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revision 1.1295 by jmc, Sat Sep 11 21:39:13 2010 UTC revision 1.1530 by mlosch, Tue Nov 8 17:00:37 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      - add code for northern and southern boundaries.
9      - reorder some loops to save some operations and so that drFBar can be scalar
10    o model/src:
11      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
12        truncation) and add diagnostics for Adams-Bashforth tendency increment.
13      - update test-exp. AD output:
14        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
15      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
16        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
17        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
18        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
19        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
20        tutorial_plume_on_slope.
21    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
22      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
23      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
24      does not even come with an F77 compiler anymore, this should not be
25      a limitation
26    
27    checkpoint63e (2011/11/06)
28    o pkg/seaice adjoint of LSR:
29      - substantially rework STORE dirs.
30      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
31        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
32        and only perform SOLV_MAX_FIXED adjoint iters.
33        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
34        always goes to same record, meaning that the last forward field will be
35        the one used in the adjoint - an approximation.
36      - now produces non-zero LSR-related gradients, and acceptable gradients for
37        An's zonal (x-z) test case (to be checked in)
38      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
39        (but these are screwed up by the thermodynamics in the first place);
40        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
41        output_adm.txt also reflects changes to seaice_lsr
42      - global_ocean.cs32x15:
43        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
44          (output_adm.seaice.txt was updated)
45        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
46          (output_adm.seaice_dynmix.txt)
47    o test-exp. exp4+stevens:
48      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
49    o pkg/seaice (lsr solver):
50      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
51        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
52      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
53      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
54        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
55      - compute (with new S/R) and print initial (+ free-driff sol. if available)
56        and final residual of linearised system.
57    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
58      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
59    o pkg/obcs: Stevens BCs (still only for east and west)
60      - fix Stevens BCs by using intermediate velocities of previous
61        time step as "baroclinic" contribution rather velocity of one grid cell
62        inside the boundaries; more consistent but makes the entire treatment
63        more complicated, requires new pickup files and two new S/Rs:
64        obcs_copy_uv_n and obcs_save_uv_n
65        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
66        (undefined by default)
67      - silently move computation of some grid factors into separate loops to
68        save some recomputations
69      - add a hack for non-linear free surface
70      - add a verification experiment to exp4 that tests this code
71    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
72    
73    checkpoint63d (2011/10/25)
74    o pkg/obcs + seaice-dynamics:
75      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
76        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
77        values (consistent with an implicit method).
78      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
79        return to older implementation (same results as before); note that none of
80        the "experimental" OBCS_SEAICE options are implemented in the new version.
81      - switch test exp. seaice_obcs to use new version (update output).
82    o pkg/seaice:
83      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
84      - add parenthesis in Water-Ice drag calculations (evp & lsr);
85      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
86        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
87      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
88        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
89    o pkg/layers:
90      - Include potential density as new coordinate (Thanks to David Munday)
91    o pkg/dic:
92      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
93        carbonate computation/output to CALC_PCO2_APPROX
94    o pkg/generic_advdiff
95      - make TAF generate code that vectorizes:
96        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
97    o model/src:
98      - improve vectorization also for adjoint code of
99        solve_tridiagonal and solve_pentadiagonal. As this requires up to
100        5 new 3D-fields, this code is only turned on for the combination of
101        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
102        for singular matrix check (only for TARGET_NEC_SX).
103      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
104        ALLOW_AUTODIFF. This flag now needs to be set outside of
105        solve_tri/pentadiagonal.F
106    o pkg/exf:
107      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
108        optional namelist EXF_NML_OBCS).
109      - add many debug-print (to trace down where pkg/cal error msg comes from)
110    o pkg/mom_vecinv/mom_vi_hdissip.F
111      - rearrange loops so that vectorization is improved and in particular
112        the adjoint routine vectorizes. The code is a little longer now, but I
113        think easier to read.
114        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
115    o pkg/seaice:
116      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
117    o pkg/exch2:
118      - alternative code (without tile x tile matrix) for cumulated (global) sum;
119        used as default; keep using matrix version in adjustment.cs-32x32x1.
120    o tools/build_options:
121      - after merging some MPI and/or multi-threads specific optfiles so that
122        the modified default optfile support both built (using genmake2 -mpi
123        for the MPI built, using genmake2 -omp for OpenMP built),
124        move now obsolete optfiles to tools/build_options/unsupported/
125       (add copy of email sent to support list in doc/optfiles_changes.txt)
126    
127    checkpoint63c (2011/09/28)
128    o pkg/ebm:
129      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
130        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
131    o pkg/seaice (SItracer pickup)
132    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
133      To be done:
134      - thorough testing of missing fields in S/R seaice_read_pickup
135      - thorough matching between generic tracers and specific fields used
136        (e.g. volume-weighted age, area-weighted age, salinity, ...)
137    o pkg/grdchk:
138      - all procs calculate and print finite-difference gradient (for testreport)
139      - change description output used by testreport;
140      - AD testing: also compare and report Finite-difference gradient;
141        => update all output_adm*.txt
142    o test exp. global_ocean_ebm:
143      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
144        and turn on exactConserve; update (fwd) output.
145    o pkg/seaice (LSR):
146      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
147      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
148        * identical results with non-CS topology (but save up to half of EXCH calls)
149        * no much changes in cs-32 verification tests since no ice at face edges
150         (differences due to convergence criteria, since nb of iterations changed)
151        * expect some differences on lat-lon-cap grid.
152        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
153    o pkg/exch2:
154      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
155        many tiles); until alternative coding is added, just add a stop.
156    o pkg/kpp:
157      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
158        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
159    o optfiles:
160      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
161        into corresponding standard one, which now support different build:
162        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
163      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
164    o pkg/obcs (seaice):
165      - add missing EXCH for uIce,vIce after applying OBCS;
166      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
167        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
168        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
169      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
170      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
171        and eedata.mth for MPI and mutlti-threaded testing.
