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revision 1.20 by adcroft, Tue May 18 15:43:59 1999 UTC revision 1.126 by jmc, Thu Jan 30 00:12:34 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 can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
7    
8    checkpoint48b_post
9    o r* coordinate added in #ifdef NONLIN_FRSURF block.
10     (modification to pressure gradient not yet implemented)
11    o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
12      (for U & V) that are used for vertical advection of momentum.
13    
14    checkpoint48a_post
15    o In preparation for r*, use temp. array to compute vertical transport
16       in flux-form momentum pkg. => change results of few test-exp.
17      Update output of: exp4, exp5, front_relax, global_ocean_pressure,
18                        lab_sea, natl_box & plume_on_slope
19    
20    checkpoint48
21    o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
22    
23    checkpoint47j_post
24    o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
25    o moved adexch from forward_step to addummy_in_stepping
26    o added exch in ctrl_map_...
27    o aveFreq.=0. at end of cost_final to avoid overwrite in
28      reverse checkpointing loop
29    o Yet more changes in gmredi:
30      * adgmredi_calc_tensor
31        avoiding all recomputation of gmredi_slope_limit
32      * adgmredi_x/y/rtransport
33        added flag for excessive storing to avoid recomp. of
34        u/v/rtans, dTdx/y/z
35        -> this is not really necessary and very memory-consuming
36      * adgmredi_slope_psi:
37        consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
38      * gmredi_slope_limit
39        re-activated full calculation of taperfct for case 'ac02'
40    o updating verification/ adjoints of carbon, global_ocean.90x40x15
41    
42    checkpoint47i_post
43    o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
44    o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
45      default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
46    o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
47    o gmredi: fix few bugs.
48    
49    checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
50    This will be a good checkpoint to plug into the ecco-branch.
51    o few modif.'s to get latest version adjointed
52      (mainly kick out code in ini_linear_phisurf)
53    o modif's to run adjoint with exactConserv
54    o case GM_BOLUS_ADVEC should be cleaned
55      S/R gmredi_slope_psi should be cleaned
56    o verification/carbon now has exactConserv=.TRUE.
57    
58    checkpoint47g_post
59    o time-average AIM output: becomes independent from statvars time-average
60      (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
61    o After TAF bug fix:
62      Tested adjoint of gmredi package.
63      Tests were done with checkpoint47 rather than with latest
64      checkpoint47f_post since the latter is broken for the adjoint
65      verification/carbon/ contains both ADM and TLM gradient checks.
66    Here they are, before they get changed/lost/stolen.
67    Mostly modif.'s to fix numerical sensitivities.
68    Gradient checks OK for
69    - GM_taper_scheme:
70      * clipping
71      * ac02
72      * linear
73      * glw91
74      * dm95
75      * ldd97
76    - GMREDI_OPTIONS:
77      * GM_VISBECK_VARIABLE_K
78      * GM_NON_UNITY_DIAGONAL
79      * GM_EXTRA_DIAGONAL
80      * GM_BOLUS_ADVEC
81    in conjunction with data.gmredi parameters to be checked in
82    in a few minutes under verification/carbon/code/
83    
84    checkpoint47f_post
85    Merging from release1_p10:
86    o modifications for using pkg/exf with pkg/seaice
87      - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
88        and SEAICE_EXTERNAL_FLUXES
89      - pkg/exf CPP options EXF_READ_EVAP and
90        EXF_NO_BULK_COMPUTATIONS
91      - usage examples are Experiments 8 and 9 in
92        verification/lab_sea/README
93      - verification/lab_sea default experiment now uses
94        pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
95    
96    checkpoint47e_post
97    o created a tag prior to creating a branch
98    
99    checkpoint47d_post
100    o fixed bug in the oceanic pressure coordinates code: vertical viscosity
101      at the bottom boundary had an erroneous half slip boundary condition
102    o added bottom drag and no slip boundary condition capabilities to
103      oceanic pressure coordinates code
104    o added new verification experiment global_ocean_pressure, this experiment is
105      also described in the tutorial section of the manual
106    checkpoint47d_pre
107    
108    checkpoint47c_post
109    o Added a verification experiment for a global cubed-sphere ocean run
110      -  verification/global_ocean.cubed32x32x30
111      -  uses pkg/therm_seaice and pkg/bulk_forcing
112    
113    o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
114    o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
115      when using P-coordinate; only implemented for atmospheric config.
