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revision 1.957 by mlosch, Wed Feb 13 07:43:39 2008 UTC revision 1.1059 by jmc, Sun Feb 1 22:37:40 2009 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/flt:
8     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
9       init_fixed & ini_varia.
10     - clean-up & simplify linear interpolation S/R:
11       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
12     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
13    o pkg/ggl90: a few modifications:
14     - fix bottom boundary condition, and interpolation of KappaE
15       near top and bottom
16     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
17     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
18     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
19    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
20      (maintain temporary backward compatibility, until next checkpoint)
21    
22    checkpoint61h
23    o pkg/diagnostics with "periodic averaging diagnostics":
24      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
25    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
26    o pkg/obcs: fix loop ranges for balancing code
27    o pkg/flt:
28     - improve criteria for finding which tile owns a float.
29     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
30    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
31      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
32      with ocean biogeo)
33    o pkg/flt:
34     - do some cleaning and fix the restart ;
35     - add output.txt in flt_example/results to get this pkg tested.
36    o genmake2: add an EXTENDED_SRC option and flag.
37       for now, cannot be turned on on command line (only through genmake_local)
38    o pkg/mdsio: read/write vector:
39     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
40     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
41       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
42     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
43      (drop to 4 digits matching for grad). But this test does not look very
44      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
45    
46    checkpoint61g
47    o pkg/flt:
48      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
49       + make OPTIONS file more standard.
50      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
51      - fix _BYTESWAPIO CPP-Flag
52      - standard reading of file-parameter "data.flt"
53      - fix argument list of S/R FLT_RESTART
54      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
55    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
56    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
57      a still unfixed compiler/optimization bug
58    
59    checkpoint61f
60    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
61      update results of global_ocean.cs32x15.icedyn test.
62    o move getcon.F from model/src to pkg/fizhi.
63    o pkg/exf: add parameter for extrapolation of temp up to the surface
64       and option to prevent negative evap (in bulk_largeyeager04 only).
65    o Prather Advection scheme: fix tracer conservation for divergent flow
66      (e.g., when using NonLin Free-Surface).
67    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
68    o gmredi (Visbeck-variable-K):
69     - add more parameters to Visbeck-variable-K.
70     - use a 5 points average for dSigmaR in Visbeck-K calculation
71       (more "homogenous": same stencil and same weights as in dSigmaH)
72     - update output of ideal_2D_oce experiment.
73    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
74      (#undef REAL4_IS_SLOW)
75     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
76       coordinate variable
77     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
78       (surface forcing fields), removes some of the functionality
79     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
80     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
81       probably not all: copy _RS surface flux fields to RL field before
82       calling DIAGNOSTICS_FILL
83     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
84       real*4 (CALL EXCH_*_RS) versions.
85     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
86       (generate new output).
87    
88    checkpoint61e
89    o gmredi (Visbeck-variable-K):
90      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
91      - change computation of Visbeck-K where Slope > Smax :        
92        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
93        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
94    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
95      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
96    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
97    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
98      does not become too large (to avoid precision problems in implicit-diffusion
99      solver); update ideal_2D_oce output.
100    o pkg ggl90:
101      - in ggl90_cal.F: compute only one set of visc/diff, used to
102        step forward TKE/T/S/momentum
103      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
104        have Prandlt =1)
105    o gmredi (fm07):
106      - add lower limit on Transition layer thickness + lower limit on 1/lambda
107      - allow to set few more params from data.gmredi
108    o pkg ggl90:
109          - add missing sqrt(2) factor in computation of mixing length
110            scale in ggl90_calc.F
111            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
112    
113    checkpoint61d
114    o adjoint modifs
115      - adapt to new field rhoInSitu
116      - allow to revert from StoreDynVars2D, StoreDynVars3D
117        to individual fields
118        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
119    o store 3-D (in-situ) density in commom block (DYNVARS.h)
120     - save 1 rho computation.
121     - no longer modify T & S inland when using down_slope pkg.
