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- Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h) For now, only in pkgs used in verification/hs94.1x64x5. - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage which are specific to TAF/TAMC).
- re-include store directives that were removed on Dec 27th. - note : this only changes the location of the calc_3d_diffusivity recomputation call, which does not change results unless packages used in forward (gmredi) are omitted in adjoint (common practice).
- move calls to GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from thermodynamics.F to inside temp_integrate.F, salt_integrate.F & ptracers_integrate - add fZon & fMer as output argument of S/R GAD_CALC_RHS
move calls to GAD_ADVECTION (Multi-Dim advection) inside temp_integrate.F and salt_integrate.F ; and similar move for PTRACERS_ADVECTION.
AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying from rTrans) to simplify dependencies (no need to store rTrans anymore in calling S/R)
add initialisation of rTrans (only for AD)
- rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER) - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER) - remove k from thermodynamics.F and move it to temp_integrate.F salt_integrate.F and ptracers_integrate.F (now done inside the tracer loop). - compute locally (in thermodynamics.F) 3-D velocity field that is used to advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT, PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE, GAD_IMPLICIT_R and PTRACERS_IMPLICIT
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