116    o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
117      NOTES: requires option NONLIN_FRSURF to be "#define".
118    o update advect_xz/results/output.txt (left from checkpoint44g_post)
119    
120    checkpoint47b_post
121    Merging from release1_p9:
122    o pkg/seaice
123      - removed GOTO's and added taf directives
124      - double precision constants to reduce the g77 (Linux)
125        to F77 (SGI) differences reported in release1_p8
126    o tools/genmake
127      - added SGI options
128    o verification/testscript
129      - updated to that of checkpoint47a_post
130    o verification/global_ocean.90x40x15/input/eedata
131      - modified for SGI f77 compatibility
132    o verification/lab_sea
133      - added description of sea-ice model
134      - added missing matlab routines
135      - added test of thermodynamics parallelization
136    
137    checkpoint47a_post
138    o new pkg: aim_v23
139     = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
140       for now, keep the same surface forcing as before.
141     - Part-Cell implemented into AIM; check that Heat & Water are conserved
142     - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
143     - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
144    o add diagnostic of surface correction term in monitor output
145    
146    o bulk_force and therm_seaice
147    - Two packages:  bulk_force (Bulk forcing)
148      and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
149    - Earlier integration from Stephaine Dutkiewicz
150      and Patrick Heimbach.
151    - Two ifdef statements for compile time,
152       ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
153    
154    checkpoint47
155    differentiable version of checkpoint46n_post
156    o bug fix in quasihydrostaticterms
157    o * "clean" adjoint code (in terms of extensive recomputations)
158        can now be obtained for all GMREDI options (i.e. for
159        - GM_VISBECK_VARIABLE_K
160        - GM_NON_UNITY_DIAGONAL
161        - GM_EXTRA_DIAGONAL
162        - GM_BOLUS_ADVEC )
163      * However, wrong gradient check problem remains unsolved.
164      * New CPP options have been introduced for different
165        tapering schemes
166    o external_fields_load now part of differentiation list
167    o pressure needs multiple storing;
168      would be nice to have store_pressure at beginning or
169      end of forward_step, e.g. by having phiHyd global (5-dim.)
170      (NB: pressure is needed for certain cases in find_rho,
171      which is also invoked through convective_adjustment).
172    o recomputations in find_rho for cases
173     'JMD95'/'UNESCO' or 'MDJWF' are OK.
174    o #define ATMOSPHERIC_LOADING should be differentiable
175    o ini_forcing shifted to begining of initialise_varia
176    o Incorporating QNVS line search routines into MITgcm
177      (this is separate code, and therefore not under pkg)
178      lsopt/, optim/
179    o Updated verification/carbon/
180      - #define GM_VISBECK_VARIABLE_K
181      - GM_taper_scheme    = 'ldd97'    
182    
183    checkpoint46n_post
184    Merging from release1_p8:
185    o verification/natl_box:
186      updating new external_fields_load routine
187    o New package: pkg/seaice
188      Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
189      The sea-ice code is based on Hibler (1979-1980).
190      Two sea-ice dynamic solvers, ADI and LSR, are included.
191      In addition to computing prognostic sea-ice variables and diagnosing
192      the forcing/external data fields that drive the ocean model,
193      SEAICE_MODEL also sets theta to the freezing point under sea-ice.
194      The implied surface heat flux is then stored in variable
195      surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
196      kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
197      non-local transport term.  Because this call precedes model
198      thermodynamics, temperature under sea-ice may not be "exactly" at
199      the freezing point by the time theta is dumped or time-averaged.
200      N.B.: fairly large differences in accuracy occur across
201            different platforms/compilers; comparison between
202            g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
203            generated output gives:
204       T           S           U           V
205      C D M    c        m  s        m  s        m  s        m  s
206      n p a R  g  m  m  e  .  m  m  e  .  m  m  e  .  m  m  e  .
207      f n k u  2  i  a  a  d  i  a  a  d  i  a  a  d  i  a  a  d
208      g d e n  d  n  x  n  .  n  x  n  .  n  x  n  .  n  x  n  .
