| 3 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 4 |
============================== |
============================== |
| 5 |
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| 6 |
ecco_c50_e33 |
checkpoint47f_post |
| 7 |
o minor changes to pkg/seaice pkg/cost/cost_ice.F |
Merging from release1_p10: |
| 8 |
and verification/natl_box_adjoint/README |
o modifications for using pkg/exf with pkg/seaice |
| 9 |
o Modif's to enable tangent linear run in ECCO environment |
- pkg/seaice CPP options SEAICE_EXTERNAL_FORCING |
| 10 |
including time-dependent forcing |
and SEAICE_EXTERNAL_FLUXES |
| 11 |
* main problem is missing call mdsreadfield out of exf_set_gen |
- pkg/exf CPP options EXF_READ_EVAP and |
| 12 |
(i.e. computation of trajectory in TLM mode) |
EXF_NO_BULK_COMPUTATIONS |
| 13 |
* incorrect g_active_write_... |
- usage examples are Experiments 8 and 9 in |
| 14 |
* (re-) init of bar files and g_bar files |
verification/lab_sea/README |
| 15 |
o Reverted back to 3-dim. tbar, sbar for SST, SSS bar files. |
- verification/lab_sea default experiment now uses |
| 16 |
o MERGES: |
pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf |
| 17 |
* obcs/ ctrl/ G. Gebbie code |
|
| 18 |
(major changes in ctrl handling, volume flux balancing etc.) |
checkpoint47e_post |
| 19 |
* cost/ ctrl/ A. Koehl code |
o created a tag prior to creating a branch |
| 20 |
- new cost contributions (new data types) |
|
| 21 |
- efficient pack/unpack for time-dependent 2-d fields |
checkpoint47d_post |
| 22 |
o replaced mutiple ctrl_get... by single generic ctrl_get_gen.F |
o fixed bug in the oceanic pressure coordinates code: vertical viscosity |
| 23 |
(except obcs) |
at the bottom boundary had an erroneous half slip boundary condition |
| 24 |
o somewhat cleaned package initialisation sequence for |
o added bottom drag and no slip boundary condition capabilities to |
| 25 |
ctrl/ cost/ ecco/ |
oceanic pressure coordinates code |
| 26 |
o extended grdchk to enable obcs gradient checks |
o added new verification experiment global_ocean_pressure, this experiment is |
| 27 |
o some generalizations for easier TLM <-> ADM switches |
also described in the tutorial section of the manual |
| 28 |
o added configuration example for parallel divided adjoint |
checkpoint47d_pre |
| 29 |
(see verification/natl_box_adjoint/code_diva_mpi/README ) |
|
| 30 |
o started verification exp. for obcs control |
checkpoint47c_post |
| 31 |
(still needs checking) |
o Added a verification experiment for a global cubed-sphere ocean run |
| 32 |
|
- verification/global_ocean.cubed32x32x30 |
| 33 |
ecco_c50_e32 |
- uses pkg/therm_seaice and pkg/bulk_forcing |
| 34 |
o Patrick's adjoint-model storage directives for pkg/seaice |
|
| 35 |
o merged with checkpoint50g_post (pkg/seaice and verification/lab_sea) |
o allow to run AIM physics with SPEEDY input files (from Franco Molteni) |
| 36 |
- added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics |
o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1) |
| 37 |
- LSR sea-ice dynamic solver moved to SouthWest B-grid location and |
when using P-coordinate; only implemented for atmospheric config. |
| 38 |
made the default because of faster convergence than ADI |
o OCEANICP & realFreshWater: include P-E direct effect on wVel ; |
| 39 |
o Modifications for adjoint of SEAICE_ALLOW_DYNAMICS |
NOTES: requires option NONLIN_FRSURF to be "#define". |
| 40 |
- extended state in checkpoint_lev... |
o update advect_xz/results/output.txt (left from checkpoint44g_post) |
|
- in lsr.F, replaced GO TO by fixed loop index (also avoid DO WHILE) |
|
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- YEAH: in lsr.F, (first) successful use of CADJ LOOP = ITERATION |
|
|
- avoid stoing in S/R budget for now |
|
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- in dynsolver.F, avoid NPSEUDO loop for adjoint |
|
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- new comlev1_lsr in the_main_loop |
|
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o Small modif's in lsopt/, optim/ to ease compilation |
|
|
New script to run optim (lsopt) |
|
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|
|
|
ecco_c50_e31 |
|
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o exf totally restructured |
|
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- replaced all exf_set_ routines by one generic exf_set_gen.F |
|
|
and made sure it's still differentiable |
|
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- split exf_getffields.F into new exf_bulkformulae.F |
|
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- exf_inscal_/exf_outscal_ suffixes consistent with field names |
|
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o New cost function: Tini-Tfin to do model spinup optimization. |
|
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o Started new verification exp for Tini-Tfin optimization. |
|
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ecco_c50_e30 |
|
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o corrected CPP option mismatch in exf_Bulk... functions for case |
|
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#define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP |
|
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o Merging from release1_p13 and from icebear5 |
|
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- bug fix for pkg/seaice dynamic solver |
