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revision 1.1315 by heimbach, Sat Oct 16 19:33:41 2010 UTC revision 1.1538 by mlosch, Tue Nov 29 17:43:32 2011 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/obcs/obcs_calc_stevens.F:
8      - join some loops to reduce number of if-statements
9      - fix a bug in code for northern and southern boundaries.
10    o pkg/seaice/seaice_init_varia.F
11      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
12        caused zero ice-velocities for the B-grid code
13    o pkg/seaice/seaice_init_fixed.F
14      - fix a bug in the initialisation of the second metric terms
15        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
16      - this affects all seaice configurations with useCurviLinearGrid = .true.
17        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
18        = .true. (default)
19      - the only verification experiment affected is global_ocean.cs32x15:
20        icedyn, seaice, and seaice_dynmix (AD)
21    o pkg/thsice/thsice_diagnostics_state.F
22      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
23        not contain garbage that can lead to surprises in diagstats_calc.F
24    o model/src:
25      - move bi,bj loops inside INTEGR_CONTINUITY ;
26      - call INTEGR_CONTINUITY directly from forward_step.F
27        (previously called from momentum_correction_step.F)
28      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
29        forward_step.F and pkg/ecco/the_main_loop.F
30    o model/src/do_oceanic_phys.F:
31      - reset addMass to zero only if useICEFRONT ;
32      - separated k-loop for rhoInSitu calculation ;
33      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
34        and at constant T,S (= WdRHOdP);
35      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
36        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
37        transport of locally-referenced potential density);
38        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
39    o gluemnc:
40      - replace ncrcat with ncks when adding variables to *.glob.nc
41      - change the way variables without record dimensions are handled so that
42        files that have variables with and without record variables can be glued:
43        add a record dimension with a new unique name to be able to differentiate
44        between variable with and without a-prior record dimensions. Remove
45        this record dimension before adding the variable to the *.glob.nc file.
46        This procedure automatically works also for grid.*.nc files that do not
47        have any record dimension.
48    o verification/cpl_aim+ocn:
49      - generate new reference output on baudelaire (gfortran, mpich2) (previously
50        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
51    o pkg/obcs/obcs_calc_stevens.F:
52      - add code for northern and southern boundaries.
53      - reorder some loops to save some operations and so that drFBar can be scalar
54    o model/src:
55      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
56        truncation) and add diagnostics for Adams-Bashforth tendency increment.
57      - update test-exp. AD output:
58        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
59      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
60        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
61        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
62        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
63        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
64        tutorial_plume_on_slope.
65    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
66      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
67      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
68      does not even come with an F77 compiler anymore, this should not be
69      a limitation
70    
71    checkpoint63e (2011/11/06)
72    o pkg/seaice adjoint of LSR:
73      - substantially rework STORE dirs.
74      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
75        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
76        and only perform SOLV_MAX_FIXED adjoint iters.
77        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
78        always goes to same record, meaning that the last forward field will be
79        the one used in the adjoint - an approximation.
80      - now produces non-zero LSR-related gradients, and acceptable gradients for
81        An's zonal (x-z) test case (to be checked in)
82      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
83        (but these are screwed up by the thermodynamics in the first place);
84        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
85        output_adm.txt also reflects changes to seaice_lsr
86      - global_ocean.cs32x15:
87        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
88          (output_adm.seaice.txt was updated)
89        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
90          (output_adm.seaice_dynmix.txt)
91    o test-exp. exp4+stevens:
92      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
93    o pkg/seaice (lsr solver):
94      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
95        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
96      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
97      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
98        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
99      - compute (with new S/R) and print initial (+ free-driff sol. if available)
100        and final residual of linearised system.
101    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
102      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
103    o pkg/obcs: Stevens BCs (still only for east and west)
104      - fix Stevens BCs by using intermediate velocities of previous
105        time step as "baroclinic" contribution rather velocity of one grid cell
106        inside the boundaries; more consistent but makes the entire treatment
107        more complicated, requires new pickup files and two new S/Rs:
108        obcs_copy_uv_n and obcs_save_uv_n
109        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
110        (undefined by default)
111      - silently move computation of some grid factors into separate loops to
112        save some recomputations
113      - add a hack for non-linear free surface
114      - add a verification experiment to exp4 that tests this code
115    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
116    
117    checkpoint63d (2011/10/25)
118    o pkg/obcs + seaice-dynamics:
119      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
120        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
121        values (consistent with an implicit method).
122      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
123        return to older implementation (same results as before); note that none of
124        the "experimental" OBCS_SEAICE options are implemented in the new version.
125      - switch test exp. seaice_obcs to use new version (update output).
126    o pkg/seaice:
127      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
128      - add parenthesis in Water-Ice drag calculations (evp & lsr);
129      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
130        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
131      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
132        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
133    o pkg/layers:
134      - Include potential density as new coordinate (Thanks to David Munday)
135    o pkg/dic:
136      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
137        carbonate computation/output to CALC_PCO2_APPROX
138    o pkg/generic_advdiff
139      - make TAF generate code that vectorizes:
140        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
141    o model/src:
142      - improve vectorization also for adjoint code of
143        solve_tridiagonal and solve_pentadiagonal. As this requires up to
144        5 new 3D-fields, this code is only turned on for the combination of
145        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
146        for singular matrix check (only for TARGET_NEC_SX).
147      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
148        ALLOW_AUTODIFF. This flag now needs to be set outside of
149        solve_tri/pentadiagonal.F
150    o pkg/exf:
151      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
152        optional namelist EXF_NML_OBCS).
