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revision 1.1664 by jmc, Mon Jun 4 21:05:46 2012 UTC revision 1.1856 by jmc, Mon Apr 22 02:41:27 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 model/src:
8      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
9      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
10      - move forcing adjustment (balancing surface forcing) in specific S/R
11        where might also be applied exchanges (if needed) to forcing arrays.
12    o pkg/shelfice:
13      - allow to specify the Ice-Shelf mass per unit area (instead of
14        shelficeLoadAnomaly) and do the conversion from one to the other
15      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
16        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
17        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
18        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
19      - update isomip experiment forward output (get machine truncation error
20        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
21    o verification/offline_exf_seaice:
22      revise data.seaice in input.thermo and input_ad and update results accordingly
23        HO = 0.2, SEAICE_areaLossFormula = 2,
24        SEAICE_growMeltByConv = .TRUE.,
25        SEAICE_doOpenWaterMelt = .TRUE.,
26      Improve consistency with input.thsice and fix the spurious 500m ice corners
27    o verification/global_ocean.cs32x15:
28      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
29        in icedyn (thsice+seaice-dyn) test and update output.
30    o verification/offline_exf_seaice:
31      - adjust list of tested variables (with testreport) and update
32        standard test output with better slection of monitored fields.
33    o pkg/cd_code:
34      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
35        experiment lab_sea.hb87
36    o tools/genmake2:
37      - change default makedepend from the system default to tools/xmakedepend:
38        When no makedepend is specified, select tools/xmakedepend it the test pass,
39        otherwise select the system default (if exist and pass the test) or
40        try to build cyrus-makedepend ; stop if none of the 3 works.
41    o pkg/exf & pkg/thsice:
42      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
43        for energy content of Precip + RunOff & Evap. Assumes:
44       1) Rain has same temp as Air.
45       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
46       3) Run-Off comes at the temp of surface water (with same Cp)
47       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
48        put directly into Latent Heat flux & should use water-vapor heat capacity.
49       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
50        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
51    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
52        (compile when SEAICE_ALLOW_JFNK is defined)
53    o pkg/thsice:
54      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
55        implementation): move THSICE_AVE call after the advection (called directly
56        from thsice_do_advect.F).
57    o verification/global_ocean.90x40x15 and OpenAD:
58      New experiment for OpenAD is identical to the one in input_ad except that
59        multiDimAdvection=.FALSE.,
60      There is still an issue with this.
61    o pkg/thsice:
62      - account for ice velocity (ocean relative velocity) in turbulent heat flux
63        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
64        and offline_exf_seaice (main test).
65    
66    checkpoint64f (2013/03/31)
67    o verification/OpenAD:
68      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
69    o verification/isomip, pkg/shelfice and OpenAD:
70      - add OpenAD setup to this exp and make shelfice package work with OpenAD
71    o verification/tutorial_global_oce_biogeo:
72      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
73    o verification/offline_exf_seaice:
74      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
75    o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
76      - add OpenAD setup to this exp and make ptracers package work with OpenAD
77    o pkg/seaice/seaice_evp.F:
78       mask the asymmetric contribution of the ice-ocean stress (when
79       the turningAngle is non-zero) over open water to avoid stripes
80       in the EVP-solutions after many EVP-substeps. This does not change
81       the verification experiment (because turningAngle=0 in that experiment),
82       but will affect other EVP solutions with turningAngle.ne.0
83    o verification, AD & TLM output:
84      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
85        additions and multiplications which affect results at machine truncation
86        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
87        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
88        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
89        digits of matching.
90    o pkg/seaice:
91       modify lsr-algorithm so that it vectorizes AND converges by using a
92       "zebra" method: split vector loop into two with step size 2; this
93       solves a general convergence problem for the JFNK solver on a vector
94       computer. It has the potential to even improve convergence for
95       non-vector machines, but it does change the results so it is turned
96       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
97       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
98    
99    checkpoint64e (2013/03/05)
100    o pkg/ecco and several verification experiments:
101       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
102       from ecco package, and revert to unified routine in model/src/
103       Adjust verification experiments accordingly, especially gloal_oce_llc90
104       Should conclude long-standing work by Gael to reconsile the_main_loop with
105       ECCO and will enable OpenAD's revolve loop in ECCO setup.
106    o pkg/generic_advdiff:
107      - implement compressible flow method for multi-dim advection (similar to
108        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
109        TAF generates many recomputations) to use it; no yet coded with implicit
110        vertical advection.
111      - change experiment advect_cs (new output) and advect_xy (same output)
112        to test compressible flow multi-dim advection.
113    o pkg/generic_advdiff:
114      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
115        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
116    o pkg/seaice:
117      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
118        bug affects two verification experiments (lab_sea and lab_sea.hb87),
119        recover old (wrong) results by setting noSlipFac = 2. in
120        seaice_calc_strainrates.F;
121      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
122      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
123        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
124      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
125    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
126      - new subroutines seaice_lsr_tridiagu/v
127      - introduce loop bounds i/jmin/max to be able to use a restricted
128        additive Schwarz method, but not used for now.
