Example #1
0
static PetscErrorCode DMTSConvertPlex(DM dm, DM *plex, PetscBool copy)
{
  PetscBool      isPlex;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscObjectTypeCompare((PetscObject) dm, DMPLEX, &isPlex);CHKERRQ(ierr);
  if (isPlex) {
    *plex = dm;
    ierr = PetscObjectReference((PetscObject) dm);CHKERRQ(ierr);
  } else {
    ierr = PetscObjectQuery((PetscObject) dm, "dm_plex", (PetscObject *) plex);CHKERRQ(ierr);
    if (!*plex) {
      ierr = DMConvert(dm,DMPLEX,plex);CHKERRQ(ierr);
      ierr = PetscObjectCompose((PetscObject) dm, "dm_plex", (PetscObject) *plex);CHKERRQ(ierr);
      if (copy) {
        PetscInt    i;
        PetscObject obj;
        const char *comps[3] = {"A","dmAux","dmCh"};

        ierr = DMCopyDMTS(dm, *plex);CHKERRQ(ierr);
        ierr = DMCopyDMSNES(dm, *plex);CHKERRQ(ierr);
        for (i = 0; i < 3; i++) {
          ierr = PetscObjectQuery((PetscObject) dm, comps[i], &obj);CHKERRQ(ierr);
          ierr = PetscObjectCompose((PetscObject) *plex, comps[i], obj);CHKERRQ(ierr);
        }
      }
    } else {
      ierr = PetscObjectReference((PetscObject) *plex);CHKERRQ(ierr);
    }
  }
  PetscFunctionReturn(0);
}
Example #2
0
PetscErrorCode private_PetscViewerDestroy_XDMF(PetscViewer *v)
{
  PetscViewer    viewer;
  DM             dm = NULL;
  long int       *bytes;
  PetscContainer container = NULL;
  PetscErrorCode ierr;
  
  PetscFunctionBegin;
  if (!v) PetscFunctionReturn(0);
  viewer = *v;
  
  ierr = PetscObjectQuery((PetscObject)viewer,"DMSwarm",(PetscObject*)&dm);CHKERRQ(ierr);
  if (dm) {
    ierr = PetscViewerASCIIPrintf(viewer,"</Grid>\n");CHKERRQ(ierr);
    ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
  }
  
  /* close xdmf header */
  ierr = PetscViewerASCIIPrintf(viewer,"</Domain>\n");CHKERRQ(ierr);
  ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPrintf(viewer,"</Xdmf>\n");CHKERRQ(ierr);
  
  ierr = PetscObjectQuery((PetscObject)viewer,"XDMFViewerContext",(PetscObject*)&container);CHKERRQ(ierr);
  if (container) {
    ierr = PetscContainerGetPointer(container,(void**)&bytes);CHKERRQ(ierr);
    ierr = PetscFree(bytes);CHKERRQ(ierr);
    ierr = PetscContainerDestroy(&container);CHKERRQ(ierr);
  }
  
  ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
  *v = NULL;
  PetscFunctionReturn(0);
}
Example #3
0
/*@C
  DMPlexTSGetGradientDM - Return gradient data layout

  Input Parameters:
+ dm - The DM
- fv - The PetscFV

  Output Parameter:
. dmGrad - The layout for gradient values

  Level: developer

.seealso: DMPlexTSGetGeometryFVM(), DMPlexTSSetRHSFunctionLocal()
@*/
PetscErrorCode DMPlexTSGetGradientDM(DM dm, PetscFV fv, DM *dmGrad)
{
  DMTS           dmts;
  PetscObject    obj;
  PetscBool      computeGradients;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm,DM_CLASSID,1);
  PetscValidHeaderSpecific(fv,PETSCFV_CLASSID,2);
  PetscValidPointer(dmGrad,3);
  ierr = PetscFVGetComputeGradients(fv, &computeGradients);CHKERRQ(ierr);
  if (!computeGradients) {*dmGrad = NULL; PetscFunctionReturn(0);}
  ierr = DMGetDMTS(dm, &dmts);CHKERRQ(ierr);
  ierr = PetscObjectQuery((PetscObject) dmts, "DMPlexTS_dmgrad_fvm", &obj);CHKERRQ(ierr);
  if (!obj) {
    DM  dmGrad;
    Vec faceGeometry, cellGeometry;

    ierr = DMPlexTSGetGeometryFVM(dm, &faceGeometry, &cellGeometry, NULL);CHKERRQ(ierr);
    ierr = DMPlexComputeGradientFVM(dm, fv, faceGeometry, cellGeometry, &dmGrad);CHKERRQ(ierr);
    ierr = PetscObjectCompose((PetscObject) dmts, "DMPlexTS_dmgrad_fvm", (PetscObject) dmGrad);CHKERRQ(ierr);
    ierr = DMDestroy(&dmGrad);CHKERRQ(ierr);
  }
  ierr = PetscObjectQuery((PetscObject) dmts, "DMPlexTS_dmgrad_fvm", (PetscObject *) dmGrad);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
Example #4
0
static PetscErrorCode PCSetUp_LSC(PC pc)
{
  PC_LSC         *lsc = (PC_LSC*)pc->data;
  Mat            L,Lp,B,C;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PCLSCAllocate_Private(pc);CHKERRQ(ierr);
  ierr = PetscObjectQuery((PetscObject)pc->mat,"LSC_L",(PetscObject*)&L);CHKERRQ(ierr);
  if (!L) {ierr = PetscObjectQuery((PetscObject)pc->pmat,"LSC_L",(PetscObject*)&L);CHKERRQ(ierr);}
  ierr = PetscObjectQuery((PetscObject)pc->pmat,"LSC_Lp",(PetscObject*)&Lp);CHKERRQ(ierr);
  if (!Lp) {ierr = PetscObjectQuery((PetscObject)pc->mat,"LSC_Lp",(PetscObject*)&Lp);CHKERRQ(ierr);}
  if (!L) {
    ierr = MatSchurComplementGetSubMatrices(pc->mat,NULL,NULL,&B,&C,NULL);CHKERRQ(ierr);
    if (!lsc->L) {
      ierr = MatMatMult(C,B,MAT_INITIAL_MATRIX,PETSC_DEFAULT,&lsc->L);CHKERRQ(ierr);
    } else {
      ierr = MatMatMult(C,B,MAT_REUSE_MATRIX,PETSC_DEFAULT,&lsc->L);CHKERRQ(ierr);
    }
    Lp = L = lsc->L;
  }
  if (lsc->scale) {
    Mat Ap;
    ierr = MatSchurComplementGetSubMatrices(pc->mat,NULL,&Ap,NULL,NULL,NULL);CHKERRQ(ierr);
    ierr = MatGetDiagonal(Ap,lsc->scale);CHKERRQ(ierr); /* Should be the mass matrix, but we don't have plumbing for that yet */
    ierr = VecReciprocal(lsc->scale);CHKERRQ(ierr);
  }
  ierr = KSPSetOperators(lsc->kspL,L,Lp);CHKERRQ(ierr);
  ierr = KSPSetFromOptions(lsc->kspL);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
Example #5
0
/*
     DMSetVI - Marks a DM as associated with a VI problem. This causes the interpolation/restriction operators to
               be restricted to only those variables NOT associated with active constraints.

*/
PetscErrorCode  DMSetVI(DM dm,IS inactive)
{
  PetscErrorCode          ierr;
  PetscContainer          isnes;
  DM_SNESVI               *dmsnesvi;

  PetscFunctionBegin;
  if (!dm) PetscFunctionReturn(0);

  ierr = PetscObjectReference((PetscObject)inactive);CHKERRQ(ierr);

  ierr = PetscObjectQuery((PetscObject)dm,"VI",(PetscObject *)&isnes);CHKERRQ(ierr);
  if (!isnes) {
    ierr = PetscContainerCreate(((PetscObject)dm)->comm,&isnes);CHKERRQ(ierr);
    ierr = PetscContainerSetUserDestroy(isnes,(PetscErrorCode (*)(void*))DMDestroy_SNESVI);CHKERRQ(ierr);
    ierr = PetscNew(DM_SNESVI,&dmsnesvi);CHKERRQ(ierr);
    ierr = PetscContainerSetPointer(isnes,(void*)dmsnesvi);CHKERRQ(ierr);
    ierr = PetscObjectCompose((PetscObject)dm,"VI",(PetscObject)isnes);CHKERRQ(ierr);
    ierr = PetscContainerDestroy(&isnes);CHKERRQ(ierr);
    dmsnesvi->createinterpolation   = dm->ops->createinterpolation;
    dm->ops->createinterpolation    = DMCreateInterpolation_SNESVI;
    dmsnesvi->coarsen            = dm->ops->coarsen;
    dm->ops->coarsen             = DMCoarsen_SNESVI;
    dmsnesvi->createglobalvector = dm->ops->createglobalvector;
    dm->ops->createglobalvector  = DMCreateGlobalVector_SNESVI;
  } else {
    ierr = PetscContainerGetPointer(isnes,(void**)&dmsnesvi);CHKERRQ(ierr);
    ierr = ISDestroy(&dmsnesvi->inactive);CHKERRQ(ierr);
  }
  ierr = DMClearGlobalVectors(dm);CHKERRQ(ierr);
  ierr = ISGetLocalSize(inactive,&dmsnesvi->n);CHKERRQ(ierr);
  dmsnesvi->inactive = inactive;
  dmsnesvi->dm       = dm;
  PetscFunctionReturn(0);
}
Example #6
0
PetscErrorCode MatMatMultNumeric_MPIAIJ_MPIAIJ(Mat A,Mat B,Mat C)
{
  PetscErrorCode     ierr;
  Mat                *seq;
  Mat_MatMatMultMPI  *mult; 
  PetscContainer     container;

  PetscFunctionBegin;
  ierr = PetscObjectQuery((PetscObject)C,"Mat_MatMatMultMPI",(PetscObject *)&container);CHKERRQ(ierr);
  if (container) {
    ierr  = PetscContainerGetPointer(container,(void **)&mult);CHKERRQ(ierr); 
  } else {
    SETERRQ(PETSC_ERR_PLIB,"Container does not exit");
  }

  seq = &mult->B_seq;
  ierr = MatGetSubMatrices(B,1,&mult->isrowb,&mult->iscolb,MAT_REUSE_MATRIX,&seq);CHKERRQ(ierr);
  mult->B_seq = *seq;
  
  seq = &mult->A_loc;
  ierr = MatGetSubMatrices(A,1,&mult->isrowa,&mult->isrowb,MAT_REUSE_MATRIX,&seq);CHKERRQ(ierr);
  mult->A_loc = *seq;

  ierr = MatMatMult_SeqAIJ_SeqAIJ(mult->A_loc,mult->B_seq,MAT_REUSE_MATRIX,0.0,&mult->C_seq);CHKERRQ(ierr);

  ierr = PetscObjectReference((PetscObject)mult->C_seq);CHKERRQ(ierr); 
  ierr = MatMerge(((PetscObject)A)->comm,mult->C_seq,B->cmap->n,MAT_REUSE_MATRIX,&C);CHKERRQ(ierr); 
  PetscFunctionReturn(0);
}
Example #7
0
static PetscErrorCode SNESComputeJacobian_DMLocal(SNES snes,Vec X,Mat A,Mat B,void *ctx)
{
  PetscErrorCode ierr;
  DM             dm;
  DMSNES_Local   *dmlocalsnes = (DMSNES_Local*)ctx;
  Vec            Xloc;

