#include #include <../src/sys/classes/viewer/impls/vtk/vtkvimpl.h> typedef struct { PetscInt nvertices; PetscInt ncells; PetscInt nconn; /* number of entries in cell->vertex connectivity array */ } PieceInfo; #if defined(PETSC_USE_REAL_SINGLE) static const char precision[] = "Float32"; #elif defined(PETSC_USE_REAL_DOUBLE) static const char precision[] = "Float64"; #else static const char precision[] = "UnknownPrecision"; #endif static PetscErrorCode TransferWrite(PetscViewer viewer,FILE *fp,PetscMPIInt srank,PetscMPIInt root,const void *send,void *recv,PetscMPIInt count,MPI_Datatype mpidatatype,PetscMPIInt tag) { PetscMPIInt rank; PetscErrorCode ierr; MPI_Comm comm; PetscFunctionBegin; ierr = PetscObjectGetComm((PetscObject)viewer,&comm);CHKERRQ(ierr); ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); if (rank == srank && rank != root) { ierr = MPI_Send((void*)send,count,mpidatatype,root,tag,comm);CHKERRQ(ierr); } else if (rank == root) { const void *buffer; if (root == srank) { /* self */ buffer = send; } else { MPI_Status status; PetscMPIInt nrecv; ierr = MPI_Recv(recv,count,mpidatatype,srank,tag,comm,&status);CHKERRQ(ierr); ierr = MPI_Get_count(&status,mpidatatype,&nrecv);CHKERRQ(ierr); if (count != nrecv) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Array size mismatch"); buffer = recv; } ierr = PetscViewerVTKFWrite(viewer,fp,buffer,count,mpidatatype);CHKERRQ(ierr); } PetscFunctionReturn(0); } static PetscErrorCode DMPlexGetVTKConnectivity(DM dm, PetscBool localized, PieceInfo *piece,PetscVTKInt **oconn,PetscVTKInt **ooffsets,PetscVTKType **otypes) { PetscErrorCode ierr; PetscSection coordSection; PetscVTKInt *conn,*offsets; PetscVTKType *types; PetscInt dim,vStart,vEnd,cStart,cEnd,pStart,pEnd,cellHeight,numLabelCells,hasLabel,c,v,countcell,countconn; PetscFunctionBegin; ierr = PetscMalloc3(piece->nconn,&conn,piece->ncells,&offsets,piece->ncells,&types);CHKERRQ(ierr); ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); ierr = DMGetDimension(dm,&dim);CHKERRQ(ierr); ierr = DMPlexGetChart(dm,&pStart,&pEnd);CHKERRQ(ierr); ierr = DMPlexGetVTKCellHeight(dm, &cellHeight);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd);CHKERRQ(ierr); ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); ierr = DMGetStratumSize(dm, "vtk", 1, &numLabelCells);CHKERRQ(ierr); hasLabel = numLabelCells > 0 ? PETSC_TRUE : PETSC_FALSE; countcell = 0; countconn = 0; for (c = cStart; c < cEnd; ++c) { PetscInt nverts,dof = 0,celltype,startoffset,nC=0; if (hasLabel) { PetscInt value; ierr = DMGetLabelValue(dm, "vtk", c, &value);CHKERRQ(ierr); if (value != 1) continue; } startoffset = countconn; if (localized) { ierr = PetscSectionGetDof(coordSection, c, &dof);CHKERRQ(ierr); } if (!dof) { PetscInt *closure = NULL; PetscInt closureSize; ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); for (v = 0; v < closureSize*2; v += 2) { if ((closure[v] >= vStart) && (closure[v] < vEnd)) { if (!localized) conn[countconn++] = closure[v] - vStart; else