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revision 1.1739 by jmc, Tue Sep 18 21:26:19 2012 UTC revision 1.1943 by jmc, Wed Nov 27 22:53:37 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 tools/build_options:
8      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
9    o coupling interface pkgs:
10        [compon_communic, atm_compon_interf & ocn_compon_interf]
11      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
12        to each S/R that needs it; remove un-used variables.
13      - change component tile registration (cpl_register.F in both compon_interf
14        and mitcomponent_tile_register.F) to pass the full list of tiles
15        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
16      - with pkg/exch2: adopt the same convention used for I/O to define mapping
17        towards coupler global array (unless W2_useE2ioLayOut=F):
18         a) can now use different tiling between atm & ocn comp.
19         b) no needs to modify the run-Off map when changing tiling (was needed
20            even if using the same tiling between atm & ocn).
21         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
22            full land tiles); not yet tested.
23      - check for valid mapping from comp. tile to coupler global array
24      - improve report of tile registration results to log file.
25    o pkg/exch2:
26      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
27        tile-registration (CPL_REGISTER);
28      - activate (un-comment) definition and setting of "W2_tileIndex" list to
29        store the local bi,bj indices of each tile;
30      - also print bi,bj in local report to log file;
31      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
32        Jun 2009 modif of pkg/exch2).
33    o testing on baudelaire:
34      - run 2 tests at a time: no significant slow down (since enough cpu) and
35        get the full set of test done earlier
36      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
37    o model/src/thermodynamics.F and routines called from it:
38      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
39        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
40        velocity (outp) by adding bolus velocity.
41      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
42        mass transport from velocity + lateral grid cell area
43      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
44      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
45     in thermodynamics.F
46      - remove k from thermodynamics.F and move it to temp_integrate.F
47        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
48        loop).
49      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
50        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
51        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
52        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
53      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
54        global_ocean.90x40x15, tutorial_global_oce_biogeo and
55        tutorial_tracer_adjsens (+ TLM output).
56    o tools/OAD_support and (verification/*/) code_oad:
57      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
58        module conversion ; remove unneeded CPP_EEOPTIONS.h.
59      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
60        version (closer to model/inc/CPP_OPTIONS.h).
61    o model/src:
62      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
63        retired list of parameters (routine FREEZE has been replace by surface
64        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
65    o pkg/gmredi:
66      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
67        velocity (same scheme but affects machine truncation) for GM_AdvForm.
68      - update output of FWD experiments: front_relax.bvp,
69        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
70    
71    checkpoint64q (2013/11/17)
72    o verification:
73      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
74        tutorial_global_oce_biogeo and global_ocean.90x40x15.
75      - generate new output (growth & melt) for seaice_itd experiment after
76        updating the input pickup_seaice files (previously wrong).
77    o pkg/cost:
78      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
79        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
80        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_TILE_RL
81          cannot be applied to var in common block).
82        o allows to get results independent of tile-per-proc setting (if using
83          slower GLOBAL_SUM_SEND_RECV option).
84      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
85        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
86        forward gradients: update output).
87      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
88        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
89    o pkg/mom_common:
90      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
91        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
92        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
93        ensure that all field value that are used are set.
94    o tutorial_deep_convection (smag3d):
95      - add missing scaling in mom_calc_smag_3d.F;
96      - set smag3D_coeff in input.smag3d such that results do not change.
97    o pkg/dic:
98      - change dic_cost.F to compute cost on each tile first and then apply
99        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
100        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
101      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
102    o eesupp/src & pkg/mdsio:
103      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
104        (from pkg/mdsio) since they are no longer used for tape IO.
105      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
106        (+ keep a copy in pkg/atm_ocn_coupler).
107    o verification/isomip:
108      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
109    o tools/build_options:
110      - optfile linux_amd64_ifort11, fast (no ieee) case:
111        to get a working restart for all experiments, add "-fp-model source"
112        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
113    
114    checkpoint64p (2013/10/20)
115    o pkg/autodiff:
116      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
117        criteria, return to simple (default) tape IO format.
118    o pkg/mdsio (+ eesupp/src):
119      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
120        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
121      - fix globalFile and singleCpuIO options using simpler global mapping.
122      - new pairs of scatter/gather vector S/R (one for each type, generated from
123        template) corresponding to simpler global mapping.
124      - adread_write.F: switch to new S/R (but leave old calls commented) and write
125        to globalFile when parameter globalFiles is set to True.
126      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
127    o pkg/autodiff:
128      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
129        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
130        missing, just add a STOP if array type do not match.
131    o pkg/exf:
132      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
133         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
134         and rename array obsSIce to exf_iceFraction.
135    o tutorial_deep_convection:
136      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
137        for now all in this exp. code dir.
138      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
139        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
140    o eesupp/src:
141      - added SINGLE_DISK_IO option because reading of parameter files on
142        very large number of processors did not work with existing set-up
143    
144    checkpoint64o (2013/09/25)
145    o pkg/atm_phys & atm_compon_interf:
146      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
147    o tools/build_options:
148      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
149        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
150        remove CPP setting (was identical to genmake2 default).
151    o pkg/gmredi & model/src: Some updating and work done on the residual model.
