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revision 1.2005 by jmc, Fri Jun 6 21:17:12 2014 UTC revision 1.2051 by jmc, Fri Aug 22 22:22:49 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 pkg/gchem:
8      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
9        pkg/dic is currently changing/updating ptracers values beyond the OB).
10    o verification (hs94):
11      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
12        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
13        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
14        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
15    o pkg/ptracers:
16      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
17        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
18      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
19        with AB-2 code (so that it get tested).
20    o model/src:
21      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
22        with AB-2 code (previously only available with AB-3 code).
23        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
24        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
25        there, by calling CYCLE_AB_TRACER).
26    o pkg/generic_advdiff:
27      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
28        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
29        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
30        S/R temp/salt/ptracers_integrate.F
31    o model/src & pkg/ptracers:
32      - remove common block variables gT,gS (in DYNVARS.h), except when
33         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
34      - remove common block variable gPtr.
35    o model/src & pkgs:
36      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
37         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
38         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
39         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
40      + change accordingly all calling S/R.
41      - use local temperature/salinity/ptracer tendency array (without bi,bj)
42        in S/R temp/salt/ptracers_integrate.F
43    o pkg/seaice:
44      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
45        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
46      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
47        in seaice_lsr
48      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
49        in s/r seaice_lsr_calc_coeffs
50    o pkg/mdsio:
51      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
52        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
53        too long (e.g., > MAX_LEN_FNAM/2 )
54    
55    checkpoint65b (2014/08/12)
56    o pkg/matrix:
57      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
58    o model/src:
59      - fix initialisation of geothermalFile; compile geothermal-flux code in
60        natl_box verification experiment.
61    o model/src & pkg/down_slope:
62      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
63      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
64        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
65        results at machine truncation level: update output of experiments
66        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
67    o pkg/diagnostics (Stats-Diags):
68      - do not cumulate the full volume when DIAGNOSTICS_FILL is
69        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
70        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
71        times (but Min,Max and StD are still wrong).
72    o model/src:
73      - add geothermal flux forcing: read in ini_forcing.F as time-constant
74        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
75    o model/src:
76      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
77        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
78        arrays are already updated while adjustments (filters, conv.adjustment) are
79        still applied later, in S/R TRACERS_CORRECTION_STEP.
80    o model/src:
81      - store in common bloc array "rhoInSitu" the virtual potential temperature
82        anomaly that is used to compute geopotential: this make the atmos code
83        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
84    o pkg/seaice/seaice_lsr.F
85      - rename integer variable ilcall to ipass (that's what it is called
86        in the residual diagnostics
87      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
88        default) for improved non-linear convergence of the first few steps
89      - adjust a few comments and add new ones to explain some of the store
90        directives
91    o pkg/generic_advdiff (& ptracers):
92      - re-work the code to check for valid advection scheme and for minimum
93        size of overlap (now stored in local common bloc in gad_advscheme.F)
94    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
95      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
96      - add an auxilliary variable "bet" and fix store directives and keys in
97        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
98        less exact gradients in my tests); but there are still
99        recomputation warning (although gradients are sort of OK), when
100        SEAICE_LSR_VECTORIZE is not defined, so this flag and
101        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
102      - update verification experiments lab_sea.
103      - change some comments in S/R seaice_calc_viscosities
104    o model/src:
105      - if staggerTimeStep=T, always apply exchange to velocity field in
106        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
107        (independent of using multi-dim advection or not); no effect on FWD run
108        but affects AD results (at machine truncation level): update output of
109        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
110        and isomip (oad: 12.d).
111    o pkg/generic_advdiff:
112      - stop if doAB_onGtGs is set to FALSE but ignored
113      - refine warning related to stability of tracer time-stepping
114        regarding internal wave dynamics.
115      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
116        on staggerTimeStep & implicitIntGravWave (will now get a warning
117        if potentially unstable).
118    o pkg/kl10:
119      - add new pkg "kl10" for mixing due to internal wave breaking, from
120        http://www.sciencedirect.com/science/article/pii/S1463500310000144
121        (contribution from Jody Klymak), tested in verification experiment
122        verification/internal_wave/input.kl10/
123    o isomip experiment:
124      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
125        (input.htd) and update the output.
126    o cd_code experiments:
127      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
128        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
129        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
130        update the corresponding output.
