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revision 1.153 by jmc, Mon May 12 21:16:45 2003 UTC revision 1.390 by jmc, Sun Nov 21 22:22:31 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 GMredi:
7      - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
8      - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
9      - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
10    o GCHEM:
11      - move call to GCHEM_FORCING_SEP, so that it is now called before
12        the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
13      - introduced a useGCHEM runtime flag and applied it everywhere.
14    o small cleaning of exch2: remove files that are also in eesupp/src
15    
16    checkpoint56
17    o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
18    o mnc: cleanup "full" files--fixes out-of-memory problem
19    o ECCO-GODAE
20      * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
21      * fully merged and updated from SIO code
22        windstress sign change affects
23        - exf_inscal_[u/v]stress
24        - sign of xx_tau[u/v] adjustments
25        - signs in cost_scat
26      * ctrl_get_gen: avoid update of tau[u/v] for first few days
27      * natl_box_adjoint updated and compressed
28      * 2-level checkpoint switch added
29        (tested in EXP. 1 of natl_box_adjoint)
30      * new switch doInitXX to avoid init. of xx_... in optimcycle=0
31    o SVD
32      * first complete, non-hacked version for SVD calculations
33      * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
34        performed via direct access files admtlm_vector.it????
35        (via ctrl_[un]pack)
36      * optimcycle is used for ARPACK iteration counter
37        (note: adxx_... is iterated, rather than xx_...; latter is constant!)
38      * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
39        and add linear transforms where necessary
40      * controls are initial/final SST, SSS (can be extended; need to check
41        ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
42    o mdsio: filename info to both stderr, stdout
43    o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
44      from sign change
45    
46    checkpoint55j_post
47    o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
48      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
49    o add consistent build directories and .cvsignore files to verification
50    o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
51    o make all subroutines 30 or less characters in length for certain older
52      compilers to work (a thorough search only turns up two routines in
53      pkg/ptracers)
54    o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
55      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
56    
57    checkpoint55i_post
58    o change arrays for total vertical diffusivity (2.D if explicit,
59      3.D if implicit) ; each ptracer uses its own background value.
60    o added mnc/NetCDF output capability to ocn_compon_interf
61      - added bits to verification/cpl_aim+ocn so that it can run on
62        ITRDA and other clusters without the mpirun "-wd" option
63    o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
64      configuration
65    o give MNC the ability to create additional files rather than
66      exceeding a specified file size limit "MNC_MAX_FILESIZE"
67      - the default is just less than 2GB which is a practical limit
68        on many systems
69    o Compute the non-local term using either KPP vertical diffusivity (=default)
70       or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
71    
72    checkpoint55h_post
73    o add verification test "vermix"
74    o remove all the *_ioinc flags and replace with the single global
75      outputTypesInclusive flag
76    o allow to set a vertical profile of vertical diffusivity for T & S
77    o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
78    o useMNC moved from data.mnc to data.pkg
79    
80    checkpoint55g_post
81    o Renaming carbon AD experiments to comply with testreport conventions
82    o Updating adjoint of Held-Suarez hs94.1x64x5
83    o Fixing directives for non-ECCO forward_step, after ECCO directives
84      have been fixed to avoid recomp. of do_oceanic_phys
85      Works well for global_ocean.90x40x15,
86      but recomp. issue remains for carbon
87    o Updating adjoint output for natl_box_adjoint after
88      pkg/ecco has been modified (see taga c55d_post)
89    
90    checkpoint55f_post
91    o rename to timeave_init_fixed
92    
93    checkpoint55e_post
94    o some delicate re-shuffle of store directives to avoid one
95      extra call of do_oceanic_physics
96      affects ecco_the_main_loop.F, do_oceanic_physics.F
97      checkpoint_lev1_directives.h
98    o NB: this may break global_ocean adjoint temporarily,
99      but it is clear how to fix it. Will do later, need this now.
100    
101    checkpoint55d_post
102    o ECCO specific cost function terms (up-to-date with 1x1 runs)
103    o ecco_cost_weights is modified to 1x1 runs
104    o modifs to allow observations to be read in as
105      single file or yearly files
106    o enable to read exf forcing fields as either
107      single file or yearly files (flag useExfYearlyFields)
108    checkpoint55d_pre
109    
110    o switch between 2-level and 3-level checkpointing
111    o add ability of MNC to write local and "partial" (eg. 2D slices where
112      the full 3D field is never actually stored) arrays to NetCDF files
113      with the correct (that is, the complete multi-dimensional) set of
114      array indicies
115      - used in mom_vecinv() to write the diagFreq output
116      - tested (demonstrated) in verification/aim.5l_cs
117    o further mnc-ification
118      - add verification/lab_sea to the list with mnc setups
119      - fix undefined mnc v-names in cd_code
120      - add kpp to mnc output (both snapshot and timeave)
121    o non-hydrostatic code
122      - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
123        in calc_gw.F
124      - defaults to viscAh
125      - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
126        friction or Leith) in non-hydrostatic mode, as long as there is
127        no biharmonic friction and/or Leigth or equivalent for vertical velocity.
