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revision 1.72 by heimbach, Thu May 30 02:38:38 2002 UTC revision 1.124 by jmc, Sun Jan 26 21:38:04 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 r* coordinate added in #ifdef NONLIN_FRSURF block.
7     (modification to pressure gradient not yet implemented)
8    o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
9      (for U & V) that are used for vertical advection of momentum.
10    
11    checkpoint48a_post
12    o In preparation for r*, use temp. array to compute vertical transport
13       in flux-form momentum pkg. => change results of few test-exp.
14      Update output of: exp4, exp5, front_relax, global_ocean_pressure,
15                        lab_sea, natl_box & plume_on_slope
16    
17    checkpoint48
18    o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
19    
20    checkpoint47j_post
21    o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
22    o moved adexch from forward_step to addummy_in_stepping
23    o added exch in ctrl_map_...
24    o aveFreq.=0. at end of cost_final to avoid overwrite in
25      reverse checkpointing loop
26    o Yet more changes in gmredi:
27      * adgmredi_calc_tensor
28        avoiding all recomputation of gmredi_slope_limit
29      * adgmredi_x/y/rtransport
30        added flag for excessive storing to avoid recomp. of
31        u/v/rtans, dTdx/y/z
32        -> this is not really necessary and very memory-consuming
33      * adgmredi_slope_psi:
34        consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
35      * gmredi_slope_limit
36        re-activated full calculation of taperfct for case 'ac02'
37    o updating verification/ adjoints of carbon, global_ocean.90x40x15
38    
39    checkpoint47i_post
40    o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
41    o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
42      default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
43    o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
44    o gmredi: fix few bugs.
45    
46    checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
47    This will be a good checkpoint to plug into the ecco-branch.
48    o few modif.'s to get latest version adjointed
49      (mainly kick out code in ini_linear_phisurf)
50    o modif's to run adjoint with exactConserv
51    o case GM_BOLUS_ADVEC should be cleaned
52      S/R gmredi_slope_psi should be cleaned
53    o verification/carbon now has exactConserv=.TRUE.
54    
55    checkpoint47g_post
56    o time-average AIM output: becomes independent from statvars time-average
57      (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
58    o After TAF bug fix:
59      Tested adjoint of gmredi package.
60      Tests were done with checkpoint47 rather than with latest
61      checkpoint47f_post since the latter is broken for the adjoint
62      verification/carbon/ contains both ADM and TLM gradient checks.
63    Here they are, before they get changed/lost/stolen.
64    Mostly modif.'s to fix numerical sensitivities.
65    Gradient checks OK for
66    - GM_taper_scheme:
67      * clipping
68      * ac02
69      * linear
70      * glw91
71      * dm95
72      * ldd97
73    - GMREDI_OPTIONS:
74      * GM_VISBECK_VARIABLE_K
75      * GM_NON_UNITY_DIAGONAL
76      * GM_EXTRA_DIAGONAL
77      * GM_BOLUS_ADVEC
78    in conjunction with data.gmredi parameters to be checked in
79    in a few minutes under verification/carbon/code/
80    
81    checkpoint47f_post
82    Merging from release1_p10:
83    o modifications for using pkg/exf with pkg/seaice
84      - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
85        and SEAICE_EXTERNAL_FLUXES
86      - pkg/exf CPP options EXF_READ_EVAP and
87        EXF_NO_BULK_COMPUTATIONS
88      - usage examples are Experiments 8 and 9 in
89        verification/lab_sea/README
90      - verification/lab_sea default experiment now uses
91        pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
92    
93    checkpoint47e_post
94    o created a tag prior to creating a branch
95    
96    checkpoint47d_post
97    o fixed bug in the oceanic pressure coordinates code: vertical viscosity
98      at the bottom boundary had an erroneous half slip boundary condition
99    o added bottom drag and no slip boundary condition capabilities to
100      oceanic pressure coordinates code
101    o added new verification experiment global_ocean_pressure, this experiment is
102      also described in the tutorial section of the manual
103    checkpoint47d_pre
104    
105    checkpoint47c_post
106    o Added a verification experiment for a global cubed-sphere ocean run
107      -  verification/global_ocean.cubed32x32x30
108      -  uses pkg/therm_seaice and pkg/bulk_forcing
109    
110    o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
111    o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
112      when using P-coordinate; only implemented for atmospheric config.
