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revision 1.1697 by jmc, Sat Jul 28 20:13:24 2012 UTC revision 1.1897 by jmc, Sat Jul 20 00:04:02 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 testreport:
8      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
9        perform additional runs (number of additional runs is "add_DIVA_runs" taken
10        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
11    o verification/lab_sea (AD test):
12      - change to test Divided Adjoint Run in this set-up (both standard AD test
13        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
14    o pkg atm_ & ocn_compon_interf:
15      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
16        staggerTimeStep implementation) and disable (retired) corresponding
17        parameter.
18    o pkg/offline:
19      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
20      - add S/R OFFLINE_CHECK to print offline parameter summary
21        and stop if loading a file that is not used;
22      - enable to calculate GMRedi tensor, KPP mixing and convective index
23        when the corresponding file(s) is/are not specified (but pkg is used).
24      - comment out resetting of monitorFreq (to endTime) since it still useful
25        for monitoring CFL numbers and checking offline fields.
26    o OpenAD:
27      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
28        smaller standard output) and generate new (smaller) output (on baudelaire
29        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
30    o model/src:
31      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
32        (where external_forcing_adjust was called) and change list of arguments;
33      - merge external_forcing_adjust.F into external_forcing_surf.F
34      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
35        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
36        previously in file "balance_relax.F", now removed); remove corresponding
37        arrays in FFIELDS.h.
38      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
39        a hack for getting back surfaceForcingS (loaded from file) when using
40        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
41      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
42        (was getting only 11 digits for AD-grad, due to different truncation
43         error in AD code).
44    
45    checkpoint64j (2013/07/04)
46    o pkg/offline:
47      - to enable the use of other features with pkg offline (e.g., obcs),
48        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
49      - comment out "allowFreezing" (now active) in 2 offline testing exp.
50    o pkg/exf ALLOW_RUNOFTEMP
51      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
52      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
53      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
54    o pkg/atm_phys:
55      - allows to add some damping on uVel,vVel (strength only function of k).
56    o verification, ad-tests:
57      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
58        global_ocean_ebm and offline_exf_seaice.thsice.
59    o verification/halfpipe_streamice:
60      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
61        flux input boundary conditions to be ignored; a fix for this bug changed
62        verification results for forward test.
63      - add adjoint test.
64    o pkg/ptracers:
65      - allow to restart without SOM pickup (resetting SOM to zero).
66    o pkg/gmredi:
67      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
68      - It uses mixing length theory and suppression by steering level effects to
69        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
70        to JPO, for more details).
71      - It also uses the diffusivity to calculate an eddy induced streamfunction
72        based on a PV closure (rather than a buoyancy closure as in GM).
73      - New files added to pkg/gmredi:
74        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
75          induced overturning streamfunction (called from gmredi_calc_tensor)
76        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
77          for use in gmredi_k3d
78        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
79          the eddy diffusivity
80    
81    checkpoint64i (2013/06/18)
82    o pkg/cheapaml:
83      - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
84        that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
85        with pkg/cheapaml.
86    o utils/python: add subpackage for cubed sphere function, first example is
87        simple cs.pcol to plot 2D fields on a map
88    o pkg/streamice:
89      - This is a new package in MITgcm, which solves dynamic equations for ice
90         sheets and ice streams
91      - At the moment it is independent of atmosphere/ocean dynamics, or any
92        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
93        ed that this will change)
94      - There is a new verification exercise that tests it, halfpipe_streamice,
95        evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
96        rectangular embayment
97      - halfpipe_streamice is forward-only for now, will have TAF test soon
98      - for questions, email dgoldber@mit.edu
99    o pkg/thsice:
100      - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
101        of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
102      - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
103         call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
104      - allow precip from pkg/cheapaml to make snow over seaice.
105    o pkg/cfc:
106      - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
107      - remove atmos CFC 2-D arrays from common bloc (now local variables)
108      - change some hard-coded constant to run time parameter for reading and
109        and interpolating atmospheric CFC ; keep same default as previously.
110      - more flexible reading of Atmos CFC (number of records no longer hard-coded)
111      - put arguments in standard order: myTime, myIter, myThid
112      - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
113        atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
114      - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
115      - new routine to print summary of CFC params and check for consistency.
116    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
117      similar to thsice_advdiff.
118      Note that for the B-grid case the routine parameters uc/vc are overwritten.
119    o pkg/cfc:
120      - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
121        update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
122      - fix interpolation of atmphspheric CFC between Sorthern and Northern
123        hemisphere value.
124    o pkg/seaice:
125      - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
126    o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
127                  so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
128      - requires an additional time level that is stored in the pickup
129      - you can start with AB2 from a pickup without this time level with
130        pickupStrictlyMatch = .false.
131    
132    checkpoint64h (2013/05/26)
133    o pkg/cheapaml:
134      - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
135        affect machine truncation (but exp cheapAML_box still pass with 13 digits).
136      - consistent treatment of uWind,vWind location: assume everywhere in
137        pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
138        (Note: was already the case for Tair,Qair advection);
139        add option (INCONSISTENT_WIND_LOCATION) to recover old results.
140      - compute diabatic forcing only in the interior (excluding overlap regions)
141      - fill in array "Qsw" (for short-wave heating);
142      - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
143        before any update (consistent with MITgcm state var diagnostics);
144      - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
145        non periodic ; + adjusted for uWind,vWind (C-grid).
