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revision 1.1687 by gforget, Wed Jul 11 21:51:27 2012 UTC revision 1.1841 by mlosch, Wed Mar 13 09:57:46 2013 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/seaice/seaice_evp.F: mask the asymmetric contribution of the ice-ocean
8      stress (when the turningAngle is non-zero) over open water to avoid
9      stripes in the EVP-solutions after many EVP-substeps. This does not change
10      the verification experiment (because turningAngle=0 in that experiment), but
11      will affect other EVP solutions with turningAngle.ne.0
12    o verification, AD & TLM output:
13      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
14        additions and multiplications which affect results at machine truncation
15        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
16        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
17        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
18        digits of matching.
19    o pkg/seaice:
20       modify lsr-algorithm so that it vectorizes AND converges by using a
21       "zebra" method: split vector loop into two with step size 2; this
22       solves a general convergence problem for the JFNK solver on a vector
23       computer. It has the potential to even improve convergence for
24       non-vector machines, but it does change the results so it is turned
25       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
26       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
27    
28    checkpoint64e (2013/03/05)
29    o pkg/ecco and several verification experiments:
30       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
31       from ecco package, and revert to unified routine in model/src/
32       Adjust verification experiments accordingly, especially gloal_oce_llc90
33       Should conclude long-standing work by Gael to reconsile the_main_loop with
34       ECCO and will enable OpenAD's revolve loop in ECCO setup.
35    o pkg/generic_advdiff:
36      - implement compressible flow method for multi-dim advection (similar to
37        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
38        TAF generates many recomputations) to use it; no yet coded with implicit
39        vertical advection.
40      - change experiment advect_cs (new output) and advect_xy (same output)
41        to test compressible flow multi-dim advection.
42    o pkg/generic_advdiff:
43      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
44        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
45    o pkg/seaice:
46      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
47        bug affects two verification experiments (lab_sea and lab_sea.hb87),
48        recover old (wrong) results by setting noSlipFac = 2. in
49        seaice_calc_strainrates.F;
50      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
51      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
52        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
53      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
54    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
55      - new subroutines seaice_lsr_tridiagu/v
56      - introduce loop bounds i/jmin/max to be able to use a restricted
57        additive Schwarz method, but not used for now.
58      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
59      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
60    o OpenAD support
61       Reorganize S/R call for overall time-stepping loop to facilitate
62       OpenAD revolve loop replacement
63       (new S/R main_do_loop.F)
64    o model/src:
65      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
66      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
67        ADAMS_BASHFORTH2.
68    o pkg/cheapaml:
69      - add new parameter (default=F, same as before) to disable full domain
70        (including land) periodicity in X & Y dir.
71      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
72        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
73        into single S/R CHEAPAML_TIMESTEP.
74    
75    checkpoint64d (2013/02/17)
76    o pkg/monitor (angular momentum):
77      - do not add Eta contribution to the total AM if using rigid-lid;
78      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
79      - horizontal discretisation: compute Zonal wind contribution separately for
80        each component (instead of from cell centered averaged) and use the 4
81        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
82      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
83        FreeSurf) if using vectorInvariant momentum.
84    o model/src (horizontal grid):
85      - move initialisation of all horizontal grid arrays to null value
86        from specific horizontal grid S/R to main S/R INI_GRID;
87      - add 2 new arrays to project model C-grid velocity on to zonal direction
88        (similar to AngleCosC & -AngleSinC but at U and V point location) and
89        compute them in S/R CALC_GRID_ANGLES.
90    o pkg/seaice: replace a hard coded parameter by a runtime parameter
91        SEAICE_JFNK_tolIter
92    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
93        preconditioner for JFNK (run LSR into the overlaps as far as possible,
94        i.e OLx/y-2, but overwrite the solution in the overlaps)
95      - extend loop range in seaice_calc_viscosity
96      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
97      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
98      - slightly modify loops in tridiagonal solver lsr-preconditioner
99      - by default remove the extra exchange in seaice_preconditioner with a
100        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
101      - modify offline_exf_seaice so that old results without RAS are reproduced
102        for output.dyn_jfnk.txt
103      in seaice_fgmres.F (unrelated to RAS)
104      - add a cpp-flag option for a re-ordered mapping (potentially more
105        efficient), but because this changes the results, turn it off by
106        default
107      - replace the save statement by local common blocks
108    o utils/matlab:
109      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
110      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
111        instead of local script "load_cs.m".
