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revision 1.1768 by mlosch, Wed Nov 14 16:43:38 2012 UTC revision 1.1961 by heimbach, Thu Jan 30 21:07:20 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/thsice
8      - corrected store directive fixes thsice adjoint gradient checks
9    o genmake2 & testreport:
10      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
11        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
12        Update testreport accordingly. No need to set "export OPENAD=true"
13        in adjoint_options/adjoint_oad anymore (will be removed later).
14    o pkg/shelfice:
15      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
16        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
17        so that surface forcing applies to k=kSurf if using pkg/shelfice.
18    o pkg/ctrl, pkg/grdchk, pkg/ecco:
19      - Changes to make GENARR more modular (i.e. invisible if not used)
20    o model/src/temp_integrate.F and salt_integrate.F
21      - re-include store directives that were removed on Dec 27th.
22    o model/src/external_forcing_surf.F
23      - add storage directives for EmPmR and PmEpR to avoid recomputation of
24        seaice_model in the adjoint that is problematic when seaice_model is
25        turned off in the adjoint. The resolved issue dated back to July when
26        EXTERNAL_FORCING_SURF call was moved.
27        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
28    o pkg/exf/exf_check.F
29      - fix a small bug again (originally found by Wentao Liu, now found again)
30      - streamline error output
31    o pkg/streamice and aim_v23:
32      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
33        Apple's /usr/bin/cpp knows what to do:
34        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
35        Target: x86_64-apple-darwin13.0.0
36    
37    checkpoint64s (2014/01/05)
38    o tools/adjoint_options:
39      - switch to fastopt.net TAF server (instead of default fastopt.de) for
40        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
41    o model/src:
42      - remove some unnecessary TAF storage directives in forward_step.F and
43        in dynamics.F (note: not always removed by TAF, e.g., double storage
44        of kappaRU,kappaRV in former version of dynamics.F).
45    o model/src & pkg/ptracers:
46      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
47        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
48        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
49      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
50      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
51      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
52    o useSingleCpuInput separates single-CPU input from single-CPU output;
53        for now only implemented for in exf_interp_read.F
54    o verification/advect_xy:
55      - fix missing EXCH call in local version of ini_salt.F and update output.
56    o momentum diagnostics:
57      - fix which deltaT is used in Total-Tendency diagnostics.
58      - fix typo in diagnostics for momentum tendency from AB.
59    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
60        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
61    
62    checkpoint64r (2013/12/08)
63    o verification/*/results:
64      - Update reference output of experiments that were passing with just 13 digits
65         (make it easier to detect future changes in results)
66    o model/src & pkg/ptracers:
67      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
68        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
69        to inside ptracers_integrate.F ; remove ptracers_advection.F
70    o coupling interface pkgs:
71        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
72      - change the config check to test the agreement of Ocean Depth
73        with ATM land/sea mask (instead of ATM orography);
74      - send to coupler the number of coupler time-steps to do for this run:
75        this allows to check for consistency and don't need anymore to be
76        specified in parameter file "data";
77      in coupler:
78      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
79      - improve report to log-file of config setting (pass log-file unit to few S/R)
80    o pkg/compon_communic:
81      - add coupling send/receive for non-tiled integer vector;
82      - add S/R to check and stop if any proc has an error (similar to
83        eesupp/src/stop_if_error.F but single thread and across Comm_World).
84    o pkg/exch2:
85      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
86        through list of all tiles my proc owns.
87    o model/src:
88      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
89        from rTrans) to simplify dependencies (no need to store rTrans anymore in
90        calling S/R); this affects AD results at machine truncation level:
91        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
92        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
93    o tools/build_options:
94      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
95    o coupling interface pkgs:
96        [compon_communic, atm_compon_interf & ocn_compon_interf]
97      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
98        to each S/R that needs it; remove un-used variables.
99      - change component tile registration (cpl_register.F in both compon_interf
100        and mitcomponent_tile_register.F) to pass the full list of tiles
101        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
102      - with pkg/exch2: adopt the same convention used for I/O to define mapping
103        towards coupler global array (unless W2_useE2ioLayOut=F):
104         a) can now use different tiling between atm & ocn comp.
105         b) no needs to modify the run-Off map when changing tiling (was needed
106            even if using the same tiling between atm & ocn).
107         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
108            full land tiles); not yet tested.
109      - check for valid mapping from comp. tile to coupler global array
110      - improve report of tile registration results to log file.
111    o pkg/exch2:
112      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
113        tile-registration (CPL_REGISTER);
114      - activate (un-comment) definition and setting of "W2_tileIndex" list to
115        store the local bi,bj indices of each tile;
116      - also print bi,bj in local report to log file;
117      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
118        Jun 2009 modif of pkg/exch2).
119    o testing on baudelaire:
120      - run 2 tests at a time: no significant slow down (since enough cpu) and
121        get the full set of test done earlier
122      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
123    o model/src/thermodynamics.F and routines called from it:
124      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
125        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
126        velocity (outp) by adding bolus velocity.