146    o pkg/seaice:
147      - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
148        add explicitly pkg/exf in experiments that currently use pkg/seaice.
149      - allows to compile pkg/seaice without pkg/exf.
150    o tools/OAD_support:
151      - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
152        of array "ourStepOf" in function rvNextAction (revolve.F90).
153    o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
154      - change pkg name (to be used with other atmospheric physics pkg)
155        but by-pass CVS when making the new pkg so that we keep the CVS history.
156    o pkg/offline:
157      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
158        (previously called from pkg/dic_surfforcing_init.F)
159    o model/src:
160      - re-order sequence of calls within packages_init_variables.F, using
161        standard order, except for:
162         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
163         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
164    o new pkg: atm_phys
165      - add entry point and source code (previously in contrib
166          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
167        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
168      - re-order sequence of calls within packages_readparms.F,
169         packages_init_fixed.F and packages_write_pickup.F
170        (but skip packages_init_variables.F because of TAF issues).
171      - update contrib/*/atm_gray/ experiment.
172    o pkg/seaice (ITD code):
173      - simplify and fix the writing of pickup-files for ITD case
174    o pkg/seaice (ITD code):
175      - introduce floe size dependent lateral melt for ITD case;
176      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
177      - update seaice_itd experiment main output.
178    o pkg/thsice:
179      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
180        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
181        changed accordingly pkg/atm2d.
182    
183    checkpoint64g (2013/05/01)
184    o pkg/exf ALLOW_RUNOFTEMP
185      - if defined,  river and glacier runoff temperature can be read-in from
186        runoftempfile; runoftempfile needs to have same format as runofffile
187    o pkg/thsice (& pkg/bulk_force):
188      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
189        for energy content of Precip + RunOff & Evap (like with pkg/exf).
190      - change computation domain to always be the interior (without overlap).
191      - fix bug (wrong overlap) when using EXF and stressReduction > 0.
192    o verification/tutorial_global_oce_biogeo:
193      - add preliminary OpenAD setup (still has problems)
194    o pkg/seaice:
195      - turn some parameters for choosing the convergence criterion of
196        the inexact Newton method (JFNK) into runtime parameters for convenience
197      - clean up seaice_calc_viscosities.F: remove/retire two options for
198        SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
199        the results of lab_sea/input because a division has been replaced by
200        a multiplication with the reciprocal (sumNorm)
201      - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
202        convergence of solver (changes results, of course), and to test some
203        new features
204    o model/src:
205      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
206      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
207      - move forcing adjustment (balancing surface forcing) in specific S/R
208        where might also be applied exchanges (if needed) to forcing arrays.
209    o pkg/shelfice:
210      - allow to specify the Ice-Shelf mass per unit area (instead of
211        shelficeLoadAnomaly) and do the conversion from one to the other
212      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
213        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
214        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
215        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
216      - update isomip experiment forward output (get machine truncation error
217        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
218    o verification/offline_exf_seaice:
219      revise data.seaice in input.thermo and input_ad and update results accordingly
220        HO = 0.2, SEAICE_areaLossFormula = 2,
221        SEAICE_growMeltByConv = .TRUE.,
222        SEAICE_doOpenWaterMelt = .TRUE.,
223      Improve consistency with input.thsice and fix the spurious 500m ice corners
224    o verification/global_ocean.cs32x15:
225      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
226        in icedyn (thsice+seaice-dyn) test and update output.
227    o verification/offline_exf_seaice:
228      - adjust list of tested variables (with testreport) and update
229        standard test output with better slection of monitored fields.
230    o pkg/cd_code:
231      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
232        experiment lab_sea.hb87
233    o tools/genmake2:
234      - change default makedepend from the system default to tools/xmakedepend:
235        When no makedepend is specified, select tools/xmakedepend it the test pass,
236        otherwise select the system default (if exist and pass the test) or
237        try to build cyrus-makedepend ; stop if none of the 3 works.
238    o pkg/exf & pkg/thsice:
239      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
240        for energy content of Precip + RunOff & Evap. Assumes:
241       1) Rain has same temp as Air.
242       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
243       3) Run-Off comes at the temp of surface water (with same Cp)
244       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
245        put directly into Latent Heat flux & should use water-vapor heat capacity.
246       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
247        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
248    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
249        (compile when SEAICE_ALLOW_JFNK is defined)
250    o pkg/thsice:
251      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
252        implementation): move THSICE_AVE call after the advection (called directly
253        from thsice_do_advect.F).
254    o verification/global_ocean.90x40x15 and OpenAD:
255      New experiment for OpenAD is identical to the one in input_ad except that
256        multiDimAdvection=.FALSE.,
257      There is still an issue with this.
258    o pkg/thsice:
259      - account for ice velocity (ocean relative velocity) in turbulent heat flux
260        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
261        and offline_exf_seaice (main test).
