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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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|
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o optim/optim_readdata.F: |
8 |
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- add some output about obcs variables that might help debugging |
9 |
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- add a check about nvarlength |
10 |
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o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec |
11 |
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o pkg/diagnostics (velocity potential): |
12 |
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- fix mask for OBCS (still problems in stream-function with OBCS); |
13 |
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- add specific parameter (default = main code CG2D params) for solver; |
14 |
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- in case of poor convergence, use solution corresponding to lowest residual. |
15 |
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o pkg/seaice/seaice_growth.F: small changes that permit vectorizable |
16 |
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adjoint code. In general statements like tmpscal=fld(i,j) are problematic |
17 |
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and should be avoided where possible. |
18 |
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o model/src (rStar): |
19 |
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- include r* effect on reference-state (PhiRef) in totPhiHyd |
20 |
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(so that it's really the potential anomaly at the cell center); |
21 |
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affect solution only if z* with full pressure in EOS. |
22 |
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- test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and |
23 |
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update output (because of z* in totPhiHyd and viscA4 changes); |
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- keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly |
25 |
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@ constant r) until interpolation at constant r is implemented. |
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o pkg/diagnostics |
27 |
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- fix RCENTER diagnostics in case cell center is not at interface middle |
28 |
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o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use |
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this eos with eosType = 'TEOS10', in data (PARM01). This eos implies |
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that THETA and SALT are "conservative temperature" and "absolute |
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salinity" |
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o pkg/ctrl |
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- fix computation of endrec in s/r ctrl_init_rec |
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- ctrl_pack/unpack_*: remove unused variables and some obsolete code |
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o pkg/seaice/seaice_growth.F |
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- fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code, |
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remove then obsolete STORE directives |
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- fix STORE directives for tice and tices, so that only the |
39 |
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appropriate part of the fields are stored (and not the entire |
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field); update global_ocean.cs32x15.seaice AD output. |
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- cosmetic changes: adjust CPP flags and indentation for better |
42 |
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legibilty |
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o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by |
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Chris Wilson) |
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o pkg/gmredi: |
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Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF), |
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and test it in verification exp. "front_relax.bvp" (update output.bvp.txt) |
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|
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checkpoint63 (2011/07/11) |
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o pkg/exch2: |
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- rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h |
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- exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the |
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(2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y |
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increments, calculates Cumul-Sum @ tile origin and sends results to each tile. |
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o pkg/diagnostics: |
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- deal with pairs of post-processed diags which are computed together; in |
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particular, re-order list of diags within 1 file to save 2nd computation. |
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- add S/R to compute velocity stream-function (called after velocity-potential |
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calculation) from divergence free transport -> new diagnostics "PsiVEL". |
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- add parameter to select grid-point location where PsiVEL == 0. |
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o eesupp/src: |
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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). |
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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 |
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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. |
86 |
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- add diagnostic of the residual sublimation freshwater flux (the freshwater |
87 |
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flux taken from the ocean if the total actual latent heat fluxes exceed |
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the maximum) |
89 |
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- remove the CPP switch around the *_FWbySublim unit change and move diagnostic |
90 |
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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. |
94 |
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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 |
101 |
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diag points to the primary (filled-up) diag to used for post processing. |
102 |
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- Update Velocity-potential computation using post-processed diag framework. |
103 |
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==> Change the ordering of fields and time-periods in MDS output file |
104 |
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when using periodic averaging: now writes one time record with the full set |
105 |
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of fields for this time period, then the next time reccord (it used to be |
106 |
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one field with the full set of time records then the next field). |
107 |
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Note: this is now similar to NetCDF (MNC) output file. <== |
108 |
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|
109 |
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checkpoint62z (2011/06/21) |
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o adjoint monitor: |
111 |
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- Add adjoint monitor output for packages exf, seaice |
112 |
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and update relevant testreport output |
113 |
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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 |
