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revision 1.697 by heimbach, Wed Jul 12 00:01:53 2006 UTC revision 1.1036 by jmc, Mon Oct 27 20:15:21 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 fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
8      (#undef REAL4_IS_SLOW)
9     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
10       coordinate variable
11     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
12       (surface forcing fields), removes some of the functionality
13     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
14     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
15       probably not all: copy _RS surface flux fields to RL field before
16       calling DIAGNOSTICS_FILL
17     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
18       real*4 (CALL EXCH_*_RS) versions.
19     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
20       (generate new output).
21    
22    checkpoint61e
23    o gmredi (Visbeck-variable-K):
24      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
25      - change computation of Visbeck-K where Slope > Smax :        
26        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
27        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
28    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
29      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
30    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
31    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
32      does not become too large (to avoid precision problems in implicit-diffusion
33      solver); update ideal_2D_oce output.
34    o pkg ggl90:
35      - in ggl90_cal.F: compute only one set of visc/diff, used to
36        step forward TKE/T/S/momentum
37      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
38        have Prandlt =1)
39    o gmredi (fm07):
40      - add lower limit on Transition layer thickness + lower limit on 1/lambda
41      - allow to set few more params from data.gmredi
42    o pkg ggl90:
43          - add missing sqrt(2) factor in computation of mixing length
44            scale in ggl90_calc.F
45            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
46    
47    checkpoint61d
48    o adjoint modifs
49      - adapt to new field rhoInSitu
50      - allow to revert from StoreDynVars2D, StoreDynVars3D
51        to individual fields
52        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
53    o store 3-D (in-situ) density in commom block (DYNVARS.h)
54     - save 1 rho computation.
55     - no longer modify T & S inland when using down_slope pkg.
56    o gad_som : allow to switch to SOM advection for T & S without corresponding
57      pickup files (using new S/R: MDS_CHECK4FILE).
58    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
59      (for useSingleCpuIO to work in multi-threaded)
60    o pkg/shelfice:
61     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
62       with SHELFICEtopoFile in data.shelfice
63     - move code for reading ice shelf topography and modifying hFacC into separate
64       subroutines of the shelfice package
65     - separate initialisation of "fixed" and "variable" variables
66     - kTopC is not (yet) replaced by kSurfC, although this is possible
67    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
68    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
69      and rename:
70      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
71      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
72    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
73    
74    checkpoint61c
75    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
76      to add mass source/sink of fluid in the interior (3-D generalisation
77      of oceanic real-fresh water flux).
78    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
79    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
80    o new pkg: down_slope
81      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
82      - presently, modify T & S inland (dwnslp_calc_rho.F).
83        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
84      - implementation for ocean in P-coords not tested.
85      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
86    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
87      (to facilitate conversion of oceanic pkg to p-coordinate).
88    o change FIND_RHO to FIND_RHO_2D :
89      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
90    o new pkg: cheapaml
91    
92    checkpoint61b
93    o exch2:
94      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
95      - no longer depend on the order sequence (N,S,E,W).
96      - 3rd exchange no longer needed (tested with 24 tiles).
97      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
98      - exch_UV_A-grid readily available (but not yet tested).
99      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
100      (both are no longer needed) in exch_uv: no effect in forward run; but
101       get truncation error differences with adjoint exch.
102    o exch2:
103     - change index-bounds storage (moved from target to local tile,
104       more intuitive this way) ; rename/remove some variables.
105     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
106    
107    checkpoint61a
108    o exch2/matlab-topology-generator:
109      fix bug in index bounds for N-S internal exchange (hard to tell if this
110      had any effect on the solution).
111    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
112      is exceeded
113    o testreport: modify syntax of awk, so that it works also with
114      awk, and not only with nawk and gawk
115    
116    checkpoint61
117    o autodiff
118      Change default for TAF usage by removing argument '-nonew_arg'
119      This changes TAF subroutine argument list (ordering of active var.)
120      Omission of this flag leads to incompatibility w.r.t. TAMC
121      To restore TAMC-compatibility, need following modifs:
122      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
123      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
124      Tested TAF version is 1.9.22
125      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
126    
127    checkpoint60
128    --->>> This is the last checkpoint for which generating the adjoint
129    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
130    --->>> by default.
131    --->>> Future checkpoints will ommit this flag by default.
132    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
133    o pkg/grdchk: Add gradient check to etan0 perturbations.
134    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
135    o pkg/autodiff: more flexibility in zeroadj.
136      model/src: modifying do_oceanic_phys.F accordingly.
137    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
138    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
139      special setup of gmredi for which the adjoint is stable
140      enough for parameter optimization.
141    o bridging the gap between eddy stress and GM.
142      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
143          along with a change in CPP option (now ALLOW_EDDYPSI).
144      -> when using GM w/ GM_AdvForm:
145          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
146          is applied either in the tracer Eq. or in momentum Eq.
147          depending on data.gmredi (intro. GM_InMomAsStress).
148      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
149      The key modifications are in model/src/taueddy_external_forcing.F
150      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
151    
152    checkpoint59r
153    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
154      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
155      fix option to read coriolis(@ cell-corner) from files with CS-grid.
