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revision 1.1980 by mlosch, Wed Apr 23 12:42:19 2014 UTC revision 1.2040 by jmc, Wed Aug 6 23:19:25 2014 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o model/src:
8      - store in common bloc array "rhoInSitu" the virtual potential temperature
9        anomaly that is used to compute geopotential: this make the atmos code
10        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
11    o pkg/seaice/seaice_lsr.F
12      - rename integer variable ilcall to ipass (that's what it is called
13        in the residual diagnostics
14      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
15        default) for improved non-linear convergence of the first few steps
16      - adjust a few comments and add new ones to explain some of the store
17        directives
18    o pkg/generic_advdiff (& ptracers):
19      - re-work the code to check for valid advection scheme and for minimum
20        size of overlap (now stored in local common bloc in gad_advscheme.F)
21    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
22      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
23      - add an auxilliary variable "bet" and fix store directives and keys in
24        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
25        less exact gradients in my tests); but there are still
26        recomputation warning (although gradients are sort of OK), when
27        SEAICE_LSR_VECTORIZE is not defined, so this flag and
28        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
29      - update verification experiments lab_sea.
30      - change some comments in S/R seaice_calc_viscosities
31    o model/src:
32      - if staggerTimeStep=T, always apply exchange to velocity field in
33        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
34        (independent of using multi-dim advection or not); no effect on FWD run
35        but affects AD results (at machine truncation level): update output of
36        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
37        and isomip (oad: 12.d).
38    o pkg/generic_advdiff:
39      - stop if doAB_onGtGs is set to FALSE but ignored
40      - refine warning related to stability of tracer time-stepping
41        regarding internal wave dynamics.
42      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
43        on staggerTimeStep & implicitIntGravWave (will now get a warning
44        if potentially unstable).
45    o pkg/kl10:
46      - add new pkg "kl10" for mixing due to internal wave breaking, from
47        http://www.sciencedirect.com/science/article/pii/S1463500310000144
48        (contribution from Jody Klymak), tested in verification experiment
49        verification/internal_wave/input.kl10/
50    o isomip experiment:
51      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
52        (input.htd) and update the output.
53    o cd_code experiments:
54      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
55        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
56        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
57        update the corresponding output.
58    o pkg/seaice:
59      - reduce the number of include files and store directives in
60        S/R seaice_lsr_tridiagu/v
61      - change the order of loops in one case in S/R seaice_lsr_tridiagv
62        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
63        get rid off one store directive (a TAF bug?)
64      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
65        S/R seaice_lsr_tridiagv to change the loop range for consistency
66      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
67      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
68        S/R seaice_lsr_tridiagu/v (requires update of
69        offline_exf_seaice/input.dyn_jfnk)
70    
71    checkpoint65a (2014/07/27)
72    o model/src:
73      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
74        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
75        (topo in p-coords, ice-shelf in z-coords); update output of experiments
76        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
77    o model/src:
78      - collect momentum forcing tendency into local 2-D array (passed as argument
79        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
80        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
81        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
82      - collect T & S forcing tendency into local 2-D array (passed as argument to
83        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
84        affects results at machine truncation level (e.g., ocean: if using
85        SHORTWAVE_HEATING and atmos:, if using FrictionHeating or (atm_Rq<>0)
86        moist correction due to vertical advection).
87      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
88        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
89        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
90        obcs_ctrl (ad & fwd grd @ 12 & 7).
91    o pkg/ptracers & diagnostics:
92      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
93        title (to avoid some unexpected truncation); sort out ptracers diags units.
94      - collect ptracer forcing tendency into local 2-D array (passed as argument
95        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
96    
97    checkpoint65 (2014/07/18)
98    o pkg/fizhi:
99      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
100        affects results at machine truncation level. Update output of experiments
101        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
102    o pkg/seaice: more clean up
103      - rename TAF common block tapes to be more consistent and remove
104        unnecessary duplicates
105      - add store directives to remove more recomputations, but use smaller
106        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
107        The idea behind this flag is to reduce the memory footprint when the
108        adjoint of the LSR is not required. As of now, defining the flag
109        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
110        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
111        For experiment offline_exf_seaice, this means on a linux box with gfortran
112        nearly a factor of 10 (but keep in mind there is mostly seaice code in
113        this experiment):
114        > size mitgcmuv_ad
115        text    data        bss     dec        hex  
116        5100659 1216  220458952  225560827  d71c8fb
117        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
118        but only a moderate increase of 36% for global_ocean.cs32x15:
119        text    data        bss     dec        hex
120        6695027 1648 1014578664 1021275339 3cdf6ccb
121        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
122      - note: there are still recomputations in global_ocean.cs32x15 and
123        offline_exf_seaice and the gradient agreement changes (gets a
124        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
125      - in general, the AD gradients still are wrong
126    o OpenAD
127      - clean up code_oad/ directories somewhat by moving files
128        dontCompile, dontTransform, keepOriginal to OAD_support/
129    o model/src:
130      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
131        (not currently tested): add dissipation terms before NLFS rescaling of
132        tendencies (previously done after).
