/[MITgcm]/MITgcm/doc/tag-index
ViewVC logotype

Diff of /MITgcm/doc/tag-index

Parent Directory Parent Directory | Revision Log Revision Log | View Revision Graph Revision Graph | View Patch Patch

revision 1.14 by cnh, Tue Sep 29 18:57:53 1998 UTC revision 1.116 by heimbach, Fri Jan 10 23:41:38 2003 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    checkpoint48
7    This will be a good checkpoint to plug into the ecco-branch.
8    o few modif.'s to get latest version adjointed
9      (mainly kick out code in ini_linear_phisurf)
10    o modif's to run adjoint with exactConserv
11    o case GM_BOLUS_ADVEC should be cleaned
12      S/R gmredi_slope_psi should be cleaned
13    o verification/carbon now has exactConserv=.TRUE.
14    
15    checkpoint47g_post
16    o time-average AIM output: becomes independent from statvars time-average
17      (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
18    o After TAF bug fix:
19      Tested adjoint of gmredi package.
20      Tests were done with checkpoint47 rather than with latest
21      checkpoint47f_post since the latter is broken for the adjoint
22      verification/carbon/ contains both ADM and TLM gradient checks.
23    Here they are, before they get changed/lost/stolen.
24    Mostly modif.'s to fix numerical sensitivities.
25    Gradient checks OK for
26    - GM_taper_scheme:
27      * clipping
28      * ac02
29      * linear
30      * glw91
31      * dm95
32      * ldd97
33    - GMREDI_OPTIONS:
34      * GM_VISBECK_VARIABLE_K
35      * GM_NON_UNITY_DIAGONAL
36      * GM_EXTRA_DIAGONAL
37      * GM_BOLUS_ADVEC
38    in conjunction with data.gmredi parameters to be checked in
39    in a few minutes under verification/carbon/code/
40    
41    checkpoint47f_post
42    Merging from release1_p10:
43    o modifications for using pkg/exf with pkg/seaice
44      - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
45        and SEAICE_EXTERNAL_FLUXES
46      - pkg/exf CPP options EXF_READ_EVAP and
47        EXF_NO_BULK_COMPUTATIONS
48      - usage examples are Experiments 8 and 9 in
49        verification/lab_sea/README
50      - verification/lab_sea default experiment now uses
51        pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
52    
53    checkpoint47e_post
54    o created a tag prior to creating a branch
55    
56    checkpoint47d_post
57    o fixed bug in the oceanic pressure coordinates code: vertical viscosity
58      at the bottom boundary had an erroneous half slip boundary condition
59    o added bottom drag and no slip boundary condition capabilities to
60      oceanic pressure coordinates code
61    o added new verification experiment global_ocean_pressure, this experiment is
62      also described in the tutorial section of the manual
63    checkpoint47d_pre
64    
65    checkpoint47c_post
66    o Added a verification experiment for a global cubed-sphere ocean run
67      -  verification/global_ocean.cubed32x32x30
68      -  uses pkg/therm_seaice and pkg/bulk_forcing
69    
70    o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
71    o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
72      when using P-coordinate; only implemented for atmospheric config.
73    o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
74      NOTES: requires option NONLIN_FRSURF to be "#define".
75    o update advect_xz/results/output.txt (left from checkpoint44g_post)
76    
77    checkpoint47b_post
78    Merging from release1_p9:
79    o pkg/seaice
80      - removed GOTO's and added taf directives
81      - double precision constants to reduce the g77 (Linux)
82        to F77 (SGI) differences reported in release1_p8
83    o tools/genmake
84      - added SGI options
85    o verification/testscript
86      - updated to that of checkpoint47a_post
87    o verification/global_ocean.90x40x15/input/eedata
88      - modified for SGI f77 compatibility
89    o verification/lab_sea
90      - added description of sea-ice model
91      - added missing matlab routines
92      - added test of thermodynamics parallelization
93    
94    checkpoint47a_post
95    o new pkg: aim_v23
96     = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
97       for now, keep the same surface forcing as before.
98     - Part-Cell implemented into AIM; check that Heat & Water are conserved
99     - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
100     - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
101    o add diagnostic of surface correction term in monitor output
102    
103    o bulk_force and therm_seaice
104    - Two packages:  bulk_force (Bulk forcing)
105      and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
106    - Earlier integration from Stephaine Dutkiewicz
107      and Patrick Heimbach.
