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revision 1.1572 by heimbach, Fri Jan 6 14:06:18 2012 UTC revision 1.1628 by dimitri, Mon Mar 19 21:48:27 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/icefront: fix bug and reorder loop in icefront_init_varia.F
8    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
9      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
10      some compilers (gfortran 4.6.0 on MacOS)
11    o momentum:
12      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
13        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
14        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
15    
16    checkpoint63k (2012/03/17)
17    o model/src:
18       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
19         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
20       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
21         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
22    o model/src: solve_*diagonal.F
23       - replace division with multiplication by inverse (similar to original version)
24         update output of AD exp. global_ocean.90x40x15.
25       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
26         to enable the use of the vectorized & differentiable solve_tridiagonal.F
27       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
28         vertical advection (to get solve_tridiagonal tested in AD mode).
29    o pkg/seaice: ECCO-CLIVAR merge:
30      1. seaice AREA relaxation
31         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
32         * runtime flag: SEAICE_tauAreaObsRelax
33      2. modified global mean cost imbalance code: CPP option
34          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
35    o another iteration on solve_*diagonal.F
36       Make choices independent of AUTODIFF
37       Default will be the adjoinable vectorized version.
38       Alternative choices are:
39       * non-adjoinable original version with low memory footprint:
40         #define SOLVE_DIAGONAL_LOWMEMORY
41       * still adjoinable but does not vectorize (k as inner-most loop):
42         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
43    o testreport
44     - add option to use a home made wrapper around "make"
45     - remove MITGCM_IEEE env. variable (no longer active)
46    o pkg/shelfice
47     - improve computation of friction velocity for velocity dependent
48       exchange coefficients: include velocities into SHELFICEBoundaryLayer
49       block to average velocities vertically
50     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
51    o Modify diagonal solvers, now three versions (upon request):
52      #ifndef SOLVE_DIAGONAL_AUTODIFF
53        1. default version (dating back a while ago)
54      #else /* def SOLVE_DIAGONAL_AUTODIFF */
55      # ifdef SOLVE_DIAGONAL_KINNER
56        2. adjoinable version with k-innermost loop (G. Forget)
57      # else
58        3. adjoinable vectorized version of 2.
59      # endif
60      #endif /* SOLVE_DIAGONAL_AUTODIFF */
61      All flags are currently set within routines, but could/should be moved to CPP-options.
62      Array bounds for 1. are as before, for 2.,3. cover the entire domain
63      (could be changed for 1. too).
64    o verification/lab_sea (fwd):
65      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
66        use 7 categories (except hb87), new solve4temp params (except salt_plume),
67        constant salinity (=4) or variable salinity (salt_plume) done through
68        SItracer.
69    o pkg/seaice:
70      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
71      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
72         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
73        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
74        SEAICE_freeze got retired) but already better than previously with
75        SEAICE_freeze=123456.7 deg.C;
76      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
77        (safer multi-threaded setting); always set SEAICEuseEVP;
78      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
79        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
80        stop if multiple specifications for the same coeff; make sure default
81        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
82    o pkg/obcs:
83      - allow to switch to upwind 1rst order advection scheme for the advective
84        flux computation at the open-boundary; disabled for adjoint built.
85    o pkg/ptracers:
86      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
87      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
88      - add parameter to decide when to start a tracer; use internal flag to
89        know which tracer to step-forward; switch this internal flag at the top
90        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
91        for adjoint built.
92    o pkg/seaice:
93      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
94      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
95      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
96    o pkg/ecco:
97      - fix writing of output file DiagnosCost_ClimSalt/Theta
98        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
99    o pkg/seaice:
100      - add missing initialisation of COR_ICE array in dynsolver.F
101      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
102        compiled either way, and is tested in all exps (multidim was only tested
103        in lab_sea ad before).
104      - cosmetic change to prepare for future addition of ITD. no change to results.
105        no defaults change.
