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revision 1.1295 by jmc, Sat Sep 11 21:39:13 2010 UTC revision 1.1519 by jmc, Tue Oct 25 12:35:08 2011 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint63d (2011/10/25)
8    o pkg/obcs + seaice-dynamics:
9      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
10        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
11        values (consistent with an implicit method).
12      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
13        return to older implementation (same results as before); note that none of
14        the "experimental" OBCS_SEAICE options are implemented in the new version.
15      - switch test exp. seaice_obcs to use new version (update output).
16    o pkg/seaice:
17      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
18      - add parenthesis in Water-Ice drag calculations (evp & lsr);
19      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
20        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
21      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
22        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
23    o pkg/layers:
24      - Include potential density as new coordinate (Thanks to David Munday)
25    o pkg/dic:
26      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
27        carbonate computation/output to CALC_PCO2_APPROX
28    o pkg/generic_advdiff
29      - make TAF generate code that vectorizes:
30        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
31    o model/src:
32      - improve vectorization also for adjoint code of
33        solve_tridiagonal and solve_pentadiagonal. As this requires up to
34        5 new 3D-fields, this code is only turned on for the combination of
35        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
36        for singular matrix check (only for TARGET_NEC_SX).
37      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
38        ALLOW_AUTODIFF. This flag now needs to be set outside of
39        solve_tri/pentadiagonal.F
40    o pkg/exf:
41      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
42        optional namelist EXF_NML_OBCS).
43      - add many debug-print (to trace down where pkg/cal error msg comes from)
44    o pkg/mom_vecinv/mom_vi_hdissip.F
45      - rearrange loops so that vectorization is improved and in particular
46        the adjoint routine vectorizes. The code is a little longer now, but I
47        think easier to read.
48        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
49    o pkg/seaice:
50      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
51    o pkg/exch2:
52      - alternative code (without tile x tile matrix) for cumulated (global) sum;
53        used as default; keep using matrix version in adjustment.cs-32x32x1.
54    o tools/build_options:
55      - after merging some MPI and/or multi-threads specific optfiles so that
56        the modified default optfile support both built (using genmake2 -mpi
57        for the MPI built, using genmake2 -omp for OpenMP built),
58        move now obsolete optfiles to tools/build_options/unsupported/
59       (add copy of email sent to support list in doc/optfiles_changes.txt)
60    
61    checkpoint63c (2011/09/28)
62    o pkg/ebm:
63      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
64        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
65    o pkg/seaice (SItracer pickup)
66    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
67      To be done:
68      - thorough testing of missing fields in S/R seaice_read_pickup
69      - thorough matching between generic tracers and specific fields used
70        (e.g. volume-weighted age, area-weighted age, salinity, ...)
71    o pkg/grdchk:
72      - all procs calculate and print finite-difference gradient (for testreport)
73      - change description output used by testreport;
74      - AD testing: also compare and report Finite-difference gradient;
75        => update all output_adm*.txt
76    o test exp. global_ocean_ebm:
77      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
78        and turn on exactConserve; update (fwd) output.
79    o pkg/seaice (LSR):
80      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
81      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
82        * identical results with non-CS topology (but save up to half of EXCH calls)
83        * no much changes in cs-32 verification tests since no ice at face edges
84         (differences due to convergence criteria, since nb of iterations changed)
85        * expect some differences on lat-lon-cap grid.
86        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
87    o pkg/exch2:
88      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
89        many tiles); until alternative coding is added, just add a stop.
90    o pkg/kpp:
91      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
92        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
93    o optfiles:
94      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
95        into corresponding standard one, which now support different build:
96        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
97      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
98    o pkg/obcs (seaice):
99      - add missing EXCH for uIce,vIce after applying OBCS;
100      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
101        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
102        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
103      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
104      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
105        and eedata.mth for MPI and mutlti-threaded testing.
106    o pkg/flt:
107      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
108      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
109      - fix pickup and trajectories + profiles output with multi-threads;
110      - add parameter to select group of fields to write along trajectory and
111        profile (default unchanged);
112      - only call PORT_RAND* function when flt_noise <> 0;
113      - add multi-threaded test for verification exp. flt_example.
114    o eesupp/src:
115      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
116      - USE_OMP_THREADING: check that number of threads (from eedata) matches
117        actual number (from env.var. setting).
118    o pkg/ebm:
119      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
120      - add multi-threaded test for verification exp. global_ocean_ebm
121    
122    checkpoint63b (2011/08/29)
123    o pkg/ebm:
124      - fix sign of runoff;
125      - update directly forcing fields (Qnet,EmPmR) to use standard
126        external_forcing_surf.F (remove ebm_forcing_surf.F);
127      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
128      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
129        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
130      - update global_ocean_ebm parameters file data and update output (fwd+ad).
131    o verification/matrix_example:
132      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
133        MPI and mutlti-threaded testing.
134    o pkg/matrix:
135      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
136      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
137      - fix for multi-threaded (remove DATA statement);
138      - use standard DIFFERENT_MULTIPLE function;
139      - add MATRIX_OPTIONS.h
140    o verification/matrix_example:
141       To allow to split the domain in several tiles, change the domain size
142        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
143        Western side) of land points.
144    o (*_)write_pickup:
145      - fix few bugs in mypackage_read/write_pickup.F
146      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
147        array of length 1 (was caught by compiler syntax-check).
148    o pkg/diagnostics (velocity potential solver):
149      - fix initialisation of main diagonal matrix (for overlap values)
150    o tools/build_options:
151      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
152        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
153      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
154        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
155        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
156        and use "-devel" testreport option for standard testing on baudelaire.
