4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
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|
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o pkg/mypackage: |
8 |
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- remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS |
9 |
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|
10 |
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checkpoint63a (2011/08/02) |
11 |
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o pkg/diagnostics (velocity potential): |
12 |
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- fix velocity-potential calculation when using OBCS: balance net inflow |
13 |
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at each level (new S/R OBCS_DIAG_BALANCE). |
14 |
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- fix some of the problems with OBCS in stream-function calculation. |
15 |
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o pkg/exf/exf_readparms.F |
16 |
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- make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF, |
17 |
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EXF_NML_OBCS) more consistent, so that you need not have these lists |
18 |
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in data.exf when they are not used. |
19 |
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o optim/optim_readdata.F: |
20 |
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- add some output about obcs variables that might help debugging |
21 |
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- add a check about nvarlength |
22 |
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o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec |
23 |
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o pkg/diagnostics (velocity potential): |
24 |
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- fix mask for OBCS (still problems in stream-function with OBCS); |
25 |
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- add specific parameter (default = main code CG2D params) for solver; |
26 |
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- in case of poor convergence, use solution corresponding to lowest residual. |
27 |
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o pkg/seaice/seaice_growth.F: small changes that permit vectorizable |
28 |
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adjoint code. In general statements like tmpscal=fld(i,j) are problematic |
29 |
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and should be avoided where possible. |
30 |
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o model/src (rStar): |
31 |
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- include r* effect on reference-state (PhiRef) in totPhiHyd |
32 |
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(so that it's really the potential anomaly at the cell center); |
33 |
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affect solution only if z* with full pressure in EOS. |
34 |
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- test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and |
35 |
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update output (because of z* in totPhiHyd and viscA4 changes); |
36 |
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- keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly |
37 |
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@ constant r) until interpolation at constant r is implemented. |
38 |
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o pkg/diagnostics |
39 |
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- fix RCENTER diagnostics in case cell center is not at interface middle |
40 |
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o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use |
41 |
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this eos with eosType = 'TEOS10', in data (PARM01). This eos implies |
42 |
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that THETA and SALT are "conservative temperature" and "absolute |
43 |
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salinity" |
44 |
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o pkg/ctrl |
45 |
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- fix computation of endrec in s/r ctrl_init_rec |
46 |
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- ctrl_pack/unpack_*: remove unused variables and some obsolete code |
47 |
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o pkg/seaice/seaice_growth.F |
48 |
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- fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code, |
49 |
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remove then obsolete STORE directives |
50 |
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- fix STORE directives for tice and tices, so that only the |
51 |
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appropriate part of the fields are stored (and not the entire |
52 |
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field); update global_ocean.cs32x15.seaice AD output. |
53 |
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- cosmetic changes: adjust CPP flags and indentation for better |
54 |
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legibilty |
55 |
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o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by |
56 |
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Chris Wilson) |
57 |
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o pkg/gmredi: |
58 |
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Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF), |
59 |
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and test it in verification exp. "front_relax.bvp" (update output.bvp.txt) |
60 |
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|
61 |
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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 |
64 |
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- exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the |
65 |
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(2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y |
66 |
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increments, calculates Cumul-Sum @ tile origin and sends results to each tile. |
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o pkg/diagnostics: |
68 |
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- deal with pairs of post-processed diags which are computed together; in |
69 |
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particular, re-order list of diags within 1 file to save 2nd computation. |
70 |
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- add S/R to compute velocity stream-function (called after velocity-potential |
71 |
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calculation) from divergence free transport -> new diagnostics "PsiVEL". |
72 |
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- add parameter to select grid-point location where PsiVEL == 0. |
73 |
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o eesupp/src: |
74 |
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new S/R to calculate cumulated sum on tiled array, corner grid-cell location |
75 |
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(specific S/R needed with exch2 topology - for now, just print an error msg) |
76 |
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o pkg/shelfice |
77 |
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- Implement friction velocity-dependent transfer coefficients following |
78 |
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Holland and Jenkins, JPO, 1999 |
79 |
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Original code by M. Losch with small modifs. |
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Enable with CPP option SHI_ALLOW_GAMMAFRICT |
81 |
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and runtime flag SHELFICEuseGammaFrict |
82 |
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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 |
85 |
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(default makedepend limitation for AD built). |
86 |
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- use cyrus_makedepend in adjustment.128x64x1 (so that it still tested). |
87 |
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o pkg/diagnostics: |
88 |
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- add run-time parameter "useMissingValue" (def=False) to fill land-point |
89 |
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(i.e., where mask=0) with MissingValue ; used only in MNC output file. |
90 |
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This replaces CPP-option DIAGNOSTICS_MISSING_VALUE. |
91 |
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- Extend the use of "missing_value" setting from data.diagnostics for the case |
92 |
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of counter-diagnostics (where fraction-weight is zero). This applies both to |
93 |
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MNC and MDS output files. |
94 |
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o pkg/seaice/seaice_growth.F: |
95 |
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- add 'a priori' cap of latent heat flux based on actual mass considerations |
96 |
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when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the |
97 |
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non-legacy seaice_solve4temp. |
98 |
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- add diagnostic of the residual sublimation freshwater flux (the freshwater |
99 |
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flux taken from the ocean if the total actual latent heat fluxes exceed |
100 |
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the maximum) |
101 |
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- remove the CPP switch around the *_FWbySublim unit change and move diagnostic |
102 |
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fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F. |
103 |
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- add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef |
104 |
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SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim). |
105 |
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- bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET. |
106 |
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- bug fix : missing part to Martin's r_FWbySublim pathological case fix. |
107 |
|
o verification 1D_ocean_ice_column: |
108 |
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made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet |
109 |
