Author: Jemma Shipton
Revision Date: 2014-10-08 15:17:20 UTC

Again mirroring Fangxin's changes from the ROM branch, this time from:

https://github.com/FluidityProject/fluidity/commit/4cb7521660339a950390076c0e7ed2cda0189073

to allow linking with petsc 3.1 when other petsc versions are present.

Author: Tim Greaves
Revision Date: 2014-06-20 10:39:35 UTC

The repository has moved to https://github.com/FluidityProject/buildscripts

Author: Dimitrios Pavlidis
Revision Date: 2014-06-12 12:47:32 UTC

last bzr commit...

Author: Richard Ferrier
Revision Date: 2014-05-30 12:09:48 UTC

Merge with fluidity trunk.

Author: Rhodri Davies
Revision Date: 2014-05-30 06:19:04 UTC

Merge in petec-legacy branch.

Author: Rhodri Davies
Revision Date: 2014-05-28 23:58:05 UTC

Merge trunk into branch.

Author: Rhodri Davies
Revision Date: 2014-05-29 00:02:52 UTC

Merge in trunk.

Author: Stephan Kramer
Revision Date: 2014-05-28 10:22:37 UTC

Properly fix .sum(axis=(1,2)) issue.
Also loosen tolerance for project_vtu test (to avoid gmsh version issues).

Author: Tim Greaves
Revision Date: 2014-05-20 15:15:36 UTC

Expanding variables in the test XML command section as in some cases the
variable assignment failed leading to a test failure.

Author: Tim Greaves
Revision Date: 2014-04-25 10:23:20 UTC

As per discussion at:
http://lists.gnu.org/archive/html/bug-libtool/2012-03/msg00004.html

libtool generation breaks for wrapped gfortran >=4.6 in some cases. This is
a different fix to the one proposed in the link above but seems to work. I'm
applying this directly to Fluidity to get a quick fix for Archer but will also
propose it as a fix to spud.

Author: Tim Greaves
Revision Date: 2014-04-17 12:52:24 UTC

Updating the Ubuntu section in 'External Libraries' to reflect a more time-
independent description of supported releases.

Author: Alexandros Avdis
Revision Date: 2014-04-15 12:39:26 UTC

Small modification giving a better error message when tidal harmonic analysis fails. When failing to compute phase it should now report which tidal constituent fails.

Author: Samuel Parkinson
Revision Date: 2014-03-25 17:08:39 UTC

revert tests and change galerkin projection routine to include halo 1 elements, but still not halo 2 elements

Author: Christopher Pain
Revision Date: 2014-03-07 17:04:28 UTC

make sure everything is up todate

Author: Zhihua Xie
Revision Date: 2014-03-06 13:33:17 UTC

small fix

Author: Stephan Kramer
Revision Date: 2014-02-20 10:43:50 UTC

Merge in trunk.

Author: Michael Lange
Revision Date: 2014-02-08 08:04:10 UTC

Make makefiles

Author: Stephan Kramer
Revision Date: 2014-01-24 16:27:36 UTC

Fix pvtu2vtu for DG pvtus.

Previously when passing a discontinuous pvtu to pvtu2vtu, it would create a continuous vtu
choosing a value at the vertex from one of the surrounding dg nodes at random. Now, it creates
a discontinuous vtu without loosing any information or accuracy.

Author: Jemma Shipton
Revision Date: 2014-01-22 14:55:37 UTC

reinstating optional argument as too much effort to remove it

Author: Stephan Kramer
Revision Date: 2014-01-14 16:12:04 UTC

Use PetscBool instead of PetscTruth.

Author: Samuel Parkinson
Revision Date: 2013-11-28 11:44:06 UTC

merge with trunk

Author: Liping Cai
Revision Date: 2013-11-22 17:42:14 UTC

set the dynamic time step is according to the value of the current source term instead of the change rate of concentrantion at the previous time step

Author: Rhodri Davies
Revision Date: 2013-11-15 01:17:18 UTC

Merge in trunk.

Author: Jon Hill
Revision Date: 2013-11-06 12:41:07 UTC

Fixes to vis slides and editing makefile for 2013

Author: Tim Greaves
Revision Date: 2013-11-01 15:40:02 UTC

** Fluidity Release 4.1.11 (lp:fluidity r4279)

This is a milestone release of Fluidity containing updates since 2013-02-27
(4.1.10, trunk r.4254) and prepared for the November Fluidity training course.

