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revision 1.15 by cnh, Wed Oct 28 03:23:17 1998 UTC revision 1.53.4.8 by heimbach, Thu Mar 21 03:57:43 2002 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    ecco_c44_e19
7    o will contain merges from main trunk
8    
9    ecco_c44_e18
10    o sponge layer code for obcs was missing
11      - added hook in external_forcing.F
12      - added storing for TAF
13    o new routine cost_init_barfiles to initialise
14      adjoint fields adtbar, adsbar, adpsbar
15      (needed in conjunction with corrected ladinit for active I/O)
16    o cleaned up and corrected order in packages_readparms, ecco_readparms
17    o corrected and simplified weights for obcs controls
18      - weight fields simplified
19      - bug fix in ctrl_pack
20      - no more write of control vector in ctrl_pack
21    o i/j index bug fixes in cost_ssh_mean
22    
23    ecco_c44_e17
24    o bug fixes in cost package
25      * wrong identifier for active I/O of monthly mean psbar
26        (cost_averagesfields, cost_ssh) xx_psbar_dummy
27      * cleaned all identifier for active I/O of monthly fields
28      * wrong ladinit in various cost routines
29    o merge with interval (chkpt44c_post - chkpt44d_post)
30      * added missing EXCLUDE_MONITOR flags
31      * changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
32        (incompatible typ in MIN/MAX expressions caused problems
33        on IBM SP3)
34      * in genmake added variable MAKEDEPEND
35        plus resetting for case SunOS
36        added timer_stats.c routine for IBM SP3
37      * removed variables in dynamics
38    
39    ecco_c44_e16
40    o new ECCO checkpoint, the first since ecco_c43_e15
41      which is branched from MITgcm.
42      All changes were merged in between (see ecco-branch-mod? tags).
43    o last changes:
44      * assuming path for TAF and TAMC are known (e.g. in $path)
45      * genmake:
46        - added tools/xmakedepend to circumvene shortcoming of
47          SUN's makedepend (size too small)
48        - invoking ../tools/xmakedepend instead of makedepend
49        - changed compiler flags for case SunOS
50    
51    ecco-branch-mod5
52    o mod's to reproduce open boundary run
53    o enable field swapping for OB's and climatology
54    o update store directives for OB control
55    o added option ALLOW_OBCS_PRESCRIBE
56    o call of getobcs now out of obcs_calc (param. list modified)
57    
58    ecco-branch-mod4
59    o this is the second part of changes necessary to reconcile
60      the natl_box_adjoint verification (with and without grdchk).
61      >>>!!! CHANGES BETWEEN THE TAGS ecco-branch-mod3 !!!<<<
62      >>>!!!                      AND ecco-branch-mod4 !!!<<<
63      >>>!!! SHOULD BE MERGED INTO THE MAIN TRUNK      !!!<<<
64      - genmake: removed $S64 overwrite for case SunOS
65      - pkg/exf: update and corrections for field swapping and obcs
66      - pkg/ecco: parameter lists for the_model_main, the_main_loop
67                  harmonized between ECCO and MITgcm
68      - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
69                      updated checkpointing_lev... lists for obcs
70      - model/src: minor changes in forward_step, plot_field
71      - pkg/mdsio: added mdsio_gl_slice
72    
73    ecco-branch-mod3
74    o this is the first part of changes necessary to reconcile
75      natl_box_adjoint verification (with and without grdchk).
76      This set of changes is relevant for ECCO only.
77      The next set/tag of changes (ecco-branch-mod4)
78      should be merged into the main trunk.
79      - update some options
80      - parameter lists of ecco_the_model_main and ecco_the_main_loop
81        differed from those of the MITgcm counterparts.
82    
83    ecco-branch-mod2
84    o update ecco-branch-mod1 to checkpoint44
85    o exclude from updates:
86      - verification/
87      - adjoint/
88      - pkg/cost
89      - pkg/ctrl
90      - pkg/ecco
91      - pkg/obcs
92      - model/src/the_model_main.F
93      - model/src/the_main_loop.F
94    
95    checkpoint44
96    o apply Shapiro filter on T&S before calc_PhiHyd (stagger time stepping)
97    o fix bug in mom_vi_del2uv
98    o added some stuff for AD
99    
100    ecco-branch-mod1
101    o based on c43
102    o replaced packages cost, ctrl, ecco, obcs
103    o removed MITgcm verif.'s, added ECCO verif.'s
104    o added lsopt, optim for line search optimization.