262    
263    checkpoint64f (2013/03/31)
264    o verification/OpenAD:
265      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
266    o verification/isomip, pkg/shelfice and OpenAD:
267      - add OpenAD setup to this exp and make shelfice package work with OpenAD
268    o verification/tutorial_global_oce_biogeo:
269      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
270    o verification/offline_exf_seaice:
271      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
272    o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
273      - add OpenAD setup to this exp and make ptracers package work with OpenAD
274    o pkg/seaice/seaice_evp.F:
275       mask the asymmetric contribution of the ice-ocean stress (when
276       the turningAngle is non-zero) over open water to avoid stripes
277       in the EVP-solutions after many EVP-substeps. This does not change
278       the verification experiment (because turningAngle=0 in that experiment),
279       but will affect other EVP solutions with turningAngle.ne.0
280    o verification, AD & TLM output:
281      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
282        additions and multiplications which affect results at machine truncation
283        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
284        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
285        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
286        digits of matching.
287    o pkg/seaice:
288       modify lsr-algorithm so that it vectorizes AND converges by using a
289       "zebra" method: split vector loop into two with step size 2; this
290       solves a general convergence problem for the JFNK solver on a vector
291       computer. It has the potential to even improve convergence for
292       non-vector machines, but it does change the results so it is turned
293       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
294       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
295    
296    checkpoint64e (2013/03/05)
297    o pkg/ecco and several verification experiments:
298       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
299       from ecco package, and revert to unified routine in model/src/
300       Adjust verification experiments accordingly, especially gloal_oce_llc90
301       Should conclude long-standing work by Gael to reconsile the_main_loop with
302       ECCO and will enable OpenAD's revolve loop in ECCO setup.
303    o pkg/generic_advdiff:
304      - implement compressible flow method for multi-dim advection (similar to
305        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
306        TAF generates many recomputations) to use it; no yet coded with implicit
307        vertical advection.
308      - change experiment advect_cs (new output) and advect_xy (same output)
309        to test compressible flow multi-dim advection.
310    o pkg/generic_advdiff:
311      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
312        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
313    o pkg/seaice:
314      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
315        bug affects two verification experiments (lab_sea and lab_sea.hb87),
316        recover old (wrong) results by setting noSlipFac = 2. in
317        seaice_calc_strainrates.F;
318      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
319      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
320        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
321      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
322    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
323      - new subroutines seaice_lsr_tridiagu/v
324      - introduce loop bounds i/jmin/max to be able to use a restricted
325        additive Schwarz method, but not used for now.
326      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
327      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
328    o OpenAD support
329       Reorganize S/R call for overall time-stepping loop to facilitate
330       OpenAD revolve loop replacement
331       (new S/R main_do_loop.F)
332    o model/src:
333      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
334      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
335        ADAMS_BASHFORTH2.
336    o pkg/cheapaml:
337      - add new parameter (default=F, same as before) to disable full domain
338        (including land) periodicity in X & Y dir.
339      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
340        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
341        into single S/R CHEAPAML_TIMESTEP.
342    
343    checkpoint64d (2013/02/17)
344    o pkg/monitor (angular momentum):
345      - do not add Eta contribution to the total AM if using rigid-lid;
346      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
347      - horizontal discretisation: compute Zonal wind contribution separately for
348        each component (instead of from cell centered averaged) and use the 4
349        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
350      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
351        FreeSurf) if using vectorInvariant momentum.
352    o model/src (horizontal grid):
353      - move initialisation of all horizontal grid arrays to null value
354        from specific horizontal grid S/R to main S/R INI_GRID;
355      - add 2 new arrays to project model C-grid velocity on to zonal direction
356        (similar to AngleCosC & -AngleSinC but at U and V point location) and
357        compute them in S/R CALC_GRID_ANGLES.
358    o pkg/seaice: replace a hard coded parameter by a runtime parameter
359        SEAICE_JFNK_tolIter
360    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
361        preconditioner for JFNK (run LSR into the overlaps as far as possible,
362        i.e OLx/y-2, but overwrite the solution in the overlaps)
363      - extend loop range in seaice_calc_viscosity
364      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
365      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
366      - slightly modify loops in tridiagonal solver lsr-preconditioner
367      - by default remove the extra exchange in seaice_preconditioner with a
368        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
369      - modify offline_exf_seaice so that old results without RAS are reproduced
370        for output.dyn_jfnk.txt
371      in seaice_fgmres.F (unrelated to RAS)
372      - add a cpp-flag option for a re-ordered mapping (potentially more
373        efficient), but because this changes the results, turn it off by
374        default
375      - replace the save statement by local common blocks
376    o utils/matlab:
377      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
378      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
379        instead of local script "load_cs.m".
380    o pkg/seaice:
381      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
382        to the scalarProductMetric and the unrolling. By chance this does not
383        change the verification experiment, because of the particular domain
384        decomposition
385    o pkg/diagnostics:
386      - change default missing_value from UNSET_RL to -999.
387    o pkg/layers: improve vectorization of layers_fluxcalc.F
388      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
389        time spent in this routine by more than a factor of 3 on an NEC-SX8
390      - step 2: replace search algorithm by a bisection algorithm found in
391        Press et al. Numerical Recipes in Fortran. This algorithm can be
392        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
393        For now, use this algorithm only for TARGET_NEC_SX defined.
394      - moved the search algorithm into a separate subroutine, that is kept
395        within the same file for automatic inlining.
396      - modified catching potential errors
397    o pkg/ecco:
398      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
399    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
400      - modifications for ALLOW_GENTIM2D_CONTROL
401      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
402      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
403      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
404      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
405    o model/src:
406      - account for moist thermodynamics in (dry) potential temperature equation;
407        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
408        and cpl_aim+ocn.
