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revision 1.1994 by mlosch, Mon May 12 14:15:52 2014 UTC revision 1.2181 by jmc, Mon Sep 14 22:14:27 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/seaice_do_ridging.F: clean up the insectarium  checkpoint65o (2015/09/14)
8    o pkg/mom_vecinv & mom_common:
9      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
10        called from there.
11      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
12        allows to use Vector-Invariant form in deep atmos and anelastic formulation
13    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
14      and Koenig-Beatty+Holland (2012)
15      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
16      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
17      - requires an extra input argument for S/R seaice_calc_viscosities
18      - tensileStrength's depth dependence is different from Itkin et al. (2015)
19        (to be changed and played with, for now exponential)
20    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
21      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
22        by AREA according to Connelly et al. (2004), JPO.
23      - For EVP and the LSR solver, the implicit part of the drag term is
24        the only non-zero term in the denominator when there is no ice (which
25        prevented running the model with zero ice-ocean drag). If
26        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
27        (or zero main diagonals BU/BV) which need to be caught. A practical
28        consequence is that for open water, the momentum equation reduce
29        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
30        they happen to be zero, often leading to a non-zero solution over
31        open water.
32    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
33        efficient EVP method.
34      - introduce area-weighted averages for e12 (analogously to
35        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
36        remain, but also changing the order of terms in the previous average
37        changed the results as much) -> update experiment
38      - add SEAICE_DELTA_SMOOTHREG code
39      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
40        TEM-code
41      - adjust loop bounds so that only required fields are computed
42      - add new averaging code for zetaZ/deltaZ (again similar to
43        seaice_calc_viscosities.F), inactive by default for now (will change
44        results again), but will replace old code eventually
45    o eesupp/src:
46      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
47        to always cumulate tile local-sum in the same order
48        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
49        Still uses MPI_Allreduce (like standard code) but on array of tiles
50        and should be faster than GLOBAL_SUM_SEND_RECV code.
51      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
52        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
53      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
54         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
55         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
56         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
57         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
58    
59    checkpoint65n (2015/07/29)
60    o pkg/thsice:
61      - add a warning when used with pkg/aim but without updating SST
62        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
63    o pkg/offline:
64      - change where Offline-Fields are loaded, from load_fields_driver.F to
65        directly within FORWARD_STEP, just after updating iter number and time;
66      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
67        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
68       These changes allow:
69        a) to recover exactly on-line results using deltaToffline=deltaTClock,
70        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
71        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
72        time-step, both with GM & KPP files and with recomputing these fields;
73        b) no needs to switch on staggerTimeStep anymore;
74        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
75      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
76    o pkg/offline:
77      - change (rarely used) offset-iteration parameter to an offset time (in s):
78        can easily recover previous offset-iter effect by setting offset-time
79        (offlineTimeOffset) to offset-iter x deltaToffline;
80      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
81        in KPP as part of surface buoyancy forcing) in offline run.
82      - fix ptracers KPP non-local term in the case where KPP is re-computed.
83    o OpenAD
84      - Adding preliminary ggl90 test to OpenAD verification.
85        Config. with ggl90 currently diverges after 64 time steps
86        so will need more work to become more stable
87      - Adding preliminary kpp test to OpenAD verification.
88        required small tweakes in kpp_routines.F
89      - Merge and update from Krishna Narayanan's contrib area:
90        * Add one variable for preliminary OpenAD DIVA
91        * Add replacement time-stepping for OpenAD DIVA
92        * genmake2 flag -diva (but only for OpenAD; preliminary)
93        * required modifs for OAD_support
94        successful preliminary test for tutorial_global_oce_biogeo/
95    o pkg/seaice:
96      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
97      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
98        delta with a smooth function in s/r seaice_calc_viscosity
99        (no effect on EVP)
100      - rename local suffix "sqr" into "sq" for more consistent variable names
101    o pkg/seaice:
102        add new parameter SEAICE_deltaMin that is used ***only***
103        for regularizing Delta (and nothing else, like the parameter
104        which is also used for all sorts of things SEAICE_EPS).
105        Defaults to SEAICE_EPS for backward compatibility only.
106    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
107        the wrong key by inialising it before use -> fixes a recomputation
108        problem but does not fix the gradient
109    o pkg/layers:
110      - move resetting of flux arrays to outside the iLa loop
111        (this caused layers_diapycnal to not work with more than one layer coord.)
112      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
113    o pkg/layers:
114      - remove from common block 3D layers fields (used to diagnose transport
115        in tracer coords) and declare them as local arrays in layers_calc.F
116    o pkg/seaice:
117      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
118        in lab_sea forward experiment (changes results -> updated)
119      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
120    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
121       computations; for SEAICE_VECTORIZE_LSR
122      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
123        sweep to the outside,
124      - remove store directives and add "CADJ loop sequential" directives
125        in analogy to model/src/solve_tridiagonal.F
126      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
127        boundaries to yield more readable code. This has also the charming side
128        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
129        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
130        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
131        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
132        an additional option)
133       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
134       but the adjoint gradients (which are affected by this change) still explode.
135    o coupler (atm & ocn _compon_interf):
136      - avoid using Exch2 IO mapping if not suitable.