106      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
107      - by lack of adequate verification experiments, I further used custom versions
108        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
109        should be correct.
110      - avoid recomputations in ad.
111    o array initialisation in adjoint mode:
112      1) pkg/mom_common/mom_calc_ke.F:
113        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
114        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
115        part this initialisation is gone, resulting in Floating Point Exception
116        (caught by open64 compiler with debug option).
117      2) model/src/convective_weights.F
118        set output convectCount over the full array range (instead of doing
119        an update): this fix a similar issue when called within recomputation (adjoint)
120        which could by-pass the initialisation (normally done in the caller S/R).
121    o pkg/seaice:
122      - final version of turbulent flux params, as agreed at MIT ice meet:
123           SEAICE_mcPheePiston (default is ~ 0.000875)
124           SEAICE_mcPheeTaper (default is 0.)
125           SEAICE_frazilFrac (defualt is 1.)
126           SEAICE_mcPheeStepFunc (default is false)
127      - changes results at trunction error level
128      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
129    o added pkg/frazil:
130      - see frazil_description.tex for details
131      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
132    o pkg/shelfice/shelfice_thermodynamics.F
133      - fix exponents for velocity dependent exchange coefficients: change
134        from 2/3(=0) to 0.66666666666666667
135      - move computation of velocity dependent exchange coefficients into
136        separate loop, so that it applies to both thermodynamics
137      - move some divisions by constants out of loops
138    
139    checkpoint63j (2012/02/16)
140    o pkg/seaice:
141      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
142      - SItracer:  added run time params, and allow coupling to ocn salinity.
143    o pkg/seaice: remove (almost) all divisions by constants within loops
144      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
145      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
146      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
147      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
148    o pkg/seaice :
149      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
150        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
151      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
152      - add permanent SItflux diag that corresponds to TFLUX but includes
153        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
154      - allow activation/testing of a fix for suspected missing term in
155        ocn-ice heat budget (to be confirmed). To test this, you want to
156        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
157        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
158      - no change in results, fwd or ad.
159    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
160      - switch to variable freezing point.
161           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
162      - bug fix : the sublimation term that was missing is now activated.
163           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
164      - bug fix : flooding sign term for SIsal0.NE.0.
165           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
166    o pkg/seaice:
167      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
168        is now the default, and the old default constant freezing point is recovered
169        with SEAICE_tempFrz0    = -1.96,
170             SEAICE_dTempFrz_dS = 0.,
171      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
172      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
173      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
174        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
175      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
176        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
177      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
178        seaice_growth r149 for legacy branch (no results change).
179      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
180        from I. Fenty).
181      - results did not change except for global_ocean.cs32x15, mostly due to the
182        switch to variable freezing point (see above item for detail).
183    o pkg/thsice:
184      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
185        seawater freezing in thsice_calc_thickn (not used).
186    o pkg/seaice: turbulent flux term specification via run time params.
187      - replace CPP switches with run time switches to facilitate testing
188      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
189                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
190      - added runtime parameter : SEAICEturbFluxFormula
191      - move Mcphee constants to SEAICE_PARAMS.h
192      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
193                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
194                 remove seaice_summary call (moved to seaice_init_fixed)
195      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
196        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
197      - seaice_summary.F : add missing report of read turbulent flux term set up
198                           and SITRACER.
199      - seaice_check.F : check range; inform and stop if retired CPPs are used
200                         (incl. SEAICE_AGE).
201      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
202             CPP switch, same computation as before for the different options.
203      - change results at the truncation level.
204    o pkg/seaice:
205      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
206        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
207        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
208      - update verification/*/input*/data.seaice:
209        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
210        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
211        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
212        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
213    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
214      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
215        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
216        difference in results only due to machine truncation.
217      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
218        MaykutPolySatVap; keep MIN_LWDOWN.
219      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
220      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
221        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
222    o pkg/salt_plume:
223      - isolate saltPlumeFlux array exch into a specific S/R called from
224        do_oceanic_phys.F
225      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
226    o verification:
227      - move untested set-up to MITgcm_contrib/verification_other.