153      - add many debug-print (to trace down where pkg/cal error msg comes from)
154    o pkg/mom_vecinv/mom_vi_hdissip.F
155      - rearrange loops so that vectorization is improved and in particular
156        the adjoint routine vectorizes. The code is a little longer now, but I
157        think easier to read.
158        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
159    o pkg/seaice:
160      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
161    o pkg/exch2:
162      - alternative code (without tile x tile matrix) for cumulated (global) sum;
163        used as default; keep using matrix version in adjustment.cs-32x32x1.
164    o tools/build_options:
165      - after merging some MPI and/or multi-threads specific optfiles so that
166        the modified default optfile support both built (using genmake2 -mpi
167        for the MPI built, using genmake2 -omp for OpenMP built),
168        move now obsolete optfiles to tools/build_options/unsupported/
169       (add copy of email sent to support list in doc/optfiles_changes.txt)
170    
171    checkpoint63c (2011/09/28)
172    o pkg/ebm:
173      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
174        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
175    o pkg/seaice (SItracer pickup)
176    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
177      To be done:
178      - thorough testing of missing fields in S/R seaice_read_pickup
179      - thorough matching between generic tracers and specific fields used
180        (e.g. volume-weighted age, area-weighted age, salinity, ...)
181    o pkg/grdchk:
182      - all procs calculate and print finite-difference gradient (for testreport)
183      - change description output used by testreport;
184      - AD testing: also compare and report Finite-difference gradient;
185        => update all output_adm*.txt
186    o test exp. global_ocean_ebm:
187      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
188        and turn on exactConserve; update (fwd) output.
189    o pkg/seaice (LSR):
190      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
191      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
192        * identical results with non-CS topology (but save up to half of EXCH calls)
193        * no much changes in cs-32 verification tests since no ice at face edges
194         (differences due to convergence criteria, since nb of iterations changed)
195        * expect some differences on lat-lon-cap grid.
196        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
197    o pkg/exch2:
198      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
199        many tiles); until alternative coding is added, just add a stop.
200    o pkg/kpp:
201      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
202        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
203    o optfiles:
204      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
205        into corresponding standard one, which now support different build:
206        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
207      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
208    o pkg/obcs (seaice):
209      - add missing EXCH for uIce,vIce after applying OBCS;
210      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
211        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
212        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
213      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
214      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
215        and eedata.mth for MPI and mutlti-threaded testing.
216    o pkg/flt:
217      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
218      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
219      - fix pickup and trajectories + profiles output with multi-threads;
220      - add parameter to select group of fields to write along trajectory and
221        profile (default unchanged);
222      - only call PORT_RAND* function when flt_noise <> 0;
223      - add multi-threaded test for verification exp. flt_example.
224    o eesupp/src:
225      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
226      - USE_OMP_THREADING: check that number of threads (from eedata) matches
227        actual number (from env.var. setting).
228    o pkg/ebm:
229      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
230      - add multi-threaded test for verification exp. global_ocean_ebm
231    
232    checkpoint63b (2011/08/29)
233    o pkg/ebm:
234      - fix sign of runoff;
235      - update directly forcing fields (Qnet,EmPmR) to use standard
236        external_forcing_surf.F (remove ebm_forcing_surf.F);
237      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
238      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
239        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
240      - update global_ocean_ebm parameters file data and update output (fwd+ad).
241    o verification/matrix_example:
242      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
243        MPI and mutlti-threaded testing.
244    o pkg/matrix:
245      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
246      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
247      - fix for multi-threaded (remove DATA statement);
248      - use standard DIFFERENT_MULTIPLE function;
249      - add MATRIX_OPTIONS.h
250    o verification/matrix_example:
251       To allow to split the domain in several tiles, change the domain size
252        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
253        Western side) of land points.
254    o (*_)write_pickup:
255      - fix few bugs in mypackage_read/write_pickup.F
256      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
257        array of length 1 (was caught by compiler syntax-check).
258    o pkg/diagnostics (velocity potential solver):
259      - fix initialisation of main diagonal matrix (for overlap values)
260    o tools/build_options:
261      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
262        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
263      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
264        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
265        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
266        and use "-devel" testreport option for standard testing on baudelaire.
267    o pkg/grdchk:
268      - Assume that all gradient-check position are within the same tile
269        corresponding to global indices (iGloTile,jGloTile) and that
270        positions (i,j indices or nbeg) are local to this tile;
271      - set tile local-indices and proc. number according to tile global-indices;
272      - remove grdchkwhichproc from namelist (retired param);
273      - send adjoint gradient to all procs so that all procs print it to STDOUT;
274      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
275    o adding package bbl (Bottom Boundary Layer)
276      description in MITgcm/pkg/bbl/bbl_description.tex
277      example/test experiment in MITgcm_contrib/bbl
278    o adjoint verifications
279      - changed 5 experiments to multi-tiles
280        * global_ocean.90x40x15
281        * obcs_ctrl
282        * offline_exf_seaice
283        * tutorial_dic_adjoffline
284        * tutorial_tracer_adjsens
285        changed reference output for those that crossed tile boundaries
286        (changed choices of gradient check positions)
287      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
288      - temporary bug fix in grdchk_loc.F for obcs
289    o genmake2 & testreport
290      - add target "obj" (just for OBJFILES files) to Makefile;
291      - add option to specify FEXTRAFLAGS on command line.
292    o pkg/mypackage:
293      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
294    
295    checkpoint63a (2011/08/02)
296    o pkg/diagnostics (velocity potential):
297      - fix velocity-potential calculation when using OBCS: balance net inflow
298        at each level (new S/R OBCS_DIAG_BALANCE).
