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revision 1.28 by adcroft, Wed Jun 21 20:11:54 2000 UTC revision 1.53.2.23 by dimitri, Fri Feb 7 03:59:42 2003 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    untagged modifications
7    o Updated useSingleCpuIO option in mdsio_writefield.F to
8      work with multi-field files, e.g., for single-file pickup.
9    
10    release1_p11
11    o Modifications for using pkg/exf with pkg/seaice
12      - improved description of the various forcing configurations
13      - added basic radiation bulk formulae to pkg/exf
14      - units/sign fix for evap computation in exf_getffields.F
15      - updated verification/global_with_exf/results/output.txt
16    o Added pkg/sbo for computing IERS Special Bureau for the Oceans
17      (SBO) core products, including oceanic mass, center-of-mass,
18      angular, and bottom pressure (see pkg/sbo/README.sbo).
19    o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
20      to avoid negative values in shallow regions.
21      - updated verification/natl_box/results/output.txt
22      - updated verification/lab_sea/results/output.txt
23    o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
24    o Added useSingleCpuIO option (see PARAMS.h).
25    
26    release1_p10
27    o modifications for using pkg/exf with pkg/seaice
28      - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
29        and SEAICE_EXTERNAL_FLUXES
30      - pkg/exf CPP options EXF_READ_EVAP and
31        EXF_NO_BULK_COMPUTATIONS
32      - usage examples are Experiments 8 and 9 in
33        verification/lab_sea/README
34      - verification/lab_sea default experiment now uses
35        pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
36    
37    release1_p9
38    o pkg/seaice
39      - removed GOTO's and added taf directives
40      - double precision constants to reduce the g77 (Linux)
41        to F77 (SGI) differences reported in release1_p8
42    o tools/genmake
43      - added SGI options
44    o verification/testscript
45      - updated to that of checkpoint47a_post
46    o verification/global_ocean.90x40x15/input/eedata
47      - modified for SGI f77 compatibility
48    o verification/lab_sea
49      - added description of sea-ice model
50      - added missing matlab routines
51      - added test of thermodynamics parallelization
52    
53    release1_p8
54    o verification/natl_box:
55      updating new external_fields_load routine
56    o New package: pkg/seaice
57      Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
58      The sea-ice code is based on Hibler (1979-1980).
59      Two sea-ice dynamic solvers, ADI and LSR, are included.
60      In addition to computing prognostic sea-ice variables and diagnosing
61      the forcing/external data fields that drive the ocean model,
62      SEAICE_MODEL also sets theta to the freezing point under sea-ice.
63      The implied surface heat flux is then stored in variable
64      surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
65      kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
66      non-local transport term.  Because this call precedes model
67      thermodynamics, temperature under sea-ice may not be "exactly" at
68      the freezing point by the time theta is dumped or time-averaged.
69      N.B.: fairly large differences in accuracy occur across
70            different platforms/compilers; comparison between
71            g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
72            generated output gives:
73       T           S           U           V
74      C D M    c        m  s        m  s        m  s        m  s
75      n p a R  g  m  m  e  .  m  m  e  .  m  m  e  .  m  m  e  .
76      f n k u  2  i  a  a  d  i  a  a  d  i  a  a  d  i  a  a  d
77      g d e n  d  n  x  n  .  n  x  n  .  n  x  n  .  n  x  n  .
78    
79      Y Y Y Y  5  5  7  7  7  8 10  9  6  6  6  6  7  5  7  5  7 FAIL  lab_sea
80    
81    release1_p7
82    o GAD:
83      - generated new common blocks to account for call of
84        same gad routines with differing traceridentities
85        (needed to modify tracerIdentity indices in GAD.h)
86      - generated separate common blocks for case useCubedSphereExchange
87        (Department of Futurology)
88      - parameter lists to gmredi_?transport: added tracerIdentity
89      - added new key indices to tamc.h
90    o external_fields_load:
91      - added this routine to TAF list
92      - needed to make some common blocks global and additional storing
93        along the same lines as exf package (checkpoint_lev?_directives.h)
94    o exf:
95      updated external forcing package
96      - bug fixes carried over from ecco-branch
97        (missing OBCS_OPTIONS.h in two routines)
98      - enable easy to use "no forcing".
99      - added exf I/O for atmospheric loading
100      - added exf I/O for runoff data
101      - transfered scaling between exf <-> MITgcm to exf namelist
102    o Adding new verification experiment global_with_exf.
103      This verification experiment is almost identical to the
104      global_ocean.90x40x15 experiment, except that it uses
105      the exf (and cal) package instead of the
106      external_fields_load routine (cf README file).
107    
108    release1_p6
109    o fixed the verification/global_ocean.90x40x15 experiment:
110     - new bathymetry (the world according to A., JMC, and M.)
