~reducedmodelling/fluidity/ROM_Non-intrusive-ann : changes

~reducedmodelling/fluidity/ROM_Non-intrusive-ann » Changes from revision 4037

From Revision 3926 to 3907

Rev	Summary	Authors	Date
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
3919	(Hopefully) minor fixes to the diamond_validation test, remo... (Hopefully) minor fixes to the diamond_validation test, removing the dependency on gtk.gdk which doesn't look to be necessary in the test (and which breaks on systems with no DISPLAY available), and adding the local copy of the diamond source to sys.path to allow diamond.debug and diamond.schema to be imported in situations where the system doesn't have a central diamond install.	Tim Greaves	12 years ago
3918	One-line fix in build system only, replacing a plain copy of... One-line fix in build system only, replacing a plain copy of bin/ in the install target of the root makefile with a find-based copy to deal with the appearance of subdirectories which are not wanted in the final install but which cause non-zero exit states of the install. The specific case being dealt with here is the tests/ directory made by the unittest target of the makefile, as spotted by Lin Zhenhua.	Tim Greaves	12 years ago
3917	A fix to ensure 'make schema' succeeds on a fresh checkout. A fix to ensure 'make schema' succeeds on a fresh checkout. This commit adds a Makefile directive to install spud-preprocess, which is required by the 'schema' directive. Note that this new directive does not interfere with the build of libspud, which is performed within its own directory. It is only called when required by 'make schema'.	Adam Candy	12 years ago
3916	One-line fix to build system only; correcting 'FLINKER' to '... One-line fix to build system only; correcting 'FLINKER' to 'FLLINKER'. Thanks to Zhenhua Lin for spotting this one!	Tim Greaves	12 years ago
3915	Relax tolerances on these two test cases slightly more again... Relax tolerances on these two test cases slightly more again from 2.0e-02 to 2.5e-02.	Brendan Tollit	12 years ago
3914	Relax two tolerances for the max GridReynoldsNumber from 1.0... Relax two tolerances for the max GridReynoldsNumber from 1.0e-02 to 2.0e-02 for these two medium test multimaterial cases, to hopefully make the i386-gcc4 build green.	Brendan Tollit	12 years ago
3913	Reverting accidental changes to ocean biology Reverting accidental changes to ocean biology	Jon Hill	12 years ago
3912	Trivial fix to the two sinking velocity test so that the use... Trivial fix to the two sinking velocity test so that the user is not asked which algorithm GMSH uses. Simple command line fix is all that is requried.	Jon Hill	12 years ago
3911	Fix for lp:928771 , making an install of libspud's spudtools... Fix for lp:928771 , making an install of libspud's spudtools into the root Fluidity directory a depenency of 'make mediumtest', and adding a rule to the root Fluidity Makefile.in to this end.	Tim Greaves	12 years ago
3910	Summary: Summary: This merge will permit the use of P2 control volumes for a tetrahedral mesh. This extends the CV faces routine to add the p2cv tet shape functions. The method to form the CV mass matrix is then changed to use a sub CV analytic approach (for p1 and p2 elements one can calculate by hand the sub CV fraction of the parent element) rather than lumping a FEM mass matrix. Routines are added to get the cv mass and compute the cv mass. Everywhere we could find that required a cv mass matrix now calls these routines. Diagnostic routines to output the CV mass and the lumped FE mass have been added. The capability to include the density in the GridReynoldsNumber diagnostic has also been added. These last two changes are included in the manual. 11 test cases are added (basic, advection, darcy, mmat, mms). A couple of test cases where changed to not output cv stats as they didnt need it. This permits p1dgp2 for multimaterial (although may well be buggy linked to other features) and is known to not work with conservative bounded mesh to mesh interpolation. This was worked on by Cian Wilson and myself and reviewed/checked by Axelle.	Brendan Tollit	12 years ago
3909	Commit purely in build system. A path error in the Makefile.... Commit purely in build system. A path error in the Makefile.in spotted by Simon Mouradian means that the flml schema was being installed in ~/.schemata rather than into ~/.diamond/schemata. This fix modifies the path to point to the correct location.	Tim Greaves	12 years ago
3908	Merging fix-multiple-material-phase-python-diagnostic branch... Merging fix-multiple-material-phase-python-diagnostic branch revisions r3897 to r3902 inclusive into trunk. Summary of change: ================== We now pass the whole states array to calculate_diagnostic_variable if a Python diagnostic algorithm is used to compute the VelocityAbsorption, VelocitySource or Viscosity diagnostic fields. Otherwise, we just pass the submaterials array. Brendan has created a test case for this (pydiag_material_phase_support_multiple_velocity_children). This resolves bug lp:800126.	Christian Jacobs	12 years ago
3907	Commit purely in build system, reverting the growing untidyn... Commit purely in build system, reverting the growing untidyness of conflicting prefixes trying to make a diamond install work from the libspud in Fluidity. This goes back to a reconfigure with the user's prefix, then installs, then reconfigures with the prefix that Fluidity expects to be used internally. This ought to resolve problems with the spud schemas not getting installed.	Tim Greaves	12 years ago