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revision 1.75 by jmc, Thu Jun 20 23:52:03 2002 UTC revision 1.129 by jmc, Sat Feb 8 03:45:30 2003 UTC
# Line 2  $Header$ Line 2  $Header$
2    
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    checkpoint48d_pre
7    o in preparation for r*:
8      new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
9      pass the 2 comp. of the grad. as arguments to momentum S/R.
10      but for the moment, only used if it does not change the results.
11    o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
12    
13    checkpoint48c_post
14    Modifications in treatment of initial flux forcing controls
15    to avoid extra storing of flux fields.
16    
17    checkpoint48c_pre
18    o Added tidal_basin_2d experiment (currently 1D!)
19    o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
20    
21    checkpoint48b_post
22    o r* coordinate added in #ifdef NONLIN_FRSURF block.
23     (modification to pressure gradient not yet implemented)
24    o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
25      (for U & V) that are used for vertical advection of momentum.
26    
27    checkpoint48a_post
28    o In preparation for r*, use temp. array to compute vertical transport
29       in flux-form momentum pkg. => change results of few test-exp.
30      Update output of: exp4, exp5, front_relax, global_ocean_pressure,
31                        lab_sea, natl_box & plume_on_slope
32    
33    checkpoint48
34    o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
35    
36    checkpoint47j_post
37    o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
38    o moved adexch from forward_step to addummy_in_stepping
39    o added exch in ctrl_map_...
40    o aveFreq.=0. at end of cost_final to avoid overwrite in
41      reverse checkpointing loop
42    o Yet more changes in gmredi:
43      * adgmredi_calc_tensor
44        avoiding all recomputation of gmredi_slope_limit
45      * adgmredi_x/y/rtransport
46        added flag for excessive storing to avoid recomp. of
47        u/v/rtans, dTdx/y/z
48        -> this is not really necessary and very memory-consuming
49      * adgmredi_slope_psi:
50        consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
51      * gmredi_slope_limit
52        re-activated full calculation of taperfct for case 'ac02'
53    o updating verification/ adjoints of carbon, global_ocean.90x40x15
54    
55    checkpoint47i_post
56    o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
57    o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
58      default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
59    o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
60    o gmredi: fix few bugs.
61    
62    checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
63    This will be a good checkpoint to plug into the ecco-branch.
64    o few modif.'s to get latest version adjointed
65      (mainly kick out code in ini_linear_phisurf)
66    o modif's to run adjoint with exactConserv
67    o case GM_BOLUS_ADVEC should be cleaned
68      S/R gmredi_slope_psi should be cleaned
69    o verification/carbon now has exactConserv=.TRUE.
70    
71    checkpoint47g_post
72    o time-average AIM output: becomes independent from statvars time-average
73      (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
74    o After TAF bug fix:
75      Tested adjoint of gmredi package.
76      Tests were done with checkpoint47 rather than with latest
77      checkpoint47f_post since the latter is broken for the adjoint
78      verification/carbon/ contains both ADM and TLM gradient checks.
79    Here they are, before they get changed/lost/stolen.
80    Mostly modif.'s to fix numerical sensitivities.
81    Gradient checks OK for
82    - GM_taper_scheme:
83      * clipping
84      * ac02
85      * linear
86      * glw91
87      * dm95
88      * ldd97
89    - GMREDI_OPTIONS:
90      * GM_VISBECK_VARIABLE_K
91      * GM_NON_UNITY_DIAGONAL
92      * GM_EXTRA_DIAGONAL
93      * GM_BOLUS_ADVEC
94    in conjunction with data.gmredi parameters to be checked in
95    in a few minutes under verification/carbon/code/
96    
97    checkpoint47f_post
98    Merging from release1_p10:
99    o modifications for using pkg/exf with pkg/seaice
100      - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
101        and SEAICE_EXTERNAL_FLUXES
102      - pkg/exf CPP options EXF_READ_EVAP and
103        EXF_NO_BULK_COMPUTATIONS
104      - usage examples are Experiments 8 and 9 in
105        verification/lab_sea/README
106      - verification/lab_sea default experiment now uses
107        pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
108    
109    checkpoint47e_post
110    o created a tag prior to creating a branch
111    
112    checkpoint47d_post
113    o fixed bug in the oceanic pressure coordinates code: vertical viscosity
114      at the bottom boundary had an erroneous half slip boundary condition
115    o added bottom drag and no slip boundary condition capabilities to
116      oceanic pressure coordinates code
117    o added new verification experiment global_ocean_pressure, this experiment is
118      also described in the tutorial section of the manual
119    checkpoint47d_pre
120    
121    checkpoint47c_post
122    o Added a verification experiment for a global cubed-sphere ocean run
123      -  verification/global_ocean.cubed32x32x30
124      -  uses pkg/therm_seaice and pkg/bulk_forcing
125    
126    o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
127    o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
128      when using P-coordinate; only implemented for atmospheric config.
