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revision 1.942 by dimitri, Fri Jan 18 01:38:33 2008 UTC revision 1.1038 by dfer, Thu Oct 30 23:38:41 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 kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
8    o gmredi (Visbeck-variable-K):
9     - add more parameters to Visbeck-variable-K.
10     - use a 5 points average for dSigmaR in Visbeck-K calculation
11       (more "homogenous": same stencil and same weights as in dSigmaH)
12     - update output of ideal_2D_oce experiment.
13    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
14      (#undef REAL4_IS_SLOW)
15     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
16       coordinate variable
17     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
18       (surface forcing fields), removes some of the functionality
19     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
20     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
21       probably not all: copy _RS surface flux fields to RL field before
22       calling DIAGNOSTICS_FILL
23     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
24       real*4 (CALL EXCH_*_RS) versions.
25     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
26       (generate new output).
27    
28    checkpoint61e
29    o gmredi (Visbeck-variable-K):
30      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
31      - change computation of Visbeck-K where Slope > Smax :        
32        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
33        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
34    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
35      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
36    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
37    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
38      does not become too large (to avoid precision problems in implicit-diffusion
39      solver); update ideal_2D_oce output.
40    o pkg ggl90:
41      - in ggl90_cal.F: compute only one set of visc/diff, used to
42        step forward TKE/T/S/momentum
43      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
44        have Prandlt =1)
45    o gmredi (fm07):
46      - add lower limit on Transition layer thickness + lower limit on 1/lambda
47      - allow to set few more params from data.gmredi
48    o pkg ggl90:
49          - add missing sqrt(2) factor in computation of mixing length
50            scale in ggl90_calc.F
51            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
52    
53    checkpoint61d
54    o adjoint modifs
55      - adapt to new field rhoInSitu
56      - allow to revert from StoreDynVars2D, StoreDynVars3D
57        to individual fields
58        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
59    o store 3-D (in-situ) density in commom block (DYNVARS.h)
60     - save 1 rho computation.
61     - no longer modify T & S inland when using down_slope pkg.
62    o gad_som : allow to switch to SOM advection for T & S without corresponding
63      pickup files (using new S/R: MDS_CHECK4FILE).
64    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
65      (for useSingleCpuIO to work in multi-threaded)
66    o pkg/shelfice:
67     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
68       with SHELFICEtopoFile in data.shelfice
69     - move code for reading ice shelf topography and modifying hFacC into separate
70       subroutines of the shelfice package
71     - separate initialisation of "fixed" and "variable" variables
72     - kTopC is not (yet) replaced by kSurfC, although this is possible
73    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
74    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
75      and rename:
76      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
77      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
78    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
79    
80    checkpoint61c
81    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
82      to add mass source/sink of fluid in the interior (3-D generalisation
83      of oceanic real-fresh water flux).
84    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
85    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
86    o new pkg: down_slope
87      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
88      - presently, modify T & S inland (dwnslp_calc_rho.F).
89        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
90      - implementation for ocean in P-coords not tested.
91      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
92    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
93      (to facilitate conversion of oceanic pkg to p-coordinate).
94    o change FIND_RHO to FIND_RHO_2D :
95      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
96    o new pkg: cheapaml
97    
98    checkpoint61b
99    o exch2:
100      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
101      - no longer depend on the order sequence (N,S,E,W).
102      - 3rd exchange no longer needed (tested with 24 tiles).
103      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
104      - exch_UV_A-grid readily available (but not yet tested).
105      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
106      (both are no longer needed) in exch_uv: no effect in forward run; but
107       get truncation error differences with adjoint exch.
108    o exch2:
109     - change index-bounds storage (moved from target to local tile,
110       more intuitive this way) ; rename/remove some variables.
111     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
112    
113    checkpoint61a
114    o exch2/matlab-topology-generator:
115      fix bug in index bounds for N-S internal exchange (hard to tell if this
116      had any effect on the solution).
