xref: /petsc/src/dm/impls/da/gr2.c (revision 57622a8ec272e2944ba90348a8875f087fbb2bc6)

/*
   Plots vectors obtained with DMDACreate2d()
*/

#include <petsc-private/dmdaimpl.h>      /*I  "petscdmda.h"   I*/
#include <petsc-private/vecimpl.h>
#include <petscdraw.h>
#include <petscviewerhdf5.h>

/*
        The data that is passed into the graphics callback
*/
typedef struct {
  PetscInt    m,n,step,k;
  PetscReal   min,max,scale;
  PetscScalar *xy,*v;
  PetscBool   showgrid;
  const char  *name0,*name1;
} ZoomCtx;

/*
       This does the drawing for one particular field
    in one particular set of coordinates. It is a callback
    called from PetscDrawZoom()
*/
#undef __FUNCT__
#define __FUNCT__ "VecView_MPI_Draw_DA2d_Zoom"
PetscErrorCode VecView_MPI_Draw_DA2d_Zoom(PetscDraw draw,void *ctx)
{
  ZoomCtx        *zctx = (ZoomCtx*)ctx;
  PetscErrorCode ierr;
  PetscInt       m,n,i,j,k,step,id,c1,c2,c3,c4;
  PetscReal      s,min,max,x1,x2,x3,x4,y_1,y2,y3,y4,xmin = PETSC_MAX_REAL,xmax = PETSC_MIN_REAL,ymin = PETSC_MAX_REAL,ymax = PETSC_MIN_REAL;
  PetscReal      xminf,xmaxf,yminf,ymaxf,w;
  PetscScalar    *v,*xy;
  char           value[16];
  size_t         len;

  PetscFunctionBegin;
  m    = zctx->m;
  n    = zctx->n;
  step = zctx->step;
  k    = zctx->k;
  v    = zctx->v;
  xy   = zctx->xy;
  s    = zctx->scale;
  min  = zctx->min;
  max  = zctx->max;

  /* PetscDraw the contour plot patch */
  for (j=0; j<n-1; j++) {
    for (i=0; i<m-1; i++) {
      id   = i+j*m;
      x1   = PetscRealPart(xy[2*id]);
      y_1  = PetscRealPart(xy[2*id+1]);
      c1   = (int)(PETSC_DRAW_BASIC_COLORS+s*(PetscClipInterval(PetscRealPart(v[k+step*id]),min,max)-min));
      xmin = PetscMin(xmin,x1);
      ymin = PetscMin(ymin,y_1);
      xmax = PetscMax(xmax,x1);
      ymax = PetscMax(ymax,y_1);

      id   = i+j*m+1;
      x2   = PetscRealPart(xy[2*id]);
      y2   = y_1;
      c2   = (int)(PETSC_DRAW_BASIC_COLORS+s*(PetscClipInterval(PetscRealPart(v[k+step*id]),min,max)-min));
      xmin = PetscMin(xmin,x2);
      xmax = PetscMax(xmax,x2);

      id   = i+j*m+1+m;
      x3   = x2;
      y3   = PetscRealPart(xy[2*id+1]);
      c3   = (int)(PETSC_DRAW_BASIC_COLORS+s*(PetscClipInterval(PetscRealPart(v[k+step*id]),min,max)-min));
      ymin = PetscMin(ymin,y3);
      ymax = PetscMax(ymax,y3);

      id = i+j*m+m;
      x4 = x1;
      y4 = y3;
      c4 = (int)(PETSC_DRAW_BASIC_COLORS+s*(PetscClipInterval(PetscRealPart(v[k+step*id]),min,max)-min));