108    - Two ifdef statements for compile time,
109       ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
110    
111    checkpoint47
112    differentiable version of checkpoint46n_post
113    o bug fix in quasihydrostaticterms
114    o * "clean" adjoint code (in terms of extensive recomputations)
115        can now be obtained for all GMREDI options (i.e. for
116        - GM_VISBECK_VARIABLE_K
117        - GM_NON_UNITY_DIAGONAL
118        - GM_EXTRA_DIAGONAL
119        - GM_BOLUS_ADVEC )
120      * However, wrong gradient check problem remains unsolved.
121      * New CPP options have been introduced for different
122        tapering schemes
123    o external_fields_load now part of differentiation list
124    o pressure needs multiple storing;
125      would be nice to have store_pressure at beginning or
126      end of forward_step, e.g. by having phiHyd global (5-dim.)
127      (NB: pressure is needed for certain cases in find_rho,
128      which is also invoked through convective_adjustment).
129    o recomputations in find_rho for cases
130     'JMD95'/'UNESCO' or 'MDJWF' are OK.
131    o #define ATMOSPHERIC_LOADING should be differentiable
132    o ini_forcing shifted to begining of initialise_varia
133    o Incorporating QNVS line search routines into MITgcm
134      (this is separate code, and therefore not under pkg)
135      lsopt/, optim/
136    o Updated verification/carbon/
137      - #define GM_VISBECK_VARIABLE_K
138      - GM_taper_scheme    = 'ldd97'    
139    
140    checkpoint46n_post
141    Merging from release1_p8:
142    o verification/natl_box:
143      updating new external_fields_load routine
144    o New package: pkg/seaice
145      Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
146      The sea-ice code is based on Hibler (1979-1980).
147      Two sea-ice dynamic solvers, ADI and LSR, are included.
148      In addition to computing prognostic sea-ice variables and diagnosing
149      the forcing/external data fields that drive the ocean model,
150      SEAICE_MODEL also sets theta to the freezing point under sea-ice.
151      The implied surface heat flux is then stored in variable
152      surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
153      kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
154      non-local transport term.  Because this call precedes model
155      thermodynamics, temperature under sea-ice may not be "exactly" at
156      the freezing point by the time theta is dumped or time-averaged.
157      N.B.: fairly large differences in accuracy occur across
158            different platforms/compilers; comparison between
159            g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
160            generated output gives:
161       T           S           U           V
162      C D M    c        m  s        m  s        m  s        m  s
163      n p a R  g  m  m  e  .  m  m  e  .  m  m  e  .  m  m  e  .
164      f n k u  2  i  a  a  d  i  a  a  d  i  a  a  d  i  a  a  d
165      g d e n  d  n  x  n  .  n  x  n  .  n  x  n  .  n  x  n  .
166    
167      Y Y Y Y  5  5  7  7  7  8 10  9  6  6  6  6  7  5  7  5  7 FAIL  lab_sea
168    o GAD:
169      - generated new common blocks to account for call of
170        same gad routines with differing traceridentities
171        (needed to modify tracerIdentity indices in GAD.h)
172      - generated separate common blocks for case useCubedSphereExchange
173        (Department of Futurology)
174      - parameter lists to gmredi_?transport: added tracerIdentity
175      - added new key indices to tamc.h
176    o external_fields_load:
177      - added this routine to TAF list
178      - needed to make some common blocks global and additional storing
179        along the same lines as exf package (checkpoint_lev?_directives.h)
180    o exf:
181      updated external forcing package
182      - bug fixes carried over from ecco-branch
183        (missing OBCS_OPTIONS.h in two routines)
184      - enable easy to use "no forcing".
185      - added exf I/O for atmospheric loading
186      - added exf I/O for runoff data
187      - transfered scaling between exf <-> MITgcm to exf namelist
188    o Adding new verification experiment global_with_exf.
189      This verification experiment is almost identical to the
190      global_ocean.90x40x15 experiment, except that it uses
191      the exf (and cal) package instead of the
192      external_fields_load routine (cf README file).
193    
194    checkpoint46m_post
195    o modified testscript to return -- when there are no lines of "%MON" output
196    o added new flag "quasiHydrostatic" for QH mode
197      and new routine quasihydrostaticterms()
198    o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
199      New routine: mom_u_coriolis_nh()
200    o fixed sign of non-hydrostatic metric terms in u and v equations.
