lp:~fluidity-core/fluidity/add-trilinos-to-acx-zoltan

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3933. By Tim Greaves on 2012-02-16

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

3932. By Tim Greaves on 2012-02-16

Adding the updated configure to complement my previous commit of aclocal.m4 and
configure.in.

3931. By Tim Greaves on 2012-02-16

An initial attempt to bring in Gerard's work on enabling trilinos detection in
pragmatic to Fluidity. Thi appears to work for detecting normal libzoltan;
tests need to be performed to see if it also works to pick up libtrilinos.

3930. By Tim Greaves on 2012-02-16

Minor Intel-specific fixes, reducing line lengths which overrun in the
middle of quoted strings.

3929. By Brendan Tollit on 2012-02-15

Correct a variable name in a ele_ngi check that was in a #ifdef DDEBUG
in assemble/Advection_Diffusion_CG.F90

3928. By Brendan Tollit on 2012-02-15

This merge will tidy up, improve, test and document the single phase porous
media Darcy flow model. This will sync the porous_media options model with
all the darcy_... test cases that have appeared over the past couple of months.
The model that used to be initiated by the porous_media option is effectively
removed as it contained code that was never finished, consistent, tested or
documented and was made by people that are not involved in Fluidity any more.
It is now favoured to define the Darcy velocity absorption field via python
diagnostics rather than a hard coded internal algorithm. Sections are added
to the manual to explain the model equations, discretisation and necessary
options.

Old tests cases are removed and new ones added.

3927. By Adam Candy on 2012-02-13

A new test case: netcdf_read_errors
This checks the errors reported when an attempt to read an invalid NetCDF file is made. Here 'invalid' refers to a file that is itself an invalid, non-conforming NetCDF file, or is of a format not supported by Fluidity.

Five types of NetCDF files are checked:
 - One which does not provide all the data requested,
 - One is missing a dimension (i.e. it provides only a 1d field),
 - One is missing the main variable,
 - One contains an incorrectly-labelled dimension (as 'lat', not 'x'), and
 - One has the variable incorrectly labelled (as 'height', not 'z').

3926. By Adam Candy on 2012-02-13

New test case: netcdf_read_free_surface
This creates a valid netCDF file containing a free surface height in the domain x,y in [-1.2,1.2]. This is read in by Fluidity as a free surface and applied as an initial condition on pressure. From this, Fluidity calculates the free surface as a diagnostic, which is provided in the outputted VTU file, alongside a field containing the analytic function used to create the netCDF file in the first place (here described in height.py). The test compares the difference between these two fields, which should be small, due to the interpolation of the netCDF file.

In summary this case tests:
 - NetCDF reader
 - Reading of a free surface and conversion into a pressure initial condition
 - Creation of the free surface diagnostic from the pressure field (including its extrapolation down from the top surface)
 - Creation of prescribed scalar fields from Python

3925. By Adam Candy on 2012-02-13

Fix to bug lp:922025. This tidies up the manner in which the pressure initial condition is set from a free-surface height field provided in a netCDF file.

Summary of changes:
 - The special case, legacy method has been removed.
 - If the input format is not recognised, the code will abort with an error detailing the problematic field and the schema path of the invalid format.
 - The 'standard' format is now named 'raw' (instead of 'other'). This is the case where no post-processing is performed on the source data, and the field is initialised by the raw data present in the netCDF file.
 - Included logging messages to indicate which field is being populated and the source netCDF file (logging level 1).
 - Logging of the post-processing applied (logging level 3).
 - For the pressure boundary condition set from a free-surface field in particular, logging level 3 will report the min and max values of the field before and after the conversion.
 - A new section in the manual describing how to initialise the pressure field by specifying the free surface height. Removal of the description of the legacy method to achieve this. Other corrections to nearby sections.

There are currently no tests, examples or longtests that are affected by the above change, but possibly user-generated initialisation flml files that do use the legacy implementation of the pressure initial condition set from free-surface netCDF. In this case, the additional logging added with this change should make it easy to identify the change required to adopt the improved version of this import.

In short, the following example highlights the change necessary:
  The option path:
    /material_phase::Ocean/scalar_field::Pressure/prognostic/initial_condition::WholeMesh/from_netcdf/format/Free-surface height

  should become:
    /material_phase::Ocean/scalar_field::Pressure/prognostic/initial_condition::WholeMesh/free_surface/from_netcdf/format/raw

  (where the file location is specified under the 'from_netcdf' node in each case).

3924. By Adam Candy on 2012-02-11

Further contributions to fixing bug lp:920944 (so it can be closed).
Two further instances of NetCDF readers now error more verbosely when the required data is not found. The reports include the coordinates (in both Cartesian and spherical, where applicable) and filename to facilitate easier debugging.

These additional changes are very similar to the change that has already gone in with the approved merge request at:
https://code.launchpad.net/~fluidity-core/fluidity/netcdferrorreporting/+merge/92443
so I have pushed them straight to the trunk.