122    o gad_som : allow to switch to SOM advection for T & S without corresponding
123      pickup files (using new S/R: MDS_CHECK4FILE).
124    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
125      (for useSingleCpuIO to work in multi-threaded)
126    o pkg/shelfice:
127     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
128       with SHELFICEtopoFile in data.shelfice
129     - move code for reading ice shelf topography and modifying hFacC into separate
130       subroutines of the shelfice package
131     - separate initialisation of "fixed" and "variable" variables
132     - kTopC is not (yet) replaced by kSurfC, although this is possible
133    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
134    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
135      and rename:
136      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
137      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
138    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
139    
140    checkpoint61c
141    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
142      to add mass source/sink of fluid in the interior (3-D generalisation
143      of oceanic real-fresh water flux).
144    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
145    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
146    o new pkg: down_slope
147      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
148      - presently, modify T & S inland (dwnslp_calc_rho.F).
149        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
150      - implementation for ocean in P-coords not tested.
151      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
152    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
153      (to facilitate conversion of oceanic pkg to p-coordinate).
154    o change FIND_RHO to FIND_RHO_2D :
155      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
156    o new pkg: cheapaml
157    
158    checkpoint61b
159    o exch2:
160      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
161      - no longer depend on the order sequence (N,S,E,W).
162      - 3rd exchange no longer needed (tested with 24 tiles).
163      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
164      - exch_UV_A-grid readily available (but not yet tested).
165      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
166      (both are no longer needed) in exch_uv: no effect in forward run; but
167       get truncation error differences with adjoint exch.
168    o exch2:
169     - change index-bounds storage (moved from target to local tile,
170       more intuitive this way) ; rename/remove some variables.
171     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
172    
173    checkpoint61a
174    o exch2/matlab-topology-generator:
175      fix bug in index bounds for N-S internal exchange (hard to tell if this
176      had any effect on the solution).
177    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
178      is exceeded
179    o testreport: modify syntax of awk, so that it works also with
180      awk, and not only with nawk and gawk
181    
182    checkpoint61
183    o autodiff
184      Change default for TAF usage by removing argument '-nonew_arg'
185      This changes TAF subroutine argument list (ordering of active var.)
186      Omission of this flag leads to incompatibility w.r.t. TAMC
187      To restore TAMC-compatibility, need following modifs:
188      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
189      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
190      Tested TAF version is 1.9.22
191      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
192    
193    checkpoint60
194    --->>> This is the last checkpoint for which generating the adjoint
195    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
196    --->>> by default.
197    --->>> Future checkpoints will ommit this flag by default.
198    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
199    o pkg/grdchk: Add gradient check to etan0 perturbations.
200    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
201    o pkg/autodiff: more flexibility in zeroadj.
202      model/src: modifying do_oceanic_phys.F accordingly.
203    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
204    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
205      special setup of gmredi for which the adjoint is stable
206      enough for parameter optimization.
207    o bridging the gap between eddy stress and GM.
208      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
209          along with a change in CPP option (now ALLOW_EDDYPSI).
210      -> when using GM w/ GM_AdvForm:
211          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
212          is applied either in the tracer Eq. or in momentum Eq.
213          depending on data.gmredi (intro. GM_InMomAsStress).
214      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
215      The key modifications are in model/src/taueddy_external_forcing.F
216      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
217    
218    checkpoint59r
219    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
220      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
221      fix option to read coriolis(@ cell-corner) from files with CS-grid.
222    o pkg/mnc: add some attributes to standard 1D-coordinate variables
223    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
224      mass points, when using mnc for output
225      - add runtime parameter (missing_value, missing_value_int) to override
226        default (which is the value of getcon('UNDEF'))
227    o pkg/mnc: prepare mnc for the actual use of missing values with the
228      diagnostics package: small fix in mnc_cw_readwrite.template and more
229      initialisation of never used fields
230      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
231      versions
232    o pkg/thsice/thsice_ini_vars.F added default initial values so that
233      thermodynamics sea ice solver does not blow up when some initial fields
234      are missing.
