/[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 1.1901 by jmc, Thu Jul 25 01:12:45 2013 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
325      - clean up code_oad/ directories somewhat by moving files
326        dontCompile, dontTransform, keepOriginal to OAD_support/
327    o model/src:
328      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
329        (not currently tested): add dissipation terms before NLFS rescaling of
330        tendencies (previously done after).
331    o pkg/diagnostics:
332      - write stats-diags in ascii file with more digits (same as in monitor).
333    o pkg/down_slope:
334      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
335        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
336    o model/src:
337      - new file "apply_forcing.F" containing all the code previously in
338        external_forcing.F, but with new argument list: pass, as new argument,
339        the current level tendency array to update (instead of a direct update
340        of the common bloc array). Change the corresponding calls.
341      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
342        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
343    o pkg/seaice/seaice_lsr, a little bit of clean up
344      - rearrange some code blocks, so that now all calculations for
345        setting up the right-hand-sides done within one single block
346        (I find that easier to read and understand)
347      - rearrange freedrift-code to reduce the number of ifdefs
348      - adjust some indentations and comments
349    
350    checkpoint64z (2014/07/10)
351    o model/src and several pkgs:
352      - change argument list of all S/R called from external_forcing.F and
353        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
354        to pass, as argument, the current level tendency array to update
355        (instead of a direct update of the common bloc array).
356      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
357      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
358    o pkg/seaice/seaice_lsr.F
359      - always initialize local arrays in seaice_lsr_tridiagu/v
360      - add more local tapes to seaice_lsr_tridiagu/v
361      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
362        keep it in bi/bj loop; this seems to be essential
363      - gradients are still wrong but only by 4-7 orders of magnitude
364        instead of 15 orders of magnitude, lab_sea improves a little
365    o pkg/seaice
366      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
367        generates unnecessary code in seaice_lsr_ad
368      - add more store directives in seaice_lsr to avoid unnecessary code
369        in seaice_lsr_ad
370      - exclude some residual computations in seaice_lsr when
371        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
372        in seaice_lsr_ad
373      - add more storing, a new tape (model/src/the_main_loop.F) and
374        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
375        and klockey should be checked by a specialist)
376      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
377        and update lab_sea after previous changes in pkg/seaice below
378    o pkg/autodiff:
379      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
380        viscFacInAd : run time parameters allowing for adjoint switches
381        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
382    o pkg/ecco:
383      - introduce cost_gencost_boxmean.F that computes a box mean
384        temperature (for use in adjoint sensitivity studies).
385    o model/src/set_defaults.F : initialize viscFacAdj to 1.
386    o pkg/mom_common/mom_calc_visc.F:
387      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
388    o pkg/seaice/seaice_summary.F:
389      - statement for SEAICEadjMODE now in autodiff_readparms.F
390    o pkg/seaice:
391      - remove some store directives and add new ones in an effort to get
392        finally rid off the recomputation warnings. This is successful
393        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
394        defined (i.e. no extensive recomputation warnings left), but there
395        are still too many recomputations on the solver iteration level
396      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
397      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
398        SEAICE_SIZE.h
399      - add a store directive in S/R seaice_calc_viscosities
400    o pkg/seaice (ITD code):
401      - fix definition of Hlimit for multi-threaded case
402      - use double precision arithmetic to compute Hlimit: this affects results;
403        update output of experiment seaice_itd.
404    o replace content of verification/seaice_itd
405      - instead of a 1D column use the configuration of offline_exf_seaice
406        to test the ice thickness distribution code with ridging
407      - this is a first shot at this experiment
408      - change of some defaults of ridging parameters SEAICEhStar (from
409        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
410        and lot of new comments.
411    
412    checkpoint64y (2014/06/20)
413    o pkg/seaice/seaice_reg_ridge.F:
414      - modify the regularization of very small volumes of ice; only check
415        total volume HEFF, and do not apply correction to individual ice
416        classes because that leads to funny patterns in the heat and fw-fluxes
417        into the ocean. Adjust seaice_itd/results/output.txt
418      - replace nITD by SEAICE_multDim in loop-ranges
419    o pkg/exf:
420      - add code to process the case field period = -12. with UV interpolation.
421      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
422        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
423    o verification/global_with_exf:
424      - switch all fields period to -12. (was previously untested) in input/data.exf
425        (but keep secondary test ".yearly" unchanged); update the reference output.