conn[countconn++] = startoffset + nC; ++nC; } } ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); } else { for (nC = 0; nC < dof/dim; nC++) conn[countconn++] = startoffset + nC; } ierr = DMPlexInvertCell(dim, nC, &conn[countconn-nC]);CHKERRQ(ierr); offsets[countcell] = countconn; nverts = countconn - startoffset; ierr = DMPlexVTKGetCellType_Internal(dm,dim,nverts,&celltype);CHKERRQ(ierr); types[countcell] = celltype; countcell++; } if (countcell != piece->ncells) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Inconsistent cell count"); if (countconn != piece->nconn) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Inconsistent connectivity count"); *oconn = conn; *ooffsets = offsets; *otypes = types; PetscFunctionReturn(0); } /* Write all fields that have been provided to the viewer Multi-block XML format with binary appended data. */ PetscErrorCode DMPlexVTKWriteAll_VTU(DM dm,PetscViewer viewer) { MPI_Comm comm; PetscSection coordSection; PetscViewer_VTK *vtk = (PetscViewer_VTK*)viewer->data; PetscViewerVTKObjectLink link; FILE *fp; PetscMPIInt rank,size,tag; PetscErrorCode ierr; PetscInt dimEmbed,cellHeight,cStart,cEnd,vStart,vEnd,numLabelCells,hasLabel,c,v,r,i; PetscBool localized; PieceInfo piece,*gpiece = NULL; void *buffer = NULL; PetscFunctionBegin; ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); #if defined(PETSC_USE_COMPLEX) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"Complex values not supported"); #endif ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); tag = ((PetscObject)viewer)->tag; ierr = PetscFOpen(comm,vtk->filename,"wb",&fp);CHKERRQ(ierr); ierr = PetscFPrintf(comm,fp,"\n");CHKERRQ(ierr); #if defined(PETSC_WORDS_BIGENDIAN) ierr = PetscFPrintf(comm,fp,"\n");CHKERRQ(ierr); #else ierr = PetscFPrintf(comm,fp,"\n");CHKERRQ(ierr); #endif ierr = PetscFPrintf(comm,fp," \n");CHKERRQ(ierr); ierr = DMGetCoordinateDim(dm, &dimEmbed);CHKERRQ(ierr); ierr = DMPlexGetVTKCellHeight(dm, &cellHeight);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd);CHKERRQ(ierr); ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); ierr = DMGetStratumSize(dm, "vtk", 1, &numLabelCells);CHKERRQ(ierr); ierr = DMGetCoordinatesLocalized(dm, &localized);CHKERRQ(ierr); ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); hasLabel = numLabelCells > 0 ? PETSC_TRUE : PETSC_FALSE; piece.nvertices = 0; piece.ncells = 0; piece.nconn = 0; if (!localized) piece.nvertices = vEnd - vStart; for (c = cStart; c < cEnd; ++c) { PetscInt dof = 0; if (hasLabel) { PetscInt value; ierr = DMGetLabelValue(dm, "vtk", c, &value);CHKERRQ(ierr); if (value != 1) continue; } if (localized) { ierr = PetscSectionGetDof(coordSection, c, &dof);CHKERRQ(ierr); } if (!dof) { PetscInt *closure = NULL; PetscInt closureSize; ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); for (v = 0; v < closureSize*2; v += 2) { if ((closure[v] >= vStart) && (closure[v] < vEnd)) { piece.nconn++; if (localized) piece.nvertices++; } } ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); } else { piece.nvertices += dof/dimEmbed; piece.nconn += dof/dimEmbed; } piece.ncells++; } if (!rank) {ierr = PetscMalloc1(size,&gpiece);CHKERRQ(ierr);} ierr = MPI_Gather((PetscInt*)&piece,sizeof(piece)/sizeof(PetscInt),MPIU_INT,(PetscInt*)gpiece,sizeof(piece)/sizeof(PetscInt),MPIU_INT,0,comm);CHKERRQ(ierr); /* * Write file header */ if (!rank) { PetscInt boffset = 0; for (r=0; r\n",gpiece[r].nvertices,gpiece[r].ncells);CHKERRQ(ierr); /* Coordinate positions */ ierr = PetscFPrintf(PETSC_COMM_SELF,fp," \n");CHKERRQ(ierr); ierr = PetscFPrintf(PETSC_COMM_SELF,fp," \n",precision,boffset);CHKERRQ(ierr); boffset += gpiece[r].nvertices*3*sizeof(PetscScalar) + sizeof(int); ierr = PetscFPrintf(PETSC_COMM_SELF,fp," \n");CHKERRQ(ierr); /* Cell connectivity */ ierr = PetscFPrintf(PETSC_COMM_SELF,fp," \n");CHKERRQ(ierr); ierr = PetscFPrintf(PETSC_COMM_SELF,fp," \n",boffset);CHKERRQ(ierr); boffset += gpiece[r].nconn*sizeof(PetscInt) + sizeof(int); ierr = PetscFPrintf(PETSC_COMM_SELF,fp," \n",boffset);CHKERRQ(ierr); boffset += gpiece[r].ncells*sizeof(PetscInt) + sizeof(int); ierr = PetscFPrintf(PETSC_COMM_SELF,fp," \n",boffset);CHKERRQ(ierr); boffset += gpiece[r].ncells*sizeof(unsigned char) + sizeof(int); ierr = PetscFPrintf(PETSC_COMM_SELF,fp," \n");CHKERRQ(ierr); /* * Cell Data headers */ ierr = PetscFPrintf(PETSC_COMM_SELF,fp," \n");CHKERRQ(ierr); ierr = PetscFPrintf(PETSC_COMM_SELF,fp," \n",boffset);CHKERRQ(ierr); boffset += gpiece[r].ncells*sizeof(int) + sizeof(int); /* all the vectors */ for (link=vtk->link; link; link=link->next) { Vec X = (Vec)link->vec; PetscInt bs,nfields,field; const char *vecname = ""; if ((link->ft != PETSC_VTK_CELL_FIELD) && (link->ft != PETSC_VTK_CELL_VECTOR_FIELD)) continue; if (((PetscObject)X)->name || link != vtk->link) { /* If the object is already named, use it. If it is past the first link, name it to disambiguate. */ ierr = PetscObjectGetName((PetscObject)X,&vecname);CHKERRQ(ierr); } ierr = PetscSectionGetDof(dm->defaultSection,cStart,&bs);CHKERRQ(ierr); ierr = PetscSectionGetNumFields(dm->defaultSection,&nfields);CHKERRQ(ierr); for (field=0,i=0; field<(nfields?nfields:1); field++) { PetscInt fbs,j; PetscFV fv = NULL; PetscObject f; PetscClassId fClass; const char *fieldname = NULL; char buf[256]; if (nfields) { /* We have user-defined fields/components */ ierr = PetscSectionGetFieldDof(dm->defaultSection,cStart,field,&fbs);CHKERRQ(ierr); ierr = PetscSectionGetFieldName(dm->defaultSection,field,&fieldname);CHKERRQ(ierr); } else fbs = bs; /* Say we have one field with 'bs' components */ ierr = DMGetField(dm,field,&f);CHKERRQ(ierr); ierr = PetscObjectGetClassId(f,&fClass);CHKERRQ(ierr); if (fClass == PETSCFV_CLASSID) { fv = (PetscFV) f; } if (!fieldname) { ierr = PetscSNPrintf(buf,sizeof(buf),"CellField%D",field);CHKERRQ(ierr); fieldname = buf; } for (j=0; j\n",precision,vecname,fieldname,compName,boffset);CHKERRQ(ierr); } else { ierr = PetscFPrintf(comm,fp," \n",precision,vecname,fieldname,j,boffset);CHKERRQ(ierr); } boffset += gpiece[r].ncells*sizeof(PetscScalar) + sizeof(int); i++; } } if (i != bs) SETERRQ2(comm,PETSC_ERR_PLIB,"Total number of field components %D != block size %D",i,bs); } ierr = PetscFPrintf(PETSC_COMM_SELF,fp," \n");CHKERRQ(ierr); /* * Point Data headers */ ierr = PetscFPrintf(PETSC_COMM_SELF,fp," \n");CHKERRQ(ierr); for (link=vtk->link; link; link=link->next) { Vec X = (Vec)link->vec; PetscInt bs,nfields,field; const char *vecname = ""; if ((link->ft != PETSC_VTK_POINT_FIELD) && (link->ft != PETSC_VTK_POINT_VECTOR_FIELD)) continue; if (((PetscObject)X)->name || link != vtk->link) { /* If the object is already named, use it. If it is past the first link, name it to disambiguate. */ ierr = PetscObjectGetName((PetscObject)X,&vecname);CHKERRQ(ierr); } ierr = PetscSectionGetDof(dm->defaultSection,vStart,&bs);CHKERRQ(ierr); ierr = PetscSectionGetNumFields(dm->defaultSection,&nfields);CHKERRQ(ierr); for (field=0,i=0; field<(nfields?nfields:1); field++) { PetscInt fbs,j; const char *fieldname = NULL; char buf[256]; if (nfields) { /* We have user-defined fields/components */ ierr = PetscSectionGetFieldDof(dm->defaultSection,vStart,field,&fbs);CHKERRQ(ierr); ierr = PetscSectionGetFieldName(dm->defaultSection,field,&fieldname);CHKERRQ(ierr); } else fbs = bs; /* Say we have one field with 'bs' components */ if (!fieldname) { ierr = PetscSNPrintf(buf,sizeof(buf),"PointField%D",field);CHKERRQ(ierr); fieldname = buf; } for (j=0; j\n",precision,vecname,fieldname,j,boffset);CHKERRQ(ierr); boffset += gpiece[r].nvertices*sizeof(PetscScalar) + sizeof(int); } } } ierr = PetscFPrintf(PETSC_COMM_SELF,fp," \n");CHKERRQ(ierr); ierr = PetscFPrintf(PETSC_COMM_SELF,fp," \n");CHKERRQ(ierr); } } ierr = PetscFPrintf(comm,fp," \n");CHKERRQ(ierr); ierr = PetscFPrintf(comm,fp," \n");CHKERRQ(ierr); ierr = PetscFPrintf(comm,fp,"_");CHKERRQ(ierr); if (!rank) { PetscInt maxsize = 0; for (r=0; r= vStart) && (closure[v] < vEnd)) { ierr = PetscSectionGetOffset(coordSection, closure[v], &off);CHKERRQ(ierr); if (dimEmbed != 3) { y[cnt*3+0] = x[off+0]; y[cnt*3+1] = (dimEmbed > 1) ? x[off+1] : 0.0; y[cnt*3+2] = 0.0; } else { y[cnt*3+0] = x[off+0]; y[cnt*3+1] = x[off+1]; y[cnt*3+2] = x[off+2]; } cnt++; } } ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); } else { ierr = PetscSectionGetOffset(coordSection, c, &off);CHKERRQ(ierr); if (dimEmbed != 3) { for (i=0; i 1) ? x[off + i*dimEmbed + 1] : 0.0; y[cnt*3+2] = 0.0; cnt++; } } else { for (i=0; i 1) ? x[i*dimEmbed+1] : 0; y[i*3+2] = 0.0; } } } nsend = piece.nvertices*3; ierr = TransferWrite(viewer,fp,r,0,y ? y : x,buffer,nsend,MPIU_SCALAR,tag);CHKERRQ(ierr); ierr = PetscFree(y);CHKERRQ(ierr); ierr = VecRestoreArrayRead(coords,&x);CHKERRQ(ierr); } { /* Connectivity, offsets, types */ PetscVTKInt *connectivity = NULL, *offsets = NULL; PetscVTKType *types = NULL; ierr = DMPlexGetVTKConnectivity(dm,localized,&piece,&connectivity,&offsets,&types);CHKERRQ(ierr); ierr = TransferWrite(viewer,fp,r,0,connectivity,buffer,piece.nconn,MPI_INT,tag);CHKERRQ(ierr); ierr = TransferWrite(viewer,fp,r,0,offsets,buffer,piece.ncells,MPI_INT,tag);CHKERRQ(ierr); ierr = TransferWrite(viewer,fp,r,0,types,buffer,piece.ncells,MPI_CHAR,tag);CHKERRQ(ierr); ierr = PetscFree3(connectivity,offsets,types);CHKERRQ(ierr); } { /* Owners (cell data) */ PetscVTKInt *owners; ierr = PetscMalloc1(piece.ncells,&owners);CHKERRQ(ierr); for (i=0; ilink; link; link=link->next) { Vec X = (Vec)link->vec; const PetscScalar *x; PetscScalar *y; PetscInt bs; if ((link->ft != PETSC_VTK_CELL_FIELD) && (link->ft != PETSC_VTK_CELL_VECTOR_FIELD)) continue; ierr = PetscSectionGetDof(dm->defaultSection,cStart,&bs);CHKERRQ(ierr); ierr = VecGetArrayRead(X,&x);CHKERRQ(ierr); ierr = PetscMalloc1(piece.ncells,&y);CHKERRQ(ierr); for (i=0; ilink; link; link=link->next) { Vec X = (Vec)link->vec; const PetscScalar *x; PetscScalar *y; PetscInt bs; if ((link->ft != PETSC_VTK_POINT_FIELD) && (link->ft != PETSC_VTK_POINT_VECTOR_FIELD)) continue; ierr = PetscSectionGetDof(dm->defaultSection,vStart,&bs);CHKERRQ(ierr); ierr = VecGetArrayRead(X,&x);CHKERRQ(ierr); ierr = PetscMalloc1(piece.nvertices,&y);CHKERRQ(ierr); for (i=0; i= vStart) && (closure[v] < vEnd)) { PetscScalar *xpoint; ierr = DMPlexPointLocalRead(dm,v,x,&xpoint);CHKERRQ(ierr); y[cnt + off++] = xpoint[i]; } } ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); } } if (cnt != piece.nvertices) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Count does not match"); ierr = TransferWrite(viewer,fp,r,0,y,buffer,piece.nvertices,MPIU_SCALAR,tag);CHKERRQ(ierr); } ierr = PetscFree(y);CHKERRQ(ierr); ierr = VecRestoreArrayRead(X,&x);CHKERRQ(ierr); } } else if (!rank) { ierr = TransferWrite(viewer,fp,r,0,NULL,buffer,gpiece[r].nvertices*3,MPIU_SCALAR,tag);CHKERRQ(ierr); /* positions */ ierr = TransferWrite(viewer,fp,r,0,NULL,buffer,gpiece[r].nconn,MPI_INT,tag);CHKERRQ(ierr); /* connectivity */ ierr = TransferWrite(viewer,fp,r,0,NULL,buffer,gpiece[r].ncells,MPI_INT,tag);CHKERRQ(ierr); /* offsets */ ierr = TransferWrite(viewer,fp,r,0,NULL,buffer,gpiece[r].ncells,MPI_CHAR,tag);CHKERRQ(ierr); /* types */ ierr = TransferWrite(viewer,fp,r,0,NULL,buffer,gpiece[r].ncells,MPI_INT,tag);CHKERRQ(ierr); /* owner rank (cells) */ /* all cell data */ for (link=vtk->link; link; link=link->next) { PetscInt bs; if ((link->ft != PETSC_VTK_CELL_FIELD) && (link->ft != PETSC_VTK_CELL_VECTOR_FIELD)) continue; ierr = PetscSectionGetDof(dm->defaultSection,cStart,&bs);CHKERRQ(ierr); for (i=0; ilink; link; link=link->next) { PetscInt bs; if ((link->ft != PETSC_VTK_POINT_FIELD) && (link->ft != PETSC_VTK_POINT_VECTOR_FIELD)) continue; ierr = PetscSectionGetDof(dm->defaultSection,vStart,&bs);CHKERRQ(ierr); for (i=0; i\n");CHKERRQ(ierr); ierr = PetscFPrintf(comm,fp,"\n");CHKERRQ(ierr); ierr = PetscFClose(comm,fp);CHKERRQ(ierr); PetscFunctionReturn(0); }