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revision 1.37 by jmc, Tue Mar 13 01:15:09 2001 UTC revision 1.87 by mlosch, Wed Sep 25 19:36:50 2002 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    
7    checkpoint46h_post
8    o cleaned up the use of rhoNil and rhoConst.
9      - rhoNil should only appear in the LINEAR equation of state, everywhere
10        else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
11        and the dynamical equations are all divided by rhoConst
12    o introduced new parameter rhoConstFresh, a reference density of fresh
13      water, to remove the fresh water flux's dependence on rhoNil. The default
14      value is 999.8 kg/m^3
15    o cleanup up external_forcing.F and external_forcing_surf.F
16      - can now be used by both OCEANIC and OCEANICP
17    checkpoint46h_pre
18    
19     Added code to convert surface volume flux (fresh water) into
20     a mass flux when using P coordinates in the ocean (OCEANICP).
21     Note: It assumes you have set rho0=rhoConst=density of fresh water.
22    
23    checkpoint46g_post
24    o Include a new diagnostic variable phiHydLow for the ocean model
25      - in z-coordinates, it is the bottom pressure anomaly
26      - in p-coordinates, it is the sea surface elevation
27      - in both cases, these variable have global drift, reflecting the mass
28        drift in z-coordinates and the volume drift in p-coordinates
29      - included time averaging for phiHydLow, be aware of the drift!
30    o depth-dependent computation of Bo_surf for pressure coordinates
31      in the ocean (buoyancyRelation='OCEANICP')
32      - requires a new routine (FIND_RHO_SCALAR) to compute density with only
33        Theta, Salinity, and Pressure in the parameter list. This routine is
34        presently contained in find_rho.F. This routine does not give the
35        correct density for 'POLY3', which would be a z-dependent reference
36        density.
37    o cleaned up find_rho
38      - removed obsolete 'eqn' from the parameter list.
39    o added two new verification experiments: gop and goz
40      (4x4 degree global ocean, 15 layers in pressure and height coordinates)
41    checkpoint46g_pre
42    
43    checkpoint46f_post
44    o Enable tangent linear (forward mode) gradient checks:
45      - extended active file handling to g_... files
46      - added TANGENT_SIMULATION to theSimulationMode
47      - extended grdchk package accordingly
48    o added tangent linear setup in verification/carbon/code_ftl
49    o added adjoint setup in verification/front_relax/code_ad
50    
51    checkpoint46e_post
52    o Added new equation of state -> MDJWF
53      - EOS of McDougall et al., 2002, JAOT, submitted
54      - caveat: the equation of state is only valid for a smaller (more
55        realistic?) range of values than JMD95P/Z and UNESCO
56      - added masks to the calculation of pressure in store_pressure
57      - added more check values for density in check_eos (ini_eos.F), some of
58        the old check values are out of the range of the MDJWF-eos, so don't
59        expect perfect matches for those
60    checkpoint46e_pre
61    
62    checkpoint46d_post
63    o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
64      'OCEANICP', also initialised field pressure correctly in ini_eos in the
65      case of pressure coordinates. eosType='JMD95Z' in
66      combination with buoyancyRelation='OCEANICP' now causes an error.
67    o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
68      in find_alpha/beta.
69    checkpoint46d_pre
70    
71    o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
72      so that JMD95Z and JMD95P give approptiate static stability in find_rho.
73    
74    checkpoint46c_post
75    o Changes necessary for ocean in p-coordinates
76     -  Added new buoyancy relation = 'OCEANICP'
77     -  Added new parameters = gravitySign (this used to be contained inside
78        the factor dRdZ which I added when we first switched to R coordinates).
79     X GM/Redi is not compatible (yet)
80     X bottom drag and no-slip need to be debugged.
81    checkpoint46c_pre
82    
83    checkpoint46b_post
84    o Added new equation of state -> JMD95Z and JMD95P
85      - EOS of Jackett and McDougall, 1995, JAOT
86      - moved all EOS parameters into EOS.h
87      - new routines ini_eos.F, store_pressure.F
88    o Added UNESCO EOS, but not recommended because it requires
89      in-situ temperature (see JMD95)
90    o Modified formatting for knudsen2.f in utils/knudsen2 and added
91      unesco.f to be used with POLY3
92    checkpoint46b_pre
93    
94    checkpoint46a_post
95    o Added (atmospheric) pressure loading
96      - new field in FFIELDS.h, etc...