299      - fix some of the problems with OBCS in stream-function calculation.
300    o pkg/exf/exf_readparms.F
301      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
302        EXF_NML_OBCS) more consistent, so that you need not have these lists
303        in data.exf when they are not used.
304    o optim/optim_readdata.F:
305      - add some output about obcs variables that might help debugging
306      - add a check about nvarlength
307    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
308    o pkg/diagnostics (velocity potential):
309      - fix mask for OBCS (still problems in stream-function with OBCS);
310      - add specific parameter (default = main code CG2D params) for solver;
311      - in case of poor convergence, use solution corresponding to lowest residual.
312    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
313      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
314      and should be avoided where possible.
315    o model/src (rStar):
316      - include r* effect on reference-state (PhiRef) in totPhiHyd
317        (so that it's really the potential anomaly at the cell center);
318        affect solution only if z* with full pressure in EOS.
319      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
320        update output (because of z* in totPhiHyd and viscA4 changes);
321      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
322        @ constant r) until interpolation at constant r is implemented.
323    o pkg/diagnostics
324      - fix RCENTER diagnostics in case cell center is not at interface middle
325    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
326      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
327      that THETA and SALT are "conservative temperature" and "absolute
328      salinity"
329    o pkg/ctrl
330      - fix computation of endrec in s/r ctrl_init_rec
331      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
332    o pkg/seaice/seaice_growth.F
333      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
334        remove then obsolete STORE directives
335      - fix STORE directives for tice and tices, so that only the
336        appropriate part of the fields are stored (and not the entire
337        field); update global_ocean.cs32x15.seaice AD output.
338      - cosmetic changes: adjust CPP flags and indentation for better
339        legibilty
340    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
341      Chris Wilson)
342    o pkg/gmredi:
343       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
344       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
345    
346    checkpoint63  (2011/07/11)
347    o pkg/exch2:
348     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
349     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
350       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
351       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
352    o pkg/diagnostics:
353     - deal with pairs of post-processed diags which are computed together; in
354       particular, re-order list of diags within 1 file to save 2nd computation.
355     - add S/R to compute velocity stream-function (called after velocity-potential
356       calculation) from divergence free transport -> new diagnostics "PsiVEL".
357     - add parameter to select grid-point location where PsiVEL == 0.
358    o eesupp/src:
359       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
360       (specific S/R needed with exch2 topology - for now, just print an error msg)
361    o pkg/shelfice
362     - Implement friction velocity-dependent transfer coefficients following
363       Holland and Jenkins, JPO, 1999
364       Original code by M. Losch with small modifs.
365       Enable with CPP option SHI_ALLOW_GAMMAFRICT
366       and runtime flag SHELFICEuseGammaFrict
367    o verification lab_sea & global_ocean.cs32x15:
368     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
369       does not miss some dependencies (but is slower) and also works with many files
370       (default makedepend limitation for AD built).
371     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
372    o pkg/diagnostics:
373     - add run-time parameter "useMissingValue" (def=False) to fill land-point
374        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
375       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
376     - Extend the use of "missing_value" setting from data.diagnostics for the case
377       of counter-diagnostics (where fraction-weight is zero). This applies both to
378       MNC and MDS output files.
379    o pkg/seaice/seaice_growth.F:
380      - add 'a priori' cap of latent heat flux based on actual mass considerations
381        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
382        non-legacy seaice_solve4temp.
383      - add diagnostic of the residual sublimation freshwater flux (the freshwater
384        flux taken from the ocean if the total actual latent heat fluxes exceed
385        the maximum)
386      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
387       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
388      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
389       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
390      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
391      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
392    o verification 1D_ocean_ice_column:
393       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
394       update results
395    o pkg/diagnostics:
396     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
397       which are not filled-up but computed from other diags ; In this case, the mate
398       diag points to the primary (filled-up) diag to used for post processing.
399     - Update Velocity-potential computation using post-processed diag framework.
400     ==> Change the ordering of fields and time-periods in MDS output file
401       when using periodic averaging: now writes one time record with the full set
402       of fields for this time period, then the next time reccord (it used to be
403       one field with the full set of time records then the next field).
404         Note: this is now similar to NetCDF (MNC) output file. <==
405    
406    checkpoint62z (2011/06/21)
407    o adjoint monitor:
408     - Add adjoint monitor output for packages exf, seaice
409       and update relevant testreport output
410    o pkg/seaice:
411     - re-order diags inits so that they appear in order in available_diagnostics.log
412     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
413       area/heff/hsnow preceeding thermodynamic growth/melt.
414     - modified diag: SIdA; output actual effect, as the description states.
415     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
416     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
417       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
418        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
419     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
420     - added diagnostics for seaice generic tracers (SItr*).
421     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
422     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
423     I. Fenty: 18-Jun-2011:
424     Minor changes to seaice package:
425     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
426        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
427       - Differentiated "regularization variables" from "floor variables"
428        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
429        * hiceMin became SEAICE_hice_reg (old hiceMin)
430          (with _reg meaning regularization variable)
431       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
432        so as to ensure energy conservation when going between phases
433      - A22 was not used anywhere
434     2) Changed regularization procedure for heffActual and hsnowActual to ensure
435        well-boundedness and smooth adjoint in seaice_growth.F
436     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
437        because the old regularization always set heffActual >= 0.05 cm
438     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
439        on AREA when HEFF > 0.
440      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
441        requiring that DISABLE_AREA_FLOOR *not* be defined
442     Affected verifications:
443      - 1D_ocean_ice_column (output.txt output_adm.txt)
444      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
445    o pkg/diagnostics:
446      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
447      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
448        (was _RL, now integer) with option = 0 to retrieve all levels.