152      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
153      - fixed up the calculation of the eddy stress and how it is added to the
154        external forcing via taueddy_external_forcing.F
155      - at the moment, it is very experimental and only works with the variable eddy
156        diffusivity calculated in gmredi_k3d.F
157    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
158        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
159    o testreport (& tools/do_tst_2+2):
160      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
161    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
162      - remove CPP='cpp -traditional -P' (this is genmake2 default)
163      - add switch (for big setups) to use 'medium' memory-model (but leave it
164        commented out for now). Note: needed with FC 19 to compile big setups.
165    o pkg/atm_compon_interf:
166      - regroup per field origin (model & pkgs) the coupling storage routines
167         (which accumalate in time each coupling field)
168      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
169        update accordingly + simplify aim_do_physics.F
170    
171    checkpoint64n (2013/08/26)
172    o pkg/bbl:
173      - update formulation to reduce dispersion of tracer properties in bbl
174      - replaced horizontal and vertical transport parameters with velocities
175      - changes results for verification/global_with_exf.yearly
176    o verification/halfpipe_streamice:
177      - change to matrix construction; update both Fwd & AD output.
178    o verification/tutorial_tracer_adjsens:
179      - OpenAD test: switch to vector-invariant momentum since fluxform with
180        rStar causes problems with OpenAD; update output.
181    o tools:
182      - genmake2: define a common prefix for all temp-file names ; move them
183        to local /tmp disk (but would be easy to move them back);
184      - xmakedepend: apply the same switch for temp-files.
185    o pkg/offline:
186      - changes for use with rStar (NLFS): assume that we continue to provide
187        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
188        output files) and apply r* scaling at each time-step (function of the time
189        varying Eta field); use normal pickup files (needed for restart with NLFS).
190    o adjoint with OpenAD:
191      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
192        package openad.  This package has to be compiled for all runs with OpenAD
193        instead of specifying code_oad_all as a modification directory.
194      - link the fortran templates from tools/OAD_support to the build directory
195        for preprocessing to avoid conflicts between different setups compiled
196        simultaneously and simplify cleanup.
197    o pkg/exf:
198      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
199        main model or other pkgs are exchanged in EXF_MAPFIELDS).
200    o model/src:
201      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
202        (similar to do_fields_blocking_exchanges.F).
203    o tools/genmake2:
204      - remove TAF output src code just before calling staf (when not doing a fresh
205        built, will stop if things go wrong with staf).
206      - fix target "adobj" (left from TAF version-2 transition)
207    o pkg/diagnostics:
208      - add a parameter to track the status of pkg/diagnostics activation;
209        this replace/extend the use of logical param "settingDiags" (to check
210        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
211        New S/R to print error message and stop when pkgStatus is not right.
212      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
213    
214    checkpoint64m (2013/08/13)
215    o model/inc:
216      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
217        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
218    o pkg/kpp & aim_v23:
219      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
220    o pkg/seaice:
221      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
222        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
223      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
224    o eesupp/src:
225      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
226        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
227    o switch to TAF version-2:
228      - add flow directives to "freeze" naming convention for ad-routines that
229        are used in I/O routines of adjoint state and associated common blocks
230        that are used in adcommon.h (backward compatible with version-1)
231      - update all ad-optfiles (in tools/adjoint_options + few local to some
232        verification exp) to switch to latest TAF version (currently 2.5.5);
233        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
234        out except for diva).
235      - the major change with TAF version-2 is that both the differentiated
236        routines and the forward routines (new) are returned as part of the TAF
237        output source code. Update genmake2 accordingly.
238      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
239        with version-2 when compared to TLM or FWD gradient); other experiments
240        output show minor changes (machine truncation level); update the few AD &
241        TLM output with 12 matching digits only (some prior to version-2 switch).
242    
243    checkpoint64l (2013/08/05)
244    o model/src:
245      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
246      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
247        when using TAF but only if using OpenAD.
248    o pkg/mom_common+fluxform+vecinv:
249      - always set horiz. viscosity arrays to background value before calling
250        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
251        only when using variable horiz. viscosity (useVariableVisc=T);
252      - simplify mom_vecinv.F (only 1 block for momViscosity).
253    o pkg/mom_common: variable horiz. viscosity in NH code
254      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
255        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
256      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
257        useBiharmonicVisc & useVariableVisc.
258      - fix old bug (already in 1rst implementation of variable horizontal viscosity
259        in calc_gw.F, version 1.27, 2006/06/20):
260        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
261        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
262      - change background horiz viscosity in vertical momentum (gW) to always be
263        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
264        any type of variable viscosity, e.g., viscAh/4Grid)
265      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
266        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
267        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
268        default viscAh,viscA4 is zero).
269    o model/src:
270      - extend length of drC & recip_drC from Nr to Nr+1.
271    o Divided Adjoint (DIVA) with MPI:
272      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
273      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
274        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
275    
276    checkpoint64k (2013/07/23)
277    o tools/OAD_support:
278      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
279        and remove it from genmake2.
280    o tools/build_options:
281      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
282        MPI_HEADER_FILES list (let genmake2 find the missing headers)
283    o verification/halfpipe_streamice:
284      - change to driving stress formulation; update both Fwd & AD output.
