PetscErrorCode DMDACreate2d(MPI_Comm comm,DMDABoundaryType bx,DMDABoundaryType by,DMDAStencilType stencil_type, PetscInt M,PetscInt N,PetscInt m,PetscInt n,PetscInt dof,PetscInt s,const PetscInt lx[],const PetscInt ly[],DM *da) { PetscErrorCode ierr; PetscFunctionBegin; ierr = DMDACreate(comm, da); CHKERRQ(ierr); ierr = DMDASetDim(*da, 2); CHKERRQ(ierr); ierr = DMDASetSizes(*da, M, N, 1); CHKERRQ(ierr); ierr = DMDASetNumProcs(*da, m, n, PETSC_DECIDE); CHKERRQ(ierr); ierr = DMDASetBoundaryType(*da, bx, by, DMDA_BOUNDARY_NONE); CHKERRQ(ierr); ierr = DMDASetDof(*da, dof); CHKERRQ(ierr); ierr = DMDASetStencilType(*da, stencil_type); CHKERRQ(ierr); ierr = DMDASetStencilWidth(*da, s); CHKERRQ(ierr); ierr = DMDASetOwnershipRanges(*da, lx, ly, NULL); CHKERRQ(ierr); /* This violates the behavior for other classes, but right now users expect negative dimensions to be handled this way */ ierr = DMSetFromOptions(*da); CHKERRQ(ierr); ierr = DMSetUp(*da); CHKERRQ(ierr); ierr = DMViewFromOptions(*da,"-dm_view"); CHKERRQ(ierr); PetscFunctionReturn(0); }
PetscErrorCode DMCreateSubDM_DA(DM dm, PetscInt numFields, PetscInt fields[], IS *is, DM *subdm) { DM_DA *da = (DM_DA*) dm->data; PetscSection section; PetscErrorCode ierr; PetscFunctionBegin; if (subdm) { PetscSF sf; Vec coords; void *ctx; /* Cannot use DMClone since the dof stuff is mixed in. Ugh ierr = DMClone(dm, subdm);CHKERRQ(ierr); */ ierr = DMCreate(PetscObjectComm((PetscObject)dm), subdm);CHKERRQ(ierr); ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr); ierr = DMSetPointSF(*subdm, sf);CHKERRQ(ierr); ierr = DMGetApplicationContext(dm, &ctx);CHKERRQ(ierr); ierr = DMSetApplicationContext(*subdm, ctx);CHKERRQ(ierr); ierr = DMGetCoordinatesLocal(dm, &coords);CHKERRQ(ierr); if (coords) { ierr = DMSetCoordinatesLocal(*subdm, coords);CHKERRQ(ierr); } else { ierr = DMGetCoordinates(dm, &coords);CHKERRQ(ierr); if (coords) {ierr = DMSetCoordinates(*subdm, coords);CHKERRQ(ierr);} } ierr = DMSetType(*subdm, DMDA);CHKERRQ(ierr); ierr = DMSetDimension(*subdm, dm->dim);CHKERRQ(ierr); ierr = DMDASetSizes(*subdm, da->M, da->N, da->P);CHKERRQ(ierr); ierr = DMDASetNumProcs(*subdm, da->m, da->n, da->p);CHKERRQ(ierr); ierr = DMDASetBoundaryType(*subdm, da->bx, da->by, da->bz);CHKERRQ(ierr); ierr = DMDASetDof(*subdm, numFields);CHKERRQ(ierr); ierr = DMDASetStencilType(*subdm, da->stencil_type);CHKERRQ(ierr); ierr = DMDASetStencilWidth(*subdm, da->s);CHKERRQ(ierr); ierr = DMDASetOwnershipRanges(*subdm, da->lx, da->ly, da->lz);CHKERRQ(ierr); } ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); if (section) { ierr = DMCreateSubDM_Section_Private(dm, numFields, fields, is, subdm);CHKERRQ(ierr); } else { if (is) { PetscInt *indices, cnt = 0, dof = da->w, i, j; ierr = PetscMalloc1(da->Nlocal*numFields/dof, &indices);CHKERRQ(ierr); for (i = da->base/dof; i < (da->base+da->Nlocal)/dof; ++i) { for (j = 0; j < numFields; ++j) { indices[cnt++] = dof*i + fields[j]; } } if (cnt != da->Nlocal*numFields/dof) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Count %d does not equal expected value %d", cnt, da->Nlocal*numFields/dof); ierr = ISCreateGeneral(PetscObjectComm((PetscObject) dm), cnt, indices, PETSC_OWN_POINTER, is);CHKERRQ(ierr); } } PetscFunctionReturn(0); }