|
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- Added SEAICE_initialHEFF to pkg/seaice |
|
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- Additional options for pkg/cost/cost_ice.F |
|
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- Updates to verification/natl_box_adjoint |
|
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- pkg/ctrl/ctrl_init.F |
|
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Fix for determination of startrec and endrec. |
|
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- pkg/cal/cal_toseconds.F |
|
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Fix for negative intervals shorter than 1 day. |
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ecco_c50_e29 |
|
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Bug fix for merging between c50 and KPP. |
|
|
ikey was passed from thermodynamics to kpp_calc via |
|
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common block rather than being recomputed in kpp_calc, |
|
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in contradiction with new key itdkey. |
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New key ikppkey created, and tamc.h headers updated. |
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ecco_c50_e28 |
|
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o major merge: |
|
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ecco-branch merged with checkpoint50 |
|
|
gmredi now available, grdchk, DIVA up-to-date for MPI |
|
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However, two outstanding problems: |
|
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- kpp adjoint is broken, needs fixing! |
|
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- a few minor modif's in handling of CPP option |
|
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ALLOW_TANGENTLINEAR_RUN in conjunction with |
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ALLOW_ECCO_OPTIMIZATION are necessary to enable |
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TLM runs with ECCO setup |
|
| 41 |
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| 42 |
ecco_c44_e27 |
checkpoint47b_post |
| 43 |
o exf: |
Merging from release1_p9: |
|
- Enable initialisation of forcing fields to constant |
|
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(runtime) values. |
|
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- in exf_getffields.F |
|
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Reduce i-/j-loop to interior domain, discarding overlaps. |
|
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That also fixes wrong TAF-key computations for key_1, key_2 |
|
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with bulf formulae. |
|
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- exf_init.F modify #ifdef for exf_init_evap |
|
|
- exf_getffieldrec.F, ctrl_getrec.F |
|
|
The following INT-usages are not safe: |
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fldsecs = int(fldsecs/fldperiod)*fldperiod |
|
|
fldcount = int(fldsecs/fldperiod) + 1 |
|
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and were modified. |
|
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- added repeatPeriod (from MAIN branch) |
|
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o grdchk: updated and merged |
|
|
- has both ADM and TLM checks |
|
|
- works for single- and multi-proc. |
|
|
- output cleaned |
|
|
- worked successfully for parallel DIVA |
|
|
Needed one update in EEPARAMS.h and updates in ctrl package |
|
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More modif's may be necessary for ECCO code to support TLM. |
|
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o autodiff: checkpoint_lev... |
|
|
- updated storing for bulk formulae (some arrays were missing) |
|
|
- added state for seaice package |
|
|
- synchronized with main branch |
|
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o DIVA: |
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|
Modif.s in |
|
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- cost_init.F |
|
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- cost_averagesfields.F |
|
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- ecco_the_main_loop.F |
|
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- ecco_the_model_main.F |
|
|
and added cost_final_restore.F cost_final_store.F |
|
|
o With these changes, it is possible to fully separate |
|
|
the first forward run to compute the cost function (mdthe_main_loop) |
|
|
and adjoint runs over individual DIVA intervals (adthe_main_loop) |
|
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into separate model executions. |
|
|
This enables better tuning of DIVA to given queue sizes. |
|
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o Loss of cost function value in consecutive DIVA runs is |
|
|
fixed by storing to 'costfinal' file. |
|
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o Appropriate call of ctrl_unpack/_pack,grdchk_main at |
|
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beginning/end of adjoint integration is accounted for. |
|
|
The current changes apply to TAF-1.4.26. |
|
|
TAF has one remaining bug, requiring one manual change |
|
|
(see MITgcm manual). |
|
|
o bug fix plus modif for ubar, vbar in cost_averagesfields |
|
|
o cal: synchronized between MAIN and ecco-branch |
|
