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revision 1.1980 by mlosch, Wed Apr 23 12:42:19 2014 UTC revision 1.2177 by mlosch, Fri Sep 4 08:08:41 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 pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
8        efficient EVP method.
9      - introduce area-weighted averages for e12 (analogously to
10        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
11        remain, but also changing the order of terms in the previous average
12        changed the results as much) -> update experiment
13      - add SEAICE_DELTA_SMOOTHREG code
14      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
15        TEM-code
16      - adjust loop bounds so that only required fields are computed
17      - add new averaging code for zetaZ/deltaZ (again similar to
18        seaice_calc_viscosities.F), inactive by default for now (will change
19        results again), but will replace old code eventually
20    o eesupp/src:
21      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
22        to always cumulate tile local-sum in the same order
23        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
24        Still uses MPI_Allreduce (like standard code) but on array of tiles
25        and should be faster than GLOBAL_SUM_SEND_RECV code.
26      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
27        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
28      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 13 more exp.:
29         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
30         fizhi-cs-aqualev20, global_ocean_ebm, matrix_example, natl_box,
31         solid-body.cs-32x32x1, tutorial_advection_in_gyre, tutorial_baroclinic_gyre
32         and tutorial_held_suarez_cs.
33    
34    checkpoint65n (2015/07/29)
35    o pkg/thsice:
36      - add a warning when used with pkg/aim but without updating SST
37        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
38    o pkg/offline:
39      - change where Offline-Fields are loaded, from load_fields_driver.F to
40        directly within FORWARD_STEP, just after updating iter number and time;
41      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
42        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
43       These changes allow:
44        a) to recover exactly on-line results using deltaToffline=deltaTClock,
45        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
46        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
47        time-step, both with GM & KPP files and with recomputing these fields;
48        b) no needs to switch on staggerTimeStep anymore;
49        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
50      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
51    o pkg/offline:
52      - change (rarely used) offset-iteration parameter to an offset time (in s):
53        can easily recover previous offset-iter effect by setting offset-time
54        (offlineTimeOffset) to offset-iter x deltaToffline;
55      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
56        in KPP as part of surface buoyancy forcing) in offline run.
57      - fix ptracers KPP non-local term in the case where KPP is re-computed.
58    o OpenAD
59      - Adding preliminary ggl90 test to OpenAD verification.
60        Config. with ggl90 currently diverges after 64 time steps
61        so will need more work to become more stable
62      - Adding preliminary kpp test to OpenAD verification.
63        required small tweakes in kpp_routines.F
64      - Merge and update from Krishna Narayanan's contrib area:
65        * Add one variable for preliminary OpenAD DIVA
66        * Add replacement time-stepping for OpenAD DIVA
67        * genmake2 flag -diva (but only for OpenAD; preliminary)
68        * required modifs for OAD_support
69        successful preliminary test for tutorial_global_oce_biogeo/
70    o pkg/seaice:
71      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
72      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
73        delta with a smooth function in s/r seaice_calc_viscosity
74        (no effect on EVP)
75      - rename local suffix "sqr" into "sq" for more consistent variable names
76    o pkg/seaice:
77        add new parameter SEAICE_deltaMin that is used ***only***
78        for regularizing Delta (and nothing else, like the parameter
79        which is also used for all sorts of things SEAICE_EPS).
80        Defaults to SEAICE_EPS for backward compatibility only.
81    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
82        the wrong key by inialising it before use -> fixes a recomputation
83        problem but does not fix the gradient
84    o pkg/layers:
85      - move resetting of flux arrays to outside the iLa loop
86        (this caused layers_diapycnal to not work with more than one layer coord.)
87      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
88    o pkg/layers:
89      - remove from common block 3D layers fields (used to diagnose transport
90        in tracer coords) and declare them as local arrays in layers_calc.F
91    o pkg/seaice:
92      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
93        in lab_sea forward experiment (changes results -> updated)
94      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
95    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
96       computations; for SEAICE_VECTORIZE_LSR
97      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
98        sweep to the outside,
99      - remove store directives and add "CADJ loop sequential" directives
100        in analogy to model/src/solve_tridiagonal.F
101      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
102        boundaries to yield more readable code. This has also the charming side
103        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
104        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
105        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
106        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
107        an additional option)
108       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
109       but the adjoint gradients (which are affected by this change) still explode.
110    o coupler (atm & ocn _compon_interf):
111      - avoid using Exch2 IO mapping if not suitable.
112    
113    checkpoint65m (2015/06/15)
114    o pkg/layers:
115      - clean-up old parameters setting (from Sep 2012):
116        + remove old parameters setting from common block (declared locally);
117        + stop if any old parameter is mixed with new parameters;
118        + check for valid or consistent parameter setting (e.g., layers_name)
119      - check that layers_bounds for Pot.Density are in the right range;
120        this is supposed to catch un-updated setting after recently shifting
121        potential density field "prho" by -1000 (now in "sigma" scale).
122    o pkg/layers:
123      - Added missing call to layers_fill for keeping track of tottend in
124        pkg/diagnostics/diagnostics_fill_state.F
125    o pkg/layers:
126      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
127        of diapycnal fluxes
128    o pkg/layers:
129      - reverted changes to interpolation to previous treatment; there
130        was never actually a problem
131    o pkg/layers:
132      - fix interpolation of layers tracers in the presence of partial cells
133      - add lots of new functionality to compute water mass transformation
134        (enabled by CPP flag LAYERS_THERMODYNAMICS)
135      - add new calls from main code (diags_oceanic_surf_flux.F,
136        thermodynamics.F, impldiff.F) and gad to save the necessary fields
137        for layers_thermodynamics calculations
138    o pkg/ptracers:
139      - add capability of stepping a passive tracer forward without advection
140        by setting PTRACERS_advScheme to 0.
