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revision 1.26 by adcroft, Mon Apr 10 14:41:52 2000 UTC revision 1.53.2.14 by heimbach, Mon Nov 11 22:04:56 2002 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    release1_p8
7    o verification/natl_box:
8      updating new external_fields_load routine
9    o New package: pkg/seaice
10      Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
11      The sea-ice code is based on Hibler (1979-1980).
12      Two sea-ice dynamic solvers, ADI and LSR, are included.
13      In addition to computing prognostic sea-ice variables and diagnosing
14      the forcing/external data fields that drive the ocean model,
15      SEAICE_MODEL also sets theta to the freezing point under sea-ice.
16      The implied surface heat flux is then stored in variable
17      surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
18      kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
19      non-local transport term.  Because this call precedes model
20      thermodynamics, temperature under sea-ice may not be "exactly" at
21      the freezing point by the time theta is dumped or time-averaged.
22      N.B.: fairly large differences in accuracy occur across
23            different platforms; comparison between
24            g77 (Linux) and ??? generated output gives:
25       T           S           U           V
26      C D M    c        m  s        m  s        m  s        m  s
27      n p a R  g  m  m  e  .  m  m  e  .  m  m  e  .  m  m  e  .
28      f n k u  2  i  a  a  d  i  a  a  d  i  a  a  d  i  a  a  d
29      g d e n  d  n  x  n  .  n  x  n  .  n  x  n  .  n  x  n  .
30    
31      Y Y Y Y  5  5  7  7  7  8 10  9  6  6  6  6  7  5  7  5  7 FAIL  lab_sea
32    
33    
34    release1_p7
35    o GAD:
36      - generated new common blocks to account for call of
37        same gad routines with differing traceridentities
38        (needed to modify tracerIdentity indices in GAD.h)
39      - generated separate common blocks for case useCubedSphereExchange
40        (Department of Futurology)
41      - parameter lists to gmredi_?transport: added tracerIdentity
42      - added new key indices to tamc.h
43    o external_fields_load:
44      - added this routine to TAF list
45      - needed to make some common blocks global and additional storing
46        along the same lines as exf package (checkpoint_lev?_directives.h)
47    o exf:
48      updated external forcing package
49      - bug fixes carried over from ecco-branch
50        (missing OBCS_OPTIONS.h in two routines)
51      - enable easy to use "no forcing".
52      - added exf I/O for atmospheric loading
53      - added exf I/O for runoff data
54      - transfered scaling between exf <-> MITgcm to exf namelist
55    o Adding new verification experiment global_with_exf.
56      This verification experiment is almost identical to the
57      global_ocean.90x40x15 experiment, except that it uses
58      the exf (and cal) package instead of the
59      external_fields_load routine (cf README file).
60    
61    release1_p6
62    o fixed the verification/global_ocean.90x40x15 experiment:
63     - new bathymetry (the world according to A., JMC, and M.)
64     - new initial fields and forcing fields (*.bin files)
65     - new POLY3.COEFFS (for the next release one should switch to a full
66       equation of state)
67     - fixed several errors and redundancies in the data file
68     - experiment uses looped cells
69     - added matlab directory with diagnostic scripts for plotting of output
70    
71    release1_p5
72    o import recent fix from MAIN branch:
73      - use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
74      - change phiMin in exp1 (to agree with documentation)
75     from checkpoint45 to checkpoint45a_post:
76      - specific exchange for X-slice domain (case Ny=1)
77      - argument futureIter of S/R obcs_calc missing in
78        exp4 & internal_wave /code
79      - solve_for_pressure : set cg2d_x to zero where OBCS are applied
80     from checkpoint44f_post to checkpoint44g_post:
81      - fix surface correction term in multiDimAdvection
82        (affects plume_on_slope results
83    o bug fix in packages_readparms (missing ALLOW_CALENDAR)
84    o bug fix in CG2D.h (correct array size for LETS_MAKE_JAM
85    o Adjoint-related bug fixes in kpp:
86      - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
87      - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
88    o added Eliassen-Palm flux hooks (dynamics,ini_fields)
89    o removed unused TAF keys iikey, idkey (dynamics,thermodynamics)
90    o flow directives:
91      - new for S/R do_the_model_io
92      - enhanced for S/R checkpoint
93    o added Eliassen Palm flux controls to gradient check package
94    o new ctrl package
95      - adopted from ECCO environment to enable optimization
96      - added Eliassen Palm fluxes to controls
97      - adjusted global_ocean.90x40x15/ and carbon/ accordingly
98    
99    release1_p4
100    o Removed f90 comments ("!")
