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revision 1.1753 by jmc, Fri Oct 19 18:52:53 2012 UTC revision 1.1959 by jmc, Fri Jan 17 22:12:57 2014 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/shelfice:
8      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
9        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
10        so that surface forcing applies to k=kSurf if using pkg/shelfice.
11    o pkg/ctrl, pkg/grdchk, pkg/ecco:
12      - Changes to make GENARR more modular (i.e. invisible if not used)
13    o model/src/temp_integrate.F and salt_integrate.F
14      - re-include store directives that were removed on Dec 27th.
15    o model/src/external_forcing_surf.F
16      - add storage directives for EmPmR and PmEpR to avoid recomputation of
17        seaice_model in the adjoint that is problematic when seaice_model is
18        turned off in the adjoint. The resolved issue dated back to July when
19        EXTERNAL_FORCING_SURF call was moved.
20        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
21    o pkg/exf/exf_check.F
22      - fix a small bug again (originally found by Wentao Liu, now found again)
23      - streamline error output
24    o pkg/streamice and aim_v23:
25      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
26        Apple's /usr/bin/cpp knows what to do:
27        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
28        Target: x86_64-apple-darwin13.0.0
29    
30    checkpoint64s (2014/01/05)
31    o tools/adjoint_options:
32      - switch to fastopt.net TAF server (instead of default fastopt.de) for
33        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
34    o model/src:
35      - remove some unnecessary TAF storage directives in forward_step.F and
36        in dynamics.F (note: not always removed by TAF, e.g., double storage
37        of kappaRU,kappaRV in former version of dynamics.F).
38    o model/src & pkg/ptracers:
39      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
40        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
41        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
42      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
43      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
44      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
45    o useSingleCpuInput separates single-CPU input from single-CPU output;
46        for now only implemented for in exf_interp_read.F
47    o verification/advect_xy:
48      - fix missing EXCH call in local version of ini_salt.F and update output.
49    o momentum diagnostics:
50      - fix which deltaT is used in Total-Tendency diagnostics.
51      - fix typo in diagnostics for momentum tendency from AB.
52    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
53        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
54    
55    checkpoint64r (2013/12/08)
56    o verification/*/results:
57      - Update reference output of experiments that were passing with just 13 digits
58         (make it easier to detect future changes in results)
59    o model/src & pkg/ptracers:
60      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
61        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
62        to inside ptracers_integrate.F ; remove ptracers_advection.F
63    o coupling interface pkgs:
64        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
65      - change the config check to test the agreement of Ocean Depth
66        with ATM land/sea mask (instead of ATM orography);
67      - send to coupler the number of coupler time-steps to do for this run:
68        this allows to check for consistency and don't need anymore to be
69        specified in parameter file "data";
70      in coupler:
71      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
72      - improve report to log-file of config setting (pass log-file unit to few S/R)
73    o pkg/compon_communic:
74      - add coupling send/receive for non-tiled integer vector;
75      - add S/R to check and stop if any proc has an error (similar to
76        eesupp/src/stop_if_error.F but single thread and across Comm_World).
77    o pkg/exch2:
78      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
79        through list of all tiles my proc owns.
80    o model/src:
81      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
82        from rTrans) to simplify dependencies (no need to store rTrans anymore in
83        calling S/R); this affects AD results at machine truncation level:
84        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
85        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
86    o tools/build_options:
87      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
88    o coupling interface pkgs:
89        [compon_communic, atm_compon_interf & ocn_compon_interf]
90      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
91        to each S/R that needs it; remove un-used variables.
92      - change component tile registration (cpl_register.F in both compon_interf
93        and mitcomponent_tile_register.F) to pass the full list of tiles
94        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
95      - with pkg/exch2: adopt the same convention used for I/O to define mapping
96        towards coupler global array (unless W2_useE2ioLayOut=F):
97         a) can now use different tiling between atm & ocn comp.
98         b) no needs to modify the run-Off map when changing tiling (was needed
99            even if using the same tiling between atm & ocn).
100         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
101            full land tiles); not yet tested.
102      - check for valid mapping from comp. tile to coupler global array
103      - improve report of tile registration results to log file.
104    o pkg/exch2:
105      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
106        tile-registration (CPL_REGISTER);
107      - activate (un-comment) definition and setting of "W2_tileIndex" list to
108        store the local bi,bj indices of each tile;
109      - also print bi,bj in local report to log file;
110      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
111        Jun 2009 modif of pkg/exch2).
112    o testing on baudelaire:
113      - run 2 tests at a time: no significant slow down (since enough cpu) and
114        get the full set of test done earlier
115      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
116    o model/src/thermodynamics.F and routines called from it:
117      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
118        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
119        velocity (outp) by adding bolus velocity.
120      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
121        mass transport from velocity + lateral grid cell area
122      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
123      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
124     in thermodynamics.F
125      - remove k from thermodynamics.F and move it to temp_integrate.F
126        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
127        loop).
128      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
129        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
130        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
131        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
132      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
133        global_ocean.90x40x15, tutorial_global_oce_biogeo and
134        tutorial_tracer_adjsens (+ TLM output).
135    o tools/OAD_support and (verification/*/) code_oad:
136      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
137        module conversion ; remove unneeded CPP_EEOPTIONS.h.
