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revision 1.19 by adcroft, Mon Mar 22 17:40:01 1999 UTC revision 1.76 by jmc, Fri Jul 12 14:52:08 2002 UTC
# Line 2  $Header$ Line 2  $Header$
2    
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
6      (affects plume_on_slope "cg2d" output)
7    o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
8    o change phiMin in exp1 (to agree with documentation)
9    o add new flags:
10     - T,S forcing inside/outside Adams-Bashforth
11     - turn off temp,salt advection and/or forcing
12     - for each tracer, define internal flag for multiDimAdvection & A-B
13    o monitor: change definition of KE to check conservation of Energy
14    
15    checkpoint45c_post
16    o Removed f90 comments ("!")
17    o Modified initialisations to enable exf package for MITgcm
18      (without invoking ECCO_PACKAGE).
19    o modifications to gradient check package (Martin Losch)
20      - enable centered differences
21      - modified format of standard output
22    
23    checkpoint45b_post
24    o cleaned exchange calls in cg2d
25    o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
26    o included CPP option SINGLE_LAYER_MODE in thermodynamics
27      to configure barotropic setup (Martin Losch)
28    o moved some initialisations within bi,bj loop in dynamics
29      (TAF flow dependency)
30    o in initialise_varia, moved call packages_init_variables
31      before convective_adjustment_init
32      (corresponding adjustment of TAF tape initialisation).
33    o in calc_diffusivity/calc_viscosity extended domain to full overlap.
34    
35    checkpoint45a_post
36    o compute Rho over the whole domain (extend iMin,jMin indices)
37    o specific exchange for X-slice domain (case Ny=1)
38    o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
39    o solve_for_pressure : set cg2d_x to zero where OBCS are applied
40    
41    checkpoint44h_post = checkpoint45
42    o Fix to restore differentiability:
43      place at which packages_init_variables is called in
44      initialise_varia is crucial for reverse control flow.
45    o modifications in GMRedi to enable stable adjoint
46      (corresponding modif's in thermodynamics, dynamics)
47    o added missing hook for sponge layer code in external_forcing
48    o modified test cost functions
49    o storing in gad_advection (plus removal of write(0,*)!
50    o missing headers TR1.h added in convective_adjustment routines
51    o errorMessageUnit set non-equal zero in eeboot
52      (conflict on some platforms, e.g. IBM SP3)
53    o modified carbon verif.
54    
55    checkpoint44h_pre
56    o vertical grid option: allow to put the Interface at the middle between
57      2 cell-centers ; replace delZ in pkg/kpp by drF.
58    o GM Advective form: Tracers are advected using the residual transport (=
59      Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
60    
61    checkpoint44g_post
62    o fix surface correction term in multiDimAdvection (affects plume_on_slope
63      results) ; ifdef missing in thermodynamics.F
64    
65    checkpoint44f_pre,checkpoint44f_post
66    o added PTRACERS package
67      This allows an arbitrary number of passive tracers to be integrated
68      forward simultaneously with the dynamicaly model.
69      + Implemented so far:
70        - basic forward algorithm (time-stepping, advection, diffusion, convection)
71        - I/O and checkpointing
72        - GM/Redi  *but*  using the GM/Redi coefficient of Salt
73      + Not implemented so far:
74        - KPP
75        - OBCS
76      + No specific example supplied (yet) but global_ocean.90x40x15 has the
77        necessary data.ptracer file. Simply use -enable=ptracers and uncomment
78        line in data.pkg.
79      + This package is disabled by default since it increases storage.
80    
81    
82    o testscript: added -cleanup option
83    o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
84                 b) enable to filter 2D fields.
85    
86    checkpoint44e_pre,post
87    o re-wrote convective adjustment to use pre-calculated weights
88      Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
89      Adds:    model/src/convective_weights.F, convectively_mixtracer.F
90      Original calls to convect() still in place.
91    
92    chkpt44d_pre,post
93    o added missing EXCLUDE_MONITOR flags
94    o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
95      (incompatible typ in MIN/MAX expressions caused problems
96      on IBM SP3)
97    o in genmake added variable MAKEDEPEND
98      plus resetting for case SunOS
99    o added timer_stats.c routine for IBM SP3
100    o removed variables in dynamics
101    !!! I forgot to create tag chkpt44d_pre !!!
102    !!! But chkpt44d_pre = chkpt44c_post    !!!