      ierr = PetscDrawTriangle(draw,x1,y_1,x2,y2,x3,y3,c1,c2,c3);CHKERRQ(ierr);
      ierr = PetscDrawTriangle(draw,x1,y_1,x3,y3,x4,y4,c1,c3,c4);CHKERRQ(ierr);
      if (zctx->showgrid) {
        ierr = PetscDrawLine(draw,x1,y_1,x2,y2,PETSC_DRAW_BLACK);CHKERRQ(ierr);
        ierr = PetscDrawLine(draw,x2,y2,x3,y3,PETSC_DRAW_BLACK);CHKERRQ(ierr);
        ierr = PetscDrawLine(draw,x3,y3,x4,y4,PETSC_DRAW_BLACK);CHKERRQ(ierr);
        ierr = PetscDrawLine(draw,x4,y4,x1,y_1,PETSC_DRAW_BLACK);CHKERRQ(ierr);
      }
    }
  }
  if (zctx->name0) {
    PetscReal xl,yl,xr,yr,x,y;
    ierr = PetscDrawGetCoordinates(draw,&xl,&yl,&xr,&yr);CHKERRQ(ierr);
    x    = xl + .3*(xr - xl);
    xl   = xl + .01*(xr - xl);
    y    = yr - .3*(yr - yl);
    yl   = yl + .01*(yr - yl);
    ierr = PetscDrawString(draw,x,yl,PETSC_DRAW_BLACK,zctx->name0);CHKERRQ(ierr);
    ierr = PetscDrawStringVertical(draw,xl,y,PETSC_DRAW_BLACK,zctx->name1);CHKERRQ(ierr);
  }
  /*
     Ideally we would use the PetscDrawAxis object to manage displaying the coordinate limits
     but that may require some refactoring.
  */
  ierr = MPI_Allreduce(&xmin,&xminf,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)draw));CHKERRQ(ierr);
  ierr = MPI_Allreduce(&xmax,&xmaxf,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)draw));CHKERRQ(ierr);
  ierr = MPI_Allreduce(&ymin,&yminf,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)draw));CHKERRQ(ierr);
  ierr = MPI_Allreduce(&ymax,&ymaxf,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)draw));CHKERRQ(ierr);
  ierr = PetscSNPrintf(value,16,"%f",xminf);CHKERRQ(ierr);
  ierr = PetscDrawString(draw,xminf,yminf - .05*(ymaxf - yminf),PETSC_DRAW_BLACK,value);CHKERRQ(ierr);
  ierr = PetscSNPrintf(value,16,"%f",xmaxf);CHKERRQ(ierr);
  ierr = PetscStrlen(value,&len);CHKERRQ(ierr);
  ierr = PetscDrawStringGetSize(draw,&w,NULL);CHKERRQ(ierr);
  ierr = PetscDrawString(draw,xmaxf - len*w,yminf - .05*(ymaxf - yminf),PETSC_DRAW_BLACK,value);CHKERRQ(ierr);
  ierr = PetscSNPrintf(value,16,"%f",yminf);CHKERRQ(ierr);
  ierr = PetscDrawString(draw,xminf - .05*(xmaxf - xminf),yminf,PETSC_DRAW_BLACK,value);CHKERRQ(ierr);
  ierr = PetscSNPrintf(value,16,"%f",ymaxf);CHKERRQ(ierr);
  ierr = PetscDrawString(draw,xminf - .05*(xmaxf - xminf),ymaxf,PETSC_DRAW_BLACK,value);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "VecView_MPI_Draw_DA2d"
PetscErrorCode VecView_MPI_Draw_DA2d(Vec xin,PetscViewer viewer)
{
  DM                 da,dac,dag;
  PetscErrorCode     ierr;
  PetscMPIInt        rank;
  PetscInt           N,s,M,w,ncoors = 4;
  const PetscInt     *lx,*ly;
  PetscReal          coors[4],ymin,ymax,xmin,xmax;
  PetscDraw          draw,popup;
  PetscBool          isnull,useports = PETSC_FALSE;
  MPI_Comm           comm;
  Vec                xlocal,xcoor,xcoorl;
  DMDABoundaryType   bx,by;
  DMDAStencilType    st;
  ZoomCtx            zctx;
  PetscDrawViewPorts *ports = NULL;
  PetscViewerFormat  format;
  PetscInt           *displayfields;
  PetscInt           ndisplayfields,i,nbounds;
  const PetscReal    *bounds;

  PetscFunctionBegin;
  zctx.showgrid = PETSC_FALSE;

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

  ierr = VecGetDM(xin,&da);CHKERRQ(ierr);
  if (!da) SETERRQ(PetscObjectComm((PetscObject)xin),PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA");

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

  ierr = DMDAGetInfo(da,0,&M,&N,0,&zctx.m,&zctx.n,0,&w,&s,&bx,&by,0,&st);CHKERRQ(ierr);
  ierr = DMDAGetOwnershipRanges(da,&lx,&ly,NULL);CHKERRQ(ierr);

  /*
        Obtain a sequential vector that is going to contain the local values plus ONE layer of
     ghosted values to draw the graphics from. We also need its corresponding DMDA (dac) that will
     update the local values pluse ONE layer of ghost values.
  */
  ierr = PetscObjectQuery((PetscObject)da,"GraphicsGhosted",(PetscObject*)&xlocal);CHKERRQ(ierr);
  if (!xlocal) {
    if (bx !=  DMDA_BOUNDARY_NONE || by !=  DMDA_BOUNDARY_NONE || s != 1 || st != DMDA_STENCIL_BOX) {
      /*
         if original da is not of stencil width one, or periodic or not a box stencil then
         create a special DMDA to handle one level of ghost points for graphics
      */
      ierr = DMDACreate2d(comm,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_STENCIL_BOX,M,N,zctx.m,zctx.n,w,1,lx,ly,&dac);CHKERRQ(ierr);
      ierr = PetscInfo(da,"Creating auxilary DMDA for managing graphics ghost points\n");CHKERRQ(ierr);
    } else {
      /* otherwise we can use the da we already have */
      dac = da;
    }
    /* create local vector for holding ghosted values used in graphics */
    ierr = DMCreateLocalVector(dac,&xlocal);CHKERRQ(ierr);
    if (dac != da) {
      /* don't keep any public reference of this DMDA, is is only available through xlocal */
      ierr = PetscObjectDereference((PetscObject)dac);CHKERRQ(ierr);
    } else {
      /* remove association between xlocal and da, because below we compose in the opposite
         direction and if we left this connect we'd get a loop, so the objects could
         never be destroyed */
      ierr = PetscObjectRemoveReference((PetscObject)xlocal,"__PETSc_dm");CHKERRQ(ierr);
    }
    ierr = PetscObjectCompose((PetscObject)da,"GraphicsGhosted",(PetscObject)xlocal);CHKERRQ(ierr);
    ierr = PetscObjectDereference((PetscObject)xlocal);CHKERRQ(ierr);
  } else {
    if (bx !=  DMDA_BOUNDARY_NONE || by !=  DMDA_BOUNDARY_NONE || s != 1 || st != DMDA_STENCIL_BOX) {
      ierr = VecGetDM(xlocal, &dac);CHKERRQ(ierr);
    } else {
      dac = da;
    }
  }

  /*
      Get local (ghosted) values of vector
  */
  ierr = DMGlobalToLocalBegin(dac,xin,INSERT_VALUES,xlocal);CHKERRQ(ierr);
  ierr = DMGlobalToLocalEnd(dac,xin,INSERT_VALUES,xlocal);CHKERRQ(ierr);
  ierr = VecGetArray(xlocal,&zctx.v);CHKERRQ(ierr);