138      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
139        version (closer to model/inc/CPP_OPTIONS.h).
140    o model/src:
141      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
142        retired list of parameters (routine FREEZE has been replace by surface
143        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
144    o pkg/gmredi:
145      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
146        velocity (same scheme but affects machine truncation) for GM_AdvForm.
147      - update output of FWD experiments: front_relax.bvp,
148        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
149    
150    checkpoint64q (2013/11/17)
151    o verification:
152      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
153        tutorial_global_oce_biogeo and global_ocean.90x40x15.
154      - generate new output (growth & melt) for seaice_itd experiment after
155        updating the input pickup_seaice files (previously wrong).
156    o pkg/cost:
157      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
158        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
159        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_TILE_RL
160          cannot be applied to var in common block).
161        o allows to get results independent of tile-per-proc setting (if using
162          slower GLOBAL_SUM_SEND_RECV option).
163      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
164        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
165        forward gradients: update output).
166      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
167        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
168    o pkg/mom_common:
169      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
170        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
171        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
172        ensure that all field value that are used are set.
173    o tutorial_deep_convection (smag3d):
174      - add missing scaling in mom_calc_smag_3d.F;
175      - set smag3D_coeff in input.smag3d such that results do not change.
176    o pkg/dic:
177      - change dic_cost.F to compute cost on each tile first and then apply
178        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
179        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
180      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
181    o eesupp/src & pkg/mdsio:
182      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
183        (from pkg/mdsio) since they are no longer used for tape IO.
184      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
185        (+ keep a copy in pkg/atm_ocn_coupler).
186    o verification/isomip:
187      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
188    o tools/build_options:
189      - optfile linux_amd64_ifort11, fast (no ieee) case:
190        to get a working restart for all experiments, add "-fp-model source"
191        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
192    
193    checkpoint64p (2013/10/20)
194    o pkg/autodiff:
195      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
196        criteria, return to simple (default) tape IO format.
197    o pkg/mdsio (+ eesupp/src):
198      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
199        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
200      - fix globalFile and singleCpuIO options using simpler global mapping.
201      - new pairs of scatter/gather vector S/R (one for each type, generated from
202        template) corresponding to simpler global mapping.
203      - adread_write.F: switch to new S/R (but leave old calls commented) and write
204        to globalFile when parameter globalFiles is set to True.
205      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
206    o pkg/autodiff:
207      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
208        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
209        missing, just add a STOP if array type do not match.
210    o pkg/exf:
211      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
212         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
213         and rename array obsSIce to exf_iceFraction.
214    o tutorial_deep_convection:
215      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
216        for now all in this exp. code dir.
217      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
218        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
219    o eesupp/src:
220      - added SINGLE_DISK_IO option because reading of parameter files on
221        very large number of processors did not work with existing set-up
222    
223    checkpoint64o (2013/09/25)
224    o pkg/atm_phys & atm_compon_interf:
225      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
226    o tools/build_options:
227      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
228        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
229        remove CPP setting (was identical to genmake2 default).
230    o pkg/gmredi & model/src: Some updating and work done on the residual model.
231      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
232      - fixed up the calculation of the eddy stress and how it is added to the
233        external forcing via taueddy_external_forcing.F
234      - at the moment, it is very experimental and only works with the variable eddy
235        diffusivity calculated in gmredi_k3d.F
236    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
237        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
238    o testreport (& tools/do_tst_2+2):
239      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
240    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
241      - remove CPP='cpp -traditional -P' (this is genmake2 default)
242      - add switch (for big setups) to use 'medium' memory-model (but leave it
243        commented out for now). Note: needed with FC 19 to compile big setups.
244    o pkg/atm_compon_interf:
245      - regroup per field origin (model & pkgs) the coupling storage routines
246         (which accumalate in time each coupling field)
247      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
248        update accordingly + simplify aim_do_physics.F
249    
250    checkpoint64n (2013/08/26)
251    o pkg/bbl:
252      - update formulation to reduce dispersion of tracer properties in bbl
253      - replaced horizontal and vertical transport parameters with velocities
254      - changes results for verification/global_with_exf.yearly
255    o verification/halfpipe_streamice:
256      - change to matrix construction; update both Fwd & AD output.
257    o verification/tutorial_tracer_adjsens:
258      - OpenAD test: switch to vector-invariant momentum since fluxform with
259        rStar causes problems with OpenAD; update output.
260    o tools:
261      - genmake2: define a common prefix for all temp-file names ; move them
262        to local /tmp disk (but would be easy to move them back);
263      - xmakedepend: apply the same switch for temp-files.
264    o pkg/offline:
265      - changes for use with rStar (NLFS): assume that we continue to provide
266        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
267        output files) and apply r* scaling at each time-step (function of the time
268        varying Eta field); use normal pickup files (needed for restart with NLFS).
269    o adjoint with OpenAD:
270      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
271        package openad.  This package has to be compiled for all runs with OpenAD
272        instead of specifying code_oad_all as a modification directory.
273      - link the fortran templates from tools/OAD_support to the build directory
274        for preprocessing to avoid conflicts between different setups compiled
275        simultaneously and simplify cleanup.
