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revision 1.127 by adcroft, Thu Jan 30 18:35:42 2003 UTC revision 1.389 by jmc, Fri Nov 19 13:55:26 2004 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    o GCHEM:
7      - move call to GCHEM_FORCING_SEP, so that it is now called before
8        the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
9      - introduced a useGCHEM runtime flag and applied it everywhere.
10    o small cleaning of exch2: remove files that are also in eesupp/src
11    
12    checkpoint56
13    o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
14    o mnc: cleanup "full" files--fixes out-of-memory problem
15    o ECCO-GODAE
16      * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
17      * fully merged and updated from SIO code
18        windstress sign change affects
19        - exf_inscal_[u/v]stress
20        - sign of xx_tau[u/v] adjustments
21        - signs in cost_scat
22      * ctrl_get_gen: avoid update of tau[u/v] for first few days
23      * natl_box_adjoint updated and compressed
24      * 2-level checkpoint switch added
25        (tested in EXP. 1 of natl_box_adjoint)
26      * new switch doInitXX to avoid init. of xx_... in optimcycle=0
27    o SVD
28      * first complete, non-hacked version for SVD calculations
29      * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
30        performed via direct access files admtlm_vector.it????
31        (via ctrl_[un]pack)
32      * optimcycle is used for ARPACK iteration counter
33        (note: adxx_... is iterated, rather than xx_...; latter is constant!)
34      * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
35        and add linear transforms where necessary
36      * controls are initial/final SST, SSS (can be extended; need to check
37        ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
38    o mdsio: filename info to both stderr, stdout
39    o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
40      from sign change
41    
42    checkpoint55j_post
43    o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
44      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
45    o add consistent build directories and .cvsignore files to verification
46    o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
47    o make all subroutines 30 or less characters in length for certain older
48      compilers to work (a thorough search only turns up two routines in
49      pkg/ptracers)
50    o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
51      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
52    
53    checkpoint55i_post
54    o change arrays for total vertical diffusivity (2.D if explicit,
55      3.D if implicit) ; each ptracer uses its own background value.
56    o added mnc/NetCDF output capability to ocn_compon_interf
57      - added bits to verification/cpl_aim+ocn so that it can run on
58        ITRDA and other clusters without the mpirun "-wd" option
59    o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
60      configuration
61    o give MNC the ability to create additional files rather than
62      exceeding a specified file size limit "MNC_MAX_FILESIZE"
63      - the default is just less than 2GB which is a practical limit
64        on many systems
65    o Compute the non-local term using either KPP vertical diffusivity (=default)
66       or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
67    
68    checkpoint55h_post
69    o add verification test "vermix"
70    o remove all the *_ioinc flags and replace with the single global
71      outputTypesInclusive flag
72    o allow to set a vertical profile of vertical diffusivity for T & S
73    o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
74    o useMNC moved from data.mnc to data.pkg
75    
76    checkpoint55g_post
77    o Renaming carbon AD experiments to comply with testreport conventions
78    o Updating adjoint of Held-Suarez hs94.1x64x5
79    o Fixing directives for non-ECCO forward_step, after ECCO directives
80      have been fixed to avoid recomp. of do_oceanic_phys
81      Works well for global_ocean.90x40x15,
82      but recomp. issue remains for carbon
83    o Updating adjoint output for natl_box_adjoint after
84      pkg/ecco has been modified (see taga c55d_post)
85    
86    checkpoint55f_post
87    o rename to timeave_init_fixed
88    
89    checkpoint55e_post
90    o some delicate re-shuffle of store directives to avoid one
91      extra call of do_oceanic_physics
92      affects ecco_the_main_loop.F, do_oceanic_physics.F
93      checkpoint_lev1_directives.h
94    o NB: this may break global_ocean adjoint temporarily,
95      but it is clear how to fix it. Will do later, need this now.
96    
97    checkpoint55d_post
98    o ECCO specific cost function terms (up-to-date with 1x1 runs)
99    o ecco_cost_weights is modified to 1x1 runs
100    o modifs to allow observations to be read in as
101      single file or yearly files
102    o enable to read exf forcing fields as either
103      single file or yearly files (flag useExfYearlyFields)
104    checkpoint55d_pre
105    
106    o switch between 2-level and 3-level checkpointing
107    o add ability of MNC to write local and "partial" (eg. 2D slices where
108      the full 3D field is never actually stored) arrays to NetCDF files
109      with the correct (that is, the complete multi-dimensional) set of
110      array indicies
111      - used in mom_vecinv() to write the diagFreq output
112      - tested (demonstrated) in verification/aim.5l_cs
113    o further mnc-ification
114      - add verification/lab_sea to the list with mnc setups
115      - fix undefined mnc v-names in cd_code
116      - add kpp to mnc output (both snapshot and timeave)
117    o non-hydrostatic code
118      - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
119        in calc_gw.F
120      - defaults to viscAh
121      - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
122        friction or Leith) in non-hydrostatic mode, as long as there is
123        no biharmonic friction and/or Leigth or equivalent for vertical velocity.
124    o pkg/cost
125      extend simple cost functions to treat time mean quantities
126      (T,U,V) via cost_accumulate_state from cost_tile
127    o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
128        be 2 times larger than the minimum size the advection scheme requires.
129        now get a perfect conservation of salt in advect_cs test-exp (updated)
130    o GGL90 (Gaspar's TKE mixed layer)
131      - add horizontal diffusion of TKE, requires exchanges in
132        do_fields_blocking_exchanges, horizontal diffusivity is zero by
133        default. In OPA there is no horizontal diffusion of TKE but the
134        mixing coefficients are computed from a horizontal average of TKE of
135        6 points or so. I think that diffusion has a little more physical
136        justification.