172    o pkg/flt:
173      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
174      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
175      - fix pickup and trajectories + profiles output with multi-threads;
176      - add parameter to select group of fields to write along trajectory and
177        profile (default unchanged);
178      - only call PORT_RAND* function when flt_noise <> 0;
179      - add multi-threaded test for verification exp. flt_example.
180    o eesupp/src:
181      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
182      - USE_OMP_THREADING: check that number of threads (from eedata) matches
183        actual number (from env.var. setting).
184    o pkg/ebm:
185      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
186      - add multi-threaded test for verification exp. global_ocean_ebm
187    
188    checkpoint63b (2011/08/29)
189    o pkg/ebm:
190      - fix sign of runoff;
191      - update directly forcing fields (Qnet,EmPmR) to use standard
192        external_forcing_surf.F (remove ebm_forcing_surf.F);
193      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
194      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
195        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
196      - update global_ocean_ebm parameters file data and update output (fwd+ad).
197    o verification/matrix_example:
198      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
199        MPI and mutlti-threaded testing.
200    o pkg/matrix:
201      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
202      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
203      - fix for multi-threaded (remove DATA statement);
204      - use standard DIFFERENT_MULTIPLE function;
205      - add MATRIX_OPTIONS.h
206    o verification/matrix_example:
207       To allow to split the domain in several tiles, change the domain size
208        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
209        Western side) of land points.
210    o (*_)write_pickup:
211      - fix few bugs in mypackage_read/write_pickup.F
212      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
213        array of length 1 (was caught by compiler syntax-check).
214    o pkg/diagnostics (velocity potential solver):
215      - fix initialisation of main diagonal matrix (for overlap values)
216    o tools/build_options:
217      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
218        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
219      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
220        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
221        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
222        and use "-devel" testreport option for standard testing on baudelaire.
223    o pkg/grdchk:
224      - Assume that all gradient-check position are within the same tile
225        corresponding to global indices (iGloTile,jGloTile) and that
226        positions (i,j indices or nbeg) are local to this tile;
227      - set tile local-indices and proc. number according to tile global-indices;
228      - remove grdchkwhichproc from namelist (retired param);
229      - send adjoint gradient to all procs so that all procs print it to STDOUT;
230      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
231    o adding package bbl (Bottom Boundary Layer)
232      description in MITgcm/pkg/bbl/bbl_description.tex
233      example/test experiment in MITgcm_contrib/bbl
234    o adjoint verifications
235      - changed 5 experiments to multi-tiles
236        * global_ocean.90x40x15
237        * obcs_ctrl
238        * offline_exf_seaice
239        * tutorial_dic_adjoffline
240        * tutorial_tracer_adjsens
241        changed reference output for those that crossed tile boundaries
242        (changed choices of gradient check positions)
243      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
244      - temporary bug fix in grdchk_loc.F for obcs
245    o genmake2 & testreport
246      - add target "obj" (just for OBJFILES files) to Makefile;
247      - add option to specify FEXTRAFLAGS on command line.
248    o pkg/mypackage:
249      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
250    
251    checkpoint63a (2011/08/02)
252    o pkg/diagnostics (velocity potential):
253      - fix velocity-potential calculation when using OBCS: balance net inflow
254        at each level (new S/R OBCS_DIAG_BALANCE).
255      - fix some of the problems with OBCS in stream-function calculation.
256    o pkg/exf/exf_readparms.F
257      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
258        EXF_NML_OBCS) more consistent, so that you need not have these lists
259        in data.exf when they are not used.
260    o optim/optim_readdata.F:
261      - add some output about obcs variables that might help debugging
262      - add a check about nvarlength
263    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
264    o pkg/diagnostics (velocity potential):
265      - fix mask for OBCS (still problems in stream-function with OBCS);
266      - add specific parameter (default = main code CG2D params) for solver;
267      - in case of poor convergence, use solution corresponding to lowest residual.
268    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
269      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
270      and should be avoided where possible.
271    o model/src (rStar):
272      - include r* effect on reference-state (PhiRef) in totPhiHyd
273        (so that it's really the potential anomaly at the cell center);
274        affect solution only if z* with full pressure in EOS.
275      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
276        update output (because of z* in totPhiHyd and viscA4 changes);
277      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
278        @ constant r) until interpolation at constant r is implemented.
279    o pkg/diagnostics
280      - fix RCENTER diagnostics in case cell center is not at interface middle
281    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
282      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
283      that THETA and SALT are "conservative temperature" and "absolute
284      salinity"
285    o pkg/ctrl
286      - fix computation of endrec in s/r ctrl_init_rec
287      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
288    o pkg/seaice/seaice_growth.F
289      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
290        remove then obsolete STORE directives
291      - fix STORE directives for tice and tices, so that only the
292        appropriate part of the fields are stored (and not the entire
293        field); update global_ocean.cs32x15.seaice AD output.
294      - cosmetic changes: adjust CPP flags and indentation for better
295        legibilty
296    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
297      Chris Wilson)
298    o pkg/gmredi:
299       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
300       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
301    
302    checkpoint63  (2011/07/11)
303    o pkg/exch2:
304     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
305     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
306       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
307       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
308    o pkg/diagnostics:
309     - deal with pairs of post-processed diags which are computed together; in
310       particular, re-order list of diags within 1 file to save 2nd computation.
311     - add S/R to compute velocity stream-function (called after velocity-potential
312       calculation) from divergence free transport -> new diagnostics "PsiVEL".
313     - add parameter to select grid-point location where PsiVEL == 0.
314    o eesupp/src:
315       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
316       (specific S/R needed with exch2 topology - for now, just print an error msg)
317    o pkg/shelfice
318     - Implement friction velocity-dependent transfer coefficients following
319       Holland and Jenkins, JPO, 1999
320       Original code by M. Losch with small modifs.
321       Enable with CPP option SHI_ALLOW_GAMMAFRICT
322       and runtime flag SHELFICEuseGammaFrict
323    o verification lab_sea & global_ocean.cs32x15:
324     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
325       does not miss some dependencies (but is slower) and also works with many files
326       (default makedepend limitation for AD built).
