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revision 1.696 by heimbach, Sat Jul 8 00:29:20 2006 UTC revision 1.993 by mlosch, Thu May 22 08:36:53 2008 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7  o take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V  o pkg/diagnostics: enforce missing_value attribute for scalar variables at
8      mass points, when using mnc for output
9      - add runtime parameter (missing_value, missing_value_int) to override
10        default (which is the value of getcon('UNDEF'))
11    o pkg/mnc: prepare mnc for the actual use of missing values with the
12      diagnostics package: small fix in mnc_cw_readwrite.template and more
13      initialisation of never used fields
14    o pkg/thsice/thsice_ini_vars.F added default initial values so that thermodynamics
15      sea ice solver does not blow up when some initial fields are missing.
16    o move from external_forcing_surf.F to ini_forcing.F
17      the p-coord. hack consisting in using pLoad to set phi0surf ;
18      update output of tutorial_global_oce_in_p (affected @ truncation level).
19    o Freshen up a bit hs94.1x64x5, notably:
20      remove rotationPeriod and tRef=5*0. (adjoint only), and add exactConserv=.TRUE.
21    o pkg/generic_advdiff:
22      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
23      applies to files where Temperature & Salinity 2nd Order moments are used.
24    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
25      this uses a dynamically allocated internal state data structure
26      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
27      and requires a fortran 90 compiler
28    
29    checkpoint59q
30    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
31       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
32    o Refresh tutorial_global_oce_biogeo, notably:
33      - change bathymetry (put back seamounts in ACC, use hFacs)
34      - change EOS (POLY3 --> JMD95Z)
35      - use Bryan-Lewis vertical diffusivity
36      - use multidimensional advection
37      - remove old virtual virtual in dic pkg, now done through ptracer pkg
38      - change a couple of parameters in dic pkg
39    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
40    o pkg/obcs: change default to OBCSfixTopo = .true.,
41      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
42      - replace "debugMode" with "debugLevel .GE. debLevB"
43    o implementation of TAF directives for gchem,cfc,dic
44    o remove "exp5" (replaced by tutorial_deep_convection).
45    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
46      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
47      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
48      --> changes results in exp4, seaice_obcs
49    o tutorial_deep_convection :
50      update the set-up and increase resolution and domain size ; start
51      from pseudo initial conditions = output at t=120mn in order to see
52      something happening when running testreport.
53    o pkg/seaice: add os7mp as an advection scheme
54                  add check for advection schemes
55                  add a flag for restoring T and S underneath sea ice
56    o pkg/my82: add netcdf-support and diagnostics
57    o thsice pkg:
58      - Now hsMax limits snow height by turning it into ice following
59        flooding scheme (and now conserving energy)
60      - Slight rewriting of the formula in thsice_calc_thick.F
61      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
62      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
63    
64    checkpoint59p
65    o gchem / dic / cfc :
66      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
67      - add new parameter files: "data.dic" & "data.cfc" ;
68      - various re-arrangement in initialisation & header file ;
69      - fix tutorial_global_oce_biogeo for multi-threaded test.
70    o pkg/dic: test for "pickup_dic" file when restarting ;
71      if no pickup-file, can restart with a re-initialised pH (same as it did
72      before) providing pickupStrictlyMatch is set to False.
73    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
74      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
75    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
76      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
77    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
78     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
79       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
80    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
81       scheme to use for vorticty-term ;
82     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
83       (with default selectVortScheme, return to original discretisation)
84     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
85    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
86    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
87      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
88      also fix diagnostics VISCAHW & VISCA4W.
89    
90    checkpoint59o
91    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
92    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
93      move a few statemens out the main loop into separate loops
94    o pkg/shelfice:
95      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
96        (kg/m^2/s), does not break tests, because in verification/isomip,
97        rhoConstFresh=rhoConst (by accident)
98      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
99      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
100        new file model/src/seawater.F, so that they are available for all pkgs.
101      - convert potential temperature into in-situ temperature. This changes the
102        isomip tests => update tests
103    o add a flag writePickupAtEnd (default=true) to be able to suppress
104      writing a pickup at the last timestep
105    o tools/mpack-1.6 :
106      - disable automake (not working) and autoconf (not needed).
107      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
108        also cleaner with much less compilation warnings.
109    o pkg/profiles:
110      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
111      (for "less than 32 characters name" compiler requirement)
112    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
113      conditions that have a different sampling frequency than S/T/U/V obcs
114    o pkg/diagnostics (stats-diags):
115      - fix global Min/Max in case 1 processor get only empty tiles
116    o genmake2: replace (4 times)
117         make genmake_tc_1.o >> genmake_warnings 2>&1
118      with
119         COMM="$CC $CFLAGS -c genmake_tc_1.c"
120         echo $COMM >> genmake_warnings
121         $COMM >> genmake_warnings 2>&1
122      to make genmake2 always see the value of CC as specified in the optfile.
