| 3 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 4 |
============================== |
============================== |
| 5 |
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| 6 |
ecco_c51_e34f |
checkpoint44g_post |
| 7 |
o added case gfdl-sgi-o3k to genmake |
o fix surface correction term in multiDimAdvection (affects plume_on_slope |
| 8 |
o added genmake option -arpack and provided default lib dir |
results) ; ifdef missing in thermodynamics.F |
| 9 |
o exf_mapfields: |
|
| 10 |
Interpolate ustress,vstress computed via exf bulk formulae |
checkpoint44f_pre,checkpoint44f_post |
| 11 |
to W/S points. Assume |
o added PTRACERS package |
| 12 |
on input: uwind,vwind on C-points |
This allows an arbitrary number of passive tracers to be integrated |
| 13 |
on output: ustress[C],vstress[C] -> fu[W],fv[S] |
forward simultaneously with the dynamicaly model. |
| 14 |
o Very prelim. preparations for forward dump&restart |
+ Implemented so far: |
| 15 |
during adjoint calculation. |
- basic forward algorithm (time-stepping, advection, diffusion, convection) |
| 16 |
|
- I/O and checkpointing |
| 17 |
ecco_C51_e34e |
- GM/Redi *but* using the GM/Redi coefficient of Salt |
| 18 |
o bug fix in cost_drifter |
+ Not implemented so far: |
| 19 |
o updating timeave package in ecco-branch to c51 |
- KPP |
| 20 |
|
- OBCS |
| 21 |
ecco_c51_e34d |
+ No specific example supplied (yet) but global_ocean.90x40x15 has the |
| 22 |
o modif's to restore TAMC compatibility |
necessary data.ptracer file. Simply use -enable=ptracers and uncomment |
| 23 |
- avoid "_d" constructs in PARAMETER declarations |
line in data.pkg. |
| 24 |
- avoid interrupting lines by comment lines |
+ This package is disabled by default since it increases storage. |
| 25 |
o Use cluster local disks for purely local I/O |
|
| 26 |
vs. globally visible disks needed for ctrl stuff |
|
| 27 |
- new active_file_loc... and mdsio_..._loc routines |
o testscript: added -cleanup option |
| 28 |
- affected packages: autodiff, ctrl, grdchk, mdsio |
o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter |
| 29 |
o bug fixes for 3d packing and I/O of sliced (xz/yz) fields |
b) enable to filter 2D fields. |
| 30 |
to increase I/O performance. |
|
| 31 |
|
checkpoint44e_pre,post |
| 32 |
ecco_c51_e34c |
o re-wrote convective adjustment to use pre-calculated weights |
| 33 |
o introducing integer flag debugLevel |
Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F |
| 34 |
- debLevZero: suppress all output |
Adds: model/src/convective_weights.F, convectively_mixtracer.F |
| 35 |
- debLevA: standard |
Original calls to convect() still in place. |
| 36 |
- debLevB: equivalent to current debugMode=.TRUE. |
|
| 37 |
o introducing pathname variable mdsioLocalDir for mdsio |
chkpt44d_pre,post |
| 38 |
that can be specified at runtime |
o added missing EXCLUDE_MONITOR flags |
| 39 |
(relevant for cluster I/O to local disk) |
o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi |
| 40 |
|
(incompatible typ in MIN/MAX expressions caused problems |
| 41 |
ecco_c51_e34b |
on IBM SP3) |
| 42 |
o Modifications of obcs |
o in genmake added variable MAKEDEPEND |
| 43 |
- bug fixes in cost package |
plus resetting for case SunOS |
| 44 |
- bug fixes in grdchk package |
o added timer_stats.c routine for IBM SP3 |
| 45 |
o new parameter maxKPPhbl in KPP |
o removed variables in dynamics |
| 46 |
o added input for obcs verification |
!!! I forgot to create tag chkpt44d_pre !!! |
| 47 |
|
!!! But chkpt44d_pre = chkpt44c_post !!! |
| 48 |
ecco_c51_e34a |
|
| 49 |
o Modifications to pkg/seaice, verification/lab_sea, and |
o real fresh water flux implemented with non-linear free-surface. |
| 50 |
verification/natl_box_adjoint for testing sea-ice adjoint code. |
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| 51 |
|
chkpt44c_pre,post |
| 52 |
ecco_c51_e34 |
o few fix (mask in shap_s2, EmPmR in external_field_load, |
| 53 |
o merging c51 into ecco-branch |
USE_NATURAL_BCS in solve_for_P); |
| 54 |
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o add arguments myIter & myTime to S/R obcs_calc & solve_for_P |
| 55 |
ecco_c50_e33a |
|
| 56 |
o first step in c51 merge |
checkpoint44b_pre/_post |
| 57 |
- redundant update in model/src/ |
o merge of relevant stuff from the ecco-branch: |
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- merge back's in autodiff, ctrl, kpp, seaice |
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ecco_c50_e33 |
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o minor changes to pkg/seaice pkg/cost/cost_ice.F |
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and verification/natl_box_adjoint/README |
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o Modif's to enable tangent linear run in ECCO environment |
|
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including time-dependent forcing |
|
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* main problem is missing call mdsreadfield out of exf_set_gen |
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(i.e. computation of trajectory in TLM mode) |
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* incorrect g_active_write_... |
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* (re-) init of bar files and g_bar files |
|
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o Reverted back to 3-dim. tbar, sbar for SST, SSS bar files. |
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o MERGES: |
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* obcs/ ctrl/ G. Gebbie code |
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(major changes in ctrl handling, volume flux balancing etc.) |
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* cost/ ctrl/ A. Koehl code |
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- new cost contributions (new data types) |
|
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- efficient pack/unpack for time-dependent 2-d fields |
|
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o replaced mutiple ctrl_get... by single generic ctrl_get_gen.F |
