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revision 1.883 by dimitri, Thu Sep 27 14:42:59 2007 UTC revision 1.992 by dimitri, Thu May 22 01:59:50 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/exf: improve vectorization by moving if-statement out of loops  o pkg/thsice/thsice_ini_vars.F added default initial values so that thermodynamics
8      sea ice solver does not blow up when some initial fields are missing.
9    o move from external_forcing_surf.F to ini_forcing.F
10      the p-coord. hack consisting in using pLoad to set phi0surf ;
11      update output of tutorial_global_oce_in_p (affected @ truncation level).
12    o Freshen up a bit hs94.1x64x5, notably:
13      remove rotationPeriod and tRef=5*0. (adjoint only), and add exactConserv=.TRUE.
14    o pkg/generic_advdiff:
15      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
16      applies to files where Temperature & Salinity 2nd Order moments are used.
17    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
18      this uses a dynamically allocated internal state data structure
19      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
20      and requires a fortran 90 compiler
21    
22    checkpoint59q
23    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
24       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
25    o Refresh tutorial_global_oce_biogeo, notably:
26      - change bathymetry (put back seamounts in ACC, use hFacs)
27      - change EOS (POLY3 --> JMD95Z)
28      - use Bryan-Lewis vertical diffusivity
29      - use multidimensional advection
30      - remove old virtual virtual in dic pkg, now done through ptracer pkg
31      - change a couple of parameters in dic pkg
32    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
33    o pkg/obcs: change default to OBCSfixTopo = .true.,
34      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
35      - replace "debugMode" with "debugLevel .GE. debLevB"
36    o implementation of TAF directives for gchem,cfc,dic
37    o remove "exp5" (replaced by tutorial_deep_convection).
38    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
39      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
40      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
41      --> changes results in exp4, seaice_obcs
42    o tutorial_deep_convection :
43      update the set-up and increase resolution and domain size ; start
44      from pseudo initial conditions = output at t=120mn in order to see
45      something happening when running testreport.
46    o pkg/seaice: add os7mp as an advection scheme
47                  add check for advection schemes
48                  add a flag for restoring T and S underneath sea ice
49    o pkg/my82: add netcdf-support and diagnostics
50    o thsice pkg:
51      - Now hsMax limits snow height by turning it into ice following
52        flooding scheme (and now conserving energy)
53      - Slight rewriting of the formula in thsice_calc_thick.F
54      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
55      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
56    
57    checkpoint59p
58    o gchem / dic / cfc :
59      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
60      - add new parameter files: "data.dic" & "data.cfc" ;
61      - various re-arrangement in initialisation & header file ;
62      - fix tutorial_global_oce_biogeo for multi-threaded test.
63    o pkg/dic: test for "pickup_dic" file when restarting ;
64      if no pickup-file, can restart with a re-initialised pH (same as it did
65      before) providing pickupStrictlyMatch is set to False.
66    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
67      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
68    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
69      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
70    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
71     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
72       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
73    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
74       scheme to use for vorticty-term ;
75     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
76       (with default selectVortScheme, return to original discretisation)
77     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
78    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
79    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
80      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
81      also fix diagnostics VISCAHW & VISCA4W.
82    
83    checkpoint59o
84    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
85    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
86      move a few statemens out the main loop into separate loops
87    o pkg/shelfice:
88      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
89        (kg/m^2/s), does not break tests, because in verification/isomip,
90        rhoConstFresh=rhoConst (by accident)
91      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
92      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
93        new file model/src/seawater.F, so that they are available for all pkgs.
94      - convert potential temperature into in-situ temperature. This changes the
95        isomip tests => update tests
96    o add a flag writePickupAtEnd (default=true) to be able to suppress
97      writing a pickup at the last timestep
98    o tools/mpack-1.6 :
99      - disable automake (not working) and autoconf (not needed).
100      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
101        also cleaner with much less compilation warnings.
