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revision 1.1743 by mlosch, Mon Sep 24 15:07:38 2012 UTC revision 1.1936 by jmc, Tue Nov 5 14:39:53 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/mom_common:
8      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
9        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
10        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
11        ensure that all field value that are used are set.
12    o tutorial_deep_convection (smag3d):
13      - add missing scaling in mom_calc_smag_3d.F;
14      - set smag3D_coeff in input.smag3d such that results do not change.
15    o pkg/dic:
16      - change dic_cost.F to compute cost on each tile first and then apply
17        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
18        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
19    o eesupp/src & pkg/mdsio:
20      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
21        (from pkg/mdsio) since they are no longer used for tape IO.
22      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
23        (+ keep a copy in pkg/atm_ocn_coupler).
24    o verification/isomip:
25      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
26    o tools/build_options:
27      - optfile linux_amd64_ifort11, fast (no ieee) case:
28        to get a working restart for all experiments, add "-fp-model source"
29        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
30    
31    checkpoint64p (2013/10/20)
32    o pkg/autodiff:
33      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
34        criteria, return to simple (default) tape IO format.
35    o pkg/mdsio (+ eesupp/src):
36      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
37        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
38      - fix globalFile and singleCpuIO options using simpler global mapping.
39      - new pairs of scatter/gather vector S/R (one for each type, generated from
40        template) corresponding to simpler global mapping.
41      - adread_write.F: switch to new S/R (but leave old calls commented) and write
42        to globalFile when parameter globalFiles is set to True.
43      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
44    o pkg/autodiff:
45      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
46        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
47        missing, just add a STOP if array type do not match.
48    o pkg/exf:
49      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
50         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
51         and rename array obsSIce to exf_iceFraction.
52    o tutorial_deep_convection:
53      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
54        for now all in this exp. code dir.
55      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
56        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
57    o eesupp/src:
58      - added SINGLE_DISK_IO option because reading of parameter files on
59        very large number of processors did not work with existing set-up
60    
61    checkpoint64o (2013/09/25)
62    o pkg/atm_phys & atm_compon_interf:
63      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
64    o tools/build_options:
65      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
66        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
67        remove CPP setting (was identical to genmake2 default).
68    o pkg/gmredi & model/src: Some updating and work done on the residual model.
69      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
70      - fixed up the calculation of the eddy stress and how it is added to the
71        external forcing via taueddy_external_forcing.F
72      - at the moment, it is very experimental and only works with the variable eddy
73        diffusivity calculated in gmredi_k3d.F
74    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
75        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
76    o testreport (& tools/do_tst_2+2):
77      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
78    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
79      - remove CPP='cpp -traditional -P' (this is genmake2 default)
80      - add switch (for big setups) to use 'medium' memory-model (but leave it
81        commented out for now). Note: needed with FC 19 to compile big setups.
82    o pkg/atm_compon_interf:
83      - regroup per field origin (model & pkgs) the coupling storage routines
84         (which accumalate in time each coupling field)
85      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
86        update accordingly + simplify aim_do_physics.F
87    
88    checkpoint64n (2013/08/26)
89    o pkg/bbl:
90      - update formulation to reduce dispersion of tracer properties in bbl
91      - replaced horizontal and vertical transport parameters with velocities
92      - changes results for verification/global_with_exf.yearly
93    o verification/halfpipe_streamice:
94      - change to matrix construction; update both Fwd & AD output.
95    o verification/tutorial_tracer_adjsens:
96      - OpenAD test: switch to vector-invariant momentum since fluxform with
97        rStar causes problems with OpenAD; update output.
98    o tools:
99      - genmake2: define a common prefix for all temp-file names ; move them
100        to local /tmp disk (but would be easy to move them back);
101      - xmakedepend: apply the same switch for temp-files.
102    o pkg/offline:
103      - changes for use with rStar (NLFS): assume that we continue to provide
104        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
105        output files) and apply r* scaling at each time-step (function of the time
106        varying Eta field); use normal pickup files (needed for restart with NLFS).
107    o adjoint with OpenAD:
108      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
109        package openad.  This package has to be compiled for all runs with OpenAD
110        instead of specifying code_oad_all as a modification directory.
111      - link the fortran templates from tools/OAD_support to the build directory
112        for preprocessing to avoid conflicts between different setups compiled
113        simultaneously and simplify cleanup.
114    o pkg/exf:
115      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
116        main model or other pkgs are exchanged in EXF_MAPFIELDS).
117    o model/src:
118      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
119        (similar to do_fields_blocking_exchanges.F).
120    o tools/genmake2:
121      - remove TAF output src code just before calling staf (when not doing a fresh
122        built, will stop if things go wrong with staf).