157    o pkg/grdchk:
158      - Assume that all gradient-check position are within the same tile
159        corresponding to global indices (iGloTile,jGloTile) and that
160        positions (i,j indices or nbeg) are local to this tile;
161      - set tile local-indices and proc. number according to tile global-indices;
162      - remove grdchkwhichproc from namelist (retired param);
163      - send adjoint gradient to all procs so that all procs print it to STDOUT;
164      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
165    o adding package bbl (Bottom Boundary Layer)
166      description in MITgcm/pkg/bbl/bbl_description.tex
167      example/test experiment in MITgcm_contrib/bbl
168    o adjoint verifications
169      - changed 5 experiments to multi-tiles
170        * global_ocean.90x40x15
171        * obcs_ctrl
172        * offline_exf_seaice
173        * tutorial_dic_adjoffline
174        * tutorial_tracer_adjsens
175        changed reference output for those that crossed tile boundaries
176        (changed choices of gradient check positions)
177      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
178      - temporary bug fix in grdchk_loc.F for obcs
179    o genmake2 & testreport
180      - add target "obj" (just for OBJFILES files) to Makefile;
181      - add option to specify FEXTRAFLAGS on command line.
182    o pkg/mypackage:
183      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
184    
185    checkpoint63a (2011/08/02)
186    o pkg/diagnostics (velocity potential):
187      - fix velocity-potential calculation when using OBCS: balance net inflow
188        at each level (new S/R OBCS_DIAG_BALANCE).
189      - fix some of the problems with OBCS in stream-function calculation.
190    o pkg/exf/exf_readparms.F
191      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
192        EXF_NML_OBCS) more consistent, so that you need not have these lists
193        in data.exf when they are not used.
194    o optim/optim_readdata.F:
195      - add some output about obcs variables that might help debugging
196      - add a check about nvarlength
197    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
198    o pkg/diagnostics (velocity potential):
199      - fix mask for OBCS (still problems in stream-function with OBCS);
200      - add specific parameter (default = main code CG2D params) for solver;
201      - in case of poor convergence, use solution corresponding to lowest residual.
202    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
203      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
204      and should be avoided where possible.
205    o model/src (rStar):
206      - include r* effect on reference-state (PhiRef) in totPhiHyd
207        (so that it's really the potential anomaly at the cell center);
208        affect solution only if z* with full pressure in EOS.
209      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
210        update output (because of z* in totPhiHyd and viscA4 changes);
211      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
212        @ constant r) until interpolation at constant r is implemented.
213    o pkg/diagnostics
214      - fix RCENTER diagnostics in case cell center is not at interface middle
215    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
216      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
217      that THETA and SALT are "conservative temperature" and "absolute
218      salinity"
219    o pkg/ctrl
220      - fix computation of endrec in s/r ctrl_init_rec
221      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
222    o pkg/seaice/seaice_growth.F
223      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
224        remove then obsolete STORE directives
225      - fix STORE directives for tice and tices, so that only the
226        appropriate part of the fields are stored (and not the entire
227        field); update global_ocean.cs32x15.seaice AD output.
228      - cosmetic changes: adjust CPP flags and indentation for better
229        legibilty
230    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
231      Chris Wilson)
232    o pkg/gmredi:
233       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
234       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
235    
236    checkpoint63  (2011/07/11)
237    o pkg/exch2:
238     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
239     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
240       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
241       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
242    o pkg/diagnostics:
243     - deal with pairs of post-processed diags which are computed together; in
244       particular, re-order list of diags within 1 file to save 2nd computation.
245     - add S/R to compute velocity stream-function (called after velocity-potential
246       calculation) from divergence free transport -> new diagnostics "PsiVEL".
247     - add parameter to select grid-point location where PsiVEL == 0.
248    o eesupp/src:
249       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
250       (specific S/R needed with exch2 topology - for now, just print an error msg)
251    o pkg/shelfice
252     - Implement friction velocity-dependent transfer coefficients following
253       Holland and Jenkins, JPO, 1999
254       Original code by M. Losch with small modifs.
255       Enable with CPP option SHI_ALLOW_GAMMAFRICT
256       and runtime flag SHELFICEuseGammaFrict
257    o verification lab_sea & global_ocean.cs32x15:
258     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
259       does not miss some dependencies (but is slower) and also works with many files
260       (default makedepend limitation for AD built).
261     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
262    o pkg/diagnostics:
263     - add run-time parameter "useMissingValue" (def=False) to fill land-point
264        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
265       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
266     - Extend the use of "missing_value" setting from data.diagnostics for the case
267       of counter-diagnostics (where fraction-weight is zero). This applies both to
268       MNC and MDS output files.
269    o pkg/seaice/seaice_growth.F:
270      - add 'a priori' cap of latent heat flux based on actual mass considerations
271        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
272        non-legacy seaice_solve4temp.
273      - add diagnostic of the residual sublimation freshwater flux (the freshwater
274        flux taken from the ocean if the total actual latent heat fluxes exceed
275        the maximum)
276      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
277       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
278      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
279       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
280      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
281      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
282    o verification 1D_ocean_ice_column:
283       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
284       update results
285    o pkg/diagnostics:
286     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
287       which are not filled-up but computed from other diags ; In this case, the mate
288       diag points to the primary (filled-up) diag to used for post processing.
289     - Update Velocity-potential computation using post-processed diag framework.
290     ==> Change the ordering of fields and time-periods in MDS output file
291       when using periodic averaging: now writes one time record with the full set
292       of fields for this time period, then the next time reccord (it used to be
293       one field with the full set of time records then the next field).