285    o tools/genmake2 and Divided Adjoint with MPI:
286      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
287      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
288      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
289        Makefile, which is set by genmake2, and check which mpi-headers are needed.
290        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
291      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
292    o testreport:
293      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
294        perform additional runs (number of additional runs is "add_DIVA_runs" taken
295        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
296    o verification/lab_sea (AD test):
297      - change to test Divided Adjoint Run in this set-up (both standard AD test
298        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
299    o pkg atm_ & ocn_compon_interf:
300      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
301        staggerTimeStep implementation) and disable (retired) corresponding
302        parameter.
303    o pkg/offline:
304      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
305      - add S/R OFFLINE_CHECK to print offline parameter summary
306        and stop if loading a file that is not used;
307      - enable to calculate GMRedi tensor, KPP mixing and convective index
308        when the corresponding file(s) is/are not specified (but pkg is used).
309      - comment out resetting of monitorFreq (to endTime) since it still useful
310        for monitoring CFL numbers and checking offline fields.
311    o OpenAD:
312      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
313        smaller standard output) and generate new (smaller) output (on baudelaire
314        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
315    o model/src:
316      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
317        (where external_forcing_adjust was called) and change list of arguments;
318      - merge external_forcing_adjust.F into external_forcing_surf.F
319      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
320        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
321        previously in file "balance_relax.F", now removed); remove corresponding
322        arrays in FFIELDS.h.
323      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
324        a hack for getting back surfaceForcingS (loaded from file) when using
325        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
326      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
327        (was getting only 11 digits for AD-grad, due to different truncation
328         error in AD code).
329    
330    checkpoint64j (2013/07/04)
331    o pkg/offline:
332      - to enable the use of other features with pkg offline (e.g., obcs),
333        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
334      - comment out "allowFreezing" (now active) in 2 offline testing exp.
335    o pkg/exf ALLOW_RUNOFTEMP
336      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
337      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
338      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
339    o pkg/atm_phys:
340      - allows to add some damping on uVel,vVel (strength only function of k).
341    o verification, ad-tests:
342      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
343        global_ocean_ebm and offline_exf_seaice.thsice.
344    o verification/halfpipe_streamice:
345      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
346        flux input boundary conditions to be ignored; a fix for this bug changed
347        verification results for forward test.
348      - add adjoint test.
349    o pkg/ptracers:
350      - allow to restart without SOM pickup (resetting SOM to zero).
351    o pkg/gmredi:
352      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
353      - It uses mixing length theory and suppression by steering level effects to
354        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
355        to JPO, for more details).
356      - It also uses the diffusivity to calculate an eddy induced streamfunction
357        based on a PV closure (rather than a buoyancy closure as in GM).
358      - New files added to pkg/gmredi:
359        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
360          induced overturning streamfunction (called from gmredi_calc_tensor)
361        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
362          for use in gmredi_k3d
363        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
364          the eddy diffusivity
365    
366    checkpoint64i (2013/06/18)
367    o pkg/cheapaml:
368      - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
369        that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
370        with pkg/cheapaml.
371    o utils/python: add subpackage for cubed sphere function, first example is
372        simple cs.pcol to plot 2D fields on a map
373    o pkg/streamice:
374      - This is a new package in MITgcm, which solves dynamic equations for ice
375         sheets and ice streams
376      - At the moment it is independent of atmosphere/ocean dynamics, or any
377        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
378        ed that this will change)
379      - There is a new verification exercise that tests it, halfpipe_streamice,
380        evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
381        rectangular embayment
382      - halfpipe_streamice is forward-only for now, will have TAF test soon
383      - for questions, email dgoldber@mit.edu
384    o pkg/thsice:
385      - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
386        of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
387      - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
388         call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
389      - allow precip from pkg/cheapaml to make snow over seaice.
390    o pkg/cfc:
391      - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
392      - remove atmos CFC 2-D arrays from common bloc (now local variables)
393      - change some hard-coded constant to run time parameter for reading and
394        and interpolating atmospheric CFC ; keep same default as previously.
395      - more flexible reading of Atmos CFC (number of records no longer hard-coded)
396      - put arguments in standard order: myTime, myIter, myThid
397      - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
398        atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
399      - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
400      - new routine to print summary of CFC params and check for consistency.
401    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
402      similar to thsice_advdiff.
403      Note that for the B-grid case the routine parameters uc/vc are overwritten.
404    o pkg/cfc:
405      - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
406        update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
407      - fix interpolation of atmphspheric CFC between Sorthern and Northern
408        hemisphere value.
409    o pkg/seaice:
410      - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
411    o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
412                  so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
413      - requires an additional time level that is stored in the pickup
414      - you can start with AB2 from a pickup without this time level with
415        pickupStrictlyMatch = .false.
416    
417    checkpoint64h (2013/05/26)
418    o pkg/cheapaml:
419      - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
420        affect machine truncation (but exp cheapAML_box still pass with 13 digits).
421      - consistent treatment of uWind,vWind location: assume everywhere in
422        pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
423        (Note: was already the case for Tair,Qair advection);
424        add option (INCONSISTENT_WIND_LOCATION) to recover old results.
