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revision 1.172 by heimbach, Fri Jul 18 21:16:49 2003 UTC revision 1.258 by heimbach, Mon Feb 23 19:20:16 2004 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    checkpoint52k_post
7    o removed top-level directory "diags"
8      - we migrated these functions to pkg/timeave a long time ago
9    o fixed bug introduced in pkg/monitor
10    o accuracy ctrlprec = 32 insuffient for gradient checks using
11      averaged fields (I/O via cost_averages)
12      -> use ctrl.h in active_file*.F to control I/O precision.
13    o paramter list of CALL ADTHE_MAIN_LOOP
14    o added initial do_the_model_io to ecco
15    o set all ...Freq to zero after cost_final
16      taveFreq, dumpFreq, pChkptFreq
17    o MAIN and ECCO differentiability restored
18    
19    checkpoint52j_post
20    o fix nchklev in tamc.h for global_ocean...
21    o Bringing flow and store directives up-to-date
22    o Really weird thing!
23      call do_the_model_io from the_main_loop with parameters
24      starttime, niter0, instead of mytime, myiter, screws up the adjoint:
25      TAF places a faulty re-call of initialise_varia
26      after cost_final call which should not be there!
27    checkpoint52j_pre
28    
29    o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
30      error messages
31    o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
32    o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
33      debug output
34    o modfied mdsio_writefield.F to handle non-global files under exch2
35    o update AIM Cubed-Sphere exp (aim.5l_cs):
36      use land, p*, and Franco.M forcing fields with fractional land-sea mask.
37    o update AIM Equatorial Channel exp:
38      use standard aim_v23 pkg and change the SST fields to be more realistic.
39    o globalFile now works with exch2
40    o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
41      mon_vort3.F to make exch2 friendly with >1 tile per cube face
42    o limit timeave output for hi-res integrations
43    
44    checkpoint52i_post
45    o removed CPP_EEOPTIONS.h from verification/*/code
46    o updated the tiling for global_ocean_pressure
47    checkpoint52i_pre
48    
49    o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
50      the old pkg/aim).
51    
52    checkpoint52h_pre
53    o shortened offending lines in exch2_send_rx?.template
54    o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
55    o genmake2: add build & execute test for NetCDF code
56    o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
57      old grid files, moved CPP_EEMACROS.h to pkg/exch2
58    o added useSingleCPUIO flag to monitor.F and mon_out.F
59    o added temporary hack for sea-ice dynamics on the cube:
60      metric terms are ignored and it is assumed that
61      there is no sea-ice on cube faces 1, 2, 4, and 5.
62    
63    checkpoint52f_post
64    o added exch2 cube routines to pkg/exch2
65    o modified hs94.cs-32x32x5 to use it
66    o added new grid files to hs94.cs-32x32x5
67    checkpoint52f_pre
68    
69    checkpoint52e_post
70    o first attempt to solve vertical advection (momemtum & T,S) Implicitly
71      for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
72    o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
73      to work with implicit vertical advection and AB ;
74    o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
75    o update output (gad_calc_rhs.F changes affect truncation error) of exp:
76     front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
77    checkpoint52e_pre
78    
79    o fix bug in impldiff when Nr=1 or Nr=2.
80    o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
81    o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
82    o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
83      ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
84    o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
85    o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
86    o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
87    
88    checkpoint52d_post
89    o re-tiled many expts to allow comparison in multi-processor mode
90      - updated output accordingly
91      - changed hs94.128x64x5 to use intial T from file rather than use the
92        random number generator
93    o add infrastructure in model routines for fizhi and gridalt packages
94    o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
95    o changes to permit hi-res, cubed-sphere, configuration
96      - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
97      - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
98      - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
99        of surface winds for the cube
100      (A verification experiment, based on global_ocean.cs32x15, but with
101       pkg/seaice turned on and with on-the-fly interpolation from the NCEP
102       Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
103       complete with example surface forcing files and matlab scripts to look
104       at the output and compare it with that of global_ocean.cs32x15.)
