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revision 1.28 by adcroft, Wed Jun 21 20:11:54 2000 UTC revision 1.81 by adcroft, Thu Aug 15 17:25:26 2002 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    checkpoint46c_post
7    o Changes necessary for ocean in p-coordinates
8     -  Added new buoyancy relation = 'OCEANICP'
9     -  Added new parameters = gravitySign (this used to be contained inside
10        the factor dRdZ which I added when we first switched to R coordinates).
11     X GM/Redi is not compatible (yet)
12     X bottom drag and no-slip need to be debugged.
13    checkpoint46c_pre
14    
15    checkpoint46b_post
16    o Added new equation of state -> JMD95Z and JMD95P
17      - EOS of Jackett and McDougall, 1995, JPO
18      - moved all EOS parameters into EOS.h
19      - new routines ini_eos.F, store_pressure.F
20    o Added UNESCO EOS, but not recommended because it requires
21      in-situ temperature (see JMD95)
22    o Modified formatting for knudsen2.f in utils/knudsen2 and added
23      unesco.f to be used with POLY3
24    checkpoint46b_pre
25    
26    checkpoint46a_post
27    o Added (atmospheric) pressure loading
28      - new field in FFIELDS.h, etc...
29      - new cpp flag ATMOSPHERIC_LOADING
30    o Changed hFacC to _hFacC in calc_phi_hyd.F
31    o Added SHORTWAVE_HEATING to some files for consistency
32    checkpoint46a_pre
33    
34    checkpoint46
35    further merges from release1_p5
36    o new ctrl package
37      - adopted from ECCO environment to enable optimization
38      - added Eliassen Palm fluxes to controls
39    o added Eliassen Palm flux controls to gradient check package
40    o cost package
41      - Compatible with new ctrl package
42      - added Eliassen Palm cost hooks
43      - modif's of existing cost functions
44    o Adjoint-related bug fixes in kpp:
45      - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
46      - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
47    o autodiff package
48      - flow directives:
49        + new for S/R do_the_model_io
50        + enhanced for S/R checkpoint
51        + new gmredi.flow
52      - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
53        disable adcommon.h/g_common.h by default.
54      - fixed problem for adjoint of global_max
55    o modified verification/carbon/
56    o New setup for adjoint of global_ocean
57    o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
58    o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
59    o incorporated hooks for sponge layer code (external_forcing.F)
60    
61    checkpoint45d_post
62    o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
63    o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
64      (affects plume_on_slope "cg2d" output)
65    o add new parameter deltaTfreesurf for free-surface time stepping
66    o exchange gT,gS when using staggerTimeStep & GM & Oly<4
67    o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
68    o change phiMin in exp1 (to agree with documentation)
69    o add new flags:
70     - T,S forcing inside/outside Adams-Bashforth
71     - turn off temp,salt advection and/or forcing
72     - for each tracer, define internal flag for multiDimAdvection & A-B
73    o monitor: change definition of KE to check conservation of Energy
74    
75    checkpoint45c_post
76    o Removed f90 comments ("!")
77    o Modified initialisations to enable exf package for MITgcm
78      (without invoking ECCO_PACKAGE).
79    o modifications to gradient check package (Martin Losch)
80      - enable centered differences
81      - modified format of standard output
82    
83    checkpoint45b_post
84    o cleaned exchange calls in cg2d
85    o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
86    o included CPP option SINGLE_LAYER_MODE in thermodynamics
87      to configure barotropic setup (Martin Losch)
88    o moved some initialisations within bi,bj loop in dynamics
89      (TAF flow dependency)
90    o in initialise_varia, moved call packages_init_variables
91      before convective_adjustment_init
92      (corresponding adjustment of TAF tape initialisation).
93    o in calc_diffusivity/calc_viscosity extended domain to full overlap.
94    
95    checkpoint45a_post
96    o compute Rho over the whole domain (extend iMin,jMin indices)
97    o specific exchange for X-slice domain (case Ny=1)
98    o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
99    o solve_for_pressure : set cg2d_x to zero where OBCS are applied
100    
101    checkpoint44h_post = checkpoint45
102    o Fix to restore differentiability:
103      place at which packages_init_variables is called in
104      initialise_varia is crucial for reverse control flow.
