[petsc-dev] DMDA_BOUNDARY_GHOSTED

[Barry Smith]

On Sep 26, 2013, at 1:10 PM, Mark F. Adams <mfadams at lbl.gov> wrote:
> 
> Also, I know this is a dumb question, and I don't really need to know this, but I can't understand this, and am very curious how code like this can work:
> 
> PetscScalar    **array;
>  ierr = DMDAVecGetArray(da, b, &array);CHKERRQ(ierr);
>  for (j=ys; j<ys+ym; j++) {
>    for (i=xs; i<xs+xm; i++) {
>      array[j][i] = ….
>    }
>  }
> 
> This is fantastic.  You seem to be doing arbitrary(ish) indexing into a multidimensional, dynamically sized, array.  Just like fortran.  I never knew you could do this and can not see how the compiler even implements this as you are not even telling it any dimension as far as I can see.  I obviously missing something very simple here.

   Yup and if xm is not too small this is fine for efficiency :-)  Never underestimate C

   Here is the magic
PetscErrorCode  VecGetArray2d(Vec x,PetscInt m,PetscInt n,PetscInt mstart,PetscInt nstart,PetscScalar **a[])

  ierr = VecGetLocalSize(x,&N);CHKERRQ(ierr);
  if (m*n != N) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Local array size %D does not match 2d array dimensions %D by %D",N,m,n);
  ierr = VecGetArray(x,&aa);CHKERRQ(ierr);

  ierr = PetscMalloc(m*sizeof(PetscScalar*),a);CHKERRQ(ierr);
  for (i=0; i<m; i++) (*a)[i] = aa + i*n - nstart;
  *a -= mstart;
  PetscFunctionReturn(0);

  Note one could even reuse the memory from a previous time and not have the malloc in here

   Barry

> 
> Mark
> 
> On Sep 26, 2013, at 12:36 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
> 
>> 
>> For vertex centered finite differences it is easy, one simply does not include the boundary nodes in the DMDA and then puts the actual Dirichlet values into the ghost slots.
>> 
>> For cell centered since the boundary value is the average of the ghost cell and the first cell I don't know how to do this because I don't know what one should put into the ghost location. Maybe include the "ghost" cell as a real point (don't use boundary_ghosted) and make the equation for that last cell force the average of that slot and its neighbor to equal the Dirichlet value.
>> 
>> 
>>  Barry
>> 
>> On Sep 26, 2013, at 11:28 AM, Matthew Knepley <knepley at gmail.com> wrote:
>> 
>>> On Thu, Sep 26, 2013 at 9:25 AM, Mark F. Adams <mfadams at lbl.gov> wrote:
>>> I am interested in making a cell centered test problem with Dirichlet BCs.  I want to go high(ish) order and doing explicit stencils (preferred) looks rather messy and I am interest in using ghost cells.  I assume this would entail using DMDA_BOUNDARY_GHOSTED.  I do not see any examples or documentation on using this other than just creating it.  Any suggestions?  I would think that there would have to be callback function for the user to set ghost values but I am not seeing anything like this around.  Perhaps I am not understand the intent of DMDA_BOUNDARY_GHOSTED.
>>> 
>>> My understanding is that it adds a single layer of ghost cells around the domain boundary. Then these show up in the gxm, etc. so that
>>> you can put values there if you want.
>>> 
>>> Matt
>>> 
>>> 
>>> Mark
>>> 
>>> 
>>> 
>>> -- 
>>> What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.
>>> -- Norbert Wiener
>> 
>