133    o pkg/diagnostics:
134      - write stats-diags in ascii file with more digits (same as in monitor).
135    o pkg/down_slope:
136      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
137        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
138    o model/src:
139      - new file "apply_forcing.F" containing all the code previously in
140        external_forcing.F, but with new argument list: pass, as new argument,
141        the current level tendency array to update (instead of a direct update
142        of the common bloc array). Change the corresponding calls.
143      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
144        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
145    o pkg/seaice/seaice_lsr, a little bit of clean up
146      - rearrange some code blocks, so that now all calculations for
147        setting up the right-hand-sides done within one single block
148        (I find that easier to read and understand)
149      - rearrange freedrift-code to reduce the number of ifdefs
150      - adjust some indentations and comments
151    
152    checkpoint64z (2014/07/10)
153    o model/src and several pkgs:
154      - change argument list of all S/R called from external_forcing.F and
155        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
156        to pass, as argument, the current level tendency array to update
157        (instead of a direct update of the common bloc array).
158      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
159      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
160    o pkg/seaice/seaice_lsr.F
161      - always initialize local arrays in seaice_lsr_tridiagu/v
162      - add more local tapes to seaice_lsr_tridiagu/v
163      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
164        keep it in bi/bj loop; this seems to be essential
165      - gradients are still wrong but only by 4-7 orders of magnitude
166        instead of 15 orders of magnitude, lab_sea improves a little
167    o pkg/seaice
168      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
169        generates unnecessary code in seaice_lsr_ad
170      - add more store directives in seaice_lsr to avoid unnecessary code
171        in seaice_lsr_ad
172      - exclude some residual computations in seaice_lsr when
173        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
174        in seaice_lsr_ad
175      - add more storing, a new tape (model/src/the_main_loop.F) and
176        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
177        and klockey should be checked by a specialist)
178      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
179        and update lab_sea after previous changes in pkg/seaice below
180    o pkg/autodiff:
181      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
182        viscFacInAd : run time parameters allowing for adjoint switches
183        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
184    o pkg/ecco:
185      - introduce cost_gencost_boxmean.F that computes a box mean
186        temperature (for use in adjoint sensitivity studies).
187    o model/src/set_defaults.F : initialize viscFacAdj to 1.
188    o pkg/mom_common/mom_calc_visc.F:
189      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
190    o pkg/seaice/seaice_summary.F:
191      - statement for SEAICEadjMODE now in autodiff_readparms.F
192    o pkg/seaice:
193      - remove some store directives and add new ones in an effort to get
194        finally rid off the recomputation warnings. This is successful
195        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
196        defined (i.e. no extensive recomputation warnings left), but there
197        are still too many recomputations on the solver iteration level
198      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
199      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
200        SEAICE_SIZE.h
201      - add a store directive in S/R seaice_calc_viscosities
202    o pkg/seaice (ITD code):
203      - fix definition of Hlimit for multi-threaded case
204      - use double precision arithmetic to compute Hlimit: this affects results;
205        update output of experiment seaice_itd.
206    o replace content of verification/seaice_itd
207      - instead of a 1D column use the configuration of offline_exf_seaice
208        to test the ice thickness distribution code with ridging
209      - this is a first shot at this experiment
210      - change of some defaults of ridging parameters SEAICEhStar (from
211        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
212        and lot of new comments.
213    
214    checkpoint64y (2014/06/20)
215    o pkg/seaice/seaice_reg_ridge.F:
216      - modify the regularization of very small volumes of ice; only check
217        total volume HEFF, and do not apply correction to individual ice
218        classes because that leads to funny patterns in the heat and fw-fluxes
219        into the ocean. Adjust seaice_itd/results/output.txt
220      - replace nITD by SEAICE_multDim in loop-ranges
221    o pkg/exf:
222      - add code to process the case field period = -12. with UV interpolation.
223      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
224        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
225    o verification/global_with_exf:
226      - switch all fields period to -12. (was previously untested) in input/data.exf
227        (but keep secondary test ".yearly" unchanged); update the reference output.
228    o pkg/cal:
229      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
230    o pkg/exf:
231      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
232        to replace logical switch "exf_verbose"
233      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
234    o pkg/sbo:
235      - update from Katherine Quinn: evaluate mass directly from density and SSH
236        (budget using Finite Volume method) instead of from bottom pressure.
