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/exch2: |
8 |
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- rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h |
9 |
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- exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the |
10 |
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(2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y |
11 |
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increments, calculates Cumul-Sum @ tile origin and sends results to each tile. |
12 |
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o pkg/diagnostics: |
13 |
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- deal with pairs of post-processed diags which are computed together; in |
14 |
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particular, re-order list of diags within 1 file to save 2nd computation. |
15 |
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- add S/R to compute velocity stream-function (called after velocity-potential |
16 |
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calculation) from divergence free transport -> new diagnostics "PsiVEL". |
17 |
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- add parameter to select grid-point location where PsiVEL == 0. |
18 |
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o eesupp/src: |
19 |
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new S/R to calculate cumulated sum on tiled array, corner grid-cell location |
20 |
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(specific S/R needed with exch2 topology - for now, just print an error msg) |
21 |
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o pkg/shelfice |
22 |
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- Implement friction velocity-dependent transfer coefficients following |
23 |
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Holland and Jenkins, JPO, 1999 |
24 |
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Original code by M. Losch with small modifs. |
25 |
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Enable with CPP option SHI_ALLOW_GAMMAFRICT |
26 |
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and runtime flag SHELFICEuseGammaFrict |
27 |
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o verification lab_sea & global_ocean.cs32x15: |
28 |
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- use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local): |
29 |
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does not miss some dependencies (but is slower) and also works with many files |
30 |
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(default makedepend limitation for AD built). |
31 |
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- use cyrus_makedepend in adjustment.128x64x1 (so that it still tested). |
32 |
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o pkg/diagnostics: |
33 |
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- add run-time parameter "useMissingValue" (def=False) to fill land-point |
34 |
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(i.e., where mask=0) with MissingValue ; used only in MNC output file. |
35 |
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This replaces CPP-option DIAGNOSTICS_MISSING_VALUE. |
36 |
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- Extend the use of "missing_value" setting from data.diagnostics for the case |
37 |
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of counter-diagnostics (where fraction-weight is zero). This applies both to |
38 |
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MNC and MDS output files. |
39 |
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o pkg/seaice/seaice_growth.F: |
40 |
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- add 'a priori' cap of latent heat flux based on actual mass considerations |
41 |
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when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the |
42 |
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non-legacy seaice_solve4temp. |
43 |
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- add diagnostic of the residual sublimation freshwater flux (the freshwater |
44 |
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flux taken from the ocean if the total actual latent heat fluxes exceed |
45 |
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the maximum) |
46 |
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- remove the CPP switch around the *_FWbySublim unit change and move diagnostic |
47 |
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fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F. |
48 |
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- add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef |
49 |
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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. |
51 |
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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 |
54 |
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update results |
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o pkg/diagnostics: |
56 |
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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 |
58 |
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diag points to the primary (filled-up) diag to used for post processing. |
59 |
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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 |
61 |
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when using periodic averaging: now writes one time record with the full set |
62 |
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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). |
