3 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
4 |
============================== |
============================== |
5 |
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6 |
release1_p17 |
o Added cost_ice for sea-ice volume sensitivity experiment. |
7 |
o added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics |
o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT |
8 |
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9 |
release1_p16 |
icebear3 |
10 |
o fixed gather/scatter inital MPI dialogue in ini_procs.F |
o Removed spurious iikey and idkey |
11 |
o pkg/seaice/lsr.F has been moved to SouthWest B-grid location |
o pkg/exf |
12 |
and has been made the default dynamic solver because of its |
- bug fix in treatment of downward radiation |
13 |
fast convergence properties relative to adi.F solver. |
o pkg/seaice |
14 |
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- added initial sea-ice thickness parameter SEAICE_initialHEFF |
15 |
release1_p15 |
o updated verification/natl_box_adjoint |
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o Added CFC-11 diagnostics, see |
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verification/global_with_CFC11/README |
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release1_p14 |
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o Added interpolation routine pkg/exf/new_interp.F for on-the-fly |
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interpolation. Enable with USE_EXF_INTERPOLATION and specify |
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input grids in data.exf |
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o Added direct pressure solver pkg/solver. |
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See pkg/solver/README.directSolver for instructions. |
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release1_p13 |
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o bug fix for pkg/seaice/adi.F dynamic solver |
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release1_p13_pre |
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o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F |
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o Added SEAICE_initialHEFF to pkg/seaice |
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o the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT |
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o Updated pkg/seaice and pkg/exf with adjoint modifications from icebear4 |
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16 |
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17 |
release1_p12 |
icebear2 |
18 |
o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf, |
o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf, |
19 |
kpp_transport_t.F, forward_step.F, and the_main_loop.F |
kpp_transport_t.F,and ecco_the_main_loop.F |
20 |
o pkg/seaice: |
o adjoint-friendly modifications to pkg/seaice |
21 |
- adjoint-friendly modifications |
o added verification/lab_sea as per release1_p12_pre |
22 |
- added a SEAICE_WRITE_PICKUP at end of the_model_main.F |
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23 |
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ecco_c44_e26 |
24 |
release1_p12_pre |
o Merging pkg/exf and pkg/seaice from cvs tag ecco_ice2 |
25 |
o Updated useSingleCpuIO option in mdsio_writefield.F to |
o exf: Modifications to correctly handle evap field for adjoint |
26 |
work with multi-field files, e.g., for single-file pickup. |
o grdchk: |
27 |
o pkg/seaice: |
Added code to perform gradient checks for bulk formulae/atmos. state |
28 |
- bug fix in growth.F: QNET for no shortwave case |
(atemp, aqh, uwind, vwind). |
29 |
- added HeffFile for specifying initial sea-ice thickness |
NOTE: |
30 |
- changed SEAICE_EXTERNAL_FLUXES wind stress implementation |
This package is out of synch with c48 package. |
31 |
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The latter also has the tangent linear gradient checks. |
32 |
release1_p11 |
Need to be merged. |
33 |
o Modifications for using pkg/exf with pkg/seaice |
o verification/natl_box_adjoint: |
34 |
- improved description of the various forcing configurations |
* added new setup: code_bulk/, input_bulk, results_bulk |
35 |
- added basic radiation bulk formulae to pkg/exf |
(Experiment 2, described in README) |
36 |
- units/sign fix for evap computation in exf_getffields.F |
uses bulk formulae and atmos. state as control instead of |
37 |
- updated verification/global_with_exf/results/output.txt |
air-sea fluxes. |
38 |
o Added pkg/sbo for computing IERS Special Bureau for the Oceans |
Performs gradient checks for first 4 elements of atemp control. |
39 |
(SBO) core products, including oceanic mass, center-of-mass, |
* changed standard verification to perform |
40 |
angular, and bottom pressure (see pkg/sbo/README.sbo). |
gradient checks on first 4 elements on hflux control. |
41 |
o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F |
* gmredi switched off (will come after merge with c48). |
42 |
to avoid negative values in shallow regions. |
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43 |
- updated verification/natl_box/results/output.txt |
ecco_c44_e25 |
44 |
- updated verification/lab_sea/results/output.txt |
o Merging some GM changes from main trunk (c47) to ecco-branch. |
45 |
o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F |
o Updating verif. natl_box_adjoint with GMRedi. |
46 |
o Added useSingleCpuIO option (see PARAMS.h). |
o Adding setup with explicit differentiaton of pressure solver. |
47 |
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o Bug fix: missing OBCS_OPTIONS.h for sponge layer code. |
48 |
release1_p10 |
o (Re-?) Commiting old bug fixes in kpp to ecco-branch |
49 |
o modifications for using pkg/exf with pkg/seaice |
(kpp_calc.F, kpp_routines.F) |
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- pkg/seaice CPP options SEAICE_EXTERNAL_FORCING |
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and SEAICE_EXTERNAL_FLUXES |