141    o pkg/diagnostics:
142      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
143    o pkg/layers:
144      - shift potential density field "prho" by -1000 for density layer averaging so
145        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
146        Note that density bin boundaries (layers_bounds in data.layers) have
147        to be set accordingly (i.e., shifted, in sigma scale).
148    o pkg/layers:
149      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
150      - fix calculation of layer non-weighted velocity and layer probability
151      - add diagnostics for pot.density used for layer averaging
152    o pkg/seaice:
153      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
154        positiveness, modify a few comments and improve variable names,
155      - the changed computation of deltaC affects most seaice-related
156        experiments at the truncation level.
157        seaice_itd.thermo is affected by far the most, with
158        only 7 digits of agreement remaining; update experiments.
159    
160    checkpoint65l (2015/05/04)
161    o pkg/shelfice:
162      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
163        factor drKp1 to zero where it is negative (ie. do not use
164        SHELFICEBoundaryLayer if hFacC>1)
165      - the same for factor drLoc in shelfice_forcing.F
166    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
167        with modules in ptracers, when using testreport option "-small_f"
168    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
169      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
170    o verification/testreport
171      - add new option -small_f
172        with this option testreport first makes the target small_f (*.f files)
173        before running make (all). This is useful for explicit inlining when
174        all sources need to be full available.
175    o pkg/exf/exf_interp.F:
176        remove previous changes related to reverse (decreasing) input grids latitude
177    
178    checkpoint65k (2015/04/01)
179    o pkg/ecco:
180        fix missing cosphi initialization; use eccoiter in place of optimcycle;
181        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
182        instead of active read/write
183    o pkg/ctrl:
184        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
185        instead of active read/write.
186    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
187        return if .NOT.useAUTODIFF
188    o pkg/seaice: add CPP brackets (cost function related).
189    o model/src:
190        add useAUTODIFF run time switch.
191    o pkg/exf/exf_interp.F:
192        add code to allow input grids with latitude starting in the north (i.e. when
193        j=1 corresponds to northern edge of field); modify global_with_exf to test
194        this feature.
195    o verification/testreport:
196      - replace "grep -A3" with POSIX conformal sed command, because there are
197        implementations of grep that cannot do contextual searches
198      - replace "cat -n" by "nl" (two occurrences), because not all implementations
199        of "cat" have the option "-n"
200    o model/src:
201        add new file gsw_teos10.F that contains 3 functions, more or less a copy
202        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
203        convert from conservative to potential temperature. For now they are not
204        called anywhere.
205    o pkg/ggl90: make "useIDEMIX" useful
206      - re-organize code in s/r ggl90_calc a little to move computations that
207        are different for idemix into separate loops (changes verification
208        experiment idemix at truncation level, 12 digits remain -> updated)
209      - requires 2 new 2D fields KappaM, verticalShear
210      - make hFacI and recip_hFacI local 3D variables that are passed to
211        s/r ggl90_idemix
212      - fix and improve some comments
213    
214    checkpoint65j (2015/02/25)
215    o pkg/openad
216      - synchronize seawater.F with version in model/src: replace routine
217        body of sw_temp by calling sw_ptmp and fix/add a few comments.
218    o pkg/mnc:
219      - change default value of pickup_read/write_mnc params to FALSE
220        (since few features are missing in reading MNC pickup files).
221    o model/src:
222      - change default (background) vertical diffusivity for salt to be the
223        temperature (background) vertical diffusivity.
224      - change background vertical diffusivity in vertical mixing pkgs ggl90,
225        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
226        This makes ptracers default diffusivity (that uses salt diffKr) more
227        consistent with vertical mixing schemes.
228    o verification/testreport:
229      - fix typo in "-pcls" option ;
230      - put temp files in /tmp (instead of in local dir)
231      - add option "-ncad" to use genmake2 new option "-nocat4ad"
232      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
233    o pkg/ggl90 (idemix code):
234      - apply few fixes ; add some missing "_d 0" ; update output of exp.
235        global_ocean.90x40x15.idemix
236    o OpenAD
237      - enable active file I/O and begin removal of work-around code
238        for OpenAD for handling control variables (memory vs. active files)
239      - new CPP options file OPENAD_OPTIONS.h
240      - revert to genarr2d gradient check for hs94.1x64x5
241      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
242      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
243    o tools/genmake2:
244      - add option for an alternative Makefile (from Martin) where multiple
245        source files are sent to TAF (instead of all in one file).
246    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
247      - code provided by Carsten Eden as an extension of ggl90
248      - so far the code is turned on within ggl90 by setting a CPP-flag at
249        compile time; a runtime flag implementation is not yet complete
250      - tested in new verification experiment global_ocean.90x40x15.idemix
251    o verification:
252      - reduce length of the AD test run by half for experiments
253        global_ocean.cs32x15 (std + thsice) and isomip
254      - enable active file I/O for OpenAD, adjust verifications accordingly
255      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
256    o verification/testreport:
257      - fix two non-POSIX sed statements so that there are no error messages
258        on Mac OS X
259      - replace hostname -s with hostname | sed 's/\..*$//'
260    o model/src/seawater.F:
261      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
262        (following the matlab code), which would have avoided the bug caught
263        by Matt (see below) in the first place
264    o pkg/shelfice:
265      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
266        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
267      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
268        ice-shelf case (i.e., within surface level).
