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revision 1.1844 by heimbach, Fri Mar 29 23:21:39 2013 UTC revision 1.1956 by gforget, Thu Jan 9 19:47:55 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 verification/isomip, pkg/shelfic and OpenAD:  o model/src/external_forcing_surf.F
8     - add storage directives for EmPmR and PmEpR to avoid recomputation of seaice_model
9       in the adjoint that is problematic when seaice_model is turned off in the adjoint.
10       The resolved issue dated back to july when EXTERNAL_FORCING_SURF call was moved.
11       Update global_ocean.cs32x15/results/output_adm.seaice_dynmix.txt accordingly.
12    
13    o pkg/exf/exf_check.F
14     - fix a small bug again (originally found by Wentao Liu, now found again)
15     - streamline error output
16    o pkg/streamice and aim_v23:
17      replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
18      Apple's /usr/bin/cpp knows what to do:
19      Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
20      Target: x86_64-apple-darwin13.0.0
21    
22    checkpoint64s (2014/01/05)
23    o tools/adjoint_options:
24      - switch to fastopt.net TAF server (instead of default fastopt.de) for
25        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
26    o model/src:
27      - remove some unnecessary TAF storage directives in forward_step.F and
28        in dynamics.F (note: not always removed by TAF, e.g., double storage
29        of kappaRU,kappaRV in former version of dynamics.F).
30    o model/src & pkg/ptracers:
31      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
32        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
33        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
34      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
35      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
36      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
37    o useSingleCpuInput separates single-CPU input from single-CPU output;
38        for now only implemented for in exf_interp_read.F
39    o verification/advect_xy:
40      - fix missing EXCH call in local version of ini_salt.F and update output.
41    o momentum diagnostics:
42      - fix which deltaT is used in Total-Tendency diagnostics.
43      - fix typo in diagnostics for momentum tendency from AB.
44    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
45        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
46    
47    checkpoint64r (2013/12/08)
48    o verification/*/results:
49      - Update reference output of experiments that were passing with just 13 digits
50         (make it easier to detect future changes in results)
51    o model/src & pkg/ptracers:
52      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
53        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
54        to inside ptracers_integrate.F ; remove ptracers_advection.F
55    o coupling interface pkgs:
56        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
57      - change the config check to test the agreement of Ocean Depth
58        with ATM land/sea mask (instead of ATM orography);
59      - send to coupler the number of coupler time-steps to do for this run:
60        this allows to check for consistency and don't need anymore to be
61        specified in parameter file "data";
62      in coupler:
63      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
64      - improve report to log-file of config setting (pass log-file unit to few S/R)
65    o pkg/compon_communic:
66      - add coupling send/receive for non-tiled integer vector;
67      - add S/R to check and stop if any proc has an error (similar to
68        eesupp/src/stop_if_error.F but single thread and across Comm_World).
69    o pkg/exch2:
70      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
71        through list of all tiles my proc owns.
72    o model/src:
73      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
74        from rTrans) to simplify dependencies (no need to store rTrans anymore in
75        calling S/R); this affects AD results at machine truncation level:
76        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
77        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
78    o tools/build_options:
79      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
80    o coupling interface pkgs:
81        [compon_communic, atm_compon_interf & ocn_compon_interf]
82      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
83        to each S/R that needs it; remove un-used variables.
84      - change component tile registration (cpl_register.F in both compon_interf
85        and mitcomponent_tile_register.F) to pass the full list of tiles
86        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
87      - with pkg/exch2: adopt the same convention used for I/O to define mapping
88        towards coupler global array (unless W2_useE2ioLayOut=F):
89         a) can now use different tiling between atm & ocn comp.
90         b) no needs to modify the run-Off map when changing tiling (was needed
91            even if using the same tiling between atm & ocn).
92         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
93            full land tiles); not yet tested.
94      - check for valid mapping from comp. tile to coupler global array
95      - improve report of tile registration results to log file.