123      - fix target "adobj" (left from TAF version-2 transition)
124    o pkg/diagnostics:
125      - add a parameter to track the status of pkg/diagnostics activation;
126        this replace/extend the use of logical param "settingDiags" (to check
127        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
128        New S/R to print error message and stop when pkgStatus is not right.
129      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
130    
131    checkpoint64m (2013/08/13)
132    o model/inc:
133      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
134        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
135    o pkg/kpp & aim_v23:
136      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
137    o pkg/seaice:
138      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
139        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
140      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
141    o eesupp/src:
142      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
143        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
144    o switch to TAF version-2:
145      - add flow directives to "freeze" naming convention for ad-routines that
146        are used in I/O routines of adjoint state and associated common blocks
147        that are used in adcommon.h (backward compatible with version-1)
148      - update all ad-optfiles (in tools/adjoint_options + few local to some
149        verification exp) to switch to latest TAF version (currently 2.5.5);
150        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
151        out except for diva).
152      - the major change with TAF version-2 is that both the differentiated
153        routines and the forward routines (new) are returned as part of the TAF
154        output source code. Update genmake2 accordingly.
155      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
156        with version-2 when compared to TLM or FWD gradient); other experiments
157        output show minor changes (machine truncation level); update the few AD &
158        TLM output with 12 matching digits only (some prior to version-2 switch).
159    
160    checkpoint64l (2013/08/05)
161    o model/src:
162      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
163      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
164        when using TAF but only if using OpenAD.
165    o pkg/mom_common+fluxform+vecinv:
166      - always set horiz. viscosity arrays to background value before calling
167        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
168        only when using variable horiz. viscosity (useVariableVisc=T);
169      - simplify mom_vecinv.F (only 1 block for momViscosity).
170    o pkg/mom_common: variable horiz. viscosity in NH code
171      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
172        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
173      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
174        useBiharmonicVisc & useVariableVisc.
175      - fix old bug (already in 1rst implementation of variable horizontal viscosity
176        in calc_gw.F, version 1.27, 2006/06/20):
177        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
178        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
179      - change background horiz viscosity in vertical momentum (gW) to always be
180        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
181        any type of variable viscosity, e.g., viscAh/4Grid)
182      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
183        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
184        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
185        default viscAh,viscA4 is zero).
186    o model/src:
187      - extend length of drC & recip_drC from Nr to Nr+1.
188    o Divided Adjoint (DIVA) with MPI:
189      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
190      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
191        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
192    
193    checkpoint64k (2013/07/23)
194    o tools/OAD_support:
195      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
196        and remove it from genmake2.
197    o tools/build_options:
198      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
199        MPI_HEADER_FILES list (let genmake2 find the missing headers)
200    o verification/halfpipe_streamice:
201      - change to driving stress formulation; update both Fwd & AD output.
202    o tools/genmake2 and Divided Adjoint with MPI:
203      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
204      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
205      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
206        Makefile, which is set by genmake2, and check which mpi-headers are needed.
207        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
208      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
209    o testreport:
210      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
211        perform additional runs (number of additional runs is "add_DIVA_runs" taken
212        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
213    o verification/lab_sea (AD test):
214      - change to test Divided Adjoint Run in this set-up (both standard AD test
215        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
216    o pkg atm_ & ocn_compon_interf:
217      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
218        staggerTimeStep implementation) and disable (retired) corresponding
219        parameter.
220    o pkg/offline:
221      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
222      - add S/R OFFLINE_CHECK to print offline parameter summary
223        and stop if loading a file that is not used;
224      - enable to calculate GMRedi tensor, KPP mixing and convective index
225        when the corresponding file(s) is/are not specified (but pkg is used).
226      - comment out resetting of monitorFreq (to endTime) since it still useful
227        for monitoring CFL numbers and checking offline fields.
228    o OpenAD:
229      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
230        smaller standard output) and generate new (smaller) output (on baudelaire
231        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
232    o model/src:
233      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
234        (where external_forcing_adjust was called) and change list of arguments;
235      - merge external_forcing_adjust.F into external_forcing_surf.F
236      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
237        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
238        previously in file "balance_relax.F", now removed); remove corresponding
239        arrays in FFIELDS.h.
240      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
241        a hack for getting back surfaceForcingS (loaded from file) when using
242        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
243      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
244        (was getting only 11 digits for AD-grad, due to different truncation
245         error in AD code).
246    
247    checkpoint64j (2013/07/04)
248    o pkg/offline:
249      - to enable the use of other features with pkg offline (e.g., obcs),
250        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
251      - comment out "allowFreezing" (now active) in 2 offline testing exp.
252    o pkg/exf ALLOW_RUNOFTEMP
253      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
254      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
255      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
256    o pkg/atm_phys:
257      - allows to add some damping on uVel,vVel (strength only function of k).
