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revision 1.31 by heimbach, Mon Nov 13 16:49:41 2000 UTC revision 1.53.2.28 by dimitri, Fri Feb 14 22:30:15 2003 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    release1_p12_pre
7    o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
8      kpp_transport_t.F, forward_step.F, and the_main_loop.F
9    o Updated useSingleCpuIO option in mdsio_writefield.F to
10      work with multi-field files, e.g., for single-file pickup.
11    o pkg/seaice:
12      - bug fix in growth.F: QNET for no shortwave case
13      - added HeffFile for specifying initial sea-ice thickness
14      - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
15      - adjoint-friendly modifications
16    
17    release1_p11
18    o Modifications for using pkg/exf with pkg/seaice
19      - improved description of the various forcing configurations
20      - added basic radiation bulk formulae to pkg/exf
21      - units/sign fix for evap computation in exf_getffields.F
22      - updated verification/global_with_exf/results/output.txt
23    o Added pkg/sbo for computing IERS Special Bureau for the Oceans
24      (SBO) core products, including oceanic mass, center-of-mass,
25      angular, and bottom pressure (see pkg/sbo/README.sbo).
26    o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
27      to avoid negative values in shallow regions.
28      - updated verification/natl_box/results/output.txt
29      - updated verification/lab_sea/results/output.txt
30    o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
31    o Added useSingleCpuIO option (see PARAMS.h).
32    
33    release1_p10
34    o modifications for using pkg/exf with pkg/seaice
35      - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
36        and SEAICE_EXTERNAL_FLUXES
37      - pkg/exf CPP options EXF_READ_EVAP and
38        EXF_NO_BULK_COMPUTATIONS
39      - usage examples are Experiments 8 and 9 in
40        verification/lab_sea/README
41      - verification/lab_sea default experiment now uses
42        pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
43    
44    release1_p9
45    o pkg/seaice
46      - removed GOTO's and added taf directives
47      - double precision constants to reduce the g77 (Linux)
48        to F77 (SGI) differences reported in release1_p8
49    o tools/genmake
50      - added SGI options
51    o verification/testscript
52      - updated to that of checkpoint47a_post
53    o verification/global_ocean.90x40x15/input/eedata
54      - modified for SGI f77 compatibility
55    o verification/lab_sea
56      - added description of sea-ice model
57      - added missing matlab routines
58      - added test of thermodynamics parallelization
59    
60    release1_p8
61    o verification/natl_box:
62      updating new external_fields_load routine
63    o New package: pkg/seaice
64      Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
65      The sea-ice code is based on Hibler (1979-1980).
66      Two sea-ice dynamic solvers, ADI and LSR, are included.
67      In addition to computing prognostic sea-ice variables and diagnosing
68      the forcing/external data fields that drive the ocean model,
69      SEAICE_MODEL also sets theta to the freezing point under sea-ice.
70      The implied surface heat flux is then stored in variable
71      surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
72      kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
73      non-local transport term.  Because this call precedes model
74      thermodynamics, temperature under sea-ice may not be "exactly" at
75      the freezing point by the time theta is dumped or time-averaged.
76      N.B.: fairly large differences in accuracy occur across
77            different platforms/compilers; comparison between
78            g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
79            generated output gives:
80       T           S           U           V
81      C D M    c        m  s        m  s        m  s        m  s
82      n p a R  g  m  m  e  .  m  m  e  .  m  m  e  .  m  m  e  .
83      f n k u  2  i  a  a  d  i  a  a  d  i  a  a  d  i  a  a  d
84      g d e n  d  n  x  n  .  n  x  n  .  n  x  n  .  n  x  n  .
85    
86      Y Y Y Y  5  5  7  7  7  8 10  9  6  6  6  6  7  5  7  5  7 FAIL  lab_sea
87    
88    release1_p7
89    o GAD:
90      - generated new common blocks to account for call of
91        same gad routines with differing traceridentities
92        (needed to modify tracerIdentity indices in GAD.h)
93      - generated separate common blocks for case useCubedSphereExchange
94        (Department of Futurology)
95      - parameter lists to gmredi_?transport: added tracerIdentity
96      - added new key indices to tamc.h
97    o external_fields_load:
98      - added this routine to TAF list
99      - needed to make some common blocks global and additional storing
100        along the same lines as exf package (checkpoint_lev?_directives.h)
101    o exf:
102      updated external forcing package
103      - bug fixes carried over from ecco-branch
104        (missing OBCS_OPTIONS.h in two routines)
105      - enable easy to use "no forcing".
