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revision 1.8 by adcroft, Wed Jul 1 22:49:29 1998 UTC revision 1.68 by jmc, Thu Mar 14 15:23:50 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 vertical grid option: allow to put the Interface at the middle between
7      2 cell-centers ; replace delZ in pkg/kpp by drF.
8    o GM Advective form: Tracers are advected using the residual transport (=
9      Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
10    
11    checkpoint44g_post
12    o fix surface correction term in multiDimAdvection (affects plume_on_slope
13      results) ; ifdef missing in thermodynamics.F
14    
15    checkpoint44f_pre,checkpoint44f_post
16    o added PTRACERS package
17      This allows an arbitrary number of passive tracers to be integrated
18      forward simultaneously with the dynamicaly model.
19      + Implemented so far:
20        - basic forward algorithm (time-stepping, advection, diffusion, convection)
21        - I/O and checkpointing
22        - GM/Redi  *but*  using the GM/Redi coefficient of Salt
23      + Not implemented so far:
24        - KPP
25        - OBCS
26      + No specific example supplied (yet) but global_ocean.90x40x15 has the
27        necessary data.ptracer file. Simply use -enable=ptracers and uncomment
28        line in data.pkg.
29      + This package is disabled by default since it increases storage.
30    
31    
32    o testscript: added -cleanup option
33    o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
34                 b) enable to filter 2D fields.
35    
36    checkpoint44e_pre,post
37    o re-wrote convective adjustment to use pre-calculated weights
38      Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
39      Adds:    model/src/convective_weights.F, convectively_mixtracer.F
40      Original calls to convect() still in place.
41    
42    chkpt44d_pre,post
43    o added missing EXCLUDE_MONITOR flags
44    o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
45      (incompatible typ in MIN/MAX expressions caused problems
46      on IBM SP3)
47    o in genmake added variable MAKEDEPEND
48      plus resetting for case SunOS
49    o added timer_stats.c routine for IBM SP3
50    o removed variables in dynamics
51    !!! I forgot to create tag chkpt44d_pre !!!
52    !!! But chkpt44d_pre = chkpt44c_post    !!!
53    
54    o real fresh water flux implemented with non-linear free-surface.
55    
56    chkpt44c_pre,post
57    o few fix (mask in shap_s2, EmPmR in external_field_load,
58      USE_NATURAL_BCS in solve_for_P);
59    o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
60    
61    checkpoint44b_pre/_post
62    o merge of relevant stuff from the ecco-branch:
63      - genmake: removed $S64 overwrite for case SunOS
64      - pkg/exf: update and corrections for field swapping and obcs
65      - pkg/ecco: parameter lists for the_model_main, the_main_loop
66                  harmonized between ECCO and MITgcm
67      - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
68                      updated checkpointing_lev... lists for obcs
69      - model/src: minor changes in forward_step, plot_field
70                   added directive for divided adjoint in the_main_loop
71      - pkg/mdsio: added mdsio_gl_slice
72    
73    o check parameters & config (chkpt44a_pre,post)
74    o OBC and NonLin_FrSurf.
75    
76    checkpoint44
77    o fix bug in mom_vi_del2uv
78    o select when filters are applied ; add options to zonal_filter (data.zonfilt)
79    o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
80    o update AIM experiments (NCEP input files)
81    o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
82    o added some stuff for AD
83    
84    checkpoint43
85    o added two new advection tests
86    o added global 4x4 degree ocean test
87    o added test of H&S94 with free surface on cube
88    o some final mods for gradient check, adjoint,...