327     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
328    o pkg/diagnostics:
329     - add run-time parameter "useMissingValue" (def=False) to fill land-point
330        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
331       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
332     - Extend the use of "missing_value" setting from data.diagnostics for the case
333       of counter-diagnostics (where fraction-weight is zero). This applies both to
334       MNC and MDS output files.
335    o pkg/seaice/seaice_growth.F:
336      - add 'a priori' cap of latent heat flux based on actual mass considerations
337        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
338        non-legacy seaice_solve4temp.
339      - add diagnostic of the residual sublimation freshwater flux (the freshwater
340        flux taken from the ocean if the total actual latent heat fluxes exceed
341        the maximum)
342      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
343       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
344      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
345       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
346      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
347      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
348    o verification 1D_ocean_ice_column:
349       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
350       update results
351    o pkg/diagnostics:
352     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
353       which are not filled-up but computed from other diags ; In this case, the mate
354       diag points to the primary (filled-up) diag to used for post processing.
355     - Update Velocity-potential computation using post-processed diag framework.
356     ==> Change the ordering of fields and time-periods in MDS output file
357       when using periodic averaging: now writes one time record with the full set
358       of fields for this time period, then the next time reccord (it used to be
359       one field with the full set of time records then the next field).
360         Note: this is now similar to NetCDF (MNC) output file. <==
361    
362    checkpoint62z (2011/06/21)
363    o adjoint monitor:
364     - Add adjoint monitor output for packages exf, seaice
365       and update relevant testreport output
366    o pkg/seaice:
367     - re-order diags inits so that they appear in order in available_diagnostics.log
368     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
369       area/heff/hsnow preceeding thermodynamic growth/melt.
370     - modified diag: SIdA; output actual effect, as the description states.
371     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
372     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
373       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
374        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
375     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
376     - added diagnostics for seaice generic tracers (SItr*).
377     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
378     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
379     I. Fenty: 18-Jun-2011:
380     Minor changes to seaice package:
381     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
382        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
383       - Differentiated "regularization variables" from "floor variables"
384        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
385        * hiceMin became SEAICE_hice_reg (old hiceMin)
386          (with _reg meaning regularization variable)
387       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
388        so as to ensure energy conservation when going between phases
389      - A22 was not used anywhere
390     2) Changed regularization procedure for heffActual and hsnowActual to ensure
391        well-boundedness and smooth adjoint in seaice_growth.F
392     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
393        because the old regularization always set heffActual >= 0.05 cm
394     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
395        on AREA when HEFF > 0.
396      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
397        requiring that DISABLE_AREA_FLOOR *not* be defined
398     Affected verifications:
399      - 1D_ocean_ice_column (output.txt output_adm.txt)
400      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
401    o pkg/diagnostics:
402      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
403      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
404        (was _RL, now integer) with option = 0 to retrieve all levels.
405      - add pieces of code to compute velocity potential at each level (new diagnostics
406        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
407        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
408      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
409        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
410        and in diagnostics_fract_fill.F (do not need a valid pointer for the
411        diagnostics counter-mate); check that definition of counter-diagnostic
412        includes a valid counter-mate (in diagnostics_set_levels.F).
413    o model/src (rStar):
414      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
415        affect solution only if z* with full pressure in EOS;
416        update output of test-exp global_ocean.90x40x15.
417    o pkg/seaice:
418      - introduce siEps=1e-5 parameter
419      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
420      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
421      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
422        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
423        as well as ice cover age and ridging index (attached to AREA).
424        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
425        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
426        Up to SItrMaxNum=3 tracers can be used simultaneously.
427    o pkg/salt_plume:
428      -introduce SPsalFRAC run time parameter that sets the fraction of the
429       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
430       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
431    o model debug options:
432      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
433        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
434      - Refine debug-msg printing selection (3 new levels):
435        debugMode  : controls printing of debug messages (sequence of S/R calls).
436        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
437         debLevZero =  0 ; /* level of disabled aux. msg printing */
438         debLevA =  1 ; /* level of minimum  aux. msg printing */
439         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
440         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
441         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
442         debLevE =  5 ; /* level of extensive debug printing */
443        New debugLevel default: with default debugMode value (=F),
444          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
445          and if debugMode=T, default debugLevel = 4 (debLevD).
446        Relation with previous settings:
447         debLevB (=2) corresponds to former debLevA (=1)
448         debLevD (=4) corresponds to former debLevB (=2)
449        Note:
450         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
451         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
452            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
453      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
454        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
455    o pkg/obcs:
456      - change OBCSfixTopo default from True to False (should not change the results);
457        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
458    o pkg/thsice:
459      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
460        2nd layer seaice sublimation (unlikely to happen)
461      - use Interior mask for OBCS in thsice_advection.F (similar to what is
462        done in gad_advection & seaice_advection).
463    o adjoint:
464      bug fix spotted by Gael Forget:
465      seaice_advection and thsice_advection still had
466      legacy CPP options to avoid CS corner updates for adjoint
467    o pkg/seaice:
468      => Change some of the defaults (2011/05/29):
469         - change SEAICEuseFluxForm default (from False to True)
470         - change DIFF1 default (from 0.004 m/s to 0. m/s)
471         And print warnings if DIFF1 is not set in data.seaice and centered
472          avection scheme is used without any diffusion.
473      also:
474      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
475      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
476      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
477        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
478        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
479      update results of test exp.:
480         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
481             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
482             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
483         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
484         seaice_obcs: output (SEAICEuseFluxForm=T)
485      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
486          for standard fwd & AD lab_sea tests (to keep the same output).
487    o pkg/seaice/seaice_growth.F:
488      - use Ian Fenty's capping formulas for actual ice
489      thickness thoughout EVOLUTION branch.
