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revision 1.871 by dimitri, Fri Sep 14 02:07:37 2007 UTC revision 1.975 by mlosch, Mon Apr 14 09:45:35 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 pkg/my82: add netcdf-support and diagnostics
8    o thsice pkg:
9      - Now hsMax limits snow heitght by turning it into ice following
10        flooding scheme (and now conserving energy)
11      - Slight rewriting of the formula in thsice_calc_thick.F
12      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
13        --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
14    
15    checkpoint59p
16    o gchem / dic / cfc :
17      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
18      - add new parameter files: "data.dic" & "data.cfc" ;
19      - various re-arrangement in initialisation & header file ;
20      - fix tutorial_global_oce_biogeo for multi-threaded test.
21    o pkg/dic: test for "pickup_dic" file when restarting ;
22      if no pickup-file, can restart with a re-initialised pH (same as it did
23      before) providing pickupStrictlyMatch is set to False.
24    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
25      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
26    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
27      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
28    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
29     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
30       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
31    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
32       scheme to use for vorticty-term ;
33     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
34       (with default selectVortScheme, return to original discretisation)
35     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
36    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
37    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
38      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
39      also fix diagnostics VISCAHW & VISCA4W.
40    
41    checkpoint59o
42    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
43    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
44      move a few statemens out the main loop into separate loops
45    o pkg/shelfice:
46      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
47        (kg/m^2/s), does not break tests, because in verification/isomip,
48        rhoConstFresh=rhoConst (by accident)
49      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
50      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
51        new file model/src/seawater.F, so that they are available for all pkgs.
52      - convert potential temperature into in-situ temperature. This changes the
53        isomip tests => update tests
54    o add a flag writePickupAtEnd (default=true) to be able to suppress
55      writing a pickup at the last timestep
56    o tools/mpack-1.6 :
57      - disable automake (not working) and autoconf (not needed).
58      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
59        also cleaner with much less compilation warnings.
60    o pkg/profiles:
61      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
62      (for "less than 32 characters name" compiler requirement)
63    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
64      conditions that have a different sampling frequency than S/T/U/V obcs
65    o pkg/diagnostics (stats-diags):
66      - fix global Min/Max in case 1 processor get only empty tiles
67    o genmake2: replace (4 times)
68         make genmake_tc_1.o >> genmake_warnings 2>&1
69      with
70         COMM="$CC $CFLAGS -c genmake_tc_1.c"
71         echo $COMM >> genmake_warnings
72         $COMM >> genmake_warnings 2>&1
73      to make genmake2 always see the value of CC as specified in the optfile.
74    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
75      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
76      - modify verification advect_cs test to test SOM-advection on CS-grid.
77    o pkg/ctrl:
78      - Rewrite of ctrl_map_ini_ecco.F,
79        introducing a generic routine (ctrl_map_ini_gen.F).
80      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
81    
82    checkpoint59n
83    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
84      number in dedicate array "hdiag":
85      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
86        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
87      - many small changes (integer format) for large number of diagnostics
88      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
89        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
90    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
91      usingSphericalGrid, this allows to define the rotated grid coordinates
92      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
93      geographical coordinates according to the inverse of the rotation defined
94      by the Euler angles, so that Coriolis parameter and online-interpolation by
95      exf works with the geographical coordinates on XC/YC/XG/YG.
96      Naturally, this feature does not work with all packages, so some
97      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
98      profiles), because there the coordinates are assumed to be regular
99      spherical grid coordinates.
100    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
101      - introduce isopycnal diffusion coefficient control.
102    o tools/adjoint_options:
103      - additional control vector components.
104    o pkg/mnc: have mnc create marginally meaning full coordinate variables
105      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
106    o pkg/mypackage:
107      - add example of read/write pickup for state-var ;
108      - add entry points to the main code for state-vars diags & write-pickup.
109    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
110      transitions for useExfYearlyFields
111      - add new subroutine that determines the file to read from for
112        use*YearlyFields = .TRUE. and .FALSE.