127      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
128        mass transport from velocity + lateral grid cell area
129      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
130      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
131     in thermodynamics.F
132      - remove k from thermodynamics.F and move it to temp_integrate.F
133        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
134        loop).
135      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
136        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
137        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
138        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
139      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
140        global_ocean.90x40x15, tutorial_global_oce_biogeo and
141        tutorial_tracer_adjsens (+ TLM output).
142    o tools/OAD_support and (verification/*/) code_oad:
143      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
144        module conversion ; remove unneeded CPP_EEOPTIONS.h.
145      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
146        version (closer to model/inc/CPP_OPTIONS.h).
147    o model/src:
148      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
149        retired list of parameters (routine FREEZE has been replace by surface
150        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
151    o pkg/gmredi:
152      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
153        velocity (same scheme but affects machine truncation) for GM_AdvForm.
154      - update output of FWD experiments: front_relax.bvp,
155        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
156    
157    checkpoint64q (2013/11/17)
158    o verification:
159      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
160        tutorial_global_oce_biogeo and global_ocean.90x40x15.
161      - generate new output (growth & melt) for seaice_itd experiment after
162        updating the input pickup_seaice files (previously wrong).
163    o pkg/cost:
164      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
165        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
166        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
167          cannot be applied to var in common block).
168        o allows to get results independent of tile-per-proc setting (if using
169          slower GLOBAL_SUM_SEND_RECV option).
170      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
171        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
172        forward gradients: update output).
173      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
174        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
175    o pkg/mom_common:
176      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
177        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
178        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
179        ensure that all field value that are used are set.
180    o tutorial_deep_convection (smag3d):
181      - add missing scaling in mom_calc_smag_3d.F;
182      - set smag3D_coeff in input.smag3d such that results do not change.
183    o pkg/dic:
184      - change dic_cost.F to compute cost on each tile first and then apply
185        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
186        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
187      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
188    o eesupp/src & pkg/mdsio:
189      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
190        (from pkg/mdsio) since they are no longer used for tape IO.
191      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
192        (+ keep a copy in pkg/atm_ocn_coupler).
193    o verification/isomip:
194      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
195    o tools/build_options:
196      - optfile linux_amd64_ifort11, fast (no ieee) case:
197        to get a working restart for all experiments, add "-fp-model source"
198        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
199    
200    checkpoint64p (2013/10/20)
201    o pkg/autodiff:
202      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
203        criteria, return to simple (default) tape IO format.
204    o pkg/mdsio (+ eesupp/src):
205      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
206        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
207      - fix globalFile and singleCpuIO options using simpler global mapping.
208      - new pairs of scatter/gather vector S/R (one for each type, generated from
209        template) corresponding to simpler global mapping.
210      - adread_write.F: switch to new S/R (but leave old calls commented) and write
211        to globalFile when parameter globalFiles is set to True.
212      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
213    o pkg/autodiff:
214      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
215        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
216        missing, just add a STOP if array type do not match.
217    o pkg/exf:
218      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
219         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
220         and rename array obsSIce to exf_iceFraction.
221    o tutorial_deep_convection:
222      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
223        for now all in this exp. code dir.
224      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
225        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
226    o eesupp/src:
227      - added SINGLE_DISK_IO option because reading of parameter files on
228        very large number of processors did not work with existing set-up
229    
230    checkpoint64o (2013/09/25)
231    o pkg/atm_phys & atm_compon_interf:
232      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
233    o tools/build_options:
234      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
235        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
236        remove CPP setting (was identical to genmake2 default).
237    o pkg/gmredi & model/src: Some updating and work done on the residual model.
238      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
239      - fixed up the calculation of the eddy stress and how it is added to the
240        external forcing via taueddy_external_forcing.F
241      - at the moment, it is very experimental and only works with the variable eddy
242        diffusivity calculated in gmredi_k3d.F
243    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
244        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
245    o testreport (& tools/do_tst_2+2):
246      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
247    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
248      - remove CPP='cpp -traditional -P' (this is genmake2 default)
249      - add switch (for big setups) to use 'medium' memory-model (but leave it
250        commented out for now). Note: needed with FC 19 to compile big setups.
251    o pkg/atm_compon_interf:
252      - regroup per field origin (model & pkgs) the coupling storage routines
253         (which accumalate in time each coupling field)
254      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
255        update accordingly + simplify aim_do_physics.F
256    
257    checkpoint64n (2013/08/26)
258    o pkg/bbl:
259      - update formulation to reduce dispersion of tracer properties in bbl
260      - replaced horizontal and vertical transport parameters with velocities
261      - changes results for verification/global_with_exf.yearly
262    o verification/halfpipe_streamice:
263      - change to matrix construction; update both Fwd & AD output.
264    o verification/tutorial_tracer_adjsens:
265      - OpenAD test: switch to vector-invariant momentum since fluxform with
266        rStar causes problems with OpenAD; update output.