490      - put treatment pathological case #2) in CPP brackets
491      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
492      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
493    o pkg/seaice:
494      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
495      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
496      also pass fac as a param, which can be 1. (to update the tendency
497      field) or the time step (to update the field itself).
498      - seaice_advdiff.F: for multidim, call seaice_diffusion with
499      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
500      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
501      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
502      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
503    o pkg/seaice:
504      diffusion with centered advection scheme (diffus.F & advect.F):
505      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
506        to just compute the laplacian of input-field.
507      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
508      - fix flux-form version in diffus.F to conserve tracer.
509      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
510       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
511    
512    checkpoint62y (2011/05/26)
513    o pkg/seaice:
514     - seaice_growth.F : in EVOLUTION branch, always include
515       a_QSWbyATM_cover in qnet (as it should be).
516     - verification/global_ocean.cs32x15 : update results accordingly
517       (output.seaice.txt output_adm.seaice.txt).
518    o pkg/seaice + obcs:
519     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
520       equivalent of assuming no tracer gradient outside the OB region.
521       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
522     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
523       after changes above);
524     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
525       only at OB location (instead of over a band of OLx width).
526    o pkg/seaice:
527     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
528       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
529    o pkg/obcs:
530      - split header file "OBCS.h" into 4 separated files:
531        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
532       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
533         (contain no conditional statement which depends on OBCS options).
534      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
535        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
536    o ctrl, cost, grdchk & autodiff pkgs:
537      - make options file more standard (like other {PKG}_OPTIONS.h file but
538        with AD_CONFIG.h); clean-up some of the included header files.
539    o pkg/obcs:
540      - do not mask tracer when applying OB (tracer == 0 could generate problems)
541      - apply tracer OB values to tracer field only at OB location (instead of
542        over a band of OLx width)
543      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
544      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
545        obcs_apply_tloc.F & obcs_apply_sloc.F
546    o obcs in model/src:
547      - call OBCS_APPLY_W only if NonHydrostatic.
548      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
549      - reset dEtaHdt and wVel to zero outside OB interior region ;
550      - leave tracer unchanged outside OB interior region: This has no effect
551        on the solution but just to prevent unrealistic tracer value outside OB.
552      - zero out velocity outside OB interior region: This has no effect on
553        the solution but just to prevent unrealistic velocity outside OB.
554    o obcs and non-lin free-surf:
555       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
556       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
557       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
558       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
559       update results of test-exp. exp4(nlfs).
560    o exp4 (nlfs) test-exp:
561       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
562       with NonLin-FreeSurf); update output.nlfs.txt
563    o obcs and 2d/3d solver norm:
564       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
565       and outside OB interior region (will allow to place OB further inside the
566       domain). Depending on the domain, can affects cg2d-Norm (previous
567       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
568       and cg3d-Norm (previous Norm was computed before canceling OB terms),
569       e.g. in tutorial_plume_on_slope.
570      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
571    o pkg rbcs:
572      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
573      - add capability to apply relaxation to horizontal velocity uVel & vVel.
574    o pkg/grdchk: add gradient check for control variable xx_shifwflx
575    o pkg/shelfice/shelfice_init_fixed.F
576      fix CPP-flag combinations
577    o pkg/seaice: Merge iceage code of Pierre Rampal
578      * update/change/correct ice age calculations
579      * add age updates for pathological cases
580      Probably needs more testing...
581    
582    checkpoint62x (2011/05/13)
583    o pkg/mom_vecinv:
584       high-order vorticity scheme: use interior masks (maskInW & S)
585       to zero-out (outside OB) gradient of vorticity.
586    o verification exp.:
587       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
588       hs94.128x64x5 and seaice_obcs ; update results.
589    o pkg/obcs:
590      fix bug in OBeta for YZ sections in obcs_exf_load.F
591    o pkg/ctrl, pkg/shelfice, and optim:
592      - add new control variable xx_shifwflx (fresh water flux underneath ice
593        shelves). This is almost as tedious as obcs-ctrl, because the
594        variables needs its own mask.
595      - add a cost function term that penalizes the deviation of xx_shifwflx
596        from the first guess (zero) in analogy to other control variables
597    o pkg/shelfice:
598      - start basic adjoint
599    o pkg/ctrl:
600      - remove extra 2D field "for good measure" when initializing in
601        ctrl_set_globfld_[xy/xz/yz].F
602      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
603      - improve error messages in ctrl_set_unpack_*
604    o OBC implementation in momentum:
605       use interior masks (maskInC,W & S) in momentum S/R:
606       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
607       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
608       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
609       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
610       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
611        (and also with Leith/Smagorinsky harmonic-viscosity).
612       Update output of experiment dome and exp4 (+nlfs).
613    o exp4 test-exp:
614      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
615        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
616        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
617        time-varying OB at Western-side for wVel (NonHyd); update output.
618      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
619        and biharmonic-viscosity ; also use prescribed time varying OB.
620    o pkg/obcs:
621      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
622    o model/src:
623      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
624      - initialise startTime & nIter0 with unlikely values: allows to set one
625        from the other without ambiguity.
626    o seaice_obcs test-exp.:
627      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
628    o pkg/obcs:
629      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
630        no longer needed with maskInC,W,S in pkg/generic_advdiff.
631    o pkg/seaice:
632      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
633        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
634      - fixed bug in the initialization of sea ice salinity variable HSALT
635        in seaice_init_varia.F  (removed dependence on ICE2WATR)
636    o fizhi-cs test exp.:
637       switch reference output convention for these 2 non-standard test-exp,
638        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
639          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
640       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
641    o model/inc:
642      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
643        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
644    o pkg/seaice:
645      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
646    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
647      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
648        and initial HSALT
649    
650    checkpoint62w (2011/04/26)
651    o pkg/mom_fluxform:
652      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
653      - use parameter "sideDragFactor" in no-slip BC side-drag part.