449      - add pieces of code to compute velocity potential at each level (new diagnostics
450        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
451        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
452      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
453        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
454        and in diagnostics_fract_fill.F (do not need a valid pointer for the
455        diagnostics counter-mate); check that definition of counter-diagnostic
456        includes a valid counter-mate (in diagnostics_set_levels.F).
457    o model/src (rStar):
458      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
459        affect solution only if z* with full pressure in EOS;
460        update output of test-exp global_ocean.90x40x15.
461    o pkg/seaice:
462      - introduce siEps=1e-5 parameter
463      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
464      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
465      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
466        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
467        as well as ice cover age and ridging index (attached to AREA).
468        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
469        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
470        Up to SItrMaxNum=3 tracers can be used simultaneously.
471    o pkg/salt_plume:
472      -introduce SPsalFRAC run time parameter that sets the fraction of the
473       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
474       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
475    o model debug options:
476      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
477        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
478      - Refine debug-msg printing selection (3 new levels):
479        debugMode  : controls printing of debug messages (sequence of S/R calls).
480        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
481         debLevZero =  0 ; /* level of disabled aux. msg printing */
482         debLevA =  1 ; /* level of minimum  aux. msg printing */
483         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
484         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
485         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
486         debLevE =  5 ; /* level of extensive debug printing */
487        New debugLevel default: with default debugMode value (=F),
488          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
489          and if debugMode=T, default debugLevel = 4 (debLevD).
490        Relation with previous settings:
491         debLevB (=2) corresponds to former debLevA (=1)
492         debLevD (=4) corresponds to former debLevB (=2)
493        Note:
494         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
495         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
496            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
497      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
498        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
499    o pkg/obcs:
500      - change OBCSfixTopo default from True to False (should not change the results);
501        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
502    o pkg/thsice:
503      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
504        2nd layer seaice sublimation (unlikely to happen)
505      - use Interior mask for OBCS in thsice_advection.F (similar to what is
506        done in gad_advection & seaice_advection).
507    o adjoint:
508      bug fix spotted by Gael Forget:
509      seaice_advection and thsice_advection still had
510      legacy CPP options to avoid CS corner updates for adjoint
511    o pkg/seaice:
512      => Change some of the defaults (2011/05/29):
513         - change SEAICEuseFluxForm default (from False to True)
514         - change DIFF1 default (from 0.004 m/s to 0. m/s)
515         And print warnings if DIFF1 is not set in data.seaice and centered
516          avection scheme is used without any diffusion.
517      also:
518      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
519      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
520      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
521        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
522        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
523      update results of test exp.:
524         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
525             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
526             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
527         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
528         seaice_obcs: output (SEAICEuseFluxForm=T)
529      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
530          for standard fwd & AD lab_sea tests (to keep the same output).
531    o pkg/seaice/seaice_growth.F:
532      - use Ian Fenty's capping formulas for actual ice
533      thickness thoughout EVOLUTION branch.
534      - put treatment pathological case #2) in CPP brackets
535      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
536      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
537    o pkg/seaice:
538      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
539      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
540      also pass fac as a param, which can be 1. (to update the tendency
541      field) or the time step (to update the field itself).
542      - seaice_advdiff.F: for multidim, call seaice_diffusion with
543      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
544      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
545      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
546      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
547    o pkg/seaice:
548      diffusion with centered advection scheme (diffus.F & advect.F):
549      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
550        to just compute the laplacian of input-field.
551      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
552      - fix flux-form version in diffus.F to conserve tracer.
553      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
554       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
555    
556    checkpoint62y (2011/05/26)
557    o pkg/seaice:
558     - seaice_growth.F : in EVOLUTION branch, always include
559       a_QSWbyATM_cover in qnet (as it should be).
560     - verification/global_ocean.cs32x15 : update results accordingly
561       (output.seaice.txt output_adm.seaice.txt).
562    o pkg/seaice + obcs:
563     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
564       equivalent of assuming no tracer gradient outside the OB region.
565       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
566     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
567       after changes above);
568     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
569       only at OB location (instead of over a band of OLx width).
570    o pkg/seaice:
571     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
572       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
573    o pkg/obcs:
574      - split header file "OBCS.h" into 4 separated files:
575        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
576       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
577         (contain no conditional statement which depends on OBCS options).
578      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
579        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
580    o ctrl, cost, grdchk & autodiff pkgs:
581      - make options file more standard (like other {PKG}_OPTIONS.h file but
582        with AD_CONFIG.h); clean-up some of the included header files.
583    o pkg/obcs:
584      - do not mask tracer when applying OB (tracer == 0 could generate problems)
585      - apply tracer OB values to tracer field only at OB location (instead of
586        over a band of OLx width)
587      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
588      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
589        obcs_apply_tloc.F & obcs_apply_sloc.F
590    o obcs in model/src:
591      - call OBCS_APPLY_W only if NonHydrostatic.
592      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
593      - reset dEtaHdt and wVel to zero outside OB interior region ;
594      - leave tracer unchanged outside OB interior region: This has no effect
595        on the solution but just to prevent unrealistic tracer value outside OB.
596      - zero out velocity outside OB interior region: This has no effect on
597        the solution but just to prevent unrealistic velocity outside OB.
598    o obcs and non-lin free-surf:
599       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
600       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
601       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
602       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
603       update results of test-exp. exp4(nlfs).
