| 4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 5 |
============================== |
============================== |
| 6 |
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| 7 |
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o new read/write pickup version: |
| 8 |
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- for now, only implemented for main (mdsio) pickup file. |
| 9 |
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- write out only what is needed to restart; merge pickup_nh , pickup_ph |
| 10 |
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and main pickup together. |
| 11 |
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- read meta file; read only what is needed to restart; stop if a field |
| 12 |
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is missing (if pickupStrictlyMatch=T, = the default) or try to restart |
| 13 |
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if it make sense (even if the restart is not perfect). |
| 14 |
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- if no meta file, assume that pickup to read corresponds exactly to |
| 15 |
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a pickup that would currently be written. |
| 16 |
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- read pickup written in the old format (until checkpoint59i) if it |
| 17 |
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recognizes an old meta file (no field-list). |
| 18 |
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- add a meta file in exp. which starts from a pickup: 2 cases: |
| 19 |
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a) minimal meta file (with just file precision) + pickupStrictlyMatch=F |
| 20 |
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e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta |
| 21 |
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b) a meta file describing the content of the associated pickup file |
| 22 |
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e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta |
| 23 |
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o pkg/mdsio & pkg/rw: |
| 24 |
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- new routine to read a meta file ; new set of routine to read |
| 25 |
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Multiple-fields file (with meta file). |
| 26 |
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o added open boundary conditions capability for seaice |
| 27 |
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HSNOW, HSALT, UICE, and VICE |
| 28 |
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|
| 29 |
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checkpoint59i |
| 30 |
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o adjoint: |
| 31 |
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* fix multiDimAdvection adjoint |
| 32 |
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(partial recomputation problem by TAF for fVerT(:,:,kDown) |
| 33 |
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and comlev1 size definition (maxpass vs. max. number of tracers) |
| 34 |
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* verification/global_ocean.90x45x15 adjoint now tests |
| 35 |
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NLFS and multiDimAdvection using DST3 (=30) |
| 36 |
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* verification/lab_sea now tests multiDimAdvection using DST3 (=30) |
| 37 |
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o pkg/kpp: add "_d 0" to real constant (if missing); |
| 38 |
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update output of exp: natl_box (10.digits); vermix (std, 7.digits) |
| 39 |
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and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits). |
| 40 |
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o prepare for "clever pickup" implementation: add new header file "RESTART.h" |
| 41 |
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for internal parameters related to restart process (formerly from PARAMS.h) |
| 42 |
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and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2. |
| 43 |
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o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed |
| 44 |
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as argument. (only atm2d & obcs write_pickup have not yet been updated) |
| 45 |
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o pkg/monitor: |
| 46 |
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- use GLOBAL_SUM_TILE instead of _GLOBAL_SUM |
| 47 |
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- fix mon_stats_rs (statistics over the full domain, even where field is zero) |
| 48 |
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- account for deep Atmosphere factor and density factor (anelastic) |
| 49 |
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o added open boundary conditions capability for seaice HEFF and AREA |
| 50 |
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o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989) |
| 51 |
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thermodynamics |
| 52 |
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- requires a little reorganization, which affects the testreport results |
| 53 |
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of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment, |
