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revision 1.157 by jmc, Thu May 22 03:24:12 2003 UTC revision 1.238 by dimitri, Sat Jan 10 00:48:49 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 added useSingleCPUIO flag to monitor.F and mon_out.F
7    
8    checkpoint52f_post
9    o added exch2 cube routines to pkg/exch2
10    o modified hs94.cs-32x32x5 to use it
11    o added new grid files to hs94.cs-32x32x5
12    checkpoint52f_pre
13    
14    checkpoint52e_post
15    o first attempt to solve vertical advection (momemtum & T,S) Implicitly
16      for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
17    o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
18      to work with implicit vertical advection and AB ;
19    o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
20    o update output (gad_calc_rhs.F changes affect truncation error) of exp:
21     front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
22    checkpoint52e_pre
23    
24    o fix bug in impldiff when Nr=1 or Nr=2.
25    o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
26    o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
27    o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
28      ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
29    o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
30    o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
31    o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
32    
33    checkpoint52d_post
34    o re-tiled many expts to allow comparison in multi-processor mode
35      - updated output accordingly
36      - changed hs94.128x64x5 to use intial T from file rather than use the
37        random number generator
38    o add infrastructure in model routines for fizhi and gridalt packages
39    o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
40    o changes to permit hi-res, cubed-sphere, configuration
41      - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
42      - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
43      - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
44        of surface winds for the cube
45      (A verification experiment, based on global_ocean.cs32x15, but with
46       pkg/seaice turned on and with on-the-fly interpolation from the NCEP
47       Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
48       complete with example surface forcing files and matlab scripts to look
49       at the output and compare it with that of global_ocean.cs32x15.)
50    o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
51       but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
52       to conform to the common rule.
53    o check-in the first version of the coupler + interfaces for multi-components
54       set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
55       - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
56       - atmosphere: use pkg aim_v23 ; no sea-ice for now.
57       - ocean and atmos. share the same horizontal grid (no interpolation).
58       - exchanges between component and coupler is done in forward_step
59    o new verification experiment, cpl_aim+ocn:
60       coupled ocean - AIM atmosphere on cs32 grid.
61    
62    checkpoint52d_pre
63    o surface flux time-av diagnostic modified for NLFS & RealFreshWater
64    o add call to AIM pendant S/R in external_forcing & external_fields_load.F
65    
66    checkpoint52c_post
67    o Fixing OPTIONS files for use of exf:
68      - ALLOW_ECCO not needed
69      - ECCO_CPPOPTIONS.h should not be included from
70        EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
71        as has been the case in the past
72      - All cal/exf related options are currently set in
73        single header file. Should remain so until we
74        agree on a consistent new policy.
75    o Removed all CPP options for cal package.
76      cal has no more CPP options.
77    o modified STOREs in GAD_ADVECTION
78    o corrected key comp. for passkey
79    
80    checkpoint52b_post
81    o new version: "thsice" of thermodynamic sea-ice pkg:
82     - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
83     - modify fluxes but do not change theta directly;
84     - light cleaning of bulk_force pkg (still needed with thsice).
85     - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
86       + output_thsice.txt to test thsice & bulk_force pkgs.
87    o put back grid & coriolis monitor output.
88    checkpoint52b_pre
89    
90    o call "do_the_model_io" at the beginning (=> dump initial state)
91    o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
92    o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
93      (need info on NUMBER_OF_PTRACERS)
94    o missing PTRACERS headers in some routines
95    o default tamc.h in pkg/autodiff supposed to crash
96      to ensure proper customization
97    
98    checkpoint52a_post
99    o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
100      - moved surfaceTendencyTice from pkg/seaice to main code
101      - subroutine FREEZE_SURFACE now limits only surface temperature
102        and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
103        => new output.txt for global_ocean.cs32x15 & global_with_exf
104      - keep the old version of FREEZE for backward compatibility;
105        global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
106      - corresponding modifs for TAF directives
107    o added surface flux output variables to TIMEAVE_STATVARS
108    o time-averaged output for pkg/ptracers
109    o fix problem with ECCO-related divided adjoint
110      snapshot file was missing some ad-variables,
111      but no warning issued by TAF
112    
113    checkpoint52a_pre
114    o some bug fixes for #undef REAL4_IS_SLOW
115    
116    checkpoint52 = ecco_c52_e35
117    o after testing adjoints of checkpoint51u_post
118    
119    checkpoint51u_post
120    o this is the post-merge tag of the ecco-branch
121      (needs another clean checkout and re-testing)
122    o various natl_box_adjoint configs and results
123      but no input fields
124    o obcs adjoint not yet merged!