97      - new cpp flag ATMOSPHERIC_LOADING
98    o Changed hFacC to _hFacC in calc_phi_hyd.F
99    o Added SHORTWAVE_HEATING to some files for consistency
100    checkpoint46a_pre
101    
102    checkpoint46
103    further merges from release1_p5
104    o new ctrl package
105      - adopted from ECCO environment to enable optimization
106      - added Eliassen Palm fluxes to controls
107    o added Eliassen Palm flux controls to gradient check package
108    o cost package
109      - Compatible with new ctrl package
110      - added Eliassen Palm cost hooks
111      - modif's of existing cost functions
112    o Adjoint-related bug fixes in kpp:
113      - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
114      - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
115    o autodiff package
116      - flow directives:
117        + new for S/R do_the_model_io
118        + enhanced for S/R checkpoint
119        + new gmredi.flow
120      - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
121        disable adcommon.h/g_common.h by default.
122      - fixed problem for adjoint of global_max
123    o modified verification/carbon/
124    o New setup for adjoint of global_ocean
125    o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
126    o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
127    o incorporated hooks for sponge layer code (external_forcing.F)
128    
129    checkpoint45d_post
130    o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
131    o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
132      (affects plume_on_slope "cg2d" output)
133    o add new parameter deltaTfreesurf for free-surface time stepping
134    o exchange gT,gS when using staggerTimeStep & GM & Oly<4
135    o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
136    o change phiMin in exp1 (to agree with documentation)
137    o add new flags:
138     - T,S forcing inside/outside Adams-Bashforth
139     - turn off temp,salt advection and/or forcing
140     - for each tracer, define internal flag for multiDimAdvection & A-B
141    o monitor: change definition of KE to check conservation of Energy
142    
143    checkpoint45c_post
144    o Removed f90 comments ("!")
145    o Modified initialisations to enable exf package for MITgcm
146      (without invoking ECCO_PACKAGE).
147    o modifications to gradient check package (Martin Losch)
148      - enable centered differences
149      - modified format of standard output
150    
151    checkpoint45b_post
152    o cleaned exchange calls in cg2d
153    o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
154    o included CPP option SINGLE_LAYER_MODE in thermodynamics
155      to configure barotropic setup (Martin Losch)
156    o moved some initialisations within bi,bj loop in dynamics
157      (TAF flow dependency)
158    o in initialise_varia, moved call packages_init_variables
159      before convective_adjustment_init
160      (corresponding adjustment of TAF tape initialisation).
161    o in calc_diffusivity/calc_viscosity extended domain to full overlap.
162    
163    checkpoint45a_post
164    o compute Rho over the whole domain (extend iMin,jMin indices)
165    o specific exchange for X-slice domain (case Ny=1)
166    o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
167    o solve_for_pressure : set cg2d_x to zero where OBCS are applied
168    
169    checkpoint44h_post = checkpoint45
170    o Fix to restore differentiability:
171      place at which packages_init_variables is called in
172      initialise_varia is crucial for reverse control flow.
173    o modifications in GMRedi to enable stable adjoint
174      (corresponding modif's in thermodynamics, dynamics)
175    o added missing hook for sponge layer code in external_forcing
176    o modified test cost functions
177    o storing in gad_advection (plus removal of write(0,*)!
178    o missing headers TR1.h added in convective_adjustment routines
179    o errorMessageUnit set non-equal zero in eeboot
180      (conflict on some platforms, e.g. IBM SP3)
181    o modified carbon verif.
182    
183    checkpoint44h_pre
184    o vertical grid option: allow to put the Interface at the middle between
185      2 cell-centers ; replace delZ in pkg/kpp by drF.
186    o GM Advective form: Tracers are advected using the residual transport (=
187      Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
188    
189    checkpoint44g_post
190    o fix surface correction term in multiDimAdvection (affects plume_on_slope
191      results) ; ifdef missing in thermodynamics.F
192    
193    checkpoint44f_pre,checkpoint44f_post
194    o added PTRACERS package
195      This allows an arbitrary number of passive tracers to be integrated
196      forward simultaneously with the dynamicaly model.
