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revision 1.1595 by gforget, Mon Feb 13 16:38:08 2012 UTC revision 1.1654 by jmc, Fri Apr 20 19:47:09 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 global_ocean.cs32x15/results: three changes following from the pkg/seaice commit below.  o ad test experiments:
8    - switch to variable freezing point.   - update and rename to "ad_optfile.local" local AD-optfile specific to a
9       particular adjoint verification experiment (in verification/*/code_ad/)
10    o pkg/seaice & pkg/exf:
11     - Part two of ECCO-CLIVAR code merges.
12       Completes merge of seaice area relax. code.
13       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
14       to be set in EXF_OPTIONS.h since this pkg controls its I/O
15       (and avoids second CPP option in SEAICE_OPTIONS.h)
16     - change default value of costIceStart & costIceEnd to a valid date.
17    o pkg/ptracers:
18     - move ptracers summary and setup check into separated S/R ; add a check for
19       valid PTRACERS_Iter0 value (error+stop or just warning).
20    o pkg/cal (+ pkg/ecco):
21     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
22       as input; and for AD, unless both are not differentiable (e.g., k index)).
23    o model/src:
24     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
25       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
26       temporary set to usingZCoords value (to be changed to F when using shelfice).
27     - hydrostatic pressure: implement partial cell near the surface also for
28       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
29       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
30    o pkg/ctrl/ctrl_init.F:
31     - add a formal parameter to s/r ctrl_init_rec to print
32       xx_$(ctrl_valiable)_file for easier debugging
33     - move call of cal_* routines into the if-block where they are really
34       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
35       to specify a startdate
36    o pkg/seaice:
37     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
38       global_ocean.cs32x15/code versions).
39     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
40       verification experiment global_ocean.cs32x15.seaice and update results.
41    o pkg/exf:
42     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
43       (according to useExfYearlyFields).
44    o pkg/cal:
45     - move calendar setting & summary (previously in cal_readparams.F) into new
46       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
47       length of the simulation is set (after SET_PARMS call); This is an attempt
48       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
49     - For safety: keep a record of pkg/cal parameter settings status
50               to allow to STOP if one pkg/cal S/R is called too early.
51     - add a stop in all basic pkg/cal subroutines if called before setting is done.
52     - modify cal_getdate.F: stop when nothing was returned;
53       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
54       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
55    
56    checkpoint63l (2012/04/04)
57    o pkg/bbl:
58      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
59        update global_with_exf output.yearly.txt file.
60    o pkg/cal:
61      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
62      - remove 2 unsused and very short (1 line only) functions ;
63      - remove unsused subroutines from AD-Diff list.
64    o model/src:
65      - start to implement clean wait to stop in initialization S/R (config_check.F,
66         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
67    o folowing PRINT_MESSAGE changes:
68      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
69    o pkg/bbl:
70      - modification so it can work with z*
71      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
72      - global_with_exf/input.yearly verification; changes output.yearly.txt
73    o eesupp/src:
74      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
75        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
76      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
77        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
78      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
79      - when using MPI, always set usingMPI=T ; set default accordingly and stop
80        if not consistent.
81      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
82        argument is zero (in case called within single-thread section).
83    o pkg/fizhi:
84        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
85        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
86    o pkg/exch2:
87      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
88        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
89      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
90        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
91        with bad ones coming from a not-yet-updated halo.
92        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
93    o pkg/frazil:
94        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
95        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
96    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
97    o verification/lab_sea
98      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
99      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
100      * nTimeSteps 3 -> 4
101      * changed reference output accordingly
102    o pkg/ctrl:
103      * fix ctrl_get_gen for xx_sst, xx_sss
104    o pkg/fizhi:
105      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
106        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
107      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
108        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
109        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
110    o pkg/gmredi:
111      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
112    o pkg/fizhi:
113      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
114        (old)aces open64 tuv test.
115    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
116    o pkg/mom_vecinv:
117      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
118        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
119        with non-lin free-surf).
120    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
121      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
122      some compilers (gfortran 4.6.0 on MacOS)
123    o momentum:
124      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
125        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
126        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
127    
128    checkpoint63k (2012/03/17)
129    o model/src:
130       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
131         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
132       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
133         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
134    o model/src: solve_*diagonal.F
135       - replace division with multiplication by inverse (similar to original version)
136         update output of AD exp. global_ocean.90x40x15.