267    o tools:
268      - genmake2: define a common prefix for all temp-file names ; move them
269        to local /tmp disk (but would be easy to move them back);
270      - xmakedepend: apply the same switch for temp-files.
271    o pkg/offline:
272      - changes for use with rStar (NLFS): assume that we continue to provide
273        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
274        output files) and apply r* scaling at each time-step (function of the time
275        varying Eta field); use normal pickup files (needed for restart with NLFS).
276    o adjoint with OpenAD:
277      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
278        package openad.  This package has to be compiled for all runs with OpenAD
279        instead of specifying code_oad_all as a modification directory.
280      - link the fortran templates from tools/OAD_support to the build directory
281        for preprocessing to avoid conflicts between different setups compiled
282        simultaneously and simplify cleanup.
283    o pkg/exf:
284      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
285        main model or other pkgs are exchanged in EXF_MAPFIELDS).
286    o model/src:
287      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
288        (similar to do_fields_blocking_exchanges.F).
289    o tools/genmake2:
290      - remove TAF output src code just before calling staf (when not doing a fresh
291        built, will stop if things go wrong with staf).
292      - fix target "adobj" (left from TAF version-2 transition)
293    o pkg/diagnostics:
294      - add a parameter to track the status of pkg/diagnostics activation;
295        this replace/extend the use of logical param "settingDiags" (to check
296        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
297        New S/R to print error message and stop when pkgStatus is not right.
298      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
299    
300    checkpoint64m (2013/08/13)
301    o model/inc:
302      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
303        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
304    o pkg/kpp & aim_v23:
305      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
306    o pkg/seaice:
307      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
308        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
309      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
310    o eesupp/src:
311      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
312        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
313    o switch to TAF version-2:
314      - add flow directives to "freeze" naming convention for ad-routines that
315        are used in I/O routines of adjoint state and associated common blocks
316        that are used in adcommon.h (backward compatible with version-1)
317      - update all ad-optfiles (in tools/adjoint_options + few local to some
318        verification exp) to switch to latest TAF version (currently 2.5.5);
319        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
320        out except for diva).
321      - the major change with TAF version-2 is that both the differentiated
322        routines and the forward routines (new) are returned as part of the TAF
323        output source code. Update genmake2 accordingly.
324      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
325        with version-2 when compared to TLM or FWD gradient); other experiments
326        output show minor changes (machine truncation level); update the few AD &
327        TLM output with 12 matching digits only (some prior to version-2 switch).
328    
329    checkpoint64l (2013/08/05)
330    o model/src:
331      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
332      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
333        when using TAF but only if using OpenAD.
334    o pkg/mom_common+fluxform+vecinv:
335      - always set horiz. viscosity arrays to background value before calling
336        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
337        only when using variable horiz. viscosity (useVariableVisc=T);
338      - simplify mom_vecinv.F (only 1 block for momViscosity).
339    o pkg/mom_common: variable horiz. viscosity in NH code
340      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
341        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
342      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
343        useBiharmonicVisc & useVariableVisc.
344      - fix old bug (already in 1rst implementation of variable horizontal viscosity
345        in calc_gw.F, version 1.27, 2006/06/20):
346        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
347        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
348      - change background horiz viscosity in vertical momentum (gW) to always be
349        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
350        any type of variable viscosity, e.g., viscAh/4Grid)
351      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
352        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
353        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
354        default viscAh,viscA4 is zero).
355    o model/src:
356      - extend length of drC & recip_drC from Nr to Nr+1.
357    o Divided Adjoint (DIVA) with MPI:
358      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
359      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
360        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
361    
362    checkpoint64k (2013/07/23)
363    o tools/OAD_support:
364      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
365        and remove it from genmake2.
366    o tools/build_options:
367      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
368        MPI_HEADER_FILES list (let genmake2 find the missing headers)
369    o verification/halfpipe_streamice:
370      - change to driving stress formulation; update both Fwd & AD output.
371    o tools/genmake2 and Divided Adjoint with MPI:
372      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
373      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
374      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
375        Makefile, which is set by genmake2, and check which mpi-headers are needed.
376        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
377      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
378    o testreport:
379      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
380        perform additional runs (number of additional runs is "add_DIVA_runs" taken
381        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
382    o verification/lab_sea (AD test):
383      - change to test Divided Adjoint Run in this set-up (both standard AD test
384        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
385    o pkg atm_ & ocn_compon_interf:
386      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
387        staggerTimeStep implementation) and disable (retired) corresponding
388        parameter.
389    o pkg/offline:
390      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
391      - add S/R OFFLINE_CHECK to print offline parameter summary
392        and stop if loading a file that is not used;
393      - enable to calculate GMRedi tensor, KPP mixing and convective index
394        when the corresponding file(s) is/are not specified (but pkg is used).