PetscErrorCode DMClone_DA(DM dm, DM *newdm) { DM_DA *da = (DM_DA *) dm->data; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMSetType(*newdm, DMDA);CHKERRQ(ierr); ierr = DMSetDimension(*newdm, dm->dim);CHKERRQ(ierr); ierr = DMDASetSizes(*newdm, da->M, da->N, da->P);CHKERRQ(ierr); ierr = DMDASetNumProcs(*newdm, da->m, da->n, da->p);CHKERRQ(ierr); ierr = DMDASetBoundaryType(*newdm, da->bx, da->by, da->bz);CHKERRQ(ierr); ierr = DMDASetDof(*newdm, da->w);CHKERRQ(ierr); ierr = DMDASetStencilType(*newdm, da->stencil_type);CHKERRQ(ierr); ierr = DMDASetStencilWidth(*newdm, da->s);CHKERRQ(ierr); ierr = DMDASetOwnershipRanges(*newdm, da->lx, da->ly, da->lz);CHKERRQ(ierr); ierr = DMSetUp(*newdm);CHKERRQ(ierr); PetscFunctionReturn(0); }
/*@C DMDACreate1d - Creates an object that will manage the communication of one-dimensional regular array data that is distributed across some processors. Collective on MPI_Comm Input Parameters: + comm - MPI communicator . bx - type of ghost cells at the boundary the array should have, if any. Use DM_BOUNDARY_NONE, DM_BOUNDARY_GHOSTED, or DM_BOUNDARY_PERIODIC. . M - global dimension of the array (use -M to indicate that it may be set to a different value from the command line with -da_grid_x <M>) . dof - number of degrees of freedom per node . s - stencil width - lx - array containing number of nodes in the X direction on each processor, or NULL. If non-null, must be of length as the number of processes in the MPI_Comm. Output Parameter: . da - the resulting distributed array object Options Database Key: + -dm_view - Calls DMView() at the conclusion of DMDACreate1d() . -da_grid_x <nx> - number of grid points in x direction; can set if M < 0 . -da_refine_x <rx> - refinement factor - -da_refine <n> - refine the DMDA n times before creating it, if M < 0 Level: beginner Notes: The array data itself is NOT stored in the DMDA, it is stored in Vec objects; The appropriate vector objects can be obtained with calls to DMCreateGlobalVector() and DMCreateLocalVector() and calls to VecDuplicate() if more are needed. .keywords: distributed array, create, one-dimensional .seealso: DMDestroy(), DMView(), DMDACreate2d(), DMDACreate3d(), DMGlobalToLocalBegin(), DMDASetRefinementFactor(), DMGlobalToLocalEnd(), DMLocalToGlobalBegin(), DMLocalToLocalBegin(), DMLocalToLocalEnd(), DMDAGetRefinementFactor(), DMDAGetInfo(), DMCreateGlobalVector(), DMCreateLocalVector(), DMDACreateNaturalVector(), DMLoad(), DMDAGetOwnershipRanges() @*/ PetscErrorCode DMDACreate1d(MPI_Comm comm, DMBoundaryType bx, PetscInt M, PetscInt dof, PetscInt s, const PetscInt lx[], DM *da) { PetscErrorCode ierr; PetscMPIInt size; PetscFunctionBegin; ierr = DMDACreate(comm, da);CHKERRQ(ierr); ierr = DMSetDimension(*da, 1);CHKERRQ(ierr); ierr = DMDASetSizes(*da, M, 1, 1);CHKERRQ(ierr); ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); ierr = DMDASetNumProcs(*da, size, PETSC_DECIDE, PETSC_DECIDE);CHKERRQ(ierr); ierr = DMDASetBoundaryType(*da, bx, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE);CHKERRQ(ierr); ierr = DMDASetDof(*da, dof);CHKERRQ(ierr); ierr = DMDASetStencilWidth(*da, s);CHKERRQ(ierr); ierr = DMDASetOwnershipRanges(*da, lx, NULL, NULL);CHKERRQ(ierr); /* This violates the behavior for other classes, but right now users expect negative dimensions to be handled this way */ ierr = DMSetFromOptions(*da);CHKERRQ(ierr); ierr = DMSetUp(*da);CHKERRQ(ierr); PetscFunctionReturn(0); }
