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revision 1.1 by cnh, Tue May 26 14:38:05 1998 UTC revision 1.67 by jmc, Wed Mar 6 02:14:02 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    o GM Advective form: Tracers are advected using the residual transport (=
7      Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
8    
9    checkpoint44g_post
10    o fix surface correction term in multiDimAdvection (affects plume_on_slope
11      results) ; ifdef missing in thermodynamics.F
12    
13    checkpoint44f_pre,checkpoint44f_post
14    o added PTRACERS package
15      This allows an arbitrary number of passive tracers to be integrated
16      forward simultaneously with the dynamicaly model.
17      + Implemented so far:
18        - basic forward algorithm (time-stepping, advection, diffusion, convection)
19        - I/O and checkpointing
20        - GM/Redi  *but*  using the GM/Redi coefficient of Salt
21      + Not implemented so far:
22        - KPP
23        - OBCS
24      + No specific example supplied (yet) but global_ocean.90x40x15 has the
25        necessary data.ptracer file. Simply use -enable=ptracers and uncomment
26        line in data.pkg.
27      + This package is disabled by default since it increases storage.
28    
29    
30    o testscript: added -cleanup option
31    o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
32                 b) enable to filter 2D fields.
33    
34    checkpoint44e_pre,post
35    o re-wrote convective adjustment to use pre-calculated weights
36      Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
37      Adds:    model/src/convective_weights.F, convectively_mixtracer.F
38      Original calls to convect() still in place.
39    
40    chkpt44d_pre,post
41    o added missing EXCLUDE_MONITOR flags
42    o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
43      (incompatible typ in MIN/MAX expressions caused problems
44      on IBM SP3)
45    o in genmake added variable MAKEDEPEND
46      plus resetting for case SunOS
47    o added timer_stats.c routine for IBM SP3
48    o removed variables in dynamics
49    !!! I forgot to create tag chkpt44d_pre !!!
50    !!! But chkpt44d_pre = chkpt44c_post    !!!
51    
52    o real fresh water flux implemented with non-linear free-surface.
53    
54    chkpt44c_pre,post
55    o few fix (mask in shap_s2, EmPmR in external_field_load,
56      USE_NATURAL_BCS in solve_for_P);
57    o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
58    
59    checkpoint44b_pre/_post
60    o merge of relevant stuff from the ecco-branch:
61      - genmake: removed $S64 overwrite for case SunOS
62      - pkg/exf: update and corrections for field swapping and obcs
63      - pkg/ecco: parameter lists for the_model_main, the_main_loop
64                  harmonized between ECCO and MITgcm
65      - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
66                      updated checkpointing_lev... lists for obcs
67      - model/src: minor changes in forward_step, plot_field
68                   added directive for divided adjoint in the_main_loop
69      - pkg/mdsio: added mdsio_gl_slice
70    
71    o check parameters & config (chkpt44a_pre,post)
72    o OBC and NonLin_FrSurf.
73    
74    checkpoint44
75    o fix bug in mom_vi_del2uv
76    o select when filters are applied ; add options to zonal_filter (data.zonfilt)
77    o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
78    o update AIM experiments (NCEP input files)
79    o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
80    o added some stuff for AD
81    
82    checkpoint43
83    o added two new advection tests
84    o added global 4x4 degree ocean test
85    o added test of H&S94 with free surface on cube
86    o some final mods for gradient check, adjoint,...