137      - clean up ggl90_calc in the hope of reducing memory usage (this hope
138        was in vain)
139      - mask tke-variable in ggl90_init
140    o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
141    o fix biharmonic diffusion on CS-grid.
142    o more obcs stuff
143      - added obcs_external_fields_load as an alternative to the EXF-pkg option
144        for reading boundary values. This routine is called from
145        obcs_prescribe_read
146      - updated obcs_check
147      - changed sponge layer relaxation parameter units for days to seconds
148      - turned off sponge layer by default
149      - changed argument list of OBCS_CALC to myTime+deltaTclock
150      - fixed about 35 bugs in obcs_external_fields_load
151    
152    checkpoint55c_post
153    o obcs stuff
154      - new runtime flags useOBCSprescribe, useOBCSbalance
155      - re-arranged obcs_calc
156      - moved exf_getobcs to obcs_prescibe_read
157        obcs_prescibe_read is called after ORLANSKI stuff
158        and independent of it (executable can contain all).
159      - updated obcs_check
160      - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
161        These may be necessary only if tangential velocities are
162        prescribed at OB, not sure, needs testing.
163    o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
164      which simplifies the calls and passes the ifc check-bounds test
165    
166    checkpoint55b_post
167    o add a 2D scalar, Z location, exchange_2 routine.
168    o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
169      to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
170      affects advect_cs results (for the wrong reason): update output.txt
171    o use a more standard discretization for biharmonic viscosity ;
172     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
173      affects results of dome set-up: update output.txt
174    o fix gad_advection.F (CubedSphere part), back to version 1.23
175    o fix bug in mom_vi_del2uv.F (CubedSphere part).
176    
177    checkpoint55a_post
178    o merged code to
179      * prescribe/read time-dependent open boundaries
180        (works in conjunction with exf, cal)
181      * sponge layer code for open boundaries
182      * each boundary N/S/E/W now has its own CPP option
183        (healthy for the adjoint)
184    
185    checkpoint55
186    o up-to-date adjoint of previous breaks
187      - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
188      - global_ocean_ebm: adjoint still needs fix (TLM ok)
189      - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
190      - carbon: * remove tr1-related adjoint verification
191                * add ptracer as control variable
192    o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
193      (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
194    
195    checkpoint54f_post
196    o in verification/carbin/ remove experiment related to
197      ALLOW_PASSIVE_TRACER (array tr1 etc)
198      code_ad/ input_ad/ results_ad
199    
200    o add two new packages
201      - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
202        + subject to optimization (memory)
203      - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
204        + subject to reordering (many GOTOs in the original code)
205        + so far opps is called for every (i,j) point, and then operates in
206          the vertical; one may want to reorder the scheme in order operate in
207          horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
208          fields)
209    o overhaul of IO so that we now have flags for MDSIO and/or MNC
210      - all verification tests compile and run with linux_ia32_g77
211      - defaults are compatible with current input files--nothing
212        should change if you were not previously using MNC
213      - MNC output has been added in numerous places (eg. timeave)
214        but there are still a few writes not yet do-able with MNC
215        (this is in progress)
216      - flags now allow for either/or/both use of MDSIO and MNC and
217        documentation will soon follow
218      - numerous small formatting cleanups for ProTeX
219    o add version info (via BUILD_INFO.h) to MNC and stdout
220    
221    checkpoint54e_post
222    o add two new packages
223      - pp81 (Packanowski and Philander, 1981), Richardson number and
224        stratification dependent mixing
225      - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
226      - these scheme operate in a similar manner as KPP (without ghat, of
227        course), however there is only one diffusivity that is used for both
228        temperature and salinity (and passive tracers)ç
229    o add offline package
230    o add "verification/dic_example" which contains a dic-gchem-ptracer setup
231      provided by Stephanie Dutkiewicz
232    o genmake2: add ability to search for C compilers and cleanup test output
233      - fixes recent SX-6 problems and should help with others (eg. HP-UX)
234    
235    checkpoint54d_post
236    o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
237    o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
238      leading to additional shift by 5 days each year of integration
239       (i.e. leading to considerable offset over the years)
240    o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
241    o start with no AB and no initial filtering (staggerTimeStep):
242      change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
243    o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
244      (external loading & cpl import/export stay in forward_step.F)
245    o update coupling interface to work with new staggerTimeStep
246    o change MDSIO ptracers_pickup.
247    o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
248    o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
249    o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
250    
251    checkpoint54c_post
252    o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
253      this affects (truncation error) output.txt of test-exp:
254       global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
255    o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
256    o change Qnet to always be the net heat flux, (+upward).
257      affects (truncation error) output of natl_box exp.: updated
258    o define the max number of passive tracers in PTRACERS_SIZE.h
259    o start to test mnc routinely in exp0
260    o add sea-ice loading (sIceLoad) as a new forcing field.
261    
262    checkpoint54b_post
263    o add testreport "-j JOBS" option for parallel builds (tested and pretty
264       impressive on Altix and Opteron systems)
265    o diagnostics can now write NetCDF files through the mnc package
266    o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
267    o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
268    o staggerTimeStep & NLFS: rescale T & S surface tendencies.
