4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
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|
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o pkg/diagnostics: |
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- deal with pairs of post-processed diags which are computed together; in |
9 |
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particular, re-order list of diags within 1 file to save 2nd computation. |
10 |
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- add S/R to compute velocity stream-function (called after velocity-potential |
11 |
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calculation) from divergence free transport -> new diagnostics "PsiVEL". |
12 |
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- add parameter to select grid-point location where PsiVEL == 0. |
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o eesupp/src: |
14 |
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new S/R to calculate cumulated sum on tiled array, corner grid-cell location |
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(specific S/R needed with exch2 topology - for now, just print an error msg) |
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o pkg/shelfice |
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- Implement friction velocity-dependent transfer coefficients following |
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Holland and Jenkins, JPO, 1999 |
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Original code by M. Losch with small modifs. |
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Enable with CPP option SHI_ALLOW_GAMMAFRICT |
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and runtime flag SHELFICEuseGammaFrict |
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o verification lab_sea & global_ocean.cs32x15: |
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- use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local): |
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does not miss some dependencies (but is slower) and also works with many files |
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(default makedepend limitation for AD built). |
26 |
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- use cyrus_makedepend in adjustment.128x64x1 (so that it still tested). |
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o pkg/diagnostics: |
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- add run-time parameter "useMissingValue" (def=False) to fill land-point |
29 |
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(i.e., where mask=0) with MissingValue ; used only in MNC output file. |
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This replaces CPP-option DIAGNOSTICS_MISSING_VALUE. |
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- Extend the use of "missing_value" setting from data.diagnostics for the case |
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of counter-diagnostics (where fraction-weight is zero). This applies both to |
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MNC and MDS output files. |
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o pkg/seaice/seaice_growth.F: |
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- add 'a priori' cap of latent heat flux based on actual mass considerations |
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when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the |
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non-legacy seaice_solve4temp. |
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- add diagnostic of the residual sublimation freshwater flux (the freshwater |
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flux taken from the ocean if the total actual latent heat fluxes exceed |
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the maximum) |
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- remove the CPP switch around the *_FWbySublim unit change and move diagnostic |
42 |
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fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F. |
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- add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef |
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SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim). |
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- bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET. |
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- bug fix : missing part to Martin's r_FWbySublim pathological case fix. |
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o verification 1D_ocean_ice_column: |
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made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet |
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update results |
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o pkg/diagnostics: |
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- Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P') |
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which are not filled-up but computed from other diags ; In this case, the mate |
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diag points to the primary (filled-up) diag to used for post processing. |
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- Update Velocity-potential computation using post-processed diag framework. |
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==> Change the ordering of fields and time-periods in MDS output file |
56 |
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when using periodic averaging: now writes one time record with the full set |
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of fields for this time period, then the next time reccord (it used to be |
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one field with the full set of time records then the next field). |
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Note: this is now similar to NetCDF (MNC) output file. <== |
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|
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checkpoint62z (2011/06/21) |
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o adjoint monitor: |
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- Add adjoint monitor output for packages exf, seaice |
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and update relevant testreport output |
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o pkg/seaice: |
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- re-order diags inits so that they appear in order in available_diagnostics.log |
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- added diags: hsnow thermo. rates of change, area preceeding ridiging process, |
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area/heff/hsnow preceeding thermodynamic growth/melt. |
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- modified diag: SIdA; output actual effect, as the description states. |
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- modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW. |
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- retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh. |
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(SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO; |
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and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO) |
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- modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates. |
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- added diagnostics for seaice generic tracers (SItr*). |
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- added SItrUnit and SItrNameLong run time param (for SItr* diags). |
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- in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'. |
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I. Fenty: 18-Jun-2011: |
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Minor changes to seaice package: |