409      - also switch to standard compiler (gfortran, was using ifort previously)
410        for fizhi-cs experiments reference output.
411    o pkg/ctrl:
412      - 1st step toward generic time-varying control variable (2D) via CPP option
413        ALLOW_GENTIM2D_CONTROL
414      - note new namelist ctrl_nml_genarr in data.ctrl
415    o verification/global_ocean.cs32x15:
416      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
417        thsice calling sequence and update "output.icedyn.txt" output file.
418    o pkg/ptracers:
419      - from Ryan A.: code to allow to restart a tracer at regular time interval
420        specifying a reset frequency and a reset-phase (for each tracers).
421    o pkg/thsice:
422      - implement new sequence of calls for thsice+seaice:
423          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
424          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
425      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
426        in CPP_OPTIONS.h) to recover old sequence;
427      - update diagnostics for Intermediate State thsice diagnostics: now filled
428        just before advection (instead of just after advection in old sequence);
429      - update output of experiment offline_exf_seaice (standard test);
430      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
431        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
432    o pkg/aim_v23:
433      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
434      - use standard pkg/mdsio routines to read & write CO2 pickup file;
435      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
436      - Implement new sequence of calls for seaice advection (with thsice and
437        seaice diffusion): do ice advection after ice-Thermodynamic (previously
438        was done before); change aim_do_physics.F (split the bi,bj loops block);
439      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
440    o pkg/thsice:
441      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
442        where just seaice diffusion is used without seaice-dynamics.
443    
444    checkpoint64c (2013/01/18)
445    o pkg/seaice:
446      - add a parameter JFNKres_tFac that can replace JFNKres_t
447        (= JFNKres_tFac*JFNKresidual before JFNK solver)
448      - add a line search option to the JFNK solver
449      - move update of u/vIce and computation of initial residual into a separate
450        routine (same file); makes the code a little easier to read (?)
451      - the line search requires computation of the residual and for some reason
452        I cannot do the update of u/vIce at the beginning of the Newton loop
453        without changing the results, so we move computation of the new residual
454        also to the end of the Newton loop, even without the line search
455    o pkg/mdsio:
456      - write missing value (corresponding to undefined array value) to meta files;
457        skip this if missing value is one (UNSET_RL would be a better value for the
458        case of undefined missing value but it's current the default missing-value);
459        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
460    o pkg/exf & thsice:
461      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
462        diagnostics) even when SHORTWAVE_HEATING is #undef;
463    o verification/cfc_example:
464      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
465        illustrate how to use it).
466    o verification/offline_exf_seaice:
467      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
468        files to only one time-record.
469      in input.thermo: narrow the 2 bands of low initial ice-concentration near
470        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
471        snapshot output; same mcPheePiston value as in thsice with
472        surf-current=0.2m/s.
473      in input.thsice: similar set-up as in input.thermo (channel with same seaice
474        initial conditions).
475    o verification/cfc_example:
476      - update file "data" with more standard choice (default rotationPeriod,
477        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
478        set deltaTFreeSurf to deltaTtracer) and update the output.
479    o pkg/layers:
480      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
481      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
482    o verification/offline_exf_seaice:
483      - set all {field}period to zero for constant-in-time forcing (not tested
484        anywhere else).
485    o verification/offline_exf_seaice:
486      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
487      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
488    o model/src:
489      - implement Finite-Volume method for (hydrostatic) presure gradient
490        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
491    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
492      - In order to be compatible with the default EVP code, this requires changing
493        the EVP code around a little; and because any small change immediately
494        breaks the lab_sea.hb87 verification experiment, the reference output is
495        updated two times (each time the remaining aggrement was only 2 digits):
496        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
497        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
498        The adjoint test lab_sea.evp also needed to be updated.
499      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
500        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
501        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
502        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
503        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
504        kept obscure, because I need to test it a little more.
505    o pkg/cheapaml:
506      - fix few incorrect type (_RL/_RS) in subroutine calls.
507    o pkg/seaice:
508      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
509        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
510    o model/src:
511      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
512        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
513        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
514    o pkg/cheapaml:
515      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
516        update output of experiment cheapAML_box.
517      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
518        and set them only in one place (cheapaml_readparms.F).
519      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
520      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
521        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
522    o model/src/the_main_loop.F:
523      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
524    o pkg/seaice:
525      - remove legacy branch code.
526      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
527    o verification/*/code*/SEAICE_OPTIONS.h:
528      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
529        SEAICE_CAP_HEFF).
530    o pkg/cheapaml:
531      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
532        to load new forcing fields.
533      - add missing "_d 0" where it's needed; + some editing (improve indentation).
534      - remove switch to "-r8" compiler option (no longer needed) in verification
535        cheapAML_box, keep same output (small trucation error differences).
536    o verification/offline_exf_seaice:
537      - add thermodynamics only test.
538    o verification/cheapAML_box:
539      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
540        keep same output (same 14 digits for cg2d).
541      - switch on "-r8" compiler option (some numerical values are missing
542        the "_d 0") and update output (only 6 digits for cg2d were preserved).
543    
544    checkpoint64b (2012/12/24)
545    o pkg/cheapaml:
546      - remove un-used variables (Qnet,EmPmR) from pickup files.
