/[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 1.1942 by jmc, Tue Nov 19 22:16:45 2013 UTC revision 1.2116 by jmc, Wed Jan 21 19:37:42 2015 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o model/src:
8      - change units of frictionHeating field from W to W/m^2
9      - fix bug in frictional heating from stratospheric drag in
10        S/R ATM_PHYS_TENDENCY_APPLY_V
11    o model/src & gmredi K3D:
12      - add frictionHeating field to pickup-files (for synchronous time-stepping)
13      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
14      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
15        and name in pickup file).
16      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
17    o model/src:
18      - move (from ini_forcing.F) initialisation of all arrays in header file
19        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
20        (since Nov 2012) with option selectAddFluid=1.
21    o pkg/shelfice:
22      - change units (+ document) of newly added field "shelfIceMassDynTendency"
23      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
24    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
25    o pkg/seaice: two new runtime parameters:
26      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
27        long overdue
28      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
29        parameterization of tensil stress for fast ice (does not do anything yet)
30    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
31        for LSR: move checking overlaps out of JFNK-if-block
32    o pkg/atm_phys:
33      - move copy of grid and dynamical fields out of atm_phys_driver.F into
34        new S/R ATM_PHYS_DYN2PHYS.
35      - fix level height for Linear Free-Surf case (to be consistent with
36        fixed-in-time pressure levels).
37    o pkg/mom_common (bottomdrag):
38      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
39        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
40        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
41    o pkg/shelfice (u/v_drag):
42      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
43      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
44        (now similar to shelfice_u_drag.F)
45      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
46        from mom_vecinv.F (similar to mom_fluxform calls).
47    o pkg/mom_common (bottomdrag):
48      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
49      - add options for alternative discretisation of velocity norm in quadratic
50        bottom drag: averaging of grid-cell-center KE to U.point and V.point
51        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
52        improves when averaging only the other component (e.g. vVel for U bottom
53        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
54      - add options (bottomVisc_pCell) to account for partial-cell in bottom
55        friction (no-slip BC) thus getting the true distance from the bottom;
56        off by default since this also reduces model stability (explicit bottom
57        friction). Changes produce different machine truncation with linear-drag
58        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
59        front_relax (bvp & mxl, 10 & 11 digits).
60    o model/src & mom pkgs:
61      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
62        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
63      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
64        just copy level Nr value to level Nr+1.
65    o doc:
66      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
67    o pkg/streamice:
68      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
69        SHELFICE.h: move array shelficemass to init_varia, initialise
70        from array shelficemassinit, which is set in init_fixed and
71        has option to be set from file; introduce array
72        shelficeMassDynTend array, set thru file in init_fixed
73      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
74        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
75        pkg/streamice
76      - shelfice_thermodynamics.F: call shelfice_step_icemass if
77        SHELFICEMassStepping = .true.
78      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
79    
80    checkpoint65h (2014/12/17)
81    o verification/global_ocean.90x40x15, global_ocean_ebm:
82      - update to generic controls.
83    o pkg/ctrl:
84      - ctrl_map_ini_genarr.F: test for igen>0
85      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
86      - move gentim2d part of ctrl_map_ini_genarr.F to
87        new separate routine : ctrl_map_ini_gentim2d.F
88      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
89        add time variable weights and cyclic controls (time mean,
90        seasonal cycle, etc) capabilities to gentim2d
91    o pkg/ecco:
92      - move reading of error, conversion to weights from
93        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
94    o global_oce_llc90, cs32:
95      - activte sbo.
96      - CTRL_SIZE.h : add maxCtrlProc.
97      - activate the new genctrl capabilities.
98      - update following reorganization of global_oce_input_fields.tar.gz  
99    o pkg/ctrl/ctrl_ad_diff.list:
100      - add missing ctrl_init_rec.f
101    o tools/OAD_support/keepOriginal:
102      - add ctrl_init_rec.F
103    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
104      - avoid recomputations of xx_gentim2d_dummy.
105    o momentum diagnostics:
106      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
107        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
108    o pkg/seaice/seaice_lsr.F:
109      - fix computation of BU/BV, make sure they are non-zero, only necessary
110        for cubed sphere exchanges and SEAICE_OLx/y>0.
