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revision 1.8 by adcroft, Wed Jul 1 22:49:29 1998 UTC revision 1.69 by heimbach, Sun Mar 24 02:44:49 2002 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    checkpoint44h_post = checkpoint45
7    o Fix to restore differentiability:
8      place at which packages_init_variables is called in
9      initialise_varia is crucial for reverse control flow.
10    o modifications in GMRedi to enable stable adjoint
11      (corresponding modif's in thermodynamics, dynamics)
12    o added missing hook for sponge layer code in external_forcing
13    o modified test cost functions
14    o storing in gad_advection (plus removal of write(0,*)!
15    o missing headers TR1.h added in convective_adjustment routines
16    o errorMessageUnit set non-equal zero in eeboot
17      (conflict on some platforms, e.g. IBM SP3)
18    o modified carbon verif.
19    
20    checkpoint44h_pre
21    o vertical grid option: allow to put the Interface at the middle between
22      2 cell-centers ; replace delZ in pkg/kpp by drF.
23    o GM Advective form: Tracers are advected using the residual transport (=
24      Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
25    
26    checkpoint44g_post
27    o fix surface correction term in multiDimAdvection (affects plume_on_slope
28      results) ; ifdef missing in thermodynamics.F
29    
30    checkpoint44f_pre,checkpoint44f_post
31    o added PTRACERS package
32      This allows an arbitrary number of passive tracers to be integrated
33      forward simultaneously with the dynamicaly model.
34      + Implemented so far:
35        - basic forward algorithm (time-stepping, advection, diffusion, convection)
36        - I/O and checkpointing
37        - GM/Redi  *but*  using the GM/Redi coefficient of Salt
38      + Not implemented so far:
39        - KPP
40        - OBCS
41      + No specific example supplied (yet) but global_ocean.90x40x15 has the
42        necessary data.ptracer file. Simply use -enable=ptracers and uncomment
43        line in data.pkg.
44      + This package is disabled by default since it increases storage.
45    
46    
47    o testscript: added -cleanup option
48    o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
49                 b) enable to filter 2D fields.
50    
51    checkpoint44e_pre,post
52    o re-wrote convective adjustment to use pre-calculated weights
53      Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
54      Adds:    model/src/convective_weights.F, convectively_mixtracer.F
55      Original calls to convect() still in place.
56    
57    chkpt44d_pre,post
58    o added missing EXCLUDE_MONITOR flags
59    o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
60      (incompatible typ in MIN/MAX expressions caused problems
61      on IBM SP3)
62    o in genmake added variable MAKEDEPEND
63      plus resetting for case SunOS
64    o added timer_stats.c routine for IBM SP3
65    o removed variables in dynamics
66    !!! I forgot to create tag chkpt44d_pre !!!
67    !!! But chkpt44d_pre = chkpt44c_post    !!!
68    
69    o real fresh water flux implemented with non-linear free-surface.
70    
71    chkpt44c_pre,post
72    o few fix (mask in shap_s2, EmPmR in external_field_load,
73      USE_NATURAL_BCS in solve_for_P);
74    o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
75    
76    checkpoint44b_pre/_post
77    o merge of relevant stuff from the ecco-branch:
78      - genmake: removed $S64 overwrite for case SunOS
79      - pkg/exf: update and corrections for field swapping and obcs
80      - pkg/ecco: parameter lists for the_model_main, the_main_loop
81                  harmonized between ECCO and MITgcm
82      - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
83                      updated checkpointing_lev... lists for obcs
84      - model/src: minor changes in forward_step, plot_field
85                   added directive for divided adjoint in the_main_loop
86      - pkg/mdsio: added mdsio_gl_slice
87    
88    o check parameters & config (chkpt44a_pre,post)
89    o OBC and NonLin_FrSurf.
90    
91    checkpoint44
92    o fix bug in mom_vi_del2uv
93    o select when filters are applied ; add options to zonal_filter (data.zonfilt)
94    o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
95    o update AIM experiments (NCEP input files)
96    o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
97    o added some stuff for AD
98    
99    checkpoint43
100    o added two new advection tests
101    o added global 4x4 degree ocean test
102    o added test of H&S94 with free surface on cube
103    o some final mods for gradient check, adjoint,...
