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revision 1.108 by dimitri, Thu Dec 5 08:43:02 2002 UTC revision 1.173 by jmc, Thu Jul 31 18:46:24 2003 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    o land pkg: read initial state from files.
7    o AIM : add stratospheric drag in the upper level
8    
9    checkpoint51d_post
10    o change function ILNBLNK (=> last non-blank char.) to return zero
11      (instead of the string length) when the string. char is empty
12    o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
13    o modif's to restore TAMC compatibility
14      - avoid "_d" constructs in PARAMETER declarations
15      - avoid interrupting lines by comment lines
16    o Use cluster local disks for purely local I/O
17      vs. globally visible disks needed for ctrl stuff
18      (merged from ecco-branch)
19      - new active_file_loc... and mdsio_..._loc routines
20      - affected packages: autodiff, ctrl, grdchk, mdsio
21    
22    checkpoint51c_post
23    o introducing integer flag debugLevel
24      - debLevZero: suppress all output
25      - debLevA: standard
26      - debLevB: equivalent to current debugMode=.TRUE.
27    o introducing pathname variable mdsioLocalDir for mdsio
28      that can be specified at runtime
29      (relevant for cluster I/O to local disk)
30    `
31    >>>checkpoint51b_post
32    adjoint of ptracers
33    o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
34    o extended state in checkpoint_lev?, etc.
35    o alternative ctrl/cost with tr1 or ptracer
36    o new comlev1_bibj_ptracers
37    o new ptracers.flow
38    o made ptracers_forcing same as external_forcing_s
39    o added verification for adjoint with ptracers
40      - adm. grdchk fail so far
41      - tlm. grdchk OK
42      - checked tapelev/comlev recomputations: OK
43    <<<checkpoint51b_pre
44    
45    checkpoint51a_post
46    o added code for biogeochemistry package
47      - new pkgs: dic, gchem
48      - new subroutine in ptracers
49    o modify code for biogeo packages
50      - in model/src and pkg/ptracers
51    
52    checkpoint51
53    o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
54      - autodiff, ctrl, exf, grdchk, seaice
55      kept separate packages
56      - cost, ecco, obcs
57    o updating verification/internal_wave, verification/lab_sea
58      (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
59    
60    checkpoint50i_post
61    o Preparing next differentiable checkpoint and sync
62      of MAIN vs. ecco-branch
63      - 1st step: this one is differentiable
64      - 2nd step: next(! not this) checkpoint will have updated packages
65                  from ecco-branch)
66    
67    checkpoint50h_post
68    o new package "land": provide surface BC for AIM.
69    o pkg/ptracers: apply exchange to all tracers after reading a pickup.
70    o AIM: use true log-P extrapolation for near surface temp (= as in
71        F.Molteni paper) ; update aim.5l_cs output.
72    o New variable in PARM03 for more flexible pickups
73    o somewhat cleaned package initialisation sequence for
74      ctrl/ cost/ ecco/ in packages_... routines
75    
76    checkpoint50g_post
77    o merged with release1_p17 (pkg/seaice and verification/lab_sea)
78      - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
79      - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
80        made the default because of faster convergence than ADI
81    
82    checkpoint50f_post
83    o exf totally restructured
84      - replaced all exf_set_ routines by one generic exf_set_gen.F
85        and made sure it's still differentiable
86      - split exf_getffields.F into new exf_bulkformulae.F
87      - exf_inscal_/exf_outscal_ suffixes consistent with field names
88      - updated adjoint/makefile and relevant verif. accordingly
89    
90    checkpoint50f_pre
91     o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
92          + change Evap over land. (update aim.5l_cs output)
93     o added missing .cvsignores and made uniform across expts
94     o changed configuration of tidal_basin_2d expt
95     o added pkg/debug functions for tracing code in fatal crashes
96     o tidied pkg/monitor to use MONITOR_OPTIONS.h
97     o new fn in pkg/monitor to stop model if solution grows too big
98     o removed lots of single quotes from comments
99    
100    checkpoint50e_post
101    o make KPP work with PTRACERS
102     - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
103       nearly a copy of kpp_transport_s
104     - there is no analogue to SurfaceTendencyS, so I have to use
105       gPtr(of the surface layer) instead
106    o add a new platform SunFire+mpi (SunFire 15000) to genmake
107    checkpoint50e_pre
108    
109    checkpoint50d_post
110    o change kpp output from multiple-record state files to single-record state
111      files analogous to write_state.F
112    o reduce the output frequency of cg3d-related stuff to the monitor frequency,
113      analogous to the cg2d-related output.
