| 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 pkg/diagnostics: |
| 8 |
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- Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P') |
| 9 |
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which are not filled-up but computed from other diags ; In this case, the mate |
| 10 |
|
diag points to the primary (filled-up) diag to used for post processing. |
| 11 |
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- Update Velocity-potential computation using post-processed diag framework. |
| 12 |
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==> Change the ordering of fields and time-periods in MDS output file |
| 13 |
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when using periodic averaging: now writes one time record with the full set |
| 14 |
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of fields for this time period, then the next time reccord (it used to be |
| 15 |
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one field with the full set of time records then the next field). |
| 16 |
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Note: this is now similar to NetCDF (MNC) output file. <== |
| 17 |
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- Extend the use of "missing_value" setting from data.diagnostics for the case |
| 18 |
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of counter-diagnostics (where fraction-weight is zero). This applies both to |
| 19 |
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MNC and MDS output files. |
| 20 |
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|
| 21 |
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checkpoint62z (2011/06/21) |
| 22 |
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o adjoint monitor: |
| 23 |
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- Add adjoint monitor output for packages exf, seaice |
| 24 |
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and update relevant testreport output |
| 25 |
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o pkg/seaice: |
| 26 |
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- re-order diags inits so that they appear in order in available_diagnostics.log |
| 27 |
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- added diags: hsnow thermo. rates of change, area preceeding ridiging process, |
| 28 |
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area/heff/hsnow preceeding thermodynamic growth/melt. |
| 29 |
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- modified diag: SIdA; output actual effect, as the description states. |
| 30 |
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- modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW. |
| 31 |
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- retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh. |
| 32 |
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(SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO; |
| 33 |
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and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO) |
| 34 |
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- modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates. |
| 35 |
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- added diagnostics for seaice generic tracers (SItr*). |
| 36 |
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- added SItrUnit and SItrNameLong run time param (for SItr* diags). |
| 37 |
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- in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'. |
| 38 |
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I. Fenty: 18-Jun-2011: |
| 39 |
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Minor changes to seaice package: |
| 40 |
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1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and |
| 41 |
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added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor) |
| 42 |
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- Differentiated "regularization variables" from "floor variables" |
| 43 |
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* areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor |
| 44 |
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* hiceMin became SEAICE_hice_reg (old hiceMin) |
| 45 |
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(with _reg meaning regularization variable) |
| 46 |
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- SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion |
| 47 |
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so as to ensure energy conservation when going between phases |
| 48 |
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- A22 was not used anywhere |
| 49 |
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2) Changed regularization procedure for heffActual and hsnowActual to ensure |
| 50 |
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well-boundedness and smooth adjoint in seaice_growth.F |
| 51 |
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3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells |
| 52 |
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because the old regularization always set heffActual >= 0.05 cm |
| 53 |
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4) Changed the model so that the default behavior is to put a small (10^-5) "floor" |
| 54 |
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on AREA when HEFF > 0. |
| 55 |
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- went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to |
| 56 |
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requiring that DISABLE_AREA_FLOOR *not* be defined |
| 57 |
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Affected verifications: |
| 58 |
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- 1D_ocean_ice_column (output.txt output_adm.txt) |
| 59 |
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- global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt) |
| 60 |
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o pkg/diagnostics: |
| 61 |
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- move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R). |
| 62 |
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- rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument |
| 63 |
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(was _RL, now integer) with option = 0 to retrieve all levels. |
