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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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o gmredi: fix few bugs and restore parameter values (e.g., Small_Number=1.D-12) |
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and scheme (e.g., Large_SlopeSqr=1.D+48) of checkpoint47f_post |
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|
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checkpoint48 |
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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 |
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o bug fix in quasihydrostaticterms |
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o * "clean" adjoint code (in terms of extensive recomputations) |
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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. |
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* New CPP options have been introduced for different |
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tapering schemes |
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o external_fields_load now part of differentiation list |
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o pressure needs multiple storing; |
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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 |
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o ini_forcing shifted to begining of initialise_varia |
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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 |
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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. |
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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 |
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non-local transport term. Because this call precedes model |
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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 |
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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 |
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o external_fields_load: |
| 179 |
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- added this routine to TAF list |
| 180 |
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- needed to make some common blocks global and additional storing |
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along the same lines as exf package (checkpoint_lev?_directives.h) |
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o exf: |
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updated external forcing package |
| 184 |
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- bug fixes carried over from ecco-branch |
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(missing OBCS_OPTIONS.h in two routines) |
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- enable easy to use "no forcing". |
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- added exf I/O for atmospheric loading |
| 188 |
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- added exf I/O for runoff data |
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- transfered scaling between exf <-> MITgcm to exf namelist |
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o Adding new verification experiment global_with_exf. |
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This verification experiment is almost identical to the |
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global_ocean.90x40x15 experiment, except that it uses |
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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 |
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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 |
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and new routine quasihydrostaticterms() |
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o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term) |
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New routine: mom_u_coriolis_nh() |
| 202 |
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o fixed sign of non-hydrostatic metric terms in u and v equations. |
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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 |
| 205 |
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o introduced flag for controllin non-hydrostatic metric terms |
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o removed gravitySign from PARM04 |
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o switched to g77/ifc from pgf77 in aim experiments |
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checkpoint46l_post |
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o made convective adjustment work with pressure coordinates: |
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- changed the direction of k-loop in convective_adjustment.F for the |
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case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation) |
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- adjusted the reference pressure k-index in convective_adjustment.F |
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- adjusted the convection condition in convect.F (in analogy to |
