/[MITgcm]/MITgcm/doc/tag-index
ViewVC logotype

Diff of /MITgcm/doc/tag-index

Parent Directory Parent Directory | Revision Log Revision Log | View Revision Graph Revision Graph | View Patch Patch

revision 1.1973 by atn, Sat Apr 5 22:51:52 2014 UTC revision 1.2088 by gforget, Thu Nov 6 20:38:45 2014 UTC
# Line 3  $Name$ Line 3  $Name$
3    
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6  <<<<<<< tag-index  
7  o pkg/salt_plume:  o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
8    - salt_plume_frac.F:  o pkg/dic: add modifications from Hajoon:
9       clean up local param names    - add iron sedimentation flux function of the flux of PO4 out of bottom layer
10       reformulate (1-frac) to frac; original 1-frac was based on swfrac code    - light attenuation: add self-shading effect by climatological Chlorophyll
11        (read from file).
12    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
13        compiles when SEAICE_ALLOW_DYNAMICS is undefined
14    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
15        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
16        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
17        approach where CPP_OPTIONS.h includes an omnipotent
18        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
19    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
20        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
21    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
22        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
23        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
24    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
25      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
26      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
27      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
28      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
29    o pkg/ctrl,ecco,exf :
30      - remove variables associated with NON-generic costs,
31        unless ECCO_CTRL_DEPRECATED is defined.
32      - remove NON-generic NON-obcs controls,
33        unless ECCO_CTRL_DEPRECATED is defined.
34    o pkg/ctrl : added ctrl_local_params.h
35    o pkg/ecco : added ecco_local_params.h
36    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
37        experiments, which will progressively be removed once the
38        experiments are revised to use only generic controls/costs.
39    
40    checkpoint65f (2014/10/13)
41    o pkg/ctrl, ecco, seaice : minor changes in headers
42    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
43        cost function and control capabilities added since checkpoint65c.
44    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
45    o pkg/ecco: increase modularity and improve logic
46      - ecco_toolbox.F (new) : basic operations that are often used,
47        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
48        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
49      - cost_gencal.F (new) : determine filnames and records.
50      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
51      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
52        and exploit the above functions leading to more compact code.
53      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
54      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
55        using_ers, using_gfo, using_mdt is now only defined within gencost)
56    o pkg/ecco: extend generic cost capabilities
57      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
58        capabilities via gencost_preproc (+ _c,_i,_r related params),
59        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
60        gencost_outputlevel arguments to cost_generic
61      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
62        and active_read, making room for gencost_preproc to take effect.
63        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
64      - pkg/ecco/cost_generic.F :
65        compute and store misfit maks*(model-data) in localdif that is
66        then used in cost and for output, output misfit if outlev.GT.0
67      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
68        rather gencost_barfile for deciding whether to write barfile
69      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
70      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
71        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
72      - pkg/ecco/ecco_summary.F : report gencost variables
73      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
74    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
75    o pkg/ecco: internal re-organization
76      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
77        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
78        mv relevant variables definition from ecco_cost.h to ecco.h,
79        make sure gencost routines only include ecco.h)
80      - throughout : add missing CCP switches, rm unused variables,
81        and rm un-necessary CPP switches
82      - throughout gencost routines : replace modelstartdate with
83        gencost_startdate when needed
84      - cost_bp_read.F : use arguments, instead of common blocs
85        so that it can be used also by (new) cost_gencost_bpv4.F
86      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
87      - ecco_phys.F : compute etanFull
88      - ecco_readparms.F : rename using_topex as using_tpj, add
89        bpv4-grace to gencost list, initialize added parameters
90      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
91    
92    checkpoint65e (2014/09/28)
93    o pkg/obcs:
94      - replaced the just-added CPP options with run-time variables
95        (see pkg/obcs/OBCS_PARAMS.h for details)
96    o pkg/obcs:
97      - add additional CPP options for sponge boundary layers
98        (see pkg/obcs/OBCS_OPTIONS.h for details)
99    o pkg/atm_phys:
100      - implement simple (obliquity only, assuming circular planet orbit)
101        seasonal cycle for incoming insolation ; used when run-time parameter
102        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
103    o pkg/exf, pkg/ecco, pkg/ctrl:
104      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
105      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
106      - implement gentim2d for xx_tauu, xx_tauv
107    o pkg/ctrl, pkg/ecco :
108      - fix and complement the generic controls implementation
109    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
110        pkg/shelfice/shelfice_thermodynamics.F,
111        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
112        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
113      - add weight in CTRL_GET_GEN calls
114    o pkg/ctrl :
115      - ctrl_get_gen.F : add weight as input parameter, and apply
116        it directly rather than using smooth_correl2Dw (to be retired).