105    
106    checkpoint43
107    o added two new advection tests
108    o added global 4x4 degree ocean test
109    o added test of H&S94 with free surface on cube
110    o some final mods for gradient check, adjoint,...
111    
112    checkpoint42
113      Fixed AD-related problems:
114    o Store directives up-to-date with re-arranged Adams-Bashforth
115      (mainly thermodynamics.F)
116    o New store directives for multi-dim. advection schemes
117      * new CPP flag ALLOW_MULTI_DIM_ADVECTION
118      * new common block and key passkey
119      (mainly gad_advection.F)
120    o Modified store directives for split of dynamics/thermodynamics
121      for the case ALLOW_KPP
122    o Cleaned argument list for timestep_tracer.F
123    
124    checkpoint41
125    o re-formatted/added comments in prologues of key subroutines
126      to work with protex
127    
128    checkpoint40
129    o moved calc_gs, calc_gt and calc_tr1 back to model/src
130    o added FLT (floats) package from Arne along with demo. experiment
131    o re-arranged Adams-Bashforth scheme for tracers to allow easier
132      implementation of forward-in-time forcing terms
133    o more mods for non-linear free-surface including new variable
134    o modified multi-dim method to work on cube
135    o bug fix in KPP (from DM)
136    
137    checkpoint40pre9
138    o added DST advection schemes
139    o fix MPI bug on SGI's
140    o modifications for non-linear free-surface
141    o fixed conditionals for fixed flow/passive tracer only mode
142    o added tension/strain form of stress tensor
143    o changes to commenting of arguments for TAF/TAMC
144    o added/updated many matlab scripts
145    o added multi-dimensional advection method for tracers
146      
147    checkpoint40pre8
148    o new package rw/
149      Added method for dumping intermediate local arrays:
150      mdsio_writetile - same as mdsio_writefield except works from inside
151                        bi,bj loop
152      mdsio_writelocal - same as mdsio_writetile except works for local
153                         arrays
154      write_local_r? - higher-level wrapper for mdsio_writelocal
155      Controlled by diagFreq. Defaults to zero (ie. no dumps)
156      Example given at end of mom_vecinv.F that dumps some local arrays.
157    o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
158      control flux-form versus vector invariant code.
159      Switch is runtime flag vectorInvariantMomentum (defaults to false)
160      or genmake -DISABLE ...
161    o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
162      (additional storing is now needed for case vecinv;
163      currently nothing implemented to switch this storing off
164      in case fluxform is used since no CPP flag available).
165    
166    checkpoint40pre7
167    o bug fix in dynamics.F
168      calc_viscosity called before k=1,Nr loop.
169    o added some #ifdef's ALLOW_PASSIVE_TRACER
170    o cleaned initialisations in ctrl_map_ini
171      related to TAF
172    
173    checkpoint40pre6
174    o split dynamics into thermodynamics & dynamics
175    o corresponding split of calc_diffusivity into
176      calc_diffusivity, calc_viscosity
177      (kpp_calc_diff, kpp_calc_visc).
178    o Added diffkr, kapgm to control variables
179    o bug fix in gmredi_slope_limit for ldd97
180    
181    checkpoint40pre5
182    o proper initialization of Adams-Bashforth time stepping
183      + uses forward step for very first step of model (iter=0)
184    o re-generated *all* output since almost all output is modified by this
185      change (sorry but we've been putting this one off for about 2 years)
186      + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
187        *not* regenerated since they are already out of date and I don't
188        want to create the impression that they are suddenly working.
189    o removed KAP stuff for DEC's
190    o modified/added many .cvsignore files in */code and */input
191    o added new expt "solid-body.cs-32x32x1"
192      + this uses an alternative form of ini_curvilinear_grid.F which
193        is not necessarily any better than the current one...
194    
195    checkpoint40pre4
196    o added re-initialisations of utrans,vtrans,rtrans in
197      calc_common_factors which are crucial for TAF.