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update results |
110 |
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o pkg/diagnostics: |
111 |
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- Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P') |
112 |
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which are not filled-up but computed from other diags ; In this case, the mate |
113 |
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diag points to the primary (filled-up) diag to used for post processing. |
114 |
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- Update Velocity-potential computation using post-processed diag framework. |
115 |
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==> Change the ordering of fields and time-periods in MDS output file |
116 |
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when using periodic averaging: now writes one time record with the full set |
117 |
|
of fields for this time period, then the next time reccord (it used to be |
118 |
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one field with the full set of time records then the next field). |
119 |
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Note: this is now similar to NetCDF (MNC) output file. <== |
120 |
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|
121 |
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checkpoint62z (2011/06/21) |
122 |
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o adjoint monitor: |
123 |
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- Add adjoint monitor output for packages exf, seaice |
124 |
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and update relevant testreport output |
125 |
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o pkg/seaice: |
126 |
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- re-order diags inits so that they appear in order in available_diagnostics.log |
127 |
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- added diags: hsnow thermo. rates of change, area preceeding ridiging process, |
128 |
|
area/heff/hsnow preceeding thermodynamic growth/melt. |
129 |
|
- modified diag: SIdA; output actual effect, as the description states. |
130 |
|
- modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW. |
131 |
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- retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh. |
132 |
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(SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO; |
133 |
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and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO) |
134 |
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- modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates. |
135 |
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- added diagnostics for seaice generic tracers (SItr*). |
136 |
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- added SItrUnit and SItrNameLong run time param (for SItr* diags). |
137 |
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- in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'. |
138 |
|
I. Fenty: 18-Jun-2011: |
139 |
|
Minor changes to seaice package: |
140 |
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1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and |
141 |
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added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor) |
142 |
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- Differentiated "regularization variables" from "floor variables" |
143 |
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* areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor |
144 |
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* hiceMin became SEAICE_hice_reg (old hiceMin) |
145 |
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(with _reg meaning regularization variable) |
146 |
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- SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion |
147 |
|
so as to ensure energy conservation when going between phases |
148 |
|
- A22 was not used anywhere |
149 |
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2) Changed regularization procedure for heffActual and hsnowActual to ensure |
150 |
|
well-boundedness and smooth adjoint in seaice_growth.F |
151 |
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3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells |
152 |
|
because the old regularization always set heffActual >= 0.05 cm |
153 |
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4) Changed the model so that the default behavior is to put a small (10^-5) "floor" |
154 |
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on AREA when HEFF > 0. |
155 |
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- went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to |
156 |
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requiring that DISABLE_AREA_FLOOR *not* be defined |
157 |
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Affected verifications: |
158 |
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- 1D_ocean_ice_column (output.txt output_adm.txt) |
159 |
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- global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt) |
160 |
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o pkg/diagnostics: |
161 |
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- move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R). |
162 |
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- rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument |
163 |
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(was _RL, now integer) with option = 0 to retrieve all levels. |
164 |
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- add pieces of code to compute velocity potential at each level (new diagnostics |
165 |
|
PhiVEL, works only when UVELMASS & VVELMASS are also turned on); |
166 |
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for now, using same params as CG2D (target-resisual, max Nb of iter ...). |
167 |
|
- fix few issues with counter diagnostics in diagnostics_setdiag.F & |
168 |
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diagstats_setdiag.F (if diagnostic counter is itself a counter diag) |
169 |
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and in diagnostics_fract_fill.F (do not need a valid pointer for the |
170 |
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diagnostics counter-mate); check that definition of counter-diagnostic |
171 |
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includes a valid counter-mate (in diagnostics_set_levels.F). |
172 |
|
o model/src (rStar): |
173 |
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- add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F); |
174 |
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affect solution only if z* with full pressure in EOS; |
175 |
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update output of test-exp global_ocean.90x40x15. |
176 |
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o pkg/seaice: |
177 |
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- introduce siEps=1e-5 parameter |
178 |
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- use areaMax in AREA update (part 4), consistent with ridging step (part 2.5). |
179 |
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- re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code. |
180 |
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- introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer. |
181 |
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For now it covers, and was tested for, ice salinity and age (attached to HEFF), |
182 |
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as well as ice cover age and ridging index (attached to AREA). |
183 |
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For now the run time parameters (in data.seaice/SEAICE_PARM03) are |
184 |
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SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA'). |
185 |
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Up to SItrMaxNum=3 tracers can be used simultaneously. |
186 |
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o pkg/salt_plume: |
187 |
|
-introduce SPsalFRAC run time parameter that sets the fraction of the |
188 |
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salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically) |
189 |
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that gets vertically redistributed (fluxed down) by pkg/salt_plume. |
190 |
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o model debug options: |
191 |
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- Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored |
192 |
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in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h). |
193 |
|
- Refine debug-msg printing selection (3 new levels): |
194 |
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debugMode : controls printing of debug messages (sequence of S/R calls). |
195 |
|
debugLevel : controls printing of algorithm-relevant auxiliary/debug messages |
196 |
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debLevZero = 0 ; /* level of disabled aux. msg printing */ |
197 |
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debLevA = 1 ; /* level of minimum aux. msg printing */ |
198 |
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debLevB = 2 ; /* level of low aux. print (report read-file opening)*/ |
199 |
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debLevC = 3 ; /* level of moderate debug prt (most pkgs debug msg) */ |
200 |
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debLevD = 4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */ |
201 |
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debLevE = 5 ; /* level of extensive debug printing */ |
202 |
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New debugLevel default: with default debugMode value (=F), |
203 |
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= 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.; |
204 |
|
and if debugMode=T, default debugLevel = 4 (debLevD). |
205 |
|
Relation with previous settings: |
206 |
|
debLevB (=2) corresponds to former debLevA (=1) |
207 |
|
debLevD (=4) corresponds to former debLevB (=2) |
208 |
|
Note: |
209 |
|
a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before); |
210 |
|
b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs); |
211 |
|
to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5) |
212 |
|
- Add new parameter (printResidualFreq, read from PARM02 namelist) to print |
213 |
|
detailed CG solvers convergence; off (=0) by default, except if debugLevel=5. |
214 |
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o pkg/obcs: |
215 |
