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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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checkpoint48a_post |
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o In preparation for r*, use temp. array to compute vertical transport |
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in flux-form momentum pkg. => change results of few test-exp. |
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Update output of: exp4, exp5, front_relax, global_ocean_pressure, |
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lab_sea, natl_box & plume_on_slope |
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checkpoint48 |
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o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D') |
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checkpoint47j_post |
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o add new exp. (ideal_2D_oce) to test "exotic" parameters and options. |
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o moved adexch from forward_step to addummy_in_stepping |
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o added exch in ctrl_map_... |
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o aveFreq.=0. at end of cost_final to avoid overwrite in |
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reverse checkpointing loop |
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o Yet more changes in gmredi: |
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* adgmredi_calc_tensor |
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avoiding all recomputation of gmredi_slope_limit |
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* adgmredi_x/y/rtransport |
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added flag for excessive storing to avoid recomp. of |
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u/v/rtans, dTdx/y/z |
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-> this is not really necessary and very memory-consuming |
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* adgmredi_slope_psi: |
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consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff |
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* gmredi_slope_limit |
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re-activated full calculation of taperfct for case 'ac02' |
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o updating verification/ adjoints of carbon, global_ocean.90x40x15 |
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checkpoint47i_post |
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o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled. |
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o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi) |
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default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post) |
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o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf) |
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o gmredi: fix few bugs. |
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checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48) |
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This will be a good checkpoint to plug into the ecco-branch. |
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o few modif.'s to get latest version adjointed |
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(mainly kick out code in ini_linear_phisurf) |
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o modif's to run adjoint with exactConserv |
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o case GM_BOLUS_ADVEC should be cleaned |
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S/R gmredi_slope_psi should be cleaned |
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o verification/carbon now has exactConserv=.TRUE. |
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checkpoint47g_post |
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o time-average AIM output: becomes independent from statvars time-average |
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(can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH) |
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o After TAF bug fix: |
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Tested adjoint of gmredi package. |
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Tests were done with checkpoint47 rather than with latest |
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checkpoint47f_post since the latter is broken for the adjoint |
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verification/carbon/ contains both ADM and TLM gradient checks. |
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Here they are, before they get changed/lost/stolen. |
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Mostly modif.'s to fix numerical sensitivities. |
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Gradient checks OK for |
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- GM_taper_scheme: |
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* clipping |
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* ac02 |
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* linear |
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* glw91 |
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* dm95 |
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* ldd97 |
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- GMREDI_OPTIONS: |
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* GM_VISBECK_VARIABLE_K |
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* GM_NON_UNITY_DIAGONAL |
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* GM_EXTRA_DIAGONAL |
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* GM_BOLUS_ADVEC |
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in conjunction with data.gmredi parameters to be checked in |
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in a few minutes under verification/carbon/code/ |
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checkpoint47f_post |
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Merging from release1_p10: |
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o modifications for using pkg/exf with pkg/seaice |
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- pkg/seaice CPP options SEAICE_EXTERNAL_FORCING |
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and SEAICE_EXTERNAL_FLUXES |
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- pkg/exf CPP options EXF_READ_EVAP and |
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EXF_NO_BULK_COMPUTATIONS |
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- usage examples are Experiments 8 and 9 in |
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verification/lab_sea/README |
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- verification/lab_sea default experiment now uses |
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pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf |
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checkpoint47e_post |
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o created a tag prior to creating a branch |
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checkpoint47d_post |
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o fixed bug in the oceanic pressure coordinates code: vertical viscosity |
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at the bottom boundary had an erroneous half slip boundary condition |
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o added bottom drag and no slip boundary condition capabilities to |
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oceanic pressure coordinates code |
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o added new verification experiment global_ocean_pressure, this experiment is |
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also described in the tutorial section of the manual |
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checkpoint47d_pre |
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checkpoint47c_post |
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o Added a verification experiment for a global cubed-sphere ocean run |
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- verification/global_ocean.cubed32x32x30 |
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- uses pkg/therm_seaice and pkg/bulk_forcing |
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o allow to run AIM physics with SPEEDY input files (from Franco Molteni) |
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o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1) |
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when using P-coordinate; only implemented for atmospheric config. |
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o OCEANICP & realFreshWater: include P-E direct effect on wVel ; |
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NOTES: requires option NONLIN_FRSURF to be "#define". |
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o update advect_xz/results/output.txt (left from checkpoint44g_post) |
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checkpoint47b_post |
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Merging from release1_p9: |
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o pkg/seaice |
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- removed GOTO's and added taf directives |
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- double precision constants to reduce the g77 (Linux) |
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to F77 (SGI) differences reported in release1_p8 |
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o tools/genmake |
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- added SGI options |
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o verification/testscript |
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- updated to that of checkpoint47a_post |
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o verification/global_ocean.90x40x15/input/eedata |
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- modified for SGI f77 compatibility |
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o verification/lab_sea |
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- added description of sea-ice model |
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- added missing matlab routines |
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- added test of thermodynamics parallelization |
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checkpoint47a_post |
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o new pkg: aim_v23 |
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= F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm. |
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for now, keep the same surface forcing as before. |
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- Part-Cell implemented into AIM; check that Heat & Water are conserved |
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- aim.5l_cs: use new aim pkg (run 10yr & get better results than before) |
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- aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg |
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o add diagnostic of surface correction term in monitor output |
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o bulk_force and therm_seaice |
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- Two packages: bulk_force (Bulk forcing) |
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and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2 |
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- Earlier integration from Stephaine Dutkiewicz |
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and Patrick Heimbach. |
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- Two ifdef statements for compile time, |
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ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE |
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checkpoint47 |
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differentiable version of checkpoint46n_post |
| 148 |
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o bug fix in quasihydrostaticterms |
| 149 |
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o * "clean" adjoint code (in terms of extensive recomputations) |
| 150 |
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can now be obtained for all GMREDI options (i.e. for |
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- GM_VISBECK_VARIABLE_K |
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- GM_NON_UNITY_DIAGONAL |
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- GM_EXTRA_DIAGONAL |
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- GM_BOLUS_ADVEC ) |
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* However, wrong gradient check problem remains unsolved. |
| 156 |
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* New CPP options have been introduced for different |
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tapering schemes |
| 158 |
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o external_fields_load now part of differentiation list |
| 159 |
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o pressure needs multiple storing; |
| 160 |
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would be nice to have store_pressure at beginning or |
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end of forward_step, e.g. by having phiHyd global (5-dim.) |
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(NB: pressure is needed for certain cases in find_rho, |
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which is also invoked through convective_adjustment). |
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o recomputations in find_rho for cases |
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'JMD95'/'UNESCO' or 'MDJWF' are OK. |
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o #define ATMOSPHERIC_LOADING should be differentiable |
| 167 |