117      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
118    o pkg/ctrl :
119      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
120        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
121      - re-activate ctrl_summary (call in ctrl_init.F)
122    o pkg/ctrl/ctrl_cost_gen.F :
123      - fix CCP brackets, remove un-necessary myiter, mytime
124    o pkg/ecco, pkg/ctrl :
125      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
126      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
127      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
128      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
129    
130    checkpoint65d (2014/09/15)
131    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
132      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
133        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
134    o pkg/ctrl/ctrl_map_ini_genarr.F :
135      - remove compilation failure
136      - replace hard coded example
137      - use ctrl_map_ini_gen2D, 3D
138    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
139      - on/off switch based upon xx_genarr2d_weight,3d
140    o src/packages_init_variables.F :
141      - regroup pkg/estimation calls
142      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
143        (moved to ctrl_init_variables)
144    o cost/cost_init_varia.F :
145      - remove ecco_cost_init_varia
146        (moved to ecco_init_varia)
147    o ctrl/ctrl_init_variables.F :
148      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
149      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
150    o ctrl/ctrl_map_ini.F :
151      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
152        (moved to ctrl_init_variables)
153    o ctrl/ctrl_map_ini_ecco.F :
154      - remove ECCO_PHYS (mv to ecco_init_varia)
155      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
156    o ecco/ecco_ad_diff.list :
157      - add ecco_init_varia.f
158    o ecco/ecco_init_varia.F
159      - new routine
160    o pkg/streamice:
161      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
162        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
163      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
164    o pkg/generic_advdiff:
165      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
166    o pkg/exf:
167      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
168         xxg_precip capability
169      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
170    o pkg/ctrl:
171      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
172    o model/src/load_fields_driver.F :
173      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
174        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
175    o OpenAD verification experiments:
176      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
177        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
178        for now, only in pkgs used in OpenAD verification experiments.
179      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
180        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
181        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
182        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
183    o OpenAD verification tests:
184      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
185      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
186        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
187      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
188        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
189    o model/src & generic_advdiff:
190      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
191        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
192        dynamics requires valid tracer forcing only over tile interior but, for
193        some diagnostics, may need to extend it over 1 point in tile halo region.
194      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
195        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
196        setting in temp/salt/ptracer_integrate.F
197    o pkg/dic:
198      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
199        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
200        in gchem_forcing_sep.F
201    o pkg/autodiff & obcs:
202      - add storage of current OB values for U & V (was already done for T & S).
203    
204    checkpoint65c (2014/08/30)
205    o pkg/dic:
206      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
207        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
208        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
209    o verification:
210      - new experiment testing OBCS and DIC pkgs, using params & output from
211        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
212        passage: take OBCS from the last year of a 2 yrs simulation and initial
213        conditions from t=1.yr while keeping the same forcing.
214    o model/src:
215      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
216        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
217    o pkg/diagnostics (Stats-Diags):
218      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
219        a) refine region where stats are computed, excluding where arrhFac=0 ;
220        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
221        c) extend regional stats over the region edges (for U or V pt location).
222    o pkg/gchem:
223      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
224        pkg/dic is currently changing/updating ptracers values beyond the OB).
225    o verification (hs94):
226      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
227        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
228        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
229        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
230    o pkg/ptracers:
231      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
232        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
233      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
234        with AB-2 code (so that it get tested).
235    o model/src:
236      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
237        with AB-2 code (previously only available with AB-3 code).
238        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
239        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
240        there, by calling CYCLE_AB_TRACER).
241    o pkg/generic_advdiff:
242      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
243        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
244        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
245        S/R temp/salt/ptracers_integrate.F
246    o model/src & pkg/ptracers:
247      - remove common block variables gT,gS (in DYNVARS.h), except when
248         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
249      - remove common block variable gPtr.
250    o model/src & pkgs:
251      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
252         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
253         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
254         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
255      + change accordingly all calling S/R.
256      - use local temperature/salinity/ptracer tendency array (without bi,bj)
257        in S/R temp/salt/ptracers_integrate.F
258    o pkg/seaice:
259      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
260        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
261      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
262        in seaice_lsr
263      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
264        in s/r seaice_lsr_calc_coeffs
265    o pkg/mdsio:
266      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
267        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
268        too long (e.g., > MAX_LEN_FNAM/2 )
269    
270    checkpoint65b (2014/08/12)
271    o pkg/matrix:
272      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
273    o model/src:
274      - fix initialisation of geothermalFile; compile geothermal-flux code in
275        natl_box verification experiment.
