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revision 1.1 by cnh, Tue May 26 14:38:05 1998 UTC revision 1.65 by adcroft, Mon Mar 4 17:26:40 2002 UTC
# Line 2  $Header$ Line 2  $Header$
2    
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    checkpoint44f_pre,checkpoint44f_post
7    o added PTRACERS package
8      This allows an arbitrary number of passive tracers to be integrated
9      forward simultaneously with the dynamicaly model.
10      + Implemented so far:
11        - basic forward algorithm (time-stepping, advection, diffusion, convection)
12        - I/O and checkpointing
13        - GM/Redi  *but*  using the GM/Redi coefficient of Salt
14      + Not implemented so far:
15        - KPP
16        - OBCS
17      + No specific example supplied (yet) but global_ocean.90x40x15 has the
18        necessary data.ptracer file. Simply use -enable=ptracers and uncomment
19        line in data.pkg.
20      + This package is disabled by default since it increases storage.
21    
22    
23    o testscript: added -cleanup option
24    o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
25                 b) enable to filter 2D fields.
26    
27    checkpoint44e_pre,post
28    o re-wrote convective adjustment to use pre-calculated weights
29      Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
30      Adds:    model/src/convective_weights.F, convectively_mixtracer.F
31      Original calls to convect() still in place.
32    
33    chkpt44d_pre,post
34    o added missing EXCLUDE_MONITOR flags
35    o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
36      (incompatible typ in MIN/MAX expressions caused problems
37      on IBM SP3)
38    o in genmake added variable MAKEDEPEND
39      plus resetting for case SunOS
40    o added timer_stats.c routine for IBM SP3
41    o removed variables in dynamics
42    !!! I forgot to create tag chkpt44d_pre !!!
43    !!! But chkpt44d_pre = chkpt44c_post    !!!
44    
45    o real fresh water flux implemented with non-linear free-surface.
46    
47    chkpt44c_pre,post
48    o few fix (mask in shap_s2, EmPmR in external_field_load,
49      USE_NATURAL_BCS in solve_for_P);
50    o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
51    
52    checkpoint44b_pre/_post
53    o merge of relevant stuff from the ecco-branch:
54      - genmake: removed $S64 overwrite for case SunOS
55      - pkg/exf: update and corrections for field swapping and obcs
56      - pkg/ecco: parameter lists for the_model_main, the_main_loop
57                  harmonized between ECCO and MITgcm
58      - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
59                      updated checkpointing_lev... lists for obcs
60      - model/src: minor changes in forward_step, plot_field
61                   added directive for divided adjoint in the_main_loop
62      - pkg/mdsio: added mdsio_gl_slice
63    
64    o check parameters & config (chkpt44a_pre,post)
65    o OBC and NonLin_FrSurf.
66    
67    checkpoint44
68    o fix bug in mom_vi_del2uv
69    o select when filters are applied ; add options to zonal_filter (data.zonfilt)
70    o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
71    o update AIM experiments (NCEP input files)
72    o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
73    o added some stuff for AD
74    
75    checkpoint43
76    o added two new advection tests
77    o added global 4x4 degree ocean test
78    o added test of H&S94 with free surface on cube
79    o some final mods for gradient check, adjoint,...
