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revision 1.50 by adcroft, Thu Sep 27 14:24:19 2001 UTC revision 1.53.4.49 by heimbach, Tue Jun 24 18:39:58 2003 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    ecco_c50_e33a
7    o first step in c51 merge
8      - redundant update in model/src/
9      - merge back's in autodiff, ctrl, kpp, seaice
10    
11    ecco_c50_e33
12    o minor changes to pkg/seaice pkg/cost/cost_ice.F
13      and verification/natl_box_adjoint/README
14    o Modif's to enable tangent linear run in ECCO environment
15      including time-dependent forcing
16      * main problem is missing call mdsreadfield out of exf_set_gen
17        (i.e. computation of trajectory in TLM mode)
18      * incorrect g_active_write_...
19      * (re-) init of bar files and g_bar files
20    o Reverted back to 3-dim. tbar, sbar for SST, SSS bar files.
21    o MERGES:
22      * obcs/ ctrl/ G. Gebbie code
23        (major changes in ctrl handling, volume flux balancing etc.)
24      * cost/ ctrl/ A. Koehl code
25        - new cost contributions (new data types)
26        - efficient pack/unpack for time-dependent 2-d fields
27    o replaced mutiple ctrl_get... by single generic ctrl_get_gen.F
28      (except obcs)
29    o somewhat cleaned package initialisation sequence for
30      ctrl/ cost/ ecco/
31    o extended grdchk to enable obcs gradient checks
32    o some generalizations for easier TLM <-> ADM switches
33    o added configuration example for parallel divided adjoint
34      (see verification/natl_box_adjoint/code_diva_mpi/README )
35    o started verification exp. for obcs control
36      (still needs checking)
37    
38    ecco_c50_e32
39    o Patrick's adjoint-model storage directives for pkg/seaice
40    o merged with checkpoint50g_post (pkg/seaice and verification/lab_sea)
41      - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
42      - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
43        made the default because of faster convergence than ADI
44    o Modifications for adjoint of SEAICE_ALLOW_DYNAMICS
45      - extended state in checkpoint_lev...
46      - in lsr.F, replaced GO TO by fixed loop index (also avoid DO WHILE)
47      - YEAH: in lsr.F, (first) successful use of CADJ LOOP = ITERATION
48      - avoid stoing in S/R budget for now
49      - in dynsolver.F, avoid NPSEUDO loop for adjoint
50      - new comlev1_lsr in the_main_loop
51    o Small modif's in lsopt/, optim/ to ease compilation
52      New script to run optim (lsopt)
53    
54    ecco_c50_e31
55    o exf totally restructured
56      - replaced all exf_set_ routines by one generic exf_set_gen.F
57        and made sure it's still differentiable
58      - split exf_getffields.F into new exf_bulkformulae.F
59      - exf_inscal_/exf_outscal_ suffixes consistent with field names
60    o New cost function: Tini-Tfin to do model spinup optimization.
61    o Started new verification exp for Tini-Tfin optimization.
62    
63    ecco_c50_e30
64    o corrected CPP option mismatch in exf_Bulk... functions for case
65      #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
66    o Merging from release1_p13 and from icebear5
67      - bug fix for pkg/seaice dynamic solver
68      - Added SEAICE_initialHEFF to pkg/seaice
69      - Additional options for pkg/cost/cost_ice.F
70      - Updates to verification/natl_box_adjoint
71      - pkg/ctrl/ctrl_init.F
72        Fix for determination of startrec and endrec.
73      - pkg/cal/cal_toseconds.F
74        Fix for negative intervals shorter than 1 day.
75    
76    ecco_c50_e29
77    Bug fix for merging between c50 and KPP.
78    ikey was passed from thermodynamics to kpp_calc via
79    common block rather than being recomputed in kpp_calc,
80    in contradiction with new key itdkey.
81    New key ikppkey created, and tamc.h headers updated.
82    
83    ecco_c50_e28
84    o major merge:
85      ecco-branch merged with checkpoint50
86      gmredi now available, grdchk, DIVA up-to-date for MPI
87      However, two outstanding problems:
88      - kpp adjoint is broken, needs fixing!
89      - a few minor modif's in handling of CPP option
90        ALLOW_TANGENTLINEAR_RUN in conjunction with
91        ALLOW_ECCO_OPTIMIZATION are necessary to enable
92        TLM runs with ECCO setup
93    
94    ecco_c44_e27
95    o exf:
96      - Enable initialisation of forcing fields to constant
97        (runtime) values.
98      - in exf_getffields.F
99        Reduce i-/j-loop to interior domain, discarding overlaps.
100        That also fixes wrong TAF-key computations for key_1, key_2
101        with bulf formulae.
