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revision 1.1844 by heimbach, Fri Mar 29 23:21:39 2013 UTC revision 1.1957 by gforget, Tue Jan 14 22:37:15 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/temp_integrate.F and salt_integrate.F
8     - re-include store directives that were removed on Dec 27th.
9    o model/src/external_forcing_surf.F
10     - add storage directives for EmPmR and PmEpR to avoid recomputation of seaice_model
11       in the adjoint that is problematic when seaice_model is turned off in the adjoint.
12       The resolved issue dated back to july when EXTERNAL_FORCING_SURF call was moved.
13       Update global_ocean.cs32x15/results/output_adm.seaice_dynmix.txt accordingly.
14    
15    o pkg/exf/exf_check.F
16     - fix a small bug again (originally found by Wentao Liu, now found again)
17     - streamline error output
18    o pkg/streamice and aim_v23:
19      replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
20      Apple's /usr/bin/cpp knows what to do:
21      Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
22      Target: x86_64-apple-darwin13.0.0
23    
24    checkpoint64s (2014/01/05)
25    o tools/adjoint_options:
26      - switch to fastopt.net TAF server (instead of default fastopt.de) for
27        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
28    o model/src:
29      - remove some unnecessary TAF storage directives in forward_step.F and
30        in dynamics.F (note: not always removed by TAF, e.g., double storage
31        of kappaRU,kappaRV in former version of dynamics.F).
32    o model/src & pkg/ptracers:
33      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
34        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
35        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
36      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
37      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
38      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
39    o useSingleCpuInput separates single-CPU input from single-CPU output;
40        for now only implemented for in exf_interp_read.F
41    o verification/advect_xy:
42      - fix missing EXCH call in local version of ini_salt.F and update output.
43    o momentum diagnostics:
44      - fix which deltaT is used in Total-Tendency diagnostics.
45      - fix typo in diagnostics for momentum tendency from AB.
46    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
47        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
48    
49    checkpoint64r (2013/12/08)
50    o verification/*/results:
51      - Update reference output of experiments that were passing with just 13 digits
52         (make it easier to detect future changes in results)
53    o model/src & pkg/ptracers:
54      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
55        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
56        to inside ptracers_integrate.F ; remove ptracers_advection.F
57    o coupling interface pkgs:
58        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
59      - change the config check to test the agreement of Ocean Depth
60        with ATM land/sea mask (instead of ATM orography);
61      - send to coupler the number of coupler time-steps to do for this run:
62        this allows to check for consistency and don't need anymore to be
63        specified in parameter file "data";
64      in coupler:
65      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
66      - improve report to log-file of config setting (pass log-file unit to few S/R)
67    o pkg/compon_communic:
68      - add coupling send/receive for non-tiled integer vector;
69      - add S/R to check and stop if any proc has an error (similar to
70        eesupp/src/stop_if_error.F but single thread and across Comm_World).
71    o pkg/exch2:
72      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
73        through list of all tiles my proc owns.
74    o model/src:
75      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
76        from rTrans) to simplify dependencies (no need to store rTrans anymore in
77        calling S/R); this affects AD results at machine truncation level:
78        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
79        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
80    o tools/build_options:
81      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
82    o coupling interface pkgs:
83        [compon_communic, atm_compon_interf & ocn_compon_interf]
84      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
85        to each S/R that needs it; remove un-used variables.
86      - change component tile registration (cpl_register.F in both compon_interf
87        and mitcomponent_tile_register.F) to pass the full list of tiles
88        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
89      - with pkg/exch2: adopt the same convention used for I/O to define mapping
90        towards coupler global array (unless W2_useE2ioLayOut=F):
91         a) can now use different tiling between atm & ocn comp.
92         b) no needs to modify the run-Off map when changing tiling (was needed
93            even if using the same tiling between atm & ocn).
94         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
95            full land tiles); not yet tested.
96      - check for valid mapping from comp. tile to coupler global array
97      - improve report of tile registration results to log file.