276    o pkg/exf:
277      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
278        main model or other pkgs are exchanged in EXF_MAPFIELDS).
279    o model/src:
280      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
281        (similar to do_fields_blocking_exchanges.F).
282    o tools/genmake2:
283      - remove TAF output src code just before calling staf (when not doing a fresh
284        built, will stop if things go wrong with staf).
285      - fix target "adobj" (left from TAF version-2 transition)
286    o pkg/diagnostics:
287      - add a parameter to track the status of pkg/diagnostics activation;
288        this replace/extend the use of logical param "settingDiags" (to check
289        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
290        New S/R to print error message and stop when pkgStatus is not right.
291      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
292    
293    checkpoint64m (2013/08/13)
294    o model/inc:
295      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
296        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
297    o pkg/kpp & aim_v23:
298      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
299    o pkg/seaice:
300      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
301        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
302      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
303    o eesupp/src:
304      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
305        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
306    o switch to TAF version-2:
307      - add flow directives to "freeze" naming convention for ad-routines that
308        are used in I/O routines of adjoint state and associated common blocks
309        that are used in adcommon.h (backward compatible with version-1)
310      - update all ad-optfiles (in tools/adjoint_options + few local to some
311        verification exp) to switch to latest TAF version (currently 2.5.5);
312        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
313        out except for diva).
314      - the major change with TAF version-2 is that both the differentiated
315        routines and the forward routines (new) are returned as part of the TAF
316        output source code. Update genmake2 accordingly.
317      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
318        with version-2 when compared to TLM or FWD gradient); other experiments
319        output show minor changes (machine truncation level); update the few AD &
320        TLM output with 12 matching digits only (some prior to version-2 switch).
321    
322    checkpoint64l (2013/08/05)
323    o model/src:
324      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
325      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
326        when using TAF but only if using OpenAD.
327    o pkg/mom_common+fluxform+vecinv:
328      - always set horiz. viscosity arrays to background value before calling
329        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
330        only when using variable horiz. viscosity (useVariableVisc=T);
331      - simplify mom_vecinv.F (only 1 block for momViscosity).
332    o pkg/mom_common: variable horiz. viscosity in NH code
333      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
334        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
335      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
336        useBiharmonicVisc & useVariableVisc.
337      - fix old bug (already in 1rst implementation of variable horizontal viscosity
338        in calc_gw.F, version 1.27, 2006/06/20):
339        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
340        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
341      - change background horiz viscosity in vertical momentum (gW) to always be
342        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
343        any type of variable viscosity, e.g., viscAh/4Grid)
344      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
345        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
346        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
347        default viscAh,viscA4 is zero).
348    o model/src:
349      - extend length of drC & recip_drC from Nr to Nr+1.
350    o Divided Adjoint (DIVA) with MPI:
351      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
352      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
353        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
354    
355    checkpoint64k (2013/07/23)
356    o tools/OAD_support:
357      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
358        and remove it from genmake2.
359    o tools/build_options:
360      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
361        MPI_HEADER_FILES list (let genmake2 find the missing headers)
362    o verification/halfpipe_streamice:
363      - change to driving stress formulation; update both Fwd & AD output.
364    o tools/genmake2 and Divided Adjoint with MPI:
365      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
366      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
367      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
368        Makefile, which is set by genmake2, and check which mpi-headers are needed.
369        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
370      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
371    o testreport:
372      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
373        perform additional runs (number of additional runs is "add_DIVA_runs" taken
374        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
375    o verification/lab_sea (AD test):
376      - change to test Divided Adjoint Run in this set-up (both standard AD test
377        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
378    o pkg atm_ & ocn_compon_interf:
379      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
380        staggerTimeStep implementation) and disable (retired) corresponding
381        parameter.
382    o pkg/offline:
383      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
384      - add S/R OFFLINE_CHECK to print offline parameter summary
385        and stop if loading a file that is not used;
386      - enable to calculate GMRedi tensor, KPP mixing and convective index
387        when the corresponding file(s) is/are not specified (but pkg is used).
388      - comment out resetting of monitorFreq (to endTime) since it still useful
389        for monitoring CFL numbers and checking offline fields.
390    o OpenAD:
391      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
392        smaller standard output) and generate new (smaller) output (on baudelaire
393        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
394    o model/src:
395      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
396        (where external_forcing_adjust was called) and change list of arguments;
397      - merge external_forcing_adjust.F into external_forcing_surf.F
398      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
399        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
400        previously in file "balance_relax.F", now removed); remove corresponding
401        arrays in FFIELDS.h.
402      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
403        a hack for getting back surfaceForcingS (loaded from file) when using
404        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
405      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
406        (was getting only 11 digits for AD-grad, due to different truncation
407         error in AD code).
408    
409    checkpoint64j (2013/07/04)
410    o pkg/offline:
411      - to enable the use of other features with pkg offline (e.g., obcs),
412        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
413      - comment out "allowFreezing" (now active) in 2 offline testing exp.
414    o pkg/exf ALLOW_RUNOFTEMP
415      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
416      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
417      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
418    o pkg/atm_phys:
419      - allows to add some damping on uVel,vVel (strength only function of k).
420    o verification, ad-tests:
421      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
422        global_ocean_ebm and offline_exf_seaice.thsice.