604    o exp4 (nlfs) test-exp:
605       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
606       with NonLin-FreeSurf); update output.nlfs.txt
607    o obcs and 2d/3d solver norm:
608       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
609       and outside OB interior region (will allow to place OB further inside the
610       domain). Depending on the domain, can affects cg2d-Norm (previous
611       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
612       and cg3d-Norm (previous Norm was computed before canceling OB terms),
613       e.g. in tutorial_plume_on_slope.
614      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
615    o pkg rbcs:
616      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
617      - add capability to apply relaxation to horizontal velocity uVel & vVel.
618    o pkg/grdchk: add gradient check for control variable xx_shifwflx
619    o pkg/shelfice/shelfice_init_fixed.F
620      fix CPP-flag combinations
621    o pkg/seaice: Merge iceage code of Pierre Rampal
622      * update/change/correct ice age calculations
623      * add age updates for pathological cases
624      Probably needs more testing...
625    
626    checkpoint62x (2011/05/13)
627    o pkg/mom_vecinv:
628       high-order vorticity scheme: use interior masks (maskInW & S)
629       to zero-out (outside OB) gradient of vorticity.
630    o verification exp.:
631       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
632       hs94.128x64x5 and seaice_obcs ; update results.
633    o pkg/obcs:
634      fix bug in OBeta for YZ sections in obcs_exf_load.F
635    o pkg/ctrl, pkg/shelfice, and optim:
636      - add new control variable xx_shifwflx (fresh water flux underneath ice
637        shelves). This is almost as tedious as obcs-ctrl, because the
638        variables needs its own mask.
639      - add a cost function term that penalizes the deviation of xx_shifwflx
640        from the first guess (zero) in analogy to other control variables
641    o pkg/shelfice:
642      - start basic adjoint
643    o pkg/ctrl:
644      - remove extra 2D field "for good measure" when initializing in
645        ctrl_set_globfld_[xy/xz/yz].F
646      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
647      - improve error messages in ctrl_set_unpack_*
648    o OBC implementation in momentum:
649       use interior masks (maskInC,W & S) in momentum S/R:
650       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
651       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
652       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
653       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
654       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
655        (and also with Leith/Smagorinsky harmonic-viscosity).
656       Update output of experiment dome and exp4 (+nlfs).
657    o exp4 test-exp:
658      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
659        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
660        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
661        time-varying OB at Western-side for wVel (NonHyd); update output.
662      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
663        and biharmonic-viscosity ; also use prescribed time varying OB.
664    o pkg/obcs:
665      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
666    o model/src:
667      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
668      - initialise startTime & nIter0 with unlikely values: allows to set one
669        from the other without ambiguity.
670    o seaice_obcs test-exp.:
671      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
672    o pkg/obcs:
673      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
674        no longer needed with maskInC,W,S in pkg/generic_advdiff.
675    o pkg/seaice:
676      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
677        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
678      - fixed bug in the initialization of sea ice salinity variable HSALT
679        in seaice_init_varia.F  (removed dependence on ICE2WATR)
680    o fizhi-cs test exp.:
681       switch reference output convention for these 2 non-standard test-exp,
682        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
683          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
684       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
685    o model/inc:
686      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
687        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
688    o pkg/seaice:
689      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
690    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
691      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
692        and initial HSALT
693    
694    checkpoint62w (2011/04/26)
695    o pkg/mom_fluxform:
696      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
697      - use parameter "sideDragFactor" in no-slip BC side-drag part.
698      - update output of exp. global_ocean.90x40x15
699    o pkg/mom_vecinv:
700      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
701    o update seaice exp.:
702      use more consistent parameter values (remove "backward compatability only":
703       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
704      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
705       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
706    o update test-exp global_ocean.90x40x15:
707      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
708      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
709      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
710      o turn on zStar & viscA4 in standard set-up (dir input/)
711        and update output files: output.txt & output.dwnslp.txt
712    o new AD-test experiment: obcs_ctrl
713      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
714    o pkg/dic:
715      fix two bugs in handling water vapour pressure in carbonate chemistry
716      and air-sea fluxes. Found by Val Bennington and Galen McKinley
717      (add DIC Option = WATERVAP_BUG to recover old results)
718      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
719    o adding allowInteriorFreezing option to check for water below freezing point
720      at depth and bring the negative heat anomaly to the surface level
721    o pkgs _fields_load:
722      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
723      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
724        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
725        rbcs to get interpolation weights and time reccord number.
726      - fix multi-threading in aim_fields_load.F
727      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
728    o external_fields_load:
729      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
730       interpolation weights) to use in a periodic time-series ; do not divide by
731       time-step to convert to integer:
732       - this fixes case where externForcingPeriod is not multiple of time-step
733          (Thanks to Christopher L. Wolfe)
734       - this fixes case where externForcingPeriod is an odd multiple of time-step
735         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
736      store index of time-record which is currently loaded:
737       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
738       - needed for the adjoint but not yet used because of extensive recomputations;
739         (to be fixed soon)
740    
741    checkpoint62v (2011/04/02)
742    o verification/1D_ocean_ice_column added to test Ian Fenty's
743      pkg/seaice_growth.F modifications for improving sea ice code differentiability
744    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
745      (new velocity statistics after changing maskInW & maskInS definition)
746    o pkg/generic_advdiff with OBCS:
747      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
748      equivalent to assumption of no tracer gradient outside the OB region.
749      This will affect the results if using obcs+biharmonic diffusion.
750      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
751    o pkg/obcs:
752      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
753      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
754      in Interior region. No impact on solution but affects Velocity monitor stats.
755    o pkg/ptracers (adjoint)
756      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
757      tape file for each tracer
758    o model/inc/src and pkg/autodiff: add parameters that allow to turn
759      of parts of the adjoint code at run time. For now, there are only
760      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
761      parameters are set in data.pkg.