258    o verification, ad-tests:
259      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
260        global_ocean_ebm and offline_exf_seaice.thsice.
261    o verification/halfpipe_streamice:
262      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
263        flux input boundary conditions to be ignored; a fix for this bug changed
264        verification results for forward test.
265      - add adjoint test.
266    o pkg/ptracers:
267      - allow to restart without SOM pickup (resetting SOM to zero).
268    o pkg/gmredi:
269      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
270      - It uses mixing length theory and suppression by steering level effects to
271        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
272        to JPO, for more details).
273      - It also uses the diffusivity to calculate an eddy induced streamfunction
274        based on a PV closure (rather than a buoyancy closure as in GM).
275      - New files added to pkg/gmredi:
276        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
277          induced overturning streamfunction (called from gmredi_calc_tensor)
278        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
279          for use in gmredi_k3d
280        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
281          the eddy diffusivity
282    
283    checkpoint64i (2013/06/18)
284    o pkg/cheapaml:
285      - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
286        that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
287        with pkg/cheapaml.
288    o utils/python: add subpackage for cubed sphere function, first example is
289        simple cs.pcol to plot 2D fields on a map
290    o pkg/streamice:
291      - This is a new package in MITgcm, which solves dynamic equations for ice
292         sheets and ice streams
293      - At the moment it is independent of atmosphere/ocean dynamics, or any
294        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
295        ed that this will change)
296      - There is a new verification exercise that tests it, halfpipe_streamice,
297        evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
298        rectangular embayment
299      - halfpipe_streamice is forward-only for now, will have TAF test soon
300      - for questions, email dgoldber@mit.edu
301    o pkg/thsice:
302      - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
303        of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
304      - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
305         call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
306      - allow precip from pkg/cheapaml to make snow over seaice.
307    o pkg/cfc:
308      - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
309      - remove atmos CFC 2-D arrays from common bloc (now local variables)
310      - change some hard-coded constant to run time parameter for reading and
311        and interpolating atmospheric CFC ; keep same default as previously.
312      - more flexible reading of Atmos CFC (number of records no longer hard-coded)
313      - put arguments in standard order: myTime, myIter, myThid
314      - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
315        atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
316      - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
317      - new routine to print summary of CFC params and check for consistency.
318    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
319      similar to thsice_advdiff.
320      Note that for the B-grid case the routine parameters uc/vc are overwritten.
321    o pkg/cfc:
322      - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
323        update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
324      - fix interpolation of atmphspheric CFC between Sorthern and Northern
325        hemisphere value.
326    o pkg/seaice:
327      - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
328    o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
329                  so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
330      - requires an additional time level that is stored in the pickup
331      - you can start with AB2 from a pickup without this time level with
332        pickupStrictlyMatch = .false.
333    
334    checkpoint64h (2013/05/26)
335    o pkg/cheapaml:
336      - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
337        affect machine truncation (but exp cheapAML_box still pass with 13 digits).
338      - consistent treatment of uWind,vWind location: assume everywhere in
339        pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
340        (Note: was already the case for Tair,Qair advection);
341        add option (INCONSISTENT_WIND_LOCATION) to recover old results.
342      - compute diabatic forcing only in the interior (excluding overlap regions)
343      - fill in array "Qsw" (for short-wave heating);
344      - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
345        before any update (consistent with MITgcm state var diagnostics);
346      - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
347        non periodic ; + adjusted for uWind,vWind (C-grid).
348    o pkg/seaice:
349      - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
350        add explicitly pkg/exf in experiments that currently use pkg/seaice.
351      - allows to compile pkg/seaice without pkg/exf.
352    o tools/OAD_support:
353      - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
354        of array "ourStepOf" in function rvNextAction (revolve.F90).
355    o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
356      - change pkg name (to be used with other atmospheric physics pkg)
357        but by-pass CVS when making the new pkg so that we keep the CVS history.
358    o pkg/offline:
359      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
360        (previously called from pkg/dic_surfforcing_init.F)
361    o model/src:
362      - re-order sequence of calls within packages_init_variables.F, using
363        standard order, except for:
364         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
365         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
366    o new pkg: atm_phys
367      - add entry point and source code (previously in contrib
368          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
369        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
370      - re-order sequence of calls within packages_readparms.F,
371         packages_init_fixed.F and packages_write_pickup.F
372        (but skip packages_init_variables.F because of TAF issues).
373      - update contrib/*/atm_gray/ experiment.
374    o pkg/seaice (ITD code):
375      - simplify and fix the writing of pickup-files for ITD case
376    o pkg/seaice (ITD code):
377      - introduce floe size dependent lateral melt for ITD case;
378      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
379      - update seaice_itd experiment main output.
380    o pkg/thsice:
381      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
382        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
383        changed accordingly pkg/atm2d.