125    o adding ECCO global 1x1 and 2x2 degree configs
126    o updated/extended some store directives for seaice
127    o pkg/ecco now containes ecco-specific part of cost function
128    o top level routines the_main_loop, forward_step
129      supersede those in model/src/
130      previous input data.cost now in data.ecco
131      (new namelist ecco_cost_nml)
132    o in ctrl/ cleaned some cross-dependencies and updated CPP options
133    
134    checkpoint51t_post
135    o this is the pre-merge tag of the ecco-branch
136    
137    checkpoint51s_post
138    o cleanup: removed various obsolete #define-s
139    o pkg/grdchk
140      - renamed 'ph-grd 3' to 'grad-res'
141      - merged from ecco-branch
142        (remaining bug fixes for obcs gradient checks)
143      - additional high-precision output for testreport
144        (grep for 'precision_grdchk_result')
145    
146    checkpoint51r_post
147    o cleaned up or removed CPP_OPTIONS.h files
148    o updated results for some of the tests to reflect the new
149      optfiles (-ieee: -O0 instead of -O3)
150    
151    checkpoint51q_post
152    o cd_code:
153      - moved cd_scheme.F -> cd_code_scheme.F
154      - separate read_checkpoint from cd_code_ini_vars.F
155      - separated cd_code part from write_checkpoint
156      - updated AD_SOURCE, generated .flow
157      - added CD_CODE_VARS.h to the_main_loop
158      - Moving cd_code specific store dir.s to pkg/cd_code
159    o ctrl package totally restructured
160      - pack/unpack now optional and decoupled from
161        xx_/adxx_ I/O
162      - ctrl_pack/unpack cleaned
163        (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
164      - confined inclusion of AD_CONFIG.h to where necessary.
165    o genmake2: changed AD dependencies from SRCFILES to AD_FILES
166    
167    checkpoint51p_post
168    o create initial cd_code package
169      - WARNING: the initialization of fields within packages
170        is broken because INI_FIELDS (where READ_CHECKPOINT is
171        called) is called *before* PACKAGES_INIT_VARIABLES.
172        This seems to be backwards since
173        1) its important to initially zero the entire field including
174           the "halo" region
175        2) zeroing needs to be done *before* reading pickup info
176           and the pickup call might or might not happen in any
177           particular run
178      - this needs an overhaul for R2
179    o cleanup verification/*/code/GMREDI_OPTIONS.h
180    o cleanup testreport
181    
182    checkpoint51o_post
183    o bringing AD-related verif's up to date with genmake2
184      - carbon/
185      - global_ocean.90x40x15/
186      - hs.94.1x64x5/
187      - (front_relax/ )
188    o (more) consistent directory structure for AD-related verif.'s
189    o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
190    o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
191    o bug fix in find_alpha.F for MDJWF:
192      - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
193        change rho -> rho-rhoConst
194      - replace call find_rho to find_rhonum
195    o initialisation of rFlx extended to full array (required by TAF)
196      and shifted to thermodynamics
197    o removed PTRACERS.h in ptracers routine
198    o added surfacetendencyPtr to S/R parameter list pracers_forcing
199    o Correcting initialisations for fVerU, fVerV.
