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revision 1.1 by cnh, Tue May 26 14:38:05 1998 UTC revision 1.53.2.6 by heimbach, Tue May 21 00:03:29 2002 UTC
# Line 2  $Header$ Line 2  $Header$
2    
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    next patch:
7    o added tangent linear setup to verification/carbon/
8    o added adjoint sensitivity setup to verification/global_ocean...
9    o moved packages_init_variables before convective_adjustment
10    
11    release1_p2
12    o fixed array boundary problem for adjoint
13      (related to partial recomputation within subroutine
14      related to dynamics -> calc_viscosity -> mom_...
15    o fixed recomputation in thermodynamics
16    o prepare (but not complete) recomputation problem in impldiff
17    o fixed problem for adjoint of global_max
18    o switched off sponge layer code in external_forcing
19    
20    release1_p1
21    o merged necessary patches:
22      - AD-related changes for GMRedi
23      - fixes i KPP (delZ -> drF)
24      - hook to OBCS songe layer code in external_forcing
25      - errorMessageUnit non-zero in eeboot.F
26      - modified test cost function and carbon verif.
27    
28    release1_chkpt44d_post = chkpt44d_post
29    
30    chkpt44d_pre,post
31    o added missing EXCLUDE_MONITOR flags
32    o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
33      (incompatible typ in MIN/MAX expressions caused problems
34      on IBM SP3)
35    o in genmake added variable MAKEDEPEND
36      plus resetting for case SunOS
37    o added timer_stats.c routine for IBM SP3
38    o removed variables in dynamics
39    
40    o real fresh water flux implemented with non-linear free-surface.
41    
42    chkpt44c_pre,post
43    o few fix (mask in shap_s2, EmPmR in external_field_load,
44      USE_NATURAL_BCS in solve_for_P);
45    o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
46    
47    checkpoint44b_pre/_post
48    o merge of relevant stuff from the ecco-branch:
49      - genmake: removed $S64 overwrite for case SunOS
50      - pkg/exf: update and corrections for field swapping and obcs
51      - pkg/ecco: parameter lists for the_model_main, the_main_loop
52                  harmonized between ECCO and MITgcm
53      - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
54                      updated checkpointing_lev... lists for obcs
55      - model/src: minor changes in forward_step, plot_field
56                   added directive for divided adjoint in the_main_loop
57      - pkg/mdsio: added mdsio_gl_slice
58    
59    o check parameters & config (chkpt44a_pre,post)
60    o OBC and NonLin_FrSurf.
61    
62    checkpoint44
63    o fix bug in mom_vi_del2uv
64    o select when filters are applied ; add options to zonal_filter (data.zonfilt)
65    o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
66    o update AIM experiments (NCEP input files)
67    o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
68    o added some stuff for AD
69    
70    checkpoint43
71    o added two new advection tests
72    o added global 4x4 degree ocean test
73    o added test of H&S94 with free surface on cube
74    o some final mods for gradient check, adjoint,...
75    
76    checkpoint42
77      Fixed AD-related problems:
78    o Store directives up-to-date with re-arranged Adams-Bashforth
79      (mainly thermodynamics.F)
80    o New store directives for multi-dim. advection schemes
81      * new CPP flag ALLOW_MULTI_DIM_ADVECTION
82      * new common block and key passkey
83      (mainly gad_advection.F)
84    o Modified store directives for split of dynamics/thermodynamics
85      for the case ALLOW_KPP
86    o Cleaned argument list for timestep_tracer.F
87    
88    checkpoint41
89    o re-formatted/added comments in prologues of key subroutines
90      to work with protex
91    
92    checkpoint40
93    o moved calc_gs, calc_gt and calc_tr1 back to model/src
94    o added FLT (floats) package from Arne along with demo. experiment
95    o re-arranged Adams-Bashforth scheme for tracers to allow easier
96      implementation of forward-in-time forcing terms
97    o more mods for non-linear free-surface including new variable
98    o modified multi-dim method to work on cube
99    o bug fix in KPP (from DM)
100    
101    checkpoint40pre9
102    o added DST advection schemes
103    o fix MPI bug on SGI's
104    o modifications for non-linear free-surface
105    o fixed conditionals for fixed flow/passive tracer only mode
106    o added tension/strain form of stress tensor
107    o changes to commenting of arguments for TAF/TAMC
108    o added/updated many matlab scripts
109    o added multi-dimensional advection method for tracers
110      
111    checkpoint40pre8
112    o new package rw/
113      Added method for dumping intermediate local arrays:
114      mdsio_writetile - same as mdsio_writefield except works from inside
115                        bi,bj loop
116      mdsio_writelocal - same as mdsio_writetile except works for local
117                         arrays
118      write_local_r? - higher-level wrapper for mdsio_writelocal
119      Controlled by diagFreq. Defaults to zero (ie. no dumps)
120      Example given at end of mom_vecinv.F that dumps some local arrays.
121    o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
122      control flux-form versus vector invariant code.