294         Note: this is now similar to NetCDF (MNC) output file. <==
295    
296    checkpoint62z (2011/06/21)
297    o adjoint monitor:
298     - Add adjoint monitor output for packages exf, seaice
299       and update relevant testreport output
300    o pkg/seaice:
301     - re-order diags inits so that they appear in order in available_diagnostics.log
302     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
303       area/heff/hsnow preceeding thermodynamic growth/melt.
304     - modified diag: SIdA; output actual effect, as the description states.
305     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
306     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
307       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
308        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
309     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
310     - added diagnostics for seaice generic tracers (SItr*).
311     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
312     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
313     I. Fenty: 18-Jun-2011:
314     Minor changes to seaice package:
315     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
316        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
317       - Differentiated "regularization variables" from "floor variables"
318        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
319        * hiceMin became SEAICE_hice_reg (old hiceMin)
320          (with _reg meaning regularization variable)
321       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
322        so as to ensure energy conservation when going between phases
323      - A22 was not used anywhere
324     2) Changed regularization procedure for heffActual and hsnowActual to ensure
325        well-boundedness and smooth adjoint in seaice_growth.F
326     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
327        because the old regularization always set heffActual >= 0.05 cm
328     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
329        on AREA when HEFF > 0.
330      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
331        requiring that DISABLE_AREA_FLOOR *not* be defined
332     Affected verifications:
333      - 1D_ocean_ice_column (output.txt output_adm.txt)
334      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
335    o pkg/diagnostics:
336      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
337      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
338        (was _RL, now integer) with option = 0 to retrieve all levels.
339      - add pieces of code to compute velocity potential at each level (new diagnostics
340        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
341        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
342      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
343        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
344        and in diagnostics_fract_fill.F (do not need a valid pointer for the
345        diagnostics counter-mate); check that definition of counter-diagnostic
346        includes a valid counter-mate (in diagnostics_set_levels.F).
347    o model/src (rStar):
348      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
349        affect solution only if z* with full pressure in EOS;
350        update output of test-exp global_ocean.90x40x15.
351    o pkg/seaice:
352      - introduce siEps=1e-5 parameter
353      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
354      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
355      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
356        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
357        as well as ice cover age and ridging index (attached to AREA).
358        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
359        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
360        Up to SItrMaxNum=3 tracers can be used simultaneously.
361    o pkg/salt_plume:
362      -introduce SPsalFRAC run time parameter that sets the fraction of the
363       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
364       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
365    o model debug options:
366      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
367        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
368      - Refine debug-msg printing selection (3 new levels):
369        debugMode  : controls printing of debug messages (sequence of S/R calls).
370        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
371         debLevZero =  0 ; /* level of disabled aux. msg printing */
372         debLevA =  1 ; /* level of minimum  aux. msg printing */
373         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
374         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
375         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
376         debLevE =  5 ; /* level of extensive debug printing */
377        New debugLevel default: with default debugMode value (=F),
378          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
379          and if debugMode=T, default debugLevel = 4 (debLevD).
380        Relation with previous settings:
381         debLevB (=2) corresponds to former debLevA (=1)
382         debLevD (=4) corresponds to former debLevB (=2)
383        Note:
384         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
385         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
386            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
387      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
388        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
389    o pkg/obcs:
390      - change OBCSfixTopo default from True to False (should not change the results);
391        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
392    o pkg/thsice:
393      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
394        2nd layer seaice sublimation (unlikely to happen)
395      - use Interior mask for OBCS in thsice_advection.F (similar to what is
396        done in gad_advection & seaice_advection).
397    o adjoint:
398      bug fix spotted by Gael Forget:
399      seaice_advection and thsice_advection still had
400      legacy CPP options to avoid CS corner updates for adjoint
401    o pkg/seaice:
402      => Change some of the defaults (2011/05/29):
403         - change SEAICEuseFluxForm default (from False to True)
404         - change DIFF1 default (from 0.004 m/s to 0. m/s)
405         And print warnings if DIFF1 is not set in data.seaice and centered
406          avection scheme is used without any diffusion.
407      also:
408      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
409      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
410      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
411        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
412        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
413      update results of test exp.:
414         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
415             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
416             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
417         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
418         seaice_obcs: output (SEAICEuseFluxForm=T)
419      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
420          for standard fwd & AD lab_sea tests (to keep the same output).
421    o pkg/seaice/seaice_growth.F:
422      - use Ian Fenty's capping formulas for actual ice
423      thickness thoughout EVOLUTION branch.
424      - put treatment pathological case #2) in CPP brackets
425      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
426      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
427    o pkg/seaice:
428      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
429      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
430      also pass fac as a param, which can be 1. (to update the tendency
431      field) or the time step (to update the field itself).
432      - seaice_advdiff.F: for multidim, call seaice_diffusion with
433      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
434      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
435      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
436      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
437    o pkg/seaice:
438      diffusion with centered advection scheme (diffus.F & advect.F):
439      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
440        to just compute the laplacian of input-field.
441      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
442      - fix flux-form version in diffus.F to conserve tracer.
443      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
444       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
445    
446    checkpoint62y (2011/05/26)
447    o pkg/seaice:
448     - seaice_growth.F : in EVOLUTION branch, always include
449       a_QSWbyATM_cover in qnet (as it should be).
450     - verification/global_ocean.cs32x15 : update results accordingly
451       (output.seaice.txt output_adm.seaice.txt).
452    o pkg/seaice + obcs:
453     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
454       equivalent of assuming no tracer gradient outside the OB region.
455       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
456     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
457       after changes above);
458     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
459       only at OB location (instead of over a band of OLx width).
460    o pkg/seaice:
461     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
462       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
463    o pkg/obcs:
464      - split header file "OBCS.h" into 4 separated files:
465        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
466       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
467         (contain no conditional statement which depends on OBCS options).
