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revision 1.1661 by mlosch, Fri May 18 12:44:21 2012 UTC revision 1.1883 by m_bates, Fri Jun 21 17:23:31 2013 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7  o pkg/shelfice:  o pkg/gmredi:
8    - add parameterisation of advective-diffusive flux into the ice shelf    - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
9      - It uses mixing length theory and suppression by steering level effects to
10        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
11        to JPO, for more details).
12      - It also uses the diffusivity to calculate an eddy induced streamfunction
13        based on a PV closure (rather than a buoyancy closure as in GM).
14      - New files added to pkg/gmredi:
15        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
16          induced overturning streamfunction (called from gmredi_calc_tensor)
17        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
18          for use in gmredi_k3d
19        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
20          the eddy diffusivity
21    
22    checkpoint64i (2013/06/18)
23    o pkg/cheapaml:
24      - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
25        that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
26        with pkg/cheapaml.
27    o utils/python: add subpackage for cubed sphere function, first example is
28        simple cs.pcol to plot 2D fields on a map
29    o pkg/streamice:
30      - This is a new package in MITgcm, which solves dynamic equations for ice
31         sheets and ice streams
32      - At the moment it is independent of atmosphere/ocean dynamics, or any
33        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
34        ed that this will change)
35      - There is a new verification exercise that tests it, halfpipe_streamice,
36        evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
37        rectangular embayment
38      - halfpipe_streamice is forward-only for now, will have TAF test soon
39      - for questions, email dgoldber@mit.edu
40    o pkg/thsice:
41      - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
42        of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
43      - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
44         call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
45      - allow precip from pkg/cheapaml to make snow over seaice.
46    o pkg/cfc:
47      - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
48      - remove atmos CFC 2-D arrays from common bloc (now local variables)
49      - change some hard-coded constant to run time parameter for reading and
50        and interpolating atmospheric CFC ; keep same default as previously.
51      - more flexible reading of Atmos CFC (number of records no longer hard-coded)
52      - put arguments in standard order: myTime, myIter, myThid
53      - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
54        atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
55      - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
56      - new routine to print summary of CFC params and check for consistency.
57    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
58      similar to thsice_advdiff.
59      Note that for the B-grid case the routine parameters uc/vc are overwritten.
60    o pkg/cfc:
61      - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
62        update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
63      - fix interpolation of atmphspheric CFC between Sorthern and Northern
64        hemisphere value.
65    o pkg/seaice:
66      - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
67    o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
68                  so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
69      - requires an additional time level that is stored in the pickup
70      - you can start with AB2 from a pickup without this time level with
71        pickupStrictlyMatch = .false.
72    
73    checkpoint64h (2013/05/26)
74    o pkg/cheapaml:
75      - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
76        affect machine truncation (but exp cheapAML_box still pass with 13 digits).
77      - consistent treatment of uWind,vWind location: assume everywhere in
78        pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
79        (Note: was already the case for Tair,Qair advection);
80        add option (INCONSISTENT_WIND_LOCATION) to recover old results.
81      - compute diabatic forcing only in the interior (excluding overlap regions)
82      - fill in array "Qsw" (for short-wave heating);
83      - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
84        before any update (consistent with MITgcm state var diagnostics);
85      - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
86        non periodic ; + adjusted for uWind,vWind (C-grid).
87    o pkg/seaice:
88      - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
89        add explicitly pkg/exf in experiments that currently use pkg/seaice.
90      - allows to compile pkg/seaice without pkg/exf.
91    o tools/OAD_support:
92      - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
93        of array "ourStepOf" in function rvNextAction (revolve.F90).
94    o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
95      - change pkg name (to be used with other atmospheric physics pkg)
96        but by-pass CVS when making the new pkg so that we keep the CVS history.
97    o pkg/offline:
98      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
99        (previously called from pkg/dic_surfforcing_init.F)
100    o model/src:
101      - re-order sequence of calls within packages_init_variables.F, using
102        standard order, except for:
103         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
104         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
105    o new pkg: atm_phys
106      - add entry point and source code (previously in contrib
107          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
108        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
109      - re-order sequence of calls within packages_readparms.F,
110         packages_init_fixed.F and packages_write_pickup.F
111        (but skip packages_init_variables.F because of TAF issues).
112      - update contrib/*/atm_gray/ experiment.
113    o pkg/seaice (ITD code):
114      - simplify and fix the writing of pickup-files for ITD case
115    o pkg/seaice (ITD code):
116      - introduce floe size dependent lateral melt for ITD case;
117      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
118      - update seaice_itd experiment main output.
119    o pkg/thsice:
120      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
121        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
122        changed accordingly pkg/atm2d.
123    
124    checkpoint64g (2013/05/01)
125    o pkg/exf ALLOW_RUNOFTEMP
126      - if defined,  river and glacier runoff temperature can be read-in from
127        runoftempfile; runoftempfile needs to have same format as runofffile
128    o pkg/thsice (& pkg/bulk_force):
129      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
130        for energy content of Precip + RunOff & Evap (like with pkg/exf).
131      - change computation domain to always be the interior (without overlap).
132      - fix bug (wrong overlap) when using EXF and stressReduction > 0.
133    o verification/tutorial_global_oce_biogeo:
134      - add preliminary OpenAD setup (still has problems)
135    o pkg/seaice:
136      - turn some parameters for choosing the convergence criterion of
137        the inexact Newton method (JFNK) into runtime parameters for convenience
138      - clean up seaice_calc_viscosities.F: remove/retire two options for
139        SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
140        the results of lab_sea/input because a division has been replaced by
141        a multiplication with the reciprocal (sumNorm)
142      - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
143        convergence of solver (changes results, of course), and to test some
144        new features
145    o model/src:
146      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
147      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
148      - move forcing adjustment (balancing surface forcing) in specific S/R
149        where might also be applied exchanges (if needed) to forcing arrays.