209    
210      Y Y Y Y  5  5  7  7  7  8 10  9  6  6  6  6  7  5  7  5  7 FAIL  lab_sea
211    o GAD:
212      - generated new common blocks to account for call of
213        same gad routines with differing traceridentities
214        (needed to modify tracerIdentity indices in GAD.h)
215      - generated separate common blocks for case useCubedSphereExchange
216        (Department of Futurology)
217      - parameter lists to gmredi_?transport: added tracerIdentity
218      - added new key indices to tamc.h
219    o external_fields_load:
220      - added this routine to TAF list
221      - needed to make some common blocks global and additional storing
222        along the same lines as exf package (checkpoint_lev?_directives.h)
223    o exf:
224      updated external forcing package
225      - bug fixes carried over from ecco-branch
226        (missing OBCS_OPTIONS.h in two routines)
227      - enable easy to use "no forcing".
228      - added exf I/O for atmospheric loading
229      - added exf I/O for runoff data
230      - transfered scaling between exf <-> MITgcm to exf namelist
231    o Adding new verification experiment global_with_exf.
232      This verification experiment is almost identical to the
233      global_ocean.90x40x15 experiment, except that it uses
234      the exf (and cal) package instead of the
235      external_fields_load routine (cf README file).
236    
237    checkpoint46m_post
238    o modified testscript to return -- when there are no lines of "%MON" output
239    o added new flag "quasiHydrostatic" for QH mode
240      and new routine quasihydrostaticterms()
241    o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
242      New routine: mom_u_coriolis_nh()
243    o fixed sign of non-hydrostatic metric terms in u and v equations.
244      Depend on correct sign of gravitySign.
245    o added work.pc* to .cvsignore in aim directories using ifc
246    o introduced flag for controllin non-hydrostatic metric terms
247    o removed gravitySign from PARM04
248    o switched to g77/ifc from pgf77 in aim experiments
249    
250    checkpoint46l_post
251    o made convective adjustment work with pressure coordinates:
252     - changed the direction of k-loop in convective_adjustment.F for the
253       case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
254     - adjusted the reference pressure k-index in convective_adjustment.F
255     - adjusted the convection condition in convect.F (in analogy to
256       calc_ivdc.F)
257     - convective_adjustment no longer computes anything on the halos
258     - removed the warnings about negative salinity from find_rho.F and
259       find_alpha.F; instead the new routine look_for_neg_salinity, called
260       at the beginning of find_rho, find_alpha, and find_beta, does a
261       check of the entire slice, if CPP-option
262       CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
263    checkpoint46l_pre
264    
265    checkpoint46k_post
266    o fixed the verification/global_ocean.90x40x15 experiment:
267     - new bathymetry (the world according to A., JMC, and M.)
268     - new initial fields and forcing fields (*.bin files)
269     - new POLY3.COEFFS (for the next release one should switch to a full
270       equation of state: JMD95P or MDJWF)
271     - fixed several errors and redundancies in the data file
272     - experiment uses looped cells
273     - added matlab directory with diagnostic scripts for plotting of output
274    
275    o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
276     - read AIM physics parameters from a file (data.aimphys)
277     - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
278    
279    checkpoint46j_post
280    o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
281    o move wVel computation at the end of the time step, in S/R integr_continuity
282    o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
283    o update timeave pkg for wVel diagnostic.
284    checkpoint46j_pre
285    
286    checkpoint46i_post
287    o Clean up AIM package (and keep the results unchanged):
288      include CPP_OPTION and use IMPLICT NONE in all routines ;
289      declare all the variables _RL ; use _d 0 for all numerical constants.
290      use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
291    
292    checkpoint46h_post
293    o cleaned up the use of rhoNil and rhoConst.
294      - rhoNil should only appear in the LINEAR equation of state, everywhere
295        else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
296        and the dynamical equations are all divided by rhoConst
297    o introduced new parameter rhoConstFresh, a reference density of fresh
298      water, to remove the fresh water flux's dependence on rhoNil. The default
299      value is 999.8 kg/m^3
300    o cleanup up external_forcing.F and external_forcing_surf.F
301      - can now be used by both OCEANIC and OCEANICP
302    checkpoint46h_pre
303    
304     Added code to convert surface volume flux (fresh water) into
305     a mass flux when using P coordinates in the ocean (OCEANICP).
306     Note: It assumes you have set rho0=rhoConst=density of fresh water.
307    
308    checkpoint46g_post
309    o Include a new diagnostic variable phiHydLow for the ocean model
310      - in z-coordinates, it is the bottom pressure anomaly
311      - in p-coordinates, it is the sea surface elevation
312      - in both cases, these variable have global drift, reflecting the mass
313        drift in z-coordinates and the volume drift in p-coordinates
314      - included time averaging for phiHydLow, be aware of the drift!