123    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
124      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
125      - modify verification advect_cs test to test SOM-advection on CS-grid.
126    o pkg/ctrl:
127      - Rewrite of ctrl_map_ini_ecco.F,
128        introducing a generic routine (ctrl_map_ini_gen.F).
129      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
130    
131    checkpoint59n
132    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
133      number in dedicate array "hdiag":
134      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
135        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
136      - many small changes (integer format) for large number of diagnostics
137      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
138        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
139    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
140      usingSphericalGrid, this allows to define the rotated grid coordinates
141      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
142      geographical coordinates according to the inverse of the rotation defined
143      by the Euler angles, so that Coriolis parameter and online-interpolation by
144      exf works with the geographical coordinates on XC/YC/XG/YG.
145      Naturally, this feature does not work with all packages, so some
146      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
147      profiles), because there the coordinates are assumed to be regular
148      spherical grid coordinates.
149    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
150      - introduce isopycnal diffusion coefficient control.
151    o tools/adjoint_options:
152      - additional control vector components.
153    o pkg/mnc: have mnc create marginally meaning full coordinate variables
154      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
155    o pkg/mypackage:
156      - add example of read/write pickup for state-var ;
157      - add entry points to the main code for state-vars diags & write-pickup.
158    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
159      transitions for useExfYearlyFields
160      - add new subroutine that determines the file to read from for
161        use*YearlyFields = .TRUE. and .FALSE.
162      - add a verification experiment to global_with_exf that tests
163        useExfYearlyFields with USE_EXF_INTERPOLATION defined
164    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
165      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
166      subroutines (which could be generated from a template, because they are
167      almost identical), for now they are included in obcs_prescribe_read.F for
168      simplicity
169    o pkg/exf:
170      - add a little more diagnostic to exf_interp_read (in analogy to
171        mds_read_field, can be turned off with debugLevel < debugLevA=1)
172      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
173        ugly but fast by unrolling short inner loops, inserting a unroll=8
174        directive in routine lagran, and splitting a loop and making do while the
175        outermost loop (the latter requires the intoduction of index arrays)
176    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
177    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
178      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
179    o verification/seaice_obcs: updated for restart test and latest options
180    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
181      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
182      for now this is only available for the C-grid code and also within
183      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
184    
185    checkpoint59m
186    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
187      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
188    o gad_som : fix flux output (& diagnostics) to have same units as other  
189      advection scheme fluxes (was previously multiplied by deltaT).  
190    o added verification/seaice_obcs both to test seaice open boundaries
191      and to provide an example matlab scrpt for generating them
192    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
193    o pkg/salt_plume: clean up salt_plume_frac.F to
194      remove redundancy in PlumeMethod 1 and 4
195    o pkg/kpp: added saltplume diagnostics
196    o pkg/obcs and pkg/seaice:
197      - do not set uice and vice to zero when OB*icefile are unspecified
198      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
199      - moved seaice tracer obcs after call to seaice_growth
200    o pkg/salt_plume: added various options for salt plume depth
201      criterion and for vertical distribution of the salt
202    
203    checkpoint59l
204    o pkg/ptracers: new version of ptracers pickup:
205      read meta file and write only fields which are needed to restart.
206      ( same logic as main pickup file ; also using pickupStrictlyMatch )
207    o pkg/seaice:
208      - add timescale for melting due to warm mixed layer as a means of
209        setting SEAICE_availHeatFrac more conveniently
210      - add a CPP-flag/runtime parameter check for flooding algorithm
211      - reformulated availHeat in seaice_growth.F to be independent of AREA
212    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
213      unit changes
214    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
215    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
216      SX vector computer.
217    o pkg/seaice:
218      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
219        seaice forcing fields can now be read only through pkg/exf
220      - removed some unused halos
221    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
222    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
223      or U/VICE from U/VWIND before computing U/VSTRESS
224    
225    checkpoint59k
226    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
227      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
228    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
229      all experiments pass when compile with un-initialised var. checking option.
230    o added pkg/salt_plume
231    o script to test restart (for now, in MITgcm_contrib/jmc_script)
232    o pkg/seaice: new read/write pickup version.
233      read meta file and write only fields which are needed to restart.
234      ( same logic as main pickup file ; also using pickupStrictlyMatch )
235    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
236    o lab_sea.hb87: modify the domain & update output.hb87.txt :
237      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
238      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
239      process. Fixed here by closing the domain at the Northern boundary.