762      This is the lazy coward's version of doing this, but still useful for
763      debugging. In order to do it right, everything needs to be moved to
764      pkg/autodiff.
765    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
766      the end; this fixes the adjoint balancing code for open boundaries.
767    o pkg/ctrl:
768      - change behavior of xx_${varname}period to be analogous to exf-conventions:
769        xx_${varname}period =   0.,  means time-independent control part
770        xx_${varname}period = -12., means one-year-periodic monthly control part
771      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
772        clean up ctrl_init a little, remove unused variables
773      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
774      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
775    
776    checkpoint62u (2011/03/15)
777    o model/src:
778      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
779        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
780      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
781        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
782    o pkg/ctrl/obcs/ecco:
783      - remove obsolete, unused, and partially broken code:
784        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
785        ALLOW_CTRL_OBCS_BALANCE
786      - put a stop statement into ecco/cost_obcsvol.F, but also add
787        cost_obcsvol to ecco_ad_diff.list
788    o pkg/ecco: fix counting cost function contributions for obcs (code
789      by Matt M.) and diffkr for diagnostics
790    o pkg/ecco, pkg/ctrl, pkg/grdchk:
791      add cost penalty terms for initial uvel, vvel, eta controls
792      and I/O for prior error files
793    o pkg/mdsio:
794       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
795       (new argument) to check for tiled file in mdsioLocalDir : this fix the
796       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
797    o pkg/ctrl:
798     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
799       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
800       unused and superfluous variables
801     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
802    o pkg/ecco
803     - enable adjoint of Stevens OB
804    o pkg/ctrl/ecco/grdchk:
805      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
806        Fortunately, we do not have any tests for the numerous cpp-flagged
807        option of "obcs as control parameters" so we will never know
808        if this is an improvement (but at least now things compile).
809      - remove an obsolete initialization from ecco_cost_init_barfiles.F
810      - fix some problems within never used ifdefs to make the code compile
811    o pkg/obcs:
812     - Refine Interior mask definition to work with more complex OB (e.g.
813       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
814       read in Interior mask from file. Check if Interior mask is consistent
815       with OB list of indices.
816    o pkg/seaice
817     - beginning code for a seaice tracer package,
818       but currently only used for seaice age: SEAICE_AGE
819       SEAICE_num = 4
820       iTracer = 1: area-weighted ice age
821               = 2: volume-weighted ice age
822               = 3, 4: template for one-year vs. multi-year ice
823       data.seaice has new namelist SEAICE_PARM03 for arrays related to
824       SEAICE_num
825    
826    checkpoint62t (2011/03/05)
827    o pkg/obcs:
828     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
829       then normal component. This ensures that the normal component is set
830       correctly even when it conficts with tangential setting from an other OB.
831       Affects results of test-experiment seaice_obcs: update the output.txt
832    o pkg/obcs:
833     - add code to monitor statistics of dynamical fields at OB.
834     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
835       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
836       - change default: balance the Net inflow through all OB (instead of balancing
837         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
838     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
839       to match Nortern OB inflow (OBCS_balanceFacN=0).
840    o pkg/seaice:
841     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
842    o pkg/seaice (seaice_growth v 1.113):
843     - reverting seaice_growth to v 1.111 in order to have code with exact bit
844       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
845       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
846       runtime flag SEAICEareaFormula is kept but is inactive
847    o model/src:
848     - add new param to scale curvilinear grid distance and area when using
849       a different sphere radius from the grid-files.
850     - test/check multi-threads EXCH applied to local variable (cg2d_x)
851    o adjoint:
852     - enable adjoint of Stevens OB
853     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
854       (a bit delicate because of potentially modified adj. common block structure;
855       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
856    
857    checkpoint62s (2011/02/15)
858    o pkg/seaice (seaice_growth v 1.112):
859     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
860       computing the ice cover tendency from effective thickness tendencies. Include
861       Ian Fenty's formula.
862     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
863       SEAICEareaFormula.
864     - simplify notations for the various d_HEFF/d_AREA terms.
865    o pkg/gmredi:
866     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
867       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
868       add a verification test-run (front_relax.bvp) to test GM_useBVP.
869    o pkg/seaice (seaice_growth v 1.111):
870     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
871     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
872       also melt ice.
873    o pkg/seaice:
874     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
875     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
876    o pkg/cheapaml:
877     - from Nico Wienders: New version of this package.
878    o pkg/flt:
879     - add CPP options to prevent floats to re-enter the opposite side of
880       a periodic domain (default: keep periodicity)
881    o pkg/gmredi:
882     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
883       (needed for multi-dim advection).
884     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
885    o model/src:
886     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
887    o tutorial_tracer_adjsens
888     - extend to NLFS and replace maskC by hFacC
889       (change reference output accordingly)
890    
891    checkpoint62r (2011/01/24)
892    o testreport:
893     - add option -deloutp (-do) to remove output file after successful run
894     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
895       extract exact list of procs from this file ; adjust COMMAND by
896       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
897    o pkg/ecco: replace old ineffective way of penalizing deviations from
898      first guess (of obcs) with code by Matt Mazloff
899    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
900      exf/cal
901      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
902        and handle case of obcs?period == 0
903        Not affected by these changes: There is still an inconsistency in
904        the computation of start/endrec for the obcs variables for ALLOW_CAL
905        defined (see comment by Menemenlis, 7-Mar-2003)
906      - make S/R ctrl_get_gen_rec return something meaningful even if
907        ALLOW_CAL is not defined
908      - ctrl_getobcs?: simplify code so that it does not need to use
909                       S/R exf_swapfields
910    o testreport:
911       allow to test MPI with different number of processors for each experiment:
912       create file "SIZE.h.mpi" in each build dir.