137    
138    checkpoint65m (2015/06/15)
139    o pkg/layers:
140      - clean-up old parameters setting (from Sep 2012):
141        + remove old parameters setting from common block (declared locally);
142        + stop if any old parameter is mixed with new parameters;
143        + check for valid or consistent parameter setting (e.g., layers_name)
144      - check that layers_bounds for Pot.Density are in the right range;
145        this is supposed to catch un-updated setting after recently shifting
146        potential density field "prho" by -1000 (now in "sigma" scale).
147    o pkg/layers:
148      - Added missing call to layers_fill for keeping track of tottend in
149        pkg/diagnostics/diagnostics_fill_state.F
150    o pkg/layers:
151      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
152        of diapycnal fluxes
153    o pkg/layers:
154      - reverted changes to interpolation to previous treatment; there
155        was never actually a problem
156    o pkg/layers:
157      - fix interpolation of layers tracers in the presence of partial cells
158      - add lots of new functionality to compute water mass transformation
159        (enabled by CPP flag LAYERS_THERMODYNAMICS)
160      - add new calls from main code (diags_oceanic_surf_flux.F,
161        thermodynamics.F, impldiff.F) and gad to save the necessary fields
162        for layers_thermodynamics calculations
163    o pkg/ptracers:
164      - add capability of stepping a passive tracer forward without advection
165        by setting PTRACERS_advScheme to 0.
166    o pkg/diagnostics:
167      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
168    o pkg/layers:
169      - shift potential density field "prho" by -1000 for density layer averaging so
170        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
171        Note that density bin boundaries (layers_bounds in data.layers) have
172        to be set accordingly (i.e., shifted, in sigma scale).
173    o pkg/layers:
174      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
175      - fix calculation of layer non-weighted velocity and layer probability
176      - add diagnostics for pot.density used for layer averaging
177    o pkg/seaice:
178      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
179        positiveness, modify a few comments and improve variable names,
180      - the changed computation of deltaC affects most seaice-related
181        experiments at the truncation level.
182        seaice_itd.thermo is affected by far the most, with
183        only 7 digits of agreement remaining; update experiments.
184    
185    checkpoint65l (2015/05/04)
186    o pkg/shelfice:
187      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
188        factor drKp1 to zero where it is negative (ie. do not use
189        SHELFICEBoundaryLayer if hFacC>1)
190      - the same for factor drLoc in shelfice_forcing.F
191    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
192        with modules in ptracers, when using testreport option "-small_f"
193    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
194      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
195    o verification/testreport
196      - add new option -small_f
197        with this option testreport first makes the target small_f (*.f files)
198        before running make (all). This is useful for explicit inlining when
199        all sources need to be full available.
200    o pkg/exf/exf_interp.F:
201        remove previous changes related to reverse (decreasing) input grids latitude
202    
203    checkpoint65k (2015/04/01)
204    o pkg/ecco:
205        fix missing cosphi initialization; use eccoiter in place of optimcycle;
206        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
207        instead of active read/write
208    o pkg/ctrl:
209        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
210        instead of active read/write.
211    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
212        return if .NOT.useAUTODIFF
213    o pkg/seaice: add CPP brackets (cost function related).
214    o model/src:
215        add useAUTODIFF run time switch.
216    o pkg/exf/exf_interp.F:
217        add code to allow input grids with latitude starting in the north (i.e. when
218        j=1 corresponds to northern edge of field); modify global_with_exf to test
219        this feature.
220    o verification/testreport:
221      - replace "grep -A3" with POSIX conformal sed command, because there are
222        implementations of grep that cannot do contextual searches
223      - replace "cat -n" by "nl" (two occurrences), because not all implementations
224        of "cat" have the option "-n"
225    o model/src:
226        add new file gsw_teos10.F that contains 3 functions, more or less a copy
227        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
228        convert from conservative to potential temperature. For now they are not
229        called anywhere.
230    o pkg/ggl90: make "useIDEMIX" useful
231      - re-organize code in s/r ggl90_calc a little to move computations that
232        are different for idemix into separate loops (changes verification
233        experiment idemix at truncation level, 12 digits remain -> updated)
234      - requires 2 new 2D fields KappaM, verticalShear
235      - make hFacI and recip_hFacI local 3D variables that are passed to
236        s/r ggl90_idemix
237      - fix and improve some comments
238    
239    checkpoint65j (2015/02/25)
240    o pkg/openad
241      - synchronize seawater.F with version in model/src: replace routine
242        body of sw_temp by calling sw_ptmp and fix/add a few comments.
243    o pkg/mnc:
244      - change default value of pickup_read/write_mnc params to FALSE
245        (since few features are missing in reading MNC pickup files).
246    o model/src:
247      - change default (background) vertical diffusivity for salt to be the
248        temperature (background) vertical diffusivity.
249      - change background vertical diffusivity in vertical mixing pkgs ggl90,
250        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
251        This makes ptracers default diffusivity (that uses salt diffKr) more
252        consistent with vertical mixing schemes.
253    o verification/testreport:
254      - fix typo in "-pcls" option ;
255      - put temp files in /tmp (instead of in local dir)
256      - add option "-ncad" to use genmake2 new option "-nocat4ad"
257      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
258    o pkg/ggl90 (idemix code):
259      - apply few fixes ; add some missing "_d 0" ; update output of exp.