128    o pkg/cost
129      extend simple cost functions to treat time mean quantities
130      (T,U,V) via cost_accumulate_state from cost_tile
131    o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
132        be 2 times larger than the minimum size the advection scheme requires.
133        now get a perfect conservation of salt in advect_cs test-exp (updated)
134    o GGL90 (Gaspar's TKE mixed layer)
135      - add horizontal diffusion of TKE, requires exchanges in
136        do_fields_blocking_exchanges, horizontal diffusivity is zero by
137        default. In OPA there is no horizontal diffusion of TKE but the
138        mixing coefficients are computed from a horizontal average of TKE of
139        6 points or so. I think that diffusion has a little more physical
140        justification.
141      - clean up ggl90_calc in the hope of reducing memory usage (this hope
142        was in vain)
143      - mask tke-variable in ggl90_init
144    o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
145    o fix biharmonic diffusion on CS-grid.
146    o more obcs stuff
147      - added obcs_external_fields_load as an alternative to the EXF-pkg option
148        for reading boundary values. This routine is called from
149        obcs_prescribe_read
150      - updated obcs_check
151      - changed sponge layer relaxation parameter units for days to seconds
152      - turned off sponge layer by default
153      - changed argument list of OBCS_CALC to myTime+deltaTclock
154      - fixed about 35 bugs in obcs_external_fields_load
155    
156    checkpoint55c_post
157    o obcs stuff
158      - new runtime flags useOBCSprescribe, useOBCSbalance
159      - re-arranged obcs_calc
160      - moved exf_getobcs to obcs_prescibe_read
161        obcs_prescibe_read is called after ORLANSKI stuff
162        and independent of it (executable can contain all).
163      - updated obcs_check
164      - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
165        These may be necessary only if tangential velocities are
166        prescribed at OB, not sure, needs testing.
167    o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
168      which simplifies the calls and passes the ifc check-bounds test
169    
170    checkpoint55b_post
171    o add a 2D scalar, Z location, exchange_2 routine.
172    o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
173      to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
174      affects advect_cs results (for the wrong reason): update output.txt
175    o use a more standard discretization for biharmonic viscosity ;
176     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
177      affects results of dome set-up: update output.txt
178    o fix gad_advection.F (CubedSphere part), back to version 1.23
179    o fix bug in mom_vi_del2uv.F (CubedSphere part).
180    
181    checkpoint55a_post
182    o merged code to
183      * prescribe/read time-dependent open boundaries
184        (works in conjunction with exf, cal)
185      * sponge layer code for open boundaries
186      * each boundary N/S/E/W now has its own CPP option
187        (healthy for the adjoint)
188    
189    checkpoint55
190    o up-to-date adjoint of previous breaks
191      - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
192      - global_ocean_ebm: adjoint still needs fix (TLM ok)
193      - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
194      - carbon: * remove tr1-related adjoint verification
195                * add ptracer as control variable
196    o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
197      (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
198    
199    checkpoint54f_post
200    o in verification/carbin/ remove experiment related to
201      ALLOW_PASSIVE_TRACER (array tr1 etc)
202      code_ad/ input_ad/ results_ad
203    
204    o add two new packages
205      - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
206        + subject to optimization (memory)
207      - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
208        + subject to reordering (many GOTOs in the original code)
209        + so far opps is called for every (i,j) point, and then operates in
210          the vertical; one may want to reorder the scheme in order operate in
211          horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
212          fields)
213    o overhaul of IO so that we now have flags for MDSIO and/or MNC
214      - all verification tests compile and run with linux_ia32_g77
215      - defaults are compatible with current input files--nothing
216        should change if you were not previously using MNC
217      - MNC output has been added in numerous places (eg. timeave)
218        but there are still a few writes not yet do-able with MNC
219        (this is in progress)
220      - flags now allow for either/or/both use of MDSIO and MNC and
221        documentation will soon follow
222      - numerous small formatting cleanups for ProTeX
223    o add version info (via BUILD_INFO.h) to MNC and stdout
224    
225    checkpoint54e_post
226    o add two new packages
227      - pp81 (Packanowski and Philander, 1981), Richardson number and
228        stratification dependent mixing
229      - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
230      - these scheme operate in a similar manner as KPP (without ghat, of
231        course), however there is only one diffusivity that is used for both
232        temperature and salinity (and passive tracers)ç
233    o add offline package
234    o add "verification/dic_example" which contains a dic-gchem-ptracer setup
235      provided by Stephanie Dutkiewicz
236    o genmake2: add ability to search for C compilers and cleanup test output
237      - fixes recent SX-6 problems and should help with others (eg. HP-UX)
238    
239    checkpoint54d_post
240    o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
241    o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
242      leading to additional shift by 5 days each year of integration
243       (i.e. leading to considerable offset over the years)
244    o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
245    o start with no AB and no initial filtering (staggerTimeStep):
246      change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
247    o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
248      (external loading & cpl import/export stay in forward_step.F)
249    o update coupling interface to work with new staggerTimeStep
250    o change MDSIO ptracers_pickup.
