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revision 1.1217 by jmc, Fri Jan 15 00:59:33 2010 UTC revision 1.1301 by jmc, Fri Sep 24 13:55:01 2010 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/seaice:
8       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
9    o pkg/seaice:
10       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
11       code (seaice_budget_ice_if.F) which enable to recover old standard
12       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
13       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
14    o model/src (rStar):
15       use simple average (not area weighted) of rStarFac at U,V point when using
16       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
17       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
18    
19    checkpoint62k (2010/09/17)
20    o adjoint
21       * changed verification/global_ocean.cs32x15 ; adjoint now tests
22         Adams-Bashforth 3 + NLFS + RSTAR
23       * some more modifs required for ECCO-GODAE v4
24    o pkg/seaice
25       add SEAICE_AGE_VOL option to use volume instead of area for
26       integrating SEAICE_AGE
27    o model/src:
28       first check-in of sigma & hybrid-sigma coordinate code ; also includes
29       non-linear free-surface parts ; but pressure-gradient not yet coded.
30    o pkg/ptracers:
31       option for ptracer to convert Salt Relax into additional EmP.
32        tested in exp. global_ocean.90x40x15.dwnslp (update output)
33    
34    checkpoint62j (2010/08/25)
35    o pkg/ggl90:
36       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
37    o pkg/dic: car_flux.F, phos_flux.F
38      - reduce number of exp-calls in order to improve performance
39      - clean up a little (replace fields by their macros, etc., fix
40        typo in CPP-flag)
41    o pkg/ggl90: minor changes
42      - GGL90diffKrS was removed --> always use GGL90diffKr
43      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
44      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
45        (commented out for now)
46      - change in max/min operations to ensure that smoothing is ok
47      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
48      - always use diffKrNrT as background profile (i.e. never use diffKr field)
49    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
50    o pkg/dic:
51      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
52        vectorization
53      - small bug fix in insol for the unlikely case of a cartesian grid
54      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
55        + now vectorize, which also removes adjoint recomputations;
56        + replace integer maksp1 by _RL maskp1
57        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
58    
59    checkpoint62i (2010/07/21)
60    o pkg/flt:
61      - with OBCS: stop floats which enter the OB region
62    o model/src:
63      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
64        for implicit vertical advection.
65    o pkg/seaice:
66     - account for melting in seaice age evolution.
67     - remove double counting of seaice ridging effect on seaice age.
68    
69    checkpoint62h (2010/06/18)
70    o pkg/exch2:
71     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
72    o tools/genmake2
73      - remove "-pdefault" option: redundant with the use of "packages.conf";
74      - remove file pkg/pkg_default : set the default as a pkg group
75        ("default_pkg_list") defined in pkg/pkg_groups;
76      - fix for case pkg/pkg_depend is missing (was hanging before);
77      - add option "-pgroups" to specify a different pkg_groups than the default.
78    o verification/adjustment.cs-32x32x1:
79       add a "minimal" set-up test (code_min & input_min) which only compiles
80       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
81    o tools/genmake2
82      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
83      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
84    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
85      files are nearly the same anyway.
86      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
87       - redefinition of tau(i,i) (by a factor of ustar)
88       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
89       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
90       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
91       - replace
92         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
93         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
94         by
95         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
96         (changes results)
97       -> exf_bulkformulae v1.22,
98          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
99          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
100                    output.txt 1.63
101           offline_exf_seaice: output.seaicetd.txt 1.7
102           seaice_obcs: output.txt 1.10)
103      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
104       -> exf_bulkformulae v1.23,
105          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
106          and global_ocean.cs32x15.icedyn (only 11 matching digits)
107      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
108    o adjoint of exch-1:
109     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
110       (note: was already like this when using EXCH-2) and remove flow dir
111       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
112     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
113     - update pkg/exch2 diff list.
114    
115    checkpoint62g (2010/05/19)
116    o eesupp/src (exch-1):
117     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
118       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
119       (renamed to exch1_*rx_cube.F).
120     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
121       to call new exch1 S/R ; update Makefile and .cvsignore.
122     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
123       exch2_xy_rx later)
124      Note: after updating your code, need to run "make clean" in eesupp/src
125    o test experiment bottom_ctrl_5x5:
126       new output_adm.txt with fewer grdchk & less monitor output.
127    o model/src:
128      remove the call to ini_cori in initialise_varia.F (just keep the usual one
129       in initialise_fixed.F). More consistent with coriolis & horizontal grid
130       beeing treated in the same way (ini_grid is not called a 2nd time).
131    o pkg/exf:
132      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
133      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
134      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
135      - cosmetic changes to exf_bulkformulae.F to make it look more like
136        exf_bulk_largeyeager04.F
137    o eesupp/src (exch-1):
138      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
139      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
140        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
141        (even without using MPI).
142      - Message mode: move RecvAck setting (indicator of buffer being ready)
143        from send_put to recv_get S/R (was useless before, but not sure if
144        it's much more useful now);
145      - Switch the order of sync: MPI-proc 1rst and then threads;
146      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
147      - fix AD code for communication mode ='get' (but not used).
148    o model/src:
149      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
150      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
151    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
152    o pkg/ctrl: require a specific set of control variables and exf-flags for
153      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
154    o model/src:
155     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
156       1rst forward sweep, to avoid over-writing output files during recomputations
157       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
158     b) 2nd version:
159      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
160      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
161         writePickupAtEnd) + seaice & ptracers output;
162      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
163    o model/src:
164      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
165    o pkg/exch2:
166      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
167      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
168    o pkg/autodiff & exch2:
169      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
170      (for now, only if ALLOW_EXCH2 is defined).
