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revision 1.1579 by jmc, Sat Jan 21 19:41:43 2012 UTC revision 1.1644 by jmc, Tue Apr 3 17:01:48 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/bbl:
8      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
9        update global_with_exf output.yearly.txt file.
10    o pkg/cal:
11      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
12      - remove 2 unsused and very short (1 line only) functions ;
13      - remove unsused subroutines from AD-Diff list.
14    o model/src:
15      - start to implement clean wait to stop in initialization S/R (config_check.F,
16         packages_check.F and pkg/obcs/obcs_check.F + pkg/mypackage)
17    o folowing PRINT_MESSAGE changes:
18      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
19    o pkg/bbl:
20      - modification so it can work with z*
21      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
22      - global_with_exf/input.yearly verification; changes output.yearly.txt
23    o eesupp/src:
24      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
25        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
26      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
27        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
28      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
29      - when using MPI, always set usingMPI=T ; set default accordingly and stop
30        if not consistent.
31      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
32        argument is zero (in case called within single-thread section).
33    o pkg/fizhi:
34        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
35        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
36    o pkg/exch2:
37      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
38        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
39      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
40        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
41        with bad ones coming from a not-yet-updated halo.
42        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
43    o pkg/frazil:
44        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
45        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
46    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
47    o verification/lab_sea
48      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
49      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
50      * nTimeSteps 3 -> 4
51      * changed reference output accordingly
52    o pkg/ctrl:
53      * fix ctrl_get_gen for xx_sst, xx_sss
54    o pkg/fizhi:
55      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
56        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
57      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
58        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
59        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
60    o pkg/gmredi:
61      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
62    o pkg/fizhi:
63      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
64        (old)aces open64 tuv test.
65    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
66    o pkg/mom_vecinv:
67      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
68        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
69        with non-lin free-surf).
70    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
71      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
72      some compilers (gfortran 4.6.0 on MacOS)
73    o momentum:
74      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
75        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
76        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
77    
78    checkpoint63k (2012/03/17)
79    o model/src:
80       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
81         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
82       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
83         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
84    o model/src: solve_*diagonal.F
85       - replace division with multiplication by inverse (similar to original version)
86         update output of AD exp. global_ocean.90x40x15.
87       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
88         to enable the use of the vectorized & differentiable solve_tridiagonal.F
89       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
90         vertical advection (to get solve_tridiagonal tested in AD mode).
91    o pkg/seaice: ECCO-CLIVAR merge:
92      1. seaice AREA relaxation
93         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
94         * runtime flag: SEAICE_tauAreaObsRelax
95      2. modified global mean cost imbalance code: CPP option
96          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
97    o another iteration on solve_*diagonal.F
98       Make choices independent of AUTODIFF
99       Default will be the adjoinable vectorized version.
100       Alternative choices are:
101       * non-adjoinable original version with low memory footprint:
102         #define SOLVE_DIAGONAL_LOWMEMORY
103       * still adjoinable but does not vectorize (k as inner-most loop):
104         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
105    o testreport
106     - add option to use a home made wrapper around "make"
107     - remove MITGCM_IEEE env. variable (no longer active)
108    o pkg/shelfice
109     - improve computation of friction velocity for velocity dependent
110       exchange coefficients: include velocities into SHELFICEBoundaryLayer
111       block to average velocities vertically
112     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
113    o Modify diagonal solvers, now three versions (upon request):
114      #ifndef SOLVE_DIAGONAL_AUTODIFF
115        1. default version (dating back a while ago)
116      #else /* def SOLVE_DIAGONAL_AUTODIFF */
117      # ifdef SOLVE_DIAGONAL_KINNER
118        2. adjoinable version with k-innermost loop (G. Forget)
119      # else
120        3. adjoinable vectorized version of 2.
121      # endif
122      #endif /* SOLVE_DIAGONAL_AUTODIFF */
123      All flags are currently set within routines, but could/should be moved to CPP-options.
124      Array bounds for 1. are as before, for 2.,3. cover the entire domain
125      (could be changed for 1. too).
