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revision 1.5.2.1 by cnh, Mon Jun 22 02:38:59 1998 UTC revision 1.66 by jmc, Tue Mar 5 15:36:06 2002 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    checkpoint44g_post
7    o fix surface correction term in multiDimAdvection (affects plume_on_slope
8      results) ; ifdef missing in thermodynamics.F
9    
10    checkpoint44f_pre,checkpoint44f_post
11    o added PTRACERS package
12      This allows an arbitrary number of passive tracers to be integrated
13      forward simultaneously with the dynamicaly model.
14      + Implemented so far:
15        - basic forward algorithm (time-stepping, advection, diffusion, convection)
16        - I/O and checkpointing
17        - GM/Redi  *but*  using the GM/Redi coefficient of Salt
18      + Not implemented so far:
19        - KPP
20        - OBCS
21      + No specific example supplied (yet) but global_ocean.90x40x15 has the
22        necessary data.ptracer file. Simply use -enable=ptracers and uncomment
23        line in data.pkg.
24      + This package is disabled by default since it increases storage.
25    
26    
27    o testscript: added -cleanup option
28    o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
29                 b) enable to filter 2D fields.
30    
31    checkpoint44e_pre,post
32    o re-wrote convective adjustment to use pre-calculated weights
33      Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
34      Adds:    model/src/convective_weights.F, convectively_mixtracer.F
35      Original calls to convect() still in place.
36    
37    chkpt44d_pre,post
38    o added missing EXCLUDE_MONITOR flags
39    o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
40      (incompatible typ in MIN/MAX expressions caused problems
41      on IBM SP3)
42    o in genmake added variable MAKEDEPEND
43      plus resetting for case SunOS
44    o added timer_stats.c routine for IBM SP3
45    o removed variables in dynamics
46    !!! I forgot to create tag chkpt44d_pre !!!
47    !!! But chkpt44d_pre = chkpt44c_post    !!!
48    
49    o real fresh water flux implemented with non-linear free-surface.
50    
51    chkpt44c_pre,post
52    o few fix (mask in shap_s2, EmPmR in external_field_load,
53      USE_NATURAL_BCS in solve_for_P);
54    o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
55    
56    checkpoint44b_pre/_post
57    o merge of relevant stuff from the ecco-branch:
58      - genmake: removed $S64 overwrite for case SunOS
59      - pkg/exf: update and corrections for field swapping and obcs
60      - pkg/ecco: parameter lists for the_model_main, the_main_loop
61                  harmonized between ECCO and MITgcm
62      - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
63                      updated checkpointing_lev... lists for obcs
64      - model/src: minor changes in forward_step, plot_field
65                   added directive for divided adjoint in the_main_loop
66      - pkg/mdsio: added mdsio_gl_slice
67    
68    o check parameters & config (chkpt44a_pre,post)
69    o OBC and NonLin_FrSurf.
70    
71    checkpoint44
72    o fix bug in mom_vi_del2uv
73    o select when filters are applied ; add options to zonal_filter (data.zonfilt)
74    o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
75    o update AIM experiments (NCEP input files)
76    o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
77    o added some stuff for AD
78    
79    checkpoint43
80    o added two new advection tests
81    o added global 4x4 degree ocean test
82    o added test of H&S94 with free surface on cube
83    o some final mods for gradient check, adjoint,...
84    
85    checkpoint42
86      Fixed AD-related problems:
87    o Store directives up-to-date with re-arranged Adams-Bashforth
88      (mainly thermodynamics.F)
89    o New store directives for multi-dim. advection schemes
90      * new CPP flag ALLOW_MULTI_DIM_ADVECTION
91      * new common block and key passkey
92      (mainly gad_advection.F)
93    o Modified store directives for split of dynamics/thermodynamics
94      for the case ALLOW_KPP
95    o Cleaned argument list for timestep_tracer.F
96    
97    checkpoint41
98    o re-formatted/added comments in prologues of key subroutines
99      to work with protex
100    
101    checkpoint40
102    o moved calc_gs, calc_gt and calc_tr1 back to model/src
103    o added FLT (floats) package from Arne along with demo. experiment
104    o re-arranged Adams-Bashforth scheme for tracers to allow easier
105      implementation of forward-in-time forcing terms
106    o more mods for non-linear free-surface including new variable
107    o modified multi-dim method to work on cube
108    o bug fix in KPP (from DM)