123      Switch is runtime flag vectorInvariantMomentum (defaults to false)
124      or genmake -DISABLE ...
125    o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
126      (additional storing is now needed for case vecinv;
127      currently nothing implemented to switch this storing off
128      in case fluxform is used since no CPP flag available).
129    
130    checkpoint40pre7
131    o bug fix in dynamics.F
132      calc_viscosity called before k=1,Nr loop.
133    o added some #ifdef's ALLOW_PASSIVE_TRACER
134    o cleaned initialisations in ctrl_map_ini
135      related to TAF
136    
137    checkpoint40pre6
138    o split dynamics into thermodynamics & dynamics
139    o corresponding split of calc_diffusivity into
140      calc_diffusivity, calc_viscosity
141      (kpp_calc_diff, kpp_calc_visc).
142    o Added diffkr, kapgm to control variables
143    o bug fix in gmredi_slope_limit for ldd97
144    
145    checkpoint40pre5
146    o proper initialization of Adams-Bashforth time stepping
147      + uses forward step for very first step of model (iter=0)
148    o re-generated *all* output since almost all output is modified by this
149      change (sorry but we've been putting this one off for about 2 years)
150      + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
151        *not* regenerated since they are already out of date and I don't
152        want to create the impression that they are suddenly working.
153    o removed KAP stuff for DEC's
154    o modified/added many .cvsignore files in */code and */input
155    o added new expt "solid-body.cs-32x32x1"
156      + this uses an alternative form of ini_curvilinear_grid.F which
157        is not necessarily any better than the current one...
158    
159    checkpoint40pre4
160    o added re-initialisations of utrans,vtrans,rtrans in
161      calc_common_factors which are crucial for TAF.
162    o extended iMin,jMin range for calc_common_factors,
163      calc_diffusivity
164    o added option ALLOW_PASSIVE_TRACER
165    o a few minor updates and fixes
166    
167    checkpoint40pre3
168    o created calc_gtr1.F for gad package
169    o split the_main_loop and re-introduced forward_step
170    o some recomputations of nIter0 for TAMC
171    
172    checkpoint40pre2
173    o Updated to latest branch of AJA, JMC
174    o Added gradient check package
175    o Added routines for passive tracer handling
176    o Added carbon sequestration sensitivity experiment
177    
178    checkpoint39
179     o Modifications and fixes to support TAMC
180       (mainly missing or wrong directives)
181     o Corrected common blocks when fooling TAMC to produce adjoint I/O
182       in addummy_in_stepping
183     o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
184     o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
185     o Included following packages:
186       cal: calendar
187       exf: external forcing
188       ecco: essential routines to control use of cal, exf
189             (NB: this is not the full ECCO environment)
190     o disabled some packages by default in genmake
191    
192    checkpoint38
193     o see notes_c37_adj.txt
194     o corrected wrong layer index in external_forcing_t
195     o replaced the_main_loop/forward_step by the_main_loop
196     o removed forceoutput from write_state
197       (replaced criteria for initial/final state)
198     o added runtime flag for pre-C35 pickups: usePickupBeforeC35
199    
200    checkpoint37
201     o mdsio.F routine split and packaged in pkg/mdsio
202       (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
203        used unless genmake -disable=mdsio)
204     o allow a more precise surface-geopotential gradient for the atmosphere
205       taking into account the change in space of Alpha (=1/rho) at the surface.
206     o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
207       (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
208     o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
209       Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
210       [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
211     o Time-Average diagnostics defined as a pseudo package "timeave".
212     o pickup files : old pickup (before c35) did not work with new code (c35
213       and after) unless activating 2 commented lines in initialise-varia.
214     o Non-Hydrostatic pickup file Pb fixed.
215     o bug with Rigid-lid version (since c35) fixed.  
216    
217    checkpoint36
218     o implement Crank-Nickelson barotropic time-stepping
219     o recover Time-Average diagnostics
220     o fix Pb in checkpoint (PR#19)
221     o AIM become a standard package ; clean unused CPP_kees
222    
223    checkpoint35
224     o subtantial rewrite of dynamics.f
225     o allows staggered time-stepping
226     o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
227     o added bottom drag (linear + quadratic)
228    
229    checkpoint34
230     o Modified exchange routines for correct reverse simulation.
231     o Added verification output to comply with bug fix in impldiff.F
232       as of c33 (exp2, natl_box).
233     o Corrected store directives in dynamics.F
234     o Corrected array boundaries in impldiff.F
235     o Corrected array dimensions in gmredi.
236       Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
237     o Added routine GLOBAL_SUM_INT to global_sum.F
238     o Added mdsio_gl.F for ECCO purposes.