913       Note: update of "-command" argument not yet implemented.
914    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
915      alleviate the need for additional 3D tapes when using
916      the non-inear free surface in the adjoint. This is done
917      by adding an 'update' of hfacc etc. to their current
918      value at the beginning of forward_step.F.
919    o pkg/seaice
920      seaice_lsr: move stress-divergence computations out of outer pseudo-
921      timestepping loop
922    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
923      up, so that the calls of the ctrl_* subroutines are really at the end
924      of the routine.
925    o pkg/gmredi:
926      allow to specify a 2-D horizontal map and a 1-D vertical profil
927      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
928    o pkg/seaice:
929      move lsr iterations from seaice_dynsolver to seaice_lsr.
930    o pkg/seaice:
931      reduce memory footprint of seaice mutldim advection tapes,
932      by using a 2D tape independent of the generic_advdiff ones,
933      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
934    
935    checkpoint62q (2010/12/29)
936    o model/src:
937      - check horizontal grid-spacing for unset or zero/negative values.
938      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
939    o pkg/flt:
940      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
941      - precision of input and output files set according to readBinaryPrec
942        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
943      - initial float position from tiled file was not converted to index space
944        (looks like a bug): fixed to make it similar to initial pos. global file.
945    o global_ocean.cs32x15:
946       change SIZE.h of AD set-up to get same tiling as with MPI.
947       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
948    o model/src:
949       add flag to control printing of domain fields (bathymetry, hFac ...) in
950       ini_mask_etc (call to plot_fieds_xy*).
951    o pkg/thsice:
952       if useEXF, some forcing fields are not valid in overlap: fixed by computing
953       over the interior only + apply EXCH at the end (like with SEAICE advection).
954    o pkg/mdsio:
955      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
956        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
957      - change barrier call for safe multi-threads access to 3-D shared buffer.
958      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
959      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
960        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
961    o pkg/flt:
962      - add fourth-order Runge-Kutta integration
963      - add basic exch2 support (only 1 facet supported so far!)
964    o pkg/mdsio+rw:
965      new S/R to read local (or tile independent) vector (read counterpart of
966       mds_writevec_loc, and front-end write_glvec_rl/rs).
967    o global_ocean.cs32x15: additional input_ad.seaice experiment
968        that uses pkg/seaice rather than pkg/thsice.
969        (using multidim advection for seaice)
970    o towards more F95 syntax for array specification in namelist:
971      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
972        of all verification experiments.
973           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
974          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
975      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
976    o global_ocean.cs32x15: additional input.seaice experiment
977        that uses pkg/seaice rather than pkg/thsice.
978    
979    checkpoint62p (2010/12/17)
980    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
981        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
982    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
983        allow for use of multim. advection in seaice adjoint.
984    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
985      - first attempt to close budgets by taking into account the freshwater
986        flux implied by the sublimation of snow and ice. So far only the
987        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
988        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
989    o eesupp/src:
990      new S/R with new option (NML_EXTENDED_F77) to change array specification
991      from F95 standard to commonly accepted extended F77 form.
992      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
993      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
994      for less tolerant f77 compiler (e.g., pgf77, g77).
995    o globalFiles:
996      commented out in parameter file "data" since it's not safe with MPI
997      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
998      in this case); no longer commented out in restart test (tst_2+2).
999    o add adTapeDir to specify a special directory where adjoint tapes are
1000      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
1001      and cannot be used together with mdsioLocalDir.
1002    o nesting pkgs:
1003      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
1004      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
1005      - add parameter files + utils dir + output from short run on beagle.
1006    o pkg/seaice:
1007        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
1008    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
1009      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
1010    
1011    checkpoint62o (2010/11/25)
1012    o pkg/exf:
1013      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
1014    o pkg/seaice:
1015      - seaice_ocean_stress: split a loop for better vectorization of the
1016        adjoint code
1017      - seaice_growth.F: fix bug in conservation of freshwater connected to
1018        capping of heff, put contribution into d_HEFFbyNEG
1019      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
1020        by something more sensible (parameters that are what their name implies)
1021      - change some defaults, so that by default exf-parameters are used for
1022        things like rhoAir, cpAir,latent/sensible heat parameters, in order
1023        to reproduce the old results, many data.seaice now contain funny values
1024        for cpAir and latent heat of sublimation
1025    o packages_readparms.F: move exf_readparms up in line so that
1026        exf-parameters are visible for other packages (e.g. seaice)
1027    o debugMode & debugLevel=2:
1028      - differentiate between debugMode & debugLevel=2:
1029        debugMode: controls printing of debug messages (sequence of S/R calls).
1030        debugLevel: controls printing of algorithm intermediate results and stats.
1031      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
1032        => allows to print debug-stats without all sequence of call messages.
1033      - switch control of debug print from debugLevel to debugMode in many S/R.
1034    o pkg/obcs (obcs-sponge):
1035        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
1036        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
1037    o pkg/generic_advdiff:
1038      - record overlap minimum size for each advection scheme;
1039      - refine criteria on overlap minimum size;
1040      - check and stop (in gad_check) if overlap size is too small.
1041    o pkg/obcs:
1042      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
1043        once, in ptracers_implicit.F)
1044      - with seaice: remove test on empty file name in obcs_apply_seaice (always
1045        apply OB values when tile has OB)
1046    o model/src, coriolis setting:
1047      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
1048        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
1049        files (selectCoriMap=3) with any grid.