276    o model/src & pkg/down_slope:
277      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
278      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
279        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
280        results at machine truncation level: update output of experiments
281        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
282    o pkg/diagnostics (Stats-Diags):
283      - do not cumulate the full volume when DIAGNOSTICS_FILL is
284        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
285        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
286        times (but Min,Max and StD are still wrong).
287    o model/src:
288      - add geothermal flux forcing: read in ini_forcing.F as time-constant
289        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
290    o model/src:
291      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
292        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
293        arrays are already updated while adjustments (filters, conv.adjustment) are
294        still applied later, in S/R TRACERS_CORRECTION_STEP.
295    o model/src:
296      - store in common bloc array "rhoInSitu" the virtual potential temperature
297        anomaly that is used to compute geopotential: this make the atmos code
298        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
299    o pkg/seaice/seaice_lsr.F
300      - rename integer variable ilcall to ipass (that's what it is called
301        in the residual diagnostics
302      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
303        default) for improved non-linear convergence of the first few steps
304      - adjust a few comments and add new ones to explain some of the store
305        directives
306    o pkg/generic_advdiff (& ptracers):
307      - re-work the code to check for valid advection scheme and for minimum
308        size of overlap (now stored in local common bloc in gad_advscheme.F)
309    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
310      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
311      - add an auxilliary variable "bet" and fix store directives and keys in
312        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
313        less exact gradients in my tests); but there are still
314        recomputation warning (although gradients are sort of OK), when
315        SEAICE_LSR_VECTORIZE is not defined, so this flag and
316        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
317      - update verification experiments lab_sea.
318      - change some comments in S/R seaice_calc_viscosities
319    o model/src:
320      - if staggerTimeStep=T, always apply exchange to velocity field in
321        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
322        (independent of using multi-dim advection or not); no effect on FWD run
323        but affects AD results (at machine truncation level): update output of
324        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
325        and isomip (oad: 12.d).
326    o pkg/generic_advdiff:
327      - stop if doAB_onGtGs is set to FALSE but ignored
328      - refine warning related to stability of tracer time-stepping
329        regarding internal wave dynamics.
330      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
331        on staggerTimeStep & implicitIntGravWave (will now get a warning
332        if potentially unstable).
333    o pkg/kl10:
334      - add new pkg "kl10" for mixing due to internal wave breaking, from
335        http://www.sciencedirect.com/science/article/pii/S1463500310000144
336        (contribution from Jody Klymak), tested in verification experiment
337        verification/internal_wave/input.kl10/
338    o isomip experiment:
339      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
340        (input.htd) and update the output.
341    o cd_code experiments:
342      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
343        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
344        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
345        update the corresponding output.
346    o pkg/seaice:
347      - reduce the number of include files and store directives in
348        S/R seaice_lsr_tridiagu/v
349      - change the order of loops in one case in S/R seaice_lsr_tridiagv
350        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
351        get rid off one store directive (a TAF bug?)
352      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
353        S/R seaice_lsr_tridiagv to change the loop range for consistency
354      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
355      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
356        S/R seaice_lsr_tridiagu/v (requires update of
357        offline_exf_seaice/input.dyn_jfnk)
358    
359    checkpoint65a (2014/07/27)
360    o model/src:
361      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
362        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
363        (topo in p-coords, ice-shelf in z-coords); update output of experiments
364        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
365    o model/src:
366      - collect momentum forcing tendency into local 2-D array (passed as argument
367        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
368        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
369        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
370      - collect T & S forcing tendency into local 2-D array (passed as argument to
371        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
372        affects results at machine truncation level (e.g., ocean: if using
373        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
374        correction due to vertical advection).
375      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
376        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
377        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
378        obcs_ctrl (ad & fwd grd @ 12 & 7).
379    o pkg/ptracers & diagnostics:
380      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
381        title (to avoid some unexpected truncation); sort out ptracers diags units.