201      Depend on correct sign of gravitySign.
202    o added work.pc* to .cvsignore in aim directories using ifc
203    o introduced flag for controllin non-hydrostatic metric terms
204    o removed gravitySign from PARM04
205    o switched to g77/ifc from pgf77 in aim experiments
206    
207    checkpoint46l_post
208    o made convective adjustment work with pressure coordinates:
209     - changed the direction of k-loop in convective_adjustment.F for the
210       case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
211     - adjusted the reference pressure k-index in convective_adjustment.F
212     - adjusted the convection condition in convect.F (in analogy to
213       calc_ivdc.F)
214     - convective_adjustment no longer computes anything on the halos
215     - removed the warnings about negative salinity from find_rho.F and
216       find_alpha.F; instead the new routine look_for_neg_salinity, called
217       at the beginning of find_rho, find_alpha, and find_beta, does a
218       check of the entire slice, if CPP-option
219       CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
220    checkpoint46l_pre
221    
222    checkpoint46k_post
223    o fixed the verification/global_ocean.90x40x15 experiment:
224     - new bathymetry (the world according to A., JMC, and M.)
225     - new initial fields and forcing fields (*.bin files)
226     - new POLY3.COEFFS (for the next release one should switch to a full
227       equation of state: JMD95P or MDJWF)
228     - fixed several errors and redundancies in the data file
229     - experiment uses looped cells
230     - added matlab directory with diagnostic scripts for plotting of output
231    
232    o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
233     - read AIM physics parameters from a file (data.aimphys)
234     - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
235    
236    checkpoint46j_post
237    o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
238    o move wVel computation at the end of the time step, in S/R integr_continuity
239    o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
240    o update timeave pkg for wVel diagnostic.
241    checkpoint46j_pre
242    
243    checkpoint46i_post
244    o Clean up AIM package (and keep the results unchanged):
245      include CPP_OPTION and use IMPLICT NONE in all routines ;
246      declare all the variables _RL ; use _d 0 for all numerical constants.
247      use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
248    
249    checkpoint46h_post
250    o cleaned up the use of rhoNil and rhoConst.
251      - rhoNil should only appear in the LINEAR equation of state, everywhere
252        else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
253        and the dynamical equations are all divided by rhoConst
254    o introduced new parameter rhoConstFresh, a reference density of fresh
255      water, to remove the fresh water flux's dependence on rhoNil. The default
256      value is 999.8 kg/m^3
257    o cleanup up external_forcing.F and external_forcing_surf.F
258      - can now be used by both OCEANIC and OCEANICP
259    checkpoint46h_pre
260    
261     Added code to convert surface volume flux (fresh water) into
262     a mass flux when using P coordinates in the ocean (OCEANICP).
263     Note: It assumes you have set rho0=rhoConst=density of fresh water.
264    
265    checkpoint46g_post
266    o Include a new diagnostic variable phiHydLow for the ocean model
267      - in z-coordinates, it is the bottom pressure anomaly
268      - in p-coordinates, it is the sea surface elevation
269      - in both cases, these variable have global drift, reflecting the mass
270        drift in z-coordinates and the volume drift in p-coordinates
271      - included time averaging for phiHydLow, be aware of the drift!
272    o depth-dependent computation of Bo_surf for pressure coordinates
273      in the ocean (buoyancyRelation='OCEANICP')
274      - requires a new routine (FIND_RHO_SCALAR) to compute density with only
275        Theta, Salinity, and Pressure in the parameter list. This routine is
276        presently contained in find_rho.F. This routine does not give the
277        correct density for 'POLY3', which would be a z-dependent reference
278        density.
279    o cleaned up find_rho
280      - removed obsolete 'eqn' from the parameter list.
281    o added two new verification experiments: gop and goz
282      (4x4 degree global ocean, 15 layers in pressure and height coordinates)
283    checkpoint46g_pre
284    
285    checkpoint46f_post
286    o Enable tangent linear (forward mode) gradient checks:
287      - extended active file handling to g_... files
288      - added TANGENT_SIMULATION to theSimulationMode
289      - extended grdchk package accordingly
290    o added tangent linear setup in verification/carbon/code_ftl
291    o added adjoint setup in verification/front_relax/code_ad
292    
293    checkpoint46e_post
294    o Added new equation of state -> MDJWF
295      - EOS of McDougall et al., 2002, JAOT, submitted
296      - caveat: the equation of state is only valid for a smaller (more
297        realistic?) range of values than JMD95P/Z and UNESCO
298      - added masks to the calculation of pressure in store_pressure
299      - added more check values for density in check_eos (ini_eos.F), some of
300        the old check values are out of the range of the MDJWF-eos, so don't
301        expect perfect matches for those
302    checkpoint46e_pre
303    
304    checkpoint46d_post
305    o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
306      'OCEANICP', also initialised field pressure correctly in ini_eos in the
307      case of pressure coordinates. eosType='JMD95Z' in
308      combination with buoyancyRelation='OCEANICP' now causes an error.