315    o depth-dependent computation of Bo_surf for pressure coordinates
316      in the ocean (buoyancyRelation='OCEANICP')
317      - requires a new routine (FIND_RHO_SCALAR) to compute density with only
318        Theta, Salinity, and Pressure in the parameter list. This routine is
319        presently contained in find_rho.F. This routine does not give the
320        correct density for 'POLY3', which would be a z-dependent reference
321        density.
322    o cleaned up find_rho
323      - removed obsolete 'eqn' from the parameter list.
324    o added two new verification experiments: gop and goz
325      (4x4 degree global ocean, 15 layers in pressure and height coordinates)
326    checkpoint46g_pre
327    
328    checkpoint46f_post
329    o Enable tangent linear (forward mode) gradient checks:
330      - extended active file handling to g_... files
331      - added TANGENT_SIMULATION to theSimulationMode
332      - extended grdchk package accordingly
333    o added tangent linear setup in verification/carbon/code_ftl
334    o added adjoint setup in verification/front_relax/code_ad
335    
336    checkpoint46e_post
337    o Added new equation of state -> MDJWF
338      - EOS of McDougall et al., 2002, JAOT, submitted
339      - caveat: the equation of state is only valid for a smaller (more
340        realistic?) range of values than JMD95P/Z and UNESCO
341      - added masks to the calculation of pressure in store_pressure
342      - added more check values for density in check_eos (ini_eos.F), some of
343        the old check values are out of the range of the MDJWF-eos, so don't
344        expect perfect matches for those
345    checkpoint46e_pre
346    
347    checkpoint46d_post
348    o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
349      'OCEANICP', also initialised field pressure correctly in ini_eos in the
350      case of pressure coordinates. eosType='JMD95Z' in
351      combination with buoyancyRelation='OCEANICP' now causes an error.
352    o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
353      in find_alpha/beta.
354    checkpoint46d_pre
355    
356    o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
357      so that JMD95Z and JMD95P give approptiate static stability in find_rho.
358    
359    checkpoint46c_post
360    o Changes necessary for ocean in p-coordinates
361     -  Added new buoyancy relation = 'OCEANICP'
362     -  Added new parameters = gravitySign (this used to be contained inside
363        the factor dRdZ which I added when we first switched to R coordinates).
364     X GM/Redi is not compatible (yet)
365     X bottom drag and no-slip need to be debugged.
366    checkpoint46c_pre
367    
368    checkpoint46b_post
369    o Added new equation of state -> JMD95Z and JMD95P
370      - EOS of Jackett and McDougall, 1995, JAOT
371      - moved all EOS parameters into EOS.h
372      - new routines ini_eos.F, store_pressure.F
373    o Added UNESCO EOS, but not recommended because it requires
374      in-situ temperature (see JMD95)
375    o Modified formatting for knudsen2.f in utils/knudsen2 and added
376      unesco.f to be used with POLY3
377    checkpoint46b_pre
378    
379    checkpoint46a_post
380    o Added (atmospheric) pressure loading
381      - new field in FFIELDS.h, etc...
382      - new cpp flag ATMOSPHERIC_LOADING
383    o Changed hFacC to _hFacC in calc_phi_hyd.F
384    o Added SHORTWAVE_HEATING to some files for consistency
385    checkpoint46a_pre
386    
387    checkpoint46
388    further merges from release1_p5
389    o new ctrl package
390      - adopted from ECCO environment to enable optimization
391      - added Eliassen Palm fluxes to controls
392    o added Eliassen Palm flux controls to gradient check package
393    o cost package
394      - Compatible with new ctrl package
395      - added Eliassen Palm cost hooks
396      - modif's of existing cost functions
397    o Adjoint-related bug fixes in kpp:
398      - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
399      - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
400    o autodiff package
401      - flow directives:
402        + new for S/R do_the_model_io
403        + enhanced for S/R checkpoint
404        + new gmredi.flow
405      - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
406        disable adcommon.h/g_common.h by default.