156    o pkg/mnc: add some attributes to standard 1D-coordinate variables
157    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
158      mass points, when using mnc for output
159      - add runtime parameter (missing_value, missing_value_int) to override
160        default (which is the value of getcon('UNDEF'))
161    o pkg/mnc: prepare mnc for the actual use of missing values with the
162      diagnostics package: small fix in mnc_cw_readwrite.template and more
163      initialisation of never used fields
164      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
165      versions
166    o pkg/thsice/thsice_ini_vars.F added default initial values so that
167      thermodynamics sea ice solver does not blow up when some initial fields
168      are missing.
169    o move from external_forcing_surf.F to ini_forcing.F
170      the p-coord. hack consisting in using pLoad to set phi0surf ;
171      update output of tutorial_global_oce_in_p (affected @ truncation level).
172    o Freshen up a bit hs94.1x64x5, notably:
173      remove rotationPeriod and tRef=5*0. (adjoint only), and add
174      exactConserv=.TRUE.
175    o pkg/generic_advdiff:
176      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
177      applies to files where Temperature & Salinity 2nd Order moments are used.
178    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
179      this uses a dynamically allocated internal state data structure
180      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
181      and requires a fortran 90 compiler
182    
183    checkpoint59q
184    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
185       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
186    o Refresh tutorial_global_oce_biogeo, notably:
187      - change bathymetry (put back seamounts in ACC, use hFacs)
188      - change EOS (POLY3 --> JMD95Z)
189      - use Bryan-Lewis vertical diffusivity
190      - use multidimensional advection
191      - remove old virtual virtual in dic pkg, now done through ptracer pkg
192      - change a couple of parameters in dic pkg
193    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
194    o pkg/obcs: change default to OBCSfixTopo = .true.,
195      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
196      - replace "debugMode" with "debugLevel .GE. debLevB"
197    o implementation of TAF directives for gchem,cfc,dic
198    o remove "exp5" (replaced by tutorial_deep_convection).
199    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
200      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
201      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
202      --> changes results in exp4, seaice_obcs
203    o tutorial_deep_convection :
204      update the set-up and increase resolution and domain size ; start
205      from pseudo initial conditions = output at t=120mn in order to see
206      something happening when running testreport.
207    o pkg/seaice: add os7mp as an advection scheme
208                  add check for advection schemes
209                  add a flag for restoring T and S underneath sea ice
210    o pkg/my82: add netcdf-support and diagnostics
211    o thsice pkg:
212      - Now hsMax limits snow height by turning it into ice following
213        flooding scheme (and now conserving energy)
214      - Slight rewriting of the formula in thsice_calc_thick.F
215      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
216      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
217    
218    checkpoint59p
219    o gchem / dic / cfc :
220      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
221      - add new parameter files: "data.dic" & "data.cfc" ;
222      - various re-arrangement in initialisation & header file ;
223      - fix tutorial_global_oce_biogeo for multi-threaded test.
224    o pkg/dic: test for "pickup_dic" file when restarting ;
225      if no pickup-file, can restart with a re-initialised pH (same as it did
226      before) providing pickupStrictlyMatch is set to False.
227    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
228      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
229    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
230      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
231    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
232     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
233       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
234    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
235       scheme to use for vorticty-term ;
236     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
237       (with default selectVortScheme, return to original discretisation)
238     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
239    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
240    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
241      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
242      also fix diagnostics VISCAHW & VISCA4W.
243    
244    checkpoint59o
245    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
246    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
247      move a few statemens out the main loop into separate loops
248    o pkg/shelfice:
249      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
250        (kg/m^2/s), does not break tests, because in verification/isomip,
251        rhoConstFresh=rhoConst (by accident)
252      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
253      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
254        new file model/src/seawater.F, so that they are available for all pkgs.
255      - convert potential temperature into in-situ temperature. This changes the
256        isomip tests => update tests
257    o add a flag writePickupAtEnd (default=true) to be able to suppress
258      writing a pickup at the last timestep
259    o tools/mpack-1.6 :
260      - disable automake (not working) and autoconf (not needed).
261      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
262        also cleaner with much less compilation warnings.
263    o pkg/profiles:
264      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
265      (for "less than 32 characters name" compiler requirement)
266    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
267      conditions that have a different sampling frequency than S/T/U/V obcs
268    o pkg/diagnostics (stats-diags):
269      - fix global Min/Max in case 1 processor get only empty tiles
270    o genmake2: replace (4 times)
271         make genmake_tc_1.o >> genmake_warnings 2>&1
272      with
273         COMM="$CC $CFLAGS -c genmake_tc_1.c"
274         echo $COMM >> genmake_warnings
275         $COMM >> genmake_warnings 2>&1
276      to make genmake2 always see the value of CC as specified in the optfile.
277    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
278      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
279      - modify verification advect_cs test to test SOM-advection on CS-grid.
280    o pkg/ctrl:
281      - Rewrite of ctrl_map_ini_ecco.F,
282        introducing a generic routine (ctrl_map_ini_gen.F).
283      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
284    
285    checkpoint59n
286    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
287      number in dedicate array "hdiag":
288      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
289        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
290      - many small changes (integer format) for large number of diagnostics
291      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
292        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
293    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
294      usingSphericalGrid, this allows to define the rotated grid coordinates
295      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
296      geographical coordinates according to the inverse of the rotation defined
297      by the Euler angles, so that Coriolis parameter and online-interpolation by
298      exf works with the geographical coordinates on XC/YC/XG/YG.
