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revision 1.195 by edhill, Fri Oct 24 05:29:35 2003 UTC revision 1.293 by jmc, Fri May 14 16:31:58 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/land: only liquid water can diffuse or run-off
7    o AIM using land: soil wetness availability account for snow
8    o added printMapIncludesZeros to EEPARMS namelist
9    
10    checkpoint53a_post
11    o restore TAMC compatiility for exf_constants.h
12      (no usage of _d in .h)
13    o Additional storing in KPP in an attempt to fix
14      TAMC problem with adjoint of KPP code.
15      (no success...)
16      Identical code works fine with TAF.
17    o Fixed verification/natl_box_adjoint experiments.
18      Initial conditions for Experiments 4 and 5 are now
19      set to "SEAICE_initialHEFF=0", which is more reasonable,
20      and hence gives results closer to that of Experiment 2.
21      Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
22    
23    checkpoint53
24    o stable checkpoint with up to date adjoint
25      TLM tests only run for 1st grdchk at the moment. Its unclear if
26      this is a code problem or a problem with resetting code for g_
27      variables that is being autogenerated wrong.
28      Otherwise:
29       o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
30       o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
31         are both still in chaos following their security messes.
32    
33    checkpoint52n_post
34    o various build (mostly genmake2) changes including:
35      - ability to build/run more easily within Cygwin and MacOS X
36      - more complicated Makefiles with a stronger dependence on Gnu Make
37    o pkg/seaice modifications
38      - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
39        of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
40        and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
41      - changed proxy for geostrophic velocity and updated
42        verification/lab_sea/results/* accordingly
43      - removed ADI dynamic solver from pkg/seaice
44      - replaced all occurrences of 1/CSTICE or 1/CSUICE
45        they caused a segmentation fault under certain circumstances
46      - removed unused field WATR
47    o bug fix in exf-package:
48      -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
49         now reflect that.
50    o small fixes in the cal-package:
51      - set reference date to first of January for the 'model'-calendar
52      - failing of cal_CheckDate in cal_FullDate now actually results in a
53        warning
54    o small modifications in exf-package to increase flexibility:
55      - change climtempfreeze from a constant to a runtime parameter that
56        is specified in data.exf_clim (default = -1.9)
57      - introduce runtime parameter windstressmax (default = 2.0) that is
58        specified in data.exf
59    o fix in pkg/thsice:
60      - update Evap (Tsf changes) to be consistent with Latent heat flux
61      - maintain snow precipitation unchanged (even if Tsf >=0).
62     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
63    
64    checkpoint52m_post
65    o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
66      this does not change any of the results, because myIter=0 in swfrac always
67      lead to jwtype=2 (the default anyway), but the call makes little sense
68      as a default
69    o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
70    o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
71      atmospheric model (AIM) to use it ; add a "slab ocean" component.
72    o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
73    o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
74    o extending useSingleCpuIO option to work with new exch2 I/O format
75      - old-style, missing-tile I/O is still accessible by defining CPP
76        option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
77    o monitor package can write to NetCDF files and/or STDOUT
78    o fix re-definition bug in MNC_GRID_INIT_ALL()
79    o doc/api_reference added
80      - a framework for building an API Reference Manual using all
81        the "protex" comments embedded in the code
82      - see pkg/generic_advdiff, pkg/mnc for examples
83    o MNC:
84      - make myThid the last argument for all subroutines
85      - new default for the grid files: NO halos
86      - add useMNC and other run-time flags
87      - separate per-file-group handling of the unlimited dimension
88      - early initialization of MNC w/ flags read at the eeboot stage
89        and lookup tables set in initialize_fixed
90      - write all MNC output to a freshly-created directory
91    o thermodynamics sea-ice (thsice) is now tested with testreport.
92    o test exp. advect_cs: use the standard cs32 grid ; update output.
93    o Added functionality to grdchk:
94      pick global i,j,k position (or nearest wet) where to perform check.