113      - add a verification experiment to global_with_exf that tests
114        useExfYearlyFields with USE_EXF_INTERPOLATION defined
115    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
116      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
117      subroutines (which could be generated from a template, because they are
118      almost identical), for now they are included in obcs_prescribe_read.F for
119      simplicity
120    o pkg/exf:
121      - add a little more diagnostic to exf_interp_read (in analogy to
122        mds_read_field, can be turned off with debugLevel < debugLevA=1)
123      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
124        ugly but fast by unrolling short inner loops, inserting a unroll=8
125        directive in routine lagran, and splitting a loop and making do while the
126        outermost loop (the latter requires the intoduction of index arrays)
127    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
128    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
129      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
130    o verification/seaice_obcs: updated for restart test and latest options
131    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
132      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
133      for now this is only available for the C-grid code and also within
134      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
135    
136    checkpoint59m
137    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
138      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
139    o gad_som : fix flux output (& diagnostics) to have same units as other  
140      advection scheme fluxes (was previously multiplied by deltaT).  
141    o added verification/seaice_obcs both to test seaice open boundaries
142      and to provide an example matlab scrpt for generating them
143    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
144    o pkg/salt_plume: clean up salt_plume_frac.F to
145      remove redundancy in PlumeMethod 1 and 4
146    o pkg/kpp: added saltplume diagnostics
147    o pkg/obcs and pkg/seaice:
148      - do not set uice and vice to zero when OB*icefile are unspecified
149      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
150      - moved seaice tracer obcs after call to seaice_growth
151    o pkg/salt_plume: added various options for salt plume depth
152      criterion and for vertical distribution of the salt
153    
154    checkpoint59l
155    o pkg/ptracers: new version of ptracers pickup:
156      read meta file and write only fields which are needed to restart.
157      ( same logic as main pickup file ; also using pickupStrictlyMatch )
158    o pkg/seaice:
159      - add timescale for melting due to warm mixed layer as a means of
160        setting SEAICE_availHeatFrac more conveniently
161      - add a CPP-flag/runtime parameter check for flooding algorithm
162      - reformulated availHeat in seaice_growth.F to be independent of AREA
163    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
164      unit changes
165    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
166    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
167      SX vector computer.
168    o pkg/seaice:
169      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
170        seaice forcing fields can now be read only through pkg/exf
171      - removed some unused halos
172    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
173    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
174      or U/VICE from U/VWIND before computing U/VSTRESS
175    
176    checkpoint59k
177    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
178      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
179    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
180      all experiments pass when compile with un-initialised var. checking option.
181    o added pkg/salt_plume
182    o script to test restart (for now, in MITgcm_contrib/jmc_script)
183    o pkg/seaice: new read/write pickup version.
184      read meta file and write only fields which are needed to restart.
185      ( same logic as main pickup file ; also using pickupStrictlyMatch )
186    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
187    o lab_sea.hb87: modify the domain & update output.hb87.txt :
188      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
189      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
190      process. Fixed here by closing the domain at the Northern boundary.
191    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
192    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
193      a set of consecutive levels in/from a 3-D array.
194    o pkg/ptracers:
195      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
196      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
197    
198    checkpoint59j
199    o in pkgs: dic, obcs, offline, rbcs:
200      standard way to compute coeff. for time interpolation between 2 time reccords
201      which retains full precision (& make results less dependent on compiler).
202      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
203    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
204      packages instead of reading ice cover and wind speed separately
205    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
206     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
207      to allow to compile customized code before the update)
208    o cleaning-up:
209      - fix CPP instruction syntax in pkg/obcs
210      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
211        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
212      - fix some threads issue in IO parts.
213    o pkg/dic:
214      - add tons of "_d 0" (--> much better testreports !)
215       and then update outputs of tutorial_global_oce_biogeo
216    o pkg/mom_fluxform:
217      add a special version of momentum advection intended to conserve momentum
218      next to a bathymetry step or a coastline edge. (default = off = #undef)
219    o new read/write pickup version:
220      - for now, only implemented for main (mdsio) pickup file.
221      - write out only what is needed to restart; merge pickup_nh , pickup_ph
222        and main pickup together.
223      - read meta file; read only what is needed to restart; stop if a field
224        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
225        if it make sense (even if the restart is not perfect).
226      - if no meta file, assume that pickup to read corresponds exactly to
227        a pickup that would currently be written.
228      - read pickup written in the old format (until checkpoint59i) if it
229        recognizes an old meta file (no field-list).
