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revision 1.47 by heimbach, Tue Aug 21 16:38:41 2001 UTC revision 1.106 by jmc, Sat Nov 23 22:39:36 2002 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    checkpoint47a_post
7    o new pkg: aim_v23
8     = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
9       for now, keep the same surface forcing as before.
10     - Part-Cell implemented into AIM; check that Heat & Water are conserved
11     - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
12     - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
13    o add diagnostic of surface correction term in monitor output
14    
15    o bulk_force and therm_seaice
16    
17    checkpoint47
18    differentiable version of checkpoint46n_post
19    o bug fix in quasihydrostaticterms
20    o * "clean" adjoint code (in terms of extensive recomputations)
21        can now be obtained for all GMREDI options (i.e. for
22        - GM_VISBECK_VARIABLE_K
23        - GM_NON_UNITY_DIAGONAL
24        - GM_EXTRA_DIAGONAL
25        - GM_BOLUS_ADVEC )
26      * However, wrong gradient check problem remains unsolved.
27      * New CPP options have been introduced for different
28        tapering schemes
29    o external_fields_load now part of differentiation list
30    o pressure needs multiple storing;
31      would be nice to have store_pressure at beginning or
32      end of forward_step, e.g. by having phiHyd global (5-dim.)
33      (NB: pressure is needed for certain cases in find_rho,
34      which is also invoked through convective_adjustment).
35    o recomputations in find_rho for cases
36     'JMD95'/'UNESCO' or 'MDJWF' are OK.
37    o #define ATMOSPHERIC_LOADING should be differentiable
38    o ini_forcing shifted to begining of initialise_varia
39    o Incorporating QNVS line search routines into MITgcm
40      (this is separate code, and therefore not under pkg)
41      lsopt/, optim/
42    o Updated verification/carbon/
43      - #define GM_VISBECK_VARIABLE_K
44      - GM_taper_scheme    = 'ldd97'    
45    
46    checkpoint46n_post
47    Merging from release1_p8:
48    o verification/natl_box:
49      updating new external_fields_load routine
50    o New package: pkg/seaice
51      Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
52      The sea-ice code is based on Hibler (1979-1980).
53      Two sea-ice dynamic solvers, ADI and LSR, are included.
54      In addition to computing prognostic sea-ice variables and diagnosing
55      the forcing/external data fields that drive the ocean model,
56      SEAICE_MODEL also sets theta to the freezing point under sea-ice.
57      The implied surface heat flux is then stored in variable
58      surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
59      kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
60      non-local transport term.  Because this call precedes model
61      thermodynamics, temperature under sea-ice may not be "exactly" at
62      the freezing point by the time theta is dumped or time-averaged.
63      N.B.: fairly large differences in accuracy occur across
64            different platforms/compilers; comparison between
65            g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
66            generated output gives:
67       T           S           U           V
68      C D M    c        m  s        m  s        m  s        m  s
69      n p a R  g  m  m  e  .  m  m  e  .  m  m  e  .  m  m  e  .
70      f n k u  2  i  a  a  d  i  a  a  d  i  a  a  d  i  a  a  d
71      g d e n  d  n  x  n  .  n  x  n  .  n  x  n  .  n  x  n  .
72    
73      Y Y Y Y  5  5  7  7  7  8 10  9  6  6  6  6  7  5  7  5  7 FAIL  lab_sea
74    o GAD:
75      - generated new common blocks to account for call of
76        same gad routines with differing traceridentities
77        (needed to modify tracerIdentity indices in GAD.h)
78      - generated separate common blocks for case useCubedSphereExchange
79        (Department of Futurology)
80      - parameter lists to gmredi_?transport: added tracerIdentity
81      - added new key indices to tamc.h
82    o external_fields_load:
83      - added this routine to TAF list
84      - needed to make some common blocks global and additional storing
85        along the same lines as exf package (checkpoint_lev?_directives.h)
86    o exf:
87      updated external forcing package
88      - bug fixes carried over from ecco-branch
89        (missing OBCS_OPTIONS.h in two routines)
90      - enable easy to use "no forcing".