95    
96    checkpoint52l_post
97    o new land formulation:
98      a) use ground enthalpy as prognostic variable to ensure exact
99         energy conservation.
100      b) account for water temperature and for latent heat of freezing
101         in all processes (rain, run-off, ground storage)
102      c) compute surface and ground temperature implicitly.
103    o aim_v23 modification for new land model:
104      a) Treat separately land / ocean / sea-ice surface fluxes
105         to allow implicit computation of land & sea-ice surface temp.
106      b) add snow precipitation.
107    checkpoint52l_pre
108    
109    o fix problem (when 1 tile is empty) in min/max monitor.
110    o fix bug in timeAve (u,vZetatave in common block)
111    o no restoring terms under ice for pkg/seaice
112    o moved SEAICE_DO_DIAGS to S/R do_the_model_io
113    o bug fix for pkg/seaice pickups
114    o change MNC call locations and add coordinate attributes
115    o mask vorticity at the corner ; affects global_ocean.cs output
116    o fix ini_curvilinear_grid ; test CS experiments with mpi
117    o aim.5l_cs: modify sea-ice fraction input file ; update output
118    o exf: Adding simple range check routine for exf fields after read
119    
120    checkpoint52k_post
121    o removed top-level directory "diags"
122      - we migrated these functions to pkg/timeave a long time ago
123    o fixed bug introduced in pkg/monitor
124    o accuracy ctrlprec = 32 insuffient for gradient checks using
125      averaged fields (I/O via cost_averages)
126      -> use ctrl.h in active_file*.F to control I/O precision.
127    o paramter list of CALL ADTHE_MAIN_LOOP
128    o added initial do_the_model_io to ecco
129    o set all ...Freq to zero after cost_final
130      taveFreq, dumpFreq, pChkptFreq
131    o MAIN and ECCO differentiability restored
132    
133    checkpoint52j_post
134    o fix nchklev in tamc.h for global_ocean...
135    o Bringing flow and store directives up-to-date
136    o Really weird thing!
137      call do_the_model_io from the_main_loop with parameters
138      starttime, niter0, instead of mytime, myiter, screws up the adjoint:
139      TAF places a faulty re-call of initialise_varia
140      after cost_final call which should not be there!
141    checkpoint52j_pre
142    
143    o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
144      error messages
145    o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
146    o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
147      debug output
148    o modfied mdsio_writefield.F to handle non-global files under exch2
149    o update AIM Cubed-Sphere exp (aim.5l_cs):
150      use land, p*, and Franco.M forcing fields with fractional land-sea mask.
151    o update AIM Equatorial Channel exp:
152      use standard aim_v23 pkg and change the SST fields to be more realistic.
153    o globalFile now works with exch2
154    o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
155      mon_vort3.F to make exch2 friendly with >1 tile per cube face
156    o limit timeave output for hi-res integrations
157    
158    checkpoint52i_post
159    o removed CPP_EEOPTIONS.h from verification/*/code
160    o updated the tiling for global_ocean_pressure
161    checkpoint52i_pre
162    
163    o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
164      the old pkg/aim).
165    
166    checkpoint52h_pre
167    o shortened offending lines in exch2_send_rx?.template
168    o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
169    o genmake2: add build & execute test for NetCDF code
170    o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
171      old grid files, moved CPP_EEMACROS.h to pkg/exch2
172    o added useSingleCPUIO flag to monitor.F and mon_out.F
173    o added temporary hack for sea-ice dynamics on the cube:
174      metric terms are ignored and it is assumed that
175      there is no sea-ice on cube faces 1, 2, 4, and 5.
176    
177    checkpoint52f_post
178    o added exch2 cube routines to pkg/exch2
179    o modified hs94.cs-32x32x5 to use it
180    o added new grid files to hs94.cs-32x32x5
181    checkpoint52f_pre
182    
183    checkpoint52e_post
184    o first attempt to solve vertical advection (momemtum & T,S) Implicitly
185      for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
186    o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
187      to work with implicit vertical advection and AB ;
188    o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
189    o update output (gad_calc_rhs.F changes affect truncation error) of exp:
190     front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
191    checkpoint52e_pre
192    
193    o fix bug in impldiff when Nr=1 or Nr=2.