269      affects (truncation error) output of lab_sea & natl_box exp.: updated
270    o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
271    
272    checkpoint54a_post
273    o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
274    o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
275    o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
276    o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
277      + internal_wave (shift in writing cg2d_ini_res)
278    checkpoint54a_pre
279    
280    o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
281      - modified verification/lab_sea and natl_box_adjoint accordingly
282    
283    checkpoint54
284    checkpoint53g_post
285    o prepare splitting of thermodynamics: store convect.counter in common block
286    o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
287      output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
288    o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
289    o new parameter "nShapS": allow to treat differently S from T (nShapT)
290    o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
291    o restore adjointability
292    
293    checkpoint53f_post
294    o modifications that affect AIM experiment results (update output.txt):
295      - no advection of S at top interface Nr (pkg/generic_advdiff)
296      - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
297    o AIM pkg:
298      - include stability function into surf.Flux derivative relative to Tsurf
299      - calculate clear-sky radiation & surface temp. change (for diagnostics)
300    
301    checkpoint53e_post
302    o merged cylindrical coord configuration
303    o added rotating_tank experiment
304    checkpoint53e_pre
305    
306    checkpoint53d_post
307    o faulks upgraded: re-generate output.txt that have changed:
308       global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
309    o Added Bryan and Lewis, 1979, vertical diffusivity profile
310    o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
311    o added Sadourny discretization of Coriolis
312      - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
313      - re-enabled use of omega3 (useAbsVorticity)
314    o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
315      vector-invariant equations
316      - note: does *NOT* yet use same variable visc. for no-slip BC's.
317    o recoded the lateral boundary conditions for non-hydrostatic w, this time
318      hopefully without new bugs
319      - still to do: biharmonic friction for non-hydrostatic w
320    o bug fix for mom_*_sidedrag: rA -> rAs,rAw
321    o regenerated output for global_ocean_ebm (using -ieee)
322    o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
323      of mom_common/
324      - simple re-arrangement of instructions within computing loop
325    checkpoint53d_pre
326    
327    checkpoint53c_post
328    o new version of coupler for AIM+thSIce and Ocean models
329     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
330     - land: change Evaporation of snow
331     - aim with thSIce: fix bug in snow-precip.
332    o changes to calc_gw.F
333     - bug fix for w^2 term near the bottom boundary
334     - (hopefully) improve the lateral slip boundary condtions for use with
335        partial/looped cells
336      - because the bug fix changes two verification experiments anyway (exp5
337        and plume on slope), change the lateral boundary condition from half slip
338        to the value of no_slip_sides
339    o ebm package wasnt quite up to the parallel task. Fixed that.
340    o Adjoint of EBM package + verification
341      * TLM OK
342      * ADM not sufficient accuracy yet (needs further testing)
343    
344    checkpoint53b_post
345    o Commiting new energy balance model to repository
346      * package is pkg/ebm
347      * verif. is verification/global_ocean_ebm
348      * references are in ebm_driver.F
349    C      * X. Wang, P. Stone and J. Marotzke, 1999:
350    C        Global thermohaline circulation. Part I:
351    C        Sensitivity to atmospheric moisture transport.
352    C        J. Climate 12(1), 71-82
353    C      * X. Wang, P. Stone and J. Marotzke, 1999:
354    C        Global thermohaline circulation. Part II:
355    C        Sensitivity with interactive transport.
356    C        J. Climate 12(1), 83-91
357    C      * M. Nakamura, P. Stone and J. Marotzke, 1994:
358    C        Destabilization of the thermohaline circulation
359    C        by atmospheric eddy transports.
360    C        J. Climate 7(12), 1870-1882
361    o Will need long integration testing.
362    checkpoint53b_pre
363    
364    o created pkg/mom_common in preparation for variable viscosity code
365    o renamed and split ini_mnc_io
366    o pkg/land: only liquid water can diffuse or run-off
367    o AIM using land: soil wetness availability account for snow
368    o added printMapIncludesZeros to EEPARMS namelist
369    
370    checkpoint53a_post
371    o restore TAMC compatiility for exf_constants.h
372      (no usage of _d in .h)
373    o Additional storing in KPP in an attempt to fix
374      TAMC problem with adjoint of KPP code.
375      (no success...)
376      Identical code works fine with TAF.
377    o Fixed verification/natl_box_adjoint experiments.
378      Initial conditions for Experiments 4 and 5 are now
379      set to "SEAICE_initialHEFF=0", which is more reasonable,
380      and hence gives results closer to that of Experiment 2.
381      Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
382    
383    checkpoint53
384    o stable checkpoint with up to date adjoint
385      TLM tests only run for 1st grdchk at the moment. Its unclear if
386      this is a code problem or a problem with resetting code for g_
387      variables that is being autogenerated wrong.
388      Otherwise:
389       o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
390       o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
391         are both still in chaos following their security messes.
392    
393    checkpoint52n_post
394    o various build (mostly genmake2) changes including:
395      - ability to build/run more easily within Cygwin and MacOS X
396      - more complicated Makefiles with a stronger dependence on Gnu Make
397    o pkg/seaice modifications
398      - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
399        of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
400        and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
401      - changed proxy for geostrophic velocity and updated
402        verification/lab_sea/results/* accordingly
403      - removed ADI dynamic solver from pkg/seaice
404      - replaced all occurrences of 1/CSTICE or 1/CSUICE
405        they caused a segmentation fault under certain circumstances
406      - removed unused field WATR
407    o bug fix in exf-package:
408      -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
409         now reflect that.
410    o small fixes in the cal-package:
411      - set reference date to first of January for the 'model'-calendar
412      - failing of cal_CheckDate in cal_FullDate now actually results in a
413        warning
414    o small modifications in exf-package to increase flexibility:
415      - change climtempfreeze from a constant to a runtime parameter that
416        is specified in data.exf_clim (default = -1.9)
417      - introduce runtime parameter windstressmax (default = 2.0) that is
418        specified in data.exf
419    o fix in pkg/thsice:
420      - update Evap (Tsf changes) to be consistent with Latent heat flux
421      - maintain snow precipitation unchanged (even if Tsf >=0).
422     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
423    
424    checkpoint52m_post
425    o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
426      this does not change any of the results, because myIter=0 in swfrac always
427      lead to jwtype=2 (the default anyway), but the call makes little sense
428      as a default
429    o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
430    o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
431      atmospheric model (AIM) to use it ; add a "slab ocean" component.
