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revision 1.106 by jmc, Sat Nov 23 22:39:36 2002 UTC revision 1.168 by stephd, Wed Jun 25 21:17:05 2003 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    checkpoint51a_post
7    o added code for biogeochemistry package
8      - new pkgs: dic, gchem
9      - new subroutine in ptracers
10    o modify code for biogeo packages
11      - in model/src and pkg/ptracers
12    
13    checkpoint51
14    o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
15      - autodiff, ctrl, exf, grdchk, seaice
16      kept separate packages
17      - cost, ecco, obcs
18    o updating verification/internal_wave, verification/lab_sea
19      (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
20    
21    checkpoint50i_post
22    o Preparing next differentiable checkpoint and sync
23      of MAIN vs. ecco-branch
24      - 1st step: this one is differentiable
25      - 2nd step: next(! not this) checkpoint will have updated packages
26                  from ecco-branch)
27    
28    checkpoint50h_post
29    o new package "land": provide surface BC for AIM.
30    o pkg/ptracers: apply exchange to all tracers after reading a pickup.
31    o AIM: use true log-P extrapolation for near surface temp (= as in
32        F.Molteni paper) ; update aim.5l_cs output.
33    o New variable in PARM03 for more flexible pickups
34    o somewhat cleaned package initialisation sequence for
35      ctrl/ cost/ ecco/ in packages_... routines
36    
37    checkpoint50g_post
38    o merged with release1_p17 (pkg/seaice and verification/lab_sea)
39      - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
40      - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
41        made the default because of faster convergence than ADI
42    
43    checkpoint50f_post
44    o exf totally restructured
45      - replaced all exf_set_ routines by one generic exf_set_gen.F
46        and made sure it's still differentiable
47      - split exf_getffields.F into new exf_bulkformulae.F
48      - exf_inscal_/exf_outscal_ suffixes consistent with field names
49      - updated adjoint/makefile and relevant verif. accordingly
50    
51    checkpoint50f_pre
52     o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
53          + change Evap over land. (update aim.5l_cs output)
54     o added missing .cvsignores and made uniform across expts
55     o changed configuration of tidal_basin_2d expt
56     o added pkg/debug functions for tracing code in fatal crashes
57     o tidied pkg/monitor to use MONITOR_OPTIONS.h
58     o new fn in pkg/monitor to stop model if solution grows too big
59     o removed lots of single quotes from comments
60    
61    checkpoint50e_post
62    o make KPP work with PTRACERS
63     - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
64       nearly a copy of kpp_transport_s
65     - there is no analogue to SurfaceTendencyS, so I have to use
66       gPtr(of the surface layer) instead
67    o add a new platform SunFire+mpi (SunFire 15000) to genmake
68    checkpoint50e_pre
69    
70    checkpoint50d_post
71    o change kpp output from multiple-record state files to single-record state
72      files analogous to write_state.F
73    o reduce the output frequency of cg3d-related stuff to the monitor frequency,
74      analogous to the cg2d-related output.
75    o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
76      so that writing to internal file fn (with length 512) fails.
77    checkpoint50d_pre
78    
79    checkpoint50c_post
80    o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
81    o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
82    o add time-average diagnostic of U*V and vertical diffusive flux for theta.
83    o bug fixed in convective adjustment diagnostic (multi-tile set-up).
84    o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
85    
86    checkpoint50c_pre
87    Merging from release1_p13:
88    o bug fix for pkg/seaice dynamic solver
89    o Added SEAICE_initialHEFF to pkg/seaice
90    
91    checkpoint50b_post
92    o store u*,v* in gU,V instead of in guNm1,gvNm1
93    o in order to put the momForcing out of the Adams-Bashforth:
94      move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
95      to timestep.F
96    o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
97    o re-generate output for highly sensitive test-exp:
98       global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
99    
100    checkpoint50b_pre
101    o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
102    o corrected CPP option mismatch in exf_Bulk... functions for case
103      #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
104    
105    checkpoint50a_post
106    o Bug fix for merging between c50 and KPP.