150    o pkg/shelfice:
151      - allow to specify the Ice-Shelf mass per unit area (instead of
152        shelficeLoadAnomaly) and do the conversion from one to the other
153      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
154        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
155        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
156        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
157      - update isomip experiment forward output (get machine truncation error
158        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
159    o verification/offline_exf_seaice:
160      revise data.seaice in input.thermo and input_ad and update results accordingly
161        HO = 0.2, SEAICE_areaLossFormula = 2,
162        SEAICE_growMeltByConv = .TRUE.,
163        SEAICE_doOpenWaterMelt = .TRUE.,
164      Improve consistency with input.thsice and fix the spurious 500m ice corners
165    o verification/global_ocean.cs32x15:
166      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
167        in icedyn (thsice+seaice-dyn) test and update output.
168    o verification/offline_exf_seaice:
169      - adjust list of tested variables (with testreport) and update
170        standard test output with better slection of monitored fields.
171    o pkg/cd_code:
172      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
173        experiment lab_sea.hb87
174    o tools/genmake2:
175      - change default makedepend from the system default to tools/xmakedepend:
176        When no makedepend is specified, select tools/xmakedepend it the test pass,
177        otherwise select the system default (if exist and pass the test) or
178        try to build cyrus-makedepend ; stop if none of the 3 works.
179    o pkg/exf & pkg/thsice:
180      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
181        for energy content of Precip + RunOff & Evap. Assumes:
182       1) Rain has same temp as Air.
183       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
184       3) Run-Off comes at the temp of surface water (with same Cp)
185       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
186        put directly into Latent Heat flux & should use water-vapor heat capacity.
187       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
188        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
189    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
190        (compile when SEAICE_ALLOW_JFNK is defined)
191    o pkg/thsice:
192      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
193        implementation): move THSICE_AVE call after the advection (called directly
194        from thsice_do_advect.F).
195    o verification/global_ocean.90x40x15 and OpenAD:
196      New experiment for OpenAD is identical to the one in input_ad except that
197        multiDimAdvection=.FALSE.,
198      There is still an issue with this.
199    o pkg/thsice:
200      - account for ice velocity (ocean relative velocity) in turbulent heat flux
201        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
202        and offline_exf_seaice (main test).
203    
204    checkpoint64f (2013/03/31)
205    o verification/OpenAD:
206      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
207    o verification/isomip, pkg/shelfice and OpenAD:
208      - add OpenAD setup to this exp and make shelfice package work with OpenAD
209    o verification/tutorial_global_oce_biogeo:
210      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
211    o verification/offline_exf_seaice:
212      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
213    o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
214      - add OpenAD setup to this exp and make ptracers package work with OpenAD
215    o pkg/seaice/seaice_evp.F:
216       mask the asymmetric contribution of the ice-ocean stress (when
217       the turningAngle is non-zero) over open water to avoid stripes
218       in the EVP-solutions after many EVP-substeps. This does not change
219       the verification experiment (because turningAngle=0 in that experiment),
220       but will affect other EVP solutions with turningAngle.ne.0
221    o verification, AD & TLM output:
222      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
223        additions and multiplications which affect results at machine truncation
224        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
225        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
226        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
227        digits of matching.
228    o pkg/seaice:
229       modify lsr-algorithm so that it vectorizes AND converges by using a
230       "zebra" method: split vector loop into two with step size 2; this
231       solves a general convergence problem for the JFNK solver on a vector
232       computer. It has the potential to even improve convergence for
233       non-vector machines, but it does change the results so it is turned
234       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
235       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
236    
237    checkpoint64e (2013/03/05)
238    o pkg/ecco and several verification experiments:
239       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
240       from ecco package, and revert to unified routine in model/src/
241       Adjust verification experiments accordingly, especially gloal_oce_llc90
242       Should conclude long-standing work by Gael to reconsile the_main_loop with
243       ECCO and will enable OpenAD's revolve loop in ECCO setup.
244    o pkg/generic_advdiff:
245      - implement compressible flow method for multi-dim advection (similar to
246        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
247        TAF generates many recomputations) to use it; no yet coded with implicit
248        vertical advection.
249      - change experiment advect_cs (new output) and advect_xy (same output)
250        to test compressible flow multi-dim advection.
251    o pkg/generic_advdiff:
252      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
253        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
254    o pkg/seaice:
255      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
256        bug affects two verification experiments (lab_sea and lab_sea.hb87),
257        recover old (wrong) results by setting noSlipFac = 2. in
258        seaice_calc_strainrates.F;
259      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
260      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
261        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
262      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
263    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
264      - new subroutines seaice_lsr_tridiagu/v
265      - introduce loop bounds i/jmin/max to be able to use a restricted
266        additive Schwarz method, but not used for now.
267      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
268      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
269    o OpenAD support
270       Reorganize S/R call for overall time-stepping loop to facilitate
271       OpenAD revolve loop replacement
272       (new S/R main_do_loop.F)
273    o model/src:
274      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
275      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
276        ADAMS_BASHFORTH2.
277    o pkg/cheapaml:
278      - add new parameter (default=F, same as before) to disable full domain
279        (including land) periodicity in X & Y dir.
280      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
281        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
282        into single S/R CHEAPAML_TIMESTEP.