129      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
130      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
131    o OpenAD support
132       Reorganize S/R call for overall time-stepping loop to facilitate
133       OpenAD revolve loop replacement
134       (new S/R main_do_loop.F)
135    o model/src:
136      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
137      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
138        ADAMS_BASHFORTH2.
139    o pkg/cheapaml:
140      - add new parameter (default=F, same as before) to disable full domain
141        (including land) periodicity in X & Y dir.
142      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
143        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
144        into single S/R CHEAPAML_TIMESTEP.
145    
146    checkpoint64d (2013/02/17)
147    o pkg/monitor (angular momentum):
148      - do not add Eta contribution to the total AM if using rigid-lid;
149      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
150      - horizontal discretisation: compute Zonal wind contribution separately for
151        each component (instead of from cell centered averaged) and use the 4
152        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
153      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
154        FreeSurf) if using vectorInvariant momentum.
155    o model/src (horizontal grid):
156      - move initialisation of all horizontal grid arrays to null value
157        from specific horizontal grid S/R to main S/R INI_GRID;
158      - add 2 new arrays to project model C-grid velocity on to zonal direction
159        (similar to AngleCosC & -AngleSinC but at U and V point location) and
160        compute them in S/R CALC_GRID_ANGLES.
161    o pkg/seaice: replace a hard coded parameter by a runtime parameter
162        SEAICE_JFNK_tolIter
163    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
164        preconditioner for JFNK (run LSR into the overlaps as far as possible,
165        i.e OLx/y-2, but overwrite the solution in the overlaps)
166      - extend loop range in seaice_calc_viscosity
167      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
168      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
169      - slightly modify loops in tridiagonal solver lsr-preconditioner
170      - by default remove the extra exchange in seaice_preconditioner with a
171        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
172      - modify offline_exf_seaice so that old results without RAS are reproduced
173        for output.dyn_jfnk.txt
174      in seaice_fgmres.F (unrelated to RAS)
175      - add a cpp-flag option for a re-ordered mapping (potentially more
176        efficient), but because this changes the results, turn it off by
177        default
178      - replace the save statement by local common blocks
179    o utils/matlab:
180      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
181      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
182        instead of local script "load_cs.m".
183    o pkg/seaice:
184      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
185        to the scalarProductMetric and the unrolling. By chance this does not
186        change the verification experiment, because of the particular domain
187        decomposition
188    o pkg/diagnostics:
189      - change default missing_value from UNSET_RL to -999.
190    o pkg/layers: improve vectorization of layers_fluxcalc.F
191      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
192        time spent in this routine by more than a factor of 3 on an NEC-SX8
193      - step 2: replace search algorithm by a bisection algorithm found in
194        Press et al. Numerical Recipes in Fortran. This algorithm can be
195        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
196        For now, use this algorithm only for TARGET_NEC_SX defined.
197      - moved the search algorithm into a separate subroutine, that is kept
198        within the same file for automatic inlining.
199      - modified catching potential errors
200    o pkg/ecco:
201      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
202    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
203      - modifications for ALLOW_GENTIM2D_CONTROL
204      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
205      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
206      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
207      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
208    o model/src:
209      - account for moist thermodynamics in (dry) potential temperature equation;
210        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
211        and cpl_aim+ocn.
212      - also switch to standard compiler (gfortran, was using ifort previously)
213        for fizhi-cs experiments reference output.
214    o pkg/ctrl:
215      - 1st step toward generic time-varying control variable (2D) via CPP option
216        ALLOW_GENTIM2D_CONTROL
217      - note new namelist ctrl_nml_genarr in data.ctrl
218    o verification/global_ocean.cs32x15:
219      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
220        thsice calling sequence and update "output.icedyn.txt" output file.
221    o pkg/ptracers:
222      - from Ryan A.: code to allow to restart a tracer at regular time interval
223        specifying a reset frequency and a reset-phase (for each tracers).
224    o pkg/thsice:
225      - implement new sequence of calls for thsice+seaice:
226          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
227          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
228      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
229        in CPP_OPTIONS.h) to recover old sequence;
230      - update diagnostics for Intermediate State thsice diagnostics: now filled
231        just before advection (instead of just after advection in old sequence);
232      - update output of experiment offline_exf_seaice (standard test);
233      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
234        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
235    o pkg/aim_v23:
236      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
237      - use standard pkg/mdsio routines to read & write CO2 pickup file;
238      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
239      - Implement new sequence of calls for seaice advection (with thsice and
240        seaice diffusion): do ice advection after ice-Thermodynamic (previously
241        was done before); change aim_do_physics.F (split the bi,bj loops block);
242      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
243    o pkg/thsice:
244      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
245        where just seaice diffusion is used without seaice-dynamics.