395      - comment out resetting of monitorFreq (to endTime) since it still useful
396        for monitoring CFL numbers and checking offline fields.
397    o OpenAD:
398      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
399        smaller standard output) and generate new (smaller) output (on baudelaire
400        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
401    o model/src:
402      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
403        (where external_forcing_adjust was called) and change list of arguments;
404      - merge external_forcing_adjust.F into external_forcing_surf.F
405      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
406        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
407        previously in file "balance_relax.F", now removed); remove corresponding
408        arrays in FFIELDS.h.
409      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
410        a hack for getting back surfaceForcingS (loaded from file) when using
411        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
412      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
413        (was getting only 11 digits for AD-grad, due to different truncation
414         error in AD code).
415    
416    checkpoint64j (2013/07/04)
417    o pkg/offline:
418      - to enable the use of other features with pkg offline (e.g., obcs),
419        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
420      - comment out "allowFreezing" (now active) in 2 offline testing exp.
421    o pkg/exf ALLOW_RUNOFTEMP
422      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
423      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
424      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
425    o pkg/atm_phys:
426      - allows to add some damping on uVel,vVel (strength only function of k).
427    o verification, ad-tests:
428      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
429        global_ocean_ebm and offline_exf_seaice.thsice.
430    o verification/halfpipe_streamice:
431      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
432        flux input boundary conditions to be ignored; a fix for this bug changed
433        verification results for forward test.
434      - add adjoint test.
435    o pkg/ptracers:
436      - allow to restart without SOM pickup (resetting SOM to zero).
437    o pkg/gmredi:
438      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
439      - It uses mixing length theory and suppression by steering level effects to
440        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
441        to JPO, for more details).
442      - It also uses the diffusivity to calculate an eddy induced streamfunction
443        based on a PV closure (rather than a buoyancy closure as in GM).
444      - New files added to pkg/gmredi:
445        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
446          induced overturning streamfunction (called from gmredi_calc_tensor)
447        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
448          for use in gmredi_k3d
449        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
450          the eddy diffusivity
451    
452    checkpoint64i (2013/06/18)
453    o pkg/cheapaml:
454      - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
455        that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
456        with pkg/cheapaml.
457    o utils/python: add subpackage for cubed sphere function, first example is
458        simple cs.pcol to plot 2D fields on a map
459    o pkg/streamice:
460      - This is a new package in MITgcm, which solves dynamic equations for ice
461         sheets and ice streams
462      - At the moment it is independent of atmosphere/ocean dynamics, or any
463        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
464        ed that this will change)
465      - There is a new verification exercise that tests it, halfpipe_streamice,
466        evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
467        rectangular embayment
468      - halfpipe_streamice is forward-only for now, will have TAF test soon
469      - for questions, email dgoldber@mit.edu
470    o pkg/thsice:
471      - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
472        of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
473      - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
474         call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
475      - allow precip from pkg/cheapaml to make snow over seaice.
476    o pkg/cfc:
477      - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
478      - remove atmos CFC 2-D arrays from common bloc (now local variables)
479      - change some hard-coded constant to run time parameter for reading and
480        and interpolating atmospheric CFC ; keep same default as previously.
481      - more flexible reading of Atmos CFC (number of records no longer hard-coded)
482      - put arguments in standard order: myTime, myIter, myThid
483      - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
484        atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
485      - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
486      - new routine to print summary of CFC params and check for consistency.
487    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
488      similar to thsice_advdiff.
489      Note that for the B-grid case the routine parameters uc/vc are overwritten.
490    o pkg/cfc:
491      - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
492        update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
493      - fix interpolation of atmphspheric CFC between Sorthern and Northern
494        hemisphere value.
495    o pkg/seaice:
496      - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
497    o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
498                  so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
499      - requires an additional time level that is stored in the pickup
500      - you can start with AB2 from a pickup without this time level with
501        pickupStrictlyMatch = .false.
502    
503    checkpoint64h (2013/05/26)
504    o pkg/cheapaml:
505      - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
506        affect machine truncation (but exp cheapAML_box still pass with 13 digits).
507      - consistent treatment of uWind,vWind location: assume everywhere in
508        pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
509        (Note: was already the case for Tair,Qair advection);
510        add option (INCONSISTENT_WIND_LOCATION) to recover old results.
511      - compute diabatic forcing only in the interior (excluding overlap regions)
512      - fill in array "Qsw" (for short-wave heating);
513      - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
514        before any update (consistent with MITgcm state var diagnostics);
515      - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
516        non periodic ; + adjusted for uWind,vWind (C-grid).
517    o pkg/seaice:
518      - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
519        add explicitly pkg/exf in experiments that currently use pkg/seaice.
520      - allows to compile pkg/seaice without pkg/exf.
521    o tools/OAD_support:
522      - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
523        of array "ourStepOf" in function rvNextAction (revolve.F90).
524    o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
525      - change pkg name (to be used with other atmospheric physics pkg)
526        but by-pass CVS when making the new pkg so that we keep the CVS history.
