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revision 1.81 by adcroft, Thu Aug 15 17:25:26 2002 UTC revision 1.131 by jmc, Sun Feb 9 03:01:58 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 New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
7    
8    checkpoint48d_post
9    o in preparation for r*:
10     a) use pre-computed gradient of hydrostatic potential:
11        changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
12     b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
13        => affects results of glob_oce_pressure (different truncation error)  
14      update output.txt of ideal_2D_oce & global_ocean_pressure
15    
16    checkpoint48d_pre
17    o in preparation for r*:
18      new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
19      pass the 2 comp. of the grad. as arguments to momentum S/R.
20      but for the moment, only used if it does not change the results.
21    o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
22    
23    checkpoint48c_post
24    Modifications in treatment of initial flux forcing controls
25    to avoid extra storing of flux fields.
26    
27    checkpoint48c_pre
28    o Added tidal_basin_2d experiment (currently 1D!)
29    o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
30    
31    checkpoint48b_post
32    o r* coordinate added in #ifdef NONLIN_FRSURF block.
33     (modification to pressure gradient not yet implemented)
34    o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
35      (for U & V) that are used for vertical advection of momentum.
36    
37    checkpoint48a_post
38    o In preparation for r*, use temp. array to compute vertical transport
39       in flux-form momentum pkg. => change results of few test-exp.
40      Update output of: exp4, exp5, front_relax, global_ocean_pressure,
41                        lab_sea, natl_box & plume_on_slope
42    
43    checkpoint48
44    o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
45    
46    checkpoint47j_post
47    o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
48    o moved adexch from forward_step to addummy_in_stepping
49    o added exch in ctrl_map_...
50    o aveFreq.=0. at end of cost_final to avoid overwrite in
51      reverse checkpointing loop
52    o Yet more changes in gmredi:
53      * adgmredi_calc_tensor
54        avoiding all recomputation of gmredi_slope_limit
55      * adgmredi_x/y/rtransport
56        added flag for excessive storing to avoid recomp. of
57        u/v/rtans, dTdx/y/z
58        -> this is not really necessary and very memory-consuming
59      * adgmredi_slope_psi:
60        consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
61      * gmredi_slope_limit
62        re-activated full calculation of taperfct for case 'ac02'
63    o updating verification/ adjoints of carbon, global_ocean.90x40x15
64    
65    checkpoint47i_post
66    o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
67    o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
68      default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
69    o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
70    o gmredi: fix few bugs.
71    
72    checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
73    This will be a good checkpoint to plug into the ecco-branch.
74    o few modif.'s to get latest version adjointed
75      (mainly kick out code in ini_linear_phisurf)
76    o modif's to run adjoint with exactConserv
77    o case GM_BOLUS_ADVEC should be cleaned
78      S/R gmredi_slope_psi should be cleaned
79    o verification/carbon now has exactConserv=.TRUE.
80    
81    checkpoint47g_post
82    o time-average AIM output: becomes independent from statvars time-average
83      (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
84    o After TAF bug fix:
85      Tested adjoint of gmredi package.
86      Tests were done with checkpoint47 rather than with latest
87      checkpoint47f_post since the latter is broken for the adjoint
88      verification/carbon/ contains both ADM and TLM gradient checks.