int main(int argc,char **argv) { PetscErrorCode ierr; KSP ksp; PC pc; Vec x,b; DM da; Mat A; PetscInt dof=1; PetscBool flg; PetscScalar zero=0.0; PetscInitialize(&argc,&argv,(char *)0,help); ierr = PetscOptionsGetInt(PETSC_NULL,"-dof",&dof,PETSC_NULL);CHKERRQ(ierr); ierr = DMDACreate(PETSC_COMM_WORLD,&da);CHKERRQ(ierr); ierr = DMDASetDim(da,3);CHKERRQ(ierr); ierr = DMDASetBoundaryType(da,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE);CHKERRQ(ierr); ierr = DMDASetStencilType(da,DMDA_STENCIL_STAR);CHKERRQ(ierr); ierr = DMDASetSizes(da,3,3,3);CHKERRQ(ierr); ierr = DMDASetNumProcs(da,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr); ierr = DMDASetDof(da,dof);CHKERRQ(ierr); ierr = DMDASetStencilWidth(da,1);CHKERRQ(ierr); ierr = DMDASetOwnershipRanges(da,PETSC_NULL,PETSC_NULL,PETSC_NULL);CHKERRQ(ierr); ierr = DMSetFromOptions(da);CHKERRQ(ierr); ierr = DMSetUp(da);CHKERRQ(ierr); ierr = DMCreateGlobalVector(da,&x);CHKERRQ(ierr); ierr = DMCreateGlobalVector(da,&b);CHKERRQ(ierr); ierr = DMCreateMatrix(da,MATAIJ,&A);CHKERRQ(ierr); ierr = VecSet(b,zero);CHKERRQ(ierr); /* Test sbaij matrix */ flg = PETSC_FALSE; ierr = PetscOptionsGetBool(PETSC_NULL,"-test_sbaij",&flg,PETSC_NULL);CHKERRQ(ierr); if (flg) { Mat sA; ierr = MatSetOption(A,MAT_SYMMETRIC,PETSC_TRUE);CHKERRQ(ierr); ierr = MatConvert(A,MATSBAIJ,MAT_INITIAL_MATRIX,&sA);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); A = sA; } ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr); ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr); ierr = KSPSetOperators(ksp,A,A,SAME_NONZERO_PATTERN);CHKERRQ(ierr); ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr); ierr = PCSetDM(pc,(DM)da);CHKERRQ(ierr); ierr = KSPSolve(ksp,b,x);CHKERRQ(ierr); /* check final residual */ flg = PETSC_FALSE; ierr = PetscOptionsGetBool(PETSC_NULL, "-check_final_residual", &flg,PETSC_NULL);CHKERRQ(ierr); if (flg){ Vec b1; PetscReal norm; ierr = KSPGetSolution(ksp,&x);CHKERRQ(ierr); ierr = VecDuplicate(b,&b1);CHKERRQ(ierr); ierr = MatMult(A,x,b1);CHKERRQ(ierr); ierr = VecAXPY(b1,-1.0,b);CHKERRQ(ierr); ierr = VecNorm(b1,NORM_2,&norm);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"Final residual %g\n",norm);CHKERRQ(ierr); ierr = VecDestroy(&b1);CHKERRQ(ierr); } ierr = KSPDestroy(&ksp);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&b);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }
PetscErrorCode DMCoarsen_DA(DM da, MPI_Comm comm,DM *daref) { PetscErrorCode ierr; PetscInt M,N,P,i; DM da2; DM_DA *dd = (DM_DA*)da->data,*dd2; PetscFunctionBegin; PetscValidHeaderSpecific(da,DM_CLASSID,1); PetscValidPointer(daref,3); if (dd->bx == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0){ M = dd->M / dd->coarsen_x; } else { M = 1 + (dd->M - 1) / dd->coarsen_x; } if (dd->by == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0){ if (dd->dim > 1) { N = dd->N / dd->coarsen_y; } else { N = 1; } } else { N = 1 + (dd->N - 1) / dd->coarsen_y; } if (dd->bz == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0){ if (dd->dim > 2) { P = dd->P / dd->coarsen_z; } else { P = 1; } } else { P = 1 + (dd->P - 1) / dd->coarsen_z; } ierr = DMDACreate(((PetscObject)da)->comm,&da2);CHKERRQ(ierr); ierr = DMSetOptionsPrefix(da2,((PetscObject)da)->prefix);CHKERRQ(ierr); ierr = DMDASetDim(da2,dd->dim);CHKERRQ(ierr); ierr = DMDASetSizes(da2,M,N,P);CHKERRQ(ierr); ierr = DMDASetNumProcs(da2,dd->m,dd->n,dd->p);CHKERRQ(ierr); ierr = DMDASetBoundaryType(da2,dd->bx,dd->by,dd->bz);CHKERRQ(ierr); ierr = DMDASetDof(da2,dd->w);CHKERRQ(ierr); ierr = DMDASetStencilType(da2,dd->stencil_type);CHKERRQ(ierr); ierr = DMDASetStencilWidth(da2,dd->s);CHKERRQ(ierr); if (dd->dim == 3) { PetscInt *lx,*ly,*lz; ierr = PetscMalloc3(dd->m,PetscInt,&lx,dd->n,PetscInt,&ly,dd->p,PetscInt,&lz);CHKERRQ(ierr); ierr = DMDACoarsenOwnershipRanges(da,(PetscBool)(dd->bx == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0),dd->s,dd->coarsen_x,dd->m,dd->lx,lx);CHKERRQ(ierr); ierr = DMDACoarsenOwnershipRanges(da,(PetscBool)(dd->by == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0),dd->s,dd->coarsen_y,dd->n,dd->ly,ly);CHKERRQ(ierr); ierr = DMDACoarsenOwnershipRanges(da,(PetscBool)(dd->bz == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0),dd->s,dd->coarsen_z,dd->p,dd->lz,lz);CHKERRQ(ierr); ierr = DMDASetOwnershipRanges(da2,lx,ly,lz);CHKERRQ(ierr); ierr = PetscFree3(lx,ly,lz);CHKERRQ(ierr); } else if (dd->dim == 2) { PetscInt *lx,*ly; ierr = PetscMalloc2(dd->m,PetscInt,&lx,dd->n,PetscInt,&ly);CHKERRQ(ierr); ierr = DMDACoarsenOwnershipRanges(da,(PetscBool)(dd->bx == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0),dd->s,dd->coarsen_x,dd->m,dd->lx,lx);CHKERRQ(ierr); ierr = DMDACoarsenOwnershipRanges(da,(PetscBool)(dd->by == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0),dd->s,dd->coarsen_y,dd->n,dd->ly,ly);CHKERRQ(ierr); ierr = DMDASetOwnershipRanges(da2,lx,ly,PETSC_NULL);CHKERRQ(ierr); ierr = PetscFree2(lx,ly);CHKERRQ(ierr); } else if (dd->dim == 1) { PetscInt *lx; ierr = PetscMalloc(dd->m*sizeof(PetscInt),&lx);CHKERRQ(ierr); ierr = DMDACoarsenOwnershipRanges(da,(PetscBool)(dd->bx == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0),dd->s,dd->coarsen_x,dd->m,dd->lx,lx);CHKERRQ(ierr); ierr = DMDASetOwnershipRanges(da2,lx,PETSC_NULL,PETSC_NULL);CHKERRQ(ierr); ierr = PetscFree(lx);CHKERRQ(ierr); } dd2 = (DM_DA*)da2->data; /* allow overloaded (user replaced) operations to be inherited by refinement clones; why are only some inherited and not all? */ /* da2->ops->createinterpolation = da->ops->createinterpolation; copying this one causes trouble for DMSetVI */ da2->ops->creatematrix = da->ops->creatematrix; da2->ops->getcoloring = da->ops->getcoloring; dd2->interptype = dd->interptype; /* copy fill information if given */ if (dd->dfill) { ierr = PetscMalloc((dd->dfill[dd->w]+dd->w+1)*sizeof(PetscInt),&dd2->dfill);CHKERRQ(ierr); ierr = PetscMemcpy(dd2->dfill,dd->dfill,(dd->dfill[dd->w]+dd->w+1)*sizeof(PetscInt));CHKERRQ(ierr); } if (dd->ofill) { ierr = PetscMalloc((dd->ofill[dd->w]+dd->w+1)*sizeof(PetscInt),&dd2->ofill);CHKERRQ(ierr); ierr = PetscMemcpy(dd2->ofill,dd->ofill,(dd->ofill[dd->w]+dd->w+1)*sizeof(PetscInt));CHKERRQ(ierr); } /* copy the refine information */ dd2->coarsen_x = dd2->refine_x = dd->coarsen_x; dd2->coarsen_y = dd2->refine_y = dd->coarsen_y; dd2->coarsen_z = dd2->refine_z = dd->coarsen_z; /* copy vector type information */ ierr = PetscFree(da2->vectype);CHKERRQ(ierr); ierr = PetscStrallocpy(da->vectype,(char**)&da2->vectype);CHKERRQ(ierr); dd2->lf = dd->lf; dd2->lj = dd->lj; da2->leveldown = da->leveldown + 1; da2->levelup = da->levelup; ierr = DMSetFromOptions(da2);CHKERRQ(ierr); ierr = DMSetUp(da2);CHKERRQ(ierr); ierr = DMViewFromOptions(da2,"-dm_view");CHKERRQ(ierr); /* inject coordinates if they are set on the fine grid */ if (da->coordinates) { DM cdaf,cdac; Vec coordsc,coordsf; VecScatter inject; ierr = DMGetCoordinateDM(da,&cdaf);CHKERRQ(ierr); ierr = DMGetCoordinates(da,&coordsf);CHKERRQ(ierr); ierr = DMGetCoordinateDM(da2,&cdac);CHKERRQ(ierr); /* force creation of the coordinate vector */ ierr = DMDASetUniformCoordinates(da2,0.0,1.0,0.0,1.0,0.0,1.0);CHKERRQ(ierr); ierr = DMGetCoordinates(da2,&coordsc);CHKERRQ(ierr); ierr = DMCreateInjection(cdac,cdaf,&inject);CHKERRQ(ierr); ierr = VecScatterBegin(inject,coordsf,coordsc,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); ierr = VecScatterEnd(inject ,coordsf,coordsc,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); ierr = VecScatterDestroy(&inject);CHKERRQ(ierr); } for (i=0; i<da->bs; i++) { const char *fieldname; ierr = DMDAGetFieldName(da,i,&fieldname);CHKERRQ(ierr); ierr = DMDASetFieldName(da2,i,fieldname);CHKERRQ(ierr); } *daref = da2; PetscFunctionReturn(0); }
