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revision 1.81 by adcroft, Thu Aug 15 17:25:26 2002 UTC revision 1.134 by dimitri, Tue Feb 18 05:33:53 2003 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    checkpoint48f_post
7    Merging from release1_p12:
8    o Modifications for using pkg/exf with pkg/seaice
9      - improved description of the various forcing configurations
10      - added basic radiation bulk formulae to pkg/exf
11      - units/sign fix for evap computation in exf_getffields.F
12      - updated verification/global_with_exf/results/output.txt
13    o Added pkg/sbo for computing IERS Special Bureau for the Oceans
14      (SBO) core products, including oceanic mass, center-of-mass,
15      angular, and bottom pressure (see pkg/sbo/README.sbo).
16    o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
17      to avoid negative values in shallow regions.
18      - updated verification/natl_box/results/output.txt
19      - updated verification/lab_sea/results/output.txt
20    o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
21    o Added useSingleCpuIO option (see PARAMS.h).
22    o Updated useSingleCpuIO option in mdsio_writefield.F to
23      work with multi-field files, e.g., for single-file pickup.
24    o pkg/seaice:
25      - bug fix in growth.F: QNET for no shortwave case
26      - added HeffFile for specifying initial sea-ice thickness
27      - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
28    o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
29      kpp_transport_t.F, forward_step.F, and the_main_loop.F
30    o pkg/seaice:
31      - adjoint-friendly modifications
32      - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
33    
34    checkpoint48e_post
35    o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
36    o dynamics: change definition of computational domain & adapt mom_fluxform
37      accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
38    o following exp works with Olx=Oly=2 (and pass through checkbounds option):
39        adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
40        exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
41        global_ocean.90x40x15 global_with_exf global_ocean_pressure
42        inverted_barometer solid-body.cs-32x32x1
43      (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
44    
45    checkpoint48d_post
46    o in preparation for r*:
47     a) use pre-computed gradient of hydrostatic potential:
48        changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
49     b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
50        => affects results of glob_oce_pressure (different truncation error)  
51      update output.txt of ideal_2D_oce & global_ocean_pressure
52    
53    checkpoint48d_pre
54    o in preparation for r*:
55      new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
56      pass the 2 comp. of the grad. as arguments to momentum S/R.
57      but for the moment, only used if it does not change the results.
58    o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
59    
60    checkpoint48c_post
61    Modifications in treatment of initial flux forcing controls
62    to avoid extra storing of flux fields.
63    
64    checkpoint48c_pre
65    o Added tidal_basin_2d experiment (currently 1D!)
66    o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
67    
68    checkpoint48b_post
69    o r* coordinate added in #ifdef NONLIN_FRSURF block.
70     (modification to pressure gradient not yet implemented)
71    o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
72      (for U & V) that are used for vertical advection of momentum.
73    
74    checkpoint48a_post
75    o In preparation for r*, use temp. array to compute vertical transport
76       in flux-form momentum pkg. => change results of few test-exp.
77      Update output of: exp4, exp5, front_relax, global_ocean_pressure,
78                        lab_sea, natl_box & plume_on_slope
79    
80    checkpoint48
81    o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
82    
83    checkpoint47j_post
84    o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
85    o moved adexch from forward_step to addummy_in_stepping
86    o added exch in ctrl_map_...
87    o aveFreq.=0. at end of cost_final to avoid overwrite in
88      reverse checkpointing loop
89    o Yet more changes in gmredi:
90      * adgmredi_calc_tensor
91        avoiding all recomputation of gmredi_slope_limit
92      * adgmredi_x/y/rtransport
93        added flag for excessive storing to avoid recomp. of
94        u/v/rtans, dTdx/y/z
95        -> this is not really necessary and very memory-consuming
96      * adgmredi_slope_psi:
97        consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
98      * gmredi_slope_limit
99        re-activated full calculation of taperfct for case 'ac02'
100    o updating verification/ adjoints of carbon, global_ocean.90x40x15
101    
102    checkpoint47i_post
103    o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
104    o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
105      default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
106    o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
107    o gmredi: fix few bugs.
108    
109    checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
110    This will be a good checkpoint to plug into the ecco-branch.
111    o few modif.'s to get latest version adjointed
112      (mainly kick out code in ini_linear_phisurf)
113    o modif's to run adjoint with exactConserv
114    o case GM_BOLUS_ADVEC should be cleaned
115      S/R gmredi_slope_psi should be cleaned
116    o verification/carbon now has exactConserv=.TRUE.
