/[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 1.1881 by m_bates, Tue Jun 18 21:30:33 2013 UTC revision 1.2061 by jahn, Fri Sep 12 17:24:38 2014 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/generic_advdiff:
8      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
9    o pkg/exf :
10      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown, xxg_precip capability
11      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
12    o pkg/ctrl :
13      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
14    o model/src/load_fields_driver.F :
15      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
16        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
17    o OpenAD verification experiments:
18      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
19        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
20        for now, only in pkgs used in OpenAD verification experiments.
21      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
22        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
23        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
24        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
25    o OpenAD verification tests:
26      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
27      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
28        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
29      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
30        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
31    o model/src & generic_advdiff:
32      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
33        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
34        dynamics requires valid tracer forcing only over tile interior but, for
35        some diagnostics, may need to extend it over 1 point in tile halo region.
36      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
37        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
38        setting in temp/salt/ptracer_integrate.F
39    o pkg/dic:
40      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
41        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
42        in gchem_forcing_sep.F
43    o pkg/autodiff & obcs:
44      - add storage of current OB values for U & V (was already done for T & S).
45    
46    checkpoint65c (2014/08/30)
47    o pkg/dic:
48      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
49        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
50        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
51    o verification:
52      - new experiment testing OBCS and DIC pkgs, using params & output from
53        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
54        passage: take OBCS from the last year of a 2 yrs simulation and initial
55        conditions from t=1.yr while keeping the same forcing.
56    o model/src:
57      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
58        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
59    o pkg/diagnostics (Stats-Diags):
60      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
61        a) refine region where stats are computed, excluding where arrhFac=0 ;
62        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
63        c) extend regional stats over the region edges (for U or V pt location).
64    o pkg/gchem:
65      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
66        pkg/dic is currently changing/updating ptracers values beyond the OB).
67    o verification (hs94):
68      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
69        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
70        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
71        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
72    o pkg/ptracers:
73      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
74        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
75      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
76        with AB-2 code (so that it get tested).
77    o model/src:
78      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
79        with AB-2 code (previously only available with AB-3 code).
80        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
81        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
82        there, by calling CYCLE_AB_TRACER).
83    o pkg/generic_advdiff:
84      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
85        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
86        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
87        S/R temp/salt/ptracers_integrate.F
88    o model/src & pkg/ptracers:
89      - remove common block variables gT,gS (in DYNVARS.h), except when
90         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
91      - remove common block variable gPtr.
92    o model/src & pkgs:
93      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
94         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
95         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
96         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
97      + change accordingly all calling S/R.
98      - use local temperature/salinity/ptracer tendency array (without bi,bj)
99        in S/R temp/salt/ptracers_integrate.F
100    o pkg/seaice:
101      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
102        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
103      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
104        in seaice_lsr
105      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
106        in s/r seaice_lsr_calc_coeffs
107    o pkg/mdsio:
108      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
109        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
110        too long (e.g., > MAX_LEN_FNAM/2 )
111    
112    checkpoint65b (2014/08/12)
113    o pkg/matrix:
114      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
115    o model/src:
116      - fix initialisation of geothermalFile; compile geothermal-flux code in
117        natl_box verification experiment.
118    o model/src & pkg/down_slope:
119      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
120      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
121        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
122        results at machine truncation level: update output of experiments
123        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
124    o pkg/diagnostics (Stats-Diags):
125      - do not cumulate the full volume when DIAGNOSTICS_FILL is
126        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
127        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
128        times (but Min,Max and StD are still wrong).
129    o model/src:
130      - add geothermal flux forcing: read in ini_forcing.F as time-constant
131        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
132    o model/src:
133      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
134        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
135        arrays are already updated while adjustments (filters, conv.adjustment) are
136        still applied later, in S/R TRACERS_CORRECTION_STEP.
137    o model/src:
138      - store in common bloc array "rhoInSitu" the virtual potential temperature
139        anomaly that is used to compute geopotential: this make the atmos code
140        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
141    o pkg/seaice/seaice_lsr.F
142      - rename integer variable ilcall to ipass (that's what it is called
143        in the residual diagnostics
144      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
145        default) for improved non-linear convergence of the first few steps
146      - adjust a few comments and add new ones to explain some of the store
147        directives
148    o pkg/generic_advdiff (& ptracers):
149      - re-work the code to check for valid advection scheme and for minimum
150        size of overlap (now stored in local common bloc in gad_advscheme.F)
151    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
152      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
153      - add an auxilliary variable "bet" and fix store directives and keys in
154        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
155        less exact gradients in my tests); but there are still
156        recomputation warning (although gradients are sort of OK), when
157        SEAICE_LSR_VECTORIZE is not defined, so this flag and
158        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
159      - update verification experiments lab_sea.