105    o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
106       but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
107       to conform to the common rule.
108    o check-in the first version of the coupler + interfaces for multi-components
109       set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
110       - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
111       - atmosphere: use pkg aim_v23 ; no sea-ice for now.
112       - ocean and atmos. share the same horizontal grid (no interpolation).
113       - exchanges between component and coupler is done in forward_step
114    o new verification experiment, cpl_aim+ocn:
115       coupled ocean - AIM atmosphere on cs32 grid.
116    
117    checkpoint52d_pre
118    o surface flux time-av diagnostic modified for NLFS & RealFreshWater
119    o add call to AIM pendant S/R in external_forcing & external_fields_load.F
120    
121    checkpoint52c_post
122    o Fixing OPTIONS files for use of exf:
123      - ALLOW_ECCO not needed
124      - ECCO_CPPOPTIONS.h should not be included from
125        EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
126        as has been the case in the past
127      - All cal/exf related options are currently set in
128        single header file. Should remain so until we
129        agree on a consistent new policy.
130    o Removed all CPP options for cal package.
131      cal has no more CPP options.
132    o modified STOREs in GAD_ADVECTION
133    o corrected key comp. for passkey
134    
135    checkpoint52b_post
136    o new version: "thsice" of thermodynamic sea-ice pkg:
137     - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
138     - modify fluxes but do not change theta directly;
139     - light cleaning of bulk_force pkg (still needed with thsice).
140     - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
141       + output_thsice.txt to test thsice & bulk_force pkgs.
142    o put back grid & coriolis monitor output.
143    checkpoint52b_pre
144    
145    o call "do_the_model_io" at the beginning (=> dump initial state)
146    o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
147    o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
148      (need info on NUMBER_OF_PTRACERS)
149    o missing PTRACERS headers in some routines
150    o default tamc.h in pkg/autodiff supposed to crash
151      to ensure proper customization
152    
153    checkpoint52a_post
154    o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
155      - moved surfaceTendencyTice from pkg/seaice to main code
156      - subroutine FREEZE_SURFACE now limits only surface temperature
157        and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
158        => new output.txt for global_ocean.cs32x15 & global_with_exf
159      - keep the old version of FREEZE for backward compatibility;
160        global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
161      - corresponding modifs for TAF directives
162    o added surface flux output variables to TIMEAVE_STATVARS
163    o time-averaged output for pkg/ptracers
164    o fix problem with ECCO-related divided adjoint
165      snapshot file was missing some ad-variables,
166      but no warning issued by TAF
167    
168    checkpoint52a_pre
169    o some bug fixes for #undef REAL4_IS_SLOW
170    
171    checkpoint52 = ecco_c52_e35
172    o after testing adjoints of checkpoint51u_post
173    
174    checkpoint51u_post
175    o this is the post-merge tag of the ecco-branch
176      (needs another clean checkout and re-testing)
177    o various natl_box_adjoint configs and results
178      but no input fields
179    o obcs adjoint not yet merged!