80    
81    checkpoint42
82      Fixed AD-related problems:
83    o Store directives up-to-date with re-arranged Adams-Bashforth
84      (mainly thermodynamics.F)
85    o New store directives for multi-dim. advection schemes
86      * new CPP flag ALLOW_MULTI_DIM_ADVECTION
87      * new common block and key passkey
88      (mainly gad_advection.F)
89    o Modified store directives for split of dynamics/thermodynamics
90      for the case ALLOW_KPP
91    o Cleaned argument list for timestep_tracer.F
92    
93    checkpoint41
94    o re-formatted/added comments in prologues of key subroutines
95      to work with protex
96    
97    checkpoint40
98    o moved calc_gs, calc_gt and calc_tr1 back to model/src
99    o added FLT (floats) package from Arne along with demo. experiment
100    o re-arranged Adams-Bashforth scheme for tracers to allow easier
101      implementation of forward-in-time forcing terms
102    o more mods for non-linear free-surface including new variable
103    o modified multi-dim method to work on cube
104    o bug fix in KPP (from DM)
105    
106    checkpoint40pre9
107    o added DST advection schemes
108    o fix MPI bug on SGI's
109    o modifications for non-linear free-surface
110    o fixed conditionals for fixed flow/passive tracer only mode
111    o added tension/strain form of stress tensor
112    o changes to commenting of arguments for TAF/TAMC
113    o added/updated many matlab scripts
114    o added multi-dimensional advection method for tracers
115      
116    checkpoint40pre8
117    o new package rw/
118      Added method for dumping intermediate local arrays:
119      mdsio_writetile - same as mdsio_writefield except works from inside
120                        bi,bj loop
121      mdsio_writelocal - same as mdsio_writetile except works for local
122                         arrays
123      write_local_r? - higher-level wrapper for mdsio_writelocal
124      Controlled by diagFreq. Defaults to zero (ie. no dumps)
125      Example given at end of mom_vecinv.F that dumps some local arrays.
126    o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
127      control flux-form versus vector invariant code.
128      Switch is runtime flag vectorInvariantMomentum (defaults to false)
129      or genmake -DISABLE ...
130    o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
131      (additional storing is now needed for case vecinv;
132      currently nothing implemented to switch this storing off
133      in case fluxform is used since no CPP flag available).
134    
135    checkpoint40pre7
136    o bug fix in dynamics.F
137      calc_viscosity called before k=1,Nr loop.
138    o added some #ifdef's ALLOW_PASSIVE_TRACER
139    o cleaned initialisations in ctrl_map_ini
140      related to TAF
141    
142    checkpoint40pre6
143    o split dynamics into thermodynamics & dynamics
144    o corresponding split of calc_diffusivity into
145      calc_diffusivity, calc_viscosity
146      (kpp_calc_diff, kpp_calc_visc).
147    o Added diffkr, kapgm to control variables
148    o bug fix in gmredi_slope_limit for ldd97
149    
150    checkpoint40pre5
151    o proper initialization of Adams-Bashforth time stepping
152      + uses forward step for very first step of model (iter=0)
153    o re-generated *all* output since almost all output is modified by this
154      change (sorry but we've been putting this one off for about 2 years)
155      + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
156        *not* regenerated since they are already out of date and I don't
157        want to create the impression that they are suddenly working.
158    o removed KAP stuff for DEC's
159    o modified/added many .cvsignore files in */code and */input
160    o added new expt "solid-body.cs-32x32x1"
161      + this uses an alternative form of ini_curvilinear_grid.F which
162        is not necessarily any better than the current one...
163    
164    checkpoint40pre4
165    o added re-initialisations of utrans,vtrans,rtrans in
166      calc_common_factors which are crucial for TAF.
167    o extended iMin,jMin range for calc_common_factors,
168      calc_diffusivity
169    o added option ALLOW_PASSIVE_TRACER
170    o a few minor updates and fixes
171    
172    checkpoint40pre3
173    o created calc_gtr1.F for gad package
174    o split the_main_loop and re-introduced forward_step
175    o some recomputations of nIter0 for TAMC
176    
177    checkpoint40pre2
178    o Updated to latest branch of AJA, JMC
179    o Added gradient check package
180    o Added routines for passive tracer handling
181    o Added carbon sequestration sensitivity experiment
182    
183    checkpoint39
184     o Modifications and fixes to support TAMC
185       (mainly missing or wrong directives)
186     o Corrected common blocks when fooling TAMC to produce adjoint I/O
187       in addummy_in_stepping
188     o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
189     o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
190     o Included following packages:
191       cal: calendar
192       exf: external forcing
193       ecco: essential routines to control use of cal, exf
194             (NB: this is not the full ECCO environment)
195     o disabled some packages by default in genmake
196    
197    checkpoint38
198     o see notes_c37_adj.txt
199     o corrected wrong layer index in external_forcing_t
200     o replaced the_main_loop/forward_step by the_main_loop
201     o removed forceoutput from write_state
202       (replaced criteria for initial/final state)
203     o added runtime flag for pre-C35 pickups: usePickupBeforeC35
204    
205    checkpoint37
206     o mdsio.F routine split and packaged in pkg/mdsio
207       (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
208        used unless genmake -disable=mdsio)
209     o allow a more precise surface-geopotential gradient for the atmosphere
210       taking into account the change in space of Alpha (=1/rho) at the surface.
