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revision 1.30 by heimbach, Mon Sep 11 23:30:54 2000 UTC revision 1.53.2.30 by dimitri, Sun Feb 16 16:28:29 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
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 pkg/seaice:
10      - adjoint-friendly modifications
11      - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
12    
13    release1_p12_pre
14    o Updated useSingleCpuIO option in mdsio_writefield.F to
15      work with multi-field files, e.g., for single-file pickup.
16    o pkg/seaice:
17      - bug fix in growth.F: QNET for no shortwave case
18      - added HeffFile for specifying initial sea-ice thickness
19      - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
20    
21    release1_p11
22    o Modifications for using pkg/exf with pkg/seaice
23      - improved description of the various forcing configurations
24      - added basic radiation bulk formulae to pkg/exf
25      - units/sign fix for evap computation in exf_getffields.F
26      - updated verification/global_with_exf/results/output.txt
27    o Added pkg/sbo for computing IERS Special Bureau for the Oceans
28      (SBO) core products, including oceanic mass, center-of-mass,
29      angular, and bottom pressure (see pkg/sbo/README.sbo).
30    o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
31      to avoid negative values in shallow regions.
32      - updated verification/natl_box/results/output.txt
33      - updated verification/lab_sea/results/output.txt
34    o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
35    o Added useSingleCpuIO option (see PARAMS.h).
36    
37    release1_p10
38    o modifications for using pkg/exf with pkg/seaice
39      - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
40        and SEAICE_EXTERNAL_FLUXES
41      - pkg/exf CPP options EXF_READ_EVAP and
42        EXF_NO_BULK_COMPUTATIONS
43      - usage examples are Experiments 8 and 9 in
44        verification/lab_sea/README
45      - verification/lab_sea default experiment now uses
46        pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
47    
48    release1_p9
49    o pkg/seaice
50      - removed GOTO's and added taf directives
51      - double precision constants to reduce the g77 (Linux)
52        to F77 (SGI) differences reported in release1_p8
53    o tools/genmake
54      - added SGI options
55    o verification/testscript
56      - updated to that of checkpoint47a_post
57    o verification/global_ocean.90x40x15/input/eedata
58      - modified for SGI f77 compatibility
59    o verification/lab_sea
60      - added description of sea-ice model
61      - added missing matlab routines
62      - added test of thermodynamics parallelization
63    
64    release1_p8
65    o verification/natl_box:
66      updating new external_fields_load routine
67    o New package: pkg/seaice
68      Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
69      The sea-ice code is based on Hibler (1979-1980).
70      Two sea-ice dynamic solvers, ADI and LSR, are included.
71      In addition to computing prognostic sea-ice variables and diagnosing
72      the forcing/external data fields that drive the ocean model,
73      SEAICE_MODEL also sets theta to the freezing point under sea-ice.
74      The implied surface heat flux is then stored in variable
75      surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
76      kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
77      non-local transport term.  Because this call precedes model
78      thermodynamics, temperature under sea-ice may not be "exactly" at
79      the freezing point by the time theta is dumped or time-averaged.
80      N.B.: fairly large differences in accuracy occur across
81            different platforms/compilers; comparison between
82            g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
83            generated output gives:
84       T           S           U           V
85      C D M    c        m  s        m  s        m  s        m  s
86      n p a R  g  m  m  e  .  m  m  e  .  m  m  e  .  m  m  e  .
87      f n k u  2  i  a  a  d  i  a  a  d  i  a  a  d  i  a  a  d
88      g d e n  d  n  x  n  .  n  x  n  .  n  x  n  .  n  x  n  .
89    
90      Y Y Y Y  5  5  7  7  7  8 10  9  6  6  6  6  7  5  7  5  7 FAIL  lab_sea
91    
92    release1_p7
93    o GAD:
94      - generated new common blocks to account for call of
95        same gad routines with differing traceridentities
96        (needed to modify tracerIdentity indices in GAD.h)
97      - generated separate common blocks for case useCubedSphereExchange
98        (Department of Futurology)
99      - parameter lists to gmredi_?transport: added tracerIdentity
100      - added new key indices to tamc.h
101    o external_fields_load:
102      - added this routine to TAF list
103      - needed to make some common blocks global and additional storing
104        along the same lines as exf package (checkpoint_lev?_directives.h)
105    o exf:
106      updated external forcing package
107      - bug fixes carried over from ecco-branch
108        (missing OBCS_OPTIONS.h in two routines)
109      - enable easy to use "no forcing".
110      - added exf I/O for atmospheric loading
111      - added exf I/O for runoff data
112      - transfered scaling between exf <-> MITgcm to exf namelist
113    o Adding new verification experiment global_with_exf.
