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revision 1.6 by adcroft, Mon Jun 22 16:09:37 1998 UTC revision 1.63 by jmc, Mon Mar 4 15:27:30 2002 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
7                 b) enable to filter 2D fields.
8    
9    checkpoint44e_pre,post
10    o re-wrote convective adjustment to use pre-calculated weights
11      Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
12      Adds:    model/src/convective_weights.F, convectively_mixtracer.F
13      Original calls to convect() still in place.
14    
15    chkpt44d_pre,post
16    o added missing EXCLUDE_MONITOR flags
17    o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
18      (incompatible typ in MIN/MAX expressions caused problems
19      on IBM SP3)
20    o in genmake added variable MAKEDEPEND
21      plus resetting for case SunOS
22    o added timer_stats.c routine for IBM SP3
23    o removed variables in dynamics
24    !!! I forgot to create tag chkpt44d_pre !!!
25    !!! But chkpt44d_pre = chkpt44c_post    !!!
26    
27    o real fresh water flux implemented with non-linear free-surface.
28    
29    chkpt44c_pre,post
30    o few fix (mask in shap_s2, EmPmR in external_field_load,
31      USE_NATURAL_BCS in solve_for_P);
32    o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
33    
34    checkpoint44b_pre/_post
35    o merge of relevant stuff from the ecco-branch:
36      - genmake: removed $S64 overwrite for case SunOS
37      - pkg/exf: update and corrections for field swapping and obcs
38      - pkg/ecco: parameter lists for the_model_main, the_main_loop
39                  harmonized between ECCO and MITgcm
40      - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
41                      updated checkpointing_lev... lists for obcs
42      - model/src: minor changes in forward_step, plot_field
43                   added directive for divided adjoint in the_main_loop
44      - pkg/mdsio: added mdsio_gl_slice
45    
46    o check parameters & config (chkpt44a_pre,post)
47    o OBC and NonLin_FrSurf.
48    
49    checkpoint44
50    o fix bug in mom_vi_del2uv
51    o select when filters are applied ; add options to zonal_filter (data.zonfilt)
52    o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
53    o update AIM experiments (NCEP input files)
54    o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
55    o added some stuff for AD
56    
57    checkpoint43
58    o added two new advection tests
59    o added global 4x4 degree ocean test
60    o added test of H&S94 with free surface on cube
61    o some final mods for gradient check, adjoint,...
62    
63    checkpoint42
64      Fixed AD-related problems:
65    o Store directives up-to-date with re-arranged Adams-Bashforth
66      (mainly thermodynamics.F)
67    o New store directives for multi-dim. advection schemes
68      * new CPP flag ALLOW_MULTI_DIM_ADVECTION
69      * new common block and key passkey
70      (mainly gad_advection.F)
71    o Modified store directives for split of dynamics/thermodynamics
72      for the case ALLOW_KPP
73    o Cleaned argument list for timestep_tracer.F
74    
75    checkpoint41
76    o re-formatted/added comments in prologues of key subroutines
77      to work with protex
78    
79    checkpoint40
80    o moved calc_gs, calc_gt and calc_tr1 back to model/src
81    o added FLT (floats) package from Arne along with demo. experiment
82    o re-arranged Adams-Bashforth scheme for tracers to allow easier
83      implementation of forward-in-time forcing terms
84    o more mods for non-linear free-surface including new variable
85    o modified multi-dim method to work on cube
86    o bug fix in KPP (from DM)
87    
88    checkpoint40pre9
89    o added DST advection schemes
90    o fix MPI bug on SGI's
91    o modifications for non-linear free-surface
92    o fixed conditionals for fixed flow/passive tracer only mode
93    o added tension/strain form of stress tensor
94    o changes to commenting of arguments for TAF/TAMC
95    o added/updated many matlab scripts
96    o added multi-dimensional advection method for tracers
97      
98    checkpoint40pre8
99    o new package rw/
100      Added method for dumping intermediate local arrays:
101      mdsio_writetile - same as mdsio_writefield except works from inside
102                        bi,bj loop
103      mdsio_writelocal - same as mdsio_writetile except works for local
104                         arrays
105      write_local_r? - higher-level wrapper for mdsio_writelocal
106      Controlled by diagFreq. Defaults to zero (ie. no dumps)
107      Example given at end of mom_vecinv.F that dumps some local arrays.
108    o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
109      control flux-form versus vector invariant code.