126    o verification/lab_sea (fwd):
127      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
128        use 7 categories (except hb87), new solve4temp params (except salt_plume),
129        constant salinity (=4) or variable salinity (salt_plume) done through
130        SItracer.
131    o pkg/seaice:
132      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
133      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
134         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
135        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
136        SEAICE_freeze got retired) but already better than previously with
137        SEAICE_freeze=123456.7 deg.C;
138      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
139        (safer multi-threaded setting); always set SEAICEuseEVP;
140      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
141        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
142        stop if multiple specifications for the same coeff; make sure default
143        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
144    o pkg/obcs:
145      - allow to switch to upwind 1rst order advection scheme for the advective
146        flux computation at the open-boundary; disabled for adjoint built.
147    o pkg/ptracers:
148      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
149      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
150      - add parameter to decide when to start a tracer; use internal flag to
151        know which tracer to step-forward; switch this internal flag at the top
152        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
153        for adjoint built.
154    o pkg/seaice:
155      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
156      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
157      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
158    o pkg/ecco:
159      - fix writing of output file DiagnosCost_ClimSalt/Theta
160        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
161    o pkg/seaice:
162      - add missing initialisation of COR_ICE array in dynsolver.F
163      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
164        compiled either way, and is tested in all exps (multidim was only tested
165        in lab_sea ad before).
166      - cosmetic change to prepare for future addition of ITD. no change to results.
167        no defaults change.
168      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
169      - by lack of adequate verification experiments, I further used custom versions
170        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
171        should be correct.
172      - avoid recomputations in ad.
173    o array initialisation in adjoint mode:
174      1) pkg/mom_common/mom_calc_ke.F:
175        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
176        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
177        part this initialisation is gone, resulting in Floating Point Exception
178        (caught by open64 compiler with debug option).
179      2) model/src/convective_weights.F
180        set output convectCount over the full array range (instead of doing
181        an update): this fix a similar issue when called within recomputation (adjoint)
182        which could by-pass the initialisation (normally done in the caller S/R).
183    o pkg/seaice:
184      - final version of turbulent flux params, as agreed at MIT ice meet:
185           SEAICE_mcPheePiston (default is ~ 0.000875)
186           SEAICE_mcPheeTaper (default is 0.)
187           SEAICE_frazilFrac (defualt is 1.)
188           SEAICE_mcPheeStepFunc (default is false)
189      - changes results at trunction error level
190      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
191    o added pkg/frazil:
192      - see frazil_description.tex for details
193      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
194    o pkg/shelfice/shelfice_thermodynamics.F
195      - fix exponents for velocity dependent exchange coefficients: change
196        from 2/3(=0) to 0.66666666666666667
197      - move computation of velocity dependent exchange coefficients into
198        separate loop, so that it applies to both thermodynamics
199      - move some divisions by constants out of loops
200    
201    checkpoint63j (2012/02/16)
202    o pkg/seaice:
203      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
204      - SItracer:  added run time params, and allow coupling to ocn salinity.
205    o pkg/seaice: remove (almost) all divisions by constants within loops
206      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
207      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
208      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
209      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
210    o pkg/seaice :
211      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
212        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
213      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
214      - add permanent SItflux diag that corresponds to TFLUX but includes
215        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
216      - allow activation/testing of a fix for suspected missing term in
217        ocn-ice heat budget (to be confirmed). To test this, you want to
218        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
219        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
220      - no change in results, fwd or ad.
221    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
222      - switch to variable freezing point.
223           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
224      - bug fix : the sublimation term that was missing is now activated.
225           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
226      - bug fix : flooding sign term for SIsal0.NE.0.
227           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
228    o pkg/seaice:
229      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
230        is now the default, and the old default constant freezing point is recovered
231        with SEAICE_tempFrz0    = -1.96,
232             SEAICE_dTempFrz_dS = 0.,
233      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
234      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
235      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
236        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
237      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
238        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
239      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
240        seaice_growth r149 for legacy branch (no results change).