547      - store tendency of advected variables into cheapaml pickup file
548        and fix the AB-2 restart.
549    o verification/offline_exf_seaice and lab_sea adjoint:
550      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
551      - switch to 4 time steps in offline, consistent with lab_sea.
552      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
553      - update results after change of experiment seaice.
554    o pkg/seaice:
555      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
556        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
557        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
558        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
559    o model/src:
560      - add run-time parameter to select CG2D solver minimum-residual solution
561        (in case of a poor convergence).
562    o pkg/seaice/seaice_lsr.F
563      - move calculation of matrix coefficients into new
564        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
565        file; the main purpose of this change is to be able to reuse the code
566        in S/R SEAICE_PRECONDITIONER
567      - modify the computation of the residual so that the mass of sea-ice
568        is not used twice; this simplifies the calculations, but since
569        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
570        not tested in testreport---this does not affect the testreport results.
571    o verification/seaice_obcs:
572      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
573        verification/lab_sea/input.salt_plume; changes results/output.txt*
574    o model/src:
575      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
576    o pkg/seaice:
577      - improve description of parameters in seaice_fgmres.F and start
578        cleaning up the code
579      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
580        second argument
581      - add a metric based on grid cell area to SEAICE_SCALPROD; update
582        results of offline_exf_seaice.dyn_jfnk
583      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
584    o pkg/aim_v23:
585      - fix an other bug in dissipation heating (grid-cell area was missing).
586    o model/src + pkg/seaice:
587      - add global (multi-tile) linear solver for pair of tri-diagonal system
588        along X and Y lines, respectively for U and V component.
589        Note: 1) MPI and cube-exchange not yet coded.
590            2) probably not accurate for poorly conditioned / large size problem.
591      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
592        default: not compiled and not used.
593    o pkg/seaice:
594      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
595        introduce bi/bj loops and use global_sum_tile_rl instead of
596        mpi_allreduce in seaice_fgmres.F
597      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
598      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
599      - add a verification experiment for JFNK in offline_exf_seaice
600    o verification:
601      - change (for now, only fwd test) offline_exf_seaice experiment:
602        use a re-entrant channel with idealized coastline (trapezoidal shape)
603        at southern boundary to explore seaice dynamics and thermodynamics
604        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
605        secondary test (input.thsice) use thermodynamics only with SST relaxation.
606      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
607    o pkg/exf:
608      - disable "sstExtrapol" when Nr=1
609    o verification:
610      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
611        to test pkg/cheapaml.
612    o pkg/aim_v23 & pkg/shap_filt:
613      - fix dissipation heating (erroneous gravity multiplication factor).
614    o pkg/seaice:
615      - remove unused field pressPre from jfnk solver
616      - rename two subroutines in seaice_preconditioner.F
617    o eesupp/src:
618       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
619    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
620       - remove wrong parts of the rhs and the lhs (were in there
621         because I did not understand the concept of this preconditioner)
622       - add an exchange between u- and v-sweep. This increases communication
623         by a factor of two but improves the convergence of jfnk. Ideally,
624         one would like the u- and v-sweep to be independent. So far within
625         undocumented ifdefs
626       - reorganize the extra computations for printing the residuals
627    o tools/genmake2:
628      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
629        since it's not necessary (and was preventing to use MNC in some cases).
630    
631    checkpoint64a (2012/11/16)
632    o pkg/autodiff:
633      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
634        autodiff_readparms.F no longer depends on calling order (within
635        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
636        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
637        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
638    o pkg/obcs:
639      - adding tidal velocity forcing capability to obcs
640        for usage example, see verification/seaice_obcs/input.tides
641    o pkg/seaice:
642      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
643        SEAICE_LSRrelaxU/V
644      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
645    o pkg/aim_v23:
646      - implement heating from friction (bottom friction and stratospheric drag).
647    o pkg/shap_filt:
648      - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
649        dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
650    o model/src:
651      - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
652        time-constant addMass field from file (addMassFile);
653      - support for heating due to friction (and Kinetic Energy dissipation):
654        add option, run-time switch and 3-D field array + support code ; each pkg
655        or S/R can add heating contribution (if there is a sink of KE); the sum is
656        accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
657    o pkg/seaice:
658      - complete merge of ITD code into seaice_growth.F
659        from MITgcm_contrib/torge/itd/code/
660        no verification so far, but Torge Martin tested
661        "1-D test case and Beaufort set up;
662        deliver okay results after 1 model year."