283    
284    checkpoint64d (2013/02/17)
285    o pkg/monitor (angular momentum):
286      - do not add Eta contribution to the total AM if using rigid-lid;
287      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
288      - horizontal discretisation: compute Zonal wind contribution separately for
289        each component (instead of from cell centered averaged) and use the 4
290        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
291      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
292        FreeSurf) if using vectorInvariant momentum.
293    o model/src (horizontal grid):
294      - move initialisation of all horizontal grid arrays to null value
295        from specific horizontal grid S/R to main S/R INI_GRID;
296      - add 2 new arrays to project model C-grid velocity on to zonal direction
297        (similar to AngleCosC & -AngleSinC but at U and V point location) and
298        compute them in S/R CALC_GRID_ANGLES.
299    o pkg/seaice: replace a hard coded parameter by a runtime parameter
300        SEAICE_JFNK_tolIter
301    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
302        preconditioner for JFNK (run LSR into the overlaps as far as possible,
303        i.e OLx/y-2, but overwrite the solution in the overlaps)
304      - extend loop range in seaice_calc_viscosity
305      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
306      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
307      - slightly modify loops in tridiagonal solver lsr-preconditioner
308      - by default remove the extra exchange in seaice_preconditioner with a
309        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
310      - modify offline_exf_seaice so that old results without RAS are reproduced
311        for output.dyn_jfnk.txt
312      in seaice_fgmres.F (unrelated to RAS)
313      - add a cpp-flag option for a re-ordered mapping (potentially more
314        efficient), but because this changes the results, turn it off by
315        default
316      - replace the save statement by local common blocks
317    o utils/matlab:
318      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
319      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
320        instead of local script "load_cs.m".
321    o pkg/seaice:
322      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
323        to the scalarProductMetric and the unrolling. By chance this does not
324        change the verification experiment, because of the particular domain
325        decomposition
326    o pkg/diagnostics:
327      - change default missing_value from UNSET_RL to -999.
328    o pkg/layers: improve vectorization of layers_fluxcalc.F
329      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
330        time spent in this routine by more than a factor of 3 on an NEC-SX8
331      - step 2: replace search algorithm by a bisection algorithm found in
332        Press et al. Numerical Recipes in Fortran. This algorithm can be
333        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
334        For now, use this algorithm only for TARGET_NEC_SX defined.
335      - moved the search algorithm into a separate subroutine, that is kept
336        within the same file for automatic inlining.
337      - modified catching potential errors
338    o pkg/ecco:
339      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
340    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
341      - modifications for ALLOW_GENTIM2D_CONTROL
342      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
343      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
344      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
345      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
346    o model/src:
347      - account for moist thermodynamics in (dry) potential temperature equation;
348        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
349        and cpl_aim+ocn.
350      - also switch to standard compiler (gfortran, was using ifort previously)
351        for fizhi-cs experiments reference output.
352    o pkg/ctrl:
353      - 1st step toward generic time-varying control variable (2D) via CPP option
354        ALLOW_GENTIM2D_CONTROL
355      - note new namelist ctrl_nml_genarr in data.ctrl
356    o verification/global_ocean.cs32x15:
357      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
358        thsice calling sequence and update "output.icedyn.txt" output file.
359    o pkg/ptracers:
360      - from Ryan A.: code to allow to restart a tracer at regular time interval
361        specifying a reset frequency and a reset-phase (for each tracers).
362    o pkg/thsice:
363      - implement new sequence of calls for thsice+seaice:
364          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
365          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
366      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
367        in CPP_OPTIONS.h) to recover old sequence;
368      - update diagnostics for Intermediate State thsice diagnostics: now filled
369        just before advection (instead of just after advection in old sequence);
370      - update output of experiment offline_exf_seaice (standard test);
371      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
372        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
373    o pkg/aim_v23:
374      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
375      - use standard pkg/mdsio routines to read & write CO2 pickup file;
376      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
377      - Implement new sequence of calls for seaice advection (with thsice and
378        seaice diffusion): do ice advection after ice-Thermodynamic (previously
379        was done before); change aim_do_physics.F (split the bi,bj loops block);
380      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
381    o pkg/thsice:
382      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
383        where just seaice diffusion is used without seaice-dynamics.
384    
385    checkpoint64c (2013/01/18)
386    o pkg/seaice:
387      - add a parameter JFNKres_tFac that can replace JFNKres_t
388        (= JFNKres_tFac*JFNKresidual before JFNK solver)
389      - add a line search option to the JFNK solver
390      - move update of u/vIce and computation of initial residual into a separate
391        routine (same file); makes the code a little easier to read (?)
392      - the line search requires computation of the residual and for some reason
393        I cannot do the update of u/vIce at the beginning of the Newton loop
394        without changing the results, so we move computation of the new residual
395        also to the end of the Newton loop, even without the line search
396    o pkg/mdsio:
397      - write missing value (corresponding to undefined array value) to meta files;
398        skip this if missing value is one (UNSET_RL would be a better value for the
399        case of undefined missing value but it's current the default missing-value);
400        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
401    o pkg/exf & thsice:
402      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
403        diagnostics) even when SHORTWAVE_HEATING is #undef;
404    o verification/cfc_example:
405      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
406        illustrate how to use it).
407    o verification/offline_exf_seaice:
408      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
409        files to only one time-record.
410      in input.thermo: narrow the 2 bands of low initial ice-concentration near
411        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
412        snapshot output; same mcPheePiston value as in thsice with
413        surf-current=0.2m/s.
414      in input.thsice: similar set-up as in input.thermo (channel with same seaice
415        initial conditions).
416    o verification/cfc_example:
417      - update file "data" with more standard choice (default rotationPeriod,
418        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
419        set deltaTFreeSurf to deltaTtracer) and update the output.
420    o pkg/layers:
421      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
422      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
423    o verification/offline_exf_seaice:
424      - set all {field}period to zero for constant-in-time forcing (not tested
425        anywhere else).