269      - add config summary in shelfice_check.F
270      - remove global variable recip_SHELFICElatentHeat and replace by a local
271        variable recip_latentHeat
272      - introduce diagnostics for friction velocity uStar (in case of
273        SHELFICEuseGammaFrict)
274      - change verification experiment isomip.htd:
275        + start from pickup (as input_ad at nIter0=8640)
276        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
277        + test SHELFICEuseGammaFrict = .TRUE.
278        + test SHELFICEadvDiffHeatFlux = .TRUE.
279    o model/src:
280      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
281        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
282        update output of experiments global_with_exf.yearly and isomip (all 6).
283    o pkg/shelfice:
284      - change setting of kTopC to also be zero where there is no ice-shelf.
285      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
286        ice-shelf is.
287      - first attempt to get RealFreshWaterFlux effects: for now, only without
288        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
289    o pkg/seaice: add the option to prescribe a fixed thickness PDF
290      for thermodynamic calculations
291      - because of divisions of the type 7/7 not exactly equal to 1, this change
292        affects results of some verification experiments by up to 4 digits:
293        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
294        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
295        adjoint: lab_sea, lab_sea.noseaicedyn
296        -> updated
297    
298    checkpoint65i (2015/01/23)
299    o model/src:
300      - change units of frictionHeating field from W to W/m^2
301      - fix bug in frictional heating from stratospheric drag in
302        S/R ATM_PHYS_TENDENCY_APPLY_V
303      - with synchronous time-stepping: move resetting to zero of frictionHeating
304        field from load_fields_driver.F to thermodynamics.F ;
305      - add diagnostics for frictional heating.
306    o model/src & gmredi K3D:
307      - add frictionHeating field to pickup-files (for synchronous time-stepping)
308      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
309      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
310        and name in pickup file).
311      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
312    o model/src:
313      - move (from ini_forcing.F) initialisation of all arrays in header file
314        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
315        (since Nov 2012) with option selectAddFluid=1.
316    o pkg/shelfice:
317      - change units (+ document) of newly added field "shelfIceMassDynTendency"
318      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
319    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
320    o pkg/seaice: two new runtime parameters:
321      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
322        long overdue
323      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
324        parameterization of tensil stress for fast ice (does not do anything yet)
325    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
326        for LSR: move checking overlaps out of JFNK-if-block
327    o pkg/atm_phys:
328      - move copy of grid and dynamical fields out of atm_phys_driver.F into
329        new S/R ATM_PHYS_DYN2PHYS.
330      - fix level height for Linear Free-Surf case (to be consistent with
331        fixed-in-time pressure levels).
332    o pkg/mom_common (bottomdrag):
333      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
334        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
335        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
336    o pkg/shelfice (u/v_drag):
337      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
338      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
339        (now similar to shelfice_u_drag.F)
340      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
341        from mom_vecinv.F (similar to mom_fluxform calls).
342    o pkg/mom_common (bottomdrag):
343      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
344      - add options for alternative discretisation of velocity norm in quadratic
345        bottom drag: averaging of grid-cell-center KE to U.point and V.point
346        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
347        improves when averaging only the other component (e.g. vVel for U bottom
348        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
349      - add options (bottomVisc_pCell) to account for partial-cell in bottom
350        friction (no-slip BC) thus getting the true distance from the bottom;
351        off by default since this also reduces model stability (explicit bottom
352        friction). Changes produce different machine truncation with linear-drag
353        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
354        front_relax (bvp & mxl, 10 & 11 digits).
355    o model/src & mom pkgs:
356      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
357        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
358      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
359        just copy level Nr value to level Nr+1.
360    o doc:
361      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
362    o pkg/streamice:
363      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
364        SHELFICE.h: move array shelficemass to init_varia, initialise
365        from array shelficemassinit, which is set in init_fixed and
366        has option to be set from file; introduce array
367        shelficeMassDynTend array, set thru file in init_fixed
368      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
369        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
370        pkg/streamice
371      - shelfice_thermodynamics.F: call shelfice_step_icemass if
372        SHELFICEMassStepping = .true.
373      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
374    
375    checkpoint65h (2014/12/17)
376    o verification/global_ocean.90x40x15, global_ocean_ebm:
377      - update to generic controls.
378    o pkg/ctrl:
379      - ctrl_map_ini_genarr.F: test for igen>0
380      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
381      - move gentim2d part of ctrl_map_ini_genarr.F to
382        new separate routine : ctrl_map_ini_gentim2d.F
383      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
384        add time variable weights and cyclic controls (time mean,
385        seasonal cycle, etc) capabilities to gentim2d
386    o pkg/ecco:
387      - move reading of error, conversion to weights from
388        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
389    o global_oce_llc90, cs32:
390      - activte sbo.
391      - CTRL_SIZE.h : add maxCtrlProc.
392      - activate the new genctrl capabilities.
393      - update following reorganization of global_oce_input_fields.tar.gz  
394    o pkg/ctrl/ctrl_ad_diff.list:
395      - add missing ctrl_init_rec.f
396    o tools/OAD_support/keepOriginal:
397      - add ctrl_init_rec.F
398    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
399      - avoid recomputations of xx_gentim2d_dummy.