103    
104    o real fresh water flux implemented with non-linear free-surface.
105    
106    chkpt44c_pre,post
107    o few fix (mask in shap_s2, EmPmR in external_field_load,
108      USE_NATURAL_BCS in solve_for_P);
109    o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
110    
111    checkpoint44b_pre/_post
112    o merge of relevant stuff from the ecco-branch:
113      - genmake: removed $S64 overwrite for case SunOS
114      - pkg/exf: update and corrections for field swapping and obcs
115      - pkg/ecco: parameter lists for the_model_main, the_main_loop
116                  harmonized between ECCO and MITgcm
117      - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
118                      updated checkpointing_lev... lists for obcs
119      - model/src: minor changes in forward_step, plot_field
120                   added directive for divided adjoint in the_main_loop
121      - pkg/mdsio: added mdsio_gl_slice
122    
123    o check parameters & config (chkpt44a_pre,post)
124    o OBC and NonLin_FrSurf.
125    
126    checkpoint44
127    o fix bug in mom_vi_del2uv
128    o select when filters are applied ; add options to zonal_filter (data.zonfilt)
129    o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
130    o update AIM experiments (NCEP input files)
131    o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
132    o added some stuff for AD
133    
134    checkpoint43
135    o added two new advection tests
136    o added global 4x4 degree ocean test
137    o added test of H&S94 with free surface on cube
138    o some final mods for gradient check, adjoint,...
139    
140    checkpoint42
141      Fixed AD-related problems:
142    o Store directives up-to-date with re-arranged Adams-Bashforth
143      (mainly thermodynamics.F)
144    o New store directives for multi-dim. advection schemes
145      * new CPP flag ALLOW_MULTI_DIM_ADVECTION
146      * new common block and key passkey
147      (mainly gad_advection.F)
148    o Modified store directives for split of dynamics/thermodynamics
149      for the case ALLOW_KPP
150    o Cleaned argument list for timestep_tracer.F
151    
152    checkpoint41
153    o re-formatted/added comments in prologues of key subroutines
154      to work with protex
155    
156    checkpoint40
157    o moved calc_gs, calc_gt and calc_tr1 back to model/src
158    o added FLT (floats) package from Arne along with demo. experiment
159    o re-arranged Adams-Bashforth scheme for tracers to allow easier
160      implementation of forward-in-time forcing terms
161    o more mods for non-linear free-surface including new variable
162    o modified multi-dim method to work on cube
163    o bug fix in KPP (from DM)
164    
165    checkpoint40pre9
166    o added DST advection schemes
167    o fix MPI bug on SGI's
168    o modifications for non-linear free-surface
169    o fixed conditionals for fixed flow/passive tracer only mode
170    o added tension/strain form of stress tensor
171    o changes to commenting of arguments for TAF/TAMC
172    o added/updated many matlab scripts
173    o added multi-dimensional advection method for tracers
174      
175    checkpoint40pre8
176    o new package rw/
177      Added method for dumping intermediate local arrays:
178      mdsio_writetile - same as mdsio_writefield except works from inside
179                        bi,bj loop
180      mdsio_writelocal - same as mdsio_writetile except works for local
181                         arrays
182      write_local_r? - higher-level wrapper for mdsio_writelocal
183      Controlled by diagFreq. Defaults to zero (ie. no dumps)
184      Example given at end of mom_vecinv.F that dumps some local arrays.
185    o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
186      control flux-form versus vector invariant code.
187      Switch is runtime flag vectorInvariantMomentum (defaults to false)
188      or genmake -DISABLE ...
189    o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
190      (additional storing is now needed for case vecinv;
191      currently nothing implemented to switch this storing off
192      in case fluxform is used since no CPP flag available).
193    
194    checkpoint40pre7
195    o bug fix in dynamics.F
196      calc_viscosity called before k=1,Nr loop.
197    o added some #ifdef's ALLOW_PASSIVE_TRACER
198    o cleaned initialisations in ctrl_map_ini
199      related to TAF
200    
201    checkpoint40pre6
202    o split dynamics into thermodynamics & dynamics
203    o corresponding split of calc_diffusivity into
204      calc_diffusivity, calc_viscosity
205      (kpp_calc_diff, kpp_calc_visc).