260        global_ocean.90x40x15.idemix
261    o OpenAD
262      - enable active file I/O and begin removal of work-around code
263        for OpenAD for handling control variables (memory vs. active files)
264      - new CPP options file OPENAD_OPTIONS.h
265      - revert to genarr2d gradient check for hs94.1x64x5
266      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
267      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
268    o tools/genmake2:
269      - add option for an alternative Makefile (from Martin) where multiple
270        source files are sent to TAF (instead of all in one file).
271    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
272      - code provided by Carsten Eden as an extension of ggl90
273      - so far the code is turned on within ggl90 by setting a CPP-flag at
274        compile time; a runtime flag implementation is not yet complete
275      - tested in new verification experiment global_ocean.90x40x15.idemix
276    o verification:
277      - reduce length of the AD test run by half for experiments
278        global_ocean.cs32x15 (std + thsice) and isomip
279      - enable active file I/O for OpenAD, adjust verifications accordingly
280      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
281    o verification/testreport:
282      - fix two non-POSIX sed statements so that there are no error messages
283        on Mac OS X
284      - replace hostname -s with hostname | sed 's/\..*$//'
285    o model/src/seawater.F:
286      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
287        (following the matlab code), which would have avoided the bug caught
288        by Matt (see below) in the first place
289    o pkg/shelfice:
290      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
291        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
292      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
293        ice-shelf case (i.e., within surface level).
294      - add config summary in shelfice_check.F
295      - remove global variable recip_SHELFICElatentHeat and replace by a local
296        variable recip_latentHeat
297      - introduce diagnostics for friction velocity uStar (in case of
298        SHELFICEuseGammaFrict)
299      - change verification experiment isomip.htd:
300        + start from pickup (as input_ad at nIter0=8640)
301        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
302        + test SHELFICEuseGammaFrict = .TRUE.
303        + test SHELFICEadvDiffHeatFlux = .TRUE.
304    o model/src:
305      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
306        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
307        update output of experiments global_with_exf.yearly and isomip (all 6).
308    o pkg/shelfice:
309      - change setting of kTopC to also be zero where there is no ice-shelf.
310      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
311        ice-shelf is.
312      - first attempt to get RealFreshWaterFlux effects: for now, only without
313        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
314    o pkg/seaice: add the option to prescribe a fixed thickness PDF
315      for thermodynamic calculations
316      - because of divisions of the type 7/7 not exactly equal to 1, this change
317        affects results of some verification experiments by up to 4 digits:
318        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
319        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
320        adjoint: lab_sea, lab_sea.noseaicedyn
321        -> updated
322    
323    checkpoint65i (2015/01/23)
324    o model/src:
325      - change units of frictionHeating field from W to W/m^2
326      - fix bug in frictional heating from stratospheric drag in
327        S/R ATM_PHYS_TENDENCY_APPLY_V
328      - with synchronous time-stepping: move resetting to zero of frictionHeating
329        field from load_fields_driver.F to thermodynamics.F ;
330      - add diagnostics for frictional heating.
331    o model/src & gmredi K3D:
332      - add frictionHeating field to pickup-files (for synchronous time-stepping)
333      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
334      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
335        and name in pickup file).
336      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
337    o model/src:
338      - move (from ini_forcing.F) initialisation of all arrays in header file
339        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
340        (since Nov 2012) with option selectAddFluid=1.
341    o pkg/shelfice:
342      - change units (+ document) of newly added field "shelfIceMassDynTendency"
343      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
344    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
345    o pkg/seaice: two new runtime parameters:
346      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
347        long overdue
348      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
349        parameterization of tensil stress for fast ice (does not do anything yet)
350    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
351        for LSR: move checking overlaps out of JFNK-if-block
352    o pkg/atm_phys:
353      - move copy of grid and dynamical fields out of atm_phys_driver.F into
354        new S/R ATM_PHYS_DYN2PHYS.
355      - fix level height for Linear Free-Surf case (to be consistent with
356        fixed-in-time pressure levels).
357    o pkg/mom_common (bottomdrag):
358      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
359        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
360        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
361    o pkg/shelfice (u/v_drag):
362      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
363      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
364        (now similar to shelfice_u_drag.F)
365      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
366        from mom_vecinv.F (similar to mom_fluxform calls).
367    o pkg/mom_common (bottomdrag):
368      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
369      - add options for alternative discretisation of velocity norm in quadratic
370        bottom drag: averaging of grid-cell-center KE to U.point and V.point
371        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
372        improves when averaging only the other component (e.g. vVel for U bottom
373        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
374      - add options (bottomVisc_pCell) to account for partial-cell in bottom
375        friction (no-slip BC) thus getting the true distance from the bottom;
376        off by default since this also reduces model stability (explicit bottom
377        friction). Changes produce different machine truncation with linear-drag
378        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
379        front_relax (bvp & mxl, 10 & 11 digits).
380    o model/src & mom pkgs:
381      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
382        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
383      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
384        just copy level Nr value to level Nr+1.