102    o pkg/profiles:
103      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
104      (for "less than 32 characters name" compiler requirement)
105    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
106      conditions that have a different sampling frequency than S/T/U/V obcs
107    o pkg/diagnostics (stats-diags):
108      - fix global Min/Max in case 1 processor get only empty tiles
109    o genmake2: replace (4 times)
110         make genmake_tc_1.o >> genmake_warnings 2>&1
111      with
112         COMM="$CC $CFLAGS -c genmake_tc_1.c"
113         echo $COMM >> genmake_warnings
114         $COMM >> genmake_warnings 2>&1
115      to make genmake2 always see the value of CC as specified in the optfile.
116    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
117      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
118      - modify verification advect_cs test to test SOM-advection on CS-grid.
119    o pkg/ctrl:
120      - Rewrite of ctrl_map_ini_ecco.F,
121        introducing a generic routine (ctrl_map_ini_gen.F).
122      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
123    
124    checkpoint59n
125    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
126      number in dedicate array "hdiag":
127      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
128        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
129      - many small changes (integer format) for large number of diagnostics
130      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
131        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
132    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
133      usingSphericalGrid, this allows to define the rotated grid coordinates
134      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
135      geographical coordinates according to the inverse of the rotation defined
136      by the Euler angles, so that Coriolis parameter and online-interpolation by
137      exf works with the geographical coordinates on XC/YC/XG/YG.
138      Naturally, this feature does not work with all packages, so some
139      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
140      profiles), because there the coordinates are assumed to be regular
141      spherical grid coordinates.
142    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
143      - introduce isopycnal diffusion coefficient control.
144    o tools/adjoint_options:
145      - additional control vector components.
146    o pkg/mnc: have mnc create marginally meaning full coordinate variables
147      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
148    o pkg/mypackage:
149      - add example of read/write pickup for state-var ;
150      - add entry points to the main code for state-vars diags & write-pickup.
151    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
152      transitions for useExfYearlyFields
153      - add new subroutine that determines the file to read from for
154        use*YearlyFields = .TRUE. and .FALSE.
155      - add a verification experiment to global_with_exf that tests
156        useExfYearlyFields with USE_EXF_INTERPOLATION defined
157    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
158      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
159      subroutines (which could be generated from a template, because they are
160      almost identical), for now they are included in obcs_prescribe_read.F for
161      simplicity
162    o pkg/exf:
163      - add a little more diagnostic to exf_interp_read (in analogy to
164        mds_read_field, can be turned off with debugLevel < debugLevA=1)
165      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
166        ugly but fast by unrolling short inner loops, inserting a unroll=8
167        directive in routine lagran, and splitting a loop and making do while the
168        outermost loop (the latter requires the intoduction of index arrays)
169    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
170    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
171      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
172    o verification/seaice_obcs: updated for restart test and latest options
173    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
174      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
175      for now this is only available for the C-grid code and also within
176      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
177    
178    checkpoint59m
179    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
180      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
181    o gad_som : fix flux output (& diagnostics) to have same units as other  
182      advection scheme fluxes (was previously multiplied by deltaT).  
183    o added verification/seaice_obcs both to test seaice open boundaries
184      and to provide an example matlab scrpt for generating them
185    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
186    o pkg/salt_plume: clean up salt_plume_frac.F to
187      remove redundancy in PlumeMethod 1 and 4
188    o pkg/kpp: added saltplume diagnostics
189    o pkg/obcs and pkg/seaice:
190      - do not set uice and vice to zero when OB*icefile are unspecified
191      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
192      - moved seaice tracer obcs after call to seaice_growth
193    o pkg/salt_plume: added various options for salt plume depth
194      criterion and for vertical distribution of the salt
195    
196    checkpoint59l
197    o pkg/ptracers: new version of ptracers pickup:
198      read meta file and write only fields which are needed to restart.
199      ( same logic as main pickup file ; also using pickupStrictlyMatch )
200    o pkg/seaice:
201      - add timescale for melting due to warm mixed layer as a means of
202        setting SEAICE_availHeatFrac more conveniently
203      - add a CPP-flag/runtime parameter check for flooding algorithm
204      - reformulated availHeat in seaice_growth.F to be independent of AREA
205    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
206      unit changes
207    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
208    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
209      SX vector computer.
210    o pkg/seaice:
211      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
212        seaice forcing fields can now be read only through pkg/exf
213      - removed some unused halos
214    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
215    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
216      or U/VICE from U/VWIND before computing U/VSTRESS
217    
218    checkpoint59k
219    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
220      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
221    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
222      all experiments pass when compile with un-initialised var. checking option.
