| 3 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 4 |
============================== |
============================== |
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| 6 |
untagged |
ecco_c44_e22 |
| 7 |
o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F |
o Finally, the merges with the Scripps cost function terms: |
| 8 |
o Added SEAICE_initialHEFF to pkg/seaice |
Various additions, modifications, quality checks. |
| 9 |
o SEAICE_WRITE_PICKUP needs to be called before WRITE_CHECKPOINT |
o Plus: Included switch ALLOW_AUTODIFF_MONITOR to handle |
| 10 |
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monitoring of adjoint state. |
| 11 |
release1_p12 |
o Plus: removed comm_stats, ini_communication_patterns from diff. list |
| 12 |
o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf, |
(no more need to "keep" MPI headers for adjoint generation) |
| 13 |
kpp_transport_t.F, forward_step.F, and the_main_loop.F |
o Plus: exf changes: |
| 14 |
o pkg/seaice: |
o added run-off routine |
| 15 |
- adjoint-friendly modifications |
o additional storing needed for ustress,vstess |
| 16 |
- added a SEAICE_WRITE_PICKUP at end of the_model_main.F |
because of state-dependent quality check |
| 17 |
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o added missing initialisations |
| 18 |
release1_p12_pre |
o Plus: genmake with MAKEDEPEND variable was still missing in ecco-branch |
| 19 |
o Updated useSingleCpuIO option in mdsio_writefield.F to |
NB: - verification/natl_box_adjoint/ 240 steps run |
| 20 |
work with multi-field files, e.g., for single-file pickup. |
* looks ok under Linux (twain.lcs.mit.edu) |
| 21 |
o pkg/seaice: |
* looks ok on MIT SUN's (fjord.mit.edu) |
| 22 |
- bug fix in growth.F: QNET for no shortwave case |
* NaN in reverse mode on Scripps SUN's at iter=214 |
| 23 |
- added HeffFile for specifying initial sea-ice thickness |
* NaN in reverse mode on IBM SP3 (BlueHorizon) at iter=204 |
| 24 |
- changed SEAICE_EXTERNAL_FLUXES wind stress implementation |
- 1 year forward int. global 2x2 deg. produces similar cost functions |
| 25 |
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* all cost terms of new code are slightly smaller (0.5 to 3%). |
| 26 |
release1_p11 |
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| 27 |
o Modifications for using pkg/exf with pkg/seaice |
ecco_c44_e21 |
| 28 |
- improved description of the various forcing configurations |
o reversed order of ctrl/cost initialisation |
| 29 |
- added basic radiation bulk formulae to pkg/exf |
o gmredi_slope_psi.F: Inconsistent types in MIN/MAX expressions |
| 30 |
- units/sign fix for evap computation in exf_getffields.F |
o modified to enable ctrl field swapping |
| 31 |
- updated verification/global_with_exf/results/output.txt |
o bug fix for global sum of ncvarlength in ctrl_init |
| 32 |
o Added pkg/sbo for computing IERS Special Bureau for the Oceans |
o no more call to ctrl_unpack from ctrl_init |
| 33 |
(SBO) core products, including oceanic mass, center-of-mass, |
o no more write of ctrl vector in ctrl_pack |
| 34 |
angular, and bottom pressure (see pkg/sbo/README.sbo). |
however, init. of control vector from ctrl_unpack |
| 35 |
o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F |
o various bug fixes & consistent nobcs handling in |
| 36 |
to avoid negative values in shallow regions. |
ctrl_pack/unpack routines (by G. Gebbie) |
| 37 |
- updated verification/natl_box/results/output.txt |
o optim package: Added obcs control part for lsopt I/O |
| 38 |
- updated verification/lab_sea/results/output.txt |
(by G. Gebbie) |
| 39 |
o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F |
o missing call to obcs_diags |
| 40 |
o Added useSingleCpuIO option (see PARAMS.h). |
o moved calls in packages_init_fixed to packages_readparms |
| 41 |
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because some quantities are needed earlier. |
| 42 |
release1_p10 |
|
| 43 |
o modifications for using pkg/exf with pkg/seaice |
ecco_c44_e20 |
| 44 |
- pkg/seaice CPP options SEAICE_EXTERNAL_FORCING |
o before major merges from the Scripps setup |
| 45 |
and SEAICE_EXTERNAL_FLUXES |
here are two small updates: |
| 46 |
- pkg/exf CPP options EXF_READ_EVAP and |
- field swapping for surface flux controls enabled |
| 47 |
EXF_NO_BULK_COMPUTATIONS |
(remains t.b.d. for atmos. state plus obcs) |
| 48 |
- usage examples are Experiments 8 and 9 in |
- bug fix in active_file.F for xz-/yz- routines |
| 49 |
verification/lab_sea/README |
- added missing xz-/yz- routines to active_file_ad.F |