87    
88    checkpoint42
89      Fixed AD-related problems:
90    o Store directives up-to-date with re-arranged Adams-Bashforth
91      (mainly thermodynamics.F)
92    o New store directives for multi-dim. advection schemes
93      * new CPP flag ALLOW_MULTI_DIM_ADVECTION
94      * new common block and key passkey
95      (mainly gad_advection.F)
96    o Modified store directives for split of dynamics/thermodynamics
97      for the case ALLOW_KPP
98    o Cleaned argument list for timestep_tracer.F
99    
100    checkpoint41
101    o re-formatted/added comments in prologues of key subroutines
102      to work with protex
103    
104    checkpoint40
105    o moved calc_gs, calc_gt and calc_tr1 back to model/src
106    o added FLT (floats) package from Arne along with demo. experiment
107    o re-arranged Adams-Bashforth scheme for tracers to allow easier
108      implementation of forward-in-time forcing terms
109    o more mods for non-linear free-surface including new variable
110    o modified multi-dim method to work on cube
111    o bug fix in KPP (from DM)
112    
113    checkpoint40pre9
114    o added DST advection schemes
115    o fix MPI bug on SGI's
116    o modifications for non-linear free-surface
117    o fixed conditionals for fixed flow/passive tracer only mode
118    o added tension/strain form of stress tensor
119    o changes to commenting of arguments for TAF/TAMC
120    o added/updated many matlab scripts
121    o added multi-dimensional advection method for tracers
122      
123    checkpoint40pre8
124    o new package rw/
125      Added method for dumping intermediate local arrays:
126      mdsio_writetile - same as mdsio_writefield except works from inside
127                        bi,bj loop
128      mdsio_writelocal - same as mdsio_writetile except works for local
129                         arrays
130      write_local_r? - higher-level wrapper for mdsio_writelocal
131      Controlled by diagFreq. Defaults to zero (ie. no dumps)
132      Example given at end of mom_vecinv.F that dumps some local arrays.
133    o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
134      control flux-form versus vector invariant code.
135      Switch is runtime flag vectorInvariantMomentum (defaults to false)
136      or genmake -DISABLE ...
137    o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
138      (additional storing is now needed for case vecinv;
139      currently nothing implemented to switch this storing off
140      in case fluxform is used since no CPP flag available).
141    
142    checkpoint40pre7
143    o bug fix in dynamics.F
144      calc_viscosity called before k=1,Nr loop.
145    o added some #ifdef's ALLOW_PASSIVE_TRACER
146    o cleaned initialisations in ctrl_map_ini
147      related to TAF
148    
149    checkpoint40pre6
150    o split dynamics into thermodynamics & dynamics
151    o corresponding split of calc_diffusivity into
152      calc_diffusivity, calc_viscosity
153      (kpp_calc_diff, kpp_calc_visc).
154    o Added diffkr, kapgm to control variables
155    o bug fix in gmredi_slope_limit for ldd97
156    
157    checkpoint40pre5
158    o proper initialization of Adams-Bashforth time stepping
159      + uses forward step for very first step of model (iter=0)
160    o re-generated *all* output since almost all output is modified by this
161      change (sorry but we've been putting this one off for about 2 years)
162      + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
163        *not* regenerated since they are already out of date and I don't
164        want to create the impression that they are suddenly working.
165    o removed KAP stuff for DEC's
166    o modified/added many .cvsignore files in */code and */input
167    o added new expt "solid-body.cs-32x32x1"
168      + this uses an alternative form of ini_curvilinear_grid.F which
169        is not necessarily any better than the current one...
170    
171    checkpoint40pre4
172    o added re-initialisations of utrans,vtrans,rtrans in
173      calc_common_factors which are crucial for TAF.
