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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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o model debug options: |
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- Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored |
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in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h). |
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- Refine debug-msg printing selection (3 new levels): |
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debugMode : controls printing of debug messages (sequence of S/R calls). |
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debugLevel : controls printing of algorithm-relevant auxiliary/debug messages |
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debLevZero = 0 ; /* level of disabled aux. msg printing */ |
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debLevA = 1 ; /* level of minimum aux. msg printing */ |
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debLevB = 2 ; /* level of low aux. print (report read-file opening)*/ |
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debLevC = 3 ; /* level of moderate debug prt (most pkgs debug msg) */ |
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debLevD = 4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */ |
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debLevE = 5 ; /* level of extensive debug printing */ |
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New debugLevel default: with default debugMode value (=F), |
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= 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.; |
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and if debugMode=T, default debugLevel = 4 (debLevD). |
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Relation with previous settings: |
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debLevB (=2) corresponds to former debLevA (=1) |
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debLevD (=4) corresponds to former debLevB (=2) |
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Note: |
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a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before); |
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b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs); |
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to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5) |
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- Add new parameter (printResidualFreq, read from PARM02 namelist) to print |
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detailed CG solvers convergence; off (=0) by default, except if debugLevel=5. |
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o pkg/obcs: |
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- change OBCSfixTopo default from True to False (should not change the results); |
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keep OBCSfixTopo=T in verification-exp. seaice_obcs. |
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o pkg/thsice: |
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- fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in |
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2nd layer seaice sublimation (unlikely to happen) |
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- use Interior mask for OBCS in thsice_advection.F (similar to what is |
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done in gad_advection & seaice_advection). |
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o adjoint: |
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bug fix spotted by Gael Forget: |
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seaice_advection and thsice_advection still had |
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legacy CPP options to avoid CS corner updates for adjoint |
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o pkg/seaice: |
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=> Change some of the defaults (2011/05/29): |
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- change SEAICEuseFluxForm default (from False to True) |
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- change DIFF1 default (from 0.004 m/s to 0. m/s) |
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And print warnings if DIFF1 is not set in data.seaice and centered |
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avection scheme is used without any diffusion. |
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also: |
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- fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F; |
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- set SEAICEdiffKh[] default in the same way as SEAICEadvSch[] |
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- stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any |
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other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with |
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#undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE. |
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update results of test exp.: |
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lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20) |
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output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200) |
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output_adm.noseaicedyn (SEAICEuseFluxForm=T) |
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offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T) |
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seaice_obcs: output (SEAICEuseFluxForm=T) |
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and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004) |
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for standard fwd & AD lab_sea tests (to keep the same output). |
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o pkg/seaice/seaice_growth.F: |
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- use Ian Fenty's capping formulas for actual ice |
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thickness thoughout EVOLUTION branch. |
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- put treatment pathological case #2) in CPP brackets |
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(ALLOW_AVOID_INFINITESIMAL_AREA, undef by default). |
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- update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly. |
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o pkg/seaice: |
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- seaice_diffusion.F : remove the min(DX,DY) factor permanently; |
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pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter; |
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also pass fac as a param, which can be 1. (to update the tendency |
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field) or the time step (to update the field itself). |
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- seaice_advdiff.F: for multidim, call seaice_diffusion with |
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e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call |
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seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step. |
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- SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F : |
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hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc. |
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o pkg/seaice: |
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diffusion with centered advection scheme (diffus.F & advect.F): |
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- simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside) |
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to just compute the laplacian of input-field. |
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- unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call. |
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- fix flux-form version in diffus.F to conserve tracer. |
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update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects |
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machine truncation) and lab_sea.salt_plume (conservative flux-form modif) |
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|
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checkpoint62y (2011/05/26) |
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o pkg/seaice: |
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- seaice_growth.F : in EVOLUTION branch, always include |
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a_QSWbyATM_cover in qnet (as it should be). |
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- verification/global_ocean.cs32x15 : update results accordingly |
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(output.seaice.txt output_adm.seaice.txt). |
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o pkg/seaice + obcs: |
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- use maskInW & maskInS in multi-dim advection and biharmonic diffusion: |
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equivalent of assuming no tracer gradient outside the OB region. |
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update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion) |
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- remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed |
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after changes above); |
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- obcs+seaice cleaning: apply seaice-tracer OB values to tracer field |
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only at OB location (instead of over a band of OLx width). |
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o pkg/seaice: |
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- fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F |
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(dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid) |
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o pkg/obcs: |
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- split header file "OBCS.h" into 4 separated files: |
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OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h |
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Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h |
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(contain no conditional statement which depends on OBCS options). |
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- move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h) |
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to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h). |
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o ctrl, cost, grdchk & autodiff pkgs: |
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- make options file more standard (like other {PKG}_OPTIONS.h file but |
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with AD_CONFIG.h); clean-up some of the included header files. |
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o pkg/obcs: |
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- do not mask tracer when applying OB (tracer == 0 could generate problems) |