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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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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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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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release1_p7 |
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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: |
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- added this routine to TAF list |
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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 |
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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 |
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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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release1_p6 |
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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) |
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- new POLY3.COEFFS (for the next release one should switch to a full |
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equation of state) |
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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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release1_p5 |
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o import recent fix from MAIN branch: |
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- use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S |
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- change phiMin in exp1 (to agree with documentation) |
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from checkpoint45 to checkpoint45a_post: |
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- specific exchange for X-slice domain (case Ny=1) |
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- argument futureIter of S/R obcs_calc missing in |
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exp4 & internal_wave /code |
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- solve_for_pressure : set cg2d_x to zero where OBCS are applied |
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from checkpoint44f_post to checkpoint44g_post: |
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- fix surface correction term in multiDimAdvection |
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(affects plume_on_slope results |
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o bug fix in packages_readparms (missing ALLOW_CALENDAR) |
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o bug fix in CG2D.h (correct array size for LETS_MAKE_JAM |
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o Adjoint-related bug fixes in kpp: |
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- kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix |
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- kpp_routines: store of Rib avoids partial recomputation bug of TAF. |
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o added Eliassen-Palm flux hooks (dynamics,ini_fields) |
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o removed unused TAF keys iikey, idkey (dynamics,thermodynamics) |
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o flow directives: |
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- new for S/R do_the_model_io |
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- enhanced for S/R checkpoint |
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o added Eliassen Palm flux controls to gradient check package |
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o new ctrl package |
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- adopted from ECCO environment to enable optimization |
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- added Eliassen Palm fluxes to controls |
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- adjusted global_ocean.90x40x15/ and carbon/ accordingly |
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release1_p4 |
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o Removed f90 comments ("!") |
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o Modified initialisations to enable exf package for MITgcm |
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(without invoking ECCO_PACKAGE). |
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o modifications to gradient check package (Martin Losch) |
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- enable centered differences |