105    o modifications in GMRedi to enable stable adjoint
106      (corresponding modif's in thermodynamics, dynamics)
107    o added missing hook for sponge layer code in external_forcing
108    o modified test cost functions
109    o storing in gad_advection (plus removal of write(0,*)!
110    o missing headers TR1.h added in convective_adjustment routines
111    o errorMessageUnit set non-equal zero in eeboot
112      (conflict on some platforms, e.g. IBM SP3)
113    o modified carbon verif.
114    
115    checkpoint44h_pre
116    o vertical grid option: allow to put the Interface at the middle between
117      2 cell-centers ; replace delZ in pkg/kpp by drF.
118    o GM Advective form: Tracers are advected using the residual transport (=
119      Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
120    
121    checkpoint44g_post
122    o fix surface correction term in multiDimAdvection (affects plume_on_slope
123      results) ; ifdef missing in thermodynamics.F
124    
125    checkpoint44f_pre,checkpoint44f_post
126    o added PTRACERS package
127      This allows an arbitrary number of passive tracers to be integrated
128      forward simultaneously with the dynamicaly model.
129      + Implemented so far:
130        - basic forward algorithm (time-stepping, advection, diffusion, convection)
131        - I/O and checkpointing
132        - GM/Redi  *but*  using the GM/Redi coefficient of Salt
133      + Not implemented so far:
134        - KPP
135        - OBCS
136      + No specific example supplied (yet) but global_ocean.90x40x15 has the
137        necessary data.ptracer file. Simply use -enable=ptracers and uncomment
138        line in data.pkg.
139      + This package is disabled by default since it increases storage.
140    
141    
142    o testscript: added -cleanup option
143    o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
144                 b) enable to filter 2D fields.
145    
146    checkpoint44e_pre,post
147    o re-wrote convective adjustment to use pre-calculated weights
148      Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
149      Adds:    model/src/convective_weights.F, convectively_mixtracer.F
150      Original calls to convect() still in place.
151    
152    chkpt44d_pre,post
153    o added missing EXCLUDE_MONITOR flags
154    o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
155      (incompatible typ in MIN/MAX expressions caused problems
156      on IBM SP3)
157    o in genmake added variable MAKEDEPEND
158      plus resetting for case SunOS
159    o added timer_stats.c routine for IBM SP3
160    o removed variables in dynamics
161    !!! I forgot to create tag chkpt44d_pre !!!
162    !!! But chkpt44d_pre = chkpt44c_post    !!!
163    
164    o real fresh water flux implemented with non-linear free-surface.
165    
166    chkpt44c_pre,post
167    o few fix (mask in shap_s2, EmPmR in external_field_load,
168      USE_NATURAL_BCS in solve_for_P);
169    o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
170    
171    checkpoint44b_pre/_post
172    o merge of relevant stuff from the ecco-branch:
173      - genmake: removed $S64 overwrite for case SunOS
174      - pkg/exf: update and corrections for field swapping and obcs
175      - pkg/ecco: parameter lists for the_model_main, the_main_loop
176                  harmonized between ECCO and MITgcm
177      - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
178                      updated checkpointing_lev... lists for obcs
179      - model/src: minor changes in forward_step, plot_field
180                   added directive for divided adjoint in the_main_loop
181      - pkg/mdsio: added mdsio_gl_slice
182    
183    o check parameters & config (chkpt44a_pre,post)
184    o OBC and NonLin_FrSurf.
185    
186    checkpoint44
187    o fix bug in mom_vi_del2uv
188    o select when filters are applied ; add options to zonal_filter (data.zonfilt)
189    o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
190    o update AIM experiments (NCEP input files)
191    o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
192    o added some stuff for AD
193    
194    checkpoint43
195    o added two new advection tests
196    o added global 4x4 degree ocean test
197    o added test of H&S94 with free surface on cube
198    o some final mods for gradient check, adjoint,...