400    o momentum diagnostics:
401      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
402        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
403    o pkg/seaice/seaice_lsr.F:
404      - fix computation of BU/BV, make sure they are non-zero, only necessary
405        for cubed sphere exchanges and SEAICE_OLx/y>0.
406        This makes calling s/r fill_cs_corner_rl obsolete (removed).
407    o verification/global_ocean.cs32x15/input.seaice
408      - add test for strong implicit coupling and restricted addtive Schwarz
409        methods for LSR
410      - update results/output.seaice.txt
411    o verification/tutorial_global_oce_biogeo:
412      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
413        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
414        update output_adm,_oadm,_tlm.txt
415    o pkg/dic:
416      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
417      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
418        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
419    o verification/tutorial_global_oce_biogeo:
420      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
421        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
422        update output_adm,_oadm,_tlm.txt
423    o eesupp/src:
424      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
425        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
426    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
427      LSR (following Hutchings et al. 2004)
428      - introduce zetaZ as a global variable (requires adjustments in
429        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
430        in seaice_calc_viscosities.F
431      - new flag SEAICEuseStrImpCpl (default off)
432      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
433        momentum equations
434      - JFNK-solver (preconditioner) adjusted to allow using this method
435        (where it does not have any positive effect)
436    o pkg/seaice
437      - add overlap for restrictive additive Schwartz method also to LSR, but
438        turn it off by default (because it only seems to work for non-cubed
439        sphere/llc topologies)
440    o pkg/autodiff
441      - add extra exchanges in addummy_in_steppging also for mnc output
442    o pkg/seaice:
443      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
444        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
445    o pkg/obcs:
446      - add option to specify domain-connected piece Id along OB though files
447        (for now, only used to diagnose PhiVel; default =1 -> global correction)
448      - modify obcs_diag_balance.F to process each connected-part separately;
449        exclude OB where Id = 0 but keep the full divergence there (-> constant
450        Psi along this portion of OB and all inflow derived from grad(Phi))
451      - add example of OB-conect files in verification/so_box_biogeo/input.
452    o pkg/diagnostics:
453      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
454      a) use non zero matrix element across OB and solve for Phi 1 grid point
455         outside OB (i.e, where tracer OBCS are applied).
456      b) global imbalance of inFlow/outFlow across OB: instead of modifying
457         velocity across OB, spread it uniformly along the OB in the RHS.
458    
459    checkpoint65g (2014/11/19)
460    o pkg/diagnostcis:
461      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
462    o pkg/my82,pp81,kl10:
463      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
464        field diffKr as background diffusivity to set minimum diffusivity value.
465    o pkg/seaice:
466      - add new parameter SEAICEuseEVPrev (for revisited EVP by
467        Bouillon et al 2013)
468      - add SEAICE_evpAlpha/Beta to namelist
469      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
470        involve trivial re-ordering of divisions/multiplications that should not
471        have any effects, but ... they do change the results of lab_sea.hb87 so
472        that only 2 digits of agreement remain, in line with the general
473        instability/fragility of the evp-code. For now, I do not care and just
474        update the verification experiment
475    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
476      - remove xx_genarr2d_numsmooth etc
477      - use xx_genarr2d_preproc etc instead
478      - carry out smooth_correl2D at initialization stage rather than during
479        time stepping.
480      - get smoothOpNb from xx_gentim2d_preproc
481    o global_oce_cs32 :
482      - add test of generic ecco capabilities.
483    o pkg/exf/exf_getsurfacefluxes.F :
484      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
485    o pkg/ctrl,ecco :
486      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
487        is defined.
488    o pkg/seaice: add diagnostics for Delta (deformation parameter)
489    o model/src:
490      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
491        diffusivity (background) is specified but ignored.
492    o verification:
493      - in testreport, convert hostname to lower case for default output dir name
494    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
495    o pkg/dic: add modifications from Hajoon:
496      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
497      - light attenuation: add self-shading effect by climatological Chlorophyll
498        (read from file).
499    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
500        compiles when SEAICE_ALLOW_DYNAMICS is undefined
501    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
502        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
503        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
504        approach where CPP_OPTIONS.h includes an omnipotent
505        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
506    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
507        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
508    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
509        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
510        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
511    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
512      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
513      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
514      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
515      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
516    o pkg/ctrl,ecco,exf :
517      - remove variables associated with NON-generic costs,
518        unless ECCO_CTRL_DEPRECATED is defined.
519      - remove NON-generic NON-obcs controls,
520        unless ECCO_CTRL_DEPRECATED is defined.
521    o pkg/ctrl : added ctrl_local_params.h
522    o pkg/ecco : added ecco_local_params.h
523    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
524        experiments, which will progressively be removed once the
525        experiments are revised to use only generic controls/costs.
526    
527    checkpoint65f (2014/10/13)
528    o pkg/ctrl, ecco, seaice : minor changes in headers
529    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
530        cost function and control capabilities added since checkpoint65c.
531    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
532    o pkg/ecco: increase modularity and improve logic
533      - ecco_toolbox.F (new) : basic operations that are often used,
534        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
535        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
536      - cost_gencal.F (new) : determine filnames and records.
537      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
538      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
539        and exploit the above functions leading to more compact code.