309    o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
310      in find_alpha/beta.
311    checkpoint46d_pre
312    
313    o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
314      so that JMD95Z and JMD95P give approptiate static stability in find_rho.
315    
316    checkpoint46c_post
317    o Changes necessary for ocean in p-coordinates
318     -  Added new buoyancy relation = 'OCEANICP'
319     -  Added new parameters = gravitySign (this used to be contained inside
320        the factor dRdZ which I added when we first switched to R coordinates).
321     X GM/Redi is not compatible (yet)
322     X bottom drag and no-slip need to be debugged.
323    checkpoint46c_pre
324    
325    checkpoint46b_post
326    o Added new equation of state -> JMD95Z and JMD95P
327      - EOS of Jackett and McDougall, 1995, JAOT
328      - moved all EOS parameters into EOS.h
329      - new routines ini_eos.F, store_pressure.F
330    o Added UNESCO EOS, but not recommended because it requires
331      in-situ temperature (see JMD95)
332    o Modified formatting for knudsen2.f in utils/knudsen2 and added
333      unesco.f to be used with POLY3
334    checkpoint46b_pre
335    
336    checkpoint46a_post
337    o Added (atmospheric) pressure loading
338      - new field in FFIELDS.h, etc...
339      - new cpp flag ATMOSPHERIC_LOADING
340    o Changed hFacC to _hFacC in calc_phi_hyd.F
341    o Added SHORTWAVE_HEATING to some files for consistency
342    checkpoint46a_pre
343    
344    checkpoint46
345    further merges from release1_p5
346    o new ctrl package
347      - adopted from ECCO environment to enable optimization
348      - added Eliassen Palm fluxes to controls
349    o added Eliassen Palm flux controls to gradient check package
350    o cost package
351      - Compatible with new ctrl package
352      - added Eliassen Palm cost hooks
353      - modif's of existing cost functions
354    o Adjoint-related bug fixes in kpp:
355      - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
356      - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
357    o autodiff package
358      - flow directives:
359        + new for S/R do_the_model_io
360        + enhanced for S/R checkpoint
361        + new gmredi.flow
362      - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
363        disable adcommon.h/g_common.h by default.
364      - fixed problem for adjoint of global_max
365    o modified verification/carbon/
366    o New setup for adjoint of global_ocean
367    o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
368    o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
369    o incorporated hooks for sponge layer code (external_forcing.F)
370    
371    checkpoint45d_post
372    o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
373    o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
374      (affects plume_on_slope "cg2d" output)
375    o add new parameter deltaTfreesurf for free-surface time stepping
376    o exchange gT,gS when using staggerTimeStep & GM & Oly<4
377    o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
378    o change phiMin in exp1 (to agree with documentation)
379    o add new flags:
380     - T,S forcing inside/outside Adams-Bashforth
381     - turn off temp,salt advection and/or forcing
382     - for each tracer, define internal flag for multiDimAdvection & A-B
383    o monitor: change definition of KE to check conservation of Energy
384    
385    checkpoint45c_post
386    o Removed f90 comments ("!")
387    o Modified initialisations to enable exf package for MITgcm
388      (without invoking ECCO_PACKAGE).
389    o modifications to gradient check package (Martin Losch)
390      - enable centered differences
391      - modified format of standard output
392    
393    checkpoint45b_post
394    o cleaned exchange calls in cg2d
395    o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
396    o included CPP option SINGLE_LAYER_MODE in thermodynamics
397      to configure barotropic setup (Martin Losch)
398    o moved some initialisations within bi,bj loop in dynamics
399      (TAF flow dependency)
400    o in initialise_varia, moved call packages_init_variables
401      before convective_adjustment_init
402      (corresponding adjustment of TAF tape initialisation).
403    o in calc_diffusivity/calc_viscosity extended domain to full overlap.