407      - fixed problem for adjoint of global_max
408    o modified verification/carbon/
409    o New setup for adjoint of global_ocean
410    o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
411    o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
412    o incorporated hooks for sponge layer code (external_forcing.F)
413    
414    checkpoint45d_post
415    o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
416    o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
417      (affects plume_on_slope "cg2d" output)
418    o add new parameter deltaTfreesurf for free-surface time stepping
419    o exchange gT,gS when using staggerTimeStep & GM & Oly<4
420    o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
421    o change phiMin in exp1 (to agree with documentation)
422    o add new flags:
423     - T,S forcing inside/outside Adams-Bashforth
424     - turn off temp,salt advection and/or forcing
425     - for each tracer, define internal flag for multiDimAdvection & A-B
426    o monitor: change definition of KE to check conservation of Energy
427    
428    checkpoint45c_post
429    o Removed f90 comments ("!")
430    o Modified initialisations to enable exf package for MITgcm
431      (without invoking ECCO_PACKAGE).
432    o modifications to gradient check package (Martin Losch)
433      - enable centered differences
434      - modified format of standard output
435    
436    checkpoint45b_post
437    o cleaned exchange calls in cg2d
438    o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
439    o included CPP option SINGLE_LAYER_MODE in thermodynamics
440      to configure barotropic setup (Martin Losch)
441    o moved some initialisations within bi,bj loop in dynamics
442      (TAF flow dependency)
443    o in initialise_varia, moved call packages_init_variables
444      before convective_adjustment_init
445      (corresponding adjustment of TAF tape initialisation).
446    o in calc_diffusivity/calc_viscosity extended domain to full overlap.
447    
448    checkpoint45a_post
449    o compute Rho over the whole domain (extend iMin,jMin indices)
450    o specific exchange for X-slice domain (case Ny=1)
451    o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
452    o solve_for_pressure : set cg2d_x to zero where OBCS are applied
453    
454    checkpoint44h_post = checkpoint45
455    o Fix to restore differentiability:
456      place at which packages_init_variables is called in
457      initialise_varia is crucial for reverse control flow.
458    o modifications in GMRedi to enable stable adjoint
459      (corresponding modif's in thermodynamics, dynamics)
460    o added missing hook for sponge layer code in external_forcing
461    o modified test cost functions
462    o storing in gad_advection (plus removal of write(0,*)!
463    o missing headers TR1.h added in convective_adjustment routines
464    o errorMessageUnit set non-equal zero in eeboot
465      (conflict on some platforms, e.g. IBM SP3)
466    o modified carbon verif.
467    
468    checkpoint44h_pre
469    o vertical grid option: allow to put the Interface at the middle between
470      2 cell-centers ; replace delZ in pkg/kpp by drF.
471    o GM Advective form: Tracers are advected using the residual transport (=
472      Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
473    
474    checkpoint44g_post
475    o fix surface correction term in multiDimAdvection (affects plume_on_slope
476      results) ; ifdef missing in thermodynamics.F
477    
478    checkpoint44f_pre,checkpoint44f_post
479    o added PTRACERS package
480      This allows an arbitrary number of passive tracers to be integrated
481      forward simultaneously with the dynamicaly model.
482      + Implemented so far:
483        - basic forward algorithm (time-stepping, advection, diffusion, convection)
484        - I/O and checkpointing
485        - GM/Redi  *but*  using the GM/Redi coefficient of Salt
486      + Not implemented so far:
487        - KPP
488        - OBCS
489      + No specific example supplied (yet) but global_ocean.90x40x15 has the
490        necessary data.ptracer file. Simply use -enable=ptracers and uncomment
491        line in data.pkg.
492      + This package is disabled by default since it increases storage.
493    
494    
495    o testscript: added -cleanup option
496    o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
497                 b) enable to filter 2D fields.
498    
499    checkpoint44e_pre,post
500    o re-wrote convective adjustment to use pre-calculated weights
501      Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
502      Adds:    model/src/convective_weights.F, convectively_mixtracer.F
503      Original calls to convect() still in place.
504    
505    chkpt44d_pre,post
506    o added missing EXCLUDE_MONITOR flags
507    o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
508      (incompatible typ in MIN/MAX expressions caused problems
509      on IBM SP3)
510    o in genmake added variable MAKEDEPEND
511      plus resetting for case SunOS
512    o added timer_stats.c routine for IBM SP3
513    o removed variables in dynamics
514    !!! I forgot to create tag chkpt44d_pre !!!
515    !!! But chkpt44d_pre = chkpt44c_post    !!!