113    o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
114      NOTES: requires option NONLIN_FRSURF to be "#define".
115    o update advect_xz/results/output.txt (left from checkpoint44g_post)
116    
117    checkpoint47b_post
118    Merging from release1_p9:
119    o pkg/seaice
120      - removed GOTO's and added taf directives
121      - double precision constants to reduce the g77 (Linux)
122        to F77 (SGI) differences reported in release1_p8
123    o tools/genmake
124      - added SGI options
125    o verification/testscript
126      - updated to that of checkpoint47a_post
127    o verification/global_ocean.90x40x15/input/eedata
128      - modified for SGI f77 compatibility
129    o verification/lab_sea
130      - added description of sea-ice model
131      - added missing matlab routines
132      - added test of thermodynamics parallelization
133    
134    checkpoint47a_post
135    o new pkg: aim_v23
136     = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
137       for now, keep the same surface forcing as before.
138     - Part-Cell implemented into AIM; check that Heat & Water are conserved
139     - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
140     - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
141    o add diagnostic of surface correction term in monitor output
142    
143    o bulk_force and therm_seaice
144    - Two packages:  bulk_force (Bulk forcing)
145      and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
146    - Earlier integration from Stephaine Dutkiewicz
147      and Patrick Heimbach.
148    - Two ifdef statements for compile time,
149       ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
150    
151    checkpoint47
152    differentiable version of checkpoint46n_post
153    o bug fix in quasihydrostaticterms
154    o * "clean" adjoint code (in terms of extensive recomputations)
155        can now be obtained for all GMREDI options (i.e. for
156        - GM_VISBECK_VARIABLE_K
157        - GM_NON_UNITY_DIAGONAL
158        - GM_EXTRA_DIAGONAL
159        - GM_BOLUS_ADVEC )
160      * However, wrong gradient check problem remains unsolved.
161      * New CPP options have been introduced for different
162        tapering schemes
163    o external_fields_load now part of differentiation list
164    o pressure needs multiple storing;
165      would be nice to have store_pressure at beginning or
166      end of forward_step, e.g. by having phiHyd global (5-dim.)
167      (NB: pressure is needed for certain cases in find_rho,
168      which is also invoked through convective_adjustment).
169    o recomputations in find_rho for cases
170     'JMD95'/'UNESCO' or 'MDJWF' are OK.
171    o #define ATMOSPHERIC_LOADING should be differentiable
172    o ini_forcing shifted to begining of initialise_varia
173    o Incorporating QNVS line search routines into MITgcm
174      (this is separate code, and therefore not under pkg)
175      lsopt/, optim/
176    o Updated verification/carbon/
177      - #define GM_VISBECK_VARIABLE_K
178      - GM_taper_scheme    = 'ldd97'    
179    
180    checkpoint46n_post
181    Merging from release1_p8:
182    o verification/natl_box:
183      updating new external_fields_load routine
184    o New package: pkg/seaice
185      Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
186      The sea-ice code is based on Hibler (1979-1980).
187      Two sea-ice dynamic solvers, ADI and LSR, are included.
188      In addition to computing prognostic sea-ice variables and diagnosing
189      the forcing/external data fields that drive the ocean model,
190      SEAICE_MODEL also sets theta to the freezing point under sea-ice.
191      The implied surface heat flux is then stored in variable
192      surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
193      kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
194      non-local transport term.  Because this call precedes model
195      thermodynamics, temperature under sea-ice may not be "exactly" at
196      the freezing point by the time theta is dumped or time-averaged.
197      N.B.: fairly large differences in accuracy occur across
198            different platforms/compilers; comparison between
199            g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
200            generated output gives:
201       T           S           U           V
202      C D M    c        m  s        m  s        m  s        m  s
203      n p a R  g  m  m  e  .  m  m  e  .  m  m  e  .  m  m  e  .
204      f n k u  2  i  a  a  d  i  a  a  d  i  a  a  d  i  a  a  d
205      g d e n  d  n  x  n  .  n  x  n  .  n  x  n  .  n  x  n  .
206    
207      Y Y Y Y  5  5  7  7  7  8 10  9  6  6  6  6  7  5  7  5  7 FAIL  lab_sea
208    o GAD:
209      - generated new common blocks to account for call of
210        same gad routines with differing traceridentities
211        (needed to modify tracerIdentity indices in GAD.h)
212      - generated separate common blocks for case useCubedSphereExchange
213        (Department of Futurology)
214      - parameter lists to gmredi_?transport: added tracerIdentity
215      - added new key indices to tamc.h
216    o external_fields_load:
217      - added this routine to TAF list
218      - needed to make some common blocks global and additional storing
219        along the same lines as exf package (checkpoint_lev?_directives.h)
220    o exf:
221      updated external forcing package
222      - bug fixes carried over from ecco-branch
223        (missing OBCS_OPTIONS.h in two routines)
224      - enable easy to use "no forcing".
