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revision 1.869 by jmc, Fri Sep 7 01:16:11 2007 UTC revision 1.974 by dfer, Fri Apr 11 21:48:34 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 thsice pkg:
8      - Now hsMax limits snow heitght by turning it into ice following
9        flooding scheme (and now conserving energy)
10      - Slight rewriting of the formula in thsice_calc_thick.F
11      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
12        --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
13    
14    checkpoint59p
15    o gchem / dic / cfc :
16      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
17      - add new parameter files: "data.dic" & "data.cfc" ;
18      - various re-arrangement in initialisation & header file ;
19      - fix tutorial_global_oce_biogeo for multi-threaded test.
20    o pkg/dic: test for "pickup_dic" file when restarting ;
21      if no pickup-file, can restart with a re-initialised pH (same as it did
22      before) providing pickupStrictlyMatch is set to False.
23    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
24      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
25    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
26      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
27    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
28     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
29       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
30    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
31       scheme to use for vorticty-term ;
32     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
33       (with default selectVortScheme, return to original discretisation)
34     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
35    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
36    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
37      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
38      also fix diagnostics VISCAHW & VISCA4W.
39    
40    checkpoint59o
41    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
42    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
43      move a few statemens out the main loop into separate loops
44    o pkg/shelfice:
45      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
46        (kg/m^2/s), does not break tests, because in verification/isomip,
47        rhoConstFresh=rhoConst (by accident)
48      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
49      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
50        new file model/src/seawater.F, so that they are available for all pkgs.
51      - convert potential temperature into in-situ temperature. This changes the
52        isomip tests => update tests
53    o add a flag writePickupAtEnd (default=true) to be able to suppress
54      writing a pickup at the last timestep
55    o tools/mpack-1.6 :
56      - disable automake (not working) and autoconf (not needed).
57      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
58        also cleaner with much less compilation warnings.
59    o pkg/profiles:
60      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
61      (for "less than 32 characters name" compiler requirement)
62    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
63      conditions that have a different sampling frequency than S/T/U/V obcs
64    o pkg/diagnostics (stats-diags):
65      - fix global Min/Max in case 1 processor get only empty tiles
66    o genmake2: replace (4 times)
67         make genmake_tc_1.o >> genmake_warnings 2>&1
68      with
69         COMM="$CC $CFLAGS -c genmake_tc_1.c"
70         echo $COMM >> genmake_warnings
71         $COMM >> genmake_warnings 2>&1
72      to make genmake2 always see the value of CC as specified in the optfile.
73    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
74      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
75      - modify verification advect_cs test to test SOM-advection on CS-grid.
76    o pkg/ctrl:
77      - Rewrite of ctrl_map_ini_ecco.F,
78        introducing a generic routine (ctrl_map_ini_gen.F).
79      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
80    
81    checkpoint59n
82    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
83      number in dedicate array "hdiag":
84      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
85        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
86      - many small changes (integer format) for large number of diagnostics
87      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
88        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
89    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
90      usingSphericalGrid, this allows to define the rotated grid coordinates
91      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
92      geographical coordinates according to the inverse of the rotation defined
93      by the Euler angles, so that Coriolis parameter and online-interpolation by
94      exf works with the geographical coordinates on XC/YC/XG/YG.
95      Naturally, this feature does not work with all packages, so some
96      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
97      profiles), because there the coordinates are assumed to be regular
98      spherical grid coordinates.
99    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
100      - introduce isopycnal diffusion coefficient control.
101    o tools/adjoint_options:
102      - additional control vector components.
103    o pkg/mnc: have mnc create marginally meaning full coordinate variables
104      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
105    o pkg/mypackage:
106      - add example of read/write pickup for state-var ;
107      - add entry points to the main code for state-vars diags & write-pickup.
108    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
109      transitions for useExfYearlyFields
110      - add new subroutine that determines the file to read from for
111        use*YearlyFields = .TRUE. and .FALSE.