527    o pkg/offline:
528      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
529        (previously called from pkg/dic_surfforcing_init.F)
530    o model/src:
531      - re-order sequence of calls within packages_init_variables.F, using
532        standard order, except for:
533         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
534         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
535    o new pkg: atm_phys
536      - add entry point and source code (previously in contrib
537          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
538        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
539      - re-order sequence of calls within packages_readparms.F,
540         packages_init_fixed.F and packages_write_pickup.F
541        (but skip packages_init_variables.F because of TAF issues).
542      - update contrib/*/atm_gray/ experiment.
543    o pkg/seaice (ITD code):
544      - simplify and fix the writing of pickup-files for ITD case
545    o pkg/seaice (ITD code):
546      - introduce floe size dependent lateral melt for ITD case;
547      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
548      - update seaice_itd experiment main output.
549    o pkg/thsice:
550      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
551        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
552        changed accordingly pkg/atm2d.
553    
554    checkpoint64g (2013/05/01)
555    o pkg/exf ALLOW_RUNOFTEMP
556      - if defined,  river and glacier runoff temperature can be read-in from
557        runoftempfile; runoftempfile needs to have same format as runofffile
558    o pkg/thsice (& pkg/bulk_force):
559      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
560        for energy content of Precip + RunOff & Evap (like with pkg/exf).
561      - change computation domain to always be the interior (without overlap).
562      - fix bug (wrong overlap) when using EXF and stressReduction > 0.
563    o verification/tutorial_global_oce_biogeo:
564      - add preliminary OpenAD setup (still has problems)
565    o pkg/seaice:
566      - turn some parameters for choosing the convergence criterion of
567        the inexact Newton method (JFNK) into runtime parameters for convenience
568      - clean up seaice_calc_viscosities.F: remove/retire two options for
569        SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
570        the results of lab_sea/input because a division has been replaced by
571        a multiplication with the reciprocal (sumNorm)
572      - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
573        convergence of solver (changes results, of course), and to test some
574        new features
575    o model/src:
576      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
577      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
578      - move forcing adjustment (balancing surface forcing) in specific S/R
579        where might also be applied exchanges (if needed) to forcing arrays.
580    o pkg/shelfice:
581      - allow to specify the Ice-Shelf mass per unit area (instead of
582        shelficeLoadAnomaly) and do the conversion from one to the other
583      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
584        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
585        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
586        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
587      - update isomip experiment forward output (get machine truncation error
588        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
589    o verification/offline_exf_seaice:
590      revise data.seaice in input.thermo and input_ad and update results accordingly
591        HO = 0.2, SEAICE_areaLossFormula = 2,
592        SEAICE_growMeltByConv = .TRUE.,
593        SEAICE_doOpenWaterMelt = .TRUE.,
594      Improve consistency with input.thsice and fix the spurious 500m ice corners
595    o verification/global_ocean.cs32x15:
596      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
597        in icedyn (thsice+seaice-dyn) test and update output.
598    o verification/offline_exf_seaice:
599      - adjust list of tested variables (with testreport) and update
600        standard test output with better slection of monitored fields.
601    o pkg/cd_code:
602      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
603        experiment lab_sea.hb87
604    o tools/genmake2:
605      - change default makedepend from the system default to tools/xmakedepend:
606        When no makedepend is specified, select tools/xmakedepend it the test pass,
607        otherwise select the system default (if exist and pass the test) or
608        try to build cyrus-makedepend ; stop if none of the 3 works.
609    o pkg/exf & pkg/thsice:
610      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
611        for energy content of Precip + RunOff & Evap. Assumes:
612       1) Rain has same temp as Air.
613       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
614       3) Run-Off comes at the temp of surface water (with same Cp)
615       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
616        put directly into Latent Heat flux & should use water-vapor heat capacity.
617       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
618        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
619    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
620        (compile when SEAICE_ALLOW_JFNK is defined)
621    o pkg/thsice:
622      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
623        implementation): move THSICE_AVE call after the advection (called directly
624        from thsice_do_advect.F).
625    o verification/global_ocean.90x40x15 and OpenAD:
626      New experiment for OpenAD is identical to the one in input_ad except that
627        multiDimAdvection=.FALSE.,
628      There is still an issue with this.
629    o pkg/thsice:
630      - account for ice velocity (ocean relative velocity) in turbulent heat flux
631        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
632        and offline_exf_seaice (main test).