299      Naturally, this feature does not work with all packages, so some
300      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
301      profiles), because there the coordinates are assumed to be regular
302      spherical grid coordinates.
303    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
304      - introduce isopycnal diffusion coefficient control.
305    o tools/adjoint_options:
306      - additional control vector components.
307    o pkg/mnc: have mnc create marginally meaning full coordinate variables
308      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
309    o pkg/mypackage:
310      - add example of read/write pickup for state-var ;
311      - add entry points to the main code for state-vars diags & write-pickup.
312    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
313      transitions for useExfYearlyFields
314      - add new subroutine that determines the file to read from for
315        use*YearlyFields = .TRUE. and .FALSE.
316      - add a verification experiment to global_with_exf that tests
317        useExfYearlyFields with USE_EXF_INTERPOLATION defined
318    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
319      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
320      subroutines (which could be generated from a template, because they are
321      almost identical), for now they are included in obcs_prescribe_read.F for
322      simplicity
323    o pkg/exf:
324      - add a little more diagnostic to exf_interp_read (in analogy to
325        mds_read_field, can be turned off with debugLevel < debugLevA=1)
326      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
327        ugly but fast by unrolling short inner loops, inserting a unroll=8
328        directive in routine lagran, and splitting a loop and making do while the
329        outermost loop (the latter requires the intoduction of index arrays)
330    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
331    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
332      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
333    o verification/seaice_obcs: updated for restart test and latest options
334    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
335      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
336      for now this is only available for the C-grid code and also within
337      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
338    
339    checkpoint59m
340    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
341      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
342    o gad_som : fix flux output (& diagnostics) to have same units as other  
343      advection scheme fluxes (was previously multiplied by deltaT).  
344    o added verification/seaice_obcs both to test seaice open boundaries
345      and to provide an example matlab scrpt for generating them
346    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
347    o pkg/salt_plume: clean up salt_plume_frac.F to
348      remove redundancy in PlumeMethod 1 and 4
349    o pkg/kpp: added saltplume diagnostics
350    o pkg/obcs and pkg/seaice:
351      - do not set uice and vice to zero when OB*icefile are unspecified
352      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
353      - moved seaice tracer obcs after call to seaice_growth
354    o pkg/salt_plume: added various options for salt plume depth
355      criterion and for vertical distribution of the salt
356    
357    checkpoint59l
358    o pkg/ptracers: new version of ptracers pickup:
359      read meta file and write only fields which are needed to restart.
360      ( same logic as main pickup file ; also using pickupStrictlyMatch )
361    o pkg/seaice:
362      - add timescale for melting due to warm mixed layer as a means of
363        setting SEAICE_availHeatFrac more conveniently
364      - add a CPP-flag/runtime parameter check for flooding algorithm
365      - reformulated availHeat in seaice_growth.F to be independent of AREA
366    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
367      unit changes
368    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
369    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
370      SX vector computer.
371    o pkg/seaice:
372      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
373        seaice forcing fields can now be read only through pkg/exf
374      - removed some unused halos
375    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
376    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
377      or U/VICE from U/VWIND before computing U/VSTRESS
378    
379    checkpoint59k
380    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
381      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
382    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
383      all experiments pass when compile with un-initialised var. checking option.
384    o added pkg/salt_plume
385    o script to test restart (for now, in MITgcm_contrib/jmc_script)
386    o pkg/seaice: new read/write pickup version.
387      read meta file and write only fields which are needed to restart.
388      ( same logic as main pickup file ; also using pickupStrictlyMatch )
389    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
390    o lab_sea.hb87: modify the domain & update output.hb87.txt :
391      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
392      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
393      process. Fixed here by closing the domain at the Northern boundary.
394    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
395    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
396      a set of consecutive levels in/from a 3-D array.
397    o pkg/ptracers:
398      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
399      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
400    
401    checkpoint59j
402    o in pkgs: dic, obcs, offline, rbcs:
403      standard way to compute coeff. for time interpolation between 2 time reccords
404      which retains full precision (& make results less dependent on compiler).
405      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
406    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
407      packages instead of reading ice cover and wind speed separately
408    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
409     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
410      to allow to compile customized code before the update)
411    o cleaning-up:
412      - fix CPP instruction syntax in pkg/obcs
413      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
414        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
415      - fix some threads issue in IO parts.
416    o pkg/dic:
417      - add tons of "_d 0" (--> much better testreports !)
418       and then update outputs of tutorial_global_oce_biogeo
419    o pkg/mom_fluxform:
420      add a special version of momentum advection intended to conserve momentum
421      next to a bathymetry step or a coastline edge. (default = off = #undef)
422    o new read/write pickup version:
423      - for now, only implemented for main (mdsio) pickup file.
424      - write out only what is needed to restart; merge pickup_nh , pickup_ph
425        and main pickup together.
426      - read meta file; read only what is needed to restart; stop if a field
427        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
428        if it make sense (even if the restart is not perfect).
429      - if no meta file, assume that pickup to read corresponds exactly to
430        a pickup that would currently be written.
431      - read pickup written in the old format (until checkpoint59i) if it
432        recognizes an old meta file (no field-list).