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- pkg/exf CPP options EXF_READ_EVAP and |
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EXF_NO_BULK_COMPUTATIONS |
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- usage examples are Experiments 8 and 9 in |
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verification/lab_sea/README |
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- verification/lab_sea default experiment now uses |
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pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf |
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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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50 |
o exf: |
o exf: |
51 |
updated external forcing package |
updated external forcing package |
52 |
- bug fixes carried over from ecco-branch |
- cleaned old exfa stuff |
53 |
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- bug fixes |
54 |
(missing OBCS_OPTIONS.h in two routines) |
(missing OBCS_OPTIONS.h in two routines) |
55 |
- enable easy to use "no forcing". |
- enable easy to use "no forcing". |
56 |
- added exf I/O for atmospheric loading |
- added exf I/O for atmospheric loading |
57 |
- added exf I/O for runoff data |
- added exf I/O for runoff data |
58 |
- transfered scaling between exf <-> MITgcm to exf namelist |
- transfered scaling between exf <-> MITgcm to exf namelist |
59 |
o Adding new verification experiment global_with_exf. |
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60 |
This verification experiment is almost identical to the |
ecco_c44_e24 |
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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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61 |
o modifications to gradient check package (Martin Losch) |
o modifications to gradient check package (Martin Losch) |
62 |
- enable centered differences |
- enable centered differences |
63 |
- modified format of standard output |
- modified format of standard output |
64 |
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o bug fix for nwettile contents |
65 |
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so far assumed global sum in first entry (1,1,k), |
66 |
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needed for global control vector |
67 |
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-> introduced new variable nwet[c/w/s]global(nr) |
68 |
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o shifts of calls to cal/exf package to be accessible |
69 |
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in MITgcm stand-alone |
70 |
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o shifted packages_init_variables before convective_adjustment_ini |
71 |
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(corresponding update of TAF tape initialisation). |
72 |
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o removed auxiliary field in impldiff |
73 |
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(caused numerical differences for GMRedi cases) |
74 |
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o updated obcs control part (G. Gebbie) |
75 |
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o removed some f90 comments ("!") |
76 |
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o Bug fixes and updates in cost package |
77 |
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* cost_final: correct multiplier mult_tauv, mult_sflux |
78 |
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* cost_hyd: added call cost_ssh |
79 |
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* cost_init_barfiles.F: replaced arrays by tmpfld's |
80 |
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* cost_readtopexmean.F: ersmask -> tpmeanmask |
81 |
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* cost_weights.F: corrected wtheta[2], wsalt[2] |
82 |
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o cleaned exchanges in cg2d.F |
83 |
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84 |
release1_p3 |
ecco_c44_e23 |
85 |
o added tangent linear setup to verification/carbon/ |
merged patches between release1_p1 and release1_p2: |
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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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86 |
o fixed array boundary problem for adjoint |
o fixed array boundary problem for adjoint |
87 |
(related to partial recomputation within subroutine |
(related to partial recomputation within subroutine |
88 |
related to dynamics -> calc_viscosity -> mom_... |
related to dynamics -> calc_viscosity -> mom_... |
90 |
o prepare (but not complete) recomputation problem in impldiff |
o prepare (but not complete) recomputation problem in impldiff |
91 |
o fixed problem for adjoint of global_max |
o fixed problem for adjoint of global_max |
92 |
o switched off sponge layer code in external_forcing |
o switched off sponge layer code in external_forcing |
93 |
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Bug fix in ctrl_mask_set_yz (spotted by G. Gebbie) |
94 |
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95 |
release1_p1 |
ecco_c44_e22 |
96 |
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o Finally, the merges with the Scripps cost function terms: |
97 |
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Various additions, modifications, quality checks. |
98 |
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o Plus: Included switch ALLOW_AUTODIFF_MONITOR to handle |
99 |
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monitoring of adjoint state. |
100 |
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o Plus: removed comm_stats, ini_communication_patterns from diff. list |
101 |
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(no more need to "keep" MPI headers for adjoint generation) |
102 |
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o Plus: exf changes: |
103 |
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o added run-off routine |
