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revision 1.1980 by mlosch, Wed Apr 23 12:42:19 2014 UTC revision 1.2178 by mlosch, Tue Sep 8 09:45:55 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: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
8      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
9        by AREA according to Connelly et al. (2004), JPO.
10      - For EVP and the LSR solver, the implicit part of the drag term is
11        the only non-zero term in the denominator when there is no ice (which
12        prevented running the model with zero ice-ocean drag). If
13        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
14        (or zero main diagonals BU/BV) which need to be caught. A practical
15        consequence is that for open water, the momentum equation reduce
16        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
17        they happen to be zero, often leading to a non-zero solution over
18        open water.
19    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
20        efficient EVP method.
21      - introduce area-weighted averages for e12 (analogously to
22        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
23        remain, but also changing the order of terms in the previous average
24        changed the results as much) -> update experiment
25      - add SEAICE_DELTA_SMOOTHREG code
26      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
27        TEM-code
28      - adjust loop bounds so that only required fields are computed
29      - add new averaging code for zetaZ/deltaZ (again similar to
30        seaice_calc_viscosities.F), inactive by default for now (will change
31        results again), but will replace old code eventually
32    o eesupp/src:
33      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
34        to always cumulate tile local-sum in the same order
35        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
36        Still uses MPI_Allreduce (like standard code) but on array of tiles
37        and should be faster than GLOBAL_SUM_SEND_RECV code.
38      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
39        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
40      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 13 more exp.:
41         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
42         fizhi-cs-aqualev20, global_ocean_ebm, matrix_example, natl_box,
43         solid-body.cs-32x32x1, tutorial_advection_in_gyre, tutorial_baroclinic_gyre
44         and tutorial_held_suarez_cs.
45    
46    checkpoint65n (2015/07/29)
47    o pkg/thsice:
48      - add a warning when used with pkg/aim but without updating SST
49        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
50    o pkg/offline:
51      - change where Offline-Fields are loaded, from load_fields_driver.F to
52        directly within FORWARD_STEP, just after updating iter number and time;
53      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
54        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
55       These changes allow:
56        a) to recover exactly on-line results using deltaToffline=deltaTClock,
57        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
58        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
59        time-step, both with GM & KPP files and with recomputing these fields;
60        b) no needs to switch on staggerTimeStep anymore;
61        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
62      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
63    o pkg/offline:
64      - change (rarely used) offset-iteration parameter to an offset time (in s):
65        can easily recover previous offset-iter effect by setting offset-time
66        (offlineTimeOffset) to offset-iter x deltaToffline;
67      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
68        in KPP as part of surface buoyancy forcing) in offline run.
69      - fix ptracers KPP non-local term in the case where KPP is re-computed.
70    o OpenAD
71      - Adding preliminary ggl90 test to OpenAD verification.
72        Config. with ggl90 currently diverges after 64 time steps
73        so will need more work to become more stable
74      - Adding preliminary kpp test to OpenAD verification.
75        required small tweakes in kpp_routines.F
76      - Merge and update from Krishna Narayanan's contrib area:
77        * Add one variable for preliminary OpenAD DIVA
78        * Add replacement time-stepping for OpenAD DIVA
79        * genmake2 flag -diva (but only for OpenAD; preliminary)
80        * required modifs for OAD_support
81        successful preliminary test for tutorial_global_oce_biogeo/
82    o pkg/seaice:
83      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
84      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
85        delta with a smooth function in s/r seaice_calc_viscosity
86        (no effect on EVP)
87      - rename local suffix "sqr" into "sq" for more consistent variable names
88    o pkg/seaice:
89        add new parameter SEAICE_deltaMin that is used ***only***
90        for regularizing Delta (and nothing else, like the parameter
91        which is also used for all sorts of things SEAICE_EPS).
92        Defaults to SEAICE_EPS for backward compatibility only.
93    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
94        the wrong key by inialising it before use -> fixes a recomputation
95        problem but does not fix the gradient
96    o pkg/layers:
97      - move resetting of flux arrays to outside the iLa loop
98        (this caused layers_diapycnal to not work with more than one layer coord.)
99      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
100    o pkg/layers:
101      - remove from common block 3D layers fields (used to diagnose transport
102        in tracer coords) and declare them as local arrays in layers_calc.F
103    o pkg/seaice:
104      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
105        in lab_sea forward experiment (changes results -> updated)
106      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
107    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
108       computations; for SEAICE_VECTORIZE_LSR
109      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
110        sweep to the outside,
111      - remove store directives and add "CADJ loop sequential" directives
112        in analogy to model/src/solve_tridiagonal.F
113      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
114        boundaries to yield more readable code. This has also the charming side
115        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
116        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
117        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
118        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
119        an additional option)
120       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
121       but the adjoint gradients (which are affected by this change) still explode.
122    o coupler (atm & ocn _compon_interf):
123      - avoid using Exch2 IO mapping if not suitable.
124    
125    checkpoint65m (2015/06/15)
126    o pkg/layers:
127      - clean-up old parameters setting (from Sep 2012):
128        + remove old parameters setting from common block (declared locally);
129        + stop if any old parameter is mixed with new parameters;
130        + check for valid or consistent parameter setting (e.g., layers_name)
131      - check that layers_bounds for Pot.Density are in the right range;
132        this is supposed to catch un-updated setting after recently shifting
133        potential density field "prho" by -1000 (now in "sigma" scale).