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- change OBCSfixTopo default from True to False (should not change the results); |
216 |
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keep OBCSfixTopo=T in verification-exp. seaice_obcs. |
217 |
|
o pkg/thsice: |
218 |
|
- fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in |
219 |
|
2nd layer seaice sublimation (unlikely to happen) |
220 |
|
- use Interior mask for OBCS in thsice_advection.F (similar to what is |
221 |
|
done in gad_advection & seaice_advection). |
222 |
|
o adjoint: |
223 |
|
bug fix spotted by Gael Forget: |
224 |
|
seaice_advection and thsice_advection still had |
225 |
|
legacy CPP options to avoid CS corner updates for adjoint |
226 |
|
o pkg/seaice: |
227 |
|
=> Change some of the defaults (2011/05/29): |
228 |
|
- change SEAICEuseFluxForm default (from False to True) |
229 |
|
- change DIFF1 default (from 0.004 m/s to 0. m/s) |
230 |
|
And print warnings if DIFF1 is not set in data.seaice and centered |
231 |
|
avection scheme is used without any diffusion. |
232 |
|
also: |
233 |
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- fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F; |
234 |
|
- set SEAICEdiffKh[] default in the same way as SEAICEadvSch[] |
235 |
|
- stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any |
236 |
|
other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with |
237 |
|
#undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE. |
238 |
|
update results of test exp.: |
239 |
|
lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20) |
240 |
|
output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200) |
241 |
|
output_adm.noseaicedyn (SEAICEuseFluxForm=T) |
242 |
|
offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T) |
243 |
|
seaice_obcs: output (SEAICEuseFluxForm=T) |
244 |
|
and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004) |
245 |
|
for standard fwd & AD lab_sea tests (to keep the same output). |
246 |
|
o pkg/seaice/seaice_growth.F: |
247 |
|
- use Ian Fenty's capping formulas for actual ice |
248 |
|
thickness thoughout EVOLUTION branch. |
249 |
|
- put treatment pathological case #2) in CPP brackets |
250 |
|
(ALLOW_AVOID_INFINITESIMAL_AREA, undef by default). |
251 |
|
- update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly. |
252 |
|
o pkg/seaice: |
253 |
|
- seaice_diffusion.F : remove the min(DX,DY) factor permanently; |
254 |
|
pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter; |
255 |
|
also pass fac as a param, which can be 1. (to update the tendency |
256 |
|
field) or the time step (to update the field itself). |
257 |
|
- seaice_advdiff.F: for multidim, call seaice_diffusion with |
258 |
|
e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call |
259 |
|
seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step. |
260 |
|
- SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F : |
261 |
|
hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc. |
262 |
|
o pkg/seaice: |
263 |
|
diffusion with centered advection scheme (diffus.F & advect.F): |
264 |
|
- simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside) |
265 |
|
to just compute the laplacian of input-field. |
266 |
|
- unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call. |
267 |
|
- fix flux-form version in diffus.F to conserve tracer. |
268 |
|
update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects |
269 |
|
machine truncation) and lab_sea.salt_plume (conservative flux-form modif) |
270 |
|
|
271 |
|
checkpoint62y (2011/05/26) |
272 |
|
o pkg/seaice: |
273 |
|
- seaice_growth.F : in EVOLUTION branch, always include |
274 |
|
a_QSWbyATM_cover in qnet (as it should be). |
275 |
|
- verification/global_ocean.cs32x15 : update results accordingly |
276 |
|
(output.seaice.txt output_adm.seaice.txt). |
277 |
|
o pkg/seaice + obcs: |
278 |
|
- use maskInW & maskInS in multi-dim advection and biharmonic diffusion: |
279 |
|
equivalent of assuming no tracer gradient outside the OB region. |
280 |
|
update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion) |
281 |
|
- remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed |
282 |
|
after changes above); |
283 |
|
- obcs+seaice cleaning: apply seaice-tracer OB values to tracer field |
284 |
|
only at OB location (instead of over a band of OLx width). |
285 |
|
o pkg/seaice: |
286 |
|
- fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F |
287 |
|
(dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid) |
288 |
|
o pkg/obcs: |
289 |
|
- split header file "OBCS.h" into 4 separated files: |
290 |
|
OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h |
291 |
|
Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h |
292 |
|
(contain no conditional statement which depends on OBCS options). |
293 |
|
- move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h) |
294 |
|
to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h). |
295 |
|
o ctrl, cost, grdchk & autodiff pkgs: |
296 |
|
- make options file more standard (like other {PKG}_OPTIONS.h file but |
297 |
|
with AD_CONFIG.h); clean-up some of the included header files. |
298 |
|
o pkg/obcs: |
299 |
|
- do not mask tracer when applying OB (tracer == 0 could generate problems) |
300 |
|
- apply tracer OB values to tracer field only at OB location (instead of |
301 |
|
over a band of OLx width) |
302 |
|
- clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R) |
303 |
|
- remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove |
304 |
|
obcs_apply_tloc.F & obcs_apply_sloc.F |
305 |
|
o obcs in model/src: |
306 |
|
- call OBCS_APPLY_W only if NonHydrostatic. |
307 |
|
- call OBCS_APPLY_ETA only if NonLinFreeSurf. |
308 |
|
- reset dEtaHdt and wVel to zero outside OB interior region ; |
309 |
|
- leave tracer unchanged outside OB interior region: This has no effect |
310 |
|
on the solution but just to prevent unrealistic tracer value outside OB. |
311 |
|
- zero out velocity outside OB interior region: This has no effect on |
312 |
|
the solution but just to prevent unrealistic velocity outside OB. |
313 |
|
o obcs and non-lin free-surf: |
314 |
|
move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F |
315 |
|
and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F |
316 |
|
+ add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR: |
317 |
|
this fixes missing EXCH + get consistent eta OB value (+ fix restart). |
318 |
|
update results of test-exp. exp4(nlfs). |
319 |
|
o exp4 (nlfs) test-exp: |
320 |
|
use OBC for Eta at Western & Eastern OB (to test prescribing Eta |
321 |
|
with NonLin-FreeSurf); update output.nlfs.txt |
322 |
|
o obcs and 2d/3d solver norm: |
323 |
|
use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB |
324 |
|
and outside OB interior region (will allow to place OB further inside the |
325 |
|
domain). Depending on the domain, can affects cg2d-Norm (previous |
326 |
|
cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl, |
327 |
|
and cg3d-Norm (previous Norm was computed before canceling OB terms), |
328 |
|
e.g. in tutorial_plume_on_slope. |
329 |
|
- update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope. |
330 |
|
o pkg rbcs: |
331 |
|
- split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h |
332 |
|
- add capability to apply relaxation to horizontal velocity uVel & vVel. |
333 |
|
o pkg/grdchk: add gradient check for control variable xx_shifwflx |
334 |
|
o pkg/shelfice/shelfice_init_fixed.F |
335 |
|
fix CPP-flag combinations |
336 |
|
o pkg/seaice: Merge iceage code of Pierre Rampal |
337 |
|
* update/change/correct ice age calculations |
338 |
|
* add age updates for pathological cases |
339 |
|
Probably needs more testing... |
340 |
|
|
341 |
|
checkpoint62x (2011/05/13) |
342 |
|
o pkg/mom_vecinv: |
343 |
|
high-order vorticity scheme: use interior masks (maskInW & S) |
344 |
|
to zero-out (outside OB) gradient of vorticity. |
345 |
|
o verification exp.: |
346 |
|
turn on "useEnergyConservingCoriolis" (better discretisation) in exp. |
347 |
|
hs94.128x64x5 and seaice_obcs ; update results. |
348 |
|
o pkg/obcs: |
349 |
|
fix bug in OBeta for YZ sections in obcs_exf_load.F |
350 |
|
o pkg/ctrl, pkg/shelfice, and optim: |
351 |
|
- add new control variable xx_shifwflx (fresh water flux underneath ice |
352 |
|
shelves). This is almost as tedious as obcs-ctrl, because the |
353 |
|
variables needs its own mask. |
354 |
|
- add a cost function term that penalizes the deviation of xx_shifwflx |
355 |
|
from the first guess (zero) in analogy to other control variables |
356 |
|
o pkg/shelfice: |
357 |
|
- start basic adjoint |
358 |
|
o pkg/ctrl: |
359 |
|
- remove extra 2D field "for good measure" when initializing in |
360 |
|
ctrl_set_globfld_[xy/xz/yz].F |
361 |
|
- replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec |
362 |
|
- improve error messages in ctrl_set_unpack_* |
363 |
|
o OBC implementation in momentum: |
364 |
|
use interior masks (maskInC,W & S) in momentum S/R: |
365 |
|
- multiply divergence, tension and some del^i.u or del^j.v by maskInC |
366 |
|
- multiply del2u,del2v by maskInW/S (biharmonic viscosity) |
367 |
|
- multiply horiz. grad of vorticity by maskInW/S (in Leith scheme) |
368 |
|
- multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd) |
369 |
|
Motivation: fix/clean implementation of OBC with biharmonic-viscosity |
370 |
|
(and also with Leith/Smagorinsky harmonic-viscosity). |
371 |
|
Update output of experiment dome and exp4 (+nlfs). |
372 |
|
o exp4 test-exp: |
373 |
|
- turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F) |
374 |
|
and prescribe time-varying OB (without pkg/exf) for zonal-velocity |
375 |
|
at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe |
376 |
|
time-varying OB at Western-side for wVel (NonHyd); update output. |
377 |
|
- add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv |
378 |
|
and biharmonic-viscosity ; also use prescribed time varying OB. |
379 |
|
o pkg/obcs: |
380 |
|
fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F |
381 |
|
o model/src: |
382 |
|
- fix startTime setting when baseTime<>0 & nIter0=0 are specified ; |
383 |
|
- initialise startTime & nIter0 with unlikely values: allows to set one |
384 |
|
from the other without ambiguity. |
385 |
|
o seaice_obcs test-exp.: |
386 |
|
add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output. |
387 |
|
o pkg/obcs: |
388 |
|
- remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer: |
389 |
|
no longer needed with maskInC,W,S in pkg/generic_advdiff. |
390 |
|
o pkg/seaice: |
391 |
|
- retired SEAICE_SALINITY and SEAICE_salinity in favor of |
392 |
|
SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively. |
393 |
|
- fixed bug in the initialization of sea ice salinity variable HSALT |
394 |
|
in seaice_init_varia.F (removed dependence on ICE2WATR) |
395 |
|
o fizhi-cs test exp.: |
396 |
|
switch reference output convention for these 2 non-standard test-exp, |
397 |
|
from: pgi 6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5) |
398 |
|
