[petsc-users] query DMPlexCreateSection

Matthew Knepley knepley at gmail.com
Fri Jan 10 19:11:19 CST 2014 

On Fri, Jan 10, 2014 at 3:09 PM, Dharmendar Reddy
<dharmareddy84 at gmail.com>wrote:

> Well,  I was wondering, if i could use:
>
> DMPlexCreateSectionBCDof (1) and DMPlexCreateSectionBCIndicesAll (2)
>

I would just do it by hand first, and then maybe we can abstract it.

   Matt


> as is done in DMPLexCreateSection
>
> http://www.mcs.anl.gov/petsc/petsc-current/src/dm/impls/plex/plex.c.html#DMPlexCreateSection
>
> Since I am trying to setup section for a problem with different number
> of fields in different domains (regions). I redid the code for initial
> section creation.
>
> So the concern is if i am to setup BC's for  the above scenario, is
> the code going to be different from the sequence of calls inside (1)
> and (2), once the initial section is defined.
>
> Thanks
> Reddy
>
> Thanks
> Reddy
>
> On Fri, Jan 10, 2014 at 2:37 PM, Brad Aagaard <baagaard at usgs.gov> wrote:
> > On 01/10/2014 11:19 AM, Dharmendar Reddy wrote:
> >>
> >> Hello,
> >>          I was able to create the petsc section as per your advice.
> >>>
> >>>    DMPlexSetChart()
> >>>    <loop over region 1>
> >>>      DMPlexSetDof() and DMPlexSetFieldDof()
> >>>    <loop over region 2>
> >>>      DMPlexSetDof() and DMPlexSetFieldDof()
> >>
> >>
> >> I could program the code upto this step.
> >>
> >>    ! Create Section
> >>    call PetscSectionCreate(comm, section, ierr)
> >>    ! This call sets the number of fields in the section. Default number
> >> of compents per field is 1
> >>    call PetscSectionSetNumFields(section, numField, ierr)
> >>    ! Set the number of componets per field
> >>    do fid=0,numField-1
> >>      call PetscSectionSetFieldComponents(section, fid, numComp(fid+1),
> >> ierr)
> >>    end do
> >>    ! Set the chart for section
> >>    call DMPlexGetChart(meshDM, cellIdStart, cellIdEnd, ierr)
> >>    call PetscSectionSetChart(section, cellIdStart, cellIdEnd, ierr)
> >>    print*,'Sucessfully set chart',cellIdStart,cellIdEnd
> >>    rgnLabel = "region"
> >>    call DMPlexGetLabelIdIS(meshDM,rgnLabel,regionIS,ierr)
> >>    call ISView(regionIS,PETSC_VIEWER_STDOUT_SELF,ierr)
> >>    call ISGetIndicesF90(regionIS, regionId, ierr)
> >>    print*, 'region', regionId
> >>    do jc=1,size(regionId) ! Loop Over region1
> >>      rgnId = regionId(jc)
> >>      call DMPlexGetStratumIS(meshDM, "region",rgnId, regionCellIS, ierr)
> >>      !print*,'Number of cells in region',rgnId
> >>      call ISGetSize(regionCellIS, numCell, ierr)
> >>      !print*,'Number of cells in region',rgnId, 'is',numCell
> >>      call ISGetIndicesF90(regionCellIS, regionCell, ierr)
> >>      do ic=1,numCell ! Get the cells of this region and loop over Cells
> >>        cellId = regionCell(ic)
> >>        ! Get the dimension of the cell
> >>        call DMPlexGetLabelValue(meshDM, "depth", cellId, cellDim, ierr)
> >>        do fid=0,numField-1 ! Loop over fields
> >>           ! Set field only if the field is defined for this region
> >>           !print*, 'settinf Field
> >> for',cellId,cellDim,fid,rgnId,numDof(fid+1,cellDim+1)
> >>           if(fieldInRegion(fid+1,rgnId)) then
> >>              call PetscSectionSetFieldDof(section, cellId, fid,
> >> numDof(fid+1,cellDim+1), ierr)
> >>           end if
> >>        end do
> >>        call  PetscSectionSetDof(section, cellId,
> >> numDofTot(cellDim+1,rgnId), ierr)
> >>      end do
> >>      call ISRestoreIndicesF90(regionCellIS, regionCell, ierr)
> >>    end do
> >>    call ISRestoreIndicesF90(regionIS, regionId, ierr)
> >>
> >>