101    o Modified initialisations to enable exf package for MITgcm
102      (without invoking ECCO_PACKAGE).
103    o modifications to gradient check package (Martin Losch)
104      - enable centered differences
105      - modified format of standard output
106    
107    release1_p3
108    o added tangent linear setup to verification/carbon/
109    o added adjoint sensitivity setup to verification/global_ocean...
110    o moved packages_init_variables before convective_adjustment
111    o output of verif. which use GMRedi brought up-to-date with
112      MAIN trunk (those were re-created after changes in GMRedi)
113    o included CPP option SINGLE_LAYER_MODE
114      to configure barotropic setup (Martin Losch).
115    o Removed auxiliary variable in impldiff
116      (caused numerical differences with MAIN trunk routine).
117    o Introduced CPP option ALLOW_AUTODIFF_MONITOR to
118      disable adcommon.h/g_common.h by default.
119    o Cleaned exchange calls in cg2d.
120    
121    release1_p2
122    o fixed array boundary problem for adjoint
123      (related to partial recomputation within subroutine
124      related to dynamics -> calc_viscosity -> mom_...
125    o fixed recomputation in thermodynamics
126    o prepare (but not complete) recomputation problem in impldiff
127    o fixed problem for adjoint of global_max
128    o switched off sponge layer code in external_forcing
129    
130    release1_p1
131    o merged necessary patches:
132      - AD-related changes for GMRedi
133      - fixes i KPP (delZ -> drF)
134      - hook to OBCS songe layer code in external_forcing
135      - errorMessageUnit non-zero in eeboot.F
136      - modified test cost function and carbon verif.
137    
138    release1_chkpt44d_post = chkpt44d_post
139    
140    chkpt44d_pre,post
141    o added missing EXCLUDE_MONITOR flags
142    o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
143      (incompatible typ in MIN/MAX expressions caused problems
144      on IBM SP3)
145    o in genmake added variable MAKEDEPEND
146      plus resetting for case SunOS
147    o added timer_stats.c routine for IBM SP3
148    o removed variables in dynamics
149    
150    o real fresh water flux implemented with non-linear free-surface.
151    
152    chkpt44c_pre,post
153    o few fix (mask in shap_s2, EmPmR in external_field_load,
154      USE_NATURAL_BCS in solve_for_P);
155    o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
156    
157    checkpoint44b_pre/_post
158    o merge of relevant stuff from the ecco-branch:
159      - genmake: removed $S64 overwrite for case SunOS
160      - pkg/exf: update and corrections for field swapping and obcs
161      - pkg/ecco: parameter lists for the_model_main, the_main_loop
162                  harmonized between ECCO and MITgcm
163      - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
164                      updated checkpointing_lev... lists for obcs
165      - model/src: minor changes in forward_step, plot_field
166                   added directive for divided adjoint in the_main_loop
167      - pkg/mdsio: added mdsio_gl_slice
168    
169    o check parameters & config (chkpt44a_pre,post)
170    o OBC and NonLin_FrSurf.
171    
172    checkpoint44
173    o fix bug in mom_vi_del2uv
174    o select when filters are applied ; add options to zonal_filter (data.zonfilt)
175    o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
176    o update AIM experiments (NCEP input files)
177    o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
178    o added some stuff for AD
179    
180    checkpoint43
181    o added two new advection tests
182    o added global 4x4 degree ocean test
183    o added test of H&S94 with free surface on cube
184    o some final mods for gradient check, adjoint,...