246    
247    checkpoint64c (2013/01/18)
248    o pkg/seaice:
249      - add a parameter JFNKres_tFac that can replace JFNKres_t
250        (= JFNKres_tFac*JFNKresidual before JFNK solver)
251      - add a line search option to the JFNK solver
252      - move update of u/vIce and computation of initial residual into a separate
253        routine (same file); makes the code a little easier to read (?)
254      - the line search requires computation of the residual and for some reason
255        I cannot do the update of u/vIce at the beginning of the Newton loop
256        without changing the results, so we move computation of the new residual
257        also to the end of the Newton loop, even without the line search
258    o pkg/mdsio:
259      - write missing value (corresponding to undefined array value) to meta files;
260        skip this if missing value is one (UNSET_RL would be a better value for the
261        case of undefined missing value but it's current the default missing-value);
262        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
263    o pkg/exf & thsice:
264      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
265        diagnostics) even when SHORTWAVE_HEATING is #undef;
266    o verification/cfc_example:
267      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
268        illustrate how to use it).
269    o verification/offline_exf_seaice:
270      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
271        files to only one time-record.
272      in input.thermo: narrow the 2 bands of low initial ice-concentration near
273        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
274        snapshot output; same mcPheePiston value as in thsice with
275        surf-current=0.2m/s.
276      in input.thsice: similar set-up as in input.thermo (channel with same seaice
277        initial conditions).
278    o verification/cfc_example:
279      - update file "data" with more standard choice (default rotationPeriod,
280        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
281        set deltaTFreeSurf to deltaTtracer) and update the output.
282    o pkg/layers:
283      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
284      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
285    o verification/offline_exf_seaice:
286      - set all {field}period to zero for constant-in-time forcing (not tested
287        anywhere else).
288    o verification/offline_exf_seaice:
289      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
290      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
291    o model/src:
292      - implement Finite-Volume method for (hydrostatic) presure gradient
293        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
294    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
295      - In order to be compatible with the default EVP code, this requires changing
296        the EVP code around a little; and because any small change immediately
297        breaks the lab_sea.hb87 verification experiment, the reference output is
298        updated two times (each time the remaining aggrement was only 2 digits):
299        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
300        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
301        The adjoint test lab_sea.evp also needed to be updated.
302      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
303        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
304        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
305        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
306        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
307        kept obscure, because I need to test it a little more.
308    o pkg/cheapaml:
309      - fix few incorrect type (_RL/_RS) in subroutine calls.
310    o pkg/seaice:
311      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
312        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
313    o model/src:
314      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
315        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
316        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
317    o pkg/cheapaml:
318      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
319        update output of experiment cheapAML_box.
320      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
321        and set them only in one place (cheapaml_readparms.F).
322      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
323      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
324        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
325    o model/src/the_main_loop.F:
326      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
327    o pkg/seaice:
328      - remove legacy branch code.
329      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
330    o verification/*/code*/SEAICE_OPTIONS.h:
331      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
332        SEAICE_CAP_HEFF).
333    o pkg/cheapaml:
334      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
335        to load new forcing fields.
336      - add missing "_d 0" where it's needed; + some editing (improve indentation).
337      - remove switch to "-r8" compiler option (no longer needed) in verification
338        cheapAML_box, keep same output (small trucation error differences).
339    o verification/offline_exf_seaice:
340      - add thermodynamics only test.
341    o verification/cheapAML_box:
342      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
343        keep same output (same 14 digits for cg2d).
344      - switch on "-r8" compiler option (some numerical values are missing
345        the "_d 0") and update output (only 6 digits for cg2d were preserved).
346    
347    checkpoint64b (2012/12/24)
348    o pkg/cheapaml:
349      - remove un-used variables (Qnet,EmPmR) from pickup files.
350      - store tendency of advected variables into cheapaml pickup file
351        and fix the AB-2 restart.
352    o verification/offline_exf_seaice and lab_sea adjoint:
353      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
354      - switch to 4 time steps in offline, consistent with lab_sea.
355      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
356      - update results after change of experiment seaice.
357    o pkg/seaice:
358      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
359        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
360        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
361        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
362    o model/src:
363      - add run-time parameter to select CG2D solver minimum-residual solution
364        (in case of a poor convergence).
365    o pkg/seaice/seaice_lsr.F
366      - move calculation of matrix coefficients into new
367        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
368        file; the main purpose of this change is to be able to reuse the code
369        in S/R SEAICE_PRECONDITIONER
370      - modify the computation of the residual so that the mass of sea-ice
371        is not used twice; this simplifies the calculations, but since
372        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
373        not tested in testreport---this does not affect the testreport results.
374    o verification/seaice_obcs:
375      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
376        verification/lab_sea/input.salt_plume; changes results/output.txt*
377    o model/src:
378      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
379    o pkg/seaice:
380      - improve description of parameters in seaice_fgmres.F and start
381        cleaning up the code
382      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
383        second argument
384      - add a metric based on grid cell area to SEAICE_SCALPROD; update
385        results of offline_exf_seaice.dyn_jfnk
386      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
387    o pkg/aim_v23:
388      - fix an other bug in dissipation heating (grid-cell area was missing).