251    o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
252    o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
253    o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
254    
255    checkpoint54c_post
256    o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
257      this affects (truncation error) output.txt of test-exp:
258       global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
259    o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
260    o change Qnet to always be the net heat flux, (+upward).
261      affects (truncation error) output of natl_box exp.: updated
262    o define the max number of passive tracers in PTRACERS_SIZE.h
263    o start to test mnc routinely in exp0
264    o add sea-ice loading (sIceLoad) as a new forcing field.
265    
266    checkpoint54b_post
267    o add testreport "-j JOBS" option for parallel builds (tested and pretty
268       impressive on Altix and Opteron systems)
269    o diagnostics can now write NetCDF files through the mnc package
270    o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
271    o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
272    o staggerTimeStep & NLFS: rescale T & S surface tendencies.
273      affects (truncation error) output of lab_sea & natl_box exp.: updated
274    o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
275    
276    checkpoint54a_post
277    o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
278    o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
279    o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
280    o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
281      + internal_wave (shift in writing cg2d_ini_res)
282    checkpoint54a_pre
283    
284    o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
285      - modified verification/lab_sea and natl_box_adjoint accordingly
286    
287    checkpoint54
288    checkpoint53g_post
289    o prepare splitting of thermodynamics: store convect.counter in common block
290    o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
291      output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
292    o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
293    o new parameter "nShapS": allow to treat differently S from T (nShapT)
294    o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
295    o restore adjointability
296    
297    checkpoint53f_post
298    o modifications that affect AIM experiment results (update output.txt):
299      - no advection of S at top interface Nr (pkg/generic_advdiff)
300      - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
301    o AIM pkg:
302      - include stability function into surf.Flux derivative relative to Tsurf
303      - calculate clear-sky radiation & surface temp. change (for diagnostics)
304    
305    checkpoint53e_post
306    o merged cylindrical coord configuration
307    o added rotating_tank experiment
308    checkpoint53e_pre
309    
310    checkpoint53d_post
311    o faulks upgraded: re-generate output.txt that have changed:
312       global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
313    o Added Bryan and Lewis, 1979, vertical diffusivity profile
314    o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
315    o added Sadourny discretization of Coriolis
316      - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
317      - re-enabled use of omega3 (useAbsVorticity)
318    o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
319      vector-invariant equations
320      - note: does *NOT* yet use same variable visc. for no-slip BC's.
321    o recoded the lateral boundary conditions for non-hydrostatic w, this time
322      hopefully without new bugs
323      - still to do: biharmonic friction for non-hydrostatic w
324    o bug fix for mom_*_sidedrag: rA -> rAs,rAw
325    o regenerated output for global_ocean_ebm (using -ieee)
326    o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
327      of mom_common/
328      - simple re-arrangement of instructions within computing loop
329    checkpoint53d_pre
330    
331    checkpoint53c_post
332    o new version of coupler for AIM+thSIce and Ocean models
333     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
334     - land: change Evaporation of snow
335     - aim with thSIce: fix bug in snow-precip.
336    o changes to calc_gw.F
337     - bug fix for w^2 term near the bottom boundary
338     - (hopefully) improve the lateral slip boundary condtions for use with
339        partial/looped cells
340      - because the bug fix changes two verification experiments anyway (exp5
341        and plume on slope), change the lateral boundary condition from half slip
342        to the value of no_slip_sides
343    o ebm package wasnt quite up to the parallel task. Fixed that.
344    o Adjoint of EBM package + verification
345      * TLM OK
346      * ADM not sufficient accuracy yet (needs further testing)
347    
348    checkpoint53b_post
349    o Commiting new energy balance model to repository
350      * package is pkg/ebm
351      * verif. is verification/global_ocean_ebm
352      * references are in ebm_driver.F
353    C      * X. Wang, P. Stone and J. Marotzke, 1999:
354    C        Global thermohaline circulation. Part I:
355    C        Sensitivity to atmospheric moisture transport.
356    C        J. Climate 12(1), 71-82
357    C      * X. Wang, P. Stone and J. Marotzke, 1999:
358    C        Global thermohaline circulation. Part II:
359    C        Sensitivity with interactive transport.
360    C        J. Climate 12(1), 83-91
361    C      * M. Nakamura, P. Stone and J. Marotzke, 1994:
362    C        Destabilization of the thermohaline circulation
363    C        by atmospheric eddy transports.
364    C        J. Climate 7(12), 1870-1882
365    o Will need long integration testing.
