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revision 1.1753 by jmc, Fri Oct 19 18:52:53 2012 UTC revision 1.1952 by jmc, Fri Dec 27 21:16:42 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 model/src & pkg/ptracers:
8      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F,
9        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
10        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
11      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
12      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
13      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
14    o useSingleCpuInput separates single-CPU input from single-CPU output;
15        for now only implemented for in exf_interp_read.F
16    o verification/advect_xy:
17      - fix missing EXCH call in local version of ini_salt.F and update output.
18    o momentum diagnostics:
19      - fix which deltaT is used in Total-Tendency diagnostics.
20      - fix typo in diagnostics for momentum tendency from AB.
21    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
22        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
23    
24    checkpoint64r (2013/12/08)
25    o verification/*/results:
26      - Update reference output of experiments that were passing with just 13 digits
27         (make it easier to detect future changes in results)
28    o model/src & pkg/ptracers:
29      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
30        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
31        to inside ptracers_integrate.F ; remove ptracers_advection.F
32    o coupling interface pkgs:
33        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
34      - change the config check to test the agreement of Ocean Depth
35        with ATM land/sea mask (instead of ATM orography);
36      - send to coupler the number of coupler time-steps to do for this run:
37        this allows to check for consistency and don't need anymore to be
38        specified in parameter file "data";
39      in coupler:
40      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
41      - improve report to log-file of config setting (pass log-file unit to few S/R)
42    o pkg/compon_communic:
43      - add coupling send/receive for non-tiled integer vector;
44      - add S/R to check and stop if any proc has an error (similar to
45        eesupp/src/stop_if_error.F but single thread and across Comm_World).
46    o pkg/exch2:
47      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
48        through list of all tiles my proc owns.
49    o model/src:
50      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
51        from rTrans) to simplify dependencies (no need to store rTrans anymore in
52        calling S/R); this affects AD results at machine truncation level:
53        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
54        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
55    o tools/build_options:
56      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
57    o coupling interface pkgs:
58        [compon_communic, atm_compon_interf & ocn_compon_interf]
59      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
60        to each S/R that needs it; remove un-used variables.
61      - change component tile registration (cpl_register.F in both compon_interf
62        and mitcomponent_tile_register.F) to pass the full list of tiles
63        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
64      - with pkg/exch2: adopt the same convention used for I/O to define mapping
65        towards coupler global array (unless W2_useE2ioLayOut=F):
66         a) can now use different tiling between atm & ocn comp.
67         b) no needs to modify the run-Off map when changing tiling (was needed
68            even if using the same tiling between atm & ocn).
69         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
70            full land tiles); not yet tested.
71      - check for valid mapping from comp. tile to coupler global array
72      - improve report of tile registration results to log file.
73    o pkg/exch2:
74      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
75        tile-registration (CPL_REGISTER);
76      - activate (un-comment) definition and setting of "W2_tileIndex" list to
77        store the local bi,bj indices of each tile;
78      - also print bi,bj in local report to log file;
79      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
80        Jun 2009 modif of pkg/exch2).
81    o testing on baudelaire:
82      - run 2 tests at a time: no significant slow down (since enough cpu) and
83        get the full set of test done earlier
84      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
85    o model/src/thermodynamics.F and routines called from it:
86      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
87        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
88        velocity (outp) by adding bolus velocity.
89      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
90        mass transport from velocity + lateral grid cell area
91      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
92      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
93     in thermodynamics.F
94      - remove k from thermodynamics.F and move it to temp_integrate.F
95        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
96        loop).
97      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
98        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
99        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
100        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
101      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
102        global_ocean.90x40x15, tutorial_global_oce_biogeo and
103        tutorial_tracer_adjsens (+ TLM output).
104    o tools/OAD_support and (verification/*/) code_oad:
105      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
106        module conversion ; remove unneeded CPP_EEOPTIONS.h.
107      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
108        version (closer to model/inc/CPP_OPTIONS.h).
109    o model/src:
110      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
111        retired list of parameters (routine FREEZE has been replace by surface
112        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
113    o pkg/gmredi:
114      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
115        velocity (same scheme but affects machine truncation) for GM_AdvForm.
116      - update output of FWD experiments: front_relax.bvp,
117        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
118    
119    checkpoint64q (2013/11/17)
120    o verification:
121      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
122        tutorial_global_oce_biogeo and global_ocean.90x40x15.
123      - generate new output (growth & melt) for seaice_itd experiment after
124        updating the input pickup_seaice files (previously wrong).
125    o pkg/cost:
126      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
127        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
128        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_TILE_RL
129          cannot be applied to var in common block).
130        o allows to get results independent of tile-per-proc setting (if using
131          slower GLOBAL_SUM_SEND_RECV option).
132      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
133        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
134        forward gradients: update output).
135      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
136        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
137    o pkg/mom_common:
138      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
139        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
140        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
141        ensure that all field value that are used are set.
142    o tutorial_deep_convection (smag3d):
143      - add missing scaling in mom_calc_smag_3d.F;
144      - set smag3D_coeff in input.smag3d such that results do not change.