114      This verification experiment is almost identical to the
115      global_ocean.90x40x15 experiment, except that it uses
116      the exf (and cal) package instead of the
117      external_fields_load routine (cf README file).
118    
119    release1_p6
120    o fixed the verification/global_ocean.90x40x15 experiment:
121     - new bathymetry (the world according to A., JMC, and M.)
122     - new initial fields and forcing fields (*.bin files)
123     - new POLY3.COEFFS (for the next release one should switch to a full
124       equation of state)
125     - fixed several errors and redundancies in the data file
126     - experiment uses looped cells
127     - added matlab directory with diagnostic scripts for plotting of output
128    
129    release1_p5
130    o import recent fix from MAIN branch:
131      - use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
132      - change phiMin in exp1 (to agree with documentation)
133     from checkpoint45 to checkpoint45a_post:
134      - specific exchange for X-slice domain (case Ny=1)
135      - argument futureIter of S/R obcs_calc missing in
136        exp4 & internal_wave /code
137      - solve_for_pressure : set cg2d_x to zero where OBCS are applied
138     from checkpoint44f_post to checkpoint44g_post:
139      - fix surface correction term in multiDimAdvection
140        (affects plume_on_slope results
141    o bug fix in packages_readparms (missing ALLOW_CALENDAR)
142    o bug fix in CG2D.h (correct array size for LETS_MAKE_JAM
143    o Adjoint-related bug fixes in kpp:
144      - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
145      - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
146    o added Eliassen-Palm flux hooks (dynamics,ini_fields)
147    o removed unused TAF keys iikey, idkey (dynamics,thermodynamics)
148    o flow directives:
149      - new for S/R do_the_model_io
150      - enhanced for S/R checkpoint
151    o added Eliassen Palm flux controls to gradient check package
152    o new ctrl package
153      - adopted from ECCO environment to enable optimization
154      - added Eliassen Palm fluxes to controls
155      - adjusted global_ocean.90x40x15/ and carbon/ accordingly
156    
157    release1_p4
158    o Removed f90 comments ("!")
159    o Modified initialisations to enable exf package for MITgcm
160      (without invoking ECCO_PACKAGE).
161    o modifications to gradient check package (Martin Losch)
162      - enable centered differences
163      - modified format of standard output
164    
165    release1_p3
166    o added tangent linear setup to verification/carbon/
167    o added adjoint sensitivity setup to verification/global_ocean...
168    o moved packages_init_variables before convective_adjustment
169    o output of verif. which use GMRedi brought up-to-date with
170      MAIN trunk (those were re-created after changes in GMRedi)
171    o included CPP option SINGLE_LAYER_MODE
172      to configure barotropic setup (Martin Losch).
173    o Removed auxiliary variable in impldiff
174      (caused numerical differences with MAIN trunk routine).
175    o Introduced CPP option ALLOW_AUTODIFF_MONITOR to
176      disable adcommon.h/g_common.h by default.
177    o Cleaned exchange calls in cg2d.
178    
179    release1_p2
180    o fixed array boundary problem for adjoint
181      (related to partial recomputation within subroutine
182      related to dynamics -> calc_viscosity -> mom_...
183    o fixed recomputation in thermodynamics
184    o prepare (but not complete) recomputation problem in impldiff
185    o fixed problem for adjoint of global_max
186    o switched off sponge layer code in external_forcing
187    
188    release1_p1
189    o merged necessary patches:
190      - AD-related changes for GMRedi
191      - fixes i KPP (delZ -> drF)
192      - hook to OBCS songe layer code in external_forcing
193      - errorMessageUnit non-zero in eeboot.F
194      - modified test cost function and carbon verif.
195    
196    release1_chkpt44d_post = chkpt44d_post
197    
198    chkpt44d_pre,post
199    o added missing EXCLUDE_MONITOR flags
200    o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
201      (incompatible typ in MIN/MAX expressions caused problems
202      on IBM SP3)
203    o in genmake added variable MAKEDEPEND
204      plus resetting for case SunOS
205    o added timer_stats.c routine for IBM SP3
206    o removed variables in dynamics
207    
208    o real fresh water flux implemented with non-linear free-surface.