423    o verification/halfpipe_streamice:
424      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
425        flux input boundary conditions to be ignored; a fix for this bug changed
426        verification results for forward test.
427      - add adjoint test.
428    o pkg/ptracers:
429      - allow to restart without SOM pickup (resetting SOM to zero).
430    o pkg/gmredi:
431      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
432      - It uses mixing length theory and suppression by steering level effects to
433        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
434        to JPO, for more details).
435      - It also uses the diffusivity to calculate an eddy induced streamfunction
436        based on a PV closure (rather than a buoyancy closure as in GM).
437      - New files added to pkg/gmredi:
438        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
439          induced overturning streamfunction (called from gmredi_calc_tensor)
440        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
441          for use in gmredi_k3d
442        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
443          the eddy diffusivity
444    
445    checkpoint64i (2013/06/18)
446    o pkg/cheapaml:
447      - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
448        that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
449        with pkg/cheapaml.
450    o utils/python: add subpackage for cubed sphere function, first example is
451        simple cs.pcol to plot 2D fields on a map
452    o pkg/streamice:
453      - This is a new package in MITgcm, which solves dynamic equations for ice
454         sheets and ice streams
455      - At the moment it is independent of atmosphere/ocean dynamics, or any
456        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
457        ed that this will change)
458      - There is a new verification exercise that tests it, halfpipe_streamice,
459        evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
460        rectangular embayment
461      - halfpipe_streamice is forward-only for now, will have TAF test soon
462      - for questions, email dgoldber@mit.edu
463    o pkg/thsice:
464      - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
465        of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
466      - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
467         call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
468      - allow precip from pkg/cheapaml to make snow over seaice.
469    o pkg/cfc:
470      - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
471      - remove atmos CFC 2-D arrays from common bloc (now local variables)
472      - change some hard-coded constant to run time parameter for reading and
473        and interpolating atmospheric CFC ; keep same default as previously.
474      - more flexible reading of Atmos CFC (number of records no longer hard-coded)
475      - put arguments in standard order: myTime, myIter, myThid
476      - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
477        atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
478      - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
479      - new routine to print summary of CFC params and check for consistency.
480    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
481      similar to thsice_advdiff.
482      Note that for the B-grid case the routine parameters uc/vc are overwritten.
483    o pkg/cfc:
484      - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
485        update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
486      - fix interpolation of atmphspheric CFC between Sorthern and Northern
487        hemisphere value.
488    o pkg/seaice:
489      - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
490    o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
491                  so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
492      - requires an additional time level that is stored in the pickup
493      - you can start with AB2 from a pickup without this time level with
494        pickupStrictlyMatch = .false.
495    
496    checkpoint64h (2013/05/26)
497    o pkg/cheapaml:
498      - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
499        affect machine truncation (but exp cheapAML_box still pass with 13 digits).
500      - consistent treatment of uWind,vWind location: assume everywhere in
501        pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
502        (Note: was already the case for Tair,Qair advection);
503        add option (INCONSISTENT_WIND_LOCATION) to recover old results.
504      - compute diabatic forcing only in the interior (excluding overlap regions)
505      - fill in array "Qsw" (for short-wave heating);
506      - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
507        before any update (consistent with MITgcm state var diagnostics);
508      - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
509        non periodic ; + adjusted for uWind,vWind (C-grid).
510    o pkg/seaice:
511      - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
512        add explicitly pkg/exf in experiments that currently use pkg/seaice.
513      - allows to compile pkg/seaice without pkg/exf.
514    o tools/OAD_support:
515      - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
516        of array "ourStepOf" in function rvNextAction (revolve.F90).
517    o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
518      - change pkg name (to be used with other atmospheric physics pkg)
519        but by-pass CVS when making the new pkg so that we keep the CVS history.
520    o pkg/offline:
521      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
522        (previously called from pkg/dic_surfforcing_init.F)
523    o model/src:
524      - re-order sequence of calls within packages_init_variables.F, using
525        standard order, except for:
526         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
527         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
528    o new pkg: atm_phys
529      - add entry point and source code (previously in contrib
530          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
531        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
532      - re-order sequence of calls within packages_readparms.F,
533         packages_init_fixed.F and packages_write_pickup.F
534        (but skip packages_init_variables.F because of TAF issues).
535      - update contrib/*/atm_gray/ experiment.
536    o pkg/seaice (ITD code):
537      - simplify and fix the writing of pickup-files for ITD case
538    o pkg/seaice (ITD code):
539      - introduce floe size dependent lateral melt for ITD case;
540      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
541      - update seaice_itd experiment main output.
542    o pkg/thsice:
543      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
544        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
545        changed accordingly pkg/atm2d.
546    
547    checkpoint64g (2013/05/01)
548    o pkg/exf ALLOW_RUNOFTEMP
549      - if defined,  river and glacier runoff temperature can be read-in from
550        runoftempfile; runoftempfile needs to have same format as runofffile
551    o pkg/thsice (& pkg/bulk_force):
552      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
553        for energy content of Precip + RunOff & Evap (like with pkg/exf).
554      - change computation domain to always be the interior (without overlap).
555      - fix bug (wrong overlap) when using EXF and stressReduction > 0.