134    o pkg/layers:
135      - Added missing call to layers_fill for keeping track of tottend in
136        pkg/diagnostics/diagnostics_fill_state.F
137    o pkg/layers:
138      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
139        of diapycnal fluxes
140    o pkg/layers:
141      - reverted changes to interpolation to previous treatment; there
142        was never actually a problem
143    o pkg/layers:
144      - fix interpolation of layers tracers in the presence of partial cells
145      - add lots of new functionality to compute water mass transformation
146        (enabled by CPP flag LAYERS_THERMODYNAMICS)
147      - add new calls from main code (diags_oceanic_surf_flux.F,
148        thermodynamics.F, impldiff.F) and gad to save the necessary fields
149        for layers_thermodynamics calculations
150    o pkg/ptracers:
151      - add capability of stepping a passive tracer forward without advection
152        by setting PTRACERS_advScheme to 0.
153    o pkg/diagnostics:
154      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
155    o pkg/layers:
156      - shift potential density field "prho" by -1000 for density layer averaging so
157        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
158        Note that density bin boundaries (layers_bounds in data.layers) have
159        to be set accordingly (i.e., shifted, in sigma scale).
160    o pkg/layers:
161      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
162      - fix calculation of layer non-weighted velocity and layer probability
163      - add diagnostics for pot.density used for layer averaging
164    o pkg/seaice:
165      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
166        positiveness, modify a few comments and improve variable names,
167      - the changed computation of deltaC affects most seaice-related
168        experiments at the truncation level.
169        seaice_itd.thermo is affected by far the most, with
170        only 7 digits of agreement remaining; update experiments.
171    
172    checkpoint65l (2015/05/04)
173    o pkg/shelfice:
174      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
175        factor drKp1 to zero where it is negative (ie. do not use
176        SHELFICEBoundaryLayer if hFacC>1)
177      - the same for factor drLoc in shelfice_forcing.F
178    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
179        with modules in ptracers, when using testreport option "-small_f"
180    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
181      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
182    o verification/testreport
183      - add new option -small_f
184        with this option testreport first makes the target small_f (*.f files)
185        before running make (all). This is useful for explicit inlining when
186        all sources need to be full available.
187    o pkg/exf/exf_interp.F:
188        remove previous changes related to reverse (decreasing) input grids latitude
189    
190    checkpoint65k (2015/04/01)
191    o pkg/ecco:
192        fix missing cosphi initialization; use eccoiter in place of optimcycle;
193        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
194        instead of active read/write
195    o pkg/ctrl:
196        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
197        instead of active read/write.
198    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
199        return if .NOT.useAUTODIFF
200    o pkg/seaice: add CPP brackets (cost function related).
201    o model/src:
202        add useAUTODIFF run time switch.
203    o pkg/exf/exf_interp.F:
204        add code to allow input grids with latitude starting in the north (i.e. when
205        j=1 corresponds to northern edge of field); modify global_with_exf to test
206        this feature.
207    o verification/testreport:
208      - replace "grep -A3" with POSIX conformal sed command, because there are
209        implementations of grep that cannot do contextual searches
210      - replace "cat -n" by "nl" (two occurrences), because not all implementations
211        of "cat" have the option "-n"
212    o model/src:
213        add new file gsw_teos10.F that contains 3 functions, more or less a copy
214        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
215        convert from conservative to potential temperature. For now they are not
216        called anywhere.
217    o pkg/ggl90: make "useIDEMIX" useful
218      - re-organize code in s/r ggl90_calc a little to move computations that
219        are different for idemix into separate loops (changes verification
220        experiment idemix at truncation level, 12 digits remain -> updated)
221      - requires 2 new 2D fields KappaM, verticalShear
222      - make hFacI and recip_hFacI local 3D variables that are passed to
223        s/r ggl90_idemix
224      - fix and improve some comments
225    
226    checkpoint65j (2015/02/25)
227    o pkg/openad
228      - synchronize seawater.F with version in model/src: replace routine
229        body of sw_temp by calling sw_ptmp and fix/add a few comments.
230    o pkg/mnc:
231      - change default value of pickup_read/write_mnc params to FALSE
232        (since few features are missing in reading MNC pickup files).
233    o model/src:
234      - change default (background) vertical diffusivity for salt to be the
235        temperature (background) vertical diffusivity.
236      - change background vertical diffusivity in vertical mixing pkgs ggl90,
237        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
238        This makes ptracers default diffusivity (that uses salt diffKr) more
239        consistent with vertical mixing schemes.
240    o verification/testreport:
241      - fix typo in "-pcls" option ;
242      - put temp files in /tmp (instead of in local dir)
243      - add option "-ncad" to use genmake2 new option "-nocat4ad"
244      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
245    o pkg/ggl90 (idemix code):
246      - apply few fixes ; add some missing "_d 0" ; update output of exp.
247        global_ocean.90x40x15.idemix
248    o OpenAD
249      - enable active file I/O and begin removal of work-around code
250        for OpenAD for handling control variables (memory vs. active files)
251      - new CPP options file OPENAD_OPTIONS.h
252      - revert to genarr2d gradient check for hs94.1x64x5
253      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
254      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
255    o tools/genmake2:
256      - add option for an alternative Makefile (from Martin) where multiple
257        source files are sent to TAF (instead of all in one file).