112    o pkg/seaice:
113      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
114        to the scalarProductMetric and the unrolling. By chance this does not
115        change the verification experiment, because of the particular domain
116        decomposition
117    o pkg/diagnostics:
118      - change default missing_value from UNSET_RL to -999.
119    o pkg/layers: improve vectorization of layers_fluxcalc.F
120      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
121        time spent in this routine by more than a factor of 3 on an NEC-SX8
122      - step 2: replace search algorithm by a bisection algorithm found in
123        Press et al. Numerical Recipes in Fortran. This algorithm can be
124        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
125        For now, use this algorithm only for TARGET_NEC_SX defined.
126      - moved the search algorithm into a separate subroutine, that is kept
127        within the same file for automatic inlining.
128      - modified catching potential errors
129    o pkg/ecco:
130      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
131    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
132      - modifications for ALLOW_GENTIM2D_CONTROL
133      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
134      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
135      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
136      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
137    o model/src:
138      - account for moist thermodynamics in (dry) potential temperature equation;
139        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
140        and cpl_aim+ocn.
141      - also switch to standard compiler (gfortran, was using ifort previously)
142        for fizhi-cs experiments reference output.
143    o pkg/ctrl:
144      - 1st step toward generic time-varying control variable (2D) via CPP option
145        ALLOW_GENTIM2D_CONTROL
146      - note new namelist ctrl_nml_genarr in data.ctrl
147    o verification/global_ocean.cs32x15:
148      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
149        thsice calling sequence and update "output.icedyn.txt" output file.
150    o pkg/ptracers:
151      - from Ryan A.: code to allow to restart a tracer at regular time interval
152        specifying a reset frequency and a reset-phase (for each tracers).
153    o pkg/thsice:
154      - implement new sequence of calls for thsice+seaice:
155          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
156          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
157      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
158        in CPP_OPTIONS.h) to recover old sequence;
159      - update diagnostics for Intermediate State thsice diagnostics: now filled
160        just before advection (instead of just after advection in old sequence);
161      - update output of experiment offline_exf_seaice (standard test);
162      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
163        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
164    o pkg/aim_v23:
165      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
166      - use standard pkg/mdsio routines to read & write CO2 pickup file;
167      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
168      - Implement new sequence of calls for seaice advection (with thsice and
169        seaice diffusion): do ice advection after ice-Thermodynamic (previously
170        was done before); change aim_do_physics.F (split the bi,bj loops block);
171      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
172    o pkg/thsice:
173      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
174        where just seaice diffusion is used without seaice-dynamics.
175    
176    checkpoint64c (2013/01/18)
177    o pkg/seaice:
178      - add a parameter JFNKres_tFac that can replace JFNKres_t
179        (= JFNKres_tFac*JFNKresidual before JFNK solver)
180      - add a line search option to the JFNK solver
181      - move update of u/vIce and computation of initial residual into a separate
182        routine (same file); makes the code a little easier to read (?)
183      - the line search requires computation of the residual and for some reason
184        I cannot do the update of u/vIce at the beginning of the Newton loop
185        without changing the results, so we move computation of the new residual
186        also to the end of the Newton loop, even without the line search
187    o pkg/mdsio:
188      - write missing value (corresponding to undefined array value) to meta files;
189        skip this if missing value is one (UNSET_RL would be a better value for the
190        case of undefined missing value but it's current the default missing-value);
191        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
192    o pkg/exf & thsice:
193      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
194        diagnostics) even when SHORTWAVE_HEATING is #undef;
195    o verification/cfc_example:
196      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
197        illustrate how to use it).
198    o verification/offline_exf_seaice:
199      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
200        files to only one time-record.
201      in input.thermo: narrow the 2 bands of low initial ice-concentration near
202        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
203        snapshot output; same mcPheePiston value as in thsice with
204        surf-current=0.2m/s.
205      in input.thsice: similar set-up as in input.thermo (channel with same seaice
206        initial conditions).
207    o verification/cfc_example:
208      - update file "data" with more standard choice (default rotationPeriod,
209        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
210        set deltaTFreeSurf to deltaTtracer) and update the output.
211    o pkg/layers:
212      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
213      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
214    o verification/offline_exf_seaice:
215      - set all {field}period to zero for constant-in-time forcing (not tested
216        anywhere else).