654      - update output of exp. global_ocean.90x40x15
655    o pkg/mom_vecinv:
656      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
657    o update seaice exp.:
658      use more consistent parameter values (remove "backward compatability only":
659       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
660      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
661       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
662    o update test-exp global_ocean.90x40x15:
663      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
664      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
665      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
666      o turn on zStar & viscA4 in standard set-up (dir input/)
667        and update output files: output.txt & output.dwnslp.txt
668    o new AD-test experiment: obcs_ctrl
669      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
670    o pkg/dic:
671      fix two bugs in handling water vapour pressure in carbonate chemistry
672      and air-sea fluxes. Found by Val Bennington and Galen McKinley
673      (add DIC Option = WATERVAP_BUG to recover old results)
674      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
675    o adding allowInteriorFreezing option to check for water below freezing point
676      at depth and bring the negative heat anomaly to the surface level
677    o pkgs _fields_load:
678      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
679      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
680        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
681        rbcs to get interpolation weights and time reccord number.
682      - fix multi-threading in aim_fields_load.F
683      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
684    o external_fields_load:
685      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
686       interpolation weights) to use in a periodic time-series ; do not divide by
687       time-step to convert to integer:
688       - this fixes case where externForcingPeriod is not multiple of time-step
689          (Thanks to Christopher L. Wolfe)
690       - this fixes case where externForcingPeriod is an odd multiple of time-step
691         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
692      store index of time-record which is currently loaded:
693       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
694       - needed for the adjoint but not yet used because of extensive recomputations;
695         (to be fixed soon)
696    
697    checkpoint62v (2011/04/02)
698    o verification/1D_ocean_ice_column added to test Ian Fenty's
699      pkg/seaice_growth.F modifications for improving sea ice code differentiability
700    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
701      (new velocity statistics after changing maskInW & maskInS definition)
702    o pkg/generic_advdiff with OBCS:
703      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
704      equivalent to assumption of no tracer gradient outside the OB region.
705      This will affect the results if using obcs+biharmonic diffusion.
706      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
707    o pkg/obcs:
708      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
709      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
710      in Interior region. No impact on solution but affects Velocity monitor stats.
711    o pkg/ptracers (adjoint)
712      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
713      tape file for each tracer
714    o model/inc/src and pkg/autodiff: add parameters that allow to turn
715      of parts of the adjoint code at run time. For now, there are only
716      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
717      parameters are set in data.pkg.
718      This is the lazy coward's version of doing this, but still useful for
719      debugging. In order to do it right, everything needs to be moved to
720      pkg/autodiff.
721    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
722      the end; this fixes the adjoint balancing code for open boundaries.
723    o pkg/ctrl:
724      - change behavior of xx_${varname}period to be analogous to exf-conventions:
725        xx_${varname}period =   0.,  means time-independent control part
726        xx_${varname}period = -12., means one-year-periodic monthly control part
727      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
728        clean up ctrl_init a little, remove unused variables
729      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
730      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
731    
732    checkpoint62u (2011/03/15)
733    o model/src:
734      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
735        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
736      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
737        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
738    o pkg/ctrl/obcs/ecco:
739      - remove obsolete, unused, and partially broken code:
740        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
741        ALLOW_CTRL_OBCS_BALANCE
742      - put a stop statement into ecco/cost_obcsvol.F, but also add
743        cost_obcsvol to ecco_ad_diff.list
744    o pkg/ecco: fix counting cost function contributions for obcs (code
745      by Matt M.) and diffkr for diagnostics
746    o pkg/ecco, pkg/ctrl, pkg/grdchk:
747      add cost penalty terms for initial uvel, vvel, eta controls
748      and I/O for prior error files
749    o pkg/mdsio:
750       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
751       (new argument) to check for tiled file in mdsioLocalDir : this fix the
752       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
753    o pkg/ctrl:
754     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
755       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
756       unused and superfluous variables
757     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
758    o pkg/ecco
759     - enable adjoint of Stevens OB
760    o pkg/ctrl/ecco/grdchk:
761      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
762        Fortunately, we do not have any tests for the numerous cpp-flagged
763        option of "obcs as control parameters" so we will never know
764        if this is an improvement (but at least now things compile).
765      - remove an obsolete initialization from ecco_cost_init_barfiles.F
766      - fix some problems within never used ifdefs to make the code compile
767    o pkg/obcs:
768     - Refine Interior mask definition to work with more complex OB (e.g.
769       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
770       read in Interior mask from file. Check if Interior mask is consistent
771       with OB list of indices.
772    o pkg/seaice
773     - beginning code for a seaice tracer package,
774       but currently only used for seaice age: SEAICE_AGE
775       SEAICE_num = 4
776       iTracer = 1: area-weighted ice age
777               = 2: volume-weighted ice age
778               = 3, 4: template for one-year vs. multi-year ice
779       data.seaice has new namelist SEAICE_PARM03 for arrays related to
780       SEAICE_num
781    
782    checkpoint62t (2011/03/05)
783    o pkg/obcs:
784     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
785       then normal component. This ensures that the normal component is set
786       correctly even when it conficts with tangential setting from an other OB.
787       Affects results of test-experiment seaice_obcs: update the output.txt
788    o pkg/obcs:
789     - add code to monitor statistics of dynamical fields at OB.
790     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
791       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
792       - change default: balance the Net inflow through all OB (instead of balancing
793         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
794     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
795       to match Nortern OB inflow (OBCS_balanceFacN=0).
796    o pkg/seaice:
797     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
798    o pkg/seaice (seaice_growth v 1.113):
799     - reverting seaice_growth to v 1.111 in order to have code with exact bit
800       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
801       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
802       runtime flag SEAICEareaFormula is kept but is inactive
803    o model/src:
804     - add new param to scale curvilinear grid distance and area when using
805       a different sphere radius from the grid-files.
806     - test/check multi-threads EXCH applied to local variable (cg2d_x)
807    o adjoint:
808     - enable adjoint of Stevens OB
809     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
810       (a bit delicate because of potentially modified adj. common block structure;
811       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
812    
813    checkpoint62s (2011/02/15)
814    o pkg/seaice (seaice_growth v 1.112):
815     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
816       computing the ice cover tendency from effective thickness tendencies. Include
817       Ian Fenty's formula.
818     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
819       SEAICEareaFormula.
820     - simplify notations for the various d_HEFF/d_AREA terms.