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1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and |
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added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor) |
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- Differentiated "regularization variables" from "floor variables" |
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* areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor |
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* hiceMin became SEAICE_hice_reg (old hiceMin) |
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(with _reg meaning regularization variable) |
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- SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion |
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so as to ensure energy conservation when going between phases |
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- A22 was not used anywhere |
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2) Changed regularization procedure for heffActual and hsnowActual to ensure |
90 |
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well-boundedness and smooth adjoint in seaice_growth.F |
91 |
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3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells |
92 |
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because the old regularization always set heffActual >= 0.05 cm |
93 |
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4) Changed the model so that the default behavior is to put a small (10^-5) "floor" |
94 |
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on AREA when HEFF > 0. |
95 |
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- went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to |
96 |
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requiring that DISABLE_AREA_FLOOR *not* be defined |
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Affected verifications: |
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- 1D_ocean_ice_column (output.txt output_adm.txt) |
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- global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt) |
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o pkg/diagnostics: |
101 |
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- move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R). |
102 |
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- rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument |
103 |
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(was _RL, now integer) with option = 0 to retrieve all levels. |
104 |
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- add pieces of code to compute velocity potential at each level (new diagnostics |
105 |
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PhiVEL, works only when UVELMASS & VVELMASS are also turned on); |
106 |
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for now, using same params as CG2D (target-resisual, max Nb of iter ...). |
107 |
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- fix few issues with counter diagnostics in diagnostics_setdiag.F & |
108 |
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diagstats_setdiag.F (if diagnostic counter is itself a counter diag) |
109 |
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and in diagnostics_fract_fill.F (do not need a valid pointer for the |
110 |
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diagnostics counter-mate); check that definition of counter-diagnostic |
111 |
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includes a valid counter-mate (in diagnostics_set_levels.F). |
112 |
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o model/src (rStar): |
113 |
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- add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F); |
114 |
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affect solution only if z* with full pressure in EOS; |
115 |
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update output of test-exp global_ocean.90x40x15. |
116 |
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o pkg/seaice: |
117 |
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- introduce siEps=1e-5 parameter |
118 |
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- use areaMax in AREA update (part 4), consistent with ridging step (part 2.5). |
119 |
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- re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code. |
120 |
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- introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer. |
121 |
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For now it covers, and was tested for, ice salinity and age (attached to HEFF), |
122 |
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as well as ice cover age and ridging index (attached to AREA). |
123 |
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For now the run time parameters (in data.seaice/SEAICE_PARM03) are |
124 |
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SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA'). |
125 |
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Up to SItrMaxNum=3 tracers can be used simultaneously. |
126 |
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o pkg/salt_plume: |
127 |
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-introduce SPsalFRAC run time parameter that sets the fraction of the |
128 |
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salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically) |
129 |
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that gets vertically redistributed (fluxed down) by pkg/salt_plume. |
130 |
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o model debug options: |
131 |
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- Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored |
132 |
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in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h). |
133 |
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- Refine debug-msg printing selection (3 new levels): |
134 |
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debugMode : controls printing of debug messages (sequence of S/R calls). |
135 |
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debugLevel : controls printing of algorithm-relevant auxiliary/debug messages |
136 |
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debLevZero = 0 ; /* level of disabled aux. msg printing */ |
137 |
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debLevA = 1 ; /* level of minimum aux. msg printing */ |
138 |
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debLevB = 2 ; /* level of low aux. print (report read-file opening)*/ |
139 |
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debLevC = 3 ; /* level of moderate debug prt (most pkgs debug msg) */ |
140 |
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debLevD = 4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */ |
141 |
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debLevE = 5 ; /* level of extensive debug printing */ |
142 |
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New debugLevel default: with default debugMode value (=F), |
143 |
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= 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.; |
144 |
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and if debugMode=T, default debugLevel = 4 (debLevD). |
145 |
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Relation with previous settings: |
146 |
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debLevB (=2) corresponds to former debLevA (=1) |
147 |
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debLevD (=4) corresponds to former debLevB (=2) |
148 |
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Note: |
149 |
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a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before); |
150 |
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b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs); |