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|
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|
icebear4 |
|
|
o Added cost_ice for sea-ice volume sensitivity experiment. |
|
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o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT |
|
|
o Reduced derivative singularities in pkg/seaice. |
|
|
o Updated verification/natl_box_adjoint |
|
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icebear3 |
|
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o Removed spurious iikey and idkey |
|
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o pkg/exf |
|
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- bug fix in treatment of downward radiation |
|
| 44 |
o pkg/seaice |
o pkg/seaice |
| 45 |
- added initial sea-ice thickness parameter SEAICE_initialHEFF |
- removed GOTO's and added taf directives |
| 46 |
o updated verification/natl_box_adjoint |
- double precision constants to reduce the g77 (Linux) |
| 47 |
|
to F77 (SGI) differences reported in release1_p8 |
| 48 |
icebear2 |
o tools/genmake |
| 49 |
o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf, |
- added SGI options |
| 50 |
kpp_transport_t.F,and ecco_the_main_loop.F |
o verification/testscript |
| 51 |
o adjoint-friendly modifications to pkg/seaice |
- updated to that of checkpoint47a_post |
| 52 |
o added verification/lab_sea as per release1_p12_pre |
o verification/global_ocean.90x40x15/input/eedata |
| 53 |
|
- modified for SGI f77 compatibility |
| 54 |
ecco_c44_e26 |
o verification/lab_sea |
| 55 |
o Merging pkg/exf and pkg/seaice from cvs tag ecco_ice2 |
- added description of sea-ice model |
| 56 |
o exf: Modifications to correctly handle evap field for adjoint |
- added missing matlab routines |
| 57 |
o grdchk: |
- added test of thermodynamics parallelization |
| 58 |
Added code to perform gradient checks for bulk formulae/atmos. state |
|
| 59 |
(atemp, aqh, uwind, vwind). |
checkpoint47a_post |
| 60 |
NOTE: |
o new pkg: aim_v23 |
| 61 |
This package is out of synch with c48 package. |
= F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm. |
| 62 |
The latter also has the tangent linear gradient checks. |
for now, keep the same surface forcing as before. |
| 63 |
Need to be merged. |
- Part-Cell implemented into AIM; check that Heat & Water are conserved |
| 64 |
o verification/natl_box_adjoint: |
- aim.5l_cs: use new aim pkg (run 10yr & get better results than before) |
| 65 |
* added new setup: code_bulk/, input_bulk, results_bulk |
- aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg |
| 66 |
(Experiment 2, described in README) |
o add diagnostic of surface correction term in monitor output |
| 67 |
uses bulk formulae and atmos. state as control instead of |
|
| 68 |
air-sea fluxes. |
o bulk_force and therm_seaice |
| 69 |
Performs gradient checks for first 4 elements of atemp control. |
- Two packages: bulk_force (Bulk forcing) |
| 70 |
* changed standard verification to perform |
and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2 |
| 71 |
gradient checks on first 4 elements on hflux control. |
- Earlier integration from Stephaine Dutkiewicz |
| 72 |
* gmredi switched off (will come after merge with c48). |
and Patrick Heimbach. |
| 73 |
|
- Two ifdef statements for compile time, |
| 74 |
ecco_c44_e25 |
ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE |
| 75 |
o Merging some GM changes from main trunk (c47) to ecco-branch. |
|
| 76 |
o Updating verif. natl_box_adjoint with GMRedi. |
checkpoint47 |
| 77 |
o Adding setup with explicit differentiaton of pressure solver. |
differentiable version of checkpoint46n_post |
| 78 |
o Bug fix: missing OBCS_OPTIONS.h for sponge layer code. |
o bug fix in quasihydrostaticterms |
| 79 |
o (Re-?) Commiting old bug fixes in kpp to ecco-branch |
o * "clean" adjoint code (in terms of extensive recomputations) |
| 80 |
(kpp_calc.F, kpp_routines.F) |
can now be obtained for all GMREDI options (i.e. for |
| 81 |
|
- GM_VISBECK_VARIABLE_K |
| 82 |
|
- GM_NON_UNITY_DIAGONAL |
| 83 |
|
- GM_EXTRA_DIAGONAL |
| 84 |
|
- GM_BOLUS_ADVEC ) |
| 85 |
|
* However, wrong gradient check problem remains unsolved. |
| 86 |
|
* New CPP options have been introduced for different |
| 87 |
|
tapering schemes |
| 88 |
|
o external_fields_load now part of differentiation list |
| 89 |
|
o pressure needs multiple storing; |
| 90 |
|
would be nice to have store_pressure at beginning or |
| 91 |
|
end of forward_step, e.g. by having phiHyd global (5-dim.) |
| 92 |
|
(NB: pressure is needed for certain cases in find_rho, |
| 93 |
|
which is also invoked through convective_adjustment). |
| 94 |
|
o recomputations in find_rho for cases |
| 95 |
|
'JMD95'/'UNESCO' or 'MDJWF' are OK. |
| 96 |
|
o #define ATMOSPHERIC_LOADING should be differentiable |
| 97 |
|
o ini_forcing shifted to begining of initialise_varia |
| 98 |
|
o Incorporating QNVS line search routines into MITgcm |
| 99 |
|
(this is separate code, and therefore not under pkg) |
| 100 |
|
lsopt/, optim/ |
| 101 |
|
o Updated verification/carbon/ |
| 102 |
|
- #define GM_VISBECK_VARIABLE_K |
| 103 |
|
- GM_taper_scheme = 'ldd97' |
| 104 |
|
|
| 105 |
|
checkpoint46n_post |
| 106 |
|
Merging from release1_p8: |
| 107 |
|
o verification/natl_box: |
| 108 |
|
updating new external_fields_load routine |
| 109 |
|
o New package: pkg/seaice |
| 110 |
|
Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle). |
