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revision 1.10 by cnh, Wed Jul 8 15:40:09 1998 UTC revision 1.71 by jmc, Wed May 1 01:35:30 2002 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    checkpoint45a_post
7    o compute Rho over the whole domain (extend iMin,jMin indices)
8    o specific exchange for X-slice domain (case Ny=1)
9    o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
10    o solve_for_pressure : set cg2d_x to zero where OBCS are applied
11    
12    checkpoint44h_post = checkpoint45
13    o Fix to restore differentiability:
14      place at which packages_init_variables is called in
15      initialise_varia is crucial for reverse control flow.
16    o modifications in GMRedi to enable stable adjoint
17      (corresponding modif's in thermodynamics, dynamics)
18    o added missing hook for sponge layer code in external_forcing
19    o modified test cost functions
20    o storing in gad_advection (plus removal of write(0,*)!
21    o missing headers TR1.h added in convective_adjustment routines
22    o errorMessageUnit set non-equal zero in eeboot
23      (conflict on some platforms, e.g. IBM SP3)
24    o modified carbon verif.
25    
26    checkpoint44h_pre
27    o vertical grid option: allow to put the Interface at the middle between
28      2 cell-centers ; replace delZ in pkg/kpp by drF.
29    o GM Advective form: Tracers are advected using the residual transport (=
30      Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
31    
32    checkpoint44g_post
33    o fix surface correction term in multiDimAdvection (affects plume_on_slope
34      results) ; ifdef missing in thermodynamics.F
35    
36    checkpoint44f_pre,checkpoint44f_post
37    o added PTRACERS package
38      This allows an arbitrary number of passive tracers to be integrated
39      forward simultaneously with the dynamicaly model.
40      + Implemented so far:
41        - basic forward algorithm (time-stepping, advection, diffusion, convection)
42        - I/O and checkpointing
43        - GM/Redi  *but*  using the GM/Redi coefficient of Salt
44      + Not implemented so far:
45        - KPP
46        - OBCS
47      + No specific example supplied (yet) but global_ocean.90x40x15 has the
48        necessary data.ptracer file. Simply use -enable=ptracers and uncomment
49        line in data.pkg.
50      + This package is disabled by default since it increases storage.
51    
52    
53    o testscript: added -cleanup option
54    o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
55                 b) enable to filter 2D fields.
56    
57    checkpoint44e_pre,post
58    o re-wrote convective adjustment to use pre-calculated weights
59      Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
60      Adds:    model/src/convective_weights.F, convectively_mixtracer.F
61      Original calls to convect() still in place.
62    
63    chkpt44d_pre,post
64    o added missing EXCLUDE_MONITOR flags
65    o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
66      (incompatible typ in MIN/MAX expressions caused problems
67      on IBM SP3)
68    o in genmake added variable MAKEDEPEND
69      plus resetting for case SunOS
70    o added timer_stats.c routine for IBM SP3
71    o removed variables in dynamics
72    !!! I forgot to create tag chkpt44d_pre !!!
73    !!! But chkpt44d_pre = chkpt44c_post    !!!
74    
75    o real fresh water flux implemented with non-linear free-surface.
76    
77    chkpt44c_pre,post
78    o few fix (mask in shap_s2, EmPmR in external_field_load,
79      USE_NATURAL_BCS in solve_for_P);
80    o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
81    
82    checkpoint44b_pre/_post
83    o merge of relevant stuff from the ecco-branch:
84      - genmake: removed $S64 overwrite for case SunOS
85      - pkg/exf: update and corrections for field swapping and obcs
86      - pkg/ecco: parameter lists for the_model_main, the_main_loop
87                  harmonized between ECCO and MITgcm
88      - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
89                      updated checkpointing_lev... lists for obcs
90      - model/src: minor changes in forward_step, plot_field
91                   added directive for divided adjoint in the_main_loop
92      - pkg/mdsio: added mdsio_gl_slice
93    
94    o check parameters & config (chkpt44a_pre,post)
95    o OBC and NonLin_FrSurf.
96    
97    checkpoint44
98    o fix bug in mom_vi_del2uv
99    o select when filters are applied ; add options to zonal_filter (data.zonfilt)
100    o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
101    o update AIM experiments (NCEP input files)
102    o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
103    o added some stuff for AD
104    
105    checkpoint43
106    o added two new advection tests
107    o added global 4x4 degree ocean test
108    o added test of H&S94 with free surface on cube
109    o some final mods for gradient check, adjoint,...