107      ikey was passed from thermodynamics to kpp_calc via
108      common block rather than being recomputed in kpp_calc,
109      in contradiction with new key itdkey.
110      New key ikppkey created, and tamc.h headers updated.
111    
112    checkpoint50
113    - 2nd step of merge with ecco-branch:
114      merge changes in ecco-branch back into main trunk
115    - bug fix in find_alpha
116    - more storing in gmredi_calc_tensor.F, kpp_routines.F
117    - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
118    - merged some sliced AD support routines
119    
120    checkpoint49
121    merged from ecco-branch:
122    o exf:
123      - Enable initialisation of forcing fields to constant
124        (runtime) values.
125      - in exf_getffields.F
126        Reduce i-/j-loop to interior domain, discarding overlaps.
127        That also fixes wrong TAF-key computations for key_1, key_2
128        with bulf formulae.
129      - exf_init.F modify #ifdef for exf_init_evap
130      - exf_getffieldrec.F, ctrl_getrec.F
131        The following INT-usages are not safe:
132          fldsecs  = int(fldsecs/fldperiod)*fldperiod
133          fldcount = int(fldsecs/fldperiod) + 1
134        and were modified.
135    o autodiff: checkpoint_lev...
136      - updated storing for bulk formulae (some arrays were missing)
137      - added state for seaice package
138      - synchronized with main branch
139    o DIVA:
140      Modif.s in
141      - the_main_loop.F
142      - the_model_main.F
143      and added cost_final_restore.F cost_final_store.F
144      o With these changes, it is possible to fully separate
145        the first forward run to compute the cost function (mdthe_main_loop)
146        and adjoint runs over individual DIVA intervals (adthe_main_loop)
147        into separate model executions.
148        This enables better tuning of DIVA to given queue sizes.
149      o Loss of cost function value in consecutive DIVA runs is
150        fixed by storing to 'costfinal' file.
151      o Appropriate call of ctrl_unpack/_pack,grdchk_main at
152        beginning/end of adjoint integration is accounted for.
153      The current changes apply to TAF-1.4.26.
154      TAF has one remaining bug, requiring one manual change
155      (see MITgcm manual).
156    o cal: synchronized between MAIN and ecco-branch
157    
158    checkpoint48i_post
159    o Changes to restore differentiability of code w.r.t. previous tag
160      (mostly adding new routines to make list and replacing
161      pressure by totPhiHyd).
162    o Updated and merged grdchk package
163      - has both ADM and TLM checks
164      - works for single- and multi-proc.
165      - output cleaned
166      - worked successfully for parallel DIVA
167    o genmake:
168      - Adding -platform=SP4
169      - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
170    o Modif. for DIVA:
171      ctrl_unpack should not be called in intermediate DIVA interval.
172      (similar thing would apply for active files such as
173      tbar, sbar, psbar, which should not be reinitialised;
174      only relevant for ecco-branch)
175    
176    checkpoint48h_post
177    o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
178    o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
179    o Added SEAICE_initialHEFF to pkg/seaice
180    o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
181    
182    checkpoint48g_post
183    --- EOS:
184    o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
185      store total Potential in totPhyHyd for diagnostics & EOS.
186    o fix restart and overlap Pb when using Z-coord and EOS funct. of P
187    --- Pressure/geopotential gradient:
188    o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
189    o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
190      ( changes results of global_ocean_pressure )
191    o NLFS + z-coord.: add eta*Rho' contribution.
192    o accurate phiHyd when using interface-W at the middle between 2 centers
193     ( changes results of ideal_2D_oce )
194    o includes r* 2nd term in potential gradient.
195    
196    checkpoint48f_post
197    Merging from release1_p12:
198    o Modifications for using pkg/exf with pkg/seaice
199      - improved description of the various forcing configurations
200      - added basic radiation bulk formulae to pkg/exf
201      - units/sign fix for evap computation in exf_getffields.F
202      - updated verification/global_with_exf/results/output.txt
203    o Added pkg/sbo for computing IERS Special Bureau for the Oceans
204      (SBO) core products, including oceanic mass, center-of-mass,
205      angular, and bottom pressure (see pkg/sbo/README.sbo).