117    
118    checkpoint47g_post
119    o time-average AIM output: becomes independent from statvars time-average
120      (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
121    o After TAF bug fix:
122      Tested adjoint of gmredi package.
123      Tests were done with checkpoint47 rather than with latest
124      checkpoint47f_post since the latter is broken for the adjoint
125      verification/carbon/ contains both ADM and TLM gradient checks.
126    Here they are, before they get changed/lost/stolen.
127    Mostly modif.'s to fix numerical sensitivities.
128    Gradient checks OK for
129    - GM_taper_scheme:
130      * clipping
131      * ac02
132      * linear
133      * glw91
134      * dm95
135      * ldd97
136    - GMREDI_OPTIONS:
137      * GM_VISBECK_VARIABLE_K
138      * GM_NON_UNITY_DIAGONAL
139      * GM_EXTRA_DIAGONAL
140      * GM_BOLUS_ADVEC
141    in conjunction with data.gmredi parameters to be checked in
142    in a few minutes under verification/carbon/code/
143    
144    checkpoint47f_post
145    Merging from release1_p10:
146    o modifications for using pkg/exf with pkg/seaice
147      - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
148        and SEAICE_EXTERNAL_FLUXES
149      - pkg/exf CPP options EXF_READ_EVAP and
150        EXF_NO_BULK_COMPUTATIONS
151      - usage examples are Experiments 8 and 9 in
152        verification/lab_sea/README
153      - verification/lab_sea default experiment now uses
154        pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
155    
156    checkpoint47e_post
157    o created a tag prior to creating a branch
158    
159    checkpoint47d_post
160    o fixed bug in the oceanic pressure coordinates code: vertical viscosity
161      at the bottom boundary had an erroneous half slip boundary condition
162    o added bottom drag and no slip boundary condition capabilities to
163      oceanic pressure coordinates code
164    o added new verification experiment global_ocean_pressure, this experiment is
165      also described in the tutorial section of the manual
166    checkpoint47d_pre
167    
168    checkpoint47c_post
169    o Added a verification experiment for a global cubed-sphere ocean run
170      -  verification/global_ocean.cubed32x32x30
171      -  uses pkg/therm_seaice and pkg/bulk_forcing
172    
173    o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
174    o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
175      when using P-coordinate; only implemented for atmospheric config.
176    o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
177      NOTES: requires option NONLIN_FRSURF to be "#define".
178    o update advect_xz/results/output.txt (left from checkpoint44g_post)
179    
180    checkpoint47b_post
181    Merging from release1_p9:
182    o pkg/seaice
183      - removed GOTO's and added taf directives
184      - double precision constants to reduce the g77 (Linux)
185        to F77 (SGI) differences reported in release1_p8
186    o tools/genmake
187      - added SGI options
188    o verification/testscript
189      - updated to that of checkpoint47a_post
190    o verification/global_ocean.90x40x15/input/eedata
191      - modified for SGI f77 compatibility
192    o verification/lab_sea
193      - added description of sea-ice model
194      - added missing matlab routines
195      - added test of thermodynamics parallelization
196    
197    checkpoint47a_post
198    o new pkg: aim_v23
199     = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
200       for now, keep the same surface forcing as before.
201     - Part-Cell implemented into AIM; check that Heat & Water are conserved
202     - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
203     - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
204    o add diagnostic of surface correction term in monitor output
205    
206    o bulk_force and therm_seaice
207    - Two packages:  bulk_force (Bulk forcing)
208      and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
209    - Earlier integration from Stephaine Dutkiewicz
210      and Patrick Heimbach.
211    - Two ifdef statements for compile time,
212       ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
213    
214    checkpoint47
215    differentiable version of checkpoint46n_post
216    o bug fix in quasihydrostaticterms
217    o * "clean" adjoint code (in terms of extensive recomputations)
218        can now be obtained for all GMREDI options (i.e. for
219        - GM_VISBECK_VARIABLE_K
220        - GM_NON_UNITY_DIAGONAL
221        - GM_EXTRA_DIAGONAL
222        - GM_BOLUS_ADVEC )
223      * However, wrong gradient check problem remains unsolved.
224      * New CPP options have been introduced for different
225        tapering schemes
226    o external_fields_load now part of differentiation list
227    o pressure needs multiple storing;
228      would be nice to have store_pressure at beginning or
229      end of forward_step, e.g. by having phiHyd global (5-dim.)
230      (NB: pressure is needed for certain cases in find_rho,
231      which is also invoked through convective_adjustment).
232    o recomputations in find_rho for cases
233     'JMD95'/'UNESCO' or 'MDJWF' are OK.