145    o pkg/dic:
146      - change dic_cost.F to compute cost on each tile first and then apply
147        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
148        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
149      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
150    o eesupp/src & pkg/mdsio:
151      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
152        (from pkg/mdsio) since they are no longer used for tape IO.
153      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
154        (+ keep a copy in pkg/atm_ocn_coupler).
155    o verification/isomip:
156      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
157    o tools/build_options:
158      - optfile linux_amd64_ifort11, fast (no ieee) case:
159        to get a working restart for all experiments, add "-fp-model source"
160        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
161    
162    checkpoint64p (2013/10/20)
163    o pkg/autodiff:
164      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
165        criteria, return to simple (default) tape IO format.
166    o pkg/mdsio (+ eesupp/src):
167      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
168        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
169      - fix globalFile and singleCpuIO options using simpler global mapping.
170      - new pairs of scatter/gather vector S/R (one for each type, generated from
171        template) corresponding to simpler global mapping.
172      - adread_write.F: switch to new S/R (but leave old calls commented) and write
173        to globalFile when parameter globalFiles is set to True.
174      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
175    o pkg/autodiff:
176      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
177        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
178        missing, just add a STOP if array type do not match.
179    o pkg/exf:
180      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
181         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
182         and rename array obsSIce to exf_iceFraction.
183    o tutorial_deep_convection:
184      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
185        for now all in this exp. code dir.
186      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
187        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
188    o eesupp/src:
189      - added SINGLE_DISK_IO option because reading of parameter files on
190        very large number of processors did not work with existing set-up
191    
192    checkpoint64o (2013/09/25)
193    o pkg/atm_phys & atm_compon_interf:
194      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
195    o tools/build_options:
196      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
197        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
198        remove CPP setting (was identical to genmake2 default).
199    o pkg/gmredi & model/src: Some updating and work done on the residual model.
200      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
201      - fixed up the calculation of the eddy stress and how it is added to the
202        external forcing via taueddy_external_forcing.F
203      - at the moment, it is very experimental and only works with the variable eddy
204        diffusivity calculated in gmredi_k3d.F
205    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
206        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
207    o testreport (& tools/do_tst_2+2):
208      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
209    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
210      - remove CPP='cpp -traditional -P' (this is genmake2 default)
211      - add switch (for big setups) to use 'medium' memory-model (but leave it
212        commented out for now). Note: needed with FC 19 to compile big setups.
213    o pkg/atm_compon_interf:
214      - regroup per field origin (model & pkgs) the coupling storage routines
215         (which accumalate in time each coupling field)
216      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
217        update accordingly + simplify aim_do_physics.F
218    
219    checkpoint64n (2013/08/26)
220    o pkg/bbl:
221      - update formulation to reduce dispersion of tracer properties in bbl
222      - replaced horizontal and vertical transport parameters with velocities
223      - changes results for verification/global_with_exf.yearly
224    o verification/halfpipe_streamice:
225      - change to matrix construction; update both Fwd & AD output.
226    o verification/tutorial_tracer_adjsens:
227      - OpenAD test: switch to vector-invariant momentum since fluxform with
228        rStar causes problems with OpenAD; update output.
229    o tools:
230      - genmake2: define a common prefix for all temp-file names ; move them
231        to local /tmp disk (but would be easy to move them back);
232      - xmakedepend: apply the same switch for temp-files.
233    o pkg/offline:
234      - changes for use with rStar (NLFS): assume that we continue to provide
235        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
236        output files) and apply r* scaling at each time-step (function of the time
237        varying Eta field); use normal pickup files (needed for restart with NLFS).
238    o adjoint with OpenAD:
239      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
240        package openad.  This package has to be compiled for all runs with OpenAD
241        instead of specifying code_oad_all as a modification directory.
242      - link the fortran templates from tools/OAD_support to the build directory
243        for preprocessing to avoid conflicts between different setups compiled
244        simultaneously and simplify cleanup.
245    o pkg/exf:
246      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
247        main model or other pkgs are exchanged in EXF_MAPFIELDS).
248    o model/src:
249      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
250        (similar to do_fields_blocking_exchanges.F).
251    o tools/genmake2:
252      - remove TAF output src code just before calling staf (when not doing a fresh
253        built, will stop if things go wrong with staf).
254      - fix target "adobj" (left from TAF version-2 transition)
255    o pkg/diagnostics:
256      - add a parameter to track the status of pkg/diagnostics activation;
257        this replace/extend the use of logical param "settingDiags" (to check
258        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
259        New S/R to print error message and stop when pkgStatus is not right.
260      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
261    
262    checkpoint64m (2013/08/13)
263    o model/inc:
264      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
265        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
266    o pkg/kpp & aim_v23:
267      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
268    o pkg/seaice:
269      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
270        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
271      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
272    o eesupp/src:
273      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
274        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
275    o switch to TAF version-2:
276      - add flow directives to "freeze" naming convention for ad-routines that
277        are used in I/O routines of adjoint state and associated common blocks
278        that are used in adcommon.h (backward compatible with version-1)
279      - update all ad-optfiles (in tools/adjoint_options + few local to some
280        verification exp) to switch to latest TAF version (currently 2.5.5);
281        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
282        out except for diva).