104    
105    checkpoint42
106      Fixed AD-related problems:
107    o Store directives up-to-date with re-arranged Adams-Bashforth
108      (mainly thermodynamics.F)
109    o New store directives for multi-dim. advection schemes
110      * new CPP flag ALLOW_MULTI_DIM_ADVECTION
111      * new common block and key passkey
112      (mainly gad_advection.F)
113    o Modified store directives for split of dynamics/thermodynamics
114      for the case ALLOW_KPP
115    o Cleaned argument list for timestep_tracer.F
116    
117    checkpoint41
118    o re-formatted/added comments in prologues of key subroutines
119      to work with protex
120    
121    checkpoint40
122    o moved calc_gs, calc_gt and calc_tr1 back to model/src
123    o added FLT (floats) package from Arne along with demo. experiment
124    o re-arranged Adams-Bashforth scheme for tracers to allow easier
125      implementation of forward-in-time forcing terms
126    o more mods for non-linear free-surface including new variable
127    o modified multi-dim method to work on cube
128    o bug fix in KPP (from DM)
129    
130    checkpoint40pre9
131    o added DST advection schemes
132    o fix MPI bug on SGI's
133    o modifications for non-linear free-surface
134    o fixed conditionals for fixed flow/passive tracer only mode
135    o added tension/strain form of stress tensor
136    o changes to commenting of arguments for TAF/TAMC
137    o added/updated many matlab scripts
138    o added multi-dimensional advection method for tracers
139      
140    checkpoint40pre8
141    o new package rw/
142      Added method for dumping intermediate local arrays:
143      mdsio_writetile - same as mdsio_writefield except works from inside
144                        bi,bj loop
145      mdsio_writelocal - same as mdsio_writetile except works for local
146                         arrays
147      write_local_r? - higher-level wrapper for mdsio_writelocal
148      Controlled by diagFreq. Defaults to zero (ie. no dumps)
149      Example given at end of mom_vecinv.F that dumps some local arrays.
150    o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
151      control flux-form versus vector invariant code.
152      Switch is runtime flag vectorInvariantMomentum (defaults to false)
153      or genmake -DISABLE ...
154    o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
155      (additional storing is now needed for case vecinv;
156      currently nothing implemented to switch this storing off
157      in case fluxform is used since no CPP flag available).
158    
159    checkpoint40pre7
160    o bug fix in dynamics.F
161      calc_viscosity called before k=1,Nr loop.
162    o added some #ifdef's ALLOW_PASSIVE_TRACER
163    o cleaned initialisations in ctrl_map_ini
164      related to TAF
165    
166    checkpoint40pre6
167    o split dynamics into thermodynamics & dynamics
168    o corresponding split of calc_diffusivity into
169      calc_diffusivity, calc_viscosity
170      (kpp_calc_diff, kpp_calc_visc).
171    o Added diffkr, kapgm to control variables
172    o bug fix in gmredi_slope_limit for ldd97
173    
174    checkpoint40pre5
175    o proper initialization of Adams-Bashforth time stepping
176      + uses forward step for very first step of model (iter=0)
177    o re-generated *all* output since almost all output is modified by this
178      change (sorry but we've been putting this one off for about 2 years)
179      + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
180        *not* regenerated since they are already out of date and I don't
181        want to create the impression that they are suddenly working.
182    o removed KAP stuff for DEC's
183    o modified/added many .cvsignore files in */code and */input
184    o added new expt "solid-body.cs-32x32x1"
185      + this uses an alternative form of ini_curvilinear_grid.F which
186        is not necessarily any better than the current one...
187    
188    checkpoint40pre4
189    o added re-initialisations of utrans,vtrans,rtrans in
190      calc_common_factors which are crucial for TAF.
191    o extended iMin,jMin range for calc_common_factors,
192      calc_diffusivity
193    o added option ALLOW_PASSIVE_TRACER
194    o a few minor updates and fixes
195    
196    checkpoint40pre3
197    o created calc_gtr1.F for gad package
198    o split the_main_loop and re-introduced forward_step
199    o some recomputations of nIter0 for TAMC
200    
201    checkpoint40pre2
202    o Updated to latest branch of AJA, JMC
203    o Added gradient check package
204    o Added routines for passive tracer handling
205    o Added carbon sequestration sensitivity experiment
206    
207    checkpoint39
208     o Modifications and fixes to support TAMC
209       (mainly missing or wrong directives)
210     o Corrected common blocks when fooling TAMC to produce adjoint I/O
211       in addummy_in_stepping
212     o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
213     o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
214     o Included following packages:
215       cal: calendar
216       exf: external forcing
217       ecco: essential routines to control use of cal, exf
218             (NB: this is not the full ECCO environment)
219     o disabled some packages by default in genmake
220    
221    checkpoint38
222     o see notes_c37_adj.txt
223     o corrected wrong layer index in external_forcing_t
224     o replaced the_main_loop/forward_step by the_main_loop
225     o removed forceoutput from write_state
226       (replaced criteria for initial/final state)
227     o added runtime flag for pre-C35 pickups: usePickupBeforeC35
228    
229    checkpoint37
230     o mdsio.F routine split and packaged in pkg/mdsio
231       (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
232        used unless genmake -disable=mdsio)
233     o allow a more precise surface-geopotential gradient for the atmosphere
234       taking into account the change in space of Alpha (=1/rho) at the surface.