433      - add a meta file in exp. which starts from a pickup: 2 cases:
434        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
435         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
436        b) a meta file describing the content of the associated pickup file
437         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
438    o pkg/mdsio & pkg/rw:
439      - new routine to read a meta file ; new set of routine to read
440        Multiple-fields file (with meta file).
441    o added open boundary conditions capability for seaice
442        HSNOW, HSALT, UICE, and VICE
443    
444    checkpoint59i
445    o adjoint:
446      * fix multiDimAdvection adjoint
447        (partial recomputation problem by TAF for fVerT(:,:,kDown)
448        and comlev1 size definition (maxpass vs. max. number of tracers)
449      * verification/global_ocean.90x45x15 adjoint now tests
450        NLFS and multiDimAdvection using DST3 (=30)
451      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
452    o pkg/kpp: add "_d 0" to real constant (if missing);
453      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
454      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
455    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
456      for internal parameters related to restart process (formerly from PARAMS.h)
457      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
458    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
459      as argument. (only atm2d & obcs write_pickup have not yet been updated)
460    o pkg/monitor:
461      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
462      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
463      - account for deep Atmosphere factor and density factor (anelastic)
464    o added open boundary conditions capability for seaice HEFF and AREA
465    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
466      thermodynamics
467      - requires a little reorganization, which affects the testreport results
468        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
469        so that now the conservative form is tested
470      - add a few comments
471    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
472    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
473    o add new diagnostics to seaice: advective, diffusive fluxes (only for
474      multidim-advection, for scheme 2 they are not filled) and transports,
475      thermodynamic growth rates
476    o change units of EmPmR (inside the code, + within coupling interface)
477      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
478      Affects results @ truncation level (cg2d match) and update output of
479       experiments: lab_sea(6), global_ocean.90x40x15(10),
480      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
481      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
482      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
483      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
484    
485    checkpoint59h
486    o pkg/exf:
487      - improve vectorization by moving if-statement out of loops in
488        exf_mapfields, exf_radiation
489      - exf_bulkformulae.F: introduce 2D fields and vectorize code
490    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
491    o testreport:
492      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
493        monitor & update offline_exf_seaice exp. output.
494      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
495    o pkg/seaice:
496      - bug fix in the evp solver: boundary conditions were affected be
497        masking of zMax/zMin (changes results)
498      - minor bug fix in boundary conditions in seaice_calc_strainrates
499        (changes results for no_slip)
500      - seaice_lsr.F: make interpolation of eta dependent on boundaries
501      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
502      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
503        stress formulation and no-slip boundary conditions
504    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
505      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
506    o pkg/seaice: a first HSALT time stepping equation has been checked in
507    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
508      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
509      without requiring DO-IF statements
510    o pkg/thsice:
511      use continuous power-law function for partition of energy between lateral
512      melting/freezing and thinning/thickening ; old code using step function
513      still available with #undef THSICE_FRACEN_POWERLAW
514      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
515    o testreport: change AD testing : check against results/output_adm.txt
516      using same scripts as for forward test.
517    
518    checkpoint59g
519    o adjoint testing: in preparation for changing testreport:
520      - output format: cost and grad written on separated lines
521      - ad output results in directory "results" (instead of "results_ad")
522    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
523    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
524    o pkg/ecco: allow user defined cost function contributions
525    o testreport:
526      Allow to choose (per experiment) the list of tested output variables
527       and the main variable (used to issue a pass/FAIL ) ;
528      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
529      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
530      Also modify printing of summary:
531       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
532       b) echo the list of tested variables in the individual summary.txt of
533          each experiment.
534    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
535      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
536      (but still depend on the tile decompostion of the domain).
537    o pkg/seaice: change a discretization detail to make the B-grid code
538      "more symmetric". This change is likely to remove all "ridges/leads" that
539      where quasi-aligned with the grid in B-grid solutions. It may also be
540      the solution to the stress coupling issues with the B-grid.
541    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
542      remove .cvsignore from input dir. (since testreport no longer run here).
543    o pkg/thsice:
544     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
545     - fix reshaping of sea-ice just after advection:
546       melt all the ice only if ice-volume is too small.
547     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
548       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
549     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
550    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
551      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
552    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
553      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
554      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
555      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
556      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
557      -> update output.txt
558    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
559     this affects truncation error: -> update output.txt of exp:
560      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
561      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
562    
563    checkpoint59f
564    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
565    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
566      a bounded range (in forward mode)
567    o pkg/ecco, ctrl, autodiff and mom_common:
568     internal parameter controls, completements of implementations
569    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
570    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
571      (not seem any difference in testing results).
572    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
573       at face corners.
574    o pkg/generic_advdiff:
575     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
576      loop range indices for computing vertical advection tendency
577      and do the calculation in the interior only (no overlap) ;
578      for now, only implemented for SOM advection (to save CPU time).
579     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
580    o exch2 adjoint
581      First set of changes:
582      - add exch2 hand-written adjoint templates
583      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
584        This will require cleanup in pkg/autodiff/*.F
585        (changed routines currently kept separate in verif. code/)
586      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
587        that used to hide exch2 or cubed-sphere specific code
588        (commented via 'cph-exch2')
589    o pkg/seaice
590      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
591    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
592       output of global_ocean.cs32x15.thsice .