1050      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
1051    o pkg/seaice/seaice_growth.F:
1052        a few cosmetic changes that reduce the number of lines of code
1053    o pkg/obcs: add boundary conditions following Stevens (1990)
1054      - the code follows old MOM/NAOSIM code
1055      - so far it is only implemented for the eastern and western boundaries
1056        and NOT for pTracers
1057    o pkg/rbcs:
1058      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
1059        beginning of the first rbcs forcing period.
1060      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
1061        offline package, i.e., one file per time, labeled by iteration number;
1062        deltaTrbcs sets the timestep with which the data was generated;
1063        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
1064      - rbcsForcingCycle=0 makes forcing non-cyclic.
1065      - make arithmetic safe for negative times and odd forcing periods.
1066    
1067    checkpoint62n (2010/11/09)
1068    o pkg/seaice:
1069        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
1070    o pkg/obcs:
1071       New S/R to copy tracer value from the OB location to narrow band region
1072        (width = same as overlap) beyond the OB: preserve OB value (needed for
1073        high-order scheme) which were overwritten by EXCH call if in overlap
1074        region. Applied to theta, salt, ptracer and advected seaice variables.
1075       With seaice: use maskInC in similar way as in gad_advection.F,
1076        in seaice_advection.F and advect.F.
1077       Update output of experiment seaice_obcs and change exp4 to test OBCS with
1078        4th order Adv.Scheme. for pasive salt and ptracer.
1079    o tools/genmake2:
1080      - when looking for an optfile (not specified), only search for Fortran compiler
1081        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
1082      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
1083        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
1084      - set default for CPP to "cpp -traditional -P" (was the case without specifying
1085        an optfile, but otherwise default was just "cpp".
1086      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
1087      - when "CC" is not set in the optfile, look for possible C compiler
1088        (instead of just setting CC=cc)
1089      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
1090        => add a ".F" to ".o" rule for source files with no "#include" (such as
1091           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
1092      - move gfortran before g77 in list of possible Fortran compiler (consistent
1093        with reference compiler switch from g77 to gfortran)
1094    o pkg/seaice:
1095      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
1096        seaice_check that stops the model, when the CPP flag is used.
1097      o seaice_growth.F: make capping of ice volume conserving by returning the
1098        capped ice as freshwater to EmPmR. This does not change the verification
1099        experiments but will change runs where the capping is acutally active
1100    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
1101      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
1102         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
1103         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
1104    o tools/genmake2:
1105      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
1106      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
1107      - clean previous genmake log files before anything else.
1108      - change Makefile to remove testreport log files (*.tr_log) and genmake log
1109        files only with "CLEAN" target (instead of "Clean");
1110    o pkg/generic_advdiff:
1111      Change OBCS in multiDim advection (gad_advection.F):
1112       Use maskInC to prevent intermediate update of tracer-field in OB regions,
1113       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
1114       which were applying future time-step OB values.
1115      This way, all explicit calculations use current-time-step OB values
1116       (simpler and more consistent).
1117      Affects results when set-up uses time-varying OBC and multi-dim advection;
1118       update output of experiment seaice_obcs.
1119    o pkg/seaice:
1120      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
1121       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
1122         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
1123      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
1124       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
1125       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
1126    o pkg aim (2010/10/26):
1127      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
1128        formulation with obliquity, eccentricity, ... as run-time parameters,
1129      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
1130        upward shortwave radition at the surface (all-sky and clear-sky).
1131    o pkg/obcs:
1132      - writing sections with globalFiles=T does not work: switch to tiled-files
1133        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
1134      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
1135      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
1136    
1137    checkpoint62m (2010/10/21)
1138    o pkg/seaice: vectorize seaice_solve4temp.F
1139      - move iterations loops outside of i/j-loops
1140      - requires 2D arrays for TB and effConduct
1141      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
1142        modified in this routine
1143      - a little bit of clean up, adjusting indentation, etc.
1144      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
1145        performance and '**TWO' by '**2' (because TWO is a float),
1146        replaced ONE, ZERO
1147  o eesupp/src:  o eesupp/src:
1148     fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube     fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
1149  o pkg/seaice/seaice_growth.F  o pkg/seaice/seaice_growth.F
# Line 39  o pkg/thsice: Line 1179  o pkg/thsice:
1179      experiments that have this flag undefined (not tested in verification);      experiments that have this flag undefined (not tested in verification);
1180      a little reorganization to save a few 2D fields and recomputations      a little reorganization to save a few 2D fields and recomputations
1181    - 1st step of revisiting thsice adjoint (major recomp. sorted out)    - 1st step of revisiting thsice adjoint (major recomp. sorted out)
1182      - 2nd step:  fix some store dirs
1183        o seems to work somewhat, i.e. using ifort but not g77
1184        o likely cause are incomplete init. or recomputation
1185        o start verification/global_ocean.cs32x15/input_ad.thsice
1186  o pkg/obcs: add support for exch2  o pkg/obcs: add support for exch2
1187    - the position of the boundary and prescribed values are specified using    - the position of the boundary and prescribed values are specified using
1188      a global domain with exch2 facets stacked      a global domain with exch2 facets stacked
# Line 400  o tools/build_options: Line 1544  o tools/build_options:
1544      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
1545  o pkg/ecco  o pkg/ecco
1546    - allow user defined cost function contributions    - allow user defined cost function contributions
1547          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
1548          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
1549    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1550        the two options are complementary.        the two options are complementary.
1551  o pkg/smooth  o pkg/smooth
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