197      + Implemented so far:
198        - basic forward algorithm (time-stepping, advection, diffusion, convection)
199        - I/O and checkpointing
200        - GM/Redi  *but*  using the GM/Redi coefficient of Salt
201      + Not implemented so far:
202        - KPP
203        - OBCS
204      + No specific example supplied (yet) but global_ocean.90x40x15 has the
205        necessary data.ptracer file. Simply use -enable=ptracers and uncomment
206        line in data.pkg.
207      + This package is disabled by default since it increases storage.
208    
209    
210    o testscript: added -cleanup option
211    o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
212                 b) enable to filter 2D fields.
213    
214    checkpoint44e_pre,post
215    o re-wrote convective adjustment to use pre-calculated weights
216      Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
217      Adds:    model/src/convective_weights.F, convectively_mixtracer.F
218      Original calls to convect() still in place.
219    
220    chkpt44d_pre,post
221    o added missing EXCLUDE_MONITOR flags
222    o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
223      (incompatible typ in MIN/MAX expressions caused problems
224      on IBM SP3)
225    o in genmake added variable MAKEDEPEND
226      plus resetting for case SunOS
227    o added timer_stats.c routine for IBM SP3
228    o removed variables in dynamics
229    !!! I forgot to create tag chkpt44d_pre !!!
230    !!! But chkpt44d_pre = chkpt44c_post    !!!
231    
232    o real fresh water flux implemented with non-linear free-surface.
233    
234    chkpt44c_pre,post
235    o few fix (mask in shap_s2, EmPmR in external_field_load,
236      USE_NATURAL_BCS in solve_for_P);
237    o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
238    
239    checkpoint44b_pre/_post
240    o merge of relevant stuff from the ecco-branch:
241      - genmake: removed $S64 overwrite for case SunOS
242      - pkg/exf: update and corrections for field swapping and obcs
243      - pkg/ecco: parameter lists for the_model_main, the_main_loop
244                  harmonized between ECCO and MITgcm
245      - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
246                      updated checkpointing_lev... lists for obcs
247      - model/src: minor changes in forward_step, plot_field
248                   added directive for divided adjoint in the_main_loop
249      - pkg/mdsio: added mdsio_gl_slice
250    
251    o check parameters & config (chkpt44a_pre,post)
252    o OBC and NonLin_FrSurf.
253    
254    checkpoint44
255    o fix bug in mom_vi_del2uv
256    o select when filters are applied ; add options to zonal_filter (data.zonfilt)
257    o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
258    o update AIM experiments (NCEP input files)
259    o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
260    o added some stuff for AD
261    
262    checkpoint43
263    o added two new advection tests
264    o added global 4x4 degree ocean test
265    o added test of H&S94 with free surface on cube
266    o some final mods for gradient check, adjoint,...
267    
268    checkpoint42
269      Fixed AD-related problems:
270    o Store directives up-to-date with re-arranged Adams-Bashforth
271      (mainly thermodynamics.F)
272    o New store directives for multi-dim. advection schemes
273      * new CPP flag ALLOW_MULTI_DIM_ADVECTION
274      * new common block and key passkey
275      (mainly gad_advection.F)
276    o Modified store directives for split of dynamics/thermodynamics
277      for the case ALLOW_KPP
278    o Cleaned argument list for timestep_tracer.F
279    
280    checkpoint41
281    o re-formatted/added comments in prologues of key subroutines
282      to work with protex
283    
284    checkpoint40
285    o moved calc_gs, calc_gt and calc_tr1 back to model/src
286    o added FLT (floats) package from Arne along with demo. experiment
287    o re-arranged Adams-Bashforth scheme for tracers to allow easier
288      implementation of forward-in-time forcing terms
289    o more mods for non-linear free-surface including new variable
290    o modified multi-dim method to work on cube
291    o bug fix in KPP (from DM)