89    Here they are, before they get changed/lost/stolen.
90    Mostly modif.'s to fix numerical sensitivities.
91    Gradient checks OK for
92    - GM_taper_scheme:
93      * clipping
94      * ac02
95      * linear
96      * glw91
97      * dm95
98      * ldd97
99    - GMREDI_OPTIONS:
100      * GM_VISBECK_VARIABLE_K
101      * GM_NON_UNITY_DIAGONAL
102      * GM_EXTRA_DIAGONAL
103      * GM_BOLUS_ADVEC
104    in conjunction with data.gmredi parameters to be checked in
105    in a few minutes under verification/carbon/code/
106    
107    checkpoint47f_post
108    Merging from release1_p10:
109    o modifications for using pkg/exf with pkg/seaice
110      - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
111        and SEAICE_EXTERNAL_FLUXES
112      - pkg/exf CPP options EXF_READ_EVAP and
113        EXF_NO_BULK_COMPUTATIONS
114      - usage examples are Experiments 8 and 9 in
115        verification/lab_sea/README
116      - verification/lab_sea default experiment now uses
117        pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
118    
119    checkpoint47e_post
120    o created a tag prior to creating a branch
121    
122    checkpoint47d_post
123    o fixed bug in the oceanic pressure coordinates code: vertical viscosity
124      at the bottom boundary had an erroneous half slip boundary condition
125    o added bottom drag and no slip boundary condition capabilities to
126      oceanic pressure coordinates code
127    o added new verification experiment global_ocean_pressure, this experiment is
128      also described in the tutorial section of the manual
129    checkpoint47d_pre
130    
131    checkpoint47c_post
132    o Added a verification experiment for a global cubed-sphere ocean run
133      -  verification/global_ocean.cubed32x32x30
134      -  uses pkg/therm_seaice and pkg/bulk_forcing
135    
136    o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
137    o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
138      when using P-coordinate; only implemented for atmospheric config.
139    o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
140      NOTES: requires option NONLIN_FRSURF to be "#define".
141    o update advect_xz/results/output.txt (left from checkpoint44g_post)
142    
143    checkpoint47b_post
144    Merging from release1_p9:
145    o pkg/seaice
146      - removed GOTO's and added taf directives
147      - double precision constants to reduce the g77 (Linux)
148        to F77 (SGI) differences reported in release1_p8
149    o tools/genmake
150      - added SGI options
151    o verification/testscript
152      - updated to that of checkpoint47a_post
153    o verification/global_ocean.90x40x15/input/eedata
154      - modified for SGI f77 compatibility
155    o verification/lab_sea
156      - added description of sea-ice model
157      - added missing matlab routines
158      - added test of thermodynamics parallelization
159    
160    checkpoint47a_post
161    o new pkg: aim_v23
162     = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
163       for now, keep the same surface forcing as before.
164     - Part-Cell implemented into AIM; check that Heat & Water are conserved
165     - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
166     - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
167    o add diagnostic of surface correction term in monitor output
168    
169    o bulk_force and therm_seaice
170    - Two packages:  bulk_force (Bulk forcing)
171      and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
172    - Earlier integration from Stephaine Dutkiewicz
173      and Patrick Heimbach.
174    - Two ifdef statements for compile time,
175       ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
176    
177    checkpoint47
178    differentiable version of checkpoint46n_post
179    o bug fix in quasihydrostaticterms
180    o * "clean" adjoint code (in terms of extensive recomputations)
181        can now be obtained for all GMREDI options (i.e. for
182        - GM_VISBECK_VARIABLE_K
183        - GM_NON_UNITY_DIAGONAL
184        - GM_EXTRA_DIAGONAL
185        - GM_BOLUS_ADVEC )
186      * However, wrong gradient check problem remains unsolved.
187      * New CPP options have been introduced for different
188        tapering schemes
189    o external_fields_load now part of differentiation list
190    o pressure needs multiple storing;
191      would be nice to have store_pressure at beginning or
192      end of forward_step, e.g. by having phiHyd global (5-dim.)
193      (NB: pressure is needed for certain cases in find_rho,
194      which is also invoked through convective_adjustment).
195    o recomputations in find_rho for cases
196     'JMD95'/'UNESCO' or 'MDJWF' are OK.
197    o #define ATMOSPHERIC_LOADING should be differentiable
198    o ini_forcing shifted to begining of initialise_varia
199    o Incorporating QNVS line search routines into MITgcm
200      (this is separate code, and therefore not under pkg)
201      lsopt/, optim/
202    o Updated verification/carbon/
203      - #define GM_VISBECK_VARIABLE_K
204      - GM_taper_scheme    = 'ldd97'    
205    
206    checkpoint46n_post
207    Merging from release1_p8:
208    o verification/natl_box:
209      updating new external_fields_load routine
210    o New package: pkg/seaice
211      Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
212      The sea-ice code is based on Hibler (1979-1980).
213      Two sea-ice dynamic solvers, ADI and LSR, are included.
214      In addition to computing prognostic sea-ice variables and diagnosing
215      the forcing/external data fields that drive the ocean model,
216      SEAICE_MODEL also sets theta to the freezing point under sea-ice.
217      The implied surface heat flux is then stored in variable
218      surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
219      kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
220      non-local transport term.  Because this call precedes model
221      thermodynamics, temperature under sea-ice may not be "exactly" at
222      the freezing point by the time theta is dumped or time-averaged.