283      - the major change with TAF version-2 is that both the differentiated
284        routines and the forward routines (new) are returned as part of the TAF
285        output source code. Update genmake2 accordingly.
286      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
287        with version-2 when compared to TLM or FWD gradient); other experiments
288        output show minor changes (machine truncation level); update the few AD &
289        TLM output with 12 matching digits only (some prior to version-2 switch).
290    
291    checkpoint64l (2013/08/05)
292    o model/src:
293      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
294      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
295        when using TAF but only if using OpenAD.
296    o pkg/mom_common+fluxform+vecinv:
297      - always set horiz. viscosity arrays to background value before calling
298        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
299        only when using variable horiz. viscosity (useVariableVisc=T);
300      - simplify mom_vecinv.F (only 1 block for momViscosity).
301    o pkg/mom_common: variable horiz. viscosity in NH code
302      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
303        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
304      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
305        useBiharmonicVisc & useVariableVisc.
306      - fix old bug (already in 1rst implementation of variable horizontal viscosity
307        in calc_gw.F, version 1.27, 2006/06/20):
308        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
309        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
310      - change background horiz viscosity in vertical momentum (gW) to always be
311        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
312        any type of variable viscosity, e.g., viscAh/4Grid)
313      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
314        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
315        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
316        default viscAh,viscA4 is zero).
317    o model/src:
318      - extend length of drC & recip_drC from Nr to Nr+1.
319    o Divided Adjoint (DIVA) with MPI:
320      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
321      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
322        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
323    
324    checkpoint64k (2013/07/23)
325    o tools/OAD_support:
326      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
327        and remove it from genmake2.
328    o tools/build_options:
329      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
330        MPI_HEADER_FILES list (let genmake2 find the missing headers)
331    o verification/halfpipe_streamice:
332      - change to driving stress formulation; update both Fwd & AD output.
333    o tools/genmake2 and Divided Adjoint with MPI:
334      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
335      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
336      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
337        Makefile, which is set by genmake2, and check which mpi-headers are needed.
338        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
339      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
340    o testreport:
341      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
342        perform additional runs (number of additional runs is "add_DIVA_runs" taken
343        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
344    o verification/lab_sea (AD test):
345      - change to test Divided Adjoint Run in this set-up (both standard AD test
346        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
347    o pkg atm_ & ocn_compon_interf:
348      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
349        staggerTimeStep implementation) and disable (retired) corresponding
350        parameter.
351    o pkg/offline:
352      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
353      - add S/R OFFLINE_CHECK to print offline parameter summary
354        and stop if loading a file that is not used;
355      - enable to calculate GMRedi tensor, KPP mixing and convective index
356        when the corresponding file(s) is/are not specified (but pkg is used).
357      - comment out resetting of monitorFreq (to endTime) since it still useful
358        for monitoring CFL numbers and checking offline fields.
359    o OpenAD:
360      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
361        smaller standard output) and generate new (smaller) output (on baudelaire
362        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
363    o model/src:
364      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
365        (where external_forcing_adjust was called) and change list of arguments;
366      - merge external_forcing_adjust.F into external_forcing_surf.F
367      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
368        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
369        previously in file "balance_relax.F", now removed); remove corresponding
370        arrays in FFIELDS.h.
371      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
372        a hack for getting back surfaceForcingS (loaded from file) when using
373        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
374      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
375        (was getting only 11 digits for AD-grad, due to different truncation
376         error in AD code).
377    
378    checkpoint64j (2013/07/04)
379    o pkg/offline:
380      - to enable the use of other features with pkg offline (e.g., obcs),
381        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
382      - comment out "allowFreezing" (now active) in 2 offline testing exp.
383    o pkg/exf ALLOW_RUNOFTEMP
384      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
385      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
386      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
387    o pkg/atm_phys:
388      - allows to add some damping on uVel,vVel (strength only function of k).
389    o verification, ad-tests:
390      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
391        global_ocean_ebm and offline_exf_seaice.thsice.
392    o verification/halfpipe_streamice:
393      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
394        flux input boundary conditions to be ignored; a fix for this bug changed
395        verification results for forward test.
396      - add adjoint test.
397    o pkg/ptracers:
398      - allow to restart without SOM pickup (resetting SOM to zero).
399    o pkg/gmredi:
400      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
401      - It uses mixing length theory and suppression by steering level effects to
402        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
403        to JPO, for more details).
404      - It also uses the diffusivity to calculate an eddy induced streamfunction
405        based on a PV closure (rather than a buoyancy closure as in GM).
406      - New files added to pkg/gmredi:
407        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
408          induced overturning streamfunction (called from gmredi_calc_tensor)
409        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
410          for use in gmredi_k3d
411        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
412          the eddy diffusivity
413    
414    checkpoint64i (2013/06/18)
415    o pkg/cheapaml:
416      - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
417        that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
418        with pkg/cheapaml.