111        This makes calling s/r fill_cs_corner_rl obsolete (removed).
112    o verification/global_ocean.cs32x15/input.seaice
113      - add test for strong implicit coupling and restricted addtive Schwarz
114        methods for LSR
115      - update results/output.seaice.txt
116    o verification/tutorial_global_oce_biogeo:
117      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
118        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
119        update output_adm,_oadm,_tlm.txt
120    o pkg/dic:
121      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
122      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
123        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
124    o verification/tutorial_global_oce_biogeo:
125      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
126        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
127        update output_adm,_oadm,_tlm.txt
128    o eesupp/src:
129      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
130        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
131    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
132      LSR (following Hutchings et al. 2004)
133      - introduce zetaZ as a global variable (requires adjustments in
134        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
135        in seaice_calc_viscosities.F
136      - new flag SEAICEuseStrImpCpl (default off)
137      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
138        momentum equations
139      - JFNK-solver (preconditioner) adjusted to allow using this method
140        (where it does not have any positive effect)
141    o pkg/seaice
142      - add overlap for restrictive additive Schwartz method also to LSR, but
143        turn it off by default (because it only seems to work for non-cubed
144        sphere/llc topologies)
145    o pkg/autodiff
146      - add extra exchanges in addummy_in_steppging also for mnc output
147    o pkg/seaice:
148      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
149        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
150    o pkg/obcs:
151      - add option to specify domain-connected piece Id along OB though files
152        (for now, only used to diagnose PhiVel; default =1 -> global correction)
153      - modify obcs_diag_balance.F to process each connected-part separately;
154        exclude OB where Id = 0 but keep the full divergence there (-> constant
155        Psi along this portion of OB and all inflow derived from grad(Phi))
156      - add example of OB-conect files in verification/so_box_biogeo/input.
157    o pkg/diagnostics:
158      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
159      a) use non zero matrix element across OB and solve for Phi 1 grid point
160         outside OB (i.e, where tracer OBCS are applied).
161      b) global imbalance of inFlow/outFlow across OB: instead of modifying
162         velocity across OB, spread it uniformly along the OB in the RHS.
163    
164    checkpoint65g (2014/11/19)
165    o pkg/diagnostcis:
166      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
167    o pkg/my82,pp81,kl10:
168      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
169        field diffKr as background diffusivity to set minimum diffusivity value.
170    o pkg/seaice:
171      - add new parameter SEAICEuseEVPrev (for revisited EVP by
172        Bouillon et al 2013)
173      - add SEAICE_evpAlpha/Beta to namelist
174      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
175        involve trivial re-ordering of divisions/multiplications that should not
176        have any effects, but ... they do change the results of lab_sea.hb87 so
177        that only 2 digits of agreement remain, in line with the general
178        instability/fragility of the evp-code. For now, I do not care and just
179        update the verification experiment
180    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
181      - remove xx_genarr2d_numsmooth etc
182      - use xx_genarr2d_preproc etc instead
183      - carry out smooth_correl2D at initialization stage rather than during
184        time stepping.
185      - get smoothOpNb from xx_gentim2d_preproc
186    o global_oce_cs32 :
187      - add test of generic ecco capabilities.
188    o pkg/exf/exf_getsurfacefluxes.F :
189      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
190    o pkg/ctrl,ecco :
191      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
192        is defined.
193    o pkg/seaice: add diagnostics for Delta (deformation parameter)
194    o model/src:
195      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
196        diffusivity (background) is specified but ignored.
197    o verification:
198      - in testreport, convert hostname to lower case for default output dir name
199    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
200    o pkg/dic: add modifications from Hajoon:
201      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
202      - light attenuation: add self-shading effect by climatological Chlorophyll
203        (read from file).
204    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
205        compiles when SEAICE_ALLOW_DYNAMICS is undefined
206    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
207        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
208        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
209        approach where CPP_OPTIONS.h includes an omnipotent
210        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
211    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
212        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
213    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
214        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
215        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
216    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
217      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
218      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
219      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
220      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
221    o pkg/ctrl,ecco,exf :
222      - remove variables associated with NON-generic costs,
223        unless ECCO_CTRL_DEPRECATED is defined.
224      - remove NON-generic NON-obcs controls,
225        unless ECCO_CTRL_DEPRECATED is defined.
226    o pkg/ctrl : added ctrl_local_params.h
227    o pkg/ecco : added ecco_local_params.h
228    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
229        experiments, which will progressively be removed once the
230        experiments are revised to use only generic controls/costs.
231    
232    checkpoint65f (2014/10/13)
233    o pkg/ctrl, ecco, seaice : minor changes in headers
234    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
235        cost function and control capabilities added since checkpoint65c.
236    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
237    o pkg/ecco: increase modularity and improve logic
238      - ecco_toolbox.F (new) : basic operations that are often used,
239        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
240        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
241      - cost_gencal.F (new) : determine filnames and records.
242      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
243      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
244        and exploit the above functions leading to more compact code.
245      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
246      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
247        using_ers, using_gfo, using_mdt is now only defined within gencost)
248    o pkg/ecco: extend generic cost capabilities
249      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
250        capabilities via gencost_preproc (+ _c,_i,_r related params),
251        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
252        gencost_outputlevel arguments to cost_generic
253      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
254        and active_read, making room for gencost_preproc to take effect.