160      - change some comments in S/R seaice_calc_viscosities
161    o model/src:
162      - if staggerTimeStep=T, always apply exchange to velocity field in
163        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
164        (independent of using multi-dim advection or not); no effect on FWD run
165        but affects AD results (at machine truncation level): update output of
166        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
167        and isomip (oad: 12.d).
168    o pkg/generic_advdiff:
169      - stop if doAB_onGtGs is set to FALSE but ignored
170      - refine warning related to stability of tracer time-stepping
171        regarding internal wave dynamics.
172      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
173        on staggerTimeStep & implicitIntGravWave (will now get a warning
174        if potentially unstable).
175    o pkg/kl10:
176      - add new pkg "kl10" for mixing due to internal wave breaking, from
177        http://www.sciencedirect.com/science/article/pii/S1463500310000144
178        (contribution from Jody Klymak), tested in verification experiment
179        verification/internal_wave/input.kl10/
180    o isomip experiment:
181      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
182        (input.htd) and update the output.
183    o cd_code experiments:
184      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
185        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
186        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
187        update the corresponding output.
188    o pkg/seaice:
189      - reduce the number of include files and store directives in
190        S/R seaice_lsr_tridiagu/v
191      - change the order of loops in one case in S/R seaice_lsr_tridiagv
192        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
193        get rid off one store directive (a TAF bug?)
194      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
195        S/R seaice_lsr_tridiagv to change the loop range for consistency
196      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
197      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
198        S/R seaice_lsr_tridiagu/v (requires update of
199        offline_exf_seaice/input.dyn_jfnk)
200    
201    checkpoint65a (2014/07/27)
202    o model/src:
203      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
204        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
205        (topo in p-coords, ice-shelf in z-coords); update output of experiments
206        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
207    o model/src:
208      - collect momentum forcing tendency into local 2-D array (passed as argument
209        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
210        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
211        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
212      - collect T & S forcing tendency into local 2-D array (passed as argument to
213        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
214        affects results at machine truncation level (e.g., ocean: if using
215        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
216        correction due to vertical advection).
217      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
218        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
219        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
220        obcs_ctrl (ad & fwd grd @ 12 & 7).
221    o pkg/ptracers & diagnostics:
222      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
223        title (to avoid some unexpected truncation); sort out ptracers diags units.
224      - collect ptracer forcing tendency into local 2-D array (passed as argument
225        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
226    
227    checkpoint65 (2014/07/18)
228    o pkg/fizhi:
229      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
230        affects results at machine truncation level. Update output of experiments
231        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
232    o pkg/seaice: more clean up
233      - rename TAF common block tapes to be more consistent and remove
234        unnecessary duplicates
235      - add store directives to remove more recomputations, but use smaller
236        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
237        The idea behind this flag is to reduce the memory footprint when the
238        adjoint of the LSR is not required. As of now, defining the flag
239        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
240        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
241        For experiment offline_exf_seaice, this means on a linux box with gfortran
242        nearly a factor of 10 (but keep in mind there is mostly seaice code in
243        this experiment):
244        > size mitgcmuv_ad
245        text    data        bss     dec        hex  
246        5100659 1216  220458952  225560827  d71c8fb
247        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
248        but only a moderate increase of 36% for global_ocean.cs32x15:
249        text    data        bss     dec        hex
250        6695027 1648 1014578664 1021275339 3cdf6ccb
251        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
252      - note: there are still recomputations in global_ocean.cs32x15 and
253        offline_exf_seaice and the gradient agreement changes (gets a
254        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
255      - in general, the AD gradients still are wrong
256    o OpenAD
257      - clean up code_oad/ directories somewhat by moving files
258        dontCompile, dontTransform, keepOriginal to OAD_support/
259    o model/src:
260      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
261        (not currently tested): add dissipation terms before NLFS rescaling of
262        tendencies (previously done after).
263    o pkg/diagnostics:
264      - write stats-diags in ascii file with more digits (same as in monitor).
265    o pkg/down_slope:
266      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
267        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
268    o model/src:
269      - new file "apply_forcing.F" containing all the code previously in
270        external_forcing.F, but with new argument list: pass, as new argument,
271        the current level tendency array to update (instead of a direct update
272        of the common bloc array). Change the corresponding calls.
273      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
274        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
275    o pkg/seaice/seaice_lsr, a little bit of clean up
276      - rearrange some code blocks, so that now all calculations for
277        setting up the right-hand-sides done within one single block
278        (I find that easier to read and understand)
279      - rearrange freedrift-code to reduce the number of ifdefs
280      - adjust some indentations and comments
281    
282    checkpoint64z (2014/07/10)
283    o model/src and several pkgs:
284      - change argument list of all S/R called from external_forcing.F and
285        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
286        to pass, as argument, the current level tendency array to update
287        (instead of a direct update of the common bloc array).