419    o utils/python: add subpackage for cubed sphere function, first example is
420        simple cs.pcol to plot 2D fields on a map
421    o pkg/streamice:
422      - This is a new package in MITgcm, which solves dynamic equations for ice
423         sheets and ice streams
424      - At the moment it is independent of atmosphere/ocean dynamics, or any
425        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
426        ed that this will change)
427      - There is a new verification exercise that tests it, halfpipe_streamice,
428        evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
429        rectangular embayment
430      - halfpipe_streamice is forward-only for now, will have TAF test soon
431      - for questions, email dgoldber@mit.edu
432    o pkg/thsice:
433      - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
434        of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
435      - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
436         call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
437      - allow precip from pkg/cheapaml to make snow over seaice.
438    o pkg/cfc:
439      - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
440      - remove atmos CFC 2-D arrays from common bloc (now local variables)
441      - change some hard-coded constant to run time parameter for reading and
442        and interpolating atmospheric CFC ; keep same default as previously.
443      - more flexible reading of Atmos CFC (number of records no longer hard-coded)
444      - put arguments in standard order: myTime, myIter, myThid
445      - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
446        atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
447      - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
448      - new routine to print summary of CFC params and check for consistency.
449    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
450      similar to thsice_advdiff.
451      Note that for the B-grid case the routine parameters uc/vc are overwritten.
452    o pkg/cfc:
453      - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
454        update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
455      - fix interpolation of atmphspheric CFC between Sorthern and Northern
456        hemisphere value.
457    o pkg/seaice:
458      - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
459    o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
460                  so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
461      - requires an additional time level that is stored in the pickup
462      - you can start with AB2 from a pickup without this time level with
463        pickupStrictlyMatch = .false.
464    
465    checkpoint64h (2013/05/26)
466    o pkg/cheapaml:
467      - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
468        affect machine truncation (but exp cheapAML_box still pass with 13 digits).
469      - consistent treatment of uWind,vWind location: assume everywhere in
470        pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
471        (Note: was already the case for Tair,Qair advection);
472        add option (INCONSISTENT_WIND_LOCATION) to recover old results.
473      - compute diabatic forcing only in the interior (excluding overlap regions)
474      - fill in array "Qsw" (for short-wave heating);
475      - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
476        before any update (consistent with MITgcm state var diagnostics);
477      - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
478        non periodic ; + adjusted for uWind,vWind (C-grid).
479    o pkg/seaice:
480      - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
481        add explicitly pkg/exf in experiments that currently use pkg/seaice.
482      - allows to compile pkg/seaice without pkg/exf.
483    o tools/OAD_support:
484      - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
485        of array "ourStepOf" in function rvNextAction (revolve.F90).
486    o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
487      - change pkg name (to be used with other atmospheric physics pkg)
488        but by-pass CVS when making the new pkg so that we keep the CVS history.
489    o pkg/offline:
490      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
491        (previously called from pkg/dic_surfforcing_init.F)
492    o model/src:
493      - re-order sequence of calls within packages_init_variables.F, using
494        standard order, except for:
495         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
496         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
497    o new pkg: atm_phys
498      - add entry point and source code (previously in contrib
499          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
500        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
501      - re-order sequence of calls within packages_readparms.F,
502         packages_init_fixed.F and packages_write_pickup.F
503        (but skip packages_init_variables.F because of TAF issues).
504      - update contrib/*/atm_gray/ experiment.
505    o pkg/seaice (ITD code):
506      - simplify and fix the writing of pickup-files for ITD case
507    o pkg/seaice (ITD code):
508      - introduce floe size dependent lateral melt for ITD case;
509      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
510      - update seaice_itd experiment main output.
511    o pkg/thsice:
512      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
513        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
514        changed accordingly pkg/atm2d.
515    
516    checkpoint64g (2013/05/01)
517    o pkg/exf ALLOW_RUNOFTEMP
518      - if defined,  river and glacier runoff temperature can be read-in from
519        runoftempfile; runoftempfile needs to have same format as runofffile
520    o pkg/thsice (& pkg/bulk_force):
521      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
522        for energy content of Precip + RunOff & Evap (like with pkg/exf).
523      - change computation domain to always be the interior (without overlap).
524      - fix bug (wrong overlap) when using EXF and stressReduction > 0.
525    o verification/tutorial_global_oce_biogeo:
526      - add preliminary OpenAD setup (still has problems)
527    o pkg/seaice:
528      - turn some parameters for choosing the convergence criterion of
529        the inexact Newton method (JFNK) into runtime parameters for convenience
530      - clean up seaice_calc_viscosities.F: remove/retire two options for
531        SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
532        the results of lab_sea/input because a division has been replaced by
533        a multiplication with the reciprocal (sumNorm)
534      - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
535        convergence of solver (changes results, of course), and to test some
536        new features
537    o model/src:
538      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
539      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
540      - move forcing adjustment (balancing surface forcing) in specific S/R
541        where might also be applied exchanges (if needed) to forcing arrays.