| 64 |
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- add pieces of code to compute velocity potential at each level (new diagnostics |
| 65 |
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PhiVEL, works only when UVELMASS & VVELMASS are also turned on); |
| 66 |
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for now, using same params as CG2D (target-resisual, max Nb of iter ...). |
| 67 |
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- fix few issues with counter diagnostics in diagnostics_setdiag.F & |
| 68 |
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diagstats_setdiag.F (if diagnostic counter is itself a counter diag) |
| 69 |
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and in diagnostics_fract_fill.F (do not need a valid pointer for the |
| 70 |
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diagnostics counter-mate); check that definition of counter-diagnostic |
| 71 |
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includes a valid counter-mate (in diagnostics_set_levels.F). |
| 72 |
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o model/src (rStar): |
| 73 |
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- add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F); |
| 74 |
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affect solution only if z* with full pressure in EOS; |
| 75 |
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update output of test-exp global_ocean.90x40x15. |
| 76 |
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o pkg/seaice: |
| 77 |
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- introduce siEps=1e-5 parameter |
| 78 |
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- use areaMax in AREA update (part 4), consistent with ridging step (part 2.5). |
| 79 |
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- re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code. |
| 80 |
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- introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer. |
| 81 |
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For now it covers, and was tested for, ice salinity and age (attached to HEFF), |
| 82 |
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as well as ice cover age and ridging index (attached to AREA). |
| 83 |
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For now the run time parameters (in data.seaice/SEAICE_PARM03) are |
| 84 |
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SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA'). |
| 85 |
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Up to SItrMaxNum=3 tracers can be used simultaneously. |
| 86 |
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o pkg/salt_plume: |
| 87 |
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-introduce SPsalFRAC run time parameter that sets the fraction of the |
| 88 |
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salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically) |
| 89 |
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that gets vertically redistributed (fluxed down) by pkg/salt_plume. |
| 90 |
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o model debug options: |
| 91 |
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- Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored |
| 92 |
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in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h). |
| 93 |
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- Refine debug-msg printing selection (3 new levels): |
| 94 |
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debugMode : controls printing of debug messages (sequence of S/R calls). |
| 95 |
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debugLevel : controls printing of algorithm-relevant auxiliary/debug messages |
| 96 |
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debLevZero = 0 ; /* level of disabled aux. msg printing */ |
| 97 |
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debLevA = 1 ; /* level of minimum aux. msg printing */ |
| 98 |
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debLevB = 2 ; /* level of low aux. print (report read-file opening)*/ |
| 99 |
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debLevC = 3 ; /* level of moderate debug prt (most pkgs debug msg) */ |
| 100 |
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debLevD = 4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */ |
| 101 |
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debLevE = 5 ; /* level of extensive debug printing */ |
| 102 |
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New debugLevel default: with default debugMode value (=F), |
| 103 |
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= 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.; |
| 104 |
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and if debugMode=T, default debugLevel = 4 (debLevD). |
| 105 |
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Relation with previous settings: |
| 106 |
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debLevB (=2) corresponds to former debLevA (=1) |
| 107 |
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debLevD (=4) corresponds to former debLevB (=2) |
| 108 |
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Note: |
| 109 |
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a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before); |
| 110 |
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b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs); |
| 111 |
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to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5) |
| 112 |
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- Add new parameter (printResidualFreq, read from PARM02 namelist) to print |
| 113 |
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detailed CG solvers convergence; off (=0) by default, except if debugLevel=5. |
| 114 |
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o pkg/obcs: |
| 115 |
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- change OBCSfixTopo default from True to False (should not change the results); |
| 116 |
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keep OBCSfixTopo=T in verification-exp. seaice_obcs. |
| 117 |
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o pkg/thsice: |
| 118 |
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- fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in |