426    o verification/offline_exf_seaice:
427      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
428      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
429    o model/src:
430      - implement Finite-Volume method for (hydrostatic) presure gradient
431        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
432    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
433      - In order to be compatible with the default EVP code, this requires changing
434        the EVP code around a little; and because any small change immediately
435        breaks the lab_sea.hb87 verification experiment, the reference output is
436        updated two times (each time the remaining aggrement was only 2 digits):
437        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
438        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
439        The adjoint test lab_sea.evp also needed to be updated.
440      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
441        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
442        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
443        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
444        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
445        kept obscure, because I need to test it a little more.
446    o pkg/cheapaml:
447      - fix few incorrect type (_RL/_RS) in subroutine calls.
448    o pkg/seaice:
449      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
450        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
451    o model/src:
452      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
453        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
454        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
455    o pkg/cheapaml:
456      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
457        update output of experiment cheapAML_box.
458      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
459        and set them only in one place (cheapaml_readparms.F).
460      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
461      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
462        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
463    o model/src/the_main_loop.F:
464      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
465    o pkg/seaice:
466      - remove legacy branch code.
467      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
468    o verification/*/code*/SEAICE_OPTIONS.h:
469      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
470        SEAICE_CAP_HEFF).
471    o pkg/cheapaml:
472      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
473        to load new forcing fields.
474      - add missing "_d 0" where it's needed; + some editing (improve indentation).
475      - remove switch to "-r8" compiler option (no longer needed) in verification
476        cheapAML_box, keep same output (small trucation error differences).
477    o verification/offline_exf_seaice:
478      - add thermodynamics only test.
479    o verification/cheapAML_box:
480      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
481        keep same output (same 14 digits for cg2d).
482      - switch on "-r8" compiler option (some numerical values are missing
483        the "_d 0") and update output (only 6 digits for cg2d were preserved).
484    
485    checkpoint64b (2012/12/24)
486    o pkg/cheapaml:
487      - remove un-used variables (Qnet,EmPmR) from pickup files.
488      - store tendency of advected variables into cheapaml pickup file
489        and fix the AB-2 restart.
490    o verification/offline_exf_seaice and lab_sea adjoint:
491      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
492      - switch to 4 time steps in offline, consistent with lab_sea.
493      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
494      - update results after change of experiment seaice.
495    o pkg/seaice:
496      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
497        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
498        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
499        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
500    o model/src:
501      - add run-time parameter to select CG2D solver minimum-residual solution
502        (in case of a poor convergence).
503    o pkg/seaice/seaice_lsr.F
504      - move calculation of matrix coefficients into new
505        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
506        file; the main purpose of this change is to be able to reuse the code
507        in S/R SEAICE_PRECONDITIONER
508      - modify the computation of the residual so that the mass of sea-ice
509        is not used twice; this simplifies the calculations, but since
510        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
511        not tested in testreport---this does not affect the testreport results.
512    o verification/seaice_obcs:
513      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
514        verification/lab_sea/input.salt_plume; changes results/output.txt*
515    o model/src:
516      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
517    o pkg/seaice:
518      - improve description of parameters in seaice_fgmres.F and start
519        cleaning up the code
520      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
521        second argument
522      - add a metric based on grid cell area to SEAICE_SCALPROD; update
523        results of offline_exf_seaice.dyn_jfnk
524      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
525    o pkg/aim_v23:
526      - fix an other bug in dissipation heating (grid-cell area was missing).
527    o model/src + pkg/seaice:
528      - add global (multi-tile) linear solver for pair of tri-diagonal system
529        along X and Y lines, respectively for U and V component.
530        Note: 1) MPI and cube-exchange not yet coded.
531            2) probably not accurate for poorly conditioned / large size problem.
532      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
533        default: not compiled and not used.
534    o pkg/seaice:
535      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
536        introduce bi/bj loops and use global_sum_tile_rl instead of
537        mpi_allreduce in seaice_fgmres.F
538      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
539      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
540      - add a verification experiment for JFNK in offline_exf_seaice
541    o verification:
542      - change (for now, only fwd test) offline_exf_seaice experiment:
543        use a re-entrant channel with idealized coastline (trapezoidal shape)
544        at southern boundary to explore seaice dynamics and thermodynamics
545        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
546        secondary test (input.thsice) use thermodynamics only with SST relaxation.
547      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
548    o pkg/exf:
549      - disable "sstExtrapol" when Nr=1
550    o verification:
551      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
552        to test pkg/cheapaml.
553    o pkg/aim_v23 & pkg/shap_filt:
554      - fix dissipation heating (erroneous gravity multiplication factor).
555    o pkg/seaice:
556      - remove unused field pressPre from jfnk solver
557      - rename two subroutines in seaice_preconditioner.F
558    o eesupp/src:
559       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
560    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
561       - remove wrong parts of the rhs and the lhs (were in there
562         because I did not understand the concept of this preconditioner)
563       - add an exchange between u- and v-sweep. This increases communication
564         by a factor of two but improves the convergence of jfnk. Ideally,
565         one would like the u- and v-sweep to be independent. So far within
566         undocumented ifdefs
567       - reorganize the extra computations for printing the residuals
568    o tools/genmake2:
569      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
570        since it's not necessary (and was preventing to use MNC in some cases).
571    
572    checkpoint64a (2012/11/16)
573    o pkg/autodiff:
574      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
575        autodiff_readparms.F no longer depends on calling order (within
576        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
577        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
578        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
579    o pkg/obcs:
580      - adding tidal velocity forcing capability to obcs
581        for usage example, see verification/seaice_obcs/input.tides
582    o pkg/seaice:
583      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
584        SEAICE_LSRrelaxU/V
585      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
586    o pkg/aim_v23:
587      - implement heating from friction (bottom friction and stratospheric drag).