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calc_ivdc.F) |
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- convective_adjustment no longer computes anything on the halos |
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- removed the warnings about negative salinity from find_rho.F and |
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find_alpha.F; instead the new routine look_for_neg_salinity, called |
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at the beginning of find_rho, find_alpha, and find_beta, does a |
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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 |
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o fixed the verification/global_ocean.90x40x15 experiment: |
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- new bathymetry (the world according to A., JMC, and M.) |
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- new initial fields and forcing fields (*.bin files) |
| 228 |
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- new POLY3.COEFFS (for the next release one should switch to a full |
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equation of state: JMD95P or MDJWF) |
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- fixed several errors and redundancies in the data file |
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- experiment uses looped cells |
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- added matlab directory with diagnostic scripts for plotting of output |
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|
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o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F: |
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- read AIM physics parameters from a file (data.aimphys) |
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- set defaults values = F.Molteni paper (Clim.Dyn., 2002) |
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checkpoint46j_post |
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o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH |
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o move wVel computation at the end of the time step, in S/R integr_continuity |
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o create specific S/R to exchange T,S before DYNAMICS (for stagger time step) |
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o update timeave pkg for wVel diagnostic. |
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checkpoint46j_pre |
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checkpoint46i_post |
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o Clean up AIM package (and keep the results unchanged): |
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include CPP_OPTION and use IMPLICT NONE in all routines ; |
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declare all the variables _RL ; use _d 0 for all numerical constants. |
| 249 |
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use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 ! |
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|
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checkpoint46h_post |
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o cleaned up the use of rhoNil and rhoConst. |
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- rhoNil should only appear in the LINEAR equation of state, everywhere |
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else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst |
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and the dynamical equations are all divided by rhoConst |
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o introduced new parameter rhoConstFresh, a reference density of fresh |
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water, to remove the fresh water flux's dependence on rhoNil. The default |
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value is 999.8 kg/m^3 |
| 259 |
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o cleanup up external_forcing.F and external_forcing_surf.F |
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- can now be used by both OCEANIC and OCEANICP |
| 261 |
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checkpoint46h_pre |
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|
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Added code to convert surface volume flux (fresh water) into |
| 264 |
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a mass flux when using P coordinates in the ocean (OCEANICP). |
| 265 |
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Note: It assumes you have set rho0=rhoConst=density of fresh water. |
| 266 |
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|
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checkpoint46g_post |
| 268 |
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o Include a new diagnostic variable phiHydLow for the ocean model |
| 269 |
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- in z-coordinates, it is the bottom pressure anomaly |
| 270 |
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- in p-coordinates, it is the sea surface elevation |
| 271 |
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- in both cases, these variable have global drift, reflecting the mass |
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drift in z-coordinates and the volume drift in p-coordinates |