91      - added exf I/O for atmospheric loading
92      - added exf I/O for runoff data
93      - transfered scaling between exf <-> MITgcm to exf namelist
94    o Adding new verification experiment global_with_exf.
95      This verification experiment is almost identical to the
96      global_ocean.90x40x15 experiment, except that it uses
97      the exf (and cal) package instead of the
98      external_fields_load routine (cf README file).
99    
100    checkpoint46m_post
101    o modified testscript to return -- when there are no lines of "%MON" output
102    o added new flag "quasiHydrostatic" for QH mode
103      and new routine quasihydrostaticterms()
104    o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
105      New routine: mom_u_coriolis_nh()
106    o fixed sign of non-hydrostatic metric terms in u and v equations.
107      Depend on correct sign of gravitySign.
108    o added work.pc* to .cvsignore in aim directories using ifc
109    o introduced flag for controllin non-hydrostatic metric terms
110    o removed gravitySign from PARM04
111    o switched to g77/ifc from pgf77 in aim experiments
112    
113    checkpoint46l_post
114    o made convective adjustment work with pressure coordinates:
115     - changed the direction of k-loop in convective_adjustment.F for the
116       case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
117     - adjusted the reference pressure k-index in convective_adjustment.F
118     - adjusted the convection condition in convect.F (in analogy to
119       calc_ivdc.F)
120     - convective_adjustment no longer computes anything on the halos
121     - removed the warnings about negative salinity from find_rho.F and
122       find_alpha.F; instead the new routine look_for_neg_salinity, called
123       at the beginning of find_rho, find_alpha, and find_beta, does a
124       check of the entire slice, if CPP-option
125       CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
126    checkpoint46l_pre
127    
128    checkpoint46k_post
129    o fixed the verification/global_ocean.90x40x15 experiment:
130     - new bathymetry (the world according to A., JMC, and M.)
131     - new initial fields and forcing fields (*.bin files)
132     - new POLY3.COEFFS (for the next release one should switch to a full
133       equation of state: JMD95P or MDJWF)
134     - fixed several errors and redundancies in the data file
135     - experiment uses looped cells
136     - added matlab directory with diagnostic scripts for plotting of output
137    
138    o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
139     - read AIM physics parameters from a file (data.aimphys)
140     - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
141    
142    checkpoint46j_post
143    o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
144    o move wVel computation at the end of the time step, in S/R integr_continuity
145    o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
146    o update timeave pkg for wVel diagnostic.
147    checkpoint46j_pre
148    
149    checkpoint46i_post
150    o Clean up AIM package (and keep the results unchanged):
151      include CPP_OPTION and use IMPLICT NONE in all routines ;
152      declare all the variables _RL ; use _d 0 for all numerical constants.
153      use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
154    
155    checkpoint46h_post
156    o cleaned up the use of rhoNil and rhoConst.
157      - rhoNil should only appear in the LINEAR equation of state, everywhere
158        else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
159        and the dynamical equations are all divided by rhoConst
160    o introduced new parameter rhoConstFresh, a reference density of fresh
161      water, to remove the fresh water flux's dependence on rhoNil. The default
162      value is 999.8 kg/m^3
163    o cleanup up external_forcing.F and external_forcing_surf.F
164      - can now be used by both OCEANIC and OCEANICP
165    checkpoint46h_pre
166    
167     Added code to convert surface volume flux (fresh water) into
168     a mass flux when using P coordinates in the ocean (OCEANICP).
169     Note: It assumes you have set rho0=rhoConst=density of fresh water.
170    
171    checkpoint46g_post
172    o Include a new diagnostic variable phiHydLow for the ocean model
173      - in z-coordinates, it is the bottom pressure anomaly
174      - in p-coordinates, it is the sea surface elevation
175      - in both cases, these variable have global drift, reflecting the mass
176        drift in z-coordinates and the volume drift in p-coordinates
177      - included time averaging for phiHydLow, be aware of the drift!