404    
405    checkpoint45a_post
406    o compute Rho over the whole domain (extend iMin,jMin indices)
407    o specific exchange for X-slice domain (case Ny=1)
408    o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
409    o solve_for_pressure : set cg2d_x to zero where OBCS are applied
410    
411    checkpoint44h_post = checkpoint45
412    o Fix to restore differentiability:
413      place at which packages_init_variables is called in
414      initialise_varia is crucial for reverse control flow.
415    o modifications in GMRedi to enable stable adjoint
416      (corresponding modif's in thermodynamics, dynamics)
417    o added missing hook for sponge layer code in external_forcing
418    o modified test cost functions
419    o storing in gad_advection (plus removal of write(0,*)!
420    o missing headers TR1.h added in convective_adjustment routines
421    o errorMessageUnit set non-equal zero in eeboot
422      (conflict on some platforms, e.g. IBM SP3)
423    o modified carbon verif.
424    
425    checkpoint44h_pre
426    o vertical grid option: allow to put the Interface at the middle between
427      2 cell-centers ; replace delZ in pkg/kpp by drF.
428    o GM Advective form: Tracers are advected using the residual transport (=
429      Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
430    
431    checkpoint44g_post
432    o fix surface correction term in multiDimAdvection (affects plume_on_slope
433      results) ; ifdef missing in thermodynamics.F
434    
435    checkpoint44f_pre,checkpoint44f_post
436    o added PTRACERS package
437      This allows an arbitrary number of passive tracers to be integrated
438      forward simultaneously with the dynamicaly model.
439      + Implemented so far:
440        - basic forward algorithm (time-stepping, advection, diffusion, convection)
441        - I/O and checkpointing
442        - GM/Redi  *but*  using the GM/Redi coefficient of Salt
443      + Not implemented so far:
444        - KPP
445        - OBCS
446      + No specific example supplied (yet) but global_ocean.90x40x15 has the
447        necessary data.ptracer file. Simply use -enable=ptracers and uncomment
448        line in data.pkg.
449      + This package is disabled by default since it increases storage.
450    
451    
452    o testscript: added -cleanup option
453    o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
454                 b) enable to filter 2D fields.
455    
456    checkpoint44e_pre,post
457    o re-wrote convective adjustment to use pre-calculated weights
458      Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
459      Adds:    model/src/convective_weights.F, convectively_mixtracer.F
460      Original calls to convect() still in place.
461    
462    chkpt44d_pre,post
463    o added missing EXCLUDE_MONITOR flags
464    o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
465      (incompatible typ in MIN/MAX expressions caused problems
466      on IBM SP3)
467    o in genmake added variable MAKEDEPEND
468      plus resetting for case SunOS
469    o added timer_stats.c routine for IBM SP3
470    o removed variables in dynamics
471    !!! I forgot to create tag chkpt44d_pre !!!
472    !!! But chkpt44d_pre = chkpt44c_post    !!!
473    
474    o real fresh water flux implemented with non-linear free-surface.
475    
476    chkpt44c_pre,post
477    o few fix (mask in shap_s2, EmPmR in external_field_load,
478      USE_NATURAL_BCS in solve_for_P);
479    o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
480    
481    checkpoint44b_pre/_post
482    o merge of relevant stuff from the ecco-branch:
483      - genmake: removed $S64 overwrite for case SunOS
484      - pkg/exf: update and corrections for field swapping and obcs
485      - pkg/ecco: parameter lists for the_model_main, the_main_loop
486                  harmonized between ECCO and MITgcm
487      - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
488                      updated checkpointing_lev... lists for obcs
489      - model/src: minor changes in forward_step, plot_field
490                   added directive for divided adjoint in the_main_loop
491      - pkg/mdsio: added mdsio_gl_slice
492    
493    o check parameters & config (chkpt44a_pre,post)
494    o OBC and NonLin_FrSurf.
495    
496    checkpoint44
497    o fix bug in mom_vi_del2uv
498    o select when filters are applied ; add options to zonal_filter (data.zonfilt)
499    o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
500    o update AIM experiments (NCEP input files)
501    o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
502    o added some stuff for AD
503    
504    checkpoint43
505    o added two new advection tests
506    o added global 4x4 degree ocean test
507    o added test of H&S94 with free surface on cube
508    o some final mods for gradient check, adjoint,...