258    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
259      - code provided by Carsten Eden as an extension of ggl90
260      - so far the code is turned on within ggl90 by setting a CPP-flag at
261        compile time; a runtime flag implementation is not yet complete
262      - tested in new verification experiment global_ocean.90x40x15.idemix
263    o verification:
264      - reduce length of the AD test run by half for experiments
265        global_ocean.cs32x15 (std + thsice) and isomip
266      - enable active file I/O for OpenAD, adjust verifications accordingly
267      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
268    o verification/testreport:
269      - fix two non-POSIX sed statements so that there are no error messages
270        on Mac OS X
271      - replace hostname -s with hostname | sed 's/\..*$//'
272    o model/src/seawater.F:
273      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
274        (following the matlab code), which would have avoided the bug caught
275        by Matt (see below) in the first place
276    o pkg/shelfice:
277      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
278        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
279      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
280        ice-shelf case (i.e., within surface level).
281      - add config summary in shelfice_check.F
282      - remove global variable recip_SHELFICElatentHeat and replace by a local
283        variable recip_latentHeat
284      - introduce diagnostics for friction velocity uStar (in case of
285        SHELFICEuseGammaFrict)
286      - change verification experiment isomip.htd:
287        + start from pickup (as input_ad at nIter0=8640)
288        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
289        + test SHELFICEuseGammaFrict = .TRUE.
290        + test SHELFICEadvDiffHeatFlux = .TRUE.
291    o model/src:
292      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
293        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
294        update output of experiments global_with_exf.yearly and isomip (all 6).
295    o pkg/shelfice:
296      - change setting of kTopC to also be zero where there is no ice-shelf.
297      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
298        ice-shelf is.
299      - first attempt to get RealFreshWaterFlux effects: for now, only without
300        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
301    o pkg/seaice: add the option to prescribe a fixed thickness PDF
302      for thermodynamic calculations
303      - because of divisions of the type 7/7 not exactly equal to 1, this change
304        affects results of some verification experiments by up to 4 digits:
305        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
306        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
307        adjoint: lab_sea, lab_sea.noseaicedyn
308        -> updated
309    
310    checkpoint65i (2015/01/23)
311    o model/src:
312      - change units of frictionHeating field from W to W/m^2
313      - fix bug in frictional heating from stratospheric drag in
314        S/R ATM_PHYS_TENDENCY_APPLY_V
315      - with synchronous time-stepping: move resetting to zero of frictionHeating
316        field from load_fields_driver.F to thermodynamics.F ;
317      - add diagnostics for frictional heating.
318    o model/src & gmredi K3D:
319      - add frictionHeating field to pickup-files (for synchronous time-stepping)
320      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
321      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
322        and name in pickup file).
323      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
324    o model/src:
325      - move (from ini_forcing.F) initialisation of all arrays in header file
326        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
327        (since Nov 2012) with option selectAddFluid=1.
328    o pkg/shelfice:
329      - change units (+ document) of newly added field "shelfIceMassDynTendency"
330      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
331    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
332    o pkg/seaice: two new runtime parameters:
333      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
334        long overdue
335      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
336        parameterization of tensil stress for fast ice (does not do anything yet)
337    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
338        for LSR: move checking overlaps out of JFNK-if-block
339    o pkg/atm_phys:
340      - move copy of grid and dynamical fields out of atm_phys_driver.F into
341        new S/R ATM_PHYS_DYN2PHYS.
342      - fix level height for Linear Free-Surf case (to be consistent with
343        fixed-in-time pressure levels).
344    o pkg/mom_common (bottomdrag):
345      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
346        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
347        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
348    o pkg/shelfice (u/v_drag):
349      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
350      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
351        (now similar to shelfice_u_drag.F)
352      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
353        from mom_vecinv.F (similar to mom_fluxform calls).
354    o pkg/mom_common (bottomdrag):
355      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
356      - add options for alternative discretisation of velocity norm in quadratic
357        bottom drag: averaging of grid-cell-center KE to U.point and V.point
358        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
359        improves when averaging only the other component (e.g. vVel for U bottom
360        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
361      - add options (bottomVisc_pCell) to account for partial-cell in bottom
362        friction (no-slip BC) thus getting the true distance from the bottom;
363        off by default since this also reduces model stability (explicit bottom
364        friction). Changes produce different machine truncation with linear-drag
365        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
366        front_relax (bvp & mxl, 10 & 11 digits).
367    o model/src & mom pkgs:
368      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
369        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
370      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
371        just copy level Nr value to level Nr+1.
372    o doc:
373      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
374    o pkg/streamice:
375      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
376        SHELFICE.h: move array shelficemass to init_varia, initialise
377        from array shelficemassinit, which is set in init_fixed and
378        has option to be set from file; introduce array
379        shelficeMassDynTend array, set thru file in init_fixed
380      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
381        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
382        pkg/streamice
383      - shelfice_thermodynamics.F: call shelfice_step_icemass if
384        SHELFICEMassStepping = .true.
385      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
386    
387    checkpoint65h (2014/12/17)
388    o verification/global_ocean.90x40x15, global_ocean_ebm:
389      - update to generic controls.
390    o pkg/ctrl:
391      - ctrl_map_ini_genarr.F: test for igen>0
392      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
393      - move gentim2d part of ctrl_map_ini_genarr.F to
394        new separate routine : ctrl_map_ini_gentim2d.F
395      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
396        add time variable weights and cyclic controls (time mean,
397        seasonal cycle, etc) capabilities to gentim2d
398    o pkg/ecco:
399      - move reading of error, conversion to weights from
400        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
401    o global_oce_llc90, cs32:
402      - activte sbo.