384    
385    checkpoint64g (2013/05/01)
386    o pkg/exf ALLOW_RUNOFTEMP
387      - if defined,  river and glacier runoff temperature can be read-in from
388        runoftempfile; runoftempfile needs to have same format as runofffile
389    o pkg/thsice (& pkg/bulk_force):
390      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
391        for energy content of Precip + RunOff & Evap (like with pkg/exf).
392      - change computation domain to always be the interior (without overlap).
393      - fix bug (wrong overlap) when using EXF and stressReduction > 0.
394    o verification/tutorial_global_oce_biogeo:
395      - add preliminary OpenAD setup (still has problems)
396    o pkg/seaice:
397      - turn some parameters for choosing the convergence criterion of
398        the inexact Newton method (JFNK) into runtime parameters for convenience
399      - clean up seaice_calc_viscosities.F: remove/retire two options for
400        SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
401        the results of lab_sea/input because a division has been replaced by
402        a multiplication with the reciprocal (sumNorm)
403      - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
404        convergence of solver (changes results, of course), and to test some
405        new features
406    o model/src:
407      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
408      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
409      - move forcing adjustment (balancing surface forcing) in specific S/R
410        where might also be applied exchanges (if needed) to forcing arrays.
411    o pkg/shelfice:
412      - allow to specify the Ice-Shelf mass per unit area (instead of
413        shelficeLoadAnomaly) and do the conversion from one to the other
414      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
415        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
416        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
417        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
418      - update isomip experiment forward output (get machine truncation error
419        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
420    o verification/offline_exf_seaice:
421      revise data.seaice in input.thermo and input_ad and update results accordingly
422        HO = 0.2, SEAICE_areaLossFormula = 2,
423        SEAICE_growMeltByConv = .TRUE.,
424        SEAICE_doOpenWaterMelt = .TRUE.,
425      Improve consistency with input.thsice and fix the spurious 500m ice corners
426    o verification/global_ocean.cs32x15:
427      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
428        in icedyn (thsice+seaice-dyn) test and update output.
429    o verification/offline_exf_seaice:
430      - adjust list of tested variables (with testreport) and update
431        standard test output with better slection of monitored fields.
432    o pkg/cd_code:
433      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
434        experiment lab_sea.hb87
435    o tools/genmake2:
436      - change default makedepend from the system default to tools/xmakedepend:
437        When no makedepend is specified, select tools/xmakedepend it the test pass,
438        otherwise select the system default (if exist and pass the test) or
439        try to build cyrus-makedepend ; stop if none of the 3 works.
440    o pkg/exf & pkg/thsice:
441      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
442        for energy content of Precip + RunOff & Evap. Assumes:
443       1) Rain has same temp as Air.
444       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
445       3) Run-Off comes at the temp of surface water (with same Cp)
446       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
447        put directly into Latent Heat flux & should use water-vapor heat capacity.
448       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
449        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
450    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
451        (compile when SEAICE_ALLOW_JFNK is defined)
452    o pkg/thsice:
453      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
454        implementation): move THSICE_AVE call after the advection (called directly
455        from thsice_do_advect.F).
456    o verification/global_ocean.90x40x15 and OpenAD:
457      New experiment for OpenAD is identical to the one in input_ad except that
458        multiDimAdvection=.FALSE.,
459      There is still an issue with this.
460    o pkg/thsice:
461      - account for ice velocity (ocean relative velocity) in turbulent heat flux
462        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
463        and offline_exf_seaice (main test).
464    
465    checkpoint64f (2013/03/31)
466    o verification/OpenAD:
467      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
468    o verification/isomip, pkg/shelfice and OpenAD:
469      - add OpenAD setup to this exp and make shelfice package work with OpenAD
470    o verification/tutorial_global_oce_biogeo:
471      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
472    o verification/offline_exf_seaice:
473      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
474    o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
475      - add OpenAD setup to this exp and make ptracers package work with OpenAD
476    o pkg/seaice/seaice_evp.F:
477       mask the asymmetric contribution of the ice-ocean stress (when
478       the turningAngle is non-zero) over open water to avoid stripes
479       in the EVP-solutions after many EVP-substeps. This does not change
480       the verification experiment (because turningAngle=0 in that experiment),
481       but will affect other EVP solutions with turningAngle.ne.0
482    o verification, AD & TLM output:
483      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
484        additions and multiplications which affect results at machine truncation
485        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
486        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
487        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
488        digits of matching.