237      - allow testreport to collect few selected SBO output ; tested in exp.
238        global_ocean.90x40x15 (after updating the results, to include SBO output).
239      - fix some multi-threading issues (in output part).
240    o model/src & most packages:
241      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
242      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
243        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
244        "data.{pkg}" exist ; and leave the S/R (return) just after.
245      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
246        + call LAND_READPARMS from packages_readparms.F
247    o pkg/seaice:
248      - remove code that resets useThSice in S/R seaice_readparms and
249        replace it by a warning in S/R seaice_check
250      - remove parameter MULTDIM, replace with nITD and runtime
251        parameter SEAICE_multDim (still hard-wired to nITD if
252        SEAICE_ITD is defined)
253    
254    checkpoint64x (2014/05/24)
255    o verification/lab_sea:
256      - update adjoint and TLM output following changes to pkg/salt_plume
257      - un-do the update after putting back local recip_Cp in few places.
258    o pkg/salt_plume: modifications by An Nguyen:
259      - add capability to do brine rejection (salt-plume) as function of
260        volume+tracers (instead of only salinity tracer).
261      - conserve volume by exchanging volume from each kLev to above to
262        accommodate in-coming brine volume
263      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
264      - switch KPP surf buoyancy due to brine forcing to 3-d
265        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
266      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
267      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
268        in East/West Arctic.
269    o pkg/sbo:
270      - incorporate modifications from Katherine Quinn to enable the use of sbo
271        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
272        output for future testreport verification (unfinished).
273    o pkg/atm_phys:
274      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
275        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
276        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
277    o pkg/seaice
278      seaice_calc_ice_strength.F: modify expression to avoid divisions
279        (affects truncation)
280      seaice_do_ridging.F: clean up the insectarium
281      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
282      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
283      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
284      - add some debugging information and error messages (warnings)
285    o model/src: modifications relatd to atmosphere p*:
286      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
287      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
288        of vertical profile tRef in geopotential background and anomaly.
289      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
290        and pkg/atm_phys.
291      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
292        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
293    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
294    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
295        not used right now, but can be used in BGC packages to fix conservation.
296    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
297        other packages too.
298    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
299        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
300    o model/src:
301      - since we have several heat capacity (even in model/src), define "recip_Cp"
302        as local variable (no longer in common block) to avoid any confusion.
303      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
304    o pkg/exf:
305      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
306        air density as function of air Temp, Humidity and atm pressure.
307    
308    checkpoint64w (2014/05/02)
309    o verification:
310      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
311        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
312        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
313        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
314        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
315    o model/src: for atmosphere in p* coords:
316      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
317      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
318        but not yet activated.
319    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
320      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
321      - this changes the results (but not for any verification experiment, because
322        none tests this), but avoids having an extra field in the restart files
323    o pkg/seaice: remove global variable TICE (not needed)
324      - replace by TICES or local variable where necessary (cost_seaice_test,
325        seaice_diagnostics_state)
326      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
327      - use specific read/write routines for reading and writing individual leves
328        of a multilevel field
329    o pkg/ctrl & model/inc:
330      - move additional anomaly fields of control vars (related to options:
331         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
332        from DYNVARS.h into new header file: CTRL_FIELDS.h
333    o pkg/seaice: some small modifications to the ridging code
334      - make fw2ObyRidge a global variable and add the freshwater flux to
335        seaice_growth
336      - pass actual thickness from seaice_prepare_ridging, so that it is
337        computed only in one place and compute it in the same way as in
338        seaice_growth
339      - initialise more fields in seaice_do_ridging that where cause floating
340        point exceptions over land
341  o pkg/seaice: preparations for ridging code and first real ridging code  o pkg/seaice: preparations for ridging code and first real ridging code
342    - move most of "PART 1" of S/R seaice_growth into a new and separate    - move most of "PART 1" of S/R seaice_growth into a new and separate
343      S/R seaice_reg_ridge that will both regularize the state variable after      S/R seaice_reg_ridge that will both regularize the state variable after
344      advection call the actual ridging routine;      advection call the actual ridging routine;
345    - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,    - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
346      d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;      d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
347    - remove ridging code from seaice_advdiff    - remove ridging code from seaice_advdiff
348    - clean up remaining part 1 of seaice_growth in an attempt to make it    - clean up remaining part 1 of seaice_growth in an attempt to make it
349      more readable (this is probably subjective)      more readable (this is probably subjective)
350    - call seaice_itd_redist once in the initialisation phase to have the initial    - call seaice_itd_redist once in the initialisation phase to have the initial
351      conditions in the correct category      conditions in the correct category

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  Added in v.1.2040

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