| 273 |
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- included time averaging for phiHydLow, be aware of the drift! |
| 274 |
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o depth-dependent computation of Bo_surf for pressure coordinates |
| 275 |
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in the ocean (buoyancyRelation='OCEANICP') |
| 276 |
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- requires a new routine (FIND_RHO_SCALAR) to compute density with only |
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Theta, Salinity, and Pressure in the parameter list. This routine is |
| 278 |
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presently contained in find_rho.F. This routine does not give the |
| 279 |
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correct density for 'POLY3', which would be a z-dependent reference |
| 280 |
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density. |
| 281 |
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o cleaned up find_rho |
| 282 |
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- removed obsolete 'eqn' from the parameter list. |
| 283 |
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o added two new verification experiments: gop and goz |
| 284 |
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(4x4 degree global ocean, 15 layers in pressure and height coordinates) |
| 285 |
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checkpoint46g_pre |
| 286 |
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|
| 287 |
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checkpoint46f_post |
| 288 |
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o Enable tangent linear (forward mode) gradient checks: |
| 289 |
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- extended active file handling to g_... files |
| 290 |
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- added TANGENT_SIMULATION to theSimulationMode |
| 291 |
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- extended grdchk package accordingly |
| 292 |
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o added tangent linear setup in verification/carbon/code_ftl |
| 293 |
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o added adjoint setup in verification/front_relax/code_ad |
| 294 |
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|
| 295 |
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checkpoint46e_post |
| 296 |
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o Added new equation of state -> MDJWF |
| 297 |
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- EOS of McDougall et al., 2002, JAOT, submitted |
| 298 |
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- caveat: the equation of state is only valid for a smaller (more |
| 299 |
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realistic?) range of values than JMD95P/Z and UNESCO |
| 300 |
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- added masks to the calculation of pressure in store_pressure |
| 301 |
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- added more check values for density in check_eos (ini_eos.F), some of |
| 302 |
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the old check values are out of the range of the MDJWF-eos, so don't |
| 303 |
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expect perfect matches for those |
| 304 |
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checkpoint46e_pre |
| 305 |
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|
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checkpoint46d_post |
| 307 |
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o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and |
| 308 |
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'OCEANICP', also initialised field pressure correctly in ini_eos in the |
| 309 |
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case of pressure coordinates. eosType='JMD95Z' in |
| 310 |
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combination with buoyancyRelation='OCEANICP' now causes an error. |
| 311 |
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o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
| 312 |
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in find_alpha/beta. |
| 313 |
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checkpoint46d_pre |
| 314 |
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|
| 315 |
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o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
| 316 |
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so that JMD95Z and JMD95P give approptiate static stability in find_rho. |
| 317 |
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|
| 318 |
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checkpoint46c_post |
| 319 |
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o Changes necessary for ocean in p-coordinates |
| 320 |
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- Added new buoyancy relation = 'OCEANICP' |
| 321 |
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- Added new parameters = gravitySign (this used to be contained inside |
| 322 |
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the factor dRdZ which I added when we first switched to R coordinates). |
| 323 |
