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revision 1.28 by adcroft, Wed Jun 21 20:11:54 2000 UTC revision 1.53.2.22 by dimitri, Wed Feb 5 09:04:34 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_p11
7    o Modifications for using pkg/exf with pkg/seaice
8      - improved description of the various forcing configurations
9      - added basic radiation bulk formulae to pkg/exf
10      - units/sign fix for evap computation in exf_getffields.F
11      - updated verification/global_with_exf/results/output.txt
12    o Added pkg/sbo for computing IERS Special Bureau for the Oceans
13      (SBO) core products, including oceanic mass, center-of-mass,
14      angular, and bottom pressure (see pkg/sbo/README.sbo).
15    o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
16      to avoid negative values in shallow regions.
17      - updated verification/natl_box/results/output.txt
18      - updated verification/lab_sea/results/output.txt
19    o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
20    o Added useSingleCpuIO option (see PARAMS.h).
21    
22    release1_p10
23    o modifications for using pkg/exf with pkg/seaice
24      - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
25        and SEAICE_EXTERNAL_FLUXES
26      - pkg/exf CPP options EXF_READ_EVAP and
27        EXF_NO_BULK_COMPUTATIONS
28      - usage examples are Experiments 8 and 9 in
29        verification/lab_sea/README
30      - verification/lab_sea default experiment now uses
31        pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
32    
33    release1_p9
34    o pkg/seaice
35      - removed GOTO's and added taf directives
36      - double precision constants to reduce the g77 (Linux)
37        to F77 (SGI) differences reported in release1_p8
38    o tools/genmake
39      - added SGI options
40    o verification/testscript
41      - updated to that of checkpoint47a_post
42    o verification/global_ocean.90x40x15/input/eedata
43      - modified for SGI f77 compatibility
44    o verification/lab_sea
45      - added description of sea-ice model
46      - added missing matlab routines
47      - added test of thermodynamics parallelization
48    
49    release1_p8
50    o verification/natl_box:
51      updating new external_fields_load routine
52    o New package: pkg/seaice
53      Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
54      The sea-ice code is based on Hibler (1979-1980).
55      Two sea-ice dynamic solvers, ADI and LSR, are included.
56      In addition to computing prognostic sea-ice variables and diagnosing
57      the forcing/external data fields that drive the ocean model,
58      SEAICE_MODEL also sets theta to the freezing point under sea-ice.
59      The implied surface heat flux is then stored in variable
60      surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
61      kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
62      non-local transport term.  Because this call precedes model
63      thermodynamics, temperature under sea-ice may not be "exactly" at
64      the freezing point by the time theta is dumped or time-averaged.
65      N.B.: fairly large differences in accuracy occur across
66            different platforms/compilers; comparison between
67            g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
68            generated output gives:
69       T           S           U           V
70      C D M    c        m  s        m  s        m  s        m  s
71      n p a R  g  m  m  e  .  m  m  e  .  m  m  e  .  m  m  e  .
72      f n k u  2  i  a  a  d  i  a  a  d  i  a  a  d  i  a  a  d
73      g d e n  d  n  x  n  .  n  x  n  .  n  x  n  .  n  x  n  .
74    
75      Y Y Y Y  5  5  7  7  7  8 10  9  6  6  6  6  7  5  7  5  7 FAIL  lab_sea
76    
77    release1_p7
78    o GAD:
79      - generated new common blocks to account for call of
80        same gad routines with differing traceridentities
81        (needed to modify tracerIdentity indices in GAD.h)
82      - generated separate common blocks for case useCubedSphereExchange
83        (Department of Futurology)
84      - parameter lists to gmredi_?transport: added tracerIdentity
85      - added new key indices to tamc.h
86    o external_fields_load:
87      - added this routine to TAF list
88      - needed to make some common blocks global and additional storing
89        along the same lines as exf package (checkpoint_lev?_directives.h)
90    o exf:
91      updated external forcing package
92      - bug fixes carried over from ecco-branch
93        (missing OBCS_OPTIONS.h in two routines)
94      - enable easy to use "no forcing".
95      - added exf I/O for atmospheric loading
96      - added exf I/O for runoff data
97      - transfered scaling between exf <-> MITgcm to exf namelist
98    o Adding new verification experiment global_with_exf.
99      This verification experiment is almost identical to the
100      global_ocean.90x40x15 experiment, except that it uses
101      the exf (and cal) package instead of the
102      external_fields_load routine (cf README file).
103    
104    release1_p6
105    o fixed the verification/global_ocean.90x40x15 experiment:
106     - new bathymetry (the world according to A., JMC, and M.)