206    o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
207      to avoid negative values in shallow regions.
208      - updated verification/natl_box/results/output.txt
209      - updated verification/lab_sea/results/output.txt
210    o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
211    o Added useSingleCpuIO option (see PARAMS.h).
212    o Updated useSingleCpuIO option in mdsio_writefield.F to
213      work with multi-field files, e.g., for single-file pickup.
214    o pkg/seaice:
215      - bug fix in growth.F: QNET for no shortwave case
216      - added HeffFile for specifying initial sea-ice thickness
217      - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
218    o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
219      kpp_transport_t.F, forward_step.F, and the_main_loop.F
220    o pkg/seaice:
221      - adjoint-friendly modifications
222      - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
223    
224    checkpoint48e_post
225    o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
226    o dynamics: change definition of computational domain & adapt mom_fluxform
227      accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
228    o following exp works with Olx=Oly=2 (and pass through checkbounds option):
229        adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
230        exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
231        global_ocean.90x40x15 global_with_exf global_ocean_pressure
232        inverted_barometer solid-body.cs-32x32x1
233      (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
234    
235    checkpoint48d_post
236    o in preparation for r*:
237     a) use pre-computed gradient of hydrostatic potential:
238        changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
239     b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
240        => affects results of glob_oce_pressure (different truncation error)  
241      update output.txt of ideal_2D_oce & global_ocean_pressure
242    
243    checkpoint48d_pre
244    o in preparation for r*:
245      new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
246      pass the 2 comp. of the grad. as arguments to momentum S/R.
247      but for the moment, only used if it does not change the results.
248    o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
249    
250    checkpoint48c_post
251    Modifications in treatment of initial flux forcing controls
252    to avoid extra storing of flux fields.
253    
254    checkpoint48c_pre
255    o Added tidal_basin_2d experiment (currently 1D!)
256    o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
257    
258    checkpoint48b_post
259    o r* coordinate added in #ifdef NONLIN_FRSURF block.
260     (modification to pressure gradient not yet implemented)
261    o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
262      (for U & V) that are used for vertical advection of momentum.
263    
264    checkpoint48a_post
265    o In preparation for r*, use temp. array to compute vertical transport
266       in flux-form momentum pkg. => change results of few test-exp.
267      Update output of: exp4, exp5, front_relax, global_ocean_pressure,
268                        lab_sea, natl_box & plume_on_slope
269    
270    checkpoint48
271    o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
272    
273    checkpoint47j_post
274    o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
275    o moved adexch from forward_step to addummy_in_stepping
276    o added exch in ctrl_map_...
277    o aveFreq.=0. at end of cost_final to avoid overwrite in
278      reverse checkpointing loop
279    o Yet more changes in gmredi:
280      * adgmredi_calc_tensor
281        avoiding all recomputation of gmredi_slope_limit
282      * adgmredi_x/y/rtransport
283        added flag for excessive storing to avoid recomp. of
284        u/v/rtans, dTdx/y/z
285        -> this is not really necessary and very memory-consuming
286      * adgmredi_slope_psi:
287        consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
288      * gmredi_slope_limit
289        re-activated full calculation of taperfct for case 'ac02'
290    o updating verification/ adjoints of carbon, global_ocean.90x40x15
291    
292    checkpoint47i_post
293    o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
294    o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
295      default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
296    o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
297    o gmredi: fix few bugs.
298    
299    checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
300    This will be a good checkpoint to plug into the ecco-branch.
301    o few modif.'s to get latest version adjointed
302      (mainly kick out code in ini_linear_phisurf)
303    o modif's to run adjoint with exactConserv
304    o case GM_BOLUS_ADVEC should be cleaned
305      S/R gmredi_slope_psi should be cleaned
306    o verification/carbon now has exactConserv=.TRUE.