225      - added exf I/O for atmospheric loading
226      - added exf I/O for runoff data
227      - transfered scaling between exf <-> MITgcm to exf namelist
228    o Adding new verification experiment global_with_exf.
229      This verification experiment is almost identical to the
230      global_ocean.90x40x15 experiment, except that it uses
231      the exf (and cal) package instead of the
232      external_fields_load routine (cf README file).
233    
234    checkpoint46m_post
235    o modified testscript to return -- when there are no lines of "%MON" output
236    o added new flag "quasiHydrostatic" for QH mode
237      and new routine quasihydrostaticterms()
238    o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
239      New routine: mom_u_coriolis_nh()
240    o fixed sign of non-hydrostatic metric terms in u and v equations.
241      Depend on correct sign of gravitySign.
242    o added work.pc* to .cvsignore in aim directories using ifc
243    o introduced flag for controllin non-hydrostatic metric terms
244    o removed gravitySign from PARM04
245    o switched to g77/ifc from pgf77 in aim experiments
246    
247    checkpoint46l_post
248    o made convective adjustment work with pressure coordinates:
249     - changed the direction of k-loop in convective_adjustment.F for the
250       case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
251     - adjusted the reference pressure k-index in convective_adjustment.F
252     - adjusted the convection condition in convect.F (in analogy to
253       calc_ivdc.F)
254     - convective_adjustment no longer computes anything on the halos
255     - removed the warnings about negative salinity from find_rho.F and
256       find_alpha.F; instead the new routine look_for_neg_salinity, called
257       at the beginning of find_rho, find_alpha, and find_beta, does a
258       check of the entire slice, if CPP-option
259       CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
260    checkpoint46l_pre
261    
262    checkpoint46k_post
263    o fixed the verification/global_ocean.90x40x15 experiment:
264     - new bathymetry (the world according to A., JMC, and M.)
265     - new initial fields and forcing fields (*.bin files)
266     - new POLY3.COEFFS (for the next release one should switch to a full
267       equation of state: JMD95P or MDJWF)
268     - fixed several errors and redundancies in the data file
269     - experiment uses looped cells
270     - added matlab directory with diagnostic scripts for plotting of output
271    
272    o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
273     - read AIM physics parameters from a file (data.aimphys)
274     - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
275    
276    checkpoint46j_post
277    o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
278    o move wVel computation at the end of the time step, in S/R integr_continuity
279    o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
280    o update timeave pkg for wVel diagnostic.
281    checkpoint46j_pre
282    
283    checkpoint46i_post
284    o Clean up AIM package (and keep the results unchanged):
285      include CPP_OPTION and use IMPLICT NONE in all routines ;
286      declare all the variables _RL ; use _d 0 for all numerical constants.
287      use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
288    
289    checkpoint46h_post
290    o cleaned up the use of rhoNil and rhoConst.
291      - rhoNil should only appear in the LINEAR equation of state, everywhere
292        else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
293        and the dynamical equations are all divided by rhoConst
294    o introduced new parameter rhoConstFresh, a reference density of fresh
295      water, to remove the fresh water flux's dependence on rhoNil. The default
296      value is 999.8 kg/m^3
297    o cleanup up external_forcing.F and external_forcing_surf.F
298      - can now be used by both OCEANIC and OCEANICP
299    checkpoint46h_pre
300    
301     Added code to convert surface volume flux (fresh water) into
302     a mass flux when using P coordinates in the ocean (OCEANICP).
303     Note: It assumes you have set rho0=rhoConst=density of fresh water.
304    
305    checkpoint46g_post
306    o Include a new diagnostic variable phiHydLow for the ocean model
307      - in z-coordinates, it is the bottom pressure anomaly
308      - in p-coordinates, it is the sea surface elevation
309      - in both cases, these variable have global drift, reflecting the mass
310        drift in z-coordinates and the volume drift in p-coordinates
311      - included time averaging for phiHydLow, be aware of the drift!
312    o depth-dependent computation of Bo_surf for pressure coordinates
313      in the ocean (buoyancyRelation='OCEANICP')
314      - requires a new routine (FIND_RHO_SCALAR) to compute density with only
315        Theta, Salinity, and Pressure in the parameter list. This routine is
316        presently contained in find_rho.F. This routine does not give the
317        correct density for 'POLY3', which would be a z-dependent reference
318        density.
319    o cleaned up find_rho
320      - removed obsolete 'eqn' from the parameter list.