366    checkpoint53b_pre
367    
368    o created pkg/mom_common in preparation for variable viscosity code
369    o renamed and split ini_mnc_io
370    o pkg/land: only liquid water can diffuse or run-off
371    o AIM using land: soil wetness availability account for snow
372    o added printMapIncludesZeros to EEPARMS namelist
373    
374    checkpoint53a_post
375    o restore TAMC compatiility for exf_constants.h
376      (no usage of _d in .h)
377    o Additional storing in KPP in an attempt to fix
378      TAMC problem with adjoint of KPP code.
379      (no success...)
380      Identical code works fine with TAF.
381    o Fixed verification/natl_box_adjoint experiments.
382      Initial conditions for Experiments 4 and 5 are now
383      set to "SEAICE_initialHEFF=0", which is more reasonable,
384      and hence gives results closer to that of Experiment 2.
385      Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
386    
387    checkpoint53
388    o stable checkpoint with up to date adjoint
389      TLM tests only run for 1st grdchk at the moment. Its unclear if
390      this is a code problem or a problem with resetting code for g_
391      variables that is being autogenerated wrong.
392      Otherwise:
393       o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
394       o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
395         are both still in chaos following their security messes.
396    
397    checkpoint52n_post
398    o various build (mostly genmake2) changes including:
399      - ability to build/run more easily within Cygwin and MacOS X
400      - more complicated Makefiles with a stronger dependence on Gnu Make
401    o pkg/seaice modifications
402      - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
403        of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
404        and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
405      - changed proxy for geostrophic velocity and updated
406        verification/lab_sea/results/* accordingly
407      - removed ADI dynamic solver from pkg/seaice
408      - replaced all occurrences of 1/CSTICE or 1/CSUICE
409        they caused a segmentation fault under certain circumstances
410      - removed unused field WATR
411    o bug fix in exf-package:
412      -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
413         now reflect that.
414    o small fixes in the cal-package:
415      - set reference date to first of January for the 'model'-calendar
416      - failing of cal_CheckDate in cal_FullDate now actually results in a
417        warning
418    o small modifications in exf-package to increase flexibility:
419      - change climtempfreeze from a constant to a runtime parameter that
420        is specified in data.exf_clim (default = -1.9)
421      - introduce runtime parameter windstressmax (default = 2.0) that is
422        specified in data.exf
423    o fix in pkg/thsice:
424      - update Evap (Tsf changes) to be consistent with Latent heat flux
425      - maintain snow precipitation unchanged (even if Tsf >=0).
426     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
427    
428    checkpoint52m_post
429    o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
430      this does not change any of the results, because myIter=0 in swfrac always
431      lead to jwtype=2 (the default anyway), but the call makes little sense
432      as a default
433    o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
434    o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
435      atmospheric model (AIM) to use it ; add a "slab ocean" component.
436    o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
437    o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
438    o extending useSingleCpuIO option to work with new exch2 I/O format
439      - old-style, missing-tile I/O is still accessible by defining CPP
440        option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
441    o monitor package can write to NetCDF files and/or STDOUT
442    o fix re-definition bug in MNC_GRID_INIT_ALL()
443    o doc/api_reference added
444      - a framework for building an API Reference Manual using all
445        the "protex" comments embedded in the code
446      - see pkg/generic_advdiff, pkg/mnc for examples
447    o MNC:
448      - make myThid the last argument for all subroutines
449      - new default for the grid files: NO halos
450      - add useMNC and other run-time flags
451      - separate per-file-group handling of the unlimited dimension
452      - early initialization of MNC w/ flags read at the eeboot stage
453        and lookup tables set in initialize_fixed
454      - write all MNC output to a freshly-created directory
455    o thermodynamics sea-ice (thsice) is now tested with testreport.
456    o test exp. advect_cs: use the standard cs32 grid ; update output.
457    o Added functionality to grdchk:
458      pick global i,j,k position (or nearest wet) where to perform check.
459    
460    checkpoint52l_post
461    o new land formulation:
462      a) use ground enthalpy as prognostic variable to ensure exact
463         energy conservation.
464      b) account for water temperature and for latent heat of freezing
465         in all processes (rain, run-off, ground storage)
466      c) compute surface and ground temperature implicitly.
467    o aim_v23 modification for new land model:
468      a) Treat separately land / ocean / sea-ice surface fluxes
469         to allow implicit computation of land & sea-ice surface temp.
470      b) add snow precipitation.
471    checkpoint52l_pre
472    
473    o fix problem (when 1 tile is empty) in min/max monitor.