to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11) |
399 |
|
reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran |
400 |
|
o model/inc: |
401 |
|
- change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4") |
402 |
|
of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS) |
403 |
|
o pkg/seaice: |
404 |
|
- fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY |
405 |
|
o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15 |
406 |
|
- updated output*.txt files due to bug fixes in salt, saltPlumeFlux, |
407 |
|
and initial HSALT |
408 |
|
|
409 |
|
checkpoint62w (2011/04/26) |
410 |
|
o pkg/mom_fluxform: |
411 |
|
- fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf. |
412 |
|
- use parameter "sideDragFactor" in no-slip BC side-drag part. |
413 |
|
- update output of exp. global_ocean.90x40x15 |
414 |
|
o pkg/mom_vecinv: |
415 |
|
mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform) |
416 |
|
o update seaice exp.: |
417 |
|
use more consistent parameter values (remove "backward compatability only": |
418 |
|
ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh) |
419 |
|
related to thermodynamics seaice. Update output (fwd+AD) of exp.: |
420 |
|
1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs |
421 |
|
o update test-exp global_ocean.90x40x15: |
422 |
|
o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis). |
423 |
|
o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.) |
424 |
|
o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params) |
425 |
|
o turn on zStar & viscA4 in standard set-up (dir input/) |
426 |
|
and update output files: output.txt & output.dwnslp.txt |
427 |
|
o new AD-test experiment: obcs_ctrl |
428 |
|
(From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector. |
429 |
|
o pkg/dic: |
430 |
|
fix two bugs in handling water vapour pressure in carbonate chemistry |
431 |
|
and air-sea fluxes. Found by Val Bennington and Galen McKinley |
432 |
|
(add DIC Option = WATERVAP_BUG to recover old results) |
433 |
|
update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline |
434 |
|
o adding allowInteriorFreezing option to check for water below freezing point |
435 |
|
at depth and bring the negative heat anomaly to the surface level |
436 |
|
o pkgs _fields_load: |
437 |
|
- extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs) |
438 |
|
- use new S/R GET_PERIODIC_INTERVAL in pkgs: |
439 |
|
bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and |
440 |
|
rbcs to get interpolation weights and time reccord number. |
441 |
|
- fix multi-threading in aim_fields_load.F |
442 |
|
- apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F |
443 |
|
o external_fields_load: |
444 |
|
new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear |
445 |
|
interpolation weights) to use in a periodic time-series ; do not divide by |
446 |
|
time-step to convert to integer: |
447 |
|
- this fixes case where externForcingPeriod is not multiple of time-step |
448 |
|
(Thanks to Christopher L. Wolfe) |
449 |
|
- this fixes case where externForcingPeriod is an odd multiple of time-step |
450 |
|
(was wrong by half of time-step); update results of tutorial_global_oce_in_p. |
451 |
|
store index of time-record which is currently loaded: |
452 |
|
- works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ; |
453 |
|
- needed for the adjoint but not yet used because of extensive recomputations; |
454 |
|
(to be fixed soon) |
455 |
|
|
456 |
|
checkpoint62v (2011/04/02) |
457 |
|
o verification/1D_ocean_ice_column added to test Ian Fenty's |
458 |
|
pkg/seaice_growth.F modifications for improving sea ice code differentiability |
459 |
|
o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope |
460 |
|
(new velocity statistics after changing maskInW & maskInS definition) |
461 |
|
o pkg/generic_advdiff with OBCS: |
462 |
|
use maksInW & maskInS in advective flux and in biharmonic diffusion calculation: |
463 |
|
equivalent to assumption of no tracer gradient outside the OB region. |
464 |
|
This will affect the results if using obcs+biharmonic diffusion. |
465 |
|
update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc) |
466 |
|
o pkg/obcs: |
467 |
|
change definition of maskInW & maskInS: leave OB edges inside (maskIn=1) |
468 |
|
(e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still |
469 |
|
in Interior region. No impact on solution but affects Velocity monitor stats. |
470 |
|
o pkg/ptracers (adjoint) |
471 |
|
New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate |
472 |
|
tape file for each tracer |
473 |
|
o model/inc/src and pkg/autodiff: add parameters that allow to turn |
474 |
|
of parts of the adjoint code at run time. For now, there are only |
475 |
|
useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These |
476 |
|
parameters are set in data.pkg. |
477 |
|
This is the lazy coward's version of doing this, but still useful for |
478 |
|
debugging. In order to do it right, everything needs to be moved to |
479 |
|
pkg/autodiff. |
480 |
|
o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at |
481 |
|
the end; this fixes the adjoint balancing code for open boundaries. |
482 |
|
o pkg/ctrl: |
483 |
|
- change behavior of xx_${varname}period to be analogous to exf-conventions: |
484 |
|
xx_${varname}period = 0., means time-independent control part |
485 |
|
xx_${varname}period = -12., means one-year-periodic monthly control part |
486 |
|
- introduce helper routine ctrl_init_rec (part of ctrl_init.F) to |
487 |
|
clean up ctrl_init a little, remove unused variables |
488 |
|
- ctrl_init: fixed the handling of the start/endrec for obcs-variables |
489 |
|
- move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec |
490 |
|
|
491 |
|
checkpoint62u (2011/03/15) |
492 |
|
o model/src: |
493 |
|
- for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in |
494 |
|
h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ; |
495 |
|
- in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to |
496 |
|
INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF. |
497 |
|
o pkg/ctrl/obcs/ecco: |
498 |
|
- remove obsolete, unused, and partially broken code: |
499 |
|
ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within |
500 |
|
ALLOW_CTRL_OBCS_BALANCE |
501 |
|
- put a stop statement into ecco/cost_obcsvol.F, but also add |
502 |
|
cost_obcsvol to ecco_ad_diff.list |
503 |
|
o pkg/ecco: fix counting cost function contributions for obcs (code |
504 |
|
by Matt M.) and diffkr for diagnostics |
505 |
|
o pkg/ecco, pkg/ctrl, pkg/grdchk: |
506 |
|
add cost penalty terms for initial uvel, vvel, eta controls |
507 |
|
and I/O for prior error files |
508 |
|
o pkg/mdsio: |
509 |
|
move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option |
510 |
|
(new argument) to check for tiled file in mdsioLocalDir : this fix the |
511 |
|
restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir. |
512 |
|
o pkg/ctrl: |
513 |
|
- ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by |
514 |
|
ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove |
515 |
|
unused and superfluous variables |
516 |
|
- ctrl_get_gen_rec.F: catch the case of xx_genperiod=0. |
517 |
|
o pkg/ecco |
518 |
|
- enable adjoint of Stevens OB |
519 |
|
o pkg/ctrl/ecco/grdchk: |
520 |
|
- remove global declaration of tmpfldx/yz and tmpfldx/yz2. |
521 |
|
Fortunately, we do not have any tests for the numerous cpp-flagged |
522 |
|
option of "obcs as control parameters" so we will never know |
523 |
|
if this is an improvement (but at least now things compile). |
524 |
|
- remove an obsolete initialization from ecco_cost_init_barfiles.F |
525 |
|
- fix some problems within never used ifdefs to make the code compile |
526 |
|
o pkg/obcs: |
527 |
|
- Refine Interior mask definition to work with more complex OB (e.g. |
528 |
|
if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to |
529 |
|
read in Interior mask from file. Check if Interior mask is consistent |
530 |
|
with OB list of indices. |
531 |
|
o pkg/seaice |
532 |
|
- beginning code for a seaice tracer package, |
533 |
|
but currently only used for seaice age: SEAICE_AGE |
534 |
|
SEAICE_num = 4 |
535 |
|
iTracer = 1: area-weighted ice age |
536 |
|
= 2: volume-weighted ice age |
537 |
|
= 3, 4: template for one-year vs. multi-year ice |
538 |
|
data.seaice has new namelist SEAICE_PARM03 for arrays related to |
539 |
|
SEAICE_num |
540 |
|
|
541 |
|
checkpoint62t (2011/03/05) |
542 |
|
o pkg/obcs: |
543 |
|
- obcs_apply_uv.F: change to a 2 steps method, first tangential component; |
544 |
|
then normal component. This ensures that the normal component is set |
545 |
|
correctly even when it conficts with tangential setting from an other OB. |
546 |
|
Affects results of test-experiment seaice_obcs: update the output.txt |
547 |
|
o pkg/obcs: |
548 |
|
- add code to monitor statistics of dynamical fields at OB. |
549 |
|
- take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW : |
550 |
|
- fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection). |
551 |
|
- change default: balance the Net inflow through all OB (instead of balancing |
552 |
|
each OB separately); keep the old method if setting OBC_balanceFacX < 0. |
553 |
|
- switch on useOBCSbalance in dome experiment: only correct Western OB outflow |
554 |
|
to match Nortern OB inflow (OBCS_balanceFacN=0). |
555 |
|
o pkg/seaice: |
556 |
|
- redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL |
557 |
|
o pkg/seaice (seaice_growth v 1.113): |
558 |
|
- reverting seaice_growth to v 1.111 in order to have code with exact bit |
559 |
|
compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge |
560 |
|
CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced |
561 |
|
runtime flag SEAICEareaFormula is kept but is inactive |
562 |
|
o model/src: |
563 |
|
- add new param to scale curvilinear grid distance and area when using |
564 |
|
a different sphere radius from the grid-files. |
565 |
|
- test/check multi-threads EXCH applied to local variable (cg2d_x) |
566 |
|
o adjoint: |
567 |
|
- enable adjoint of Stevens OB |
568 |
|
- add dummy_in_dynamics to enable extraction of ADJrhoinsitu |
569 |
|
(a bit delicate because of potentially modified adj. common block structure; |
570 |
|
current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later) |
571 |
|
|
572 |
|
checkpoint62s (2011/02/15) |
573 |
|
o pkg/seaice (seaice_growth v 1.112): |
574 |
|
- introduce SEAICEareaFormula run time parameter, which selects the recipe for |
575 |
|
computing the ice cover tendency from effective thickness tendencies. Include |
576 |
|
Ian Fenty's formula. |
577 |
|
- remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using |
578 |
|
SEAICEareaFormula. |
579 |
|
- simplify notations for the various d_HEFF/d_AREA terms. |
580 |
|
o pkg/gmredi: |
581 |
|
- add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code |
582 |
|
from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative; |
583 |
|
add a verification test-run (front_relax.bvp) to test GM_useBVP. |
584 |
