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revision 1.95 by adcroft, Tue Nov 5 19:14:26 2002 UTC revision 1.153 by jmc, Mon May 12 21:16:45 2003 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    checkpoint50c_post
7    o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
8    o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
9    o add time-average diagnostic of U*V and vertical diffusive flux for theta.
10    o bug fixed in convective adjustment diagnostic (multi-tile set-up).
11    o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
12    
13    checkpoint50c_pre
14    Merging from release1_p13:
15    o bug fix for pkg/seaice dynamic solver
16    o Added SEAICE_initialHEFF to pkg/seaice
17    
18    checkpoint50b_post
19    o store u*,v* in gU,V instead of in guNm1,gvNm1
20    o in order to put the momForcing out of the Adams-Bashforth:
21      move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
22      to timestep.F
23    o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
24    o re-generate output for highly sensitive test-exp:
25       global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
26    
27    checkpoint50b_pre
28    o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
29    o corrected CPP option mismatch in exf_Bulk... functions for case
30      #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
31    
32    checkpoint50a_post
33    o Bug fix for merging between c50 and KPP.
34      ikey was passed from thermodynamics to kpp_calc via
35      common block rather than being recomputed in kpp_calc,
36      in contradiction with new key itdkey.
37      New key ikppkey created, and tamc.h headers updated.
38    
39    checkpoint50
40    - 2nd step of merge with ecco-branch:
41      merge changes in ecco-branch back into main trunk
42    - bug fix in find_alpha
43    - more storing in gmredi_calc_tensor.F, kpp_routines.F
44    - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
45    - merged some sliced AD support routines
46    
47    checkpoint49
48    merged from ecco-branch:
49    o exf:
50      - Enable initialisation of forcing fields to constant
51        (runtime) values.
52      - in exf_getffields.F
53        Reduce i-/j-loop to interior domain, discarding overlaps.
54        That also fixes wrong TAF-key computations for key_1, key_2
55        with bulf formulae.
56      - exf_init.F modify #ifdef for exf_init_evap
57      - exf_getffieldrec.F, ctrl_getrec.F
58        The following INT-usages are not safe:
59          fldsecs  = int(fldsecs/fldperiod)*fldperiod
60          fldcount = int(fldsecs/fldperiod) + 1
61        and were modified.
62    o autodiff: checkpoint_lev...
63      - updated storing for bulk formulae (some arrays were missing)
64      - added state for seaice package
65      - synchronized with main branch
66    o DIVA:
67      Modif.s in
68      - the_main_loop.F
69      - the_model_main.F
70      and added cost_final_restore.F cost_final_store.F
71      o With these changes, it is possible to fully separate
72        the first forward run to compute the cost function (mdthe_main_loop)
73        and adjoint runs over individual DIVA intervals (adthe_main_loop)
74        into separate model executions.
75        This enables better tuning of DIVA to given queue sizes.
76      o Loss of cost function value in consecutive DIVA runs is
77        fixed by storing to 'costfinal' file.
78      o Appropriate call of ctrl_unpack/_pack,grdchk_main at
79        beginning/end of adjoint integration is accounted for.
80      The current changes apply to TAF-1.4.26.
81      TAF has one remaining bug, requiring one manual change
82      (see MITgcm manual).
83    o cal: synchronized between MAIN and ecco-branch
84    
85    checkpoint48i_post
86    o Changes to restore differentiability of code w.r.t. previous tag
87      (mostly adding new routines to make list and replacing
88      pressure by totPhiHyd).
89    o Updated and merged grdchk package
90      - has both ADM and TLM checks
91      - works for single- and multi-proc.
92      - output cleaned
93      - worked successfully for parallel DIVA
94    o genmake:
95      - Adding -platform=SP4
96      - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
97    o Modif. for DIVA:
98      ctrl_unpack should not be called in intermediate DIVA interval.
99      (similar thing would apply for active files such as
100      tbar, sbar, psbar, which should not be reinitialised;
101      only relevant for ecco-branch)
102    
103    checkpoint48h_post
104    o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
105    o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
106    o Added SEAICE_initialHEFF to pkg/seaice
107    o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
108    
109    checkpoint48g_post
110    --- EOS:
111    o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
112      store total Potential in totPhyHyd for diagnostics & EOS.