382      - collect ptracer forcing tendency into local 2-D array (passed as argument
383        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
384    
385    checkpoint65 (2014/07/18)
386    o pkg/fizhi:
387      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
388        affects results at machine truncation level. Update output of experiments
389        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
390    o pkg/seaice: more clean up
391      - rename TAF common block tapes to be more consistent and remove
392        unnecessary duplicates
393      - add store directives to remove more recomputations, but use smaller
394        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
395        The idea behind this flag is to reduce the memory footprint when the
396        adjoint of the LSR is not required. As of now, defining the flag
397        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
398        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
399        For experiment offline_exf_seaice, this means on a linux box with gfortran
400        nearly a factor of 10 (but keep in mind there is mostly seaice code in
401        this experiment):
402        > size mitgcmuv_ad
403        text    data        bss     dec        hex  
404        5100659 1216  220458952  225560827  d71c8fb
405        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
406        but only a moderate increase of 36% for global_ocean.cs32x15:
407        text    data        bss     dec        hex
408        6695027 1648 1014578664 1021275339 3cdf6ccb
409        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
410      - note: there are still recomputations in global_ocean.cs32x15 and
411        offline_exf_seaice and the gradient agreement changes (gets a
412        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
413      - in general, the AD gradients still are wrong
414    o OpenAD
415      - clean up code_oad/ directories somewhat by moving files
416        dontCompile, dontTransform, keepOriginal to OAD_support/
417    o model/src:
418      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
419        (not currently tested): add dissipation terms before NLFS rescaling of
420        tendencies (previously done after).
421    o pkg/diagnostics:
422      - write stats-diags in ascii file with more digits (same as in monitor).
423    o pkg/down_slope:
424      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
425        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
426    o model/src:
427      - new file "apply_forcing.F" containing all the code previously in
428        external_forcing.F, but with new argument list: pass, as new argument,
429        the current level tendency array to update (instead of a direct update
430        of the common bloc array). Change the corresponding calls.
431      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
432        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
433    o pkg/seaice/seaice_lsr, a little bit of clean up
434      - rearrange some code blocks, so that now all calculations for
435        setting up the right-hand-sides done within one single block
436        (I find that easier to read and understand)
437      - rearrange freedrift-code to reduce the number of ifdefs
438      - adjust some indentations and comments
439    
440    checkpoint64z (2014/07/10)
441    o model/src and several pkgs:
442      - change argument list of all S/R called from external_forcing.F and
443        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
444        to pass, as argument, the current level tendency array to update
445        (instead of a direct update of the common bloc array).
446      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
447      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
448    o pkg/seaice/seaice_lsr.F
449      - always initialize local arrays in seaice_lsr_tridiagu/v
450      - add more local tapes to seaice_lsr_tridiagu/v
451      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
452        keep it in bi/bj loop; this seems to be essential
453      - gradients are still wrong but only by 4-7 orders of magnitude
454        instead of 15 orders of magnitude, lab_sea improves a little
455    o pkg/seaice
456      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
457        generates unnecessary code in seaice_lsr_ad
458      - add more store directives in seaice_lsr to avoid unnecessary code
459        in seaice_lsr_ad
460      - exclude some residual computations in seaice_lsr when
461        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
462        in seaice_lsr_ad
463      - add more storing, a new tape (model/src/the_main_loop.F) and
464        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
465        and klockey should be checked by a specialist)
466      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
467        and update lab_sea after previous changes in pkg/seaice below
468    o pkg/autodiff:
469      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
470        viscFacInAd : run time parameters allowing for adjoint switches
471        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
472  o pkg/ecco:  o pkg/ecco:
473    - cost_gencost_seaicev4.F:    - introduce cost_gencost_boxmean.F that computes a box mean
474       reformulate proxy cost as function of sst and local param SEAICE_freeze      temperature (for use in adjoint sensitivity studies).
475       change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]  o model/src/set_defaults.F : initialize viscFacAdj to 1.
476    - add stop statement if old names siv4-[sst,vol] are used  o pkg/mom_common/mom_calc_visc.F:
477    - add snapshots + cost reports for atmospheric longwave    - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
478    - remove factor 0.1 in front of wtau[u,v]  o pkg/seaice/seaice_summary.F:
479    - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with    - statement for SEAICEadjMODE now in autodiff_readparms.F
480       ALLOW_TMI_SST_COST_CONTRIBUTION  o pkg/seaice:
481  o pkg/smooth:    - remove some store directives and add new ones in an effort to get
482    - move param smooth2Ddiffnbt to pkg/ecco      finally rid off the recomputation warnings. This is successful
483  =======      when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
484        defined (i.e. no extensive recomputation warnings left), but there
485        are still too many recomputations on the solver iteration level
486      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
487      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
488        SEAICE_SIZE.h
489      - add a store directive in S/R seaice_calc_viscosities
490    o pkg/seaice (ITD code):
491      - fix definition of Hlimit for multi-threaded case
492      - use double precision arithmetic to compute Hlimit: this affects results;
493        update output of experiment seaice_itd.