104 |
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o additional storing needed for ustress,vstess |
105 |
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because of state-dependent quality check |
106 |
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o added missing initialisations |
107 |
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o Plus: genmake with MAKEDEPEND variable was still missing in ecco-branch |
108 |
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NB: - verification/natl_box_adjoint/ 240 steps run |
109 |
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* looks ok under Linux (twain.lcs.mit.edu) |
110 |
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* looks ok on MIT SUN's (fjord.mit.edu) |
111 |
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* NaN in reverse mode on Scripps SUN's at iter=214 |
112 |
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* NaN in reverse mode on IBM SP3 (BlueHorizon) at iter=204 |
113 |
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- 1 year forward int. global 2x2 deg. produces similar cost functions |
114 |
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* all cost terms of new code are slightly smaller (0.5 to 3%). |
115 |
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116 |
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ecco_c44_e21 |
117 |
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o reversed order of ctrl/cost initialisation |
118 |
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o gmredi_slope_psi.F: Inconsistent types in MIN/MAX expressions |
119 |
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o modified to enable ctrl field swapping |
120 |
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o bug fix for global sum of ncvarlength in ctrl_init |
121 |
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o no more call to ctrl_unpack from ctrl_init |
122 |
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o no more write of ctrl vector in ctrl_pack |
123 |
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however, init. of control vector from ctrl_unpack |
124 |
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o various bug fixes & consistent nobcs handling in |
125 |
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ctrl_pack/unpack routines (by G. Gebbie) |
126 |
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o optim package: Added obcs control part for lsopt I/O |
127 |
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(by G. Gebbie) |
128 |
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o missing call to obcs_diags |
129 |
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o moved calls in packages_init_fixed to packages_readparms |
130 |
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because some quantities are needed earlier. |
131 |
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132 |
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ecco_c44_e20 |
133 |
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o before major merges from the Scripps setup |
134 |
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here are two small updates: |
135 |
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- field swapping for surface flux controls enabled |
136 |
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(remains t.b.d. for atmos. state plus obcs) |
137 |
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- bug fix in active_file.F for xz-/yz- routines |
138 |
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- added missing xz-/yz- routines to active_file_ad.F |
139 |
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140 |
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ecco_c44_e19 |
141 |
o merged necessary patches: |
o merged necessary patches: |
142 |
- AD-related changes for GMRedi |
- AD-related changes for GMRedi |
143 |
- fixes i KPP (delZ -> drF) |
- fixes i KPP (delZ -> drF) |
144 |
- hook to OBCS songe layer code in external_forcing |
- hook to OBCS songe layer code in external_forcing |
145 |
- errorMessageUnit non-zero in eeboot.F |
- errorMessageUnit non-zero in eeboot.F |
146 |
- modified test cost function and carbon verif. |
- included GMREDI, EXACT_CONSERV to natl_box_adjoint verif. |
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release1_chkpt44d_post = chkpt44d_post |
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147 |
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148 |
chkpt44d_pre,post |
ecco_c44_e18 |
149 |
o added missing EXCLUDE_MONITOR flags |
o sponge layer code for obcs was missing |
150 |
o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi |
- added hook in external_forcing.F |
151 |
(incompatible typ in MIN/MAX expressions caused problems |
- added storing for TAF |
152 |
on IBM SP3) |
o new routine cost_init_barfiles to initialise |
153 |
o in genmake added variable MAKEDEPEND |
adjoint fields adtbar, adsbar, adpsbar |
154 |
plus resetting for case SunOS |
(needed in conjunction with corrected ladinit for active I/O) |
155 |
o added timer_stats.c routine for IBM SP3 |
o cleaned up and corrected order in packages_readparms, ecco_readparms |
156 |
o removed variables in dynamics |
o corrected and simplified weights for obcs controls |
157 |
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- weight fields simplified |
158 |
o real fresh water flux implemented with non-linear free-surface. |
- bug fix in ctrl_pack |
159 |
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- no more write of control vector in ctrl_pack |
160 |
chkpt44c_pre,post |
o i/j index bug fixes in cost_ssh_mean |
161 |
o few fix (mask in shap_s2, EmPmR in external_field_load, |
|
162 |
USE_NATURAL_BCS in solve_for_P); |
ecco_c44_e17 |
163 |
o add arguments myIter & myTime to S/R obcs_calc & solve_for_P |
o bug fixes in cost package |
164 |
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* wrong identifier for active I/O of monthly mean psbar |
165 |
checkpoint44b_pre/_post |