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o ini_forcing shifted to begining of initialise_varia |
| 168 |
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o Incorporating QNVS line search routines into MITgcm |
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(this is separate code, and therefore not under pkg) |
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lsopt/, optim/ |
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o Updated verification/carbon/ |
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- #define GM_VISBECK_VARIABLE_K |
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- GM_taper_scheme = 'ldd97' |
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checkpoint46n_post |
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Merging from release1_p8: |
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o verification/natl_box: |
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updating new external_fields_load routine |
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o New package: pkg/seaice |
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Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle). |
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The sea-ice code is based on Hibler (1979-1980). |
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Two sea-ice dynamic solvers, ADI and LSR, are included. |
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In addition to computing prognostic sea-ice variables and diagnosing |
| 184 |
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the forcing/external data fields that drive the ocean model, |
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SEAICE_MODEL also sets theta to the freezing point under sea-ice. |
| 186 |
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The implied surface heat flux is then stored in variable |
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surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and |
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kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the |
| 189 |
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non-local transport term. Because this call precedes model |
| 190 |
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thermodynamics, temperature under sea-ice may not be "exactly" at |
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the freezing point by the time theta is dumped or time-averaged. |
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N.B.: fairly large differences in accuracy occur across |
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different platforms/compilers; comparison between |
| 194 |
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g77 (Linux) and F77 (SGI Origin 2000/MIPSpro) |
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generated output gives: |
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T S U V |
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C D M c m s m s m s m s |
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n p a R g m m e . m m e . m m e . m m e . |
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f n k u 2 i a a d i a a d i a a d i a a d |
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g d e n d n x n . n x n . n x n . n x n . |
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Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea |
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o GAD: |
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- generated new common blocks to account for call of |
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same gad routines with differing traceridentities |
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(needed to modify tracerIdentity indices in GAD.h) |
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- generated separate common blocks for case useCubedSphereExchange |
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(Department of Futurology) |
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- parameter lists to gmredi_?transport: added tracerIdentity |
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- added new key indices to tamc.h |
| 211 |
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o external_fields_load: |
| 212 |
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- added this routine to TAF list |
| 213 |
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- needed to make some common blocks global and additional storing |
| 214 |
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along the same lines as exf package (checkpoint_lev?_directives.h) |
| 215 |
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o exf: |
| 216 |
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updated external forcing package |
| 217 |
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- bug fixes carried over from ecco-branch |
| 218 |
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(missing OBCS_OPTIONS.h in two routines) |
| 219 |
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- enable easy to use "no forcing". |
| 220 |
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- added exf I/O for atmospheric loading |
| 221 |
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- added exf I/O for runoff data |
| 222 |
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- transfered scaling between exf <-> MITgcm to exf namelist |
| 223 |
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o Adding new verification experiment global_with_exf. |
| 224 |
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This verification experiment is almost identical to the |
| 225 |
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global_ocean.90x40x15 experiment, except that it uses |
| 226 |
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the exf (and cal) package instead of the |
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external_fields_load routine (cf README file). |
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checkpoint46m_post |
| 230 |
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o modified testscript to return -- when there are no lines of "%MON" output |
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o added new flag "quasiHydrostatic" for QH mode |
| 232 |
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and new routine quasihydrostaticterms() |
| 233 |
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o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term) |
| 234 |
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New routine: mom_u_coriolis_nh() |
| 235 |
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o fixed sign of non-hydrostatic metric terms in u and v equations. |
| 236 |
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Depend on correct sign of gravitySign. |
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o added work.pc* to .cvsignore in aim directories using ifc |
| 238 |
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o introduced flag for controllin non-hydrostatic metric terms |
| 239 |
