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revision 1.892 by jmc, Mon Oct 15 00:30:04 2007 UTC revision 1.994 by mlosch, Thu May 22 12:22:13 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/diagnostics: enforce missing_value attribute for scalar variables at
8      mass points, when using mnc for output
9      - add runtime parameter (missing_value, missing_value_int) to override
10        default (which is the value of getcon('UNDEF'))
11    o pkg/mnc: prepare mnc for the actual use of missing values with the
12      diagnostics package: small fix in mnc_cw_readwrite.template and more
13      initialisation of never used fields
14      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
15      versions
16    o pkg/thsice/thsice_ini_vars.F added default initial values so that
17      thermodynamics sea ice solver does not blow up when some initial fields
18      are missing.
19    o move from external_forcing_surf.F to ini_forcing.F
20      the p-coord. hack consisting in using pLoad to set phi0surf ;
21      update output of tutorial_global_oce_in_p (affected @ truncation level).
22    o Freshen up a bit hs94.1x64x5, notably:
23      remove rotationPeriod and tRef=5*0. (adjoint only), and add
24      exactConserv=.TRUE.
25    o pkg/generic_advdiff:
26      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
27      applies to files where Temperature & Salinity 2nd Order moments are used.
28    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
29      this uses a dynamically allocated internal state data structure
30      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
31      and requires a fortran 90 compiler
32    
33    checkpoint59q
34    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
35       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
36    o Refresh tutorial_global_oce_biogeo, notably:
37      - change bathymetry (put back seamounts in ACC, use hFacs)
38      - change EOS (POLY3 --> JMD95Z)
39      - use Bryan-Lewis vertical diffusivity
40      - use multidimensional advection
41      - remove old virtual virtual in dic pkg, now done through ptracer pkg
42      - change a couple of parameters in dic pkg
43    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
44    o pkg/obcs: change default to OBCSfixTopo = .true.,
45      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
46      - replace "debugMode" with "debugLevel .GE. debLevB"
47    o implementation of TAF directives for gchem,cfc,dic
48    o remove "exp5" (replaced by tutorial_deep_convection).
49    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
50      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
51      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
52      --> changes results in exp4, seaice_obcs
53    o tutorial_deep_convection :
54      update the set-up and increase resolution and domain size ; start
55      from pseudo initial conditions = output at t=120mn in order to see
56      something happening when running testreport.
57    o pkg/seaice: add os7mp as an advection scheme
58                  add check for advection schemes
59                  add a flag for restoring T and S underneath sea ice
60    o pkg/my82: add netcdf-support and diagnostics
61    o thsice pkg:
62      - Now hsMax limits snow height by turning it into ice following
63        flooding scheme (and now conserving energy)
64      - Slight rewriting of the formula in thsice_calc_thick.F
65      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
66      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
67    
68    checkpoint59p
69    o gchem / dic / cfc :
70      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
71      - add new parameter files: "data.dic" & "data.cfc" ;
72      - various re-arrangement in initialisation & header file ;
73      - fix tutorial_global_oce_biogeo for multi-threaded test.
74    o pkg/dic: test for "pickup_dic" file when restarting ;
75      if no pickup-file, can restart with a re-initialised pH (same as it did
76      before) providing pickupStrictlyMatch is set to False.
77    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
78      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
79    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
80      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
81    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
82     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
83       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
84    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
85       scheme to use for vorticty-term ;
86     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
87       (with default selectVortScheme, return to original discretisation)
88     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
89    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
90    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
91      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
92      also fix diagnostics VISCAHW & VISCA4W.
93    
94    checkpoint59o
95    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
96    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
97      move a few statemens out the main loop into separate loops
98    o pkg/shelfice:
99      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
100        (kg/m^2/s), does not break tests, because in verification/isomip,
101        rhoConstFresh=rhoConst (by accident)
102      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
103      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
104        new file model/src/seawater.F, so that they are available for all pkgs.
105      - convert potential temperature into in-situ temperature. This changes the
106        isomip tests => update tests
107    o add a flag writePickupAtEnd (default=true) to be able to suppress
108      writing a pickup at the last timestep
109    o tools/mpack-1.6 :
110      - disable automake (not working) and autoconf (not needed).
111      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
112        also cleaner with much less compilation warnings.