255        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
256      - pkg/ecco/cost_generic.F :
257        compute and store misfit maks*(model-data) in localdif that is
258        then used in cost and for output, output misfit if outlev.GT.0
259      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
260        rather gencost_barfile for deciding whether to write barfile
261      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
262      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
263        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
264      - pkg/ecco/ecco_summary.F : report gencost variables
265      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
266    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
267    o pkg/ecco: internal re-organization
268      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
269        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
270        mv relevant variables definition from ecco_cost.h to ecco.h,
271        make sure gencost routines only include ecco.h)
272      - throughout : add missing CCP switches, rm unused variables,
273        and rm un-necessary CPP switches
274      - throughout gencost routines : replace modelstartdate with
275        gencost_startdate when needed
276      - cost_bp_read.F : use arguments, instead of common blocs
277        so that it can be used also by (new) cost_gencost_bpv4.F
278      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
279      - ecco_phys.F : compute etanFull
280      - ecco_readparms.F : rename using_topex as using_tpj, add
281        bpv4-grace to gencost list, initialize added parameters
282      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
283    
284    checkpoint65e (2014/09/28)
285    o pkg/obcs:
286      - replaced the just-added CPP options with run-time variables
287        (see pkg/obcs/OBCS_PARAMS.h for details)
288    o pkg/obcs:
289      - add additional CPP options for sponge boundary layers
290        (see pkg/obcs/OBCS_OPTIONS.h for details)
291    o pkg/atm_phys:
292      - implement simple (obliquity only, assuming circular planet orbit)
293        seasonal cycle for incoming insolation ; used when run-time parameter
294        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
295    o pkg/exf, pkg/ecco, pkg/ctrl:
296      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
297      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
298      - implement gentim2d for xx_tauu, xx_tauv
299    o pkg/ctrl, pkg/ecco :
300      - fix and complement the generic controls implementation
301    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
302        pkg/shelfice/shelfice_thermodynamics.F,
303        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
304        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
305      - add weight in CTRL_GET_GEN calls
306    o pkg/ctrl :
307      - ctrl_get_gen.F : add weight as input parameter, and apply
308        it directly rather than using smooth_correl2Dw (to be retired).
309      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
310    o pkg/ctrl :
311      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
312        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
313      - re-activate ctrl_summary (call in ctrl_init.F)
314    o pkg/ctrl/ctrl_cost_gen.F :
315      - fix CCP brackets, remove un-necessary myiter, mytime
316    o pkg/ecco, pkg/ctrl :
317      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
318      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
319      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
320      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
321    
322    checkpoint65d (2014/09/15)
323    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
324      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
325        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
326    o pkg/ctrl/ctrl_map_ini_genarr.F :
327      - remove compilation failure
328      - replace hard coded example
329      - use ctrl_map_ini_gen2D, 3D
330    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
331      - on/off switch based upon xx_genarr2d_weight,3d
332    o src/packages_init_variables.F :
333      - regroup pkg/estimation calls
334      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
335        (moved to ctrl_init_variables)
336    o cost/cost_init_varia.F :
337      - remove ecco_cost_init_varia
338        (moved to ecco_init_varia)
339    o ctrl/ctrl_init_variables.F :
340      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
341      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
342    o ctrl/ctrl_map_ini.F :
343      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
344        (moved to ctrl_init_variables)
345    o ctrl/ctrl_map_ini_ecco.F :
346      - remove ECCO_PHYS (mv to ecco_init_varia)
347      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
348    o ecco/ecco_ad_diff.list :
349      - add ecco_init_varia.f
350    o ecco/ecco_init_varia.F
351      - new routine
352    o pkg/streamice:
353      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
354        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
355      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
356    o pkg/generic_advdiff:
357      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
358    o pkg/exf:
359      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
360         xxg_precip capability
361      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
362    o pkg/ctrl:
363      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
364    o model/src/load_fields_driver.F :
365      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
366        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
367    o OpenAD verification experiments:
368      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
369        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
370        for now, only in pkgs used in OpenAD verification experiments.
371      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
372        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
373        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
374        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
375    o OpenAD verification tests:
376      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
377      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
378        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
379      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
380        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
381    o model/src & generic_advdiff:
382      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
383        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
384        dynamics requires valid tracer forcing only over tile interior but, for
385        some diagnostics, may need to extend it over 1 point in tile halo region.
386      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
387        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
388        setting in temp/salt/ptracer_integrate.F
389    o pkg/dic:
390      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
391        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
392        in gchem_forcing_sep.F
393    o pkg/autodiff & obcs:
394      - add storage of current OB values for U & V (was already done for T & S).
395    
396    checkpoint65c (2014/08/30)
397    o pkg/dic:
398      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
399        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
400        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
401    o verification:
402      - new experiment testing OBCS and DIC pkgs, using params & output from
403        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
404        passage: take OBCS from the last year of a 2 yrs simulation and initial
405        conditions from t=1.yr while keeping the same forcing.
406    o model/src:
407      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
408        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
409    o pkg/diagnostics (Stats-Diags):
410      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
411        a) refine region where stats are computed, excluding where arrhFac=0 ;
412        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
413        c) extend regional stats over the region edges (for U or V pt location).
414    o pkg/gchem:
415      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
416        pkg/dic is currently changing/updating ptracers values beyond the OB).
417    o verification (hs94):
418      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
419        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
420        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
421        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
422    o pkg/ptracers:
423      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
424        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
425      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
426        with AB-2 code (so that it get tested).
427    o model/src:
428      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
429        with AB-2 code (previously only available with AB-3 code).
430        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
431        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
432        there, by calling CYCLE_AB_TRACER).