307    
308    checkpoint47g_post
309    o time-average AIM output: becomes independent from statvars time-average
310      (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
311    o After TAF bug fix:
312      Tested adjoint of gmredi package.
313      Tests were done with checkpoint47 rather than with latest
314      checkpoint47f_post since the latter is broken for the adjoint
315      verification/carbon/ contains both ADM and TLM gradient checks.
316    Here they are, before they get changed/lost/stolen.
317    Mostly modif.'s to fix numerical sensitivities.
318    Gradient checks OK for
319    - GM_taper_scheme:
320      * clipping
321      * ac02
322      * linear
323      * glw91
324      * dm95
325      * ldd97
326    - GMREDI_OPTIONS:
327      * GM_VISBECK_VARIABLE_K
328      * GM_NON_UNITY_DIAGONAL
329      * GM_EXTRA_DIAGONAL
330      * GM_BOLUS_ADVEC
331    in conjunction with data.gmredi parameters to be checked in
332    in a few minutes under verification/carbon/code/
333    
334    checkpoint47f_post
335    Merging from release1_p10:
336    o modifications for using pkg/exf with pkg/seaice
337      - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
338        and SEAICE_EXTERNAL_FLUXES
339      - pkg/exf CPP options EXF_READ_EVAP and
340        EXF_NO_BULK_COMPUTATIONS
341      - usage examples are Experiments 8 and 9 in
342        verification/lab_sea/README
343      - verification/lab_sea default experiment now uses
344        pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
345    
346    checkpoint47e_post
347    o created a tag prior to creating a branch
348    
349    checkpoint47d_post
350    o fixed bug in the oceanic pressure coordinates code: vertical viscosity
351      at the bottom boundary had an erroneous half slip boundary condition
352    o added bottom drag and no slip boundary condition capabilities to
353      oceanic pressure coordinates code
354    o added new verification experiment global_ocean_pressure, this experiment is
355      also described in the tutorial section of the manual
356    checkpoint47d_pre
357    
358    checkpoint47c_post
359    o Added a verification experiment for a global cubed-sphere ocean run
360      -  verification/global_ocean.cubed32x32x30
361      -  uses pkg/therm_seaice and pkg/bulk_forcing
362    
363    o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
364    o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
365      when using P-coordinate; only implemented for atmospheric config.
366    o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
367      NOTES: requires option NONLIN_FRSURF to be "#define".
368    o update advect_xz/results/output.txt (left from checkpoint44g_post)
369    
370    checkpoint47b_post
371    Merging from release1_p9:
372    o pkg/seaice
373      - removed GOTO's and added taf directives
374      - double precision constants to reduce the g77 (Linux)
375        to F77 (SGI) differences reported in release1_p8
376    o tools/genmake
377      - added SGI options
378    o verification/testscript
379      - updated to that of checkpoint47a_post
380    o verification/global_ocean.90x40x15/input/eedata
381      - modified for SGI f77 compatibility
382    o verification/lab_sea
383      - added description of sea-ice model
384      - added missing matlab routines
385      - added test of thermodynamics parallelization
386    
387  checkpoint47a_post  checkpoint47a_post
388  o new pkg: aim_v23  o new pkg: aim_v23
389   = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.   = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
# Line 13  o new pkg: aim_v23 Line 394  o new pkg: aim_v23
394  o add diagnostic of surface correction term in monitor output  o add diagnostic of surface correction term in monitor output
395    
396  o bulk_force and therm_seaice  o bulk_force and therm_seaice
397    - Two packages:  bulk_force (Bulk forcing)
398      and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
399    - Earlier integration from Stephaine Dutkiewicz
400      and Patrick Heimbach.
401    - Two ifdef statements for compile time,
402       ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
403    
404  checkpoint47  checkpoint47
405  differentiable version of checkpoint46n_post  differentiable version of checkpoint46n_post

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