|
o pkg/seaice (seaice_growth v 1.111): |
585 |
|
- for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's. |
586 |
|
- the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to |
587 |
|
also melt ice. |
588 |
|
o pkg/seaice: |
589 |
|
- McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty). |
590 |
|
- can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h |
591 |
|
o pkg/cheapaml: |
592 |
|
- from Nico Wienders: New version of this package. |
593 |
|
o pkg/flt: |
594 |
|
- add CPP options to prevent floats to re-enter the opposite side of |
595 |
|
a periodic domain (default: keep periodicity) |
596 |
|
o pkg/gmredi: |
597 |
|
- apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners |
598 |
|
(needed for multi-dim advection). |
599 |
|
- switch on GM Advective form in global_ocean.cs32x15 and update output.txt |
600 |
|
o model/src: |
601 |
|
- fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run. |
602 |
|
o tutorial_tracer_adjsens |
603 |
|
- extend to NLFS and replace maskC by hFacC |
604 |
|
(change reference output accordingly) |
605 |
|
|
606 |
|
checkpoint62r (2011/01/24) |
607 |
|
o testreport: |
608 |
|
- add option -deloutp (-do) to remove output file after successful run |
609 |
|
- add option -mfile (-mf) for MPI machile-file and for each test-exp, |
610 |
|
extract exact list of procs from this file ; adjust COMMAND by |
611 |
|
replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs. |
612 |
|
o pkg/ecco: replace old ineffective way of penalizing deviations from |
613 |
|
first guess (of obcs) with code by Matt Mazloff |
614 |
|
o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without |
615 |
|
exf/cal |
616 |
|
- ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl |
617 |
|
and handle case of obcs?period == 0 |
618 |
|
Not affected by these changes: There is still an inconsistency in |
619 |
|
the computation of start/endrec for the obcs variables for ALLOW_CAL |
620 |
|
defined (see comment by Menemenlis, 7-Mar-2003) |
621 |
|
- make S/R ctrl_get_gen_rec return something meaningful even if |
622 |
|
ALLOW_CAL is not defined |
623 |
|
- ctrl_getobcs?: simplify code so that it does not need to use |
624 |
|
S/R exf_swapfields |
625 |
|
o testreport: |
626 |
|
allow to test MPI with different number of processors for each experiment: |
627 |
|
create file "SIZE.h.mpi" in each build dir. |
628 |
|
Note: update of "-command" argument not yet implemented. |
629 |
|
o model/src, pkg/autodiff, pkg/ecco, pkg/seaice: |
630 |
|
alleviate the need for additional 3D tapes when using |
631 |
|
the non-inear free surface in the adjoint. This is done |
632 |
|
by adding an 'update' of hfacc etc. to their current |
633 |
|
value at the beginning of forward_step.F. |
634 |
|
o pkg/seaice |
635 |
|
seaice_lsr: move stress-divergence computations out of outer pseudo- |
636 |
|
timestepping loop |
637 |
|
o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD' |
638 |
|
up, so that the calls of the ctrl_* subroutines are really at the end |
639 |
|
of the routine. |
640 |
|
o pkg/gmredi: |
641 |
|
allow to specify a 2-D horizontal map and a 1-D vertical profil |
642 |
|
as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity. |
643 |
|
o pkg/seaice: |
644 |
|
move lsr iterations from seaice_dynsolver to seaice_lsr. |
645 |
|
o pkg/seaice: |
646 |
|
reduce memory footprint of seaice mutldim advection tapes, |
647 |
|
by using a 2D tape independent of the generic_advdiff ones, |
648 |
|
and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc. |
649 |
|
|
650 |
|
checkpoint62q (2010/12/29) |
651 |
|
o model/src: |
652 |
|
- check horizontal grid-spacing for unset or zero/negative values. |
653 |
|
- change AD test hs94.1x64x5 to be truly a 2-D set-up. |
654 |
|
o pkg/flt: |
655 |
|
- use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR |
656 |
|
- precision of input and output files set according to readBinaryPrec |
657 |
|
and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits. |
658 |
|
- initial float position from tiled file was not converted to index space |
659 |
|
(looks like a bug): fixed to make it similar to initial pos. global file. |
660 |
|
o global_ocean.cs32x15: |
661 |
|
change SIZE.h of AD set-up to get same tiling as with MPI. |
662 |
|
Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11) |
663 |
|
o model/src: |
664 |
|
add flag to control printing of domain fields (bathymetry, hFac ...) in |
665 |
|
ini_mask_etc (call to plot_fieds_xy*). |
666 |
|
o pkg/thsice: |
667 |
|
if useEXF, some forcing fields are not valid in overlap: fixed by computing |
668 |
|
over the interior only + apply EXCH at the end (like with SEAICE advection). |
669 |
|
o pkg/mdsio: |
670 |
|
- add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer |
671 |
|
to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS. |
672 |
|
- change barrier call for safe multi-threads access to 3-D shared buffer. |
673 |
|
- MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones) |
674 |
|
- replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and |
675 |
|
remove the 4 S/R MDS_PASS_WH_R4/8toRL/S. |
676 |
|
o pkg/flt: |
677 |
|
- add fourth-order Runge-Kutta integration |
678 |
|
- add basic exch2 support (only 1 facet supported so far!) |
679 |
|
o pkg/mdsio+rw: |
680 |
|
new S/R to read local (or tile independent) vector (read counterpart of |
681 |
|
mds_writevec_loc, and front-end write_glvec_rl/rs). |
682 |
|
o global_ocean.cs32x15: additional input_ad.seaice experiment |
683 |
|
that uses pkg/seaice rather than pkg/thsice. |
684 |
|
(using multidim advection for seaice) |
685 |
|
o towards more F95 syntax for array specification in namelist: |
686 |
|
- change "data.diagnostics" (data.ptracers was changed before checkpoint62p) |
687 |
|
of all verification experiments. |
688 |
|
e.g.: line: fields(1,3)='ETAN ','ETANSQ ', |
689 |
|
was changed to: fields(1:2,3)='ETAN ','ETANSQ ', |
690 |
|
- finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles |
691 |
|
o global_ocean.cs32x15: additional input.seaice experiment |
692 |
|
that uses pkg/seaice rather than pkg/thsice. |
693 |
|
|
694 |
|
checkpoint62p (2010/12/17) |
695 |
|
o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it |
696 |
|
to THSICE_SIZE.h to avoid conflict with pkg/seaice. |
697 |
|
o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint. |
698 |
|
allow for use of multim. advection in seaice adjoint. |
699 |
|
o pkg/seaice: add diagnostics for snow precipitation and sublimation flux |
700 |
|
- first attempt to close budgets by taking into account the freshwater |
701 |
|
flux implied by the sublimation of snow and ice. So far only the |
702 |
|
volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag |
703 |
|
SEAICE_ADD_SUBLIMATION_TO_FWBUDGET |
704 |
|
o eesupp/src: |
705 |
|
new S/R with new option (NML_EXTENDED_F77) to change array specification |
706 |
|
from F95 standard to commonly accepted extended F77 form. |
707 |
|
This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5) |
708 |
|
and to revert back to the original syntax (with -DNML_EXTENDED_F77) |
709 |
|
for less tolerant f77 compiler (e.g., pgf77, g77). |
710 |
|
o globalFiles: |
711 |
|
commented out in parameter file "data" since it's not safe with MPI |
712 |
|
(e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much |
713 |
|
in this case); no longer commented out in restart test (tst_2+2). |
714 |
|
o add adTapeDir to specify a special directory where adjoint tapes are |
715 |
|
written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05 |
716 |
|
and cannot be used together with mdsioLocalDir. |
717 |
|
o nesting pkgs: |
718 |
|
- packages_init_variables : put call to OBCS_INIT_VARIABLES in last position |
719 |
|
- update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino) |
720 |
|
- add parameter files + utils dir + output from short run on beagle. |
721 |
|
o pkg/seaice: |
722 |
|
fix seaice_growth.F store directives; update results of exp. lab_sea.ad |
723 |
|
o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid |
724 |
|
unnecessary copying in adjoint code, requires new parameter NMAX_ITER |
725 |
|
|
726 |
|
checkpoint62o (2010/11/25) |
727 |
|
o pkg/exf: |
728 |
|
- change CPP option EXF_VERBOSE to run-time logical param exf_verbose. |
729 |
|
o pkg/seaice: |
730 |
|
- seaice_ocean_stress: split a loop for better vectorization of the |
731 |
|
adjoint code |
732 |
|
- seaice_growth.F: fix bug in conservation of freshwater connected to |
733 |
|
capping of heff, put contribution into d_HEFFbyNEG |
734 |
|
- replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat |
735 |
|
by something more sensible (parameters that are what their name implies) |
736 |
|
- change some defaults, so that by default exf-parameters are used for |
737 |
|
things like rhoAir, cpAir,latent/sensible heat parameters, in order |
738 |
|
to reproduce the old results, many data.seaice now contain funny values |
739 |
|
for cpAir and latent heat of sublimation |
740 |
|
o packages_readparms.F: move exf_readparms up in line so that |
741 |
|
exf-parameters are visible for other packages (e.g. seaice) |
742 |
|
o debugMode & debugLevel=2: |
743 |
|
- differentiate between debugMode & debugLevel=2: |
744 |
|
debugMode: controls printing of debug messages (sequence of S/R calls). |
745 |
|
debugLevel: controls printing of algorithm intermediate results and stats. |
746 |
|
- remove "if debugLevel=2 => debugMode" but keep "debugMode => debugLevel=2"; |
747 |
|
=> allows to print debug-stats without all sequence of call messages. |
748 |
|
- switch control of debug print from debugLevel to debugMode in many S/R. |
749 |
|
o pkg/obcs (obcs-sponge): |
750 |
|
fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the |
751 |
|
call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge) |
752 |
|
o pkg/generic_advdiff: |
753 |
|
- record overlap minimum size for each advection scheme; |
754 |
|
- refine criteria on overlap minimum size; |
755 |
|
- check and stop (in gad_check) if overlap size is too small. |
756 |
|
o pkg/obcs: |
757 |
|
- with ptracers: remove multiple calls to obcs_apply_ptracer (only done |
758 |
|
once, in ptracers_implicit.F) |
759 |
|
- with seaice: remove test on empty file name in obcs_apply_seaice (always |
760 |
|
apply OB values when tile has OB) |
761 |
|
o model/src, coriolis setting: |
762 |
|
- integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical |
763 |
|
useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from |
764 |
|
files (selectCoriMap=3) with any grid. |
765 |
|
- add parameter "fPrime" for constant second Coriolis coeff (default=0). |
766 |
|
o pkg/seaice/seaice_growth.F: |
767 |
|
a few cosmetic changes that reduce the number of lines of code |
768 |
|
o pkg/obcs: add boundary conditions following Stevens (1990) |
769 |
|
- the code follows old MOM/NAOSIM code |
770 |
|
- so far it is only implemented for the eastern and western boundaries |
771 |
|
and NOT for pTracers |
772 |
|
o pkg/rbcs: |