403      - CTRL_SIZE.h : add maxCtrlProc.
404      - activate the new genctrl capabilities.
405      - update following reorganization of global_oce_input_fields.tar.gz  
406    o pkg/ctrl/ctrl_ad_diff.list:
407      - add missing ctrl_init_rec.f
408    o tools/OAD_support/keepOriginal:
409      - add ctrl_init_rec.F
410    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
411      - avoid recomputations of xx_gentim2d_dummy.
412    o momentum diagnostics:
413      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
414        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
415    o pkg/seaice/seaice_lsr.F:
416      - fix computation of BU/BV, make sure they are non-zero, only necessary
417        for cubed sphere exchanges and SEAICE_OLx/y>0.
418        This makes calling s/r fill_cs_corner_rl obsolete (removed).
419    o verification/global_ocean.cs32x15/input.seaice
420      - add test for strong implicit coupling and restricted addtive Schwarz
421        methods for LSR
422      - update results/output.seaice.txt
423    o verification/tutorial_global_oce_biogeo:
424      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
425        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
426        update output_adm,_oadm,_tlm.txt
427    o pkg/dic:
428      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
429      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
430        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
431    o verification/tutorial_global_oce_biogeo:
432      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
433        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
434        update output_adm,_oadm,_tlm.txt
435    o eesupp/src:
436      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
437        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
438    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
439      LSR (following Hutchings et al. 2004)
440      - introduce zetaZ as a global variable (requires adjustments in
441        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
442        in seaice_calc_viscosities.F
443      - new flag SEAICEuseStrImpCpl (default off)
444      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
445        momentum equations
446      - JFNK-solver (preconditioner) adjusted to allow using this method
447        (where it does not have any positive effect)
448    o pkg/seaice
449      - add overlap for restrictive additive Schwartz method also to LSR, but
450        turn it off by default (because it only seems to work for non-cubed
451        sphere/llc topologies)
452    o pkg/autodiff
453      - add extra exchanges in addummy_in_steppging also for mnc output
454    o pkg/seaice:
455      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
456        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
457    o pkg/obcs:
458      - add option to specify domain-connected piece Id along OB though files
459        (for now, only used to diagnose PhiVel; default =1 -> global correction)
460      - modify obcs_diag_balance.F to process each connected-part separately;
461        exclude OB where Id = 0 but keep the full divergence there (-> constant
462        Psi along this portion of OB and all inflow derived from grad(Phi))
463      - add example of OB-conect files in verification/so_box_biogeo/input.
464    o pkg/diagnostics:
465      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
466      a) use non zero matrix element across OB and solve for Phi 1 grid point
467         outside OB (i.e, where tracer OBCS are applied).
468      b) global imbalance of inFlow/outFlow across OB: instead of modifying
469         velocity across OB, spread it uniformly along the OB in the RHS.
470    
471    checkpoint65g (2014/11/19)
472    o pkg/diagnostcis:
473      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
474    o pkg/my82,pp81,kl10:
475      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
476        field diffKr as background diffusivity to set minimum diffusivity value.
477    o pkg/seaice:
478      - add new parameter SEAICEuseEVPrev (for revisited EVP by
479        Bouillon et al 2013)
480      - add SEAICE_evpAlpha/Beta to namelist
481      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
482        involve trivial re-ordering of divisions/multiplications that should not
483        have any effects, but ... they do change the results of lab_sea.hb87 so
484        that only 2 digits of agreement remain, in line with the general
485        instability/fragility of the evp-code. For now, I do not care and just
486        update the verification experiment
487    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
488      - remove xx_genarr2d_numsmooth etc
489      - use xx_genarr2d_preproc etc instead
490      - carry out smooth_correl2D at initialization stage rather than during
491        time stepping.
492      - get smoothOpNb from xx_gentim2d_preproc
493    o global_oce_cs32 :
494      - add test of generic ecco capabilities.
495    o pkg/exf/exf_getsurfacefluxes.F :
496      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
497    o pkg/ctrl,ecco :
498      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
499        is defined.
500    o pkg/seaice: add diagnostics for Delta (deformation parameter)
501    o model/src:
502      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
503        diffusivity (background) is specified but ignored.
504    o verification:
505      - in testreport, convert hostname to lower case for default output dir name
506    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
507    o pkg/dic: add modifications from Hajoon:
508      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
509      - light attenuation: add self-shading effect by climatological Chlorophyll
510        (read from file).
511    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
512        compiles when SEAICE_ALLOW_DYNAMICS is undefined
513    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
514        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
515        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
516        approach where CPP_OPTIONS.h includes an omnipotent
517        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
518    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
519        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
520    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
521        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
522        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
523    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
524      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
525      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
526      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
527      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
528    o pkg/ctrl,ecco,exf :
529      - remove variables associated with NON-generic costs,
530        unless ECCO_CTRL_DEPRECATED is defined.
531      - remove NON-generic NON-obcs controls,
532        unless ECCO_CTRL_DEPRECATED is defined.
533    o pkg/ctrl : added ctrl_local_params.h
534    o pkg/ecco : added ecco_local_params.h
535    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
536        experiments, which will progressively be removed once the
537        experiments are revised to use only generic controls/costs.