174    o extended iMin,jMin range for calc_common_factors,
175      calc_diffusivity
176    o added option ALLOW_PASSIVE_TRACER
177    o a few minor updates and fixes
178    
179    checkpoint40pre3
180    o created calc_gtr1.F for gad package
181    o split the_main_loop and re-introduced forward_step
182    o some recomputations of nIter0 for TAMC
183    
184    checkpoint40pre2
185    o Updated to latest branch of AJA, JMC
186    o Added gradient check package
187    o Added routines for passive tracer handling
188    o Added carbon sequestration sensitivity experiment
189    
190    checkpoint39
191     o Modifications and fixes to support TAMC
192       (mainly missing or wrong directives)
193     o Corrected common blocks when fooling TAMC to produce adjoint I/O
194       in addummy_in_stepping
195     o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
196     o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
197     o Included following packages:
198       cal: calendar
199       exf: external forcing
200       ecco: essential routines to control use of cal, exf
201             (NB: this is not the full ECCO environment)
202     o disabled some packages by default in genmake
203    
204    checkpoint38
205     o see notes_c37_adj.txt
206     o corrected wrong layer index in external_forcing_t
207     o replaced the_main_loop/forward_step by the_main_loop
208     o removed forceoutput from write_state
209       (replaced criteria for initial/final state)
210     o added runtime flag for pre-C35 pickups: usePickupBeforeC35
211    
212    checkpoint37
213     o mdsio.F routine split and packaged in pkg/mdsio
214       (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
215        used unless genmake -disable=mdsio)
216     o allow a more precise surface-geopotential gradient for the atmosphere
217       taking into account the change in space of Alpha (=1/rho) at the surface.
218     o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
219       (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
220     o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
221       Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
222       [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
223     o Time-Average diagnostics defined as a pseudo package "timeave".
224     o pickup files : old pickup (before c35) did not work with new code (c35
225       and after) unless activating 2 commented lines in initialise-varia.
226     o Non-Hydrostatic pickup file Pb fixed.
227     o bug with Rigid-lid version (since c35) fixed.  
228    
229    checkpoint36
230     o implement Crank-Nickelson barotropic time-stepping
231     o recover Time-Average diagnostics
232     o fix Pb in checkpoint (PR#19)
233     o AIM become a standard package ; clean unused CPP_kees
234    
235    checkpoint35
236     o subtantial rewrite of dynamics.f
237     o allows staggered time-stepping
238     o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
239     o added bottom drag (linear + quadratic)
240    
241    checkpoint34
242     o Modified exchange routines for correct reverse simulation.
243     o Added verification output to comply with bug fix in impldiff.F
244       as of c33 (exp2, natl_box).
245     o Corrected store directives in dynamics.F
246     o Corrected array boundaries in impldiff.F
247     o Corrected array dimensions in gmredi.
248       Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
249     o Added routine GLOBAL_SUM_INT to global_sum.F
250     o Added mdsio_gl.F for ECCO purposes.
251    
252    checkpoint33
253     o Fixed bug in lower BC in impldiff.F
254     o Fixed confusion about units of forcing arrays in FFIELDS.h
255       namely Fu,Fv,Qnet,Qsw,EmPmR:
256       - Removed verification/natl_box/code/external_fields_scale.F
257         (did not differ from that in model/src)
258       - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
259         (see FFIELDS.h for description)
260       - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
261         kpp_calc.F and kpp_transport_t.F
262       - Removed model/src/external_fields_scale.F and calls to it
263       - verification/natl_box uses flux data with "atmospheric" sign so
264         a special version of external_fields_load.F is used to
265         change the data as it's read in. This way, the arrays
266         have the right units and signs at all times tha a user could
267         possibly use them.
268     o Corrected genmake to delete a temporary file during configuration
269    
270    checkpoint32
271     o Scaling of forcing fields moved from external_forcing.F to
272       external_fields_scale.F, called directly after loading fields.
273     o Surface relaxation terms added to surface tendency fields in
274       extra subroutine.
275     o impldiff.F changed to avoid storing by TAMC of huge intermediate
276       fields.
277     o Changes in GMRedi to comply with packaging structure.
278     o Modifications and bug fixes in KPP package.
279     o Verification experiment for KPP added (verification/nat_box/)
280    
281    checkpoint31
282     o Packages interface brought in line with defined standard
283       -> new routines packages_...F
284       -> changes in initialise_fixed.F, initialise_varia.F
285       -> enables initialisation interface for ECCO package
286     o Rescaling of external forcing fields immediately after read
287       (removed from external_forcing.F)
288       -> new: surface_fields_scale.F
289       -> affects ini_foorcing.F, external_fields_load.F
290     o Computation of surface tendencies before tendency updates.