239    
240    checkpoint33
241     o Fixed bug in lower BC in impldiff.F
242     o Fixed confusion about units of forcing arrays in FFIELDS.h
243       namely Fu,Fv,Qnet,Qsw,EmPmR:
244       - Removed verification/natl_box/code/external_fields_scale.F
245         (did not differ from that in model/src)
246       - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
247         (see FFIELDS.h for description)
248       - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
249         kpp_calc.F and kpp_transport_t.F
250       - Removed model/src/external_fields_scale.F and calls to it
251       - verification/natl_box uses flux data with "atmospheric" sign so
252         a special version of external_fields_load.F is used to
253         change the data as it's read in. This way, the arrays
254         have the right units and signs at all times tha a user could
255         possibly use them.
256     o Corrected genmake to delete a temporary file during configuration
257    
258    checkpoint32
259     o Scaling of forcing fields moved from external_forcing.F to
260       external_fields_scale.F, called directly after loading fields.
261     o Surface relaxation terms added to surface tendency fields in
262       extra subroutine.
263     o impldiff.F changed to avoid storing by TAMC of huge intermediate
264       fields.
265     o Changes in GMRedi to comply with packaging structure.
266     o Modifications and bug fixes in KPP package.
267     o Verification experiment for KPP added (verification/nat_box/)
268    
269    checkpoint31
270     o Packages interface brought in line with defined standard
271       -> new routines packages_...F
272       -> changes in initialise_fixed.F, initialise_varia.F
273       -> enables initialisation interface for ECCO package
274     o Rescaling of external forcing fields immediately after read
275       (removed from external_forcing.F)
276       -> new: surface_fields_scale.F
277       -> affects ini_foorcing.F, external_fields_load.F
278     o Computation of surface tendencies before tendency updates.
279       -> new: external_forcing_surf.F
280     o Change of variable names useGMRedi, useKPP, useECCO
281     o Further changes in dynamics.F, impldiff.F for TAMC
282     o Tested for experiments 0, 2, 4.
283       - not yet tested for GMRedi.
284       - not yet tested for KPP.
285    
286    checkpoint30
287     o Updates for OBCs
288     o New experiment for test OBCs (internal_wave)
289     o New output.txt in verification/exp4/results/
290     o Updates for KPP: calculation of viscosity corrected, new variables
291       kpp_dumpFreq and kpp_taveFreq
292     o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
293       and entry for T90 in genmake
294    
295    checkpoint29
296     o packaged KPP and GM/Redi
297    
298    checkpoint28
299     o Corrected initialization of hFacMin for difference vertical coordinates
300     o Modified calculation of partial cell thickness to more robust algorithm
301     o config_summary.F: replaced write_1D_... by write_0D_...
302       read_write.F: added subroutines write_0D_...
303     o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
304       included some initialisations required for TAMC.
305     o routine calc_isoslopes: modified sqrt computation to make it
306       differentiable for zero argument.
307     o routines dynamics, impldiff:
308       included store directives and tape key computations required for TAMC.
309     o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
310    
311    checkpoint27
312     o fixed calc_isoslopes() to so that cancellation of terms in tensor
313       formulation works properly with variable resolution.
314     o restructured the calling tree between the_model_main() and dynamics()
315     o split initialise() into initialise_fixed() and initialise_varia()
316     o introduced initialization file pSurfInitFile for free surface (cg2d_x)
317       in new routine ini_psurf()
318    
319    checkpoint26
320     o moved some #ifdef in optional routines to encompass everything
321       except the argument declarations. This was using up some memory.
322     o fixed macros like _ADT to work with both versions of Linux cpp
323     o cleaned up some unused and uninitialized variables
324       (helps when debugging with strict compile options)
325     o split up CPP_EEOPTIONS.h into options and macros
326       (macros are now in eesupp/inc/CPP_EEMACROS.h)
327     o patch for 2 processor JAM mode
328    
329    checkpoint25
330     o updates for OBCs and NH
331     o dramatically reduced memory usage
332     o added "JAM" routines for use on Artic network
333     o parameterization of convection by implicit vertical diffusion
334     o added a diagnostic of convective index
335     o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
336       (this is was partly for OBCs and NH but also in anticipation of
337        an explicit free-surface option)
338     o initial state input files for U and V
339    
340    checkpoint24
341     o Removed some spurious "REAL"s
342     o Updated KPP to latest version from JPL
343     o Added a COS(latitude) in horizontal viscosity
344    
345    checkpoint23
346     o Added del^4 diffusion for salt and temperature
347     o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
348    
349    checkpoint22
350     o Made many small changes: implicit none, format(i5), etc...