663      - complete merge of SEAICE_SIZE.h into all relevant routines
664      - move computation of eta at Z-points into calc_viscosities
665        + introduce global field etaZ
666        + add different methods for computing etaZ, for now the old
667          method (simple averages of eta to Z-points) is hardwired
668        + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
669          seaice_preconditioner
670      - simplify computations for SEAICE_ZETA_SMOOTHREG
671      - seaice_preconditioner:
672        + replace one remaining press by pressLoc (mistake)
673        + adjust printing of residuals
674      - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
675        + add (SEAICE.h) and rename some counters (initiliased in
676          seaice_init_fixed.F)
677        + add _BEGIN/END_MASTER (myThid)  around print statements
678        + print total number of iterations and failures over SEAICE_monFreq
679          interval to STDOUT
680      - move control over output-messages by fgmres to seaice_jfnk to save
681        some operations
682      - move resetting initial guess for fgmres outside of seaice_fgmres_driver
683        in order to make restarts with sol .ne. zero (fgmres with restarts)
684        (seaice_jfnk.F, seaice_fgmres.F)
685      - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
686        a serious convergence problem when open boundaries are involved
687    o pkg/ggl90: fix computation of control volumes for the case of
688      ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
689      up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
690    o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
691    o pkg/autodiff
692      - Add inAdMode switch for SEAICEuseDYNAMICS:
693        SEAICEuseDYNAMICSinAdMode
694        (extend logic in ADAUTODIFF_INADMODE_SET)
695    o pkg/seaice
696      - Step 1 of merging ice-thickness distribution (ITD) code from
697        MITgcm_contrib/torge/itd/ (author: Torge Martin)
698        The code implements concept laid out in Thorndike et al. (1975);
699        code is enabled via CPP flag SEAICE_ITD
700        nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
701        code is not complete yet!!
702      - SEAICE_SIZE.h now included in almost all seaice routines
703    o verification (using seaice):
704      - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
705        global_ocean.cs32x15.seaice ; update results.
706      - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
707      - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
708        offline_exf_seaice (previously compiling B-grid).
709    o pkg/exf:
710      - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
711        to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
712        forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
713    o pkg/layers (adjust changes from Sept 19):
714      - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
715        this allows to remove "layers_maxNum" dimension from all layers arrays.
716    o pkg/layers (adjust changes from Sept 19):
717      - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
718      - snap-shot extended to all type of layers (not just the 1rst type);
719      - remove layers variables when corresponding CPP option is undef.
720    o pkg/layers:
721      - rename pkg/layers variable and add new output (layer exist & un-weighted
722        velocity in layer)
723    o pkg/seaice:
724      - simplify (?) ocean-drag coefficent computations by using
725        the same routine in all three solvers (saves some code lines)
726      - remove global fields DRAGA and DRAGS from C-grid code and
727        declare them locally in lsr.F (the only place where they are
728        still used)
729      - update AD output of lab_sea.evp (very sensitive anyway).
730    o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
731      (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
732      and SEAICEuseJFNK=.true. A few things to note:
733      - involves a FGMRES, that is parallel but very inefficient,
734        because of many scalar products (global sums) in the Gram-Schmidt
735        orthogonalization method. Needs to be replaced. Original code
736        from J.-F. Lemieux
737      - preconditioner for FGMRES is a stripped down version of LSOR
738      - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
739        preconditioner. For the preconditioner, the default is set to 10.
740      - Jacobian times vector is computed with finite differences
741      - marginally related to JFNK-solver: add a smooth regularization for
742        zeta with tanh that will improve convergence (Lemieux and Tremblay,
743        2009) for any implicit solver (not implemented for EVP because EVP
744        does not need this regularization in the first place). Define
745        SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
746    o eesupp/src:
747      - check in genmake2 that intrinsic S/R flush is available.
748      - add S/R to flush IO unit (if intrinsic S/R flush is available)
749      - flush standard & error msg unit before MPI termination
750      - if debugMode, flush IO unit after printing msg
751    o pkg/ctrl:
752      - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
753        to ctrl_set_unpack_xyz.
754    
755    checkpoint64 (2012/10/09)
756    o pkg/shelfice
757      - in mom_fluxform.F, mom_vecinv.F:
758        CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
759        Bug fix KappaRU -> KappaRV
760        does not change verification/isomip but may change other setups
761        (presumably constant KappaRU=KappaRV)
762      - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
763    o pkg/obcs:
764      - fixed some indexing bugs in obcs_seaice_sponge.F
765      - added obcs relaxation subroutines for HSALT and HSNOW
766      - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
767    o pkg/seaice:
768      - add "multicategory" parameterization for snow in analogy to ice,
769        default is off for now.
770    o pkg/obcs:
771      - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
772        see verification/seaice_obcs/input.seaiceSponge for example application.
773      - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
774        index setting by master-thread. This fix multi-threads Pb in previous modifs.
775    o pkg/layers :
776      - add diagnostics to pkg/layers
777      - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
778        (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
779    o pkg/generic_advdiff/gad_implicit_r.F :
780      - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
781    o pkg/seaice/seaice_growth.F:
782      - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
783    o pkg/obcs:
784      - change default setting of OBCS_UVICE_OLD from defined to undef;
785      - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
786        in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
787      - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
788      - change OB null index value (OB_indexNone) to -99 ; this fix the problem
789        with Southern & Western OB at a tile edge (at least in a simple set-up).
790    o pkg/obcs:
791      - change settings of OB index in case OB coincides with tile edge (shared by
792        2 tiles), so that common OB location is registered by both tiles (instead of
793        only 1). However, for Southern and Western OB, index value = 0 is not
794        recognized as valid OB index (=default null value) and needs to be fixed.
795      - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
796      - new parameter "OB_indexNone" for null index value (for now, still zero)
797        to replace hard-coded null index value of zero.
798    o pkg/exch2:
799      - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
800        always check buffer-size (but outside the loop); move checking for valid
801        index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
802        print each tile and point connection only if |W2_printMsg|>= 2 and 3.