538    
539    checkpoint65f (2014/10/13)
540    o pkg/ctrl, ecco, seaice : minor changes in headers
541    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
542        cost function and control capabilities added since checkpoint65c.
543    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
544    o pkg/ecco: increase modularity and improve logic
545      - ecco_toolbox.F (new) : basic operations that are often used,
546        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
547        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
548      - cost_gencal.F (new) : determine filnames and records.
549      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
550      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
551        and exploit the above functions leading to more compact code.
552      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
553      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
554        using_ers, using_gfo, using_mdt is now only defined within gencost)
555    o pkg/ecco: extend generic cost capabilities
556      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
557        capabilities via gencost_preproc (+ _c,_i,_r related params),
558        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
559        gencost_outputlevel arguments to cost_generic
560      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
561        and active_read, making room for gencost_preproc to take effect.
562        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
563      - pkg/ecco/cost_generic.F :
564        compute and store misfit maks*(model-data) in localdif that is
565        then used in cost and for output, output misfit if outlev.GT.0
566      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
567        rather gencost_barfile for deciding whether to write barfile
568      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
569      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
570        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
571      - pkg/ecco/ecco_summary.F : report gencost variables
572      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
573    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
574    o pkg/ecco: internal re-organization
575      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
576        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
577        mv relevant variables definition from ecco_cost.h to ecco.h,
578        make sure gencost routines only include ecco.h)
579      - throughout : add missing CCP switches, rm unused variables,
580        and rm un-necessary CPP switches
581      - throughout gencost routines : replace modelstartdate with
582        gencost_startdate when needed
583      - cost_bp_read.F : use arguments, instead of common blocs
584        so that it can be used also by (new) cost_gencost_bpv4.F
585      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
586      - ecco_phys.F : compute etanFull
587      - ecco_readparms.F : rename using_topex as using_tpj, add
588        bpv4-grace to gencost list, initialize added parameters
589      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
590    
591    checkpoint65e (2014/09/28)
592    o pkg/obcs:
593      - replaced the just-added CPP options with run-time variables
594        (see pkg/obcs/OBCS_PARAMS.h for details)
595    o pkg/obcs:
596      - add additional CPP options for sponge boundary layers
597        (see pkg/obcs/OBCS_OPTIONS.h for details)
598    o pkg/atm_phys:
599      - implement simple (obliquity only, assuming circular planet orbit)
600        seasonal cycle for incoming insolation ; used when run-time parameter
601        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
602    o pkg/exf, pkg/ecco, pkg/ctrl:
603      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
604      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
605      - implement gentim2d for xx_tauu, xx_tauv
606    o pkg/ctrl, pkg/ecco :
607      - fix and complement the generic controls implementation
608    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
609        pkg/shelfice/shelfice_thermodynamics.F,
610        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
611        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
612      - add weight in CTRL_GET_GEN calls
613    o pkg/ctrl :
614      - ctrl_get_gen.F : add weight as input parameter, and apply
615        it directly rather than using smooth_correl2Dw (to be retired).
616      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
617    o pkg/ctrl :
618      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
619        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
620      - re-activate ctrl_summary (call in ctrl_init.F)
621    o pkg/ctrl/ctrl_cost_gen.F :
622      - fix CCP brackets, remove un-necessary myiter, mytime
623    o pkg/ecco, pkg/ctrl :
624      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
625      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
626      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
627      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
628    
629    checkpoint65d (2014/09/15)
630    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
631      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
632        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
633    o pkg/ctrl/ctrl_map_ini_genarr.F :
634      - remove compilation failure
635      - replace hard coded example
636      - use ctrl_map_ini_gen2D, 3D
637    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
638      - on/off switch based upon xx_genarr2d_weight,3d
639    o src/packages_init_variables.F :
640      - regroup pkg/estimation calls
641      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
642        (moved to ctrl_init_variables)
643    o cost/cost_init_varia.F :
644      - remove ecco_cost_init_varia
645        (moved to ecco_init_varia)
646    o ctrl/ctrl_init_variables.F :
647      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
648      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
649    o ctrl/ctrl_map_ini.F :
650      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
651        (moved to ctrl_init_variables)
652    o ctrl/ctrl_map_ini_ecco.F :
653      - remove ECCO_PHYS (mv to ecco_init_varia)
654      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
655    o ecco/ecco_ad_diff.list :
656      - add ecco_init_varia.f
657    o ecco/ecco_init_varia.F
658      - new routine
659    o pkg/streamice:
660      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
661        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
662      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
663    o pkg/generic_advdiff:
664      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
665    o pkg/exf:
666      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
667         xxg_precip capability
668      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
669    o pkg/ctrl:
670      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
671    o model/src/load_fields_driver.F :
672      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
673        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
674    o OpenAD verification experiments:
675      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
676        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
677        for now, only in pkgs used in OpenAD verification experiments.
678      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
679        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
680        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
681        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
682    o OpenAD verification tests:
683      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
684      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
685        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
686      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
687        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
688    o model/src & generic_advdiff:
689      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
690        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
691        dynamics requires valid tracer forcing only over tile interior but, for
692        some diagnostics, may need to extend it over 1 point in tile halo region.
693      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
694        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
695        setting in temp/salt/ptracer_integrate.F
696    o pkg/dic:
697      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
698        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
699        in gchem_forcing_sep.F
700    o pkg/autodiff & obcs:
701      - add storage of current OB values for U & V (was already done for T & S).