171    o pkg/autodiff:
172      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
173        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
174       + clean-up comments (_RS is not always real*4)
175      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
176      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
177        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
178    o testreport (AD-tests):
179      no longer link files from dir "../input" (1rst link files from
180      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
181    
182    checkpoint62f (2010/04/29)
183    o model/src/the_main_loop.F:
184      adjust store directives for seaice evp and multicategory according to
185      pkg/ecco/the_main_loop.F
186    o adjoint:
187      global_sum_ad was incomplete (noted many times by many people ;)
188      nice description by Jean U. as follows:
189      * allreduce(var) in global_sum.F can be interpreted as
190        reduce(sum) followed by broadcast of sum.
191      * The adjoint of that is
192        sum(adjoint) followed by broadcast(summed adjoint value)
193        or in other words, allreduce(sum, adjoint vars)
194      We were missing the sum(adjoint)!
195      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
196      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
197      The fix should produce 16-digit accuracy between
198      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
199      multi-CPU single-tile (e.g. nSx=1, nPx-2)
200      We'll probably change this yet again shortly
201    o eesupp/src:
202      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
203    o pkg/icefront
204      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
205        specification of addmass array based on a 2D field, which is added
206        at bottommost wet level at each horizontal location.
207    o model/src:
208     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
209     layout; (not always compatible with delX,delY setting; commented out for now).
210    o pkg/exch2:
211     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
212     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
213    
214    checkpoint62e (2010/04/15)
215    o pkg/obcs:
216      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
217    o pkg/dic:
218      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
219        (note: not presently tested in any forward verification exp.)
220       update tutorial_global_oce_biogeo AD output file.
221    o pkg/exf:
222      - account for the variation of albedo as a function of zenith angle
223        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
224    o build_options:
225     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
226    o pkg/dic:
227      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
228      - use binary pickup file for restart;
229      - initialise atmos-CO2 box from dic_pCO2 parameter;
230      - fix multi-threaded.
231    o pkg/rbcs:
232     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
233       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
234     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
235       and update output.txt
236    o pkg/kpp:
237     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
238     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
239       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
240       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
241     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
242       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
243    o pkg/offline:
244      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
245      (bug was added in version 1.10 on 2007-08-23).
246    o pkg/offline:
247      - no need to specify periodicExternalForcing, etc ... to use offline pack
248      - offline input files no longer just single prec --> parameter offlineLoadPrec
249    o verification/lab_sea:
250      change AD test to multi-tile setup and update all 4 AD output.
251      NOTE: while cost function values remain very similar,
252      gradients are very different, although gradient checks are self-consistent
253      Should try to get to the bottom of this (cost function summation order?)
254    o pkg/dic:
255      in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
256      a weakness of TAF that drops part of double precision in log10 derivative.
257      <= changes removed since problem has been fixed in current TAF version 1.9.71
258      update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
259    o pkg/ecco:
260      add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
261      update all 4 lab_sea AD output.
262    
263    checkpoint62d (2010/03/22)
264    o build_options:
265      remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
266    o remove unbalanced quote (single or double) in commented line of source code
267      (may cause some warning with some preprocessor/makedepend versions).
268    o pkg/seaice:
269      fix seaice_model.F for adjoint (gael) and update AD results of experiments
270       lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
271    o testreport:
272      add option '-runonly' (short: '-ro') to just do the run part (without make).
273    o eesupp: remove JAM communication code (obsolete).
274    o add option to genmake2 & testreport to switch "_RS" type to "real*4"
275      (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
276      to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
277      (update also the output).
278    
279    checkpoint62c (2010/03/02)
280    o tools/build_options :
281       move (some) old optfiles from build_options/ to build_options/unsupported/
282    o model/src and pkg/exf
283       surface relaxation -- separating data and data.exf options
284       The point is to ensure that we specify the surface relaxation
285       either in data or in data.exf (but not half and half) and to
286       avoid an accidental relaxation to 0 (which happened if a time
287       scale was specified but the file name was left empty)
288    o model/src model/inc and pkg/mom_common
289       ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
290       => addition to the viscosity field as computed by others schemes
291    o tools/build_options:
292      - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
293        but keep the former optfile for few weeks for smooth transition
294    o pkg/ecco
295      - allow user defined cost function contributions
296            CPP: ALLOW_USERCOST_CONTRIBUTION
297            USAGE: compute contributions in cost_usercost_all.F
298      - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
299          the two options are complementary.
300    o pkg/smooth
301      - migration from contrib to the main repository
302    
303    checkpoint62b (2010/01/26)
304    o pkg/monitor:
305      - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
306        (in case someone forgot to update customized pieces of code)
307    o nonHydrostatic:
308      - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
309      - add a simple 2-D experiment (short_surf_wave) to test it.
310    o pkg/icefront:
311       adding the shell of, and the hooks to, a new package that
312       will model melting and freezing of vertical glacier ice fronts
313    o momentum:
314      add diagnostics of momentum tendency from Hydrostatic pressure gradient
315       (without surf.pressure term: would need a 2nd filling since implicit term).
316    o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
317      two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
318      cannot deal with the former
319    o cleaning:
320      - remove all (except OpenAD) old TLM output from results_ad dirs.
321      - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
322      - comment out maskH definition (replaced by maskInC)
323    o pkg/monitor:
324      - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
325        & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
326    
327    checkpoint62a (2010/01/15)
328    o model/src:
329      - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
330  o pkg/diagnostics:  o pkg/diagnostics:
331    - add optional level number diagnostics (i.e., level number to be define    - add optional level number diagnostics (i.e., level number to be define
332      explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".      explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".

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