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(except obcs) |
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o somewhat cleaned package initialisation sequence for |
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ctrl/ cost/ ecco/ |
|
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o extended grdchk to enable obcs gradient checks |
|
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o some generalizations for easier TLM <-> ADM switches |
|
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o added configuration example for parallel divided adjoint |
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(see verification/natl_box_adjoint/code_diva_mpi/README ) |
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o started verification exp. for obcs control |
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(still needs checking) |
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ecco_c50_e32 |
|
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o Patrick's adjoint-model storage directives for pkg/seaice |
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o merged with checkpoint50g_post (pkg/seaice and verification/lab_sea) |
|
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- added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics |
|
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- LSR sea-ice dynamic solver moved to SouthWest B-grid location and |
|
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made the default because of faster convergence than ADI |
|
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o Modifications for adjoint of SEAICE_ALLOW_DYNAMICS |
|
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- extended state in checkpoint_lev... |
|
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- 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 |
|
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- 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 |
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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 |
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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. |
|
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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 |
|
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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 |
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ecco_c44_e27 |
|
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o exf: |
|
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- 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 |
|
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- exf_getffieldrec.F, ctrl_getrec.F |
|
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The following INT-usages are not safe: |
|
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fldsecs = int(fldsecs/fldperiod)*fldperiod |
|
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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 |
|
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- has both ADM and TLM checks |
|
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- works for single- and multi-proc. |
|
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- output cleaned |
|
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- worked successfully for parallel DIVA |
|
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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... |
|
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- updated storing for bulk formulae (some arrays were missing) |
|
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- added state for seaice package |
|
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- 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 |
|
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and added cost_final_restore.F cost_final_store.F |
|
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o With these changes, it is possible to fully separate |
|
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the first forward run to compute the cost function (mdthe_main_loop) |
|
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and adjoint runs over individual DIVA intervals (adthe_main_loop) |
|
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into separate model executions. |
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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 |
|
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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. |
|
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The current changes apply to TAF-1.4.26. |
|
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TAF has one remaining bug, requiring one manual change |
|
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(see MITgcm manual). |
|
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o bug fix plus modif for ubar, vbar in cost_averagesfields |
|
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o cal: synchronized between MAIN and ecco-branch |
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icebear4 |
|
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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 |
|
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o Reduced derivative singularities in pkg/seaice. |
|
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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 |
|
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o pkg/seaice |
|
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- added initial sea-ice thickness parameter SEAICE_initialHEFF |
|
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o updated verification/natl_box_adjoint |
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icebear2 |
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o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf, |