821    o pkg/gmredi:
822     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
823       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
824       add a verification test-run (front_relax.bvp) to test GM_useBVP.
825    o pkg/seaice (seaice_growth v 1.111):
826     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
827     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
828       also melt ice.
829    o pkg/seaice:
830     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
831     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
832    o pkg/cheapaml:
833     - from Nico Wienders: New version of this package.
834    o pkg/flt:
835     - add CPP options to prevent floats to re-enter the opposite side of
836       a periodic domain (default: keep periodicity)
837    o pkg/gmredi:
838     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
839       (needed for multi-dim advection).
840     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
841    o model/src:
842     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
843    o tutorial_tracer_adjsens
844     - extend to NLFS and replace maskC by hFacC
845       (change reference output accordingly)
846    
847    checkpoint62r (2011/01/24)
848    o testreport:
849     - add option -deloutp (-do) to remove output file after successful run
850     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
851       extract exact list of procs from this file ; adjust COMMAND by
852       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
853    o pkg/ecco: replace old ineffective way of penalizing deviations from
854      first guess (of obcs) with code by Matt Mazloff
855    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
856      exf/cal
857      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
858        and handle case of obcs?period == 0
859        Not affected by these changes: There is still an inconsistency in
860        the computation of start/endrec for the obcs variables for ALLOW_CAL
861        defined (see comment by Menemenlis, 7-Mar-2003)
862      - make S/R ctrl_get_gen_rec return something meaningful even if
863        ALLOW_CAL is not defined
864      - ctrl_getobcs?: simplify code so that it does not need to use
865                       S/R exf_swapfields
866    o testreport:
867       allow to test MPI with different number of processors for each experiment:
868       create file "SIZE.h.mpi" in each build dir.
869       Note: update of "-command" argument not yet implemented.
870    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
871      alleviate the need for additional 3D tapes when using
872      the non-inear free surface in the adjoint. This is done
873      by adding an 'update' of hfacc etc. to their current
874      value at the beginning of forward_step.F.
875    o pkg/seaice
876      seaice_lsr: move stress-divergence computations out of outer pseudo-
877      timestepping loop
878    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
879      up, so that the calls of the ctrl_* subroutines are really at the end
880      of the routine.
881    o pkg/gmredi:
882      allow to specify a 2-D horizontal map and a 1-D vertical profil
883      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
884    o pkg/seaice:
885      move lsr iterations from seaice_dynsolver to seaice_lsr.
886    o pkg/seaice:
887      reduce memory footprint of seaice mutldim advection tapes,
888      by using a 2D tape independent of the generic_advdiff ones,
889      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
890    
891    checkpoint62q (2010/12/29)
892    o model/src:
893      - check horizontal grid-spacing for unset or zero/negative values.
894      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
895    o pkg/flt:
896      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
897      - precision of input and output files set according to readBinaryPrec
898        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
899      - initial float position from tiled file was not converted to index space
900        (looks like a bug): fixed to make it similar to initial pos. global file.
901    o global_ocean.cs32x15:
902       change SIZE.h of AD set-up to get same tiling as with MPI.
903       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
904    o model/src:
905       add flag to control printing of domain fields (bathymetry, hFac ...) in
906       ini_mask_etc (call to plot_fieds_xy*).
907    o pkg/thsice:
908       if useEXF, some forcing fields are not valid in overlap: fixed by computing
909       over the interior only + apply EXCH at the end (like with SEAICE advection).
910    o pkg/mdsio:
911      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
912        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
913      - change barrier call for safe multi-threads access to 3-D shared buffer.
914      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
915      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
916        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
917    o pkg/flt:
918      - add fourth-order Runge-Kutta integration
919      - add basic exch2 support (only 1 facet supported so far!)
920    o pkg/mdsio+rw:
921      new S/R to read local (or tile independent) vector (read counterpart of
922       mds_writevec_loc, and front-end write_glvec_rl/rs).
923    o global_ocean.cs32x15: additional input_ad.seaice experiment
924        that uses pkg/seaice rather than pkg/thsice.
925        (using multidim advection for seaice)
926    o towards more F95 syntax for array specification in namelist:
927      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
928        of all verification experiments.
929           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
930          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
931      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
932    o global_ocean.cs32x15: additional input.seaice experiment
933        that uses pkg/seaice rather than pkg/thsice.
934    
935    checkpoint62p (2010/12/17)
936    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
937        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
938    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
939        allow for use of multim. advection in seaice adjoint.
940    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
941      - first attempt to close budgets by taking into account the freshwater
942        flux implied by the sublimation of snow and ice. So far only the
943        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
944        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
945    o eesupp/src:
946      new S/R with new option (NML_EXTENDED_F77) to change array specification
947      from F95 standard to commonly accepted extended F77 form.
948      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
949      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
950      for less tolerant f77 compiler (e.g., pgf77, g77).
951    o globalFiles:
952      commented out in parameter file "data" since it's not safe with MPI
953      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
954      in this case); no longer commented out in restart test (tst_2+2).
955    o add adTapeDir to specify a special directory where adjoint tapes are
956      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
957      and cannot be used together with mdsioLocalDir.
958    o nesting pkgs:
959      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
960      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
961      - add parameter files + utils dir + output from short run on beagle.