433    o pkg/generic_advdiff:
434      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
435        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
436        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
437        S/R temp/salt/ptracers_integrate.F
438    o model/src & pkg/ptracers:
439      - remove common block variables gT,gS (in DYNVARS.h), except when
440         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
441      - remove common block variable gPtr.
442    o model/src & pkgs:
443      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
444         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
445         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
446         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
447      + change accordingly all calling S/R.
448      - use local temperature/salinity/ptracer tendency array (without bi,bj)
449        in S/R temp/salt/ptracers_integrate.F
450    o pkg/seaice:
451      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
452        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
453      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
454        in seaice_lsr
455      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
456        in s/r seaice_lsr_calc_coeffs
457    o pkg/mdsio:
458      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
459        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
460        too long (e.g., > MAX_LEN_FNAM/2 )
461    
462    checkpoint65b (2014/08/12)
463    o pkg/matrix:
464      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
465    o model/src:
466      - fix initialisation of geothermalFile; compile geothermal-flux code in
467        natl_box verification experiment.
468    o model/src & pkg/down_slope:
469      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
470      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
471        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
472        results at machine truncation level: update output of experiments
473        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
474    o pkg/diagnostics (Stats-Diags):
475      - do not cumulate the full volume when DIAGNOSTICS_FILL is
476        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
477        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
478        times (but Min,Max and StD are still wrong).
479    o model/src:
480      - add geothermal flux forcing: read in ini_forcing.F as time-constant
481        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
482    o model/src:
483      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
484        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
485        arrays are already updated while adjustments (filters, conv.adjustment) are
486        still applied later, in S/R TRACERS_CORRECTION_STEP.
487    o model/src:
488      - store in common bloc array "rhoInSitu" the virtual potential temperature
489        anomaly that is used to compute geopotential: this make the atmos code
490        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
491    o pkg/seaice/seaice_lsr.F
492      - rename integer variable ilcall to ipass (that's what it is called
493        in the residual diagnostics
494      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
495        default) for improved non-linear convergence of the first few steps
496      - adjust a few comments and add new ones to explain some of the store
497        directives
498    o pkg/generic_advdiff (& ptracers):
499      - re-work the code to check for valid advection scheme and for minimum
500        size of overlap (now stored in local common bloc in gad_advscheme.F)
501    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
502      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
503      - add an auxilliary variable "bet" and fix store directives and keys in
504        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
505        less exact gradients in my tests); but there are still
506        recomputation warning (although gradients are sort of OK), when
507        SEAICE_LSR_VECTORIZE is not defined, so this flag and
508        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
509      - update verification experiments lab_sea.
510      - change some comments in S/R seaice_calc_viscosities
511    o model/src:
512      - if staggerTimeStep=T, always apply exchange to velocity field in
513        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
514        (independent of using multi-dim advection or not); no effect on FWD run
515        but affects AD results (at machine truncation level): update output of
516        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
517        and isomip (oad: 12.d).
518    o pkg/generic_advdiff:
519      - stop if doAB_onGtGs is set to FALSE but ignored
520      - refine warning related to stability of tracer time-stepping
521        regarding internal wave dynamics.
522      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
523        on staggerTimeStep & implicitIntGravWave (will now get a warning
524        if potentially unstable).
525    o pkg/kl10:
526      - add new pkg "kl10" for mixing due to internal wave breaking, from
527        http://www.sciencedirect.com/science/article/pii/S1463500310000144
528        (contribution from Jody Klymak), tested in verification experiment
529        verification/internal_wave/input.kl10/
530    o isomip experiment:
531      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
532        (input.htd) and update the output.
533    o cd_code experiments:
534      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
535        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
536        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
537        update the corresponding output.
538    o pkg/seaice:
539      - reduce the number of include files and store directives in
540        S/R seaice_lsr_tridiagu/v
541      - change the order of loops in one case in S/R seaice_lsr_tridiagv
542        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
543        get rid off one store directive (a TAF bug?)
544      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
545        S/R seaice_lsr_tridiagv to change the loop range for consistency
546      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
547      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
548        S/R seaice_lsr_tridiagu/v (requires update of
549        offline_exf_seaice/input.dyn_jfnk)
550    
551    checkpoint65a (2014/07/27)
552    o model/src:
553      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
554        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
555        (topo in p-coords, ice-shelf in z-coords); update output of experiments
556        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
557    o model/src:
558      - collect momentum forcing tendency into local 2-D array (passed as argument
559        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
560        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
561        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
562      - collect T & S forcing tendency into local 2-D array (passed as argument to
563        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
564        affects results at machine truncation level (e.g., ocean: if using
565        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
566        correction due to vertical advection).
567      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
568        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
569        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
570        obcs_ctrl (ad & fwd grd @ 12 & 7).
571    o pkg/ptracers & diagnostics:
572      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
573        title (to avoid some unexpected truncation); sort out ptracers diags units.