556    o verification/tutorial_global_oce_biogeo:
557      - add preliminary OpenAD setup (still has problems)
558    o pkg/seaice:
559      - turn some parameters for choosing the convergence criterion of
560        the inexact Newton method (JFNK) into runtime parameters for convenience
561      - clean up seaice_calc_viscosities.F: remove/retire two options for
562        SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
563        the results of lab_sea/input because a division has been replaced by
564        a multiplication with the reciprocal (sumNorm)
565      - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
566        convergence of solver (changes results, of course), and to test some
567        new features
568    o model/src:
569      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
570      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
571      - move forcing adjustment (balancing surface forcing) in specific S/R
572        where might also be applied exchanges (if needed) to forcing arrays.
573    o pkg/shelfice:
574      - allow to specify the Ice-Shelf mass per unit area (instead of
575        shelficeLoadAnomaly) and do the conversion from one to the other
576      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
577        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
578        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
579        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
580      - update isomip experiment forward output (get machine truncation error
581        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
582    o verification/offline_exf_seaice:
583      revise data.seaice in input.thermo and input_ad and update results accordingly
584        HO = 0.2, SEAICE_areaLossFormula = 2,
585        SEAICE_growMeltByConv = .TRUE.,
586        SEAICE_doOpenWaterMelt = .TRUE.,
587      Improve consistency with input.thsice and fix the spurious 500m ice corners
588    o verification/global_ocean.cs32x15:
589      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
590        in icedyn (thsice+seaice-dyn) test and update output.
591    o verification/offline_exf_seaice:
592      - adjust list of tested variables (with testreport) and update
593        standard test output with better slection of monitored fields.
594    o pkg/cd_code:
595      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
596        experiment lab_sea.hb87
597    o tools/genmake2:
598      - change default makedepend from the system default to tools/xmakedepend:
599        When no makedepend is specified, select tools/xmakedepend it the test pass,
600        otherwise select the system default (if exist and pass the test) or
601        try to build cyrus-makedepend ; stop if none of the 3 works.
602    o pkg/exf & pkg/thsice:
603      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
604        for energy content of Precip + RunOff & Evap. Assumes:
605       1) Rain has same temp as Air.
606       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
607       3) Run-Off comes at the temp of surface water (with same Cp)
608       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
609        put directly into Latent Heat flux & should use water-vapor heat capacity.
610       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
611        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
612    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
613        (compile when SEAICE_ALLOW_JFNK is defined)
614    o pkg/thsice:
615      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
616        implementation): move THSICE_AVE call after the advection (called directly
617        from thsice_do_advect.F).
618    o verification/global_ocean.90x40x15 and OpenAD:
619      New experiment for OpenAD is identical to the one in input_ad except that
620        multiDimAdvection=.FALSE.,
621      There is still an issue with this.
622    o pkg/thsice:
623      - account for ice velocity (ocean relative velocity) in turbulent heat flux
624        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
625        and offline_exf_seaice (main test).
626    
627    checkpoint64f (2013/03/31)
628    o verification/OpenAD:
629      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
630    o verification/isomip, pkg/shelfice and OpenAD:
631      - add OpenAD setup to this exp and make shelfice package work with OpenAD
632    o verification/tutorial_global_oce_biogeo:
633      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
634    o verification/offline_exf_seaice:
635      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
636    o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
637      - add OpenAD setup to this exp and make ptracers package work with OpenAD
638    o pkg/seaice/seaice_evp.F:
639       mask the asymmetric contribution of the ice-ocean stress (when
640       the turningAngle is non-zero) over open water to avoid stripes
641       in the EVP-solutions after many EVP-substeps. This does not change
642       the verification experiment (because turningAngle=0 in that experiment),
643       but will affect other EVP solutions with turningAngle.ne.0
644    o verification, AD & TLM output:
645      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
646        additions and multiplications which affect results at machine truncation
647        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
648        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
649        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
650        digits of matching.
651    o pkg/seaice:
652       modify lsr-algorithm so that it vectorizes AND converges by using a
653       "zebra" method: split vector loop into two with step size 2; this
654       solves a general convergence problem for the JFNK solver on a vector
655       computer. It has the potential to even improve convergence for
656       non-vector machines, but it does change the results so it is turned
657       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
658       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
659    
660    checkpoint64e (2013/03/05)
661    o pkg/ecco and several verification experiments:
662       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
663       from ecco package, and revert to unified routine in model/src/
664       Adjust verification experiments accordingly, especially gloal_oce_llc90
665       Should conclude long-standing work by Gael to reconsile the_main_loop with
666       ECCO and will enable OpenAD's revolve loop in ECCO setup.
667    o pkg/generic_advdiff:
668      - implement compressible flow method for multi-dim advection (similar to
669        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
670        TAF generates many recomputations) to use it; no yet coded with implicit
671        vertical advection.
672      - change experiment advect_cs (new output) and advect_xy (same output)
673        to test compressible flow multi-dim advection.
674    o pkg/generic_advdiff:
675      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
676        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
677    o pkg/seaice:
678      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
679        bug affects two verification experiments (lab_sea and lab_sea.hb87),
680        recover old (wrong) results by setting noSlipFac = 2. in
681        seaice_calc_strainrates.F;
682      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
683      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
684        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
685      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
686    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
687      - new subroutines seaice_lsr_tridiagu/v
688      - introduce loop bounds i/jmin/max to be able to use a restricted
689        additive Schwarz method, but not used for now.