235    o move from external_forcing_surf.F to ini_forcing.F
236      the p-coord. hack consisting in using pLoad to set phi0surf ;
237      update output of tutorial_global_oce_in_p (affected @ truncation level).
238    o Freshen up a bit hs94.1x64x5, notably:
239      remove rotationPeriod and tRef=5*0. (adjoint only), and add
240      exactConserv=.TRUE.
241    o pkg/generic_advdiff:
242      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
243      applies to files where Temperature & Salinity 2nd Order moments are used.
244    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
245      this uses a dynamically allocated internal state data structure
246      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
247      and requires a fortran 90 compiler
248    
249    checkpoint59q
250    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
251       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
252    o Refresh tutorial_global_oce_biogeo, notably:
253      - change bathymetry (put back seamounts in ACC, use hFacs)
254      - change EOS (POLY3 --> JMD95Z)
255      - use Bryan-Lewis vertical diffusivity
256      - use multidimensional advection
257      - remove old virtual virtual in dic pkg, now done through ptracer pkg
258      - change a couple of parameters in dic pkg
259    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
260    o pkg/obcs: change default to OBCSfixTopo = .true.,
261      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
262      - replace "debugMode" with "debugLevel .GE. debLevB"
263    o implementation of TAF directives for gchem,cfc,dic
264    o remove "exp5" (replaced by tutorial_deep_convection).
265    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
266      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
267      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
268      --> changes results in exp4, seaice_obcs
269    o tutorial_deep_convection :
270      update the set-up and increase resolution and domain size ; start
271      from pseudo initial conditions = output at t=120mn in order to see
272      something happening when running testreport.
273    o pkg/seaice: add os7mp as an advection scheme
274                  add check for advection schemes
275                  add a flag for restoring T and S underneath sea ice
276    o pkg/my82: add netcdf-support and diagnostics
277    o thsice pkg:
278      - Now hsMax limits snow height by turning it into ice following
279        flooding scheme (and now conserving energy)
280      - Slight rewriting of the formula in thsice_calc_thick.F
281      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
282      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
283    
284    checkpoint59p
285    o gchem / dic / cfc :
286      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
287      - add new parameter files: "data.dic" & "data.cfc" ;
288      - various re-arrangement in initialisation & header file ;
289      - fix tutorial_global_oce_biogeo for multi-threaded test.
290    o pkg/dic: test for "pickup_dic" file when restarting ;
291      if no pickup-file, can restart with a re-initialised pH (same as it did
292      before) providing pickupStrictlyMatch is set to False.
293    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
294      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
295    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
296      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
297    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
298     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
299       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
300    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
301       scheme to use for vorticty-term ;
302     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
303       (with default selectVortScheme, return to original discretisation)
304     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
305    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
306    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
307      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
308      also fix diagnostics VISCAHW & VISCA4W.
309    
310    checkpoint59o
311    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
312    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
313      move a few statemens out the main loop into separate loops
314    o pkg/shelfice:
315      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
316        (kg/m^2/s), does not break tests, because in verification/isomip,
317        rhoConstFresh=rhoConst (by accident)
318      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
319      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
320        new file model/src/seawater.F, so that they are available for all pkgs.
321      - convert potential temperature into in-situ temperature. This changes the
322        isomip tests => update tests
323    o add a flag writePickupAtEnd (default=true) to be able to suppress
324      writing a pickup at the last timestep
325    o tools/mpack-1.6 :
326      - disable automake (not working) and autoconf (not needed).
327      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
328        also cleaner with much less compilation warnings.
329    o pkg/profiles:
330      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
331      (for "less than 32 characters name" compiler requirement)
332    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
333      conditions that have a different sampling frequency than S/T/U/V obcs
334    o pkg/diagnostics (stats-diags):
335      - fix global Min/Max in case 1 processor get only empty tiles
336  o genmake2: replace (4 times)  o genmake2: replace (4 times)
337       make genmake_tc_1.o >> genmake_warnings 2>&1       make genmake_tc_1.o >> genmake_warnings 2>&1
338    with    with

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