474    o fix bug in timeAve (u,vZetatave in common block)
475    o no restoring terms under ice for pkg/seaice
476    o moved SEAICE_DO_DIAGS to S/R do_the_model_io
477    o bug fix for pkg/seaice pickups
478    o change MNC call locations and add coordinate attributes
479    o mask vorticity at the corner ; affects global_ocean.cs output
480    o fix ini_curvilinear_grid ; test CS experiments with mpi
481    o aim.5l_cs: modify sea-ice fraction input file ; update output
482    o exf: Adding simple range check routine for exf fields after read
483    
484    checkpoint52k_post
485    o removed top-level directory "diags"
486      - we migrated these functions to pkg/timeave a long time ago
487    o fixed bug introduced in pkg/monitor
488    o accuracy ctrlprec = 32 insuffient for gradient checks using
489      averaged fields (I/O via cost_averages)
490      -> use ctrl.h in active_file*.F to control I/O precision.
491    o paramter list of CALL ADTHE_MAIN_LOOP
492    o added initial do_the_model_io to ecco
493    o set all ...Freq to zero after cost_final
494      taveFreq, dumpFreq, pChkptFreq
495    o MAIN and ECCO differentiability restored
496    
497    checkpoint52j_post
498    o fix nchklev in tamc.h for global_ocean...
499    o Bringing flow and store directives up-to-date
500    o Really weird thing!
501      call do_the_model_io from the_main_loop with parameters
502      starttime, niter0, instead of mytime, myiter, screws up the adjoint:
503      TAF places a faulty re-call of initialise_varia
504      after cost_final call which should not be there!
505    checkpoint52j_pre
506    
507    o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
508      error messages
509    o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
510    o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
511      debug output
512    o modfied mdsio_writefield.F to handle non-global files under exch2
513    o update AIM Cubed-Sphere exp (aim.5l_cs):
514      use land, p*, and Franco.M forcing fields with fractional land-sea mask.
515    o update AIM Equatorial Channel exp:
516      use standard aim_v23 pkg and change the SST fields to be more realistic.
517    o globalFile now works with exch2
518    o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
519      mon_vort3.F to make exch2 friendly with >1 tile per cube face
520    o limit timeave output for hi-res integrations
521    
522    checkpoint52i_post
523    o removed CPP_EEOPTIONS.h from verification/*/code
524    o updated the tiling for global_ocean_pressure
525    checkpoint52i_pre
526    
527    o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
528      the old pkg/aim).
529    
530    checkpoint52h_pre
531    o shortened offending lines in exch2_send_rx?.template
532    o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
533    o genmake2: add build & execute test for NetCDF code
534    o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
535      old grid files, moved CPP_EEMACROS.h to pkg/exch2
536    o added useSingleCPUIO flag to monitor.F and mon_out.F
537    o added temporary hack for sea-ice dynamics on the cube:
538      metric terms are ignored and it is assumed that
539      there is no sea-ice on cube faces 1, 2, 4, and 5.
540    
541    checkpoint52f_post
542    o added exch2 cube routines to pkg/exch2
543    o modified hs94.cs-32x32x5 to use it
544    o added new grid files to hs94.cs-32x32x5
545    checkpoint52f_pre
546    
547    checkpoint52e_post
548    o first attempt to solve vertical advection (momemtum & T,S) Implicitly
549      for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
550    o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
551      to work with implicit vertical advection and AB ;
552    o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
553    o update output (gad_calc_rhs.F changes affect truncation error) of exp:
554     front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
555    checkpoint52e_pre
556    
557    o fix bug in impldiff when Nr=1 or Nr=2.
558    o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
559    o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
560    o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
561      ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
562    o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
563    o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
564    o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
565    
566    checkpoint52d_post
567    o re-tiled many expts to allow comparison in multi-processor mode
568      - updated output accordingly
569      - changed hs94.128x64x5 to use intial T from file rather than use the
570        random number generator
571    o add infrastructure in model routines for fizhi and gridalt packages
572    o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
573    o changes to permit hi-res, cubed-sphere, configuration
574      - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
575      - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
576      - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
577        of surface winds for the cube
578      (A verification experiment, based on global_ocean.cs32x15, but with
579       pkg/seaice turned on and with on-the-fly interpolation from the NCEP
580       Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
581       complete with example surface forcing files and matlab scripts to look
582       at the output and compare it with that of global_ocean.cs32x15.)
583    o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
584       but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
585       to conform to the common rule.
586    o check-in the first version of the coupler + interfaces for multi-components
587       set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
588       - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
589       - atmosphere: use pkg aim_v23 ; no sea-ice for now.
590       - ocean and atmos. share the same horizontal grid (no interpolation).
591       - exchanges between component and coupler is done in forward_step
592    o new verification experiment, cpl_aim+ocn:
593       coupled ocean - AIM atmosphere on cs32 grid.
594    
595    checkpoint52d_pre
596    o surface flux time-av diagnostic modified for NLFS & RealFreshWater
597    o add call to AIM pendant S/R in external_forcing & external_fields_load.F
598    
599    checkpoint52c_post
600    o Fixing OPTIONS files for use of exf:
601      - ALLOW_ECCO not needed
602      - ECCO_CPPOPTIONS.h should not be included from
603        EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
604        as has been the case in the past
605      - All cal/exf related options are currently set in
606        single header file. Should remain so until we
607        agree on a consistent new policy.