129    o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
130      NOTES: requires option NONLIN_FRSURF to be "#define".
131    o update advect_xz/results/output.txt (left from checkpoint44g_post)
132    
133    checkpoint47b_post
134    Merging from release1_p9:
135    o pkg/seaice
136      - removed GOTO's and added taf directives
137      - double precision constants to reduce the g77 (Linux)
138        to F77 (SGI) differences reported in release1_p8
139    o tools/genmake
140      - added SGI options
141    o verification/testscript
142      - updated to that of checkpoint47a_post
143    o verification/global_ocean.90x40x15/input/eedata
144      - modified for SGI f77 compatibility
145    o verification/lab_sea
146      - added description of sea-ice model
147      - added missing matlab routines
148      - added test of thermodynamics parallelization
149    
150    checkpoint47a_post
151    o new pkg: aim_v23
152     = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
153       for now, keep the same surface forcing as before.
154     - Part-Cell implemented into AIM; check that Heat & Water are conserved
155     - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
156     - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
157    o add diagnostic of surface correction term in monitor output
158    
159    o bulk_force and therm_seaice
160    - Two packages:  bulk_force (Bulk forcing)
161      and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
162    - Earlier integration from Stephaine Dutkiewicz
163      and Patrick Heimbach.
164    - Two ifdef statements for compile time,
165       ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
166    
167    checkpoint47
168    differentiable version of checkpoint46n_post
169    o bug fix in quasihydrostaticterms
170    o * "clean" adjoint code (in terms of extensive recomputations)
171        can now be obtained for all GMREDI options (i.e. for
172        - GM_VISBECK_VARIABLE_K
173        - GM_NON_UNITY_DIAGONAL
174        - GM_EXTRA_DIAGONAL
175        - GM_BOLUS_ADVEC )
176      * However, wrong gradient check problem remains unsolved.
177      * New CPP options have been introduced for different
178        tapering schemes
179    o external_fields_load now part of differentiation list
180    o pressure needs multiple storing;
181      would be nice to have store_pressure at beginning or
182      end of forward_step, e.g. by having phiHyd global (5-dim.)
183      (NB: pressure is needed for certain cases in find_rho,
184      which is also invoked through convective_adjustment).
185    o recomputations in find_rho for cases
186     'JMD95'/'UNESCO' or 'MDJWF' are OK.
187    o #define ATMOSPHERIC_LOADING should be differentiable
188    o ini_forcing shifted to begining of initialise_varia
189    o Incorporating QNVS line search routines into MITgcm
190      (this is separate code, and therefore not under pkg)
191      lsopt/, optim/
192    o Updated verification/carbon/
193      - #define GM_VISBECK_VARIABLE_K
194      - GM_taper_scheme    = 'ldd97'    
195    
196    checkpoint46n_post
197    Merging from release1_p8:
198    o verification/natl_box:
199      updating new external_fields_load routine
200    o New package: pkg/seaice
201      Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
202      The sea-ice code is based on Hibler (1979-1980).
203      Two sea-ice dynamic solvers, ADI and LSR, are included.
204      In addition to computing prognostic sea-ice variables and diagnosing
205      the forcing/external data fields that drive the ocean model,
206      SEAICE_MODEL also sets theta to the freezing point under sea-ice.
207      The implied surface heat flux is then stored in variable
208      surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
209      kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
210      non-local transport term.  Because this call precedes model
211      thermodynamics, temperature under sea-ice may not be "exactly" at
212      the freezing point by the time theta is dumped or time-averaged.
213      N.B.: fairly large differences in accuracy occur across
214            different platforms/compilers; comparison between
215            g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
216            generated output gives:
217       T           S           U           V
218      C D M    c        m  s        m  s        m  s        m  s
219      n p a R  g  m  m  e  .  m  m  e  .  m  m  e  .  m  m  e  .
220      f n k u  2  i  a  a  d  i  a  a  d  i  a  a  d  i  a  a  d
221      g d e n  d  n  x  n  .  n  x  n  .  n  x  n  .  n  x  n  .
