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revision 1.1549 by jmc, Thu Dec 15 22:45:47 2011 UTC revision 1.1613 by jmc, Thu Mar 8 17:29:36 2012 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/ptracers:
8      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
9      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
10      - add parameter to decide when to start a tracer; use internal flag to
11        know which tracer to step-forward; switch this internal flag at the top
12        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
13        for adjoint built.
14    o pkg/seaice:
15      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
16      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
17      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
18    o pkg/ecco:
19      - fix writing of output file DiagnosCost_ClimSalt/Theta
20        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
21    o pkg/seaice:
22      - add missing initialisation of COR_ICE array in dynsolver.F
23      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
24        compiled either way, and is tested in all exps (multidim was only tested
25        in lab_sea ad before).
26      - cosmetic change to prepare for future addition of ITD. no change to results.
27        no defaults change.
28      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
29      - by lack of adequate verification experiments, I further used custom versions
30        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
31        should be correct.
32      - avoid recomputations in ad.
33    o array initialisation in adjoint mode:
34      1) pkg/mom_common/mom_calc_ke.F:
35        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
36        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
37        part this initialisation is gone, resulting in Floating Point Exception
38        (caught by open64 compiler with debug option).
39      2) model/src/convective_weights.F
40        set output convectCount over the full array range (instead of doing
41        an update): this fix a similar issue when called within recomputation (adjoint)
42        which could by-pass the initialisation (normally done in the caller S/R).
43    o pkg/seaice:
44      - final version of turbulent flux params, as agreed at MIT ice meet:
45           SEAICE_mcPheePiston (default is ~ 0.000875)
46           SEAICE_mcPheeTaper (default is 0.)
47           SEAICE_frazilFrac (defualt is 1.)
48           SEAICE_mcPheeStepFunc (default is false)
49      - changes results at trunction error level
50      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
51    o added pkg/frazil:
52      - see frazil_description.tex for details
53      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
54    o pkg/shelfice/shelfice_thermodynamics.F
55      - fix exponents for velocity dependent exchange coefficients: change
56        from 2/3(=0) to 0.66666666666666667
57      - move computation of velocity dependent exchange coefficients into
58        separate loop, so that it applies to both thermodynamics
59      - move some divisions by constants out of loops
60    
61    checkpoint63j (2012/02/16)
62    o pkg/seaice:
63      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
64      - SItracer:  added run time params, and allow coupling to ocn salinity.
65    o pkg/seaice: remove (almost) all divisions by constants within loops
66      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
67      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
68      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
69      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
70    o pkg/seaice :
71      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
72        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
73      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
74      - add permanent SItflux diag that corresponds to TFLUX but includes
75        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
76      - allow activation/testing of a fix for suspected missing term in
77        ocn-ice heat budget (to be confirmed). To test this, you want to
78        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
79        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
80      - no change in results, fwd or ad.
81    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
82      - switch to variable freezing point.
83           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
84      - bug fix : the sublimation term that was missing is now activated.
85           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
86      - bug fix : flooding sign term for SIsal0.NE.0.
87           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
88    o pkg/seaice:
89      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
90        is now the default, and the old default constant freezing point is recovered
91        with SEAICE_tempFrz0    = -1.96,
92             SEAICE_dTempFrz_dS = 0.,
93      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
94      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
95      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
96        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
97      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
98        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
99      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
100        seaice_growth r149 for legacy branch (no results change).
101      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
102        from I. Fenty).
103      - results did not change except for global_ocean.cs32x15, mostly due to the
104        switch to variable freezing point (see above item for detail).
105    o pkg/thsice:
106      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
107        seawater freezing in thsice_calc_thickn (not used).
108    o pkg/seaice: turbulent flux term specification via run time params.
109      - replace CPP switches with run time switches to facilitate testing
110      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
111                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
112      - added runtime parameter : SEAICEturbFluxFormula
113      - move Mcphee constants to SEAICE_PARAMS.h
114      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
115                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
116                 remove seaice_summary call (moved to seaice_init_fixed)
117      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
118        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
119      - seaice_summary.F : add missing report of read turbulent flux term set up
120                           and SITRACER.
121      - seaice_check.F : check range; inform and stop if retired CPPs are used
122                         (incl. SEAICE_AGE).
123      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
124             CPP switch, same computation as before for the different options.
125      - change results at the truncation level.