The main policy decision following the release of 4.1.11 is that Fluidity only
supports GCC as a compiler for building. Since Intel moved to 12.0 all Intel
compilers have contained critical-for-us Fortran bugs which have not been
resolved, and there are no signs that a resolution is near as of this release.
Hence, with 11.1(>.074) being unavailable from Intel, GCC remains the only
supported compiler to build Fluidity.

Known bugs include the non-functional CGAL build, and a known issue with the
libspud build when built with CC, CXX, and FC set to MPI compilers. Neither are
expected to be an issue for the majority of users.

Key changes since 4.1.10 include:

* Adding prescribed normal flow boundary condition
* New equation type ‘shallow water’
* Test overhaul for cluster environments
* Improved support for internal boundaries, in particular 2d adaptivity.
* Removed ALGENCAN support
* Testharness no longer requires PYTHONPATH to be set
* PETSc auto detection added for common install locations
* tcmalloc used for non-debug Fluidity when available
* Removed use_compressible_projection_method option

Author: psalinas
Revision Date: 2013-10-31 19:03:59 UTC

Some changes

Author: Cian Wilson
Revision Date: 2013-10-29 10:16:15 UTC

Updates to tests to remove deprecated use_compressible_projection_method option.

Author: Satoshi Kimura
Revision Date: 2013-10-25 15:24:16 UTC

Merge the trunk

Author: Jon Hill
Revision Date: 2013-10-11 07:51:55 UTC

Merge from trunk

Author: Doru Bercea
Revision Date: 2013-10-07 13:20:49 UTC

Using assign to trigger caching.

Author: psalinas
Revision Date: 2013-10-03 17:06:13 UTC

Added LOC_U_SOURCE, a way to calculate SOUGI_X and more fixes.

Author: David Ham
Revision Date: 2013-09-24 11:04:36 UTC

put mass matrix version of explicit wave equation back in

Author: David Ham
Revision Date: 2013-09-19 14:21:16 UTC

test of external facet integral

Author: Florian Rathgeber
Revision Date: 2013-09-18 00:38:12 UTC

core_types: Add common base class FunctionSpaceBase

Serves as the base class for all types of FunctionSpaces and takes a
mesh and an element as constructor arguments.

Author: Jemma Shipton
Revision Date: 2013-09-06 14:30:24 UTC

update branch to get some tests

Author: David Ham
Revision Date: 2013-09-06 13:40:10 UTC

Less problematic name for test python script

Author: Lawrence Mitchell
Revision Date: 2013-09-03 15:11:22 UTC

Add more docstrings

Author: David Ham
Revision Date: 2013-09-02 14:58:31 UTC

Plausibly complete helmholtz test

Author: Jemma Shipton
Revision Date: 2013-07-26 12:41:39 UTC

script for generating cubed sphere meshes in parallel

Author: Jon Hill
Revision Date: 2013-07-19 09:34:48 UTC

Tweaking tolerance

Author: Michael Lange
Revision Date: 2013-07-15 16:56:23 UTC

Shuffling use statements for Intel v13

Author: Adam Candy
Revision Date: 2013-07-04 15:04:45 UTC

Revert merge 4202, which is causing failures in current trunk.

Author: Jemma Shipton
Revision Date: 2013-06-13 11:05:09 UTC

rt1 Williamson 2 test

Author: Jon Hill
Revision Date: 2013-06-05 11:50:53 UTC

Removing the chaining from non-radial extrudes using sigma layer, similar to bug 1099943. Fixes https://bugs.launchpad.net/fluidity/+bug/1183080

Author: Michael Lange
Revision Date: 2013-05-27 16:23:12 UTC

Adding detector re-initialisation from NetCDF checkpoint.

Author: Jon Hill
Revision Date: 2013-05-19 09:42:51 UTC

Merge from trunk

Author: Stephan Kramer
Revision Date: 2013-05-18 13:41:19 UTC

Mesh movement according to ice melt.

To use choose ice_melt as mesh movement scheme and add a prescribed field
"ThermalConductivity" with the conductivity values for water and ice in the
corresponding regions. As the ice melt depends on the normal temperature
gradient at the interface you'll need enough resolution to resolve the
diffusive boundary layer.