178    o depth-dependent computation of Bo_surf for pressure coordinates
179      in the ocean (buoyancyRelation='OCEANICP')
180      - requires a new routine (FIND_RHO_SCALAR) to compute density with only
181        Theta, Salinity, and Pressure in the parameter list. This routine is
182        presently contained in find_rho.F. This routine does not give the
183        correct density for 'POLY3', which would be a z-dependent reference
184        density.
185    o cleaned up find_rho
186      - removed obsolete 'eqn' from the parameter list.
187    o added two new verification experiments: gop and goz
188      (4x4 degree global ocean, 15 layers in pressure and height coordinates)
189    checkpoint46g_pre
190    
191    checkpoint46f_post
192    o Enable tangent linear (forward mode) gradient checks:
193      - extended active file handling to g_... files
194      - added TANGENT_SIMULATION to theSimulationMode
195      - extended grdchk package accordingly
196    o added tangent linear setup in verification/carbon/code_ftl
197    o added adjoint setup in verification/front_relax/code_ad
198    
199    checkpoint46e_post
200    o Added new equation of state -> MDJWF
201      - EOS of McDougall et al., 2002, JAOT, submitted
202      - caveat: the equation of state is only valid for a smaller (more
203        realistic?) range of values than JMD95P/Z and UNESCO
204      - added masks to the calculation of pressure in store_pressure
205      - added more check values for density in check_eos (ini_eos.F), some of
206        the old check values are out of the range of the MDJWF-eos, so don't
207        expect perfect matches for those
208    checkpoint46e_pre
209    
210    checkpoint46d_post
211    o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
212      'OCEANICP', also initialised field pressure correctly in ini_eos in the
213      case of pressure coordinates. eosType='JMD95Z' in
214      combination with buoyancyRelation='OCEANICP' now causes an error.
215    o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
216      in find_alpha/beta.
217    checkpoint46d_pre
218    
219    o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
220      so that JMD95Z and JMD95P give approptiate static stability in find_rho.
221    
222    checkpoint46c_post
223    o Changes necessary for ocean in p-coordinates
224     -  Added new buoyancy relation = 'OCEANICP'
225     -  Added new parameters = gravitySign (this used to be contained inside
226        the factor dRdZ which I added when we first switched to R coordinates).
227     X GM/Redi is not compatible (yet)
228     X bottom drag and no-slip need to be debugged.
229    checkpoint46c_pre
230    
231    checkpoint46b_post
232    o Added new equation of state -> JMD95Z and JMD95P
233      - EOS of Jackett and McDougall, 1995, JAOT
234      - moved all EOS parameters into EOS.h
235      - new routines ini_eos.F, store_pressure.F
236    o Added UNESCO EOS, but not recommended because it requires
237      in-situ temperature (see JMD95)
238    o Modified formatting for knudsen2.f in utils/knudsen2 and added
239      unesco.f to be used with POLY3
240    checkpoint46b_pre
241    
242    checkpoint46a_post
243    o Added (atmospheric) pressure loading
244      - new field in FFIELDS.h, etc...
245      - new cpp flag ATMOSPHERIC_LOADING
246    o Changed hFacC to _hFacC in calc_phi_hyd.F
247    o Added SHORTWAVE_HEATING to some files for consistency
248    checkpoint46a_pre
249    
250    checkpoint46
251    further merges from release1_p5
252    o new ctrl package
253      - adopted from ECCO environment to enable optimization
254      - added Eliassen Palm fluxes to controls
255    o added Eliassen Palm flux controls to gradient check package
256    o cost package
257      - Compatible with new ctrl package
258      - added Eliassen Palm cost hooks
259      - modif's of existing cost functions
260    o Adjoint-related bug fixes in kpp:
261      - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
262      - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
263    o autodiff package
264      - flow directives:
265        + new for S/R do_the_model_io
266        + enhanced for S/R checkpoint
267        + new gmredi.flow
268      - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
269        disable adcommon.h/g_common.h by default.