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

  /*
      Determine the min and max  coordinates in plot
  */
  ierr     = VecStrideMin(xcoor,0,NULL,&xmin);CHKERRQ(ierr);
  ierr     = VecStrideMax(xcoor,0,NULL,&xmax);CHKERRQ(ierr);
  ierr     = VecStrideMin(xcoor,1,NULL,&ymin);CHKERRQ(ierr);
  ierr     = VecStrideMax(xcoor,1,NULL,&ymax);CHKERRQ(ierr);
  coors[0] = xmin - .05*(xmax- xmin); coors[2] = xmax + .05*(xmax - xmin);
  coors[1] = ymin - .05*(ymax- ymin); coors[3] = ymax + .05*(ymax - ymin);
  ierr     = PetscInfo4(da,"Preparing DMDA 2d contour plot coordinates %g %g %g %g\n",(double)coors[0],(double)coors[1],(double)coors[2],(double)coors[3]);CHKERRQ(ierr);

  ierr = PetscOptionsGetRealArray(NULL,"-draw_coordinates",coors,&ncoors,NULL);CHKERRQ(ierr);

  /*
       get local ghosted version of coordinates
  */
  ierr = PetscObjectQuery((PetscObject)da,"GraphicsCoordinateGhosted",(PetscObject*)&xcoorl);CHKERRQ(ierr);
  if (!xcoorl) {
    /* create DMDA to get local version of graphics */
    ierr = DMDACreate2d(comm,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_STENCIL_BOX,M,N,zctx.m,zctx.n,2,1,lx,ly,&dag);CHKERRQ(ierr);
    ierr = PetscInfo(dag,"Creating auxilary DMDA for managing graphics coordinates ghost points\n");CHKERRQ(ierr);
    ierr = DMCreateLocalVector(dag,&xcoorl);CHKERRQ(ierr);
    ierr = PetscObjectCompose((PetscObject)da,"GraphicsCoordinateGhosted",(PetscObject)xcoorl);CHKERRQ(ierr);
    ierr = PetscObjectDereference((PetscObject)dag);CHKERRQ(ierr);
    ierr = PetscObjectDereference((PetscObject)xcoorl);CHKERRQ(ierr);
  } else {
    ierr = VecGetDM(xcoorl,&dag);CHKERRQ(ierr);
  }
  ierr = DMGlobalToLocalBegin(dag,xcoor,INSERT_VALUES,xcoorl);CHKERRQ(ierr);
  ierr = DMGlobalToLocalEnd(dag,xcoor,INSERT_VALUES,xcoorl);CHKERRQ(ierr);
  ierr = VecGetArray(xcoorl,&zctx.xy);CHKERRQ(ierr);

  /*
        Get information about size of area each processor must do graphics for
  */
  ierr = DMDAGetInfo(dac,0,&M,&N,0,0,0,0,&zctx.step,0,&bx,&by,0,0);CHKERRQ(ierr);
  ierr = DMDAGetGhostCorners(dac,0,0,0,&zctx.m,&zctx.n,0);CHKERRQ(ierr);

  ierr = PetscOptionsGetBool(NULL,"-draw_contour_grid",&zctx.showgrid,NULL);CHKERRQ(ierr);

  ierr = DMDASelectFields(da,&ndisplayfields,&displayfields);CHKERRQ(ierr);

  ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr);
  ierr = PetscOptionsGetBool(NULL,"-draw_ports",&useports,NULL);CHKERRQ(ierr);
  if (useports || format == PETSC_VIEWER_DRAW_PORTS) {
    ierr       = PetscDrawSynchronizedClear(draw);CHKERRQ(ierr);
    ierr       = PetscDrawViewPortsCreate(draw,ndisplayfields,&ports);CHKERRQ(ierr);
    zctx.name0 = 0;
    zctx.name1 = 0;
  } else {
    ierr = DMDAGetCoordinateName(da,0,&zctx.name0);CHKERRQ(ierr);
    ierr = DMDAGetCoordinateName(da,1,&zctx.name1);CHKERRQ(ierr);
  }

  /*
     Loop over each field; drawing each in a different window
  */
  for (i=0; i<ndisplayfields; i++) {
    zctx.k = displayfields[i];
    if (useports) {
      ierr = PetscDrawViewPortsSet(ports,i);CHKERRQ(ierr);
    } else {
      ierr = PetscViewerDrawGetDraw(viewer,i,&draw);CHKERRQ(ierr);
    }

    /*
        Determine the min and max color in plot
    */
    ierr = VecStrideMin(xin,zctx.k,NULL,&zctx.min);CHKERRQ(ierr);
    ierr = VecStrideMax(xin,zctx.k,NULL,&zctx.max);CHKERRQ(ierr);
    if (zctx.k < nbounds) {
      zctx.min = bounds[2*zctx.k];
      zctx.max = bounds[2*zctx.k+1];
    }
    if (zctx.min == zctx.max) {
      zctx.min -= 1.e-12;
      zctx.max += 1.e-12;
    }

    if (!rank) {
      const char *title;

      ierr = DMDAGetFieldName(da,zctx.k,&title);CHKERRQ(ierr);
      if (title) {
        ierr = PetscDrawSetTitle(draw,title);CHKERRQ(ierr);
      }
    }
    ierr = PetscDrawSetCoordinates(draw,coors[0],coors[1],coors[2],coors[3]);CHKERRQ(ierr);
    ierr = PetscInfo2(da,"DMDA 2d contour plot min %g max %g\n",(double)zctx.min,(double)zctx.max);CHKERRQ(ierr);