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X GM/Redi is not compatible (yet) |
| 324 |
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X bottom drag and no-slip need to be debugged. |
| 325 |
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checkpoint46c_pre |
| 326 |
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|
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checkpoint46b_post |
| 328 |
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o Added new equation of state -> JMD95Z and JMD95P |
| 329 |
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- EOS of Jackett and McDougall, 1995, JAOT |
| 330 |
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- moved all EOS parameters into EOS.h |
| 331 |
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- new routines ini_eos.F, store_pressure.F |
| 332 |
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o Added UNESCO EOS, but not recommended because it requires |
| 333 |
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in-situ temperature (see JMD95) |
| 334 |
|
o Modified formatting for knudsen2.f in utils/knudsen2 and added |
| 335 |
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unesco.f to be used with POLY3 |
| 336 |
|
checkpoint46b_pre |
| 337 |
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|
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checkpoint46a_post |
| 339 |
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o Added (atmospheric) pressure loading |
| 340 |
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- new field in FFIELDS.h, etc... |
| 341 |
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- new cpp flag ATMOSPHERIC_LOADING |
| 342 |
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o Changed hFacC to _hFacC in calc_phi_hyd.F |
| 343 |
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o Added SHORTWAVE_HEATING to some files for consistency |
| 344 |
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checkpoint46a_pre |
| 345 |
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|
| 346 |
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checkpoint46 |
| 347 |
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further merges from release1_p5 |
| 348 |
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o new ctrl package |
| 349 |
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- adopted from ECCO environment to enable optimization |
| 350 |
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- added Eliassen Palm fluxes to controls |
| 351 |
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o added Eliassen Palm flux controls to gradient check package |
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o cost package |
| 353 |
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- Compatible with new ctrl package |
| 354 |
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- added Eliassen Palm cost hooks |
| 355 |
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- modif's of existing cost functions |
| 356 |
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o Adjoint-related bug fixes in kpp: |
| 357 |
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- kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix |
| 358 |
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- kpp_routines: store of Rib avoids partial recomputation bug of TAF. |
| 359 |
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o autodiff package |
| 360 |
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- flow directives: |
| 361 |
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+ new for S/R do_the_model_io |
| 362 |
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+ enhanced for S/R checkpoint |
| 363 |
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+ new gmredi.flow |
| 364 |
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- Introduced CPP option ALLOW_AUTODIFF_MONITOR to |
| 365 |
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disable adcommon.h/g_common.h by default. |
| 366 |
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- fixed problem for adjoint of global_max |
| 367 |
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o modified verification/carbon/ |
| 368 |
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o New setup for adjoint of global_ocean |
| 369 |
|
o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F) |
| 370 |
|
o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F) |
| 371 |
|
o incorporated hooks for sponge layer code (external_forcing.F) |
| 372 |
|
|
| 373 |
|
checkpoint45d_post |
| 374 |
|
o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F) |
| 375 |
|
o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S |
| 376 |
|
(affects plume_on_slope "cg2d" output) |
| 377 |
|
o add new parameter deltaTfreesurf for free-surface time stepping |
| 378 |
|
o exchange gT,gS when using staggerTimeStep & GM & Oly<4 |
| 379 |
|
o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B |
| 380 |
|
o change phiMin in exp1 (to agree with documentation) |
| 381 |
|
o add new flags: |
| 382 |
|
- T,S forcing inside/outside Adams-Bashforth |
| 383 |
|
- turn off temp,salt advection and/or forcing |
| 384 |
|
- for each tracer, define internal flag for multiDimAdvection & A-B |
| 385 |
|
o monitor: change definition of KE to check conservation of Energy |
| 386 |
|
|
| 387 |
|
checkpoint45c_post |
| 388 |
|
o Removed f90 comments ("!") |
| 389 |
|