113    o fix restart and overlap Pb when using Z-coord and EOS funct. of P
114    --- Pressure/geopotential gradient:
115    o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
116    o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
117      ( changes results of global_ocean_pressure )
118    o NLFS + z-coord.: add eta*Rho' contribution.
119    o accurate phiHyd when using interface-W at the middle between 2 centers
120     ( changes results of ideal_2D_oce )
121    o includes r* 2nd term in potential gradient.
122    
123    checkpoint48f_post
124    Merging from release1_p12:
125    o Modifications for using pkg/exf with pkg/seaice
126      - improved description of the various forcing configurations
127      - added basic radiation bulk formulae to pkg/exf
128      - units/sign fix for evap computation in exf_getffields.F
129      - updated verification/global_with_exf/results/output.txt
130    o Added pkg/sbo for computing IERS Special Bureau for the Oceans
131      (SBO) core products, including oceanic mass, center-of-mass,
132      angular, and bottom pressure (see pkg/sbo/README.sbo).
133    o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
134      to avoid negative values in shallow regions.
135      - updated verification/natl_box/results/output.txt
136      - updated verification/lab_sea/results/output.txt
137    o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
138    o Added useSingleCpuIO option (see PARAMS.h).
139    o Updated useSingleCpuIO option in mdsio_writefield.F to
140      work with multi-field files, e.g., for single-file pickup.
141    o pkg/seaice:
142      - bug fix in growth.F: QNET for no shortwave case
143      - added HeffFile for specifying initial sea-ice thickness
144      - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
145    o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
146      kpp_transport_t.F, forward_step.F, and the_main_loop.F
147    o pkg/seaice:
148      - adjoint-friendly modifications
149      - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
150    
151    checkpoint48e_post
152    o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
153    o dynamics: change definition of computational domain & adapt mom_fluxform
154      accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
155    o following exp works with Olx=Oly=2 (and pass through checkbounds option):
156        adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
157        exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
158        global_ocean.90x40x15 global_with_exf global_ocean_pressure
159        inverted_barometer solid-body.cs-32x32x1
160      (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
161    
162    checkpoint48d_post
163    o in preparation for r*:
164     a) use pre-computed gradient of hydrostatic potential:
165        changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
166     b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
167        => affects results of glob_oce_pressure (different truncation error)  
168      update output.txt of ideal_2D_oce & global_ocean_pressure
169    
170    checkpoint48d_pre
171    o in preparation for r*:
172      new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
173      pass the 2 comp. of the grad. as arguments to momentum S/R.
174      but for the moment, only used if it does not change the results.
175    o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
176    
177    checkpoint48c_post
178    Modifications in treatment of initial flux forcing controls
179    to avoid extra storing of flux fields.
180    
181    checkpoint48c_pre
182    o Added tidal_basin_2d experiment (currently 1D!)
183    o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
184    
185    checkpoint48b_post
186    o r* coordinate added in #ifdef NONLIN_FRSURF block.
187     (modification to pressure gradient not yet implemented)
188    o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
189      (for U & V) that are used for vertical advection of momentum.
190    
191    checkpoint48a_post
192    o In preparation for r*, use temp. array to compute vertical transport
193       in flux-form momentum pkg. => change results of few test-exp.
194      Update output of: exp4, exp5, front_relax, global_ocean_pressure,
195                        lab_sea, natl_box & plume_on_slope
196    
197    checkpoint48
198    o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
199    
200    checkpoint47j_post
201    o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
202    o moved adexch from forward_step to addummy_in_stepping
203    o added exch in ctrl_map_...
204    o aveFreq.=0. at end of cost_final to avoid overwrite in
205      reverse checkpointing loop
206    o Yet more changes in gmredi:
207      * adgmredi_calc_tensor
208        avoiding all recomputation of gmredi_slope_limit
209      * adgmredi_x/y/rtransport
210        added flag for excessive storing to avoid recomp. of
211        u/v/rtans, dTdx/y/z
212        -> this is not really necessary and very memory-consuming
213      * adgmredi_slope_psi:
214        consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
215      * gmredi_slope_limit
216        re-activated full calculation of taperfct for case 'ac02'
217    o updating verification/ adjoints of carbon, global_ocean.90x40x15
218    
219    checkpoint47i_post
220    o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
221    o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
222      default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
223    o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
224    o gmredi: fix few bugs.