194    o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
195    o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
196    o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
197      ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
198    o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
199    o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
200    o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
201    
202    checkpoint52d_post
203    o re-tiled many expts to allow comparison in multi-processor mode
204      - updated output accordingly
205      - changed hs94.128x64x5 to use intial T from file rather than use the
206        random number generator
207    o add infrastructure in model routines for fizhi and gridalt packages
208    o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
209    o changes to permit hi-res, cubed-sphere, configuration
210      - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
211      - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
212      - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
213        of surface winds for the cube
214      (A verification experiment, based on global_ocean.cs32x15, but with
215       pkg/seaice turned on and with on-the-fly interpolation from the NCEP
216       Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
217       complete with example surface forcing files and matlab scripts to look
218       at the output and compare it with that of global_ocean.cs32x15.)
219    o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
220       but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
221       to conform to the common rule.
222    o check-in the first version of the coupler + interfaces for multi-components
223       set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
224       - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
225       - atmosphere: use pkg aim_v23 ; no sea-ice for now.
226       - ocean and atmos. share the same horizontal grid (no interpolation).
227       - exchanges between component and coupler is done in forward_step
228    o new verification experiment, cpl_aim+ocn:
229       coupled ocean - AIM atmosphere on cs32 grid.
230    
231    checkpoint52d_pre
232    o surface flux time-av diagnostic modified for NLFS & RealFreshWater
233    o add call to AIM pendant S/R in external_forcing & external_fields_load.F
234    
235    checkpoint52c_post
236    o Fixing OPTIONS files for use of exf:
237      - ALLOW_ECCO not needed
238      - ECCO_CPPOPTIONS.h should not be included from
239        EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
240        as has been the case in the past
241      - All cal/exf related options are currently set in
242        single header file. Should remain so until we
243        agree on a consistent new policy.
244    o Removed all CPP options for cal package.
245      cal has no more CPP options.
246    o modified STOREs in GAD_ADVECTION
247    o corrected key comp. for passkey
248    
249    checkpoint52b_post
250    o new version: "thsice" of thermodynamic sea-ice pkg:
251     - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
252     - modify fluxes but do not change theta directly;
253     - light cleaning of bulk_force pkg (still needed with thsice).
254     - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
255       + output_thsice.txt to test thsice & bulk_force pkgs.
256    o put back grid & coriolis monitor output.
257    checkpoint52b_pre
258    
259    o call "do_the_model_io" at the beginning (=> dump initial state)
260    o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
261    o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
262      (need info on NUMBER_OF_PTRACERS)
263    o missing PTRACERS headers in some routines
264    o default tamc.h in pkg/autodiff supposed to crash
265      to ensure proper customization
266    
267    checkpoint52a_post
268    o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
269      - moved surfaceTendencyTice from pkg/seaice to main code
270      - subroutine FREEZE_SURFACE now limits only surface temperature
271        and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
272        => new output.txt for global_ocean.cs32x15 & global_with_exf
273      - keep the old version of FREEZE for backward compatibility;
274        global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
275      - corresponding modifs for TAF directives
276    o added surface flux output variables to TIMEAVE_STATVARS
277    o time-averaged output for pkg/ptracers
278    o fix problem with ECCO-related divided adjoint
279      snapshot file was missing some ad-variables,
280      but no warning issued by TAF
281    
282    checkpoint52a_pre
283    o some bug fixes for #undef REAL4_IS_SLOW
284    
285    checkpoint52 = ecco_c52_e35
286    o after testing adjoints of checkpoint51u_post
287    
288    checkpoint51u_post
289    o this is the post-merge tag of the ecco-branch
290      (needs another clean checkout and re-testing)
291    o various natl_box_adjoint configs and results
292      but no input fields
293    o obcs adjoint not yet merged!
