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Changes to allow for atmospheric integration builds of the code
Changes for new exchange routines which do general tile <-> tile connectivity, variable width overlap regions and provide hooks for shared memory and DMA protocols like Arctic, Memory Channel etc..
Consistent isomorphism chages
E-implemented the theta* and salt* time-stepping scheme. We did this so that theta/salt/u/v would all be at the same time-level at the end of dynamics() to make I/O easier.
Added code to bring "salt" up-to-date with "theta". One caveat is that implicit diffusion of salt is done with the diffusivity of theta. We'll sort this out later. In explicit mode, diffKzS is used.
Changes to support topography, hydrography and forcing from files
Various corrections: o do_gterm_blocking..() is fixed to work with new time-stepping o CPP_OPTIONS.h now contains #define ALLOW_CD
Merge of GM Redi and spherical polar and inplicit diffusion and CD. Everything for a global run is now included, however, still some discrepancies with GM Redi.
Implemented implicit vertical diffusion (tracers only). Involved introducing a "total" diffusivity array (local 3D) calculated by calc_diffusivity(). Made some small changes to time-stepping algorithm. Switched on by setting implicitZdiffusion. (note: *Not* fully tested with topography. But when switched off this does produce identical results)
Swapped the time-stepping algorithm around (just a little bit). We now officially use the predictor-corrector terminology. We make the prediction step at the end of the dynamics() section and store the result in the gUNm1, gVNm1, gTNm1 arrays. The "tricky" part is that at the beginning of the dynamics section, where the "correction" is made, theses arrays must be initialised at the beginning of any run. A new routine init_predictor() does this. This is "all" in preparation for implicit diffusion. Let's hope it's enough...
Further memory saving macros for particular grids
Added extra IO features - runtime on/off flags - more reporting of configuration
Moved the "K loop" from timestep() upto dynamics(). dynamics() now contains all K loops (two infact).
Removed development debuggin
Further $Id to $Header conversions
Initial revision
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