199    
200    checkpoint42
201      Fixed AD-related problems:
202    o Store directives up-to-date with re-arranged Adams-Bashforth
203      (mainly thermodynamics.F)
204    o New store directives for multi-dim. advection schemes
205      * new CPP flag ALLOW_MULTI_DIM_ADVECTION
206      * new common block and key passkey
207      (mainly gad_advection.F)
208    o Modified store directives for split of dynamics/thermodynamics
209      for the case ALLOW_KPP
210    o Cleaned argument list for timestep_tracer.F
211    
212    checkpoint41
213    o re-formatted/added comments in prologues of key subroutines
214      to work with protex
215    
216    checkpoint40
217    o moved calc_gs, calc_gt and calc_tr1 back to model/src
218    o added FLT (floats) package from Arne along with demo. experiment
219    o re-arranged Adams-Bashforth scheme for tracers to allow easier
220      implementation of forward-in-time forcing terms
221    o more mods for non-linear free-surface including new variable
222    o modified multi-dim method to work on cube
223    o bug fix in KPP (from DM)
224    
225    checkpoint40pre9
226    o added DST advection schemes
227    o fix MPI bug on SGI's
228    o modifications for non-linear free-surface
229    o fixed conditionals for fixed flow/passive tracer only mode
230    o added tension/strain form of stress tensor
231    o changes to commenting of arguments for TAF/TAMC
232    o added/updated many matlab scripts
233    o added multi-dimensional advection method for tracers
234      
235    checkpoint40pre8
236    o new package rw/
237      Added method for dumping intermediate local arrays:
238      mdsio_writetile - same as mdsio_writefield except works from inside
239                        bi,bj loop
240      mdsio_writelocal - same as mdsio_writetile except works for local
241                         arrays
242      write_local_r? - higher-level wrapper for mdsio_writelocal
243      Controlled by diagFreq. Defaults to zero (ie. no dumps)
244      Example given at end of mom_vecinv.F that dumps some local arrays.
245    o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
246      control flux-form versus vector invariant code.
247      Switch is runtime flag vectorInvariantMomentum (defaults to false)
248      or genmake -DISABLE ...
249    o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
250      (additional storing is now needed for case vecinv;
251      currently nothing implemented to switch this storing off
252      in case fluxform is used since no CPP flag available).
253    
254    checkpoint40pre7
255    o bug fix in dynamics.F
256      calc_viscosity called before k=1,Nr loop.
257    o added some #ifdef's ALLOW_PASSIVE_TRACER
258    o cleaned initialisations in ctrl_map_ini
259      related to TAF
260    
261    checkpoint40pre6
262    o split dynamics into thermodynamics & dynamics
263    o corresponding split of calc_diffusivity into
264      calc_diffusivity, calc_viscosity
265      (kpp_calc_diff, kpp_calc_visc).
266    o Added diffkr, kapgm to control variables
267    o bug fix in gmredi_slope_limit for ldd97
268    
269    checkpoint40pre5
270    o proper initialization of Adams-Bashforth time stepping
271      + uses forward step for very first step of model (iter=0)
272    o re-generated *all* output since almost all output is modified by this
273      change (sorry but we've been putting this one off for about 2 years)
274      + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
275        *not* regenerated since they are already out of date and I don't
276        want to create the impression that they are suddenly working.
277    o removed KAP stuff for DEC's
278    o modified/added many .cvsignore files in */code and */input
279    o added new expt "solid-body.cs-32x32x1"
280      + this uses an alternative form of ini_curvilinear_grid.F which
281        is not necessarily any better than the current one...
282    
283    checkpoint40pre4
284    o added re-initialisations of utrans,vtrans,rtrans in
285      calc_common_factors which are crucial for TAF.
286    o extended iMin,jMin range for calc_common_factors,
287      calc_diffusivity
288    o added option ALLOW_PASSIVE_TRACER
289    o a few minor updates and fixes
290    
291    checkpoint40pre3
292    o created calc_gtr1.F for gad package
293    o split the_main_loop and re-introduced forward_step
294    o some recomputations of nIter0 for TAMC
295    
296    checkpoint40pre2
297    o Updated to latest branch of AJA, JMC
298    o Added gradient check package
299    o Added routines for passive tracer handling
300    o Added carbon sequestration sensitivity experiment
301    
302    checkpoint39
303     o Modifications and fixes to support TAMC
304       (mainly missing or wrong directives)
305     o Corrected common blocks when fooling TAMC to produce adjoint I/O
306       in addummy_in_stepping
307     o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
308     o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
309     o Included following packages:
310       cal: calendar
311       exf: external forcing
312       ecco: essential routines to control use of cal, exf
313             (NB: this is not the full ECCO environment)
314     o disabled some packages by default in genmake
315    
316    checkpoint38
317     o see notes_c37_adj.txt
318     o corrected wrong layer index in external_forcing_t
319     o replaced the_main_loop/forward_step by the_main_loop
320     o removed forceoutput from write_state
321       (replaced criteria for initial/final state)
322     o added runtime flag for pre-C35 pickups: usePickupBeforeC35
323    
324    checkpoint37
325     o mdsio.F routine split and packaged in pkg/mdsio
326       (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
327        used unless genmake -disable=mdsio)
328     o allow a more precise surface-geopotential gradient for the atmosphere
329       taking into account the change in space of Alpha (=1/rho) at the surface.