223      N.B.: fairly large differences in accuracy occur across
224            different platforms/compilers; comparison between
225            g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
226            generated output gives:
227       T           S           U           V
228      C D M    c        m  s        m  s        m  s        m  s
229      n p a R  g  m  m  e  .  m  m  e  .  m  m  e  .  m  m  e  .
230      f n k u  2  i  a  a  d  i  a  a  d  i  a  a  d  i  a  a  d
231      g d e n  d  n  x  n  .  n  x  n  .  n  x  n  .  n  x  n  .
232    
233      Y Y Y Y  5  5  7  7  7  8 10  9  6  6  6  6  7  5  7  5  7 FAIL  lab_sea
234    o GAD:
235      - generated new common blocks to account for call of
236        same gad routines with differing traceridentities
237        (needed to modify tracerIdentity indices in GAD.h)
238      - generated separate common blocks for case useCubedSphereExchange
239        (Department of Futurology)
240      - parameter lists to gmredi_?transport: added tracerIdentity
241      - added new key indices to tamc.h
242    o external_fields_load:
243      - added this routine to TAF list
244      - needed to make some common blocks global and additional storing
245        along the same lines as exf package (checkpoint_lev?_directives.h)
246    o exf:
247      updated external forcing package
248      - bug fixes carried over from ecco-branch
249        (missing OBCS_OPTIONS.h in two routines)
250      - enable easy to use "no forcing".
251      - added exf I/O for atmospheric loading
252      - added exf I/O for runoff data
253      - transfered scaling between exf <-> MITgcm to exf namelist
254    o Adding new verification experiment global_with_exf.
255      This verification experiment is almost identical to the
256      global_ocean.90x40x15 experiment, except that it uses
257      the exf (and cal) package instead of the
258      external_fields_load routine (cf README file).
259    
260    checkpoint46m_post
261    o modified testscript to return -- when there are no lines of "%MON" output
262    o added new flag "quasiHydrostatic" for QH mode
263      and new routine quasihydrostaticterms()
264    o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
265      New routine: mom_u_coriolis_nh()
266    o fixed sign of non-hydrostatic metric terms in u and v equations.
267      Depend on correct sign of gravitySign.
268    o added work.pc* to .cvsignore in aim directories using ifc
269    o introduced flag for controllin non-hydrostatic metric terms
270    o removed gravitySign from PARM04
271    o switched to g77/ifc from pgf77 in aim experiments
272    
273    checkpoint46l_post
274    o made convective adjustment work with pressure coordinates:
275     - changed the direction of k-loop in convective_adjustment.F for the
276       case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
277     - adjusted the reference pressure k-index in convective_adjustment.F
278     - adjusted the convection condition in convect.F (in analogy to
279       calc_ivdc.F)
280     - convective_adjustment no longer computes anything on the halos
281     - removed the warnings about negative salinity from find_rho.F and
282       find_alpha.F; instead the new routine look_for_neg_salinity, called
283       at the beginning of find_rho, find_alpha, and find_beta, does a
284       check of the entire slice, if CPP-option
285       CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
286    checkpoint46l_pre
287    
288    checkpoint46k_post
289    o fixed the verification/global_ocean.90x40x15 experiment:
290     - new bathymetry (the world according to A., JMC, and M.)
291     - new initial fields and forcing fields (*.bin files)
292     - new POLY3.COEFFS (for the next release one should switch to a full
293       equation of state: JMD95P or MDJWF)
294     - fixed several errors and redundancies in the data file
295     - experiment uses looped cells
296     - added matlab directory with diagnostic scripts for plotting of output
297    
298    o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
299     - read AIM physics parameters from a file (data.aimphys)
300     - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
301    
302    checkpoint46j_post
303    o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
304    o move wVel computation at the end of the time step, in S/R integr_continuity
305    o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
306    o update timeave pkg for wVel diagnostic.
307    checkpoint46j_pre
308    
309    checkpoint46i_post
310    o Clean up AIM package (and keep the results unchanged):
311      include CPP_OPTION and use IMPLICT NONE in all routines ;
312      declare all the variables _RL ; use _d 0 for all numerical constants.