198    o extended iMin,jMin range for calc_common_factors,
199      calc_diffusivity
200    o added option ALLOW_PASSIVE_TRACER
201    o a few minor updates and fixes
202    
203    checkpoint40pre3
204    o created calc_gtr1.F for gad package
205    o split the_main_loop and re-introduced forward_step
206    o some recomputations of nIter0 for TAMC
207    
208    checkpoint40pre2
209    o Updated to latest branch of AJA, JMC
210    o Added gradient check package
211    o Added routines for passive tracer handling
212    o Added carbon sequestration sensitivity experiment
213    
214    checkpoint39
215     o Modifications and fixes to support TAMC
216       (mainly missing or wrong directives)
217     o Corrected common blocks when fooling TAMC to produce adjoint I/O
218       in addummy_in_stepping
219     o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
220     o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
221     o Included following packages:
222       cal: calendar
223       exf: external forcing
224       ecco: essential routines to control use of cal, exf
225             (NB: this is not the full ECCO environment)
226     o disabled some packages by default in genmake
227    
228    checkpoint38
229     o see notes_c37_adj.txt
230     o corrected wrong layer index in external_forcing_t
231     o replaced the_main_loop/forward_step by the_main_loop
232     o removed forceoutput from write_state
233       (replaced criteria for initial/final state)
234     o added runtime flag for pre-C35 pickups: usePickupBeforeC35
235    
236    checkpoint37
237     o mdsio.F routine split and packaged in pkg/mdsio
238       (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
239        used unless genmake -disable=mdsio)
240     o allow a more precise surface-geopotential gradient for the atmosphere
241       taking into account the change in space of Alpha (=1/rho) at the surface.
242     o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
243       (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
244     o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
245       Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
246       [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
247     o Time-Average diagnostics defined as a pseudo package "timeave".
248     o pickup files : old pickup (before c35) did not work with new code (c35
249       and after) unless activating 2 commented lines in initialise-varia.
250     o Non-Hydrostatic pickup file Pb fixed.
251     o bug with Rigid-lid version (since c35) fixed.  
252    
253    checkpoint36
254     o implement Crank-Nickelson barotropic time-stepping
255     o recover Time-Average diagnostics
256     o fix Pb in checkpoint (PR#19)
257     o AIM become a standard package ; clean unused CPP_kees
258    
259    checkpoint35
260     o subtantial rewrite of dynamics.f
261     o allows staggered time-stepping
262     o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
263     o added bottom drag (linear + quadratic)
264    
265    checkpoint34
266     o Modified exchange routines for correct reverse simulation.
267     o Added verification output to comply with bug fix in impldiff.F
268       as of c33 (exp2, natl_box).
269     o Corrected store directives in dynamics.F
270     o Corrected array boundaries in impldiff.F
271     o Corrected array dimensions in gmredi.
272       Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
273     o Added routine GLOBAL_SUM_INT to global_sum.F
274     o Added mdsio_gl.F for ECCO purposes.
275    
276    checkpoint33
277     o Fixed bug in lower BC in impldiff.F
278     o Fixed confusion about units of forcing arrays in FFIELDS.h
279       namely Fu,Fv,Qnet,Qsw,EmPmR:
280       - Removed verification/natl_box/code/external_fields_scale.F
281         (did not differ from that in model/src)
282       - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
283         (see FFIELDS.h for description)
284       - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
285         kpp_calc.F and kpp_transport_t.F
286       - Removed model/src/external_fields_scale.F and calls to it
287       - verification/natl_box uses flux data with "atmospheric" sign so
288         a special version of external_fields_load.F is used to
289         change the data as it's read in. This way, the arrays
290         have the right units and signs at all times tha a user could
291         possibly use them.
292     o Corrected genmake to delete a temporary file during configuration
293    
294    checkpoint32
295     o Scaling of forcing fields moved from external_forcing.F to
296       external_fields_scale.F, called directly after loading fields.
297     o Surface relaxation terms added to surface tendency fields in
298       extra subroutine.
299     o impldiff.F changed to avoid storing by TAMC of huge intermediate
300       fields.
301     o Changes in GMRedi to comply with packaging structure.
302     o Modifications and bug fixes in KPP package.
303     o Verification experiment for KPP added (verification/nat_box/)
304    
305    checkpoint31
306     o Packages interface brought in line with defined standard
307       -> new routines packages_...F
308       -> changes in initialise_fixed.F, initialise_varia.F
309       -> enables initialisation interface for ECCO package
310     o Rescaling of external forcing fields immediately after read
311       (removed from external_forcing.F)
312       -> new: surface_fields_scale.F
313       -> affects ini_foorcing.F, external_fields_load.F
314     o Computation of surface tendencies before tendency updates.