385    o doc:
386      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
387    o pkg/streamice:
388      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
389        SHELFICE.h: move array shelficemass to init_varia, initialise
390        from array shelficemassinit, which is set in init_fixed and
391        has option to be set from file; introduce array
392        shelficeMassDynTend array, set thru file in init_fixed
393      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
394        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
395        pkg/streamice
396      - shelfice_thermodynamics.F: call shelfice_step_icemass if
397        SHELFICEMassStepping = .true.
398      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
399    
400    checkpoint65h (2014/12/17)
401    o verification/global_ocean.90x40x15, global_ocean_ebm:
402      - update to generic controls.
403    o pkg/ctrl:
404      - ctrl_map_ini_genarr.F: test for igen>0
405      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
406      - move gentim2d part of ctrl_map_ini_genarr.F to
407        new separate routine : ctrl_map_ini_gentim2d.F
408      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
409        add time variable weights and cyclic controls (time mean,
410        seasonal cycle, etc) capabilities to gentim2d
411    o pkg/ecco:
412      - move reading of error, conversion to weights from
413        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
414    o global_oce_llc90, cs32:
415      - activte sbo.
416      - CTRL_SIZE.h : add maxCtrlProc.
417      - activate the new genctrl capabilities.
418      - update following reorganization of global_oce_input_fields.tar.gz  
419    o pkg/ctrl/ctrl_ad_diff.list:
420      - add missing ctrl_init_rec.f
421    o tools/OAD_support/keepOriginal:
422      - add ctrl_init_rec.F
423    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
424      - avoid recomputations of xx_gentim2d_dummy.
425    o momentum diagnostics:
426      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
427        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
428    o pkg/seaice/seaice_lsr.F:
429      - fix computation of BU/BV, make sure they are non-zero, only necessary
430        for cubed sphere exchanges and SEAICE_OLx/y>0.
431        This makes calling s/r fill_cs_corner_rl obsolete (removed).
432    o verification/global_ocean.cs32x15/input.seaice
433      - add test for strong implicit coupling and restricted addtive Schwarz
434        methods for LSR
435      - update results/output.seaice.txt
436    o verification/tutorial_global_oce_biogeo:
437      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
438        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
439        update output_adm,_oadm,_tlm.txt
440    o pkg/dic:
441      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
442      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
443        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
444    o verification/tutorial_global_oce_biogeo:
445      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
446        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
447        update output_adm,_oadm,_tlm.txt
448    o eesupp/src:
449      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
450        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
451    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
452      LSR (following Hutchings et al. 2004)
453      - introduce zetaZ as a global variable (requires adjustments in
454        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
455        in seaice_calc_viscosities.F
456      - new flag SEAICEuseStrImpCpl (default off)
457      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
458        momentum equations
459      - JFNK-solver (preconditioner) adjusted to allow using this method
460        (where it does not have any positive effect)
461    o pkg/seaice
462      - add overlap for restrictive additive Schwartz method also to LSR, but
463        turn it off by default (because it only seems to work for non-cubed
464        sphere/llc topologies)
465    o pkg/autodiff
466      - add extra exchanges in addummy_in_steppging also for mnc output
467    o pkg/seaice:
468      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
469        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
470    o pkg/obcs:
471      - add option to specify domain-connected piece Id along OB though files
472        (for now, only used to diagnose PhiVel; default =1 -> global correction)
473      - modify obcs_diag_balance.F to process each connected-part separately;
474        exclude OB where Id = 0 but keep the full divergence there (-> constant
475        Psi along this portion of OB and all inflow derived from grad(Phi))
476      - add example of OB-conect files in verification/so_box_biogeo/input.
477    o pkg/diagnostics:
478      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
479      a) use non zero matrix element across OB and solve for Phi 1 grid point
480         outside OB (i.e, where tracer OBCS are applied).
481      b) global imbalance of inFlow/outFlow across OB: instead of modifying
482         velocity across OB, spread it uniformly along the OB in the RHS.
483    
484    checkpoint65g (2014/11/19)
485    o pkg/diagnostcis:
486      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
487    o pkg/my82,pp81,kl10:
488      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
489        field diffKr as background diffusivity to set minimum diffusivity value.
490    o pkg/seaice:
491      - add new parameter SEAICEuseEVPrev (for revisited EVP by
492        Bouillon et al 2013)
493      - add SEAICE_evpAlpha/Beta to namelist
494      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
495        involve trivial re-ordering of divisions/multiplications that should not
496        have any effects, but ... they do change the results of lab_sea.hb87 so
497        that only 2 digits of agreement remain, in line with the general
498        instability/fragility of the evp-code. For now, I do not care and just
499        update the verification experiment
500    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
501      - remove xx_genarr2d_numsmooth etc
502      - use xx_genarr2d_preproc etc instead
503      - carry out smooth_correl2D at initialization stage rather than during
504        time stepping.
505      - get smoothOpNb from xx_gentim2d_preproc
506    o global_oce_cs32 :
507      - add test of generic ecco capabilities.
508    o pkg/exf/exf_getsurfacefluxes.F :
509      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
510    o pkg/ctrl,ecco :
511      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
512        is defined.
513    o pkg/seaice: add diagnostics for Delta (deformation parameter)
514    o model/src:
515      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
516        diffusivity (background) is specified but ignored.
