2090:   if (network->vltog) {
2091:     PetscFree(network->vltog);
2092:   }
2093:   if (network->vertex.sf) {
2094:     PetscSFDestroy(&network->vertex.sf);
2095:   }
2096:   /* edge */
2097:   ISLocalToGlobalMappingDestroy(&network->edge.mapping);
2098:   PetscSectionDestroy(&network->edge.DofSection);
2099:   PetscSectionDestroy(&network->edge.GlobalDofSection);
2100:   if (network->edge.sf) {
2101:     PetscSFDestroy(&network->edge.sf);
2102:   }
2103:   DMDestroy(&network->plex);
2104:   PetscSectionDestroy(&network->DataSection);
2105:   PetscSectionDestroy(&network->DofSection);

2107:   for (j=0; j<network->nsubnet; j++) {
2108:     PetscFree(network->subnet[j].edges);
2109:   }
2110:   PetscFree(network->subnetvtx);

2112:   PetscFree(network->subnet);
2113:   PetscFree(network->componentdataarray);
2114:   PetscFree2(network->header,network->cvalue);
2115:   PetscFree(network);
2116:   return(0);
2117: }

2119: PetscErrorCode DMView_Network(DM dm,PetscViewer viewer)
2120: {
2122:   DM_Network     *network = (DM_Network*)dm->data;
2123:   PetscBool      iascii;
2124:   PetscMPIInt    rank;
2125:   PetscInt       p,nsubnet;

2128:   if (!dm->setupcalled) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONGSTATE,"Must call DMSetUp() first");
2129:   MPI_Comm_rank(PetscObjectComm((PetscObject)dm),&rank);
2132:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);
2133:   if (iascii) {
2134:     const PetscInt    *cone,*vtx,*edges;
2135:     PetscInt          vfrom,vto,i,j,nv,ne;

2137:     nsubnet = network->nsubnet - network->ncsubnet; /* num of subnetworks */
2138:     PetscViewerASCIIPushSynchronized(viewer);
2139:     PetscViewerASCIISynchronizedPrintf(viewer, "  [%d] nsubnet: %D; nsubnetCouple: %D; nEdges: %D; nVertices: %D\n",rank,nsubnet,network->ncsubnet,network->nEdges,network->nVertices);

2141:     for (i=0; i<nsubnet; i++) {
2142:       DMNetworkGetSubnetworkInfo(dm,i,&nv,&ne,&vtx,&edges);
2143:       if (ne) {
2144:         PetscViewerASCIISynchronizedPrintf(viewer, "     Subnet %D: nEdges %D, nVertices %D\n",i,ne,nv);
2145:         for (j=0; j<ne; j++) {
2146:           p = edges[j];
2147:           DMNetworkGetConnectedVertices(dm,p,&cone);
2148:           DMNetworkGetGlobalVertexIndex(dm,cone[0],&vfrom);
2149:           DMNetworkGetGlobalVertexIndex(dm,cone[1],&vto);
2150:           DMNetworkGetGlobalEdgeIndex(dm,edges[j],&p);
2151:           PetscViewerASCIISynchronizedPrintf(viewer, "       edge %D: %D----> %D\n",p,vfrom,vto);
2152:         }
2153:       }
2154:     }
2155:     /* Coupling subnets */
2156:     nsubnet = network->nsubnet;
2157:     for (; i<nsubnet; i++) {
2158:       DMNetworkGetSubnetworkInfo(dm,i,&nv,&ne,&vtx,&edges);
2159:       if (ne) {
2160:         PetscViewerASCIISynchronizedPrintf(viewer, "     Subnet %D (couple): nEdges %D, nVertices %D\n",i,ne,nv);
2161:         for (j=0; j<ne; j++) {
2162:           p = edges[j];
2163:           DMNetworkGetConnectedVertices(dm,p,&cone);
2164:           DMNetworkGetGlobalVertexIndex(dm,cone[0],&vfrom);
2165:           DMNetworkGetGlobalVertexIndex(dm,cone[1],&vto);
2166:           DMNetworkGetGlobalEdgeIndex(dm,edges[j],&p);
2167:           PetscViewerASCIISynchronizedPrintf(viewer, "       edge %D: %D----> %D\n",p,vfrom,vto);
2168:         }
2169:       }
2170:     }
2171:     PetscViewerFlush(viewer);
2172:     PetscViewerASCIIPopSynchronized(viewer);
2173:   } else SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Viewer type %s not yet supported for DMNetwork writing", ((PetscObject)viewer)->type_name);
2174:   return(0);
2175: }