217    o verification/offline_exf_seaice:
218      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
219      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
220    o model/src:
221      - implement Finite-Volume method for (hydrostatic) presure gradient
222        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
223    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
224      - In order to be compatible with the default EVP code, this requires changing
225        the EVP code around a little; and because any small change immediately
226        breaks the lab_sea.hb87 verification experiment, the reference output is
227        updated two times (each time the remaining aggrement was only 2 digits):
228        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
229        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
230        The adjoint test lab_sea.evp also needed to be updated.
231      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
232        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
233        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
234        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
235        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
236        kept obscure, because I need to test it a little more.
237    o pkg/cheapaml:
238      - fix few incorrect type (_RL/_RS) in subroutine calls.
239    o pkg/seaice:
240      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
241        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
242    o model/src:
243      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
244        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
245        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
246    o pkg/cheapaml:
247      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
248        update output of experiment cheapAML_box.
249      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
250        and set them only in one place (cheapaml_readparms.F).
251      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
252      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
253        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
254    o model/src/the_main_loop.F:
255      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
256    o pkg/seaice:
257      - remove legacy branch code.
258      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
259    o verification/*/code*/SEAICE_OPTIONS.h:
260      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
261        SEAICE_CAP_HEFF).
262    o pkg/cheapaml:
263      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
264        to load new forcing fields.
265      - add missing "_d 0" where it's needed; + some editing (improve indentation).
266      - remove switch to "-r8" compiler option (no longer needed) in verification
267        cheapAML_box, keep same output (small trucation error differences).
268    o verification/offline_exf_seaice:
269      - add thermodynamics only test.
270    o verification/cheapAML_box:
271      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
272        keep same output (same 14 digits for cg2d).
273      - switch on "-r8" compiler option (some numerical values are missing
274        the "_d 0") and update output (only 6 digits for cg2d were preserved).
275    
276    checkpoint64b (2012/12/24)
277    o pkg/cheapaml:
278      - remove un-used variables (Qnet,EmPmR) from pickup files.
279      - store tendency of advected variables into cheapaml pickup file
280        and fix the AB-2 restart.
281    o verification/offline_exf_seaice and lab_sea adjoint:
282      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
283      - switch to 4 time steps in offline, consistent with lab_sea.
284      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
285      - update results after change of experiment seaice.
286    o pkg/seaice:
287      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
288        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
289        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
290        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
291    o model/src:
292      - add run-time parameter to select CG2D solver minimum-residual solution
293        (in case of a poor convergence).
294    o pkg/seaice/seaice_lsr.F
295      - move calculation of matrix coefficients into new
296        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
297        file; the main purpose of this change is to be able to reuse the code
298        in S/R SEAICE_PRECONDITIONER
299      - modify the computation of the residual so that the mass of sea-ice
300        is not used twice; this simplifies the calculations, but since
301        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
302        not tested in testreport---this does not affect the testreport results.
303    o verification/seaice_obcs:
304      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
305        verification/lab_sea/input.salt_plume; changes results/output.txt*
306    o model/src:
307      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
308    o pkg/seaice:
309      - improve description of parameters in seaice_fgmres.F and start
310        cleaning up the code
311      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
312        second argument
313      - add a metric based on grid cell area to SEAICE_SCALPROD; update
314        results of offline_exf_seaice.dyn_jfnk
315      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
316    o pkg/aim_v23:
317      - fix an other bug in dissipation heating (grid-cell area was missing).
318    o model/src + pkg/seaice:
319      - add global (multi-tile) linear solver for pair of tri-diagonal system
320        along X and Y lines, respectively for U and V component.
321        Note: 1) MPI and cube-exchange not yet coded.
322            2) probably not accurate for poorly conditioned / large size problem.
323      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
324        default: not compiled and not used.
325    o pkg/seaice:
326      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
327        introduce bi/bj loops and use global_sum_tile_rl instead of
328        mpi_allreduce in seaice_fgmres.F
329      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
330      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
331      - add a verification experiment for JFNK in offline_exf_seaice
332    o verification:
333      - change (for now, only fwd test) offline_exf_seaice experiment:
334        use a re-entrant channel with idealized coastline (trapezoidal shape)
335        at southern boundary to explore seaice dynamics and thermodynamics
336        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
337        secondary test (input.thsice) use thermodynamics only with SST relaxation.