494    o replace content of verification/seaice_itd
495      - instead of a 1D column use the configuration of offline_exf_seaice
496        to test the ice thickness distribution code with ridging
497      - this is a first shot at this experiment
498      - change of some defaults of ridging parameters SEAICEhStar (from
499        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
500        and lot of new comments.
501    
502    checkpoint64y (2014/06/20)
503    o pkg/seaice/seaice_reg_ridge.F:
504      - modify the regularization of very small volumes of ice; only check
505        total volume HEFF, and do not apply correction to individual ice
506        classes because that leads to funny patterns in the heat and fw-fluxes
507        into the ocean. Adjust seaice_itd/results/output.txt
508      - replace nITD by SEAICE_multDim in loop-ranges
509    o pkg/exf:
510      - add code to process the case field period = -12. with UV interpolation.
511      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
512        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
513    o verification/global_with_exf:
514      - switch all fields period to -12. (was previously untested) in input/data.exf
515        (but keep secondary test ".yearly" unchanged); update the reference output.
516    o pkg/cal:
517      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
518    o pkg/exf:
519      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
520        to replace logical switch "exf_verbose"
521      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
522    o pkg/sbo:
523      - update from Katherine Quinn: evaluate mass directly from density and SSH
524        (budget using Finite Volume method) instead of from bottom pressure.
525      - allow testreport to collect few selected SBO output ; tested in exp.
526        global_ocean.90x40x15 (after updating the results, to include SBO output).
527      - fix some multi-threading issues (in output part).
528    o model/src & most packages:
529      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
530      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
531        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
532        "data.{pkg}" exist ; and leave the S/R (return) just after.
533      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
534        + call LAND_READPARMS from packages_readparms.F
535    o pkg/seaice:
536      - remove code that resets useThSice in S/R seaice_readparms and
537        replace it by a warning in S/R seaice_check
538      - remove parameter MULTDIM, replace with nITD and runtime
539        parameter SEAICE_multDim (still hard-wired to nITD if
540        SEAICE_ITD is defined)
541    
542    checkpoint64x (2014/05/24)
543    o verification/lab_sea:
544      - update adjoint and TLM output following changes to pkg/salt_plume
545      - un-do the update after putting back local recip_Cp in few places.
546    o pkg/salt_plume: modifications by An Nguyen:
547      - add capability to do brine rejection (salt-plume) as function of
548        volume+tracers (instead of only salinity tracer).
549      - conserve volume by exchanging volume from each kLev to above to
550        accommodate in-coming brine volume
551      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
552      - switch KPP surf buoyancy due to brine forcing to 3-d
553        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
554      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
555      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
556        in East/West Arctic.
557    o pkg/sbo:
558      - incorporate modifications from Katherine Quinn to enable the use of sbo
559        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
560        output for future testreport verification (unfinished).
561    o pkg/atm_phys:
562      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
563        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
564        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
565    o pkg/seaice
566      seaice_calc_ice_strength.F: modify expression to avoid divisions
567        (affects truncation)
568      seaice_do_ridging.F: clean up the insectarium
569      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
570      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
571      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
572      - add some debugging information and error messages (warnings)
573    o model/src: modifications relatd to atmosphere p*:
574      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
575      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
576        of vertical profile tRef in geopotential background and anomaly.
577      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
578        and pkg/atm_phys.
579      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
580        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
581    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
582    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
583        not used right now, but can be used in BGC packages to fix conservation.
584    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
585        other packages too.
586    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
587        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
588    o model/src:
589      - since we have several heat capacity (even in model/src), define "recip_Cp"
590        as local variable (no longer in common block) to avoid any confusion.
591      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
592    o pkg/exf:
593      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
594        air density as function of air Temp, Humidity and atm pressure.
595    
596    checkpoint64w (2014/05/02)
597    o verification:
598      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
599        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
600        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
601        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
602        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
603    o model/src: for atmosphere in p* coords:
604      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
605      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
606        but not yet activated.