2177: PetscErrorCode DMGlobalToLocalBegin_Network(DM dm, Vec g, InsertMode mode, Vec l)
2178: {
2180:   DM_Network     *network = (DM_Network*)dm->data;

2183:   DMGlobalToLocalBegin(network->plex,g,mode,l);
2184:   return(0);
2185: }

2187: PetscErrorCode DMGlobalToLocalEnd_Network(DM dm, Vec g, InsertMode mode, Vec l)
2188: {
2190:   DM_Network     *network = (DM_Network*)dm->data;

2193:   DMGlobalToLocalEnd(network->plex,g,mode,l);
2194:   return(0);
2195: }

2197: PetscErrorCode DMLocalToGlobalBegin_Network(DM dm, Vec l, InsertMode mode, Vec g)
2198: {
2200:   DM_Network     *network = (DM_Network*)dm->data;

2203:   DMLocalToGlobalBegin(network->plex,l,mode,g);
2204:   return(0);
2205: }

2207: PetscErrorCode DMLocalToGlobalEnd_Network(DM dm, Vec l, InsertMode mode, Vec g)
2208: {
2210:   DM_Network     *network = (DM_Network*)dm->data;

2213:   DMLocalToGlobalEnd(network->plex,l,mode,g);
2214:   return(0);
2215: }

2217: /*@
2218:   DMNetworkGetVertexLocalToGlobalOrdering - Get vertex global index

2220:   Not collective

2222:   Input Parameters:
2223: + dm - the dm object
2224: - vloc - local vertex ordering, start from 0

2226:   Output Parameters:
2227: .  vg  - global vertex ordering, start from 0

2229:   Level: advanced

2231: .seealso: DMNetworkSetVertexLocalToGlobalOrdering()
2232: @*/
2233: PetscErrorCode DMNetworkGetVertexLocalToGlobalOrdering(DM dm,PetscInt vloc,PetscInt *vg)
2234: {
2235:   DM_Network  *network = (DM_Network*)dm->data;
2236:   PetscInt    *vltog = network->vltog;

2239:   if (!vltog) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_ARG_WRONGSTATE,"Must call DMNetworkSetVertexLocalToGlobalOrdering() first");
2240:   *vg = vltog[vloc];
2241:   return(0);
2242: }

2244: /*@
2245:   DMNetworkSetVertexLocalToGlobalOrdering - Create and setup vertex local to global map

2247:   Collective

2249:   Input Parameters:
2250: . dm - the dm object

2252:   Level: advanced

2254: .seealso: DMNetworkGetGlobalVertexIndex()
2255: @*/
2256: PetscErrorCode DMNetworkSetVertexLocalToGlobalOrdering(DM dm)
2257: {
2258:   PetscErrorCode    ierr;
2259:   DM_Network        *network=(DM_Network*)dm->data;
2260:   MPI_Comm          comm;
2261:   PetscMPIInt       rank,size,*displs,*recvcounts,remoterank;
2262:   PetscBool         ghost;
2263:   PetscInt          *vltog,nroots,nleaves,i,*vrange,k,N,lidx;
2264:   const PetscSFNode *iremote;
2265:   PetscSF           vsf;
2266:   Vec               Vleaves,Vleaves_seq;
2267:   VecScatter        ctx;
2268:   PetscScalar       *varr,val;
2269:   const PetscScalar *varr_read;

2272:   PetscObjectGetComm((PetscObject)dm,&comm);
2273:   MPI_Comm_size(comm,&size);
2274:   MPI_Comm_rank(comm,&rank);

2276:   if (size == 1) {
2277:     nroots = network->vEnd - network->vStart;
2278:     PetscMalloc1(nroots, &vltog);
2279:     for (i=0; i<nroots; i++) vltog[i] = i;
2280:     network->vltog = vltog;
2281:     return(0);
2282:   }

2284:   if (!network->distributecalled) SETERRQ(comm, PETSC_ERR_ARG_WRONGSTATE,"Must call DMNetworkDistribute() first");
2285:   if (network->vltog) {
2286:     PetscFree(network->vltog);
2287:   }