112      - add a verification experiment to global_with_exf that tests
113        useExfYearlyFields with USE_EXF_INTERPOLATION defined
114    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
115      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
116      subroutines (which could be generated from a template, because they are
117      almost identical), for now they are included in obcs_prescribe_read.F for
118      simplicity
119    o pkg/exf:
120      - add a little more diagnostic to exf_interp_read (in analogy to
121        mds_read_field, can be turned off with debugLevel < debugLevA=1)
122      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
123        ugly but fast by unrolling short inner loops, inserting a unroll=8
124        directive in routine lagran, and splitting a loop and making do while the
125        outermost loop (the latter requires the intoduction of index arrays)
126    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
127    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
128      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
129    o verification/seaice_obcs: updated for restart test and latest options
130    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
131      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
132      for now this is only available for the C-grid code and also within
133      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
134    
135    checkpoint59m
136    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
137      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
138    o gad_som : fix flux output (& diagnostics) to have same units as other  
139      advection scheme fluxes (was previously multiplied by deltaT).  
140    o added verification/seaice_obcs both to test seaice open boundaries
141      and to provide an example matlab scrpt for generating them
142    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
143    o pkg/salt_plume: clean up salt_plume_frac.F to
144      remove redundancy in PlumeMethod 1 and 4
145    o pkg/kpp: added saltplume diagnostics
146    o pkg/obcs and pkg/seaice:
147      - do not set uice and vice to zero when OB*icefile are unspecified
148      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
149      - moved seaice tracer obcs after call to seaice_growth
150    o pkg/salt_plume: added various options for salt plume depth
151      criterion and for vertical distribution of the salt
152    
153    checkpoint59l
154    o pkg/ptracers: new version of ptracers pickup:
155      read meta file and write only fields which are needed to restart.
156      ( same logic as main pickup file ; also using pickupStrictlyMatch )
157    o pkg/seaice:
158      - add timescale for melting due to warm mixed layer as a means of
159        setting SEAICE_availHeatFrac more conveniently
160      - add a CPP-flag/runtime parameter check for flooding algorithm
161      - reformulated availHeat in seaice_growth.F to be independent of AREA
162    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
163      unit changes
164    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
165    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
166      SX vector computer.
167    o pkg/seaice:
168      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
169        seaice forcing fields can now be read only through pkg/exf
170      - removed some unused halos
171    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
172    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
173      or U/VICE from U/VWIND before computing U/VSTRESS
174    
175    checkpoint59k
176    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
177      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
178    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
179      all experiments pass when compile with un-initialised var. checking option.
180    o added pkg/salt_plume
181    o script to test restart (for now, in MITgcm_contrib/jmc_script)
182    o pkg/seaice: new read/write pickup version.
183      read meta file and write only fields which are needed to restart.
184      ( same logic as main pickup file ; also using pickupStrictlyMatch )
185    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
186    o lab_sea.hb87: modify the domain & update output.hb87.txt :
187      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
188      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
189      process. Fixed here by closing the domain at the Northern boundary.
190    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
191    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
192      a set of consecutive levels in/from a 3-D array.
193    o pkg/ptracers:
194      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
195      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
196    
197    checkpoint59j
198    o in pkgs: dic, obcs, offline, rbcs:
199      standard way to compute coeff. for time interpolation between 2 time reccords
200      which retains full precision (& make results less dependent on compiler).
201      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
202    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
203      packages instead of reading ice cover and wind speed separately
204    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
205     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
206      to allow to compile customized code before the update)
207    o cleaning-up:
208      - fix CPP instruction syntax in pkg/obcs
209      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
210        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
211      - fix some threads issue in IO parts.
212    o pkg/dic:
213      - add tons of "_d 0" (--> much better testreports !)
214       and then update outputs of tutorial_global_oce_biogeo
215    o pkg/mom_fluxform:
216      add a special version of momentum advection intended to conserve momentum
217      next to a bathymetry step or a coastline edge. (default = off = #undef)
218    o new read/write pickup version:
219      - for now, only implemented for main (mdsio) pickup file.
220      - write out only what is needed to restart; merge pickup_nh , pickup_ph
221        and main pickup together.
222      - read meta file; read only what is needed to restart; stop if a field
223        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
224        if it make sense (even if the restart is not perfect).
225      - if no meta file, assume that pickup to read corresponds exactly to
226        a pickup that would currently be written.