| 111 |
|
The sea-ice code is based on Hibler (1979-1980). |
| 112 |
|
Two sea-ice dynamic solvers, ADI and LSR, are included. |
| 113 |
|
In addition to computing prognostic sea-ice variables and diagnosing |
| 114 |
|
the forcing/external data fields that drive the ocean model, |
| 115 |
|
SEAICE_MODEL also sets theta to the freezing point under sea-ice. |
| 116 |
|
The implied surface heat flux is then stored in variable |
| 117 |
|
surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and |
| 118 |
|
kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the |
| 119 |
|
non-local transport term. Because this call precedes model |
| 120 |
|
thermodynamics, temperature under sea-ice may not be "exactly" at |
| 121 |
|
the freezing point by the time theta is dumped or time-averaged. |
| 122 |
|
N.B.: fairly large differences in accuracy occur across |
| 123 |
|
different platforms/compilers; comparison between |
| 124 |
|
g77 (Linux) and F77 (SGI Origin 2000/MIPSpro) |
| 125 |
|
generated output gives: |
| 126 |
|
T S U V |
| 127 |
|
C D M c m s m s m s m s |
| 128 |
|
n p a R g m m e . m m e . m m e . m m e . |
| 129 |
|
f n k u 2 i a a d i a a d i a a d i a a d |
| 130 |
|
g d e n d n x n . n x n . n x n . n x n . |
| 131 |
|
|
| 132 |
|
Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea |
| 133 |
|
o GAD: |
| 134 |
|
- generated new common blocks to account for call of |
| 135 |
|
same gad routines with differing traceridentities |
| 136 |
|
(needed to modify tracerIdentity indices in GAD.h) |
| 137 |
|
- generated separate common blocks for case useCubedSphereExchange |
| 138 |
|
(Department of Futurology) |
| 139 |
|
- parameter lists to gmredi_?transport: added tracerIdentity |
| 140 |
|
- added new key indices to tamc.h |
| 141 |
|
o external_fields_load: |
| 142 |
|
- added this routine to TAF list |
| 143 |
|
- needed to make some common blocks global and additional storing |
| 144 |
|
along the same lines as exf package (checkpoint_lev?_directives.h) |
| 145 |
o exf: |
o exf: |
| 146 |
updated external forcing package |
updated external forcing package |
| 147 |
- cleaned old exfa stuff |
- bug fixes carried over from ecco-branch |
|
- bug fixes |
|
| 148 |
(missing OBCS_OPTIONS.h in two routines) |
(missing OBCS_OPTIONS.h in two routines) |
| 149 |
- enable easy to use "no forcing". |
- enable easy to use "no forcing". |
| 150 |
- added exf I/O for atmospheric loading |
- added exf I/O for atmospheric loading |
| 151 |
- added exf I/O for runoff data |
- added exf I/O for runoff data |
| 152 |
- transfered scaling between exf <-> MITgcm to exf namelist |
- transfered scaling between exf <-> MITgcm to exf namelist |
| 153 |
|
o Adding new verification experiment global_with_exf. |
| 154 |
ecco_c44_e24 |
This verification experiment is almost identical to the |
| 155 |
|
global_ocean.90x40x15 experiment, except that it uses |
| 156 |
|
the exf (and cal) package instead of the |
| 157 |
|
external_fields_load routine (cf README file). |
| 158 |
|
|
| 159 |
|
checkpoint46m_post |
| 160 |
|
o modified testscript to return -- when there are no lines of "%MON" output |
| 161 |
|
o added new flag "quasiHydrostatic" for QH mode |
| 162 |
|
and new routine quasihydrostaticterms() |
| 163 |
|
o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term) |
| 164 |
|
New routine: mom_u_coriolis_nh() |
| 165 |
|
o fixed sign of non-hydrostatic metric terms in u and v equations. |
| 166 |
|
Depend on correct sign of gravitySign. |
| 167 |
|
o added work.pc* to .cvsignore in aim directories using ifc |
| 168 |
|
o introduced flag for controllin non-hydrostatic metric terms |
| 169 |
|
o removed gravitySign from PARM04 |
| 170 |
|
o switched to g77/ifc from pgf77 in aim experiments |
| 171 |
|
|
| 172 |
|
checkpoint46l_post |
| 173 |
|
o made convective adjustment work with pressure coordinates: |
| 174 |
|
- changed the direction of k-loop in convective_adjustment.F for the |
| 175 |
|
case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation) |
| 176 |
|
- adjusted the reference pressure k-index in convective_adjustment.F |
| 177 |
|
- adjusted the convection condition in convect.F (in analogy to |
| 178 |
|
calc_ivdc.F) |
| 179 |
|
- convective_adjustment no longer computes anything on the halos |
| 180 |
|
- removed the warnings about negative salinity from find_rho.F and |
| 181 |
|
find_alpha.F; instead the new routine look_for_neg_salinity, called |
| 182 |
|
at the beginning of find_rho, find_alpha, and find_beta, does a |
| 183 |
|
check of the entire slice, if CPP-option |
| 184 |
|
CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined |
| 185 |
|
checkpoint46l_pre |
| 186 |
|
|
| 187 |
|
checkpoint46k_post |
| 188 |
|
o fixed the verification/global_ocean.90x40x15 experiment: |
| 189 |
|
- new bathymetry (the world according to A., JMC, and M.) |
| 190 |
|
- new initial fields and forcing fields (*.bin files) |
| 191 |
|
- new POLY3.COEFFS (for the next release one should switch to a full |
| 192 |
|
equation of state: JMD95P or MDJWF) |
| 193 |
|
- fixed several errors and redundancies in the data file |
| 194 |
|
- experiment uses looped cells |
| 195 |
|
- added matlab directory with diagnostic scripts for plotting of output |
| 196 |
|
|
| 197 |
|
o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F: |
| 198 |
|
- read AIM physics parameters from a file (data.aimphys) |
| 199 |