517    o verification:
518      - in testreport, convert hostname to lower case for default output dir name
519    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
520    o pkg/dic: add modifications from Hajoon:
521      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
522      - light attenuation: add self-shading effect by climatological Chlorophyll
523        (read from file).
524    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
525        compiles when SEAICE_ALLOW_DYNAMICS is undefined
526    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
527        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
528        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
529        approach where CPP_OPTIONS.h includes an omnipotent
530        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
531    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
532        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
533    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
534        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
535        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
536    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
537      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
538      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
539      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
540      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
541    o pkg/ctrl,ecco,exf :
542      - remove variables associated with NON-generic costs,
543        unless ECCO_CTRL_DEPRECATED is defined.
544      - remove NON-generic NON-obcs controls,
545        unless ECCO_CTRL_DEPRECATED is defined.
546    o pkg/ctrl : added ctrl_local_params.h
547    o pkg/ecco : added ecco_local_params.h
548    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
549        experiments, which will progressively be removed once the
550        experiments are revised to use only generic controls/costs.
551    
552    checkpoint65f (2014/10/13)
553    o pkg/ctrl, ecco, seaice : minor changes in headers
554    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
555        cost function and control capabilities added since checkpoint65c.
556    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
557    o pkg/ecco: increase modularity and improve logic
558      - ecco_toolbox.F (new) : basic operations that are often used,
559        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
560        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
561      - cost_gencal.F (new) : determine filnames and records.
562      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
563      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
564        and exploit the above functions leading to more compact code.
565      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
566      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
567        using_ers, using_gfo, using_mdt is now only defined within gencost)
568    o pkg/ecco: extend generic cost capabilities
569      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
570        capabilities via gencost_preproc (+ _c,_i,_r related params),
571        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
572        gencost_outputlevel arguments to cost_generic
573      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
574        and active_read, making room for gencost_preproc to take effect.
575        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
576      - pkg/ecco/cost_generic.F :
577        compute and store misfit maks*(model-data) in localdif that is
578        then used in cost and for output, output misfit if outlev.GT.0
579      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
580        rather gencost_barfile for deciding whether to write barfile
581      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
582      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
583        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
584      - pkg/ecco/ecco_summary.F : report gencost variables
585      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
586    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
587    o pkg/ecco: internal re-organization
588      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
589        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
590        mv relevant variables definition from ecco_cost.h to ecco.h,
591        make sure gencost routines only include ecco.h)
592      - throughout : add missing CCP switches, rm unused variables,
593        and rm un-necessary CPP switches
594      - throughout gencost routines : replace modelstartdate with
595        gencost_startdate when needed
596      - cost_bp_read.F : use arguments, instead of common blocs
597        so that it can be used also by (new) cost_gencost_bpv4.F
598      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
599      - ecco_phys.F : compute etanFull
600      - ecco_readparms.F : rename using_topex as using_tpj, add
601        bpv4-grace to gencost list, initialize added parameters
602      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
603    
604    checkpoint65e (2014/09/28)
605    o pkg/obcs:
606      - replaced the just-added CPP options with run-time variables
607        (see pkg/obcs/OBCS_PARAMS.h for details)
608    o pkg/obcs:
609      - add additional CPP options for sponge boundary layers
610        (see pkg/obcs/OBCS_OPTIONS.h for details)
611    o pkg/atm_phys:
612      - implement simple (obliquity only, assuming circular planet orbit)
613        seasonal cycle for incoming insolation ; used when run-time parameter
614        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
615    o pkg/exf, pkg/ecco, pkg/ctrl:
616      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
617      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
618      - implement gentim2d for xx_tauu, xx_tauv
619    o pkg/ctrl, pkg/ecco :
620      - fix and complement the generic controls implementation
621    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
622        pkg/shelfice/shelfice_thermodynamics.F,
623        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
624        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
625      - add weight in CTRL_GET_GEN calls
626    o pkg/ctrl :
627      - ctrl_get_gen.F : add weight as input parameter, and apply
628        it directly rather than using smooth_correl2Dw (to be retired).
629      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
630    o pkg/ctrl :
631      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
632        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
633      - re-activate ctrl_summary (call in ctrl_init.F)
634    o pkg/ctrl/ctrl_cost_gen.F :
635      - fix CCP brackets, remove un-necessary myiter, mytime
636    o pkg/ecco, pkg/ctrl :
637      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
638      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
639      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
640      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
641    
642    checkpoint65d (2014/09/15)
643    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
644      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
645        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
646    o pkg/ctrl/ctrl_map_ini_genarr.F :
647      - remove compilation failure
648      - replace hard coded example
649      - use ctrl_map_ini_gen2D, 3D
650    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
651      - on/off switch based upon xx_genarr2d_weight,3d
652    o src/packages_init_variables.F :
653      - regroup pkg/estimation calls
654      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
655        (moved to ctrl_init_variables)
656    o cost/cost_init_varia.F :
657      - remove ecco_cost_init_varia
658        (moved to ecco_init_varia)
659    o ctrl/ctrl_init_variables.F :
660      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
661      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
662    o ctrl/ctrl_map_ini.F :
663      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
664        (moved to ctrl_init_variables)
665    o ctrl/ctrl_map_ini_ecco.F :
666      - remove ECCO_PHYS (mv to ecco_init_varia)
667      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
668    o ecco/ecco_ad_diff.list :
669      - add ecco_init_varia.f
670    o ecco/ecco_init_varia.F
671      - new routine
672    o pkg/streamice:
673      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
674        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
675      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
676    o pkg/generic_advdiff:
677      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
678    o pkg/exf:
679      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
680         xxg_precip capability
681      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
682    o pkg/ctrl:
683      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
684    o model/src/load_fields_driver.F :
685      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
686        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
687    o OpenAD verification experiments:
688      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
689        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
690        for now, only in pkgs used in OpenAD verification experiments.