113    o pkg/profiles:
114      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
115      (for "less than 32 characters name" compiler requirement)
116    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
117      conditions that have a different sampling frequency than S/T/U/V obcs
118    o pkg/diagnostics (stats-diags):
119      - fix global Min/Max in case 1 processor get only empty tiles
120    o genmake2: replace (4 times)
121         make genmake_tc_1.o >> genmake_warnings 2>&1
122      with
123         COMM="$CC $CFLAGS -c genmake_tc_1.c"
124         echo $COMM >> genmake_warnings
125         $COMM >> genmake_warnings 2>&1
126      to make genmake2 always see the value of CC as specified in the optfile.
127    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
128      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
129      - modify verification advect_cs test to test SOM-advection on CS-grid.
130    o pkg/ctrl:
131      - Rewrite of ctrl_map_ini_ecco.F,
132        introducing a generic routine (ctrl_map_ini_gen.F).
133      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
134    
135    checkpoint59n
136    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
137      number in dedicate array "hdiag":
138      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
139        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
140      - many small changes (integer format) for large number of diagnostics
141      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
142        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
143    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
144      usingSphericalGrid, this allows to define the rotated grid coordinates
145      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
146      geographical coordinates according to the inverse of the rotation defined
147      by the Euler angles, so that Coriolis parameter and online-interpolation by
148      exf works with the geographical coordinates on XC/YC/XG/YG.
149      Naturally, this feature does not work with all packages, so some
150      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
151      profiles), because there the coordinates are assumed to be regular
152      spherical grid coordinates.
153    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
154      - introduce isopycnal diffusion coefficient control.
155    o tools/adjoint_options:
156      - additional control vector components.
157    o pkg/mnc: have mnc create marginally meaning full coordinate variables
158      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
159    o pkg/mypackage:
160      - add example of read/write pickup for state-var ;
161      - add entry points to the main code for state-vars diags & write-pickup.
162    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
163      transitions for useExfYearlyFields
164      - add new subroutine that determines the file to read from for
165        use*YearlyFields = .TRUE. and .FALSE.
166      - add a verification experiment to global_with_exf that tests
167        useExfYearlyFields with USE_EXF_INTERPOLATION defined
168    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
169      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
170      subroutines (which could be generated from a template, because they are
171      almost identical), for now they are included in obcs_prescribe_read.F for
172      simplicity
173    o pkg/exf:
174      - add a little more diagnostic to exf_interp_read (in analogy to
175        mds_read_field, can be turned off with debugLevel < debugLevA=1)
176      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
177        ugly but fast by unrolling short inner loops, inserting a unroll=8
178        directive in routine lagran, and splitting a loop and making do while the
179        outermost loop (the latter requires the intoduction of index arrays)
180    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
181    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
182      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
183    o verification/seaice_obcs: updated for restart test and latest options
184    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
185      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
186      for now this is only available for the C-grid code and also within
187      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
188    
189    checkpoint59m
190    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
191      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
192    o gad_som : fix flux output (& diagnostics) to have same units as other  
193      advection scheme fluxes (was previously multiplied by deltaT).  
194    o added verification/seaice_obcs both to test seaice open boundaries
195      and to provide an example matlab scrpt for generating them
196    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
197    o pkg/salt_plume: clean up salt_plume_frac.F to
198      remove redundancy in PlumeMethod 1 and 4
199    o pkg/kpp: added saltplume diagnostics
200    o pkg/obcs and pkg/seaice:
201      - do not set uice and vice to zero when OB*icefile are unspecified
202      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
203      - moved seaice tracer obcs after call to seaice_growth
204    o pkg/salt_plume: added various options for salt plume depth
205      criterion and for vertical distribution of the salt
206    
207    checkpoint59l
208    o pkg/ptracers: new version of ptracers pickup:
209      read meta file and write only fields which are needed to restart.
210      ( same logic as main pickup file ; also using pickupStrictlyMatch )
211    o pkg/seaice:
212      - add timescale for melting due to warm mixed layer as a means of
213        setting SEAICE_availHeatFrac more conveniently
214      - add a CPP-flag/runtime parameter check for flooding algorithm
215      - reformulated availHeat in seaice_growth.F to be independent of AREA
216    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
217      unit changes
218    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
219    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
220      SX vector computer.
221    o pkg/seaice:
222      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
223        seaice forcing fields can now be read only through pkg/exf
224      - removed some unused halos
225    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
226    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
227      or U/VICE from U/VWIND before computing U/VSTRESS
228    
229    checkpoint59k
230    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
231      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
232    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
233      all experiments pass when compile with un-initialised var. checking option.
