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revision 1.911 by jmc, Sun Nov 25 22:28:30 2007 UTC revision 1.1027 by jmc, Tue Oct 7 20:59:20 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 gmredi(fm07):
8      - add lower limit on Transition layer thickness D + lower limit on D/lambda
9      - allow to set few more params from data.gmredi
10    o pkg ggl90:
11          - add missing sqrt(2) factor in computation of mixing length
12            scale in ggl90_calc.F
13            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
14    
15    checkpoint61d
16    o adjoint modifs
17      - adapt to new field rhoInSitu
18      - allow to revert from StoreDynVars2D, StoreDynVars3D
19        to individual fields
20        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
21    o store 3-D (in-situ) density in commom block (DYNVARS.h)
22     - save 1 rho computation.
23     - no longer modify T & S inland when using down_slope pkg.
24    o gad_som : allow to switch to SOM advection for T & S without corresponding
25      pickup files (using new S/R: MDS_CHECK4FILE).
26    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
27      (for useSingleCpuIO to work in multi-threaded)
28    o pkg/shelfice:
29     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
30       with SHELFICEtopoFile in data.shelfice
31     - move code for reading ice shelf topography and modifying hFacC into separate
32       subroutines of the shelfice package
33     - separate initialisation of "fixed" and "variable" variables
34     - kTopC is not (yet) replaced by kSurfC, although this is possible
35    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
36    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
37      and rename:
38      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
39      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
40    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
41    
42    checkpoint61c
43    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
44      to add mass source/sink of fluid in the interior (3-D generalisation
45      of oceanic real-fresh water flux).
46    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
47    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
48    o new pkg: down_slope
49      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
50      - presently, modify T & S inland (dwnslp_calc_rho.F).
51        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
52      - implementation for ocean in P-coords not tested.
53      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
54    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
55      (to facilitate conversion of oceanic pkg to p-coordinate).
56    o change FIND_RHO to FIND_RHO_2D :
57      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
58    o new pkg: cheapaml
59    
60    checkpoint61b
61    o exch2:
62      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
63      - no longer depend on the order sequence (N,S,E,W).
64      - 3rd exchange no longer needed (tested with 24 tiles).
65      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
66      - exch_UV_A-grid readily available (but not yet tested).
67      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
68      (both are no longer needed) in exch_uv: no effect in forward run; but
69       get truncation error differences with adjoint exch.
70    o exch2:
71     - change index-bounds storage (moved from target to local tile,
72       more intuitive this way) ; rename/remove some variables.
73     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
74    
75    checkpoint61a
76    o exch2/matlab-topology-generator:
77      fix bug in index bounds for N-S internal exchange (hard to tell if this
78      had any effect on the solution).
79    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
80      is exceeded
81    o testreport: modify syntax of awk, so that it works also with
82      awk, and not only with nawk and gawk
83    
84    checkpoint61
85    o autodiff
86      Change default for TAF usage by removing argument '-nonew_arg'
87      This changes TAF subroutine argument list (ordering of active var.)
88      Omission of this flag leads to incompatibility w.r.t. TAMC
89      To restore TAMC-compatibility, need following modifs:
90      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
91      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
92      Tested TAF version is 1.9.22
93      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
94    
95    checkpoint60
96    --->>> This is the last checkpoint for which generating the adjoint
97    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
98    --->>> by default.
99    --->>> Future checkpoints will ommit this flag by default.
100    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
101    o pkg/grdchk: Add gradient check to etan0 perturbations.
102    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
103    o pkg/autodiff: more flexibility in zeroadj.
104      model/src: modifying do_oceanic_phys.F accordingly.
105    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
106    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
107      special setup of gmredi for which the adjoint is stable
108      enough for parameter optimization.
109    o bridging the gap between eddy stress and GM.
110      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
111          along with a change in CPP option (now ALLOW_EDDYPSI).
112      -> when using GM w/ GM_AdvForm:
113          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
114          is applied either in the tracer Eq. or in momentum Eq.
115          depending on data.gmredi (intro. GM_InMomAsStress).
116      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
117      The key modifications are in model/src/taueddy_external_forcing.F
118      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
119    
120    checkpoint59r
121    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
122      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
123      fix option to read coriolis(@ cell-corner) from files with CS-grid.