691      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
692        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
693        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
694        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
695    o OpenAD verification tests:
696      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
697      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
698        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
699      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
700        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
701    o model/src & generic_advdiff:
702      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
703        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
704        dynamics requires valid tracer forcing only over tile interior but, for
705        some diagnostics, may need to extend it over 1 point in tile halo region.
706      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
707        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
708        setting in temp/salt/ptracer_integrate.F
709    o pkg/dic:
710      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
711        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
712        in gchem_forcing_sep.F
713    o pkg/autodiff & obcs:
714      - add storage of current OB values for U & V (was already done for T & S).
715    
716    checkpoint65c (2014/08/30)
717    o pkg/dic:
718      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
719        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
720        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
721    o verification:
722      - new experiment testing OBCS and DIC pkgs, using params & output from
723        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
724        passage: take OBCS from the last year of a 2 yrs simulation and initial
725        conditions from t=1.yr while keeping the same forcing.
726    o model/src:
727      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
728        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
729    o pkg/diagnostics (Stats-Diags):
730      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
731        a) refine region where stats are computed, excluding where arrhFac=0 ;
732        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
733        c) extend regional stats over the region edges (for U or V pt location).
734    o pkg/gchem:
735      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
736        pkg/dic is currently changing/updating ptracers values beyond the OB).
737    o verification (hs94):
738      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
739        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
740        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
741        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
742    o pkg/ptracers:
743      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
744        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
745      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
746        with AB-2 code (so that it get tested).
747    o model/src:
748      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
749        with AB-2 code (previously only available with AB-3 code).
750        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
751        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
752        there, by calling CYCLE_AB_TRACER).
753    o pkg/generic_advdiff:
754      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
755        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
756        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
757        S/R temp/salt/ptracers_integrate.F
758    o model/src & pkg/ptracers:
759      - remove common block variables gT,gS (in DYNVARS.h), except when
760         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
761      - remove common block variable gPtr.
762    o model/src & pkgs:
763      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
764         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
765         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
766         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
767      + change accordingly all calling S/R.
768      - use local temperature/salinity/ptracer tendency array (without bi,bj)
769        in S/R temp/salt/ptracers_integrate.F
770    o pkg/seaice:
771      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
772        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
773      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
774        in seaice_lsr
775      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
776        in s/r seaice_lsr_calc_coeffs
777    o pkg/mdsio:
778      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
779        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
780        too long (e.g., > MAX_LEN_FNAM/2 )
781    
782    checkpoint65b (2014/08/12)
783    o pkg/matrix:
784      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
785    o model/src:
786      - fix initialisation of geothermalFile; compile geothermal-flux code in
787        natl_box verification experiment.
788    o model/src & pkg/down_slope:
789      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
790      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
791        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
792        results at machine truncation level: update output of experiments
793        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
794    o pkg/diagnostics (Stats-Diags):
795      - do not cumulate the full volume when DIAGNOSTICS_FILL is
796        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
797        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
798        times (but Min,Max and StD are still wrong).
799    o model/src:
800      - add geothermal flux forcing: read in ini_forcing.F as time-constant
801        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
802    o model/src:
803      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
804        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
805        arrays are already updated while adjustments (filters, conv.adjustment) are
806        still applied later, in S/R TRACERS_CORRECTION_STEP.
807    o model/src:
808      - store in common bloc array "rhoInSitu" the virtual potential temperature
809        anomaly that is used to compute geopotential: this make the atmos code
810        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
811    o pkg/seaice/seaice_lsr.F
812      - rename integer variable ilcall to ipass (that's what it is called
813        in the residual diagnostics
814      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
815        default) for improved non-linear convergence of the first few steps
816      - adjust a few comments and add new ones to explain some of the store
817        directives
818    o pkg/generic_advdiff (& ptracers):
819      - re-work the code to check for valid advection scheme and for minimum
820        size of overlap (now stored in local common bloc in gad_advscheme.F)
821    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
822      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
823      - add an auxilliary variable "bet" and fix store directives and keys in
824        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
825        less exact gradients in my tests); but there are still
826        recomputation warning (although gradients are sort of OK), when
827        SEAICE_LSR_VECTORIZE is not defined, so this flag and
828        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
829      - update verification experiments lab_sea.
830      - change some comments in S/R seaice_calc_viscosities
831    o model/src:
832      - if staggerTimeStep=T, always apply exchange to velocity field in
833        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
834        (independent of using multi-dim advection or not); no effect on FWD run
835        but affects AD results (at machine truncation level): update output of
836        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
837        and isomip (oad: 12.d).