185    
186    checkpoint42
187      Fixed AD-related problems:
188    o Store directives up-to-date with re-arranged Adams-Bashforth
189      (mainly thermodynamics.F)
190    o New store directives for multi-dim. advection schemes
191      * new CPP flag ALLOW_MULTI_DIM_ADVECTION
192      * new common block and key passkey
193      (mainly gad_advection.F)
194    o Modified store directives for split of dynamics/thermodynamics
195      for the case ALLOW_KPP
196    o Cleaned argument list for timestep_tracer.F
197    
198    checkpoint41
199    o re-formatted/added comments in prologues of key subroutines
200      to work with protex
201    
202    checkpoint40
203    o moved calc_gs, calc_gt and calc_tr1 back to model/src
204    o added FLT (floats) package from Arne along with demo. experiment
205    o re-arranged Adams-Bashforth scheme for tracers to allow easier
206      implementation of forward-in-time forcing terms
207    o more mods for non-linear free-surface including new variable
208    o modified multi-dim method to work on cube
209    o bug fix in KPP (from DM)
210    
211    checkpoint40pre9
212    o added DST advection schemes
213    o fix MPI bug on SGI's
214    o modifications for non-linear free-surface
215    o fixed conditionals for fixed flow/passive tracer only mode
216    o added tension/strain form of stress tensor
217    o changes to commenting of arguments for TAF/TAMC
218    o added/updated many matlab scripts
219    o added multi-dimensional advection method for tracers
220      
221    checkpoint40pre8
222    o new package rw/
223      Added method for dumping intermediate local arrays:
224      mdsio_writetile - same as mdsio_writefield except works from inside
225                        bi,bj loop
226      mdsio_writelocal - same as mdsio_writetile except works for local
227                         arrays
228      write_local_r? - higher-level wrapper for mdsio_writelocal
229      Controlled by diagFreq. Defaults to zero (ie. no dumps)
230      Example given at end of mom_vecinv.F that dumps some local arrays.
231    o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
232      control flux-form versus vector invariant code.
233      Switch is runtime flag vectorInvariantMomentum (defaults to false)
234      or genmake -DISABLE ...
235    o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
236      (additional storing is now needed for case vecinv;
237      currently nothing implemented to switch this storing off
238      in case fluxform is used since no CPP flag available).
239    
240    checkpoint40pre7
241    o bug fix in dynamics.F
242      calc_viscosity called before k=1,Nr loop.
243    o added some #ifdef's ALLOW_PASSIVE_TRACER
244    o cleaned initialisations in ctrl_map_ini
245      related to TAF
246    
247    checkpoint40pre6
248    o split dynamics into thermodynamics & dynamics
249    o corresponding split of calc_diffusivity into
250      calc_diffusivity, calc_viscosity
251      (kpp_calc_diff, kpp_calc_visc).
252    o Added diffkr, kapgm to control variables
253    o bug fix in gmredi_slope_limit for ldd97
254    
255    checkpoint40pre5
256    o proper initialization of Adams-Bashforth time stepping
257      + uses forward step for very first step of model (iter=0)
258    o re-generated *all* output since almost all output is modified by this
259      change (sorry but we've been putting this one off for about 2 years)
260      + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
261        *not* regenerated since they are already out of date and I don't
262        want to create the impression that they are suddenly working.
263    o removed KAP stuff for DEC's
264    o modified/added many .cvsignore files in */code and */input
265    o added new expt "solid-body.cs-32x32x1"
266      + this uses an alternative form of ini_curvilinear_grid.F which
267        is not necessarily any better than the current one...
268    
269    checkpoint40pre4
270    o added re-initialisations of utrans,vtrans,rtrans in
271      calc_common_factors which are crucial for TAF.
272    o extended iMin,jMin range for calc_common_factors,
273      calc_diffusivity
274    o added option ALLOW_PASSIVE_TRACER
275    o a few minor updates and fixes
276    
277    checkpoint40pre3
278    o created calc_gtr1.F for gad package
279    o split the_main_loop and re-introduced forward_step
280    o some recomputations of nIter0 for TAMC
281    
282    checkpoint40pre2
283    o Updated to latest branch of AJA, JMC
284    o Added gradient check package
285    o Added routines for passive tracer handling
286    o Added carbon sequestration sensitivity experiment
287    
288    checkpoint39
289     o Modifications and fixes to support TAMC
290       (mainly missing or wrong directives)
291     o Corrected common blocks when fooling TAMC to produce adjoint I/O
292       in addummy_in_stepping
293     o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
294     o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
295     o Included following packages:
296       cal: calendar
297       exf: external forcing
298       ecco: essential routines to control use of cal, exf
299             (NB: this is not the full ECCO environment)
300     o disabled some packages by default in genmake
301    
302    checkpoint38
303     o see notes_c37_adj.txt
304     o corrected wrong layer index in external_forcing_t
305     o replaced the_main_loop/forward_step by the_main_loop
306     o removed forceoutput from write_state
307       (replaced criteria for initial/final state)
308     o added runtime flag for pre-C35 pickups: usePickupBeforeC35
309    
310    checkpoint37
311     o mdsio.F routine split and packaged in pkg/mdsio
312       (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
313        used unless genmake -disable=mdsio)
314     o allow a more precise surface-geopotential gradient for the atmosphere
315       taking into account the change in space of Alpha (=1/rho) at the surface.
316     o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
317       (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
318     o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
319       Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
320       [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
321     o Time-Average diagnostics defined as a pseudo package "timeave".