117    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
118      is exceeded
119    o testreport: modify syntax of awk, so that it works also with
120      awk, and not only with nawk and gawk
121    
122    checkpoint61
123    o autodiff
124      Change default for TAF usage by removing argument '-nonew_arg'
125      This changes TAF subroutine argument list (ordering of active var.)
126      Omission of this flag leads to incompatibility w.r.t. TAMC
127      To restore TAMC-compatibility, need following modifs:
128      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
129      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
130      Tested TAF version is 1.9.22
131      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
132    
133    checkpoint60
134    --->>> This is the last checkpoint for which generating the adjoint
135    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
136    --->>> by default.
137    --->>> Future checkpoints will ommit this flag by default.
138    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
139    o pkg/grdchk: Add gradient check to etan0 perturbations.
140    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
141    o pkg/autodiff: more flexibility in zeroadj.
142      model/src: modifying do_oceanic_phys.F accordingly.
143    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
144    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
145      special setup of gmredi for which the adjoint is stable
146      enough for parameter optimization.
147    o bridging the gap between eddy stress and GM.
148      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
149          along with a change in CPP option (now ALLOW_EDDYPSI).
150      -> when using GM w/ GM_AdvForm:
151          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
152          is applied either in the tracer Eq. or in momentum Eq.
153          depending on data.gmredi (intro. GM_InMomAsStress).
154      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
155      The key modifications are in model/src/taueddy_external_forcing.F
156      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
157    
158    checkpoint59r
159    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
160      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
161      fix option to read coriolis(@ cell-corner) from files with CS-grid.
162    o pkg/mnc: add some attributes to standard 1D-coordinate variables
163    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
164      mass points, when using mnc for output
165      - add runtime parameter (missing_value, missing_value_int) to override
166        default (which is the value of getcon('UNDEF'))
167    o pkg/mnc: prepare mnc for the actual use of missing values with the
168      diagnostics package: small fix in mnc_cw_readwrite.template and more
169      initialisation of never used fields
170      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
171      versions
172    o pkg/thsice/thsice_ini_vars.F added default initial values so that
173      thermodynamics sea ice solver does not blow up when some initial fields
174      are missing.
175    o move from external_forcing_surf.F to ini_forcing.F
176      the p-coord. hack consisting in using pLoad to set phi0surf ;
177      update output of tutorial_global_oce_in_p (affected @ truncation level).
178    o Freshen up a bit hs94.1x64x5, notably:
179      remove rotationPeriod and tRef=5*0. (adjoint only), and add
180      exactConserv=.TRUE.
181    o pkg/generic_advdiff:
182      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
183      applies to files where Temperature & Salinity 2nd Order moments are used.
184    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
185      this uses a dynamically allocated internal state data structure
186      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
187      and requires a fortran 90 compiler
188    
189    checkpoint59q
190    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
191       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
192    o Refresh tutorial_global_oce_biogeo, notably:
193      - change bathymetry (put back seamounts in ACC, use hFacs)
194      - change EOS (POLY3 --> JMD95Z)
195      - use Bryan-Lewis vertical diffusivity
196      - use multidimensional advection
197      - remove old virtual virtual in dic pkg, now done through ptracer pkg
198      - change a couple of parameters in dic pkg
199    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
200    o pkg/obcs: change default to OBCSfixTopo = .true.,
201      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
202      - replace "debugMode" with "debugLevel .GE. debLevB"
203    o implementation of TAF directives for gchem,cfc,dic
204    o remove "exp5" (replaced by tutorial_deep_convection).
205    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
206      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
207      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
208      --> changes results in exp4, seaice_obcs
209    o tutorial_deep_convection :
210      update the set-up and increase resolution and domain size ; start
211      from pseudo initial conditions = output at t=120mn in order to see
212      something happening when running testreport.
213    o pkg/seaice: add os7mp as an advection scheme
214                  add check for advection schemes
215                  add a flag for restoring T and S underneath sea ice
216    o pkg/my82: add netcdf-support and diagnostics
217    o thsice pkg:
218      - Now hsMax limits snow height by turning it into ice following
219        flooding scheme (and now conserving energy)
220      - Slight rewriting of the formula in thsice_calc_thick.F
221      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
222      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
223    
224    checkpoint59p
225    o gchem / dic / cfc :
226      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
227      - add new parameter files: "data.dic" & "data.cfc" ;
228      - various re-arrangement in initialisation & header file ;
229      - fix tutorial_global_oce_biogeo for multi-threaded test.