593    
594    checkpoint59e
595    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
596      for B-grid vector (not yet tested) and C-grid vector (<- only used
597      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
598    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
599      (#ifdef ALLOW_SALT_PLUME)
600    o gather_2d/scatter_2d: removed halo regions
601    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
602      scheme and the corresponding test case (under front_relax dir). For now,
603      only available with Skew-flux form and not yet tested in realistic set-up.
604      adjoint: store directives updated, but gradient checks deteriorated,
605      so maybe GM/Redi adjoint is now broken.
606    o seaice adjoint
607      * add AREA, HEFF, HSNOW as control variable
608        (should not change lab_sea results)
609      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
610    o pkg/seaice:
611      * added computation of saltFlux in seaice_growth;
612        For time being, sea ice salinity is assumed constant
613        contribution of snow flooding to freshening of sea ice is neglected.
614        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
615        defaults to 0.0 in order to maintain backward compatibility.
616        Typical values for SEAICE_salinity are 4 to 10 g/kg.
617      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
618      * added SEAICE_availHeatFrac, which specifies fraction of surface level
619        heat content used to melt or grow ice
620      * commented out cap of HICE: it helps keep ice thinner
621      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
622      * applied OBCS T/S mask to HEFFM sea ice mask
623    
624    checkpoint59d
625    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
626     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
627     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
628    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
629     and change default value of parameter "GM_Small_Number";
630     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
631       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
632       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
633    o pkg/ecco: cost function when applying pkg/smooth to controls
634    o pkg/ctrl: add forcingPrecond run time parameter
635    o pkg/seaice:
636     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
637     - fix bug in metric terms of u-equation in LSR solver (implicit part),
638       changes verification/lab_sea
639     - rearrange implicit part of u-equation in LSR solver to make it easier to
640       read, understand, and debug. This causes changes at the truncation level.
641     - fix (serious) bug in the boundary conditions (sign error in the implicit
642       part) of the LSR solver. Changes all LSR results.
643     - fixed problem with HSNOW initialization to avoid thick snow when AREA
644       is initilized with small values - does not change lab_sea results.
645     - added HsnowFile initialization capability
646    o pkg/smooth: addition to model/src and pkg/ctrl so allow
647     initialization of pkg/smooth and application to control vector
648    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
649    o dependencies: pkg/profiles requires pkg/cal
650    o pkg/profiles:
651     - added option ALLOW_PROFILES_GENERICGRID
652         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
653         that interpolation information (grid points and coefficients) is provided
654         within the netcdf input files.
655         -> sample matlab scripts can be found in MITgcm_contrib/gael
656         that allow you to prepare netcdf input files.
657     - also modified: cleaner include statements, cleaner error print statements,
658       cleaner stops when error, and more tests of the netcdf input files consistency.
659    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
660    o pkg/seaice:
661     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
662       requires a new routine: seaice_diagnostics_fill.F
663     - make sure that seaice does not move if not forced (pressure replacement
664       method, Hibler and Ip, 1995), changes results
665     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
666     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
667       It is turned off by default (=-1.), because it changes the results.
668     - make it possible to read AREA from a file, too.
669    
670    checkpoint59c
671    o add S/R and diagnostics for oceanic mixed-layer depth
672    o move GMRedi call after all vertical mixing schemes (including KPP)
673    o pkg/thsice:
674     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
675      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
676    o pkg/obcs:
677     - bug fix for balance code
678    o pkg/seaice:
679      - allow values of SEAICE_elasticParm > 1
680      - add new parameter SEAICE_evpTauRelax as an alternative
681        to SEAICE_elasticParm
682      - make lsr boundary conditions free slip (by default), changes result
683      - add code for no slip boundary conditions for lsr
684      - set minimum of zeta to zero (and not 4e8) (changes results)
685      - add a cap on AREA after advecting AREA if seaice_growth is not called
686    o change calculation of Visbeck K:
687      - no longer depend on tapering scheme; instead, compute slope (limited
688        by GM_maxSlope). this is equivalent to what was comuted before with
689        clipping or linear tappering.
690      - fix vertical averaging (wrong by 1/2 level)
691      - leave the old version (but will not be maintained) within
692        #ifdef OLD_VISBECK_CALC / #endif
693      - update output of exp. ideal_2D_oce
694    o change error catch in calc_r_star to improve vectorization
695    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
696      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
697    o adjoint:
698      Re-organized adjoint checkpointing according to Matt Mazloff
699      (but with modifs/completions/cleanups)
700      Storing is now bundled into large arrays to optimized I/O
701      (and second step in cleanup of the_main_loop)
702    
703    checkpoint59b
704    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
705      - export/import (between ocean & coupler) fields needed for ocean DIC.
706    o pkg/seaice:
707      - get rid of three more exchanges seaice_calc_viscosities (required
708        different loop boundaries in seaice_lsr and seaice_ocean_stress)
709      - bug fix in seaice_ocean_stress (update of lab_sea required)
710      - reduce loop boundaries to necessary minimum also in seaice_evp
711      - go back to the old way of computing deltaC/Z as the adjoint likes that
712        better
713    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
714      passive tracer to an Age Tracer) + update output.txt
715    o pkg/exf:
716      - implement A-grid / C-grid selection for wind-stress input files.