180    o adding ECCO global 1x1 and 2x2 degree configs
181    o updated/extended some store directives for seaice
182    o pkg/ecco now containes ecco-specific part of cost function
183    o top level routines the_main_loop, forward_step
184      supersede those in model/src/
185      previous input data.cost now in data.ecco
186      (new namelist ecco_cost_nml)
187    o in ctrl/ cleaned some cross-dependencies and updated CPP options
188    
189    checkpoint51t_post
190    o this is the pre-merge tag of the ecco-branch
191    
192    checkpoint51s_post
193    o cleanup: removed various obsolete #define-s
194    o pkg/grdchk
195      - renamed 'ph-grd 3' to 'grad-res'
196      - merged from ecco-branch
197        (remaining bug fixes for obcs gradient checks)
198      - additional high-precision output for testreport
199        (grep for 'precision_grdchk_result')
200    
201    checkpoint51r_post
202    o cleaned up or removed CPP_OPTIONS.h files
203    o updated results for some of the tests to reflect the new
204      optfiles (-ieee: -O0 instead of -O3)
205    
206    checkpoint51q_post
207    o cd_code:
208      - moved cd_scheme.F -> cd_code_scheme.F
209      - separate read_checkpoint from cd_code_ini_vars.F
210      - separated cd_code part from write_checkpoint
211      - updated AD_SOURCE, generated .flow
212      - added CD_CODE_VARS.h to the_main_loop
213      - Moving cd_code specific store dir.s to pkg/cd_code
214    o ctrl package totally restructured
215      - pack/unpack now optional and decoupled from
216        xx_/adxx_ I/O
217      - ctrl_pack/unpack cleaned
218        (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
219      - confined inclusion of AD_CONFIG.h to where necessary.
220    o genmake2: changed AD dependencies from SRCFILES to AD_FILES
221    
222    checkpoint51p_post
223    o create initial cd_code package
224      - WARNING: the initialization of fields within packages
225        is broken because INI_FIELDS (where READ_CHECKPOINT is
226        called) is called *before* PACKAGES_INIT_VARIABLES.
227        This seems to be backwards since
228        1) its important to initially zero the entire field including
229           the "halo" region
230        2) zeroing needs to be done *before* reading pickup info
231           and the pickup call might or might not happen in any
232           particular run
233      - this needs an overhaul for R2
234    o cleanup verification/*/code/GMREDI_OPTIONS.h
235    o cleanup testreport
236    
237    checkpoint51o_post
238    o bringing AD-related verif's up to date with genmake2
239      - carbon/
240      - global_ocean.90x40x15/
241      - hs.94.1x64x5/
242      - (front_relax/ )
243    o (more) consistent directory structure for AD-related verif.'s
244    o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
245    o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
246    o bug fix in find_alpha.F for MDJWF:
247      - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
248        change rho -> rho-rhoConst
249      - replace call find_rho to find_rhonum
250    o initialisation of rFlx extended to full array (required by TAF)
251      and shifted to thermodynamics
252    o removed PTRACERS.h in ptracers routine
253    o added surfacetendencyPtr to S/R parameter list pracers_forcing
254    o Correcting initialisations for fVerU, fVerV.
255    o helping TAF to recognize dependency on kUp for
256      fVerU, fVerV
257    o Replacing delZ by delR in pkg/ctrl/
258    checkpoint51o_pre
259    
260    o undid all of cp51 pending some cleanups and discussion
261    o added the [#include "AD_CONFIG.h"] statement to all files that need
262       it for adjoint/tl #defines
263     o re-worked the build logic in genmake2 to support AD_CONFIG.h
264     o removed tools/genmake since it no longer works
265    
266    checkpoint51n_post
267    o modifications to make FREEZE flux visible to pkg/kpp
268      - moved surfaceTendencyTice from pkg/seaice to main code
269      - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
270      - subroutine FREEZE now limits only surface temperature
271        (this means new output.txt for global_ocean.90x40x15,
272         global_ocean.cs32x15, and global_with_exf)
273    o added surface flux output variables to TIMEAVE_STATVARS
274    
275    checkpoint51n_pre
276    o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
277    o added [#include "AD_CONFIG.h"] to all files that use the following
278      defines:
279      - ALLOW_ADJOINT_RUN
280      - ALLOW_TANGENTLINEAR_RUN
281      - ALLOW_ECCO_OPTIMIZATION
282    
283    checkpoint51m_post
284    o incorporating changes to get TAMC/TAF working in genmake2
285      - added new TAMC/TAF targets to the Makefile
286      - various cleanups related to package handling
287      - these changes should have no impact on the forward model
288    
289    checkpoint51l_post
290    o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
291     - faster algorithm for cal_addtime.F
292     - higher precision arithmetic, where needed
293     - pkg/exf *startdate variables changed from calendar date to
294       model integration time
295    
296    checkpoint51l_pre
297    o add salt flux to forcing fields (used when salty sea-ice forms or melts)
298    o enable to apply restoring on S & T only in a latitude band.