200    o helping TAF to recognize dependency on kUp for
201      fVerU, fVerV
202    o Replacing delZ by delR in pkg/ctrl/
203    checkpoint51o_pre
204    
205    o undid all of cp51 pending some cleanups and discussion
206    o added the [#include "AD_CONFIG.h"] statement to all files that need
207       it for adjoint/tl #defines
208     o re-worked the build logic in genmake2 to support AD_CONFIG.h
209     o removed tools/genmake since it no longer works
210    
211    checkpoint51n_post
212    o modifications to make FREEZE flux visible to pkg/kpp
213      - moved surfaceTendencyTice from pkg/seaice to main code
214      - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
215      - subroutine FREEZE now limits only surface temperature
216        (this means new output.txt for global_ocean.90x40x15,
217         global_ocean.cs32x15, and global_with_exf)
218    o added surface flux output variables to TIMEAVE_STATVARS
219    
220    checkpoint51n_pre
221    o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
222    o added [#include "AD_CONFIG.h"] to all files that use the following
223      defines:
224      - ALLOW_ADJOINT_RUN
225      - ALLOW_TANGENTLINEAR_RUN
226      - ALLOW_ECCO_OPTIMIZATION
227    
228    checkpoint51m_post
229    o incorporating changes to get TAMC/TAF working in genmake2
230      - added new TAMC/TAF targets to the Makefile
231      - various cleanups related to package handling
232      - these changes should have no impact on the forward model
233    
234    checkpoint51l_post
235    o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
236     - faster algorithm for cal_addtime.F
237     - higher precision arithmetic, where needed
238     - pkg/exf *startdate variables changed from calendar date to
239       model integration time
240    
241    checkpoint51l_pre
242    o add salt flux to forcing fields (used when salty sea-ice forms or melts)
243    o enable to apply restoring on S & T only in a latitude band.
244    o update output (external_forcing_surf modif. change truncation errors)
245       global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
246    
247    checkpoint51k_post
248    o change default to: useNHMTerms=.FALSE.
249     - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
250       adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
251     - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
252        exp1, ideal_2D_oce
253     - change data file of oceanic exp (leave the results unchanged for now)
254       exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
255    o set gravitySign automatically according to the vertical coordinate used
256      (and change sign: back to "logical" value: +1 when R increases downward)
257    o added an include barrier to the default CPP_OPTIONS.h and
258      removed the #include "PACKAGES_CONFIG.h" from it
259    o fix a bug in mom_fluxform (from chk51j_post)
260    
261    checkpoint51j_post
262    o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
263    o adjusted some flow directives (dynamics, thermodynamics)
264    o added cubed-sphere case to test cost function
265    o heckpoint_lev?_directives.h now include
266      pkg-specific directives, whenever those are enabled.
267    o Moving pkg-specific flow directives to corresponding pkg
268      Moving pkg-specific differentiation list to corresponding pkg
269      Moving pkg-specific checkpoint-lev storing to corresponding pkg
270      ---> conventions are
271           - pkg_ad.flow
272           - pkg_ad_diff.list
273           - pkg_ad_check_lev?_dir.h
274    
275    checkpoint51i_post
276    o merge of the branch-genmake2
277      - knowingly breaks the older genmake
278      - automatic generation of all ALLOW_${PKG_NAME} defines
279      - new testreport supersedes older testscript
280    o large number of package inclusion and header cleanups
281    checkpoint51i_pre
282    
283    o new output for adjoin of global ocean vector invariant
284    o fix for checkpoint of thermodynamic seaice and bulk_force
285    o Steph gchem various cleanups
286    
287    checkpoint 51h_pre
288    o fixed some single quotes
289    o modify gchem pkg to be more versatile
290    o modifications to clean up dic pkg
291    o add pkg/cfc
292    
293    checkpoint51g_post
294    o provide links for ARPACK and ADM*TLM
295    o start removing verification/vero/
296    o update AD-related stuff
297      (in particular some IF-statements in model/src/ routines)
298    o adding to verification/global_ocean.90x40x15/ adjoint of
299      vector invariant setup
300    
301    checkpoint51f_post
302    o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
303    o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
304      of tracer Green's fucntions for ocean inversion project.
305    
306    checkpoint51f_pre
307    o Added on-the-fly spatial interpolation capability
308        "USE_EXF_INTERPOLATION" to pkg/exf.
309      - This is a temporary Cartesian-grid hack until
310        the super-duper ESMF coupler becomes available.