  PetscFunctionBegin;
  ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
  if (dmlocalsnes->jacobianlocal) {
    ierr = DMGetLocalVector(dm,&Xloc);CHKERRQ(ierr);
    ierr = VecZeroEntries(Xloc);CHKERRQ(ierr);
    if (dmlocalsnes->boundarylocal) {ierr = (*dmlocalsnes->boundarylocal)(dm,Xloc,dmlocalsnes->boundarylocalctx);CHKERRQ(ierr);}
    ierr = DMGlobalToLocalBegin(dm,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
    ierr = DMGlobalToLocalEnd(dm,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
    CHKMEMQ;
    ierr = (*dmlocalsnes->jacobianlocal)(dm,Xloc,A,B,dmlocalsnes->jacobianlocalctx);CHKERRQ(ierr);
    CHKMEMQ;
    ierr = DMRestoreLocalVector(dm,&Xloc);CHKERRQ(ierr);
  } else {
    MatFDColoring fdcoloring;
    ierr = PetscObjectQuery((PetscObject)dm,"DMDASNES_FDCOLORING",(PetscObject*)&fdcoloring);CHKERRQ(ierr);
    if (!fdcoloring) {
      ISColoring coloring;

      ierr = DMCreateColoring(dm,dm->coloringtype,&coloring);CHKERRQ(ierr);
      ierr = MatFDColoringCreate(B,coloring,&fdcoloring);CHKERRQ(ierr);
      ierr = ISColoringDestroy(&coloring);CHKERRQ(ierr);
      switch (dm->coloringtype) {
      case IS_COLORING_GLOBAL:
        ierr = MatFDColoringSetFunction(fdcoloring,(PetscErrorCode (*)(void))SNESComputeFunction_DMLocal,dmlocalsnes);CHKERRQ(ierr);
        break;
      default: SETERRQ1(PetscObjectComm((PetscObject)snes),PETSC_ERR_SUP,"No support for coloring type '%s'",ISColoringTypes[dm->coloringtype]);
      }
      ierr = PetscObjectSetOptionsPrefix((PetscObject)fdcoloring,((PetscObject)dm)->prefix);CHKERRQ(ierr);
      ierr = MatFDColoringSetFromOptions(fdcoloring);CHKERRQ(ierr);
      ierr = MatFDColoringSetUp(B,coloring,fdcoloring);CHKERRQ(ierr);
      ierr = PetscObjectCompose((PetscObject)dm,"DMDASNES_FDCOLORING",(PetscObject)fdcoloring);CHKERRQ(ierr);
      ierr = PetscObjectDereference((PetscObject)fdcoloring);CHKERRQ(ierr);

      /* The following breaks an ugly reference counting loop that deserves a paragraph. MatFDColoringApply() will call
       * VecDuplicate() with the state Vec and store inside the MatFDColoring. This Vec will duplicate the Vec, but the
       * MatFDColoring is composed with the DM. We dereference the DM here so that the reference count will eventually
       * drop to 0. Note the code in DMDestroy() that exits early for a negative reference count. That code path will be
       * taken when the PetscObjectList for the Vec inside MatFDColoring is destroyed.
       */
      ierr = PetscObjectDereference((PetscObject)dm);CHKERRQ(ierr);
    }
    ierr  = MatFDColoringApply(B,fdcoloring,X,snes);CHKERRQ(ierr);
  }
  /* This will be redundant if the user called both, but it's too common to forget. */
  if (A != B) {
    ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}
Example #8
0
PetscErrorCode  SNESComputeJacobianDefaultColor(SNES snes,Vec x1,Mat J,Mat B,void *ctx)
{
  MatFDColoring  color = (MatFDColoring)ctx;
  PetscErrorCode ierr;
  DM             dm;
  MatColoring    mc;
  ISColoring     iscoloring;
  PetscBool      hascolor;
  PetscBool      solvec,matcolor = PETSC_FALSE;

  PetscFunctionBegin;
  if (color) PetscValidHeaderSpecific(color,MAT_FDCOLORING_CLASSID,6);
  if (!color) {ierr  = PetscObjectQuery((PetscObject)B,"SNESMatFDColoring",(PetscObject*)&color);CHKERRQ(ierr);}

  if (!color) {
    ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
    ierr = DMHasColoring(dm,&hascolor);CHKERRQ(ierr);
    matcolor = PETSC_FALSE;
    ierr = PetscOptionsGetBool(((PetscObject)snes)->options,((PetscObject)snes)->prefix,"-snes_fd_color_use_mat",&matcolor,NULL);CHKERRQ(ierr);
    if (hascolor && !matcolor) {
      ierr = DMCreateColoring(dm,IS_COLORING_GLOBAL,&iscoloring);CHKERRQ(ierr);
      ierr = MatFDColoringCreate(B,iscoloring,&color);CHKERRQ(ierr);
      ierr = MatFDColoringSetFunction(color,(PetscErrorCode (*)(void))SNESComputeFunctionCtx,NULL);CHKERRQ(ierr);
      ierr = MatFDColoringSetFromOptions(color);CHKERRQ(ierr);
      ierr = MatFDColoringSetUp(B,iscoloring,color);CHKERRQ(ierr);
      ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr);
    } else {
      ierr = MatColoringCreate(B,&mc);CHKERRQ(ierr);
      ierr = MatColoringSetDistance(mc,2);CHKERRQ(ierr);
      ierr = MatColoringSetType(mc,MATCOLORINGSL);CHKERRQ(ierr);
      ierr = MatColoringSetFromOptions(mc);CHKERRQ(ierr);
      ierr = MatColoringApply(mc,&iscoloring);CHKERRQ(ierr);
      ierr = MatColoringDestroy(&mc);CHKERRQ(ierr);
      ierr = MatFDColoringCreate(B,iscoloring,&color);CHKERRQ(ierr);
      ierr = MatFDColoringSetFunction(color,(PetscErrorCode (*)(void))SNESComputeFunctionCtx,NULL);CHKERRQ(ierr);
      ierr = MatFDColoringSetFromOptions(color);CHKERRQ(ierr);
      ierr = MatFDColoringSetUp(B,iscoloring,color);CHKERRQ(ierr);
      ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr);
    }
    ierr = PetscObjectCompose((PetscObject)B,"SNESMatFDColoring",(PetscObject)color);CHKERRQ(ierr);
    ierr = PetscObjectDereference((PetscObject)color);CHKERRQ(ierr);
  }

  /* F is only usable if there is no RHS on the SNES and the full solution corresponds to x1 */
  ierr = VecEqual(x1,snes->vec_sol,&solvec);CHKERRQ(ierr);
  if (!snes->vec_rhs && solvec) {
    Vec F;
    ierr = SNESGetFunction(snes,&F,NULL,NULL);CHKERRQ(ierr);
    ierr = MatFDColoringSetF(color,F);CHKERRQ(ierr);
  }
  ierr = MatFDColoringApply(B,color,x1,snes);CHKERRQ(ierr);
  if (J != B) {
    ierr = MatAssemblyBegin(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatAssemblyEnd(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}
Example #9
0
File: theta.c Project: Kun-Qu/petsc
static PetscErrorCode TSThetaGetX0AndXdot(TS ts,DM dm,Vec *X0,Vec *Xdot)
{
  TS_Theta       *th = (TS_Theta*)ts->data;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  if (X0) {
    if (dm && dm != ts->dm) {
      ierr = PetscObjectQuery((PetscObject)dm,"TSTheta_X0",(PetscObject*)X0);CHKERRQ(ierr);
      if (!*X0) SETERRQ(((PetscObject)ts)->comm,PETSC_ERR_ARG_INCOMP,"TSTheta_X0 has not been composed with DM from SNES");
    } else *X0 = ts->vec_sol;
  }
  if (Xdot) {
    if (dm && dm != ts->dm) {
      ierr = PetscObjectQuery((PetscObject)dm,"TSTheta_Xdot",(PetscObject*)Xdot);CHKERRQ(ierr);
      if (!*Xdot) SETERRQ(((PetscObject)ts)->comm,PETSC_ERR_ARG_INCOMP,"TSTheta_Xdot has not been composed with DM from SNES");
    } else *Xdot = th->Xdot;
  }
  PetscFunctionReturn(0);
}
Example #10
0
/*
     DMCreateInterpolation_SNESVI - Modifieds the interpolation obtained from the DM by removing all rows and columns associated with active constraints.

*/
PetscErrorCode  DMCreateInterpolation_SNESVI(DM dm1,DM dm2,Mat *mat,Vec *vec)
{
  PetscErrorCode          ierr;
  PetscContainer          isnes;
  DM_SNESVI               *dmsnesvi1,*dmsnesvi2;
  Mat                     interp;

  PetscFunctionBegin;
  ierr = PetscObjectQuery((PetscObject)dm1,"VI",(PetscObject *)&isnes);CHKERRQ(ierr);
  if (!isnes) SETERRQ(((PetscObject)dm1)->comm,PETSC_ERR_PLIB,"Composed VI data structure is missing");
  ierr = PetscContainerGetPointer(isnes,(void**)&dmsnesvi1);CHKERRQ(ierr);
  ierr = PetscObjectQuery((PetscObject)dm2,"VI",(PetscObject *)&isnes);CHKERRQ(ierr);
  if (!isnes) SETERRQ(((PetscObject)dm2)->comm,PETSC_ERR_PLIB,"Composed VI data structure is missing");
  ierr = PetscContainerGetPointer(isnes,(void**)&dmsnesvi2);CHKERRQ(ierr);

  ierr = (*dmsnesvi1->createinterpolation)(dm1,dm2,&interp,PETSC_NULL);CHKERRQ(ierr);
  ierr = MatGetSubMatrix(interp,dmsnesvi2->inactive,dmsnesvi1->inactive,MAT_INITIAL_MATRIX,mat);CHKERRQ(ierr);
  ierr = MatDestroy(&interp);CHKERRQ(ierr);
  *vec = 0;
  PetscFunctionReturn(0);
}
Example #11
0
/*
     DMCreateGlobalVector_SNESVI - Creates global vector of the size of the reduced space

*/
PetscErrorCode  DMCreateGlobalVector_SNESVI(DM dm,Vec *vec)
{
  PetscErrorCode          ierr;
  PetscContainer          isnes;
  DM_SNESVI               *dmsnesvi;

