Hmm, I've been tricked apparently. What I thought was PETSc writing out VTK was actually PFLOTRAN writing out VTK from PETSc data structures.
On a day-to-day basis I tend to use HDF5, and I've checked that that does, in fact, work with only PETSc, and only a few lines of PETSc. Follow/run example: http://www.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-current/src/dm/da/examples/tutorials/ex9.c.html Then load that in python with h5py and view with matplotlib: In [1]: import h5py In [2]: ex9 = h5py.File('hdf5output') In [3]: ex9 Out[3]: <HDF5 file "hdf5output" (mode r+, 142.7k)> In [4]: ex9.keys() Out[4]: ['Vec_0x84000000_0'] In [5]: vec = ex9[ex9.keys()[0]] In [6]: vec Out[6]: <HDF5 dataset "Vec_0x84000000_0": shape (90, 100, 2), type "<f8"> In [7]: vec.shape # vec was created from a 2D DA, size (90,100), with 2 dofs Out[7]: (90, 100, 2) In [8]: from matplotlib import pyplot as plt In [9]: plt.imshow(vec[:,:,0].transpose(), origin='lower') Out[9]: <matplotlib.image.AxesImage object at 0x2310850> In [10]: plt.colorbar() Out[10]: <matplotlib.colorbar.Colorbar instance at 0x2313320> In [11]: plt.show() The downside of this option is that, in order for hdf5 files to work in anything but python (which is smart enough to use introspection on the file itself) you need a special viewer (the VisIt people call this a "flavor" of HDF5), see http://visitusers.org/index.php?title=VisIt_and_HDF5 These work on both VisIt and Paraview, but I've never tried to write one myself, so I don't know how ugly they are. They basically specify the layout of the hdf5 file. Note that if you go with the HDF5 option, you'll likely want to move to petsc-dev, which includes more HDF5 functionality, such as groups. Ethan On Thu, 2011-07-07 at 08:21 -0600, Andrew T Barker wrote: > > Should PETSc ship some Python code to > > read IS's, Vec's, Mat's in binary format? > > Yes. Please. > > I have played with matplotlib some to view Petsc output (vtk), with mixed > results. I wonder if Ethan would be willing to share an example or two? > > Best, > > Andrew -- ------------------------------------ Ethan Coon Post-Doctoral Researcher Applied Mathematics - T-5 Los Alamos National Laboratory 505-665-8289 http://www.ldeo.columbia.edu/~ecoon/ ------------------------------------