322     o pickup files : old pickup (before c35) did not work with new code (c35
323       and after) unless activating 2 commented lines in initialise-varia.
324     o Non-Hydrostatic pickup file Pb fixed.
325     o bug with Rigid-lid version (since c35) fixed.  
326    
327    checkpoint36
328     o implement Crank-Nickelson barotropic time-stepping
329     o recover Time-Average diagnostics
330     o fix Pb in checkpoint (PR#19)
331     o AIM become a standard package ; clean unused CPP_kees
332    
333    checkpoint35
334     o subtantial rewrite of dynamics.f
335     o allows staggered time-stepping
336     o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
337     o added bottom drag (linear + quadratic)
338    
339    checkpoint34
340     o Modified exchange routines for correct reverse simulation.
341     o Added verification output to comply with bug fix in impldiff.F
342       as of c33 (exp2, natl_box).
343     o Corrected store directives in dynamics.F
344     o Corrected array boundaries in impldiff.F
345     o Corrected array dimensions in gmredi.
346       Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
347     o Added routine GLOBAL_SUM_INT to global_sum.F
348     o Added mdsio_gl.F for ECCO purposes.
349    
350    checkpoint33
351     o Fixed bug in lower BC in impldiff.F
352     o Fixed confusion about units of forcing arrays in FFIELDS.h
353       namely Fu,Fv,Qnet,Qsw,EmPmR:
354       - Removed verification/natl_box/code/external_fields_scale.F
355         (did not differ from that in model/src)
356       - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
357         (see FFIELDS.h for description)
358       - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
359         kpp_calc.F and kpp_transport_t.F
360       - Removed model/src/external_fields_scale.F and calls to it
361       - verification/natl_box uses flux data with "atmospheric" sign so
362         a special version of external_fields_load.F is used to
363         change the data as it's read in. This way, the arrays
364         have the right units and signs at all times tha a user could
365         possibly use them.
366     o Corrected genmake to delete a temporary file during configuration
367    
368    checkpoint32
369     o Scaling of forcing fields moved from external_forcing.F to
370       external_fields_scale.F, called directly after loading fields.
371     o Surface relaxation terms added to surface tendency fields in
372       extra subroutine.
373     o impldiff.F changed to avoid storing by TAMC of huge intermediate
374       fields.
375     o Changes in GMRedi to comply with packaging structure.
376     o Modifications and bug fixes in KPP package.
377     o Verification experiment for KPP added (verification/nat_box/)
378    
379    checkpoint31
380     o Packages interface brought in line with defined standard
381       -> new routines packages_...F
382       -> changes in initialise_fixed.F, initialise_varia.F
383       -> enables initialisation interface for ECCO package
384     o Rescaling of external forcing fields immediately after read
385       (removed from external_forcing.F)
386       -> new: surface_fields_scale.F
387       -> affects ini_foorcing.F, external_fields_load.F
388     o Computation of surface tendencies before tendency updates.
389       -> new: external_forcing_surf.F
390     o Change of variable names useGMRedi, useKPP, useECCO
391     o Further changes in dynamics.F, impldiff.F for TAMC
392     o Tested for experiments 0, 2, 4.
393       - not yet tested for GMRedi.
394       - not yet tested for KPP.
395    
396    checkpoint30
397     o Updates for OBCs
398     o New experiment for test OBCs (internal_wave)
399     o New output.txt in verification/exp4/results/
400     o Updates for KPP: calculation of viscosity corrected, new variables
401       kpp_dumpFreq and kpp_taveFreq
402     o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
403       and entry for T90 in genmake
404    
405    checkpoint29
406     o packaged KPP and GM/Redi
407    
408    checkpoint28
409     o Corrected initialization of hFacMin for difference vertical coordinates
410     o Modified calculation of partial cell thickness to more robust algorithm
411     o config_summary.F: replaced write_1D_... by write_0D_...
412       read_write.F: added subroutines write_0D_...
413     o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
414       included some initialisations required for TAMC.
415     o routine calc_isoslopes: modified sqrt computation to make it
416       differentiable for zero argument.
417     o routines dynamics, impldiff:
418       included store directives and tape key computations required for TAMC.
419     o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
420    
421  checkpoint27  checkpoint27
422   o fixed calc_isoslopes() to so that cancellation of terms in tensor   o fixed calc_isoslopes() to so that cancellation of terms in tensor
423     formulation works properly with variable resolution.     formulation works properly with variable resolution.

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