|
- set defaults values = F.Molteni paper (Clim.Dyn., 2002) |
| 200 |
|
|
| 201 |
|
checkpoint46j_post |
| 202 |
|
o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH |
| 203 |
|
o move wVel computation at the end of the time step, in S/R integr_continuity |
| 204 |
|
o create specific S/R to exchange T,S before DYNAMICS (for stagger time step) |
| 205 |
|
o update timeave pkg for wVel diagnostic. |
| 206 |
|
checkpoint46j_pre |
| 207 |
|
|
| 208 |
|
checkpoint46i_post |
| 209 |
|
o Clean up AIM package (and keep the results unchanged): |
| 210 |
|
include CPP_OPTION and use IMPLICT NONE in all routines ; |
| 211 |
|
declare all the variables _RL ; use _d 0 for all numerical constants. |
| 212 |
|
use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 ! |
| 213 |
|
|
| 214 |
|
checkpoint46h_post |
| 215 |
|
o cleaned up the use of rhoNil and rhoConst. |
| 216 |
|
- rhoNil should only appear in the LINEAR equation of state, everywhere |
| 217 |
|
else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst |
| 218 |
|
and the dynamical equations are all divided by rhoConst |
| 219 |
|
o introduced new parameter rhoConstFresh, a reference density of fresh |
| 220 |
|
water, to remove the fresh water flux's dependence on rhoNil. The default |
| 221 |
|
value is 999.8 kg/m^3 |
| 222 |
|
o cleanup up external_forcing.F and external_forcing_surf.F |
| 223 |
|
- can now be used by both OCEANIC and OCEANICP |
| 224 |
|
checkpoint46h_pre |
| 225 |
|
|
| 226 |
|
Added code to convert surface volume flux (fresh water) into |
| 227 |
|
a mass flux when using P coordinates in the ocean (OCEANICP). |
| 228 |
|
Note: It assumes you have set rho0=rhoConst=density of fresh water. |
| 229 |
|
|
| 230 |
|
checkpoint46g_post |
| 231 |
|
o Include a new diagnostic variable phiHydLow for the ocean model |
| 232 |
|
- in z-coordinates, it is the bottom pressure anomaly |
| 233 |
|
- in p-coordinates, it is the sea surface elevation |
| 234 |
|
- in both cases, these variable have global drift, reflecting the mass |
| 235 |
|
drift in z-coordinates and the volume drift in p-coordinates |
| 236 |
|
- included time averaging for phiHydLow, be aware of the drift! |
| 237 |
|
o depth-dependent computation of Bo_surf for pressure coordinates |
| 238 |
|
in the ocean (buoyancyRelation='OCEANICP') |
| 239 |
|
- requires a new routine (FIND_RHO_SCALAR) to compute density with only |
| 240 |
|
Theta, Salinity, and Pressure in the parameter list. This routine is |
| 241 |
|
presently contained in find_rho.F. This routine does not give the |
| 242 |
|
correct density for 'POLY3', which would be a z-dependent reference |
| 243 |
|
density. |
| 244 |
|
o cleaned up find_rho |
| 245 |
|
- removed obsolete 'eqn' from the parameter list. |
| 246 |
|
o added two new verification experiments: gop and goz |
| 247 |
|
(4x4 degree global ocean, 15 layers in pressure and height coordinates) |
| 248 |
|
checkpoint46g_pre |
| 249 |
|
|
| 250 |
|
checkpoint46f_post |
| 251 |
|
o Enable tangent linear (forward mode) gradient checks: |
| 252 |
|
- extended active file handling to g_... files |
| 253 |
|
- added TANGENT_SIMULATION to theSimulationMode |
| 254 |
|
- extended grdchk package accordingly |
| 255 |
|
o added tangent linear setup in verification/carbon/code_ftl |
| 256 |
|
o added adjoint setup in verification/front_relax/code_ad |
| 257 |
|
|
| 258 |
|
checkpoint46e_post |
| 259 |
|
o Added new equation of state -> MDJWF |
| 260 |
|
- EOS of McDougall et al., 2002, JAOT, submitted |
| 261 |
|
- caveat: the equation of state is only valid for a smaller (more |
| 262 |
|
realistic?) range of values than JMD95P/Z and UNESCO |
| 263 |
|
- added masks to the calculation of pressure in store_pressure |
| 264 |
|
- added more check values for density in check_eos (ini_eos.F), some of |
| 265 |
|
the old check values are out of the range of the MDJWF-eos, so don't |
| 266 |
|
expect perfect matches for those |
| 267 |
|
checkpoint46e_pre |
| 268 |
|
|
| 269 |
|
checkpoint46d_post |
| 270 |
|
o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and |
| 271 |
|
'OCEANICP', also initialised field pressure correctly in ini_eos in the |
| 272 |
|
case of pressure coordinates. eosType='JMD95Z' in |
| 273 |
|
combination with buoyancyRelation='OCEANICP' now causes an error. |
| 274 |
|
o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
| 275 |
|
in find_alpha/beta. |
| 276 |
|
checkpoint46d_pre |
| 277 |
|
|
| 278 |
|
o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
| 279 |
|
so that JMD95Z and JMD95P give approptiate static stability in find_rho. |
| 280 |
|
|
| 281 |
|
checkpoint46c_post |
| 282 |
|
o Changes necessary for ocean in p-coordinates |
| 283 |
|
- Added new buoyancy relation = 'OCEANICP' |
| 284 |
|
- Added new parameters = gravitySign (this used to be contained inside |
| 285 |
|
the factor dRdZ which I added when we first switched to R coordinates). |
| 286 |
|
X GM/Redi is not compatible (yet) |
| 287 |
|
X bottom drag and no-slip need to be debugged. |
| 288 |
|
checkpoint46c_pre |
| 289 |
|
|
| 290 |
|
checkpoint46b_post |
| 291 |
|
o Added new equation of state -> JMD95Z and JMD95P |
| 292 |
|
- EOS of Jackett and McDougall, 1995, JAOT |
| 293 |
|
- moved all EOS parameters into EOS.h |
| 294 |
|
- new routines ini_eos.F, store_pressure.F |
| 295 |
|
o Added UNESCO EOS, but not recommended because it requires |
| 296 |
|