131    o pkg/seaice:
132      - reduce the number of include files and store directives in
133        S/R seaice_lsr_tridiagu/v
134      - change the order of loops in one case in S/R seaice_lsr_tridiagv
135        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
136        get rid off one store directive (a TAF bug?)
137      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
138        S/R seaice_lsr_tridiagv to change the loop range for consistency
139      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
140      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
141        S/R seaice_lsr_tridiagu/v (requires update of
142        offline_exf_seaice/input.dyn_jfnk)
143    
144    checkpoint65a (2014/07/27)
145    o model/src:
146      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
147        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
148        (topo in p-coords, ice-shelf in z-coords); update output of experiments
149        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
150    o model/src:
151      - collect momentum forcing tendency into local 2-D array (passed as argument
152        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
153        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
154        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
155      - collect T & S forcing tendency into local 2-D array (passed as argument to
156        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
157        affects results at machine truncation level (e.g., ocean: if using
158        SHORTWAVE_HEATING and atmos:, if using FrictionHeating or (atm_Rq<>0)
159        moist correction due to vertical advection).
160      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
161        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
162        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
163        obcs_ctrl (ad & fwd grd @ 12 & 7).
164    o pkg/ptracers & diagnostics:
165      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
166        title (to avoid some unexpected truncation); sort out ptracers diags units.
167      - collect ptracer forcing tendency into local 2-D array (passed as argument
168        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
169    
170    checkpoint65 (2014/07/18)
171    o pkg/fizhi:
172      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
173        affects results at machine truncation level. Update output of experiments
174        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
175    o pkg/seaice: more clean up
176      - rename TAF common block tapes to be more consistent and remove
177        unnecessary duplicates
178      - add store directives to remove more recomputations, but use smaller
179        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
180        The idea behind this flag is to reduce the memory footprint when the
181        adjoint of the LSR is not required. As of now, defining the flag
182        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
183        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
184        For experiment offline_exf_seaice, this means on a linux box with gfortran
185        nearly a factor of 10 (but keep in mind there is mostly seaice code in
186        this experiment):
187        > size mitgcmuv_ad
188        text    data        bss     dec        hex  
189        5100659 1216  220458952  225560827  d71c8fb
190        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
191        but only a moderate increase of 36% for global_ocean.cs32x15:
192        text    data        bss     dec        hex
193        6695027 1648 1014578664 1021275339 3cdf6ccb
194        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
195      - note: there are still recomputations in global_ocean.cs32x15 and
196        offline_exf_seaice and the gradient agreement changes (gets a
197        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
198      - in general, the AD gradients still are wrong
199    o OpenAD
200      - clean up code_oad/ directories somewhat by moving files
201        dontCompile, dontTransform, keepOriginal to OAD_support/
202    o model/src:
203      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
204        (not currently tested): add dissipation terms before NLFS rescaling of
205        tendencies (previously done after).
206    o pkg/diagnostics:
207      - write stats-diags in ascii file with more digits (same as in monitor).
208    o pkg/down_slope:
209      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
210        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
211    o model/src:
212      - new file "apply_forcing.F" containing all the code previously in
213        external_forcing.F, but with new argument list: pass, as new argument,
214        the current level tendency array to update (instead of a direct update
215        of the common bloc array). Change the corresponding calls.
216      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
217        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
218    o pkg/seaice/seaice_lsr, a little bit of clean up
219      - rearrange some code blocks, so that now all calculations for
220        setting up the right-hand-sides done within one single block
221        (I find that easier to read and understand)
222      - rearrange freedrift-code to reduce the number of ifdefs
223      - adjust some indentations and comments
224    
225    checkpoint64z (2014/07/10)
226    o model/src and several pkgs:
227      - change argument list of all S/R called from external_forcing.F and
228        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
229        to pass, as argument, the current level tendency array to update
230        (instead of a direct update of the common bloc array).