64 |
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Note: this is now similar to NetCDF (MNC) output file. <== |
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|
66 |
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checkpoint62z (2011/06/21) |
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o adjoint monitor: |
68 |
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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 |
72 |
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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. |
74 |
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- modified diag: SIdA; output actual effect, as the description states. |
75 |
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- modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW. |
76 |
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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) |
79 |
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- modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates. |
80 |
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- added diagnostics for seaice generic tracers (SItr*). |
81 |
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- added SItrUnit and SItrNameLong run time param (for SItr* diags). |
82 |
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- in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'. |
83 |
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I. Fenty: 18-Jun-2011: |
84 |
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Minor changes to seaice package: |
85 |
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1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and |
86 |
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added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor) |
87 |
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- Differentiated "regularization variables" from "floor variables" |
88 |
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* areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor |
89 |
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* hiceMin became SEAICE_hice_reg (old hiceMin) |
90 |
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(with _reg meaning regularization variable) |
91 |
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- SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion |
92 |
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so as to ensure energy conservation when going between phases |
93 |
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- A22 was not used anywhere |
94 |
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2) Changed regularization procedure for heffActual and hsnowActual to ensure |
95 |
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well-boundedness and smooth adjoint in seaice_growth.F |
96 |
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3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells |
97 |
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because the old regularization always set heffActual >= 0.05 cm |
98 |
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4) Changed the model so that the default behavior is to put a small (10^-5) "floor" |
99 |
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on AREA when HEFF > 0. |
100 |
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- went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to |
101 |
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requiring that DISABLE_AREA_FLOOR *not* be defined |
102 |
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Affected verifications: |
103 |
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- 1D_ocean_ice_column (output.txt output_adm.txt) |
104 |
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- global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt) |
105 |
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o pkg/diagnostics: |
106 |
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- move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R). |
107 |
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- rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument |
108 |
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(was _RL, now integer) with option = 0 to retrieve all levels. |
109 |
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- add pieces of code to compute velocity potential at each level (new diagnostics |
110 |
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PhiVEL, works only when UVELMASS & VVELMASS are also turned on); |
111 |
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for now, using same params as CG2D (target-resisual, max Nb of iter ...). |
112 |
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- fix few issues with counter diagnostics in diagnostics_setdiag.F & |
113 |
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diagstats_setdiag.F (if diagnostic counter is itself a counter diag) |
114 |
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and in diagnostics_fract_fill.F (do not need a valid pointer for the |
115 |
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diagnostics counter-mate); check that definition of counter-diagnostic |
116 |
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includes a valid counter-mate (in diagnostics_set_levels.F). |
117 |
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o model/src (rStar): |
118 |
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- add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F); |
119 |
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affect solution only if z* with full pressure in EOS; |
120 |
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update output of test-exp global_ocean.90x40x15. |