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- modified format of standard output |
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release1_p3 |
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o added tangent linear setup to verification/carbon/ |
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o added adjoint sensitivity setup to verification/global_ocean... |
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o moved packages_init_variables before convective_adjustment |
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o output of verif. which use GMRedi brought up-to-date with |
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MAIN trunk (those were re-created after changes in GMRedi) |
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o included CPP option SINGLE_LAYER_MODE |
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to configure barotropic setup (Martin Losch). |
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o Removed auxiliary variable in impldiff |
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(caused numerical differences with MAIN trunk routine). |
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o Introduced CPP option ALLOW_AUTODIFF_MONITOR to |
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disable adcommon.h/g_common.h by default. |
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o Cleaned exchange calls in cg2d. |
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release1_p2 |
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o fixed array boundary problem for adjoint |
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(related to partial recomputation within subroutine |
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related to dynamics -> calc_viscosity -> mom_... |
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o fixed recomputation in thermodynamics |
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o prepare (but not complete) recomputation problem in impldiff |
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o fixed problem for adjoint of global_max |
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o switched off sponge layer code in external_forcing |
|
| 50 |
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| 51 |
release1_p1 |
ecco_c44_e19 |
| 52 |
o merged necessary patches: |
o merged necessary patches: |
| 53 |
- AD-related changes for GMRedi |
- AD-related changes for GMRedi |
| 54 |
- fixes i KPP (delZ -> drF) |
- fixes i KPP (delZ -> drF) |
| 55 |
- hook to OBCS songe layer code in external_forcing |
- hook to OBCS songe layer code in external_forcing |
| 56 |
- errorMessageUnit non-zero in eeboot.F |
- errorMessageUnit non-zero in eeboot.F |
| 57 |
- modified test cost function and carbon verif. |
- included GMREDI, EXACT_CONSERV to natl_box_adjoint verif. |
| 58 |
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| 59 |
release1_chkpt44d_post = chkpt44d_post |
ecco_c44_e18 |
| 60 |
|
o sponge layer code for obcs was missing |
| 61 |
chkpt44d_pre,post |
- added hook in external_forcing.F |
| 62 |
o added missing EXCLUDE_MONITOR flags |
- added storing for TAF |
| 63 |
o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi |
o new routine cost_init_barfiles to initialise |
| 64 |
(incompatible typ in MIN/MAX expressions caused problems |
adjoint fields adtbar, adsbar, adpsbar |
| 65 |
on IBM SP3) |
(needed in conjunction with corrected ladinit for active I/O) |
| 66 |
o in genmake added variable MAKEDEPEND |
o cleaned up and corrected order in packages_readparms, ecco_readparms |
| 67 |
plus resetting for case SunOS |
o corrected and simplified weights for obcs controls |
| 68 |
o added timer_stats.c routine for IBM SP3 |
- weight fields simplified |
| 69 |
o removed variables in dynamics |
- bug fix in ctrl_pack |
| 70 |
|
- no more write of control vector in ctrl_pack |
| 71 |
o real fresh water flux implemented with non-linear free-surface. |
o i/j index bug fixes in cost_ssh_mean |
| 72 |
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|
| 73 |
chkpt44c_pre,post |
ecco_c44_e17 |
| 74 |
o few fix (mask in shap_s2, EmPmR in external_field_load, |
o bug fixes in cost package |
| 75 |
USE_NATURAL_BCS in solve_for_P); |
* wrong identifier for active I/O of monthly mean psbar |
| 76 |
o add arguments myIter & myTime to S/R obcs_calc & solve_for_P |
(cost_averagesfields, cost_ssh) xx_psbar_dummy |
| 77 |
|
* cleaned all identifier for active I/O of monthly fields |
| 78 |
checkpoint44b_pre/_post |
* wrong ladinit in various cost routines |
| 79 |