126    o pkg/seaice:
127      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
128        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
129        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
130      - update verification/*/input*/data.seaice:
131        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
132        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
133        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
134        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
135    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
136      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
137        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
138        difference in results only due to machine truncation.
139      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
140        MaykutPolySatVap; keep MIN_LWDOWN.
141      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
142      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
143        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
144    o pkg/salt_plume:
145      - isolate saltPlumeFlux array exch into a specific S/R called from
146        do_oceanic_phys.F
147      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
148    o verification:
149      - move untested set-up to MITgcm_contrib/verification_other.
150    o pkg/seaice:
151      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
152    o pkg/seaice:
153      - seaice_solve4temp.F (keeping results unchanged):
154        * add 2 future run-time params to select which saturation vapor pressure
155          formula is used and how post-iteration fluxes are set.
156          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
157        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
158          the linearized expression to stay consistent with tsurf finding.
159      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
160        can be < 0.
161    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
162      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
163        conductive heat flux F_c , and add it explicitly when updating tsurf as
164        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
165        so that now F_ia has a consistent meaning through the entire routine.
166        This causes differences at truncation level: update output of fwd exp.
167        global_ocean.cs32x15.seaice.
168    o pkg/seaice:
169      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
170        of arrays, sign/direction of fluxes; no effect on results.
171      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
172        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
173        note: this should have been done before changing celsius2K default.
174      - to keep results unchanged, add back old value of celsius2K in verification
175        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
176      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
177        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
178        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
179        freezing temp is consistent with value in seaice_growth.F ; this causes
180        differences at machine truncation level: update lab_sea AD output (3/4).
181    o pkg/seaice:
182      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
183        and climsst/sss even when using seaice (to prevent calculation that might
184        use SST on land); does not affect any verification exp.
185      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
186        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
187    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
188      over land (non-legacy code)
189    o vectorize salt_plume package:
190      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
191      - this code computes plumebk everywhere (also over land), thus requires
192        code to avoid divisions by zero and catch the case of kLev=Nr.
193      - efficiency of salt_plume_frac is still sub-optimal
194    o tools (genmake2):
195      - fix makefile NAME specification (option: -makefile NAME) by adding
196        "-f $MAKEFILE" in few places where it was missing including makedepend
197        command (contribution from Paul).
198    
199    checkpoint63i (2012/01/24)
200    o model/src:
201      - add factorized versions of some EOS code to find_rho.F,
202        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
203    o model/src:
204      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
205      - change default celsius2K from 273.16 to 273.15
206      - to keep results unchanged, add back old value of celsius2K in verification
207        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
208         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
209    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
210      to make TAF generate vectorizable code
211    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
212       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
213       have flags that do this more efficiently.
214    o pkg/diagnostics/diagstats_calc.F
215      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
216    o pkg/obcs (with exch2):
217      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
218        and remove code (in obcs_readparms.F) which was based on EXCH of indices
219        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
220    o pkg/exf and seaice exp:
221      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
222        so that switching off area & heff advection flags does not affect results.
223      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
224      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
225        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
226        results of verification experiments: 1D_ocean_ice_column(fwd),
227        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
228        and offline_exf_seaice (all 4).
229    o pkg/seaice:
230      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
231        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
232      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
233        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
234        not multi-dim advection;
235      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
236        SHORTWAVE_HEATING #undef.
237    o optim: make Makefile more robust (?)
238    o pkg/obcs:
239      * fix treatment of obcs_read_pickup for TAF
240    o pkg/shelfice:
241      * add missing initialisation of num_shifwflx
242      * new adjoint verification exp. for isomip
243      * change Prandtl and Schmidt numbers from generic formulations
244        (in terms of model diffus. and visc.) to separate runtime
245        parameters, with Holland and Jenkins (1999) default values.
246    o pkg/exf (interpolation):
247      - extended input field (2 rows) near the N & S poles:
248        * fill in with the symetric value (when even Nb of data in longitude)
249        * add average value at the poles only for scalar quantities ; for vector
250          component interpolation, skip the averaging and keep duplicated values,
251          unless the 2 components have same location (uvInterp=T) in which case
252          interpolate the 2 components together using S/R EXF_INTERP_UV.
253      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
254        together: this allows to account properly for local orientation when
255        averaging at N & S pole.
256      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
257        exf-interpolation near N & S poles. Undef by default.