| 54 |
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so that now the conservative form is tested |
| 55 |
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- add a few comments |
| 56 |
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o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code* |
| 57 |
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o add a little bit of code to gad_os7mp_adv_?.F to help vectorization |
| 58 |
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o add new diagnostics to seaice: advective, diffusive fluxes (only for |
| 59 |
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multidim-advection, for scheme 2 they are not filled) and transports, |
| 60 |
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thermodynamic growth rates |
| 61 |
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o change units of EmPmR (inside the code) from m/s to kg/m2/s (mass flux) but |
| 62 |
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leave input file unchanged. Affects results @ truncation level (cg2d match) |
| 63 |
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and update output of experiments: lab_sea(6), global_ocean.90x40x15(10), |
| 64 |
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global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11) |
| 65 |
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+ adjoint results: global_ocean_ebm(11) and lab_sea (12). |
| 66 |
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Next: will retire convertEmP2rUnit (simply using mass2rUnit instead). |
| 67 |
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|
| 68 |
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checkpoint59h |
| 69 |
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o pkg/exf: |
| 70 |
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- improve vectorization by moving if-statement out of loops in |
| 71 |
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exf_mapfields, exf_radiation |
| 72 |
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- exf_bulkformulae.F: introduce 2D fields and vectorize code |
| 73 |
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o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package |
| 74 |
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o testreport: |
| 75 |
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- allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE |
| 76 |
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monitor & update offline_exf_seaice exp. output. |
| 77 |
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- AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost) |
| 78 |
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o pkg/seaice: |
| 79 |
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- bug fix in the evp solver: boundary conditions were affected be |
| 80 |
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masking of zMax/zMin (changes results) |
| 81 |
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- minor bug fix in boundary conditions in seaice_calc_strainrates |
| 82 |
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(changes results for no_slip) |
| 83 |
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- seaice_lsr.F: make interpolation of eta dependent on boundaries |
| 84 |
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- replace hardcoded lower limit for zeta (zMin) by runtime parameter |
| 85 |
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- add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean |
| 86 |
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stress formulation and no-slip boundary conditions |
| 87 |
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o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP |
| 88 |
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in gad_calc_rhs.F ; add few safety stops in initialisation phase. |
| 89 |
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o pkg/seaice: a first HSALT time stepping equation has been checked in |
| 90 |
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o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV |
| 91 |
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in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem |
| 92 |
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without requiring DO-IF statements |
| 93 |
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o pkg/thsice: |
| 94 |
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use continuous power-law function for partition of energy between lateral |
| 95 |
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melting/freezing and thinning/thickening ; old code using step function |
| 96 |
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still available with #undef THSICE_FRACEN_POWERLAW |
| 97 |
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update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice |
| 98 |
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o testreport: change AD testing : check against results/output_adm.txt |
| 99 |
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using same scripts as for forward test. |
| 100 |
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|
| 101 |
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checkpoint59g |
| 102 |
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o adjoint testing: in preparation for changing testreport: |