89    
90    checkpoint42
91      Fixed AD-related problems:
92    o Store directives up-to-date with re-arranged Adams-Bashforth
93      (mainly thermodynamics.F)
94    o New store directives for multi-dim. advection schemes
95      * new CPP flag ALLOW_MULTI_DIM_ADVECTION
96      * new common block and key passkey
97      (mainly gad_advection.F)
98    o Modified store directives for split of dynamics/thermodynamics
99      for the case ALLOW_KPP
100    o Cleaned argument list for timestep_tracer.F
101    
102    checkpoint41
103    o re-formatted/added comments in prologues of key subroutines
104      to work with protex
105    
106    checkpoint40
107    o moved calc_gs, calc_gt and calc_tr1 back to model/src
108    o added FLT (floats) package from Arne along with demo. experiment
109    o re-arranged Adams-Bashforth scheme for tracers to allow easier
110      implementation of forward-in-time forcing terms
111    o more mods for non-linear free-surface including new variable
112    o modified multi-dim method to work on cube
113    o bug fix in KPP (from DM)
114    
115    checkpoint40pre9
116    o added DST advection schemes
117    o fix MPI bug on SGI's
118    o modifications for non-linear free-surface
119    o fixed conditionals for fixed flow/passive tracer only mode
120    o added tension/strain form of stress tensor
121    o changes to commenting of arguments for TAF/TAMC
122    o added/updated many matlab scripts
123    o added multi-dimensional advection method for tracers
124      
125    checkpoint40pre8
126    o new package rw/
127      Added method for dumping intermediate local arrays:
128      mdsio_writetile - same as mdsio_writefield except works from inside
129                        bi,bj loop
130      mdsio_writelocal - same as mdsio_writetile except works for local
131                         arrays
132      write_local_r? - higher-level wrapper for mdsio_writelocal
133      Controlled by diagFreq. Defaults to zero (ie. no dumps)
134      Example given at end of mom_vecinv.F that dumps some local arrays.
135    o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
136      control flux-form versus vector invariant code.
137      Switch is runtime flag vectorInvariantMomentum (defaults to false)
138      or genmake -DISABLE ...
139    o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
140      (additional storing is now needed for case vecinv;
141      currently nothing implemented to switch this storing off
142      in case fluxform is used since no CPP flag available).
143    
144    checkpoint40pre7
145    o bug fix in dynamics.F
146      calc_viscosity called before k=1,Nr loop.
147    o added some #ifdef's ALLOW_PASSIVE_TRACER
148    o cleaned initialisations in ctrl_map_ini
149      related to TAF
150    
151    checkpoint40pre6
152    o split dynamics into thermodynamics & dynamics
153    o corresponding split of calc_diffusivity into
154      calc_diffusivity, calc_viscosity
155      (kpp_calc_diff, kpp_calc_visc).
156    o Added diffkr, kapgm to control variables
157    o bug fix in gmredi_slope_limit for ldd97
158    
159    checkpoint40pre5
160    o proper initialization of Adams-Bashforth time stepping
161      + uses forward step for very first step of model (iter=0)
162    o re-generated *all* output since almost all output is modified by this
163      change (sorry but we've been putting this one off for about 2 years)
164      + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
165        *not* regenerated since they are already out of date and I don't
166        want to create the impression that they are suddenly working.
167    o removed KAP stuff for DEC's
168    o modified/added many .cvsignore files in */code and */input
169    o added new expt "solid-body.cs-32x32x1"
170      + this uses an alternative form of ini_curvilinear_grid.F which
171        is not necessarily any better than the current one...
172    
173    checkpoint40pre4
174    o added re-initialisations of utrans,vtrans,rtrans in
175      calc_common_factors which are crucial for TAF.
176    o extended iMin,jMin range for calc_common_factors,
177      calc_diffusivity
178    o added option ALLOW_PASSIVE_TRACER
179    o a few minor updates and fixes
180    
181    checkpoint40pre3
182    o created calc_gtr1.F for gad package
183    o split the_main_loop and re-introduced forward_step
184    o some recomputations of nIter0 for TAMC
185    
186    checkpoint40pre2
187    o Updated to latest branch of AJA, JMC
188    o Added gradient check package
189    o Added routines for passive tracer handling
190    o Added carbon sequestration sensitivity experiment
191    
192    checkpoint39
193     o Modifications and fixes to support TAMC
194       (mainly missing or wrong directives)
195     o Corrected common blocks when fooling TAMC to produce adjoint I/O
196       in addummy_in_stepping
197     o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
198     o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
199     o Included following packages:
200       cal: calendar
201       exf: external forcing
202       ecco: essential routines to control use of cal, exf
203             (NB: this is not the full ECCO environment)
204     o disabled some packages by default in genmake
205    
206    checkpoint38
207     o see notes_c37_adj.txt
208     o corrected wrong layer index in external_forcing_t
209     o replaced the_main_loop/forward_step by the_main_loop
210     o removed forceoutput from write_state
211       (replaced criteria for initial/final state)
212     o added runtime flag for pre-C35 pickups: usePickupBeforeC35
213    
214    checkpoint37
215     o mdsio.F routine split and packaged in pkg/mdsio
216       (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
217        used unless genmake -disable=mdsio)
218     o allow a more precise surface-geopotential gradient for the atmosphere
219       taking into account the change in space of Alpha (=1/rho) at the surface.