717      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
718      for now, in exf_bulk_largeyeager04.F only :
719      - change implementation for case where windspeed + 2. components wind-stress
720        are read-in. AND use rhoConstFresh to convert evap.
721    o pkg/seaice:
722      - use correct EXCH_UV for wind-forcing (on A-grid).
723      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
724        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
725    o pkg/exf:
726      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
727      EXF_INTERPOLATION:
728      - merge global_with_exf/code version of exf_interp_read.F
729        to the main code ;
730      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
731        reading the file ; Important: This options needs to be defined to recover
732        previous code.
733        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
734      - no longer loose real*8 precision along the way when using exf_iprec=64.
735    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
736      - change discretisation of evp-solver in order to avoid another exchange
737        (changes lab_sea) and clean up a little
738      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
739        help the adjoint (this also changes the results slightly)
740      - add a few "_d 0" where they had been missing in seaice_evp.F
741      - cleaning up: remove unused seaice_calc_rhs.F
742    o pkg/exf: some cleaning-up:
743      - change various "constants" into runtime parameters
744      - cleaned-up Large&Yeager04 routine which should eventually
745        replace exf_bulkformulae.F (changed names of S/R and CPP)
746        and merged various ALLOW_ATM_WIND options
747     only used with thsice pkg (in thsice_get_exf.F):
748      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
749        which are used when useStabilityFct_overIce=TRUE (= the default)
750      - change default values of ice & snow emissivity and scale downward LW
751        by ice & snow emissivity.
752    o pkg/thsice:
753     fix few little problems, in thsice_calc_thickn.F:
754      - growth vertically (and not laterally) if iceFrac == iceMaskMax
755      - melt only laterally if hIce < hThinIce (as the comments say)
756      and in thsice_extend.F:
757      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
758      - start to form ice as soon as the minimum ice-volume is reachable.
759     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
760      and cpl_aim+ocn
761    o pkg/kpp
762     - move computation of surface related input fields to KPP into a new
763       subroutine kpp_forcing_surf.F
764     - remove wrong (within bi,bj loops) EXCH calls.
765     - little cleaning (add argument myThid in last position, cvs header ...)
766     - for now, fix conservation problem by exchanging KPPviscAz (may not
767       be the best fix)
768    o pkg/seaice
769     - check for inconsistent evp parameter/cpp-flag combination
770     - remove leftover errIO flat for obsolete name list error handling
771    o OpenAD
772     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
773    
774    checkpoint59a
775    o pkg/seaice: some parameter clarifications and a little bit of clean up
776    o pkg/thsice: rename run-time parameters:
777       himin       -> hIceMin
778       himin0      -> hThinIce
779       hihig       -> hThickIce
780       i0          -> i0swFrac
781       transCoef   -> bMeltCoef
782       frac_energy -> fracMelting
783      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
784       with default values (for now) that do not change the results.
785      remove old version of thsice vars advection in pkg/seaice.
786    o in FFIELDS.h:
787      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
788      - make pLoad & sIceLoad always available (but still only used if
789         ATMOSPHERIC_LOADING is #define).
790    o pkg/kpp: replaced _KPP_RL with _RL
791    o bug fixes for vertical diffusivity computations when both KPP and
792        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
793        are no longer updating the vertical diffusivity array
794        (passed as argument) but are (re-) setting those arrays.
795    o pkg/seaice: fix bug in evp solver, while doing that
796      - change (improve?) discretization of stress computations for both
797        cgrid-lsr and evp solver
798      - add a new routine to compute strain rates
799      - the above changes lab_sea results
800      - add no slip conditions for evp solver (off by default), lsr-version
801        may follow
802      - fix exchange for shear at Z-points (does not change lab_sea)
803      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
804        (to force the user to pick a time step since there is not "safe" way
805        of choosing it)
806      - add principal stress diagnostics
807      - rearrange fields for evp a little to avoid having to call a: too many
808        exchanges and b: exchanges for stress trensor components which we do
809        not have.
810      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
811        of evp, complete rewrite for lsr case (latter is does not yet work
812        in all cases)
813    o pkg/kpp: add code to have mixing in shelf ice caverns
814      - add myThid to all kpp routines (long overdue)
815    
816    checkpoint59
817    o pkg/exf:
818      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
819        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
820      - move exf header files from lower_case.h to UPPER_CASE.h ;
821        add missing cvs Header & Name
822      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
823      - add namelist param. selectStressGridPosition, exf_monFreq
824      - retire many _CLIM routines, and remove data.exf_clim
825        + params moved to data.exf
826        + climsst, climsss now handled by exf_set_gen, i.e.
827          climss?period=0 refers to constant field,
828          climss?period=-12 to monthly forcing
829      - split up namelists in data.exf
830    o pkg/seaice:
831      - remove seaice_exch and seaice_exch_uv
832      - remove superfluous exchange of theta
833      - add myThid to seaice_budget_ocean/ice
834      - add new interface for atmospheric wind forcing (C-grid only)
835        + new routine
836        + two new field (taux, tauy for stress over ice)
837        + removed one global field (DAIRN) for C-grid case only
838    o pkg/thsise
839      - 2nd set of modifs for thsice adjoint in conjunction with exf
840    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
841    
842    checkpoint58y_post
843    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
844      vertical diffusivity, similar to that in MOM4; turned on using
845      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
846      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
847    o Added capability for 3D specification of background vertical diffusion
848      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
849      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
850      "data" file that contains the 3D vertical diffusivity coefficients.