int main(int argc,char **argv) { PetscErrorCode ierr; KSP ksp; PC pc; Vec x,b; DM da; Mat A,Atrans; PetscInt dof=1,M=8; PetscBool flg,trans=PETSC_FALSE; ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr; ierr = PetscOptionsGetInt(NULL,NULL,"-dof",&dof,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,NULL,"-M",&M,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,NULL,"-trans",&trans,NULL);CHKERRQ(ierr); ierr = DMDACreate(PETSC_COMM_WORLD,&da);CHKERRQ(ierr); ierr = DMSetDimension(da,3);CHKERRQ(ierr); ierr = DMDASetBoundaryType(da,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE);CHKERRQ(ierr); ierr = DMDASetStencilType(da,DMDA_STENCIL_STAR);CHKERRQ(ierr); ierr = DMDASetSizes(da,M,M,M);CHKERRQ(ierr); ierr = DMDASetNumProcs(da,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr); ierr = DMDASetDof(da,dof);CHKERRQ(ierr); ierr = DMDASetStencilWidth(da,1);CHKERRQ(ierr); ierr = DMDASetOwnershipRanges(da,NULL,NULL,NULL);CHKERRQ(ierr); ierr = DMSetFromOptions(da);CHKERRQ(ierr); ierr = DMSetUp(da);CHKERRQ(ierr); ierr = DMCreateGlobalVector(da,&x);CHKERRQ(ierr); ierr = DMCreateGlobalVector(da,&b);CHKERRQ(ierr); ierr = ComputeRHS(da,b);CHKERRQ(ierr); ierr = DMSetMatType(da,MATBAIJ);CHKERRQ(ierr); ierr = DMSetFromOptions(da);CHKERRQ(ierr); ierr = DMCreateMatrix(da,&A);CHKERRQ(ierr); ierr = ComputeMatrix(da,A);CHKERRQ(ierr); /* A is non-symmetric. Make A = 0.5*(A + Atrans) symmetric for testing icc and cholesky */ ierr = MatTranspose(A,MAT_INITIAL_MATRIX,&Atrans);CHKERRQ(ierr); ierr = MatAXPY(A,1.0,Atrans,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr); ierr = MatScale(A,0.5);CHKERRQ(ierr); ierr = MatDestroy(&Atrans);CHKERRQ(ierr); /* Test sbaij matrix */ flg = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,NULL, "-test_sbaij1", &flg,NULL);CHKERRQ(ierr); if (flg) { Mat sA; PetscBool issymm; ierr = MatIsTranspose(A,A,0.0,&issymm);CHKERRQ(ierr); if (issymm) { ierr = MatSetOption(A,MAT_SYMMETRIC,PETSC_TRUE);CHKERRQ(ierr); } else {ierr = PetscPrintf(PETSC_COMM_WORLD,"Warning: A is non-symmetric\n");CHKERRQ(ierr);} ierr = MatConvert(A,MATSBAIJ,MAT_INITIAL_MATRIX,&sA);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); A = sA; } ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr); ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr); ierr = KSPSetOperators(ksp,A,A);CHKERRQ(ierr); ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr); ierr = PCSetDM(pc,(DM)da);CHKERRQ(ierr); if (trans) { ierr = KSPSolveTranspose(ksp,b,x);CHKERRQ(ierr); } else { ierr = KSPSolve(ksp,b,x);CHKERRQ(ierr); } /* check final residual */ flg = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,NULL, "-check_final_residual", &flg,NULL);CHKERRQ(ierr); if (flg) { Vec b1; PetscReal norm; ierr = KSPGetSolution(ksp,&x);CHKERRQ(ierr); ierr = VecDuplicate(b,&b1);CHKERRQ(ierr); ierr = MatMult(A,x,b1);CHKERRQ(ierr); ierr = VecAXPY(b1,-1.0,b);CHKERRQ(ierr); ierr = VecNorm(b1,NORM_2,&norm);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"Final residual %g\n",norm);CHKERRQ(ierr); ierr = VecDestroy(&b1);CHKERRQ(ierr); } ierr = KSPDestroy(&ksp);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&b);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