234    o #define ATMOSPHERIC_LOADING should be differentiable
235    o ini_forcing shifted to begining of initialise_varia
236    o Incorporating QNVS line search routines into MITgcm
237      (this is separate code, and therefore not under pkg)
238      lsopt/, optim/
239    o Updated verification/carbon/
240      - #define GM_VISBECK_VARIABLE_K
241      - GM_taper_scheme    = 'ldd97'    
242    
243    checkpoint46n_post
244    Merging from release1_p8:
245    o verification/natl_box:
246      updating new external_fields_load routine
247    o New package: pkg/seaice
248      Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
249      The sea-ice code is based on Hibler (1979-1980).
250      Two sea-ice dynamic solvers, ADI and LSR, are included.
251      In addition to computing prognostic sea-ice variables and diagnosing
252      the forcing/external data fields that drive the ocean model,
253      SEAICE_MODEL also sets theta to the freezing point under sea-ice.
254      The implied surface heat flux is then stored in variable
255      surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
256      kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
257      non-local transport term.  Because this call precedes model
258      thermodynamics, temperature under sea-ice may not be "exactly" at
259      the freezing point by the time theta is dumped or time-averaged.
260      N.B.: fairly large differences in accuracy occur across
261            different platforms/compilers; comparison between
262            g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
263            generated output gives:
264       T           S           U           V
265      C D M    c        m  s        m  s        m  s        m  s
266      n p a R  g  m  m  e  .  m  m  e  .  m  m  e  .  m  m  e  .
267      f n k u  2  i  a  a  d  i  a  a  d  i  a  a  d  i  a  a  d
268      g d e n  d  n  x  n  .  n  x  n  .  n  x  n  .  n  x  n  .
269    
270      Y Y Y Y  5  5  7  7  7  8 10  9  6  6  6  6  7  5  7  5  7 FAIL  lab_sea
271    o GAD:
272      - generated new common blocks to account for call of
273        same gad routines with differing traceridentities
274        (needed to modify tracerIdentity indices in GAD.h)
275      - generated separate common blocks for case useCubedSphereExchange
276        (Department of Futurology)
277      - parameter lists to gmredi_?transport: added tracerIdentity
278      - added new key indices to tamc.h
279    o external_fields_load:
280      - added this routine to TAF list
281      - needed to make some common blocks global and additional storing
282        along the same lines as exf package (checkpoint_lev?_directives.h)
283    o exf:
284      updated external forcing package
285      - bug fixes carried over from ecco-branch
286        (missing OBCS_OPTIONS.h in two routines)
287      - enable easy to use "no forcing".
288      - added exf I/O for atmospheric loading
289      - added exf I/O for runoff data
290      - transfered scaling between exf <-> MITgcm to exf namelist
291    o Adding new verification experiment global_with_exf.
292      This verification experiment is almost identical to the
293      global_ocean.90x40x15 experiment, except that it uses
294      the exf (and cal) package instead of the
295      external_fields_load routine (cf README file).
296    
297    checkpoint46m_post
298    o modified testscript to return -- when there are no lines of "%MON" output
299    o added new flag "quasiHydrostatic" for QH mode
300      and new routine quasihydrostaticterms()
301    o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
302      New routine: mom_u_coriolis_nh()
303    o fixed sign of non-hydrostatic metric terms in u and v equations.
304      Depend on correct sign of gravitySign.
305    o added work.pc* to .cvsignore in aim directories using ifc
306    o introduced flag for controllin non-hydrostatic metric terms
307    o removed gravitySign from PARM04
308    o switched to g77/ifc from pgf77 in aim experiments
309    
310    checkpoint46l_post
311    o made convective adjustment work with pressure coordinates:
312     - changed the direction of k-loop in convective_adjustment.F for the
313       case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
314     - adjusted the reference pressure k-index in convective_adjustment.F
315     - adjusted the convection condition in convect.F (in analogy to
316       calc_ivdc.F)
317     - convective_adjustment no longer computes anything on the halos
318     - removed the warnings about negative salinity from find_rho.F and
319       find_alpha.F; instead the new routine look_for_neg_salinity, called
320       at the beginning of find_rho, find_alpha, and find_beta, does a
321       check of the entire slice, if CPP-option
322       CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
323    checkpoint46l_pre
324    
325    checkpoint46k_post
326    o fixed the verification/global_ocean.90x40x15 experiment:
327     - new bathymetry (the world according to A., JMC, and M.)
328     - new initial fields and forcing fields (*.bin files)
329     - new POLY3.COEFFS (for the next release one should switch to a full
330       equation of state: JMD95P or MDJWF)
331     - fixed several errors and redundancies in the data file
332     - experiment uses looped cells
333     - added matlab directory with diagnostic scripts for plotting of output
334    
335    o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
336     - read AIM physics parameters from a file (data.aimphys)
337     - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
338    
339    checkpoint46j_post
340    o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
341    o move wVel computation at the end of the time step, in S/R integr_continuity
342    o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
343    o update timeave pkg for wVel diagnostic.