227      - read pickup written in the old format (until checkpoint59i) if it
228        recognizes an old meta file (no field-list).
229      - add a meta file in exp. which starts from a pickup: 2 cases:
230        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
231         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
232        b) a meta file describing the content of the associated pickup file
233         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
234    o pkg/mdsio & pkg/rw:
235      - new routine to read a meta file ; new set of routine to read
236        Multiple-fields file (with meta file).
237    o added open boundary conditions capability for seaice
238        HSNOW, HSALT, UICE, and VICE
239    
240    checkpoint59i
241    o adjoint:
242      * fix multiDimAdvection adjoint
243        (partial recomputation problem by TAF for fVerT(:,:,kDown)
244        and comlev1 size definition (maxpass vs. max. number of tracers)
245      * verification/global_ocean.90x45x15 adjoint now tests
246        NLFS and multiDimAdvection using DST3 (=30)
247      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
248    o pkg/kpp: add "_d 0" to real constant (if missing);
249      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
250      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
251    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
252      for internal parameters related to restart process (formerly from PARAMS.h)
253      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
254    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
255      as argument. (only atm2d & obcs write_pickup have not yet been updated)
256    o pkg/monitor:
257      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
258      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
259      - account for deep Atmosphere factor and density factor (anelastic)
260    o added open boundary conditions capability for seaice HEFF and AREA
261    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
262      thermodynamics
263      - requires a little reorganization, which affects the testreport results
264        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
265        so that now the conservative form is tested
266      - add a few comments
267    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
268    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
269    o add new diagnostics to seaice: advective, diffusive fluxes (only for
270      multidim-advection, for scheme 2 they are not filled) and transports,
271      thermodynamic growth rates
272    o change units of EmPmR (inside the code, + within coupling interface)
273      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
274      Affects results @ truncation level (cg2d match) and update output of
275       experiments: lab_sea(6), global_ocean.90x40x15(10),
276      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
277      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
278      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
279      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
280    
281    checkpoint59h
282    o pkg/exf:
283      - improve vectorization by moving if-statement out of loops in
284        exf_mapfields, exf_radiation
285      - exf_bulkformulae.F: introduce 2D fields and vectorize code
286    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
287    o testreport:
288      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
289        monitor & update offline_exf_seaice exp. output.
290      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
291    o pkg/seaice:
292      - bug fix in the evp solver: boundary conditions were affected be
293        masking of zMax/zMin (changes results)
294      - minor bug fix in boundary conditions in seaice_calc_strainrates
295        (changes results for no_slip)
296      - seaice_lsr.F: make interpolation of eta dependent on boundaries
297      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
298      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
299        stress formulation and no-slip boundary conditions
300    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
301      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
302    o pkg/seaice: a first HSALT time stepping equation has been checked in
303    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
304      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
305      without requiring DO-IF statements
306    o pkg/thsice:
307      use continuous power-law function for partition of energy between lateral
308      melting/freezing and thinning/thickening ; old code using step function
309      still available with #undef THSICE_FRACEN_POWERLAW
310      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
311    o testreport: change AD testing : check against results/output_adm.txt
312      using same scripts as for forward test.
313    
314    checkpoint59g
315    o adjoint testing: in preparation for changing testreport:
316      - output format: cost and grad written on separated lines
317      - ad output results in directory "results" (instead of "results_ad")
318    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
319    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
320    o pkg/ecco: allow user defined cost function contributions
321  o testreport:  o testreport:
322    Allow to choose (per experiment) the list of tested output variables    Allow to choose (per experiment) the list of tested output variables
323     and the main variable (used to issue a pass/FAIL ) ;     and the main variable (used to issue a pass/FAIL ) ;
324    - 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
325    - 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] ;
326    Also modify printing of summary:    Also modify printing of summary:
327     a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)     a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
328     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 271  o in FFIELDS.h: Line 585  o in FFIELDS.h:
585       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
586  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
587  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
588      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
589        are no longer updating the vertical diffusivity array
590        (passed as argument) but are (re-) setting those arrays.
591  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
592    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
593      cgrid-lsr and evp solver      cgrid-lsr and evp solver

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