/[MITgcm]/MITgcm/doc/tag-index
ViewVC logotype

Diff of /MITgcm/doc/tag-index

Parent Directory Parent Directory | Revision Log Revision Log | View Revision Graph Revision Graph | View Patch Patch

revision 1.1738 by jmc, Mon Sep 17 22:32:32 2012 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 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
626    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:
631      - add OpenAD setup to this exp and make ptracers package work with OpenAD
632    o pkg/seaice/seaice_evp.F:
633       mask the asymmetric contribution of the ice-ocean stress (when
634       the turningAngle is non-zero) over open water to avoid stripes
635       in the EVP-solutions after many EVP-substeps. This does not change
636       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:
639      - 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
641        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
642        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
643        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
644        digits of matching.
645    o pkg/seaice:
646       modify lsr-algorithm so that it vectorizes AND converges by using a
647       "zebra" method: split vector loop into two with step size 2; this
648       solves a general convergence problem for the JFNK solver on a vector
649       computer. It has the potential to even improve convergence for
650       non-vector machines, but it does change the results so it is turned
651       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
652       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
653    
654    checkpoint64e (2013/03/05)
655    o pkg/ecco and several verification experiments:
656       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
657       from ecco package, and revert to unified routine in model/src/
658       Adjust verification experiments accordingly, especially gloal_oce_llc90
659       Should conclude long-standing work by Gael to reconsile the_main_loop with
660       ECCO and will enable OpenAD's revolve loop in ECCO setup.
661    o pkg/generic_advdiff:
662      - implement compressible flow method for multi-dim advection (similar to
663        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
664        TAF generates many recomputations) to use it; no yet coded with implicit
665        vertical advection.
666      - change experiment advect_cs (new output) and advect_xy (same output)
667        to test compressible flow multi-dim advection.
668    o pkg/generic_advdiff:
669      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
670        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
671    o pkg/seaice:
672      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
673        bug affects two verification experiments (lab_sea and lab_sea.hb87),
674        recover old (wrong) results by setting noSlipFac = 2. in
675        seaice_calc_strainrates.F;
676      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
677      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
678        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
679      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
680    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
681      - new subroutines seaice_lsr_tridiagu/v
682      - introduce loop bounds i/jmin/max to be able to use a restricted
683        additive Schwarz method, but not used for now.
684      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
685      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
686    o OpenAD support
687       Reorganize S/R call for overall time-stepping loop to facilitate
688       OpenAD revolve loop replacement
689       (new S/R main_do_loop.F)
690    o model/src:
691      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
692      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
693        ADAMS_BASHFORTH2.
694    o pkg/cheapaml:
695      - add new parameter (default=F, same as before) to disable full domain
696        (including land) periodicity in X & Y dir.
697      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
698        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
699        into single S/R CHEAPAML_TIMESTEP.
700    
701    checkpoint64d (2013/02/17)
702    o pkg/monitor (angular momentum):
703      - do not add Eta contribution to the total AM if using rigid-lid;
704      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
705      - horizontal discretisation: compute Zonal wind contribution separately for
706        each component (instead of from cell centered averaged) and use the 4
707        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
708      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
709        FreeSurf) if using vectorInvariant momentum.
710    o model/src (horizontal grid):
711      - move initialisation of all horizontal grid arrays to null value
712        from specific horizontal grid S/R to main S/R INI_GRID;
713      - add 2 new arrays to project model C-grid velocity on to zonal direction
714        (similar to AngleCosC & -AngleSinC but at U and V point location) and
715        compute them in S/R CALC_GRID_ANGLES.
716    o pkg/seaice: replace a hard coded parameter by a runtime parameter
717        SEAICE_JFNK_tolIter
718    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
719        preconditioner for JFNK (run LSR into the overlaps as far as possible,
720        i.e OLx/y-2, but overwrite the solution in the overlaps)
721      - extend loop range in seaice_calc_viscosity
722      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
723      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
724      - slightly modify loops in tridiagonal solver lsr-preconditioner
725      - by default remove the extra exchange in seaice_preconditioner with a
726        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
727      - modify offline_exf_seaice so that old results without RAS are reproduced
728        for output.dyn_jfnk.txt
729      in seaice_fgmres.F (unrelated to RAS)
730      - add a cpp-flag option for a re-ordered mapping (potentially more
731        efficient), but because this changes the results, turn it off by
732        default
733      - replace the save statement by local common blocks
734    o utils/matlab:
735      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
736      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
737        instead of local script "load_cs.m".