574      - collect ptracer forcing tendency into local 2-D array (passed as argument
575        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
576    
577    checkpoint65 (2014/07/18)
578    o pkg/fizhi:
579      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
580        affects results at machine truncation level. Update output of experiments
581        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
582    o pkg/seaice: more clean up
583      - rename TAF common block tapes to be more consistent and remove
584        unnecessary duplicates
585      - add store directives to remove more recomputations, but use smaller
586        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
587        The idea behind this flag is to reduce the memory footprint when the
588        adjoint of the LSR is not required. As of now, defining the flag
589        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
590        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
591        For experiment offline_exf_seaice, this means on a linux box with gfortran
592        nearly a factor of 10 (but keep in mind there is mostly seaice code in
593        this experiment):
594        > size mitgcmuv_ad
595        text    data        bss     dec        hex
596        5100659 1216  220458952  225560827  d71c8fb
597        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
598        but only a moderate increase of 36% for global_ocean.cs32x15:
599        text    data        bss     dec        hex
600        6695027 1648 1014578664 1021275339 3cdf6ccb
601        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
602      - note: there are still recomputations in global_ocean.cs32x15 and
603        offline_exf_seaice and the gradient agreement changes (gets a
604        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
605      - in general, the AD gradients still are wrong
606    o OpenAD
607      - clean up code_oad/ directories somewhat by moving files
608        dontCompile, dontTransform, keepOriginal to OAD_support/
609    o model/src:
610      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
611        (not currently tested): add dissipation terms before NLFS rescaling of
612        tendencies (previously done after).
613    o pkg/diagnostics:
614      - write stats-diags in ascii file with more digits (same as in monitor).
615    o pkg/down_slope:
616      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
617        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
618    o model/src:
619      - new file "apply_forcing.F" containing all the code previously in
620        external_forcing.F, but with new argument list: pass, as new argument,
621        the current level tendency array to update (instead of a direct update
622        of the common bloc array). Change the corresponding calls.
623      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
624        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
625    o pkg/seaice/seaice_lsr, a little bit of clean up
626      - rearrange some code blocks, so that now all calculations for
627        setting up the right-hand-sides done within one single block
628        (I find that easier to read and understand)
629      - rearrange freedrift-code to reduce the number of ifdefs
630      - adjust some indentations and comments
631    
632    checkpoint64z (2014/07/10)
633    o model/src and several pkgs:
634      - change argument list of all S/R called from external_forcing.F and
635        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
636        to pass, as argument, the current level tendency array to update
637        (instead of a direct update of the common bloc array).
638      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
639      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
640    o pkg/seaice/seaice_lsr.F
641      - always initialize local arrays in seaice_lsr_tridiagu/v
642      - add more local tapes to seaice_lsr_tridiagu/v
643      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
644        keep it in bi/bj loop; this seems to be essential
645      - gradients are still wrong but only by 4-7 orders of magnitude
646        instead of 15 orders of magnitude, lab_sea improves a little
647    o pkg/seaice
648      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
649        generates unnecessary code in seaice_lsr_ad
650      - add more store directives in seaice_lsr to avoid unnecessary code
651        in seaice_lsr_ad
652      - exclude some residual computations in seaice_lsr when
653        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
654        in seaice_lsr_ad
655      - add more storing, a new tape (model/src/the_main_loop.F) and
656        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
657        and klockey should be checked by a specialist)
658      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
659        and update lab_sea after previous changes in pkg/seaice below
660    o pkg/autodiff:
661      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
662        viscFacInAd : run time parameters allowing for adjoint switches
663        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
664    o pkg/ecco:
665      - introduce cost_gencost_boxmean.F that computes a box mean
666        temperature (for use in adjoint sensitivity studies).
667    o model/src/set_defaults.F : initialize viscFacAdj to 1.
668    o pkg/mom_common/mom_calc_visc.F:
669      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
670    o pkg/seaice/seaice_summary.F:
671      - statement for SEAICEadjMODE now in autodiff_readparms.F
672    o pkg/seaice:
673      - remove some store directives and add new ones in an effort to get
674        finally rid off the recomputation warnings. This is successful
675        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
676        defined (i.e. no extensive recomputation warnings left), but there
677        are still too many recomputations on the solver iteration level
678      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
679      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
680        SEAICE_SIZE.h
681      - add a store directive in S/R seaice_calc_viscosities
682    o pkg/seaice (ITD code):
683      - fix definition of Hlimit for multi-threaded case
684      - use double precision arithmetic to compute Hlimit: this affects results;
685        update output of experiment seaice_itd.
686    o replace content of verification/seaice_itd
687      - instead of a 1D column use the configuration of offline_exf_seaice
688        to test the ice thickness distribution code with ridging
689      - this is a first shot at this experiment
690      - change of some defaults of ridging parameters SEAICEhStar (from
691        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
692        and lot of new comments.
693    
694    checkpoint64y (2014/06/20)
695    o pkg/seaice/seaice_reg_ridge.F:
696      - modify the regularization of very small volumes of ice; only check
697        total volume HEFF, and do not apply correction to individual ice
698        classes because that leads to funny patterns in the heat and fw-fluxes
699        into the ocean. Adjust seaice_itd/results/output.txt
700      - replace nITD by SEAICE_multDim in loop-ranges
701    o pkg/exf:
702      - add code to process the case field period = -12. with UV interpolation.