228    o pkg/seaice:
229      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
230    o pkg/seaice:
231      - seaice_solve4temp.F (keeping results unchanged):
232        * add 2 future run-time params to select which saturation vapor pressure
233          formula is used and how post-iteration fluxes are set.
234          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
235        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
236          the linearized expression to stay consistent with tsurf finding.
237      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
238        can be < 0.
239    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
240      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
241        conductive heat flux F_c , and add it explicitly when updating tsurf as
242        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
243        so that now F_ia has a consistent meaning through the entire routine.
244        This causes differences at truncation level: update output of fwd exp.
245        global_ocean.cs32x15.seaice.
246    o pkg/seaice:
247      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
248        of arrays, sign/direction of fluxes; no effect on results.
249      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
250        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
251        note: this should have been done before changing celsius2K default.
252      - to keep results unchanged, add back old value of celsius2K in verification
253        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
254      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
255        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
256        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
257        freezing temp is consistent with value in seaice_growth.F ; this causes
258        differences at machine truncation level: update lab_sea AD output (3/4).
259    o pkg/seaice:
260      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
261        and climsst/sss even when using seaice (to prevent calculation that might
262        use SST on land); does not affect any verification exp.
263      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
264        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
265    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
266      over land (non-legacy code)
267    o vectorize salt_plume package:
268      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
269      - this code computes plumebk everywhere (also over land), thus requires
270        code to avoid divisions by zero and catch the case of kLev=Nr.
271      - efficiency of salt_plume_frac is still sub-optimal
272    o tools (genmake2):
273      - fix makefile NAME specification (option: -makefile NAME) by adding
274        "-f $MAKEFILE" in few places where it was missing including makedepend
275        command (contribution from Paul).
276    
277    checkpoint63i (2012/01/24)
278    o model/src:
279      - add factorized versions of some EOS code to find_rho.F,
280        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
281    o model/src:
282      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
283      - change default celsius2K from 273.16 to 273.15
284      - to keep results unchanged, add back old value of celsius2K in verification
285        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
286         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
287    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
288      to make TAF generate vectorizable code
289    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
290       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
291       have flags that do this more efficiently.
292    o pkg/diagnostics/diagstats_calc.F
293      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
294    o pkg/obcs (with exch2):
295      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
296        and remove code (in obcs_readparms.F) which was based on EXCH of indices
297        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
298    o pkg/exf and seaice exp:
299      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
300        so that switching off area & heff advection flags does not affect results.
301      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
302      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
303        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
304        results of verification experiments: 1D_ocean_ice_column(fwd),
305        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
306        and offline_exf_seaice (all 4).
307    o pkg/seaice:
308      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
309        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
310      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
311        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
312        not multi-dim advection;
313      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
314        SHORTWAVE_HEATING #undef.
315  o optim: make Makefile more robust (?)  o optim: make Makefile more robust (?)
316  o pkg/obcs:  o pkg/obcs:
317    * fix treatment of obcs_read_pickup for TAF    * fix treatment of obcs_read_pickup for TAF
318  o pkg/shelfice:  o pkg/shelfice:
319    * add missing initialisation of num_shifwflx    * add missing initialisation of num_shifwflx
320    * new adjoint verification exp. for isomip    * new adjoint verification exp. for isomip
321    * change Prandtl and Schmidt numbers from generic formulations    * change Prandtl and Schmidt numbers from generic formulations
322      (in terms of model diffus. and visc.) to separate runtime      (in terms of model diffus. and visc.) to separate runtime
323      parameters, with Holland and Jenkins (1999) default values.      parameters, with Holland and Jenkins (1999) default values.
324  o pkg/exf (interpolation):  o pkg/exf (interpolation):
325    - extended input field (2 rows) near the N & S poles:    - extended input field (2 rows) near the N & S poles:

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