110    
111    checkpoint42
112      Fixed AD-related problems:
113    o Store directives up-to-date with re-arranged Adams-Bashforth
114      (mainly thermodynamics.F)
115    o New store directives for multi-dim. advection schemes
116      * new CPP flag ALLOW_MULTI_DIM_ADVECTION
117      * new common block and key passkey
118      (mainly gad_advection.F)
119    o Modified store directives for split of dynamics/thermodynamics
120      for the case ALLOW_KPP
121    o Cleaned argument list for timestep_tracer.F
122    
123    checkpoint41
124    o re-formatted/added comments in prologues of key subroutines
125      to work with protex
126    
127    checkpoint40
128    o moved calc_gs, calc_gt and calc_tr1 back to model/src
129    o added FLT (floats) package from Arne along with demo. experiment
130    o re-arranged Adams-Bashforth scheme for tracers to allow easier
131      implementation of forward-in-time forcing terms
132    o more mods for non-linear free-surface including new variable
133    o modified multi-dim method to work on cube
134    o bug fix in KPP (from DM)
135    
136    checkpoint40pre9
137    o added DST advection schemes
138    o fix MPI bug on SGI's
139    o modifications for non-linear free-surface
140    o fixed conditionals for fixed flow/passive tracer only mode
141    o added tension/strain form of stress tensor
142    o changes to commenting of arguments for TAF/TAMC
143    o added/updated many matlab scripts
144    o added multi-dimensional advection method for tracers
145      
146    checkpoint40pre8
147    o new package rw/
148      Added method for dumping intermediate local arrays:
149      mdsio_writetile - same as mdsio_writefield except works from inside
150                        bi,bj loop
151      mdsio_writelocal - same as mdsio_writetile except works for local
152                         arrays
153      write_local_r? - higher-level wrapper for mdsio_writelocal
154      Controlled by diagFreq. Defaults to zero (ie. no dumps)
155      Example given at end of mom_vecinv.F that dumps some local arrays.
156    o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
157      control flux-form versus vector invariant code.
158      Switch is runtime flag vectorInvariantMomentum (defaults to false)
159      or genmake -DISABLE ...
160    o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
161      (additional storing is now needed for case vecinv;
162      currently nothing implemented to switch this storing off
163      in case fluxform is used since no CPP flag available).
164    
165    checkpoint40pre7
166    o bug fix in dynamics.F
167      calc_viscosity called before k=1,Nr loop.
168    o added some #ifdef's ALLOW_PASSIVE_TRACER
169    o cleaned initialisations in ctrl_map_ini
170      related to TAF
171    
172    checkpoint40pre6
173    o split dynamics into thermodynamics & dynamics
174    o corresponding split of calc_diffusivity into
175      calc_diffusivity, calc_viscosity
176      (kpp_calc_diff, kpp_calc_visc).
177    o Added diffkr, kapgm to control variables
178    o bug fix in gmredi_slope_limit for ldd97
179    
180    checkpoint40pre5
181    o proper initialization of Adams-Bashforth time stepping
182      + uses forward step for very first step of model (iter=0)
183    o re-generated *all* output since almost all output is modified by this
184      change (sorry but we've been putting this one off for about 2 years)
185      + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
186        *not* regenerated since they are already out of date and I don't
187        want to create the impression that they are suddenly working.
188    o removed KAP stuff for DEC's
189    o modified/added many .cvsignore files in */code and */input
190    o added new expt "solid-body.cs-32x32x1"
191      + this uses an alternative form of ini_curvilinear_grid.F which
192        is not necessarily any better than the current one...
193    
194    checkpoint40pre4
195    o added re-initialisations of utrans,vtrans,rtrans in
196      calc_common_factors which are crucial for TAF.
197    o extended iMin,jMin range for calc_common_factors,
198      calc_diffusivity
199    o added option ALLOW_PASSIVE_TRACER
200    o a few minor updates and fixes
201    
202    checkpoint40pre3
203    o created calc_gtr1.F for gad package
204    o split the_main_loop and re-introduced forward_step
205    o some recomputations of nIter0 for TAMC
206    
207    checkpoint40pre2
208    o Updated to latest branch of AJA, JMC
209    o Added gradient check package
210    o Added routines for passive tracer handling
211    o Added carbon sequestration sensitivity experiment
212    
213    checkpoint39
214     o Modifications and fixes to support TAMC
215       (mainly missing or wrong directives)
216     o Corrected common blocks when fooling TAMC to produce adjoint I/O
217       in addummy_in_stepping
218     o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
219     o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
220     o Included following packages:
221       cal: calendar
222       exf: external forcing
223       ecco: essential routines to control use of cal, exf
224             (NB: this is not the full ECCO environment)
225     o disabled some packages by default in genmake
226    
227    checkpoint38
228     o see notes_c37_adj.txt
229     o corrected wrong layer index in external_forcing_t
230     o replaced the_main_loop/forward_step by the_main_loop
231     o removed forceoutput from write_state
232       (replaced criteria for initial/final state)
233     o added runtime flag for pre-C35 pickups: usePickupBeforeC35
234    
235    checkpoint37
236     o mdsio.F routine split and packaged in pkg/mdsio
237       (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
238        used unless genmake -disable=mdsio)
239     o allow a more precise surface-geopotential gradient for the atmosphere
240       taking into account the change in space of Alpha (=1/rho) at the surface.