114    o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
115      so that writing to internal file fn (with length 512) fails.
116    checkpoint50d_pre
117    
118    checkpoint50c_post
119    o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
120    o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
121    o add time-average diagnostic of U*V and vertical diffusive flux for theta.
122    o bug fixed in convective adjustment diagnostic (multi-tile set-up).
123    o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
124    
125    checkpoint50c_pre
126    Merging from release1_p13:
127    o bug fix for pkg/seaice dynamic solver
128    o Added SEAICE_initialHEFF to pkg/seaice
129    
130    checkpoint50b_post
131    o store u*,v* in gU,V instead of in guNm1,gvNm1
132    o in order to put the momForcing out of the Adams-Bashforth:
133      move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
134      to timestep.F
135    o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
136    o re-generate output for highly sensitive test-exp:
137       global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
138    
139    checkpoint50b_pre
140    o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
141    o corrected CPP option mismatch in exf_Bulk... functions for case
142      #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
143    
144    checkpoint50a_post
145    o Bug fix for merging between c50 and KPP.
146      ikey was passed from thermodynamics to kpp_calc via
147      common block rather than being recomputed in kpp_calc,
148      in contradiction with new key itdkey.
149      New key ikppkey created, and tamc.h headers updated.
150    
151    checkpoint50
152    - 2nd step of merge with ecco-branch:
153      merge changes in ecco-branch back into main trunk
154    - bug fix in find_alpha
155    - more storing in gmredi_calc_tensor.F, kpp_routines.F
156    - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
157    - merged some sliced AD support routines
158    
159    checkpoint49
160    merged from ecco-branch:
161    o exf:
162      - Enable initialisation of forcing fields to constant
163        (runtime) values.
164      - in exf_getffields.F
165        Reduce i-/j-loop to interior domain, discarding overlaps.
166        That also fixes wrong TAF-key computations for key_1, key_2
167        with bulf formulae.
168      - exf_init.F modify #ifdef for exf_init_evap
169      - exf_getffieldrec.F, ctrl_getrec.F
170        The following INT-usages are not safe:
171          fldsecs  = int(fldsecs/fldperiod)*fldperiod
172          fldcount = int(fldsecs/fldperiod) + 1
173        and were modified.
174    o autodiff: checkpoint_lev...
175      - updated storing for bulk formulae (some arrays were missing)
176      - added state for seaice package
177      - synchronized with main branch
178    o DIVA:
179      Modif.s in
180      - the_main_loop.F
181      - the_model_main.F
182      and added cost_final_restore.F cost_final_store.F
183      o With these changes, it is possible to fully separate
184        the first forward run to compute the cost function (mdthe_main_loop)
185        and adjoint runs over individual DIVA intervals (adthe_main_loop)
186        into separate model executions.
187        This enables better tuning of DIVA to given queue sizes.
188      o Loss of cost function value in consecutive DIVA runs is
189        fixed by storing to 'costfinal' file.
190      o Appropriate call of ctrl_unpack/_pack,grdchk_main at
191        beginning/end of adjoint integration is accounted for.
192      The current changes apply to TAF-1.4.26.
193      TAF has one remaining bug, requiring one manual change
194      (see MITgcm manual).
195    o cal: synchronized between MAIN and ecco-branch
196    
197    checkpoint48i_post
198    o Changes to restore differentiability of code w.r.t. previous tag
199      (mostly adding new routines to make list and replacing
200      pressure by totPhiHyd).
201    o Updated and merged grdchk package
202      - has both ADM and TLM checks
203      - works for single- and multi-proc.