738    o pkg/seaice:
739      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
740        to the scalarProductMetric and the unrolling. By chance this does not
741        change the verification experiment, because of the particular domain
742        decomposition
743    o pkg/diagnostics:
744      - change default missing_value from UNSET_RL to -999.
745    o pkg/layers: improve vectorization of layers_fluxcalc.F
746      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
747        time spent in this routine by more than a factor of 3 on an NEC-SX8
748      - step 2: replace search algorithm by a bisection algorithm found in
749        Press et al. Numerical Recipes in Fortran. This algorithm can be
750        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
751        For now, use this algorithm only for TARGET_NEC_SX defined.
752      - moved the search algorithm into a separate subroutine, that is kept
753        within the same file for automatic inlining.
754      - modified catching potential errors
755    o pkg/ecco:
756      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
757    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
758      - modifications for ALLOW_GENTIM2D_CONTROL
759      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
760      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
761      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
762      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
763    o model/src:
764      - account for moist thermodynamics in (dry) potential temperature equation;
765        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
766        and cpl_aim+ocn.
767      - also switch to standard compiler (gfortran, was using ifort previously)
768        for fizhi-cs experiments reference output.
769    o pkg/ctrl:
770      - 1st step toward generic time-varying control variable (2D) via CPP option
771        ALLOW_GENTIM2D_CONTROL
772      - note new namelist ctrl_nml_genarr in data.ctrl
773    o verification/global_ocean.cs32x15:
774      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
775        thsice calling sequence and update "output.icedyn.txt" output file.
776    o pkg/ptracers:
777      - from Ryan A.: code to allow to restart a tracer at regular time interval
778        specifying a reset frequency and a reset-phase (for each tracers).
779    o pkg/thsice:
780      - implement new sequence of calls for thsice+seaice:
781          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
782          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
783      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
784        in CPP_OPTIONS.h) to recover old sequence;
785      - update diagnostics for Intermediate State thsice diagnostics: now filled
786        just before advection (instead of just after advection in old sequence);
787      - update output of experiment offline_exf_seaice (standard test);
788      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
789        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
790    o pkg/aim_v23:
791      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
792      - use standard pkg/mdsio routines to read & write CO2 pickup file;
793      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
794      - Implement new sequence of calls for seaice advection (with thsice and
795        seaice diffusion): do ice advection after ice-Thermodynamic (previously
796        was done before); change aim_do_physics.F (split the bi,bj loops block);
797      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
798    o pkg/thsice:
799      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
800        where just seaice diffusion is used without seaice-dynamics.
801    
802    checkpoint64c (2013/01/18)
803    o pkg/seaice:
804      - add a parameter JFNKres_tFac that can replace JFNKres_t
805        (= JFNKres_tFac*JFNKresidual before JFNK solver)
806      - add a line search option to the JFNK solver
807      - move update of u/vIce and computation of initial residual into a separate
808        routine (same file); makes the code a little easier to read (?)
809      - the line search requires computation of the residual and for some reason
810        I cannot do the update of u/vIce at the beginning of the Newton loop
811        without changing the results, so we move computation of the new residual
812        also to the end of the Newton loop, even without the line search
813    o pkg/mdsio:
814      - write missing value (corresponding to undefined array value) to meta files;
815        skip this if missing value is one (UNSET_RL would be a better value for the
816        case of undefined missing value but it's current the default missing-value);
817        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
818    o pkg/exf & thsice:
819      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
820        diagnostics) even when SHORTWAVE_HEATING is #undef;
821    o verification/cfc_example:
822      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
823        illustrate how to use it).
824    o verification/offline_exf_seaice:
825      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
826        files to only one time-record.
827      in input.thermo: narrow the 2 bands of low initial ice-concentration near
828        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
829        snapshot output; same mcPheePiston value as in thsice with
830        surf-current=0.2m/s.
831      in input.thsice: similar set-up as in input.thermo (channel with same seaice
832        initial conditions).
833    o verification/cfc_example:
834      - update file "data" with more standard choice (default rotationPeriod,
835        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
836        set deltaTFreeSurf to deltaTtracer) and update the output.
837    o pkg/layers:
838      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
839      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
840    o verification/offline_exf_seaice:
841      - set all {field}period to zero for constant-in-time forcing (not tested
842        anywhere else).