2289:   DMNetworkSetSubMap_private(network->vStart,network->vEnd,&network->vertex.mapping);
2290:   PetscSFGetSubSF(network->plex->sf, network->vertex.mapping, &network->vertex.sf);
2291:   vsf = network->vertex.sf;

2293:   PetscMalloc3(size+1,&vrange,size+1,&displs,size,&recvcounts);
2294:   PetscSFGetGraph(vsf,&nroots,&nleaves,NULL,&iremote);

2296:   for (i=0; i<size; i++) { displs[i] = i; recvcounts[i] = 1;}

2298:   i         = nroots - nleaves; /* local number of vertices, excluding ghosts */
2299:   vrange[0] = 0;
2300:   MPI_Allgatherv(&i,1,MPIU_INT,vrange+1,recvcounts,displs,MPIU_INT,comm);
2301:   for (i=2; i<size+1; i++) {vrange[i] += vrange[i-1];}

2303:   PetscMalloc1(nroots, &vltog);
2304:   network->vltog = vltog;

2306:   /* Set vltog for non-ghost vertices */
2307:   k = 0;
2308:   for (i=0; i<nroots; i++) {
2309:     DMNetworkIsGhostVertex(dm,i+network->vStart,&ghost);
2310:     if (ghost) continue;
2311:     vltog[i] = vrange[rank] + k++;
2312:   }
2313:   PetscFree3(vrange,displs,recvcounts);

2315:   /* Set vltog for ghost vertices */
2316:   /* (a) create parallel Vleaves and sequential Vleaves_seq to convert local iremote[*].index to global index */
2317:   VecCreate(comm,&Vleaves);
2318:   VecSetSizes(Vleaves,2*nleaves,PETSC_DETERMINE);
2319:   VecSetFromOptions(Vleaves);
2320:   VecGetArray(Vleaves,&varr);
2321:   for (i=0; i<nleaves; i++) {
2322:     varr[2*i]   = (PetscScalar)(iremote[i].rank);  /* rank of remote process */
2323:     varr[2*i+1] = (PetscScalar)(iremote[i].index); /* local index in remote process */
2324:   }
2325:   VecRestoreArray(Vleaves,&varr);

2327:   /* (b) scatter local info to remote processes via VecScatter() */
2328:   VecScatterCreateToAll(Vleaves,&ctx,&Vleaves_seq);
2329:   VecScatterBegin(ctx,Vleaves,Vleaves_seq,INSERT_VALUES,SCATTER_FORWARD);
2330:   VecScatterEnd(ctx,Vleaves,Vleaves_seq,INSERT_VALUES,SCATTER_FORWARD);

2332:   /* (c) convert local indices to global indices in parallel vector Vleaves */
2333:   VecGetSize(Vleaves_seq,&N);
2334:   VecGetArrayRead(Vleaves_seq,&varr_read);
2335:   for (i=0; i<N; i+=2) {
2336:     remoterank = (PetscMPIInt)PetscRealPart(varr_read[i]);
2337:     if (remoterank == rank) {
2338:       k = i+1; /* row number */
2339:       lidx = (PetscInt)PetscRealPart(varr_read[i+1]);
2340:       val  = (PetscScalar)vltog[lidx]; /* global index for non-ghost vertex computed above */
2341:       VecSetValues(Vleaves,1,&k,&val,INSERT_VALUES);
2342:     }
2343:   }
2344:   VecRestoreArrayRead(Vleaves_seq,&varr_read);
2345:   VecAssemblyBegin(Vleaves);
2346:   VecAssemblyEnd(Vleaves);

2348:   /* (d) Set vltog for ghost vertices by copying local values of Vleaves */
2349:   VecGetArrayRead(Vleaves,&varr_read);
2350:   k = 0;
2351:   for (i=0; i<nroots; i++) {
2352:     DMNetworkIsGhostVertex(dm,i+network->vStart,&ghost);
2353:     if (!ghost) continue;
2354:     vltog[i] = (PetscInt)PetscRealPart(varr_read[2*k+1]); k++;
2355:   }
2356:   VecRestoreArrayRead(Vleaves,&varr_read);

2358:   VecDestroy(&Vleaves);
2359:   VecDestroy(&Vleaves_seq);
2360:   VecScatterDestroy(&ctx);
2361:   return(0);
2362: }