338      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
339    o pkg/exf:
340      - disable "sstExtrapol" when Nr=1
341    o verification:
342      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
343        to test pkg/cheapaml.
344    o pkg/aim_v23 & pkg/shap_filt:
345      - fix dissipation heating (erroneous gravity multiplication factor).
346    o pkg/seaice:
347      - remove unused field pressPre from jfnk solver
348      - rename two subroutines in seaice_preconditioner.F
349    o eesupp/src:
350       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
351    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
352       - remove wrong parts of the rhs and the lhs (were in there
353         because I did not understand the concept of this preconditioner)
354       - add an exchange between u- and v-sweep. This increases communication
355         by a factor of two but improves the convergence of jfnk. Ideally,
356         one would like the u- and v-sweep to be independent. So far within
357         undocumented ifdefs
358       - reorganize the extra computations for printing the residuals
359    o tools/genmake2:
360      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
361        since it's not necessary (and was preventing to use MNC in some cases).
362    
363    checkpoint64a (2012/11/16)
364    o pkg/autodiff:
365      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
366        autodiff_readparms.F no longer depends on calling order (within
367        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
368        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
369        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
370    o pkg/obcs:
371      - adding tidal velocity forcing capability to obcs
372        for usage example, see verification/seaice_obcs/input.tides
373    o pkg/seaice:
374      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
375        SEAICE_LSRrelaxU/V
376      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
377    o pkg/aim_v23:
378      - implement heating from friction (bottom friction and stratospheric drag).
379    o pkg/shap_filt:
380      - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
381        dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
382    o model/src:
383      - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
384        time-constant addMass field from file (addMassFile);
385      - support for heating due to friction (and Kinetic Energy dissipation):
386        add option, run-time switch and 3-D field array + support code ; each pkg
387        or S/R can add heating contribution (if there is a sink of KE); the sum is
388        accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
389    o pkg/seaice:
390      - complete merge of ITD code into seaice_growth.F
391        from MITgcm_contrib/torge/itd/code/
392        no verification so far, but Torge Martin tested
393        "1-D test case and Beaufort set up;
394        deliver okay results after 1 model year."
395      - complete merge of SEAICE_SIZE.h into all relevant routines
396      - move computation of eta at Z-points into calc_viscosities
397        + introduce global field etaZ
398        + add different methods for computing etaZ, for now the old
399          method (simple averages of eta to Z-points) is hardwired
400        + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
401          seaice_preconditioner
402      - simplify computations for SEAICE_ZETA_SMOOTHREG
403      - seaice_preconditioner:
404        + replace one remaining press by pressLoc (mistake)
405        + adjust printing of residuals
406      - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
407        + add (SEAICE.h) and rename some counters (initiliased in
408          seaice_init_fixed.F)
409        + add _BEGIN/END_MASTER (myThid)  around print statements
410        + print total number of iterations and failures over SEAICE_monFreq
411          interval to STDOUT
412      - move control over output-messages by fgmres to seaice_jfnk to save
413        some operations
414      - move resetting initial guess for fgmres outside of seaice_fgmres_driver
415        in order to make restarts with sol .ne. zero (fgmres with restarts)
416        (seaice_jfnk.F, seaice_fgmres.F)
417      - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
418        a serious convergence problem when open boundaries are involved
419    o pkg/ggl90: fix computation of control volumes for the case of
420      ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
421      up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
422    o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
423    o pkg/autodiff
424      - Add inAdMode switch for SEAICEuseDYNAMICS:
425        SEAICEuseDYNAMICSinAdMode
426        (extend logic in ADAUTODIFF_INADMODE_SET)
427    o pkg/seaice
428      - Step 1 of merging ice-thickness distribution (ITD) code from
429        MITgcm_contrib/torge/itd/ (author: Torge Martin)
430        The code implements concept laid out in Thorndike et al. (1975);
431        code is enabled via CPP flag SEAICE_ITD
432        nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
433        code is not complete yet!!
434      - SEAICE_SIZE.h now included in almost all seaice routines
435    o verification (using seaice):
436      - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
437        global_ocean.cs32x15.seaice ; update results.
438      - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
439      - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
440        offline_exf_seaice (previously compiling B-grid).