489    o pkg/seaice:
490       modify lsr-algorithm so that it vectorizes AND converges by using a
491       "zebra" method: split vector loop into two with step size 2; this
492       solves a general convergence problem for the JFNK solver on a vector
493       computer. It has the potential to even improve convergence for
494       non-vector machines, but it does change the results so it is turned
495       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
496       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
497    
498    checkpoint64e (2013/03/05)
499    o pkg/ecco and several verification experiments:
500       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
501       from ecco package, and revert to unified routine in model/src/
502       Adjust verification experiments accordingly, especially gloal_oce_llc90
503       Should conclude long-standing work by Gael to reconsile the_main_loop with
504       ECCO and will enable OpenAD's revolve loop in ECCO setup.
505    o pkg/generic_advdiff:
506      - implement compressible flow method for multi-dim advection (similar to
507        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
508        TAF generates many recomputations) to use it; no yet coded with implicit
509        vertical advection.
510      - change experiment advect_cs (new output) and advect_xy (same output)
511        to test compressible flow multi-dim advection.
512    o pkg/generic_advdiff:
513      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
514        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
515    o pkg/seaice:
516      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
517        bug affects two verification experiments (lab_sea and lab_sea.hb87),
518        recover old (wrong) results by setting noSlipFac = 2. in
519        seaice_calc_strainrates.F;
520      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
521      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
522        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
523      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
524    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
525      - new subroutines seaice_lsr_tridiagu/v
526      - introduce loop bounds i/jmin/max to be able to use a restricted
527        additive Schwarz method, but not used for now.
528      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
529      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
530    o OpenAD support
531       Reorganize S/R call for overall time-stepping loop to facilitate
532       OpenAD revolve loop replacement
533       (new S/R main_do_loop.F)
534    o model/src:
535      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
536      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
537        ADAMS_BASHFORTH2.
538    o pkg/cheapaml:
539      - add new parameter (default=F, same as before) to disable full domain
540        (including land) periodicity in X & Y dir.
541      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
542        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
543        into single S/R CHEAPAML_TIMESTEP.
544    
545    checkpoint64d (2013/02/17)
546    o pkg/monitor (angular momentum):
547      - do not add Eta contribution to the total AM if using rigid-lid;
548      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
549      - horizontal discretisation: compute Zonal wind contribution separately for
550        each component (instead of from cell centered averaged) and use the 4
551        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
552      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
553        FreeSurf) if using vectorInvariant momentum.
554    o model/src (horizontal grid):
555      - move initialisation of all horizontal grid arrays to null value
556        from specific horizontal grid S/R to main S/R INI_GRID;
557      - add 2 new arrays to project model C-grid velocity on to zonal direction
558        (similar to AngleCosC & -AngleSinC but at U and V point location) and
559        compute them in S/R CALC_GRID_ANGLES.
560    o pkg/seaice: replace a hard coded parameter by a runtime parameter
561        SEAICE_JFNK_tolIter
562    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
563        preconditioner for JFNK (run LSR into the overlaps as far as possible,
564        i.e OLx/y-2, but overwrite the solution in the overlaps)
565      - extend loop range in seaice_calc_viscosity
566      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
567      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
568      - slightly modify loops in tridiagonal solver lsr-preconditioner
569      - by default remove the extra exchange in seaice_preconditioner with a
570        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
571      - modify offline_exf_seaice so that old results without RAS are reproduced
572        for output.dyn_jfnk.txt
573      in seaice_fgmres.F (unrelated to RAS)
574      - add a cpp-flag option for a re-ordered mapping (potentially more
575        efficient), but because this changes the results, turn it off by
576        default
577      - replace the save statement by local common blocks
578    o utils/matlab:
579      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
580      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
581        instead of local script "load_cs.m".
582    o pkg/seaice:
583      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
584        to the scalarProductMetric and the unrolling. By chance this does not
585        change the verification experiment, because of the particular domain
586        decomposition
587    o pkg/diagnostics:
588      - change default missing_value from UNSET_RL to -999.
589    o pkg/layers: improve vectorization of layers_fluxcalc.F
590      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
591        time spent in this routine by more than a factor of 3 on an NEC-SX8
592      - step 2: replace search algorithm by a bisection algorithm found in
593        Press et al. Numerical Recipes in Fortran. This algorithm can be
594        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
595        For now, use this algorithm only for TARGET_NEC_SX defined.
596      - moved the search algorithm into a separate subroutine, that is kept
597        within the same file for automatic inlining.
598      - modified catching potential errors
599    o pkg/ecco:
600      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
601    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
602      - modifications for ALLOW_GENTIM2D_CONTROL
603      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
604      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
605      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
606      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
607    o model/src:
608      - account for moist thermodynamics in (dry) potential temperature equation;
609        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
610        and cpl_aim+ocn.
611      - also switch to standard compiler (gfortran, was using ifort previously)
612        for fizhi-cs experiments reference output.
