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revision 1.1214 by jmc, Tue Jan 12 00:23:23 2010 UTC revision 1.1300 by jmc, Thu Sep 23 22:53:26 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       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
9       code (seaice_budget_ice_if.F) which enable to recover old standard
10       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
11       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
12    o model/src (rStar):
13       use simple average (not area weighted) of rStarFac at U,V point when using
14       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
15       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
16    
17    checkpoint62k (2010/09/17)
18    o adjoint
19       * changed verification/global_ocean.cs32x15 ; adjoint now tests
20         Adams-Bashforth 3 + NLFS + RSTAR
21       * some more modifs required for ECCO-GODAE v4
22    o pkg/seaice
23       add SEAICE_AGE_VOL option to use volume instead of area for
24       integrating SEAICE_AGE
25    o model/src:
26       first check-in of sigma & hybrid-sigma coordinate code ; also includes
27       non-linear free-surface parts ; but pressure-gradient not yet coded.
28    o pkg/ptracers:
29       option for ptracer to convert Salt Relax into additional EmP.
30        tested in exp. global_ocean.90x40x15.dwnslp (update output)
31    
32    checkpoint62j (2010/08/25)
33    o pkg/ggl90:
34       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
35    o pkg/dic: car_flux.F, phos_flux.F
36      - reduce number of exp-calls in order to improve performance
37      - clean up a little (replace fields by their macros, etc., fix
38        typo in CPP-flag)
39    o pkg/ggl90: minor changes
40      - GGL90diffKrS was removed --> always use GGL90diffKr
41      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
42      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
43        (commented out for now)
44      - change in max/min operations to ensure that smoothing is ok
45      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
46      - always use diffKrNrT as background profile (i.e. never use diffKr field)
47    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
48    o pkg/dic:
49      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
50        vectorization
51      - small bug fix in insol for the unlikely case of a cartesian grid
52      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
53        + now vectorize, which also removes adjoint recomputations;
54        + replace integer maksp1 by _RL maskp1
55        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
56    
57    checkpoint62i (2010/07/21)
58    o pkg/flt:
59      - with OBCS: stop floats which enter the OB region
60    o model/src:
61      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
62        for implicit vertical advection.
63    o pkg/seaice:
64     - account for melting in seaice age evolution.
65     - remove double counting of seaice ridging effect on seaice age.
66    
67    checkpoint62h (2010/06/18)
68    o pkg/exch2:
69     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
70    o tools/genmake2
71      - remove "-pdefault" option: redundant with the use of "packages.conf";
72      - remove file pkg/pkg_default : set the default as a pkg group
73        ("default_pkg_list") defined in pkg/pkg_groups;
74      - fix for case pkg/pkg_depend is missing (was hanging before);
75      - add option "-pgroups" to specify a different pkg_groups than the default.
76    o verification/adjustment.cs-32x32x1:
77       add a "minimal" set-up test (code_min & input_min) which only compiles
78       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
79    o tools/genmake2
80      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
81      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
82    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
83      files are nearly the same anyway.
84      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
85       - redefinition of tau(i,i) (by a factor of ustar)
86       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
87       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
88       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
89       - replace
90         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
91         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
92         by
93         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
94         (changes results)
95       -> exf_bulkformulae v1.22,
96          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
97          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
98                    output.txt 1.63
99           offline_exf_seaice: output.seaicetd.txt 1.7
100           seaice_obcs: output.txt 1.10)
101      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
102       -> exf_bulkformulae v1.23,
103          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
104          and global_ocean.cs32x15.icedyn (only 11 matching digits)
105      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
106    o adjoint of exch-1:
107     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
108       (note: was already like this when using EXCH-2) and remove flow dir
109       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
110     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
111     - update pkg/exch2 diff list.
112    
113    checkpoint62g (2010/05/19)
114    o eesupp/src (exch-1):
115     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
116       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
117       (renamed to exch1_*rx_cube.F).