96    o pkg/exch2:
97      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
98        tile-registration (CPL_REGISTER);
99      - activate (un-comment) definition and setting of "W2_tileIndex" list to
100        store the local bi,bj indices of each tile;
101      - also print bi,bj in local report to log file;
102      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
103        Jun 2009 modif of pkg/exch2).
104    o testing on baudelaire:
105      - run 2 tests at a time: no significant slow down (since enough cpu) and
106        get the full set of test done earlier
107      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
108    o model/src/thermodynamics.F and routines called from it:
109      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
110        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
111        velocity (outp) by adding bolus velocity.
112      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
113        mass transport from velocity + lateral grid cell area
114      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
115      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
116     in thermodynamics.F
117      - remove k from thermodynamics.F and move it to temp_integrate.F
118        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
119        loop).
120      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
121        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
122        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
123        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
124      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
125        global_ocean.90x40x15, tutorial_global_oce_biogeo and
126        tutorial_tracer_adjsens (+ TLM output).
127    o tools/OAD_support and (verification/*/) code_oad:
128      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
129        module conversion ; remove unneeded CPP_EEOPTIONS.h.
130      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
131        version (closer to model/inc/CPP_OPTIONS.h).
132    o model/src:
133      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
134        retired list of parameters (routine FREEZE has been replace by surface
135        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
136    o pkg/gmredi:
137      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
138        velocity (same scheme but affects machine truncation) for GM_AdvForm.
139      - update output of FWD experiments: front_relax.bvp,
140        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
141    
142    checkpoint64q (2013/11/17)
143    o verification:
144      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
145        tutorial_global_oce_biogeo and global_ocean.90x40x15.
146      - generate new output (growth & melt) for seaice_itd experiment after
147        updating the input pickup_seaice files (previously wrong).
148    o pkg/cost:
149      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
150        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
151        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_TILE_RL
152          cannot be applied to var in common block).
153        o allows to get results independent of tile-per-proc setting (if using
154          slower GLOBAL_SUM_SEND_RECV option).
155      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
156        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
157        forward gradients: update output).
158      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
159        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
160    o pkg/mom_common:
161      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
162        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
163        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
164        ensure that all field value that are used are set.
165    o tutorial_deep_convection (smag3d):
166      - add missing scaling in mom_calc_smag_3d.F;
167      - set smag3D_coeff in input.smag3d such that results do not change.
168    o pkg/dic:
169      - change dic_cost.F to compute cost on each tile first and then apply
170        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
171        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
172      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
173    o eesupp/src & pkg/mdsio:
174      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
175        (from pkg/mdsio) since they are no longer used for tape IO.
176      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
177        (+ keep a copy in pkg/atm_ocn_coupler).
178    o verification/isomip:
179      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
180    o tools/build_options:
181      - optfile linux_amd64_ifort11, fast (no ieee) case:
182        to get a working restart for all experiments, add "-fp-model source"
183        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
184    
185    checkpoint64p (2013/10/20)
186    o pkg/autodiff:
187      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
188        criteria, return to simple (default) tape IO format.
189    o pkg/mdsio (+ eesupp/src):
190      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
191        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
192      - fix globalFile and singleCpuIO options using simpler global mapping.
193      - new pairs of scatter/gather vector S/R (one for each type, generated from
194        template) corresponding to simpler global mapping.
195      - adread_write.F: switch to new S/R (but leave old calls commented) and write
196        to globalFile when parameter globalFiles is set to True.
197      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
198    o pkg/autodiff:
199      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
200        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
201        missing, just add a STOP if array type do not match.
202    o pkg/exf:
203      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
204         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
205         and rename array obsSIce to exf_iceFraction.
206    o tutorial_deep_convection:
207      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
208        for now all in this exp. code dir.
209      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
210        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
211    o eesupp/src:
212      - added SINGLE_DISK_IO option because reading of parameter files on
213        very large number of processors did not work with existing set-up
214    
215    checkpoint64o (2013/09/25)
216    o pkg/atm_phys & atm_compon_interf:
217      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
218    o tools/build_options:
219      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
220        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
221        remove CPP setting (was identical to genmake2 default).
222    o pkg/gmredi & model/src: Some updating and work done on the residual model.
223      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
224      - fixed up the calculation of the eddy stress and how it is added to the
225        external forcing via taueddy_external_forcing.F
226      - at the moment, it is very experimental and only works with the variable eddy
227        diffusivity calculated in gmredi_k3d.F
228    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
229        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
230    o testreport (& tools/do_tst_2+2):
231      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
232    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
233      - remove CPP='cpp -traditional -P' (this is genmake2 default)
234      - add switch (for big setups) to use 'medium' memory-model (but leave it
235        commented out for now). Note: needed with FC 19 to compile big setups.