843    o verification/offline_exf_seaice:
844      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
845      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
846    o model/src:
847      - implement Finite-Volume method for (hydrostatic) presure gradient
848        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
849    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
850      - In order to be compatible with the default EVP code, this requires changing
851        the EVP code around a little; and because any small change immediately
852        breaks the lab_sea.hb87 verification experiment, the reference output is
853        updated two times (each time the remaining aggrement was only 2 digits):
854        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
855        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
856        The adjoint test lab_sea.evp also needed to be updated.
857      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
858        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
859        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
860        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
861        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
862        kept obscure, because I need to test it a little more.
863    o pkg/cheapaml:
864      - fix few incorrect type (_RL/_RS) in subroutine calls.
865    o pkg/seaice:
866      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
867        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
868    o model/src:
869      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
870        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
871        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
872    o pkg/cheapaml:
873      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
874        update output of experiment cheapAML_box.
875      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
876        and set them only in one place (cheapaml_readparms.F).
877      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
878      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
879        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
880    o model/src/the_main_loop.F:
881      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
882    o pkg/seaice:
883      - remove legacy branch code.
884      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
885    o verification/*/code*/SEAICE_OPTIONS.h:
886      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
887        SEAICE_CAP_HEFF).
888    o pkg/cheapaml:
889      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
890        to load new forcing fields.
891      - add missing "_d 0" where it's needed; + some editing (improve indentation).
892      - remove switch to "-r8" compiler option (no longer needed) in verification
893        cheapAML_box, keep same output (small trucation error differences).
894    o verification/offline_exf_seaice:
895      - add thermodynamics only test.
896    o verification/cheapAML_box:
897      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
898        keep same output (same 14 digits for cg2d).
899      - switch on "-r8" compiler option (some numerical values are missing
900        the "_d 0") and update output (only 6 digits for cg2d were preserved).
901    
902    checkpoint64b (2012/12/24)
903    o pkg/cheapaml:
904      - remove un-used variables (Qnet,EmPmR) from pickup files.
905      - store tendency of advected variables into cheapaml pickup file
906        and fix the AB-2 restart.
907    o verification/offline_exf_seaice and lab_sea adjoint:
908      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
909      - switch to 4 time steps in offline, consistent with lab_sea.
910      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
911      - update results after change of experiment seaice.
912    o pkg/seaice:
913      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
914        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
915        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
916        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
917    o model/src:
918      - add run-time parameter to select CG2D solver minimum-residual solution
919        (in case of a poor convergence).
920    o pkg/seaice/seaice_lsr.F
921      - move calculation of matrix coefficients into new
922        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
923        file; the main purpose of this change is to be able to reuse the code
924        in S/R SEAICE_PRECONDITIONER
925      - modify the computation of the residual so that the mass of sea-ice
926        is not used twice; this simplifies the calculations, but since
927        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
928        not tested in testreport---this does not affect the testreport results.
929    o verification/seaice_obcs:
930      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
931        verification/lab_sea/input.salt_plume; changes results/output.txt*
932    o model/src:
933      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
934    o pkg/seaice:
935      - improve description of parameters in seaice_fgmres.F and start
936        cleaning up the code
937      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
938        second argument
939      - add a metric based on grid cell area to SEAICE_SCALPROD; update
940        results of offline_exf_seaice.dyn_jfnk
941      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
942    o pkg/aim_v23:
943      - fix an other bug in dissipation heating (grid-cell area was missing).
944    o model/src + pkg/seaice:
945      - add global (multi-tile) linear solver for pair of tri-diagonal system
946        along X and Y lines, respectively for U and V component.
947        Note: 1) MPI and cube-exchange not yet coded.
948            2) probably not accurate for poorly conditioned / large size problem.
949      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
950        default: not compiled and not used.
951    o pkg/seaice:
952      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
953        introduce bi/bj loops and use global_sum_tile_rl instead of
954        mpi_allreduce in seaice_fgmres.F
955      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
956      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
957      - add a verification experiment for JFNK in offline_exf_seaice
958    o verification:
959      - change (for now, only fwd test) offline_exf_seaice experiment:
960        use a re-entrant channel with idealized coastline (trapezoidal shape)
961        at southern boundary to explore seaice dynamics and thermodynamics
962        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
963        secondary test (input.thsice) use thermodynamics only with SST relaxation.
964      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
965    o pkg/exf:
966      - disable "sstExtrapol" when Nr=1
967    o verification:
968      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
969        to test pkg/cheapaml.
