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STOREs not necessary for DISABLE_SIGMA_CODE
Attempt to make adjoint work again for arctic210x192x50 setup (currently broken)
Pieces that are needed to use model/src/forward_step.F and model/src/forward_step.F along with pkg/ecco. This capability is still in testing phase. So, for now, the added code is commented out using CPP ifdefs.
Small changes (mostly for pkg/thsice)
Storage directives allowing the use of Adam-Bashforth-3 time stepping in adjoint.
Prerequisite for adjoint of ggl90.
Add state for pkg/offline
Temporary(?) stores for annual balance.
Add includes.
Modify checkpointing to fit large mdsio vector stores to file (partly revert to individual field storing rather than to StoreDynVars2, StoreDynVars3D for large tile sizes).
Some fixes for verification/tutorial_global_oce_optim/
implementing TAF directives for gchem,cfc,dic
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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