[petsc-users] DMPlex tetrahedra facets orientation
Matthew Knepley
knepley at gmail.com
Mon Mar 8 12:22:39 CST 2021
On Mon, Mar 8, 2021 at 11:18 AM Nicolas Barral <
nicolas.barral at math.u-bordeaux.fr> wrote:
> On 08/03/2021 15:55, Matthew Knepley wrote:
> > On Mon, Mar 8, 2021 at 4:02 AM Nicolas Barral
> > <nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>> wrote:
> >
> > On 07/03/2021 22:56, Matthew Knepley wrote:
> > > On Sun, Mar 7, 2021 at 4:51 PM Nicolas Barral
> > > <nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>> wrote:
> > >
> > >
> > > On 07/03/2021 22:30, Matthew Knepley wrote:
> > > > On Sun, Mar 7, 2021 at 4:13 PM Nicolas Barral
> > > > <nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>
> > > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>>> wrote:
> > > >
> > > > On 07/03/2021 16:54, Matthew Knepley wrote:
> > > > > On Sun, Mar 7, 2021 at 8:52 AM Nicolas Barral
> > > > > <nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>
> > > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>>
> > > > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>
> > > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>>>> wrote:
> > > > >
> > > > > Matt,
> > > > >
> > > > > Thanks for your answer.
> > > > >
> > > > > However, DMPlexComputeCellGeometryFVM does not
> > compute
> > > what I
> > > > need
> > > > > (normals of height 1 entities). I can't find any
> > > function doing
> > > > > that, is
> > > > > there one ?
> > > > >
> > > > >
> > > > > The normal[] in DMPlexComputeCellGeometryFVM() is
> > exactly what
> > > > you want.
> > > > > What does not look right to you?
> > > >
> > > >
> > > > So it turns out it's not what I want because I need
> > > non-normalized
> > > > normals. It doesn't seem like I can easily retrieve
> > the norm,
> > > can I?
> > > >
> > > >
> > > > You just want area-weighted normals I think, which means
> > that you
> > > just
> > > > multiply by the area,
> > > > which comes back in the same function.
> > > >
> > >
> > > Ah by the area times 2, of course, my bad.
> > > Do you order height-1 elements in a certain way ? I need to
> > access the
> > > facet (resp. edge) opposite to a vertex in a tet (resp.
> > triangle).
> > >
> > >
> > > Yes. Now that I have pretty much settled on it, I will put it in
> the
> > > manual. It is currently here:
> > >
> > >
> >
> https://gitlab.com/petsc/petsc/-/blob/main/src/dm/impls/plex/plexinterpolate.c#L56
> > >
> > > All normals are outward facing, but hopefully the ordering in the
> > sourse
> > > file makes sense.
> >
> > Thanks Matt, but I'm not sure I understand well. What I do so far is:
> >
> > ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr);
> > for (i=0; i<dim+1; ++i) {
> > f = cone[i];
> > ierr = DMPlexComputeCellGeometryFVM(dm, f, &area, NULL,
> > &vn[i*dim]);CHKERRQ(ierr);
> > if (dim == 3) { area *= 2; }
> > for (j=0; j<dim; ++j) { vn[i*dim+j] *= area; }
> >
> > So in 3D, it seems that:
> > (vn[9],vn[10],vn[11]) is the inward normal to the facet opposing
> vertex0
> > (vn[6],vn[7],vn[8]) " "
> 1
> > (vn[3],vn[4],vn[5]) " "
> 2
> > (vn[0],vn[1],vn[2]) " "
> 3
> >
> > in 2D:
> > (vn[2],vn[3]) is a normal to the edge opposing vertex 0
> > (vn[4],vn[5]) " " 1
> > (vn[0],vn[1]) " " 2
> > Yet in 2D, whether the normals are inward or outward does not seem
> > consistent across elements.
> >
> > What am I wrongly assuming ?
> >
> >
> > Ah, I see the problem. I probably need another function. You can tell
> > that not many people use Plex this way yet.
> > The logic for what you want is embedded my traversal, but it simple:
> >
> > ierr = DMPlexGetConeSize(dm, c, &coneSize);CHKERRQ(ierr);
> > ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr);
> > ierr = DMPlexGetConeOrientation(dm, c, &ornt);CHKERRQ(ierr);
> > for (i=0; i<coneSize; ++i) {
> > f = cone[i];
> > flip = ornt[i] >= 0 ? 1 : -1;
> > ierr = DMPlexComputeCellGeometryFVM(dm, f, &area, NULL,
> > &vn[i*dim]);CHKERRQ(ierr);
> > if (dim == 3) { area *= 2; }
> > for (j=0; j<dim; ++j) { vn[i*dim+j] *= area * flip; }
> > I could make a function that returns all normals, properly oriented. It
> > would just do this.
>
> Ah this works now, thanks Matt. Toby is correct, it is ultimately
> related to Jacobians, and what I need can be done differently, not sure
> it's clearer though.
>
> Out of curiosity, what is the logic in the facet ordering ?