204      - output cleaned
205      - worked successfully for parallel DIVA
206    o genmake:
207      - Adding -platform=SP4
208      - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
209    o Modif. for DIVA:
210      ctrl_unpack should not be called in intermediate DIVA interval.
211      (similar thing would apply for active files such as
212      tbar, sbar, psbar, which should not be reinitialised;
213      only relevant for ecco-branch)
214    
215    checkpoint48h_post
216    o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
217    o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
218    o Added SEAICE_initialHEFF to pkg/seaice
219    o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
220    
221    checkpoint48g_post
222    --- EOS:
223    o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
224      store total Potential in totPhyHyd for diagnostics & EOS.
225    o fix restart and overlap Pb when using Z-coord and EOS funct. of P
226    --- Pressure/geopotential gradient:
227    o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
228    o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
229      ( changes results of global_ocean_pressure )
230    o NLFS + z-coord.: add eta*Rho' contribution.
231    o accurate phiHyd when using interface-W at the middle between 2 centers
232     ( changes results of ideal_2D_oce )
233    o includes r* 2nd term in potential gradient.
234    
235    checkpoint48f_post
236    Merging from release1_p12:
237    o Modifications for using pkg/exf with pkg/seaice
238      - improved description of the various forcing configurations
239      - added basic radiation bulk formulae to pkg/exf
240      - units/sign fix for evap computation in exf_getffields.F
241      - updated verification/global_with_exf/results/output.txt
242    o Added pkg/sbo for computing IERS Special Bureau for the Oceans
243      (SBO) core products, including oceanic mass, center-of-mass,
244      angular, and bottom pressure (see pkg/sbo/README.sbo).
245    o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
246      to avoid negative values in shallow regions.
247      - updated verification/natl_box/results/output.txt
248      - updated verification/lab_sea/results/output.txt
249    o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
250    o Added useSingleCpuIO option (see PARAMS.h).
251    o Updated useSingleCpuIO option in mdsio_writefield.F to
252      work with multi-field files, e.g., for single-file pickup.
253    o pkg/seaice:
254      - bug fix in growth.F: QNET for no shortwave case
255      - added HeffFile for specifying initial sea-ice thickness
256      - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
257    o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
258      kpp_transport_t.F, forward_step.F, and the_main_loop.F
259    o pkg/seaice:
260      - adjoint-friendly modifications
261      - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
262    
263    checkpoint48e_post
264    o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
265    o dynamics: change definition of computational domain & adapt mom_fluxform
266      accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
267    o following exp works with Olx=Oly=2 (and pass through checkbounds option):
268        adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
269        exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
270        global_ocean.90x40x15 global_with_exf global_ocean_pressure
271        inverted_barometer solid-body.cs-32x32x1
272      (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
273    
274    checkpoint48d_post
275    o in preparation for r*:
276     a) use pre-computed gradient of hydrostatic potential:
277        changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
278     b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
279        => affects results of glob_oce_pressure (different truncation error)  
280      update output.txt of ideal_2D_oce & global_ocean_pressure
281    
282    checkpoint48d_pre
283    o in preparation for r*:
284      new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
285      pass the 2 comp. of the grad. as arguments to momentum S/R.
286      but for the moment, only used if it does not change the results.
287    o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
288    
289    checkpoint48c_post
290    Modifications in treatment of initial flux forcing controls
291    to avoid extra storing of flux fields.
292    
293    checkpoint48c_pre
294    o Added tidal_basin_2d experiment (currently 1D!)
295    o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
296    
297    checkpoint48b_post
298    o r* coordinate added in #ifdef NONLIN_FRSURF block.
299     (modification to pressure gradient not yet implemented)
300    o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
301      (for U & V) that are used for vertical advection of momentum.
302    
303    checkpoint48a_post
304    o In preparation for r*, use temp. array to compute vertical transport
305       in flux-form momentum pkg. => change results of few test-exp.