    ierr = PetscDrawGetPopup(draw,&popup);CHKERRQ(ierr);
    if (popup) {ierr = PetscDrawScalePopup(popup,zctx.min,zctx.max);CHKERRQ(ierr);}

    zctx.scale = (245.0 - PETSC_DRAW_BASIC_COLORS)/(zctx.max - zctx.min);

    ierr = PetscDrawZoom(draw,VecView_MPI_Draw_DA2d_Zoom,&zctx);CHKERRQ(ierr);
  }
  ierr = PetscFree(displayfields);CHKERRQ(ierr);
  ierr = PetscDrawViewPortsDestroy(ports);CHKERRQ(ierr);

  ierr = VecRestoreArray(xcoorl,&zctx.xy);CHKERRQ(ierr);
  ierr = VecRestoreArray(xlocal,&zctx.v);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}


#if defined(PETSC_HAVE_HDF5)
#undef __FUNCT__
#define __FUNCT__ "VecView_MPI_HDF5_DA"
PetscErrorCode VecView_MPI_HDF5_DA(Vec xin,PetscViewer viewer)
{
  DM             dm;
  DM_DA          *da;
  hid_t          filespace;  /* file dataspace identifier */
  hid_t          chunkspace; /* chunk dataset property identifier */
  hid_t          plist_id;   /* property list identifier */
  hid_t          dset_id;    /* dataset identifier */
  hid_t          memspace;   /* memory dataspace identifier */
  hid_t          file_id;
  hid_t          group;
  hid_t          scalartype; /* scalar type (H5T_NATIVE_FLOAT or H5T_NATIVE_DOUBLE) */
  herr_t         status;
  hsize_t        dim;
  hsize_t        maxDims[6], dims[6], chunkDims[6], count[6], offset[6];
  PetscInt       timestep;
  PetscScalar    *x;
  const char     *vecname;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscViewerHDF5OpenGroup(viewer, &file_id, &group);CHKERRQ(ierr);
  ierr = PetscViewerHDF5GetTimestep(viewer, &timestep);CHKERRQ(ierr);

  ierr = VecGetDM(xin,&dm);CHKERRQ(ierr);
  if (!dm) SETERRQ(PetscObjectComm((PetscObject)xin),PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA");
  da = (DM_DA*)dm->data;

  /* Create the dataspace for the dataset.
   *
   * dims - holds the current dimensions of the dataset
   *
   * maxDims - holds the maximum dimensions of the dataset (unlimited
   * for the number of time steps with the current dimensions for the
   * other dimensions; so only additional time steps can be added).
   *
   * chunkDims - holds the size of a single time step (required to
   * permit extending dataset).
   */
  dim = 0;
  if (timestep >= 0) {
    dims[dim]      = timestep+1;
    maxDims[dim]   = H5S_UNLIMITED;
    chunkDims[dim] = 1;
    ++dim;
  }
  if (da->dim == 3) {
    ierr           = PetscHDF5IntCast(da->P,dims+dim);CHKERRQ(ierr);
    maxDims[dim]   = dims[dim];
    chunkDims[dim] = dims[dim];
    ++dim;
  }
  if (da->dim > 1) {
    ierr           = PetscHDF5IntCast(da->N,dims+dim);CHKERRQ(ierr);
    maxDims[dim]   = dims[dim];
    chunkDims[dim] = dims[dim];
    ++dim;
  }
  ierr           = PetscHDF5IntCast(da->M,dims+dim);CHKERRQ(ierr);
  maxDims[dim]   = dims[dim];
  chunkDims[dim] = dims[dim];
  ++dim;
  if (da->w > 1) {
    ierr           = PetscHDF5IntCast(da->w,dims+dim);CHKERRQ(ierr);
    maxDims[dim]   = dims[dim];
    chunkDims[dim] = dims[dim];
    ++dim;
  }
#if defined(PETSC_USE_COMPLEX)
  dims[dim]      = 2;
  maxDims[dim]   = dims[dim];
  chunkDims[dim] = dims[dim];
  ++dim;
#endif
  filespace = H5Screate_simple(dim, dims, maxDims);
  if (filespace == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Screate_simple()");

#if defined(PETSC_USE_REAL_SINGLE)
  scalartype = H5T_NATIVE_FLOAT;
#elif defined(PETSC_USE_REAL___FLOAT128)
#error "HDF5 output with 128 bit floats not supported."
#else
  scalartype = H5T_NATIVE_DOUBLE;
#endif

  /* Create the dataset with default properties and close filespace */
  ierr = PetscObjectGetName((PetscObject)xin,&vecname);CHKERRQ(ierr);
  if (!H5Lexists(group, vecname, H5P_DEFAULT)) {
    /* Create chunk */
    chunkspace = H5Pcreate(H5P_DATASET_CREATE);
    if (chunkspace == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Pcreate()");
    status = H5Pset_chunk(chunkspace, dim, chunkDims);CHKERRQ(status);

#if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800)
    dset_id = H5Dcreate2(group, vecname, scalartype, filespace, H5P_DEFAULT, chunkspace, H5P_DEFAULT);
#else
    dset_id = H5Dcreate(group, vecname, scalartype, filespace, H5P_DEFAULT);
#endif
    if (dset_id == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Dcreate2()");
  } else {
    dset_id = H5Dopen2(group, vecname, H5P_DEFAULT);
    status  = H5Dset_extent(dset_id, dims);CHKERRQ(status);
  }
  status = H5Sclose(filespace);CHKERRQ(status);