211     o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
212       (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
213     o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
214       Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
215       [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
216     o Time-Average diagnostics defined as a pseudo package "timeave".
217     o pickup files : old pickup (before c35) did not work with new code (c35
218       and after) unless activating 2 commented lines in initialise-varia.
219     o Non-Hydrostatic pickup file Pb fixed.
220     o bug with Rigid-lid version (since c35) fixed.  
221    
222    checkpoint36
223     o implement Crank-Nickelson barotropic time-stepping
224     o recover Time-Average diagnostics
225     o fix Pb in checkpoint (PR#19)
226     o AIM become a standard package ; clean unused CPP_kees
227    
228    checkpoint35
229     o subtantial rewrite of dynamics.f
230     o allows staggered time-stepping
231     o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
232     o added bottom drag (linear + quadratic)
233    
234    checkpoint34
235     o Modified exchange routines for correct reverse simulation.
236     o Added verification output to comply with bug fix in impldiff.F
237       as of c33 (exp2, natl_box).
238     o Corrected store directives in dynamics.F
239     o Corrected array boundaries in impldiff.F
240     o Corrected array dimensions in gmredi.
241       Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
242     o Added routine GLOBAL_SUM_INT to global_sum.F
243     o Added mdsio_gl.F for ECCO purposes.
244    
245    checkpoint33
246     o Fixed bug in lower BC in impldiff.F
247     o Fixed confusion about units of forcing arrays in FFIELDS.h
248       namely Fu,Fv,Qnet,Qsw,EmPmR:
249       - Removed verification/natl_box/code/external_fields_scale.F
250         (did not differ from that in model/src)
251       - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
252         (see FFIELDS.h for description)
253       - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
254         kpp_calc.F and kpp_transport_t.F
255       - Removed model/src/external_fields_scale.F and calls to it
256       - verification/natl_box uses flux data with "atmospheric" sign so
257         a special version of external_fields_load.F is used to
258         change the data as it's read in. This way, the arrays
259         have the right units and signs at all times tha a user could
260         possibly use them.
261     o Corrected genmake to delete a temporary file during configuration
262    
263    checkpoint32
264     o Scaling of forcing fields moved from external_forcing.F to
265       external_fields_scale.F, called directly after loading fields.
266     o Surface relaxation terms added to surface tendency fields in
267       extra subroutine.
268     o impldiff.F changed to avoid storing by TAMC of huge intermediate
269       fields.
270     o Changes in GMRedi to comply with packaging structure.
271     o Modifications and bug fixes in KPP package.
272     o Verification experiment for KPP added (verification/nat_box/)
273    
274    checkpoint31
275     o Packages interface brought in line with defined standard
276       -> new routines packages_...F
277       -> changes in initialise_fixed.F, initialise_varia.F
278       -> enables initialisation interface for ECCO package
279     o Rescaling of external forcing fields immediately after read
280       (removed from external_forcing.F)
281       -> new: surface_fields_scale.F
282       -> affects ini_foorcing.F, external_fields_load.F
283     o Computation of surface tendencies before tendency updates.