151 |
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to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5) |
152 |
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- Add new parameter (printResidualFreq, read from PARM02 namelist) to print |
153 |
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detailed CG solvers convergence; off (=0) by default, except if debugLevel=5. |
154 |
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o pkg/obcs: |
155 |
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- change OBCSfixTopo default from True to False (should not change the results); |
156 |
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keep OBCSfixTopo=T in verification-exp. seaice_obcs. |
157 |
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o pkg/thsice: |
158 |
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- fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in |
159 |
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2nd layer seaice sublimation (unlikely to happen) |
160 |
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- use Interior mask for OBCS in thsice_advection.F (similar to what is |
161 |
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done in gad_advection & seaice_advection). |
162 |
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o adjoint: |
163 |
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bug fix spotted by Gael Forget: |
164 |
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seaice_advection and thsice_advection still had |
165 |
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legacy CPP options to avoid CS corner updates for adjoint |
166 |
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o pkg/seaice: |
167 |
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=> Change some of the defaults (2011/05/29): |
168 |
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- change SEAICEuseFluxForm default (from False to True) |
169 |
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- change DIFF1 default (from 0.004 m/s to 0. m/s) |
170 |
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And print warnings if DIFF1 is not set in data.seaice and centered |
171 |
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avection scheme is used without any diffusion. |
172 |
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also: |
173 |
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- fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F; |
174 |
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- set SEAICEdiffKh[] default in the same way as SEAICEadvSch[] |
175 |
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- stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any |
176 |
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other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with |
177 |
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#undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE. |
178 |
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update results of test exp.: |
179 |
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lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20) |
180 |
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output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200) |
181 |
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output_adm.noseaicedyn (SEAICEuseFluxForm=T) |
182 |
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offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T) |
183 |
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seaice_obcs: output (SEAICEuseFluxForm=T) |
184 |
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and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004) |
185 |
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for standard fwd & AD lab_sea tests (to keep the same output). |
186 |
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o pkg/seaice/seaice_growth.F: |
187 |
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- use Ian Fenty's capping formulas for actual ice |
188 |
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thickness thoughout EVOLUTION branch. |
189 |
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- put treatment pathological case #2) in CPP brackets |
190 |
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(ALLOW_AVOID_INFINITESIMAL_AREA, undef by default). |
191 |
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- update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly. |
192 |
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o pkg/seaice: |
193 |
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- seaice_diffusion.F : remove the min(DX,DY) factor permanently; |
194 |
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pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter; |
195 |
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also pass fac as a param, which can be 1. (to update the tendency |
196 |
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field) or the time step (to update the field itself). |
197 |
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- seaice_advdiff.F: for multidim, call seaice_diffusion with |
198 |
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e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call |
199 |
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seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step. |
200 |
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- SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F : |
201 |
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hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc. |
202 |
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o pkg/seaice: |
203 |
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diffusion with centered advection scheme (diffus.F & advect.F): |
204 |
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- simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside) |
205 |
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to just compute the laplacian of input-field. |
206 |
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- unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call. |
207 |
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- fix flux-form version in diffus.F to conserve tracer. |
208 |
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update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects |
209 |
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machine truncation) and lab_sea.salt_plume (conservative flux-form modif) |
210 |
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|
211 |
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checkpoint62y (2011/05/26) |
212 |
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o pkg/seaice: |
213 |
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- seaice_growth.F : in EVOLUTION branch, always include |
214 |
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a_QSWbyATM_cover in qnet (as it should be). |
215 |
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- verification/global_ocean.cs32x15 : update results accordingly |
216 |
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(output.seaice.txt output_adm.seaice.txt). |
217 |
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o pkg/seaice + obcs: |
218 |
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- use maskInW & maskInS in multi-dim advection and biharmonic diffusion: |
219 |
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equivalent of assuming no tracer gradient outside the OB region. |
220 |
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update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion) |
221 |
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- remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed |
222 |
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after changes above); |
223 |
|
- obcs+seaice cleaning: apply seaice-tracer OB values to tracer field |
224 |
