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revision 1.2033 by mlosch, Tue Jul 29 16:29:56 2014 UTC revision 1.2075 by gforget, Mon Sep 29 17:16:46 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/seaice:  o pkg/ecco: internal re-organization
8      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
9        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
10        mv relevant variables definition from ecco_cost.h to ecco.h,
11        make sure gencost routines only include ecco.h)
12      - throughout : add missing CCP switches, rm unused variables,
13        and rm un-necessary CPP switches
14      - throughout gencost routines : replace modelstartdate with
15        gencost_startdate when needed
16      - cost_bp_read.F : use arguments, instead of common blocs
17        so that it can be used also by (new) cost_gencost_bpv4.F
18      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
19      - ecco_phys.F : compute etanFull
20      - ecco_readparms.F : rename using_topex as using_tpj, add
21        bpv4-grace to gencost list, initialize added parameters
22      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
23    
24    checkpoint65e (2014/09/28)
25    o pkg/obcs:
26      - replaced the just-added CPP options with run-time variables
27        (see pkg/obcs/OBCS_PARAMS.h for details)
28    o pkg/obcs:
29      - add additional CPP options for sponge boundary layers
30        (see pkg/obcs/OBCS_OPTIONS.h for details)
31    o pkg/atm_phys:
32      - implement simple (obliquity only, assuming circular planet orbit)
33        seasonal cycle for incoming insolation ; used when run-time parameter
34        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
35    o pkg/exf, pkg/ecco, pkg/ctrl:
36      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
37      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
38      - implement gentim2d for xx_tauu, xx_tauv
39    o pkg/ctrl, pkg/ecco :
40      - fix and complement the generic controls implementation
41    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
42        pkg/shelfice/shelfice_thermodynamics.F,
43        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
44        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
45      - add weight in CTRL_GET_GEN calls
46    o pkg/ctrl :
47      - ctrl_get_gen.F : add weight as input parameter, and apply
48        it directly rather than using smooth_correl2Dw (to be retired).
49      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
50    o pkg/ctrl :
51      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
52        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
53      - re-activate ctrl_summary (call in ctrl_init.F)
54    o pkg/ctrl/ctrl_cost_gen.F :
55      - fix CCP brackets, remove un-necessary myiter, mytime
56    o pkg/ecco, pkg/ctrl :
57      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
58      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
59      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
60      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
61    
62    checkpoint65d (2014/09/15)
63    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
64      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
65        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
66    o pkg/ctrl/ctrl_map_ini_genarr.F :
67      - remove compilation failure
68      - replace hard coded example
69      - use ctrl_map_ini_gen2D, 3D
70    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
71      - on/off switch based upon xx_genarr2d_weight,3d
72    o src/packages_init_variables.F :
73      - regroup pkg/estimation calls
74      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
75        (moved to ctrl_init_variables)
76    o cost/cost_init_varia.F :
77      - remove ecco_cost_init_varia
78        (moved to ecco_init_varia)
79    o ctrl/ctrl_init_variables.F :
80      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
81      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
82    o ctrl/ctrl_map_ini.F :
83      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
84        (moved to ctrl_init_variables)
85    o ctrl/ctrl_map_ini_ecco.F :
86      - remove ECCO_PHYS (mv to ecco_init_varia)
87      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
88    o ecco/ecco_ad_diff.list :
89      - add ecco_init_varia.f
90    o ecco/ecco_init_varia.F
91      - new routine
92    o pkg/streamice:
93      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
94        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
95      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
96    o pkg/generic_advdiff:
97      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
98    o pkg/exf:
99      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
100         xxg_precip capability
101      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
102    o pkg/ctrl:
103      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
104    o model/src/load_fields_driver.F :
105      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
106        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
107    o OpenAD verification experiments:
108      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
109        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
110        for now, only in pkgs used in OpenAD verification experiments.
111      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
112        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
113        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
114        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
115    o OpenAD verification tests:
116      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
117      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
118        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
119      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
120        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
121    o model/src & generic_advdiff:
122      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
123        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
124        dynamics requires valid tracer forcing only over tile interior but, for
125        some diagnostics, may need to extend it over 1 point in tile halo region.
126      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
127        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
128        setting in temp/salt/ptracer_integrate.F
129    o pkg/dic:
130      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
131        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
132        in gchem_forcing_sep.F
133    o pkg/autodiff & obcs:
134      - add storage of current OB values for U & V (was already done for T & S).
135    
136    checkpoint65c (2014/08/30)
137    o pkg/dic:
138      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
139        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
140        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
141    o verification:
142      - new experiment testing OBCS and DIC pkgs, using params & output from
143        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
144        passage: take OBCS from the last year of a 2 yrs simulation and initial
145        conditions from t=1.yr while keeping the same forcing.
146    o model/src:
147      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
148        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
149    o pkg/diagnostics (Stats-Diags):
150      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
151        a) refine region where stats are computed, excluding where arrhFac=0 ;
152        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
153        c) extend regional stats over the region edges (for U or V pt location).
154    o pkg/gchem:
155      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
156        pkg/dic is currently changing/updating ptracers values beyond the OB).
157    o verification (hs94):
158      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
159        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
160        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
161        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
162    o pkg/ptracers:
163      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
164        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
165      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
166        with AB-2 code (so that it get tested).
167    o model/src:
168      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
169        with AB-2 code (previously only available with AB-3 code).
170        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
171        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
172        there, by calling CYCLE_AB_TRACER).
