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

~reducedmodelling/fluidity/ROM_Non-intrusive-ann » Changes to assemble/Diagnostic_fields_wrapper.F90 from revision 4037

From Revision 4037 to 462

Rev	Summary	Authors	Date
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
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
3459	Finally getting rid of new_options logical. Finally getting rid of new_options logical. !------------------------------------------------------------------------ ! Global flag for whether we are running off the new xml options file. ! Legacy variable - to be removed in the future !------------------------------------------------------------------------ logical, parameter :: new_options = .true. Today is the future!	Stephan Kramer	13 years ago
3136	Merging branch revisions r15698 and r15771 into trunk. Merging branch revisions r15698 and r15771 into trunk. Summary of branch changes: ------------------------------------------------------------------------ r15771 \| ctj10 \| 2011-03-09 02:01:53 +0000 (Wed, 09 Mar 2011) \| 7 lines - Made a right hash of things...committing several fixes to the calculate_sum_velocity_divergence subroutine with help from Cian and Stephan. - Added additional ewrite's to Multiphase.F90. - Changed a SumVelocityDivergence-related FLExit message in Diagnostic_fields_wrapper.F90. ------------------------------------------------------------------------ r15698 \| ctj10 \| 2011-03-02 00:03:32 +0000 (Wed, 02 Mar 2011) \| 3 lines Added a new diagnostic scalar field called 'SumVelocityDivergence' which holds \sum{div(vfrac*u)} (summed up over all phases), calculated by the new subroutine 'calculate_sum_velocity_divergence'.	ctj10	13 years ago
3022	- Merging branch revision r15543 into trunk. Branch now sync... - Merging branch revision r15543 into trunk. Branch now synchronised with trunk. Summary of branch changes: ------------------------------------------------------------------------ r15543 \| ctj10 \| 2011-02-16 18:04:48 +0000 (Wed, 16 Feb 2011) \| 7 lines - Brought the calculate_diagnostic_phase_volume_fraction call out of calculate_momentum_diagnostics as a temporary bug fix. Only the submaterials were being used to compute the diagnostic PhaseVolumeFraction, leading to incorrect results. - Also calling calculate_diagnostic_phase_volume_fraction in Diagnostic_fields_wrapper.F90. - Added a 1D version of the mphase_gravity test case committed in r15499 (also tagged as 'special' for now).	ctj10	13 years ago
3019	- Merging branch revisions r15410, r15498 and r15527 into tr... - Merging branch revisions r15410, r15498 and r15527 into trunk. Summary of branch changes: ------------------------------------------------------------------------ r15410 \| ctj10 \| 2011-02-03 19:02:15 +0000 (Thu, 03 Feb 2011) \| 3 lines - Multiplying mass element, viscosity element, buoyancy element, and C^T contributions by PhaseVolumeFraction (if multi-phase). ------------------------------------------------------------------------ r15498 \| ctj10 \| 2011-02-11 20:18:32 +0000 (Fri, 11 Feb 2011) \| 16 lines In Momentum_CG.F90: ------------------- - Using a new variable called 'coefficient_detwei' for femtools function (shape_shape, etc) arguments, in case detwei also has to be multiplied by the non-linear volume fraction (nvfrac_gi) among other things. This avoids the need for duplicate function calls with a different detwei argument for multi-phase simulations. - Multiplying advection term through by the non-linear volume fraction. We're only considering the non-conservative form (i.e. beta=0) for now - we will sort the rest out later. - In mass term: removed multiplications by the volume fraction in the moving mesh stuff. - Removed multiplications by the volume fraction in the viscosity term for now. In Multiphase.F90: ------------------ - Setting the intent of 'nvfrac' in get_nonlinear_volume_fraction to intent(inout). ------------------------------------------------------------------------ r15527 \| ctj10 \| 2011-02-16 00:46:40 +0000 (Wed, 16 Feb 2011) \| 7 lines - Subroutine 'get_phase_submaterials' now keeps track of the phase's index within the submaterials array. - Calls to calculate_momentum_diagnostics and calculate_densities now use the submaterials array for multi-phase flow simulations. - Added a PhaseVolumeFraction field to each phase in the mphase_identical_velocities test case and removed the unnecessary MaterialVolumeFraction fields. - Added dependencies on Multiphase.F90 in assemble/Makefile.in. - Set up an array of mass matrices in Momentum_Equation.F90	ctj10	13 years ago
2609	Additional functionality for initialising and modelling an e... Additional functionality for initialising and modelling an equilibrium ice shelf state, porting in further changes from the iceshelf branch. This is all under ongoing development with the options temporarily residing under: /ocean_forcing/shelf/ This code allows the generation of a large-scale perturbation in the free-surface through several approaches: - body force to effectively displace the fluid - requires a spin up - body force in combination with an free-surface initial condition (implemented in r14692) - initial perturbation of eta0 All three approaches work fine for an unstratified ocean (with a zero perturbation density), and with increasing accuracy. Code is also in place to take into account constant and linear variations in perturbation density (i.e. a linear ocean stratification in the latter), and hence inhomogeneities in ice density. The methods applied here are easily generalised to arbitrary functions of ocean stratification. The constant and linear variation cases are implemented for testing. The unstratified case is not yet fully solved, and improvements to the methods will follow. This commit includes the changes made in several commits in the iceshelf branch. The mapping of the position field to pressure space that went in with commit r14731 (by rbn00) was missed in the merge of the trunk Tidal_Modelling.F90 into the iceshelf branch and this commit includes the iceshelf commit which brought this change back in. The node loop which contained an option path call that skramer originally pointed out, that was fixed by r14731 also, is ported back in and additionally modified to eliminate a further test per node loop.	asc	13 years ago
