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revision 1.187 by jmc, Thu Oct 16 17:14:34 2003 UTC revision 1.287 by dimitri, Wed May 5 00:23:37 2004 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    o pkg/seaice modifications
7      - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
8        of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
9        and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
10      - changed proxy for geostrophic velocity and updated
11        verification/lab_sea/results/* accordingly
12      - removed ADI dynamic solver from pkg/seaice
13      - replaced all occurrences of 1/CSTICE or 1/CSUICE
14        they caused a segmentation fault under certain circumstances
15      - removed unused field WATR
16    o bug fix in exf-package:
17      -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
18         now reflect that.
19    o small fixes in the cal-package:
20      - set reference date to first of January for the 'model'-calendar
21      - failing of cal_CheckDate in cal_FullDate now actually results in a
22        warning
23    o small modifications in exf-package to increase flexibility:
24      - change climtempfreeze from a constant to a runtime parameter that
25        is specified in data.exf_clim (default = -1.9)
26      - introduce runtime parameter windstressmax (default = 2.0) that is
27        specified in data.exf
28    o fix in pkg/thsice:
29      - update Evap (Tsf changes) to be consistent with Latent heat flux
30      - maintain snow precipitation unchanged (even if Tsf >=0).
31     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
32    
33    checkpoint52m_post
34    o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
35      this does not change any of the results, because myIter=0 in swfrac always
36      lead to jwtype=2 (the default anyway), but the call makes little sense
37      as a default
38    o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
39    o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
40      atmospheric model (AIM) to use it ; add a "slab ocean" component.
41    o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
42    o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
43    o extending useSingleCpuIO option to work with new exch2 I/O format
44      - old-style, missing-tile I/O is still accessible by defining CPP
45        option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
46    o monitor package can write to NetCDF files and/or STDOUT
47    o fix re-definition bug in MNC_GRID_INIT_ALL()
48    o doc/api_reference added
49      - a framework for building an API Reference Manual using all
50        the "protex" comments embedded in the code
51      - see pkg/generic_advdiff, pkg/mnc for examples
52    o MNC:
53      - make myThid the last argument for all subroutines
54      - new default for the grid files: NO halos
55      - add useMNC and other run-time flags
56      - separate per-file-group handling of the unlimited dimension
57      - early initialization of MNC w/ flags read at the eeboot stage
58        and lookup tables set in initialize_fixed
59      - write all MNC output to a freshly-created directory
60    o thermodynamics sea-ice (thsice) is now tested with testreport.
61    o test exp. advect_cs: use the standard cs32 grid ; update output.
62    o Added functionality to grdchk:
63      pick global i,j,k position (or nearest wet) where to perform check.
64    
65    checkpoint52l_post
66    o new land formulation:
67      a) use ground enthalpy as prognostic variable to ensure exact
68         energy conservation.
69      b) account for water temperature and for latent heat of freezing
70         in all processes (rain, run-off, ground storage)
71      c) compute surface and ground temperature implicitly.
72    o aim_v23 modification for new land model:
73      a) Treat separately land / ocean / sea-ice surface fluxes
74         to allow implicit computation of land & sea-ice surface temp.
75      b) add snow precipitation.
76    checkpoint52l_pre
77    
78    o fix problem (when 1 tile is empty) in min/max monitor.
79    o fix bug in timeAve (u,vZetatave in common block)
80    o no restoring terms under ice for pkg/seaice
81    o moved SEAICE_DO_DIAGS to S/R do_the_model_io
82    o bug fix for pkg/seaice pickups
83    o change MNC call locations and add coordinate attributes
84    o mask vorticity at the corner ; affects global_ocean.cs output
85    o fix ini_curvilinear_grid ; test CS experiments with mpi
86    o aim.5l_cs: modify sea-ice fraction input file ; update output
87    o exf: Adding simple range check routine for exf fields after read
88    
89    checkpoint52k_post
90    o removed top-level directory "diags"
91      - we migrated these functions to pkg/timeave a long time ago
92    o fixed bug introduced in pkg/monitor
93    o accuracy ctrlprec = 32 insuffient for gradient checks using
94      averaged fields (I/O via cost_averages)
95      -> use ctrl.h in active_file*.F to control I/O precision.