425      - compute diabatic forcing only in the interior (excluding overlap regions)
426      - fill in array "Qsw" (for short-wave heating);
427      - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
428        before any update (consistent with MITgcm state var diagnostics);
429      - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
430        non periodic ; + adjusted for uWind,vWind (C-grid).
431    o pkg/seaice:
432      - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
433        add explicitly pkg/exf in experiments that currently use pkg/seaice.
434      - allows to compile pkg/seaice without pkg/exf.
435    o tools/OAD_support:
436      - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
437        of array "ourStepOf" in function rvNextAction (revolve.F90).
438    o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
439      - change pkg name (to be used with other atmospheric physics pkg)
440        but by-pass CVS when making the new pkg so that we keep the CVS history.
441    o pkg/offline:
442      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
443        (previously called from pkg/dic_surfforcing_init.F)
444    o model/src:
445      - re-order sequence of calls within packages_init_variables.F, using
446        standard order, except for:
447         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
448         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
449    o new pkg: atm_phys
450      - add entry point and source code (previously in contrib
451          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
452        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
453      - re-order sequence of calls within packages_readparms.F,
454         packages_init_fixed.F and packages_write_pickup.F
455        (but skip packages_init_variables.F because of TAF issues).
456      - update contrib/*/atm_gray/ experiment.
457    o pkg/seaice (ITD code):
458      - simplify and fix the writing of pickup-files for ITD case
459    o pkg/seaice (ITD code):
460      - introduce floe size dependent lateral melt for ITD case;
461      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
462      - update seaice_itd experiment main output.
463    o pkg/thsice:
464      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
465        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
466        changed accordingly pkg/atm2d.
467    
468    checkpoint64g (2013/05/01)
469    o pkg/exf ALLOW_RUNOFTEMP
470      - if defined,  river and glacier runoff temperature can be read-in from
471        runoftempfile; runoftempfile needs to have same format as runofffile
472    o pkg/thsice (& pkg/bulk_force):
473      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
474        for energy content of Precip + RunOff & Evap (like with pkg/exf).
475      - change computation domain to always be the interior (without overlap).
476      - fix bug (wrong overlap) when using EXF and stressReduction > 0.
477    o verification/tutorial_global_oce_biogeo:
478      - add preliminary OpenAD setup (still has problems)
479    o pkg/seaice:
480      - turn some parameters for choosing the convergence criterion of
481        the inexact Newton method (JFNK) into runtime parameters for convenience
482      - clean up seaice_calc_viscosities.F: remove/retire two options for
483        SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
484        the results of lab_sea/input because a division has been replaced by
485        a multiplication with the reciprocal (sumNorm)
486      - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
487        convergence of solver (changes results, of course), and to test some
488        new features
489    o model/src:
490      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
491      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
492      - move forcing adjustment (balancing surface forcing) in specific S/R
493        where might also be applied exchanges (if needed) to forcing arrays.
494    o pkg/shelfice:
495      - allow to specify the Ice-Shelf mass per unit area (instead of
496        shelficeLoadAnomaly) and do the conversion from one to the other
497      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
498        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
499        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
500        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
501      - update isomip experiment forward output (get machine truncation error
502        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
503    o verification/offline_exf_seaice:
504      revise data.seaice in input.thermo and input_ad and update results accordingly
505        HO = 0.2, SEAICE_areaLossFormula = 2,
506        SEAICE_growMeltByConv = .TRUE.,
507        SEAICE_doOpenWaterMelt = .TRUE.,
508      Improve consistency with input.thsice and fix the spurious 500m ice corners
509    o verification/global_ocean.cs32x15:
510      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
511        in icedyn (thsice+seaice-dyn) test and update output.
512    o verification/offline_exf_seaice:
513      - adjust list of tested variables (with testreport) and update
514        standard test output with better slection of monitored fields.
515    o pkg/cd_code:
516      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
517        experiment lab_sea.hb87
518    o tools/genmake2:
519      - change default makedepend from the system default to tools/xmakedepend:
520        When no makedepend is specified, select tools/xmakedepend it the test pass,
521        otherwise select the system default (if exist and pass the test) or
522        try to build cyrus-makedepend ; stop if none of the 3 works.
523    o pkg/exf & pkg/thsice:
524      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
525        for energy content of Precip + RunOff & Evap. Assumes:
526       1) Rain has same temp as Air.
527       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
528       3) Run-Off comes at the temp of surface water (with same Cp)
529       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
530        put directly into Latent Heat flux & should use water-vapor heat capacity.
531       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
532        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
533    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
534        (compile when SEAICE_ALLOW_JFNK is defined)
535    o pkg/thsice:
536      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
537        implementation): move THSICE_AVE call after the advection (called directly
538        from thsice_do_advect.F).
539    o verification/global_ocean.90x40x15 and OpenAD:
540      New experiment for OpenAD is identical to the one in input_ad except that
541        multiDimAdvection=.FALSE.,
542      There is still an issue with this.
543    o pkg/thsice:
544      - account for ice velocity (ocean relative velocity) in turbulent heat flux
545        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
546        and offline_exf_seaice (main test).