107     - new initial fields and forcing fields (*.bin files)
108     - new POLY3.COEFFS (for the next release one should switch to a full
109       equation of state)
110     - fixed several errors and redundancies in the data file
111     - experiment uses looped cells
112     - added matlab directory with diagnostic scripts for plotting of output
113    
114    release1_p5
115    o import recent fix from MAIN branch:
116      - use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
117      - change phiMin in exp1 (to agree with documentation)
118     from checkpoint45 to checkpoint45a_post:
119      - specific exchange for X-slice domain (case Ny=1)
120      - argument futureIter of S/R obcs_calc missing in
121        exp4 & internal_wave /code
122      - solve_for_pressure : set cg2d_x to zero where OBCS are applied
123     from checkpoint44f_post to checkpoint44g_post:
124      - fix surface correction term in multiDimAdvection
125        (affects plume_on_slope results
126    o bug fix in packages_readparms (missing ALLOW_CALENDAR)
127    o bug fix in CG2D.h (correct array size for LETS_MAKE_JAM
128    o Adjoint-related bug fixes in kpp:
129      - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
130      - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
131    o added Eliassen-Palm flux hooks (dynamics,ini_fields)
132    o removed unused TAF keys iikey, idkey (dynamics,thermodynamics)
133    o flow directives:
134      - new for S/R do_the_model_io
135      - enhanced for S/R checkpoint
136    o added Eliassen Palm flux controls to gradient check package
137    o new ctrl package
138      - adopted from ECCO environment to enable optimization
139      - added Eliassen Palm fluxes to controls
140      - adjusted global_ocean.90x40x15/ and carbon/ accordingly
141    
142    release1_p4
143    o Removed f90 comments ("!")
144    o Modified initialisations to enable exf package for MITgcm
145      (without invoking ECCO_PACKAGE).
146    o modifications to gradient check package (Martin Losch)
147      - enable centered differences
148      - modified format of standard output
149    
150    release1_p3
151    o added tangent linear setup to verification/carbon/
152    o added adjoint sensitivity setup to verification/global_ocean...
153    o moved packages_init_variables before convective_adjustment
154    o output of verif. which use GMRedi brought up-to-date with
155      MAIN trunk (those were re-created after changes in GMRedi)
156    o included CPP option SINGLE_LAYER_MODE
157      to configure barotropic setup (Martin Losch).
158    o Removed auxiliary variable in impldiff
159      (caused numerical differences with MAIN trunk routine).
160    o Introduced CPP option ALLOW_AUTODIFF_MONITOR to
161      disable adcommon.h/g_common.h by default.
162    o Cleaned exchange calls in cg2d.
163    
164    release1_p2
165    o fixed array boundary problem for adjoint
166      (related to partial recomputation within subroutine
167      related to dynamics -> calc_viscosity -> mom_...
168    o fixed recomputation in thermodynamics
169    o prepare (but not complete) recomputation problem in impldiff
170    o fixed problem for adjoint of global_max
171    o switched off sponge layer code in external_forcing
172    
173    release1_p1
174    o merged necessary patches:
175      - AD-related changes for GMRedi
176      - fixes i KPP (delZ -> drF)
177      - hook to OBCS songe layer code in external_forcing
178      - errorMessageUnit non-zero in eeboot.F
179      - modified test cost function and carbon verif.
180    
181    release1_chkpt44d_post = chkpt44d_post
182    
183    chkpt44d_pre,post
184    o added missing EXCLUDE_MONITOR flags
185    o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
186      (incompatible typ in MIN/MAX expressions caused problems
187      on IBM SP3)
188    o in genmake added variable MAKEDEPEND
189      plus resetting for case SunOS
190    o added timer_stats.c routine for IBM SP3
191    o removed variables in dynamics
192    
193    o real fresh water flux implemented with non-linear free-surface.
194    
195    chkpt44c_pre,post
196    o few fix (mask in shap_s2, EmPmR in external_field_load,
197      USE_NATURAL_BCS in solve_for_P);
198    o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
199    
200    checkpoint44b_pre/_post
201    o merge of relevant stuff from the ecco-branch:
202      - genmake: removed $S64 overwrite for case SunOS
203      - pkg/exf: update and corrections for field swapping and obcs
204      - pkg/ecco: parameter lists for the_model_main, the_main_loop
205                  harmonized between ECCO and MITgcm
206      - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
207                      updated checkpointing_lev... lists for obcs
208      - model/src: minor changes in forward_step, plot_field
209                   added directive for divided adjoint in the_main_loop
210      - pkg/mdsio: added mdsio_gl_slice
211    
212    o check parameters & config (chkpt44a_pre,post)
213    o OBC and NonLin_FrSurf.