426    o pkg/cal:
427      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
428    o pkg/exf:
429      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
430        to replace logical switch "exf_verbose"
431      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
432    o pkg/sbo:
433      - update from Katherine Quinn: evaluate mass directly from density and SSH
434        (budget using Finite Volume method) instead of from bottom pressure.
435      - allow testreport to collect few selected SBO output ; tested in exp.
436        global_ocean.90x40x15 (after updating the results, to include SBO output).
437      - fix some multi-threading issues (in output part).
438    o model/src & most packages:
439      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
440      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
441        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
442        "data.{pkg}" exist ; and leave the S/R (return) just after.
443      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
444        + call LAND_READPARMS from packages_readparms.F
445    o pkg/seaice:
446      - remove code that resets useThSice in S/R seaice_readparms and
447        replace it by a warning in S/R seaice_check
448      - remove parameter MULTDIM, replace with nITD and runtime
449        parameter SEAICE_multDim (still hard-wired to nITD if
450        SEAICE_ITD is defined)
451    
452    checkpoint64x (2014/05/24)
453    o verification/lab_sea:
454      - update adjoint and TLM output following changes to pkg/salt_plume
455      - un-do the update after putting back local recip_Cp in few places.
456    o pkg/salt_plume: modifications by An Nguyen:
457      - add capability to do brine rejection (salt-plume) as function of
458        volume+tracers (instead of only salinity tracer).
459      - conserve volume by exchanging volume from each kLev to above to
460        accommodate in-coming brine volume
461      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
462      - switch KPP surf buoyancy due to brine forcing to 3-d
463        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
464      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
465      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
466        in East/West Arctic.
467    o pkg/sbo:
468      - incorporate modifications from Katherine Quinn to enable the use of sbo
469        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
470        output for future testreport verification (unfinished).
471    o pkg/atm_phys:
472      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
473        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
474        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
475    o pkg/seaice
476      seaice_calc_ice_strength.F: modify expression to avoid divisions
477        (affects truncation)
478      seaice_do_ridging.F: clean up the insectarium
479      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
480      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
481      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
482      - add some debugging information and error messages (warnings)
483    o model/src: modifications relatd to atmosphere p*:
484      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
485      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
486        of vertical profile tRef in geopotential background and anomaly.
487      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
488        and pkg/atm_phys.
489      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
490        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
491    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
492    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
493        not used right now, but can be used in BGC packages to fix conservation.
494    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
495        other packages too.
496    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
497        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
498    o model/src:
499      - since we have several heat capacity (even in model/src), define "recip_Cp"
500        as local variable (no longer in common block) to avoid any confusion.
501      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
502    o pkg/exf:
503      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
504        air density as function of air Temp, Humidity and atm pressure.
505    
506    checkpoint64w (2014/05/02)
507    o verification:
508      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
509        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
510        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
511        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
512        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
513    o model/src: for atmosphere in p* coords:
514      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
515      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
516        but not yet activated.
517    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
518      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
519      - this changes the results (but not for any verification experiment, because
520        none tests this), but avoids having an extra field in the restart files
521    o pkg/seaice: remove global variable TICE (not needed)
522      - replace by TICES or local variable where necessary (cost_seaice_test,
523        seaice_diagnostics_state)
524      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
525      - use specific read/write routines for reading and writing individual leves
526        of a multilevel field
527    o pkg/ctrl & model/inc:
528      - move additional anomaly fields of control vars (related to options:
529         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
530        from DYNVARS.h into new header file: CTRL_FIELDS.h
531    o pkg/seaice: some small modifications to the ridging code
532      - make fw2ObyRidge a global variable and add the freshwater flux to
533        seaice_growth
534      - pass actual thickness from seaice_prepare_ridging, so that it is
535        computed only in one place and compute it in the same way as in
536        seaice_growth
537      - initialise more fields in seaice_do_ridging that where cause floating
538        point exceptions over land
539    o pkg/seaice: preparations for ridging code and first real ridging code
540      - move most of "PART 1" of S/R seaice_growth into a new and separate
541        S/R seaice_reg_ridge that will both regularize the state variable after
542        advection call the actual ridging routine;
543      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
544        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
545      - remove ridging code from seaice_advdiff
546      - clean up remaining part 1 of seaice_growth in an attempt to make it
547        more readable (this is probably subjective)
548      - call seaice_itd_redist once in the initialisation phase to have the initial
549        conditions in the correct category
550      - finally: add new ridging routine for ITD code
551    
552    checkpoint64v (2014/04/11)
553    o pkg/ecco:
554      - add runtime parameters mdt[start,end]date[1,2]
555      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
556    o pkg/seaice:
557      - make deltaC a global variable, so that it can be used in ridging code
558      - first step towards ridging: introduce new routines that compute
559        ice strength based on ridging parameters
560      - add diagnostic for HSNOWITD
561      - add opnWtrFrac as a global variable (required for ridging scheme)
562    o pkg/salt_plume + pkg/seaice/seaice_growth.F
563      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
564        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
565    o verification/hs94.1x64x5:
566      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
567      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
568    o autodiff:
569      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
570        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
571        For now, only in pkgs used in verification/hs94.1x64x5.
572      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
573        which are specific to TAF/TAMC).
574      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
575        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
576        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
577      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
578        building mitgcmuv_ad (make adAll).
579    o pkg/ecco:
580      - cost_gencost_seaicev4.F:
581         reformulate proxy cost as function of sst and local param SEAICE_freeze
582         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
583      - add stop statement if old names siv4-[sst,vol] are used
584      - add snapshots + cost reports for atmospheric longwave
585      - remove factor 0.1 in front of wtau[u,v]
586      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
587         ALLOW_TMI_SST_COST_CONTRIBUTION
588    o pkg/atm_phys:
589      - add some diagnostics for Short-wave and for convection S/R.
590    o pkg/seaice/seaice_growth:
591      - fix a bug in the lateral melt parameterization for SEAICE_ITD
592        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
593      - rearrange loop order for better vector code in the same code block
594      - rewrite the floeDiameter formula to have fewer divisions
595      -  (miraculously) none of this changes the results of seaice_itd
596    o pkg/smooth:
597      - move param smooth2Ddiffnbt to pkg/ecco
598    o pkg/salt_plume:
599      - salt_plume_frac.F:
600         clean up local param names
601         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
602    o pkg/rw:
603      - add RS version of S/R READ_MFLDS_LEV.
604    o pkg/streamice:
605      - fix the restart test by writing/reading pickup_streamice files.
606    o pkg/seaice:
607      - refine checks for jfnk-related parameters
608      - comment out if statement with SEAICEuseIMEX parameter as long as there
609        is no IMEX code to avoid confusion and surprises
610    
611    checkpoint64u (2014/03/07)
612    o verification/MLAdjust:
613      - rename secondary test suffix:
614         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
615         0.leithD -> AhFlxF  + switch to flux-form
616         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
617         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
618    o pkg/mom_vecinv:
619      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
620        to be before mom_calc_visc.F)
621      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
622      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
623        this is simpler for the adjoint and for diagnostics.
624    o model/src + pkg/momentum:
625      - add input files for  2-D additional Western and Southern cell-edge wall
626         (e.g., to add "thin-wall" where it is =1).
627      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
628        using 2nd hFacZ that is computed from initial (fix domain) hFac
629      - known limitations of thin wall implementation: not yet coded for sigma
630        coords; not working with CD-scheme neither.
631    o pkg/seaice:
632      - rename recently introduced parameters from (wrong name) AB to
633        BDF (backward difference time discretisation)
634      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
635    o tools/adjoint_options:
636      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
637    
638    checkpoint64t (2014/02/01)
639    o pkg/ecco
640      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
641        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
642      - replace hard-coded record number and period which only work for monthly
643        with read-in runtime param that works for other periods (month,day,year)
644    o pkg/thsice
645      - corrected store directive fixes thsice adjoint gradient checks
646    o genmake2 & testreport:
647      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
648        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
649        Update testreport accordingly. No need to set "export OPENAD=true"
650        in adjoint_options/adjoint_oad anymore (will be removed later).
651    o pkg/shelfice:
652      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
653        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
654        so that surface forcing applies to k=kSurf if using pkg/shelfice.
655    o pkg/ctrl, pkg/grdchk, pkg/ecco:
656      - Changes to make GENARR more modular (i.e. invisible if not used)
657    o model/src/temp_integrate.F and salt_integrate.F
658      - re-include store directives that were removed on Dec 27th.