284       -> new: external_forcing_surf.F
285     o Change of variable names useGMRedi, useKPP, useECCO
286     o Further changes in dynamics.F, impldiff.F for TAMC
287     o Tested for experiments 0, 2, 4.
288       - not yet tested for GMRedi.
289       - not yet tested for KPP.
290    
291    checkpoint30
292     o Updates for OBCs
293     o New experiment for test OBCs (internal_wave)
294     o New output.txt in verification/exp4/results/
295     o Updates for KPP: calculation of viscosity corrected, new variables
296       kpp_dumpFreq and kpp_taveFreq
297     o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
298       and entry for T90 in genmake
299    
300    checkpoint29
301     o packaged KPP and GM/Redi
302    
303    checkpoint28
304     o Corrected initialization of hFacMin for difference vertical coordinates
305     o Modified calculation of partial cell thickness to more robust algorithm
306     o config_summary.F: replaced write_1D_... by write_0D_...
307       read_write.F: added subroutines write_0D_...
308     o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
309       included some initialisations required for TAMC.
310     o routine calc_isoslopes: modified sqrt computation to make it
311       differentiable for zero argument.
312     o routines dynamics, impldiff:
313       included store directives and tape key computations required for TAMC.
314     o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
315    
316    checkpoint27
317     o fixed calc_isoslopes() to so that cancellation of terms in tensor
318       formulation works properly with variable resolution.
319     o restructured the calling tree between the_model_main() and dynamics()
320     o split initialise() into initialise_fixed() and initialise_varia()
321     o introduced initialization file pSurfInitFile for free surface (cg2d_x)
322       in new routine ini_psurf()
323    
324    checkpoint26
325     o moved some #ifdef in optional routines to encompass everything
326       except the argument declarations. This was using up some memory.
327     o fixed macros like _ADT to work with both versions of Linux cpp
328     o cleaned up some unused and uninitialized variables
329       (helps when debugging with strict compile options)
330     o split up CPP_EEOPTIONS.h into options and macros
331       (macros are now in eesupp/inc/CPP_EEMACROS.h)
332     o patch for 2 processor JAM mode
333    
334    checkpoint25
335     o updates for OBCs and NH
336     o dramatically reduced memory usage
337     o added "JAM" routines for use on Artic network
338     o parameterization of convection by implicit vertical diffusion
339     o added a diagnostic of convective index
340     o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
341       (this is was partly for OBCs and NH but also in anticipation of
342        an explicit free-surface option)
343     o initial state input files for U and V
344    
345    checkpoint24
346     o Removed some spurious "REAL"s
347     o Updated KPP to latest version from JPL
348     o Added a COS(latitude) in horizontal viscosity
349    
350    checkpoint23
351     o Added del^4 diffusion for salt and temperature
352     o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
353    
354    checkpoint22
355     o Made many small changes: implicit none, format(i5), etc...
356     o Introduced KPP mixing scheme (compiles and runs but *not* tested)
357    
358    checkpoint21
359     o Introduced new I/O package that supports direct-access records (mdsio.F)
360     o Split-up mid-level I/O routines
361     o Updated input data for experiments 0,1,2,4 and 5
362     o Finally removed the genmake.* scripts (everyone seems happy with genmake)
363    
364    checkpoint20
365     o Tidied up open-boundaries some more
366     o Added non-hydrostatic code
367     o Fixed some input data
368     o Modified MPI start-up to work in "coupled" context.
369    
370    checkpoint19
371     o Tidied up directory structure for verification experiments.
372     o Added new code for open boundaries.
373     o Corrected advective terms near boundaries.
374     o Added CPP flag for "old UV" geometry and corrected spherical geometry.
375     o Implemented free-slip/no-slip BCs and del^4 dissipation.
376     o Split default parameters out of ini_parms.F into set_defaults.F.