  PetscFunctionBegin;
  ierr = PetscObjectQuery((PetscObject)dm,"VI",(PetscObject *)&isnes);CHKERRQ(ierr);
  if (!isnes) SETERRQ(((PetscObject)dm)->comm,PETSC_ERR_PLIB,"Composed SNES is missing");
  ierr = PetscContainerGetPointer(isnes,(void**)&dmsnesvi);CHKERRQ(ierr);
  ierr = VecCreateMPI(((PetscObject)dm)->comm,dmsnesvi->n,PETSC_DETERMINE,vec);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
Example #12
0
PetscErrorCode  SNESComputeJacobianDefaultColor(SNES snes,Vec x1,Mat *J,Mat *B,MatStructure *flag,void *ctx)
{
  MatFDColoring  color = (MatFDColoring)ctx;
  PetscErrorCode ierr;
  DM             dm;
  PetscErrorCode (*func)(SNES,Vec,Vec,void*);
  Vec            F;
  void           *funcctx;
  ISColoring     iscoloring;
  PetscBool      hascolor;
  PetscBool      solvec;

  PetscFunctionBegin;
  if (color) PetscValidHeaderSpecific(color,MAT_FDCOLORING_CLASSID,6);
  else {ierr  = PetscObjectQuery((PetscObject)*B,"SNESMatFDColoring",(PetscObject*)&color);CHKERRQ(ierr);}
  *flag = SAME_NONZERO_PATTERN;
  ierr  = SNESGetFunction(snes,&F,&func,&funcctx);CHKERRQ(ierr);
  if (!color) {
    ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
    ierr = DMHasColoring(dm,&hascolor);CHKERRQ(ierr);
    if (hascolor) {
      ierr = DMCreateColoring(dm,IS_COLORING_GLOBAL,&iscoloring);CHKERRQ(ierr);
      ierr = MatFDColoringCreate(*B,iscoloring,&color);CHKERRQ(ierr);
      ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr);
      ierr = MatFDColoringSetFunction(color,(PetscErrorCode (*)(void))func,funcctx);CHKERRQ(ierr);
      ierr = MatFDColoringSetFromOptions(color);CHKERRQ(ierr);
    } else {
      ierr = MatGetColoring(*B,MATCOLORINGSL,&iscoloring);CHKERRQ(ierr);
      ierr = MatFDColoringCreate(*B,iscoloring,&color);CHKERRQ(ierr);
      ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr);
      ierr = MatFDColoringSetFunction(color,(PetscErrorCode (*)(void))func,(void*)funcctx);CHKERRQ(ierr);
      ierr = MatFDColoringSetFromOptions(color);CHKERRQ(ierr);
    }
    ierr = PetscObjectCompose((PetscObject)*B,"SNESMatFDColoring",(PetscObject)color);CHKERRQ(ierr);
    ierr = PetscObjectDereference((PetscObject)color);CHKERRQ(ierr);
  }

  /* F is only usable if there is no RHS on the SNES and the full solution corresponds to x1 */
  ierr = VecEqual(x1,snes->vec_sol,&solvec);CHKERRQ(ierr);
  if (!snes->vec_rhs && solvec) {
    ierr = MatFDColoringSetF(color,F);CHKERRQ(ierr);
  }
  ierr = MatFDColoringApply(*B,color,x1,flag,snes);CHKERRQ(ierr);
  if (*J != *B) {
    ierr = MatAssemblyBegin(*J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatAssemblyEnd(*J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}
Example #13
0
/*@
  DMPlexTSGetGeometryFVM - Return precomputed geometric data

  Input Parameter:
. dm - The DM

  Output Parameters:
+ facegeom - The values precomputed from face geometry
. cellgeom - The values precomputed from cell geometry
- minRadius - The minimum radius over the mesh of an inscribed sphere in a cell

  Level: developer

.seealso: DMPlexTSSetRHSFunctionLocal()
@*/
PetscErrorCode DMPlexTSGetGeometryFVM(DM dm, Vec *facegeom, Vec *cellgeom, PetscReal *minRadius)
{
  DMTS           dmts;
  PetscObject    obj;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm,DM_CLASSID,1);
  ierr = DMGetDMTS(dm, &dmts);CHKERRQ(ierr);
  ierr = PetscObjectQuery((PetscObject) dmts, "DMPlexTS_facegeom_fvm", &obj);CHKERRQ(ierr);
  if (!obj) {
    Vec cellgeom, facegeom;

    ierr = DMPlexComputeGeometryFVM(dm, &cellgeom, &facegeom);CHKERRQ(ierr);
    ierr = PetscObjectCompose((PetscObject) dmts, "DMPlexTS_facegeom_fvm", (PetscObject) facegeom);CHKERRQ(ierr);
    ierr = PetscObjectCompose((PetscObject) dmts, "DMPlexTS_cellgeom_fvm", (PetscObject) cellgeom);CHKERRQ(ierr);
    ierr = VecDestroy(&facegeom);CHKERRQ(ierr);
    ierr = VecDestroy(&cellgeom);CHKERRQ(ierr);
  }
  if (facegeom) {PetscValidPointer(facegeom, 2); ierr = PetscObjectQuery((PetscObject) dmts, "DMPlexTS_facegeom_fvm", (PetscObject *) facegeom);CHKERRQ(ierr);}
  if (cellgeom) {PetscValidPointer(cellgeom, 3); ierr = PetscObjectQuery((PetscObject) dmts, "DMPlexTS_cellgeom_fvm", (PetscObject *) cellgeom);CHKERRQ(ierr);}
  if (minRadius) {ierr = DMPlexGetMinRadius(dm, minRadius);CHKERRQ(ierr);}
  PetscFunctionReturn(0);
}
Example #14
0
PetscErrorCode MatDestroy_SeqAIJ_RARt(Mat A)
{
  PetscErrorCode ierr;
  PetscContainer container;
  Mat_RARt       *rart=PETSC_NULL;

  PetscFunctionBegin;
  ierr = PetscObjectQuery((PetscObject)A,"Mat_RARt",(PetscObject *)&container);CHKERRQ(ierr);
  if (!container) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Container does not exit");
  ierr = PetscContainerGetPointer(container,(void **)&rart);CHKERRQ(ierr);
  A->ops->destroy   = rart->destroy;
  if (A->ops->destroy) {
    ierr = (*A->ops->destroy)(A);CHKERRQ(ierr);
  }
  ierr = PetscObjectCompose((PetscObject)A,"Mat_RARt",0);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
Example #15
0
PetscErrorCode MatDestroy_MPIAIJ_MatMatMult(Mat A)
{
  PetscErrorCode     ierr;
  PetscContainer     container;
  Mat_MatMatMultMPI  *mult=PETSC_NULL;

  PetscFunctionBegin;
  ierr = PetscObjectQuery((PetscObject)A,"Mat_MatMatMultMPI",(PetscObject *)&container);CHKERRQ(ierr);
  if (container) {
    ierr = PetscContainerGetPointer(container,(void **)&mult);CHKERRQ(ierr);
  } else {
    SETERRQ(PETSC_ERR_PLIB,"Container does not exit");
  }
  A->ops->destroy = mult->MatDestroy;
  ierr = PetscObjectCompose((PetscObject)A,"Mat_MatMatMultMPI",0);CHKERRQ(ierr);
  ierr = (*A->ops->destroy)(A);CHKERRQ(ierr);
  ierr = PetscContainerDestroy(container);CHKERRQ(ierr); 
  PetscFunctionReturn(0);
}
Example #16
0
PetscErrorCode MatRARtNumeric_SeqAIJ_SeqAIJ(Mat A,Mat R,Mat C)
{
  PetscErrorCode        ierr;
  Mat_RARt              *rart;
  PetscContainer        container;
  MatTransposeColoring  matcoloring;
  Mat                   Rt,RARt;
  PetscLogDouble        Mult_sp_den=0.0,app1=0.0,app2=0.0,t0,tf;

  PetscFunctionBegin;
  ierr = PetscObjectQuery((PetscObject)C,"Mat_RARt",(PetscObject *)&container);CHKERRQ(ierr);
  if (!container) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Container does not exit");
  ierr  = PetscContainerGetPointer(container,(void **)&rart);CHKERRQ(ierr);

  /* Get dense Rt by Apply MatTransposeColoring to R */
  matcoloring = rart->matcoloring;
  Rt          = rart->Rt;
  ierr = PetscGetTime(&t0);CHKERRQ(ierr);
  ierr = MatTransColoringApplySpToDen(matcoloring,R,Rt);CHKERRQ(ierr);
  ierr = PetscGetTime(&tf);CHKERRQ(ierr);
  app1 += tf - t0;

  /* Get dense RARt = R*A*Rt */
  ierr = PetscGetTime(&t0);CHKERRQ(ierr);
  RARt = rart->RARt;
  ierr = MatMatMatMultNumeric_SeqAIJ_SeqAIJ_SeqDense(R,A,Rt,RARt,rart->work);CHKERRQ(ierr);
  ierr = PetscGetTime(&tf);CHKERRQ(ierr);
  Mult_sp_den += tf - t0;

  /* Recover C from C_dense */
  ierr = PetscGetTime(&t0);CHKERRQ(ierr);
  ierr = MatTransColoringApplyDenToSp(matcoloring,RARt,C);CHKERRQ(ierr);
  ierr = PetscGetTime(&tf);CHKERRQ(ierr);
  app2 += tf - t0;

#if defined(PETSC_USE_INFO)
  ierr = PetscInfo4(C,"Num = ColorApp %g + %g + Mult_sp_den %g  = %g\n",app1,app2,Mult_sp_den,app1+app2+Mult_sp_den);CHKERRQ(ierr);
#endif
  PetscFunctionReturn(0);
}
Example #17
0
PetscErrorCode MatDuplicate_MPIAIJ_MatMatMult(Mat A, MatDuplicateOption op, Mat *M) 
{
  PetscErrorCode     ierr;
  Mat_MatMatMultMPI  *mult; 
  PetscContainer     container;