222    
223      Y Y Y Y  5  5  7  7  7  8 10  9  6  6  6  6  7  5  7  5  7 FAIL  lab_sea
224    o GAD:
225      - generated new common blocks to account for call of
226        same gad routines with differing traceridentities
227        (needed to modify tracerIdentity indices in GAD.h)
228      - generated separate common blocks for case useCubedSphereExchange
229        (Department of Futurology)
230      - parameter lists to gmredi_?transport: added tracerIdentity
231      - added new key indices to tamc.h
232    o external_fields_load:
233      - added this routine to TAF list
234      - needed to make some common blocks global and additional storing
235        along the same lines as exf package (checkpoint_lev?_directives.h)
236    o exf:
237      updated external forcing package
238      - bug fixes carried over from ecco-branch
239        (missing OBCS_OPTIONS.h in two routines)
240      - enable easy to use "no forcing".
241      - added exf I/O for atmospheric loading
242      - added exf I/O for runoff data
243      - transfered scaling between exf <-> MITgcm to exf namelist
244    o Adding new verification experiment global_with_exf.
245      This verification experiment is almost identical to the
246      global_ocean.90x40x15 experiment, except that it uses
247      the exf (and cal) package instead of the
248      external_fields_load routine (cf README file).
249    
250    checkpoint46m_post
251    o modified testscript to return -- when there are no lines of "%MON" output
252    o added new flag "quasiHydrostatic" for QH mode
253      and new routine quasihydrostaticterms()
254    o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
255      New routine: mom_u_coriolis_nh()
256    o fixed sign of non-hydrostatic metric terms in u and v equations.
257      Depend on correct sign of gravitySign.
258    o added work.pc* to .cvsignore in aim directories using ifc
259    o introduced flag for controllin non-hydrostatic metric terms
260    o removed gravitySign from PARM04
261    o switched to g77/ifc from pgf77 in aim experiments
262    
263    checkpoint46l_post
264    o made convective adjustment work with pressure coordinates:
265     - changed the direction of k-loop in convective_adjustment.F for the
266       case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
267     - adjusted the reference pressure k-index in convective_adjustment.F
268     - adjusted the convection condition in convect.F (in analogy to
269       calc_ivdc.F)
270     - convective_adjustment no longer computes anything on the halos
271     - removed the warnings about negative salinity from find_rho.F and
272       find_alpha.F; instead the new routine look_for_neg_salinity, called
273       at the beginning of find_rho, find_alpha, and find_beta, does a
274       check of the entire slice, if CPP-option
275       CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
276    checkpoint46l_pre
277    
278    checkpoint46k_post
279    o fixed the verification/global_ocean.90x40x15 experiment:
280     - new bathymetry (the world according to A., JMC, and M.)
281     - new initial fields and forcing fields (*.bin files)
282     - new POLY3.COEFFS (for the next release one should switch to a full
283       equation of state: JMD95P or MDJWF)
284     - fixed several errors and redundancies in the data file
285     - experiment uses looped cells
286     - added matlab directory with diagnostic scripts for plotting of output
287    
288    o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
289     - read AIM physics parameters from a file (data.aimphys)
290     - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
291    
292    checkpoint46j_post
293    o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
294    o move wVel computation at the end of the time step, in S/R integr_continuity
295    o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
296    o update timeave pkg for wVel diagnostic.
297    checkpoint46j_pre
298    
299    checkpoint46i_post
300    o Clean up AIM package (and keep the results unchanged):
301      include CPP_OPTION and use IMPLICT NONE in all routines ;
302      declare all the variables _RL ; use _d 0 for all numerical constants.
303      use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
304    
305    checkpoint46h_post
306    o cleaned up the use of rhoNil and rhoConst.
307      - rhoNil should only appear in the LINEAR equation of state, everywhere
308        else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
309        and the dynamical equations are all divided by rhoConst
310    o introduced new parameter rhoConstFresh, a reference density of fresh
311      water, to remove the fresh water flux's dependence on rhoNil. The default
312      value is 999.8 kg/m^3
313    o cleanup up external_forcing.F and external_forcing_surf.F
314      - can now be used by both OCEANIC and OCEANICP
315    checkpoint46h_pre
316    
317     Added code to convert surface volume flux (fresh water) into
318     a mass flux when using P coordinates in the ocean (OCEANICP).
319     Note: It assumes you have set rho0=rhoConst=density of fresh water.
320    
321    checkpoint46g_post
322    o Include a new diagnostic variable phiHydLow for the ocean model
323      - in z-coordinates, it is the bottom pressure anomaly
324      - in p-coordinates, it is the sea surface elevation
325      - in both cases, these variable have global drift, reflecting the mass
326        drift in z-coordinates and the volume drift in p-coordinates
327      - included time averaging for phiHydLow, be aware of the drift!