311      - See verification/global_with_exf/README for usage example.
312      - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
313        flags and modified pkg/seaice accordingly.
314    o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
315        and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
316        non-local transport term.
317    
318    checkpoint51e_post
319    o pkg/mom_vecinv:
320      - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
321      - add time-ave diagnostic of vorticity advection.
322    o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
323    o atmospheric geopotential: - include water vapor effect;
324                                - use p^kappa in p* scaling.
325    o land pkg: read initial state from files.
326    o AIM : add stratospheric drag in the upper level
327    
328    checkpoint51d_post
329    o change function ILNBLNK (=> last non-blank char.) to return zero
330      (instead of the string length) when the string. char is empty
331    o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
332    o modif's to restore TAMC compatibility
333      - avoid "_d" constructs in PARAMETER declarations
334      - avoid interrupting lines by comment lines
335    o Use cluster local disks for purely local I/O
336      vs. globally visible disks needed for ctrl stuff
337      (merged from ecco-branch)
338      - new active_file_loc... and mdsio_..._loc routines
339      - affected packages: autodiff, ctrl, grdchk, mdsio
340    
341    checkpoint51c_post
342    o introducing integer flag debugLevel
343      - debLevZero: suppress all output
344      - debLevA: standard
345      - debLevB: equivalent to current debugMode=.TRUE.
346    o introducing pathname variable mdsioLocalDir for mdsio
347      that can be specified at runtime
348      (relevant for cluster I/O to local disk)
349    `
350    >>>checkpoint51b_post
351    adjoint of ptracers
352    o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
353    o extended state in checkpoint_lev?, etc.
354    o alternative ctrl/cost with tr1 or ptracer
355    o new comlev1_bibj_ptracers
356    o new ptracers.flow
357    o made ptracers_forcing same as external_forcing_s
358    o added verification for adjoint with ptracers
359      - adm. grdchk fail so far
360      - tlm. grdchk OK
361      - checked tapelev/comlev recomputations: OK
362    <<<checkpoint51b_pre
363    
364    checkpoint51a_post
365    o added code for biogeochemistry package
366      - new pkgs: dic, gchem
367      - new subroutine in ptracers
368    o modify code for biogeo packages
369      - in model/src and pkg/ptracers
370    
371    checkpoint51
372    o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
373      - autodiff, ctrl, exf, grdchk, seaice
374      kept separate packages
375      - cost, ecco, obcs
376    o updating verification/internal_wave, verification/lab_sea
377      (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
378    
379    checkpoint50i_post
380    o Preparing next differentiable checkpoint and sync
381      of MAIN vs. ecco-branch
382      - 1st step: this one is differentiable
383      - 2nd step: next(! not this) checkpoint will have updated packages
384                  from ecco-branch)
385    
386    checkpoint50h_post
387    o new package "land": provide surface BC for AIM.
388    o pkg/ptracers: apply exchange to all tracers after reading a pickup.
389    o AIM: use true log-P extrapolation for near surface temp (= as in
390        F.Molteni paper) ; update aim.5l_cs output.
391    o New variable in PARM03 for more flexible pickups
392    o somewhat cleaned package initialisation sequence for
393      ctrl/ cost/ ecco/ in packages_... routines
394    
395    checkpoint50g_post
396    o merged with release1_p17 (pkg/seaice and verification/lab_sea)
397      - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
398      - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
399        made the default because of faster convergence than ADI
400    
401    checkpoint50f_post
402    o exf totally restructured
403      - replaced all exf_set_ routines by one generic exf_set_gen.F
404        and made sure it's still differentiable
405      - split exf_getffields.F into new exf_bulkformulae.F
406      - exf_inscal_/exf_outscal_ suffixes consistent with field names
407      - updated adjoint/makefile and relevant verif. accordingly
408    
409    checkpoint50f_pre
410   o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;   o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
411        + change Evap over land. (update aim.5l_cs output)        + change Evap over land. (update aim.5l_cs output)
412   o added missing .cvsignores and made uniform across expts   o added missing .cvsignores and made uniform across expts

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