> >> Now I need to work on the code for BC. Can you help me with a bit more
> >> detail here.
> >>>
> >>>    <loop over BC>
> >>>      DMPlexSetConstraintDof() and DMPlexSetFieldConstraintDof()
> >
> >
> > Use DMPlexSetConstraintDof() to set the number of DOF constrained at each
> > point on the BC. DMPlexSetFieldConstraintDof() is used if you have
> multiple
> > fields in a section.
> >
> >
> >>>    DMPlexSetUp()
> >>>    <loop over BC>
> >>>      DMPlexSetConstraintIndices() and DMPlexSetFieldConstraintIndices()
> >
> >
> > Use DMPlexSetConstraintIndices() to set the indices of the DOF that are
> > constrained.
> >
> > For example, one might constrain the DOF normal and/or tangential to a
> > boundary in an elasticity problem. You first set the size for all the
> > points, allocate via DMPlexSetUp, and then set the indices for the
> > constrained DOF at each point.
> >
> > Regards,
> > Brad
> >
> >
> >> On Thu, Jan 2, 2014 at 9:56 AM, Matthew Knepley <knepley at gmail.com>
> wrote:
> >>>
> >>> On Thu, Jan 2, 2014 at 4:11 AM, Dharmendar Reddy
> >>> <dharmareddy84 at gmail.com>
> >>> wrote:
> >>>>
> >>>>
> >>>> Hello,
> >>>>           I am trying to use DMPlexCreateSection from fortran. I was
> >>>> able to solve a Poisson equation earlier using DMPlex for handling
> >>>> mesh data.
> >>>>
> >>>> Now i need to solve a system of equations: (poisson + continuity
> >>>> equations)
> >>>>
> >>>> - div (grad phi) = (C + n)  --- (1)
> >>>>    div (J ) = 0  ---------------  (2)
> >>>>    J = n grad(phi)
> >>>> ( C is constant)
> >>>> Simulation domain is defined as, rectangular regions 1 and 2 shown
> >>>> below.
> >>>>
> >>>> -------------
> >>>> |     1        |
> >>>> -------------
> >>>> |               |
> >>>> |       2      |
> >>>> |               |
> >>>> --------------
> >>>>
> >>>> Now, equation 1 is defined in region 1 and 2
> >>>> and equation 2 is defined only for region 2.
> >>>>
> >>>> How do i setup the section  ? DMPlexCreateSection applies the given
> >>>> DOF layout  per cell to all cells in the mesh.
> >>>>
> >>>> I am not sure if all the function calls inside
> >>>> DMPlexCreateSectionIntial and DMPlexCreateSectionBCDof  are accessible
> >>>> from Fotran.
> >>>
> >>>
> >>>
> >>> You don't want them anyway since they apply to the whole domain. The
> >>> control
> >>> flow could be:
> >>>
> >>>    DMPlexSetChart()
> >>>    <loop over region 1>
> >>>      DMPlexSetDof() and DMPlexSetFieldDof()
> >>>    <loop over region 2>
> >>>      DMPlexSetDof() and DMPlexSetFieldDof()
> >>>    <loop over BC>
> >>>      DMPlexSetConstraintDof() and DMPlexSetFieldConstraintDof()
> >>>    DMPlexSetUp()
> >>>    <loop over BC>
> >>>      DMPlexSetConstraintIndices() and DMPlexSetFieldConstraintIndices()
> >>>
> >>> We could try and package some of this up if it looks generic.
> >>>
> >>>    Thanks,
> >>>
> >>>       Matt
> >>>
> >>>>
> >>>> Thanks
> >>>> Reddy
> >>>>
> >>>> --
> >>>> -----------------------------------------------------
> >>>> Dharmendar Reddy Palle
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> --
> >>> 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
> >>
> >>
> >>
> >>
> >
>
>
>
> --
> -----------------------------------------------------
> Dharmendar Reddy Palle
> Graduate Student
> Microelectronics Research center,
> University of Texas at Austin,
> 10100 Burnet Road, Bldg. 160
> MER 2.608F, TX 78758-4445
> e-mail: dharmareddy84 at gmail.com
> Phone: +1-512-350-9082
> United States of America.
> Homepage: https://webspace.utexas.edu/~dpr342
>



-- 
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20140110/527a7b8d/attachment.html>

More information about the petsc-users mailing list