509    
510    checkpoint42
511      Fixed AD-related problems:
512    o Store directives up-to-date with re-arranged Adams-Bashforth
513      (mainly thermodynamics.F)
514    o New store directives for multi-dim. advection schemes
515      * new CPP flag ALLOW_MULTI_DIM_ADVECTION
516      * new common block and key passkey
517      (mainly gad_advection.F)
518    o Modified store directives for split of dynamics/thermodynamics
519      for the case ALLOW_KPP
520    o Cleaned argument list for timestep_tracer.F
521    
522    checkpoint41
523    o re-formatted/added comments in prologues of key subroutines
524      to work with protex
525    
526    checkpoint40
527    o moved calc_gs, calc_gt and calc_tr1 back to model/src
528    o added FLT (floats) package from Arne along with demo. experiment
529    o re-arranged Adams-Bashforth scheme for tracers to allow easier
530      implementation of forward-in-time forcing terms
531    o more mods for non-linear free-surface including new variable
532    o modified multi-dim method to work on cube
533    o bug fix in KPP (from DM)
534    
535    checkpoint40pre9
536    o added DST advection schemes
537    o fix MPI bug on SGI's
538    o modifications for non-linear free-surface
539    o fixed conditionals for fixed flow/passive tracer only mode
540    o added tension/strain form of stress tensor
541    o changes to commenting of arguments for TAF/TAMC
542    o added/updated many matlab scripts
543    o added multi-dimensional advection method for tracers
544      
545    checkpoint40pre8
546    o new package rw/
547      Added method for dumping intermediate local arrays:
548      mdsio_writetile - same as mdsio_writefield except works from inside
549                        bi,bj loop
550      mdsio_writelocal - same as mdsio_writetile except works for local
551                         arrays
552      write_local_r? - higher-level wrapper for mdsio_writelocal
553      Controlled by diagFreq. Defaults to zero (ie. no dumps)
554      Example given at end of mom_vecinv.F that dumps some local arrays.
555    o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
556      control flux-form versus vector invariant code.
557      Switch is runtime flag vectorInvariantMomentum (defaults to false)
558      or genmake -DISABLE ...
559    o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
560      (additional storing is now needed for case vecinv;
561      currently nothing implemented to switch this storing off
562      in case fluxform is used since no CPP flag available).
563    
564    checkpoint40pre7
565    o bug fix in dynamics.F
566      calc_viscosity called before k=1,Nr loop.
567    o added some #ifdef's ALLOW_PASSIVE_TRACER
568    o cleaned initialisations in ctrl_map_ini
569      related to TAF
570    
571    checkpoint40pre6
572    o split dynamics into thermodynamics & dynamics
573    o corresponding split of calc_diffusivity into
574      calc_diffusivity, calc_viscosity
575      (kpp_calc_diff, kpp_calc_visc).
576    o Added diffkr, kapgm to control variables
577    o bug fix in gmredi_slope_limit for ldd97
578    
579    checkpoint40pre5
580    o proper initialization of Adams-Bashforth time stepping
581      + uses forward step for very first step of model (iter=0)
582    o re-generated *all* output since almost all output is modified by this
583      change (sorry but we've been putting this one off for about 2 years)
584      + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
585        *not* regenerated since they are already out of date and I don't
586        want to create the impression that they are suddenly working.
587    o removed KAP stuff for DEC's
588    o modified/added many .cvsignore files in */code and */input
589    o added new expt "solid-body.cs-32x32x1"
590      + this uses an alternative form of ini_curvilinear_grid.F which
591        is not necessarily any better than the current one...
592    
593    checkpoint40pre4
594    o added re-initialisations of utrans,vtrans,rtrans in
595      calc_common_factors which are crucial for TAF.