838    o pkg/generic_advdiff:
839      - stop if doAB_onGtGs is set to FALSE but ignored
840      - refine warning related to stability of tracer time-stepping
841        regarding internal wave dynamics.
842      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
843        on staggerTimeStep & implicitIntGravWave (will now get a warning
844        if potentially unstable).
845    o pkg/kl10:
846      - add new pkg "kl10" for mixing due to internal wave breaking, from
847        http://www.sciencedirect.com/science/article/pii/S1463500310000144
848        (contribution from Jody Klymak), tested in verification experiment
849        verification/internal_wave/input.kl10/
850    o isomip experiment:
851      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
852        (input.htd) and update the output.
853    o cd_code experiments:
854      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
855        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
856        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
857        update the corresponding output.
858    o pkg/seaice:
859      - reduce the number of include files and store directives in
860        S/R seaice_lsr_tridiagu/v
861      - change the order of loops in one case in S/R seaice_lsr_tridiagv
862        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
863        get rid off one store directive (a TAF bug?)
864      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
865        S/R seaice_lsr_tridiagv to change the loop range for consistency
866      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
867      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
868        S/R seaice_lsr_tridiagu/v (requires update of
869        offline_exf_seaice/input.dyn_jfnk)
870    
871    checkpoint65a (2014/07/27)
872    o model/src:
873      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
874        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
875        (topo in p-coords, ice-shelf in z-coords); update output of experiments
876        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
877    o model/src:
878      - collect momentum forcing tendency into local 2-D array (passed as argument
879        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
880        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
881        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
882      - collect T & S forcing tendency into local 2-D array (passed as argument to
883        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
884        affects results at machine truncation level (e.g., ocean: if using
885        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
886        correction due to vertical advection).
887      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
888        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
889        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
890        obcs_ctrl (ad & fwd grd @ 12 & 7).
891    o pkg/ptracers & diagnostics:
892      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
893        title (to avoid some unexpected truncation); sort out ptracers diags units.
894      - collect ptracer forcing tendency into local 2-D array (passed as argument
895        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
896    
897    checkpoint65 (2014/07/18)
898    o pkg/fizhi:
899      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
900        affects results at machine truncation level. Update output of experiments
901        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
902    o pkg/seaice: more clean up
903      - rename TAF common block tapes to be more consistent and remove
904        unnecessary duplicates
905      - add store directives to remove more recomputations, but use smaller
906        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
907        The idea behind this flag is to reduce the memory footprint when the
908        adjoint of the LSR is not required. As of now, defining the flag
909        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
910        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
911        For experiment offline_exf_seaice, this means on a linux box with gfortran
912        nearly a factor of 10 (but keep in mind there is mostly seaice code in
913        this experiment):
914        > size mitgcmuv_ad
915        text    data        bss     dec        hex
916        5100659 1216  220458952  225560827  d71c8fb
917        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
918        but only a moderate increase of 36% for global_ocean.cs32x15:
919        text    data        bss     dec        hex
920        6695027 1648 1014578664 1021275339 3cdf6ccb
921        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
922      - note: there are still recomputations in global_ocean.cs32x15 and
923        offline_exf_seaice and the gradient agreement changes (gets a
924        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
925      - in general, the AD gradients still are wrong
926    o OpenAD
927      - clean up code_oad/ directories somewhat by moving files
928        dontCompile, dontTransform, keepOriginal to OAD_support/
929    o model/src:
930      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
931        (not currently tested): add dissipation terms before NLFS rescaling of
932        tendencies (previously done after).
933    o pkg/diagnostics:
934      - write stats-diags in ascii file with more digits (same as in monitor).
935    o pkg/down_slope:
936      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
937        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
938    o model/src:
939      - new file "apply_forcing.F" containing all the code previously in
940        external_forcing.F, but with new argument list: pass, as new argument,
941        the current level tendency array to update (instead of a direct update
942        of the common bloc array). Change the corresponding calls.
943      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
944        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
945    o pkg/seaice/seaice_lsr, a little bit of clean up
946      - rearrange some code blocks, so that now all calculations for
947        setting up the right-hand-sides done within one single block
948        (I find that easier to read and understand)
949      - rearrange freedrift-code to reduce the number of ifdefs
950      - adjust some indentations and comments
951    
952    checkpoint64z (2014/07/10)
953    o model/src and several pkgs:
954      - change argument list of all S/R called from external_forcing.F and
955        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
956        to pass, as argument, the current level tendency array to update
957        (instead of a direct update of the common bloc array).
958      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
959      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
960    o pkg/seaice/seaice_lsr.F
961      - always initialize local arrays in seaice_lsr_tridiagu/v
962      - add more local tapes to seaice_lsr_tridiagu/v
963      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
964        keep it in bi/bj loop; this seems to be essential
965      - gradients are still wrong but only by 4-7 orders of magnitude
966        instead of 15 orders of magnitude, lab_sea improves a little
967    o pkg/seaice
968      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
969        generates unnecessary code in seaice_lsr_ad
970      - add more store directives in seaice_lsr to avoid unnecessary code
971        in seaice_lsr_ad
972      - exclude some residual computations in seaice_lsr when
973        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
974        in seaice_lsr_ad
975      - add more storing, a new tape (model/src/the_main_loop.F) and
976        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
977        and klockey should be checked by a specialist)
978      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
979        and update lab_sea after previous changes in pkg/seaice below
980    o pkg/autodiff:
981      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
982        viscFacInAd : run time parameters allowing for adjoint switches
983        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
984    o pkg/ecco:
985      - introduce cost_gencost_boxmean.F that computes a box mean
986        temperature (for use in adjoint sensitivity studies).