389    o model/src + pkg/seaice:
390      - add global (multi-tile) linear solver for pair of tri-diagonal system
391        along X and Y lines, respectively for U and V component.
392        Note: 1) MPI and cube-exchange not yet coded.
393            2) probably not accurate for poorly conditioned / large size problem.
394      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
395        default: not compiled and not used.
396    o pkg/seaice:
397      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
398        introduce bi/bj loops and use global_sum_tile_rl instead of
399        mpi_allreduce in seaice_fgmres.F
400      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
401      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
402      - add a verification experiment for JFNK in offline_exf_seaice
403    o verification:
404      - change (for now, only fwd test) offline_exf_seaice experiment:
405        use a re-entrant channel with idealized coastline (trapezoidal shape)
406        at southern boundary to explore seaice dynamics and thermodynamics
407        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
408        secondary test (input.thsice) use thermodynamics only with SST relaxation.
409      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
410    o pkg/exf:
411      - disable "sstExtrapol" when Nr=1
412    o verification:
413      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
414        to test pkg/cheapaml.
415    o pkg/aim_v23 & pkg/shap_filt:
416      - fix dissipation heating (erroneous gravity multiplication factor).
417    o pkg/seaice:
418      - remove unused field pressPre from jfnk solver
419      - rename two subroutines in seaice_preconditioner.F
420    o eesupp/src:
421       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
422    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
423       - remove wrong parts of the rhs and the lhs (were in there
424         because I did not understand the concept of this preconditioner)
425       - add an exchange between u- and v-sweep. This increases communication
426         by a factor of two but improves the convergence of jfnk. Ideally,
427         one would like the u- and v-sweep to be independent. So far within
428         undocumented ifdefs
429       - reorganize the extra computations for printing the residuals
430    o tools/genmake2:
431      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
432        since it's not necessary (and was preventing to use MNC in some cases).
433    
434    checkpoint64a (2012/11/16)
435    o pkg/autodiff:
436      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
437        autodiff_readparms.F no longer depends on calling order (within
438        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
439        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
440        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
441    o pkg/obcs:
442      - adding tidal velocity forcing capability to obcs
443        for usage example, see verification/seaice_obcs/input.tides
444    o pkg/seaice:
445      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
446        SEAICE_LSRrelaxU/V
447      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
448    o pkg/aim_v23:
449      - implement heating from friction (bottom friction and stratospheric drag).
450    o pkg/shap_filt:
451      - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
452        dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
453    o model/src:
454      - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
455        time-constant addMass field from file (addMassFile);
456      - support for heating due to friction (and Kinetic Energy dissipation):
457        add option, run-time switch and 3-D field array + support code ; each pkg
458        or S/R can add heating contribution (if there is a sink of KE); the sum is
459        accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
460    o pkg/seaice:
461      - complete merge of ITD code into seaice_growth.F
462        from MITgcm_contrib/torge/itd/code/
463        no verification so far, but Torge Martin tested
464        "1-D test case and Beaufort set up;
465        deliver okay results after 1 model year."
466      - complete merge of SEAICE_SIZE.h into all relevant routines
467      - move computation of eta at Z-points into calc_viscosities
468        + introduce global field etaZ
469        + add different methods for computing etaZ, for now the old
470          method (simple averages of eta to Z-points) is hardwired
471        + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
472          seaice_preconditioner
473      - simplify computations for SEAICE_ZETA_SMOOTHREG
474      - seaice_preconditioner:
475        + replace one remaining press by pressLoc (mistake)
476        + adjust printing of residuals
477      - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
478        + add (SEAICE.h) and rename some counters (initiliased in
479          seaice_init_fixed.F)
480        + add _BEGIN/END_MASTER (myThid)  around print statements
481        + print total number of iterations and failures over SEAICE_monFreq
482          interval to STDOUT
483      - move control over output-messages by fgmres to seaice_jfnk to save
484        some operations
485      - move resetting initial guess for fgmres outside of seaice_fgmres_driver
486        in order to make restarts with sol .ne. zero (fgmres with restarts)
487        (seaice_jfnk.F, seaice_fgmres.F)
488      - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
489        a serious convergence problem when open boundaries are involved
490    o pkg/ggl90: fix computation of control volumes for the case of
491      ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
492      up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
493    o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
494    o pkg/autodiff
495      - Add inAdMode switch for SEAICEuseDYNAMICS:
496        SEAICEuseDYNAMICSinAdMode
497        (extend logic in ADAUTODIFF_INADMODE_SET)
498    o pkg/seaice
499      - Step 1 of merging ice-thickness distribution (ITD) code from
500        MITgcm_contrib/torge/itd/ (author: Torge Martin)
501        The code implements concept laid out in Thorndike et al. (1975);
502        code is enabled via CPP flag SEAICE_ITD
503        nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
504        code is not complete yet!!