236    o pkg/atm_compon_interf:
237      - regroup per field origin (model & pkgs) the coupling storage routines
238         (which accumalate in time each coupling field)
239      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
240        update accordingly + simplify aim_do_physics.F
241    
242    checkpoint64n (2013/08/26)
243    o pkg/bbl:
244      - update formulation to reduce dispersion of tracer properties in bbl
245      - replaced horizontal and vertical transport parameters with velocities
246      - changes results for verification/global_with_exf.yearly
247    o verification/halfpipe_streamice:
248      - change to matrix construction; update both Fwd & AD output.
249    o verification/tutorial_tracer_adjsens:
250      - OpenAD test: switch to vector-invariant momentum since fluxform with
251        rStar causes problems with OpenAD; update output.
252    o tools:
253      - genmake2: define a common prefix for all temp-file names ; move them
254        to local /tmp disk (but would be easy to move them back);
255      - xmakedepend: apply the same switch for temp-files.
256    o pkg/offline:
257      - changes for use with rStar (NLFS): assume that we continue to provide
258        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
259        output files) and apply r* scaling at each time-step (function of the time
260        varying Eta field); use normal pickup files (needed for restart with NLFS).
261    o adjoint with OpenAD:
262      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
263        package openad.  This package has to be compiled for all runs with OpenAD
264        instead of specifying code_oad_all as a modification directory.
265      - link the fortran templates from tools/OAD_support to the build directory
266        for preprocessing to avoid conflicts between different setups compiled
267        simultaneously and simplify cleanup.
268    o pkg/exf:
269      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
270        main model or other pkgs are exchanged in EXF_MAPFIELDS).
271    o model/src:
272      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
273        (similar to do_fields_blocking_exchanges.F).
274    o tools/genmake2:
275      - remove TAF output src code just before calling staf (when not doing a fresh
276        built, will stop if things go wrong with staf).
277      - fix target "adobj" (left from TAF version-2 transition)
278    o pkg/diagnostics:
279      - add a parameter to track the status of pkg/diagnostics activation;
280        this replace/extend the use of logical param "settingDiags" (to check
281        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
282        New S/R to print error message and stop when pkgStatus is not right.
283      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
284    
285    checkpoint64m (2013/08/13)
286    o model/inc:
287      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
288        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
289    o pkg/kpp & aim_v23:
290      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
291    o pkg/seaice:
292      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
293        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
294      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
295    o eesupp/src:
296      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
297        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
298    o switch to TAF version-2:
299      - add flow directives to "freeze" naming convention for ad-routines that
300        are used in I/O routines of adjoint state and associated common blocks
301        that are used in adcommon.h (backward compatible with version-1)
302      - update all ad-optfiles (in tools/adjoint_options + few local to some
303        verification exp) to switch to latest TAF version (currently 2.5.5);
304        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
305        out except for diva).
306      - the major change with TAF version-2 is that both the differentiated
307        routines and the forward routines (new) are returned as part of the TAF
308        output source code. Update genmake2 accordingly.
309      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
310        with version-2 when compared to TLM or FWD gradient); other experiments
311        output show minor changes (machine truncation level); update the few AD &
312        TLM output with 12 matching digits only (some prior to version-2 switch).
313    
314    checkpoint64l (2013/08/05)
315    o model/src:
316      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
317      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
318        when using TAF but only if using OpenAD.
319    o pkg/mom_common+fluxform+vecinv:
320      - always set horiz. viscosity arrays to background value before calling
321        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
322        only when using variable horiz. viscosity (useVariableVisc=T);
323      - simplify mom_vecinv.F (only 1 block for momViscosity).
324    o pkg/mom_common: variable horiz. viscosity in NH code
325      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
326        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
327      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
328        useBiharmonicVisc & useVariableVisc.