516    
517    o real fresh water flux implemented with non-linear free-surface.
518    
519    chkpt44c_pre,post
520    o few fix (mask in shap_s2, EmPmR in external_field_load,
521      USE_NATURAL_BCS in solve_for_P);
522    o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
523    
524    checkpoint44b_pre/_post
525    o merge of relevant stuff from the ecco-branch:
526      - genmake: removed $S64 overwrite for case SunOS
527      - pkg/exf: update and corrections for field swapping and obcs
528      - pkg/ecco: parameter lists for the_model_main, the_main_loop
529                  harmonized between ECCO and MITgcm
530      - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
531                      updated checkpointing_lev... lists for obcs
532      - model/src: minor changes in forward_step, plot_field
533                   added directive for divided adjoint in the_main_loop
534      - pkg/mdsio: added mdsio_gl_slice
535    
536    o check parameters & config (chkpt44a_pre,post)
537    o OBC and NonLin_FrSurf.
538    
539    checkpoint44
540    o fix bug in mom_vi_del2uv
541    o select when filters are applied ; add options to zonal_filter (data.zonfilt)
542    o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
543    o update AIM experiments (NCEP input files)
544    o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
545    o added some stuff for AD
546    
547    checkpoint43
548    o added two new advection tests
549    o added global 4x4 degree ocean test
550    o added test of H&S94 with free surface on cube
551    o some final mods for gradient check, adjoint,...
552    
553    checkpoint42
554      Fixed AD-related problems:
555    o Store directives up-to-date with re-arranged Adams-Bashforth
556      (mainly thermodynamics.F)
557    o New store directives for multi-dim. advection schemes
558      * new CPP flag ALLOW_MULTI_DIM_ADVECTION
559      * new common block and key passkey
560      (mainly gad_advection.F)
561    o Modified store directives for split of dynamics/thermodynamics
562      for the case ALLOW_KPP
563    o Cleaned argument list for timestep_tracer.F
564    
565    checkpoint41
566    o re-formatted/added comments in prologues of key subroutines
567      to work with protex
568    
569    checkpoint40
570    o moved calc_gs, calc_gt and calc_tr1 back to model/src
571    o added FLT (floats) package from Arne along with demo. experiment
572    o re-arranged Adams-Bashforth scheme for tracers to allow easier
573      implementation of forward-in-time forcing terms
574    o more mods for non-linear free-surface including new variable
575    o modified multi-dim method to work on cube
576    o bug fix in KPP (from DM)
577    
578    checkpoint40pre9
579    o added DST advection schemes
580    o fix MPI bug on SGI's
581    o modifications for non-linear free-surface
582    o fixed conditionals for fixed flow/passive tracer only mode
583    o added tension/strain form of stress tensor
584    o changes to commenting of arguments for TAF/TAMC
585    o added/updated many matlab scripts
586    o added multi-dimensional advection method for tracers
587      
588    checkpoint40pre8
589    o new package rw/
590      Added method for dumping intermediate local arrays:
591      mdsio_writetile - same as mdsio_writefield except works from inside
592                        bi,bj loop
593      mdsio_writelocal - same as mdsio_writetile except works for local
594                         arrays
595      write_local_r? - higher-level wrapper for mdsio_writelocal
596      Controlled by diagFreq. Defaults to zero (ie. no dumps)
597      Example given at end of mom_vecinv.F that dumps some local arrays.
598    o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
599      control flux-form versus vector invariant code.
600      Switch is runtime flag vectorInvariantMomentum (defaults to false)
601      or genmake -DISABLE ...
602    o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
603      (additional storing is now needed for case vecinv;
604      currently nothing implemented to switch this storing off
605      in case fluxform is used since no CPP flag available).
606    
607    checkpoint40pre7
608    o bug fix in dynamics.F
609      calc_viscosity called before k=1,Nr loop.
610    o added some #ifdef's ALLOW_PASSIVE_TRACER
611    o cleaned initialisations in ctrl_map_ini
612      related to TAF
613    
614    checkpoint40pre6
615    o split dynamics into thermodynamics & dynamics
616    o corresponding split of calc_diffusivity into
617      calc_diffusivity, calc_viscosity
618      (kpp_calc_diff, kpp_calc_visc).