  PetscFunctionBegin;
  ierr = PetscObjectQuery((PetscObject)A,"Mat_MatMatMultMPI",(PetscObject *)&container);CHKERRQ(ierr);
  if (container) {
    ierr  = PetscContainerGetPointer(container,(void **)&mult);CHKERRQ(ierr); 
  } else {
    SETERRQ(PETSC_ERR_PLIB,"Container does not exit");
  }
  /* Note: the container is not duplicated, because it requires deep copying of
     several large data sets (see PetscContainerDestroy_Mat_MatMatMultMPI()).
     These data sets are only used for repeated calling of MatMatMultNumeric(). 
     *M is unlikely being used in this way. Thus we create *M with pure mpiaij format */
  ierr = (*mult->MatDuplicate)(A,op,M);CHKERRQ(ierr);
  (*M)->ops->destroy   = mult->MatDestroy;   /* = MatDestroy_MPIAIJ, *M doesn't duplicate A's container! */
  (*M)->ops->duplicate = mult->MatDuplicate; /* = MatDuplicate_MPIAIJ */
  PetscFunctionReturn(0);
}
Example #18
0
/*
    obj - the PETSc object where the scalar pointer came from
    base - the Fortran array address
    addr - the Fortran offset from base
    N    - the amount of data

    lx   - the array space that is to be passed to XXXXRestoreArray()
*/
PetscErrorCode PetscScalarAddressFromFortran(PetscObject obj,PetscScalar *base,size_t addr,PetscInt N,PetscScalar **lx)
{
  PetscErrorCode ierr;
  PetscInt       shift;
  PetscContainer container;
  PetscScalar    *tlx;

  ierr = PetscObjectQuery(obj,"GetArrayPtr",(PetscObject *)&container);CHKERRQ(ierr);
  if (container) {
    ierr  = PetscContainerGetPointer(container,(void**)lx);CHKERRQ(ierr);
    tlx   = base + addr;

    shift = *(PetscInt*)*lx;
    ierr  = PetscMemcpy(*lx,tlx,N*sizeof(PetscScalar));CHKERRQ(ierr);
    tlx   = (PetscScalar*)(((char *)tlx) - shift);
    ierr = PetscFree(tlx);CHKERRQ(ierr);
    ierr = PetscContainerDestroy(&container);CHKERRQ(ierr);
    ierr = PetscObjectCompose(obj,"GetArrayPtr",0);CHKERRQ(ierr);
  } else {
    *lx = base + addr;
  }
  return 0;
}
Example #19
0
static PetscErrorCode DMPlexVTKWriteAll_ASCII(DM dm, PetscViewer viewer)
{
  MPI_Comm                 comm;
  PetscViewer_VTK          *vtk = (PetscViewer_VTK*) viewer->data;
  FILE                     *fp;
  PetscViewerVTKObjectLink link;
  PetscSection             coordSection, globalCoordSection;
  PetscLayout              vLayout;
  Vec                      coordinates;
  PetscReal                lengthScale;
  PetscInt                 vMax, totVertices, totCells;
  PetscBool                hasPoint = PETSC_FALSE, hasCell = PETSC_FALSE, writePartition = PETSC_FALSE;
  PetscErrorCode           ierr;

  PetscFunctionBegin;
  ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr);
  ierr = PetscFOpen(comm, vtk->filename, "wb", &fp);CHKERRQ(ierr);
  ierr = PetscFPrintf(comm, fp, "# vtk DataFile Version 2.0\n");CHKERRQ(ierr);
  ierr = PetscFPrintf(comm, fp, "Simplicial Mesh Example\n");CHKERRQ(ierr);
  ierr = PetscFPrintf(comm, fp, "ASCII\n");CHKERRQ(ierr);
  ierr = PetscFPrintf(comm, fp, "DATASET UNSTRUCTURED_GRID\n");CHKERRQ(ierr);
  /* Vertices */
  ierr = DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale);CHKERRQ(ierr);
  ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
  ierr = PetscSectionCreateGlobalSection(coordSection, dm->sf, PETSC_FALSE, PETSC_FALSE, &globalCoordSection);CHKERRQ(ierr);
  ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
  ierr = DMPlexGetHybridBounds(dm, NULL, NULL, NULL, &vMax);CHKERRQ(ierr);
  if (vMax >= 0) {
    PetscInt pStart, pEnd, p, localSize = 0;

    ierr = PetscSectionGetChart(globalCoordSection, &pStart, &pEnd);CHKERRQ(ierr);
    pEnd = PetscMin(pEnd, vMax);
    for (p = pStart; p < pEnd; ++p) {
      PetscInt dof;

      ierr = PetscSectionGetDof(globalCoordSection, p, &dof);CHKERRQ(ierr);
      if (dof > 0) ++localSize;
    }
    ierr = PetscLayoutCreate(PetscObjectComm((PetscObject)dm), &vLayout);CHKERRQ(ierr);
    ierr = PetscLayoutSetLocalSize(vLayout, localSize);CHKERRQ(ierr);
    ierr = PetscLayoutSetBlockSize(vLayout, 1);CHKERRQ(ierr);
    ierr = PetscLayoutSetUp(vLayout);CHKERRQ(ierr);
  } else {
    ierr = PetscSectionGetPointLayout(PetscObjectComm((PetscObject)dm), globalCoordSection, &vLayout);CHKERRQ(ierr);
  }
  ierr = PetscLayoutGetSize(vLayout, &totVertices);CHKERRQ(ierr);
  ierr = PetscFPrintf(comm, fp, "POINTS %d double\n", totVertices);CHKERRQ(ierr);
  ierr = DMPlexVTKWriteSection_ASCII(dm, coordSection, globalCoordSection, coordinates, fp, 3, PETSC_DETERMINE, lengthScale);CHKERRQ(ierr);
  /* Cells */
  ierr = DMPlexVTKWriteCells_ASCII(dm, fp, &totCells);CHKERRQ(ierr);
  /* Vertex fields */
  for (link = vtk->link; link; link = link->next) {
    if ((link->ft == PETSC_VTK_POINT_FIELD) || (link->ft == PETSC_VTK_POINT_VECTOR_FIELD)) hasPoint = PETSC_TRUE;
    if ((link->ft == PETSC_VTK_CELL_FIELD)  || (link->ft == PETSC_VTK_CELL_VECTOR_FIELD))  hasCell  = PETSC_TRUE;
  }
  if (hasPoint) {
    ierr = PetscFPrintf(comm, fp, "POINT_DATA %d\n", totVertices);CHKERRQ(ierr);
    for (link = vtk->link; link; link = link->next) {
      Vec          X = (Vec) link->vec;
      DM           dmX;
      PetscSection section, globalSection, newSection = NULL;
      const char   *name;
      PetscInt     enforceDof = PETSC_DETERMINE;

      if ((link->ft != PETSC_VTK_POINT_FIELD) && (link->ft != PETSC_VTK_POINT_VECTOR_FIELD)) continue;
      if (link->ft == PETSC_VTK_POINT_VECTOR_FIELD) enforceDof = 3;
      ierr = PetscObjectGetName(link->vec, &name);CHKERRQ(ierr);
      ierr = VecGetDM(X, &dmX);CHKERRQ(ierr);
      if (dmX) {
        DMLabel  subpointMap, subpointMapX;
        PetscInt dim, dimX, pStart, pEnd, qStart, qEnd;

        ierr = DMGetDefaultSection(dmX, &section);CHKERRQ(ierr);
        /* Here is where we check whether dmX is a submesh of dm */
        ierr = DMGetDimension(dm,  &dim);CHKERRQ(ierr);
        ierr = DMGetDimension(dmX, &dimX);CHKERRQ(ierr);
        ierr = DMPlexGetChart(dm,  &pStart, &pEnd);CHKERRQ(ierr);
        ierr = DMPlexGetChart(dmX, &qStart, &qEnd);CHKERRQ(ierr);
        ierr = DMPlexGetSubpointMap(dm,  &subpointMap);CHKERRQ(ierr);
        ierr = DMPlexGetSubpointMap(dmX, &subpointMapX);CHKERRQ(ierr);
        if (((dim != dimX) || ((pEnd-pStart) < (qEnd-qStart))) && subpointMap && !subpointMapX) {
          const PetscInt *ind = NULL;
          IS              subpointIS;
          PetscInt        n = 0, q;

          ierr = PetscSectionGetChart(section, &qStart, &qEnd);CHKERRQ(ierr);
          ierr = DMPlexCreateSubpointIS(dm, &subpointIS);CHKERRQ(ierr);
          if (subpointIS) {
            ierr = ISGetLocalSize(subpointIS, &n);CHKERRQ(ierr);
            ierr = ISGetIndices(subpointIS, &ind);CHKERRQ(ierr);
          }
          ierr = PetscSectionCreate(comm, &newSection);CHKERRQ(ierr);
          ierr = PetscSectionSetChart(newSection, pStart, pEnd);CHKERRQ(ierr);
          for (q = qStart; q < qEnd; ++q) {
            PetscInt dof, off, p;

            ierr = PetscSectionGetDof(section, q, &dof);CHKERRQ(ierr);
            if (dof) {
              ierr = PetscFindInt(q, n, ind, &p);CHKERRQ(ierr);
              if (p >= pStart) {
                ierr = PetscSectionSetDof(newSection, p, dof);CHKERRQ(ierr);
                ierr = PetscSectionGetOffset(section, q, &off);CHKERRQ(ierr);
                ierr = PetscSectionSetOffset(newSection, p, off);CHKERRQ(ierr);
              }
            }
          }
          if (subpointIS) {
            ierr = ISRestoreIndices(subpointIS, &ind);CHKERRQ(ierr);
            ierr = ISDestroy(&subpointIS);CHKERRQ(ierr);
          }
          /* No need to setup section */
          section = newSection;
        }
      } else {
        ierr = PetscObjectQuery(link->vec, "section", (PetscObject*) &section);CHKERRQ(ierr);
        if (!section) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Vector %s had no PetscSection composed with it", name);
      }
      if (!section) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Vector %s had no PetscSection composed with it", name);
      ierr = PetscSectionCreateGlobalSection(section, dm->sf, PETSC_FALSE, PETSC_FALSE, &globalSection);CHKERRQ(ierr);
      ierr = DMPlexVTKWriteField_ASCII(dm, section, globalSection, X, name, fp, enforceDof, PETSC_DETERMINE, 1.0);CHKERRQ(ierr);
      ierr = PetscSectionDestroy(&globalSection);CHKERRQ(ierr);
      if (newSection) {ierr = PetscSectionDestroy(&newSection);CHKERRQ(ierr);}
    }
  }
  /* Cell Fields */
  ierr = PetscOptionsGetBool(((PetscObject) dm)->prefix, "-dm_view_partition", &writePartition, NULL);CHKERRQ(ierr);
  if (hasCell || writePartition) {
    ierr = PetscFPrintf(comm, fp, "CELL_DATA %d\n", totCells);CHKERRQ(ierr);
    for (link = vtk->link; link; link = link->next) {
      Vec          X = (Vec) link->vec;
      DM           dmX;
      PetscSection section, globalSection;
      const char   *name;
      PetscInt     enforceDof = PETSC_DETERMINE;

      if ((link->ft != PETSC_VTK_CELL_FIELD) && (link->ft != PETSC_VTK_CELL_VECTOR_FIELD)) continue;
      if (link->ft == PETSC_VTK_CELL_VECTOR_FIELD) enforceDof = 3;
      ierr = PetscObjectGetName(link->vec, &name);CHKERRQ(ierr);
      ierr = VecGetDM(X, &dmX);CHKERRQ(ierr);
      if (dmX) {
        ierr = DMGetDefaultSection(dmX, &section);CHKERRQ(ierr);
      } else {
        PetscContainer c;

        ierr = PetscObjectQuery(link->vec, "section", (PetscObject*) &c);CHKERRQ(ierr);
        if (!c) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Vector %s had no PetscSection composed with it", name);
        ierr = PetscContainerGetPointer(c, (void**) &section);CHKERRQ(ierr);
      }
      if (!section) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Vector %s had no PetscSection composed with it", name);
      ierr = PetscSectionCreateGlobalSection(section, dm->sf, PETSC_FALSE, PETSC_FALSE, &globalSection);CHKERRQ(ierr);
      ierr = DMPlexVTKWriteField_ASCII(dm, section, globalSection, X, name, fp, enforceDof, PETSC_DETERMINE, 1.0);CHKERRQ(ierr);
      ierr = PetscSectionDestroy(&globalSection);CHKERRQ(ierr);
    }
    if (writePartition) {
      ierr = PetscFPrintf(comm, fp, "SCALARS partition int 1\n");CHKERRQ(ierr);
      ierr = PetscFPrintf(comm, fp, "LOOKUP_TABLE default\n");CHKERRQ(ierr);
      ierr = DMPlexVTKWritePartition_ASCII(dm, fp);CHKERRQ(ierr);
    }
  }
  /* Cleanup */
  ierr = PetscSectionDestroy(&globalCoordSection);CHKERRQ(ierr);
  ierr = PetscLayoutDestroy(&vLayout);CHKERRQ(ierr);
  ierr = PetscFClose(comm, fp);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
Example #20
0
PetscErrorCode private_DMSwarmView_XDMF(DM dm,PetscViewer viewer)
{
  PetscBool      isswarm = PETSC_FALSE;
  const char     *viewername;
  char           datafile[PETSC_MAX_PATH_LEN];
  PetscViewer    fviewer;
  PetscInt       k,ng,dim;
  Vec            dvec;
  long int       *bytes = NULL;
  PetscContainer container = NULL;
  const char     *dmname;
  PetscErrorCode ierr;
  