773 |
|
- replace rbcsInIter by rbcsForcingOffset, the time in seconds at the |
774 |
|
beginning of the first rbcs forcing period. |
775 |
|
- add option rbcsSingleTimeFiles that makes rbcs read forcing data like the |
776 |
|
offline package, i.e., one file per time, labeled by iteration number; |
777 |
|
deltaTrbcs sets the timestep with which the data was generated; |
778 |
|
rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset. |
779 |
|
- rbcsForcingCycle=0 makes forcing non-cyclic. |
780 |
|
- make arithmetic safe for negative times and odd forcing periods. |
781 |
|
|
782 |
|
checkpoint62n (2010/11/09) |
783 |
|
o pkg/seaice: |
784 |
|
fix masking in free-drift S/R ; update results of exp. lab_sea.fd |
785 |
|
o pkg/obcs: |
786 |
|
New S/R to copy tracer value from the OB location to narrow band region |
787 |
|
(width = same as overlap) beyond the OB: preserve OB value (needed for |
788 |
|
high-order scheme) which were overwritten by EXCH call if in overlap |
789 |
|
region. Applied to theta, salt, ptracer and advected seaice variables. |
790 |
|
With seaice: use maskInC in similar way as in gad_advection.F, |
791 |
|
in seaice_advection.F and advect.F. |
792 |
|
Update output of experiment seaice_obcs and change exp4 to test OBCS with |
793 |
|
4th order Adv.Scheme. for pasive salt and ptracer. |
794 |
|
o tools/genmake2: |
795 |
|
- when looking for an optfile (not specified), only search for Fortran compiler |
796 |
|
(remove sym-link test + setting of CPP + makedepend check + C-compiler check) |
797 |
|
- in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm |
798 |
|
(instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong) |
799 |
|
- set default for CPP to "cpp -traditional -P" (was the case without specifying |
800 |
|
an optfile, but otherwise default was just "cpp". |
801 |
|
- comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from) |
802 |
|
- when "CC" is not set in the optfile, look for possible C compiler |
803 |
|
(instead of just setting CC=cc) |
804 |
|
- put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes: |
805 |
|
=> add a ".F" to ".o" rule for source files with no "#include" (such as |
806 |
|
port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS. |
807 |
|
- move gfortran before g77 in list of possible Fortran compiler (consistent |
808 |
|
with reference compiler switch from g77 to gfortran) |
809 |
|
o pkg/seaice: |
810 |
|
o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to |
811 |
|
seaice_check that stops the model, when the CPP flag is used. |
812 |
|
o seaice_growth.F: make capping of ice volume conserving by returning the |
813 |
|
capped ice as freshwater to EmPmR. This does not change the verification |
814 |
|
experiments but will change runs where the capping is acutally active |
815 |
|
o change reference platform+compiler from faulks+g77 to baudelaire+gfortran |
816 |
|
(except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5, |
817 |
|
global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD), |
818 |
|
lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd) |
819 |
|
o tools/genmake2: |
820 |
|
- merge genmake_warnings & genmake_errors into 1 log file: "genmake.log") |
821 |
|
- change DUMPSTATE default to false (can use "-ds" option to switch it to T) |
822 |
|
- clean previous genmake log files before anything else. |
823 |
|
- change Makefile to remove testreport log files (*.tr_log) and genmake log |
824 |
|
files only with "CLEAN" target (instead of "Clean"); |
825 |
|
o pkg/generic_advdiff: |
826 |
|
Change OBCS in multiDim advection (gad_advection.F): |
827 |
|
Use maskInC to prevent intermediate update of tracer-field in OB regions, |
828 |
|
thus keeping current-time-step OB values; and remove the call to OBCS_APPLY |
829 |
|
which were applying future time-step OB values. |
830 |
|
This way, all explicit calculations use current-time-step OB values |
831 |
|
(simpler and more consistent). |
832 |
|
Affects results when set-up uses time-varying OBC and multi-dim advection; |
833 |
|
update output of experiment seaice_obcs. |
834 |
|
o pkg/seaice: |
835 |
|
move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h: |
836 |
|
this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH & |
837 |
|
SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY. |
838 |
|
Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY |
839 |
|
but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp |
840 |
|
unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h) |
841 |
|
o pkg aim (2010/10/26): |
842 |
|
- Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation |
843 |
|
formulation with obliquity, eccentricity, ... as run-time parameters, |
844 |
|
- Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and |
845 |
|
upward shortwave radition at the surface (all-sky and clear-sky). |
846 |
|
o pkg/obcs: |
847 |
|
- writing sections with globalFiles=T does not work: switch to tiled-files |
848 |
|
when writing sections for OBCS (change pkg/rw/write_rec.F accordingly). |
849 |
|
- fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F |
850 |
|
- apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs |
851 |
|
|
852 |
|
checkpoint62m (2010/10/21) |
853 |
|
o pkg/seaice: vectorize seaice_solve4temp.F |
854 |
|
- move iterations loops outside of i/j-loops |
855 |
|
- requires 2D arrays for TB and effConduct |
856 |
|
- add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is |
857 |
|
modified in this routine |
858 |
|
- a little bit of clean up, adjusting indentation, etc. |
859 |
|
- replaced a few TEN**a by exp(a*log(10.)) in new code for better |
860 |
|
performance and '**TWO' by '**2' (because TWO is a float), |
861 |
|
replaced ONE, ZERO |
862 |
|
o eesupp/src: |
863 |
|
fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube |
864 |
|
o pkg/seaice/seaice_growth.F |
865 |
|
Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and |
866 |
|
merging process. The merged routine has two branches, and one activates the 'evolution' |
867 |
|
branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now). |
868 |
|
In summary, here is what the '10/10 revision' did consist of |
869 |
|
part 1: seaice_growth.F revisions 1.71 to 1.75 |
870 |
|
- Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged. |
871 |
|
The emphasis here was on improving readability (e.g. by trying to use meaningful |
872 |
|
variable names) and modularity (e.g. by adding arrays to store heff etc. updates). |
873 |
|
part 1.5: |
874 |
|
- revising the lab_sea experiment to make it a more useful (i.e. stable |
875 |
|
and representative of an actual model run). This was done by generating a |
876 |
|
(winter) pickup to start from, switching back the main experiment dynamic |
877 |
|
solver from evp to lsr, having one of the experiments use the free drift solution. |
878 |
|
part 2: seaice_growth.F revisions 1.76 to 1.85 |
879 |
|
- Sorting out hard-coded constants that prevented heat and fresh water conservation. |
880 |
|
- Sorting out the various fields units and sign (set early on and reset at the end) |
881 |
|
to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and |
882 |
|
fresh water stock is 'effective ice meters', and >0 implies more ice/snow. |
883 |
|
- Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks, |
884 |
|
and simplifying logical expressions to further improve readibility. |
885 |
|
part 3: seaice_growth.F revisions 1.86 to 1.89 |
886 |
|
- Re-organize the blocks of code more logically. |
887 |
|
- Merging the '_if.F' pieces that add something new. |
888 |
|
o pkg/thsice: |
889 |
|
- vectorize thsice_solve4temp and thsice_get_exf. |
890 |
|
Problem: thsice_solve4temp has an unvectorizable statement that |
891 |
|
might also be problematic for TAF |
892 |
|
- thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This |
893 |
|
does not change the verifcation experiment, but will change all |
894 |
|
experiments that have this flag undefined (not tested in verification); |
895 |
|
a little reorganization to save a few 2D fields and recomputations |
896 |
|
- 1st step of revisiting thsice adjoint (major recomp. sorted out) |
897 |
|
- 2nd step: fix some store dirs |
898 |
|
o seems to work somewhat, i.e. using ifort but not g77 |
899 |
|
o likely cause are incomplete init. or recomputation |
900 |
|
o start verification/global_ocean.cs32x15/input_ad.thsice |
901 |
|
o pkg/obcs: add support for exch2 |
902 |
|
- the position of the boundary and prescribed values are specified using |
903 |
|
a global domain with exch2 facets stacked |
904 |
|
- in x for N,S boundaries (like W2_mapIO=-1) |
905 |
|
- in y for E,W boundaries (so E,W boundaries do not overlap) |
906 |
|
o pkg/mdsio: add support for writing global sections with exch2 |
907 |
|
file layout is as for obcs described above: |
908 |
|
- for x-z sections, facets are stacked in x (like W2_mapIO=-1) |
909 |
|
- for y-z sections, facets are stacked in y |
910 |
|
o pkg/thsice: |
911 |
|
- change a few routines for better vectorization: thsice_albedo.F, |
912 |
|
thsice_step_temp.F, and in thsice_calc_thickn.F. Results are |
913 |
|
not affected, but in particular the latter routine has changed |
914 |
|
dramatically (not necessarily easier to read now). |
915 |
|
- re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops |
916 |
|
iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF. |
917 |
|
o verification/lab_sea: |
918 |
|
- overhaul of the forward model experiments. The main motivation |
919 |
|
for this revision is that lab_sea has proven quite fragile (when |
920 |
|
changing the sea-ice code, and switching platforms) to a point |
921 |
|
when failures were very hard to attribute to specific code problems. |
922 |
|
- the suspected reason for this fragility is noise amplification by evp so, |
923 |
|
to start with, we decided to replace evp with lsr in the main experiment. |
924 |
|
- the input.lsr experiment thus became obsolete and was removed. |
925 |
|
- it was replaced with the input.fd experiment that uses an |
926 |
|
analytical "free drift" solution as the ice velocity field. |
927 |
|
- Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp) |
928 |
|
will hopefully allow us to discriminate problems due to dynamic solvers |
929 |
|
from problems due to the thermodynamic code. input.salt_plume (lsr) allows |
930 |
|
us to test additional options, along with the salt plume package. |
931 |
|
- Finally a pickup was generated (at the end of a one year run) to |
932 |
|
make the tests more representative of an actual model run. Previously |
933 |
|
the tests starting point was a 1m thickness of ice everywhere. |
934 |
|
o pkg/seaice: |
935 |
|
- introducing S\R seaice_freedrift.F that compute the |
936 |
|
analytical solution to an approximate ice momentum |
937 |
|
equation (i.e. the simple stress/coriolis balance). |
938 |
|
- define SEAICE_ALLOW_FREEDRIFT to trigger the computation |
939 |
|
of the free drift velocity field, and enable its use. |
940 |
|