613    o pkg/ctrl:
614      - 1st step toward generic time-varying control variable (2D) via CPP option
615        ALLOW_GENTIM2D_CONTROL
616      - note new namelist ctrl_nml_genarr in data.ctrl
617    o verification/global_ocean.cs32x15:
618      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
619        thsice calling sequence and update "output.icedyn.txt" output file.
620    o pkg/ptracers:
621      - from Ryan A.: code to allow to restart a tracer at regular time interval
622        specifying a reset frequency and a reset-phase (for each tracers).
623    o pkg/thsice:
624      - implement new sequence of calls for thsice+seaice:
625          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
626          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
627      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
628        in CPP_OPTIONS.h) to recover old sequence;
629      - update diagnostics for Intermediate State thsice diagnostics: now filled
630        just before advection (instead of just after advection in old sequence);
631      - update output of experiment offline_exf_seaice (standard test);
632      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
633        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
634    o pkg/aim_v23:
635      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
636      - use standard pkg/mdsio routines to read & write CO2 pickup file;
637      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
638      - Implement new sequence of calls for seaice advection (with thsice and
639        seaice diffusion): do ice advection after ice-Thermodynamic (previously
640        was done before); change aim_do_physics.F (split the bi,bj loops block);
641      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
642    o pkg/thsice:
643      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
644        where just seaice diffusion is used without seaice-dynamics.
645    
646    checkpoint64c (2013/01/18)
647    o pkg/seaice:
648      - add a parameter JFNKres_tFac that can replace JFNKres_t
649        (= JFNKres_tFac*JFNKresidual before JFNK solver)
650      - add a line search option to the JFNK solver
651      - move update of u/vIce and computation of initial residual into a separate
652        routine (same file); makes the code a little easier to read (?)
653      - the line search requires computation of the residual and for some reason
654        I cannot do the update of u/vIce at the beginning of the Newton loop
655        without changing the results, so we move computation of the new residual
656        also to the end of the Newton loop, even without the line search
657    o pkg/mdsio:
658      - write missing value (corresponding to undefined array value) to meta files;
659        skip this if missing value is one (UNSET_RL would be a better value for the
660        case of undefined missing value but it's current the default missing-value);
661        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
662    o pkg/exf & thsice:
663      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
664        diagnostics) even when SHORTWAVE_HEATING is #undef;
665    o verification/cfc_example:
666      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
667        illustrate how to use it).
668    o verification/offline_exf_seaice:
669      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
670        files to only one time-record.
671      in input.thermo: narrow the 2 bands of low initial ice-concentration near
672        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
673        snapshot output; same mcPheePiston value as in thsice with
674        surf-current=0.2m/s.
675      in input.thsice: similar set-up as in input.thermo (channel with same seaice
676        initial conditions).
677    o verification/cfc_example:
678      - update file "data" with more standard choice (default rotationPeriod,
679        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
680        set deltaTFreeSurf to deltaTtracer) and update the output.
681    o pkg/layers:
682      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
683      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
684    o verification/offline_exf_seaice:
685      - set all {field}period to zero for constant-in-time forcing (not tested
686        anywhere else).
687    o verification/offline_exf_seaice:
688      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
689      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
690    o model/src:
691      - implement Finite-Volume method for (hydrostatic) presure gradient
692        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
693    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
694      - In order to be compatible with the default EVP code, this requires changing
695        the EVP code around a little; and because any small change immediately
696        breaks the lab_sea.hb87 verification experiment, the reference output is
697        updated two times (each time the remaining aggrement was only 2 digits):
698        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
699        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
700        The adjoint test lab_sea.evp also needed to be updated.
701      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
702        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
703        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
704        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
705        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
706        kept obscure, because I need to test it a little more.
707    o pkg/cheapaml:
708      - fix few incorrect type (_RL/_RS) in subroutine calls.
709    o pkg/seaice:
710      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
711        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
712    o model/src:
713      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
714        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
715        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
716    o pkg/cheapaml:
717      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
718        update output of experiment cheapAML_box.
719      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
720        and set them only in one place (cheapaml_readparms.F).
721      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
722      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
723        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
724    o model/src/the_main_loop.F:
725      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
726    o pkg/seaice:
727      - remove legacy branch code.
728      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
729    o verification/*/code*/SEAICE_OPTIONS.h:
730      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
731        SEAICE_CAP_HEFF).
732    o pkg/cheapaml:
733      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
734        to load new forcing fields.
735      - add missing "_d 0" where it's needed; + some editing (improve indentation).
736      - remove switch to "-r8" compiler option (no longer needed) in verification
737        cheapAML_box, keep same output (small trucation error differences).
738    o verification/offline_exf_seaice:
739      - add thermodynamics only test.
740    o verification/cheapAML_box:
741      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
742        keep same output (same 14 digits for cg2d).