441    o pkg/exf:
442      - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
443        to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
444        forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
445    o pkg/layers (adjust changes from Sept 19):
446      - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
447        this allows to remove "layers_maxNum" dimension from all layers arrays.
448    o pkg/layers (adjust changes from Sept 19):
449      - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
450      - snap-shot extended to all type of layers (not just the 1rst type);
451      - remove layers variables when corresponding CPP option is undef.
452    o pkg/layers:
453      - rename pkg/layers variable and add new output (layer exist & un-weighted
454        velocity in layer)
455    o pkg/seaice:
456      - simplify (?) ocean-drag coefficent computations by using
457        the same routine in all three solvers (saves some code lines)
458      - remove global fields DRAGA and DRAGS from C-grid code and
459        declare them locally in lsr.F (the only place where they are
460        still used)
461      - update AD output of lab_sea.evp (very sensitive anyway).
462    o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
463      (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
464      and SEAICEuseJFNK=.true. A few things to note:
465      - involves a FGMRES, that is parallel but very inefficient,
466        because of many scalar products (global sums) in the Gram-Schmidt
467        orthogonalization method. Needs to be replaced. Original code
468        from J.-F. Lemieux
469      - preconditioner for FGMRES is a stripped down version of LSOR
470      - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
471        preconditioner. For the preconditioner, the default is set to 10.
472      - Jacobian times vector is computed with finite differences
473      - marginally related to JFNK-solver: add a smooth regularization for
474        zeta with tanh that will improve convergence (Lemieux and Tremblay,
475        2009) for any implicit solver (not implemented for EVP because EVP
476        does not need this regularization in the first place). Define
477        SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
478    o eesupp/src:
479      - check in genmake2 that intrinsic S/R flush is available.
480      - add S/R to flush IO unit (if intrinsic S/R flush is available)
481      - flush standard & error msg unit before MPI termination
482      - if debugMode, flush IO unit after printing msg
483    o pkg/ctrl:
484      - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
485        to ctrl_set_unpack_xyz.
486    
487    checkpoint64 (2012/10/09)
488    o pkg/shelfice
489      - in mom_fluxform.F, mom_vecinv.F:
490        CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
491        Bug fix KappaRU -> KappaRV
492        does not change verification/isomip but may change other setups
493        (presumably constant KappaRU=KappaRV)
494      - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
495    o pkg/obcs:
496      - fixed some indexing bugs in obcs_seaice_sponge.F
497      - added obcs relaxation subroutines for HSALT and HSNOW
498      - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
499    o pkg/seaice:
500      - add "multicategory" parameterization for snow in analogy to ice,
501        default is off for now.
502    o pkg/obcs:
503      - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
504        see verification/seaice_obcs/input.seaiceSponge for example application.
505      - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
506        index setting by master-thread. This fix multi-threads Pb in previous modifs.
507    o pkg/layers :
508      - add diagnostics to pkg/layers
509      - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
510        (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
511    o pkg/generic_advdiff/gad_implicit_r.F :
512      - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
513    o pkg/seaice/seaice_growth.F:
514      - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
515    o pkg/obcs:
516      - change default setting of OBCS_UVICE_OLD from defined to undef;
517      - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
518        in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
519      - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
520      - change OB null index value (OB_indexNone) to -99 ; this fix the problem
521        with Southern & Western OB at a tile edge (at least in a simple set-up).
522    o pkg/obcs:
523      - change settings of OB index in case OB coincides with tile edge (shared by
524        2 tiles), so that common OB location is registered by both tiles (instead of
525        only 1). However, for Southern and Western OB, index value = 0 is not
526        recognized as valid OB index (=default null value) and needs to be fixed.
527      - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
528      - new parameter "OB_indexNone" for null index value (for now, still zero)
529        to replace hard-coded null index value of zero.
530    o pkg/exch2:
531      - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
532        always check buffer-size (but outside the loop); move checking for valid
533        index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
534        print each tile and point connection only if |W2_printMsg|>= 2 and 3.
535    o pkg/ctrl (pack & unpack):
536      - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
537        (locally defined) for different variables (+ remove the variable-specific
538        file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
539        (to be extended to other local file names in ctrl.h).