288      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
289      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
290    o pkg/seaice/seaice_lsr.F
291      - always initialize local arrays in seaice_lsr_tridiagu/v
292      - add more local tapes to seaice_lsr_tridiagu/v
293      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
294        keep it in bi/bj loop; this seems to be essential
295      - gradients are still wrong but only by 4-7 orders of magnitude
296        instead of 15 orders of magnitude, lab_sea improves a little
297    o pkg/seaice
298      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
299        generates unnecessary code in seaice_lsr_ad
300      - add more store directives in seaice_lsr to avoid unnecessary code
301        in seaice_lsr_ad
302      - exclude some residual computations in seaice_lsr when
303        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
304        in seaice_lsr_ad
305      - add more storing, a new tape (model/src/the_main_loop.F) and
306        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
307        and klockey should be checked by a specialist)
308      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
309        and update lab_sea after previous changes in pkg/seaice below
310    o pkg/autodiff:
311      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
312        viscFacInAd : run time parameters allowing for adjoint switches
313        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
314    o pkg/ecco:
315      - introduce cost_gencost_boxmean.F that computes a box mean
316        temperature (for use in adjoint sensitivity studies).
317    o model/src/set_defaults.F : initialize viscFacAdj to 1.
318    o pkg/mom_common/mom_calc_visc.F:
319      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
320    o pkg/seaice/seaice_summary.F:
321      - statement for SEAICEadjMODE now in autodiff_readparms.F
322    o pkg/seaice:
323      - remove some store directives and add new ones in an effort to get
324        finally rid off the recomputation warnings. This is successful
325        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
326        defined (i.e. no extensive recomputation warnings left), but there
327        are still too many recomputations on the solver iteration level
328      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
329      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
330        SEAICE_SIZE.h
331      - add a store directive in S/R seaice_calc_viscosities
332    o pkg/seaice (ITD code):
333      - fix definition of Hlimit for multi-threaded case
334      - use double precision arithmetic to compute Hlimit: this affects results;
335        update output of experiment seaice_itd.
336    o replace content of verification/seaice_itd
337      - instead of a 1D column use the configuration of offline_exf_seaice
338        to test the ice thickness distribution code with ridging
339      - this is a first shot at this experiment
340      - change of some defaults of ridging parameters SEAICEhStar (from
341        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
342        and lot of new comments.
343    
344    checkpoint64y (2014/06/20)
345    o pkg/seaice/seaice_reg_ridge.F:
346      - modify the regularization of very small volumes of ice; only check
347        total volume HEFF, and do not apply correction to individual ice
348        classes because that leads to funny patterns in the heat and fw-fluxes
349        into the ocean. Adjust seaice_itd/results/output.txt
350      - replace nITD by SEAICE_multDim in loop-ranges
351    o pkg/exf:
352      - add code to process the case field period = -12. with UV interpolation.
353      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
354        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
355    o verification/global_with_exf:
356      - switch all fields period to -12. (was previously untested) in input/data.exf
357        (but keep secondary test ".yearly" unchanged); update the reference output.
358    o pkg/cal:
359      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
360    o pkg/exf:
361      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
362        to replace logical switch "exf_verbose"
363      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
364    o pkg/sbo:
365      - update from Katherine Quinn: evaluate mass directly from density and SSH
366        (budget using Finite Volume method) instead of from bottom pressure.
367      - allow testreport to collect few selected SBO output ; tested in exp.
368        global_ocean.90x40x15 (after updating the results, to include SBO output).
369      - fix some multi-threading issues (in output part).
370    o model/src & most packages:
371      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
372      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
373        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
374        "data.{pkg}" exist ; and leave the S/R (return) just after.
375      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
376        + call LAND_READPARMS from packages_readparms.F
377    o pkg/seaice:
378      - remove code that resets useThSice in S/R seaice_readparms and
379        replace it by a warning in S/R seaice_check
380      - remove parameter MULTDIM, replace with nITD and runtime
381        parameter SEAICE_multDim (still hard-wired to nITD if
382        SEAICE_ITD is defined)
383    
384    checkpoint64x (2014/05/24)
385    o verification/lab_sea:
386      - update adjoint and TLM output following changes to pkg/salt_plume
387      - un-do the update after putting back local recip_Cp in few places.
388    o pkg/salt_plume: modifications by An Nguyen:
389      - add capability to do brine rejection (salt-plume) as function of
390        volume+tracers (instead of only salinity tracer).
391      - conserve volume by exchanging volume from each kLev to above to
392        accommodate in-coming brine volume
393      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
394      - switch KPP surf buoyancy due to brine forcing to 3-d
395        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
396      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
397      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
398        in East/West Arctic.