329      - fix old bug (already in 1rst implementation of variable horizontal viscosity
330        in calc_gw.F, version 1.27, 2006/06/20):
331        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
332        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
333      - change background horiz viscosity in vertical momentum (gW) to always be
334        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
335        any type of variable viscosity, e.g., viscAh/4Grid)
336      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
337        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
338        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
339        default viscAh,viscA4 is zero).
340    o model/src:
341      - extend length of drC & recip_drC from Nr to Nr+1.
342    o Divided Adjoint (DIVA) with MPI:
343      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
344      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
345        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
346    
347    checkpoint64k (2013/07/23)
348    o tools/OAD_support:
349      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
350        and remove it from genmake2.
351    o tools/build_options:
352      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
353        MPI_HEADER_FILES list (let genmake2 find the missing headers)
354    o verification/halfpipe_streamice:
355      - change to driving stress formulation; update both Fwd & AD output.
356    o tools/genmake2 and Divided Adjoint with MPI:
357      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
358      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
359      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
360        Makefile, which is set by genmake2, and check which mpi-headers are needed.
361        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
362      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
363    o testreport:
364      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
365        perform additional runs (number of additional runs is "add_DIVA_runs" taken
366        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
367    o verification/lab_sea (AD test):
368      - change to test Divided Adjoint Run in this set-up (both standard AD test
369        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
370    o pkg atm_ & ocn_compon_interf:
371      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
372        staggerTimeStep implementation) and disable (retired) corresponding
373        parameter.
374    o pkg/offline:
375      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
376      - add S/R OFFLINE_CHECK to print offline parameter summary
377        and stop if loading a file that is not used;
378      - enable to calculate GMRedi tensor, KPP mixing and convective index
379        when the corresponding file(s) is/are not specified (but pkg is used).
380      - comment out resetting of monitorFreq (to endTime) since it still useful
381        for monitoring CFL numbers and checking offline fields.
382    o OpenAD:
383      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
384        smaller standard output) and generate new (smaller) output (on baudelaire
385        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
386    o model/src:
387      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
388        (where external_forcing_adjust was called) and change list of arguments;
389      - merge external_forcing_adjust.F into external_forcing_surf.F
390      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
391        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
392        previously in file "balance_relax.F", now removed); remove corresponding
393        arrays in FFIELDS.h.
394      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
395        a hack for getting back surfaceForcingS (loaded from file) when using
396        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
397      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
398        (was getting only 11 digits for AD-grad, due to different truncation
399         error in AD code).
400    
401    checkpoint64j (2013/07/04)
402    o pkg/offline:
403      - to enable the use of other features with pkg offline (e.g., obcs),
404        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
405      - comment out "allowFreezing" (now active) in 2 offline testing exp.
406    o pkg/exf ALLOW_RUNOFTEMP
407      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
408      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
409      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
410    o pkg/atm_phys:
411      - allows to add some damping on uVel,vVel (strength only function of k).
412    o verification, ad-tests:
413      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
414        global_ocean_ebm and offline_exf_seaice.thsice.
415    o verification/halfpipe_streamice:
416      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
417        flux input boundary conditions to be ignored; a fix for this bug changed
418        verification results for forward test.
419      - add adjoint test.
420    o pkg/ptracers:
421      - allow to restart without SOM pickup (resetting SOM to zero).
422    o pkg/gmredi:
423      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
424      - It uses mixing length theory and suppression by steering level effects to
425        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
426        to JPO, for more details).
427      - It also uses the diffusivity to calculate an eddy induced streamfunction
428        based on a PV closure (rather than a buoyancy closure as in GM).
429      - New files added to pkg/gmredi:
430        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
431          induced overturning streamfunction (called from gmredi_calc_tensor)
432        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
433          for use in gmredi_k3d
434        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
435          the eddy diffusivity
436    
437    checkpoint64i (2013/06/18)
438    o pkg/cheapaml:
439      - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
440        that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
441        with pkg/cheapaml.
442    o utils/python: add subpackage for cubed sphere function, first example is
443        simple cs.pcol to plot 2D fields on a map
444    o pkg/streamice:
445      - This is a new package in MITgcm, which solves dynamic equations for ice
446         sheets and ice streams
447      - At the moment it is independent of atmosphere/ocean dynamics, or any
448        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
449        ed that this will change)
450      - There is a new verification exercise that tests it, halfpipe_streamice,
451        evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
452        rectangular embayment
453      - halfpipe_streamice is forward-only for now, will have TAF test soon
454      - for questions, email dgoldber@mit.edu
455    o pkg/thsice:
456      - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
457        of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
458      - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
459         call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
460      - allow precip from pkg/cheapaml to make snow over seaice.