106      - added exf I/O for atmospheric loading
107      - added exf I/O for runoff data
108      - transfered scaling between exf <-> MITgcm to exf namelist
109    o Adding new verification experiment global_with_exf.
110      This verification experiment is almost identical to the
111      global_ocean.90x40x15 experiment, except that it uses
112      the exf (and cal) package instead of the
113      external_fields_load routine (cf README file).
114    
115    release1_p6
116    o fixed the verification/global_ocean.90x40x15 experiment:
117     - new bathymetry (the world according to A., JMC, and M.)
118     - new initial fields and forcing fields (*.bin files)
119     - new POLY3.COEFFS (for the next release one should switch to a full
120       equation of state)
121     - fixed several errors and redundancies in the data file
122     - experiment uses looped cells
123     - added matlab directory with diagnostic scripts for plotting of output
124    
125    release1_p5
126    o import recent fix from MAIN branch:
127      - use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
128      - change phiMin in exp1 (to agree with documentation)
129     from checkpoint45 to checkpoint45a_post:
130      - specific exchange for X-slice domain (case Ny=1)
131      - argument futureIter of S/R obcs_calc missing in
132        exp4 & internal_wave /code
133      - solve_for_pressure : set cg2d_x to zero where OBCS are applied
134     from checkpoint44f_post to checkpoint44g_post:
135      - fix surface correction term in multiDimAdvection
136        (affects plume_on_slope results
137    o bug fix in packages_readparms (missing ALLOW_CALENDAR)
138    o bug fix in CG2D.h (correct array size for LETS_MAKE_JAM
139    o Adjoint-related bug fixes in kpp:
140      - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
141      - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
142    o added Eliassen-Palm flux hooks (dynamics,ini_fields)
143    o removed unused TAF keys iikey, idkey (dynamics,thermodynamics)
144    o flow directives:
145      - new for S/R do_the_model_io
146      - enhanced for S/R checkpoint
147    o added Eliassen Palm flux controls to gradient check package
148    o new ctrl package
149      - adopted from ECCO environment to enable optimization
150      - added Eliassen Palm fluxes to controls
151      - adjusted global_ocean.90x40x15/ and carbon/ accordingly
152    
153    release1_p4
154    o Removed f90 comments ("!")
155    o Modified initialisations to enable exf package for MITgcm
156      (without invoking ECCO_PACKAGE).
157    o modifications to gradient check package (Martin Losch)
158      - enable centered differences
159      - modified format of standard output
160    
161    release1_p3
162    o added tangent linear setup to verification/carbon/
163    o added adjoint sensitivity setup to verification/global_ocean...
164    o moved packages_init_variables before convective_adjustment
165    o output of verif. which use GMRedi brought up-to-date with
166      MAIN trunk (those were re-created after changes in GMRedi)
167    o included CPP option SINGLE_LAYER_MODE
168      to configure barotropic setup (Martin Losch).
169    o Removed auxiliary variable in impldiff
170      (caused numerical differences with MAIN trunk routine).
171    o Introduced CPP option ALLOW_AUTODIFF_MONITOR to
172      disable adcommon.h/g_common.h by default.
173    o Cleaned exchange calls in cg2d.
174    
175    release1_p2
176    o fixed array boundary problem for adjoint
177      (related to partial recomputation within subroutine
178      related to dynamics -> calc_viscosity -> mom_...
179    o fixed recomputation in thermodynamics
180    o prepare (but not complete) recomputation problem in impldiff
181    o fixed problem for adjoint of global_max
182    o switched off sponge layer code in external_forcing
183    
184    release1_p1
185    o merged necessary patches:
186      - AD-related changes for GMRedi
187      - fixes i KPP (delZ -> drF)
188      - hook to OBCS songe layer code in external_forcing
189      - errorMessageUnit non-zero in eeboot.F
190      - modified test cost function and carbon verif.
191    
192    release1_chkpt44d_post = chkpt44d_post
193    
194    chkpt44d_pre,post
195    o added missing EXCLUDE_MONITOR flags
196    o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
197      (incompatible typ in MIN/MAX expressions caused problems
198      on IBM SP3)
199    o in genmake added variable MAKEDEPEND
200      plus resetting for case SunOS
201    o added timer_stats.c routine for IBM SP3
202    o removed variables in dynamics
203    
204    o real fresh water flux implemented with non-linear free-surface.