| 103 |
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- output format: cost and grad written on separated lines |
| 104 |
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- ad output results in directory "results" (instead of "results_ad") |
| 105 |
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o pkg/seaice: adding ice salinity HSALT as a prognostic variable |
| 106 |
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o pkg/seaice: changes for using pkg/seaice with pkg/obcs |
| 107 |
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o pkg/ecco: allow user defined cost function contributions |
| 108 |
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o testreport: |
| 109 |
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Allow to choose (per experiment) the list of tested output variables |
| 110 |
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and the main variable (used to issue a pass/FAIL ) ; |
| 111 |
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- for now, done by adding the specific list in file: [exp]/input/tr_checklist |
| 112 |
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- default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ; |
| 113 |
|
Also modify printing of summary: |
| 114 |
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a) ">" NN "<" indicates the "main" variable (used for pass/FAIL) |
| 115 |
|
b) echo the list of tested variables in the individual summary.txt of |
| 116 |
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each experiment. |
| 117 |
|
o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of |
| 118 |
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threads and number of processes (with #define GLOBAL_SUM_SEND_RECV) |
| 119 |
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(but still depend on the tile decompostion of the domain). |
| 120 |
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o pkg/seaice: change a discretization detail to make the B-grid code |
| 121 |
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"more symmetric". This change is likely to remove all "ridges/leads" that |
| 122 |
|
where quasi-aligned with the grid in B-grid solutions. It may also be |
| 123 |
|
the solution to the stress coupling issues with the B-grid. |
| 124 |
|
o each tested exp: add a "run" directory with a standard ".cvsignore" file ; |
| 125 |
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remove .cvsignore from input dir. (since testreport no longer run here). |
| 126 |
|
o pkg/thsice: |
| 127 |
|
- cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h" |
| 128 |
|
- fix reshaping of sea-ice just after advection: |
| 129 |
|
melt all the ice only if ice-volume is too small. |
| 130 |
|
- re-visit lateral/thinning repartition of melting (modifs from May 04, 2007): |
| 131 |
|
prevent lateral melting if sea-ice fraction is too close to iceMaskMin ; |
| 132 |
|
and update experiment global_ocean.cs32x15.icedyn (+start from pickup files). |
| 133 |
|
o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water |
| 134 |
|
tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged. |
| 135 |
|
o define mass2rUnit & rUnit2mass as units conversion factor, used for surface |
| 136 |
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forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit |
| 137 |
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(z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse; |
| 138 |
|
and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error |
| 139 |
|
of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16 |
| 140 |
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-> update output.txt |
| 141 |
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o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME): |
| 142 |
|
this affects truncation error: -> update output.txt of exp: |
| 143 |
|
global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr, |
| 144 |
|
ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon. |
| 145 |
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|
| 146 |
|
checkpoint59f |
| 147 |
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o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode) |
| 148 |
|
o pkg/ctrl: ctrl_bound forces parameter corrections to stay in |
| 149 |
|
a bounded range (in forward mode) |
| 150 |
|
o pkg/ecco, ctrl, autodiff and mom_common: |
| 151 |
|
internal parameter controls, completements of implementations |
| 152 |
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o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy. |
| 153 |
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o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ; |
| 154 |
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(not seem any difference in testing results). |
| 155 |
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o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains |
| 156 |
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at face corners. |
| 157 |
|
o pkg/generic_advdiff: |
| 158 |
|
- in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR) |
| 159 |
|
loop range indices for computing vertical advection tendency |
| 160 |
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and do the calculation in the interior only (no overlap) ; |
| 161 |
|
for now, only implemented for SOM advection (to save CPU time). |
| 162 |
|
- add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment) |
| 163 |
|