432    o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
433    o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
434    o extending useSingleCpuIO option to work with new exch2 I/O format
435      - old-style, missing-tile I/O is still accessible by defining CPP
436        option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
437    o monitor package can write to NetCDF files and/or STDOUT
438    o fix re-definition bug in MNC_GRID_INIT_ALL()
439    o doc/api_reference added
440      - a framework for building an API Reference Manual using all
441        the "protex" comments embedded in the code
442      - see pkg/generic_advdiff, pkg/mnc for examples
443    o MNC:
444      - make myThid the last argument for all subroutines
445      - new default for the grid files: NO halos
446      - add useMNC and other run-time flags
447      - separate per-file-group handling of the unlimited dimension
448      - early initialization of MNC w/ flags read at the eeboot stage
449        and lookup tables set in initialize_fixed
450      - write all MNC output to a freshly-created directory
451    o thermodynamics sea-ice (thsice) is now tested with testreport.
452    o test exp. advect_cs: use the standard cs32 grid ; update output.
453    o Added functionality to grdchk:
454      pick global i,j,k position (or nearest wet) where to perform check.
455    
456    checkpoint52l_post
457    o new land formulation:
458      a) use ground enthalpy as prognostic variable to ensure exact
459         energy conservation.
460      b) account for water temperature and for latent heat of freezing
461         in all processes (rain, run-off, ground storage)
462      c) compute surface and ground temperature implicitly.
463    o aim_v23 modification for new land model:
464      a) Treat separately land / ocean / sea-ice surface fluxes
465         to allow implicit computation of land & sea-ice surface temp.
466      b) add snow precipitation.
467    checkpoint52l_pre
468    
469    o fix problem (when 1 tile is empty) in min/max monitor.
470    o fix bug in timeAve (u,vZetatave in common block)
471    o no restoring terms under ice for pkg/seaice
472    o moved SEAICE_DO_DIAGS to S/R do_the_model_io
473    o bug fix for pkg/seaice pickups
474    o change MNC call locations and add coordinate attributes
475    o mask vorticity at the corner ; affects global_ocean.cs output
476    o fix ini_curvilinear_grid ; test CS experiments with mpi
477    o aim.5l_cs: modify sea-ice fraction input file ; update output
478    o exf: Adding simple range check routine for exf fields after read
479    
480    checkpoint52k_post
481    o removed top-level directory "diags"
482      - we migrated these functions to pkg/timeave a long time ago
483    o fixed bug introduced in pkg/monitor
484    o accuracy ctrlprec = 32 insuffient for gradient checks using
485      averaged fields (I/O via cost_averages)
486      -> use ctrl.h in active_file*.F to control I/O precision.
487    o paramter list of CALL ADTHE_MAIN_LOOP
488    o added initial do_the_model_io to ecco
489    o set all ...Freq to zero after cost_final
490      taveFreq, dumpFreq, pChkptFreq
491    o MAIN and ECCO differentiability restored
492    
493    checkpoint52j_post
494    o fix nchklev in tamc.h for global_ocean...
495    o Bringing flow and store directives up-to-date
496    o Really weird thing!
497      call do_the_model_io from the_main_loop with parameters
498      starttime, niter0, instead of mytime, myiter, screws up the adjoint:
499      TAF places a faulty re-call of initialise_varia
500      after cost_final call which should not be there!
501    checkpoint52j_pre
502    
503    o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
504      error messages
505    o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
506    o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
507      debug output
508    o modfied mdsio_writefield.F to handle non-global files under exch2
509    o update AIM Cubed-Sphere exp (aim.5l_cs):
510      use land, p*, and Franco.M forcing fields with fractional land-sea mask.
511    o update AIM Equatorial Channel exp:
512      use standard aim_v23 pkg and change the SST fields to be more realistic.
513    o globalFile now works with exch2
514    o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
515      mon_vort3.F to make exch2 friendly with >1 tile per cube face
516    o limit timeave output for hi-res integrations
517    
518    checkpoint52i_post
519    o removed CPP_EEOPTIONS.h from verification/*/code
520    o updated the tiling for global_ocean_pressure
521    checkpoint52i_pre
522    
523    o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
524      the old pkg/aim).
525    
526    checkpoint52h_pre
527    o shortened offending lines in exch2_send_rx?.template
528    o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
529    o genmake2: add build & execute test for NetCDF code
530    o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
531      old grid files, moved CPP_EEMACROS.h to pkg/exch2
532    o added useSingleCPUIO flag to monitor.F and mon_out.F
533    o added temporary hack for sea-ice dynamics on the cube:
534      metric terms are ignored and it is assumed that
535      there is no sea-ice on cube faces 1, 2, 4, and 5.
536    
537    checkpoint52f_post
538    o added exch2 cube routines to pkg/exch2
539    o modified hs94.cs-32x32x5 to use it
540    o added new grid files to hs94.cs-32x32x5
541    checkpoint52f_pre
542    
543    checkpoint52e_post
544    o first attempt to solve vertical advection (momemtum & T,S) Implicitly
545      for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
546    o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
547      to work with implicit vertical advection and AB ;
548    o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
549    o update output (gad_calc_rhs.F changes affect truncation error) of exp:
550     front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
551    checkpoint52e_pre
552    
553    o fix bug in impldiff when Nr=1 or Nr=2.
554    o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
555    o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
556    o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
557      ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
558    o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
559    o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
560    o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
561    
562    checkpoint52d_post
563    o re-tiled many expts to allow comparison in multi-processor mode
564      - updated output accordingly
565      - changed hs94.128x64x5 to use intial T from file rather than use the
566        random number generator
567    o add infrastructure in model routines for fizhi and gridalt packages
568    o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
569    o changes to permit hi-res, cubed-sphere, configuration
570      - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
571      - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
572      - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
573        of surface winds for the cube
574      (A verification experiment, based on global_ocean.cs32x15, but with
575       pkg/seaice turned on and with on-the-fly interpolation from the NCEP
576       Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
577       complete with example surface forcing files and matlab scripts to look
578       at the output and compare it with that of global_ocean.cs32x15.)