399    o pkg/sbo:
400      - incorporate modifications from Katherine Quinn to enable the use of sbo
401        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
402        output for future testreport verification (unfinished).
403    o pkg/atm_phys:
404      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
405        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
406        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
407    o pkg/seaice
408      seaice_calc_ice_strength.F: modify expression to avoid divisions
409        (affects truncation)
410      seaice_do_ridging.F: clean up the insectarium
411      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
412      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
413      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
414      - add some debugging information and error messages (warnings)
415    o model/src: modifications relatd to atmosphere p*:
416      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
417      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
418        of vertical profile tRef in geopotential background and anomaly.
419      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
420        and pkg/atm_phys.
421      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
422        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
423    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
424    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
425        not used right now, but can be used in BGC packages to fix conservation.
426    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
427        other packages too.
428    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
429        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
430    o model/src:
431      - since we have several heat capacity (even in model/src), define "recip_Cp"
432        as local variable (no longer in common block) to avoid any confusion.
433      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
434    o pkg/exf:
435      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
436        air density as function of air Temp, Humidity and atm pressure.
437    
438    checkpoint64w (2014/05/02)
439    o verification:
440      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
441        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
442        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
443        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
444        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
445    o model/src: for atmosphere in p* coords:
446      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
447      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
448        but not yet activated.
449    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
450      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
451      - this changes the results (but not for any verification experiment, because
452        none tests this), but avoids having an extra field in the restart files
453    o pkg/seaice: remove global variable TICE (not needed)
454      - replace by TICES or local variable where necessary (cost_seaice_test,
455        seaice_diagnostics_state)
456      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
457      - use specific read/write routines for reading and writing individual leves
458        of a multilevel field
459    o pkg/ctrl & model/inc:
460      - move additional anomaly fields of control vars (related to options:
461         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
462        from DYNVARS.h into new header file: CTRL_FIELDS.h
463    o pkg/seaice: some small modifications to the ridging code
464      - make fw2ObyRidge a global variable and add the freshwater flux to
465        seaice_growth
466      - pass actual thickness from seaice_prepare_ridging, so that it is
467        computed only in one place and compute it in the same way as in
468        seaice_growth
469      - initialise more fields in seaice_do_ridging that where cause floating
470        point exceptions over land
471    o pkg/seaice: preparations for ridging code and first real ridging code
472      - move most of "PART 1" of S/R seaice_growth into a new and separate
473        S/R seaice_reg_ridge that will both regularize the state variable after
474        advection call the actual ridging routine;
475      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
476        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
477      - remove ridging code from seaice_advdiff
478      - clean up remaining part 1 of seaice_growth in an attempt to make it
479        more readable (this is probably subjective)
480      - call seaice_itd_redist once in the initialisation phase to have the initial
481        conditions in the correct category
482      - finally: add new ridging routine for ITD code
483    
484    checkpoint64v (2014/04/11)
485    o pkg/ecco:
486      - add runtime parameters mdt[start,end]date[1,2]
487      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
488    o pkg/seaice:
489      - make deltaC a global variable, so that it can be used in ridging code
490      - first step towards ridging: introduce new routines that compute
491        ice strength based on ridging parameters
492      - add diagnostic for HSNOWITD
493      - add opnWtrFrac as a global variable (required for ridging scheme)
494    o pkg/salt_plume + pkg/seaice/seaice_growth.F
495      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
496        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
497    o verification/hs94.1x64x5:
498      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
499      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
500    o autodiff:
501      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
502        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
503        For now, only in pkgs used in verification/hs94.1x64x5.
504      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
505        which are specific to TAF/TAMC).
506      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
507        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
508        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
509      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
510        building mitgcmuv_ad (make adAll).
511    o pkg/ecco:
512      - cost_gencost_seaicev4.F:
513         reformulate proxy cost as function of sst and local param SEAICE_freeze
514         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
515      - add stop statement if old names siv4-[sst,vol] are used
516      - add snapshots + cost reports for atmospheric longwave
517      - remove factor 0.1 in front of wtau[u,v]
518      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
519         ALLOW_TMI_SST_COST_CONTRIBUTION
520    o pkg/atm_phys:
521      - add some diagnostics for Short-wave and for convection S/R.
522    o pkg/seaice/seaice_growth:
523      - fix a bug in the lateral melt parameterization for SEAICE_ITD
524        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
525      - rearrange loop order for better vector code in the same code block
526      - rewrite the floeDiameter formula to have fewer divisions
527      -  (miraculously) none of this changes the results of seaice_itd
528    o pkg/smooth:
529      - move param smooth2Ddiffnbt to pkg/ecco
530    o pkg/salt_plume:
531      - salt_plume_frac.F:
532         clean up local param names
533         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
534    o pkg/rw:
535      - add RS version of S/R READ_MFLDS_LEV.