291       -> new: external_forcing_surf.F
292     o Change of variable names useGMRedi, useKPP, useECCO
293     o Further changes in dynamics.F, impldiff.F for TAMC
294     o Tested for experiments 0, 2, 4.
295       - not yet tested for GMRedi.
296       - not yet tested for KPP.
297    
298    checkpoint30
299     o Updates for OBCs
300     o New experiment for test OBCs (internal_wave)
301     o New output.txt in verification/exp4/results/
302     o Updates for KPP: calculation of viscosity corrected, new variables
303       kpp_dumpFreq and kpp_taveFreq
304     o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
305       and entry for T90 in genmake
306    
307    checkpoint29
308     o packaged KPP and GM/Redi
309    
310    checkpoint28
311     o Corrected initialization of hFacMin for difference vertical coordinates
312     o Modified calculation of partial cell thickness to more robust algorithm
313     o config_summary.F: replaced write_1D_... by write_0D_...
314       read_write.F: added subroutines write_0D_...
315     o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
316       included some initialisations required for TAMC.
317     o routine calc_isoslopes: modified sqrt computation to make it
318       differentiable for zero argument.
319     o routines dynamics, impldiff:
320       included store directives and tape key computations required for TAMC.
321     o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
322    
323    checkpoint27
324     o fixed calc_isoslopes() to so that cancellation of terms in tensor
325       formulation works properly with variable resolution.
326     o restructured the calling tree between the_model_main() and dynamics()
327     o split initialise() into initialise_fixed() and initialise_varia()
328     o introduced initialization file pSurfInitFile for free surface (cg2d_x)
329       in new routine ini_psurf()
330    
331    checkpoint26
332     o moved some #ifdef in optional routines to encompass everything
333       except the argument declarations. This was using up some memory.
334     o fixed macros like _ADT to work with both versions of Linux cpp
335     o cleaned up some unused and uninitialized variables
336       (helps when debugging with strict compile options)
337     o split up CPP_EEOPTIONS.h into options and macros
338       (macros are now in eesupp/inc/CPP_EEMACROS.h)
339     o patch for 2 processor JAM mode
340    
341    checkpoint25
342     o updates for OBCs and NH
343     o dramatically reduced memory usage
344     o added "JAM" routines for use on Artic network
345     o parameterization of convection by implicit vertical diffusion
346     o added a diagnostic of convective index
347     o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
348       (this is was partly for OBCs and NH but also in anticipation of
349        an explicit free-surface option)
350     o initial state input files for U and V
351    
352    checkpoint24
353     o Removed some spurious "REAL"s
354     o Updated KPP to latest version from JPL
355     o Added a COS(latitude) in horizontal viscosity
356    
357    checkpoint23
358     o Added del^4 diffusion for salt and temperature
359     o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
360    
361    checkpoint22
362     o Made many small changes: implicit none, format(i5), etc...
363     o Introduced KPP mixing scheme (compiles and runs but *not* tested)
364    
365    checkpoint21
366     o Introduced new I/O package that supports direct-access records (mdsio.F)
367     o Split-up mid-level I/O routines
368     o Updated input data for experiments 0,1,2,4 and 5
369     o Finally removed the genmake.* scripts (everyone seems happy with genmake)
370    
371    checkpoint20
372     o Tidied up open-boundaries some more
373     o Added non-hydrostatic code
374     o Fixed some input data
375     o Modified MPI start-up to work in "coupled" context.
376    
377    checkpoint19
378     o Tidied up directory structure for verification experiments.
379     o Added new code for open boundaries.
380     o Corrected advective terms near boundaries.
381     o Added CPP flag for "old UV" geometry and corrected spherical geometry.
382     o Implemented free-slip/no-slip BCs and del^4 dissipation.
383     o Split default parameters out of ini_parms.F into set_defaults.F.