851    o ice dynamics (pkg/seaice) with thsice thermodynamics:
852      - add code within pkg thsice to advect & diffuse sea-ice fields
853      similar to (and will replace) what has been added in  seaice_advdiff.F,
854      but: - conserving Mass, Heat & Salt.
855           - better when using non-linear advection scheme (not yet fully tested)
856           - can also be used in atmospheric set-up (for now, only the diffusion).
857    
858    checkpoint58x_post
859    o IO option for global-file compact format:
860      - add options when generating topology (utils/exch2/matlab-topology-generator)
861      - add I/O capability (pkg/mdsio).
862      - adapt utils/matlab/rdmds.m to read this format.
863      for now long-line format not yet supported by pkg/mdsio (& exch2).
864    o shelfice: add a few diagnostics
865    
866    checkpoint58w_post
867    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
868      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
869      (and replace horiVertRatio in NH code).
870      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
871                         and tutorial_plume_on_slope (sensitive to truncation)
872    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
873      directly to drive seaice model (C-grid only)
874    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
875     - reintroduce computation of wind from stress,
876     - compute tau (in exf_bulkformulae.F) from windstress averaged to
877       mass points to avoid tau = 0
878     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
879    o rdmnc.m: make it work with "global" files created with gluemnc
880    o rdmnc.m : some improvements in dealing with singleton dimension
881      (tested on all testreport mnc output files).
882    o genmake2: disable pkg/profiles if netcdf test fails.
883    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
884    o move call to cal_readparms up to make calendar parameters/variable available
885      to all packages
886    
887    checkpoint58v_post
888    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
889      useDynP_inEos_Zc tested.
890    o pkg/exf: changes to properly interpolate/mask/scale initial fields
891    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
892      and portions thereof.  See read_cs.txt for description and examples.
893    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
894      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
895      following the great-circle arc between those 2 points.
896    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
897      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
898    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
899     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
900     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
901     - still needs work (not working with some options ; efficiency to improve)
902       and serious testing.
903     - use this scheme for temperature & salinity in 2 advection test exp.:
904       advect_xy & advect_xz, respectively.
905    
906    checkpoint58u_post
907    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
908    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
909    o testreport: add option "-skipdir" to skip some test.
910    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
911      momentum calculation.
912    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
913    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
914      remove checkpoint.F and the_correction_step.F (no longer used);
915      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
916    o add option (linFSConserveTr) to correct for tracer source/sink due to
917      Linear Free surface
918    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
919    o pkg/thsice: fix reading mnc-pickups
920    
921    checkpoint58t_post
922    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
923    o pkg/mdsio:
924     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
925       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
926       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
927     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
928     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
929       either MDS_READ_FIELD or MDS_WRITE_FIELD )
930     - new S/R (to replace MDSWRITEMETA), which allows to write more
931       informations (variable names, time ...) to meta files.
932     - modify rdmds.m to give back the meta file content.
933    o pkg/diagnostics: change vertical interpolation to be safer, and more
934       flexible (define p-levels to interpolate to in data.diagnostics);
935      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
936       diagnostic pointer.
937    o pkg/seaice: more cleaning up of seaice_growth, added many comments
938    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
939    o fix multi-category seaice:
940     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
941       SEAICE_MULTICATEGORY
942     - fix short wave heat flux
943    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
944       and allow to use EVP solver. Change forward lab_sea: test both EVP
945       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
946    o Initial check-in of lab_sea adjoint
947      (very similar to natl_box_adjoint/code_seaice)
948      * used C-grid and EVP solver
949      * used KPP, GM/Redi
950      * uses inAdExact=.TRUE.
951      * gradient checks fail for both ADM and TLM
952        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
953        f.d. gradients actually seem more problematic than ADM, TLM gradients;
954        issue is related to forward mismatch between g77 an ifort
955    o pkg/seaice: overhaul of thermodynamics
956     - growth.F and groatb.F are replaced by new routine seaice_growth.F
957     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
958     - move a few global fields out of SEAICE.h into seaice_growth.F and
959       make them 2D (FICE/QNETO/ ...)
960     - remove FO (it is the same as QNETO)
961     - introduce a few local fields to avoid modifying external fields such
962       as atemp, etc.