102      - exf_init.F modify #ifdef for exf_init_evap
103      - exf_getffieldrec.F, ctrl_getrec.F
104        The following INT-usages are not safe:
105          fldsecs  = int(fldsecs/fldperiod)*fldperiod
106          fldcount = int(fldsecs/fldperiod) + 1
107        and were modified.
108      - added repeatPeriod (from MAIN branch)
109    o grdchk: updated and merged
110      - has both ADM and TLM checks
111      - works for single- and multi-proc.
112      - output cleaned
113      - worked successfully for parallel DIVA
114      Needed one update in EEPARAMS.h and updates in ctrl package
115      More modif's may be necessary for ECCO code to support TLM.
116    o autodiff: checkpoint_lev...
117      - updated storing for bulk formulae (some arrays were missing)
118      - added state for seaice package
119      - synchronized with main branch
120    o DIVA:
121      Modif.s in
122      - cost_init.F
123      - cost_averagesfields.F
124      - ecco_the_main_loop.F
125      - ecco_the_model_main.F
126      and added cost_final_restore.F cost_final_store.F
127      o With these changes, it is possible to fully separate
128        the first forward run to compute the cost function (mdthe_main_loop)
129        and adjoint runs over individual DIVA intervals (adthe_main_loop)
130        into separate model executions.
131        This enables better tuning of DIVA to given queue sizes.
132      o Loss of cost function value in consecutive DIVA runs is
133        fixed by storing to 'costfinal' file.
134      o Appropriate call of ctrl_unpack/_pack,grdchk_main at
135        beginning/end of adjoint integration is accounted for.
136      The current changes apply to TAF-1.4.26.
137      TAF has one remaining bug, requiring one manual change
138      (see MITgcm manual).
139    o bug fix plus modif for ubar, vbar in cost_averagesfields
140    o cal: synchronized between MAIN and ecco-branch
141    
142    icebear4
143    o Added cost_ice for sea-ice volume sensitivity experiment.
144    o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
145    o Reduced derivative singularities in pkg/seaice.
146    o Updated verification/natl_box_adjoint
147    
148    icebear3
149    o Removed spurious iikey and idkey
150    o pkg/exf
151      - bug fix in treatment of downward radiation
152    o pkg/seaice
153      - added initial sea-ice thickness parameter SEAICE_initialHEFF
154    o updated verification/natl_box_adjoint
155    
156    icebear2
157    o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
158      kpp_transport_t.F,and ecco_the_main_loop.F
159    o adjoint-friendly modifications to pkg/seaice
160    o added verification/lab_sea as per release1_p12_pre
161    
162    ecco_c44_e26
163    o Merging pkg/exf and pkg/seaice from cvs tag ecco_ice2
164    o exf: Modifications to correctly handle evap field for adjoint
165    o grdchk:
166      Added code to perform gradient checks for bulk formulae/atmos. state
167      (atemp, aqh, uwind, vwind).
168      NOTE:
169      This package is out of synch with c48 package.
170      The latter also has the tangent linear gradient checks.
171      Need to be merged.
172    o verification/natl_box_adjoint:
173      * added new setup: code_bulk/, input_bulk, results_bulk
174        (Experiment 2, described in README)
175        uses bulk formulae and atmos. state as control instead of
176        air-sea fluxes.
177        Performs gradient checks for first 4 elements of atemp control.
178      * changed standard verification to perform
179        gradient checks on first 4 elements on hflux control.
180      * gmredi switched off (will come after merge with c48).
181    
182    ecco_c44_e25
183    o Merging some GM changes from main trunk (c47) to ecco-branch.
184    o Updating verif. natl_box_adjoint with GMRedi.
185    o Adding setup with explicit differentiaton of pressure solver.
186    o Bug fix: missing OBCS_OPTIONS.h for sponge layer code.
187    o (Re-?) Commiting old bug fixes in kpp to ecco-branch
188      (kpp_calc.F, kpp_routines.F)
189    o exf:
190      updated external forcing package
191      - cleaned old exfa stuff
192      - bug fixes
193        (missing OBCS_OPTIONS.h in two routines)
194      - enable easy to use "no forcing".
195      - added exf I/O for atmospheric loading
196      - added exf I/O for runoff data
197      - transfered scaling between exf <-> MITgcm to exf namelist
198    
199    ecco_c44_e24
200    o modifications to gradient check package (Martin Losch)
201      - enable centered differences
202      - modified format of standard output
203    o bug fix for nwettile contents
204      so far assumed global sum  in first entry (1,1,k),
205      needed for global control vector
206      -> introduced new variable nwet[c/w/s]global(nr)
207    o shifts of calls to cal/exf package to be accessible
208      in MITgcm stand-alone
209    o shifted packages_init_variables before convective_adjustment_ini
210      (corresponding update of TAF tape initialisation).