344    checkpoint46j_pre
345    
346    checkpoint46i_post
347    o Clean up AIM package (and keep the results unchanged):
348      include CPP_OPTION and use IMPLICT NONE in all routines ;
349      declare all the variables _RL ; use _d 0 for all numerical constants.
350      use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
351    
352    checkpoint46h_post
353    o cleaned up the use of rhoNil and rhoConst.
354      - rhoNil should only appear in the LINEAR equation of state, everywhere
355        else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
356        and the dynamical equations are all divided by rhoConst
357    o introduced new parameter rhoConstFresh, a reference density of fresh
358      water, to remove the fresh water flux's dependence on rhoNil. The default
359      value is 999.8 kg/m^3
360    o cleanup up external_forcing.F and external_forcing_surf.F
361      - can now be used by both OCEANIC and OCEANICP
362    checkpoint46h_pre
363    
364     Added code to convert surface volume flux (fresh water) into
365     a mass flux when using P coordinates in the ocean (OCEANICP).
366     Note: It assumes you have set rho0=rhoConst=density of fresh water.
367    
368    checkpoint46g_post
369    o Include a new diagnostic variable phiHydLow for the ocean model
370      - in z-coordinates, it is the bottom pressure anomaly
371      - in p-coordinates, it is the sea surface elevation
372      - in both cases, these variable have global drift, reflecting the mass
373        drift in z-coordinates and the volume drift in p-coordinates
374      - included time averaging for phiHydLow, be aware of the drift!
375    o depth-dependent computation of Bo_surf for pressure coordinates
376      in the ocean (buoyancyRelation='OCEANICP')
377      - requires a new routine (FIND_RHO_SCALAR) to compute density with only
378        Theta, Salinity, and Pressure in the parameter list. This routine is
379        presently contained in find_rho.F. This routine does not give the
380        correct density for 'POLY3', which would be a z-dependent reference
381        density.
382    o cleaned up find_rho
383      - removed obsolete 'eqn' from the parameter list.
384    o added two new verification experiments: gop and goz
385      (4x4 degree global ocean, 15 layers in pressure and height coordinates)
386    checkpoint46g_pre
387    
388    checkpoint46f_post
389    o Enable tangent linear (forward mode) gradient checks:
390      - extended active file handling to g_... files
391      - added TANGENT_SIMULATION to theSimulationMode
392      - extended grdchk package accordingly
393    o added tangent linear setup in verification/carbon/code_ftl
394    o added adjoint setup in verification/front_relax/code_ad
395    
396    checkpoint46e_post
397    o Added new equation of state -> MDJWF
398      - EOS of McDougall et al., 2002, JAOT, submitted
399      - caveat: the equation of state is only valid for a smaller (more
400        realistic?) range of values than JMD95P/Z and UNESCO
401      - added masks to the calculation of pressure in store_pressure
402      - added more check values for density in check_eos (ini_eos.F), some of
403        the old check values are out of the range of the MDJWF-eos, so don't
404        expect perfect matches for those
405    checkpoint46e_pre
406    
407    checkpoint46d_post
408    o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
409      'OCEANICP', also initialised field pressure correctly in ini_eos in the
410      case of pressure coordinates. eosType='JMD95Z' in
411      combination with buoyancyRelation='OCEANICP' now causes an error.
412    o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
413      in find_alpha/beta.
414    checkpoint46d_pre
415    
416    o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
417      so that JMD95Z and JMD95P give approptiate static stability in find_rho.
418    
419  checkpoint46c_post  checkpoint46c_post
420  o Changes necessary for ocean in p-coordinates  o Changes necessary for ocean in p-coordinates
421   -  Added new buoyancy relation = 'OCEANICP'   -  Added new buoyancy relation = 'OCEANICP'
# Line 14  checkpoint46c_pre Line 427  checkpoint46c_pre
427    
428  checkpoint46b_post  checkpoint46b_post
429  o Added new equation of state -> JMD95Z and JMD95P  o Added new equation of state -> JMD95Z and JMD95P
430    - EOS of Jackett and McDougall, 1995, JPO    - EOS of Jackett and McDougall, 1995, JAOT
431    - moved all EOS parameters into EOS.h    - moved all EOS parameters into EOS.h
432    - new routines ini_eos.F, store_pressure.F    - new routines ini_eos.F, store_pressure.F
433  o Added UNESCO EOS, but not recommended because it requires  o Added UNESCO EOS, but not recommended because it requires

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