579    o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
580       but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
581       to conform to the common rule.
582    o check-in the first version of the coupler + interfaces for multi-components
583       set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
584       - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
585       - atmosphere: use pkg aim_v23 ; no sea-ice for now.
586       - ocean and atmos. share the same horizontal grid (no interpolation).
587       - exchanges between component and coupler is done in forward_step
588    o new verification experiment, cpl_aim+ocn:
589       coupled ocean - AIM atmosphere on cs32 grid.
590    
591    checkpoint52d_pre
592    o surface flux time-av diagnostic modified for NLFS & RealFreshWater
593    o add call to AIM pendant S/R in external_forcing & external_fields_load.F
594    
595    checkpoint52c_post
596    o Fixing OPTIONS files for use of exf:
597      - ALLOW_ECCO not needed
598      - ECCO_CPPOPTIONS.h should not be included from
599        EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
600        as has been the case in the past
601      - All cal/exf related options are currently set in
602        single header file. Should remain so until we
603        agree on a consistent new policy.
604    o Removed all CPP options for cal package.
605      cal has no more CPP options.
606    o modified STOREs in GAD_ADVECTION
607    o corrected key comp. for passkey
608    
609    checkpoint52b_post
610    o new version: "thsice" of thermodynamic sea-ice pkg:
611     - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
612     - modify fluxes but do not change theta directly;
613     - light cleaning of bulk_force pkg (still needed with thsice).
614     - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
615       + output_thsice.txt to test thsice & bulk_force pkgs.
616    o put back grid & coriolis monitor output.
617    checkpoint52b_pre
618    
619    o call "do_the_model_io" at the beginning (=> dump initial state)
620    o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
621    o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
622      (need info on NUMBER_OF_PTRACERS)
623    o missing PTRACERS headers in some routines
624    o default tamc.h in pkg/autodiff supposed to crash
625      to ensure proper customization
626    
627    checkpoint52a_post
628    o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
629      - moved surfaceTendencyTice from pkg/seaice to main code
630      - subroutine FREEZE_SURFACE now limits only surface temperature
631        and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
632        => new output.txt for global_ocean.cs32x15 & global_with_exf
633      - keep the old version of FREEZE for backward compatibility;
634        global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
635      - corresponding modifs for TAF directives
636    o added surface flux output variables to TIMEAVE_STATVARS
637    o time-averaged output for pkg/ptracers
638    o fix problem with ECCO-related divided adjoint
639      snapshot file was missing some ad-variables,
640      but no warning issued by TAF
641    
642    checkpoint52a_pre
643    o some bug fixes for #undef REAL4_IS_SLOW
644    
645    checkpoint52 = ecco_c52_e35
646    o after testing adjoints of checkpoint51u_post
647    
648    checkpoint51u_post
649    o this is the post-merge tag of the ecco-branch
650      (needs another clean checkout and re-testing)
651    o various natl_box_adjoint configs and results
652      but no input fields
653    o obcs adjoint not yet merged!
654    o adding ECCO global 1x1 and 2x2 degree configs
655    o updated/extended some store directives for seaice
656    o pkg/ecco now containes ecco-specific part of cost function
657    o top level routines the_main_loop, forward_step
658      supersede those in model/src/
659      previous input data.cost now in data.ecco
660      (new namelist ecco_cost_nml)
661    o in ctrl/ cleaned some cross-dependencies and updated CPP options
662    
663    checkpoint51t_post
664    o this is the pre-merge tag of the ecco-branch
665    
666    checkpoint51s_post
667    o cleanup: removed various obsolete #define-s
668    o pkg/grdchk
669      - renamed 'ph-grd 3' to 'grad-res'
670      - merged from ecco-branch
671        (remaining bug fixes for obcs gradient checks)
672      - additional high-precision output for testreport
673        (grep for 'precision_grdchk_result')
674    
675    checkpoint51r_post
676    o cleaned up or removed CPP_OPTIONS.h files
677    o updated results for some of the tests to reflect the new
678      optfiles (-ieee: -O0 instead of -O3)
679    
680    checkpoint51q_post
681    o cd_code:
682      - moved cd_scheme.F -> cd_code_scheme.F
683      - separate read_checkpoint from cd_code_ini_vars.F
684      - separated cd_code part from write_checkpoint
685      - updated AD_SOURCE, generated .flow
686      - added CD_CODE_VARS.h to the_main_loop
687      - Moving cd_code specific store dir.s to pkg/cd_code
688    o ctrl package totally restructured
689      - pack/unpack now optional and decoupled from
690        xx_/adxx_ I/O
691      - ctrl_pack/unpack cleaned
692        (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
693      - confined inclusion of AD_CONFIG.h to where necessary.
694    o genmake2: changed AD dependencies from SRCFILES to AD_FILES
695    
696    checkpoint51p_post
697    o create initial cd_code package
698      - WARNING: the initialization of fields within packages
699        is broken because INI_FIELDS (where READ_CHECKPOINT is
700        called) is called *before* PACKAGES_INIT_VARIABLES.