299    o update output (external_forcing_surf modif. change truncation errors)
300       global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
301    
302    checkpoint51k_post
303    o change default to: useNHMTerms=.FALSE.
304     - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
305       adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
306     - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
307        exp1, ideal_2D_oce
308     - change data file of oceanic exp (leave the results unchanged for now)
309       exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
310    o set gravitySign automatically according to the vertical coordinate used
311      (and change sign: back to "logical" value: +1 when R increases downward)
312    o added an include barrier to the default CPP_OPTIONS.h and
313      removed the #include "PACKAGES_CONFIG.h" from it
314    o fix a bug in mom_fluxform (from chk51j_post)
315    
316    checkpoint51j_post
317    o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
318    o adjusted some flow directives (dynamics, thermodynamics)
319    o added cubed-sphere case to test cost function
320    o heckpoint_lev?_directives.h now include
321      pkg-specific directives, whenever those are enabled.
322    o Moving pkg-specific flow directives to corresponding pkg
323      Moving pkg-specific differentiation list to corresponding pkg
324      Moving pkg-specific checkpoint-lev storing to corresponding pkg
325      ---> conventions are
326           - pkg_ad.flow
327           - pkg_ad_diff.list
328           - pkg_ad_check_lev?_dir.h
329    
330    checkpoint51i_post
331    o merge of the branch-genmake2
332      - knowingly breaks the older genmake
333      - automatic generation of all ALLOW_${PKG_NAME} defines
334      - new testreport supersedes older testscript
335    o large number of package inclusion and header cleanups
336    checkpoint51i_pre
337    
338    o new output for adjoin of global ocean vector invariant
339    o fix for checkpoint of thermodynamic seaice and bulk_force
340    o Steph gchem various cleanups
341    
342    checkpoint 51h_pre
343    o fixed some single quotes
344    o modify gchem pkg to be more versatile
345    o modifications to clean up dic pkg
346    o add pkg/cfc
347    
348    checkpoint51g_post
349    o provide links for ARPACK and ADM*TLM
350    o start removing verification/vero/
351    o update AD-related stuff
352      (in particular some IF-statements in model/src/ routines)
353    o adding to verification/global_ocean.90x40x15/ adjoint of
354      vector invariant setup
355    
356    checkpoint51f_post
357    o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
358    o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
359      of tracer Green's fucntions for ocean inversion project.
360    
361    checkpoint51f_pre
362    o Added on-the-fly spatial interpolation capability
363        "USE_EXF_INTERPOLATION" to pkg/exf.
364      - This is a temporary Cartesian-grid hack until
365        the super-duper ESMF coupler becomes available.
366      - See verification/global_with_exf/README for usage example.
367      - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
368        flags and modified pkg/seaice accordingly.
369    o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
370        and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
371        non-local transport term.
372    
373    checkpoint51e_post
374    o pkg/mom_vecinv:
375      - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
376      - add time-ave diagnostic of vorticity advection.
377    o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
378    o atmospheric geopotential: - include water vapor effect;
379                                - use p^kappa in p* scaling.
380    o land pkg: read initial state from files.
381    o AIM : add stratospheric drag in the upper level
382    
383  checkpoint51d_post  checkpoint51d_post
384    o change function ILNBLNK (=> last non-blank char.) to return zero
385      (instead of the string length) when the string. char is empty
386  o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)  o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
387  o modif's to restore TAMC compatibility  o modif's to restore TAMC compatibility
388    - avoid "_d" constructs in PARAMETER declarations    - avoid "_d" constructs in PARAMETER declarations

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