608    o Removed all CPP options for cal package.
609      cal has no more CPP options.
610    o modified STOREs in GAD_ADVECTION
611    o corrected key comp. for passkey
612    
613    checkpoint52b_post
614    o new version: "thsice" of thermodynamic sea-ice pkg:
615     - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
616     - modify fluxes but do not change theta directly;
617     - light cleaning of bulk_force pkg (still needed with thsice).
618     - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
619       + output_thsice.txt to test thsice & bulk_force pkgs.
620    o put back grid & coriolis monitor output.
621    checkpoint52b_pre
622    
623    o call "do_the_model_io" at the beginning (=> dump initial state)
624    o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
625    o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
626      (need info on NUMBER_OF_PTRACERS)
627    o missing PTRACERS headers in some routines
628    o default tamc.h in pkg/autodiff supposed to crash
629      to ensure proper customization
630    
631    checkpoint52a_post
632    o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
633      - moved surfaceTendencyTice from pkg/seaice to main code
634      - subroutine FREEZE_SURFACE now limits only surface temperature
635        and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
636        => new output.txt for global_ocean.cs32x15 & global_with_exf
637      - keep the old version of FREEZE for backward compatibility;
638        global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
639      - corresponding modifs for TAF directives
640    o added surface flux output variables to TIMEAVE_STATVARS
641    o time-averaged output for pkg/ptracers
642    o fix problem with ECCO-related divided adjoint
643      snapshot file was missing some ad-variables,
644      but no warning issued by TAF
645    
646    checkpoint52a_pre
647    o some bug fixes for #undef REAL4_IS_SLOW
648    
649    checkpoint52 = ecco_c52_e35
650    o after testing adjoints of checkpoint51u_post
651    
652    checkpoint51u_post
653    o this is the post-merge tag of the ecco-branch
654      (needs another clean checkout and re-testing)
655    o various natl_box_adjoint configs and results
656      but no input fields
657    o obcs adjoint not yet merged!
658    o adding ECCO global 1x1 and 2x2 degree configs
659    o updated/extended some store directives for seaice
660    o pkg/ecco now containes ecco-specific part of cost function
661    o top level routines the_main_loop, forward_step
662      supersede those in model/src/
663      previous input data.cost now in data.ecco
664      (new namelist ecco_cost_nml)
665    o in ctrl/ cleaned some cross-dependencies and updated CPP options
666    
667    checkpoint51t_post
668    o this is the pre-merge tag of the ecco-branch
669    
670    checkpoint51s_post
671    o cleanup: removed various obsolete #define-s
672    o pkg/grdchk
673      - renamed 'ph-grd 3' to 'grad-res'
674      - merged from ecco-branch
675        (remaining bug fixes for obcs gradient checks)
676      - additional high-precision output for testreport
677        (grep for 'precision_grdchk_result')
678    
679    checkpoint51r_post
680    o cleaned up or removed CPP_OPTIONS.h files
681    o updated results for some of the tests to reflect the new
682      optfiles (-ieee: -O0 instead of -O3)
683    
684    checkpoint51q_post
685    o cd_code:
686      - moved cd_scheme.F -> cd_code_scheme.F
687      - separate read_checkpoint from cd_code_ini_vars.F
688      - separated cd_code part from write_checkpoint
689      - updated AD_SOURCE, generated .flow
690      - added CD_CODE_VARS.h to the_main_loop
691      - Moving cd_code specific store dir.s to pkg/cd_code
692    o ctrl package totally restructured
693      - pack/unpack now optional and decoupled from
694        xx_/adxx_ I/O
695      - ctrl_pack/unpack cleaned
696        (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
697      - confined inclusion of AD_CONFIG.h to where necessary.
698    o genmake2: changed AD dependencies from SRCFILES to AD_FILES
699    
700    checkpoint51p_post
701    o create initial cd_code package
702      - WARNING: the initialization of fields within packages
703        is broken because INI_FIELDS (where READ_CHECKPOINT is
704        called) is called *before* PACKAGES_INIT_VARIABLES.
705        This seems to be backwards since
706        1) its important to initially zero the entire field including
707           the "halo" region
708        2) zeroing needs to be done *before* reading pickup info
709           and the pickup call might or might not happen in any
710           particular run
711      - this needs an overhaul for R2
712    o cleanup verification/*/code/GMREDI_OPTIONS.h
713    o cleanup testreport
714    
715    checkpoint51o_post
716    o bringing AD-related verif's up to date with genmake2
717      - carbon/
718      - global_ocean.90x40x15/
719      - hs.94.1x64x5/
720      - (front_relax/ )
721    o (more) consistent directory structure for AD-related verif.'s
722    o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
723    o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
724    o bug fix in find_alpha.F for MDJWF:
725      - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
726        change rho -> rho-rhoConst
727      - replace call find_rho to find_rhonum
728    o initialisation of rFlx extended to full array (required by TAF)
729      and shifted to thermodynamics
730    o removed PTRACERS.h in ptracers routine
731    o added surfacetendencyPtr to S/R parameter list pracers_forcing
732    o Correcting initialisations for fVerU, fVerV.