Author: Xiaohu Guo
Revision Date: 2013-05-13 10:30:37 UTC

add more timing hooks

Author: Michael Lange
Revision Date: 2013-05-01 16:33:10 UTC

Initial set of changes to get configure going:
 * Make configure cross-compile-aware
 * Make configure BG/Q-aware
 * Identify LAPACK with dsyevx (provided by IBM ESSL)
 * Bypass PETSc version check

Author: Frank Milthaler
Revision Date: 2013-04-29 15:19:30 UTC

updating the parallel test: running on 2, 3, 4 procs

Author: Tim Greaves
Revision Date: 2013-03-13 13:27:46 UTC

Initial round of updates to the manual, based on an updated set of instructions
including the gcc 4.7 build.

Author: Stephan Kramer
Revision Date: 2013-03-09 19:26:15 UTC

Also merging in schema fixes (that I'd done by hand on this branch already).

Author: Stephan Kramer
Revision Date: 2013-03-09 19:24:36 UTC

Undoing incorrect schema changes (now identical to trunk).

Author: Stephan Kramer
Revision Date: 2013-03-07 14:39:45 UTC

Merging in trunk.

Author: Gerard
Revision Date: 2013-02-19 02:24:55 UTC

Bug fixes

Author: Jemma Shipton
Revision Date: 2013-02-21 22:00:09 UTC

unittest for quad meshes

Author: Jefferson Gomes
Revision Date: 2013-02-19 17:14:58 UTC

deleting legacy comments

Author: Jon Hill
Revision Date: 2013-02-16 19:15:38 UTC

So the diff was incorrect - error between keyboard and chair - so merging across

Author: Gerard
Revision Date: 2013-02-09 09:37:52 UTC

Added profiling print to darcy_impes main.

Author: Mark Filipiak
Revision Date: 2013-02-04 16:20:23 UTC

Remove unnecessary and undesirable exact coordinate remapping.

Author: Jon Hill
Revision Date: 2013-01-15 15:53:47 UTC

Argh, merge from trunk *and* a tweak to configure to get hector to compile

Author: Gerard
Revision Date: 2013-01-04 14:02:00 UTC

Re-instate some old ad stuff - with changes to make it less crap for porting

Author: Michael Lange
Revision Date: 2012-12-22 13:20:25 UTC

Adding writes for vector fields.

Author: Stephan Kramer
Revision Date: 2012-12-11 23:45:22 UTC

Hopefully fixing the intel debug build.

For some bizarre reason intel started to choke on a bit of debugging code, code that is perfectly legal and hasn't changed for a long time. However on reading the code I realized the debugging check was actually incorrect. So hopefully fixing that will also placate the intel compiler.

Author: James Robert Percival
Revision Date: 2012-12-10 18:53:30 UTC

Sufficient changes to ensure that surface are correctly calculated on CV faces for tetrahedral meshes, as tested by resurrected test_cv_faces femtools unittest.

Author: Mark Filipiak
Revision Date: 2012-11-29 12:08:44 UTC

Merge from trunk.

Author: Alexandros Avdis
Revision Date: 2012-11-09 18:10:19 UTC

Merging the latest corrections from fix_coord_transformations.

Author: Michael Lange
Revision Date: 2012-11-09 15:02:00 UTC

Inverting Zoltan's mapping to fix Hilbert SFC re-ordering in fldecomp.

Author: David Ham
Revision Date: 2012-11-03 14:54:19 UTC

merge from trunk

Author: Jemma Shipton
Revision Date: 2012-10-30 16:17:08 UTC

work in progress

Author: Jemma Shipton
Revision Date: 2012-10-23 14:54:53 UTC

get global numbering fix for quads from trunk

Author: Alexandros Avdis
Revision Date: 2012-10-23 11:10:26 UTC

Merge in of trunk, to keep present branch up-to-date.

Author: Simon Mouradian
Revision Date: 2012-10-19 12:48:57 UTC

Boundaries treated as closed by default.

Author: Stephan Kramer
Revision Date: 2012-10-16 15:14:15 UTC

Should have been added in last commit.

Author: Tim Greaves
Revision Date: 2012-10-11 09:12:38 UTC

Trivial change testing buildbot

Author: Simon Mouradian
Revision Date: 2012-10-09 20:00:15 UTC

revert last trunk merge, something broke

Author: Adam Candy
Revision Date: 2012-09-17 20:04:30 UTC

The relationship of a generic scalar field to the density in the linear equation of state has the wrong sign.
This commit fixes the code. tests and examples need to be checked.