>
The order of faces in a cell was somewhat arbitrary. However, I wanted that
select vertices from closure(cell) = vertices before interpolation of cell
so the canonical orientation of face should have the vertices such that
they give
me the order of vertices I expect in cell-vertex meshes. This way
Uninterpolate(Interpolate(dm))
is idempotent.
Thanks,
Matt
> Thanks
>
> --
> Nicolas
>
> >
> > Thanks,
> >
> > Matt
> >
> > Thanks,
> >
> > --
> > Nicolas
> >
> > >
> > > Thanks,
> > >
> > > Matt
> > >
> > > Thanks
> > >
> > > --
> > > Nicolas
> > >
> > >
> > > > Thanks,
> > > >
> > > > Matt
> > > >
> > > > If not, I'll fallback to computing them by hand for
> > now. Is the
> > > > following assumption safe or do I have to use
> > > DMPlexGetOrientedFace?
> > > > > if I call P0P1P2P3 a tet and note x the cross
> > product,
> > > > > P3P2xP3P1 is the outward normal to face P1P2P3
> > > > > P0P2xP0P3 " P0P2P3
> > > > > P3P1xP3P0 " P0P1P3
> > > > > P0P1xP0P2 " P0P1P2
> > > >
> > > > Thanks
> > > >
> > > > --
> > > > Nicolas
> > > > >
> > > > > Thanks,
> > > > >
> > > > > Matt
> > > > >
> > > > > So far I've been doing it by hand, and after a
> > lot of
> > > > experimenting the
> > > > > past weeks, it seems that if I call P0P1P2P3 a
> > tetrahedron
> > > > and note x
> > > > > the cross product,
> > > > > P3P2xP3P1 is the outward normal to face P1P2P3
> > > > > P0P2xP0P3 " P0P2P3
> > > > > P3P1xP3P0 " P0P1P3
> > > > > P0P1xP0P2 " P0P1P2
> > > > > Have I been lucky but can't expect it to be
> true ?
> > > > >
> > > > > (Alternatively, there is a link between the
> normals
> > > and the
> > > > element
> > > > > Jacobian, but I don't know the formula and can
> > find them)
> > > > >
> > > > >
> > > > > Thanks,
> > > > >
> > > > > --
> > > > > Nicolas
> > > > >
> > > > > On 08/02/2021 15:19, Matthew Knepley wrote:
> > > > > > On Mon, Feb 8, 2021 at 6:01 AM Nicolas Barral
> > > > > > <nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>
> > > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>>
> > > > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>
> > > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>>>
> > > > > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>
> > > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>>
> > > > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>
> > > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>>>>> wrote:
> > > > > >
> > > > > > Hi all,
> > > > > >
> > > > > > Can I make any assumption on the
> > orientation of
> > > triangular
> > > > > facets in a
> > > > > > tetrahedral plex ? I need the inward
> facet
> > > normals. Do
> > > > I need
> > > > > to use
> > > > > > DMPlexGetOrientedFace or can I rely on
> > either
> > > the tet
> > > > vertices
> > > > > > ordering,
> > > > > > or the faces ordering ? Could
> > > > DMPlexGetRawFaces_Internal be
> > > > > enough ?
> > > > > >
> > > > > >
> > > > > > You can do it by hand, but you have to
> > account for
> > > the face
> > > > > orientation
> > > > > > relative to the cell. That is what
> > > > > > DMPlexGetOrientedFace() does. I think it
> > would be
> > > easier
> > > > to use the
> > > > > > function below.
> > > > > >
> > > > > > Alternatively, is there a function that
> > > computes the
> > > > normals
> > > > > - without
> > > > > > bringing out the big guns ?
> > > > > >
> > > > > >
> > > > > > This will compute the normals
> > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/DMPLEX/DMPlexComputeCellGeometryFVM.html
> > > > > > Should not be too heavy weight.
> > > > > >
> > > > > > THanks,
> > > > > >
> > > > > > Matt
> > > > > >
> > > > > > Thanks
> > > > > >
> > > > > > --
> > > > > > Nicolas
> > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > > 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
> > > > > >
> > > > > > https://www.cse.buffalo.edu/~knepley/
> > > > > <http://www.cse.buffalo.edu/~knepley/>
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > 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
> > > > >
> > > > > https://www.cse.buffalo.edu/~knepley/
> > > > <http://www.cse.buffalo.edu/~knepley/>
> > > >
> > > >
> > > >
> > > > --
> > > > 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
> > > >
> > > > https://www.cse.buffalo.edu/~knepley/
> > > <http://www.cse.buffalo.edu/~knepley/>
> > >
> > >
> > >
> > > --
> > > 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
> > >
> > > https://www.cse.buffalo.edu/~knepley/
> > <http://www.cse.buffalo.edu/~knepley/>
> >
> >
> >
> > --
> > 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
> >
> > https://www.cse.buffalo.edu/~knepley/ <
> http://www.cse.buffalo.edu/~knepley/>
>
--
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
https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20210308/af3da83d/attachment-0001.html>
More information about the petsc-users
mailing list