223    o added pkg/salt_plume
224    o script to test restart (for now, in MITgcm_contrib/jmc_script)
225    o pkg/seaice: new read/write pickup version.
226      read meta file and write only fields which are needed to restart.
227      ( same logic as main pickup file ; also using pickupStrictlyMatch )
228    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
229    o lab_sea.hb87: modify the domain & update output.hb87.txt :
230      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
231      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
232      process. Fixed here by closing the domain at the Northern boundary.
233    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
234    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
235      a set of consecutive levels in/from a 3-D array.
236    o pkg/ptracers:
237      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
238      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
239    
240    checkpoint59j
241    o in pkgs: dic, obcs, offline, rbcs:
242      standard way to compute coeff. for time interpolation between 2 time reccords
243      which retains full precision (& make results less dependent on compiler).
244      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
245    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
246      packages instead of reading ice cover and wind speed separately
247    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
248     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
249      to allow to compile customized code before the update)
250    o cleaning-up:
251      - fix CPP instruction syntax in pkg/obcs
252      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
253        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
254      - fix some threads issue in IO parts.
255    o pkg/dic:
256      - add tons of "_d 0" (--> much better testreports !)
257       and then update outputs of tutorial_global_oce_biogeo
258    o pkg/mom_fluxform:
259      add a special version of momentum advection intended to conserve momentum
260      next to a bathymetry step or a coastline edge. (default = off = #undef)
261    o new read/write pickup version:
262      - for now, only implemented for main (mdsio) pickup file.
263      - write out only what is needed to restart; merge pickup_nh , pickup_ph
264        and main pickup together.
265      - read meta file; read only what is needed to restart; stop if a field
266        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
267        if it make sense (even if the restart is not perfect).
268      - if no meta file, assume that pickup to read corresponds exactly to
269        a pickup that would currently be written.
270      - read pickup written in the old format (until checkpoint59i) if it
271        recognizes an old meta file (no field-list).
272      - add a meta file in exp. which starts from a pickup: 2 cases:
273        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
274         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
275        b) a meta file describing the content of the associated pickup file
276         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
277    o pkg/mdsio & pkg/rw:
278      - new routine to read a meta file ; new set of routine to read
279        Multiple-fields file (with meta file).
280    o added open boundary conditions capability for seaice
281        HSNOW, HSALT, UICE, and VICE
282    
283    checkpoint59i
284    o adjoint:
285      * fix multiDimAdvection adjoint
286        (partial recomputation problem by TAF for fVerT(:,:,kDown)
287        and comlev1 size definition (maxpass vs. max. number of tracers)
288      * verification/global_ocean.90x45x15 adjoint now tests
289        NLFS and multiDimAdvection using DST3 (=30)
290      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
291    o pkg/kpp: add "_d 0" to real constant (if missing);
292      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
293      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
294    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
295      for internal parameters related to restart process (formerly from PARAMS.h)
296      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
297    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
298      as argument. (only atm2d & obcs write_pickup have not yet been updated)
299    o pkg/monitor:
300      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
301      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
302      - account for deep Atmosphere factor and density factor (anelastic)
303    o added open boundary conditions capability for seaice HEFF and AREA
304    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
305      thermodynamics
306      - requires a little reorganization, which affects the testreport results
307        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
308        so that now the conservative form is tested
309      - add a few comments
310    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
311    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
312    o add new diagnostics to seaice: advective, diffusive fluxes (only for
313      multidim-advection, for scheme 2 they are not filled) and transports,
314      thermodynamic growth rates
315    o change units of EmPmR (inside the code, + within coupling interface)
316      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
317      Affects results @ truncation level (cg2d match) and update output of
318       experiments: lab_sea(6), global_ocean.90x40x15(10),
319      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
320      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
321      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
322      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
323    
324    checkpoint59h
325    o pkg/exf:
326      - improve vectorization by moving if-statement out of loops in
327        exf_mapfields, exf_radiation
328      - exf_bulkformulae.F: introduce 2D fields and vectorize code
329  o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package  o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
330  o testreport:  o testreport:
331    - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE    - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE

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