743      - switch on "-r8" compiler option (some numerical values are missing
744        the "_d 0") and update output (only 6 digits for cg2d were preserved).
745    
746    checkpoint64b (2012/12/24)
747    o pkg/cheapaml:
748      - remove un-used variables (Qnet,EmPmR) from pickup files.
749      - store tendency of advected variables into cheapaml pickup file
750        and fix the AB-2 restart.
751    o verification/offline_exf_seaice and lab_sea adjoint:
752      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
753      - switch to 4 time steps in offline, consistent with lab_sea.
754      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
755      - update results after change of experiment seaice.
756    o pkg/seaice:
757      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
758        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
759        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
760        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
761    o model/src:
762      - add run-time parameter to select CG2D solver minimum-residual solution
763        (in case of a poor convergence).
764    o pkg/seaice/seaice_lsr.F
765      - move calculation of matrix coefficients into new
766        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
767        file; the main purpose of this change is to be able to reuse the code
768        in S/R SEAICE_PRECONDITIONER
769      - modify the computation of the residual so that the mass of sea-ice
770        is not used twice; this simplifies the calculations, but since
771        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
772        not tested in testreport---this does not affect the testreport results.
773    o verification/seaice_obcs:
774      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
775        verification/lab_sea/input.salt_plume; changes results/output.txt*
776    o model/src:
777      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
778    o pkg/seaice:
779      - improve description of parameters in seaice_fgmres.F and start
780        cleaning up the code
781      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
782        second argument
783      - add a metric based on grid cell area to SEAICE_SCALPROD; update
784        results of offline_exf_seaice.dyn_jfnk
785      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
786    o pkg/aim_v23:
787      - fix an other bug in dissipation heating (grid-cell area was missing).
788    o model/src + pkg/seaice:
789      - add global (multi-tile) linear solver for pair of tri-diagonal system
790        along X and Y lines, respectively for U and V component.
791        Note: 1) MPI and cube-exchange not yet coded.
792            2) probably not accurate for poorly conditioned / large size problem.
793      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
794        default: not compiled and not used.
795    o pkg/seaice:
796      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
797        introduce bi/bj loops and use global_sum_tile_rl instead of
798        mpi_allreduce in seaice_fgmres.F
799      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
800      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
801      - add a verification experiment for JFNK in offline_exf_seaice
802    o verification:
803      - change (for now, only fwd test) offline_exf_seaice experiment:
804        use a re-entrant channel with idealized coastline (trapezoidal shape)
805        at southern boundary to explore seaice dynamics and thermodynamics
806        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
807        secondary test (input.thsice) use thermodynamics only with SST relaxation.
808      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
809    o pkg/exf:
810      - disable "sstExtrapol" when Nr=1
811    o verification:
812      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
813        to test pkg/cheapaml.
814    o pkg/aim_v23 & pkg/shap_filt:
815      - fix dissipation heating (erroneous gravity multiplication factor).
816    o pkg/seaice:
817      - remove unused field pressPre from jfnk solver
818      - rename two subroutines in seaice_preconditioner.F
819    o eesupp/src:
820       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
821    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
822       - remove wrong parts of the rhs and the lhs (were in there
823         because I did not understand the concept of this preconditioner)
824       - add an exchange between u- and v-sweep. This increases communication
825         by a factor of two but improves the convergence of jfnk. Ideally,
826         one would like the u- and v-sweep to be independent. So far within
827         undocumented ifdefs
828       - reorganize the extra computations for printing the residuals
829    o tools/genmake2:
830      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
831        since it's not necessary (and was preventing to use MNC in some cases).
832    
833    checkpoint64a (2012/11/16)
834    o pkg/autodiff:
835      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
836        autodiff_readparms.F no longer depends on calling order (within
837        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
838        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
839        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
840    o pkg/obcs:
841      - adding tidal velocity forcing capability to obcs
842        for usage example, see verification/seaice_obcs/input.tides
843    o pkg/seaice:
844      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
845        SEAICE_LSRrelaxU/V
846      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
847    o pkg/aim_v23:
848      - implement heating from friction (bottom friction and stratospheric drag).
849    o pkg/shap_filt:
850      - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
851        dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
852    o model/src:
853      - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
854        time-constant addMass field from file (addMassFile);
855      - support for heating due to friction (and Kinetic Energy dissipation):
856        add option, run-time switch and 3-D field array + support code ; each pkg
857        or S/R can add heating contribution (if there is a sink of KE); the sum is
858        accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
859    o pkg/seaice:
860      - complete merge of ITD code into seaice_growth.F
861        from MITgcm_contrib/torge/itd/code/
862        no verification so far, but Torge Martin tested
863        "1-D test case and Beaufort set up;
864        deliver okay results after 1 model year."