  PetscFunctionBegin;
  ierr = PetscObjectQuery((PetscObject)viewer,"XDMFViewerContext",(PetscObject*)&container);CHKERRQ(ierr);
  if (container) {
    ierr = PetscContainerGetPointer(container,(void**)&bytes);CHKERRQ(ierr);
  } else SETERRQ(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP,"Valid to find attached data XDMFViewerContext");
  
  ierr = PetscObjectTypeCompare((PetscObject)dm,DMSWARM,&isswarm);CHKERRQ(ierr);
  if (!isswarm) SETERRQ(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP,"Only valid for DMSwarm");
  
  ierr = PetscObjectCompose((PetscObject)viewer,"DMSwarm",(PetscObject)dm);CHKERRQ(ierr);
  
  ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
  ierr = PetscObjectGetName((PetscObject)dm,&dmname);CHKERRQ(ierr);
  if (!dmname) {
    ierr = DMGetOptionsPrefix(dm,&dmname);CHKERRQ(ierr);
  }
  if (!dmname) {
    ierr = PetscViewerASCIIPrintf(viewer,"<Grid Name=\"DMSwarm\" GridType=\"Uniform\">\n");CHKERRQ(ierr);
  } else {
    ierr = PetscViewerASCIIPrintf(viewer,"<Grid Name=\"DMSwarm[%s]\" GridType=\"Uniform\">\n",dmname);CHKERRQ(ierr);
  }
  
  /* create a sub-viewer for topology, geometry and all data fields */
  /* name is viewer.name + "_swarm_fields.pbin" */
  ierr = PetscViewerCreate(PetscObjectComm((PetscObject)viewer),&fviewer);CHKERRQ(ierr);
  ierr = PetscViewerSetType(fviewer,PETSCVIEWERBINARY);CHKERRQ(ierr);
  ierr = PetscViewerBinarySetSkipHeader(fviewer,PETSC_TRUE);CHKERRQ(ierr);
  ierr = PetscViewerBinarySetSkipInfo(fviewer,PETSC_TRUE);CHKERRQ(ierr);
  ierr = PetscViewerFileSetMode(fviewer,FILE_MODE_WRITE);CHKERRQ(ierr);
  
  ierr = PetscViewerFileGetName(viewer,&viewername);CHKERRQ(ierr);
  ierr = private_CreateDataFileNameXDMF(viewername,datafile);CHKERRQ(ierr);
  ierr = PetscViewerFileSetName(fviewer,datafile);CHKERRQ(ierr);
  
  ierr = DMSwarmGetSize(dm,&ng);CHKERRQ(ierr);
  
  /* write topology header */
  ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPrintf(viewer,"<Topology Dimensions=\"%D\" TopologyType=\"Mixed\">\n",ng);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPrintf(viewer,"<DataItem Format=\"Binary\" Endian=\"Big\" DataType=\"Int\" Dimensions=\"%D\" Seek=\"%D\">\n",ng*3,bytes[0]);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPrintf(viewer,"%s\n",datafile);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPrintf(viewer,"</DataItem>\n");CHKERRQ(ierr);
  ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPrintf(viewer,"</Topology>\n");CHKERRQ(ierr);
  ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
  
  /* write topology data */
  for (k=0; k<ng; k++) {
    PetscInt pvertex[3];
    
    pvertex[0] = 1;
    pvertex[1] = 1;
    pvertex[2] = k;
    ierr = PetscViewerBinaryWrite(fviewer,pvertex,3,PETSC_INT,PETSC_FALSE);CHKERRQ(ierr);
  }
  bytes[0] += sizeof(PetscInt) * ng * 3;
  
  /* write geometry header */
  ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
  ierr = DMGetDimension(dm,&dim);CHKERRQ(ierr);
  switch (dim) {
    case 1:
      SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for 1D");
      break;
    case 2:
      ierr = PetscViewerASCIIPrintf(viewer,"<Geometry Type=\"XY\">\n");CHKERRQ(ierr);
      break;
    case 3:
      ierr = PetscViewerASCIIPrintf(viewer,"<Geometry Type=\"XYZ\">\n");CHKERRQ(ierr);
      break;
  }
  ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPrintf(viewer,"<DataItem Format=\"Binary\" Endian=\"Big\" DataType=\"Float\" Precision=\"8\" Dimensions=\"%D %D\" Seek=\"%D\">\n",ng,dim,bytes[0]);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPrintf(viewer,"%s\n",datafile);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPrintf(viewer,"</DataItem>\n");CHKERRQ(ierr);
  ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPrintf(viewer,"</Geometry>\n");CHKERRQ(ierr);
  ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
  
  /* write geometry data */
  ierr = DMSwarmCreateGlobalVectorFromField(dm,DMSwarmPICField_coor,&dvec);CHKERRQ(ierr);
  ierr = VecView(dvec,fviewer);CHKERRQ(ierr);
  ierr = DMSwarmDestroyGlobalVectorFromField(dm,DMSwarmPICField_coor,&dvec);CHKERRQ(ierr);
  bytes[0] += sizeof(PetscReal) * ng * dim;
  
  ierr = PetscViewerDestroy(&fviewer);CHKERRQ(ierr);
  
  PetscFunctionReturn(0);
}
Example #21
0
PetscErrorCode private_ISView_Swarm_XDMF(IS is,PetscViewer viewer)
{
  long int       *bytes = NULL;
  PetscContainer container = NULL;
  const char     *viewername;
  char           datafile[PETSC_MAX_PATH_LEN];
  PetscViewer    fviewer;
  PetscInt       N,bs;
  const char     *vecname;
  char           fieldname[PETSC_MAX_PATH_LEN];
  PetscErrorCode ierr;
  
  PetscFunctionBegin;
  ierr = PetscObjectQuery((PetscObject)viewer,"XDMFViewerContext",(PetscObject*)&container);CHKERRQ(ierr);
  if (container) {
    ierr = PetscContainerGetPointer(container,(void**)&bytes);CHKERRQ(ierr);
  } else SETERRQ(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP,"Valid to find attached data XDMFViewerContext");
  
  ierr = PetscViewerFileGetName(viewer,&viewername);CHKERRQ(ierr);
  ierr = private_CreateDataFileNameXDMF(viewername,datafile);CHKERRQ(ierr);
  
  /* re-open a sub-viewer for all data fields */
  /* name is viewer.name + "_swarm_fields.pbin" */
  ierr = PetscViewerCreate(PetscObjectComm((PetscObject)viewer),&fviewer);CHKERRQ(ierr);
  ierr = PetscViewerSetType(fviewer,PETSCVIEWERBINARY);CHKERRQ(ierr);
  ierr = PetscViewerBinarySetSkipHeader(fviewer,PETSC_TRUE);CHKERRQ(ierr);
  ierr = PetscViewerBinarySetSkipInfo(fviewer,PETSC_TRUE);CHKERRQ(ierr);
  ierr = PetscViewerFileSetMode(fviewer,FILE_MODE_APPEND);CHKERRQ(ierr);
  ierr = PetscViewerFileSetName(fviewer,datafile);CHKERRQ(ierr);
  
  ierr = ISGetSize(is,&N);CHKERRQ(ierr);
  ierr = ISGetBlockSize(is,&bs);CHKERRQ(ierr);
  N = N/bs;
  ierr = PetscObjectGetName((PetscObject)is,&vecname);CHKERRQ(ierr);
  if (!vecname) {
    ierr = PetscSNPrintf(fieldname,PETSC_MAX_PATH_LEN-1,"swarmfield_%D",((PetscObject)is)->tag);CHKERRQ(ierr);
  } else {
    ierr = PetscSNPrintf(fieldname,PETSC_MAX_PATH_LEN-1,"%s",vecname);CHKERRQ(ierr);
  }
  
  /* write data header */
  ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPrintf(viewer,"<Attribute Center=\"Node\" Name=\"%s\" Type=\"None\">\n",fieldname);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
  if (bs == 1) {
    ierr = PetscViewerASCIIPrintf(viewer,"<DataItem Format=\"Binary\" Endian=\"Big\" DataType=\"Int\" Precision=\"4\" Dimensions=\"%D\" Seek=\"%D\">\n",N,bytes[0]);CHKERRQ(ierr);
  } else {
    ierr = PetscViewerASCIIPrintf(viewer,"<DataItem Format=\"Binary\" Endian=\"Big\" DataType=\"Int\" Precision=\"4\" Dimensions=\"%D %D\" Seek=\"%D\">\n",N,bs,bytes[0]);CHKERRQ(ierr);
  }
  ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPrintf(viewer,"%s\n",datafile);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPrintf(viewer,"</DataItem>\n");CHKERRQ(ierr);
  ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPrintf(viewer,"</Attribute>\n");CHKERRQ(ierr);
  ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
  
  /* write data */
  ierr = ISView(is,fviewer);CHKERRQ(ierr);
  bytes[0] += sizeof(PetscInt) * N * bs;
  
  ierr = PetscViewerDestroy(&fviewer);CHKERRQ(ierr);
  
  PetscFunctionReturn(0);
}
Example #22
0
/*
    Performs an efficient scatter on the rows of B needed by this process; this is
    a modification of the VecScatterBegin_() routines.
*/
PetscErrorCode MatMPIDenseScatter(Mat A,Mat B,Mat C,Mat *outworkB)
{
  Mat_MPIAIJ             *aij = (Mat_MPIAIJ*)A->data;
  PetscErrorCode         ierr;
  PetscScalar            *b,*w,*svalues,*rvalues;
  VecScatter             ctx = aij->Mvctx; 
  VecScatter_MPI_General *from = (VecScatter_MPI_General*) ctx->fromdata;
  VecScatter_MPI_General *to   = ( VecScatter_MPI_General*) ctx->todata;
  PetscInt               i,j,k;
  PetscInt               *sindices,*sstarts,*rindices,*rstarts;
  PetscMPIInt            *sprocs,*rprocs,nrecvs;
  MPI_Request            *swaits,*rwaits;
  MPI_Comm               comm = ((PetscObject)A)->comm;
  PetscMPIInt            tag = ((PetscObject)ctx)->tag,ncols = B->cmap->N, nrows = aij->B->cmap->n,imdex,nrowsB = B->rmap->n;
  MPI_Status             status;
  MPIAIJ_MPIDense        *contents;
  PetscContainer         cont;
  Mat                    workB;