121 |
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o pkg/seaice: |
122 |
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- introduce siEps=1e-5 parameter |
123 |
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- use areaMax in AREA update (part 4), consistent with ridging step (part 2.5). |
124 |
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- re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code. |
125 |
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- introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer. |
126 |
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For now it covers, and was tested for, ice salinity and age (attached to HEFF), |
127 |
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as well as ice cover age and ridging index (attached to AREA). |
128 |
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For now the run time parameters (in data.seaice/SEAICE_PARM03) are |
129 |
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SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA'). |
130 |
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Up to SItrMaxNum=3 tracers can be used simultaneously. |
131 |
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o pkg/salt_plume: |
132 |
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-introduce SPsalFRAC run time parameter that sets the fraction of the |
133 |
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salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically) |
134 |
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that gets vertically redistributed (fluxed down) by pkg/salt_plume. |
135 |
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o model debug options: |
136 |
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- Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored |
137 |
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in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h). |
138 |
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- Refine debug-msg printing selection (3 new levels): |
139 |
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debugMode : controls printing of debug messages (sequence of S/R calls). |
140 |
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debugLevel : controls printing of algorithm-relevant auxiliary/debug messages |
141 |
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debLevZero = 0 ; /* level of disabled aux. msg printing */ |
142 |
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debLevA = 1 ; /* level of minimum aux. msg printing */ |
143 |
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debLevB = 2 ; /* level of low aux. print (report read-file opening)*/ |
144 |
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debLevC = 3 ; /* level of moderate debug prt (most pkgs debug msg) */ |
145 |
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debLevD = 4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */ |
146 |
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debLevE = 5 ; /* level of extensive debug printing */ |
147 |
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New debugLevel default: with default debugMode value (=F), |
148 |
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= 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.; |
149 |
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and if debugMode=T, default debugLevel = 4 (debLevD). |
150 |
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Relation with previous settings: |
151 |
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debLevB (=2) corresponds to former debLevA (=1) |
152 |
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debLevD (=4) corresponds to former debLevB (=2) |
153 |
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Note: |
154 |
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a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before); |
155 |
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b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs); |
156 |
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to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5) |
157 |
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- Add new parameter (printResidualFreq, read from PARM02 namelist) to print |
158 |
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detailed CG solvers convergence; off (=0) by default, except if debugLevel=5. |
159 |
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o pkg/obcs: |
160 |
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- change OBCSfixTopo default from True to False (should not change the results); |
161 |
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keep OBCSfixTopo=T in verification-exp. seaice_obcs. |
162 |
|
o pkg/thsice: |
163 |
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- fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in |
164 |
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2nd layer seaice sublimation (unlikely to happen) |
165 |
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- use Interior mask for OBCS in thsice_advection.F (similar to what is |
166 |
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done in gad_advection & seaice_advection). |
167 |
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o adjoint: |
168 |
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bug fix spotted by Gael Forget: |
169 |
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seaice_advection and thsice_advection still had |
170 |
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legacy CPP options to avoid CS corner updates for adjoint |
171 |
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o pkg/seaice: |
172 |