690      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
691      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
692    o OpenAD support
693       Reorganize S/R call for overall time-stepping loop to facilitate
694       OpenAD revolve loop replacement
695       (new S/R main_do_loop.F)
696    o model/src:
697      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
698      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
699        ADAMS_BASHFORTH2.
700    o pkg/cheapaml:
701      - add new parameter (default=F, same as before) to disable full domain
702        (including land) periodicity in X & Y dir.
703      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
704        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
705        into single S/R CHEAPAML_TIMESTEP.
706    
707    checkpoint64d (2013/02/17)
708    o pkg/monitor (angular momentum):
709      - do not add Eta contribution to the total AM if using rigid-lid;
710      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
711      - horizontal discretisation: compute Zonal wind contribution separately for
712        each component (instead of from cell centered averaged) and use the 4
713        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
714      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
715        FreeSurf) if using vectorInvariant momentum.
716    o model/src (horizontal grid):
717      - move initialisation of all horizontal grid arrays to null value
718        from specific horizontal grid S/R to main S/R INI_GRID;
719      - add 2 new arrays to project model C-grid velocity on to zonal direction
720        (similar to AngleCosC & -AngleSinC but at U and V point location) and
721        compute them in S/R CALC_GRID_ANGLES.
722    o pkg/seaice: replace a hard coded parameter by a runtime parameter
723        SEAICE_JFNK_tolIter
724    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
725        preconditioner for JFNK (run LSR into the overlaps as far as possible,
726        i.e OLx/y-2, but overwrite the solution in the overlaps)
727      - extend loop range in seaice_calc_viscosity
728      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
729      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
730      - slightly modify loops in tridiagonal solver lsr-preconditioner
731      - by default remove the extra exchange in seaice_preconditioner with a
732        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
733      - modify offline_exf_seaice so that old results without RAS are reproduced
734        for output.dyn_jfnk.txt
735      in seaice_fgmres.F (unrelated to RAS)
736      - add a cpp-flag option for a re-ordered mapping (potentially more
737        efficient), but because this changes the results, turn it off by
738        default
739      - replace the save statement by local common blocks
740    o utils/matlab:
741      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
742      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
743        instead of local script "load_cs.m".
744    o pkg/seaice:
745      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
746        to the scalarProductMetric and the unrolling. By chance this does not
747        change the verification experiment, because of the particular domain
748        decomposition
749    o pkg/diagnostics:
750      - change default missing_value from UNSET_RL to -999.
751    o pkg/layers: improve vectorization of layers_fluxcalc.F
752      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
753        time spent in this routine by more than a factor of 3 on an NEC-SX8
754      - step 2: replace search algorithm by a bisection algorithm found in
755        Press et al. Numerical Recipes in Fortran. This algorithm can be
756        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
757        For now, use this algorithm only for TARGET_NEC_SX defined.
758      - moved the search algorithm into a separate subroutine, that is kept
759        within the same file for automatic inlining.
760      - modified catching potential errors
761    o pkg/ecco:
762      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
763    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
764      - modifications for ALLOW_GENTIM2D_CONTROL
765      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
766      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
767      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
768      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
769    o model/src:
770      - account for moist thermodynamics in (dry) potential temperature equation;
771        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
772        and cpl_aim+ocn.
773      - also switch to standard compiler (gfortran, was using ifort previously)
774        for fizhi-cs experiments reference output.
775    o pkg/ctrl:
776      - 1st step toward generic time-varying control variable (2D) via CPP option
777        ALLOW_GENTIM2D_CONTROL
778      - note new namelist ctrl_nml_genarr in data.ctrl
779    o verification/global_ocean.cs32x15:
780      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
781        thsice calling sequence and update "output.icedyn.txt" output file.
782    o pkg/ptracers:
783      - from Ryan A.: code to allow to restart a tracer at regular time interval
784        specifying a reset frequency and a reset-phase (for each tracers).
785    o pkg/thsice:
786      - implement new sequence of calls for thsice+seaice:
787          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
788          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
789      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
790        in CPP_OPTIONS.h) to recover old sequence;
791      - update diagnostics for Intermediate State thsice diagnostics: now filled
792        just before advection (instead of just after advection in old sequence);
793      - update output of experiment offline_exf_seaice (standard test);
794      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
795        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
796    o pkg/aim_v23:
797      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
798      - use standard pkg/mdsio routines to read & write CO2 pickup file;
799      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
800      - Implement new sequence of calls for seaice advection (with thsice and
801        seaice diffusion): do ice advection after ice-Thermodynamic (previously
802        was done before); change aim_do_physics.F (split the bi,bj loops block);
803      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
804    o pkg/thsice:
805      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
806        where just seaice diffusion is used without seaice-dynamics.
807    
808    checkpoint64c (2013/01/18)
809    o pkg/seaice:
810      - add a parameter JFNKres_tFac that can replace JFNKres_t
811        (= JFNKres_tFac*JFNKresidual before JFNK solver)
812      - add a line search option to the JFNK solver
813      - move update of u/vIce and computation of initial residual into a separate
814        routine (same file); makes the code a little easier to read (?)