733    o helping TAF to recognize dependency on kUp for
734      fVerU, fVerV
735    o Replacing delZ by delR in pkg/ctrl/
736    checkpoint51o_pre
737    
738    o undid all of cp51 pending some cleanups and discussion
739    o added the [#include "AD_CONFIG.h"] statement to all files that need
740       it for adjoint/tl #defines
741     o re-worked the build logic in genmake2 to support AD_CONFIG.h
742     o removed tools/genmake since it no longer works
743    
744    checkpoint51n_post
745    o modifications to make FREEZE flux visible to pkg/kpp
746      - moved surfaceTendencyTice from pkg/seaice to main code
747      - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
748      - subroutine FREEZE now limits only surface temperature
749        (this means new output.txt for global_ocean.90x40x15,
750         global_ocean.cs32x15, and global_with_exf)
751    o added surface flux output variables to TIMEAVE_STATVARS
752    
753    checkpoint51n_pre
754    o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
755    o added [#include "AD_CONFIG.h"] to all files that use the following
756      defines:
757      - ALLOW_ADJOINT_RUN
758      - ALLOW_TANGENTLINEAR_RUN
759      - ALLOW_ECCO_OPTIMIZATION
760    
761    checkpoint51m_post
762    o incorporating changes to get TAMC/TAF working in genmake2
763      - added new TAMC/TAF targets to the Makefile
764      - various cleanups related to package handling
765      - these changes should have no impact on the forward model
766    
767    checkpoint51l_post
768    o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
769     - faster algorithm for cal_addtime.F
770     - higher precision arithmetic, where needed
771     - pkg/exf *startdate variables changed from calendar date to
772       model integration time
773    
774    checkpoint51l_pre
775    o add salt flux to forcing fields (used when salty sea-ice forms or melts)
776    o enable to apply restoring on S & T only in a latitude band.
777    o update output (external_forcing_surf modif. change truncation errors)
778       global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
779    
780    checkpoint51k_post
781    o change default to: useNHMTerms=.FALSE.
782     - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
783       adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
784     - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
785        exp1, ideal_2D_oce
786     - change data file of oceanic exp (leave the results unchanged for now)
787       exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
788    o set gravitySign automatically according to the vertical coordinate used
789      (and change sign: back to "logical" value: +1 when R increases downward)
790    o added an include barrier to the default CPP_OPTIONS.h and
791      removed the #include "PACKAGES_CONFIG.h" from it
792    o fix a bug in mom_fluxform (from chk51j_post)
793    
794    checkpoint51j_post
795    o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
796    o adjusted some flow directives (dynamics, thermodynamics)
797    o added cubed-sphere case to test cost function
798    o heckpoint_lev?_directives.h now include
799      pkg-specific directives, whenever those are enabled.
800    o Moving pkg-specific flow directives to corresponding pkg
801      Moving pkg-specific differentiation list to corresponding pkg
802      Moving pkg-specific checkpoint-lev storing to corresponding pkg
803      ---> conventions are
804           - pkg_ad.flow
805           - pkg_ad_diff.list
806           - pkg_ad_check_lev?_dir.h
807    
808    checkpoint51i_post
809    o merge of the branch-genmake2
810      - knowingly breaks the older genmake
811      - automatic generation of all ALLOW_${PKG_NAME} defines
812      - new testreport supersedes older testscript
813    o large number of package inclusion and header cleanups
814    checkpoint51i_pre
815    
816    o new output for adjoin of global ocean vector invariant
817    o fix for checkpoint of thermodynamic seaice and bulk_force
818    o Steph gchem various cleanups
819    
820    checkpoint 51h_pre
821    o fixed some single quotes
822    o modify gchem pkg to be more versatile
823    o modifications to clean up dic pkg
824    o add pkg/cfc
825    
826    checkpoint51g_post
827    o provide links for ARPACK and ADM*TLM
828    o start removing verification/vero/
829    o update AD-related stuff
830      (in particular some IF-statements in model/src/ routines)
831    o adding to verification/global_ocean.90x40x15/ adjoint of
832      vector invariant setup
833    
834    checkpoint51f_post
835    o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
836    o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
837      of tracer Green's fucntions for ocean inversion project.
838    
839    checkpoint51f_pre
840    o Added on-the-fly spatial interpolation capability
841        "USE_EXF_INTERPOLATION" to pkg/exf.
842      - This is a temporary Cartesian-grid hack until
843        the super-duper ESMF coupler becomes available.
844      - See verification/global_with_exf/README for usage example.
845      - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
846        flags and modified pkg/seaice accordingly.