540      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
541      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
542        using_ers, using_gfo, using_mdt is now only defined within gencost)
543    o pkg/ecco: extend generic cost capabilities
544      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
545        capabilities via gencost_preproc (+ _c,_i,_r related params),
546        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
547        gencost_outputlevel arguments to cost_generic
548      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
549        and active_read, making room for gencost_preproc to take effect.
550        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
551      - pkg/ecco/cost_generic.F :
552        compute and store misfit maks*(model-data) in localdif that is
553        then used in cost and for output, output misfit if outlev.GT.0
554      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
555        rather gencost_barfile for deciding whether to write barfile
556      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
557      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
558        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
559      - pkg/ecco/ecco_summary.F : report gencost variables
560      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
561    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
562    o pkg/ecco: internal re-organization
563      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
564        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
565        mv relevant variables definition from ecco_cost.h to ecco.h,
566        make sure gencost routines only include ecco.h)
567      - throughout : add missing CCP switches, rm unused variables,
568        and rm un-necessary CPP switches
569      - throughout gencost routines : replace modelstartdate with
570        gencost_startdate when needed
571      - cost_bp_read.F : use arguments, instead of common blocs
572        so that it can be used also by (new) cost_gencost_bpv4.F
573      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
574      - ecco_phys.F : compute etanFull
575      - ecco_readparms.F : rename using_topex as using_tpj, add
576        bpv4-grace to gencost list, initialize added parameters
577      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
578    
579    checkpoint65e (2014/09/28)
580    o pkg/obcs:
581      - replaced the just-added CPP options with run-time variables
582        (see pkg/obcs/OBCS_PARAMS.h for details)
583    o pkg/obcs:
584      - add additional CPP options for sponge boundary layers
585        (see pkg/obcs/OBCS_OPTIONS.h for details)
586    o pkg/atm_phys:
587      - implement simple (obliquity only, assuming circular planet orbit)
588        seasonal cycle for incoming insolation ; used when run-time parameter
589        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
590    o pkg/exf, pkg/ecco, pkg/ctrl:
591      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
592      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
593      - implement gentim2d for xx_tauu, xx_tauv
594    o pkg/ctrl, pkg/ecco :
595      - fix and complement the generic controls implementation
596    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
597        pkg/shelfice/shelfice_thermodynamics.F,
598        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
599        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
600      - add weight in CTRL_GET_GEN calls
601    o pkg/ctrl :
602      - ctrl_get_gen.F : add weight as input parameter, and apply
603        it directly rather than using smooth_correl2Dw (to be retired).
604      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
605    o pkg/ctrl :
606      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
607        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
608      - re-activate ctrl_summary (call in ctrl_init.F)
609    o pkg/ctrl/ctrl_cost_gen.F :
610      - fix CCP brackets, remove un-necessary myiter, mytime
611    o pkg/ecco, pkg/ctrl :
612      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
613      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
614      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
615      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
616    
617    checkpoint65d (2014/09/15)
618    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
619      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
620        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
621    o pkg/ctrl/ctrl_map_ini_genarr.F :
622      - remove compilation failure
623      - replace hard coded example
624      - use ctrl_map_ini_gen2D, 3D
625    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
626      - on/off switch based upon xx_genarr2d_weight,3d
627    o src/packages_init_variables.F :
628      - regroup pkg/estimation calls
629      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
630        (moved to ctrl_init_variables)
631    o cost/cost_init_varia.F :
632      - remove ecco_cost_init_varia
633        (moved to ecco_init_varia)
634    o ctrl/ctrl_init_variables.F :
635      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
636      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
637    o ctrl/ctrl_map_ini.F :
638      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
639        (moved to ctrl_init_variables)
640    o ctrl/ctrl_map_ini_ecco.F :
641      - remove ECCO_PHYS (mv to ecco_init_varia)
642      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
643    o ecco/ecco_ad_diff.list :
644      - add ecco_init_varia.f
645    o ecco/ecco_init_varia.F
646      - new routine
647    o pkg/streamice:
648      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
649        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
650      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
651    o pkg/generic_advdiff:
652      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
653    o pkg/exf:
654      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
655         xxg_precip capability
656      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
657    o pkg/ctrl:
658      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
659    o model/src/load_fields_driver.F :
660      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
661        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
662    o OpenAD verification experiments:
663      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
664        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
665        for now, only in pkgs used in OpenAD verification experiments.
666      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
667        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
668        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
669        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
670    o OpenAD verification tests:
671      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
672      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
673        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
674      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
675        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
676    o model/src & generic_advdiff:
677      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
678        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
679        dynamics requires valid tracer forcing only over tile interior but, for
680        some diagnostics, may need to extend it over 1 point in tile halo region.
681      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
682        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
683        setting in temp/salt/ptracer_integrate.F
684    o pkg/dic:
685      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
686        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
687        in gchem_forcing_sep.F
688    o pkg/autodiff & obcs:
689      - add storage of current OB values for U & V (was already done for T & S).
690    
691    checkpoint65c (2014/08/30)
692    o pkg/dic:
693      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
694        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
695        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
696    o verification:
697      - new experiment testing OBCS and DIC pkgs, using params & output from
698        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
699        passage: take OBCS from the last year of a 2 yrs simulation and initial
700        conditions from t=1.yr while keeping the same forcing.
701    o model/src:
702      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
703        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
704    o pkg/diagnostics (Stats-Diags):
705      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
706        a) refine region where stats are computed, excluding where arrhFac=0 ;
707        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
708        c) extend regional stats over the region edges (for U or V pt location).