in-situ temperature (see JMD95) |
| 297 |
|
o Modified formatting for knudsen2.f in utils/knudsen2 and added |
| 298 |
|
unesco.f to be used with POLY3 |
| 299 |
|
checkpoint46b_pre |
| 300 |
|
|
| 301 |
|
checkpoint46a_post |
| 302 |
|
o Added (atmospheric) pressure loading |
| 303 |
|
- new field in FFIELDS.h, etc... |
| 304 |
|
- new cpp flag ATMOSPHERIC_LOADING |
| 305 |
|
o Changed hFacC to _hFacC in calc_phi_hyd.F |
| 306 |
|
o Added SHORTWAVE_HEATING to some files for consistency |
| 307 |
|
checkpoint46a_pre |
| 308 |
|
|
| 309 |
|
checkpoint46 |
| 310 |
|
further merges from release1_p5 |
| 311 |
|
o new ctrl package |
| 312 |
|
- adopted from ECCO environment to enable optimization |
| 313 |
|
- added Eliassen Palm fluxes to controls |
| 314 |
|
o added Eliassen Palm flux controls to gradient check package |
| 315 |
|
o cost package |
| 316 |
|
- Compatible with new ctrl package |
| 317 |
|
- added Eliassen Palm cost hooks |
| 318 |
|
- modif's of existing cost functions |
| 319 |
|
o Adjoint-related bug fixes in kpp: |
| 320 |
|
- kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix |
| 321 |
|
- kpp_routines: store of Rib avoids partial recomputation bug of TAF. |
| 322 |
|
o autodiff package |
| 323 |
|
- flow directives: |
| 324 |
|
+ new for S/R do_the_model_io |
| 325 |
|
+ enhanced for S/R checkpoint |
| 326 |
|
+ new gmredi.flow |
| 327 |
|
- Introduced CPP option ALLOW_AUTODIFF_MONITOR to |
| 328 |
|
disable adcommon.h/g_common.h by default. |
| 329 |
|
- fixed problem for adjoint of global_max |
| 330 |
|
o modified verification/carbon/ |
| 331 |
|
o New setup for adjoint of global_ocean |
| 332 |
|
o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F) |
| 333 |
|
o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F) |
| 334 |
|
o incorporated hooks for sponge layer code (external_forcing.F) |
| 335 |
|
|
| 336 |
|
checkpoint45d_post |
| 337 |
|
o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F) |
| 338 |
|
o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S |
| 339 |
|
(affects plume_on_slope "cg2d" output) |
| 340 |
|
o add new parameter deltaTfreesurf for free-surface time stepping |
| 341 |
|
o exchange gT,gS when using staggerTimeStep & GM & Oly<4 |
| 342 |
|
o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B |
| 343 |
|
o change phiMin in exp1 (to agree with documentation) |
| 344 |
|
o add new flags: |
| 345 |
|
- T,S forcing inside/outside Adams-Bashforth |
| 346 |
|
- turn off temp,salt advection and/or forcing |
| 347 |
|
- for each tracer, define internal flag for multiDimAdvection & A-B |
| 348 |
|
o monitor: change definition of KE to check conservation of Energy |
| 349 |
|
|
| 350 |
|
checkpoint45c_post |
| 351 |
|
o Removed f90 comments ("!") |
| 352 |
|
o Modified initialisations to enable exf package for MITgcm |
| 353 |
|
(without invoking ECCO_PACKAGE). |
| 354 |
o modifications to gradient check package (Martin Losch) |
o modifications to gradient check package (Martin Losch) |
| 355 |
- enable centered differences |
- enable centered differences |
| 356 |
- modified format of standard output |
- modified format of standard output |
| 357 |
o bug fix for nwettile contents |
|
| 358 |
so far assumed global sum in first entry (1,1,k), |
checkpoint45b_post |
| 359 |
needed for global control vector |
o cleaned exchange calls in cg2d |
| 360 |
-> introduced new variable nwet[c/w/s]global(nr) |
o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step |
| 361 |
o shifts of calls to cal/exf package to be accessible |
o included CPP option SINGLE_LAYER_MODE in thermodynamics |
| 362 |
in MITgcm stand-alone |
to configure barotropic setup (Martin Losch) |
| 363 |
o shifted packages_init_variables before convective_adjustment_ini |
o moved some initialisations within bi,bj loop in dynamics |
| 364 |
(corresponding update of TAF tape initialisation). |
(TAF flow dependency) |
| 365 |
o removed auxiliary field in impldiff |
o in initialise_varia, moved call packages_init_variables |
| 366 |
(caused numerical differences for GMRedi cases) |
before convective_adjustment_init |
| 367 |
o updated obcs control part (G. Gebbie) |
(corresponding adjustment of TAF tape initialisation). |
| 368 |
o removed some f90 comments ("!") |
o in calc_diffusivity/calc_viscosity extended domain to full overlap. |
| 369 |
o Bug fixes and updates in cost package |
|
| 370 |
* cost_final: correct multiplier mult_tauv, mult_sflux |
checkpoint45a_post |
| 371 |
* cost_hyd: added call cost_ssh |
o compute Rho over the whole domain (extend iMin,jMin indices) |
| 372 |
* cost_init_barfiles.F: replaced arrays by tmpfld's |
o specific exchange for X-slice domain (case Ny=1) |
| 373 |
* cost_readtopexmean.F: ersmask -> tpmeanmask |
o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code |
| 374 |
* cost_weights.F: corrected wtheta[2], wsalt[2] |
o solve_for_pressure : set cg2d_x to zero where OBCS are applied |
| 375 |
o cleaned exchanges in cg2d.F |
|
| 376 |
|
checkpoint44h_post = checkpoint45 |
| 377 |
ecco_c44_e23 |
o Fix to restore differentiability: |
| 378 |
merged patches between release1_p1 and release1_p2: |
place at which packages_init_variables is called in |
| 379 |
o fixed array boundary problem for adjoint |
initialise_varia is crucial for reverse control flow. |
| 380 |
(related to partial recomputation within subroutine |
o modifications in GMRedi to enable stable adjoint |
| 381 |