o Modified initialisations to enable exf package for MITgcm |
| 390 |
|
(without invoking ECCO_PACKAGE). |
| 391 |
|
o modifications to gradient check package (Martin Losch) |
| 392 |
|
- enable centered differences |
| 393 |
|
- modified format of standard output |
| 394 |
|
|
| 395 |
|
checkpoint45b_post |
| 396 |
|
o cleaned exchange calls in cg2d |
| 397 |
|
o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step |
| 398 |
|
o included CPP option SINGLE_LAYER_MODE in thermodynamics |
| 399 |
|
to configure barotropic setup (Martin Losch) |
| 400 |
|
o moved some initialisations within bi,bj loop in dynamics |
| 401 |
|
(TAF flow dependency) |
| 402 |
|
o in initialise_varia, moved call packages_init_variables |
| 403 |
|
before convective_adjustment_init |
| 404 |
|
(corresponding adjustment of TAF tape initialisation). |
| 405 |
|
o in calc_diffusivity/calc_viscosity extended domain to full overlap. |
| 406 |
|
|
| 407 |
|
checkpoint45a_post |
| 408 |
|
o compute Rho over the whole domain (extend iMin,jMin indices) |
| 409 |
|
o specific exchange for X-slice domain (case Ny=1) |
| 410 |
|
o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code |
| 411 |
|
o solve_for_pressure : set cg2d_x to zero where OBCS are applied |
| 412 |
|
|
| 413 |
|
checkpoint44h_post = checkpoint45 |
| 414 |
|
o Fix to restore differentiability: |
| 415 |
|
place at which packages_init_variables is called in |
| 416 |
|
initialise_varia is crucial for reverse control flow. |
| 417 |
|
o modifications in GMRedi to enable stable adjoint |
| 418 |
|
(corresponding modif's in thermodynamics, dynamics) |
| 419 |
|
o added missing hook for sponge layer code in external_forcing |
| 420 |
|
o modified test cost functions |
| 421 |
|
o storing in gad_advection (plus removal of write(0,*)! |
| 422 |
|
o missing headers TR1.h added in convective_adjustment routines |
| 423 |
|
o errorMessageUnit set non-equal zero in eeboot |
| 424 |
|
(conflict on some platforms, e.g. IBM SP3) |
| 425 |
|
o modified carbon verif. |
| 426 |
|
|
| 427 |
|
checkpoint44h_pre |
| 428 |
|
o vertical grid option: allow to put the Interface at the middle between |
| 429 |
|
2 cell-centers ; replace delZ in pkg/kpp by drF. |
| 430 |
|
o GM Advective form: Tracers are advected using the residual transport (= |
| 431 |
|
Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form. |
| 432 |
|
|
| 433 |
|
checkpoint44g_post |
| 434 |
|
o fix surface correction term in multiDimAdvection (affects plume_on_slope |
| 435 |
|
results) ; ifdef missing in thermodynamics.F |
| 436 |
|
|
| 437 |
|
checkpoint44f_pre,checkpoint44f_post |
| 438 |
|
o added PTRACERS package |
| 439 |
|
This allows an arbitrary number of passive tracers to be integrated |
| 440 |
|
forward simultaneously with the dynamicaly model. |
| 441 |
|
+ Implemented so far: |
| 442 |
|
- basic forward algorithm (time-stepping, advection, diffusion, convection) |
| 443 |
|
- I/O and checkpointing |
| 444 |
|
- GM/Redi *but* using the GM/Redi coefficient of Salt |
| 445 |
|
+ Not implemented so far: |
| 446 |
|
- KPP |
| 447 |
|
- OBCS |
| 448 |
|
+ No specific example supplied (yet) but global_ocean.90x40x15 has the |
| 449 |
|
necessary data.ptracer file. Simply use -enable=ptracers and uncomment |
| 450 |
|
line in data.pkg. |
| 451 |
|
+ This package is disabled by default since it increases storage. |
| 452 |
|
|
| 453 |
|
|
| 454 |
|
o testscript: added -cleanup option |
| 455 |
|
o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter |
| 456 |
|
b) enable to filter 2D fields. |
| 457 |
|
|
| 458 |
|
checkpoint44e_pre,post |
| 459 |
|
o re-wrote convective adjustment to use pre-calculated weights |
| 460 |
|
Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F |
| 461 |
|
Adds: model/src/convective_weights.F, convectively_mixtracer.F |
| 462 |
|
Original calls to convect() still in place. |
| 463 |
|
|
| 464 |
|
chkpt44d_pre,post |
| 465 |
|
o added missing EXCLUDE_MONITOR flags |
| 466 |
|
o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi |
| 467 |
|
(incompatible typ in MIN/MAX expressions caused problems |
| 468 |
|
on IBM SP3) |
| 469 |
|
o in genmake added variable MAKEDEPEND |
| 470 |
|
plus resetting for case SunOS |
| 471 |
|
o added timer_stats.c routine for IBM SP3 |
| 472 |
|
o removed variables in dynamics |
| 473 |
|
!!! I forgot to create tag chkpt44d_pre !!! |
| 474 |
|
!!! But chkpt44d_pre = chkpt44c_post !!! |
| 475 |
|
|
| 476 |
|
o real fresh water flux implemented with non-linear free-surface. |
| 477 |
|
|
| 478 |
|
chkpt44c_pre,post |
| 479 |
|
o few fix (mask in shap_s2, EmPmR in external_field_load, |
| 480 |
|
USE_NATURAL_BCS in solve_for_P); |
| 481 |
|
o add arguments myIter & myTime to S/R obcs_calc & solve_for_P |
| 482 |
|
|
| 483 |
|
checkpoint44b_pre/_post |
| 484 |
|
o merge of relevant stuff from the ecco-branch: |
| 485 |
|
- genmake: removed $S64 overwrite for case SunOS |
| 486 |
|
- pkg/exf: update and corrections for field swapping and obcs |
| 487 |
|
- pkg/ecco: parameter lists for the_model_main, the_main_loop |
| 488 |
|
harmonized between ECCO and MITgcm |
| 489 |
|
- pkg/autodiff: added flow directives for obcs, mdsio_gl_slice |
| 490 |
|
updated checkpointing_lev... lists for obcs |
| 491 |
|
- model/src: minor changes in forward_step, plot_field |
| 492 |
|
added directive for divided adjoint in the_main_loop |
| 493 |
|
- pkg/mdsio: added mdsio_gl_slice |
| 494 |
|
|
| 495 |
|