709    o pkg/gchem:
710      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
711        pkg/dic is currently changing/updating ptracers values beyond the OB).
712    o verification (hs94):
713      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
714        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
715        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
716        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
717    o pkg/ptracers:
718      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
719        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
720      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
721        with AB-2 code (so that it get tested).
722    o model/src:
723      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
724        with AB-2 code (previously only available with AB-3 code).
725        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
726        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
727        there, by calling CYCLE_AB_TRACER).
728    o pkg/generic_advdiff:
729      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
730        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
731        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
732        S/R temp/salt/ptracers_integrate.F
733    o model/src & pkg/ptracers:
734      - remove common block variables gT,gS (in DYNVARS.h), except when
735         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
736      - remove common block variable gPtr.
737    o model/src & pkgs:
738      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
739         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
740         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
741         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
742      + change accordingly all calling S/R.
743      - use local temperature/salinity/ptracer tendency array (without bi,bj)
744        in S/R temp/salt/ptracers_integrate.F
745    o pkg/seaice:
746      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
747        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
748      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
749        in seaice_lsr
750      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
751        in s/r seaice_lsr_calc_coeffs
752    o pkg/mdsio:
753      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
754        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
755        too long (e.g., > MAX_LEN_FNAM/2 )
756    
757    checkpoint65b (2014/08/12)
758    o pkg/matrix:
759      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
760    o model/src:
761      - fix initialisation of geothermalFile; compile geothermal-flux code in
762        natl_box verification experiment.
763    o model/src & pkg/down_slope:
764      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
765      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
766        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
767        results at machine truncation level: update output of experiments
768        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
769    o pkg/diagnostics (Stats-Diags):
770      - do not cumulate the full volume when DIAGNOSTICS_FILL is
771        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
772        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
773        times (but Min,Max and StD are still wrong).
774    o model/src:
775      - add geothermal flux forcing: read in ini_forcing.F as time-constant
776        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
777    o model/src:
778      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
779        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
780        arrays are already updated while adjustments (filters, conv.adjustment) are
781        still applied later, in S/R TRACERS_CORRECTION_STEP.
782    o model/src:
783      - store in common bloc array "rhoInSitu" the virtual potential temperature
784        anomaly that is used to compute geopotential: this make the atmos code
785        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
786    o pkg/seaice/seaice_lsr.F
787      - rename integer variable ilcall to ipass (that's what it is called
788        in the residual diagnostics
789      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
790        default) for improved non-linear convergence of the first few steps
791      - adjust a few comments and add new ones to explain some of the store
792        directives
793    o pkg/generic_advdiff (& ptracers):
794      - re-work the code to check for valid advection scheme and for minimum
795        size of overlap (now stored in local common bloc in gad_advscheme.F)
796    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
797      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
798      - add an auxilliary variable "bet" and fix store directives and keys in
799        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
800        less exact gradients in my tests); but there are still
801        recomputation warning (although gradients are sort of OK), when
802        SEAICE_LSR_VECTORIZE is not defined, so this flag and
803        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
804      - update verification experiments lab_sea.
805      - change some comments in S/R seaice_calc_viscosities
806    o model/src:
807      - if staggerTimeStep=T, always apply exchange to velocity field in
808        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
809        (independent of using multi-dim advection or not); no effect on FWD run
810        but affects AD results (at machine truncation level): update output of
811        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
812        and isomip (oad: 12.d).
813    o pkg/generic_advdiff:
814      - stop if doAB_onGtGs is set to FALSE but ignored
815      - refine warning related to stability of tracer time-stepping
816        regarding internal wave dynamics.
817      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
818        on staggerTimeStep & implicitIntGravWave (will now get a warning
819        if potentially unstable).
820    o pkg/kl10:
821      - add new pkg "kl10" for mixing due to internal wave breaking, from
822        http://www.sciencedirect.com/science/article/pii/S1463500310000144
823        (contribution from Jody Klymak), tested in verification experiment
824        verification/internal_wave/input.kl10/
825    o isomip experiment:
826      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
827        (input.htd) and update the output.
828    o cd_code experiments:
829      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
830        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
831        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
832        update the corresponding output.
833    o pkg/seaice:
834      - reduce the number of include files and store directives in
835        S/R seaice_lsr_tridiagu/v
836      - change the order of loops in one case in S/R seaice_lsr_tridiagv
837        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
838        get rid off one store directive (a TAF bug?)
839      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
840        S/R seaice_lsr_tridiagv to change the loop range for consistency
841      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
842      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
843        S/R seaice_lsr_tridiagu/v (requires update of
844        offline_exf_seaice/input.dyn_jfnk)
845    
846    checkpoint65a (2014/07/27)
847    o model/src:
848      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
849        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
850        (topo in p-coords, ice-shelf in z-coords); update output of experiments
851        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
852    o model/src:
853      - collect momentum forcing tendency into local 2-D array (passed as argument
854        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
855        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
856        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
857      - collect T & S forcing tendency into local 2-D array (passed as argument to
858        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
859        affects results at machine truncation level (e.g., ocean: if using
860        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
861        correction due to vertical advection).
862      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
863        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
864        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
865        obcs_ctrl (ad & fwd grd @ 12 & 7).
866    o pkg/ptracers & diagnostics:
867      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
868        title (to avoid some unexpected truncation); sort out ptracers diags units.