542    o pkg/shelfice:
543      - allow to specify the Ice-Shelf mass per unit area (instead of
544        shelficeLoadAnomaly) and do the conversion from one to the other
545      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
546        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
547        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
548        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
549      - update isomip experiment forward output (get machine truncation error
550        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
551    o verification/offline_exf_seaice:
552      revise data.seaice in input.thermo and input_ad and update results accordingly
553        HO = 0.2, SEAICE_areaLossFormula = 2,
554        SEAICE_growMeltByConv = .TRUE.,
555        SEAICE_doOpenWaterMelt = .TRUE.,
556      Improve consistency with input.thsice and fix the spurious 500m ice corners
557    o verification/global_ocean.cs32x15:
558      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
559        in icedyn (thsice+seaice-dyn) test and update output.
560    o verification/offline_exf_seaice:
561      - adjust list of tested variables (with testreport) and update
562        standard test output with better slection of monitored fields.
563    o pkg/cd_code:
564      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
565        experiment lab_sea.hb87
566    o tools/genmake2:
567      - change default makedepend from the system default to tools/xmakedepend:
568        When no makedepend is specified, select tools/xmakedepend it the test pass,
569        otherwise select the system default (if exist and pass the test) or
570        try to build cyrus-makedepend ; stop if none of the 3 works.
571    o pkg/exf & pkg/thsice:
572      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
573        for energy content of Precip + RunOff & Evap. Assumes:
574       1) Rain has same temp as Air.
575       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
576       3) Run-Off comes at the temp of surface water (with same Cp)
577       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
578        put directly into Latent Heat flux & should use water-vapor heat capacity.
579       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
580        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
581    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
582        (compile when SEAICE_ALLOW_JFNK is defined)
583    o pkg/thsice:
584      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
585        implementation): move THSICE_AVE call after the advection (called directly
586        from thsice_do_advect.F).
587    o verification/global_ocean.90x40x15 and OpenAD:
588      New experiment for OpenAD is identical to the one in input_ad except that
589        multiDimAdvection=.FALSE.,
590      There is still an issue with this.
591    o pkg/thsice:
592      - account for ice velocity (ocean relative velocity) in turbulent heat flux
593        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
594        and offline_exf_seaice (main test).
595    
596    checkpoint64f (2013/03/31)
597    o verification/OpenAD:
598      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
599    o verification/isomip, pkg/shelfice and OpenAD:
600      - add OpenAD setup to this exp and make shelfice package work with OpenAD
601    o verification/tutorial_global_oce_biogeo:
602      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
603    o verification/offline_exf_seaice:
604      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
605    o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
606      - add OpenAD setup to this exp and make ptracers package work with OpenAD
607    o pkg/seaice/seaice_evp.F:
608       mask the asymmetric contribution of the ice-ocean stress (when
609       the turningAngle is non-zero) over open water to avoid stripes
610       in the EVP-solutions after many EVP-substeps. This does not change
611       the verification experiment (because turningAngle=0 in that experiment),
612       but will affect other EVP solutions with turningAngle.ne.0
613    o verification, AD & TLM output:
614      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
615        additions and multiplications which affect results at machine truncation
616        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
617        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
618        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
619        digits of matching.
620    o pkg/seaice:
621       modify lsr-algorithm so that it vectorizes AND converges by using a
622       "zebra" method: split vector loop into two with step size 2; this
623       solves a general convergence problem for the JFNK solver on a vector
624       computer. It has the potential to even improve convergence for
625       non-vector machines, but it does change the results so it is turned
626       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
627       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
628    
629    checkpoint64e (2013/03/05)
630    o pkg/ecco and several verification experiments:
631       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
632       from ecco package, and revert to unified routine in model/src/
633       Adjust verification experiments accordingly, especially gloal_oce_llc90
634       Should conclude long-standing work by Gael to reconsile the_main_loop with
635       ECCO and will enable OpenAD's revolve loop in ECCO setup.
636    o pkg/generic_advdiff:
637      - implement compressible flow method for multi-dim advection (similar to
638        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
639        TAF generates many recomputations) to use it; no yet coded with implicit
640        vertical advection.
641      - change experiment advect_cs (new output) and advect_xy (same output)
642        to test compressible flow multi-dim advection.
643    o pkg/generic_advdiff:
644      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
645        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
646    o pkg/seaice:
647      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
648        bug affects two verification experiments (lab_sea and lab_sea.hb87),
649        recover old (wrong) results by setting noSlipFac = 2. in
650        seaice_calc_strainrates.F;
651      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
652      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
653        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
654      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
655    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
656      - new subroutines seaice_lsr_tridiagu/v
657      - introduce loop bounds i/jmin/max to be able to use a restricted
658        additive Schwarz method, but not used for now.
659      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
660      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
661    o OpenAD support
662       Reorganize S/R call for overall time-stepping loop to facilitate
663       OpenAD revolve loop replacement
664       (new S/R main_do_loop.F)
665    o model/src:
666      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
667      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
668        ADAMS_BASHFORTH2.
669    o pkg/cheapaml:
670      - add new parameter (default=F, same as before) to disable full domain
671        (including land) periodicity in X & Y dir.