o check parameters & config (chkpt44a_pre,post) |
| 496 |
|
o OBC and NonLin_FrSurf. |
| 497 |
|
|
| 498 |
|
checkpoint44 |
| 499 |
|
o fix bug in mom_vi_del2uv |
| 500 |
|
o select when filters are applied ; add options to zonal_filter (data.zonfilt) |
| 501 |
|
o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection) |
| 502 |
|
o update AIM experiments (NCEP input files) |
| 503 |
|
o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf) |
| 504 |
|
o added some stuff for AD |
| 505 |
|
|
| 506 |
|
checkpoint43 |
| 507 |
|
o added two new advection tests |
| 508 |
|
o added global 4x4 degree ocean test |
| 509 |
|
o added test of H&S94 with free surface on cube |
| 510 |
|
o some final mods for gradient check, adjoint,... |
| 511 |
|
|
| 512 |
|
checkpoint42 |
| 513 |
|
Fixed AD-related problems: |
| 514 |
|
o Store directives up-to-date with re-arranged Adams-Bashforth |
| 515 |
|
(mainly thermodynamics.F) |
| 516 |
|
o New store directives for multi-dim. advection schemes |
| 517 |
|
* new CPP flag ALLOW_MULTI_DIM_ADVECTION |
| 518 |
|
* new common block and key passkey |
| 519 |
|
(mainly gad_advection.F) |
| 520 |
|
o Modified store directives for split of dynamics/thermodynamics |
| 521 |
|
for the case ALLOW_KPP |
| 522 |
|
o Cleaned argument list for timestep_tracer.F |
| 523 |
|
|
| 524 |
|
checkpoint41 |
| 525 |
|
o re-formatted/added comments in prologues of key subroutines |
| 526 |
|
to work with protex |
| 527 |
|
|
| 528 |
|
checkpoint40 |
| 529 |
|
o moved calc_gs, calc_gt and calc_tr1 back to model/src |
| 530 |
|
o added FLT (floats) package from Arne along with demo. experiment |
| 531 |
|
o re-arranged Adams-Bashforth scheme for tracers to allow easier |
| 532 |
|
implementation of forward-in-time forcing terms |
| 533 |
|
o more mods for non-linear free-surface including new variable |
| 534 |
|
o modified multi-dim method to work on cube |
| 535 |
|
o bug fix in KPP (from DM) |
| 536 |
|
|
| 537 |
|
checkpoint40pre9 |
| 538 |
|
o added DST advection schemes |
| 539 |
|
o fix MPI bug on SGI's |
| 540 |
|
o modifications for non-linear free-surface |
| 541 |
|
o fixed conditionals for fixed flow/passive tracer only mode |
| 542 |
|
o added tension/strain form of stress tensor |
| 543 |
|
o changes to commenting of arguments for TAF/TAMC |
| 544 |
|
o added/updated many matlab scripts |
| 545 |
|
o added multi-dimensional advection method for tracers |
| 546 |
|
|
| 547 |
|
checkpoint40pre8 |
| 548 |
|
o new package rw/ |
| 549 |
|
Added method for dumping intermediate local arrays: |
| 550 |
|
mdsio_writetile - same as mdsio_writefield except works from inside |
| 551 |
|
bi,bj loop |
| 552 |
|
mdsio_writelocal - same as mdsio_writetile except works for local |
| 553 |
|
arrays |
| 554 |
|
write_local_r? - higher-level wrapper for mdsio_writelocal |
| 555 |
|
Controlled by diagFreq. Defaults to zero (ie. no dumps) |
| 556 |
|
Example given at end of mom_vecinv.F that dumps some local arrays. |
| 557 |
|
o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to |
| 558 |
|
control flux-form versus vector invariant code. |
| 559 |
|
Switch is runtime flag vectorInvariantMomentum (defaults to false) |
| 560 |
|
or genmake -DISABLE ... |
| 561 |
|
o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F |
| 562 |
|
(additional storing is now needed for case vecinv; |
| 563 |
|
currently nothing implemented to switch this storing off |
| 564 |
|
in case fluxform is used since no CPP flag available). |
| 565 |
|
|
| 566 |
|
checkpoint40pre7 |
| 567 |
|
o bug fix in dynamics.F |
| 568 |
|
calc_viscosity called before k=1,Nr loop. |
| 569 |
|
o added some #ifdef's ALLOW_PASSIVE_TRACER |
| 570 |
|
o cleaned initialisations in ctrl_map_ini |
| 571 |
|
related to TAF |
| 572 |
|
|
| 573 |
|
checkpoint40pre6 |
| 574 |
|
o split dynamics into thermodynamics & dynamics |
| 575 |
|
o corresponding split of calc_diffusivity into |
| 576 |
|
calc_diffusivity, calc_viscosity |
| 577 |
|
(kpp_calc_diff, kpp_calc_visc). |
| 578 |
|
o Added diffkr, kapgm to control variables |
| 579 |
|
o bug fix in gmredi_slope_limit for ldd97 |
| 580 |
|
|
| 581 |
|
checkpoint40pre5 |
| 582 |
|
o proper initialization of Adams-Bashforth time stepping |
| 583 |
|
+ uses forward step for very first step of model (iter=0) |
| 584 |
|
o re-generated *all* output since almost all output is modified by this |
| 585 |
|
change (sorry but we've been putting this one off for about 2 years) |
| 586 |
|
+ natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were |
| 587 |
|
*not* regenerated since they are already out of date and I don't |
| 588 |
|
want to create the impression that they are suddenly working. |
| 589 |
|
o removed KAP stuff for DEC's |
| 590 |
|
o modified/added many .cvsignore files in */code and */input |
| 591 |
|
o added new expt "solid-body.cs-32x32x1" |
| 592 |
|
+ this uses an alternative form of ini_curvilinear_grid.F which |
| 593 |
|
is not necessarily any better than the current one... |
| 594 |
|
|
| 595 |
|
checkpoint40pre4 |
| 596 |
|
o added re-initialisations of utrans,vtrans,rtrans in |
| 597 |
|
calc_common_factors which are crucial for TAF. |
| 598 |
|
o extended iMin,jMin range for calc_common_factors, |
| 599 |
|
calc_diffusivity |
| 600 |
|
o added option ALLOW_PASSIVE_TRACER |
| 601 |
|
o a few minor updates and fixes |
| 602 |
|
|
| 603 |
|
checkpoint40pre3 |
| 604 |
|
o created calc_gtr1.F for gad package |
| 605 |
|