240    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
241    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
242      a set of consecutive levels in/from a 3-D array.
243    o pkg/ptracers:
244      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
245      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
246    
247    checkpoint59j
248    o in pkgs: dic, obcs, offline, rbcs:
249      standard way to compute coeff. for time interpolation between 2 time reccords
250      which retains full precision (& make results less dependent on compiler).
251      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
252    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
253      packages instead of reading ice cover and wind speed separately
254    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
255     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
256      to allow to compile customized code before the update)
257    o cleaning-up:
258      - fix CPP instruction syntax in pkg/obcs
259      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
260        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
261      - fix some threads issue in IO parts.
262    o pkg/dic:
263      - add tons of "_d 0" (--> much better testreports !)
264       and then update outputs of tutorial_global_oce_biogeo
265    o pkg/mom_fluxform:
266      add a special version of momentum advection intended to conserve momentum
267      next to a bathymetry step or a coastline edge. (default = off = #undef)
268    o new read/write pickup version:
269      - for now, only implemented for main (mdsio) pickup file.
270      - write out only what is needed to restart; merge pickup_nh , pickup_ph
271        and main pickup together.
272      - read meta file; read only what is needed to restart; stop if a field
273        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
274        if it make sense (even if the restart is not perfect).
275      - if no meta file, assume that pickup to read corresponds exactly to
276        a pickup that would currently be written.
277      - read pickup written in the old format (until checkpoint59i) if it
278        recognizes an old meta file (no field-list).
279      - add a meta file in exp. which starts from a pickup: 2 cases:
280        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
281         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
282        b) a meta file describing the content of the associated pickup file
283         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
284    o pkg/mdsio & pkg/rw:
285      - new routine to read a meta file ; new set of routine to read
286        Multiple-fields file (with meta file).
287    o added open boundary conditions capability for seaice
288        HSNOW, HSALT, UICE, and VICE
289    
290    checkpoint59i
291    o adjoint:
292      * fix multiDimAdvection adjoint
293        (partial recomputation problem by TAF for fVerT(:,:,kDown)
294        and comlev1 size definition (maxpass vs. max. number of tracers)
295      * verification/global_ocean.90x45x15 adjoint now tests
296        NLFS and multiDimAdvection using DST3 (=30)
297      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
298    o pkg/kpp: add "_d 0" to real constant (if missing);
299      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
300      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
301    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
302      for internal parameters related to restart process (formerly from PARAMS.h)
303      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
304    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
305      as argument. (only atm2d & obcs write_pickup have not yet been updated)
306    o pkg/monitor:
307      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
308      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
309      - account for deep Atmosphere factor and density factor (anelastic)
310    o added open boundary conditions capability for seaice HEFF and AREA
311    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
312      thermodynamics
313      - requires a little reorganization, which affects the testreport results
314        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
315        so that now the conservative form is tested
316      - add a few comments
317    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
318    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
319    o add new diagnostics to seaice: advective, diffusive fluxes (only for
320      multidim-advection, for scheme 2 they are not filled) and transports,
321      thermodynamic growth rates
322    o change units of EmPmR (inside the code, + within coupling interface)
323      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
324      Affects results @ truncation level (cg2d match) and update output of
325       experiments: lab_sea(6), global_ocean.90x40x15(10),
326      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
327      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
328      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
329      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
330    
331    checkpoint59h
332    o pkg/exf:
333      - improve vectorization by moving if-statement out of loops in
334        exf_mapfields, exf_radiation
335      - exf_bulkformulae.F: introduce 2D fields and vectorize code
336    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
337    o testreport:
338      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
339        monitor & update offline_exf_seaice exp. output.
340      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
341    o pkg/seaice:
342      - bug fix in the evp solver: boundary conditions were affected be
343        masking of zMax/zMin (changes results)
344      - minor bug fix in boundary conditions in seaice_calc_strainrates
345        (changes results for no_slip)
346      - seaice_lsr.F: make interpolation of eta dependent on boundaries
347      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
348      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
349        stress formulation and no-slip boundary conditions
350    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
351      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
352    o pkg/seaice: a first HSALT time stepping equation has been checked in
353    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
354      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
355      without requiring DO-IF statements
356    o pkg/thsice:
357      use continuous power-law function for partition of energy between lateral
358      melting/freezing and thinning/thickening ; old code using step function
359      still available with #undef THSICE_FRACEN_POWERLAW
360      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
361    o testreport: change AD testing : check against results/output_adm.txt
362      using same scripts as for forward test.