547    
548    checkpoint64f (2013/03/31)
549    o verification/OpenAD:
550      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
551    o verification/isomip, pkg/shelfice and OpenAD:
552      - add OpenAD setup to this exp and make shelfice package work with OpenAD
553    o verification/tutorial_global_oce_biogeo:
554      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
555    o verification/offline_exf_seaice:
556      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
557    o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
558      - add OpenAD setup to this exp and make ptracers package work with OpenAD
559    o pkg/seaice/seaice_evp.F:
560       mask the asymmetric contribution of the ice-ocean stress (when
561       the turningAngle is non-zero) over open water to avoid stripes
562       in the EVP-solutions after many EVP-substeps. This does not change
563       the verification experiment (because turningAngle=0 in that experiment),
564       but will affect other EVP solutions with turningAngle.ne.0
565    o verification, AD & TLM output:
566      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
567        additions and multiplications which affect results at machine truncation
568        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
569        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
570        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
571        digits of matching.
572    o pkg/seaice:
573       modify lsr-algorithm so that it vectorizes AND converges by using a
574       "zebra" method: split vector loop into two with step size 2; this
575       solves a general convergence problem for the JFNK solver on a vector
576       computer. It has the potential to even improve convergence for
577       non-vector machines, but it does change the results so it is turned
578       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
579       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
580    
581    checkpoint64e (2013/03/05)
582    o pkg/ecco and several verification experiments:
583       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
584       from ecco package, and revert to unified routine in model/src/
585       Adjust verification experiments accordingly, especially gloal_oce_llc90
586       Should conclude long-standing work by Gael to reconsile the_main_loop with
587       ECCO and will enable OpenAD's revolve loop in ECCO setup.
588    o pkg/generic_advdiff:
589      - implement compressible flow method for multi-dim advection (similar to
590        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
591        TAF generates many recomputations) to use it; no yet coded with implicit
592        vertical advection.
593      - change experiment advect_cs (new output) and advect_xy (same output)
594        to test compressible flow multi-dim advection.
595    o pkg/generic_advdiff:
596      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
597        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
598    o pkg/seaice:
599      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
600        bug affects two verification experiments (lab_sea and lab_sea.hb87),
601        recover old (wrong) results by setting noSlipFac = 2. in
602        seaice_calc_strainrates.F;
603      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
604      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
605        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
606      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
607    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
608      - new subroutines seaice_lsr_tridiagu/v
609      - introduce loop bounds i/jmin/max to be able to use a restricted
610        additive Schwarz method, but not used for now.
611      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
612      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
613    o OpenAD support
614       Reorganize S/R call for overall time-stepping loop to facilitate
615       OpenAD revolve loop replacement
616       (new S/R main_do_loop.F)
617    o model/src:
618      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
619      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
620        ADAMS_BASHFORTH2.
621    o pkg/cheapaml:
622      - add new parameter (default=F, same as before) to disable full domain
623        (including land) periodicity in X & Y dir.
624      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
625        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
626        into single S/R CHEAPAML_TIMESTEP.
627    
628    checkpoint64d (2013/02/17)
629    o pkg/monitor (angular momentum):
630      - do not add Eta contribution to the total AM if using rigid-lid;
631      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
632      - horizontal discretisation: compute Zonal wind contribution separately for
633        each component (instead of from cell centered averaged) and use the 4
634        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
635      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
636        FreeSurf) if using vectorInvariant momentum.
637    o model/src (horizontal grid):
638      - move initialisation of all horizontal grid arrays to null value
639        from specific horizontal grid S/R to main S/R INI_GRID;
640      - add 2 new arrays to project model C-grid velocity on to zonal direction
641        (similar to AngleCosC & -AngleSinC but at U and V point location) and
642        compute them in S/R CALC_GRID_ANGLES.
643    o pkg/seaice: replace a hard coded parameter by a runtime parameter
644        SEAICE_JFNK_tolIter
645    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
646        preconditioner for JFNK (run LSR into the overlaps as far as possible,
647        i.e OLx/y-2, but overwrite the solution in the overlaps)
648      - extend loop range in seaice_calc_viscosity
649      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
650      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
651      - slightly modify loops in tridiagonal solver lsr-preconditioner
652      - by default remove the extra exchange in seaice_preconditioner with a
653        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
654      - modify offline_exf_seaice so that old results without RAS are reproduced
655        for output.dyn_jfnk.txt
656      in seaice_fgmres.F (unrelated to RAS)
657      - add a cpp-flag option for a re-ordered mapping (potentially more
658        efficient), but because this changes the results, turn it off by
659        default
660      - replace the save statement by local common blocks
661    o utils/matlab:
662      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
663      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
664        instead of local script "load_cs.m".
665    o pkg/seaice:
666      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
667        to the scalarProductMetric and the unrolling. By chance this does not
668        change the verification experiment, because of the particular domain
669        decomposition
670    o pkg/diagnostics:
671      - change default missing_value from UNSET_RL to -999.
672    o pkg/layers: improve vectorization of layers_fluxcalc.F
673      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
674        time spent in this routine by more than a factor of 3 on an NEC-SX8
675      - step 2: replace search algorithm by a bisection algorithm found in
676        Press et al. Numerical Recipes in Fortran. This algorithm can be
677        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
678        For now, use this algorithm only for TARGET_NEC_SX defined.
679      - moved the search algorithm into a separate subroutine, that is kept
680        within the same file for automatic inlining.