588    o pkg/shap_filt:
589      - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
590        dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
591    o model/src:
592      - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
593        time-constant addMass field from file (addMassFile);
594      - support for heating due to friction (and Kinetic Energy dissipation):
595        add option, run-time switch and 3-D field array + support code ; each pkg
596        or S/R can add heating contribution (if there is a sink of KE); the sum is
597        accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
598    o pkg/seaice:
599      - complete merge of ITD code into seaice_growth.F
600        from MITgcm_contrib/torge/itd/code/
601        no verification so far, but Torge Martin tested
602        "1-D test case and Beaufort set up;
603        deliver okay results after 1 model year."
604      - complete merge of SEAICE_SIZE.h into all relevant routines
605      - move computation of eta at Z-points into calc_viscosities
606        + introduce global field etaZ
607        + add different methods for computing etaZ, for now the old
608          method (simple averages of eta to Z-points) is hardwired
609        + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
610          seaice_preconditioner
611      - simplify computations for SEAICE_ZETA_SMOOTHREG
612      - seaice_preconditioner:
613        + replace one remaining press by pressLoc (mistake)
614        + adjust printing of residuals
615      - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
616        + add (SEAICE.h) and rename some counters (initiliased in
617          seaice_init_fixed.F)
618        + add _BEGIN/END_MASTER (myThid)  around print statements
619        + print total number of iterations and failures over SEAICE_monFreq
620          interval to STDOUT
621      - move control over output-messages by fgmres to seaice_jfnk to save
622        some operations
623      - move resetting initial guess for fgmres outside of seaice_fgmres_driver
624        in order to make restarts with sol .ne. zero (fgmres with restarts)
625        (seaice_jfnk.F, seaice_fgmres.F)
626      - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
627        a serious convergence problem when open boundaries are involved
628    o pkg/ggl90: fix computation of control volumes for the case of
629      ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
630      up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
631    o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
632    o pkg/autodiff
633      - Add inAdMode switch for SEAICEuseDYNAMICS:
634        SEAICEuseDYNAMICSinAdMode
635        (extend logic in ADAUTODIFF_INADMODE_SET)
636    o pkg/seaice
637      - Step 1 of merging ice-thickness distribution (ITD) code from
638        MITgcm_contrib/torge/itd/ (author: Torge Martin)
639        The code implements concept laid out in Thorndike et al. (1975);
640        code is enabled via CPP flag SEAICE_ITD
641        nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
642        code is not complete yet!!
643      - SEAICE_SIZE.h now included in almost all seaice routines
644    o verification (using seaice):
645      - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
646        global_ocean.cs32x15.seaice ; update results.
647      - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
648      - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
649        offline_exf_seaice (previously compiling B-grid).
650    o pkg/exf:
651      - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
652        to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
653        forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
654    o pkg/layers (adjust changes from Sept 19):
655      - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
656        this allows to remove "layers_maxNum" dimension from all layers arrays.
657    o pkg/layers (adjust changes from Sept 19):
658      - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
659      - snap-shot extended to all type of layers (not just the 1rst type);
660      - remove layers variables when corresponding CPP option is undef.
661    o pkg/layers:
662      - rename pkg/layers variable and add new output (layer exist & un-weighted
663        velocity in layer)
664    o pkg/seaice:
665      - simplify (?) ocean-drag coefficent computations by using
666        the same routine in all three solvers (saves some code lines)
667      - remove global fields DRAGA and DRAGS from C-grid code and
668        declare them locally in lsr.F (the only place where they are
669        still used)
670      - update AD output of lab_sea.evp (very sensitive anyway).
671    o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
672      (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
673      and SEAICEuseJFNK=.true. A few things to note:
674      - involves a FGMRES, that is parallel but very inefficient,
675        because of many scalar products (global sums) in the Gram-Schmidt
676        orthogonalization method. Needs to be replaced. Original code
677        from J.-F. Lemieux
678      - preconditioner for FGMRES is a stripped down version of LSOR
679      - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
680        preconditioner. For the preconditioner, the default is set to 10.
681      - Jacobian times vector is computed with finite differences
682      - marginally related to JFNK-solver: add a smooth regularization for
683        zeta with tanh that will improve convergence (Lemieux and Tremblay,
684        2009) for any implicit solver (not implemented for EVP because EVP
685        does not need this regularization in the first place). Define
686        SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
687    o eesupp/src:
688      - check in genmake2 that intrinsic S/R flush is available.
689      - add S/R to flush IO unit (if intrinsic S/R flush is available)
690      - flush standard & error msg unit before MPI termination
691      - if debugMode, flush IO unit after printing msg
692    o pkg/ctrl:
693      - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
694        to ctrl_set_unpack_xyz.
695    
696    checkpoint64 (2012/10/09)
697    o pkg/shelfice
698      - in mom_fluxform.F, mom_vecinv.F:
699        CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
700        Bug fix KappaRU -> KappaRV
701        does not change verification/isomip but may change other setups
702        (presumably constant KappaRU=KappaRV)
703      - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
704    o pkg/obcs:
705      - fixed some indexing bugs in obcs_seaice_sponge.F
706      - added obcs relaxation subroutines for HSALT and HSNOW
707      - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
708    o pkg/seaice:
709      - add "multicategory" parameterization for snow in analogy to ice,
710        default is off for now.
711    o pkg/obcs:
712      - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
713        see verification/seaice_obcs/input.seaiceSponge for example application.
714      - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
715        index setting by master-thread. This fix multi-threads Pb in previous modifs.
716    o pkg/layers :
717      - add diagnostics to pkg/layers
718      - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
719        (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
720    o pkg/generic_advdiff/gad_implicit_r.F :
721      - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
722    o pkg/seaice/seaice_growth.F:
723      - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
724    o pkg/obcs:
725      - change default setting of OBCS_UVICE_OLD from defined to undef;
726      - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
727        in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
728      - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
729      - change OB null index value (OB_indexNone) to -99 ; this fix the problem
730        with Southern & Western OB at a tile edge (at least in a simple set-up).