  PetscFunctionBegin;
  ierr = PetscObjectQuery((PetscObject)C,"workB",(PetscObject*)&cont);CHKERRQ(ierr);
  ierr = PetscContainerGetPointer(cont,(void**)&contents);CHKERRQ(ierr);

  workB = *outworkB = contents->workB;
  if (nrows != workB->rmap->n) SETERRQ2(PETSC_ERR_PLIB,"Number of rows of workB %D not equal to columns of aij->B %D",nrows,workB->cmap->n);
  sindices  = to->indices;
  sstarts   = to->starts;
  sprocs    = to->procs;
  swaits    = contents->swaits;
  svalues   = contents->svalues;

  rindices  = from->indices;
  rstarts   = from->starts;
  rprocs    = from->procs;
  rwaits    = contents->rwaits;
  rvalues   = contents->rvalues;

  ierr = MatGetArray(B,&b);CHKERRQ(ierr);
  ierr = MatGetArray(workB,&w);CHKERRQ(ierr);

  for (i=0; i<from->n; i++) {
    ierr = MPI_Irecv(rvalues+ncols*rstarts[i],ncols*(rstarts[i+1]-rstarts[i]),MPIU_SCALAR,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr);
  } 

  for (i=0; i<to->n; i++) {
    /* pack a message at a time */
    CHKMEMQ;
    for (j=0; j<sstarts[i+1]-sstarts[i]; j++){
      for (k=0; k<ncols; k++) {
        svalues[ncols*(sstarts[i] + j) + k] = b[sindices[sstarts[i]+j] + nrowsB*k];
      }
    }
    CHKMEMQ;
    ierr = MPI_Isend(svalues+ncols*sstarts[i],ncols*(sstarts[i+1]-sstarts[i]),MPIU_SCALAR,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr);
  }

  nrecvs = from->n;
  while (nrecvs) {
    ierr = MPI_Waitany(from->n,rwaits,&imdex,&status);CHKERRQ(ierr);
    nrecvs--;
    /* unpack a message at a time */
    CHKMEMQ;
    for (j=0; j<rstarts[imdex+1]-rstarts[imdex]; j++){
      for (k=0; k<ncols; k++) {
        w[rindices[rstarts[imdex]+j] + nrows*k] = rvalues[ncols*(rstarts[imdex] + j) + k];
      }
    }
    CHKMEMQ;
  }
  if (to->n) {ierr = MPI_Waitall(to->n,swaits,to->sstatus);CHKERRQ(ierr)}
Example #23
0
/*
     DMCoarsen_SNESVI - Computes the regular coarsened DM then computes additional information about its inactive set

*/
PetscErrorCode  DMCoarsen_SNESVI(DM dm1,MPI_Comm comm,DM *dm2)
{
  PetscErrorCode          ierr;
  PetscContainer          isnes;
  DM_SNESVI               *dmsnesvi1;
  Vec                     finemarked,coarsemarked;
  IS                      inactive;
  VecScatter              inject;
  const PetscInt          *index;
  PetscInt                n,k,cnt = 0,rstart,*coarseindex;
  PetscScalar             *marked;

  PetscFunctionBegin;
  ierr = PetscObjectQuery((PetscObject)dm1,"VI",(PetscObject *)&isnes);CHKERRQ(ierr);
  if (!isnes) SETERRQ(((PetscObject)dm1)->comm,PETSC_ERR_PLIB,"Composed VI data structure is missing");
  ierr = PetscContainerGetPointer(isnes,(void**)&dmsnesvi1);CHKERRQ(ierr);

  /* get the original coarsen */
  ierr = (*dmsnesvi1->coarsen)(dm1,comm,dm2);CHKERRQ(ierr);

  /* not sure why this extra reference is needed, but without the dm2 disappears too early */
  ierr = PetscObjectReference((PetscObject)*dm2);CHKERRQ(ierr);

  /* need to set back global vectors in order to use the original injection */
  ierr = DMClearGlobalVectors(dm1);CHKERRQ(ierr);
  dm1->ops->createglobalvector = dmsnesvi1->createglobalvector;
  ierr = DMCreateGlobalVector(dm1,&finemarked);CHKERRQ(ierr);
  ierr = DMCreateGlobalVector(*dm2,&coarsemarked);CHKERRQ(ierr);

  /*
     fill finemarked with locations of inactive points
  */
  ierr = ISGetIndices(dmsnesvi1->inactive,&index);CHKERRQ(ierr);
  ierr = ISGetLocalSize(dmsnesvi1->inactive,&n);CHKERRQ(ierr);
  ierr = VecSet(finemarked,0.0);CHKERRQ(ierr);
  for (k=0;k<n;k++){
      ierr = VecSetValue(finemarked,index[k],1.0,INSERT_VALUES);CHKERRQ(ierr);
  }
  ierr = VecAssemblyBegin(finemarked);CHKERRQ(ierr);
  ierr = VecAssemblyEnd(finemarked);CHKERRQ(ierr);

  ierr = DMCreateInjection(*dm2,dm1,&inject);CHKERRQ(ierr);
  ierr = VecScatterBegin(inject,finemarked,coarsemarked,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
  ierr = VecScatterEnd(inject,finemarked,coarsemarked,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
  ierr = VecScatterDestroy(&inject);CHKERRQ(ierr);

  /*
     create index set list of coarse inactive points from coarsemarked
  */
  ierr = VecGetLocalSize(coarsemarked,&n);CHKERRQ(ierr);
  ierr = VecGetOwnershipRange(coarsemarked,&rstart,PETSC_NULL);CHKERRQ(ierr);
  ierr = VecGetArray(coarsemarked,&marked);CHKERRQ(ierr);
  for (k=0; k<n; k++) {
    if (marked[k] != 0.0) cnt++;
  }
  ierr = PetscMalloc(cnt*sizeof(PetscInt),&coarseindex);CHKERRQ(ierr);
  cnt  = 0;
  for (k=0; k<n; k++) {
    if (marked[k] != 0.0) coarseindex[cnt++] = k + rstart;
  }
  ierr = VecRestoreArray(coarsemarked,&marked);CHKERRQ(ierr);
  ierr = ISCreateGeneral(((PetscObject)coarsemarked)->comm,cnt,coarseindex,PETSC_OWN_POINTER,&inactive);CHKERRQ(ierr);

  ierr = DMClearGlobalVectors(dm1);CHKERRQ(ierr);
  dm1->ops->createglobalvector = DMCreateGlobalVector_SNESVI;
  ierr = DMSetVI(*dm2,inactive);CHKERRQ(ierr);

  ierr = VecDestroy(&finemarked);CHKERRQ(ierr);
  ierr = VecDestroy(&coarsemarked);CHKERRQ(ierr);
  ierr = ISDestroy(&inactive);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
Example #24
0
static PetscErrorCode SNESComputeJacobian_DMDA(SNES snes,Vec X,Mat *A,Mat *B,MatStructure *mstr,void *ctx)
{
  PetscErrorCode ierr;
  DM             dm;
  DMSNES_DA      *dmdasnes = (DMSNES_DA*)ctx;
  DMDALocalInfo  info;
  Vec            Xloc;
  void           *x;

  PetscFunctionBegin;
  if (!dmdasnes->residuallocal) SETERRQ(PetscObjectComm((PetscObject)snes),PETSC_ERR_PLIB,"Corrupt context");
  ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);

  if (dmdasnes->jacobianlocal) {
    ierr = DMGetLocalVector(dm,&Xloc);CHKERRQ(ierr);
    ierr = DMGlobalToLocalBegin(dm,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
    ierr = DMGlobalToLocalEnd(dm,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
    ierr = DMDAGetLocalInfo(dm,&info);CHKERRQ(ierr);
    ierr = DMDAVecGetArray(dm,Xloc,&x);CHKERRQ(ierr);
    CHKMEMQ;
    ierr = (*dmdasnes->jacobianlocal)(&info,x,*A,*B,mstr,dmdasnes->jacobianlocalctx);CHKERRQ(ierr);
    CHKMEMQ;
    ierr = DMDAVecRestoreArray(dm,Xloc,&x);CHKERRQ(ierr);
    ierr = DMRestoreLocalVector(dm,&Xloc);CHKERRQ(ierr);
  } else {
    MatFDColoring fdcoloring;
    ierr = PetscObjectQuery((PetscObject)dm,"DMDASNES_FDCOLORING",(PetscObject*)&fdcoloring);CHKERRQ(ierr);
    if (!fdcoloring) {
      ISColoring coloring;

      ierr = DMCreateColoring(dm,dm->coloringtype,&coloring);CHKERRQ(ierr);
      ierr = MatFDColoringCreate(*B,coloring,&fdcoloring);CHKERRQ(ierr);
      ierr = ISColoringDestroy(&coloring);CHKERRQ(ierr);
      switch (dm->coloringtype) {
      case IS_COLORING_GLOBAL:
        ierr = MatFDColoringSetFunction(fdcoloring,(PetscErrorCode (*)(void))SNESComputeFunction_DMDA,dmdasnes);CHKERRQ(ierr);
        break;
      default: SETERRQ1(PetscObjectComm((PetscObject)snes),PETSC_ERR_SUP,"No support for coloring type '%s'",ISColoringTypes[dm->coloringtype]);
      }
      ierr = PetscObjectSetOptionsPrefix((PetscObject)fdcoloring,((PetscObject)dm)->prefix);CHKERRQ(ierr);
      ierr = MatFDColoringSetFromOptions(fdcoloring);CHKERRQ(ierr);
      ierr = PetscObjectCompose((PetscObject)dm,"DMDASNES_FDCOLORING",(PetscObject)fdcoloring);CHKERRQ(ierr);
      ierr = PetscObjectDereference((PetscObject)fdcoloring);CHKERRQ(ierr);