258      - add debug check/print on 1rst iter if debugLevel >=2.
259    o pkg/exf:
260      - change masking flags definition (no longer "parameter"), put them in
261        common block and set them in S/R EXF_INIT_FIXED.
262      - change recognized masking flag from s,u,v to c,w,s since the mask
263        to use (maskC,W,S) depends on position on model grid and has little to
264        do with scalar/vector difference; fix masking if using P-coordinates.
265      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
266        and update results of exp. global_with_exf (x2).
267      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
268    o pkg/obcs
269      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
270    o pkg/exf (interpolation):
271      - assume periodicity in X only if input field cover full longitude range.
272      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
273        and should vectorise).
274      - fix input lat of the 2 added row (in case we provide N.pole data).
275    
276    checkpoint63h (2011/12/30)
277    o pkg/seaice:
278      - change declaration of UVM from _RL to _RS in order to get B-grid
279        uIce,vIce monitor when _RS = real*4
280    o pkg/offline:
281      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
282      - compute vertical velocity if not read from file (switch on exactConserv
283        & staggerTimeStep);
284      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
285    o verification:
286      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
287        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
288        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
289      - update output of exp. global_ocean.cs32x15.viscA4 after changing
290        grid-file angles (used here for coriolis-3d);
291      - remove (or gzip) few files not needed to run fizhi-cs experiments.
292    o pkg/exf (vector interpolation):
293      - rotate vector component toward local grid-axis orientation using grid-angles
294        (stored in GRID.h) instead of locally computed rotation angle; keep old code
295        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
296    o pkg/seaice:
297      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
298        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
299    o pkg/PKG_OPTIONS.h files:
300      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
301        outside of the #ifdef ALLOW_THISPKG / #endif block.
302      - update verification/*/code/PKG_OPTIONS.h files.
303    o add a verification experiment (offline_exf_seaice/input.seaice) that test
304      the B-grid LSOR solver
305    o pkg/seaice: sort out emissivity and long wave radiation step 2:
306      - add emissivity for snow and ice as new run-time parameters
307        (unfortunately) that default to the corresponding exf values; this
308        changes results in most verification experiments so that for backward
309        compatibility these parameter have to be set explicitly to inconsistent
310        values (ugly);
311      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
312        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
313        until we agree how to handle this bug properly
314    o pkg/exf (interpolation):
315      - add a set of run-time param ({inputfield}_interpMethod), one for
316        each interpolated input field, to select the interpolation method
317        with a value of zero switching off the interpolation;
318      - print interpolation parameters to standard output;
319      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
320        (to use instead runoff_interpMethod=0 in data.exf).
321      - simplify default setting of interpolation parameters (for all fields,
322        set position to match model grid cell-center position, leading to trivial
323        interpolation in case of regular Lat-Lon grid) and fix for the case of
324        non-uniform delY.
325    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
326       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
327       this factor is absolutely required, because the lw exitance (= out-going
328       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
329       where the reflectivity rho = 1-emissivity for conservation reasons. Once
330       this is established, we can remove the CPP-Flag (if we want to).
331    o pkg/seaice:
332      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
333        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
334      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
335        what the name implies (and not emissivity*BoltzmannConstant), this means
336        the old default value of 5.5e-8 now means
337        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
338        S/R exf_readparms
339      - FV-discretization of the B-grid LSOR solver, turn on with
340        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
341        of the calling routine dynsolver, so that B and C-grid code look a
342        little more alike.
343      - fix index bugs in ostres.F (B-grid code)
344    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
345    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
346      default for SEAICE_emissivity, if useEXF; requires setting a wrong
347      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
348      backward compatiblity
349    o model/src: use sigmaR in calc_ivdc
350    
351    checkpoint63g (2011/12/16)
352    o pkg/seaice/seaice_growth.F:
353      fix heat conservation of the coupled ocean-seaice system.
354      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
355      solid vs liquid water treatment is resolved via QNET.
356    o pkg/seaice/seaice_growth.F:
357      add missing term for sublimation in saltFlux, which was breaking conservation.
358    o pkg/seaice/seaice_model.F:
359      Remove this patholigical case treatment in evolution branch,
360      where it is un-necessary and breaks conservation.
361      Update global_ocean.cs32x15/results accordingly for
362      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
363  o model/src:  o model/src:
364    useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in    useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
365    external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.    external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.

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