970    o pkg/aim_v23 & pkg/shap_filt:
971      - fix dissipation heating (erroneous gravity multiplication factor).
972    o pkg/seaice:
973      - remove unused field pressPre from jfnk solver
974      - rename two subroutines in seaice_preconditioner.F
975    o eesupp/src:
976       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
977    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
978       - remove wrong parts of the rhs and the lhs (were in there
979         because I did not understand the concept of this preconditioner)
980       - add an exchange between u- and v-sweep. This increases communication
981         by a factor of two but improves the convergence of jfnk. Ideally,
982         one would like the u- and v-sweep to be independent. So far within
983         undocumented ifdefs
984       - reorganize the extra computations for printing the residuals
985    o tools/genmake2:
986      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
987        since it's not necessary (and was preventing to use MNC in some cases).
988    
989    checkpoint64a (2012/11/16)
990    o pkg/autodiff:
991      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
992        autodiff_readparms.F no longer depends on calling order (within
993        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
994        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
995        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
996    o pkg/obcs:
997      - adding tidal velocity forcing capability to obcs
998        for usage example, see verification/seaice_obcs/input.tides
999    o pkg/seaice:
1000      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
1001        SEAICE_LSRrelaxU/V
1002      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
1003    o pkg/aim_v23:
1004      - implement heating from friction (bottom friction and stratospheric drag).
1005    o pkg/shap_filt:
1006      - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
1007        dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
1008    o model/src:
1009      - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
1010        time-constant addMass field from file (addMassFile);
1011      - support for heating due to friction (and Kinetic Energy dissipation):
1012        add option, run-time switch and 3-D field array + support code ; each pkg
1013        or S/R can add heating contribution (if there is a sink of KE); the sum is
1014        accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
1015    o pkg/seaice:
1016      - complete merge of ITD code into seaice_growth.F
1017        from MITgcm_contrib/torge/itd/code/
1018        no verification so far, but Torge Martin tested
1019        "1-D test case and Beaufort set up;
1020        deliver okay results after 1 model year."
1021      - complete merge of SEAICE_SIZE.h into all relevant routines
1022      - move computation of eta at Z-points into calc_viscosities
1023        + introduce global field etaZ
1024        + add different methods for computing etaZ, for now the old
1025          method (simple averages of eta to Z-points) is hardwired
1026        + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
1027          seaice_preconditioner
1028      - simplify computations for SEAICE_ZETA_SMOOTHREG
1029      - seaice_preconditioner:
1030        + replace one remaining press by pressLoc (mistake)
1031        + adjust printing of residuals
1032      - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
1033        + add (SEAICE.h) and rename some counters (initiliased in
1034          seaice_init_fixed.F)
1035        + add _BEGIN/END_MASTER (myThid)  around print statements
1036        + print total number of iterations and failures over SEAICE_monFreq
1037          interval to STDOUT
1038      - move control over output-messages by fgmres to seaice_jfnk to save
1039        some operations
1040      - move resetting initial guess for fgmres outside of seaice_fgmres_driver
1041        in order to make restarts with sol .ne. zero (fgmres with restarts)
1042        (seaice_jfnk.F, seaice_fgmres.F)
1043      - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
1044        a serious convergence problem when open boundaries are involved
1045    o pkg/ggl90: fix computation of control volumes for the case of
1046      ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
1047      up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
1048    o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
1049    o pkg/autodiff
1050      - Add inAdMode switch for SEAICEuseDYNAMICS:
1051        SEAICEuseDYNAMICSinAdMode
1052        (extend logic in ADAUTODIFF_INADMODE_SET)
1053    o pkg/seaice
1054      - Step 1 of merging ice-thickness distribution (ITD) code from
1055        MITgcm_contrib/torge/itd/ (author: Torge Martin)
1056        The code implements concept laid out in Thorndike et al. (1975);
1057        code is enabled via CPP flag SEAICE_ITD
1058        nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
1059        code is not complete yet!!
1060      - SEAICE_SIZE.h now included in almost all seaice routines
1061    o verification (using seaice):
1062      - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
1063        global_ocean.cs32x15.seaice ; update results.
1064      - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
1065      - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
1066        offline_exf_seaice (previously compiling B-grid).
1067    o pkg/exf:
1068      - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
1069        to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
1070        forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
1071    o pkg/layers (adjust changes from Sept 19):
1072      - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
1073        this allows to remove "layers_maxNum" dimension from all layers arrays.