/* DMPatchZoom - Create a version of the coarse patch (identified by rank) with halo on communicator commz Collective on DM Input Parameters: + dm - the DM . rank - the rank which holds the given patch - commz - the new communicator for the patch Output Parameters: + dmz - the patch DM . sfz - the PetscSF mapping the patch+halo to the zoomed version . sfzr - the PetscSF mapping the patch to the restricted zoomed version Level: intermediate Note: All processes in commz should have the same rank (could autosplit comm) .seealso: DMPatchSolve() */ PetscErrorCode DMPatchZoom(DM dm, Vec X, MatStencil lower, MatStencil upper, MPI_Comm commz, DM *dmz, PetscSF *sfz, PetscSF *sfzr) { DMDAStencilType st; MatStencil blower, bupper, loclower, locupper; IS is; const PetscInt *ranges, *indices; PetscInt *localPoints = NULL; PetscSFNode *remotePoints = NULL; PetscInt dim, dof; PetscInt M, N, P, rM, rN, rP, halo = 1, sxb, syb, szb, sxr, syr, szr, exr, eyr, ezr, mxb, myb, mzb, i, j, k, q; PetscMPIInt size; PetscErrorCode ierr; PetscFunctionBegin; ierr = MPI_Comm_size(PetscObjectComm((PetscObject)dm), &size);CHKERRQ(ierr); /* Create patch DM */ ierr = DMDAGetInfo(dm, &dim, &M, &N, &P, 0,0,0, &dof, 0,0,0,0, &st);CHKERRQ(ierr); /* Get piece for rank r, expanded by halo */ bupper.i = PetscMin(M, upper.i + halo); blower.i = PetscMax(lower.i - halo, 0); bupper.j = PetscMin(N, upper.j + halo); blower.j = PetscMax(lower.j - halo, 0); bupper.k = PetscMin(P, upper.k + halo); blower.k = PetscMax(lower.k - halo, 0); rM = bupper.i - blower.i; rN = bupper.j - blower.j; rP = bupper.k - blower.k; if (commz != MPI_COMM_NULL) { ierr = DMDACreate(commz, dmz);CHKERRQ(ierr); ierr = DMSetDimension(*dmz, dim);CHKERRQ(ierr); ierr = DMDASetSizes(*dmz, rM, rN, rP);CHKERRQ(ierr); ierr = DMDASetNumProcs(*dmz, PETSC_DECIDE, PETSC_DECIDE, PETSC_DECIDE);CHKERRQ(ierr); ierr = DMDASetBoundaryType(*dmz, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE);CHKERRQ(ierr); ierr = DMDASetDof(*dmz, dof);CHKERRQ(ierr); ierr = DMDASetStencilType(*dmz, st);CHKERRQ(ierr); ierr = DMDASetStencilWidth(*dmz, 0);CHKERRQ(ierr); ierr = DMDASetOwnershipRanges(*dmz, NULL, NULL, NULL);CHKERRQ(ierr); ierr = DMSetFromOptions(*dmz);CHKERRQ(ierr); ierr = DMSetUp(*dmz);CHKERRQ(ierr); ierr = DMDAGetCorners(*dmz, &sxb, &syb, &szb, &mxb, &myb, &mzb);CHKERRQ(ierr); sxr = PetscMax(sxb, lower.i - blower.i); syr = PetscMax(syb, lower.j - blower.j); szr = PetscMax(szb, lower.k - blower.k); exr = PetscMin(sxb+mxb, upper.i - blower.i); eyr = PetscMin(syb+myb, upper.j - blower.j); ezr = PetscMin(szb+mzb, upper.k - blower.k); ierr = PetscMalloc2(rM*rN*rP,&localPoints,rM*rN*rP,&remotePoints);CHKERRQ(ierr); } else { sxr = syr = szr = exr = eyr = ezr = sxb = syb = szb = mxb = myb = mzb = 0; } /* Create SF for restricted map */ ierr = VecGetOwnershipRanges(X,&ranges);CHKERRQ(ierr); loclower.i = blower.i + sxr; locupper.i = blower.i + exr; loclower.j = blower.j + syr; locupper.j = blower.j + eyr; loclower.k = blower.k + szr; locupper.k = blower.k + ezr; ierr = DMDACreatePatchIS(dm, &loclower, &locupper, &is);CHKERRQ(ierr); ierr = ISGetIndices(is, &indices);CHKERRQ(ierr); q = 0; for (k = szb; k < szb+mzb; ++k) { if ((k < szr) || (k >= ezr)) continue; for (j = syb; j < syb+myb; ++j) { if ((j < syr) || (j >= eyr)) continue; for (i = sxb; i < sxb+mxb; ++i) { const PetscInt lp = ((k-szb)*rN + (j-syb))*rM + i-sxb; PetscInt r; if ((i < sxr) || (i >= exr)) continue; localPoints[q] = lp; ierr = PetscFindInt(indices[q], size+1, ranges, &r);CHKERRQ(ierr); remotePoints[q].rank = r < 0 ? -(r+1) - 1 : r; remotePoints[q].index = indices[q] - ranges[remotePoints[q].rank]; ++q; } } } ierr = ISRestoreIndices(is, &indices);CHKERRQ(ierr); ierr = ISDestroy(&is);CHKERRQ(ierr); ierr = PetscSFCreate(PetscObjectComm((PetscObject)dm), sfzr);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) *sfzr, "Restricted Map");CHKERRQ(ierr); ierr = PetscSFSetGraph(*sfzr, M*N*P, q, localPoints, PETSC_COPY_VALUES, remotePoints, PETSC_COPY_VALUES);CHKERRQ(ierr); /* Create SF for buffered map */ loclower.i = blower.i + sxb; locupper.i = blower.i + sxb+mxb; loclower.j = blower.j + syb; locupper.j = blower.j + syb+myb; loclower.k = blower.k + szb; locupper.k = blower.k + szb+mzb; ierr = DMDACreatePatchIS(dm, &loclower, &locupper, &is);CHKERRQ(ierr); ierr = ISGetIndices(is, &indices);CHKERRQ(ierr); q = 0; for (k = szb; k < szb+mzb; ++k) { for (j = syb; j < syb+myb; ++j) { for (i = sxb; i < sxb+mxb; ++i, ++q) { PetscInt r; localPoints[q] = q; ierr = PetscFindInt(indices[q], size+1, ranges, &r);CHKERRQ(ierr); remotePoints[q].rank = r < 0 ? -(r+1) - 1 : r; remotePoints[q].index = indices[q] - ranges[remotePoints[q].rank]; } } } ierr = ISRestoreIndices(is, &indices);CHKERRQ(ierr); ierr = ISDestroy(&is);CHKERRQ(ierr); ierr = PetscSFCreate(PetscObjectComm((PetscObject)dm), sfz);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) *sfz, "Buffered Map");CHKERRQ(ierr); ierr = PetscSFSetGraph(*sfz, M*N*P, q, localPoints, PETSC_COPY_VALUES, remotePoints, PETSC_COPY_VALUES);CHKERRQ(ierr); ierr = PetscFree2(localPoints, remotePoints);CHKERRQ(ierr); PetscFunctionReturn(0); }
PETSC_EXTERN void PETSC_STDCALL dmdasetownershipranges_(DM da, PetscInt lx[], PetscInt ly[], PetscInt lz[], int *__ierr ){ *__ierr = DMDASetOwnershipRanges( (DM)PetscToPointer((da) ),lx,ly,lz); }
PetscErrorCode DMRefine_DA(DM da,MPI_Comm comm,DM *daref) { PetscErrorCode ierr; PetscInt M,N,P,i; DM da2; DM_DA *dd = (DM_DA*)da->data,*dd2; PetscFunctionBegin; PetscValidHeaderSpecific(da,DM_CLASSID,1); PetscValidPointer(daref,3); if (dd->bx == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0) { M = dd->refine_x*dd->M; } else { M = 1 + dd->refine_x*(dd->M - 1); } if (dd->by == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0) { if (dd->dim > 1) { N = dd->refine_y*dd->N; } else { N = 1; } } else { N = 1 + dd->refine_y*(dd->N - 1); } if (dd->bz == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0) { if (dd->dim > 2) { P = dd->refine_z*dd->P; } else { P = 1; } } else { P = 1 + dd->refine_z*(dd->P - 1); } ierr = DMDACreate(PetscObjectComm((PetscObject)da),&da2);CHKERRQ(ierr); ierr = DMSetOptionsPrefix(da2,((PetscObject)da)->prefix);CHKERRQ(ierr); ierr = DMDASetDim(da2,dd->dim);CHKERRQ(ierr); ierr = DMDASetSizes(da2,M,N,P);CHKERRQ(ierr); ierr = DMDASetNumProcs(da2,dd->m,dd->n,dd->p);CHKERRQ(ierr); ierr = DMDASetBoundaryType(da2,dd->bx,dd->by,dd->bz);CHKERRQ(ierr); ierr = DMDASetDof(da2,dd->w);CHKERRQ(ierr); ierr = DMDASetStencilType(da2,dd->stencil_type);CHKERRQ(ierr); ierr = DMDASetStencilWidth(da2,dd->s);CHKERRQ(ierr); if (dd->dim == 3) { PetscInt *lx,*ly,*lz; ierr = PetscMalloc3(dd->m,&lx,dd->n,&ly,dd->p,&lz);CHKERRQ(ierr); ierr = DMDARefineOwnershipRanges(da,(PetscBool)(dd->bx == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0),dd->s,dd->refine_x,dd->m,dd->lx,lx);CHKERRQ(ierr); ierr = DMDARefineOwnershipRanges(da,(PetscBool)(dd->by == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0),dd->s,dd->refine_y,dd->n,dd->ly,ly);CHKERRQ(ierr); ierr = DMDARefineOwnershipRanges(da,(PetscBool)(dd->bz == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0),dd->s,dd->refine_z,dd->p,dd->lz,lz);CHKERRQ(ierr); ierr = DMDASetOwnershipRanges(da2,lx,ly,lz);CHKERRQ(ierr); ierr = PetscFree3(lx,ly,lz);CHKERRQ(ierr); } else if (dd->dim == 2) { PetscInt *lx,*ly; ierr = PetscMalloc2(dd->m,&lx,dd->n,&ly);CHKERRQ(ierr); ierr = DMDARefineOwnershipRanges(da,(PetscBool)(dd->bx == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0),dd->s,dd->refine_x,dd->m,dd->lx,lx);CHKERRQ(ierr); ierr = DMDARefineOwnershipRanges(da,(PetscBool)(dd->by == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0),dd->s,dd->refine_y,dd->n,dd->ly,ly);CHKERRQ(ierr); ierr = DMDASetOwnershipRanges(da2,lx,ly,NULL);CHKERRQ(ierr); ierr = PetscFree2(lx,ly);CHKERRQ(ierr); } else if (dd->dim == 1) { PetscInt *lx; ierr = PetscMalloc1(dd->m,&lx);CHKERRQ(ierr); ierr = DMDARefineOwnershipRanges(da,(PetscBool)(dd->bx == DMDA_BOUNDARY_PERIODIC || dd->interptype == DMDA_Q0),dd->s,dd->refine_x,dd->m,dd->lx,lx);CHKERRQ(ierr); ierr = DMDASetOwnershipRanges(da2,lx,NULL,NULL);CHKERRQ(ierr); ierr = PetscFree(lx);CHKERRQ(ierr); } dd2 = (DM_DA*)da2->data; /* allow overloaded (user replaced) operations to be inherited by refinement clones */ da2->ops->creatematrix = da->ops->creatematrix; /* da2->ops->createinterpolation = da->ops->createinterpolation; this causes problem with SNESVI */ da2->ops->getcoloring = da->ops->getcoloring; dd2->interptype = dd->interptype; /* copy fill information if given */ if (dd->dfill) { ierr = PetscMalloc1((dd->dfill[dd->w]+dd->w+1),&dd2->dfill);CHKERRQ(ierr); ierr = PetscMemcpy(dd2->dfill,dd->dfill,(dd->dfill[dd->w]+dd->w+1)*sizeof(PetscInt));CHKERRQ(ierr); } if (dd->ofill) { ierr = PetscMalloc1((dd->ofill[dd->w]+dd->w+1),&dd2->ofill);CHKERRQ(ierr); ierr = PetscMemcpy(dd2->ofill,dd->ofill,(dd->ofill[dd->w]+dd->w+1)*sizeof(PetscInt));CHKERRQ(ierr); } /* copy the refine information */ dd2->coarsen_x = dd2->refine_x = dd->refine_x; dd2->coarsen_y = dd2->refine_y = dd->refine_y; dd2->coarsen_z = dd2->refine_z = dd->refine_z; /* copy vector type information */ ierr = DMSetVecType(da2,da->vectype);CHKERRQ(ierr); dd2->lf = dd->lf; dd2->lj = dd->lj; da2->leveldown = da->leveldown; da2->levelup = da->levelup + 1; ierr = DMSetFromOptions(da2);CHKERRQ(ierr); ierr = DMSetUp(da2);CHKERRQ(ierr); /* interpolate coordinates if they are set on the coarse grid */ if (da->coordinates) { DM cdaf,cdac; Vec coordsc,coordsf; Mat II; ierr = DMGetCoordinateDM(da,&cdac);CHKERRQ(ierr); ierr = DMGetCoordinates(da,&coordsc);CHKERRQ(ierr); ierr = DMGetCoordinateDM(da2,&cdaf);CHKERRQ(ierr); /* force creation of the coordinate vector */ ierr = DMDASetUniformCoordinates(da2,0.0,1.0,0.0,1.0,0.0,1.0);CHKERRQ(ierr); ierr = DMGetCoordinates(da2,&coordsf);CHKERRQ(ierr); ierr = DMCreateInterpolation(cdac,cdaf,&II,NULL);CHKERRQ(ierr); ierr = MatInterpolate(II,coordsc,coordsf);CHKERRQ(ierr); ierr = MatDestroy(&II);CHKERRQ(ierr); } for (i=0; i<da->bs; i++) { const char *fieldname; ierr = DMDAGetFieldName(da,i,&fieldname);CHKERRQ(ierr); ierr = DMDASetFieldName(da2,i,fieldname);CHKERRQ(ierr); } *daref = da2; PetscFunctionReturn(0); }