461    o pkg/cfc:
462      - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
463      - remove atmos CFC 2-D arrays from common bloc (now local variables)
464      - change some hard-coded constant to run time parameter for reading and
465        and interpolating atmospheric CFC ; keep same default as previously.
466      - more flexible reading of Atmos CFC (number of records no longer hard-coded)
467      - put arguments in standard order: myTime, myIter, myThid
468      - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
469        atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
470      - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
471      - new routine to print summary of CFC params and check for consistency.
472    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
473      similar to thsice_advdiff.
474      Note that for the B-grid case the routine parameters uc/vc are overwritten.
475    o pkg/cfc:
476      - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
477        update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
478      - fix interpolation of atmphspheric CFC between Sorthern and Northern
479        hemisphere value.
480    o pkg/seaice:
481      - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
482    o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
483                  so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
484      - requires an additional time level that is stored in the pickup
485      - you can start with AB2 from a pickup without this time level with
486        pickupStrictlyMatch = .false.
487    
488    checkpoint64h (2013/05/26)
489    o pkg/cheapaml:
490      - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
491        affect machine truncation (but exp cheapAML_box still pass with 13 digits).
492      - consistent treatment of uWind,vWind location: assume everywhere in
493        pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
494        (Note: was already the case for Tair,Qair advection);
495        add option (INCONSISTENT_WIND_LOCATION) to recover old results.
496      - compute diabatic forcing only in the interior (excluding overlap regions)
497      - fill in array "Qsw" (for short-wave heating);
498      - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
499        before any update (consistent with MITgcm state var diagnostics);
500      - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
501        non periodic ; + adjusted for uWind,vWind (C-grid).
502    o pkg/seaice:
503      - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
504        add explicitly pkg/exf in experiments that currently use pkg/seaice.
505      - allows to compile pkg/seaice without pkg/exf.
506    o tools/OAD_support:
507      - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
508        of array "ourStepOf" in function rvNextAction (revolve.F90).
509    o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
510      - change pkg name (to be used with other atmospheric physics pkg)
511        but by-pass CVS when making the new pkg so that we keep the CVS history.
512    o pkg/offline:
513      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
514        (previously called from pkg/dic_surfforcing_init.F)
515    o model/src:
516      - re-order sequence of calls within packages_init_variables.F, using
517        standard order, except for:
518         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
519         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
520    o new pkg: atm_phys
521      - add entry point and source code (previously in contrib
522          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
523        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
524      - re-order sequence of calls within packages_readparms.F,
525         packages_init_fixed.F and packages_write_pickup.F
526        (but skip packages_init_variables.F because of TAF issues).
527      - update contrib/*/atm_gray/ experiment.
528    o pkg/seaice (ITD code):
529      - simplify and fix the writing of pickup-files for ITD case
530    o pkg/seaice (ITD code):
531      - introduce floe size dependent lateral melt for ITD case;
532      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
533      - update seaice_itd experiment main output.
534    o pkg/thsice:
535      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
536        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
537        changed accordingly pkg/atm2d.
538    
539    checkpoint64g (2013/05/01)
540    o pkg/exf ALLOW_RUNOFTEMP
541      - if defined,  river and glacier runoff temperature can be read-in from
542        runoftempfile; runoftempfile needs to have same format as runofffile
543    o pkg/thsice (& pkg/bulk_force):
544      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
545        for energy content of Precip + RunOff & Evap (like with pkg/exf).
546      - change computation domain to always be the interior (without overlap).
547      - fix bug (wrong overlap) when using EXF and stressReduction > 0.