659    o model/src/external_forcing_surf.F
660      - add storage directives for EmPmR and PmEpR to avoid recomputation of
661        seaice_model in the adjoint that is problematic when seaice_model is
662        turned off in the adjoint. The resolved issue dated back to July when
663        EXTERNAL_FORCING_SURF call was moved.
664        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
665    o pkg/exf/exf_check.F
666      - fix a small bug again (originally found by Wentao Liu, now found again)
667      - streamline error output
668    o pkg/streamice and aim_v23:
669      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
670        Apple's /usr/bin/cpp knows what to do:
671        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
672        Target: x86_64-apple-darwin13.0.0
673    
674    checkpoint64s (2014/01/05)
675    o tools/adjoint_options:
676      - switch to fastopt.net TAF server (instead of default fastopt.de) for
677        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
678    o model/src:
679      - remove some unnecessary TAF storage directives in forward_step.F and
680        in dynamics.F (note: not always removed by TAF, e.g., double storage
681        of kappaRU,kappaRV in former version of dynamics.F).
682    o model/src & pkg/ptracers:
683      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
684        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
685        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
686      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
687      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
688      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
689    o useSingleCpuInput separates single-CPU input from single-CPU output;
690        for now only implemented for in exf_interp_read.F
691    o verification/advect_xy:
692      - fix missing EXCH call in local version of ini_salt.F and update output.
693    o momentum diagnostics:
694      - fix which deltaT is used in Total-Tendency diagnostics.
695      - fix typo in diagnostics for momentum tendency from AB.
696    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
697        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
698    
699    checkpoint64r (2013/12/08)
700    o verification/*/results:
701      - Update reference output of experiments that were passing with just 13 digits
702         (make it easier to detect future changes in results)
703    o model/src & pkg/ptracers:
704      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
705        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
706        to inside ptracers_integrate.F ; remove ptracers_advection.F
707    o coupling interface pkgs:
708        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
709      - change the config check to test the agreement of Ocean Depth
710        with ATM land/sea mask (instead of ATM orography);
711      - send to coupler the number of coupler time-steps to do for this run:
712        this allows to check for consistency and don't need anymore to be
713        specified in parameter file "data";
714      in coupler:
715      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
716      - improve report to log-file of config setting (pass log-file unit to few S/R)
717    o pkg/compon_communic:
718      - add coupling send/receive for non-tiled integer vector;
719      - add S/R to check and stop if any proc has an error (similar to
720        eesupp/src/stop_if_error.F but single thread and across Comm_World).
721    o pkg/exch2:
722      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
723        through list of all tiles my proc owns.
724    o model/src:
725      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
726        from rTrans) to simplify dependencies (no need to store rTrans anymore in
727        calling S/R); this affects AD results at machine truncation level:
728        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
729        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
730    o tools/build_options:
731      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
732    o coupling interface pkgs:
733        [compon_communic, atm_compon_interf & ocn_compon_interf]
734      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
735        to each S/R that needs it; remove un-used variables.
736      - change component tile registration (cpl_register.F in both compon_interf
737        and mitcomponent_tile_register.F) to pass the full list of tiles
738        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
739      - with pkg/exch2: adopt the same convention used for I/O to define mapping
740        towards coupler global array (unless W2_useE2ioLayOut=F):
741         a) can now use different tiling between atm & ocn comp.
742         b) no needs to modify the run-Off map when changing tiling (was needed
743            even if using the same tiling between atm & ocn).
744         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
745            full land tiles); not yet tested.
746      - check for valid mapping from comp. tile to coupler global array
747      - improve report of tile registration results to log file.
748    o pkg/exch2:
749      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
750        tile-registration (CPL_REGISTER);
751      - activate (un-comment) definition and setting of "W2_tileIndex" list to
752        store the local bi,bj indices of each tile;
753      - also print bi,bj in local report to log file;
754      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
755        Jun 2009 modif of pkg/exch2).
756    o testing on baudelaire:
757      - run 2 tests at a time: no significant slow down (since enough cpu) and
758        get the full set of test done earlier
759      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
760    o model/src/thermodynamics.F and routines called from it:
761      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
762        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
763        velocity (outp) by adding bolus velocity.
764      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
765        mass transport from velocity + lateral grid cell area
766      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
767      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
768     in thermodynamics.F
769      - remove k from thermodynamics.F and move it to temp_integrate.F
770        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
771        loop).