540    o pkg/flt:
541      - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
542    o pkg/mdsio:
543      - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
544    o tools/genmake2:
545      - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
546        (added by Alistair in version 1.51 for building without make depend);
547      - remove Header files list (H_SRC_FILES) from the dependence of targets
548         ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
549        place in version 1.23): this save going through staf when unrelated header
550        file has been modified.
551       Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
552        "make depend" step, still need to do "make links" before "make adtaf".
553    o eesupp/src (+ few pkg src files) & genmake2:
554      - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
555      - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
556      - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
557         upper/lower case ; account for space between "#" and undef/define)
558    o pkg/flt (with exch2):
559      - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
560      - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
561    
562    checkpoint63s (2012/09/05)
563    o pkg/ecco:
564      - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
565      - add more relevant #ifdef ALLOW_SMOOTH ones.
566      - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
567    o pkg/ctrl:
568      - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
569        ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
570      - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
571        doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
572        ctrlSmoothCorrel3D (new).
573        The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
574      - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
575      - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
576        controls when useAtmWind, and vice versa.
577      - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
578      - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
579          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
580      - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
581          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
582      - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
583        replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
584    o pkg/smooth:
585      - remove un-necessary includes.
586      - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
587        Those CPP options were never defined, and not necessary.
588    o model/src:
589      - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
590      - standard treatment of useSMOOTH.
591    o pkg/autodiff:
592      - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
593        useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
594    o pkg/exch2:
595      - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
596        + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
597      - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
598        and tiles to process mapping.
599      - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
600        moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
601        rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
602        from w2_eeboot.F to w2_readparms.F.
603    o eesupp/src:
604      - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
605        ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
606        also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
607      - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
608        is defined (remove condition on usingMPI) to match cases where MPI_INIT
609        has been called.
610      - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
611      - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
612        (so that on 1 proc, get same myPid independently of usingMPI)
613      - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
614        useCubedSphereExchange with EXCH-1 (safer).
615      - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
616    o pkg/ggl90:
617      - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
618        used in ALLOW_GGL90_SMOOTH code.
619    o pkg/flt:
620      - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
621        floats at the Southern end of the domain).
622    o eesupp/inc:
623      - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
624        but not used (and not to be used) anywhere, just for documentation.
625    o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
626      - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
627        a) can damage previously written records in any other multi-record files.
628        b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
629    o tools/genmake2:
630      - define variable MAKE within Makefile and use it in place of 'make';
631      - update AD_CONFIG.h (if needed) before building any of the executable
632        (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
633        and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
634      - always print usual warning comment 'this file is automatically generated'
635        from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
636    o pkg/cheapaml:
637      - updated to correspond to the code used in accepted paper (Nico Wienders).
638    o pkg/exf:
639        added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
640        ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
641        and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
642    o pkg/exf, autodiff, ctrl, ecco and seaice:
643        remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
644    o pkg/ctrl, ecco:
645        allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
646        Depending on useAtmWind, one is inactive, and the other is active (see
647        exf_getffields.F/exf_getsurfacefluxes.F).
648    o tools/genmake2:
649      - improve error msg when failing in 2nd test of check_for_broken_Ff
650      - fix option '-makefile' short-name (-mf according to genmake2 -help)
651      - source local config file "genmake_local" just after processing the genmake2
652        command arguments (previously done before processing arg).
653    o pkg/grdchk:
654      - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
655        to this routine from cost_final has been dropped in g_cost_final)
656      - improve printed information (more explicit msg, no longer using "print *,"
657         fix fcpertminus printed value).
658    o model/src:
659      - move call to COST_INIT_VARIA out of packages_init_variables.F directly
660        into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
661        this prevents getting cost-funct reset in adinitialise_varia recomputations.
662    o pkg/dic:
663      - move initialisation of "freefe" array from from dic_biotic_forcing.F to
664        fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
665    o pkg/grdchk:
666      - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
667      - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
668    o pkg/autodiff/ctrl/grdchk :
669      - attempt to sort out what works and what does not,
670        with regard to I/O, and to warn/stop accordingly.
671    o pkg/grdchk:
672      - attempt to fix grdchk in the case of useSingleCpuIO.
673      - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
674       statements were moved from grdchk_main.F and into
675       grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
676      - a global sum is applied to record numbers icvrec/layer
677       out of grdchk_loc so that they be passed to I/O routines.
678    o pkg/smooth:
679      - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
680        smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
681    o verification/testreport:
682      - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
683      - can also use compressed (gzip) reference output file;
684      - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
685        to be easier to collect by testreport.