118     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
119       to call new exch1 S/R ; update Makefile and .cvsignore.
120     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
121       exch2_xy_rx later)
122      Note: after updating your code, need to run "make clean" in eesupp/src
123    o test experiment bottom_ctrl_5x5:
124       new output_adm.txt with fewer grdchk & less monitor output.
125    o model/src:
126      remove the call to ini_cori in initialise_varia.F (just keep the usual one
127       in initialise_fixed.F). More consistent with coriolis & horizontal grid
128       beeing treated in the same way (ini_grid is not called a 2nd time).
129    o pkg/exf:
130      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
131      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
132      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
133      - cosmetic changes to exf_bulkformulae.F to make it look more like
134        exf_bulk_largeyeager04.F
135    o eesupp/src (exch-1):
136      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
137      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
138        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
139        (even without using MPI).
140      - Message mode: move RecvAck setting (indicator of buffer being ready)
141        from send_put to recv_get S/R (was useless before, but not sure if
142        it's much more useful now);
143      - Switch the order of sync: MPI-proc 1rst and then threads;
144      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
145      - fix AD code for communication mode ='get' (but not used).
146    o model/src:
147      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
148      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
149    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
150    o pkg/ctrl: require a specific set of control variables and exf-flags for
151      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
152    o model/src:
153     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
154       1rst forward sweep, to avoid over-writing output files during recomputations
155       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
156     b) 2nd version:
157      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
158      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
159         writePickupAtEnd) + seaice & ptracers output;
160      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
161    o model/src:
162      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
163    o pkg/exch2:
164      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
165      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
166    o pkg/autodiff & exch2:
167      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
168      (for now, only if ALLOW_EXCH2 is defined).
169    o pkg/autodiff:
170      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
171        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
172       + clean-up comments (_RS is not always real*4)
173      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
174      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
175        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
176    o testreport (AD-tests):
177      no longer link files from dir "../input" (1rst link files from
178      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
179    
180    checkpoint62f (2010/04/29)
181    o model/src/the_main_loop.F:
182      adjust store directives for seaice evp and multicategory according to
183      pkg/ecco/the_main_loop.F
184    o adjoint:
185      global_sum_ad was incomplete (noted many times by many people ;)
186      nice description by Jean U. as follows:
187      * allreduce(var) in global_sum.F can be interpreted as
188        reduce(sum) followed by broadcast of sum.
189      * The adjoint of that is
190        sum(adjoint) followed by broadcast(summed adjoint value)
191        or in other words, allreduce(sum, adjoint vars)
192      We were missing the sum(adjoint)!
193      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
194      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
195      The fix should produce 16-digit accuracy between
196      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
197      multi-CPU single-tile (e.g. nSx=1, nPx-2)
198      We'll probably change this yet again shortly
199    o eesupp/src:
200      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
201    o pkg/icefront
202      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
203        specification of addmass array based on a 2D field, which is added
204        at bottommost wet level at each horizontal location.
205    o model/src:
206     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
207     layout; (not always compatible with delX,delY setting; commented out for now).
208    o pkg/exch2:
209     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
210     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
211    
212    checkpoint62e (2010/04/15)
213    o pkg/obcs:
214      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
215    o pkg/dic:
216      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
217        (note: not presently tested in any forward verification exp.)
218       update tutorial_global_oce_biogeo AD output file.
219    o pkg/exf:
220      - account for the variation of albedo as a function of zenith angle
221        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
222    o build_options:
223     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
224    o pkg/dic:
225      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
226      - use binary pickup file for restart;
227      - initialise atmos-CO2 box from dic_pCO2 parameter;
228      - fix multi-threaded.
229    o pkg/rbcs:
230     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
231       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
232     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
233       and update output.txt
234    o pkg/kpp:
235     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
236     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
237       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
238       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
239     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
240       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
241    o pkg/offline:
242      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
243      (bug was added in version 1.10 on 2007-08-23).