  /* Each process defines a dataset and writes it to the hyperslab in the file */
  dim = 0;
  if (timestep >= 0) {
    offset[dim] = timestep;
    ++dim;
  }
  if (da->dim == 3) {ierr = PetscHDF5IntCast(da->zs,offset + dim++);CHKERRQ(ierr);}
  if (da->dim > 1)  {ierr = PetscHDF5IntCast(da->ys,offset + dim++);CHKERRQ(ierr);}
  ierr = PetscHDF5IntCast(da->xs/da->w,offset + dim++);CHKERRQ(ierr);
  if (da->w > 1) offset[dim++] = 0;
#if defined(PETSC_USE_COMPLEX)
  offset[dim++] = 0;
#endif
  dim = 0;
  if (timestep >= 0) {
    count[dim] = 1;
    ++dim;
  }
  if (da->dim == 3) {ierr = PetscHDF5IntCast(da->ze - da->zs,count + dim++);CHKERRQ(ierr);}
  if (da->dim > 1)  {ierr = PetscHDF5IntCast(da->ye - da->ys,count + dim++);CHKERRQ(ierr);}
  ierr = PetscHDF5IntCast((da->xe - da->xs)/da->w,count + dim++);CHKERRQ(ierr);
  if (da->w > 1) {ierr = PetscHDF5IntCast(da->w,count + dim++);CHKERRQ(ierr);}
#if defined(PETSC_USE_COMPLEX)
  count[dim++] = 2;
#endif
  memspace = H5Screate_simple(dim, count, NULL);
  if (memspace == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Screate_simple()");

  filespace = H5Dget_space(dset_id);
  if (filespace == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Dget_space()");
  status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, count, NULL);CHKERRQ(status);

  /* Create property list for collective dataset write */
  plist_id = H5Pcreate(H5P_DATASET_XFER);
  if (plist_id == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Pcreate()");
#if defined(PETSC_HAVE_H5PSET_FAPL_MPIO)
  status = H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);CHKERRQ(status);
#endif
  /* To write dataset independently use H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT) */

  ierr   = VecGetArray(xin, &x);CHKERRQ(ierr);
  status = H5Dwrite(dset_id, scalartype, memspace, filespace, plist_id, x);CHKERRQ(status);
  status = H5Fflush(file_id, H5F_SCOPE_GLOBAL);CHKERRQ(status);
  ierr   = VecRestoreArray(xin, &x);CHKERRQ(ierr);

  /* Close/release resources */
  if (group != file_id) {
    status = H5Gclose(group);CHKERRQ(status);
  }
  status = H5Pclose(plist_id);CHKERRQ(status);
  status = H5Sclose(filespace);CHKERRQ(status);
  status = H5Sclose(memspace);CHKERRQ(status);
  status = H5Dclose(dset_id);CHKERRQ(status);
  ierr   = PetscInfo1(xin,"Wrote Vec object with name %s\n",vecname);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
#endif

extern PetscErrorCode VecView_MPI_Draw_DA1d(Vec,PetscViewer);

#if defined(PETSC_HAVE_MPIIO)
#undef __FUNCT__
#define __FUNCT__ "DMDAArrayMPIIO"
static PetscErrorCode DMDAArrayMPIIO(DM da,PetscViewer viewer,Vec xin,PetscBool write)
{
  PetscErrorCode    ierr;
  MPI_File          mfdes;
  PetscMPIInt       gsizes[4],lsizes[4],lstarts[4],asiz,dof;
  MPI_Datatype      view;
  const PetscScalar *array;
  MPI_Offset        off;
  MPI_Aint          ub,ul;
  PetscInt          type,rows,vecrows,tr[2];
  DM_DA             *dd = (DM_DA*)da->data;

  PetscFunctionBegin;
  ierr = VecGetSize(xin,&vecrows);CHKERRQ(ierr);
  if (!write) {
    /* Read vector header. */
    ierr = PetscViewerBinaryRead(viewer,tr,2,PETSC_INT);CHKERRQ(ierr);
    type = tr[0];
    rows = tr[1];
    if (type != VEC_FILE_CLASSID) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_ARG_WRONG,"Not vector next in file");
    if (rows != vecrows) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_ARG_SIZ,"Vector in file not same size as DMDA vector");
  } else {
    tr[0] = VEC_FILE_CLASSID;
    tr[1] = vecrows;
    ierr  = PetscViewerBinaryWrite(viewer,tr,2,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr);
  }

  ierr       = PetscMPIIntCast(dd->w,&dof);CHKERRQ(ierr);
  gsizes[0]  = dof;
  ierr       = PetscMPIIntCast(dd->M,gsizes+1);CHKERRQ(ierr);
  ierr       = PetscMPIIntCast(dd->N,gsizes+2);CHKERRQ(ierr);
  ierr       = PetscMPIIntCast(dd->P,gsizes+1);CHKERRQ(ierr);
  lsizes[0]  = dof;
  ierr       = PetscMPIIntCast((dd->xe-dd->xs)/dof,lsizes+1);CHKERRQ(ierr);
  ierr       = PetscMPIIntCast(dd->ye-dd->ys,lsizes+2);CHKERRQ(ierr);
  ierr       = PetscMPIIntCast(dd->ze-dd->zs,lsizes+3);CHKERRQ(ierr);
  lstarts[0] = 0;
  ierr       = PetscMPIIntCast(dd->xs/dof,lstarts+1);CHKERRQ(ierr);
  ierr       = PetscMPIIntCast(dd->ys,lstarts+2);CHKERRQ(ierr);
  ierr       = PetscMPIIntCast(dd->zs,lstarts+3);CHKERRQ(ierr);
  ierr       = MPI_Type_create_subarray(dd->dim+1,gsizes,lsizes,lstarts,MPI_ORDER_FORTRAN,MPIU_SCALAR,&view);CHKERRQ(ierr);
  ierr       = MPI_Type_commit(&view);CHKERRQ(ierr);