681      - modified catching potential errors
682    o pkg/ecco:
683      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
684    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
685      - modifications for ALLOW_GENTIM2D_CONTROL
686      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
687      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
688      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
689      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
690    o model/src:
691      - account for moist thermodynamics in (dry) potential temperature equation;
692        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
693        and cpl_aim+ocn.
694      - also switch to standard compiler (gfortran, was using ifort previously)
695        for fizhi-cs experiments reference output.
696    o pkg/ctrl:
697      - 1st step toward generic time-varying control variable (2D) via CPP option
698        ALLOW_GENTIM2D_CONTROL
699      - note new namelist ctrl_nml_genarr in data.ctrl
700    o verification/global_ocean.cs32x15:
701      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
702        thsice calling sequence and update "output.icedyn.txt" output file.
703    o pkg/ptracers:
704      - from Ryan A.: code to allow to restart a tracer at regular time interval
705        specifying a reset frequency and a reset-phase (for each tracers).
706    o pkg/thsice:
707      - implement new sequence of calls for thsice+seaice:
708          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
709          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
710      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
711        in CPP_OPTIONS.h) to recover old sequence;
712      - update diagnostics for Intermediate State thsice diagnostics: now filled
713        just before advection (instead of just after advection in old sequence);
714      - update output of experiment offline_exf_seaice (standard test);
715      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
716        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
717    o pkg/aim_v23:
718      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
719      - use standard pkg/mdsio routines to read & write CO2 pickup file;
720      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
721      - Implement new sequence of calls for seaice advection (with thsice and
722        seaice diffusion): do ice advection after ice-Thermodynamic (previously
723        was done before); change aim_do_physics.F (split the bi,bj loops block);
724      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
725    o pkg/thsice:
726      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
727        where just seaice diffusion is used without seaice-dynamics.
728    
729    checkpoint64c (2013/01/18)
730    o pkg/seaice:
731      - add a parameter JFNKres_tFac that can replace JFNKres_t
732        (= JFNKres_tFac*JFNKresidual before JFNK solver)
733      - add a line search option to the JFNK solver
734      - move update of u/vIce and computation of initial residual into a separate
735        routine (same file); makes the code a little easier to read (?)
736      - the line search requires computation of the residual and for some reason
737        I cannot do the update of u/vIce at the beginning of the Newton loop
738        without changing the results, so we move computation of the new residual
739        also to the end of the Newton loop, even without the line search
740    o pkg/mdsio:
741      - write missing value (corresponding to undefined array value) to meta files;
742        skip this if missing value is one (UNSET_RL would be a better value for the
743        case of undefined missing value but it's current the default missing-value);
744        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
745    o pkg/exf & thsice:
746      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
747        diagnostics) even when SHORTWAVE_HEATING is #undef;
748    o verification/cfc_example:
749      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
750        illustrate how to use it).
751    o verification/offline_exf_seaice:
752      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
753        files to only one time-record.
754      in input.thermo: narrow the 2 bands of low initial ice-concentration near
755        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
756        snapshot output; same mcPheePiston value as in thsice with
757        surf-current=0.2m/s.
758      in input.thsice: similar set-up as in input.thermo (channel with same seaice
759        initial conditions).
760    o verification/cfc_example:
761      - update file "data" with more standard choice (default rotationPeriod,
762        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
763        set deltaTFreeSurf to deltaTtracer) and update the output.
764    o pkg/layers:
765      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
766      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
767    o verification/offline_exf_seaice:
768      - set all {field}period to zero for constant-in-time forcing (not tested
769        anywhere else).
770    o verification/offline_exf_seaice:
771      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
772      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
773    o model/src:
774      - implement Finite-Volume method for (hydrostatic) presure gradient
775        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
776    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
777      - In order to be compatible with the default EVP code, this requires changing
778        the EVP code around a little; and because any small change immediately
779        breaks the lab_sea.hb87 verification experiment, the reference output is
780        updated two times (each time the remaining aggrement was only 2 digits):
781        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
782        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
783        The adjoint test lab_sea.evp also needed to be updated.
784      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
785        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
786        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
787        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
788        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
789        kept obscure, because I need to test it a little more.
790    o pkg/cheapaml:
791      - fix few incorrect type (_RL/_RS) in subroutine calls.
792    o pkg/seaice:
793      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
794        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
795    o model/src:
796      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
797        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
798        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
799    o pkg/cheapaml:
800      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
801        update output of experiment cheapAML_box.
802      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
803        and set them only in one place (cheapaml_readparms.F).
804      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
805      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
806        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
807    o model/src/the_main_loop.F:
808      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
809    o pkg/seaice:
810      - remove legacy branch code.
811      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
812    o verification/*/code*/SEAICE_OPTIONS.h:
813      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
814        SEAICE_CAP_HEFF).
815    o pkg/cheapaml:
816      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
817        to load new forcing fields.
818      - add missing "_d 0" where it's needed; + some editing (improve indentation).
819      - remove switch to "-r8" compiler option (no longer needed) in verification
820        cheapAML_box, keep same output (small trucation error differences).
821    o verification/offline_exf_seaice:
822      - add thermodynamics only test.