701        This seems to be backwards since
702        1) its important to initially zero the entire field including
703           the "halo" region
704        2) zeroing needs to be done *before* reading pickup info
705           and the pickup call might or might not happen in any
706           particular run
707      - this needs an overhaul for R2
708    o cleanup verification/*/code/GMREDI_OPTIONS.h
709    o cleanup testreport
710    
711    checkpoint51o_post
712    o bringing AD-related verif's up to date with genmake2
713      - carbon/
714      - global_ocean.90x40x15/
715      - hs.94.1x64x5/
716      - (front_relax/ )
717    o (more) consistent directory structure for AD-related verif.'s
718    o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
719    o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
720    o bug fix in find_alpha.F for MDJWF:
721      - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
722        change rho -> rho-rhoConst
723      - replace call find_rho to find_rhonum
724    o initialisation of rFlx extended to full array (required by TAF)
725      and shifted to thermodynamics
726    o removed PTRACERS.h in ptracers routine
727    o added surfacetendencyPtr to S/R parameter list pracers_forcing
728    o Correcting initialisations for fVerU, fVerV.
729    o helping TAF to recognize dependency on kUp for
730      fVerU, fVerV
731    o Replacing delZ by delR in pkg/ctrl/
732    checkpoint51o_pre
733    
734    o undid all of cp51 pending some cleanups and discussion
735    o added the [#include "AD_CONFIG.h"] statement to all files that need
736       it for adjoint/tl #defines
737     o re-worked the build logic in genmake2 to support AD_CONFIG.h
738     o removed tools/genmake since it no longer works
739    
740    checkpoint51n_post
741    o modifications to make FREEZE flux visible to pkg/kpp
742      - moved surfaceTendencyTice from pkg/seaice to main code
743      - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
744      - subroutine FREEZE now limits only surface temperature
745        (this means new output.txt for global_ocean.90x40x15,
746         global_ocean.cs32x15, and global_with_exf)
747    o added surface flux output variables to TIMEAVE_STATVARS
748    
749    checkpoint51n_pre
750    o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
751    o added [#include "AD_CONFIG.h"] to all files that use the following
752      defines:
753      - ALLOW_ADJOINT_RUN
754      - ALLOW_TANGENTLINEAR_RUN
755      - ALLOW_ECCO_OPTIMIZATION
756    
757    checkpoint51m_post
758    o incorporating changes to get TAMC/TAF working in genmake2
759      - added new TAMC/TAF targets to the Makefile
760      - various cleanups related to package handling
761      - these changes should have no impact on the forward model
762    
763    checkpoint51l_post
764    o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
765     - faster algorithm for cal_addtime.F
766     - higher precision arithmetic, where needed
767     - pkg/exf *startdate variables changed from calendar date to
768       model integration time
769    
770    checkpoint51l_pre
771    o add salt flux to forcing fields (used when salty sea-ice forms or melts)
772    o enable to apply restoring on S & T only in a latitude band.
773    o update output (external_forcing_surf modif. change truncation errors)
774       global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
775    
776    checkpoint51k_post
777    o change default to: useNHMTerms=.FALSE.
778     - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
779       adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
780     - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
781        exp1, ideal_2D_oce
782     - change data file of oceanic exp (leave the results unchanged for now)
783       exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
784    o set gravitySign automatically according to the vertical coordinate used
785      (and change sign: back to "logical" value: +1 when R increases downward)
786    o added an include barrier to the default CPP_OPTIONS.h and
787      removed the #include "PACKAGES_CONFIG.h" from it
788    o fix a bug in mom_fluxform (from chk51j_post)
789    
790    checkpoint51j_post
791    o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
792    o adjusted some flow directives (dynamics, thermodynamics)
793    o added cubed-sphere case to test cost function
794    o heckpoint_lev?_directives.h now include
795      pkg-specific directives, whenever those are enabled.
796    o Moving pkg-specific flow directives to corresponding pkg
797      Moving pkg-specific differentiation list to corresponding pkg
798      Moving pkg-specific checkpoint-lev storing to corresponding pkg
799      ---> conventions are
800           - pkg_ad.flow
801           - pkg_ad_diff.list
802           - pkg_ad_check_lev?_dir.h
803    
804    checkpoint51i_post
805    o merge of the branch-genmake2
806      - knowingly breaks the older genmake
807      - automatic generation of all ALLOW_${PKG_NAME} defines
808      - new testreport supersedes older testscript
809    o large number of package inclusion and header cleanups
810    checkpoint51i_pre
811    
812    o new output for adjoin of global ocean vector invariant
813    o fix for checkpoint of thermodynamic seaice and bulk_force
814    o Steph gchem various cleanups
815    
816    checkpoint 51h_pre
817    o fixed some single quotes
818    o modify gchem pkg to be more versatile
819    o modifications to clean up dic pkg
820    o add pkg/cfc
821    
822    checkpoint51g_post
823    o provide links for ARPACK and ADM*TLM
824    o start removing verification/vero/
825    o update AD-related stuff
826      (in particular some IF-statements in model/src/ routines)
827    o adding to verification/global_ocean.90x40x15/ adjoint of
828      vector invariant setup
829    
830    checkpoint51f_post
831    o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
832    o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
833      of tracer Green's fucntions for ocean inversion project.
834    
835    checkpoint51f_pre
836    o Added on-the-fly spatial interpolation capability
837        "USE_EXF_INTERPOLATION" to pkg/exf.
838      - This is a temporary Cartesian-grid hack until
839        the super-duper ESMF coupler becomes available.
840      - See verification/global_with_exf/README for usage example.
841      - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
842        flags and modified pkg/seaice accordingly.
843    o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
844        and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
845        non-local transport term.
846    
847    checkpoint51e_post
848    o pkg/mom_vecinv:
849      - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
850      - add time-ave diagnostic of vorticity advection.
851    o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
852    o atmospheric geopotential: - include water vapor effect;
853                                - use p^kappa in p* scaling.
854    o land pkg: read initial state from files.