306      Update output of: exp4, exp5, front_relax, global_ocean_pressure,
307                        lab_sea, natl_box & plume_on_slope
308    
309    checkpoint48
310    o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
311    
312    checkpoint47j_post
313    o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
314    o moved adexch from forward_step to addummy_in_stepping
315    o added exch in ctrl_map_...
316    o aveFreq.=0. at end of cost_final to avoid overwrite in
317      reverse checkpointing loop
318    o Yet more changes in gmredi:
319      * adgmredi_calc_tensor
320        avoiding all recomputation of gmredi_slope_limit
321      * adgmredi_x/y/rtransport
322        added flag for excessive storing to avoid recomp. of
323        u/v/rtans, dTdx/y/z
324        -> this is not really necessary and very memory-consuming
325      * adgmredi_slope_psi:
326        consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
327      * gmredi_slope_limit
328        re-activated full calculation of taperfct for case 'ac02'
329    o updating verification/ adjoints of carbon, global_ocean.90x40x15
330    
331    checkpoint47i_post
332    o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
333    o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
334      default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
335    o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
336    o gmredi: fix few bugs.
337    
338    checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
339    This will be a good checkpoint to plug into the ecco-branch.
340    o few modif.'s to get latest version adjointed
341      (mainly kick out code in ini_linear_phisurf)
342    o modif's to run adjoint with exactConserv
343    o case GM_BOLUS_ADVEC should be cleaned
344      S/R gmredi_slope_psi should be cleaned
345    o verification/carbon now has exactConserv=.TRUE.
346    
347    checkpoint47g_post
348    o time-average AIM output: becomes independent from statvars time-average
349      (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
350    o After TAF bug fix:
351      Tested adjoint of gmredi package.
352      Tests were done with checkpoint47 rather than with latest
353      checkpoint47f_post since the latter is broken for the adjoint
354      verification/carbon/ contains both ADM and TLM gradient checks.
355    Here they are, before they get changed/lost/stolen.
356    Mostly modif.'s to fix numerical sensitivities.
357    Gradient checks OK for
358    - GM_taper_scheme:
359      * clipping
360      * ac02
361      * linear
362      * glw91
363      * dm95
364      * ldd97
365    - GMREDI_OPTIONS:
366      * GM_VISBECK_VARIABLE_K
367      * GM_NON_UNITY_DIAGONAL
368      * GM_EXTRA_DIAGONAL
369      * GM_BOLUS_ADVEC
370    in conjunction with data.gmredi parameters to be checked in
371    in a few minutes under verification/carbon/code/
372    
373    checkpoint47f_post
374    Merging from release1_p10:
375    o modifications for using pkg/exf with pkg/seaice
376      - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
377        and SEAICE_EXTERNAL_FLUXES
378      - pkg/exf CPP options EXF_READ_EVAP and
379        EXF_NO_BULK_COMPUTATIONS
380      - usage examples are Experiments 8 and 9 in
381        verification/lab_sea/README
382      - verification/lab_sea default experiment now uses
383        pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
384    
385    checkpoint47e_post
386    o created a tag prior to creating a branch
387    
388    checkpoint47d_post
389    o fixed bug in the oceanic pressure coordinates code: vertical viscosity
390      at the bottom boundary had an erroneous half slip boundary condition
391    o added bottom drag and no slip boundary condition capabilities to
392      oceanic pressure coordinates code
393    o added new verification experiment global_ocean_pressure, this experiment is
394      also described in the tutorial section of the manual
395    checkpoint47d_pre
396    
397    checkpoint47c_post
398    o Added a verification experiment for a global cubed-sphere ocean run
399      -  verification/global_ocean.cubed32x32x30
400      -  uses pkg/therm_seaice and pkg/bulk_forcing
401    
402    o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
403    o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
404      when using P-coordinate; only implemented for atmospheric config.
405    o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
406      NOTES: requires option NONLIN_FRSURF to be "#define".
407    o update advect_xz/results/output.txt (left from checkpoint44g_post)
408    
409  checkpoint47b_post  checkpoint47b_post
410  Merging from release1_p9:  Merging from release1_p9:
411  o pkg/seaice  o pkg/seaice

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