115 |
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- added diags: hsnow thermo. rates of change, area preceeding ridiging process, |
116 |
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area/heff/hsnow preceeding thermodynamic growth/melt. |
117 |
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- modified diag: SIdA; output actual effect, as the description states. |
118 |
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- modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW. |
119 |
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- retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh. |
120 |
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(SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO; |
121 |
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and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO) |
122 |
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- modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates. |
123 |
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- added diagnostics for seaice generic tracers (SItr*). |
124 |
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- added SItrUnit and SItrNameLong run time param (for SItr* diags). |
125 |
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- in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'. |
126 |
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I. Fenty: 18-Jun-2011: |
127 |
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Minor changes to seaice package: |
128 |
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1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and |
129 |
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added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor) |
130 |
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- Differentiated "regularization variables" from "floor variables" |
131 |
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* areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor |
132 |
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* hiceMin became SEAICE_hice_reg (old hiceMin) |
133 |
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(with _reg meaning regularization variable) |
134 |
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- SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion |
135 |
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so as to ensure energy conservation when going between phases |
136 |
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- A22 was not used anywhere |
137 |
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2) Changed regularization procedure for heffActual and hsnowActual to ensure |
138 |
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well-boundedness and smooth adjoint in seaice_growth.F |
139 |
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3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells |
140 |
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because the old regularization always set heffActual >= 0.05 cm |
141 |
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4) Changed the model so that the default behavior is to put a small (10^-5) "floor" |
142 |
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on AREA when HEFF > 0. |
143 |
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- went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to |
144 |
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requiring that DISABLE_AREA_FLOOR *not* be defined |
145 |
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Affected verifications: |
146 |
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- 1D_ocean_ice_column (output.txt output_adm.txt) |
147 |
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- global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt) |
148 |
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o pkg/diagnostics: |
149 |
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- move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R). |
150 |
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- rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument |
151 |
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(was _RL, now integer) with option = 0 to retrieve all levels. |
152 |
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- add pieces of code to compute velocity potential at each level (new diagnostics |
153 |
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PhiVEL, works only when UVELMASS & VVELMASS are also turned on); |
154 |
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for now, using same params as CG2D (target-resisual, max Nb of iter ...). |
155 |
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- fix few issues with counter diagnostics in diagnostics_setdiag.F & |
156 |
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diagstats_setdiag.F (if diagnostic counter is itself a counter diag) |
157 |
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and in diagnostics_fract_fill.F (do not need a valid pointer for the |
158 |
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diagnostics counter-mate); check that definition of counter-diagnostic |
159 |
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includes a valid counter-mate (in diagnostics_set_levels.F). |
160 |
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o model/src (rStar): |
161 |
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- add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F); |
162 |
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affect solution only if z* with full pressure in EOS; |
163 |
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update output of test-exp global_ocean.90x40x15. |
164 |
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o pkg/seaice: |
165 |
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- introduce siEps=1e-5 parameter |
166 |
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- use areaMax in AREA update (part 4), consistent with ridging step (part 2.5). |
167 |
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- re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code. |
168 |
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- introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer. |
169 |
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For now it covers, and was tested for, ice salinity and age (attached to HEFF), |
170 |
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as well as ice cover age and ridging index (attached to AREA). |
171 |
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For now the run time parameters (in data.seaice/SEAICE_PARM03) are |
172 |
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SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA'). |
173 |
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Up to SItrMaxNum=3 tracers can be used simultaneously. |
174 |
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o pkg/salt_plume: |
175 |
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-introduce SPsalFRAC run time parameter that sets the fraction of the |
176 |
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salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically) |
177 |
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that gets vertically redistributed (fluxed down) by pkg/salt_plume. |
178 |
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o model debug options: |
179 |
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- Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored |
180 |
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in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h). |
181 |
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- Refine debug-msg printing selection (3 new levels): |
182 |
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debugMode : controls printing of debug messages (sequence of S/R calls). |
183 |
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debugLevel : controls printing of algorithm-relevant auxiliary/debug messages |
184 |
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debLevZero = 0 ; /* level of disabled aux. msg printing */ |
185 |
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debLevA = 1 ; /* level of minimum aux. msg printing */ |
186 |
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debLevB = 2 ; /* level of low aux. print (report read-file opening)*/ |
187 |