703      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
704        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
705    o verification/global_with_exf:
706      - switch all fields period to -12. (was previously untested) in input/data.exf
707        (but keep secondary test ".yearly" unchanged); update the reference output.
708    o pkg/cal:
709      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
710    o pkg/exf:
711      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
712        to replace logical switch "exf_verbose"
713      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
714    o pkg/sbo:
715      - update from Katherine Quinn: evaluate mass directly from density and SSH
716        (budget using Finite Volume method) instead of from bottom pressure.
717      - allow testreport to collect few selected SBO output ; tested in exp.
718        global_ocean.90x40x15 (after updating the results, to include SBO output).
719      - fix some multi-threading issues (in output part).
720    o model/src & most packages:
721      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
722      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
723        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
724        "data.{pkg}" exist ; and leave the S/R (return) just after.
725      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
726        + call LAND_READPARMS from packages_readparms.F
727    o pkg/seaice:
728      - remove code that resets useThSice in S/R seaice_readparms and
729        replace it by a warning in S/R seaice_check
730      - remove parameter MULTDIM, replace with nITD and runtime
731        parameter SEAICE_multDim (still hard-wired to nITD if
732        SEAICE_ITD is defined)
733    
734    checkpoint64x (2014/05/24)
735    o verification/lab_sea:
736      - update adjoint and TLM output following changes to pkg/salt_plume
737      - un-do the update after putting back local recip_Cp in few places.
738    o pkg/salt_plume: modifications by An Nguyen:
739      - add capability to do brine rejection (salt-plume) as function of
740        volume+tracers (instead of only salinity tracer).
741      - conserve volume by exchanging volume from each kLev to above to
742        accommodate in-coming brine volume
743      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
744      - switch KPP surf buoyancy due to brine forcing to 3-d
745        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
746      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
747      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
748        in East/West Arctic.
749    o pkg/sbo:
750      - incorporate modifications from Katherine Quinn to enable the use of sbo
751        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
752        output for future testreport verification (unfinished).
753    o pkg/atm_phys:
754      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
755        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
756        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
757    o pkg/seaice
758      seaice_calc_ice_strength.F: modify expression to avoid divisions
759        (affects truncation)
760      seaice_do_ridging.F: clean up the insectarium
761      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
762      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
763      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
764      - add some debugging information and error messages (warnings)
765    o model/src: modifications relatd to atmosphere p*:
766      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
767      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
768        of vertical profile tRef in geopotential background and anomaly.
769      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
770        and pkg/atm_phys.
771      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
772        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
773    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
774    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
775        not used right now, but can be used in BGC packages to fix conservation.
776    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
777        other packages too.
778    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
779        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
780    o model/src:
781      - since we have several heat capacity (even in model/src), define "recip_Cp"
782        as local variable (no longer in common block) to avoid any confusion.
783      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
784    o pkg/exf:
785      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
786        air density as function of air Temp, Humidity and atm pressure.
787    
788    checkpoint64w (2014/05/02)
789    o verification:
790      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
791        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
792        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
793        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
794        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
795    o model/src: for atmosphere in p* coords:
796      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
797      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
798        but not yet activated.
799    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
800      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
801      - this changes the results (but not for any verification experiment, because
802        none tests this), but avoids having an extra field in the restart files
803    o pkg/seaice: remove global variable TICE (not needed)
804      - replace by TICES or local variable where necessary (cost_seaice_test,
805        seaice_diagnostics_state)
806      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
807      - use specific read/write routines for reading and writing individual leves
808        of a multilevel field
809    o pkg/ctrl & model/inc:
810      - move additional anomaly fields of control vars (related to options:
811         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
812        from DYNVARS.h into new header file: CTRL_FIELDS.h
813    o pkg/seaice: some small modifications to the ridging code
814      - make fw2ObyRidge a global variable and add the freshwater flux to
815        seaice_growth
816      - pass actual thickness from seaice_prepare_ridging, so that it is
817        computed only in one place and compute it in the same way as in
818        seaice_growth
819      - initialise more fields in seaice_do_ridging that where cause floating
820        point exceptions over land
821    o pkg/seaice: preparations for ridging code and first real ridging code
822      - move most of "PART 1" of S/R seaice_growth into a new and separate
823        S/R seaice_reg_ridge that will both regularize the state variable after
824        advection call the actual ridging routine;
825      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
826        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
827      - remove ridging code from seaice_advdiff
828      - clean up remaining part 1 of seaice_growth in an attempt to make it
829        more readable (this is probably subjective)
830      - call seaice_itd_redist once in the initialisation phase to have the initial
831        conditions in the correct category
832      - finally: add new ridging routine for ITD code
833    
834    checkpoint64v (2014/04/11)
835    o pkg/ecco:
836      - add runtime parameters mdt[start,end]date[1,2]
837      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
838    o pkg/seaice:
839      - make deltaC a global variable, so that it can be used in ridging code
840      - first step towards ridging: introduce new routines that compute
841        ice strength based on ridging parameters
842      - add diagnostic for HSNOWITD
843      - add opnWtrFrac as a global variable (required for ridging scheme)
844    o pkg/salt_plume + pkg/seaice/seaice_growth.F
845      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
846        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
847    o verification/hs94.1x64x5:
848      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
849      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
850    o autodiff:
851      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
852        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
853        For now, only in pkgs used in verification/hs94.1x64x5.
854      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
855        which are specific to TAF/TAMC).