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kpp_transport_t.F,and ecco_the_main_loop.F |
|
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o adjoint-friendly modifications to pkg/seaice |
|
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o added verification/lab_sea as per release1_p12_pre |
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ecco_c44_e26 |
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o Merging pkg/exf and pkg/seaice from cvs tag ecco_ice2 |
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o exf: Modifications to correctly handle evap field for adjoint |
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o grdchk: |
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Added code to perform gradient checks for bulk formulae/atmos. state |
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(atemp, aqh, uwind, vwind). |
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NOTE: |
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This package is out of synch with c48 package. |
|
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The latter also has the tangent linear gradient checks. |
|
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Need to be merged. |
|
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o verification/natl_box_adjoint: |
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* added new setup: code_bulk/, input_bulk, results_bulk |
|
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(Experiment 2, described in README) |
|
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uses bulk formulae and atmos. state as control instead of |
|
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air-sea fluxes. |
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Performs gradient checks for first 4 elements of atemp control. |
|
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* changed standard verification to perform |
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gradient checks on first 4 elements on hflux control. |
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* gmredi switched off (will come after merge with c48). |
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ecco_c44_e25 |
|
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o Merging some GM changes from main trunk (c47) to ecco-branch. |
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o Updating verif. natl_box_adjoint with GMRedi. |
|
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o Adding setup with explicit differentiaton of pressure solver. |
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o Bug fix: missing OBCS_OPTIONS.h for sponge layer code. |
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o (Re-?) Commiting old bug fixes in kpp to ecco-branch |
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(kpp_calc.F, kpp_routines.F) |
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o exf: |
|
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updated external forcing package |
|
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- cleaned old exfa stuff |
|
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- bug fixes |
|
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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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ecco_c44_e24 |
|
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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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o bug fix for nwettile contents |
|
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so far assumed global sum in first entry (1,1,k), |
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needed for global control vector |
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-> introduced new variable nwet[c/w/s]global(nr) |
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o shifts of calls to cal/exf package to be accessible |
|
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in MITgcm stand-alone |
|
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o shifted packages_init_variables before convective_adjustment_ini |
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(corresponding update of TAF tape initialisation). |
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o removed auxiliary field in impldiff |
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(caused numerical differences for GMRedi cases) |
|
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o updated obcs control part (G. Gebbie) |
|
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o removed some f90 comments ("!") |
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o Bug fixes and updates in cost package |
|
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* cost_final: correct multiplier mult_tauv, mult_sflux |
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* cost_hyd: added call cost_ssh |
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* cost_init_barfiles.F: replaced arrays by tmpfld's |
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* cost_readtopexmean.F: ersmask -> tpmeanmask |
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* cost_weights.F: corrected wtheta[2], wsalt[2] |
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o cleaned exchanges in cg2d.F |
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ecco_c44_e23 |
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merged patches between release1_p1 and 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 |
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Bug fix in ctrl_mask_set_yz (spotted by G. Gebbie) |
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ecco_c44_e22 |
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o Finally, the merges with the Scripps cost function terms: |
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Various additions, modifications, quality checks. |
|
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o Plus: Included switch ALLOW_AUTODIFF_MONITOR to handle |