235     o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
236       (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
237     o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
238       Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
239       [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
240     o Time-Average diagnostics defined as a pseudo package "timeave".
241     o pickup files : old pickup (before c35) did not work with new code (c35
242       and after) unless activating 2 commented lines in initialise-varia.
243     o Non-Hydrostatic pickup file Pb fixed.
244     o bug with Rigid-lid version (since c35) fixed.  
245    
246    checkpoint36
247     o implement Crank-Nickelson barotropic time-stepping
248     o recover Time-Average diagnostics
249     o fix Pb in checkpoint (PR#19)
250     o AIM become a standard package ; clean unused CPP_kees
251    
252    checkpoint35
253     o subtantial rewrite of dynamics.f
254     o allows staggered time-stepping
255     o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
256     o added bottom drag (linear + quadratic)
257    
258    checkpoint34
259     o Modified exchange routines for correct reverse simulation.
260     o Added verification output to comply with bug fix in impldiff.F
261       as of c33 (exp2, natl_box).
262     o Corrected store directives in dynamics.F
263     o Corrected array boundaries in impldiff.F
264     o Corrected array dimensions in gmredi.
265       Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
266     o Added routine GLOBAL_SUM_INT to global_sum.F
267     o Added mdsio_gl.F for ECCO purposes.
268    
269    checkpoint33
270     o Fixed bug in lower BC in impldiff.F
271     o Fixed confusion about units of forcing arrays in FFIELDS.h
272       namely Fu,Fv,Qnet,Qsw,EmPmR:
273       - Removed verification/natl_box/code/external_fields_scale.F
274         (did not differ from that in model/src)
275       - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
276         (see FFIELDS.h for description)
277       - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
278         kpp_calc.F and kpp_transport_t.F
279       - Removed model/src/external_fields_scale.F and calls to it
280       - verification/natl_box uses flux data with "atmospheric" sign so
281         a special version of external_fields_load.F is used to
282         change the data as it's read in. This way, the arrays
283         have the right units and signs at all times tha a user could
284         possibly use them.
285     o Corrected genmake to delete a temporary file during configuration
286    
287    checkpoint32
288     o Scaling of forcing fields moved from external_forcing.F to
289       external_fields_scale.F, called directly after loading fields.
290     o Surface relaxation terms added to surface tendency fields in
291       extra subroutine.
292     o impldiff.F changed to avoid storing by TAMC of huge intermediate
293       fields.
294     o Changes in GMRedi to comply with packaging structure.
295     o Modifications and bug fixes in KPP package.
296     o Verification experiment for KPP added (verification/nat_box/)
297    
298    checkpoint31
299     o Packages interface brought in line with defined standard
300       -> new routines packages_...F
301       -> changes in initialise_fixed.F, initialise_varia.F
302       -> enables initialisation interface for ECCO package
303     o Rescaling of external forcing fields immediately after read
304       (removed from external_forcing.F)
305       -> new: surface_fields_scale.F
306       -> affects ini_foorcing.F, external_fields_load.F
307     o Computation of surface tendencies before tendency updates.
308       -> new: external_forcing_surf.F
309     o Change of variable names useGMRedi, useKPP, useECCO
310     o Further changes in dynamics.F, impldiff.F for TAMC
311     o Tested for experiments 0, 2, 4.
312       - not yet tested for GMRedi.
313       - not yet tested for KPP.
314    
315    checkpoint30
316     o Updates for OBCs
317     o New experiment for test OBCs (internal_wave)
318     o New output.txt in verification/exp4/results/
319     o Updates for KPP: calculation of viscosity corrected, new variables
320       kpp_dumpFreq and kpp_taveFreq
321     o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
322       and entry for T90 in genmake
323    
324    checkpoint29
325     o packaged KPP and GM/Redi
326    
327    checkpoint28
328     o Corrected initialization of hFacMin for difference vertical coordinates
329     o Modified calculation of partial cell thickness to more robust algorithm
330     o config_summary.F: replaced write_1D_... by write_0D_...
331       read_write.F: added subroutines write_0D_...
332     o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
333       included some initialisations required for TAMC.
334     o routine calc_isoslopes: modified sqrt computation to make it
335       differentiable for zero argument.
336     o routines dynamics, impldiff:
337       included store directives and tape key computations required for TAMC.