  ierr = PetscViewerBinaryGetMPIIODescriptor(viewer,&mfdes);CHKERRQ(ierr);
  ierr = PetscViewerBinaryGetMPIIOOffset(viewer,&off);CHKERRQ(ierr);
  ierr = MPI_File_set_view(mfdes,off,MPIU_SCALAR,view,(char*)"native",MPI_INFO_NULL);CHKERRQ(ierr);
  ierr = VecGetArrayRead(xin,&array);CHKERRQ(ierr);
  asiz = lsizes[1]*(lsizes[2] > 0 ? lsizes[2] : 1)*(lsizes[3] > 0 ? lsizes[3] : 1)*dof;
  if (write) {
    ierr = MPIU_File_write_all(mfdes,(PetscScalar*)array,asiz,MPIU_SCALAR,MPI_STATUS_IGNORE);CHKERRQ(ierr);
  } else {
    ierr = MPIU_File_read_all(mfdes,(PetscScalar*)array,asiz,MPIU_SCALAR,MPI_STATUS_IGNORE);CHKERRQ(ierr);
  }
  ierr = MPI_Type_get_extent(view,&ul,&ub);CHKERRQ(ierr);
  ierr = PetscViewerBinaryAddMPIIOOffset(viewer,ub);CHKERRQ(ierr);
  ierr = VecRestoreArrayRead(xin,&array);CHKERRQ(ierr);
  ierr = MPI_Type_free(&view);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
#endif

#undef __FUNCT__
#define __FUNCT__ "VecView_MPI_DA"
PetscErrorCode  VecView_MPI_DA(Vec xin,PetscViewer viewer)
{
  DM                da;
  PetscErrorCode    ierr;
  PetscInt          dim;
  Vec               natural;
  PetscBool         isdraw,isvtk;
#if defined(PETSC_HAVE_HDF5)
  PetscBool         ishdf5;
#endif
  const char        *prefix,*name;
  PetscViewerFormat format;

  PetscFunctionBegin;
  ierr = VecGetDM(xin,&da);CHKERRQ(ierr);
  if (!da) SETERRQ(PetscObjectComm((PetscObject)xin),PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA");
  ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr);
  ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERVTK,&isvtk);CHKERRQ(ierr);
#if defined(PETSC_HAVE_HDF5)
  ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERHDF5,&ishdf5);CHKERRQ(ierr);
#endif
  if (isdraw) {
    ierr = DMDAGetInfo(da,&dim,0,0,0,0,0,0,0,0,0,0,0,0);CHKERRQ(ierr);
    if (dim == 1) {
      ierr = VecView_MPI_Draw_DA1d(xin,viewer);CHKERRQ(ierr);
    } else if (dim == 2) {
      ierr = VecView_MPI_Draw_DA2d(xin,viewer);CHKERRQ(ierr);
    } else SETERRQ1(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"Cannot graphically view vector associated with this dimensional DMDA %D",dim);
  } else if (isvtk) {           /* Duplicate the Vec and hold a reference to the DM */
    Vec Y;
    ierr = PetscObjectReference((PetscObject)da);CHKERRQ(ierr);
    ierr = VecDuplicate(xin,&Y);CHKERRQ(ierr);
    if (((PetscObject)xin)->name) {
      /* If xin was named, copy the name over to Y. The duplicate names are safe because nobody else will ever see Y. */
      ierr = PetscObjectSetName((PetscObject)Y,((PetscObject)xin)->name);CHKERRQ(ierr);
    }
    ierr = VecCopy(xin,Y);CHKERRQ(ierr);
    ierr = PetscViewerVTKAddField(viewer,(PetscObject)da,DMDAVTKWriteAll,PETSC_VTK_POINT_FIELD,(PetscObject)Y);CHKERRQ(ierr);
#if defined(PETSC_HAVE_HDF5)
  } else if (ishdf5) {
    ierr = VecView_MPI_HDF5_DA(xin,viewer);CHKERRQ(ierr);
#endif
  } else {
#if defined(PETSC_HAVE_MPIIO)
    PetscBool isbinary,isMPIIO;

    ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr);
    if (isbinary) {
      ierr = PetscViewerBinaryGetMPIIO(viewer,&isMPIIO);CHKERRQ(ierr);
      if (isMPIIO) {
        ierr = DMDAArrayMPIIO(da,viewer,xin,PETSC_TRUE);CHKERRQ(ierr);
        PetscFunctionReturn(0);
      }
    }
#endif

    /* call viewer on natural ordering */
    ierr = PetscObjectGetOptionsPrefix((PetscObject)xin,&prefix);CHKERRQ(ierr);
    ierr = DMDACreateNaturalVector(da,&natural);CHKERRQ(ierr);
    ierr = PetscObjectSetOptionsPrefix((PetscObject)natural,prefix);CHKERRQ(ierr);
    ierr = DMDAGlobalToNaturalBegin(da,xin,INSERT_VALUES,natural);CHKERRQ(ierr);
    ierr = DMDAGlobalToNaturalEnd(da,xin,INSERT_VALUES,natural);CHKERRQ(ierr);
    ierr = PetscObjectGetName((PetscObject)xin,&name);CHKERRQ(ierr);
    ierr = PetscObjectSetName((PetscObject)natural,name);CHKERRQ(ierr);

    ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr);
    if (format == PETSC_VIEWER_BINARY_MATLAB) {
      /* temporarily remove viewer format so it won't trigger in the VecView() */
      ierr = PetscViewerSetFormat(viewer,PETSC_VIEWER_DEFAULT);CHKERRQ(ierr);
    }

    ierr = VecView(natural,viewer);CHKERRQ(ierr);

    if (format == PETSC_VIEWER_BINARY_MATLAB) {
      MPI_Comm    comm;
      FILE        *info;
      const char  *fieldname;
      char        fieldbuf[256];
      PetscInt    dim,ni,nj,nk,pi,pj,pk,dof,n;

      /* set the viewer format back into the viewer */
      ierr = PetscViewerSetFormat(viewer,format);CHKERRQ(ierr);
      ierr = PetscObjectGetComm((PetscObject)viewer,&comm);CHKERRQ(ierr);
      ierr = PetscViewerBinaryGetInfoPointer(viewer,&info);CHKERRQ(ierr);
      ierr = DMDAGetInfo(da,&dim,&ni,&nj,&nk,&pi,&pj,&pk,&dof,0,0,0,0,0);CHKERRQ(ierr);
      ierr = PetscFPrintf(comm,info,"#--- begin code written by PetscViewerBinary for MATLAB format ---#\n");CHKERRQ(ierr);
      ierr = PetscFPrintf(comm,info,"#$$ tmp = PetscBinaryRead(fd); \n");CHKERRQ(ierr);
      if (dim == 1) { ierr = PetscFPrintf(comm,info,"#$$ tmp = reshape(tmp,%d,%d);\n",dof,ni);CHKERRQ(ierr); }
      if (dim == 2) { ierr = PetscFPrintf(comm,info,"#$$ tmp = reshape(tmp,%d,%d,%d);\n",dof,ni,nj);CHKERRQ(ierr); }
      if (dim == 3) { ierr = PetscFPrintf(comm,info,"#$$ tmp = reshape(tmp,%d,%d,%d,%d);\n",dof,ni,nj,nk);CHKERRQ(ierr); }

      for (n=0; n<dof; n++) {
        ierr = DMDAGetFieldName(da,n,&fieldname);CHKERRQ(ierr);
        if (!fieldname || !fieldname[0]) {
          ierr = PetscSNPrintf(fieldbuf,sizeof fieldbuf,"field%D",n);CHKERRQ(ierr);
          fieldname = fieldbuf;
        }
        if (dim == 1) { ierr = PetscFPrintf(comm,info,"#$$ Set.%s.%s = squeeze(tmp(%d,:))';\n",name,fieldname,n+1);CHKERRQ(ierr); }
        if (dim == 2) { ierr = PetscFPrintf(comm,info,"#$$ Set.%s.%s = squeeze(tmp(%d,:,:))';\n",name,fieldname,n+1);CHKERRQ(ierr); }
        if (dim == 3) { ierr = PetscFPrintf(comm,info,"#$$ Set.%s.%s = permute(squeeze(tmp(%d,:,:,:)),[2 1 3]);\n",name,fieldname,n+1);CHKERRQ(ierr);}
      }
      ierr = PetscFPrintf(comm,info,"#$$ clear tmp; \n");CHKERRQ(ierr);
      ierr = PetscFPrintf(comm,info,"#--- end code written by PetscViewerBinary for MATLAB format ---#\n\n");CHKERRQ(ierr);
    }

    ierr = VecDestroy(&natural);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}

#if defined(PETSC_HAVE_HDF5)
#undef __FUNCT__
#define __FUNCT__ "VecLoad_HDF5_DA"
PetscErrorCode VecLoad_HDF5_DA(Vec xin, PetscViewer viewer)
{
  DM             da;
  PetscErrorCode ierr;
  hsize_t        dim;
  hsize_t        count[5];
  hsize_t        offset[5];
  PetscInt       cnt = 0;
  PetscScalar    *x;
  const char     *vecname;
  hid_t          filespace; /* file dataspace identifier */
  hid_t          plist_id;  /* property list identifier */
  hid_t          dset_id;   /* dataset identifier */
  hid_t          memspace;  /* memory dataspace identifier */
  hid_t          file_id;
  herr_t         status;
  DM_DA          *dd;

  PetscFunctionBegin;
  ierr = PetscViewerHDF5GetFileId(viewer, &file_id);CHKERRQ(ierr);
  ierr = VecGetDM(xin,&da);CHKERRQ(ierr);
  dd   = (DM_DA*)da->data;

  /* Create the dataspace for the dataset */
  ierr = PetscHDF5IntCast(dd->dim + ((dd->w == 1) ? 0 : 1),&dim);CHKERRQ(ierr);
#if defined(PETSC_USE_COMPLEX)
  dim++;
#endif

  /* Create the dataset with default properties and close filespace */
  ierr = PetscObjectGetName((PetscObject)xin,&vecname);CHKERRQ(ierr);
#if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800)
  dset_id = H5Dopen2(file_id, vecname, H5P_DEFAULT);
#else
  dset_id = H5Dopen(file_id, vecname);
#endif
  if (dset_id == -1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Dopen2() with Vec named %s",vecname);
  filespace = H5Dget_space(dset_id);