98    o pkg/exch2:
99      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
100        tile-registration (CPL_REGISTER);
101      - activate (un-comment) definition and setting of "W2_tileIndex" list to
102        store the local bi,bj indices of each tile;
103      - also print bi,bj in local report to log file;
104      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
105        Jun 2009 modif of pkg/exch2).
106    o testing on baudelaire:
107      - run 2 tests at a time: no significant slow down (since enough cpu) and
108        get the full set of test done earlier
109      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
110    o model/src/thermodynamics.F and routines called from it:
111      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
112        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
113        velocity (outp) by adding bolus velocity.
114      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
115        mass transport from velocity + lateral grid cell area
116      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
117      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
118     in thermodynamics.F
119      - remove k from thermodynamics.F and move it to temp_integrate.F
120        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
121        loop).
122      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
123        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
124        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
125        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
126      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
127        global_ocean.90x40x15, tutorial_global_oce_biogeo and
128        tutorial_tracer_adjsens (+ TLM output).
129    o tools/OAD_support and (verification/*/) code_oad:
130      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
131        module conversion ; remove unneeded CPP_EEOPTIONS.h.
132      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
133        version (closer to model/inc/CPP_OPTIONS.h).
134    o model/src:
135      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
136        retired list of parameters (routine FREEZE has been replace by surface
137        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
138    o pkg/gmredi:
139      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
140        velocity (same scheme but affects machine truncation) for GM_AdvForm.
141      - update output of FWD experiments: front_relax.bvp,
142        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
143    
144    checkpoint64q (2013/11/17)
145    o verification:
146      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
147        tutorial_global_oce_biogeo and global_ocean.90x40x15.
148      - generate new output (growth & melt) for seaice_itd experiment after
149        updating the input pickup_seaice files (previously wrong).
150    o pkg/cost:
151      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
152        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
153        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_TILE_RL
154          cannot be applied to var in common block).
155        o allows to get results independent of tile-per-proc setting (if using
156          slower GLOBAL_SUM_SEND_RECV option).
157      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
158        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
159        forward gradients: update output).
160      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
161        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
162    o pkg/mom_common:
163      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
164        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
165        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
166        ensure that all field value that are used are set.
167    o tutorial_deep_convection (smag3d):
168      - add missing scaling in mom_calc_smag_3d.F;
169      - set smag3D_coeff in input.smag3d such that results do not change.
170    o pkg/dic:
171      - change dic_cost.F to compute cost on each tile first and then apply
172        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
173        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
174      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
175    o eesupp/src & pkg/mdsio:
176      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
177        (from pkg/mdsio) since they are no longer used for tape IO.
178      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
179        (+ keep a copy in pkg/atm_ocn_coupler).
180    o verification/isomip:
181      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
182    o tools/build_options:
183      - optfile linux_amd64_ifort11, fast (no ieee) case:
184        to get a working restart for all experiments, add "-fp-model source"
185        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
186    
187    checkpoint64p (2013/10/20)
188    o pkg/autodiff:
189      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
190        criteria, return to simple (default) tape IO format.
191    o pkg/mdsio (+ eesupp/src):
192      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
193        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
194      - fix globalFile and singleCpuIO options using simpler global mapping.
195      - new pairs of scatter/gather vector S/R (one for each type, generated from
196        template) corresponding to simpler global mapping.
197      - adread_write.F: switch to new S/R (but leave old calls commented) and write
198        to globalFile when parameter globalFiles is set to True.
199      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
200    o pkg/autodiff:
201      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
202        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
203        missing, just add a STOP if array type do not match.
204    o pkg/exf:
205      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
206         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
207         and rename array obsSIce to exf_iceFraction.
208    o tutorial_deep_convection:
209      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
210        for now all in this exp. code dir.
211      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
212        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
213    o eesupp/src:
214      - added SINGLE_DISK_IO option because reading of parameter files on
215        very large number of processors did not work with existing set-up
216    
217    checkpoint64o (2013/09/25)
218    o pkg/atm_phys & atm_compon_interf:
219      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
220    o tools/build_options:
221      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
222        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
223        remove CPP setting (was identical to genmake2 default).
224    o pkg/gmredi & model/src: Some updating and work done on the residual model.