377    
378    checkpoint18
379     o Further changes for optional code generation with
380       CPP - ugh!
381    
382    checkpoint17
383     o Beginning to incorporating modularity
384       for supporting atmos. and ocean configs.
385     o Small changes for TAMC complinace
386     o New ultra simple test case. Barotropic box
387       configuration "exp0".
388    
389    checkpoint16
390     o Minor changes to exchange routines to support
391       accumulation in reverse mode. Adjoint of an
392       assignment is an addition.
393     o Changes to support compilation by TAMC (LR(1)
394       syntax) and by g77 under Linux ( 72 character
395       limit ).
396    
397    checkpoint15
398     Rewrote exchange routines to allow
399     o General tile <-> tile connectivity.
400     o TAMC reverse mode flag ( is this really needed? )
401     o Variable width overlap and exchange region widths.
402     o Hooks for sharing data via DMA, Arctic, Memory Channel,
403       shmput/shmget, VIA, SYSV shmem and every other cool
404       communication method.
405    
406    checkpoint14
407     Consistent isomorphism chages made. These allow dynamical core
408     to support both pressure and meters as a vertical coordinate.
409    
410    checkpoint13
411     Release which corrects global_max problem and a couple
412     of KGM time-averaging diagnostic errors. Also contains
413     a double-gyre experiment setup as well as the baseline
414     4 degree global template. The double gyre template is
415     organised to allow it to be applied automatically to
416     the baseline configuration.
417    
418    branch-point-rdot
419     A few tidy-ups have been made bt the real point of this
420     check-point (excuse the pun) is to allow a branch to be
421     made for the purposes of adding the rDot alterations.
422     I don't want to commit the rDot to the main-trunk until
423     we've actually tested it...
424    
425    checkpoint12
426     Tidy up and added generic genmake script (formerly
427     configure script).
428     Released to testers.
429    
430    checkpoint11
431     Re-arranged initialise() and introduced ini_vertical_grid()
432     and ini_masks_etc().
433    
434    checkpoint10
435     Introduced the configure script.
436     Separated out the diags package.
437     Added template for writing time-averages of tile/intermediate quantities.
438     Updated SIZE.h in exp2 and made the data big-endian.
439    
440    checkpoint9
441     MPI fix. Filename changes (meta/data). salbin*y stuff.
442     General tidy-up.
443     SST.bin SSS.bin added to verification/exp2
444    
445    checkpoint8
446     Inludes time-dependant forcing and time-averaging.
447     Works at 4x4 and 2.8125x2.8125 global
448    
449    checkpoint7-4degree-ref
450     Branch from checkpoint7. Released for application to
451     global modeling and general modeling - process studies, regional
452     model etc..
453     Configured for verification/exp2 - 4 degree global, two process.
454    
455    checkpoint7
456     Created by cnh
457     Simple 4 degree global simulation
458     configuration.
459     Includes climatological wind,
460     hydrography, bathymetry etc
461     Does not include Heat Flux and E-P
462    
463    checkpoint6
464     Created by cnh
465     merged checkpoint5 with CD and
466     spherical polar code.
467     Still some problems with GM Redi
468     abd full topography.
469    
470    checkpoint5
471     Created by AJA
472     contains updates to GM Redi
473     and reordered timestepping loop
474     for Implicit Diffusion.
475    
476    checkpoint4
477     Created by cnh
478     Contains memory saving macros ( _rdxc etc..) for when
479     grid variations are limited.
480     Contains polynomial coeffs for EOS and knudsen program
481     for generation.
482    
483  checkpoint3  checkpoint3
484   Created by cnh   Created by cnh
485   Added extra flags for runtime options   Added extra flags for runtime options
# Line 20  checkpoint1 Line 498  checkpoint1
498   Restructured kloop in dynamics.F   Restructured kloop in dynamics.F
499   Added non-linear EOS   Added non-linear EOS
500    
501  baseline - Original checked in code  baseline
502     Original checked in code
503    

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