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o removed gravitySign from PARM04 |
| 240 |
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o switched to g77/ifc from pgf77 in aim experiments |
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checkpoint46l_post |
| 243 |
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o made convective adjustment work with pressure coordinates: |
| 244 |
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- changed the direction of k-loop in convective_adjustment.F for the |
| 245 |
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case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation) |
| 246 |
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- adjusted the reference pressure k-index in convective_adjustment.F |
| 247 |
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- adjusted the convection condition in convect.F (in analogy to |
| 248 |
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calc_ivdc.F) |
| 249 |
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- convective_adjustment no longer computes anything on the halos |
| 250 |
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- removed the warnings about negative salinity from find_rho.F and |
| 251 |
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find_alpha.F; instead the new routine look_for_neg_salinity, called |
| 252 |
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at the beginning of find_rho, find_alpha, and find_beta, does a |
| 253 |
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check of the entire slice, if CPP-option |
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CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined |
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checkpoint46l_pre |
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checkpoint46k_post |
| 258 |
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o fixed the verification/global_ocean.90x40x15 experiment: |
| 259 |
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- new bathymetry (the world according to A., JMC, and M.) |
| 260 |
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- new initial fields and forcing fields (*.bin files) |
| 261 |
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- new POLY3.COEFFS (for the next release one should switch to a full |
| 262 |
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equation of state: JMD95P or MDJWF) |
| 263 |
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- fixed several errors and redundancies in the data file |
| 264 |
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- experiment uses looped cells |
| 265 |
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- added matlab directory with diagnostic scripts for plotting of output |
| 266 |
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|
| 267 |
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o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F: |
| 268 |
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- read AIM physics parameters from a file (data.aimphys) |
| 269 |
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- set defaults values = F.Molteni paper (Clim.Dyn., 2002) |
| 270 |
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| 271 |
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checkpoint46j_post |
| 272 |
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o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH |
| 273 |
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o move wVel computation at the end of the time step, in S/R integr_continuity |
| 274 |
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o create specific S/R to exchange T,S before DYNAMICS (for stagger time step) |
| 275 |
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o update timeave pkg for wVel diagnostic. |
| 276 |
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checkpoint46j_pre |
| 277 |
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| 278 |
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checkpoint46i_post |
| 279 |
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o Clean up AIM package (and keep the results unchanged): |
| 280 |
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include CPP_OPTION and use IMPLICT NONE in all routines ; |
| 281 |
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declare all the variables _RL ; use _d 0 for all numerical constants. |
| 282 |
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use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 ! |
| 283 |
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|
| 284 |
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checkpoint46h_post |
| 285 |
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o cleaned up the use of rhoNil and rhoConst. |
| 286 |
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- rhoNil should only appear in the LINEAR equation of state, everywhere |
| 287 |
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else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst |
| 288 |
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and the dynamical equations are all divided by rhoConst |
| 289 |
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o introduced new parameter rhoConstFresh, a reference density of fresh |
| 290 |
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water, to remove the fresh water flux's dependence on rhoNil. The default |
| 291 |
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value is 999.8 kg/m^3 |
| 292 |
|
o cleanup up external_forcing.F and external_forcing_surf.F |
| 293 |
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- can now be used by both OCEANIC and OCEANICP |
| 294 |
|
checkpoint46h_pre |
| 295 |
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|
| 296 |
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Added code to convert surface volume flux (fresh water) into |
| 297 |
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a mass flux when using P coordinates in the ocean (OCEANICP). |
| 298 |
|
Note: It assumes you have set rho0=rhoConst=density of fresh water. |
| 299 |
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|
| 300 |
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checkpoint46g_post |
| 301 |
|
o Include a new diagnostic variable phiHydLow for the ocean model |
| 302 |
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- in z-coordinates, it is the bottom pressure anomaly |
| 303 |
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- in p-coordinates, it is the sea surface elevation |
| 304 |
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- in both cases, these variable have global drift, reflecting the mass |
| 305 |
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drift in z-coordinates and the volume drift in p-coordinates |
| 306 |
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- included time averaging for phiHydLow, be aware of the drift! |
| 307 |
|
o depth-dependent computation of Bo_surf for pressure coordinates |
| 308 |
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in the ocean (buoyancyRelation='OCEANICP') |