702    
703    checkpoint65c (2014/08/30)
704    o pkg/dic:
705      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
706        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
707        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
708    o verification:
709      - new experiment testing OBCS and DIC pkgs, using params & output from
710        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
711        passage: take OBCS from the last year of a 2 yrs simulation and initial
712        conditions from t=1.yr while keeping the same forcing.
713    o model/src:
714      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
715        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
716    o pkg/diagnostics (Stats-Diags):
717      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
718        a) refine region where stats are computed, excluding where arrhFac=0 ;
719        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
720        c) extend regional stats over the region edges (for U or V pt location).
721    o pkg/gchem:
722      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
723        pkg/dic is currently changing/updating ptracers values beyond the OB).
724    o verification (hs94):
725      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
726        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
727        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
728        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
729    o pkg/ptracers:
730      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
731        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
732      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
733        with AB-2 code (so that it get tested).
734    o model/src:
735      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
736        with AB-2 code (previously only available with AB-3 code).
737        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
738        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
739        there, by calling CYCLE_AB_TRACER).
740    o pkg/generic_advdiff:
741      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
742        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
743        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
744        S/R temp/salt/ptracers_integrate.F
745    o model/src & pkg/ptracers:
746      - remove common block variables gT,gS (in DYNVARS.h), except when
747         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
748      - remove common block variable gPtr.
749    o model/src & pkgs:
750      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
751         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
752         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
753         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
754      + change accordingly all calling S/R.
755      - use local temperature/salinity/ptracer tendency array (without bi,bj)
756        in S/R temp/salt/ptracers_integrate.F
757    o pkg/seaice:
758      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
759        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
760      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
761        in seaice_lsr
762      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
763        in s/r seaice_lsr_calc_coeffs
764    o pkg/mdsio:
765      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
766        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
767        too long (e.g., > MAX_LEN_FNAM/2 )
768    
769    checkpoint65b (2014/08/12)
770    o pkg/matrix:
771      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
772    o model/src:
773      - fix initialisation of geothermalFile; compile geothermal-flux code in
774        natl_box verification experiment.
775    o model/src & pkg/down_slope:
776      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
777      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
778        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
779        results at machine truncation level: update output of experiments
780        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
781    o pkg/diagnostics (Stats-Diags):
782      - do not cumulate the full volume when DIAGNOSTICS_FILL is
783        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
784        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
785        times (but Min,Max and StD are still wrong).
786    o model/src:
787      - add geothermal flux forcing: read in ini_forcing.F as time-constant
788        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
789    o model/src:
790      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
791        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
792        arrays are already updated while adjustments (filters, conv.adjustment) are
793        still applied later, in S/R TRACERS_CORRECTION_STEP.
794    o model/src:
795      - store in common bloc array "rhoInSitu" the virtual potential temperature
796        anomaly that is used to compute geopotential: this make the atmos code
797        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
798    o pkg/seaice/seaice_lsr.F
799      - rename integer variable ilcall to ipass (that's what it is called
800        in the residual diagnostics
801      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
802        default) for improved non-linear convergence of the first few steps
803      - adjust a few comments and add new ones to explain some of the store
804        directives
805    o pkg/generic_advdiff (& ptracers):
806      - re-work the code to check for valid advection scheme and for minimum
807        size of overlap (now stored in local common bloc in gad_advscheme.F)
808    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
809      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
810      - add an auxilliary variable "bet" and fix store directives and keys in
811        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
812        less exact gradients in my tests); but there are still
813        recomputation warning (although gradients are sort of OK), when
814        SEAICE_LSR_VECTORIZE is not defined, so this flag and
815        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
816      - update verification experiments lab_sea.
817      - change some comments in S/R seaice_calc_viscosities
818    o model/src:
819      - if staggerTimeStep=T, always apply exchange to velocity field in
820        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
821        (independent of using multi-dim advection or not); no effect on FWD run
822        but affects AD results (at machine truncation level): update output of
823        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
824        and isomip (oad: 12.d).
825    o pkg/generic_advdiff:
826      - stop if doAB_onGtGs is set to FALSE but ignored
827      - refine warning related to stability of tracer time-stepping
828        regarding internal wave dynamics.
829      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
830        on staggerTimeStep & implicitIntGravWave (will now get a warning
831        if potentially unstable).
832    o pkg/kl10:
833      - add new pkg "kl10" for mixing due to internal wave breaking, from
834        http://www.sciencedirect.com/science/article/pii/S1463500310000144
835        (contribution from Jody Klymak), tested in verification experiment
836        verification/internal_wave/input.kl10/
837    o isomip experiment:
838      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
839        (input.htd) and update the output.
840    o cd_code experiments:
841      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
842        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
843        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
844        update the corresponding output.
845    o pkg/seaice:
846      - reduce the number of include files and store directives in
847        S/R seaice_lsr_tridiagu/v
848      - change the order of loops in one case in S/R seaice_lsr_tridiagv
849        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
850        get rid off one store directive (a TAF bug?)
851      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
852        S/R seaice_lsr_tridiagv to change the loop range for consistency
853      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
854      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
855        S/R seaice_lsr_tridiagu/v (requires update of
856        offline_exf_seaice/input.dyn_jfnk)
857    
858    checkpoint65a (2014/07/27)
859    o model/src:
860      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
861        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
862        (topo in p-coords, ice-shelf in z-coords); update output of experiments
863        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
864    o model/src:
865      - collect momentum forcing tendency into local 2-D array (passed as argument
866        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
867        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
868        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
869      - collect T & S forcing tendency into local 2-D array (passed as argument to
870        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
871        affects results at machine truncation level (e.g., ocean: if using
872        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
873        correction due to vertical advection).