214    
215    checkpoint44
216    o fix bug in mom_vi_del2uv
217    o select when filters are applied ; add options to zonal_filter (data.zonfilt)
218    o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
219    o update AIM experiments (NCEP input files)
220    o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
221    o added some stuff for AD
222    
223    checkpoint43
224    o added two new advection tests
225    o added global 4x4 degree ocean test
226    o added test of H&S94 with free surface on cube
227    o some final mods for gradient check, adjoint,...
228    
229    checkpoint42
230      Fixed AD-related problems:
231    o Store directives up-to-date with re-arranged Adams-Bashforth
232      (mainly thermodynamics.F)
233    o New store directives for multi-dim. advection schemes
234      * new CPP flag ALLOW_MULTI_DIM_ADVECTION
235      * new common block and key passkey
236      (mainly gad_advection.F)
237    o Modified store directives for split of dynamics/thermodynamics
238      for the case ALLOW_KPP
239    o Cleaned argument list for timestep_tracer.F
240    
241    checkpoint41
242    o re-formatted/added comments in prologues of key subroutines
243      to work with protex
244    
245    checkpoint40
246    o moved calc_gs, calc_gt and calc_tr1 back to model/src
247    o added FLT (floats) package from Arne along with demo. experiment
248    o re-arranged Adams-Bashforth scheme for tracers to allow easier
249      implementation of forward-in-time forcing terms
250    o more mods for non-linear free-surface including new variable
251    o modified multi-dim method to work on cube
252    o bug fix in KPP (from DM)
253    
254    checkpoint40pre9
255    o added DST advection schemes
256    o fix MPI bug on SGI's
257    o modifications for non-linear free-surface
258    o fixed conditionals for fixed flow/passive tracer only mode
259    o added tension/strain form of stress tensor
260    o changes to commenting of arguments for TAF/TAMC
261    o added/updated many matlab scripts
262    o added multi-dimensional advection method for tracers
263      
264    checkpoint40pre8
265    o new package rw/
266      Added method for dumping intermediate local arrays:
267      mdsio_writetile - same as mdsio_writefield except works from inside
268                        bi,bj loop
269      mdsio_writelocal - same as mdsio_writetile except works for local
270                         arrays
271      write_local_r? - higher-level wrapper for mdsio_writelocal
272      Controlled by diagFreq. Defaults to zero (ie. no dumps)
273      Example given at end of mom_vecinv.F that dumps some local arrays.
274    o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
275      control flux-form versus vector invariant code.
276      Switch is runtime flag vectorInvariantMomentum (defaults to false)
277      or genmake -DISABLE ...
278    o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
279      (additional storing is now needed for case vecinv;
280      currently nothing implemented to switch this storing off
281      in case fluxform is used since no CPP flag available).
282    
283    checkpoint40pre7
284    o bug fix in dynamics.F
285      calc_viscosity called before k=1,Nr loop.
286    o added some #ifdef's ALLOW_PASSIVE_TRACER
287    o cleaned initialisations in ctrl_map_ini
288      related to TAF
289    
290    checkpoint40pre6
291    o split dynamics into thermodynamics & dynamics
292    o corresponding split of calc_diffusivity into
293      calc_diffusivity, calc_viscosity
294      (kpp_calc_diff, kpp_calc_visc).
295    o Added diffkr, kapgm to control variables
296    o bug fix in gmredi_slope_limit for ldd97
297    
298    checkpoint40pre5
299    o proper initialization of Adams-Bashforth time stepping
300      + uses forward step for very first step of model (iter=0)
301    o re-generated *all* output since almost all output is modified by this
302      change (sorry but we've been putting this one off for about 2 years)
303      + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
304        *not* regenerated since they are already out of date and I don't
305        want to create the impression that they are suddenly working.
306    o removed KAP stuff for DEC's
307    o modified/added many .cvsignore files in */code and */input
308    o added new expt "solid-body.cs-32x32x1"
309      + this uses an alternative form of ini_curvilinear_grid.F which
310        is not necessarily any better than the current one...
311    
312    checkpoint40pre4
313    o added re-initialisations of utrans,vtrans,rtrans in
314      calc_common_factors which are crucial for TAF.