270      - fixed problem for adjoint of global_max
271    o modified verification/carbon/
272    o New setup for adjoint of global_ocean
273    o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
274    o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
275    o incorporated hooks for sponge layer code (external_forcing.F)
276    
277    checkpoint45d_post
278    o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
279    o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
280      (affects plume_on_slope "cg2d" output)
281    o add new parameter deltaTfreesurf for free-surface time stepping
282    o exchange gT,gS when using staggerTimeStep & GM & Oly<4
283    o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
284    o change phiMin in exp1 (to agree with documentation)
285    o add new flags:
286     - T,S forcing inside/outside Adams-Bashforth
287     - turn off temp,salt advection and/or forcing
288     - for each tracer, define internal flag for multiDimAdvection & A-B
289    o monitor: change definition of KE to check conservation of Energy
290    
291    checkpoint45c_post
292    o Removed f90 comments ("!")
293    o Modified initialisations to enable exf package for MITgcm
294      (without invoking ECCO_PACKAGE).
295    o modifications to gradient check package (Martin Losch)
296      - enable centered differences
297      - modified format of standard output
298    
299    checkpoint45b_post
300    o cleaned exchange calls in cg2d
301    o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
302    o included CPP option SINGLE_LAYER_MODE in thermodynamics
303      to configure barotropic setup (Martin Losch)
304    o moved some initialisations within bi,bj loop in dynamics
305      (TAF flow dependency)
306    o in initialise_varia, moved call packages_init_variables
307      before convective_adjustment_init
308      (corresponding adjustment of TAF tape initialisation).
309    o in calc_diffusivity/calc_viscosity extended domain to full overlap.
310    
311    checkpoint45a_post
312    o compute Rho over the whole domain (extend iMin,jMin indices)
313    o specific exchange for X-slice domain (case Ny=1)
314    o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
315    o solve_for_pressure : set cg2d_x to zero where OBCS are applied
316    
317    checkpoint44h_post = checkpoint45
318    o Fix to restore differentiability:
319      place at which packages_init_variables is called in
320      initialise_varia is crucial for reverse control flow.
321    o modifications in GMRedi to enable stable adjoint
322      (corresponding modif's in thermodynamics, dynamics)
323    o added missing hook for sponge layer code in external_forcing
324    o modified test cost functions
325    o storing in gad_advection (plus removal of write(0,*)!
326    o missing headers TR1.h added in convective_adjustment routines
327    o errorMessageUnit set non-equal zero in eeboot
328      (conflict on some platforms, e.g. IBM SP3)
329    o modified carbon verif.
330    
331    checkpoint44h_pre
332    o vertical grid option: allow to put the Interface at the middle between
333      2 cell-centers ; replace delZ in pkg/kpp by drF.
334    o GM Advective form: Tracers are advected using the residual transport (=
335      Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
336    
337    checkpoint44g_post
338    o fix surface correction term in multiDimAdvection (affects plume_on_slope
339      results) ; ifdef missing in thermodynamics.F
340    
341    checkpoint44f_pre,checkpoint44f_post
342    o added PTRACERS package
343      This allows an arbitrary number of passive tracers to be integrated
344      forward simultaneously with the dynamicaly model.
345      + Implemented so far:
346        - basic forward algorithm (time-stepping, advection, diffusion, convection)
347        - I/O and checkpointing
348        - GM/Redi  *but*  using the GM/Redi coefficient of Salt
349      + Not implemented so far:
350        - KPP
351        - OBCS
352      + No specific example supplied (yet) but global_ocean.90x40x15 has the
353        necessary data.ptracer file. Simply use -enable=ptracers and uncomment
354        line in data.pkg.
355      + This package is disabled by default since it increases storage.
356    
357    
358    o testscript: added -cleanup option
359    o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
360                 b) enable to filter 2D fields.