205    
206    chkpt44c_pre,post
207    o few fix (mask in shap_s2, EmPmR in external_field_load,
208      USE_NATURAL_BCS in solve_for_P);
209    o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
210    
211    checkpoint44b_pre/_post
212    o merge of relevant stuff from the ecco-branch:
213      - genmake: removed $S64 overwrite for case SunOS
214      - pkg/exf: update and corrections for field swapping and obcs
215      - pkg/ecco: parameter lists for the_model_main, the_main_loop
216                  harmonized between ECCO and MITgcm
217      - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
218                      updated checkpointing_lev... lists for obcs
219      - model/src: minor changes in forward_step, plot_field
220                   added directive for divided adjoint in the_main_loop
221      - pkg/mdsio: added mdsio_gl_slice
222    
223    o check parameters & config (chkpt44a_pre,post)
224    o OBC and NonLin_FrSurf.
225    
226    checkpoint44
227    o fix bug in mom_vi_del2uv
228    o select when filters are applied ; add options to zonal_filter (data.zonfilt)
229    o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
230    o update AIM experiments (NCEP input files)
231    o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
232    o added some stuff for AD
233    
234    checkpoint43
235    o added two new advection tests
236    o added global 4x4 degree ocean test
237    o added test of H&S94 with free surface on cube
238    o some final mods for gradient check, adjoint,...
239    
240    checkpoint42
241      Fixed AD-related problems:
242    o Store directives up-to-date with re-arranged Adams-Bashforth
243      (mainly thermodynamics.F)
244    o New store directives for multi-dim. advection schemes
245      * new CPP flag ALLOW_MULTI_DIM_ADVECTION
246      * new common block and key passkey
247      (mainly gad_advection.F)
248    o Modified store directives for split of dynamics/thermodynamics
249      for the case ALLOW_KPP
250    o Cleaned argument list for timestep_tracer.F
251    
252    checkpoint41
253    o re-formatted/added comments in prologues of key subroutines
254      to work with protex
255    
256    checkpoint40
257    o moved calc_gs, calc_gt and calc_tr1 back to model/src
258    o added FLT (floats) package from Arne along with demo. experiment
259    o re-arranged Adams-Bashforth scheme for tracers to allow easier
260      implementation of forward-in-time forcing terms
261    o more mods for non-linear free-surface including new variable
262    o modified multi-dim method to work on cube
263    o bug fix in KPP (from DM)
264    
265    checkpoint40pre9
266    o added DST advection schemes
267    o fix MPI bug on SGI's
268    o modifications for non-linear free-surface
269    o fixed conditionals for fixed flow/passive tracer only mode
270    o added tension/strain form of stress tensor
271    o changes to commenting of arguments for TAF/TAMC
272    o added/updated many matlab scripts
273    o added multi-dimensional advection method for tracers
274      
275    checkpoint40pre8
276    o new package rw/
277      Added method for dumping intermediate local arrays:
278      mdsio_writetile - same as mdsio_writefield except works from inside
279                        bi,bj loop
280      mdsio_writelocal - same as mdsio_writetile except works for local
281                         arrays
282      write_local_r? - higher-level wrapper for mdsio_writelocal
283      Controlled by diagFreq. Defaults to zero (ie. no dumps)
284      Example given at end of mom_vecinv.F that dumps some local arrays.
285    o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
286      control flux-form versus vector invariant code.
287      Switch is runtime flag vectorInvariantMomentum (defaults to false)
288      or genmake -DISABLE ...
289    o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
290      (additional storing is now needed for case vecinv;
291      currently nothing implemented to switch this storing off
292      in case fluxform is used since no CPP flag available).
293    
294    checkpoint40pre7
295    o bug fix in dynamics.F
296      calc_viscosity called before k=1,Nr loop.
297    o added some #ifdef's ALLOW_PASSIVE_TRACER
298    o cleaned initialisations in ctrl_map_ini
299      related to TAF
300    
301    checkpoint40pre6
302    o split dynamics into thermodynamics & dynamics
303    o corresponding split of calc_diffusivity into
304      calc_diffusivity, calc_viscosity
305      (kpp_calc_diff, kpp_calc_visc).
306    o Added diffkr, kapgm to control variables
307    o bug fix in gmredi_slope_limit for ldd97
308    
309    checkpoint40pre5
310    o proper initialization of Adams-Bashforth time stepping
311      + uses forward step for very first step of model (iter=0)
312    o re-generated *all* output since almost all output is modified by this
313      change (sorry but we've been putting this one off for about 2 years)
314      + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
315        *not* regenerated since they are already out of date and I don't
316        want to create the impression that they are suddenly working.