1074    o pkg/layers (adjust changes from Sept 19):
1075      - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
1076      - snap-shot extended to all type of layers (not just the 1rst type);
1077      - remove layers variables when corresponding CPP option is undef.
1078    o pkg/layers:
1079      - rename pkg/layers variable and add new output (layer exist & un-weighted
1080        velocity in layer)
1081    o pkg/seaice:
1082      - simplify (?) ocean-drag coefficent computations by using
1083        the same routine in all three solvers (saves some code lines)
1084      - remove global fields DRAGA and DRAGS from C-grid code and
1085        declare them locally in lsr.F (the only place where they are
1086        still used)
1087      - update AD output of lab_sea.evp (very sensitive anyway).
1088    o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
1089      (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
1090      and SEAICEuseJFNK=.true. A few things to note:
1091      - involves a FGMRES, that is parallel but very inefficient,
1092        because of many scalar products (global sums) in the Gram-Schmidt
1093        orthogonalization method. Needs to be replaced. Original code
1094        from J.-F. Lemieux
1095      - preconditioner for FGMRES is a stripped down version of LSOR
1096      - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
1097        preconditioner. For the preconditioner, the default is set to 10.
1098      - Jacobian times vector is computed with finite differences
1099      - marginally related to JFNK-solver: add a smooth regularization for
1100        zeta with tanh that will improve convergence (Lemieux and Tremblay,
1101        2009) for any implicit solver (not implemented for EVP because EVP
1102        does not need this regularization in the first place). Define
1103        SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
1104    o eesupp/src:
1105      - check in genmake2 that intrinsic S/R flush is available.
1106      - add S/R to flush IO unit (if intrinsic S/R flush is available)
1107      - flush standard & error msg unit before MPI termination
1108      - if debugMode, flush IO unit after printing msg
1109    o pkg/ctrl:
1110      - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
1111        to ctrl_set_unpack_xyz.
1112    
1113    checkpoint64 (2012/10/09)
1114    o pkg/shelfice
1115      - in mom_fluxform.F, mom_vecinv.F:
1116        CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
1117        Bug fix KappaRU -> KappaRV
1118        does not change verification/isomip but may change other setups
1119        (presumably constant KappaRU=KappaRV)
1120      - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
1121    o pkg/obcs:
1122      - fixed some indexing bugs in obcs_seaice_sponge.F
1123      - added obcs relaxation subroutines for HSALT and HSNOW
1124      - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
1125    o pkg/seaice:
1126      - add "multicategory" parameterization for snow in analogy to ice,
1127        default is off for now.
1128    o pkg/obcs:
1129      - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
1130        see verification/seaice_obcs/input.seaiceSponge for example application.
1131      - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
1132        index setting by master-thread. This fix multi-threads Pb in previous modifs.
1133    o pkg/layers :
1134      - add diagnostics to pkg/layers
1135      - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
1136        (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
1137    o pkg/generic_advdiff/gad_implicit_r.F :
1138      - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
1139    o pkg/seaice/seaice_growth.F:
1140      - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
1141    o pkg/obcs:
1142      - change default setting of OBCS_UVICE_OLD from defined to undef;
1143      - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
1144        in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
1145      - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
1146      - change OB null index value (OB_indexNone) to -99 ; this fix the problem
1147        with Southern & Western OB at a tile edge (at least in a simple set-up).
1148  o pkg/obcs:  o pkg/obcs:
1149    - change settings of OB index in case OB coincides with tile edge (shared by    - change settings of OB index in case OB coincides with tile edge (shared by
1150      2 tiles), so that common OB location is registered by both tiles (instead of      2 tiles), so that common OB location is registered by both tiles (instead of
1151      only 1). However, for Southern and Western OB, index value = 0 is not      only 1). However, for Southern and Western OB, index value = 0 is not
1152      recognized as valid OB index (=default null value) and needs to be fixed.      recognized as valid OB index (=default null value) and needs to be fixed.
1153    - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)    - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
1154    - new parameter "OB_indexNone" for null index value (for now, still zero)    - new parameter "OB_indexNone" for null index value (for now, still zero)
1155      to replace hard-coded null index value of zero.      to replace hard-coded null index value of zero.
1156  o pkg/exch2:  o pkg/exch2:
1157    - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:    - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
Legend:
Removed from v.1.1738  
changed lines
  Added in v.1.1957
  ViewVC Help
Powered by ViewVC 1.1.22