536    o pkg/streamice:
537      - fix the restart test by writing/reading pickup_streamice files.
538    o pkg/seaice:
539      - refine checks for jfnk-related parameters
540      - comment out if statement with SEAICEuseIMEX parameter as long as there
541        is no IMEX code to avoid confusion and surprises
542    
543    checkpoint64u (2014/03/07)
544    o verification/MLAdjust:
545      - rename secondary test suffix:
546         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
547         0.leithD -> AhFlxF  + switch to flux-form
548         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
549         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
550    o pkg/mom_vecinv:
551      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
552        to be before mom_calc_visc.F)
553      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
554      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
555        this is simpler for the adjoint and for diagnostics.
556    o model/src + pkg/momentum:
557      - add input files for  2-D additional Western and Southern cell-edge wall
558         (e.g., to add "thin-wall" where it is =1).
559      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
560        using 2nd hFacZ that is computed from initial (fix domain) hFac
561      - known limitations of thin wall implementation: not yet coded for sigma
562        coords; not working with CD-scheme neither.
563    o pkg/seaice:
564      - rename recently introduced parameters from (wrong name) AB to
565        BDF (backward difference time discretisation)
566      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
567    o tools/adjoint_options:
568      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
569    
570    checkpoint64t (2014/02/01)
571    o pkg/ecco
572      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
573        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
574      - replace hard-coded record number and period which only work for monthly
575        with read-in runtime param that works for other periods (month,day,year)
576    o pkg/thsice
577      - corrected store directive fixes thsice adjoint gradient checks
578    o genmake2 & testreport:
579      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
580        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
581        Update testreport accordingly. No need to set "export OPENAD=true"
582        in adjoint_options/adjoint_oad anymore (will be removed later).
583    o pkg/shelfice:
584      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
585        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
586        so that surface forcing applies to k=kSurf if using pkg/shelfice.
587    o pkg/ctrl, pkg/grdchk, pkg/ecco:
588      - Changes to make GENARR more modular (i.e. invisible if not used)
589    o model/src/temp_integrate.F and salt_integrate.F
590      - re-include store directives that were removed on Dec 27th.
591    o model/src/external_forcing_surf.F
592      - add storage directives for EmPmR and PmEpR to avoid recomputation of
593        seaice_model in the adjoint that is problematic when seaice_model is
594        turned off in the adjoint. The resolved issue dated back to July when
595        EXTERNAL_FORCING_SURF call was moved.
596        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
597    o pkg/exf/exf_check.F
598      - fix a small bug again (originally found by Wentao Liu, now found again)
599      - streamline error output
600    o pkg/streamice and aim_v23:
601      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
602        Apple's /usr/bin/cpp knows what to do:
603        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
604        Target: x86_64-apple-darwin13.0.0
605    
606    checkpoint64s (2014/01/05)
607    o tools/adjoint_options:
608      - switch to fastopt.net TAF server (instead of default fastopt.de) for
609        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
610    o model/src:
611      - remove some unnecessary TAF storage directives in forward_step.F and
612        in dynamics.F (note: not always removed by TAF, e.g., double storage
613        of kappaRU,kappaRV in former version of dynamics.F).
614    o model/src & pkg/ptracers:
615      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
616        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
617        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
618      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
619      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
620      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
621    o useSingleCpuInput separates single-CPU input from single-CPU output;
622        for now only implemented for in exf_interp_read.F
623    o verification/advect_xy:
624      - fix missing EXCH call in local version of ini_salt.F and update output.
625    o momentum diagnostics:
626      - fix which deltaT is used in Total-Tendency diagnostics.
627      - fix typo in diagnostics for momentum tendency from AB.
628    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
629        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
630    
631    checkpoint64r (2013/12/08)
632    o verification/*/results:
633      - Update reference output of experiments that were passing with just 13 digits
634         (make it easier to detect future changes in results)
635    o model/src & pkg/ptracers:
636      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
637        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
638        to inside ptracers_integrate.F ; remove ptracers_advection.F
639    o coupling interface pkgs:
640        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
641      - change the config check to test the agreement of Ocean Depth
642        with ATM land/sea mask (instead of ATM orography);
643      - send to coupler the number of coupler time-steps to do for this run:
644        this allows to check for consistency and don't need anymore to be
645        specified in parameter file "data";
646      in coupler:
647      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
648      - improve report to log-file of config setting (pass log-file unit to few S/R)
649    o pkg/compon_communic:
650      - add coupling send/receive for non-tiled integer vector;
651      - add S/R to check and stop if any proc has an error (similar to
652        eesupp/src/stop_if_error.F but single thread and across Comm_World).