468      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
469        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
470    o ctrl, cost, grdchk & autodiff pkgs:
471      - make options file more standard (like other {PKG}_OPTIONS.h file but
472        with AD_CONFIG.h); clean-up some of the included header files.
473    o pkg/obcs:
474      - do not mask tracer when applying OB (tracer == 0 could generate problems)
475      - apply tracer OB values to tracer field only at OB location (instead of
476        over a band of OLx width)
477      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
478      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
479        obcs_apply_tloc.F & obcs_apply_sloc.F
480    o obcs in model/src:
481      - call OBCS_APPLY_W only if NonHydrostatic.
482      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
483      - reset dEtaHdt and wVel to zero outside OB interior region ;
484      - leave tracer unchanged outside OB interior region: This has no effect
485        on the solution but just to prevent unrealistic tracer value outside OB.
486      - zero out velocity outside OB interior region: This has no effect on
487        the solution but just to prevent unrealistic velocity outside OB.
488    o obcs and non-lin free-surf:
489       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
490       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
491       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
492       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
493       update results of test-exp. exp4(nlfs).
494    o exp4 (nlfs) test-exp:
495       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
496       with NonLin-FreeSurf); update output.nlfs.txt
497    o obcs and 2d/3d solver norm:
498       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
499       and outside OB interior region (will allow to place OB further inside the
500       domain). Depending on the domain, can affects cg2d-Norm (previous
501       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
502       and cg3d-Norm (previous Norm was computed before canceling OB terms),
503       e.g. in tutorial_plume_on_slope.
504      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
505    o pkg rbcs:
506      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
507      - add capability to apply relaxation to horizontal velocity uVel & vVel.
508    o pkg/grdchk: add gradient check for control variable xx_shifwflx
509    o pkg/shelfice/shelfice_init_fixed.F
510      fix CPP-flag combinations
511    o pkg/seaice: Merge iceage code of Pierre Rampal
512      * update/change/correct ice age calculations
513      * add age updates for pathological cases
514      Probably needs more testing...
515    
516    checkpoint62x (2011/05/13)
517    o pkg/mom_vecinv:
518       high-order vorticity scheme: use interior masks (maskInW & S)
519       to zero-out (outside OB) gradient of vorticity.
520    o verification exp.:
521       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
522       hs94.128x64x5 and seaice_obcs ; update results.
523    o pkg/obcs:
524      fix bug in OBeta for YZ sections in obcs_exf_load.F
525    o pkg/ctrl, pkg/shelfice, and optim:
526      - add new control variable xx_shifwflx (fresh water flux underneath ice
527        shelves). This is almost as tedious as obcs-ctrl, because the
528        variables needs its own mask.
529      - add a cost function term that penalizes the deviation of xx_shifwflx
530        from the first guess (zero) in analogy to other control variables
531    o pkg/shelfice:
532      - start basic adjoint
533    o pkg/ctrl:
534      - remove extra 2D field "for good measure" when initializing in
535        ctrl_set_globfld_[xy/xz/yz].F
536      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
537      - improve error messages in ctrl_set_unpack_*
538    o OBC implementation in momentum:
539       use interior masks (maskInC,W & S) in momentum S/R:
540       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
541       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
542       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
543       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
544       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
545        (and also with Leith/Smagorinsky harmonic-viscosity).
546       Update output of experiment dome and exp4 (+nlfs).
547    o exp4 test-exp:
548      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
549        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
550        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
551        time-varying OB at Western-side for wVel (NonHyd); update output.
552      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
553        and biharmonic-viscosity ; also use prescribed time varying OB.
554    o pkg/obcs:
555      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
556    o model/src:
557      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
558      - initialise startTime & nIter0 with unlikely values: allows to set one
559        from the other without ambiguity.
560    o seaice_obcs test-exp.:
561      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
562    o pkg/obcs:
563      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
564        no longer needed with maskInC,W,S in pkg/generic_advdiff.
565    o pkg/seaice:
566      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
567        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
568      - fixed bug in the initialization of sea ice salinity variable HSALT
569        in seaice_init_varia.F  (removed dependence on ICE2WATR)
570    o fizhi-cs test exp.:
571       switch reference output convention for these 2 non-standard test-exp,
572        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
573          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
574       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
575    o model/inc:
576      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
577        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
578    o pkg/seaice:
579      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
580    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
581      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
582        and initial HSALT
583    
584    checkpoint62w (2011/04/26)
585    o pkg/mom_fluxform:
586      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
587      - use parameter "sideDragFactor" in no-slip BC side-drag part.
588      - update output of exp. global_ocean.90x40x15
589    o pkg/mom_vecinv:
590      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
591    o update seaice exp.:
592      use more consistent parameter values (remove "backward compatability only":
593       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
594      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
595       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
596    o update test-exp global_ocean.90x40x15:
597      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
598      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
599      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
600      o turn on zStar & viscA4 in standard set-up (dir input/)
601        and update output files: output.txt & output.dwnslp.txt
602    o new AD-test experiment: obcs_ctrl
603      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
604    o pkg/dic:
605      fix two bugs in handling water vapour pressure in carbonate chemistry
606      and air-sea fluxes. Found by Val Bennington and Galen McKinley
607      (add DIC Option = WATERVAP_BUG to recover old results)
608      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
609    o adding allowInteriorFreezing option to check for water below freezing point
610      at depth and bring the negative heat anomaly to the surface level
611    o pkgs _fields_load:
612      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
613      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
614        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
615        rbcs to get interpolation weights and time reccord number.