865      - complete merge of SEAICE_SIZE.h into all relevant routines
866      - move computation of eta at Z-points into calc_viscosities
867        + introduce global field etaZ
868        + add different methods for computing etaZ, for now the old
869          method (simple averages of eta to Z-points) is hardwired
870        + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
871          seaice_preconditioner
872      - simplify computations for SEAICE_ZETA_SMOOTHREG
873      - seaice_preconditioner:
874        + replace one remaining press by pressLoc (mistake)
875        + adjust printing of residuals
876      - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
877        + add (SEAICE.h) and rename some counters (initiliased in
878          seaice_init_fixed.F)
879        + add _BEGIN/END_MASTER (myThid)  around print statements
880        + print total number of iterations and failures over SEAICE_monFreq
881          interval to STDOUT
882      - move control over output-messages by fgmres to seaice_jfnk to save
883        some operations
884      - move resetting initial guess for fgmres outside of seaice_fgmres_driver
885        in order to make restarts with sol .ne. zero (fgmres with restarts)
886        (seaice_jfnk.F, seaice_fgmres.F)
887      - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
888        a serious convergence problem when open boundaries are involved
889    o pkg/ggl90: fix computation of control volumes for the case of
890      ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
891      up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
892    o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
893    o pkg/autodiff
894      - Add inAdMode switch for SEAICEuseDYNAMICS:
895        SEAICEuseDYNAMICSinAdMode
896        (extend logic in ADAUTODIFF_INADMODE_SET)
897    o pkg/seaice
898      - Step 1 of merging ice-thickness distribution (ITD) code from
899        MITgcm_contrib/torge/itd/ (author: Torge Martin)
900        The code implements concept laid out in Thorndike et al. (1975);
901        code is enabled via CPP flag SEAICE_ITD
902        nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
903        code is not complete yet!!
904      - SEAICE_SIZE.h now included in almost all seaice routines
905    o verification (using seaice):
906      - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
907        global_ocean.cs32x15.seaice ; update results.
908      - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
909      - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
910        offline_exf_seaice (previously compiling B-grid).
911    o pkg/exf:
912      - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
913        to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
914        forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
915    o pkg/layers (adjust changes from Sept 19):
916      - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
917        this allows to remove "layers_maxNum" dimension from all layers arrays.
918    o pkg/layers (adjust changes from Sept 19):
919      - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
920      - snap-shot extended to all type of layers (not just the 1rst type);
921      - remove layers variables when corresponding CPP option is undef.
922    o pkg/layers:
923      - rename pkg/layers variable and add new output (layer exist & un-weighted
924        velocity in layer)
925    o pkg/seaice:
926      - simplify (?) ocean-drag coefficent computations by using
927        the same routine in all three solvers (saves some code lines)
928      - remove global fields DRAGA and DRAGS from C-grid code and
929        declare them locally in lsr.F (the only place where they are
930        still used)
931      - update AD output of lab_sea.evp (very sensitive anyway).
932    o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
933      (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
934      and SEAICEuseJFNK=.true. A few things to note:
935      - involves a FGMRES, that is parallel but very inefficient,
936        because of many scalar products (global sums) in the Gram-Schmidt
937        orthogonalization method. Needs to be replaced. Original code
938        from J.-F. Lemieux
939      - preconditioner for FGMRES is a stripped down version of LSOR
940      - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
941        preconditioner. For the preconditioner, the default is set to 10.
942      - Jacobian times vector is computed with finite differences
943      - marginally related to JFNK-solver: add a smooth regularization for
944        zeta with tanh that will improve convergence (Lemieux and Tremblay,
945        2009) for any implicit solver (not implemented for EVP because EVP
946        does not need this regularization in the first place). Define
947        SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
948    o eesupp/src:
949      - check in genmake2 that intrinsic S/R flush is available.
950      - add S/R to flush IO unit (if intrinsic S/R flush is available)
951      - flush standard & error msg unit before MPI termination
952      - if debugMode, flush IO unit after printing msg
953    o pkg/ctrl:
954      - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
955        to ctrl_set_unpack_xyz.
956    
957    checkpoint64 (2012/10/09)
958    o pkg/shelfice
959      - in mom_fluxform.F, mom_vecinv.F:
960        CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
961        Bug fix KappaRU -> KappaRV
962        does not change verification/isomip but may change other setups
963        (presumably constant KappaRU=KappaRV)
964      - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
965    o pkg/obcs:
966      - fixed some indexing bugs in obcs_seaice_sponge.F
967      - added obcs relaxation subroutines for HSALT and HSNOW
968      - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
969  o pkg/seaice:  o pkg/seaice:
970    - add "multicategory" parameterization for snow in analogy to ice,    - add "multicategory" parameterization for snow in analogy to ice,
971      default is off for now.      default is off for now.
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