109    
110    checkpoint40pre9
111    o added DST advection schemes
112    o fix MPI bug on SGI's
113    o modifications for non-linear free-surface
114    o fixed conditionals for fixed flow/passive tracer only mode
115    o added tension/strain form of stress tensor
116    o changes to commenting of arguments for TAF/TAMC
117    o added/updated many matlab scripts
118    o added multi-dimensional advection method for tracers
119      
120    checkpoint40pre8
121    o new package rw/
122      Added method for dumping intermediate local arrays:
123      mdsio_writetile - same as mdsio_writefield except works from inside
124                        bi,bj loop
125      mdsio_writelocal - same as mdsio_writetile except works for local
126                         arrays
127      write_local_r? - higher-level wrapper for mdsio_writelocal
128      Controlled by diagFreq. Defaults to zero (ie. no dumps)
129      Example given at end of mom_vecinv.F that dumps some local arrays.
130    o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
131      control flux-form versus vector invariant code.
132      Switch is runtime flag vectorInvariantMomentum (defaults to false)
133      or genmake -DISABLE ...
134    o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
135      (additional storing is now needed for case vecinv;
136      currently nothing implemented to switch this storing off
137      in case fluxform is used since no CPP flag available).
138    
139    checkpoint40pre7
140    o bug fix in dynamics.F
141      calc_viscosity called before k=1,Nr loop.
142    o added some #ifdef's ALLOW_PASSIVE_TRACER
143    o cleaned initialisations in ctrl_map_ini
144      related to TAF
145    
146    checkpoint40pre6
147    o split dynamics into thermodynamics & dynamics
148    o corresponding split of calc_diffusivity into
149      calc_diffusivity, calc_viscosity
150      (kpp_calc_diff, kpp_calc_visc).
151    o Added diffkr, kapgm to control variables
152    o bug fix in gmredi_slope_limit for ldd97
153    
154    checkpoint40pre5
155    o proper initialization of Adams-Bashforth time stepping
156      + uses forward step for very first step of model (iter=0)
157    o re-generated *all* output since almost all output is modified by this
158      change (sorry but we've been putting this one off for about 2 years)
159      + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
160        *not* regenerated since they are already out of date and I don't
161        want to create the impression that they are suddenly working.
162    o removed KAP stuff for DEC's
163    o modified/added many .cvsignore files in */code and */input
164    o added new expt "solid-body.cs-32x32x1"
165      + this uses an alternative form of ini_curvilinear_grid.F which
166        is not necessarily any better than the current one...
167    
168    checkpoint40pre4
169    o added re-initialisations of utrans,vtrans,rtrans in
170      calc_common_factors which are crucial for TAF.
171    o extended iMin,jMin range for calc_common_factors,
172      calc_diffusivity
173    o added option ALLOW_PASSIVE_TRACER
174    o a few minor updates and fixes
175    
176    checkpoint40pre3
177    o created calc_gtr1.F for gad package
178    o split the_main_loop and re-introduced forward_step
179    o some recomputations of nIter0 for TAMC
180    
181    checkpoint40pre2
182    o Updated to latest branch of AJA, JMC
183    o Added gradient check package
184    o Added routines for passive tracer handling
185    o Added carbon sequestration sensitivity experiment
186    
187    checkpoint39
188     o Modifications and fixes to support TAMC
189       (mainly missing or wrong directives)
190     o Corrected common blocks when fooling TAMC to produce adjoint I/O
191       in addummy_in_stepping
192     o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
193     o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
194     o Included following packages:
195       cal: calendar
196       exf: external forcing
197       ecco: essential routines to control use of cal, exf
198             (NB: this is not the full ECCO environment)
199     o disabled some packages by default in genmake
200    
201    checkpoint38
202     o see notes_c37_adj.txt
203     o corrected wrong layer index in external_forcing_t
204     o replaced the_main_loop/forward_step by the_main_loop
205     o removed forceoutput from write_state
206       (replaced criteria for initial/final state)
207     o added runtime flag for pre-C35 pickups: usePickupBeforeC35
208    
209    checkpoint37
210     o mdsio.F routine split and packaged in pkg/mdsio
211       (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
212        used unless genmake -disable=mdsio)
213     o allow a more precise surface-geopotential gradient for the atmosphere
214       taking into account the change in space of Alpha (=1/rho) at the surface.
215     o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
216       (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
217     o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
218       Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
219       [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
220     o Time-Average diagnostics defined as a pseudo package "timeave".
221     o pickup files : old pickup (before c35) did not work with new code (c35
222       and after) unless activating 2 commented lines in initialise-varia.
223     o Non-Hydrostatic pickup file Pb fixed.
224     o bug with Rigid-lid version (since c35) fixed.  