616      - fix multi-threading in aim_fields_load.F
617      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
618    o external_fields_load:
619      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
620       interpolation weights) to use in a periodic time-series ; do not divide by
621       time-step to convert to integer:
622       - this fixes case where externForcingPeriod is not multiple of time-step
623          (Thanks to Christopher L. Wolfe)
624       - this fixes case where externForcingPeriod is an odd multiple of time-step
625         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
626      store index of time-record which is currently loaded:
627       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
628       - needed for the adjoint but not yet used because of extensive recomputations;
629         (to be fixed soon)
630    
631    checkpoint62v (2011/04/02)
632    o verification/1D_ocean_ice_column added to test Ian Fenty's
633      pkg/seaice_growth.F modifications for improving sea ice code differentiability
634    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
635      (new velocity statistics after changing maskInW & maskInS definition)
636    o pkg/generic_advdiff with OBCS:
637      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
638      equivalent to assumption of no tracer gradient outside the OB region.
639      This will affect the results if using obcs+biharmonic diffusion.
640      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
641    o pkg/obcs:
642      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
643      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
644      in Interior region. No impact on solution but affects Velocity monitor stats.
645    o pkg/ptracers (adjoint)
646      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
647      tape file for each tracer
648    o model/inc/src and pkg/autodiff: add parameters that allow to turn
649      of parts of the adjoint code at run time. For now, there are only
650      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
651      parameters are set in data.pkg.
652      This is the lazy coward's version of doing this, but still useful for
653      debugging. In order to do it right, everything needs to be moved to
654      pkg/autodiff.
655    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
656      the end; this fixes the adjoint balancing code for open boundaries.
657    o pkg/ctrl:
658      - change behavior of xx_${varname}period to be analogous to exf-conventions:
659        xx_${varname}period =   0.,  means time-independent control part
660        xx_${varname}period = -12., means one-year-periodic monthly control part
661      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
662        clean up ctrl_init a little, remove unused variables
663      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
664      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
665    
666    checkpoint62u (2011/03/15)
667    o model/src:
668      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
669        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
670      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
671        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
672    o pkg/ctrl/obcs/ecco:
673      - remove obsolete, unused, and partially broken code:
674        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
675        ALLOW_CTRL_OBCS_BALANCE
676      - put a stop statement into ecco/cost_obcsvol.F, but also add
677        cost_obcsvol to ecco_ad_diff.list
678    o pkg/ecco: fix counting cost function contributions for obcs (code
679      by Matt M.) and diffkr for diagnostics
680    o pkg/ecco, pkg/ctrl, pkg/grdchk:
681      add cost penalty terms for initial uvel, vvel, eta controls
682      and I/O for prior error files
683    o pkg/mdsio:
684       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
685       (new argument) to check for tiled file in mdsioLocalDir : this fix the
686       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
687    o pkg/ctrl:
688     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
689       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
690       unused and superfluous variables
691     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
692    o pkg/ecco
693     - enable adjoint of Stevens OB
694    o pkg/ctrl/ecco/grdchk:
695      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
696        Fortunately, we do not have any tests for the numerous cpp-flagged
697        option of "obcs as control parameters" so we will never know
698        if this is an improvement (but at least now things compile).
699      - remove an obsolete initialization from ecco_cost_init_barfiles.F
700      - fix some problems within never used ifdefs to make the code compile
701    o pkg/obcs:
702     - Refine Interior mask definition to work with more complex OB (e.g.
703       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
704       read in Interior mask from file. Check if Interior mask is consistent
705       with OB list of indices.
706    o pkg/seaice
707     - beginning code for a seaice tracer package,
708       but currently only used for seaice age: SEAICE_AGE
709       SEAICE_num = 4
710       iTracer = 1: area-weighted ice age
711               = 2: volume-weighted ice age
712               = 3, 4: template for one-year vs. multi-year ice
713       data.seaice has new namelist SEAICE_PARM03 for arrays related to
714       SEAICE_num
715    
716    checkpoint62t (2011/03/05)
717    o pkg/obcs:
718     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
719       then normal component. This ensures that the normal component is set
720       correctly even when it conficts with tangential setting from an other OB.
721       Affects results of test-experiment seaice_obcs: update the output.txt
722    o pkg/obcs:
723     - add code to monitor statistics of dynamical fields at OB.
724     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
725       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
726       - change default: balance the Net inflow through all OB (instead of balancing
727         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
728     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
729       to match Nortern OB inflow (OBCS_balanceFacN=0).
730    o pkg/seaice:
731     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
732    o pkg/seaice (seaice_growth v 1.113):
733     - reverting seaice_growth to v 1.111 in order to have code with exact bit
734       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
735       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
736       runtime flag SEAICEareaFormula is kept but is inactive
737    o model/src:
738     - add new param to scale curvilinear grid distance and area when using
739       a different sphere radius from the grid-files.
740     - test/check multi-threads EXCH applied to local variable (cg2d_x)
741    o adjoint:
742     - enable adjoint of Stevens OB
743     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
744       (a bit delicate because of potentially modified adj. common block structure;
745       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
746    
747    checkpoint62s (2011/02/15)
748    o pkg/seaice (seaice_growth v 1.112):
749     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
750       computing the ice cover tendency from effective thickness tendencies. Include
751       Ian Fenty's formula.
752     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
753       SEAICEareaFormula.
754     - simplify notations for the various d_HEFF/d_AREA terms.
755    o pkg/gmredi:
756     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
757       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
758       add a verification test-run (front_relax.bvp) to test GM_useBVP.
759    o pkg/seaice (seaice_growth v 1.111):
760     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
761     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
762       also melt ice.
763    o pkg/seaice:
764     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
765     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
766    o pkg/cheapaml:
767     - from Nico Wienders: New version of this package.
