lp:fluidity/stable

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3559. By Tim Bond on 2011-12-06

lp:fluidity/stable is now deprecated in favour of lp:fluidity/4.1 but will be
retained for the moment; bringing up to date with 4.1.1 with this merge.

3558. By Tim Bond on 2011-11-07

An update of fluidity/stable to mirror the new fluidity/4.1.0 release.

This is a major step forward, long-delayed after many problems with the
Fluidity testing framework over the past couple of months.

Normal service in terms of regular fluidity/stable updates with changelogs
is expected to resume from this point.

3557. By Tim Bond on 2011-08-30

Updating stable-trunk to match trunk revision 3567.

Changelog:

* Bugfix for Intel 11.x unit testing
* Bugfix for bug 832197 dealing with problems using old versions of scipy

There remain known unit-test problems using Intel 11.x (as yet not formally
supported by Fluidity).

3556. By Tim Bond on 2011-08-22

Updating stable trunk to mirror trunk revіsion 3565.

Changelog:

* Bug fix in vector_field_addto_field_scale_field. If we remap scale then we
  should use the remapped field, not the original

* Put in a dependency on include/version.h. This fixes a race condition
  exposed with make -j since the recent change to how the version number
  is handled.

* Bug fix to Momentum_DG when using implicity_buoyancy. The interface to
  ele_grad_at_quad got changed a while back and this one was missed or reverted

* Switching the indices of an array in Momentum_CG which seems to have been
  missed when the ele_grad_at_quad interface was updated a while back.

* Spud updated to revision 452 and some updates to the build process to deal
  with python install locations.

* Branch merge from diagnostic-python-spud, mostly written by Nan Mao:

    This branch contains the features that let the embedded python interpreter
    in fluidity access the spud dictionary of fluidity's options.

    Use it as follows:

      import libspud
      libspud.get_option("/simulation_name")

    It only works for Python >= 2.7, so if you want your code to work on 2.6 or
    before, you need to guard with an

      if sys.version_info[1] > 6

    This branch also contains some minor fixes for compiling fluidity against;
    sometimes things were using the system one, and sometimes things were using
    the libspud/ directory.

    This branch also updates libspud/ to be the latest spud trunk. Those
    changes have been reviewed earlier in other merge requests.

3555. By Tim Bond on 2011-08-17

Updating lp:fluidity/stable to mirror r3558 of the development trunk.

Changeѕ since previous update:

* Fix for bug https://launchpad.net/bugs/814667
  - Fix invalid element in adaptivity_options schema
  - Relax-NG doesn't allow mixing string and data in a single group in an
    element, so don't do it.

* Fix for bug https://launchpad.net/bugs/822355
  - Bug-fix in interpolation manager for periodic meshes.

* Extensions to the python-state system to expose CSR matrices.

  User code can access CSR matrices like:

    m = state.csr_matrices['PressureMeshMassMatrix']

  The interface is quite extensive, as it subclasses scipy.sparse.csr_matrix.
  So you can do almost anything with it: multiply it by a vector
  (m * field.val), solve mu = b (scipy.sparse.linalg.spsolve), etc.

  Note that it only exposes CSR matrices that happened to exist in state when
  it was passed to calculate_diagnostic_fields. In many cases, that appears to
  be precisely 0. One can test this by adding a call to

    get_mass_matrix(state, velocity_mesh)

  just before the call to calculate_diagnostic_variables.

* Bugfixes for https://launchpad.net/bugs/814839
               https://launchpad.net/bugs/815814

  - Move version definition out of include/confdefs.h

  - Setting the version number of Fluidity during configure is the wrong
    thing to do, and writing it into include/confdefs.h doubly so.
    Instead, add a new rule to the top-level Makefile to generate
    include/version.h. If you need to know __FLUIDITY_VERSION__ you must
    now explicitly include version.h as well confdefs.h.

  - Remove any last vestiges of svnversion from the configure scripts.

3554. By Tim Bond on 2011-08-10

Reverting 3553; this fixes 4.6 but breaks Intel 10, and the latter is more
important to us at the moment.

3553. By Tim Bond on 2011-08-10

Small bufix targetting bug:

   https://bugs.launchpad.net/fluidity/+bug/823966

swapping the order of the parmetis and zoltan checks in configure.in
to fix a linking bug using gcc 4.6 on oneiric.

3552. By Cian Wilson on 2011-08-09

Bugfix pointed out by hhiester. cv_stats were not parallel safe.

3551. By Jon Hill on 2011-08-08

Fix for the failing flredecomp test. Probably better ways to fix this long term, but this will suffice for now

3550. By Adam Candy on 2011-08-02

Bringing partition.cpp back - effectively revoking r3549 (apologies for the break in history).