225    
226    checkpoint36
227     o implement Crank-Nickelson barotropic time-stepping
228     o recover Time-Average diagnostics
229     o fix Pb in checkpoint (PR#19)
230     o AIM become a standard package ; clean unused CPP_kees
231    
232    checkpoint35
233     o subtantial rewrite of dynamics.f
234     o allows staggered time-stepping
235     o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
236     o added bottom drag (linear + quadratic)
237    
238    checkpoint34
239     o Modified exchange routines for correct reverse simulation.
240     o Added verification output to comply with bug fix in impldiff.F
241       as of c33 (exp2, natl_box).
242     o Corrected store directives in dynamics.F
243     o Corrected array boundaries in impldiff.F
244     o Corrected array dimensions in gmredi.
245       Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
246     o Added routine GLOBAL_SUM_INT to global_sum.F
247     o Added mdsio_gl.F for ECCO purposes.
248    
249    checkpoint33
250     o Fixed bug in lower BC in impldiff.F
251     o Fixed confusion about units of forcing arrays in FFIELDS.h
252       namely Fu,Fv,Qnet,Qsw,EmPmR:
253       - Removed verification/natl_box/code/external_fields_scale.F
254         (did not differ from that in model/src)
255       - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
256         (see FFIELDS.h for description)
257       - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
258         kpp_calc.F and kpp_transport_t.F
259       - Removed model/src/external_fields_scale.F and calls to it
260       - verification/natl_box uses flux data with "atmospheric" sign so
261         a special version of external_fields_load.F is used to
262         change the data as it's read in. This way, the arrays
263         have the right units and signs at all times tha a user could
264         possibly use them.
265     o Corrected genmake to delete a temporary file during configuration
266    
267    checkpoint32
268     o Scaling of forcing fields moved from external_forcing.F to
269       external_fields_scale.F, called directly after loading fields.
270     o Surface relaxation terms added to surface tendency fields in
271       extra subroutine.
272     o impldiff.F changed to avoid storing by TAMC of huge intermediate
273       fields.
274     o Changes in GMRedi to comply with packaging structure.
275     o Modifications and bug fixes in KPP package.
276     o Verification experiment for KPP added (verification/nat_box/)
277    
278    checkpoint31
279     o Packages interface brought in line with defined standard
280       -> new routines packages_...F
281       -> changes in initialise_fixed.F, initialise_varia.F
282       -> enables initialisation interface for ECCO package
283     o Rescaling of external forcing fields immediately after read
284       (removed from external_forcing.F)
285       -> new: surface_fields_scale.F
286       -> affects ini_foorcing.F, external_fields_load.F
287     o Computation of surface tendencies before tendency updates.
288       -> new: external_forcing_surf.F
289     o Change of variable names useGMRedi, useKPP, useECCO
290     o Further changes in dynamics.F, impldiff.F for TAMC
291     o Tested for experiments 0, 2, 4.
292       - not yet tested for GMRedi.
293       - not yet tested for KPP.
294    
295    checkpoint30
296     o Updates for OBCs
297     o New experiment for test OBCs (internal_wave)
298     o New output.txt in verification/exp4/results/
299     o Updates for KPP: calculation of viscosity corrected, new variables
300       kpp_dumpFreq and kpp_taveFreq
301     o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
302       and entry for T90 in genmake
303    
304    checkpoint29
305     o packaged KPP and GM/Redi
306    
307    checkpoint28
308     o Corrected initialization of hFacMin for difference vertical coordinates
309     o Modified calculation of partial cell thickness to more robust algorithm
310     o config_summary.F: replaced write_1D_... by write_0D_...
311       read_write.F: added subroutines write_0D_...
312     o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
313       included some initialisations required for TAMC.
314     o routine calc_isoslopes: modified sqrt computation to make it
315       differentiable for zero argument.
316     o routines dynamics, impldiff:
317       included store directives and tape key computations required for TAMC.
318     o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
319    
320    checkpoint27
321     o fixed calc_isoslopes() to so that cancellation of terms in tensor
322       formulation works properly with variable resolution.
323     o restructured the calling tree between the_model_main() and dynamics()
324     o split initialise() into initialise_fixed() and initialise_varia()
325     o introduced initialization file pSurfInitFile for free surface (cg2d_x)
326       in new routine ini_psurf()
327    
328    checkpoint26
329     o moved some #ifdef in optional routines to encompass everything
330       except the argument declarations. This was using up some memory.