768    o pkg/flt:
769     - add CPP options to prevent floats to re-enter the opposite side of
770       a periodic domain (default: keep periodicity)
771    o pkg/gmredi:
772     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
773       (needed for multi-dim advection).
774     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
775    o model/src:
776     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
777    o tutorial_tracer_adjsens
778     - extend to NLFS and replace maskC by hFacC
779       (change reference output accordingly)
780    
781    checkpoint62r (2011/01/24)
782    o testreport:
783     - add option -deloutp (-do) to remove output file after successful run
784     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
785       extract exact list of procs from this file ; adjust COMMAND by
786       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
787    o pkg/ecco: replace old ineffective way of penalizing deviations from
788      first guess (of obcs) with code by Matt Mazloff
789    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
790      exf/cal
791      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
792        and handle case of obcs?period == 0
793        Not affected by these changes: There is still an inconsistency in
794        the computation of start/endrec for the obcs variables for ALLOW_CAL
795        defined (see comment by Menemenlis, 7-Mar-2003)
796      - make S/R ctrl_get_gen_rec return something meaningful even if
797        ALLOW_CAL is not defined
798      - ctrl_getobcs?: simplify code so that it does not need to use
799                       S/R exf_swapfields
800    o testreport:
801       allow to test MPI with different number of processors for each experiment:
802       create file "SIZE.h.mpi" in each build dir.
803       Note: update of "-command" argument not yet implemented.
804    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
805      alleviate the need for additional 3D tapes when using
806      the non-inear free surface in the adjoint. This is done
807      by adding an 'update' of hfacc etc. to their current
808      value at the beginning of forward_step.F.
809    o pkg/seaice
810      seaice_lsr: move stress-divergence computations out of outer pseudo-
811      timestepping loop
812    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
813      up, so that the calls of the ctrl_* subroutines are really at the end
814      of the routine.
815    o pkg/gmredi:
816      allow to specify a 2-D horizontal map and a 1-D vertical profil
817      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
818    o pkg/seaice:
819      move lsr iterations from seaice_dynsolver to seaice_lsr.
820    o pkg/seaice:
821      reduce memory footprint of seaice mutldim advection tapes,
822      by using a 2D tape independent of the generic_advdiff ones,
823      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
824    
825    checkpoint62q (2010/12/29)
826    o model/src:
827      - check horizontal grid-spacing for unset or zero/negative values.
828      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
829    o pkg/flt:
830      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
831      - precision of input and output files set according to readBinaryPrec
832        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
833      - initial float position from tiled file was not converted to index space
834        (looks like a bug): fixed to make it similar to initial pos. global file.
835    o global_ocean.cs32x15:
836       change SIZE.h of AD set-up to get same tiling as with MPI.
837       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
838    o model/src:
839       add flag to control printing of domain fields (bathymetry, hFac ...) in
840       ini_mask_etc (call to plot_fieds_xy*).
841    o pkg/thsice:
842       if useEXF, some forcing fields are not valid in overlap: fixed by computing
843       over the interior only + apply EXCH at the end (like with SEAICE advection).
844    o pkg/mdsio:
845      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
846        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
847      - change barrier call for safe multi-threads access to 3-D shared buffer.
848      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
849      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
850        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
851    o pkg/flt:
852      - add fourth-order Runge-Kutta integration
853      - add basic exch2 support (only 1 facet supported so far!)
854    o pkg/mdsio+rw:
855      new S/R to read local (or tile independent) vector (read counterpart of
856       mds_writevec_loc, and front-end write_glvec_rl/rs).
857    o global_ocean.cs32x15: additional input_ad.seaice experiment
858        that uses pkg/seaice rather than pkg/thsice.
859        (using multidim advection for seaice)
860    o towards more F95 syntax for array specification in namelist:
861      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
862        of all verification experiments.
863           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
864          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
865      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
866    o global_ocean.cs32x15: additional input.seaice experiment
867        that uses pkg/seaice rather than pkg/thsice.
868    
869    checkpoint62p (2010/12/17)
870    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
871        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
872    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
873        allow for use of multim. advection in seaice adjoint.
874    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
875      - first attempt to close budgets by taking into account the freshwater
876        flux implied by the sublimation of snow and ice. So far only the
877        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
878        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
879    o eesupp/src:
880      new S/R with new option (NML_EXTENDED_F77) to change array specification
881      from F95 standard to commonly accepted extended F77 form.
882      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
883      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
884      for less tolerant f77 compiler (e.g., pgf77, g77).
885    o globalFiles:
886      commented out in parameter file "data" since it's not safe with MPI
887      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
888      in this case); no longer commented out in restart test (tst_2+2).
889    o add adTapeDir to specify a special directory where adjoint tapes are
890      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
891      and cannot be used together with mdsioLocalDir.
892    o nesting pkgs:
893      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
894      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
895      - add parameter files + utils dir + output from short run on beagle.
896    o pkg/seaice:
897        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
898    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
899      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
900    
901    checkpoint62o (2010/11/25)
902    o pkg/exf:
903      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
904    o pkg/seaice:
905      - seaice_ocean_stress: split a loop for better vectorization of the
906        adjoint code
907      - seaice_growth.F: fix bug in conservation of freshwater connected to
908        capping of heff, put contribution into d_HEFFbyNEG
909      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
910        by something more sensible (parameters that are what their name implies)
911      - change some defaults, so that by default exf-parameters are used for
912        things like rhoAir, cpAir,latent/sensible heat parameters, in order
913        to reproduce the old results, many data.seaice now contain funny values
914        for cpAir and latent heat of sublimation
915    o packages_readparms.F: move exf_readparms up in line so that
916        exf-parameters are visible for other packages (e.g. seaice)
917    o debugMode & debugLevel=2:
918      - differentiate between debugMode & debugLevel=2:
919        debugMode: controls printing of debug messages (sequence of S/R calls).