220     o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
221       (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
222     o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
223       Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
224       [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
225     o Time-Average diagnostics defined as a pseudo package "timeave".
226     o pickup files : old pickup (before c35) did not work with new code (c35
227       and after) unless activating 2 commented lines in initialise-varia.
228     o Non-Hydrostatic pickup file Pb fixed.
229     o bug with Rigid-lid version (since c35) fixed.  
230    
231    checkpoint36
232     o implement Crank-Nickelson barotropic time-stepping
233     o recover Time-Average diagnostics
234     o fix Pb in checkpoint (PR#19)
235     o AIM become a standard package ; clean unused CPP_kees
236    
237    checkpoint35
238     o subtantial rewrite of dynamics.f
239     o allows staggered time-stepping
240     o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
241     o added bottom drag (linear + quadratic)
242    
243    checkpoint34
244     o Modified exchange routines for correct reverse simulation.
245     o Added verification output to comply with bug fix in impldiff.F
246       as of c33 (exp2, natl_box).
247     o Corrected store directives in dynamics.F
248     o Corrected array boundaries in impldiff.F
249     o Corrected array dimensions in gmredi.
250       Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
251     o Added routine GLOBAL_SUM_INT to global_sum.F
252     o Added mdsio_gl.F for ECCO purposes.
253    
254    checkpoint33
255     o Fixed bug in lower BC in impldiff.F
256     o Fixed confusion about units of forcing arrays in FFIELDS.h
257       namely Fu,Fv,Qnet,Qsw,EmPmR:
258       - Removed verification/natl_box/code/external_fields_scale.F
259         (did not differ from that in model/src)
260       - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
261         (see FFIELDS.h for description)
262       - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
263         kpp_calc.F and kpp_transport_t.F
264       - Removed model/src/external_fields_scale.F and calls to it
265       - verification/natl_box uses flux data with "atmospheric" sign so
266         a special version of external_fields_load.F is used to
267         change the data as it's read in. This way, the arrays
268         have the right units and signs at all times tha a user could
269         possibly use them.
270     o Corrected genmake to delete a temporary file during configuration
271    
272    checkpoint32
273     o Scaling of forcing fields moved from external_forcing.F to
274       external_fields_scale.F, called directly after loading fields.
275     o Surface relaxation terms added to surface tendency fields in
276       extra subroutine.
277     o impldiff.F changed to avoid storing by TAMC of huge intermediate
278       fields.
279     o Changes in GMRedi to comply with packaging structure.
280     o Modifications and bug fixes in KPP package.
281     o Verification experiment for KPP added (verification/nat_box/)
282    
283    checkpoint31
284     o Packages interface brought in line with defined standard
285       -> new routines packages_...F
286       -> changes in initialise_fixed.F, initialise_varia.F
287       -> enables initialisation interface for ECCO package
288     o Rescaling of external forcing fields immediately after read
289       (removed from external_forcing.F)
290       -> new: surface_fields_scale.F
291       -> affects ini_foorcing.F, external_fields_load.F
292     o Computation of surface tendencies before tendency updates.
293       -> new: external_forcing_surf.F
294     o Change of variable names useGMRedi, useKPP, useECCO
295     o Further changes in dynamics.F, impldiff.F for TAMC
296     o Tested for experiments 0, 2, 4.
297       - not yet tested for GMRedi.
298       - not yet tested for KPP.
299    
300    checkpoint30
301     o Updates for OBCs
302     o New experiment for test OBCs (internal_wave)
303     o New output.txt in verification/exp4/results/
304     o Updates for KPP: calculation of viscosity corrected, new variables
305       kpp_dumpFreq and kpp_taveFreq
306     o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
307       and entry for T90 in genmake
308    
309    checkpoint29
310     o packaged KPP and GM/Redi
311    
312    checkpoint28
313     o Corrected initialization of hFacMin for difference vertical coordinates
314     o Modified calculation of partial cell thickness to more robust algorithm
315     o config_summary.F: replaced write_1D_... by write_0D_...
316       read_write.F: added subroutines write_0D_...
317     o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
318       included some initialisations required for TAMC.
319     o routine calc_isoslopes: modified sqrt computation to make it
320       differentiable for zero argument.
321     o routines dynamics, impldiff:
322       included store directives and tape key computations required for TAMC.
323     o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
324    
325    checkpoint27
326     o fixed calc_isoslopes() to so that cancellation of terms in tensor
327       formulation works properly with variable resolution.