363    
364    checkpoint59g
365    o adjoint testing: in preparation for changing testreport:
366      - output format: cost and grad written on separated lines
367      - ad output results in directory "results" (instead of "results_ad")
368    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
369    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
370    o pkg/ecco: allow user defined cost function contributions
371    o testreport:
372      Allow to choose (per experiment) the list of tested output variables
373       and the main variable (used to issue a pass/FAIL ) ;
374      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
375      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
376      Also modify printing of summary:
377       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
378       b) echo the list of tested variables in the individual summary.txt of
379          each experiment.
380    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
381      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
382      (but still depend on the tile decompostion of the domain).
383    o pkg/seaice: change a discretization detail to make the B-grid code
384      "more symmetric". This change is likely to remove all "ridges/leads" that
385      where quasi-aligned with the grid in B-grid solutions. It may also be
386      the solution to the stress coupling issues with the B-grid.
387    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
388      remove .cvsignore from input dir. (since testreport no longer run here).
389    o pkg/thsice:
390     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
391     - fix reshaping of sea-ice just after advection:
392       melt all the ice only if ice-volume is too small.
393     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
394       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
395     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
396    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
397      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
398    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
399      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
400      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
401      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
402      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
403      -> update output.txt
404    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
405     this affects truncation error: -> update output.txt of exp:
406      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
407      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
408    
409    checkpoint59f
410    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
411    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
412      a bounded range (in forward mode)
413    o pkg/ecco, ctrl, autodiff and mom_common:
414     internal parameter controls, completements of implementations
415    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
416    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
417      (not seem any difference in testing results).
418    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
419       at face corners.
420    o pkg/generic_advdiff:
421     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
422      loop range indices for computing vertical advection tendency
423      and do the calculation in the interior only (no overlap) ;
424      for now, only implemented for SOM advection (to save CPU time).
425     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
426    o exch2 adjoint
427      First set of changes:
428      - add exch2 hand-written adjoint templates
429      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
430        This will require cleanup in pkg/autodiff/*.F
431        (changed routines currently kept separate in verif. code/)
432      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
433        that used to hide exch2 or cubed-sphere specific code
434        (commented via 'cph-exch2')
435    o pkg/seaice
436      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
437    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
438       output of global_ocean.cs32x15.thsice .
439    
440    checkpoint59e
441    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
442      for B-grid vector (not yet tested) and C-grid vector (<- only used
443      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
444    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
445      (#ifdef ALLOW_SALT_PLUME)
446    o gather_2d/scatter_2d: removed halo regions
447    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
448      scheme and the corresponding test case (under front_relax dir). For now,
449      only available with Skew-flux form and not yet tested in realistic set-up.
450      adjoint: store directives updated, but gradient checks deteriorated,
451      so maybe GM/Redi adjoint is now broken.
452    o seaice adjoint
453      * add AREA, HEFF, HSNOW as control variable
454        (should not change lab_sea results)
455      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
456    o pkg/seaice:
457      * added computation of saltFlux in seaice_growth;
458        For time being, sea ice salinity is assumed constant
459        contribution of snow flooding to freshening of sea ice is neglected.
460        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
461        defaults to 0.0 in order to maintain backward compatibility.
462        Typical values for SEAICE_salinity are 4 to 10 g/kg.
463      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
464      * added SEAICE_availHeatFrac, which specifies fraction of surface level
465        heat content used to melt or grow ice
466      * commented out cap of HICE: it helps keep ice thinner
467      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
468      * applied OBCS T/S mask to HEFFM sea ice mask
469    
470    checkpoint59d
471    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
472     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
473     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
474    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
475     and change default value of parameter "GM_Small_Number";
476     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
477       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
478       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
479    o pkg/ecco: cost function when applying pkg/smooth to controls
480    o pkg/ctrl: add forcingPrecond run time parameter
481    o pkg/seaice:
482     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
483     - fix bug in metric terms of u-equation in LSR solver (implicit part),
484       changes verification/lab_sea
485     - rearrange implicit part of u-equation in LSR solver to make it easier to
486       read, understand, and debug. This causes changes at the truncation level.
487     - fix (serious) bug in the boundary conditions (sign error in the implicit
488       part) of the LSR solver. Changes all LSR results.
489     - fixed problem with HSNOW initialization to avoid thick snow when AREA
490       is initilized with small values - does not change lab_sea results.
491     - added HsnowFile initialization capability
492    o pkg/smooth: addition to model/src and pkg/ctrl so allow
493     initialization of pkg/smooth and application to control vector
494    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
495    o dependencies: pkg/profiles requires pkg/cal
496    o pkg/profiles:
497     - added option ALLOW_PROFILES_GENERICGRID
498         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
499         that interpolation information (grid points and coefficients) is provided
500         within the netcdf input files.