|
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monitoring of adjoint state. |
|
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o Plus: removed comm_stats, ini_communication_patterns from diff. list |
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(no more need to "keep" MPI headers for adjoint generation) |
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o Plus: exf changes: |
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o added run-off routine |
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o additional storing needed for ustress,vstess |
|
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because of state-dependent quality check |
|
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o added missing initialisations |
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o Plus: genmake with MAKEDEPEND variable was still missing in ecco-branch |
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NB: - verification/natl_box_adjoint/ 240 steps run |
|
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* looks ok under Linux (twain.lcs.mit.edu) |
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* looks ok on MIT SUN's (fjord.mit.edu) |
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* NaN in reverse mode on Scripps SUN's at iter=214 |
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* NaN in reverse mode on IBM SP3 (BlueHorizon) at iter=204 |
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- 1 year forward int. global 2x2 deg. produces similar cost functions |
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* all cost terms of new code are slightly smaller (0.5 to 3%). |
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ecco_c44_e21 |
|
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o reversed order of ctrl/cost initialisation |
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o gmredi_slope_psi.F: Inconsistent types in MIN/MAX expressions |
|
|
o modified to enable ctrl field swapping |
|
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o bug fix for global sum of ncvarlength in ctrl_init |
|
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o no more call to ctrl_unpack from ctrl_init |
|
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o no more write of ctrl vector in ctrl_pack |
|
|
however, init. of control vector from ctrl_unpack |
|
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o various bug fixes & consistent nobcs handling in |
|
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ctrl_pack/unpack routines (by G. Gebbie) |
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o optim package: Added obcs control part for lsopt I/O |
|
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(by G. Gebbie) |
|
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o missing call to obcs_diags |
|
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o moved calls in packages_init_fixed to packages_readparms |
|
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because some quantities are needed earlier. |
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ecco_c44_e20 |
|
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o before major merges from the Scripps setup |
|
|
here are two small updates: |
|
|
- field swapping for surface flux controls enabled |
|
|
(remains t.b.d. for atmos. state plus obcs) |
|
|
- bug fix in active_file.F for xz-/yz- routines |
|
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- added missing xz-/yz- routines to active_file_ad.F |
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ecco_c44_e19 |
|
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o merged necessary patches: |
|
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- AD-related changes for GMRedi |
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- fixes i KPP (delZ -> drF) |
|
|
- hook to OBCS songe layer code in external_forcing |
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- errorMessageUnit non-zero in eeboot.F |
|
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- included GMREDI, EXACT_CONSERV to natl_box_adjoint verif. |
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ecco_c44_e18 |
|
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o sponge layer code for obcs was missing |
|
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- added hook in external_forcing.F |
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- added storing for TAF |
|
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o new routine cost_init_barfiles to initialise |
|
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adjoint fields adtbar, adsbar, adpsbar |
|
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(needed in conjunction with corrected ladinit for active I/O) |
|
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o cleaned up and corrected order in packages_readparms, ecco_readparms |
|
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o corrected and simplified weights for obcs controls |
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- weight fields simplified |
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- bug fix in ctrl_pack |
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- no more write of control vector in ctrl_pack |
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o i/j index bug fixes in cost_ssh_mean |
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ecco_c44_e17 |
|
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o bug fixes in cost package |
|
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* wrong identifier for active I/O of monthly mean psbar |
|
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(cost_averagesfields, cost_ssh) xx_psbar_dummy |
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* cleaned all identifier for active I/O of monthly fields |
|
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* wrong ladinit in various cost routines |