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debLevC = 3 ; /* level of moderate debug prt (most pkgs debug msg) */ |
188 |
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debLevD = 4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */ |
189 |
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debLevE = 5 ; /* level of extensive debug printing */ |
190 |
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New debugLevel default: with default debugMode value (=F), |
191 |
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= 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.; |
192 |
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and if debugMode=T, default debugLevel = 4 (debLevD). |
193 |
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Relation with previous settings: |
194 |
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debLevB (=2) corresponds to former debLevA (=1) |
195 |
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debLevD (=4) corresponds to former debLevB (=2) |
196 |
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Note: |
197 |
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a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before); |
198 |
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b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs); |
199 |
|
to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5) |
200 |
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- Add new parameter (printResidualFreq, read from PARM02 namelist) to print |
201 |
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detailed CG solvers convergence; off (=0) by default, except if debugLevel=5. |
202 |
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o pkg/obcs: |
203 |
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- change OBCSfixTopo default from True to False (should not change the results); |
204 |
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keep OBCSfixTopo=T in verification-exp. seaice_obcs. |
205 |
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o pkg/thsice: |
206 |
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- fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in |
207 |
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2nd layer seaice sublimation (unlikely to happen) |
208 |
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- use Interior mask for OBCS in thsice_advection.F (similar to what is |
209 |
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done in gad_advection & seaice_advection). |
210 |
|
o adjoint: |
211 |
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bug fix spotted by Gael Forget: |
212 |
|
seaice_advection and thsice_advection still had |
213 |
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legacy CPP options to avoid CS corner updates for adjoint |
214 |
|
o pkg/seaice: |
215 |
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=> Change some of the defaults (2011/05/29): |
216 |
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- change SEAICEuseFluxForm default (from False to True) |
217 |
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- change DIFF1 default (from 0.004 m/s to 0. m/s) |
218 |
|
And print warnings if DIFF1 is not set in data.seaice and centered |
219 |
|
avection scheme is used without any diffusion. |
220 |
|
also: |
221 |
|
- fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F; |
222 |
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- set SEAICEdiffKh[] default in the same way as SEAICEadvSch[] |
223 |
|
- stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any |
224 |
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other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with |
225 |
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#undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE. |
226 |
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update results of test exp.: |
227 |
|
lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20) |
228 |
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output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200) |
229 |
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output_adm.noseaicedyn (SEAICEuseFluxForm=T) |
230 |
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offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T) |
231 |
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seaice_obcs: output (SEAICEuseFluxForm=T) |
232 |
|
and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004) |
233 |
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for standard fwd & AD lab_sea tests (to keep the same output). |
234 |
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o pkg/seaice/seaice_growth.F: |
235 |
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- use Ian Fenty's capping formulas for actual ice |
236 |
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thickness thoughout EVOLUTION branch. |
237 |
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- put treatment pathological case #2) in CPP brackets |
238 |
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(ALLOW_AVOID_INFINITESIMAL_AREA, undef by default). |
239 |
|
- update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly. |
240 |
|
o pkg/seaice: |
241 |
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- seaice_diffusion.F : remove the min(DX,DY) factor permanently; |
242 |
|
pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter; |
243 |
|
also pass fac as a param, which can be 1. (to update the tendency |
244 |
|
field) or the time step (to update the field itself). |
245 |
|
- seaice_advdiff.F: for multidim, call seaice_diffusion with |
246 |
|
e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call |
247 |
|
seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step. |
248 |
|
- SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F : |
249 |
|
hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc. |
250 |
|
o pkg/seaice: |
251 |
|
diffusion with centered advection scheme (diffus.F & advect.F): |
252 |
|
- simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside) |
253 |
|
to just compute the laplacian of input-field. |
254 |
|
- unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call. |
255 |
|
- fix flux-form version in diffus.F to conserve tracer. |
256 |
|
update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects |
257 |
|
machine truncation) and lab_sea.salt_plume (conservative flux-form modif) |
258 |
|
|
259 |
|
checkpoint62y (2011/05/26) |
260 |
|
o pkg/seaice: |
261 |
|
- seaice_growth.F : in EVOLUTION branch, always include |
262 |
|
a_QSWbyATM_cover in qnet (as it should be). |
263 |
|
- verification/global_ocean.cs32x15 : update results accordingly |
264 |
|
(output.seaice.txt output_adm.seaice.txt). |
265 |
|
o pkg/seaice + obcs: |
266 |
|
- use maskInW & maskInS in multi-dim advection and biharmonic diffusion: |
267 |
|
equivalent of assuming no tracer gradient outside the OB region. |
268 |
|
update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion) |
269 |
|
- remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed |
270 |
|
after changes above); |
271 |
|
- obcs+seaice cleaning: apply seaice-tracer OB values to tracer field |
272 |
|
only at OB location (instead of over a band of OLx width). |
273 |
|
o pkg/seaice: |
274 |
|
- fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F |
275 |
|
(dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid) |
276 |
o pkg/obcs: |
o pkg/obcs: |
277 |
- split header file "OBCS.h" into 4 separated files: |
- split header file "OBCS.h" into 4 separated files: |
278 |
OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h |
OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h |
279 |
Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h |
Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h |
280 |
(contain no conditional statement that depends on OBCS options). |
(contain no conditional statement which depends on OBCS options). |
281 |
|
- move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h) |
282 |
|
to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h). |
283 |
o ctrl, cost, grdchk & autodiff pkgs: |
o ctrl, cost, grdchk & autodiff pkgs: |
284 |
- make options file more standard (like other {PKG}_OPTIONS.h file but |
- make options file more standard (like other {PKG}_OPTIONS.h file but |
285 |
with AD_CONFIG.h); clean-up some of the included header files. |
with AD_CONFIG.h); clean-up some of the included header files. |