241      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
242        from I. Fenty).
243      - results did not change except for global_ocean.cs32x15, mostly due to the
244        switch to variable freezing point (see above item for detail).
245    o pkg/thsice:
246      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
247        seawater freezing in thsice_calc_thickn (not used).
248    o pkg/seaice: turbulent flux term specification via run time params.
249      - replace CPP switches with run time switches to facilitate testing
250      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
251                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
252      - added runtime parameter : SEAICEturbFluxFormula
253      - move Mcphee constants to SEAICE_PARAMS.h
254      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
255                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
256                 remove seaice_summary call (moved to seaice_init_fixed)
257      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
258        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
259      - seaice_summary.F : add missing report of read turbulent flux term set up
260                           and SITRACER.
261      - seaice_check.F : check range; inform and stop if retired CPPs are used
262                         (incl. SEAICE_AGE).
263      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
264             CPP switch, same computation as before for the different options.
265      - change results at the truncation level.
266    o pkg/seaice:
267      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
268        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
269        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
270      - update verification/*/input*/data.seaice:
271        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
272        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
273        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
274        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
275    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
276      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
277        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
278        difference in results only due to machine truncation.
279      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
280        MaykutPolySatVap; keep MIN_LWDOWN.
281      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
282      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
283        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
284    o pkg/salt_plume:
285      - isolate saltPlumeFlux array exch into a specific S/R called from
286        do_oceanic_phys.F
287      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
288    o verification:
289      - move untested set-up to MITgcm_contrib/verification_other.
290    o pkg/seaice:
291      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
292    o pkg/seaice:
293      - seaice_solve4temp.F (keeping results unchanged):
294        * add 2 future run-time params to select which saturation vapor pressure
295          formula is used and how post-iteration fluxes are set.
296          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
297        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
298          the linearized expression to stay consistent with tsurf finding.
299      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
300        can be < 0.
301    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
302      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
303        conductive heat flux F_c , and add it explicitly when updating tsurf as
304        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
305        so that now F_ia has a consistent meaning through the entire routine.
306        This causes differences at truncation level: update output of fwd exp.
307        global_ocean.cs32x15.seaice.
308    o pkg/seaice:
309      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
310        of arrays, sign/direction of fluxes; no effect on results.
311      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
312        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
313        note: this should have been done before changing celsius2K default.
314      - to keep results unchanged, add back old value of celsius2K in verification
315        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
316      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
317        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
318        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
319        freezing temp is consistent with value in seaice_growth.F ; this causes
320        differences at machine truncation level: update lab_sea AD output (3/4).
321    o pkg/seaice:
322      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
323        and climsst/sss even when using seaice (to prevent calculation that might
324        use SST on land); does not affect any verification exp.
325      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
326        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
327    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
328      over land (non-legacy code)
329    o vectorize salt_plume package:
330      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
331      - this code computes plumebk everywhere (also over land), thus requires
332        code to avoid divisions by zero and catch the case of kLev=Nr.
333      - efficiency of salt_plume_frac is still sub-optimal
334    o tools (genmake2):
335      - fix makefile NAME specification (option: -makefile NAME) by adding
336        "-f $MAKEFILE" in few places where it was missing including makedepend
337        command (contribution from Paul).
338    
339    checkpoint63i (2012/01/24)
340    o model/src:
341      - add factorized versions of some EOS code to find_rho.F,
342        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
343  o model/src:  o model/src:
344    - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;    - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
345    - change default celsius2K from 273.16 to 273.15    - change default celsius2K from 273.16 to 273.15
346    - to keep results unchanged, add back old value of celsius2K in verification    - to keep results unchanged, add back old value of celsius2K in verification
347      exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd) &      exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
348       global_ocean.cs32x15(seaice).       global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
349  o model/src: add a little initialisation trick to find_rho.F and find_alpha.F  o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
350    to make TAF generate vectorizable code    to make TAF generate vectorizable code
351  o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.  o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
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