317    o removed KAP stuff for DEC's
318    o modified/added many .cvsignore files in */code and */input
319    o added new expt "solid-body.cs-32x32x1"
320      + this uses an alternative form of ini_curvilinear_grid.F which
321        is not necessarily any better than the current one...
322    
323    checkpoint40pre4
324    o added re-initialisations of utrans,vtrans,rtrans in
325      calc_common_factors which are crucial for TAF.
326    o extended iMin,jMin range for calc_common_factors,
327      calc_diffusivity
328    o added option ALLOW_PASSIVE_TRACER
329    o a few minor updates and fixes
330    
331    checkpoint40pre3
332    o created calc_gtr1.F for gad package
333    o split the_main_loop and re-introduced forward_step
334    o some recomputations of nIter0 for TAMC
335    
336    checkpoint40pre2
337    o Updated to latest branch of AJA, JMC
338    o Added gradient check package
339    o Added routines for passive tracer handling
340    o Added carbon sequestration sensitivity experiment
341    
342    checkpoint39
343     o Modifications and fixes to support TAMC
344       (mainly missing or wrong directives)
345     o Corrected common blocks when fooling TAMC to produce adjoint I/O
346       in addummy_in_stepping
347     o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
348     o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
349     o Included following packages:
350       cal: calendar
351       exf: external forcing
352       ecco: essential routines to control use of cal, exf
353             (NB: this is not the full ECCO environment)
354     o disabled some packages by default in genmake
355    
356    checkpoint38
357     o see notes_c37_adj.txt
358     o corrected wrong layer index in external_forcing_t
359     o replaced the_main_loop/forward_step by the_main_loop
360     o removed forceoutput from write_state
361       (replaced criteria for initial/final state)
362     o added runtime flag for pre-C35 pickups: usePickupBeforeC35
363    
364    checkpoint37
365     o mdsio.F routine split and packaged in pkg/mdsio
366       (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
367        used unless genmake -disable=mdsio)
368     o allow a more precise surface-geopotential gradient for the atmosphere
369       taking into account the change in space of Alpha (=1/rho) at the surface.
370     o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
371       (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
372     o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
373       Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
374       [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
375     o Time-Average diagnostics defined as a pseudo package "timeave".
376     o pickup files : old pickup (before c35) did not work with new code (c35
377       and after) unless activating 2 commented lines in initialise-varia.
378     o Non-Hydrostatic pickup file Pb fixed.
379     o bug with Rigid-lid version (since c35) fixed.  
380    
381    checkpoint36
382     o implement Crank-Nickelson barotropic time-stepping
383     o recover Time-Average diagnostics
384     o fix Pb in checkpoint (PR#19)
385     o AIM become a standard package ; clean unused CPP_kees
386    
387    checkpoint35
388     o subtantial rewrite of dynamics.f
389     o allows staggered time-stepping
390     o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
391     o added bottom drag (linear + quadratic)
392    
393    checkpoint34
394     o Modified exchange routines for correct reverse simulation.
395     o Added verification output to comply with bug fix in impldiff.F
396       as of c33 (exp2, natl_box).
397     o Corrected store directives in dynamics.F
398     o Corrected array boundaries in impldiff.F
399     o Corrected array dimensions in gmredi.
400       Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
401     o Added routine GLOBAL_SUM_INT to global_sum.F
402     o Added mdsio_gl.F for ECCO purposes.
403    
404    checkpoint33
405     o Fixed bug in lower BC in impldiff.F
406     o Fixed confusion about units of forcing arrays in FFIELDS.h
407       namely Fu,Fv,Qnet,Qsw,EmPmR:
408       - Removed verification/natl_box/code/external_fields_scale.F
409         (did not differ from that in model/src)
410       - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
411         (see FFIELDS.h for description)
412       - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
413         kpp_calc.F and kpp_transport_t.F
414       - Removed model/src/external_fields_scale.F and calls to it
415       - verification/natl_box uses flux data with "atmospheric" sign so
416         a special version of external_fields_load.F is used to
417         change the data as it's read in. This way, the arrays
418         have the right units and signs at all times tha a user could
419         possibly use them.
420     o Corrected genmake to delete a temporary file during configuration
421    
422  checkpoint32  checkpoint32
423   o Scaling of forcing fields moved from external_forcing.F to   o Scaling of forcing fields moved from external_forcing.F to
424     external_fields_scale.F, called directly after loading fields.     external_fields_scale.F, called directly after loading fields.

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