328     o restructured the calling tree between the_model_main() and dynamics()
329     o split initialise() into initialise_fixed() and initialise_varia()
330     o introduced initialization file pSurfInitFile for free surface (cg2d_x)
331       in new routine ini_psurf()
332    
333    checkpoint26
334     o moved some #ifdef in optional routines to encompass everything
335       except the argument declarations. This was using up some memory.
336     o fixed macros like _ADT to work with both versions of Linux cpp
337     o cleaned up some unused and uninitialized variables
338       (helps when debugging with strict compile options)
339     o split up CPP_EEOPTIONS.h into options and macros
340       (macros are now in eesupp/inc/CPP_EEMACROS.h)
341     o patch for 2 processor JAM mode
342    
343    checkpoint25
344     o updates for OBCs and NH
345     o dramatically reduced memory usage
346     o added "JAM" routines for use on Artic network
347     o parameterization of convection by implicit vertical diffusion
348     o added a diagnostic of convective index
349     o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
350       (this is was partly for OBCs and NH but also in anticipation of
351        an explicit free-surface option)
352     o initial state input files for U and V
353    
354    checkpoint24
355     o Removed some spurious "REAL"s
356     o Updated KPP to latest version from JPL
357     o Added a COS(latitude) in horizontal viscosity
358    
359    checkpoint23
360     o Added del^4 diffusion for salt and temperature
361     o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
362    
363    checkpoint22
364     o Made many small changes: implicit none, format(i5), etc...
365     o Introduced KPP mixing scheme (compiles and runs but *not* tested)
366    
367    checkpoint21
368     o Introduced new I/O package that supports direct-access records (mdsio.F)
369     o Split-up mid-level I/O routines
370     o Updated input data for experiments 0,1,2,4 and 5
371     o Finally removed the genmake.* scripts (everyone seems happy with genmake)
372    
373    checkpoint20
374     o Tidied up open-boundaries some more
375     o Added non-hydrostatic code
376     o Fixed some input data
377     o Modified MPI start-up to work in "coupled" context.
378    
379    checkpoint19
380     o Tidied up directory structure for verification experiments.
381     o Added new code for open boundaries.
382     o Corrected advective terms near boundaries.
383     o Added CPP flag for "old UV" geometry and corrected spherical geometry.
384     o Implemented free-slip/no-slip BCs and del^4 dissipation.
385     o Split default parameters out of ini_parms.F into set_defaults.F.
386    
387    checkpoint18
388     o Further changes for optional code generation with
389       CPP - ugh!
390    
391    checkpoint17
392     o Beginning to incorporating modularity
393       for supporting atmos. and ocean configs.
394     o Small changes for TAMC complinace
395     o New ultra simple test case. Barotropic box
396       configuration "exp0".
397    
398    checkpoint16
399     o Minor changes to exchange routines to support
400       accumulation in reverse mode. Adjoint of an
401       assignment is an addition.
402     o Changes to support compilation by TAMC (LR(1)
403       syntax) and by g77 under Linux ( 72 character
404       limit ).
405    
406    checkpoint15
407     Rewrote exchange routines to allow
408     o General tile <-> tile connectivity.
409     o TAMC reverse mode flag ( is this really needed? )
410     o Variable width overlap and exchange region widths.
411     o Hooks for sharing data via DMA, Arctic, Memory Channel,
412       shmput/shmget, VIA, SYSV shmem and every other cool
413       communication method.
414    
415    checkpoint14
416     Consistent isomorphism chages made. These allow dynamical core
417     to support both pressure and meters as a vertical coordinate.
418    
419    checkpoint13
420     Release which corrects global_max problem and a couple
421     of KGM time-averaging diagnostic errors. Also contains
422     a double-gyre experiment setup as well as the baseline
423     4 degree global template. The double gyre template is
424     organised to allow it to be applied automatically to
425     the baseline configuration.
426    
427    branch-point-rdot
428     A few tidy-ups have been made bt the real point of this
429     check-point (excuse the pun) is to allow a branch to be
430     made for the purposes of adding the rDot alterations.
431     I don't want to commit the rDot to the main-trunk until
432     we've actually tested it...
433    
434    checkpoint12
435     Tidy up and added generic genmake script (formerly
436     configure script).
437     Released to testers.
438    
439    checkpoint11
440     Re-arranged initialise() and introduced ini_vertical_grid()
441     and ini_masks_etc().
442    
443  checkpoint10  checkpoint10
444   Introduced the configure script.   Introduced the configure script.
445   Separated out the diags package.   Separated out the diags package.

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