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revision 1.2024 by heimbach, Tue Jul 15 23:07:57 2014 UTC revision 1.2067 by gforget, Fri Sep 19 21:03:11 2014 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    
8    o pkg/ctrl :
9     - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
10       ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
11     - re-activate ctrl_summary (call in ctrl_init.F)
12    o pkg/ctrl/ctrl_cost_gen.F :
13     - rename ctrl_cost_gen2d input parameters {wmean_gen,wgen,genmask}
14       as {xx_gen_wmean,xx_gen_weight,xx_gen_mask}
15     - add ctrl_cost_gen3d for ARR3D (ctrl_cost_gen2d is for ARR2D,TIM2D)
16    o pkg/ctrl/CTRL_GENARR.h :
17     - add objf_genarr2d,  num_genarr2d, mult_genarr2d
18     - add objf_genarr3d,  num_genarr3d, mult_genarr3d
19     - add wgenarr2d, wgenarr3d
20    o pkg/ctrl/ctrl_readparms.F :
21     - add mult_genarr2d,mult_genarr3d in namelist
22    o pkg/ctrl_map_ini_genarr.F :
23     - bug fixes
24    o pkg/ctrl/ctrl_cost_driver.F :
25     - remove un-necessary cal.h, fix CCP brackets, remove un-necessary
26       myiter, mytime, add return
27    o pkg/ctrl/ctrl_cost_gen.F :
28     - fix CCP brackets, remove un-necessary myiter, mytime
29    o pkg/ecco :
30       - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
31       - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
32       - update cost_forcing_gen calls in cost_forcing.F
33       - update cost_genctrl call in ecco_cost_driver.F
34       - update ecco_ad_diff.list accordingly
35    o pkg/ctrl :
36       - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
37       - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
38       - update ctrl_ad_diff.list accordingly
39    
40    checkpoint65d (2014/09/15)
41    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
42      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
43        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
44    o pkg/ctrl/ctrl_map_ini_genarr.F :
45      - remove compilation failure
46      - replace hard coded example
47      - use ctrl_map_ini_gen2D, 3D
48    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
49      - on/off switch based upon xx_genarr2d_weight,3d
50    o src/packages_init_variables.F :
51      - regroup pkg/estimation calls
52      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
53        (moved to ctrl_init_variables)
54    o cost/cost_init_varia.F :
55      - remove ecco_cost_init_varia
56        (moved to ecco_init_varia)
57    o ctrl/ctrl_init_variables.F :
58      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
59      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
60    o ctrl/ctrl_map_ini.F :
61      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
62        (moved to ctrl_init_variables)
63    o ctrl/ctrl_map_ini_ecco.F :
64      - remove ECCO_PHYS (mv to ecco_init_varia)
65      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
66    o ecco/ecco_ad_diff.list :
67      - add ecco_init_varia.f
68    o ecco/ecco_init_varia.F
69      - new routine
70    o pkg/streamice:
71      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
72        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
73      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
74    o pkg/generic_advdiff:
75      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
76    o pkg/exf:
77      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
78         xxg_precip capability
79      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
80    o pkg/ctrl:
81      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
82    o model/src/load_fields_driver.F :
83      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
84        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
85    o OpenAD verification experiments:
86      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
87        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
88        for now, only in pkgs used in OpenAD verification experiments.
89      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
90        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
91        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
92        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
93    o OpenAD verification tests:
94      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
95      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
96        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
97      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
98        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
99    o model/src & generic_advdiff:
100      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
101        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
102        dynamics requires valid tracer forcing only over tile interior but, for
103        some diagnostics, may need to extend it over 1 point in tile halo region.
104      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
105        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
106        setting in temp/salt/ptracer_integrate.F
107    o pkg/dic:
108      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
109        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
110        in gchem_forcing_sep.F
111    o pkg/autodiff & obcs:
112      - add storage of current OB values for U & V (was already done for T & S).
113    
114    checkpoint65c (2014/08/30)
115    o pkg/dic:
116      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
117        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
118        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
119    o verification:
120      - new experiment testing OBCS and DIC pkgs, using params & output from
121        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
122        passage: take OBCS from the last year of a 2 yrs simulation and initial
123        conditions from t=1.yr while keeping the same forcing.
124    o model/src:
125      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
126        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
127    o pkg/diagnostics (Stats-Diags):
128      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
129        a) refine region where stats are computed, excluding where arrhFac=0 ;
130        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
131        c) extend regional stats over the region edges (for U or V pt location).
132    o pkg/gchem:
133      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
134        pkg/dic is currently changing/updating ptracers values beyond the OB).
135    o verification (hs94):
136      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
137        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
138        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
139        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
140    o pkg/ptracers:
141      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
142        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
143      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
144        with AB-2 code (so that it get tested).
145    o model/src:
146      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
147        with AB-2 code (previously only available with AB-3 code).
148        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
149        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
150        there, by calling CYCLE_AB_TRACER).
151    o pkg/generic_advdiff:
152      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
153        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
154        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
155        S/R temp/salt/ptracers_integrate.F
156    o model/src & pkg/ptracers:
157      - remove common block variables gT,gS (in DYNVARS.h), except when
158         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
159      - remove common block variable gPtr.
160    o model/src & pkgs:
161      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
162         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
163         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
164         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
165      + change accordingly all calling S/R.
166      - use local temperature/salinity/ptracer tendency array (without bi,bj)
167        in S/R temp/salt/ptracers_integrate.F
168    o pkg/seaice:
169      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
170        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
171      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
172        in seaice_lsr
173      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
174        in s/r seaice_lsr_calc_coeffs
175    o pkg/mdsio:
176      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
177        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
178        too long (e.g., > MAX_LEN_FNAM/2 )
179    
180    checkpoint65b (2014/08/12)
181    o pkg/matrix:
182      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
183    o model/src:
184      - fix initialisation of geothermalFile; compile geothermal-flux code in
185        natl_box verification experiment.