596    o extended iMin,jMin range for calc_common_factors,
597      calc_diffusivity
598    o added option ALLOW_PASSIVE_TRACER
599    o a few minor updates and fixes
600    
601    checkpoint40pre3
602    o created calc_gtr1.F for gad package
603    o split the_main_loop and re-introduced forward_step
604    o some recomputations of nIter0 for TAMC
605    
606    checkpoint40pre2
607    o Updated to latest branch of AJA, JMC
608    o Added gradient check package
609    o Added routines for passive tracer handling
610    o Added carbon sequestration sensitivity experiment
611    
612    checkpoint39
613     o Modifications and fixes to support TAMC
614       (mainly missing or wrong directives)
615     o Corrected common blocks when fooling TAMC to produce adjoint I/O
616       in addummy_in_stepping
617     o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
618     o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
619     o Included following packages:
620       cal: calendar
621       exf: external forcing
622       ecco: essential routines to control use of cal, exf
623             (NB: this is not the full ECCO environment)
624     o disabled some packages by default in genmake
625    
626    checkpoint38
627     o see notes_c37_adj.txt
628     o corrected wrong layer index in external_forcing_t
629     o replaced the_main_loop/forward_step by the_main_loop
630     o removed forceoutput from write_state
631       (replaced criteria for initial/final state)
632     o added runtime flag for pre-C35 pickups: usePickupBeforeC35
633    
634    checkpoint37
635     o mdsio.F routine split and packaged in pkg/mdsio
636       (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
637        used unless genmake -disable=mdsio)
638     o allow a more precise surface-geopotential gradient for the atmosphere
639       taking into account the change in space of Alpha (=1/rho) at the surface.
640     o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
641       (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
642     o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
643       Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
644       [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
645     o Time-Average diagnostics defined as a pseudo package "timeave".
646     o pickup files : old pickup (before c35) did not work with new code (c35
647       and after) unless activating 2 commented lines in initialise-varia.
648     o Non-Hydrostatic pickup file Pb fixed.
649     o bug with Rigid-lid version (since c35) fixed.  
650    
651    checkpoint36
652     o implement Crank-Nickelson barotropic time-stepping
653     o recover Time-Average diagnostics
654     o fix Pb in checkpoint (PR#19)
655     o AIM become a standard package ; clean unused CPP_kees
656    
657    checkpoint35
658     o subtantial rewrite of dynamics.f
659     o allows staggered time-stepping
660     o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
661     o added bottom drag (linear + quadratic)
662    
663    checkpoint34
664     o Modified exchange routines for correct reverse simulation.
665     o Added verification output to comply with bug fix in impldiff.F
666       as of c33 (exp2, natl_box).
667     o Corrected store directives in dynamics.F
668     o Corrected array boundaries in impldiff.F
669     o Corrected array dimensions in gmredi.
670       Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
671     o Added routine GLOBAL_SUM_INT to global_sum.F
672     o Added mdsio_gl.F for ECCO purposes.
673    
674    checkpoint33
675     o Fixed bug in lower BC in impldiff.F
676     o Fixed confusion about units of forcing arrays in FFIELDS.h
677       namely Fu,Fv,Qnet,Qsw,EmPmR:
678       - Removed verification/natl_box/code/external_fields_scale.F
679         (did not differ from that in model/src)
680       - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
681         (see FFIELDS.h for description)
682       - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
683         kpp_calc.F and kpp_transport_t.F
684       - Removed model/src/external_fields_scale.F and calls to it
685       - verification/natl_box uses flux data with "atmospheric" sign so
686         a special version of external_fields_load.F is used to
687         change the data as it's read in. This way, the arrays
688         have the right units and signs at all times tha a user could
689         possibly use them.
690     o Corrected genmake to delete a temporary file during configuration
691    
692    checkpoint32
693     o Scaling of forcing fields moved from external_forcing.F to
694       external_fields_scale.F, called directly after loading fields.
695     o Surface relaxation terms added to surface tendency fields in
696       extra subroutine.
697     o impldiff.F changed to avoid storing by TAMC of huge intermediate
698       fields.
699     o Changes in GMRedi to comply with packaging structure.
700     o Modifications and bug fixes in KPP package.
701     o Verification experiment for KPP added (verification/nat_box/)
702    
703    checkpoint31
704     o Packages interface brought in line with defined standard
705       -> new routines packages_...F
706       -> changes in initialise_fixed.F, initialise_varia.F
707       -> enables initialisation interface for ECCO package
708     o Rescaling of external forcing fields immediately after read
709       (removed from external_forcing.F)
710       -> new: surface_fields_scale.F
711       -> affects ini_foorcing.F, external_fields_load.F
712     o Computation of surface tendencies before tendency updates.
713       -> new: external_forcing_surf.F
714     o Change of variable names useGMRedi, useKPP, useECCO
715     o Further changes in dynamics.F, impldiff.F for TAMC
716     o Tested for experiments 0, 2, 4.
717       - not yet tested for GMRedi.
718       - not yet tested for KPP.