292    
293    checkpoint40pre9
294    o added DST advection schemes
295    o fix MPI bug on SGI's
296    o modifications for non-linear free-surface
297    o fixed conditionals for fixed flow/passive tracer only mode
298    o added tension/strain form of stress tensor
299    o changes to commenting of arguments for TAF/TAMC
300    o added/updated many matlab scripts
301    o added multi-dimensional advection method for tracers
302      
303    checkpoint40pre8
304    o new package rw/
305      Added method for dumping intermediate local arrays:
306      mdsio_writetile - same as mdsio_writefield except works from inside
307                        bi,bj loop
308      mdsio_writelocal - same as mdsio_writetile except works for local
309                         arrays
310      write_local_r? - higher-level wrapper for mdsio_writelocal
311      Controlled by diagFreq. Defaults to zero (ie. no dumps)
312      Example given at end of mom_vecinv.F that dumps some local arrays.
313    o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
314      control flux-form versus vector invariant code.
315      Switch is runtime flag vectorInvariantMomentum (defaults to false)
316      or genmake -DISABLE ...
317    o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
318      (additional storing is now needed for case vecinv;
319      currently nothing implemented to switch this storing off
320      in case fluxform is used since no CPP flag available).
321    
322    checkpoint40pre7
323    o bug fix in dynamics.F
324      calc_viscosity called before k=1,Nr loop.
325    o added some #ifdef's ALLOW_PASSIVE_TRACER
326    o cleaned initialisations in ctrl_map_ini
327      related to TAF
328    
329    checkpoint40pre6
330    o split dynamics into thermodynamics & dynamics
331    o corresponding split of calc_diffusivity into
332      calc_diffusivity, calc_viscosity
333      (kpp_calc_diff, kpp_calc_visc).
334    o Added diffkr, kapgm to control variables
335    o bug fix in gmredi_slope_limit for ldd97
336    
337    checkpoint40pre5
338    o proper initialization of Adams-Bashforth time stepping
339      + uses forward step for very first step of model (iter=0)
340    o re-generated *all* output since almost all output is modified by this
341      change (sorry but we've been putting this one off for about 2 years)
342      + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
343        *not* regenerated since they are already out of date and I don't
344        want to create the impression that they are suddenly working.
345    o removed KAP stuff for DEC's
346    o modified/added many .cvsignore files in */code and */input
347    o added new expt "solid-body.cs-32x32x1"
348      + this uses an alternative form of ini_curvilinear_grid.F which
349        is not necessarily any better than the current one...
350    
351    checkpoint40pre4
352    o added re-initialisations of utrans,vtrans,rtrans in
353      calc_common_factors which are crucial for TAF.
354    o extended iMin,jMin range for calc_common_factors,
355      calc_diffusivity
356    o added option ALLOW_PASSIVE_TRACER
357    o a few minor updates and fixes
358    
359    checkpoint40pre3
360    o created calc_gtr1.F for gad package
361    o split the_main_loop and re-introduced forward_step
362    o some recomputations of nIter0 for TAMC
363    
364    checkpoint40pre2
365    o Updated to latest branch of AJA, JMC
366    o Added gradient check package
367    o Added routines for passive tracer handling
368    o Added carbon sequestration sensitivity experiment
369    
370    checkpoint39
371     o Modifications and fixes to support TAMC
372       (mainly missing or wrong directives)
373     o Corrected common blocks when fooling TAMC to produce adjoint I/O
374       in addummy_in_stepping
375     o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
376     o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
377     o Included following packages:
378       cal: calendar
379       exf: external forcing
380       ecco: essential routines to control use of cal, exf
381             (NB: this is not the full ECCO environment)
382     o disabled some packages by default in genmake
383    
384    checkpoint38
385     o see notes_c37_adj.txt
386     o corrected wrong layer index in external_forcing_t
387     o replaced the_main_loop/forward_step by the_main_loop
388     o removed forceoutput from write_state
389       (replaced criteria for initial/final state)
390     o added runtime flag for pre-C35 pickups: usePickupBeforeC35
391    
392  checkpoint37  checkpoint37
393   o mdsio.F routine split and packaged in pkg/mdsio   o mdsio.F routine split and packaged in pkg/mdsio
394     (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not     (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not

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