| 119 |
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2nd layer seaice sublimation (unlikely to happen) |
| 120 |
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- use Interior mask for OBCS in thsice_advection.F (similar to what is |
| 121 |
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done in gad_advection & seaice_advection). |
| 122 |
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o adjoint: |
| 123 |
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bug fix spotted by Gael Forget: |
| 124 |
|
seaice_advection and thsice_advection still had |
| 125 |
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legacy CPP options to avoid CS corner updates for adjoint |
| 126 |
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o pkg/seaice: |
| 127 |
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=> Change some of the defaults (2011/05/29): |
| 128 |
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- change SEAICEuseFluxForm default (from False to True) |
| 129 |
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- change DIFF1 default (from 0.004 m/s to 0. m/s) |
| 130 |
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And print warnings if DIFF1 is not set in data.seaice and centered |
| 131 |
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avection scheme is used without any diffusion. |
| 132 |
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also: |
| 133 |
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- fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F; |
| 134 |
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- set SEAICEdiffKh[] default in the same way as SEAICEadvSch[] |
| 135 |
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- stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any |
| 136 |
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other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with |
| 137 |
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#undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE. |
| 138 |
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update results of test exp.: |
| 139 |
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lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20) |
| 140 |
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output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200) |
| 141 |
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output_adm.noseaicedyn (SEAICEuseFluxForm=T) |
| 142 |
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offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T) |
| 143 |
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seaice_obcs: output (SEAICEuseFluxForm=T) |
| 144 |
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and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004) |
| 145 |
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for standard fwd & AD lab_sea tests (to keep the same output). |
| 146 |
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o pkg/seaice/seaice_growth.F: |
| 147 |
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- use Ian Fenty's capping formulas for actual ice |
| 148 |
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thickness thoughout EVOLUTION branch. |
| 149 |
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- put treatment pathological case #2) in CPP brackets |
| 150 |
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(ALLOW_AVOID_INFINITESIMAL_AREA, undef by default). |
| 151 |
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- update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly. |
| 152 |
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o pkg/seaice: |
| 153 |
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- seaice_diffusion.F : remove the min(DX,DY) factor permanently; |
| 154 |
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pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter; |
| 155 |
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also pass fac as a param, which can be 1. (to update the tendency |
| 156 |
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field) or the time step (to update the field itself). |
| 157 |
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- seaice_advdiff.F: for multidim, call seaice_diffusion with |
| 158 |
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e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call |
| 159 |
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seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step. |
| 160 |
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- SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F : |
| 161 |
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hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc. |
| 162 |
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o pkg/seaice: |
| 163 |
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diffusion with centered advection scheme (diffus.F & advect.F): |
| 164 |
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- simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside) |
| 165 |
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to just compute the laplacian of input-field. |
| 166 |
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- unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call. |
| 167 |
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- fix flux-form version in diffus.F to conserve tracer. |
| 168 |
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update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects |
| 169 |
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machine truncation) and lab_sea.salt_plume (conservative flux-form modif) |
| 170 |
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|
| 171 |
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checkpoint62y (2011/05/26) |
| 172 |
|
o pkg/seaice: |
| 173 |
|
- seaice_growth.F : in EVOLUTION branch, always include |
| 174 |
|
a_QSWbyATM_cover in qnet (as it should be). |
| 175 |
|
- verification/global_ocean.cs32x15 : update results accordingly |
| 176 |
|
(output.seaice.txt output_adm.seaice.txt). |
| 177 |
|
o pkg/seaice + obcs: |
| 178 |
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- use maskInW & maskInS in multi-dim advection and biharmonic diffusion: |
| 179 |
|
equivalent of assuming no tracer gradient outside the OB region. |
| 180 |
|
update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion) |
| 181 |