231      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
232      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
233    o pkg/seaice/seaice_lsr.F
234      - always initialize local arrays in seaice_lsr_tridiagu/v
235      - add more local tapes to seaice_lsr_tridiagu/v
236      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
237        keep it in bi/bj loop; this seems to be essential
238      - gradients are still wrong but only by 4-7 orders of magnitude
239        instead of 15 orders of magnitude, lab_sea improves a little
240    o pkg/seaice
241      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
242        generates unnecessary code in seaice_lsr_ad
243      - add more store directives in seaice_lsr to avoid unnecessary code
244        in seaice_lsr_ad
245      - exclude some residual computations in seaice_lsr when
246        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
247        in seaice_lsr_ad
248      - add more storing, a new tape (model/src/the_main_loop.F) and
249        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
250        and klockey should be checked by a specialist)
251      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
252        and update lab_sea after previous changes in pkg/seaice below
253    o pkg/autodiff:
254      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
255        viscFacInAd : run time parameters allowing for adjoint switches
256        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
257    o pkg/ecco:
258      - introduce cost_gencost_boxmean.F that computes a box mean
259        temperature (for use in adjoint sensitivity studies).
260    o model/src/set_defaults.F : initialize viscFacAdj to 1.
261    o pkg/mom_common/mom_calc_visc.F:
262      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
263    o pkg/seaice/seaice_summary.F:
264      - statement for SEAICEadjMODE now in autodiff_readparms.F
265    o pkg/seaice:
266      - remove some store directives and add new ones in an effort to get
267        finally rid off the recomputation warnings. This is successful
268        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
269        defined (i.e. no extensive recomputation warnings left), but there
270        are still too many recomputations on the solver iteration level
271      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
272      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
273        SEAICE_SIZE.h
274      - add a store directive in S/R seaice_calc_viscosities
275    o pkg/seaice (ITD code):
276      - fix definition of Hlimit for multi-threaded case
277      - use double precision arithmetic to compute Hlimit: this affects results;
278        update output of experiment seaice_itd.
279    o replace content of verification/seaice_itd
280      - instead of a 1D column use the configuration of offline_exf_seaice
281        to test the ice thickness distribution code with ridging
282      - this is a first shot at this experiment
283      - change of some defaults of ridging parameters SEAICEhStar (from
284        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
285        and lot of new comments.
286    
287    checkpoint64y (2014/06/20)
288    o pkg/seaice/seaice_reg_ridge.F:
289      - modify the regularization of very small volumes of ice; only check
290        total volume HEFF, and do not apply correction to individual ice
291        classes because that leads to funny patterns in the heat and fw-fluxes
292        into the ocean. Adjust seaice_itd/results/output.txt
293      - replace nITD by SEAICE_multDim in loop-ranges
294    o pkg/exf:
295      - add code to process the case field period = -12. with UV interpolation.
296      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
297        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
298  o verification/global_with_exf:  o verification/global_with_exf:
299    - swith all fields period to -12. (was previously untested) in input/data.exf    - switch all fields period to -12. (was previously untested) in input/data.exf
300      (but keep secondary test ".yearly" unchanged); update the reference output.      (but keep secondary test ".yearly" unchanged); update the reference output.
301  o pkg/cal:  o pkg/cal:
302    - new calendar type "noLeapYear" for 365 days calendar without any leap year.    - new calendar type "noLeapYear" for 365 days calendar without any leap year.
303  o pkg/exf:  o pkg/exf:
304    - new integer parameter "exf_debugLev" (default set to main model debugLevel)    - new integer parameter "exf_debugLev" (default set to main model debugLevel)
305      to replace logical switch "exf_verbose"      to replace logical switch "exf_verbose"
306    - report in STDOUT when loading a new reccord (if exf_debugLev >= 3)    - report in STDOUT when loading a new record (if exf_debugLev >= 3)
307  o pkg/sbo:  o pkg/sbo:
308    - update from Katherine Quinn: evaluate mass directly from density and SSH    - update from Katherine Quinn: evaluate mass directly from density and SSH
309      (budget using Finite Volume method) instead of from bottom pressure.      (budget using Finite Volume method) instead of from bottom pressure.
# Line 28  o model/src & most packages: Line 319  o model/src & most packages:
319      + call LAND_READPARMS from packages_readparms.F      + call LAND_READPARMS from packages_readparms.F
320  o pkg/seaice:  o pkg/seaice:
321    - remove code that resets useThSice in S/R seaice_readparms and    - remove code that resets useThSice in S/R seaice_readparms and
322      replace by a warning in S/R seaice_check      replace it by a warning in S/R seaice_check
323    - remove parameter MULTDIM, replace with nITD and runtime    - remove parameter MULTDIM, replace with nITD and runtime
324      parameter SEAICE_multDim (still hard-wired to nITD if      parameter SEAICE_multDim (still hard-wired to nITD if
325      SEAICE_ITD is defined)      SEAICE_ITD is defined)

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