920        debugLevel: controls printing of algorithm intermediate results and stats.
921      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
922        => allows to print debug-stats without all sequence of call messages.
923      - switch control of debug print from debugLevel to debugMode in many S/R.
924    o pkg/obcs (obcs-sponge):
925        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
926        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
927    o pkg/generic_advdiff:
928      - record overlap minimum size for each advection scheme;
929      - refine criteria on overlap minimum size;
930      - check and stop (in gad_check) if overlap size is too small.
931    o pkg/obcs:
932      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
933        once, in ptracers_implicit.F)
934      - with seaice: remove test on empty file name in obcs_apply_seaice (always
935        apply OB values when tile has OB)
936    o model/src, coriolis setting:
937      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
938        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
939        files (selectCoriMap=3) with any grid.
940      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
941    o pkg/seaice/seaice_growth.F:
942        a few cosmetic changes that reduce the number of lines of code
943    o pkg/obcs: add boundary conditions following Stevens (1990)
944      - the code follows old MOM/NAOSIM code
945      - so far it is only implemented for the eastern and western boundaries
946        and NOT for pTracers
947    o pkg/rbcs:
948      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
949        beginning of the first rbcs forcing period.
950      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
951        offline package, i.e., one file per time, labeled by iteration number;
952        deltaTrbcs sets the timestep with which the data was generated;
953        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
954      - rbcsForcingCycle=0 makes forcing non-cyclic.
955      - make arithmetic safe for negative times and odd forcing periods.
956    
957    checkpoint62n (2010/11/09)
958    o pkg/seaice:
959        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
960    o pkg/obcs:
961       New S/R to copy tracer value from the OB location to narrow band region
962        (width = same as overlap) beyond the OB: preserve OB value (needed for
963        high-order scheme) which were overwritten by EXCH call if in overlap
964        region. Applied to theta, salt, ptracer and advected seaice variables.
965       With seaice: use maskInC in similar way as in gad_advection.F,
966        in seaice_advection.F and advect.F.
967       Update output of experiment seaice_obcs and change exp4 to test OBCS with
968        4th order Adv.Scheme. for pasive salt and ptracer.
969    o tools/genmake2:
970      - when looking for an optfile (not specified), only search for Fortran compiler
971        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
972      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
973        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
974      - set default for CPP to "cpp -traditional -P" (was the case without specifying
975        an optfile, but otherwise default was just "cpp".
976      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
977      - when "CC" is not set in the optfile, look for possible C compiler
978        (instead of just setting CC=cc)
979      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
980        => add a ".F" to ".o" rule for source files with no "#include" (such as
981           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
982      - move gfortran before g77 in list of possible Fortran compiler (consistent
983        with reference compiler switch from g77 to gfortran)
984    o pkg/seaice:
985      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
986        seaice_check that stops the model, when the CPP flag is used.
987      o seaice_growth.F: make capping of ice volume conserving by returning the
988        capped ice as freshwater to EmPmR. This does not change the verification
989        experiments but will change runs where the capping is acutally active
990    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
991      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
992         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
993         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
994    o tools/genmake2:
995      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
996      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
997      - clean previous genmake log files before anything else.
998      - change Makefile to remove testreport log files (*.tr_log) and genmake log
999        files only with "CLEAN" target (instead of "Clean");
1000    o pkg/generic_advdiff:
1001      Change OBCS in multiDim advection (gad_advection.F):
1002       Use maskInC to prevent intermediate update of tracer-field in OB regions,
1003       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
1004       which were applying future time-step OB values.
1005      This way, all explicit calculations use current-time-step OB values
1006       (simpler and more consistent).
1007      Affects results when set-up uses time-varying OBC and multi-dim advection;
1008       update output of experiment seaice_obcs.
1009    o pkg/seaice:
1010      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
1011       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
1012         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
1013      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
1014       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
1015       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
1016    o pkg aim (2010/10/26):
1017      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
1018        formulation with obliquity, eccentricity, ... as run-time parameters,
1019      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
1020        upward shortwave radition at the surface (all-sky and clear-sky).
1021    o pkg/obcs:
1022      - writing sections with globalFiles=T does not work: switch to tiled-files
1023        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
1024      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
1025      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
1026    
1027    checkpoint62m (2010/10/21)
1028    o pkg/seaice: vectorize seaice_solve4temp.F
1029      - move iterations loops outside of i/j-loops
1030      - requires 2D arrays for TB and effConduct
1031      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
1032        modified in this routine
1033      - a little bit of clean up, adjusting indentation, etc.
1034      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
1035        performance and '**TWO' by '**2' (because TWO is a float),
1036        replaced ONE, ZERO
1037    o eesupp/src:
1038       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
1039    o pkg/seaice/seaice_growth.F
1040      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
1041      merging process. The merged routine has two branches, and one activates the 'evolution'
1042      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
1043      In summary, here is what the '10/10 revision' did consist of
1044        part 1: seaice_growth.F revisions 1.71 to 1.75
1045          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
1046            The emphasis here was on improving readability (e.g. by trying to use meaningful
1047            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
1048        part 1.5:
1049          - revising the lab_sea experiment to make it a more useful (i.e. stable
1050            and representative of an actual model run). This was done by generating a
1051            (winter) pickup to start from, switching back the main experiment dynamic
1052            solver from evp to lsr, having one of the experiments use the free drift solution.