874      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
875        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
876        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
877        obcs_ctrl (ad & fwd grd @ 12 & 7).
878    o pkg/ptracers & diagnostics:
879      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
880        title (to avoid some unexpected truncation); sort out ptracers diags units.
881      - collect ptracer forcing tendency into local 2-D array (passed as argument
882        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
883    
884    checkpoint65 (2014/07/18)
885    o pkg/fizhi:
886      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
887        affects results at machine truncation level. Update output of experiments
888        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
889    o pkg/seaice: more clean up
890      - rename TAF common block tapes to be more consistent and remove
891        unnecessary duplicates
892      - add store directives to remove more recomputations, but use smaller
893        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
894        The idea behind this flag is to reduce the memory footprint when the
895        adjoint of the LSR is not required. As of now, defining the flag
896        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
897        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
898        For experiment offline_exf_seaice, this means on a linux box with gfortran
899        nearly a factor of 10 (but keep in mind there is mostly seaice code in
900        this experiment):
901        > size mitgcmuv_ad
902        text    data        bss     dec        hex
903        5100659 1216  220458952  225560827  d71c8fb
904        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
905        but only a moderate increase of 36% for global_ocean.cs32x15:
906        text    data        bss     dec        hex
907        6695027 1648 1014578664 1021275339 3cdf6ccb
908        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
909      - note: there are still recomputations in global_ocean.cs32x15 and
910        offline_exf_seaice and the gradient agreement changes (gets a
911        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
912      - in general, the AD gradients still are wrong
913    o OpenAD
914      - clean up code_oad/ directories somewhat by moving files
915        dontCompile, dontTransform, keepOriginal to OAD_support/
916    o model/src:
917      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
918        (not currently tested): add dissipation terms before NLFS rescaling of
919        tendencies (previously done after).
920    o pkg/diagnostics:
921      - write stats-diags in ascii file with more digits (same as in monitor).
922    o pkg/down_slope:
923      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
924        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
925    o model/src:
926      - new file "apply_forcing.F" containing all the code previously in
927        external_forcing.F, but with new argument list: pass, as new argument,
928        the current level tendency array to update (instead of a direct update
929        of the common bloc array). Change the corresponding calls.
930      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
931        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
932    o pkg/seaice/seaice_lsr, a little bit of clean up
933      - rearrange some code blocks, so that now all calculations for
934        setting up the right-hand-sides done within one single block
935        (I find that easier to read and understand)
936      - rearrange freedrift-code to reduce the number of ifdefs
937      - adjust some indentations and comments
938    
939    checkpoint64z (2014/07/10)
940    o model/src and several pkgs:
941      - change argument list of all S/R called from external_forcing.F and
942        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
943        to pass, as argument, the current level tendency array to update
944        (instead of a direct update of the common bloc array).
945      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
946      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
947    o pkg/seaice/seaice_lsr.F
948      - always initialize local arrays in seaice_lsr_tridiagu/v
949      - add more local tapes to seaice_lsr_tridiagu/v
950      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
951        keep it in bi/bj loop; this seems to be essential
952      - gradients are still wrong but only by 4-7 orders of magnitude
953        instead of 15 orders of magnitude, lab_sea improves a little
954    o pkg/seaice
955      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
956        generates unnecessary code in seaice_lsr_ad
957      - add more store directives in seaice_lsr to avoid unnecessary code
958        in seaice_lsr_ad
959      - exclude some residual computations in seaice_lsr when
960        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
961        in seaice_lsr_ad
962      - add more storing, a new tape (model/src/the_main_loop.F) and
963        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
964        and klockey should be checked by a specialist)
965      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
966        and update lab_sea after previous changes in pkg/seaice below
967    o pkg/autodiff:
968      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
969        viscFacInAd : run time parameters allowing for adjoint switches
970        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
971    o pkg/ecco:
972      - introduce cost_gencost_boxmean.F that computes a box mean
973        temperature (for use in adjoint sensitivity studies).
974    o model/src/set_defaults.F : initialize viscFacAdj to 1.
975    o pkg/mom_common/mom_calc_visc.F:
976      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
977    o pkg/seaice/seaice_summary.F:
978      - statement for SEAICEadjMODE now in autodiff_readparms.F
979    o pkg/seaice:
980      - remove some store directives and add new ones in an effort to get
981        finally rid off the recomputation warnings. This is successful
982        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
983        defined (i.e. no extensive recomputation warnings left), but there
984        are still too many recomputations on the solver iteration level
985      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
986      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
987        SEAICE_SIZE.h
988      - add a store directive in S/R seaice_calc_viscosities
989    o pkg/seaice (ITD code):
990      - fix definition of Hlimit for multi-threaded case
991      - use double precision arithmetic to compute Hlimit: this affects results;
992        update output of experiment seaice_itd.
993    o replace content of verification/seaice_itd
994      - instead of a 1D column use the configuration of offline_exf_seaice
995        to test the ice thickness distribution code with ridging
996      - this is a first shot at this experiment
997      - change of some defaults of ridging parameters SEAICEhStar (from
998        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
999        and lot of new comments.