110      Switch is runtime flag vectorInvariantMomentum (defaults to false)
111      or genmake -DISABLE ...
112    o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
113      (additional storing is now needed for case vecinv;
114      currently nothing implemented to switch this storing off
115      in case fluxform is used since no CPP flag available).
116    
117    checkpoint40pre7
118    o bug fix in dynamics.F
119      calc_viscosity called before k=1,Nr loop.
120    o added some #ifdef's ALLOW_PASSIVE_TRACER
121    o cleaned initialisations in ctrl_map_ini
122      related to TAF
123    
124    checkpoint40pre6
125    o split dynamics into thermodynamics & dynamics
126    o corresponding split of calc_diffusivity into
127      calc_diffusivity, calc_viscosity
128      (kpp_calc_diff, kpp_calc_visc).
129    o Added diffkr, kapgm to control variables
130    o bug fix in gmredi_slope_limit for ldd97
131    
132    checkpoint40pre5
133    o proper initialization of Adams-Bashforth time stepping
134      + uses forward step for very first step of model (iter=0)
135    o re-generated *all* output since almost all output is modified by this
136      change (sorry but we've been putting this one off for about 2 years)
137      + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
138        *not* regenerated since they are already out of date and I don't
139        want to create the impression that they are suddenly working.
140    o removed KAP stuff for DEC's
141    o modified/added many .cvsignore files in */code and */input
142    o added new expt "solid-body.cs-32x32x1"
143      + this uses an alternative form of ini_curvilinear_grid.F which
144        is not necessarily any better than the current one...
145    
146    checkpoint40pre4
147    o added re-initialisations of utrans,vtrans,rtrans in
148      calc_common_factors which are crucial for TAF.
149    o extended iMin,jMin range for calc_common_factors,
150      calc_diffusivity
151    o added option ALLOW_PASSIVE_TRACER
152    o a few minor updates and fixes
153    
154    checkpoint40pre3
155    o created calc_gtr1.F for gad package
156    o split the_main_loop and re-introduced forward_step
157    o some recomputations of nIter0 for TAMC
158    
159    checkpoint40pre2
160    o Updated to latest branch of AJA, JMC
161    o Added gradient check package
162    o Added routines for passive tracer handling
163    o Added carbon sequestration sensitivity experiment
164    
165    checkpoint39
166     o Modifications and fixes to support TAMC
167       (mainly missing or wrong directives)
168     o Corrected common blocks when fooling TAMC to produce adjoint I/O
169       in addummy_in_stepping
170     o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
171     o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
172     o Included following packages:
173       cal: calendar
174       exf: external forcing
175       ecco: essential routines to control use of cal, exf
176             (NB: this is not the full ECCO environment)
177     o disabled some packages by default in genmake
178    
179    checkpoint38
180     o see notes_c37_adj.txt
181     o corrected wrong layer index in external_forcing_t
182     o replaced the_main_loop/forward_step by the_main_loop
183     o removed forceoutput from write_state
184       (replaced criteria for initial/final state)
185     o added runtime flag for pre-C35 pickups: usePickupBeforeC35
186    
187    checkpoint37
188     o mdsio.F routine split and packaged in pkg/mdsio
189       (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
190        used unless genmake -disable=mdsio)
191     o allow a more precise surface-geopotential gradient for the atmosphere
192       taking into account the change in space of Alpha (=1/rho) at the surface.
193     o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
194       (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
195     o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
196       Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
197       [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
198     o Time-Average diagnostics defined as a pseudo package "timeave".
199     o pickup files : old pickup (before c35) did not work with new code (c35
200       and after) unless activating 2 commented lines in initialise-varia.
201     o Non-Hydrostatic pickup file Pb fixed.
202     o bug with Rigid-lid version (since c35) fixed.  
203    
204    checkpoint36
205     o implement Crank-Nickelson barotropic time-stepping
206     o recover Time-Average diagnostics
207     o fix Pb in checkpoint (PR#19)
208     o AIM become a standard package ; clean unused CPP_kees
209    
210    checkpoint35
211     o subtantial rewrite of dynamics.f
212     o allows staggered time-stepping
213     o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
214     o added bottom drag (linear + quadratic)
215    
216    checkpoint34
217     o Modified exchange routines for correct reverse simulation.