      /* The following breaks an ugly reference counting loop that deserves a paragraph. MatFDColoringApply() will call
       * VecDuplicate() with the state Vec and store inside the MatFDColoring. This Vec will duplicate the Vec, but the
       * MatFDColoring is composed with the DM. We dereference the DM here so that the reference count will eventually
       * drop to 0. Note the code in DMDestroy() that exits early for a negative reference count. That code path will be
       * taken when the PetscObjectList for the Vec inside MatFDColoring is destroyed.
       */
      ierr = PetscObjectDereference((PetscObject)dm);CHKERRQ(ierr);
    }
    *mstr = SAME_NONZERO_PATTERN;
    ierr  = MatFDColoringApply(*B,fdcoloring,X,mstr,snes);CHKERRQ(ierr);
  }
  /* This will be redundant if the user called both, but it's too common to forget. */
  if (*A != *B) {
    ierr = MatAssemblyBegin(*A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatAssemblyEnd(*A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}
Example #25
0
File: gr1.c Project: Kun-Qu/petsc
PetscErrorCode VecView_MPI_Draw_DA1d(Vec xin,PetscViewer v)
{
  DM                da;
  PetscErrorCode    ierr;
  PetscMPIInt       rank,size,tag1,tag2;
  PetscInt          i,n,N,step,istart,isize,j,nbounds;
  MPI_Status        status;
  PetscReal         coors[4],ymin,ymax,min,max,xmin,xmax,tmp,xgtmp;
  const PetscScalar *array,*xg;
  PetscDraw         draw;
  PetscBool         isnull,showpoints = PETSC_FALSE;
  MPI_Comm          comm;
  PetscDrawAxis     axis;
  Vec               xcoor;
  DMDABoundaryType  bx;
  const PetscReal   *bounds;
  PetscInt          *displayfields;
  PetscInt          k,ndisplayfields;
  PetscBool         flg,hold;

  PetscFunctionBegin;
  ierr = PetscViewerDrawGetDraw(v,0,&draw);CHKERRQ(ierr);
  ierr = PetscDrawIsNull(draw,&isnull);CHKERRQ(ierr); if (isnull) PetscFunctionReturn(0);
  ierr = PetscViewerDrawGetBounds(v,&nbounds,&bounds);CHKERRQ(ierr);

  ierr = PetscObjectQuery((PetscObject)xin,"DM",(PetscObject*)&da);CHKERRQ(ierr);
  if (!da) SETERRQ(((PetscObject)xin)->comm,PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA");

  ierr = PetscOptionsGetBool(PETSC_NULL,"-draw_vec_mark_points",&showpoints,PETSC_NULL);CHKERRQ(ierr);

  ierr = DMDAGetInfo(da,0,&N,0,0,0,0,0,&step,0,&bx,0,0,0);CHKERRQ(ierr);
  ierr = DMDAGetCorners(da,&istart,0,0,&isize,0,0);CHKERRQ(ierr);
  ierr = VecGetArrayRead(xin,&array);CHKERRQ(ierr);
  ierr = VecGetLocalSize(xin,&n);CHKERRQ(ierr);
  n    = n/step;

  /* get coordinates of nodes */
  ierr = DMDAGetCoordinates(da,&xcoor);CHKERRQ(ierr);
  if (!xcoor) {
    ierr = DMDASetUniformCoordinates(da,0.0,1.0,0.0,0.0,0.0,0.0);CHKERRQ(ierr);
    ierr = DMDAGetCoordinates(da,&xcoor);CHKERRQ(ierr);
  }
  ierr = VecGetArrayRead(xcoor,&xg);CHKERRQ(ierr);

  ierr = PetscObjectGetComm((PetscObject)xin,&comm);CHKERRQ(ierr);
  ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 
  ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);

  /*
      Determine the min and max x coordinate in plot 
  */
  if (!rank) {
    xmin = PetscRealPart(xg[0]);
  } 
  if (rank == size-1) {
    xmax = PetscRealPart(xg[n-1]);
  }
  ierr = MPI_Bcast(&xmin,1,MPIU_REAL,0,comm);CHKERRQ(ierr);
  ierr = MPI_Bcast(&xmax,1,MPIU_REAL,size-1,comm);CHKERRQ(ierr);

  ierr = PetscMalloc(step*sizeof(PetscInt),&displayfields);CHKERRQ(ierr);
  for (i=0; i<step; i++) displayfields[i] = i;
  ndisplayfields = step;
  ierr = PetscOptionsGetIntArray(PETSC_NULL,"-draw_fields",displayfields,&ndisplayfields,&flg);CHKERRQ(ierr);
  if (!flg) ndisplayfields = step;
  for (k=0; k<ndisplayfields; k++) {
    j = displayfields[k];
    ierr = PetscViewerDrawGetDraw(v,k,&draw);CHKERRQ(ierr);
    ierr = PetscDrawCheckResizedWindow(draw);CHKERRQ(ierr);

    /*
        Determine the min and max y coordinate in plot 
    */
    min = 1.e20; max = -1.e20;
    for (i=0; i<n; i++) {
      if (PetscRealPart(array[j+i*step]) < min) min = PetscRealPart(array[j+i*step]);
      if (PetscRealPart(array[j+i*step]) > max) max = PetscRealPart(array[j+i*step]);
    }
    if (min + 1.e-10 > max) {
      min -= 1.e-5;
      max += 1.e-5;
    }
    if (j < nbounds) {
      min = PetscMin(min,bounds[2*j]);
      max = PetscMax(max,bounds[2*j+1]);
    }

    ierr = MPI_Reduce(&min,&ymin,1,MPIU_REAL,MPIU_MIN,0,comm);CHKERRQ(ierr);
    ierr = MPI_Reduce(&max,&ymax,1,MPIU_REAL,MPIU_MAX,0,comm);CHKERRQ(ierr);

    ierr = PetscViewerDrawGetHold(v,&hold);CHKERRQ(ierr);
    if (!hold) {
      ierr = PetscDrawSynchronizedClear(draw);CHKERRQ(ierr);
    }
    ierr = PetscViewerDrawGetDrawAxis(v,k,&axis);CHKERRQ(ierr);
    ierr = PetscLogObjectParent(draw,axis);CHKERRQ(ierr);
    if (!rank) {
      const char *title;

      ierr = PetscDrawAxisSetLimits(axis,xmin,xmax,ymin,ymax);CHKERRQ(ierr);
      ierr = PetscDrawAxisDraw(axis);CHKERRQ(ierr);
      ierr = PetscDrawGetCoordinates(draw,coors,coors+1,coors+2,coors+3);CHKERRQ(ierr);
      ierr = DMDAGetFieldName(da,j,&title);CHKERRQ(ierr);
      if (title) {ierr = PetscDrawSetTitle(draw,title);CHKERRQ(ierr);}
    }
    ierr = MPI_Bcast(coors,4,MPIU_REAL,0,comm);CHKERRQ(ierr);
    if (rank) {
      ierr = PetscDrawSetCoordinates(draw,coors[0],coors[1],coors[2],coors[3]);CHKERRQ(ierr);
    }

    /* draw local part of vector */
    ierr = PetscObjectGetNewTag((PetscObject)xin,&tag1);CHKERRQ(ierr);
    ierr = PetscObjectGetNewTag((PetscObject)xin,&tag2);CHKERRQ(ierr);
    if (rank < size-1) { /*send value to right */
      ierr = MPI_Send((void*)&array[j+(n-1)*step],1,MPIU_REAL,rank+1,tag1,comm);CHKERRQ(ierr);
      ierr = MPI_Send((void*)&xg[n-1],1,MPIU_REAL,rank+1,tag1,comm);CHKERRQ(ierr);
    }
    if (!rank && bx == DMDA_BOUNDARY_PERIODIC && size > 1) { /* first processor sends first value to last */
      ierr = MPI_Send((void*)&array[j],1,MPIU_REAL,size-1,tag2,comm);CHKERRQ(ierr);
    }

    for (i=1; i<n; i++) {
      ierr = PetscDrawLine(draw,PetscRealPart(xg[i-1]),PetscRealPart(array[j+step*(i-1)]),PetscRealPart(xg[i]),PetscRealPart(array[j+step*i]),PETSC_DRAW_RED);CHKERRQ(ierr);
      if (showpoints) {
        ierr = PetscDrawPoint(draw,PetscRealPart(xg[i-1]),PetscRealPart(array[j+step*(i-1)]),PETSC_DRAW_BLACK);CHKERRQ(ierr);
      }
    }
    if (rank) { /* receive value from left */
      ierr = MPI_Recv(&tmp,1,MPIU_REAL,rank-1,tag1,comm,&status);CHKERRQ(ierr);
      ierr = MPI_Recv(&xgtmp,1,MPIU_REAL,rank-1,tag1,comm,&status);CHKERRQ(ierr);
      ierr = PetscDrawLine(draw,xgtmp,tmp,PetscRealPart(xg[0]),PetscRealPart(array[j]),PETSC_DRAW_RED);CHKERRQ(ierr);
      if (showpoints) {
        ierr = PetscDrawPoint(draw,xgtmp,tmp,PETSC_DRAW_BLACK);CHKERRQ(ierr);
      }
    }
    if (rank == size-1 && bx == DMDA_BOUNDARY_PERIODIC && size > 1) {
      ierr = MPI_Recv(&tmp,1,MPIU_REAL,0,tag2,comm,&status);CHKERRQ(ierr);
      ierr = PetscDrawLine(draw,PetscRealPart(xg[n-2]),PetscRealPart(array[j+step*(n-1)]),PetscRealPart(xg[n-1]),tmp,PETSC_DRAW_RED);CHKERRQ(ierr);
      if (showpoints) {
        ierr = PetscDrawPoint(draw,PetscRealPart(xg[n-2]),PetscRealPart(array[j+step*(n-1)]),PETSC_DRAW_BLACK);CHKERRQ(ierr);
      }
    }
    ierr = PetscDrawSynchronizedFlush(draw);CHKERRQ(ierr);
    ierr = PetscDrawPause(draw);CHKERRQ(ierr);
  }
  ierr = PetscFree(displayfields);CHKERRQ(ierr);
  ierr = VecRestoreArrayRead(xcoor,&xg);CHKERRQ(ierr);
  ierr = VecRestoreArrayRead(xin,&array);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
Example #26
0
File: dmi.c Project: plguhur/petsc
/* This assumes that the DM has been cloned prior to the call */
PetscErrorCode DMCreateSubDM_Section_Private(DM dm, PetscInt numFields, PetscInt fields[], IS *is, DM *subdm)
{
  PetscSection   section, sectionGlobal;
  PetscInt      *subIndices;
  PetscInt       subSize = 0, subOff = 0, nF, f, pStart, pEnd, p;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  if (!numFields) PetscFunctionReturn(0);
  ierr = DMGetDefaultSection(dm, &section);CHKERRQ(ierr);
  ierr = DMGetDefaultGlobalSection(dm, &sectionGlobal);CHKERRQ(ierr);
  if (!section) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Must set default section for DM before splitting fields");
  if (!sectionGlobal) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Must set default global section for DM before splitting fields");
  ierr = PetscSectionGetNumFields(section, &nF);CHKERRQ(ierr);
  if (numFields > nF) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Number of requested fields %d greater than number of DM fields %d", numFields, nF);
  if (is) {
    ierr = PetscSectionGetChart(sectionGlobal, &pStart, &pEnd);CHKERRQ(ierr);
    for (p = pStart; p < pEnd; ++p) {
      PetscInt gdof;

      ierr = PetscSectionGetDof(sectionGlobal, p, &gdof);CHKERRQ(ierr);
      if (gdof > 0) {
        for (f = 0; f < numFields; ++f) {
          PetscInt fdof, fcdof;

          ierr     = PetscSectionGetFieldDof(section, p, fields[f], &fdof);CHKERRQ(ierr);
          ierr     = PetscSectionGetFieldConstraintDof(section, p, fields[f], &fcdof);CHKERRQ(ierr);
          subSize += fdof-fcdof;
        }
      }
    }
    ierr = PetscMalloc1(subSize, &subIndices);CHKERRQ(ierr);
    for (p = pStart; p < pEnd; ++p) {
      PetscInt gdof, goff;

      ierr = PetscSectionGetDof(sectionGlobal, p, &gdof);CHKERRQ(ierr);
      if (gdof > 0) {
        ierr = PetscSectionGetOffset(sectionGlobal, p, &goff);CHKERRQ(ierr);
        for (f = 0; f < numFields; ++f) {
          PetscInt fdof, fcdof, fc, f2, poff = 0;