To actually use the free drift solution as the model ice |
941 |
|
velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice. |
942 |
|
o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata" |
943 |
|
|
944 |
|
checkpoint62l (2010/10/04) |
945 |
|
o pkg/seaice: |
946 |
|
-fix the USE_ORIGINAL_SBI version (for variable freezing point); |
947 |
|
-use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new |
948 |
|
version (with USE_ORIGINAL_SBI undef); |
949 |
|
o add hooks for new packages OASIS, the package will follow |
950 |
|
(hooks exclude the seaice pkg for now) |
951 |
|
o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO |
952 |
|
Option to use mdsio_read_whalos.F/mdsio_write_whalos.F, |
953 |
|
rather than mdsio_readvector.F/mdsio_writevector.F, within |
954 |
|
adread_adwrite.F to read/write adjoint-related tapes to disk. |
955 |
|
o eesupp and pkg/mdsio: ALLOW_WHIO |
956 |
|
Option to write/read 2D fields to files including tiles halos. |
957 |
|
The main purpose is for adjoint related "tape I/O". |
958 |
|
The secondary purpose is for debugging phases. |
959 |
|
A word on those rather specifically intended purposes. |
960 |
|
The code was meant to be stripped down to the bare minimum. |
961 |
|
Typically, there is a unique and basic mapping to the global |
962 |
|
buffer (tile by tile, then proc by proc, then level by level), and |
963 |
|
byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not |
964 |
|
meant to generate user friendly outputs of various shapes and forms. |
965 |
|
Rather it is intended, for the knowledgeabale developers, |
966 |
|
to be largely independent of the many mdsio options, to allow |
967 |
|
outputs of tiles+halos in debugging phases and in adjoint runs, |
968 |
|
and to allow some flexibility in tuning (adoint) I/O depending on each |
969 |
|
file system behavior. With regard to tuning, most of the potential knobs |
970 |
|
(to leave files open, to allocate the I/O indep. of usesinglecpuio, |
971 |
|
to specify directories, to specify the typical size of I/O calls, etc.) |
972 |
|
are not yet included, and will be added if they prove useful. |
973 |
|
o pkg/seaice: |
974 |
|
fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F |
975 |
|
o pkg/seaice: |
976 |
|
new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty |
977 |
|
code (seaice_budget_ice_if.F) which enable to recover old standard |
978 |
|
code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined. |
979 |
|
temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F. |
980 |
|
o model/src (rStar): |
981 |
|
use simple average (not area weighted) of rStarFac at U,V point when using |
982 |
|
vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection) |
983 |
|
update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20. |
984 |
|
|
985 |
|
checkpoint62k (2010/09/17) |
986 |
|
o adjoint |
987 |
|
* changed verification/global_ocean.cs32x15 ; adjoint now tests |
988 |
|
Adams-Bashforth 3 + NLFS + RSTAR |
989 |
|
* some more modifs required for ECCO-GODAE v4 |
990 |
|
o pkg/seaice |
991 |
|
add SEAICE_AGE_VOL option to use volume instead of area for |
992 |
|
integrating SEAICE_AGE |
993 |
|
o model/src: |
994 |
|
first check-in of sigma & hybrid-sigma coordinate code ; also includes |
995 |
|
non-linear free-surface parts ; but pressure-gradient not yet coded. |
996 |
|
o pkg/ptracers: |
997 |
|
option for ptracer to convert Salt Relax into additional EmP. |
998 |
|
tested in exp. global_ocean.90x40x15.dwnslp (update output) |
999 |
|
|
1000 |
|
checkpoint62j (2010/08/25) |
1001 |
|
o pkg/ggl90: |
1002 |
|
other minor changes: remove 3-D temp array gTKE (+ add argument myIter) |
1003 |
|
o pkg/dic: car_flux.F, phos_flux.F |
1004 |
|
- reduce number of exp-calls in order to improve performance |
1005 |
|
- clean up a little (replace fields by their macros, etc., fix |
1006 |
|
typo in CPP-flag) |
1007 |
|
o pkg/ggl90: minor changes |
1008 |
|
- GGL90diffKrS was removed --> always use GGL90diffKr |
1009 |
|
- GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV |
1010 |
|
- hack of mxlMaxFlag=2 --> ensure mixing between first and second level |
1011 |
|
(commented out for now) |
1012 |
|
- change in max/min operations to ensure that smoothing is ok |
1013 |
|
- smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr) |
1014 |
|
- always use diffKrNrT as background profile (i.e. never use diffKr field) |
1015 |
|
o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj) |
1016 |
|
o pkg/dic: |
1017 |
|
- model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better |
1018 |
|
vectorization |
1019 |
|
- small bug fix in insol for the unlikely case of a cartesian grid |
1020 |
|
- towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F |
1021 |
|
+ now vectorize, which also removes adjoint recomputations; |
1022 |
|
+ replace integer maksp1 by _RL maskp1 |
1023 |
|
+ replace a**x by exp(x*log(a)) in phos_flux.F for speed |
1024 |
|
|
1025 |
|
checkpoint62i (2010/07/21) |
1026 |
|
o pkg/flt: |
1027 |
|
- with OBCS: stop floats which enter the OB region |
1028 |
|
o model/src: |
1029 |
|
- use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones) |
1030 |
|
for implicit vertical advection. |
1031 |
|
o pkg/seaice: |
1032 |
|
- account for melting in seaice age evolution. |
1033 |
|
- remove double counting of seaice ridging effect on seaice age. |
1034 |
|
|
1035 |
|
checkpoint62h (2010/06/18) |
1036 |
|
o pkg/exch2: |
1037 |
|
- remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1). |
1038 |
|
o tools/genmake2 |
1039 |
|
- remove "-pdefault" option: redundant with the use of "packages.conf"; |
1040 |
|
- remove file pkg/pkg_default : set the default as a pkg group |
1041 |
|
("default_pkg_list") defined in pkg/pkg_groups; |
1042 |
|
- fix for case pkg/pkg_depend is missing (was hanging before); |
1043 |
|
- add option "-pgroups" to specify a different pkg_groups than the default. |
1044 |
|
o verification/adjustment.cs-32x32x1: |
1045 |
|
add a "minimal" set-up test (code_min & input_min) which only compiles |
1046 |
|
eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc. |
1047 |
|
o tools/genmake2 |
1048 |
|
- extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg])) |
1049 |
|
- fix details of checking for mnc & profile pkg when NetCDF is unavailable. |
1050 |
|
o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these |
1051 |
|
files are nearly the same anyway. |
1052 |
|
Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04: |
1053 |
|
- redefinition of tau(i,i) (by a factor of ustar) |
1054 |
|
- 1./exf(Const/T) -> exf(-Const/T) (big change in the results) |
1055 |
|
- replace rhonil by rhoConstFresh in computation of evap (bug fix) |
1056 |
|
- replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results) |
1057 |
|
- replace |
1058 |
|
rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh ) |
1059 |
|
shn = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j) |
1060 |
|
by |
1061 |
|
shn = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh ) |
1062 |
|
(changes results) |
1063 |
|
-> exf_bulkformulae v1.22, |
1064 |
|
update verification experiments lab_sea, offline_exf_seaice, seaice_obcs |
1065 |
|
(lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13, |
1066 |
|
output.txt 1.63 |
1067 |
|
offline_exf_seaice: output.seaicetd.txt 1.7 |
1068 |
|
seaice_obcs: output.txt 1.10) |
1069 |
|
Step 2: do the actual merge and remove exf_bulk_largeyeager04.F |
1070 |
|
-> exf_bulkformulae v1.23, |
1071 |
|
unfortunately requires updating lab_sea.salt_plume (6 matching digits), |
1072 |
|
and global_ocean.cs32x15.icedyn (only 11 matching digits) |
1073 |
|
Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice. |
1074 |
|
o adjoint of exch-1: |
1075 |
|
- pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list) |
1076 |
|
(note: was already like this when using EXCH-2) and remove flow dir |
1077 |
|
and hand-written AD version of high-level EXCH S/R (pkg/autodiff); |
1078 |
|
- provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow); |
1079 |
|
- update pkg/exch2 diff list. |
1080 |
|
|
1081 |
|
checkpoint62g (2010/05/19) |
1082 |
|
o eesupp/src (exch-1): |
1083 |
|
- split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F) |
1084 |
|
and remove argument "simulationMode"; same thing for all exch_*rx_cube.F |
1085 |
|
(renamed to exch1_*rx_cube.F). |
1086 |
|
- change accordingly exch_*_rx.template and AD version in pkg/autodiff |
1087 |
|
to call new exch1 S/R ; update Makefile and .cvsignore. |
1088 |
|
- replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove |
1089 |
|
exch2_xy_rx later) |
1090 |
|
Note: after updating your code, need to run "make clean" in eesupp/src |
1091 |
|
o test experiment bottom_ctrl_5x5: |
1092 |
|
new output_adm.txt with fewer grdchk & less monitor output. |
1093 |
|
o model/src: |
1094 |
|
remove the call to ini_cori in initialise_varia.F (just keep the usual one |
1095 |
|
in initialise_fixed.F). More consistent with coriolis & horizontal grid |
1096 |
|
beeing treated in the same way (ini_grid is not called a 2nd time). |
1097 |
|
o pkg/exf: |
1098 |
|
- rewrite exf_bulk_largeyeager04.F for better vectorization, changes |
1099 |
|
global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated |
1100 |
|
- fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now) |
1101 |
|
- cosmetic changes to exf_bulkformulae.F to make it look more like |
1102 |
|
exf_bulk_largeyeager04.F |
1103 |
|
o eesupp/src (exch-1): |
1104 |
|
- Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1). |
1105 |
|
- Separate buffer filling and MPI sending: allow EXCH-1 to work for local |
1106 |
|
array (non-shared) when using MPI+MTH. Also reduces number of BARRIER |
1107 |
|
(even without using MPI). |
1108 |
|
- Message mode: move RecvAck setting (indicator of buffer being ready) |
1109 |
|
from send_put to recv_get S/R (was useless before, but not sure if |
1110 |
|
it's much more useful now); |
1111 |
|
- Switch the order of sync: MPI-proc 1rst and then threads; |
1112 |
|
- take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead. |
1113 |
|
- fix AD code for communication mode ='get' (but not used). |
1114 |
|
o model/src: |
1115 |
|
initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does |
1116 |
|
not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp). |
1117 |
|
o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API |
1118 |
|
o pkg/ctrl: require a specific set of control variables and exf-flags for |
1119 |
|
adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied) |
1120 |
|
o model/src: |
1121 |
|
a) 1rst version of a new driver S/R to turn-off output freq and flags after the |
1122 |
|
1rst forward sweep, to avoid over-writing output files during recomputations |
1123 |
|
recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?) |
1124 |
|
b) 2nd version: |
1125 |
|
- add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO); |
1126 |
|
- switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast, |
1127 |
|