96    o paramter list of CALL ADTHE_MAIN_LOOP
97    o added initial do_the_model_io to ecco
98    o set all ...Freq to zero after cost_final
99      taveFreq, dumpFreq, pChkptFreq
100    o MAIN and ECCO differentiability restored
101    
102    checkpoint52j_post
103    o fix nchklev in tamc.h for global_ocean...
104    o Bringing flow and store directives up-to-date
105    o Really weird thing!
106      call do_the_model_io from the_main_loop with parameters
107      starttime, niter0, instead of mytime, myiter, screws up the adjoint:
108      TAF places a faulty re-call of initialise_varia
109      after cost_final call which should not be there!
110    checkpoint52j_pre
111    
112    o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
113      error messages
114    o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
115    o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
116      debug output
117    o modfied mdsio_writefield.F to handle non-global files under exch2
118    o update AIM Cubed-Sphere exp (aim.5l_cs):
119      use land, p*, and Franco.M forcing fields with fractional land-sea mask.
120    o update AIM Equatorial Channel exp:
121      use standard aim_v23 pkg and change the SST fields to be more realistic.
122    o globalFile now works with exch2
123    o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
124      mon_vort3.F to make exch2 friendly with >1 tile per cube face
125    o limit timeave output for hi-res integrations
126    
127    checkpoint52i_post
128    o removed CPP_EEOPTIONS.h from verification/*/code
129    o updated the tiling for global_ocean_pressure
130    checkpoint52i_pre
131    
132    o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
133      the old pkg/aim).
134    
135    checkpoint52h_pre
136    o shortened offending lines in exch2_send_rx?.template
137    o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
138    o genmake2: add build & execute test for NetCDF code
139    o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
140      old grid files, moved CPP_EEMACROS.h to pkg/exch2
141    o added useSingleCPUIO flag to monitor.F and mon_out.F
142    o added temporary hack for sea-ice dynamics on the cube:
143      metric terms are ignored and it is assumed that
144      there is no sea-ice on cube faces 1, 2, 4, and 5.
145    
146    checkpoint52f_post
147    o added exch2 cube routines to pkg/exch2
148    o modified hs94.cs-32x32x5 to use it
149    o added new grid files to hs94.cs-32x32x5
150    checkpoint52f_pre
151    
152    checkpoint52e_post
153    o first attempt to solve vertical advection (momemtum & T,S) Implicitly
154      for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
155    o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
156      to work with implicit vertical advection and AB ;
157    o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
158    o update output (gad_calc_rhs.F changes affect truncation error) of exp:
159     front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
160    checkpoint52e_pre
161    
162    o fix bug in impldiff when Nr=1 or Nr=2.
163    o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
164    o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
165    o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
166      ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
167    o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
168    o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
169    o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
170    
171    checkpoint52d_post
172    o re-tiled many expts to allow comparison in multi-processor mode
173      - updated output accordingly
174      - changed hs94.128x64x5 to use intial T from file rather than use the
175        random number generator
176    o add infrastructure in model routines for fizhi and gridalt packages
177    o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
178    o changes to permit hi-res, cubed-sphere, configuration
179      - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
180      - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
181      - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
182        of surface winds for the cube
183      (A verification experiment, based on global_ocean.cs32x15, but with
184       pkg/seaice turned on and with on-the-fly interpolation from the NCEP
185       Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
186       complete with example surface forcing files and matlab scripts to look
187       at the output and compare it with that of global_ocean.cs32x15.)
188    o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
189       but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
190       to conform to the common rule.
191    o check-in the first version of the coupler + interfaces for multi-components
192       set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
193       - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
194       - atmosphere: use pkg aim_v23 ; no sea-ice for now.
195       - ocean and atmos. share the same horizontal grid (no interpolation).