313      use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
314    
315    checkpoint46h_post
316    o cleaned up the use of rhoNil and rhoConst.
317      - rhoNil should only appear in the LINEAR equation of state, everywhere
318        else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
319        and the dynamical equations are all divided by rhoConst
320    o introduced new parameter rhoConstFresh, a reference density of fresh
321      water, to remove the fresh water flux's dependence on rhoNil. The default
322      value is 999.8 kg/m^3
323    o cleanup up external_forcing.F and external_forcing_surf.F
324      - can now be used by both OCEANIC and OCEANICP
325    checkpoint46h_pre
326    
327     Added code to convert surface volume flux (fresh water) into
328     a mass flux when using P coordinates in the ocean (OCEANICP).
329     Note: It assumes you have set rho0=rhoConst=density of fresh water.
330    
331    checkpoint46g_post
332    o Include a new diagnostic variable phiHydLow for the ocean model
333      - in z-coordinates, it is the bottom pressure anomaly
334      - in p-coordinates, it is the sea surface elevation
335      - in both cases, these variable have global drift, reflecting the mass
336        drift in z-coordinates and the volume drift in p-coordinates
337      - included time averaging for phiHydLow, be aware of the drift!
338    o depth-dependent computation of Bo_surf for pressure coordinates
339      in the ocean (buoyancyRelation='OCEANICP')
340      - requires a new routine (FIND_RHO_SCALAR) to compute density with only
341        Theta, Salinity, and Pressure in the parameter list. This routine is
342        presently contained in find_rho.F. This routine does not give the
343        correct density for 'POLY3', which would be a z-dependent reference
344        density.
345    o cleaned up find_rho
346      - removed obsolete 'eqn' from the parameter list.
347    o added two new verification experiments: gop and goz
348      (4x4 degree global ocean, 15 layers in pressure and height coordinates)
349    checkpoint46g_pre
350    
351    checkpoint46f_post
352    o Enable tangent linear (forward mode) gradient checks:
353      - extended active file handling to g_... files
354      - added TANGENT_SIMULATION to theSimulationMode
355      - extended grdchk package accordingly
356    o added tangent linear setup in verification/carbon/code_ftl
357    o added adjoint setup in verification/front_relax/code_ad
358    
359    checkpoint46e_post
360    o Added new equation of state -> MDJWF
361      - EOS of McDougall et al., 2002, JAOT, submitted
362      - caveat: the equation of state is only valid for a smaller (more
363        realistic?) range of values than JMD95P/Z and UNESCO
364      - added masks to the calculation of pressure in store_pressure
365      - added more check values for density in check_eos (ini_eos.F), some of
366        the old check values are out of the range of the MDJWF-eos, so don't
367        expect perfect matches for those
368    checkpoint46e_pre
369    
370    checkpoint46d_post
371    o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
372      'OCEANICP', also initialised field pressure correctly in ini_eos in the
373      case of pressure coordinates. eosType='JMD95Z' in
374      combination with buoyancyRelation='OCEANICP' now causes an error.
375    o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
376      in find_alpha/beta.
377    checkpoint46d_pre
378    
379    o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
380      so that JMD95Z and JMD95P give approptiate static stability in find_rho.
381    
382  checkpoint46c_post  checkpoint46c_post
383  o Changes necessary for ocean in p-coordinates  o Changes necessary for ocean in p-coordinates
384   -  Added new buoyancy relation = 'OCEANICP'   -  Added new buoyancy relation = 'OCEANICP'
# Line 14  checkpoint46c_pre Line 390  checkpoint46c_pre
390    
391  checkpoint46b_post  checkpoint46b_post
392  o Added new equation of state -> JMD95Z and JMD95P  o Added new equation of state -> JMD95Z and JMD95P
393    - EOS of Jackett and McDougall, 1995, JPO    - EOS of Jackett and McDougall, 1995, JAOT
394    - moved all EOS parameters into EOS.h    - moved all EOS parameters into EOS.h
395    - new routines ini_eos.F, store_pressure.F    - new routines ini_eos.F, store_pressure.F
396  o Added UNESCO EOS, but not recommended because it requires  o Added UNESCO EOS, but not recommended because it requires

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