111     - new initial fields and forcing fields (*.bin files)
112     - new POLY3.COEFFS (for the next release one should switch to a full
113       equation of state)
114     - fixed several errors and redundancies in the data file
115     - experiment uses looped cells
116     - added matlab directory with diagnostic scripts for plotting of output
117    
118    release1_p5
119    o import recent fix from MAIN branch:
120      - use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
121      - change phiMin in exp1 (to agree with documentation)
122     from checkpoint45 to checkpoint45a_post:
123      - specific exchange for X-slice domain (case Ny=1)
124      - argument futureIter of S/R obcs_calc missing in
125        exp4 & internal_wave /code
126      - solve_for_pressure : set cg2d_x to zero where OBCS are applied
127     from checkpoint44f_post to checkpoint44g_post:
128      - fix surface correction term in multiDimAdvection
129        (affects plume_on_slope results
130    o bug fix in packages_readparms (missing ALLOW_CALENDAR)
131    o bug fix in CG2D.h (correct array size for LETS_MAKE_JAM
132    o Adjoint-related bug fixes in kpp:
133      - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
134      - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
135    o added Eliassen-Palm flux hooks (dynamics,ini_fields)
136    o removed unused TAF keys iikey, idkey (dynamics,thermodynamics)
137    o flow directives:
138      - new for S/R do_the_model_io
139      - enhanced for S/R checkpoint
140    o added Eliassen Palm flux controls to gradient check package
141    o new ctrl package
142      - adopted from ECCO environment to enable optimization
143      - added Eliassen Palm fluxes to controls
144      - adjusted global_ocean.90x40x15/ and carbon/ accordingly
145    
146    release1_p4
147    o Removed f90 comments ("!")
148    o Modified initialisations to enable exf package for MITgcm
149      (without invoking ECCO_PACKAGE).
150    o modifications to gradient check package (Martin Losch)
151      - enable centered differences
152      - modified format of standard output
153    
154    release1_p3
155    o added tangent linear setup to verification/carbon/
156    o added adjoint sensitivity setup to verification/global_ocean...
157    o moved packages_init_variables before convective_adjustment
158    o output of verif. which use GMRedi brought up-to-date with
159      MAIN trunk (those were re-created after changes in GMRedi)
160    o included CPP option SINGLE_LAYER_MODE
161      to configure barotropic setup (Martin Losch).
162    o Removed auxiliary variable in impldiff
163      (caused numerical differences with MAIN trunk routine).
164    o Introduced CPP option ALLOW_AUTODIFF_MONITOR to
165      disable adcommon.h/g_common.h by default.
166    o Cleaned exchange calls in cg2d.
167    
168    release1_p2
169    o fixed array boundary problem for adjoint
170      (related to partial recomputation within subroutine
171      related to dynamics -> calc_viscosity -> mom_...
172    o fixed recomputation in thermodynamics
173    o prepare (but not complete) recomputation problem in impldiff
174    o fixed problem for adjoint of global_max
175    o switched off sponge layer code in external_forcing
176    
177    release1_p1
178    o merged necessary patches:
179      - AD-related changes for GMRedi
180      - fixes i KPP (delZ -> drF)
181      - hook to OBCS songe layer code in external_forcing
182      - errorMessageUnit non-zero in eeboot.F
183      - modified test cost function and carbon verif.
184    
185    release1_chkpt44d_post = chkpt44d_post
186    
187    chkpt44d_pre,post
188    o added missing EXCLUDE_MONITOR flags
189    o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
190      (incompatible typ in MIN/MAX expressions caused problems
191      on IBM SP3)
192    o in genmake added variable MAKEDEPEND
193      plus resetting for case SunOS
194    o added timer_stats.c routine for IBM SP3
195    o removed variables in dynamics
196    
197    o real fresh water flux implemented with non-linear free-surface.
198    
199    chkpt44c_pre,post
200    o few fix (mask in shap_s2, EmPmR in external_field_load,
201      USE_NATURAL_BCS in solve_for_P);
202    o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
203    
204    checkpoint44b_pre/_post
205    o merge of relevant stuff from the ecco-branch:
206      - genmake: removed $S64 overwrite for case SunOS
207      - pkg/exf: update and corrections for field swapping and obcs
208      - pkg/ecco: parameter lists for the_model_main, the_main_loop
209                  harmonized between ECCO and MITgcm
210      - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
211                      updated checkpointing_lev... lists for obcs
212      - model/src: minor changes in forward_step, plot_field
213                   added directive for divided adjoint in the_main_loop
214      - pkg/mdsio: added mdsio_gl_slice
215    
216    o check parameters & config (chkpt44a_pre,post)
217    o OBC and NonLin_FrSurf.