196       - exchanges between component and coupler is done in forward_step
197    o new verification experiment, cpl_aim+ocn:
198       coupled ocean - AIM atmosphere on cs32 grid.
199    
200    checkpoint52d_pre
201    o surface flux time-av diagnostic modified for NLFS & RealFreshWater
202    o add call to AIM pendant S/R in external_forcing & external_fields_load.F
203    
204    checkpoint52c_post
205    o Fixing OPTIONS files for use of exf:
206      - ALLOW_ECCO not needed
207      - ECCO_CPPOPTIONS.h should not be included from
208        EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
209        as has been the case in the past
210      - All cal/exf related options are currently set in
211        single header file. Should remain so until we
212        agree on a consistent new policy.
213    o Removed all CPP options for cal package.
214      cal has no more CPP options.
215    o modified STOREs in GAD_ADVECTION
216    o corrected key comp. for passkey
217    
218    checkpoint52b_post
219    o new version: "thsice" of thermodynamic sea-ice pkg:
220     - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
221     - modify fluxes but do not change theta directly;
222     - light cleaning of bulk_force pkg (still needed with thsice).
223     - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
224       + output_thsice.txt to test thsice & bulk_force pkgs.
225    o put back grid & coriolis monitor output.
226    checkpoint52b_pre
227    
228    o call "do_the_model_io" at the beginning (=> dump initial state)
229    o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
230    o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
231      (need info on NUMBER_OF_PTRACERS)
232    o missing PTRACERS headers in some routines
233    o default tamc.h in pkg/autodiff supposed to crash
234      to ensure proper customization
235    
236    checkpoint52a_post
237    o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
238      - moved surfaceTendencyTice from pkg/seaice to main code
239      - subroutine FREEZE_SURFACE now limits only surface temperature
240        and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
241        => new output.txt for global_ocean.cs32x15 & global_with_exf
242      - keep the old version of FREEZE for backward compatibility;
243        global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
244      - corresponding modifs for TAF directives
245    o added surface flux output variables to TIMEAVE_STATVARS
246    o time-averaged output for pkg/ptracers
247    o fix problem with ECCO-related divided adjoint
248      snapshot file was missing some ad-variables,
249      but no warning issued by TAF
250    
251    checkpoint52a_pre
252    o some bug fixes for #undef REAL4_IS_SLOW
253    
254    checkpoint52 = ecco_c52_e35
255    o after testing adjoints of checkpoint51u_post
256    
257    checkpoint51u_post
258    o this is the post-merge tag of the ecco-branch
259      (needs another clean checkout and re-testing)
260    o various natl_box_adjoint configs and results
261      but no input fields
262    o obcs adjoint not yet merged!
263    o adding ECCO global 1x1 and 2x2 degree configs
264    o updated/extended some store directives for seaice
265    o pkg/ecco now containes ecco-specific part of cost function
266    o top level routines the_main_loop, forward_step
267      supersede those in model/src/
268      previous input data.cost now in data.ecco
269      (new namelist ecco_cost_nml)
270    o in ctrl/ cleaned some cross-dependencies and updated CPP options
271    
272    checkpoint51t_post
273    o this is the pre-merge tag of the ecco-branch
274    
275    checkpoint51s_post
276    o cleanup: removed various obsolete #define-s
277    o pkg/grdchk
278      - renamed 'ph-grd 3' to 'grad-res'
279      - merged from ecco-branch
280        (remaining bug fixes for obcs gradient checks)
281      - additional high-precision output for testreport
282        (grep for 'precision_grdchk_result')
283    
284    checkpoint51r_post
285    o cleaned up or removed CPP_OPTIONS.h files
286    o updated results for some of the tests to reflect the new
287      optfiles (-ieee: -O0 instead of -O3)
288    
289    checkpoint51q_post
290    o cd_code:
291      - moved cd_scheme.F -> cd_code_scheme.F
292      - separate read_checkpoint from cd_code_ini_vars.F
293      - separated cd_code part from write_checkpoint
294      - updated AD_SOURCE, generated .flow
295      - added CD_CODE_VARS.h to the_main_loop
296      - Moving cd_code specific store dir.s to pkg/cd_code
297    o ctrl package totally restructured
298      - pack/unpack now optional and decoupled from
299        xx_/adxx_ I/O
300      - ctrl_pack/unpack cleaned
301        (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
302      - confined inclusion of AD_CONFIG.h to where necessary.