330     o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
331       (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
332     o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
333       Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
334       [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
335     o Time-Average diagnostics defined as a pseudo package "timeave".
336     o pickup files : old pickup (before c35) did not work with new code (c35
337       and after) unless activating 2 commented lines in initialise-varia.
338     o Non-Hydrostatic pickup file Pb fixed.
339     o bug with Rigid-lid version (since c35) fixed.  
340    
341    checkpoint36
342     o implement Crank-Nickelson barotropic time-stepping
343     o recover Time-Average diagnostics
344     o fix Pb in checkpoint (PR#19)
345     o AIM become a standard package ; clean unused CPP_kees
346    
347    checkpoint35
348     o subtantial rewrite of dynamics.f
349     o allows staggered time-stepping
350     o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
351     o added bottom drag (linear + quadratic)
352    
353    checkpoint34
354     o Modified exchange routines for correct reverse simulation.
355     o Added verification output to comply with bug fix in impldiff.F
356       as of c33 (exp2, natl_box).
357     o Corrected store directives in dynamics.F
358     o Corrected array boundaries in impldiff.F
359     o Corrected array dimensions in gmredi.
360       Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
361     o Added routine GLOBAL_SUM_INT to global_sum.F
362     o Added mdsio_gl.F for ECCO purposes.
363    
364    checkpoint33
365     o Fixed bug in lower BC in impldiff.F
366     o Fixed confusion about units of forcing arrays in FFIELDS.h
367       namely Fu,Fv,Qnet,Qsw,EmPmR:
368       - Removed verification/natl_box/code/external_fields_scale.F
369         (did not differ from that in model/src)
370       - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
371         (see FFIELDS.h for description)
372       - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
373         kpp_calc.F and kpp_transport_t.F
374       - Removed model/src/external_fields_scale.F and calls to it
375       - verification/natl_box uses flux data with "atmospheric" sign so
376         a special version of external_fields_load.F is used to
377         change the data as it's read in. This way, the arrays
378         have the right units and signs at all times tha a user could
379         possibly use them.
380     o Corrected genmake to delete a temporary file during configuration
381    
382    checkpoint32
383     o Scaling of forcing fields moved from external_forcing.F to
384       external_fields_scale.F, called directly after loading fields.
385     o Surface relaxation terms added to surface tendency fields in
386       extra subroutine.
387     o impldiff.F changed to avoid storing by TAMC of huge intermediate
388       fields.
389     o Changes in GMRedi to comply with packaging structure.
390     o Modifications and bug fixes in KPP package.
391     o Verification experiment for KPP added (verification/nat_box/)
392    
393    checkpoint31
394     o Packages interface brought in line with defined standard
395       -> new routines packages_...F
396       -> changes in initialise_fixed.F, initialise_varia.F
397       -> enables initialisation interface for ECCO package
398     o Rescaling of external forcing fields immediately after read
399       (removed from external_forcing.F)
400       -> new: surface_fields_scale.F
401       -> affects ini_foorcing.F, external_fields_load.F
402     o Computation of surface tendencies before tendency updates.
403       -> new: external_forcing_surf.F
404     o Change of variable names useGMRedi, useKPP, useECCO
405     o Further changes in dynamics.F, impldiff.F for TAMC
406     o Tested for experiments 0, 2, 4.
407       - not yet tested for GMRedi.
408       - not yet tested for KPP.
409    
410    checkpoint30
411     o Updates for OBCs
412     o New experiment for test OBCs (internal_wave)
413     o New output.txt in verification/exp4/results/
414     o Updates for KPP: calculation of viscosity corrected, new variables
415       kpp_dumpFreq and kpp_taveFreq
416     o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
417       and entry for T90 in genmake
418    
419  checkpoint29  checkpoint29
420   o packaged KPP and GM/Redi   o packaged KPP and GM/Redi
421    

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