241     o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
242       (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
243     o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
244       Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
245       [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
246     o Time-Average diagnostics defined as a pseudo package "timeave".
247     o pickup files : old pickup (before c35) did not work with new code (c35
248       and after) unless activating 2 commented lines in initialise-varia.
249     o Non-Hydrostatic pickup file Pb fixed.
250     o bug with Rigid-lid version (since c35) fixed.  
251    
252    checkpoint36
253     o implement Crank-Nickelson barotropic time-stepping
254     o recover Time-Average diagnostics
255     o fix Pb in checkpoint (PR#19)
256     o AIM become a standard package ; clean unused CPP_kees
257    
258    checkpoint35
259     o subtantial rewrite of dynamics.f
260     o allows staggered time-stepping
261     o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
262     o added bottom drag (linear + quadratic)
263    
264    checkpoint34
265     o Modified exchange routines for correct reverse simulation.
266     o Added verification output to comply with bug fix in impldiff.F
267       as of c33 (exp2, natl_box).
268     o Corrected store directives in dynamics.F
269     o Corrected array boundaries in impldiff.F
270     o Corrected array dimensions in gmredi.
271       Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
272     o Added routine GLOBAL_SUM_INT to global_sum.F
273     o Added mdsio_gl.F for ECCO purposes.
274    
275    checkpoint33
276     o Fixed bug in lower BC in impldiff.F
277     o Fixed confusion about units of forcing arrays in FFIELDS.h
278       namely Fu,Fv,Qnet,Qsw,EmPmR:
279       - Removed verification/natl_box/code/external_fields_scale.F
280         (did not differ from that in model/src)
281       - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
282         (see FFIELDS.h for description)
283       - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
284         kpp_calc.F and kpp_transport_t.F
285       - Removed model/src/external_fields_scale.F and calls to it
286       - verification/natl_box uses flux data with "atmospheric" sign so
287         a special version of external_fields_load.F is used to
288         change the data as it's read in. This way, the arrays
289         have the right units and signs at all times tha a user could
290         possibly use them.
291     o Corrected genmake to delete a temporary file during configuration
292    
293    checkpoint32
294     o Scaling of forcing fields moved from external_forcing.F to
295       external_fields_scale.F, called directly after loading fields.
296     o Surface relaxation terms added to surface tendency fields in
297       extra subroutine.
298     o impldiff.F changed to avoid storing by TAMC of huge intermediate
299       fields.
300     o Changes in GMRedi to comply with packaging structure.
301     o Modifications and bug fixes in KPP package.
302     o Verification experiment for KPP added (verification/nat_box/)
303    
304    checkpoint31
305     o Packages interface brought in line with defined standard
306       -> new routines packages_...F
307       -> changes in initialise_fixed.F, initialise_varia.F
308       -> enables initialisation interface for ECCO package
309     o Rescaling of external forcing fields immediately after read
310       (removed from external_forcing.F)
311       -> new: surface_fields_scale.F
312       -> affects ini_foorcing.F, external_fields_load.F
313     o Computation of surface tendencies before tendency updates.
314       -> new: external_forcing_surf.F
315     o Change of variable names useGMRedi, useKPP, useECCO
316     o Further changes in dynamics.F, impldiff.F for TAMC
317     o Tested for experiments 0, 2, 4.
318       - not yet tested for GMRedi.
319       - not yet tested for KPP.
320    
321    checkpoint30
322     o Updates for OBCs
323     o New experiment for test OBCs (internal_wave)
324     o New output.txt in verification/exp4/results/
325     o Updates for KPP: calculation of viscosity corrected, new variables
326       kpp_dumpFreq and kpp_taveFreq
327     o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
328       and entry for T90 in genmake
329    
330    checkpoint29
331     o packaged KPP and GM/Redi
332    
333    checkpoint28
334     o Corrected initialization of hFacMin for difference vertical coordinates
335     o Modified calculation of partial cell thickness to more robust algorithm
336     o config_summary.F: replaced write_1D_... by write_0D_...
337       read_write.F: added subroutines write_0D_...
338     o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
339       included some initialisations required for TAMC.
