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revision 1.1598 by mlosch, Tue Feb 14 16:42:44 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/seaice: remove (almost) all divisions by constants within loops  o pkg/bbl:
8    in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d    - 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    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    those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
209  o pkg/seaice :    output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
210    - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula.EQ.  o pkg/seaice :
211    1 or 2, using newly added run time parameter SEAICE_availHeatTaper.    - 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.    - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
214    - add permanent SItflux diag that corresponds to TFLUX but includes    - add permanent SItflux diag that corresponds to TFLUX but includes
215    ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.      ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
216    - allow activation/testing of a fix for suspected missing term in    - 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      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      undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
219    SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.      SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
220    - no change in results, fwd or ad.    - no change in results, fwd or ad.
221  o global_ocean.cs32x15/results: three changes following from the pkg/seaice commit below.  o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
222    - switch to variable freezing point.    - switch to variable freezing point.
223         Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.         Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
224    - bug fix : the sublimation term that was missing is now activated.    - bug fix : the sublimation term that was missing is now activated.
225         Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.         Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
226    - bug fix : flooding sign term for SIsal0.NE.0.    - bug fix : flooding sign term for SIsal0.NE.0.
227         Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.         Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
228  o pkg/seaice:  o pkg/seaice:
229    - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT    - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
230   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
231   SEAICE_tempFrz0    = -1.96,      with SEAICE_tempFrz0    = -1.96,
232   SEAICE_dTempFrz_dS = 0.,           SEAICE_dTempFrz_dS = 0.,
233    - 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)
234    - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.    - 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    - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
236   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.
237    - 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)
238   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).
239    - 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
240   seaice_growth r149 for legacy branch (no results change).      seaice_growth r149 for legacy branch (no results change).
241    - 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
242    - results did not change except for global_ocean.cs32x15, mostly due to the switch      from I. Fenty).
243    to variable freezing point (see above item for detail).    - 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:  o pkg/thsice:
246    - fix and simplify interface to salt_plume pkg ; diagnose directly amount of    - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
247      seawater freezing in thsice_calc_thickn (not used).      seawater freezing in thsice_calc_thickn (not used).
248  o pkg/seaice: turbulent flux term specification via run time params.  o pkg/seaice: turbulent flux term specification via run time params.
249    - replace CPP switches with run time switches to facilitate testing    - replace CPP switches with run time switches to facilitate testing
250    - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX, GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR    - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
251                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
252    - added runtime parameter : SEAICEturbFluxFormula    - added runtime parameter : SEAICEturbFluxFormula
253    - move Mcphee constants to SEAICE_PARAMS.h    - move Mcphee constants to SEAICE_PARAMS.h
254    - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;    - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
255      SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply); remove               SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
256      seaice_summary call (moved to seaice_init_fixed)               remove seaice_summary call (moved to seaice_init_fixed)
257    - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on    - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
258      SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)      SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
259    - 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
260    - seaice_check.F : check range; inform and stop if retired CPPs are used (incl. SEAICE_AGE).                         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    - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
264          CPP switch, same computation as before for the different options.           CPP switch, same computation as before for the different options.
265    - change results at the truncation level.    - change results at the truncation level.
266  o pkg/seaice:  o pkg/seaice:
267    - 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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