328    o depth-dependent computation of Bo_surf for pressure coordinates
329      in the ocean (buoyancyRelation='OCEANICP')
330      - requires a new routine (FIND_RHO_SCALAR) to compute density with only
331        Theta, Salinity, and Pressure in the parameter list. This routine is
332        presently contained in find_rho.F. This routine does not give the
333        correct density for 'POLY3', which would be a z-dependent reference
334        density.
335    o cleaned up find_rho
336      - removed obsolete 'eqn' from the parameter list.
337    o added two new verification experiments: gop and goz
338      (4x4 degree global ocean, 15 layers in pressure and height coordinates)
339    checkpoint46g_pre
340    
341    checkpoint46f_post
342    o Enable tangent linear (forward mode) gradient checks:
343      - extended active file handling to g_... files
344      - added TANGENT_SIMULATION to theSimulationMode
345      - extended grdchk package accordingly
346    o added tangent linear setup in verification/carbon/code_ftl
347    o added adjoint setup in verification/front_relax/code_ad
348    
349    checkpoint46e_post
350    o Added new equation of state -> MDJWF
351      - EOS of McDougall et al., 2002, JAOT, submitted
352      - caveat: the equation of state is only valid for a smaller (more
353        realistic?) range of values than JMD95P/Z and UNESCO
354      - added masks to the calculation of pressure in store_pressure
355      - added more check values for density in check_eos (ini_eos.F), some of
356        the old check values are out of the range of the MDJWF-eos, so don't
357        expect perfect matches for those
358    checkpoint46e_pre
359    
360    checkpoint46d_post
361    o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
362      'OCEANICP', also initialised field pressure correctly in ini_eos in the
363      case of pressure coordinates. eosType='JMD95Z' in
364      combination with buoyancyRelation='OCEANICP' now causes an error.
365    o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
366      in find_alpha/beta.
367    checkpoint46d_pre
368    
369    o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
370      so that JMD95Z and JMD95P give approptiate static stability in find_rho.
371    
372    checkpoint46c_post
373    o Changes necessary for ocean in p-coordinates
374     -  Added new buoyancy relation = 'OCEANICP'
375     -  Added new parameters = gravitySign (this used to be contained inside
376        the factor dRdZ which I added when we first switched to R coordinates).
377     X GM/Redi is not compatible (yet)
378     X bottom drag and no-slip need to be debugged.
379    checkpoint46c_pre
380    
381    checkpoint46b_post
382    o Added new equation of state -> JMD95Z and JMD95P
383      - EOS of Jackett and McDougall, 1995, JAOT
384      - moved all EOS parameters into EOS.h
385      - new routines ini_eos.F, store_pressure.F
386    o Added UNESCO EOS, but not recommended because it requires
387      in-situ temperature (see JMD95)
388    o Modified formatting for knudsen2.f in utils/knudsen2 and added
389      unesco.f to be used with POLY3
390    checkpoint46b_pre
391    
392    checkpoint46a_post
393    o Added (atmospheric) pressure loading
394      - new field in FFIELDS.h, etc...
395      - new cpp flag ATMOSPHERIC_LOADING
396    o Changed hFacC to _hFacC in calc_phi_hyd.F
397    o Added SHORTWAVE_HEATING to some files for consistency
398    checkpoint46a_pre
399    
400    checkpoint46
401    further merges from release1_p5
402    o new ctrl package
403      - adopted from ECCO environment to enable optimization
404      - added Eliassen Palm fluxes to controls
405    o added Eliassen Palm flux controls to gradient check package
406    o cost package
407      - Compatible with new ctrl package
408      - added Eliassen Palm cost hooks
409      - modif's of existing cost functions
410    o Adjoint-related bug fixes in kpp:
411      - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
412      - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
413    o autodiff package
414      - flow directives:
415        + new for S/R do_the_model_io
416        + enhanced for S/R checkpoint
417        + new gmredi.flow
418      - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
419        disable adcommon.h/g_common.h by default.
420      - fixed problem for adjoint of global_max
421    o modified verification/carbon/
422    o New setup for adjoint of global_ocean
423    o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
424    o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
425    o incorporated hooks for sponge layer code (external_forcing.F)
426    
427    checkpoint45d_post
428    o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
429    o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
430      (affects plume_on_slope "cg2d" output)
431    o add new parameter deltaTfreesurf for free-surface time stepping
432    o exchange gT,gS when using staggerTimeStep & GM & Oly<4
433  o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B  o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
434  o change phiMin in exp1 (to agree with documentation)  o change phiMin in exp1 (to agree with documentation)
435  o add new flags:  o add new flags:

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