244    o pkg/offline:
245      - no need to specify periodicExternalForcing, etc ... to use offline pack
246      - offline input files no longer just single prec --> parameter offlineLoadPrec
247    o verification/lab_sea:
248      change AD test to multi-tile setup and update all 4 AD output.
249      NOTE: while cost function values remain very similar,
250      gradients are very different, although gradient checks are self-consistent
251      Should try to get to the bottom of this (cost function summation order?)
252    o pkg/dic:
253      in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
254      a weakness of TAF that drops part of double precision in log10 derivative.
255      <= changes removed since problem has been fixed in current TAF version 1.9.71
256      update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
257    o pkg/ecco:
258      add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
259      update all 4 lab_sea AD output.
260    
261    checkpoint62d (2010/03/22)
262    o build_options:
263      remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
264    o remove unbalanced quote (single or double) in commented line of source code
265      (may cause some warning with some preprocessor/makedepend versions).
266    o pkg/seaice:
267      fix seaice_model.F for adjoint (gael) and update AD results of experiments
268       lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
269    o testreport:
270      add option '-runonly' (short: '-ro') to just do the run part (without make).
271    o eesupp: remove JAM communication code (obsolete).
272    o add option to genmake2 & testreport to switch "_RS" type to "real*4"
273      (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
274      to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
275      (update also the output).
276    
277    checkpoint62c (2010/03/02)
278    o tools/build_options :
279       move (some) old optfiles from build_options/ to build_options/unsupported/
280    o model/src and pkg/exf
281       surface relaxation -- separating data and data.exf options
282       The point is to ensure that we specify the surface relaxation
283       either in data or in data.exf (but not half and half) and to
284       avoid an accidental relaxation to 0 (which happened if a time
285       scale was specified but the file name was left empty)
286    o model/src model/inc and pkg/mom_common
287       ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
288       => addition to the viscosity field as computed by others schemes
289    o tools/build_options:
290      - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
291        but keep the former optfile for few weeks for smooth transition
292    o pkg/ecco
293      - allow user defined cost function contributions
294            CPP: ALLOW_USERCOST_CONTRIBUTION
295            USAGE: compute contributions in cost_usercost_all.F
296      - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
297          the two options are complementary.
298    o pkg/smooth
299      - migration from contrib to the main repository
300    
301    checkpoint62b (2010/01/26)
302    o pkg/monitor:
303      - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
304        (in case someone forgot to update customized pieces of code)
305    o nonHydrostatic:
306      - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
307      - add a simple 2-D experiment (short_surf_wave) to test it.
308    o pkg/icefront:
309       adding the shell of, and the hooks to, a new package that
310       will model melting and freezing of vertical glacier ice fronts
311    o momentum:
312      add diagnostics of momentum tendency from Hydrostatic pressure gradient
313       (without surf.pressure term: would need a 2nd filling since implicit term).
314    o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
315      two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
316      cannot deal with the former
317    o cleaning:
318      - remove all (except OpenAD) old TLM output from results_ad dirs.
319      - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
320      - comment out maskH definition (replaced by maskInC)
321    o pkg/monitor:
322      - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
323        & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
324    
325    checkpoint62a (2010/01/15)
326    o model/src:
327      - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
328    o pkg/diagnostics:
329      - add optional level number diagnostics (i.e., level number to be define
330        explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
331      - strictly check for valid parser-code(10) ;
332      - check if adding diag to the list from the right place.
333    o pkg/longstep:
334      - change parameters and fix tracer conservation with rstar/nonlinear free surface
335    o diagnostics:
336     - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer
337       S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics.
338  o pkg/diagnostics:  o pkg/diagnostics:
339   - Add option for writing vertical integral (sum of selected levels) of an output   - Add option for writing vertical integral (sum of selected levels) of an output
340      field instead of writing output field levels. Activate this option on a per      field instead of writing output field levels. Activate this option on a per

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