2392	Changing isntances of Chris' person email address to the gro... Changing isntances of Chris' person email address to the group software email address, and removing some rogue tabs at the same time to allow me to commit the changes.	tmb1	13 years ago
2091	Minor change to sediment diagnostics to prevent them being c... Minor change to sediment diagnostics to prevent them being called when there's no sediment in the system.	jhill1	13 years ago
2080	Bug fixes and optimisation of code to compute spontaneous po... Bug fixes and optimisation of code to compute spontaneous potentials in porous media. Also added several options to allow some of the necessary fields to be defined at run time rather than at compile time.	mgulamal	13 years ago
1997	Taking the derivative of a discontinuous field is not suppor... Taking the derivative of a discontinuous field is not supported in most diagnostic algorithms. Checks for this however were missing and fluidity would happily provide you with the wrong answer. The following diagnostic algorithms do not work for discontinuous source fields and now give an appropriate error message: grad, div, perp, curl_2d, curl, scalar_advection, vector_advection, scalar_laplacian, vector_laplacian and strain_rate. Removing "Gradient" and "TemperatureGradient" diagnostic fields as these provide exactly the same funtionality as the "grad" diagnostic algorithm.	skramer	13 years ago
1534	This commit adds a fixed mesh wetting and drying algorithm. This commit adds a fixed mesh wetting and drying algorithm. Note: Wetting and drying is still in an early stage should be only used for testing. The basic idea of the new wetting and drying algorithm is to decouple the pressure and free surface in dry areas. This decoupling is controlled by a scalar field called "WettingDryingAlpha" which can be added as a diagnostic field: If WettingDryingAlpha is zero at a point, this point is regarded as wet and the free surface and pressure are fully coupled. If WettingDryingAlpha is one at a point, this point is regarded as dry and the free surface and pressure are fully decoupled. In that case, the free surface height is set to the bathymetry depth plus a small (user specified) offset d0. Therefore, a small waterlayer is always maintained. A no-normal flow boundary condition is applied on the dry surface. The transition between coupled and decoupled happens linearly with a second auxiliary variable dmin with d0<dmin (normally d0=dmin/2 is a good value). At the momement mesh movement has to be used in combination with wetting and drying.	sf1409	13 years ago
1407	commiting the multiply connected streamfunction diagnostic (... commiting the multiply connected streamfunction diagnostic (this will eventually replace the diagnostic streamfunction once other tests are completed). Updated the schema etc following this change. Also add a test case to check correct boundary conditions are applied in serial, periodic and parallel	am2008	14 years ago
1120	A first sweep of tidying up the control volume code (not inc... A first sweep of tidying up the control volume code (not including the coupled cv code, which still needs some work). Ordering things a bit better has allowed new options for removing mass terms or advection terms (though quite why you'd want to model a purely diffusive equation using cv is beyond me) which brings the cv code into line with other subroutines. Convergence tests have been added for these, which, as they exclude the mass, are nice and fast so allow different face values to be tested (which, shockingly, wasn't done in mms before). The refactoring should also give a small optimisation to the AdvectionDiffusion equation, as it no longer unecessarily multiplies by a Density. I've also removed the default values from options that have to be specified in the options file. This does however mean that prognostic Density needs a TBETA now so some tests (and long tests in a separate commit) therefore needed updating. This commit also allows the use of diffusion with equation types other than AdvectionDiffusion, though (BIG WARNING HERE) this has not been tested at all! Deleting some unused and unmaintained code, options, tools and special tests.	cwilson	14 years ago
993	Adding some more options to the Vorticity and Vorticity2D di... Adding some more options to the Vorticity and Vorticity2D diagnostics	maddison	14 years ago
986	A fix for the qg PV recalculation issue that doesn't mess up... A fix for the qg PV recalculation issue that doesn't mess up everybody else's time fields. Thanks to jhill and Cian for reporting and helping me sort it out.	jemma	14 years ago
980	Added optional velocity_name argument to solve_advection_dif... Added optional velocity_name argument to solve_advection_diffusion_dg so it can be called from qg_strat, in line with what is currently done in solve_field_equation_cg. Also, some minor changes to allow adaptivity to be called from qg_strat, in particular the function recalculate now checks if a field is diagnostic otherwise calculate_diagnostic_variables tried to recalculate the prognostic PotentialVorticity field used by qg_strat.	jemma	14 years ago
971	- Fixing a bug with Geostrophic and HydrostaticPressures whe... - Fixing a bug with Geostrophic and HydrostaticPressures when assembling with a discontinuous test space and running in parallel. This was the cause of the strange behaviour I was seeing when extruding in parallel so not Stephan's fault at all - sorry! - Adding a tests for extrusion in 1+1d in serial and parallel (yes, they're stagnant pools of water). - Deleting the magic name diagnostic field ElementOwner since it produced the wrong answer (which may have been the cause of some of the confusion in yesterday's meeting) as there is already a diagnostic_algorithm to replace it. Adjusting appropriate test cases. - diagnostic_algorithms.rng appears to have been out of date (only wrt a comment though).	cwilson	14 years ago
931	Removing the old balanced velocity diagnostics Removing the old balanced velocity diagnostics	maddison	14 years ago
462	Deleting a "use metric_diagnostics" Deleting a "use metric_diagnostics"	maddison	14 years ago

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