211    o removed auxiliary field in impldiff
212      (caused numerical differences for GMRedi cases)
213    o updated obcs control part (G. Gebbie)
214    o removed some f90 comments ("!")
215    o Bug fixes and updates in cost package
216     * cost_final: correct multiplier mult_tauv, mult_sflux
217     * cost_hyd: added call cost_ssh
218     * cost_init_barfiles.F: replaced arrays by tmpfld's
219     * cost_readtopexmean.F: ersmask -> tpmeanmask
220     * cost_weights.F: corrected wtheta[2], wsalt[2]
221    o cleaned exchanges in cg2d.F
222    
223    ecco_c44_e23
224    merged patches between release1_p1 and release1_p2:
225    o fixed array boundary problem for adjoint
226      (related to partial recomputation within subroutine
227      related to dynamics -> calc_viscosity -> mom_...
228    o fixed recomputation in thermodynamics
229    o prepare (but not complete) recomputation problem in impldiff
230    o fixed problem for adjoint of global_max
231    o switched off sponge layer code in external_forcing
232    Bug fix in ctrl_mask_set_yz (spotted by G. Gebbie)
233    
234    ecco_c44_e22
235    o Finally, the merges with the Scripps cost function terms:
236      Various additions, modifications, quality checks.
237    o Plus: Included switch ALLOW_AUTODIFF_MONITOR to handle
238      monitoring of adjoint state.
239    o Plus: removed comm_stats, ini_communication_patterns from diff. list
240      (no more need to "keep" MPI headers for adjoint generation)
241    o Plus: exf changes:
242      o added run-off routine
243      o additional storing needed for ustress,vstess
244        because of state-dependent quality check
245      o added missing initialisations
246    o Plus: genmake with MAKEDEPEND variable was still missing in ecco-branch
247    NB: - verification/natl_box_adjoint/ 240 steps run
248          * looks ok under Linux (twain.lcs.mit.edu)
249          * looks ok on MIT SUN's (fjord.mit.edu)
250          * NaN in reverse mode on Scripps SUN's at iter=214
251          * NaN in reverse mode on IBM SP3 (BlueHorizon) at iter=204
252        - 1 year forward int. global 2x2 deg. produces similar cost functions
253          * all cost terms of new code are slightly smaller (0.5 to 3%).
254    
255    ecco_c44_e21
256    o reversed order of ctrl/cost initialisation
257    o gmredi_slope_psi.F: Inconsistent types in MIN/MAX expressions
258    o modified to enable ctrl field swapping
259    o bug fix for global sum of ncvarlength in ctrl_init
260    o no more call to ctrl_unpack from ctrl_init
261    o no more write of ctrl vector in ctrl_pack
262      however, init. of control vector from ctrl_unpack
263    o various bug fixes & consistent nobcs handling in
264      ctrl_pack/unpack routines (by G. Gebbie)
265    o optim package: Added obcs control part for lsopt I/O
266      (by G. Gebbie)
267    o missing call to obcs_diags
268    o moved calls in packages_init_fixed to packages_readparms
269      because some quantities are needed earlier.
270    
271    ecco_c44_e20
272    o before major merges from the Scripps setup
273      here are two small updates:
274      - field swapping for surface flux controls enabled
275        (remains t.b.d. for atmos. state plus obcs)
276      - bug fix in active_file.F for xz-/yz- routines
277      - added missing xz-/yz- routines to active_file_ad.F
278    
279    ecco_c44_e19
280    o merged necessary patches:
281      - AD-related changes for GMRedi
282      - fixes i KPP (delZ -> drF)
283      - hook to OBCS songe layer code in external_forcing
284      - errorMessageUnit non-zero in eeboot.F
285      - included GMREDI, EXACT_CONSERV to natl_box_adjoint verif.