686      - update existing TLM output (half out-of-date by more than 3 yrs).
687      - report NETCDF & LAPACK settings (from genmake2) in output dir.
688      - report run-time in each individual summary (previously only for AD test);
689        for TLM test, add also TAF version.
690      - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
691    
692    checkpoint63r (2012/08/15)
693    o tools/genmake2:
694      - fix Makefile for target ftlall (+ update files to clean after make ftlall)
695    o pkg/ecco/ecco_cost_final.F :
696      - fix fc print statements (to stdout and costfunction0000) so
697        that the printed value is always after the global sum.
698    o pkg/seaice/seaice_dynsolver.F :
699      - fix ice strength assymptote at SEAICE_area_max<1
700        (no change for the standard case of SEAICE_area_max=1)
701    o some cleaning:
702      - pkg source files: ensure that all *.F files from each pkg included the
703        corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
704        only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
705        code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
706        includes;
707      - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
708      - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
709        is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
710        ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
711      - update option-file CPP_OPTIONS.h of all AD experiments:
712        * no longer include PACKAGES_CONFIG.h ;
713        * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
714        * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
715          including ECCO_CPPOPTIONS.h).
716    o pkg/cost, pkg/ctrl, pkg/ecco option-file:
717      - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
718        separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
719        not necessary accurate).
720      - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
721        pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
722        deliberately break compilation (a remainder that it needs to be customized)
723      - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
724      - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
725      - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
726    o tools/genamke2:
727      - check for lapack.
728    o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
729      - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
730        jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
731        from both packages.
732      - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
733      - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
734      - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
735        of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
736    o pkg/cost : add comments to explain special and/or untested setups.
737    o pkg/exf:
738      - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
739        (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
740    o verification/*/code_ad:
741      mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
742      - reccord when this file is included (define ECCO_CPPOPTIONS_H)
743      - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
744        allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
745    o pkg/seaice :
746      - added possibility to change ice strength/PRESS0 relationship to
747        HEFF, according to the following run time parameters
748        SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
749        SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
750        SEAICEpresH0   :: HEFF threshold for ice strength            (m)
751    o pkg/ggl90 :
752      - added run time flag mxlSurfFlag to include the code that ensure
753        mixing between first and second level (previously included as a comment)
754    o verification/1D_ocean_ice_column/input_ad/data.autodiff :
755      - add test of newly added dumpAdByRec=T option where
756        we write all records to one file per variable.
757    o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
758      - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
759        to check that this code is ok with taf and compiles in adjoint.
760    o pkg/autodiff :
761      - added run time param dumpAdByRec : ad dump format switch.
762        If true then write all records to one file per variable.
763        Else write one file per record (remains the default).
764      - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
765    o pkg/seaice:
766     - Added SEAICEuseTILT run time switch : if set to
767       false then omit the tilt term in seaice dynamics.
768     - Fix free drift calculation.
769    o pkg/shelfice:
770      When initializing SHELFICEDragQuadratic, set default to be
771      consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
772      but retain option to set it independently
773      (inconsistenty spotted by Veronique Dansereau)
774    o eesupp/inc:
775      - in EEPARAMS.h, add real-type constant for some frequently used simple number
776         (0,1,2,1/2), with name explicitly referring to RS/RL type.
777    o model/src:
778      - move balancing of relaxation terms to new S/R balance_relax.F.
779    o pkg/autodiff:
780      re-write active I/O high-level (control) S/R:
781      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
782      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
783      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
784        MDS_READ/WRITE_FIELD); change loops to multi-threads.
785      - update and merge active_file_control_slice.flow into active_file_control.flow
786      - update the calls in lower level S/R (active_file.F, active_file_g.F and
787        active_file_ad.F) keeping the argument list and function unchanged.
788      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
789        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
790      - new low-level active I/O routines, one for each type (RL/RS), for active var
791        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
792        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
793        right type.
794    o autodiff and RS=real*4:
795      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
796        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
797      - change argument type of 3-D mask argument to _RS to match type in the call
798        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
799    o pkg/thsice:
800      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
801      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
802        fresh-water flux: uniform correction or proportional to local precip.