218     o Added verification output to comply with bug fix in impldiff.F
219       as of c33 (exp2, natl_box).
220     o Corrected store directives in dynamics.F
221     o Corrected array boundaries in impldiff.F
222     o Corrected array dimensions in gmredi.
223       Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
224     o Added routine GLOBAL_SUM_INT to global_sum.F
225     o Added mdsio_gl.F for ECCO purposes.
226    
227    checkpoint33
228     o Fixed bug in lower BC in impldiff.F
229     o Fixed confusion about units of forcing arrays in FFIELDS.h
230       namely Fu,Fv,Qnet,Qsw,EmPmR:
231       - Removed verification/natl_box/code/external_fields_scale.F
232         (did not differ from that in model/src)
233       - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
234         (see FFIELDS.h for description)
235       - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
236         kpp_calc.F and kpp_transport_t.F
237       - Removed model/src/external_fields_scale.F and calls to it
238       - verification/natl_box uses flux data with "atmospheric" sign so
239         a special version of external_fields_load.F is used to
240         change the data as it's read in. This way, the arrays
241         have the right units and signs at all times tha a user could
242         possibly use them.
243     o Corrected genmake to delete a temporary file during configuration
244    
245    checkpoint32
246     o Scaling of forcing fields moved from external_forcing.F to
247       external_fields_scale.F, called directly after loading fields.
248     o Surface relaxation terms added to surface tendency fields in
249       extra subroutine.
250     o impldiff.F changed to avoid storing by TAMC of huge intermediate
251       fields.
252     o Changes in GMRedi to comply with packaging structure.
253     o Modifications and bug fixes in KPP package.
254     o Verification experiment for KPP added (verification/nat_box/)
255    
256    checkpoint31
257     o Packages interface brought in line with defined standard
258       -> new routines packages_...F
259       -> changes in initialise_fixed.F, initialise_varia.F
260       -> enables initialisation interface for ECCO package
261     o Rescaling of external forcing fields immediately after read
262       (removed from external_forcing.F)
263       -> new: surface_fields_scale.F
264       -> affects ini_foorcing.F, external_fields_load.F
265     o Computation of surface tendencies before tendency updates.
266       -> new: external_forcing_surf.F
267     o Change of variable names useGMRedi, useKPP, useECCO
268     o Further changes in dynamics.F, impldiff.F for TAMC
269     o Tested for experiments 0, 2, 4.
270       - not yet tested for GMRedi.
271       - not yet tested for KPP.
272    
273    checkpoint30
274     o Updates for OBCs
275     o New experiment for test OBCs (internal_wave)
276     o New output.txt in verification/exp4/results/
277     o Updates for KPP: calculation of viscosity corrected, new variables
278       kpp_dumpFreq and kpp_taveFreq
279     o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
280       and entry for T90 in genmake
281    
282    checkpoint29
283     o packaged KPP and GM/Redi
284    
285    checkpoint28
286     o Corrected initialization of hFacMin for difference vertical coordinates
287     o Modified calculation of partial cell thickness to more robust algorithm
288     o config_summary.F: replaced write_1D_... by write_0D_...
289       read_write.F: added subroutines write_0D_...
290     o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
291       included some initialisations required for TAMC.
292     o routine calc_isoslopes: modified sqrt computation to make it
293       differentiable for zero argument.
294     o routines dynamics, impldiff:
295       included store directives and tape key computations required for TAMC.
296     o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
297    
298    checkpoint27
299     o fixed calc_isoslopes() to so that cancellation of terms in tensor
300       formulation works properly with variable resolution.
301     o restructured the calling tree between the_model_main() and dynamics()
302     o split initialise() into initialise_fixed() and initialise_varia()
303     o introduced initialization file pSurfInitFile for free surface (cg2d_x)
304       in new routine ini_psurf()
305    
306    checkpoint26
307     o moved some #ifdef in optional routines to encompass everything
308       except the argument declarations. This was using up some memory.