772      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
773        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
774        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
775        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
776      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
777        global_ocean.90x40x15, tutorial_global_oce_biogeo and
778        tutorial_tracer_adjsens (+ TLM output).
779    o tools/OAD_support and (verification/*/) code_oad:
780      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
781        module conversion ; remove unneeded CPP_EEOPTIONS.h.
782      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
783        version (closer to model/inc/CPP_OPTIONS.h).
784    o model/src:
785      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
786        retired list of parameters (routine FREEZE has been replace by surface
787        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
788    o pkg/gmredi:
789      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
790        velocity (same scheme but affects machine truncation) for GM_AdvForm.
791      - update output of FWD experiments: front_relax.bvp,
792        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
793    
794    checkpoint64q (2013/11/17)
795    o verification:
796      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
797        tutorial_global_oce_biogeo and global_ocean.90x40x15.
798      - generate new output (growth & melt) for seaice_itd experiment after
799        updating the input pickup_seaice files (previously wrong).
800    o pkg/cost:
801      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
802        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
803        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
804          cannot be applied to var in common block).
805        o allows to get results independent of tile-per-proc setting (if using
806          slower GLOBAL_SUM_SEND_RECV option).
807      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
808        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
809        forward gradients: update output).
810      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
811        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
812    o pkg/mom_common:
813      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
814        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
815        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
816        ensure that all field value that are used are set.
817    o tutorial_deep_convection (smag3d):
818      - add missing scaling in mom_calc_smag_3d.F;
819      - set smag3D_coeff in input.smag3d such that results do not change.
820    o pkg/dic:
821      - change dic_cost.F to compute cost on each tile first and then apply
822        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
823        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
824      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
825    o eesupp/src & pkg/mdsio:
826      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
827        (from pkg/mdsio) since they are no longer used for tape IO.
828      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
829        (+ keep a copy in pkg/atm_ocn_coupler).
830    o verification/isomip:
831      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
832    o tools/build_options:
833      - optfile linux_amd64_ifort11, fast (no ieee) case:
834        to get a working restart for all experiments, add "-fp-model source"
835        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
836    
837    checkpoint64p (2013/10/20)
838    o pkg/autodiff:
839      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
840        criteria, return to simple (default) tape IO format.
841    o pkg/mdsio (+ eesupp/src):
842      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
843        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
844      - fix globalFile and singleCpuIO options using simpler global mapping.
845      - new pairs of scatter/gather vector S/R (one for each type, generated from
846        template) corresponding to simpler global mapping.
847      - adread_write.F: switch to new S/R (but leave old calls commented) and write
848        to globalFile when parameter globalFiles is set to True.
849      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
850    o pkg/autodiff:
851      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
852        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
853        missing, just add a STOP if array type do not match.
854    o pkg/exf:
855      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
856         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
857         and rename array obsSIce to exf_iceFraction.
858    o tutorial_deep_convection:
859      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
860        for now all in this exp. code dir.
861      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
862        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
863    o eesupp/src:
864      - added SINGLE_DISK_IO option because reading of parameter files on
865        very large number of processors did not work with existing set-up
866    
867    checkpoint64o (2013/09/25)
868    o pkg/atm_phys & atm_compon_interf:
869      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
870    o tools/build_options:
871      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
872        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
873        remove CPP setting (was identical to genmake2 default).
874    o pkg/gmredi & model/src: Some updating and work done on the residual model.
875      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
876      - fixed up the calculation of the eddy stress and how it is added to the
877        external forcing via taueddy_external_forcing.F
878      - at the moment, it is very experimental and only works with the variable eddy
879        diffusivity calculated in gmredi_k3d.F
880    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
881        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
882    o testreport (& tools/do_tst_2+2):
883      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
884    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
885      - remove CPP='cpp -traditional -P' (this is genmake2 default)
886      - add switch (for big setups) to use 'medium' memory-model (but leave it
887        commented out for now). Note: needed with FC 19 to compile big setups.
888    o pkg/atm_compon_interf:
889      - regroup per field origin (model & pkgs) the coupling storage routines
890         (which accumalate in time each coupling field)
891      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
892        update accordingly + simplify aim_do_physics.F
893    
894    checkpoint64n (2013/08/26)
895    o pkg/bbl:
896      - update formulation to reduce dispersion of tracer properties in bbl
897      - replaced horizontal and vertical transport parameters with velocities
898      - changes results for verification/global_with_exf.yearly
899    o verification/halfpipe_streamice:
900      - change to matrix construction; update both Fwd & AD output.