869      - collect ptracer forcing tendency into local 2-D array (passed as argument
870        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
871    
872    checkpoint65 (2014/07/18)
873    o pkg/fizhi:
874      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
875        affects results at machine truncation level. Update output of experiments
876        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
877    o pkg/seaice: more clean up
878      - rename TAF common block tapes to be more consistent and remove
879        unnecessary duplicates
880      - add store directives to remove more recomputations, but use smaller
881        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
882        The idea behind this flag is to reduce the memory footprint when the
883        adjoint of the LSR is not required. As of now, defining the flag
884        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
885        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
886        For experiment offline_exf_seaice, this means on a linux box with gfortran
887        nearly a factor of 10 (but keep in mind there is mostly seaice code in
888        this experiment):
889        > size mitgcmuv_ad
890        text    data        bss     dec        hex
891        5100659 1216  220458952  225560827  d71c8fb
892        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
893        but only a moderate increase of 36% for global_ocean.cs32x15:
894        text    data        bss     dec        hex
895        6695027 1648 1014578664 1021275339 3cdf6ccb
896        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
897      - note: there are still recomputations in global_ocean.cs32x15 and
898        offline_exf_seaice and the gradient agreement changes (gets a
899        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
900      - in general, the AD gradients still are wrong
901    o OpenAD
902      - clean up code_oad/ directories somewhat by moving files
903        dontCompile, dontTransform, keepOriginal to OAD_support/
904    o model/src:
905      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
906        (not currently tested): add dissipation terms before NLFS rescaling of
907        tendencies (previously done after).
908    o pkg/diagnostics:
909      - write stats-diags in ascii file with more digits (same as in monitor).
910    o pkg/down_slope:
911      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
912        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
913    o model/src:
914      - new file "apply_forcing.F" containing all the code previously in
915        external_forcing.F, but with new argument list: pass, as new argument,
916        the current level tendency array to update (instead of a direct update
917        of the common bloc array). Change the corresponding calls.
918      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
919        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
920    o pkg/seaice/seaice_lsr, a little bit of clean up
921      - rearrange some code blocks, so that now all calculations for
922        setting up the right-hand-sides done within one single block
923        (I find that easier to read and understand)
924      - rearrange freedrift-code to reduce the number of ifdefs
925      - adjust some indentations and comments
926    
927    checkpoint64z (2014/07/10)
928    o model/src and several pkgs:
929      - change argument list of all S/R called from external_forcing.F and
930        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
931        to pass, as argument, the current level tendency array to update
932        (instead of a direct update of the common bloc array).
933      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
934      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
935    o pkg/seaice/seaice_lsr.F
936      - always initialize local arrays in seaice_lsr_tridiagu/v
937      - add more local tapes to seaice_lsr_tridiagu/v
938      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
939        keep it in bi/bj loop; this seems to be essential
940      - gradients are still wrong but only by 4-7 orders of magnitude
941        instead of 15 orders of magnitude, lab_sea improves a little
942    o pkg/seaice
943      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
944        generates unnecessary code in seaice_lsr_ad
945      - add more store directives in seaice_lsr to avoid unnecessary code
946        in seaice_lsr_ad
947      - exclude some residual computations in seaice_lsr when
948        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
949        in seaice_lsr_ad
950      - add more storing, a new tape (model/src/the_main_loop.F) and
951        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
952        and klockey should be checked by a specialist)
953      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
954        and update lab_sea after previous changes in pkg/seaice below
955    o pkg/autodiff:
956      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
957        viscFacInAd : run time parameters allowing for adjoint switches
958        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
959    o pkg/ecco:
960      - introduce cost_gencost_boxmean.F that computes a box mean
961        temperature (for use in adjoint sensitivity studies).
962    o model/src/set_defaults.F : initialize viscFacAdj to 1.
963    o pkg/mom_common/mom_calc_visc.F:
964      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
965    o pkg/seaice/seaice_summary.F:
966      - statement for SEAICEadjMODE now in autodiff_readparms.F
967    o pkg/seaice:
968      - remove some store directives and add new ones in an effort to get
969        finally rid off the recomputation warnings. This is successful
970        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
971        defined (i.e. no extensive recomputation warnings left), but there
972        are still too many recomputations on the solver iteration level
973      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
974      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
975        SEAICE_SIZE.h
976      - add a store directive in S/R seaice_calc_viscosities
977    o pkg/seaice (ITD code):
978      - fix definition of Hlimit for multi-threaded case
979      - use double precision arithmetic to compute Hlimit: this affects results;
980        update output of experiment seaice_itd.
981    o replace content of verification/seaice_itd
982      - instead of a 1D column use the configuration of offline_exf_seaice
983        to test the ice thickness distribution code with ridging
984      - this is a first shot at this experiment
985      - change of some defaults of ridging parameters SEAICEhStar (from
986        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
987        and lot of new comments.
988    
989    checkpoint64y (2014/06/20)
990    o pkg/seaice/seaice_reg_ridge.F:
991      - modify the regularization of very small volumes of ice; only check
992        total volume HEFF, and do not apply correction to individual ice
993        classes because that leads to funny patterns in the heat and fw-fluxes
994        into the ocean. Adjust seaice_itd/results/output.txt
995      - replace nITD by SEAICE_multDim in loop-ranges
996    o pkg/exf:
997      - add code to process the case field period = -12. with UV interpolation.