315       -> new: external_forcing_surf.F
316     o Change of variable names useGMRedi, useKPP, useECCO
317     o Further changes in dynamics.F, impldiff.F for TAMC
318     o Tested for experiments 0, 2, 4.
319       - not yet tested for GMRedi.
320       - not yet tested for KPP.
321    
322    checkpoint30
323     o Updates for OBCs
324     o New experiment for test OBCs (internal_wave)
325     o New output.txt in verification/exp4/results/
326     o Updates for KPP: calculation of viscosity corrected, new variables
327       kpp_dumpFreq and kpp_taveFreq
328     o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
329       and entry for T90 in genmake
330    
331    checkpoint29
332     o packaged KPP and GM/Redi
333    
334    checkpoint28
335     o Corrected initialization of hFacMin for difference vertical coordinates
336     o Modified calculation of partial cell thickness to more robust algorithm
337     o config_summary.F: replaced write_1D_... by write_0D_...
338       read_write.F: added subroutines write_0D_...
339     o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
340       included some initialisations required for TAMC.
341     o routine calc_isoslopes: modified sqrt computation to make it
342       differentiable for zero argument.
343     o routines dynamics, impldiff:
344       included store directives and tape key computations required for TAMC.
345     o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
346    
347    checkpoint27
348     o fixed calc_isoslopes() to so that cancellation of terms in tensor
349       formulation works properly with variable resolution.
350     o restructured the calling tree between the_model_main() and dynamics()
351     o split initialise() into initialise_fixed() and initialise_varia()
352     o introduced initialization file pSurfInitFile for free surface (cg2d_x)
353       in new routine ini_psurf()
354    
355    checkpoint26
356     o moved some #ifdef in optional routines to encompass everything
357       except the argument declarations. This was using up some memory.
358     o fixed macros like _ADT to work with both versions of Linux cpp
359     o cleaned up some unused and uninitialized variables
360       (helps when debugging with strict compile options)
361     o split up CPP_EEOPTIONS.h into options and macros
362       (macros are now in eesupp/inc/CPP_EEMACROS.h)
363     o patch for 2 processor JAM mode
364    
365    checkpoint25
366     o updates for OBCs and NH
367     o dramatically reduced memory usage
368     o added "JAM" routines for use on Artic network
369     o parameterization of convection by implicit vertical diffusion
370     o added a diagnostic of convective index
371     o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
372       (this is was partly for OBCs and NH but also in anticipation of
373        an explicit free-surface option)
374     o initial state input files for U and V
375    
376    checkpoint24
377     o Removed some spurious "REAL"s
378     o Updated KPP to latest version from JPL
379     o Added a COS(latitude) in horizontal viscosity
380    
381    checkpoint23
382     o Added del^4 diffusion for salt and temperature
383     o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
384    
385    checkpoint22
386     o Made many small changes: implicit none, format(i5), etc...
387     o Introduced KPP mixing scheme (compiles and runs but *not* tested)
388    
389    checkpoint21
390     o Introduced new I/O package that supports direct-access records (mdsio.F)
391     o Split-up mid-level I/O routines
392     o Updated input data for experiments 0,1,2,4 and 5
393     o Finally removed the genmake.* scripts (everyone seems happy with genmake)
394    
395    checkpoint20
396     o Tidied up open-boundaries some more
397     o Added non-hydrostatic code
398     o Fixed some input data
399     o Modified MPI start-up to work in "coupled" context.
400    
401    checkpoint19
402     o Tidied up directory structure for verification experiments.
403     o Added new code for open boundaries.
404     o Corrected advective terms near boundaries.
405     o Added CPP flag for "old UV" geometry and corrected spherical geometry.
406     o Implemented free-slip/no-slip BCs and del^4 dissipation.
407     o Split default parameters out of ini_parms.F into set_defaults.F.
408    
409    checkpoint18
410     o Further changes for optional code generation with
411       CPP - ugh!
412    
413    checkpoint17
414     o Beginning to incorporating modularity
415       for supporting atmos. and ocean configs.
416     o Small changes for TAMC complinace
417     o New ultra simple test case. Barotropic box
418       configuration "exp0".
419    
420  checkpoint16  checkpoint16
421   o Minor changes to exchange routines to support   o Minor changes to exchange routines to support
422     accumulation in reverse mode. Adjoint of an     accumulation in reverse mode. Adjoint of an

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