o merge of relevant stuff from the ecco-branch: |
o merge with interval (chkpt44c_post - chkpt44d_post) |
| 80 |
|
* added missing EXCLUDE_MONITOR flags |
| 81 |
|
* changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi |
| 82 |
|
(incompatible typ in MIN/MAX expressions caused problems |
| 83 |
|
on IBM SP3) |
| 84 |
|
* in genmake added variable MAKEDEPEND |
| 85 |
|
plus resetting for case SunOS |
| 86 |
|
added timer_stats.c routine for IBM SP3 |
| 87 |
|
* removed variables in dynamics |
| 88 |
|
|
| 89 |
|
ecco_c44_e16 |
| 90 |
|
o new ECCO checkpoint, the first since ecco_c43_e15 |
| 91 |
|
which is branched from MITgcm. |
| 92 |
|
All changes were merged in between (see ecco-branch-mod? tags). |
| 93 |
|
o last changes: |
| 94 |
|
* assuming path for TAF and TAMC are known (e.g. in $path) |
| 95 |
|
* genmake: |
| 96 |
|
- added tools/xmakedepend to circumvene shortcoming of |
| 97 |
|
SUN's makedepend (size too small) |
| 98 |
|
- invoking ../tools/xmakedepend instead of makedepend |
| 99 |
|
- changed compiler flags for case SunOS |
| 100 |
|
|
| 101 |
|
ecco-branch-mod5 |
| 102 |
|
o mod's to reproduce open boundary run |
| 103 |
|
o enable field swapping for OB's and climatology |
| 104 |
|
o update store directives for OB control |
| 105 |
|
o added option ALLOW_OBCS_PRESCRIBE |
| 106 |
|
o call of getobcs now out of obcs_calc (param. list modified) |
| 107 |
|
|
| 108 |
|
ecco-branch-mod4 |
| 109 |
|
o this is the second part of changes necessary to reconcile |
| 110 |
|
the natl_box_adjoint verification (with and without grdchk). |
| 111 |
|
>>>!!! CHANGES BETWEEN THE TAGS ecco-branch-mod3 !!!<<< |
| 112 |
|
>>>!!! AND ecco-branch-mod4 !!!<<< |
| 113 |
|
>>>!!! SHOULD BE MERGED INTO THE MAIN TRUNK !!!<<< |
| 114 |
- genmake: removed $S64 overwrite for case SunOS |
- genmake: removed $S64 overwrite for case SunOS |
| 115 |
- pkg/exf: update and corrections for field swapping and obcs |
- pkg/exf: update and corrections for field swapping and obcs |
| 116 |
- pkg/ecco: parameter lists for the_model_main, the_main_loop |
- pkg/ecco: parameter lists for the_model_main, the_main_loop |
| 118 |
- pkg/autodiff: added flow directives for obcs, mdsio_gl_slice |
- pkg/autodiff: added flow directives for obcs, mdsio_gl_slice |
| 119 |
updated checkpointing_lev... lists for obcs |
updated checkpointing_lev... lists for obcs |
| 120 |
- model/src: minor changes in forward_step, plot_field |
- model/src: minor changes in forward_step, plot_field |
|
added directive for divided adjoint in the_main_loop |
|
| 121 |
- pkg/mdsio: added mdsio_gl_slice |
- pkg/mdsio: added mdsio_gl_slice |
| 122 |
|
|
| 123 |
o check parameters & config (chkpt44a_pre,post) |
ecco-branch-mod3 |
| 124 |
o OBC and NonLin_FrSurf. |
o this is the first part of changes necessary to reconcile |
| 125 |
|
natl_box_adjoint verification (with and without grdchk). |
| 126 |
|
This set of changes is relevant for ECCO only. |
| 127 |
|
The next set/tag of changes (ecco-branch-mod4) |
| 128 |
|
should be merged into the main trunk. |
| 129 |
|
- update some options |
| 130 |
|
- parameter lists of ecco_the_model_main and ecco_the_main_loop |
| 131 |
|
differed from those of the MITgcm counterparts. |
| 132 |
|
|
| 133 |
|
ecco-branch-mod2 |
| 134 |
|
o update ecco-branch-mod1 to checkpoint44 |
| 135 |
|
o exclude from updates: |
| 136 |
|
- verification/ |
| 137 |
|
- adjoint/ |
| 138 |
|
- pkg/cost |
| 139 |
|
- pkg/ctrl |
| 140 |
|
- pkg/ecco |
| 141 |
|
- pkg/obcs |
| 142 |
|
- model/src/the_model_main.F |
| 143 |
|
- model/src/the_main_loop.F |
| 144 |
|
|
| 145 |
checkpoint44 |
checkpoint44 |
| 146 |
|
o apply Shapiro filter on T&S before calc_PhiHyd (stagger time stepping) |
| 147 |
o fix bug in mom_vi_del2uv |
o fix bug in mom_vi_del2uv |
|
o select when filters are applied ; add options to zonal_filter (data.zonfilt) |
|
|
o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection) |
|
|
o update AIM experiments (NCEP input files) |
|
|
o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf) |
|
| 148 |
o added some stuff for AD |
o added some stuff for AD |
| 149 |
|
|
| 150 |
|
ecco-branch-mod1 |
| 151 |
|
o based on c43 |
| 152 |
|
o replaced packages cost, ctrl, ecco, obcs |
| 153 |
|
o removed MITgcm verif.'s, added ECCO verif.'s |
| 154 |
|
o added lsopt, optim for line search optimization. |
| 155 |
|
|
| 156 |
checkpoint43 |
checkpoint43 |
| 157 |
o added two new advection tests |
o added two new advection tests |
| 158 |
o added global 4x4 degree ocean test |
o added global 4x4 degree ocean test |
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