672      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
673        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
674        into single S/R CHEAPAML_TIMESTEP.
675    
676    checkpoint64d (2013/02/17)
677    o pkg/monitor (angular momentum):
678      - do not add Eta contribution to the total AM if using rigid-lid;
679      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
680      - horizontal discretisation: compute Zonal wind contribution separately for
681        each component (instead of from cell centered averaged) and use the 4
682        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
683      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
684        FreeSurf) if using vectorInvariant momentum.
685    o model/src (horizontal grid):
686      - move initialisation of all horizontal grid arrays to null value
687        from specific horizontal grid S/R to main S/R INI_GRID;
688      - add 2 new arrays to project model C-grid velocity on to zonal direction
689        (similar to AngleCosC & -AngleSinC but at U and V point location) and
690        compute them in S/R CALC_GRID_ANGLES.
691    o pkg/seaice: replace a hard coded parameter by a runtime parameter
692        SEAICE_JFNK_tolIter
693    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
694        preconditioner for JFNK (run LSR into the overlaps as far as possible,
695        i.e OLx/y-2, but overwrite the solution in the overlaps)
696      - extend loop range in seaice_calc_viscosity
697      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
698      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
699      - slightly modify loops in tridiagonal solver lsr-preconditioner
700      - by default remove the extra exchange in seaice_preconditioner with a
701        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
702      - modify offline_exf_seaice so that old results without RAS are reproduced
703        for output.dyn_jfnk.txt
704      in seaice_fgmres.F (unrelated to RAS)
705      - add a cpp-flag option for a re-ordered mapping (potentially more
706        efficient), but because this changes the results, turn it off by
707        default
708      - replace the save statement by local common blocks
709    o utils/matlab:
710      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
711      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
712        instead of local script "load_cs.m".
713    o pkg/seaice:
714      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
715        to the scalarProductMetric and the unrolling. By chance this does not
716        change the verification experiment, because of the particular domain
717        decomposition
718    o pkg/diagnostics:
719      - change default missing_value from UNSET_RL to -999.
720    o pkg/layers: improve vectorization of layers_fluxcalc.F
721      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
722        time spent in this routine by more than a factor of 3 on an NEC-SX8
723      - step 2: replace search algorithm by a bisection algorithm found in
724        Press et al. Numerical Recipes in Fortran. This algorithm can be
725        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
726        For now, use this algorithm only for TARGET_NEC_SX defined.
727      - moved the search algorithm into a separate subroutine, that is kept
728        within the same file for automatic inlining.
729      - modified catching potential errors
730    o pkg/ecco:
731      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
732    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
733      - modifications for ALLOW_GENTIM2D_CONTROL
734      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
735      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
736      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
737      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
738    o model/src:
739      - account for moist thermodynamics in (dry) potential temperature equation;
740        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
741        and cpl_aim+ocn.
742      - also switch to standard compiler (gfortran, was using ifort previously)
743        for fizhi-cs experiments reference output.
744    o pkg/ctrl:
745      - 1st step toward generic time-varying control variable (2D) via CPP option
746        ALLOW_GENTIM2D_CONTROL
747      - note new namelist ctrl_nml_genarr in data.ctrl
748    o verification/global_ocean.cs32x15:
749      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
750        thsice calling sequence and update "output.icedyn.txt" output file.
751    o pkg/ptracers:
752      - from Ryan A.: code to allow to restart a tracer at regular time interval
753        specifying a reset frequency and a reset-phase (for each tracers).
754    o pkg/thsice:
755      - implement new sequence of calls for thsice+seaice:
756          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
757          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
758      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
759        in CPP_OPTIONS.h) to recover old sequence;
760      - update diagnostics for Intermediate State thsice diagnostics: now filled
761        just before advection (instead of just after advection in old sequence);
762      - update output of experiment offline_exf_seaice (standard test);
763      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
764        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
765    o pkg/aim_v23:
766      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
767      - use standard pkg/mdsio routines to read & write CO2 pickup file;
768      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
769      - Implement new sequence of calls for seaice advection (with thsice and
770        seaice diffusion): do ice advection after ice-Thermodynamic (previously
771        was done before); change aim_do_physics.F (split the bi,bj loops block);
772      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
773    o pkg/thsice:
774      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
775        where just seaice diffusion is used without seaice-dynamics.
776    
777    checkpoint64c (2013/01/18)
778    o pkg/seaice:
779      - add a parameter JFNKres_tFac that can replace JFNKres_t
780        (= JFNKres_tFac*JFNKresidual before JFNK solver)
781      - add a line search option to the JFNK solver
782      - move update of u/vIce and computation of initial residual into a separate
783        routine (same file); makes the code a little easier to read (?)