731    o pkg/obcs:
732      - change settings of OB index in case OB coincides with tile edge (shared by
733        2 tiles), so that common OB location is registered by both tiles (instead of
734        only 1). However, for Southern and Western OB, index value = 0 is not
735        recognized as valid OB index (=default null value) and needs to be fixed.
736      - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
737      - new parameter "OB_indexNone" for null index value (for now, still zero)
738        to replace hard-coded null index value of zero.
739    o pkg/exch2:
740      - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
741        always check buffer-size (but outside the loop); move checking for valid
742        index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
743        print each tile and point connection only if |W2_printMsg|>= 2 and 3.
744    o pkg/ctrl (pack & unpack):
745      - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
746        (locally defined) for different variables (+ remove the variable-specific
747        file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
748        (to be extended to other local file names in ctrl.h).
749    o pkg/flt:
750      - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
751    o pkg/mdsio:
752      - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
753    o tools/genmake2:
754      - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
755        (added by Alistair in version 1.51 for building without make depend);
756      - remove Header files list (H_SRC_FILES) from the dependence of targets
757         ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
758        place in version 1.23): this save going through staf when unrelated header
759        file has been modified.
760       Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
761        "make depend" step, still need to do "make links" before "make adtaf".
762    o eesupp/src (+ few pkg src files) & genmake2:
763      - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
764      - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
765      - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
766         upper/lower case ; account for space between "#" and undef/define)
767    o pkg/flt (with exch2):
768      - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
769      - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
770    
771    checkpoint63s (2012/09/05)
772    o pkg/ecco:
773      - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
774      - add more relevant #ifdef ALLOW_SMOOTH ones.
775      - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
776    o pkg/ctrl:
777      - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
778        ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
779      - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
780        doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
781        ctrlSmoothCorrel3D (new).
782        The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
783      - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
784      - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
785        controls when useAtmWind, and vice versa.
786      - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
787      - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
788          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
789      - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
790          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
791      - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
792        replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
793    o pkg/smooth:
794      - remove un-necessary includes.
795      - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
796        Those CPP options were never defined, and not necessary.
797    o model/src:
798      - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
799      - standard treatment of useSMOOTH.
800    o pkg/autodiff:
801      - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
802        useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
803    o pkg/exch2:
804      - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
805        + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
806      - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
807        and tiles to process mapping.
808      - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
809        moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
810        rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
811        from w2_eeboot.F to w2_readparms.F.
812    o eesupp/src:
813      - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
814        ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
815        also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
816      - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
817        is defined (remove condition on usingMPI) to match cases where MPI_INIT
818        has been called.
819      - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
820      - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
821        (so that on 1 proc, get same myPid independently of usingMPI)
822      - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
823        useCubedSphereExchange with EXCH-1 (safer).
824      - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
825    o pkg/ggl90:
826      - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
827        used in ALLOW_GGL90_SMOOTH code.
828    o pkg/flt:
829      - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
830        floats at the Southern end of the domain).
831    o eesupp/inc:
832      - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
833        but not used (and not to be used) anywhere, just for documentation.
834    o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
835      - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
836        a) can damage previously written records in any other multi-record files.
837        b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
838    o tools/genmake2:
839      - define variable MAKE within Makefile and use it in place of 'make';
840      - update AD_CONFIG.h (if needed) before building any of the executable
841        (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
842        and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
843      - always print usual warning comment 'this file is automatically generated'
844        from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
845    o pkg/cheapaml:
846      - updated to correspond to the code used in accepted paper (Nico Wienders).
847    o pkg/exf:
848        added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
849        ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
850        and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
851    o pkg/exf, autodiff, ctrl, ecco and seaice:
852        remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
853    o pkg/ctrl, ecco:
854        allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
855        Depending on useAtmWind, one is inactive, and the other is active (see
856        exf_getffields.F/exf_getsurfacefluxes.F).
857    o tools/genmake2:
858      - improve error msg when failing in 2nd test of check_for_broken_Ff
859      - fix option '-makefile' short-name (-mf according to genmake2 -help)
860      - source local config file "genmake_local" just after processing the genmake2
861        command arguments (previously done before processing arg).
862    o pkg/grdchk:
863      - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
864        to this routine from cost_final has been dropped in g_cost_final)
865      - improve printed information (more explicit msg, no longer using "print *,"
866         fix fcpertminus printed value).
867    o model/src:
868      - move call to COST_INIT_VARIA out of packages_init_variables.F directly
869        into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
870        this prevents getting cost-funct reset in adinitialise_varia recomputations.
871    o pkg/dic:
872      - move initialisation of "freefe" array from from dic_biotic_forcing.F to
873        fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
874    o pkg/grdchk:
875      - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
876      - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
877    o pkg/autodiff/ctrl/grdchk :
878      - attempt to sort out what works and what does not,
879        with regard to I/O, and to warn/stop accordingly.
880    o pkg/grdchk:
881      - attempt to fix grdchk in the case of useSingleCpuIO.
882      - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
883       statements were moved from grdchk_main.F and into
884       grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
885      - a global sum is applied to record numbers icvrec/layer
886       out of grdchk_loc so that they be passed to I/O routines.
887    o pkg/smooth:
888      - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
889        smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
890    o verification/testreport:
891      - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
892      - can also use compressed (gzip) reference output file;
893      - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
894        to be easier to collect by testreport.
895      - update existing TLM output (half out-of-date by more than 3 yrs).
896      - report NETCDF & LAPACK settings (from genmake2) in output dir.