653    o pkg/exch2:
654      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
655        through list of all tiles my proc owns.
656    o model/src:
657      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
658        from rTrans) to simplify dependencies (no need to store rTrans anymore in
659        calling S/R); this affects AD results at machine truncation level:
660        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
661        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
662    o tools/build_options:
663      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
664    o coupling interface pkgs:
665        [compon_communic, atm_compon_interf & ocn_compon_interf]
666      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
667        to each S/R that needs it; remove un-used variables.
668      - change component tile registration (cpl_register.F in both compon_interf
669        and mitcomponent_tile_register.F) to pass the full list of tiles
670        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
671      - with pkg/exch2: adopt the same convention used for I/O to define mapping
672        towards coupler global array (unless W2_useE2ioLayOut=F):
673         a) can now use different tiling between atm & ocn comp.
674         b) no needs to modify the run-Off map when changing tiling (was needed
675            even if using the same tiling between atm & ocn).
676         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
677            full land tiles); not yet tested.
678      - check for valid mapping from comp. tile to coupler global array
679      - improve report of tile registration results to log file.
680    o pkg/exch2:
681      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
682        tile-registration (CPL_REGISTER);
683      - activate (un-comment) definition and setting of "W2_tileIndex" list to
684        store the local bi,bj indices of each tile;
685      - also print bi,bj in local report to log file;
686      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
687        Jun 2009 modif of pkg/exch2).
688    o testing on baudelaire:
689      - run 2 tests at a time: no significant slow down (since enough cpu) and
690        get the full set of test done earlier
691      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
692    o model/src/thermodynamics.F and routines called from it:
693      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
694        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
695        velocity (outp) by adding bolus velocity.
696      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
697        mass transport from velocity + lateral grid cell area
698      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
699      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
700     in thermodynamics.F
701      - remove k from thermodynamics.F and move it to temp_integrate.F
702        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
703        loop).
704      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
705        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
706        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
707        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
708      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
709        global_ocean.90x40x15, tutorial_global_oce_biogeo and
710        tutorial_tracer_adjsens (+ TLM output).
711    o tools/OAD_support and (verification/*/) code_oad:
712      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
713        module conversion ; remove unneeded CPP_EEOPTIONS.h.
714      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
715        version (closer to model/inc/CPP_OPTIONS.h).
716    o model/src:
717      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
718        retired list of parameters (routine FREEZE has been replace by surface
719        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
720    o pkg/gmredi:
721      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
722        velocity (same scheme but affects machine truncation) for GM_AdvForm.
723      - update output of FWD experiments: front_relax.bvp,
724        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
725    
726    checkpoint64q (2013/11/17)
727    o verification:
728      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
729        tutorial_global_oce_biogeo and global_ocean.90x40x15.
730      - generate new output (growth & melt) for seaice_itd experiment after
731        updating the input pickup_seaice files (previously wrong).
732    o pkg/cost:
733      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
734        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
735        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
736          cannot be applied to var in common block).
737        o allows to get results independent of tile-per-proc setting (if using
738          slower GLOBAL_SUM_SEND_RECV option).
739      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
740        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
741        forward gradients: update output).
742      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
743        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
744    o pkg/mom_common:
745      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
746        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
747        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
748        ensure that all field value that are used are set.
749    o tutorial_deep_convection (smag3d):
750      - add missing scaling in mom_calc_smag_3d.F;
751      - set smag3D_coeff in input.smag3d such that results do not change.
752    o pkg/dic:
753      - change dic_cost.F to compute cost on each tile first and then apply
754        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
755        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
756      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
757    o eesupp/src & pkg/mdsio:
758      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
759        (from pkg/mdsio) since they are no longer used for tape IO.
760      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
761        (+ keep a copy in pkg/atm_ocn_coupler).
762    o verification/isomip:
763      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
764    o tools/build_options:
765      - optfile linux_amd64_ifort11, fast (no ieee) case:
766        to get a working restart for all experiments, add "-fp-model source"
767        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
768    
769    checkpoint64p (2013/10/20)
770    o pkg/autodiff:
771      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
772        criteria, return to simple (default) tape IO format.
773    o pkg/mdsio (+ eesupp/src):
774      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
775        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
776      - fix globalFile and singleCpuIO options using simpler global mapping.
777      - new pairs of scatter/gather vector S/R (one for each type, generated from
778        template) corresponding to simpler global mapping.
779      - adread_write.F: switch to new S/R (but leave old calls commented) and write
780        to globalFile when parameter globalFiles is set to True.
781      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
782    o pkg/autodiff:
783      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
784        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
785        missing, just add a STOP if array type do not match.
786    o pkg/exf:
787      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
788         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
789         and rename array obsSIce to exf_iceFraction.