1053        part 2: seaice_growth.F revisions 1.76 to 1.85
1054          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
1055          - Sorting out the various fields units and sign (set early on and reset at the end)
1056            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
1057            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
1058          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
1059            and simplifying logical expressions to further improve readibility.
1060        part 3: seaice_growth.F revisions 1.86 to 1.89
1061          - Re-organize the blocks of code more logically.
1062          - Merging the '_if.F' pieces that add something new.
1063    o pkg/thsice:
1064      - vectorize thsice_solve4temp and thsice_get_exf.
1065        Problem: thsice_solve4temp has an unvectorizable statement that
1066        might also be problematic for TAF
1067      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
1068        does not change the verifcation experiment, but will change all
1069        experiments that have this flag undefined (not tested in verification);
1070        a little reorganization to save a few 2D fields and recomputations
1071      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
1072      - 2nd step:  fix some store dirs
1073        o seems to work somewhat, i.e. using ifort but not g77
1074        o likely cause are incomplete init. or recomputation
1075        o start verification/global_ocean.cs32x15/input_ad.thsice
1076    o pkg/obcs: add support for exch2
1077      - the position of the boundary and prescribed values are specified using
1078        a global domain with exch2 facets stacked
1079        - in x for N,S boundaries (like W2_mapIO=-1)
1080        - in y for E,W boundaries (so E,W boundaries do not overlap)
1081    o pkg/mdsio: add support for writing global sections with exch2
1082        file layout is as for obcs described above:
1083        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
1084        - for y-z sections, facets are stacked in y
1085    o pkg/thsice:
1086       - change a few routines for better vectorization: thsice_albedo.F,
1087         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
1088         not affected, but in particular the latter routine has changed
1089         dramatically (not necessarily easier to read now).
1090       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
1091       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
1092    o verification/lab_sea:
1093      - overhaul of the forward model experiments. The main motivation
1094        for this revision is that lab_sea has proven quite fragile (when
1095        changing the sea-ice code, and switching platforms) to a point
1096        when failures were very hard to attribute to specific code problems.
1097      - the suspected reason for this fragility is noise amplification by evp so,
1098        to start with, we decided to replace evp with lsr in the main experiment.
1099      - the input.lsr experiment thus became obsolete and was removed.
1100      - it was replaced with the input.fd experiment that uses an
1101        analytical "free drift" solution as the ice velocity field.
1102      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
1103        will hopefully allow us to discriminate problems due to dynamic solvers
1104        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
1105        us to test additional options, along with the salt plume package.
1106      - Finally a pickup was generated (at the end of a one year run) to
1107        make the tests more representative of an actual model run. Previously
1108        the tests starting point was a 1m thickness of ice everywhere.
1109    o pkg/seaice:
1110      - introducing S\R seaice_freedrift.F that compute the
1111        analytical solution to an approximate ice momentum
1112        equation (i.e. the simple stress/coriolis balance).
1113      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
1114        of the free drift velocity field, and enable its use.
1115        To actually use the free drift solution as the model ice
1116        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
1117    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
1118    
1119    checkpoint62l (2010/10/04)
1120    o pkg/seaice:
1121      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
1122      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
1123       version (with USE_ORIGINAL_SBI undef);
1124    o add hooks for new packages OASIS, the package will follow
1125      (hooks exclude the seaice pkg for now)
1126    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
1127      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
1128      rather than mdsio_readvector.F/mdsio_writevector.F, within
1129      adread_adwrite.F to read/write adjoint-related tapes to disk.
1130    o eesupp and pkg/mdsio: ALLOW_WHIO
1131      Option to write/read 2D fields to files including tiles halos.
1132      The main purpose is for adjoint related "tape I/O".
1133      The secondary purpose is for debugging phases.
1134      A word on those rather specifically intended purposes.
1135      The code was meant to be stripped down to the bare minimum.
1136      Typically, there is a unique and basic mapping to the global
1137      buffer (tile by tile, then proc by proc, then level by level), and
1138      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
1139      meant to generate user friendly outputs of various shapes and forms.
1140      Rather it is intended, for the knowledgeabale developers,
1141      to be largely independent of the many mdsio options, to allow
1142      outputs of tiles+halos in debugging phases and in adjoint runs,
1143      and to allow some flexibility in tuning (adoint) I/O depending on each
1144      file system behavior. With regard to tuning, most of the potential knobs
1145      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
1146      to specify directories, to specify the typical size of I/O calls, etc.)
1147      are not yet included, and will be added if they prove useful.
1148    o pkg/seaice:
1149       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
1150    o pkg/seaice:
1151       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
1152       code (seaice_budget_ice_if.F) which enable to recover old standard
1153       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
1154       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
1155    o model/src (rStar):
1156       use simple average (not area weighted) of rStarFac at U,V point when using
1157       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
1158       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
1159    
1160    checkpoint62k (2010/09/17)
1161    o adjoint
1162       * changed verification/global_ocean.cs32x15 ; adjoint now tests
1163         Adams-Bashforth 3 + NLFS + RSTAR
1164       * some more modifs required for ECCO-GODAE v4
1165    o pkg/seaice
1166       add SEAICE_AGE_VOL option to use volume instead of area for
1167       integrating SEAICE_AGE
1168  o model/src:  o model/src:
1169     first check-in of sigma & hybrid-sigma coordinate code ; also includes     first check-in of sigma & hybrid-sigma coordinate code ; also includes
1170     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 1434  o tools/build_options:
1434      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
1435  o pkg/ecco  o pkg/ecco
1436    - allow user defined cost function contributions    - allow user defined cost function contributions
1437          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
1438          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
1439    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1440        the two options are complementary.        the two options are complementary.
1441  o pkg/smooth  o pkg/smooth
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