June 12 -- June 18

This week I have implemented a JSPlot library, which allows to use matplotlib API, but plot into your web browser:
http://github.com/certik/jsplot
(Scroll down a little bit to see the screenshots and examples.)

This was the last missing piece to be able to develop with FEMhub (I don't have a root access to my computer, running RHEL5). Now I have the full Python stack working (scipy, all the solvers, mayavi, ...), plus nice plotting in the browser.

I have spent several days investigating how to write weak forms for the radial Dirac equation as well as how to derive the action for it. It turns out, that one takes the Lagrangian from quantum electrodynamics (QED), converts it to spherical coordinates (which you can imagine is a hell of a job) and then integrates over angles and what remains is the Lagrangian (resp. action) for the radial Dirac equation. People used that in the literature a lot, but I just could not figure out where they take the functional from. So that part is clear and then I went to coding.

Here are the commits for JSPlot:

Ondrej Certik (38):
      Initial commit
      Make index.html work
      README added
      Hook up raphael
      Serve raphael-min.js locally
      Plot simpler stuff
      Works fine
      plots work
      Download all the raphael stuff locally
      raphael.html added
      Use {% url %}
      Use simpler urls
      Typo fix
      Flotr demo added
      Use flotr in the index page
      Don't recalculate
      Add data by hand
      Generate the data in Python
      Add another flotr demo
      Example mpl plot added
      jsplot example added
      runserver.py added
      Hook it up with jsplot
      Add a screenshot
      Better README added
      README improved
      Show some testing data
      Use better testing data
      License added
      setup.py added
      Use testing data if data == []
      Just return from the function on CTRL-C
      spkg-install added
      prepend the .. path, instead of append
      Use the proper local files in ./manage.py
      Turn off points
      Fix a bug
      Add grid and legend

I fixed some scipy warnings in hermes2d:

ondrej@crow:~/repos/hermes2d(master)$ git weekreport 
Ondrej Certik (4):
      hermes_common updated
      Fix the other SciPy warning in Python wrappers
      Update the generated .cpp file
      update hermes_common

I have fixed Python wrappers in hermes1d, made the Schroedinger example work again:

ondrej@crow:~/repos/hermes1d(master)$ git weekreport 
Ondrej Certik (19):
      Use jsplot if available
      Build everything for now
      Make the Python wrappers work again
      Fix the lhs/rhs/residual to build properly
      Polish the forms a little bit
      Enable assembling
      Implement c2py_Mesh
      Use c2py_Mesh in the schroedinger example
      Update insert_matrix in Schroedinger
      Fixed the rest in Schroedinger
      copy_mesh_to_vector() and copy_vector_to_mesh() added to the Mesh class
      Use JSPlot
      Linearizer.get_xy() fixed
      Implement Mesh.copy_vector_to_mesh() and use it from get_xy()
      Use CooMatrix to assemble
      Implement pysparse solver
      Polish the numpy solver
      Polish the printing a little bit
      Rename assemble_jacobian() to assemble_matrix()

I fixed some build issues with FEMhub:

ondrej@crow:~/repos/femhub(master)$ git weekreport 
Ondrej Certik (3):
      Add gnutls dependency for Python
      opencdk added
      Fix libgpg_error to build in parallel

and I have some more patches to the build system in my "pu" branch at github:

* 44398d8 (github/pu) Use absolute paths in "femhub -i"
* 2b17bf0 Fix "femhub --devel-install" to normalize the paths
* 3b41261 Make "femhub --shell" stay in the current directory

I still need to test that femhub builds fine with those (it always takes quite some testing to make sure it builds properly).