505      - SEAICE_SIZE.h now included in almost all seaice routines
506    o verification (using seaice):
507      - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
508        global_ocean.cs32x15.seaice ; update results.
509      - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
510      - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
511        offline_exf_seaice (previously compiling B-grid).
512    o pkg/exf:
513      - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
514        to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
515        forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
516    o pkg/layers (adjust changes from Sept 19):
517      - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
518        this allows to remove "layers_maxNum" dimension from all layers arrays.
519    o pkg/layers (adjust changes from Sept 19):
520      - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
521      - snap-shot extended to all type of layers (not just the 1rst type);
522      - remove layers variables when corresponding CPP option is undef.
523    o pkg/layers:
524      - rename pkg/layers variable and add new output (layer exist & un-weighted
525        velocity in layer)
526    o pkg/seaice:
527      - simplify (?) ocean-drag coefficent computations by using
528        the same routine in all three solvers (saves some code lines)
529      - remove global fields DRAGA and DRAGS from C-grid code and
530        declare them locally in lsr.F (the only place where they are
531        still used)
532      - update AD output of lab_sea.evp (very sensitive anyway).
533    o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
534      (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
535      and SEAICEuseJFNK=.true. A few things to note:
536      - involves a FGMRES, that is parallel but very inefficient,
537        because of many scalar products (global sums) in the Gram-Schmidt
538        orthogonalization method. Needs to be replaced. Original code
539        from J.-F. Lemieux
540      - preconditioner for FGMRES is a stripped down version of LSOR
541      - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
542        preconditioner. For the preconditioner, the default is set to 10.
543      - Jacobian times vector is computed with finite differences
544      - marginally related to JFNK-solver: add a smooth regularization for
545        zeta with tanh that will improve convergence (Lemieux and Tremblay,
546        2009) for any implicit solver (not implemented for EVP because EVP
547        does not need this regularization in the first place). Define
548        SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
549    o eesupp/src:
550      - check in genmake2 that intrinsic S/R flush is available.
551      - add S/R to flush IO unit (if intrinsic S/R flush is available)
552      - flush standard & error msg unit before MPI termination
553      - if debugMode, flush IO unit after printing msg
554    o pkg/ctrl:
555      - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
556        to ctrl_set_unpack_xyz.
557    
558    checkpoint64 (2012/10/09)
559    o pkg/shelfice
560      - in mom_fluxform.F, mom_vecinv.F:
561        CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
562        Bug fix KappaRU -> KappaRV
563        does not change verification/isomip but may change other setups
564        (presumably constant KappaRU=KappaRV)
565      - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
566    o pkg/obcs:
567      - fixed some indexing bugs in obcs_seaice_sponge.F
568      - added obcs relaxation subroutines for HSALT and HSNOW
569      - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
570    o pkg/seaice:
571      - add "multicategory" parameterization for snow in analogy to ice,
572        default is off for now.
573    o pkg/obcs:
574      - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
575        see verification/seaice_obcs/input.seaiceSponge for example application.
576      - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
577        index setting by master-thread. This fix multi-threads Pb in previous modifs.
578    o pkg/layers :
579      - add diagnostics to pkg/layers
580      - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
581        (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
582    o pkg/generic_advdiff/gad_implicit_r.F :
583      - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
584    o pkg/seaice/seaice_growth.F:
585      - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
586    o pkg/obcs:
587      - change default setting of OBCS_UVICE_OLD from defined to undef;
588      - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
589        in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
590      - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
591      - change OB null index value (OB_indexNone) to -99 ; this fix the problem
592        with Southern & Western OB at a tile edge (at least in a simple set-up).
593    o pkg/obcs:
594      - change settings of OB index in case OB coincides with tile edge (shared by
595        2 tiles), so that common OB location is registered by both tiles (instead of
596        only 1). However, for Southern and Western OB, index value = 0 is not
597        recognized as valid OB index (=default null value) and needs to be fixed.
598      - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
599      - new parameter "OB_indexNone" for null index value (for now, still zero)
600        to replace hard-coded null index value of zero.
601    o pkg/exch2:
602      - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
603        always check buffer-size (but outside the loop); move checking for valid
604        index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
605        print each tile and point connection only if |W2_printMsg|>= 2 and 3.
606    o pkg/ctrl (pack & unpack):
607      - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
608        (locally defined) for different variables (+ remove the variable-specific
609        file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
610        (to be extended to other local file names in ctrl.h).
611    o pkg/flt:
612      - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
613    o pkg/mdsio:
614      - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
615    o tools/genmake2:
616      - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
617        (added by Alistair in version 1.51 for building without make depend);
618      - remove Header files list (H_SRC_FILES) from the dependence of targets
619         ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
620        place in version 1.23): this save going through staf when unrelated header
621        file has been modified.
622       Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
623        "make depend" step, still need to do "make links" before "make adtaf".