o split the_main_loop and re-introduced forward_step |
| 606 |
|
o some recomputations of nIter0 for TAMC |
| 607 |
|
|
| 608 |
|
checkpoint40pre2 |
| 609 |
|
o Updated to latest branch of AJA, JMC |
| 610 |
|
o Added gradient check package |
| 611 |
|
o Added routines for passive tracer handling |
| 612 |
|
o Added carbon sequestration sensitivity experiment |
| 613 |
|
|
| 614 |
|
checkpoint39 |
| 615 |
|
o Modifications and fixes to support TAMC |
| 616 |
|
(mainly missing or wrong directives) |
| 617 |
|
o Corrected common blocks when fooling TAMC to produce adjoint I/O |
| 618 |
|
in addummy_in_stepping |
| 619 |
|
o Updated verification/vero/ (bug fixes in code/, correct pickups in input/) |
| 620 |
|
o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs. |
| 621 |
|
o Included following packages: |
| 622 |
|
cal: calendar |
| 623 |
|
exf: external forcing |
| 624 |
|
ecco: essential routines to control use of cal, exf |
| 625 |
|
(NB: this is not the full ECCO environment) |
| 626 |
|
o disabled some packages by default in genmake |
| 627 |
|
|
| 628 |
|
checkpoint38 |
| 629 |
|
o see notes_c37_adj.txt |
| 630 |
|
o corrected wrong layer index in external_forcing_t |
| 631 |
|
o replaced the_main_loop/forward_step by the_main_loop |
| 632 |
|
o removed forceoutput from write_state |
| 633 |
|
(replaced criteria for initial/final state) |
| 634 |
|
o added runtime flag for pre-C35 pickups: usePickupBeforeC35 |
| 635 |
|
|
| 636 |
|
checkpoint37 |
| 637 |
|
o mdsio.F routine split and packaged in pkg/mdsio |
| 638 |
|
(mdsio.F and mdsio_gl.F still exist in eesupp/src but are not |
| 639 |
|
used unless genmake -disable=mdsio) |
| 640 |
|
o allow a more precise surface-geopotential gradient for the atmosphere |
| 641 |
|
taking into account the change in space of Alpha (=1/rho) at the surface. |
| 642 |
|
o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit] |
| 643 |
|
(ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa]) |
| 644 |
|
o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and |
| 645 |
|
Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential |
| 646 |
|
[m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere). |
| 647 |
|
o Time-Average diagnostics defined as a pseudo package "timeave". |
| 648 |
|
o pickup files : old pickup (before c35) did not work with new code (c35 |
| 649 |
|
and after) unless activating 2 commented lines in initialise-varia. |
| 650 |
|
o Non-Hydrostatic pickup file Pb fixed. |
| 651 |
|
o bug with Rigid-lid version (since c35) fixed. |
| 652 |
|
|
| 653 |
|
checkpoint36 |
| 654 |
|
o implement Crank-Nickelson barotropic time-stepping |
| 655 |
|
o recover Time-Average diagnostics |
| 656 |
|
o fix Pb in checkpoint (PR#19) |
| 657 |
|
o AIM become a standard package ; clean unused CPP_kees |
| 658 |
|
|
| 659 |
|
checkpoint35 |
| 660 |
|
o subtantial rewrite of dynamics.f |
| 661 |
|
o allows staggered time-stepping |
| 662 |
|
o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt |
| 663 |
|
o added bottom drag (linear + quadratic) |
| 664 |
|
|
| 665 |
|
checkpoint34 |
| 666 |
|
o Modified exchange routines for correct reverse simulation. |
| 667 |
|
o Added verification output to comply with bug fix in impldiff.F |
| 668 |
|
as of c33 (exp2, natl_box). |
| 669 |
|
o Corrected store directives in dynamics.F |
| 670 |
|
o Corrected array boundaries in impldiff.F |
| 671 |
|
o Corrected array dimensions in gmredi. |
| 672 |
|
Added temporary scalars to avoid storage by TAMC (gmredi, kpp). |
| 673 |
|
o Added routine GLOBAL_SUM_INT to global_sum.F |
| 674 |
|
o Added mdsio_gl.F for ECCO purposes. |
| 675 |
|
|
| 676 |
|
checkpoint33 |
| 677 |
|
o Fixed bug in lower BC in impldiff.F |
| 678 |
|
o Fixed confusion about units of forcing arrays in FFIELDS.h |
| 679 |
|
namely Fu,Fv,Qnet,Qsw,EmPmR: |
| 680 |
|
- Removed verification/natl_box/code/external_fields_scale.F |
| 681 |
|
(did not differ from that in model/src) |
| 682 |
|
- Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units |
| 683 |
|
(see FFIELDS.h for description) |
| 684 |
|
- Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F, |
| 685 |
|
kpp_calc.F and kpp_transport_t.F |
| 686 |
|
- Removed model/src/external_fields_scale.F and calls to it |
| 687 |
|
- verification/natl_box uses flux data with "atmospheric" sign so |
| 688 |
|
a special version of external_fields_load.F is used to |
| 689 |
|
change the data as it's read in. This way, the arrays |
| 690 |
|
have the right units and signs at all times tha a user could |
| 691 |
|
possibly use them. |
| 692 |
|
o Corrected genmake to delete a temporary file during configuration |
| 693 |
|
|
| 694 |
|
checkpoint32 |
| 695 |
|
o Scaling of forcing fields moved from external_forcing.F to |
| 696 |
|
external_fields_scale.F, called directly after loading fields. |
| 697 |
|
o Surface relaxation terms added to surface tendency fields in |
| 698 |
|
extra subroutine. |
| 699 |
|
o impldiff.F changed to avoid storing by TAMC of huge intermediate |
| 700 |
|
fields. |
| 701 |
|
o Changes in GMRedi to comply with packaging structure. |
| 702 |
|
o Modifications and bug fixes in KPP package. |
| 703 |
|
o Verification experiment for KPP added (verification/nat_box/) |
| 704 |
|
|
| 705 |
|
checkpoint31 |
| 706 |
|
o Packages interface brought in line with defined standard |
| 707 |
|
-> new routines packages_...F |
| 708 |
|
-> changes in initialise_fixed.F, initialise_varia.F |