286    
287    ecco_c44_e18
288    o sponge layer code for obcs was missing
289      - added hook in external_forcing.F
290      - added storing for TAF
291    o new routine cost_init_barfiles to initialise
292      adjoint fields adtbar, adsbar, adpsbar
293      (needed in conjunction with corrected ladinit for active I/O)
294    o cleaned up and corrected order in packages_readparms, ecco_readparms
295    o corrected and simplified weights for obcs controls
296      - weight fields simplified
297      - bug fix in ctrl_pack
298      - no more write of control vector in ctrl_pack
299    o i/j index bug fixes in cost_ssh_mean
300    
301    ecco_c44_e17
302    o bug fixes in cost package
303      * wrong identifier for active I/O of monthly mean psbar
304        (cost_averagesfields, cost_ssh) xx_psbar_dummy
305      * cleaned all identifier for active I/O of monthly fields
306      * wrong ladinit in various cost routines
307    o merge with interval (chkpt44c_post - chkpt44d_post)
308      * added missing EXCLUDE_MONITOR flags
309      * changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
310        (incompatible typ in MIN/MAX expressions caused problems
311        on IBM SP3)
312      * in genmake added variable MAKEDEPEND
313        plus resetting for case SunOS
314        added timer_stats.c routine for IBM SP3
315      * removed variables in dynamics
316    
317    ecco_c44_e16
318    o new ECCO checkpoint, the first since ecco_c43_e15
319      which is branched from MITgcm.
320      All changes were merged in between (see ecco-branch-mod? tags).
321    o last changes:
322      * assuming path for TAF and TAMC are known (e.g. in $path)
323      * genmake:
324        - added tools/xmakedepend to circumvene shortcoming of
325          SUN's makedepend (size too small)
326        - invoking ../tools/xmakedepend instead of makedepend
327        - changed compiler flags for case SunOS
328    
329    ecco-branch-mod5
330    o mod's to reproduce open boundary run
331    o enable field swapping for OB's and climatology
332    o update store directives for OB control
333    o added option ALLOW_OBCS_PRESCRIBE
334    o call of getobcs now out of obcs_calc (param. list modified)
335    
336    ecco-branch-mod4
337    o this is the second part of changes necessary to reconcile
338      the natl_box_adjoint verification (with and without grdchk).
339      >>>!!! CHANGES BETWEEN THE TAGS ecco-branch-mod3 !!!<<<
340      >>>!!!                      AND ecco-branch-mod4 !!!<<<
341      >>>!!! SHOULD BE MERGED INTO THE MAIN TRUNK      !!!<<<
342      - genmake: removed $S64 overwrite for case SunOS
343      - pkg/exf: update and corrections for field swapping and obcs
344      - pkg/ecco: parameter lists for the_model_main, the_main_loop
345                  harmonized between ECCO and MITgcm
346      - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
347                      updated checkpointing_lev... lists for obcs
348      - model/src: minor changes in forward_step, plot_field
349      - pkg/mdsio: added mdsio_gl_slice
350    
351    ecco-branch-mod3
352    o this is the first part of changes necessary to reconcile
353      natl_box_adjoint verification (with and without grdchk).
354      This set of changes is relevant for ECCO only.
355      The next set/tag of changes (ecco-branch-mod4)
356      should be merged into the main trunk.
357      - update some options
358      - parameter lists of ecco_the_model_main and ecco_the_main_loop
359        differed from those of the MITgcm counterparts.
360    
361    ecco-branch-mod2
362    o update ecco-branch-mod1 to checkpoint44
363    o exclude from updates:
364      - verification/
365      - adjoint/
366      - pkg/cost
367      - pkg/ctrl
368      - pkg/ecco
369      - pkg/obcs
370      - model/src/the_model_main.F
371      - model/src/the_main_loop.F
372    
373    checkpoint44
374    o apply Shapiro filter on T&S before calc_PhiHyd (stagger time stepping)
375    o fix bug in mom_vi_del2uv
376    o added some stuff for AD
377    
378    ecco-branch-mod1
379    o based on c43
380    o replaced packages cost, ctrl, ecco, obcs
381    o removed MITgcm verif.'s, added ECCO verif.'s
382    o added lsopt, optim for line search optimization.
383    
384    checkpoint43
385    o added two new advection tests
386    o added global 4x4 degree ocean test
387    o added test of H&S94 with free surface on cube
388    o some final mods for gradient check, adjoint,...
389    
390    checkpoint42
391      Fixed AD-related problems:
392    o Store directives up-to-date with re-arranged Adams-Bashforth
393      (mainly thermodynamics.F)
394    o New store directives for multi-dim. advection schemes
395      * new CPP flag ALLOW_MULTI_DIM_ADVECTION
396      * new common block and key passkey
397      (mainly gad_advection.F)
398    o Modified store directives for split of dynamics/thermodynamics
399      for the case ALLOW_KPP
400    o Cleaned argument list for timestep_tracer.F
401    
402    checkpoint41
403    o re-formatted/added comments in prologues of key subroutines
404      to work with protex
405    
406  checkpoint40  checkpoint40
407  o moved calc_gs, calc_gt and calc_tr1 back to model/src  o moved calc_gs, calc_gt and calc_tr1 back to model/src
408  o added FLT (floats) package from Arne along with demo. experiment  o added FLT (floats) package from Arne along with demo. experiment

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