548    o verification/tutorial_global_oce_biogeo:
549      - add preliminary OpenAD setup (still has problems)
550    o pkg/seaice:
551      - turn some parameters for choosing the convergence criterion of
552        the inexact Newton method (JFNK) into runtime parameters for convenience
553      - clean up seaice_calc_viscosities.F: remove/retire two options for
554        SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
555        the results of lab_sea/input because a division has been replaced by
556        a multiplication with the reciprocal (sumNorm)
557      - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
558        convergence of solver (changes results, of course), and to test some
559        new features
560    o model/src:
561      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
562      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
563      - move forcing adjustment (balancing surface forcing) in specific S/R
564        where might also be applied exchanges (if needed) to forcing arrays.
565    o pkg/shelfice:
566      - allow to specify the Ice-Shelf mass per unit area (instead of
567        shelficeLoadAnomaly) and do the conversion from one to the other
568      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
569        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
570        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
571        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
572      - update isomip experiment forward output (get machine truncation error
573        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
574    o verification/offline_exf_seaice:
575      revise data.seaice in input.thermo and input_ad and update results accordingly
576        HO = 0.2, SEAICE_areaLossFormula = 2,
577        SEAICE_growMeltByConv = .TRUE.,
578        SEAICE_doOpenWaterMelt = .TRUE.,
579      Improve consistency with input.thsice and fix the spurious 500m ice corners
580    o verification/global_ocean.cs32x15:
581      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
582        in icedyn (thsice+seaice-dyn) test and update output.
583    o verification/offline_exf_seaice:
584      - adjust list of tested variables (with testreport) and update
585        standard test output with better slection of monitored fields.
586    o pkg/cd_code:
587      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
588        experiment lab_sea.hb87
589    o tools/genmake2:
590      - change default makedepend from the system default to tools/xmakedepend:
591        When no makedepend is specified, select tools/xmakedepend it the test pass,
592        otherwise select the system default (if exist and pass the test) or
593        try to build cyrus-makedepend ; stop if none of the 3 works.
594    o pkg/exf & pkg/thsice:
595      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
596        for energy content of Precip + RunOff & Evap. Assumes:
597       1) Rain has same temp as Air.
598       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
599       3) Run-Off comes at the temp of surface water (with same Cp)
600       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
601        put directly into Latent Heat flux & should use water-vapor heat capacity.
602       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
603        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
604    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
605        (compile when SEAICE_ALLOW_JFNK is defined)
606    o pkg/thsice:
607      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
608        implementation): move THSICE_AVE call after the advection (called directly
609        from thsice_do_advect.F).
610    o verification/global_ocean.90x40x15 and OpenAD:
611      New experiment for OpenAD is identical to the one in input_ad except that
612        multiDimAdvection=.FALSE.,
613      There is still an issue with this.
614    o pkg/thsice:
615      - account for ice velocity (ocean relative velocity) in turbulent heat flux
616        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
617        and offline_exf_seaice (main test).
618    
619    checkpoint64f (2013/03/31)
620    o verification/OpenAD:
621      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
622    o verification/isomip, pkg/shelfice and OpenAD:
623    - add OpenAD setup to this exp and make shelfice package work with OpenAD    - add OpenAD setup to this exp and make shelfice package work with OpenAD
624  o verification/offline_exf_seaice: replace adjoint experiment.  o verification/tutorial_global_oce_biogeo:
625      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
626    o verification/offline_exf_seaice:
627      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
628  o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:  o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
629    - add OpenAD setup to this exp and make ptracers package work with OpenAD    - add OpenAD setup to this exp and make ptracers package work with OpenAD
630  o pkg/seaice/seaice_evp.F: mask the asymmetric contribution of the ice-ocean  o pkg/seaice/seaice_evp.F:
631    stress (when the turningAngle is non-zero) over open water to avoid     mask the asymmetric contribution of the ice-ocean stress (when
632    stripes in the EVP-solutions after many EVP-substeps. This does not change     the turningAngle is non-zero) over open water to avoid stripes
633    the verification experiment (because turningAngle=0 in that experiment), but     in the EVP-solutions after many EVP-substeps. This does not change
634    will affect other EVP solutions with turningAngle.ne.0     the verification experiment (because turningAngle=0 in that experiment),
635       but will affect other EVP solutions with turningAngle.ne.0
636  o verification, AD & TLM output:  o verification, AD & TLM output:
637    - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple    - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
638      additions and multiplications which affect results at machine truncation      additions and multiplications which affect results at machine truncation

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