790    o tutorial_deep_convection:
791      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
792        for now all in this exp. code dir.
793      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
794        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
795    o eesupp/src:
796      - added SINGLE_DISK_IO option because reading of parameter files on
797        very large number of processors did not work with existing set-up
798    
799    checkpoint64o (2013/09/25)
800    o pkg/atm_phys & atm_compon_interf:
801      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
802    o tools/build_options:
803      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
804        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
805        remove CPP setting (was identical to genmake2 default).
806    o pkg/gmredi & model/src: Some updating and work done on the residual model.
807      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
808      - fixed up the calculation of the eddy stress and how it is added to the
809        external forcing via taueddy_external_forcing.F
810      - at the moment, it is very experimental and only works with the variable eddy
811        diffusivity calculated in gmredi_k3d.F
812    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
813        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
814    o testreport (& tools/do_tst_2+2):
815      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
816    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
817      - remove CPP='cpp -traditional -P' (this is genmake2 default)
818      - add switch (for big setups) to use 'medium' memory-model (but leave it
819        commented out for now). Note: needed with FC 19 to compile big setups.
820    o pkg/atm_compon_interf:
821      - regroup per field origin (model & pkgs) the coupling storage routines
822         (which accumalate in time each coupling field)
823      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
824        update accordingly + simplify aim_do_physics.F
825    
826    checkpoint64n (2013/08/26)
827    o pkg/bbl:
828      - update formulation to reduce dispersion of tracer properties in bbl
829      - replaced horizontal and vertical transport parameters with velocities
830      - changes results for verification/global_with_exf.yearly
831    o verification/halfpipe_streamice:
832      - change to matrix construction; update both Fwd & AD output.
833    o verification/tutorial_tracer_adjsens:
834      - OpenAD test: switch to vector-invariant momentum since fluxform with
835        rStar causes problems with OpenAD; update output.
836    o tools:
837      - genmake2: define a common prefix for all temp-file names ; move them
838        to local /tmp disk (but would be easy to move them back);
839      - xmakedepend: apply the same switch for temp-files.
840    o pkg/offline:
841      - changes for use with rStar (NLFS): assume that we continue to provide
842        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
843        output files) and apply r* scaling at each time-step (function of the time
844        varying Eta field); use normal pickup files (needed for restart with NLFS).
845    o adjoint with OpenAD:
846      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
847        package openad.  This package has to be compiled for all runs with OpenAD
848        instead of specifying code_oad_all as a modification directory.
849      - link the fortran templates from tools/OAD_support to the build directory
850        for preprocessing to avoid conflicts between different setups compiled
851        simultaneously and simplify cleanup.
852    o pkg/exf:
853      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
854        main model or other pkgs are exchanged in EXF_MAPFIELDS).
855    o model/src:
856      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
857        (similar to do_fields_blocking_exchanges.F).
858    o tools/genmake2:
859      - remove TAF output src code just before calling staf (when not doing a fresh
860        built, will stop if things go wrong with staf).
861      - fix target "adobj" (left from TAF version-2 transition)
862    o pkg/diagnostics:
863      - add a parameter to track the status of pkg/diagnostics activation;
864        this replace/extend the use of logical param "settingDiags" (to check
865        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
866        New S/R to print error message and stop when pkgStatus is not right.
867      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
868    
869    checkpoint64m (2013/08/13)
870    o model/inc:
871      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
872        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
873    o pkg/kpp & aim_v23:
874      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
875    o pkg/seaice:
876      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
877        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
878      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
879    o eesupp/src:
880      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
881        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
882    o switch to TAF version-2:
883      - add flow directives to "freeze" naming convention for ad-routines that
884        are used in I/O routines of adjoint state and associated common blocks
885        that are used in adcommon.h (backward compatible with version-1)
886      - update all ad-optfiles (in tools/adjoint_options + few local to some
887        verification exp) to switch to latest TAF version (currently 2.5.5);
888        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
889        out except for diva).
890      - the major change with TAF version-2 is that both the differentiated
891        routines and the forward routines (new) are returned as part of the TAF
892        output source code. Update genmake2 accordingly.
893      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
894        with version-2 when compared to TLM or FWD gradient); other experiments
895        output show minor changes (machine truncation level); update the few AD &
896        TLM output with 12 matching digits only (some prior to version-2 switch).
897    
898    checkpoint64l (2013/08/05)
899    o model/src:
900      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
901      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
902        when using TAF but only if using OpenAD.
903    o pkg/mom_common+fluxform+vecinv:
904      - always set horiz. viscosity arrays to background value before calling
905        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
906        only when using variable horiz. viscosity (useVariableVisc=T);
907      - simplify mom_vecinv.F (only 1 block for momViscosity).