633    
634    checkpoint64f (2013/03/31)
635    o verification/OpenAD:
636      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
637    o verification/isomip, pkg/shelfice and OpenAD:
638      - add OpenAD setup to this exp and make shelfice package work with OpenAD
639    o verification/tutorial_global_oce_biogeo:
640      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
641    o verification/offline_exf_seaice:
642      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
643    o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
644      - add OpenAD setup to this exp and make ptracers package work with OpenAD
645    o pkg/seaice/seaice_evp.F:
646       mask the asymmetric contribution of the ice-ocean stress (when
647       the turningAngle is non-zero) over open water to avoid stripes
648       in the EVP-solutions after many EVP-substeps. This does not change
649       the verification experiment (because turningAngle=0 in that experiment),
650       but will affect other EVP solutions with turningAngle.ne.0
651    o verification, AD & TLM output:
652      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
653        additions and multiplications which affect results at machine truncation
654        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
655        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
656        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
657        digits of matching.
658    o pkg/seaice:
659       modify lsr-algorithm so that it vectorizes AND converges by using a
660       "zebra" method: split vector loop into two with step size 2; this
661       solves a general convergence problem for the JFNK solver on a vector
662       computer. It has the potential to even improve convergence for
663       non-vector machines, but it does change the results so it is turned
664       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
665       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
666    
667    checkpoint64e (2013/03/05)
668    o pkg/ecco and several verification experiments:
669       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
670       from ecco package, and revert to unified routine in model/src/
671       Adjust verification experiments accordingly, especially gloal_oce_llc90
672       Should conclude long-standing work by Gael to reconsile the_main_loop with
673       ECCO and will enable OpenAD's revolve loop in ECCO setup.
674    o pkg/generic_advdiff:
675      - implement compressible flow method for multi-dim advection (similar to
676        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
677        TAF generates many recomputations) to use it; no yet coded with implicit
678        vertical advection.
679      - change experiment advect_cs (new output) and advect_xy (same output)
680        to test compressible flow multi-dim advection.
681    o pkg/generic_advdiff:
682      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
683        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
684    o pkg/seaice:
685      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
686        bug affects two verification experiments (lab_sea and lab_sea.hb87),
687        recover old (wrong) results by setting noSlipFac = 2. in
688        seaice_calc_strainrates.F;
689      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
690      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
691        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
692      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
693    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
694      - new subroutines seaice_lsr_tridiagu/v
695      - introduce loop bounds i/jmin/max to be able to use a restricted
696        additive Schwarz method, but not used for now.
697      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
698      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
699    o OpenAD support
700       Reorganize S/R call for overall time-stepping loop to facilitate
701       OpenAD revolve loop replacement
702       (new S/R main_do_loop.F)
703    o model/src:
704      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
705      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
706        ADAMS_BASHFORTH2.
707    o pkg/cheapaml:
708      - add new parameter (default=F, same as before) to disable full domain
709        (including land) periodicity in X & Y dir.
710      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
711        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
712        into single S/R CHEAPAML_TIMESTEP.
713    
714    checkpoint64d (2013/02/17)
715    o pkg/monitor (angular momentum):
716      - do not add Eta contribution to the total AM if using rigid-lid;
717      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
718      - horizontal discretisation: compute Zonal wind contribution separately for
719        each component (instead of from cell centered averaged) and use the 4
720        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
721      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
722        FreeSurf) if using vectorInvariant momentum.
723    o model/src (horizontal grid):
724      - move initialisation of all horizontal grid arrays to null value
725        from specific horizontal grid S/R to main S/R INI_GRID;
726      - add 2 new arrays to project model C-grid velocity on to zonal direction
727        (similar to AngleCosC & -AngleSinC but at U and V point location) and
728        compute them in S/R CALC_GRID_ANGLES.
729    o pkg/seaice: replace a hard coded parameter by a runtime parameter
730        SEAICE_JFNK_tolIter
731    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
732        preconditioner for JFNK (run LSR into the overlaps as far as possible,
733        i.e OLx/y-2, but overwrite the solution in the overlaps)
734      - extend loop range in seaice_calc_viscosity
735      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
736      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
737      - slightly modify loops in tridiagonal solver lsr-preconditioner
738      - by default remove the extra exchange in seaice_preconditioner with a
739        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
740      - modify offline_exf_seaice so that old results without RAS are reproduced
741        for output.dyn_jfnk.txt
742      in seaice_fgmres.F (unrelated to RAS)
743      - add a cpp-flag option for a re-ordered mapping (potentially more
744        efficient), but because this changes the results, turn it off by
745        default
746      - replace the save statement by local common blocks
747    o utils/matlab:
748      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
749      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
750        instead of local script "load_cs.m".
751    o pkg/seaice:
752      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
753        to the scalarProductMetric and the unrolling. By chance this does not
754        change the verification experiment, because of the particular domain
755        decomposition
756    o pkg/diagnostics:
757      - change default missing_value from UNSET_RL to -999.
758    o pkg/layers: improve vectorization of layers_fluxcalc.F
759      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
760        time spent in this routine by more than a factor of 3 on an NEC-SX8
761      - step 2: replace search algorithm by a bisection algorithm found in
762        Press et al. Numerical Recipes in Fortran. This algorithm can be
763        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
764        For now, use this algorithm only for TARGET_NEC_SX defined.
765      - moved the search algorithm into a separate subroutine, that is kept
766        within the same file for automatic inlining.