607    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
608      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
609      - this changes the results (but not for any verification experiment, because
610        none tests this), but avoids having an extra field in the restart files
611    o pkg/seaice: remove global variable TICE (not needed)
612      - replace by TICES or local variable where necessary (cost_seaice_test,
613        seaice_diagnostics_state)
614      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
615      - use specific read/write routines for reading and writing individual leves
616        of a multilevel field
617    o pkg/ctrl & model/inc:
618      - move additional anomaly fields of control vars (related to options:
619         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
620        from DYNVARS.h into new header file: CTRL_FIELDS.h
621    o pkg/seaice: some small modifications to the ridging code
622      - make fw2ObyRidge a global variable and add the freshwater flux to
623        seaice_growth
624      - pass actual thickness from seaice_prepare_ridging, so that it is
625        computed only in one place and compute it in the same way as in
626        seaice_growth
627      - initialise more fields in seaice_do_ridging that where cause floating
628        point exceptions over land
629    o pkg/seaice: preparations for ridging code and first real ridging code
630      - move most of "PART 1" of S/R seaice_growth into a new and separate
631        S/R seaice_reg_ridge that will both regularize the state variable after
632        advection call the actual ridging routine;
633      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
634        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
635      - remove ridging code from seaice_advdiff
636      - clean up remaining part 1 of seaice_growth in an attempt to make it
637        more readable (this is probably subjective)
638      - call seaice_itd_redist once in the initialisation phase to have the initial
639        conditions in the correct category
640      - finally: add new ridging routine for ITD code
641    
642    checkpoint64v (2014/04/11)
643    o pkg/ecco:
644      - add runtime parameters mdt[start,end]date[1,2]
645      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
646    o pkg/seaice:
647      - make deltaC a global variable, so that it can be used in ridging code
648      - first step towards ridging: introduce new routines that compute
649        ice strength based on ridging parameters
650      - add diagnostic for HSNOWITD
651      - add opnWtrFrac as a global variable (required for ridging scheme)
652    o pkg/salt_plume + pkg/seaice/seaice_growth.F
653      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
654        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
655    o verification/hs94.1x64x5:
656      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
657      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
658  o autodiff:  o autodiff:
659    - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,    - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
660      and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)      and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
661      For now, only in pkgs used in verification/hs94.1x64x5.      For now, only in pkgs used in verification/hs94.1x64x5.
662    - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage    - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
663      which are specific to TAF/TAMC).      which are specific to TAF/TAMC).
664    - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:    - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
665      since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad      since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
666      is compiled), this simplifies/reduces which *_OPTIONS.h file to include.      is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
667    - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when    - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
668      building mitgcmuv_ad (make adAll).      building mitgcmuv_ad (make adAll).
669  o pkg/atm_phys:  o pkg/ecco:
670      - cost_gencost_seaicev4.F:
671         reformulate proxy cost as function of sst and local param SEAICE_freeze
672         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
673      - add stop statement if old names siv4-[sst,vol] are used
674      - add snapshots + cost reports for atmospheric longwave
675      - remove factor 0.1 in front of wtau[u,v]
676      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
677         ALLOW_TMI_SST_COST_CONTRIBUTION
678    o pkg/atm_phys:
679    - add some diagnostics for Short-wave and for convection S/R.    - add some diagnostics for Short-wave and for convection S/R.
680  o pkg/seaice/seaice_growth:  o pkg/seaice/seaice_growth:
681    - fix a bug in the lateral melt parameterization for SEAICE_ITD    - fix a bug in the lateral melt parameterization for SEAICE_ITD
682      in seaice_growth; tempFrz needs to be computed inside the i/j-loop      in seaice_growth; tempFrz needs to be computed inside the i/j-loop
683    - rearrange loop order for better vector code in the same code block    - rearrange loop order for better vector code in the same code block
684    - rewrite the floeDiameter formula to have fewer divisions    - rewrite the floeDiameter formula to have fewer divisions
685    -  (miraculously) none of this changes the results of seaice_itd    -  (miraculously) none of this changes the results of seaice_itd
686  >>>>>>> 1.1972  o pkg/smooth:
687      - move param smooth2Ddiffnbt to pkg/ecco
688    o pkg/salt_plume:
689      - salt_plume_frac.F:
690         clean up local param names
691         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
692  o pkg/rw:  o pkg/rw:
693    - add RS version of S/R READ_MFLDS_LEV.    - add RS version of S/R READ_MFLDS_LEV.
694  o pkg/streamice:  o pkg/streamice:
Legend:
Removed from v.1.1973  
changed lines
  Added in v.1.2088
  ViewVC Help
Powered by ViewVC 1.1.22