124    o pkg/mnc: add some attributes to standard 1D-coordinate variables
125    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
126      mass points, when using mnc for output
127      - add runtime parameter (missing_value, missing_value_int) to override
128        default (which is the value of getcon('UNDEF'))
129    o pkg/mnc: prepare mnc for the actual use of missing values with the
130      diagnostics package: small fix in mnc_cw_readwrite.template and more
131      initialisation of never used fields
132      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
133      versions
134    o pkg/thsice/thsice_ini_vars.F added default initial values so that
135      thermodynamics sea ice solver does not blow up when some initial fields
136      are missing.
137    o move from external_forcing_surf.F to ini_forcing.F
138      the p-coord. hack consisting in using pLoad to set phi0surf ;
139      update output of tutorial_global_oce_in_p (affected @ truncation level).
140    o Freshen up a bit hs94.1x64x5, notably:
141      remove rotationPeriod and tRef=5*0. (adjoint only), and add
142      exactConserv=.TRUE.
143    o pkg/generic_advdiff:
144      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
145      applies to files where Temperature & Salinity 2nd Order moments are used.
146    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
147      this uses a dynamically allocated internal state data structure
148      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
149      and requires a fortran 90 compiler
150    
151    checkpoint59q
152    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
153       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
154    o Refresh tutorial_global_oce_biogeo, notably:
155      - change bathymetry (put back seamounts in ACC, use hFacs)
156      - change EOS (POLY3 --> JMD95Z)
157      - use Bryan-Lewis vertical diffusivity
158      - use multidimensional advection
159      - remove old virtual virtual in dic pkg, now done through ptracer pkg
160      - change a couple of parameters in dic pkg
161    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
162    o pkg/obcs: change default to OBCSfixTopo = .true.,
163      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
164      - replace "debugMode" with "debugLevel .GE. debLevB"
165    o implementation of TAF directives for gchem,cfc,dic
166    o remove "exp5" (replaced by tutorial_deep_convection).
167    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
168      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
169      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
170      --> changes results in exp4, seaice_obcs
171    o tutorial_deep_convection :
172      update the set-up and increase resolution and domain size ; start
173      from pseudo initial conditions = output at t=120mn in order to see
174      something happening when running testreport.
175    o pkg/seaice: add os7mp as an advection scheme
176                  add check for advection schemes
177                  add a flag for restoring T and S underneath sea ice
178    o pkg/my82: add netcdf-support and diagnostics
179    o thsice pkg:
180      - Now hsMax limits snow height by turning it into ice following
181        flooding scheme (and now conserving energy)
182      - Slight rewriting of the formula in thsice_calc_thick.F
183      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
184      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
185    
186    checkpoint59p
187    o gchem / dic / cfc :
188      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
189      - add new parameter files: "data.dic" & "data.cfc" ;
190      - various re-arrangement in initialisation & header file ;
191      - fix tutorial_global_oce_biogeo for multi-threaded test.
192    o pkg/dic: test for "pickup_dic" file when restarting ;
193      if no pickup-file, can restart with a re-initialised pH (same as it did
194      before) providing pickupStrictlyMatch is set to False.
195    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
196      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
197    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
198      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
199    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
200     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
201       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
202    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
203       scheme to use for vorticty-term ;
204     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
205       (with default selectVortScheme, return to original discretisation)
206     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
207    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
208    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
209      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
210      also fix diagnostics VISCAHW & VISCA4W.
211    
212    checkpoint59o
213    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
214    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
215      move a few statemens out the main loop into separate loops
216    o pkg/shelfice:
217      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
218        (kg/m^2/s), does not break tests, because in verification/isomip,
219        rhoConstFresh=rhoConst (by accident)
220      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
221      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
222        new file model/src/seawater.F, so that they are available for all pkgs.
223      - convert potential temperature into in-situ temperature. This changes the
224        isomip tests => update tests
225    o add a flag writePickupAtEnd (default=true) to be able to suppress
226      writing a pickup at the last timestep
227    o tools/mpack-1.6 :
228      - disable automake (not working) and autoconf (not needed).
229      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
230        also cleaner with much less compilation warnings.
231    o pkg/profiles:
232      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
233      (for "less than 32 characters name" compiler requirement)
234    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
235      conditions that have a different sampling frequency than S/T/U/V obcs
236    o pkg/diagnostics (stats-diags):
237      - fix global Min/Max in case 1 processor get only empty tiles
238    o genmake2: replace (4 times)
239         make genmake_tc_1.o >> genmake_warnings 2>&1
240      with
241         COMM="$CC $CFLAGS -c genmake_tc_1.c"
242         echo $COMM >> genmake_warnings
243         $COMM >> genmake_warnings 2>&1
244      to make genmake2 always see the value of CC as specified in the optfile.