o exch2 adjoint |
| 164 |
|
First set of changes: |
| 165 |
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- add exch2 hand-written adjoint templates |
| 166 |
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- exch2 hand-written no longer use TAF-flag 'nownew_arg' |
| 167 |
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This will require cleanup in pkg/autodiff/*.F |
| 168 |
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(changed routines currently kept separate in verif. code/) |
| 169 |
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- Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC |
| 170 |
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that used to hide exch2 or cubed-sphere specific code |
| 171 |
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(commented via 'cph-exch2') |
| 172 |
|
o pkg/seaice |
| 173 |
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- Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE. |
| 174 |
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o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update |
| 175 |
|
output of global_ocean.cs32x15.thsice . |
| 176 |
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|
| 177 |
|
checkpoint59e |
| 178 |
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o exch2: new S/R that only use the cube-tracer (center-position) exchange: |
| 179 |
|
for B-grid vector (not yet tested) and C-grid vector (<- only used |
| 180 |
|
when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined). |
| 181 |
|
o starting implementation of Duffy et al. (GRL 1999) salt plume scheme |
| 182 |
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(#ifdef ALLOW_SALT_PLUME) |
| 183 |
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o gather_2d/scatter_2d: removed halo regions |
| 184 |
|
o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007 |
| 185 |
|
scheme and the corresponding test case (under front_relax dir). For now, |
| 186 |
|
only available with Skew-flux form and not yet tested in realistic set-up. |
| 187 |
|
adjoint: store directives updated, but gradient checks deteriorated, |
| 188 |
|
so maybe GM/Redi adjoint is now broken. |
| 189 |
|
o seaice adjoint |
| 190 |
|
* add AREA, HEFF, HSNOW as control variable |
| 191 |
|
(should not change lab_sea results) |
| 192 |
|
* CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40 |
| 193 |
|
o pkg/seaice: |
| 194 |
|
* added computation of saltFlux in seaice_growth; |
| 195 |
|
For time being, sea ice salinity is assumed constant |
| 196 |
|
contribution of snow flooding to freshening of sea ice is neglected. |
| 197 |
|
SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it |
| 198 |
|
defaults to 0.0 in order to maintain backward compatibility. |
| 199 |
|
Typical values for SEAICE_salinity are 4 to 10 g/kg. |
| 200 |
|
* replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F |
| 201 |
|
* added SEAICE_availHeatFrac, which specifies fraction of surface level |
| 202 |
|
heat content used to melt or grow ice |
| 203 |
|
* commented out cap of HICE: it helps keep ice thinner |
| 204 |
|
* reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option |
| 205 |
|
* applied OBCS T/S mask to HEFFM sea ice mask |
| 206 |
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|
| 207 |
|
checkpoint59d |
| 208 |
|
o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array |
| 209 |
|
for {PKG} state variables, and called from DO_STATEVARS_DIAGS. |
| 210 |
|
(keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics) |
| 211 |
|
o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0" |
| 212 |
|
and change default value of parameter "GM_Small_Number"; |
| 213 |
|
update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15, |
| 214 |
|
global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf, |
| 215 |
|
tutorial_global_oce_biogeo, tutorial_global_oce_latlon |
| 216 |
|
o pkg/ecco: cost function when applying pkg/smooth to controls |
| 217 |
|
o pkg/ctrl: add forcingPrecond run time parameter |
| 218 |
|
o pkg/seaice: |
| 219 |
|
- replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code |
| 220 |
|
- fix bug in metric terms of u-equation in LSR solver (implicit part), |
| 221 |
|
changes verification/lab_sea |
| 222 |
|
- rearrange implicit part of u-equation in LSR solver to make it easier to |
| 223 |
|
read, understand, and debug. This causes changes at the truncation level. |
| 224 |
|
- fix (serious) bug in the boundary conditions (sign error in the implicit |
| 225 |
|
part) of the LSR solver. Changes all LSR results. |
| 226 |
|
- fixed problem with HSNOW initialization to avoid thick snow when AREA |
| 227 |
|
is initilized with small values - does not change lab_sea results. |
| 228 |
|
- added HsnowFile initialization capability |
| 229 |
|
o pkg/smooth: addition to model/src and pkg/ctrl so allow |
| 230 |
|
initialization of pkg/smooth and application to control vector |
| 231 |
|
o pkg/seaice: fix another bug in the LSR no-slip boundary conditons |
| 232 |
|
o dependencies: pkg/profiles requires pkg/cal |
| 233 |
|
o pkg/profiles: |
| 234 |
|
- added option ALLOW_PROFILES_GENERICGRID |
| 235 |
|
-> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming |
| 236 |
|
that interpolation information (grid points and coefficients) is provided |
| 237 |
|
within the netcdf input files. |
| 238 |
|
-> sample matlab scripts can be found in MITgcm_contrib/gael |
| 239 |
|
that allow you to prepare netcdf input files. |
| 240 |
|