225      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
226      - fixed up the calculation of the eddy stress and how it is added to the
227        external forcing via taueddy_external_forcing.F
228      - at the moment, it is very experimental and only works with the variable eddy
229        diffusivity calculated in gmredi_k3d.F
230    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
231        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
232    o testreport (& tools/do_tst_2+2):
233      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
234    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
235      - remove CPP='cpp -traditional -P' (this is genmake2 default)
236      - add switch (for big setups) to use 'medium' memory-model (but leave it
237        commented out for now). Note: needed with FC 19 to compile big setups.
238    o pkg/atm_compon_interf:
239      - regroup per field origin (model & pkgs) the coupling storage routines
240         (which accumalate in time each coupling field)
241      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
242        update accordingly + simplify aim_do_physics.F
243    
244    checkpoint64n (2013/08/26)
245    o pkg/bbl:
246      - update formulation to reduce dispersion of tracer properties in bbl
247      - replaced horizontal and vertical transport parameters with velocities
248      - changes results for verification/global_with_exf.yearly
249    o verification/halfpipe_streamice:
250      - change to matrix construction; update both Fwd & AD output.
251    o verification/tutorial_tracer_adjsens:
252      - OpenAD test: switch to vector-invariant momentum since fluxform with
253        rStar causes problems with OpenAD; update output.
254    o tools:
255      - genmake2: define a common prefix for all temp-file names ; move them
256        to local /tmp disk (but would be easy to move them back);
257      - xmakedepend: apply the same switch for temp-files.
258    o pkg/offline:
259      - changes for use with rStar (NLFS): assume that we continue to provide
260        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
261        output files) and apply r* scaling at each time-step (function of the time
262        varying Eta field); use normal pickup files (needed for restart with NLFS).
263    o adjoint with OpenAD:
264      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
265        package openad.  This package has to be compiled for all runs with OpenAD
266        instead of specifying code_oad_all as a modification directory.
267      - link the fortran templates from tools/OAD_support to the build directory
268        for preprocessing to avoid conflicts between different setups compiled
269        simultaneously and simplify cleanup.
270    o pkg/exf:
271      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
272        main model or other pkgs are exchanged in EXF_MAPFIELDS).
273    o model/src:
274      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
275        (similar to do_fields_blocking_exchanges.F).
276    o tools/genmake2:
277      - remove TAF output src code just before calling staf (when not doing a fresh
278        built, will stop if things go wrong with staf).
279      - fix target "adobj" (left from TAF version-2 transition)
280    o pkg/diagnostics:
281      - add a parameter to track the status of pkg/diagnostics activation;
282        this replace/extend the use of logical param "settingDiags" (to check
283        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
284        New S/R to print error message and stop when pkgStatus is not right.
285      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
286    
287    checkpoint64m (2013/08/13)
288    o model/inc:
289      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
290        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
291    o pkg/kpp & aim_v23:
292      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
293    o pkg/seaice:
294      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
295        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
296      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
297    o eesupp/src:
298      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
299        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
300    o switch to TAF version-2:
301      - add flow directives to "freeze" naming convention for ad-routines that
302        are used in I/O routines of adjoint state and associated common blocks
303        that are used in adcommon.h (backward compatible with version-1)
304      - update all ad-optfiles (in tools/adjoint_options + few local to some
305        verification exp) to switch to latest TAF version (currently 2.5.5);
306        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
307        out except for diva).
308      - the major change with TAF version-2 is that both the differentiated
309        routines and the forward routines (new) are returned as part of the TAF
310        output source code. Update genmake2 accordingly.
311      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
312        with version-2 when compared to TLM or FWD gradient); other experiments
313        output show minor changes (machine truncation level); update the few AD &
314        TLM output with 12 matching digits only (some prior to version-2 switch).
315    
316    checkpoint64l (2013/08/05)
317    o model/src:
318      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
319      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
320        when using TAF but only if using OpenAD.
321    o pkg/mom_common+fluxform+vecinv:
322      - always set horiz. viscosity arrays to background value before calling
323        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
324        only when using variable horiz. viscosity (useVariableVisc=T);
325      - simplify mom_vecinv.F (only 1 block for momViscosity).
326    o pkg/mom_common: variable horiz. viscosity in NH code
327      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
328        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
329      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
330        useBiharmonicVisc & useVariableVisc.