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only at OB location (instead of over a band of OLx width). |
225 |
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o pkg/seaice: |
226 |
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- fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F |
227 |
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(dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid) |
228 |
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o pkg/obcs: |
229 |
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- split header file "OBCS.h" into 4 separated files: |
230 |
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OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h |
231 |
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Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h |
232 |
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(contain no conditional statement which depends on OBCS options). |
233 |
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- move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h) |
234 |
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to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h). |
235 |
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o ctrl, cost, grdchk & autodiff pkgs: |
236 |
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- make options file more standard (like other {PKG}_OPTIONS.h file but |
237 |
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with AD_CONFIG.h); clean-up some of the included header files. |
238 |
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o pkg/obcs: |
239 |
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- do not mask tracer when applying OB (tracer == 0 could generate problems) |
240 |
|
- apply tracer OB values to tracer field only at OB location (instead of |
241 |
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over a band of OLx width) |
242 |
|
- clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R) |
243 |
|
- remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove |
244 |
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obcs_apply_tloc.F & obcs_apply_sloc.F |
245 |
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o obcs in model/src: |
246 |
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- call OBCS_APPLY_W only if NonHydrostatic. |
247 |
|
- call OBCS_APPLY_ETA only if NonLinFreeSurf. |
248 |
|
- reset dEtaHdt and wVel to zero outside OB interior region ; |
249 |
|
- leave tracer unchanged outside OB interior region: This has no effect |
250 |
|
on the solution but just to prevent unrealistic tracer value outside OB. |
251 |
|
- zero out velocity outside OB interior region: This has no effect on |
252 |
|
the solution but just to prevent unrealistic velocity outside OB. |
253 |
|
o obcs and non-lin free-surf: |
254 |
|
move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F |
255 |
|
and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F |
256 |
|
+ add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR: |
257 |
|
this fixes missing EXCH + get consistent eta OB value (+ fix restart). |
258 |
|
update results of test-exp. exp4(nlfs). |
259 |
|
o exp4 (nlfs) test-exp: |
260 |
|
use OBC for Eta at Western & Eastern OB (to test prescribing Eta |
261 |
|
with NonLin-FreeSurf); update output.nlfs.txt |
262 |
|
o obcs and 2d/3d solver norm: |
263 |
|
use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB |
264 |
|
and outside OB interior region (will allow to place OB further inside the |
265 |
|
domain). Depending on the domain, can affects cg2d-Norm (previous |
266 |
|
cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl, |
267 |
|
and cg3d-Norm (previous Norm was computed before canceling OB terms), |
268 |
|
e.g. in tutorial_plume_on_slope. |
269 |
|
- update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope. |
270 |
|
o pkg rbcs: |
271 |
|
- split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h |
272 |
|
- add capability to apply relaxation to horizontal velocity uVel & vVel. |
273 |
|
o pkg/grdchk: add gradient check for control variable xx_shifwflx |
274 |
|
o pkg/shelfice/shelfice_init_fixed.F |
275 |
|
fix CPP-flag combinations |
276 |
|
o pkg/seaice: Merge iceage code of Pierre Rampal |
277 |
|
* update/change/correct ice age calculations |
278 |
|
* add age updates for pathological cases |
279 |
|
Probably needs more testing... |
280 |
|
|
281 |
|
checkpoint62x (2011/05/13) |
282 |
|
o pkg/mom_vecinv: |
283 |
|
high-order vorticity scheme: use interior masks (maskInW & S) |
284 |
|
to zero-out (outside OB) gradient of vorticity. |
285 |
|
o verification exp.: |
286 |
|
turn on "useEnergyConservingCoriolis" (better discretisation) in exp. |
287 |
|
hs94.128x64x5 and seaice_obcs ; update results. |
288 |
|
o pkg/obcs: |
289 |
|
fix bug in OBeta for YZ sections in obcs_exf_load.F |
290 |
|
o pkg/ctrl, pkg/shelfice, and optim: |
291 |
|
- add new control variable xx_shifwflx (fresh water flux underneath ice |
292 |
|
shelves). This is almost as tedious as obcs-ctrl, because the |
293 |
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variables needs its own mask. |
294 |
|
- add a cost function term that penalizes the deviation of xx_shifwflx |
295 |
|
from the first guess (zero) in analogy to other control variables |
296 |
|
o pkg/shelfice: |
297 |
|
- start basic adjoint |
298 |
|
o pkg/ctrl: |
299 |
|
- remove extra 2D field "for good measure" when initializing in |
300 |
|
ctrl_set_globfld_[xy/xz/yz].F |
301 |
|
- replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec |
302 |
|
- improve error messages in ctrl_set_unpack_* |
303 |
|
o OBC implementation in momentum: |
304 |
|
use interior masks (maskInC,W & S) in momentum S/R: |
305 |
|
- multiply divergence, tension and some del^i.u or del^j.v by maskInC |
306 |
|
- multiply del2u,del2v by maskInW/S (biharmonic viscosity) |
307 |
|
- multiply horiz. grad of vorticity by maskInW/S (in Leith scheme) |
308 |
|
- multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd) |
309 |
|
Motivation: fix/clean implementation of OBC with biharmonic-viscosity |
310 |
|
(and also with Leith/Smagorinsky harmonic-viscosity). |
311 |
|
Update output of experiment dome and exp4 (+nlfs). |
312 |
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o exp4 test-exp: |
313 |
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- turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F) |
314 |
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and prescribe time-varying OB (without pkg/exf) for zonal-velocity |
315 |
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at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe |
316 |
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time-varying OB at Western-side for wVel (NonHyd); update output. |
317 |
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- add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv |
318 |
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and biharmonic-viscosity ; also use prescribed time varying OB. |
319 |
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o pkg/obcs: |
320 |
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fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F |
321 |
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o model/src: |
322 |
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- fix startTime setting when baseTime<>0 & nIter0=0 are specified ; |
323 |
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- initialise startTime & nIter0 with unlikely values: allows to set one |
324 |
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from the other without ambiguity. |
325 |
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o seaice_obcs test-exp.: |
326 |
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add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output. |
327 |
o pkg/obcs: |
o pkg/obcs: |
328 |
- remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer: |
- remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer: |
329 |
no longer needed with maskInC,W,S in pkg/generic_advdiff. |
no longer needed with maskInC,W,S in pkg/generic_advdiff. |