234    o added pkg/salt_plume
235    o script to test restart (for now, in MITgcm_contrib/jmc_script)
236    o pkg/seaice: new read/write pickup version.
237      read meta file and write only fields which are needed to restart.
238      ( same logic as main pickup file ; also using pickupStrictlyMatch )
239    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
240    o lab_sea.hb87: modify the domain & update output.hb87.txt :
241      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
242      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
243      process. Fixed here by closing the domain at the Northern boundary.
244    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
245    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
246      a set of consecutive levels in/from a 3-D array.
247    o pkg/ptracers:
248      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
249      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
250    
251    checkpoint59j
252    o in pkgs: dic, obcs, offline, rbcs:
253      standard way to compute coeff. for time interpolation between 2 time reccords
254      which retains full precision (& make results less dependent on compiler).
255      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
256    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
257      packages instead of reading ice cover and wind speed separately
258    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
259     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
260      to allow to compile customized code before the update)
261    o cleaning-up:
262      - fix CPP instruction syntax in pkg/obcs
263      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
264        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
265      - fix some threads issue in IO parts.
266    o pkg/dic:
267      - add tons of "_d 0" (--> much better testreports !)
268       and then update outputs of tutorial_global_oce_biogeo
269    o pkg/mom_fluxform:
270      add a special version of momentum advection intended to conserve momentum
271      next to a bathymetry step or a coastline edge. (default = off = #undef)
272    o new read/write pickup version:
273      - for now, only implemented for main (mdsio) pickup file.
274      - write out only what is needed to restart; merge pickup_nh , pickup_ph
275        and main pickup together.
276      - read meta file; read only what is needed to restart; stop if a field
277        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
278        if it make sense (even if the restart is not perfect).
279      - if no meta file, assume that pickup to read corresponds exactly to
280        a pickup that would currently be written.
281      - read pickup written in the old format (until checkpoint59i) if it
282        recognizes an old meta file (no field-list).
283      - add a meta file in exp. which starts from a pickup: 2 cases:
284        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
285         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
286        b) a meta file describing the content of the associated pickup file
287         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
288    o pkg/mdsio & pkg/rw:
289      - new routine to read a meta file ; new set of routine to read
290        Multiple-fields file (with meta file).
291    o added open boundary conditions capability for seaice
292        HSNOW, HSALT, UICE, and VICE
293    
294    checkpoint59i
295    o adjoint:
296      * fix multiDimAdvection adjoint
297        (partial recomputation problem by TAF for fVerT(:,:,kDown)
298        and comlev1 size definition (maxpass vs. max. number of tracers)
299      * verification/global_ocean.90x45x15 adjoint now tests
300        NLFS and multiDimAdvection using DST3 (=30)
301      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
302    o pkg/kpp: add "_d 0" to real constant (if missing);
303      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
304      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
305    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
306      for internal parameters related to restart process (formerly from PARAMS.h)
307      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
308    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
309      as argument. (only atm2d & obcs write_pickup have not yet been updated)
310  o pkg/monitor:  o pkg/monitor:
311    - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM    - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
312    - fix mon_stats_rs (statistics over the full domain, even where field is zero)    - fix mon_stats_rs (statistics over the full domain, even where field is zero)
# Line 20  o add a little bit of code to gad_os7mp_ Line 323  o add a little bit of code to gad_os7mp_
323  o add new diagnostics to seaice: advective, diffusive fluxes (only for  o add new diagnostics to seaice: advective, diffusive fluxes (only for
324    multidim-advection, for scheme 2 they are not filled) and transports,    multidim-advection, for scheme 2 they are not filled) and transports,
325    thermodynamic growth rates    thermodynamic growth rates
326  o change units of EmPmR (inside the code) from m/s to kg/m2/s (mass flux) but  o change units of EmPmR (inside the code, + within coupling interface)
327    leave input file unchanged. Affects results @ truncation level (cg2d match)    from m/s to kg/m2/s (mass flux) but leave input file unchanged.
328    and update output of experiments: lab_sea(6), global_ocean.90x40x15(10),    Affects results @ truncation level (cg2d match) and update output of
329       experiments: lab_sea(6), global_ocean.90x40x15(10),
330    global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)    global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
331    + adjoint results: global_ocean_ebm(11) and lab_sea (12).    + adjoint results: global_ocean_ebm(11) and lab_sea (12).
332      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
333    Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).    Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
334    
335  checkpoint59h  checkpoint59h

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