1000    
1001    checkpoint64y (2014/06/20)
1002    o pkg/seaice/seaice_reg_ridge.F:
1003      - modify the regularization of very small volumes of ice; only check
1004        total volume HEFF, and do not apply correction to individual ice
1005        classes because that leads to funny patterns in the heat and fw-fluxes
1006        into the ocean. Adjust seaice_itd/results/output.txt
1007      - replace nITD by SEAICE_multDim in loop-ranges
1008    o pkg/exf:
1009      - add code to process the case field period = -12. with UV interpolation.
1010      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
1011        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
1012    o verification/global_with_exf:
1013      - switch all fields period to -12. (was previously untested) in input/data.exf
1014        (but keep secondary test ".yearly" unchanged); update the reference output.
1015    o pkg/cal:
1016      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
1017    o pkg/exf:
1018      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
1019        to replace logical switch "exf_verbose"
1020      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
1021    o pkg/sbo:
1022      - update from Katherine Quinn: evaluate mass directly from density and SSH
1023        (budget using Finite Volume method) instead of from bottom pressure.
1024      - allow testreport to collect few selected SBO output ; tested in exp.
1025        global_ocean.90x40x15 (after updating the results, to include SBO output).
1026      - fix some multi-threading issues (in output part).
1027    o model/src & most packages:
1028      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
1029      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
1030        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
1031        "data.{pkg}" exist ; and leave the S/R (return) just after.
1032      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
1033        + call LAND_READPARMS from packages_readparms.F
1034    o pkg/seaice:
1035      - remove code that resets useThSice in S/R seaice_readparms and
1036        replace it by a warning in S/R seaice_check
1037      - remove parameter MULTDIM, replace with nITD and runtime
1038        parameter SEAICE_multDim (still hard-wired to nITD if
1039        SEAICE_ITD is defined)
1040    
1041    checkpoint64x (2014/05/24)
1042    o verification/lab_sea:
1043      - update adjoint and TLM output following changes to pkg/salt_plume
1044      - un-do the update after putting back local recip_Cp in few places.
1045    o pkg/salt_plume: modifications by An Nguyen:
1046      - add capability to do brine rejection (salt-plume) as function of
1047        volume+tracers (instead of only salinity tracer).
1048      - conserve volume by exchanging volume from each kLev to above to
1049        accommodate in-coming brine volume
1050      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
1051      - switch KPP surf buoyancy due to brine forcing to 3-d
1052        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
1053      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
1054      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
1055        in East/West Arctic.
1056    o pkg/sbo:
1057      - incorporate modifications from Katherine Quinn to enable the use of sbo
1058        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
1059        output for future testreport verification (unfinished).
1060    o pkg/atm_phys:
1061      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
1062        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
1063        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
1064    o pkg/seaice
1065      seaice_calc_ice_strength.F: modify expression to avoid divisions
1066        (affects truncation)
1067      seaice_do_ridging.F: clean up the insectarium
1068      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
1069      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
1070      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
1071      - add some debugging information and error messages (warnings)
1072    o model/src: modifications relatd to atmosphere p*:
1073      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
1074      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
1075        of vertical profile tRef in geopotential background and anomaly.
1076      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
1077        and pkg/atm_phys.
1078      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
1079        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
1080    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
1081    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
1082        not used right now, but can be used in BGC packages to fix conservation.
1083    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
1084        other packages too.
1085    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
1086        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
1087    o model/src:
1088      - since we have several heat capacity (even in model/src), define "recip_Cp"
1089        as local variable (no longer in common block) to avoid any confusion.
1090      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
1091    o pkg/exf:
1092      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
1093        air density as function of air Temp, Humidity and atm pressure.
1094    
1095    checkpoint64w (2014/05/02)
1096    o verification:
1097      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
1098        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
1099        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
1100        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
1101        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
1102    o model/src: for atmosphere in p* coords:
1103      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
1104      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
1105        but not yet activated.
1106    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
1107      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
1108      - this changes the results (but not for any verification experiment, because
1109        none tests this), but avoids having an extra field in the restart files
1110    o pkg/seaice: remove global variable TICE (not needed)
1111      - replace by TICES or local variable where necessary (cost_seaice_test,
1112        seaice_diagnostics_state)
1113      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
1114      - use specific read/write routines for reading and writing individual leves
1115        of a multilevel field
1116    o pkg/ctrl & model/inc:
1117      - move additional anomaly fields of control vars (related to options:
1118         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
1119        from DYNVARS.h into new header file: CTRL_FIELDS.h
1120    o pkg/seaice: some small modifications to the ridging code
1121      - make fw2ObyRidge a global variable and add the freshwater flux to
1122        seaice_growth
1123      - pass actual thickness from seaice_prepare_ridging, so that it is
1124        computed only in one place and compute it in the same way as in
1125        seaice_growth
1126      - initialise more fields in seaice_do_ridging that where cause floating
1127        point exceptions over land
1128  o pkg/seaice: preparations for ridging code and first real ridging code  o pkg/seaice: preparations for ridging code and first real ridging code
1129    - 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
1130      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
1131      advection call the actual ridging routine;      advection call the actual ridging routine;
1132    - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,    - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
1133      d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;      d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
1134    - remove ridging code from seaice_advdiff    - remove ridging code from seaice_advdiff
1135    - 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
1136      more readable (this is probably subjective)      more readable (this is probably subjective)
1137    - 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
1138      conditions in the correct category      conditions in the correct category
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