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- with INCLUDE_IMPLVERTADV_CODE defined, also call MOM_U,V_IMPLICIT_R & GAD_IMPLICIT_R (instead of IMPLDIFF) when just implicitViscosity and implicitDiffusion (respectively) are used (even without momImplVertAdv or temp,salt,PTRACERS_ImplVertAdv).
simplify iMin,iMax,jMin,jMax settings
- allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS) with AB-2 code (previously only available with AB-3 code). Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done there, by calling CYCLE_AB_TRACER).
- change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS, and update corresponding calls in S/R temp/salt/ptracers_integrate.F
- change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G, IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT, GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T. - use local temperature/salinity/ptracer tendency array (without bi,bj) in S/R temp/salt/ptracers_integrate.F ;
- push the k loop inside S/R TIMESTEP_TRACER (and call it outside the k loop). - call S/R DWNSLP_APPLY before TIMESTEP_TRACER;
move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer_integrate.F so that theta,salt and pTracers arrays are already updated when leaving S/R THERMODYANMICS while adjustments (filters, conv.adjustment) are still applied later, in S/R TRACERS_CORRECTION_STEP.
change implemetation of AB on tracer (doAB_onGtGs=F, not AB on tendency): store AB(Tr)=Tr^(n+1/2) into gtNm(m2) instead of directly in theta,salt. This fix some forcing-term calculation (e.g., relaxation) that should not be computed from AB(Tr) but instead directly from Tr.
- collect forcing tendency into local 2-D array (passed as argument to apply_forcing S/R); add 3-D diagnostics for forcing tendency.
- drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; for NLFS case, use new recip_hFac value in order to conserve tracer.
- new file "apply_forcing.F" containing all the code previously in external_forcing.F, but with new argument list: pass, as new argument, the current level tendency array to update (instead of a direct update of the common bloc array). Change the corresponding calls.
- 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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