963    
964    checkpoint58s_post
965    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
966      changed exf_set_gen.F so that
967        genperiod=0 means input file is one time-constant field and
968        genperiod=-12 means input file contains 12 monthly means
969    o CG2D: use pre-computed solver main-diagonal (stored in common block);
970      this affects truncation error ; generate new output file for exp. which
971      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
972        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
973        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
974        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
975        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
976        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
977    o start implementation of deep-atmosphere and anelastic formulation
978    o verification: remove 2nd copy of input files and use script "prepare_run"
979      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
980    o mom_common/vecinv/fluxform: fix a few initialisation isssues
981    o profiles: fix for multithreaded case
982    
983    o diagnostics: rename few diags:
984      s/'PRESSURE'/'RCENTER '/g
985      s/'TICE    '/'oceFreez'/g
986      s/'TAUX    '/'oceTAUX '/g
987      s/'TAUY    '/'oceTAUY '/g
988      s/'SWFLUX  '/'oceQsw  '/g
989      s/DIFx/DFxE/g
990      s/DIFy/DFyE/g
991      and add few ocean-forcing diagnostics:
992      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
993    o modifications to pkg/seaice/growth.F and budget.F, which change results of
994      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
995      as actual snow thickness.  It now refers everywhere to effective snow
996      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
997    
998    checkpoint58r_post
999    o modifications to pkg/seaice/growth.F, which change results of
1000      lab_sea experiment: fixes pertain to melting snow over open water, to
1001      masking EVAP under sea ice, and to using the correct AREA variable for
1002      computations of EVAP, PRECIP, HSNOW, and GHEFF
1003    o add ability to read bathy, salt, and theta using MNC (off by def)
1004    o add flooding algorithm and advection of HSNOW for pkg/seaice;
1005      both are turned off by default and do no change any results
1006    o seaice advection with pkg/thsice: a step toward the use of non-linear
1007      advection scheme, but #ifdef or commented out for now (requires more EXCH).
1008    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
1009      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
1010      in natl_box (affects results @ truncation level: update output.txt)
1011    o multi-threading and IO:
1012      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
1013      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
1014        (needed to work with SingleCpuIO): tested in all verif. exp.
1015    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
1016      affects the results (but none of the verification test uses this scheme).
1017    o Adding some pkg/diagnostics capability to pkg/seaice
1018      (will certainly be subject to changes)
1019    o ctrl: adding new control variables:
1020      lwflux, lwdown, evap, snowprecip, apressure, runoff
1021    
1022    checkpoint58q_post
1023    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
1024      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
1025      high_res_cube configuration by 4% on Columbia.
1026    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
1027      add (in global_with_exf/code) a version of EXF_INTERP_READ without
1028      dynamical allocation (seems to work in multi-threaded).
1029    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
1030      single CPU io) so that TAF does not have to see EESUPPORT.h
1031    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
1032    
1033    checkpoint58p_post
1034    o obcs: stop if obcs is used with useCDscheme = .true.
1035    o shelfice:
1036     - fix a sign error so that no slip at shelfice interface works
1037     - remove stop for combination non-hydrostatic code and shelfice. That does
1038       not mean, that the results are correct, but at least they are numerically
1039       stable
1040    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
1041    o added adjoint exch routined for all exch*3d* routines
1042      and updated flow directives
1043    
1044    checkpoint58o_post
1045    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
1046      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
1047    o change controling S/R for writing pickup file (new S/R do_write_pickup)
1048      and clean-up reading/writing of pickup files.
1049    o fix local version of read/write pickup (NH part) in rotating_tank/code
1050    o simplify EXCH interface:
1051     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
1052     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
1053    o added the regrid package
1054    o shelfice:
1055     - add a simple boundary layer scheme to reduce noise
1056     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
1057    
1058    checkpoint58n_post
1059    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
1060       local variable (not in common block).
1061    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
1062      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
1063      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
1064        to work with SingleCpuIO.
1065    o add "_d 0" to real constant of pkg/cfc subroutines ;
1066       update exp. cfc_exemple & tutorial_cfc_offline output files.
1067    o multi-threading and IO:
1068      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
1069        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
1070      - barrier before and after reading.
1071      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
1072      - avoid using MDS_WRITELOCAL for LAND pkg output.
1073      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
1074        common-block variables ; Allows multi-threading with master-thread IO.
1075    o change default MAX_NO_THREADS from 32 to 4 ;
1076      and stop cleanly when MAX_NO_THREADS is too small.
1077    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
1078    
1079    checkpoint58m_post
1080    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
1081       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
1082    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
1083       keep global_ocean.90x40x15 (for AD testing) with former secondary test
1084       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
1085    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
1086        add MITgcm_tutorials (= code + all the tutorials)
1087    o ecco, option to compute cost for total ssh (mean+anom)
1088    o consistent with addition of ptracer and ssh in pkg/profiles
1089    o profiles: adding ptracer and ssh
1090    o testreport: change multi-test output-file name
1091      (from output.txt.{name} to output.{name}.txt)
1092    o profiles: now ok for mutli-tiles case
1093    o seaice: add 4 parameters for different advection schemes for area,
1094      (effective) seaice thickness, enthalphy, and snow height. Their default
1095      is the standard parameter SEAICEadvScheme
1096    o calc_gw:
1097     - add cosFacU in zonal viscous flux (harmonic.visc.).
1098     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
1099       of tutorial_plume_on_slope.
1100    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
1101    o calc_gw: true flux-form, account for horizontal grid spacing.
1102      update rotating_tank results, but not plume_on_slope (affected at
1103      truncation level, 11 digits).
1104    
1105  checkpoint58l_post  checkpoint58l_post
1106  o take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V  o calc_gw:
1107     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
1108     - remove side-drag for now (need to fix it); update plume_on_slope results.
1109     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
1110  o commit code to make SST/SSS weights spatially variable  o commit code to make SST/SSS weights spatially variable
1111    (based on either variable in-situ or variable initial T/S weights)    (based on either variable in-situ or variable initial T/S weights)
1112  o pkg/ecco:  o pkg/ecco:
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