186    o model/src & pkg/down_slope:
187      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
188      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
189        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
190        results at machine truncation level: update output of experiments
191        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
192    o pkg/diagnostics (Stats-Diags):
193      - do not cumulate the full volume when DIAGNOSTICS_FILL is
194        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
195        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
196        times (but Min,Max and StD are still wrong).
197    o model/src:
198      - add geothermal flux forcing: read in ini_forcing.F as time-constant
199        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
200    o model/src:
201      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
202        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
203        arrays are already updated while adjustments (filters, conv.adjustment) are
204        still applied later, in S/R TRACERS_CORRECTION_STEP.
205    o model/src:
206      - store in common bloc array "rhoInSitu" the virtual potential temperature
207        anomaly that is used to compute geopotential: this make the atmos code
208        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
209    o pkg/seaice/seaice_lsr.F
210      - rename integer variable ilcall to ipass (that's what it is called
211        in the residual diagnostics
212      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
213        default) for improved non-linear convergence of the first few steps
214      - adjust a few comments and add new ones to explain some of the store
215        directives
216    o pkg/generic_advdiff (& ptracers):
217      - re-work the code to check for valid advection scheme and for minimum
218        size of overlap (now stored in local common bloc in gad_advscheme.F)
219    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
220      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
221      - add an auxilliary variable "bet" and fix store directives and keys in
222        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
223        less exact gradients in my tests); but there are still
224        recomputation warning (although gradients are sort of OK), when
225        SEAICE_LSR_VECTORIZE is not defined, so this flag and
226        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
227      - update verification experiments lab_sea.
228      - change some comments in S/R seaice_calc_viscosities
229    o model/src:
230      - if staggerTimeStep=T, always apply exchange to velocity field in
231        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
232        (independent of using multi-dim advection or not); no effect on FWD run
233        but affects AD results (at machine truncation level): update output of
234        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
235        and isomip (oad: 12.d).
236    o pkg/generic_advdiff:
237      - stop if doAB_onGtGs is set to FALSE but ignored
238      - refine warning related to stability of tracer time-stepping
239        regarding internal wave dynamics.
240      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
241        on staggerTimeStep & implicitIntGravWave (will now get a warning
242        if potentially unstable).
243    o pkg/kl10:
244      - add new pkg "kl10" for mixing due to internal wave breaking, from
245        http://www.sciencedirect.com/science/article/pii/S1463500310000144
246        (contribution from Jody Klymak), tested in verification experiment
247        verification/internal_wave/input.kl10/
248    o isomip experiment:
249      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
250        (input.htd) and update the output.
251    o cd_code experiments:
252      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
253        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
254        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
255        update the corresponding output.
256    o pkg/seaice:
257      - reduce the number of include files and store directives in
258        S/R seaice_lsr_tridiagu/v
259      - change the order of loops in one case in S/R seaice_lsr_tridiagv
260        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
261        get rid off one store directive (a TAF bug?)
262      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
263        S/R seaice_lsr_tridiagv to change the loop range for consistency
264      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
265      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
266        S/R seaice_lsr_tridiagu/v (requires update of
267        offline_exf_seaice/input.dyn_jfnk)
268    
269    checkpoint65a (2014/07/27)
270    o model/src:
271      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
272        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
273        (topo in p-coords, ice-shelf in z-coords); update output of experiments
274        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
275    o model/src:
276      - collect momentum forcing tendency into local 2-D array (passed as argument
277        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
278        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
279        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
280      - collect T & S forcing tendency into local 2-D array (passed as argument to
281        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
282        affects results at machine truncation level (e.g., ocean: if using
283        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
284        correction due to vertical advection).
285      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
286        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
287        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
288        obcs_ctrl (ad & fwd grd @ 12 & 7).
289    o pkg/ptracers & diagnostics:
290      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
291        title (to avoid some unexpected truncation); sort out ptracers diags units.
292      - collect ptracer forcing tendency into local 2-D array (passed as argument
293        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
294    
295    checkpoint65 (2014/07/18)
296    o pkg/fizhi:
297      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
298        affects results at machine truncation level. Update output of experiments
299        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
300    o pkg/seaice: more clean up
301      - rename TAF common block tapes to be more consistent and remove
302        unnecessary duplicates
303      - add store directives to remove more recomputations, but use smaller
304        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
305        The idea behind this flag is to reduce the memory footprint when the
306        adjoint of the LSR is not required. As of now, defining the flag
307        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
308        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
309        For experiment offline_exf_seaice, this means on a linux box with gfortran
310        nearly a factor of 10 (but keep in mind there is mostly seaice code in
311        this experiment):
312        > size mitgcmuv_ad
313        text    data        bss     dec        hex  
314        5100659 1216  220458952  225560827  d71c8fb
315        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
316        but only a moderate increase of 36% for global_ocean.cs32x15:
317        text    data        bss     dec        hex
318        6695027 1648 1014578664 1021275339 3cdf6ccb
319        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
320      - note: there are still recomputations in global_ocean.cs32x15 and
321        offline_exf_seaice and the gradient agreement changes (gets a
322        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
323      - in general, the AD gradients still are wrong
324  o OpenAD  o OpenAD
325    - clean up code_oad/ directories somewhat by moving files    - clean up code_oad/ directories somewhat by moving files
326      dontCompile, dontTransform, keepOriginal to OAD_support/      dontCompile, dontTransform, keepOriginal to OAD_support/

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