206    o Added diffkr, kapgm to control variables
207    o bug fix in gmredi_slope_limit for ldd97
208    
209    checkpoint40pre5
210    o proper initialization of Adams-Bashforth time stepping
211      + uses forward step for very first step of model (iter=0)
212    o re-generated *all* output since almost all output is modified by this
213      change (sorry but we've been putting this one off for about 2 years)
214      + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
215        *not* regenerated since they are already out of date and I don't
216        want to create the impression that they are suddenly working.
217    o removed KAP stuff for DEC's
218    o modified/added many .cvsignore files in */code and */input
219    o added new expt "solid-body.cs-32x32x1"
220      + this uses an alternative form of ini_curvilinear_grid.F which
221        is not necessarily any better than the current one...
222    
223    checkpoint40pre4
224    o added re-initialisations of utrans,vtrans,rtrans in
225      calc_common_factors which are crucial for TAF.
226    o extended iMin,jMin range for calc_common_factors,
227      calc_diffusivity
228    o added option ALLOW_PASSIVE_TRACER
229    o a few minor updates and fixes
230    
231    checkpoint40pre3
232    o created calc_gtr1.F for gad package
233    o split the_main_loop and re-introduced forward_step
234    o some recomputations of nIter0 for TAMC
235    
236    checkpoint40pre2
237    o Updated to latest branch of AJA, JMC
238    o Added gradient check package
239    o Added routines for passive tracer handling
240    o Added carbon sequestration sensitivity experiment
241    
242    checkpoint39
243     o Modifications and fixes to support TAMC
244       (mainly missing or wrong directives)
245     o Corrected common blocks when fooling TAMC to produce adjoint I/O
246       in addummy_in_stepping
247     o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
248     o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
249     o Included following packages:
250       cal: calendar
251       exf: external forcing
252       ecco: essential routines to control use of cal, exf
253             (NB: this is not the full ECCO environment)
254     o disabled some packages by default in genmake
255    
256    checkpoint38
257     o see notes_c37_adj.txt
258     o corrected wrong layer index in external_forcing_t
259     o replaced the_main_loop/forward_step by the_main_loop
260     o removed forceoutput from write_state
261       (replaced criteria for initial/final state)
262     o added runtime flag for pre-C35 pickups: usePickupBeforeC35
263    
264    checkpoint37
265     o mdsio.F routine split and packaged in pkg/mdsio
266       (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
267        used unless genmake -disable=mdsio)
268     o allow a more precise surface-geopotential gradient for the atmosphere
269       taking into account the change in space of Alpha (=1/rho) at the surface.
270     o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
271       (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
272     o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
273       Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
274       [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
275     o Time-Average diagnostics defined as a pseudo package "timeave".
276     o pickup files : old pickup (before c35) did not work with new code (c35
277       and after) unless activating 2 commented lines in initialise-varia.
278     o Non-Hydrostatic pickup file Pb fixed.
279     o bug with Rigid-lid version (since c35) fixed.  
280    
281    checkpoint36
282     o implement Crank-Nickelson barotropic time-stepping
283     o recover Time-Average diagnostics
284     o fix Pb in checkpoint (PR#19)
285     o AIM become a standard package ; clean unused CPP_kees
286    
287    checkpoint35
288     o subtantial rewrite of dynamics.f
289     o allows staggered time-stepping
290     o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
291     o added bottom drag (linear + quadratic)
292    
293    checkpoint34
294     o Modified exchange routines for correct reverse simulation.
295     o Added verification output to comply with bug fix in impldiff.F
296       as of c33 (exp2, natl_box).
297     o Corrected store directives in dynamics.F
298     o Corrected array boundaries in impldiff.F
299     o Corrected array dimensions in gmredi.
300       Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
301     o Added routine GLOBAL_SUM_INT to global_sum.F
302     o Added mdsio_gl.F for ECCO purposes.
303    
304    checkpoint33
305     o Fixed bug in lower BC in impldiff.F
306     o Fixed confusion about units of forcing arrays in FFIELDS.h
307       namely Fu,Fv,Qnet,Qsw,EmPmR:
308       - Removed verification/natl_box/code/external_fields_scale.F
309         (did not differ from that in model/src)
310       - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
311         (see FFIELDS.h for description)
312       - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
313         kpp_calc.F and kpp_transport_t.F
314       - Removed model/src/external_fields_scale.F and calls to it
315       - verification/natl_box uses flux data with "atmospheric" sign so
316         a special version of external_fields_load.F is used to
317         change the data as it's read in. This way, the arrays
318         have the right units and signs at all times tha a user could
319         possibly use them.