901    o verification/tutorial_tracer_adjsens:
902      - OpenAD test: switch to vector-invariant momentum since fluxform with
903        rStar causes problems with OpenAD; update output.
904    o tools:
905      - genmake2: define a common prefix for all temp-file names ; move them
906        to local /tmp disk (but would be easy to move them back);
907      - xmakedepend: apply the same switch for temp-files.
908    o pkg/offline:
909      - changes for use with rStar (NLFS): assume that we continue to provide
910        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
911        output files) and apply r* scaling at each time-step (function of the time
912        varying Eta field); use normal pickup files (needed for restart with NLFS).
913    o adjoint with OpenAD:
914      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
915        package openad.  This package has to be compiled for all runs with OpenAD
916        instead of specifying code_oad_all as a modification directory.
917      - link the fortran templates from tools/OAD_support to the build directory
918        for preprocessing to avoid conflicts between different setups compiled
919        simultaneously and simplify cleanup.
920    o pkg/exf:
921      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
922        main model or other pkgs are exchanged in EXF_MAPFIELDS).
923    o model/src:
924      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
925        (similar to do_fields_blocking_exchanges.F).
926    o tools/genmake2:
927      - remove TAF output src code just before calling staf (when not doing a fresh
928        built, will stop if things go wrong with staf).
929      - fix target "adobj" (left from TAF version-2 transition)
930    o pkg/diagnostics:
931      - add a parameter to track the status of pkg/diagnostics activation;
932        this replace/extend the use of logical param "settingDiags" (to check
933        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
934        New S/R to print error message and stop when pkgStatus is not right.
935      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
936    
937    checkpoint64m (2013/08/13)
938    o model/inc:
939      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
940        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
941    o pkg/kpp & aim_v23:
942      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
943    o pkg/seaice:
944      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
945        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
946      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
947    o eesupp/src:
948      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
949        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
950    o switch to TAF version-2:
951      - add flow directives to "freeze" naming convention for ad-routines that
952        are used in I/O routines of adjoint state and associated common blocks
953        that are used in adcommon.h (backward compatible with version-1)
954      - update all ad-optfiles (in tools/adjoint_options + few local to some
955        verification exp) to switch to latest TAF version (currently 2.5.5);
956        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
957        out except for diva).
958      - the major change with TAF version-2 is that both the differentiated
959        routines and the forward routines (new) are returned as part of the TAF
960        output source code. Update genmake2 accordingly.
961      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
962        with version-2 when compared to TLM or FWD gradient); other experiments
963        output show minor changes (machine truncation level); update the few AD &
964        TLM output with 12 matching digits only (some prior to version-2 switch).
965    
966    checkpoint64l (2013/08/05)
967    o model/src:
968      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
969      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
970        when using TAF but only if using OpenAD.
971    o pkg/mom_common+fluxform+vecinv:
972      - always set horiz. viscosity arrays to background value before calling
973        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
974        only when using variable horiz. viscosity (useVariableVisc=T);
975      - simplify mom_vecinv.F (only 1 block for momViscosity).
976    o pkg/mom_common: variable horiz. viscosity in NH code
977      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
978        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
979      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
980        useBiharmonicVisc & useVariableVisc.
981      - fix old bug (already in 1rst implementation of variable horizontal viscosity
982        in calc_gw.F, version 1.27, 2006/06/20):
983        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
984        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
985      - change background horiz viscosity in vertical momentum (gW) to always be
986        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
987        any type of variable viscosity, e.g., viscAh/4Grid)
988      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
989        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
990        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
991        default viscAh,viscA4 is zero).
992    o model/src:
993      - extend length of drC & recip_drC from Nr to Nr+1.
994  o Divided Adjoint (DIVA) with MPI:  o Divided Adjoint (DIVA) with MPI:
995    - genmake2: do not create local ./mpi_headers dir when no file to copy into.    - genmake2: do not create local ./mpi_headers dir when no file to copy into.
996    - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT    - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
Legend:
Removed from v.1.1901  
changed lines
  Added in v.1.2067
  ViewVC Help
Powered by ViewVC 1.1.22