815      - the line search requires computation of the residual and for some reason
816        I cannot do the update of u/vIce at the beginning of the Newton loop
817        without changing the results, so we move computation of the new residual
818        also to the end of the Newton loop, even without the line search
819    o pkg/mdsio:
820      - write missing value (corresponding to undefined array value) to meta files;
821        skip this if missing value is one (UNSET_RL would be a better value for the
822        case of undefined missing value but it's current the default missing-value);
823        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
824    o pkg/exf & thsice:
825      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
826        diagnostics) even when SHORTWAVE_HEATING is #undef;
827    o verification/cfc_example:
828      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
829        illustrate how to use it).
830    o verification/offline_exf_seaice:
831      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
832        files to only one time-record.
833      in input.thermo: narrow the 2 bands of low initial ice-concentration near
834        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
835        snapshot output; same mcPheePiston value as in thsice with
836        surf-current=0.2m/s.
837      in input.thsice: similar set-up as in input.thermo (channel with same seaice
838        initial conditions).
839    o verification/cfc_example:
840      - update file "data" with more standard choice (default rotationPeriod,
841        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
842        set deltaTFreeSurf to deltaTtracer) and update the output.
843    o pkg/layers:
844      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
845      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
846    o verification/offline_exf_seaice:
847      - set all {field}period to zero for constant-in-time forcing (not tested
848        anywhere else).
849    o verification/offline_exf_seaice:
850      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
851      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
852    o model/src:
853      - implement Finite-Volume method for (hydrostatic) presure gradient
854        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
855    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
856      - In order to be compatible with the default EVP code, this requires changing
857        the EVP code around a little; and because any small change immediately
858        breaks the lab_sea.hb87 verification experiment, the reference output is
859        updated two times (each time the remaining aggrement was only 2 digits):
860        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
861        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
862        The adjoint test lab_sea.evp also needed to be updated.
863      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
864        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
865        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
866        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
867        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
868        kept obscure, because I need to test it a little more.
869    o pkg/cheapaml:
870      - fix few incorrect type (_RL/_RS) in subroutine calls.
871    o pkg/seaice:
872      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
873        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
874    o model/src:
875      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
876        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
877        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
878    o pkg/cheapaml:
879      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
880        update output of experiment cheapAML_box.
881      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
882        and set them only in one place (cheapaml_readparms.F).
883      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
884      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
885        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
886    o model/src/the_main_loop.F:
887      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
888    o pkg/seaice:
889      - remove legacy branch code.
890      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
891    o verification/*/code*/SEAICE_OPTIONS.h:
892      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
893        SEAICE_CAP_HEFF).
894    o pkg/cheapaml:
895      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
896        to load new forcing fields.
897      - add missing "_d 0" where it's needed; + some editing (improve indentation).
898      - remove switch to "-r8" compiler option (no longer needed) in verification
899        cheapAML_box, keep same output (small trucation error differences).
900    o verification/offline_exf_seaice:
901      - add thermodynamics only test.
902    o verification/cheapAML_box:
903      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
904        keep same output (same 14 digits for cg2d).
905      - switch on "-r8" compiler option (some numerical values are missing
906        the "_d 0") and update output (only 6 digits for cg2d were preserved).
907    
908    checkpoint64b (2012/12/24)
909    o pkg/cheapaml:
910      - remove un-used variables (Qnet,EmPmR) from pickup files.
911      - store tendency of advected variables into cheapaml pickup file
912        and fix the AB-2 restart.
913    o verification/offline_exf_seaice and lab_sea adjoint:
914      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
915      - switch to 4 time steps in offline, consistent with lab_sea.
916      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
917      - update results after change of experiment seaice.
918    o pkg/seaice:
919      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
920        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
921        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
922        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
923    o model/src:
924      - add run-time parameter to select CG2D solver minimum-residual solution
925        (in case of a poor convergence).
926    o pkg/seaice/seaice_lsr.F
927      - move calculation of matrix coefficients into new
928        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
929        file; the main purpose of this change is to be able to reuse the code
930        in S/R SEAICE_PRECONDITIONER
931      - modify the computation of the residual so that the mass of sea-ice
932        is not used twice; this simplifies the calculations, but since
933        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
934        not tested in testreport---this does not affect the testreport results.
935    o verification/seaice_obcs:
936      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
937        verification/lab_sea/input.salt_plume; changes results/output.txt*
938    o model/src:
939      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
940    o pkg/seaice:
941      - improve description of parameters in seaice_fgmres.F and start
942        cleaning up the code
943      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
944        second argument
945      - add a metric based on grid cell area to SEAICE_SCALPROD; update
946        results of offline_exf_seaice.dyn_jfnk
947      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
948    o pkg/aim_v23:
949      - fix an other bug in dissipation heating (grid-cell area was missing).
950    o model/src + pkg/seaice:
951      - add global (multi-tile) linear solver for pair of tri-diagonal system
952        along X and Y lines, respectively for U and V component.
953        Note: 1) MPI and cube-exchange not yet coded.
954            2) probably not accurate for poorly conditioned / large size problem.
955      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
956        default: not compiled and not used.