619    o Added diffkr, kapgm to control variables
620    o bug fix in gmredi_slope_limit for ldd97
621    
622    checkpoint40pre5
623    o proper initialization of Adams-Bashforth time stepping
624      + uses forward step for very first step of model (iter=0)
625    o re-generated *all* output since almost all output is modified by this
626      change (sorry but we've been putting this one off for about 2 years)
627      + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
628        *not* regenerated since they are already out of date and I don't
629        want to create the impression that they are suddenly working.
630    o removed KAP stuff for DEC's
631    o modified/added many .cvsignore files in */code and */input
632    o added new expt "solid-body.cs-32x32x1"
633      + this uses an alternative form of ini_curvilinear_grid.F which
634        is not necessarily any better than the current one...
635    
636    checkpoint40pre4
637    o added re-initialisations of utrans,vtrans,rtrans in
638      calc_common_factors which are crucial for TAF.
639    o extended iMin,jMin range for calc_common_factors,
640      calc_diffusivity
641    o added option ALLOW_PASSIVE_TRACER
642    o a few minor updates and fixes
643    
644    checkpoint40pre3
645    o created calc_gtr1.F for gad package
646    o split the_main_loop and re-introduced forward_step
647    o some recomputations of nIter0 for TAMC
648    
649    checkpoint40pre2
650    o Updated to latest branch of AJA, JMC
651    o Added gradient check package
652    o Added routines for passive tracer handling
653    o Added carbon sequestration sensitivity experiment
654    
655    checkpoint39
656     o Modifications and fixes to support TAMC
657       (mainly missing or wrong directives)
658     o Corrected common blocks when fooling TAMC to produce adjoint I/O
659       in addummy_in_stepping
660     o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
661     o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
662     o Included following packages:
663       cal: calendar
664       exf: external forcing
665       ecco: essential routines to control use of cal, exf
666             (NB: this is not the full ECCO environment)
667     o disabled some packages by default in genmake
668    
669    checkpoint38
670     o see notes_c37_adj.txt
671     o corrected wrong layer index in external_forcing_t
672     o replaced the_main_loop/forward_step by the_main_loop
673     o removed forceoutput from write_state
674       (replaced criteria for initial/final state)
675     o added runtime flag for pre-C35 pickups: usePickupBeforeC35
676    
677    checkpoint37
678     o mdsio.F routine split and packaged in pkg/mdsio
679       (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
680        used unless genmake -disable=mdsio)
681     o allow a more precise surface-geopotential gradient for the atmosphere
682       taking into account the change in space of Alpha (=1/rho) at the surface.
683     o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
684       (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
685     o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
686       Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
687       [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
688     o Time-Average diagnostics defined as a pseudo package "timeave".
689     o pickup files : old pickup (before c35) did not work with new code (c35
690       and after) unless activating 2 commented lines in initialise-varia.
691     o Non-Hydrostatic pickup file Pb fixed.
692     o bug with Rigid-lid version (since c35) fixed.  
693    
694    checkpoint36
695     o implement Crank-Nickelson barotropic time-stepping
696     o recover Time-Average diagnostics
697     o fix Pb in checkpoint (PR#19)
698     o AIM become a standard package ; clean unused CPP_kees
699    
700    checkpoint35
701     o subtantial rewrite of dynamics.f
702     o allows staggered time-stepping
703     o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
704     o added bottom drag (linear + quadratic)
705    
706    checkpoint34
707     o Modified exchange routines for correct reverse simulation.
708     o Added verification output to comply with bug fix in impldiff.F
709       as of c33 (exp2, natl_box).
710     o Corrected store directives in dynamics.F
711     o Corrected array boundaries in impldiff.F
712     o Corrected array dimensions in gmredi.
713       Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
714     o Added routine GLOBAL_SUM_INT to global_sum.F
715     o Added mdsio_gl.F for ECCO purposes.
716    
717    checkpoint33
718     o Fixed bug in lower BC in impldiff.F
719     o Fixed confusion about units of forcing arrays in FFIELDS.h
720       namely Fu,Fv,Qnet,Qsw,EmPmR:
721       - Removed verification/natl_box/code/external_fields_scale.F
722         (did not differ from that in model/src)
723       - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
724         (see FFIELDS.h for description)
725       - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
726         kpp_calc.F and kpp_transport_t.F
727       - Removed model/src/external_fields_scale.F and calls to it
728       - verification/natl_box uses flux data with "atmospheric" sign so
729         a special version of external_fields_load.F is used to
730         change the data as it's read in. This way, the arrays
731         have the right units and signs at all times tha a user could
732         possibly use them.