225    
226    checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
227    This will be a good checkpoint to plug into the ecco-branch.
228    o few modif.'s to get latest version adjointed
229      (mainly kick out code in ini_linear_phisurf)
230    o modif's to run adjoint with exactConserv
231    o case GM_BOLUS_ADVEC should be cleaned
232      S/R gmredi_slope_psi should be cleaned
233    o verification/carbon now has exactConserv=.TRUE.
234    
235    checkpoint47g_post
236    o time-average AIM output: becomes independent from statvars time-average
237      (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
238    o After TAF bug fix:
239      Tested adjoint of gmredi package.
240      Tests were done with checkpoint47 rather than with latest
241      checkpoint47f_post since the latter is broken for the adjoint
242      verification/carbon/ contains both ADM and TLM gradient checks.
243    Here they are, before they get changed/lost/stolen.
244    Mostly modif.'s to fix numerical sensitivities.
245    Gradient checks OK for
246    - GM_taper_scheme:
247      * clipping
248      * ac02
249      * linear
250      * glw91
251      * dm95
252      * ldd97
253    - GMREDI_OPTIONS:
254      * GM_VISBECK_VARIABLE_K
255      * GM_NON_UNITY_DIAGONAL
256      * GM_EXTRA_DIAGONAL
257      * GM_BOLUS_ADVEC
258    in conjunction with data.gmredi parameters to be checked in
259    in a few minutes under verification/carbon/code/
260    
261    checkpoint47f_post
262    Merging from release1_p10:
263    o modifications for using pkg/exf with pkg/seaice
264      - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
265        and SEAICE_EXTERNAL_FLUXES
266      - pkg/exf CPP options EXF_READ_EVAP and
267        EXF_NO_BULK_COMPUTATIONS
268      - usage examples are Experiments 8 and 9 in
269        verification/lab_sea/README
270      - verification/lab_sea default experiment now uses
271        pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
272    
273    checkpoint47e_post
274    o created a tag prior to creating a branch
275    
276    checkpoint47d_post
277    o fixed bug in the oceanic pressure coordinates code: vertical viscosity
278      at the bottom boundary had an erroneous half slip boundary condition
279    o added bottom drag and no slip boundary condition capabilities to
280      oceanic pressure coordinates code
281    o added new verification experiment global_ocean_pressure, this experiment is
282      also described in the tutorial section of the manual
283    checkpoint47d_pre
284    
285    checkpoint47c_post
286    o Added a verification experiment for a global cubed-sphere ocean run
287      -  verification/global_ocean.cubed32x32x30
288      -  uses pkg/therm_seaice and pkg/bulk_forcing
289    
290    o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
291    o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
292      when using P-coordinate; only implemented for atmospheric config.
293    o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
294      NOTES: requires option NONLIN_FRSURF to be "#define".
295    o update advect_xz/results/output.txt (left from checkpoint44g_post)
296    
297    checkpoint47b_post
298    Merging from release1_p9:
299    o pkg/seaice
300      - removed GOTO's and added taf directives
301      - double precision constants to reduce the g77 (Linux)
302        to F77 (SGI) differences reported in release1_p8
303    o tools/genmake
304      - added SGI options
305    o verification/testscript
306      - updated to that of checkpoint47a_post
307    o verification/global_ocean.90x40x15/input/eedata
308      - modified for SGI f77 compatibility
309    o verification/lab_sea
310      - added description of sea-ice model
311      - added missing matlab routines
312      - added test of thermodynamics parallelization
313    
314    checkpoint47a_post
315    o new pkg: aim_v23
316     = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
317       for now, keep the same surface forcing as before.
318     - Part-Cell implemented into AIM; check that Heat & Water are conserved
319     - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
320     - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
321    o add diagnostic of surface correction term in monitor output
322    
323    o bulk_force and therm_seaice
324    - Two packages:  bulk_force (Bulk forcing)
325      and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
326    - Earlier integration from Stephaine Dutkiewicz
327      and Patrick Heimbach.
328    - Two ifdef statements for compile time,
329       ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
330    
331    checkpoint47
332    differentiable version of checkpoint46n_post
333    o bug fix in quasihydrostaticterms
334    o * "clean" adjoint code (in terms of extensive recomputations)
335        can now be obtained for all GMREDI options (i.e. for
336        - GM_VISBECK_VARIABLE_K
337        - GM_NON_UNITY_DIAGONAL
338        - GM_EXTRA_DIAGONAL
339        - GM_BOLUS_ADVEC )
340      * However, wrong gradient check problem remains unsolved.