957    o pkg/seaice:
958      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
959        introduce bi/bj loops and use global_sum_tile_rl instead of
960        mpi_allreduce in seaice_fgmres.F
961      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
962      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
963      - add a verification experiment for JFNK in offline_exf_seaice
964    o verification:
965      - change (for now, only fwd test) offline_exf_seaice experiment:
966        use a re-entrant channel with idealized coastline (trapezoidal shape)
967        at southern boundary to explore seaice dynamics and thermodynamics
968        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
969        secondary test (input.thsice) use thermodynamics only with SST relaxation.
970      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
971    o pkg/exf:
972      - disable "sstExtrapol" when Nr=1
973    o verification:
974      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
975        to test pkg/cheapaml.
976    o pkg/aim_v23 & pkg/shap_filt:
977      - fix dissipation heating (erroneous gravity multiplication factor).
978    o pkg/seaice:
979      - remove unused field pressPre from jfnk solver
980      - rename two subroutines in seaice_preconditioner.F
981    o eesupp/src:
982       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
983    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
984       - remove wrong parts of the rhs and the lhs (were in there
985         because I did not understand the concept of this preconditioner)
986       - add an exchange between u- and v-sweep. This increases communication
987         by a factor of two but improves the convergence of jfnk. Ideally,
988         one would like the u- and v-sweep to be independent. So far within
989         undocumented ifdefs
990       - reorganize the extra computations for printing the residuals
991    o tools/genmake2:
992      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
993        since it's not necessary (and was preventing to use MNC in some cases).
994    
995    checkpoint64a (2012/11/16)
996    o pkg/autodiff:
997      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
998        autodiff_readparms.F no longer depends on calling order (within
999        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
1000        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
1001        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
1002    o pkg/obcs:
1003      - adding tidal velocity forcing capability to obcs
1004        for usage example, see verification/seaice_obcs/input.tides
1005    o pkg/seaice:
1006      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
1007        SEAICE_LSRrelaxU/V
1008      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
1009    o pkg/aim_v23:
1010      - implement heating from friction (bottom friction and stratospheric drag).
1011    o pkg/shap_filt:
1012      - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
1013        dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
1014    o model/src:
1015      - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
1016        time-constant addMass field from file (addMassFile);
1017      - support for heating due to friction (and Kinetic Energy dissipation):
1018        add option, run-time switch and 3-D field array + support code ; each pkg
1019        or S/R can add heating contribution (if there is a sink of KE); the sum is
1020        accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
1021    o pkg/seaice:
1022      - complete merge of ITD code into seaice_growth.F
1023        from MITgcm_contrib/torge/itd/code/
1024        no verification so far, but Torge Martin tested
1025        "1-D test case and Beaufort set up;
1026        deliver okay results after 1 model year."
1027      - complete merge of SEAICE_SIZE.h into all relevant routines
1028      - move computation of eta at Z-points into calc_viscosities
1029        + introduce global field etaZ
1030        + add different methods for computing etaZ, for now the old
1031          method (simple averages of eta to Z-points) is hardwired
1032        + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
1033          seaice_preconditioner
1034      - simplify computations for SEAICE_ZETA_SMOOTHREG
1035      - seaice_preconditioner:
1036        + replace one remaining press by pressLoc (mistake)
1037        + adjust printing of residuals
1038      - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
1039        + add (SEAICE.h) and rename some counters (initiliased in
1040          seaice_init_fixed.F)
1041        + add _BEGIN/END_MASTER (myThid)  around print statements
1042        + print total number of iterations and failures over SEAICE_monFreq
1043          interval to STDOUT
1044      - move control over output-messages by fgmres to seaice_jfnk to save
1045        some operations
1046      - move resetting initial guess for fgmres outside of seaice_fgmres_driver
1047        in order to make restarts with sol .ne. zero (fgmres with restarts)
1048        (seaice_jfnk.F, seaice_fgmres.F)
1049      - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
1050        a serious convergence problem when open boundaries are involved
1051    o pkg/ggl90: fix computation of control volumes for the case of
1052      ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
1053      up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
1054    o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
1055    o pkg/autodiff
1056      - Add inAdMode switch for SEAICEuseDYNAMICS:
1057        SEAICEuseDYNAMICSinAdMode
1058        (extend logic in ADAUTODIFF_INADMODE_SET)
1059    o pkg/seaice
1060      - Step 1 of merging ice-thickness distribution (ITD) code from
1061        MITgcm_contrib/torge/itd/ (author: Torge Martin)
1062        The code implements concept laid out in Thorndike et al. (1975);
1063        code is enabled via CPP flag SEAICE_ITD
1064        nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
1065        code is not complete yet!!
1066      - SEAICE_SIZE.h now included in almost all seaice routines
1067    o verification (using seaice):
1068      - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
1069        global_ocean.cs32x15.seaice ; update results.
1070      - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
1071      - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
1072        offline_exf_seaice (previously compiling B-grid).
1073    o pkg/exf:
1074      - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
1075        to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
1076        forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
1077  o pkg/layers (adjust changes from Sept 19):  o pkg/layers (adjust changes from Sept 19):
1078    - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)    - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
1079      this allows to remove "layers_maxNum" dimension from all layers arrays.      this allows to remove "layers_maxNum" dimension from all layers arrays.
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