803    o pkg/ctrl (pack & unpack):
804      - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
805        (locally defined) for different variables (+ remove the variable-specific
806        file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
807        (to be extended to other local file names in ctrl.h).
808    o pkg/flt:
809      - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
810    o pkg/mdsio:
811      - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
812    o tools/genmake2:
813      - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
814        (added by Alistair in version 1.51 for building without make depend);
815      - remove Header files list (H_SRC_FILES) from the dependence of targets
816         ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
817        place in version 1.23): this save going through staf when unrelated header
818        file has been modified.
819       Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
820        "make depend" step, still need to do "make links" before "make adtaf".
821    o eesupp/src (+ few pkg src files) & genmake2:
822      - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
823      - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
824      - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
825         upper/lower case ; account for space between "#" and undef/define)
826    o pkg/flt (with exch2):
827      - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
828      - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
829    
830    checkpoint63s (2012/09/05)
831    o pkg/ecco:
832      - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
833      - add more relevant #ifdef ALLOW_SMOOTH ones.
834      - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
835    o pkg/ctrl:
836      - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
837        ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
838      - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
839        doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
840        ctrlSmoothCorrel3D (new).
841        The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
842      - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
843      - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
844        controls when useAtmWind, and vice versa.
845      - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
846      - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
847          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
848      - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
849          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
850      - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
851        replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
852    o pkg/smooth:
853      - remove un-necessary includes.
854      - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
855        Those CPP options were never defined, and not necessary.
856    o model/src:
857      - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
858      - standard treatment of useSMOOTH.
859    o pkg/autodiff:
860      - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
861        useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
862    o pkg/exch2:
863      - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
864        + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
865      - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
866        and tiles to process mapping.
867      - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
868        moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
869        rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
870        from w2_eeboot.F to w2_readparms.F.
871    o eesupp/src:
872      - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
873        ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
874        also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
875      - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
876        is defined (remove condition on usingMPI) to match cases where MPI_INIT
877        has been called.
878      - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
879      - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
880        (so that on 1 proc, get same myPid independently of usingMPI)
881      - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
882        useCubedSphereExchange with EXCH-1 (safer).
883      - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
884    o pkg/ggl90:
885      - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
886        used in ALLOW_GGL90_SMOOTH code.
887    o pkg/flt:
888      - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
889        floats at the Southern end of the domain).
890    o eesupp/inc:
891      - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
892        but not used (and not to be used) anywhere, just for documentation.
893    o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
894      - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
895        a) can damage previously written records in any other multi-record files.
896        b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
897    o tools/genmake2:
898      - define variable MAKE within Makefile and use it in place of 'make';
899      - update AD_CONFIG.h (if needed) before building any of the executable
900        (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
901        and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
902      - always print usual warning comment 'this file is automatically generated'
903        from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
904    o pkg/cheapaml:
905      - updated to correspond to the code used in accepted paper (Nico Wienders).
906    o pkg/exf:
907        added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
908        ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
909        and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
910    o pkg/exf, autodiff, ctrl, ecco and seaice:
911        remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
912    o pkg/ctrl, ecco:
913        allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
914        Depending on useAtmWind, one is inactive, and the other is active (see
915        exf_getffields.F/exf_getsurfacefluxes.F).
916    o tools/genmake2:
917      - improve error msg when failing in 2nd test of check_for_broken_Ff
918      - fix option '-makefile' short-name (-mf according to genmake2 -help)
919      - source local config file "genmake_local" just after processing the genmake2
920        command arguments (previously done before processing arg).
921    o pkg/grdchk:
922      - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
923        to this routine from cost_final has been dropped in g_cost_final)
924      - improve printed information (more explicit msg, no longer using "print *,"
925         fix fcpertminus printed value).
926    o model/src:
927      - move call to COST_INIT_VARIA out of packages_init_variables.F directly
928        into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
929        this prevents getting cost-funct reset in adinitialise_varia recomputations.
930    o pkg/dic:
931      - move initialisation of "freefe" array from from dic_biotic_forcing.F to
932        fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
933    o pkg/grdchk:
934      - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
935      - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
936    o pkg/autodiff/ctrl/grdchk :
937      - attempt to sort out what works and what does not,
938        with regard to I/O, and to warn/stop accordingly.
939    o pkg/grdchk:
940      - attempt to fix grdchk in the case of useSingleCpuIO.
941      - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
942       statements were moved from grdchk_main.F and into
943       grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
944      - a global sum is applied to record numbers icvrec/layer
945       out of grdchk_loc so that they be passed to I/O routines.
946    o pkg/smooth:
947      - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
948        smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
949    o verification/testreport:
950      - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
951      - can also use compressed (gzip) reference output file;
952      - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
953        to be easier to collect by testreport.
954      - update existing TLM output (half out-of-date by more than 3 yrs).
955      - report NETCDF & LAPACK settings (from genmake2) in output dir.
956      - report run-time in each individual summary (previously only for AD test);
957        for TLM test, add also TAF version.
958      - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
959    
960    checkpoint63r (2012/08/15)
961    o tools/genmake2:
962      - fix Makefile for target ftlall (+ update files to clean after make ftlall)
963    o pkg/ecco/ecco_cost_final.F :
964      - fix fc print statements (to stdout and costfunction0000) so
965        that the printed value is always after the global sum.