624    o eesupp/src (+ few pkg src files) & genmake2:
625      - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
626      - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
627      - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
628         upper/lower case ; account for space between "#" and undef/define)
629    o pkg/flt (with exch2):
630      - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
631      - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
632    
633    checkpoint63s (2012/09/05)
634    o pkg/ecco:
635      - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
636      - add more relevant #ifdef ALLOW_SMOOTH ones.
637      - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
638    o pkg/ctrl:
639      - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
640        ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
641      - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
642        doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
643        ctrlSmoothCorrel3D (new).
644        The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
645      - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
646      - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
647        controls when useAtmWind, and vice versa.
648      - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
649      - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
650          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
651      - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
652          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
653      - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
654        replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
655    o pkg/smooth:
656      - remove un-necessary includes.
657      - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
658        Those CPP options were never defined, and not necessary.
659    o model/src:
660      - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
661      - standard treatment of useSMOOTH.
662    o pkg/autodiff:
663      - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
664        useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
665    o pkg/exch2:
666      - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
667        + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
668      - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
669        and tiles to process mapping.
670      - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
671        moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
672        rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
673        from w2_eeboot.F to w2_readparms.F.
674    o eesupp/src:
675      - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
676        ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
677        also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
678      - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
679        is defined (remove condition on usingMPI) to match cases where MPI_INIT
680        has been called.
681      - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
682      - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
683        (so that on 1 proc, get same myPid independently of usingMPI)
684      - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
685        useCubedSphereExchange with EXCH-1 (safer).
686      - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
687    o pkg/ggl90:
688      - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
689        used in ALLOW_GGL90_SMOOTH code.
690    o pkg/flt:
691      - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
692        floats at the Southern end of the domain).
693    o eesupp/inc:
694      - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
695        but not used (and not to be used) anywhere, just for documentation.
696    o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
697      - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
698        a) can damage previously written records in any other multi-record files.
699        b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
700    o tools/genmake2:
701      - define variable MAKE within Makefile and use it in place of 'make';
702      - update AD_CONFIG.h (if needed) before building any of the executable
703        (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
704        and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
705      - always print usual warning comment 'this file is automatically generated'
706        from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
707    o pkg/cheapaml:
708      - updated to correspond to the code used in accepted paper (Nico Wienders).
709    o pkg/exf:
710        added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
711        ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
712        and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
713    o pkg/exf, autodiff, ctrl, ecco and seaice:
714        remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
715    o pkg/ctrl, ecco:
716        allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
717        Depending on useAtmWind, one is inactive, and the other is active (see
718        exf_getffields.F/exf_getsurfacefluxes.F).
719    o tools/genmake2:
720      - improve error msg when failing in 2nd test of check_for_broken_Ff
721      - fix option '-makefile' short-name (-mf according to genmake2 -help)
722      - source local config file "genmake_local" just after processing the genmake2
723        command arguments (previously done before processing arg).
724    o pkg/grdchk:
725      - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
726        to this routine from cost_final has been dropped in g_cost_final)
727      - improve printed information (more explicit msg, no longer using "print *,"
728         fix fcpertminus printed value).
729    o model/src:
730      - move call to COST_INIT_VARIA out of packages_init_variables.F directly
731        into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
732        this prevents getting cost-funct reset in adinitialise_varia recomputations.
733    o pkg/dic:
734      - move initialisation of "freefe" array from from dic_biotic_forcing.F to
735        fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
736    o pkg/grdchk:
737      - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
738      - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
739    o pkg/autodiff/ctrl/grdchk :
740      - attempt to sort out what works and what does not,
741        with regard to I/O, and to warn/stop accordingly.
742    o pkg/grdchk:
743      - attempt to fix grdchk in the case of useSingleCpuIO.
744      - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
745       statements were moved from grdchk_main.F and into
746       grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
747      - a global sum is applied to record numbers icvrec/layer
748       out of grdchk_loc so that they be passed to I/O routines.
749    o pkg/smooth:
750      - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
751        smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
752    o verification/testreport:
753      - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
754      - can also use compressed (gzip) reference output file;
755      - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
756        to be easier to collect by testreport.
757      - update existing TLM output (half out-of-date by more than 3 yrs).
758      - report NETCDF & LAPACK settings (from genmake2) in output dir.
759      - report run-time in each individual summary (previously only for AD test);
760        for TLM test, add also TAF version.
761      - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
762    
763    checkpoint63r (2012/08/15)
764    o tools/genmake2:
765      - fix Makefile for target ftlall (+ update files to clean after make ftlall)
766    o pkg/ecco/ecco_cost_final.F :
767      - fix fc print statements (to stdout and costfunction0000) so
768        that the printed value is always after the global sum.
769    o pkg/seaice/seaice_dynsolver.F :
770      - fix ice strength assymptote at SEAICE_area_max<1
771        (no change for the standard case of SEAICE_area_max=1)
772    o some cleaning:
773      - pkg source files: ensure that all *.F files from each pkg included the
774        corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
775        only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
776        code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
777        includes;
778      - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
779      - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
780        is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
781        ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
782      - update option-file CPP_OPTIONS.h of all AD experiments:
783        * no longer include PACKAGES_CONFIG.h ;
784        * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
785        * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
786          including ECCO_CPPOPTIONS.h).
