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Avoid extensive recomp. warnings for verification/tutorial_tracer_adjsens
- modifications for ALLOW_GENTIM2D_CONTROL.
Remove some stores here.
Prepare store for new GAD variables.
Extra stores for ALLOW_CG2D_NSA && NONLIN_FRSURF
Add more hooks to pkg.
- pkg/autodiff: checkpoint_lev2_directives.h etc. bug fix - pkg/mdsio: mdsio_write_whalos.F/mdsio_read_whalos.F remove mdsioLocalDir and useSingleCpuIO (to handle those externally) pass locSingleCPUIO as a parameter (that may be useSingleCpuIO) if non zero file id is provided, then omit file opening/closing - pkg/autodiff: adread_adwrite.F pass useSingleCpuIO as the locSingleCPUIO parameter
o model/src, pkg/autodiff, pkg/ecco, pkg/seaice: alleviate the need for additional 3D tapes when using the non-inear free surface in the adjoint. This is done by adding an 'update' of hfacc etc. to their current value at the beginning of forward_step.F.
Add hooks to SHELFICE adjoint.
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.
Starting thsice adjoint
Extend cMean fields to ALLOW_COST_TEST
First step for a NLFS adjoint o initially suppress rStar (new flag DISABLE_RSTAR_CODE) o new init. routines for calc_r_star, calc_surf_dr o still need to deal with ini_masks_etc o testreport seemed happy
Add newly introduced saltFlux0/1
o Fixing directives for non-ECCO forward_step, after ECCO directives have been fixed to avoid recomp. of do_oceanic_phys o Works well for global_ocean.90x40x15, but recomp. issue remains for carbon
extend simple cost functions to treat time mean quantities o cost_tile called from forward_step o cost_accumulate_state called from cost_tile
o bringing adjoint up to date for sheduled c55
Keeping up with JMC's latest modifs.
Fixing adjoint for head of MAIN branch.
o Adjoint for EBM package (needs further testing) o bug fix for parallel EBM in ebm_zonalmean.F
modified one store dir.
keeping up-to-speed with Ben & Jerrys
o convert all "INCLUDE_EXTERNAL_FORCING_PACKAGE" defines to the more consistent ALLOW_EXF o passed all the basic verification tests on shelley
Moving cd_code specific store dir.s to pkg/cd_code
o add a "cd_code" package and update all the verification tests so that they use the new package instead of "INCLUDE_CD_CODE"
checkpoint_lev?_directives.h now include pkg-specific directives, whenever those are enabled.
Bringing autodiff/ up to date with code
o extended state in checkpoint_lev?, etc. o new ptracers.flow
Merging for c51 vs. e34
Preparing next round of sync MAIN vs. ecco-branch and adjoint of next checkpoint.
move STORE empmr to always store it.
Synchronized between MAIN and ecco-branch.
Changes to restore differentiability of code w.r.t. previous tag (mostly adding new routines to make list and replacing pressure by totPhiHyd).
Modifications in treatment of initial flux forcing controls to avoid extra storing of flux fields.
Bringing differentiability up to date.
Merging from release1_p8 branch:
o external_fields_load:
- added this routine to TAF list
- needed to make some common blocks global and additional storing
along the same lines as exf package (checkpoint_lev?_directives.h)
o merge of relevant stuff from the ecco-branch:
- genmake: removed $S64 overwrite for case SunOS
- pkg/exf: update and corrections for field swapping and obcs
- pkg/ecco: parameter lists for the_model_main, the_main_loop
harmonized between ECCO and MITgcm
- pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
updated checkpointing_lev... lists for obcs
- model/src: minor changes in forward_step, plot_field
added directive for divided adjoint in the_main_loop
- pkg/mdsio: added mdsio_gl_slice
Transfering major checkpoint store directive blocks to separate header files. Files are included in the_main_loop (lev3, lev2) and forward_step (lev1).
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