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=> Change some of the defaults (2011/05/29): |
173 |
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- change SEAICEuseFluxForm default (from False to True) |
174 |
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- change DIFF1 default (from 0.004 m/s to 0. m/s) |
175 |
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And print warnings if DIFF1 is not set in data.seaice and centered |
176 |
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avection scheme is used without any diffusion. |
177 |
|
also: |
178 |
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- fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F; |
179 |
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- set SEAICEdiffKh[] default in the same way as SEAICEadvSch[] |
180 |
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- stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any |
181 |
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other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with |
182 |
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#undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE. |
183 |
|
update results of test exp.: |
184 |
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lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20) |
185 |
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output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200) |
186 |
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output_adm.noseaicedyn (SEAICEuseFluxForm=T) |
187 |
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offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T) |
188 |
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seaice_obcs: output (SEAICEuseFluxForm=T) |
189 |
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and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004) |
190 |
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for standard fwd & AD lab_sea tests (to keep the same output). |
191 |
|
o pkg/seaice/seaice_growth.F: |
192 |
|
- use Ian Fenty's capping formulas for actual ice |
193 |
|
thickness thoughout EVOLUTION branch. |
194 |
|
- put treatment pathological case #2) in CPP brackets |
195 |
|
(ALLOW_AVOID_INFINITESIMAL_AREA, undef by default). |
196 |
|
- update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly. |
197 |
|
o pkg/seaice: |
198 |
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- seaice_diffusion.F : remove the min(DX,DY) factor permanently; |
199 |
|
pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter; |
200 |
|
also pass fac as a param, which can be 1. (to update the tendency |
201 |
|
field) or the time step (to update the field itself). |
202 |
|
- seaice_advdiff.F: for multidim, call seaice_diffusion with |
203 |
|
e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call |
204 |
|
seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step. |
205 |
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- SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F : |
206 |
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hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc. |
207 |
|
o pkg/seaice: |
208 |
|
diffusion with centered advection scheme (diffus.F & advect.F): |
209 |
|
- simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside) |
210 |
|
to just compute the laplacian of input-field. |
211 |
|
- unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call. |
212 |
|
- fix flux-form version in diffus.F to conserve tracer. |
213 |
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update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects |
214 |
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machine truncation) and lab_sea.salt_plume (conservative flux-form modif) |
215 |
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|
216 |
|
checkpoint62y (2011/05/26) |
217 |
|
o pkg/seaice: |
218 |
|
- seaice_growth.F : in EVOLUTION branch, always include |
219 |
|
a_QSWbyATM_cover in qnet (as it should be). |
220 |
|
- verification/global_ocean.cs32x15 : update results accordingly |
221 |
|
(output.seaice.txt output_adm.seaice.txt). |
222 |
|
o pkg/seaice + obcs: |
223 |
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- use maskInW & maskInS in multi-dim advection and biharmonic diffusion: |
224 |
|
equivalent of assuming no tracer gradient outside the OB region. |
225 |
|
update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion) |
226 |
|
- remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed |
227 |
|
after changes above); |
228 |
|
- obcs+seaice cleaning: apply seaice-tracer OB values to tracer field |
229 |
|
only at OB location (instead of over a band of OLx width). |
230 |
|
o pkg/seaice: |
231 |
|
- fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F |
232 |
|
(dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid) |
233 |
|
o pkg/obcs: |
234 |
|
- split header file "OBCS.h" into 4 separated files: |
235 |
|
OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h |
236 |
|
Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h |
237 |
|
(contain no conditional statement which depends on OBCS options). |
238 |
|
- move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h) |
239 |
|
to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h). |
240 |
|
o ctrl, cost, grdchk & autodiff pkgs: |
241 |
|
- make options file more standard (like other {PKG}_OPTIONS.h file but |
242 |
|
with AD_CONFIG.h); clean-up some of the included header files. |
243 |
|
o pkg/obcs: |
244 |
|
- do not mask tracer when applying OB (tracer == 0 could generate problems) |
245 |
|
- apply tracer OB values to tracer field only at OB location (instead of |
246 |
|
over a band of OLx width) |
247 |
|
- clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R) |
248 |
|
- remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove |
249 |
|
obcs_apply_tloc.F & obcs_apply_sloc.F |
250 |
|
o obcs in model/src: |
251 |
|
- call OBCS_APPLY_W only if NonHydrostatic. |
252 |
|
- call OBCS_APPLY_ETA only if NonLinFreeSurf. |
253 |
|
- reset dEtaHdt and wVel to zero outside OB interior region ; |
254 |
|
- leave tracer unchanged outside OB interior region: This has no effect |
255 |
|
on the solution but just to prevent unrealistic tracer value outside OB. |
256 |
|
- zero out velocity outside OB interior region: This has no effect on |
257 |
|
the solution but just to prevent unrealistic velocity outside OB. |
258 |
|
o obcs and non-lin free-surf: |
259 |
|
move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F |
260 |
|
and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F |
261 |
|
+ add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR: |
262 |
|
this fixes missing EXCH + get consistent eta OB value (+ fix restart). |
263 |
|
update results of test-exp. exp4(nlfs). |
264 |
|
o exp4 (nlfs) test-exp: |
265 |
|
use OBC for Eta at Western & Eastern OB (to test prescribing Eta |
266 |
|
with NonLin-FreeSurf); update output.nlfs.txt |
267 |
|
o obcs and 2d/3d solver norm: |
268 |
|
use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB |
269 |
|
and outside OB interior region (will allow to place OB further inside the |
270 |
|
domain). Depending on the domain, can affects cg2d-Norm (previous |
271 |
|
cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl, |
272 |
|
and cg3d-Norm (previous Norm was computed before canceling OB terms), |
273 |
|
e.g. in tutorial_plume_on_slope. |
274 |
|
- update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope. |
275 |
|
o pkg rbcs: |
276 |
|
- split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h |
277 |
|
- add capability to apply relaxation to horizontal velocity uVel & vVel. |
278 |
|
o pkg/grdchk: add gradient check for control variable xx_shifwflx |
279 |
|
o pkg/shelfice/shelfice_init_fixed.F |
280 |
|
fix CPP-flag combinations |
281 |
|
o pkg/seaice: Merge iceage code of Pierre Rampal |
282 |
|
* update/change/correct ice age calculations |
283 |
|
* add age updates for pathological cases |
284 |
|
Probably needs more testing... |
285 |
|
|
286 |
|
checkpoint62x (2011/05/13) |
287 |
|
o pkg/mom_vecinv: |
288 |
|
high-order vorticity scheme: use interior masks (maskInW & S) |
289 |
|
to zero-out (outside OB) gradient of vorticity. |
290 |
|
o verification exp.: |
291 |
|
turn on "useEnergyConservingCoriolis" (better discretisation) in exp. |
292 |
|
hs94.128x64x5 and seaice_obcs ; update results. |
293 |
|
o pkg/obcs: |
294 |
|
fix bug in OBeta for YZ sections in obcs_exf_load.F |
295 |
|
o pkg/ctrl, pkg/shelfice, and optim: |
296 |
|
- add new control variable xx_shifwflx (fresh water flux underneath ice |
297 |
|
shelves). This is almost as tedious as obcs-ctrl, because the |
298 |
|
variables needs its own mask. |
299 |
|
- add a cost function term that penalizes the deviation of xx_shifwflx |
300 |
|
from the first guess (zero) in analogy to other control variables |
301 |
|
o pkg/shelfice: |
302 |
|
- start basic adjoint |
303 |
|
o pkg/ctrl: |
304 |
|
- remove extra 2D field "for good measure" when initializing in |
305 |
|
ctrl_set_globfld_[xy/xz/yz].F |
306 |
|
- replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec |
307 |
|
- improve error messages in ctrl_set_unpack_* |
308 |
|
o OBC implementation in momentum: |
309 |
|
use interior masks (maskInC,W & S) in momentum S/R: |
310 |
|
- multiply divergence, tension and some del^i.u or del^j.v by maskInC |
311 |
|
- multiply del2u,del2v by maskInW/S (biharmonic viscosity) |
312 |
|
- multiply horiz. grad of vorticity by maskInW/S (in Leith scheme) |
313 |
|
- multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd) |
314 |
|
Motivation: fix/clean implementation of OBC with biharmonic-viscosity |
315 |
|
(and also with Leith/Smagorinsky harmonic-viscosity). |
316 |
|
Update output of experiment dome and exp4 (+nlfs). |
317 |
|
o exp4 test-exp: |
318 |
|
- turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F) |
319 |
|
and prescribe time-varying OB (without pkg/exf) for zonal-velocity |
320 |
|
at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe |
321 |
|
time-varying OB at Western-side for wVel (NonHyd); update output. |
322 |
|
- add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv |
323 |
|
and biharmonic-viscosity ; also use prescribed time varying OB. |
324 |
|
o pkg/obcs: |
325 |
|
fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F |
326 |
|
o model/src: |
327 |
|
- fix startTime setting when baseTime<>0 & nIter0=0 are specified ; |
328 |
|
- initialise startTime & nIter0 with unlikely values: allows to set one |
329 |
|
from the other without ambiguity. |
330 |
|
o seaice_obcs test-exp.: |
331 |
|
add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output. |
332 |
|
o pkg/obcs: |
333 |
|
- remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer: |
334 |
|
no longer needed with maskInC,W,S in pkg/generic_advdiff. |
335 |
|
o pkg/seaice: |
336 |
|
- retired SEAICE_SALINITY and SEAICE_salinity in favor of |
337 |
|
SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively. |
338 |
|
- fixed bug in the initialization of sea ice salinity variable HSALT |
339 |
|
in seaice_init_varia.F (removed dependence on ICE2WATR) |
340 |
|
o fizhi-cs test exp.: |
341 |
|
switch reference output convention for these 2 non-standard test-exp, |
342 |
|
from: pgi 6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5) |
343 |
|
to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11) |
344 |
|
reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran |
345 |
|
o model/inc: |
346 |
|