962    o pkg/seaice:
963        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
964    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
965      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
966    
967    checkpoint62o (2010/11/25)
968    o pkg/exf:
969      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
970    o pkg/seaice:
971      - seaice_ocean_stress: split a loop for better vectorization of the
972        adjoint code
973      - seaice_growth.F: fix bug in conservation of freshwater connected to
974        capping of heff, put contribution into d_HEFFbyNEG
975      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
976        by something more sensible (parameters that are what their name implies)
977      - change some defaults, so that by default exf-parameters are used for
978        things like rhoAir, cpAir,latent/sensible heat parameters, in order
979        to reproduce the old results, many data.seaice now contain funny values
980        for cpAir and latent heat of sublimation
981    o packages_readparms.F: move exf_readparms up in line so that
982        exf-parameters are visible for other packages (e.g. seaice)
983    o debugMode & debugLevel=2:
984      - differentiate between debugMode & debugLevel=2:
985        debugMode: controls printing of debug messages (sequence of S/R calls).
986        debugLevel: controls printing of algorithm intermediate results and stats.
987      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
988        => allows to print debug-stats without all sequence of call messages.
989      - switch control of debug print from debugLevel to debugMode in many S/R.
990    o pkg/obcs (obcs-sponge):
991        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
992        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
993    o pkg/generic_advdiff:
994      - record overlap minimum size for each advection scheme;
995      - refine criteria on overlap minimum size;
996      - check and stop (in gad_check) if overlap size is too small.
997    o pkg/obcs:
998      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
999        once, in ptracers_implicit.F)
1000      - with seaice: remove test on empty file name in obcs_apply_seaice (always
1001        apply OB values when tile has OB)
1002    o model/src, coriolis setting:
1003      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
1004        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
1005        files (selectCoriMap=3) with any grid.
1006      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
1007    o pkg/seaice/seaice_growth.F:
1008        a few cosmetic changes that reduce the number of lines of code
1009    o pkg/obcs: add boundary conditions following Stevens (1990)
1010      - the code follows old MOM/NAOSIM code
1011      - so far it is only implemented for the eastern and western boundaries
1012        and NOT for pTracers
1013    o pkg/rbcs:
1014      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
1015        beginning of the first rbcs forcing period.
1016      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
1017        offline package, i.e., one file per time, labeled by iteration number;
1018        deltaTrbcs sets the timestep with which the data was generated;
1019        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
1020      - rbcsForcingCycle=0 makes forcing non-cyclic.
1021      - make arithmetic safe for negative times and odd forcing periods.
1022    
1023    checkpoint62n (2010/11/09)
1024    o pkg/seaice:
1025        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
1026    o pkg/obcs:
1027       New S/R to copy tracer value from the OB location to narrow band region
1028        (width = same as overlap) beyond the OB: preserve OB value (needed for
1029        high-order scheme) which were overwritten by EXCH call if in overlap
1030        region. Applied to theta, salt, ptracer and advected seaice variables.
1031       With seaice: use maskInC in similar way as in gad_advection.F,
1032        in seaice_advection.F and advect.F.
1033       Update output of experiment seaice_obcs and change exp4 to test OBCS with
1034        4th order Adv.Scheme. for pasive salt and ptracer.
1035    o tools/genmake2:
1036      - when looking for an optfile (not specified), only search for Fortran compiler
1037        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
1038      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
1039        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
1040      - set default for CPP to "cpp -traditional -P" (was the case without specifying
1041        an optfile, but otherwise default was just "cpp".
1042      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
1043      - when "CC" is not set in the optfile, look for possible C compiler
1044        (instead of just setting CC=cc)
1045      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
1046        => add a ".F" to ".o" rule for source files with no "#include" (such as
1047           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
1048      - move gfortran before g77 in list of possible Fortran compiler (consistent
1049        with reference compiler switch from g77 to gfortran)
1050    o pkg/seaice:
1051      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
1052        seaice_check that stops the model, when the CPP flag is used.
1053      o seaice_growth.F: make capping of ice volume conserving by returning the
1054        capped ice as freshwater to EmPmR. This does not change the verification
1055        experiments but will change runs where the capping is acutally active
1056    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
1057      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
1058         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
1059         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
1060    o tools/genmake2:
1061      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
1062      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
1063      - clean previous genmake log files before anything else.
1064      - change Makefile to remove testreport log files (*.tr_log) and genmake log
1065        files only with "CLEAN" target (instead of "Clean");
1066    o pkg/generic_advdiff:
1067      Change OBCS in multiDim advection (gad_advection.F):
1068       Use maskInC to prevent intermediate update of tracer-field in OB regions,
1069       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
1070       which were applying future time-step OB values.
1071      This way, all explicit calculations use current-time-step OB values
1072       (simpler and more consistent).
1073      Affects results when set-up uses time-varying OBC and multi-dim advection;
1074       update output of experiment seaice_obcs.
1075    o pkg/seaice:
1076      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
1077       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
1078         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
1079      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
1080       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
1081       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
1082    o pkg aim (2010/10/26):
1083      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
1084        formulation with obliquity, eccentricity, ... as run-time parameters,
1085      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
1086        upward shortwave radition at the surface (all-sky and clear-sky).
1087    o pkg/obcs:
1088      - writing sections with globalFiles=T does not work: switch to tiled-files
1089        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
1090      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
1091      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
1092    
1093    checkpoint62m (2010/10/21)
1094    o pkg/seaice: vectorize seaice_solve4temp.F
1095      - move iterations loops outside of i/j-loops
1096      - requires 2D arrays for TB and effConduct
1097      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
1098        modified in this routine
1099      - a little bit of clean up, adjusting indentation, etc.
1100      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
1101        performance and '**TWO' by '**2' (because TWO is a float),
1102        replaced ONE, ZERO
1103    o eesupp/src:
1104       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
1105    o pkg/seaice/seaice_growth.F
1106      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
1107      merging process. The merged routine has two branches, and one activates the 'evolution'
1108      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
1109      In summary, here is what the '10/10 revision' did consist of
1110        part 1: seaice_growth.F revisions 1.71 to 1.75
1111          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
1112            The emphasis here was on improving readability (e.g. by trying to use meaningful
1113            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
1114        part 1.5:
1115          - revising the lab_sea experiment to make it a more useful (i.e. stable
1116            and representative of an actual model run). This was done by generating a
1117            (winter) pickup to start from, switching back the main experiment dynamic
1118            solver from evp to lsr, having one of the experiments use the free drift solution.