897      - report run-time in each individual summary (previously only for AD test);
898        for TLM test, add also TAF version.
899      - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
900    
901    checkpoint63r (2012/08/15)
902    o tools/genmake2:
903      - fix Makefile for target ftlall (+ update files to clean after make ftlall)
904    o pkg/ecco/ecco_cost_final.F :
905      - fix fc print statements (to stdout and costfunction0000) so
906        that the printed value is always after the global sum.
907    o pkg/seaice/seaice_dynsolver.F :
908      - fix ice strength assymptote at SEAICE_area_max<1
909        (no change for the standard case of SEAICE_area_max=1)
910    o some cleaning:
911      - pkg source files: ensure that all *.F files from each pkg included the
912        corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
913        only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
914        code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
915        includes;
916      - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
917      - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
918        is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
919        ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
920      - update option-file CPP_OPTIONS.h of all AD experiments:
921        * no longer include PACKAGES_CONFIG.h ;
922        * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
923        * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
924          including ECCO_CPPOPTIONS.h).
925    o pkg/cost, pkg/ctrl, pkg/ecco option-file:
926      - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
927        separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
928        not necessary accurate).
929      - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
930        pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
931        deliberately break compilation (a remainder that it needs to be customized)
932      - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
933      - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
934      - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
935    o tools/genamke2:
936      - check for lapack.
937    o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
938      - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
939        jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
940        from both packages.
941      - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
942      - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
943      - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
944        of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
945    o pkg/cost : add comments to explain special and/or untested setups.
946    o pkg/exf:
947      - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
948        (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
949    o verification/*/code_ad:
950      mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
951      - reccord when this file is included (define ECCO_CPPOPTIONS_H)
952      - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
953        allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
954    o pkg/seaice :
955      - added possibility to change ice strength/PRESS0 relationship to
956        HEFF, according to the following run time parameters
957        SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
958        SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
959        SEAICEpresH0   :: HEFF threshold for ice strength            (m)
960    o pkg/ggl90 :
961      - added run time flag mxlSurfFlag to include the code that ensure
962        mixing between first and second level (previously included as a comment)
963    o verification/1D_ocean_ice_column/input_ad/data.autodiff :
964      - add test of newly added dumpAdByRec=T option where
965        we write all records to one file per variable.
966    o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
967      - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
968        to check that this code is ok with taf and compiles in adjoint.
969    o pkg/autodiff :
970      - added run time param dumpAdByRec : ad dump format switch.
971        If true then write all records to one file per variable.
972        Else write one file per record (remains the default).
973      - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
974    o pkg/seaice:
975     - Added SEAICEuseTILT run time switch : if set to
976       false then omit the tilt term in seaice dynamics.
977     - Fix free drift calculation.
978    o pkg/shelfice:
979      When initializing SHELFICEDragQuadratic, set default to be
980      consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
981      but retain option to set it independently
982      (inconsistenty spotted by Veronique Dansereau)
983    o eesupp/inc:
984      - in EEPARAMS.h, add real-type constant for some frequently used simple number
985         (0,1,2,1/2), with name explicitly referring to RS/RL type.
986    o model/src:
987      - move balancing of relaxation terms to new S/R balance_relax.F.
988    o pkg/autodiff:
989      re-write active I/O high-level (control) S/R:
990      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
991      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
992      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
993        MDS_READ/WRITE_FIELD); change loops to multi-threads.
994      - update and merge active_file_control_slice.flow into active_file_control.flow
995      - update the calls in lower level S/R (active_file.F, active_file_g.F and
996        active_file_ad.F) keeping the argument list and function unchanged.
997      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
998        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
999      - new low-level active I/O routines, one for each type (RL/RS), for active var
1000        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
1001        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
1002        right type.
1003    o autodiff and RS=real*4:
1004      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
1005        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
1006      - change argument type of 3-D mask argument to _RS to match type in the call
1007        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
1008    o pkg/thsice:
1009      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
1010      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
1011        fresh-water flux: uniform correction or proportional to local precip.
1012    o pkg/ctrl:
1013      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
1014      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
1015                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
1016      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
1017    
1018    checkpoint63q (2012/07/30)
1019    o pkg/autodiff:
1020      note about monitor and snap-shot of ad-variables:
1021      a) need to apply ADEXCH before monitor or output of ad-vars to include
1022       overlap contributions (was done for adjDump but missing for monitor).
1023      b) since ADEXCH implies adding overlap values to interior array, machine
1024       truncation error is expected when adding an ADEXCH call in the middle of
1025       the time-stepping (although mathematically identical).
1026      modifs:
1027      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
1028        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
1029      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
1030        apply ADEXCH before monitor or snap-shot of ad-variables:
1031           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
1032      - implement new method (copy+adexch) for snap-shot and monitor of main model
1033        ad-vars (initially not used by default -> output unchanged).
1034      - change default (set to 2) to use new method and update few output_adm.txt
1035        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
1036        and both tutorial_tracer_adjsens tests).
1037      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
1038        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
1039    o pkg/ctrl:
1040      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
1041      generic control variables via
1042      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
1043      Only required customization should be S/R ctrl_map_ini_genarr.F
1044      (routine in repository contains example)
1045    o pkg/exf:
1046      - fix and refine checking of surface-relaxation setting when using EXF
1047    o verification (adjoint exp):
1048      - reduce length of simulation by half for experiment global_ocean.cs32x15
1049        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
1050    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
1051      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
1052        of KE that can occur with aggressive optimization
1053      + put quadratic bottom drag calculation in separated loops (only done if
1054        using bottomDragQuadratic)
1055    o model/src: CG2D_NSA
1056      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
1057         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
1058      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
1059         change cg2d residual target to be expressed in Wunits (=> do not normalise
1060         RHS ; this fix global_max Pb with TAF); update output.
1061    o verification/tutorial_tracer_adjsens:
1062       improve parameter consistency (and get rid of warnings):
1063       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
1064       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
1065       - use staggerTimeStep (for stability) in som81; use default rotation period.