719    
720    checkpoint30
721     o Updates for OBCs
722     o New experiment for test OBCs (internal_wave)
723     o New output.txt in verification/exp4/results/
724     o Updates for KPP: calculation of viscosity corrected, new variables
725       kpp_dumpFreq and kpp_taveFreq
726     o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
727       and entry for T90 in genmake
728    
729    checkpoint29
730     o packaged KPP and GM/Redi
731    
732    checkpoint28
733     o Corrected initialization of hFacMin for difference vertical coordinates
734     o Modified calculation of partial cell thickness to more robust algorithm
735     o config_summary.F: replaced write_1D_... by write_0D_...
736       read_write.F: added subroutines write_0D_...
737     o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
738       included some initialisations required for TAMC.
739     o routine calc_isoslopes: modified sqrt computation to make it
740       differentiable for zero argument.
741     o routines dynamics, impldiff:
742       included store directives and tape key computations required for TAMC.
743     o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
744    
745    checkpoint27
746     o fixed calc_isoslopes() to so that cancellation of terms in tensor
747       formulation works properly with variable resolution.
748     o restructured the calling tree between the_model_main() and dynamics()
749     o split initialise() into initialise_fixed() and initialise_varia()
750     o introduced initialization file pSurfInitFile for free surface (cg2d_x)
751       in new routine ini_psurf()
752    
753    checkpoint26
754     o moved some #ifdef in optional routines to encompass everything
755       except the argument declarations. This was using up some memory.
756     o fixed macros like _ADT to work with both versions of Linux cpp
757     o cleaned up some unused and uninitialized variables
758       (helps when debugging with strict compile options)
759     o split up CPP_EEOPTIONS.h into options and macros
760       (macros are now in eesupp/inc/CPP_EEMACROS.h)
761     o patch for 2 processor JAM mode
762    
763    checkpoint25
764     o updates for OBCs and NH
765     o dramatically reduced memory usage
766     o added "JAM" routines for use on Artic network
767     o parameterization of convection by implicit vertical diffusion
768     o added a diagnostic of convective index
769     o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
770       (this is was partly for OBCs and NH but also in anticipation of
771        an explicit free-surface option)
772     o initial state input files for U and V
773    
774    checkpoint24
775     o Removed some spurious "REAL"s
776     o Updated KPP to latest version from JPL
777     o Added a COS(latitude) in horizontal viscosity
778    
779    checkpoint23
780     o Added del^4 diffusion for salt and temperature
781     o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
782    
783    checkpoint22
784     o Made many small changes: implicit none, format(i5), etc...
785     o Introduced KPP mixing scheme (compiles and runs but *not* tested)
786    
787    checkpoint21
788     o Introduced new I/O package that supports direct-access records (mdsio.F)
789     o Split-up mid-level I/O routines
790     o Updated input data for experiments 0,1,2,4 and 5
791     o Finally removed the genmake.* scripts (everyone seems happy with genmake)
792    
793    checkpoint20
794     o Tidied up open-boundaries some more
795     o Added non-hydrostatic code
796     o Fixed some input data
797     o Modified MPI start-up to work in "coupled" context.
798    
799    checkpoint19
800     o Tidied up directory structure for verification experiments.
801     o Added new code for open boundaries.
802     o Corrected advective terms near boundaries.
803     o Added CPP flag for "old UV" geometry and corrected spherical geometry.
804     o Implemented free-slip/no-slip BCs and del^4 dissipation.
805     o Split default parameters out of ini_parms.F into set_defaults.F.
806    
807    checkpoint18
808     o Further changes for optional code generation with
809       CPP - ugh!
810    
811    checkpoint17
812     o Beginning to incorporating modularity
813       for supporting atmos. and ocean configs.
814     o Small changes for TAMC complinace
815     o New ultra simple test case. Barotropic box
816       configuration "exp0".
817    
818    checkpoint16
819     o Minor changes to exchange routines to support
820       accumulation in reverse mode. Adjoint of an
821       assignment is an addition.
822     o Changes to support compilation by TAMC (LR(1)
823       syntax) and by g77 under Linux ( 72 character
824       limit ).
825    
826  checkpoint15  checkpoint15
827   Rewrote exchange routines to allow   Rewrote exchange routines to allow
828   o General tile <-> tile connectivity.   o General tile <-> tile connectivity.

Legend:
Removed from v.1.14  
changed lines
  Added in v.1.116

  ViewVC Help
Powered by ViewVC 1.1.22