1119        part 2: seaice_growth.F revisions 1.76 to 1.85
1120          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
1121          - Sorting out the various fields units and sign (set early on and reset at the end)
1122            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
1123            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
1124          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
1125            and simplifying logical expressions to further improve readibility.
1126        part 3: seaice_growth.F revisions 1.86 to 1.89
1127          - Re-organize the blocks of code more logically.
1128          - Merging the '_if.F' pieces that add something new.
1129    o pkg/thsice:
1130      - vectorize thsice_solve4temp and thsice_get_exf.
1131        Problem: thsice_solve4temp has an unvectorizable statement that
1132        might also be problematic for TAF
1133      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
1134        does not change the verifcation experiment, but will change all
1135        experiments that have this flag undefined (not tested in verification);
1136        a little reorganization to save a few 2D fields and recomputations
1137      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
1138      - 2nd step:  fix some store dirs
1139        o seems to work somewhat, i.e. using ifort but not g77
1140        o likely cause are incomplete init. or recomputation
1141        o start verification/global_ocean.cs32x15/input_ad.thsice
1142    o pkg/obcs: add support for exch2
1143      - the position of the boundary and prescribed values are specified using
1144        a global domain with exch2 facets stacked
1145        - in x for N,S boundaries (like W2_mapIO=-1)
1146        - in y for E,W boundaries (so E,W boundaries do not overlap)
1147    o pkg/mdsio: add support for writing global sections with exch2
1148        file layout is as for obcs described above:
1149        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
1150        - for y-z sections, facets are stacked in y
1151    o pkg/thsice:
1152       - change a few routines for better vectorization: thsice_albedo.F,
1153         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
1154         not affected, but in particular the latter routine has changed
1155         dramatically (not necessarily easier to read now).
1156       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
1157       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
1158    o verification/lab_sea:
1159      - overhaul of the forward model experiments. The main motivation
1160        for this revision is that lab_sea has proven quite fragile (when
1161        changing the sea-ice code, and switching platforms) to a point
1162        when failures were very hard to attribute to specific code problems.
1163      - the suspected reason for this fragility is noise amplification by evp so,
1164        to start with, we decided to replace evp with lsr in the main experiment.
1165      - the input.lsr experiment thus became obsolete and was removed.
1166      - it was replaced with the input.fd experiment that uses an
1167        analytical "free drift" solution as the ice velocity field.
1168      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
1169        will hopefully allow us to discriminate problems due to dynamic solvers
1170        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
1171        us to test additional options, along with the salt plume package.
1172      - Finally a pickup was generated (at the end of a one year run) to
1173        make the tests more representative of an actual model run. Previously
1174        the tests starting point was a 1m thickness of ice everywhere.
1175    o pkg/seaice:
1176      - introducing S\R seaice_freedrift.F that compute the
1177        analytical solution to an approximate ice momentum
1178        equation (i.e. the simple stress/coriolis balance).
1179      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
1180        of the free drift velocity field, and enable its use.
1181        To actually use the free drift solution as the model ice
1182        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
1183    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
1184    
1185    checkpoint62l (2010/10/04)
1186    o pkg/seaice:
1187      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
1188      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
1189       version (with USE_ORIGINAL_SBI undef);
1190    o add hooks for new packages OASIS, the package will follow
1191      (hooks exclude the seaice pkg for now)
1192    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
1193      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
1194      rather than mdsio_readvector.F/mdsio_writevector.F, within
1195      adread_adwrite.F to read/write adjoint-related tapes to disk.
1196    o eesupp and pkg/mdsio: ALLOW_WHIO
1197      Option to write/read 2D fields to files including tiles halos.
1198      The main purpose is for adjoint related "tape I/O".
1199      The secondary purpose is for debugging phases.
1200      A word on those rather specifically intended purposes.
1201      The code was meant to be stripped down to the bare minimum.
1202      Typically, there is a unique and basic mapping to the global
1203      buffer (tile by tile, then proc by proc, then level by level), and
1204      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
1205      meant to generate user friendly outputs of various shapes and forms.
1206      Rather it is intended, for the knowledgeabale developers,
1207      to be largely independent of the many mdsio options, to allow
1208      outputs of tiles+halos in debugging phases and in adjoint runs,
1209      and to allow some flexibility in tuning (adoint) I/O depending on each
1210      file system behavior. With regard to tuning, most of the potential knobs
1211      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
1212      to specify directories, to specify the typical size of I/O calls, etc.)
1213      are not yet included, and will be added if they prove useful.
1214    o pkg/seaice:
1215       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
1216    o pkg/seaice:
1217       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
1218       code (seaice_budget_ice_if.F) which enable to recover old standard
1219       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
1220       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
1221    o model/src (rStar):
1222       use simple average (not area weighted) of rStarFac at U,V point when using
1223       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
1224       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
1225    
1226    checkpoint62k (2010/09/17)
1227    o adjoint
1228       * changed verification/global_ocean.cs32x15 ; adjoint now tests
1229         Adams-Bashforth 3 + NLFS + RSTAR
1230       * some more modifs required for ECCO-GODAE v4
1231    o pkg/seaice
1232       add SEAICE_AGE_VOL option to use volume instead of area for
1233       integrating SEAICE_AGE
1234  o model/src:  o model/src:
1235     first check-in of sigma & hybrid-sigma coordinate code ; also includes     first check-in of sigma & hybrid-sigma coordinate code ; also includes
1236     non-linear free-surface parts ; but pressure-gradient not yet coded.     non-linear free-surface parts ; but pressure-gradient not yet coded.
# Line 273  o tools/build_options: Line 1500  o tools/build_options:
1500      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
1501  o pkg/ecco  o pkg/ecco
1502    - allow user defined cost function contributions    - allow user defined cost function contributions
1503          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
1504          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
1505    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1506        the two options are complementary.        the two options are complementary.
1507  o pkg/smooth  o pkg/smooth
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