767      - modified catching potential errors
768    o pkg/ecco:
769      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
770    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
771      - modifications for ALLOW_GENTIM2D_CONTROL
772      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
773      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
774      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
775      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
776    o model/src:
777      - account for moist thermodynamics in (dry) potential temperature equation;
778        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
779        and cpl_aim+ocn.
780      - also switch to standard compiler (gfortran, was using ifort previously)
781        for fizhi-cs experiments reference output.
782    o pkg/ctrl:
783      - 1st step toward generic time-varying control variable (2D) via CPP option
784        ALLOW_GENTIM2D_CONTROL
785      - note new namelist ctrl_nml_genarr in data.ctrl
786    o verification/global_ocean.cs32x15:
787      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
788        thsice calling sequence and update "output.icedyn.txt" output file.
789    o pkg/ptracers:
790      - from Ryan A.: code to allow to restart a tracer at regular time interval
791        specifying a reset frequency and a reset-phase (for each tracers).
792    o pkg/thsice:
793      - implement new sequence of calls for thsice+seaice:
794          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
795          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
796      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
797        in CPP_OPTIONS.h) to recover old sequence;
798      - update diagnostics for Intermediate State thsice diagnostics: now filled
799        just before advection (instead of just after advection in old sequence);
800      - update output of experiment offline_exf_seaice (standard test);
801      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
802        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
803    o pkg/aim_v23:
804      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
805      - use standard pkg/mdsio routines to read & write CO2 pickup file;
806      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
807      - Implement new sequence of calls for seaice advection (with thsice and
808        seaice diffusion): do ice advection after ice-Thermodynamic (previously
809        was done before); change aim_do_physics.F (split the bi,bj loops block);
810      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
811    o pkg/thsice:
812      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
813        where just seaice diffusion is used without seaice-dynamics.
814    
815    checkpoint64c (2013/01/18)
816    o pkg/seaice:
817      - add a parameter JFNKres_tFac that can replace JFNKres_t
818        (= JFNKres_tFac*JFNKresidual before JFNK solver)
819      - add a line search option to the JFNK solver
820      - move update of u/vIce and computation of initial residual into a separate
821        routine (same file); makes the code a little easier to read (?)
822      - the line search requires computation of the residual and for some reason
823        I cannot do the update of u/vIce at the beginning of the Newton loop
824        without changing the results, so we move computation of the new residual
825        also to the end of the Newton loop, even without the line search
826    o pkg/mdsio:
827      - write missing value (corresponding to undefined array value) to meta files;
828        skip this if missing value is one (UNSET_RL would be a better value for the
829        case of undefined missing value but it's current the default missing-value);
830        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
831    o pkg/exf & thsice:
832      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
833        diagnostics) even when SHORTWAVE_HEATING is #undef;
834    o verification/cfc_example:
835      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
836        illustrate how to use it).
837    o verification/offline_exf_seaice:
838      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
839        files to only one time-record.
840      in input.thermo: narrow the 2 bands of low initial ice-concentration near
841        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
842        snapshot output; same mcPheePiston value as in thsice with
843        surf-current=0.2m/s.
844      in input.thsice: similar set-up as in input.thermo (channel with same seaice
845        initial conditions).
846    o verification/cfc_example:
847      - update file "data" with more standard choice (default rotationPeriod,
848        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
849        set deltaTFreeSurf to deltaTtracer) and update the output.
850    o pkg/layers:
851      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
852      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
853    o verification/offline_exf_seaice:
854      - set all {field}period to zero for constant-in-time forcing (not tested
855        anywhere else).
856    o verification/offline_exf_seaice:
857      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
858      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
859    o model/src:
860      - implement Finite-Volume method for (hydrostatic) presure gradient
861        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
862    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
863      - In order to be compatible with the default EVP code, this requires changing
864        the EVP code around a little; and because any small change immediately
865        breaks the lab_sea.hb87 verification experiment, the reference output is
866        updated two times (each time the remaining aggrement was only 2 digits):
867        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
868        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
869        The adjoint test lab_sea.evp also needed to be updated.
870      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
871        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
872        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
873        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
874        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
875        kept obscure, because I need to test it a little more.
876    o pkg/cheapaml:
877      - fix few incorrect type (_RL/_RS) in subroutine calls.
878    o pkg/seaice:
879      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
880        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
881    o model/src:
882      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
883        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
884        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
885    o pkg/cheapaml:
886      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
887        update output of experiment cheapAML_box.
888      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
889        and set them only in one place (cheapaml_readparms.F).
890      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
891      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
892        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
893    o model/src/the_main_loop.F:
894      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
895    o pkg/seaice:
896      - remove legacy branch code.
897      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
898    o verification/*/code*/SEAICE_OPTIONS.h:
899      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
900        SEAICE_CAP_HEFF).
901    o pkg/cheapaml:
902      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
903        to load new forcing fields.