733     o Corrected genmake to delete a temporary file during configuration
734    
735    checkpoint32
736     o Scaling of forcing fields moved from external_forcing.F to
737       external_fields_scale.F, called directly after loading fields.
738     o Surface relaxation terms added to surface tendency fields in
739       extra subroutine.
740     o impldiff.F changed to avoid storing by TAMC of huge intermediate
741       fields.
742     o Changes in GMRedi to comply with packaging structure.
743     o Modifications and bug fixes in KPP package.
744     o Verification experiment for KPP added (verification/nat_box/)
745    
746    checkpoint31
747     o Packages interface brought in line with defined standard
748       -> new routines packages_...F
749       -> changes in initialise_fixed.F, initialise_varia.F
750       -> enables initialisation interface for ECCO package
751     o Rescaling of external forcing fields immediately after read
752       (removed from external_forcing.F)
753       -> new: surface_fields_scale.F
754       -> affects ini_foorcing.F, external_fields_load.F
755     o Computation of surface tendencies before tendency updates.
756       -> new: external_forcing_surf.F
757     o Change of variable names useGMRedi, useKPP, useECCO
758     o Further changes in dynamics.F, impldiff.F for TAMC
759     o Tested for experiments 0, 2, 4.
760       - not yet tested for GMRedi.
761       - not yet tested for KPP.
762    
763    checkpoint30
764     o Updates for OBCs
765     o New experiment for test OBCs (internal_wave)
766     o New output.txt in verification/exp4/results/
767     o Updates for KPP: calculation of viscosity corrected, new variables
768       kpp_dumpFreq and kpp_taveFreq
769     o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
770       and entry for T90 in genmake
771    
772    checkpoint29
773     o packaged KPP and GM/Redi
774    
775    checkpoint28
776     o Corrected initialization of hFacMin for difference vertical coordinates
777     o Modified calculation of partial cell thickness to more robust algorithm
778     o config_summary.F: replaced write_1D_... by write_0D_...
779       read_write.F: added subroutines write_0D_...
780     o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
781       included some initialisations required for TAMC.
782     o routine calc_isoslopes: modified sqrt computation to make it
783       differentiable for zero argument.
784     o routines dynamics, impldiff:
785       included store directives and tape key computations required for TAMC.
786     o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
787    
788    checkpoint27
789     o fixed calc_isoslopes() to so that cancellation of terms in tensor
790       formulation works properly with variable resolution.
791     o restructured the calling tree between the_model_main() and dynamics()
792     o split initialise() into initialise_fixed() and initialise_varia()
793     o introduced initialization file pSurfInitFile for free surface (cg2d_x)
794       in new routine ini_psurf()
795    
796    checkpoint26
797     o moved some #ifdef in optional routines to encompass everything
798       except the argument declarations. This was using up some memory.
799     o fixed macros like _ADT to work with both versions of Linux cpp
800     o cleaned up some unused and uninitialized variables
801       (helps when debugging with strict compile options)
802     o split up CPP_EEOPTIONS.h into options and macros
803       (macros are now in eesupp/inc/CPP_EEMACROS.h)
804     o patch for 2 processor JAM mode
805    
806    checkpoint25
807     o updates for OBCs and NH
808     o dramatically reduced memory usage
809     o added "JAM" routines for use on Artic network
810     o parameterization of convection by implicit vertical diffusion
811     o added a diagnostic of convective index
812     o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
813       (this is was partly for OBCs and NH but also in anticipation of
814        an explicit free-surface option)
815     o initial state input files for U and V
816    
817    checkpoint24
818     o Removed some spurious "REAL"s
819     o Updated KPP to latest version from JPL
820     o Added a COS(latitude) in horizontal viscosity
821    
822    checkpoint23
823     o Added del^4 diffusion for salt and temperature
824     o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
825    
826    checkpoint22
827     o Made many small changes: implicit none, format(i5), etc...
828     o Introduced KPP mixing scheme (compiles and runs but *not* tested)
829    
830  checkpoint21  checkpoint21
831   o Introduced new I/O package that supports direct-access records (mdsio.F)   o Introduced new I/O package that supports direct-access records (mdsio.F)
832   o Split-up mid-level I/O routines   o Split-up mid-level I/O routines

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