987    o model/src/set_defaults.F : initialize viscFacAdj to 1.
988    o pkg/mom_common/mom_calc_visc.F:
989      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
990    o pkg/seaice/seaice_summary.F:
991      - statement for SEAICEadjMODE now in autodiff_readparms.F
992    o pkg/seaice:
993      - remove some store directives and add new ones in an effort to get
994        finally rid off the recomputation warnings. This is successful
995        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
996        defined (i.e. no extensive recomputation warnings left), but there
997        are still too many recomputations on the solver iteration level
998      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
999      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
1000        SEAICE_SIZE.h
1001      - add a store directive in S/R seaice_calc_viscosities
1002    o pkg/seaice (ITD code):
1003      - fix definition of Hlimit for multi-threaded case
1004      - use double precision arithmetic to compute Hlimit: this affects results;
1005        update output of experiment seaice_itd.
1006    o replace content of verification/seaice_itd
1007      - instead of a 1D column use the configuration of offline_exf_seaice
1008        to test the ice thickness distribution code with ridging
1009      - this is a first shot at this experiment
1010      - change of some defaults of ridging parameters SEAICEhStar (from
1011        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
1012        and lot of new comments.
1013    
1014    checkpoint64y (2014/06/20)
1015    o pkg/seaice/seaice_reg_ridge.F:
1016      - modify the regularization of very small volumes of ice; only check
1017        total volume HEFF, and do not apply correction to individual ice
1018        classes because that leads to funny patterns in the heat and fw-fluxes
1019        into the ocean. Adjust seaice_itd/results/output.txt
1020      - replace nITD by SEAICE_multDim in loop-ranges
1021    o pkg/exf:
1022      - add code to process the case field period = -12. with UV interpolation.
1023      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
1024        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
1025    o verification/global_with_exf:
1026      - switch all fields period to -12. (was previously untested) in input/data.exf
1027        (but keep secondary test ".yearly" unchanged); update the reference output.
1028    o pkg/cal:
1029      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
1030    o pkg/exf:
1031      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
1032        to replace logical switch "exf_verbose"
1033      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
1034    o pkg/sbo:
1035      - update from Katherine Quinn: evaluate mass directly from density and SSH
1036        (budget using Finite Volume method) instead of from bottom pressure.
1037      - allow testreport to collect few selected SBO output ; tested in exp.
1038        global_ocean.90x40x15 (after updating the results, to include SBO output).
1039      - fix some multi-threading issues (in output part).
1040    o model/src & most packages:
1041      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
1042      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
1043        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
1044        "data.{pkg}" exist ; and leave the S/R (return) just after.
1045      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
1046        + call LAND_READPARMS from packages_readparms.F
1047    o pkg/seaice:
1048      - remove code that resets useThSice in S/R seaice_readparms and
1049        replace it by a warning in S/R seaice_check
1050      - remove parameter MULTDIM, replace with nITD and runtime
1051        parameter SEAICE_multDim (still hard-wired to nITD if
1052        SEAICE_ITD is defined)
1053    
1054    checkpoint64x (2014/05/24)
1055    o verification/lab_sea:
1056      - update adjoint and TLM output following changes to pkg/salt_plume
1057      - un-do the update after putting back local recip_Cp in few places.
1058    o pkg/salt_plume: modifications by An Nguyen:
1059      - add capability to do brine rejection (salt-plume) as function of
1060        volume+tracers (instead of only salinity tracer).
1061      - conserve volume by exchanging volume from each kLev to above to
1062        accommodate in-coming brine volume
1063      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
1064      - switch KPP surf buoyancy due to brine forcing to 3-d
1065        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
1066      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
1067      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
1068        in East/West Arctic.
1069    o pkg/sbo:
1070      - incorporate modifications from Katherine Quinn to enable the use of sbo
1071        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
1072        output for future testreport verification (unfinished).
1073    o pkg/atm_phys:
1074      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
1075        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
1076        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
1077    o pkg/seaice
1078      seaice_calc_ice_strength.F: modify expression to avoid divisions
1079        (affects truncation)
1080      seaice_do_ridging.F: clean up the insectarium
1081    - fix a bug that was compensated by areaScaling (-> remove areaScaling code)    - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
1082    - added SEAICEsnowFracRidge to redistributed snow (2nd bug)    - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
1083    - set closing/openingRate to zero where no extra iteration is need (3rd bug)    - set closing/openingRate to zero where no extra iteration is need (3rd bug)
1084    - add some debugging information and error messages (warnings)    - add some debugging information and error messages (warnings)
1085  o model/src: modifications relatd to atmosphere p*:  o model/src: modifications relatd to atmosphere p*:
1086    - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)    - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
1087    - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead    - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
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