855    o AIM : add stratospheric drag in the upper level
856    
857    checkpoint51d_post
858    o change function ILNBLNK (=> last non-blank char.) to return zero
859      (instead of the string length) when the string. char is empty
860    o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
861    o modif's to restore TAMC compatibility
862      - avoid "_d" constructs in PARAMETER declarations
863      - avoid interrupting lines by comment lines
864    o Use cluster local disks for purely local I/O
865      vs. globally visible disks needed for ctrl stuff
866      (merged from ecco-branch)
867      - new active_file_loc... and mdsio_..._loc routines
868      - affected packages: autodiff, ctrl, grdchk, mdsio
869    
870    checkpoint51c_post
871    o introducing integer flag debugLevel
872      - debLevZero: suppress all output
873      - debLevA: standard
874      - debLevB: equivalent to current debugMode=.TRUE.
875    o introducing pathname variable mdsioLocalDir for mdsio
876      that can be specified at runtime
877      (relevant for cluster I/O to local disk)
878    `
879    >>>checkpoint51b_post
880    adjoint of ptracers
881    o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
882    o extended state in checkpoint_lev?, etc.
883    o alternative ctrl/cost with tr1 or ptracer
884    o new comlev1_bibj_ptracers
885    o new ptracers.flow
886    o made ptracers_forcing same as external_forcing_s
887    o added verification for adjoint with ptracers
888      - adm. grdchk fail so far
889      - tlm. grdchk OK
890      - checked tapelev/comlev recomputations: OK
891    <<<checkpoint51b_pre
892    
893    checkpoint51a_post
894    o added code for biogeochemistry package
895      - new pkgs: dic, gchem
896      - new subroutine in ptracers
897    o modify code for biogeo packages
898      - in model/src and pkg/ptracers
899    
900    checkpoint51
901    o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
902      - autodiff, ctrl, exf, grdchk, seaice
903      kept separate packages
904      - cost, ecco, obcs
905    o updating verification/internal_wave, verification/lab_sea
906      (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
907    
908    checkpoint50i_post
909    o Preparing next differentiable checkpoint and sync
910      of MAIN vs. ecco-branch
911      - 1st step: this one is differentiable
912      - 2nd step: next(! not this) checkpoint will have updated packages
913                  from ecco-branch)
914    
915    checkpoint50h_post
916    o new package "land": provide surface BC for AIM.
917    o pkg/ptracers: apply exchange to all tracers after reading a pickup.
918    o AIM: use true log-P extrapolation for near surface temp (= as in
919        F.Molteni paper) ; update aim.5l_cs output.
920    o New variable in PARM03 for more flexible pickups
921    o somewhat cleaned package initialisation sequence for
922      ctrl/ cost/ ecco/ in packages_... routines
923    
924    checkpoint50g_post
925    o merged with release1_p17 (pkg/seaice and verification/lab_sea)
926      - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
927      - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
928        made the default because of faster convergence than ADI
929    
930    checkpoint50f_post
931    o exf totally restructured
932      - replaced all exf_set_ routines by one generic exf_set_gen.F
933        and made sure it's still differentiable
934      - split exf_getffields.F into new exf_bulkformulae.F
935      - exf_inscal_/exf_outscal_ suffixes consistent with field names
936      - updated adjoint/makefile and relevant verif. accordingly
937    
938    checkpoint50f_pre
939     o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
940          + change Evap over land. (update aim.5l_cs output)
941     o added missing .cvsignores and made uniform across expts
942     o changed configuration of tidal_basin_2d expt
943     o added pkg/debug functions for tracing code in fatal crashes
944     o tidied pkg/monitor to use MONITOR_OPTIONS.h
945     o new fn in pkg/monitor to stop model if solution grows too big
946     o removed lots of single quotes from comments
947    
948    checkpoint50e_post
949    o make KPP work with PTRACERS
950     - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
951       nearly a copy of kpp_transport_s
952     - there is no analogue to SurfaceTendencyS, so I have to use
953       gPtr(of the surface layer) instead
954    o add a new platform SunFire+mpi (SunFire 15000) to genmake
955    checkpoint50e_pre
956    
957    checkpoint50d_post
958    o change kpp output from multiple-record state files to single-record state
959      files analogous to write_state.F
960    o reduce the output frequency of cg3d-related stuff to the monitor frequency,
961      analogous to the cg2d-related output.
962    o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
963      so that writing to internal file fn (with length 512) fails.
964    checkpoint50d_pre
965    
966    checkpoint50c_post
967    o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
968    o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
969    o add time-average diagnostic of U*V and vertical diffusive flux for theta.
970    o bug fixed in convective adjustment diagnostic (multi-tile set-up).
971    o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
972    
973    checkpoint50c_pre
974    Merging from release1_p13:
975    o bug fix for pkg/seaice dynamic solver
976    o Added SEAICE_initialHEFF to pkg/seaice
977    
978    checkpoint50b_post
979    o store u*,v* in gU,V instead of in guNm1,gvNm1
980    o in order to put the momForcing out of the Adams-Bashforth:
981      move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
982      to timestep.F
983    o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
984    o re-generate output for highly sensitive test-exp:
985       global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
986    
987    checkpoint50b_pre
988    o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
989    o corrected CPP option mismatch in exf_Bulk... functions for case
990      #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
991    
992    checkpoint50a_post
993    o Bug fix for merging between c50 and KPP.
994      ikey was passed from thermodynamics to kpp_calc via
995      common block rather than being recomputed in kpp_calc,
996      in contradiction with new key itdkey.
997      New key ikppkey created, and tamc.h headers updated.
998    
999    checkpoint50
1000    - 2nd step of merge with ecco-branch:
1001      merge changes in ecco-branch back into main trunk
1002    - bug fix in find_alpha
1003    - more storing in gmredi_calc_tensor.F, kpp_routines.F
1004    - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
1005    - merged some sliced AD support routines
1006    
1007    checkpoint49
1008    merged from ecco-branch:
1009    o exf:
1010      - Enable initialisation of forcing fields to constant
1011        (runtime) values.