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- apply tracer OB values to tracer field only at OB location (instead of |
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over a band of OLx width) |
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- clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R) |
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- remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove |
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obcs_apply_tloc.F & obcs_apply_sloc.F |
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o obcs in model/src: |
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- call OBCS_APPLY_W only if NonHydrostatic. |
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- call OBCS_APPLY_ETA only if NonLinFreeSurf. |
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- reset dEtaHdt and wVel to zero outside OB interior region ; |
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- leave tracer unchanged outside OB interior region: This has no effect |
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on the solution but just to prevent unrealistic tracer value outside OB. |
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- zero out velocity outside OB interior region: This has no effect on |
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the solution but just to prevent unrealistic velocity outside OB. |
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o obcs and non-lin free-surf: |
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move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F |
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and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F |
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+ add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR: |
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this fixes missing EXCH + get consistent eta OB value (+ fix restart). |
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update results of test-exp. exp4(nlfs). |
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o exp4 (nlfs) test-exp: |
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use OBC for Eta at Western & Eastern OB (to test prescribing Eta |
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with NonLin-FreeSurf); update output.nlfs.txt |
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o obcs and 2d/3d solver norm: |
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use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB |
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and outside OB interior region (will allow to place OB further inside the |
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domain). Depending on the domain, can affects cg2d-Norm (previous |
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cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl, |
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and cg3d-Norm (previous Norm was computed before canceling OB terms), |
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e.g. in tutorial_plume_on_slope. |
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- update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope. |
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o pkg rbcs: |
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- split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h |
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- add capability to apply relaxation to horizontal velocity uVel & vVel. |
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o pkg/grdchk: add gradient check for control variable xx_shifwflx |
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o pkg/shelfice/shelfice_init_fixed.F |
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fix CPP-flag combinations |
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o pkg/seaice: Merge iceage code of Pierre Rampal |
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* update/change/correct ice age calculations |
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* add age updates for pathological cases |
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Probably needs more testing... |
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|
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checkpoint62x (2011/05/13) |
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o pkg/mom_vecinv: |
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high-order vorticity scheme: use interior masks (maskInW & S) |
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to zero-out (outside OB) gradient of vorticity. |
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o verification exp.: |
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turn on "useEnergyConservingCoriolis" (better discretisation) in exp. |
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hs94.128x64x5 and seaice_obcs ; update results. |
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o pkg/obcs: |
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fix bug in OBeta for YZ sections in obcs_exf_load.F |
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o pkg/ctrl, pkg/shelfice, and optim: |
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- add new control variable xx_shifwflx (fresh water flux underneath ice |
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shelves). This is almost as tedious as obcs-ctrl, because the |
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variables needs its own mask. |
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- add a cost function term that penalizes the deviation of xx_shifwflx |
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from the first guess (zero) in analogy to other control variables |
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o pkg/shelfice: |
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- start basic adjoint |
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o pkg/ctrl: |
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- remove extra 2D field "for good measure" when initializing in |
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ctrl_set_globfld_[xy/xz/yz].F |
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- replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec |
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- improve error messages in ctrl_set_unpack_* |
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o OBC implementation in momentum: |
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use interior masks (maskInC,W & S) in momentum S/R: |
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- multiply divergence, tension and some del^i.u or del^j.v by maskInC |
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- multiply del2u,del2v by maskInW/S (biharmonic viscosity) |
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- multiply horiz. grad of vorticity by maskInW/S (in Leith scheme) |
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- multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd) |
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Motivation: fix/clean implementation of OBC with biharmonic-viscosity |
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(and also with Leith/Smagorinsky harmonic-viscosity). |
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Update output of experiment dome and exp4 (+nlfs). |
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o exp4 test-exp: |
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- turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F) |
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and prescribe time-varying OB (without pkg/exf) for zonal-velocity |
| 192 |
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at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe |
| 193 |
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time-varying OB at Western-side for wVel (NonHyd); update output. |
| 194 |
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- add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv |
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and biharmonic-viscosity ; also use prescribed time varying OB. |
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o pkg/obcs: |
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fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F |
| 198 |
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o model/src: |
| 199 |
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- fix startTime setting when baseTime<>0 & nIter0=0 are specified ; |
| 200 |
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- initialise startTime & nIter0 with unlikely values: allows to set one |
| 201 |
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from the other without ambiguity. |
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o seaice_obcs test-exp.: |
| 203 |
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add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output. |
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o pkg/obcs: |
| 205 |
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- remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer: |
| 206 |
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no longer needed with maskInC,W,S in pkg/generic_advdiff. |
| 207 |
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o pkg/seaice: |
| 208 |
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- retired SEAICE_SALINITY and SEAICE_salinity in favor of |
| 209 |
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SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively. |
| 210 |
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- fixed bug in the initialization of sea ice salinity variable HSALT |
| 211 |
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in seaice_init_varia.F (removed dependence on ICE2WATR) |
| 212 |
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o fizhi-cs test exp.: |
| 213 |
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switch reference output convention for these 2 non-standard test-exp, |
| 214 |
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from: pgi 6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5) |
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to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11) |
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reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran |
| 217 |
o model/inc: |
o model/inc: |
| 218 |
- change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4") |
- change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4") |
| 219 |
of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS) |
of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS) |
| 220 |
o pkg/seaice: |
o pkg/seaice: |
| 221 |
- fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY |
- fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY |
| 222 |
o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15 |
o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15 |
| 223 |
- updated affected output*.txt files due to salt and saltPlumeFlux bug fix |
- updated output*.txt files due to bug fixes in salt, saltPlumeFlux, |
| 224 |
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and initial HSALT |
| 225 |
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|
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checkpoint62w (2011/04/26) |
checkpoint62w (2011/04/26) |
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o pkg/mom_fluxform: |
o pkg/mom_fluxform: |
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