501         -> sample matlab scripts can be found in MITgcm_contrib/gael
502         that allow you to prepare netcdf input files.
503     - also modified: cleaner include statements, cleaner error print statements,
504       cleaner stops when error, and more tests of the netcdf input files consistency.
505    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
506    o pkg/seaice:
507     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
508       requires a new routine: seaice_diagnostics_fill.F
509     - make sure that seaice does not move if not forced (pressure replacement
510       method, Hibler and Ip, 1995), changes results
511     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
512     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
513       It is turned off by default (=-1.), because it changes the results.
514     - make it possible to read AREA from a file, too.
515    
516    checkpoint59c
517    o add S/R and diagnostics for oceanic mixed-layer depth
518    o move GMRedi call after all vertical mixing schemes (including KPP)
519    o pkg/thsice:
520     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
521      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
522    o pkg/obcs:
523     - bug fix for balance code
524    o pkg/seaice:
525      - allow values of SEAICE_elasticParm > 1
526      - add new parameter SEAICE_evpTauRelax as an alternative
527        to SEAICE_elasticParm
528      - make lsr boundary conditions free slip (by default), changes result
529      - add code for no slip boundary conditions for lsr
530      - set minimum of zeta to zero (and not 4e8) (changes results)
531      - add a cap on AREA after advecting AREA if seaice_growth is not called
532    o change calculation of Visbeck K:
533      - no longer depend on tapering scheme; instead, compute slope (limited
534        by GM_maxSlope). this is equivalent to what was comuted before with
535        clipping or linear tappering.
536      - fix vertical averaging (wrong by 1/2 level)
537      - leave the old version (but will not be maintained) within
538        #ifdef OLD_VISBECK_CALC / #endif
539      - update output of exp. ideal_2D_oce
540    o change error catch in calc_r_star to improve vectorization
541    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
542      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
543    o adjoint:
544      Re-organized adjoint checkpointing according to Matt Mazloff
545      (but with modifs/completions/cleanups)
546      Storing is now bundled into large arrays to optimized I/O
547      (and second step in cleanup of the_main_loop)
548    
549    checkpoint59b
550    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
551      - export/import (between ocean & coupler) fields needed for ocean DIC.
552    o pkg/seaice:
553      - get rid of three more exchanges seaice_calc_viscosities (required
554        different loop boundaries in seaice_lsr and seaice_ocean_stress)
555      - bug fix in seaice_ocean_stress (update of lab_sea required)
556      - reduce loop boundaries to necessary minimum also in seaice_evp
557      - go back to the old way of computing deltaC/Z as the adjoint likes that
558        better
559    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
560      passive tracer to an Age Tracer) + update output.txt
561    o pkg/exf:
562      - implement A-grid / C-grid selection for wind-stress input files.
563      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
564      for now, in exf_bulk_largeyeager04.F only :
565      - change implementation for case where windspeed + 2. components wind-stress
566        are read-in. AND use rhoConstFresh to convert evap.
567    o pkg/seaice:
568      - use correct EXCH_UV for wind-forcing (on A-grid).
569      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
570        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
571    o pkg/exf:
572      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
573      EXF_INTERPOLATION:
574      - merge global_with_exf/code version of exf_interp_read.F
575        to the main code ;
576      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
577        reading the file ; Important: This options needs to be defined to recover
578        previous code.
579        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
580      - no longer loose real*8 precision along the way when using exf_iprec=64.
581    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
582      - change discretisation of evp-solver in order to avoid another exchange
583        (changes lab_sea) and clean up a little
584      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
585        help the adjoint (this also changes the results slightly)
586      - add a few "_d 0" where they had been missing in seaice_evp.F
587      - cleaning up: remove unused seaice_calc_rhs.F
588    o pkg/exf: some cleaning-up:
589      - change various "constants" into runtime parameters
590      - cleaned-up Large&Yeager04 routine which should eventually
591        replace exf_bulkformulae.F (changed names of S/R and CPP)
592        and merged various ALLOW_ATM_WIND options
593     only used with thsice pkg (in thsice_get_exf.F):
594      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
595        which are used when useStabilityFct_overIce=TRUE (= the default)
596      - change default values of ice & snow emissivity and scale downward LW
597        by ice & snow emissivity.
598    o pkg/thsice:
599     fix few little problems, in thsice_calc_thickn.F:
600      - growth vertically (and not laterally) if iceFrac == iceMaskMax
601      - melt only laterally if hIce < hThinIce (as the comments say)
602      and in thsice_extend.F:
603      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
604      - start to form ice as soon as the minimum ice-volume is reachable.
