[petsc-dev] DMComplex and Coordinates

[Matthew Knepley]

On Wed, Sep 26, 2012 at 5:37 PM, Chris Eldred <chris.eldred at gmail.com>wrote:

> Will there be a way to set coordinates if I am using a homemade mesh
> generator?
>

Sure, here is me doing this by hand (from complexcreate.c):

  /* Build coordinates */
  ierr = DMComplexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
  ierr = PetscSectionSetChart(coordSection, numEdges, numEdges +
numVertices);CHKERRQ(ierr);
  for (v = numEdges; v < numEdges+numVertices; ++v) {
    ierr = PetscSectionSetDof(coordSection, v, 2);CHKERRQ(ierr);
  }
  ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr);
  ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr);
  ierr = VecCreate(((PetscObject) dm)->comm, &coordinates);CHKERRQ(ierr);
  ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
  ierr = VecSetFromOptions(coordinates);CHKERRQ(ierr);
  ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
  for (vy = 0; vy <= edges[1]; ++vy) {
    for (vx = 0; vx <= edges[0]; ++vx) {
      coords[(vy*(edges[0]+1)+vx)*2+0] = lower[0] + ((upper[0] -
lower[0])/edges[0])*vx;
      coords[(vy*(edges[0]+1)+vx)*2+1] = lower[1] + ((upper[1] -
lower[1])/edges[1])*vy;
    }
  }
  ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
  ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr);


> What about having coordinates for the edges/faces/cells as well (to be
> interpreted as we want)?


Yep, just give them a dof in the Section and set the values.

   Matt


> On Wed, Sep 26, 2012 at 3:34 PM, Matthew Knepley <knepley at gmail.com>
> wrote:
> > On Wed, Sep 26, 2012 at 5:24 PM, Chris Eldred <chris.eldred at gmail.com>
> > wrote:
> >>
> >> On the subject:
> >>
> >> How do coordinates work for user-defined DMComplex objects? What
> >> determines the Coordinate section (and which points does it contain?)?
> >> How is the coordinate vector set?
> >
> >
> > I am just rewriting this. Now it will be
> >
> >   DMGetCoordinateDM(DM, DM *)
> >   DMGetCoordinates(DM, Vec *)
> >   DMGetCoordinatesLocal(DM, Vec *)
> >
> > and there is a convenience
> >
> >   DMComplexGetCoordinateSection(DM, PetscSection *)
> >
> > By default, I read in the vertex coordinates from the mesh generator.
> > However,
> > the idea is that you can interpret the coordinates however you want. We
> just
> > give you a DM and a vector. You can construct the section however you
> want,
> > although without vertex coordinates some default things will not work,
> like
> > VTK
> > output.
> >
> >     Matt
> >
> >>
> >>
> >> --
> >> Chris Eldred
> >> DOE Computational Science Graduate Fellow
> >> Graduate Student, Atmospheric Science, Colorado State University
> >> B.S. Applied Computational Physics, Carnegie Mellon University, 2009
> >> chris.eldred at gmail.com
> >
> >
> >
> >
> > --
> > 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
>
>
>
> --
> Chris Eldred
> DOE Computational Science Graduate Fellow
> Graduate Student, Atmospheric Science, Colorado State University
> B.S. Applied Computational Physics, Carnegie Mellon University, 2009
> chris.eldred at gmail.com
>



-- 
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
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