294    o adding ECCO global 1x1 and 2x2 degree configs
295    o updated/extended some store directives for seaice
296    o pkg/ecco now containes ecco-specific part of cost function
297    o top level routines the_main_loop, forward_step
298      supersede those in model/src/
299      previous input data.cost now in data.ecco
300      (new namelist ecco_cost_nml)
301    o in ctrl/ cleaned some cross-dependencies and updated CPP options
302    
303    checkpoint51t_post
304    o this is the pre-merge tag of the ecco-branch
305    
306    checkpoint51s_post
307    o cleanup: removed various obsolete #define-s
308    o pkg/grdchk
309      - renamed 'ph-grd 3' to 'grad-res'
310      - merged from ecco-branch
311        (remaining bug fixes for obcs gradient checks)
312      - additional high-precision output for testreport
313        (grep for 'precision_grdchk_result')
314    
315    checkpoint51r_post
316    o cleaned up or removed CPP_OPTIONS.h files
317    o updated results for some of the tests to reflect the new
318      optfiles (-ieee: -O0 instead of -O3)
319    
320    checkpoint51q_post
321    o cd_code:
322      - moved cd_scheme.F -> cd_code_scheme.F
323      - separate read_checkpoint from cd_code_ini_vars.F
324      - separated cd_code part from write_checkpoint
325      - updated AD_SOURCE, generated .flow
326      - added CD_CODE_VARS.h to the_main_loop
327      - Moving cd_code specific store dir.s to pkg/cd_code
328    o ctrl package totally restructured
329      - pack/unpack now optional and decoupled from
330        xx_/adxx_ I/O
331      - ctrl_pack/unpack cleaned
332        (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
333      - confined inclusion of AD_CONFIG.h to where necessary.
334    o genmake2: changed AD dependencies from SRCFILES to AD_FILES
335    
336    checkpoint51p_post
337    o create initial cd_code package
338      - WARNING: the initialization of fields within packages
339        is broken because INI_FIELDS (where READ_CHECKPOINT is
340        called) is called *before* PACKAGES_INIT_VARIABLES.
341        This seems to be backwards since
342        1) its important to initially zero the entire field including
343           the "halo" region
344        2) zeroing needs to be done *before* reading pickup info
345           and the pickup call might or might not happen in any
346           particular run
347      - this needs an overhaul for R2
348    o cleanup verification/*/code/GMREDI_OPTIONS.h
349    o cleanup testreport
350    
351    checkpoint51o_post
352    o bringing AD-related verif's up to date with genmake2
353      - carbon/
354      - global_ocean.90x40x15/
355      - hs.94.1x64x5/
356      - (front_relax/ )
357    o (more) consistent directory structure for AD-related verif.'s
358    o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
359    o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
360    o bug fix in find_alpha.F for MDJWF:
361      - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
362        change rho -> rho-rhoConst
363      - replace call find_rho to find_rhonum
364    o initialisation of rFlx extended to full array (required by TAF)
365      and shifted to thermodynamics
366    o removed PTRACERS.h in ptracers routine
367    o added surfacetendencyPtr to S/R parameter list pracers_forcing
368    o Correcting initialisations for fVerU, fVerV.
369    o helping TAF to recognize dependency on kUp for
370      fVerU, fVerV
371    o Replacing delZ by delR in pkg/ctrl/
372    checkpoint51o_pre
373    
374  o undid all of cp51 pending some cleanups and discussion  o undid all of cp51 pending some cleanups and discussion
375    o added the [#include "AD_CONFIG.h"] statement to all files that need
376       it for adjoint/tl #defines
377     o re-worked the build logic in genmake2 to support AD_CONFIG.h
378     o removed tools/genmake since it no longer works
379    
380  checkpoint51n_post  checkpoint51n_post
381  o modifications to make FREEZE flux visible to pkg/kpp  o modifications to make FREEZE flux visible to pkg/kpp

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