209    
210    chkpt44c_pre,post
211    o few fix (mask in shap_s2, EmPmR in external_field_load,
212      USE_NATURAL_BCS in solve_for_P);
213    o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
214    
215    checkpoint44b_pre/_post
216    o merge of relevant stuff from the ecco-branch:
217      - genmake: removed $S64 overwrite for case SunOS
218      - pkg/exf: update and corrections for field swapping and obcs
219      - pkg/ecco: parameter lists for the_model_main, the_main_loop
220                  harmonized between ECCO and MITgcm
221      - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
222                      updated checkpointing_lev... lists for obcs
223      - model/src: minor changes in forward_step, plot_field
224                   added directive for divided adjoint in the_main_loop
225      - pkg/mdsio: added mdsio_gl_slice
226    
227    o check parameters & config (chkpt44a_pre,post)
228    o OBC and NonLin_FrSurf.
229    
230    checkpoint44
231    o fix bug in mom_vi_del2uv
232    o select when filters are applied ; add options to zonal_filter (data.zonfilt)
233    o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
234    o update AIM experiments (NCEP input files)
235    o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
236    o added some stuff for AD
237    
238    checkpoint43
239    o added two new advection tests
240    o added global 4x4 degree ocean test
241    o added test of H&S94 with free surface on cube
242    o some final mods for gradient check, adjoint,...
243    
244    checkpoint42
245      Fixed AD-related problems:
246    o Store directives up-to-date with re-arranged Adams-Bashforth
247      (mainly thermodynamics.F)
248    o New store directives for multi-dim. advection schemes
249      * new CPP flag ALLOW_MULTI_DIM_ADVECTION
250      * new common block and key passkey
251      (mainly gad_advection.F)
252    o Modified store directives for split of dynamics/thermodynamics
253      for the case ALLOW_KPP
254    o Cleaned argument list for timestep_tracer.F
255    
256    checkpoint41
257    o re-formatted/added comments in prologues of key subroutines
258      to work with protex
259    
260    checkpoint40
261    o moved calc_gs, calc_gt and calc_tr1 back to model/src
262    o added FLT (floats) package from Arne along with demo. experiment
263    o re-arranged Adams-Bashforth scheme for tracers to allow easier
264      implementation of forward-in-time forcing terms
265    o more mods for non-linear free-surface including new variable
266    o modified multi-dim method to work on cube
267    o bug fix in KPP (from DM)
268    
269    checkpoint40pre9
270    o added DST advection schemes
271    o fix MPI bug on SGI's
272    o modifications for non-linear free-surface
273    o fixed conditionals for fixed flow/passive tracer only mode
274    o added tension/strain form of stress tensor
275    o changes to commenting of arguments for TAF/TAMC
276    o added/updated many matlab scripts
277    o added multi-dimensional advection method for tracers
278      
279    checkpoint40pre8
280    o new package rw/
281      Added method for dumping intermediate local arrays:
282      mdsio_writetile - same as mdsio_writefield except works from inside
283                        bi,bj loop
284      mdsio_writelocal - same as mdsio_writetile except works for local
285                         arrays
286      write_local_r? - higher-level wrapper for mdsio_writelocal
287      Controlled by diagFreq. Defaults to zero (ie. no dumps)
288      Example given at end of mom_vecinv.F that dumps some local arrays.
289    o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
290      control flux-form versus vector invariant code.
291      Switch is runtime flag vectorInvariantMomentum (defaults to false)
292      or genmake -DISABLE ...
293    o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
294      (additional storing is now needed for case vecinv;
295      currently nothing implemented to switch this storing off
296      in case fluxform is used since no CPP flag available).
297    
298    checkpoint40pre7
299    o bug fix in dynamics.F
300      calc_viscosity called before k=1,Nr loop.
301    o added some #ifdef's ALLOW_PASSIVE_TRACER
302    o cleaned initialisations in ctrl_map_ini
303      related to TAF
304    
305    checkpoint40pre6
306    o split dynamics into thermodynamics & dynamics
307    o corresponding split of calc_diffusivity into
308      calc_diffusivity, calc_viscosity
309      (kpp_calc_diff, kpp_calc_visc).
310    o Added diffkr, kapgm to control variables
311    o bug fix in gmredi_slope_limit for ldd97
312    
313    checkpoint40pre5
314    o proper initialization of Adams-Bashforth time stepping
315      + uses forward step for very first step of model (iter=0)
316    o re-generated *all* output since almost all output is modified by this
317      change (sorry but we've been putting this one off for about 2 years)
318      + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
319        *not* regenerated since they are already out of date and I don't
320        want to create the impression that they are suddenly working.
321    o removed KAP stuff for DEC's
322    o modified/added many .cvsignore files in */code and */input
323    o added new expt "solid-body.cs-32x32x1"
324      + this uses an alternative form of ini_curvilinear_grid.F which
325        is not necessarily any better than the current one...