- change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4") |
347 |
|
of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS) |
348 |
|
o pkg/seaice: |
349 |
|
- fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY |
350 |
|
o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15 |
351 |
|
- updated output*.txt files due to bug fixes in salt, saltPlumeFlux, |
352 |
|
and initial HSALT |
353 |
|
|
354 |
|
checkpoint62w (2011/04/26) |
355 |
|
o pkg/mom_fluxform: |
356 |
|
- fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf. |
357 |
|
- use parameter "sideDragFactor" in no-slip BC side-drag part. |
358 |
|
- update output of exp. global_ocean.90x40x15 |
359 |
|
o pkg/mom_vecinv: |
360 |
|
mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform) |
361 |
|
o update seaice exp.: |
362 |
|
use more consistent parameter values (remove "backward compatability only": |
363 |
|
ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh) |
364 |
|
related to thermodynamics seaice. Update output (fwd+AD) of exp.: |
365 |
|
1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs |
366 |
|
o update test-exp global_ocean.90x40x15: |
367 |
|
o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis). |
368 |
|
o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.) |
369 |
|
o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params) |
370 |
|
o turn on zStar & viscA4 in standard set-up (dir input/) |
371 |
|
and update output files: output.txt & output.dwnslp.txt |
372 |
|
o new AD-test experiment: obcs_ctrl |
373 |
|
(From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector. |
374 |
|
o pkg/dic: |
375 |
|
fix two bugs in handling water vapour pressure in carbonate chemistry |
376 |
|
and air-sea fluxes. Found by Val Bennington and Galen McKinley |
377 |
|
(add DIC Option = WATERVAP_BUG to recover old results) |
378 |
|
update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline |
379 |
|
o adding allowInteriorFreezing option to check for water below freezing point |
380 |
|
at depth and bring the negative heat anomaly to the surface level |
381 |
|
o pkgs _fields_load: |
382 |
|
- extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs) |
383 |
|
- use new S/R GET_PERIODIC_INTERVAL in pkgs: |
384 |
|
bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and |
385 |
|
rbcs to get interpolation weights and time reccord number. |
386 |
|
- fix multi-threading in aim_fields_load.F |
387 |
|
- apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F |
388 |
|
o external_fields_load: |
389 |
|
new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear |
390 |
|
interpolation weights) to use in a periodic time-series ; do not divide by |
391 |
|
time-step to convert to integer: |
392 |
|
- this fixes case where externForcingPeriod is not multiple of time-step |
393 |
|
(Thanks to Christopher L. Wolfe) |
394 |
|
- this fixes case where externForcingPeriod is an odd multiple of time-step |
395 |
|
(was wrong by half of time-step); update results of tutorial_global_oce_in_p. |
396 |
|
store index of time-record which is currently loaded: |
397 |
|
- works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ; |
398 |
|
- needed for the adjoint but not yet used because of extensive recomputations; |
399 |
|
(to be fixed soon) |
400 |
|
|
401 |
|
checkpoint62v (2011/04/02) |
402 |
|
o verification/1D_ocean_ice_column added to test Ian Fenty's |
403 |
|
pkg/seaice_growth.F modifications for improving sea ice code differentiability |
404 |
|
o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope |
405 |
|
(new velocity statistics after changing maskInW & maskInS definition) |
406 |
|
o pkg/generic_advdiff with OBCS: |
407 |
|
use maksInW & maskInS in advective flux and in biharmonic diffusion calculation: |
408 |
|
equivalent to assumption of no tracer gradient outside the OB region. |
409 |
|
This will affect the results if using obcs+biharmonic diffusion. |
410 |
|
update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc) |
411 |
|
o pkg/obcs: |
412 |
|
change definition of maskInW & maskInS: leave OB edges inside (maskIn=1) |
413 |
|
(e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still |
414 |
|
in Interior region. No impact on solution but affects Velocity monitor stats. |
415 |
|
o pkg/ptracers (adjoint) |
416 |
|
New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate |
417 |
|
tape file for each tracer |
418 |
|
o model/inc/src and pkg/autodiff: add parameters that allow to turn |
419 |
|
of parts of the adjoint code at run time. For now, there are only |
420 |
|
useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These |
421 |
|
parameters are set in data.pkg. |
422 |
|
This is the lazy coward's version of doing this, but still useful for |
423 |
|
debugging. In order to do it right, everything needs to be moved to |
424 |
|
pkg/autodiff. |
425 |
|
o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at |
426 |
|
the end; this fixes the adjoint balancing code for open boundaries. |
427 |
|
o pkg/ctrl: |
428 |
|
- change behavior of xx_${varname}period to be analogous to exf-conventions: |
429 |
|
xx_${varname}period = 0., means time-independent control part |
430 |
|
xx_${varname}period = -12., means one-year-periodic monthly control part |
431 |
|
- introduce helper routine ctrl_init_rec (part of ctrl_init.F) to |
432 |
|
clean up ctrl_init a little, remove unused variables |
433 |
|
- ctrl_init: fixed the handling of the start/endrec for obcs-variables |
434 |
|
- move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec |
435 |
|
|
436 |
|
checkpoint62u (2011/03/15) |
437 |
|
o model/src: |
438 |
|
- for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in |
439 |
|
h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ; |
440 |
|
- in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to |