- also modified: cleaner include statements, cleaner error print statements, |
| 241 |
|
cleaner stops when error, and more tests of the netcdf input files consistency. |
| 242 |
|
o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs. |
| 243 |
|
o pkg/seaice: |
| 244 |
|
- move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this |
| 245 |
|
requires a new routine: seaice_diagnostics_fill.F |
| 246 |
|
- make sure that seaice does not move if not forced (pressure replacement |
| 247 |
|
method, Hibler and Ip, 1995), changes results |
| 248 |
|
- and new damping criterion for EVP solver according to Hunke, JCP, 2001 |
| 249 |
|
- SEAICE_evpDampC = > 0. turns it on (615. is the recommended value). |
| 250 |
|
It is turned off by default (=-1.), because it changes the results. |
| 251 |
|
- make it possible to read AREA from a file, too. |
| 252 |
|
|
| 253 |
|
checkpoint59c |
| 254 |
|
o add S/R and diagnostics for oceanic mixed-layer depth |
| 255 |
|
o move GMRedi call after all vertical mixing schemes (including KPP) |
| 256 |
|
o pkg/thsice: |
| 257 |
|
- ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs |
| 258 |
|
(melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice |
| 259 |
|
o pkg/obcs: |
| 260 |
|
- bug fix for balance code |
| 261 |
|
o pkg/seaice: |
| 262 |
|
- allow values of SEAICE_elasticParm > 1 |
| 263 |
|
- add new parameter SEAICE_evpTauRelax as an alternative |
| 264 |
|
to SEAICE_elasticParm |
| 265 |
|
- make lsr boundary conditions free slip (by default), changes result |
| 266 |
|
- add code for no slip boundary conditions for lsr |
| 267 |
|
- set minimum of zeta to zero (and not 4e8) (changes results) |
| 268 |
|
- add a cap on AREA after advecting AREA if seaice_growth is not called |
| 269 |
|
o change calculation of Visbeck K: |
| 270 |
|
- no longer depend on tapering scheme; instead, compute slope (limited |
| 271 |
|
by GM_maxSlope). this is equivalent to what was comuted before with |
| 272 |
|
clipping or linear tappering. |
| 273 |
|
- fix vertical averaging (wrong by 1/2 level) |
| 274 |
|
- leave the old version (but will not be maintained) within |
| 275 |
|
#ifdef OLD_VISBECK_CALC / #endif |
| 276 |
|
- update output of exp. ideal_2D_oce |
| 277 |
|
o change error catch in calc_r_star to improve vectorization |
| 278 |
|
o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and |
| 279 |
|
add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf). |
| 280 |
|
o adjoint: |
| 281 |
|
Re-organized adjoint checkpointing according to Matt Mazloff |
| 282 |
|
(but with modifs/completions/cleanups) |
| 283 |
|
Storing is now bundled into large arrays to optimized I/O |
| 284 |
|
(and second step in cleanup of the_main_loop) |
| 285 |
|
|
| 286 |
|
checkpoint59b |
| 287 |
|
o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d): |
| 288 |
|
- export/import (between ocean & coupler) fields needed for ocean DIC. |
| 289 |
|
o pkg/seaice: |
| 290 |
|
- get rid of three more exchanges seaice_calc_viscosities (required |
| 291 |
|
different loop boundaries in seaice_lsr and seaice_ocean_stress) |
| 292 |
|
- bug fix in seaice_ocean_stress (update of lab_sea required) |
| 293 |
|
- reduce loop boundaries to necessary minimum also in seaice_evp |
| 294 |
|
- go back to the old way of computing deltaC/Z as the adjoint likes that |
| 295 |
|
better |
| 296 |
|
o Refresh of tutorial_global_oce_latlon (includes changing salinity-like |
| 297 |
|
passive tracer to an Age Tracer) + update output.txt |
| 298 |
o pkg/exf: |
o pkg/exf: |
| 299 |
- implement A-grid / C-grid selection for wind-stress input files. |
- implement A-grid / C-grid selection for wind-stress input files. |
| 300 |
- clean-up exf_wind.F (remove us, use wspeed instead ; add wStress) |
- clean-up exf_wind.F (remove us, use wspeed instead ; add wStress) |
| 335 |
o pkg/thsice: |
o pkg/thsice: |
| 336 |
fix few little problems, in thsice_calc_thickn.F: |
fix few little problems, in thsice_calc_thickn.F: |
| 337 |
- growth vertically (and not laterally) if iceFrac == iceMaskMax |
- growth vertically (and not laterally) if iceFrac == iceMaskMax |
| 338 |
- melt laterally only if hIce < hThinIce (as the comments say) |
- melt only laterally if hIce < hThinIce (as the comments say) |
| 339 |
and in thsice_extend.F: |
and in thsice_extend.F: |
| 340 |
- allow to form ice even when iceFrac == iceMaskMax (by increasing thickness) |
- allow to form ice even when iceFrac == iceMaskMax (by increasing thickness) |
| 341 |
- start to form ice as soon as the minimum ice-volume is reachable. |
- start to form ice as soon as the minimum ice-volume is reachable. |
| 372 |
ATMOSPHERIC_LOADING is #define). |
ATMOSPHERIC_LOADING is #define). |
| 373 |
o pkg/kpp: replaced _KPP_RL with _RL |
o pkg/kpp: replaced _KPP_RL with _RL |
| 374 |
o bug fixes for vertical diffusivity computations when both KPP and |
o bug fixes for vertical diffusivity computations when both KPP and |
| 375 |
3D diffusivity arrays are used. |
3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F |
| 376 |
|
are no longer updating the vertical diffusivity array |
| 377 |
|
(passed as argument) but are (re-) setting those arrays. |
| 378 |
o pkg/seaice: fix bug in evp solver, while doing that |
o pkg/seaice: fix bug in evp solver, while doing that |
| 379 |
- change (improve?) discretization of stress computations for both |
- change (improve?) discretization of stress computations for both |
| 380 |
cgrid-lsr and evp solver |
cgrid-lsr and evp solver |
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