341      * New CPP options have been introduced for different
342        tapering schemes
343    o external_fields_load now part of differentiation list
344    o pressure needs multiple storing;
345      would be nice to have store_pressure at beginning or
346      end of forward_step, e.g. by having phiHyd global (5-dim.)
347      (NB: pressure is needed for certain cases in find_rho,
348      which is also invoked through convective_adjustment).
349    o recomputations in find_rho for cases
350     'JMD95'/'UNESCO' or 'MDJWF' are OK.
351    o #define ATMOSPHERIC_LOADING should be differentiable
352    o ini_forcing shifted to begining of initialise_varia
353    o Incorporating QNVS line search routines into MITgcm
354      (this is separate code, and therefore not under pkg)
355      lsopt/, optim/
356    o Updated verification/carbon/
357      - #define GM_VISBECK_VARIABLE_K
358      - GM_taper_scheme    = 'ldd97'    
359    
360    checkpoint46n_post
361    Merging from release1_p8:
362    o verification/natl_box:
363      updating new external_fields_load routine
364    o New package: pkg/seaice
365      Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
366      The sea-ice code is based on Hibler (1979-1980).
367      Two sea-ice dynamic solvers, ADI and LSR, are included.
368      In addition to computing prognostic sea-ice variables and diagnosing
369      the forcing/external data fields that drive the ocean model,
370      SEAICE_MODEL also sets theta to the freezing point under sea-ice.
371      The implied surface heat flux is then stored in variable
372      surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
373      kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
374      non-local transport term.  Because this call precedes model
375      thermodynamics, temperature under sea-ice may not be "exactly" at
376      the freezing point by the time theta is dumped or time-averaged.
377      N.B.: fairly large differences in accuracy occur across
378            different platforms/compilers; comparison between
379            g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
380            generated output gives:
381       T           S           U           V
382      C D M    c        m  s        m  s        m  s        m  s
383      n p a R  g  m  m  e  .  m  m  e  .  m  m  e  .  m  m  e  .
384      f n k u  2  i  a  a  d  i  a  a  d  i  a  a  d  i  a  a  d
385      g d e n  d  n  x  n  .  n  x  n  .  n  x  n  .  n  x  n  .
386    
387      Y Y Y Y  5  5  7  7  7  8 10  9  6  6  6  6  7  5  7  5  7 FAIL  lab_sea
388    o GAD:
389      - generated new common blocks to account for call of
390        same gad routines with differing traceridentities
391        (needed to modify tracerIdentity indices in GAD.h)
392      - generated separate common blocks for case useCubedSphereExchange
393        (Department of Futurology)
394      - parameter lists to gmredi_?transport: added tracerIdentity
395      - added new key indices to tamc.h
396    o external_fields_load:
397      - added this routine to TAF list
398      - needed to make some common blocks global and additional storing
399        along the same lines as exf package (checkpoint_lev?_directives.h)
400    o exf:
401      updated external forcing package
402      - bug fixes carried over from ecco-branch
403        (missing OBCS_OPTIONS.h in two routines)
404      - enable easy to use "no forcing".
405      - added exf I/O for atmospheric loading
406      - added exf I/O for runoff data
407      - transfered scaling between exf <-> MITgcm to exf namelist
408    o Adding new verification experiment global_with_exf.
409      This verification experiment is almost identical to the
410      global_ocean.90x40x15 experiment, except that it uses
411      the exf (and cal) package instead of the
412      external_fields_load routine (cf README file).
413    
414    checkpoint46m_post
415    o modified testscript to return -- when there are no lines of "%MON" output
416    o added new flag "quasiHydrostatic" for QH mode
417      and new routine quasihydrostaticterms()
418    o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
419      New routine: mom_u_coriolis_nh()
420    o fixed sign of non-hydrostatic metric terms in u and v equations.
421      Depend on correct sign of gravitySign.
422    o added work.pc* to .cvsignore in aim directories using ifc
423    o introduced flag for controllin non-hydrostatic metric terms
424  o removed gravitySign from PARM04  o removed gravitySign from PARM04
425  o switched to g77/ifc from pgf77 in aim experiments  o switched to g77/ifc from pgf77 in aim experiments
426    

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