related to dynamics -> calc_viscosity -> mom_... |
(corresponding modif's in thermodynamics, dynamics) |
| 382 |
o fixed recomputation in thermodynamics |
o added missing hook for sponge layer code in external_forcing |
| 383 |
o prepare (but not complete) recomputation problem in impldiff |
o modified test cost functions |
| 384 |
o fixed problem for adjoint of global_max |
o storing in gad_advection (plus removal of write(0,*)! |
| 385 |
o switched off sponge layer code in external_forcing |
o missing headers TR1.h added in convective_adjustment routines |
| 386 |
Bug fix in ctrl_mask_set_yz (spotted by G. Gebbie) |
o errorMessageUnit set non-equal zero in eeboot |
| 387 |
|
(conflict on some platforms, e.g. IBM SP3) |
| 388 |
ecco_c44_e22 |
o modified carbon verif. |
| 389 |
o Finally, the merges with the Scripps cost function terms: |
|
| 390 |
Various additions, modifications, quality checks. |
checkpoint44h_pre |
| 391 |
o Plus: Included switch ALLOW_AUTODIFF_MONITOR to handle |
o vertical grid option: allow to put the Interface at the middle between |
| 392 |
monitoring of adjoint state. |
2 cell-centers ; replace delZ in pkg/kpp by drF. |
| 393 |
o Plus: removed comm_stats, ini_communication_patterns from diff. list |
o GM Advective form: Tracers are advected using the residual transport (= |
| 394 |
(no more need to "keep" MPI headers for adjoint generation) |
Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form. |
| 395 |
o Plus: exf changes: |
|
| 396 |
o added run-off routine |
checkpoint44g_post |
| 397 |
o additional storing needed for ustress,vstess |
o fix surface correction term in multiDimAdvection (affects plume_on_slope |
| 398 |
because of state-dependent quality check |
results) ; ifdef missing in thermodynamics.F |
| 399 |
o added missing initialisations |
|
| 400 |
o Plus: genmake with MAKEDEPEND variable was still missing in ecco-branch |
checkpoint44f_pre,checkpoint44f_post |
| 401 |
NB: - verification/natl_box_adjoint/ 240 steps run |
o added PTRACERS package |
| 402 |
* looks ok under Linux (twain.lcs.mit.edu) |
This allows an arbitrary number of passive tracers to be integrated |
| 403 |
* looks ok on MIT SUN's (fjord.mit.edu) |
forward simultaneously with the dynamicaly model. |
| 404 |
* NaN in reverse mode on Scripps SUN's at iter=214 |
+ Implemented so far: |
| 405 |
* NaN in reverse mode on IBM SP3 (BlueHorizon) at iter=204 |
- basic forward algorithm (time-stepping, advection, diffusion, convection) |
| 406 |
- 1 year forward int. global 2x2 deg. produces similar cost functions |
- I/O and checkpointing |
| 407 |
* all cost terms of new code are slightly smaller (0.5 to 3%). |
- GM/Redi *but* using the GM/Redi coefficient of Salt |
| 408 |
|
+ Not implemented so far: |
| 409 |
ecco_c44_e21 |
- KPP |
| 410 |
o reversed order of ctrl/cost initialisation |
- OBCS |
| 411 |
o gmredi_slope_psi.F: Inconsistent types in MIN/MAX expressions |
+ No specific example supplied (yet) but global_ocean.90x40x15 has the |
| 412 |
o modified to enable ctrl field swapping |
necessary data.ptracer file. Simply use -enable=ptracers and uncomment |
| 413 |
o bug fix for global sum of ncvarlength in ctrl_init |
line in data.pkg. |
| 414 |
o no more call to ctrl_unpack from ctrl_init |
+ This package is disabled by default since it increases storage. |
| 415 |
o no more write of ctrl vector in ctrl_pack |
|
| 416 |
however, init. of control vector from ctrl_unpack |
|
| 417 |
o various bug fixes & consistent nobcs handling in |
o testscript: added -cleanup option |
| 418 |
ctrl_pack/unpack routines (by G. Gebbie) |
o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter |
| 419 |
o optim package: Added obcs control part for lsopt I/O |
b) enable to filter 2D fields. |
| 420 |
(by G. Gebbie) |
|
| 421 |
o missing call to obcs_diags |
checkpoint44e_pre,post |
| 422 |
o moved calls in packages_init_fixed to packages_readparms |
o re-wrote convective adjustment to use pre-calculated weights |
| 423 |
because some quantities are needed earlier. |
Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F |
| 424 |
|
Adds: model/src/convective_weights.F, convectively_mixtracer.F |
| 425 |
ecco_c44_e20 |
Original calls to convect() still in place. |
| 426 |
o before major merges from the Scripps setup |
|
| 427 |
here are two small updates: |
chkpt44d_pre,post |
| 428 |
- field swapping for surface flux controls enabled |
o added missing EXCLUDE_MONITOR flags |
| 429 |
(remains t.b.d. for atmos. state plus obcs) |
o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi |
| 430 |
- bug fix in active_file.F for xz-/yz- routines |
(incompatible typ in MIN/MAX expressions caused problems |
| 431 |
- added missing xz-/yz- routines to active_file_ad.F |
on IBM SP3) |
| 432 |
|
o in genmake added variable MAKEDEPEND |
| 433 |
ecco_c44_e19 |
plus resetting for case SunOS |
| 434 |
o merged necessary patches: |
o added timer_stats.c routine for IBM SP3 |
| 435 |
- AD-related changes for GMRedi |
o removed variables in dynamics |
| 436 |
- fixes i KPP (delZ -> drF) |
!!! I forgot to create tag chkpt44d_pre !!! |
| 437 |
- hook to OBCS songe layer code in external_forcing |
!!! But chkpt44d_pre = chkpt44c_post !!! |
| 438 |
- errorMessageUnit non-zero in eeboot.F |
|
| 439 |
- included GMREDI, EXACT_CONSERV to natl_box_adjoint verif. |
o real fresh water flux implemented with non-linear free-surface. |
| 440 |
|
|
| 441 |
ecco_c44_e18 |