803    o pkg/ctrl:
804      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
805      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
806                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
807      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
808    
809    checkpoint63q (2012/07/30)
810    o pkg/autodiff:
811      note about monitor and snap-shot of ad-variables:
812      a) need to apply ADEXCH before monitor or output of ad-vars to include
813       overlap contributions (was done for adjDump but missing for monitor).
814      b) since ADEXCH implies adding overlap values to interior array, machine
815       truncation error is expected when adding an ADEXCH call in the middle of
816       the time-stepping (although mathematically identical).
817      modifs:
818      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
819        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
820      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
821        apply ADEXCH before monitor or snap-shot of ad-variables:
822           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
823      - implement new method (copy+adexch) for snap-shot and monitor of main model
824        ad-vars (initially not used by default -> output unchanged).
825      - change default (set to 2) to use new method and update few output_adm.txt
826        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
827        and both tutorial_tracer_adjsens tests).
828      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
829        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
830    o pkg/ctrl:
831      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
832      generic control variables via
833      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
834      Only required customization should be S/R ctrl_map_ini_genarr.F
835      (routine in repository contains example)
836    o pkg/exf:
837      - fix and refine checking of surface-relaxation setting when using EXF
838    o verification (adjoint exp):
839      - reduce length of simulation by half for experiment global_ocean.cs32x15
840        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
841    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
842      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
843        of KE that can occur with aggressive optimization
844      + put quadratic bottom drag calculation in separated loops (only done if
845        using bottomDragQuadratic)
846    o model/src: CG2D_NSA
847      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
848         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
849      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
850         change cg2d residual target to be expressed in Wunits (=> do not normalise
851         RHS ; this fix global_max Pb with TAF); update output.
852    o verification/tutorial_tracer_adjsens:
853       improve parameter consistency (and get rid of warnings):
854       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
855       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
856       - use staggerTimeStep (for stability) in som81; use default rotation period.
857    o pkg/exch2:
858      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
859        reset to 0 = 1 long line in X)
860    o pkg/mdsio:
861      - fix reading of dimensions from meta file for large-size domain
862    o model/src:
863      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
864      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
865        Cubed-Sphere Exch with CS-corners inside the domain;
866        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
867        globalArea and to set hasWetCSCorners.
868      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
869        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
870      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
871        useCDscheme and useCubedSphereExchange).
872    o pkg/seaice/seaice_growth.F :
873      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
874        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
875        when the previous code was not correct.
876      - in all cases diagnoze the boundary condition mismatch to SIaaflux
877      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
878        that term to QNET (essentially to set the melt/freeze water to 0degC).
879        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
880  o verification/global_ocean.cs32x15/input.seaice :  o verification/global_ocean.cs32x15/input.seaice :
881   - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.    - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
882   - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).    - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
883   - update results (output.seaice.txt) accordingly.    - update results (output.seaice.txt) accordingly.
884  o verification/lab_sea/input/data.seaice :  o verification/lab_sea/input/data.seaice :
885   - remove SEAICEheatConsFix, which is now be tested    - remove SEAICEheatConsFix, which is now be tested
886     in global_ocean.cs32x15. The presently coded fix      in global_ocean.cs32x15. The presently coded fix
887     is only consistent with real fresh water + nlfs.      is only consistent with real fresh water + nlfs.
888   - update results (output.txt) accordingly.    - update results (output.txt) accordingly.
889  o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).  o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
890  o AD_CONFIG.h file:  o AD_CONFIG.h file:
891   - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;    - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
892   - remove #include "AD_CONFIG.h" from all included OPTIONS files and    - remove #include "AD_CONFIG.h" from all included OPTIONS files and
893     add it explicitly in each fortran src file where it is needed.      add it explicitly in each fortran src file where it is needed.
894     motivation: header file AD_CONFIG.h is generated/modified after "make depend"      motivation: header file AD_CONFIG.h is generated/modified after "make depend"
895     thus introducing potentially wrong dependency; therefore, better to include      thus introducing potentially wrong dependency; therefore, better to include
896     it only where it's really needed, and after any other included OPTIONS file      it only where it's really needed, and after any other included OPTIONS file
897     (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN      (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
898     or ALLOW_TANGENTLINEAR_RUN).      or ALLOW_TANGENTLINEAR_RUN).
899    
900  checkpoint63p (2012/07/06)  checkpoint63p (2012/07/06)
901  o pkg/autodiff:  o pkg/autodiff:
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