908    o pkg/mom_common: variable horiz. viscosity in NH code
909      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
910        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
911      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
912        useBiharmonicVisc & useVariableVisc.
913      - fix old bug (already in 1rst implementation of variable horizontal viscosity
914        in calc_gw.F, version 1.27, 2006/06/20):
915        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
916        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
917      - change background horiz viscosity in vertical momentum (gW) to always be
918        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
919        any type of variable viscosity, e.g., viscAh/4Grid)
920      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
921        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
922        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
923        default viscAh,viscA4 is zero).
924    o model/src:
925      - extend length of drC & recip_drC from Nr to Nr+1.
926    o Divided Adjoint (DIVA) with MPI:
927      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
928      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
929        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
930    
931    checkpoint64k (2013/07/23)
932    o tools/OAD_support:
933      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
934        and remove it from genmake2.
935    o tools/build_options:
936      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
937        MPI_HEADER_FILES list (let genmake2 find the missing headers)
938    o verification/halfpipe_streamice:
939      - change to driving stress formulation; update both Fwd & AD output.
940    o tools/genmake2 and Divided Adjoint with MPI:
941      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
942      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
943      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
944        Makefile, which is set by genmake2, and check which mpi-headers are needed.
945        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
946      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
947    o testreport:
948      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
949        perform additional runs (number of additional runs is "add_DIVA_runs" taken
950        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
951    o verification/lab_sea (AD test):
952      - change to test Divided Adjoint Run in this set-up (both standard AD test
953        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
954    o pkg atm_ & ocn_compon_interf:
955      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
956        staggerTimeStep implementation) and disable (retired) corresponding
957        parameter.
958    o pkg/offline:
959      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
960      - add S/R OFFLINE_CHECK to print offline parameter summary
961        and stop if loading a file that is not used;
962      - enable to calculate GMRedi tensor, KPP mixing and convective index
963        when the corresponding file(s) is/are not specified (but pkg is used).
964      - comment out resetting of monitorFreq (to endTime) since it still useful
965        for monitoring CFL numbers and checking offline fields.
966    o OpenAD:
967      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
968        smaller standard output) and generate new (smaller) output (on baudelaire
969        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
970    o model/src:
971      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
972        (where external_forcing_adjust was called) and change list of arguments;
973      - merge external_forcing_adjust.F into external_forcing_surf.F
974      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
975        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
976        previously in file "balance_relax.F", now removed); remove corresponding
977        arrays in FFIELDS.h.
978      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
979        a hack for getting back surfaceForcingS (loaded from file) when using
980        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
981      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
982        (was getting only 11 digits for AD-grad, due to different truncation
983         error in AD code).
984    
985    checkpoint64j (2013/07/04)
986    o pkg/offline:
987      - to enable the use of other features with pkg offline (e.g., obcs),
988        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
989      - comment out "allowFreezing" (now active) in 2 offline testing exp.
990    o pkg/exf ALLOW_RUNOFTEMP
991      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
992      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
993      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
994    o pkg/atm_phys:
995      - allows to add some damping on uVel,vVel (strength only function of k).
996    o verification, ad-tests:
997      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
998        global_ocean_ebm and offline_exf_seaice.thsice.
999    o verification/halfpipe_streamice:
1000      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
1001        flux input boundary conditions to be ignored; a fix for this bug changed
1002        verification results for forward test.
1003      - add adjoint test.
1004    o pkg/ptracers:
1005      - allow to restart without SOM pickup (resetting SOM to zero).
1006    o pkg/gmredi:
1007      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
1008      - It uses mixing length theory and suppression by steering level effects to
1009        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
1010        to JPO, for more details).
1011      - It also uses the diffusivity to calculate an eddy induced streamfunction
1012        based on a PV closure (rather than a buoyancy closure as in GM).
1013      - New files added to pkg/gmredi:
1014        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
1015          induced overturning streamfunction (called from gmredi_calc_tensor)
1016        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
1017          for use in gmredi_k3d
1018        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
1019          the eddy diffusivity
1020    
1021  checkpoint64i (2013/06/18)  checkpoint64i (2013/06/18)
1022  o pkg/cheapaml:  o pkg/cheapaml:
# Line 40  o pkg/cfc: Line 1053  o pkg/cfc:
1053      atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.      atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
1054    - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf    - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
1055    - new routine to print summary of CFC params and check for consistency.    - new routine to print summary of CFC params and check for consistency.
1056    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
1057      similar to thsice_advdiff.
1058      Note that for the B-grid case the routine parameters uc/vc are overwritten.
1059  o pkg/cfc:  o pkg/cfc:
1060    - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);    - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
1061      update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.      update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
Legend:
Removed from v.1.1881  
changed lines
  Added in v.1.2061
  ViewVC Help
Powered by ViewVC 1.1.22