309     o fixed macros like _ADT to work with both versions of Linux cpp
310     o cleaned up some unused and uninitialized variables
311       (helps when debugging with strict compile options)
312     o split up CPP_EEOPTIONS.h into options and macros
313       (macros are now in eesupp/inc/CPP_EEMACROS.h)
314     o patch for 2 processor JAM mode
315    
316    checkpoint25
317     o updates for OBCs and NH
318     o dramatically reduced memory usage
319     o added "JAM" routines for use on Artic network
320     o parameterization of convection by implicit vertical diffusion
321     o added a diagnostic of convective index
322     o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
323       (this is was partly for OBCs and NH but also in anticipation of
324        an explicit free-surface option)
325     o initial state input files for U and V
326    
327    checkpoint24
328     o Removed some spurious "REAL"s
329     o Updated KPP to latest version from JPL
330     o Added a COS(latitude) in horizontal viscosity
331    
332    checkpoint23
333     o Added del^4 diffusion for salt and temperature
334     o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
335    
336    checkpoint22
337     o Made many small changes: implicit none, format(i5), etc...
338     o Introduced KPP mixing scheme (compiles and runs but *not* tested)
339    
340    checkpoint21
341     o Introduced new I/O package that supports direct-access records (mdsio.F)
342     o Split-up mid-level I/O routines
343     o Updated input data for experiments 0,1,2,4 and 5
344     o Finally removed the genmake.* scripts (everyone seems happy with genmake)
345    
346    checkpoint20
347     o Tidied up open-boundaries some more
348     o Added non-hydrostatic code
349     o Fixed some input data
350     o Modified MPI start-up to work in "coupled" context.
351    
352    checkpoint19
353     o Tidied up directory structure for verification experiments.
354     o Added new code for open boundaries.
355     o Corrected advective terms near boundaries.
356     o Added CPP flag for "old UV" geometry and corrected spherical geometry.
357     o Implemented free-slip/no-slip BCs and del^4 dissipation.
358     o Split default parameters out of ini_parms.F into set_defaults.F.
359    
360    checkpoint18
361     o Further changes for optional code generation with
362       CPP - ugh!
363    
364    checkpoint17
365     o Beginning to incorporating modularity
366       for supporting atmos. and ocean configs.
367     o Small changes for TAMC complinace
368     o New ultra simple test case. Barotropic box
369       configuration "exp0".
370    
371    checkpoint16
372     o Minor changes to exchange routines to support
373       accumulation in reverse mode. Adjoint of an
374       assignment is an addition.
375     o Changes to support compilation by TAMC (LR(1)
376       syntax) and by g77 under Linux ( 72 character
377       limit ).
378    
379    checkpoint15
380     Rewrote exchange routines to allow
381     o General tile <-> tile connectivity.
382     o TAMC reverse mode flag ( is this really needed? )
383     o Variable width overlap and exchange region widths.
384     o Hooks for sharing data via DMA, Arctic, Memory Channel,
385       shmput/shmget, VIA, SYSV shmem and every other cool
386       communication method.
387    
388    checkpoint14
389     Consistent isomorphism chages made. These allow dynamical core
390     to support both pressure and meters as a vertical coordinate.
391    
392    checkpoint13
393     Release which corrects global_max problem and a couple
394     of KGM time-averaging diagnostic errors. Also contains
395     a double-gyre experiment setup as well as the baseline
396     4 degree global template. The double gyre template is
397     organised to allow it to be applied automatically to
398     the baseline configuration.
399    
400    branch-point-rdot
401     A few tidy-ups have been made bt the real point of this
402     check-point (excuse the pun) is to allow a branch to be
403     made for the purposes of adding the rDot alterations.
404     I don't want to commit the rDot to the main-trunk until
405     we've actually tested it...
406    
407    checkpoint12
408     Tidy up and added generic genmake script (formerly
409     configure script).
410     Released to testers.
411    
412    checkpoint11
413     Re-arranged initialise() and introduced ini_vertical_grid()
414     and ini_masks_etc().
415    
416    checkpoint10
417     Introduced the configure script.
418     Separated out the diags package.
419     Added template for writing time-averages of tile/intermediate quantities.
420     Updated SIZE.h in exp2 and made the data big-endian.
421    
422    checkpoint9
423     MPI fix. Filename changes (meta/data). salbin*y stuff.
424     General tidy-up.
425     SST.bin SSS.bin added to verification/exp2
426    
427  checkpoint8  checkpoint8
428   Inludes time-dependant forcing and time-averaging.   Inludes time-dependant forcing and time-averaging.
429   Works at 4x4 and 2.8125x2.8125 global   Works at 4x4 and 2.8125x2.8125 global

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