137       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
138         to enable the use of the vectorized & differentiable solve_tridiagonal.F
139       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
140         vertical advection (to get solve_tridiagonal tested in AD mode).
141    o pkg/seaice: ECCO-CLIVAR merge:
142      1. seaice AREA relaxation
143         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
144         * runtime flag: SEAICE_tauAreaObsRelax
145      2. modified global mean cost imbalance code: CPP option
146          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
147    o another iteration on solve_*diagonal.F
148       Make choices independent of AUTODIFF
149       Default will be the adjoinable vectorized version.
150       Alternative choices are:
151       * non-adjoinable original version with low memory footprint:
152         #define SOLVE_DIAGONAL_LOWMEMORY
153       * still adjoinable but does not vectorize (k as inner-most loop):
154         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
155    o testreport
156     - add option to use a home made wrapper around "make"
157     - remove MITGCM_IEEE env. variable (no longer active)
158    o pkg/shelfice
159     - improve computation of friction velocity for velocity dependent
160       exchange coefficients: include velocities into SHELFICEBoundaryLayer
161       block to average velocities vertically
162     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
163    o Modify diagonal solvers, now three versions (upon request):
164      #ifndef SOLVE_DIAGONAL_AUTODIFF
165        1. default version (dating back a while ago)
166      #else /* def SOLVE_DIAGONAL_AUTODIFF */
167      # ifdef SOLVE_DIAGONAL_KINNER
168        2. adjoinable version with k-innermost loop (G. Forget)
169      # else
170        3. adjoinable vectorized version of 2.
171      # endif
172      #endif /* SOLVE_DIAGONAL_AUTODIFF */
173      All flags are currently set within routines, but could/should be moved to CPP-options.
174      Array bounds for 1. are as before, for 2.,3. cover the entire domain
175      (could be changed for 1. too).
176    o verification/lab_sea (fwd):
177      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
178        use 7 categories (except hb87), new solve4temp params (except salt_plume),
179        constant salinity (=4) or variable salinity (salt_plume) done through
180        SItracer.
181    o pkg/seaice:
182      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
183      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
184         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
185        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
186        SEAICE_freeze got retired) but already better than previously with
187        SEAICE_freeze=123456.7 deg.C;
188      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
189        (safer multi-threaded setting); always set SEAICEuseEVP;
190      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
191        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
192        stop if multiple specifications for the same coeff; make sure default
193        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
194    o pkg/obcs:
195      - allow to switch to upwind 1rst order advection scheme for the advective
196        flux computation at the open-boundary; disabled for adjoint built.
197    o pkg/ptracers:
198      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
199      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
200      - add parameter to decide when to start a tracer; use internal flag to
201        know which tracer to step-forward; switch this internal flag at the top
202        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
203        for adjoint built.
204    o pkg/seaice:
205      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
206      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
207      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
208    o pkg/ecco:
209      - fix writing of output file DiagnosCost_ClimSalt/Theta
210        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
211    o pkg/seaice:
212      - add missing initialisation of COR_ICE array in dynsolver.F
213      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
214        compiled either way, and is tested in all exps (multidim was only tested
215        in lab_sea ad before).
216      - cosmetic change to prepare for future addition of ITD. no change to results.
217        no defaults change.
218      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
219      - by lack of adequate verification experiments, I further used custom versions
220        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
221        should be correct.
222      - avoid recomputations in ad.
223    o array initialisation in adjoint mode:
224      1) pkg/mom_common/mom_calc_ke.F:
225        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
226        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
227        part this initialisation is gone, resulting in Floating Point Exception
228        (caught by open64 compiler with debug option).
229      2) model/src/convective_weights.F
230        set output convectCount over the full array range (instead of doing
231        an update): this fix a similar issue when called within recomputation (adjoint)
232        which could by-pass the initialisation (normally done in the caller S/R).