|
- remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed |
| 182 |
|
after changes above); |
| 183 |
|
- obcs+seaice cleaning: apply seaice-tracer OB values to tracer field |
| 184 |
|
only at OB location (instead of over a band of OLx width). |
| 185 |
|
o pkg/seaice: |
| 186 |
|
- fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F |
| 187 |
|
(dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid) |
| 188 |
|
o pkg/obcs: |
| 189 |
|
- split header file "OBCS.h" into 4 separated files: |
| 190 |
|
OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h |
| 191 |
|
Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h |
| 192 |
|
(contain no conditional statement which depends on OBCS options). |
| 193 |
|
- move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h) |
| 194 |
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to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h). |
| 195 |
|
o ctrl, cost, grdchk & autodiff pkgs: |
| 196 |
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- make options file more standard (like other {PKG}_OPTIONS.h file but |
| 197 |
|
with AD_CONFIG.h); clean-up some of the included header files. |
| 198 |
|
o pkg/obcs: |
| 199 |
|
- do not mask tracer when applying OB (tracer == 0 could generate problems) |
| 200 |
|
- apply tracer OB values to tracer field only at OB location (instead of |
| 201 |
|
over a band of OLx width) |
| 202 |
|
- clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R) |
| 203 |
|
- remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove |
| 204 |
|
obcs_apply_tloc.F & obcs_apply_sloc.F |
| 205 |
|
o obcs in model/src: |
| 206 |
|
- call OBCS_APPLY_W only if NonHydrostatic. |
| 207 |
|
- call OBCS_APPLY_ETA only if NonLinFreeSurf. |
| 208 |
|
- reset dEtaHdt and wVel to zero outside OB interior region ; |
| 209 |
|
- leave tracer unchanged outside OB interior region: This has no effect |
| 210 |
|
on the solution but just to prevent unrealistic tracer value outside OB. |
| 211 |
|
- zero out velocity outside OB interior region: This has no effect on |
| 212 |
|
the solution but just to prevent unrealistic velocity outside OB. |
| 213 |
|
o obcs and non-lin free-surf: |
| 214 |
|
move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F |
| 215 |
|
and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F |
| 216 |
|
+ add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR: |
| 217 |
|
this fixes missing EXCH + get consistent eta OB value (+ fix restart). |
| 218 |
|
update results of test-exp. exp4(nlfs). |
| 219 |
|
o exp4 (nlfs) test-exp: |
| 220 |
|
use OBC for Eta at Western & Eastern OB (to test prescribing Eta |
| 221 |
|
with NonLin-FreeSurf); update output.nlfs.txt |
| 222 |
|
o obcs and 2d/3d solver norm: |
| 223 |
|
use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB |
| 224 |
|
and outside OB interior region (will allow to place OB further inside the |
| 225 |
|
domain). Depending on the domain, can affects cg2d-Norm (previous |
| 226 |
|
cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl, |
| 227 |
|
and cg3d-Norm (previous Norm was computed before canceling OB terms), |
| 228 |
|
e.g. in tutorial_plume_on_slope. |
| 229 |
|
- update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope. |
| 230 |
|
o pkg rbcs: |
| 231 |
|
- split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h |
| 232 |
|
- add capability to apply relaxation to horizontal velocity uVel & vVel. |
| 233 |
|
o pkg/grdchk: add gradient check for control variable xx_shifwflx |
| 234 |
|
o pkg/shelfice/shelfice_init_fixed.F |
| 235 |
|
fix CPP-flag combinations |
| 236 |
|
o pkg/seaice: Merge iceage code of Pierre Rampal |
| 237 |
|
* update/change/correct ice age calculations |
| 238 |
|
* add age updates for pathological cases |
| 239 |
|
Probably needs more testing... |
| 240 |
|
|
| 241 |
|
checkpoint62x (2011/05/13) |
| 242 |
|
o pkg/mom_vecinv: |
| 243 |
|
high-order vorticity scheme: use interior masks (maskInW & S) |
| 244 |
|
to zero-out (outside OB) gradient of vorticity. |
| 245 |
|
o verification exp.: |
| 246 |
|
turn on "useEnergyConservingCoriolis" (better discretisation) in exp. |
| 247 |
|
hs94.128x64x5 and seaice_obcs ; update results. |
| 248 |
|
o pkg/obcs: |
| 249 |
|
fix bug in OBeta for YZ sections in obcs_exf_load.F |
| 250 |
|
o pkg/ctrl, pkg/shelfice, and optim: |
| 251 |
|
- add new control variable xx_shifwflx (fresh water flux underneath ice |
| 252 |
|
shelves). This is almost as tedious as obcs-ctrl, because the |
| 253 |
|
variables needs its own mask. |
| 254 |
|
- add a cost function term that penalizes the deviation of xx_shifwflx |
| 255 |
|
from the first guess (zero) in analogy to other control variables |
| 256 |
|
o pkg/shelfice: |
| 257 |
|
- start basic adjoint |
| 258 |
|
o pkg/ctrl: |
| 259 |
|
- remove extra 2D field "for good measure" when initializing in |
| 260 |
|
ctrl_set_globfld_[xy/xz/yz].F |
| 261 |
|
- replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec |
| 262 |
|
- improve error messages in ctrl_set_unpack_* |
| 263 |
|
o OBC implementation in momentum: |
| 264 |
|
use interior masks (maskInC,W & S) in momentum S/R: |
| 265 |
|
- multiply divergence, tension and some del^i.u or del^j.v by maskInC |
| 266 |
|
- multiply del2u,del2v by maskInW/S (biharmonic viscosity) |
| 267 |
|
- multiply horiz. grad of vorticity by maskInW/S (in Leith scheme) |
| 268 |
|
- multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd) |
| 269 |
|
Motivation: fix/clean implementation of OBC with biharmonic-viscosity |
| 270 |
|
(and also with Leith/Smagorinsky harmonic-viscosity). |
| 271 |
|
Update output of experiment dome and exp4 (+nlfs). |
| 272 |
o exp4 test-exp: |
o exp4 test-exp: |
| 273 |
|
- turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F) |
| 274 |
|
and prescribe time-varying OB (without pkg/exf) for zonal-velocity |
| 275 |
|
at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe |
| 276 |
|
time-varying OB at Western-side for wVel (NonHyd); update output. |
| 277 |
- add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv |
- add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv |
| 278 |
and biharmonic-viscosity ; prescribe time varying OB but without pkg/exf. |
and biharmonic-viscosity ; also use prescribed time varying OB. |
| 279 |
o pkg/obcs: |
o pkg/obcs: |
| 280 |
fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F |
fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F |
| 281 |
o model/src: |
o model/src: |
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