823    o verification/cheapAML_box:
824      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
825        keep same output (same 14 digits for cg2d).
826      - switch on "-r8" compiler option (some numerical values are missing
827        the "_d 0") and update output (only 6 digits for cg2d were preserved).
828    
829    checkpoint64b (2012/12/24)
830    o pkg/cheapaml:
831      - remove un-used variables (Qnet,EmPmR) from pickup files.
832      - store tendency of advected variables into cheapaml pickup file
833        and fix the AB-2 restart.
834    o verification/offline_exf_seaice and lab_sea adjoint:
835      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
836      - switch to 4 time steps in offline, consistent with lab_sea.
837      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
838      - update results after change of experiment seaice.
839    o pkg/seaice:
840      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
841        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
842        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
843        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
844    o model/src:
845      - add run-time parameter to select CG2D solver minimum-residual solution
846        (in case of a poor convergence).
847    o pkg/seaice/seaice_lsr.F
848      - move calculation of matrix coefficients into new
849        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
850        file; the main purpose of this change is to be able to reuse the code
851        in S/R SEAICE_PRECONDITIONER
852      - modify the computation of the residual so that the mass of sea-ice
853        is not used twice; this simplifies the calculations, but since
854        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
855        not tested in testreport---this does not affect the testreport results.
856    o verification/seaice_obcs:
857      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
858        verification/lab_sea/input.salt_plume; changes results/output.txt*
859    o model/src:
860      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
861    o pkg/seaice:
862      - improve description of parameters in seaice_fgmres.F and start
863        cleaning up the code
864      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
865        second argument
866      - add a metric based on grid cell area to SEAICE_SCALPROD; update
867        results of offline_exf_seaice.dyn_jfnk
868      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
869    o pkg/aim_v23:
870      - fix an other bug in dissipation heating (grid-cell area was missing).
871    o model/src + pkg/seaice:
872      - add global (multi-tile) linear solver for pair of tri-diagonal system
873        along X and Y lines, respectively for U and V component.
874        Note: 1) MPI and cube-exchange not yet coded.
875            2) probably not accurate for poorly conditioned / large size problem.
876      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
877        default: not compiled and not used.
878    o pkg/seaice:
879      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
880        introduce bi/bj loops and use global_sum_tile_rl instead of
881        mpi_allreduce in seaice_fgmres.F
882      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
883      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
884      - add a verification experiment for JFNK in offline_exf_seaice
885    o verification:
886      - change (for now, only fwd test) offline_exf_seaice experiment:
887        use a re-entrant channel with idealized coastline (trapezoidal shape)
888        at southern boundary to explore seaice dynamics and thermodynamics
889        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
890        secondary test (input.thsice) use thermodynamics only with SST relaxation.
891      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
892    o pkg/exf:
893      - disable "sstExtrapol" when Nr=1
894    o verification:
895      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
896        to test pkg/cheapaml.
897    o pkg/aim_v23 & pkg/shap_filt:
898      - fix dissipation heating (erroneous gravity multiplication factor).
899    o pkg/seaice:
900      - remove unused field pressPre from jfnk solver
901      - rename two subroutines in seaice_preconditioner.F
902    o eesupp/src:
903       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
904    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
905       - remove wrong parts of the rhs and the lhs (were in there
906         because I did not understand the concept of this preconditioner)
907       - add an exchange between u- and v-sweep. This increases communication
908         by a factor of two but improves the convergence of jfnk. Ideally,
909         one would like the u- and v-sweep to be independent. So far within
910         undocumented ifdefs
911       - reorganize the extra computations for printing the residuals
912    o tools/genmake2:
913      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
914        since it's not necessary (and was preventing to use MNC in some cases).
915    
916    checkpoint64a (2012/11/16)
917    o pkg/autodiff:
918      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
919        autodiff_readparms.F no longer depends on calling order (within
920        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
921        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
922        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
923    o pkg/obcs:
924      - adding tidal velocity forcing capability to obcs
925        for usage example, see verification/seaice_obcs/input.tides
926    o pkg/seaice:
927      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
928        SEAICE_LSRrelaxU/V
929      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
930    o pkg/aim_v23:
931      - implement heating from friction (bottom friction and stratospheric drag).
932    o pkg/shap_filt:
933      - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
934        dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
935    o model/src:
936      - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
937        time-constant addMass field from file (addMassFile);
938      - support for heating due to friction (and Kinetic Energy dissipation):
939        add option, run-time switch and 3-D field array + support code ; each pkg
940        or S/R can add heating contribution (if there is a sink of KE); the sum is
941        accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
942    o pkg/seaice:
943      - complete merge of ITD code into seaice_growth.F
944        from MITgcm_contrib/torge/itd/code/
945        no verification so far, but Torge Martin tested
946        "1-D test case and Beaufort set up;
947        deliver okay results after 1 model year."