218    
219    checkpoint44
220    o fix bug in mom_vi_del2uv
221    o select when filters are applied ; add options to zonal_filter (data.zonfilt)
222    o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
223    o update AIM experiments (NCEP input files)
224    o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
225    o added some stuff for AD
226    
227    checkpoint43
228    o added two new advection tests
229    o added global 4x4 degree ocean test
230    o added test of H&S94 with free surface on cube
231    o some final mods for gradient check, adjoint,...
232    
233    checkpoint42
234      Fixed AD-related problems:
235    o Store directives up-to-date with re-arranged Adams-Bashforth
236      (mainly thermodynamics.F)
237    o New store directives for multi-dim. advection schemes
238      * new CPP flag ALLOW_MULTI_DIM_ADVECTION
239      * new common block and key passkey
240      (mainly gad_advection.F)
241    o Modified store directives for split of dynamics/thermodynamics
242      for the case ALLOW_KPP
243    o Cleaned argument list for timestep_tracer.F
244    
245    checkpoint41
246    o re-formatted/added comments in prologues of key subroutines
247      to work with protex
248    
249    checkpoint40
250    o moved calc_gs, calc_gt and calc_tr1 back to model/src
251    o added FLT (floats) package from Arne along with demo. experiment
252    o re-arranged Adams-Bashforth scheme for tracers to allow easier
253      implementation of forward-in-time forcing terms
254    o more mods for non-linear free-surface including new variable
255    o modified multi-dim method to work on cube
256    o bug fix in KPP (from DM)
257    
258    checkpoint40pre9
259    o added DST advection schemes
260    o fix MPI bug on SGI's
261    o modifications for non-linear free-surface
262    o fixed conditionals for fixed flow/passive tracer only mode
263    o added tension/strain form of stress tensor
264    o changes to commenting of arguments for TAF/TAMC
265    o added/updated many matlab scripts
266    o added multi-dimensional advection method for tracers
267      
268    checkpoint40pre8
269    o new package rw/
270      Added method for dumping intermediate local arrays:
271      mdsio_writetile - same as mdsio_writefield except works from inside
272                        bi,bj loop
273      mdsio_writelocal - same as mdsio_writetile except works for local
274                         arrays
275      write_local_r? - higher-level wrapper for mdsio_writelocal
276      Controlled by diagFreq. Defaults to zero (ie. no dumps)
277      Example given at end of mom_vecinv.F that dumps some local arrays.
278    o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
279      control flux-form versus vector invariant code.
280      Switch is runtime flag vectorInvariantMomentum (defaults to false)
281      or genmake -DISABLE ...
282    o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
283      (additional storing is now needed for case vecinv;
284      currently nothing implemented to switch this storing off
285      in case fluxform is used since no CPP flag available).
286    
287    checkpoint40pre7
288    o bug fix in dynamics.F
289      calc_viscosity called before k=1,Nr loop.
290    o added some #ifdef's ALLOW_PASSIVE_TRACER
291    o cleaned initialisations in ctrl_map_ini
292      related to TAF
293    
294    checkpoint40pre6
295    o split dynamics into thermodynamics & dynamics
296    o corresponding split of calc_diffusivity into
297      calc_diffusivity, calc_viscosity
298      (kpp_calc_diff, kpp_calc_visc).
299    o Added diffkr, kapgm to control variables
300    o bug fix in gmredi_slope_limit for ldd97
301    
302    checkpoint40pre5
303    o proper initialization of Adams-Bashforth time stepping
304      + uses forward step for very first step of model (iter=0)
305    o re-generated *all* output since almost all output is modified by this
306      change (sorry but we've been putting this one off for about 2 years)
307      + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
308        *not* regenerated since they are already out of date and I don't
309        want to create the impression that they are suddenly working.
310    o removed KAP stuff for DEC's
311    o modified/added many .cvsignore files in */code and */input
312    o added new expt "solid-body.cs-32x32x1"
313      + this uses an alternative form of ini_curvilinear_grid.F which
314        is not necessarily any better than the current one...
315    
316    checkpoint40pre4
317    o added re-initialisations of utrans,vtrans,rtrans in
318      calc_common_factors which are crucial for TAF.