| 709 |
|
-> enables initialisation interface for ECCO package |
| 710 |
|
o Rescaling of external forcing fields immediately after read |
| 711 |
|
(removed from external_forcing.F) |
| 712 |
|
-> new: surface_fields_scale.F |
| 713 |
|
-> affects ini_foorcing.F, external_fields_load.F |
| 714 |
|
o Computation of surface tendencies before tendency updates. |
| 715 |
|
-> new: external_forcing_surf.F |
| 716 |
|
o Change of variable names useGMRedi, useKPP, useECCO |
| 717 |
|
o Further changes in dynamics.F, impldiff.F for TAMC |
| 718 |
|
o Tested for experiments 0, 2, 4. |
| 719 |
|
- not yet tested for GMRedi. |
| 720 |
|
- not yet tested for KPP. |
| 721 |
|
|
| 722 |
|
checkpoint30 |
| 723 |
|
o Updates for OBCs |
| 724 |
|
o New experiment for test OBCs (internal_wave) |
| 725 |
|
o New output.txt in verification/exp4/results/ |
| 726 |
|
o Updates for KPP: calculation of viscosity corrected, new variables |
| 727 |
|
kpp_dumpFreq and kpp_taveFreq |
| 728 |
|
o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.) |
| 729 |
|
and entry for T90 in genmake |
| 730 |
|
|
| 731 |
|
checkpoint29 |
| 732 |
|
o packaged KPP and GM/Redi |
| 733 |
|
|
| 734 |
|
checkpoint28 |
| 735 |
|
o Corrected initialization of hFacMin for difference vertical coordinates |
| 736 |
|
o Modified calculation of partial cell thickness to more robust algorithm |
| 737 |
|
o config_summary.F: replaced write_1D_... by write_0D_... |
| 738 |
|
read_write.F: added subroutines write_0D_... |
| 739 |
|
o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho: |
| 740 |
|
included some initialisations required for TAMC. |
| 741 |
|
o routine calc_isoslopes: modified sqrt computation to make it |
| 742 |
|
differentiable for zero argument. |
| 743 |
|
o routines dynamics, impldiff: |
| 744 |
|
included store directives and tape key computations required for TAMC. |
| 745 |
|
o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC |
| 746 |
|
|
| 747 |
|
checkpoint27 |
| 748 |
|
o fixed calc_isoslopes() to so that cancellation of terms in tensor |
| 749 |
|
formulation works properly with variable resolution. |
| 750 |
|
o restructured the calling tree between the_model_main() and dynamics() |
| 751 |
|
o split initialise() into initialise_fixed() and initialise_varia() |
| 752 |
|
o introduced initialization file pSurfInitFile for free surface (cg2d_x) |
| 753 |
|
in new routine ini_psurf() |
| 754 |
|
|
| 755 |
|
checkpoint26 |
| 756 |
|
o moved some #ifdef in optional routines to encompass everything |
| 757 |
|
except the argument declarations. This was using up some memory. |
| 758 |
|
o fixed macros like _ADT to work with both versions of Linux cpp |
| 759 |
|
o cleaned up some unused and uninitialized variables |
| 760 |
|
(helps when debugging with strict compile options) |
| 761 |
|
o split up CPP_EEOPTIONS.h into options and macros |
| 762 |
|
(macros are now in eesupp/inc/CPP_EEMACROS.h) |
| 763 |
|
o patch for 2 processor JAM mode |
| 764 |
|
|
| 765 |
|
checkpoint25 |
| 766 |
|
o updates for OBCs and NH |
| 767 |
|
o dramatically reduced memory usage |
| 768 |
|
o added "JAM" routines for use on Artic network |
| 769 |
|
o parameterization of convection by implicit vertical diffusion |
| 770 |
|
o added a diagnostic of convective index |
| 771 |
|
o moved call to calc_divg_hat() from dynamics() to solve_for_pressure() |
| 772 |
|
(this is was partly for OBCs and NH but also in anticipation of |
| 773 |
|
an explicit free-surface option) |
| 774 |
|
o initial state input files for U and V |
| 775 |
|
|
| 776 |
|
checkpoint24 |
| 777 |
|
o Removed some spurious "REAL"s |
| 778 |
|
o Updated KPP to latest version from JPL |
| 779 |
|
o Added a COS(latitude) in horizontal viscosity |
| 780 |
|
|
| 781 |
|
checkpoint23 |
| 782 |
|
o Added del^4 diffusion for salt and temperature |
| 783 |
|
o Multiple minor fixes (implicit none's, arguments to global_sum, etc.) |
| 784 |
|
|
| 785 |
|
checkpoint22 |
| 786 |
|
o Made many small changes: implicit none, format(i5), etc... |
| 787 |
|
o Introduced KPP mixing scheme (compiles and runs but *not* tested) |
| 788 |
|
|
| 789 |
|
checkpoint21 |
| 790 |
|
o Introduced new I/O package that supports direct-access records (mdsio.F) |
| 791 |
|
o Split-up mid-level I/O routines |
| 792 |
|
o Updated input data for experiments 0,1,2,4 and 5 |
| 793 |
|
o Finally removed the genmake.* scripts (everyone seems happy with genmake) |
| 794 |
|
|
| 795 |
|
checkpoint20 |
| 796 |
|
o Tidied up open-boundaries some more |
| 797 |
|
o Added non-hydrostatic code |
| 798 |
|
o Fixed some input data |
| 799 |
|
o Modified MPI start-up to work in "coupled" context. |
| 800 |
|
|
| 801 |
|
checkpoint19 |
| 802 |
|
o Tidied up directory structure for verification experiments. |
| 803 |
|
o Added new code for open boundaries. |
| 804 |
|
o Corrected advective terms near boundaries. |
| 805 |
|
o Added CPP flag for "old UV" geometry and corrected spherical geometry. |
| 806 |
|
o Implemented free-slip/no-slip BCs and del^4 dissipation. |
| 807 |
|
o Split default parameters out of ini_parms.F into set_defaults.F. |
| 808 |
|
|
| 809 |
|
checkpoint18 |
| 810 |
|
o Further changes for optional code generation with |
| 811 |
|
CPP - ugh! |
| 812 |
|
|
| 813 |
checkpoint17 |
checkpoint17 |
| 814 |
o Beginning to incorporating modularity |
o Beginning to incorporating modularity |
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