856      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
857        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
858        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
859      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
860        building mitgcmuv_ad (make adAll).
861    o pkg/ecco:
862      - cost_gencost_seaicev4.F:
863         reformulate proxy cost as function of sst and local param SEAICE_freeze
864         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
865      - add stop statement if old names siv4-[sst,vol] are used
866      - add snapshots + cost reports for atmospheric longwave
867      - remove factor 0.1 in front of wtau[u,v]
868      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
869         ALLOW_TMI_SST_COST_CONTRIBUTION
870    o pkg/atm_phys:
871      - add some diagnostics for Short-wave and for convection S/R.
872    o pkg/seaice/seaice_growth:
873      - fix a bug in the lateral melt parameterization for SEAICE_ITD
874        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
875      - rearrange loop order for better vector code in the same code block
876      - rewrite the floeDiameter formula to have fewer divisions
877      -  (miraculously) none of this changes the results of seaice_itd
878    o pkg/smooth:
879      - move param smooth2Ddiffnbt to pkg/ecco
880    o pkg/salt_plume:
881      - salt_plume_frac.F:
882         clean up local param names
883         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
884    o pkg/rw:
885      - add RS version of S/R READ_MFLDS_LEV.
886    o pkg/streamice:
887      - fix the restart test by writing/reading pickup_streamice files.
888    o pkg/seaice:
889      - refine checks for jfnk-related parameters
890      - comment out if statement with SEAICEuseIMEX parameter as long as there
891        is no IMEX code to avoid confusion and surprises
892    
893    checkpoint64u (2014/03/07)
894    o verification/MLAdjust:
895      - rename secondary test suffix:
896         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
897         0.leithD -> AhFlxF  + switch to flux-form
898         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
899         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
900    o pkg/mom_vecinv:
901      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
902        to be before mom_calc_visc.F)
903      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
904      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
905        this is simpler for the adjoint and for diagnostics.
906    o model/src + pkg/momentum:
907      - add input files for  2-D additional Western and Southern cell-edge wall
908         (e.g., to add "thin-wall" where it is =1).
909      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
910        using 2nd hFacZ that is computed from initial (fix domain) hFac
911      - known limitations of thin wall implementation: not yet coded for sigma
912        coords; not working with CD-scheme neither.
913    o pkg/seaice:
914      - rename recently introduced parameters from (wrong name) AB to
915        BDF (backward difference time discretisation)
916      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
917    o tools/adjoint_options:
918      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
919    
920    checkpoint64t (2014/02/01)
921    o pkg/ecco
922      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
923        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
924      - replace hard-coded record number and period which only work for monthly
925        with read-in runtime param that works for other periods (month,day,year)
926    o pkg/thsice
927      - corrected store directive fixes thsice adjoint gradient checks
928    o genmake2 & testreport:
929      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
930        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
931        Update testreport accordingly. No need to set "export OPENAD=true"
932        in adjoint_options/adjoint_oad anymore (will be removed later).
933    o pkg/shelfice:
934      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
935        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
936        so that surface forcing applies to k=kSurf if using pkg/shelfice.
937    o pkg/ctrl, pkg/grdchk, pkg/ecco:
938      - Changes to make GENARR more modular (i.e. invisible if not used)
939    o model/src/temp_integrate.F and salt_integrate.F
940      - re-include store directives that were removed on Dec 27th.
941    o model/src/external_forcing_surf.F
942      - add storage directives for EmPmR and PmEpR to avoid recomputation of
943        seaice_model in the adjoint that is problematic when seaice_model is
944        turned off in the adjoint. The resolved issue dated back to July when
945        EXTERNAL_FORCING_SURF call was moved.
946        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
947    o pkg/exf/exf_check.F
948      - fix a small bug again (originally found by Wentao Liu, now found again)
949      - streamline error output
950    o pkg/streamice and aim_v23:
951      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
952        Apple's /usr/bin/cpp knows what to do:
953        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
954        Target: x86_64-apple-darwin13.0.0
955    
956    checkpoint64s (2014/01/05)
957    o tools/adjoint_options:
958      - switch to fastopt.net TAF server (instead of default fastopt.de) for
959        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
960    o model/src:
961      - remove some unnecessary TAF storage directives in forward_step.F and
962        in dynamics.F (note: not always removed by TAF, e.g., double storage
963        of kappaRU,kappaRV in former version of dynamics.F).
964    o model/src & pkg/ptracers:
965      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
966        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
967        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
968      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
969      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
970      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
971    o useSingleCpuInput separates single-CPU input from single-CPU output;
972        for now only implemented for in exf_interp_read.F
973    o verification/advect_xy:
974      - fix missing EXCH call in local version of ini_salt.F and update output.