605     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
606      and cpl_aim+ocn
607    o pkg/kpp
608     - move computation of surface related input fields to KPP into a new
609       subroutine kpp_forcing_surf.F
610     - remove wrong (within bi,bj loops) EXCH calls.
611     - little cleaning (add argument myThid in last position, cvs header ...)
612     - for now, fix conservation problem by exchanging KPPviscAz (may not
613       be the best fix)
614    o pkg/seaice
615     - check for inconsistent evp parameter/cpp-flag combination
616     - remove leftover errIO flat for obsolete name list error handling
617    o OpenAD
618     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
619    
620    checkpoint59a
621    o pkg/seaice: some parameter clarifications and a little bit of clean up
622    o pkg/thsice: rename run-time parameters:
623       himin       -> hIceMin
624       himin0      -> hThinIce
625       hihig       -> hThickIce
626       i0          -> i0swFrac
627       transCoef   -> bMeltCoef
628       frac_energy -> fracMelting
629      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
630       with default values (for now) that do not change the results.
631      remove old version of thsice vars advection in pkg/seaice.
632    o in FFIELDS.h:
633      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
634      - make pLoad & sIceLoad always available (but still only used if
635         ATMOSPHERIC_LOADING is #define).
636    o pkg/kpp: replaced _KPP_RL with _RL
637    o bug fixes for vertical diffusivity computations when both KPP and
638        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
639        are no longer updating the vertical diffusivity array
640        (passed as argument) but are (re-) setting those arrays.
641    o pkg/seaice: fix bug in evp solver, while doing that
642      - change (improve?) discretization of stress computations for both
643        cgrid-lsr and evp solver
644      - add a new routine to compute strain rates
645      - the above changes lab_sea results
646      - add no slip conditions for evp solver (off by default), lsr-version
647        may follow
648      - fix exchange for shear at Z-points (does not change lab_sea)
649      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
650        (to force the user to pick a time step since there is not "safe" way
651        of choosing it)
652      - add principal stress diagnostics
653      - rearrange fields for evp a little to avoid having to call a: too many
654        exchanges and b: exchanges for stress trensor components which we do
655        not have.
656      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
657        of evp, complete rewrite for lsr case (latter is does not yet work
658        in all cases)
659    o pkg/kpp: add code to have mixing in shelf ice caverns
660      - add myThid to all kpp routines (long overdue)
661    
662    checkpoint59
663    o pkg/exf:
664      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
665        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
666      - move exf header files from lower_case.h to UPPER_CASE.h ;
667        add missing cvs Header & Name
668      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
669      - add namelist param. selectStressGridPosition, exf_monFreq
670      - retire many _CLIM routines, and remove data.exf_clim
671        + params moved to data.exf
672        + climsst, climsss now handled by exf_set_gen, i.e.
673          climss?period=0 refers to constant field,
674          climss?period=-12 to monthly forcing
675      - split up namelists in data.exf
676    o pkg/seaice:
677      - remove seaice_exch and seaice_exch_uv
678      - remove superfluous exchange of theta
679      - add myThid to seaice_budget_ocean/ice
680      - add new interface for atmospheric wind forcing (C-grid only)
681        + new routine
682        + two new field (taux, tauy for stress over ice)
683        + removed one global field (DAIRN) for C-grid case only
684    o pkg/thsise
685      - 2nd set of modifs for thsice adjoint in conjunction with exf
686    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
687    
688    checkpoint58y_post
689    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
690      vertical diffusivity, similar to that in MOM4; turned on using
691      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
692      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
693    o Added capability for 3D specification of background vertical diffusion
694      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
695      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
696      "data" file that contains the 3D vertical diffusivity coefficients.
697    o ice dynamics (pkg/seaice) with thsice thermodynamics:
698      - add code within pkg thsice to advect & diffuse sea-ice fields
699      similar to (and will replace) what has been added in  seaice_advdiff.F,
700      but: - conserving Mass, Heat & Salt.
701           - better when using non-linear advection scheme (not yet fully tested)
702           - can also be used in atmospheric set-up (for now, only the diffusion).
703    
704    checkpoint58x_post
705    o IO option for global-file compact format:
706      - add options when generating topology (utils/exch2/matlab-topology-generator)
707      - add I/O capability (pkg/mdsio).
708      - adapt utils/matlab/rdmds.m to read this format.
709      for now long-line format not yet supported by pkg/mdsio (& exch2).
710    o shelfice: add a few diagnostics
711    
712    checkpoint58w_post
713    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
714      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
715      (and replace horiVertRatio in NH code).