chkpt44c_pre,post |
| 442 |
o sponge layer code for obcs was missing |
o few fix (mask in shap_s2, EmPmR in external_field_load, |
| 443 |
- added hook in external_forcing.F |
USE_NATURAL_BCS in solve_for_P); |
| 444 |
- added storing for TAF |
o add arguments myIter & myTime to S/R obcs_calc & solve_for_P |
| 445 |
o new routine cost_init_barfiles to initialise |
|
| 446 |
adjoint fields adtbar, adsbar, adpsbar |
checkpoint44b_pre/_post |
| 447 |
(needed in conjunction with corrected ladinit for active I/O) |
o merge of relevant stuff from the ecco-branch: |
|
o cleaned up and corrected order in packages_readparms, ecco_readparms |
|
|
o corrected and simplified weights for obcs controls |
|
|
- weight fields simplified |
|
|
- bug fix in ctrl_pack |
|
|
- no more write of control vector in ctrl_pack |
|
|
o i/j index bug fixes in cost_ssh_mean |
|
|
|
|
|
ecco_c44_e17 |
|
|
o bug fixes in cost package |
|
|
* wrong identifier for active I/O of monthly mean psbar |
|
|
(cost_averagesfields, cost_ssh) xx_psbar_dummy |
|
|
* cleaned all identifier for active I/O of monthly fields |
|
|
* wrong ladinit in various cost routines |
|
|
o merge with interval (chkpt44c_post - chkpt44d_post) |
|
|
* added missing EXCLUDE_MONITOR flags |
|
|
* changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi |
|
|
(incompatible typ in MIN/MAX expressions caused problems |
|
|
on IBM SP3) |
|
|
* in genmake added variable MAKEDEPEND |
|
|
plus resetting for case SunOS |
|
|
added timer_stats.c routine for IBM SP3 |
|
|
* removed variables in dynamics |
|
|
|
|
|
ecco_c44_e16 |
|
|
o new ECCO checkpoint, the first since ecco_c43_e15 |
|
|
which is branched from MITgcm. |
|
|
All changes were merged in between (see ecco-branch-mod? tags). |
|
|
o last changes: |
|
|
* assuming path for TAF and TAMC are known (e.g. in $path) |
|
|
* genmake: |
|
|
- added tools/xmakedepend to circumvene shortcoming of |
|
|
SUN's makedepend (size too small) |
|
|
- invoking ../tools/xmakedepend instead of makedepend |
|
|
- changed compiler flags for case SunOS |
|
|
|
|
|
ecco-branch-mod5 |
|
|
o mod's to reproduce open boundary run |
|
|
o enable field swapping for OB's and climatology |
|
|
o update store directives for OB control |
|
|
o added option ALLOW_OBCS_PRESCRIBE |
|
|
o call of getobcs now out of obcs_calc (param. list modified) |
|
|
|
|
|
ecco-branch-mod4 |
|
|
o this is the second part of changes necessary to reconcile |
|
|
the natl_box_adjoint verification (with and without grdchk). |
|
|
>>>!!! CHANGES BETWEEN THE TAGS ecco-branch-mod3 !!!<<< |
|
|
>>>!!! AND ecco-branch-mod4 !!!<<< |
|
|
>>>!!! SHOULD BE MERGED INTO THE MAIN TRUNK !!!<<< |
|
| 448 |
- genmake: removed $S64 overwrite for case SunOS |
- genmake: removed $S64 overwrite for case SunOS |
| 449 |
- pkg/exf: update and corrections for field swapping and obcs |
- pkg/exf: update and corrections for field swapping and obcs |
| 450 |
- pkg/ecco: parameter lists for the_model_main, the_main_loop |
- pkg/ecco: parameter lists for the_model_main, the_main_loop |
| 452 |
- pkg/autodiff: added flow directives for obcs, mdsio_gl_slice |
- pkg/autodiff: added flow directives for obcs, mdsio_gl_slice |
| 453 |
updated checkpointing_lev... lists for obcs |
updated checkpointing_lev... lists for obcs |
| 454 |
- model/src: minor changes in forward_step, plot_field |
- model/src: minor changes in forward_step, plot_field |
| 455 |
|
added directive for divided adjoint in the_main_loop |
| 456 |
- pkg/mdsio: added mdsio_gl_slice |
- pkg/mdsio: added mdsio_gl_slice |
| 457 |
|
|
| 458 |
ecco-branch-mod3 |
o check parameters & config (chkpt44a_pre,post) |
| 459 |
o this is the first part of changes necessary to reconcile |
o OBC and NonLin_FrSurf. |
|
natl_box_adjoint verification (with and without grdchk). |
|
|
This set of changes is relevant for ECCO only. |
|
|
The next set/tag of changes (ecco-branch-mod4) |
|
|
should be merged into the main trunk. |
|
|
- update some options |
|
|
- parameter lists of ecco_the_model_main and ecco_the_main_loop |
|
|
differed from those of the MITgcm counterparts. |
|
|
|
|
|
ecco-branch-mod2 |
|
|
o update ecco-branch-mod1 to checkpoint44 |
|
|
o exclude from updates: |
|
|
- verification/ |
|
|
- adjoint/ |
|
|
- pkg/cost |
|
|
- pkg/ctrl |
|
|
- pkg/ecco |
|
|
- pkg/obcs |
|
|
- model/src/the_model_main.F |
|
|
- model/src/the_main_loop.F |
|
| 460 |
|
|
| 461 |
checkpoint44 |
checkpoint44 |
|
o apply Shapiro filter on T&S before calc_PhiHyd (stagger time stepping) |
|
| 462 |
o fix bug in mom_vi_del2uv |
o fix bug in mom_vi_del2uv |
| 463 |
|
o select when filters are applied ; add options to zonal_filter (data.zonfilt) |
| 464 |
|
o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection) |
| 465 |
|
o update AIM experiments (NCEP input files) |
| 466 |
|
o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf) |
| 467 |
o added some stuff for AD |
o added some stuff for AD |
| 468 |
|
|
|
ecco-branch-mod1 |
|
|
o based on c43 |
|
|
o replaced packages cost, ctrl, ecco, obcs |
|
|
o removed MITgcm verif.'s, added ECCO verif.'s |
|
|
o added lsopt, optim for line search optimization. |
|
|
|
|
| 469 |
checkpoint43 |
checkpoint43 |
| 470 |
o added two new advection tests |
o added two new advection tests |
| 471 |
o added global 4x4 degree ocean test |
o added global 4x4 degree ocean test |
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