On Wed, Mar 16, 2016 at 7:23 AM, gouarin <[email protected]>
wrote:
> Hi,
>
> I try to use PETSc to solve BEM problem so I need to construct a surface
> with 3D coordinates. First of all, I would like to plot the mesh and I
> think that the output of the viewer is completely wrong.
>
> Here is a Python example
>
> import sys, petsc4py
> petsc4py.init(sys.argv)
> import numpy as np
> import petsc4py.PETSc as petsc
>
>
> coords = np.array([[0, 0, 0],
> [1, 0, 0],
> [0, 1, 0],
> [1, 1, 0],
> [0, 0, 1],
> [1, 0, 1],
> [0, 1, 1],
> [1, 1, 1],
> ], dtype=np.double)
>
> cells = np.array([[0, 1, 3, 2],
> [1, 5, 7, 3],
> [0, 4, 6, 2],
> [2, 3, 6, 7],
>
This quad is mis-specified, since 3-6 is a diagonal.
> [0, 1, 5, 4],
> [4, 5, 7, 6],
> ], dtype=np.int32)
>
> dm = petsc.DMPlex().createFromCellList(2, cells, coords,
> interpolate=False, comm=petsc.COMM_WORLD)
>
> viewer = petsc.Viewer().createHDF5('cube.h5', 'w')
> dm.view(viewer)
>
> If you look at the cells in the cube.h5, the numbering of the points is
> wrong.
>
I rewrote this in C, and I can visualize the surface. I then run it using
./ex18 -dm_view hdf5:dm.h5
and process that file
./bin/petsc_gen_xdmf.py dm.h5
This won't quite work when you have interpolate = PETSC_FALSE, because then
I do not force the 'viz' output,
however it can be forced with a viewer format.
Thanks,
Matt
> Thanks,
> Loic
> --
> Loic Gouarin
> Laboratoire de Mathématiques
> Université Paris-Sud
> Bâtiment 425
> 91405 Orsay Cedex
> France
> Tel: (+33) 1 69 15 60 14
> Fax: (+33) 1 69 15 67 18
>
--
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
static char help[] = "Test surface meshes";
#include <petscdmplex.h>
#undef __FUNCT__
#define __FUNCT__ "main"
int main(int argc, char **argv) {
DM dm, dist;
Mat mat;
PetscInt dim = 2;
PetscBool interpolate = PETSC_TRUE;
PetscInt cells[24] = {0, 2, 3, 1, 1, 3, 7, 5, 0, 4, 6, 2, 2, 6, 7, 3, 0, 1, 5, 4, 4, 5, 7, 6};
PetscReal coords[24] = {0, 0, 0, 1, 0, 0, 0, 1, 0, 1, 1, 0, 0, 0, 1, 1, 0, 1, 0, 1, 1, 1, 1, 1};
PetscErrorCode ierr;
ierr = PetscInitialize(&argc, &argv, NULL, help); CHKERRQ(ierr);
ierr = DMPlexCreateFromCellList(PETSC_COMM_WORLD, dim, 6, 8, 4, interpolate, cells, 3, coords, &dm); CHKERRQ(ierr);
ierr = DMPlexDistribute(dm, 0, NULL, &dist); CHKERRQ(ierr);
if (dist) {
ierr = DMDestroy(&dm);CHKERRQ(ierr);
dm = dist;
}
ierr = DMViewFromOptions(dm, NULL, "-dm_view");CHKERRQ(ierr);
ierr = DMDestroy(&dm);CHKERRQ(ierr);
PetscFinalize();
return 0;
}