351     o Introduced KPP mixing scheme (compiles and runs but *not* tested)
352    
353    checkpoint21
354     o Introduced new I/O package that supports direct-access records (mdsio.F)
355     o Split-up mid-level I/O routines
356     o Updated input data for experiments 0,1,2,4 and 5
357     o Finally removed the genmake.* scripts (everyone seems happy with genmake)
358    
359    checkpoint20
360     o Tidied up open-boundaries some more
361     o Added non-hydrostatic code
362     o Fixed some input data
363     o Modified MPI start-up to work in "coupled" context.
364    
365    checkpoint19
366     o Tidied up directory structure for verification experiments.
367     o Added new code for open boundaries.
368     o Corrected advective terms near boundaries.
369     o Added CPP flag for "old UV" geometry and corrected spherical geometry.
370     o Implemented free-slip/no-slip BCs and del^4 dissipation.
371     o Split default parameters out of ini_parms.F into set_defaults.F.
372    
373    checkpoint18
374     o Further changes for optional code generation with
375       CPP - ugh!
376    
377    checkpoint17
378     o Beginning to incorporating modularity
379       for supporting atmos. and ocean configs.
380     o Small changes for TAMC complinace
381     o New ultra simple test case. Barotropic box
382       configuration "exp0".
383    
384    checkpoint16
385     o Minor changes to exchange routines to support
386       accumulation in reverse mode. Adjoint of an
387       assignment is an addition.
388     o Changes to support compilation by TAMC (LR(1)
389       syntax) and by g77 under Linux ( 72 character
390       limit ).
391    
392    checkpoint15
393     Rewrote exchange routines to allow
394     o General tile <-> tile connectivity.
395     o TAMC reverse mode flag ( is this really needed? )
396     o Variable width overlap and exchange region widths.
397     o Hooks for sharing data via DMA, Arctic, Memory Channel,
398       shmput/shmget, VIA, SYSV shmem and every other cool
399       communication method.
400    
401    checkpoint14
402     Consistent isomorphism chages made. These allow dynamical core
403     to support both pressure and meters as a vertical coordinate.
404    
405    checkpoint13
406     Release which corrects global_max problem and a couple
407     of KGM time-averaging diagnostic errors. Also contains
408     a double-gyre experiment setup as well as the baseline
409     4 degree global template. The double gyre template is
410     organised to allow it to be applied automatically to
411     the baseline configuration.
412    
413    branch-point-rdot
414     A few tidy-ups have been made bt the real point of this
415     check-point (excuse the pun) is to allow a branch to be
416     made for the purposes of adding the rDot alterations.
417     I don't want to commit the rDot to the main-trunk until
418     we've actually tested it...
419    
420    checkpoint12
421     Tidy up and added generic genmake script (formerly
422     configure script).
423     Released to testers.
424    
425    checkpoint11
426     Re-arranged initialise() and introduced ini_vertical_grid()
427     and ini_masks_etc().
428    
429    checkpoint10
430     Introduced the configure script.
431     Separated out the diags package.
432     Added template for writing time-averages of tile/intermediate quantities.
433     Updated SIZE.h in exp2 and made the data big-endian.
434    
435    checkpoint9
436     MPI fix. Filename changes (meta/data). salbin*y stuff.
437     General tidy-up.
438     SST.bin SSS.bin added to verification/exp2
439    
440    checkpoint8
441     Inludes time-dependant forcing and time-averaging.
442     Works at 4x4 and 2.8125x2.8125 global
443    
444    checkpoint7-4degree-ref
445     Branch from checkpoint7. Released for application to
446     global modeling and general modeling - process studies, regional
447     model etc..
448     Configured for verification/exp2 - 4 degree global, two process.
449    
450    checkpoint7
451     Created by cnh
452     Simple 4 degree global simulation
453     configuration.
454     Includes climatological wind,
455     hydrography, bathymetry etc
456     Does not include Heat Flux and E-P
457    
458    checkpoint6
459     Created by cnh
460     merged checkpoint5 with CD and
461     spherical polar code.
462     Still some problems with GM Redi
463     abd full topography.
464    
465    checkpoint5
466     Created by AJA
467     contains updates to GM Redi
468     and reordered timestepping loop
469     for Implicit Diffusion.
470    
471    checkpoint4
472     Created by cnh
473     Contains memory saving macros ( _rdxc etc..) for when
474     grid variations are limited.
475     Contains polynomial coeffs for EOS and knudsen program
476     for generation.
477    
478  checkpoint3  checkpoint3
479   Created by cnh   Created by cnh
480   Added extra flags for runtime options   Added extra flags for runtime options
# Line 20  checkpoint1 Line 493  checkpoint1
493   Restructured kloop in dynamics.F   Restructured kloop in dynamics.F
494   Added non-linear EOS   Added non-linear EOS
495    
496  baseline - Original checked in code  baseline
497     Original checked in code
498    

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