904      - add missing "_d 0" where it's needed; + some editing (improve indentation).
905      - remove switch to "-r8" compiler option (no longer needed) in verification
906        cheapAML_box, keep same output (small trucation error differences).
907    o verification/offline_exf_seaice:
908      - add thermodynamics only test.
909    o verification/cheapAML_box:
910      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
911        keep same output (same 14 digits for cg2d).
912      - switch on "-r8" compiler option (some numerical values are missing
913        the "_d 0") and update output (only 6 digits for cg2d were preserved).
914    
915    checkpoint64b (2012/12/24)
916    o pkg/cheapaml:
917      - remove un-used variables (Qnet,EmPmR) from pickup files.
918      - store tendency of advected variables into cheapaml pickup file
919        and fix the AB-2 restart.
920    o verification/offline_exf_seaice and lab_sea adjoint:
921      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
922      - switch to 4 time steps in offline, consistent with lab_sea.
923      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
924      - update results after change of experiment seaice.
925    o pkg/seaice:
926      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
927        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
928        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
929        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
930    o model/src:
931      - add run-time parameter to select CG2D solver minimum-residual solution
932        (in case of a poor convergence).
933    o pkg/seaice/seaice_lsr.F
934      - move calculation of matrix coefficients into new
935        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
936        file; the main purpose of this change is to be able to reuse the code
937        in S/R SEAICE_PRECONDITIONER
938      - modify the computation of the residual so that the mass of sea-ice
939        is not used twice; this simplifies the calculations, but since
940        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
941        not tested in testreport---this does not affect the testreport results.
942    o verification/seaice_obcs:
943      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
944        verification/lab_sea/input.salt_plume; changes results/output.txt*
945    o model/src:
946      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
947    o pkg/seaice:
948      - improve description of parameters in seaice_fgmres.F and start
949        cleaning up the code
950      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
951        second argument
952      - add a metric based on grid cell area to SEAICE_SCALPROD; update
953        results of offline_exf_seaice.dyn_jfnk
954      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
955    o pkg/aim_v23:
956      - fix an other bug in dissipation heating (grid-cell area was missing).
957    o model/src + pkg/seaice:
958      - add global (multi-tile) linear solver for pair of tri-diagonal system
959        along X and Y lines, respectively for U and V component.
960        Note: 1) MPI and cube-exchange not yet coded.
961            2) probably not accurate for poorly conditioned / large size problem.
962      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
963        default: not compiled and not used.
964    o pkg/seaice:
965      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
966        introduce bi/bj loops and use global_sum_tile_rl instead of
967        mpi_allreduce in seaice_fgmres.F
968      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
969      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
970      - add a verification experiment for JFNK in offline_exf_seaice
971    o verification:
972      - change (for now, only fwd test) offline_exf_seaice experiment:
973        use a re-entrant channel with idealized coastline (trapezoidal shape)
974        at southern boundary to explore seaice dynamics and thermodynamics
975        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
976        secondary test (input.thsice) use thermodynamics only with SST relaxation.
977      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
978    o pkg/exf:
979      - disable "sstExtrapol" when Nr=1
980    o verification:
981      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
982        to test pkg/cheapaml.
983    o pkg/aim_v23 & pkg/shap_filt:
984      - fix dissipation heating (erroneous gravity multiplication factor).
985    o pkg/seaice:
986      - remove unused field pressPre from jfnk solver
987      - rename two subroutines in seaice_preconditioner.F
988    o eesupp/src:
989       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
990    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
991       - remove wrong parts of the rhs and the lhs (were in there
992         because I did not understand the concept of this preconditioner)
993       - add an exchange between u- and v-sweep. This increases communication
994         by a factor of two but improves the convergence of jfnk. Ideally,
995         one would like the u- and v-sweep to be independent. So far within
996         undocumented ifdefs
997       - reorganize the extra computations for printing the residuals
998    o tools/genmake2:
999      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
1000        since it's not necessary (and was preventing to use MNC in some cases).
1001    
1002    checkpoint64a (2012/11/16)
1003    o pkg/autodiff:
1004      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
1005        autodiff_readparms.F no longer depends on calling order (within
1006        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
1007        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
1008        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
1009    o pkg/obcs:
1010      - adding tidal velocity forcing capability to obcs
1011        for usage example, see verification/seaice_obcs/input.tides
1012  o pkg/seaice:  o pkg/seaice:
1013    - turn the LSR-relaxation parameters WFAU/V into runtime parameters    - turn the LSR-relaxation parameters WFAU/V into runtime parameters
1014      SEAICE_LSRrelaxU/V      SEAICE_LSRrelaxU/V
1015      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
1016  o pkg/aim_v23:  o pkg/aim_v23:
1017    - implement heating from friction (bottom friction and stratospheric drag).    - implement heating from friction (bottom friction and stratospheric drag).
1018  o pkg/shap_filt:  o pkg/shap_filt:
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