784      - the line search requires computation of the residual and for some reason
785        I cannot do the update of u/vIce at the beginning of the Newton loop
786        without changing the results, so we move computation of the new residual
787        also to the end of the Newton loop, even without the line search
788    o pkg/mdsio:
789      - write missing value (corresponding to undefined array value) to meta files;
790        skip this if missing value is one (UNSET_RL would be a better value for the
791        case of undefined missing value but it's current the default missing-value);
792        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
793    o pkg/exf & thsice:
794      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
795        diagnostics) even when SHORTWAVE_HEATING is #undef;
796    o verification/cfc_example:
797      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
798        illustrate how to use it).
799    o verification/offline_exf_seaice:
800      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
801        files to only one time-record.
802      in input.thermo: narrow the 2 bands of low initial ice-concentration near
803        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
804        snapshot output; same mcPheePiston value as in thsice with
805        surf-current=0.2m/s.
806      in input.thsice: similar set-up as in input.thermo (channel with same seaice
807        initial conditions).
808    o verification/cfc_example:
809      - update file "data" with more standard choice (default rotationPeriod,
810        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
811        set deltaTFreeSurf to deltaTtracer) and update the output.
812    o pkg/layers:
813      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
814      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
815    o verification/offline_exf_seaice:
816      - set all {field}period to zero for constant-in-time forcing (not tested
817        anywhere else).
818    o verification/offline_exf_seaice:
819      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
820      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
821    o model/src:
822      - implement Finite-Volume method for (hydrostatic) presure gradient
823        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
824    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
825      - In order to be compatible with the default EVP code, this requires changing
826        the EVP code around a little; and because any small change immediately
827        breaks the lab_sea.hb87 verification experiment, the reference output is
828        updated two times (each time the remaining aggrement was only 2 digits):
829        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
830        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
831        The adjoint test lab_sea.evp also needed to be updated.
832      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
833        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
834        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
835        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
836        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
837        kept obscure, because I need to test it a little more.
838    o pkg/cheapaml:
839      - fix few incorrect type (_RL/_RS) in subroutine calls.
840    o pkg/seaice:
841      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
842        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
843    o model/src:
844      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
845        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
846        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
847    o pkg/cheapaml:
848      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
849        update output of experiment cheapAML_box.
850      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
851        and set them only in one place (cheapaml_readparms.F).
852      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
853      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
854        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
855    o model/src/the_main_loop.F:
856      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
857    o pkg/seaice:
858      - remove legacy branch code.
859      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
860    o verification/*/code*/SEAICE_OPTIONS.h:
861      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
862        SEAICE_CAP_HEFF).
863    o pkg/cheapaml:
864      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
865        to load new forcing fields.
866      - add missing "_d 0" where it's needed; + some editing (improve indentation).
867      - remove switch to "-r8" compiler option (no longer needed) in verification
868        cheapAML_box, keep same output (small trucation error differences).
869    o verification/offline_exf_seaice:
870      - add thermodynamics only test.
871    o verification/cheapAML_box:
872      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
873        keep same output (same 14 digits for cg2d).
874      - switch on "-r8" compiler option (some numerical values are missing
875        the "_d 0") and update output (only 6 digits for cg2d were preserved).
876    
877    checkpoint64b (2012/12/24)
878    o pkg/cheapaml:
879      - remove un-used variables (Qnet,EmPmR) from pickup files.
880      - store tendency of advected variables into cheapaml pickup file
881        and fix the AB-2 restart.
882    o verification/offline_exf_seaice and lab_sea adjoint:
883      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
884      - switch to 4 time steps in offline, consistent with lab_sea.
885      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
886      - update results after change of experiment seaice.
887    o pkg/seaice:
888      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
889        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
890        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
891        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
892    o model/src:
893      - add run-time parameter to select CG2D solver minimum-residual solution
894        (in case of a poor convergence).
895    o pkg/seaice/seaice_lsr.F
896      - move calculation of matrix coefficients into new
897        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
898        file; the main purpose of this change is to be able to reuse the code
899        in S/R SEAICE_PRECONDITIONER
900      - modify the computation of the residual so that the mass of sea-ice
901        is not used twice; this simplifies the calculations, but since
902        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
903        not tested in testreport---this does not affect the testreport results.
904    o verification/seaice_obcs:
905      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
906        verification/lab_sea/input.salt_plume; changes results/output.txt*
907    o model/src:
908      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
909    o pkg/seaice:
910      - improve description of parameters in seaice_fgmres.F and start
911        cleaning up the code
912      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
913        second argument
914      - add a metric based on grid cell area to SEAICE_SCALPROD; update
915        results of offline_exf_seaice.dyn_jfnk
916      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
917    o pkg/aim_v23:
918      - fix an other bug in dissipation heating (grid-cell area was missing).
919    o model/src + pkg/seaice:
920      - add global (multi-tile) linear solver for pair of tri-diagonal system
921        along X and Y lines, respectively for U and V component.
922        Note: 1) MPI and cube-exchange not yet coded.
923            2) probably not accurate for poorly conditioned / large size problem.
924      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
925        default: not compiled and not used.