writePickupAtEnd) + seaice & ptracers output; |
1128 |
|
- do not switch off MNC flags (otherwise, won't get admonitor netcdf file) |
1129 |
|
o model/src: |
1130 |
|
- new S/R rotate_uv2en_rl (..._rs) that rotates vector fields. |
1131 |
|
o pkg/exch2: |
1132 |
|
- remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ; |
1133 |
|
- add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch). |
1134 |
|
o pkg/autodiff & exch2: |
1135 |
|
process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF |
1136 |
|
(for now, only if ALLOW_EXCH2 is defined). |
1137 |
|
o pkg/autodiff: |
1138 |
|
- include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F |
1139 |
|
(not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly. |
1140 |
|
+ clean-up comments (_RS is not always real*4) |
1141 |
|
- fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R) |
1142 |
|
- add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2: |
1143 |
|
was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs. |
1144 |
|
o testreport (AD-tests): |
1145 |
|
no longer link files from dir "../input" (1rst link files from |
1146 |
|
"../input_ad.[xx]" if secondary test "xx" and then from "../input_ad") |
1147 |
|
|
1148 |
|
checkpoint62f (2010/04/29) |
1149 |
|
o model/src/the_main_loop.F: |
1150 |
|
adjust store directives for seaice evp and multicategory according to |
1151 |
|
pkg/ecco/the_main_loop.F |
1152 |
|
o adjoint: |
1153 |
|
global_sum_ad was incomplete (noted many times by many people ;) |
1154 |
|
nice description by Jean U. as follows: |
1155 |
|
* allreduce(var) in global_sum.F can be interpreted as |
1156 |
|
reduce(sum) followed by broadcast of sum. |
1157 |
|
* The adjoint of that is |
1158 |
|
sum(adjoint) followed by broadcast(summed adjoint value) |
1159 |
|
or in other words, allreduce(sum, adjoint vars) |
1160 |
|
We were missing the sum(adjoint)! |
1161 |
|
Benign, except(!) for "global" scalars appearing in tile loops (bi,bj) |
1162 |
|
(noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset). |
1163 |
|
The fix should produce 16-digit accuracy between |
1164 |
|
single-CPU multi-tile (e.g. nSx=2, nPx=1) and |
1165 |
|
multi-CPU single-tile (e.g. nSx=1, nPx-2) |
1166 |
|
We'll probably change this yet again shortly |
1167 |
|
o eesupp/src: |
1168 |
|
- fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?) |
1169 |
|
o pkg/icefront |
1170 |
|
- ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving |
1171 |
|
specification of addmass array based on a 2D field, which is added |
1172 |
|
at bottommost wet level at each horizontal location. |
1173 |
|
o model/src: |
1174 |
|
horizontal grid initialisation (other than curvilinear): add code for Exch2 IO |
1175 |
|
layout; (not always compatible with delX,delY setting; commented out for now). |
1176 |
|
o pkg/exch2: |
1177 |
|
change tile to processor setting (case nSy*nPy > 1): allows default model mapping |
1178 |
|
(myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config. |
1179 |
|
|
1180 |
|
checkpoint62e (2010/04/15) |
1181 |
|
o pkg/obcs: |
1182 |
|
- fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert). |
1183 |
|
o pkg/dic: |
1184 |
|
-fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up; |
1185 |
|
(note: not presently tested in any forward verification exp.) |
1186 |
|
update tutorial_global_oce_biogeo AD output file. |
1187 |
|
o pkg/exf: |
1188 |
|
- account for the variation of albedo as a function of zenith angle |
1189 |
|
by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h |
1190 |
|
o build_options: |
1191 |
|
- rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas" |
1192 |
|
o pkg/dic: |
1193 |
|
change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart: |
1194 |
|
- use binary pickup file for restart; |
1195 |
|
- initialise atmos-CO2 box from dic_pCO2 parameter; |
1196 |
|
- fix multi-threaded. |
1197 |
|
o pkg/rbcs: |
1198 |
|
- clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ; |
1199 |
|
change (+ fix IO calls) type of array RBC_mask from _RL to _RS. |
1200 |
|
- add RBCS to exp4 passive tracer 01 (rbcs was previously untested) |
1201 |
|
and update output.txt |
1202 |
|
o pkg/kpp: |
1203 |
|
- add diagnostics for KPP non-local flux of Temp, Salinity and pTracers; |
1204 |
|
- change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS |
1205 |
|
(= ratio of KPP non-local (salt) flux relative to surface-flux) when |
1206 |
|
using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat '); |
1207 |
|
- change pkg/offline to read-in average KPPghat*KPPdiffKzS from file |
1208 |
|
KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile). |
1209 |
|
o pkg/offline: |
1210 |
|
fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor |
1211 |
|
(bug was added in version 1.10 on 2007-08-23). |
1212 |
|
o pkg/offline: |
1213 |
|
- no need to specify periodicExternalForcing, etc ... to use offline pack |
1214 |
|
- offline input files no longer just single prec --> parameter offlineLoadPrec |
1215 |
|
o verification/lab_sea: |
1216 |
|
change AD test to multi-tile setup and update all 4 AD output. |
1217 |
|
NOTE: while cost function values remain very similar, |
1218 |
|
gradients are very different, although gradient checks are self-consistent |
1219 |
|
Should try to get to the bottom of this (cost function summation order?) |
1220 |
|
o pkg/dic: |
1221 |
|
in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid |
1222 |
|
a weakness of TAF that drops part of double precision in log10 derivative. |
1223 |
|
<= changes removed since problem has been fixed in current TAF version 1.9.71 |
1224 |
|
update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo. |
1225 |
|
o pkg/ecco: |
1226 |
|
add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F |
1227 |
|
update all 4 lab_sea AD output. |
1228 |
|
|
1229 |
|
checkpoint62d (2010/03/22) |
1230 |
|
o build_options: |
1231 |
|
remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles. |
1232 |
|
o remove unbalanced quote (single or double) in commented line of source code |
1233 |
|
(may cause some warning with some preprocessor/makedepend versions). |
1234 |
|
o pkg/seaice: |
1235 |
|
fix seaice_model.F for adjoint (gael) and update AD results of experiments |
1236 |
|
lab_sea (std + evp + noseaicedyn) and offline_exf_seaice. |
1237 |
|
o testreport: |
1238 |
|
add option '-runonly' (short: '-ro') to just do the run part (without make). |
1239 |
|
o eesupp: remove JAM communication code (obsolete). |
1240 |
|
o add option to genmake2 & testreport to switch "_RS" type to "real*4" |
1241 |
|
(if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return |
1242 |
|
to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1 |
1243 |
|
(update also the output). |
1244 |
|
|
1245 |
|
checkpoint62c (2010/03/02) |
1246 |
|
o tools/build_options : |
1247 |
|
move (some) old optfiles from build_options/ to build_options/unsupported/ |
1248 |
|
o model/src and pkg/exf |
1249 |
|
surface relaxation -- separating data and data.exf options |
1250 |
|
The point is to ensure that we specify the surface relaxation |
1251 |
|
either in data or in data.exf (but not half and half) and to |
1252 |
|
avoid an accidental relaxation to 0 (which happened if a time |
1253 |
|
scale was specified but the file name was left empty) |
1254 |
|
o model/src model/inc and pkg/mom_common |
1255 |
|
ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity |
1256 |
|
=> addition to the viscosity field as computed by others schemes |
1257 |
|
o tools/build_options: |
1258 |
|
- rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile) |
1259 |
|
but keep the former optfile for few weeks for smooth transition |
1260 |
|
o pkg/ecco |
1261 |
|
- allow user defined cost function contributions |
1262 |
|
CPP: ALLOW_USERCOST_CONTRIBUTION |
1263 |
|
USAGE: compute contributions in cost_usercost_all.F |
1264 |
|
- note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was. |
1265 |
|
the two options are complementary. |
1266 |
|
o pkg/smooth |
1267 |
|
- migration from contrib to the main repository |
1268 |
|
|
1269 |
|
checkpoint62b (2010/01/26) |
1270 |
|
o pkg/monitor: |
1271 |
|
- change back mon_printstats_rl.F & mon_stats_rl.F and add a stop |
1272 |
|
(in case someone forgot to update customized pieces of code) |
1273 |
|
o nonHydrostatic: |
1274 |
|
- add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested); |
1275 |
|
- add a simple 2-D experiment (short_surf_wave) to test it. |
1276 |
|
o pkg/icefront: |
1277 |
|
adding the shell of, and the hooks to, a new package that |
1278 |
|
will model melting and freezing of vertical glacier ice fronts |
1279 |
|
o momentum: |
1280 |
|
add diagnostics of momentum tendency from Hydrostatic pressure gradient |
1281 |
|
(without surf.pressure term: would need a 2nd filling since implicit term). |
1282 |
|
o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace |
1283 |
|
two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR |
1284 |
|
cannot deal with the former |
1285 |
|
o cleaning: |
1286 |
|
- remove all (except OpenAD) old TLM output from results_ad dirs. |
1287 |
|
- remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R) |
1288 |
|
- comment out maskH definition (replaced by maskInC) |
1289 |
|
o pkg/monitor: |
1290 |
|
- change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl |
1291 |
|
& mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs. |
1292 |
|
|
1293 |
|
checkpoint62a (2010/01/15) |
1294 |
|
o model/src: |
1295 |
|
- bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4) |
1296 |
|
o pkg/diagnostics: |
1297 |
|
- add optional level number diagnostics (i.e., level number to be define |
1298 |
|
explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X". |
1299 |
|
- strictly check for valid parser-code(10) ; |
1300 |
|
- check if adding diag to the list from the right place. |
1301 |
|
o pkg/longstep: |
1302 |
|
- change parameters and fix tracer conservation with rstar/nonlinear free surface |
1303 |
|
o diagnostics: |
1304 |
|
- in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer |
1305 |
|
S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics. |
1306 |
|
o pkg/diagnostics: |
1307 |
|
- Add option for writing vertical integral (sum of selected levels) of an output |
1308 |
|
field instead of writing output field levels. Activate this option on a per |
1309 |
|
output-file basis, by setting the 2nd character of fileflag to 'I'. |
1310 |
|
- Add field-specific information relative to level integral in 3rd postion |
1311 |
|
of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate |
1312 |
|
vertically (x level-thickness x hFac), "r"=same but without hFac. |
1313 |
o do_the_model_io: |
o do_the_model_io: |
1314 |
- pass end-of-model-run flag as argument, from forward_step to diagnostics_write: |
- pass end-of-model-run flag as argument, from forward_step to diagnostics_write: |
1315 |
in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before |
in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before |