230      - add a meta file in exp. which starts from a pickup: 2 cases:
231        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
232         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
233        b) a meta file describing the content of the associated pickup file
234         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
235    o pkg/mdsio & pkg/rw:
236      - new routine to read a meta file ; new set of routine to read
237        Multiple-fields file (with meta file).
238    o added open boundary conditions capability for seaice
239        HSNOW, HSALT, UICE, and VICE
240    
241    checkpoint59i
242    o adjoint:
243      * fix multiDimAdvection adjoint
244        (partial recomputation problem by TAF for fVerT(:,:,kDown)
245        and comlev1 size definition (maxpass vs. max. number of tracers)
246      * verification/global_ocean.90x45x15 adjoint now tests
247        NLFS and multiDimAdvection using DST3 (=30)
248      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
249    o pkg/kpp: add "_d 0" to real constant (if missing);
250      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
251      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
252    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
253      for internal parameters related to restart process (formerly from PARAMS.h)
254      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
255    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
256      as argument. (only atm2d & obcs write_pickup have not yet been updated)
257    o pkg/monitor:
258      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
259      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
260      - account for deep Atmosphere factor and density factor (anelastic)
261    o added open boundary conditions capability for seaice HEFF and AREA
262    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
263      thermodynamics
264      - requires a little reorganization, which affects the testreport results
265        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
266        so that now the conservative form is tested
267      - add a few comments
268    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
269    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
270    o add new diagnostics to seaice: advective, diffusive fluxes (only for
271      multidim-advection, for scheme 2 they are not filled) and transports,
272      thermodynamic growth rates
273    o change units of EmPmR (inside the code, + within coupling interface)
274      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
275      Affects results @ truncation level (cg2d match) and update output of
276       experiments: lab_sea(6), global_ocean.90x40x15(10),
277      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
278      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
279      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
280      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
281    
282    checkpoint59h
283    o pkg/exf:
284      - improve vectorization by moving if-statement out of loops in
285        exf_mapfields, exf_radiation
286      - exf_bulkformulae.F: introduce 2D fields and vectorize code
287    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
288    o testreport:
289      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
290        monitor & update offline_exf_seaice exp. output.
291      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
292    o pkg/seaice:
293      - bug fix in the evp solver: boundary conditions were affected be
294        masking of zMax/zMin (changes results)
295      - minor bug fix in boundary conditions in seaice_calc_strainrates
296        (changes results for no_slip)
297      - seaice_lsr.F: make interpolation of eta dependent on boundaries
298      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
299      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
300        stress formulation and no-slip boundary conditions
301    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
302      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
303    o pkg/seaice: a first HSALT time stepping equation has been checked in
304    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
305      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
306      without requiring DO-IF statements
307    o pkg/thsice:
308      use continuous power-law function for partition of energy between lateral
309      melting/freezing and thinning/thickening ; old code using step function
310      still available with #undef THSICE_FRACEN_POWERLAW
311      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
312    o testreport: change AD testing : check against results/output_adm.txt
313      using same scripts as for forward test.
314    
315    checkpoint59g
316    o adjoint testing: in preparation for changing testreport:
317      - output format: cost and grad written on separated lines
318      - ad output results in directory "results" (instead of "results_ad")
319    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
320  o pkg/seaice: changes for using pkg/seaice with pkg/obcs  o pkg/seaice: changes for using pkg/seaice with pkg/obcs
321  o pkg/ecco: allow user defined cost function contributions  o pkg/ecco: allow user defined cost function contributions
322  o testreport:  o testreport:
323    Allow to choose (per experiment) the list of tested output variables    Allow to choose (per experiment) the list of tested output variables
324     and the main variable (used to issue a pass/FAIL ) ;     and the main variable (used to issue a pass/FAIL ) ;
325    - for now, done by adding the specific list in file: [exp]/input/tr_checklist    - for now, done by adding the specific list in file: [exp]/input/tr_checklist
326    - default is unchange: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;    - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
327    Also modify printing of summary:    Also modify printing of summary:
328     a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)     a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
329     b) echo the list of tested variables in the individual summary.txt of     b) echo the list of tested variables in the individual summary.txt of
# Line 273  o in FFIELDS.h: Line 586  o in FFIELDS.h:
586       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
587  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
588  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
589      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
590        are no longer updating the vertical diffusivity array
591        (passed as argument) but are (re-) setting those arrays.
592  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
593    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
594      cgrid-lsr and evp solver      cgrid-lsr and evp solver

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