1012      - in exf_getffields.F
1013        Reduce i-/j-loop to interior domain, discarding overlaps.
1014        That also fixes wrong TAF-key computations for key_1, key_2
1015        with bulf formulae.
1016      - exf_init.F modify #ifdef for exf_init_evap
1017      - exf_getffieldrec.F, ctrl_getrec.F
1018        The following INT-usages are not safe:
1019          fldsecs  = int(fldsecs/fldperiod)*fldperiod
1020          fldcount = int(fldsecs/fldperiod) + 1
1021        and were modified.
1022    o autodiff: checkpoint_lev...
1023      - updated storing for bulk formulae (some arrays were missing)
1024      - added state for seaice package
1025      - synchronized with main branch
1026    o DIVA:
1027      Modif.s in
1028      - the_main_loop.F
1029      - the_model_main.F
1030      and added cost_final_restore.F cost_final_store.F
1031      o With these changes, it is possible to fully separate
1032        the first forward run to compute the cost function (mdthe_main_loop)
1033        and adjoint runs over individual DIVA intervals (adthe_main_loop)
1034        into separate model executions.
1035        This enables better tuning of DIVA to given queue sizes.
1036      o Loss of cost function value in consecutive DIVA runs is
1037        fixed by storing to 'costfinal' file.
1038      o Appropriate call of ctrl_unpack/_pack,grdchk_main at
1039        beginning/end of adjoint integration is accounted for.
1040      The current changes apply to TAF-1.4.26.
1041      TAF has one remaining bug, requiring one manual change
1042      (see MITgcm manual).
1043    o cal: synchronized between MAIN and ecco-branch
1044    
1045    checkpoint48i_post
1046    o Changes to restore differentiability of code w.r.t. previous tag
1047      (mostly adding new routines to make list and replacing
1048      pressure by totPhiHyd).
1049    o Updated and merged grdchk package
1050      - has both ADM and TLM checks
1051      - works for single- and multi-proc.
1052      - output cleaned
1053      - worked successfully for parallel DIVA
1054    o genmake:
1055      - Adding -platform=SP4
1056      - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
1057    o Modif. for DIVA:
1058      ctrl_unpack should not be called in intermediate DIVA interval.
1059      (similar thing would apply for active files such as
1060      tbar, sbar, psbar, which should not be reinitialised;
1061      only relevant for ecco-branch)
1062    
1063    checkpoint48h_post
1064    o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
1065    o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
1066    o Added SEAICE_initialHEFF to pkg/seaice
1067    o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
1068    
1069    checkpoint48g_post
1070    --- EOS:
1071    o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
1072      store total Potential in totPhyHyd for diagnostics & EOS.
1073    o fix restart and overlap Pb when using Z-coord and EOS funct. of P
1074    --- Pressure/geopotential gradient:
1075    o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
1076    o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
1077      ( changes results of global_ocean_pressure )
1078    o NLFS + z-coord.: add eta*Rho' contribution.
1079    o accurate phiHyd when using interface-W at the middle between 2 centers
1080     ( changes results of ideal_2D_oce )
1081    o includes r* 2nd term in potential gradient.
1082    
1083    checkpoint48f_post
1084    Merging from release1_p12:
1085    o Modifications for using pkg/exf with pkg/seaice
1086      - improved description of the various forcing configurations
1087      - added basic radiation bulk formulae to pkg/exf
1088      - units/sign fix for evap computation in exf_getffields.F
1089      - updated verification/global_with_exf/results/output.txt
1090    o Added pkg/sbo for computing IERS Special Bureau for the Oceans
1091      (SBO) core products, including oceanic mass, center-of-mass,
1092      angular, and bottom pressure (see pkg/sbo/README.sbo).
1093    o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
1094      to avoid negative values in shallow regions.
1095      - updated verification/natl_box/results/output.txt
1096      - updated verification/lab_sea/results/output.txt
1097    o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
1098    o Added useSingleCpuIO option (see PARAMS.h).
1099    o Updated useSingleCpuIO option in mdsio_writefield.F to
1100      work with multi-field files, e.g., for single-file pickup.
1101    o pkg/seaice:
1102      - bug fix in growth.F: QNET for no shortwave case
1103      - added HeffFile for specifying initial sea-ice thickness
1104      - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
1105    o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
1106      kpp_transport_t.F, forward_step.F, and the_main_loop.F
1107    o pkg/seaice:
1108      - adjoint-friendly modifications
1109      - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
1110    
1111    checkpoint48e_post
1112    o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
1113    o dynamics: change definition of computational domain & adapt mom_fluxform
1114      accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
1115    o following exp works with Olx=Oly=2 (and pass through checkbounds option):
1116        adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
1117        exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
1118        global_ocean.90x40x15 global_with_exf global_ocean_pressure
1119        inverted_barometer solid-body.cs-32x32x1
1120      (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
1121    
1122    checkpoint48d_post
1123    o in preparation for r*:
1124     a) use pre-computed gradient of hydrostatic potential:
1125        changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
1126     b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
1127        => affects results of glob_oce_pressure (different truncation error)  
1128      update output.txt of ideal_2D_oce & global_ocean_pressure
1129    
1130    checkpoint48d_pre
1131    o in preparation for r*:
1132      new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
1133      pass the 2 comp. of the grad. as arguments to momentum S/R.
1134      but for the moment, only used if it does not change the results.
1135    o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
1136    
1137    checkpoint48c_post
1138    Modifications in treatment of initial flux forcing controls
1139    to avoid extra storing of flux fields.
1140    
1141    checkpoint48c_pre
1142  o Added tidal_basin_2d experiment (currently 1D!)  o Added tidal_basin_2d experiment (currently 1D!)
1143  o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)  o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
1144    
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