          /* Can get rid of this loop by storing field information in the global section */
          for (f2 = 0; f2 < fields[f]; ++f2) {
            ierr  = PetscSectionGetFieldDof(section, p, f2, &fdof);CHKERRQ(ierr);
            ierr  = PetscSectionGetFieldConstraintDof(section, p, f2, &fcdof);CHKERRQ(ierr);
            poff += fdof-fcdof;
          }
          ierr = PetscSectionGetFieldDof(section, p, fields[f], &fdof);CHKERRQ(ierr);
          ierr = PetscSectionGetFieldConstraintDof(section, p, fields[f], &fcdof);CHKERRQ(ierr);
          for (fc = 0; fc < fdof-fcdof; ++fc, ++subOff) {
            subIndices[subOff] = goff+poff+fc;
          }
        }
      }
    }
    ierr = ISCreateGeneral(PetscObjectComm((PetscObject)dm), subSize, subIndices, PETSC_OWN_POINTER, is);CHKERRQ(ierr);
  }
  if (subdm) {
    PetscSection subsection;
    PetscBool    haveNull = PETSC_FALSE;
    PetscInt     f, nf = 0;

    ierr = PetscSectionCreateSubsection(section, numFields, fields, &subsection);CHKERRQ(ierr);
    ierr = DMSetDefaultSection(*subdm, subsection);CHKERRQ(ierr);
    ierr = PetscSectionDestroy(&subsection);CHKERRQ(ierr);
    for (f = 0; f < numFields; ++f) {
      (*subdm)->nullspaceConstructors[f] = dm->nullspaceConstructors[fields[f]];
      if ((*subdm)->nullspaceConstructors[f]) {
        haveNull = PETSC_TRUE;
        nf       = f;
      }
    }
    if (haveNull && is) {
      MatNullSpace nullSpace;

      ierr = (*(*subdm)->nullspaceConstructors[nf])(*subdm, nf, &nullSpace);CHKERRQ(ierr);
      ierr = PetscObjectCompose((PetscObject) *is, "nullspace", (PetscObject) nullSpace);CHKERRQ(ierr);
      ierr = MatNullSpaceDestroy(&nullSpace);CHKERRQ(ierr);
    }
    if (dm->prob) {
      PetscInt Nf;

      ierr = PetscDSGetNumFields(dm->prob, &Nf);CHKERRQ(ierr);
      if (nF != Nf) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "The number of DM fields %d does not match the number of Section fields %d", Nf, nF);
      ierr = DMSetNumFields(*subdm, numFields);CHKERRQ(ierr);
      for (f = 0; f < numFields; ++f) {
        PetscObject disc;

        ierr = DMGetField(dm, fields[f], &disc);CHKERRQ(ierr);
        ierr = DMSetField(*subdm, f, disc);CHKERRQ(ierr);
      }
      if (numFields == 1 && is) {
        PetscObject disc, space, pmat;

        ierr = DMGetField(*subdm, 0, &disc);CHKERRQ(ierr);
        ierr = PetscObjectQuery(disc, "nullspace", &space);CHKERRQ(ierr);
        if (space) {ierr = PetscObjectCompose((PetscObject) *is, "nullspace", space);CHKERRQ(ierr);}
        ierr = PetscObjectQuery(disc, "nearnullspace", &space);CHKERRQ(ierr);
        if (space) {ierr = PetscObjectCompose((PetscObject) *is, "nearnullspace", space);CHKERRQ(ierr);}
        ierr = PetscObjectQuery(disc, "pmat", &pmat);CHKERRQ(ierr);
        if (pmat) {ierr = PetscObjectCompose((PetscObject) *is, "pmat", pmat);CHKERRQ(ierr);}
      }
    }
  }
#if 0
  /* We need a way to filter the original SF for given fields:
       - Keeping the original section around it too much I think
       - We could keep the distributed section, and subset it
   */
  if (dm->sfNatural) {
    PetscSF sfNatural;

    ierr = PetscSectionCreateSubsection(dm->originalSection, numFields, fields, &(*subdm)->originalSection);CHKERRQ(ierr);
    ierr = DMPlexCreateGlobalToNaturalPetscSF(*subdm, &sfNatural);CHKERRQ(ierr);
    ierr = DMPlexSetGlobalToNaturalPetscSF(*subdm, sfNatural);CHKERRQ(ierr);
  }
#endif
  PetscFunctionReturn(0);
}
Example #27
0
File: dmi.c Project: ZJLi2013/petsc
/* This assumes that the DM has been cloned prior to the call */
PetscErrorCode DMCreateSubDM_Section_Private(DM dm, PetscInt numFields, PetscInt fields[], IS *is, DM *subdm)
{
  PetscSection   section, sectionGlobal;
  PetscInt      *subIndices;
  PetscInt       subSize = 0, subOff = 0, nF, f, pStart, pEnd, p;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  if (!numFields) PetscFunctionReturn(0);
  ierr = DMGetDefaultSection(dm, &section);CHKERRQ(ierr);
  ierr = DMGetDefaultGlobalSection(dm, &sectionGlobal);CHKERRQ(ierr);
  if (!section) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Must set default section for DM before splitting fields");
  if (!sectionGlobal) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Must set default global section for DM before splitting fields");
  ierr = PetscSectionGetNumFields(section, &nF);CHKERRQ(ierr);
  if (numFields > nF) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Number of requested fields %d greater than number of DM fields %d", numFields, nF);
  if (is) {
    ierr = PetscSectionGetChart(sectionGlobal, &pStart, &pEnd);CHKERRQ(ierr);
    for (p = pStart; p < pEnd; ++p) {
      PetscInt gdof;

      ierr = PetscSectionGetDof(sectionGlobal, p, &gdof);CHKERRQ(ierr);
      if (gdof > 0) {
        for (f = 0; f < numFields; ++f) {
          PetscInt fdof, fcdof;

          ierr     = PetscSectionGetFieldDof(section, p, fields[f], &fdof);CHKERRQ(ierr);
          ierr     = PetscSectionGetFieldConstraintDof(section, p, fields[f], &fcdof);CHKERRQ(ierr);
          subSize += fdof-fcdof;
        }
      }
    }
    ierr = PetscMalloc1(subSize, &subIndices);CHKERRQ(ierr);
    for (p = pStart; p < pEnd; ++p) {
      PetscInt gdof, goff;

      ierr = PetscSectionGetDof(sectionGlobal, p, &gdof);CHKERRQ(ierr);
      if (gdof > 0) {
        ierr = PetscSectionGetOffset(sectionGlobal, p, &goff);CHKERRQ(ierr);
        for (f = 0; f < numFields; ++f) {
          PetscInt fdof, fcdof, fc, f2, poff = 0;

          /* Can get rid of this loop by storing field information in the global section */
          for (f2 = 0; f2 < fields[f]; ++f2) {
            ierr  = PetscSectionGetFieldDof(section, p, f2, &fdof);CHKERRQ(ierr);
            ierr  = PetscSectionGetFieldConstraintDof(section, p, f2, &fcdof);CHKERRQ(ierr);
            poff += fdof-fcdof;
          }
          ierr = PetscSectionGetFieldDof(section, p, fields[f], &fdof);CHKERRQ(ierr);
          ierr = PetscSectionGetFieldConstraintDof(section, p, fields[f], &fcdof);CHKERRQ(ierr);
          for (fc = 0; fc < fdof-fcdof; ++fc, ++subOff) {
            subIndices[subOff] = goff+poff+fc;
          }
        }
      }
    }
    ierr = ISCreateGeneral(PetscObjectComm((PetscObject)dm), subSize, subIndices, PETSC_OWN_POINTER, is);CHKERRQ(ierr);
  }
  if (subdm) {
    PetscSection subsection;
    PetscBool    haveNull = PETSC_FALSE;
    PetscInt     f, nf = 0;

    ierr = PetscSectionCreateSubsection(section, numFields, fields, &subsection);CHKERRQ(ierr);
    ierr = DMSetDefaultSection(*subdm, subsection);CHKERRQ(ierr);
    ierr = PetscSectionDestroy(&subsection);CHKERRQ(ierr);
    for (f = 0; f < numFields; ++f) {
      (*subdm)->nullspaceConstructors[f] = dm->nullspaceConstructors[fields[f]];
      if ((*subdm)->nullspaceConstructors[f]) {
        haveNull = PETSC_TRUE;
        nf       = f;
      }
    }
    if (haveNull) {
      MatNullSpace nullSpace;

      ierr = (*(*subdm)->nullspaceConstructors[nf])(*subdm, nf, &nullSpace);CHKERRQ(ierr);
      ierr = PetscObjectCompose((PetscObject) *is, "nullspace", (PetscObject) nullSpace);CHKERRQ(ierr);
      ierr = MatNullSpaceDestroy(&nullSpace);CHKERRQ(ierr);
    }
    if (dm->fields) {
      if (nF != dm->numFields) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "The number of DM fields %d does not match the number of Section fields %d", dm->numFields, nF);
      ierr = DMSetNumFields(*subdm, numFields);CHKERRQ(ierr);
      for (f = 0; f < numFields; ++f) {
        ierr = PetscObjectListDuplicate(dm->fields[fields[f]]->olist, &(*subdm)->fields[f]->olist);CHKERRQ(ierr);
      }
      if (numFields == 1) {
        MatNullSpace space;
        Mat          pmat;

        ierr = PetscObjectQuery((*subdm)->fields[0], "nullspace", (PetscObject*) &space);CHKERRQ(ierr);
        if (space) {ierr = PetscObjectCompose((PetscObject) *is, "nullspace", (PetscObject) space);CHKERRQ(ierr);}
        ierr = PetscObjectQuery((*subdm)->fields[0], "nearnullspace", (PetscObject*) &space);CHKERRQ(ierr);
        if (space) {ierr = PetscObjectCompose((PetscObject) *is, "nearnullspace", (PetscObject) space);CHKERRQ(ierr);}
        ierr = PetscObjectQuery((*subdm)->fields[0], "pmat", (PetscObject*) &pmat);CHKERRQ(ierr);
        if (pmat) {ierr = PetscObjectCompose((PetscObject) *is, "pmat", (PetscObject) pmat);CHKERRQ(ierr);}
      }
    }
  }
  PetscFunctionReturn(0);
}