321    o added two new verification experiments: gop and goz
322      (4x4 degree global ocean, 15 layers in pressure and height coordinates)
323    checkpoint46g_pre
324    
325    checkpoint46f_post
326    o Enable tangent linear (forward mode) gradient checks:
327      - extended active file handling to g_... files
328      - added TANGENT_SIMULATION to theSimulationMode
329      - extended grdchk package accordingly
330    o added tangent linear setup in verification/carbon/code_ftl
331    o added adjoint setup in verification/front_relax/code_ad
332    
333    checkpoint46e_post
334    o Added new equation of state -> MDJWF
335      - EOS of McDougall et al., 2002, JAOT, submitted
336      - caveat: the equation of state is only valid for a smaller (more
337        realistic?) range of values than JMD95P/Z and UNESCO
338      - added masks to the calculation of pressure in store_pressure
339      - added more check values for density in check_eos (ini_eos.F), some of
340        the old check values are out of the range of the MDJWF-eos, so don't
341        expect perfect matches for those
342    checkpoint46e_pre
343    
344    checkpoint46d_post
345    o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
346      'OCEANICP', also initialised field pressure correctly in ini_eos in the
347      case of pressure coordinates. eosType='JMD95Z' in
348      combination with buoyancyRelation='OCEANICP' now causes an error.
349    o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
350      in find_alpha/beta.
351    checkpoint46d_pre
352    
353    o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
354      so that JMD95Z and JMD95P give approptiate static stability in find_rho.
355    
356    checkpoint46c_post
357    o Changes necessary for ocean in p-coordinates
358     -  Added new buoyancy relation = 'OCEANICP'
359     -  Added new parameters = gravitySign (this used to be contained inside
360        the factor dRdZ which I added when we first switched to R coordinates).
361     X GM/Redi is not compatible (yet)
362     X bottom drag and no-slip need to be debugged.
363    checkpoint46c_pre
364    
365    checkpoint46b_post
366    o Added new equation of state -> JMD95Z and JMD95P
367      - EOS of Jackett and McDougall, 1995, JAOT
368      - moved all EOS parameters into EOS.h
369      - new routines ini_eos.F, store_pressure.F
370    o Added UNESCO EOS, but not recommended because it requires
371      in-situ temperature (see JMD95)
372    o Modified formatting for knudsen2.f in utils/knudsen2 and added
373      unesco.f to be used with POLY3
374    checkpoint46b_pre
375    
376    checkpoint46a_post
377    o Added (atmospheric) pressure loading
378      - new field in FFIELDS.h, etc...
379      - new cpp flag ATMOSPHERIC_LOADING
380    o Changed hFacC to _hFacC in calc_phi_hyd.F
381    o Added SHORTWAVE_HEATING to some files for consistency
382    checkpoint46a_pre
383    
384    checkpoint46
385    further merges from release1_p5
386    o new ctrl package
387      - adopted from ECCO environment to enable optimization
388      - added Eliassen Palm fluxes to controls
389    o added Eliassen Palm flux controls to gradient check package
390    o cost package
391      - Compatible with new ctrl package
392      - added Eliassen Palm cost hooks
393      - modif's of existing cost functions
394    o Adjoint-related bug fixes in kpp:
395      - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
396      - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
397    o autodiff package
398      - flow directives:
399        + new for S/R do_the_model_io
400        + enhanced for S/R checkpoint
401        + new gmredi.flow
402      - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
403        disable adcommon.h/g_common.h by default.
404      - fixed problem for adjoint of global_max
405    o modified verification/carbon/
406    o New setup for adjoint of global_ocean
407    o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
408    o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
409    o incorporated hooks for sponge layer code (external_forcing.F)
410    
411    checkpoint45d_post
412    o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
413    o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
414      (affects plume_on_slope "cg2d" output)
415    o add new parameter deltaTfreesurf for free-surface time stepping
416    o exchange gT,gS when using staggerTimeStep & GM & Oly<4
417    o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
418    o change phiMin in exp1 (to agree with documentation)
419    o add new flags:
420     - T,S forcing inside/outside Adams-Bashforth
421     - turn off temp,salt advection and/or forcing
422     - for each tracer, define internal flag for multiDimAdvection & A-B
423    o monitor: change definition of KE to check conservation of Energy
424    
425    checkpoint45c_post
426    o Removed f90 comments ("!")
427    o Modified initialisations to enable exf package for MITgcm
428      (without invoking ECCO_PACKAGE).
429    o modifications to gradient check package (Martin Losch)
430      - enable centered differences
431      - modified format of standard output
432    
433  checkpoint45b_post  checkpoint45b_post
434  o cleaned exchange calls in cg2d  o cleaned exchange calls in cg2d
435  o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step  o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step

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