847    o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
848        and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
849        non-local transport term.
850    
851    checkpoint51e_post
852    o pkg/mom_vecinv:
853      - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
854      - add time-ave diagnostic of vorticity advection.
855    o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
856    o atmospheric geopotential: - include water vapor effect;
857                                - use p^kappa in p* scaling.
858    o land pkg: read initial state from files.
859    o AIM : add stratospheric drag in the upper level
860    
861    checkpoint51d_post
862    o change function ILNBLNK (=> last non-blank char.) to return zero
863      (instead of the string length) when the string. char is empty
864    o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
865    o modif's to restore TAMC compatibility
866      - avoid "_d" constructs in PARAMETER declarations
867      - avoid interrupting lines by comment lines
868    o Use cluster local disks for purely local I/O
869      vs. globally visible disks needed for ctrl stuff
870      (merged from ecco-branch)
871      - new active_file_loc... and mdsio_..._loc routines
872      - affected packages: autodiff, ctrl, grdchk, mdsio
873    
874    checkpoint51c_post
875    o introducing integer flag debugLevel
876      - debLevZero: suppress all output
877      - debLevA: standard
878      - debLevB: equivalent to current debugMode=.TRUE.
879    o introducing pathname variable mdsioLocalDir for mdsio
880      that can be specified at runtime
881      (relevant for cluster I/O to local disk)
882    `
883    >>>checkpoint51b_post
884    adjoint of ptracers
885    o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
886    o extended state in checkpoint_lev?, etc.
887    o alternative ctrl/cost with tr1 or ptracer
888    o new comlev1_bibj_ptracers
889    o new ptracers.flow
890    o made ptracers_forcing same as external_forcing_s
891    o added verification for adjoint with ptracers
892      - adm. grdchk fail so far
893      - tlm. grdchk OK
894      - checked tapelev/comlev recomputations: OK
895    <<<checkpoint51b_pre
896    
897    checkpoint51a_post
898    o added code for biogeochemistry package
899      - new pkgs: dic, gchem
900      - new subroutine in ptracers
901    o modify code for biogeo packages
902      - in model/src and pkg/ptracers
903    
904    checkpoint51
905    o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
906      - autodiff, ctrl, exf, grdchk, seaice
907      kept separate packages
908      - cost, ecco, obcs
909    o updating verification/internal_wave, verification/lab_sea
910      (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
911    
912    checkpoint50i_post
913    o Preparing next differentiable checkpoint and sync
914      of MAIN vs. ecco-branch
915      - 1st step: this one is differentiable
916      - 2nd step: next(! not this) checkpoint will have updated packages
917                  from ecco-branch)
918    
919    checkpoint50h_post
920    o new package "land": provide surface BC for AIM.
921    o pkg/ptracers: apply exchange to all tracers after reading a pickup.
922    o AIM: use true log-P extrapolation for near surface temp (= as in
923        F.Molteni paper) ; update aim.5l_cs output.
924    o New variable in PARM03 for more flexible pickups
925    o somewhat cleaned package initialisation sequence for
926      ctrl/ cost/ ecco/ in packages_... routines
927    
928    checkpoint50g_post
929    o merged with release1_p17 (pkg/seaice and verification/lab_sea)
930      - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
931      - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
932        made the default because of faster convergence than ADI
933    
934    checkpoint50f_post
935    o exf totally restructured
936      - replaced all exf_set_ routines by one generic exf_set_gen.F
937        and made sure it's still differentiable
938      - split exf_getffields.F into new exf_bulkformulae.F
939      - exf_inscal_/exf_outscal_ suffixes consistent with field names
940      - updated adjoint/makefile and relevant verif. accordingly
941    
942    checkpoint50f_pre
943     o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
944          + change Evap over land. (update aim.5l_cs output)
945     o added missing .cvsignores and made uniform across expts
946     o changed configuration of tidal_basin_2d expt
947     o added pkg/debug functions for tracing code in fatal crashes
948     o tidied pkg/monitor to use MONITOR_OPTIONS.h
949     o new fn in pkg/monitor to stop model if solution grows too big
950     o removed lots of single quotes from comments
951    
952    checkpoint50e_post
953    o make KPP work with PTRACERS
954     - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
955       nearly a copy of kpp_transport_s
956     - there is no analogue to SurfaceTendencyS, so I have to use
957       gPtr(of the surface layer) instead
958    o add a new platform SunFire+mpi (SunFire 15000) to genmake
959    checkpoint50e_pre
960    
961    checkpoint50d_post
962    o change kpp output from multiple-record state files to single-record state
963      files analogous to write_state.F
964    o reduce the output frequency of cg3d-related stuff to the monitor frequency,
965      analogous to the cg2d-related output.
966    o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
967      so that writing to internal file fn (with length 512) fails.
968    checkpoint50d_pre
969    
970  checkpoint50c_post  checkpoint50c_post
971  o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)  o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
972  o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.  o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
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