| 309 |
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- requires a new routine (FIND_RHO_SCALAR) to compute density with only |
| 310 |
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Theta, Salinity, and Pressure in the parameter list. This routine is |
| 311 |
|
presently contained in find_rho.F. This routine does not give the |
| 312 |
|
correct density for 'POLY3', which would be a z-dependent reference |
| 313 |
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density. |
| 314 |
|
o cleaned up find_rho |
| 315 |
|
- removed obsolete 'eqn' from the parameter list. |
| 316 |
|
o added two new verification experiments: gop and goz |
| 317 |
|
(4x4 degree global ocean, 15 layers in pressure and height coordinates) |
| 318 |
|
checkpoint46g_pre |
| 319 |
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|
| 320 |
|
checkpoint46f_post |
| 321 |
|
o Enable tangent linear (forward mode) gradient checks: |
| 322 |
|
- extended active file handling to g_... files |
| 323 |
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- added TANGENT_SIMULATION to theSimulationMode |
| 324 |
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- extended grdchk package accordingly |
| 325 |
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o added tangent linear setup in verification/carbon/code_ftl |
| 326 |
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o added adjoint setup in verification/front_relax/code_ad |
| 327 |
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|
| 328 |
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checkpoint46e_post |
| 329 |
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o Added new equation of state -> MDJWF |
| 330 |
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- EOS of McDougall et al., 2002, JAOT, submitted |
| 331 |
|
- caveat: the equation of state is only valid for a smaller (more |
| 332 |
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realistic?) range of values than JMD95P/Z and UNESCO |
| 333 |
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- added masks to the calculation of pressure in store_pressure |
| 334 |
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- added more check values for density in check_eos (ini_eos.F), some of |
| 335 |
|
the old check values are out of the range of the MDJWF-eos, so don't |
| 336 |
|
expect perfect matches for those |
| 337 |
|
checkpoint46e_pre |
| 338 |
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|
| 339 |
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checkpoint46d_post |
| 340 |
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o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and |
| 341 |
|
'OCEANICP', also initialised field pressure correctly in ini_eos in the |
| 342 |
|
case of pressure coordinates. eosType='JMD95Z' in |
| 343 |
|
combination with buoyancyRelation='OCEANICP' now causes an error. |
| 344 |
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o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
| 345 |
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in find_alpha/beta. |
| 346 |
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checkpoint46d_pre |
| 347 |
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|
| 348 |
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o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
| 349 |
|
so that JMD95Z and JMD95P give approptiate static stability in find_rho. |
| 350 |
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|
| 351 |
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checkpoint46c_post |
| 352 |
|
o Changes necessary for ocean in p-coordinates |
| 353 |
|
- Added new buoyancy relation = 'OCEANICP' |
| 354 |
|
- Added new parameters = gravitySign (this used to be contained inside |
| 355 |
|
the factor dRdZ which I added when we first switched to R coordinates). |
| 356 |
|
X GM/Redi is not compatible (yet) |
| 357 |
|
X bottom drag and no-slip need to be debugged. |
| 358 |
|
checkpoint46c_pre |
| 359 |
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|
| 360 |
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checkpoint46b_post |
| 361 |
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o Added new equation of state -> JMD95Z and JMD95P |
| 362 |
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- EOS of Jackett and McDougall, 1995, JAOT |
| 363 |
|
- moved all EOS parameters into EOS.h |
| 364 |
|
- new routines ini_eos.F, store_pressure.F |
| 365 |
|
o Added UNESCO EOS, but not recommended because it requires |
| 366 |
|
in-situ temperature (see JMD95) |
| 367 |
|
o Modified formatting for knudsen2.f in utils/knudsen2 and added |
| 368 |
|
unesco.f to be used with POLY3 |
| 369 |
|
checkpoint46b_pre |
| 370 |
|
|
| 371 |
|
checkpoint46a_post |
| 372 |
|
o Added (atmospheric) pressure loading |
| 373 |
|
- new field in FFIELDS.h, etc... |
| 374 |
|
- new cpp flag ATMOSPHERIC_LOADING |
| 375 |
|
o Changed hFacC to _hFacC in calc_phi_hyd.F |
| 376 |
|
o Added SHORTWAVE_HEATING to some files for consistency |
| 377 |
|
checkpoint46a_pre |
| 378 |
|
|
| 379 |
|
checkpoint46 |
| 380 |
|
further merges from release1_p5 |
| 381 |
|
o new ctrl package |
| 382 |
|
- adopted from ECCO environment to enable optimization |
| 383 |
|
- added Eliassen Palm fluxes to controls |
| 384 |
|
o added Eliassen Palm flux controls to gradient check package |
| 385 |
|
o cost package |
| 386 |
|
- Compatible with new ctrl package |
| 387 |
|
- added Eliassen Palm cost hooks |
| 388 |
|
- modif's of existing cost functions |
| 389 |
|
o Adjoint-related bug fixes in kpp: |
| 390 |
|
- kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix |
| 391 |
|
- kpp_routines: store of Rib avoids partial recomputation bug of TAF. |
| 392 |
|
o autodiff package |
| 393 |
|
- flow directives: |
| 394 |
|
+ new for S/R do_the_model_io |
| 395 |
|
+ enhanced for S/R checkpoint |
| 396 |
|
+ new gmredi.flow |
| 397 |
|
- Introduced CPP option ALLOW_AUTODIFF_MONITOR to |
| 398 |
|
disable adcommon.h/g_common.h by default. |
| 399 |
|
- fixed problem for adjoint of global_max |
| 400 |
|
o modified verification/carbon/ |
| 401 |
|
o New setup for adjoint of global_ocean |
| 402 |
|
o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F) |
| 403 |
|
o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F) |
| 404 |
|
o incorporated hooks for sponge layer code (external_forcing.F) |
| 405 |
|
|
| 406 |
|
checkpoint45d_post |
| 407 |
|
o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F) |
| 408 |
|
o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S |
| 409 |
|
(affects plume_on_slope "cg2d" output) |
| 410 |
|
o add new parameter deltaTfreesurf for free-surface time stepping |
| 411 |
|
o exchange gT,gS when using staggerTimeStep & GM & Oly<4 |
| 412 |
o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B |
o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B |
| 413 |
o change phiMin in exp1 (to agree with documentation) |
o change phiMin in exp1 (to agree with documentation) |
| 414 |
o add new flags: |
o add new flags: |
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