975    o momentum diagnostics:
976      - fix which deltaT is used in Total-Tendency diagnostics.
977      - fix typo in diagnostics for momentum tendency from AB.
978    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
979        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
980    
981    checkpoint64r (2013/12/08)
982    o verification/*/results:
983      - Update reference output of experiments that were passing with just 13 digits
984         (make it easier to detect future changes in results)
985    o model/src & pkg/ptracers:
986      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
987        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
988        to inside ptracers_integrate.F ; remove ptracers_advection.F
989    o coupling interface pkgs:
990        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
991      - change the config check to test the agreement of Ocean Depth
992        with ATM land/sea mask (instead of ATM orography);
993      - send to coupler the number of coupler time-steps to do for this run:
994        this allows to check for consistency and don't need anymore to be
995        specified in parameter file "data";
996      in coupler:
997      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
998      - improve report to log-file of config setting (pass log-file unit to few S/R)
999    o pkg/compon_communic:
1000      - add coupling send/receive for non-tiled integer vector;
1001      - add S/R to check and stop if any proc has an error (similar to
1002        eesupp/src/stop_if_error.F but single thread and across Comm_World).
1003    o pkg/exch2:
1004      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
1005        through list of all tiles my proc owns.
1006    o model/src:
1007      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
1008        from rTrans) to simplify dependencies (no need to store rTrans anymore in
1009        calling S/R); this affects AD results at machine truncation level:
1010        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
1011        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
1012    o tools/build_options:
1013      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
1014    o coupling interface pkgs:
1015        [compon_communic, atm_compon_interf & ocn_compon_interf]
1016      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
1017        to each S/R that needs it; remove un-used variables.
1018      - change component tile registration (cpl_register.F in both compon_interf
1019        and mitcomponent_tile_register.F) to pass the full list of tiles
1020        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
1021      - with pkg/exch2: adopt the same convention used for I/O to define mapping
1022        towards coupler global array (unless W2_useE2ioLayOut=F):
1023         a) can now use different tiling between atm & ocn comp.
1024         b) no needs to modify the run-Off map when changing tiling (was needed
1025            even if using the same tiling between atm & ocn).
1026         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
1027            full land tiles); not yet tested.
1028      - check for valid mapping from comp. tile to coupler global array
1029      - improve report of tile registration results to log file.
1030    o pkg/exch2:
1031      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
1032        tile-registration (CPL_REGISTER);
1033      - activate (un-comment) definition and setting of "W2_tileIndex" list to
1034        store the local bi,bj indices of each tile;
1035      - also print bi,bj in local report to log file;
1036      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
1037        Jun 2009 modif of pkg/exch2).
1038    o testing on baudelaire:
1039      - run 2 tests at a time: no significant slow down (since enough cpu) and
1040        get the full set of test done earlier
1041      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
1042  o model/src/thermodynamics.F and routines called from it:  o model/src/thermodynamics.F and routines called from it:
1043    - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &    - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
1044      gmredi_calc_wflow.F) to update eulerian velocity (input) into residual      gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
# Line 23  o model/src/thermodynamics.F and routine Line 1058  o model/src/thermodynamics.F and routine
1058    - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,    - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
1059      global_ocean.90x40x15, tutorial_global_oce_biogeo and      global_ocean.90x40x15, tutorial_global_oce_biogeo and
1060      tutorial_tracer_adjsens (+ TLM output).      tutorial_tracer_adjsens (+ TLM output).
1061  o toolm/OAD_support and (verification/*/) code_oad:  o tools/OAD_support and (verification/*/) code_oad:
1062    - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to    - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
1063      module conversion ; remove unneeded CPP_EEOPTIONS.h.      module conversion ; remove unneeded CPP_EEOPTIONS.h.
1064    - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard    - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
1065      version (closer to model/incCPP_OPTIONS.h).      version (closer to model/inc/CPP_OPTIONS.h).
1066  o model/src:  o model/src:
1067    - remove parameter "useOldFreezing" from PARAMS.h and push it to the    - remove parameter "useOldFreezing" from PARAMS.h and push it to the
1068      retired list of parameters (routine FREEZE has been replace by surface      retired list of parameters (routine FREEZE has been replace by surface
# Line 47  o verification: Line 1082  o verification:
1082  o pkg/cost:  o pkg/cost:
1083    - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL    - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
1084      (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:      (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
1085      o this fixes global-sum value if multi-threads (since GLOBAL_SUM_TILE_RL      o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
1086        cannot be applied to var in common block).        cannot be applied to var in common block).
1087      o allows to get results independent of tile-per-proc setting (if using      o allows to get results independent of tile-per-proc setting (if using
1088        slower GLOBAL_SUM_SEND_RECV option).        slower GLOBAL_SUM_SEND_RECV option).
Legend:
Removed from v.1.1942  
changed lines
  Added in v.1.2116
  ViewVC Help
Powered by ViewVC 1.1.22