948      - complete merge of SEAICE_SIZE.h into all relevant routines
949      - move computation of eta at Z-points into calc_viscosities
950        + introduce global field etaZ
951        + add different methods for computing etaZ, for now the old
952          method (simple averages of eta to Z-points) is hardwired
953        + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
954          seaice_preconditioner
955      - simplify computations for SEAICE_ZETA_SMOOTHREG
956      - seaice_preconditioner:
957        + replace one remaining press by pressLoc (mistake)
958        + adjust printing of residuals
959      - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
960        + add (SEAICE.h) and rename some counters (initiliased in
961          seaice_init_fixed.F)
962        + add _BEGIN/END_MASTER (myThid)  around print statements
963        + print total number of iterations and failures over SEAICE_monFreq
964          interval to STDOUT
965      - move control over output-messages by fgmres to seaice_jfnk to save
966        some operations
967      - move resetting initial guess for fgmres outside of seaice_fgmres_driver
968        in order to make restarts with sol .ne. zero (fgmres with restarts)
969        (seaice_jfnk.F, seaice_fgmres.F)
970      - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
971        a serious convergence problem when open boundaries are involved
972    o pkg/ggl90: fix computation of control volumes for the case of
973      ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
974      up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
975    o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
976    o pkg/autodiff
977      - Add inAdMode switch for SEAICEuseDYNAMICS:
978        SEAICEuseDYNAMICSinAdMode
979        (extend logic in ADAUTODIFF_INADMODE_SET)
980    o pkg/seaice
981      - Step 1 of merging ice-thickness distribution (ITD) code from
982        MITgcm_contrib/torge/itd/ (author: Torge Martin)
983        The code implements concept laid out in Thorndike et al. (1975);
984        code is enabled via CPP flag SEAICE_ITD
985        nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
986        code is not complete yet!!
987      - SEAICE_SIZE.h now included in almost all seaice routines
988    o verification (using seaice):
989      - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
990        global_ocean.cs32x15.seaice ; update results.
991      - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
992      - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
993        offline_exf_seaice (previously compiling B-grid).
994    o pkg/exf:
995      - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
996        to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
997        forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
998    o pkg/layers (adjust changes from Sept 19):
999      - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
1000        this allows to remove "layers_maxNum" dimension from all layers arrays.
1001    o pkg/layers (adjust changes from Sept 19):
1002      - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
1003      - snap-shot extended to all type of layers (not just the 1rst type);
1004      - remove layers variables when corresponding CPP option is undef.
1005    o pkg/layers:
1006      - rename pkg/layers variable and add new output (layer exist & un-weighted
1007        velocity in layer)
1008    o pkg/seaice:
1009      - simplify (?) ocean-drag coefficent computations by using
1010        the same routine in all three solvers (saves some code lines)
1011      - remove global fields DRAGA and DRAGS from C-grid code and
1012        declare them locally in lsr.F (the only place where they are
1013        still used)
1014      - update AD output of lab_sea.evp (very sensitive anyway).
1015    o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
1016      (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
1017      and SEAICEuseJFNK=.true. A few things to note:
1018      - involves a FGMRES, that is parallel but very inefficient,
1019        because of many scalar products (global sums) in the Gram-Schmidt
1020        orthogonalization method. Needs to be replaced. Original code
1021        from J.-F. Lemieux
1022      - preconditioner for FGMRES is a stripped down version of LSOR
1023      - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
1024        preconditioner. For the preconditioner, the default is set to 10.
1025      - Jacobian times vector is computed with finite differences
1026      - marginally related to JFNK-solver: add a smooth regularization for
1027        zeta with tanh that will improve convergence (Lemieux and Tremblay,
1028        2009) for any implicit solver (not implemented for EVP because EVP
1029        does not need this regularization in the first place). Define
1030        SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
1031    o eesupp/src:
1032      - check in genmake2 that intrinsic S/R flush is available.
1033      - add S/R to flush IO unit (if intrinsic S/R flush is available)
1034      - flush standard & error msg unit before MPI termination
1035      - if debugMode, flush IO unit after printing msg
1036    o pkg/ctrl:
1037      - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
1038        to ctrl_set_unpack_xyz.
1039    
1040    checkpoint64 (2012/10/09)
1041    o pkg/shelfice
1042      - in mom_fluxform.F, mom_vecinv.F:
1043        CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
1044        Bug fix KappaRU -> KappaRV
1045        does not change verification/isomip but may change other setups
1046        (presumably constant KappaRU=KappaRV)
1047      - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
1048    o pkg/obcs:
1049      - fixed some indexing bugs in obcs_seaice_sponge.F
1050      - added obcs relaxation subroutines for HSALT and HSNOW
1051      - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
1052    o pkg/seaice:
1053      - add "multicategory" parameterization for snow in analogy to ice,
1054        default is off for now.
1055    o pkg/obcs:
1056      - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
1057        see verification/seaice_obcs/input.seaiceSponge for example application.
1058      - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
1059        index setting by master-thread. This fix multi-threads Pb in previous modifs.
1060    o pkg/layers :
1061      - add diagnostics to pkg/layers
1062      - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
1063        (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
1064    o pkg/generic_advdiff/gad_implicit_r.F :
1065      - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
1066    o pkg/seaice/seaice_growth.F:
1067      - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
1068  o pkg/obcs:  o pkg/obcs:
1069    - change default setting of OBCS_UVICE_OLD from defined to undef;    - change default setting of OBCS_UVICE_OLD from defined to undef;
1070    - use new parameter OB_indexNone for null index value (instead of hard-coded 0)    - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
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