173    o pkg/generic_advdiff:
174      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
175        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
176        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
177        S/R temp/salt/ptracers_integrate.F
178    o model/src & pkg/ptracers:
179      - remove common block variables gT,gS (in DYNVARS.h), except when
180         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
181      - remove common block variable gPtr.
182    o model/src & pkgs:
183      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
184         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
185         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
186         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
187      + change accordingly all calling S/R.
188      - use local temperature/salinity/ptracer tendency array (without bi,bj)
189        in S/R temp/salt/ptracers_integrate.F
190    o pkg/seaice:
191      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
192        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
193      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
194        in seaice_lsr
195      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
196        in s/r seaice_lsr_calc_coeffs
197    o pkg/mdsio:
198      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
199        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
200        too long (e.g., > MAX_LEN_FNAM/2 )
201    
202    checkpoint65b (2014/08/12)
203    o pkg/matrix:
204      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
205    o model/src:
206      - fix initialisation of geothermalFile; compile geothermal-flux code in
207        natl_box verification experiment.
208    o model/src & pkg/down_slope:
209      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
210      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
211        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
212        results at machine truncation level: update output of experiments
213        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
214    o pkg/diagnostics (Stats-Diags):
215      - do not cumulate the full volume when DIAGNOSTICS_FILL is
216        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
217        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
218        times (but Min,Max and StD are still wrong).
219    o model/src:
220      - add geothermal flux forcing: read in ini_forcing.F as time-constant
221        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
222    o model/src:
223      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
224        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
225        arrays are already updated while adjustments (filters, conv.adjustment) are
226        still applied later, in S/R TRACERS_CORRECTION_STEP.
227    o model/src:
228      - store in common bloc array "rhoInSitu" the virtual potential temperature
229        anomaly that is used to compute geopotential: this make the atmos code
230        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
231    o pkg/seaice/seaice_lsr.F
232      - rename integer variable ilcall to ipass (that's what it is called
233        in the residual diagnostics
234      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
235        default) for improved non-linear convergence of the first few steps
236      - adjust a few comments and add new ones to explain some of the store
237        directives
238    o pkg/generic_advdiff (& ptracers):
239      - re-work the code to check for valid advection scheme and for minimum
240        size of overlap (now stored in local common bloc in gad_advscheme.F)
241    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
242      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
243      - add an auxilliary variable "bet" and fix store directives and keys in
244        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
245        less exact gradients in my tests); but there are still
246        recomputation warning (although gradients are sort of OK), when
247        SEAICE_LSR_VECTORIZE is not defined, so this flag and
248        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
249      - update verification experiments lab_sea.
250      - change some comments in S/R seaice_calc_viscosities
251    o model/src:
252      - if staggerTimeStep=T, always apply exchange to velocity field in
253        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
254        (independent of using multi-dim advection or not); no effect on FWD run
255        but affects AD results (at machine truncation level): update output of
256        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
257        and isomip (oad: 12.d).
258    o pkg/generic_advdiff:
259      - stop if doAB_onGtGs is set to FALSE but ignored
260      - refine warning related to stability of tracer time-stepping
261        regarding internal wave dynamics.
262      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
263        on staggerTimeStep & implicitIntGravWave (will now get a warning
264        if potentially unstable).
265    o pkg/kl10:
266      - add new pkg "kl10" for mixing due to internal wave breaking, from
267        http://www.sciencedirect.com/science/article/pii/S1463500310000144
268        (contribution from Jody Klymak), tested in verification experiment
269        verification/internal_wave/input.kl10/
270    o isomip experiment:
271      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
272        (input.htd) and update the output.
273    o cd_code experiments:
274      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
275        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
276        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
277        update the corresponding output.
278    o pkg/seaice:
279    - reduce the number of include files and store directives in    - reduce the number of include files and store directives in
280      S/R seaice_lsr_tridiagu/v      S/R seaice_lsr_tridiagu/v
281    - change the order of loops in one case in S/R seaice_lsr_tridiagv    - change the order of loops in one case in S/R seaice_lsr_tridiagv
282      (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to      (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
283      get rid off one store directive (a TAF bug?)      get rid off one store directive (a TAF bug?)
284    - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in    - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
285      S/R seaice_lsr_tridiagv to change the loop range for consistency      S/R seaice_lsr_tridiagv to change the loop range for consistency
286    - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v    - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
287    - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in    - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
288      S/R seaice_lsr_tridiagu/v (requires update of      S/R seaice_lsr_tridiagu/v (requires update of
289      offline_exf_seaice/input.dyn_jfnk)      offline_exf_seaice/input.dyn_jfnk)
290    
291  checkpoint65a (2014/07/27)  checkpoint65a (2014/07/27)
292  o model/src:  o model/src:
# Line 31  o model/src: Line 302  o model/src:
302    - collect T & S forcing tendency into local 2-D array (passed as argument to    - collect T & S forcing tendency into local 2-D array (passed as argument to
303      apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.      apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
304      affects results at machine truncation level (e.g., ocean: if using      affects results at machine truncation level (e.g., ocean: if using
305      SHORTWAVE_HEATING and atmos:, if using FrictionHeating or (atm_Rq<>0)      SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
306      moist correction due to vertical advection).      correction due to vertical advection).
307    - update output of experiments: fizhi-cs-32x32x40 (13 digits),    - update output of experiments: fizhi-cs-32x32x40 (13 digits),
308      global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:      global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
309      seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),      seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),

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