1066    o pkg/exch2:
1067      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
1068        reset to 0 = 1 long line in X)
1069    o pkg/mdsio:
1070      - fix reading of dimensions from meta file for large-size domain
1071    o model/src:
1072      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
1073      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
1074        Cubed-Sphere Exch with CS-corners inside the domain;
1075        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
1076        globalArea and to set hasWetCSCorners.
1077      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
1078        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
1079      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
1080        useCDscheme and useCubedSphereExchange).
1081    o pkg/seaice/seaice_growth.F :
1082      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
1083        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
1084        when the previous code was not correct.
1085      - in all cases diagnoze the boundary condition mismatch to SIaaflux
1086      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
1087        that term to QNET (essentially to set the melt/freeze water to 0degC).
1088        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
1089    o verification/global_ocean.cs32x15/input.seaice :
1090      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
1091      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
1092      - update results (output.seaice.txt) accordingly.
1093    o verification/lab_sea/input/data.seaice :
1094      - remove SEAICEheatConsFix, which is now be tested
1095        in global_ocean.cs32x15. The presently coded fix
1096        is only consistent with real fresh water + nlfs.
1097      - update results (output.txt) accordingly.
1098    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
1099    o AD_CONFIG.h file:
1100      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
1101      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
1102        add it explicitly in each fortran src file where it is needed.
1103        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
1104        thus introducing potentially wrong dependency; therefore, better to include
1105        it only where it's really needed, and after any other included OPTIONS file
1106        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
1107        or ALLOW_TANGENTLINEAR_RUN).
1108    
1109    checkpoint63p (2012/07/06)
1110    o pkg/autodiff:
1111      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
1112      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
1113        which are now read from new parameter file "data.autodiff" (inAdExact
1114        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
1115      - add file "data.autodiff" in all verification/*/input_ad/ directories.
1116      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
1117        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
1118    o verification/tutorial_tracer_adjsens/
1119      - add extra sub-verification which uses "SOM" advection scheme
1120        (2nd Order-Moment Advection Scheme, Prather Limiter) with
1121          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
1122        and in data:
1123          multiDimAdvection=.TRUE.,
1124          tempAdvScheme=81,
1125          saltAdvScheme=81,
1126    o model/src:
1127      - introduce ALLOW_BALANCE_RELAX which allow the removal
1128       of the global mean of relaxation terms by setting
1129       balanceThetaClimRelax and balanceSaltClimRelax
1130      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
1131       This case is now treated appropriately in seaice_growth.F
1132    o pkg/seaice:
1133      - do balanceEmPmR and balanceQnet based on the net fluxes
1134        (SItflux) that enter the ocean+ice system rather than QNET
1135        and EMPMR. Works best in real fresh water.
1136      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
1137        out of the diagnotics bloc, and stored in global arrays.
1138    
1139    checkpoint63o (2012/06/29)
1140    o vertical mixing schemes:
1141      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
1142      - replace computation of density (in Function STATE1, opps_calc.F) by a call
1143        to S/R FIND_RHO_SCALAR
1144      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
1145        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
1146        affects output (vermix.ggl90) at truncation level.
1147    o testreport:
1148      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
1149        (nSx,nSy) for the number of threads (from eedata.mth)
1150    o model/src:
1151      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
1152        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
1153    o verification/tutorial_tracer_adjsens/
1154      - compile with ALLOW_CG2D_NSA
1155      - run with nonlinFreeSurf=3
1156      - update reference output_adm.txt
1157    o tools/genmake2:
1158      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
1159        refine usePROFILES switching off (only when NetCDF is not available).
1160    o verification (atmospheric set-up):
1161      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
1162    o pkg/profiles : refine profiles and files handling.
1163    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
1164    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
1165      - changes to use model/src/the_main_loop.F rather than the ecco version
1166        in ecco type adjoint runs.
1167    o model/src:
1168      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
1169      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
1170      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
1171    o model/src:
1172      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
1173        update output of test experiment bottom_ctrl_5x5.
1174    o pkg/generic_advdiff:
1175      - implement vertical bi-harmonic diffusion (for now, only for T & S and
1176        only explicitly).
1177    o verification/bottom_ctrl_5x5/
1178      update reference output (results changed quite some time ago,
1179      not sure when; but new reference results look ok in terms of grdchk)
1180    o verification/1D_ocean_ice_column/
1181      For verification purposes, the exact adjoint rather than an approx.
1182      should be used (e.g., to comare against F.D. or TLM).
1183      removed autodiff_inadmode*_ad.F routines in code_ad/
1184      Update results/ accordingly.
1185    o pkg/cal:
1186      - change cal_getdate.F so that output date is function of input time only
1187        (less ambiguous, not mixed up with input iteration number).
1188      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
1189    o pkg/diagnostics:
1190      - implement calendarDumps also for stats-diags
1191      - implement calendarDumps also for snap-shot output (negative freq)
1192      - for now, ignores calendarDumps if non-zero phase-lag.
1193    
1194    checkpoint63n (2012/06/04)
1195    o model/src:
1196      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
1197        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
1198      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
1199        similar to calc_r_star.F); update results of experiment internal_wave and
1200        tutorial_global_oce_in_p (affected @ truncation level).
1201    o pkg/shelfice:
1202      - add parameterisation of advective-diffusive flux into the ice shelf
1203      according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd      according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
1204    - simply eps3/3a computation    - simply eps3/3a computation
1205  o eesupp:  o eesupp:
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