Author: Alexandros Avdis
Revision Date: 2012-09-09 09:35:13 UTC

Added test case (MMS) of advection-diffusion of passive tracer, P1DG discretisation, compact discontinuous Galerkin, and a combination of Neumman and Diriclet boundary conditions across the domain boundaries.

Author: Rhodri Davies
Revision Date: 2012-09-07 13:48:36 UTC

Change things to intent inout for testing

Author: James Robert Percival
Revision Date: 2012-08-29 11:54:11 UTC

merging Metis changes from DARWIN port branch

Author: Adam Candy
Revision Date: 2012-08-24 11:37:34 UTC

Trunk merge.

Author: Adam Candy
Revision Date: 2012-08-23 22:48:35 UTC

Remove print statements used for unittest debugging.

Author: Stephan Kramer
Revision Date: 2012-06-27 09:44:56 UTC

Merging from trunk.

Author: Fiona Reid
Revision Date: 2012-06-20 13:43:03 UTC

Changed petsccg -> petscpccg for PETSc 3.3 compatibility and used LINKER instead
of FLLINKER for several tool binaries (periodise, test_laplacian, test_trace_space
and visualise_elements as they failed to link with FLLINKER.

Author: Tim Greaves
Revision Date: 2012-05-30 20:48:37 UTC

Fix test #2.

Author: Jon Hill
Revision Date: 2012-05-01 10:43:17 UTC

Merge from trunk

Author: Alexandros Avdis
Revision Date: 2012-04-25 16:30:27 UTC

Fix rotate2ll.

Author: Patrick Farrell
Revision Date: 2012-04-16 13:08:17 UTC

Merge from trunk.

Author: Gerard
Revision Date: 2012-04-12 13:46:03 UTC

Use SIGHUP to cause a checkpoint at the end of the next timestep. SIGHUP is cleared once the checkpoint has started.

Author: Dimitrios Pavlidis
Revision Date: 2012-03-30 10:17:18 UTC

clean up velocity field initialisation a bit and allocate the correct size for u, v, w

Author: Frank Milthaler
Revision Date: 2012-03-28 14:52:57 UTC

move ocean_forcing to embedded_models; change relevant code; changed flml in tests, longtests and example

Author: Stephan Kramer
Revision Date: 2012-03-27 11:16:41 UTC

Fix initialising prescribed fields from "netcdf" format in parallel.

Author: Simon Funke
Revision Date: 2012-03-26 14:54:06 UTC

Merge from trunk

Author: Jon Hill
Revision Date: 2012-03-02 14:02:21 UTC

Fixing typos

Author: Jon Hill
Revision Date: 2012-02-28 21:36:27 UTC

Merge from trunk

Author: Tim Greaves
Revision Date: 2012-02-16 20:28:06 UTC

Additional setuptools aclocal.m4 routine added in error; removing.

Author: Frank Milthaler
Revision Date: 2012-02-09 18:17:43 UTC

minor tweaks/clean up on implicit solids and fixed a memory leak (lumped_mass_matrix_fluid and lumped_inverse_mass_matrix_fluid) in supermesh_force and intersections of solid/fluid elements are now inserted in an unsorted ilist

Author: Stephan Kramer
Revision Date: 2012-02-07 20:44:29 UTC

Some changes in petsc_solve_petsc_csr routines:
 petsc_solve_setup_petsc_csr now returns a petsc matrix and petsc_numbering object. Usually this will just be matrix%M and matrix%row_numbering. But this will be different when I have implemented reordering for petsc_csr_matrix type.
Remove some unused variables. In particular this removes an unused argument from setup_ksp_from_options.

Author: Adam Candy
Revision Date: 2012-01-18 17:21:24 UTC

There is now an option to control whether the slope limiting for the vertex-based Kuzmin scheme is applied directly to the velocity or to the velocity tendency in the momentum equation solve. This is controlled by the schema node at:

 ...velocity/prognostic/temporal_discretisation/discontinuous_galerkin/limit_slope_apply_to_tendency

Note this commit switches the default behaviour *back* to applying it to the velocity.

Author: Jon Hill
Revision Date: 2012-01-03 10:14:11 UTC

Adding test i forgot in last commit