441 |
|
INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF. |
442 |
|
o pkg/ctrl/obcs/ecco: |
443 |
|
- remove obsolete, unused, and partially broken code: |
444 |
|
ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within |
445 |
|
ALLOW_CTRL_OBCS_BALANCE |
446 |
|
- put a stop statement into ecco/cost_obcsvol.F, but also add |
447 |
|
cost_obcsvol to ecco_ad_diff.list |
448 |
|
o pkg/ecco: fix counting cost function contributions for obcs (code |
449 |
|
by Matt M.) and diffkr for diagnostics |
450 |
|
o pkg/ecco, pkg/ctrl, pkg/grdchk: |
451 |
|
add cost penalty terms for initial uvel, vvel, eta controls |
452 |
|
and I/O for prior error files |
453 |
|
o pkg/mdsio: |
454 |
|
move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option |
455 |
|
(new argument) to check for tiled file in mdsioLocalDir : this fix the |
456 |
|
restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir. |
457 |
|
o pkg/ctrl: |
458 |
|
- ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by |
459 |
|
ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove |
460 |
|
unused and superfluous variables |
461 |
|
- ctrl_get_gen_rec.F: catch the case of xx_genperiod=0. |
462 |
|
o pkg/ecco |
463 |
|
- enable adjoint of Stevens OB |
464 |
|
o pkg/ctrl/ecco/grdchk: |
465 |
|
- remove global declaration of tmpfldx/yz and tmpfldx/yz2. |
466 |
|
Fortunately, we do not have any tests for the numerous cpp-flagged |
467 |
|
option of "obcs as control parameters" so we will never know |
468 |
|
if this is an improvement (but at least now things compile). |
469 |
|
- remove an obsolete initialization from ecco_cost_init_barfiles.F |
470 |
|
- fix some problems within never used ifdefs to make the code compile |
471 |
|
o pkg/obcs: |
472 |
|
- Refine Interior mask definition to work with more complex OB (e.g. |
473 |
|
if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to |
474 |
|
read in Interior mask from file. Check if Interior mask is consistent |
475 |
|
with OB list of indices. |
476 |
|
o pkg/seaice |
477 |
|
- beginning code for a seaice tracer package, |
478 |
|
but currently only used for seaice age: SEAICE_AGE |
479 |
|
SEAICE_num = 4 |
480 |
|
iTracer = 1: area-weighted ice age |
481 |
|
= 2: volume-weighted ice age |
482 |
|
= 3, 4: template for one-year vs. multi-year ice |
483 |
|
data.seaice has new namelist SEAICE_PARM03 for arrays related to |
484 |
|
SEAICE_num |
485 |
|
|
486 |
|
checkpoint62t (2011/03/05) |
487 |
|
o pkg/obcs: |
488 |
|
- obcs_apply_uv.F: change to a 2 steps method, first tangential component; |
489 |
|
then normal component. This ensures that the normal component is set |
490 |
|
correctly even when it conficts with tangential setting from an other OB. |
491 |
|
Affects results of test-experiment seaice_obcs: update the output.txt |
492 |
|
o pkg/obcs: |
493 |
|
- add code to monitor statistics of dynamical fields at OB. |
494 |
|
- take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW : |
495 |
|
- fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection). |
496 |
|
- change default: balance the Net inflow through all OB (instead of balancing |
497 |
|
each OB separately); keep the old method if setting OBC_balanceFacX < 0. |
498 |
|
- switch on useOBCSbalance in dome experiment: only correct Western OB outflow |
499 |
|
to match Nortern OB inflow (OBCS_balanceFacN=0). |
500 |
|
o pkg/seaice: |
501 |
|
- redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL |
502 |
|
o pkg/seaice (seaice_growth v 1.113): |
503 |
|
- reverting seaice_growth to v 1.111 in order to have code with exact bit |
504 |
|
compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge |
505 |
|
CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced |
506 |
|
runtime flag SEAICEareaFormula is kept but is inactive |
507 |
|
o model/src: |
508 |
|
- add new param to scale curvilinear grid distance and area when using |
509 |
|
a different sphere radius from the grid-files. |
510 |
|
- test/check multi-threads EXCH applied to local variable (cg2d_x) |
511 |
|
o adjoint: |
512 |
|
- enable adjoint of Stevens OB |
513 |
|
- add dummy_in_dynamics to enable extraction of ADJrhoinsitu |
514 |
|
(a bit delicate because of potentially modified adj. common block structure; |
515 |
|
current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later) |
516 |
|
|
517 |
|
checkpoint62s (2011/02/15) |
518 |
|
o pkg/seaice (seaice_growth v 1.112): |
519 |
|
- introduce SEAICEareaFormula run time parameter, which selects the recipe for |
520 |
|
computing the ice cover tendency from effective thickness tendencies. Include |
521 |
|
Ian Fenty's formula. |
522 |
|
- remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using |
523 |
|
SEAICEareaFormula. |
524 |
|
- simplify notations for the various d_HEFF/d_AREA terms. |
525 |
|
o pkg/gmredi: |
526 |
|
- add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code |
527 |
|
from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative; |
528 |
|
add a verification test-run (front_relax.bvp) to test GM_useBVP. |
529 |
|
o pkg/seaice (seaice_growth v 1.111): |
530 |
|
- for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's. |
531 |
|
- the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to |
532 |
|
also melt ice. |
533 |
|
o pkg/seaice: |
534 |
|
- McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty). |
535 |
|
- can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h |
536 |
|
o pkg/cheapaml: |
537 |
|
- from Nico Wienders: New version of this package. |
538 |
o pkg/flt: |
o pkg/flt: |
539 |
- add CPP options to prevent floats to re-enter the opposite side of |
- add CPP options to prevent floats to re-enter the opposite side of |
540 |
a periodic domain (default: keep periodicity) |
a periodic domain (default: keep periodicity) |