340     o routine calc_isoslopes: modified sqrt computation to make it
341       differentiable for zero argument.
342     o routines dynamics, impldiff:
343       included store directives and tape key computations required for TAMC.
344     o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
345    
346    checkpoint27
347     o fixed calc_isoslopes() to so that cancellation of terms in tensor
348       formulation works properly with variable resolution.
349     o restructured the calling tree between the_model_main() and dynamics()
350     o split initialise() into initialise_fixed() and initialise_varia()
351     o introduced initialization file pSurfInitFile for free surface (cg2d_x)
352       in new routine ini_psurf()
353    
354    checkpoint26
355     o moved some #ifdef in optional routines to encompass everything
356       except the argument declarations. This was using up some memory.
357     o fixed macros like _ADT to work with both versions of Linux cpp
358     o cleaned up some unused and uninitialized variables
359       (helps when debugging with strict compile options)
360     o split up CPP_EEOPTIONS.h into options and macros
361       (macros are now in eesupp/inc/CPP_EEMACROS.h)
362     o patch for 2 processor JAM mode
363    
364    checkpoint25
365     o updates for OBCs and NH
366     o dramatically reduced memory usage
367     o added "JAM" routines for use on Artic network
368     o parameterization of convection by implicit vertical diffusion
369     o added a diagnostic of convective index
370     o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
371       (this is was partly for OBCs and NH but also in anticipation of
372        an explicit free-surface option)
373     o initial state input files for U and V
374    
375    checkpoint24
376     o Removed some spurious "REAL"s
377     o Updated KPP to latest version from JPL
378     o Added a COS(latitude) in horizontal viscosity
379    
380    checkpoint23
381     o Added del^4 diffusion for salt and temperature
382     o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
383    
384    checkpoint22
385     o Made many small changes: implicit none, format(i5), etc...
386     o Introduced KPP mixing scheme (compiles and runs but *not* tested)
387    
388    checkpoint21
389     o Introduced new I/O package that supports direct-access records (mdsio.F)
390     o Split-up mid-level I/O routines
391     o Updated input data for experiments 0,1,2,4 and 5
392     o Finally removed the genmake.* scripts (everyone seems happy with genmake)
393    
394    checkpoint20
395     o Tidied up open-boundaries some more
396     o Added non-hydrostatic code
397     o Fixed some input data
398     o Modified MPI start-up to work in "coupled" context.
399    
400    checkpoint19
401     o Tidied up directory structure for verification experiments.
402     o Added new code for open boundaries.
403     o Corrected advective terms near boundaries.
404     o Added CPP flag for "old UV" geometry and corrected spherical geometry.
405     o Implemented free-slip/no-slip BCs and del^4 dissipation.
406     o Split default parameters out of ini_parms.F into set_defaults.F.
407    
408    checkpoint18
409     o Further changes for optional code generation with
410       CPP - ugh!
411    
412    checkpoint17
413     o Beginning to incorporating modularity
414       for supporting atmos. and ocean configs.
415     o Small changes for TAMC complinace
416     o New ultra simple test case. Barotropic box
417       configuration "exp0".
418    
419    checkpoint16
420     o Minor changes to exchange routines to support
421       accumulation in reverse mode. Adjoint of an
422       assignment is an addition.
423     o Changes to support compilation by TAMC (LR(1)
424       syntax) and by g77 under Linux ( 72 character
425       limit ).
426    
427    checkpoint15
428     Rewrote exchange routines to allow
429     o General tile <-> tile connectivity.
430     o TAMC reverse mode flag ( is this really needed? )
431     o Variable width overlap and exchange region widths.
432     o Hooks for sharing data via DMA, Arctic, Memory Channel,
433       shmput/shmget, VIA, SYSV shmem and every other cool
434       communication method.
435    
436    checkpoint14
437     Consistent isomorphism chages made. These allow dynamical core
438     to support both pressure and meters as a vertical coordinate.
439    
440    checkpoint13
441     Release which corrects global_max problem and a couple
442     of KGM time-averaging diagnostic errors. Also contains
443     a double-gyre experiment setup as well as the baseline
444     4 degree global template. The double gyre template is
445     organised to allow it to be applied automatically to
446     the baseline configuration.
447    
448    branch-point-rdot
449     A few tidy-ups have been made bt the real point of this
450     check-point (excuse the pun) is to allow a branch to be
451     made for the purposes of adding the rDot alterations.
452     I don't want to commit the rDot to the main-trunk until
453     we've actually tested it...
454    
455  checkpoint12  checkpoint12
456   Tidy up and added generic genmake script (formerly   Tidy up and added generic genmake script (formerly
457   configure script).   configure script).

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