331     o fixed macros like _ADT to work with both versions of Linux cpp
332     o cleaned up some unused and uninitialized variables
333       (helps when debugging with strict compile options)
334     o split up CPP_EEOPTIONS.h into options and macros
335       (macros are now in eesupp/inc/CPP_EEMACROS.h)
336     o patch for 2 processor JAM mode
337    
338    checkpoint25
339     o updates for OBCs and NH
340     o dramatically reduced memory usage
341     o added "JAM" routines for use on Artic network
342     o parameterization of convection by implicit vertical diffusion
343     o added a diagnostic of convective index
344     o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
345       (this is was partly for OBCs and NH but also in anticipation of
346        an explicit free-surface option)
347     o initial state input files for U and V
348    
349    checkpoint24
350     o Removed some spurious "REAL"s
351     o Updated KPP to latest version from JPL
352     o Added a COS(latitude) in horizontal viscosity
353    
354    checkpoint23
355     o Added del^4 diffusion for salt and temperature
356     o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
357    
358    checkpoint22
359     o Made many small changes: implicit none, format(i5), etc...
360     o Introduced KPP mixing scheme (compiles and runs but *not* tested)
361    
362    checkpoint21
363     o Introduced new I/O package that supports direct-access records (mdsio.F)
364     o Split-up mid-level I/O routines
365     o Updated input data for experiments 0,1,2,4 and 5
366     o Finally removed the genmake.* scripts (everyone seems happy with genmake)
367    
368    checkpoint20
369     o Tidied up open-boundaries some more
370     o Added non-hydrostatic code
371     o Fixed some input data
372     o Modified MPI start-up to work in "coupled" context.
373    
374    checkpoint19
375     o Tidied up directory structure for verification experiments.
376     o Added new code for open boundaries.
377     o Corrected advective terms near boundaries.
378     o Added CPP flag for "old UV" geometry and corrected spherical geometry.
379     o Implemented free-slip/no-slip BCs and del^4 dissipation.
380     o Split default parameters out of ini_parms.F into set_defaults.F.
381    
382    checkpoint18
383     o Further changes for optional code generation with
384       CPP - ugh!
385    
386    checkpoint17
387     o Beginning to incorporating modularity
388       for supporting atmos. and ocean configs.
389     o Small changes for TAMC complinace
390     o New ultra simple test case. Barotropic box
391       configuration "exp0".
392    
393    checkpoint16
394     o Minor changes to exchange routines to support
395       accumulation in reverse mode. Adjoint of an
396       assignment is an addition.
397     o Changes to support compilation by TAMC (LR(1)
398       syntax) and by g77 under Linux ( 72 character
399       limit ).
400    
401    checkpoint15
402     Rewrote exchange routines to allow
403     o General tile <-> tile connectivity.
404     o TAMC reverse mode flag ( is this really needed? )
405     o Variable width overlap and exchange region widths.
406     o Hooks for sharing data via DMA, Arctic, Memory Channel,
407       shmput/shmget, VIA, SYSV shmem and every other cool
408       communication method.
409    
410    checkpoint14
411     Consistent isomorphism chages made. These allow dynamical core
412     to support both pressure and meters as a vertical coordinate.
413    
414    checkpoint13
415     Release which corrects global_max problem and a couple
416     of KGM time-averaging diagnostic errors. Also contains
417     a double-gyre experiment setup as well as the baseline
418     4 degree global template. The double gyre template is
419     organised to allow it to be applied automatically to
420     the baseline configuration.
421    
422    branch-point-rdot
423     A few tidy-ups have been made bt the real point of this
424     check-point (excuse the pun) is to allow a branch to be
425     made for the purposes of adding the rDot alterations.
426     I don't want to commit the rDot to the main-trunk until
427     we've actually tested it...
428    
429    checkpoint12
430     Tidy up and added generic genmake script (formerly
431     configure script).
432     Released to testers.
433    
434    checkpoint11
435     Re-arranged initialise() and introduced ini_vertical_grid()
436     and ini_masks_etc().
437    
438    checkpoint10
439     Introduced the configure script.
440     Separated out the diags package.
441     Added template for writing time-averages of tile/intermediate quantities.
442     Updated SIZE.h in exp2 and made the data big-endian.
443    
444    checkpoint9
445     MPI fix. Filename changes (meta/data). salbin*y stuff.
446     General tidy-up.
447     SST.bin SSS.bin added to verification/exp2
448    
449    checkpoint8
450     Inludes time-dependant forcing and time-averaging.
451     Works at 4x4 and 2.8125x2.8125 global
452    
453  checkpoint7-4degree-ref  checkpoint7-4degree-ref
454   Branch from checkpoint7. Released for application to   Branch from checkpoint7. Released for application to
455   global modeling and general modeling - process studies, regional   global modeling and general modeling - process studies, regional

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