~pefarrell/fluidity/fix-intel-12 : changes

~pefarrell/fluidity/fix-intel-12 » Changes from revision 3957

From Revision 3939 to 3920

Rev	Summary	Authors	Date
3939	Relax two tolerances for the intel build for this recently a... Relax two tolerances for the intel build for this recently added test. 5.0e-03 --> 8.0e-03 (integral of tracer) 5.0e-04 --> 6.0e-04 (min of tracer)	Brendan Tollit	12 years ago
3938	Small correction to last merge. Only use the relevant variab... Small correction to last merge. Only use the relevant variables from Global parameters and correct some repetetive English in a couple of FLExit's.	Brendan Tollit	12 years ago
3937	Remove the porosity from the DG_CourantNumber and ControlVol... Remove the porosity from the DG_CourantNumber and ControlVolumeCFLNumber diagnostic fields. Add three new diagnostic fields being InterstitialVelocityCGCourantNumber, InterstitialVelocityCVCourantNumber and InterstitialVelocityDGCourantNumber which are only for porous media flow where the Darcy velocity (= porosity * interstitial velocity) is solved for. These are magic named diagnostic fields rather than algorithm names due to the way the courant number fields are already used. Everywhere in the options where ControlVolumeCFLNumber can be selected (such as CV face value schemes) permit the selection of InterstitialVelocityCVCourantNumber. For CV (or coupled CV) discretised fields there is a restriction that all the 'porosity' fields used must be the same with the same theta averaging also, due to the way this is obtained from one call in Field_Equations_CV. The default options when used satisfy this constraint. For adaptive time stepping also permit the selection of InterstitialVelocityCGCourantNumber. If an InterstitialVelocityCG/CV CourantNumber is used for adaptive time stepping then always force its calculation in this routine as the options here may be different to a field that may exist in the state. For a scalar field discretised with DG add the small new capability to select which Courant number field to use for the temporal sub cycling with the available selections being DG_CourantNumber and InterstitialVelocityDGCourantNumber. To avoid changing all the test cases, by default if not activated this option will do as before and use DG_CourantNumber. Add a copy of a short darcy flow test case that now discretises the tracer with DG using subcycling and adaptive time stepping related to the new interstitial velocity courant number fields. Adjust all relevant darcy test cases to also test this. Add a routine in assemble/Porous_Media.F90 to find the theta averaged porosity field, to avoid a code copy in the adv-diff CG/CV/DG routines. Add to the manual a description of the three new diagnostic fields and adjust the configuring Porous media flow section as required.	Brendan Tollit	12 years ago
3936	Remove the finest simulation (_E) from the Burgers MMS repla... Remove the finest simulation (_E) from the Burgers MMS replay test. This should hopefully speed up the test so that it falls within buildbot's 20-minute limit ..	Patrick Farrell	12 years ago
3935	Forgot an option check. Sorry for the noise. Forgot an option check. Sorry for the noise.	Axelle Vire	12 years ago
3934	Correct Brendan's option check regarding the use of CV for c... Correct Brendan's option check regarding the use of CV for continuity with two-way coupling. Apologies that it hasn't been done before the merge.	Axelle Vire	12 years ago
3933	Relax a tolerance on this test with Brendan's consent. The t... Relax a tolerance on this test with Brendan's consent. The test was passing locally but failed on independent buildbot branches.	Axelle Vire	12 years ago
3932	Loose the tolerance on this test slightly (with Brendan's co... Loose the tolerance on this test slightly (with Brendan's consent) since it makes the trunk fails locally on my Maverick machine.	Axelle Vire	12 years ago
3931	Bug-fix for SampleNetCDF which is used in tidal boundary con... Bug-fix for SampleNetCDF which is used in tidal boundary conditions. This bug would occur whenever a node was interpolated that is located exactly on one any of the constant longitutde or latitude lines of the input netcdf grid. In this case instead of interpolating between the value of the 2 nearest nodes, the value was extrapolated. This code clearly needs some more tests. Coming up...	Stephan Kramer	12 years ago
3930	Minor Intel-specific fixes, reducing line lengths which over... Minor Intel-specific fixes, reducing line lengths which overrun in the middle of quoted strings.	Tim Greaves	12 years ago
3929	Correct a variable name in a ele_ngi check that was in a #if... Correct a variable name in a ele_ngi check that was in a #ifdef DDEBUG in assemble/Advection_Diffusion_CG.F90	Brendan Tollit	12 years ago
3928	This merge will tidy up, improve, test and document the sing... 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.	Brendan Tollit	12 years ago
3927	A new test case: netcdf_read_errors 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').	Adam Candy	12 years ago
3926	New test case: netcdf_read_free_surface 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	Adam Candy	12 years ago
3925	Fix to bug lp:922025. This tidies up the manner in which the... 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).	Adam Candy	12 years ago
3924	Further contributions to fixing bug lp:920944 (so it can be ... 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.	Adam Candy	12 years ago
3923	Contributes to fixing bug lp:920944. Contributes to fixing bug lp:920944. The netCDF reader used when reading a file specified under ../from_netcdf/file options now gives more feedback when the point requested is not present. It reports the coordinates and filename to facilitate easier debugging. This fixes the problem reported by Yi HanSoo, where the error from the reader was ambiguous as to which points could not be located in which file. We may need to make similar changes to other instances of NetCDF reads in the code, or better, unify them all into one routine. Merge request made and approved at: https://code.launchpad.net/~fluidity-core/fluidity/netcdferrorreporting/+merge/92443	Adam Candy	12 years ago
3922	A new test case: a P1DG-P2 version of the 2d gyre (gyre_2d). A new test case: a P1DG-P2 version of the 2d gyre (gyre_2d). Fangxin asked me how to set this up yesterday for Travers, so I thought it's worth adding it to the tests. The diagnostic needed adjusting to account for the existance of negative velocities in the y-coordinate direction along the Western boundary (since we apply the Dirichlet no-slip conditions weakly here).	Adam Candy	12 years ago
3921	Correction of a mistake in a logging message of the gyre_2d ... Correction of a mistake in a logging message of the gyre_2d test.	Adam Candy	12 years ago
3920	Bringing Fluidity's version of libspud up to date with r.515... Bringing Fluidity's version of libspud up to date with r.515 of the libspud trunk.	Tim Greaves	12 years ago

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