  /* Each process defines a dataset and reads it from the hyperslab in the file */
  cnt = 0;
  if (dd->dim == 3) {ierr = PetscHDF5IntCast(dd->zs,offset + cnt++);CHKERRQ(ierr);}
  if (dd->dim > 1)  {ierr = PetscHDF5IntCast(dd->ys,offset + cnt++);CHKERRQ(ierr);}
  ierr = PetscHDF5IntCast(dd->xs/dd->w,offset + cnt++);CHKERRQ(ierr);
  if (dd->w > 1) offset[cnt++] = 0;
#if defined(PETSC_USE_COMPLEX)
  offset[cnt++] = 0;
#endif
  cnt = 0;
  if (dd->dim == 3) {ierr = PetscHDF5IntCast(dd->ze - dd->zs,count + cnt++);CHKERRQ(ierr);}
  if (dd->dim > 1)  {ierr = PetscHDF5IntCast(dd->ye - dd->ys,count + cnt++);CHKERRQ(ierr);}
  ierr = PetscHDF5IntCast((dd->xe - dd->xs)/dd->w,count + cnt++);CHKERRQ(ierr);
  if (dd->w > 1) {ierr = PetscHDF5IntCast(dd->w,count + cnt++);CHKERRQ(ierr);}
#if defined(PETSC_USE_COMPLEX)
  count[cnt++] = 2;
#endif
  memspace = H5Screate_simple(dim, count, NULL);
  if (memspace == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Screate_simple()");

  status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, count, NULL);CHKERRQ(status);

  /* Create property list for collective dataset write */
  plist_id = H5Pcreate(H5P_DATASET_XFER);
  if (plist_id == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Pcreate()");
#if defined(PETSC_HAVE_H5PSET_FAPL_MPIO)
  status = H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);CHKERRQ(status);
#endif
  /* To write dataset independently use H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT) */

  ierr   = VecGetArray(xin, &x);CHKERRQ(ierr);
  status = H5Dread(dset_id, H5T_NATIVE_DOUBLE, memspace, filespace, plist_id, x);CHKERRQ(status);
  ierr   = VecRestoreArray(xin, &x);CHKERRQ(ierr);

  /* Close/release resources */
  status = H5Pclose(plist_id);CHKERRQ(status);
  status = H5Sclose(filespace);CHKERRQ(status);
  status = H5Sclose(memspace);CHKERRQ(status);
  status = H5Dclose(dset_id);CHKERRQ(status);
  PetscFunctionReturn(0);
}
#endif

#undef __FUNCT__
#define __FUNCT__ "VecLoad_Binary_DA"
PetscErrorCode VecLoad_Binary_DA(Vec xin, PetscViewer viewer)
{
  DM             da;
  PetscErrorCode ierr;
  Vec            natural;
  const char     *prefix;
  PetscInt       bs;
  PetscBool      flag;
  DM_DA          *dd;
#if defined(PETSC_HAVE_MPIIO)
  PetscBool isMPIIO;
#endif

  PetscFunctionBegin;
  ierr = VecGetDM(xin,&da);CHKERRQ(ierr);
  dd   = (DM_DA*)da->data;
#if defined(PETSC_HAVE_MPIIO)
  ierr = PetscViewerBinaryGetMPIIO(viewer,&isMPIIO);CHKERRQ(ierr);
  if (isMPIIO) {
    ierr = DMDAArrayMPIIO(da,viewer,xin,PETSC_FALSE);CHKERRQ(ierr);
    PetscFunctionReturn(0);
  }
#endif

  ierr = PetscObjectGetOptionsPrefix((PetscObject)xin,&prefix);CHKERRQ(ierr);
  ierr = DMDACreateNaturalVector(da,&natural);CHKERRQ(ierr);
  ierr = PetscObjectSetName((PetscObject)natural,((PetscObject)xin)->name);CHKERRQ(ierr);
  ierr = PetscObjectSetOptionsPrefix((PetscObject)natural,prefix);CHKERRQ(ierr);
  ierr = VecLoad(natural,viewer);CHKERRQ(ierr);
  ierr = DMDANaturalToGlobalBegin(da,natural,INSERT_VALUES,xin);CHKERRQ(ierr);
  ierr = DMDANaturalToGlobalEnd(da,natural,INSERT_VALUES,xin);CHKERRQ(ierr);
  ierr = VecDestroy(&natural);CHKERRQ(ierr);
  ierr = PetscInfo(xin,"Loading vector from natural ordering into DMDA\n");CHKERRQ(ierr);
  ierr = PetscOptionsGetInt(((PetscObject)xin)->prefix,"-vecload_block_size",&bs,&flag);CHKERRQ(ierr);
  if (flag && bs != dd->w) {
    ierr = PetscInfo2(xin,"Block size in file %D not equal to DMDA's dof %D\n",bs,dd->w);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "VecLoad_Default_DA"
PetscErrorCode  VecLoad_Default_DA(Vec xin, PetscViewer viewer)
{
  PetscErrorCode ierr;
  DM             da;
  PetscBool      isbinary;
#if defined(PETSC_HAVE_HDF5)
  PetscBool ishdf5;
#endif

  PetscFunctionBegin;
  ierr = VecGetDM(xin,&da);CHKERRQ(ierr);
  if (!da) SETERRQ(PetscObjectComm((PetscObject)xin),PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA");

#if defined(PETSC_HAVE_HDF5)
  ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERHDF5,&ishdf5);CHKERRQ(ierr);
#endif
  ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr);

  if (isbinary) {
    ierr = VecLoad_Binary_DA(xin,viewer);CHKERRQ(ierr);
#if defined(PETSC_HAVE_HDF5)
  } else if (ishdf5) {
    ierr = VecLoad_HDF5_DA(xin,viewer);CHKERRQ(ierr);
#endif
  } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Viewer type %s not supported for vector loading", ((PetscObject)viewer)->type_name);
  PetscFunctionReturn(0);
}