320     o Corrected genmake to delete a temporary file during configuration
321    
322    checkpoint32
323     o Scaling of forcing fields moved from external_forcing.F to
324       external_fields_scale.F, called directly after loading fields.
325     o Surface relaxation terms added to surface tendency fields in
326       extra subroutine.
327     o impldiff.F changed to avoid storing by TAMC of huge intermediate
328       fields.
329     o Changes in GMRedi to comply with packaging structure.
330     o Modifications and bug fixes in KPP package.
331     o Verification experiment for KPP added (verification/nat_box/)
332    
333    checkpoint31
334     o Packages interface brought in line with defined standard
335       -> new routines packages_...F
336       -> changes in initialise_fixed.F, initialise_varia.F
337       -> enables initialisation interface for ECCO package
338     o Rescaling of external forcing fields immediately after read
339       (removed from external_forcing.F)
340       -> new: surface_fields_scale.F
341       -> affects ini_foorcing.F, external_fields_load.F
342     o Computation of surface tendencies before tendency updates.
343       -> new: external_forcing_surf.F
344     o Change of variable names useGMRedi, useKPP, useECCO
345     o Further changes in dynamics.F, impldiff.F for TAMC
346     o Tested for experiments 0, 2, 4.
347       - not yet tested for GMRedi.
348       - not yet tested for KPP.
349    
350    checkpoint30
351     o Updates for OBCs
352     o New experiment for test OBCs (internal_wave)
353     o New output.txt in verification/exp4/results/
354     o Updates for KPP: calculation of viscosity corrected, new variables
355       kpp_dumpFreq and kpp_taveFreq
356     o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
357       and entry for T90 in genmake
358    
359    checkpoint29
360     o packaged KPP and GM/Redi
361    
362    checkpoint28
363     o Corrected initialization of hFacMin for difference vertical coordinates
364     o Modified calculation of partial cell thickness to more robust algorithm
365     o config_summary.F: replaced write_1D_... by write_0D_...
366       read_write.F: added subroutines write_0D_...
367     o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
368       included some initialisations required for TAMC.
369     o routine calc_isoslopes: modified sqrt computation to make it
370       differentiable for zero argument.
371     o routines dynamics, impldiff:
372       included store directives and tape key computations required for TAMC.
373     o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
374    
375    checkpoint27
376     o fixed calc_isoslopes() to so that cancellation of terms in tensor
377       formulation works properly with variable resolution.
378     o restructured the calling tree between the_model_main() and dynamics()
379     o split initialise() into initialise_fixed() and initialise_varia()
380     o introduced initialization file pSurfInitFile for free surface (cg2d_x)
381       in new routine ini_psurf()
382    
383    checkpoint26
384     o moved some #ifdef in optional routines to encompass everything
385       except the argument declarations. This was using up some memory.
386     o fixed macros like _ADT to work with both versions of Linux cpp
387     o cleaned up some unused and uninitialized variables
388       (helps when debugging with strict compile options)
389     o split up CPP_EEOPTIONS.h into options and macros
390       (macros are now in eesupp/inc/CPP_EEMACROS.h)
391     o patch for 2 processor JAM mode
392    
393    checkpoint25
394     o updates for OBCs and NH
395     o dramatically reduced memory usage
396     o added "JAM" routines for use on Artic network
397     o parameterization of convection by implicit vertical diffusion
398     o added a diagnostic of convective index
399     o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
400       (this is was partly for OBCs and NH but also in anticipation of
401        an explicit free-surface option)
402     o initial state input files for U and V
403    
404    checkpoint24
405     o Removed some spurious "REAL"s
406     o Updated KPP to latest version from JPL
407     o Added a COS(latitude) in horizontal viscosity
408    
409    checkpoint23
410     o Added del^4 diffusion for salt and temperature
411     o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
412    
413    checkpoint22
414     o Made many small changes: implicit none, format(i5), etc...
415     o Introduced KPP mixing scheme (compiles and runs but *not* tested)
416    
417    checkpoint21
418     o Introduced new I/O package that supports direct-access records (mdsio.F)
419     o Split-up mid-level I/O routines
420     o Updated input data for experiments 0,1,2,4 and 5
421     o Finally removed the genmake.* scripts (everyone seems happy with genmake)
422    
423  checkpoint20  checkpoint20
424   o Tidied up open-boundaries some more   o Tidied up open-boundaries some more

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