716      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
717                         and tutorial_plume_on_slope (sensitive to truncation)
718    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
719      directly to drive seaice model (C-grid only)
720    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
721     - reintroduce computation of wind from stress,
722     - compute tau (in exf_bulkformulae.F) from windstress averaged to
723       mass points to avoid tau = 0
724     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
725    o rdmnc.m: make it work with "global" files created with gluemnc
726    o rdmnc.m : some improvements in dealing with singleton dimension
727      (tested on all testreport mnc output files).
728    o genmake2: disable pkg/profiles if netcdf test fails.
729    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
730    o move call to cal_readparms up to make calendar parameters/variable available
731      to all packages
732    
733    checkpoint58v_post
734    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
735      useDynP_inEos_Zc tested.
736    o pkg/exf: changes to properly interpolate/mask/scale initial fields
737    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
738      and portions thereof.  See read_cs.txt for description and examples.
739    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
740      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
741      following the great-circle arc between those 2 points.
742    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
743      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
744    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
745     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
746     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
747     - still needs work (not working with some options ; efficiency to improve)
748       and serious testing.
749     - use this scheme for temperature & salinity in 2 advection test exp.:
750       advect_xy & advect_xz, respectively.
751    
752    checkpoint58u_post
753    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
754    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
755    o testreport: add option "-skipdir" to skip some test.
756    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
757      momentum calculation.
758    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
759    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
760      remove checkpoint.F and the_correction_step.F (no longer used);
761      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
762    o add option (linFSConserveTr) to correct for tracer source/sink due to
763      Linear Free surface
764    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
765    o pkg/thsice: fix reading mnc-pickups
766    
767    checkpoint58t_post
768    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
769    o pkg/mdsio:
770     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
771       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
772       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
773     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
774     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
775       either MDS_READ_FIELD or MDS_WRITE_FIELD )
776     - new S/R (to replace MDSWRITEMETA), which allows to write more
777       informations (variable names, time ...) to meta files.
778     - modify rdmds.m to give back the meta file content.
779    o pkg/diagnostics: change vertical interpolation to be safer, and more
780       flexible (define p-levels to interpolate to in data.diagnostics);
781      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
782       diagnostic pointer.
783    o pkg/seaice: more cleaning up of seaice_growth, added many comments
784    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
785    o fix multi-category seaice:
786     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
787       SEAICE_MULTICATEGORY
788     - fix short wave heat flux
789    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
790       and allow to use EVP solver. Change forward lab_sea: test both EVP
791       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
792    o Initial check-in of lab_sea adjoint
793      (very similar to natl_box_adjoint/code_seaice)
794      * used C-grid and EVP solver
795      * used KPP, GM/Redi
796      * uses inAdExact=.TRUE.
797      * gradient checks fail for both ADM and TLM
798        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
799        f.d. gradients actually seem more problematic than ADM, TLM gradients;
800        issue is related to forward mismatch between g77 an ifort
801    o pkg/seaice: overhaul of thermodynamics
802     - growth.F and groatb.F are replaced by new routine seaice_growth.F
803     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
804     - move a few global fields out of SEAICE.h into seaice_growth.F and
805       make them 2D (FICE/QNETO/ ...)
806     - remove FO (it is the same as QNETO)
807     - introduce a few local fields to avoid modifying external fields such
808       as atemp, etc.
809    
810    checkpoint58s_post
811    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
812      changed exf_set_gen.F so that
813        genperiod=0 means input file is one time-constant field and
814        genperiod=-12 means input file contains 12 monthly means
815    o CG2D: use pre-computed solver main-diagonal (stored in common block);
816      this affects truncation error ; generate new output file for exp. which
817      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
818        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
819        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
820        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
821        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
822        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
823    o start implementation of deep-atmosphere and anelastic formulation
824    o verification: remove 2nd copy of input files and use script "prepare_run"
825      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
826    o mom_common/vecinv/fluxform: fix a few initialisation isssues
827    o profiles: fix for multithreaded case
828    
829    o diagnostics: rename few diags:
830      s/'PRESSURE'/'RCENTER '/g
831      s/'TICE    '/'oceFreez'/g
832      s/'TAUX    '/'oceTAUX '/g
833      s/'TAUY    '/'oceTAUY '/g
834      s/'SWFLUX  '/'oceQsw  '/g
835      s/DIFx/DFxE/g
836      s/DIFy/DFyE/g
837      and add few ocean-forcing diagnostics:
838      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
839    o modifications to pkg/seaice/growth.F and budget.F, which change results of
840      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
841      as actual snow thickness.  It now refers everywhere to effective snow
842      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
843    
844    checkpoint58r_post
845    o modifications to pkg/seaice/growth.F, which change results of
846      lab_sea experiment: fixes pertain to melting snow over open water, to
847      masking EVAP under sea ice, and to using the correct AREA variable for
848      computations of EVAP, PRECIP, HSNOW, and GHEFF
849    o add ability to read bathy, salt, and theta using MNC (off by def)
850    o add flooding algorithm and advection of HSNOW for pkg/seaice;
851      both are turned off by default and do no change any results
852    o seaice advection with pkg/thsice: a step toward the use of non-linear
853      advection scheme, but #ifdef or commented out for now (requires more EXCH).