326    
327    checkpoint40pre4
328    o added re-initialisations of utrans,vtrans,rtrans in
329      calc_common_factors which are crucial for TAF.
330    o extended iMin,jMin range for calc_common_factors,
331      calc_diffusivity
332    o added option ALLOW_PASSIVE_TRACER
333    o a few minor updates and fixes
334    
335    checkpoint40pre3
336    o created calc_gtr1.F for gad package
337    o split the_main_loop and re-introduced forward_step
338    o some recomputations of nIter0 for TAMC
339    
340    checkpoint40pre2
341    o Updated to latest branch of AJA, JMC
342    o Added gradient check package
343    o Added routines for passive tracer handling
344    o Added carbon sequestration sensitivity experiment
345    
346    checkpoint39
347     o Modifications and fixes to support TAMC
348       (mainly missing or wrong directives)
349     o Corrected common blocks when fooling TAMC to produce adjoint I/O
350       in addummy_in_stepping
351     o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
352     o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
353     o Included following packages:
354       cal: calendar
355       exf: external forcing
356       ecco: essential routines to control use of cal, exf
357             (NB: this is not the full ECCO environment)
358     o disabled some packages by default in genmake
359    
360    checkpoint38
361     o see notes_c37_adj.txt
362     o corrected wrong layer index in external_forcing_t
363     o replaced the_main_loop/forward_step by the_main_loop
364     o removed forceoutput from write_state
365       (replaced criteria for initial/final state)
366     o added runtime flag for pre-C35 pickups: usePickupBeforeC35
367    
368    checkpoint37
369     o mdsio.F routine split and packaged in pkg/mdsio
370       (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
371        used unless genmake -disable=mdsio)
372     o allow a more precise surface-geopotential gradient for the atmosphere
373       taking into account the change in space of Alpha (=1/rho) at the surface.
374     o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
375       (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
376     o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
377       Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
378       [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
379     o Time-Average diagnostics defined as a pseudo package "timeave".
380     o pickup files : old pickup (before c35) did not work with new code (c35
381       and after) unless activating 2 commented lines in initialise-varia.
382     o Non-Hydrostatic pickup file Pb fixed.
383     o bug with Rigid-lid version (since c35) fixed.  
384    
385    checkpoint36
386     o implement Crank-Nickelson barotropic time-stepping
387     o recover Time-Average diagnostics
388     o fix Pb in checkpoint (PR#19)
389     o AIM become a standard package ; clean unused CPP_kees
390    
391    checkpoint35
392     o subtantial rewrite of dynamics.f
393     o allows staggered time-stepping
394     o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
395     o added bottom drag (linear + quadratic)
396    
397    checkpoint34
398     o Modified exchange routines for correct reverse simulation.
399     o Added verification output to comply with bug fix in impldiff.F
400       as of c33 (exp2, natl_box).
401     o Corrected store directives in dynamics.F
402     o Corrected array boundaries in impldiff.F
403     o Corrected array dimensions in gmredi.
404       Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
405     o Added routine GLOBAL_SUM_INT to global_sum.F
406     o Added mdsio_gl.F for ECCO purposes.
407    
408    checkpoint33
409     o Fixed bug in lower BC in impldiff.F
410     o Fixed confusion about units of forcing arrays in FFIELDS.h
411       namely Fu,Fv,Qnet,Qsw,EmPmR:
412       - Removed verification/natl_box/code/external_fields_scale.F
413         (did not differ from that in model/src)
414       - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
415         (see FFIELDS.h for description)
416       - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
417         kpp_calc.F and kpp_transport_t.F
418       - Removed model/src/external_fields_scale.F and calls to it
419       - verification/natl_box uses flux data with "atmospheric" sign so
420         a special version of external_fields_load.F is used to
421         change the data as it's read in. This way, the arrays
422         have the right units and signs at all times tha a user could
423         possibly use them.
424     o Corrected genmake to delete a temporary file during configuration
425    
426    checkpoint32
427     o Scaling of forcing fields moved from external_forcing.F to
428       external_fields_scale.F, called directly after loading fields.
429     o Surface relaxation terms added to surface tendency fields in
430       extra subroutine.
431     o impldiff.F changed to avoid storing by TAMC of huge intermediate
432       fields.
433     o Changes in GMRedi to comply with packaging structure.
434     o Modifications and bug fixes in KPP package.
435     o Verification experiment for KPP added (verification/nat_box/)
436    
437  checkpoint31  checkpoint31
438   o Packages interface brought in line with defined standard   o Packages interface brought in line with defined standard
439     -> new routines packages_...F     -> new routines packages_...F

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