966    o pkg/seaice/seaice_dynsolver.F :
967      - fix ice strength assymptote at SEAICE_area_max<1
968        (no change for the standard case of SEAICE_area_max=1)
969    o some cleaning:
970      - pkg source files: ensure that all *.F files from each pkg included the
971        corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
972        only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
973        code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
974        includes;
975      - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
976      - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
977        is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
978        ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
979      - update option-file CPP_OPTIONS.h of all AD experiments:
980        * no longer include PACKAGES_CONFIG.h ;
981        * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
982        * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
983          including ECCO_CPPOPTIONS.h).
984    o pkg/cost, pkg/ctrl, pkg/ecco option-file:
985      - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
986        separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
987        not necessary accurate).
988      - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
989        pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
990        deliberately break compilation (a remainder that it needs to be customized)
991      - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
992      - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
993      - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
994    o tools/genamke2:
995      - check for lapack.
996    o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
997      - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
998        jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
999        from both packages.
1000      - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
1001      - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
1002      - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
1003        of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
1004    o pkg/cost : add comments to explain special and/or untested setups.
1005    o pkg/exf:
1006      - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
1007        (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
1008    o verification/*/code_ad:
1009      mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
1010      - reccord when this file is included (define ECCO_CPPOPTIONS_H)
1011      - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
1012        allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
1013    o pkg/seaice :
1014      - added possibility to change ice strength/PRESS0 relationship to
1015        HEFF, according to the following run time parameters
1016        SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
1017        SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
1018        SEAICEpresH0   :: HEFF threshold for ice strength            (m)
1019    o pkg/ggl90 :
1020      - added run time flag mxlSurfFlag to include the code that ensure
1021        mixing between first and second level (previously included as a comment)
1022    o verification/1D_ocean_ice_column/input_ad/data.autodiff :
1023      - add test of newly added dumpAdByRec=T option where
1024        we write all records to one file per variable.
1025    o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
1026      - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
1027        to check that this code is ok with taf and compiles in adjoint.
1028    o pkg/autodiff :
1029      - added run time param dumpAdByRec : ad dump format switch.
1030        If true then write all records to one file per variable.
1031        Else write one file per record (remains the default).
1032      - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
1033    o pkg/seaice:
1034     - Added SEAICEuseTILT run time switch : if set to
1035       false then omit the tilt term in seaice dynamics.
1036     - Fix free drift calculation.
1037    o pkg/shelfice:
1038      When initializing SHELFICEDragQuadratic, set default to be
1039      consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
1040      but retain option to set it independently
1041      (inconsistenty spotted by Veronique Dansereau)
1042    o eesupp/inc:
1043      - in EEPARAMS.h, add real-type constant for some frequently used simple number
1044         (0,1,2,1/2), with name explicitly referring to RS/RL type.
1045    o model/src:
1046      - move balancing of relaxation terms to new S/R balance_relax.F.
1047    o pkg/autodiff:
1048      re-write active I/O high-level (control) S/R:
1049      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
1050      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
1051      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
1052        MDS_READ/WRITE_FIELD); change loops to multi-threads.
1053      - update and merge active_file_control_slice.flow into active_file_control.flow
1054      - update the calls in lower level S/R (active_file.F, active_file_g.F and
1055        active_file_ad.F) keeping the argument list and function unchanged.
1056      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
1057        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
1058      - new low-level active I/O routines, one for each type (RL/RS), for active var
1059        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
1060        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
1061        right type.
1062    o autodiff and RS=real*4:
1063      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
1064        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
1065      - change argument type of 3-D mask argument to _RS to match type in the call
1066        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
1067    o pkg/thsice:
1068      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
1069      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
1070        fresh-water flux: uniform correction or proportional to local precip.
1071    o pkg/ctrl:
1072      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
1073      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
1074                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
1075      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
1076    
1077    checkpoint63q (2012/07/30)
1078  o pkg/autodiff:  o pkg/autodiff:
1079    note about monitor and snap-shot of ad-variables:    note about monitor and snap-shot of ad-variables:
1080    a) need to apply ADEXCH before monitor or output of ad-vars to include    a) need to apply ADEXCH before monitor or output of ad-vars to include
# Line 12  o pkg/autodiff: Line 1083  o pkg/autodiff:
1083     truncation error is expected when adding an ADEXCH call in the middle of     truncation error is expected when adding an ADEXCH call in the middle of
1084     the time-stepping (although mathematically identical).     the time-stepping (although mathematically identical).
1085    modifs:    modifs:
1086      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
1087        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
1088    - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to    - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
1089      apply ADEXCH before monitor or snap-shot of ad-variables:      apply ADEXCH before monitor or snap-shot of ad-variables:
1090         =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.         =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
1091    - implement new method (copy+adexch) for snap-shot and monitor of main model    - implement new method (copy+adexch) for snap-shot and monitor of main model
1092      ad-vars (but not yet used by default).      ad-vars (initially not used by default -> output unchanged).
1093    - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars    - change default (set to 2) to use new method and update few output_adm.txt
1094      declaration (adEddyPsiX,adEddyPsiY in adcommon.h).      with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
1095        and both tutorial_tracer_adjsens tests).
1096      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
1097        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
1098  o pkg/ctrl:  o pkg/ctrl:
1099    enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of    enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
1100    generic control variables via    generic control variables via
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