233    o pkg/seaice:
234      - final version of turbulent flux params, as agreed at MIT ice meet:
235           SEAICE_mcPheePiston (default is ~ 0.000875)
236           SEAICE_mcPheeTaper (default is 0.)
237           SEAICE_frazilFrac (defualt is 1.)
238           SEAICE_mcPheeStepFunc (default is false)
239      - changes results at trunction error level
240      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
241    o added pkg/frazil:
242      - see frazil_description.tex for details
243      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
244    o pkg/shelfice/shelfice_thermodynamics.F
245      - fix exponents for velocity dependent exchange coefficients: change
246        from 2/3(=0) to 0.66666666666666667
247      - move computation of velocity dependent exchange coefficients into
248        separate loop, so that it applies to both thermodynamics
249      - move some divisions by constants out of loops
250    
251    checkpoint63j (2012/02/16)
252    o pkg/seaice:
253      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
254      - SItracer:  added run time params, and allow coupling to ocn salinity.
255    o pkg/seaice: remove (almost) all divisions by constants within loops
256      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
257      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
258      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
259      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
260    o pkg/seaice :
261      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
262        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
263      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
264      - add permanent SItflux diag that corresponds to TFLUX but includes
265        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
266      - allow activation/testing of a fix for suspected missing term in
267        ocn-ice heat budget (to be confirmed). To test this, you want to
268        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
269        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
270      - no change in results, fwd or ad.
271    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
272      - switch to variable freezing point.
273         Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.         Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
274    - bug fix : the sublimation term that was missing is now activated.    - bug fix : the sublimation term that was missing is now activated.
275         Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.         Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
276    - bug fix : flooding sign term for SIsal0.NE.0.    - bug fix : flooding sign term for SIsal0.NE.0.
277         Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.         Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
278  o pkg/seaice:  o pkg/seaice:
279    - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT    - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
280   is now the default, and the old default constant freezing point is recovered with      is now the default, and the old default constant freezing point is recovered
281   SEAICE_tempFrz0    = -1.96,      with SEAICE_tempFrz0    = -1.96,
282   SEAICE_dTempFrz_dS = 0.,           SEAICE_dTempFrz_dS = 0.,
283    - retire SEAICE_freeze that was the old way of specifycing the constant freezing point.    - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
284    - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.    - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
285    - bug fix (thanks to M. Losch) : the sublimation term that was missing is now    - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
286   activated. To reproduce old results that had this bug define SEAICE_DISABLE_SUBLIM.      activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
287    - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)    - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
288   was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).      was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
289    - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in    - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
290   seaice_growth r149 for legacy branch (no results change).      seaice_growth r149 for legacy branch (no results change).
291    - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code from I. Fenty).    - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
292    - results did not change except for global_ocean.cs32x15, mostly due to the switch      from I. Fenty).
293    to variable freezing point (see above item for detail).    - results did not change except for global_ocean.cs32x15, mostly due to the
294        switch to variable freezing point (see above item for detail).
295  o pkg/thsice:  o pkg/thsice:
296    - fix and simplify interface to salt_plume pkg ; diagnose directly amount of    - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
297      seawater freezing in thsice_calc_thickn (not used).      seawater freezing in thsice_calc_thickn (not used).
298  o pkg/seaice: turbulent flux term specification via run time params.  o pkg/seaice: turbulent flux term specification via run time params.
299    - replace CPP switches with run time switches to facilitate testing    - replace CPP switches with run time switches to facilitate testing
300    - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX, GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR    - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
301                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
302    - added runtime parameter : SEAICEturbFluxFormula    - added runtime parameter : SEAICEturbFluxFormula
303    - move Mcphee constants to SEAICE_PARAMS.h    - move Mcphee constants to SEAICE_PARAMS.h
304    - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;    - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
305      SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply); remove               SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
306      seaice_summary call (moved to seaice_init_fixed)               remove seaice_summary call (moved to seaice_init_fixed)
307    - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on    - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
308      SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)      SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
309    - seaice_summary.F : add missing report of read turbulent flux term set up (and SITRACER).    - seaice_summary.F : add missing report of read turbulent flux term set up
310    - seaice_check.F : check range; inform and stop if retired CPPs are used (incl. SEAICE_AGE).                         and SITRACER.
311      - seaice_check.F : check range; inform and stop if retired CPPs are used
312                         (incl. SEAICE_AGE).
313    - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without    - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
314          CPP switch, same computation as before for the different options.           CPP switch, same computation as before for the different options.
315    - change results at the truncation level.    - change results at the truncation level.
316  o pkg/seaice:  o pkg/seaice:
317    - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:    - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
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