315    o extended iMin,jMin range for calc_common_factors,
316      calc_diffusivity
317    o added option ALLOW_PASSIVE_TRACER
318    o a few minor updates and fixes
319    
320    checkpoint40pre3
321    o created calc_gtr1.F for gad package
322    o split the_main_loop and re-introduced forward_step
323    o some recomputations of nIter0 for TAMC
324    
325    checkpoint40pre2
326    o Updated to latest branch of AJA, JMC
327    o Added gradient check package
328    o Added routines for passive tracer handling
329    o Added carbon sequestration sensitivity experiment
330    
331    checkpoint39
332     o Modifications and fixes to support TAMC
333       (mainly missing or wrong directives)
334     o Corrected common blocks when fooling TAMC to produce adjoint I/O
335       in addummy_in_stepping
336     o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
337     o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
338     o Included following packages:
339       cal: calendar
340       exf: external forcing
341       ecco: essential routines to control use of cal, exf
342             (NB: this is not the full ECCO environment)
343     o disabled some packages by default in genmake
344    
345    checkpoint38
346     o see notes_c37_adj.txt
347     o corrected wrong layer index in external_forcing_t
348     o replaced the_main_loop/forward_step by the_main_loop
349     o removed forceoutput from write_state
350       (replaced criteria for initial/final state)
351     o added runtime flag for pre-C35 pickups: usePickupBeforeC35
352    
353    checkpoint37
354     o mdsio.F routine split and packaged in pkg/mdsio
355       (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
356        used unless genmake -disable=mdsio)
357     o allow a more precise surface-geopotential gradient for the atmosphere
358       taking into account the change in space of Alpha (=1/rho) at the surface.
359     o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
360       (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
361     o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
362       Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
363       [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
364     o Time-Average diagnostics defined as a pseudo package "timeave".
365     o pickup files : old pickup (before c35) did not work with new code (c35
366       and after) unless activating 2 commented lines in initialise-varia.
367     o Non-Hydrostatic pickup file Pb fixed.
368     o bug with Rigid-lid version (since c35) fixed.  
369    
370    checkpoint36
371     o implement Crank-Nickelson barotropic time-stepping
372     o recover Time-Average diagnostics
373     o fix Pb in checkpoint (PR#19)
374     o AIM become a standard package ; clean unused CPP_kees
375    
376    checkpoint35
377     o subtantial rewrite of dynamics.f
378     o allows staggered time-stepping
379     o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
380     o added bottom drag (linear + quadratic)
381    
382    checkpoint34
383     o Modified exchange routines for correct reverse simulation.
384     o Added verification output to comply with bug fix in impldiff.F
385       as of c33 (exp2, natl_box).
386     o Corrected store directives in dynamics.F
387     o Corrected array boundaries in impldiff.F
388     o Corrected array dimensions in gmredi.
389       Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
390     o Added routine GLOBAL_SUM_INT to global_sum.F
391     o Added mdsio_gl.F for ECCO purposes.
392    
393    checkpoint33
394     o Fixed bug in lower BC in impldiff.F
395     o Fixed confusion about units of forcing arrays in FFIELDS.h
396       namely Fu,Fv,Qnet,Qsw,EmPmR:
397       - Removed verification/natl_box/code/external_fields_scale.F
398         (did not differ from that in model/src)
399       - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
400         (see FFIELDS.h for description)
401       - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
402         kpp_calc.F and kpp_transport_t.F
403       - Removed model/src/external_fields_scale.F and calls to it
404       - verification/natl_box uses flux data with "atmospheric" sign so
405         a special version of external_fields_load.F is used to
406         change the data as it's read in. This way, the arrays
407         have the right units and signs at all times tha a user could
408         possibly use them.
409     o Corrected genmake to delete a temporary file during configuration
410    
411    checkpoint32
412     o Scaling of forcing fields moved from external_forcing.F to
413       external_fields_scale.F, called directly after loading fields.
414     o Surface relaxation terms added to surface tendency fields in
415       extra subroutine.
416     o impldiff.F changed to avoid storing by TAMC of huge intermediate
417       fields.
418     o Changes in GMRedi to comply with packaging structure.
419     o Modifications and bug fixes in KPP package.
420     o Verification experiment for KPP added (verification/nat_box/)
421    
422    checkpoint31
423     o Packages interface brought in line with defined standard
424       -> new routines packages_...F
425       -> changes in initialise_fixed.F, initialise_varia.F
426       -> enables initialisation interface for ECCO package
427     o Rescaling of external forcing fields immediately after read
428       (removed from external_forcing.F)
429       -> new: surface_fields_scale.F
430       -> affects ini_foorcing.F, external_fields_load.F
431     o Computation of surface tendencies before tendency updates.
432       -> new: external_forcing_surf.F
433     o Change of variable names useGMRedi, useKPP, useECCO
434     o Further changes in dynamics.F, impldiff.F for TAMC
435     o Tested for experiments 0, 2, 4.
436       - not yet tested for GMRedi.
437       - not yet tested for KPP.
438    
439    checkpoint30
440     o Updates for OBCs
441     o New experiment for test OBCs (internal_wave)
442     o New output.txt in verification/exp4/results/
443     o Updates for KPP: calculation of viscosity corrected, new variables
444       kpp_dumpFreq and kpp_taveFreq
445     o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
446       and entry for T90 in genmake
447    
448  checkpoint29  checkpoint29
449   o packaged KPP and GM/Redi   o packaged KPP and GM/Redi
450    

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