787    o pkg/cost, pkg/ctrl, pkg/ecco option-file:
788      - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
789        separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
790        not necessary accurate).
791      - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
792        pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
793        deliberately break compilation (a remainder that it needs to be customized)
794      - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
795      - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
796      - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
797    o tools/genamke2:
798      - check for lapack.
799    o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
800      - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
801        jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
802        from both packages.
803      - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
804      - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
805      - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
806        of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
807    o pkg/cost : add comments to explain special and/or untested setups.
808    o pkg/exf:
809      - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
810        (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
811    o verification/*/code_ad:
812      mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
813      - reccord when this file is included (define ECCO_CPPOPTIONS_H)
814      - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
815        allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
816    o pkg/seaice :
817      - added possibility to change ice strength/PRESS0 relationship to
818        HEFF, according to the following run time parameters
819        SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
820        SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
821        SEAICEpresH0   :: HEFF threshold for ice strength            (m)
822    o pkg/ggl90 :
823      - added run time flag mxlSurfFlag to include the code that ensure
824        mixing between first and second level (previously included as a comment)
825    o verification/1D_ocean_ice_column/input_ad/data.autodiff :
826      - add test of newly added dumpAdByRec=T option where
827        we write all records to one file per variable.
828    o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
829      - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
830        to check that this code is ok with taf and compiles in adjoint.
831    o pkg/autodiff :
832      - added run time param dumpAdByRec : ad dump format switch.
833        If true then write all records to one file per variable.
834        Else write one file per record (remains the default).
835      - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
836    o pkg/seaice:
837     - Added SEAICEuseTILT run time switch : if set to
838       false then omit the tilt term in seaice dynamics.
839     - Fix free drift calculation.
840    o pkg/shelfice:
841      When initializing SHELFICEDragQuadratic, set default to be
842      consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
843      but retain option to set it independently
844      (inconsistenty spotted by Veronique Dansereau)
845    o eesupp/inc:
846      - in EEPARAMS.h, add real-type constant for some frequently used simple number
847         (0,1,2,1/2), with name explicitly referring to RS/RL type.
848    o model/src:
849      - move balancing of relaxation terms to new S/R balance_relax.F.
850    o pkg/autodiff:
851      re-write active I/O high-level (control) S/R:
852      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
853      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
854      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
855        MDS_READ/WRITE_FIELD); change loops to multi-threads.
856      - update and merge active_file_control_slice.flow into active_file_control.flow
857      - update the calls in lower level S/R (active_file.F, active_file_g.F and
858        active_file_ad.F) keeping the argument list and function unchanged.
859      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
860        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
861      - new low-level active I/O routines, one for each type (RL/RS), for active var
862        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
863        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
864        right type.
865    o autodiff and RS=real*4:
866      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
867        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
868      - change argument type of 3-D mask argument to _RS to match type in the call
869        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
870    o pkg/thsice:
871      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
872      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
873        fresh-water flux: uniform correction or proportional to local precip.
874    o pkg/ctrl:
875      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
876      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
877                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
878      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
879    
880    checkpoint63q (2012/07/30)
881    o pkg/autodiff:
882      note about monitor and snap-shot of ad-variables:
883      a) need to apply ADEXCH before monitor or output of ad-vars to include
884       overlap contributions (was done for adjDump but missing for monitor).
885      b) since ADEXCH implies adding overlap values to interior array, machine
886       truncation error is expected when adding an ADEXCH call in the middle of
887       the time-stepping (although mathematically identical).
888      modifs:
889      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
890        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
891      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
892        apply ADEXCH before monitor or snap-shot of ad-variables:
893           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
894      - implement new method (copy+adexch) for snap-shot and monitor of main model
895        ad-vars (initially not used by default -> output unchanged).
896      - change default (set to 2) to use new method and update few output_adm.txt
897        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
898        and both tutorial_tracer_adjsens tests).
899      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
900        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
901    o pkg/ctrl:
902      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
903      generic control variables via
904      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
905      Only required customization should be S/R ctrl_map_ini_genarr.F
906      (routine in repository contains example)
907    o pkg/exf:
908      - fix and refine checking of surface-relaxation setting when using EXF
909    o verification (adjoint exp):
910      - reduce length of simulation by half for experiment global_ocean.cs32x15
911        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
912    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
913      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
914        of KE that can occur with aggressive optimization
915      + put quadratic bottom drag calculation in separated loops (only done if
916        using bottomDragQuadratic)
917    o model/src: CG2D_NSA
918      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
919         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
920      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
921         change cg2d residual target to be expressed in Wunits (=> do not normalise
922         RHS ; this fix global_max Pb with TAF); update output.
923    o verification/tutorial_tracer_adjsens:
924       improve parameter consistency (and get rid of warnings):
925       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
926       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
927       - use staggerTimeStep (for stability) in som81; use default rotation period.