384    
385    checkpoint18
386     o Further changes for optional code generation with
387       CPP - ugh!
388    
389    checkpoint17
390     o Beginning to incorporating modularity
391       for supporting atmos. and ocean configs.
392     o Small changes for TAMC complinace
393     o New ultra simple test case. Barotropic box
394       configuration "exp0".
395    
396    checkpoint16
397     o Minor changes to exchange routines to support
398       accumulation in reverse mode. Adjoint of an
399       assignment is an addition.
400     o Changes to support compilation by TAMC (LR(1)
401       syntax) and by g77 under Linux ( 72 character
402       limit ).
403    
404    checkpoint15
405     Rewrote exchange routines to allow
406     o General tile <-> tile connectivity.
407     o TAMC reverse mode flag ( is this really needed? )
408     o Variable width overlap and exchange region widths.
409     o Hooks for sharing data via DMA, Arctic, Memory Channel,
410       shmput/shmget, VIA, SYSV shmem and every other cool
411       communication method.
412    
413    checkpoint14
414     Consistent isomorphism chages made. These allow dynamical core
415     to support both pressure and meters as a vertical coordinate.
416    
417    checkpoint13
418     Release which corrects global_max problem and a couple
419     of KGM time-averaging diagnostic errors. Also contains
420     a double-gyre experiment setup as well as the baseline
421     4 degree global template. The double gyre template is
422     organised to allow it to be applied automatically to
423     the baseline configuration.
424    
425    branch-point-rdot
426     A few tidy-ups have been made bt the real point of this
427     check-point (excuse the pun) is to allow a branch to be
428     made for the purposes of adding the rDot alterations.
429     I don't want to commit the rDot to the main-trunk until
430     we've actually tested it...
431    
432    checkpoint12
433     Tidy up and added generic genmake script (formerly
434     configure script).
435     Released to testers.
436    
437    checkpoint11
438     Re-arranged initialise() and introduced ini_vertical_grid()
439     and ini_masks_etc().
440    
441    checkpoint10
442     Introduced the configure script.
443     Separated out the diags package.
444     Added template for writing time-averages of tile/intermediate quantities.
445     Updated SIZE.h in exp2 and made the data big-endian.
446    
447    checkpoint9
448     MPI fix. Filename changes (meta/data). salbin*y stuff.
449     General tidy-up.
450     SST.bin SSS.bin added to verification/exp2
451    
452    checkpoint8
453     Inludes time-dependant forcing and time-averaging.
454     Works at 4x4 and 2.8125x2.8125 global
455    
456    checkpoint7-4degree-ref
457     Branch from checkpoint7. Released for application to
458     global modeling and general modeling - process studies, regional
459     model etc..
460     Configured for verification/exp2 - 4 degree global, two process.
461    
462    checkpoint7
463     Created by cnh
464     Simple 4 degree global simulation
465     configuration.
466     Includes climatological wind,
467     hydrography, bathymetry etc
468     Does not include Heat Flux and E-P
469    
470    checkpoint6
471     Created by cnh
472     merged checkpoint5 with CD and
473     spherical polar code.
474     Still some problems with GM Redi
475     abd full topography.
476    
477    checkpoint5
478     Created by AJA
479     contains updates to GM Redi
480     and reordered timestepping loop
481     for Implicit Diffusion.
482    
483    checkpoint4
484     Created by cnh
485     Contains memory saving macros ( _rdxc etc..) for when
486     grid variations are limited.
487     Contains polynomial coeffs for EOS and knudsen program
488     for generation.
489    
490  checkpoint3  checkpoint3
491   Created by cnh   Created by cnh
492   Added extra flags for runtime options   Added extra flags for runtime options
# Line 20  checkpoint1 Line 505  checkpoint1
505   Restructured kloop in dynamics.F   Restructured kloop in dynamics.F
506   Added non-linear EOS   Added non-linear EOS
507    
508  baseline - Original checked in code  baseline
509     Original checked in code
510    

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