361    
362    checkpoint44e_pre,post
363    o re-wrote convective adjustment to use pre-calculated weights
364      Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
365      Adds:    model/src/convective_weights.F, convectively_mixtracer.F
366      Original calls to convect() still in place.
367    
368    chkpt44d_pre,post
369    o added missing EXCLUDE_MONITOR flags
370    o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
371      (incompatible typ in MIN/MAX expressions caused problems
372      on IBM SP3)
373    o in genmake added variable MAKEDEPEND
374      plus resetting for case SunOS
375    o added timer_stats.c routine for IBM SP3
376    o removed variables in dynamics
377    !!! I forgot to create tag chkpt44d_pre !!!
378    !!! But chkpt44d_pre = chkpt44c_post    !!!
379    
380    o real fresh water flux implemented with non-linear free-surface.
381    
382    chkpt44c_pre,post
383    o few fix (mask in shap_s2, EmPmR in external_field_load,
384      USE_NATURAL_BCS in solve_for_P);
385    o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
386    
387    checkpoint44b_pre/_post
388    o merge of relevant stuff from the ecco-branch:
389      - genmake: removed $S64 overwrite for case SunOS
390      - pkg/exf: update and corrections for field swapping and obcs
391      - pkg/ecco: parameter lists for the_model_main, the_main_loop
392                  harmonized between ECCO and MITgcm
393      - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
394                      updated checkpointing_lev... lists for obcs
395      - model/src: minor changes in forward_step, plot_field
396                   added directive for divided adjoint in the_main_loop
397      - pkg/mdsio: added mdsio_gl_slice
398    
399    o check parameters & config (chkpt44a_pre,post)
400    o OBC and NonLin_FrSurf.
401    
402    checkpoint44
403    o fix bug in mom_vi_del2uv
404    o select when filters are applied ; add options to zonal_filter (data.zonfilt)
405    o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
406    o update AIM experiments (NCEP input files)
407    o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
408    o added some stuff for AD
409    
410    checkpoint43
411    o added two new advection tests
412    o added global 4x4 degree ocean test
413    o added test of H&S94 with free surface on cube
414    o some final mods for gradient check, adjoint,...
415    
416    checkpoint42
417      Fixed AD-related problems:
418    o Store directives up-to-date with re-arranged Adams-Bashforth
419      (mainly thermodynamics.F)
420    o New store directives for multi-dim. advection schemes
421      * new CPP flag ALLOW_MULTI_DIM_ADVECTION
422      * new common block and key passkey
423      (mainly gad_advection.F)
424    o Modified store directives for split of dynamics/thermodynamics
425      for the case ALLOW_KPP
426    o Cleaned argument list for timestep_tracer.F
427    
428    checkpoint41
429    o re-formatted/added comments in prologues of key subroutines
430      to work with protex
431    
432  checkpoint40  checkpoint40
433  o all changes of checkpoint40pre?  o moved calc_gs, calc_gt and calc_tr1 back to model/src
434    o added FLT (floats) package from Arne along with demo. experiment
435    o re-arranged Adams-Bashforth scheme for tracers to allow easier
436      implementation of forward-in-time forcing terms
437    o more mods for non-linear free-surface including new variable
438    o modified multi-dim method to work on cube
439    o bug fix in KPP (from DM)
440    
441    checkpoint40pre9
442    o added DST advection schemes
443    o fix MPI bug on SGI's
444    o modifications for non-linear free-surface
445    o fixed conditionals for fixed flow/passive tracer only mode
446    o added tension/strain form of stress tensor
447    o changes to commenting of arguments for TAF/TAMC
448    o added/updated many matlab scripts
449    o added multi-dimensional advection method for tracers
450      
451    checkpoint40pre8
452  o new package rw/  o new package rw/
453    Added method for dumping intermediate local arrays:    Added method for dumping intermediate local arrays:
454    mdsio_writetile - same as mdsio_writefield except works from inside    mdsio_writetile - same as mdsio_writefield except works from inside

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