331      - fix old bug (already in 1rst implementation of variable horizontal viscosity
332        in calc_gw.F, version 1.27, 2006/06/20):
333        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
334        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
335      - change background horiz viscosity in vertical momentum (gW) to always be
336        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
337        any type of variable viscosity, e.g., viscAh/4Grid)
338      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
339        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
340        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
341        default viscAh,viscA4 is zero).
342    o model/src:
343      - extend length of drC & recip_drC from Nr to Nr+1.
344    o Divided Adjoint (DIVA) with MPI:
345      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
346      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
347        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
348    
349    checkpoint64k (2013/07/23)
350    o tools/OAD_support:
351      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
352        and remove it from genmake2.
353    o tools/build_options:
354      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
355        MPI_HEADER_FILES list (let genmake2 find the missing headers)
356    o verification/halfpipe_streamice:
357      - change to driving stress formulation; update both Fwd & AD output.
358    o tools/genmake2 and Divided Adjoint with MPI:
359      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
360      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
361      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
362        Makefile, which is set by genmake2, and check which mpi-headers are needed.
363        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
364      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
365    o testreport:
366      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
367        perform additional runs (number of additional runs is "add_DIVA_runs" taken
368        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
369    o verification/lab_sea (AD test):
370      - change to test Divided Adjoint Run in this set-up (both standard AD test
371        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
372    o pkg atm_ & ocn_compon_interf:
373      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
374        staggerTimeStep implementation) and disable (retired) corresponding
375        parameter.
376    o pkg/offline:
377      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
378      - add S/R OFFLINE_CHECK to print offline parameter summary
379        and stop if loading a file that is not used;
380      - enable to calculate GMRedi tensor, KPP mixing and convective index
381        when the corresponding file(s) is/are not specified (but pkg is used).
382      - comment out resetting of monitorFreq (to endTime) since it still useful
383        for monitoring CFL numbers and checking offline fields.
384    o OpenAD:
385      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
386        smaller standard output) and generate new (smaller) output (on baudelaire
387        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
388    o model/src:
389      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
390        (where external_forcing_adjust was called) and change list of arguments;
391      - merge external_forcing_adjust.F into external_forcing_surf.F
392      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
393        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
394        previously in file "balance_relax.F", now removed); remove corresponding
395        arrays in FFIELDS.h.
396      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
397        a hack for getting back surfaceForcingS (loaded from file) when using
398        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
399      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
400        (was getting only 11 digits for AD-grad, due to different truncation
401         error in AD code).
402    
403    checkpoint64j (2013/07/04)
404    o pkg/offline:
405      - to enable the use of other features with pkg offline (e.g., obcs),
406        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
407      - comment out "allowFreezing" (now active) in 2 offline testing exp.
408    o pkg/exf ALLOW_RUNOFTEMP
409      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
410      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
411      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
412    o pkg/atm_phys:
413      - allows to add some damping on uVel,vVel (strength only function of k).
414    o verification, ad-tests:
415      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
416        global_ocean_ebm and offline_exf_seaice.thsice.
417    o verification/halfpipe_streamice:
418      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
419        flux input boundary conditions to be ignored; a fix for this bug changed
420        verification results for forward test.
421      - add adjoint test.
422    o pkg/ptracers:
423      - allow to restart without SOM pickup (resetting SOM to zero).
424    o pkg/gmredi:
425      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
426      - It uses mixing length theory and suppression by steering level effects to
427        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
428        to JPO, for more details).
429      - It also uses the diffusivity to calculate an eddy induced streamfunction
430        based on a PV closure (rather than a buoyancy closure as in GM).
431      - New files added to pkg/gmredi:
432        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
433          induced overturning streamfunction (called from gmredi_calc_tensor)
434        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
435          for use in gmredi_k3d
436        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
437          the eddy diffusivity
438    
439    checkpoint64i (2013/06/18)
440    o pkg/cheapaml:
441      - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
442        that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
443        with pkg/cheapaml.