(cost_averagesfields, cost_ssh) xx_psbar_dummy |
166 |
o merge of relevant stuff from the ecco-branch: |
* cleaned all identifier for active I/O of monthly fields |
167 |
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* wrong ladinit in various cost routines |
168 |
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o merge with interval (chkpt44c_post - chkpt44d_post) |
169 |
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* added missing EXCLUDE_MONITOR flags |
170 |
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* changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi |
171 |
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(incompatible typ in MIN/MAX expressions caused problems |
172 |
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on IBM SP3) |
173 |
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* in genmake added variable MAKEDEPEND |
174 |
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plus resetting for case SunOS |
175 |
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added timer_stats.c routine for IBM SP3 |
176 |
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* removed variables in dynamics |
177 |
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178 |
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ecco_c44_e16 |
179 |
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o new ECCO checkpoint, the first since ecco_c43_e15 |
180 |
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which is branched from MITgcm. |
181 |
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All changes were merged in between (see ecco-branch-mod? tags). |
182 |
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o last changes: |
183 |
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* assuming path for TAF and TAMC are known (e.g. in $path) |
184 |
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* genmake: |
185 |
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- added tools/xmakedepend to circumvene shortcoming of |
186 |
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SUN's makedepend (size too small) |
187 |
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- invoking ../tools/xmakedepend instead of makedepend |
188 |
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- changed compiler flags for case SunOS |
189 |
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190 |
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ecco-branch-mod5 |
191 |
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o mod's to reproduce open boundary run |
192 |
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o enable field swapping for OB's and climatology |
193 |
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o update store directives for OB control |
194 |
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o added option ALLOW_OBCS_PRESCRIBE |
195 |
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o call of getobcs now out of obcs_calc (param. list modified) |
196 |
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197 |
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ecco-branch-mod4 |
198 |
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o this is the second part of changes necessary to reconcile |
199 |
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the natl_box_adjoint verification (with and without grdchk). |
200 |
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>>>!!! CHANGES BETWEEN THE TAGS ecco-branch-mod3 !!!<<< |
201 |
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>>>!!! AND ecco-branch-mod4 !!!<<< |
202 |
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>>>!!! SHOULD BE MERGED INTO THE MAIN TRUNK !!!<<< |
203 |
- genmake: removed $S64 overwrite for case SunOS |
- genmake: removed $S64 overwrite for case SunOS |
204 |
- pkg/exf: update and corrections for field swapping and obcs |
- pkg/exf: update and corrections for field swapping and obcs |
205 |
- pkg/ecco: parameter lists for the_model_main, the_main_loop |
- pkg/ecco: parameter lists for the_model_main, the_main_loop |
207 |
- pkg/autodiff: added flow directives for obcs, mdsio_gl_slice |
- pkg/autodiff: added flow directives for obcs, mdsio_gl_slice |
208 |
updated checkpointing_lev... lists for obcs |
updated checkpointing_lev... lists for obcs |
209 |
- 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 |
|
210 |
- pkg/mdsio: added mdsio_gl_slice |
- pkg/mdsio: added mdsio_gl_slice |
211 |
|
|
212 |
o check parameters & config (chkpt44a_pre,post) |
ecco-branch-mod3 |
213 |
o OBC and NonLin_FrSurf. |
o this is the first part of changes necessary to reconcile |
214 |
|
natl_box_adjoint verification (with and without grdchk). |
215 |
|
This set of changes is relevant for ECCO only. |
216 |
|
The next set/tag of changes (ecco-branch-mod4) |
217 |
|
should be merged into the main trunk. |
218 |
|
- update some options |
219 |
|
- parameter lists of ecco_the_model_main and ecco_the_main_loop |
220 |
|
differed from those of the MITgcm counterparts. |
221 |
|
|
222 |
|
ecco-branch-mod2 |
223 |
|
o update ecco-branch-mod1 to checkpoint44 |
224 |
|
o exclude from updates: |
225 |
|
- verification/ |
226 |
|
- adjoint/ |
227 |
|
- pkg/cost |
228 |
|
- pkg/ctrl |
229 |
|
- pkg/ecco |
230 |
|
- pkg/obcs |
231 |
|
- model/src/the_model_main.F |
232 |
|
- model/src/the_main_loop.F |
233 |
|
|
234 |
checkpoint44 |
checkpoint44 |
235 |
|
o apply Shapiro filter on T&S before calc_PhiHyd (stagger time stepping) |
236 |
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) |
|
237 |
o added some stuff for AD |
o added some stuff for AD |
238 |
|
|
239 |
|
ecco-branch-mod1 |
240 |
|
o based on c43 |
241 |
|
o replaced packages cost, ctrl, ecco, obcs |
242 |
|
o removed MITgcm verif.'s, added ECCO verif.'s |
243 |
|
o added lsopt, optim for line search optimization. |
244 |
|
|
245 |
checkpoint43 |
checkpoint43 |
246 |
o added two new advection tests |
o added two new advection tests |
247 |
o added global 4x4 degree ocean test |
o added global 4x4 degree ocean test |