338     o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
339    
340    checkpoint27
341     o fixed calc_isoslopes() to so that cancellation of terms in tensor
342       formulation works properly with variable resolution.
343     o restructured the calling tree between the_model_main() and dynamics()
344     o split initialise() into initialise_fixed() and initialise_varia()
345     o introduced initialization file pSurfInitFile for free surface (cg2d_x)
346       in new routine ini_psurf()
347    
348    checkpoint26
349     o moved some #ifdef in optional routines to encompass everything
350       except the argument declarations. This was using up some memory.
351     o fixed macros like _ADT to work with both versions of Linux cpp
352     o cleaned up some unused and uninitialized variables
353       (helps when debugging with strict compile options)
354     o split up CPP_EEOPTIONS.h into options and macros
355       (macros are now in eesupp/inc/CPP_EEMACROS.h)
356     o patch for 2 processor JAM mode
357    
358    checkpoint25
359     o updates for OBCs and NH
360     o dramatically reduced memory usage
361     o added "JAM" routines for use on Artic network
362     o parameterization of convection by implicit vertical diffusion
363     o added a diagnostic of convective index
364     o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
365       (this is was partly for OBCs and NH but also in anticipation of
366        an explicit free-surface option)
367     o initial state input files for U and V
368    
369    checkpoint24
370     o Removed some spurious "REAL"s
371     o Updated KPP to latest version from JPL
372     o Added a COS(latitude) in horizontal viscosity
373    
374    checkpoint23
375     o Added del^4 diffusion for salt and temperature
376     o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
377    
378    checkpoint22
379     o Made many small changes: implicit none, format(i5), etc...
380     o Introduced KPP mixing scheme (compiles and runs but *not* tested)
381    
382    checkpoint21
383     o Introduced new I/O package that supports direct-access records (mdsio.F)
384     o Split-up mid-level I/O routines
385     o Updated input data for experiments 0,1,2,4 and 5
386     o Finally removed the genmake.* scripts (everyone seems happy with genmake)
387    
388    checkpoint20
389     o Tidied up open-boundaries some more
390     o Added non-hydrostatic code
391     o Fixed some input data
392     o Modified MPI start-up to work in "coupled" context.
393    
394    checkpoint19
395     o Tidied up directory structure for verification experiments.
396     o Added new code for open boundaries.
397     o Corrected advective terms near boundaries.
398     o Added CPP flag for "old UV" geometry and corrected spherical geometry.
399     o Implemented free-slip/no-slip BCs and del^4 dissipation.
400     o Split default parameters out of ini_parms.F into set_defaults.F.
401    
402    checkpoint18
403     o Further changes for optional code generation with
404       CPP - ugh!
405    
406    checkpoint17
407     o Beginning to incorporating modularity
408       for supporting atmos. and ocean configs.
409     o Small changes for TAMC complinace
410     o New ultra simple test case. Barotropic box
411       configuration "exp0".
412    
413    checkpoint16
414     o Minor changes to exchange routines to support
415       accumulation in reverse mode. Adjoint of an
416       assignment is an addition.
417     o Changes to support compilation by TAMC (LR(1)
418       syntax) and by g77 under Linux ( 72 character
419       limit ).
420    
421    checkpoint15
422     Rewrote exchange routines to allow
423     o General tile <-> tile connectivity.
424     o TAMC reverse mode flag ( is this really needed? )
425     o Variable width overlap and exchange region widths.
426     o Hooks for sharing data via DMA, Arctic, Memory Channel,
427       shmput/shmget, VIA, SYSV shmem and every other cool
428       communication method.
429    
430    checkpoint14
431     Consistent isomorphism chages made. These allow dynamical core
432     to support both pressure and meters as a vertical coordinate.
433    
434    checkpoint13
435     Release which corrects global_max problem and a couple
436     of KGM time-averaging diagnostic errors. Also contains
437     a double-gyre experiment setup as well as the baseline
438     4 degree global template. The double gyre template is
439     organised to allow it to be applied automatically to
440     the baseline configuration.
441    
442    branch-point-rdot
443     A few tidy-ups have been made bt the real point of this
444     check-point (excuse the pun) is to allow a branch to be
445     made for the purposes of adding the rDot alterations.
446     I don't want to commit the rDot to the main-trunk until
447     we've actually tested it...
448    
449    checkpoint12
450     Tidy up and added generic genmake script (formerly
451     configure script).
452     Released to testers.
453    
454    checkpoint11
455     Re-arranged initialise() and introduced ini_vertical_grid()
456     and ini_masks_etc().
457    
458  checkpoint10  checkpoint10
459   Introduced the configure script.   Introduced the configure script.
460   Separated out the diags package.   Separated out the diags package.

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