245    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
246      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
247      - modify verification advect_cs test to test SOM-advection on CS-grid.
248    o pkg/ctrl:
249      - Rewrite of ctrl_map_ini_ecco.F,
250        introducing a generic routine (ctrl_map_ini_gen.F).
251      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
252    
253    checkpoint59n
254    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
255      number in dedicate array "hdiag":
256      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
257        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
258      - many small changes (integer format) for large number of diagnostics
259      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
260        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
261    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
262      usingSphericalGrid, this allows to define the rotated grid coordinates
263      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
264      geographical coordinates according to the inverse of the rotation defined
265      by the Euler angles, so that Coriolis parameter and online-interpolation by
266      exf works with the geographical coordinates on XC/YC/XG/YG.
267      Naturally, this feature does not work with all packages, so some
268      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
269      profiles), because there the coordinates are assumed to be regular
270      spherical grid coordinates.
271    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
272      - introduce isopycnal diffusion coefficient control.
273    o tools/adjoint_options:
274      - additional control vector components.
275    o pkg/mnc: have mnc create marginally meaning full coordinate variables
276      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
277    o pkg/mypackage:
278      - add example of read/write pickup for state-var ;
279      - add entry points to the main code for state-vars diags & write-pickup.
280    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
281      transitions for useExfYearlyFields
282      - add new subroutine that determines the file to read from for
283        use*YearlyFields = .TRUE. and .FALSE.
284      - add a verification experiment to global_with_exf that tests
285        useExfYearlyFields with USE_EXF_INTERPOLATION defined
286    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
287      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
288      subroutines (which could be generated from a template, because they are
289      almost identical), for now they are included in obcs_prescribe_read.F for
290      simplicity
291    o pkg/exf:
292      - add a little more diagnostic to exf_interp_read (in analogy to
293        mds_read_field, can be turned off with debugLevel < debugLevA=1)
294      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
295        ugly but fast by unrolling short inner loops, inserting a unroll=8
296        directive in routine lagran, and splitting a loop and making do while the
297        outermost loop (the latter requires the intoduction of index arrays)
298    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
299    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
300      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
301    o verification/seaice_obcs: updated for restart test and latest options
302    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
303      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
304      for now this is only available for the C-grid code and also within
305      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
306    
307    checkpoint59m
308    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
309      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
310    o gad_som : fix flux output (& diagnostics) to have same units as other  
311      advection scheme fluxes (was previously multiplied by deltaT).  
312    o added verification/seaice_obcs both to test seaice open boundaries
313      and to provide an example matlab scrpt for generating them
314    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
315    o pkg/salt_plume: clean up salt_plume_frac.F to
316      remove redundancy in PlumeMethod 1 and 4
317    o pkg/kpp: added saltplume diagnostics
318    o pkg/obcs and pkg/seaice:
319      - do not set uice and vice to zero when OB*icefile are unspecified
320      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
321      - moved seaice tracer obcs after call to seaice_growth
322    o pkg/salt_plume: added various options for salt plume depth
323      criterion and for vertical distribution of the salt
324    
325    checkpoint59l
326    o pkg/ptracers: new version of ptracers pickup:
327      read meta file and write only fields which are needed to restart.
328      ( same logic as main pickup file ; also using pickupStrictlyMatch )
329    o pkg/seaice:
330      - add timescale for melting due to warm mixed layer as a means of
331        setting SEAICE_availHeatFrac more conveniently
332      - add a CPP-flag/runtime parameter check for flooding algorithm
333      - reformulated availHeat in seaice_growth.F to be independent of AREA
334    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
335      unit changes
336    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
337    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
338      SX vector computer.
339    o pkg/seaice:
340      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
341        seaice forcing fields can now be read only through pkg/exf
342      - removed some unused halos
343    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
344    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
345      or U/VICE from U/VWIND before computing U/VSTRESS
346    
347    checkpoint59k
348    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
349      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
350    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
351      all experiments pass when compile with un-initialised var. checking option.
352    o added pkg/salt_plume
353  o script to test restart (for now, in MITgcm_contrib/jmc_script)  o script to test restart (for now, in MITgcm_contrib/jmc_script)
354  o pkg/seaice: new read/write pickup version.  o pkg/seaice: new read/write pickup version.
355    read meta file and write only fields which are needed to restart.    read meta file and write only fields which are needed to restart.

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