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o merge with interval (chkpt44c_post - chkpt44d_post) |
|
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* added missing EXCLUDE_MONITOR flags |
|
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* 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 |
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ecco_c44_e16 |
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o new ECCO checkpoint, the first since ecco_c43_e15 |
|
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which is branched from MITgcm. |
|
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All changes were merged in between (see ecco-branch-mod? tags). |
|
|
o last changes: |
|
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* assuming path for TAF and TAMC are known (e.g. in $path) |
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* genmake: |
|
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- added tools/xmakedepend to circumvene shortcoming of |
|
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SUN's makedepend (size too small) |
|
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- invoking ../tools/xmakedepend instead of makedepend |
|
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- changed compiler flags for case SunOS |
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ecco-branch-mod5 |
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o mod's to reproduce open boundary run |
|
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o enable field swapping for OB's and climatology |
|
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o update store directives for OB control |
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o added option ALLOW_OBCS_PRESCRIBE |
|
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o call of getobcs now out of obcs_calc (param. list modified) |
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ecco-branch-mod4 |
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o this is the second part of changes necessary to reconcile |
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the natl_box_adjoint verification (with and without grdchk). |
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>>>!!! CHANGES BETWEEN THE TAGS ecco-branch-mod3 !!!<<< |
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>>>!!! AND ecco-branch-mod4 !!!<<< |
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>>>!!! SHOULD BE MERGED INTO THE MAIN TRUNK !!!<<< |
|
| 58 |
- genmake: removed $S64 overwrite for case SunOS |
- genmake: removed $S64 overwrite for case SunOS |
| 59 |
- pkg/exf: update and corrections for field swapping and obcs |
- pkg/exf: update and corrections for field swapping and obcs |
| 60 |
- pkg/ecco: parameter lists for the_model_main, the_main_loop |
- pkg/ecco: parameter lists for the_model_main, the_main_loop |
| 62 |
- pkg/autodiff: added flow directives for obcs, mdsio_gl_slice |
- pkg/autodiff: added flow directives for obcs, mdsio_gl_slice |
| 63 |
updated checkpointing_lev... lists for obcs |
updated checkpointing_lev... lists for obcs |
| 64 |
- model/src: minor changes in forward_step, plot_field |
- model/src: minor changes in forward_step, plot_field |
| 65 |
|
added directive for divided adjoint in the_main_loop |
| 66 |
- pkg/mdsio: added mdsio_gl_slice |
- pkg/mdsio: added mdsio_gl_slice |
| 67 |
|
|
| 68 |
ecco-branch-mod3 |
o check parameters & config (chkpt44a_pre,post) |
| 69 |
o this is the first part of changes necessary to reconcile |
o OBC and NonLin_FrSurf. |
|
natl_box_adjoint verification (with and without grdchk). |
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This set of changes is relevant for ECCO only. |
|
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The next set/tag of changes (ecco-branch-mod4) |
|
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should be merged into the main trunk. |
|
|
- update some options |
|
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- parameter lists of ecco_the_model_main and ecco_the_main_loop |
|
|
differed from those of the MITgcm counterparts. |
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|
|
|
|
ecco-branch-mod2 |
|
|
o update ecco-branch-mod1 to checkpoint44 |
|
|
o exclude from updates: |
|
|
- verification/ |
|
|
- adjoint/ |
|
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- pkg/cost |
|
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- pkg/ctrl |
|
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- pkg/ecco |
|
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- pkg/obcs |
|
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- model/src/the_model_main.F |
|
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- model/src/the_main_loop.F |
|
| 70 |
|
|
| 71 |
checkpoint44 |
checkpoint44 |
|
o apply Shapiro filter on T&S before calc_PhiHyd (stagger time stepping) |
|
| 72 |
o fix bug in mom_vi_del2uv |
o fix bug in mom_vi_del2uv |
| 73 |
|
o select when filters are applied ; add options to zonal_filter (data.zonfilt) |
| 74 |
|
o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection) |
| 75 |
|
o update AIM experiments (NCEP input files) |
| 76 |
|
o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf) |
| 77 |
o added some stuff for AD |
o added some stuff for AD |
| 78 |
|
|
|
ecco-branch-mod1 |
|
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o based on c43 |
|
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o replaced packages cost, ctrl, ecco, obcs |
|
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o removed MITgcm verif.'s, added ECCO verif.'s |
|
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o added lsopt, optim for line search optimization. |
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|
|
| 79 |
checkpoint43 |
checkpoint43 |
| 80 |
o added two new advection tests |
o added two new advection tests |
| 81 |
o added global 4x4 degree ocean test |
o added global 4x4 degree ocean test |
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