926    o pkg/seaice:
927      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
928        introduce bi/bj loops and use global_sum_tile_rl instead of
929        mpi_allreduce in seaice_fgmres.F
930      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
931      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
932      - add a verification experiment for JFNK in offline_exf_seaice
933    o verification:
934      - change (for now, only fwd test) offline_exf_seaice experiment:
935        use a re-entrant channel with idealized coastline (trapezoidal shape)
936        at southern boundary to explore seaice dynamics and thermodynamics
937        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
938        secondary test (input.thsice) use thermodynamics only with SST relaxation.
939      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
940    o pkg/exf:
941      - disable "sstExtrapol" when Nr=1
942    o verification:
943      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
944        to test pkg/cheapaml.
945    o pkg/aim_v23 & pkg/shap_filt:
946      - fix dissipation heating (erroneous gravity multiplication factor).
947    o pkg/seaice:
948      - remove unused field pressPre from jfnk solver
949      - rename two subroutines in seaice_preconditioner.F
950    o eesupp/src:
951       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
952    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
953       - remove wrong parts of the rhs and the lhs (were in there
954         because I did not understand the concept of this preconditioner)
955       - add an exchange between u- and v-sweep. This increases communication
956         by a factor of two but improves the convergence of jfnk. Ideally,
957         one would like the u- and v-sweep to be independent. So far within
958         undocumented ifdefs
959       - reorganize the extra computations for printing the residuals
960    o tools/genmake2:
961      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
962        since it's not necessary (and was preventing to use MNC in some cases).
963    
964    checkpoint64a (2012/11/16)
965    o pkg/autodiff:
966      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
967        autodiff_readparms.F no longer depends on calling order (within
968        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
969        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
970        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
971    o pkg/obcs:
972      - adding tidal velocity forcing capability to obcs
973        for usage example, see verification/seaice_obcs/input.tides
974    o pkg/seaice:
975      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
976        SEAICE_LSRrelaxU/V
977      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
978    o pkg/aim_v23:
979      - implement heating from friction (bottom friction and stratospheric drag).
980    o pkg/shap_filt:
981      - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
982        dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
983    o model/src:
984      - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
985        time-constant addMass field from file (addMassFile);
986      - support for heating due to friction (and Kinetic Energy dissipation):
987        add option, run-time switch and 3-D field array + support code ; each pkg
988        or S/R can add heating contribution (if there is a sink of KE); the sum is
989        accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
990    o pkg/seaice:
991      - complete merge of ITD code into seaice_growth.F
992        from MITgcm_contrib/torge/itd/code/
993        no verification so far, but Torge Martin tested
994        "1-D test case and Beaufort set up;
995        deliver okay results after 1 model year."
996      - complete merge of SEAICE_SIZE.h into all relevant routines
997      - move computation of eta at Z-points into calc_viscosities
998        + introduce global field etaZ
999        + add different methods for computing etaZ, for now the old
1000          method (simple averages of eta to Z-points) is hardwired
1001        + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
1002          seaice_preconditioner
1003      - simplify computations for SEAICE_ZETA_SMOOTHREG
1004      - seaice_preconditioner:
1005        + replace one remaining press by pressLoc (mistake)
1006        + adjust printing of residuals
1007      - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
1008        + add (SEAICE.h) and rename some counters (initiliased in
1009          seaice_init_fixed.F)
1010        + add _BEGIN/END_MASTER (myThid)  around print statements
1011        + print total number of iterations and failures over SEAICE_monFreq
1012          interval to STDOUT
1013      - move control over output-messages by fgmres to seaice_jfnk to save
1014        some operations
1015      - move resetting initial guess for fgmres outside of seaice_fgmres_driver
1016        in order to make restarts with sol .ne. zero (fgmres with restarts)
1017        (seaice_jfnk.F, seaice_fgmres.F)
1018      - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
1019        a serious convergence problem when open boundaries are involved
1020    o pkg/ggl90: fix computation of control volumes for the case of
1021      ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
1022      up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
1023    o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
1024    o pkg/autodiff
1025      - Add inAdMode switch for SEAICEuseDYNAMICS:
1026        SEAICEuseDYNAMICSinAdMode
1027        (extend logic in ADAUTODIFF_INADMODE_SET)
1028    o pkg/seaice
1029      - Step 1 of merging ice-thickness distribution (ITD) code from
1030        MITgcm_contrib/torge/itd/ (author: Torge Martin)
1031        The code implements concept laid out in Thorndike et al. (1975);
1032        code is enabled via CPP flag SEAICE_ITD
1033        nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
1034        code is not complete yet!!
1035      - SEAICE_SIZE.h now included in almost all seaice routines
1036    o verification (using seaice):
1037      - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
1038        global_ocean.cs32x15.seaice ; update results.
1039      - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
1040      - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
1041        offline_exf_seaice (previously compiling B-grid).
1042    o pkg/exf:
1043      - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
1044        to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
1045        forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
1046  o pkg/layers (adjust changes from Sept 19):  o pkg/layers (adjust changes from Sept 19):
1047    - 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)
1048      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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