444    o utils/python: add subpackage for cubed sphere function, first example is
445        simple cs.pcol to plot 2D fields on a map
446    o pkg/streamice:
447      - This is a new package in MITgcm, which solves dynamic equations for ice
448         sheets and ice streams
449      - At the moment it is independent of atmosphere/ocean dynamics, or any
450        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
451        ed that this will change)
452      - There is a new verification exercise that tests it, halfpipe_streamice,
453        evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
454        rectangular embayment
455      - halfpipe_streamice is forward-only for now, will have TAF test soon
456      - for questions, email dgoldber@mit.edu
457    o pkg/thsice:
458      - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
459        of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
460      - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
461         call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
462      - allow precip from pkg/cheapaml to make snow over seaice.
463    o pkg/cfc:
464      - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
465      - remove atmos CFC 2-D arrays from common bloc (now local variables)
466      - change some hard-coded constant to run time parameter for reading and
467        and interpolating atmospheric CFC ; keep same default as previously.
468      - more flexible reading of Atmos CFC (number of records no longer hard-coded)
469      - put arguments in standard order: myTime, myIter, myThid
470      - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
471        atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
472      - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
473      - new routine to print summary of CFC params and check for consistency.
474    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
475      similar to thsice_advdiff.
476      Note that for the B-grid case the routine parameters uc/vc are overwritten.
477    o pkg/cfc:
478      - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
479        update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
480      - fix interpolation of atmphspheric CFC between Sorthern and Northern
481        hemisphere value.
482    o pkg/seaice:
483      - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
484    o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
485                  so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
486      - requires an additional time level that is stored in the pickup
487      - you can start with AB2 from a pickup without this time level with
488        pickupStrictlyMatch = .false.
489    
490    checkpoint64h (2013/05/26)
491    o pkg/cheapaml:
492      - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
493        affect machine truncation (but exp cheapAML_box still pass with 13 digits).
494      - consistent treatment of uWind,vWind location: assume everywhere in
495        pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
496        (Note: was already the case for Tair,Qair advection);
497        add option (INCONSISTENT_WIND_LOCATION) to recover old results.
498      - compute diabatic forcing only in the interior (excluding overlap regions)
499      - fill in array "Qsw" (for short-wave heating);
500      - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
501        before any update (consistent with MITgcm state var diagnostics);
502      - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
503        non periodic ; + adjusted for uWind,vWind (C-grid).
504    o pkg/seaice:
505      - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
506        add explicitly pkg/exf in experiments that currently use pkg/seaice.
507      - allows to compile pkg/seaice without pkg/exf.
508    o tools/OAD_support:
509      - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
510        of array "ourStepOf" in function rvNextAction (revolve.F90).
511    o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
512      - change pkg name (to be used with other atmospheric physics pkg)
513        but by-pass CVS when making the new pkg so that we keep the CVS history.
514    o pkg/offline:
515      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
516        (previously called from pkg/dic_surfforcing_init.F)
517    o model/src:
518      - re-order sequence of calls within packages_init_variables.F, using
519        standard order, except for:
520         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
521         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
522    o new pkg: atm_phys
523      - add entry point and source code (previously in contrib
524          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
525        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
526      - re-order sequence of calls within packages_readparms.F,
527         packages_init_fixed.F and packages_write_pickup.F
528        (but skip packages_init_variables.F because of TAF issues).
529      - update contrib/*/atm_gray/ experiment.
530    o pkg/seaice (ITD code):
531      - simplify and fix the writing of pickup-files for ITD case
532    o pkg/seaice (ITD code):
533      - introduce floe size dependent lateral melt for ITD case;
534      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
535      - update seaice_itd experiment main output.
536    o pkg/thsice:
537      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
538        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
539        changed accordingly pkg/atm2d.
540    
541    checkpoint64g (2013/05/01)
542    o pkg/exf ALLOW_RUNOFTEMP
543      - if defined,  river and glacier runoff temperature can be read-in from
544        runoftempfile; runoftempfile needs to have same format as runofffile
545    o pkg/thsice (& pkg/bulk_force):
546      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
547        for energy content of Precip + RunOff & Evap (like with pkg/exf).
548      - change computation domain to always be the interior (without overlap).
549      - fix bug (wrong overlap) when using EXF and stressReduction > 0.