303    o genmake2: changed AD dependencies from SRCFILES to AD_FILES
304    
305    checkpoint51p_post
306    o create initial cd_code package
307      - WARNING: the initialization of fields within packages
308        is broken because INI_FIELDS (where READ_CHECKPOINT is
309        called) is called *before* PACKAGES_INIT_VARIABLES.
310        This seems to be backwards since
311        1) its important to initially zero the entire field including
312           the "halo" region
313        2) zeroing needs to be done *before* reading pickup info
314           and the pickup call might or might not happen in any
315           particular run
316      - this needs an overhaul for R2
317    o cleanup verification/*/code/GMREDI_OPTIONS.h
318    o cleanup testreport
319    
320    checkpoint51o_post
321    o bringing AD-related verif's up to date with genmake2
322      - carbon/
323      - global_ocean.90x40x15/
324      - hs.94.1x64x5/
325      - (front_relax/ )
326    o (more) consistent directory structure for AD-related verif.'s
327    o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
328    o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
329    o bug fix in find_alpha.F for MDJWF:
330      - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
331        change rho -> rho-rhoConst
332      - replace call find_rho to find_rhonum
333    o initialisation of rFlx extended to full array (required by TAF)
334      and shifted to thermodynamics
335    o removed PTRACERS.h in ptracers routine
336    o added surfacetendencyPtr to S/R parameter list pracers_forcing
337    o Correcting initialisations for fVerU, fVerV.
338    o helping TAF to recognize dependency on kUp for
339      fVerU, fVerV
340    o Replacing delZ by delR in pkg/ctrl/
341    checkpoint51o_pre
342    
343    o undid all of cp51 pending some cleanups and discussion
344    o added the [#include "AD_CONFIG.h"] statement to all files that need
345       it for adjoint/tl #defines
346     o re-worked the build logic in genmake2 to support AD_CONFIG.h
347     o removed tools/genmake since it no longer works
348    
349    checkpoint51n_post
350    o modifications to make FREEZE flux visible to pkg/kpp
351      - moved surfaceTendencyTice from pkg/seaice to main code
352      - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
353      - subroutine FREEZE now limits only surface temperature
354        (this means new output.txt for global_ocean.90x40x15,
355         global_ocean.cs32x15, and global_with_exf)
356    o added surface flux output variables to TIMEAVE_STATVARS
357    
358    checkpoint51n_pre
359    o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
360    o added [#include "AD_CONFIG.h"] to all files that use the following
361      defines:
362      - ALLOW_ADJOINT_RUN
363      - ALLOW_TANGENTLINEAR_RUN
364      - ALLOW_ECCO_OPTIMIZATION
365    
366    checkpoint51m_post
367    o incorporating changes to get TAMC/TAF working in genmake2
368      - added new TAMC/TAF targets to the Makefile
369      - various cleanups related to package handling
370      - these changes should have no impact on the forward model
371    
372    checkpoint51l_post
373    o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
374     - faster algorithm for cal_addtime.F
375     - higher precision arithmetic, where needed
376     - pkg/exf *startdate variables changed from calendar date to
377       model integration time
378    
379    checkpoint51l_pre
380    o add salt flux to forcing fields (used when salty sea-ice forms or melts)
381    o enable to apply restoring on S & T only in a latitude band.
382    o update output (external_forcing_surf modif. change truncation errors)
383       global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
384    
385  checkpoint51k_post  checkpoint51k_post
386  o change default to: useNHMTerms=.FALSE.  o change default to: useNHMTerms=.FALSE.
387   - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):   - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):

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