998      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
999        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
1000    o verification/global_with_exf:
1001      - switch all fields period to -12. (was previously untested) in input/data.exf
1002        (but keep secondary test ".yearly" unchanged); update the reference output.
1003    o pkg/cal:
1004      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
1005    o pkg/exf:
1006      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
1007        to replace logical switch "exf_verbose"
1008      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
1009    o pkg/sbo:
1010      - update from Katherine Quinn: evaluate mass directly from density and SSH
1011        (budget using Finite Volume method) instead of from bottom pressure.
1012      - allow testreport to collect few selected SBO output ; tested in exp.
1013        global_ocean.90x40x15 (after updating the results, to include SBO output).
1014      - fix some multi-threading issues (in output part).
1015    o model/src & most packages:
1016      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
1017      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
1018        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
1019        "data.{pkg}" exist ; and leave the S/R (return) just after.
1020      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
1021        + call LAND_READPARMS from packages_readparms.F
1022    o pkg/seaice:
1023      - remove code that resets useThSice in S/R seaice_readparms and
1024        replace it by a warning in S/R seaice_check
1025      - remove parameter MULTDIM, replace with nITD and runtime
1026        parameter SEAICE_multDim (still hard-wired to nITD if
1027        SEAICE_ITD is defined)
1028    
1029    checkpoint64x (2014/05/24)
1030    o verification/lab_sea:
1031      - update adjoint and TLM output following changes to pkg/salt_plume
1032      - un-do the update after putting back local recip_Cp in few places.
1033    o pkg/salt_plume: modifications by An Nguyen:
1034      - add capability to do brine rejection (salt-plume) as function of
1035        volume+tracers (instead of only salinity tracer).
1036      - conserve volume by exchanging volume from each kLev to above to
1037        accommodate in-coming brine volume
1038      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
1039      - switch KPP surf buoyancy due to brine forcing to 3-d
1040        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
1041      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
1042      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
1043        in East/West Arctic.
1044    o pkg/sbo:
1045      - incorporate modifications from Katherine Quinn to enable the use of sbo
1046        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
1047        output for future testreport verification (unfinished).
1048    o pkg/atm_phys:
1049      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
1050        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
1051        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
1052    o pkg/seaice
1053      seaice_calc_ice_strength.F: modify expression to avoid divisions
1054        (affects truncation)
1055      seaice_do_ridging.F: clean up the insectarium
1056      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
1057      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
1058      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
1059      - add some debugging information and error messages (warnings)
1060    o model/src: modifications relatd to atmosphere p*:
1061      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
1062      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
1063        of vertical profile tRef in geopotential background and anomaly.
1064      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
1065        and pkg/atm_phys.
1066      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
1067        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
1068    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
1069    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
1070        not used right now, but can be used in BGC packages to fix conservation.
1071    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
1072        other packages too.
1073    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
1074        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
1075    o model/src:
1076      - since we have several heat capacity (even in model/src), define "recip_Cp"
1077        as local variable (no longer in common block) to avoid any confusion.
1078      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
1079    o pkg/exf:
1080      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
1081        air density as function of air Temp, Humidity and atm pressure.
1082    
1083    checkpoint64w (2014/05/02)
1084    o verification:
1085      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
1086        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
1087        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
1088        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
1089        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
1090    o model/src: for atmosphere in p* coords:
1091      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
1092      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
1093        but not yet activated.
1094    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
1095      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
1096      - this changes the results (but not for any verification experiment, because
1097        none tests this), but avoids having an extra field in the restart files
1098    o pkg/seaice: remove global variable TICE (not needed)
1099      - replace by TICES or local variable where necessary (cost_seaice_test,
1100        seaice_diagnostics_state)
1101      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
1102      - use specific read/write routines for reading and writing individual leves
1103        of a multilevel field
1104    o pkg/ctrl & model/inc:
1105      - move additional anomaly fields of control vars (related to options:
1106         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
1107        from DYNVARS.h into new header file: CTRL_FIELDS.h
1108    o pkg/seaice: some small modifications to the ridging code
1109      - make fw2ObyRidge a global variable and add the freshwater flux to
1110        seaice_growth
1111      - pass actual thickness from seaice_prepare_ridging, so that it is
1112        computed only in one place and compute it in the same way as in
1113        seaice_growth
1114      - initialise more fields in seaice_do_ridging that where cause floating
1115        point exceptions over land
1116  o pkg/seaice: preparations for ridging code and first real ridging code  o pkg/seaice: preparations for ridging code and first real ridging code
1117    - move most of "PART 1" of S/R seaice_growth into a new and separate    - move most of "PART 1" of S/R seaice_growth into a new and separate
1118      S/R seaice_reg_ridge that will both regularize the state variable after      S/R seaice_reg_ridge that will both regularize the state variable after
1119      advection call the actual ridging routine;      advection call the actual ridging routine;
1120    - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,    - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
1121      d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;      d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
1122    - remove ridging code from seaice_advdiff    - remove ridging code from seaice_advdiff
1123    - clean up remaining part 1 of seaice_growth in an attempt to make it    - clean up remaining part 1 of seaice_growth in an attempt to make it
1124      more readable (this is probably subjective)      more readable (this is probably subjective)
1125    - call seaice_itd_redist once in the initialisation phase to have the initial    - call seaice_itd_redist once in the initialisation phase to have the initial
1126      conditions in the correct category      conditions in the correct category
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