319    o extended iMin,jMin range for calc_common_factors,
320      calc_diffusivity
321    o added option ALLOW_PASSIVE_TRACER
322    o a few minor updates and fixes
323    
324    checkpoint40pre3
325    o created calc_gtr1.F for gad package
326    o split the_main_loop and re-introduced forward_step
327    o some recomputations of nIter0 for TAMC
328    
329    checkpoint40pre2
330    o Updated to latest branch of AJA, JMC
331    o Added gradient check package
332    o Added routines for passive tracer handling
333    o Added carbon sequestration sensitivity experiment
334    
335    checkpoint39
336     o Modifications and fixes to support TAMC
337       (mainly missing or wrong directives)
338     o Corrected common blocks when fooling TAMC to produce adjoint I/O
339       in addummy_in_stepping
340     o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
341     o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
342     o Included following packages:
343       cal: calendar
344       exf: external forcing
345       ecco: essential routines to control use of cal, exf
346             (NB: this is not the full ECCO environment)
347     o disabled some packages by default in genmake
348    
349    checkpoint38
350     o see notes_c37_adj.txt
351     o corrected wrong layer index in external_forcing_t
352     o replaced the_main_loop/forward_step by the_main_loop
353     o removed forceoutput from write_state
354       (replaced criteria for initial/final state)
355     o added runtime flag for pre-C35 pickups: usePickupBeforeC35
356    
357    checkpoint37
358     o mdsio.F routine split and packaged in pkg/mdsio
359       (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
360        used unless genmake -disable=mdsio)
361     o allow a more precise surface-geopotential gradient for the atmosphere
362       taking into account the change in space of Alpha (=1/rho) at the surface.
363     o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
364       (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
365     o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
366       Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
367       [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
368     o Time-Average diagnostics defined as a pseudo package "timeave".
369     o pickup files : old pickup (before c35) did not work with new code (c35
370       and after) unless activating 2 commented lines in initialise-varia.
371     o Non-Hydrostatic pickup file Pb fixed.
372     o bug with Rigid-lid version (since c35) fixed.  
373    
374    checkpoint36
375     o implement Crank-Nickelson barotropic time-stepping
376     o recover Time-Average diagnostics
377     o fix Pb in checkpoint (PR#19)
378     o AIM become a standard package ; clean unused CPP_kees
379    
380    checkpoint35
381     o subtantial rewrite of dynamics.f
382     o allows staggered time-stepping
383     o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
384     o added bottom drag (linear + quadratic)
385    
386    checkpoint34
387     o Modified exchange routines for correct reverse simulation.
388     o Added verification output to comply with bug fix in impldiff.F
389       as of c33 (exp2, natl_box).
390     o Corrected store directives in dynamics.F
391     o Corrected array boundaries in impldiff.F
392     o Corrected array dimensions in gmredi.
393       Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
394     o Added routine GLOBAL_SUM_INT to global_sum.F
395     o Added mdsio_gl.F for ECCO purposes.
396    
397    checkpoint33
398     o Fixed bug in lower BC in impldiff.F
399     o Fixed confusion about units of forcing arrays in FFIELDS.h
400       namely Fu,Fv,Qnet,Qsw,EmPmR:
401       - Removed verification/natl_box/code/external_fields_scale.F
402         (did not differ from that in model/src)
403       - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
404         (see FFIELDS.h for description)
405       - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
406         kpp_calc.F and kpp_transport_t.F
407       - Removed model/src/external_fields_scale.F and calls to it
408       - verification/natl_box uses flux data with "atmospheric" sign so
409         a special version of external_fields_load.F is used to
410         change the data as it's read in. This way, the arrays
411         have the right units and signs at all times tha a user could
412         possibly use them.
413     o Corrected genmake to delete a temporary file during configuration
414    
415    checkpoint32
416     o Scaling of forcing fields moved from external_forcing.F to
417       external_fields_scale.F, called directly after loading fields.
418     o Surface relaxation terms added to surface tendency fields in
419       extra subroutine.
420     o impldiff.F changed to avoid storing by TAMC of huge intermediate
421       fields.
422     o Changes in GMRedi to comply with packaging structure.
423     o Modifications and bug fixes in KPP package.
424     o Verification experiment for KPP added (verification/nat_box/)
425    
426    checkpoint31
427     o Packages interface brought in line with defined standard
428       -> new routines packages_...F
429       -> changes in initialise_fixed.F, initialise_varia.F
430       -> enables initialisation interface for ECCO package
431     o Rescaling of external forcing fields immediately after read
432       (removed from external_forcing.F)
433       -> new: surface_fields_scale.F
434       -> affects ini_foorcing.F, external_fields_load.F
435     o Computation of surface tendencies before tendency updates.
436       -> new: external_forcing_surf.F
437     o Change of variable names useGMRedi, useKPP, useECCO
438     o Further changes in dynamics.F, impldiff.F for TAMC
439     o Tested for experiments 0, 2, 4.
440       - not yet tested for GMRedi.
441       - not yet tested for KPP.
442    
443    checkpoint30
444     o Updates for OBCs
445     o New experiment for test OBCs (internal_wave)
446     o New output.txt in verification/exp4/results/
447     o Updates for KPP: calculation of viscosity corrected, new variables
448       kpp_dumpFreq and kpp_taveFreq
449     o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
450       and entry for T90 in genmake
451    
452  checkpoint29  checkpoint29
453   o packaged KPP and GM/Redi   o packaged KPP and GM/Redi
454    

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