854    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
855      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
856      in natl_box (affects results @ truncation level: update output.txt)
857    o multi-threading and IO:
858      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
859      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
860        (needed to work with SingleCpuIO): tested in all verif. exp.
861    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
862      affects the results (but none of the verification test uses this scheme).
863    o Adding some pkg/diagnostics capability to pkg/seaice
864      (will certainly be subject to changes)
865    o ctrl: adding new control variables:
866      lwflux, lwdown, evap, snowprecip, apressure, runoff
867    
868    checkpoint58q_post
869    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
870      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
871      high_res_cube configuration by 4% on Columbia.
872    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
873      add (in global_with_exf/code) a version of EXF_INTERP_READ without
874      dynamical allocation (seems to work in multi-threaded).
875    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
876      single CPU io) so that TAF does not have to see EESUPPORT.h
877    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
878    
879    checkpoint58p_post
880    o obcs: stop if obcs is used with useCDscheme = .true.
881    o shelfice:
882     - fix a sign error so that no slip at shelfice interface works
883     - remove stop for combination non-hydrostatic code and shelfice. That does
884       not mean, that the results are correct, but at least they are numerically
885       stable
886    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
887    o added adjoint exch routined for all exch*3d* routines
888      and updated flow directives
889    
890    checkpoint58o_post
891    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
892      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
893    o change controling S/R for writing pickup file (new S/R do_write_pickup)
894      and clean-up reading/writing of pickup files.
895    o fix local version of read/write pickup (NH part) in rotating_tank/code
896    o simplify EXCH interface:
897     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
898     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
899    o added the regrid package
900    o shelfice:
901     - add a simple boundary layer scheme to reduce noise
902     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
903    
904    checkpoint58n_post
905    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
906       local variable (not in common block).
907    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
908      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
909      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
910        to work with SingleCpuIO.
911    o add "_d 0" to real constant of pkg/cfc subroutines ;
912       update exp. cfc_exemple & tutorial_cfc_offline output files.
913    o multi-threading and IO:
914      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
915        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
916      - barrier before and after reading.
917      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
918      - avoid using MDS_WRITELOCAL for LAND pkg output.
919      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
920        common-block variables ; Allows multi-threading with master-thread IO.
921    o change default MAX_NO_THREADS from 32 to 4 ;
922      and stop cleanly when MAX_NO_THREADS is too small.
923    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
924    
925    checkpoint58m_post
926    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
927       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
928    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
929       keep global_ocean.90x40x15 (for AD testing) with former secondary test
930       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
931    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
932        add MITgcm_tutorials (= code + all the tutorials)
933    o ecco, option to compute cost for total ssh (mean+anom)
934    o consistent with addition of ptracer and ssh in pkg/profiles
935    o profiles: adding ptracer and ssh
936    o testreport: change multi-test output-file name
937      (from output.txt.{name} to output.{name}.txt)
938    o profiles: now ok for mutli-tiles case
939    o seaice: add 4 parameters for different advection schemes for area,
940      (effective) seaice thickness, enthalphy, and snow height. Their default
941      is the standard parameter SEAICEadvScheme
942    o calc_gw:
943     - add cosFacU in zonal viscous flux (harmonic.visc.).
944     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
945       of tutorial_plume_on_slope.
946    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
947    o calc_gw: true flux-form, account for horizontal grid spacing.
948      update rotating_tank results, but not plume_on_slope (affected at
949      truncation level, 11 digits).
950    
951    checkpoint58l_post
952    o calc_gw:
953     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
954     - remove side-drag for now (need to fix it); update plume_on_slope results.
955     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
956  o commit code to make SST/SSS weights spatially variable  o commit code to make SST/SSS weights spatially variable
957    (based on either variable in-situ or variable initial T/S weights)    (based on either variable in-situ or variable initial T/S weights)
958  o pkg/ecco:  o pkg/ecco:
# Line 15  o pkg/ecco: Line 963  o pkg/ecco:
963      (sflxumm, sfluxmm2, bal_sfluxmm)      (sflxumm, sfluxmm2, bal_sfluxmm)
964    * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,    * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
965      including separate counting and multipliers      including separate counting and multipliers
966    o pkg/rbcs
967      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
968    
969  checkpoint58k_post  checkpoint58k_post
970  o testreport:  o testreport:

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