550    o verification/tutorial_global_oce_biogeo:
551      - add preliminary OpenAD setup (still has problems)
552    o pkg/seaice:
553      - turn some parameters for choosing the convergence criterion of
554        the inexact Newton method (JFNK) into runtime parameters for convenience
555      - clean up seaice_calc_viscosities.F: remove/retire two options for
556        SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
557        the results of lab_sea/input because a division has been replaced by
558        a multiplication with the reciprocal (sumNorm)
559      - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
560        convergence of solver (changes results, of course), and to test some
561        new features
562    o model/src:
563      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
564      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
565      - move forcing adjustment (balancing surface forcing) in specific S/R
566        where might also be applied exchanges (if needed) to forcing arrays.
567    o pkg/shelfice:
568      - allow to specify the Ice-Shelf mass per unit area (instead of
569        shelficeLoadAnomaly) and do the conversion from one to the other
570      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
571        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
572        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
573        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
574      - update isomip experiment forward output (get machine truncation error
575        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
576    o verification/offline_exf_seaice:
577      revise data.seaice in input.thermo and input_ad and update results accordingly
578        HO = 0.2, SEAICE_areaLossFormula = 2,
579        SEAICE_growMeltByConv = .TRUE.,
580        SEAICE_doOpenWaterMelt = .TRUE.,
581      Improve consistency with input.thsice and fix the spurious 500m ice corners
582    o verification/global_ocean.cs32x15:
583      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
584        in icedyn (thsice+seaice-dyn) test and update output.
585    o verification/offline_exf_seaice:
586      - adjust list of tested variables (with testreport) and update
587        standard test output with better slection of monitored fields.
588    o pkg/cd_code:
589      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
590        experiment lab_sea.hb87
591    o tools/genmake2:
592      - change default makedepend from the system default to tools/xmakedepend:
593        When no makedepend is specified, select tools/xmakedepend it the test pass,
594        otherwise select the system default (if exist and pass the test) or
595        try to build cyrus-makedepend ; stop if none of the 3 works.
596    o pkg/exf & pkg/thsice:
597      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
598        for energy content of Precip + RunOff & Evap. Assumes:
599       1) Rain has same temp as Air.
600       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
601       3) Run-Off comes at the temp of surface water (with same Cp)
602       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
603        put directly into Latent Heat flux & should use water-vapor heat capacity.
604       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
605        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
606    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
607        (compile when SEAICE_ALLOW_JFNK is defined)
608    o pkg/thsice:
609      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
610        implementation): move THSICE_AVE call after the advection (called directly
611        from thsice_do_advect.F).
612    o verification/global_ocean.90x40x15 and OpenAD:
613      New experiment for OpenAD is identical to the one in input_ad except that
614        multiDimAdvection=.FALSE.,
615      There is still an issue with this.
616    o pkg/thsice:
617      - account for ice velocity (ocean relative velocity) in turbulent heat flux
618        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
619        and offline_exf_seaice (main test).
620    
621    checkpoint64f (2013/03/31)
622    o verification/OpenAD:
623      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
624    o verification/isomip, pkg/shelfice and OpenAD:
625    - 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
626  o verification/offline_exf_seaice: replace adjoint experiment.  o verification/tutorial_global_oce_biogeo:
627      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
628    o verification/offline_exf_seaice:
629      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
630  o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:  o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
631    - 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
632  o pkg/seaice/seaice_evp.F: mask the asymmetric contribution of the ice-ocean  o pkg/seaice/seaice_evp.F:
633    stress (when the turningAngle is non-zero) over open water to avoid     mask the asymmetric contribution of the ice-ocean stress (when
634    stripes in the EVP-solutions after many EVP-substeps. This does not change     the turningAngle is non-zero) over open water to avoid stripes
635    the verification experiment (because turningAngle=0 in that experiment), but     in the EVP-solutions after many EVP-substeps. This does not change
636    will affect other EVP solutions with turningAngle.ne.0     the verification experiment (because turningAngle=0 in that experiment),
637       but will affect other EVP solutions with turningAngle.ne.0
638  o verification, AD & TLM output:  o verification, AD & TLM output:
639    - 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
640      additions and multiplications which affect results at machine truncation      additions and multiplications which affect results at machine truncation

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