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Update NLFS adjoint.
Fix TAF problems when including correction code for source/sink of tracer due to the linear free surface (S/R CALC_WSURF_TR) (I had removed the ifndef ALLOW_AUTODIFF_TAMC, thought it was trivial)
Re-organized adjoint checkpointing according to Matt Mazloff (but with modifs/completions/cleanups) Storing is now bundled into large arrays to optimized I/O (and second step in cleanup of the_main_loop)
Change CADJ STORE pattern after removing some #ifdef ALLOW_EXF ... #ELSE ... #ENDIF structures.
o Changes in cost to compute \bar{T*V} instead of \bar{T}*{V}
o one fix in pkg/flt
o ecco_readparms namelist was incomplete for new control terms o seaice load added to stored state o slightly more storing in do_oceanic_phys
Making the "last interal means" cMean* always available within cost package
o Add hooks for rbcs checkpointing o Add rbcs_init_varia
Modifications for bottom topography control o replace hFacC by _hFacC at various places o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL o add non-self-adjoint cg2d_nsa o update autodiff support routines o re-initialise hfac after ctrl_depth_ini o works for 5x5 box, doesnt work for global_ocean.90x40x15
Now rstar adjoint.
Extend cMean fields to ALLOW_COST_TEST
Implement 4-level checkpointing. Needed for high-res. runs with large global files to be able to limit tapelev size (otherwise a potential show-stopper).
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