928    o pkg/exch2:
929      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
930        reset to 0 = 1 long line in X)
931    o pkg/mdsio:
932      - fix reading of dimensions from meta file for large-size domain
933    o model/src:
934      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
935      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
936        Cubed-Sphere Exch with CS-corners inside the domain;
937        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
938        globalArea and to set hasWetCSCorners.
939      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
940        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
941      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
942        useCDscheme and useCubedSphereExchange).
943    o pkg/seaice/seaice_growth.F :
944      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
945        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
946        when the previous code was not correct.
947      - in all cases diagnoze the boundary condition mismatch to SIaaflux
948      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
949        that term to QNET (essentially to set the melt/freeze water to 0degC).
950        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
951    o verification/global_ocean.cs32x15/input.seaice :
952      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
953      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
954      - update results (output.seaice.txt) accordingly.
955    o verification/lab_sea/input/data.seaice :
956      - remove SEAICEheatConsFix, which is now be tested
957        in global_ocean.cs32x15. The presently coded fix
958        is only consistent with real fresh water + nlfs.
959      - update results (output.txt) accordingly.
960    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
961    o AD_CONFIG.h file:
962      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
963      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
964        add it explicitly in each fortran src file where it is needed.
965        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
966        thus introducing potentially wrong dependency; therefore, better to include
967        it only where it's really needed, and after any other included OPTIONS file
968        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
969        or ALLOW_TANGENTLINEAR_RUN).
970    
971    checkpoint63p (2012/07/06)
972    o pkg/autodiff:
973      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
974      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
975        which are now read from new parameter file "data.autodiff" (inAdExact
976        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
977      - add file "data.autodiff" in all verification/*/input_ad/ directories.
978      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
979        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
980    o verification/tutorial_tracer_adjsens/
981      - add extra sub-verification which uses "SOM" advection scheme
982        (2nd Order-Moment Advection Scheme, Prather Limiter) with
983          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
984        and in data:
985          multiDimAdvection=.TRUE.,
986          tempAdvScheme=81,
987          saltAdvScheme=81,
988    o model/src:
989      - introduce ALLOW_BALANCE_RELAX which allow the removal
990       of the global mean of relaxation terms by setting
991       balanceThetaClimRelax and balanceSaltClimRelax
992      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
993       This case is now treated appropriately in seaice_growth.F
994    o pkg/seaice:
995      - do balanceEmPmR and balanceQnet based on the net fluxes
996        (SItflux) that enter the ocean+ice system rather than QNET
997        and EMPMR. Works best in real fresh water.
998      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
999        out of the diagnotics bloc, and stored in global arrays.
1000    
1001    checkpoint63o (2012/06/29)
1002    o vertical mixing schemes:
1003      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
1004      - replace computation of density (in Function STATE1, opps_calc.F) by a call
1005        to S/R FIND_RHO_SCALAR
1006      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
1007        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
1008        affects output (vermix.ggl90) at truncation level.
1009    o testreport:
1010      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
1011        (nSx,nSy) for the number of threads (from eedata.mth)
1012    o model/src:
1013      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
1014        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
1015    o verification/tutorial_tracer_adjsens/
1016      - compile with ALLOW_CG2D_NSA
1017      - run with nonlinFreeSurf=3
1018      - update reference output_adm.txt
1019    o tools/genmake2:
1020      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
1021        refine usePROFILES switching off (only when NetCDF is not available).
1022    o verification (atmospheric set-up):
1023      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
1024    o pkg/profiles : refine profiles and files handling.
1025    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
1026    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
1027      - changes to use model/src/the_main_loop.F rather than the ecco version
1028        in ecco type adjoint runs.
1029    o model/src:
1030      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
1031      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
1032      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
1033    o model/src:
1034      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
1035        update output of test experiment bottom_ctrl_5x5.
1036    o pkg/generic_advdiff:
1037      - implement vertical bi-harmonic diffusion (for now, only for T & S and
1038        only explicitly).
1039    o verification/bottom_ctrl_5x5/
1040      update reference output (results changed quite some time ago,
1041      not sure when; but new reference results look ok in terms of grdchk)
1042    o verification/1D_ocean_ice_column/
1043      For verification purposes, the exact adjoint rather than an approx.
1044      should be used (e.g., to comare against F.D. or TLM).
1045      removed autodiff_inadmode*_ad.F routines in code_ad/
1046      Update results/ accordingly.
1047    o pkg/cal:
1048      - change cal_getdate.F so that output date is function of input time only
1049        (less ambiguous, not mixed up with input iteration number).
1050      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
1051    o pkg/diagnostics:
1052      - implement calendarDumps also for stats-diags
1053      - implement calendarDumps also for snap-shot output (negative freq)
1054      - for now, ignores calendarDumps if non-zero phase-lag.
1055    
1056  checkpoint63n (2012/06/04)  checkpoint63n (2012/06/04)
1057  o model/src:  o model/src:
1058    - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)    - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
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