230    o pkg/dic: test for "pickup_dic" file when restarting ;
231      if no pickup-file, can restart with a re-initialised pH (same as it did
232      before) providing pickupStrictlyMatch is set to False.
233    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
234      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
235    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
236      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
237    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
238     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
239       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
240    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
241       scheme to use for vorticty-term ;
242     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
243       (with default selectVortScheme, return to original discretisation)
244     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
245    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
246    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
247      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
248      also fix diagnostics VISCAHW & VISCA4W.
249    
250    checkpoint59o
251    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
252    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
253      move a few statemens out the main loop into separate loops
254    o pkg/shelfice:
255      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
256        (kg/m^2/s), does not break tests, because in verification/isomip,
257        rhoConstFresh=rhoConst (by accident)
258      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
259      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
260        new file model/src/seawater.F, so that they are available for all pkgs.
261      - convert potential temperature into in-situ temperature. This changes the
262        isomip tests => update tests
263    o add a flag writePickupAtEnd (default=true) to be able to suppress
264      writing a pickup at the last timestep
265    o tools/mpack-1.6 :
266      - disable automake (not working) and autoconf (not needed).
267      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
268        also cleaner with much less compilation warnings.
269    o pkg/profiles:
270      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
271      (for "less than 32 characters name" compiler requirement)
272    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
273      conditions that have a different sampling frequency than S/T/U/V obcs
274    o pkg/diagnostics (stats-diags):
275      - fix global Min/Max in case 1 processor get only empty tiles
276    o genmake2: replace (4 times)
277         make genmake_tc_1.o >> genmake_warnings 2>&1
278      with
279         COMM="$CC $CFLAGS -c genmake_tc_1.c"
280         echo $COMM >> genmake_warnings
281         $COMM >> genmake_warnings 2>&1
282      to make genmake2 always see the value of CC as specified in the optfile.
283    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
284      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
285      - modify verification advect_cs test to test SOM-advection on CS-grid.
286    o pkg/ctrl:
287      - Rewrite of ctrl_map_ini_ecco.F,
288        introducing a generic routine (ctrl_map_ini_gen.F).
289      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
290    
291    checkpoint59n
292    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
293      number in dedicate array "hdiag":
294      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
295        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
296      - many small changes (integer format) for large number of diagnostics
297      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
298        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
299    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
300      usingSphericalGrid, this allows to define the rotated grid coordinates
301      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
302      geographical coordinates according to the inverse of the rotation defined
303      by the Euler angles, so that Coriolis parameter and online-interpolation by
304      exf works with the geographical coordinates on XC/YC/XG/YG.
305      Naturally, this feature does not work with all packages, so some
306      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
307      profiles), because there the coordinates are assumed to be regular
308      spherical grid coordinates.
309    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
310      - introduce isopycnal diffusion coefficient control.
311    o tools/adjoint_options:
312      - additional control vector components.
313    o pkg/mnc: have mnc create marginally meaning full coordinate variables
314      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
315    o pkg/mypackage:
316      - add example of read/write pickup for state-var ;
317      - add entry points to the main code for state-vars diags & write-pickup.
318    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
319      transitions for useExfYearlyFields
320      - add new subroutine that determines the file to read from for
321        use*YearlyFields = .TRUE. and .FALSE.
322      - add a verification experiment to global_with_exf that tests
323        useExfYearlyFields with USE_EXF_INTERPOLATION defined
324    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
325      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
326      subroutines (which could be generated from a template, because they are
327      almost identical), for now they are included in obcs_prescribe_read.F for
328      simplicity
329    o pkg/exf:
330      - add a little more diagnostic to exf_interp_read (in analogy to
331        mds_read_field, can be turned off with debugLevel < debugLevA=1)
332      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
333        ugly but fast by unrolling short inner loops, inserting a unroll=8
334        directive in routine lagran, and splitting a loop and making do while the
335        outermost loop (the latter requires the intoduction of index arrays)
336  o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice  o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
337  o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver  o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
338    http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html    http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html

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