[petsc-users] PETSc recommended visualization packages

On 14 July 2011 18:33, Ethan Coon wrote: > On Thu, 2011-07-14 at 17:47 -0300, Lisandro Dalcin wrote: > >> >> 1) readMatDense() is wrong. The I,J,V arrays are the CSR structure, >> not the COO (coordinate) format, Then you cannot simply: >> > > Ok, thanks, I wasn't sure of which format you were usi

[petsc-users] PETSc recommended visualization packages

On 14 July 2011 16:22, Ethan Coon wrote: > Attached patch takes Lisandro's matio.py and puts it in a > PetscBinaryRead.py that reads a binary with (potentially) multiple Petsc > objects, deciphers the contents of the file from the header, and returns > numpy objects. ?It's basically the same as th

[petsc-users] PETSc recommended visualization packages

On Thu, 2011-07-14 at 17:47 -0300, Lisandro Dalcin wrote: > > 1) readMatDense() is wrong. The I,J,V arrays are the CSR structure, > not the COO (coordinate) format, Then you cannot simply: > >for i,j,v in zip(I,J,V): > mat[i,j] = v > > I think you have to: > > for row, rsta

[petsc-users] PETSc recommended visualization packages

Ethan, Excellent. I have the matlab programs in a subdirectory called matlab. Will there be several of these? So should we have a bin/python subdirectory for them? Barry On Jul 14, 2011, at 2:22 PM, Ethan Coon wrote: > Attached patch takes Lisandro's matio.py and puts it in a

[petsc-users] PETSc recommended visualization packages

I suppose it's possible, eventually. Much of the matlab stuff is related to the socket and the "wrappers", which exist in petsc4py instead. There may be a few though -- PetscBinaryWrite.py at least. Ethan On Thu, 2011-07-14 at 14:38 -0500, Barry Smith wrote: > Ethan, > >Excellent. > >

[petsc-users] PETSc recommended visualization packages

Attached patch takes Lisandro's matio.py and puts it in a PetscBinaryRead.py that reads a binary with (potentially) multiple Petsc objects, deciphers the contents of the file from the header, and returns numpy objects. It's basically the same as the PetscBinaryRead.m I've tested this on Vecs, but

[petsc-users] PETSc recommended visualization packages

Brad, Do you have examples of the way you encode mesh informations (connectivity table, block of elements, edges, vertices) in hdf5 files, and of the xdmf files that describe that layout? As I said in a previous message, I find the xdmf format documentation quite lacking. I also use Sieve to

[petsc-users] PETSc recommended visualization packages

On Thu, Jul 7, 2011 at 5:12 PM, Ethan Coon wrote: > Hmm, I've been tricked apparently. What I thought was PETSc writing out > VTK was actually PFLOTRAN writing out VTK from PETSc data structures. > PETSc will write out VTK if you a) set the PETSC_VIEWER_ASCII_VTK format b) view the DA fir

[petsc-users] PETSc recommended visualization packages: Xdmf and HDF5

Blaise- I constructed my Xdmf writer based on the documentation at http://www.xdmf.org/index.php/XDMF_Model_and_Format. The documentation is vague but I was able to figure most things out with a little trial and error. An example pair of HDF5 and Xdmf files is attached. The code is in the PyL

[petsc-users] PETSc recommended visualization packages

Ethan- I think writing an Xdmf file that points to the datasets in an HDF5 file is probably easier than creating a viewer. For PyLith we write the HDF5 file and a corresponding Xdmf file. This allows us to simply open the Xdmf file in ParaView; I think VisIt supports this as well. Brad On 07

[petsc-users] PETSc recommended visualization packages

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 examp

[petsc-users] PETSc recommended visualization packages

> 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

[petsc-users] PETSc recommended visualization packages

On 6 July 2011 11:41, Ethan Coon wrote: > Both Paraview and Visit generally make ugly axes/colorbars/keys/etc. ?In my > opinion they both look fine for presentations and my own viewing, but are not > really acceptable for publication-quality. ?For things run on a > reasonably-sized problem, mat

[petsc-users] PETSc recommended visualization packages

On Wed, 2011-07-06 at 12:24 -0300, Lisandro Dalcin wrote: > On 6 July 2011 11:41, Ethan Coon wrote: > > Both Paraview and Visit generally make ugly axes/colorbars/keys/etc. In my > > opinion they both look fine for presentations and my own viewing, but are > > not really acceptable for publicat

[petsc-users] PETSc recommended visualization packages

Both Paraview and Visit generally make ugly axes/colorbars/keys/etc. In my opinion they both look fine for presentations and my own viewing, but are not really acceptable for publication-quality. For things run on a reasonably-sized problem, matplotlib (using either h5py to read hdf5, pyvtk to

[petsc-users] PETSc recommended visualization packages

Hi, Let me add to Barry's frustration. I have spent most the last week trying to render animations of reasonably large computations (about 25M 3d unstructured elements divided in up to 25,000 exodusII files). - Paraview is simple to get started with in the GUI. In theory, it is scriptable in p

[petsc-users] PETSc recommended visualization packages

On 5 July 2011 12:53, Brad Aagaard wrote: > Hi, > > I agree with Blaise's assessment of ParaView. It is good for quick and > dirty visualization, but its scripting interface is very limited. > > MayaVi provides a GUI along with high-level API access to VTK data > structures through Python. One can

[petsc-users] PETSc recommended visualization packages

https://wci.llnl.gov/codes/visit/ This one. I agree the name is too generic to find it with just visit. I always use "visit llnl". 2011/7/5 Stephen Wornom : > Jed Brown wrote: >> >> On Mon, Jul 4, 2011 at 21:44, Barry Smith > > wrote: >> >> ? ?What are the recommende

[petsc-users] PETSc recommended visualization packages

Jed Brown wrote: > On Mon, Jul 4, 2011 at 21:44, Barry Smith > wrote: > > What are the recommended visualization packages for use with PETSc > (for example making movies of contour plots and isosurfaces) and > what are the recommended data formats to use t

[petsc-users] PETSc recommended visualization packages

Hi, I agree with Blaise's assessment of ParaView. It is good for quick and dirty visualization, but its scripting interface is very limited. MayaVi provides a GUI along with high-level API access to VTK data structures through Python. One can update/modify the data values through the API without

[petsc-users] PETSc recommended visualization packages

On Mon, Jul 4, 2011 at 21:44, Barry Smith wrote: > What are the recommended visualization packages for use with PETSc (for > example making movies of contour plots and isosurfaces) and what are the > recommended data formats to use to save Vecs for visualization? VisIt and ParaView are the prim

[petsc-users] PETSc recommended visualization packages

What are the recommended visualization packages for use with PETSc (for example making movies of contour plots and isosurfaces) and what are the recommended data formats to use to save Vecs for visualization? Thanks Barry